Biology subjects

Smith, D. C.

Publications and source records attributed to Smith, D. C..

5 recordsLinked to original sources

bioRxiv2026

Seafloor topography structures subseafloor microbial communities in the Puerto Rico Trench

The influence of seafloor topography on subseafloor microbial communities is poorly understood. In this study, we systematically sampled subseafloor sedimentary microbial communities and pore-water geochemistry at bathyal, abyssal, and hadal water depths of the Puerto Rico Trench. The Puerto Rico Trench exhibits vertical relief of over 8 km with seafloor topography shaped by active plate tectonics and characterized by a very steep southern wall and active mass wasting. Sampling across these features, we find that subseafloor microbial communities are influenced by topography in the following two ways. First, subseafloor sediment in the deepest part of the trench is anoxic, enriched in organic matter due to mass transport of sediment from shallower water depths, and contains an anaerobic subseafloor community that is quite distinct from the anaerobic subseafloor community in anoxic sediment at bathyal depths. The difference between these bathyal and hadal subseafloor anaerobic communities is consistent with influence of water-depth-related physical properties on subseafloor community composition. Second, subseafloor sediment remains oxygenated for meters below seafloor on steep slopes within the bathyal zone, an abyssal topographic high within the trench, and the abyssal plain seaward of the trench subseafloor, likely due to limited sediment accumulation, which selects for the presence of aerobic microbial communities. The difference between these bathyal and abyssal aerobic subseafloor communities and the anaerobic communities at bathyal and hadal depths reflects the role of seafloor topography in structuring subseafloor availability of redox reactants, which in turn drives the activities and composition of subseafloor microbial communities.

microbiology↗

bioRxiv2026

Piezophilic activity dominates the Puerto Rico Trench deep subseafloor biosphere

Hydrostatic pressure is a defining feature of the deep ocean, yet how it structures microbial activity across the subseafloor biosphere is poorly understood. Here, we assess pressure effects on anabolic activity in seafloor and subseafloor communities across a margin-to-hadal-to-abyssal transect of the Puerto Rico Trench region (493-8,385 m water depth). Community-level responses to pressure reverse with burial, revealing a previously unrecognized shift toward piezophily in resident subseafloor communities down to 20 meters below seafloor (mbsf). In pressure-incubation experiments, atmospheric pressure yielded higher proportions of active cells in surficial sediments, whereas in situ pressure yielded higher proportions in the subseafloor. Pressure also structured active-community composition; in trench-axis sediments extending to 8.35 mbsf, JS1/Atribacterota populations belonging to geographically widespread hadal lineages exhibited a physiological response to in situ pressure, indicative of subseafloor piezophily. These findings suggest that hydrostatic pressure acts as an ecological filter after burial, favoring piezophilic traits that may support microbial persistence in the deep subseafloor biosphere.

microbiology↗

bioRxiv2023

Network analysis reveals strain-dependent response to misfolded tau aggregates

Mouse genetic backgrounds have been shown to modulate amyloid accumulation and propagation of tau aggregates. Previous research into these effects has highlighted the importance of studying the impact of genetic heterogeneity on modeling Alzheimers disease. However, it is unknown what mechanisms underly these effects of genetic background on modeling Alzheimers disease, specifically tau aggregate-driven pathogenicity. In this study, we induced tau aggregation in wild-derived mice by expressing MAPT (P301L). To investigate the effect of genetic background on the action of tau aggregates, we performed RNA sequencing with brains of 6-month-old C57BL/6J, CAST/EiJ, PWK/PhJ, and WSB/EiJ mice (n=64). We also measured tau seeding activity in the cortex of these mice. We identified three gene signatures: core transcriptional signature, unique signature for each wild-derived genetic background, and tau seeding-associated signature. Our data suggest that microglial response to tau seeds is elevated in CAST/EiJ and PWK/PhJ mice. Together, our study provides the first evidence that mouse genetic context influences the seeding of tau. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=198 HEIGHT=200 SRC="FIGDIR/small/526029v1_ufig1.gif" ALT="Figure 1"> View larger version (51K): org.highwire.dtl.DTLVardef@1c99217org.highwire.dtl.DTLVardef@965522org.highwire.dtl.DTLVardef@1af4105org.highwire.dtl.DTLVardef@d5ea98_HPS_FORMAT_FIGEXP M_FIG C_FIG SUMMARYSeeding of tau predates the phosphorylation and spreading of tau aggregates. Acri and colleagues report transcriptomic responses to tau and elevated tau seeds in wild-derived mice. This paper creates a rich resource by combining genetics, tau biosensor assays, and transcriptomics.

neuroscience↗

bioRxiv2020

From people to Panthera: Natural SARS-CoV-2 infection in tigers and lions at the Bronx Zoo

We describe the first cases of natural SARS-CoV-2 infection detected in animals in the United States. In March 2020, four tigers and three lions at the Bronx Zoo developed mild respiratory signs. SARS-CoV-2 RNA was detected by rRT-PCR in respiratory secretions and/or feces from all seven affected animals; viral RNA and/or antibodies were detected in their keepers. SARS-CoV-2 was isolated from respiratory secretions or feces from three affected animals; in situ hybridization co-localized viral RNA with cellular damage. Whole genome sequence and haplotype network analyses showed tigers and lions were infected with two different SARS-CoV-2 strains, suggesting independent viral introductions. The source of SARS-CoV-2 infection in the lions is unknown. Epidemiological data and genetic similarities between keeper and tiger viruses indicate human to animal transmission.

pathology↗

bioRxiv2018

Transcriptional and electrophysiological aberrations in an induced pluripotent stem cell-derived model of spinocerebellar ataxia type 7

Spinocerebellar ataxia type 7 (SCA7) is an inherited neurodegenerative disease caused by a polyglutamine repeat expansion in the ATXN7 gene. Patients with this disease suffer from a degeneration of their cerebellar Purkinje neurons and retinal photoreceptors that result in a progressive ataxia and loss of vision. As with many neurodegenerative diseases, studies of pathogenesis have been hindered by a lack of disease-relevant models. To this end, we have generated induced pluripotent stem cells (iPSCs) from a cohort of SCA7 patients in South Africa. First, we differentiated the SCA7 affected iPSCs into neurons which showed evidence of a transcriptional phenotype affecting components of STAGA (ATXN7 and KAT2A) and the heat shock protein pathway (DNAJA1 and HSP70). We then performed electrophysiology on the SCA7 iPSC-derived neurons and found that these cells show features of functional aberrations. Lastly, we were able to differentiate the SCA7 iPSCs into retinal photoreceptors that also showed similar transcriptional aberrations to the SCA7 neurons. Our findings demonstrate that iPSC-derived neurons and photoreceptors from SCA7 patients express molecular and electrophysiological differences that are indicative of impaired neuronal health. We hope that these findings will contribute towards the ongoing efforts to establish the cell-derived models of neurodegenerative diseases that are needed to develop patient-specific treatments.

neuroscience↗