Biology subjects

Ghosh, T.

Publications and source records attributed to Ghosh, T..

At least 19 recordsLinked to original sources

bioRxiv2026

Assessment of Microbial Consortia for Biogenic Mineralization Potential of Lead (Pb) using Microbiologically Induced Calcite Precipitation and Nitrate Reduction

Groundwater contamination by lead and nitrate exceeding the permissible limits of the World Health Organization (WHO) and the Bureau of Indian Standards (BIS) of 10 ppb lead and 45 to 50 ppm nitrate poses a severe health risk of systemic toxicity in humans and animals. Microbial nitrate reduction coupled with microbiologically induced calcite precipitation (MICP) proved to be a novel bioremediation strategy to transform soluble lead nitrate into insoluble lead biominerals. This study presents statistical optimization of operational parameters for nitrate reduction and co-precipitation of biogenic lead carbonate-calcium carbonate by nitrate-reducing bacterial consortia. The SEM, TEM with SEAD, and XRD analysis of the biomineral confirmed lead carbonate co-precipitation with CaCO3. A two-level factorial design was applied to screen significant variables and interactive factors that influence nitrate reduction and biomineral precipitation. The highest nitrate reduction, maximum ammonia production, and biogenic Pb-mineralization efficiency of > 90% were obtained at the optimum conditions (initial nitrate requirement of 600 ppm, temperature 37 oC, pH 8, and carbon content of 5.5 g/L) compared to those obtained under the common process parameters. ANOVA with a high correlation coefficient (R2 > 0.99) corroborated the linear model for the biogenic mineralization process. This study on the biogenic removal of Pb by nitrate-reducing bacterial consortia revealed possible opportunities for large-scale treatment of Pb-contaminated surface and subsurface water bodies.

microbiology↗

bioRxiv2026

Nonparametric kernel-based detection of spatially variable genes with adaptive shrinkage and scalable multi-sample inference

AO_SCPLOWBSTRACTC_SCPLOWIdentifying spatially variable genes (SVGs), genes whose expression varies coherently across tissue space, is a central analytic goal in spatially resolved transcriptomics. Current methods rank spatially variable genes using either significance probabilities from parametric models or effect sizes such as the proportion of spatial variance, but parametric approaches impose distributional assumptions, such as Gaussian processes or negative binomial models, that may be violated for sparse or zero-inflated data. Furthermore, most detection tools cannot jointly model multiple biological replicates, and no existing framework provides both nonparametric significance probabilities and stabilized effect-size estimates with formal uncertainty quantification. Here, we introduce CytoKspace, a nonparametric framework that combines a sparse exponential kernel constructed from nearest-neighbor graphs with a quadratic-form test statistic and adaptive permutation testing. CytoKspace employs a multi-stage adaptive permutation schedule that yields substantial computational savings over fixed-permutation baselines, an adaptive shrinkage layer built on empirical Bayes estimation that stabilizes raw spatial effect sizes and provides posterior estimates with local false sign rates, and a scalable multi-sample extension via Fisher combination of significance probabilities and inverse-variance-weighted meta-analysis that accommodates studies with multiple biological replicates. In extensive simulations across a broad range of sample sizes, gene counts, spatially variable gene fractions, and effect sizes, as well as in applications to two real datasets from the Visium and seqFISH platforms, CytoKspace demonstrates competitive sensitivity, well-calibrated false positive rates, and practical computational requirements compared to existing methods. A software implementation of our method is freely available at https://github.com/Ghoshlab/CytoKspace.

bioinformatics↗

bioRxiv2026

HetNetEX: Exact Asymptotic Inference in Heterogeneous Biomedical Knowledge Graphs

Heterogeneous biomedical knowledge networks (hetnets) integrate disparate data types, drugs, genes, diseases, and pathways, across independent sources; Hetionet (https://het.io) is a widely used example. A standard approach for assessing connectivity significance is XSwap, which permutes the hetnet P times and fits a gamma-hurdle null model to the degree-weighted path count (DWPC), pooling permuted values across pairs with matching source and target degrees to increase the effective sample size. This permutation approach has been highly successful in practice, but it faces four practical constraints in large graphs: (1) a finite resolution for the smallest reportable p-values, (2) computational cost that grows prohibitive at path lengths L [≥] 4 or 5, (3) a variance model (Var {propto} {micro}2) that departs from the configuration-model form (1 +{kappa} ){micro}, and (4) O(P 10m L) runtime. To complement this approach, we present HetNetEX (Heterogeneous Network EXact inference), which computes the null DWPC distribution analytically from degree sequences using the configuration model in O(Ln) time. In simulations at P = 200 across L = 1-4, HetNetEX achieves Spearman{rho} > 0.96 concordance with XSwap rankings while being >10,000x faster and providing analytical p-values without a resolution ceiling. High-degree pairs show larger XSwap sampling error than low-degree pairs, reflecting the finite-sample nature of permutation that analytical computation avoids.

systems biology↗

bioRxiv2026

A Dual-Function Guanidinium Scaffold that Couples Copper Sequestration with Redox Protection in Wilson disease

Wilson disease (WD) is caused due to mutations in the copper ATPase gene ATP7B, that result in accumulation of labile copper pools and the consequent disruption of cellular redox homeostasis through uncontrolled copper-mediated reactive oxygen species generation. Current therapies mainly depend on high-affinity copper chelation to lower metal burden which sometimes also strip copper from cuproproteins and may disturb physiological copper-dependent processes. It also does not directly suppress pathological copper reactivity i.e., free radical generation, a major driver of WD progression. To overcome these limitations, we have rationally designed Gua-Cu-3, a C-symmetric guanidinium-based molecule that can chelate labile copper without metal stripping from cuproproteins due to moderate binding affinity and it has intrinsic antioxidant activity within a single nanosheet-forming supramolecular self-assembly. Spectroscopic, calorimetric, and computational analyses revealed controlled multivalent copper coordination (Kd = 95.4 M) while radical-scavenging and hydroxyl-radical inhibition assays further revealed potent redox-regulatory activity. In cellular models of copper overload, Gua-Cu-3 treatment reduces ATP7B trafficking from trans-Golgi network, confirming effective intracellular copper sequestration. This was accompanied by a marked reduction in oxidative stress, reduction of translocation of Nrf2 in nucleus and of HO-1 expression, thereby limiting lipid peroxidation which leads to restoration of cellular homeostasis, including improved lysosomal integrity, reduced endoplasmic reticulum stress, decreased mitochondrial superoxide levels, and diminished apoptosis. Importantly, the protective effects extended, beyond cultured cells, Gua-Cu-3 attenuates oxidative stress in ATP7B-homolog-deficient C. elegans and rescues copper-induced developmental defects in zebrafish, outperforming D-penicillamine, which is currently in use for Wilson disease management. These findings establish Gua-Cu-3 as a molecularly designed supramolecular copper-reactivity buffer that couples-controlled copper sequestration with redox regulation which is distinct from conventional copper depletion and provides a framework for treating Wilson disease and other disorders associated with metal dyshomeostasis and oxidative stress.

Cell Biology↗

bioRxiv2026

Demographic history, geographic distance, and landscape features shape the genetic divergence of wild tigers in northeast India

Habitat fragmentation creates small, isolated populations vulnerable to inbreeding, genetic drift, and high genetic load. For conservation management, it is essential to distinguish contemporary landscape resistance from historical demographic processes as drivers of these genetic patterns, especially for conservation priority regions such as northeast India which intersects two major tiger conservation landscapes. We studied the genetic structure and landscape connectivity of tigers across four protected areas in northeast India: Kaziranga, Manas, Orang, and Nameri, using faecal samples. From 741 samples collected over two field seasons, we identified 654 confirmed tiger specimens. Using methylation-based enrichment and ddRAD-seq of 176 samples, we generated a high-quality dataset of 3091 SNPs across 44 individuals. Population structure analyses identified three genetically distinct clusters: Kaziranga-Nameri, Manas, and Orang. Isolation-by-distance and landscape resistance explained 13% and 17% of the observed genetic divergence, respectively, with human settlements influencing gene flow. Orangs pronounced divergence from Kaziranga, despite geographic proximity and corridors, suggests a post-bottleneck founder effect, as evidenced by reduced heterozygosity (Ho = 0.24), nucleotide diversity (pi = 0.24), and effective population size (Ne = 1.3). These findings reveal that demographic and genetic recovery can decouple: Orangs population has recently grown, yet genome-wide evidence shows ongoing genetic erosion that monitoring has not detected. Similar patterns have been reported in other Indian tiger populations, indicating that such decoupling may be systemic. Target 4 of the Kunming-Montreal Global Biodiversity Framework requires explicit genetic diversity monitoring; this study demonstrates that non-invasive genomics can operationalise that mandate at a conservation-relevant scale.

evolutionary biology↗

bioRxiv2026

SLD5/GINS4 controls dynein-dependent centrosome maturation and exposes a candidate mitotic vulnerability in cancer.

Faithful proliferation requires coordinated DNA replication with centrosome maturation and spindle-pole integrity. SLD5, encoded by GINS4, is a core component of the GINS replication complex and is frequently elevated in tumors, but whether it links replication-associated cancer states to centrosome control has remained unclear. Here, we show that GINS4/SLD5 is recurrently upregulated across human cancers at transcript and protein levels and marks tumor programs enriched for DNA replication, chromosome segregation, and mitotic control. In cancer cells, Sld5 depletion dispersed PCM1, AZI1, and CEP290-positive centriolar satellites without eliminating these satellite proteins, reduced dynein heavy chain expression, and destabilized dynein-dynactin localization at spindle poles. Direct depletion of dynein heavy chain, co-depletion analyses, and pharmacological inhibition of dynein motor activity with ciliobrevin D phenocopied Sld5 loss, causing satellite dispersion, defective recruitment of PLK1, Aurora A, CEP192, and CEP215 to centrosomes, and multipolar spindle formation. These defects occurred without detectable DNA damage or checkpoint activation, indicating a non-canonical Sld5 function beyond its role in the replisome. Cancer dependency and kinase network analyses further nominate SLD5-associated mitotic and checkpoint pathways as therapeutic targets. Our findings identify SLD5/GINS4 as a regulator of dynein-dependent centrosome maturation and a candidate vulnerability in replication-driven cancers, with potential value for biomarker-guided therapeutic stratification. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=136 SRC="FIGDIR/small/723511v1_ufig1.gif" ALT="Figure 1"> View larger version (53K): org.highwire.dtl.DTLVardef@525d9org.highwire.dtl.DTLVardef@1f7d7eeorg.highwire.dtl.DTLVardef@815586org.highwire.dtl.DTLVardef@115f286_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗

bioRxiv2025

The transcription factor BCL11A restores differentiation potential to aged oligodendrocyte progenitor cells

In young animals, oligodendrocyte progenitor cells (OPCs) undergo robust differentiation, progressing through stages to become pre-myelinating oligodendrocytes (Pre-OL) and ultimately myelinating oligodendrocytes (OLs). However, OPCs from aged animals have reduced differentiation ability. This disrupts myelin maintenance in the central nervous system (CNS), leading to a lack of remyelination following demyelinating injury and impaired adaptive myelination as a mechanism of learning. To uncover novel factors essential for restoring resilience in aged OPCs, we employed a data-driven approach involving the development of a computational pipeline, gSWITCH (accessible at: https://altoslabs.shinyapps.io/gSWITCH/), that allows for capture of precise dynamic gene expression patterns to pinpoint potential switch genes during lineage progression. Using gSWITCH to identify potential switch genes crucial for OPCs, we conducted a comparative analysis of gene expression in OPCs isolated from young and aged animals. This revealed a group of transcription factors with decreased expression in aged OPCs. Further analysis of transcription factor binding site enrichment in OPC switches highlighted Bcl11a, a zinc finger transcription factor that could potentially serve as a master regulator of many switch genes. Ectopic overexpression of Bcl11a in aged OPCs did not enhance their proliferation; however, it significantly enhanced their differentiation into OLs. Overexpression of Bcl11a in aged mice, followed by demyelination injury in spinal cord white matter, significantly increased the differentiation of OPCs into OLs within the injury region compared to control aged mice. Furthermore, we found that Bcl11a is absent in invertebrates and has undergone pervasive purifying selection throughout vertebrate evolution, constraining its amino-acid sequence by eliminating deleterious mutations. Our study shows that reversing the age-related decline of this evolutionarily conserved factor in aged OPCs restores their impaired capacity for differentiation.

neuroscience↗

bioRxiv2025

Novel truncating Desmin mutation Arg150Stop disrupts structural integrity and cellular homeostasis by formation of persistent aggregate-like structure

Desminopathies are a heterogeneous group of myofibrillar myopathies defined by the presence of desmin-positive aggregates that compromise cytoskeletal integrity in skeletal and cardiac muscle. Although desmin knockout models and several truncating mutations typically result in a functional null phenotype without inclusion body formation, the molecular consequences of specific stop-gain variants remain poorly understood. In this study, we investigated the pathogenic mechanism of a novel DES nonsense mutation, NM_001927.4:c.448C>T; p.(Arg150Stop), previously identified in an Indian patient with congenital myopathy. This premature stop codon lies within the Linker 1A domain and is predicted to generate a truncated protein lacking the C-terminal tail. To delineate its functional consequences, we used two complementary experimental approaches: transient overexpression of the R150X mutant in skeletal and cardiac myocytes, and a CRISPR/Cas9-engineered homozygous R150X cardiomyocyte line (Des-R150X-CRISPR). Both models consistently revealed the formation of persistent aggregate-like structures, in striking contrast to desmin knockout systems that do not generate inclusions. These aggregate-like structures disrupted actin filament organization, impaired filament bundling, and induced organelle mislocalization. Biochemical analysis indicated that the aggregates were resistant to proteasomal degradation, yet they were partially cleared by autophagy, underscoring a role for protein quality control pathways in modulating disease severity. Importantly, the Des-R150X-CRISPR line demonstrated aggregate-driven pathology at endogenous levels, confirming that this mutation acts through a toxic gain-of-function mechanism rather than simple loss of desmin function. Our findings establish the Arg150Stop variant as a mechanistically distinct truncating mutation that generates aggregation-prone protein rather than a null state. By reproducing hallmark features of desminopathy in a physiologically relevant human cell models, this work not only broadens the known pathogenic spectrum of DES variants but also highlights aggregate formation as a central driver of cellular dysfunction and a promising therapeutic target in desminopathies.

cell biology↗

bioRxiv2025

Ancient bridges, modern threat: Conserving landscape heterogeneity ensures sustenance of living root-bridges in Meghalaya

The Anthropocene, marked by rapid biodiversity loss, has renewed attention on natures contributions to people, which include ecological, cultural, and spiritual values. A striking example of such nature-culture interactions are the living root-bridges of Meghalaya, India, where Khasi people ingeniously train the aerial roots of Ficus elastica across river valleys to form natural bridges. These structures, currently under consideration for UNESCO World Heritage recognition, exemplify sustainable resource use in one of the wettest and most landslide-prone regions of the world. However, increasing tourism and unregulated construction is threatening to this nature culture relationship in a biodiversity hotspot. In such situations, understanding the factors governing the geneflow is vital to the preservation of interactions between the pollinating fig wasps, the fig tree and its seed dispersers. Despite its ecological and cultural significance, little is known about the population biology or dispersal potential of F. elastica. Here, we investigated dispersal potential of natural populations of F. elastica across Meghalaya. Using ddRAD-SNP genotyping ([~]12K SNPs from 308 individuals), we detected four genetic clusters corresponding to E. Khasi, W. Khasi, W. Jaintia, and Ribhoi hills. Redundancy analysis and resistance modelling revealed that wind regimes and topography jointly structure these populations, enabling gene flow within but not across river valleys. Analysis of spatial distribution of related individuals indicates short dispersal distance of 1-4km varying across different populations. Given F. elasticas association with riparian ecosystems, and with UNESCO recognition pending, our study underscores the need for strict guidelines to curb habitat destruction and ensure the long-term survival of both the species and its cultural legacy.

ecology↗

bioRxiv2025

A high sensitivity strategy to screen NAD(P)H-dependent oxidoreductase activity by coupled enzyme cascade

Enzymes play a pivotal role in "green chemistry" as tools for biocatalysis. Oxidoreductase enzymes are especially useful for carrying out key electron transfer (redox) steps towards a wide range of chemical transformations (e.g., asymmetric hydrogenation, oxygenation, hydroxylation, epoxidation, or Baeyer-Villiger oxidation) that might not otherwise be available to chemists through conventional (nonbiological) synthetic approaches. The ability to screen oxidoreductase activity is important in identifying useful biocatalysts from nature, and also towards engineering novel ones through directed evolution. Many valuable redox enzymes are dependent upon NAD(P)H as an electron donating co-substrate (or conversely, upon NAD(P)+ as an electron acceptor), and the common method to detect their activity is to monitor the change in absorbance at 340 nm as NAD(P)H is converted to NAD(P)+ (or vice versa). The limited sensitivity of this method presents a challenge in detecting very low levels of oxidoreductase activity, and this can prove very difficult to begin engineering enzymes as improved biocatalysts when the rates of natural enzymes may be slow for a desired redox reaction. Herein, we report a fluorescence-based, enzyme cascade-coupled system that we have developed to detect oxidoreductase activity with orders of magnitude more sensitivity than conventional absorbance-based assays. While recycling NAD(P)H from NAD(P)+, the coupled enzyme cascade triggers cleavage of a fluorogenically labeled probe, releasing a strong fluorescent signal. This allows detection of very low levels of a specific oxidoreductase activity that we may wish to magnify by directed evolution using our assay in high-throughput screening.

biochemistry↗

bioRxiv2025

A novel molecular sexing method for Greater One-horned Rhinoceros (Rhinoceros unicornis) for reliable demographic assessments

Accurate assessment of demographic parameters is crucial for conserving endangered species. The Greater One-horned Rhinoceros (Rhinoceros unicornis), a sexually monomorphic species, lacks a validated molecular sexing protocol for diverse biological samples. This study established a multi-marker molecular sexing protocol using blood, tissue, horn, and dung samples from all wild populations in India. The optimized multiplex strategy that involves three sex-linked markers: ZF, AMESC, and TSRY, enabled simultaneous amplification of X-and Y-chromosome-specific fragments in degraded samples. Testing with 286 individual rhino samples from seven parks (5 blood, 180 tissue, seven horn, and 94 dung) led to a [~]92% (195 M: 69 F) success rate. Overall, this approach validates a molecular sexing protocol with increased reliability and fewer amplification failures, facilitating large-scale demographic studies. Future research should utilize this method to examine the sex ratio of all existing Indian rhino populations across their range, ensuring their future persistence and management.

ecology↗

bioRxiv2025

Non-canonical regulation of the plasma membrane copper transporter CTR1 through modulation of membrane mechanical properties

We describe a non-canonical, membrane receptor-like regulation of the human copper transporter CTR1 in response to copper stimuli. CTR1 is the sole high-affinity trimeric plasma-membrane copper-importing channel that self-regulates by undergoing endocytosis to limit copper uptake. We observed that preceding copper-induced endocytosis, CTR1 forms clusters on the plasma membrane, a phenomenon that is typically observed in membrane receptors. We deciphered the mechanism of CTR1 clustering and studied its ramifications on plasma membrane physical properties harboring the clusters that favors endocytosis. Membrane tension and fluctuation are fundamental regulators of pre- and post-endocytic events. Using coarse-grain MD simulation and coupled Interference Reflection Microscopy-Total Internal Reflection Fluorescence Microscopy we demonstrated that CTR1 clusters induce positive membrane curvature, increase in local membrane tension and decrease in local membrane fluctuation; alterations that favors formation of endocytic pits. Clustering is facilitated by copper-sequestering Methionine rich extracellular amino-terminus of CTR1. MD-simulations and IRM-TIRF imaging revealed that CTR1 clustering is facilitated by membrane cholesterol, depletion of which delays CTR1 endocytosis. CTR1 clustering promotes clathrin-coated pit formation that engages recruitment of adapter protein AP-2. To summarize, we report a hitherto unknown pre-endocytic receptor-like phenomenon of ligand-induced clustering of a metal channel, that in-turn regulates self-endocytosis by modulating membrane properties.

cell biology↗

bioRxiv2025

Actin contractility and endocytosis create apico-basal tension gradient in HeLa cells

The functions of the plasma membrane of a cell are coupled to its mechanical state. To understand the players that contribute to the tight regulation of membrane mechanics with its local heterogeneities, the tension of the cell membrane requires to be mapped out from the basal to the apical membrane. In this work, optical-trap-based tension measurements performed at two axial (z) planes per cell reveal an apico-basal gradient, that is understood better on comparison with basal membrane mechanics and membrane compaction measurements by a combination of high resolution microscopy (IRM) and fluorescence lifetime (Flipper-TR) measurements, respectively. While the apico-basal gradient in the apparent tension (low to high) was found to depend on an intact actin cytoskeleton, analysing the colocalization of the cortical actin with the motor protein myosin and the actin-membrane linker ezrin suggested that cytoskeleton contractility is a major determinant of the patterned tension. Tension-sensitive lifetime of Flipper-TR, validated the gradient but failed to catch the dependence on actin due to the dual and opposite effects of tension on lifetime. Finally, measurements utilizing fluorescently tagged transferrin (Tf) demonstrated that the functional state of the membrane also showed similar height dependence. Thus, planes where tension maximized showed a peak in accumulation of Tf colocalizing with clathrin indicative of the presence of more pits. This enabled us to demonstrate that cells exist in tightly regulated patterned tension states that is coupled to their cytoskeleton as well membrane functions like endocytosis. Significance StatementThe cell membrane is protective but also highly dynamic - performing a diverse set of functions usually via membrane shape changes. These functions affect membrane mechanics but are also mechano-regulated. Mapping the state of cell surface mechanics or tension of live cells is therefore of fundamental importance. Interestingly, recent works have suggested that membrane tension can be non-uniform. However, no single tension-measuring technique can truly reach every part of the cell. Our work addresses this issue where we map tension in live HeLa cells using multifarious approaches including the measurement of tether forces, membrane fluctuations, and lipid compaction. We show that at the top/apical surface, the membrane-tension is lower than that at the midplane. The observed gradient resembles that of the state of endocytosis and controlled acto-myosin contractility.

biophysics↗

bioRxiv2024

Phosphatidylinositol-3,5-bisphosphate mediated vacuolar morphology modulation is integral to ethanol stress response

Vacuoles enlarge in response to ethanol. We used quantitative imaging to show that even brief exposure to ethanol causes a rapid transition from multilobed vacuoles to a single compartment. Vacuole unlobing is essential as mutants restricted for vacuole fusion exhibit greater ethanol sensitivity. This response involves the inhibition of vacuole fission via downregulation of the activity of Fab1, a lipid kinase generating the signaling lipid phosphatidylinositol-3,5-bisphosphate. Ethanol exposure results in the redistribution of a phosphatidylinositol-3,5-bisphosphate sensor from the perivauolar dots to the cytoplasm and the dissociation of the effector of this lipid, Atg18, from the vacuolar membrane to the cytoplasm. Impaired Atg18 membrane recruitment also entails a loss of interaction between a scaffold of the Fab1 complex, Vac14, and Atg18. A hyperactive Fab1 mutant, with elevated pools of phosphatidylinositol-3,5-bisphosphate, shows delayed vacuole enlargement; the partial relocation of the phosphatidylinositol-3,5-bisphosphate probe to the perivacuolar dots and of Atg18 to the vacuole membrane. Since Atg18 is responsible for vacuole fragmentation, our results show that, under ethanol stress, cells actively regulate vacuole morphology by modulating phosphatidylinositol-3,5-bisphosphate levels.

cell biology↗

bioRxiv2024

Divergent Functions of Late ESCRT Components in Giardia lamblia: Insights from Subcellular Distributions and Protein Interactions

Giardia lamblia, a human gut pathogen, possesses a minimal ESCRT (Endosomal Sorting Complex Required for Transport) machinery. Paradoxically, there are multiple paralogs of some late-ESCRT components. There are three paralogs for Vps4, GlVps4a, GlVps4b, and GlVps4c, and two for Vps46, GlVps46a, and GlVps46b. This study addressed whether these paralogs discharge overlapping and/or distinct cellular functions by determining the sub-cellular distribution of the paralogs in trophozoites and during encysting. Consistent with the distribution of orthologs in model organisms, most of these components were found to be associated with various cellular membranes, particularly in regions of acute membrane bending. Some of these paralogs are also associated with microtubule structures, such as cytoplasmic axonemes and the median body. Considering their diverse sub-cellular distributions, it is likely that they perform non-overlapping functions within the cell. Furthermore, their redistribution during encystation indicates that they may play a role in the morphological and functional changes accompanying this transition. The study also characterized GlIst1, an ESCRT-III accessory protein that undergoes unique post-translational myristoylation at lysine 43, potentially aiding its membrane recruitment. GlIst1 selectively interacts with GlVps4b through non-canonical MIT-MIM interactions. GlIst1 also exhibits selective interaction with GlVps46b. Such selective interaction of GlIst1 with only specific paralogs of GlVps4 and GlVps46 further underscores the distinct cellular roles of these paralogs. Author SummaryGiardia lamblia, a unicellular protozoan parasite, is the causative agent of giardiasis, a water-transmitted disease affecting millions globally. This disease poses a substantial threat to public health, especially in less developed countries, where clean water and proper sanitation are scarce. The parasite manifests in two morphologically distinct forms, trophozoites and cysts. Transformation between these forms is essential for the organisms survival, spread, and infection processes. Trophozoites, the active and motile form of Giardia, inhabit the small intestine of the host and trigger infections. These trophozoites can transform into cysts through encystation, enabling the parasite to endure harsh external environments and spread between hosts through contaminated water or food sources. The transition between these states necessitates extensive membrane restructuring. Such changes are likely to involve the Endosomal Sorting Complex Required for Transport (ESCRT) machinery, as it has been shown to participate in both prokaryotic and eukaryotic membrane remodeling events. Our research sheds light on the ESCRT machinery in G. lamblia, a crucial membrane-shaping system that may facilitate the transition between trophozoites and cysts. The ESCRT machinery in G. lamblia is distinct from that in yeast and humans, representing one of the most basic ESCRT systems. Our investigation provides valuable information about the intracellular distribution of various late-ESCRT components under different conditions, their potential functions, and their interactions with other late-ESCRT components. These findings may contribute significantly to our understanding of the basic operation of the ESCRT machinery in this parasite.

cell biology↗

bioRxiv2024

Two paralogues of N-ethylmaleimide sensitive factor: An exception to the minimal vesicular trafficking machinery of Giardia

Vesicular trafficking plays a critical role in the survival of the human gut pathogen Giardia lamblia as it drives nutrient uptake and morphological stage transition. Unlike most eukaryotes, Giardia has a minimal vesicular trafficking machinery. Herein, we report a rare exception to this minimalism wherein two paralogues of NSF, a crucial factor driving vesicular trafficking by uncoupling the cis-SNARE bundle, are present in this unicellular parasite. While GlNSF114776 and GlNSF112681 share very high sequence homology, they are likely to have distinct cellular roles as they exhibit differences in their affinities towards the Gl-SNAPs and display non-overlapping distribution in encysting trophozoites. Under multiple stress conditions (nutritional, oxidative and nitrosative), while GlNSF112681 remains at peripheral vesicles, GlNSF114776 relocalizes to the anterior flagella-associated striated fibres, indicating a possible role in regulating flagellar motility. At this location, GlNSF114776 is likely to perform a 20S complex independent function as neither Gl-SNAPs nor GlSNAREs are present there. The two paralogues are likely needed for stress adaptation as both copies have also been retained in Giardia genomes isolated from clinical samples. This non-canonical function of the GlNSF114776 may have evolved to support the unique architecture and motility of the anterior flagella.

cell biology↗

bioRxiv2024

cytoKernel: Robust kernel embeddings for assessing differential expression of single cell data

High-throughput sequencing of single-cell data can be used to rigorously evlauate cell specification and enable intricate variations between groups or conditions. Many popular existing methods for differential expression target differences in aggregate measurements (mean, median, sum) and limit their approaches to detect only global differential changes. We present a robust method for differential expression of single-cell data using a kernel-based score test, cytoKernel. cytoKernel is specifically designed to assess the differential expression of single cell RNA sequencing and high-dimensional flow or mass cytometry data using the full probability distribution pattern. cytoKernel is based on kernel embeddings which employs the probability distributions of the single cell data, by calculating the pairwise divergence/distance between distributions of subjects. It can detect both patterns involving aggregate changes, as well as more elusive variations that are often overlooked due to the multimodal characteristics of single cell data. We performed extensive benchmarks across both simulated and real data sets from mass cytometry data and single-cell RNA sequencing. The cytoKernel procedure effectively controls the False Discovery Rate (FDR) and shows favourable performance compared to existing methods. The method is able to identify more differential patterns than existing approaches. We apply cytoKernel to assess gene expression and protein marker expression differences from cell subpopulations in various publicly available single-cell RNAseq and mass cytometry data sets. The methods described in this paper are implemented in the open-source R package cytoKernel, which is freely available from Bioconductor at http://bioconductor.org/packages/cytoKernel.

bioinformatics↗

bioRxiv2024

Optimising future rhino population management strategies using insights from genetic health assessments across India

Various species conservation paradigms are facing enormous challenges during the ongoing Anthropocene. While the widely-used reintroduction/translocation-based approaches have supported many endangered species population recoveries, they seldom use detailed genetic information during initial planning. The Indian greater one-horned rhino typifies such assisted migration-driven species recovery, but currently facing long-term survival concerns due to their mostly small, isolated populations reaching respective carrying capacities. We assessed nation-wide rhino genetic health, identified suitable source populations and provided future translocation scenarios for all extant and proposed rhino habitats. Analyses with 504 unique rhino genotypes across all seven Indian rhino-bearing parks revealed six genetically-isolated populations with overall moderately low genetic diversity. Our results showed that Kaziranga and Manas NPs (Assam) to have the best rhino genetic health, whereas Jaldapara and Gorumara NPs (West Bengal) undergoing strong genetic erosions. Forward genetic simulations suggested that annual supplementation efforts from only few Assam rhino populations (Kaziranga NP, Orang NP and Pobitora WLS) are best suited for genetic rescue of most of the extant populations. Overall, the genetic diversity and differentiation patterns mimics the complex evolutionary history and individual recovery histories. We suggest park-specific management solutions (ranging from protection measures, grassland restoration, livestock and conflict management, regular supplementation events etc.) to ensure the species long-term persistence and prevent the alarming loss of grassland habitats and its associate biodiversity. We insist on utilising such genetic health indices-driven population management solutions to identify targeted mitigative measures in other species.

genetics↗