Biology subjects

Passow, C. N.

Publications and source records attributed to Passow, C. N..

4 recordsLinked to original sources

bioRxiv2020

Repeated evolution of circadian clock dysregulation in cavefish populations

Circadian rhythms are nearly ubiquitous throughout nature, suggesting they are critical for survival in diverse environments. Organisms inhabiting environments with arrhythmic days, such as caves, offer a unique opportunity to study the evolution of circadian rhythms in response to changing ecological pressures. Here we demonstrate that the cave environment has led to the repeated disruption of the biological clock across multiple populations of Mexican cavefish, with the circadian transcriptome showing widespread reductions in rhythmicity and changes to the timing of the activation/repression of genes in the core pacemaker. Then, we investigate the function of two genes with decreased rhythmic expression in cavefish. Mutants of these genes phenocopy reductions in sleep seen in multiple cave populations, suggesting a link between circadian dysregulation and sleep reduction. Altogether, our results reveal that evolution in an arrhythmic environment has resulted in dysregulation to the biological clock across multiple populations by diverse molecular mechanisms.

evolutionary biology↗

bioRxiv2019

Unique transcriptional signatures of sleep loss across independently evolved cavefish populations

Animals respond to sleep loss with compensatory rebound sleep, and this is thought to be critical for the maintenance of physiological homeostasis. Sleep duration varies dramatically across animal species, but it is not known whether evolutionary differences in sleep duration are associated with differences in sleep homeostasis. The Mexican cavefish, Astyanax mexicanus, has emerged as a powerful model for studying the evolution of sleep. While eyed surface populations of A. mexicanus sleep approximately eight hours each day, multiple blind cavefish populations have converged on sleep patterns that total as little as two hours each day, providing the opportunity to examine whether the evolution of sleep loss is accompanied by changes in sleep homeostasis. Here, we examine the behavioral and molecular response to sleep deprivation across four independent populations of A. mexicanus. Our behavioral analysis indicates that surface fish and all three cavefish populations display robust recovery sleep during the day following nighttime sleep deprivation, suggesting sleep homeostasis remains intact in cavefish. We profiled transcriptome-wide changes associated with sleep deprivation in surface fish and cavefish. While the total number of differentially expressed genes was not greater for the surface population, the surface population exhibited the highest number of uniquely differentially expressed genes than any other population. Strikingly, a majority of the differentially expressed genes are unique to individual cave populations, suggesting unique expression responses are exhibited across independently evolved cavefish populations. Together, these findings suggest sleep homeostasis is intact in cavefish despite a dramatic reduction in overall sleep duration.

evolutionary biology↗

bioRxiv2018

Performance of gene expression analyses using de novo assembled transcripts in polyploid species

MotivationQuality of gene expression analyses using de novo assembled transcripts in species experienced recent polyploidization is yet unexplored.\n\nResultsFive plant species with various polyploidy history were used for differential gene expression (DGE) analyses. DGE analyses using putative genes inferred by Trinity performed similar to or better than Corset and Grouper in precision, but lower in sensitivity. In species that lack polyploidy event in the past few million years, DGE analyses using de novo assembled transcriptome identified 50-76% of the differentially expressed genes recovered by mapping reads to the reference genes. However, in species with more recent polyploidy event, the percentage decreased to 7-30%. In addition, 7-89% of differentially expressed genes from de novo assembly are contaminations. Gene co-expression network analyses using de novo assemblies vs. mapping to the reference genes recovered the same module that significantly correlated with treatment in one of the five species tested.\n\nAvailability and ImplementationCommands and scripts used in this study are available at https://bitbucket.org/lychen83/chen_et_al_2018_benchmark_dge/; Analysis files are available at Dryad doi: XXXXXX.\n\nContactlychen83@qq.com\n\nSupplementary informationSupplementary data are available at Bioinformatics online

bioinformatics↗

bioRxiv2018

RNAlater and flash freezing storage methods nonrandomly influence observed gene expression in RNAseq experiments

RNA-sequencing is a popular next-generation sequencing technique for assaying genome-wide gene expression profiles. Nonetheless, it is susceptible to biases that are introduced by sample handling prior gene expression measurements. Two of the most common methods for preserving samples in both field-based and laboratory conditions are submersion in RNAlater and flash freezing in liquid nitrogen. Flash freezing in liquid nitrogen can be impractical, particularly for field collections. RNAlater is a solution for stabilizing tissue for longer-term storage as it rapidly permeates tissue to protect cellular RNA. In this study, we assessed genome-wide expression patterns in 30 day old fry collected from the same brood at the same time point that were flash-frozen in liquid nitrogen and stored at -80{degrees}C or submerged and stored in RNAlater at room temperature, simulating conditions of fieldwork. We show that sample storage is a significant factor influencing observed differential gene expression. In particular, genes with elevated GC content exhibit higher observed expression levels in liquid nitrogen flash-freezing relative to RNAlater-storage. Further, genes with higher expression in RNAlater relative to liquid nitrogen experience disproportionate enrichment for functional categories, many of which are involved in RNA processing. This suggests that RNAlater may elicit a physiological response that has the potential to bias biological interpretations of expression studies. The biases introduced to observed gene expression arising from mimicking many field-based studies are substantial and should not be ignored.

genomics↗