Biology subjects

Akin, S.

Publications and source records attributed to Akin, S..

3 recordsLinked to original sources

bioRxiv2025

What determines trophic niche breadth? A global analysis of freshwater fishes using isospaces

Trophic niche is one of the most tractable dimensions of a species niche. Several hypotheses have been proposed to explain global variation in species trophic niches, but empirical tests are limited. Stable isotope analysis (SIA) of {delta}{superscript 1}3C (a proxy for basal sources) and {delta}{superscript 1} N (a proxy for vertical trophic position) has increasingly been used to estimate trophic niche variation. We performed SIA on a dataset of over 33,000 stable isotope samples from freshwater fishes across six ecoregions. For 541 populations (358 species), we estimated the size of {delta}{superscript 1}3C x {delta}{superscript 1} N isospace--a bivariate representation of trophic niche breadth. We evaluated isospace variation in relation to environmental factors, species traits, and sampling scale, testing both novel and long-standing hypotheses about the drivers of trophic niche variation. A Boosted Regression Tree Model best predicted isospace, with environmental and trait-based variables among the strongest predictors. Fish isospaces were broader in regions with warmer temperatures, higher humidity, and precipitation variability, suggesting that more productive, diverse, and seasonal ecosystems are associated with broader trophic niches. Conversely, isospace size declined with increasing basin fish richness, which may reflect heightened interspecific competition or historical competitive exclusion. Isospace size was slightly smaller in large lakes compared to rivers, streams, and small lakes. Within-population variation in body size was strongly and positively associated with isospace size, highlighting the role of ontogenetic dietary shifts. Fish with truncate-rounded fins had broader isospaces than those with forked-lunate fins, likely due to the former having more limited movement and greater spatial isolation that resulted in greater between-individual niche variation. Primary consumers had larger isospaces than intermediate and top consumers. Predators showed relationships consistent those observed from analysis encompassing all trophic guilds, but non-predators deviated with regards to four variables--solar radiation, basin richness, average body size, and caudal fin aspect ratio. Isospace size increased with the number of sampled individuals, habitats and years surveyed. Although isospace patterns have well-documented limitations as trophic ecology metrics, our findings nonetheless conform with several longstanding hypotheses for trophic niche variation and stimulate new ideas about environmental and biological drivers of niche breadth.

ecology↗

bioRxiv2024

Sedentary lifestyle induces oxidative stress and atrophy in rat skeletal muscle

Abundant evidence indicates that skeletal muscle is an important endocrine organ that plays a key role in regulating metabolic homeostasis. Therefore, maintaining healthy skeletal muscles is essential to good health. While it is established that prolonged skeletal muscle inactivity results in both oxidative stress and muscle atrophy, it remains unknown if the change from an active to a sedentary lifestyle promotes a similar increase in oxidative stress and locomotor muscle atrophy. We tested the hypothesis that the transition from active to sedentary living results in the rapid development of oxidative damage and fiber atrophy in locomotor skeletal muscles. Adult Wistar rats were randomly divided into control (CON; n=8) and sedentary (SED; n=8) groups. During a seven-day experimental period, animals in the CON group were housed in standard size cages permitting free movement, while animals in the SED group were housed in small cages that promoted sedentary behavior. At the end of the experimental protocol, soleus muscles were removed and the activities of antioxidant enzymes superoxide dismutase (SOD), catalase (CAT), and glutathione peroxidase (GPX) were determined along with two biomarkers of muscle oxidative stress (i.e., levels of advanced protein oxidation (AOPP) and 4-hydroxynonenal (4-HNE)). Living in the reduced-size cage resulted in muscle atrophy as evidenced by a 17.2% decrease in the soleus to body weight ratio (P<0.001). Moreover, the activities of SOD, CAT and GPX in the soleus muscle were significantly decreased in SED animals compared to CON (P<0.05). Finally, compared to CON, sedentary living increased both AOPP and 4-HNE levels in muscles of SED animals (P<0.001 and P <0.05, respectively). These findings provide the first evidence that the transition from an active to sedentary lifestyle results in the rapid onset of oxidative stress and atrophy in locomotor skeletal muscles. Importantly, these results suggest that an impaired antioxidant defense contributes to sedentary behavior-induced oxidative stress in locomotor muscles.

physiology↗

bioRxiv2023

Accessibility and activity of transcriptional regulatory elements during sea urchin embryogenesis and differentiation

Transcriptional regulatory elements (TREs) are the primary nodes of the gene regulatory networks that control development. TREs are identified by PRO-seq and their accessibility by ATAC-seq during sea urchin embryonic development and differentiation. Our analysis identifies surprisingly early accessibility in 4-cell cleavage embryo TREs that is not necessarily followed by subsequent transcription, and an excess of ATAC-seq peaks transcriptionally disengaged during the stages analyzed. Embryonic accessibility shifts are driven by transcriptionally engaged TREs, and PRO-seq transcriptional differences at TREs provide more contrast among embryonic stages than ATAC-seq accessibility differences. TRE accessibility reaches a maximum around the 20-hour late blastula, which coincides with major embryo regionalizations. At the same time, a large number of distal TREs become transcriptionally disengaged, in support of an early Pol II primed model for developmental gene regulation that eventually resolves in transcriptional activation or silencing. A transcriptional potency model based on labile nucleosome TRE occupancy driven by DNA sequences and the prevalence of histone variants is proposed in order to explain the basal accessibility of transcriptionally inactive TREs during early embryogenesis. Summary statementGenomic profiles deciphering the location and activity of regulatory elements that control gene expression suggest general mechanisms of regulatory potency in early sea urchin embryos.

developmental biology↗