The CHARMM36 force field for lipids is widely used in simulations of lipid bilayers. The CHARMM family of force fields were developed for use with the mTIP3P water model. This water model has an anomalously high dielectric constant and low viscosity, which limits...

["Biochemistry","Biophysics","Computational Biology"]
doi:10.7717/peerj.5472

Sponges are ubiquitous on coral reefs, mostly long lived and therefore adaptive to changing environmental conditions. They feed on organic matter withdrawn from the passing water and they may harbor microorganisms (endosymbionts), which contribute to their nutrition....

["Ecology","Marine Biology","Biological Oceanography"]
doi:10.7717/peerj.5460

The invasive Asian shore crab, Hemigrapsus sanguineus, is ubiquitous in the rocky intertidal zone of the western North Atlantic. A likely contributor to this colonization is that H. sanguineus is able to handle a wide range of salinities, and is thus more likely...

["Marine Biology","Biological Oceanography"]
doi:10.7717/peerj.5446

Background Spatial scale is important when studying ecological processes. The Greater sage-grouse (Centrocercus urophasianus) is a large sexually dimorphic tetraonid that is endemic to the sagebrush biome of western North America. The impacts of oil and gas (OAG)...

["Conservation Biology","Ecology","Natural Resource Management","Environmental Impacts"]
doi:10.7717/peerj.5417

Background Nonsteroidal anti-inflammatory drugs (NSAIDs) are frequently used in clinical practice, which can have adverse effects on the osteoblast. The objective of this study was to determine the effect of NSAIDs on the osteoblast by analyzing the gene expression...

["Drugs and Devices","Pharmacology"]
doi:10.7717/peerj.5415

Roads may have an important negative effect on animal dispersal rate and mortality and thus the functioning of local populations. However, road verges may be surrogate habitats for invertebrates. This creates a conservation dilemma around the impact of roads on...

["Biodiversity","Conservation Biology","Ecology","Entomology","Zoology"]
doi:10.7717/peerj.5413

Antarctica, with its severe conditions, is poor in terrestrial fauna species. However, an increase in human presence together with climate change may cause an influx of non-native species. Here we report a significant increase in colonized area of one of the few...

["Biodiversity","Conservation Biology","Ecology","Ecosystem Science"]
doi:10.7717/peerj.5408

Background Acute kidney injury (AKI) is associated with a significant increase in morbidity, mortality, and health care costs. In intensive care units (ICU), AKI is commonly multifactorial and frequently involves diverse factors, such as hypovolemia, sepsis, and...

["Nephrology","Pharmacology","Public Health"]
doi:10.7717/peerj.5405

Background Tar seep deposits in South America historically are well-known for their rich record of fossil mammals, contrasting with only a few formal reports of reptile remains. Here we report a new snake fauna recovered from two tar pits from Venezuela. The fossil...

["Biogeography","Evolutionary Studies","Paleontology","Taxonomy","Zoology"]
doi:10.7717/peerj.5402

A residue from the primary treatment of a Wastewater Treatment Plant (WWTP) was used to isolate filamentous fungi with lipase production potential. Two of the 27 isolated fungi presented high hydrolysis index and were selected for lipase production by solid-state...

["Biotechnology","Environmental Contamination and Remediation","Green Chemistry"]
doi:10.7717/peerj.5368

We investigated a pantropical sub-family and genus of damselfishes, the sergeant-majors (Pomacentridae: Abudefdufinae: Abudefduf), to identify the tempo and mechanisms of speciation in the lineage. We examined sequence capture data from 500 loci and 20 species,...

["Biodiversity","Biogeography","Zoology"]
doi:10.7717/peerj.5357

Background Bacteria, archaea, viruses and fungi live in various plant compartments including leaves and roots. These plant-associated microbial communities have many effects on host fitness and function. Global climate change is impacting plant species distributions,...

["Ecology","Genomics","Microbiology","Plant Science","Climate Change Biology"]
doi:10.7717/peerj.5293

Selection of the right reference gene(s) is crucial in the analysis and interpretation of gene expression data. The aim of the present study was to discover and validate a minimal set of internal control genes in head and neck tumor studies. We analyzed data from...

["Genomics","Oncology"]
doi:10.7717/peerj.5207
589 downloads
658 views

Phylogenetic comparative methods (PCMs), especially ones based on linear models, have played a central role in understanding species’ trait evolution. These methods, however, usually assume that phylogenetic trees are known without error or uncertainty, but this...

["Computational Biology","Evolutionary Studies","Genetics","Taxonomy","Statistics"]
doi:10.7287/peerj.preprints.1216v2
223 downloads
671 views

From microorganisms to the largest macroorganisms, much of Earth’s biodiversity is subject to forces of physical turnover. Residence time is the ratio of an ecosystem’s size to its rate of flow and provides a means for understanding the influence of physical turnover...

["Biodiversity","Ecology","Ecosystem Science","Microbiology"]
doi:10.7287/peerj.preprints.2727v3

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