Browsing by Keyword "Evolutionary Modeling"

Now showing items 1-13 of 13

    • Can You Sequence Ecology? Metagenomics of Adaptive Diversification 

      Marx, Christopher J (Public Library of Science, 2013)
      Few areas of science have benefited more from the expansion in sequencing capability than the study of microbial communities. Can sequence data, besides providing hypotheses of the functions the members possess, detect the ...

    • Cycling Empirical Antibiotic Therapy in Hospitals: Meta-Analysis and Models 

      Abel, Sören; Kouyos, Roger; Viechtbauer, Wolfgang; Bonhoeffer, Sebastian (Public Library of Science, 2014)
      The rise of resistance together with the shortage of new broad-spectrum antibiotics underlines the urgency of optimizing the use of available drugs to minimize disease burden. Theoretical studies suggest that coordinating ...

    • The Evolution of Cell-to-Cell Communication in a Sporulating Bacterium 

      van Gestel, Jordi; Nowak, Martin A.; Tarnita, Corina (Public Library of Science, 2012)
      Traditionally microorganisms were considered to be autonomous organisms that could be studied in isolation. However, over the last decades cell-to-cell communication has been found to be ubiquitous. By secreting molecular ...

    • Exploring the miRNA Regulatory Network Using Evolutionary Correlations 

      Obermayer, Benedikt; Levine, Erel (Public Library of Science, 2014)
      Post-transcriptional regulation by miRNAs is a widespread and highly conserved phenomenon in metazoans, with several hundreds to thousands of conserved binding sites for each miRNA, and up to two thirds of all genes under ...

    • NSAIDs Modulate Clonal Evolution in Barrett's Esophagus 

      Kostadinov, Rumen L.; Kuhner, Mary K.; Li, Xiaohong; Sanchez, Carissa A.; Galipeau, Patricia C.; Paulson, Thomas G.; Sather, Cassandra L.; Srivastava, Amitabh; Odze, Robert D.; Blount, Patricia L.; Vaughan, Thomas L.; Reid, Brian J.; Maley, Carlo C. (Public Library of Science, 2013)
      Cancer is considered an outcome of decades-long clonal evolution fueled by acquisition of somatic genomic abnormalities (SGAs). Non-steroidal anti-inflammatory drugs (NSAIDs) have been shown to reduce cancer risk, including ...

    • Positively Selected Sites in Cetacean Myoglobins Contribute to Protein Stability 

      Dasmeh, Pouria; Serohijos, Adrian; Kepp, Kasper P.; Shakhnovich, Eugene Isaacovitch (Public Library of Science, 2013)
      Since divergence ∼50 Ma ago from their terrestrial ancestors, cetaceans underwent a series of adaptations such as a ∼10–20 fold increase in myoglobin (Mb) concentration in skeletal muscle, critical for increasing oxygen ...

    • The role of deleterious passengers in cancer 

      McFarland, Christopher Dennis (2014-10-21)
      The development of cancer from a population of precancerous cells is a rapid evolutionary process. During progression, cells evolve several new traits for survive and proliferation via a few key `driver' mutations. However, ...

    • Selection for Replicases in Protocells 

      Bianconi, Ginestra; Zhao, Kun; Chen, Irene; Nowak, Martin A. (Public Library of Science, 2013)
      We consider a world of nucleotide sequences and protocells. The sequences have the property of spontaneous self-replication. Some sequences - so-called replicases - have enzymatic activity in the sense of enhancing the ...

    • Sine Systemate Chaos? A Versatile Tool for Earthworm Taxonomy: Non-Destructive Imaging of Freshly Fixed and Museum Specimens Using Micro-Computed Tomography 

      Fernández, Rosa; Kvist, Sebastian; Lenihan, Jennifer; Giribet, Gonzalo; Ziegler, Alexander (Public Library of Science, 2014)
      In spite of the high relevance of lumbricid earthworms (‘Oligochaeta’: Lumbricidae) for soil structure and functioning, the taxonomy of this group of terrestrial invertebrates remains in a quasi-chaotic state. Earthworm ...

    • Structure, Dynamics and Implied Gating Mechanism of a Human Cyclic Nucleotide-Gated Channel 

      Gofman, Yana; Schärfe, Charlotta; Marks, Debora S.; Haliloglu, Turkan; Ben-Tal, Nir (Public Library of Science, 2014)
      Cyclic nucleotide-gated (CNG) ion channels are nonselective cation channels, essential for visual and olfactory sensory transduction. Although the channels include voltage-sensor domains (VSDs), their conductance is thought ...

    • Transmission of Single and Multiple Viral Variants in Primary HIV-1 Subtype C Infection 

      Moyo, Sikhulile; van Widenfelt, Erik; Vartanian, Jean-Pierre; Novitsky, Vladimir A.; Wang, Rui; Margolin, Lauren; Baca, Jeannie; Rossenkhan, Raabya; Essex, Myron Elmer (Public Library of Science, 2011)
      To address whether sequences of viral gag and env quasispecies collected during the early post-acute period can be utilized to determine multiplicity of transmitted HIV's, recently developed approaches for analysis of viral ...

    • A Universal Trend among Proteomes Indicates an Oily Last Common Ancestor 

      Mannige, Ranjan V.; Brooks, Charles L.; Shakhnovich, Eugene Isaacovitch (Public Library of Science, 2012)
      Despite progresses in ancestral protein sequence reconstruction, much needs to be unraveled about the nature of the putative last common ancestral proteome that served as the prototype of all extant lifeforms. Here, we ...

    • Within-Host Bacterial Diversity Hinders Accurate Reconstruction of Transmission Networks from Genomic Distance Data 

      Worby, Colin J.; Lipsitch, Marc; Hanage, William P. (Public Library of Science, 2014)
      The prospect of using whole genome sequence data to investigate bacterial disease outbreaks has been keenly anticipated in many quarters, and the large-scale collection and sequencing of isolates from cases is becoming ...