Insights into the genomic features and lifestyle of B1 subcluster mycobacteriophages.

Bacteriophages infecting Mycobacterium smegmatis mc2155 are numerous and, hence, are classified into clusters based on nucleotide sequence similarity. Analyzing phages belonging to clusters/subclusters can help gain deeper insights into their biological features and potential therapeutic applications. In this study, for genomic characterization of B1 subcluster mycobacteriophages, a framework of online tools was developed, which enabled functional annotation of about 55% of the previously deemed hypothetical proteins in B1 phages. We also studied the phenotype, lysogeny status, and antimycobacterial activity of 10 B1 phages against biofilm and an antibiotic-resistant M. smegmatis strain (4XR1). All 10 phages belonged to the Siphoviridae family, appeared temperate based on their spontaneous release from the putative lysogens and showed antibiofilm activity. The highest inhibitory and disruptive effects on biofilm were 64% and 46%, respectively. This systematic characterization using a combination of genomic and experimental tools is a promising approach to furthering our understanding of viral dark matter.

Systematic review and meta-analysis of human Toll-like receptors genetic polymorphisms for susceptibility to tuberculosis infection.

Epidemiological data from the world health organization (WHO) show that Globally an estimated 10 million (range, 8.9-11.0 million) people around the world were infected with TB in 2019. M.tuberculosis (M.tb) is the major cause of tuberculosis. Infection with M.tb has varied host immune responses because of the host genetic factor and its response to the infection. Genetic polymorphism in TLRs imparts susceptibility or resistance to the host against several diseases. In the present study, a systematic review and meta-analysis were performed to describe the relationship among various TLRs and SNPs involved in M.tb infection and their association with susceptibility to pulmonary tuberculosis in various populations of the world. PubMed and Scihub databases from 2008 to 2019 were searched and 58 articles were shortlisted for the present study to explore the association between TLRs gene polymorphisms and susceptibility to tuberculosis infection. The combined analysis showed that the polymorphisms TLR1 (rs5743618), TLR1 (rs4833095), TLR2 (-196 to -174) del, TLR2 (rs3804099), TLR4 (rs4986790), TLR4 (rs4986791), TLR4 (rs7873784), TLR6 (rs5743810), TLR8 (rs3764880), TLR9 (rs5743836), TLR9 (rs352139) were significantly associated with TB disease in certain ethnic population. In our meta-analysis study, we have also found variations between studies in some polymorphism, for example. The TLR1 (rs 5743618), TLR2 (rs5743708), TLR4 Asp299Gly, TLR4 Thr399Ile, TLR4 (rs7873784), TLR6 (rs5743810), TLR9 (rs5743836) was associated with the protection against TB. Meta-analysis was performed between polymorphisms and pulmonary tuberculosis to define increase or decrease in susceptibility to tuberculosis in various populations, which indicated that a relationship exists between SNPs/host genetic factors and susceptibility or resistance in patients suffering from pulmonary tuberculosis our finding concludes that this gene polymorphism may be associated with susceptibility to TB. The present study adds value to the various researches and studies going on various populations of the world in better understanding the role of TLR polymorphism in TB.

Dimension reduction of subjective motivational values toward child gender tool tested in women of reproductive age from a hospital in rural area of Himachal Pradesh, India.

BACKGROUND: A novel subjective Motivational Value toward Child Gender (MVCG) tool was developed using the theoretical construct of 10 motivational domains described by Shalom H Schwartz. OBJECTIVE: The study aimed to summarize the pattern of correlations of (MVCG) in women of reproductive age in Himachal Pradesh, India. METHODS: A cross-sectional study was conducted from October 2018 to November 2019 among a sample of 355 women. Required data were collected through an interviewer-administered questionnaire. Maximum likelihood exploratory factor analysis (EFA) with oblique rotation was done with Bartlett's test sphericity and Kaiser-Meyer-Olkin test. RESULTS: A total of 28 (53.8%) questions loaded on eight factors explaining maximum variance (68.7%). Reliability analysis of these questions, with high loadings on extracted factors, of the questionnaire, observed with poor Cronbach's alpha of 0.61 and intraclass cluster coefficient (ICC) 0.49. However, selected domains such as tradition, power, achievement, self-direction, and benevolence were observed with a good Cronbach's alpha and ICC. CONCLUSION: MCVG is novel tool in its kind with well scalable properties in measuring subjective motivational values towards child gender. After EFA, total questions across 10 domains reduced from 52 to 28, across 8 domains, loaded on 8 factors with good reliability and agreement.

Identification and differential expression of serotransferrin and apolipoprotein A-I in the plasma of HIV-1 patients treated with first-line antiretroviral therapy.

BACKGROUND: Plasma proteins are known to interfere the drug metabolism during therapy. As limited information is available regarding the role of plasma proteins in HIV drug resistance during ART in HIV/AIDS patients, the present study aimed to identify and characterize the differentially expressed plasma proteins in the drug resistant and drug respondent groups of HIV-1 infected patients with > 6 years of first line ART. METHODS: Four-drug resistant (treatment failure) and four-drug respondent (treatment responder) patients were selected for plasma proteomic analysis based on viral load and drug resistance associated mutations from a cohort study designed on the first line ART patients who were enrolled in the antiretroviral therapy center, Sarojini Naidu Medical College, Agra, India from December 2009 to November 2016. After depleting high abundant proteins, plasma proteins were resolved using two-dimensional gel electrophoresis on IPG strips, pH range of 3-10. Spots were selected in the gel based on the density of staining which was common in the drug resistant and drug respondent groups separately. The fold change of each spot was calculated using image-J. Each protein spot was identified using the matrix assisted laser desorption/ionization-time of flight/time of flight (MALDI-TOF/TOF) after tryptic digestion. Peptide peaks were identified through flex analysis version 3.3, and a search against a protein data base using the internal Mascot. Gene ontology study was completed through STRING v.11 and Panther15.0. RESULTS: Out of eight spots from 2D gel samples analyzed by MALDITOF/TOF, two proteins were found to have significant score (> 56) after Flex analysis. These two proteins were identified to be apolipoprotein A1 and serotransferrin. The fold change expression of these two proteins were analyzed in drug resistant and drug respondent group. Apolipoprotein-A1 and serotransferrin were observed to be expressed 1.76 and 1.13-fold more respectively in drug respondent group compared to drug resistant group. The gene ontology analysis revealed the involvement of these two proteins in various important physiological processes. CONCLUSION: Apolipoprotein A-I and serotransferrin were found to be expressed more in drug respondent group compared to drug resistant group.

Autoantibodies in acquired myasthenia gravis: Clinical phenotype and immunological correlation.

BACKGROUND: Data on antibody profile in myasthenia gravis (MG) from India are limited. OBJECTIVES: To investigate antibody profile in patients with MG and their clinical correlates. PATIENTS AND METHODS: Patients of MG (n = 85, M:F::1.1:1, mean age: 39.29 ± 17.3 years, mean symptom duration: 72.94 ± 91.8 months) were evaluated for clinical features, MG foundation of America (MGFA) score, response to treatment, and outcome at last follow-up. Antibodies to acetylcholine receptor (AChR), muscle-specific kinase (MUSK), titin and ryanodine receptor (RYR) were analysed using ELISA. RESULTS: Based on the regional distribution of weakness, the cohort could be categorized as: generalized: 60, ocular: 16 and oculo-bulbar: 9. Sixty patients were followed up for a mean duration of 26.74 ± 13.8 months. Outcome at last follow-up was as follows: remission-22, no remission-33 and dead-5. AChR and MUSK antibodies were detected in 58 and 8 patients, respectively. Frequency of generalized MG, worse MGFA score during the disease course and thymomatous histology significantly correlated with presence of AChR-antibodies, though outcome at last follow-up was comparable between AChR-antibody positive and negative groups. Patients with MUSK antibodies had oculo-bulbar or generalized MG and frequent respiratory crisis, but majority improved or remitted with treatment. Titin antibodies were detected in 31.8% and RYR antibodies in 32.9%. Their presence did not correlate with age at onset of MG, severity or presence of thymoma. CONCLUSION: This report highlights the spectrum of antibodies in MG in an Indian cohort. AChR-antibody positivity correlated with clinical severity. Outcome was good in majority of MUSK antibody-positive MG. The role of other antibodies, complementary vs epiphenomenon, remains open.

Significance of immune response to Mycobacterium tuberculosis culture filtrate protein antigens in cerebrospinal fluid of tuberculous meningitis patients: A search for diagnostic marker.

Mycobacterium tuberculosis (H37Ra) culture filtrate proteins (CFP) are explored as a diagnostic marker for tuberculous meningitis (TBM). Cerebrospinal fluid (CSF) samples from patients were categorized as confirmed (n = 47), suspected (n = 20), and non-TBM (n = 25) cases. Immune response by Western blot revealed TBM CSF samples are having heterogeneous response to CFP. CFP ELISA was 92% sensitive and 38.30% specific. ODs of confirmed TBM and non-TBM cases were significantly different (P < 0.0001) and also the suspected TBM and non-TBM cases (P = 0.0001). No significant difference noticed in TBM and suspected TBM (P = 0.90). Thus, CFP can be a better biomarker for the diagnosis of TBM.

Comparative Evaluation of Multiplex PCR, RLEP PCR and LAMP PCR in Urine, Stool and Blood Samples for the Diagnosis of Pediatric Leprosy - A Cross-Sectional Study.

OBJECTIVE: To compare the diagnostic efficacy of Multiplex polymerase chain reaction (PCR), Mycobacterium leprae-specific repetitive element (RLEP) PCR and loop-mediated isothermal amplification (LAMP) PCR in the diagnosis of pediatric leprosy as an alternative to slit-skin smear (SSS) examination. METHODS: A cross-sectional study was performed on 26 children aged 0-18 years with characteristic skin lesions of leprosy. SSS examination for acid fast bacilli (AFB) was performed for all children. Additionally, urine, stool and blood samples were tested by three PCR techniques - Multiplex, RLEP and LAMP. The results of these tests were compared with each other and with results of SSS examination for acid fast bacilli (AFB) using appropriate statistical tests. RESULTS: Out of 26 patients studied, SSS examination was positive for AFB in 7 cases (26.9%). In blood samples, the positivity of Multiplex PCR, RLEP PCR and LAMP PCR was 84.6%, 80.8%, and 80.8%, respectively. Multiplex PCR in blood samples was positive in 100% (n = 7) of SSS positive cases and 84.2% (16 out of 19) of the SSS negative cases (P < 0.001). The positivity of all PCR methods in urine and stool samples was significantly lesser than in blood. CONCLUSION: Multiplex PCR in blood sample is a superior diagnostic tool for pediatric leprosy compared to RLEP PCR and LAMP PCR, as well as SSS examination.

Comparative evaluation of ELISA and dot-blot for the diagnosis of tuberculous meningitis.

Tuberculous meningitis is a central nervous system tuberculosis caused by M. tuberculosis. It causes high mortality if delayed in diagnosis and treatment. In this comparative study, Cerebrospinal fluid from TBM and non TBM patients were analyzed by ELISA and Dot-blot for anti-tuberculous antibodies. About 70% of the TBM samples showed positivity by Dot-blot and 72.5% by ELISA. Among the non TBM controls, 2.9% showed positivity by Dot-blot and 4.4% by ELISA. Both methods did not differ significantly as seen by Fisher's exact test (p = 0.50). Thus, Dot-blot could be an easy alternative to ELISA for quick diagnosis of TBM.

Magnetite-supported montmorillonite (K10) (nanocat-Fe-Si-K10): an efficient green catalyst for multicomponent synthesis of amidoalkyl naphthol.

Montmorillonite (K10) loaded on magnetite silica-coated nanoparticles was made using simple co-precipitation methods. The prepared nanocat-Fe-Si-K10 was analyzed using some techniques including field emission-scanning electron microscopy (FE-SEM), inductive coupling plasma-optical emission spectroscopy (ICP-OES), X-ray diffraction (XRD), thermo-gravimetric analysis (TGA), Fourier transmission-infrared spectra (FT-IR), energy dispersive X-ray spectroscopy (EDS), and wavelength-dispersive spectroscopy (WDX). The catalytic activity of the synthesized nanocat-Fe-Si-K10 has been examined in one-pot multicomponent transformations for the synthesis of 1-amidoalkyl 2-naphthol derivatives under solvent-free conditions. Nanocat-Fe-Si-K10 was determined to be very active, having the ability to be reused 15 times without significant loss of catalytic activity. The suggested technique has several advantages, including excellent yield, minimum reaction time, a straightforward workup, and catalyst recycling, all of which are essential green synthetic aspects.

Mycobacteriophage D29 Lysin B exhibits promising anti-mycobacterial activity against drug-resistant Mycobacterium tuberculosis.

IMPORTANCE: To combat the rapidly emerging drug-resistant M. tuberculosis, it is now essential to look for alternative therapeutics. Mycobacteriophages can be considered as efficient therapeutics due to their natural ability to infect and kill mycobacteria including M. tuberculosis. Here, we have exploited the mycolyl-arabinogalactan esterase property of LysB encoded from mycobacteriophage D29. This study is novel in terms of targeting a multi-drug-resistant pathogenic strain of M. tuberculosis with LysB and also examining the combination of anti-TB drugs and LysB. All the experiments include external administration of LysB. Therefore, the remarkable lytic activity of LysB overcomes the difficulty to enter the complex cell envelope of mycobacteria. Targeting the intracellularly located M. tuberculosis by LysB and non-toxicity to macrophages take the process of the development of LysB as a drug one step ahead, and also, the interaction studies with rifampicin and isoniazid will help to form a new treatment regimen against tuberculosis.

Enhanced Electrochemical Performance of Disordered Rocksalt Cathodes Enabled by a Graphite Conductive Additive.

Cobalt-free cation-disordered rocksalt (DRX) cathodes are a promising class of materials for next-generation Li-ion batteries. Although they have high theoretical specific capacities (>300 mA h/g) and moderate operating voltages (∼3.5 V vs Li/Li+), DRX cathodes typically require a high carbon content (up to 30 wt %) to fully utilize the active material which has a detrimental impact on cell-level energy density. To assess pathways to reduce the electrode's carbon content, the present study investigates how the carbon's microstructure and loading (10-20 wt %) influence the performance of DRX cathodes with the nominal composition Li1.2Mn0.5Ti0.3O1.9F0.1. While electrodes prepared with conventional disordered carbon additives (C65 and ketjenblack) exhibit rapid capacity fade due to an unstable cathode/electrolyte interface, DRX cathodes containing 10 wt % graphite show superior cycling performance (e.g., reversible capacities ∼260 mA h/g with 85% capacity retention after 50 cycles) and rate capability (∼135 mA h/g at 1000 mA/g). A suite of characterization tools was employed to evaluate the performance differences among these composite electrodes. Overall, these results indicate that the superior performance of the graphite-based cathodes is largely attributed to the: (i) formation of a uniform graphitic coating on DRX particles which protects the surface from parasitic reactions at high states of charge and (ii) homogeneous dispersion of the active material and carbon throughout the composite cathode which provides a robust electronically conductive network that can withstand repeated charge-discharge cycles. Overall, this study provides key scientific insights on how the carbon microstructure and electrode processing influence the performance of DRX cathodes. Based on these results, exploration of alternative routes to apply graphitic coatings is recommended to further optimize the material performance.

Enhancing the Electrode Gravimetric Capacity of Li1.2Mn0.4Ti0.4O2 Cathode Using Interfacial Carbon Deposition and Carbon Nanotube-Mediated Electrical Percolation.

Mn-based cation-disordered rocksalt oxides (Mn-DRX) are emerging as promising cathode materials for next-generation Li-ion batteries due to their high specific capacities and cobalt- and nickel-free characteristic. However, to reach the usable capacity, solid-state synthesized Mn-DRX materials require activation via postsynthetic ball milling, typically incorporating more than 20 wt % conductive carbon that adversely reduces the electrode-level gravimetric capacity. To address this issue, we first deposit amorphous carbon on the surface of the Li1.2Mn0.4Ti0.4O2 (LMTO) particles to increase the electrical conductivity by 5 orders of magnitude. Although the cathode material gravimetric first charge capacity reaches 180 mAh/g, its highly irreversible behavior leads to a first discharge capacity of 70 mAh/g. Subsequently, to ensure a good electrical percolation network, the LMTO material is ball-milled with a multiwall carbon nanotube (CNT) to obtain a 78.7 wt % LMTO active material loading in the cathode electrode (LMTO-CNT). As a result, a 210 mAh/g cathode electrode gravimetric first charge and 165 mAh/g first discharge capacity values are obtained, compared to the respective capacity values of 222 and 155 mAh/g for the LMTO material ball-milled with 20 wt % SuperP C65 electrode (LMTO-SP). After 50 cycles, LMTO-CNT delivers a 121 mAh/g electrode gravimetric discharge capacity, largely outperforming the value of 44 mAh/g of LMTO-SP. Our study demonstrates that while ball milling is necessary to achieve a significant amount of capacity of LMTO, a careful selection of additives, such as CNT, effectively reduces the required carbon quantity to achieve a higher electrode gravimetric discharge capacity.

SWATH-MS analysis of plasma proteins among Indian HIV-1 infected patients.

The identification and characterization of plasma proteins in drug resistant and drug sensitive in HIV-1 infected/AIDS patients were carried out using the SWATH-MS protocol. In total, 204 proteins were identified and quantified, 57 proteins were differentially expressed, out of which 25 proteins were down regulated and 32 proteins were up regulated in drug resistant patients. Six proteins such as complement C4-A, immunoglobulin heavy variable 1-2, carboxylic ester hydrolase, fibulin-1, immunoglobulin lambda constant7, secreted phosphoprotein 24 were differentially expressed in individuals with drug resistant HIV as compared to individuals with drug sensitive HIV. Gene ontology of 57 differentially expressed proteins was analysed and documented.

In-vivo studies on Transitmycin, a potent Mycobacterium tuberculosis inhibitor.

This study involves the in-vitro and in-vivo anti-TB potency and in-vivo safety of Transitmycin (TR) (PubChem CID:90659753)- identified to be a novel secondary metabolite derived from Streptomyces sp (R2). TR was tested in-vitro against drug resistant TB clinical isolates (n = 49). 94% of DR-TB strains (n = 49) were inhibited by TR at 10µg ml-1. In-vivo safety and efficacy studies showed that 0.005mg kg-1 of TR is toxic to mice, rats and guinea pigs, while 0.001mg kg-1 is safe, infection load did not reduce. TR is a potent DNA intercalator and also targets RecA and methionine aminopeptidases of Mycobacterium. Analogue 47 of TR was designed using in-silico based molecule detoxification approaches and SAR analysis. The multiple targeting nature of the TR brightens the chances of the analogues of TR to be a potent TB therapeutic molecule even though the parental compound is toxic. Analog 47 of TR is proposed to have non-DNA intercalating property and lesser in-vivo toxicity with high functional potency. This study attempts to develop a novel anti-TB molecule from microbial sources. Though the parental compound is toxic, its analogs are designed to be safe through in-silico approaches. However, further laboratory validations on this claim need to be carried out before labelling it as a promising anti-TB molecule.

Pathogen-specific TLR2 protein activation programs macrophages to induce Wnt-beta-catenin signaling.

Innate immunity recognizes and resists various pathogens; however, the mechanisms regulating pathogen versus nonpathogen discrimination are still imprecisely understood. Here, we demonstrate that pathogen-specific activation of TLR2 upon infection with Mycobacterium bovis BCG, in comparison with other pathogenic microbes, including Salmonella typhimurium and Staphylococcus aureus, programs macrophages for robust up-regulation of signaling cohorts of Wnt-ß-catenin signaling. Signaling perturbations or genetic approaches suggest that infection-mediated stimulation of Wnt-ß-catenin is vital for activation of Notch1 signaling. Interestingly, inducible NOS (iNOS) activity is pivotal for TLR2-mediated activation of Wnt-ß-catenin signaling as iNOS(-/-) mice demonstrated compromised ability to trigger activation of Wnt-ß-catenin signaling as well as Notch1-mediated cellular responses. Intriguingly, TLR2-driven integration of iNOS/NO, Wnt-ß-catenin, and Notch1 signaling contributes to its capacity to regulate the battery of genes associated with T(Reg) cell lineage commitment. These findings reveal a role for differential stimulation of TLR2 in deciding the strength of Wnt-ß-catenin signaling, which together with signals from Notch1 contributes toward the modulation of a defined set of effector functions in macrophages and thus establishes a conceptual framework for the development of novel therapeutics.

Nitric oxide is involved in Mycobacterium bovis bacillus Calmette-Guérin-activated Jagged1 and Notch1 signaling.

Pathogenic mycobacteria have evolved unique strategies to survive within the hostile environment of macrophages. Modulation of key signaling cascades by NO, generated by the host during infection, assumes critical importance in overall cell-fate decisions. We show that NO is a critical factor in Mycobacterium bovis bacillus Calmette-Guérin-mediated Notch1 activation, as the generation of activated Notch1 or expression of Notch1 target genes matrix metalloproteinase-9 (MMP-9) or Hes1 was abrogated in macrophages derived from inducible NO synthase (iNOS) knockout (iNOS(-/-)), but not from wild-type, mice. Interestingly, expression of the Notch1 ligand Jagged1 was compromised in M. bovis bacillus Calmette-Guérin-stimulated iNOS(-/-) macrophages, and loss of Jagged1 expression or Notch1 signaling could be rescued by NO donors. Signaling perturbations or genetic approaches implicated that robust expression of MMP-9 or Hes1 required synergy and cross talk between TLR2 and canonical Notch1-PI3K cascade. Further, CSL/RBP-Jk contributed to TLR2-mediated expression of MMP-9 or Hes1. Correlative evidence shows that, in a murine model for CNS tuberculosis, this mechanism operates in vivo only in brains derived from WT but not from iNOS(-/-) mice. Importantly, we demonstrate the activation of Notch1 signaling in vivo in granulomatous lesions in the brains of Mycobacterium tuberculosis-infected human patients with tuberculous meningitis. Current investigation identifies NO as a pathological link that modulates direct cooperation of TLR2 with Notch1-PI3K signaling or Jagged1 to regulate specific components of TLR2 responses. These findings provide new insights into mechanisms by which Notch1, TLR2, and NO signals are integrated in a cross talk that modulates a defined set of effector functions in macrophages.

PE_PGRS antigens of Mycobacterium tuberculosis induce maturation and activation of human dendritic cells.

Mycobacterium tuberculosis, the causative agent of pulmonary tuberculosis, infects one-third of the world's population. Activation of host immune responses for containment of mycobacterial infections involves participation of innate immune cells, such as dendritic cells (DCs). DCs are sentinels of the immune system and are important for eliciting both primary and secondary immune responses to pathogens. In this context, to understand the molecular pathogenesis of tuberculosis and host response to mycobacteria and to conceive prospective vaccine candidates, it is important to understand how cell wall Ags of M. tuberculosis and, in particular, the proline-glutamic acid_polymorphic guanine-cytosine-rich sequence (PE_PGRS) family of proteins modulate DC maturation and function. In this study, we demonstrate that two cell wall-associated/secretory PE_PGRS proteins, PE_PGRS 17 (Rv0978c) and PE_PGRS 11 (Rv0754), recognize TLR2, induce maturation and activation of human DCs, and enhance the ability of DCs to stimulate CD4(+) T cells. We further found that PE_PGRS protein-mediated activation of DCs involves participation of ERK1/2, p38 MAPK, and NF-kappaB signaling pathways. Priming of human DCs with IFN-gamma further augmented PE_PGRS 17 or PE_PGRS 11 Ag-induced DC maturation and secretion of key proinflammatory cytokines. Our results suggest that by activating DCs, PE_PGRS proteins, important mycobacterial cell wall Ags, could potentially contribute in the initiation of innate immune responses during tuberculosis infection and hence regulate the clinical course of tuberculosis.