Biology subjects

Hussain, T.

Publications and source records attributed to Hussain, T..

At least 19 recordsLinked to original sources

bioRxiv2026

An LSEC-focused computational drug repurposing platform for liver fibrosis: Identification of vorinostat and other LSEC-protective candidates

Liver sinusoidal endothelial cells (LSECs) are increasingly recognized as a critical yet underexplored cell type in anti-fibrotic drug development. This study presents a computational drug screening platform integrating LSEC-specific transcriptomic analysis across simple steatosis, fibrotic nonalcoholic steatohepatitis (NASH), and cirrhosis, with tiered gene signature selection combining machine learning, large language model-assisted curation, gene safety assessment, and Connectivity Map-based screening using human endothelial perturbational profiles. The platform identifies 6 clinical-stage and 8 preclinical candidates with LSEC-protective potential. Among these, vorinostat (SAHA), a clinically approved histone deacetylase (HDAC) inhibitor, is selected for experimental validation. In hepatocyte-specific Asah1-deficient mice fed a Paigen diet, SAHA attenuates hepatic inflammation, fibrosis, LSEC dysfunction, and portal hemodynamic abnormalities, with effects confirmed in a hepatotoxin (CCl4)-induced fibrosis model. High mobility group box 1 (HMGB1) is identified as a key hepatocyte-derived paracrine mediator of LSEC injury through Transwell co-culture and glycyrrhizin rescue. Vorinostat dose-dependently reverses HMGB1-induced LSEC dysfunction across inflammation, capillarization, fibrogenesis, and vasoconstriction, associated with endothelial transcription factor reprogramming including KLF2 upregulation, validated in primary LSECs and in vivo. SAHA also protected LSECs from TNF--induced inflammation and reduced monocyte adhesion. These findings establish an LSEC-focused drug repurposing framework and identify candidates for LSEC-protective anti-fibrotic therapy. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=129 SRC="FIGDIR/small/727430v1_ufig1.gif" ALT="Figure 1"> View larger version (23K): org.highwire.dtl.DTLVardef@41e95dorg.highwire.dtl.DTLVardef@1401031org.highwire.dtl.DTLVardef@e72fc4org.highwire.dtl.DTLVardef@1f11347_HPS_FORMAT_FIGEXP M_FIG C_FIG

pharmacology and toxicology↗

bioRxiv2026

IL-1α drives a tumor-stroma-neutrophil axis through inflammatory fibroblast activation in head and neck cancer

In head and neck squamous cell carcinoma (HNSCC), high tumor-associated neutrophil (TAN) density is a robust biomarker of poor prognosis. TANs predominantly localize to the stroma and their intratumoral density strongly correlates with adverse outcome. Here, we investigated how tumor-stroma communication regulates TAN recruitment, activation, and spatial organization. We identified interleukin-1 (IL-1), released by viable or necrotic tumor cells, as an upstream signal that induces an inflammatory cancer associated fibroblast (iCAF)-like transcriptional program in patient-derived mesenchymal stromal cells (MSCs) of the oral cavity. IL-1-stimulated MSCs secrete factors associated with neutrophil recruitment, survival, and function, together with mediators of extracellular matrix remodeling and angiogenesis. Notably, the IL-1-induced iCAF-like transcriptional program closely resembles CAF subsets in HNSCC that are associated with poor clinical outcome. Functionally, conditioned media from IL-1-stimulated MSCs promoted tumor growth and enhanced polymorphonuclear neutrophil survival, activation, trans-well migration and infiltration into spheroids, in vitro. In zebrafish xenografts, co-injection of IL-1-overexpressing tumor cells and MSCs markedly amplified neutrophil infiltration. TCGA analysis demonstrated robust correlations between the IL-1-induced MSC gene signature and neutrophil signatures across multiple TAN subsets in human HNSCC. Spatial analysis of HNSCC tissues showed that stromal regions adjacent to IL1A-positive tumor islets were enriched for CXCL8/CSF3 double-positive cells and exhibited increased TAN density, including higher frequencies of NE- and MPO-positive neutrophils. Collectively, these findings define an IL-1-dependent tumor-stroma signaling circuit that links tumor inflammation to stromal remodeling and neutrophil infiltration in HNSCC. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=180 SRC="FIGDIR/small/700440v1_ufig1.gif" ALT="Figure 1"> View larger version (47K): org.highwire.dtl.DTLVardef@f8d282org.highwire.dtl.DTLVardef@1c4575aorg.highwire.dtl.DTLVardef@1430cfcorg.highwire.dtl.DTLVardef@1098887_HPS_FORMAT_FIGEXP M_FIG Graphical abstract: IL-1 drives tumor-stroma communication and neutrophil recruitment in HNSCC. Here, we describe a mechanism in HNSCC that promotes high tumor-associated neutrophil (TAN) density, a biomarker associated with poor prognosis. Tumor-derived IL-1 activates stromal cells to adopt an inflammatory phenotype, resulting in the release of CXCL8, GM-CSF, and G-CSF to enhance neutrophil recruitment, activation, and survival. IL1A-positive tumor islets are surrounded by CXCL8/CSF3-rich stroma with elevated TAN densities in both tumor and stromal compartments. These TANs exhibit increased frequencies of MPO- and NE-positive cells, revealing a spatially organized inflammatory tumor microenvironment. Figure was created using BioRender. C_FIG

cancer biology↗

bioRxiv2025

Assessing Drought Resilience and Identification of High Yielding Upland Rice Varieties through Phenology, Growth and Yield Traits

Drought stress is the major yield limiting factor in upland rice production where the moisture availability is highly variable. Understanding and evaluating how upland rice responds to drought stress is critical to improving resilience and yield stability. In this study performance of sixteen upland rice varieties were evaluated under non-stressed, moderately stressed and highly stressed conditions. Drought stress was introduced by irrigating upland rice at 70% and 50% field capacity (FC) whereas non-stress treatment was irrigated at 100% FC. Irrigation in moderately stressed and highly stressed conditions was also withheld for six days at lateral crop stages to observe temporary wilting by inducing a stress interval. Data on agronomic traits of upland rice was collected in three experimental replications. Results indicated that performance of upland rice varieties was significantly altered under stress conditions and highest performance was observed under non-stressed conditions. Yield losses for short duration and long duration varieties ranged 35-60% and 24-62% under moderate stress whereas it ranged 43-78% and 52-73% under highly stressed conditions, respectively. Overall varieties Dawk Kha, Khao/ Sai and Dawk Pa-yawm, indicated higher stability under stressed conditions therefore, these long duration varieties could be used for obtaining better yields under diverse agroclimatic conditions and under unpredicted weather patterns. Short duration Ma-led-nai-fai and long duration Goo Meung Lung and Bow Leb Nahag could be used for acquiring traits for higher tillering and panicle bearing capacity. Short heighted varieties such as Jao Daeng, Sahm Deuan and Ma-led-nai-fai could be used in breeding for short heighted new varieties to overcome lodging concerns. Strong significant association of GMP, STI, MPRO, MHAR with grain yield under non-stressed, moderately stressed and highly stressed conditions indicated that these indices were appropriate for their use as selection criteria for drought resilience.

plant biology↗

bioRxiv2025

Evaluating Field Corn Yield and Plant and Soil Nutrient Concentrations Under Application of Synthetic Fertilizer and Dairy Manure

Application of manure in field corn has the potential to sustain corn yields and reduce nutrient leaching in soil profile. A field trial with randomized complete block design was conducted on Adkins fine sandy loam soil to evaluate the impact of application of manure and synthetic fertilizer on nutrient concentrations (N, P, K and S) in plant and soil and field corn yield. Experimental treatments included an application of synthetic fertilizer (NPK) and dairy manure application at 5-, 10- and 15-tons acre-1 in addition to a non-fertilized control. All the manure was applied before planting. Corn was manually harvested, and plants were separated into leaves, stems and cobs to determine dry weights. Post harvest soil sampling was performed at 0-30, 30-60 and 60-90 cm soil depths. Results indicated that in-season leaf nutrient concentration was significantly different among applied treatments. Application of synthetic fertilizer resulted in the highest plant height (116 in) and produced higher corn yield (45.5 tons acre-1) compared to control and application of dairy manure. Application of manure at 5 tons acre-1 produced higher corn yield (35.5 tons acre-1) compared to manure application at 10 (25.9 tons acre-1) and 15 tons acre-1 (26.1 tons acre-1). A similar trend was observed for leaf, stem and cobs fresh and dry weights. Nutrient recovery was higher under application of synthetic fertilizer followed by application of manure at 5 tons acre-1. Soil nutrient analysis indicated no significant impact on N, P, K and S concentration among treatments except for NH4+-N. However, nutrient concentration significantly varied under different soil depths. Results suggest that a combination of synthetic fertilizer application and manure might be a practical approach for balanced nutrient supply for field corn. Further investigations are necessary to explore the potential of manure application to ensure balanced nutrient supply, improved yields and reduced nutrient losses in field corn. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=134 SRC="FIGDIR/small/676050v1_ufig1.gif" ALT="Figure 1"> View larger version (53K): org.highwire.dtl.DTLVardef@422c9eorg.highwire.dtl.DTLVardef@7f6342org.highwire.dtl.DTLVardef@14dbed5org.highwire.dtl.DTLVardef@12ba515_HPS_FORMAT_FIGEXP M_FIG C_FIG Credit: Photographs taken and experimental data generated by T. Hussain during postdoctoral research at OSU.

plant biology↗

bioRxiv2025

Growth and Yield Response of Soft White Common Spring Wheat (SWCSW) Varieties under Different Nitrogen Fertilizations and Plant Growth Regulators Applications

Application of plant growth regulators (PGRs) is often reported beneficial in wheat to achieve various targets including lodging resistance. However, research evidence on the application of PGRs in Soft White Common Spring Wheat (SWCSW) varieties is limited particularly in Columbia Basin. Therefore, our objectives were to evaluate the effects of PGRs on SWCSW varieties exposed to different nitrogen (N) application levels. Two widely grown SWCSW varieties, Louise and Diva were planted for two growing seasons using split plot design with four replications. Crop growth (stem height and diameter), yield and yield attributes (grain numbers per head, head numbers per fit, grain weight), quality characteristics (test weight, protein content) and lodging score were recorded following the application of PGRs at tillering (GS21-26), stem elongation (GS30-32), and flag leaf emergence (GS37-39) stages combined with high N fertilization. No lodging was observed during first season whereas it was witnessed during second season, and we observed a variable but positive response particularly under application of CC-C, TE, CC-BC and CC-AB. An increase in stem diameter and reduction in stem height were observed under PGR application which indirectly contributed to stem strength and reduced lodging. Although impact of PGRs application on grain numbers, head numbers grain yield and grain weight were non-significant and variable, we observed an improved performance of these attributes such as higher grain yield was observed under application of CC-B and CC-BC. The grain yield of Louise and Diva was similar at low and high N input. These results indicate that application of 168 kg N ha-1 is sufficient for an acceptable grain productivity and to gain agronomic returns. As we observed a significant seasonal impact and variations in the performance of SWCSW varieties, future research should consider long term evaluations to evaluate the impacts of PGRs on soft white common spring wheat varieties.

plant biology↗

bioRxiv2025

Organ-specific immune responses are strain-dependent in a mouse model of Cryptococcus neoformans brain infection

Cryptococcal meningitis remains the top cause of death from an invasive fungal infection in humans, responsible for [~]100,000 deaths annually of vulnerable patients with underlying immune deficiencies. Animal models of cryptococcal meningitis are important for understanding the immune parameters that correlate with protection. However, modelling this infection in mice is challenging. There is wide variability in infection routes, doses and mouse background used in the field, which makes understanding phenotypes of mutants and immune interventions difficult to broadly apply. Our intention was to create a resource for the field on how Cryptococcus neoformans strain influences analysis of organ-specific immune responses in an intravenous mouse model of cryptococcal meningitis, focusing on impact of the fungal strain while keeping mouse genetic background (C57BL/6J) and infection route constant. We quantified myeloid and lymphoid cell recruitment and fungal-specific CD4 T-cell activation, correlating these results with fungal burdens in mice infected with the commonly used reference strain H99 or with two recently isolated clinical strains that were the same molecular type (VNI) or an unrelated type (VNB). We also analysed how dose used in murine infection models affected brain immune responses during C. neoformans infection. Our work reveals intriguing patterns of organ-specific immunity that are dependent on C. neoformans strain but not always explained by virulence potential, raising important questions for the field regarding the impact of C. neoformans strain on cellular immune responses in experimental animal models.

immunology↗

bioRxiv2025

Pulsatile flow dynamics determine pulmonary arterial architecture

Single ventricle congenital heart disease (SV-CHD) is a uniformly lethal condition requiring the Glenn surgery, which as a side effect eliminates arterial pulsatility and contributes to pulmonary vascular complications. In Glenn patients, we quantified pulsatility loss in each dimension of force (flow, pressure, and stretch) using cardiac catheterization and MRI. To model and investigate the individual impact of each dimension of pulsatility loss on the pulmonary vasculature, we applied isolated pulsatile and non-pulsatile mechanical stimuli to pulmonary arterial endothelial cells (ECs) in vitro. We found that each dimension of force triggered distinct transcriptional responses, revealing force-specific regulation of structural and signaling pathways. Pulsatile stretch uniquely stimulated EC secretion of PDGFB, a key driver of vascular smooth muscle cell (vSMC) recruitment. In a rat Glenn model, loss of pulsatility led to vascular wall thinning, confirming in vivo relevance. Our findings uncover a mechanistic link between endothelial stretch sensing and PDGFB-mediated EC-vSMC crosstalk, essential for maintaining pulmonary artery architecture. Clinically, these insights suggest that restoring or mimicking pulsatile forces may help preserve vascular integrity and prevent remodeling in SV-CHD patients.

cell biology↗

bioRxiv2025

Structural insights into the recruitment of viral Type 2 IRES to ribosomal preinitiation complex for protein synthesis

Picornaviruses employ internal ribosome entry sites (IRESs) in their genomic RNA to hijack the hosts translational machinery. The picornavirus, Encephalomyocarditis virus, employs a type 2 IRES present in its 5UTR and requires 43S ribosomal preinitiation complex (PIC), the central domain of eukaryotic initiation factor (eIF) 4G, eIF4A, and an essential ITAF (IRES trans-acting factor)-polypyrimidine tract binding protein 1 (PTB1) to form 48S PIC. In this study, we have used cryo-electron microscopy (cryo-EM) to determine the structure of EMCV IRES-bound mammalian 48S PIC in a scanning-arrested closed state at the start codon. The EMCV IRES domains contacts initiator tRNA (tRNAi) and 40S head at the inter-subunit interface, which reveals an altogether unique mechanism used by viruses to capture host translational machinery for its protein synthesis. The tRNAi is held away from the 40S body in contrast to canonical cap-dependent translation while the domain I apical region of EMCV IRES mimics 28S rRNA of 60S to interact with 40S ribosomal head proteins-uS13 and uS19. The structural analysis account for numerous biochemical studies on Type 2 IRES and shows how Type 2 IRES interacts with 43S PIC to form 48S PIC. This study provides mechanistic insights for understanding EMCV IRES-mediated translation initiation, which could be extrapolated to other IRESs sharing similar motifs and factor requirements including type 1 viral IRESs.

biophysics↗

bioRxiv2025

B-cell-Specific Wwox Deletion Promotes Plasmablastic Tumor Development and Pro-Inflammatory Signatures in a Myeloma Mouse Model

Deletions and translocations affecting WWOX accompanied by loss of expression are frequently observed in B cell neoplasms and are linked to poor prognosis. Our previous research showed that Wwox deletion early in B cell development induces genomic instability, neoplastic transformation, and monoclonal gammopathies in mice. In this study, by crossing Cd19 Wwox knockout (KO) with Vk*MYC myeloma model mice, we generated a model with concurrent Wwox deletion and MYC activation, reproducing two common oncogenic alterations in B and plasma cell cancers. We observed that Vk*MYC:Wwox KO mice exhibited significantly reduced survival rates primarily due to the development of plasmablastic plasmacytomas and lymphomas. Transcriptome profiling from bone marrow derived Cd138+ plasma cells and plasmablastic tumors revealed enrichment of biofunctions related to tumorigenic phenotype and inflammation activation upon Wwox deletion in Vk*MYC mice. Wwox KO plasmablastic tumors displayed mutations affecting classical cancer genes, DNA damage response (DDR) genes, as well as overexpression of Aid/Apobec family members associated to hypermutation and DDR mutational signatures. These findings illustrate the significant pathobiological effects of B cell specific Wwox deletion and support a relevant role for WWOX loss of function in B cell neoplastic progression towards more aggressive phenotypes.

cancer biology↗

bioRxiv2025

Therapeutic Potential of PRMT1 as a Critical Survival Dependency Target in Multiple Myeloma

Multiple myeloma (MM) is a neoplasm of antibody-producing plasma cells and is the second most prevalent hematological malignancy worldwide. Development of drug resistance and disease relapse significantly impede the success of MM treatment, highlighting the critical need to discover novel therapeutic targets. In a custom CRISPR/Cas9 screen targeting 197 DNA damage response-related genes, Protein Arginine N-Methyltransferase 1 (PRMT1) emerged as a top hit, revealing it as a potential therapeutic vulnerability and survival dependency in MM cells. PRMT1, a major Type I PRMT enzyme, catalyzes the asymmetric transfer of methyl groups to arginine residues, influencing gene transcription and protein function through post-translational modification. Dysregulation or overexpression of PRMT1 has been observed in various malignancies including MM and is linked to chemoresistance. Treatment with the Type I PRMT inhibitor GSK3368715 resulted in a dose-dependent reduction in cell survival across a panel of MM cell lines. This was accompanied by reduced levels of asymmetric dimethylation of arginine (ADMA) and increased arginine monomethylation (MMA) in MM cells. Cell cycle analysis revealed an accumulation of cells in the G0/G1 phase and a reduction in the S phase upon GSK3368715 treatment. Additionally, PRMT1 inhibition led to a significant downregulation of genes involved in cell proliferation, DNA replication, and DNA damage response (DDR), likely inducing genomic instability and impairing tumor growth. This was supported by Reverse Phase Protein Array (RPPA) analyses, which revealed a significant reduction in levels of proteins associated with cell cycle regulation and DDR pathways. Overall, our findings indicate that MM cells critically depend on PRMT1 for survival, highlighting the therapeutic potential of PRMT1 inhibition in treating MM.

cancer biology↗

bioRxiv2024

Odoribacter splanchnicus mitigates Salmonella-induced gut inflammation and its associated pathogenesis via its secreted bacteriocin

Foodborne pathogens pose a major global health hazard, worsened by drug-resistant strains. Therefore, designing novel therapeutic strategies is crucial. Here, we identified the protective role of gut-commensal Odoribacter splanchnicus (OS) against Salmonella in mice by promoting colonization resistance, preserving gut barrier integrity, and preventing acute inflammation and biofilm formation. In vitro, both OS and their culture supernatant inhibited Salmonella biofilm formation, intracellular proliferation in human intestinal cells, and virulence gene expression. Further, our results depicted that OSs protective role acts over a broad spectrum as it confers protection against Gram-positive, Listeria monocytogenes and Gram-negative, Salmonella Typhimurium. Notably, OS conferred protection even when administered post-infection in mice, highlighting its therapeutic potential. Using several biochemical and proteomics approaches, we characterized key OS-secreted molecules that limit intracellular Salmonella and Listeria replication in human intestinal epithelial cells by regulating key virulence effectors and flagella. Collectively, our study establishes OS as the broad-spectrum protective agent against Salmonella and Listeria infections, with promising therapeutic potential. Author SummaryFoodborne pathogens such as Salmonella and Listeria continue to threaten global health, especially with the rise of antibiotic resistance. In this study, we identify the gut commensal bacterium Odoribacter splanchnicus (OS) as a potent protectant against these pathogens. Using a mouse model, we show that OS enhances colonization resistance, maintains gut barrier integrity, and prevents both inflammation and biofilm formation during infection. Remarkably, OS also limits pathogen proliferation and virulence gene expression in human intestinal cells. These protective effects are mediated by both live OS and its secreted molecules within culture supernatant. Importantly, OS administration post-infection also conferred protection, indicating strong therapeutic potential. Biochemical and proteomic analyses revealed OS-secreted factors that suppress key virulence and motility pathways in pathogens. Our findings establish Odoribacter splanchnicus as a promising broad-spectrum biotherapeutic agent against major foodborne infections. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=93 SRC="FIGDIR/small/609322v4_ufig1.gif" ALT="Figure 1"> View larger version (33K): org.highwire.dtl.DTLVardef@7ea42corg.highwire.dtl.DTLVardef@4c8074org.highwire.dtl.DTLVardef@855350org.highwire.dtl.DTLVardef@120decc_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

bioRxiv2024

Divergent cytokine and transcriptional signatures control functional T follicular helper cell heterogeneity

Adaptive immune responses protect against multiple classes of pathogens, including viral, bacterial, fungal, and helminth infections. In all these settings, CD4+ T follicular helper (Tfh) cells tailor high-affinity class-switched B cells responses. How Tfh lineage sovereignty is established while allowing for this context-specific functional heterogeneity is unclear. Here, we identify Tfh transcriptional networks in response to diverse infections. While Bcl-6 is the transcriptional linchpin of the core Tfh signature, this is overlayed with pathogen-specific transcriptional modules that shape Tfh function. Cytokine-transcriptional Tfh programing in mouse and human lymphoid tissue demonstrated that type I interferon and TGF{beta} signaling direct individual Tfh subpopulations to instruct B cell output. Here, we provide a transcriptional map and cell surface resource to interrogate Tfh diversity in humans and mice. This resource can be leveraged to further understand the origins of immune flexibility, perform immune monitoring in infection and antibody-mediated diseases and to develop context-specific vaccines. ONE-SENTENCE SUMMARYDalit, Tan and colleagues provide a resource that functionally and transcriptionally profiles T follicular helper cells (Tfh) during diverse pathogen responses to reveal a blueprint for transcriptional flexibility and new tools to interrogate Tfh heterogeneity in mice and humans.

immunology↗

bioRxiv2024

Nuclear pore complexes undergo Nup221 exchange during blood stage asexual replication of Plasmodium parasites.

Plasmodium parasites, the causative agents of malaria, undergo closed mitosis without breakdown of the nuclear envelope. Unlike closed mitosis in yeast, P. berghei parasites undergo multiple rounds of asynchronous nuclear divisions in a shared cytoplasm which results in a multinucleated organism prior to formation of daughter cells within an infected red blood cell. During this replication process, intact nuclear pore complexes (NPCs) and their component nucleoporins play critical roles in parasite growth, facilitating selective bi-directional nucleocytoplasmic transport and genome organization. Here we utilize ultrastructure expansion microscopy (U-ExM) to investigate P. berghei nucleoporins at the single nucleus level throughout the 24-hour blood-stage replication cycle. Our findings reveal that these Nups are evenly distributed around the nuclei and organized in a rosete structure previously undescribed around the centriolar plaque, which is responsible for intranuclear microtubule nucleation during mitosis. By adapting the recombination-induced tag exchange (RITE) system to P. berghei, we provide evidence of NPC maintenance, demonstrating Nup221 turnover during parasite asexual replication. Our data shed light on the distribution of NPCs and their homeostasis during the blood-stage replication of P. berghei parasites. Summary StatementEmploying ultrastructure expansion microscopy and the RITE system, this study unveils Nup221 turnover in nuclear pore complexes of Plasmodium parasites, shedding light on their replication mechanisms.

cell biology↗

bioRxiv2023

Atomic structure of wheat ribosome reveals unique features of the plant ribosomes

Ribosomes from plants have unique plant-specific features that may aid in rapid gene expression and regulation in response to changing environmental conditions due to their sessile nature. Here, we present high-resolution cryo-electron microscopy structures of the 60S and 80S ribosomes from wheat, a monocot staple crop plant (Triticum aestivum). We compare wheat ribosome with closely related ribosomes from a dicot plant and other eukaryotes from yeast to humans. While plant ribosomes have unique plant-specific rRNA modification (Cm1847) in peptide exit tunnel, Zinc-finger motif in eL34 is absent and uL4 is extended making an exclusive interaction network. We note striking differences in eL15-Helix 11 (25S) interaction network, eL6-Expansion segment 7 assembly and certain rRNA chemical modifications between monocot and dicot ribosomes. Among eukaryotic ribosomes, we observe that rRNA modification (Gm75) in 5.8S rRNA is highly conserved and a base flipping (G1506) in peptide exit tunnel, and these features are likely involved in sensing nascent peptide. Finally, we discuss importance of universal conservation of three consecutive rRNA modifications in all ribosomes for their interaction with A-site aminoacyl-tRNA.

plant biology↗

bioRxiv2023

Indigenous cattle of Sri Lanka: Genetic and phylogeographic relationship with Zebu of Indus valley and South Indian origin

The present study reports the population structure, genetic admixture and phylogeography of island cattle breeds of Sri Lanka viz. Batu Harak, Thawalam and White cattle. Moderately high level of genetic diversity was observed. Estimates of inbreeding for Thawalam and White cattle breeds were relatively high with 6.1% and 7.2% respectively. Genetic differentiation of Sri Lankan Zebu (Batu Harak and White cattle) was lowest with Red Sindhi among Indus valley zebu while it was lowest with Hallikar among the South Indian cattle. Global F statistics showed 6.5% differences among all the investigated zebu cattle breeds and 1.9% differences among Sri Lankan zebu breeds. The Sri Lankan zebu cattle breeds showed strong genetic relationships with Hallikar cattle, an ancient breed considered to be ancestor for most Mysore type draught cattle breeds of South India. Genetic admixture analysis revealed high levels of breed purity in Lanka White cattle with >97% zebu ancestry while significant taurine admixture was observed in Batu Harak and Thawalam cattle. Two major zebu haplogroups, I1 and I2 were observed in Sri Lankan zebu with the former predominating the later in all the three breeds. A total of 112 haplotypes were observed in the studied breeds, of which 50 haplotypes were found in Sri Lankan zebu cattle. Mismatch analysis revealed unimodal distribution in all the three breeds indicating population expansion. The sum of squared deviations (SSD) and raggedness index were non-significant in both the lineages of all the three breeds except for I1 lineage of Thawalam cattle (P<0.01) and I2 lineage of Batu Harak cattle (P<0.05). The results of neutrality tests revealed negative Tajimas D values for both the lineages of Batu Harak (P>0.05) and White cattle (P>0.05) indicating an excess of low frequency polymorphisms and demographic expansion. Genetic dilution of native zebu cattle germplasm is a cause for concern and it is imperative that national breeding organizations consider establishing conservation units for the three native cattle breeds to maintain breed purity and initiate genetic improvement programs.

genetics↗

bioRxiv2023

Yeast eukaryotic initiation factor 4B remodels the mRNA entry site on the small ribosomal subunit

Eukaryotic initiation factor 4B (eIF4B) belongs to the eIF4 group of factors that help in mRNA recruitment to the ribosomal preinitiation complex (PIC) in all eukaryotic organisms. eIF4B stimulates the helicase activity of eIF4A and helps in the formation of the 48S PIC by facilitating mRNA recruitment. However, there is no clear understanding of the location of eIF4B on the 40S and how eIF4B helps in the recruitment of mRNAs. In this work using cryo-electron microscopy, we show that yeast eIF4B binds to the 40S ribosomal subunit at the mRNA entry channel making contacts with ribosomal proteins uS10, uS3, and eS10 and ribosomal rRNA helix h16. The yeast eIF4B position on the 40S overlaps with the RRM domain of eIF3g indicating that the binding of eIF4B may trigger the relocation of the eIF3 b-g-i module to the subunit interface. The 40S head is in partially open conformation that may facilitate the release of eIF3j and hence aid mRNA recruitment and scanning. The structural analysis of yeast eIF4B-bound ribosomal complex provides insight into possible events during mRNA recruitment.

biophysics↗

bioRxiv2022

WWOX P47T loss-of-function mutation induces epilepsy, progressive neuroinflammation, and cerebellar degeneration in mice phenocopying human SCAR12

WWOX gene loss-of-function (LoF) has been associated with neuropathologies resulting in developmental, epileptic, and ataxic phenotypes of varying severity based on the level of WWOX dysfunction. WWOX gene biallelic germline variant p.Pro47Thr (P47T) has been causally associated with a new form of autosomal recessive cerebellar ataxia with epilepsy and intellectual disability (SCAR12). This mutation affects the WW1 protein binding domain of WWOX, impairing its ability to interact with canonical proline-proline-X-tyrosine motifs in partner proteins. We generated a mutant knock-in mouse model of Wwox P47T that phenocopies SCAR12. WwoxP47T/P47T mice displayed epilepsy, profound social behavior and cognition deficits, and poor motor coordination, and unlike KO models that survive only for 1 month, live beyond 1 year of age. These deficits progressed with age, and mice became practically immobile, suggesting severe cerebellar dysfunction. WwoxP47T/P47T mice exhibited signs of progressive neuroinflammation with elevated astro-microgliosis that increased with age. The cerebellar cortex displayed significantly reduced molecular and granular layer thickness and a strikingly reduced number of Purkinje cells with degenerated dendrites. Transcriptome profiling from various brain regions from these Wwox LoF mice highlighted widespread changes in neuronal and glial pathways, enrichment of bioprocesses related to neuroinflammation and severe cerebellar dysfunction, activation of pathways compatible with compensatory neurogenesis along with major suppression of gene networks associated with excitability, neuronal cell differentiation and brain development. Our results show significant pathobiological effects and potential mechanisms through which WWOX LoF leads to epilepsy, cerebellar neurodegeneration, neuroinflammation, and ataxia. Additionally, the mouse model described here will be a useful tool for the study of WWOX in common neurodegenerative conditions in which it has been identified as a novel risk factor.

neuroscience↗

bioRxiv2022

The PTEX pore component EXP2 is important for intrahepatic development during the Plasmodium liver stage

During vertebrate infection, obligate intracellular malaria parasites develop within a parasitophorous vacuole which constitutes the interface between the parasite and its hepatocyte or erythrocyte host cells. To transcend this barrier, Plasmodium spp. utilize a dual-function pore formed by EXP2 for nutrient transport and, in the context of the PTEX translocon, effector protein export across the vacuole membrane. While critical to blood stage survival, less is known about EXP2/PTEX function in the liver stage, although major differences in the export mechanism are indicated by absence of the PTEX unfoldase HSP101 in the intrahepatic vacuole. Here, we employed the glucosamine-activated glmS ribozyme to study the role of EXP2 during Plasmodium berghei liver stage development in hepatoma cells. Insertion of the glmS sequence into the exp2 3UTR enabled glucosamine-dependent depletion of EXP2 after hepatocyte invasion, allowing separation of EXP2 function during intrahepatic development from a recently reported role in hepatocyte invasion. Post-invasion EXP2 knockdown reduced parasite size and largely abolished expression of the mid to late liver stage marker LISP2. As an orthogonal approach to monitor development, EXP2-glmS parasites and controls were engineered to express nanoluciferase. Activation of glmS after invasion substantially decreased luminescence in hepatoma monolayers and in culture supernatants at later time points corresponding with merosome detachment that marks the culmination of liver stage development. Collectively, our findings extend the utility of the glmS ribozyme to study protein function in the liver stage and reveal EXP2 is important for intrahepatic parasite development, indicating PTEX components also function at the hepatocyte-parasite interface.

microbiology↗