Integrative analysis discovers Imidurea as dual multitargeted inhibitor of CD69, CD40, SHP2, lysozyme, GATA3, cCBL, and S-cysteinase from SARS-CoV-2 and M. tuberculosis.

Two of the deadliest infectious diseases, COVID-19 and tuberculosis (TB), have combined to establish a worldwide pandemic, wreaking havoc on economies and claiming countless lives. The optimised, multitargeted medications may diminish resistance and counter them together. Based on computational expression studies, 183 genes were co-expressed in COVID-19 and TB blood samples. We used the multisampling screening algorithms on the top ten co-expressed genes (CD40, SHP2, Lysozyme, GATA3, cCBL, SIVmac239 Nef, CD69, S-adenosylhomocysteinase, Chemokine Receptor-7, and Membrane Protein). Imidurea is a multitargeted inhibitor for COVID-19 and TB, as confirmed by extensive screening and post-filtering utilising MM\GBSA algorithms. Imidurea has shown docking and MM\GBSA scores of -8.21 to -4.75 Kcal/mol and -64.16 to -29.38 Kcal/mol, respectively. The DFT, pharmacokinetics, and interaction patterns suggest that Imidurea may be a drug candidate, and all ten complexes were tested for stability and bond strength using 100 ns for all MD atoms. The modelling findings showed the complex's repurposing potential, with a cumulative deviation and fluctuation of <2 Å and significant intermolecular interaction, which validated the possibilities. Finally, an inhibition test was performed to confirm our in-silico findings on SARS-CoV-2 Delta variant infection, which was suppressed by adding imidurea to Vero E6 cells after infection.

Liver metastases - An unusual cause of portal hypertension: A case report.

Introduction: Portal hypertension is a rare complication of liver metastases. The study highlights that clinician should be aware of conditions mimicking cirrhosis with similar clinical presentation and imaging findings. Case presentation: We present the case of a 29-year-old non-alcoholic lady who presented to our hospital with a history of two months of progressive, painless abdominal distension and progressively increasing yellowish discoloration of the eyes. Physical examination, laboratory investigations, and imaging tests led to a diagnosis of multiple metastases from breast carcinoma to the liver leading to portal hypertension after exclusion of other causes of portal hypertension. However, after three weeks of presentation to the hospital, the patient died before any therapeutic measures were initiated to address breast carcinoma. Clinical discussion: Liver metastasis from primary breast carcinoma rarely presents with clinical symptoms of portal hypertension. Although portal hypertension secondary to pseudocirrhosis, predominantly linked to ongoing chemotherapy for known cancers, has been previously described in case studies, our case had an unusual presentation leading to diagnostic uncertainty. Conclusion: Our case highlights the rare cause of liver metastasis secondary to breast carcinoma, which presented as portal hypertension.

Dual effects of NV-CoV-2 biomimetic polymer: An antiviral regimen against COVID-19.

Remdesivir (RDV) is the only antiviral drug approved for COVID-19 therapy by the FDA. Another drug LAGEVRIO™ (molnupiravir) though has not been approved yet by FDA but has been authorized on December 23, 2021, for emergency use to treat adults with mild-to moderate COVID-19 symptoms and for whom alternative COVID-19 treatment options are not clinically appropriate. The fact is that the efficacy of RDV is, however, limited in vivo though it is highly promising in vitro against SARS-CoV-2 virus. In this paper we are focusing on the action mechanism of RDV and how it can be improved in vivo. The stability of RDV alone and on encapsulation with our platform technology based polymer NV-387 (NV-CoV-2), were compared in presence of plasma in vitro and in vivo. Furthermore, a non-clinical pharmacology study of NV-CoV-2 (Polymer) and NV CoV-2 (Polymer encapsulated Remdesivir) in both NL-63 infected and uninfected rats was done. In addition, the antiviral activity of NV-CoV-2 and NV-CoV-2-R was compared with RDV in a cell culture study. The results are (i) NV-CoV-2 polymer encapsulation protects RDV from plasma-mediated catabolism in both in vitro and in vivo, studies; (ii) Body weight measurements of the normal (uninfected) rats after administration of the test materials (NV-CoV-2 and NV-CoV-2-R) showed no toxic effects. (iii) Body weight measurements and survival rates of the NL-63 infected rats were similar to the uninfected rats after treatment with NV-CoV-2 and NV-CoV-2-R. Overall, the efficacy as an antiviral regimens were found in this order as below; NV-CoV-2-R > NV-CoV-2 > RDV. Our platform technology based NV-387-encapsulated-RDV (NV-CoV-2-R) drug has a dual effect against different variants of the coronaviruses. First, NV-CoV-2 is an antiviral regimen. Secondly, RDV is protected from plasma-mediated degradation in transit. All together, NV-CoV-2-R is the safest and efficient regimen against COVID-19.

Comfort care plan to periviable infants: associated decision reversals and missed opportunity of antenatal steroids.

OBJECTIVE: This study aims to identify how often families of periviable infants had a care plan stating whether to provide active or comfort care and how often the care plan was reversed, close to or after the delivery. STUDY DESIGN: In this retrospective study, we reviewed the medical records of all mother-infant dyads (single or twin infants with no known congenital anomalies) who were delivered between 23 0/7 and 24 6/7 weeks gestational age from January 2012 to December 2016. RESULT: Ninety-nine women met the inclusion criteria - 6 (6%) did not have a care plan available, 85 women (86%) chose for active care and received antenatal steroids (ANS). Six women (6%) who chose comfort care and two women (2%) who chose limited resuscitation during antenatal counseling opted out of the ANS. Two thirds of the women (4/6) who initially opted for comfort care later desired active care, while none of the women who chose active care reversed their decisions. CONCLUSION: The majorities of the families (94%) had a prenatal care plan in place. Two-thirds (4/6) of the families who opted for comfort care changed their decisions resulting in a missed opportunity for ANS.

Single-Cell Genomics: Enabling the Functional Elucidation of Infectious Diseases in Multi-Cell Genomes.

Since the time when detection of gene expression in single cells by microarrays to the Next Generation Sequencing (NGS) enabled Single Cell Genomics (SCG), it has played a pivotal role to understand and elucidate the functional role of cellular heterogeneity. Along this journey to becoming a key player in the capture of the individuality of cells, SCG overcame many milestones, including scale, speed, sensitivity and sample costs (4S). There have been many important experimental and computational innovations in the efficient analysis and interpretation of SCG data. The increasing role of AI in SCG data analysis has further enhanced its applicability in building models for clinical intervention. Furthermore, SCG has been instrumental in the delineation of the role of cellular heterogeneity in specific diseases, including cancer and infectious diseases. The understanding of the role of differential immune responses in driving coronavirus disease-2019 (COVID-19) disease severity and clinical outcomes has been greatly aided by SCG. With many variants of concern (VOC) in sight, it would be of great importance to further understand the immune response specificity vis-a-vis the immune cell repertoire, the identification of novel cell types, and antibody response. Given the potential of SCG to play an integral part in the multi-omics approach to the study of the host-pathogen interaction and its outcomes, our review attempts to highlight its strengths, its implications for infectious disease biology, and its current limitations. We conclude that the application of SCG would be a critical step towards future pandemic preparedness.

Development of central precocious puberty following cannabinoid use for paediatric epilepsy: causal or coincidence?

Research suggests a role for cannabidiol oil in managing certain forms of paediatric onset epilepsy. However, studies on the impact of cannabis on the hypothalamo-pituitary-gonadal (HPG) axis have conflicting results. Delta-9-tetrahydrocannabinol (Δ9-THC) acutely inhibits gonadotropin-releasing hormone in the hypothalamus, reducing testosterone levels by 65% in rhesus monkeys. Additionally, there have been reports of pubertal arrest and delayed puberty in male cannabis users. In contrast, other studies have reported higher testosterone levels following long-term cannabis use.A 2-year-old boy presented with testicular enlargement, increased penile length and growth of coarse pubic hair developing over 6 months. His mother procured cannabidiol oil online, which he started taking 7 months earlier for severe epilepsy refractory to medical management. Subsequent investigations confirmed central precocious puberty. While it is unclear whether the precocious puberty is a direct consequence of HPG axis activation by Δ9-THC, this case demonstrates a temporal association between cannabis use and development of precocious puberty.

Detection of Colonic Polyps During Colonoscopy in a Tertiary Care Center of Nepal.

BACKGROUND: Colorectal cancer is the third leading cause of cancer death in the world. Most colon cancer develop from the polyps. Data on the prevalence of colorectal polyps in Nepal is lacking. The objective was to determine the prevalence of colorectal polyps, site of occurrence and adenomas among various age groups. All polyps after removal by polypectomy was sent for histopathological examination. METHODS: Study was done in 1027 consecutive patients who underwent colonoscopy in the pre-specified time after excluding patients with colorectal cancer, Inflammatory Bowel Disease and polyposis syndromes. RESULTS: Among 1027 patients, the mean age was 45 years. 292 (28.43%) were below 40 years, whereas, 735 (71.57%) were above 40 years. Polyps were detected in 12.95% of overall patients and in 9.73% of patients over age 40. The most common location of polyps was rectum (46.62%). 43.61% were adenomatous polyps, 11.28% were hyperplastic polyps, 18.05% were juvenile polyps, 22.56% were inflammatory polyps and 1.50% were malignant adenocarcinoma. Polyp detection rate was 12.95%, whereas adenoma detection rate was 5.84%. 46.55% had advanced adenomas. A positive correlation between the size of polyp and adenomatous variety was found [Chi-square value ?2 = 8.42 (>3.841), p value <0.05]. Prevalence of adenomatous polyps was significantly higher above the age of 40 [Chi-square value ?2 = 11.53 (>3.841), p value<0.05].  Conclusions: The prevalence of polyp increases with age. With increasing age and size of polyp, the prevalence of adenomatous polyp increases significantly. One out of every eight people over 40 years had a colonic polyp.

Myg1 exonuclease couples the nuclear and mitochondrial translational programs through RNA processing.

Semi-autonomous functioning of mitochondria in eukaryotic cell necessitates coordination with nucleus. Several RNA species fine-tune mitochondrial processes by synchronizing with the nuclear program, however the involved components remain enigmatic. In this study, we identify a widely conserved dually localized protein Myg1, and establish its role as a 3'-5' RNA exonuclease. We employ mouse melanoma cells, and knockout of the Myg1 ortholog in Saccharomyces cerevisiae with complementation using human Myg1 to decipher the conserved role of Myg1 in selective RNA processing. Localization of Myg1 to nucleolus and mitochondrial matrix was studied through imaging and confirmed by sub-cellular fractionation studies. We developed Silexoseqencing, a methodology to map the RNAse trail at single-nucleotide resolution, and identified in situ cleavage by Myg1 on specific transcripts in the two organelles. In nucleolus, Myg1 processes pre-ribosomal RNA involved in ribosome assembly and alters cytoplasmic translation. In mitochondrial matrix, Myg1 processes 3'-termini of the mito-ribosomal and messenger RNAs and controls translation of mitochondrial proteins. We provide a molecular link to the possible involvement of Myg1 in chronic depigmenting disorder vitiligo. Our study identifies a key component involved in regulating spatially segregated organellar RNA processing and establishes the evolutionarily conserved ribonuclease as a coordinator of nucleo-mitochondrial crosstalk.

Design of novel multi-epitope vaccines against severe acute respiratory syndrome validated through multistage molecular interaction and dynamics.

Severe acute respiratory syndrome (SARS) is endemic in South China and is continuing to spread worldwide since the 2003 outbreak, affecting human population of 37 countries till present. SARS is caused by the severe acute respiratory syndrome Coronavirus (SARS-CoV). In the present study, we have designed two multi-epitope vaccines (MEVs) composed of cytotoxic T lymphocyte (CTL), helper T lymphocyte (HTL) and B cell epitopes overlap, bearing the potential to elicit cellular as well as humoral immune response. We have used truncated (residues 10-153) Onchocerca volvulus activation-associated secreted protein-1 as molecular adjuvants at N-terminal of both the MEVs. Selected overlapping epitopes of both the MEVs were further validated for stable molecular interactions with their respective human leukocyte antigen class I and II allele binders. Moreover, CTL epitopes were further studied for their molecular interaction with transporter associated with antigen processing. Furthermore, after tertiary structure modelling, both the MEVs were validated for their stable molecular interaction with Toll-like receptors 2 and 4. Codon-optimized cDNA of both the MEVs was analysed for their potential high level of expression in the mammalian cell line (Human) needed for their further in vivo testing. Overall, the present study proposes in silico validated design of two MEVs against SARS composed of specific epitopes with the potential to cause a high level of SARS-CoV specific cellular as well as humoral immune response. Communicated by Ramaswamy H. Sarma.

Cerebral venous sinus thrombosis as a warning signal for double positive crescentic glomerulonephritis in a young male with complete renal recovery.

Double positive crescentic glomerulonephritis is relatively rare in young population and has variable outcomes. Although increased incidence of deep venous thrombosis in antineutrophil cytoplasmic antibody-associated vasculitis has been reported, cerebral venous sinus thrombosis (CVT) is very rare. We present a young male who presented with CVT followed by rapidly progressive crescentic glomerulonephritis and with appropriate therapeutic modalities he had complete renal and partial neurological recovery.

First Degree Relatives of Patients with Celiac Disease Harbour an Intestinal Transcriptomic Signature that Might Protect them from Enterocyte Damage.

INTRODUCTION: Celiac disease (CeD) is an autoimmune enteropathy which affects approximately 0.7% of the global population. While first-degree relatives (FDR) of patients with CeD have a 7.5% risk of developing enteropathy, many remain protected. Therefore, intestinal mucosa of FDR might have protective compensatory mechanisms against immunological injury. We have explored the protective mechanisms that may be active in intestinal mucosa of FDR. METHODS: Intestinal mucosal biopsies (4-5 pieces) from treatment naïve patients with CeD (n = 12), FDR (n = 12) (anti-tTG negative) and controls (n = 12) (anti-tTG negative) were obtained from each individual and subjected to microarray analysis using HT-12-v4 Human Expression BeadChips (Illumina). Differential gene expression analysis was carried out among CeD, FDR and controls; and resulting gene lists were analyzed using gene ontology and pathway enrichment tools. RESULTS: Patients with CeD, FDR and control groups displayed significant differential gene expression. Thirty seven genes were upregulated and 372 were downregulated in the intestinal mucosa of FDR in comparison to CeD and controls. Pseudogenes constituted about 18% (315/1751) of FDR differentially expressed genes, and formed "clusters" that associated uniquely with individual study groups. The three study groups segregated into distinct clusters in unsupervised (PCA) and supervised (random forests) modelling approaches. Pathways analysis revealed an emphasis on crypt-villous maintenance and immune regulation in the intestinal mucosa of FDR. CONCLUSIONS: Our analysis suggests that the intestinal mucosa of celiac FDR consist of a unique molecular phenotype that is distinct from CeD and controls. The transcriptomic landscape of FDR promotes maintenance of crypt-villous axis and modulation of immune mechanisms. These differences clearly demonstrate the existence of compensatory protective mechanisms in the FDR intestinal mucosa.

A-C Estrogens as Potent and Selective Estrogen Receptor-Beta Agonists (SERBAs) to Enhance Memory Consolidation under Low-Estrogen Conditions.

Estrogen receptor-beta (ERß) is a drug target for memory consolidation in postmenopausal women. Herein is reported a series of potent and selective ERß agonists (SERBAs) with in vivo efficacy that are A-C estrogens, lacking the B and D estrogen rings. The most potent and selective A-C estrogen is selective for activating ER relative to seven other nuclear hormone receptors, with a surprising 750-fold selectivity for the ß over α isoform and with EC50s of 20-30 nM in cell-based and direct binding assays. Comparison of potency in different assays suggests that the ER isoform selectivity is related to the compound's ability to drive the productive conformational change needed to activate transcription. The compound also shows in vivo efficacy after microinfusion into the dorsal hippocampus and after intraperitoneal injection (0.5 mg/kg) or oral gavage (0.5 mg/kg). This simple yet novel A-C estrogen is selective, brain penetrant, and facilitates memory consolidation.

Adipocyte Model of Mycobacterium tuberculosis Infection Reveals Differential Availability of Iron to Bacilli in the Lipid-Rich Caseous Environment.

Mycobacterium tuberculosis, a successful human pathogen, utilizes multiple carbon sources from the host but adapts to a fatty-acid-rich environment in vivo We sought to delineate the physiologic response of M. tuberculosis to a lipid-rich environment by using differentiated adipocytes as a model system. Global transcriptome profiling based on RNA sequencing was performed for bacilli from infected adipocytes and preadipocytes. Genes involved in de novo fatty acid synthesis were downregulated, while those predicted to be involved in triglyceride biosynthesis were upregulated, in bacilli isolated from adipocytes, indicating reliance on host-derived fatty acids. Transcription factor network analysis indicated suppression of IdeR-regulated genes, suggesting decreased iron uptake by M. tuberculosis in the adipocyte model. This suppression of iron uptake coincided with higher ferritin and iron levels in adipocytes than in preadipocytes. In accord with the role of iron in mediating oxidative stress, we observed upregulation of genes involved in mitigating oxidative stress in M. tuberculosis isolated from adipocytes. We provide evidence that oleic acid, a major host-derived fatty acid, helps reduce the bacterial cytoplasm, thereby providing a safe haven for an M. tuberculosis mutant that is sensitive to iron-mediated oxidative stress. Via an independent mechanism, host ferritin is also able to rescue the growth of this mutant. Our work highlights the inherent synergy between macronutrients and micronutrients of the host environment that converge to provide resilience to the pathogen. This complex synergy afforded by the adipocyte model of infection will aid in the identification of genes required by M. tuberculosis in a caseous host environment.

Mapping Protein Binding Sites and Conformational Epitopes Using Cysteine Labeling and Yeast Surface Display.

We describe a facile method for mapping protein:ligand binding sites and conformational epitopes. The method uses a combination of Cys scanning mutagenesis, chemical labeling, and yeast surface display. While Ala scanning is widely used for similar purposes, often mutation to Ala (or other amino acids) has little effect on binding, except at hotspot residues. Many residues in physical contact with a binding partner are insensitive to substitution with Ala. In contrast, we show that labeling of Cys residues in a binding site consistently abrogates binding. We couple this methodology to yeast surface display and deep sequencing to map conformational epitopes targeted by both monoclonal antibodies and polyclonal sera as well as a protein:ligand binding site. The method does not require purified protein, can distinguish buried and exposed residues, and can be extended to other display formats, including mammalian cells and viruses, emphasizing its wide applicability.

Early versus late inguinal hernia repair in extremely low-birthweight infants.

OBJECTIVE: Compare outcomes of extremely low-birthweight (ELBW) infants following early (before discharge) versus late (after discharge) inguinal hernia (IH) repair. STUDY DESIGN: In a retrospective study of ELBW infants with IH, data were abstracted for clinical characteristics, IH and related outcomes. RESULT: Of the 39/252 (15.4%) ELBW infants who developed IH, those with early (59%) versus late (41%) repair were comparable in birth weight (753 ± 158 versus 744 ± 131 g, p = 0.84), gestation age (26 ± 2 versus 26.2 ± 2 weeks, p = 0.92), with comparable rate of broncopulmonary dysplasia (87% versus 75%, p = 0.41), but early repair group had prolonged respiratory support (60.6 ± 28.6 versus 39 ± 30 days, p = 0.032). Both groups had comparable diagnosis to repair interval (51.2 ± 29.2 versus 60.5 ± 30.6 days, p = 0.38) and early repair group has earlier corrected gestation (41.6 ± 3.9 versus 45.4 ± 4.6 weeks, p < 0.01) at time of repair. Post-IH repair complications (incarceration, postoperative apnea, infections, recurrence and testicular atrophy) were not different. CONCLUSIONS: We did not find significant differences in outcomes of IH in early and late repair groups of ELBW infants.

Alu-miRNA interactions modulate transcript isoform diversity in stress response and reveal signatures of positive selection.

Primate-specific Alus harbor different regulatory features, including miRNA targets. In this study, we provide evidence for miRNA-mediated modulation of transcript isoform levels during heat-shock response through exaptation of Alu-miRNA sites in mature mRNA. We performed genome-wide expression profiling coupled with functional validation of miRNA target sites within exonized Alus, and analyzed conservation of these targets across primates. We observed that two miRNAs (miR-15a-3p and miR-302d-3p) elevated in stress response, target RAD1, GTSE1, NR2C1, FKBP9 and UBE2I exclusively within Alu. These genes map onto the p53 regulatory network. Ectopic overexpression of miR-15a-3p downregulates GTSE1 and RAD1 at the protein level and enhances cell survival. This Alu-mediated fine-tuning seems to be unique to humans as evident from the absence of orthologous sites in other primate lineages. We further analyzed signatures of selection on Alu-miRNA targets in the genome, using 1000 Genomes Phase-I data. We found that 198 out of 3177 Alu-exonized genes exhibit signatures of selection within Alu-miRNA sites, with 60 of them containing SNPs supported by multiple evidences (global-FST > 0.3, pair-wise-FST > 0.5, Fay-Wu's H < -20, iHS > 2.0, high ΔDAF) and implicated in p53 network. We propose that by affecting multiple genes, Alu-miRNA interactions have the potential to facilitate population-level adaptations in response to environmental challenges.