Genomes and Genes
Experts and Doctors on biological models in Princeton, Florida, United States
Locale: Princeton, Florida, United States
Topic: biological models
- Okada K, Comaniciu D, Krishnan A. Robust anisotropic Gaussian fitting for volumetric characterization of pulmonary nodules in multislice CT. IEEE Trans Med Imaging. 2005;24:409-23 pubmed..This system processes each 33-voxel volume-of-interest by an average of 2 s with a 2.4-GHz Intel CPU. Our solution is generic and can be applied for the analysis of blob-like structures in various other applications. ..
- Nadell C, Xavier J, Foster K. The sociobiology of biofilms. FEMS Microbiol Rev. 2009;33:206-24 pubmed publisher..Biofilms will typically result from a balance between competition and cooperation, and we argue that understanding this balance is central to building a complete and predictive model of biofilm formation. ..
- Goodrich J, Clouse K, Schupbach T. Hrb27C, Sqd and Otu cooperatively regulate gurken RNA localization and mediate nurse cell chromosome dispersion in Drosophila oogenesis. Development. 2004;131:1949-58 pubmed..All three mutants share another phenotype, persistent polytene nurse cell chromosomes. Our analyses support dual cooperative roles for Sqd, Hrb27C and Otu during Drosophila oogenesis. ..
- Ruiz N. Bioinformatics identification of MurJ (MviN) as the peptidoglycan lipid II flippase in Escherichia coli. Proc Natl Acad Sci U S A. 2008;105:15553-7 pubmed publisher..Because of its essential nature, MurJ could serve as a target in the continuing search for antimicrobial compounds. ..
- Boer V, Crutchfield C, Bradley P, Botstein D, Rabinowitz J. Growth-limiting intracellular metabolites in yeast growing under diverse nutrient limitations. Mol Biol Cell. 2010;21:198-211 pubmed publisher..The complete data can be accessed at the interactive website http://growthrate.princeton.edu/metabolome. ..
- Bartumeus F, Giuggioli L, Louzao M, Bretagnolle V, Oro D, Levin S. Fishery discards impact on seabird movement patterns at regional scales. Curr Biol. 2010;20:215-22 pubmed publisher..Our results demonstrate human involvement on landscape-level behavioral ecology and provide a new ecosystemic approach in the study of fishery-seabird interactions. ..
- Riley T, Yu X, Sontag E, Levine A. The p53HMM algorithm: using profile hidden markov models to detect p53-responsive genes. BMC Bioinformatics. 2009;10:111 pubmed publisher..These methods may also boost performance when applied to other transcription factor binding sites. ..
- Yan Y, Denef N, Schupbach T. The vacuolar proton pump, V-ATPase, is required for notch signaling and endosomal trafficking in Drosophila. Dev Cell. 2009;17:387-402 pubmed publisher..Our results demonstrate that Rbcn-3 affects Notch signaling and trafficking through regulating V-ATPase function, which implies that the acidification of an intracellular compartment in the receiving cells is crucial for signaling. ..
- Persikov A, Osada R, Singh M. Predicting DNA recognition by Cys2His2 zinc finger proteins. Bioinformatics. 2009;25:22-9 pubmed publisher..An online tool for predicting ZF DNA binding is available at http://compbio.cs.princeton.edu/zf/. ..
- Gjorevski N, Nelson C. Bidirectional extracellular matrix signaling during tissue morphogenesis. Cytokine Growth Factor Rev. 2009;20:459-65 pubmed publisher..We also discuss the implications for successful engineering of functional tissues ex vivo. ..
- Lupashin V, Waters M. t-SNARE activation through transient interaction with a rab-like guanosine triphosphatase. Science. 1997;276:1255-8 pubmed..The data suggest that the Rab protein Ypt1p transiently interacts with the t-SNARE Sed5p and results in displacement of the negative regulator Sly1p, allowing subsequent formation of the v-SNARE-t-SNARE targeting complex. ..
- Kavousanakis M, Kanodia J, Kim Y, Kevrekidis I, Shvartsman S. A compartmental model for the bicoid gradient. Dev Biol. 2010;345:12-7 pubmed publisher..We formulate a compartmental model, constrain its parameters by experimental data, and demonstrate that it provides an adequate description of the Bcd gradient dynamics. ..
- Shiozaki E, Chai J, Rigotti D, Riedl S, Li P, Srinivasula S, et al. Mechanism of XIAP-mediated inhibition of caspase-9. Mol Cell. 2003;11:519-27 pubmed..Thus, XIAP sequesters caspase-9 in a monomeric state, which serves to prevent catalytic activity. These studies, in conjunction with other observations, define a unified mechanism for the activation of all caspases. ..
- Deshpande G, Calhoun G, Jinks T, Polydorides A, Schedl P. Nanos downregulates transcription and modulates CTD phosphorylation in the soma of early Drosophila embryos. Mech Dev. 2005;122:645-57 pubmed..Finally, we present evidence indicating that the suppression of transcription in the soma by Nos protein is important for normal embryonic development. ..
- Wolanin P, Baker M, Francis N, Thomas D, Derosier D, Stock J. Self-assembly of receptor/signaling complexes in bacterial chemotaxis. Proc Natl Acad Sci U S A. 2006;103:14313-8 pubmed..To understand this structure in its cellular context, we propose a model involving parallel membrane segments in receptor-mediated CheA activation in vivo. ..
- Ureta A, Endres R, Wingreen N, Silhavy T. Kinetic analysis of the assembly of the outer membrane protein LamB in Escherichia coli mutants each lacking a secretion or targeting factor in a different cellular compartment. J Bacteriol. 2007;189:446-54 pubmed
- Sample C, Shvartsman S. Multiscale modeling of diffusion in the early Drosophila embryo. Proc Natl Acad Sci U S A. 2010;107:10092-6 pubmed publisher..A similar approach can be used to analyze the dynamics of all three maternal morphogen gradients in Drosophila. ..
- Paterson J, Ydenberg C, Rose M. Dynamic localization of yeast Fus2p to an expanding ring at the cell fusion junction during mating. J Cell Biol. 2008;181:697-709 pubmed publisher..In zygotes, Fus2p-GFP forms a dilating ring at the cell junction, returning to the nucleus at the completion of cell fusion. ..
- Endres R, Oleksiuk O, Hansen C, Meir Y, Sourjik V, Wingreen N. Variable sizes of Escherichia coli chemoreceptor signaling teams. Mol Syst Biol. 2008;4:211 pubmed publisher..This variation of signaling-team size shows that receptor cooperativity is dynamic and likely optimized for sensing noisy ligand concentrations. ..
- Tagkopoulos I, Liu Y, Tavazoie S. Predictive behavior within microbial genetic networks. Science. 2008;320:1313-7 pubmed publisher..We further show that these internal correlations reflect a true associative learning paradigm, because they show rapid decoupling upon exposure to novel environments. ..
- Keymer J, Endres R, Skoge M, Meir Y, Wingreen N. Chemosensing in Escherichia coli: two regimes of two-state receptors. Proc Natl Acad Sci U S A. 2006;103:1786-91 pubmed..e., high Hill coefficient. For homogeneous receptors, we predict an observable transition between regime I and regime II with increasing receptor methylation or amidation. ..
- Ungar D, Oka T, Krieger M, Hughson F. Retrograde transport on the COG railway. Trends Cell Biol. 2006;16:113-20 pubmed..This hypothesis explains the impact of COG mutations by postulating that they impair the retrograde flow of resident Golgi proteins needed to maintain normal Golgi structure and function. ..
- Gregor T, Tank D, Wieschaus E, Bialek W. Probing the limits to positional information. Cell. 2007;130:153-64 pubmed
- O Connor D, Wittenberg G, Wang S. Dissection of bidirectional synaptic plasticity into saturable unidirectional processes. J Neurophysiol. 2005;94:1565-73 pubmed..Variation in the distribution of initial synaptic strengths predicts a form of metaplasticity and can account for differences in learning rules observed under several physiological and genetic manipulations...
- Lenz D, Mok K, Lilley B, Kulkarni R, Wingreen N, Bassler B. The small RNA chaperone Hfq and multiple small RNAs control quorum sensing in Vibrio harveyi and Vibrio cholerae. Cell. 2004;118:69-82 pubmed publisher..We propose that Hfq, together with these sRNAs, creates an ultrasensitive regulatory switch that controls the critical transition into the high cell density, quorum-sensing mode...
- Ruvinsky I, Gibson Brown J. Genetic and developmental bases of serial homology in vertebrate limb evolution. Development. 2000;127:5233-44 pubmed
- Reeves G, Kalifa R, Klein D, Lemmon M, Shvartsman S. Computational analysis of EGFR inhibition by Argos. Dev Biol. 2005;284:523-35 pubmed..Thus, the spatial range of Argos does not have to be tightly regulated or may act at different ranges in distinct developmental contexts. ..
- Norvell A, Kelley R, Wehr K, Schupbach T. Specific isoforms of squid, a Drosophila hnRNP, perform distinct roles in Gurken localization during oogenesis. Genes Dev. 1999;13:864-76 pubmed..These results demonstrate the isoform-specific contributions of individual hnRNP proteins in the regulation of a specific mRNA. Moreover, these data suggest a novel role for hnRNPs in localization and translational regulation of mRNAs. ..
- Wu J, Hu M, Chai J, Seoane J, Huse M, Li C, et al. Crystal structure of a phosphorylated Smad2. Recognition of phosphoserine by the MH2 domain and insights on Smad function in TGF-beta signaling. Mol Cell. 2001;8:1277-89 pubmed..These observations define a bifunctional role for the MH2 domain as a pSer-X-pSer binding module in receptor Ser/Thr kinase signaling pathways. ..
- Malinverni J, Silhavy T. An ABC transport system that maintains lipid asymmetry in the gram-negative outer membrane. Proc Natl Acad Sci U S A. 2009;106:8009-14 pubmed publisher..We propose that the Mla pathway constitutes a bacterial intermembrane PL trafficking system...
- Wang S, Arellano Santoyo H, Combs P, Shaevitz J. Actin-like cytoskeleton filaments contribute to cell mechanics in bacteria. Proc Natl Acad Sci U S A. 2010;107:9182-5 pubmed publisher..These data are the first evidence that the bacterial cytoskeleton contributes to the mechanical integrity of a cell in much the same way as it does in eukaryotes. ..
- Osnas E, Dobson A. Evolution of virulence when transmission occurs before disease. Biol Lett. 2010;6:505-8 pubmed publisher..This model predicts that ESS virulence is highly dependent on the timing of transmission and pathology after infection; thus, pathogen evolution may either increase or decrease virulence after emergence in a new host. ..
- Gordon D. Recent advances in elucidating the role of the microsomal triglyceride transfer protein in apolipoprotein B lipoprotein assembly. Curr Opin Lipidol. 1997;8:131-7 pubmed..Thus, microsomal triglyceride transfer protein appears to control the number of apolipoprotein B lipoprotein particles secreted but not the lipid composition. ..
- Vitousek M, Romero L, Tarlow E, Cyr N, Wikelski M. Island tameness: an altered cardiovascular stress response in Galápagos marine iguanas. Physiol Behav. 2010;99:544-8 pubmed publisher..Understanding how the response to predators differs in predator-naïve species could enable the design of maximally effective techniques for inducing an anti-predator response in these vulnerable species...
- Clouse K, Ferguson S, Schupbach T. Squid, Cup, and PABP55B function together to regulate gurken translation in Drosophila. Dev Biol. 2008;313:713-24 pubmed..These data also provide the first evidence of a link between the complex of commonly used trans-acting factors and Enc, a factor that is required for grk translation. ..
- Higgins J, Hoffman S, Dworkin S. Rethinking gender, heterosexual men, and women's vulnerability to HIV/AIDS. Am J Public Health. 2010;100:435-45 pubmed publisher..We also call for an expanded model that acknowledges biology, gender inequality, and gendered power relations but also directly examines social structure, gender, and HIV risk for heterosexual women and men. ..
- Kinney J, Murugan A, Callan C, Cox E. Using deep sequencing to characterize the biophysical mechanism of a transcriptional regulatory sequence. Proc Natl Acad Sci U S A. 2010;107:9158-63 pubmed publisher..The principles of our method can also be applied to a wide range of other problems in molecular biology. ..
- Meighan C, Schwarzbauer J. Control of C. elegans hermaphrodite gonad size and shape by vab-3/Pax6-mediated regulation of integrin receptors. Genes Dev. 2007;21:1615-20 pubmed..These results demonstrate concomitant, but distinct roles in migration for each integrin. Notably, transcriptional control of migration termination provides a new mechanism for regulation of morphogenesis and organ size. ..
- McMillen T, Holmes P. An elastic rod model for anguilliform swimming. J Math Biol. 2006;53:843-86 pubmed
- Gjorevski N, Nelson C. Endogenous patterns of mechanical stress are required for branching morphogenesis. Integr Biol (Camb). 2010;2:424-34 pubmed publisher..These data suggest that the pattern and magnitude of mechanical stress across epithelial tissues cooperate with biochemical signals to specify branching pattern. ..