Setu: a pipeline for the robust assembly of SARS-CoV-2 genomes.

Setu is an efficient pipeline integrating currently available open source bioinformatic tools to perform rapid de novo assembly to assist tracking of severe acute respiratory syndrome coronavirus 2 genome evolution in clinical data, being particularly useful for institutions with limited computing resources or personnel not familiar with bioinformatic pipelines.

RNA-Seq data analysis reveals novel nonsense mutations in the NPR3 gene leading to the progression of intellectual disability disorder.

Intellectual disability (ID) is a progressive disorder that affects around 1-3% of the world's population. The heterogeneity of intellectual disability makes it difficult to diagnose as a complete disease. Genetic factors and major mutations play a noticeable role in the development and progression of ID. There is a high need to explore novel variants that may lead to new insights into the progressive aspects of ID. In the current course of study, 31 samples of ID from different studies available on GEO (GSE77742, GSE74263, GSE90682, GSE98476, GSE108887, GSE145710, and PRJEB21964) datasets were taken for the study. These datasets were analyzed for differential gene expression and single nucleotide polymorphism (SNPs). The SNPs of high impact were compared with the differentially expressed genes. Comparison leads to the identification of the priority gene ie NPR3 gene. The identified priority gene further was evaluated for the effect of the mutation using a Mutation Taster. Structure comparison analysis of the wild and mutated proteins of the NPR3 gene was further carried out by UCSF Chimera. Structural analysis reveals the anomalies in protein expression affecting the regulations of the NPR3 gene. These findings identified a novel nonsense mutation (E222*) in the downregulated NPR3 gene that leads to anomalies in the regulation of its protein expression. This missense mutation reveals a major role in causing ID. Our study concludes that the decrease in the expression of the NPR3 gene causes delayed sensory, motor, and physiological functions of the human brain leading to neurodevelopmental delay that causes ID.

Correlation between acne and insulin resistance; experience from central India.

Introduction: Acne is a common dermatological condition primarily seen in teenage and adolescent patients and is a major concern for cosmological issues. Along with environmental factors, the proliferation of basal keratinocytes in the sebaceous-pilosebaceous unit, abnormal desquamation of follicular corneocytes, and metabolic abnormalities play a significant role in the pathogenesis of acne development. Aim: To study the causal relation between acne vulgaris and insulin resistance by calculating Homeostatic Model Assessment for Insulin Resistance (HOMA-IR) and identify the relation between insulin resistance and the severity of acne. Materials and Methods: This was a retrospective study, where the data of patients with persistent Acne Vulgaris who were referred to the Endocrine department for evaluation of the hormonal and metabolic causes for acne vulgaris were analysed. The patient's clinical records were evaluated in whom there was no significant hormonal or metabolic abnormality identified known to cause persistent acne were included after proper consent and HOMA-IR was calculated. Results: Of several patients with persistent acne, 150 patients were included in our study with the male-to-female ratio was 23:27. The mean age of patients was 33.2 years. The mean HOMA-IR in our acne patients was 1.62 ranging from 0.9-3.7. Sixty four (42.67%) patients had HOMA-IR more than 2.0, thereby suggesting insulin resistance. Conclusion: Our study suggests the prevalence of insulin resistance in 42.67% of patients with acne, thereby providing the possibility of use of insulin modifiers as an adjunct acne treatment and stratifying the possible risk of metabolic syndrome in patients with acne. Also recommended is the control of dietary factors and lifestyle modification for the management of acne with insulin resistance.

Chitosan nanoplatform for the co-delivery of palbociclib and ultra-small magnesium nanoclusters: dual receptor targeting, therapy and imaging.

Theranostic nanoparticles have gained significant attention in cancer diagnosis and therapy. In this study, estrone (ES) and folic acid (FA) functionalized single and dual receptor targeted theranostic chitosan nanoparticles were developed for breast cancer imaging and therapy. These nanoparticles (NPs) were loaded with palbociclib (PB) and ultra-small magnesium nanoclusters (UMN). The developed nontargeted theranostic NPs (PB-UMN-CS-NPs), estrogen receptor targeted theranostic NPs (PB-UMN-CS-ES-NPs), folate receptor targeted theranostic NPs (PB-UMN-CS-FA-NPs), and dual targeted theranostic NPs (PB-UMN-CS-ES-FA-NPs) have particle sizes of 178.4 ± 1.21 nm, 181.6± 1.35 nm, 185.1± 1.33 nm, and 198.2± 1.43 nm with surface charges of +19.02± 0.382 mV, +13.89±0.410 mV, +16.72±0.527 mV and +15.23±0.377 mV, respectively. Cytotoxicity studies on estrogen receptor (ER) and folate receptor (FR) expressing breast cancer cells revealed that dual-targeted theranostic NPs (PB-UMN-CS-FA-ES-NPs) were more effective, inhibiting cell growth by 54.17 and 42.23 times in MCF-7 and T-47D cells compared to free PB, respectively. Additionally, developed NPs were capable of inhibiting the cell cycle progression of MCF-7 cells from the G1 phase to the S phase more efficiently compared to free PB. Ultrasound and photoacoustic (USG/PA) imaging demonstrated that dual targeted theranostic NPs were capable of effectively reducing hypoxic tumor volume and significantly suppressing tumor vascularity compared to free PB, nontargeted, FR targeted and ER targeted NPs. Moreover, in vivo optical imaging demonstrated tumor specific accumulation of the dual-targeted theranostic NPs. Furthermore, in vitro hemocompatibility and histopathological studies confirmed the biocompatibility of developed nanoformulations.

Br - nanoconjugate enhances the antibacterial efficacy of nimboloide against Flavobacterium columnare infection in Labeo rohita: A nanoinformatics approach.

BACKGROUND: The bacterial pathogen, Flavobacterium columnare causes columnaris disease in Labeo rohita globally. Major effects of this bacterial infection include skin rashes and gill necrosis. Nimbolide, the key ingredient of the leaf extract of Azadirachta indica possesses anti-bacterial properties effective against many microorganisms. Nano-informatics plays a promising role in drug development and its delivery against infections caused by multi-drug-resistant bacteria. Currently, studies in the disciplines of dentistry, food safety, bacteriology, mycology, virology, and parasitology are being conducted to learn more about the wide anti-virulence activity of nimbolide. METHODS: The toxicity of nimbolide was predicted to determine its dosage for treating bacterial infection in Labeo rohita. Further, comparative 3-D structure prediction and docking studies are done for nimbolide conjugated nanoparticles with several key target receptors to determine better natural ligands against columnaris disease. The nanoparticle conjugates are being designed using in-silico approaches to study molecular docking interactions with the target receptor. RESULTS: Bromine conjugated nimbolide shows the best molecular interaction with the target receptors of selected species ie L rohita. Nimbolide comes under the class III level of toxic compound so, attempts are made to reduce the dosage of the compound without compromising its efficiency. Further, bromine is also used as a common surfactant and can eliminate heavy metals from wastewater. CONCLUSION: The dosage of bromine-conjugated nimbolide can be reduced to a non-toxic level and thus the efficiency of the Nimbolide can be increased. Moreover, it can be used to synthesize nanoparticle composites which have potent antibacterial activity towards both gram-positive and gram-negative bacteria. This material also forms a good coating on the surface and kills both airborne and waterborne bacteria.

Comparative Transcriptomics Data Profiling Reveals E2F Targets as an Important Biological Pathway Overexpressed in Intellectual Disability Disorder.

Intellectual disability (ID) is an early childhood neurodevelopmental disorder that is characterized by impaired intellectual functioning and adaptive behavior. It is one of the major concerns in the field of neurodevelopmental disorders across the globe. Diversified approaches have been put forward to overcome this problem. Among all these approaches, high throughput transcriptomic analysis has taken an important dimension. The identification of genes causing ID rapidly increased over the past 3 to 5 years owing to the use of sophisticated high throughput sequencing platforms. Early monitoring and preventions are much important for such disorder as their progression occurs during fetal development. This study is an attempt to identify differentially expressed genes (DEGs) and upregulated biological processes involved in development of ID patients through comparative analysis of available transcriptomics data. A total of 7 transcriptomic studies were retrieved from National Center for Biotechnology Information (NCBI) and were subjected to quality check and trimming prior to alignment. The normalization and differential expression analysis were carried out using DESeq2 and EdgeR packages of Rstudio to identify DEGs in ID. In progression of the study, functional enrichment analysis of the results obtained from both DESeq2 and EdgeR was done using gene set enrichment analysis (GSEA) tool to identify major upregulated biological processes involved in ID. Our findings concluded that monitoring the level of E2F targets, estrogen, and genes related to oxidative phosphorylation, DNA repair, and glycolysis during the developmental stage of an individual can help in the early detection of ID disorder.

Deployment of in-silico analysis to reveal the antibacterial profiles of Allium sativum against Aeromonas hydrophila.

The key challenges in aquaculture are the emergence of antimicrobial resistance in fish cultivation due to the frequent use of antibiotics. Over the past three decades, this led to a major threat in the persistence of multidrug-resistant bacteria. Aeromonas hydrophila is a Gram-negative bacterium, a common causative agent of motile bacterial septicemia in fisheries. Combining these two key factors of the presented narrative, the essential type II topoisomerase enzyme 'DNA gyrase' (encoded by the gyrA and gyrB genes) as a potential drug target in Aeromonas hydrophila was taken, retrieve its sequence from UniProtKB (Id-A0KKQ2), constructs the 3-D structure using SWISS-MODEL (in absence of the experimental structure), and performs an in-silico screening of selected drug-like compounds (25 antibacterial phytochemicals) most of which are bioactive compounds of A. sativum through molecular docking. Quercetin a derivative of A. sativum was observed as a more potent drug molecule than other studied molecules based on ligand binding energy as docking score -7.812, showed highly encouraging results, supported by a study using structural dynamics of the receptor-ligand complex for a duration of 100 ns by Molecular Dynamic Simulations and confirm binding stability with MM-GBSA calculations. This study also provides theoretical grounds for drug discovery against other pathogenic bacteria posing threats to the ecosystem. Switching to herbal products is the best way to combat the plurality of problems to avoid seen or unseen post-treatment side effects.Communicated by Ramaswamy H. Sarma.

Baroreflex sensitivity is impaired in survivors of mild COVID-19 at 3-6 months of clinical recovery; association with carotid artery stiffness.

The association between the stiffening of barosensitive regions of central arteries and the derangements in baroreflex functions remains unexplored in COVID-19 survivors. Fifty-seven survivors of mild COVID-19 (defined as presence of upper respiratory tract symptoms and/or fever without shortness of breath or hypoxia; SpO2 > 93%), with an age range of 22-66 years (27 females) participated at 3-6 months of recovering from the acute phase of RT-PCR positive COVID-19. Healthy volunteers whose baroreflex sensitivity (BRS) and arterial stiffness data were acquired prior to the onset of the pandemic constituted the control group. BRS was found to be significantly lower in the COVID survivor group for the systolic blood pressure-based sequences (BRSSBP ) [9.78 (7.16-17.74) ms/mmHg vs 16.5 (11.25-23.78) ms/mmHg; p = 0.0253]. The COVID survivor group showed significantly higher carotid ß stiffness index [7.16 (5.75-8.18) vs 5.64 (4.34-6.96); (p = 0.0004)], and pulse wave velocity ß (PWVß ) [5.67 (4.96-6.32) m/s vs 5.12 (4.37-5.41) m/s; p = 0.0002]. BRS quantified by both the sequence and spectral methods showed an inverse correlation with PWVß in the male survivors. Impairment of BRS in the male survivors of mild COVID-19 at 3-6 months of clinical recovery shows association with carotid artery stiffness.

COVID Variants, Villain and Victory: A Bioinformatics Perspective.

The SARS-CoV-2 virus, a novel member of the Coronaviridae family, is responsible for the viral infection known as Coronavirus Disease 2019 (COVID-19). In response to the urgent and critical need for rapid detection, diagnosis, analysis, interpretation, and treatment of COVID-19, a wide variety of bioinformatics tools have been developed. Given the virulence of SARS-CoV-2, it is crucial to explore the pathophysiology of the virus. We intend to examine how bioinformatics, in conjunction with next-generation sequencing techniques, can be leveraged to improve current diagnostic tools and streamline vaccine development for emerging SARS-CoV-2 variants. We also emphasize how bioinformatics, in general, can contribute to critical areas of biomedicine, including clinical diagnostics, SARS-CoV-2 genomic surveillance and its evolution, identification of potential drug targets, and development of therapeutic strategies. Currently, state-of-the-art bioinformatics tools have helped overcome technical obstacles with respect to genomic surveillance and have assisted in rapid detection, diagnosis, and delivering precise treatment to individuals on time.

Effects of school-level and area-level socio-economic factors on elementary school student COVID-19 infections: a population-based observational study.

OBJECTIVES: To estimate the variability of the cumulative incidence of SARS-CoV-2 infections among elementary school students attributable to individual schools and/or their geographic areas, and to ascertain whether socio-economic characteristics of school populations and/or geographic areas may be predictive of this variability. DESIGN: Population-based observational study of SARS-CoV-2 infections among elementary school children. SETTING: 3994 publicly funded elementary schools in 491 forward sortation areas (designated geographic unit based on first three characters of Canadian postal code), Ontario, Canada, September 2020 to April 2021. PARTICIPANTS: All students attending publicly funded elementary schools with a positive molecular test for SARS-CoV-2 reported by the Ontario Ministry of Education. MAIN OUTCOME MEASURES: Cumulative incidence of laboratory-confirmed elementary school student SARS-CoV-2 infections in Ontario, 2020-21 school year. RESULTS: A multilevel modelling approach was used to estimate the effects of socio-economic factors at the school and area levels on the cumulative incidence of elementary school student SARS-CoV-2 infections. At the school level (level 1), the proportion of the student body from low-income households was positively associated with cumulative incidence (ß=0.083, p<0.001). At the area level (level 2), all dimensions of marginalisation were significantly related to cumulative incidence. Ethnic concentration (ß=0.454, p<0.001), residential instability (ß=0.356, p<0.001) and material deprivation (ß=0.212, p<0.001) were positively related, while dependency (ß=-0.204, p<0.001) was negatively related. Area-related marginalisation variables explained 57.6% of area variability in cumulative incidence. School-related variables explained 1.2% of school variability in cumulative incidence. CONCLUSIONS: The socio-economic characteristics of the geographic area of schools were more important in accounting for the cumulative incidence of SARS-CoV-2 elementary school student infections than individual school characteristics. Schools in marginalised areas should be prioritised for infection prevention measures and education continuity and recovery plans.

Molecular docking approaches and its significance in assessing the antioxidant properties in different compounds.

In the last few years, the significance of antioxidant compounds and their properties has attracted great interest from the scientific community. The role of an antioxidant in managing & regulating oxidative stress and also in the protection of the human body from severe adverse effects due to excess release of free radicles or reactive oxygen species (ROS) is remarkable. From aiding protection & combating severe illnesses such as cancer, neurodegeneration, aging, and diabetes to being a vital part of the treatment of SARs-CoV-19 is of great importance. Therefore, the study of anti-oxidants is of great importance in human sustenance. Additionally, molecular docking techniques and their various mathematical features help in understanding the molecular interactions of anti-oxidants based on their lowest binding energy. The evaluation of the binding score between two constituent molecules will provide insight as to the binding process and also suggest possible novel therapeutic targets for the treatment of diseases. In this chapter, we will discuss the significance of molecular docking techniques in the study of antioxidant compounds.

A meta-analysis of differentially expressed and regulatory genes with their functional enrichment analysis for brain transcriptome data in autism spectrum disorder.

Autism spectrum disorder (ASD) is a complex neurodevelopmental condition characterized by persistent challenges in social interactions and repetitive behavioral patterns. It is a significant problem emerging worldwide, as one in 100 children is affected by this disorder globally. In this study, a meta-analysis was performed for the identification of differentially expressed genes (DEGs) along with the expression analysis of regulatory genes. Functional enrichment analysis was an integral part of current findings to notify the significant pathways of this complex disorder. The study was conducted with two RNA-Seq datasets, viz., GSE64018 and GSE62098, for ASD patients and control samples from the GEO database. The identification of up-regulatory and down-regulatory genes was performed by the interaction analysis of transcription factors (TF) and DEGs. As an outcome of the meta-analysis, 2543 DEGs were identified as common across both of the datasets in which 1402 DEGs exhibited upregulation and 1130 genes have shown downregulation. In network analysis, upregulatory genes have shown strong interaction while downregulatory genes exhibit weak or null interaction. Further, in the enrichment analysis of screened upregulatory DEGs, three major significant pathways were identified namely the ATP synthesis pathway, FAS signaling pathway, and the Huntington's disease pathway. The common expression of CYC 1 gene in all the identified pathways has indicated that it is an important key regulator gene for the majorly associated pathways. The study concludes that all the potential DEGs were found to show their related high expression in neurobiological regulations specifically with ASD.Communicated by Ramaswamy S. Sarma.

Effect of Yoga Based Cardiac Rehabilitation on Blood Pressure Variability and Baroreflex Sensitivity: RCT in Patients Post MI.

To assess the effects of 12 weeks Yoga based Cardiac Rehabilitation program on Blood Pressure Variability and Baroreflex Sensitivity in Eighty patients post myocardial infarction. Randomized controlled trial with two parallel groups. A tertiary care institution in India. The Yoga group received 13 hospital-based structured yoga sessions in adjunct to the standard care. Control Group participants received enhanced standard care involving three brief educational sessions on importance of diet and physical activity. Beat to beat arterial pressure variability and baroreflex sensitivity was determined non-invasively. Baseline measurement was done at 3 weeks post Myocardial Infarction. The measurements were repeated at 13th week and at 26th week post MI. There was no significant difference between the groups in time domain indices of SBP variability. At 26th week post MI, after normalization the Low Frequency power increased in the yoga group as compared to the decrease in the standard care group (p = 0.02). Though the High Frequency power increased in both the groups, the magnitude of increase was higher in the standard care group (p = 0.005). However, the total power increased significantly in yoga group with a concurrent decrease in standard care group (p = < 0.001). The SBP All BRS was significantly different between the groups with an increase in the yoga group and a decline in standard care group (p = 0.003) at 13th week. A short-term Yoga based cardiac rehabilitation has additive effects in improving baroreflex sensitivity and dampening blood pressure variability post myocardial infarction in patients under optimal medication.The main trial is registered in Clinical Trials Registry-India (CTRI) (Ref. No: CTRI/2012/02/002408). In addition, CTRI has also been registered for the sub-study. (Ref. No: CTRI/2017/09/009925).

White light-emitting, biocompatible, water-soluble metallic magnesium nanoclusters for bioimaging applications.

Ultra-small (1.6 nm), water-soluble, white light-emitting (WLE), highly stable (∼8 months) BSA templated metallic (Mg0) nanoclusters (fluorescent magnesium nanoclusters = FMNCs) is developed using the green and facile route. Synthesis was facilitated by the reduction of magnesium salt, where template bovine serum albumin is utilized as a reducing agent and ascorbic acid act as a capping agent to impart stability in water, thereby obtaining stabilized Mg0nanoclusters In solution, stabilized Mg0nanoclusters produce white light (450-620 nm with FWHM ∼120 nm) upon 366 nm light excitation. This white light emission was found to have a CIE coordinate of 0.30, 0.33 [pure white light CIE (0.33, 0.33)]. Taking advantage of WLE and ultrasmall size, FMNCs were used forin vitrofluorescence imaging of HaCaT cell lines, yielding blue (τ= 2.94 ns, with a relative of QY = 1.2 % w.r.t QS), green (τ= 3.07 ns; relative quantum yield of 4.6% w.r.t R6G) and red (τ= 0.3 ns) images. Further, incubation of FMNCs with HEK293 (Human embryonic kidney cell) and cancerous MDA-MB-231 (Breast cancer cell line) human cell lines yielded 100 % cell viability. Current work is envisioned to contribute significantly in the area of science, engineering, and nanomedicine.

Deciphering the role of precursor miR-12136 and miR-8485 in the progression of intellectual disability (ID).

The short, non-coding RNAs known as miRNA modulate the expression of human protein-coding genes. About 90 % of genes in humans are controlled by the expression of miRNA. The dysfunction of these miRNA target genes leads to many human diseases, including neurodevelopmental disorders as well. Intellectual disability (ID) is a neurodevelopmental disorder that is characterized by adaptive behavior and intellectual functioning which includes logical reasoning, ability in learning, practical intelligence, and verbal skills. Identification of miRNA involved in ID and their associated target genes can help in the identification of diagnostic biomarkers related to ID at a very early age. The present study is an attempt to identify miRNA and their associated target genes that play an important role in the development of intellectual disability patients through the meta-analysis of available transcriptome data. A total of 6 transcriptomic studies were retrieved from NCBI and were subjected to quality check and trimming before alignment. The normalization and identification of differentially expressed miRNA were carried out using the EdgeR package of R studio. Further, the gene targets of downregulated miRNA were identified using miRDB. The system biology approaches were also applied to the study to identify the hub target genes and the diseases associated with main miRNAs.

A molecular dynamics simulation study of the ACE2 receptor with screened natural inhibitors to identify novel drug candidate against COVID-19.

BACKGROUND & OBJECTIVES: The massive outbreak of Novel Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV-2) has turned out to be a serious global health issue worldwide. Currently, no drugs or vaccines are available for the treatment of COVID-19. The current computational study was attempted to identify a novel therapeutic inhibitor against novel SARS-CoV-2 using in silico drug discovery pipeline. METHODS: In the present study, the human angiotensin-converting enzyme 2 (ACE2) receptor was the target for the designing of drugs against the deadly virus. The 3D structure of the receptor was modeled & validated using a Swiss-model, Procheck & Errat server. A molecular docking study was performed between a group of natural & synthetic compounds having proven anti-viral activity with ACE2 receptor using Autodock tool 1.5.6. The molecular dynamics simulation study was performed using Desmond v 12 to evaluate the stability and interaction of the ACE2 receptor with a ligand. RESULTS: Based on the lowest binding energy, confirmation, and H-bond interaction, cinnamic acid (-5.20 kcal/mol), thymoquinone (-4.71 kcal/mol), and andrographolide (Kalmegh) (-4.00 kcal/mol) were screened out showing strong binding affinity to the active site of ACE2 receptor. MD simulations suggest that cinnamic acid, thymoquinone, and andrographolide (Kalmegh) could efficiently activate the biological pathway without changing the conformation in the binding site of the ACE2 receptor. The bioactivity and drug-likeness properties of compounds show their better pharmacological property and safer to use. INTERPRETATION & CONCLUSIONS: The study concludes the high potential of cinnamic acid, thymoquinone, and andrographolide against the SARS-CoV-2 ACE2 receptor protein. Thus, the molecular docking and MD simulation study will aid in understanding the molecular interaction between ligand and receptor binding site, thereby leading to novel therapeutic intervention.