Biology subjects

Kumar, M.

Publications and source records attributed to Kumar, M..

At least 37 records · Page 2Linked to original sources

bioRxiv2026

Pathology of dose dependent inocula of H5N8 avian influenza viruses in experimentally infected chicken

In the present study, we assessed the pathogenicity of H5N8 avian influenza viruses belongs to the clade 2.3.4.4b in chicken. Birds of three different dose groups, 102, 104, and 106 EID50 were used in the study. No mortality was observed in 102 EID0 group. Percent cumulative mortality of 104 and 106 EID50 group was 66.67 and 100 %, respectively. Varying duration of MDT of 3.2 and 2 days was observed in 104 and 106 EID50 group, respectively. The CID50 of virus was found to be 104.5 EID50. High no. of viral RNA copies were found both in oropharyngeal and cloacal swabs and in various organs of birds infected in 104 and 106 EID50 group. Significant gross and histological changes and presence of viral antigen in various organs were observed in 104 and 106 EID50 group. So, the study concludes that Indian HPAI, H5N8 isolates are highly pathogenic in nature to chicken by affecting most organs systemically. CID50 of this H5N8 virus indicates poor adaption in chicken and it implies poor transmission possibility of this virus for host species in field condition. Though this virus is highly pathogenic in nature as that of HPAI, H5N1 viruses, absence of endothelial staining in most organ attributes variation in replication process and pathogenesis from HPAI, H5N1 viruses. Hence, further studies need to be done to elucidate the pathobiology of this virus in various bird species. HighlightsO_LIH5N8 virus belong to the clade 2.3.4.4b, Indian isolate is highly pathogenic in nature as that of HPAIV, H5N1. C_LIO_LIThe dose inocula, 102 EID50 is noninfectious to chicken. C_LIO_LIThe dose inocula, 104 and 106 EID50 had caused significant mortality in the inoculated chicken with MDT of 2 and 3.2 days, respectively. C_LIO_LIH5N8 virus was detected with high viral titres in clocal and oral shedding and in multiple organ with the dose inocula, 104 and 106 EID50. C_LIO_LI104 and 106 EID50 of H5N8 inocula virus caused significant gross and histological changes in multiple organs and viral antigens were detected in respective organs. C_LI

microbiology↗

bioRxiv2026

Atlas of lysine acetylation in the mouse

Lysine acetylation has widespread ramifications from genetic regulatory effects to modulation of enzymatic function. With improved acetyl-lysine enrichment technologies and advances in mass spectrometer speed and sensitivity, we present a comprehensive atlas of the mouse acetylome comprising 17,952 unique lysine acetylation sites across 4,340 proteins and 15 tissues. This resource, which nearly doubles the known mouse acetyl-lysine catalog, shows at least 14% of the acetylome is shared across tissues. We focus our investigation on several acetylated proteins, including ribosomal acetylation and its potential to extend ribosomal half-life in the liver and pancreas. Additionally, we identify a novel acetylation event in the active site of carnitine O-acetyltransferase (Crat) that also mirrors tissue-specific Crat activity. By integrating these data with human pathogenic variants, we identify acetyl-lysine residues on cardiac troponin and homogentisate dioxygenase that likely mimic disease-causing mutations. This resource provides a foundational framework for investigating protein acetylation in metabolic health and disease.

biochemistry↗

bioRxiv2026

Cribriform Plate Microenvironment Assembles a Suppressive Myeloid Network during EAE-induced Neuroinflammation

During neuroinflammation, CD11c+CD11b+ myeloid cells accumulate at the cribriform plate, a key cerebrospinal fluid (CSF) and antigen outflow site in mice. At this site, podoplanin (PDPN)-expressing cells, including lymphatic vessels and meningeal layers, expand to create a distinct drainage microenvironment. In this study we sought to characterize myeloid cells which populate this region using a mouse model of neuroinflammation, experimental autoimmune encephalomyelitis (EAE). Utilizing a combination of immunohistochemistry, flow cytometry, and scRNAseq, we report that macrophages and dendritic cells (DCs) from this region display unique expressional signatures related to tolerance, cell death, and reduced inflammatory profile. Together this data supports that myeloid retention at the cribriform plate and olfactory bulb meninges promotes a local immunosuppressive environment.

immunology↗

bioRxiv2025

Gonadal Hormone Status Dictates Neurobehavioral, Metabolic and Immunological Benefits of Ketogenic Diet in Female Mice through Gut-Metabolic-Brain Axis

The ketogenic diet (KD) is recognized for its broad therapeutic potential across metabolic, neurological, immunological, and aging-related domains; however, its efficacy and durability in females remain underexplored. This study investigated the effects of a short-term, intermittent KD on neurobehavioral function, lipid metabolism, immune response, and gut microbiota composition in sham-operated (intact) and ovariectomized (OVX, estrogen-deficient) female mice, aiming to delineate the interactions between diet and gonadal hormones. In sham females, KD reduced circulating estradiol levels and induced low-grade systemic inflammation, without producing measurable behavioral benefits. Conversely, KD exhibited reduced compulsivity, anxiety, and depression-like behaviors with improved well-being in OVX females, suggesting enhanced neurobehavioral resilience under estrogen-deficient conditions. Biochemical analyses revealed KD-induced hyperlipidemia in both groups, although the lipid load was attenuated in OVX mice. KD further decreased low-density lipoprotein cholesterol but led to uremia and histopathological evidence of hepatic steatosis and fibrosis in OVX females, despite unaltered liver function markers. 16S rRNA sequencing revealed hormone-dependent remodelling of the gut microbiota, characterised by distinct compositional shifts between the sham and OVX cohorts. Correlation analyses linked microbial alterations to improved lipid profiles and reduced anxiodepressive behaviors, implicating the gut-metabolic-brain axis in mediating the effects of KD. Collectively, these findings suggest that KD confers neurobehavioral and metabolic benefits in the absence of ovarian hormones but may also pose risks to the liver and kidneys. These results highlight ketogenic nutrition as a potential non-pharmacological strategy to mitigate menopause- and aging-associated neurobehavioral, metabolic, and immune dysfunctions through modulation of the gut microbiota.

neuroscience↗

bioRxiv2025

Right-Lateralized Maladaptive Topological Reorganization in Hyperthyroidism

Hyperthyroidism (HT) has been associated with cognitive impairments, but the structural connectomic and molecular mechanisms underlying these deficits remain poorly understood. In this study, we investigated large-scale brain network reorganization using structural connectivity derived from diffusion MRI in patients with 30 hyperthyroidism and 28 matched control participants. Subject level connectomes were analyzed to characterize network topology, with a specific focus on hub architecture, nodal alterations, and hemispheric reorganization. To probe molecular underpinnings, we integrated normative neurotransmitter receptor and transporter density maps with network metrics, assessing their correspondence to observed connectomic disruptions. Individuals with hyperthyroidism exhibited increased structural connectivity, particularly in mid- and long-range connections, alongside disrupted network topology. These changes were characterized by reduced modularity, increased characteristic path length and hub reorganization, most prominently in subcortical and right-hemisphere regions. Importantly, network alterations were functionally relevant, as metrics showed significant associations with clinical and cognitive variables, including FT4 levels, BMI, and perceptuomotor performance in the hyperthyroid group. Spatial neuromolecular correspondence analyses further revealed that DAT, 5-HT2A, and NET were closely aligned with topological changes. Moreover, neurotransmitter-weighted within-module degree z-scores moderately predicted TSH levels in HT. Our findings demonstrate that hyperthyroidism is associated with an increase in redundant, spatially extended white matter connections and a marked right-lateralized asymmetry in network organization. Furthermore, serotonergic (5-HT1a) and dopaminergic (DAT) systems consistently contributed to the modulation of intra-modular hubness, suggesting their role in maladaptive structural reorganization that may underlie perceptuomotor dysfunction in hyperthyroidism.

neuroscience↗

bioRxiv2025

hpGRISZ: a high-performance fluorescent biosensor for in vivo imaging of synaptic zinc dynamics

Despite the crucial role of synaptic Zn2+ in neurotransmission and neural processing, direct in vivo measurement of Zn2+ transients has remained challenging due to the limited responsiveness of existing fluorescent indicators. Here we report hpGRISZ (high-performance green indicator for synaptic Zn2+), an ultraresponsive turn-on green fluorescent biosensor engineered through iterative linker optimization, mutagenesis, and directed evolution. hpGRISZ exhibits exceptional brightness, thermostability, and a large fluorescence response (F/F0 {approx} 25) with micromolar affinity suitable for detecting extracellular synaptic Zn2+ release. We comprehensively characterized hpGRISZ in vitro, in mammalian cells, and in vivo. A membrane-anchored version of hpGRISZ traffics robustly to the cell surface under physiological conditions, where it retains strong responsiveness and supports wide-field, two-photon, and fiber photometry recordings in awake mice. These assays revealed synaptic Zn2+ dynamics across distinct brain regions and neuronal circuits. Together, our findings establish hpGRISZ as a powerful tool for dissecting zinc signaling in neural circuits and as a prototype for next-generation genetically encoded biosensors for in vivo imaging.

neuroscience↗

bioRxiv2025

Diverse ancestral myosin motors generate and segregate distinct types of nanocluster-rich domains at the plasma membrane

Molecular organization of the plasma membrane (PM) at nano and micron scales is critical for its function in all living cells. This emerges not only from the self-assembly of lipids and proteins but also from active forces originating in the underlying cytoskeletal cortex. These forces drive membrane molecules into non-equilibrium steady state patterns such as nanoclusters. However, the molecular agents connecting membrane organization with cytoskeletal dynamics and stresses have remained unknown. Here we show that two classes of ubiquitous ancestral non-muscle myosins are deployed for the organization of different types of membrane components. Inner-leaflet localized Class I myosins link outer-leaflet GPI-anchored molecules to juxta-membrane actin-filaments, whereas the more cortically-localized Class II myosins operate on transmembrane proteins endowed with actin-binding capacity. Consistent with an active Flory Huggins theory for phase separation, these observations show that the distinct motor-driven membrane molecules generate spatially segregated mesoscale domains, enriched in nanoclusters derived from different myosin classes. Moreover, chemically reversible post-translational modifications such as palmitoylation enable concatenation of these domains by enhancing affinity of the membrane domain constituents for each other. We anticipate that the segregation potential of the ATP-fueled cell membrane is made available for the crucial purpose of modulating information transduction because it can be regulated in space and time during the construction of signaling cascades, underpinning functional plasma membrane organization.

cell biology↗

bioRxiv2025

Multimodal Imaging and Logistic Weighted Cognitive Scores for Classification of MCI, AD, and FTD Subtypes

BackgroundDifferentiating between mild cognitive impairment (MCI), Alzheimers disease (AD), and frontotemporal dementia (FTD) subtypes remains a clinical challenge due to overlapping cognitive symptoms, structural atrophy, and metabolic patterns, especially in the early stages. Multimodal classification approaches integrating neuroimaging and cognitive scores may offer early and accurate characterization and subsequently improved diagnostic precision. MethodsIn this study, we included 100 participants (50 AD, 30 FTD, including 14 bvFTD and 16 PPA, and 20 MCI) who underwent simultaneous structural MRI and FDG-PET imaging. Cortical thickness (CTH) from anatomical MRI and standardized uptake values from FDG-PET were extracted using FreeSurfer and PETSurfer pipelines, respectively. CTH and FDG-PET features were combined into a single vector through a logistic weighting function derived from ACE-III scores, capturing the progressive nature of cognitive decline in dementia. A Naive Bayes classifier was then trained to differentiate diagnostic groups based on the merged features. ResultsThe model achieved classification accuracies of 83% for MCI vs. dementia (AD + FTD), 85% for MCI vs. FTD, 87% for MCI vs. PPA, 71% for MCI vs. bvFTD, 64% for MCI vs. AD, and 69% for AD vs. FTD. The overall classification accuracy was 68%, with the highest discriminative performance observed in separating MCI from FTD subtypes. ConclusionsThis study presents a novel, cognition-weighted multimodal approach combining structural and metabolic imaging to enhance the classification of neurodegenerative syndromes. Findings from this study, underscore the potential of integrating ACE-III scores with neuroimaging biomarkers for accurate characterization and, early-stage differentiation of MCI, AD, and FTD variants.

neuroscience↗

bioRxiv2025

Lipoxin B4 Mitigates TRPV4-Activated Muller Cell Gliosis During Ocular Hypertension

PurposeMuller glia play dual roles in glaucoma, contributing to both retinal homeostasis and neuroinflammation; their activation by elevated intraocular pressure through the mechanosensitive channel TRPV4 promotes a reactive state that drives retinal ganglion cell (RGC) loss. Lipoxin B4 (LXB4), an endogenous lipid mediator produced by retinal astrocytes, has been shown to suppress glial reactivity and directly protect RGCs. This study investigated whether LXB4 modulates TRPV4-driven Muller glial activation and inflammation and whether Muller glia themselves contribute to this retinal lipoxin pathway. MethodsOcular hypertension (OHT) was induced in mice via a silicone oil model, and reactive Muller glia were isolated via magnetic sorting for transcriptomic analysis. In vitro, primary and immortalized Muller glia were treated with a TRPV4 agonist with or without LXB4. Glial reactivity was assessed by flow cytometry, immunostaining, qPCR, and western blotting. LC-MS/MS-based lipidomics was used to quantify lipoxin pathway metabolites, and single-cell RNA-seq was used to examine transcriptional responses to LXB4 treatment. GFAP and TRPV4 expression was evaluated via immunohistochemistry in retinal sections. ResultsRNA bulk-sequencing analysis and qPCR revealed that Muller glia express both 5- and 15-lipoxygenase. Lipidomic analysis confirmed that the lipoxin pathway is functional and that Muller glia endogenously produce LXB4, establishing this essential cell type as a source of anti-inflammatory and neuroprotective LXB4 in the retina. TRPV4 activation induced a reactive glial phenotype characterized by increased GFAP and IL6 expression, increased STAT3 phosphorylation, and increased production of lipoxins, suggesting that biomechanical stress simultaneously triggers both gliosis and protective lipid signaling. Treatment with LXB4 suppressed TRPV4-induced gliosis in vitro by downregulating IL6 and inhibiting STAT3 activation, and in vivo by reducing the expression of Stat3, Il6, and TNF- during OHT while attenuating TRPV4 upregulation in Muller glia. ConclusionMuller glia are a significant source of LXB4 in the retina. This neuroprotective Muller glia pathway is amplified during chronic TRPV4 activation to counter-regulate gliosis. The findings support targeting of the TRPV4-lipoxin pathway as a potential approach to protect against OHT-induced neurodegeneration in glaucoma.

molecular biology↗

bioRxiv2025

Expanding the Global Map of Protein Post Translational Modifications with Immunoaffinity Enrichment and nDIA Analysis on the Orbitrap Astral Mass Spectrometer

Post-translational modifications (PTMs) contribute greatly to the diversity of the human proteome by affecting protein structure, function, interactions, stability, localization, and more. The study of PTMs is essential to understand various cellular functions, disease mechanisms, and aid in the development of biomarkers and design of therapeutic targets. Owing to their diversity, dynamic nature, and low stoichiometry compared to unmodified proteome counterparts, the analysis of PTMs remains challenging. In this study, immunoaffinity enrichment of PTM peptides was combined with analysis using Data Dependent Acquisition (DDA) and narrow window Data Independent Acquisition (nDIA) on the Orbitrap Astral mass spectrometer (MS) as well as comparative analysis using the Orbitrap Fusion Lumos MS for Ubiquitination, Phosphorylation, Acetylation, Succinylation, and Methylation. Human cell line and mouse tissue samples at various input peptide amounts were immuno-enriched and mass spectrometry data was acquired on both instruments to assess depth of coverage and number of novel sites identified. The study identified a total of 88,731 unique ubiquitin sites, 64,397 phosphorylation sites (43,721 phosphoserine, 8,414 phosphothreonine and 12,262 phosphotyrosine), 11,629 acetylation, 5,272 succinylation and 1,461 mono-methylation sites. In half the acquisition time, nDIA analysis of immuno-enriched samples on Orbitrap Astral MS provided much greater depth of coverage for all PTMs compared to DDA analysis on Orbitrap Fusion Lumos MS, with up to 33-fold more PTM peptides identified and quantified. Overall, the data presented in this study demonstrates the need for enrichment for PTM detection and the utility of combining antibody-based peptide capture and nDIA on the Orbitrap Astral MS as powerful tools for discovery and profiling of protein post-translational modifications in cells and tissues.

biochemistry↗

bioRxiv2025

Integrated transcriptomic analyses identifies host-targeting repurposing drugs for hepatitis C virus infection and related hepatocellular carcinoma

Hepatitis C virus (HCV) infection is a major risk factor in developing hepatocellular carcinoma (HCC). Drug development for HCV infection and HCC treatment is needed owing to treatment failure due to viral resistance and tumor heterogeneity. We analysed transcriptomic data of human liver tissues from multiple studies to identify differentially expressed genes in four study groups: (HCV+ vs Control); (HCV+HCC+ vs Control); (HCV+ AND HCV+HCC+ vs Control); and (HCV+HCC+ vs HCV+) respectively. We identified 597, 1321, 923, and 1526 upregulated and 474, 558, 336, and 989 downregulated genes for above respective studied groups. We performed functional, pathway enrichment, and protein-protein interaction analyses for identified upregulated genes. We identified and prioritized 39, 57, 58, and 110 repurposing drugs for 9, 17, 14, and 33 non-essential upregulated target genes based on drug group, action, and literature evidence. We also performed mutational analysis of key target genes. We found several dysregulated genes such as CTLA4, GPC3, MDK, TUBB2B etc. and many novel target genes like CACNB4, HTR7, IGHG1, SLC22A12, etc. We identified several potential repurposing drugs namely asenapine, cabergoline, dequalinium, epinastine, methysergide, loxapine, lurasidone, etc. This study identified prospective repurposing drugs using host-targeting approach for HCV infection and related HCC treatment.

bioinformatics↗

bioRxiv2025

Nutritional Ketosis Attenuates Sucrose Bingeing-Induced Behavioral Deficits by Improving Synaptic Plasticity and Anti-Inflammatory Signalling in the Prefrontal Cortex of Male and Female Mice

Binge eating, one of the defining characteristics of binge eating disorder, has been linked to poor health span. Animals, like humans, selectively binge on highly palatable foods, implying that the binge-like behavior is motivated by hedonic rather than metabolic signals. Given the association between reward processing and food intake, this study explored sex-specific underlying biological mechanisms, including synaptic, neuroimmune and neurometabolic correlates of binge-like sucrose drinking, compulsivity and anxiety-like behaviors, utilizing a preclinical model of hedonic sucrose drinking. Throughout the experiment, male and female mice binged on a sweet solution when given food ad libitum with free access and a choice between water and a 10% (w/v) sucrose solution, with females consuming more sucrose. The sucrose intake was positively correlated with transcription of genes for dopamine receptors (Drd1, Drd2) in the PFC of male and female mice. Sucrose-bingeing increased PFC neuroinflammation, concomitantly increasing region-specific blood-brain barrier permeability in males. Sucrose bingeing elevated the transcription of glucose metabolism genes (Slc2a3, Glo1) while inhibiting ketone oxidation pathway genes (Slc16a1, Oxct1, Acat1) in the PFC of males and females. Nutritional ketosis attenuated sucrose bingeing, compulsivity and anxiety-like behaviors in sucrose-dependent male and female mice by suppressing the transcription of reward-related genes (Drd1, Drd2) while promoting an anti-inflammatory neuroimmune microenvironment in the PFC of male and female mice in a sex-dependent manner. Overall, this study identified synaptic, neuroimmune and neurometabolic mechanisms as novel druggable targets and nutritional ketosis as a potential therapy for diseases where binge-like eating, compulsivity and anxiety-like behaviors are the main symptoms, such as binge eating disorder. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=195 SRC="FIGDIR/small/651641v1_ufig1.gif" ALT="Figure 1"> View larger version (54K): org.highwire.dtl.DTLVardef@f4f91dorg.highwire.dtl.DTLVardef@10f0f9forg.highwire.dtl.DTLVardef@1caa2baorg.highwire.dtl.DTLVardef@81a2e1_HPS_FORMAT_FIGEXP M_FIG C_FIG

neuroscience↗

bioRxiv2025

Loss of cep57 function induces G1 arrest and microcephaly

Faithful chromosome segregation and coordinated cell-cycle progression are essential for maintaining genome stability and preserving progenitor populations during vertebrate embryogenesis. Although pathogenic CEP57 variants are associated with developmental disorders including aneuploidy and microcephaly, the molecular mechanisms by which CEP57 coordinates these processes remain poorly understood. Here, we identify Cep57 as a previously unrecognized regulator of chromosome segregation, G1/S transition, centrosome integrity, and genome surveillance during early zebrafish embryogenesis. Cep57 localizes to both the nucleus and centrosomes of zebrafish blastulae, indicating probable dual functions in nuclear cell cycle regulation and centrosome organization. Our results show that Cep57 associates with Rad21, Smc1, and Smc3, revealing an unexpected functional link between Cep57 and the cohesin complex. Loss of Cep57 results in Rad21 depletion, destabilization of the cohesin complex, chromosome segregation errors resulting in supernumerary nuclei, and disruption of pericentriolar material organization, demonstrating a critical role in maintaining mitotic fidelity. We further show that Cep57 interacts with Geminin and promotes an Rb1-dependent G1/S checkpoint, whereas Cep57 deficiency causes widespread cell cycle dysregulation, genome instability, and apoptosis. Quantitative proteomic analyses reveal robust activation of DNA damage and checkpoint signaling pathways, consistent with engagement of genome surveillance mechanisms following Cep57 loss. Importantly, these cellular abnormalities precede extensive neural apoptosis, depletion of neuroprogenitor populations, and the emergence of microcephaly-associated phenotypes. Collectively, our findings establish Cep57 as a cohesin-associated integrator of chromosome segregation, cell cycle progression, and genome stability that is essential for neural progenitor maintenance during vertebrate embryogenesis, thereby expanding its functional repertoire far beyond its canonical role in centrosome regulation.

developmental biology↗

bioRxiv2025

AGO2 slicing of a domesticated retrotransposon is necessary for normal vasculature development

Argonaute-mediated RNA slicing is an ancient genome-defense mechanism linked to transposon repression. Although RNAi is no longer a major repeat-control pathway in mammals, AGO2 has retained catalytic activity, and this activity is essential for postnatal viability. The physiological targets that explain this requirement have remained unknown. Here we show that mammalian AGO2 slicing is required to restrain Rtl1, an imprinted domesticated retrotransposon whose cleavage is directed by miRNAs from the miR-433[~]127 cluster. Loss of AGO2 catalysis derepresses Rtl1 and causes endothelial defects and lethal neonatal muscle failure. Mechanistically, RTL1 is an oligomerization-prone retrotransposon-derived protein whose excess expression in muscle induces a non-aggregate proteostasis-stress state characterized by increased proteasome-dependent activity, reduced nascent protein synthesis, and depletion of mitochondrial, calcium-handling, and contractile gene programs. Thus, an essential function of mammalian AGO2 catalysis is to restrain a domesticated transposon-derived protein whose uncontrolled expression compromises endothelial and skeletal muscle function. These findings reveal how an ancestral transposon-Argonaute regulatory interaction has been repurposed to support mammalian development and survival.

developmental biology↗

bioRxiv2025

A high-resolution genomic study of the Pama-Nyungan speaking Yolngu people of northeast Arnhem Land, Australia.

ObjectivesAbout 300 Aboriginal languages were spoken in Australia. These were classified into two groups: Pama-Nyungan (PN), comprised of one language Family, and Non-Pama-Nyungan (NPN) with more than 20 language Families. The Yolngu people belong to the larger PN Family and live in Arnhem Land in northern Australia. They are surrounded by groups who speak NPN languages. This study, using nuclear genomic and mitochondrial DNA data, was undertaken to shed light on the origins of the Yolngu people and their language. The nuclear genomic sequences of Yolngu people were compared to those of other Indigenous Australians, as well as Papuan, African, East Asian and European people. Materials and methodsWith the agreement of Indigenous participants, samples were collected from 13 Yolngu individuals and 4 people from neighbouring NPN speakers and their nuclear genomes sequenced to a 30lil coverage. Using the short-read DNA BGISEQ-500 technology, these sequences were mapped to a reference genome and identified [~]24.86 million Single Nucleotide Variants (SNVs). The Yolngu SNVs were then compared to those of 36 individuals from 10 other Indigenous populations/locations across Australia and four worldwide populations using multidimensional scaling, population structure, F3 statistics and phylogenetic analyses. ResultsUsing the above methods, we infer that Yolngu speakers are closely related to neighbouring NPN speakers, followed by the Weipa population. No European or East Asian admixture was detected in the genomes of the Yolngu speakers studied here, which contrasts with the genomes of many other PN speakers that have been studied. Our results show that Yolngu speakers are more closely related to other PN speakers in the northeast of Australia than to those in central and western Australia studied here. Yolngu and the other Australian populations from this study share Papuans as an out-group. DiscussionThe study presented here provides an account of the nuclear and mitochondrial genomic diversity within the PN Yolngu Aboriginal population. The results show the Yolngu sample and their NPN neighbours have a strong genetic relationship. They also offer evidence of ancestral links between the Yolngu and PN-speaking populations in Cape York. From earlier fingerprint studies, consistent with the genomic results shown here, we suggest that there was a movement of people from the east into northeast Arnhem Land, associated with the flooding of the Sahul Shelf, and that this occurred between about 11 Kya and 8 Kya ago. Several Yolngu myths point to such a movement. It is suggested that the spread of the PN language or its speakers may have influenced the population structure of the Yolngu. Further genomic studies, with larger samples, of populations to the east of the Yolngu around the Gulf of Carpentaria into Cape York are required to test this hypothesis. Our results imply that PN did not spread with the movement of people across the continent, rather, the PN languages diffused among the different populations. It seems clear that the languages dispersed and not the people. The low level of relatedness detected between the Yolngu people and the people of the central arid desert of Australia suggests a long period of separation with different patterns of migration. Beyond Australia, Yolngu are most closely related to the Papuan people of New Guinea.

genetics↗

bioRxiv2025

The experimentally evolved fluconazole-resistant Clade II isolates of Candidozyma auris exhibit a distinct lipid compositional landscape, highlighting intra-clade sphingolipid heterogeneity

The intrinsic resistance of Candidozyma auris to antifungal drugs poses a major therapeutic challenge, with conventional resistance mechanisms providing only partial explanations. Sphingolipids (SLs), known for their interclade heterogeneity, play a crucial role in antifungal resistance. This study examined the SL landscape in two drug-susceptible clade II isolates, C-line and P-line, from distinct geographical origins, which were experimentally evolved to develop stable fluconazole (FLC) resistance. The progenitors displayed distinct SL profiles, P1 had higher PhytoCer and OHPhytoCer, indicating a more active acidic SL biosynthesis branch, whereas C1 exhibited elevated OHGlcCer, OHCer, and LCBs, reflecting a greater role of the neutral biosynthesis branch. The principal component analysis (PCA) also confirmed distinct segregation of the two progenitors. Upon evolution, P1.1 and C1.1 adaptors showed significant SL alterations. P1.1 exhibited PhytoCer enrichment, while C1.1 showed reduced OHGlcCer alongside increased PhytoCer, dhCer and OHPhytoCer levels. Notably, OHGlcCer remained unchanged in P1.1, whereas LCBs and OHPhytoCer decreased compared to P1. Despite these lineage-specific differences between the progenitors, both evolved replicates exhibited increased PhytoCer as a common denominator like what is also observed in clinical FLC-resistant isolates. These findings highlight intra-clade SL variability and suggest that specific SLs contribute to FLC resistance in C. auris.

microbiology↗

bioRxiv2025

Modeling the Aging Human Lung: Generation of a Senescent Human Lung Organoid Culture System

IntroductionThe aging lung enters into a state of irreversible cellular growth arrest characterized by senescence. While senescence is beneficial in preventing oncogenic cell proliferation, it becomes detrimental when persistent, promoting chronic inflammation and fibrosis through the senescence-associated secretory phenotype (SASP). Such senescence-related pathophysiological processes play key roles in lung diseases like chronic obstructive pulmonary disease (COPD) and idiopathic pulmonary fibrosis (IPF). However, few models accurately represent senescence in the human lung. MethodsTo generate a human lung senescence in vitro model, we first generated a human induced pluripotent stem cell (hiPSC)-derived lung organoid (LO) system which was dissociated into monolayers and air-liquid interface (ALI) cultures to enhance visualization and allow uniform exposure to agents. Cellular senescence was induced using doxorubicin, a DNA-damaging agent. Senescence markers, such as {beta}-galactosidase ({beta}-gal) activity, SASP cytokine production and secretion, cell morphology, proliferative capacity, and barrier integrity were evaluated to validate the senescent phenotype. ResultsThe doxorubicin-induced senescent hiPSC-derived lung cells demonstrated the hallmark characteristics of cellular senescence, including increased {beta}-gal activity and increased production of the pro-inflammatory SASP cytokine IL-6 and increased secretion of TNF-. Senescent cells displayed enlarged morphology, decreased proliferation, and reduced wound repair capacity. Barrier integrity was impaired with decreased electrical resistance, and increased permeability, as well as expression of abnormal tight junction proteins and increased fibrosis, all consistent with the senescent lung. ConclusionOur hiPSC-derived lung cell senescent model reproduces key aspects of human lung senescence and offer an in vitro tool for studying age-related lung disease mechanisms and therapeutic interventions. This model has potential applications in exploring the impact of environmental factors (e.g., toxins, infectious pathogens, etc.) on the senescent lung and assessing treatments that could mitigate pathologies associated with pulmonary aging including barrier impairment, inflammation and fibrosis.

cell biology↗

bioRxiv2025

CD8+ T cells mediate vaccination-induced lymphatic containment of latent Mycobacterium tuberculosis infection following immunosuppression, while B cells are dispensable

It is estimated that two billion people are latently infected with Mycobacterium tuberculosis (Mtb), the causative agent of tuberculosis (TB). Latent Mtb infection (LTBI) can occur in multiple organs, including the lymphatics. The risk of LTBI reactivation increases in immunocompromised conditions, such as coinfection with human immunodeficiency virus (HIV), and during treatment of autoimmune diseases and organ transplantation. The immunological correlates of protection against TB, including against reactivation of LTBI, remain largely elusive. Here, we used a mouse model of latent lymphatic Mtb infection to dissect the immunological mechanisms underlying LTBI containment versus reactivation. We show that immunosuppression-mediated reactivation of lymphatic LTBI and the subsequent spread to non-lymphatic organs can be prevented by vaccination with multiple recombinant BCG (rBCG) strains despite the deficiency of CD4+ T cells. Using spatial transcriptomics, multi-parameter imaging, network analysis and bioinformatic integration of histopathological images, we reveal that immunosuppression is associated with a distinct repositioning of non-CD4 immune cells at the edge of TB lesions within the infection-draining cervical lymph nodes. While B cells increased in numbers, they are dispensable for the containment of LTBI. Lymphatic Mtb infection in different immune cell-deficient mouse strains, antibody-mediated cell depletion and adoptive transfer experiments into highly susceptible mice unequivocally show that vaccination-mediated prevention of LTBI reactivation is critically dependent on CD8+ T cells. These findings have profound implications for our understanding of immunity to TB and the management of LTBI. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=92 SRC="FIGDIR/small/634479v1_ufig1.gif" ALT="Figure 1"> View larger version (26K): org.highwire.dtl.DTLVardef@151fdd6org.highwire.dtl.DTLVardef@1efed47org.highwire.dtl.DTLVardef@c2e7e0org.highwire.dtl.DTLVardef@555c7_HPS_FORMAT_FIGEXP M_FIG C_FIG

immunology↗