Biology subjects

Warren, D. E.

Publications and source records attributed to Warren, D. E..

5 recordsLinked to original sources

bioRxiv2025

A new chromosome-level genome assembly for western painted turtle Chrysemys picta belli, a model for extreme physiological adaptations

The western painted turtle, Chrysemys picta bellii, has the greatest tolerance to anoxia of any tetrapod studied to date. These turtles reside in the northern United States and southern Canada, and survive months of anoxia while submerged in ice-locked ponds and bogs. Reference genomes provide an important resource for elucidating the molecular bases for such unique physiological traits. An initial reference genome for this species was published in 2013, but the assembly is highly fragmented which poses several limitations for downstream analyses and biological interpretation. In this study, we created a new and improved assembly by combining PacBio HiFi, 10x Genomics Chromium, Hi-C sequence data and BioNano optical mapping derived from a single individual to generate a new haplotype-resolved chromosome-level assembly for C. picta bellii, called "SLU_Cpb5.0". The genome size of the primary assembly is 2.372 Gb with a scaffold N50 of 133.6 Mb, which is a 6.5-fold improvement over the existing assembly. Genome annotation of SLU_Cpb5.0 revealed 12,242 novel genes compared to previous assemblies. Our PacBio Iso-Seq RNA sequencing data for twelve tissues unraveled over 100,000 novel transcript isoforms and 4,325 novel genes that were not annotated by standard NCBI pipeline. We also observed distinct patterns of tissue-specific isoform expression, creating a robust foundation for future characterization of the functions of these genes. The improved genome assembly and annotation will facilitate comparative genomics studies to better understand the genetic basis of C.picta belliis extreme physiological adaptations and other aspects of its biology.

genomics↗

bioRxiv2022

Responses of the in vitro turtle brain to visual and auditory stimuli during severe hypoxia

North American pond turtles (Emydidae) are renowned for their ability to survive extreme hypoxia and anoxia, which enables several species to overwinter in ice-locked, anoxic freshwater ponds and bogs for months. Centrally important for surviving these conditions is a profound metabolic suppression, which enables ATP demands to be met entirely with glycolysis. Despite this, turtles have occasionally been observed exploring their natural and laboratory environments while anoxic and can still respond to sensory stimuli. To better understand whether anoxia limits a special sensory function, we recorded evoked potentials in a reduced brain preparation, in vitro, that was perfused with severely hypoxic artificial cerebral spinal fluid (aCSF). For recordings of visual responses, an LED light was flashed onto retinal eyecups while evoked potentials were recorded from the retina or the optic tectum. For recordings of auditory responses, a piezo motor-controlled glass actuator vibrated the tympanic membrane while evoked potentials were recorded from the cochlear nuclei. We found that visual responses decreased even with moderately hypoxic perfusate (aCSF PO2 = 30-60 torr) and completely abolished under severe hypoxia. In contrast, the evoked response within the cochlear nuclei was unattenuated with severe hypoxia (aCSF PO2 < 20 torr). These data provide further support that pond turtles have a limited ability to sense visual information in their environment even while moderately hypoxic, but that auditory input may become a principal avenue of sensory perception during extreme diving in this species. Summary StatementSevere hypoxia attenuates the visual, but not auditory responses in a reduced brain preparation from a pond turtle.

physiology↗

bioRxiv2021

Skeletal Muscle Histidine Containing Dipeptide Contents are Increased in Freshwater Turtles (Chrysemys picta bellii) with Cold-Acclimation

Freshwater turtles found in higher latitudes can experience extreme challenges to acid-base homeostasis while overwintering, due to a combination of cold temperatures along with the potential for environmental hypoxia. Histidine containing dipeptides (HCDs; carnosine, anserine and balenine) may facilitate pH regulation in response to these challenges, through their role as pH buffers. We measured the HCDs content of three tissues (liver, cardiac muscle and skeletal muscle) from the anoxia-tolerant painted turtle (Chrysemys picta bellii) acclimated to either 3 or 20{degrees}C. HCDs were detected in all tissues, with the highest content shown in the skeletal muscle. Turtles acclimated to 3{degrees}C had more HCD in their skeletal muscle than those acclimated to 20{degrees}C (carnosine = 20.8{+/-}4.5 vs 12.5{+/-}5.9 mmol{middle dot}kg DM-1; ES = 1.59 (95%CI: 0.16 - 3.00), P = 0.013). The higher HCD content observed in the skeletal muscle of the cold-acclimated turtles suggests a role in acid-base regulation in response to physiological challenges associated with living in the cold, with the increase possibly related to the temperature sensitivity of carnosines dissociation constant and buffering power of the skeletal muscle during anoxic submergence. HighlightsO_LIpH regulation is a major challenge for overwintering freshwater turtles. C_LIO_LIHistidine containing dipeptides are important intracellular buffers. C_LIO_LITurtles acclimated to 3{degrees}C had higher HCD content than those at 20{degrees}C. C_LIO_LIHCDs may be important pH regulators in cold-acclimated turtles. C_LI

physiology↗

bioRxiv2021

Cold-acclimation induces life stage-specific responses in the cardiac proteome of Western painted turtles (Chrysemys picta bellii): implications for anoxia tolerance

Western painted turtles (Chrysemys picta bellii) are the most anoxia-tolerant tetrapod. Survival time improves at low temperature and during ontogeny, such that adults acclimated to 3{degrees}C survive far longer without oxygen than either warm-acclimated adults or cold-acclimated hatchlings. Since protein synthesis is rapidly suppressed to save energy at the onset of anoxia exposure, this study tested the hypothesis that cold-acclimation would evoke preparatory changes in protein expression that would support enhanced anoxia survival in adult but not hatchling turtles. To test this, adult and hatchling turtles were acclimated to either 20{degrees}C (warm) or 3{degrees}C (cold) for 5 weeks, and then the heart ventricles were collected for quantitative proteomic analysis using labeled isobaric tags and mass spectrometry. The relative abundances of 1316 identified proteins were compared between temperatures and developmental stages. The effect of cold-acclimation on the cardiac proteome was most evident when life stage was included as a covariable, suggesting that ontogenic differences in anoxia tolerance may be predicated on successful maturation of the heart from its hatchling to adult form and, only after this maturation occurs, will cold-acclimation induce protein expression changes appropriate for supporting heart function during prolonged anoxia. The main differences between the hatchling and adult cardiac proteomes reflect an increase in metabolic scope that included more myoglobin and increased investment in both aerobic and anaerobic energy pathways. Mitochondrial structure and function were key targets of life stage- and temperature-induced changes to the cardiac proteome, including reduced complex II proteins in cold-acclimated adults that may help down-regulate the electron transport system and avoid succinate accumulation during anoxia. Therefore, targeted cold-induced changes to the cardiac proteome may be a contributing mechanism for stagespecific anoxia tolerance in turtles.

physiology↗

bioRxiv2017

Surgically disconnected temporal pole exhibits resting functional connectivity with remote brain regions

Functional connectivity, as measured by resting-state fMRI, has proven a powerful method for studying brain systems in the context of behavior, development, and disease states. However, the relationship of functional connectivity to structural connectivity remains unclear. If functional connectivity relies on structural connectivity, then anatomical isolation of a brain region should eliminate functional connectivity with other brain regions. We tested this by measuring functional connectivity of the surgically disconnected temporal pole in resection patients (N=5; mean age 37; 2F, 3M). Functional connectivity was evaluated based on coactivation of whole-brain fMRI data with the average low-frequency BOLD signal from disconnected tissue in each patient. In sharp contrast to our prediction, we observed significant functional connectivity between the disconnected temporal pole and remote brain regions in each disconnection case. These findings raise important questions about the neural bases of functional connectivity measures derived from the fMRI BOLD signal.

neuroscience↗