Genome-Scale Community Model-Guided Development of Bacterial Coculture for Lignocellulose Bioconversion.

Microbial communities have shown promising potential in degrading complex biopolymers, producing value-added products through collaborative metabolic functionality. Hence, developing synthetic microbial consortia has become a predominant technique for various biotechnological applications. However, diverse microbial entities in a consortium can engage in distinct biochemical interactions that pose challenges in developing mutualistic communities.

A putative mycobacterial GDP-mannose dependent α-mannosyltransferase Rv0225 acts as PimC: an study.

The complex cell envelope of pathogenic mycobacteria provides a strong barrier against the host immune system and various antibiotics. Phosphatidyl-myo-inositol mannosides (PIMs), lipomannan (LM), and lipoarabinomannan (LAM) are structurally important elements of mycobacterial cell envelope and also play crucial roles in modulating the host immune functions. At the cytoplasmic side of the mycobacterial inner membrane, phosphatidyl-myo-inositol (PI) is mannosylated by α-mannosyltransferases PimA and PimB' to synthesize PIM using GDP-mannose (GDPM) as the mannose donor.

A new species of the genus Ceraphron Jurine (Hymenoptera: Ceraphronidae) from India.

Ceraphron initium sp. nov. is described and illustrated from Nagaland state of India based on male specimens.

Light-Responsive Aldehyde-Reduction Catalysis Through Catalyst Encapsulation.

We report a light-responsive tetrahedral metal-organic capsule that binds a perrhenate catalyst, which is released selectively upon irradiation with 350 nm light, turning on the catalytic reduction of organic carbonyls by hydrosilanes. The catalytic activity can be switched off by heating at 75 °C for 2.5 h, which stimulates capsule reformation and catalyst re-encapsulation.

The neuroprotective effect of short-chain fatty acids against hypoxia-reperfusion injury.

Gut microbe-derived short-chain fatty acids (SCFAs) are known to have a profound impact on various brain functions, including cognition, mood, and overall neurological health. However, their role, if any, in protecting against hypoxic injury and ischemic stroke has not been extensively studied. In this study, we investigated the effects of two major SCFAs abundant in the gut, propionate (P) and butyrate (B), on hypoxia-reperfusion injury using a neuronal cell line and a zebrafish model.

Genome-Scale Metabolic Model Reconstruction and Investigation into the Fluxome of the Fast-Growing Cyanobacterium sp. PCC 11901.

The ability to convert atmospheric CO and light into biomass and value-added chemicals makes cyanobacteria a promising resource microbial host for biotechnological applications. A newly discovered fastest-growing cyanobacterial strain, sp. PCC 11901, has been reported to have the highest biomass accumulation rate, making it a preferred target host for producing renewable fuels, value-added biochemicals, and natural products.

Protocol for genome-scale differential flux analysis to interrogate metabolic differences from gene expression data.

Deciphering the functional differences between diseased and healthy cells requires understanding the alterations in biochemical flux patterns. We present a genome-scale differential flux analysis (GS-DFA) protocol to elucidate these metabolic disparities by integrating condition-specific gene expression data into the human genome-scale metabolic model (humanGEM). In this protocol, we describe the steps to normalize and integrate data into the humanGEM and analyze differential flux across the biochemical network between diseased and healthy cells.

Rational Engineering of a β-Glucosidase (H0HC94) from Glycosyl Hydrolase Family I (GH1) to Improve Catalytic Performance on Cellobiose.

The conversion of lignocellulosic feedstocks by cellulases to glucose is a critical step in biofuel production. β-Glucosidases catalyze the final step in cellulose breakdown, producing glucose, and are often the rate-limiting step in biomass hydrolysis. The specific activity of most natural and engineered β-glucosidase is higher on the artificial substrate -nitrophenyl β-d-glucopyranoside (NPGlc) than on the natural substrate, cellobiose.

Genome-scale community modelling elucidates the metabolic interaction in Indian type-2 diabetic gut microbiota.

Type-2 diabetes (T2D) is a rapidly growing multifactorial metabolic disorder that induces the onset of various diseases in the human body. The compositional and metabolic shift of the gut microbiota is a crucial factor behind T2D. Hence, gaining insight into the metabolic profile of the gut microbiota is essential for revealing their role in regulating the metabolism of T2D patients.

Machine learning for the advancement of genome-scale metabolic modeling.

Constraint-based modeling (CBM) has evolved as the core systems biology tool to map the interrelations between genotype, phenotype, and external environment. The recent advancement of high-throughput experimental approaches and multi-omics strategies has generated a plethora of new and precise information from wide-ranging biological domains. On the other hand, the continuously growing field of machine learning (ML) and its specialized branch of deep learning (DL) provide essential computational architectures for decoding complex and heterogeneous biological data.

Alpha globin gene alterations modifying the phenotype of homozygous beta thalassaemia.

The phenotype of β-thalassemia varies widely. The primary determinant is the type of beta-globin gene mutation; however, there are secondary and tertiary modifiers also as associated alpha mutations, polymorphisms, as well as coinheritance of mutations affecting other related systems. Co-inheritance of alpha thalassemia mutations is known to ameliorate the severity of HbE-β thalassemia.

Assessment and process optimization of high throughput biofabrication of immunocompetent breast cancer model for drug screening applications.

Recent advancements in 3D cancer modeling have significantly enhanced our ability to delve into the intricacies of carcinogenesis. Despite the pharmaceutical industry's substantial investment of both capital and time in the drug screening and development pipeline, a concerning trend persists: drug candidates screened on conventional cancer models exhibit a dismal success rate in clinical trials. One pivotal factor contributing to this discrepancy is the absence of drug testing on pathophysiologically biomimetic 3D cancer models during pre-clinical stages.

Mechanistic insights into on-surface reactions from isothermal temperature-programmed X-ray photoelectron spectroscopy.

On-surface synthesis often proceeds under kinetic control due to the irreversibility of key reaction steps, rendering kinetic studies pivotal. The accurate quantification of reaction rates also bears potential for unveiling reaction mechanisms. Temperature-Programmed X-ray Photoelectron Spectroscopy (TP-XPS) has emerged as an analytical tool for kinetic studies with splendid chemical and sufficient temporal resolution.

Light-Driven Purification of Progesterone from Steroid Mixtures Using a Photoresponsive Metal-Organic Capsule.

Chemical separations are expensive, consuming 10-15% of humanity's global energy budget. Many current separation methods employ thermal energy for distillation, often through the combustion of carbon-containing fuels, or extractions and crystallizations from organic solvents, which must then be discarded or redistilled, with a substantial energetic cost. The direct use of renewable energy sources, such as light, could enable the development of novel separations processes, as is required for the transition away from fossil fuel use.

Surgical Outcome of Basal Ganglia Hemorrhage: A Retrospective Analysis of Nearly 3,000 Cases over 10 Years.

 Basal ganglia hemorrhage (BGH) is a severe neurologic condition associated with significant morbidity and mortality, and its optimal management remains a topic of debate. Our study assessed the surgical outcomes of BGH patients at the 3-month mark using the modified Rankin Scale (mRS).  This retrospective observational study was conducted over 10 years at an advanced neuro-specialty hospital in Eastern India, including patients who underwent decompressive craniotomy and hematoma evacuation.

Subthalamic Deep Brain Stimulation in Parkinson's Disease: A Boon or Bane - A Single Centre Retrospective Observational Study from India.

 Subthalamic deep brain stimulation (STN-DBS) for refractory Parkinson's disease (PD) is more of a modality of treatment that is empirical, for which a physiological explanation is being sought. This study was done to determine the outcome and complications of patients undergoing STN-DBS for PD.  This retrospective observational cohort study was conducted in an advanced neuromedicine facility in eastern India for 9 years (August 2013-August 2022), which included all patients undergoing STN-DBS.

Influence of polymorphisms in TNF-α and IL1β on susceptibility to alcohol induced liver diseases and therapeutic potential of miR-124-3p impeding TNF-α/IL1β mediated multi-cellular signaling in liver microenvironment.

Background And Aims: Alcoholic liver disease (ALD) is the leading cause of the liver cirrhosis related death worldwide. Excessive alcohol consumption resulting enhanced gut permeability which trigger sensitization of inflammatory cells to bacterial endotoxins and induces secretion of cytokines, chemokines leading to activation of stellate cells, neutrophil infiltration and hepatocyte injury followed by steatohepatitis, fibrosis and cirrhosis. But all chronic alcoholics are not susceptible to ALD.

Deciphering the mannose transfer mechanism of mycobacterial PimE by molecular dynamics simulations.

Phosphatidyl-myo-inositol mannosides (PIMs), Lipomannan (LM), and Lipoarabinomannan (LAM) are essential components of the cell envelopes of mycobacteria. At the beginning of the biosynthesis of these compounds, phosphatidylinositol (PI) is mannosylated and acylated by various enzymes to produce Ac1/2PIM4, which is used to synthesize either Ac1/2PIM6 or LM/LAM. The protein PimE, a membrane-bound glycosyltransferase (GT-C), catalyzes the addition of a mannose group to Ac1PIM4 to produce Ac1PIM5, using polyprenolphosphate mannose (PPM) as the mannose donor.

Molecular insights into mutation-induced conformational changes in Acetyl CoA Carboxylase for improved activity.

Acetyl-CoA carboxylase (ACCase) is crucial for fatty acid biosynthesis and has potential applications in lipid accumulation and advanced biofuel production. Mutations like S659A and S1157A in Saccharomyces cerevisiae ACCase remove the Snf1-regulation sites, resulting in increased enzyme activity with positive effects on the fatty acid pathway. However, the molecular-level understanding of these mutations on ACCase activity remains unexplored.

Reconstruction of a Genome-Scale Metabolic Model of and Its Application for Lipid Production under Three Trophic Modes.

Green microalgae have emerged as beneficial feedstocks for biofuel production. A systems-level understanding of the biochemical network is needed to harness the microalgal metabolic capacity for bioproduction. Genome-scale metabolic modeling (GEM) showed immense potential in rational metabolic engineering, utilizing biochemical flux distribution analysis.

Elucidating the Ionic Liquid-Induced Mixed Inhibition of GH1 β-Glucosidase H0HC94.

Deciphering the ionic liquid (IL) tolerance of glycoside hydrolases (GHs) to improve their hydrolysis efficiency for fermentable sugar synthesis in the "one-pot" process has long been a hurdle for researchers. In this work, we employed experimental and theoretical approaches to investigate the 1-ethyl-3-methylimidazolium acetate ([CCim][MeCO])-induced inhibition of GH1 β-glucosidase (H0HC94) from 5A. At 10-15% [CCim][MeCO] concentration, H0HC94 experiences competitive inhibition ( = 0.

Grace, Inspiration, Fulfillment, Timeless, Soulful (GIFTS): The Why and How of Podcasts for Recognition and Mentoring of Faculty in Medicine.

This commentary offers the reader an alternative to mentoring through the use of PODCASTS. By providing the listener with an understanding of the challenges and opportunities for self-reflection and sharing of experiences by the interviewees, we are impacting the listener attitudes and future goals through lessons learned.

Leukoreduction of red blood cell units decreases dysregulatory micro RNAs during routine storage: An observational study with In-silico analysis.

Background: Red Blood cells (RBCs) bring about harmful consequences during storage. MicroRNA (miRNA) dysregulation in stored RBCs could represent potential biomarkers of storage lesions. Although leukoreduction prevents damage to RBCs, it is uncertain whether leukoreduction of RBCs would impact the dysregulation of miRNAs during storage.