Biology subjects

Ramakrishnan, J.

Publications and source records attributed to Ramakrishnan, J..

5 recordsLinked to original sources

bioRxiv2025

Deciphering the global genomic landscape of C. neoformans: Population dynamics, molecular epidemiology and genomic signatures of pathogenicity

The study investigates global genomic surveillance of Cryptococcus neoformans over three decades to elucidate genetic diversity, incorporating serotypes, molecular types, STs and mating types, phylogenomics, virulence-associated determinants, antifungal resistance, and pangenome profiles. Across 139 study genomes, the isolates exhibited nineteen distinct sequence types (STs), among which ST5 (63%) was the most prevalent. The predominance of MAT mating type 91% mirrors enhanced virulence, environmental adaptability and clonal expansion, enabling its persistence without MATa (9%) counterparts. The phylogenomic analysis revealed, there is no distinct clustering of isolates from clinical and environmental settings, indicating a high level of genome conservation across sources. Core-accessory genome partitioning and ortholog-based clustering revealed clonal population dominance of the VNI lineage across continents, alongside clear divergence from the VNIV lineage. Virulence gene analysis highlighted conserved expression of capsular genes, phospholipase gene, iron acquisition genes and superoxide dismutase genes, while point mutations and aneuploidy in ERG11 and AFR1 suggested potential azole-resistance mechanisms. This study delivers a holistic assessment of global genomic diversity in the C. neoformans population, emphasising evolutionary conservation, lineage-specific divergence, and adaptability to environment, host and anti-fungal treatments.

bioinformatics↗

bioRxiv2025

Deciphering the Survival Strategies of the Entomopathogenic Nematode Steinernema carpocapsae Using Rapid Desiccation Assisted by Nanoparticle-Based Emulsion

Water retention is essential for survival under desiccating conditions, especially for entomopathogenic nematodes (EPNs) used as biocontrol agents. Foliar application of EPNs causes rapid desiccation (RD), severely reducing their survival and efficacy. We investigated the physiological and molecular responses of Steinernema carpocapsae to RD, delivered in a novel nanoparticle-stabilized emulsion to improve tolerance under variable humidity. We hypothesized that the formulation would enhance EPNs survival, by promoting early stress-responsive pathways and water-retention mechanisms. Formulated nematodes exhibited delayed water loss and increased survival under low humidity compared with non-formulated controls. The emulsion mitigated RD by enhanced hydration retention and reduced water loss, effects that were strongly associated with differential trehalose accumulation. In addition, maintenance of basement membrane integrity and cytoskeletal organization, emerged as a critical component of desiccation. These findings advance understanding of RD tolerance in EPNs and demonstrate how tailored formulation strategies can protect biocontrol agents under desiccation stress.

developmental biology↗

bioRxiv2024

Hybrid Genome Sequence of Cryptococcus neoformans of Indian origin and comparative genome analysis

ObjectivesThe Indian isolate of Cryptococcus neoformans underwent complete genome sequencing to elucidate its genomic architecture and functional characteristics. Furthermore, this study aimed to comprehensively characterize the virulence factors (virulome), antibiotic resistance genes (resistome), and the pan-genome of C. neoformans spp. through a comparative genomic analysis, providing insights into the genetic diversity and evolutionary relationships among strains. MethodsThe genomic data of a clinical strain of C. neoformans was assembled and annotated by MaSuRCA5 and Braker tool. Along with this, the assembled genomic data of the 11 strains were retrieved from NCBI datasets. The comparative virulome, resistome, phylogeny and of the 12 C. neoformans genomes were analyzed using DFVF, AFRbase, BLAST, CLUSTAL Omega, MEGAX, and Orthovenn3, respectively. ResultsThe sequenced isolate was identified as a member of the Cryptococcus neoformans var. grubii subspecies. Notably, virulence-related genes comprise approximately 4.8% of the total genome. A comparative genomic analysis of 12 study genomes revealed variations in virulence patterns, including differences in melanization, immune evasion, blood-brain barrier evasion, transcriptional regulation, and oxidative stress response. The phylogenetic study using MLST and orthologous clusters categorized the subspecies grubii and neoformans in different clades. Pan-genome analysis showed that 73.6% of orthologous gene clusters and 77.72% of orthologous proteins were conserved across all 12 study genomes, indicating a shared core genome. Furthermore, the evolutionary relatedness study of the pan-genome revealed gene expansion and contraction events among the study strains. ConclusionThis pioneering study presents the first comprehensive genomic and comparative genomic analysis of Cryptococcus sp., incorporating data on virulence genes, antibiotic resistance, and pan-genome dynamics. Key findings reveal that strains Cn, H99, and JEC21 harbor crucial virulence genes associated with infection severity. While all study strains possess genes promoting antifungal resistance (AFR), most lack specific single nucleotide polymorphisms defining AFR. Consistent with pan-genome analysis, our results show significant gene expansion and contraction events in these strains. This study underscores the importance of bioinformatic tools for efficient whole-genome analysis and large-scale comparative genomics research.

genomics↗

bioRxiv2024

Elucidating the effect of cations on Klebsiella pneumoniae biofilm and related genes

K. pneumoniae is a non-motile, encapsulated bacterium from the Enterobacteriaceae family. The illnesses related to this opportunistic pathogen are pneumonia, Urinary Tract Infection (UTI), pyogenic liver abscess, endophthalmitis, and meningitis. Among them, UTI is predominant due to its biofilm formation leading to the mortality of 150 million people worldwide. The function of monovalent and divalent ions on Klebsiella biofilm, aside from physiochemical variables, remains unclear. Hence the present study was performed to analyze the role of K+, Ca2+, Na+, Mg2+, NH+4 in biofilm formation and its influence on biofilm-related genes. Among the tested cations, K+ and Ca2+ yielded strong biofilm in clinical and environment isolates in pH between 6.5 to 9.5. Increasing Ca2+ ions concertation reduced the Klebsiella biofilm. When compared to the hypercalciuria condition (Ca2+ level > 5 mM), 2.5 mM resulted in high biofilm mass. Cations concurrently enhanced the size of the capsule and cell density of Klebsiella but were not correlated with biofilm mass. Expression of the LPS gene (WbaG) either in planktonic or biofilm stage promoted biofilm formation in the presence of K+, Ca2+ and Na+. Whereas, expression of fimbriae genes (FimH and mrkD) was co- regulation, and capsule genes (RmpA and Wcab) were absent. Stating, the primary component needed for the Klebsiella biofilm is not the capsule or fimbriae, rather LPS. Resulting as a potent target in the treatment of Klebsiella biofilm in UTI. To the best of our knowledge, this is the first kind of study on the effect of cation ions on biofilm and planktonic cells of Klebsiella spp. and demonstrating the role of LPS biosynthesis gene (WbaG) in biofilm development.

microbiology↗

bioRxiv2019

Biofilm of Klebsiella pneumoniae minimize phagocytosis and cytokine expression by macrophage cell line

Infectious bacteria in biofilm mode are involved in many of persistent infections. Owing to its importance in clinical settings many in vitro and in vivo studies have analysed the structural and functional properties of biofilm, its resistance to antibiotic exposure etc. Currently the immune mechanism toward the clearance of biofilm infections is being investigated. K. pneumoniae is one of the major leading causes of biofilm infections on indwelling medical devices. There was no previous literature that demonstrates the interactions of macrophage cells lines and Klebsiella biofilm, as the first report, we investigated the in vitro response of Klebsiella biofilm to phagocytosis and cytokine expression. We developed an in vitro model to study the interactions of Kebsiella biofilm and macrophage. The phagocytosis assay was performed for heat inactivated and live biofilm. A similar phagocytic response against both biofilms were observed when these cells were exposed to RAW 264.7 macrophages. Also, the expressions of TLR2, iNOS, inflammatory cytokines such as IL-{beta}1, IFN-{gamma}, IL-6, IL-12, IL-4, TNF- and anti-inflammatory cytokines, IL-10 during phagocytosis were analysed. These results collectively demonstrated that the rate of phagocytosis was an average of 15% for both biofilms. Also, when activated macrophage was exposed to heat-inactivated or live biofilms, there was a significant increase in proinflammatory cytokine genes together with expected increase in TLR2 and iNOS. Thus, it is clear that macrophage response against biofilm producing K. pneumoniae results in increase in phagocytic rate and a corresponding increase in inflammatory cytokine gene expression which could be important for clearing K. pneumoniae cells.

immunology↗