Comprehensive analysis of small RNA-seq data reveals that combination of miRNA with its isomiRs increase the accuracy of target prediction in <i>Arabidopsis thaliana</i>

<div><p>Along with the canonical miRNA, distinct miRNA-like sequences called sibling miRNAs (sib-miRs) are generated from the same pre-miRNA. Among them, isomeric sequences featuring slight variations at the terminals, relative to the canonical miRNA, constitute a pool of isomeric sibling miRNAs (isomiRs). Despite the high prevalence of isomiRs in eukaryotes, their features and relevance remain elusive. In this study, we performed a comprehensive analysis of mature precursor miRNA (pre-miRNA) sequences from <i>Arabidopsis</i> to understand their features and regulatory targets. The influence of isomiR terminal heterogeneity in target binding was examined comprehensively. Our comprehensive analyses suggested a novel computational strategy that utilizes miRNA and its isomiRs to enhance the accuracy of their regulatory target prediction in <i>Arabidopsis</i>. A few targets are shared by several members of isomiRs; however, this phenomenon was not typical. Gene Ontology (GO) enrichment analysis showed that commonly targeted mRNAs were enriched for certain GO terms. Moreover, comparison of these commonly targeted genes with validated targets from published data demonstrated that the validated targets are bound by most isomiRs and not only the canonical miRNA. Furthermore, the biological role of isomiRs in target cleavage was supported by degradome data. Incorporating this finding, we predicted potential target genes of several miRNAs and confirmed them by experimental assays. This study proposes a novel strategy to improve the accuracy of predicting miRNA targets through combined use of miRNA with its isomiRs.</p></div

Additional file 1 of Emergence of multidrug-resistant Bacillus spp. derived from animal feed, food and human diarrhea in South-Eastern Bangladesh

Additional file 1: Figure S1. Cultural morphology and Grams staining  of isolated Bacillus spp. Figure S2.16srDNA gene of the isolated Bacillus spp. by PCR test. Figure S3. Toxin genes (nheA, nheB, nheC, cytK) of isolated Bacillus spp. by PCR test. Figure S4. Toxin genes (hblA, hblC, hblD, entFM) of isolated Bacillus spp. by PCR test. Figure S5. Antibiotic resistance genes of isolated Bacillus spp. by PCR test. Table S1. Strains and source of selected Bacillus spp. Table S2. Biochemical characteristics of Bacillus spp. Table S3. Primers of toxin gene and 16srRNA gene and PCR protocol used in this study. Table S4. Overall antimicrobial susceptibility profile of Bacillus spp. Table S5. Overall antimicrobial susceptibility profiles of 7 Bacillus species. Table S6. Distributions of antibiotic genes among animal feed, food and diarrhea. Table S7. Prevalence of ARGs of Bacillus spp. in animal feed, food and diarrhea. Table S8. Prevalence of ARGs of 7 Bacillus species. Table S9. Distributions of ARGs among 7 Bacillus species. Table S10. MDR profiles of B. cereus, B. subtilis, B. amyloliquefaciens, B. licheniformis, B. thuringiensis, B. megaterium and B. coagulans. Table S11. Species wise percentage of MAR index >0.2. Table S12. Sample wise percentage of MAR index >0.2. Table S13. MIC break point of Antibiotic used. Table S14. PCR protocol of antibiotic resistant gene primer used in this study

DataSheet1_Computational insights into the stereo-selectivity of catechins for the inhibition of the cancer therapeutic target EGFR kinase.pdf

The epidermal growth factor receptor (EGFR) plays a crucial role in regulating cellular growth and survival, and its dysregulation is implicated in various cancers, making it a prime target for cancer therapy. Natural compounds known as catechins have garnered attention as promising anticancer agents. These compounds exert their anticancer effects through diverse mechanisms, primarily by inhibiting receptor tyrosine kinases (RTKs), a protein family that includes the notable member EGFR. Catechins, characterized by two chiral centers and stereoisomerism, demonstrate variations in chemical and physical properties due to differences in the spatial orientation of atoms. Although previous studies have explored the membrane fluidity effects and transport across cellular membranes, the stereo-selectivity of catechins concerning EGFR kinase inhibition remains unexplored. In this study, we investigated the stereo-selectivity of catechins in inhibiting EGFR kinase, both in its wild-type and in the prevalent L858R mutant. Computational analyses indicated that all stereoisomers, including the extensively studied catechin (−)-EGCG, effectively bound within the ATP-binding site, potentially inhibiting EGFR kinase activity. Notably, gallated catechins emerged as superior EGFR inhibitors to their non-gallated counterparts, revealing intriguing binding trends. The top four stereoisomers exhibiting high dock scores and binding energies with wild-type EGFR comprise (−)-CG (−)-GCG (+)-CG, and (−)-EGCG. To assess dynamic behavior and stability, molecular dynamics simulations over 100 ns were conducted for the top-ranked catechin (−)-CG and the widely investigated catechin (−)-EGCG with EGFR kinase. This study enhances our understanding of how the stereoisomeric nature of a drug influences inhibitory potential, providing insights that could guide the selection of specific stereoisomers for improved efficacy inexisting drugs.</p

Subsistence Farming, Agrobiodiversity, and Sustainable Agriculture: A Case Study

<div><p>Subsistence farming still predominates in many places across the globe including India. Crops and livestock are often integral key components of subsistence farming practiced generally by smallholder farmers. A precise documentation of traditional farming practices involving native diversity with overall objectives of their conservation and showcasing their role in addressing livelihood security of farmers was done in the present study. This case study was undertaken in three underprivileged districts of India representing specific agroecosystems. The outcome of the study could help develop a policy framework for bringing sustainable agricultural development to subsistence farming agroecosystems. It could also help in exploring and advocating the potential of various suggested “add-value” interventions to native agrobiodiversity in addressing livelihood security of farmers.</p></div

Table_1_Association of household fuel with acute respiratory infection (ARI) under-five years children in Bangladesh.docx

In developing countries, acute respiratory infections (ARIs) cause a significant number of deaths among children. According to Bangladesh Demographic and Health Survey (BDHS), about 25% of the deaths in children under-five years are caused by ARI in Bangladesh every year. Low-income families frequently rely on wood, coal, and animal excrement for cooking. However, it is unclear whether using alternative fuels offers a health benefit over solid fuels. To clear this doubt, we conducted a study to investigate the effects of fuel usage on ARI in children. In this study, we used the latest BDHS 2017–18 survey data collected by the Government of Bangladesh (GoB) and estimated the effects of fuel use on ARI by constructing multivariable logistic regression models. From the analysis, we found that the crude (the only type of fuel in the model) odds ratio (OR) for ARI is 1.69 [95% confidence interval (CI): 1.06–2.71]. This suggests that children in families using contaminated fuels are 69.3% more likely to experience an ARI episode than children in households using clean fuels. After adjusting for cooking fuel, type of roof material, child's age (months), and sex of the child–the effect of solid fuels is similar to the adjusted odds ratio (AOR) for ARI (OR: 1.69, 95% CI: 1.05–2.72). This implies that an ARI occurrence is 69.2% more likely when compared to the effect of clean fuel. This study found a statistically significant association between solid fuel consumption and the occurrence of ARI in children in households. The correlation between indoor air pollution and clinical parameters of ARI requires further investigation. Our findings will also help other researchers and policymakers to take comprehensive actions by considering fuel type as a risk factor as well as taking proper steps to solve this issue.</p