Biology subjects

Ganesh, A.

Publications and source records attributed to Ganesh, A..

12 recordsLinked to original sources

bioRxiv2026

Early Spatiotemporal Deficits Become Competitive Advantages During Collective Expansion

Rapid spatial expansion into new territory is fundamental to population persistence, ecological dominance, and evolutionary success. Every race for space is initiated by founding populations, yet how their initial spatiotemporal conditions shape the outcome remains unclear. Here, by combining nonlinear theory with quantitative microbial experiments, we show that collective motility can overturn the classical logic of priority effects. Populations expanding by individual motility retain the expected advantage of an earlier start or a larger initial footprint. By contrast, under collective motility, nonlinear density-dependent feedback enables initially lagging populations to accelerate, transforming early deficits into long-term competitive advantage. Optimization predicts that this advantage is maximized when the delay scales log-linearly with initial density. We validate this scaling behavior across diverse swarming microbes, revealing a general regulatory strategy for competitive range expansion. Competition and evolution experiments further show that this behavior is adaptive and robustly preserved. Together, our results establish a quantitative framework linking the initial organization of founding populations to final spatial outcomes, helping explain how organisms regulate early dynamics to shape ecological success in space. SignificanceRapid expansion into new territory often decides who will dominate. To understand this contest, we focused on how the race begins. We built a theoretical framework linking the initial conditions of founding populations to long-run competitive outcomes, then tested its predictions experimentally in microbial populations by controlling inoculum, quantifying range expansion, competing strains head-to-head, and performing laboratory evolution. Our results show that history is not merely the starting point of range expansion, but part of the regulatory strategy for winning space. This work provides a mechanistic framework for quantitatively thinking about range expansion across systems, from microbial colonization and biological invasions to infection spread, cancer metastasis and developmental migration.

ecology↗

bioRxiv2026

The Chromosome-Scale Genome of Phyllanthus niruri Reveals Candidate Genes and a Putative Biosynthetic Framework for Phyllanthin Formation.

Phyllanthus niruri (Phyllanthaceae) is a medicinally important herb known for producing phyllanthin, a bioactive dibenzylbutane lignan with reported hepatoprotective and antioxidant properties. However, the biosynthetic basis of phyllanthin production remains unresolved, largely due to the absence of a reference genome for the species. We report a Chromosome-Scale Assembly of P. niruri generated by integrating PacBio HiFi long reads and Illumina short reads, followed by reference-guided scaffolding against Phyllanthus cochinchinensis. The assembly has an L50 of 7 and 97.6% BUSCO completeness. Annotation predicted 19,254 protein-coding genes (91.1% functionally annotated), with phenylpropanoid biosynthesis emerging as the most enriched specialized-metabolism pathway in the genome. Using pathway-guided genome mining, structural similarity analysis, and comparative metabolic reconstruction, we propose a putative biosynthetic pathway for phyllanthin originating from the phenylpropanoid-lignan branch through secoisolariciresinol-like intermediates, followed by terminal O-methylation reactions. A total of 305 unique candidate genes associated with the proposed pathway were identified, including expanded families of dirigent proteins, peroxidases, secoisolariciresinol dehydrogenases, and O-methyltransferases. Comparative transcriptomic analyses across related Phyllanthus species further supported the proposed pathway through coordinated expression of lignan-associated genes and tissue-specific enrichment of O-methyltransferases. This work provides the first reference genome for P. niruri and a prioritized candidate gene set for functional characterization of phyllanthin biosynthesis.

genomics↗

bioRxiv2026

Characterization of programmed cell death pathways activated in Mycobacterium tuberculosis-infected human macrophages

Mycobacterium tuberculosis (Mtb) primarily infects human lung macrophages, which serve as its major replication niche. Mtb can manipulate host macrophage cell death pathways to its advantage by inhibiting apoptosis and inducing necrotic cell death. However, the specific necrotic cell death pathway activated in human macrophages after Mtb infection remains unclear. Here, we used the THP-1 cell line and primary human monocyte-derived macrophage (hMDM) to analyze multiple programmed cell death pathways during days 1-3 after Mtb infection. Confocal microscopic analysis demonstrates that Mtb-infected THP-1 cells or hMDMs rarely exhibited apoptosis. Immunoblotting shows that Mtb induces significant CASP3 and GSDME activation in THP-1 cells, but not in hMDMs. We show that Mtb, in THP-1 cells but not hMDM, induces a significant increase in GSDMD cleavage, a hallmark of pyroptosis. MLKL phosphorylation was not observed in THP-1 cells or hMDMs during Mtb infections, indicating an absence of necroptosis. No changes in ferroptosis markers such as GPX4 expression or lipid peroxidation levels were detected. Time-lapse live-cell imaging revealed no lysosomal membrane permeabilization prior to plasma membrane rupture (PMR). However, we observed DNA release from Mtb-infected THP-1 cells and hMDMs after PMR. The DNA released from THP-1 cells exhibits low levels of myeloperoxidase and histone H3 citrullination. High-resolution confocal imaging shows that Mtb is associated with the released DNA. We demonstrate that pyroptosis induction in THP-1 cells is dispensable for the DNA release and cell death induction. In conclusion, our results reveal that Mtb-triggered cell death in hMDMs bypasses canonical cell death pathways like apoptosis, pyroptosis, necroptosis, and ferroptosis. Instead, cell death in both THP-1 cells and hMDMs correlates with DNA release, potentially through a pathway similar to NETosis in neutrophils.

cell biology↗

bioRxiv2025

Benchmarking Framework to Catalyze Individual Human Genome Projects

Individual human genome projects still aim for chromosome-level gapless assemblies, which rely on high-coverage reads from multiple long-read sequencing platforms using a multiplicity of assembly pipelines. Moreover, the dependence on DNA derived from primary cell lines for these assemblies makes such projects prohibitively expensive to scale for individual genome initiatives and to catalyze clinical applications. Over the past decades, genome assembly quality has advanced remarkably from draft assemblies in the early 2010s, to chromosome-level assemblies using error-prone long reads in the late 2010s, to the recent T2T gapless assemblies enabled by high-quality next-generation long-read technologies. That said, a systematic evaluation of trade-offs from assemblies obtained at various coverages, starting at 3x, from a single long-read sequencing platform, is critical for developing a cost-effective and practical strategy for catalyzing individual genome initiative. Here, by assembling contigs at various coverage levels through downsampling of existing PacBio HiFi reads from three individuals, we demonstrate that high-quality assemblies, as measured by standard assembly metrics and DNA-level linearity relative to a reference across most chromosomes (developed inhouse), can be achieved at approximately 12x coverage. Interestingly, starting at coverages as low as 6x, assembly metrics, including BUSCO scores and DNA-level linearity, begin to saturate, suggesting minimal trade-offs. Furthermore, we show that known structural variants (e.g., the 8p23.1 inversion) can be reliably identified even at 6x coverage. Together, these results suggest that cost-effective strategies can be developed to advance individual genome initiatives potentially from PacBio HiFi reads from a single SMRT cell per human genome.

bioinformatics↗

bioRxiv2024

NLRP11 is required for canonical NLRP3 and non-canonical inflammasome activation during human macrophage infection with mycobacteria

The NLRP11 protein is only expressed in primates and participates in the activation of the canonical NLRP3 and non-canonical NLRP3 inflammasome activation after infection with gram-negative bacteria. Here, we generated a series of defined NLRP11 deletion mutants to further analyze the role of NLRP11 in NLRP3 inflammasome activation. Like the complete NLRP11 deletion mutant (NLRP11-/-), the NLRP11 mutant lacking the NACHT and LRR domains (NLRP11{Delta}N_LRR) showed reduced activation of the canonical NLRP3 inflammasome, whereas a pyrin domain mutant (NLRP11{Delta}PYD) had no effect on NLRP3 activation. The NLRP11-/- and NLRP11{Delta}N_LRR mutants but not the NLRP11{Delta}PYD mutant also displayed reduced activation of caspase-4 during infection with the intracytosolic, gram-negative pathogen Shigella flexneri. We found that the human adapted, acid-fast pathogen Mycobacterium tuberculosis and the opportunistic pathogen M. kansasii both activate the non-canonical NLRP11 inflammasome in a caspase-4/5-dependent pathway. In conclusion, we show that NLRP11 functions in the non-canonical caspase-4/5 inflammasome activation pathway and the canonical NRLP3 inflammasome pathway, and that NLRP11 is required for full recognition of mycobacteria by each of these pathways. Our work extends the spectrum of bacterial pathogen recognition by the non-canonical NLRP11-caspase4/5 pathway beyond gram-negative bacteria. IMPORTANCEThe activation of inflammasome complexes plays a crucial role in intracellular pathogen detection. NLRP11 and caspase-4 are essential for recognizing lipopolysaccharide (LPS), a molecule found in gram-negative bacteria such as the human pathogens Shigella spp., which activate both canonical NLRP3 and non-canonical inflammasome pathways. Through a series of deletion mutants, we demonstrate that the NACHT and LRR domains of NLRP11, but not its pyrin domain, are critical for detection of S. flexneri. Notably, our research reveals that the acid-fast bacterium M. tuberculosis is also detected by NLRP11 and caspase-4, despite not producing LPS. These findings significantly expand the range of pathogens recognized by NLRP11 and caspase-4 to now include acid - fast bacteria that do not contain LPS and underscore the versatility of these innate immune components in pathogen detection.

immunology↗

bioRxiv2024

The first assembled chromosome-level genome of an individual from Karnataka, India

We present the first chromosome-level assembled genome of an individual from Karnataka, India (KIn1), using de novo assembly of 12x coverage of PacBio HiFi reads generated in-house and 30x Hi-C data from the most ethnically related individual to KIn1 from Andhra Pradesh (HG04712), publicly available under International Genome Sample Resource (IGSR). We achieved an N50 of 137 Mb and an L50 of 9--very close to the maximum achievable N50 of 147 Mb and minimum achievable L50 of 8 respectively for human genomes. A comparison of the KIn1 assembly with assemblies of four other individual genomes from a Puerto Rican (PR1), Ashkenazi (Ash1), Hans Chinese (Hans1), and Northern European (T2T) reported to date from resources like IGSR and/or Genome-in-a-Bottle (GIBR) collections shows that the longest scaffolds from KIn1 cover 80-90% of the reference chromosomes and exhibit near collinearity. We find a unique inversion in the chromosome 7 euchromatic region and other major translocations in chromosomes 17 and 20 in KIn1. We also produced a chromosome-level assembly for another individual from Punjab, Lahore (HG03492), for use in our comparison. The analysis of variants among select IGSR individuals using the KIn1 assembly as a reference reveals that the Indian Telugu from the UK (ITU) population in IGSR is ethnically closest to KIn1, followed by the Sri Lankan Tamil from the UK (STU) as representatives of South Asian ancestry.

genomics↗

bioRxiv2024

Salmonella Typhimurium infection inhibits macrophage IFNbeta signaling in a TLR4-dependent manner

Type I Interferons (IFNs) generally have a protective role during viral infections, but their function during bacterial infections is dependent on the bacterial species. Legionella pneumophila, Shigella sonnei and Mycobacterium tuberculosis can inhibit type I IFN signaling. Here we examined the role of type I IFN, specifically IFN{beta}, in the context of Salmonella enterica serovar Typhimurium (STm) macrophage infections and the capacity of STm to inhibit type I IFN signaling. We demonstrate that IFN{beta} has no effect on the intracellular growth of STm in infected bone marrow derived macrophages (BMDMs) derived from C57BL/6 mice. STm infection inhibits IFN{beta} signaling but not IFN{gamma} signaling in a murine macrophage cell line. We show that this inhibition is independent of the type III and type VI secretion systems expressed by STm and is also independent of bacterial phagocytosis. The inhibition is Toll-like receptor 4 (TLR4)-dependent as the TLR4 ligand, lipopolysaccharide (LPS), alone is sufficient to inhibit IFN{beta}-mediated signaling and STm-infected, TLR4-deficient BMDMs do not exhibit inhibited IFN{beta} signaling. In summary, we show that macrophages exposed to STm have reduced IFN{beta} signaling via crosstalk with TLR4 signaling, and that IFN{beta} signaling does not affect cell autonomous host defense against STm.

microbiology↗

bioRxiv2023

Targeted hypermutation of putative antigen sensors in multicellular bacteria

Diversity-generating retroelements (DGRs) are used by bacteria, archaea and viruses as a targeted mutagenesis tool. Through error-prone reverse transcription, DGRs introduce random mutations at specific genomic loci, enabling rapid evolution of these targeted genes. However, the function and benefits of DGR-diversified proteins in cellular hosts remains elusive. We find that 85% of DGRs from one of the major monophyletic lineages of DGR reverse transcriptases are encoded by multicellular bacteria, which often have two or more DGR loci in their genomes. Using the multicellular purple sulfur bacterium Thiohalocapsa sp. PB-PSB1 as an example, we characterized nine distinct DGR loci that cumulatively lead to more than 10294 possible different combinations of target polypeptides. With environmental metagenomes from individual Thiohalocapsa aggregates, we show that most of PB-PSB1s DGR targets are diversified across its biogeographic range, with spatial heterogeneity in the diversity of each locus. In PSB1 and other members of this lineage of cellular DGRs, diversified target genes are associated with NACHT-domain anti-phage defenses and putative ternary conflict systems previously shown to be enriched in multicellular bacteria. We propose that these DGR-diversified target genes act as antigen sensors that confer a form of adaptive immunity to their multicellular consortia. These findings have implications for the emergence of multicellularity, as the NACHT-domain anti-phage systems and ternary systems share both domain homology and conceptual similarities with the innate immune and programmed cell death pathways of plants and metazoans. SignificanceTo defend themselves against predators, bacteria employ a wide range of conflict systems, some of which are enriched in multicellular bacteria. Here, we show that numerous multicellular bacteria use related diversity-generating retroelements (DGRs) to diversify such conflict systems. Error-prone reverse transcription in DGRs introduces random, targeted mutations and rapid diversification. We used Thiohalocapsa PB-PSB1, a member of multicellular bacterial consortia, as a model to study this association between conflict systems and DGRs. We characterized the natural diversity of PB-PSB1 DGRs and propose they function as hypervariable antigen sensors. The accumulation of such DGR-diversified defense systems in multicellular bacteria emphasizes the fitness advantage of a rapidly diversifying immune system for the evolution of multicellularity.

microbiology↗

bioRxiv2023

Diversity at single nucleotide to pangenome scales among sulfur cycling bacteria in salt marshes

Sulfur-oxidizing and sulfate-reducing bacteria in salt marsh sediments are major controllers of ecosystem-scale carbon cycling. Cross-site comparisons of S-cycling communities are difficult given the rampant uncultured microbial diversity in sediment, yet comparisons are essential for revealing biogeographic, phylogenetic and functionally significant variation. Here, we use deep shotgun metagenomic sequencing data to construct and compare metagenome-assembled genomes (MAGs) of sulfur-cycling bacteria from Massachusetts and Alabama salt marshes that contrast in seasonality and sediment organic matter content. Samples were collected from sediments under Sporobolus alterniflorus and Sporobolus pumilus in separate MA vegetation zones, and under Sporobolus alterniflorus and Juncus roemerianus co-rooted in AL marsh. We grouped metagenomic data by plant species and site and identified 38 MAGs that included pathways for dissimilatory sulfate reduction or sulfide oxidation. Phylogenetic analyses indicated that 30 of the 38 were affiliated with uncultivated lineages. Read-mapping to MAGs showed significant differentiation of AL and MA samples, differentiation of samples taken in S. alterniflorus and S. pumilus vegetation zones in MA, but no differentiation of samples taken under S. alterniflorus and J. roemerianus that were rooted together in AL marsh. Pangenomic analyses of eight ubiquitous MAGs also detected site- and vegetation-specific genomic features, including varied sulfur-cycling operons, carbon fixation pathways, fixed single nucleotide variants, and active diversity-generating retroelements. This genetic diversity, detected at multiple scales even within uncultured groups, suggests evolutionary relationships affected by distance and local environment, and demonstrates differential microbial capacities for sulfur and carbon cycling in salt marsh sediments. ImportanceSalt marshes are known for their significant carbon storage capacity, and sulfur cycling is closely linked with the ecosystem-scale carbon cycling in these ecosystems. Sulfate reducers are the major decomposers in salt marsh systems, and sulfur-oxidizing bacteria remove sulfide, a toxic byproduct of sulfate reduction, supporting the productivity of marsh plants. To date, the complexity of coastal environments, heterogeneity of the rhizosphere, high microbial diversity and uncultured majority hindered our understanding of the genomic diversity of sulfur-cycling microbes in salt marshes. Here we use comparative genomics to overcome these challenges and provide an in-depth characterization of microbial diversity in salt marshes. We characterize sulfur-cycling communities across distinct sites and plant species and uncover extensive genomic diversity at the taxon level and specific genomic features present in MAGs affiliated with sulfur-cycling uncultivated lineages. Our work provides insights into the partnerships in salt marshes and a roadmap for multiscale analyses of diversity in complex biological systems.

ecology↗

bioRxiv2022

Modification of blood-based (IgG) to salivary-based (IgA) ELISA for Inflammatory Bowel Disease Diagnostic: Tumor necrosis factor (TNF) alpha quantification

Approximately 1.6 million people in the United States are struggling with Inflammatory bowel disease. Even though there are a number of diagnostic tools present, including MRI, CT scan, and laboratory tests, the public still lacks access to diagnostic tools due to their expensive costs and needs for the labor of trained phlebotomists. In response, this study focused on modification from blood based enzyme-linked immunoassay (ELISA) to salivary based ELISA in order to expand its accessibility. A 1mL saliva sample was spiked with 1 {+/-} 0.01 g/mL lyophilized IgG TNF proteins, and the unspiked saliva was used as a control to test the modified diagnostic. Saliva samples were processed through centrifugation and syringe filtration steps. The change in color between a serum and salivary ELISA kit using either centrifugation or syringe filtration steps was measured by a Color Analysis app that compared red, green and blue values and a microtiter plate reader. The new protocol of salivary-based ELISA lost sensitivity from 31.5pg/mL to 15.6pg/mL of TNF protein concentration. The best centrifugation method was when a combination of stock saliva and buffer was used before spiking the sample. This means that we can modify the current serum based diagnostic tool to a salivary diagnostic using centrifugation to filter the sample and implement it in developing countries due to its lower cost.

bioengineering↗

bioRxiv2022

Identification of a TNF-TNFR-like system in malaria vectors (Anopheles stephensi) likely to influence Plasmodium resistance

Identification of Plasmodium-resistance genes in malaria vectors remains an elusive goal despite the recent availability of high-quality genomes of several mosquito vectors. An. stephensi, with its three distinctly-identifiable forms at the egg stage, correlating with varying vector competence, offers an ideal species to discover functional mosquito genes implicated in Plasmodium resistance. Recently, the genomes of several strains of An. stephensi of the type-form, known to display high vectorial capacity, have been reported. Here, we report a chromosomal-level assembly of an intermediate-form of An. stephensi strain (IndInt), shown to have reduced vectorial capacity relative to a strain of type-form (IndCh). The contig level assembly with a L50 of 4 was scaffolded into chromosomes by using the genome of IndCh as the reference. The final assembly shows a heterozygous paracentric inversion, 3Li, involving 8 Mbp, which is syntenic to the extensively-studied 2La inversion implicated in Plasmodium resistance in An. gambiae involving 21 Mbp. Deep annotation of genes within the 3Li region in IndInt assembly using the state-of-the-art protein-fold prediction and other annotation tools reveals the presence of a TNF-like gene, which is the homolog of the eiger gene in Drosophila. Subsequent chromosome-wide searches revealed homologs of wengen (wgn) and grindelwald (grnd) genes in IndInt, which are known to be the receptors for eiger in Drosophila. We have identified all the genes in IndInt required for eiger-mediated signaling by analogy to TNF-TNFR system, suggesting the presence of a functionally active eiger signaling pathway present in IndInt. Comparative genomics of high-quality genome assemblies of the three type-forms with that of IndInt, reveals structurally disruptive mutations in eiger gene in all three strains of the type-form, alluding to compromised innate immunity in the type-form as the cause of high vectorial capacity in these strains. This is the first report of the presence of an intact evolutionarily-conserved TNF-TNFR signaling system in malaria vectors, with a potential role in Plasmodium resistance.

genomics↗

bioRxiv2021

A SARS-CoV-2 spike ferritin nanoparticle vaccine protects against heterologous challenge with B.1.1.7 and B.1.351 virus variants in Syrian golden hamsters

The emergence of SARS-CoV-2 variants of concern (VOC) requires adequate coverage of vaccine protection. We evaluated whether a spike ferritin nanoparticle vaccine (SpFN), adjuvanted with the Army Liposomal Formulation QS21 (ALFQ), conferred protection against the B.1.1.7 and B.1.351 VOCs in Syrian golden hamsters. SpFN-ALFQ was administered as either single or double-vaccination (0 and 4 week) regimens, using a high (10 g) or low (0.2 g) immunogen dose. Animals were intranasally challenged at week 11. Binding antibody responses were comparable between high- and low-dose groups. Neutralizing antibody titers were equivalent against WA1, B.1.1.7, and B.1.351 variants following two high dose two vaccinations. SpFN-ALFQ vaccination protected against SARS-CoV-2-induced disease and viral replication following intranasal B.1.1.7 or B.1.351 challenge, as evidenced by reduced weight loss, lung pathology, and lung and nasal turbinate viral burden. These data support the development of SpFN-ALFQ as a broadly protective, next-generation SARS-CoV-2 vaccine.

immunology↗