Biology subjects

Chowdhury, J.

Publications and source records attributed to Chowdhury, J..

5 recordsLinked to original sources

bioRxiv2026

Stepwise Proteinase K Digestion Improves Genomic DNA Yield and Purity from Goat Semen: A Comparative Pilot Study of Five Extraction Protocols

Background: Genomic DNA of high quality is a prerequisite for molecular genetic analyses. However, DNA extraction from goat semen is frequently challenged by highly compacted sperm chromatin and the presence of enzymatic inhibitors within the seminal plasma. Objectives: This pilot study aimed to identify a reliable and cost-effective method for isolating high-quality genomic DNA from caprine semen. Methods: Five extraction protocols were evaluated: an unmodified blood protocol (Protocol B), two modifications of a sperm protocol (Modified Protocols 1 and 2), and a stool protocol (Protocol BS) using a commercial spin-column kit (Kit A), alongside a second commercial silica membrane kit (Kit B). Three technical replicates per protocol were processed from a single frozen semen straw of a Black Bengal buck (with one replicate evaluated for Protocol B). Extracted DNA was evaluated based on concentration, purity (absorbance ratios A260/A280 and A260/A230), cost per sample, and PCR amplification success of the mitochondrial hypervariable region 1 (HVR1). Results: Modified Protocol 2 utilizing 100 uL of semen and two sequential 1.5-hour proteinase K incubations at 55 degrees C yielded the highest normalized DNA concentration (mean +/- SD: 55.9 +/- 30.4 ng/uL semen), optimal purity ratios (A260/A280 = 1.78; A260/A230 = 2.06), and the lowest cost per nanogram of DNA (INR 0.073 +/- 0.037). All extracts from this protocol were successfully amplified via PCR. While the Kruskal-Wallis test for normalized yield did not reach statistical significance (p = 0.075), rendering yield differences exploratory, Modified Protocol 2 demonstrated the strongest overall performance. Conclusions: Modified Protocol 2 offers a promising, cost-efficient workflow for caprine sperm DNA isolation. Given that this pilot study sampled a single animal, these findings must be validated using biological replicates from multiple bucks prior to widespread implementation.

molecular biology↗

bioRxiv2026

Modifying integrated nursery management through the lens of mycorrhizal ecology improves radiata pine seedling performance and reshapes root mycobiome structure at operational industry scale

Early management decisions in operational forestry are critical for plantation success because it strongly influences seedling quality at planting. Beyond shaping seedling morphology, nursery inputs can also restructure root-associated fungal communities which has consequences for nutrient acquisition, stress tolerance and disease suppression after planting. In this study, we altered nutrient and fungicide inputs based on mycorrhizal ecological theory and quantified the effects of these treatments on key dimensions of the growth performance of radiata pine seedlings. In parallel, we profiled the root-associated mycobiome, assigning fungal taxa to functional guilds and summarizing their richness, diversity, relative abundance and community structure. Using a composite performance index that integrates the key morphological and health measures into a single response variable, together with conventional statistical models with machine learning approaches, we identified management practises that promote both plant performance and a favourable root fungal community and determined the consistent microbiome changes linked to overall quality of the seedlings. These results suggest that microbial feedback loops occur even in highly managed nursery conditions. More broadly, by combining a composite performance index with predictive modelling, we provide a practical way to test complex management combinations and identify microbiome features associated with high-quality planting stock.

ecology↗

bioRxiv2025

Amino acid biostimulant increases pine photosynthetic efficiency and growth through optimised mycobiome and nitrogen assimilation

BackgroundAmino-acid biostimulants have emerged as powerful alternatives to conventional inorganic nitrogen fertilisers, yet their potential in forestry species like radiata pine (Pinus radiata) remains largely unexplored. In this study, we reveal physiological mechanisms of enhanced growth of radiata pine seedlings that are achieved by substituting standard inorganic fertigation, either partially or entirely, with amino-acid-based biostimulants. ResultsAmino-acid fertigation notably increased shoot biomass, plant height, and collar diameter. Critically, this approach reshaped the root fungal community, selectively enriching fungi with diverse ecological roles, including several taxa known for auxin production. These microbial shifts correlated directly with elevated auxin concentrations observed in needle tissues, providing a plausible mechanism for the enhanced growth. Machine learning models further identified key fungal genera that strongly associated with plant biomass, reinforcing microbiome shifts as a contributing mechanism to enhanced growth. Additionally, amino-acid fertigation improved nitrogen assimilation, correlating positively with increased chlorophyll content and photosynthetic efficiency. ConclusionsOur findings highlight that the transition from inorganic source to amino-acid biostimulants not only enhances plant growth and nitrogen use but also promotes a beneficial root microbiome, thereby offering a sustainable pathway to nursery production of radiata pine.

plant biology↗

bioRxiv2023

A Parasite Odyssey: An RNA virus concealed in Toxoplasma gondii

We are entering a "Platinum Age of Virus Discovery", an era marked by exponential growth in the discovery of virus biodiversity, and driven by advances in metagenomics and computational analysis. In the ecosystem of a human (or any animal) there are more species of viruses than simply those directly infecting the animal cells. Viruses can infect all organisms constituting the microbiome, including bacteria, fungi, and unicellular parasites. Thus the complexity of possible interactions between host, microbe, and viruses is unfathomable. To understand this interaction network we must employ computationally-assisted virology as a means of analyzing and interpreting the millions of available samples to make inferences about the ways in which viruses may intersect human health. From a computational viral screen of human neuronal datasets, we identified a novel narnavirus Apocryptovirus odysseus (Ao) which likely infects the neurotropic parasite Toxoplasma gondii. Previously, several parasitic protozoan viruses (PPVs) have been mechanistically established as triggers of host innate responses, and here we present in silico evidence that Ao is a plausible pro-inflammatory factor in human and mouse cells infected by T. gondii. T. gondii infects billions of people worldwide, yet the prognosis of toxoplasmosis disease is highly variable, and PPVs like Ao could function as a hitherto undescribed hypervirulence factor. In a broader screen of over 7.6 million samples, we explored phylogenetically-proximal viruses to Ao and discovered 19 Apocryptovirus species, all found in libraries annotated as vertebrate transcriptome or metatranscriptomes. While the Narnavirus samples making up this genus-like clade are derived from sheep, goat, bat, rabbit, chicken, and pigeon samples, the presence of virus is strongly predictive of parasitic (Apicomplexa) nucleic acid co-occurrence, supporting that these are a clade of parasite-infecting viruses. This is a computational proof-of-concept study in which we rapidly analyze millions of datasets from which we distilled a mechanistically, ecologically, and phylogenetically refined hypothesis. We predict this highly diverged Ao RNA virus is biologically a T. gondii infection, and that Ao, and other viruses like it, will modulate this disease which afflicts billions worldwide.

microbiology↗

bioRxiv2022

Laccaria bicolor pectin methylesterases are involved in ectomycorrhiza development with Populus tremula x Populus tremuloides

O_LIThe development of ectomycorrhizal (ECM) symbioses between soil fungi and tree roots requires modification of root cell-walls. The pectin-mediated adhesion between adjacent root cells loosens to accommodate fungal hyphae in the Hartig Net, facilitating nutrient exchange between partners. We investigated the role of fungal pectin modifying enzymes in Laccaria bicolor for ECM formation with Populus tremula x Populus tremuloides. C_LIO_LIWe combine transcriptomics of cell-wall related enzymes in both partners during ECM formation, immunolocalization of pectin (Homogalacturonan, HG) epitopes in different methylesterification states, pectin methylesterase (PME) activity assays and functional analyses of transgenic L. bicolor to uncover pectin modification mechanisms and the requirement of fungal pectin methylesterases (LbPMEs) for ECM formation. C_LIO_LIImmunolocalization identified remodelling of pectin towards de-esterified HG during ECM formation, which was accompanied by increased LbPME1 expression and PME activity. Overexpression or RNAi of the ECM-induced LbPME1 in transgenic L. bicolor lines led to reduced ECM formation. Hartig Nets formed with LbPME1 RNAi lines were shallower, whereas those formed with LbPME1 over-expressors were deeper. C_LIO_LIThis suggests that LbPME1 plays a role in ECM formation potentially through HG-de-esterification, which initiates loosening of adjacent root cells to facilitate Hartig Net formation. C_LI

plant biology↗