Biology subjects

Anderson, T.

Publications and source records attributed to Anderson, T..

At least 19 recordsLinked to original sources

bioRxiv2026

Scarless regeneration requires post-translational proteolytic regulation via macrophage-derived Legumain

Macrophages express proteolytic factors in response to injury but how proteases are deployed and regulated during regeneration are incompletely defined. Beyond their transcriptomic expression, activity of individual proteases is defined both by their unique substrate specificity and post-translational modifications of their active forms. Here we show a key role for the lysosomal protease Legumain in controlling ECM dynamics and post-translational processing of the regenerative proteome. Injury interface-targeted Ctsla localization and post-translational processing requires Lgmn in macrophages. Extracellular cues from physical remodeling control differentiation state and injury response of ligament resident fibroblasts. Loss of ECM turnover, including localized Fibronectin 1a/b remodeling, impairs dedifferentiation in legumain mutants and leads to fibrotic scarring. Taken together, we demonstrate a role for macrophage-derived lysosomal proteases as specialized tools required to fine-tune proteome composition and function in regeneration.

cell biology↗

bioRxiv2026

Widespread occurrence of bovine-like and new viruses in wild deer across the United States

Over the past several decades, deer populations in North America have grown considerably, resulting in frequent contact with humans and livestock, and increased potential for pathogen spillover. Despite the importance of pathogen spillover among humans, wildlife, and livestock, the diversity of viruses present in deer remains largely unknown. Using a metagenomic high-throughput sequencing approach, we characterized viral communities in the upper respiratory tracts of live mule deer (Odocoileus hemionus) and white-tailed deer (Odocoileus virginianus) captured at fourteen study sites in nine states across the United States. We identified vertebrate-infecting viruses in both deer species at all but two of the study sites, located in Illinois and Utah. Viral richness did not vary among species or study sites. However, viral community composition was different across study sites but not among deer species. Amongst the detected viral sequences, several originate from or were closely related to viruses previously described in humans (e.g., severe acute respiratory syndrome coronavirus 2) and livestock (e.g., bovine-like coronavirus). We also documented viruses recently discovered in deer, such as CHeRI orbivirus 1. Finally, we identified several new putative viruses in the Picornaviridae, Rhabdoviridae and Tobaniviridae families, including a novel Aphthovirus related to bovine rhinitis A virus in both deer species, across seven states and nine study sites. Our findings expand the understanding of viral diversity in two deer species across the United States, providing important insights for managing pathogens at the wildlife, livestock, and human interface.

microbiology↗

bioRxiv2026

A multivalent mRNA-lipid nanoparticle vaccine containing eight hemagglutinin antigens elicited broad neutralizing antibody responses and protected against influenza A virus challenge in swine.

The diversity within H1 and H3 subtype influenza A viruses (IAV) in swine prevents effective vaccine control approaches with inactivated whole-virus vaccines. We addressed the challenge of controlling co-circulating hemagglutinin (HA) clades of swine IAV with the development of a multivalent mRNA-lipid nanoparticle (LNP) vaccine expressing 8 HA proteins to maximize genetic coverage. We applied a computational approach to select eight HA genes that represented 95% of the observed IAV detected in the United States between 2022 and 2025. Piglets were vaccinated and boosted intramuscularly with either individual HA mRNA-LNP or an 8-HA multivalent mRNA-LNP. Serum was collected to evaluate systemic antibody levels. Twenty-one days post-boost, pigs were challenged with a field relevant H1 1A.3.3.3-c3 IAV strain. The 8-HA multivalent mRNA-LNP vaccine induced neutralizing antibodies against all eight antigens and vaccinees were protected against lung lesions, with lesion scores similar to non-challenged animals. Homologous monovalent vaccination significantly reduced IAV detection in nasal secretions and in the lungs. Heterologous monovalent vaccination was not cross-protective but did not induce vaccine-associated enhanced respiratory disease. We provide evidence that monovalent and multivalent mRNA-LNP influenza vaccines elicited neutralizing antibody responses in pigs and protected against viral challenge. The versatility and capacity for rapidly updating the mRNA-LNP vaccine platform make it an appealing tool to improve animal health and minimize the circulation and diversity of IAV in swine. ImportanceInfluenza A virus is an important respiratory pathogen in swine, and zoonotic transmission of swine strains to humans remains a public health risk. Control strategies against IAV in swine herds rely heavily on biosecurity measures and vaccination. However, the antigenic diversity of IAV circulating in swine challenges current vaccination programs, and there is a need for broadly protective vaccines or platforms that can rapidly update components to reflect circulating diversity. mRNA-LNP vaccines have emerged as promising vaccine platforms, offering simultaneous delivery of multiple antigens, rapid development, scalable manufacturing, and potent immunogenicity. In this study, we assessed the immunogenicity and protective capacity of monovalent and multivalent mRNA-LNP vaccines encoding eight representative IAV HA antigens. To our knowledge, this is the first study to objectively select multiple representative endemic swine IAV strains by quantifying genetic diversity within the phylogeny and to apply this selection to rationally design and evaluate a multivalent HA mRNA-based influenza vaccine in the swine model.

microbiology↗

bioRxiv2026

Thalamic nuclei insights into Alzheimer's disease

INTRODUCTIONThalamic nuclei support multiple cognitive processes, yet their integrity in biologically-defined Alzheimers disease (AD) remains unknown. METHODAmyloid status was determined using PET Centiloids >24 in 1,327 participants from ADNI. Combined with clinical diagnosis, this yielded six groups: amyloid-negative or positive CN-MCI-dementia/AD. Thalamic nuclei volumes were extracted from T1-weighted MRI using the HIPS-THOMAS algorithm. RESULTSLarge volume reductions in the anteroventral, mediodorsal, and pulvinar nuclei were observed in amyloid-positive MCI and AD. Reduced volumes were also evident in amyloid-positive CN, supporting preclinical AD. Adding the anteroventral nucleus improved cognitive status classification in Random Forest analyses. A phenotypic model integrating thalamic nuclei clearly distinguished amyloid-positive groups from amyloid-negative CN and reclassified non-AD patients with 68% of amyloid-negative MCI subjects as CN-like, and 27% of amyloid-positive CN as MCI-like. DISCUSSIONThalamic volumetry from conventional T1-weighted MRI enhances clinical insight into AD and provides a practical biomarker for disease intervention.

neuroscience↗

bioRxiv2026

Source-space EEG functional connectivity and prediction of cognition in Parkinsons disease: No added benefit of individualized head models over standard templates

IntroductionCognitive decline is a major non-motor feature of Parkinsons disease (PD), but reliable and accessible biomarkers remain limited. Resting-state electroencephalography (EEG) is a promising candidate because it is low-cost, portable, and well suited to repeated assessment. Recent work has increasingly focused on source-space functional connectivity (FC) for the prediction of cognition. However, the influence of source modelling based on an individualized MRI-based head model relative to that based on standard template model is unknown. MethodsTo compare these two source-space EEG FC methods, we analysed EEG data from the New Zealand Parkinsons Progression Programme, including 136 people with PD and 51 age-similar controls. Source space resting-state EEG, parcellated with the HCP-MMP1 atlas, was used to derive amplitude envelope correlation (AEC) and debiased weighted phase lag index (dwPLI) across six canonical frequency bands. The resulting twenty-four FC modalities were evaluated using six machine-learning regression algorithms within a nested cross-validation framework. ResultsTheta-, alpha-, and beta-band FC showed the most consistent prediction of global cognition. The strongest performance was observed for theta- and alpha-band AEC and dwPLI features (max R{superscript 2} = 0.170, 95% CI = 0.067-0.262; max r = 0.439, 95% CI = 0.328-0.537). Standard and individualized head models showed comparable predictive performance across nearly all modalities. The feature-importance neuroanatomical patterns for Cole-Anticevic networks were also similar between the two head-model options. ConclusionsWe found that source-space resting-state EEG FC can predict cognitive performance in PD. The comparability of the two head models suggests that the more user-friendly and less resource-intensive standard template head model is sufficient for this purpose. This supports feasible, scalable, and clinically accessible EEG-based FC biomarkers of cognition in PD.

neuroscience↗

bioRxiv2026

Hypothalamus amyloid levels are associated with early sex-dependent alterations in energy homeostasis in TgF344-AD rats

We reported previously that diet-induced obesity exacerbates early-stage Alzheimers disease (AD)-like pathology in TgF344-AD rats. Our findings also suggested that TgF344-AD rats may be prone to weight gain during early AD development, which we assessed here. Energy intake, body composition, and the impact of glucose administration on blood glucose were also assessed. Body temperature, intrascapular brown adipose tissue (iBAT) mass, and iBAT uncoupling protein-1 (UCP1) expression were used as indicators of thermogenic function. Soluble amyloid {beta}40 (A{beta}40) and A{beta}42 were quantified in hypothalamus. Male TgF344-AD rats began to outweigh wildtype (WT) littermates by 5 weeks of age; this increase emerged later in female TgF344-AD rats (~5 months). Female TgF344-AD rats ingested more energy from chow and a high fat, high sugar (HFHS) diet, gained more weight on the HFHS diet, and had lower UCP1 than WT rats, effects not observed in male TgF344-AD rats. Surprisingly, male and female TgF344-AD rats had increased body temperatures. This was restricted to the dark phase in females, which is when they ingest excess calories. Finally, the HFHS diet disrupted glucose regulation in male but not female TgF344-AD rats. These findings suggest that increases in energy intake and decreases in UCP1 may contribute to the additional weight gain in female TgF344-AD rats. The causes for these increases in males remain unclear. Hypothalamic A{beta}42 correlated with glucose dysregulation in male TgF344-AD rats and BAT mass in female TgF344-AD rats, raising the possibility that increases in A{beta}42 in hypothalamus produce sex-specific disruptions in energy homeostasis.

neuroscience↗

bioRxiv2025

Impact of Maternal Antibodies and Weaning Stress on the Replication and Transmission of Human H3N2 Influenza A in Piglets

Modern swine production facilitates indoor respiratory contact between human employees and pigs in their care, creating conditions for interspecies transmission of influenza A virus (IAV). Sow vaccination is routinely practiced in the U.S. to transfer maternal derived antibodies (MDA) to piglets. Weaning is a highly stressful period for piglets that requires increased human interaction. This study investigates the effect of maternal antibodies on the susceptibility of weaned piglets to a human-origin H3N2 IAV. Weaned piglets often possess mixed immunity from MDA, which may be antigenically matched or mismatched to circulating viruses. Given the repeated spillover of human seasonal H3N2 into swine, we specifically examined how matched and mismatched MDA, acquired from vaccinated sows, influenced piglet susceptibility. Additionally, we assessed the impact of weaning-related stress on the outcome of viral challenge. The H3N2 virus was generated by reverse genetics to mimic the 2010.1 H3N2 introduction from humans to swine. Challenged seeder piglets were divided by immune and weaning status. Two days post inoculation, naive direct contact pigs were placed with seeders. IAV qRT-PCR and virus titration were performed on nasal swabs and bronchoalveolar lavage fluid to evaluate shedding and transmission kinetics. Matched MDA were effective in reducing shedding in challenged pigs and minimizing transmission to contacts. There was an increase in shedding and transmission in weaned pigs compared to littermates that remained on the sow. These results identify critical control points in production where changing practices could mitigate human-to-swine and swine-to-swine transmission to prevent establishment of novel lineages in pig populations. ImportanceDefining the factors that increase the susceptibility of pigs to infection with human influenza A viruses (IAV) is critical to understand why those viruses transmit to the new host. IAV is frequently detected in nursing pigs, where it was shown that maternal derived antibodies (MDA) may reduce clinical signs but may not prevent infection and transmission. Infected weaned piglets can then move viruses from the sow farm to offsite nurseries, where they can cause outbreaks with clinical disease as MDA wanes. Determining management practices that can be modified to reduce interspecies transmission of viruses to pigs is economically beneficial to the swine industry and could help define measures to prevent new spillover events. Reducing spillover of human IAV into pig populations also benefits public health by reducing genomic and phenotypic diversity in swine and the subsequent potential for zoonotic transmission.

immunology↗

bioRxiv2025

Template switching by coronavirus polymerase requires helicase activity and is stimulated by remdesivir and molnupiravir

Polymerase template switching is an essential mechanism in coronaviruses (CoVs) that enables both sub-genomic (sg) RNA synthesis and increases genomic diversity via RNA recombination. Despite its importance, the molecular mechanism of CoV polymerase template switching remains unclear. Using magnetic tweezers, we show that the CoV non-structural protein (nsp) 13-helicase drives polymerase template switching, followed by copy-back RNA synthesis. This activity requires nsp13-helicase ATPase activity and a duplex RNA downstream of the CoV polymerase. This novel function of nsp13-helicase is targeted by the nucleotide analogs remdesivir and molnupiravir, whose incorporation in the nascent strand increases CoV polymerase template switching probability, leading to defective RNA production. We propose a novel mechanism of action where incorporation of these analogs dramatically reduces full length genome copy number by stimulating polymerase template switching. Our study further demonstrates nsp13-helicases central role in CoV replication and how this enzyme function can be indirectly targeted by analogs.

microbiology↗

bioRxiv2025

Evidence for the Transient Presence of Atypical Astrocytes in Mice Following a Single, Closed-Head Mild Traumatic Brain Injury

Mild traumatic brain injury (mTBI) affects roughly 42 million people each year, causes a variety of physical, behavioral, and cognitive symptoms, and increases the risk for developing neurological disorders, including post-traumatic headache (PTH) and Alzheimers disease (AD). Multiple molecular and cellular changes occur following mTBI; here we focus on astrocytes - cells that respond to brain injury and are critical to maintaining neuronal and circuit homeostasis. While some astrocytes become reactive after mTBI, others adopt an atypical state characterized by the loss of multiple functional astrocyte proteins, including glutamate transporters (GLT-1, GLAST) and ion channels (Kir4.1), without upregulation of prototypical reactive astrocyte markers (glial fibrillary acidic protein [GFAP]). Previous studies have shown that repeated mTBI causes atypical astrocytes (AtAs) that can persist for months, but we know much less about whether a single mTBI causes similar astrocyte phenotypes. To address this, we employed a closed-head mild traumatic brain injury (chmTBI) model in male and female mice and quantified the abundance of AtAs both acutely (3-days) and chronically (1-month) after a single injury. We found that 3-days after chmTBI, AtAs were present in areas subject to blunt force trauma (BFT), consistent with previous reports, as well as in other brain regions presumably affected by diffuse injury. One month after chmTBI, however, the proportion of AtAs was similar between chmTBI and sham injured mice, thereby suggesting AtAs do not persist long term in this model. Consistent with previous studies, this chmTBI model did not induce significant GFAP-positive reactive astrocytes as assayed using immunohistochemistry, at either timepoint. Overall, we show an increase in AtAs 3-days after a single chmTBI that returns to sham levels when examined 1-month after injury. This suggests that after a single mTBI, AtAs are present but do not persist long term, unlike in repeated mTBI where AtAs persist for months after injury.

neuroscience↗

bioRxiv2025

Effect of combined Respiratory Muscle Training on Sleep and Cardiovascular Biometrics in a non-clinical cohort

Study objectivesSleep disruption is a growing health problem, affecting a significant portion of the adult population worldwide. Insufficient sleep has various short- and long-term consequences, including an elevated risk of cardiovascular and metabolic diseases. Previous research has demonstrated that resistive respiratory muscle training (RMT) can enhance both sleep quality and cardiovascular health in individuals diagnosed with obstructive sleep apnea, underscoring its efficacy as a non-pharmacological therapeutic strategy for this patient group. However, the effects of RMT on sleep and cardiovascular parameters have not been investigated in non-clinical populations. MethodsThis prospective study investigated the effects of combined inspiratory and expiratory RMT (cRMT) on sleep parameters and cardiovascular biometrics, specifically heart rate variability (HRV), in a non-clinical adult cohort. Utilizing a wearable device for remote data collection, this randomized controlled trial included 67 participants divided into good and poor sleeper groups based on historical sleep data. During a five-week intervention period, participants in the intervention group underwent cRMT using a Breather Fit device, while control group participants did not receive the intervention. ResultsStudy findings demonstrate a significant increase in overnight HRV metrics during the intervention period compared to the baseline, indicating improved autonomic cardiac function. However, no significant changes were observed in any parameters of sleep quality. ConclusionThese results suggest that cRMT may enhance cardiovascular health by improving autonomic function in non-clinical populations without directly affecting sleep quality. This study underscores the potential of RMT as a non-pharmacological intervention to improve cardiovascular health, warranting further investigation in future studies. Brief summaryO_LICurrent Knowledge/Study Rationale: Insufficient, disrupted, or ineffective sleep is prevalent and can increase the risk of developing cardiovascular disease (CVD). While respiratory muscle training has been found effective in improving sleep and cardiovascular parameters in sleep apnea, its effect in healthy people with or without sleep issues is unknown. C_LIO_LIStudy Impact: This study demonstrates significant benefits of RMT on CVD metrics including HR and HRV, indicating improved autonomic cardiac function. These findings highlight the potential of RMT as a non-pharmacological intervention to improve cardiovascular health. C_LI

physiology↗

bioRxiv2025

Phylo-rs: an extensible phylogenetic analysis library in Rust

We introduce Phylo-rs: a fast, extensible, general-purpose library for phylogenetic analysis and inference written in the Rust programming language. Phylo-rs leverages a combination of speed, memory-safety, and native WebAssembly support offered by Rust to provide a robust set of memory-efficient data structures and elementary phylogenetic algorithms. Phylo-rs is focused on efficient and convenient deployment of software aimed at large-scale phylogenetic analysis and inference. Phylo-rs is available under an open-source license on GitHub at https://github.com/sriram98v/phylo-rs, with documentation available at https://docs.rs/phylo/latest/phylo/.

bioinformatics↗

bioRxiv2025

Pooled long-read sequencing for structural variant characterization in schistosome populations

Pooled sequencing provides a rapid cost-effective approach to assess genetic variation segregating within populations of organisms. However, such studies are typically limited to single nucleotide variants and small indels ([≤] 50bp), and have not been used for structural variants (SVs; >50bp) which impact large portions of most genomes and may significantly impact phenotype. Here, we examined SVs circulating in five laboratory populations of the human parasite Schistosoma mansoni by generating long-read sequences from pools of worms (92 -152 per population). We were able identify and genotype 17,446 SVs, representing 6.5% of the genome despite challenges in identifying low frequency variants. SVs included deletions (n=8,525), duplications (n=131), insertions (n=8,410), inversions (n=311), and translocations (n=69) and were enriched in repeat regions. More than half (59%) of the SVs were shared between [≥]4 populations, but 12% were found in only one of the five populations. Within this subset, we identified 168 population-specific SVs that were at-or-near fixation (>95% alternate allele frequency) in one population but missing (<5%) in the other four populations. Five of these variants impact the coding sequence of 6 genes. We also identified 8 SVs with extreme allele frequency differences between populations within quantitative trait loci for biomedically important pathogen phenotypes (drug resistance, larval stage production) identified in prior genetic mapping studies. These results demonstrate that long-read sequence data from pooled individuals is a viable method to quickly catalogue SVs circulating within populations. Furthermore, some of these variants may be responsible for, or linked to, regions experiencing, population-specific directional selection. Significance StatementStructural variants (SVs) are large genomic variants that are frequently overlooked despite being the largest source of genetic variation within a population. This is because large SVs are expensive and difficult to genotype relative to single nucleotide variants or small indels, so are typically overlooked in population studies. This study attempts to solve these problems by using pooled samples and long-read sequencing to survey SVs circulating in five laboratory populations of the human parasite, Schistosoma mansoni. We were able to identify 17,446 SVs that impact 6.5% of the genome. A number of these SVs may be linked to population-specific adaptations. We also found 8 SVs that were associated with known parasitic traits from previous studies. This work highlights the value of long-read sequencing of pooled samples to document genetic diversity and provides a new method for exploring the role of SVs in parasite evolution and pathogenicity.

genomics↗

bioRxiv2024

Dynamic cell fate plasticity and tissue integration drive functional synovial joint regeneration

Adult mammalian synovial joints have limited regenerative capacity, where injuries heal with mechanically inferior fibrotic tissues. Here we developed a unilateral whole-joint resection model in adult zebrafish to advance our understanding of how to stimulate regrowth of native synovial joint tissues. Using a combination of microCT, histological, live imaging, and single-cell RNA sequencing (scRNAseq) approaches after complete removal of all joint tissues, we find de novo regeneration of articular cartilage, ligament, and synovium into a functional joint. Clonal lineage tracing and scRNAseq implicate a multipotent, neural crest-derived population in the adult skeleton as a cell source for these regenerating tissues. Together, our findings reveal latent molecular and cellular programs within the adult skeleton that are deployed to regenerate a complex joint with lubricated articular cartilage.

developmental biology↗

bioRxiv2024

Host population structure and rare dispersal events drive leptospirosis transmission patterns among Rattus norvegicus in Boston, Massachusetts, US

Leptospirosis (caused by pathogenic bacteria in the genus Leptospira) is prevalent worldwide but more common in tropical and subtropical regions. Transmission can occur following direct exposure to infected urine from reservoir hosts, such as rats, or a urine-contaminated environment, which then can serve as an infection source for additional rats and other mammals, including humans. The brown rat, Rattus norvegicus, is an important reservoir of leptospirosis in urban settings. We investigated leptospirosis among brown rats in Boston, Massachusetts and hypothesized that rat dispersal in this urban setting influences the movement, persistence, and diversity of Leptospira. We analyzed DNA from 328 rat kidney samples collected from 17 sites in Boston over a seven-year period (2016-2022); 59 rats representing 12 of 17 sites were positive for Leptospira. We used 21 neutral microsatellite loci to genotype 311 rats and utilized the resulting data to investigate genetic connectivity among sampling sites. We generated whole genome sequences for 28 Leptospira isolates obtained from frozen and fresh tissue from some of the 59 Leptospira-positive rat kidneys. When isolates were not obtained, we attempted Leptospira genomic DNA capture and enrichment, which yielded 14 additional Leptospira genomes from rats. We also generated an enriched Leptospira genome from a 2018 human case in Boston. We found evidence of high genetic structure and limited dispersal among rat populations that is likely influenced by major roads and/or other unknown dispersal barriers, resulting in distinct rat population groups within the city; at certain sites these groups persisted for multiple years. We identified multiple distinct phylogenetic clades of L. interrogans among rats, with specific clades tightly linked to distinct rat populations. This pattern suggests L. interrogans persists in local rat populations and movement of leptospirosis in this urban rat community is driven by rat dispersal. Finally, our genomic analyses of the 2018 human leptospirosis case in Boston suggests a link to rats as the source. These findings will be useful for guiding rat control and human leptospirosis mitigation efforts in this and other urban settings.

molecular biology↗

bioRxiv2023

A single locus determines praziquantel response in Schistosoma mansoni

We previously performed a genome-wide association study (GWAS) to identify the genetic basis of praziquantel (PZQ) response in schistosomes, identifying two quantitative trait loci (QTL) situated on chromosome 2 and chromosome 3. We reanalyzed this GWAS using the latest (v10) genome assembly showing that a single locus on chromosome 3, rather than two independent loci, determines drug response. These results reveal that praziquantel response is monogenic and demonstrates the importance of high-quality genomic information.

genetics↗

bioRxiv2023

An FPGA-based hardware accelerator supporting sensitivesequence homology filtering with profile hidden Markovmodels

BackgroundSequence alignment lies at the heart of genome sequence annotation. While the BLAST suite of alignment tools has long held an important role in alignment-based sequence database search, greater sensitivity is achieved through the use of profile hidden Markov models (pHMMs). The Forward algorithm that provides much of pHMMs sensitivity is relatively slow, motivating extensive efforts to increase speed. Numerous researchers have devised methods to improve pHMM alignment speed using hardware accelerators such as graphics processing units (GPUs) and field programmable gate arrays (FPGAs). Here, we describe an FPGA hardware accelerator for a key bottleneck step in the analysis pipeline employed by the popular pHMM aligment tool, HMMER. HMMER accelerates pHMM Forward alignment by screening most sequence with a series of filters that rapidly approximate the result of computing full Forward alignment. The first of these filters, the Single Segment ungapped Viterbi (SSV) algorithm, is designed to filter out 98% of non-related inputs and accounts for 70% of the overall runtime of the DNA search tool nhmmer in common use cases. SSV is an ideal target for hardware acceleration due to its limited data dependency structure. ResultsWe present Hardware Accelerated single segment Viterbi Additional Coprocessor (HAVAC), an FPGA-based hardware accelerator for the SSV algorithm. The core HAVAC kernel calculates the SSV matrix at 1739 GCUPS on a Xilinx Alveo U50 FPGA accelerator card, [~] 227x faster than the optimized SSV implementation in nhmmer. Accounting for PCI-e data transfer data processing, HAVAC is 65x faster than nhmmers SSV with one thread and 35x faster than nhmmer with four threads, and uses [~] 31% the energy of a traditional high end Intel CPU. Because these computations are performed on a co-processor, the host CPU remain free to simultaneously compute downstream pHMM alignment and later post-processing. Author summarySequence alignment lies at the heart of genome sequence annotation, and must be both fast and accurate. Signals of relationships between sequences are obscured over time by mutational forces, so that alignment and annotation of the full diversity of life demands highly sensitive tools. Profile hidden Markov models (pHMMs) provide the greatest sensitivity in the face of diversity, but are relatively slow. Here, we describe an approach to improving the speed of pHMM search that leverages field programmable gate arrays - hardware devices that can be configured to implement arbitrary digital circuits to achieve impressive parallelism and energy efficiency. Our tool, HAVAC, accelerates one key bottleneck step in the analysis pipeline employed by the popular pHMM aligment tool, HMMER. HAVAC produces a [~] 60x speedup over the analogous stage in HMMER. HAVAC can be implemented as a part of a larger sequence homology search tool for faster search times and reduced energy usage. Interested users can download HAVAC on github at https://github.com/TravisWheelerLab/HAVAC.

bioinformatics↗

bioRxiv2023

Ligament injury in adult zebrafish triggers ECM remodeling and cell dedifferentiation for scar-free regeneration

After traumatic injury, healing of mammalian ligaments is typically associated with fibrotic scarring as opposed to scar-free regeneration. In contrast, here we show that the ligament supporting the jaw joint of adult zebrafish is capable of rapid and complete scar-free healing. Following surgical transection of the jaw joint ligament, we observe breakdown of ligament tissue adjacent to the cut sites, expansion of mesenchymal tissue within the wound site, and then remodeling of extracellular matrix (ECM) to a normal ligament morphology. Lineage tracing of mature ligamentocytes following transection shows that they dedifferentiate, undergo cell cycle re-entry, and contribute to the regenerated ligament. Single-cell RNA sequencing of the regenerating ligament reveals dynamic expression of ECM genes in neural-crest-derived mesenchymal cells, as well as diverse immune cells expressing the endopeptidase-encoding gene legumain. Analysis of legumain mutant zebrafish shows a requirement for early ECM remodeling and efficient ligament regeneration. Our study establishes a new model of adult scar-free ligament regeneration and highlights roles of immune-mesenchyme cross-talk in ECM remodeling that initiates regeneration. HighlightsO_LIRapid regeneration of the jaw joint ligament in adult zebrafish C_LIO_LIDedifferentiation of mature ligamentocytes contributes to regeneration C_LIO_LIscRNAseq reveals dynamic ECM remodeling and immune activation during regeneration C_LIO_LIRequirement of Legumain for ECM remodeling and ligament healing C_LI

molecular biology↗

bioRxiv2023

Dynamic Effects of Ventral Hippocampal NRG3/ERBB4 Signaling on Nicotine Withdrawal-Induced Responses

Tobacco smoking remains a leading cause of preventable death in the United States, with a less than 5% success rate for smokers attempting to quit. High relapse rates have been linked to several genetic factors, indicating that the mechanistic relationship between genes and drugs of abuse is a valuable avenue for the development of novel smoking cessation therapies. For example, various single nucleotide polymorphisms (SNPs) in the gene for neuregulin 3 (NRG3) and its cognate receptor, the receptor tyrosine-protein kinase erbB-4 (ERBB4), have been linked to nicotine addiction. Our lab has previously shown that ERBB4 plays a role in anxiety-like behavior during nicotine withdrawal (WD); however, the neuronal mechanisms and circuit-specific effects of NRG3-ERBB4 signaling during nicotine and WD are unknown. The present study utilizes genetic, biochemical, and functional approaches to examine the anxiety-related behavioral and functional role of NRG3-ERBB4 signaling, specifically in the ventral hippocampus (VH). We report that 24hWD from nicotine is associated with altered synaptic expression of VH NRG3 and ERBB4, and genetic disruption of VH ErbB4 leads to an elimination of anxiety-like behaviors induced during 24hWD. Moreover, we observed attenuation of GABAergic transmission as well as alterations in Ca2+-dependent network activity in the ventral CA1 area of VH ErbB4 knock-down mice during 24hWD. Our findings further highlight contributions of the NRG3-ERBB4 signaling pathway to anxiety-related behaviors seen during nicotine WD.

neuroscience↗