Characterisation of Indian gut microbiome for B-vitamin production and its comparison with Chinese cohort

The human gut microbiota can biosynthesize essential micronutrients such as B-vitamins and is also known for its metabolic cooperative behaviour. The present study characterises such B-vitamin biosynthesizers, their biosynthetic pathways, explores their prevalence and abundance, examines how lifestyle or diet affects them in multiple Indian cohorts and compares it with the Chinese cohort. To achieve this, publicly available faecal metagenome data of healthy individuals from multiple Indian (two urban and three tribal populations) and a Chinese cohort were analysed. The distribution of prevalence and abundance of B-vitamin biosynthesizers showed similar profiles to that of the entire gut community of the Indian cohort, and there were 28 B-vitamin biosynthesizers that had modest or higher prevalence and abundance. The omnivorous diet affected only the prevalence of a few B-vitamin biosynthesizers; however, lifestyle and/or location affected both prevalence and abundance. A comparison with the Chinese cohort showed that fourteen B-vitamin biosynthesizers were significantly more prevalent and abundant in Chinese as compared with Indian samples (False Discovery Rate (FDR) <= 0·05). The metabolic potential of the entire gut community for B-vitamin production showed that within India, the tribal cohort has a higher abundance of B-vitamin biosynthesis pathways as compared with two urban cohorts namely, Bhopal and Kasargod, and comparison with the Chinese cohort revealed a higher abundance in the latter group. Potential metabolic cooperative behaviour of the Indian gut microbiome for biosynthesis of the B-vitamins showed multiple pairs of species showed theoretical complementarity for complete biosynthetic pathways genes of thiamine, riboflavin, niacin and pantothenate.

Reverse Engineering in Biotechnology: The Role of Genetic Engineering in Synthetic Biology

Synthetic biology is built on genetic engineering and principles of design engineering, which provides control over the biological functions of interest. This chapter explores the uses, processes, and applications of genetic engineering in synthetic biology. The chapter provides a brief history and course of development of the field of synthetic biology and genetic engineering and their unbreakable association. Next, the chapter delves into materials and methods and the applications of synthetic biology. This includes discussing the generally used components of genetic engineering to design new functions into organisms and even the general steps that are part of any synthetic biology experiment. Lastly, the chapter also explains the use of the materials and methodology discussed in solving a specific problem related to a model mentioned in the paper titled "Development of Integrase-mediated differentiation circuits to improve evolutionary stability in E. coli." It explains how by using genetic engineering a synthetic biology-related problem was solved efficiently.

Computational Inference of Gene Regulatory Network Using Genome-wide ChIP-X Data

Gene regulatory network is the architecture of transcription factors (TFs) and their gene targets, which help in controlling their expression as required by a phenotype during various environmental perturbations. Inferring the regulatory network from the high-throughput data needs an algorithmic approach involving statistical analysis. There are several interaction databases such as JASPAR and SwissRegulon that provide information for TFs-targets pair interaction, which are estimated based on experimental and prediction procedures. These repositories are majorly used for predicting the complex structure of GRNs either with or without gene expression data. Here we described and discussed the step-wise procedures to extract the interaction data for a desired set of target-TFs from the JASPAR database, and used that information to infer the network by using the igraph library. Further, we also mentioned the important parameters for analyzing the different properties of the network. The described procedure will be helpful in discerning the GRN based on the set of TF-gene pairs.

Methodological analysis of CTRI registered clinical trials on Ayurveda interventions for COVID-19 management

BACKGROUND

Clinical trial protocols provide important methodological information and are expected to be detailed. During COVID-19 pandemic several studies has been registered on CTRI regarding ayurveda for COVID-19. However, there is accumulating evidence that many protocols do not address important study elements. Therefore it is critical to analyze the clinical trial protocols and methodology of ayurveda clinical trials regarding COVID-19 registered on CTRI.

OBJECTIVE

To assess the methodological aspects of CTRI registered ayurveda trial for COVID-19, based upon available trial protocols, during 2020 and 2021.

MATERIALS AND METHODS

We searched the CTRI database for interventional trials protocols regarding ayurveda for COVID-19, during the year 2020 and 2021. We assessed the protocols for several methodological aspects such as study design, sample size, randomization, blinding, intervention (duration and type) and outcomes.

RESULTS

Total 140 clinical trial protocols were analyzed. The highest numbers of studies were registered in May, June, and July 2020 with steady decline thereafter despite rising COVID-19 cases. Total 90 trials were randomized and only 29 are blinded, however majority of the trials did not mention methods of randomization and blinding. Sample size in hospital-based studies ranged from 30 -500 and in community-based studies from 500-80000, however, sample size calculation details were not mentioned in the protocol. Most common intervention used were guduchi, ashwagandha, yashtimadhu, AYUSH-64, curcumin and chyavanprash.

CONCLUSION

Although there was a surge of clinical trials on CTRI regarding ayurveda for COVID -19, the methodological quality is not up to the mark with large scope for improvement.

Global Transcriptional Regulators Fine-Tune the Translational and Metabolic Efficiency for Optimal Growth of Escherichia coli

Global transcriptional regulators coordinate complex genetic interactions that bestow better adaptability for an organism against external and internal perturbations. These transcriptional regulators are known to control an enormous array of genes with diverse functionalities. However, regulator-driven molecular mechanisms that underpin precisely tuned translational and metabolic processes conducive for rapid exponential growth remain obscure. Here, we comprehensively reveal the fundamental role of global transcriptional regulators FNR, ArcA, and IHF in sustaining translational and metabolic efficiency under glucose fermentative conditions in Escherichia coli By integrating high-throughput gene expression profiles and absolute intracellular metabolite concentrations, we illustrate that these regulators are crucial in maintaining nitrogen homeostasis, govern expression of otherwise unnecessary or hedging genes, and exert tight control on metabolic bottleneck steps. Furthermore, we characterize changes in expression and activity profiles of other coregulators associated with these dysregulated metabolic pathways, determining the regulatory interactions within the transcriptional regulatory network. Such systematic findings emphasize their importance in optimizing the proteome allocation toward metabolic enzymes as well as ribosomes, facilitating condition-specific phenotypic outcomes. Consequentially, we reveal that disruption of this inherent trade-off between ribosome and metabolic proteome economy due to the loss of regulators resulted in lowered growth rates. Moreover, our findings reinforce that the accumulations of intracellular metabolites in the event of proteome repartitions negatively affects the glucose uptake. Overall, by extending the three-partition proteome allocation theory concordant with multi-omics measurements, we elucidate the physiological consequences of loss of global regulators on central carbon metabolism restraining the organism to attain maximal biomass synthesis.IMPORTANCE Cellular proteome allocation in response to environmental or internal perturbations governs their eventual phenotypic outcome. This entails striking an effective balance between amino acid biosynthesis by metabolic proteins and its consumption by ribosomes. However, the global transcriptional regulator-driven molecular mechanisms that underpin their coordination remains unexplored. Here, we emphasize that global transcriptional regulators, known to control expression of a myriad of genes, are fundamental for precisely tuning the translational and metabolic efficiencies that define the growth optimality. Towards this, we systematically characterized the single deletion effect of FNR, ArcA, and IHF regulators of Escherichia coli on exponential growth under anaerobic glucose fermentative conditions. Their absence disrupts the stringency of proteome allocation, which manifests as impairment in key metabolic processes and an accumulation of intracellular metabolites. Furthermore, by incorporating an extension to the empirical growth laws, we quantitatively demonstrate the general design principles underlying the existence of these regulators in E. coli.

Role of enhanced glucocorticoid receptor sensitivity in inflammation in PTSD: insights from computational model for circadian-neuroendocrine-immune interactions

Although glucocorticoid resistance contributes to increased inflammation, individuals with posttraumatic stress disorder (PTSD) exhibit increased glucocorticoid receptor (GR) sensitivity along with increased inflammation. It is not clear how inflammation coexists with a hyperresponsive hypothalamic-pituitary-adrenal (HPA) axis. To understand this better, we developed and analyzed an integrated mathematical model for the HPA axis and the immune system. We performed mathematical simulations for a dexamethasone (DEX) suppression test and IC₅₀-dexamethasone for cytokine suppression by varying model parameters. The model analysis suggests that increasing the steepness of the dose-response curve for GR activity may reduce anti-inflammatory effects of GRs at the ambient glucocorticoid levels, thereby increasing proinflammatory response. The adaptive response of proinflammatory cytokine-mediated stimulatory effects on the HPA axis is reduced due to dominance of the GR-mediated negative feedback on the HPA axis. To verify these hypotheses, we analyzed the clinical data on neuroendocrine variables and cytokines obtained from war-zone veterans with and without PTSD. We observed significant group differences for cortisol and ACTH suppression tests, proinflammatory cytokines TNFα and IL6, high-sensitivity C-reactive protein, promoter methylation of GR gene, and IC_50-DEX for lysozyme suppression. Causal inference modeling revealed significant associations between cortisol suppression and post-DEX cortisol decline, promoter methylation of human GR gene exon 1F (NR3C1-1F), IC_50-DEX, and proinflammatory cytokines. We noted significant mediation effects of NR3C1-1F promoter methylation on inflammatory cytokines through changes in GR sensitivity. Our findings suggest that increased GR sensitivity may contribute to increased inflammation; therefore, interventions to restore GR sensitivity may normalize inflammation in PTSD.

Mechanistic inferences on metabolic dysfunction in posttraumatic stress disorder from an integrated model and multiomic analysis: role of glucocorticoid receptor sensitivity

Posttraumatic stress disorder (PTSD) is associated with neuroendocrine alterations and metabolic abnormalities; however, how metabolism is affected by neuroendocrine disturbances is unclear. The data from combat-exposed veterans with PTSD show increased glycolysis to lactate flux, reduced TCA cycle flux, impaired amino acid and lipid metabolism, insulin resistance, inflammation, and hypersensitive hypothalamic-pituitary-adrenal (HPA) axis. To analyze whether the co-occurrence of multiple metabolic abnormalities is independent or arises from an underlying regulatory defect, we employed a systems biological approach using an integrated mathematical model and multiomic analysis. The models for hepatic metabolism, HPA axis, inflammation, and regulatory signaling were integrated to perform metabolic control analysis (MCA) with respect to the observations from our clinical data. We combined the metabolomics, neuroendocrine, clinical laboratory, and cytokine data from combat-exposed veterans with and without PTSD to characterize the differences in regulatory effects. MCA revealed mechanistic association of the HPA axis and inflammation with metabolic dysfunction consistent with PTSD. This was supported by the data using correlational and causal analysis that revealed significant associations between cortisol suppression, high-sensitivity C-reactive protein, homeostatic model assessment of insulin resistance, γ-glutamyltransferase, hypoxanthine, and several metabolites. Causal mediation analysis indicates that the effects of enhanced glucocorticoid receptor sensitivity (GRS) on glycolytic pathway, gluconeogenic and branched-chain amino acids, triglycerides, and hepatic function are jointly mediated by inflammation, insulin resistance, oxidative stress, and energy deficit. Our analysis suggests that the interventions to normalize GRS and inflammation may help to manage features of metabolic dysfunction in PTSD.

Computational Analysis of Insulin-Glucagon Signalling Network: Implications of Bistability to Metabolic Homeostasis and Disease states

Insulin and glucagon control plasma macronutrient homeostasis through their signalling network composed of multiple feedback and crosstalk interactions. To understand how these interactions contribute to metabolic homeostasis and disease states, we analysed the steady state response of metabolic regulation (catabolic or anabolic) with respect to structural and input perturbations in the integrated signalling network, for varying levels of plasma glucose. Structural perturbations revealed: the positive feedback of AKT on IRS is responsible for the bistability in anabolic zone (glucose >5.5 mmol); the positive feedback of calcium on cAMP is responsible for ensuring ultrasensitive response in catabolic zone (glucose <4.5 mmol); the crosstalk between AKT and PDE3 is responsible for efficient catabolic response under low glucose condition; the crosstalk between DAG and PKC regulates the span of anabolic bistable region with respect to plasma glucose levels. The macronutrient perturbations revealed: varying plasma amino acids and fatty acids from normal to high levels gradually shifted the bistable response towards higher glucose range, eventually making the response catabolic or unresponsive to increasing glucose levels. The analysis reveals that certain macronutrient composition may be more conducive to homeostasis than others. The network perturbations that may contribute to disease states such as diabetes, obesity and cancer are discussed.

Influence of plasma macronutrient levels on hepatic metabolism: role of regulatory networks in homeostasis and disease states

Multilevel regulations by metabolic, signaling and transcription pathways form a complex network that works to provide robust metabolic regulation in the liver. This analysis indicates that dietary perturbations in these networks can lead to insulin resistance.

Control of cholesterol homeostasis by entero-hepatic bile transport – the role of feedback mechanisms

Cholesterol homeostasis is achieved through a tight regulation between synthesis, dietary absorption, utilization of bile salts, and excretion in the entero-hepatic compartment.

Fluorosis in Maharashtra

In all 241 school going children from the adjacent villages in Rajura taluka of Chandrapur district in Maharashtra were screened for dental fluorosis. Additionally 38 adult persons were also screened. The population in these villages appears to be at risk for fluorosis. Water fluoride level of 20 ppm from the village Dhoptala is the highest reported fluoride concentration in drinking water sources in the state. The entire area needs further investigations.