Cohort Profile: Real-Time Insights of COVID-19 in India (RTI COVID-India).

BACKGROUND: The coronavirus disease (COVID) pandemic caused disruption globally and was particularly distressing in low- and middle-income countries such as India. This study aimed to provide population representative estimates of COVID-related outcomes in India over time and characterize how COVID-related changes and impacts differ by key socioeconomic groups across the life course. METHODS: The sample was leveraged from an existing nationally representative study on cognition and dementia in India: Harmonized Diagnostic Assessment of Dementia for the Longitudinal Aging Study in India (LASI-DAD). The wave-1 of LASI-DAD enrolled 4096 older adults aged 60 years and older in 3316 households from 18 states and union territories of India. Out of the 3316 LASI-DAD households, 2704 with valid phone numbers were contacted and invited to participate in the Real-Time Insights COVID-19 in India (RTI COVID-India) study. RTI COVID-India was a bi-monthly phone survey that provided insight into the individual's knowledge, attitudes, and behaviour towards COVID-19 and changes in the household's economic and health conditions throughout the pandemic. The survey was started in May 2020 and 9 rounds of data have been collected. FINDINGS TILL DATE: Out of the 2704 LASI-DAD households with valid phone numbers, 1766 households participated in the RTI COVID-India survey at least once. Participants were in the age range of 18-102 years, 49% were female, 66% resided in rural area. Across all rounds, there was a higher report of infection among respondents aged 60-69 years. There was a greater prevalence of COVID-19 diagnosis reported in urban (23.0%) compared to rural areas (9.8%). Respondents with higher education had a greater prevalence of COVID-19 diagnosis compared to those with lower or no formal education. Highest prevalence of COVID-19 diagnosis was reported from high economic status compared to middle and low economic status households. Comparing education gradients in experiencing COVID-19 symptoms and being diagnosed, we observe an opposite pattern: respondents with no formal schooling reported the highest level of experiencing COVID-19 symptoms, whereas the greatest proportion of the respondents with secondary school or higher education reported being diagnosed with COVID-19. FUTURE PLANS: The study group will analyse the data collected showing the real-time changes throughout the pandemic and will make the data widely available for researchers to conduct further studies.

Role of proline-rich tyrosine kinase 2 (Pyk2) in the pathogenesis of Alzheimer's disease.

Alzheimer's disease (AD), a progressive neurodegenerative disorder, is the most common form of dementia in the elderly. Two major pathological hallmarks have been identified for AD: extracellular amyloid plaques and intracellular neurofibrillary tangles (NFT). Recently, proline-rich tyrosine kinase 2 (Pyk2), which belongs to the focal adhesion kinase (FAK) non-receptor tyrosine kinase family, was recognized to contribute significantly towards the pathogenesis of AD. Pyk2 can influence the formation of amyloid plaques as well as NFTs. The kinase can directly phosphorylate tau, which is a significant component of NFTs and enhances tau pathology. Several competitive inhibitors have been developed for Pyk2, tested in several cancer models, as Pyk2 is known to be overexpressed under those conditions. The current review article discusses the possible mechanistic pathways by which Pyk2 can influence the pathogenesis of AD. Besides, it describes various inhibitors for Pyk2 and their potential role as therapeutics for AD in the future.

Design and in vitro analysis of SIRT2 inhibitor targeting Parkinson's disease.

Inhibition of Sirtuin2 (SIRT2) protein rescues the α-synuclein toxicity in vitro and in vivo models of Parkinson's disease (PD). Thioacetyl group can structurally mimic the acetyl group and restrain the deacetylating p53 reaction by SIRT2. This work evaluated the biological activity of designed pentapeptides inhibitor containing N-thioacetyl-lysine against SIRT2. Pentapeptide by introducing thioacetyl-lysine as an inhibitor of SIRT2 was screened by molecular docking and synthesized by solid phase method. The inhibition of pure recombinant SIRT2 as well as SIRT2 in serum of PD patients by peptide was done by fluorescent activity assay. The inhibition of SIRT2 was assessed in PC12 cell line by measuring acetylated α-tubulin level. The peptide YKK(ε-thioAc)AM and HRK(ε-thioAc)AM were found to be SIRT2 inhibitors by molecular docking. However, YKK(ε-thioAc)AM was more specific towards SIRT2 than SIRT1 (Sirtuin1). It inhibited recombinant SIRT2 by IC50 value of 0.15 µM and KD values 9.92 × 10-8/M. It also inhibited serum SIRT2 of PD. It increased the acetylation of α-tubulin in PC12 neuroblastoma cells which is essential for maintaining the microtubular cell functions of brain. It can be concluded that novel peptide YKK(ε-thioAc)AM may be a platform for therapeutic agent for Parkinson's disease targeting SIRT2.

Serum sestrins: potential predictive molecule in human sarcopenia.

BACKGROUND: The aging trajectory from a state of robustness and good health proceeds from sarcopenia to frailty followed by disability and death due to decline in skeletal muscle mass and function. Sarcopenia is now formally recognized as a muscle disease with an ICD-10-MC diagnosis code. The autophagic response seems to be affected in the skeletal muscle during aging contributing to sarcopenia. Sestrins (Sesns) proteins play a critical role in autophagy induction under cellular stress conditions. AIMS: The study aims to identify sarcopenia in older adults using Asian Working group guidelines (AWGS) to determine clinically relevant cut-off levels for diagnosis and their association with antioxidant protein Sesns. METHODS: The study recruited 102 older adults attending Geriatric medicine OPD AIIMS, New Delhi, India. The level of serum Sesns were evaluated by Surface Plasmon Resonance (SPR) and validated by immunoblotting. Fifty older adults were diagnosed as sarcopenics according to AWGS. RESULTS: Sesn 1 (p = 0.0448) and Sesn 2 (p < 0.0001) levels were significantly reduced in sarcopenic compared to non-sarcopenic. ROC analysis showed a better cut-off of Sesn 2; 10.104 ng/µL with 92% sensitivity and 84% specificity. Even after adjusting the values with respect to confounding factors, Sesn levels remained significantly reduced in sarcopenics (p < 0.030). DISCUSSION: The level of Sesn 2 showed positive co-relation with the characteristics of sarcopenia. This study first time reported the concentration of serum sestrin in sarcopenic older adults. CONCLUSION: It can be concluded that sarcopenia can be diagnosed at the early stage by using the serum sestrin scale as one of the potential biomarker.

Induction of p73, Δ133p53, Δ160p53, pAKT lead to neuroprotection via DNA repair by 5-LOX inhibition.

The inflammatory process plays a key role in neurodegenerative disorder. The inflammatory molecule, 5-lipooxygenase (5-LOX), protein is involved in the pathologic phenotype of AD which includes Aß amyloid deposition and tau hyperphosphorylation. This study aims to identify the mechanistic role in neuroprotection by 5-LOX inhibitor in neurotoxic SH-SY5Y cell line model by evaluating different cell survival pathway. The neurotoxic SH-SY5Y cells were developed by the treatment of Aß25-35. The cells were then treated with 5-LOX peptide inhibitor, YWCS to prevent neurotoxicity reported earlier from our lab. The effect of 5-LOX inhibition on cell survival pathways were determined by western blot experiment with different doses of peptide by using polyclonal anti body of p53, anti-Akt and anti-phosphorylated Akt. Immunoprecipitation and mass spectroscopic studies were done to identify the altered proteins appeared on the blot. Over expression of phosphorylated Akt and 3 bands on p53 lane blot other than p53 were observed. Three bands were identified as isoforms of p53 which correspond to p73, Δ133p53 and Δ160p53 in the cells treated only with 80 µM of YWCS compare to untreated cells. However, no alteration of total p53 and Akt were observed in treated cells. The results exposed the novel mechanistic pathway of neuroprotection by 5-LOX inhibition is likely to be mediated by DNA DSB repair through p53 isoforms and PI3K/Akt pathway. Our finding has opened a new window in the therapeutic approach for the prevention of AD.

p38 MAP kinases: plausible diagnostic and prognostic serum protein marker of non small cell lung cancer.

INTRODUCTION: p38 MAPK signaling molecules plays a dual role in cancer, both progression and suppression. Elevated expression of p38α was reported in lung cancer tissue in rat model. Our objective was to explore the concentration of all 4 isoforms of p38MAPK in serum of Non Small Cell Lung Cancer (NSCLC). MATERIAL AND METHODS: The blood samples were collected from 77 NSCLC patients, 52 ethically matched healthy controls and 18 follow up patients were collected as some patients expired and some discontinued the treatment. The concentration of all isoforms of p38 (p38α, p38ß, p38γ, and p38δ) were evaluated by Surface Plasmon Resonance (SPR) technology. RESULT: The levels of all isoforms of serum p38 were significantly elevated at pre-therapy compare to control. Only p38α expression was significantly associated with tumor stage and its expression reduced after treatment which is then validated by western blot. However, no changes were observed in other isoforms after therapy. CONCLUSION: Our study revealed that, p38α is more efficient among all the isoform to predict the disease accurately and it can be concluded that p38 MAPK may be used as diagnostic as well as prognostic marker of NSCLC disease.

Structural insights of Mycobacterium GTPase-Obg and anti-sigma-F factor Usfx interaction.

An essential protein for bacterial growth, GTPase-Obg (Obg), is known to play an unknown but crucial role in stress response as its expression increases in Mycobacterium under stress conditions. It is well reported that Obg interacts with anti-sigma-F factor Usfx; however, a detailed analysis and structural characterization of their physical interaction remain undone. In view of above-mentioned points, this study was conceptualized for performing binding analysis and structural characterization of Obg-Usfx interaction. The binding studies were performed by surface plasmon resonance, while in silico docking analysis was done to identify crucial residues responsible for Obg-Usfx interaction. Surface plasmon resonance results clearly suggest that N-terminal and G domains of Obg mainly contribute to Usfx binding. Also, binding constants display strong affinity that was further evident by intermolecular hydrogen bonds and hydrophobic interactions in the predicted complex. Strong interaction between Obg and Usfx supports the view that Obg plays an important role in stress response, essentially required for Mycobacterium survival. As concluded by various studies that Obg is crucial for Mycobacterium survival under stress, this structural information may help us in designing novel and potential inhibitors against resistant Mycobacterium strains.

DS6: anticandidal, antibiofilm peptide against Candida tropicalis and exhibit synergy with commercial drug.

Antifungal peptides have gained interest as therapeutic agents in recent years because of increased multidrug resistance against present antifungal drugs. This study designed, synthesized and characterized antifungal activity of a small peptide analogue, DS6. This peptide was designed using the template from the N-terminal part of the antifungal protein, Aspergillus giganteous. DS6 inhibited Candida tropicalis (ATCC 13803), as well as its clinical isolates. DS6 was found to be a fungicidal, killing the fungus very rapidly. DS6 is also non-toxic to human cells. Synergistic interactions of DS6 with amphotericin B and fluconazole were also evident. DS6 is membrane lytic and exhibits antibiofilm activity against C. tropicalis. In conclusion, DS6 may have utility as an alternative antifungal therapy for C. tropicalis. Copyright © 2017 European Peptide Society and John Wiley & Sons, Ltd.

Estimation of Serum YKL-40 by Real-Time Surface Plasmon Resonance Technology in North-Indian Asthma Patients.

BACKGROUND: Many studies reported for estimating serum YKL-40 using ELISA or RIA methods. This study introduces the plausible utilization of real-time surface plasmon resonance (SPR) technology in investigating the expression of serum YKL-40 protein levels and ELISA method for serum IgE in bronchial asthma. METHODS: A commercially available BIAcore 2000 instrument, based on SPR technology, was utilized for assessing serum YKL-40 levels in a control sample size of 45 and active sample size of 97. Antibody immobilization was optimized to obtain the best sensor performance and a sensitive analytic detection. A commercially available ELISA kit was utilized for detecting serum IgE to estimate allergic condition-associated asthma. RESULTS: The results of SPR technology could distinctly classify with highly statistical significance, the asthma severities by estimating the elevated levels of YKL-40 in blood sera of minute quantities (up to 0.33 ng/ml), and thus differentiates superior utility in comparison with ELISA method. No statistically significant correlation of YKL-40 and IgE was observed. CONCLUSIONS: Serum YKL-40 may be used as a protein marker in classifying asthma severity by applying SPR technology as a reliable, label-free, highly sensitive, and cost-effective tool.

Serum 5-LOX: a progressive protein marker for breast cancer and new approach for therapeutic target.

Lipoxygenase (LOX) pathway has emerged to have a role in carcinogenesis. There is an evidence that both 12-LOX and 5-LOX have procarcinogenic role. We have previously reported the elevated level of serum 12-LOX in breast cancer patients. This study evaluated the serum level of 5-LOX in breast cancer patients and its in vitro inhibition assessment with peptide inhibitor YWCS. The level of 5-LOX was determined by surface plasmon resonance (SPR). The peptide inhibitor of 5-LOX was designed by molecular modeling and kinetic assay was performed by spectrophotometry. The siRNA mediated 5-LOX gene silencing was performed to investigate the effect on proliferation of MDA-MB-231, breast cancer cell line. The serum 5-LOX level in breast cancer (5.69±1.97ng/µl) was almost 2-fold elevated compared to control (3.53±1.0ng/µl) (P < 0.0001). The peptide YWCS had shown competitive inhibitory effects with IC50, 2.2 µM and dissociation constant (K D), 4.92×10(-8) M. The siRNA mediated knockdown of 5-LOX, resulted in the decreased gene expression for 5-LOX and increased cell death in MDA-MB-231 cell line and thereby play a key role in reducing tumor proliferation. Thus, it can be concluded that 5-LOX is one of the potential serum protein marker for breast cancer and a promising therapeutic target for the same.

NFκB-p50 as a blood based protein marker for early diagnosis and prognosis of head and neck squamous cell carcinoma.

Head and neck squamous cell carcinoma (HNSCC) is the major health concern in Indian population. Despite of advanced treatment the mortality rate for this disease has not been improved very much. Current research focused on development of protein marker for the diagnosis and prognosis of HNSCC. The case control study was performed with 125 HNSCC patients and 104 control cases. The level of p50 and IκBα proteins in serum were evaluated at pre and post therapy by label free real time surface plasmon resonance (SPR) and western blot analysis. The serum p50 concentration were significantly (P < 0.0001) higher at the time of diagnosis i.e. pre therapy (Mean ± SD = 27.06 ± 4.88 ng/µl) as compared to controls (Mean ± SD = 16.96 ± 4.04 ng/µl) while it decline at post therapy (Mean ± SD = 21.01 ± 4.98 ng/µl). Similarly, the concentration of IκBα protein in serum were slightly higher at pre therapy (Mean ± SD = 8.33 ± 1.85 ng/µl) as compared to controls (Mean ± SD = 7.27 ± 1.84 ng/µl) and declined at post therapy (Mean ± SD = 7.09 ± 1.24 ng/µl). The level of p50 was also high at the early stage of the disease. The specificity and sensitivity of p50 proteins obtained from ROC analysis revealed the potentiality to be diagnostic protein marker for HNSCC for its accuracy in the study cohort.

von Willebrand factor antagonizes nitric oxide synthase to promote insulin resistance during hypoxia.

Hypoxic respiratory diseases or hypoxia exposures are frequently accompanied by glucose intolerance and impaired nitric oxide (NO) availability. However, the molecular mechanism responsible for impaired NO production and insulin resistance (IR) during hypoxia remains obscure. In this study, we investigated the possible mechanism of impaired NO production and IR during hypoxia in a mouse model. Mice were exposed to hypoxia for different periods of time (0-24 h), and parameters of IR and endothelial dysfunctions were analyzed. Exposure to hypoxia resulted in a time-dependent increase in IR as well as multimeric forms of von Willebrand factor (vWF) and subsequently a decrease in eNOS activity. Preincubation with plasma of hypoxia-exposed animals (different time points) or human vWF inhibited insulin-induced NO production in a dose-dependent manner; larger doses of insulin reversed the effect. In contrast, preincubation of vWF-immunodepleted plasma failed to inhibit insulin-induced NO production, whereas vWF immunoneutralization abolished the effect of hypoxia-induced IR and D-[U-(14)C]glucose uptake. Furthermore, the interactions between vWF and eNOS were studied by far-Western blotting, co-immunoprecipitation, and surface plasma resonance spectroscopy. Kinetic analyses showed that the dissociation constant (KD), inhibitory constant (Ki), and half-maximal inhibitory concentration (IC50) were 1.79 × 10(-8) M, 250 pM, and 18.31 pM, respectively, suggesting that vWF binds to eNOS with a high affinity and greater efficacy for activator (insulin) inhibition. These results indicated that vWF, an antagonist of eNOS, inhibits insulin-induced NO production and causes IR.

A novel antimicrobial peptide derived from modified N-terminal domain of bovine lactoferrin: design, synthesis, activity against multidrug-resistant bacteria and Candida.

Lactoferrin (LF) is believed to contribute to the host's defense against microbial infections. This work focuses on the antibacterial and antifungal activities of a designed peptide, L10 (WFRKQLKW) by modifying the first eight N-terminal residues of bovine LF by selective homologous substitution of amino acids on the basis of hydrophobicity, L10 has shown potent antibacterial and antifungal properties against clinically isolated extended spectrum beta lactamases (ESBL), producing gram-negative bacteria as well as Candida strains with minimal inhibitory concentrations (MIC) ranging from 1 to 8 µg/mL and 6.5 µg/mL, respectively. The peptide was found to be least hemolytic at a concentration of 800 µg/mL. Interaction with lipopolysaccharide (LPS) and lipid A (LA) suggests that the peptide targets the membrane of gram-negative bacteria. The membrane interactive nature of the peptide, both antibacterial and antifungal, was further confirmed by visual observations employing electron microscopy. Further analyses, by means of propidium iodide based flow cytometry, also supported the membrane permeabilization of Candida cells. The peptide was also found to possess anti-inflammatory properties, by virtue of its ability to inhibit cyclooxygenase-2 (COX-2). L10 therefore emerges as a potential therapeutic remedial solution for infections caused by ESBL positive, gram-negative bacteria and multidrug-resistant (MDR) fungal strains, on account of its multifunctional activities. This study may open up new approach to develop and design novel antimicrobials.

Development of peptide inhibitor as a therapeutic agent against head and neck squamous cell carcinoma (HNSCC) targeting p38alpha MAP kinase.

BACKGROUND: The p38alpha MAP kinase pathway is involved in inflammation, cell differentiation, growth, apoptosis and production of pro-inflammatory cytokines TNF-alpha and IL-1beta. The overproduction of these cytokines plays an important role in cancer. The aim of this work was to design a peptide inhibitor on the basis of structural information of the active site of p38alpha. METHODS: A tetrapeptide, VWCS as p38alpha inhibitor was designed on the basis of structural information of the ATP binding site by molecular modeling. The inhibition study of peptide with p38alpha was performed by ELISA, binding study by Surface Plasmon Resonance and anti-proliferative assays by MTT and flow cytometry. RESULTS: The percentage inhibition of designed VWCS against pure p38alpha protein and serum of HNSCC patients was 70.30 and 71.5%, respectively. The biochemical assay demonstrated the K(D) and IC50 of the selective peptide as 7.22 x 10(-9) M and 20.08 nM, respectively. The VWCS as inhibitor significantly reduced viability of oral cancer KB cell line with an IC50 value of 10 microM and induced apoptosis by activating Caspase 3 and 7. CONCLUSIONS: VWCS efficiently interacted at the ATP binding pocket of p38alpha with high potency and can be used as a potent inhibitor in case of HNSCC. GENERAL SIGNIFICANCE: VWCS can act as an anticancer agent as it potentially inhibits the cell growth and induces apoptosis in oral cancer cell-line in a dose as well as time dependent manner. Hence, p38alpha MAP kinase inhibitor can be a potential therapeutic agent for human oral cancer.

Identification and molecular characterization of a novel splice variant of human 5- lipoxygenase gene.

5-Lipoxygenase (5-LO) is one of the members of Lipoxygenase family. It breaks down arachidonic acid to pro-inflammatory compounds like leukotrienes. Leukotriene plays a major role in the inflammatory process. In this study, while cloning full length 5-LO, a novel splice variant of 5-LO (t5-LO) was found to be expressed in HepG2 cell line. The complete ORF of t5-LO is 420 bp long, expressing 139 amino acid long proteins from N-terminal. The splice variant of 5-LO was cloned, expressed, purified in bacterial system and characterized by MS/MS and western blot experiments. The full length 5-LO is 674 amino acids long encoded by 2,025 bp long ORF. RT-PCR and western blot revealed that t5-LO is extensively expressed in HepG2 cell line.

Trajectories and correlates of poor mental health in India over the course of the COVID-19 pandemic: a nationwide survey.

INTRODUCTION: The COVID-19 pandemic had large impacts on mental health; however, most existing evidence is focused on the initial lockdown period and high-income contexts. By assessing trajectories of mental health symptoms in India over 2 years, we aim to understand the effect of later time periods and pandemic characteristics on mental health in a lower-middle income context. METHODS: We used data from the Real-Time Insights of COVID-19 in India cohort study (N=3709). We used covariate-adjusted linear regression models with generalised estimating equations to assess associations between mental health (Patient Health Questionnaire (PHQ-4) score; range 0-12) and pandemic periods as well as pandemic characteristics (COVID-19 cases and deaths, government stringency, self-reported financial impact, COVID-19 infection in the household) and explored effect modification by age, gender and rural/urban residence. RESULTS: Mental health symptoms dropped immediately following the lockdown period but rose again during the delta and omicron waves. Associations between mental health and later pandemic stages were stronger for adults 45 years of age and older (p<0.001). PHQ-4 scores were significantly associated with all pandemic characteristics considered, including estimated COVID-19 deaths (PHQ-4 difference of 0.10 units; 95% CI 0.06 to 0.13), government stringency index (0.14 units; 95% CI 0.11 to 0.18), self-reported major financial impacts (1.20 units; 95% CI 1.09 to 1.32) and COVID-19 infection in the household (0.36 units; 95% CI 0.23 to 0.50). CONCLUSION: While the lockdown period and associated financial stress had the largest mental health impacts on Indian adults, the effects of the pandemic on mental health persisted over time, especially among middle-aged and older adults. Results highlight the importance of investments in mental health supports and services to address the consequences of cyclical waves of infections and disease burden due to COVID-19 or other emerging pandemics.

Quantification of COX-2 Level in Alzheimer's Disease Patients to Develop Potential Blood-Based Biomarker for Early Diagnosis and Therapeutic Target.

Background: Alzheimer's disease (AD) is a progressive neurodegenerative disease and symptoms develop gradually over many years. The current direction for medication development in AD is focused on neuro-inflammation and oxidative stress. Amyloid-ß (Aß) deposition activates microglia leading to neuro-inflammation and neurodegeneration induced by activation of COX-2 via NFκB p50 in glioblastoma cells. Objective: The study aimed to evaluate the concentration of COX-2 and NFκB p50 in serum of AD, mild cognitive impairment (MCI), and geriatric control (GC) and to establish a blood-based biomarker for early diagnosis and its therapeutic implications. Methods: Proteins and their mRNA level in blood of study groups were measured by surface plasmon resonance (SPR) and quantitative polymerase chain reaction (qPCR), respectively. The level of protein was further validated by western blot. The binding study of designed peptide against COX-2 by molecular docking was verified by SPR. The rescue of neurotoxicity by peptide was also checked by MTT assay on SH-SY5Y cells (neuroblastoma cell line). Results: Proteins and mRNA were highly expressed in AD and MCI compared to GC. However, COX-2 decreases with disease duration. The peptide showed binding affinity with COX-2 with low dissociation constant in SPR and rescued the neurotoxicity of SH-SY5Y cells by decreasing the level of Aß, tau, and pTau proteins. Conclusions: It can be concluded that COX-2 protein can serve as a potential blood-based biomarker for early detection and can be a good platform for therapeutic intervention for AD.

Clinical Significance of MUC4 and Associated Proteins in Pancreatic and Periampullary Cancers.

OBJECTIVE: This study primarily aimed to assess the expression of MUC4 in patients with pancreatic ductal adenocarcinoma (PDAC) as compared with controls and assess its clinical relevance. MATERIALS AND METHODS: Serum MUC4 levels and MUC4 gene expression in snap-frozen tissue were analyzed through surface plasmon resonance and quantitative polymerase chain reaction, respectively. Tumor tissues and control tissues were analyzed for MUC4 and other mucins through immunohistochemistry. RESULT: MUC4 expression in tumor tissue was found to be significantly elevated in PDAC patients as compared with chronic pancreatitis tissues and normal pancreatic tissues. Periampullary carcinoma and cholangiocarcinoma tissue also showed increased expression of MUC4 and other mucins. CONCLUSIONS: Differential expression of MUC4 in pancreatic tumor tissues can help to differentiate PDAC from benign conditions.

50,000 years of Evolutionary History of India: Insights from ~2,700 Whole Genome Sequences.

India has been underrepresented in whole genome sequencing studies. We generated 2,762 high coverage genomes from India-including individuals from most geographic regions, speakers of all major languages, and tribal and caste groups-providing a comprehensive survey of genetic variation in India. With these data, we reconstruct the evolutionary history of India through space and time at fine scales. We show that most Indians derive ancestry from three ancestral groups related to ancient Iranian farmers, Eurasian Steppe pastoralists and South Asian hunter-gatherers. We uncover a common source of Iranian-related ancestry from early Neolithic cultures of Central Asia into the ancestors of Ancestral South Indians (ASI), Ancestral North Indians (ANI), Austro-asiatic-related and East Asian-related groups in India. Following these admixtures, India experienced a major demographic shift towards endogamy, resulting in extensive homozygosity and identity-by-descent sharing among individuals. At deep time scales, Indians derive around 1-2% of their ancestry from gene flow from archaic hominins, Neanderthals and Denisovans. By assembling the surviving fragments of archaic ancestry in modern Indians, we recover ~1.5 Gb (or 50%) of the introgressing Neanderthal and ~0.6 Gb (or 20%) of the introgressing Denisovan genomes, more than any other previous archaic ancestry study. Moreover, Indians have the largest variation in Neanderthal ancestry, as well as the highest amount of population-specific Neanderthal segments among worldwide groups. Finally, we demonstrate that most of the genetic variation in Indians stems from a single major migration out of Africa that occurred around 50,000 years ago, with minimal contribution from earlier migration waves. Together, these analyses provide a detailed view of the population history of India and underscore the value of expanding genomic surveys to diverse groups outside Europe.

Structural studies on molecular interactions between camel peptidoglycan recognition protein, CPGRP-S, and peptidoglycan moieties N-acetylglucosamine and N-acetylmuramic acid.

Peptidoglycan (PGN) consists of repeating units of N-acetylglucosamine (GlcNAc) and N-acetylmuramic acid (MurNAc), which are cross-linked by short peptides. It is well known that PGN forms a major cell wall component of bacteria making it an important ligand for the recognition by peptidoglycan recognition proteins (PGRPs) of the host. The binding studies showed that PGN, GlcNAc, and MurNAc bind to camel PGRP-S (CPGRP-S) with affinities corresponding to dissociation constants of 1.3 × 10(-9), 2.6 × 10(-7), and 1.8 × 10(-7) M, respectively. The crystal structure determinations of the complexes of CPGRP-S with GlcNAc and MurNAc showed that the structures consist of four crystallographically independent molecules, A, B, C, and D, in the asymmetric unit that exists as A-B and C-D units of two neighboring linear polymers. The structure determinations showed that compounds GlcNAc and MurNAc bound to CPGRP-S at the same subsite in molecule C. Both GlcNAc and MurNAc form several hydrogen bonds and extensive hydrophobic interactions with protein atoms, indicating the specific nature of their bindings. Flow cytometric studies showed that PGN enhanced the secretions of TNF-α and IL-6 from human peripheral blood mononuclear cells. The introduction of CPGRP-S to the PGN-challenged cultured peripheral blood mononuclear cells reduced the expressions of proinflammatory cytokines, TNF-α and IL-6. This showed that CPGRP-S inhibited PGN-induced production of proinflammatory cytokines and down-regulated macrophage-mediated inflammation, indicating its potential applications as an antibacterial agent.