Biology subjects

Ray, T.

Publications and source records attributed to Ray, T..

10 recordsLinked to original sources

bioRxiv2025

Copy number of the blaNDM-1 gene (New Delhi metallo-β-lactamase-1) and meropenem susceptibility in Enterobacterales: Consideration for treatment with meropenem?

Some Enterobacterales carrying blaNDM were still susceptible to meropenem, exhibiting meropenem minimum inhibitory concentration (MIC) values below the clinical breakpoint. As this phenomenon is a rare observation, this study investigated the underlying regulatory mechanisms contributing to the low MIC values and evaluated the efficacy of meropenem as a therapeutic preference for such isolates. Six clinical blaNDM-positive Enterobacterales exhibited meropenem MICs between 0.5-2.0 mg/L. Successful transmission of blaNDM into recipient E. coli J53 indicated its presence on plasmids. Conventional Sanger and whole-genome sequencing revealed that no truncation or deletion was observed within blaNDM or its core promoter region up to 120 bp upstream. Quantitative real-time PCR of blaNDM showed significantly lower expression levels of blaNDM, i.e., 0.2-0.5 in study isolates, compared to a clinical blaNDM-possessing isolate (expression=1) exhibiting a high meropenem MIC value (64 mg/L). Droplet digital PCR (ddPCR) further demonstrated that these isolates carried a lower copy number of the blaNDM gene, compared to the blaNDM-possessing isolate with high meropenem MIC (64 mg/L). Furthermore, the in vitro time-kill assay exhibited bactericidal efficacy of meropenem >3 log10 decrease in cfu/mL over the 24 hours from the starting inoculum. Administration of meropenem in in vivo neutropenic mice produced a 4-log cfu reduction compared to untreated controls at the start of dosing. Our data suggest that a reduction in blaNDM gene dosage, reflecting lower expression of blaNDM, correlates with lower meropenem MIC values. Meropenem is effective against these isolates when the meropenem MICs for the isolates are 0.5-2.0 mg/L. ImportanceThe production of NDM by Enterobacterales poses one of the most urgent global public health threats due to its plasmid-mediated spread, leading to treatment failure by exhibiting high MICs against a broad-spectrum of antibiotics. However, in rare instances, blaNDM-1-positive clinical Enterobacterales with unexpectedly low meropenem MICs (0.5-2.0 mg/L) raise a further question of reconsidering meropenem as a potential therapeutic option in these specific cases. This study identified that low MICs were associated with reduced expression and lower copy number of the plasmid-mediated blaNDM gene, despite intact promoter regions. Both in vitro and in vivo assays validated the bactericidal activity of meropenem against these isolates. The study raised an argument about the potential limitations of relying solely on genotypic detection of resistance genes for therapeutic decision-making, which emphasises the need for further investigation. As a safe medication, repurposing meropenem for neonatal treatment may eliminate the need for other toxic drugs.

microbiology↗

bioRxiv2024

Diversity-enhanced canopy space occupation and leaf functional diversity jointly promote overyielding in tropical tree communities

Understanding the mechanisms that drive biodiversity-productivity relationships is critical for guiding forest restoration. Although complementarity among trees in the canopy space has been suggested as a key mechanism for greater productivity in mixed-species tree communities, empirical evidence remains limited. Here, we used data from a tropical tree diversity experiment to disentangle the effects of tree species richness and community functional characteristics (community-weighted mean and functional diversity of leaf traits) on canopy space filling, and how these effects are related to overyielding. We found that canopy space filling was largely explained by species identity effects rather than tree diversity effects. Communities with a high abundance of species with conservative leaf traits were those with most densely packed canopies. Overall, a higher canopy space filling translated into an enhanced wood productivity, with communities associated with a high taxonomic and functional diversity being the most productive. Importantly, most communities (83%) produced more wood volume than the average of their constituent species in monoculture (i.e. most communities overyielded). Our results show that overyielding increased with leaf functional diversity and positive net biodiversity effects on canopy space filling, which mainly arose due to a high taxonomic diversity. These findings suggest that both taxonomic diversity-enhanced canopy space filling and canopy leaf diversity are important drivers for overyielding in mixed-species forests. Consequently, restoration initiatives should promote stands with functionally diverse canopies by selecting tree species with large interspecific differences in leaf nutrition, as well as leaf and branch morphology to optimize carbon capture in young forest stands.

ecology↗

bioRxiv2023

Mycorrhizal fungi modulate tree diversity effects on nutrient dynamics

Species-specific differences in nutrient acquisition strategies allow for complementary use of resources among plants in mixtures, which may be further shaped by mycorrhizal associations. However, empirical evidence of these relationships is scarce, particularly for tree communities. We investigated the impact of tree species richness and mycorrhizal types, arbuscular mycorrhizal fungi (AM) and ectomycorrhizal fungi (EM), on the above- and belowground carbon (C), nitrogen (N), and phosphorus (P) dynamics. Soil and microbial biomass elemental pools did not strongly respond to tree species richness or mycorrhizal type. Tree species richness increased foliage C and P pools depending on mycorrhizal type. Additive partitioning analyses showed that net biodiversity effects for C, N, P pools in EM tree communities, and N pools in AM tree communities, were driven by selection effects, while mixtures of both mycorrhizal types were influenced by complementarity effects. Furthermore, tree species richness enhanced soil nitrate uptake over two years but had no impact on ammonium and phosphate levels. Our results indicate that positive effects of tree diversity on aboveground nutrient storage are mediated by complementary mycorrhizal strategies. Given the prevalence of anthropogenic impacts on tree species richness globally, these results may have important implications for reforestation of multifunctional forests.

ecology↗

bioRxiv2023

The impact of kit, environment and sampling contamination on the observed microbiome of bovine milk

Contaminants can easily outnumber bacteria that originate within the milk itself, milk microbiome research currently suffers from a critical knowledge gap; namely, does non-mastitis bovine milk contain a native microbiome? In this study, we sampled external and internal mammary epithelium, stripped and cisternal milk, used numerous negative controls to identify potential sources of microbial contamination. Two algorithms were used to mathematically remove this contamination and to track potential movement of microbes among our samples. Our results suggest that majority (i.e., >75%) of the sequence data generated from bovine milk and mammary epithelium samples represents contaminating DNA. The contaminants in milk samples were primarily sourced from the DNA extraction kits and the internal and external skin of the teat, while the teat canal and apex samples were mainly contaminated during the sampling process. After decontamination, the milk microbiome displayed a more dispersed, less diverse and compositionally distinct bacterial profile compared with the teat skin samples. Similar microbial compositions were observed between cisternal and stripped milk samples, as well as between teat apex and canal samples. Staphylococcus and Acinetobacter were the predominant genera detected in the sequences of milk samples, and bacterial culture showed growth of Staphylococcus and Corynebacterium spp. in 50% (7/14) of stripped milk samples and growth of Staphylococcus spp. in 7% (1/14) of cisternal milk samples. Our study suggests that microbiome data generated from milk samples obtained from clinically healthy bovine udders may be heavily biased by contaminants that enter the sample during the sample collection and processing workflows. ImportanceObtaining a non-contaminated sample of bovine milk is challenging due to the nature of the sampling environment and the route by which milk is typically extracted from the mammary gland. Furthermore, the very low bacterial biomass of bovine milk exacerbates the impacts of contaminant sequences in downstream analyses, which can lead to severe biases. Our finding showed that bovine milk contains very low bacterial biomass, and each contamination event (including sampling procedure and DNA extraction process) introduces bacteria and/or DNA fragments that easily outnumber the native bacterial cells. This finding has important implications for our ability to draw robust conclusions from milk microbiome data, especially if the data have not been subjected to rigorous decontamination procedures. Based on these findings, we strongly urge researchers to include numerous negative controls into their sampling and sample processing workflows; and to utilize several complementary methods for identifying potential contaminants within the resulting sequence data. These measures will improve the accuracy, reliability, reproducibility, and interpretability of milk microbiome data and research.

microbiology↗

bioRxiv2023

Exploring associations between the teat apex metagenome and Staphylococcus aureus intramammary infection risk in primiparous cows under organic directives

The primary objective of this study was to identify associations between teat apex microbiome and Staphylococcus aureus intramammary infection (IMI) risk in primiparous cows during the first 5 weeks after calving. We performed a case-control study using shotgun metagenomics of the teat apex and culture-based milk data collected longitudinally from 710 primiparous cows on 5 organic dairy farms. We observed a strong association between S. aureus DNA in the metagenomic teat apex data prior to parturition and the odds of S. aureus IMI after parturition (OR = 38.9, 95% CI: 14.84-102.21). Differential abundance analysis confirmed this association, with cases having a 23.8 higher log fold change (LFC) in abundance of S. aureus in their samples compared to controls. Of the most prevalent microorganisms in controls, those associated with a lower risk of post-calving S. aureus IMI included Microbacterium phage Min 1 (OR = 0.37, 95% CI: 0.25-0.53), Corynebacterium efficiens (OR = 0.53, 95% CI: 0.30-0.94), Kocuria polaris (OR = 0.54, 95% CI: 0.35-0.82), Micrococcus terreus (OR = 0.64, 95% CI: 0.44-0.93) and Dietzia alimentaria (OR = 0.45, 95% CI: 0.26-0.75). Microcin B17 was the most prevalent antibacterial peptide on the teat apex of cases and controls (99.7% in both groups). The predicted abundance of Microcin B17 was also higher in cases compared to controls (LFC 0.26). Cow and farm random effects often explained a large proportion of the observed variability in the teat apex microbiome, suggesting that our results need to be interpreted within the context of the random effects. IMPORTANCEIntramammary infections (IMI) caused by Staphylococcus aureus remain an important problem for the organic dairy industry. The microbiome on the external skin of the teat apex may play a role in mitigating S. aureus IMI risk, in particular the production of antimicrobial peptides (AMPs) by commensal microbes. However, current studies of the teat apex microbiome utilize a 16S approach, which precludes detection of genomics features such as AMPs. Therefore, further research using a shotgun metagenomic approach is needed to understand what role pre-partum teat apex microbiome dynamics play in IMI risk.

ecology↗

bioRxiv2023

Metallo-protease Peptidase M84 from Bacillus altitudinis induces ROS dependent apoptosis in ovarian cancer cells by targeting PAR-1

In pursuit of isolating novel anticancer proteases from environmental microbial isolates, we have purified and identified an extracellular metallo-protease from Bacillus altitudinis named Peptidase M84. This protease selectively triggered apoptosis in human ovarian adenocarcinoma cells (PA-1, SKOV3) and mouse ovarian carcinoma cells (ID8), in addition to exhibiting no significant effect on normal human epithelial ovarian cell (IOSE) and mouse peritoneal macrophage (PEM[FE]) cell viabilities. Protease activated receptor-1 (PAR-1); a GPCR which is reported to be overexpressed in ovarian cancer cells was identified as a novel target of Peptidase M84. We observed that Peptidase M84 induced PAR-1 overexpression along with activating its downstream signalling effectors NF{kappa}B and MAPK to promote excessive reactive oxygen species (ROS) generation in ovarian cancer cells. This disrupted mitochondrial membrane potential, allowed cytosolic release of mitochondrial cytochrome c, increased the Bax (pro-apoptotic) to Bcl-2 (anti-apoptotic) ratio and promoted DNA damage to evoke apoptotic death of the ovarian cancer cells. Peptidase M84 also reduced nuclear ki-67 expression in these malignant cells to render an anti-proliferative role. In in vivo set-up, weekly intraperitoneal administration of Peptidase M84 (12 {micro}g/kg body-weight) in the ID8 mice model significantly diminished ascitic fluid accumulation through induction of oxidative stress, increasing murine survival rates by 60%. Collectively, our in vitro and in vivo findings suggested that Peptidase M84 triggered PAR-1 mediated oxidative stress to act as an apoptosis inducer in ovarian cancer cells. This established Peptidase M84 as a promising drug candidate for receptor mediated targeted-therapy of ovarian cancer. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=158 HEIGHT=200 SRC="FIGDIR/small/556500v2_ufig1.gif" ALT="Figure 1"> View larger version (51K): org.highwire.dtl.DTLVardef@6b0a19org.highwire.dtl.DTLVardef@1640510org.highwire.dtl.DTLVardef@1888b49org.highwire.dtl.DTLVardef@1708114_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗

bioRxiv2023

Tree diversity increases productivity through enhancing structural complexity across mycorrhizal types

Tree species diversity plays a central role for forest productivity, but factors driving positive biodiversity-productivity relationships remain poorly understood. In a biodiversity experiment manipulating tree diversity and mycorrhizal associations, we examined the roles of above- and belowground processes in modulating wood productivity in young temperate tree communities, as well as potential underlying mechanisms. We found that tree species richness increased forest productivity indirectly by enhancing structural complexity within communities. After six years, structurally complex communities were twice as productive as structurally simple stands. This pattern was consistent across stands with different mycorrhizal associations. Our results also demonstrate that taxonomic diversity and functional variation in shade tolerance, but not phenotypic plasticity, are key drivers of structural complexity in mixtures, which in turn lead to overyielding. Consideration of stand structural complexity appears to be a crucial element in predicting carbon sequestration in the early successional stages of mixed-species forests.

ecology↗

bioRxiv2020

Indigenous knowledge of plant uses by the community of Batiaghata, Khulna, Bangladesh

Southwestern region of Bangladesh is very rich in floral diversity, and their diversified uses. An extensive survey was conducted to investigate ethnobotanical applications of botanical species by the community of Khulna, Bangladesh. We focused on plants and community relationships, identify the most important species used, determine the relative importance of the species surveyed and calculated the Fidelity level (FI) and Cultural Significance Index (CSI) concerning individual species. In total, we have listed 136 species of 114 genera under 52 families, of which 32% (45 species) were used for folk medicine. Inheritance of traditional knowledge of medicinal plants was the primary source of knowledge acquisition through oral transmission over the generations. However, only 34% of the informants were traditional herbal practitioners. Most of the medicinal uses are primly associated with anti-inflammatory, anti-microbial, antiseptic, expectorant, antidote, fever reduction, and pain relief.

scientific communication and education↗

bioRxiv2020

Gatekeeper transcription factors regulate switch between lineage preservation and cell plasticity

Reprogramming somatic cells to pluripotency by repressing lineage-instructive transcription factors (TFs) alone has not been pursued because lineage specification is thought to be regulated by transcriptional regulatory networks (TRNs) comprising of multiple TFs rather than by single pivotal "gatekeeper" TFs. Utilizing an intra-species somatic cell hybrid model, we identified Snai2 and Prrx1 as the most critical determinants of mesenchymal commitment in rat embryonic fibroblasts (REFs) and demonstrate that siRNA-mediated knockdown of either of these master regulators is adequate to convert REFs into functional adipocytes, chondrocytes or osteocytes without requiring exogenous TFs or small molecule cocktails. Furthermore, knockdown of Snai2 alone proved sufficient to transform REFs to dedifferentiated pluripotent stem-like cells (dPSCs) that formed embryoid bodies capable of triple germ-layer differentiation. These findings suggest that inhibition of a single gatekeeper TF in a lineage committed cell is adequate for acquisition of cell plasticity and reprogramming without requiring permanent genetic modification. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=143 SRC="FIGDIR/small/999433v1_ufig1.gif" ALT="Figure 1"> View larger version (25K): org.highwire.dtl.DTLVardef@1acdb83org.highwire.dtl.DTLVardef@17fb3ddorg.highwire.dtl.DTLVardef@f994c9org.highwire.dtl.DTLVardef@197541e_HPS_FORMAT_FIGEXP M_FIG C_FIG Schematic diagram depicting transdifferentiation of REFs into adipocytes, osteocytes, chondrocytes and dedifferentiation into MSCs on individual treatment with siSnai2 or siPrrx1. dPSCs were generated only in the siSnai2 group.

cell biology↗

bioRxiv2017

An epithelial-mesenchymal-amoeboid transition gene signature reveals molecular subtypes of breast cancer progression and metastasis

Cancer cells within a tumor are known to display varying degrees of metastatic propensity but the molecular basis underlying such heterogeneity remains unclear. We analyzed genome-wide gene expression data obtained from primary tumors of lymph node-negative breast cancer patients using a novel metastasis biology-based Epithelial-Mesenchymal-Amoeboid Transition (EMAT) gene signature, and identified subtypes associated with distinct prognostic profiles. EMAT subtype status improved prognosis accuracy of clinical parameters and statistically outperformed traditional breast cancer intrinsic subtypes even after adjusting for treatment variables. Additionally, analysis of 3D spheroids from an in vitro isogenic model of breast cancer progression reveals that EMAT subtypes display progression from premalignant to malignant and pre-invasive to invasive cancer. EMAT classification is a biologically informed method to assess metastasis risk in early stage, lymph node-negative breast cancer patients.

cancer biology↗