Modeling a global regulatory network of Methanothermobacter thermautotrophicus strain ∆H

Methanogens and what they tell us about how life might survive on Mars

Space exploration and research are uncovering the potential for terrestrial life to survive in outer space, as well as the environmental factors that affect life during interplanetary transfer. The presence of methane in the Martian atmosphere suggests the possibility of methanogens, either extant or extinct, on Mars. Understanding how methanogens survive and adapt under space-exposed conditions is crucial for understanding the implications of extraterrestrial life. In this article, we discuss methanogens as model organisms for obtaining energy transducers and producing methane in a simulated Martian environment. We also explore the chemical evolution of cellular composition and growth maintenance to support survival in extraterrestrial environments. Neutral selective pressure is imposed on the chemical composition of cellular components to increase cell survival and reduce growth under physiological conditions. Energy limitation is an evolutionary driver of macromolecular polymerization, growth maintenance, and survival fitness of methanogens. Methanogens grown in a Martian environment may exhibit global alterations in their metabolic function and gene expression at the system scale. A space systems biology approach would further elucidate molecular survival mechanisms and adaptation to a drastic outer space environment. Therefore, identifying a genetically stable methanogenic community is essential for biomethane production from waste recycling to achieve sustainable space-life support functions.

Initiation of Apoptotic Pathway by the Cell-Free Supernatant Synthesized from Weissella cibaria Through In-Silico and In-Vitro Methods

Globally, colorectal cancer is the most prevalent type of cancer. Even though multiple treatments such as surgery, radiation, chemotherapy, and immunotherapy are available, the adverse effects caused in patients seem remarkable. Therefore, the current work was deliberated to prepare the metabolites (cell-free supernatant-CFS) from Weissella cibaria RK-3-1 to conduct in-silico and in-vitro-based anticancer assays. First, the active biomolecules present in the CFS were screened using a GC-MS analyzer. In addition, in-silico-based pharmacokinetic and docking studies were performed to confirm the anticancer potential of metabolites. In-silico results suggested that the bioactive compounds such as filicinic acid, dibutyl phthalate, and 4H-pyran-4-one,2,3-dihydro-3,5-dihydroxy-6-methyl present in CFS possessed significant molecular docking interactions with anticancer hub proteins. Furthermore, in-vitro results displayed the inhibition of cell proliferation in HT-29 cells at an IC50 value of 22.5 ± 1.3 µg/ml with the least significant effect on HEK-293 cell lines. Moreover, bacterial metabolites-controlled cell proliferation during the cell cycle's synthesis phase (S). Furthermore, the gene expression results confirm the increased expression of Bad, Bax, Bcl2, caspase-3, and cytochrome-C genes involved in the intrinsic apoptotic pathway. Hence, our findings from the in-silico and the in-vitro study confirm the anticancer potential of cell free-supernatant synthesized by W. cibaria.

A comprehensive review on methane's dual role: effects in climate change and potential as a carbon-neutral energy source

The unprecedented population and anthropogenic activity rise have challenged the future look up for shifts in global temperature and climate patterns. Anthropogenic activities such as land fillings, building dams, wetlands converting to lands, combustion of biomass, deforestation, mining, and the gas and coal industries have directly or indirectly increased catastrophic methane (CH4) emissions at an alarming rate. Methane is 25 times more potent trapping heat when compared to carbon dioxide (CO2) in the atmosphere. A rise in atmospheric methane, on a 20-year time scale, has an impact of 80 times greater than that of CO2. With increased population growth, waste generation is rising and is predicted to reach 6 Mt by 2025. CH4 emitted from landfills is a significant source that accounts for 40% of overall global methane emissions. Various mitigation and emissions reduction strategies could significantly reduce the global CH4 burden at a cost comparable to the parallel and necessary CO2 reduction measures, reversing the CH4 burden to pathways that achieve the goals of the Paris Agreement. CH4 mitigation directly benefits climate change, has collateral impacts on the economy, human health, and agriculture, and considerably supports CO2 mitigation. Utilizing the CO2 from the environment, methanogens produce methane and lower their carbon footprint. NGOs and the general public should act on time to overcome atmospheric methane emissions by utilizing the raw source for producing carbon-neutral fuel. However, more research potential is required for green energy production and to consider investigating the untapped potential of methanogens for dependable energy generation.

The genome of Symbiodiniaceae-associated Stutzerimonas frequens CAM01 reveals a broad spectrum of antibiotic resistance genes indicating anthropogenic drift in the Palk Bay coral reef of south-eastern India

An increase in antibiotic pollution in reef areas will lead to the emergence of antibiotic-resistant bacteria, leading to ecological disturbances in the sensitive coral holobiont. This study provides insights into the genome of antibiotics-resistant Stutzerimonas frequens CAM01, isolated from Favites-associated Symbiodiniaceae of a near-shore polluted reef of Palk Bay, India. The draft genome contains 4.67 Mbp in size with 52 contigs. Further genome analysis revealed the presence of four antibiotic-resistant genes, namely, adeF, rsmA, APH (3")-Ib, and APH (6)-Id that provide resistance by encoding resistance-nodulation-cell division (RND) antibiotic efflux pump and aminoglycoside phosphotransferase. The isolate showed resistance against 73% of the antibiotics tested, concurrent with the predicted AMR genes. Four secondary metabolites, namely Aryl polyene, NRPS-independent-siderophore, terpenes, and ectoine were detected in the isolate, which may play a role in virulence and pathogenicity adaptation in microbes. This study provides key insights into the genome of Stutzerimonas frequens CAM01 and highlights the emergence of antibiotic-resistant bacteria in coral reef ecosystems.

GC-MS and Network Pharmacology Analysis of the Ayurvedic Fermented Medicine, Chandanasava, Against Chronic Kidney and Cardiovascular Diseases

Chandanasava is an Ayurvedic polyherbal fermented traditional medicine (FTM) used by traditional practitioners for millennia. Nevertheless, the mode of action and functional targets are still unknown. The current study includes a pharmacological network analysis to identify the Chandanasava compounds interacting with target proteins involved in chronic kidney disease (CKD) and cardiovascular disease (CVD). Sixty-one Chandanasava phytochemicals were obtained by GC-MS and screened using the Traditional Chinese Medicine Systems Pharmacology Database (TCMSP). The disease target genes were obtained from DisGeNET and GeneCards databases. Forty-five phytocompounds and 135 potential targets were screened for CKD and CVD target proteins and protein interaction networks were constructed. The pharmacological network was deciphered employing target proteins involved in the mechanical action of Chandanasava. The results indicated that 10 bioactive compounds exhibited higher binding affinity patterns with the screened 42 CKD and CVD target proteins. Gene Ontology and KEGG analysis revealed target pathways involved in CKD and CVD, which were further explored by detailed analysis and network-coupled drug profile screening. The molecular docking results showed piperine and melatonin as effective inhibitors/regulators of the hub genes of CKD and CVD. The current study establishing authentic bioactive compounds in FTM is based on deeper insights into recognized Ayurvedic medicines. Representing the workflow of the network pharmacological analysis.

Brassica juncea (L.) Czern. leaves alleviate adjuvant-induced rheumatoid arthritis in rats via modulating the finest disease targets - IL2RA, IL18 and VEGFA

Brassica juncea (BJ) is a familiar edible crop, which has been used as a dietary ingredient and to prepare anti-inflammatory/anti-arthritic formulations in Ayurveda. But, the scientific validation or confirmation of its therapeutic properties is very limited. This study was performed to determine the efficiency of BJ leaves for the treatment of Rheumatoid arthritis using in vivo and in silico systems. Standard in vitro procedures was followed to study the total phenolic, flavonoid contents and free radical scavenging ability of the extracts of BJ. The effective extract was screened and the presence of bioactive chemicals was studied using HPLC. Further, the possible therapeutic actions of the BJ active principles against the disease targets were studied using PPI networking and docking analysis. IL2RA, IL18 and VEGFA are found to be the potential RA target and the compounds detected from BJ extract have shown great binding efficiency towards the target from molecular docking study. The resulting complexes were then subject to 100 ns molecular dynamics simulation studies with the GROMACS package to analyze the stability of docked protein-ligand complexes and to assess the fluctuation and conformational changes during protein-ligand interactions. To confirm the anti-arthritic activity of BJ, the extract was tested in CFA-induced arthritic Wistar rats. The test groups administered with BJ extract showed retrieval of altered hematological parameters and substantial recovery from inflammation and degeneration of rat hind paw.Communicated by Ramaswamy H. Sarma.

Genomics insights of SARS-CoV-2 (COVID-19) into target-based drug discovery

Coronavirus disease (COVID-19) pandemic is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). COVID-19 is a global health emergency and no clinically approved vaccines or antiviral drugs available to date. Intensive research on SARS-CoV-2 is urgently warranted to understand its pathogenesis and virulence mechanisms and to discover target-based antiviral therapeutics. Among various research logics, current bioinformatics highlights novel testable hypotheses for systematic drug repositioning and designing against COVID-19. A total of 121 articles related to bioinformatics facets of this virus were collected from the PubMed Central. The content of each investigation was comprehensively reviewed, manually curated, and included herein. Interestingly, 109 COVID-19-related literature published in 2020 (January-June) were included in this review. The present article emphasizes novel resource development on its genome structure, evolution, therapeutic targets, drug designing, and drug repurposing strategies. Genome organization, the function of coding genes, origin, and evolution of SARS-CoV-2 is described in detail. Genomic insights into understanding the structure-function relationships of drug targets including spike, main protease, and RNA-dependent RNA polymerase of SARS-CoV-2 are discussed intensively. Several molecular docking and systems pharmacology approaches have been investigated some promising antiviral drugs against SARS-CoV-2 based on its genomic characteristics, pathogenesis mechanism, and host specificity. Perhaps, the present genomic insights of this virus will provide a lead to the researchers to design or repurpose of antiviral drugs soon and future directions to control the spread of COVID-19.

Comparative genomic analysis reveals starvation survival systems in Methanothermobacter thermautotrophicus ΔH

Methanothermobacter thermautotrophicus ΔH (MTH) is a thermophilic hydrogenotrophic methanogenic archaeon capable of reducing CO₂ with H₂ to produce methane gas. It is the potential candidate in the biomethanation of CO₂ and CO in anaerobic reactors and biogas upgrading process. However, systematic studies addressing its genome conservation and function remain scant in this genome. In this study, we have evaluated its evolutionary resemblance and metabolic discrepancy, particularly in starvation survival systems by comparing the genomic contexts with Methanothermobacter marburgensis str. Marburg (MMG) and Methanobacterium formicicum DSM 1535 (MFO). The phylogenomic analysis of this study indicated that there was a strong phylogenomic signal among MTH, MMG, and MFO in the whole-genome tree. DNA replication machinery was conserved in the MTH genome and might have evolved at different evolution rates. Genome synteny analysis observed collinearity of either gene orders or gene families has to be maintained with syntenic blocks located in the syntenic out-paralogs. A genome-wide metabolic analysis identified some unique putative metabolic subsystems in MTH, which are proposed to determine its growth characteristics in diverse environments. MTH genome comprised of 93 unique genes-coding for starvation survival and stress-response proteins. These proteins confer its adaptation to nutritional deprivation and other abiotic stresses. MTH has a typical system to withstand its growth and cell viability during stable operation and recovery after prolonged starvation. Thus, the present work will provide an insight to improve the genome refinement and metabolic reconstruction in parallel to other closely related species.