Biology subjects

Thapa, S.

Publications and source records attributed to Thapa, S..

At least 19 recordsLinked to original sources

bioRxiv2026

Isolation of postnatal human neural stem cells

While it was once thought that neurogenesis is complete by birth, it is now apparent that the human brain continues to generate new neurons postnatally, at least into childhood. While much attention has been focused on postnatally-born neurons, their presumed progenitor - the postnatal neural stem cell (NSC) - remains poorly characterized. Using index sorting, we identify and prospectively isolate two subsets of NSCs from the postnatal human brain, and describe their differentiation dynamics using clonal barcoding and in vivo xenotransplantation. We demonstrate an A2B5+EGFR+ population biased towards interneuron and oligodendrocyte fates (NINO), and an A2B5-EGFRhi population biased towards an astrocyte fate (NAC). Profiling of human brains across lifespan shows that the frequency of NSCs declined exponentially across the first two decades of life, but stabilized thereafter, still present in the brains of donors as old as 90 years. Our study provides a framework for the functional study of postnatal human NSCs and their potential roles in development, aging, and disease.

neuroscience↗

bioRxiv2026

A Human Vocal Fold Organ-On-Chip for Studying Platform-Dependent Mucosal Responses to Particulate Matter

BackgroundCoarse particulate matter (PM10) deposits at the vocal fold (VF) mucosa, yet upper airway responses remain poorly characterized. Existing in vitro VF models use monocultures that lack the stratified epithelium, lamina propria, and physiological perfusion. We developed a chip-based co-culture model of human VF mucosa and applied it to acute PM10 exposure. MethodsVocal fold organ-on-chip (VF-OOC) paired primary VF fibroblasts with either immortalized laryngeal epithelial cells (iLEC) or induced pluripotent stem cells (iPSC)-derived VF epithelial cells. Transwell and 2D chip cultures were controls. Epithelia matured at an air-liquid interface on fibroblast-embedded collagen over a perfused microchannel. PM10 urban dust (0 to 400 {micro}g/mL) was applied for 24 hours. Responses were assessed by histology, immunofluorescence, transmission electron microscopy, qPCR, and ELISA. ResultsVF-OOC produced a thicker stratified epithelium with upregulated barrier, mucin, and extracellular matrix genes versus transwell controls. Intercellular junctions and basement membrane matched adult human VF mucosa. PM10 remained at the epithelial surface across all doses. TranswelliLEC downregulated basal markers (TP63, KRT5, KRT14). VF-OOCiLEC upregulated MUC1 and HAS3, consistent with an adaptive mucosal response. VF-OOCiPSC additionally induced suprabasal, junctional, extracellular matrix, and cytokine genes largely absent in iLEC and transwell formats. ConclusionsVF-OOC reproduced key features of native human VF mucosa and captured distinct, platform-specific responses to PM10 that differed by epithelial cell source. By introducing new approach methodologies (NAMs) into laryngology, this platform extends respiratory toxicology to the upper airway beyond bronchial and alveolar compartments and allows mechanistic studies of exposure-linked diseases such as laryngitis.

cell biology↗

bioRxiv2026

Rubicon modulates neuroimmune responses following traumatic brain injury

Traumatic brain injury (TBI) elicits robust neuroinflammation and oxidative stress, coupled with an acute inhibition of macro-autophagy (autophagy) in neurons and microglia. Rubicon (Rubcn), a Beclin1 interacting protein that suppresses autophagy and mediates LC3-associated phagocytosis and endocytosis (LAP/LANDO), influences inflammatory signaling in metabolic, neurodegenerative, and inflammaging diseases; yet its role in acquired brain injury has not been defined. Using a controlled cortical impact model, we investigated the role of Rubicon in acute neuroinflammatory responses following injury by comparing wild-type and Rubcn-mutant mice. Bulk-RNA sequencing of injured cortex revealed attenuated induction of inflammatory pathways and reduced activation of pro-inflammatory microglial/macrophage phenotype in injured Rubcn-mutant mice. Rubcn-mutant mice demonstrated less pronounced inhibition of autophagy during the acute phase of injury. Although the inflammatory dicerences were transient, Rubicon mutant mice exhibited improved motor coordination and gait stability during recovery. Proteomic analyses revealed the presence of a truncated Rubicon protein in the mutant mice and identified the negative regulator of reactive oxygen species (NRROS) as a novel interactor of Rubicon. Consistent with this interaction, Rubcn-mutant mice displayed markedly reduced oxidative damage, indicated by decreased lipid peroxidation after injury. Together, these findings indicate that Rubicon promotes acute neuroinflammatory and oxidative stress responses following TBI by modulating autophagy and ROS production. Rubicon mediated pathways may serve as therapeutic targets that ocer a neuroprotective strategy to improve outcomes after TBI.

neuroscience↗

bioRxiv2026

SpliceRead: Improving Canonical and Non-Canonical Splice Site Prediction with Residual Blocks and Synthetic Data Augmentation

Accurate splice site prediction is fundamental to understanding gene expression and its associated disorders. However, most existing models are biased toward frequent canonical sites, limiting their ability to detect rare but biologically important non-canonical variants. These models often rely heavily on large, imbalanced datasets that fail to capture the sequence diversity of non-canonical sites, leading to high false-negative rates. Here, we present SpliceRead, a novel deep learning model designed to improve the classification of both canonical and non-canonical splice sites using a combination of residual convolutional blocks and synthetic data augmentation. SpliceRead employs a data augmentation method to generate diverse non-canonical sequences and uses residual connections to enhance gradient flow and capture subtle genomic features. Trained and tested on a multi-species dataset of 400- and 600-nucleotide sequences, SpliceRead consistently outperforms state-of-the-art models across all key metrics, including F1-score, accuracy, precision, and recall. Notably, it achieves a substantially lower non-canonical misclassification rate than baseline methods. Extensive evaluations, including cross-validation, cross-species testing, and input-length generalization, confirm its robustness and adaptability. SpliceRead offers a powerful, generalizable framework for splice site prediction, particularly in challenging, low-frequency sequence scenarios, and paves the way for more accurate gene annotation in both model and non-model organisms.The open sourced code of SpliceRead and a detailed documentation is available at The open-sourced code of SpliceRead and detailed documentation are available at https://github.com/OluwadareLab/SpliceRead.

bioinformatics↗

bioRxiv2026

ASPECT: Alternative Splicing Event Classification with Transformers

MotivationAlternative splicing (AS) is a fundamental regulatory mechanism that expands transcriptomic and proteomic diversity by generating multiple mRNA isoforms from a single gene. Aberrant AS has been implicated in numerous diseases through the production of dysfunctional or pathogenic protein variants. However, much of the existing AS research has focused predominantly on exon skipping and constitutive splicing, with comparatively limited attention to other biologically relevant AS event types. Moreover, many current computational approaches rely on short genomic sequence windows and conventional deep learning architectures, which may limit their ability to capture broader regulatory context associated with complex splicing decisions. Bridging these methodological and conceptual gaps is essential for advancing comprehensive AS characterization and improving our understanding of its role in human health and disease. ResultsWe present ASPECT, an alternative splicing event classification framework built upon DNABERT-2 with Byte Pair Encoding (BPE) tokenization. Across multiple binary alternative splicing event pair classification tasks, ASPECT achieves consistently strong performance as measured by AUC, F1-score,and accuracy, demonstrating reliable discrimination between closely related splicing event types. Importantly, ASPECT demonstrates consistent performance when applied to TCGA BRCA cancer-associated splicing events reconstructed from SpliceSeq annotations, supporting its applicability beyond the canonical splicing events used for training. AvailabilityThe open-source code, data, and detailed documentation used in this study are available at https://github.com/OluwadareLab/ASPECT. ContactOluwatosin.Oluwadare@unt.edu Supplementary informationN/A

bioinformatics↗

bioRxiv2025

Harnessing Lytic Phages for Biofilm Control in Carbapenem-Resistant Klebsiella pneumoniae Causing Urinary Tract Infection

BackgroundKlebsiella pneumoniae is a major opportunistic pathogen with rising multidrug resistance and biofilm-related infections. Molecular and phage characterization is crucial to understand resistance mechanisms and explore alternative therapies such as phage therapy. MethodsWe performed whole-genome sequencing and antibiotic susceptibility testing of hospital-isolated Klebsiella pneumoniae (KP6697). MLST, plasmid replicon analysis, and resistance gene identification were conducted using bioinformatics. Phage isolation, electron microscopy-based morphological and biofilm analysis, and evaluation of lytic activity, stability, and host range were performed. Phage genome sequencing and annotation identified functional genes. ResultsThe host strain Klebsiella pneumoniae (KP6697) was multidrug-resistant, exhibiting resistance to 18 of 22 tested antibiotics, and genome analysis identified ST16 with eight plasmid replicons and 23 resistance genes, including blaCTX-M-15, blaNDM-5, and blaOXA-181. Functional annotations revealed extensive metabolic versatility and a rich repertoire of genes for biofilm formation, quorum sensing, secretion systems, and stress response. A lytic phage, Phage_KP6697_Omshanti, was isolated and classified as a Caudoviricetes member with a 45.3kb genome encoding lysis, replication, and structural genes. It demonstrated short latency, high burst size, thermal and pH stability, and broad host range against CRKP and other MDR strains. Importantly, microscopy confirmed its ability to inhibit and degrade biofilms at multiple stages, highlighting strong therapeutic potential. ConclusionComprehensive analysis of carbapenem-resistant K. pneumoniae (KP6697) revealed multidrug resistance and strong biofilm formation. The lytic phage Phage_KP6697_Omshanti, with depolymerase and endolysin activity, disrupted biofilms, and its stability, high burst size, and genomic traits suggest potential as an anti-CRKP agent, especially with antibiotics IMPORTANCEKlebsiella pneumoniae is increasing multidrug resistance and robust biofilm formation pose severe clinical challenges, limiting treatment options. Understanding the molecular basis of its resistance and exploiting bacteriophages with strong biofilm-disrupting properties provide promising alternative therapeutic strategies. This study highlights the isolation and genomic characterization of a lytic phage with potent anti-biofilm activity against carbapenem-resistant K. pneumoniae, underscoring its potential in combating resistant infections.

microbiology↗

bioRxiv2025

Lysosomal multi-omics reveals altered sphingolipid catabolism as driver of lysosomal dysfunction in the aging brain.

Recent data indicate that lipid composition has profound influence on the brain function and that changes in lipid homeostasis affect brain aging and predisposition to neurodegenerative diseases. Lipids dynamically reside in multiple intracellular locations and their organellar distribution is important for specific interactions and biological function. During brain aging lipid changes have been specifically noted in lysosomes, but the identity of the accumulated lipids, their interactions with other biomolecules such as proteins, and their functional relevance have not been characterized. We used mass spectrometry (MS) to assess longitudinal changes in the lipidome and proteome of lysosomes isolated from the mouse cortex, from the age of 3- to 24-months. Our statistical and machine learning analyses identified two factors demonstrating predictive power for age and differences in both lipids and proteins. Of these, factor 1 was the best predictor of sample age. Factor 1 lipids with the highest feature importance included multiple species of hexosylceramides (HexCer) and their sulfonated derivatives, sulfatides (SHexCer), all of which increased with age. Increased factor 1 proteins included myelin proteins, select sphingolipid catabolism enzymes and proteins associated with lysosomal storage diseases. Our analyses suggested that mechanisms underlying factor 1 encompass the combination of an age-dependent increase in lysosomal delivery of myelin components and alterations in lysosomal sphingolipid catabolism favoring degradation of sphingomyelin over HexCer. The overall age-related lysosomal changes resembled those observed in lysosomal storage diseases, particularly Gaucher disease, where accumulation of HexCer species is associated with lysosomal dysfunction. To corroborate factor 1 predictions, we employed a combination of biochemical, imaging and flow cytometry approaches, which confirmed alterations in sphingolipid catabolism and lysosomal accumulation of myelin components. These changes were associated with age-related alteration in lysosomal morphology, lysosomal dysfunction and inhibition of autophagy in both neurons and microglia. Our findings indicate that factors contributing to lysosomal aging resemble those observed in lysosomal storage diseases and underscore the significance of organelle-specific analyses for dissecting mechanisms contributing to brain aging.

neuroscience↗

bioRxiv2025

Inhibition of autophagy-lysosomal function exacerbates microglial and monocyte lipid metabolism reprograming and dysfunction after brain injury

CNS has an overall higher level of lipids than all tissues except adipose and contains up to 25% of total body cholesterol. Recent data demonstrate a complex crosstalk between lipid metabolism and inflammation, suggesting potential contribution of the lipid-rich brain environment to neuroinflammation. While recent data support the importance of brain lipid environment to inflammatory changes observed in age related chronic neurodegenerative diseases, in vivo interactions between lipid environment, lipid metabolism and neuroinflammation in acute brain disease and injury remain poorly understood. Here we utilize a mouse model of traumatic brain injury (TBI) to demonstrate that acute neurotrauma leads to widespread lipid metabolism reprograming in all microglial and brain associated and infiltrating monocyte populations. Additionally, we identify unique microglial and monocyte populations with higher degree of lipid metabolism reprograming and pronounced accumulation of neutral storage lipids, including cholesteryl esters and triglycerides. These lipids accumulate not only in lipid droplets but also in the microglial and monocyte lysosomes and are associated with lysosomal dysfunction and inhibition of autophagy after TBI. Our data indicate that lipid accumulation in these cells is the result of altered lipid handling rather than lipid synthesis and is triggered by phagocytosis of lipid-rich myelin debris generated after TBI. Finally, we use mice with autophagy defects in microglia and monocytes to demonstrate that further inhibition of autophagy leads to more pronounced lipid metabolism reprograming and exacerbated cellular lipid accumulation. Our data suggest a pathological feedback loop, where lipid phagocytosis causes inhibition of autophagy-lysosomal function, which in turn exacerbates cellular lipid retention, reprograming and inflammation.

neuroscience↗

bioRxiv2025

rapunzel5 is necessary for normal hematopoietic development in zebrafish

The molecular mechanisms regulating the highly complex process of hematopoiesis in vertebrates is still enigmatic. This system begins with the controlled differentiation of adult hematopoietic stem and progenitor cells (HSPCs), which can proliferate and generate all types of mature blood cells. Identifying the underlying factors and mechanisms that allow HSPCs to differentiate and proliferate is an essential issue in stem cell biology and tissue homeostasis; disruptions in these processes can cause severe diseases. A transcriptomic screen of hematopoietic-supportive zebrafish stromal tissues identified rapunzel5 (rpz5) was likely involved in vertebrate hematopoiesis. We performed loss-of-function experiments in zebrafish embryos at the one-cell-stage with morpholinos to determine if blood cell production was affected by rpz5. rpz5 knockdown resulted in reduced amounts of red blood cells, myeloid cells, and thrombocytes, and adding back exogenous rpz5 rescued these deficiencies. Further analysis with methylcellulose assays indicated that there was also a significant reduction in HSPCs following rpz5 reduction. Together, these findings suggest that zebrafish rpz5 is essential for normal formation, differentiation, and proliferation of HSPCs, specifically down the erythroid and myeloid pathway. Fully understanding the roles of novel genes such as rpz5 is essential for understanding the evolution of vertebrate hematopoiesis and for treating hematological diseases in the future.

genetics↗

bioRxiv2024

Horizontal transfer of nuclear DNA in transmissible cancer

Although somatic cell genomes are usually entirely clonally inherited, nuclear DNA exchange between cells of an organism can occur sporadically by cell fusion, phagocytosis or other mechanisms1-3. This phenomenon has long been noted in the context of cancer, where it could be envisaged that DNA horizontal transfer plays a functional role in disease evolution4-13. However, an understanding of the frequency and significance of this process in naturally occurring tumours is lacking. The host-tumour genetic discordance of transmissible cancers, malignant clones which pass between animals as allogeneic grafts, provides an opportunity to investigate this. We screened for host-to-tumour horizontal transfer of nuclear DNA in 174 tumours from three transmissible cancers affecting dogs and Tasmanian devils, and detected a single instance in the canine transmissible venereal tumour (CTVT). This involved introduction of a 15-megabase dicentric genetic element, composed of 11 rearranged fragments of six chromosomes, to a CTVT sublineage occurring in Asia around 2,000 years ago. The element forms the short arm of a small submetacentric chromosome, and derives from a dog with ancestry associated with the ancient Middle East. The introduced DNA fragment is transcriptionally active and has adopted the expression profile of CTVT. Its 143 genes do not, however, confer any obvious advantage to its spatially restricted CTVT sublineage. Our findings indicate that nuclear DNA horizontal transfer, although likely a rare event in tumour evolution, provides a viable mechanism for the acquisition of genetic material in naturally occurring cancer genomes.

cancer biology↗

bioRxiv2024

Preventing escape and malfunction of recoded cells due to tRNA base changes

Engineering the genetic code restricts DNA transfer (cellular bioisolation) and enables new chemistries via non-standard amino acid incorporation. These distinct properties make recoded cells state-of-the-art safe technologies. However, evolutionary pressures may endanger the longevity of the recoding. Here, we reveal that recoded Escherichia coli lacking 18,214 serine codons and two tRNASer can express wild-type antibiotic resistance genes and escape up to seven orders of magnitude faster than expected. We show a two-step escape process whereby recoded cells mistranslate antibiotic resistance genes to survive until modified or mutated tRNAs reintroduce serine into unassigned codons. We developed genetic-code-sensitive kill switches that sense serine incorporation and prevent cellular escape while preserving encoding of three distinct non-standard amino acids. This work lays the foundation for the long-term controlled function of cells that incorporate new chemistries, with implications for the design, use, and biosafety of synthetic genomes in clinical and environmental applications where physical containment is insufficient.

synthetic biology↗

bioRxiv2024

Prevalence of Class 1 integron in disease-causing carbapenem-resistant Escherichia coli in a tertiary hospital in Kathmandu, Nepal

BackgroundHigh prevalence of carbapenem resistance genes have been abundantly reported within clinical E. coli in Nepal but their co-prevalence with class-1 integron is poorly documented. These Class I Integrons play pivotal role in evolution and spread of antimicrobial resistance (AMR). Therefore, it is necessary to highlight their epidemiological significance, so this study determined the prevalence of Class 1 integrons within Carbapenem resistance Escherichia coli (CREc) population. MethodsFifty-two clinical E. coli with confirmed resistance to Meropenem were collected between January 2020-April 2022 in Kathmandu Model Hospital, and undergone antimicrobial susceptibility testing for 11 antimicrobial classes. Carbapenemase production was confirmed by eCIM and mCIM methods. Presence of Class I integron and carbapenemase genes, blaNDM-1, blaKPC, blaIMP, blaVIM, blaOXA-23, blaOXA-48, was confirmed by PCR method. ResultsThe result revealed 92.3% (n=48/52) of the isolates harbored intI1 gene. Among integron-positive population, 97.9% (n=47/48) were carbapenemase producers which were further identified as metallo {beta}-lactamase (MBL) producers (82.9%, n=39/47) and serine {beta}-lactamase (SBL) producer (17%, n=8/47). Carbapenemase gene blaNDM-1 (79.2%, n=38/48) was highly prevalent within integron-positive isolates, followed by blaOXA-23 (62.5%, n=30/48) and blaOXA-48 (54.2%, n=26/48). All integron-positive CREc isolates were resistant to minimum 16 antibiotics tested, but were susceptible to Colistin, Polymixin B, and Tigecycline. ConclusionIn conclusion, Class 1 integrons were highly prevalent within clinical CREc in Nepal, and their co-prevalence with other CRE gene is concerning due to possibility of wider spread. Therefore, an in-depth genomic analysis of Class 1 integrons is needed to understand the integron mediated AMR in high risk clones like CREc and inform intervention measures to stop spread of such pathogens.

microbiology↗

bioRxiv2023

Decreased fucosylation impacts epithelial integrity and increases risk for COPD.

COPD causes significant morbidity and mortality worldwide. Epithelial damage is fundamental to disease pathogenesis, although the mechanisms driving disease remain undefined. Published evidence from a COPD cohort (SPIROMICS) and confirmed in a second cohort (COPDgene) demonstrate a polymorphism in Fucosyltransferese-2 (FUT2) is a trans-pQTL for E-cadherin, which is critical in COPD pathogenesis. We found by MALDI-TOF analysis that FUT2 increased terminal fucosylation of E-cadherin. Using atomic force microscopy, we found that FUT2-dependent fucosylation enhanced E-cadherin-E-cadherin bond strength, mediating the improvement in monolayer integrity. Tracheal epithelial cells from Fut2-/- mice have reduced epithelial integrity, which is recovered with reconstitution of Fut2. Overexpression of FUT2 in COPD derived epithelia rescues barrier function. Fut2-/- mice show increased susceptibility in an elastase model of disease developing both emphysema and fibrosis. We propose this is due to the role of FUT2 in proliferation and cell differentiation. Overexpression of FUT2 significantly increased proliferation. Loss of Fut2 results in accumulation of Spc+ cells suggesting a failure of alveolar type 2 cells to undergo transdifferentiation to alveolar type 1. Using a combination of population data, genetically manipulated mouse models, and patient-derived cells, we present a novel mechanism by which post-translational modifications modulate tissue pathology and serve as a proof of concept for the development of a disease-modifying target in COPD.

cell biology↗

bioRxiv2023

Home-field advantage affects the local adaptive interaction between Andropogon gerardii ecotypes and rhizobiome

Due to climate change, drought frequencies and severities are predicted to increase across the United States. Plant responses and adaptation to stresses depend on plant genetic and environmental factors. Understanding the effect of those factors on plant performance is required to predict the species responses to environmental change. We used reciprocal gardens planted with distinct regional Andropogon gerardii ecotypes adapted to dry, mesic, and wet environments to characterize their rhizosphere communities using 16S rRNA metabarcode sequencing. Even though the local microbial pool was the main driver of these rhizosphere communities, the significant plant ecotype effect highlighted active microbial recruitment in the rhizosphere driven by ecotype or plant genetic background. Our data also suggest that ecotypes were more successful in recruiting rhizosphere community members unique to their local homesites, supporting the "home field advantage" hypothesis. These unique homesite microbes may represent microbial specialists that are linked to plant stress responses. Further, our data support ecotypic variation in the recruitment of congeneric but distinct bacterial variants, highlighting the nuanced effects of plant ecotypes on the rhizosphere microbiome recruitment. Our results should facilitate expanded studies on understanding the complexity of plant host interactions with local soil microbes and identification of functional potential of recruited microbes. Our study has the potential to aid in predicting ecosystem responses to climate change and the impact of management on restoration practices. ImportanceIn this study, we used reciprocal gardens located across a sharp precipitation gradient to characterize rhizosphere communities of distinct dry, mesic, and wet regional Andropogon gerardii ecotypes. We used16S rRNA amplicon sequencing and focused oligotyping analysis and showed that even though the location was the main driver of the microbial communities, ecotypes could potentially recruit distinct bacterial populations. We showed that different A. gerardii ecotypes were more successful in overall community recruitment and recruitment of microbes unique to the "home" environment, when growing at their "home site". We found evidence for "home field advantage" interactions between the host and associated rhizobiomes, and the capability of ecotypes to recruit specialized microbes that were potentially linked to plant stress responses. Our study provides insights into the understanding of factors effecting the plant adaptation, improving management strategies, and predicting of the future landscape under the changing climate.

microbiology↗

bioRxiv2022

HIV-1 preintegration complex preferentially integrates the viral DNA into nucleosomes containing trimethylated histone 3-lysine 36 modification

HIV-1 DNA integration into the host chromosomes is carried out by the preintegration complex (PIC). The PIC contains the viral DNA, virally encoded integrase enzyme and other critical viral/host factors. The PIC-associated viral DNA is preferentially integrated into gene bodies of actively transcribing genes. Here, we identify a biochemical mechanism underlying the preference of PIC-mediated viral DNA integration (PIC-VDI). Specifically, we observed that the PIC-VDI into human chromatin is preferred over the genomic DNA. Surprisingly, nucleosome core particles without any histone modifications were not preferred for PIC-VDI when compared to the analogous naked DNA. However, PIC-VDI was markedly enhanced with nucleosomes containing the trimethylated histone 3 lysine 36 (H3K36me3), an epigenetic mark linked to HIV-1 DNA integration preference. Interestingly, we observed that nucleosomes with flanking linker DNA promoted PIC-VDI in the presence of LEDGF/p75. We also discovered that nucleosomes with linker DNA and H3K36me3 served as the optimal substrate for PIC-VDI. Mapping of the integration sites within these substrates identified preference of specific regions of the nucleosome core DNA for integration. Finally, we provide biochemical and genetic evidence that histone H1 protein, that condenses the chromatin, negatively regulates HIV-1 DNA integration, consistent with the integration preference for open chromatin structure. Collectively, these results identify the role of specific chromatin marks that drive HIV-1 integration preference and define the optimal substrate requirement for efficient DNA integration by the PIC.

microbiology↗

bioRxiv2021

Bacteria but not fungi communities differ among perennial grassland ecotypic rhizosphere under abiotic environmental stress

Environmental change, especially frequent droughts, is predicted to detrimentally impact the North American perennial grasslands. Consistent dry spells will affect plant communities as well as their associated rhizobiomes, possibly altering the plant host performance under environmental stress. Therefore, there is a need to understand the impact of drought on the rhizobiome, and how the rhizobiome may modulate host performance and ameliorate its response to drought stress. In this study, we analyzed bacterial and fungal communities in the rhizospheres of three ecotypes (dry, mesic, and wet) of a dominant prairie grass, Andropogon gerardii. The ecotypes were established in 2010 in a common garden design and grown for a decade under persistent dry conditions at the arid margin of the species range in Colby Kansas. The experiment aimed to answer whether and to what extent do the different ecotypes maintain or recruit distinct rhizobiomes after ten years in an arid climate. In order to answer this question, we screened the bacterial and fungal rhizobiome profiles of the ecotypes under the arid conditions of western KS as a surrogate for future climate environmental stress using 16S rRNA and ITS2 metabarcoding sequencing. Under these conditions, bacterial communities differed compositionally among the A. gerardii ecotypes, whereas the fungal communities did not. The ecotypes were instrumental in driving the differences among bacterial rhizobiomes, as the ecotypes maintained distinct bacterial rhizobiomes even after ten years at the edge of the host species range. This study will aid us to optimize plant productivity through the use of different ecotypes under future abiotic environmental stress, especially drought.

bioinformatics↗

bioRxiv2021

HIV-1 Mutants that Escape the Cytotoxic T-Lymphocytes are Defective in Viral DNA Integration

ABSTRACT HIV-1 replication is durably controlled in certain untreated HIV-1-infected individuals expressing particular human leukocyte antigens (HLA). These HLAs tag infected cells for elimination by presenting specific viral epitopes to CD8+ cytotoxic T-lymphocytes (CTL). In individuals expressing HLA-B27, CTLs primarily target the capsid protein (CA)-derived KK10 epitope. Selection of CA mutation R264K helps HIV-1 escape the CTL response but severely diminishes virus infectivity. Here we report that the R264K mutation-associated infectivity defect arises primarily from impaired viral DNA integration. Strikingly, selection of the compensatory CA mutation S173A or depletion of host cyclophilin A largely rescues the R264K-associated integration and infectivity defects. Collectively, our study reveals novel mechanistic insights into the fitness defect incurred by an HIV-1 variant escaping a CA-directed CTL response.

microbiology↗

bioRxiv2021

Knockout of E-cadherin in adult mouse epithelium results in emphysema and airway disease

Chronic obstructive pulmonary disease (COPD) is a devastating lung disease, characterized by a progressive decline in lung function, alveolar loss (emphysema), and airflow limitation due to excessive mucus secretion (chronic bronchitis), that can occur even after the injurious agent is removed. It is slated to rise to the 3rd leading cause of death due to chronic disease by 2030 globally, and the 4th leading cause of death due to chronic disease in the USA. While there is substantial evidence indicating loss of E-cadherin in the lung epithelium of patients with COPD, it is not known if this is causal to the disease. We investigated if loss of E-cadherin can result in lung disease using in both in vitro models of primary, differentiated human cells and in mouse models. Using a cell type-specific promoter using Cre/LoxP mice system to knock-out E- cadherin in ciliated and alveolar epithelial cell (Type 1 and Type 2) populations in adult mouse models, we determined that loss of E-cadherin caused airspace enlargement, as well as increased airway hyperresponsiveness indicating that it does have a causative role in causing COPD. Strategies to upregulate CDH1 (encodes for E-cadherin) in CHBEs and cigarette-smoke injured NHBEs can rescue the dysfunctional epithelium.

cell biology↗