Biology subjects

Prakash, D.

Publications and source records attributed to Prakash, D..

6 recordsLinked to original sources

bioRxiv2025

Functional Characterization of 123 Genes from Mycobacteriophage LeBron Uncovers Cytotoxic Gene Families in Cluster L1

Bacteriophages represent a vast reservoir of genetic diversity however, functional annotation remains a major challenge, as most predicted gene products lack detectable similarity to characterized gene families. Experimental approaches such as systematic overexpression screens provide an avenue for identifying phage genes that influence bacterial physiology. Here, we report an overexpression screen of all 123 predicted protein-coding genes from Cluster L1 mycobacteriophage LeBron, the first representative of this cluster to undergo genome-wide functional analysis. Expression assays in Mycobacterium smegmatis revealed that 39 genes (32%) impaired host growth, with nineteen of these toxic genes (49%) assigned no known function. The proportion of cytotoxic genes observed in LeBron is comparable to findings from Clusters K and F, despite minimal sequence conservation across clusters. Interestingly, a subset of LeBrons toxic genes appear to be functionally analogous to previously identified toxic genes in other clusters, suggesting conserved biological activities carried out by non-homologous proteins. Additionally, this analysis uncovered several novel gene families that elicit strong cytotoxic effects, expanding the known catalog of phage-derived bacterial growth inhibitors. These results provide new insights into phage gene functions and demonstrate the value of genome-wide expression screening for uncovering conserved and cluster-specific interactions between bacteriophages and their hosts.

microbiology↗

bioRxiv2025

Fabrication of a Parali (Rice Straws) Biomass & Herbal Based Filtration System for Sustainable Rural Water Purification

Access to safe drinking water remains a serious challenge in rural India, where traditional chemical and membrane-based filtering systems are often unavailable due to their high cost, energy requirements, and maintenance demands. This work develops and validates a low-cost, eco-friendly herbal filtration system for Mubarakpur hamlet by combining the antibacterial properties of plant extracts with natural filter media. The physical, chemical, and microbiological properties of the water samples collected from ponds, wells, sewage, and tap sources included turbidity, pH, COD, BOD, heavy metals, and bacterial load. Herbal extracts derived from Neem (Azadirachta indica), Bael (Aegle marmelos), Lemon, Amla, Moringa, Garlic, and Ginger had bactericidal effects when tested for antimicrobial activity; however, the peels of Bael and Lemon exhibited the best inhibition of Streptobacillus species. A six-layer prototype filtration device including cotton cloth, charcoal, parali biomass, gravel, sand, and a layer of herbal extract was created as a result of these findings. The extracts of lemon and bael exhibited the greatest inhibition of Streptobacillus species when tested for antibacterial activity. A six-layer prototype filtration device including cotton cloth, charcoal, parali biomass, gravel, sand, and a layer of herbal extract was created as a result of these findings. Laboratory testing of the small prototype revealed significant improvements in water quality: the microbial load dropped from 2,000,000 CFU/mL to 0 CFU/mL, the turbidity went from 300 NTU to 0.8 NTU, the COD decreased from 1000 mg/L to 9 mg/L, and the BOD decreased from 200 mg/L to 3.5 mg/L. Lead levels in tap water (0.02 mg/L) were also reduced to undetectable levels.

bioengineering↗

bioRxiv2025

Exploring the Microbial Geobiological Pattern Across the Serpentinization Sites through Metagenomic and Elemental Composition Analyses

It is well-known that ultramafic rocks can continuously generate hydrogen through the serpentinization process associated with dynamic geochemical and geobiological interactions. This study aims to gain an improved understanding of these dynamic processes through the understanding of diverse microbial populations in order to maximize the geologic hydrogen production potential. The water samples were collected from a near surface serpentinite site in Northern California, USA. Elemental analyses of these water samples revealed the presence of essential dissolved minerals such as magnesium, calcium, and potassium, along with trace elements including iron, cobalt, and nickel. These elements act as cofactors for enzymes involved in microbial metabolic processes and Non-metric Multidimensional Scaling analysis supports this corelation. Furthermore, the analysis of total organic carbon (TOC) showed significant levels of organic carbon, suggesting a link with biological carbon cycling processes. Metagenomic analysis uncovered a diverse microbial community of hydrogen-fueled microbial consortia at the sampling sites, encompassing hydrogenogenic and hydrogenotrophic microorganisms. We examine hydrogen-metabolizing communities, including sulfate-reducing bacteria, acetogens, and methanogens, supported by diversity in hydrogenase enzymes across various sampling sites. These observations are corroborated by genomic accession data and abundance profiling of genes associated with acetogenesis, methanogenesis, and carbon monoxide metabolism. These investigations provide new insights into hydrogen-metabolizing microorganisms in northern California and propose frameworks for optimizing hydrogen production through the inhibition of hydrogen metabolism. O_FIG O_LINKSMALLFIG WIDTH=155 HEIGHT=200 SRC="FIGDIR/small/678891v1_ufig1.gif" ALT="Figure 1"> View larger version (49K): org.highwire.dtl.DTLVardef@11e5041org.highwire.dtl.DTLVardef@126ea56org.highwire.dtl.DTLVardef@1e2cd4forg.highwire.dtl.DTLVardef@11537f2_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIThe association of the serpentinization process with dynamic geochemical and geobiological interactions. C_LIO_LIMetagenomic study found an assorted microbial community of hydrogen-fueled consortia at the different sampling sites in Northern California C_LIO_LIHydrogen-metabolizing communities counted, including sulfate-reducing bacteria, acetogens, and methanogens. C_LI

microbiology↗

bioRxiv2025

Screening of Natural Plant Extracts for Antimicrobial Activity Against Streptobacillus moniliformis

The rise of antimicrobial resistance has driven the search for alternative antibacterial agents, including plant-based compounds. This study evaluates the antimicrobial potential of selected herbal extracts against Streptobacillus moniliformis using the agar well diffusion method. The tested extracts included Tulsi leaves (Ocimum sanctum), Neem leaves (Azadirachta indica), Bael leaves (Aegle marmelos), Adarak peels (Zingiber officinalef), Moringa seeds and leaves (Moringa oleifera), Dalchini (Cinnamomum verum), Lemon/Orange peels (Citrus limon and Citrus sinensis), and Ginger peels (Zingiber officinale). Among these, Bael leaves and Lemon peels demonstrated significant antibacterial activity, forming distinct zones of inhibition. In contrast, Neem and Moringa extracts did not inhibit bacterial growth. The observed antimicrobial activity is likely due to the presence of bioactive compounds such as flavonoids, tannins, and essential oils, which may disrupt bacterial cell walls and metabolic processes. Notably, S. moniliformis exhibited limited survival in culture, while other bacterial strains showed minimal resistance. These findings suggest that certain herbal extracts, particularly Bael leaves and Lemon peels, may serve as natural antimicrobial agents against S. moniliformis. Further studies are required to isolate and characterize the active compounds responsible for this antibacterial activity to explore their potential in developing alternative antimicrobial therapies.

microbiology↗

bioRxiv2022

Pyrrole produced by Pseudomonas aeruginosa influences olfactory food choice of Caenorhabditis elegans

Sense of smell can influence dietary choices in animals. So far, most of the research has focused on how animals respond to distinct odors when they are introduced individually. However, it remains unclear how animals evaluate foods that contain a bouquet of olfactory cues with contrasting effects. Here, we utilize Caenorhabditis elegans as a bacterivore to ask if odors produced by dietary bacteria can regulate worms food preferences. We show that the bacterium Pseudomonas aeruginosa produces a relatively small quantity of a new attractant for C. elegans. We identify the odor as a heterocyclic compound called pyrrole. We find that pyrrole contributes to the sensory decision-making of worms in diet preference assays. Using specific neuronal ablation lines and calcium response assays, we show that AWA odor sensory neurons of worms are necessary for sensing pyrrole. In all, we show that specific odors produced by bacteria can influence food choice behavior of animals.

animal behavior and cognition↗

bioRxiv2018

Two-component systems regulate swarming in Pseudomonas aeruginosa PA14

Swarming in Pseudomonas aeruginosa is a quorum-dependant motility over semi-solid surfaces. On soft agar, P. aeruginosa exhibits a dendritic swarm pattern, with multiple levels of branching. Swarm patterns vary considerably depending upon the experimental design. In the present study, we show that the swarm pattern is plastic and media dependent. We define several quantifiable, macroscale features of the swarm to study the plasticity observed across media. Further, through a targeted screen of 113 genes encoding two-component system (TCS) components, we show that 44 TCS genes regulate PA14 swarming in a contextual fashion. However, only four TCS genes are essential for swarming. Many swarming-defective TCS mutants are highly efficient in biofilm formation indicating an antagonistic relationship between swarming and biofilm states in P. aeruginosa.

microbiology↗