Biology subjects

Roberts, M. D.

Publications and source records attributed to Roberts, M. D..

23 records · Page 2Linked to original sources

bioRxiv2022

Weaker selection on genes with treatment-specific expression may limit plasticity evolution in Arabidopsis thaliana

Differential gene expression between environments often underlies phenotypic plasticity. However, environment-specific expression patterns are hypothesized to relax selection on genes, and thus limit plasticity evolution. We collated over 27 terabases of RNA-sequencing data on Arabidopsis thaliana from over 300 peer-reviewed studies and 200 treatment conditions to investigate this hypothesis. Consistent with relaxed selection, genes with more treatment-specific expression have higher levels of nucleotide diversity and divergence at nonsynonymous sites but lack stronger signals of positive selection. This result persisted even after controlling for expression level, gene length, GC content, the tissue specificity of expression, and technical variation between studies. Overall, our investigation supports the existence of a hypothesized trade-off between the environment specificity of a genes expression and the strength of selection on said gene in A. thaliana. Future studies should leverage multiple genome-scale datasets to tease apart the contributions of many variables in limiting plasticity evolution.

evolutionary biology↗

bioRxiv2022

The topological shape of gene expression across the evolution of flowering plants

Since they emerged ~125 million years ago, flowering plants have evolved to dominate the terrestrial landscape and survive in the most inhospitable environments on earth. At their core, these adaptations have been shaped by changes in numerous, interconnected pathways and genes that collectively give rise to emergent biological phenomena. Linking gene expression to morphological outcomes remains a grand challenge in biology, and new approaches are needed to begin to address this gap. Here, we implemented topological data analysis (TDA) to summarize the high dimensionality and noisiness of gene expression data using lens functions that delineate plant tissue and stress responses. Using this framework, we created a topological representation of the shape of gene expression across plant evolution, development, and environment for the phylogenetically diverse flowering plants. The TDA-based Mapper graphs form a well-defined gradient of tissues from leaves to seeds, or from healthy to stressed samples, depending on the lens function. This suggests there are distinct and conserved expression patterns across angiosperms that delineate different tissue types or responses to biotic and abiotic stresses. Genes that correlate with the tissue lens function are enriched in central processes such as photosynthetic, growth and development, housekeeping, or stress responses. Together, our results highlight the power of TDA for analyzing complex biological data and reveal a core expression backbone that defines plant form and function. Significance statementA grand challenge in biology is to link gene expression to phenotypes across evolution, development, and the environment, but efforts have been hindered by biological complexity and dataset heterogeneity. Here, we implemented topological data analysis across thousands of gene expression datasets in phylogenetically diverse flowering plants. We created a topological representation of gene expression across plants and observed well-defined gradients of tissues from leaves to seeds, or from healthy to environmentally stressed. Using this framework, we identified a core and deeply conserved expression backbone that defines plant form and function, with key patterns that delineate plant tissues, abiotic, and biotic stresses. Our results highlight the power of topological approaches for analyzing complex biological datasets.

plant biology↗

bioRxiv2021

Naked mole-rat and Damaraland mole-rat exhibit lower respiration in mitochondria, cellular and organismal levels

Naked mole-rats (NMR) and Damaraland mole-rats (DMR) are the only two eusocial mammals known. Both species exhibit extraordinary longevity for their body size, high tolerance to hypoxia and oxidative stress and high reproductive output; these collectively defy the concept that all life-history traits should be negatively correlated. However, when life-history traits share similar underpinning physiological mechanisms, these may be positively associated with each other. Here, we propose that the bioenergetic properties of mole-rats share a potential common mechanism. We adopted a top-down perspective measuring the bioenergetic properties at the organismal, cellular, and molecular level in both species and the biological significance of these properties were compared with the same measures in Siberian hamsters and C57BL/6 mice, chosen for their similar body size to the mole-rat species. We found mole-rats shared several bioenergetic properties that differed from their comparator species, including low basal metabolic rates, a high dependence on glycolysis rather than on oxidative phosphorylation for ATP production, and low proton conductance across the mitochondrial inner membrane. These shared mole-rat features could be a result of evolutionary adaptation to tolerating variable oxygen atmospheres, in particular hypoxia, and may in turn be one of the molecular mechanisms underlying their extremely long lifespans.

physiology↗

bioRxiv2021

Resistance training rejuvenates the mitochondrial methylome in aged human skeletal muscle

Resistance training (RT) alters skeletal muscle nuclear DNA methylation patterns (or the methylome). However, no study has examined if RT affects the mitochondrial DNA (mtDNA) methylome. Herein, ten older untrained males (65{+/-}7 years old) performed six weeks of full-body RT (twice weekly). Body composition and knee extensor torque were assessed prior to and 72 hours following the last RT session. Vastus lateralis (VL) biopsies were also obtained. VL DNA was subjected to reduced representation bisulfite sequencing providing excellent coverage across the ~16-kilobase mtDNA methylome (254 CpG sites). Various biochemical assays were also performed, and older male data were compared to younger trained males (22{+/-}2 years old, n=7). RT increased whole-body lean tissue mass (p=0.017), VL thickness (p=0.012), and knee extensor torque (p=0.029) in older males. RT also profoundly affected the mtDNA methylome in older males, as 63% (159/254) of the CpG sites demonstrated reduced methylation (p<0.05). Notably, several mtDNA sites presented a more "youthful" signature after RT in older males when comparisons were made to younger males. The 1.12 kilobase D-loop/control region on mtDNA, which regulates mtDNA replication and transcription, possessed enriched hypomethylation in older males following RT. Enhanced expression of mitochondrial H- and L-strand genes and increases in mitochondrial complex III and IV protein levels were also observed (p<0.05). This is the first study to show RT alters the mtDNA methylome in skeletal muscle. Observed methylome alterations may enhance mitochondrial transcription, and RT remarkably evokes mitochondrial methylome profiles to mimic a more youthful signature in older males.

molecular biology↗

bioRxiv2019

PHYSIOLOGICAL DIFFERENCES BETWEEN ADVANCED CROSSFIT ATHLETES, RECREATIONAL CROSSFIT PARTICIPANTS, AND PHYSICALLY-ACTIVE ADULTS

This investigation examined anthropometric, hormonal, and physiological differences between advanced (ADV; n = 8, 27.8 {+/-} 4.2 years, 170 {+/-} 11 cm, 79.8 {+/-} 13.3 kg) and recreational (REC; n = 8, 33.5 {+/-} 8.1 years, 172 {+/-} 14 cm, 76.3 {+/-} 19.5 kg) CrossFit (CF) trained participants in comparison to physically-active controls (CON; n = 7, 27.5 {+/-} 6.7 years, 171 {+/-} 14 cm, 74.5 {+/-} 14.3 kg). ADV and REC were distinguished by their past competitive success. REC and CON were resistance-trained (>2 years) and exercised on 3-5 days{middle dot}wk-1 for the past year, but CON utilized traditional resistance and cardiovascular exercise. All participants provided a fasted, resting blood sample and completed assessments of resting metabolic rate, body composition, muscle morphology, isometric mid-thigh pull strength, peak aerobic capacity, and a 3-minute maximal cycle ergometer sprint across two separate occasions (separated by 3-7 days). Blood samples were analyzed for testosterone, cortisol, and insulin-like growth factor-1. One-way analysis of variance revealed ADV to possess lower body fat percentage (6.7-8.3%, p = 0.007), greater bone and non-bone lean mass (12.5-26.8%, p [≤] 0.028), muscle morphology characteristics (14.2-59.9%, p < 0.05), isometric strength characteristics (15.4-41.8%, p < 0.05), peak aerobic capacity (18.8-19.1%, p = 0.002), and anaerobic performance (15.4-51.1%, p [≤] 0.023) compared to both REC and CON. No differences were seen between REC and CON, or between all groups for resting metabolic rate or hormone concentrations. These data suggest ADV possess several physiological advantages over REC and CON, whereas similar physiological characteristics were present in individuals who have been regularly participating in either CF or resistance and cardiovascular training for the past year.

physiology↗