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Biology subjects

Das, S. K.

Publications and source records attributed to Das, S. K..

At least 19 recordsLinked to original sources

An Efficient Microfluidic Platform for Organ-Specific CyclicMultiaxial Loading and Differentiation of Progenitor Cells

Mechanical loading is a fundamental regulator of tissue development, maturation, and function, yet existing in vitro systems predominantly apply uniaxial load/strain to cell-laden hydrogels, limiting their ability to reproduce physiologically relevant multiaxial on-chip tissue mechanics. Here, we present an engineered system to apply controlled multiaxial mechanical loading to real scaffolds with undifferentiated cells. The system enables programmable cyclic stretching and relaxation at the cell scaffold level and is compatible with both cell-laden native scaffold and engineered soft tissues. We have quantified the strain field experienced by the tissue with distinct mechanical loading periods using computation simulations and validated these with systematic experiments, demonstrating reproducible and various organ-relevant multiaxial strain profiles. As proof of concept, we applied the approach to human cardiac tissues, where cyclic multiaxial mechanical loading of mononuclear cells laden native tissue scaffold promoted cardiac structural organization and supports the emergence of spontaneous contractile activity. This approach provides a generalizable method for reproducing physiologically relevant tissue mechanics in vitro and enables systematic investigation of mechano-regulation across a plethora of human tissues.

bioengineering↗

Gut microbiome-associated adaptability of suckermouth catfish inhabiting the polluted Buriganga River: insights into heavy-metal-remediating microorganisms

The suckermouth catfish (SMCF), known for its pollutant tolerance and high invasiveness, is prevalent in the heavily contaminated Buriganga River in Bangladesh. This waterway, contaminated with a variety of pollutants, including heavy metals, has experienced the near-complete disappearance of native fish populations; however, the suckermouth catfish demonstrates remarkable adaptability in this environment. One objective of this study is to elucidate the role of the gut microbiome in SMCFs' adaptation to this severely polluted habitat. We performed next-generation sequencing (NGS) of gut contents from SMCFs to analyze the gut microbial profiles of the fish samples. The results indicated that the suckermouth catfish's gut is enriched with microbial communities, including Paraclostridium, Klebsiella, Staphylococcus, Bacillus, and Pseudomonas, which have the potential to remediate pollutants, including heavy metals. The subsequent aim of this research is to isolate and identify bacteria from the SMCF gut capable of remediating multiple heavy metals. We isolated three isolates with the potential to remediate multiple heavy metals and identified them as Staphylococcus pasteuri SD, Morganella morganii SAS1, and Sporosarcina saromensis SAS using partial 16S rRNA gene amplicon sequencing and conventional techniques. All isolates showed distinct capabilities for remediating multiple heavy metals. Notably, S. pasteuri showed the highest lead (Pb) bioaccumulation (36.28%), S. saromensis showed the highest chromium (Cr) uptake (39.22%), and M. morganii showed the highest nickel (Ni) uptake (35.90%). Furthermore, these isolates exhibited remarkable metal-tolerance profiles, with maximum tolerable concentrations ranging from 125 ppm to 1000 ppm, and sustained healthy growth under metal-supplemented conditions throughout a 48-hour incubation period. This validates their potential to remediate multiple heavy metals. Collectively, the results underscore the ecological adaptability of suckermouth catfish in polluted aquatic environments, which is associated with their gut microbiome, and highlight the bioremediation potential of these gut-derived microbes as effective agents for mitigating heavy metal contamination.

microbiology↗

Metal homeostasis is remodeled in response to different quiescence triggers

Cells can enter a reversible non-proliferative state called quiescence either spontaneously or in response to nutrient deprivations. Metal ions are essential nutrients and play wide-ranging regulatory and signaling roles in biological processes. We previously showed that zinc is an essential nutrient for the mammalian cell cycle as zinc deprivation drives cells into quiescence, and this quiescent state is associated with changes in iron, copper, and manganese, suggesting broad remodeling of metal homeostasis. Here we examine whether metal remodeling is a general feature of quiescence by inducing quiescence via different triggers (zinc deficiency, serum starvation, and growth factor withdrawal) in MCF10A cells. Fluorescence microscopy and elemental analysis reveal significant trigger-dependent changes in the labile and total metal pools of quiescent cells. To gain insight into these differences, we carried out RNA sequencing and differential expression analysis, focusing on metal associated, metal regulatory, and metal homeostasis genes. While core quiescence pathways are shared across triggers, quiescence states remain molecularly distinct. A significant percent of 2458 metal homeostasis annotated genes are differentially expressed including 55% in starvation-induced quiescence, 50% in zinc deficiency-induced quiescence and 21% in growth factor withdrawal-induced quiescence. Our results also showed unique alteration of genes involved in major metal dependent processes including antioxidant activity, oxidative phosphorylation, heme metabolism, and chromatin accessibility in different quiescence states. Overall, this work demonstrates that metal homeostasis is systematically rewired during cellular quiescence with associated effects on genes that regulate critical biological processes. Significance StatementCells constantly evaluate their nutrient and energy status and integrate these signals into proliferation-quiescence decisions. Quiescence prevents cells from passing damage to daughter cells. Metals are essential micronutrients for biological processes. While limitation of zinc can drive cells into quiescence and alter other metals, how metals are remodeled and whether this is a common feature of quiescence was unknown. Here we examined three quiescence triggers by modifying growth media and serum, the primary source of metals. We report significant changes in labile and total Cu, Fe, Zn and Mn pools, and metal associated genes in response to distinct quiescence triggers. These changes converge on mitochondrial function, cellular antioxidant activity, and heme biosynthesis in a trigger specific manner.

cell biology↗

ACTIVATED CASO₄-INDUCED VACUOLATION AS A QUANTITATIVE PLATFORM FOR PHAGOCYTOSIS-DRIVEN DRUG SCREENING

Cytoplasmic vacuolization is a fundamental process associated with phagocytosis, lysosomal acidification, and autophagy, yet robust in-vitro models for its quantification and pharmacological screening remainlimitedor insufficiently established. In this study, we demonstrate that thermally activated calcium sulfate (ACS) induces extensive vacuolation across mammalian cell lines including HeLa, RAW 264.7, 3T3-L1, and SH-SY5Y, thereby establishing a versatile platform to study vacuole biogenesis. To ensure reproducibility, particle heterogeneity was addressed using sedimentation-based fractionation, with homogeneous suspensions obtained at the 5th minute producing stable and consistent vacuole formation. Vacuolation was subsequently quantified by Neutral Red (NR) uptake, dose and time dependent response analyses confirmed direct correlation between ACS concentration and vacuole induction. The assay was validated with bafilomycin A1 (BFA1), a selective V-ATPase inhibitor, which served as a positive control and demonstrated concentration and time dependent inhibition of vacuole formation and acidification. Building on this framework, ten commercially available drugs were screened, revealing distinct profiles ranging from early cytotoxicity, strong vacuole inhibition to partial suppression or negligible effects. This dual capacity to discriminate between vacuole inhibition and cytotoxic responses highlights the utility of ACS-induced vacuolization as a sensitive and scalable in vitro platform. Collectively, our findings position this system as a tractable assay for mechanistic studies of vacuole biology and a functional screening tool for identifying modulators of lysosomal and phagocytic pathways relevant to infection, Lysosomal Disorders, and Phagocytotic dysfunction disorders. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=109 SRC="FIGDIR/small/711143v1_ufig1.gif" ALT="Figure 1"> View larger version (23K): org.highwire.dtl.DTLVardef@e5b920org.highwire.dtl.DTLVardef@1dd1072org.highwire.dtl.DTLVardef@62ae59org.highwire.dtl.DTLVardef@a468bf_HPS_FORMAT_FIGEXP M_FIG C_FIG

cell biology↗

Biological Mechanisms of Strength Preservation During Calorie Restriction-Induced Weight Loss Among Young- to Middle-Aged Adults without Obesity

PurposeWeight loss is often pursued to improve cardiometabolic health and quality of life. However, rapid weight loss can lead to reductions in lean soft tissue mass and strength to compromise body composition and functional ability. Thus, identifying molecular predictors of muscular strength preservation during weight loss is critical to mitigating these effects. MethodsWe conducted a secondary analysis of the CALERIETM (Comprehensive Assessment of Long-term Effects of Reducing Intake of Energy) trial, a two-year randomized controlled study of caloric restriction (CR) or ad-libitum intake in healthy adults without obesity. Among 198 participants, changes in whole-body mass and knee extensor strength were assessed over the first 12 months of the study which was primarily characterized by weight loss. Transcriptomic profiling was conducted in a subset of 42 participants who provided skeletal muscle samples. Linear regression was used to model the relationship between strength change and gene expression change, while controlling for changes in whole-body mass. Gene set enrichment analysis (GSEA) was performed using Hallmark pathways. Individual-level pathway analysis was performed via gene set variation analysis (GSVA). ResultsWe identified 96 out of 198 individuals (48.5%) who maintained or improved strength relative to body mass during weight loss (i.e. individuals with residuals > 0). Transcriptomics analysis on a subset of 42 individuals revealed 151 genes significantly associated with change in strength after accounting for change in whole-body mass (p < 0.01). Hub genes were identified as HSP90AA1 ({beta} = 34.45, SE = 7.32, p <0.001), EIF3A ({beta} = 36.14, SE = 10.27, p < 0.001), EIF5B ({beta} = 49.94, SE = 11.28, p < 0.001), and H3C1 ({beta} = -15.87, SE = 4.85, p < 0.001). GSEA revealed significant involvement of pathways related to cellular proliferation, immune regulation, protein secretion, and checkpoint control processes. GSVA identified a similar set of pathways. ConclusionsThese findings highlight molecular pathways supporting strength retention during CR-induced weight loss. Heat-shock protein, HSP90AA1, warrants further investigation as a candidate target for preserving muscle strength during interventions aimed at weight reduction.

molecular biology↗

Dynamic Supercoiling Sponsors Transcription Amplification by MYC

MYC dysregulation occurs in most cancers provoking, profound changes in gene expression. Although sometimes considered to be an E-box-dependent transcription factor, an alternate model posits MYC to be a universal amplifier of active genes. Although MYC is associated with accelerated pause release, the full extent of its participation in the transcription cycle remains poorly illuminated. MYC also stimulates topoisomerases to resolve topological issues that complicate DNA transactions; whether and how this stimulation is coordinated with or independent of its transcriptional role has not been examined. We have developed a genetic tool that discriminates between MYCs ability to activate versus amplify reporter gene expression in any cell. This system enables the interrogation of genes, cofactors, and compounds that execute or modulate MYC activity. Using a combination of biochemical and cellular assays, we reveal the dynamic interplay between MYC-driven transcription amplification and DNA supercoiling. The early stages of transcription are highly sensitive to the level of DNA supercoiling. Reducing the activity of TOP1 either through genetic knockdown or low-dose inhibition potentiates transcription amplification by MYC. This enhancement is associated with pre-initiation complex (PIC) stabilization by DNA supercoiling. MYC helps to mobilize these stabilized PICs. Significance StatementMYC is dysregulated in most cancers, yet its precise functions in transcription are poorly understood. Using a genetic system that distinguishes transcriptional activation from amplification, we reveal a functional interplay between MYC-driven amplification and DNA supercoiling. Reduced topoisomerase I activity increases DNA-supercoiling that in turn stabilizes PICs to provide more substrate for MYC-dependent transcription amplification. Thus, DNA topology as a critical regulator of MYC-dependent transcription.

molecular biology↗

Optimization of mRNA Synthesis and its Cell Expression for Vaccine Development

In vitro transcription (IVT) is a versatile procedure that facilitates template-directed synthesis of RNA molecules of any sequence, from short oligonucleotides to those of several kilobases, in quantities ranging from micrograms to milligrams. This technique, involving the engineering of a template with a bacteriophage promoter sequence, enables the synthesis of RNA for use in a variety of applications including structural studies, biochemical assays, and as functional molecules. Messenger RNA (mRNA) therapy has tremendous potential in regenerative medicine, disease treatment, and vaccination. Synthetic mRNA leverages the cells natural translation machinery to produce proteins, with the ability to transfect cells and induce expression of target proteins under physiological conditions until it is eventually degraded. In this study, we explore the impact of pseudouridine ({Psi})-modified mRNA in enhancing RNA stability, translational efficiency, and immune compatibility for therapeutic use. By optimizing IVT conditions and employing cellulose-based purification techniques, we successfully synthesized high-quality, modified mRNA that demonstrated superior functional performance. Luciferase and GFP mRNA, synthesized with pseudouridine-modified rNTPs, exhibited improved stability, reduced immune activation, and enhanced translation efficiency in HEK293 cells. A sevenfold increase in luciferase activity and elevated GFP fluorescence confirmed the higher protein expression capabilities of the modified mRNA. Furthermore, cellulose bead purification effectively separated single-stranded RNA from double-stranded RNA contaminants, ensuring minimal immune response and maximizing transfection efficiency. These findings highlight the potential of pseudouridine-modified mRNA and refined purification methods for advancing mRNA-based therapies, from vaccines to protein-replacement treatments, setting the foundation for scalable, clinical-grade RNA production.

cell biology↗

Exploring Microbial Dynamics: The Role of Commensals in Healthy and Dandruff-Affected Scalps

The human scalp harbors a diverse microbial community that plays a crucial role in scalp health and disease. This study aimed to analyze the microbiome of both healthy and dandruff-affected scalps to elucidate microbial composition differences and potential associations with dandruff pathology. Samples were collected from three healthy and three dandruff-affected individuals, and the V4 region of the 16S rRNA gene and the ITS1 region were sequenced to characterize bacterial and fungal communities, respectively. Taxonomic analysis identified 5 dominant phyla and 31 genera within the samples, revealing a shift from Actinomycetota dominance in healthy scalps to Basidiomycota dominance in dandruff-affected scalps. Notably, the fungal phylum Ascomycota, including Malassezia, was also more abundant in dandruff-affected scalps. This transition emphasizes the intricate interactions among microbial communities and their potential impact on scalp health. These findings suggest specific microbial shifts are associated with dandruff, highlighting the potential for targeted therapeutic strategies that modulate the scalp microbiome to improve scalp health. Further research is needed to elucidate the specific interactions between these microbial groups and their impact on scalp health.

microbiology↗

THE CORRELATION BETWEEN REDOX ACTIVITY AND ANTIMICROBIAL PROPERTIES OF PYOCYANIN FROM Pseudomonas aeruginosa

Pseudomonas aeruginosa, a metabolically versatile gram-negative bacterium, has garnered attention for its ability to thrive in diverse environments and its capacity to produce pyocyanin, a secondary metabolite with multifunctional properties. Pyocyanin, a redox-active phenazine compound, plays a critical role in mediating the ecological competitiveness of P. aeruginosa through its antimicrobial, biofilm-modulating, and reactive oxygen species (ROS)-generating activities. Beyond its contributions to bacterial virulence, pyocyanin demonstrates significant potential in various industrial and biomedical applications due to its redox properties and ability to function under diverse environmental conditions. This study investigates the electrochemical behaviour and pH-dependent antimicrobial activity of pyocyanin to evaluate its applicability in environmental and medical fields. Soil-derived P. aeruginosa isolates were cultured for pyocyanin (PYO) production, and the pigment was characterized using UV-visible spectroscopy to get its spectral integrity. Electrochemical analysis through cyclic voltammetry revealed enhanced redox activity in acidic environments and stable functionality in alkaline conditions. Antimicrobial assays demonstrated that pyocyanin exhibited optimal activity at neutral to slightly alkaline pH, effectively inhibiting bacterial and fungal growth, while extreme acidic conditions reduced its efficacy. The findings highlight pyocyanins versatility as both a redox mediator and an antimicrobial agent. In medical contexts, its pH-sensitive activity aligns well with physiological conditions, offering promise for combating multidrug-resistant pathogens. Future optimization of pyocyanin biosynthesis, particularly through cost-effective and scalable methods, could unlock its full potential in biotechnological and therapeutic innovations.

microbiology↗

DNA barcoding and species delimitation based on four Chloroplast loci to identify species within the Elaeocarpaceae family

AbstractDNA barcoding is an indispensable taxonomic tool for plant species identification. The present research successfully amplified the four coding regions of plastid namely; matK, rpoB, ndhJ, and accD, sequenced, and submitted it to NCBI Genbank after verification. This study evaluated the significance of single (matK, rpoB, ndhJ, and accD) and two-locus plastid loci (rpoB+matK, ndhJ+matK, accD+matK) and examined their abilities for species identification and phylogenetic construction of Elaeocarpaceae plants. The average aligned length for matK, rpoB, ndhJ, accD, ndhJ+matK, rpoB+matK, and accD+matK was 395 bp, 538 bp, 477 bp, 254 bp, 872 bp, 937 bp, and 649 bp, respectively. The highest substitution rate was recorded in the rpoB (18.47%), followed by ndhJ (17.38%), accD (14.00%), and matK (11.23%). The number of variable sites, segregating sites (S), nucleotide diversity (Pi), and mutations (Eta) were observed to be highest in the matK region. Evolutionary relationship based on the Neighbor-joining method demonstrated that candidate barcode sequences were competent for identifying Crinodendron, Elaeocarpus, Sloanea, and Vallea species. A significant barcoding gap was identified in two barcoding regions (matK and ndhJ+matK). The species-specific barcodes for the genus Elaeocarpus were generated based on Single Nucleotide Polymorphism (SNP) analysis. This study offers novel strategies for effectively identifying species within Elaeocarpaceae and lays the foundation for germplasm conservation and utilization.

bioinformatics↗

Phytochemical Characterization of Bio-active Compounds in Hydroethanolic Extract of Elaeocarpus ganitrus leaves using HPLC, LC-MS, and HPTLC Analyses

Bioactive compounds have various applications in different industries, including food, pharmaceutical, and cosmetic industries, demonstrating the need to identify the best-standardized technique to screen the phytochemical profile of medicinal plants. This study aimed to characterize the bioactive compounds in the hydroethanolic extracts of Elaeocarpus ganitrus leaves using various analytical techniques: HPLC, LC-MS, and HPTLC. Air-dried leaves of E. ganitrus were extracted with 70% ethanol. The phytochemical composition of crude extracts was analyzed by the High performance liquid chromatography (HPLC) method, and a total of 93 compounds, including 46 flavonoids, 17 phenols, 14 polyphenols, 3 phenolic acid, 3 phenolic glycosides, 2 flavonoid glycosides, 2 glycosides, 2 phenylpropanoid glycoside, 1 hydroxycinnamic acid, 1 lignan, 1 tannin, and 1 terpene glycoside were detected and quantified. The Liquid chromatography mass spectrometry (LC-MS) analyses identified 11 major eleven compounds: quercetin (803.0215 {micro}g/L), gallic acid (726.13 {micro}g/L), ferulic acid (652.34 {micro}g/L), chlorogenic acid (651.021{micro}g/L), pinocembrin (264.11 {micro}g/L), p-aminobenzoic acid (251.021 {micro}g/L), epicatechin (246.02 {micro}g/L), catechin (161.51 {micro}g/L), caffeic acid (123.31 {micro}g/L), syringaldehyde (116.31 {micro}g/L), and naringenin (106.31 {micro}g/L). The chemical fingerprinting was carried out by high performance thin layer chromatography (HPTLC), and HPTLC fingerprint qualitatively revealed a predominant amount of gallic acid (48.64 %), curcumin (15.21 %), caffeic acid (12.19 %) and cinnamic acid (6.50 %). A significant amount of bioactive constituents in a hydroethanolic extract of E. ganitrus leaves indicates the plants therapeutic potential, including antioxidant, anti-inflammatory, antidiabetic, anticancer, neuroprotective, and cardio-protective activities.

biochemistry↗

Development of Specific barcodes for identification of Aloe species based on chloroplast DNA barcoding

DNA barcoding is currently an effective and extensively used tool for species identification. The chloroplast matK (maturase K) and rbcL (Ribulose-bisphosphate large subunit) are one of the most variable coding genes of angiosperms and have been recommended as a universal barcode for land plants. Aloe is a large genus of around 500 species, and most species are widely used for traditional medicinal purposes worldwide, viz., Aloe vera, Aloe ferox, Aloe arborescens, and Aloe maculate. This study evaluated the two chloroplast DNA barcodes (matK and rbcL) to develop a theoretical base for species identification and germplasm conservation of Aloe species. The Maximum Parsimony analysis was conducted to study the evolutionary relatedness of Aloe sequences using matK and rbcL sequences retrieved from the NCBI database. The results revealed that 49 Aloe accessions were segregated into four major clades based on the matK sequence. Likewise, the 29 Aloe accessions were distributed into two major clades based on the rbcL sequence. SNP (Single Nucleotide Polymorphism) site analysis was conducted to obtain the specific barcode of Aloe species and generate the corresponding DNA QR code that electronic devices could immediately recognize. This study provides innovative research methods for efficient species identification of the genus Aloe and indicates the possibility of correctly identifying, discriminating, and documenting the Aloe species.

molecular biology↗

Histone H3 tail modifications regulate structure and dynamics of the H1 C-terminal domain within nucleosomes

Despite their importance, how linker histone H1s interact in chromatin and especially how the highly positively charged and intrinsically disordered H1 C-terminal domain (CTD) binds and stabilizes nucleosomes and higher-order chromatin structures remains unclear. Using single-molecule FRET we found that about half of the H1 CTDs in H1-nucleosome complexes exhibit well-defined FRET values indicative of distinct, static conformations, while the remainder of the population exhibits dynamically changing values, similar to that observed for H1 in the absence of nucleosomes. We also find that the first 30 residues of the CTD participate in relatively localized interactions with the first [~]20 bp of linker DNA, and that two separate regions in the CTD contribute to H1-dependent organization of linker DNA, consistent with some non-random CTD-linker DNA interactions. Finally, our data show that acetylation mimetics within the histone H3 tail induce decondensation and enhanced dynamics of the nucleosome-bound H1 CTD. (148 words)

biophysics↗

Spontaneous Histone Exchange Between Nucleosomes

The nucleosome is the fundamental gene-packing unit in eukaryotes. Nucleosomes comprise [~]147 bp DNA wrapped around an octameric histone protein core composed of two H2A-H2B dimers and one (H3-H4)2 tetramer. The strong yet flexible DNA-histone interactions are a physical basis of the dynamic regulation of genes packaged in chromatin. The dynamic nature of DNA-histone interactions implies that nucleosomes dissociate DNA-histone contacts transiently and repeatedly. This kinetic instability may lead to spontaneous nucleosome disassembly or histone exchange between nucleosomes. At a high nucleosome concentration, nucleosome-nucleosome collisions and subsequent histone exchange would be a more likely pathway, where nucleosomes act as their own histone chaperone. The spontaneous histone exchange would serve as a mechanism for maintaining the overall chromatin stability although it has never been reported. We employed three-color single-molecule FRET (smFRET) to demonstrate that histone H2A-H2B dimers are exchanged spontaneously between nucleosomes and that the time scale is on a few tens of seconds at a physiological nucleosome concentration. The rate of histone exchange increases at a higher monovalent salt concentration, with histone acetylated nucleosomes, and in the presence of histone chaperone Nap1, while it remains unchanged at a higher temperature, and decreases upon DNA methylation. These results support histone exchange via transient and repetitive partial disassembly of the nucleosome and corroborate spontaneous histone diffusion in a compact chromatin context, modulating the local concentrations of histone modifications and variants.

biophysics↗

Transgenic Mouse Models Establish a Protective Role of Type 1 IFN Response in SARS-CoV-2 infection-related Immunopathology

Type 1 interferon (IFN-I) response is the first line of host defense against invading viruses. In the absence of definite mouse models, the role of IFN-I in SARS-CoV-2 infections remained to be perplexing. Here, we developed two mouse models, one with constitutively high IFN-I response (hACE2; Irgm1-/-) and the other with dampened IFN-I response (hACE2; Ifnar1-/-) to comprehend the role of IFN-I response during SARS-CoV-2 invasion. We found that hACE2; Irgm1-/- mice were resistant to lethal SARS-CoV-2 infection with substantially reduced cytokine storm and immunopathology. In striking contrast, a severe SARS-CoV-2 infection along with immune cells infiltration, inflammatory response, and enhanced pathology was observed in the lungs of hACE2; Ifnar1-/- mice. Additionally, hACE2; Ifnar1-/- mice were highly susceptible to SARS-CoV-2 neuroinvasion in the brain accompanied by immune cell infiltration, microglia/astrocytes activation, cytokine response, and demyelination of neurons. The hACE2; Irgm1-/- Ifnar1-/- double knockout mice or hACE2; Irgm1-/- mice treated with STING or RIPK2 pharmacological inhibitors displayed loss of the protective phenotypes observed in hACE2; Irgm1-/- mice suggesting that heightened IFN-I response accounts for the observed immunity. Taken together, we explicitly demonstrate that IFN-I protects from lethal SARS-CoV-2 infection, and Irgm1 (IRGM) could be an excellent therapeutic target. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=133 SRC="FIGDIR/small/520843v1_ufig1.gif" ALT="Figure 1"> View larger version (51K): org.highwire.dtl.DTLVardef@a3aad4org.highwire.dtl.DTLVardef@12452fcorg.highwire.dtl.DTLVardef@1c43dc0org.highwire.dtl.DTLVardef@b2167d_HPS_FORMAT_FIGEXP M_FIG C_FIG

immunology↗

Description of Halopseudomonas maritima sp. nov., based on phylogenomic analysis

A novel bacterium, strain RR6T of the genus Halopseudomonas, was isolated from the sea sand from Paradip port area, India. Cells are Gram-stain-negative, rod-shaped, aerobic, non-sporulating and motile. The major cellular fatty acids of RR6T were C10:0 3OH, C12:0, C16:1 w7c/16:1 w6c, 18:1 w7c and/or 18:1 w6c and C16:0. The predominant polar lipids were phosphatidylglycerol (PG), diphosphatidylglycerol (DPG), phosphatidylethanolamine (PE), phosphatidylcholine (PC), unidentified phospholipid (PL) and unidentified lipids (L1-L2). The genome size of the strain RR6 was 3.93 Mb. The genomic G+C content was 61.3%. Gene ontology study showed a significant fraction of genes were associated with biological processes (53%), followed by molecular function (36%) and cellular components (11%). Comparisons of 16S rRNA gene sequences revealed 99.73 - 99.87 % sequence similarity with the closely related type strains of the genus Halopseudomonas. The average nucleotide identity (ANI) and average amino acid identity (AAI) of RR6T with reference strains of closely related species of the genus Halopseudomonas were below 95-96, and the corresponding in-silico DNA-DNA hybridization (DDH) values were below 70 %. A phylogenomic tree based on core genome analysis supported these results. Genotypic and phenotypic characteristics of RR6T indicate that the strain represents a novel species of the genus Halopseudomonas and the name Halopseudomonas maritima sp. nov. is proposed. The type strain is RR6T (= NBRC 115418T = TBRC 15628T).

microbiology↗

In silico analysis of Bacopa monnieri (L.) Wettst. compounds for drug development against Neurodegenerative Disorders

Neurotrophins play a crucial role in the development and regulation of neurons. Alterations in the functioning of these Neurotrophins leads to several Neurodegenerative Disorders. Albeit engineered medications which are accessible for the treatment of Neurodegenerative Disorders, due to their numerous side-effects, it becomes imperative to formulate and synthesize novel drug candidates. Plants could be utilized as an alternative for these manufactured medications because of their low incidental effects in contrast with the engineered drugs. Bacopa monnieri has been traditionally known to be utilized to treat Neurodegenerative Disorders. Therefore, in current study an in-silico based study was carried out to evaluate the pharmacological effect of Bacopa monnieri. Molecular Docking was carried out to screen the active phytochemicals of Bacopa monnieri which can act as potential drug candidates against the causative proteins of Neurodegenerative Disorders. A total of 105 biologically active phytochemicals from Bacopa monnieri were docked against the receptors of brain-derived neurotrophic factor, neurotrophin-3, neurotrophin-4, and nerve growth factor. Based on molecular docking study it was observed that the phytocompounds Vitamin E, Benzene propanoic acid, 3,5-bis(1,1dimethylethyl)4-hydroxy-, methyl ester (BPA), Stigmasterol, and Nonacosane of Bacopa monnieri significantly fits to the active residues of the four selected drug targets. Further Molecular Dynamics simulation study was performed to examine the stability of the binding of these phytochemicals with the selected targets. Drug likeness properties as well as related physico-chemical properties were analyzed through ADMETox study. Our findings suggested that the phytocompounds Vitamin E, BPA, Stigmasterol and Nonacosane significantly bind against brain-derived neurotrophic factor, neurotrophin-3, neurotrophin4, and nerve growth factor, respectively which may be the potential drug candidates for the treatment of neurodegenerative disorders. Graphic Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=140 SRC="FIGDIR/small/486025v1_ufig1.gif" ALT="Figure 1"> View larger version (55K): org.highwire.dtl.DTLVardef@2c39aforg.highwire.dtl.DTLVardef@17f4fd9org.highwire.dtl.DTLVardef@1534e13org.highwire.dtl.DTLVardef@2ad383_HPS_FORMAT_FIGEXP M_FIG C_FIG

pharmacology and toxicology↗