Systematic design of pulse dosing to eradicate persister bacteria.

A small fraction of infectious bacteria use persistence as a strategy to survive exposure to antibiotics. Periodic pulse dosing of antibiotics has long been considered a potentially effective strategy towards eradication of persisters. Recent studies have demonstrated through in vitro experiments that it is indeed feasible to achieve such effectiveness. However, systematic design of periodic pulse dosing regimens to treat persisters is currently lacking. Here we rigorously develop a methodology for the systematic design of optimal periodic pulse dosing strategies for rapid eradication of persisters. A key outcome of the theoretical analysis, on which the proposed methodology is based, is that bactericidal effectiveness of periodic pulse dosing depends mainly on the ratio of durations of the corresponding on and off parts of the pulse. Simple formulas for critical and optimal values of this ratio are derived. The proposed methodology is supported by computer simulations and in vitro experiments.

Recent advancement of nano-biochar for the remediation of heavy metals and emerging contaminants: Mechanism, adsorption kinetic model, plant growth and development.

Even though researches have shown that biochar can improve soil-health and plant-growth even in harsh environments and get rid of harmful heavy metals and new contaminants, it is still not sustainable, affordable, or effective enough. Therefore, scientists are required to develop nanomaterials in order to preserve numerous aquatic and terrestrial species. The carbonaceous chemical known as nano-biochar (N-BC) can be used to get rid of metal contamination and emerging contaminants. However, techniques to reduce hetero-aggregation and agglomeration of nano-biochar are needed that lead to the emergence of emerging nano-biochar (EN-BC) in order to maximise its capacity for adsorption of nano-biochar. To address concerns in regards to the expanding human population and sustain a healthy community, it is imperative to address the problems associated with toxic heavy metals, emerging contaminants, and other abiotic stressors that are threatening agricultural development. Nano-biochar can provide an effective solution for removal of emerging contaminants, toxic heavy metals, and non-degradable substance. This review provides the detailed functional mechanistic and kinetics of nano-biochar, its effectiveness in promoting plant growth, and soil health under abiotic stress. Nonetheless, this review paper has comprehensively illustrated various adsorption study models that will be employed in future research.

Synergistic regulation of hydrogen sulfide and nitric oxide on biochemical components, exopolysaccharides, and nitrogen metabolism in nickel stressed rice field cyanobacteria.

The present study examined the regulatory mechanism of hydrogen sulfide (H2S) and nitric oxide (NO) in nickel (Ni) stressed cyanobacteria viz., Nostoc muscorum and Anabaena sp. by analyzing growth, photosynthetic pigments, biochemical components (protein and carbohydrate), exopolysaccharides (EPS), inorganic nitrogen content, and activity of enzymes comprised in nitrogen metabolism and Ni accumulation. The 1 µM Ni substantially diminished growth by 18% and 22% in N. muscorum and Anabaena sp. respectively, along with declining the pigment contents (Chl a/Car ratio and phycobiliproteins), and biochemical components. It also exerted negative impacts on inorganic uptake of nitrate and nitrite contents; nitrate reductase and nitrite reductase; and ammonium assimilating enzymes (glutamine synthetase, glutamate synthase, and glutamate dehydrogenase exhibited a reverse trend) activities. Nonetheless, the adverse impact of Ni can be mitigated through the exogenous supplementation of NaHS [sodium hydrosulfide (8 µM); H2S donor] and SNP [sodium nitroprusside (10 µM); NO donor] which showed substantial improvement on growth, pigments, nitrogen metabolism, and EPS layer and noticeably occurred as a consequence of a substantial reduction in Ni accumulation content which minimized the toxicity effects. The accumulation of Ni on both the cyanobacterial cell surface (EPS layer) are confirmed by the SEM-EDX analysis. Further, the addition of NO scavenger (PTIO; 20 µM) and inhibitor of NO (L-NAME; 100 µM); and H2S scavenger (HT; 20 µM) and H2S inhibitor (PAG; 50 µM) reversed the positive responses of H2S and NO and damages were more prominent under Ni stress thereby, suggesting the downstream signaling of H2S on NO-mediated alleviation. Thus, this study concludes the crosstalk mechanism of H2S and NO in the mitigation of Ni-induced toxicity in rice field cyanobacteria.

Differential gene expression analysis of RAGE-S100A6 complex for target selection and the design of novel inhibitors for anticancer drug discovery.

Receptor for advanced glycation end products (RAGE), a member of the immunoglobulin family, interactions with its ligands trigger downstream signaling and induce an inflammatory response linked to diabetes, inflammation, carcinogenesis, cardiovascular disease, and a variety of other human disorders. The interaction of RAGE and S100A6 has been associated with a variety of malignancies. For the control of RAGE-related illnesses, there is a great demand for more specialized drug options. To identify the most effective target for combating human malignancies associated with RAGE-S100A6 complex, we conducted single and differential gene expression analyses of S100A6 and RAGE, comparing normal and malignant tissues. Further, a structure-based virtual screening was conducted using the ZINC15 database. The chosen compounds were then subjected to a molecular docking investigation on the RAGE active site region, recognized by the various cancer-related RAGE ligands. An optimized RAGE structure was screened against a library of drug-like molecules. The screening results suggested that three promising compounds were presented as the top acceptable drug-like molecules with a high binding affinity at the RAGE V-domain catalytic region. We depicted that these compounds may be potential RAGE inhibitors and could be used to produce a successful medication against human cancer and other RAGE-related diseases based on their various assorted parameters, binding energy, hydrogen bonding, ADMET characteristics, etc. MD simulation on a time scale of 50 ns was used to test the stability of the RAGE-inhibitor complexes. Therefore, targeting RAGE and its ligands using these drug-like molecules may be an effective therapeutic approach.

Establishment of decellularized extracellular matrix scaffold derived from caprine pancreas as a novel alternative template over porcine pancreatic scaffold for prospective biomedical application.

In this study, the caprine pancreas has been presented as an alternative to the porcine organ for pancreatic xenotransplantation with lesser risk factors. The obtained caprine pancreas underwent a systematic cycle of detergent perfusion for decellularization. It was perfused using anionic (0.5% w/v sodium dodecyl sulfate) as well as non-ionic (0.1% v/v triton X-100, t-octyl phenoxy polyethoxy ethanol) detergents and washed intermittently with 1XPBS supplemented with 0.1% v/v antibiotic and nucleases in a gravitation-driven set-up. After 48 h, a white decellularized pancreas was obtained, and its extracellular matrix (ECM) content was examined for scaffold-like properties. The ECM content was assessed for removal of cellular content, and nuclear material was evaluated with temporal H&E staining. Quantified DNA was found to be present in a negligible amount in the resultant decellularized pancreas tissue (DPT), thus prohibiting it from triggering any immunogenicity. Collagen and fibronectin were confirmed to be preserved upon trichrome and immunohistochemical staining, respectively. SEM and AFM images reveal interconnected collagen fibril networks in the DPT, confirming that collagen was unaffected. sGAG was visualized using Prussian blue staining and quantified with DMMB assay, where DPT has effectively retained this ECM component. Uniaxial tensile analysis revealed that DPT possesses better elasticity than NPT (native pancreatic tissue). Physical parameters like tensile strength, stiffness, biodegradation, and swelling index were retained in the DPT with negligible loss. The cytocompatibility analysis of DPT has shown no cytotoxic effect for up to 72 h on normal insulin-producing cells (MIN-6) and cancerous glioblastoma (LN229) cells in vitro. The scaffold was recellularized using isolated mouse islets, which have established in vitro cell proliferation for up to 9 days. The scaffold received at the end of the decellularization cycle was found to be non-toxic to the cells, retained biological and physical properties of the native ECM, suitable for recellularization, and can be used as a safer and better alternative as a transplantable organ from a xenogeneic source.

Tempol and silymarin rescue from zinc-induced degeneration of dopaminergic neurons through modulation of oxidative stress and inflammation.

Oxidative stress and inflammation are the key players in the toxic manifestation of sporadic Parkinson's disease and zinc (Zn)-induced dopaminergic neurodegeneration. A synthetic superoxide dismutase (SOD) mimetic, tempol, and a naturally occurring antioxidant, silymarin protect against oxidative stress-mediated damage. The study intended to explore the effects of tempol and silymarin against Zn-induced dopaminergic neurodegeneration. Exposure to Zn produced neurobehavioral deficits and striatal dopamine depletion. Zn reduced glutathione content and glutathione-S-transferase activity and increased lipid peroxidation, superoxide dismutase activity, and level of pro-inflammatory mediators [nuclear factor-kappa B (NF-κB), tumor necrosis factor-alpha (TNF-α), interleukin-1 beta (IL-1ß), and interleukin-6 (IL-6)]. Zn also attenuated the expression of tyrosine hydoxylase (TH), vesicular monoamine transporter 2 (VMAT-2), mitochondrial B-cell lymphoma-2 (Bcl-2), and procaspase-3 and 9 proteins and number of TH-positive neurons. Conversely, Zn elevated the expression of dopamine transporter (DAT) and mitochondrial Bcl-2-associated X (Bax) protein along with mitochondrial cytochrome c release. Administration of tempol significantly alleviated Zn-induced motor impairments, dopamine depletion, reduction in TH expression, and loss of TH-positive neurons similar to silymarin. Silymarin mitigated Zn-induced oxidative stress and inflammation and restored the expression of dopamine transporters and levels of pro-apoptotic proteins akin to tempol. The results demonstrate that both tempol and silymarin protect against Zn-induced dopaminergic neuronal loss through the suppression of oxidative stress and inflammation.

Development of clove oil based nanoencapsulated biopesticide employing mesoporous nanosilica synthesized from paddy straw via bioinspired sol-gel route.

Paddy straw (PS) burning is a concerning issue in South Asian countries, clamoring for exploring alternative management strategies. Being a rich source of silica, PS can be a potential nanosilica (SiNPs) source. The current study reports a pioneering approach for green synthesis of high-purity mesoporous SiNPs by sol-gel method using the aqueous extract of Sapindus mukorossi seed pericarp as a stabilizer. The mesoporous nature of SiNPs was harnessed as a carrier for the essential oil to develop the carrier-based formulation. SiNPs were characterized using XRD, EDX, FTIR, FE-SEM, TEM, AFM, DLS, water contact angle, and BET analysis. The synthesized SiNPs possessed a spheroid morphology with an average particle size of 20.34 ± 2.64 nm. XRD results confirmed its amorphous nature. The mesoporous nature of SiNPs was confirmed using BET analysis which showed a cumulative pore volume of 2.059 cm3/g and a high surface area of 746.32 m2/g. The SiNPs were further loaded with clove essential oil (CEO), and the encapsulation of CEO was assessed using UV-Vis, FTIR, and BET analysis. The in-vitro antifungal activity of CEO and CEO-loaded SiNPs (CEO-SiNPs) was evaluated using the agar plate assay. UV-Vis results depicted 62.64% encapsulation of CEO in SiNPs. The antifungal efficacy of CEO-SiNPs against F. oxysporum exhibited minimum inhibitory concentration (MIC), i.e., 125 mg/L, while the MIC of CEO was found to be 250 mg/L. The study delivers new insights into the holistic utilization of PS and propitious contribution toward the circular economy and Sustainable Development Goals (SDGs).

GM1 ganglioside modifies microglial and neuroinflammatory responses to α-synuclein in the rat AAV-A53T α-synuclein model of Parkinson's disease.

Among the pathological events associated with the dopaminergic neurodegeneration characteristic of Parkinson's disease (PD) are the accumulation of toxic forms of α-synuclein and microglial activation associated with neuroinflammation. Although numerous other processes may participate in the pathogenesis of PD, the two factors mentioned above may play critical roles in the initiation and progression of dopamine neuron degeneration in PD. In this study, we employed a slowly progressing model of PD using adeno-associated virus-mediated expression of human A53T α-synuclein into the substantia nigra on one side of the brain and examined the microglial response in the striatum on the injected side compared to the non-injected (control) side. We further examined the extent to which administration of the neuroprotective ganglioside GM1 influenced α-synuclein-induced glial responses. Changes in a number of microglial morphological measures (i.e., process length, number of endpoints, fractal dimension, lacunarity, density, and cell perimeter) were indicative of the presence of activated microglial and an inflammatory response on the injected side of the brain, compared to the control side. In GM1-treated animals, no significant differences in microglial morphology were observed between the injected and control striata. Follow-up studies showed that mRNA expression for several inflammation-related genes was increased on the A53T α-synuclein injected side vs. the non-injected side in saline-treated animals and that such changes were not observed in GM1-treated animals. These data show that inhibition of microglial activation and potentially damaging neuroinflammation by GM1 ganglioside administration may be among the many factors that contribute to the neuroprotective effects of GM1 in this model and possibly in human PD.

Molecular insights into the differential efflux mechanism of Rv1634 protein, a multidrug transporter of major facilitator superfamily in Mycobacterium tuberculosis.

Currently, multidrug-resistant tuberculosis (MDR-TB) is a public health crisis and a major health security threat globally. In Mycobacterium tuberculosis (Mtb), major facilitator superfamily (MFS) is the largest group of secondary active transporters. Along with the transport of their natural substrates, MFS proteins were involved in a drug efflux mechanism that ultimately lead to resistance against available anti-TB drugs in Mtb. In the present study, the three-dimensional structure model of an MFS protein, Rv1634, a probable multidrug transporter from Mtb, was generated using homology modeling. The protein structure model was found in inward-open conformation having 14 transmembrane helices. In addition, a central transport channel was deduced across the protein, and a single binding pocket was identified halfway through the central cavity by structural alignment with the homologous protein structures. Further, Rv1634 protein was studied based on the differential structural behavior of apo and ligand-bound forms. All the protein systems were inserted into a phospholipid bilayer to characterize the conformational dynamics of the protein using molecular dynamics (MD) simulations. Detailed analysis of the MD trajectories showed the diverse substrate specificity of the binding pocket for the antibiotics that caused differential movement in the ciprofloxacin and norfloxacin, to which Mtb strains have now become resistant. The expulsion of the drugs outside the bacterial cell occurs through the alternating-access mechanism of N and C-terminal domains, which is intriguing and essential to the understanding the drug resistance mechanism in pathogenic bacteria.

Predicting sequence and structural features of effective piRNA target binding sites.

Piwi-interacting RNA (piRNA) targets are usually identified through base pairing between the piRNA seed region and complementary bases on the target mRNAs, which often results in false predictions. Cross-linking immunoprecipitation (CLIP) study emerges as a promising method that enables accurate identification of PIWI-clade-based targets containing RNA-binding sites. In the present study, we have analyzed the piRNA-target CLIP-Seq datasets to uncover the additional characteristic features of piRNA targets. We studied important sequence and structural features using IP+ and IP- set targets that might enhance the accuracy of target site predictions. Analysis has revealed substantial enrichment of AU in target sites as well as in and around the 30 nts upstream and downstream of target sites in IP+ set relative to IP- set that might be contributing to lowering the minimal folding energy of target sites of IP+ set that might be easing the base pairing between piRNA and their targets. We have also found a lower MFE threshold (en) and higher miRanda score for piRNA targets. Interestingly, we have found that majority of the target sites are residing within 3'UTR, suggesting 3'UTR as a preferential target site like that of miRNA targets. Thus, we hypothesize that our findings on additional key features of piRNA target sites might be valuable in identifying the potential targets of piRNA accurately, which will aid in decrypting their functional importance.

Deciphering the role of Trichoderma sp. bioactives in combating the wilt causing cell wall degrading enzyme polygalacturonase produced by Fusarium oxysporum: An in-silico approach.

The cell wall degrading enzymes polygalacturonase (PG) secreted by Fusarium oxysporum f. sp. radicis-lycopersici (FOL) is testified to trigger Fusarium crown and root rot disease in tomato crops; instigated due to the degradation of the pectin. Trichoderma sp. is documented as a potential biocontrol agent playing a pivotal role in plant health and disease management. An in-silico approach employing homology modelling, molecular docking, molecular dynamics (MD) simulation and MMPBSA was employed to assess the prospective role of bioactives produced by Trichoderma sp. in combating the PG2 enzyme. The studies revealed that amongst the wide range of bioactives screened, Trichodermamide B produced by T. harzianum and Viridin, Virone, and Trichosetin produced by T. virens emerged as the potential inhibitors of the PG2. Docking results revealed that the complexes possessed most stable energy for Trichodermamide B (-8.1 kcal/mol) followed by Viridin (-7.7 kcal/mol), Virone (-7.1 kcal/mol), and Trichosetin (-7 kcal/mol), respectively. Interaction studies of FOL with T. virens and T. harzianum reported an inhibition of 83.33% and 75.87%, respectively. The structural rigidity and stability of the docked complex was confirmed through MD simulations evaluated across multiple descriptors from the simulation trajectories. Further, MMPBSA analysis validated the results that binding of the enzyme to the screened ligands was spontaneous. The study unravels new insights on the versatile potential of Trichoderma sp. Bioactives as a prospective agent for the inhibition of cell-wall degrading enzymes secreted by phytopathogens. The proposed study can be implemented for design of bioformulations that serve the role of biopesticide, promising a sustainable alternate to chemical-based products.

miR-34a negatively regulates cell cycle factor Cdt2/DTL in HPV infected cervical cancer cells.

MicroRNAs have emerged as an important regulator of cell cycle and various other cellular processes. Aberration in microRNAs has been linked with development of several cancers and other diseases but still very little is known about the mechanism by which they regulate these cellular events. High risk human papilloma virus (HR HPV) is the causative agent of 99% of cervical cancer cases which attenuates multiple tumor suppressors and checkpoint factors of the host cell. The viral proteins also stabilize many oncogenic factors, including an essential cell cycle regulator Cdt2/DTL which in turn promotes cell transformation and proliferation. In this study, we report that a micro-RNA, miR-34a by suppressing HPV E6 protein, destabilizes Cdt2/DTL protein level in HPV infected cervical cancer cell lines. Destabilization of Cdt2 stabilizes pro-apoptotic and onco-suppressor proteins like p21 and Set8 and suppresses cell proliferation, invasion and migration capabilities of the HPV positive cervical cancer cells. Overexpression of either HPV E6 or Cdt2 genes along with miR-34a restored back the suppressed proliferation rate. This study is the first-ever report to show that miR-34a regulates cell cycle factor Cdt2 by suppressing viral E6 protein level, thus opening up the possibility of exploring miR-34a as a specific therapy for cervical cancer treatment.

Evaluating complete surface-associated and secretory proteome of Leishmania donovani for discovering novel vaccines and diagnostic targets.

The protozoa Leishmania donovani causes visceral leishmaniasis (kala-azar), the third most common vector-borne disease. The visceral organs, particularly the spleen, liver, and bone marrow, are affected by the disease. The lack of effective treatment regimens makes curing and eradicating the disease difficult. The availability of complete L. donovani genome/proteome data allows for the development of specific and efficient vaccine candidates using the reverse vaccinology method, while utilizing the unique sequential and structural features of potential antigenic proteins to induce protective T cell and B cell responses. Such shortlisted candidates may then be tested quickly for their efficacy in the laboratory and later in clinical settings. These antigens will also be useful for designing antigen-based next-generation sero-diagnostic assays. L. donovani's cell surface-associated proteins and secretory proteins are among the first interacting entities to be exposed to the host immune machinery. As a result, potential antigenic epitope peptides derived from these proteins could serve as competent vaccine components. We used a stepwise filtering-based in silico approach to identify the entire surface-associated and secretory proteome of L. donovani, which may provide rationally selected most exposed antigenic proteins. Our study identified 12 glycosylphosphatidylinositol-anchored proteins, 45 transmembrane helix-containing proteins, and 73 secretory proteins as potent antigens unique to L. donovani. In addition, we used immunoinformatics to identify B and T cell epitopes in them. Out of the shortlisted surface-associated and secretory proteome, 66 protein targets were found to have the most potential overlapping B cell and T cell epitopes (linear and conformational; MHC class I and MHC class II).

Dose- and sex-dependent effects of phlebotomy-induced anemia on the neonatal mouse hippocampal transcriptome.

BACKGROUND: Phlebotomy-induced anemia (PIA) is universal and variable in degree among preterm infants and may contribute to neurodevelopmental risk. In mice, PIA causes brain tissue hypoxia, iron deficiency, and long-term sex-dependent neurobehavioral abnormalities. The neuroregulatory molecular pathways disrupted by PIA underlying these effects are unknown. METHODS: Male and female pups were phlebotomized daily from postnatal day (P)3-P14 via facial venipuncture to target hematocrits of 25% (moderate, mPIA) and 18% (severe, sPIA). P14 hippocampal RNA from non-bled control and PIA mice was sequenced by next-generation sequencing to identify differentially expressed genes (DEGs) that were analyzed using Ingenuity Pathway Analysis. RESULTS: mPIA females showed the least DEGs (0.5% of >22,000 genes) whereas sPIA females had the most (8.6%), indicating a dose-dependent effect. mPIA and sPIA males showed similar changes in gene expression (5.3% and 4.7%, respectively), indicating a threshold effect at mPIA. The pattern of altered genes induced by PIA indicates sex-specific and anemia-dose-dependent effects with increased pro-inflammation in females and decreased neurodevelopment in males. CONCLUSION: These gene-expression changes may underlie the reduced recognition memory function in male and abnormal social-cognitive behavior in female adult mice following neonatal PIA. These results parallel clinical studies demonstrating sex-specific behavioral outcomes as a function of neonatal anemia. IMPACT: Phlebotomy-induced anemia (PIA) in neonatal mice results in an altered hippocampal transcriptome and the severity of changes are dependent upon degree of anemia and sex of neonatal mice. The reported findings provide context to the sex-specific outcomes that have been reported in transfusion threshold clinical trials of preterm infants and therefore may inform treatment strategies that may be based on sex. These data advance the field by showing that consequences of PIA may be based in sex-specific transcriptomic alterations. Such changes may also result from other causes of neonatal anemia that also affect term infants.

Recalibrating the Non-Communicable Diseases risk prediction tools for the rural population of Western India.

BACKGROUND: The aim of the present study was to recalibrate the effectiveness of Indian Diabetes Risk Score (IDRS) and Community-Based Assessment Checklist (CBAC) by opportunistic screening of Diabetes Mellitus (DM) and Hypertension (HT) among the people attending health centres, and estimating the risk of fatal and non-fatal Cardio-Vascular Diseases (CVDs) among them using WHO/ISH charts. METHODS: All the people aged ≥ 30 years attending the health centers were screened for DM and HT. Weight, height, waist circumference, and hip circumferences were measured, and BMI and Waist-Hip Ratio (WHR) were calculated. Risk categorization of all participants was done using IDRS, CBAC, and WHO/ISH risk prediction charts. Individuals diagnosed with DM or HT were started on treatment. The data was recorded using Epicollect5 and was analyzed using SPSS v.23 and MedCalc v.19.8. ROC curves were plotted for DM and HT with the IDRS, CBAC score, and anthropometric parameters. Sensitivity (SN), specificity (SP), Positive Predictive Value (PPV), Negative Predictive Value (NPV), Accuracy and Youden's index were calculated for different cut-offs of IDRS and CBAC scores. RESULTS: A total of 942 participants were included for the screening, out of them, 9.2% (95% CI: 7.45-11.31) were diagnosed with DM for the first time. Hypertension was detected among 25.7% (95% CI: 22.9-28.5) of the participants. A total of 447 (47.3%) participants were found with IDRS score ≥ 60, and 276 (29.3%) with CBAC score > 4. As much as 26.1% were at moderate to higher risk (≥ 10%) of developing CVDs. Area Under the Curve (AUC) for IDRS in predicting DM was 0.64 (0.58-0.70), with 67.1% SN and 55.2% SP (Youden's Index 0.22). While the AUC for CBAC was 0.59 (0.53-0.65). For hypertension both the AUCs were 0.66 (0.62-0.71) and 0.63 (0.59-0.67), respectively. CONCLUSIONS: IDRS was found to have the maximum AUC and sensitivity thereby demonstrating its usefulness as compared to other tools for screening of both diabetes and hypertension. It thus has the potential to expose the hidden NCD iceberg. Hence, we propose IDRS as a useful tool in screening of Diabetes and Hypertension in rural India.

Microbiome of Pukzing Cave in India shows high antimicrobial activity against plant and animal pathogens.

Pukzing cave, the largest cave of Mizoram, India was explored for bacterial diversity. Culture dependent method revealed 235 bacterial isolates using three different treatments. Identity of the microbial species was confirmed by 16S rDNA sequencing. The highest bacterial population was recovered from heat treatment (n = 97;41.2%) followed by normal (n = 79;33.6%) and cold treatment (n = 59;25.1%) indicating dominance of moderate thermophiles. Antimicrobial potential of isolates showed 20.4% isolates having antimicrobial ability against tested pathogens. Amplicon sequencing of PKSI, PKSII and NRP specific genes revealed presence of AMP genes in the microbial population. Six microbial pathogens were selected for screening as they are well known for different disease cause organism in various fields such as agriculture and human health. Cave environment harbors unique microbial flora and hypervariable region V4 is more informative. Higher activity of AMP assay against these microbes indicates that cave microbial communities could be potential source of future genomic resources.

Deciphering the Potential of Pre and Pro-Vitamin D of Mushrooms against Mpro and PLpro Proteases of COVID-19: An In Silico Approach.

Vitamin D's role in combating the SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2), the virus causing COVID-19, has been established in unveiling viable inhibitors of COVID-19. The current study investigated the role of pre and pro-vitamin D bioactives from edible mushrooms against Mpro and PLpro proteases of SARS-CoV-2 by computational experiments. The bioactives of mushrooms, specifically ergosterol (provitamin D2), 7-dehydrocholesterol (provitamin-D3), 22,23-dihydroergocalciferol (provitamin-D4), cholecalciferol (vitamin-D3), and ergocalciferol (vitamin D2) were screened against Mpro and PLpro. Molecular docking analyses of the generated bioactive protease complexes unravelled the differential docking energies, which ranged from -7.5 kcal/mol to -4.5 kcal/mol. Ergosterol exhibited the lowest binding energy (-7.5 kcal/mol) against Mpro and PLpro (-5.9 kcal/mol). The Molecular Mechanics Poisson-Boltzmann Surface Area (MMPBSA) and MD simulation analyses indicated that the generated complexes were stable, thus affirming the putative binding of the bioactives to viral proteases. Considering the pivotal role of vitamin D bioactives, their direct interactions against SARS-CoV-2 proteases highlight the promising role of bioactives present in mushrooms as potent nutraceuticals against COVID-19.

Biosorptive and Biodegradative Mechanistic Approach for the Decolorization of Congo Red Dye by Aspergillus Species.

In this work, Aspergillus terreus GS28 and Aspergillus flavus CR500 isolated from industrial waste sludge examined for the decolorization of Congo red (CR) dye. The rate of CR decolorization raised due to optimum pH, temperature, carbon, nitrogen, and heavy metals. In the comparative study, A. terreus has the maximum ability (95%) to decolorize CR (≈ 100 mg L-1) as compared with A. flavus (92.96%) under optimized condition after 120 h. GC-MS and FTIR analysis of the fungal-metabolite and fungal-biomass shows bio-degradation and biosorption processes respectively. The degraded products were benzenepropanic (Rt-26.147), 3, 4-diaminonapthelene-1-sulfonic acid, and benzenedicarboxylic acid (Rt-26.660) by A. terreus, and benzenedicarboxylic acid (Rt-41.467) by A. flavus. The phytotoxicity assay revealed that a decrease in toxicity of the degraded product towards the growth and germination rate of two plant seeds compared to CR. Thus, the finding suggests that both the fungi act promising CR remediation candidates, induces restoration of CR polluted wastewater and save soil-land.

Climate-specific biosynthetic gene clusters in populations of a lichen-forming fungus.

Natural products can contribute to abiotic stress tolerance in plants and fungi. We hypothesize that biosynthetic gene clusters (BGCs), the genomic elements that underlie natural product biosynthesis, display structured differences along elevation gradients. We analysed biosynthetic gene variation in natural populations of the lichen-forming fungus Umbilicaria pustulata. We collected a total of 600 individuals from the Mediterranean and cold-temperate climates. Population genomic analyses indicate that U. pustulata contains three clusters that are highly differentiated between the Mediterranean and cold-temperate populations. One entire cluster is exclusively present in cold-temperate populations, and a second cluster is putatively dysfunctional in all cold-temperate populations. In the third cluster variation is fixed in all cold-temperate populations due to hitchhiking. In these two clusters the presence of consistent allele frequency differences among replicate populations/gradients suggests that selection rather than drift is driving the pattern. We advocate that the landscape of fungal biosynthetic genes is shaped by both positive and hitchhiking selection. We demonstrate, for the first time, the presence of climate-associated BGCs and BGC variations in lichen-forming fungi. While the associated secondary metabolites of the candidate clusters are presently unknown, our study paves the way for targeted discovery of natural products with ecological significance.

Fetal inflammation induces acute immune tolerance in the neonatal rat hippocampus.

BACKGROUND: Infants born preterm due to chorioamnionitis are frequently affected by a fetal inflammatory response syndrome (FIRS) and then by subsequent postnatal infections. FIRS and postnatal systemic inflammatory events independently contribute to poor neurocognitive outcomes of preterm infants. Developmental integrity of the hippocampus is crucial for intact neurocognitive outcomes in preterms and hippocampally dependent behaviors are particularly vulnerable to preterm systemic inflammation. How FIRS modulates the hippocampal immune response to acute postnatal inflammatory events is not well understood. METHODS: Prenatal LPS exposed (FIRS) and control neonatal rats received i.p. LPS or saline at postnatal day (P) 5. On P7, immune response was evaluated in the hippocampus of four treatment groups by measuring gene expression of inflammatory mediators and cytosolic and nuclear NFκB pathway proteins. Microglial activation was determined by CD11b+ and Iba1+ immunohistochemistry (IHC) and inflammatory gene expression of isolated microglia. Astrocyte reactivity was measured using Gfap+ IHC. RESULTS: Postnatal LPS resulted in a robust hippocampal inflammatory response. In contrast, FIRS induced by prenatal LPS attenuated the response to postnatal LPS exposure, evidenced by decreased gene expression of inflammatory mediators, decreased nuclear NFκB p65 protein, and fewer activated CD11b+ and Iba1+ microglia. Isolated microglia demonstrated inflammatory gene upregulation to postnatal LPS without evidence of immune tolerance by prenatal LPS. CONCLUSION: Prenatal LPS exposure induced immune tolerance to subsequent postnatal LPS exposure in the hippocampus. Microglia demonstrate a robust inflammatory response to postnatal LPS, but only a partial immune tolerance response.