PUBLICATIONS ARCHIVE


Summer 2021 Publications

Shamal M. Gunawardhana, Erik D. Holmstrom (2021) Apolar chemical environments compact unfolded RNAs and can promote folding.Biophysical Reports

Ly CY, Yu C, McDonald PR, Roy A, Johnson DK, Davido DJ (2021) Simple and rapid high-throughput assay to identify HSV-1 ICP0 transactivation inhibitors.Antiviral Res.

Schultz CW, Dhir T, McCarthy GA, Nevler A, DuHadaway JB, McCoy MD, Jiang W, Brown SZ, Goetz A, Jain A, Calvert VS, Vishwakarma V, Wang D, Dang H, Cassel J, Summer R, Shaghaghi H, Pommier Y, Baechler AS, Pishvaian MJ, Golan T, Yeo CJ, Petricoin EF, Prendergast GC, Salvino JM, Singh PK, Dixon DA and Brody JR (2021) The FDA approved anthelmintic Pyrvinium Pamoate inhibits pancreatic cancer cells in nutrient depleted conditions by targeting the mitochondria.Molecular Cancer Therapeutics.

Keffeler EC, Iyer VS, Henderson AJ, Huck IL, Schwarting N, Cortez A, Hancock LE (2021) Activity of CcpA-regulated GH18 family glycosyl hydrolases that contribute to nutrient acquisition and fitness in Enterococcus faecalis.Infect Immun.

Keffeler EC, Parthasarathy S, Abdullahi ZH, Hancock LE (2021)Metabolism of poly-β1,4-N-acetylglucosamine substrates and importation of N-acetylglucosamine and glucosamine by Enterococcus faecalis.  J Bacteriol.

Parthasarathy S, Wang X, Carr KR, Varahan S, Hancock EB, Hancock LE (2021)SigV mediates lysozyme resistance in Enterococcus faecalis via RsiV and PgdA.J Bacteriol.

January 2021 Publications

Hyewon Park, Haeyoung Kim, Victoria Hassebroek, Yoshiaki Azuma, Chad Slawson, and Mizuki Azuma. (2020) Chromosomal localization of Ewing sarcoma EWSR1/FLI1 protein promotes the induction of aneuploidyJ. Biological Chemistry.

Clinton Rice, Stuart J. Macdonald, Xiaochen Wang, and Robert Ward (2020).The Broad Transcription Factor Links Hormonal Signaling, Gene Expression, and Cellular Morphogenesis Events During Drosophila Imaginal Disc DevelopmentGenetics.

December 2020 Publications

Tom Hill and Rob Unckless. (2020) Recurrent evolution of high virulence in isolated populations of a DNA viruseLife.

Christian Gomez and Kristi Neufeld. (2020) Elevated Adenomatous Polyposis Coli in Goblet Cells is Associated with Inflammation in Mouse and Human ColonExperimental Physiology.

Thelma Chiremba and Kristi Neufeld. (2020) Constitutive Musashi1 expression impairs mouse postnatal development and intestinal homeostasisMolecular Biology of the Cell.

November 2020 Publications

Wang, J. and Miao, Y*. (2020) Peptide Gaussian accelerated molecular dynamics (Pep-GaMD): Enhanced sampling and free energy and kinetics calculations of peptide bindingJournal of Chemical Physics.

Conrad M, Soldner CA, Miao Y, & Sticht H. (2020) Agonist Binding and G Protein Coupling in Histamine H2 Receptor: A Molecular Dynamics StudyInternational Journal of Molecular Sciences.

Tom Hill and Rob Unckless. (2020) Adaptation, ancestral variation and gene flow in a ’Sky island’ Drosophila speciesMolecular Ecology.

Legrand N, Dixon DA, Sobolewski C. (2020) Stress granules in colorectal cancer: Current knowledge and potential therapeutic applications. World J Gastroenterol.

C.D. Heer, L.S. Voth, D.J. Sanderson, Y.M.O. Alhammad, M.S. Schmidt, S.A.J. Trammell, S. Perlman, M.S. Cohen, A.R. Fehr, and C. Brenner. (2020). Coronavirus and PARP expression dysregulate the NAD Metabolome: a potentially actionable component of innate immunityJ Biol Chem.

S. Ghosh, T.A. Dellibovi-Ragheb, E. Pak, Q. Qui, M. Fisher, P.M. Takvorian, C. Bleck, V. Hsu, A.R. Fehr, S. Perlman, S.R. Achar, M.R. Straus, G.R. Whittaker, C.A.M. de Haan, G. Altan-Bonnet, and N. Altan-Bonnet. (2020) B-Coronaviruses use lysosomal organelles for cellular egressCell In press.

Y.M.O. Alhammad, M.M. Kashipathy, A. Roy, J.P. Gagne, L. Nonfoux, P. McDonald, P. Gao, K.P. Battaile, D.K. Johnson, G.G. Poirier, S. Lovell, and A.R. Fehr. (2020) The SARS-CoV-2 conserved macrodomain is a highly efficient ADP-ribosylhydrolaseJ Virol. In press.

Jennifer R Klaus, Pauline M L Coulon, Pratik Koirala, Mohammad R Seyedsayamdost, Eric Déziel, Josephine R Chandler. (2020)  Secondary metabolites from the Burkholderia pseudomallei complex: structure, ecology, and evolutionJ. Industrial Mcrb. & Biotech.

Jennifer R Klaus, Charlotte Majerczyk, Stephanie Moon, Natalie A Eppler, Sierra Smith, Emily Tuma, Marie-Christine Groleau, Kyle L Asfahl, Nicole E Smalley, Hillary S Hayden, Marianne Piochon, Patrick Ball, Ajai A Dandekar, Charles Gauthier, Eric Déziel, Josephine R Chandler. (2020) Burkholderia thailandensis methylated hydroxy-alkylquinolines: biosynthesis and antimicrobial activity in co-cultures. AEM.

October 2020 Publications

Rajhans Sharma, Sriram KK, Erik D. Holmstrom, Fredrik Westerlund. (2020) Real-time compaction of nanoconfined DNA by an intrinsically disordered macromolecular counterionBiochemical and Biophysical Research Communications. doi.org/10.1016/j.bbrc.2020.06.051

Rob Unckless with several other authors. (2020)  Resistance to natural and synthetic gene drive systems.  J Evol Biol. 2020;00:1–16. This review is the culmination of a workshop that took place in the Swiss Alps.

Dong R, Chen P, Polireddy K, Wu X, Wang T, Ramesh R, Dixon DAXu L, Aubé J, and Chen Q. (2020) An RNA-binding protein, Hu-antigen R, in pancreatic cancer epithelial to mesenchymal transition, metastasis, and cancer stem cellsMol Cancer Ther. 2020; 17(10), 2029-2041. PMID: 32879054

Hassebroek VA, Park H, Pandey N, Lerbakken BT, Aksenova V, Arnaoutov A, Dasso M, Azuma Y. (2020)  PICH regulates the abundance and localization of SUMOylated proteins on mitotic chromosomes. (2020) Mol Biol Cell. doi: 10.1091/mbc.E20-03-0180. Online ahead of print.PMID: 32877270

Aaron J Rudeen, Justin T. Douglas, Minli Xing, W. Hayes McDonald, Audrey L Lamb, and Kristi L Neufeld. (2020) The 15-aa repeat region of Adenomatous polyposis coli is intrinsically disordered and retains conformational flexibility upon binding β-catenin. Biochemistry. PMID: 32941008 DOI: 10.1021/acs.biochem.0c00479

September 2020 Publications

Dimond ZE, Hefty PS. (2020) Comprehensive genome analysis and comparisons of the swine pathogen, Chlamydia suis reveals unique ORFs and candidate host-specificity factors.  Pathog Dis.  PMID: 32639528 DOI: 10.1093/femspd/ftaa035

Parker, T.W.Rudeen, A.J.Neufeld, K.L. (2020) Oncogenic Serine 45-Deleted β-Catenin Remains Susceptible to Wnt Stimulation and APC Regulation in Human ColonocytesCancers 2020, 12(8), 2114. Special Issue "Targeting Wnt Signaling in Cancer: Opportunities Abound If We Can Avoid the Sword of Damocles"

María Angélica Bravo Núñez, Ibrahim M Sabbarini, Lauren E Eide, Robert L Unckless, Sarah E Zanders. (2020) Atypical meiosis can be adaptive in outcrossed Schizosaccharomyces pombe due to wtf meiotic drivers.  eLife 2020;9:e57936 DOI: 10.7554/eLife.57936

Zhang P, Wu X, Gardashova G, Yang Y, Zhang Y, Xu L*, and Zeng Y*. (2020) Molecular and Functional Extracellular Vesicle Analysis using Nanopatterned Microchips Monitors Tumor Progression and MetastasisScience Translational Medicine 12:eaaz2878 (Featured as cover story). *Correspondence. PMID: 32522804

Liu S, Huang Z, Tang A, Wu X, Aube J, Xu L, Xing C, and Huang Y. (2020) Inhibition of RNA-binding protein HuR reduces glomerulosclerosis in experimental nephritisClinical Science (Lond) 2020; 134(12):1433-1448. PMID: 32478392

Lan L, Liu J, Xing M, Smith AR, Wang J, Wu X, Appelman C, Li K, Roy A, Gowthaman R, Karanicolas J, Somoza AD, Wang CCC, Miao Y, De Guzman R, Oakley BR, Neufeld KL, and Xu L. (2020) Identification and Validation of an Aspergillus nidulans Secondary Metabolite Derivative as an Inhibitor of the Musashi-RNA InteractionCancers (Basel) 2020; 12(8). (in press) PMID: 32784494

August 2020 Publications

Miao, Y*, Bhattarai, A., and Wang, J. (2020) Ligand Gaussian accelerated molecular dynamics (LiGaMD): Characterization of ligand binding thermodynamics and kineticsJournal of Chemical Theory and Computation, Published Online

Gao, Y.; Cao, D.; Pawnikar, S.; John, K. P.; Ahn, H. M.; Hill, S.; Ha, J. M.; Parikh, P.; Ogilvie, C.; Swain, A.; Yang, A.; Bell, A.; Salazar, A.; Miao, Y.*; Liang, B.* (2020) Structure of the Human Respiratory Syncytial Virus M2-1 Protein in Complex with a Short Positive-Sense Gene-End RNAStructure 2020, In press (Undergraduate)

Juhoon So, Minwook Kim, Seung‐Hoon Lee, Sungjin Ko, Daniel A Lee, Hyewon Park, Mizuki Azuma, Michael J Parsons, David Prober, Donghun Shin. (2020) Attenuating the EGFR‐ERK‐SOX9 axis promotes liver progenitor cell‐mediated liver regeneration in zebrafish. Hepatology 28 Jun 2020, PMID: 32602149

Nadia Efimova, Changsong Yang, Jonathan X. Chia, Ning Li, Christopher J. Lengner, Kristi L. Neufeld, Tatyana M. Svitkina. (2020) Branched actin networks are assembled on microtubules by adenomatous polyposis coli for targeted membrane protrusion. Journal of Cell Biology 219 (9): e202003091, PMID: 32597939.

July 2020 Publications

Parthasarathy S, Jordan LD, Schwarting N, Woods MA, Abdullahi Z, Varahan S, Passos PMS, Miller B, Hancock LE. (2020) Involvement of Chromosomally Encoded Homologs of the RRNPP Protein Family in Enterococcus faecalis Biofilm Formation and UTI Pathogenesis J Bacteriol. 2020 Jun 15:JB.00063-20. doi: 10.1128/JB.00063-20. Online ahead of print. PMID: 32540933

Matthew E. Ochs, Matthew P. Josephson, and Erik A. Lundquist. (2020) The Predicted RNA-Binding Protein ETR-1/CELF1 Acts in Muscles To Regulate Neuroblast Migration in Caenorhabditis elegans G3: Genes, Genomes, Genetics. doi:10.1534/g3.120.401182. Early online May 12, 2020.

June 2020 Publications

Bhattarai, A., Devkota, S., Bhattarai, S., Wolfe, M. S.* and Miao, Y.* (2020) Mechanisms of gamma-secretase activation and substrate processing. BioRxiv, ACS Central Science 2020. In Press.

May 2020 Publications

Yousef M.O. Alhammad and Anthony R. FehrThe Viral Macrodomain Counters Host Antiviral ADP-ribosylation. Viruses 2020, Mar 31;12(4):E384

Bhattarai, A., Wang, J., and Miao, Y.* Retrospective Ensemble Docking of Allosteric Modulators in an Adenosine G-Protein-Coupled Receptor, BBA - General Subjects 2020, 1864 (8), 129615.

Pawnikar, S. and Miao, Y.* Pathway and Mechanism of Drug Binding to Chemokine Receptors Revealed by Accelerated Molecular Simulations, Future Medicinal Chemistry, In press.

Macdonald SJ and Highfill CA. A naturally-occurring 22-bp coding deletion in Ugt86Dd reduces nicotine resistance in Drosophila melanogasterBMC Res Notes. 2020;13(1):188.

Frawley, D., Greco, C., Oakley, B., Alhussain, M.M., Fleming, A.B., Keller, N.P. and Bayram, Ö. The tetrameric pheromone module SteC-MkkB-MpkB-SteD regulates asexual sporulation, sclerotia formation and aflatoxin production in Aspergillus flavusCell Microbiol 2020, e13192.

Bastos, R.W., Valero, C., Silva, L.P., Schoen, T., Drott, M., Brauer, V., Silva-Rocha, R., Lind, A., Steenwyk, J.L., Rokas, A., Rodrigues, F., Resendiz-Sharpe, A., Lagrou, K., Marcet-Houben, M., Gabaldón, T., McDonnell, E., Reid, I., Tsang, A., Oakley, B.R., Loures, F.V., Almeida, F., Huttenlocher, A., Keller, N.P., Ries, L.N.A. and Goldman, G.H. Functional Characterization of Clinical Isolates of the Opportunistic Fungal Pathogen Aspergillus nidulansmSphere 2020, 5,  (on line, page numbers not yet assigned.)

Xiaoqing Wu, Gulhumay Gardashova, Lan Lan, Shuang Han, Cuncong Zhong, Rebecca T Marquez, Lanjing Wei, Spencer Wood, Sudeshna Roy, Ragul Gowthaman, John Karanicolas, Fei P Gao, Dan A Dixon, Danny R Welch, Ling Li, Min Ji, Jeffrey Aubé, Liang XuTargeting the interaction between RNA-binding protein HuR and FOXQ1 suppresses breast cancer invasion and metastasisCommunications Biology 2020; 3(1):193. 

April 2020 Publications

Albert Zhang, Brian D. Ackley, and Dong Yan.  Vitamin B12 Regulates Glial Migration and Synapse Formation through Isoform-Specific Control of PTP3/LAR PRTP Expression.  Cell Reports 2020; 30(12): 3981-3988.

Meagan Kurland, Bryn O’Meara, Dana K. Tucker, and Brian Ackley.  The Hox Gene egl-5 Acts as a Terminal Selector for VD13 Development via Wnt SignalingJ. Dev. Biol. 2020; 8(1): 5.

Anabel Soldano, Huili Yao, Josephine R. Chandler, and Mario Rivera.  Inhibiting Iron Mobilization from Bacterioferritin in Pseudomonas aeruginosa Impairs Biofilm Formation Irrespective of Environmental Iron Availability.  ACS Infect Dis. 2020; 6(3): 447-458.

E. Peter Greenberg, Josephine R. Chandler, and Mohammad R. Seyedsayamdost.  The Chemistry and Biology of Bactobolin: A 10-Year Collaboration with Natural Product Chemist Extraordinaire Jon Clardy.  J. Nat. Prod. 2020; 83(3): 738-743.

Brittny R. Smith and Stuart J. Macdonald.  Dissecting the Genetic Basis of Variation in Drosophila Sleep Using a Multiparental QTL Mapping ResourceGenes 2020; 11(3): E294.

March 2020 Publications

Joanne R. Chapman, Maureen A. Dowell, Rosanna Chan, and Robert L. UncklessThe genetic basis of natural variation in Drosophila melanogaster immune defense against Enterococcus faecalisGenes 2020; 11 (2): 234.

Taybor W Parker and Kristi L Neufeld. APC controls Wnt-induced β-catenin destruction complex recruitment in human colonocytes. Science Reports. 2020 Feb 19; 10(1):2957 PMID: 32076059

Frawley, D., C. Greco, B. Oakley, M. M. Alhussain, A. B. Fleming, N. P. Keller, and Ö. Bayram. The tetrameric pheromone module SteC-MkkB-MpkB-SteD regulates asexual sporulation, sclerotia formation and aflatoxin production in Aspergillus flavus. Cellular Microbiology 2020 Feb 18; (accepted and now available on line)

A.R. Fehr, S.A. Singh, C.M. Kerr, S. Mukai, H. Higashi, and M. Aikawa. 2020. The impact of PARPs and ADP-ribosylation on inflammation and host-pathogen interactions. Genes Dev. 2020 Feb 6. doi: 10.1101/gad.334425.119.

February 2020 Publications

Schultz, C.W., Preet, R., Dhir, T., Dixon, D.A.* and Brody, J.R.* Wiley Interdiscip. Rev. RNA. 2020; Understanding and targeting the disease-related RNA binding protein HuRin press. *Co-corresponding authors.

January 2020 Publications

A.R. FehrBacterial Artificial Chromosome-Based Lambda Red Recombination with the I-SceI Homing Endonuclease for Genetic Alteration of MERS-CoVMethods Mol. Biol. 2020; 2099:53-68

Schuler B, Borgia A, Borgia M, Heidarsson P, Holmstrom E, Nettels D, and Sottini A.  Binding without folding – the biomolecular function of disordered polyelectrolyte complexes.  Current Opinion in Structural Biology 2020; 60:66-76.

Liu H, Marquez RT, Wu X, Li K, Vadlamani S, Li S, Wang Y, Xu L, Wu D.  A non-intrusive evaluation method for tumor-targeting characteristics of nanomedicinesbased on in vivo near-infrared fluorescence imagingJ Mater Chem B 2019; 7(31):4751-4757.

Lan L, Xing M, Kashipathy MM, Douglas JT, Gao P, Battaile KP, Hanzlik RP, Lovell S, and Xu L.  Crystal and solution structures of human oncoprotein musashi-2 N-terminal RNA recognition motif 1Proteins: Structure, Function and Bioinformatics 2019. PMID: 31603583 (in press)

December 2019 Publications

M.E. Grunewald, M.G. Shaban, S.R. Mackin, A.R. Fehr, and Stanley Perlman. 2019. Murine coronavirus infection activates AhR in an IDO1-independent manner contributing to cytokine modulation and pro-viral TiPARP expression. J Virol. doi: 10.1128/JVI.01743-19. [Epub ahead of print]

R.L. Unckless and H.A. Orr. 2019. The population genetics of evolutionary rescue in diploids: X chromosomal vs. autosomal rescue. The American Naturalist. doi: 10.1086/707139

Pandey N, Keifenheim D, Yoshida MM, Hassebroek VA, Soroka C, Azuma Y, Clarke DJ. Topoisomerase II SUMOylation activates a metaphase checkpoint via Haspin and Aurora B kinases. J Cell Biol. 2019 Nov 11. pii: jcb.201807189. doi: 10.1083/jcb.201807189. [Epub ahead of print]

 

November 2019 Publications

Hanson, Mark A., Lemaitre, Bruno, and Unckless, Robert L. (2019). Dynamic evolution of antimicrobial peptides underscores trade-offs between immunity and ecological fitnessFrontiers in Immunology 10.3389.

Chakraborty M, Emerson JJ, Macdonald SJ, Long AD. (2019). Structural variants exhibit widespread allelic heterogeneity and shape variation in complex traitsNature Communications 10: 4872.

McFarlane JS, Zhang J, Wang S, Lei X, Moran GR, Lamb AL (2019).  Staphylopine and pseudopaline dehydrogenases catalyze reversible reactions and produce stereospecific metallophores.  Journal of Biological Chemistry. [Epub ahead of print]

 

October 2019 Publications

Chapman, JR, T Hill and RL Unckless. 2019. Balancing selection drives the maintenance of genetic variation in Drosophila antimicrobial peptidesGenome Biology and Evolution (Early online). doi: 10.1093/gbe/evz191.

Hill, T and RL Unckless. 2019. A deep learning approach for detecting copy number variation in next generation sequencingG3: Genes, Genomes, Genetics (Early online). doi: 10.1534/g3.119.400596.

Lea, JK and RL Unckless. 2019. An assessment of the immune costs associated with meiotic drive chromosomes in DrosophilaProceedings of the Royal Society B. 286: 20191534. doi: 10.1098/rspb.2019.1534.

 

September 2019 Publications

Wang, J., and Miao, Y. (2019) Mechanistic Insights into Specific G Protein Interactions with Adenosine ReceptorsJ. Phys. Chem. B, 123, 6462-6473.

Scott D. LaBrie, Zoë E. Dimond, Kelly S. Harrison, Srishti Baid, Jason Wickstrum, Robert J. Suchland, P. Scott Hefty. (2019) Transposon Mutagenesis in Chlamydia trachomatis Identifies CT339 as a ComEC Homolog Important for DNA Uptake and Lateral Gene TransferMBio, 2019, 10(4), e01343-19.

Moran GR, Lamb AL. (2019) The tenured itch: ready to treat your midcareer malaise?  ASBMB Today, 18(7), 49-50.

Wang DStoveken HMZucca SDao MOrlandi CSong CMasuho IJohnston COpperman KJGiles ACGill MSLundquist EAGrill BMartemyanov KA. (2019) Genetic behavioral screen identifies an orphan anti-opioid systemScience, 15 Aug 2019 first release.

 

August 2019 Publications

Benomar S, Evans K, Unckless R and Chandler JR. Efflux pumps in Chromobacterium species increase antibiotic resistance and promote survival in a co-culture competition model. AEM In press.

Zanders, SE and RL Unckless. 2019. Fertility costs of meiotic drivers. Current Biology 29: R512-520.

Koseva BS, Hackett JL, Zhou Y, Harris BR, Kelly JK, Greenfield MD, Gleason JM, Macdonald SJ. 2019. Quantitative Genetic Mapping and Genome Assembly in the Lesser Wax Moth Achroia grisella. Genes, Genomes, Genetics 9: 2349-2361.

Grau, M. F., R. Entwistle, C. E. Oakley, C. C. C. Wang, and B. R. Oakley. 2019. Overexpression of an LaeA-like Methyltransferase Upregulates Secondary Metabolite Production in Aspergillus nidulans. ACS Chem Biol 14:1643-1651.

Zeng Y, Ma J, Xu L, Wu D. Natural Product Gossypol and Its Derivatives in Precision Cancer Medicine. Curr Med Chem 2019; 26(10):1849-1873. PMID: 28545375.

 

July 2019 Publications

Gujar MR, Stricker AM, Lundquist EA (2019) RHO-1 and the Rho GEF RHGF-1 interact with UNC-6/Netrin signaling to regulate growth cone protrusion and microtubule organization in Caenorhabditis elegansPLoS Genet 15(6): e1007960.

McFarlane JS, Ronnebaum TA, Meneely KM, Chilton A, Fenton AW, Lamb AL.  Changes in the allosteric site of human liver pyruvate kinase upon activator binding include the breakage of an intersubunit cation-π bond.  Acta Crystallogr F Struct Biol Commun. 75, 461-469.

Tom Hill, Boryana S. Koseva, Robert L. UncklessThe Genome of Drosophila innubila Reveals Lineage-Specific Patterns of Selection in Immune Genes” in Molecular Biology and EvolutionMol.Biol.Evol. 36(7):1405-1417.

 

June 2019 Publications

Matthew E. Grunewald, Yating Chen, Chad Kuny, Takashi Maejima, Robert Lease, Dana Ferraris, Masanori Aikawa, Christopher S. Sullivan, Stanley Perlman, Anthony R. Fehr (2019) The coronavirus macrodomain is required to prevent PARP-mediated inhibition of virus replication and enhancement of IFN expression. PLOS Pathogens. May 16.

Duxbury, E.ML., Day, J.P., Vespasiani, D.M., Thüringer,Y.,  Tolosana, I., Smith.S.CL., Tagliaferri, L., Kamacioglu, A., Lindsley, I., Love, L., Unckless, R.L., Jiggins, F.M., Longdon, B., (2019) Host-pathogen coevolution increases genetic variation in susceptibility to infection. eLife. Apr 30.

Baker, H.A., Fabian, C.J., Hastings, R.C., Dixon, D.A., Nydegger, J.L., Phillips, T.A., Powers, K.R., Kimler, B.F. (2019) Circulating adipose stromal cells as a response biomarker in phase II energy balance trials of obese breast cancer survivors and high-risk women. Breast Cancer Res. Treat. Apr 30

Al-Hashimi, H., Chiarellie, T., Lundquist, E.A., Buechner, M., Novel exc Genes Involved in Formation of the Tubular Excretory Canals of Caenorhabditis elegans. G3: Genes/Genomes/Genetics on May 7. G3 (Bethesda). 2019 May 7;9(5):1339-1353. doi: 10.1534/g3.119.200626. PMID: 30885922

 

May 2019 Publications

Everman, E. R., McNeil, C. L., Hackett, J. L., Bain, C. L. and Macdonald, S. J. (2019) Dissection of complex, fitness-related traits in multiple Drosophila mapping populations offers insight into the genetic control of stress resistance. Genetics 211: 1449-1467.

New, J., Subramaniam, D., Ramalingam, S., Enders, J., Sayed, A.A.A., Ponnurangam, S., Standing, D. Ramamoorthy, P., O'Neil, M., Dixon, D.A., Umar, S., Jensen, R.A., Thomas, S.M. and Anant, S. Pleotropic role of RNA binding protein CELF2 in Autophagy Induction. Molecular Carcinogenesis. 2019; 1-10.

 

April 2019 Publications

Monteleone, N.J., Moore, A.E., Iacona, J.R., Lutz, C.S  and Dixon, D.A. miR-21-mediated regulation of 15-hydroxyprostaglandin dehydrogenase in colon cancer. Scientific Reports, 2019.

Elramli, N., Karahoda, B., Bayram, Ö. S. Frawley, D., Ulas, M., Oakley, C. E., Oakley, B. R., Seiler, S. and Bayram, Ö. (In Press) Assembly of a heptameric STRPAK complex is required for coordination of light-dependent multicellular fungal development with secondary metabolism in Aspergillus nidulansIn Press: PLoS Genetics. 

Horio, T., Szewczy, E., Oakley, C. E., Osmani, A. H., Osmani, S. A. and Oakley, B. R. (2019) SUMOlock reveals a more complete Aspergillus nidulans SUMOylome. Fungal Genet. Biol. 127:50-59.

 

March 2019 Publications

Legrand N, Dixon DA, Sobolewski C. AU-rich elements-binding proteins in colorectal cancer. World J Gastrointest Oncol 2019; 11(2): 71-90

 

February 2019 Publications

Mutreja Y, Combs B, Gamblin TC (2018) FTDP-17 mutations alter the aggregation and microtubule stabilization propensity of tau in an isoform-specific fashionBiochemistry. In Press. DOI: 10.1021/acs.biochem.8b01039

Kenjic N, Hoag MR, Moraski GC, Caperelli CA, Moran GR, Lamb AL.  PvdF of pyoverdin biosynthesis is a structurally unique N10-formyltetrahydrofolate-dependent formyltransferase.  Arch Biochem Biophys [Epub ahead of print]

Green LC, Anthony SR, Slone S, Lanzillotta L, Nieman ML, Wu X, Robbins N, Jones SM, Roy S, Owens Iii AP, Aube J, Xu L, Lorenz JN, Blaxall BC, Rubinstein J, Benoit JB, Tranter M. Human antigen R as a therapeutic target in pathological cardiac hypertrophy. JCI Insight. 2019 Jan 22. [Epub ahead of print] PubMed PMID: 30668549.

 

January 2019 Publications

Ronnebaum TA, McFarlane JS, Prisinzano TE, Booker SJ, Lamb AL (2018). Stuffed methyltransferase domain catalyzes the penultimate step of pyochelin biosynthesisBiochemistry. In Press.  DOI: 10.1021/acs.biochem.8b00716

December 2018 Publications

Miao, Y.*, Bhattarai, A., Nguyen, A. T., Christopoulos, A., and May, L. T. (2018) Structural Basis for Binding of Allosteric Drug Leads in the Adenosine A1 Receptor, Scientific Reports, 8:16836.https://doi.org/10.1038/s41598-018-35266-x 

 

November 2018 Publications

Michelle F. Grau, Ruth Entwistle, Yi-Ming Chiang, Manmeet Ahuja, C. Elizabeth Oakley, Tomohiro Akashi, Clay C. C. Wang, Richard B. Todd, and Berl R. Oakley.  Hybrid Transcription Factor Engineering Activates the Silent Secondary Metabolite Gene Cluster for (+)-Asperlin in Aspergillus nidulans.  ACS Chem Biol, Article ASAP

Bhattarai, A., and Miao, Y.* Gaussian accelerated molecular dynamics for elucidation of drug pathwaysExpert Opinion On Drug Discovery. In Press

Zhang, J., Wang, N., Miao, Y.*, Hauser, F., Rappel, W.-J., McCammon, J. A., and Schroeder, J.* Identification of SLAC1 anion channel residues required for CO2/bicarbonate sensing and regulation of stomatal movementsProc Natl Acad Sci, In Press

Utesch, T., Catalina, A. d. M., Schattenberg, C., Paege, N., Schmieder, P., Krause, E., Miao, Y., McCammon, J. A., Meyer, V., Jung, S., and Mroginski, M. A Computational Modeling Approach Predicts Interaction of the Antifungal Protein AFP from Aspergillus giganteus with Fungal Membranes via Its γ-Core MotifmSphere, 3(5), e00377-18

 

October 2018 Publications

Al-Hashimi H, Hall DH, Ackley BD, Lundquist EA, Buechner M “Intermediate filaments EXC-2 and IFA-4 Maintain Luminal Structure of the Tubular Excretory Canals in Caenorhabditis elegans” Genetics, v. 210, issue 2, pp. 637-652..

McFarlane JS, Hagen R, Chilton AS, Forbes D, Lamb AL, Ellis HR.. Not as easy as π: an insertional residue does not explain the π-helix gain-of-function in two component FMN reductases. Protein Science [Epub ahead of print]

Li J, Smith AR, Marquez RT, Li J, Li K, Lan L, Wu X, Zhao L, Ren F, Wang Y, Wang Y, Jia B, Xu L, Chang Z. MicroRNA-383 acts as a tumor suppressor in colorectal cancer by modulating CREPT/RPRD1B expression. Molecular Carcinogenesis 2018; 57(10):1408-1420. 

Lan L, Liu H, Smith AR, Appelman C, Yu J, Larsen S, Marquez RT, Wu X, Liu FY, Gao P, Gowthaman R, Karanicolas J, De Guzman RN, Rogers S, Aubé J, Neufeld KLXu LNatural product derivative Gossypolone inhibits Musashi family of RNA-binding proteins. BMC Cancer 2018; 18(1):809.

 

September 2018 Publications

Bandyopadhyay A, Wang H, Ray JCJLineage space and the propensity of bacterial cells to undergo growth transitions. PLoS Comput Biol. 2018 Aug 22;14(8):e1006380. doi: 10.1371/journal.pcbi.1006380

McElfresh GC, Ray JCJ. 2018. Intergenerational Cellular Signal Transfer and Erasure. In: The interplay of thermodynamics and computation in natural and artificial systems. D. Wolpert, C. Kempes, J. Grochow and P. Stadler, Eds. Santa Fe Institute Press.

Franklin MW, Slusky JSGTight Turns of Outer Membrane Proteins: An Analysis of Sequence, Structure, and Hydrogen Bonding. J Mol Biol. 2018 Sep 14;430(18 Pt B):3251-3265. doi: 10.1016/j.jmb.2018.06.013. Epub 2018 Jun 23.

Kato J, Dey S, Soto JE, Butan C, Wilkinson MC, De Guzman RN, Galan JE. A protein secreted by the Salmonella type III secretion system controls needle filament assemblyeLife, 7, e35886, 2018. 

Gujar MR, Sundararajan L, Stricker A, Lundquist EAControl of Growth Cone Polarity, Microtubule Accumulation, and Protrusion by UNC-6/Netrin and Its Receptors in Caenorhabditis elegans. Genetics. 2018 Jul 25. pii: genetics.301234.2018. doi: 10.1534/genetics.118.301234. [Epub ahead of print]PMID:30045855

 

August 2018 Publications

Davido DJ, Tu EM, Wang H, Korom M, Gazquez Casals A, Reddy PJ, Mostafa HH, Combs B, Haenchen SD, Morrison LA. Attenuated HSV-1 expressing a mutant form of ICP6 stimulates a strong immune response that protects mice against HSV-1-induced corneal disease. J Virol. 2018 Jun 27. pii: JVI.01036-18. doi: 10.1128/JVI.01036-18. [Epub ahead of print]

V. Paolillo (Lundquist lab), C.B. Jenkinson, T. Horio, B.R. Oakley Cyclins in aspergilli: Phylogenetic and functional analyses of group I cyclins. in Science Direct June 2018.

 

July 2018 Publications

Hill T (Unckless Lab), Betancourt AJ Extensive exchange of transposable elements in the Drosophila pseudoobscura group in Mobile DNA. 2018

 

June 2018 Publications

Abisado R, Benomar S, Klaus JR, Dandekar AA, Chandler JRBacterial quorum sensing and microbial community interactions. MBio 2018 May 22;9(3). pii: e02331-17. doi: 10.1128/mBio.02331-17.

Klaus JR, Deay J, Neuenswander B, Hursh W, Gao Z, Bouddhara T, Williams TD, Douglas J, Monize K, Martins P, Majerczyk C, Seyedsayamdost MR, Peterson BR, Rivera M, Chandler JRMalleilactone is a Burkholderia pseudomallei virulence factor regulated by antibiotics and quorum sensing. Journal of Bacteriology. 2018 May 7. pii: JB.00008-18. doi: 10.1128/JB.00008-18. [Epub ahead of print]

Miao Y Acceleration of Biomolecular Kinetics in Gaussian Accelerated Molecular Dynamics. Journal of Chemical Physics, 149(7):072308. 2018.

 

May 2018 Publications

Preet R, Dixon DAMutant KRAS Exosomes Influence the Metabolic State of the Colon Microenvironment Cellular and Molecular Gastroenterology and Hepatology, Volume 5, Issue 4, 2018, Pages 627-629.e6.

Alan JKRobinson SKMagsig KLDemarco RSLundquist EAThe Atypical Rho GTPase CHW-1 Works with SAX-3/Robo To Mediate Axon Guidance in Caenorhabditis elegans 2018 Apr 13. pii: g3.200148.2018. doi: 10.1534/g3.118.200148. [Epub ahead of print]

McFarlane JS, Davis CL, Lamb AL.  Staphylopine, pseudopaline, and yersinopine dehydrogenases: a structural and kinetic analysis of a new functional class of opine dehydrogenase.  J. Biol. Chem.  [Epub ahead of print]

 

April 2018 Publications

CL Shelton, Lamb AL.  Unraveling the structure and mechanism of the MST(ery) Enzymes.  Trends Biochem Sci.  [Epub ahead of print]

Huang YM, McCammon JA, Miao YReplica exchange Gaussian accelerated molecular dynamics: Improved enhanced sampling and free energy calculationJ Chem Theory Comput, 2018 Article ASAP, DOI: 10.1021/acs.jctc.7b01226. 

Miao Y, McCammon JA Mechanism of the G-Protein Mimetic Nanobody Binding to a Muscarinic G-Protein-Coupled ReceptorProc Natl Acad Sci U S A, 2018 In Press, DOI: 10.1073/pnas.1800756115.

Y Zeng, J Liu, S Yang, W Liu, L Xu, R Wang. Time-lapse live cell imaging to monitor doxorubicin release from DNA origami nanostructures. Journal of Materials Chemistry B, 2018.

 

March 2018 Publications

Brody JR, Dixon DAComplex HuR function in pancreatic cancer cellsWiley Interdiscip Rev RNA. 2018 Feb 16. DOI: 10.1002/wrna.1469.

Miao Y, Huang YM, Walker R, McCammon JA, & Chang C-eA. Ligand Binding Pathways and Conformational Transitions of the HIV ProteaseBiochemistry, DOI: 10.1021/acs.biochem.7b01248.

Peng W, Furuuchi N, Aslanukova L, Huang YH, Brown SZ, Jiang W, Addya S, Vishwakarma V, Peters E, Brody JR, Dixon DA, Sawicki JA. Elevated HuR in Pancreas Promotes a Pancreatitis-Like Inflammatory Microenvironment That Facilitates Tumor DevelopmentMol Cell Biol.  2018 Jan 16;38(3). pii: e00427-17. doi: 10.1128/MCB.00427-17.

Ronnebaum TA, Lamb AL.. Nonribosomal peptides for iron acquisition: pyochelin biosynthesis as a case study.  Current Opinion in Structural Biology 53, 1-11.

Smith, BR, Unckless, RLDraft Genome Sequence of Lysinibacillus fusiformis Strain Juneja, a Laboratory-Derived Pathogen of Drosophila melanogaster. Genome Announcements 6: e01571-17.

 

February 2018 Publications

Evans KC, Benomar S, Camuy-Vélez LA, Nasseri EB, Wang X, Neuenswander B, Chandler JR.  Quorum-sensing control of antibiotic resistance stabilizes cooperation in Chromobacterium violaceum. The ISME J 2018 10.1038/s41396-018-0047-7.

Mostafa HH, Thompson TW, Konen AJ, Haenchen SD, Hilliard JG, Macdonald SJ, Morrison LA, Davido DJHerpes Simplex Virus 1 Mutant with Point Mutations in UL39 Is Impaired for Acute Viral Replication in Mice, Establishment of Latency, and Explant-Induced Reactivation.J Virol. 2018 Jan 10. pii: JVI.01654-17. doi: 10.1128/JVI.01654-17.

Muralidharan R, Mehta M, Ahmed R, Roy S, Xu L, Aubé J, Chen A, Zhao YD, Herman T, Ramesh R, Munshi A. HuR-targeted small molecule inhibitor exhibits cytotoxicity towards human lung cancer cells. Scientific Reports2017; 7:9694.

Ni Z, He J, Wu Y, Hu C, Dai X, Yan X, Li B, Li X, Xiong H, Li Y, Li S, Xu L, Li Y, Lian J, He F. AKT-mediated phosphorylation of ATG4B impairs mitochondrial activity and enhances the Warburg effect in hepatocellular carcinoma cellsAutophagy [Epub ahead of print].

Dohn, J, Grubbs A, Oakley E,  Oakley BNew multi-marker strains and complementing genes for Aspergillus nidulans molecular biologyFungal Genetics and Biology [Epub ahead of print].

 

January 2018 Publications

Hill T and Unckless RLThe dynamic evolution of theDrosophila innubila Nudivirus” in Infection, Genetics and Evolution. ScienceDirect 2017 S1567134817303933

Bardai FH, Wang L, Mutreja Y, Yenjerla M, Gamblin TC, Feany MB. A conserved cytoskeletal signaling cascade mediates neurotoxicity of FTDP-17 tau mutations in vivo. Journal of Neuroscience, 14 November 2017, 1550-17.

Mutreja Y and Gamblin TCOptimization of in vitro conditions to study the arachidonic acid induction of 4R isoforms of the microtubule-associated protein tau. Methods in Cell Biology 141:65-88.

McFarlane JS, Lamb ALBiosynthesis of an Opine Metallophore by Pseudomonas aeruginosa. Biochemistry 56(45): 5967-5971.

Yu J, Lan L, Lewin SJ, Rogers SA, Roy A, Wu X, Gao P, Karanicolas J, Aube J, Sun B, and Xu LIdentification of novel small molecule Beclin 1 mimetics activating autophagyOncotarget 2017; 8(31):51355. PMC5584254.

December 2017/January 2018 Publications

Hill T and Unckless RL. The dynamic evolution of the Drosophila innubila Nudivirus” in Infection, Genetics and Evolution. ScienceDirect 2017 S1567134817303933

Bardai FH, Wang L, Mutreja Y, Yenjerla M, Gamblin TC, Feany MB. A conserved cytoskeletal signaling cascade mediates neurotoxicity of FTDP-17 tau mutations in vivo. Journal of Neuroscience, 14 November 2017, 1550-17.

Mutreja Y and Gamblin TC. Optimization of in vitro conditions to study the arachidonic acid induction of 4R isoforms of the microtubule-associated protein tau. Methods in Cell Biology 141:65-88.

McFarlane JS, Lamb AL. Biosynthesis of an Opine Metallophore by Pseudomonas aeruginosaBiochemistry 56(45): 5967-5971.

Yu J, Lan L, Lewin SJ, Rogers SA, Roy A, Wu X, Gao P, Karanicolas J, Aube J, Sun B, and Xu L. Identification of novel small molecule Beclin 1 mimetics activating autophagy. Oncotarget 2017; 8(31):51355. PMC5584254.

 

November 2017 Publications

Hill T and Unckless RL. Baculovirus molecular evolution via gene turnover and recurrent positive selection of key genes. Journal of Virology (Early Online) JVI.01319-17.  

Highfill CA, Tran JH, Nguyen SKT, Moldenhauer TR, Wang X, Macdonald SJ. Naturally Segregating Variation at Ugt86Dd Contributes to Nicotine Resistance in Drosophila melanogaster. Genetics 2017, 207:311-325.

Gujar MR, Stricker AM, Lundquist EA. Flavin monooxygenases regulate Caenorhabditis elegans axon guidance and growth cone protrusion with UNC-6/Netrin signaling and Rac GTPases.PLoS Genet. 2017 Aug 31;13(8):e1006998. doi: 10.1371/journal.pgen.1006998. eCollection 2017 Aug.

 

September 2017 Publications

Zeng Y, Ma J, Xu L, Wu D. Natural Product Gossypol and Its Derivatives in Precision Cancer Medicine. Current Medicinal Chemistry. 2017 (in press).

Yu J, Zhao X, Zhang N, You C, Yao G, Zhu J, Xu L, and Sun B. Identification of novel 3-nitroacridines as autophagy inducers in gastric cancer cells. New Journal of Chemistry2017; 41(10):4087-4095.

Zheng Y-G, Wu X-Q, Su J, Jiang P, Xu L, Gao J, Cai B, and Ji M. Design and synthesis of a novel photoaffinity probe for labelling egf receptor tyrosine kinases. Journal of Enzyme Inhibition and Medicinal Chemistry 2017; 32(1):954-959.

 

August 2017 Publications

Rowland MA, Greenbaum JM, Deeds EJ.  Crosstalk and the evolvability of intracellular communication.  Nature Communications 8: 16009.

 

July 2017 Publications

Najarro MA, Hackett JL, Macdonald SJ. Loci Contributing to Boric Acid Toxicity in Two Reference Populations of Drosophila melanogasterG3 (Bethesda) 7(6):1631-1641.

Sorger R, Bachman JA, Smith A, Sorger PK, Deeds EJ.  Fundamental trade-offs between information flow in single cells and cellular populations.  Proceedings of the National Academy of Sciences USA 114(22): 555-5760.

 

June 2017 Publications

Zhang P, Wang X, Fan A, Zheng Y, Liu X, Wang S, Zou H, Oakley BR, Keller NP, Yin WP.  A cryptic pigment biosynthetic pathway uncovered by heterologous expression is essential for conidial development in Pestalotiopsis fici. Mol Microbiol.  [Epub ahead of print]

Peterson B, Xu L, Levy M.  Targeting multiple receptors on a cell surface for specific cell targeting.  US Patent No.  US 9,636,419, issued May 2.

 

May 2017 Publications

Eshelman K, Yao H, Punchi Hewage AN, Deay JJ, Chandler JR, Rivera M.  Inhibiting the BfrB:Bfd interaction in Pseudomonas causes irreversible iron accumulation in bacterioferritn and iron deficiency in the bacterial cytosol.  Metallomics [Epub ahead of print]

Kaur K, Wu X, Fields JK, Johnson DK, Lan L, Pratt M, Somoza AD, Wang CCC, Karanicolas J, Oakley BRXu LDe Guzman RN.  The fungal natural product azaphilone-9 binds to HuR and inhibits HuR-RNA interaction in vitro.  PLoS One 12(4):e0175471.

 

February 2017 Publications

Gao FJ, Shi L, Hines T, Hebbar S, Neufeld KL, Smith DS.  Insulin signaling regulates a functional interaction between Adenomatous Polyposis Coli (APC) and cytoplasmic dynein.  Molecular Biology of the Cell. [Epub ahead of print]

Josephson MP, Aliani R, Norris ML, Ochs ME, Gujar M, Lundquist EA.  The Caenorhabditis elegans NF2/Merlin Molecule NFM-1 Non-autonomously Regulates Neuroblast Migration and Interacts Genetically with the Guidance Cue SLT-1/Slit.  Genetics [Epub ahead of print]

Nussinov R, Papin JA, Vakser I.  Computing the dynamic supramolecular structural proteome.  PLoS Computational Biology 13: e1005290.

Sung CT, Chang S-L, Entwistle R, Ahn G, Lin T-S, Petrova V, Yeh H-H, Praseuth MB, Chiang Y-M, Oakley BR, Wang CCC.  Overexpression of a three-gene conidial pigment biosynthetic pathway in Aspergillus nidulans reveals the first NRPS known to acetylate tryptophan. Fungal Genetics and Biology [Epub ahead of print]

Wolfe AR, Ernlund A, McGuinness W, Lehmann C, Carl K, Balmaceda N, Neufeld KL.  Suppression of intestinal tumorigenesis in Apc mutant mice by Musashi-1 deletion.  Journal of Cell Science [Epub ahead of print]

Summer 2021 Publications

Shamal M. Gunawardhana, Erik D. Holmstrom (2021) Apolar chemical environments compact unfolded RNAs and can promote folding.Biophysical Reports

Ly CY, Yu C, McDonald PR, Roy A, Johnson DK, Davido DJ (2021) Simple and rapid high-throughput assay to identify HSV-1 ICP0 transactivation inhibitors.Antiviral Res.

Schultz CW, Dhir T, McCarthy GA, Nevler A, DuHadaway JB, McCoy MD, Jiang W, Brown SZ, Goetz A, Jain A, Calvert VS, Vishwakarma V, Wang D, Dang H, Cassel J, Summer R, Shaghaghi H, Pommier Y, Baechler AS, Pishvaian MJ, Golan T, Yeo CJ, Petricoin EF, Prendergast GC, Salvino JM, Singh PK, Dixon DA and Brody JR (2021) The FDA approved anthelmintic Pyrvinium Pamoate inhibits pancreatic cancer cells in nutrient depleted conditions by targeting the mitochondria.Molecular Cancer Therapeutics.

Keffeler EC, Iyer VS, Henderson AJ, Huck IL, Schwarting N, Cortez A, Hancock LE (2021) Activity of CcpA-regulated GH18 family glycosyl hydrolases that contribute to nutrient acquisition and fitness in Enterococcus faecalis.Infect Immun.

Keffeler EC, Parthasarathy S, Abdullahi ZH, Hancock LE (2021)Metabolism of poly-β1,4-N-acetylglucosamine substrates and importation of N-acetylglucosamine and glucosamine by Enterococcus faecalis.  J Bacteriol.

Parthasarathy S, Wang X, Carr KR, Varahan S, Hancock EB, Hancock LE (2021)SigV mediates lysozyme resistance in Enterococcus faecalis via RsiV and PgdA.J Bacteriol.

January 2021 Publications

Hyewon Park, Haeyoung Kim, Victoria Hassebroek, Yoshiaki Azuma, Chad Slawson, and Mizuki Azuma. (2020) Chromosomal localization of Ewing sarcoma EWSR1/FLI1 protein promotes the induction of aneuploidyJ. Biological Chemistry.

Clinton Rice, Stuart J. Macdonald, Xiaochen Wang, and Robert Ward (2020).The Broad Transcription Factor Links Hormonal Signaling, Gene Expression, and Cellular Morphogenesis Events During Drosophila Imaginal Disc DevelopmentGenetics.

December 2020 Publications

Tom Hill and Rob Unckless. (2020) Recurrent evolution of high virulence in isolated populations of a DNA viruseLife.

Christian Gomez and Kristi Neufeld. (2020) Elevated Adenomatous Polyposis Coli in Goblet Cells is Associated with Inflammation in Mouse and Human ColonExperimental Physiology.

Thelma Chiremba and Kristi Neufeld. (2020) Constitutive Musashi1 expression impairs mouse postnatal development and intestinal homeostasisMolecular Biology of the Cell.

November 2020 Publications

Wang, J. and Miao, Y*. (2020) Peptide Gaussian accelerated molecular dynamics (Pep-GaMD): Enhanced sampling and free energy and kinetics calculations of peptide bindingJournal of Chemical Physics.

Conrad M, Soldner CA, Miao Y, & Sticht H. (2020) Agonist Binding and G Protein Coupling in Histamine H2 Receptor: A Molecular Dynamics StudyInternational Journal of Molecular Sciences.

Tom Hill and Rob Unckless. (2020) Adaptation, ancestral variation and gene flow in a ’Sky island’ Drosophila speciesMolecular Ecology.

Legrand N, Dixon DA, Sobolewski C. (2020) Stress granules in colorectal cancer: Current knowledge and potential therapeutic applications. World J Gastroenterol.

C.D. Heer, L.S. Voth, D.J. Sanderson, Y.M.O. Alhammad, M.S. Schmidt, S.A.J. Trammell, S. Perlman, M.S. Cohen, A.R. Fehr, and C. Brenner. (2020). Coronavirus and PARP expression dysregulate the NAD Metabolome: a potentially actionable component of innate immunityJ Biol Chem.

S. Ghosh, T.A. Dellibovi-Ragheb, E. Pak, Q. Qui, M. Fisher, P.M. Takvorian, C. Bleck, V. Hsu, A.R. Fehr, S. Perlman, S.R. Achar, M.R. Straus, G.R. Whittaker, C.A.M. de Haan, G. Altan-Bonnet, and N. Altan-Bonnet. (2020) B-Coronaviruses use lysosomal organelles for cellular egressCell In press.

Y.M.O. Alhammad, M.M. Kashipathy, A. Roy, J.P. Gagne, L. Nonfoux, P. McDonald, P. Gao, K.P. Battaile, D.K. Johnson, G.G. Poirier, S. Lovell, and A.R. Fehr. (2020) The SARS-CoV-2 conserved macrodomain is a highly efficient ADP-ribosylhydrolaseJ Virol. In press.

Jennifer R Klaus, Pauline M L Coulon, Pratik Koirala, Mohammad R Seyedsayamdost, Eric Déziel, Josephine R Chandler. (2020)  Secondary metabolites from the Burkholderia pseudomallei complex: structure, ecology, and evolutionJ. Industrial Mcrb. & Biotech.

Jennifer R Klaus, Charlotte Majerczyk, Stephanie Moon, Natalie A Eppler, Sierra Smith, Emily Tuma, Marie-Christine Groleau, Kyle L Asfahl, Nicole E Smalley, Hillary S Hayden, Marianne Piochon, Patrick Ball, Ajai A Dandekar, Charles Gauthier, Eric Déziel, Josephine R Chandler. (2020) Burkholderia thailandensis methylated hydroxy-alkylquinolines: biosynthesis and antimicrobial activity in co-cultures. AEM.

October 2020 Publications

Rajhans Sharma, Sriram KK, Erik D. Holmstrom, Fredrik Westerlund. (2020) Real-time compaction of nanoconfined DNA by an intrinsically disordered macromolecular counterionBiochemical and Biophysical Research Communications. doi.org/10.1016/j.bbrc.2020.06.051

Rob Unckless with several other authors. (2020)  Resistance to natural and synthetic gene drive systems.  J Evol Biol. 2020;00:1–16. This review is the culmination of a workshop that took place in the Swiss Alps.

Dong R, Chen P, Polireddy K, Wu X, Wang T, Ramesh R, Dixon DAXu L, Aubé J, and Chen Q. (2020) An RNA-binding protein, Hu-antigen R, in pancreatic cancer epithelial to mesenchymal transition, metastasis, and cancer stem cellsMol Cancer Ther. 2020; 17(10), 2029-2041. PMID: 32879054

Hassebroek VA, Park H, Pandey N, Lerbakken BT, Aksenova V, Arnaoutov A, Dasso M, Azuma Y. (2020)  PICH regulates the abundance and localization of SUMOylated proteins on mitotic chromosomes. (2020) Mol Biol Cell. doi: 10.1091/mbc.E20-03-0180. Online ahead of print.PMID: 32877270

Aaron J Rudeen, Justin T. Douglas, Minli Xing, W. Hayes McDonald, Audrey L Lamb, and Kristi L Neufeld. (2020) The 15-aa repeat region of Adenomatous polyposis coli is intrinsically disordered and retains conformational flexibility upon binding β-catenin. Biochemistry. PMID: 32941008 DOI: 10.1021/acs.biochem.0c00479

September 2020 Publications

Dimond ZE, Hefty PS. (2020) Comprehensive genome analysis and comparisons of the swine pathogen, Chlamydia suis reveals unique ORFs and candidate host-specificity factors.  Pathog Dis.  PMID: 32639528 DOI: 10.1093/femspd/ftaa035

Parker, T.W.Rudeen, A.J.Neufeld, K.L. (2020) Oncogenic Serine 45-Deleted β-Catenin Remains Susceptible to Wnt Stimulation and APC Regulation in Human ColonocytesCancers 2020, 12(8), 2114. Special Issue "Targeting Wnt Signaling in Cancer: Opportunities Abound If We Can Avoid the Sword of Damocles"

María Angélica Bravo Núñez, Ibrahim M Sabbarini, Lauren E Eide, Robert L Unckless, Sarah E Zanders. (2020) Atypical meiosis can be adaptive in outcrossed Schizosaccharomyces pombe due to wtf meiotic drivers.  eLife 2020;9:e57936 DOI: 10.7554/eLife.57936

Zhang P, Wu X, Gardashova G, Yang Y, Zhang Y, Xu L*, and Zeng Y*. (2020) Molecular and Functional Extracellular Vesicle Analysis using Nanopatterned Microchips Monitors Tumor Progression and MetastasisScience Translational Medicine 12:eaaz2878 (Featured as cover story). *Correspondence. PMID: 32522804

Liu S, Huang Z, Tang A, Wu X, Aube J, Xu L, Xing C, and Huang Y. (2020) Inhibition of RNA-binding protein HuR reduces glomerulosclerosis in experimental nephritisClinical Science (Lond) 2020; 134(12):1433-1448. PMID: 32478392

Lan L, Liu J, Xing M, Smith AR, Wang J, Wu X, Appelman C, Li K, Roy A, Gowthaman R, Karanicolas J, Somoza AD, Wang CCC, Miao Y, De Guzman R, Oakley BR, Neufeld KL, and Xu L. (2020) Identification and Validation of an Aspergillus nidulans Secondary Metabolite Derivative as an Inhibitor of the Musashi-RNA InteractionCancers (Basel) 2020; 12(8). (in press) PMID: 32784494

August 2020 Publications

Miao, Y*, Bhattarai, A., and Wang, J. (2020) Ligand Gaussian accelerated molecular dynamics (LiGaMD): Characterization of ligand binding thermodynamics and kineticsJournal of Chemical Theory and Computation, Published Online

Gao, Y.; Cao, D.; Pawnikar, S.; John, K. P.; Ahn, H. M.; Hill, S.; Ha, J. M.; Parikh, P.; Ogilvie, C.; Swain, A.; Yang, A.; Bell, A.; Salazar, A.; Miao, Y.*; Liang, B.* (2020) Structure of the Human Respiratory Syncytial Virus M2-1 Protein in Complex with a Short Positive-Sense Gene-End RNAStructure 2020, In press (Undergraduate)

Juhoon So, Minwook Kim, Seung‐Hoon Lee, Sungjin Ko, Daniel A Lee, Hyewon Park, Mizuki Azuma, Michael J Parsons, David Prober, Donghun Shin. (2020) Attenuating the EGFR‐ERK‐SOX9 axis promotes liver progenitor cell‐mediated liver regeneration in zebrafish. Hepatology 28 Jun 2020, PMID: 32602149

Nadia Efimova, Changsong Yang, Jonathan X. Chia, Ning Li, Christopher J. Lengner, Kristi L. Neufeld, Tatyana M. Svitkina. (2020) Branched actin networks are assembled on microtubules by adenomatous polyposis coli for targeted membrane protrusion. Journal of Cell Biology 219 (9): e202003091, PMID: 32597939.

July 2020 Publications

Parthasarathy S, Jordan LD, Schwarting N, Woods MA, Abdullahi Z, Varahan S, Passos PMS, Miller B, Hancock LE. (2020) Involvement of Chromosomally Encoded Homologs of the RRNPP Protein Family in Enterococcus faecalis Biofilm Formation and UTI Pathogenesis J Bacteriol. 2020 Jun 15:JB.00063-20. doi: 10.1128/JB.00063-20. Online ahead of print. PMID: 32540933

Matthew E. Ochs, Matthew P. Josephson, and Erik A. Lundquist. (2020) The Predicted RNA-Binding Protein ETR-1/CELF1 Acts in Muscles To Regulate Neuroblast Migration in Caenorhabditis elegans G3: Genes, Genomes, Genetics. doi:10.1534/g3.120.401182. Early online May 12, 2020.

June 2020 Publications

Bhattarai, A., Devkota, S., Bhattarai, S., Wolfe, M. S.* and Miao, Y.* (2020) Mechanisms of gamma-secretase activation and substrate processing. BioRxiv, ACS Central Science 2020. In Press.

May 2020 Publications

Yousef M.O. Alhammad and Anthony R. FehrThe Viral Macrodomain Counters Host Antiviral ADP-ribosylation. Viruses 2020, Mar 31;12(4):E384

Bhattarai, A., Wang, J., and Miao, Y.* Retrospective Ensemble Docking of Allosteric Modulators in an Adenosine G-Protein-Coupled Receptor, BBA - General Subjects 2020, 1864 (8), 129615.

Pawnikar, S. and Miao, Y.* Pathway and Mechanism of Drug Binding to Chemokine Receptors Revealed by Accelerated Molecular Simulations, Future Medicinal Chemistry, In press.

Macdonald SJ and Highfill CA. A naturally-occurring 22-bp coding deletion in Ugt86Dd reduces nicotine resistance in Drosophila melanogasterBMC Res Notes. 2020;13(1):188.

Frawley, D., Greco, C., Oakley, B., Alhussain, M.M., Fleming, A.B., Keller, N.P. and Bayram, Ö. The tetrameric pheromone module SteC-MkkB-MpkB-SteD regulates asexual sporulation, sclerotia formation and aflatoxin production in Aspergillus flavusCell Microbiol 2020, e13192.

Bastos, R.W., Valero, C., Silva, L.P., Schoen, T., Drott, M., Brauer, V., Silva-Rocha, R., Lind, A., Steenwyk, J.L., Rokas, A., Rodrigues, F., Resendiz-Sharpe, A., Lagrou, K., Marcet-Houben, M., Gabaldón, T., McDonnell, E., Reid, I., Tsang, A., Oakley, B.R., Loures, F.V., Almeida, F., Huttenlocher, A., Keller, N.P., Ries, L.N.A. and Goldman, G.H. Functional Characterization of Clinical Isolates of the Opportunistic Fungal Pathogen Aspergillus nidulansmSphere 2020, 5,  (on line, page numbers not yet assigned.)

Xiaoqing Wu, Gulhumay Gardashova, Lan Lan, Shuang Han, Cuncong Zhong, Rebecca T Marquez, Lanjing Wei, Spencer Wood, Sudeshna Roy, Ragul Gowthaman, John Karanicolas, Fei P Gao, Dan A Dixon, Danny R Welch, Ling Li, Min Ji, Jeffrey Aubé, Liang XuTargeting the interaction between RNA-binding protein HuR and FOXQ1 suppresses breast cancer invasion and metastasisCommunications Biology 2020; 3(1):193. 

April 2020 Publications

Albert Zhang, Brian D. Ackley, and Dong Yan.  Vitamin B12 Regulates Glial Migration and Synapse Formation through Isoform-Specific Control of PTP3/LAR PRTP Expression.  Cell Reports 2020; 30(12): 3981-3988.

Meagan Kurland, Bryn O’Meara, Dana K. Tucker, and Brian Ackley.  The Hox Gene egl-5 Acts as a Terminal Selector for VD13 Development via Wnt SignalingJ. Dev. Biol. 2020; 8(1): 5.

Anabel Soldano, Huili Yao, Josephine R. Chandler, and Mario Rivera.  Inhibiting Iron Mobilization from Bacterioferritin in Pseudomonas aeruginosa Impairs Biofilm Formation Irrespective of Environmental Iron Availability.  ACS Infect Dis. 2020; 6(3): 447-458.

E. Peter Greenberg, Josephine R. Chandler, and Mohammad R. Seyedsayamdost.  The Chemistry and Biology of Bactobolin: A 10-Year Collaboration with Natural Product Chemist Extraordinaire Jon Clardy.  J. Nat. Prod. 2020; 83(3): 738-743.

Brittny R. Smith and Stuart J. Macdonald.  Dissecting the Genetic Basis of Variation in Drosophila Sleep Using a Multiparental QTL Mapping ResourceGenes 2020; 11(3): E294.

March 2020 Publications

Joanne R. Chapman, Maureen A. Dowell, Rosanna Chan, and Robert L. UncklessThe genetic basis of natural variation in Drosophila melanogaster immune defense against Enterococcus faecalisGenes 2020; 11 (2): 234.

Taybor W Parker and Kristi L Neufeld. APC controls Wnt-induced β-catenin destruction complex recruitment in human colonocytes. Science Reports. 2020 Feb 19; 10(1):2957 PMID: 32076059

Frawley, D., C. Greco, B. Oakley, M. M. Alhussain, A. B. Fleming, N. P. Keller, and Ö. Bayram. The tetrameric pheromone module SteC-MkkB-MpkB-SteD regulates asexual sporulation, sclerotia formation and aflatoxin production in Aspergillus flavus. Cellular Microbiology 2020 Feb 18; (accepted and now available on line)

A.R. Fehr, S.A. Singh, C.M. Kerr, S. Mukai, H. Higashi, and M. Aikawa. 2020. The impact of PARPs and ADP-ribosylation on inflammation and host-pathogen interactions. Genes Dev. 2020 Feb 6. doi: 10.1101/gad.334425.119.

February 2020 Publications

Schultz, C.W., Preet, R., Dhir, T., Dixon, D.A.* and Brody, J.R.* Wiley Interdiscip. Rev. RNA. 2020; Understanding and targeting the disease-related RNA binding protein HuRin press. *Co-corresponding authors.

January 2020 Publications

A.R. FehrBacterial Artificial Chromosome-Based Lambda Red Recombination with the I-SceI Homing Endonuclease for Genetic Alteration of MERS-CoVMethods Mol. Biol. 2020; 2099:53-68

Schuler B, Borgia A, Borgia M, Heidarsson P, Holmstrom E, Nettels D, and Sottini A.  Binding without folding – the biomolecular function of disordered polyelectrolyte complexes.  Current Opinion in Structural Biology 2020; 60:66-76.

Liu H, Marquez RT, Wu X, Li K, Vadlamani S, Li S, Wang Y, Xu L, Wu D.  A non-intrusive evaluation method for tumor-targeting characteristics of nanomedicinesbased on in vivo near-infrared fluorescence imagingJ Mater Chem B 2019; 7(31):4751-4757.

Lan L, Xing M, Kashipathy MM, Douglas JT, Gao P, Battaile KP, Hanzlik RP, Lovell S, and Xu L.  Crystal and solution structures of human oncoprotein musashi-2 N-terminal RNA recognition motif 1Proteins: Structure, Function and Bioinformatics 2019. PMID: 31603583 (in press)

December 2019 Publications

M.E. Grunewald, M.G. Shaban, S.R. Mackin, A.R. Fehr, and Stanley Perlman. 2019. Murine coronavirus infection activates AhR in an IDO1-independent manner contributing to cytokine modulation and pro-viral TiPARP expression. J Virol. doi: 10.1128/JVI.01743-19. [Epub ahead of print]

R.L. Unckless and H.A. Orr. 2019. The population genetics of evolutionary rescue in diploids: X chromosomal vs. autosomal rescue. The American Naturalist. doi: 10.1086/707139

Pandey N, Keifenheim D, Yoshida MM, Hassebroek VA, Soroka C, Azuma Y, Clarke DJ. Topoisomerase II SUMOylation activates a metaphase checkpoint via Haspin and Aurora B kinases. J Cell Biol. 2019 Nov 11. pii: jcb.201807189. doi: 10.1083/jcb.201807189. [Epub ahead of print]

 

November 2019 Publications

Hanson, Mark A., Lemaitre, Bruno, and Unckless, Robert L. (2019). Dynamic evolution of antimicrobial peptides underscores trade-offs between immunity and ecological fitnessFrontiers in Immunology 10.3389.

Chakraborty M, Emerson JJ, Macdonald SJ, Long AD. (2019). Structural variants exhibit widespread allelic heterogeneity and shape variation in complex traitsNature Communications 10: 4872.

McFarlane JS, Zhang J, Wang S, Lei X, Moran GR, Lamb AL (2019).  Staphylopine and pseudopaline dehydrogenases catalyze reversible reactions and produce stereospecific metallophores.  Journal of Biological Chemistry. [Epub ahead of print]

 

October 2019 Publications

Chapman, JR, T Hill and RL Unckless. 2019. Balancing selection drives the maintenance of genetic variation in Drosophila antimicrobial peptidesGenome Biology and Evolution (Early online). doi: 10.1093/gbe/evz191.

Hill, T and RL Unckless. 2019. A deep learning approach for detecting copy number variation in next generation sequencingG3: Genes, Genomes, Genetics (Early online). doi: 10.1534/g3.119.400596.

Lea, JK and RL Unckless. 2019. An assessment of the immune costs associated with meiotic drive chromosomes in DrosophilaProceedings of the Royal Society B. 286: 20191534. doi: 10.1098/rspb.2019.1534.

 

September 2019 Publications

Wang, J., and Miao, Y. (2019) Mechanistic Insights into Specific G Protein Interactions with Adenosine ReceptorsJ. Phys. Chem. B, 123, 6462-6473.

Scott D. LaBrie, Zoë E. Dimond, Kelly S. Harrison, Srishti Baid, Jason Wickstrum, Robert J. Suchland, P. Scott Hefty. (2019) Transposon Mutagenesis in Chlamydia trachomatis Identifies CT339 as a ComEC Homolog Important for DNA Uptake and Lateral Gene TransferMBio, 2019, 10(4), e01343-19.

Moran GR, Lamb AL. (2019) The tenured itch: ready to treat your midcareer malaise?  ASBMB Today, 18(7), 49-50.

Wang DStoveken HMZucca SDao MOrlandi CSong CMasuho IJohnston COpperman KJGiles ACGill MSLundquist EAGrill BMartemyanov KA. (2019) Genetic behavioral screen identifies an orphan anti-opioid systemScience, 15 Aug 2019 first release.

 

August 2019 Publications

Benomar S, Evans K, Unckless R and Chandler JR. Efflux pumps in Chromobacterium species increase antibiotic resistance and promote survival in a co-culture competition model. AEM In press.

Zanders, SE and RL Unckless. 2019. Fertility costs of meiotic drivers. Current Biology 29: R512-520.

Koseva BS, Hackett JL, Zhou Y, Harris BR, Kelly JK, Greenfield MD, Gleason JM, Macdonald SJ. 2019. Quantitative Genetic Mapping and Genome Assembly in the Lesser Wax Moth Achroia grisella. Genes, Genomes, Genetics 9: 2349-2361.

Grau, M. F., R. Entwistle, C. E. Oakley, C. C. C. Wang, and B. R. Oakley. 2019. Overexpression of an LaeA-like Methyltransferase Upregulates Secondary Metabolite Production in Aspergillus nidulans. ACS Chem Biol 14:1643-1651.

Zeng Y, Ma J, Xu L, Wu D. Natural Product Gossypol and Its Derivatives in Precision Cancer Medicine. Curr Med Chem 2019; 26(10):1849-1873. PMID: 28545375.

 

July 2019 Publications

Gujar MR, Stricker AM, Lundquist EA (2019) RHO-1 and the Rho GEF RHGF-1 interact with UNC-6/Netrin signaling to regulate growth cone protrusion and microtubule organization in Caenorhabditis elegansPLoS Genet 15(6): e1007960.

McFarlane JS, Ronnebaum TA, Meneely KM, Chilton A, Fenton AW, Lamb AL.  Changes in the allosteric site of human liver pyruvate kinase upon activator binding include the breakage of an intersubunit cation-π bond.  Acta Crystallogr F Struct Biol Commun. 75, 461-469.

Tom Hill, Boryana S. Koseva, Robert L. UncklessThe Genome of Drosophila innubila Reveals Lineage-Specific Patterns of Selection in Immune Genes” in Molecular Biology and EvolutionMol.Biol.Evol. 36(7):1405-1417.

 

June 2019 Publications

Matthew E. Grunewald, Yating Chen, Chad Kuny, Takashi Maejima, Robert Lease, Dana Ferraris, Masanori Aikawa, Christopher S. Sullivan, Stanley Perlman, Anthony R. Fehr (2019) The coronavirus macrodomain is required to prevent PARP-mediated inhibition of virus replication and enhancement of IFN expression. PLOS Pathogens. May 16.

Duxbury, E.ML., Day, J.P., Vespasiani, D.M., Thüringer,Y.,  Tolosana, I., Smith.S.CL., Tagliaferri, L., Kamacioglu, A., Lindsley, I., Love, L., Unckless, R.L., Jiggins, F.M., Longdon, B., (2019) Host-pathogen coevolution increases genetic variation in susceptibility to infection. eLife. Apr 30.

Baker, H.A., Fabian, C.J., Hastings, R.C., Dixon, D.A., Nydegger, J.L., Phillips, T.A., Powers, K.R., Kimler, B.F. (2019) Circulating adipose stromal cells as a response biomarker in phase II energy balance trials of obese breast cancer survivors and high-risk women. Breast Cancer Res. Treat. Apr 30

Al-Hashimi, H., Chiarellie, T., Lundquist, E.A., Buechner, M., Novel exc Genes Involved in Formation of the Tubular Excretory Canals of Caenorhabditis elegans. G3: Genes/Genomes/Genetics on May 7. G3 (Bethesda). 2019 May 7;9(5):1339-1353. doi: 10.1534/g3.119.200626. PMID: 30885922

 

May 2019 Publications

Everman, E. R., McNeil, C. L., Hackett, J. L., Bain, C. L. and Macdonald, S. J. (2019) Dissection of complex, fitness-related traits in multiple Drosophila mapping populations offers insight into the genetic control of stress resistance. Genetics 211: 1449-1467.

New, J., Subramaniam, D., Ramalingam, S., Enders, J., Sayed, A.A.A., Ponnurangam, S., Standing, D. Ramamoorthy, P., O'Neil, M., Dixon, D.A., Umar, S., Jensen, R.A., Thomas, S.M. and Anant, S. Pleotropic role of RNA binding protein CELF2 in Autophagy Induction. Molecular Carcinogenesis. 2019; 1-10.

 

April 2019 Publications

Monteleone, N.J., Moore, A.E., Iacona, J.R., Lutz, C.S  and Dixon, D.A. miR-21-mediated regulation of 15-hydroxyprostaglandin dehydrogenase in colon cancer. Scientific Reports, 2019.

Elramli, N., Karahoda, B., Bayram, Ö. S. Frawley, D., Ulas, M., Oakley, C. E., Oakley, B. R., Seiler, S. and Bayram, Ö. (In Press) Assembly of a heptameric STRPAK complex is required for coordination of light-dependent multicellular fungal development with secondary metabolism in Aspergillus nidulansIn Press: PLoS Genetics. 

Horio, T., Szewczy, E., Oakley, C. E., Osmani, A. H., Osmani, S. A. and Oakley, B. R. (2019) SUMOlock reveals a more complete Aspergillus nidulans SUMOylome. Fungal Genet. Biol. 127:50-59.

 

March 2019 Publications

Legrand N, Dixon DA, Sobolewski C. AU-rich elements-binding proteins in colorectal cancer. World J Gastrointest Oncol 2019; 11(2): 71-90

 

February 2019 Publications

Mutreja Y, Combs B, Gamblin TC (2018) FTDP-17 mutations alter the aggregation and microtubule stabilization propensity of tau in an isoform-specific fashionBiochemistry. In Press. DOI: 10.1021/acs.biochem.8b01039

Kenjic N, Hoag MR, Moraski GC, Caperelli CA, Moran GR, Lamb AL.  PvdF of pyoverdin biosynthesis is a structurally unique N10-formyltetrahydrofolate-dependent formyltransferase.  Arch Biochem Biophys [Epub ahead of print]

Green LC, Anthony SR, Slone S, Lanzillotta L, Nieman ML, Wu X, Robbins N, Jones SM, Roy S, Owens Iii AP, Aube J, Xu L, Lorenz JN, Blaxall BC, Rubinstein J, Benoit JB, Tranter M. Human antigen R as a therapeutic target in pathological cardiac hypertrophy. JCI Insight. 2019 Jan 22. [Epub ahead of print] PubMed PMID: 30668549.

 

January 2019 Publications

Ronnebaum TA, McFarlane JS, Prisinzano TE, Booker SJ, Lamb AL (2018). Stuffed methyltransferase domain catalyzes the penultimate step of pyochelin biosynthesisBiochemistry. In Press.  DOI: 10.1021/acs.biochem.8b00716

December 2018 Publications

Miao, Y.*, Bhattarai, A., Nguyen, A. T., Christopoulos, A., and May, L. T. (2018) Structural Basis for Binding of Allosteric Drug Leads in the Adenosine A1 Receptor, Scientific Reports, 8:16836.https://doi.org/10.1038/s41598-018-35266-x 

 

November 2018 Publications

Michelle F. Grau, Ruth Entwistle, Yi-Ming Chiang, Manmeet Ahuja, C. Elizabeth Oakley, Tomohiro Akashi, Clay C. C. Wang, Richard B. Todd, and Berl R. Oakley.  Hybrid Transcription Factor Engineering Activates the Silent Secondary Metabolite Gene Cluster for (+)-Asperlin in Aspergillus nidulans.  ACS Chem Biol, Article ASAP

Bhattarai, A., and Miao, Y.* Gaussian accelerated molecular dynamics for elucidation of drug pathwaysExpert Opinion On Drug Discovery. In Press

Zhang, J., Wang, N., Miao, Y.*, Hauser, F., Rappel, W.-J., McCammon, J. A., and Schroeder, J.* Identification of SLAC1 anion channel residues required for CO2/bicarbonate sensing and regulation of stomatal movementsProc Natl Acad Sci, In Press

Utesch, T., Catalina, A. d. M., Schattenberg, C., Paege, N., Schmieder, P., Krause, E., Miao, Y., McCammon, J. A., Meyer, V., Jung, S., and Mroginski, M. A Computational Modeling Approach Predicts Interaction of the Antifungal Protein AFP from Aspergillus giganteus with Fungal Membranes via Its γ-Core MotifmSphere, 3(5), e00377-18

 

October 2018 Publications

Al-Hashimi H, Hall DH, Ackley BD, Lundquist EA, Buechner M “Intermediate filaments EXC-2 and IFA-4 Maintain Luminal Structure of the Tubular Excretory Canals in Caenorhabditis elegans” Genetics, v. 210, issue 2, pp. 637-652..

McFarlane JS, Hagen R, Chilton AS, Forbes D, Lamb AL, Ellis HR.. Not as easy as π: an insertional residue does not explain the π-helix gain-of-function in two component FMN reductases. Protein Science [Epub ahead of print]

Li J, Smith AR, Marquez RT, Li J, Li K, Lan L, Wu X, Zhao L, Ren F, Wang Y, Wang Y, Jia B, Xu L, Chang Z. MicroRNA-383 acts as a tumor suppressor in colorectal cancer by modulating CREPT/RPRD1B expression. Molecular Carcinogenesis 2018; 57(10):1408-1420. 

Lan L, Liu H, Smith AR, Appelman C, Yu J, Larsen S, Marquez RT, Wu X, Liu FY, Gao P, Gowthaman R, Karanicolas J, De Guzman RN, Rogers S, Aubé J, Neufeld KLXu LNatural product derivative Gossypolone inhibits Musashi family of RNA-binding proteins. BMC Cancer 2018; 18(1):809.

 

September 2018 Publications

Bandyopadhyay A, Wang H, Ray JCJLineage space and the propensity of bacterial cells to undergo growth transitions. PLoS Comput Biol. 2018 Aug 22;14(8):e1006380. doi: 10.1371/journal.pcbi.1006380

McElfresh GC, Ray JCJ. 2018. Intergenerational Cellular Signal Transfer and Erasure. In: The interplay of thermodynamics and computation in natural and artificial systems. D. Wolpert, C. Kempes, J. Grochow and P. Stadler, Eds. Santa Fe Institute Press.

Franklin MW, Slusky JSGTight Turns of Outer Membrane Proteins: An Analysis of Sequence, Structure, and Hydrogen Bonding. J Mol Biol. 2018 Sep 14;430(18 Pt B):3251-3265. doi: 10.1016/j.jmb.2018.06.013. Epub 2018 Jun 23.

Kato J, Dey S, Soto JE, Butan C, Wilkinson MC, De Guzman RN, Galan JE. A protein secreted by the Salmonella type III secretion system controls needle filament assemblyeLife, 7, e35886, 2018. 

Gujar MR, Sundararajan L, Stricker A, Lundquist EAControl of Growth Cone Polarity, Microtubule Accumulation, and Protrusion by UNC-6/Netrin and Its Receptors in Caenorhabditis elegans. Genetics. 2018 Jul 25. pii: genetics.301234.2018. doi: 10.1534/genetics.118.301234. [Epub ahead of print]PMID:30045855

 

August 2018 Publications

Davido DJ, Tu EM, Wang H, Korom M, Gazquez Casals A, Reddy PJ, Mostafa HH, Combs B, Haenchen SD, Morrison LA. Attenuated HSV-1 expressing a mutant form of ICP6 stimulates a strong immune response that protects mice against HSV-1-induced corneal disease. J Virol. 2018 Jun 27. pii: JVI.01036-18. doi: 10.1128/JVI.01036-18. [Epub ahead of print]

V. Paolillo (Lundquist lab), C.B. Jenkinson, T. Horio, B.R. Oakley Cyclins in aspergilli: Phylogenetic and functional analyses of group I cyclins. in Science Direct June 2018.

 

July 2018 Publications

Hill T (Unckless Lab), Betancourt AJ Extensive exchange of transposable elements in the Drosophila pseudoobscura group in Mobile DNA. 2018

 

June 2018 Publications

Abisado R, Benomar S, Klaus JR, Dandekar AA, Chandler JRBacterial quorum sensing and microbial community interactions. MBio 2018 May 22;9(3). pii: e02331-17. doi: 10.1128/mBio.02331-17.

Klaus JR, Deay J, Neuenswander B, Hursh W, Gao Z, Bouddhara T, Williams TD, Douglas J, Monize K, Martins P, Majerczyk C, Seyedsayamdost MR, Peterson BR, Rivera M, Chandler JRMalleilactone is a Burkholderia pseudomallei virulence factor regulated by antibiotics and quorum sensing. Journal of Bacteriology. 2018 May 7. pii: JB.00008-18. doi: 10.1128/JB.00008-18. [Epub ahead of print]

Miao Y Acceleration of Biomolecular Kinetics in Gaussian Accelerated Molecular Dynamics. Journal of Chemical Physics, 149(7):072308. 2018.

 

May 2018 Publications

Preet R, Dixon DAMutant KRAS Exosomes Influence the Metabolic State of the Colon Microenvironment Cellular and Molecular Gastroenterology and Hepatology, Volume 5, Issue 4, 2018, Pages 627-629.e6.

Alan JKRobinson SKMagsig KLDemarco RSLundquist EAThe Atypical Rho GTPase CHW-1 Works with SAX-3/Robo To Mediate Axon Guidance in Caenorhabditis elegans 2018 Apr 13. pii: g3.200148.2018. doi: 10.1534/g3.118.200148. [Epub ahead of print]

McFarlane JS, Davis CL, Lamb AL.  Staphylopine, pseudopaline, and yersinopine dehydrogenases: a structural and kinetic analysis of a new functional class of opine dehydrogenase.  J. Biol. Chem.  [Epub ahead of print]

 

April 2018 Publications

CL Shelton, Lamb AL.  Unraveling the structure and mechanism of the MST(ery) Enzymes.  Trends Biochem Sci.  [Epub ahead of print]

Huang YM, McCammon JA, Miao YReplica exchange Gaussian accelerated molecular dynamics: Improved enhanced sampling and free energy calculationJ Chem Theory Comput, 2018 Article ASAP, DOI: 10.1021/acs.jctc.7b01226. 

Miao Y, McCammon JA Mechanism of the G-Protein Mimetic Nanobody Binding to a Muscarinic G-Protein-Coupled ReceptorProc Natl Acad Sci U S A, 2018 In Press, DOI: 10.1073/pnas.1800756115.

Y Zeng, J Liu, S Yang, W Liu, L Xu, R Wang. Time-lapse live cell imaging to monitor doxorubicin release from DNA origami nanostructures. Journal of Materials Chemistry B, 2018.

 

March 2018 Publications

Brody JR, Dixon DAComplex HuR function in pancreatic cancer cellsWiley Interdiscip Rev RNA. 2018 Feb 16. DOI: 10.1002/wrna.1469.

Miao Y, Huang YM, Walker R, McCammon JA, & Chang C-eA. Ligand Binding Pathways and Conformational Transitions of the HIV ProteaseBiochemistry, DOI: 10.1021/acs.biochem.7b01248.

Peng W, Furuuchi N, Aslanukova L, Huang YH, Brown SZ, Jiang W, Addya S, Vishwakarma V, Peters E, Brody JR, Dixon DA, Sawicki JA. Elevated HuR in Pancreas Promotes a Pancreatitis-Like Inflammatory Microenvironment That Facilitates Tumor DevelopmentMol Cell Biol.  2018 Jan 16;38(3). pii: e00427-17. doi: 10.1128/MCB.00427-17.

Ronnebaum TA, Lamb AL.. Nonribosomal peptides for iron acquisition: pyochelin biosynthesis as a case study.  Current Opinion in Structural Biology 53, 1-11.

Smith, BR, Unckless, RLDraft Genome Sequence of Lysinibacillus fusiformis Strain Juneja, a Laboratory-Derived Pathogen of Drosophila melanogaster. Genome Announcements 6: e01571-17.

 

February 2018 Publications

Evans KC, Benomar S, Camuy-Vélez LA, Nasseri EB, Wang X, Neuenswander B, Chandler JR.  Quorum-sensing control of antibiotic resistance stabilizes cooperation in Chromobacterium violaceum. The ISME J 2018 10.1038/s41396-018-0047-7.

Mostafa HH, Thompson TW, Konen AJ, Haenchen SD, Hilliard JG, Macdonald SJ, Morrison LA, Davido DJHerpes Simplex Virus 1 Mutant with Point Mutations in UL39 Is Impaired for Acute Viral Replication in Mice, Establishment of Latency, and Explant-Induced Reactivation.J Virol. 2018 Jan 10. pii: JVI.01654-17. doi: 10.1128/JVI.01654-17.

Muralidharan R, Mehta M, Ahmed R, Roy S, Xu L, Aubé J, Chen A, Zhao YD, Herman T, Ramesh R, Munshi A. HuR-targeted small molecule inhibitor exhibits cytotoxicity towards human lung cancer cells. Scientific Reports2017; 7:9694.

Ni Z, He J, Wu Y, Hu C, Dai X, Yan X, Li B, Li X, Xiong H, Li Y, Li S, Xu L, Li Y, Lian J, He F. AKT-mediated phosphorylation of ATG4B impairs mitochondrial activity and enhances the Warburg effect in hepatocellular carcinoma cellsAutophagy [Epub ahead of print].

Dohn, J, Grubbs A, Oakley E,  Oakley BNew multi-marker strains and complementing genes for Aspergillus nidulans molecular biologyFungal Genetics and Biology [Epub ahead of print].

 

January 2018 Publications

Hill T and Unckless RLThe dynamic evolution of theDrosophila innubila Nudivirus” in Infection, Genetics and Evolution. ScienceDirect 2017 S1567134817303933

Bardai FH, Wang L, Mutreja Y, Yenjerla M, Gamblin TC, Feany MB. A conserved cytoskeletal signaling cascade mediates neurotoxicity of FTDP-17 tau mutations in vivo. Journal of Neuroscience, 14 November 2017, 1550-17.

Mutreja Y and Gamblin TCOptimization of in vitro conditions to study the arachidonic acid induction of 4R isoforms of the microtubule-associated protein tau. Methods in Cell Biology 141:65-88.

McFarlane JS, Lamb ALBiosynthesis of an Opine Metallophore by Pseudomonas aeruginosa. Biochemistry 56(45): 5967-5971.

Yu J, Lan L, Lewin SJ, Rogers SA, Roy A, Wu X, Gao P, Karanicolas J, Aube J, Sun B, and Xu LIdentification of novel small molecule Beclin 1 mimetics activating autophagyOncotarget 2017; 8(31):51355. PMC5584254.

December 2017/January 2018 Publications

Hill T and Unckless RL. The dynamic evolution of the Drosophila innubila Nudivirus” in Infection, Genetics and Evolution. ScienceDirect 2017 S1567134817303933

Bardai FH, Wang L, Mutreja Y, Yenjerla M, Gamblin TC, Feany MB. A conserved cytoskeletal signaling cascade mediates neurotoxicity of FTDP-17 tau mutations in vivo. Journal of Neuroscience, 14 November 2017, 1550-17.

Mutreja Y and Gamblin TC. Optimization of in vitro conditions to study the arachidonic acid induction of 4R isoforms of the microtubule-associated protein tau. Methods in Cell Biology 141:65-88.

McFarlane JS, Lamb AL. Biosynthesis of an Opine Metallophore by Pseudomonas aeruginosaBiochemistry 56(45): 5967-5971.

Yu J, Lan L, Lewin SJ, Rogers SA, Roy A, Wu X, Gao P, Karanicolas J, Aube J, Sun B, and Xu L. Identification of novel small molecule Beclin 1 mimetics activating autophagy. Oncotarget 2017; 8(31):51355. PMC5584254.

 

November 2017 Publications

Hill T and Unckless RL. Baculovirus molecular evolution via gene turnover and recurrent positive selection of key genes. Journal of Virology (Early Online) JVI.01319-17.  

Highfill CA, Tran JH, Nguyen SKT, Moldenhauer TR, Wang X, Macdonald SJ. Naturally Segregating Variation at Ugt86Dd Contributes to Nicotine Resistance in Drosophila melanogaster. Genetics 2017, 207:311-325.

Gujar MR, Stricker AM, Lundquist EA. Flavin monooxygenases regulate Caenorhabditis elegans axon guidance and growth cone protrusion with UNC-6/Netrin signaling and Rac GTPases.PLoS Genet. 2017 Aug 31;13(8):e1006998. doi: 10.1371/journal.pgen.1006998. eCollection 2017 Aug.

 

September 2017 Publications

Zeng Y, Ma J, Xu L, Wu D. Natural Product Gossypol and Its Derivatives in Precision Cancer Medicine. Current Medicinal Chemistry. 2017 (in press).

Yu J, Zhao X, Zhang N, You C, Yao G, Zhu J, Xu L, and Sun B. Identification of novel 3-nitroacridines as autophagy inducers in gastric cancer cells. New Journal of Chemistry2017; 41(10):4087-4095.

Zheng Y-G, Wu X-Q, Su J, Jiang P, Xu L, Gao J, Cai B, and Ji M. Design and synthesis of a novel photoaffinity probe for labelling egf receptor tyrosine kinases. Journal of Enzyme Inhibition and Medicinal Chemistry 2017; 32(1):954-959.

 

August 2017 Publications

Rowland MA, Greenbaum JM, Deeds EJ.  Crosstalk and the evolvability of intracellular communication.  Nature Communications 8: 16009.

 

July 2017 Publications

Najarro MA, Hackett JL, Macdonald SJ. Loci Contributing to Boric Acid Toxicity in Two Reference Populations of Drosophila melanogasterG3 (Bethesda) 7(6):1631-1641.

Sorger R, Bachman JA, Smith A, Sorger PK, Deeds EJ.  Fundamental trade-offs between information flow in single cells and cellular populations.  Proceedings of the National Academy of Sciences USA 114(22): 555-5760.

 

June 2017 Publications

Zhang P, Wang X, Fan A, Zheng Y, Liu X, Wang S, Zou H, Oakley BR, Keller NP, Yin WP.  A cryptic pigment biosynthetic pathway uncovered by heterologous expression is essential for conidial development in Pestalotiopsis fici. Mol Microbiol.  [Epub ahead of print]

Peterson B, Xu L, Levy M.  Targeting multiple receptors on a cell surface for specific cell targeting.  US Patent No.  US 9,636,419, issued May 2.

 

May 2017 Publications

Eshelman K, Yao H, Punchi Hewage AN, Deay JJ, Chandler JR, Rivera M.  Inhibiting the BfrB:Bfd interaction in Pseudomonas causes irreversible iron accumulation in bacterioferritn and iron deficiency in the bacterial cytosol.  Metallomics [Epub ahead of print]

Kaur K, Wu X, Fields JK, Johnson DK, Lan L, Pratt M, Somoza AD, Wang CCC, Karanicolas J, Oakley BRXu LDe Guzman RN.  The fungal natural product azaphilone-9 binds to HuR and inhibits HuR-RNA interaction in vitro.  PLoS One 12(4):e0175471.

 

February 2017 Publications

Gao FJ, Shi L, Hines T, Hebbar S, Neufeld KL, Smith DS.  Insulin signaling regulates a functional interaction between Adenomatous Polyposis Coli (APC) and cytoplasmic dynein.  Molecular Biology of the Cell. [Epub ahead of print]

Josephson MP, Aliani R, Norris ML, Ochs ME, Gujar M, Lundquist EA.  The Caenorhabditis elegans NF2/Merlin Molecule NFM-1 Non-autonomously Regulates Neuroblast Migration and Interacts Genetically with the Guidance Cue SLT-1/Slit.  Genetics [Epub ahead of print]

Nussinov R, Papin JA, Vakser I.  Computing the dynamic supramolecular structural proteome.  PLoS Computational Biology 13: e1005290.

Sung CT, Chang S-L, Entwistle R, Ahn G, Lin T-S, Petrova V, Yeh H-H, Praseuth MB, Chiang Y-M, Oakley BR, Wang CCC.  Overexpression of a three-gene conidial pigment biosynthetic pathway in Aspergillus nidulans reveals the first NRPS known to acetylate tryptophan. Fungal Genetics and Biology [Epub ahead of print]

Wolfe AR, Ernlund A, McGuinness W, Lehmann C, Carl K, Balmaceda N, Neufeld KL.  Suppression of intestinal tumorigenesis in Apc mutant mice by Musashi-1 deletion.  Journal of Cell Science [Epub ahead of print]

December 2016 Publications

Cloud-Richardson, Smith BR, Macdonald SJ.  Genetic dissection of intraspecific variation in a male-specific sexual trait in Drosophila melanogaster.  Heredity 117, 417-26.

 

November 2016 Publications

Beaupre BA, Roman JV, Hoag MR, Meneely KM, Silvaggi NR, Lamb AL, Moran GR.  Ligand binding phenomena that pertain to the metabolic function of renalase.  Arch Biochem Biophys 612, 46-56.

Blanco FF, Preet R, Aguado A, Vishwakarma V, Stevens LE, Vyas A, Padhye S, Xu L, Weir SJ, Anant S, Meisner-Kober N, Brody JR, and Dixon DA. Impact of HuR inhibition by the small molecule MS-444 on colorectal cancer cell tumorigenesis. Oncotarget [Epub ahead of print]

Oakley CE, Ahuja M, Sun WW, Entwistle R, Akashi T, Yaegashi J, Guo CJ, Cerqueira GC, Wortman JR, Wang CC, Chiang YM, Oakley BR. Discovery of McrA, a master regulator of Aspergillus secondary metabolism. Mol Microbiol [Epub ahead of print]

Sun J, Chen Y, Li K, Huang Y, Fu X, Zhang X, Zhao W, Wei Y, Xu L, Zhang P, Venkataramanan R, and Li S. A prodrug micellar carrier assembled from polymers with pendant farnesyl thiosalicylic acid moieties for improved delivery of paclitaxel. Acta Biomaterialia 43, 282-291

 

October 2016 Publications

Hackett JL, Wang X, Smith BR, Macdonald SJ.  Mapping QTL Contributing to Variation in Posterior Lobe Morphology between Strains of Drosophila melanogaster.  PLoS One. 11: e0162573

Huang W, Beer RL, Delaspre F, Wang G, Edelman HE, Park H, Azuma M, Parsons MJ.  Sox9b is a mediator of retinoic acid signaling restricting endocrine progenitor differentiation.  Developmental Biology 418, 28-39.

Li J, Wehmeyer G, Lovell S, Battaile KP, Egan SM. 1.65 Å resolution structure of AraC family transcriptional activator ToxT from Vibrio cholera.  Acta Cryst.  F72:726-731.

Meneely KM, Ronnebaum TA, Riley AP, Prisinzano TE, Lamb AL. (2016)  Holo structure and steady state kinetics of the thiazolinyl imine reductases for siderophore biosynthesis.  Biochemistry 55, 5423-33.

Slone S, Anthony SR, Wu X, Benoit JB, Aube J, Xu L, Tranter M.  Activation of HuR downstream of p38 MAPK promotes cardiomyocyte hypertrophy. Cellular Signaling 28, 1735-1741.

Xu B-Q, Fu Z-G, Meng Y, Wu X-Q, Wu B, Xu L, Jiang J-L, Li L, and Chen Z-N. Gemcitabine enhances cell invasion via activating HAb18G/CD147-EGFR-pSTAT3 signaling. Oncotarget [Epub ahead of print]

 

September 2016 Publications

Highfill CA, Reeves GA, Macdonald SJ.  Genetic analysis of variation in lifespan using a multiparental advanced intercross Drosophila mapping population.  BMC Genet.  17:113.

Im W, Liang J, Olson A, Zhou HX, Vajda S, Vakser IA.  Challenges in structural approaches to cell modeling.  J Mol Biol 428: 2943-64.

Park H, Galbraith R, Turner T, Mehojah J, Azuma M.  Loss of Ewing sarcoma EWS allele promotes tumorigenesis by inducing chromosomal instability in zebrafish.  Sci Rep doi.10.1038/srep32297.

 

August 2016 Publications

Meneely KM, Sundlov JA, Gulick AM, Moran GR, Lamb AL.  An open and shut case: the role of magnesium in MST enzymes.  J. Am. Chem. Soc.  [Epub ahead of print]

Josephson MP, Miltner AM, Lundquist EA. Non-autonomous Roles of MAB-5/Hox and the Secreted Basement Membrane Molecule SPON-1/F-spondin in Caenorhabditis elegans Neuronal Migration. Genetics. 2016 May 25. pii: genetics.116.188367. [Epub ahead of print]

Reiner DJ, Lundquist EA. Small GTPases. WormBook. 2016 May 24:1-99. doi: 10.1895/wormbook.1.67.2. [Epub ahead of print]

 

July 2016 Publications

Gruseendorf KA, Trezza CJ, Salem AT, Al-Hashimi H, Mattingly BC, Kampmeyer DE, Khan L, Hall DH, Gobel V, Ackley BDBuechner M. Facilitation of Endosomal Recycling by an IRG Protein Homologue Maintains Apical Tubule Structure in Caenorhabditis elegansGenetics [Epub ahead of print]

Sridharan V, Azuma Y.  SUMO-interacting motifs (SIMs) in Polo-like kinase 1-interacting checkpoint helicase (PICH) ensure proper chromosome segregation during mitosis.  Cell Cycle [Epub ahead of print]

Yeh HH, Ahuja M, Chiang YM, Oakley CE, Moore S, Yoon O, Hajovsky H, Bok JW, Keller NP, Wang CC, Oakley BR.  Resistance gene-guided genomie mining: serial promoter exchanges in Aspergillus nidulans reveal the biosynthetic pathway for fellutamide B, a proteasome inhibitor.  ACS Chem Biol [Epub ahead of print]

Yoshida MM, Ting L, Gygi SP, Azuma Y.  SUMOylation of DNA topoisomerase IIα regulates histone H3 kinase Haspin and H3 phosphorylation in mitosis.  J. Cell Biol 213: 665-78.

 

June 2016 Publications

Basha A, Basha F, Ali SK, Hanson PR, Oakley BR, Hajovsky H, Mitscher LA.  Onychomycosis and its Chemotherapy. Curr Med Chem 23: 1609-1624.

Lanza C, Tan EP, Zhang Z, Machacek M, Brinker AE, Azuma M,  Slawson C.  Reduced O-GlcNAcase expression promotes mitotic errors and spindle defects.  Cell Cycle 15: 1363-75.

Tseng BS, Majerczyk CD, Passos da Silva D, Chandler JR, Greenberg EP, Parsek MR.  Quorum sensing influences Buukholderia thailandensis biofilm development and matric production.  J Bacteriol [Epub ahead of print]

 

May 2016 Publications

Nariya MK, Israeli J, Shi JJ, Deeds EJ.  Mathematical model for length control by the timing of substrate switching in the type III secreation system.  PLoS Comput Biol: e1004851.

 

April 2016 Publications

Ray JCJ.  Survival of Phenotypic Information during Cellular Growth Transitions.  ACS Synth Biol. {Epub ahead of print].

Ray JCJ, Wickersheim ML, Jalihal AP, Adeshina YO, Cooper TF, Balázsi G. Cellular Growth Arrest and Persistence from Enzyme Saturation.  PLoS Comput Biol. 12(3):e1004825.

Wang X, Hinshaw KC, Macdonald SJChandler JR.  Draft genome sequence of Chromobacterium violaceum strain CV017.  Genome Accounc 4(2): e00080-16.

Wu X, Tang W, Marquez RT, Li K, Highfill CA, He F, Lian J, Lin J, Fuchs JR, Ji M, Li L, Xu L.  Overcoming chem/radio-resistance of pancreatic cancer by inhibiting STAT3 signaling.  Oncotarget [Epub ahead of print].

 

March 2016 Publications

Josephson MP, Chai Y, Ou G, Lundquist EA.  EGL-20/Wnt and MAB-5/Hox Act Sequentially to Inhibit Anterior Migration of Neuroblasts in C. elegans.  PLoS One: e0148658.

 

February 2016 Publications

Johnson DK, Karanicolas J.  Ultra-high-throughput structure-based virtual screening for small-molecule inhibitors of protein-protein interactions.  J. Chem. Inf. Model. [Epub ahead of print]

 

January 2016 Publications

Najarro MA, Hackett JL, Smith BR, Highfill CA, King EG, Long AD, Macdonald SJ.  Identifying loci contributing to natural variation in xenobiotic resistance in Drosophila.  PLoS Genet 11(11): e1005663.

Wiley EO, Fuiten AM, Doosey MH, Lohman BK, Merkes C, Azuma M.  The caudal skeleton of the zebrafish, Danio rerio, from a phylogenetic perspective: a polyural interpretation of homologous structures.  Copeia 103 (4), 740-750.

December 2015 Publications

Chiang Y-M, Ahuja M., Oakley CE, Entwistle R, Asokan A, Zutz C, Wang CC, Oakley BR. Development of genetic dereplication strain in Aspergillus nidulans results in the discovery of Aspercryptin. Angew Chem Int Ed Eng [Epub ahead of print]

LaFayette S, Houle D, Beaudoin T, Wojewodka G, Radzioch D,  Hoffman L, Burns J, Dandekar A, Smalley N, Chandler JR, Zlosnik J, Speert D, Bernier J, Matouk E, Brochiero E, Rousseau S, Nguyen D. Cystic fibrosis-adapted Pseudomonas aeruginosa quorum sensing lasR mutants cause hyper-inflammatory responses. Science Adv 1: e1500199

November 2015 Publications

Barta ML, Battaile KP, Lovell S, Hefty PS.  Hypothetical Protein CT398 (CdsZ) Interacts with σ54 (RpoN)-Holoenzyme and the Type III Secretion Export Apparatus in Chlamydia trachomatis.  Protein Sci [Epub ahead of print]

Gonzalez C, Ray JCJ, Manhard M, Adams RM, Nevozhay D, Morozov AV, Balazsi G.  Stress-response balance drives the evolution of a network module and its host genome.  Mol Systems Biol 11: 827.

Oakley BR, Paolillo V, Zheng Y.  gamma-tubulin complexes in microtubule nucleation and beyond.  Mol Biol Cell 26: 2957-2962.

Truong TT, Seyedsayamdost M, Greenberg EP, Chandler JR.  A Burkholderia thailandensis acyl-homoserine lactone-independent LuxR homolog that activates production of the cytotoxin malleilactone.  J. Bacteriol [Eub ahead of print]

 

August 2015 Publications

Fowler AM, Shinogle HE, Davido DJ.  Development of a novel cell-based assay to monitor the transactivation activity of the HSV-1 protein ICP0.  Antiviral Res 120: 1-6.

Gowthaman R, Lyskov S, Karanicolas J.  DARC 2.0: Improved docking and virtual screening at protein interaction sites.  PLoS One 10(7):e0131612.

Gowthaman R, Miller SA, Robers S, Khowsathit J, Lan L, Bai N, Johnson DK, Liu C, Xu L, Anbanandam A, Aube J, Roy A, Karanicolas J.  DARC: Mapping surface topography by ray-casting for effective virtual screening at protein interaction sites.  J. Med Chem.  [Epub ahead of print]

Guo C-J, Sun W-W, Bruno KS, Oakley BR, Keller NP, Wang CCC.  Spatial regulation of a common precursor from two distinct genes generates metabolite diversity. Chemical Science [In Press]

Ryu H, Yoshida MM, Sridharan V, Kumagai A, Dunphy WG, Dasso M, Azuma Y.  SUMOylation of the C_terminal domain of DNA topoisomerase IIa regulates the centromeric localization of Claspin.  Cell Cycle [Epub ahead of print]

Smalley NE, An D, Parsek M, Chandler JR, Dandekar A. Quorum sensing protects Pseudomonas aeruginosa against cheating by other species in a laboratory co-culture model.  J Bacteriol [EPub ahead of print]

Sundararajan L, Norris ML, Lundquist EA.  SDN-1/Syndecan Acts in Parallel to the Transmembrane Molecule MIG-13 to Promote Anterior Neuroblast Migration.  G3 (Bethesda) [Epub ahead of print].

Wang B, Li K, Jin M, Qiu R, Liu B, Oakley BR, Xiang X.  The Aspergillus nidulans bimC4 mutation provides an excellent tool for identification of kinesin-14 inhibitors. Fungal Genet. Biol. 82:51-55.

 

July 2015 Publications

Newton AH, Danahy DB, Chan MA, Benedict SH.  Timely blockade of ICAM-1.LFA-1 interaction prevents disease onset in a mouse model of emphysema.  Immunotherapy [Epub ahead of print]

 

June 2015 Publications

Gilmore MS, Rauch M, Ramsey MM, Himes PR, Varahan S, Manson JM, Lebreton F, Hancock LE.  Pheromone killing of multidrug-resistant Enterococcus faecalis V583 by native commensal strains.  Proc Natl Acad Sci USA [Epub ahead of print]

Hartin SN, Hudson ML, Yingling C, Ackley BD.  A synthetic lethal screen identifies a role for Lin-44/Wnt in C. elegans embryogenesis.  PLoS One: e0121397.

Lamb AL.  Breaking a pathogen’s iron will: inhibiting siderophore production as an antimicrobial strategy.  Biochim Biophys Acta 1854, 1054-1070.

Shogan BD, Belogortseva N, Luong PM, Zaborin A, Lax S, Bethel C, Ward M, Muldoon JP, Singer M, An G, Umanskiy K, Konda V, Shakhsheer B, Luo J, Klabbers R, Hancock LE, Gilbert J, Zaborina O, Alverdy JC.  Collagen Degradation and MMP9 activation by Enterococcus faecalis contribute to intestinal anastomotic leak.  Sci Transl Med 7(286):286ra68.

 

May 2015 Publications

Boutell C, Davido DJ. A quantitative assay to monitor HSV-1 ICP0 ubiquitin ligase activity in vitroMethods 2015 Apr 8 [Epub ahead of print]

 Lan L, Appelman C, Smith AR, Yu J, Larsen S, Marquez RT, Wu X, Gao P, Roy A, Anbanandam A, Gowthaman R, Karanicolas JDe Guzman RN, Rogers SA, Aube J, Ji M, Cohen RS, Neufeld KLXu L. Natural product (–)-gossypol inhibits colon cancer cell growth by targeting RNA-binding protein Musashi-1. Molecular Oncology 2015 (in press)

Paranjape SR, Riley AP, Somoza AD, Oakley CE, Wang CC, Prisinzano TE, Oakley BRGamblin TC. Azaphilones Inhibit Tau Aggregation and Dissolve Tau Aggregates in Vitro. ACS Chemical Neuroscience 2015 Apr 15 [Epub ahead of print]

Smith AR, Marquez RT, Tsao W-C, Pathak S, Roy A, Ping J, Wilkerson B, Lan L, Meng W, Neufeld KL, Sun X-F, Xu L. Tumor Suppressive microRNA-137 Negatively Regulates Musashi-1 in Colorectal Cancer. Oncotarget 2015 (in press).

 

April 2015 Publications

Mostafa HH, van Loben Sels JM, Davido DJ. HSV-1 upregulates p35, alters CDK-5 localization, and stimulates CDK-5 kinase activity during acute infection in neurons. J Virol. 2015 Feb 18. pii: JVI.00106-15.

Rowland MA, Harrison B, Deeds EJ.  Phosphatase specificity and pathway insulation in signaling networks.  Biophys J. 108(4): 986-96.

Wani PS, Rowland MA, Ondracek A, Deeds EJ, Roelofs J.  Maturation of the proteasome core particle induces an affinity switch that controls regulatory particle association. Nat Commun. 6: 6384-95.

Wu X, Lan L, Wilson DM, Marquez RT, Tsao W-C, Gao P, Roy A, Turner B, McDonald P, Tunge JA, Rogers SA, Dixon DA, Aube J, and Xu L. Identification and validation of novel small molecule disruptors of HuR-mRNA interaction. ACS Chem Biol 2015 [Epub ahead of print]

 

March 2015 Publications

Johnson DK, Karanicolas J.  Selectivity of small-molecule inhibitors of protein interactions can be driven by protein surface fluctuations.  PLoS Comput Biol: e1004081.

Liu H, Li K, Xu L, Wu D. Bilayered near-infrared fluorescent nanoparticles based on low molecular weight PEI for tumor-targeted in vivo imaging. Journal of Nanoparticle Research 16: 2784.

Zeineldin, M. & Neufeld, K.L. “New insights from animal models of colon cancer: Inflammation control as a new facet on the tumor suppressor APC gem” Gastrointestinal Cancer: Targets and Therapy: 2015:5: 39—52

 

February 2015 Publications

Amunts A, Fiedorczuk K, Truong TT, Chandler JR, Greenberg EP, Ramakrishnan V.  Bactobolin A binds to a site on the 70S ribosome distinct from previously seen antibiotics. J Mol Biol [Epub ahead of print]

Kuczera K.  Molecular modeling of peptides.  Methods Mol Biol 1268: 15-41.

Merkes C, Turkalo TK, Wilder N, Park H, Wenger LW, Lewin SJ, Azuma M.  Ewing sarcoma Ewsa protein regulates chondrogenesis of Meckel’s cartilage through modulation of Sox9 in zebrafish. PLoS ONE: e0116627.

Sridharan V, Park H, Ryu H, Azuma Y.  SUMOylation regulates Polo-like kinase 1-interacting checkpoint helicase (PICH) during mitosis.  J Biol Chem. [Epub ahead of print]

 

January 2015 Publications

Deng L, Shang L, Bai S, Chen J, He X, Trevino RM, Chen S, Li X, Meng X, Yu B, Wang X, Liu Y, McDermott SP, Ariazi AE, Ginestier C, Ibarra I, Ke J, Luther TK, Clouthier SG, Xu L, Shan G, Song E, Yao H, Hannon GJ, Weiss SJ, Wicha MS, Liu S. microRNA100 inhibits self-renewal of breast cancer stem-like cells and breast tumor development. Cancer Research 74, 6648-6660.

Edgerton H, Paolillo V, Oakley BR.  Spatial regulation of the spindle assembly checkpoint and anaphase promoting complex in Aspergillus nidulans.  Molecular Microbiology.  [Epub ahead of print]

Lamb AL, Kappock TJ, Silvaggi NR.  You are lost without a map: navigating the sea of protein structures.  Biochim Biophys Acta [Epub ahead of print]

Li K, Liu H, Gao W, Chen M, Zeng Y, Liu J, Xu L, Wu D.  Mulberry-like dual-drug complicated nanocarriers assembled with apogossypolone amphiphilic starch micelles and doxorubicin hyaluronic acid nanoparticles for tumor combination and targeted therapy.  Biomaterials 2015; 39(1):131-144.

Lu J, Zhao W, Liu H, Marquez R, Huang Y, Zhang Y, Li J, Xie W, Venkataramanan R, Xu L, Li S.  An Improved D-α-Tocopherol-Based Nanocarrier for Targeted Delivery of Doxorubicin with Reversal of Multidrug Resistance.  Journal of Controlled Release [Epub ahead of print]

Smith MC, Box AC, Haug JS, Lane WS, Davido DJ.  A Phospho-SIM in the Antiviral Protein PML is Required for Its Recruitment to HSV-1 Genomes.  Cells 3, 1131-1158.

Tewary SK, Liang L, Lin Z, Lynn A, Cotmore SF, Tattersall P, Zhao H, Tang L.  Structures of minute virus of mice replication initiator protein N-terminal domain: Insights into DNA nicking and origin binding.  Virology.  [Epub ahead of print]

Wang B, Chen L, Ni Z, Dai X, Qin L, Wu Y, Li X, Xu L, Lian J, He F.  Hsp90 inhibitor 17-AAG sensitizes Bcl-2 inhibitor (-)-gossypol by suppressing ERK-mediated protective autophagy and Mcl-1 accumulation in hepatocellular carcinoma cells.  Experimental Cell Research, 2014. 328(2):379-387.

December 2014 Publications

Kemege K, Hickey JM, Barta ML, Wickstrum J, Balwalli N, Lovell S, Battaile KP, Hefty PS.  Chlamydia trachomatis protein CT009 is a structural and functional homolog to the key morphogenesis component RodZ and interacts with division septal plane localized MreB.  Mol Micrbiol [Epub ahead of print]

Norris AD, Sundararajan L, Morgan DE, Roberts ZJ, Lundquist EA.  The UNC-6/Netrin receptors UNC-40/DCC and UNC-5 inhibit growth cone filopodial protrusion via UNC-73/Trio, Rac-like GTPases and UNC-33/CRMP.  Development 141: 4395-405.

November 2014 Publications

Chilton AS, Ellis AL, Lamb AL.  Structure of an Aspergillus fumigatus old yellow enzymes (EasA) involved in ergot alkaloid biosynthesis.  Acta Crystallogr F Struct Biol Commun.  70: 1328-32.

Long AD, Macdonald SJ, King EG.  Dissecting complex traits using the Drosophila Synthetic Population Resource. Trends in Genetics 30: 488–495.

Lu J, Zhao W, Huang Y, Liu H, Marquez R, Gibbs RB, Li J, Venkataramanan R, Xu L, Li S, Li S. Targeted Delivery of Doxorubicin by Folic Acid-Decorated Dual Functional Nanocarrier. Mol Pharm [Epub ahead of print].

Meneely KM, Luo Q, Riley AP, Taylor B, Roy A, Stein RL, Prisinzano TE, Lamb AL.  Expanding the results of a high throughput screen against an isochorismate-pyruvate lyase to enzymes of a similar scaffold or mechanism.  Bioorg Med Chem.  22: 5961-69.

October 2014 Publications

Barta ML, Thomas K, Yuan H, Lovell S, Battaile KP, Schramm VL, Hefty PS.  Structural and Biochemical Characterization of Chlamydia trachomatis Hypothetical Protein CT263 Supports that Menaquinone Synthesis Occurs through the Futalosine Pathway.  J. Biol. Chem.  [Epub ahead of print]

Conlin PL, Chandler JR, Kerr B.  Games of life and death: antibiotic resistance and production through the lens of evolutionary game theory.  Curr Opin Micro 21: 35-44.

Liu H, Li K, Lan L, Ma J, Zeng Y, Xu L, Wu D.  Double-layered hyaluronic acid/stearic acid-modified polyethyleneimine nanoparticles encapsulating (−)-gossypol: a nanocarrier for chiral anticancer drugs. Journal of Materials Chemistry B. 2014, 2(32):5238-5248.

Marriage TN, EG King, AD Long, SJ Macdonald.  Fine-mapping nicotine resistance loci in Drosophila using a multiparent advanced generation intercross population. Genetics 198: 45–57

Rathinavelan T, Lara-Tejero M, Lefebre M, Chatterjee S, McShan AC, Guo DC, Tang C, Galan JE, De Guzman RN. NMR model of PrgI-SipD interaction and its implications in the needle-tip assembly of the Salmonella type III secretion system.  J Mol Biol.  426: 2958-69.

Varahan S, Harms N, Gilmore MS, Tomich JM, Hancock LE.  An ABC Transporter Is Required for Secretion of Peptide Sex Pheromones in Enterococcus faecalis.  MBio. 2014 Sep 23;5(5). pii: e01726-14. doi: 10.1128/mBio.01726-14.

September 2014 Publications

Jain P, Li J, Porubsky P, Neuenswander B, Egan SM, Aube J, Rogers SA.  3-Substituted Biquinolinium Inhibitors of AraC Family Transcriptional Activator VirF from S. flexneri Obtained Through In Situ Chemical Ionization of 3,4-Disubstituted Dihydroquinolines.  Res Avd. [Epub ahead of print]

Park H, Turkalo TK, Nelson K, Folmsbee SS, Robb C, Roper B, Azuma M.  Ewing sarcoma EWS protein regulates midzone formation by recruiting Auroroa B kinase to the midzone.  Cell Cycle 13, 2391-2399.

Stetler DA¸ Davis C, Leavitt K, Schriger I, Benson K, Bhakta S, Wang LC, Oben C, Watters M, Haghnegahdar T and Bortolato M.  Association of low-activity MAOA allelic variants with violent crime in incarcerated offenders.  J Psychiatr Res [Epub ahead of print]

Zhou B, Yang K, Wills E, Tang L, Baines JD.  A Mutation in the DNA Polymerase Accessory Factor of Herpes Simplex Virus 1 Restores Viral DNA Replication in the Presence of Raltegravir.  J Virol. [Epub ahead of print]

August 2014 Publications

Al-Ani G, Briggs K, Malik SS, Conner M, Azuma Y, Fischer CJ.  Quantitative determination of binding of ISWI to nucleosomes and DNA shows allosteric regulation of DNA binding by nucleotides.  Biochemistry 53, 4334-4345.

Al-Ani G, Malik SS, Eastlund A, Briggs K, Fischer CJ.  ISWI remodels nucleosomes through a random walk.  Biochemistry 53, 4346-57.

Timmons L, Luna H, Martinez J, Moore Z, Nagarajan V, Kemege JM, Asad N.  Systematic comparison of bacterial feeding strains for increased yield of Caenorhabditis elegans males by RNA interference-induced non-disjunction FEBS letters [Epub ahead of print]

Qin J, Yang B, Xu B, Smith A, Xu L, Yuan J, Li L.  Concurrent CD44s and STAT3 expression in human clear cell  renal cellular carcinoma and its impact on survival. International Journal of Clinical and Experimental Pathology 2014, 7(6):3236.

Zhang P, Huang Y, Hoa L, Marquez R, Lu J, Zhao W, Zhang X, Goa X, Li J, Venkataramanan R, Xu L, Li S.  A PEG-Fmoc conjugate as a nanocarrier for paclitaxel. Biomaterials 2014, 35(25):7146-7156.  

July 2014 Publications

Sundararajan L, Norris ML, Schoneich S, Ackley BD, Lundquist EA.  The fat-like cadherin CDH-4 acts cell non-autonomously in anterior-posterior neuroblast migration.  Dev Biol.  [Epub ahead of print]

Zeineldin M, Jensen D, Paranjape SR, Parelkar NK, Jokar I, Vielhauer GA, Neufeld KL. Human Cancer Xenografts in Outbred Nude Mice Can Be Confounded by Polymorphisms in a Modifier of Tumorigenesis  Genetics. [Epub ahead of print]

Zeineldin M, Miller MA, Sullivan R, Neufeld KL. Nuclear Adenomatous polyposis coli suppresses colitis-associated tumorigenesis in mice  Carcinogenesis [Epub ahead of print]

June 2014 Publications

Chiang Y-M, Wang C C C, Oakley BR. (2014) Analyzing fungal secondary metabolite genes and gene clusters.  In Natural Products: Discourse, Diversity & Design. (Edited by A. Osbourn, R. Goss and G. Carter), John Wiley & Sons, Hoboken, N.J.  pp 175-193.

King EG, Sanderson BJ, McNeil CL, Long AD, Macdonald SJ.  Genetic dissection of the Drosophila melanogaster female head transcriptome reveals widespread allelic heterogeneity.  PLoS Genet: e1004322.

Lanfranca MP, Mostafa HH, Davido DJ.  HSV-1 ICP0: an E3 ligase that counteracts host intrinsic and innate immunity.  Cells 3: 438-54.

Newton AH, Benedict SH.  Low density lipoprotein promotes human naïve T cell differentiation to Th1 cells.  Hum Immunol [Epub ahead of print]

Wang B, Ni Z, Dai X, Qin L, Li X, Xu L, Lian J, and He F. The Bcl-2/xL inhibitor ABT-263 increases the stability of Mcl-1 mRNA and protein in hepatocellular carcinoma cells. Mol Cancer 13: 98.

May 2014 Publications

Barta ML, Hickey JM, Anbanandam A, Dyer K, Hammel M, Hefty PS.  Atypical response regulator ChxR from Chlamydia trachomatis is structrurally posed for DNA binding.  PLoS One.  2014 Mar 19; 9(3):e91760.

Ni Z, Wang B, Dai X, Ding W, Yang T, Li X, Lewin S, Xu L, Lian J, He F.  HCC cells with high levels of Bcl-2 are resistant to ABT-737 via activation of the ROS-JNK-autophagy pathway.  Free Radic Biol Med 70, 194-203.

Osaka I, Hefty PS.  Lipopolysaccharid-binding alkylpolamine DS-96 inhibits Chlamydia trachomatis infection by blocking attachment and entry.  Antimicrob Agents Chemother [Epub ahead of print]

Rowland MA, Deeds EJ.  Crosstalk and the evolution of specificity in two-component signaling.  Proc Nat Acad Sci USA.  [Epub ahead of print]

April 2014 Publications

Liu T, Sanchez JF, Chiang Y-M, Oakley BR, Wang CCC.  Rational Domain Swaps Reveal Insights about Chain Length Control by Ketosynthase Domains in Fungal Nonreducing Polyketide Synthases. Org Lett 16, 1676-9.

Wang L, Yang H, Palmbos PL, Ney G, Detzler TA, Coleman D, Leflein J, Davis M, Zhang M, Tang W, Hicks JK, Helchowski CM, Prasad J, Lawrence TS, Xu L, Yu X, Canman CE, Ljungman M, Simeone DM.  ATDC/TRIM29 phosphorylation by ATM/MAPKAP Kinase 2 mediates radioresistance in pancreatic cancer cells.  Cancer Res 74, 1778-88.

March 2014 Publications

Frederick RE, Ojha S, Lamb AL, Dubois JL.  How pH modulates the reactivity and selectivity of a siderophore-associated flavin monooxygenase.  Biochemistry.  [Epub ahead of print]

Jas GS, Middaugh CR, Kuczera K.  Non-exponential kinetics and a complete folding pathway of an α-Helical Heteropeptide: Direct Observation and Comprehensive Molecular Dynamics.  J. Phys. Chem B 118:639-647.

Li L, Hoa X, Qin J, He F, Smith A, Zhang M, Simeone DM, Qiao XT, Chen ZN, Lawrence TS, Xu L.  Antibody against CD44s inhibits pancreatic tumor initation and postradiation recurrence in mice.  Gastroenterology.  [Epub ahead of print]

February 2014 Publications

Lothrop AP, Snider GW, Flemer S Jr, Ruggles EL, Davidson RS, Lamb AL, Hondal RJ.  Compensating for the absence of selenocysteine in high-molecular weight thioredoxin reductases: the electrophilic activation hypothesis.  Biochemistry [Epub ahead of print].

Paranjape, SR, Chiang, YM, Sanchez, JF, Entwistle, R, Wang, CC, Oakley, BR, Gamblin, TC. Inhibition of Tau Aggregation by Three Aspergillus nidulans Secondary Metabolites: 2,ω-Dihydroxyemodin, Asperthecin and Asperbenzaldehyde. Planta Medica 80(1):77-85.

Rankin CA, Galeva NA, Bae K, Ahmad MN, Witte TM, Richter ML.  Isolated RING2 domain of Parkin is sufficient for E2-dependent E3 ligase activity.  Biochemistry 53: 225-34.

Tewary SK, Zhao H, Deng X, Qiu J, Tang L. The human parvovirus B19 non-structural protein 1 N-terminal domain specifically binds to the origin of replication in the viral DNA. Virology. [Epub ahead of print].

January 2014 Publications

Barta ML, Lovell S, Sinclair AN, Battaile KP, Hefty PS.  Chlamydia trachomatis CT771 (nudH) is an asymmetric Ap4A hydrolase.  Biochemistry [Epub ahead of print].

Basha A, Basha F, Ali SK, Hanson PR, Mitscher LA, Oakley BR.  Recent Progress in the Chemotherapy of Human Fungal Diseases. Emphasis on 1,3-beta-Glucan Synthase and Chitin Synthase Inhibitors. Curr Med Chem 20, 4859-4887.

Li L, Tang W, Wu X, Karnak D, Meng X, Thompson R, Hao X, Li Y, Qiao XT, Lin J, Fuchs J, Simeone DM, Chen ZN, Lawrence TS, Xu L.  HAb18G/CD147 promotes pSTAT3-mediated pancreatic cancer development via CD44s.  Clin Cancer Res 19, 6703-15.

Yaegashi J, Oakley BR, Wang CC.  Recent advances in genome mining of secondary metabolite biosynthetic gene clusters and the development of heterologous expression systems in Aspergillus nidulans.  J Ind Microbiol Biotechnol [Epub ahead of print].

Xia T, Diprimio N, Keppel TR, Vo B, Fraser K, Battaile KP, Egan C, Bystroff C, Lovell S, Weiss DD, Anderson JC, Karanicolas J.  The designability of protein switches by chemical rescue of structure: mechanisms of inactivation and reactivation.  J Am Chem Soc 135: 18840-9.

December 2013 Publications

Alan JK, Struckhoff EC, Lundquist EA.  Multiple cytoskeletal pathways and PI3K signaling mediate CDC-42-induced neuronal protrusion in C. elegans.  Small GTPases [Epub ahead of print].

November 2013 Publications

Alan JK, Lundquist EA.  Mutationally activated Rho GTPases in cancer.  Small GTPases  [Epub ahead of print].

Barta ML, Hickey J, Kemege KE, Lovell S, Battaile KP, Hefty PS.  Structure of CT584 from Chlamydia trachomatis refined to 3.05 Å resolution.  Acta Cryst F69, 1196-1201.

Mostafa HH, Davido DJ.  HSV-1 ICP22 but not US1.5 is Required for Efficient Acute Replication in Mice and VICE Domain Formation.  J Virol [Epub ahead of print]

Perusina Lanfranca M, Mostafa HH, Davido DJ.  Two overlapping regions within the N-terminal half of the HSV-1 E3 ubiquitin ligase ICP0 facilitate the degradation and dissociation of PML and dissociation of Sp100 from ND10.  J Virol [Epub ahead of print]

Suderman R, Deeds EJ.  Machines vs. ensembles: effective MAPK signaling through heterogeneous sets of proteins complexes.  PLoS Comput Biol 9(10): e1003278.

Syed LU, Zhang-Swisher L, Huff H, Rochford C, Wang F, Liu J, Wu J, Richter M, Balivada S, Troyer D, Li J.  Luminol-labeled gold nanoparticles for ultrasensitive chemiluminescence-based chemical analysis.  Analyst 138, 5600-5609.

Wang S, Wang G, Tang G, Wang R, Nikolovska-Coleska Z, Yang D, and Xu L.  Small molecule inhibitors of anti-apoptotic BCL-2 family members and the uses thereof.  United States Patent No. US 8,557,812, issued on Oct. 15, 2013.

Wickstrum J, Sammons LR, Restivo KN, Hefty PS.  Conditional gene expression in Chlamydia trachomatis using the Tet system. PLoS One 8(10): e76743.

October 2013 Publications

Cridland JM, Macdonald SJ, Long AD, Thornton KR. Abundance and distribution of transposable elements in two Drosophila QTL mapping resources. Molecular Biology and Evolution 30: 2311–2327.>

Koppolu V, Osaka I, Skredenske JM, Kettle B, Hefty PS, Li J,Egan SM.   Small Molecule Inhibitor of Shigella flexneri Master Virulence Regulator, VirF.  Infection and Immunity.  [Epub ahead of print]

Kundrotas PJ, Vakser IA, Janin J. Structural templates for modeling homodimer. Protein Science. [Epub ahead of print]

Meneely KM, Luo Q, Lamb AL.  Redesign of MST enzymes to target lyase activity instead promotes mutase and dehydratase activities.  Archives of Biochemistry and Biophysics. [Epub ahead of print]

September 2013 Publications

Anishchenko I, Kundrotas PJ, Tuzikov AV, Vakser IA.  Protein models: The Grand Challenge of protein docking, Proteins [Epub ahead of print]

Kislukhin G, King EG, Walters KN, Macdonald SJ, and Long AD.  The genetic architecture of methotrexate toxicity is similar in Drosophila melanogaster and humans. G3: Genes, Genomes, Genetics 3: 1301–1310.

Kundrotas PJ, Vakser IA. Protein-protein alternative binding modes do not overlap, Protein Sci. 22:1141-1145.  Highlighted in “In This Issue” section.

Kundrotas PJ, Vakser IA. Global and local structural similarity in protein-protein complexes: Implications for template-based docking, Proteins [Epub ahead of print]

Meneely KM, Luo Q, Dhar P, Lamb AL.  Lysine221 is the general base residue of the isochorismate synthase from Pseudomonas aeruginosa (PchA) in a reaction that is diffusion limited.  Arch.  Biochem. Biophys.  [Epub ahead of print]

Ruvinsky AM, Kirys T, Tuzikov AV, Vakser IA. Ensemble-based characterization of unbound and bound states on protein energy landscape. Protein Sci. 22: 734-744.

Tewary SK, Zhao H, Shen W, Qiu J, Tang L.  Structure of the NS1 protein N-terminal origin-recognition/nickase domain from the emerging human bocavirus.  J Virol. [Epub ahead of print]

August 2013 Publications

Gowthaman R, Deeds EJ, Karanicolas J.  The structural properties of non-traditional drug targets present new challenges for virtual screening.  J. Chem. Inf. Model [Epub ahead of print].

July 2013 Publications

Dotson AL, Novikova L, Stehno-Bittel L, Benedict SH.  Elimination of T cell reactivity to pancreatic  β cells and partial preservation of β cell activity by peptide blockade of LFA-1:ICAM-1 interaction with the NOD mouse model.  Clinical Immunology 148, 149-161.

Novikova L, Smirnova IV, Rawal S, Dotson AL, Benedict SH, Stehno-Bittel L.  Variations in rodent models of type 1 diabetes: islet morphology.  J. Diabetes Res. 2013:965832.

Oakley BR (2013). Aspergillus nidulans. In Brenner’s Encyclopedia of Genetics (Second Edition), Editors-in-Chief: S. Maloy, and K. Hughes, eds. (San Diego: Academic Press), pp. 212-215.

Zhao H, Christensen TE, Kamau YN, Tang L.  Structures of the phage Sf6 large terminase provide new insights into DNA translocation and cleavage. Proc Natl Acad Sci USA 110, 8075-80.

June 2013 Publications

Caylor RC, Jin Y, Ackley BD.  The Caenorhabditis elegans voltage-gated calcium channel subunits UNC-2 and UNC-36 and the calcium-dependent kinase UNC-43/CaMKII regulate neuromuscular junction morphology.  Neural Dev. 8: 10.

Chiang YM, Oakley CE, Ahuja M, Entwistle R, Schultz A, Chang SL, Sung CT, Wang CCC, Oakley BR.  An Efficient System for Heterologous Expression of Secondary Metabolite Genes in Aspergillus nidulans.  J. Am. Chem. Soc. 135, 7720-7731.

Rice SA, Davido DJ.  HSV-1 ICP22: hijacking host nuclear functions to enhance viral infection.  Future Microbiol 8, 311-21.

Tamayo JV, Gujar M, Macdonald SJ, Lundquist EA.  Functional transcriptomic analysis of the role of MAB-5/Hox in Q neuroblast migration in Caenorhabditis elegans.  BMC Genomics 14: 304.

Yaegashi J, Praseuth MB, Tyan SW, Sanchez JF, Entwistle R, Chiang YM, Oakley BR, Wang CC.  Molecular genetic characterization of the biosynthesis cluster of a prenylated isoindolinone alkaloid aspernidine A in Asptergillus nidulans.  Org Lett [Epub ahead of print].

May 2013 Publications

Chatterjee S, Chaudhury S, McShan AC, Kaur K, De Guzman RN.  Structure and biophysics of type III secretion in bacteria.  Biochemistry 52, 2508-17.

Sigamani SS, Zhao H, Kamau YN, Baines JD, Tang L.  The structure of the herpes simplex virus DNA-packaging terminase pUL15 nuclease domain suggests an evolutionary lineage among eukaryotic and prokaryotic viruses.  J Virol [Epub ahead of print]

Zeineldin M, Neufeld KL.  Understanding the phenotypic variation in rodent models with germline apc mutations.  Cancer Res 73, 2389-99.

April 2013 Publications

Jo S, Lee HS, Skolnick J, Im W.  Restricted N-glycan conformational space in the PDB and its implication in glycan structure modeling.  PLoS Comput Biol: e1002946.

Johnson DK, Karanicolas J.  Druggable protein interaction sites are more predisposed to surface pocket formation than the rest of the protein surface.  PLoS Comput Biol: e1002951.

Lu J, Huang Y, Zhao W, Marquez RT, Meng X, Li J, Gao X, Venkataramanan R, Wang Z, Li S.  PEG-derived embelin as a nanomicellar carrier for delivery of paclitaxel to breast and prostate cancers.  Biomaterials 24, 1591-1600.

Osaka I, Hefty PS.  A simple resazurin-based microplate assay for measuring Chlamydia infections.  Antimicrob Agents Chemother.  [Epub ahead of print]>

Park S, Im W.  Two dimensional window exchange umbrella sampling for transmembrane helix assembly. J Chem Theory Comput.  9: 13-17.

Smith MC, Goddard ET, Perusina Lanfranca M, Davido DJ.  hTERT extends the life of human fibroblasts without compromising type 1 interferon signaling.  PLoS One: e58233.

 

March 2013 Publications

Dentler W.  A role for the membrane in regulating chlamydomonas flagellar length.  PLoS One.  8: e53366.

Huarcaya Najarro E, Ackley BD.  C. elegans fmi-1/flamingo and Wnt pathway components interact genetically to control the anteroposterior neurite growth of the VD GABAergic neurons.  Dev Biol [Epub ahead of print]

Lee KI, Pastor RW, Andersen OS, Im W.  Assessing smectic liquid-crystal continuum models for elastic bilayer deformations.  Chem Phys Lipids [Epub ahead of print]

Skredenske JM, Koppolu V, Kolin A, Deng J, Kettle B, Taylor B, Egan SE. Identification of a Small Molecule Inhibitor of Bacterial AraC Family Activators. Journal of Biomolecular Screening.  [Epub ahead of print]

Takusagawa F.  Microsomal prostaglandin E synthase type-2 (mPGES2) is a GSH-dependent heme protein, and dithiothreitol dissociates the bound-heme to produce active PVD2 synthase in vitro.  J Biol Chem [Epub ahead of print]

Cheng P, Ni Z, Dai X, Wang B, Smith AR, Xu L, Wu D, He F, Lian J.  The novel BH-3 mimetic apogossypolone induces beclin-1- and ROS-mediated autophagy in human hepatocellular cells.  Cell Death and Disease 4, e489.

Wang H, Davido DJ, Morrison LA.  HSV-1 strain McKrae is more neuroinvasive than HSV-1 KOS after corneal or vaginal incoluation in mice.  Virus Res.  [Epub ahead of print]

Yeh HH, Chang SL, Chiang YM, Bruno KS, Oakley BR, Wu TK, Wang CC.  Engineering fungal nonreducing polyketide synthetase by heterologous expression and domain swapping.  Org Lett 15: 756-759.

February 2013 Publications

Bender A, Woydziak ZR, Branden , Zhou Z, Ackley BD, Peterson BR.  Novel acid-activated fluorophores reveal a dynamic wave of protons in the intestine of Ceanorhabditis elegans.  ACS Chem Biol  [Epub ahead of print]

Khan LA, Zhang H, Abraham N, Sun L, Fleming JT, Buechner M, Hall DH, Gobel V.  Intracellular lumen extension requires ERM-1-dependent apical memebrane expansion and AQP-8-mediated flux.  Nature Cell Biology.  [Epub ahead of print]

Vakser IA.  Low-resolution structural modeling of protein interactome.  Curr Opin Struct Biol [Epub ahead of print]

Zeineldin M, Neufeld KL.  More than two decades of Apc modeling in rodents.  Biochim Biophys Acta.  [Epub ahead of print]

January 2013 Publications

Asad N, Aw WY, Timmons L.   Natural and Unanticipated Modifiers of RNAi Activity in Caenorhabditiselegans. PLoS One 7(11) e50191 (2012) 

Jo S, Jiang W, Lee HS, Roux B, Im W. CHARMM-GUI Ligand Binder for Absolute Binding Free Energy Calculations and Its Application. J ChemInf Model. 2012 Dec 20. [Epub ahead of print]

Marquez RT, Tsao BW, Faust NF and Xu L. Drug resistance and molecular cancer therapy: Apoptosis vs. Autophagy. In: Justine Rudner, ed., Apoptosis. Chapter. InTech. 2013 (in press).

Mostafa HH, Thompson TW, Davido DJ. N-terminal phosphorylation sites of herpes simplex virus type 1 ICP0 differentially regulate its activities and enhance viral replication. J Virol.2012 Dec 5. [Epub ahead of print]

Rowland, M. A., Fontana, W. and Deeds, E. J. Crosstalk and competition in signaling networks. Biophys. J.103:2389-98.  This article is the focus of a “New and Notable” column in Biophysical Journal.

December 2012 Publications

Guo C-J, Knox B, Chiang, Y-M, Lo H-C, Sanchez J, Lee K-H, Oakley B, Bruno K, Wang C. Molecular genetic characterization of a cluster in A. terreus for biosynthesis of the meroterpenoid terretonin. Org. Lett. 14:5684-5687.

Sundararajan L, Lundquist EA.  The Transmembrane Proteins UNC-40/DCC, PTP-3/LAR, and MIG-21 Control Anterior-posterior Neuroblast Migration with Left-right Functional Asymmetry in Caenorhabditis elegansGenetics 2012 Oct 10. [Epub ahead of print]

Combs, B. and Gamblin, T.C. FTDP-17 Mutations Induce Distinct Effects on Aggregation and Microtubule Interactions. Biochemistry 2012, 51(43): 8597-8607.

Lee, H.S. and Im, W. Identification of Ligand Templates using Local Structure Alignment for Structure-Based Drug Design. J Chem Inf Model. 2012 Oct 22;52(10):2784-95. Epub 2012 Sep 28.

Meneely, K.M., and Lamb, A.L. Two structures of a thiazolinyl imine reductase from Yersinia enterocolitica provide insight into catalysis and binding to the nonribosomal peptide synthetase module of HMWP1. Biochemistry. 2012 Oct 23. [Epub ahead of print]

Oakley, C. E., Edgerton-Morgan, H., Oakley, B. R., Tools for Manipulation of Secondary Metabolism Pathways: Rapid Promoter Replacements and Gene Deletions in Aspergillus nidulans. Methods Mol Biol 2012, 944, 143-161.

Zeineldin, M. and Neufeld, K., Isolation of Epithelial Cells from Mouse Gastrointestinal Tract for Western Blot or RNA analysis. Bio-protocol, invited, peer-reviewed.
Featured protocol under fields of "Molecular Biology" and "Cell Biology"

Zhao, H., Kamau, Y., Christensen, T. and Tang, L., Structural and functional studies of the bacteriophage Sf6 terminase small subunit reveal a DNA-spooling device facilitated by structural plasticity. J. Mol. Biol. 423, 3, 413-26.

PREPARATION OF REGULATORY T CELLS USING ICAM-1 CO-STIMULATION
U.S. Patent Application Serial No. 12/122,377
Benedict, S, Williams K, Dotson, A

November 2012 Publications

Combs, B. and Gamblin, T.C. FTDP-17 Mutations Induce Distinct Effects on Aggregation and Microtubule Interactions. Biochemistry 2012, 51(43): 8597-8607.
http://www.ncbi.nlm.nih.gov/pubmed/23043292

Jo, S. and Im, W. Glycan fragment database: a database of PDB-based glycan 3D structures. Nucleic Acids Res. 2012 Oct 26. [Epub ahead of print]
http://www.ncbi.nlm.nih.gov/pubmed/23104379

Lee, H.S. and Im, W. Identification of Ligand Templates using Local Structure Alignment for Structure-Based Drug Design. J Chem Inf Model. 2012 Oct 22;52(10):2784-95. Epub 2012 Sep 28.
http://www.ncbi.nlm.nih.gov/pubmed/22978550

Meneely, K.M., and Lamb, A.L. Two structures of a thiazolinyl imine reductase from Yersinia enterocolitica provide insight into catalysis and binding to the nonribosomal peptide synthetase module of HMWP1. Biochemistry. 2012 Oct 23. [Epub ahead of print]
http://www.ncbi.nlm.nih.gov/pubmed/23066849

Oakley, C. E., Edgerton-Morgan, H., Oakley, B. R., Tools for Manipulation of Secondary Metabolism Pathways: Rapid Promoter Replacements and Gene Deletions in Aspergillus nidulans. Methods Mol Biol 2012, 944, 143-161.
http://www.ncbi.nlm.nih.gov/pubmed/23065614

Zeineldin, M. and Neufeld, K., Isolation of Epithelial Cells from Mouse Gastrointestinal Tract for Western Blot or RNA analysis. Bio-protocol, invited, peer-reviewed.
http://www.bio-protocol.org/wenzhang.aspx?id=292
Featured protocol under fields of "Molecular Biology" and "Cell Biology"
http://www.bio-protocol.org/fllist.aspx?fl1=1&fweek1=1
http://www.bio-protocol.org/fllist.aspx?fl1=4&fweek1=1

Zhao, H., Kamau, Y., Christensen, T. and Tang, L., Structural and functional studies of the bacteriophage Sf6 terminase small subunit reveal a DNA-spooling device facilitated by structural plasticity. J. Mol. Biol. 423, 3, 413-26.
http://www.ncbi.nlm.nih.gov/pubmed/22858866

PREPARATION OF REGULATORY T CELLS USING ICAM-1 CO-STIMULATION
U.S. Patent Application Serial No. 12/122,377
Benedict, S, Williams K, Dotson, A

October 2012 Publications

Olucha J, Meneely KM, Lamb AL. Modification of residue 42 of the active site loop with a lysine-mimetic side chain rescues isochorismate-pyruvate lyase activity in Pseudomonas aeruginosa PchB. Biochemistry. 51: 7525-7532.
http://www.ncbi.nlm.nih.gov/pubmed/22970849

Sudharsan R, Azuma Y. The SUMO ligase PIAS1 regulates UV-induced apoptosis by recruiting Daxx to SUMOylated foci. J. Cell Sci. [Epub ahead of print].
http://www.ncbi.nlm.nih.gov/pubmed/22976298

September 2012 Publications

Edgerton-Morgan H, Oakley BR. γ-Tubulin plays a key role in inactivating APC/CCdh1 at the G1-S boundary. J Cell Biol. 2012 Aug 27. [Epub ahead of print]
http://www.ncbi.nlm.nih.gov/pubmed/22927465

King EG, Merkes CM, McNeil CL, Hoofer SR, Sen S, Broman KW, Long AD, Macdonald SJ.
Genetic dissection of a model complex trait using the Drosophila Synthetic Population Resource.Genome Res. 2012 Aug;22(8):1558-66. Epub 2012 Apr 10.
http://www.ncbi.nlm.nih.gov/pubmed/22496517

Macdonald SJ, Mostafa HH, Morrison LA, Davido DJ. Genome Sequence of Herpes Simplex Virus 1 Strain McKrae.J Virol. 2012 Sep;86(17):9540-1.
http://www.ncbi.nlm.nih.gov/pubmed/22879612

Soukup, A. A., Y. M. Chiang, J. W. Bok, Y. Reyes-Dominguez, B. R. Oakley, C. C. Wang, J. Strauss, and N. P. Keller. 2012. Overexpression of the Aspergillusnidulans histone 4 acetyltransferaseEsaA increases activation of secondary metabolite production. MolMicrobiol.
http://www.ncbi.nlm.nih.gov/pubmed/22882998

August 2012 Publications

Entwistle RA, Rizk RS, Cheng DM, Lushington GH, Himes RH, Gupta ML Jr.  Differentiating between models of epothilone binding to microtubules using tubulin mutagenesis, cytotoxicity, and molecular modeling.  ChemMedChem.  2012 Jul 16 [Epub ahead of print]
http://www.ncbi.nlm.nih.gov/pubmed/22807375

King EG, Macdonald SJ, Long AD. Properties and power of the Drosophila Synthetic Population Resource for the routine dissection of complex traits. Genetics 2012, 191: 935-49.
http://www.ncbi.nlm.nih.gov/pubmed/22505626

Klionsky DJ1. . .Xu L996. . .et al.  Guidelines for the use and interpretation of assays for monitoring autophagy.  Autophagy 8, 445-544.
http://www.landesbioscience.com/journals/3/article/19496/

Lee HS, Jo S, Lim HS, Im W.  Application of binding free energy calculations to prediction of binding modes and affinities of MDM2 and MDMX inhibitors.  J Chem Inf Model.  2012 Jul 6.  [Epub ahead of print]
http://www.ncbi.nlm.nih.gov/pubmed/22731511

July 2012 Publications

Biswas S, Benedict SH, Lynch SG, LeVine SM.  Potential immunological consequences of pharmacological suppression of grastric acid production in patients with multiple sclerosis.BMC Medicine, 10:57.
http://www.ncbi.nlm.nih.gov/pubmed/22676575

Deckert K, Budiardjo SJ, Brunner LC, Lovell S, Karanicolas J. Designing allosteric control into enzymes by chemical rescue of structure.  J. Amer. Chem. Soc. 134: 10055-60.
http://www.ncbi.nlm.nih.gov/pubmed/22655749

Kirys T, RuvinskyAM, Tuzikov AV, Vakser IA.  Rotamer libraries and probabilities of transition between rotamers for the side chains in protein-protein binding.Proteins 2012 Apr 27 [Epub ahead of print]
http://www.ncbi.nlm.nih.gov/pubmed/22544766

Kundrotas PJ, Zhu Z, Janin J, Vakser IA.Templates are available to model nearly all complexes of structurally characterized proteins.  Proc. Natl. Acad. Sci. USA 109: 9438-41.
http://www.ncbi.nlm.nih.gov/pubmed/22645367

Yeh H, Chiang Y, Entwistle R, Ahuja M, Lee K, Bruno K, Wu T, Oakley BR, Wang C. Molecular genetic analysis reveals that a nonribosomal peptide synthase-like (NRPS-like) gene in Aspergillus nidulans is responsible for microperfuranone biosynthesis.  Appl. Microbiol. Biotechnol.  2012 May 25 [Epub ahead of print]
http://www.ncbi.nlm.nih.gov/pubmed/22627757

Zhong D, Lefebre M, Kaur K, McDowell MA, Gdowski C, Jo S, Wang Y, Benedict SH, Lea SM, Galan JE, De Guzman RN.  The Salmonella type III secretion system inner rod protein PrgJ is partially folded.  J. Biol. Chem. 2012 May 31 [Epub ahead of print]
http://www.ncbi.nlm.nih.gov/pubmed/22654099

June 2012 Publications

Demarco RS, Struckhoff EC, Lundquist EA.  The Rac GTP exchange factor TIAM-1 acts with CDC-42 and the guidance receptor UNC-40/DCC in neuronal protrusion and axon guidance. PLoS Genetics 2012, 8:4, e1002665.
http://www.ncbi.nlm.nih.gov/pubmed/22570618

Macdonald SJ, Mostafa HH, Morrison LA, Davido DJ.Genome Sequence of Herpes Simplex Virus 1 Strain KOS.J Virol. 2012 Jun;86(11):6371-2.
http://www.ncbi.nlm.nih.gov/pubmed/22570244

Osaka I, Hills JM, Kieweg SL, Shinogle HE, Moore DS, Hefty PS.  An automated image-based method for rapid analysis of Chlamydia infection as a tool for screening antichlamydial agents.Antimicrob Agents Chemother2012 May 21 [Epub ahead of print]
http://www.ncbi.nlm.nih.gov/pubmed/22615279

May 2012 Publications

Ahuja M, Chiang YM, Chang SL, Praseuth MB, Entwistle R, Sanchez JF, Lo HC, Yeh HH, Oakley BR, Wang CC. Illuminating the diversity of aromatic polyketide synthases in Aspergillus nidulans. J Am Chem Soc
[Epub ahead of print]
http://www.ncbi.nlm.nih.gov/pubmed/22510154

Cheng X, Im W. NMR observable-based structure refinement of DAP12-NKG2C activating immunoreceptor complex in explicit membranes. Biophys J 102: L27-9.
http://www.ncbi.nlm.nih.gov/pubmed/22500771

Kim T, Lee KU, Morris P, Pastor RW, Andersen OS, Im W. Influence of hydrophobic mismatch on structures and dynamics of gramicidin a and lipid bilayers. Biophys J 102: 1551-60.
http://www.ncbi.nlm.nih.gov/pubmed/22500755

O'Bryhim BE, Radel J, Macdonald SJ, Symons RC. The genetic control of avascular area in mouse oxygen-induced retinopathy. Molecular Vision 2012; 18: 377-89.
http://www.ncbi.nlm.nih.gov/pubmed/22355249

Park S, Kim T, Im W. Transmembrane helix assembly by window exchange umbrella sampling. Phys Rev Lett 108: 108102.
http://www.ncbi.nlm.nih.gov/pubmed/22463457

Sanchez JF, Entwistle R, Corcoran D, Oakley BR, Wang CC. Identification and molecular genetic analysis of the cichorine cluster in Aspergillus nidulans. In press: Med Chem Comm Available on line.
http://pubs.rsc.org/en/content/articlepdf/2012/md/c2md20055d

April 2012 Publications

Karanicolas J. Designing orthogonal signaling pathways: How to fit in with the surroundings. Proc Natl Acad Sci U S A. 2012 Mar 26. [Epub ahead of print]
http://www.ncbi.nlm.nih.gov/pubmed/22451928

Najarro EH, Wong L, Zhen M, Carpio EP, Goncharov A, Garriga G, Lundquist EA, Jin Y, Ackley BD. Caenorhabditis elegans Flamingo Cadherin fmi-1 Regulates GABAergic Neuronal Development. J Neurosci. 32(12):4196-211 (2012)
http://www.ncbi.nlm.nih.gov/pubmed/22442082

Deeds EJ, Krivine J, Feret J, Danos V, Fontana W. Combinatorial complexity and compositional drift in protein interaction networks. PLoS One. 7(3):e32032 (2012)
http://www.ncbi.nlm.nih.gov/pubmed/22412851

Wacker MJ, Tevis O, Hanke J, Howard T, Gilbert W, Orr JA. Characterization of thromboxane A(2) receptor and TRPV1 mRNA expression in cultured sensory neurons. Neurosci Lett. 2012 Mar 7. [Epub ahead of print]
http://www.ncbi.nlm.nih.gov/pubmed/22425716

March 2012 Publications

Deeds EJ, Bachman JA, Fontana W. Optimizing ring assembly reveals the strength of weak interactions. Proc. Natl. Acad. Sci. USA 109(7): 2348-53. http://www.ncbi.nlm.nih.gov/pubmed/22308356

Lo HC, Entwistle R, Guo CJ, Ahuja M, Szewczyk E, Hung JH, Chiang YM, Oakley BR. Wang CC. Two separate gene clusters encode the biosynthetic pathway for the meroterpenoids, austinol and dehydroaustinol in Aspergillus nidulans. J Am Chem Soc 2012 Feb 13 [Epub ahead of print] http://www.ncbi.nlm.nih.gov/pubmed/22329759

Somoza AD, Lee KH, Chiang YM, Oakley BR, Wang CC. Reengineering an azaphilone biosynthesis pathway in Aspergillus nidulins to create lipoxygenase inhibitors. Org. Lett. 2012 Feb 1 [Epub ahead of print] http://www.ncbi.nlm.nih.gov/pubmed/22296232

Taheri-Talesh N, Xiong Y, Oakley BR. The functions of myosin II and myosin V homologs in tip growth and septation in Aspergillus nidulans. PLoS One 7, e31218. http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0031…

February 2012 Publications

Devore NM and Scott EE. Structures of cyctochrome P450 17A1 with prostate cancer drugs abiraterone and TOK-001. Nature 2012 Jan 22 [Epub ahead of print]
http://www.ncbi.nlm.nih.gov/pubmed/22266943

Estrada DF, Conner M, Joer SC and De Guzman RN. The structure of the hantavirus zinc finger domain is conserved and represents the only natively folded region of the Gn cytoplasmic tail. Front Microbiol 2:251.
http://www.ncbi.nlm.nih.gov/pubmed/22203819

Lian J, Ni Z, Dai X, Su C, Smith AR and Xu L, and He F. Sorafenib sensitizes (-)-gossypol-induced growth suppression in androgen-independent prostate cancer cells via Mcl-1 inhibition and Bak activation. Molecular Cancer Therapeutics 2011, Dec. in press
http://www.ncbi.nlm.nih.gov/pubmed/22188816

Marquez RT and Xu L. Bcl2:Beclin 1 complex: multiple mechanisms regulating autophagy/apoptosis toggle switch. Am J Cancer Res 2012;2(2). (in press)
http://www.ajcr.us/ajcr0000098A.html

Simeone DM, Ljungman M, Xu L, Wang L and He F. Compositions and methods for treating cancer. US Patent No. US 8,088749, issued on Jan. 3, 2012.

Voss K, Combs B, Patterson KR, Binder LI and Gamblin TC. Hsp70 alters tau function and aggregation in an isoform specific manner. Biochemistry 2012 Jan 10 [Epub ahead of print]
http://www.ncbi.nlm.nih.gov/pubmed/22236337

January 2012 Publications

Alan JK, Lundquist EA. Analysis of Rho GTPase function in axon pathfinding using Caenorhabditis elegans. Methods Mol Biol 827:339-58.
http://www.ncbi.nlm.nih.gov/pubmed/22144285

December 2016 Publications

Cloud-Richardson, Smith BR, Macdonald SJ.  Genetic dissection of intraspecific variation in a male-specific sexual trait in Drosophila melanogaster.  Heredity 117, 417-26.

 

November 2016 Publications

Beaupre BA, Roman JV, Hoag MR, Meneely KM, Silvaggi NR, Lamb AL, Moran GR.  Ligand binding phenomena that pertain to the metabolic function of renalase.  Arch Biochem Biophys 612, 46-56.

Blanco FF, Preet R, Aguado A, Vishwakarma V, Stevens LE, Vyas A, Padhye S, Xu L, Weir SJ, Anant S, Meisner-Kober N, Brody JR, and Dixon DA. Impact of HuR inhibition by the small molecule MS-444 on colorectal cancer cell tumorigenesis. Oncotarget [Epub ahead of print]

Oakley CE, Ahuja M, Sun WW, Entwistle R, Akashi T, Yaegashi J, Guo CJ, Cerqueira GC, Wortman JR, Wang CC, Chiang YM, Oakley BR. Discovery of McrA, a master regulator of Aspergillus secondary metabolism. Mol Microbiol [Epub ahead of print]

Sun J, Chen Y, Li K, Huang Y, Fu X, Zhang X, Zhao W, Wei Y, Xu L, Zhang P, Venkataramanan R, and Li S. A prodrug micellar carrier assembled from polymers with pendant farnesyl thiosalicylic acid moieties for improved delivery of paclitaxel. Acta Biomaterialia 43, 282-291

 

October 2016 Publications

Hackett JL, Wang X, Smith BR, Macdonald SJ.  Mapping QTL Contributing to Variation in Posterior Lobe Morphology between Strains of Drosophila melanogaster.  PLoS One. 11: e0162573

Huang W, Beer RL, Delaspre F, Wang G, Edelman HE, Park H, Azuma M, Parsons MJ.  Sox9b is a mediator of retinoic acid signaling restricting endocrine progenitor differentiation.  Developmental Biology 418, 28-39.

Li J, Wehmeyer G, Lovell S, Battaile KP, Egan SM. 1.65 Å resolution structure of AraC family transcriptional activator ToxT from Vibrio cholera.  Acta Cryst.  F72:726-731.

Meneely KM, Ronnebaum TA, Riley AP, Prisinzano TE, Lamb AL. (2016)  Holo structure and steady state kinetics of the thiazolinyl imine reductases for siderophore biosynthesis.  Biochemistry 55, 5423-33.

Slone S, Anthony SR, Wu X, Benoit JB, Aube J, Xu L, Tranter M.  Activation of HuR downstream of p38 MAPK promotes cardiomyocyte hypertrophy. Cellular Signaling 28, 1735-1741.

Xu B-Q, Fu Z-G, Meng Y, Wu X-Q, Wu B, Xu L, Jiang J-L, Li L, and Chen Z-N. Gemcitabine enhances cell invasion via activating HAb18G/CD147-EGFR-pSTAT3 signaling. Oncotarget [Epub ahead of print]

 

September 2016 Publications

Highfill CA, Reeves GA, Macdonald SJ.  Genetic analysis of variation in lifespan using a multiparental advanced intercross Drosophila mapping population.  BMC Genet.  17:113.

Im W, Liang J, Olson A, Zhou HX, Vajda S, Vakser IA.  Challenges in structural approaches to cell modeling.  J Mol Biol 428: 2943-64.

Park H, Galbraith R, Turner T, Mehojah J, Azuma M.  Loss of Ewing sarcoma EWS allele promotes tumorigenesis by inducing chromosomal instability in zebrafish.  Sci Rep doi.10.1038/srep32297.

 

August 2016 Publications

Meneely KM, Sundlov JA, Gulick AM, Moran GR, Lamb AL.  An open and shut case: the role of magnesium in MST enzymes.  J. Am. Chem. Soc.  [Epub ahead of print]

Josephson MP, Miltner AM, Lundquist EA. Non-autonomous Roles of MAB-5/Hox and the Secreted Basement Membrane Molecule SPON-1/F-spondin in Caenorhabditis elegans Neuronal Migration. Genetics. 2016 May 25. pii: genetics.116.188367. [Epub ahead of print]

Reiner DJ, Lundquist EA. Small GTPases. WormBook. 2016 May 24:1-99. doi: 10.1895/wormbook.1.67.2. [Epub ahead of print]

 

July 2016 Publications

Gruseendorf KA, Trezza CJ, Salem AT, Al-Hashimi H, Mattingly BC, Kampmeyer DE, Khan L, Hall DH, Gobel V, Ackley BDBuechner M. Facilitation of Endosomal Recycling by an IRG Protein Homologue Maintains Apical Tubule Structure in Caenorhabditis elegansGenetics [Epub ahead of print]

Sridharan V, Azuma Y.  SUMO-interacting motifs (SIMs) in Polo-like kinase 1-interacting checkpoint helicase (PICH) ensure proper chromosome segregation during mitosis.  Cell Cycle [Epub ahead of print]

Yeh HH, Ahuja M, Chiang YM, Oakley CE, Moore S, Yoon O, Hajovsky H, Bok JW, Keller NP, Wang CC, Oakley BR.  Resistance gene-guided genomie mining: serial promoter exchanges in Aspergillus nidulans reveal the biosynthetic pathway for fellutamide B, a proteasome inhibitor.  ACS Chem Biol [Epub ahead of print]

Yoshida MM, Ting L, Gygi SP, Azuma Y.  SUMOylation of DNA topoisomerase IIα regulates histone H3 kinase Haspin and H3 phosphorylation in mitosis.  J. Cell Biol 213: 665-78.

 

June 2016 Publications

Basha A, Basha F, Ali SK, Hanson PR, Oakley BR, Hajovsky H, Mitscher LA.  Onychomycosis and its Chemotherapy. Curr Med Chem 23: 1609-1624.

Lanza C, Tan EP, Zhang Z, Machacek M, Brinker AE, Azuma M,  Slawson C.  Reduced O-GlcNAcase expression promotes mitotic errors and spindle defects.  Cell Cycle 15: 1363-75.

Tseng BS, Majerczyk CD, Passos da Silva D, Chandler JR, Greenberg EP, Parsek MR.  Quorum sensing influences Buukholderia thailandensis biofilm development and matric production.  J Bacteriol [Epub ahead of print]

 

May 2016 Publications

Nariya MK, Israeli J, Shi JJ, Deeds EJ.  Mathematical model for length control by the timing of substrate switching in the type III secreation system.  PLoS Comput Biol: e1004851.

 

April 2016 Publications

Ray JCJ.  Survival of Phenotypic Information during Cellular Growth Transitions.  ACS Synth Biol. {Epub ahead of print].

Ray JCJ, Wickersheim ML, Jalihal AP, Adeshina YO, Cooper TF, Balázsi G. Cellular Growth Arrest and Persistence from Enzyme Saturation.  PLoS Comput Biol. 12(3):e1004825.

Wang X, Hinshaw KC, Macdonald SJChandler JR.  Draft genome sequence of Chromobacterium violaceum strain CV017.  Genome Accounc 4(2): e00080-16.

Wu X, Tang W, Marquez RT, Li K, Highfill CA, He F, Lian J, Lin J, Fuchs JR, Ji M, Li L, Xu L.  Overcoming chem/radio-resistance of pancreatic cancer by inhibiting STAT3 signaling.  Oncotarget [Epub ahead of print].

 

March 2016 Publications

Josephson MP, Chai Y, Ou G, Lundquist EA.  EGL-20/Wnt and MAB-5/Hox Act Sequentially to Inhibit Anterior Migration of Neuroblasts in C. elegans.  PLoS One: e0148658.

 

February 2016 Publications

Johnson DK, Karanicolas J.  Ultra-high-throughput structure-based virtual screening for small-molecule inhibitors of protein-protein interactions.  J. Chem. Inf. Model. [Epub ahead of print]

 

January 2016 Publications

Najarro MA, Hackett JL, Smith BR, Highfill CA, King EG, Long AD, Macdonald SJ.  Identifying loci contributing to natural variation in xenobiotic resistance in Drosophila.  PLoS Genet 11(11): e1005663.

Wiley EO, Fuiten AM, Doosey MH, Lohman BK, Merkes C, Azuma M.  The caudal skeleton of the zebrafish, Danio rerio, from a phylogenetic perspective: a polyural interpretation of homologous structures.  Copeia 103 (4), 740-750.

December 2015 Publications

Chiang Y-M, Ahuja M., Oakley CE, Entwistle R, Asokan A, Zutz C, Wang CC, Oakley BR. Development of genetic dereplication strain in Aspergillus nidulans results in the discovery of Aspercryptin. Angew Chem Int Ed Eng [Epub ahead of print]

LaFayette S, Houle D, Beaudoin T, Wojewodka G, Radzioch D,  Hoffman L, Burns J, Dandekar A, Smalley N, Chandler JR, Zlosnik J, Speert D, Bernier J, Matouk E, Brochiero E, Rousseau S, Nguyen D. Cystic fibrosis-adapted Pseudomonas aeruginosa quorum sensing lasR mutants cause hyper-inflammatory responses. Science Adv 1: e1500199

November 2015 Publications

Barta ML, Battaile KP, Lovell S, Hefty PS.  Hypothetical Protein CT398 (CdsZ) Interacts with σ54 (RpoN)-Holoenzyme and the Type III Secretion Export Apparatus in Chlamydia trachomatis.  Protein Sci [Epub ahead of print]

Gonzalez C, Ray JCJ, Manhard M, Adams RM, Nevozhay D, Morozov AV, Balazsi G.  Stress-response balance drives the evolution of a network module and its host genome.  Mol Systems Biol 11: 827.

Oakley BR, Paolillo V, Zheng Y.  gamma-tubulin complexes in microtubule nucleation and beyond.  Mol Biol Cell 26: 2957-2962.

Truong TT, Seyedsayamdost M, Greenberg EP, Chandler JR.  A Burkholderia thailandensis acyl-homoserine lactone-independent LuxR homolog that activates production of the cytotoxin malleilactone.  J. Bacteriol [Eub ahead of print]

 

August 2015 Publications

Fowler AM, Shinogle HE, Davido DJ.  Development of a novel cell-based assay to monitor the transactivation activity of the HSV-1 protein ICP0.  Antiviral Res 120: 1-6.

Gowthaman R, Lyskov S, Karanicolas J.  DARC 2.0: Improved docking and virtual screening at protein interaction sites.  PLoS One 10(7):e0131612.

Gowthaman R, Miller SA, Robers S, Khowsathit J, Lan L, Bai N, Johnson DK, Liu C, Xu L, Anbanandam A, Aube J, Roy A, Karanicolas J.  DARC: Mapping surface topography by ray-casting for effective virtual screening at protein interaction sites.  J. Med Chem.  [Epub ahead of print]

Guo C-J, Sun W-W, Bruno KS, Oakley BR, Keller NP, Wang CCC.  Spatial regulation of a common precursor from two distinct genes generates metabolite diversity. Chemical Science [In Press]

Ryu H, Yoshida MM, Sridharan V, Kumagai A, Dunphy WG, Dasso M, Azuma Y.  SUMOylation of the C_terminal domain of DNA topoisomerase IIa regulates the centromeric localization of Claspin.  Cell Cycle [Epub ahead of print]

Smalley NE, An D, Parsek M, Chandler JR, Dandekar A. Quorum sensing protects Pseudomonas aeruginosa against cheating by other species in a laboratory co-culture model.  J Bacteriol [EPub ahead of print]

Sundararajan L, Norris ML, Lundquist EA.  SDN-1/Syndecan Acts in Parallel to the Transmembrane Molecule MIG-13 to Promote Anterior Neuroblast Migration.  G3 (Bethesda) [Epub ahead of print].

Wang B, Li K, Jin M, Qiu R, Liu B, Oakley BR, Xiang X.  The Aspergillus nidulans bimC4 mutation provides an excellent tool for identification of kinesin-14 inhibitors. Fungal Genet. Biol. 82:51-55.

 

July 2015 Publications

Newton AH, Danahy DB, Chan MA, Benedict SH.  Timely blockade of ICAM-1.LFA-1 interaction prevents disease onset in a mouse model of emphysema.  Immunotherapy [Epub ahead of print]

 

June 2015 Publications

Gilmore MS, Rauch M, Ramsey MM, Himes PR, Varahan S, Manson JM, Lebreton F, Hancock LE.  Pheromone killing of multidrug-resistant Enterococcus faecalis V583 by native commensal strains.  Proc Natl Acad Sci USA [Epub ahead of print]

Hartin SN, Hudson ML, Yingling C, Ackley BD.  A synthetic lethal screen identifies a role for Lin-44/Wnt in C. elegans embryogenesis.  PLoS One: e0121397.

Lamb AL.  Breaking a pathogen’s iron will: inhibiting siderophore production as an antimicrobial strategy.  Biochim Biophys Acta 1854, 1054-1070.

Shogan BD, Belogortseva N, Luong PM, Zaborin A, Lax S, Bethel C, Ward M, Muldoon JP, Singer M, An G, Umanskiy K, Konda V, Shakhsheer B, Luo J, Klabbers R, Hancock LE, Gilbert J, Zaborina O, Alverdy JC.  Collagen Degradation and MMP9 activation by Enterococcus faecalis contribute to intestinal anastomotic leak.  Sci Transl Med 7(286):286ra68.

 

May 2015 Publications

Boutell C, Davido DJ. A quantitative assay to monitor HSV-1 ICP0 ubiquitin ligase activity in vitroMethods 2015 Apr 8 [Epub ahead of print]

 Lan L, Appelman C, Smith AR, Yu J, Larsen S, Marquez RT, Wu X, Gao P, Roy A, Anbanandam A, Gowthaman R, Karanicolas JDe Guzman RN, Rogers SA, Aube J, Ji M, Cohen RS, Neufeld KLXu L. Natural product (–)-gossypol inhibits colon cancer cell growth by targeting RNA-binding protein Musashi-1. Molecular Oncology 2015 (in press)

Paranjape SR, Riley AP, Somoza AD, Oakley CE, Wang CC, Prisinzano TE, Oakley BRGamblin TC. Azaphilones Inhibit Tau Aggregation and Dissolve Tau Aggregates in Vitro. ACS Chemical Neuroscience 2015 Apr 15 [Epub ahead of print]

Smith AR, Marquez RT, Tsao W-C, Pathak S, Roy A, Ping J, Wilkerson B, Lan L, Meng W, Neufeld KL, Sun X-F, Xu L. Tumor Suppressive microRNA-137 Negatively Regulates Musashi-1 in Colorectal Cancer. Oncotarget 2015 (in press).

 

April 2015 Publications

Mostafa HH, van Loben Sels JM, Davido DJ. HSV-1 upregulates p35, alters CDK-5 localization, and stimulates CDK-5 kinase activity during acute infection in neurons. J Virol. 2015 Feb 18. pii: JVI.00106-15.

Rowland MA, Harrison B, Deeds EJ.  Phosphatase specificity and pathway insulation in signaling networks.  Biophys J. 108(4): 986-96.

Wani PS, Rowland MA, Ondracek A, Deeds EJ, Roelofs J.  Maturation of the proteasome core particle induces an affinity switch that controls regulatory particle association. Nat Commun. 6: 6384-95.

Wu X, Lan L, Wilson DM, Marquez RT, Tsao W-C, Gao P, Roy A, Turner B, McDonald P, Tunge JA, Rogers SA, Dixon DA, Aube J, and Xu L. Identification and validation of novel small molecule disruptors of HuR-mRNA interaction. ACS Chem Biol 2015 [Epub ahead of print]

 

March 2015 Publications

Johnson DK, Karanicolas J.  Selectivity of small-molecule inhibitors of protein interactions can be driven by protein surface fluctuations.  PLoS Comput Biol: e1004081.

Liu H, Li K, Xu L, Wu D. Bilayered near-infrared fluorescent nanoparticles based on low molecular weight PEI for tumor-targeted in vivo imaging. Journal of Nanoparticle Research 16: 2784.

Zeineldin, M. & Neufeld, K.L. “New insights from animal models of colon cancer: Inflammation control as a new facet on the tumor suppressor APC gem” Gastrointestinal Cancer: Targets and Therapy: 2015:5: 39—52

 

February 2015 Publications

Amunts A, Fiedorczuk K, Truong TT, Chandler JR, Greenberg EP, Ramakrishnan V.  Bactobolin A binds to a site on the 70S ribosome distinct from previously seen antibiotics. J Mol Biol [Epub ahead of print]

Kuczera K.  Molecular modeling of peptides.  Methods Mol Biol 1268: 15-41.

Merkes C, Turkalo TK, Wilder N, Park H, Wenger LW, Lewin SJ, Azuma M.  Ewing sarcoma Ewsa protein regulates chondrogenesis of Meckel’s cartilage through modulation of Sox9 in zebrafish. PLoS ONE: e0116627.

Sridharan V, Park H, Ryu H, Azuma Y.  SUMOylation regulates Polo-like kinase 1-interacting checkpoint helicase (PICH) during mitosis.  J Biol Chem. [Epub ahead of print]

 

January 2015 Publications

Deng L, Shang L, Bai S, Chen J, He X, Trevino RM, Chen S, Li X, Meng X, Yu B, Wang X, Liu Y, McDermott SP, Ariazi AE, Ginestier C, Ibarra I, Ke J, Luther TK, Clouthier SG, Xu L, Shan G, Song E, Yao H, Hannon GJ, Weiss SJ, Wicha MS, Liu S. microRNA100 inhibits self-renewal of breast cancer stem-like cells and breast tumor development. Cancer Research 74, 6648-6660.

Edgerton H, Paolillo V, Oakley BR.  Spatial regulation of the spindle assembly checkpoint and anaphase promoting complex in Aspergillus nidulans.  Molecular Microbiology.  [Epub ahead of print]

Lamb AL, Kappock TJ, Silvaggi NR.  You are lost without a map: navigating the sea of protein structures.  Biochim Biophys Acta [Epub ahead of print]

Li K, Liu H, Gao W, Chen M, Zeng Y, Liu J, Xu L, Wu D.  Mulberry-like dual-drug complicated nanocarriers assembled with apogossypolone amphiphilic starch micelles and doxorubicin hyaluronic acid nanoparticles for tumor combination and targeted therapy.  Biomaterials 2015; 39(1):131-144.

Lu J, Zhao W, Liu H, Marquez R, Huang Y, Zhang Y, Li J, Xie W, Venkataramanan R, Xu L, Li S.  An Improved D-α-Tocopherol-Based Nanocarrier for Targeted Delivery of Doxorubicin with Reversal of Multidrug Resistance.  Journal of Controlled Release [Epub ahead of print]

Smith MC, Box AC, Haug JS, Lane WS, Davido DJ.  A Phospho-SIM in the Antiviral Protein PML is Required for Its Recruitment to HSV-1 Genomes.  Cells 3, 1131-1158.

Tewary SK, Liang L, Lin Z, Lynn A, Cotmore SF, Tattersall P, Zhao H, Tang L.  Structures of minute virus of mice replication initiator protein N-terminal domain: Insights into DNA nicking and origin binding.  Virology.  [Epub ahead of print]

Wang B, Chen L, Ni Z, Dai X, Qin L, Wu Y, Li X, Xu L, Lian J, He F.  Hsp90 inhibitor 17-AAG sensitizes Bcl-2 inhibitor (-)-gossypol by suppressing ERK-mediated protective autophagy and Mcl-1 accumulation in hepatocellular carcinoma cells.  Experimental Cell Research, 2014. 328(2):379-387.

December 2014 Publications

Kemege K, Hickey JM, Barta ML, Wickstrum J, Balwalli N, Lovell S, Battaile KP, Hefty PS.  Chlamydia trachomatis protein CT009 is a structural and functional homolog to the key morphogenesis component RodZ and interacts with division septal plane localized MreB.  Mol Micrbiol [Epub ahead of print]

Norris AD, Sundararajan L, Morgan DE, Roberts ZJ, Lundquist EA.  The UNC-6/Netrin receptors UNC-40/DCC and UNC-5 inhibit growth cone filopodial protrusion via UNC-73/Trio, Rac-like GTPases and UNC-33/CRMP.  Development 141: 4395-405.

November 2014 Publications

Chilton AS, Ellis AL, Lamb AL.  Structure of an Aspergillus fumigatus old yellow enzymes (EasA) involved in ergot alkaloid biosynthesis.  Acta Crystallogr F Struct Biol Commun.  70: 1328-32.

Long AD, Macdonald SJ, King EG.  Dissecting complex traits using the Drosophila Synthetic Population Resource. Trends in Genetics 30: 488–495.

Lu J, Zhao W, Huang Y, Liu H, Marquez R, Gibbs RB, Li J, Venkataramanan R, Xu L, Li S, Li S. Targeted Delivery of Doxorubicin by Folic Acid-Decorated Dual Functional Nanocarrier. Mol Pharm [Epub ahead of print].

Meneely KM, Luo Q, Riley AP, Taylor B, Roy A, Stein RL, Prisinzano TE, Lamb AL.  Expanding the results of a high throughput screen against an isochorismate-pyruvate lyase to enzymes of a similar scaffold or mechanism.  Bioorg Med Chem.  22: 5961-69.

October 2014 Publications

Barta ML, Thomas K, Yuan H, Lovell S, Battaile KP, Schramm VL, Hefty PS.  Structural and Biochemical Characterization of Chlamydia trachomatis Hypothetical Protein CT263 Supports that Menaquinone Synthesis Occurs through the Futalosine Pathway.  J. Biol. Chem.  [Epub ahead of print]

Conlin PL, Chandler JR, Kerr B.  Games of life and death: antibiotic resistance and production through the lens of evolutionary game theory.  Curr Opin Micro 21: 35-44.

Liu H, Li K, Lan L, Ma J, Zeng Y, Xu L, Wu D.  Double-layered hyaluronic acid/stearic acid-modified polyethyleneimine nanoparticles encapsulating (−)-gossypol: a nanocarrier for chiral anticancer drugs. Journal of Materials Chemistry B. 2014, 2(32):5238-5248.

Marriage TN, EG King, AD Long, SJ Macdonald.  Fine-mapping nicotine resistance loci in Drosophila using a multiparent advanced generation intercross population. Genetics 198: 45–57

Rathinavelan T, Lara-Tejero M, Lefebre M, Chatterjee S, McShan AC, Guo DC, Tang C, Galan JE, De Guzman RN. NMR model of PrgI-SipD interaction and its implications in the needle-tip assembly of the Salmonella type III secretion system.  J Mol Biol.  426: 2958-69.

Varahan S, Harms N, Gilmore MS, Tomich JM, Hancock LE.  An ABC Transporter Is Required for Secretion of Peptide Sex Pheromones in Enterococcus faecalis.  MBio. 2014 Sep 23;5(5). pii: e01726-14. doi: 10.1128/mBio.01726-14.

September 2014 Publications

Jain P, Li J, Porubsky P, Neuenswander B, Egan SM, Aube J, Rogers SA.  3-Substituted Biquinolinium Inhibitors of AraC Family Transcriptional Activator VirF from S. flexneri Obtained Through In Situ Chemical Ionization of 3,4-Disubstituted Dihydroquinolines.  Res Avd. [Epub ahead of print]

Park H, Turkalo TK, Nelson K, Folmsbee SS, Robb C, Roper B, Azuma M.  Ewing sarcoma EWS protein regulates midzone formation by recruiting Auroroa B kinase to the midzone.  Cell Cycle 13, 2391-2399.

Stetler DA¸ Davis C, Leavitt K, Schriger I, Benson K, Bhakta S, Wang LC, Oben C, Watters M, Haghnegahdar T and Bortolato M.  Association of low-activity MAOA allelic variants with violent crime in incarcerated offenders.  J Psychiatr Res [Epub ahead of print]

Zhou B, Yang K, Wills E, Tang L, Baines JD.  A Mutation in the DNA Polymerase Accessory Factor of Herpes Simplex Virus 1 Restores Viral DNA Replication in the Presence of Raltegravir.  J Virol. [Epub ahead of print]

August 2014 Publications

Al-Ani G, Briggs K, Malik SS, Conner M, Azuma Y, Fischer CJ.  Quantitative determination of binding of ISWI to nucleosomes and DNA shows allosteric regulation of DNA binding by nucleotides.  Biochemistry 53, 4334-4345.

Al-Ani G, Malik SS, Eastlund A, Briggs K, Fischer CJ.  ISWI remodels nucleosomes through a random walk.  Biochemistry 53, 4346-57.

Timmons L, Luna H, Martinez J, Moore Z, Nagarajan V, Kemege JM, Asad N.  Systematic comparison of bacterial feeding strains for increased yield of Caenorhabditis elegans males by RNA interference-induced non-disjunction FEBS letters [Epub ahead of print]

Qin J, Yang B, Xu B, Smith A, Xu L, Yuan J, Li L.  Concurrent CD44s and STAT3 expression in human clear cell  renal cellular carcinoma and its impact on survival. International Journal of Clinical and Experimental Pathology 2014, 7(6):3236.

Zhang P, Huang Y, Hoa L, Marquez R, Lu J, Zhao W, Zhang X, Goa X, Li J, Venkataramanan R, Xu L, Li S.  A PEG-Fmoc conjugate as a nanocarrier for paclitaxel. Biomaterials 2014, 35(25):7146-7156.  

July 2014 Publications

Sundararajan L, Norris ML, Schoneich S, Ackley BD, Lundquist EA.  The fat-like cadherin CDH-4 acts cell non-autonomously in anterior-posterior neuroblast migration.  Dev Biol.  [Epub ahead of print]

Zeineldin M, Jensen D, Paranjape SR, Parelkar NK, Jokar I, Vielhauer GA, Neufeld KL. Human Cancer Xenografts in Outbred Nude Mice Can Be Confounded by Polymorphisms in a Modifier of Tumorigenesis  Genetics. [Epub ahead of print]

Zeineldin M, Miller MA, Sullivan R, Neufeld KL. Nuclear Adenomatous polyposis coli suppresses colitis-associated tumorigenesis in mice  Carcinogenesis [Epub ahead of print]

June 2014 Publications

Chiang Y-M, Wang C C C, Oakley BR. (2014) Analyzing fungal secondary metabolite genes and gene clusters.  In Natural Products: Discourse, Diversity & Design. (Edited by A. Osbourn, R. Goss and G. Carter), John Wiley & Sons, Hoboken, N.J.  pp 175-193.

King EG, Sanderson BJ, McNeil CL, Long AD, Macdonald SJ.  Genetic dissection of the Drosophila melanogaster female head transcriptome reveals widespread allelic heterogeneity.  PLoS Genet: e1004322.

Lanfranca MP, Mostafa HH, Davido DJ.  HSV-1 ICP0: an E3 ligase that counteracts host intrinsic and innate immunity.  Cells 3: 438-54.

Newton AH, Benedict SH.  Low density lipoprotein promotes human naïve T cell differentiation to Th1 cells.  Hum Immunol [Epub ahead of print]

Wang B, Ni Z, Dai X, Qin L, Li X, Xu L, Lian J, and He F. The Bcl-2/xL inhibitor ABT-263 increases the stability of Mcl-1 mRNA and protein in hepatocellular carcinoma cells. Mol Cancer 13: 98.

May 2014 Publications

Barta ML, Hickey JM, Anbanandam A, Dyer K, Hammel M, Hefty PS.  Atypical response regulator ChxR from Chlamydia trachomatis is structrurally posed for DNA binding.  PLoS One.  2014 Mar 19; 9(3):e91760.

Ni Z, Wang B, Dai X, Ding W, Yang T, Li X, Lewin S, Xu L, Lian J, He F.  HCC cells with high levels of Bcl-2 are resistant to ABT-737 via activation of the ROS-JNK-autophagy pathway.  Free Radic Biol Med 70, 194-203.

Osaka I, Hefty PS.  Lipopolysaccharid-binding alkylpolamine DS-96 inhibits Chlamydia trachomatis infection by blocking attachment and entry.  Antimicrob Agents Chemother [Epub ahead of print]

Rowland MA, Deeds EJ.  Crosstalk and the evolution of specificity in two-component signaling.  Proc Nat Acad Sci USA.  [Epub ahead of print]

April 2014 Publications

Liu T, Sanchez JF, Chiang Y-M, Oakley BR, Wang CCC.  Rational Domain Swaps Reveal Insights about Chain Length Control by Ketosynthase Domains in Fungal Nonreducing Polyketide Synthases. Org Lett 16, 1676-9.

Wang L, Yang H, Palmbos PL, Ney G, Detzler TA, Coleman D, Leflein J, Davis M, Zhang M, Tang W, Hicks JK, Helchowski CM, Prasad J, Lawrence TS, Xu L, Yu X, Canman CE, Ljungman M, Simeone DM.  ATDC/TRIM29 phosphorylation by ATM/MAPKAP Kinase 2 mediates radioresistance in pancreatic cancer cells.  Cancer Res 74, 1778-88.

March 2014 Publications

Frederick RE, Ojha S, Lamb AL, Dubois JL.  How pH modulates the reactivity and selectivity of a siderophore-associated flavin monooxygenase.  Biochemistry.  [Epub ahead of print]

Jas GS, Middaugh CR, Kuczera K.  Non-exponential kinetics and a complete folding pathway of an α-Helical Heteropeptide: Direct Observation and Comprehensive Molecular Dynamics.  J. Phys. Chem B 118:639-647.

Li L, Hoa X, Qin J, He F, Smith A, Zhang M, Simeone DM, Qiao XT, Chen ZN, Lawrence TS, Xu L.  Antibody against CD44s inhibits pancreatic tumor initation and postradiation recurrence in mice.  Gastroenterology.  [Epub ahead of print]

February 2014 Publications

Lothrop AP, Snider GW, Flemer S Jr, Ruggles EL, Davidson RS, Lamb AL, Hondal RJ.  Compensating for the absence of selenocysteine in high-molecular weight thioredoxin reductases: the electrophilic activation hypothesis.  Biochemistry [Epub ahead of print].

Paranjape, SR, Chiang, YM, Sanchez, JF, Entwistle, R, Wang, CC, Oakley, BR, Gamblin, TC. Inhibition of Tau Aggregation by Three Aspergillus nidulans Secondary Metabolites: 2,ω-Dihydroxyemodin, Asperthecin and Asperbenzaldehyde. Planta Medica 80(1):77-85.

Rankin CA, Galeva NA, Bae K, Ahmad MN, Witte TM, Richter ML.  Isolated RING2 domain of Parkin is sufficient for E2-dependent E3 ligase activity.  Biochemistry 53: 225-34.

Tewary SK, Zhao H, Deng X, Qiu J, Tang L. The human parvovirus B19 non-structural protein 1 N-terminal domain specifically binds to the origin of replication in the viral DNA. Virology. [Epub ahead of print].

January 2014 Publications

Barta ML, Lovell S, Sinclair AN, Battaile KP, Hefty PS.  Chlamydia trachomatis CT771 (nudH) is an asymmetric Ap4A hydrolase.  Biochemistry [Epub ahead of print].

Basha A, Basha F, Ali SK, Hanson PR, Mitscher LA, Oakley BR.  Recent Progress in the Chemotherapy of Human Fungal Diseases. Emphasis on 1,3-beta-Glucan Synthase and Chitin Synthase Inhibitors. Curr Med Chem 20, 4859-4887.

Li L, Tang W, Wu X, Karnak D, Meng X, Thompson R, Hao X, Li Y, Qiao XT, Lin J, Fuchs J, Simeone DM, Chen ZN, Lawrence TS, Xu L.  HAb18G/CD147 promotes pSTAT3-mediated pancreatic cancer development via CD44s.  Clin Cancer Res 19, 6703-15.

Yaegashi J, Oakley BR, Wang CC.  Recent advances in genome mining of secondary metabolite biosynthetic gene clusters and the development of heterologous expression systems in Aspergillus nidulans.  J Ind Microbiol Biotechnol [Epub ahead of print].

Xia T, Diprimio N, Keppel TR, Vo B, Fraser K, Battaile KP, Egan C, Bystroff C, Lovell S, Weiss DD, Anderson JC, Karanicolas J.  The designability of protein switches by chemical rescue of structure: mechanisms of inactivation and reactivation.  J Am Chem Soc 135: 18840-9.

December 2013 Publications

Alan JK, Struckhoff EC, Lundquist EA.  Multiple cytoskeletal pathways and PI3K signaling mediate CDC-42-induced neuronal protrusion in C. elegans.  Small GTPases [Epub ahead of print].

November 2013 Publications

Alan JK, Lundquist EA.  Mutationally activated Rho GTPases in cancer.  Small GTPases  [Epub ahead of print].

Barta ML, Hickey J, Kemege KE, Lovell S, Battaile KP, Hefty PS.  Structure of CT584 from Chlamydia trachomatis refined to 3.05 Å resolution.  Acta Cryst F69, 1196-1201.

Mostafa HH, Davido DJ.  HSV-1 ICP22 but not US1.5 is Required for Efficient Acute Replication in Mice and VICE Domain Formation.  J Virol [Epub ahead of print]

Perusina Lanfranca M, Mostafa HH, Davido DJ.  Two overlapping regions within the N-terminal half of the HSV-1 E3 ubiquitin ligase ICP0 facilitate the degradation and dissociation of PML and dissociation of Sp100 from ND10.  J Virol [Epub ahead of print]

Suderman R, Deeds EJ.  Machines vs. ensembles: effective MAPK signaling through heterogeneous sets of proteins complexes.  PLoS Comput Biol 9(10): e1003278.

Syed LU, Zhang-Swisher L, Huff H, Rochford C, Wang F, Liu J, Wu J, Richter M, Balivada S, Troyer D, Li J.  Luminol-labeled gold nanoparticles for ultrasensitive chemiluminescence-based chemical analysis.  Analyst 138, 5600-5609.

Wang S, Wang G, Tang G, Wang R, Nikolovska-Coleska Z, Yang D, and Xu L.  Small molecule inhibitors of anti-apoptotic BCL-2 family members and the uses thereof.  United States Patent No. US 8,557,812, issued on Oct. 15, 2013.

Wickstrum J, Sammons LR, Restivo KN, Hefty PS.  Conditional gene expression in Chlamydia trachomatis using the Tet system. PLoS One 8(10): e76743.

October 2013 Publications

Cridland JM, Macdonald SJ, Long AD, Thornton KR. Abundance and distribution of transposable elements in two Drosophila QTL mapping resources. Molecular Biology and Evolution 30: 2311–2327.>

Koppolu V, Osaka I, Skredenske JM, Kettle B, Hefty PS, Li J,Egan SM.   Small Molecule Inhibitor of Shigella flexneri Master Virulence Regulator, VirF.  Infection and Immunity.  [Epub ahead of print]

Kundrotas PJ, Vakser IA, Janin J. Structural templates for modeling homodimer. Protein Science. [Epub ahead of print]

Meneely KM, Luo Q, Lamb AL.  Redesign of MST enzymes to target lyase activity instead promotes mutase and dehydratase activities.  Archives of Biochemistry and Biophysics. [Epub ahead of print]

September 2013 Publications

Anishchenko I, Kundrotas PJ, Tuzikov AV, Vakser IA.  Protein models: The Grand Challenge of protein docking, Proteins [Epub ahead of print]

Kislukhin G, King EG, Walters KN, Macdonald SJ, and Long AD.  The genetic architecture of methotrexate toxicity is similar in Drosophila melanogaster and humans. G3: Genes, Genomes, Genetics 3: 1301–1310.

Kundrotas PJ, Vakser IA. Protein-protein alternative binding modes do not overlap, Protein Sci. 22:1141-1145.  Highlighted in “In This Issue” section.

Kundrotas PJ, Vakser IA. Global and local structural similarity in protein-protein complexes: Implications for template-based docking, Proteins [Epub ahead of print]

Meneely KM, Luo Q, Dhar P, Lamb AL.  Lysine221 is the general base residue of the isochorismate synthase from Pseudomonas aeruginosa (PchA) in a reaction that is diffusion limited.  Arch.  Biochem. Biophys.  [Epub ahead of print]

Ruvinsky AM, Kirys T, Tuzikov AV, Vakser IA. Ensemble-based characterization of unbound and bound states on protein energy landscape. Protein Sci. 22: 734-744.

Tewary SK, Zhao H, Shen W, Qiu J, Tang L.  Structure of the NS1 protein N-terminal origin-recognition/nickase domain from the emerging human bocavirus.  J Virol. [Epub ahead of print]

August 2013 Publications

Gowthaman R, Deeds EJ, Karanicolas J.  The structural properties of non-traditional drug targets present new challenges for virtual screening.  J. Chem. Inf. Model [Epub ahead of print].

July 2013 Publications

Dotson AL, Novikova L, Stehno-Bittel L, Benedict SH.  Elimination of T cell reactivity to pancreatic  β cells and partial preservation of β cell activity by peptide blockade of LFA-1:ICAM-1 interaction with the NOD mouse model.  Clinical Immunology 148, 149-161.

Novikova L, Smirnova IV, Rawal S, Dotson AL, Benedict SH, Stehno-Bittel L.  Variations in rodent models of type 1 diabetes: islet morphology.  J. Diabetes Res. 2013:965832.

Oakley BR (2013). Aspergillus nidulans. In Brenner’s Encyclopedia of Genetics (Second Edition), Editors-in-Chief: S. Maloy, and K. Hughes, eds. (San Diego: Academic Press), pp. 212-215.

Zhao H, Christensen TE, Kamau YN, Tang L.  Structures of the phage Sf6 large terminase provide new insights into DNA translocation and cleavage. Proc Natl Acad Sci USA 110, 8075-80.

June 2013 Publications

Caylor RC, Jin Y, Ackley BD.  The Caenorhabditis elegans voltage-gated calcium channel subunits UNC-2 and UNC-36 and the calcium-dependent kinase UNC-43/CaMKII regulate neuromuscular junction morphology.  Neural Dev. 8: 10.

Chiang YM, Oakley CE, Ahuja M, Entwistle R, Schultz A, Chang SL, Sung CT, Wang CCC, Oakley BR.  An Efficient System for Heterologous Expression of Secondary Metabolite Genes in Aspergillus nidulans.  J. Am. Chem. Soc. 135, 7720-7731.

Rice SA, Davido DJ.  HSV-1 ICP22: hijacking host nuclear functions to enhance viral infection.  Future Microbiol 8, 311-21.

Tamayo JV, Gujar M, Macdonald SJ, Lundquist EA.  Functional transcriptomic analysis of the role of MAB-5/Hox in Q neuroblast migration in Caenorhabditis elegans.  BMC Genomics 14: 304.

Yaegashi J, Praseuth MB, Tyan SW, Sanchez JF, Entwistle R, Chiang YM, Oakley BR, Wang CC.  Molecular genetic characterization of the biosynthesis cluster of a prenylated isoindolinone alkaloid aspernidine A in Asptergillus nidulans.  Org Lett [Epub ahead of print].

May 2013 Publications

Chatterjee S, Chaudhury S, McShan AC, Kaur K, De Guzman RN.  Structure and biophysics of type III secretion in bacteria.  Biochemistry 52, 2508-17.

Sigamani SS, Zhao H, Kamau YN, Baines JD, Tang L.  The structure of the herpes simplex virus DNA-packaging terminase pUL15 nuclease domain suggests an evolutionary lineage among eukaryotic and prokaryotic viruses.  J Virol [Epub ahead of print]

Zeineldin M, Neufeld KL.  Understanding the phenotypic variation in rodent models with germline apc mutations.  Cancer Res 73, 2389-99.

April 2013 Publications

Jo S, Lee HS, Skolnick J, Im W.  Restricted N-glycan conformational space in the PDB and its implication in glycan structure modeling.  PLoS Comput Biol: e1002946.

Johnson DK, Karanicolas J.  Druggable protein interaction sites are more predisposed to surface pocket formation than the rest of the protein surface.  PLoS Comput Biol: e1002951.

Lu J, Huang Y, Zhao W, Marquez RT, Meng X, Li J, Gao X, Venkataramanan R, Wang Z, Li S.  PEG-derived embelin as a nanomicellar carrier for delivery of paclitaxel to breast and prostate cancers.  Biomaterials 24, 1591-1600.

Osaka I, Hefty PS.  A simple resazurin-based microplate assay for measuring Chlamydia infections.  Antimicrob Agents Chemother.  [Epub ahead of print]>

Park S, Im W.  Two dimensional window exchange umbrella sampling for transmembrane helix assembly. J Chem Theory Comput.  9: 13-17.

Smith MC, Goddard ET, Perusina Lanfranca M, Davido DJ.  hTERT extends the life of human fibroblasts without compromising type 1 interferon signaling.  PLoS One: e58233.

 

March 2013 Publications

Dentler W.  A role for the membrane in regulating chlamydomonas flagellar length.  PLoS One.  8: e53366.

Huarcaya Najarro E, Ackley BD.  C. elegans fmi-1/flamingo and Wnt pathway components interact genetically to control the anteroposterior neurite growth of the VD GABAergic neurons.  Dev Biol [Epub ahead of print]

Lee KI, Pastor RW, Andersen OS, Im W.  Assessing smectic liquid-crystal continuum models for elastic bilayer deformations.  Chem Phys Lipids [Epub ahead of print]

Skredenske JM, Koppolu V, Kolin A, Deng J, Kettle B, Taylor B, Egan SE. Identification of a Small Molecule Inhibitor of Bacterial AraC Family Activators. Journal of Biomolecular Screening.  [Epub ahead of print]

Takusagawa F.  Microsomal prostaglandin E synthase type-2 (mPGES2) is a GSH-dependent heme protein, and dithiothreitol dissociates the bound-heme to produce active PVD2 synthase in vitro.  J Biol Chem [Epub ahead of print]

Cheng P, Ni Z, Dai X, Wang B, Smith AR, Xu L, Wu D, He F, Lian J.  The novel BH-3 mimetic apogossypolone induces beclin-1- and ROS-mediated autophagy in human hepatocellular cells.  Cell Death and Disease 4, e489.

Wang H, Davido DJ, Morrison LA.  HSV-1 strain McKrae is more neuroinvasive than HSV-1 KOS after corneal or vaginal incoluation in mice.  Virus Res.  [Epub ahead of print]

Yeh HH, Chang SL, Chiang YM, Bruno KS, Oakley BR, Wu TK, Wang CC.  Engineering fungal nonreducing polyketide synthetase by heterologous expression and domain swapping.  Org Lett 15: 756-759.

February 2013 Publications

Bender A, Woydziak ZR, Branden , Zhou Z, Ackley BD, Peterson BR.  Novel acid-activated fluorophores reveal a dynamic wave of protons in the intestine of Ceanorhabditis elegans.  ACS Chem Biol  [Epub ahead of print]

Khan LA, Zhang H, Abraham N, Sun L, Fleming JT, Buechner M, Hall DH, Gobel V.  Intracellular lumen extension requires ERM-1-dependent apical memebrane expansion and AQP-8-mediated flux.  Nature Cell Biology.  [Epub ahead of print]

Vakser IA.  Low-resolution structural modeling of protein interactome.  Curr Opin Struct Biol [Epub ahead of print]

Zeineldin M, Neufeld KL.  More than two decades of Apc modeling in rodents.  Biochim Biophys Acta.  [Epub ahead of print]

January 2013 Publications

Asad N, Aw WY, Timmons L.   Natural and Unanticipated Modifiers of RNAi Activity in Caenorhabditiselegans. PLoS One 7(11) e50191 (2012) 

Jo S, Jiang W, Lee HS, Roux B, Im W. CHARMM-GUI Ligand Binder for Absolute Binding Free Energy Calculations and Its Application. J ChemInf Model. 2012 Dec 20. [Epub ahead of print]

Marquez RT, Tsao BW, Faust NF and Xu L. Drug resistance and molecular cancer therapy: Apoptosis vs. Autophagy. In: Justine Rudner, ed., Apoptosis. Chapter. InTech. 2013 (in press).

Mostafa HH, Thompson TW, Davido DJ. N-terminal phosphorylation sites of herpes simplex virus type 1 ICP0 differentially regulate its activities and enhance viral replication. J Virol.2012 Dec 5. [Epub ahead of print]

Rowland, M. A., Fontana, W. and Deeds, E. J. Crosstalk and competition in signaling networks. Biophys. J.103:2389-98.  This article is the focus of a “New and Notable” column in Biophysical Journal.

December 2012 Publications

Guo C-J, Knox B, Chiang, Y-M, Lo H-C, Sanchez J, Lee K-H, Oakley B, Bruno K, Wang C. Molecular genetic characterization of a cluster in A. terreus for biosynthesis of the meroterpenoid terretonin. Org. Lett. 14:5684-5687.

Sundararajan L, Lundquist EA.  The Transmembrane Proteins UNC-40/DCC, PTP-3/LAR, and MIG-21 Control Anterior-posterior Neuroblast Migration with Left-right Functional Asymmetry in Caenorhabditis elegansGenetics 2012 Oct 10. [Epub ahead of print]

Combs, B. and Gamblin, T.C. FTDP-17 Mutations Induce Distinct Effects on Aggregation and Microtubule Interactions. Biochemistry 2012, 51(43): 8597-8607.

Lee, H.S. and Im, W. Identification of Ligand Templates using Local Structure Alignment for Structure-Based Drug Design. J Chem Inf Model. 2012 Oct 22;52(10):2784-95. Epub 2012 Sep 28.

Meneely, K.M., and Lamb, A.L. Two structures of a thiazolinyl imine reductase from Yersinia enterocolitica provide insight into catalysis and binding to the nonribosomal peptide synthetase module of HMWP1. Biochemistry. 2012 Oct 23. [Epub ahead of print]

Oakley, C. E., Edgerton-Morgan, H., Oakley, B. R., Tools for Manipulation of Secondary Metabolism Pathways: Rapid Promoter Replacements and Gene Deletions in Aspergillus nidulans. Methods Mol Biol 2012, 944, 143-161.

Zeineldin, M. and Neufeld, K., Isolation of Epithelial Cells from Mouse Gastrointestinal Tract for Western Blot or RNA analysis. Bio-protocol, invited, peer-reviewed.
Featured protocol under fields of "Molecular Biology" and "Cell Biology"

Zhao, H., Kamau, Y., Christensen, T. and Tang, L., Structural and functional studies of the bacteriophage Sf6 terminase small subunit reveal a DNA-spooling device facilitated by structural plasticity. J. Mol. Biol. 423, 3, 413-26.

PREPARATION OF REGULATORY T CELLS USING ICAM-1 CO-STIMULATION
U.S. Patent Application Serial No. 12/122,377
Benedict, S, Williams K, Dotson, A

November 2012 Publications

Combs, B. and Gamblin, T.C. FTDP-17 Mutations Induce Distinct Effects on Aggregation and Microtubule Interactions. Biochemistry 2012, 51(43): 8597-8607.
http://www.ncbi.nlm.nih.gov/pubmed/23043292

Jo, S. and Im, W. Glycan fragment database: a database of PDB-based glycan 3D structures. Nucleic Acids Res. 2012 Oct 26. [Epub ahead of print]
http://www.ncbi.nlm.nih.gov/pubmed/23104379

Lee, H.S. and Im, W. Identification of Ligand Templates using Local Structure Alignment for Structure-Based Drug Design. J Chem Inf Model. 2012 Oct 22;52(10):2784-95. Epub 2012 Sep 28.
http://www.ncbi.nlm.nih.gov/pubmed/22978550

Meneely, K.M., and Lamb, A.L. Two structures of a thiazolinyl imine reductase from Yersinia enterocolitica provide insight into catalysis and binding to the nonribosomal peptide synthetase module of HMWP1. Biochemistry. 2012 Oct 23. [Epub ahead of print]
http://www.ncbi.nlm.nih.gov/pubmed/23066849

Oakley, C. E., Edgerton-Morgan, H., Oakley, B. R., Tools for Manipulation of Secondary Metabolism Pathways: Rapid Promoter Replacements and Gene Deletions in Aspergillus nidulans. Methods Mol Biol 2012, 944, 143-161.
http://www.ncbi.nlm.nih.gov/pubmed/23065614

Zeineldin, M. and Neufeld, K., Isolation of Epithelial Cells from Mouse Gastrointestinal Tract for Western Blot or RNA analysis. Bio-protocol, invited, peer-reviewed.
http://www.bio-protocol.org/wenzhang.aspx?id=292
Featured protocol under fields of "Molecular Biology" and "Cell Biology"
http://www.bio-protocol.org/fllist.aspx?fl1=1&fweek1=1
http://www.bio-protocol.org/fllist.aspx?fl1=4&fweek1=1

Zhao, H., Kamau, Y., Christensen, T. and Tang, L., Structural and functional studies of the bacteriophage Sf6 terminase small subunit reveal a DNA-spooling device facilitated by structural plasticity. J. Mol. Biol. 423, 3, 413-26.
http://www.ncbi.nlm.nih.gov/pubmed/22858866

PREPARATION OF REGULATORY T CELLS USING ICAM-1 CO-STIMULATION
U.S. Patent Application Serial No. 12/122,377
Benedict, S, Williams K, Dotson, A

October 2012 Publications

Olucha J, Meneely KM, Lamb AL. Modification of residue 42 of the active site loop with a lysine-mimetic side chain rescues isochorismate-pyruvate lyase activity in Pseudomonas aeruginosa PchB. Biochemistry. 51: 7525-7532.
http://www.ncbi.nlm.nih.gov/pubmed/22970849

Sudharsan R, Azuma Y. The SUMO ligase PIAS1 regulates UV-induced apoptosis by recruiting Daxx to SUMOylated foci. J. Cell Sci. [Epub ahead of print].
http://www.ncbi.nlm.nih.gov/pubmed/22976298

September 2012 Publications

Edgerton-Morgan H, Oakley BR. γ-Tubulin plays a key role in inactivating APC/CCdh1 at the G1-S boundary. J Cell Biol. 2012 Aug 27. [Epub ahead of print]
http://www.ncbi.nlm.nih.gov/pubmed/22927465

King EG, Merkes CM, McNeil CL, Hoofer SR, Sen S, Broman KW, Long AD, Macdonald SJ.
Genetic dissection of a model complex trait using the Drosophila Synthetic Population Resource.Genome Res. 2012 Aug;22(8):1558-66. Epub 2012 Apr 10.
http://www.ncbi.nlm.nih.gov/pubmed/22496517

Macdonald SJ, Mostafa HH, Morrison LA, Davido DJ. Genome Sequence of Herpes Simplex Virus 1 Strain McKrae.J Virol. 2012 Sep;86(17):9540-1.
http://www.ncbi.nlm.nih.gov/pubmed/22879612

Soukup, A. A., Y. M. Chiang, J. W. Bok, Y. Reyes-Dominguez, B. R. Oakley, C. C. Wang, J. Strauss, and N. P. Keller. 2012. Overexpression of the Aspergillusnidulans histone 4 acetyltransferaseEsaA increases activation of secondary metabolite production. MolMicrobiol.
http://www.ncbi.nlm.nih.gov/pubmed/22882998

August 2012 Publications

Entwistle RA, Rizk RS, Cheng DM, Lushington GH, Himes RH, Gupta ML Jr.  Differentiating between models of epothilone binding to microtubules using tubulin mutagenesis, cytotoxicity, and molecular modeling.  ChemMedChem.  2012 Jul 16 [Epub ahead of print]
http://www.ncbi.nlm.nih.gov/pubmed/22807375

King EG, Macdonald SJ, Long AD. Properties and power of the Drosophila Synthetic Population Resource for the routine dissection of complex traits. Genetics 2012, 191: 935-49.
http://www.ncbi.nlm.nih.gov/pubmed/22505626

Klionsky DJ1. . .Xu L996. . .et al.  Guidelines for the use and interpretation of assays for monitoring autophagy.  Autophagy 8, 445-544.
http://www.landesbioscience.com/journals/3/article/19496/

Lee HS, Jo S, Lim HS, Im W.  Application of binding free energy calculations to prediction of binding modes and affinities of MDM2 and MDMX inhibitors.  J Chem Inf Model.  2012 Jul 6.  [Epub ahead of print]
http://www.ncbi.nlm.nih.gov/pubmed/22731511

July 2012 Publications

Biswas S, Benedict SH, Lynch SG, LeVine SM.  Potential immunological consequences of pharmacological suppression of grastric acid production in patients with multiple sclerosis.BMC Medicine, 10:57.
http://www.ncbi.nlm.nih.gov/pubmed/22676575

Deckert K, Budiardjo SJ, Brunner LC, Lovell S, Karanicolas J. Designing allosteric control into enzymes by chemical rescue of structure.  J. Amer. Chem. Soc. 134: 10055-60.
http://www.ncbi.nlm.nih.gov/pubmed/22655749

Kirys T, RuvinskyAM, Tuzikov AV, Vakser IA.  Rotamer libraries and probabilities of transition between rotamers for the side chains in protein-protein binding.Proteins 2012 Apr 27 [Epub ahead of print]
http://www.ncbi.nlm.nih.gov/pubmed/22544766

Kundrotas PJ, Zhu Z, Janin J, Vakser IA.Templates are available to model nearly all complexes of structurally characterized proteins.  Proc. Natl. Acad. Sci. USA 109: 9438-41.
http://www.ncbi.nlm.nih.gov/pubmed/22645367

Yeh H, Chiang Y, Entwistle R, Ahuja M, Lee K, Bruno K, Wu T, Oakley BR, Wang C. Molecular genetic analysis reveals that a nonribosomal peptide synthase-like (NRPS-like) gene in Aspergillus nidulans is responsible for microperfuranone biosynthesis.  Appl. Microbiol. Biotechnol.  2012 May 25 [Epub ahead of print]
http://www.ncbi.nlm.nih.gov/pubmed/22627757

Zhong D, Lefebre M, Kaur K, McDowell MA, Gdowski C, Jo S, Wang Y, Benedict SH, Lea SM, Galan JE, De Guzman RN.  The Salmonella type III secretion system inner rod protein PrgJ is partially folded.  J. Biol. Chem. 2012 May 31 [Epub ahead of print]
http://www.ncbi.nlm.nih.gov/pubmed/22654099

June 2012 Publications

Demarco RS, Struckhoff EC, Lundquist EA.  The Rac GTP exchange factor TIAM-1 acts with CDC-42 and the guidance receptor UNC-40/DCC in neuronal protrusion and axon guidance. PLoS Genetics 2012, 8:4, e1002665.
http://www.ncbi.nlm.nih.gov/pubmed/22570618

Macdonald SJ, Mostafa HH, Morrison LA, Davido DJ.Genome Sequence of Herpes Simplex Virus 1 Strain KOS.J Virol. 2012 Jun;86(11):6371-2.
http://www.ncbi.nlm.nih.gov/pubmed/22570244

Osaka I, Hills JM, Kieweg SL, Shinogle HE, Moore DS, Hefty PS.  An automated image-based method for rapid analysis of Chlamydia infection as a tool for screening antichlamydial agents.Antimicrob Agents Chemother2012 May 21 [Epub ahead of print]
http://www.ncbi.nlm.nih.gov/pubmed/22615279

May 2012 Publications

Ahuja M, Chiang YM, Chang SL, Praseuth MB, Entwistle R, Sanchez JF, Lo HC, Yeh HH, Oakley BR, Wang CC. Illuminating the diversity of aromatic polyketide synthases in Aspergillus nidulans. J Am Chem Soc
[Epub ahead of print]
http://www.ncbi.nlm.nih.gov/pubmed/22510154

Cheng X, Im W. NMR observable-based structure refinement of DAP12-NKG2C activating immunoreceptor complex in explicit membranes. Biophys J 102: L27-9.
http://www.ncbi.nlm.nih.gov/pubmed/22500771

Kim T, Lee KU, Morris P, Pastor RW, Andersen OS, Im W. Influence of hydrophobic mismatch on structures and dynamics of gramicidin a and lipid bilayers. Biophys J 102: 1551-60.
http://www.ncbi.nlm.nih.gov/pubmed/22500755

O'Bryhim BE, Radel J, Macdonald SJ, Symons RC. The genetic control of avascular area in mouse oxygen-induced retinopathy. Molecular Vision 2012; 18: 377-89.
http://www.ncbi.nlm.nih.gov/pubmed/22355249

Park S, Kim T, Im W. Transmembrane helix assembly by window exchange umbrella sampling. Phys Rev Lett 108: 108102.
http://www.ncbi.nlm.nih.gov/pubmed/22463457

Sanchez JF, Entwistle R, Corcoran D, Oakley BR, Wang CC. Identification and molecular genetic analysis of the cichorine cluster in Aspergillus nidulans. In press: Med Chem Comm Available on line.
http://pubs.rsc.org/en/content/articlepdf/2012/md/c2md20055d

April 2012 Publications

Karanicolas J. Designing orthogonal signaling pathways: How to fit in with the surroundings. Proc Natl Acad Sci U S A. 2012 Mar 26. [Epub ahead of print]
http://www.ncbi.nlm.nih.gov/pubmed/22451928

Najarro EH, Wong L, Zhen M, Carpio EP, Goncharov A, Garriga G, Lundquist EA, Jin Y, Ackley BD. Caenorhabditis elegans Flamingo Cadherin fmi-1 Regulates GABAergic Neuronal Development. J Neurosci. 32(12):4196-211 (2012)
http://www.ncbi.nlm.nih.gov/pubmed/22442082

Deeds EJ, Krivine J, Feret J, Danos V, Fontana W. Combinatorial complexity and compositional drift in protein interaction networks. PLoS One. 7(3):e32032 (2012)
http://www.ncbi.nlm.nih.gov/pubmed/22412851

Wacker MJ, Tevis O, Hanke J, Howard T, Gilbert W, Orr JA. Characterization of thromboxane A(2) receptor and TRPV1 mRNA expression in cultured sensory neurons. Neurosci Lett. 2012 Mar 7. [Epub ahead of print]
http://www.ncbi.nlm.nih.gov/pubmed/22425716

March 2012 Publications

Deeds EJ, Bachman JA, Fontana W. Optimizing ring assembly reveals the strength of weak interactions. Proc. Natl. Acad. Sci. USA 109(7): 2348-53. http://www.ncbi.nlm.nih.gov/pubmed/22308356

Lo HC, Entwistle R, Guo CJ, Ahuja M, Szewczyk E, Hung JH, Chiang YM, Oakley BR. Wang CC. Two separate gene clusters encode the biosynthetic pathway for the meroterpenoids, austinol and dehydroaustinol in Aspergillus nidulans. J Am Chem Soc 2012 Feb 13 [Epub ahead of print] http://www.ncbi.nlm.nih.gov/pubmed/22329759

Somoza AD, Lee KH, Chiang YM, Oakley BR, Wang CC. Reengineering an azaphilone biosynthesis pathway in Aspergillus nidulins to create lipoxygenase inhibitors. Org. Lett. 2012 Feb 1 [Epub ahead of print] http://www.ncbi.nlm.nih.gov/pubmed/22296232

Taheri-Talesh N, Xiong Y, Oakley BR. The functions of myosin II and myosin V homologs in tip growth and septation in Aspergillus nidulans. PLoS One 7, e31218. http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0031…

February 2012 Publications

Devore NM and Scott EE. Structures of cyctochrome P450 17A1 with prostate cancer drugs abiraterone and TOK-001. Nature 2012 Jan 22 [Epub ahead of print]
http://www.ncbi.nlm.nih.gov/pubmed/22266943

Estrada DF, Conner M, Joer SC and De Guzman RN. The structure of the hantavirus zinc finger domain is conserved and represents the only natively folded region of the Gn cytoplasmic tail. Front Microbiol 2:251.
http://www.ncbi.nlm.nih.gov/pubmed/22203819

Lian J, Ni Z, Dai X, Su C, Smith AR and Xu L, and He F. Sorafenib sensitizes (-)-gossypol-induced growth suppression in androgen-independent prostate cancer cells via Mcl-1 inhibition and Bak activation. Molecular Cancer Therapeutics 2011, Dec. in press
http://www.ncbi.nlm.nih.gov/pubmed/22188816

Marquez RT and Xu L. Bcl2:Beclin 1 complex: multiple mechanisms regulating autophagy/apoptosis toggle switch. Am J Cancer Res 2012;2(2). (in press)
http://www.ajcr.us/ajcr0000098A.html

Simeone DM, Ljungman M, Xu L, Wang L and He F. Compositions and methods for treating cancer. US Patent No. US 8,088749, issued on Jan. 3, 2012.

Voss K, Combs B, Patterson KR, Binder LI and Gamblin TC. Hsp70 alters tau function and aggregation in an isoform specific manner. Biochemistry 2012 Jan 10 [Epub ahead of print]
http://www.ncbi.nlm.nih.gov/pubmed/22236337

January 2012 Publications

Alan JK, Lundquist EA. Analysis of Rho GTPase function in axon pathfinding using Caenorhabditis elegans. Methods Mol Biol 827:339-58.
http://www.ncbi.nlm.nih.gov/pubmed/22144285

November 2011 Publications

Lee KI, Jo S, Egwolf B, Roux B, Pastor RW, Im W.  Web interface for borwnian dynamics simulation of ion transport and its applications to beta-barrel pores.  J. ComputChem 2011 Nov 21 [Epub ahead of print]

Moore CL, Huang MH, RobbennoltSA, Voss K, Combs B, Gamblin TC, Goux WJ.Secondary nucleating sequences affect kinetics and thermodynamics of tau aggregation. Biochemistry. 2011 Nov 15 [Epub ahead of print]

Patterson KR, Ward SM, Combs B, Voss K, Kanaan NM, Morfini G, Brady ST, Gamblin TC, Binder LI.  Heat Shock Protein 70 Prevents both Tau Aggregation and the Inhibitory Effects of Preexisting Tau Aggregates on Fast Axonal Transport.  Biochemistry50, 10300

October 2011 Publications

Kemege KE, Hickey JM, Lovell S, Battaile KP, Zhang Y, Hefty PS. Ab initio structural modeling and experimental validation of Chlamydia trachomatis protein CT296 reveals structural similarity with Fe(II) 2-oxoflutarate dependent enzymes. J. Bacteriol. 2011 Sep 30 [Epub ahead of print]

McNeil CL, Bain CL, Macdonald SJ. Multiple Quantitative Trait Loci Influence the Shape of a Male-Specific Genital Structure in Drosophila melanogaster Genes, Genomes, Genetics 1: 343-351.
 

September 2011 Publications

Combs B, Voss KR and Gamblin TC. Pseudohyperphosphorylation has differential effects on polymerization and function of tau isoforms. Biochemistry 2011 Sep 26. [Epub ahead of print]

Mostafa HH, Thompson TW, Kushnir AS, Haenchen SD, Bayless AM, Hilliard JG, Link MA, Pitcher LA, Loveday E, Schaffer PA, Davido DJ. Herpes Simplex Virus Type 1 ICP0 Phosphorylation Site Mutants are Attenuated for Viral Replication and Impaired for Explant-Induced Reactivation. J Virol. 2011 Sep 21. [Epub ahead of print]

Norris, AD, and Lundquist, EA. UNC-6/Netrin and its receptors UNC-5 and UNC-40/DCC modulate growth cone protrusion in vivo in C. elegans. Development 2011, 138:4433-4442.

Williams KM, Dotson AL, Otto AR, Kohlmeier JE, Benedict SH. Choice of resident costimulatory molecule can influence cell fate in human naïve CD4+ T cell differentiation. Cell Immunol. 2011 Aug 27. [Epub ahead of print]

Wu X, Li M, Tang W, Zheng Y, Lian J, Xu L, and Ji M. Design, synthesis and in vitro antitumor activity evaluation of novel 4-pyrrylamino quinazoline derivatives. Chem Biol Drug Design 2011 Sep 3, [Epub ahead of print]

Zeineldin M, Cunningham J, McGuinness W, Alltizer P, Cowley B, Blanchat B, Xu W, Pinson D and Neufeld KL. A knock-in mouse model reveals roles for nuclear Apc in cell proliferation, Wnt signal inhibition and tumor suppression. Oncogene. 2011 Sep 26, [Epub ahead of print]

 

 

August 2011 Publications

Hofmann FT, Lindemann C, Salia H, Adamitzki P, Karanicolas J, Seebeck FP.  A phosphoarginine containing peptide as an artificial SH2 ligand.ChemCommun.  [Epub ahead of print]

Jo S, Song KC, Desaire H, Mackerell AD Jr, Im W.  Glycan reader: automated sugar identification nd simulation preparation for carbohydrates and glycoproteins.  JComput Chem.[Epub ahead of print]

Lamb AL.  Pericyclic reactions catalyzed by chorismate-utilizing enzymes.  Biochemistry.  50: 7476-7483.

Liu S, Vakser IA.  DECK: distance and environment-dependent, coarse-grained, knowledge-based potentials for protein-protein docking.  BMC Bioinformatics.12:280.

Liu T, Chiang YM, Somoza AD, Oakley BR, Wang CC.  Engineering an “unnatural” natural product by swapping polyketide synthase domains in Aspergillusnidulans.J Am Chem Soc. 133:13314-6.

Mattingly BC, Buechner M.  The FGD homologue EXC-5 regulates apical trafficking in C. eleganstubules.  Develop Biol[Epub ahead of print]

Olucha J, Lamb AL.Mechanistic and structural studies of the N-hydroxylatingflavoproteinmonooxygenases.Bioorg. Chem. [Epub ahead of print]

Rui H, Kumar R, Im W.  Membrane tension, lipid adaptation, conformational changes and energetics in MscL gating.Biophys J.  101: 671-9.

Szewczyk E, Oakley BR. Microtubule dynamics in mitosis in Aspergillus nidulans.Fungal Genet Biol

July 2011 Publications

Hickey JM, Lovell S, Battaile KP, Middaugh CR, Hefty PS. "The atypical response regulator ChxR has structural characteristics and dimer interface interactions that are unique within the OmpR/PhoB subfamily. J. Biol. Chem. [Epub ahead of print]

Olucha J, Meneely KM, Chilton AS, Lamb AL."Two structures of an N-hydroxylating flavoprotein monooxygenase: the ornithine hydroxylase from Pseudomonas aeruginosa." J. Biol. Chem. [Epub ahead of print]

Olucha J, Ouellette AN, Luo Q, Lamb AL."pH dependence of catalysis by Pseudomonas aeruginosa isochorismate-pyruvate lyase: implications for transition state stabilization and the role of lysine 42." Biochemistry.[Epub ahead of print]

Smith MC, Boutell C, Davido DJ. "HSC-1 ICP0: paving the way for viral replication. Future Virol. 6, 421-429.

Smith MC, Bayless AM, Goddard ET, Davido DJ. "CK2 inhibitors increase the sensitivity of HSV-1 to interferon-β." Antiviral Res.[Epub ahead of print]

June 2011 Publications

Estrada DF, De Guzman RN. “Structural characterization of the crimean-congo hemorrhagic fever virus gn tail provides insight into virus assembly.” J Biol Chem 286: 21678-86.

Jo S, Im W. “Transmembrane helix orientation and dynamics: insights from ensemble dynamics with solid-state NMR observables.” Biophys J. 100: 2913-21.

Kim T, Jo S, Im W. “Solid-State NMR Ensemble Dynamics as a Mediator between Experiment and Simulation.”  Biophys J. 100: 2922-8.

Parthasarathy S, Altuve A, Terzyan S, Zhang X, Kuczera K, Rivera M, Benson DR. “Accommodating a nonconservative internal mutation by water-mediated hydrogen bonding between β-sheet strands: a comparison of human and rat type B (mitochondrial) cytochrome b(5).” Biochemistry. [Epub ahead of print]

Rankin CA, Roy A, Zhang Y, Richter M. “Parkin, a top level manager in the cell's sanitation department.” Open Biochem 5:9-26.

Sievers SA, Karanicolas J, Chang HW, Zhao A, Jiang L, Zirafi O, Stevens JT, Münch J, Baker D & Eisenberg D. “Structure-based design of non-natural amino-acid inhibitors of amyloid fibril formation.” Nature. [Epub ahead of print]

May 2011 Publications

Xu J, Lan L, Bogard N, Mattione C, and Cohen RS. "Rab11 Is Required for Epithelial Cell Viability, Terminal Differentiation, and Suppression of Tumor-Like Growth in the Drosophila Egg Chamber." PloS One. 6(5): e20180.

Song KC, Livanec PW, Klauda JB, Kuczera K, Dunn RC, Im W. "Orientations of fluorescent lipid analogue BODIPY-PC to probe lipid membrane properties: insights from molecular dynamics simulations." J. Phys. Chem. B 115: 6157–65.

Chaguturu R. "Conference report: the Screening Asia Conference 2010: an update." Future Med. Chem. 3: 513

April 2011 Publications

Deeds EJ, Savage V and Fontana W. Curvature in metabolic scaling: A reply to MacKay. J. Theor. Biol. [Epub ahead of print]

Luo Q, Meneely KM and Lamb AL. Entropic and enthalpic components of catalysis in the mutase and lyase activities of Pseudomonas aeruginosa PchB. J. Am. Chem. Soc. [Epub ahead of print]

Giles SS, Soukup AA, Lauer C, Shaaban M, Lin A, Oakley BR, Wang CC, and Keller NP. Cryptic Aspergillus nidulans antimicrobial. Appl Environ Microbiol.

DeSano JT, Lawrence, TW and Xu L. Chapter 15, “MicroRNAs: Small but Critical Regulators of Cancer Stem Cells” in: Cancer Stem Cells Theories and Practice, Stanley Shostak, Ed.

March 2011 Publications

Sanchez JF, Entwistle R, Hung J-H, Yaegashi J, Jain S, Chiang Y-M, Wang CCC, Oakley BR. Genome-based deletion analysis reveals the prenyl xanthose biosynthesis pathway in Aspergillus nidulas. J. Am. Chem. Soc. 133: 4010-7.

Demarco RS and Lundquist EA "RACK"-ing up the effectors: Receptor for activated C kinase acts downstream of Rac GTPase signaling in growth cone outgrowth. Small GTPases 2:1, 1-4; January/February 2011

Karanicolas J, Corn JE, Chen I, Joachimiak, LA, Dym O, Peck SH, Albeck S, Unger T, Hu W, Liu G, Delbecq S, Montelione GT, Spiegel CP, Liu DR and Baker D. A De Novo Protein Binding Pair By Computational Design and Directed Evolution. Molecular Cell 42:1-11.

February 2011 Publications

Lee KI, Rui H, Pastor RW, Im W. Brownian dynamics simulations of ion transport through the VDAC. Biophys. J. 100: 611–9.

Lian J, Wu X, He F, Karnak D, Tang W, Meng Y, Xiang D, Ji M, Lawrence TS and Xu L. A natural BH3 mimetic induces autophagy in apoptosis-resistant prostate cancer via modulating Bcl-2-Beclin1 interaction at endoplasmic reticulum. Cell Death Differ. 18: 60–71.

Rathinavelan T, Tang C and De Guzman RN. Characterization of the Interaction between the Salmonella Type III Secretion System Tip Protein SipD and the Needle Protein PrgI by Paramagnetic Relaxation Enhancement. J. Biol. Chem. 286: 4922–30.

Rui H, Lee KI, Pastor RW, Im W. Molecular dynamics studies of ion permeation in VDAC. Biophys. J. 100: 602–10.

January 2011 Publications

Spears E, Neufeld KL. "A novel double-negative feedback loop between adenomatous polyposis coli and musashi1 in colon epithelia." J Biol Chem. 2011 Jan 3. [Epub ahead of print]

Palmer JM, Mallaredy S, Perry DW, Sanchez JF, Thiesen JM, Szewczyk E, Oakley BR, Wang CCC, Keller NP, Mirabito PM. "Telomere position effect is regulated by heterochromatin associated proteins and NkuA in Aspergillus nidulans."  Microbiology 156, 3522-3531.

Dai Y, DeSano J, Tang W, Meng X, Meng Y, Burstein E, Lawrence TS, Xu L. "Natural proteasome inhibitor celastrol suppresses androgen-independent prostate cancer progression by modulating apoptotic protein and NF-kappaB." PloS One. 5(12): e14153.

Dai Y, DeSano J, Yang Q, Tang W, Meng Y, Burstein E, Lawrence TS, Xu L. "Natural IAP inhibitor embelin enhances therapeutic efficacy of ionizing radiation in prostate cancer." Am J Cancer Res 1(2), 128-143.

December 2010 Publications

Lan L, Lin S, Zhang S, Cohen RS. “Evidence for a Transport-Trap Mode of Drosophila melanogaster gurken mRNA Localization.” PLoS One 5(11).

Ryu H, Furuta M, Kirkpatrick D, Gygi SP, Azuma Y. “PIASy-dependent SUMOylation regulates DNA topoisomerase II{alpha} activity.” J Cell Biol. 191(4):783-94. 

Zhao H, Sequeira RD, Galeva NA, Tang L. “The host outer membrane proteins OmpA and OmpC are associated with the Shigella phage Sf6 virion.” Virology. 2010 Nov 9. [Epub ahead of print]

Hegefeld WA, Chen SE, Deleon KY, Kuczera K, Jas GS. “Helix Formation in a Pentapeptide: Experiment and Force-field Dependent Dynamics.” J Phys Chem A. 114(47):12391-402.

Hickey JM, Weldon L, Hefty PS. “The Atypical OmpR/PhoB Response Regulator, ChxR, from Chlamydia trachomatis forms Homodimers in vivo and Binds a Direct Repeat of Nucleotide Sequences.” J Bacteriol. 2010 Nov 5. [Epub ahead of print]

Priyadarshi A, Tang L. “Crystallization and preliminary crystallographic analysis of the type III secretion translocator chaperone SicA from Salmonella enterica.” Acta Crystallogr Sect F Struct Biol Cryst Commun. 66(Pt 11):1533-5.

Chatterjee S, Zhong D, Nordhues BA, Battaile KP, Lovell SW, De Guzman RN. “The crystal structures of the Salmonella type III secretion system tip protein SipD in complex with deoxycholate and chenodeoxycholate.” Protein Sci. 2010 Oct 28. [Epub ahead of print]

Jo S, Rui H, Lim JB, Klauda JB, Im W. Cholesterol flip-flop: insights from free energy simulation studies. J Phys Chem B. 114(42):13342-8. 

Ashton GH, Morton JP, Myant K, Phesse TJ, Ridgway RA, Marsh V, Wilkins JA, Athineos D, Muncan V, Kemp R, Neufeld K, Clevers H, Brunton V, Winton DJ, Wang X, Sears RC, Clarke AR, Frame MC, Sansom OJ. “Focal adhesion kinase is required for intestinal regeneration and tumorigenesis downstream of Wnt/c-Myc signaling.” Dev Cell 19(2):259-69. 

Demarco RS and Lundquist EA. "RACK-1 acts with Rac GTPase signaling and UNC-115/abLIM in Caenorhabditis elegans axon pathfinding and cell migration." PLoS Genetics 6(11):e1001215. 

November 2010 Publications

Lian J, Karnak D, and Xu L. “The Bcl-2-Beclin 1 interaction in (-)-gossypol-induced autophagy versus apoptosis in prostate cancer cells.” Autophagy 6(8). Epub Oct. 25, 2010.

Pan X, Thompson R, Meng X, Wu D, and Xu L. “Tumor-targeted RNA-interference: functional non-viral nanovectors.” Am J Cancer Res 1(1):32-49.

Ruvinsky AM and Vakser IA. “Sequence composition and environment effects on residue fluctuations in protein structures.” J Chem Phys 133(15): 155101.

September 2010 Publications

Dyer JO, Demarco RS, Lundquist EA “Distinct roles of Rac GTPases and the UNC-73/Trio and PIX-1 Rac GTP exchange factors in neuroblast protrusion and migration in C. elegans” Small GTPases 1, 44-61. 

Jepkorir G, Rodríguez JC, Rui H, Im W, Lovell S, Battaile KP, Alontaga AY, Yukl ET, Moënne-Loccoz P, Rivera M. “Structural, NMR Spectroscopic, and Computational Investigation of Hemin Loading in the Hemophore HasAp from Pseudomonas aeruginosa.” J Am Chem Soc. 132: 9857-72.

Kim T, Im W. “Revisiting hydrophobic mismatch with free energy simulation studies of transmembrane hielix tilt and rotation.” Biophys J 99: 175-83

Nayak, Tania, Edgerton-Morgan, Heather, Horio, Tetsuya, Xiong, Yi, De Souza, Colin P., Osmani, Stephen A. and Oakley, Berl R. “γ-Tubulin regulates the anaphase-promoting complex/cyclosome during interphase.” J. Cell Biol. 190, 317-330

Rui H, Im W. “Protegrin-1 orientation and physicochemical properties in membrane bilayers studied by potential of mean force calculations.” J Comput Chem. [Epub ahead of print] 

July 2010 Publications

Rui H, Im W. Protegrin-1 orientation and physicochemical properties in membrane bilayers studied by potential of mean force calculations. J Comput Chem. [Epub ahead of print] 

Jepkorir G, Rodríguez JC, Rui H, Im W, Lovell S, Battaile KP, Alontaga AY, Yukl ET, Moënne-Loccoz P, Rivera M. Structural, NMR Spectroscopic, and Computational Investigation of Hemin Loading in the Hemophore HasAp from Pseudomonas aeruginosa. J Am Chem Soc. [Epub ahead of print]

May 2010 Publications

Ryu H, Al-Ani G, Deckert K, Kirkpatrick D, Gygi SP, Dasso M, Azuma Y.“PIASy mediates SUMO-2/3 conjugation of poly(ADP-ribose) polymerase 1 (PARP1) on mitotic chromosomes.”J. Biol. Chem. 285: 14415-23. 

Zhang L, Nebane NM, Wennerberg K, Li Y, Neubauer V, Hobrath JV, McKellip S, Rasmussen L, Shindo N, Sosa M, Maddry JA, Ananthan S, Piazza GA, White EL, Harsay E. “A High-Throughput Screen for Chemical Inhibitors of Exocytic Transport in Yeast.”

Wang Y, Nordhues BA, Zhong D, De Guzman RN. “NMR characterization of the interaction of the Salmonella type III secretion system protein SipD and bile salts.”Biochemistry 18, 42290

Chiang YM, Oakley BR, Keller NP, Wang CC. Unraveling polyketide synthesis in members of the genus Aspergillus, Appl Microbiol Biotechnol. 2010 May; 86(6)

April 2010 Publications

Chiang, Y. M., Szewczyk, E., Davidson, A. D., Entwistle, R., Keller, N. P., Wang, C. C., and Oakley, B. R. Characterization of the Aspergillus nidulans monodictyphenone gene cluster, Applied and Environmental Microbiology 76, 2067-2074

Kundrotas, P. J., and Vakser, I. A. Accuracy of protein-protein binding sites in high-throughput template-based modeling, PLoS Computational Biology 6, e1000727.

Wang, Y., Coffey, R. J., Osheroff, N., and Neufeld, K. L. Topoisomerase IIalpha binding domains of adenomatous polyposis coli influence cell cycle progression and aneuploidy, PloS one 5, 

March 2010 Publications

Sanchez, J. F., Chiang, Y. M., Szewczyk, E., Davidson, A. D., Ahuja, M., Elizabeth Oakley, C., Woo Bok, J., Keller, N., Oakley, B. R., and Wang, C. C. Molecular genetic analysis of the orsellinic acid/F9775 gene cluster of Aspergillus nidulans, Molecular bioSystems 6, 587-593.

Wang, X., and Ward, R. E. Sec61alpha is required for dorsal closure during Drosophila embryogenesis through its regulation of Dpp signaling, Developmental Dynamics 239, 784-797.
 

February 2010 Publications

Rathinavelan, T., Zhang, L., Picking, W. L., Weis, D. D., De Guzman, R. N., and Im, W. A repulsive electrostatic mechanism for protein export through the type III secretion apparatus, Biophysical Journal 98, 452-461.

Zhao, H., Finch, C. J., Sequeira, R. D., Johnson, B. A., Johnson, J. E., Casjens, S. R., and Tang, L. Crystal structure of the DNA-recognition component of the bacterial virus Sf6 genome-packaging machine, Proceedings of the National Academy of Sciences of the United States of America 107, 

January 2010 Publications

Kundrotas, P. J., Zhu, Z., and Vakser, I. A. GWIDD: Genome-wide protein docking database, Nucleic Acids Research 38, D513-517.

Wickstrum, J. R., Skredenske, J. M., Balasubramaniam, V., Jones, K., and Egan, S. M. The AraC/XylS family activator RhaS negatively autoregulates rhaSR expression by preventing cyclic AMP receptor protein activation, Journal of Bacteriology 192, 225-232.

Zhang, L., Huang, M., and Harsay, E. A chemical genetic screen for modulators of exocytic transport identifies inhibitors of a transport mechanism linked to GTR2 function, Eukaryotic Cell 9, 116-126.

November 2011 Publications

Lee KI, Jo S, Egwolf B, Roux B, Pastor RW, Im W.  Web interface for borwnian dynamics simulation of ion transport and its applications to beta-barrel pores.  J. ComputChem 2011 Nov 21 [Epub ahead of print]

Moore CL, Huang MH, RobbennoltSA, Voss K, Combs B, Gamblin TC, Goux WJ.Secondary nucleating sequences affect kinetics and thermodynamics of tau aggregation. Biochemistry. 2011 Nov 15 [Epub ahead of print]

Patterson KR, Ward SM, Combs B, Voss K, Kanaan NM, Morfini G, Brady ST, Gamblin TC, Binder LI.  Heat Shock Protein 70 Prevents both Tau Aggregation and the Inhibitory Effects of Preexisting Tau Aggregates on Fast Axonal Transport.  Biochemistry50, 10300

October 2011 Publications

Kemege KE, Hickey JM, Lovell S, Battaile KP, Zhang Y, Hefty PS. Ab initio structural modeling and experimental validation of Chlamydia trachomatis protein CT296 reveals structural similarity with Fe(II) 2-oxoflutarate dependent enzymes. J. Bacteriol. 2011 Sep 30 [Epub ahead of print]

McNeil CL, Bain CL, Macdonald SJ. Multiple Quantitative Trait Loci Influence the Shape of a Male-Specific Genital Structure in Drosophila melanogaster Genes, Genomes, Genetics 1: 343-351.
 

September 2011 Publications

Combs B, Voss KR and Gamblin TC. Pseudohyperphosphorylation has differential effects on polymerization and function of tau isoforms. Biochemistry 2011 Sep 26. [Epub ahead of print]

Mostafa HH, Thompson TW, Kushnir AS, Haenchen SD, Bayless AM, Hilliard JG, Link MA, Pitcher LA, Loveday E, Schaffer PA, Davido DJ. Herpes Simplex Virus Type 1 ICP0 Phosphorylation Site Mutants are Attenuated for Viral Replication and Impaired for Explant-Induced Reactivation. J Virol. 2011 Sep 21. [Epub ahead of print]

Norris, AD, and Lundquist, EA. UNC-6/Netrin and its receptors UNC-5 and UNC-40/DCC modulate growth cone protrusion in vivo in C. elegans. Development 2011, 138:4433-4442.

Williams KM, Dotson AL, Otto AR, Kohlmeier JE, Benedict SH. Choice of resident costimulatory molecule can influence cell fate in human naïve CD4+ T cell differentiation. Cell Immunol. 2011 Aug 27. [Epub ahead of print]

Wu X, Li M, Tang W, Zheng Y, Lian J, Xu L, and Ji M. Design, synthesis and in vitro antitumor activity evaluation of novel 4-pyrrylamino quinazoline derivatives. Chem Biol Drug Design 2011 Sep 3, [Epub ahead of print]

Zeineldin M, Cunningham J, McGuinness W, Alltizer P, Cowley B, Blanchat B, Xu W, Pinson D and Neufeld KL. A knock-in mouse model reveals roles for nuclear Apc in cell proliferation, Wnt signal inhibition and tumor suppression. Oncogene. 2011 Sep 26, [Epub ahead of print]

 

 

August 2011 Publications

Hofmann FT, Lindemann C, Salia H, Adamitzki P, Karanicolas J, Seebeck FP.  A phosphoarginine containing peptide as an artificial SH2 ligand.ChemCommun.  [Epub ahead of print]

Jo S, Song KC, Desaire H, Mackerell AD Jr, Im W.  Glycan reader: automated sugar identification nd simulation preparation for carbohydrates and glycoproteins.  JComput Chem.[Epub ahead of print]

Lamb AL.  Pericyclic reactions catalyzed by chorismate-utilizing enzymes.  Biochemistry.  50: 7476-7483.

Liu S, Vakser IA.  DECK: distance and environment-dependent, coarse-grained, knowledge-based potentials for protein-protein docking.  BMC Bioinformatics.12:280.

Liu T, Chiang YM, Somoza AD, Oakley BR, Wang CC.  Engineering an “unnatural” natural product by swapping polyketide synthase domains in Aspergillusnidulans.J Am Chem Soc. 133:13314-6.

Mattingly BC, Buechner M.  The FGD homologue EXC-5 regulates apical trafficking in C. eleganstubules.  Develop Biol[Epub ahead of print]

Olucha J, Lamb AL.Mechanistic and structural studies of the N-hydroxylatingflavoproteinmonooxygenases.Bioorg. Chem. [Epub ahead of print]

Rui H, Kumar R, Im W.  Membrane tension, lipid adaptation, conformational changes and energetics in MscL gating.Biophys J.  101: 671-9.

Szewczyk E, Oakley BR. Microtubule dynamics in mitosis in Aspergillus nidulans.Fungal Genet Biol

July 2011 Publications

Hickey JM, Lovell S, Battaile KP, Middaugh CR, Hefty PS. "The atypical response regulator ChxR has structural characteristics and dimer interface interactions that are unique within the OmpR/PhoB subfamily. J. Biol. Chem. [Epub ahead of print]

Olucha J, Meneely KM, Chilton AS, Lamb AL."Two structures of an N-hydroxylating flavoprotein monooxygenase: the ornithine hydroxylase from Pseudomonas aeruginosa." J. Biol. Chem. [Epub ahead of print]

Olucha J, Ouellette AN, Luo Q, Lamb AL."pH dependence of catalysis by Pseudomonas aeruginosa isochorismate-pyruvate lyase: implications for transition state stabilization and the role of lysine 42." Biochemistry.[Epub ahead of print]

Smith MC, Boutell C, Davido DJ. "HSC-1 ICP0: paving the way for viral replication. Future Virol. 6, 421-429.

Smith MC, Bayless AM, Goddard ET, Davido DJ. "CK2 inhibitors increase the sensitivity of HSV-1 to interferon-β." Antiviral Res.[Epub ahead of print]

June 2011 Publications

Estrada DF, De Guzman RN. “Structural characterization of the crimean-congo hemorrhagic fever virus gn tail provides insight into virus assembly.” J Biol Chem 286: 21678-86.

Jo S, Im W. “Transmembrane helix orientation and dynamics: insights from ensemble dynamics with solid-state NMR observables.” Biophys J. 100: 2913-21.

Kim T, Jo S, Im W. “Solid-State NMR Ensemble Dynamics as a Mediator between Experiment and Simulation.”  Biophys J. 100: 2922-8.

Parthasarathy S, Altuve A, Terzyan S, Zhang X, Kuczera K, Rivera M, Benson DR. “Accommodating a nonconservative internal mutation by water-mediated hydrogen bonding between β-sheet strands: a comparison of human and rat type B (mitochondrial) cytochrome b(5).” Biochemistry. [Epub ahead of print]

Rankin CA, Roy A, Zhang Y, Richter M. “Parkin, a top level manager in the cell's sanitation department.” Open Biochem 5:9-26.

Sievers SA, Karanicolas J, Chang HW, Zhao A, Jiang L, Zirafi O, Stevens JT, Münch J, Baker D & Eisenberg D. “Structure-based design of non-natural amino-acid inhibitors of amyloid fibril formation.” Nature. [Epub ahead of print]

May 2011 Publications

Xu J, Lan L, Bogard N, Mattione C, and Cohen RS. "Rab11 Is Required for Epithelial Cell Viability, Terminal Differentiation, and Suppression of Tumor-Like Growth in the Drosophila Egg Chamber." PloS One. 6(5): e20180.

Song KC, Livanec PW, Klauda JB, Kuczera K, Dunn RC, Im W. "Orientations of fluorescent lipid analogue BODIPY-PC to probe lipid membrane properties: insights from molecular dynamics simulations." J. Phys. Chem. B 115: 6157–65.

Chaguturu R. "Conference report: the Screening Asia Conference 2010: an update." Future Med. Chem. 3: 513

April 2011 Publications

Deeds EJ, Savage V and Fontana W. Curvature in metabolic scaling: A reply to MacKay. J. Theor. Biol. [Epub ahead of print]

Luo Q, Meneely KM and Lamb AL. Entropic and enthalpic components of catalysis in the mutase and lyase activities of Pseudomonas aeruginosa PchB. J. Am. Chem. Soc. [Epub ahead of print]

Giles SS, Soukup AA, Lauer C, Shaaban M, Lin A, Oakley BR, Wang CC, and Keller NP. Cryptic Aspergillus nidulans antimicrobial. Appl Environ Microbiol.

DeSano JT, Lawrence, TW and Xu L. Chapter 15, “MicroRNAs: Small but Critical Regulators of Cancer Stem Cells” in: Cancer Stem Cells Theories and Practice, Stanley Shostak, Ed.

March 2011 Publications

Sanchez JF, Entwistle R, Hung J-H, Yaegashi J, Jain S, Chiang Y-M, Wang CCC, Oakley BR. Genome-based deletion analysis reveals the prenyl xanthose biosynthesis pathway in Aspergillus nidulas. J. Am. Chem. Soc. 133: 4010-7.

Demarco RS and Lundquist EA "RACK"-ing up the effectors: Receptor for activated C kinase acts downstream of Rac GTPase signaling in growth cone outgrowth. Small GTPases 2:1, 1-4; January/February 2011

Karanicolas J, Corn JE, Chen I, Joachimiak, LA, Dym O, Peck SH, Albeck S, Unger T, Hu W, Liu G, Delbecq S, Montelione GT, Spiegel CP, Liu DR and Baker D. A De Novo Protein Binding Pair By Computational Design and Directed Evolution. Molecular Cell 42:1-11.

February 2011 Publications

Lee KI, Rui H, Pastor RW, Im W. Brownian dynamics simulations of ion transport through the VDAC. Biophys. J. 100: 611–9.

Lian J, Wu X, He F, Karnak D, Tang W, Meng Y, Xiang D, Ji M, Lawrence TS and Xu L. A natural BH3 mimetic induces autophagy in apoptosis-resistant prostate cancer via modulating Bcl-2-Beclin1 interaction at endoplasmic reticulum. Cell Death Differ. 18: 60–71.

Rathinavelan T, Tang C and De Guzman RN. Characterization of the Interaction between the Salmonella Type III Secretion System Tip Protein SipD and the Needle Protein PrgI by Paramagnetic Relaxation Enhancement. J. Biol. Chem. 286: 4922–30.

Rui H, Lee KI, Pastor RW, Im W. Molecular dynamics studies of ion permeation in VDAC. Biophys. J. 100: 602–10.

January 2011 Publications

Spears E, Neufeld KL. "A novel double-negative feedback loop between adenomatous polyposis coli and musashi1 in colon epithelia." J Biol Chem. 2011 Jan 3. [Epub ahead of print]

Palmer JM, Mallaredy S, Perry DW, Sanchez JF, Thiesen JM, Szewczyk E, Oakley BR, Wang CCC, Keller NP, Mirabito PM. "Telomere position effect is regulated by heterochromatin associated proteins and NkuA in Aspergillus nidulans."  Microbiology 156, 3522-3531.

Dai Y, DeSano J, Tang W, Meng X, Meng Y, Burstein E, Lawrence TS, Xu L. "Natural proteasome inhibitor celastrol suppresses androgen-independent prostate cancer progression by modulating apoptotic protein and NF-kappaB." PloS One. 5(12): e14153.

Dai Y, DeSano J, Yang Q, Tang W, Meng Y, Burstein E, Lawrence TS, Xu L. "Natural IAP inhibitor embelin enhances therapeutic efficacy of ionizing radiation in prostate cancer." Am J Cancer Res 1(2), 128-143.

December 2010 Publications

Lan L, Lin S, Zhang S, Cohen RS. “Evidence for a Transport-Trap Mode of Drosophila melanogaster gurken mRNA Localization.” PLoS One 5(11).

Ryu H, Furuta M, Kirkpatrick D, Gygi SP, Azuma Y. “PIASy-dependent SUMOylation regulates DNA topoisomerase II{alpha} activity.” J Cell Biol. 191(4):783-94. 

Zhao H, Sequeira RD, Galeva NA, Tang L. “The host outer membrane proteins OmpA and OmpC are associated with the Shigella phage Sf6 virion.” Virology. 2010 Nov 9. [Epub ahead of print]

Hegefeld WA, Chen SE, Deleon KY, Kuczera K, Jas GS. “Helix Formation in a Pentapeptide: Experiment and Force-field Dependent Dynamics.” J Phys Chem A. 114(47):12391-402.

Hickey JM, Weldon L, Hefty PS. “The Atypical OmpR/PhoB Response Regulator, ChxR, from Chlamydia trachomatis forms Homodimers in vivo and Binds a Direct Repeat of Nucleotide Sequences.” J Bacteriol. 2010 Nov 5. [Epub ahead of print]

Priyadarshi A, Tang L. “Crystallization and preliminary crystallographic analysis of the type III secretion translocator chaperone SicA from Salmonella enterica.” Acta Crystallogr Sect F Struct Biol Cryst Commun. 66(Pt 11):1533-5.

Chatterjee S, Zhong D, Nordhues BA, Battaile KP, Lovell SW, De Guzman RN. “The crystal structures of the Salmonella type III secretion system tip protein SipD in complex with deoxycholate and chenodeoxycholate.” Protein Sci. 2010 Oct 28. [Epub ahead of print]

Jo S, Rui H, Lim JB, Klauda JB, Im W. Cholesterol flip-flop: insights from free energy simulation studies. J Phys Chem B. 114(42):13342-8. 

Ashton GH, Morton JP, Myant K, Phesse TJ, Ridgway RA, Marsh V, Wilkins JA, Athineos D, Muncan V, Kemp R, Neufeld K, Clevers H, Brunton V, Winton DJ, Wang X, Sears RC, Clarke AR, Frame MC, Sansom OJ. “Focal adhesion kinase is required for intestinal regeneration and tumorigenesis downstream of Wnt/c-Myc signaling.” Dev Cell 19(2):259-69. 

Demarco RS and Lundquist EA. "RACK-1 acts with Rac GTPase signaling and UNC-115/abLIM in Caenorhabditis elegans axon pathfinding and cell migration." PLoS Genetics 6(11):e1001215. 

November 2010 Publications

Lian J, Karnak D, and Xu L. “The Bcl-2-Beclin 1 interaction in (-)-gossypol-induced autophagy versus apoptosis in prostate cancer cells.” Autophagy 6(8). Epub Oct. 25, 2010.

Pan X, Thompson R, Meng X, Wu D, and Xu L. “Tumor-targeted RNA-interference: functional non-viral nanovectors.” Am J Cancer Res 1(1):32-49.

Ruvinsky AM and Vakser IA. “Sequence composition and environment effects on residue fluctuations in protein structures.” J Chem Phys 133(15): 155101.

September 2010 Publications

Dyer JO, Demarco RS, Lundquist EA “Distinct roles of Rac GTPases and the UNC-73/Trio and PIX-1 Rac GTP exchange factors in neuroblast protrusion and migration in C. elegans” Small GTPases 1, 44-61. 

Jepkorir G, Rodríguez JC, Rui H, Im W, Lovell S, Battaile KP, Alontaga AY, Yukl ET, Moënne-Loccoz P, Rivera M. “Structural, NMR Spectroscopic, and Computational Investigation of Hemin Loading in the Hemophore HasAp from Pseudomonas aeruginosa.” J Am Chem Soc. 132: 9857-72.

Kim T, Im W. “Revisiting hydrophobic mismatch with free energy simulation studies of transmembrane hielix tilt and rotation.” Biophys J 99: 175-83

Nayak, Tania, Edgerton-Morgan, Heather, Horio, Tetsuya, Xiong, Yi, De Souza, Colin P., Osmani, Stephen A. and Oakley, Berl R. “γ-Tubulin regulates the anaphase-promoting complex/cyclosome during interphase.” J. Cell Biol. 190, 317-330

Rui H, Im W. “Protegrin-1 orientation and physicochemical properties in membrane bilayers studied by potential of mean force calculations.” J Comput Chem. [Epub ahead of print] 

July 2010 Publications

Rui H, Im W. Protegrin-1 orientation and physicochemical properties in membrane bilayers studied by potential of mean force calculations. J Comput Chem. [Epub ahead of print] 

Jepkorir G, Rodríguez JC, Rui H, Im W, Lovell S, Battaile KP, Alontaga AY, Yukl ET, Moënne-Loccoz P, Rivera M. Structural, NMR Spectroscopic, and Computational Investigation of Hemin Loading in the Hemophore HasAp from Pseudomonas aeruginosa. J Am Chem Soc. [Epub ahead of print]

May 2010 Publications

Ryu H, Al-Ani G, Deckert K, Kirkpatrick D, Gygi SP, Dasso M, Azuma Y.“PIASy mediates SUMO-2/3 conjugation of poly(ADP-ribose) polymerase 1 (PARP1) on mitotic chromosomes.”J. Biol. Chem. 285: 14415-23. 

Zhang L, Nebane NM, Wennerberg K, Li Y, Neubauer V, Hobrath JV, McKellip S, Rasmussen L, Shindo N, Sosa M, Maddry JA, Ananthan S, Piazza GA, White EL, Harsay E. “A High-Throughput Screen for Chemical Inhibitors of Exocytic Transport in Yeast.”

Wang Y, Nordhues BA, Zhong D, De Guzman RN. “NMR characterization of the interaction of the Salmonella type III secretion system protein SipD and bile salts.”Biochemistry 18, 42290

Chiang YM, Oakley BR, Keller NP, Wang CC. Unraveling polyketide synthesis in members of the genus Aspergillus, Appl Microbiol Biotechnol. 2010 May; 86(6)

April 2010 Publications

Chiang, Y. M., Szewczyk, E., Davidson, A. D., Entwistle, R., Keller, N. P., Wang, C. C., and Oakley, B. R. Characterization of the Aspergillus nidulans monodictyphenone gene cluster, Applied and Environmental Microbiology 76, 2067-2074

Kundrotas, P. J., and Vakser, I. A. Accuracy of protein-protein binding sites in high-throughput template-based modeling, PLoS Computational Biology 6, e1000727.

Wang, Y., Coffey, R. J., Osheroff, N., and Neufeld, K. L. Topoisomerase IIalpha binding domains of adenomatous polyposis coli influence cell cycle progression and aneuploidy, PloS one 5, 

March 2010 Publications

Sanchez, J. F., Chiang, Y. M., Szewczyk, E., Davidson, A. D., Ahuja, M., Elizabeth Oakley, C., Woo Bok, J., Keller, N., Oakley, B. R., and Wang, C. C. Molecular genetic analysis of the orsellinic acid/F9775 gene cluster of Aspergillus nidulans, Molecular bioSystems 6, 587-593.

Wang, X., and Ward, R. E. Sec61alpha is required for dorsal closure during Drosophila embryogenesis through its regulation of Dpp signaling, Developmental Dynamics 239, 784-797.
 

February 2010 Publications

Rathinavelan, T., Zhang, L., Picking, W. L., Weis, D. D., De Guzman, R. N., and Im, W. A repulsive electrostatic mechanism for protein export through the type III secretion apparatus, Biophysical Journal 98, 452-461.

Zhao, H., Finch, C. J., Sequeira, R. D., Johnson, B. A., Johnson, J. E., Casjens, S. R., and Tang, L. Crystal structure of the DNA-recognition component of the bacterial virus Sf6 genome-packaging machine, Proceedings of the National Academy of Sciences of the United States of America 107, 

January 2010 Publications

Kundrotas, P. J., Zhu, Z., and Vakser, I. A. GWIDD: Genome-wide protein docking database, Nucleic Acids Research 38, D513-517.

Wickstrum, J. R., Skredenske, J. M., Balasubramaniam, V., Jones, K., and Egan, S. M. The AraC/XylS family activator RhaS negatively autoregulates rhaSR expression by preventing cyclic AMP receptor protein activation, Journal of Bacteriology 192, 225-232.

Zhang, L., Huang, M., and Harsay, E. A chemical genetic screen for modulators of exocytic transport identifies inhibitors of a transport mechanism linked to GTR2 function, Eukaryotic Cell 9, 116-126.