Biology subjects

Allen, M. S.

Publications and source records attributed to Allen, M. S..

7 recordsLinked to original sources

bioRxiv2026

Integrating conventional tagging and acoustic telemetry improves estimates of post-release survival in a highly targeted reef fish

Accurate estimation of post-release survival is fundamental to fisheries stock assessment and effective management. Conventional tag-return studies and acoustic telemetry are commonly used to estimate this probability, yet each approach has limitations when applied independently. Using gag (Mycteroperca microlepis) as a case study, we integrated data from a large-scale conventional tagging program and an acoustic telemetry experiment within a discrete-time statistical modeling framework that links relative recapture risk with telemetry-derived fate. This approach enabled estimation of post-release survival across a broad gradient of capture depths representative of recreational fishing conditions. Estimated survival was high in shallow waters ({approx}97%) but declined with increasing capture depth, consistent with depth-related barotrauma. Applying model predictions to depth distributions from the recreational fishery yielded annual and monthly post-release survival probabilities. Annual estimates were consistent with values assumed in recent stock assessments, while monthly values highlighted seasonal patterns potentially relevant for management. This integrated framework advances post-release survival estimation by combining the extensive sample sizes and environmental coverage characteristic of conventional tagging data with the direct fate observations provided by acoustic telemetry, and offers a transferable approach for other highly targeted fisheries.

ecology↗

bioRxiv2024

Gut Microbiota and DTI Microstructural Brain Alterations in Rodents Due to Morphine Self-Administration

The opioid epidemic is an evolving health crisis in need of interventions that target all domains of maladaptive changes due to chronic use and abuse. Opioids are known for their effects on the opioid and dopaminergic systems, in addition to neurocircuitry changes that mediate changes in behavior; however, new research lines are looking at complementary changes in the brain and gut. The gut-brain axis (GBA) is a bidirectional signaling process that permits feedback between the brain and gut and is altered in subjects with opioid use disorders. In this work, we determine longitudinal, non-invasive, and in-vivo complementary changes in the brain and gut in rodents trained to self-administer morphine for two weeks using MRI and 16S rDNA analysis of fecal matter. We assess the changes occurring during both an acute phase (early in the self-administration process, after two days of self-administration) and a chronic phase (late in the self-administration process, after two weeks of self-administration), with all measurements benchmarked against baseline (naive, non-drug state). Rats were surgically implanted with an intravenous jugular catheter for self-administration of morphine. Rats were allowed to choose between an active lever, which delivers a single infusion of morphine (0.4 mg/kg/infusion), or an inactive lever, which had no consequence upon pressing. Animals were scanned in a 7T MRI scanner three times (baseline, acute, and chronic), and before scanning, fecal matter was collected from each rat. After the last scan session, a subset of animals was euthanized, and brains were preserved for immunohistochemistry analysis. We found early changes in gut microbiota diversity and specific abundance as early as the acute phase that persisted into the chronic phase. In MRI, we identified alterations in diffusivity indices both within subjects and between groups, showing a main effect in the striatum, thalamus, and somatosensory cortex. Finally, immunohistochemistry analyses revealed increased neuroinflammatory markers in the thalamus of rats exposed to morphine. Overall, we demonstrate that morphine self-administration shapes the brain and gut microbiota. In conclusion, gut changes precede the anatomical effects observed in MRI features, with neuroinflammation emerging as a crucial link mediating communication between the gut and the brain. This highlights neuroinflammation as a potential target in addressing the impacts of opioid use.

neuroscience↗

bioRxiv2022

Breeding the phenylketonuria mouse: novel dietary regimen enables breeding of female C57BL/6J mice homozygous for the Pahenu2 mutation without fostering.

The Pahenu2 mutation in C57BL/6J mice is a well characterized model for studying phenylketonuria (PKU), with Pahenu2 homozygotes displaying heightened blood phenylalanine and other characteristics of PKU. Pahenu2 homozygous females do not successfully rear young on any conventional diet due to their disease status. The most commonly used successful breeding strategy is crossing Pahenu2 heterozygous females with homozygous mutant males; producing litters of 50% homozygous and 50% heterozygous animals. In many treatment studies the heterozygous pups produced are not useable, but add to experimental costs and total animals used. To this end our lab created a dietary regimen with reduced phenylalanine and increased large neutral amino acid content, enabling homozygous mating. Phenylalanine levels in homozygous females and males on the new diet are significantly lower than that of homozygous females and males on traditional diets (p = 1.35x10-4 and p = 1.5x10-5 respectively). Litters born to Pahenu2 homozygous mothers on this diet demonstrate no significant difference in litter size compared to litters born to heterozygous mothers (p > 0.75). No observable defects were noted in litters born from homozygous crosses. This dietary regimen enables litter production of 100% Pahenu2 homozygous animals for investigators who wish to rapidly expand their Pahenu2 mouse colony size or do not require heterozygous littermate controls in their PKU studies.

genetics↗

bioRxiv2022

Hurricane Harvey Impacts on Water Quality and Microbial Communities in Houston, TX Waterbodies

Hurricanes, and other extreme weather events, can temporarily alter the structure of coastal systems and generate floodwaters that are contaminated with fecal-associated microbes; however, every coastal system and extreme weather event is unique, so identification of trends and commonalities in these episodic events is challenging. To improve our understanding of the resilience of coastal systems to the disturbance of extreme weather events and the risk exposure to floodwaters poses to the public, we monitored water quality, fecal indicator bacteria (FIB) at three stations within Clear Lake, an estuary between Houston and Galveston, and three stations in bayous that feed into the estuary. Water samples were collected immediately before Hurricane Harvey (pre-HH, August 25th, 2017), immediately after (HH, August 30th) and then throughout the fall of 2017 (post-HH). FIB levels were monitored by culturing E. coli and Enterococci. Microbial community structure was profiled by high throughput sequencing of PCR-amplified 16S rRNA gene fragments. Water quality and FIB data was also compared to historical data for these water body segments. Before Harvey, salinity within Clear Lake ranged from 9 to 11 practical salinity units (PSU). Immediately after the storm, salinity dropped to < 1 PSU and then gradually increased to pre-storm and historical levels over two months. Dissolved inorganic nutrient levels were also relatively low immediately after Harvey and returned, within a couple of months, to pre-HH and historical levels. FIB levels were elevated immediately after the storm; however, after one week, E. coli levels had decreased to acceptable levels for freshwater. Enterococci levels collected several weeks after the storm were within the range of historical levels for these water bodies. Microbial community structure shifted from a system dominated by Cyanobacteria sp. before HH to a system dominated by Proteobacteria and Bacteroidetes immediately after. Further, several sequences observed only in floodwater showed similarity to sequences previously reported for samples collected following Hurricane Irene. These changes in beta diversity corresponded to salinity and nitrate/nitrite concentrations. Differential abundance analysis of metabolic pathways, predicted from 16S sequences, suggested that pathways associated with virulence and antibiotic resistance were elevated in floodwater. Overall, these results suggest that recovery of the Clear Lake system following Hurricane Harvey took at least a month and floodwater generated from these extreme events may have high levels of fecal contamination, antibiotic resistant bacteria and bacteria rarely observed in other systems.

microbiology↗

bioRxiv2020

Testing the efficacy of lionfish traps in the northern Gulf of Mexico

Spearfishing is currently the primary approach for removing invasive Indo-Pacific lionfish (Pterois volitans/miles complex) to mitigate their impacts to western Atlantic marine ecosystems. However, a substantial portion of lionfish spawning biomass is beyond the depth limits of SCUBA. Innovative technologies may offer an alternative means to target lionfish and allow for the development of a deepwater lionfish trap fishery, but the removal efficiency and potential environmental impacts of traps have not been evaluated. We tested a collapsible non-containment trap (the Gittings trap) near artificial reefs in the northern Gulf of Mexico. A total of 327 lionfish and 28 native fishes (4 of which regulated species) recruited to traps (i.e., number of fish observed within the trap footprint) during 82 trap sets, catching 144 lionfish and 29 native species. Lionfish recruitment was highest for single (versus paired) traps deployed <15 m from reefs with a 1-day soak time, for which mean lionfish and native species recruitment per trap were approximately 5 and 0.1, respectively. Gittings traps selected for larger lionfish (mean size 277 mm total length) compared to spearfishing (mean size 258 mm). Community impacts from Gittings traps appeared minimal given recruitment patterns and catch rates were >10X higher for lionfish versus native fishes. Gittings traps did not move on the bottom during two major storm events; however, further testing will be necessary to test trap movement with surface buoys. Additional research should also focus on design and operational modifications to improve Gittings trap deployment success (68% successfully opened on the seabed) and reduce lionfish escapement (56% escaped from traps upon retrieval). While removal efficiency for lionfish (12-24%) was far below that of spearfishing, study results demonstrate Gittings traps are suitable for future testing on deepwater natural reefs, which constitute >90% of the regions reef habitat.

ecology↗

bioRxiv2019

Saving large fish through harvest slots outperforms the classical minimum-length limit when the aim is to achieve multiple harvest and catch-related fisheries objectives

We address the problem of optimal size-selective exploitation in an age-structured fish population model by systematically examining how density- and size-dependency in growth, mortality and fecundity affect optimal harvesting patterns when judged against a set of common fisheries objectives. Five key insights are derived. First, while minimum-length limits often maximize the biomass yield, exploitation using harvest slots (i.e., regulations that protect both immature and very large individuals) can generate within 95% of maximum yield, and harvest slots generally maximize the number of fish that are harvested. Second, density-dependence in growth and size-dependent mortality predict more liberal optimal size-limits than those derived under assumptions of no density and size-dependence. Third, strong density-dependence in growth maximizes the production of trophy fish in the catch only when some modest harvest is introduced; the same holds for numbers harvested, when the stock-recruitment function follows the Ricker-type. Fourth, the inclusion of size-dependent maternal effects on fecundity or egg viability has only limited effects on optimal size limits, unless the increase in fecundity with mass ("hyperallometry") is very large. Extreme hyperallometry in fecundity also shifts the optimal size-limit for biomass yield from the traditional minimum-length limit to a harvest slot. Fifth, harvest slots generally provide the best compromises among multiple objectives. We conclude that harvest slots, or more generally dome-shaped selectivity to harvest, can outperform the standard minimum-length selectivity. The exact configuration of optimal size limits crucially depends on objectives, local fishing pressure, the stock-recruitment function and the density and size-dependency of growth, mortality and fecundity.

ecology↗

bioRxiv2018

Immunological responses to the relapsing fever spirochete Borrelia turicatae in infected Rhesus macaques: implications for pathogenesis and diagnosis.

The global public health impact of relapsing fever (RF) spirochetosis is significant, as the pathogens exist on five of seven continents. The hallmark sign of infection is episodic fever and the greatest threat is to the unborn. With the goal of better understanding the specificity of B cell responses and the role of immune responses in pathogenicity, we infected Rhesus macaques with Borrelia turicatae (a new world RF spirochete species) by tick bite and monitored the immune responses generated in response to the pathogen. Specifically, we evaluated inflammatory mediator induction by the pathogen, host antibody responses to specific antigens, and peripheral lymphocyte population dynamics. Our results indicate that B. turicatae elicits from peripheral blood cells key inflammatory response mediators (IL-1{beta} and TNF-) which are associated with pre-term abortion. Moreover, a global decline in peripheral B cell populations was observed in all animals at 14 days post-infection. Serological responses were also evaluated to assess the antigenicity of three surface proteins, BipA, BrpA and Bta112. Interestingly, a distinction was observed between antibodies generated in non-human primates (NHPs) and mice. Our results provide support for the nonhuman primate model not only in studies of prenatal pathogenesis, but for diagnostic and vaccine antigen identification and testing.

immunology↗