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Recent Publications

2014

    Featuring CMB laboratories and FSU graduate students.


    Aluvila, S., T. Mandal, E. Hustedt, P. Fajer, J.Y. Choe, and K.J. Oh. 2014. Organization of the mitochondrial apoptotic BAK pore: oligomerization of the BAK homodimers. J Biol Chem. 289:2537-2551.

    Bass, H.W., E.E. Wear, T.J. Lee, G.G. Hoffman, H.K. Gumber, G.C. Allen, W.F. Thompson, and L. Hanley-Bowdoin. 2014. A maize root tip system to study DNA replication programmes in somatic and endocycling nuclei during plant development. J Exp Bot. 65:2747-2756.

    Bradshaw, M.D., and B.J. Gaffney. 2014. Fluctuations of an Exposed pi-Helix Involved in Lipoxygenase Substrate Recognition. Biochemistry. 53:5102-5110.

    Brewer, T.E., M. Elizabeth Stroupe, and K.M. Jones. 2014. The genome, proteome and phylogenetic analysis of Sinorhizobium meliloti phage PhiM12, the founder of a new group of T4-superfamily phages. Virology. 450-451:84-97.

    Brunet, N.M., P.B. Chase, G. Mihajlovic, and B. Schoffstall. 2014. Ca(2+)-regulatory function of the inhibitory peptide region of cardiac troponin I is aided by the C-terminus of cardiac troponin T: Effects of familial hypertrophic cardiomyopathy mutations cTnI R145G and cTnT R278C, alone and in combination, on filament sliding. Arch Biochem Biophys. 552-553:11-20.

    Caudle, S.B., C.R. Miller, and D.R. Rokyta. 2014. Environment determines epistatic patterns for a ssDNA virus. Genetics. 196:267-279.

    Cui, H., D. Kong, X. Liu, and Y. Hao. 2014. SCARECROW, SCR-LIKE 23 and SHORT-ROOT control bundle sheath cell fate and function in Arabidopsis thaliana. Plant J. 78:319-327.

    Darrow, E.M., and B.P. Chadwick. 2014. A novel tRNA variable number tandem repeat at human chromosome 1q23.3 is implicated as a boundary element based on conservation of a CTCF motif in mouse. Nucleic Acids Res. 42:6421-6435.

    Darrow, E.M., A.P. Seberg, S. Das, D.M. Figueroa, Z. Sun, S.C. Moseley, and B.P. Chadwick. 2014. A region of euchromatin coincides with an extensive tandem repeat on the mouse (Mus musculus) inactive X chromosome. Chromosome Res. 22:335-350.

    Easton, E.E., E.M. Darrow, T. Spears, and D. Thistle. 2014. The mitochondrial genomes of Amphiascoides atopus and Schizopera knabeni (Harpacticoida: Miraciidae) reveal similarities between the copepod orders Harpacticoida and Poecilostomatoida. Gene. 538:123-137.

    Gao, X., C. Wang, and H. Cui. 2014. Identification of bundle sheath cell fate factors provides new tools for C3-to-C4 engineering. Plant Signal Behav. 9:e29162.

    Jean-Francois, F.L., J. Dai, L. Yu, A. Myrick, E. Rubin, P.G. Fajer, L. Song, H.X. Zhou, and T.A. Cross. 2014. Binding of MgtR, a Salmonella transmembrane regulatory peptide, to MgtC, a Mycobacterium tuberculosis virulence factor: a structural study. J Mol Biol. 426:436-446.

    Li, P., H. Jin, and H.G. Yu. 2014. Condensin suppresses recombination and regulates double-strand break processing at the repetitive rDNA array to ensure proper chromosome segregation during meiosis in budding yeast. Mol Biol Cell.  2014 Aug 7. pii: mbc.E14-05-0957. [Epub ahead of print]

    Lu, J., H. Li, M. Hu, T. Sasaki, A. Baccei, D.M. Gilbert, J.S. Liu, J.J. Collins, and P.H. Lerou. 2014. The distribution of genomic variations in human iPSCs is related to replication-timing reorganization during reprogramming. Cell Rep. 7:70-78.

    Lupinek, C., E. Wollmann, A. Baar, S. Banerjee, H. Breiteneder, B.M. Broecker, M. Bublin, M. Curin, S. Flicker, T. Garmatiuk, H. Hochwallner, I. Mittermann, S. Pahr, Y. Resch, K.H. Roux, B. Srinivasan, S. Stentzel, S. Vrtala, L.N. Willison, M. Wickman, K.C. Lodrup-Carlsen, J.M. Anto, J. Bousquet, C. Bachert, D. Ebner, T. Schlederer, C. Harwanegg, and R. Valenta. 2014. Advances in allergen-microarray technology for diagnosis and monitoring of allergy: the MeDALL allergen-chip. Methods. 66:106-119.

    Madzima, T.F., J. Huang, and K.M. McGinnis. 2014. Chromatin structure and gene expression changes associated with loss of MOP1 activity in Zea mays. Epigenetics. 9.

    Margres, M.J., J.J. McGivern, K.P. Wray, M. Seavy, K. Calvin, and D.R. Rokyta. 2014. Linking the transcriptome and proteome to characterize the venom of the eastern diamondback rattlesnake (Crotalus adamanteus). J Proteomics. 96:145-158.

    Murphy, S.P., H.K. Gumber, Y. Mao, and H.W. Bass. 2014. A dynamic meiotic SUN belt includes the zygotene-stage telomere bouquet and is disrupted in chromosome segregation mutants of maize (Zea mays L.). Front Plant Sci. 5:314.

    Pope, B.D., and D.M. Gilbert. 2014. Genetics: Up and down in Down's syndrome. Nature. 508:323-324.

    Sexton, B.S., D. Avey, B.R. Druliner, J.A. Fincher, D.L. Vera, D.J. Grau, M.L. Borowsky, S. Gupta, S.B. Girimurugan, E. Chicken, J. Zhang, W.S. Noble, F. Zhu, R.E. Kingston, and J.H. Dennis. 2014. The spring-loaded genome: nucleosome redistributions are widespread, transient, and DNA-directed. Genome Res. 24:251-259.

    Sexton, B.S., B.R. Druliner, D. Avey, F. Zhu, and J.H. Dennis. 2014. Changes in nucleosome occupancy occur in a chromosome specific manner. Genomics Data. 16 June 2014, DOI: 10.1016/j.gdata.2014.06.006.

    Sima, J., and D.M. Gilbert. 2014. Complex correlations: replication timing and mutational landscapes during cancer and genome evolution. Curr Opin Genet Dev. 25:93-100.

    Stroupe, M.E., T.E. Brewer, D.R. Sousa, and K.M. Jones. 2014. The structure of Sinorhizobium meliloti phage PhiM12, which has a novel T=19l triangulation number and is the founder of a new group of T4-superfamily phages. Virology. 450-451:205-212.

    Tamori, Y., and W.M. Deng. 2014. Compensatory cellular hypertrophy: the other strategy for tissue homeostasis. Trends Cell Biol. 24:230-237.

    Taylor, K.A., M. Feig, C.L. Brooks, 3rd, P.M. Fagnant, S. Lowey, and K.M. Trybus. 2014. Role of the essential light chain in the activation of smooth muscle myosin by regulatory light chain phosphorylation. J Struct Biol. 185:375-382.

    Thiebaud, N., M.C. Johnson, J.L. Butler, G.A. Bell, K.L. Ferguson, A.R. Fadool, J.C. Fadool, A.M. Gale, D.S. Gale, and D.A. Fadool. 2014. Hyperlipidemic diet causes loss of olfactory sensory neurons, reduces olfactory discrimination, and disrupts odor-reversal learning. J Neurosci. 34:6970-6984.

    van der Linde, K., E. Fumagalli, G. Roman, and L.C. Lyons. 2014. The FlyBar: administering alcohol to flies. J Vis Exp.

    Willison, L.N., S.K. Sathe, and K.H. Roux. 2014. Production and analysis of recombinant tree nut allergens. Methods. 66:34-43.

    Wu, X., E.M. Lee, C. Hammack, J.M. Robotham, M. Basu, J. Lang, M.A. Brinton, and H. Tang. 2014. Cell Death-Inducing DFFA-Like Effector b Is Required for Hepatitis C Virus Entry into Hepatocytes. J Virol. 88:8433-8444.

    Yoshimatsu, T., P.R. Williams, F.D. D'Orazi, S.C. Suzuki, J.M. Fadool, W.T. Allison, P.A. Raymond, and R.O. Wong. 2014. Transmission from the dominant input shapes the stereotypic ratio of photoreceptor inputs onto horizontal cells. Nat Commun. 5:3699.

    Yu, F., Y. Peng, Q. Wang, Y. Shi, L. Si, H. Wang, Y. Zheng, E. Lee, S. Xiao, M. Yu, Y. Li, C. Zhang, H. Tang, C. Wang, L. Zhang, and D. Zhou. 2014. Development of bivalent oleanane-type triterpenes as potent HCV entry inhibitors. Eur J Med Chem. 77:258-268.


2013

    Chadwick, B.P., and K.C. Scott. 2013. Molecular versatility: the many faces and functions of noncoding RNA. Chromosome Res. 21:555-559.

    Chase, P.B., M.P. Szczypinski, and E.P. Soto. 2013. Nuclear tropomyosin and troponin in striated muscle: new roles in a new locale? J Muscle Res Cell Motil. 34:275-284.

    Cordina, N.M., C.K. Liew, D.A. Gell, P.G. Fajer, J.P. Mackay, and L.J. Brown. 2013. Effects of calcium binding and the hypertrophic cardiomyopathy A8V mutation on the dynamic equilibrium between closed and open conformations of the regulatory N-domain of isolated cardiac troponin C. Biochemistry. 52:1950-1962.

    Culver-Cochran, A.E., and B.P. Chadwick. 2013. Loss of WSTF results in spontaneous fluctuations of heterochromatin formation and resolution, combined with substantial changes to gene expression. BMC Genomics. 14:740.

    Darrow, E.M., and B.P. Chadwick. 2013. Boosting transcription by transcription: enhancer-associated transcripts. Chromosome Res. 21:713-724.

    Druliner, B.R., J.A. Fincher, B.S. Sexton, D.L. Vera, M. Roche, S. Lyle, and J.H. Dennis. 2013. Chromatin patterns associated with lung adenocarcinoma progression. Cell Cycle. 12:1536-1543.

    Fincher, J.A., D.L. Vera, D.D. Hughes, K.M. McGinnis, J.H. Dennis, and H.W. Bass. 2013. Genome-wide prediction of nucleosome occupancy in maize reveals plant chromatin structural features at genes and other elements at multiple scales. Plant Physiol. 162:1127-1141.

    Frausto, S.D., E. Lee, and H. Tang. 2013. Cyclophilins as modulators of viral replication. Viruses. 5:1684-1701.

    Garreta, A., S.P. Val-Moraes, Q. Garcia-Fernandez, M. Busquets, C. Juan, A. Oliver, A. Ortiz, B.J. Gaffney, I. Fita, A. Manresa, and X. Carpena. 2013. Structure and interaction with phospholipids of a prokaryotic lipoxygenase from Pseudomonas aeruginosa. FASEB J. 27:4811-4821.

    Graumann, K., H.W. Bass, and G. Parry. 2013. SUNrises on the International Plant Nucleus Consortium: SEB Salzburg 2012. Nucleus. 4:3-7.

    Howe, E.S., S.P. Murphy, and H.W. Bass. 2013. Three-dimensional acrylamide fluorescence in situ hybridization for plant cells. In Plant Meiosis.  Methods and Protocols. Vol. 990. W.P. Pawlowski, M. Grelon, and S.A. Armstrong, editors. Humana Press. 53-66.

    Huang, Y.C., L. Smith, J. Poulton, and W.M. Deng. 2013. The microRNA miR-7 regulates Tramtrack69 in a developmental switch in Drosophila follicle cells. Development. 140:897-905.

    Johnson, M.C., K.C. Biju, J. Hoffman, and D.A. Fadool. 2013. Odor enrichment sculpts the abundance of olfactory bulb mitral cells. Neurosci Lett. 541:173-178.

    Jones, K.M., H.C. Mendis, and C. Queiroux. 2013. Single-plant, sterile microcosms for nodulation and growth of the legume plant Medicago truncatula with the rhizobial symbiont Sinorhizobium meliloti. J Vis Exp., e50916, doi:10.3791/50916.

    Karatzaferi, C., and P.B. Chase. 2013. Muscle fatigue and muscle weakness: what we know and what we wish we did. Front Physiol. 4:125.

    Kirkland, B., Z. Wang, P. Zhang, S. Takebayashi, S. Lenhert, D.M. Gilbert, and J. Guan. 2013. Low-cost fabrication of centimetre-scale periodic arrays of single plasmid DNA molecules. Lab Chip. 13:3367-3372.

    Labonne, J.D., J.E. Dorweiler, and K.M. McGinnis. 2013. Changes in nucleosome position at transcriptional start sites of specific genes in Zea mays mediator of paramutation1 mutants. Epigenetics. 8:398-408.

    Liu, Y., B. Kirkland, J. Shirley, Z. Wang, P. Zhang, J. Stembridge, W. Wong, S. Takebayashi, D.M. Gilbert, S. Lenhert, and J. Guan. 2013. Development of a single-cell array for large-scale DNA fluorescence in situ hybridization. Lab Chip. 13:1316-1324.

    Loong*, C.K., A.K. Takeda*, M.A. Badr, J.S. Rogers, and P.B. Chase. 2013. Slowed Dynamics of Thin Filament Regulatory Units Reduces Ca-Sensitivity of Cardiac Biomechanical Function. Cell Mol Bioeng. 6:183-198.

    Margres, M.J., K. Aronow, J. Loyacano, and D.R. Rokyta. 2013. The venom-gland transcriptome of the eastern coral snake (Micrurus fulvius) reveals high venom complexity in the intragenomic evolution of venoms. BMC Genomics. 14:531.

    Martinez, J.S., A.M. Lehaf, J.B. Schlenoff, and T.C. Keller, 3rd. 2013. Cell durotaxis on polyelectrolyte multilayers with photogenerated gradients of modulus. Biomacromolecules. 14:1311-1320.

    Mendis, H.C., C. Queiroux, T.E. Brewer, O.M. Davis, B.K. Washburn, and K.M. Jones. 2013. The succinoglycan endoglycanase encoded by exoK is required for efficient symbiosis of Sinorhizobium meliloti 1021 with the host plants Medicago truncatula and Medicago sativa (Alfalfa). Mol Plant Microbe Interact. 26:1089-1105.

    Michel, M., J.S. Gardner, C.L. Green, C.L. Organ, and L.C. Lyons. 2013. Protein phosphatase-dependent circadian regulation of intermediate-term associative memory. J Neurosci. 33:4605-4613.

    Pope, B.D., O.M. Aparicio, and D.M. Gilbert. 2013. SnapShot: Replication timing. Cell. 152:1390-1390 e1391.

    Pope, B.D., and D.M. Gilbert. 2013. The replication domain model: regulating replicon firing in the context of large-scale chromosome architecture. J Mol Biol. 425:4690-4695.

    Rokyta, D.R., K.P. Wray, and M.J. Margres. 2013. The genesis of an exceptionally lethal venom in the timber rattlesnake (Crotalus horridus) revealed through comparative venom-gland transcriptomics. BMC Genomics. 14:394.

    Saade, C.J., K. Alvarez-Delfin, and J.M. Fadool. 2013. Rod photoreceptors protect from cone degeneration-induced retinal remodeling and restore visual responses in zebrafish. J Neurosci. 33:1804-1814.

    Sackman, A.M., and D.R. Rokyta. 2013. The adaptive potential of hybridization demonstrated with bacteriophages. J Mol Evol. 77:221-230.

    Sousa, D.R., S.M. Stagg, and M.E. Stroupe. 2013. Cryo-EM structures of the actin:tropomyosin filament reveal the mechanism for the transition from C- to M-state. J Mol Biol. 425:4544-4555.

    Takebayashi, S., I. Lei, T. Ryba, T. Sasaki, V. Dileep, D. Battaglia, X. Gao, P. Fang, Y. Fan, M.A. Esteban, J. Tang, G.R. Crabtree, Z. Wang, and D.M. Gilbert. 2013. Murine esBAF chromatin remodeling complex subunits BAF250a and Brg1 are necessary to maintain and reprogram pluripotency-specific replication timing of select replication domains. Epigenetics Chromatin. 6:42.

    Tamori, Y., and W.M. Deng. 2013. Tissue repair through cell competition and compensatory cellular hypertrophy in postmitotic epithelia. Dev Cell. 25:350-363.

    Tian, A.G., Y. Tamori, Y.C. Huang, N.T. Melendez, and W.M. Deng. 2013. Efficient EGFR signaling and dorsal-ventral axis patterning requires syntaxin dependent Gurken trafficking. Dev Biol. 373:349-358.

    Tucker, K., S. Cho, N. Thiebaud, M.X. Henderson, and D.A. Fadool. 2013. Glucose sensitivity of mouse olfactory bulb neurons is conveyed by a voltage-gated potassium channel. J Physiol. 591:2541-2561.

    Willison, L.N., Q. Zhang, M. Su, S.S. Teuber, S.K. Sathe, and K.H. Roux. 2013. Conformational epitope mapping of Pru du 6, a major allergen from almond nut. Mol Immunol. 55:253-263.

    Winkler, H., and K.A. Taylor. 2013. Marker-free dual-axis tilt series alignment. J Struct Biol. 182:117-124.

    Winkler, H., S. Wu, and K.A. Taylor. 2013. Electron tomography of paracrystalline 2D arrays. Methods Mol Biol. 955:427-460.

    Zhan, N., G. Palui, H. Grise, H. Tang, I. Alabugin, and H. Mattoussi. 2013. Combining ligand design with photoligation to provide compact, colloidally stable, and easy to conjugate quantum dots. ACS Appl Mater Interfaces. 5:2861-2869.

2012

    Asumda, F.Z., and P.B. Chase. 2012. Nuclear cardiac troponin and tropomyosin are expressed early in cardiac differentiation of rat mesenchymal stem cells. Differentiation. 83:106-115.

    Baumann, B.A., D.W. Taylor, Z. Huang, F. Tama, P.M. Fagnant, K.M. Trybus, and K.A. Taylor. 2012. Phosphorylated smooth muscle heavy meromyosin shows an open conformation linked to activation. Journal of molecular biology. 415:274-287.

    Boerner, S., and K.M. McGinnis. 2012. Computational identification and functional predictions of long noncoding RNA in Zea mays. PLoS One. 7:e43047.

    Brunet, N.M., G. Mihajlovic, K. Aledealat, F. Wang, P. Xiong, S. von Molnar, and P.B. Chase. 2012. Micromechanical thermal assays of Ca2+-regulated thin-filament function and modulation by hypertrophic cardiomyopathy mutants of human cardiac troponin. J Biomed Biotechnol. 2012:657523.

    Castoe, T.A., E.L. Braun, A.M. Bronikowski, C.L. Cox, A.R. Rabosky, A.P. Jason de Koning, J. Dobry, M.K. Fujita, M.W. Giorgianni, A. Hargreaves, C.V. Henkel, S.P. Mackessy, D. O'Meally, D.R. Rokyta, S.M. Secor, J.W. Streicher, K.P. Wray, K.D. Yokoyama, and D.D. Pollock. 2012. Report from the first snake genomics and integrative biology meeting. Stand Genomic Sci. 7:150-152.

    Chandra, T., K. Kirschner, J.Y. Thuret, B.D. Pope, T. Ryba, S. Newman, K. Ahmed, S.A. Samarajiwa, R. Salama, T. Carroll, R. Stark, R. Janky, M. Narita, L. Xue, A. Chicas, S. Nunez, R. Janknecht, Y. Hayashi-Takanaka, M.D. Wilson, A. Marshall, D.T. Odom, M.M. Babu, D.P. Bazett-Jones, S. Tavare, P.A. Edwards, S.W. Lowe, H. Kimura, and D.M. Gilbert. 2012. Independence of repressive histone marks and chromatin compaction during senescent heterochromatic layer formation. Mol Cell. 47:203-214.

    Cordina, N.M., C.K. Liew, D.A. Gell, P.G. Fajer, J.P. Mackay, and L.J. Brown. 2012. Interdomain orientation of cardiac troponin C characterized by paramagnetic relaxation enhancement NMR reveals a compact state. Protein Sci. 21:1376-1387.

    Cornacchia, D., V. Dileep, J.P. Quivy, R. Foti, F. Tili, R. Santarella-Mellwig, C. Antony, G. Almouzni, D.M. Gilbert, and S.B. Buonomo. 2012. Mouse Rif1 is a key regulator of the replication-timing programme in mammalian cells. EMBO J. 31:3678-3690.

    Corthell, J.T., D.A. Fadool, and P.Q. Trombley. 2012. Connexin and AMPA receptor expression changes over time in the rat olfactory bulb. Neuroscience. 222C:38-48.

    Cui, H. 2012. Killing two birds with one stone: transcriptional regulators coordinate development and stress responses in plants. Plant Signal Behav. 7:701-703.

    Cui, H., Y. Hao, and D. Kong. 2012. SCARECROW has a SHORT-ROOT-independent role in modulating the sugar response. Plant physiology. 158:1769-1778.

    Culver-Cochran, A.E., and B.P. Chadwick. 2012. The WSTF-ISWI chromatin remodeling complex transiently associates with the human inactive X chromosome during late S-phase prior to BRCA1 and gamma-H2AX. PLoS One. 7(e50023):1-15.

    Dileep, V., R. Didier, and D.M. Gilbert. 2012. Genome-wide analysis of replication timing in mammalian cells: troubleshooting problems encountered when comparing different cell types. Methods in enzymology. 57:165-169.

    Eichten, S.R., N.A. Ellis, I. Makarevitch, C.T. Yeh, J.I. Gent, L. Guo, K.M. McGinnis, X. Zhang, P.S. Schnable, M.W. Vaughn, R.K. Dawe, and N.M. Springer. 2012. Spreading of heterochromatin is limited to specific families of maize retrotransposons. PLoS Genet. 8:e1003127.

    Fajer, P.G., G.M. Bou-Assaf, and A.G. Marshall. 2012. Improved sequence resolution by global analysis of overlapped peptides in hydrogen/deuterium exchange mass spectrometry. J Am Soc Mass Spectrom. 23:1202-1208.

    Figueroa, D.M., and H.W. Bass. 2012. Development of pachytene FISH maps for six maize chromosomes and their integration with other maize maps for insights into genome structure variation. Chromosome Res. 20:363-380.

    Figueroa, D.M., F.I. Amarillo, and H.W. Bass. 2012. Cytogenetic mapping in plants. In Plant Genetics and Genomics: Crops and Models. Vol. 4. H.W. Bass and J.A. Birchler, editors. Springer New York. 79–119.

    Gaffney, B.J., M.D. Bradshaw, S.D. Frausto, F. Wu, J.H. Freed, and P. Borbat. 2012. Locating a lipid at the portal to the lipoxygenase active site. Biophys J. 103:2134-2144.

    Grise, H., S. Frausto, T. Logan, and H. Tang. 2012. A conserved tandem cyclophilin-binding site in hepatitis C virus nonstructural protein 5A regulates Alisporivir susceptibility. J Virol. 86:4811-4822.

    Hao, Y., and H. Cui. 2012. SHORT-ROOT regulates vascular patterning, but not apical meristematic activity in the Arabidopsis root through cytokinin homeostasis. Plant Signal Behav. 7:314-317.

    Hira, S.M., K. Aledealat, K.S. Chen, M. Field, G.J. Sullivan, P.B. Chase, P. Xiong, S. von Molnar, and G.F. Strouse. 2012. Detection of target ssDNA using a microfabricated Hall magnetometer with correlated optical readout. J Biomed Biotechnol. 2012:492730.

    Horakova, A.H., J.M. Calabrese, C.R. McLaughlin, D.C. Tremblay, T. Magnuson, and B.P. Chadwick. 2012. The mouse DXZ4 homolog retains Ctcf binding and proximity to Pls3 despite substantial organizational differences compared to the primate macrosatellite. Genome Biol. 13:R70.

    Horakova, A.H., S.C. Moseley, C.R. McLaughlin, D.C. Tremblay, and B.P. Chadwick. 2012. The macrosatellite DXZ4 mediates CTCF-dependent long-range intrachromosomal interactions on the human inactive X chromosome. Hum Mol Genet. 21:4367-4377.

    Howe, E.S., T.E. Clemente, and H.W. Bass. 2012. Maize histone H2B-mCherry: a new fluorescent chromatin marker for somatic and meiotic chromosome research. DNA Cell Biol. 31:925-938.

    Ippoliti, P.J., N.A. Delateur, K.M. Jones, and P.J. Beuning. 2012. Multiple strategies for translesion synthesis in bacteria. Cells. 1:799-831.

    Jin, F., H. Liu, P. Li, H.G. Yu, and Y. Wang. 2012. Loss of function of the Cik1/Kar3 motor complex results in chromosomes with syntelic attachment that are sensed by the tension checkpoint. PLoS Genet. 8:e1002492.

    Jin, H., M. Avey, and H.G. Yu. 2012. Is cohesin required for spindle-pole-body/centrosome cohesion? Commun Integr Biol. 5:26-29.

    Jones, K.M. 2012. Increased production of the exopolysaccharide succinoglycan enhances Sinorhizobium meliloti 1021 symbiosis with the host plant Medicago truncatula. J Bacteriol. 194:4322-4331.

    Kusi-Appiah, A.E., N. Vafai, P.J. Cranfill, M.W. Davidson, and S. Lenhert. 2012. Lipid multilayer microarrays for in vitro liposomal drug delivery and screening. Biomaterials. 33:4187-4194.

    Lenhert, S., and F.G. Vellanti. 2012. Drug discovery: a view through the looking glass. Future Med Chem. 4:2011-2013.

    Lerch, T.F., J.K. O'Donnell, N.L. Meyer, Q. Xie, K.A. Taylor, S.M. Stagg, and M.S. Chapman. 2012. Structure of AAV-DJ, a retargeted gene therapy vector: cryo-electron microscopy at 4.5 A resolution. Structure. 20:1310-1320.

    Liang, Q., B. Fu, F. Wu, X. Li, Y. Yuan, and F. Zhu. 2012. ORF45 of Kaposi's sarcoma-associated herpesvirus inhibits phosphorylation of interferon regulatory factor 7 by IKKepsilon and TBK1 as an alternative substrate. J Virol. 86:10162-10172.

    Loong, C.K., M.A. Badr, and P.B. Chase. 2012. Tropomyosin flexural rigidity and single ca(2+) regulatory unit dynamics: implications for cooperative regulation of cardiac muscle contraction and cardiomyocyte hypertrophy. Front Physiol. 3:80.

    Loong, C.K., H.X. Zhou, and P.B. Chase. 2012. Familial hypertrophic cardiomyopathy related E180G mutation increases flexibility of human cardiac alpha-tropomyosin. FEBS Lett. 586:3503-3507.

    Loong, C.K., H.X. Zhou, and P.B. Chase. 2012. Persistence length of human cardiac alpha-tropomyosin measured by single molecule direct probe microscopy. PLoS One. 7:e39676.

    Mast, T.G., and D.A. Fadool. 2012. Mature and precursor brain-derived neurotrophic factor have individual roles in the mouse olfactory bulb. PLoS One. 7:e31978.

    McCraw, D.M., J.K. O'Donnell, K.A. Taylor, S.M. Stagg, and M.S. Chapman. 2012. Structure of adeno-associated virus-2 in complex with neutralizing monoclonal antibody A20. Virology. 431:40-49.

    Michel, M., C.L. Green, J.S. Gardner, C.L. Organ, and L.C. Lyons. 2012. Massed training-induced intermediate-term operant memory in aplysia requires protein synthesis and multiple persistent kinase cascades. J Neurosci. 32:4581-4591.

    Mitsakakis, K., S. Sekula-Neuner, S. Lenhert, H. Fuchs, and E. Gizeli. 2012. Convergence of dip-pen nanolithography and acoustic biosensors towards a rapid-analysis multi-sample microsystem. Analyst. 137:3076-3082.

    Moseley, S.C., R. Rizkallah, D.C. Tremblay, B.R. Anderson, M.M. Hurt, and B.P. Chadwick. 2012. YY1 associates with the macrosatellite DXZ4 on the inactive X chromosome and binds with CTCF to a hypomethylated form in some male carcinomas. Nucleic Acids Res. 40:1596-1608.

    Murphy, S.P., and H.W. Bass. 2012. The maize (Zea mays) desynaptic (dy) mutation defines a pathway for meiotic chromosome segregation, linking nuclear morphology, telomere distribution and synapsis. J Cell Sci. 125:3681-3690.

    Murphy, S.P., and H.W. Bass. 2012. Genetics and cytology of meiotic chromosome behavior in plants. . In Plant Genetics and Genomics: Crops and Models. Vol. 4. H.W. Bass and J.A. Birchler, editors. Springer New York. 193–229.

    Nafday, O.A., T.W. Lowry, and S. Lenhert. 2012. Multifunctional lipid multilayer stamping. Small. 8:1021-1028.

    Nag, A., J.M. Robotham, and H. Tang. 2012. Suppression of viral RNA binding and the assembly of infectious hepatitis C virus particles in vitro by cyclophilin inhibitors. J Virol. 86:12616-12624.

    Palouzier-Paulignan, B., M.C. Lacroix, P. Aime, C. Baly, M. Caillol, P. Congar, A.K. Julliard, K. Tucker, and D.A. Fadool. 2012. Olfaction under metabolic influences. Chem Senses. 37:769-797.

    Pearson, V.M., C.R. Miller, and D.R. Rokyta. 2012. The consistency of beneficial fitness effects of mutations across diverse genetic backgrounds. PLoS One. 7:e43864.

    Pope, B.D., T. Chandra, Q. Buckley, M. Hoare, T. Ryba, F.K. Wiseman, A. Kuta, M.D. Wilson, D.T. Odom, and D.M. Gilbert. 2012. Replication-timing boundaries facilitate cell-type and species-specific regulation of a rearranged human chromosome in mouse. Hum Mol Genet. 21:4162-4170.

    Queiroux, C., B.K. Washburn, O.M. Davis, J. Stewart, T.E. Brewer, M.R. Lyons, and K.M. Jones. 2012. A comparative genomics screen identifies a Sinorhizobium meliloti 1021 sodM-like gene strongly expressed within host plant nodules. BMC Microbiol. 12:74.

    Rokyta, D.R., A.R. Lemmon, M.J. Margres, and K. Aronow. 2012. The venom-gland transcriptome of the eastern diamondback rattlesnake (Crotalus adamanteus). BMC Genomics. 13:312.

    Ryba, T., D. Battaglia, B.H. Chang, J.W. Shirley, Q. Buckley, B.D. Pope, M. Devidas, B.J. Druker, and D.M. Gilbert. 2012. Abnormal developmental control of replication-timing domains in pediatric acute lymphoblastic leukemia. Genome Res. 22:1833-1844.

    Smith, K.W., and M.E. Stroupe. 2012. Mutational analysis of sulfite reductase hemoprotein reveals the mechanism for coordinated electron and proton transfer. Biochemistry. 51:9857-9868.

    Stamatoyannopoulos, J.A., M. Snyder, R. Hardison, B. Ren, T. Gingeras, D.M. Gilbert, M. Groudine, M. Bender, R. Kaul, T. Canfield, E. Giste, A. Johnson, M. Zhang, G. Balasundaram, R. Byron, V. Roach, P.J. Sabo, R. Sandstrom, A.S. Stehling, R.E. Thurman, S.M. Weissman, P. Cayting, M. Hariharan, J. Lian, Y. Cheng, S.G. Landt, Z. Ma, B.J. Wold, J. Dekker, G.E. Crawford, C.A. Keller, W. Wu, C. Morrissey, S.A. Kumar, T. Mishra, D. Jain, M. Byrska-Bishop, D. Blankenberg, B.R. Lajoie, G. Jain, A. Sanyal, K.B. Chen, O. Denas, J. Taylor, G.A. Blobel, M.J. Weiss, M. Pimkin, W. Deng, G.K. Marinov, B.A. Williams, K.I. Fisher-Aylor, G. Desalvo, A. Kiralusha, D. Trout, H. Amrhein, A. Mortazavi, L. Edsall, D. McCleary, S. Kuan, Y. Shen, F. Yue, Z. Ye, C.A. Davis, C. Zaleski, S. Jha, C. Xue, A. Dobin, W. Lin, M. Fastuca, H. Wang, R. Guigo, S. Djebali, J. Lagarde, T. Ryba, T. Sasaki, V.S. Malladi, M.S. Cline, V.M. Kirkup, K. Learned, K.R. Rosenbloom, W.J. Kent, E.A. Feingold, P.J. Good, M. Pazin, R.F. Lowdon, and L.B. Adams. 2012. An encyclopedia of mouse DNA elements (Mouse ENCODE). Genome Biol. 13:418.

    Takebayashi, S., V. Dileep, T. Ryba, J.H. Dennis, and D.M. Gilbert. 2012. Chromatin-interaction compartment switch at developmentally regulated chromosomal domains reveals an unusual principle of chromatin folding. Proc Natl Acad Sci USA. 109:12574-12579.

    Talbert, P.B., K. Ahmad, G. Almouzni, J. Ausio, F. Berger, P.L. Bhalla, W.M. Bonner, W.Z. Cande, B.P. Chadwick, S.W. Chan, G.A. Cross, L. Cui, S.I. Dimitrov, D. Doenecke, J.M. Eirin-Lopez, M.A. Gorovsky, S.B. Hake, B.A. Hamkalo, S. Holec, S.E. Jacobsen, K. Kamieniarz, S. Khochbin, A.G. Ladurner, D. Landsman, J.A. Latham, B. Loppin, H.S. Malik, W.F. Marzluff, J.R. Pehrson, J. Postberg, R. Schneider, M.B. Singh, M.M. Smith, E. Thompson, M.E. Torres-Padilla, D.J. Tremethick, B.M. Turner, J.H. Waterborg, H. Wollmann, R. Yelagandula, B. Zhu, and S. Henikoff. 2012. A unified phylogeny-based nomenclature for histone variants. Epigenetics Chromatin. 5:7.

    Tucker, K.R., S.J. Godbey, N. Thiebaud, and D.A. Fadool. 2012. Olfactory ability and object memory in three mouse models of varying body weight, metabolic hormones, and adiposity. Physiol Behav. 107:424-432.

    Winbush, A., D. Reed, P.L. Chang, S.V. Nuzhdin, L.C. Lyons, and M.N. Arbeitman. 2012. Identification of gene expression changes associated with long-term memory of courtship rejection in Drosophila males. G3. 2:1437-1445.

    Wu, S., J. Liu, M.C. Reedy, R.J. Perz-Edwards, R.T. Tregear, H. Winkler, C. Franzini-Armstrong, H. Sasaki, C. Lucaveche, Y.E. Goldman, M.K. Reedy, and K.A. Taylor. 2012. Structural changes in isometrically contracting insect flight muscle trapped following a mechanical perturbation. PLoS One. 7:e39422.

    Wu, X., J.M. Robotham, E. Lee, S. Dalton, N.M. Kneteman, D.M. Gilbert, and H. Tang. 2012. Productive hepatitis C virus infection of stem cell-derived hepatocytes reveals a critical transition to viral permissiveness during differentiation. PLoS Pathog. 8:e1002617.

2011

    Asumda, F.Z., and P.B. Chase. 2011. Age-related changes in rat bone-marrow mesenchymal stem cell plasticity. BMC Cell Biol. 12:44.

    Bai, F., A. Weis, A.K. Takeda, P.B. Chase, and M. Kawai. 2011. Enhanced active cross-bridges during diastole: molecular pathogenesis of tropomyosin's HCM mutations. Biophys J. 100:1014-1023.

    Bou-Assaf, G.M., J.E. Chamoun, M.R. Emmett, P.G. Fajer, and A.G. Marshall. 2011. Complexation and Calcium-Induced Conformational Changes in the Cardiac Troponin Complex Monitored by Hydrogen/Deuterium Exchange and FT-ICR Mass Spectrometry. Int J Mass Spectrom. 302:116-124.

    Brockerhoff, S.E., and J.M. Fadool. 2011. Genetics of photoreceptor degeneration and regeneration in zebrafish. Cell Mol Life Sci. 68:651-659.

    Brown, A.N., N. Lauter, D.L. Vera, K.A. McLaughlin-Large, T.M. Steele, N.C. Fredette, and H.W. Bass. 2011. QTL Mapping and Candidate Gene Analysis of Telomere Length Control Factors in Maize (Zea mays L.). G3. 1:437-450.

    Bush, D.J., O. Kirillova, S.A. Clark, O. Davulcu, F. Fabiola, Q. Xie, T. Somasundaram, W.R. Ellington, and M.S. Chapman. 2011. The structure of lombricine kinase: implications for phosphagen kinase conformational changes. The Journal of biological chemistry. 286:9338-9350.

    Cheng, Y., K.S. Chen, N.L. Meyer, J. Yuan, L.S. Hirst, P.B. Chase, and P. Xiong. 2011. Functionalized SnO(2) nanobelt field-effect transistor sensors for label-free detection of cardiac troponin. Biosensors & bioelectronics. 26:4538-4544.

    Collins, A., A. Warrington, K.A. Taylor, and T. Svitkina. 2011. Structural organization of the actin cytoskeleton at sites of clathrin-mediated endocytosis. Curr Biol. 21:1167-1175.

    Cui, H., Y. Hao, M. Kovtun, V. Stolc, X.W. Deng, H. Sakakibara, and M. Kojima. 2011. Genome-wide direct target analysis reveals a role for SHORT-ROOT in root vascular patterning through cytokinin homeostasis. Plant physiology. 157:1221-1231.

    Fadool, D.A., K. Tucker, and P. Pedarzani. 2011. Mitral cells of the olfactory bulb perform metabolic sensing and are disrupted by obesity at the level of the Kv1.3 ion channel. PLoS One. 6:e24921.

    Figueroa, D.M., J.D. Davis, C. Strobel, M.S. Conejo, K.D. Beckham, B.C. Ring, and H.W. Bass. 2011. The selection and use of sorghum (Sorghum propinquum) bacterial artificial chromosomes as cytogenetic FISH probes for maize (Zea mays L.). J Biomed Biotechnol. 2011:386862.

    Gilbert, D.M., and L.L. Wallrath. 2011. Chromatin and chromosomes. Mol Biol Cell. 22:717.

    Hoffman, G.G., and W.R. Ellington. 2011. Arginine kinase isoforms in the closest protozoan relative of metazoans. Comparative biochemistry and physiology. Part D, Genomics & proteomics. 6:171-177.

    Hu, G., J. Liu, K.A. Taylor, and K.H. Roux. 2011. Structural comparison of HIV-1 envelope spikes with and without the V1/V2 loop. J Virol. 85:2741-2750.

    Kshirsagar, H.H., P. Fajer, G.M. Sharma, K.H. Roux, and S.K. Sathe. 2011. Biochemical and spectroscopic characterization of almond and cashew nut seed 11S legumins, amandin and anacardein. J Agric Food Chem. 59:386-393.

    Kuang, E., B. Fu, Q. Liang, J. Myoung, and F. Zhu. 2011. Phosphorylation of eukaryotic translation initiation factor 4B (EIF4B) by open reading frame 45/p90 ribosomal S6 kinase (ORF45/RSK) signaling axis facilitates protein translation during Kaposi sarcoma-associated herpesvirus (KSHV) lytic replication. J Biol Chem. 286:41171-41182.

    Kuipers, M.A., T.J. Stasevich, T. Sasaki, K.A. Wilson, K.L. Hazelwood, J.G. McNally, M.W. Davidson, and D.M. Gilbert. 2011. Highly stable loading of Mcm proteins onto chromatin in living cells requires replication to unload. The Journal of cell biology. 192:29-41.

    Li, P., H. Jin, M.L. Hoang, and H.G. Yu. 2011. Tracking chromosome dynamics in live yeast cells: coordinated movement of rDNA homologs and anaphase disassembly of the nucleolus during meiosis. Chromosome Res. 19:1013-1026.

    Liang, Q., H. Deng, C.W. Sun, T.M. Townes, and F. Zhu. 2011. Negative regulation of IRF7 activation by activating transcription factor 4 suggests a cross-regulation between the IFN responses and the cellular integrated stress responses. Journal of Immunology. 186:1001-1010.

    Liang, Q., H. Deng, X. Li, X. Wu, Q. Tang, T.H. Chang, H. Peng, F.J. Rauscher, 3rd, K. Ozato, and F. Zhu. 2011. Tripartite motif-containing protein 28 is a small ubiquitin-related modifier E3 ligase and negative regulator of IFN regulatory factor 7. Journal of Immunology. 187:4754-4763.

    Lin, W., H. Jin, X. Liu, K. Hampton, and H.G. Yu. 2011. Scc2 regulates gene expression by recruiting cohesin to the chromosome as a transcriptional activator during yeast meiosis. Mol Biol Cell. 22:1985-1996.

    Lin, W., M. Wang, H. Jin, and H.G. Yu. 2011. Cohesin plays a dual role in gene regulation and sister-chromatid cohesion during meiosis in Saccharomyces cerevisiae. Genetics. 187:1041-1051.

    Lubelsky, Y., T. Sasaki, M.A. Kuipers, I. Lucas, M.M. Le Beau, S. Carignon, M. Debatisse, J.A. Prinz, J.H. Dennis, and D.M. Gilbert. 2011. Pre-replication complex proteins assemble at regions of low nucleosome occupancy within the Chinese hamster dihydrofolate reductase initiation zone. Nucleic acids research. 39:3141-3155.

    Lyons, L.C. 2011. Critical role of the circadian clock in memory formation: lessons from Aplysia. Front Mol Neurosci. 4:52.

    Madzima, T.F., E.S. Mills, J.M. Gardiner, and K.M. McGinnis. 2011. Identification of epigenetic regulators of a transcriptionally silenced transgene in maize. G3. 1:75-83.

    Martinez, J.S., T.C. Keller, 3rd, and J.B. Schlenoff. 2011. Cytotoxicity of free versus multilayered polyelectrolytes. Biomacromolecules. 12:4063-4070.

    Mathur, M.C., P.B. Chase, and J.M. Chalovich. 2011. Several cardiomyopathy causing mutations on tropomyosin either destabilize the active state of actomyosin or alter the binding properties of tropomyosin. Biochem Biophys Res Commun. 406:74-78.

    McLaughlin, C.R., and B.P. Chadwick. 2011. Characterization of DXZ4 conservation in primates implies important functional roles for CTCF binding, array expression and tandem repeat organization on the X chromosome. Genome Biol. 12:R37.

    Michel, M., C.L. Green, A. Eskin, and L.C. Lyons. 2011. PKG-mediated MAPK signaling is necessary for long-term operant memory in Aplysia. Learn Mem. 18:108-117.

    Michel, M., C.L. Green, and L.C. Lyons. 2011. PKA and PKC are required for long-term but not short-term in vivo operant memory in Aplysia. Learn Mem. 18:19-23.

    Morris, A.C., M.A. Forbes-Osborne, L.S. Pillai, and J.M. Fadool. 2011. Microarray analysis of XOPS-mCFP zebrafish retina identifies genes associated with rod photoreceptor degeneration and regeneration. Invest Ophthalmol Vis Sci. 52:2255-2266.

    Nafday, O.A., and S. Lenhert. 2011. High-throughput optical quality control of lipid multilayers fabricated by dip-pen nanolithography. Nanotechnology. 22:225301.

    Newcomer, R.G., M.D. Moussallem, T.C. Keller, J.B. Schlenoff, and Q.X. Sang. 2011. Human coronary artery smooth muscle cell responses to bioactive polyelectrolyte multilayer interfaces. Biotechnology research international. 2011:854068.

    Pope, B.D., K. Tsumagari, D. Battaglia, T. Ryba, I. Hiratani, M. Ehrlich, and D.M. Gilbert. 2011. DNA replication timing is maintained genome-wide in primary human myoblasts independent of D4Z4 contraction in FSH muscular dystrophy. PLoS One. 6:e27413.

    Poulton, J.S., Y.C. Huang, L. Smith, J. Sun, N. Leake, J. Schleede, L.M. Stevens, and W.M. Deng. 2011. The microRNA pathway regulates the temporal pattern of Notch signaling in Drosophila follicle cells. Development. 138:1737-1745.

    Rayes, R.F., T. Kalai, K. Hideg, M.A. Geeves, and P.G. Fajer. 2011. Dynamics of tropomyosin in muscle fibers as monitored by saturation transfer EPR of bi-functional probe. PLoS One. 6:e21277.

    Rokyta, D.R., P. Joyce, S.B. Caudle, C. Miller, C.J. Beisel, and H.A. Wichman. 2011. Epistasis between beneficial mutations and the phenotype-to-fitness Map for a ssDNA virus. PLoS Genet. 7:e1002075.

    Rokyta, D.R., K.P. Wray, A.R. Lemmon, E.M. Lemmon, and S.B. Caudle. 2011. A high-throughput venom-gland transcriptome for the Eastern Diamondback Rattlesnake (Crotalus adamanteus) and evidence for pervasive positive selection across toxin classes. Toxicon. 57:657-671.

    Ryba, T., Battaglia, D., Pope, B.D., Hiratani, I. and Gilbert, D.M. (2011) Genome-Scale Analysis of Replication Timing: from Bench to Bioinformatics. Nature protocols 6:870-895

    Ryba, T., I. Hiratani, T. Sasaki, D. Battaglia, M. Kulik, J. Zhang, S. Dalton, and D. M. Gilbert. (2011) Replication Timing: A Fingerprint for Cell Identity and Pluripotency. PLoS COMPUTATIONAL BIOL 7:e1002225

    Schoffstall, B., V.A. LaBarbera, N.M. Brunet, B.J. Gavino, L. Herring, S. Heshmati, B.H. Kraft, V. Inchausti, N.L. Meyer, D. Moonoo, A.K. Takeda, and P.B. Chase. 2011. Interaction between troponin and myosin enhances contractile activity of myosin in cardiac muscle. DNA Cell Biol. 30:653-659.

    Sharma, G.M., A. Irsigler, P. Dhanarajan, R. Ayuso, L. Bardina, H.A. Sampson, K.H. Roux, and S.K. Sathe. 2011. Cloning and characterization of an 11S legumin, Car i 4, a major allergen in pecan. Journal of agricultural and food chemistry. 59:9542-9552.

    Shimabukuro, K., N. Noda, M. Stewart, and T.M. Roberts. 2011. Reconstitution of amoeboid motility in vitro identifies a motor-independent mechanism for cell body retraction. Current biology : CB. 21:1727-1731.

    Shirk, K., H. Jin, T.H. Giddings, Jr., M. Winey, and H.G. Yu. 2011. The Aurora kinase Ipl1 is necessary for spindle pole body cohesion during budding yeast meiosis. Journal of cell science. 124:2891-2896.

    Shirley, J.W., S. Ty, S. Takebayashi, X. Liu, and D.M. Gilbert. 2011. FISH Finder: a high-throughput tool for analyzing FISH images. Bioinformatics. 27:933-938.

    Tremblay, D.C., S. Moseley, and B.P. Chadwick. 2011. Variation in array size, monomer composition and expression of the macrosatellite DXZ4. PLoS One. 6:e18969.

    van der Linde, K., and L.C. Lyons. 2011. Circadian modulation of acute alcohol sensitivity Circadian modulation of acute alcohol sensitivity but not acute tolerance in Drosophila. Chronobiol Int. 28:397-406.

    Vileno, B., J. Chamoun, H. Liang, P. Brewer, B.D. Haldeman, K.C. Facemyer, B. Salzameda, L. Song, H.C. Li, C.R. Cremo, and P.G. Fajer. 2011. Broad disorder and the allosteric mechanism of myosin II regulation by phosphorylation. Proc Natl Acad Sci U S A. 108:8218-8223.

    Wang, F., N.M. Brunet, J.R. Grubich, E.A. Bienkiewicz, T.M. Asbury, L.A. Compton, G. Mihajlovic, V.F. Miller, and P.B. Chase. 2011. Facilitated cross-bridge interactions with thin filaments by familial hypertrophic cardiomyopathy mutations in alpha-tropomyosin. Journal of biomedicine & biotechnology. 2011:435271.

    Willison, L.N., P. Tripathi, G. Sharma, S.S. Teuber, S.K. Sathe, and K.H. Roux. 2011. Cloning, expression and patient IgE reactivity of recombinant Pru du 6, an 11S globulin from almond. International archives of allergy and immunology. 156:267-281.

    Zhang, Q., L.N. Willison, P. Tripathi, S.K. Sathe, K.H. Roux, M.R. Emmett, G.T. Blakney, H.M. Zhang, and A.G. Marshall. 2011. Epitope mapping of a 95 kDa antigen in complex with antibody by solution-phase amide backbone hydrogen/deuterium exchange monitored by Fourier transform ion cyclotron resonance mass spectrometry. Analytical chemistry. 83:7129-7136.

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