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Total of 334 results See all subject areas
microbiology

Evolutionary studies of clustered regularly interspaced short palindromic repeats (CRISPRs) and their associated (cas) genes can provide insights into host-pathogen co-evolutionary dynamics and the frequency at which different genomic events (e.g., horizontal vs....

["Evolutionary Studies","Genomics","Microbiology","Infectious Diseases"]
doi:10.7717/peerj.340

Background. As whole genome sequence data from bacterial isolates becomes cheaper to generate, computational methods are needed to correlate sequence data with biological observations. Here we present the large-scale BLAST score ratio (LS-BSR) pipeline, which rapidly...

["Bioinformatics","Computational Biology","Genomics","Microbiology"]
doi:10.7717/peerj.332

Mementos encapsulate memories and serve as triggers for their recollections. By using a purple pigment producing bacterium as “ink” for writing on agar, a picture memento depicting the initials of students’ names was created, to help them remember the strong friendships...

["Microbiology","Science and Medical Education"]
doi:10.7287/peerj.preprints.349v1

It has been widely accepted that aphids and their primary endosymbiotic bacteria Buchnera have strictly parallel diversification relationship. As the first reported case of insect-bacteria cospeciation, this parallel diversification hypothesis has been prevalent,...

["Entomology","Evolutionary Studies","Genetics","Microbiology","Zoology"]
doi:10.7287/peerj.preprints.346v1

A multitude of studies have looked at the in vivo and in vitro behavior of the lac repressor binding to DNA and effector molecules in order to study transcriptional repression, however these studies are not always reconcilable. Here we use in vitro transcription...

["Biochemistry","Biophysics","Mathematical Biology","Microbiology","Molecular Biology"]
doi:10.7287/peerj.preprints.317v1

Caenorhabditis elegans is commonly used as an infection model for pathogenesis studies in Pseudomonas aeruginosa. While the standard virulence assays rely on the slow and fast killing or paralysis of nematodes, here we developed a behaviour assay to monitor the...

["Microbiology","Infectious Diseases"]
doi:10.7287/peerj.preprints.313v1

Bacteria were long assumed to be monoploid, maintaining one copy of a circular chromosome. In recent years it became obvious that the majority of species in several phylogenetic groups of prokaryotes are oligoploid or polyploid, e.g. in halophilic and methanogenic...

["Biochemistry","Genetics","Genomics","Microbiology","Molecular Biology"]
doi:10.7287/peerj.preprints.306v1

Chronic wounds are a major global health problem. Their management is difficult and costly, and the development of antibiotic resistance by both planktonic and biofilm-associated bacteria necessitates the use of alternative wound treatments. Honey is now being...

["Microbiology","Infectious Diseases"]
doi:10.7717/peerj.326

Brown-headed Cowbirds (Molothrus ater) are the most widespread avian brood parasite in North America, laying their eggs in the nests of approximately 250 host species that raise the cowbird nestlings as their own. It is currently unknown how these heterospecific...

["Evolutionary Studies","Genetics","Microbiology","Zoology"]
doi:10.7717/peerj.321

Molecular surveys of aphotic habitats have indicated the presence of major uncultured lineages phylogenetically classified as members of the Cyanobacteria. One of these lineages has recently been proposed as a non-photosynthetic sister phylum to the Cyanobacteria,...

["Genomics","Microbiology"]
doi:10.7287/peerj.preprints.204v2

Mycobacterium species have a complex cAMP regulatory network indicated by the high number of adenylate cyclases annotated in their genomes. However the need for a high level of redundancy in adenylate cyclase genes remains unknown. We have used semiquantitiative...

["Microbiology","Infectious Diseases"]
doi:10.7717/peerj.298

During the period of March 2004 to December 2007, samples of aerial litter (dead but still attached plant parts) and ground litter (dead plant material on the ground) were collected from 81 study sites representing a wide range of latitudes (34°S to 50°S) and a...

["Biogeography","Ecology","Microbiology"]
doi:10.7717/peerj.296

Many microbial, fungal, or oomcyete populations violate assumptions for population genetic analysis because these populations are clonal, admixed, partially clonal, and/or sexual. Furthermore, few tools exist that are specifically designed for analyzing data from...

["Bioinformatics","Genetics","Microbiology","Mycology","Computational Science"]
doi:10.7717/peerj.281

Metagenomics is a valuable tool for the study of microbial communities but has been limited by the difficulty of “binning” the resulting sequences into groups corresponding to the individual species and strains that constitute the community. Moreover, there are...

["Bioengineering","Bioinformatics","Computational Biology","Genomics","Microbiology"]
doi:10.7287/peerj.preprints.260v1

Microbes require several complex organic molecules for growth. A species may obtain a required factor by taking up molecules released by other species or by synthesizing the molecule. The patterns of uptake and synthesis set a flow of resources through the multiple...

["Evolutionary Studies","Mathematical Biology","Microbiology"]
doi:10.7717/peerj.267

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