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Chowdhury, N.

Publications and source records attributed to Chowdhury, N..

18 recordsLinked to original sources

ChatGEM: An Agentic Architecture Enabling Interactive Simulation of Genome-Scale Metabolic Models

Genome-scale metabolic models (GEMs) are powerful tools for predicting cellular phenotypes and guiding microbial strain engineering, yet broad adoption remains challenging due to the computational expertise required. To overcome that, we present ChatGEM, an agentic platform that enables interactive GEM simulation through natural language. Built on the multi-agent ADEPT framework, ChatGEM integrates COBRApy within a retrieval-augmented generation (RAG) architecture that coordinates code generation and execution through specialized agents. Benchmarking across three tasks of increasing complexity showed that RAG-enabled code generation improved the mean overall performance score from 2.63 to 4.20 while reducing the execution time significantly starting from routine to complex tasks. Application of ChatGEM using an enzyme-constrained GEM (ecGEM) for four engineered Pseudomonas putida KT2440 strains identified the constitutive strain as the optimal chassis for succinate overproduction using a succinate leakage index - a prediction observed experimentally. Therefore, ChatGEM democratizes metabolic modeling by enabling researchers without computational expertise to perform sophisticated GEM-based analyses through natural language, and, hence, accelerating scientific discovery.

systems biology↗

Wnt stimulation and inhibition in the development and phenotype of patient-derived gallbladder organoids

Gallbladder cancer (GBC) is a highly lethal malignancy with limited experimental models to study disease biology or evaluate therapeutic responses. Although canonical Wnt activation is commonly used for patient-derived organoid (PDO) development and expansion, gallbladder PDOs has also been generated under Wnt-inhibitory conditions. No comparative assessment has determined how Wnt pathway modulation influences gallbladder PDO development, phenotype or drug response. This study systematically compared the impact of canonical Wnt activation (WNTAct medium containing CHIR99021) versus inhibition (WNTInh medium containing DKK1) on the establishment, propagation, molecular features and therapeutic responses of PDOs generated from malignant or non-malignant gallbladder tissues derived from the same patient. Both media supported successful PDO generation with comparable efficiency, preserving biliary epithelial functions and marker expression. Transcriptomic profiling confirmed selective enrichment of canonical Wnt target genes in PDOs generated in WNTAct cultures. WNTAct conditions enabled markedly superior long-term propagation, whereas WNTInh cultures more consistently retained the dysplastic features in malignant samples. Gemcitabine response assays demonstrated significantly greater drug sensitivity in PDOs grown in WNTAct medium, a phenotype reversible upon media switching but requiring extended adaptation, indicating a dynamic and context-dependent influence of Wnt signaling on chemotherapeutic vulnerability. Collectively, the findings reveal a trade-off between long-term propagation and histological fidelity in gallbladder PDOs and show that Wnt signaling modulates gemcitabine sensitivity in a reversible manner. This comparative framework provides practical guidance for selecting culture conditions for gallbladder PDO based disease modelling and precision oncology applications.

cell biology↗

Dissipation of lysosome pH impairs formation and collapses existing LPS-induced lysosome tubules in macrophages

While lysosomes are typically globular in morphology, lipopolysaccharide-activated macrophages reorganize lysosomes into an expanded tubular network. Here, we sought to determine if the V-ATPase and the lysosomal pH contribute to LPS-mediated lysosome tubulation in macrophages. We found that inhibition of the V-ATPase prevented lysosome tubulation and collapsed preformed tubules. However, the V-ATPase also controls mTORC1 activity, which itself is needed for tubulation. To distinguish between lysosomal pH and mTORC1, we turned to NH4Cl, which alkalinized lysosomal pH but did not interfere with mTORC1; yet NH4Cl blocked tubulation showing that an acidic lysosomal pH is needed for lysosome remodelling. Moreover, clamping the pH to either acidic or alkaline pH caused tubules to collapse, indicating that the pH gradient promotes tubulation, rather than a specific pH. These effects were not due to altered microtubule organization or impaired lysosome motility, suggesting that motors remained associated with lysosomes. On the other hand, while LPS did not alter the average pH of spherical or tubular lysosomes, growing tubules displayed a more acidic peripheral end relative to the pericentral end. Based on this observation, we propose that a localized pH gradient along the tubule may enable tubulation by modulating factors that catalyse tubule growth.

cell biology↗

Insights into gallbladder cancer pathogenesis from a living organoid gallbladder cholangiocyte biorepository

Gallbladder cancer (GBC) while rare worldwide has a high prevalence in India. Pathogenesis is unclear and outcomes poor. Gallbladder cholangiocyte organoids (GCOs) or gallbladder carcinoma organoids (GBCOs) were developed and serially propagated from surgically resected gallbladder tissues with benign or malignant diseases, respectively. Patient derived organoids (PDOs) were derived from 15 normal; 58 inflamed; 12 xanthogranulomatous cholecystitis (XGC); 5 pre-invasive neoplasm and 13 invasive malignant gallbladder pathologies. Protocol optimisation achieved 58% (69/119) success in organoid generation and expansion. Organoids maintained tight junction integrity; P-gp pump and enzymatic activity; preserved tissue-specific gene and protein marker expression; histological features and genetic variations. Cryopreserved organoids from 62 patients with primary tissue and high-quality DNA, RNA and protein derivatives have been banked. In gene expression analyses of tissue, XGC samples clustered with malignant subtypes, separate from benign pathologies. Derived XGC organoids showed a similar clustering. Enriched hallmark pathways in XGC support neoplastic change through chronic inflammation. PDOs generated from different gallbladder pathologies are a promising model to investigate the pathogenesis of GBC. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=199 SRC="FIGDIR/small/651639v1_ufig1.gif" ALT="Figure 1"> View larger version (69K): org.highwire.dtl.DTLVardef@465f3dorg.highwire.dtl.DTLVardef@16c5f0org.highwire.dtl.DTLVardef@11d4807org.highwire.dtl.DTLVardef@163d072_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗

The effect of prolonged elbow pain and rTMS on cortical inhibition: A TMS-EEG study

IntroductionRecent studies using combined transcranial magnetic stimulation (TMS) and electroencephalography (EEG) have shown that pain leads to an increase in the N45 peak of the TMS-evoked potential (TEP), which is mediated by GABAergic inhibition. Conversely, 10Hz repetitive TMS (10Hz-rTMS), which provides pain relief, reduces the N45 peak. However, these studies used brief pain stimuli (lasting minutes), limiting their clinical relevance. The present study determined the effect of pain and 10Hz-rTMS on the N45 peak in a prolonged pain model (lasting several days) induced by nerve growth factor (NGF) injection to the elbow muscle. Materials and MethodsExperiment 1: TEPs were measured in 22 healthy participants on Day 0 (pre-NGF), Day 2 (peak pain), and Day 7 (pain resolution). Experiment 2: We examined the effect of 5 days of active (n=16) or sham (n=16) rTMS to the left primary motor cortex (M1) on the N45 peak during prolonged NGF-induced pain, with TEPs measured on Day 0 and Day 4 (post-rTMS). ResultsExperiment 1: While no overall change in the N45 peak was seen, a correlation emerged between higher pain severity on Day 2 and a larger increase in the N45 peak. Experiment 2: Active rTMS reduced the N45 peak on Day 4 vs. Day 0, with no effect in the sham group. ConclusionOur findings suggest that (i) higher pain severity correlates with an increase in the N45 peak, and (ii) rTMS decreases cortical inhibition in a model of prolonged experimental pain. This study extends previous research by demonstrating a link between pain perception and cortical inhibition within a prolonged pain context.

neuroscience↗

Glutamate is a key nutrient for Porphyromonas gingivalis growth and survival during intracellular autophagic life under nutritionally limited conditions

Porphyromonas gingivalis survives in special autophagic vacuoles that serve as major replicative habitats in human primary gingival epithelial cells (GECs). As an asaccharolytic strict anaerobe, P. gingivalis is dependent on amino acids and peptides for nutrient sources. However, it is largely unknown as to P. gingivalis metabolic processing under the nutritionally limited intracellular environments such the vacuoles, especially the preferred amino acids and associated-metabolic machineries. Here we elucidate that a Glutamate (Glu) catabolic enzyme, glutamate dehydrogenase (GdhA) is highly enriched in the isolated P. gingivalis-containing vacuoles. Interestingly, we found that P. gingivalis induces conversion of intracellular glutamine pool to Glu determined by analyses of the P. gingivalis-containing vacuoles and the whole infected-GECs. Critically, exogenous Glu-Glu dipeptide, a simple precursor of Glu, significantly increases the size of isolated intact P. gingivalis containing-vacuoles and live wild-type P. gingivalis numbers in GECs. In contrast, the isogenic GdhA-deficient-strain, {Delta}gdhA displayed a significant growth defect with collapsed-vacuoles in GECs. Next, we confirmed that P. gingivalis uptakes 14C-Glu and it preferentially utilizes Glu-Glu-dipeptide using a nutritionally reduced Tryptic-Soy-Broth (TSB) media supplemented with Glu-Glu. Contrary, {Delta}gdhA-strain showed no detectable growth especially in nutritionally reduced TSB media with Glu-Glu. Using Atomic-Force-Microscopy, we observed that, wild-type P. gingivalis but not {Delta}gdhA strain notably increased the cell volume upon Glu-Glu supplementation, an indicator of higher metabolism and growth. Utilization of a human gingiva-mimicking organoid-system further validated the importance of Glu as an essential nutrient for the intramucosal colonization of P. gingivalis via the protected replicative vacuoles in GECs. ImportanceThis study reveals that P. gingivalis heavily depends on preferential utilization of Glutamate (Glu) for autophagic vacuolar growth and survival in human GECs. Several novel observations are made to support this: (i) GdhA of P. gingivalis is highly enriched in these vacuoles, (ii) P. gingivalis induces a large conversion of intracellular glutamine to Glu, (iii) size of vacuoles are significantly increased in the presence of Glu-Glu in P. gingivalis wild-type strain infection which is opposite in a {Delta}gdhA strain, (iv) P. gingivalis uptakes 14C-Glu and preferentially utilizes Glu-Glu dipeptide, (v) similarly, wild-type strain shows growth increase in a nutritionally reduced bacterial culture media, and (vi) finally, Glu-Glu supplementation increases bacterial cell-volume of P. gingivalis wild-type but not {Delta}gdhA strain, an indicator of higher metabolism and growth. Taken together, this study highlights the pathophysiological importance of Glu for P. gingivalis growth-rate, biomass induction and survival in nutritionally limited host subcellular environments.

microbiology↗

Porphyromonas gingivalis activates Heat-Shock-Protein 27 to drive a LC3C-specific pro-bacterial form of select autophagy that is redox sensitive for intracellular survival in human gingival mucosa

Porphyromonas gingivalis, a major oral pathobiont, evades canonical host pathogen clearance in human primary gingival epithelial cells (GECs) by initiating a non-canonical variant of autophagy consisting of Microtubule-associated protein 1A/1B-light chain 3 (LC3)-rich autophagosomes, which then act as replicative niches. Simultaneously, P. gingivalis inhibits apoptosis and oxidative-stress, including extracellular-ATP (eATP)-mediated reactive-oxygen-species (ROS) production via phosphorylating Heat Shock Protein 27 (HSp27) with the bacterial nucleoside-diphosphate-kinase (Ndk). Here, we have mechanistically identified that P. gingivalis-mediated induction of HSp27 is crucial for the recruitment of the LC3 isoform, LC3C, to drive the formation of live P. gingivalis-containing Beclin1-ATG14-rich autophagosomes that are redox sensitive and non-degrading. HSp27 depletions of both infected GECs and gingiva-mimicking organotypic-culture systems resulted in the collapse of P. gingivalis-mediated autophagosomes, and abolished P. gingivalis-induced LC3C-specific autophagic-flux in a HSp27-dependent manner. Concurrently, HSp27 depletion accompanied by eATP treatment abrogated protracted Beclin 1-ATG14 partnering and decreased live intracellular P. gingivalis levels. These events were only partially restored via treatments with the antioxidant N-acetyl cysteine (NAC), which rescued the cellular redox environment independent of HSp27. Moreover, the temporal phosphorylation of HSp27 by the bacterial Ndk results in HSp27 tightly partnering with LC3C, hindering LC3C canonical cleavage, extending Beclin 1-ATG14 association, and halting canonical maturation. These findings pinpoint how HSp27 pleiotropically serves as a major platform-molecule, redox regulator, and stepwise modulator of LC3C during P. gingivalis-mediated non-canonical autophagy. Thus, our findings can determine specific molecular strategies for interfering with the host-adapted P. gingivalis successful mucosal colonization and oral dysbiosis.

microbiology↗

Peak alpha frequency is not significantly altered by five days of experimental pain and repetitive transcranial stimulation of the left dorsolateral prefrontal cortex

Repetitive transcranial magnetic stimulation (rTMS) holds promise as a non-invasive pain treatment. Given the link between individual peak alpha frequency (PAF) of resting-state electroencephalographic recordings and pain sensitivity, and the potential for rTMS to modulate PAF, we investigated these relationships through a secondary analysis of established rTMS-induced analgesia in an experimental model of sustained muscle pain. In a randomised, single-blind, sham-controlled experiment, 30 healthy adults underwent either active (n=15) or sham (n=15) high-frequency rTMS (20 min) to the left dorsolateral prefrontal cortex for five consecutive days following induction of sustained experimental pain by nerve growth factor (NGF) injected into the right extensor carpi radialis brevis muscle. The pain intensity was assessed daily for 14 days on a numerical rating scale (NRS). PAF of the resting state electroencephalography (5 min) was assessed before and one day after the five rTMS treatment days. The pre-registered analysis revealed no significant changes in PAF following five consecutive days of active (from 9.90{+/-}0.39 Hz to 9.95{+/-}0.38 Hz) or sham (from 9.86{+/-}0.44 Hz to 9.81{+/-}0.35 Hz) rTMS, suggesting that the impact of rTMS on NGF-induced pain is independent of PAF modulation. However, exploratory analysis indicated an association between a larger absolute difference in baseline PAF to 10 Hz (i.e. the rTMS frequency) and higher NRS pain ratings at Day 5 in participants receiving active rTMS. This suggests rTMS is more efficient when delivered close to individual PAF or for those with PAF around 10 Hz, necessitating further exploration of PAFs role in rTMS-induced pain relief.

neuroscience↗

Unique territorial and sub-chromosomal organization revealed in the holocentric moth Bombyx mori

Hallmarks of multicellular eukaryotic genome organization are chromosome territories, compartments, and loop-extrusion-mediated structures, including TADs. However, these are mainly observed in model organisms, and most eukaryotes remain unexplored. Using Hi-C in the silkworm Bombyx mori we discover a novel chromatin folding structure, compartment S, which is "secluded" from the rest of the chromosome. This compartment exhibits loop extrusion features and a unique genetic and epigenetic landscape, and it localizes towards the periphery of chromosome territories. While euchromatin and heterochromatin display preferential compartmental contacts, S domains are remarkably devoid of contacts with other regions, including with other S domains. Polymer simulations show that this contact pattern can only be explained by high loop-extrusion activity within compartment S, combined with low extrusion elsewhere through the genome. This unique, targeted extrusion represents a novel phenomenon and underscores how evolutionarily conserved mechanisms--compartmentalization and loop extrusion--can be repurposed to create new 3D genome architectures.

genomics↗

Effects of nicotine compared to placebo gum on sensitivity to pain and mediating effects of peak alpha frequency

Recent research has linked individual peak alpha frequency (PAF) to pain sensitivity, but whether PAF alterations can influence pain remains unclear. Our study investigated the effects of nicotine on pain sensitivity and whether pain changes are mediated by PAF changes. In a randomised, double-blind, placebo-controlled experiment, 62 healthy adults (18-44 years) received either 4 mg nicotine (n=29) or placebo gum (n=33). Resting state EEG and pain ratings during prolonged heat and pressure models were collected before and after nicotine intake. The nicotine group showed a small decrease in heat-pain ratings compared to placebo group when controlling confounders, and a small increase in PAF across the scalp from pre- to post-gum, both with and without confounder adjustment. These effects were most pronounced in the central-parietal and right-frontal electrodes. However, mediation analysis did not support the notion that PAF changes mediate nicotines effects on pain sensitivity. While a growing body of literature supports a link between PAF and both acute and chronic pain, further work is needed to understand the mechanisms of this link.

neuroscience↗

Multiplexed fluorescence and scatter detection with single cell resolution using on-chip fiber optics for droplet microfluidic applications

Droplet microfluidics has emerged as a critical component of several high-throughput single cell analysis techniques in biomedical research and diagnostics. However, while there has been significant progress in the individual assays being developed, multi-parametric optical sensing of droplets and their encapsulated contents remains challenging. The current common approach of microscopy based high-speed imaging of droplets is technically complex and requires expensive instrumentation limiting their large-scale adoption. Here we have adapted the principles of the widely established technique of flow cytometry to a novel optofluidic setup - the OptiDrop platform, with on-chip detection of scatter and multiple fluorescence signals from microfluidic droplets and their contents using optical fibers. The highly customizable on-chip optical fiber-based signal detection system enables simplified, miniaturized, low-cost, multi-parametric sensing of optical signals with high sensitivity and single cell resolution within each droplet. Our work on differential expression analysis of the Major Histocompatibility Complex (MHC) protein in response to IFN{gamma} stimulation further demonstrates the OptiDrop platforms capabilities in sensitively detecting cell surface biomarkers using fluorescently labeled antibodies. The OptiDrop platform thus combines the versatility of flow cytometry with the power of droplet microfluidics to provide wide-ranging optical sensing solutions for research and diagnostics.

bioengineering↗

Intramuscular injection of nerve growth factor as a model of temporomandibular disorder: nature, time-course, and sex differences characterising the pain experience

BackgroundTemporomandibular disorder (TMD) is a common condition that frequently transitions to chronic symptoms. Experimental pain models that mimic the symptoms of clinical TMD may be useful in understanding the mechanisms, and sex differences, present in this disorder. Here we aimed to comprehensively characterise the nature and time-course of pain, functional impairment and hyperalgesia induced by repeated intramuscular injection of nerve growth factor (NGF) into the masseter muscle, and to investigate sex differences in the NGF-induced pain experience. Methods94 healthy individuals participated in a longitudinal observational study with 30-day follow-up. NGF was injected into the right masseter muscle on Day 0 and Day 2. Participants attended laboratory sessions to assess pain (Numerical Rating Scale; NRS), functional limitation (mouth opening distance, Jaw Functional Limitation Scale; JFLS) and mechanical sensitization (pressure pain thresholds; PPTs) on Days 0, 2 and 5 and completed twice daily electronic pain dairies from Day 0 to day 30. ResultsPeak pain averaged 2.0/10 (95 % CI: 1.6-2.4) at rest and 4.3/10 (95 % CI: 3.9-4.8) on chewing. Pain-free mouth opening distance reduced from 5.0 cm (95 % CI: 4.8-5.1 cm) on Day 0 to 3.7 cm (95 % CI: 3.5-3.9 cm) on Day 5. The greatest reduction in PPTs was observed over the masseter muscle. Females experienced higher pain, greater functional impairment, and greater sensitivity to mechanical stimuli than males. ConclusionIntramuscular injection of NGF is a useful model with which to explore the mechanisms, and sex differences, present in clinical TMD.

neuroscience↗

Heterochromatin diversity modulates genome compartmentalization and loop extrusion barriers

Two dominant processes organizing chromosomes are loop extrusion and the compartmental segregation of active and inactive chromatin. The molecular players involved in loop extrusion during interphase, cohesin and CTCF, have been extensively studied and experimentally validated. However, neither the molecular determinants nor the functional roles of compartmentalization are well understood. Here, we distinguish three inactive chromatin states using contact frequency profiling, comprising two types of heterochromatin and a previously uncharacterized inactive state exhibiting a neutral interaction preference. We find that heterochromatin marked by long continuous stretches of H3K9me3, HP1 and HP1{beta} correlates with a conserved signature of strong compartmentalization and is abundant in HCT116 colon cancer cells. We demonstrate that disruption of DNA methyltransferase activity dramatically remodels genome compartmentalization as a consequence of the loss of H3K9me3 and HP1 binding. Interestingly, H3K9me3-HP1/{beta} is replaced by the neutral inactive state and retains late replication timing. Furthermore, we show that H3K9me3-HP1/{beta} heterochromatin is permissive to loop extrusion by cohesin but refractory to CTCF, explaining a paucity of visible loop extrusion-associated patterns in Hi-C. Accordingly, CTCF loop extrusion barriers are reactivated upon loss of H3K9me3-HP1/{beta}, not as a result of canonical demethylation of the CTCF binding motif but due to an intrinsic resistance of H3K9me3-HP1/{beta} heterochromatin to CTCF binding. Together, our work reveals a dynamic structural and organizational diversity of the inactive portion of the genome and establishes new connections between the regulation of chromatin state and chromosome organization, including an interplay between DNA methylation, compartmentalization and loop extrusion. HighlightsO_LIThree inactive chromatin states are distinguishable by long-range contact frequencies in HCT116, respectively associated with H3K9me3, H3K27me3 and a H3K9me2 state with neutral contact preferences. C_LIO_LIH3K9me3-HP1/{beta} heterochromatin has a high degree of homotypic affinity and is permissive to loop extrusion but depleted in extrusion barriers. C_LIO_LIDisrupting DNA methylation causes widespread loss of H3K9me3-HP1/{beta} and dramatic remodeling of genome compartmentalization. C_LIO_LIH3K9me3-HP1/{beta} is replaced by the neutral inactive state, which gains CTCF loop extrusion barriers and associated contact frequency patterns. C_LIO_LIDNA methylation suppresses CTCF binding via two distinct mechanisms. C_LI

genomics↗

Castration-mediated IL-8 Promotes Myeloid Infiltration and Prostate Cancer Progression

Immunotherapy is a treatment for many types of cancer, primarily due to deep and durable clinical responses mediated by immune checkpoint blockade (ICB)1, 2. Prostate cancer is a notable exception in that it is generally unresponsive to ICB. The standard treatment for advanced prostate cancer is androgen-deprivation therapy (ADT), a form of castration (CTX). ADT is initially effective, but over time patients eventually develop castration-resistant prostate cancer (CRPC). Here, we focused on defining tumor-cell intrinsic factors that contribute to prostate cancer progression and resistance to immunotherapy. We analyzed cancer cells isolated from castration-sensitive and castration-resistant prostate tumors, and discovered that castration resulted in significant secretion of Interleukin-8 (IL-8) and its likely murine homolog Cxcl15. These chemokines drove subsequent intra-tumoral infiltration with polymorphonuclear myeloid-derived suppressor cells (PMN-MDSCs), promoting tumor progression. PMN-MDSC infiltration was abrogated when IL-8 was deleted from prostate cancer epithelial cells using CRISPR/Cas9, or when PMN-MDSC migration was blocked with antibodies against the IL-8 receptor CXCR2. Blocking PMN-MDSC infiltration in combination with anti-CTLA-4 delayed the onset of castration resistance and increased the density of polyfunctional CD8 T cells in tumors. Taken together, our findings establish castration-mediated IL-8 secretion and subsequent PMN-MDSC infiltration as a key suppressive mechanism in the progression of prostate cancer. Targeting of the IL-8/CXCR2 axis around the time of ADT, in combination with ICB, represents a novel therapeutic approach to delay prostate cancer progression to advanced disease.

cancer biology↗

Catestatin improves insulin sensitivity in diet-induced obese mice: in vivo and in silico validation

Obesity is characterized by a state of chronic, unresolved inflammation in insulin-targeted tissues. Obesity-induced inflammation accumulates proinflammatory macrophages in adipose tissue and liver. Proinflammatory cytokines released from tissue macrophages inhibits insulin sensitivity. Chromogranin A (CgA) peptide catestatin (CST: hCgA352-372) improves obesity-induced hepatic insulin resistance by reducing inflammation and inhibiting proinflammatory macrophage infiltration. Obesity leads to inflammation-induced endoplasmic reticulum (ER) stress and insulin resistance. We reasoned that the anti-inflammatory effects of CST would alleviate ER stress. CST decreased obesity-induced ER dilation in hepatocytes and macrophages. CST reduced phosphorylation of UPR signaling molecules and increased phosphorylation of insulin signaling molecules. We developed an in silico state space model mimicking dynamics of integrated ER stress and insulin pathways. Proportional-Integral-Derivative (PID) controllers helped in checking whether the reduction of phosphorylated PERK resulting in attenuation of ER stress, resembling CST effect, could enhance insulin sensitivity. The simulation results showed CST not only decreased ER stress but also enhanced insulin sensitivity. Simulation results also revealed that enhancement of AKT phosphorylation overcame effects of high ER stress to achieve insulin sensitivity.

systems biology↗

Novel cholera toxin variant and ToxT regulon in environmental Vibrio mimicus strains: potential resources for the evolution of Vibrio cholerae hybrid strains

Atypical El Tor strains of Vibrio cholerae O1 harboring variant ctxB genes of cholera toxin (CT) are gradually becoming a major cause of recent cholera epidemics. Vibrio mimicus occasionally contains virulence factors associated with cholera, e.g., CT, encoded by ctxAB on CTX[FE] genome; and TCP, the CTX[FE]-specific receptor. This study carried out extensive molecular characterization of CTX[FE] and ToxT regulon in ctx+ve strains of V. mimicus isolated from the Bengal coast. Southern hybridization, PCR, and DNA sequencing of virulence related-genes revealed the presence of an El Tor type CTX prophage (CTXET) carrying a novel ctxAB, tandem copies of environmental type pre-CTX prophage (pre-CTXEnv), and RS1 elements, which were organized in an array of RS1-CTXET-RS1-pre-CTXEnv-pre-CTXEnv. Additionally, a novel variant of tcpA and toxT respectively, showing clonal lineage to a phylogenetic clade of V. cholerae non-O1/O139, was identified. The V. mimicus strains lacked the RTX and TLC elements, and Vibrio seventh pandemic islands of the El Tor strains, but contained five heptamer (TTTTGAT) repeats in ctxAB promoter region like some classical strains of V. cholerae O1. PFGE analysis showed all the ctx+ve V. mimicus strains were clonally related. However, their in vitro CT production and in vivo toxigenecity were variable, which could be explained by differential transcription of virulence genes along with ToxR regulon. Taken together, our findings strongly suggest that environmental V. mimicus strains act as potential reservoir of atypical virulence factors, including variant CT and ToxT regulon, and may contribute to the evolution of V. cholerae hybrid strains.\n\nIMPORTANCENatural diversification of CTX[FE] and ctxAB genes certainly influences disease severity and shifting patterns in major etiological agents of cholera, e.g., the overwhelming emergence of hybrid El Tor variants, replacing the prototype El Tor strains of V. cholerae. This study showing the occurrence of CTXET comprising a novel variant of ctxAB in V. mimicus points out a previously unnoticed evolutionary event, independent to that of the El Tor strains of V. cholerae. Identification and cluster analysis of the newly-discovered alleles of tcpA and toxT indicates their horizontal transfer from an uncommon clone of V. cholerae. The genomic content of ToxT regulon, and tandemly arranged multiple pre-CTX[FE]Env and a CTX[FE]ET in V. mimicus probably act as salient raw materials inducing natural recombination among the hallmark virulence genes of hybrid V. cholerae strains. This study will facilitate deeper understanding of the evolution of new variant CT and ToxT regulon, influencing cholera epidemiology.

microbiology↗

Viable But Non-Culturable Cells Are Persister Cells

Bacteria have two dormant phenotypes: the viable but non-culturable (VBNC) state and the persister state. Both resting stages arise without mutation and both have been linked to chronic infections; however, persister cells revive rapidly whereas the cell population called VBNC is reported to not resuscitate. Here we investigated the relatedness of the two stress-induced phenotypes at the single-cell level by using transmission electron microscopy and fluorescent microscopy to examine cell morphology and by quantifying cell resuscitation. Using the classic starvation conditions to create VBNC cells, we found that the majority of the remaining Escherichia coli population are spherical, have empty cytosol, and fail to resuscitate; however, some of the spherical cells under these classic VBNC-inducing conditions resuscitate immediately (most probably those with dense cytosol). Critically, all the culturable cells became persister cells within 14 days of starvation. We found that the persister cells initially are rodlike, have clear but limited membrane damage, can resuscitate immediately, and gradually become spherical by aging. After 24 h, only rod-shaped persister cells survive, and all the spherical cells lyse. Both cell populations formed under the VBNC-inducing conditions and the persister cells are metabolically inactive. Therefore, the bacterial population consists of dead cells and persister cells in the VBNC-inducing conditions; i.e., the non-lysed particles that do not resuscitate are dead, and the dormant cells that resuscitate are persister cells. Hence, \"VBNC\" and \"persister\" describe the same dormant phenotype.

microbiology↗

Stability of Commonly Used Haematological Parameters in Samples Stored at 33°C, 22°C and 4°C

AimThis study aimed to investigate the analytical bias and imprecision in haematological parameters induced by storage at 4{degrees}C, 22{degrees}C and 33 {degrees}C.\n\nMethodsThree K2EDTA anticoagulated vials of blood were collected from each of twenty blood donors and stored at 4{degrees}C, 22{degrees}C and 33{degrees}C respectively. Readings from each vial were taken at 0, 4, 6, 12, 24, 48 and 72 hours after collection on the Sysmex XP-100 analyser. The mean and median shift of the parameters relative to the baseline and the coefficient of variation for each time-temperature combination were calculated. The shift was compared to the maximum acceptable bias.\n\nResultsHaemoglobin, Red Blood Cell Count, White Blood Cell Count, Mean Corpuscular Haemoglobin were stable for at least twenty four hours at 33{degrees}C. Haematocrit, Mean Corpuscular Volume and Platelet Counts were stable for less than four hours at 33{degrees}C. All the above parameters were stable for longer at 22{degrees}C and 4{degrees}C. The three-part differential count showed instability within four hours at 33 {degrees}C.\n\nConclusionsStrict pre-analytical control is needed at 33{degrees}C or above due to the marked instability of most parameters. However, Haemoglobin, Red Blood Cell Count, White Blood Cell Count and Mean Corpuscular Haemoglobin remain relatively stable even at 33{degrees}C.\n\nKey MessageHaematology samples exposed to temperatures of 33{degrees}C or above show rapid change in MCV, HCT,MCHC, RDW, Platelet Counts and three-part differential counts. Settings where prolonged exposure to these temperatures cannot be avoided should rely on the more stable parameters of Haemoglobin, RBC Counts, MCH and WBC Counts.

pathology↗