Search bioRxiv⌕ Search

Biology subjects

Cassidy, K.

Publications and source records attributed to Cassidy, K..

2 recordsLinked to original sources

Population-specific drivers of reproductive phenology in a widespread large carnivore, the gray wolf

Animals often rely on cues from the environment to time reproduction with optimal conditions. However, for most species, which environmental cues are used and how their use varies across a species distribution remains poorly understood. The gray wolf (Canis lupus) is found across a broad latitudinal range (12{degrees}N to 83{degrees}N) and diverse natural habitats, making them an ideal study species to explore these questions. Using 1,261 estimated birth dates of wild and captive wolves across their global range, we investigated how environmental variables influence reproductive phenology in this widespread large carnivore. Birth dates for wild wolves ranged from November 22nd for Indian wolves (18{degrees}N) to June 15th for Arctic wolves (80{degrees}N). The best predictor of timing of birth was increasing daylength during the mating season, followed by precipitation variability during the year. The timing of birth in captive wolves was highly similar to wild wolves at same latitudes, suggesting they use similar environmental cues to time reproduction. Near the equator where photoperiod is more stable, wolves remained seasonal and likely use climatic cues to time reproduction. Our work reveals populations may use different environmental cues to time reproduction, a characteristic that likely facilitates adaptation to diverse environments.

ecology↗

PyLipID: A Python package for analysis of protein-lipid interactions from MD simulations

Lipids play important modulatory and structural roles for membrane proteins. Molecular dynamics simulations are frequently used to provide insights into the nature of these proteinlipid interactions. Systematic comparative analysis requires tools that provide algorithms for objective assessment of such interactions. We introduce PyLipID, a python package for the identification and characterization of specific lipid interactions and binding sites on membrane proteins from molecular dynamics simulations. PyLipID uses a community analysis approach for binding site detection, calculating lipid residence times for both the individual protein residues and the detected binding sites. To assist structural analysis, PyLipID produces representative bound lipid poses from simulation data, using a density-based scoring function. To estimate residue contacts robustly, PyLipID uses a dual-cutoff scheme to differentiate between lipid conformational rearrangements whilst bound from full dissociation events. In addition to the characterization of protein-lipid interactions, PyLipID is applicable to analysis of the interactions of membrane proteins with other ligands. By combining automated analysis, efficient algorithms, and open-source distribution, PyLipID facilitates the systematic analysis of lipid interactions from large simulation datasets of multiple species of membrane proteins. ToC Graphic O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=143 SRC="FIGDIR/small/452312v1_ufig1.gif" ALT="Figure 1"> View larger version (53K): org.highwire.dtl.DTLVardef@1f6530corg.highwire.dtl.DTLVardef@c639d5org.highwire.dtl.DTLVardef@1fef967org.highwire.dtl.DTLVardef@a80446_HPS_FORMAT_FIGEXP M_FIG C_FIG

biophysics↗