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Biology subjects

Matthew MacManes

Publications and source records attributed to Matthew MacManes.

3 recordsLinked to original sources

Physiological and biochemical changes associated with experimental dehydration in the desert adapted cactus mouse, Peromyscus eremicus

Characterizing traits critical for adaptation to a given environment is an important first step in understanding how phenotypes evolve. How animals adapt to the extreme heat and aridity commonplace to deserts represents is an exceptionally interesting example of these processes, and has been the focus of study for decades. In contrast to those studies, where experiments are conducted on either wild animals or captive animals held in non-desert conditions, the study described here leverages a unique environmental chamber that replicates desert conditions for captive Peromyscus eremicus (cactus mouse). Here we establish baseline values for daily water intake and for serum electrolytes, as well as the response of these variables to experimental dehydration. In brief, P. eremicus daily water intake is very low. Its serum electrolytes are distinct from many previously studied animals, and its response to acute dehydration is profound, though not suggestive of renal impairment, which is atypical of mammals.\n\nSummary statementThe establishment of baseline values for serum electrolytes and water intake, as well as their response to acute dehydration is critical for characterizing the physiology necessary for desert survival.\n\nConflict of Interest StatementThe authors declare no conflict of interest.

Zoology

PALADIN:Protein Alignment for Functional Profiling Whole Metagenome Shotgun Data

Whole metagenome shotgun sequencing is a powerful approach for assaying the functional potential of microbial communities. Presently, we lack tools that efficiently and accurately align DNA reads against protein references, the technique necessary for constructing a functional profile. Here, we present PALADIN--a novel modification of Burrows-Wheeler Aligner that provides more accurate alignment and orders-of-magnitude improved efficiency by directly mapping in protein space.

Bioinformatics

Brain Transcriptional Profiles of Male Alternative Reproductive Tactics and Females in Bluegill Sunfish

Bluegill sunfish are one of the classic systems for studying male alternative reproductive tactics (ARTs) in teleost fishes. In this species, there are two distinct life histories: parental and cuckolder, encompassing three reproductive tactics, parental, satellite, and sneaker. The parental life history is fixed, whereas individuals who enter the cuckolder life history transition from the sneaker to the satellite tactic as they grow. For this study, we used RNAseq to characterize the brain transcriptome of the three male tactics and females during spawning to identify gene categories associated with each tactic and identify potential candidate genes influencing their different spawning behaviors. We found that sneaker males had higher levels of gene differentiation compared to the other two male tactics. Sneaker males also had high expression in ionotropic glutamate receptor genes, specifically AMPA receptors, which may be important for increased working spatial memory while attempting to cuckold parental males at their nests. Larger differences in gene expression also occurred among male tactics than between males and females. We found significant expression differences in several candidate genes that were previously identified in other species with ARTs and suggest a previously undescribed role for cAMP-responsive element modulator (crem) in influencing parental male behaviors during spawning.

Genomics