Biology subjects

Smith, J. K.

Publications and source records attributed to Smith, J. K..

8 recordsLinked to original sources

bioRxiv2025

De novo recovery of Ghana virus, an African bat Henipavirus, reveals differential tropism and attenuated pathogenicity compared to Nipah virus

Henipaviruses (HNVs) like Nipah (NiV) and Hendra (HeV) viruses represent severe zoonotic threats. Ghana virus (GhV), identified in 2012, is the only African bat henipavirus with a near-complete genome assembly. However, without isolates in culture, GhV biology, pathogenicity, and zoonotic potential remain poorly understood. Using reverse genetics, we recovered a full-length infectious clone of GhV at BSL-4 following rational reconstruction of its incomplete 3' leader and modification of a non-canonical transcriptional initiation site. GhV demonstrated restricted receptor tropism (ephrin-B2 but not ephrin-B3) and distinct innate immune antagonism. Replication was attenuated in primary human cells, but was enhanced in bat cells. In Syrian golden hamsters, GhV infection caused no disease or mortality. Furthermore, a chimeric NiV encoding the GhV receptor-binding protein was completely attenuated in vivo, implicating ephrin-B3 receptor usage as a critical determinant of HNV pathogenesis. These findings elucidate GhV zoonotic potential and inform strategies for virus surveillance and control. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=200 SRC="FIGDIR/small/679836v1_ufig1.gif" ALT="Figure 1"> View larger version (64K): org.highwire.dtl.DTLVardef@1e5addcorg.highwire.dtl.DTLVardef@1f96850org.highwire.dtl.DTLVardef@12f842eorg.highwire.dtl.DTLVardef@8f013c_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

bioRxiv2025

Surface Expansion Regionalization of the Hippocampus in Early Brain Development

The hippocampal formation is implicated in a myriad of crucial functions, particularly centered around memory and emotion, with distinct subdivisions fulfilling specific roles. However, there is no consensus on the spatial organization of these subdivisions, given that the functional connectivity and gene expression-based parcellation along its longitudinal axis differs from the histology-based parcellation along its medial-lateral axis. The dynamic nonuniform surface expansion of the hippocampus during early development reflects the underlying changes of microstructure and functional connectivity, providing important clues on hippocampal subdivisions. Moreover, the thin and convoluted properties bring out the hippocampal maturity largely in the form of expanding surface area. We thus unprecedentedly explore the development-based surface area regionalization and patterns of the hippocampus by leveraging 513 high-quality longitudinal MRI scans during the first two postnatal years. Our findings imply two discrete hippocampal developmental patterns, featuring one pattern of subdivisions along the anterior-posterior axis (head, regions 1 and 5; body, regions 2, 4, 6, and 7; tail, region 3) and the other one along the medial-lateral axis (subiculum, regions 4, 5, and 6; CA fields, regions 1, 2, and 7). Most of the resulting 7 subdivisions exhibit region-specific and nonlinear spatiotemporal surface area expansion patterns with an initial high growth, followed by a transition to low increase. Each subregion displays bilaterally symmetric pattern. The medial portion of the hippocampal head experiences the most rapid surface area expansion. These results provide important references for exploring the fine-grained organization and development of the hippocampus and its intricate cognitions.

neuroscience↗

bioRxiv2022

Structural and Dynamic Basis of DNA Capture and Translocation by Mitochondrial Twinkle Helicase

Twinkle is the sole helicase responsible for mitochondrial DNA replication. Twinkle can selfload onto and unwind mitochondrial DNA. Nearly 60 mutations on Twinkle have been linked to human mitochondrial diseases. Using cryo-electron microscopy (cryo-EM) and High-speed atomic force microscope (HS-AFM), we obtained the atomic-resolution structure of a vertebrate Twinkle homolog with DNA and captured in real-time how Twinkle is self-loaded onto DNA. Our data highlight the essential role of the non-catalytic N-terminal domain of Twinkle. The N-terminal domain interacts with the helicase domain to stabilize Twinkle hexamers during translocation and the new domain-domain interface is a hotspot for disease-related mutations. The N-terminal domains can protrude approximately 5 nm to capture nearby DNA and initialize Twinkle loading onto DNA. Moreover, structural analysis and subunit doping experiments suggest that Twinkle hydrolyzes ATP stochastically, which explains the low efficiency of Twinkle DNA unwinding and implicates additional regulations of Twinkle during mitochondrial DNA replication.

biochemistry↗

bioRxiv2021

Nipah virus Bangladesh infection elicits organ-specific innate and inflammatory responses in the marmoset model

The common marmoset (Callithrix jacchus) is increasingly recognized as an ideal non-human primate (NHP) at high-biocontainment due to its smaller size and relative ease of handling. Here, we evaluated the susceptibility and pathogenesis of Nipah virus Bangladesh strain (NiVB) infection in marmosets at biosafety level 4. Infection via the intranasal and intratracheal route resulted in fatal disease in all four infected marmosets. Three developed pulmonary edema and hemorrhage as well as multi-focal hemorrhagic lymphadenopathy, while one recapitulated neurologic clinical symptoms and cardiomyopathy on gross pathology. Organ-specific innate and inflammatory responses were characterized by RNA-seq in six different tissues from infected and control marmosets. Notably, a unique transcriptome was revealed in the brainstem of the marmoset exhibiting neurological symptoms. Our results provide a more comprehensive understanding of NiV pathogenesis in an accessible and novel NHP model, closely reflecting clinical disease as observed in NiV patients.

microbiology↗

bioRxiv2021

Small molecule SWELL1-LRRC8 complex induction improves glycemic control and nonalcoholic fatty liver disease in murine Type 2 diabetes

Type 2 diabetes (T2D) is associated with insulin resistance, impaired insulin secretion from the pancreatic {beta}-cell, and nonalcoholic fatty liver disease (NAFLD). SWELL1 (LRRC8a) ablation impairs adipose and skeletal muscle insulin-pAKT2 signaling, {beta}-cell insulin secretion and glycemic control - suggesting that SWELL1-LRRC8 complex dysfunction contributes to T2D pathogenesis. Here, we show that ICl,SWELL and SWELL1 protein are reduced in adipose and {beta}-cells in murine and human T2D. Combining cryo-electron microscopy, molecular docking, medicinal chemistry, and functional studies, we define a structure activity relationship to rationally-designed active derivatives (SN-40X) of a SWELL1 channel inhibitor (DCPIB/SN-401), that bind the SWELL1-LRRC8 hexameric complex, restore SWELL1-LRRC8 protein, plasma membrane trafficking, signaling and islet insulin secretion via SWELL1-dependent mechanisms. In vivo, SN-401 and active SN-40X compounds restore glycemic control and prevents NAFLD by improving insulin-sensitivity and insulin secretion in murine T2D. These findings demonstrate that small molecule SWELL1 modulators restore SWELL1-dependent insulin-sensitivity and insulin secretion in T2D and may represent a first-in-class therapeutic approach for T2D and NAFLD.

physiology↗

bioRxiv2020

Furin Cleavage Site Is Key to SARS-CoV-2 Pathogenesis

SARS-CoV-2 has resulted in a global pandemic and shutdown economies around the world. Sequence analysis indicates that the novel coronavirus (CoV) has an insertion of a furin cleavage site (PRRAR) in its spike protein. Absent in other group 2B CoVs, the insertion may be a key factor in the replication and virulence of SARS-CoV-2. To explore this question, we generated a SARS-CoV-2 mutant lacking the furin cleavage site ({Delta}PRRA) in the spike protein. This mutant virus replicated with faster kinetics and improved fitness in Vero E6 cells. The mutant virus also had reduced spike protein processing as compared to wild-type SARS-CoV-2. In contrast, the {Delta}PRRA had reduced replication in Calu3 cells, a human respiratory cell line, and had attenuated disease in a hamster pathogenesis model. Despite the reduced disease, the {Delta}PRRA mutant offered robust protection from SARS-CoV-2 rechallenge. Importantly, plaque reduction neutralization tests (PRNT50) with COVID-19 patient sera and monoclonal antibodies against the receptor-binding domain found a shift, with the mutant virus resulting in consistently reduced PRNT50 titers. Together, these results demonstrate a critical role for the furin cleavage site insertion in SARS-CoV-2 replication and pathogenesis. In addition, these findings illustrate the importance of this insertion in evaluating neutralization and other downstream SARS-CoV-2 assays. ImportanceAs COVID-19 has impacted the world, understanding how SARS-CoV-2 replicates and causes virulence offers potential pathways to disrupt its disease. By removing the furin cleavage site, we demonstrate the importance of this insertion to SARS-CoV-2 replication and pathogenesis. In addition, the findings with Vero cells indicate the likelihood of cell culture adaptations in virus stocks that can influence reagent generation and interpretation of a wide range of data including neutralization and drug efficacy. Overall, our work highlights the importance of this key motif in SARS-CoV-2 infection and pathogenesis. Article SummaryA deletion of the furin cleavage site in SARS-CoV-2 amplifies replication in Vero cells, but attenuates replication in respiratory cells and pathogenesis in vivo. Loss of the furin site also reduces susceptibility to neutralization in vitro.

microbiology↗

bioRxiv2018

Effects of endophyte infected tall fescue seed and red clover isoflavones on rumen microbial populations, fiber fermentation, and volatile fatty acids in vitro

Negative impacts of endophyte-infected Lolium arundinaceum (Darbyshire) (tall fescue) are responsible for over $2 billion in losses to livestock producers annually. While the influence of endophyte-infected tall fescue has been studied for decades, mitigation methods have not been clearly elucidated. Isoflavones found in Trifolium pretense (red clover) have been the subject of recent research regarding tall fescue toxicosis mitigation. Therefore, the aim of this study was to determine the effect of ergovaline and red clover isoflavones on rumen microbial populations, fiber degradation, and volatile fatty acids (VFA) in an in vitro system. Using a dose of 1.10 mg x L-1, endophyte-infected or endophyte-free tall fescue seed was added to ANKOM fiber bags with or without 2.19 mg of isoflavones in the form of a control, powder, or pulverized tablet, resulting in a 2 x 3 factorial arrangements of treatments. Measurements of pH, VFA, bacterial taxa, as well as the disappearance of neutral detergent fiber (aNDF), acid detergent fiber (ADF), and crude protein (CP) were taken after 48 h of incubation. aNDF disappearance values were significantly altered by seed type (P = 0.003) and isoflavone treatment (P = 0.005), and ADF disappearance values were significantly different in a seed x isoflavone treatment interaction (P [≤] 0.05). A seed x isoflavone treatment interaction was also observed with respect to CP disappearance (P [≤] 0.05). Seventeen bacterial taxa were significantly altered by seed x isoflavone treatment interaction groups (P [≤] 0.05), six bacterial taxa were increased by isoflavones (P [≤] 0.05), and eleven bacterial taxa were altered by seed type (P [≤] 0.05). Due to the beneficial effect of isoflavones on tall fescue seed fiber degradation, these compounds may be viable options for mitigating fescue toxicosis. Further research should be conducted to determine physiological implications as well as microbiological changes in vivo.

microbiology↗

bioRxiv2017

AFQ-Browser: Supporting reproducible human neuroscience research through browser-based visualization tools

Human neuroscience research faces several challenges with regards to reproducibility. While scientists are generally aware that data sharing is an important component of reproducible research, it is not always clear how to usefully share data in a manner that allows other labs to understand and reproduce published findings. Here we describe a new open source tool, AFQ-Browser, that builds an interactive website as a companion to a published diffusion MRI study. Because AFQ-browser is portable -- it runs in any modern web-browser -- it can facilitate transparency and data sharing. Moreover, by leveraging new web-visualization technologies to create linked views between different dimensions of a diffusion MRI dataset (anatomy, quantitative diffusion metrics, subject metadata), AFQ-Browser facilitates exploratory data analysis, fueling new scientific discoveries based on previously published datasets. In an era where Big Data is playing an increasingly prominent role in scientific discovery, so will browser-based tools for exploring high-dimensional datasets, communicating scientific discoveries, sharing and aggregating data across labs, and publishing data alongside manuscripts.

neuroscience↗