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

BACKGROUND: Antimicrobial resistance poses a huge risk to human health worldwide, while Bangladesh is confronting the most severe challenge between the food supply and the huge consumption of antibiotics annually. More importantly, probiotics containing Bacillus spp. are claimed to be an alternative to antimicrobial stewardship programs. However, their antibiotic resistance remains elusive. Thus, we employed the antimicrobial susceptibility test and PCR to assess the prevalence of resistance, including multidrug resistance (MDR) and resito-genotyping of isolated Bacillus spp. RESULTS: The phenotypic profile showed that Bacillus spp. were 100% sensitive to gentamicin (2 µg/mL), whereas lowered sensitivity to levofloxacin (67.8%, 0.5-1 µg/mL), ciprofloxacin (62.3%, 0.5-1 µg/mL), clindamycin (52.2%, 0.25-0.5 µg/mL), amoxicillin-clavulanic acid (37.6%, 0.06 µg/mL), azithromycin (33.4%, 1-2 µg/mL), tetracycline (25.6%, 2-4 µg/mL), nitrofurantoin (21.1%, 16-32 µg/mL), co-trimoxazole (19.2%, 2 µg/mL), and erythromycin (18.8%, 0.25-0.5 µg/mL). The strains were completely resistant to penicillin, amoxicillin-clavulanic acid, cefixime, ceftriaxone, vancomycin, and co-trimoxazole, and a species-specific trend was seen in both phenotypic and genotypic resistance patterns. Genotypic resistance indicated prevalence of the bla1 (71.5%), tetA (33%), erm1 (27%), blaTEM (13.1%), blaCTX-M-1/blaCTX-M-2 /sul1 (10.1%), blaSHV (9.6%), and qnrS (4.1%) genes. The ß-lactamase resistance gene bla1 was found in all penicillin-resistant (MIC ≥ 32 µg/mL) Bacillus spp. One hundred ninety-one isolates (89.6%) were MDR, with 100% from diarrhea, 90.3% from food, and 88.7% from animal feed. CONCLUSION: Based on the MIC value and profile analysis of antibiotic resistance genes, this is the first study that Bacillus spp. antimicrobial susceptibilities have been identified in Bangladesh, and our study will shed light on the adverse effects of feed-borne Bacillus spp. emerging from animal feed to the food chain. A comprehensive investigation is urgently needed by policymakers on tolerance limits and harmful effects in the animal industry.

Arachidonic acid supplementation attenuates adipocyte inflammation but not adiposity in high fat diet induced obese mice.

Obesity is associated with low-grade chronic inflammation and has a remarkable role in the pathophysiology of metabolic complications. In triggering these inflammatory responses, the arachidonic acid (AA) cascade plays a key role. However, there is a lack of data on how supplementary AA would affect obesity, adipose tissue inflammation, and the AA cascade in obesity. This study aims to investigate how AA supplementation affects obesity, adipocyte morphology, inflammation, and AA cascade signaling. Male Swiss Albino mice were used in our experiment. The mice were fed high-fat diets to induce obesity, and these obese mice were treated with two different doses of AA for 3 weeks. A normal diet non-obese group and an untreated obese group were kept as controls. Bodyweight and daily food intake data were recorded during that period. After the treatment period, blood serum and white adipose tissue of the experimental mice were collected for colorimetric lipid profile tests, histology, and mRNA extraction. The ΔΔCT method was employed for calculating the relative mRNA expression of target genes. The findings of our study suggest that AA has no significant effects on body weight, visceral adiposity, adipose tissue morphology, and serum lipid profile. However, AA treatment has resulted in a significant down-regulation of pro-inflammatory markers as well as the COX pathway. Besides, up-regulation of 12/15-LOX has been observed, indicating the metabolism pathway of supplementary AA through the LOX pathway. Our findings indicate that AA treatment may not provide significant benefits in terms of body weight, visceral fat mass, or serum lipid profile. However, it has effectively alleviated obesity-induced adipocyte inflammation in high-fat diet-induced obese mice.

Aspirin attenuates the expression of adhesion molecules, risk of obesity, and adipose tissue inflammation in high-fat diet-induced obese mice.

The prevalence of obesity is increasing at an alarming rate and keeps on being one of the significant challenges of this century. Obesity promotes adipose tissue hypertrophy and causes the release of different pro-inflammatory cytokines, playing a significant role in the pathophysiology of metabolic syndrome. Aspirin is known as a potent anti-inflammatory drug, but its role in adipogenesis, adipocyte-specific inflammation, and metabolic syndrome is not well characterized. Thus, in this experiment, we aimed to determine the effect of low-dose aspirin on obesity, obesity-induced inflammation, and metabolic syndrome. High-fat diet-induced obese female mice (Swiss Albino) were used in our study. Mice were fed on a normal diet, a high-fat diet, and a low dose of aspirin (LDA) in the presence of a high-fat diet for 11 weeks. Body weight, lipid profile, adipose tissue size, and inflammatory status were analyzed after that period. The ∆∆CT method was used to calculate the relative mRNA expression of target genes. Treatment with a low dose of aspirin resulted in a significant reduction of body weight, visceral fat mass and serum total cholesterols, serum and adipose tissue triglycerides, and blood glucose levels in high-fat diet-induced obese mice compared to the untreated obese group. Consistent with these biochemical results, a significant reduction in mRNA expression of different genes like PPARγ, GLUT4, IL-6, TNFα, MCP-1, ICAM-I, and VCAM-I associated with adipogenesis and inflammation were noticed. Overall, current study findings indicate that low-dose aspirin reduces obesity, hyperlipidemia, adipocyte-specific inflammation, and metabolic syndrome in high-fat diet-induced obese mice.

pssRNAit: A Web Server for Designing Effective and Specific Plant siRNAs with Genome-Wide Off-Target Assessment.

We report an advanced web server, the plant-specific small noncoding RNA interference tool pssRNAit, which can be used to design a pool of small interfering RNAs (siRNAs) for highly effective, specific, and nontoxic gene silencing in plants. In developing this tool, we integrated the transcript dataset of plants, several rules governing gene silencing, and a series of computational models of the biological mechanism of the RNA interference (RNAi) pathway. The designed pool of siRNAs can be used to construct a long double-strand RNA and expressed through virus-induced gene silencing (VIGS) or synthetic transacting siRNA vectors for gene silencing. We demonstrated the performance of pssRNAit by designing and expressing the VIGS constructs to silence Phytoene desaturase (PDS) or a ribosomal protein-encoding gene, RPL10 (QM), in Nicotiana benthamiana We analyzed the expression levels of predicted intended-target and off-target genes using reverse transcription quantitative PCR. We further conducted an RNA-sequencing-based transcriptome analysis to assess genome-wide off-target gene silencing triggered by the fragments that were designed by pssRNAit, targeting different homologous regions of the PDS gene. Our analyses confirmed the high accuracy of siRNA constructs designed using pssRNAit The pssRNAit server, freely available at https://plantgrn.noble.org/pssRNAit/, supports the design of highly effective and specific RNAi, VIGS, or synthetic transacting siRNA constructs for high-throughput functional genomics and trait improvement in >160 plant species.

Determinants and dynamics of food insecurity during COVID-19 in rural Bangladesh.

COVID-19 has threatened food security of the poor due to the lockdown of markets amidst poor institutions and lack of social safety nets in the developing world. To provide rapid evidence on the determinants and dynamics of food insecurity and to understand the coping strategies adopted by rural households during the pandemic, we carried out a telephone survey of roughly 10,000 rural households in Bangladesh, three weeks after the country went into lockdown. We found that roughly 90% of households reported experiencing a negative income shock after the countrywide lockdown was implemented. Households that primarily depend on daily casual labor for their income were affected the most, while households with regular jobs were affected the least in terms of food insecurity. Households adversely hit by income shock due to the pandemic were also found to rely more on past savings, food stocks, and loans from various sources to cope with the food crisis. When we followed-up 2402 households, about 3 to 4 weeks after the first survey, to understand the dynamics of food insecurity, we found that food insecurity increased significantly across households and began affecting groups that were in an advantageous position during the first survey. This poses a threat to the poor as food security has already worsened since the crisis hit and would presumably worsen further in the future unless rapid measures are taken to attenuate it at the earliest.

Clinical evaluation of dengue and identification of risk factors for severe disease: protocol for a multicentre study in 8 countries.

BACKGROUND: The burden of dengue continues to increase globally, with an estimated 100 million clinically apparent infections occurring each year. Although most dengue infections are asymptomatic, patients can present with a wide spectrum of clinical symptoms ranging from mild febrile illness through to severe manifestations of bleeding, organ impairment, and hypovolaemic shock due to a systemic vascular leak syndrome. Clinical diagnosis of dengue and identification of which patients are likely to develop severe disease remain challenging. This study aims to improve diagnosis and clinical management through approaches designed a) to differentiate between dengue and other common febrile illness within 72 h of fever onset, and b) among patients with dengue to identify markers that are predictive of the likelihood of evolving to a more severe disease course. METHOD/DESIGN: This is a prospective multi-centre observational study aiming to enrol 7-8000 participants aged ≥ 5 years presenting with a febrile illness consistent with dengue to outpatient health facilities in 8 countries across Asia and Latin America. Patients presenting within 72 h of fever onset who do not exhibit signs of severe disease are eligible for the study. A broad range of clinical and laboratory parameters are assessed daily for up to 6 days during the acute illness, and also at a follow up visit 1 week later. DISCUSSION: Data from this large cohort of patients, enrolled early with undifferentiated fever, will be used to develop a practical diagnostic algorithm and a robust clinical case definition for dengue. Additionally, among patients with confirmed dengue we aim to identify simple clinical and laboratory parameters associated with progression to a more severe disease course. We will also investigate early virological and serological correlates of severe disease, and examine genetic associations in this large heterogeneous cohort. In addition the results will be used to assess the new World Health Organization classification scheme for dengue in practice, and to update the guidelines for "Integrated Management of Childhood Illness" used in dengue-endemic countries. TRIAL REGISTRATION: NCT01550016. Registration Date: March 7, 2012.

ANTIGENIC AND GENETIC CHARACTERIZATION OF INFLUENZA B VIRUSES IN 2012 FROM SLUMS, DHAKA, BANGLADESH.

Nasal and throat swab samples were collected from 400 subjects with influenza-like illness during June to September, 2012 from two heavily crowded slums, Rayerbazar and Hazaribagh, situated southeast of Dhaka, Bangladesh. Forty-one samples were positive for influenza B virus using quantitative RT-PCR, but no influenza A virus was detected. Antigenic characterization revealed that the influenza B viruses were of Yamagata and Victoria lineages, which was confirmed from genetic analysis of hemagglutinin (HA) and neuraminidase (NA) genes. Co-circulation of influenza B viruses of both Yamagata and Victoria lineages in the slums of Dhaka indicates that introduction of a tetravalent vaccine formulation that includes both of these influenza B virus lineages would be more effective in this population.

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

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 Arabidopsis 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 Arabidopsis. 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.

Migraine among women with endometriosis: a hospital-based case-control study in Bangladesh.

BACKGROUND: Endometriosis is a disease among women of reproductive age, which causes several health problems, such as dysmenorrhea, dyspareunia, and subfertility. In addition, it increases psychological stress and often results in marital disharmony. Similarly, migraine is more frequent among this group of women. Several studies have shown an association between endometriosis and migraine among groups of populations completely different from Bangladesh. OBJECTIVE: This study aimed to identify the association between endometriosis and migraine among the Bangladeshi population. STUDY DESIGN: This nonrandomized case-control study was conducted with cases of endometriosis and controls without endometriosis who were confirmed by laparoscopy or laparotomy. Among the study participants, cases of migraine in 1 group of respondents who were already diagnosed as patients of migraine were identified, and the others with complaints of headaches were further confirmed by a medicine specialist. Patients were recruited from the Department of Obstetrics and Gynecology at the Bangladesh Institute of Research and Rehabilitation in Diabetes, Endocrine and Metabolic Disorders General Hospital and Ibrahim Medical College. The study was approved by the ethical review committee of the Bangladesh Institute of Research and Rehabilitation in Diabetes, Endocrine and Metabolic Disorders General Hospital. Multivariate logistic regression was used to identify the association between endometriosis and migraine using odds ratios and 95% confidence intervals. RESULTS: Of 1496 patients who underwent laparoscopy or laparotomy during the study period, the frequency of endometriosis was found to be 12.7%. A total of 190 patients with confirmed endometriosis cases and an equal number of controls without endometriosis were enrolled, maintaining the age distribution of the controls similar to that of the cases. Compared with controls, the distribution of age, body mass index, education, and marital status of the patients with endometriosis were similar. The average ages of respondents were 30.6 years in both the case and control groups. Regarding occupation, cases included more students than controls (12% vs 0%, respectively). The odds of suffering from dysmenorrhea and dyspareunia among the cases were 3.3 (95% confidence interval, 2.66-4.15; P<.001) and 9.5 (95% confidence interval, 5.3-17.9; P<.001) times higher than that of controls, respectively. In addition, the odds of menstrual irregularity was 60% lower among the cases than among controls (odds ratio, 0.4; 95% confidence interval, 0.24-0.64; P<.001). No significant difference was observed in having primary subfertility and secondary subfertility among the 2 groups of respondents. Univariate regression analysis showed that patients with endometriosis have 6.13 times higher odds (95% confidence interval, 2.50-18.40; P<.001) of having a migraine and 2.00 times higher odds (95% confidence interval, 1.2-3.2; P=.01) of having a headache than controls. Furthermore, the age- and body mass index-adjusted multivariate model showed that patients with endometriosis have 5.4 times higher odds of having migraine than patients without endometriosis (95% confidence interval, 2.11-16.4; P<.001). In addition, the higher the age of reproductive-age women, the higher the odds of having migraine. A 1-year increase in age increases the odds of having migraine by 23% (odds ratio, 1.23; 95% confidence interval, 1.13-1.16; P<.001). CONCLUSION: Our results support the association between endometriosis and migraine among the Bangladeshi population, which is similar to relevant studies conducted in other geographic locations. The groups of physicians who treat patients suffering from the 2 diseases, endometriosis and migraine, should keep this interrelationship in mind to ensure a better quality of life for the patient.

Adsorbents from rice husk and shrimp shell for effective removal of heavy metals and reactive dyes in water.

Widespread contamination by heavy metals (HMs) and dyes poses a major health risk to people and ecosystems requiring effective treatment. In this work, rice husk (RH) and shrimp shells were extracted to obtain amorphous silica and chitosan, respectively, which were utilized to produce nano-chitosan-coated silica (NCCS). To ensure the stability of the nanoparticles, silica was freeze-dried after being coated with nano-chitosan. Functional groups (-NH2, -OH, P]O) from chitosan nanoparticles (CNPs) were introduced to the surface of silica during this process. Dyes such as brilliant green (BG), methylene blue (MB) and reactive brown (RB) as well as HMs (Cr6+, Pb2+, Cd2+, Ni2+) were removed by adsorbents. CNPs showed the highest adsorption capacity for RB (59.52 mg/g) among dyes and Cr6+ (42.55 mg/g) among HMs. CNPs showed the highest adsorption capacity for HMs among different adsorbents. Although NCCS and CNPs showed similar adsorption capabilities for HMs and dyes, NCCS showed the best stability. The adsorption performance decreased as RB > Cr6+ > MB > BG > Pb2+ > Cd2+ > Ni2+. The adsorption reactions followed both pseudo-first-order and second-order kinetics, and was spontaneous from thermodynamic analysis. In summary, the waste-derived adsorbents demonstrated excellent potential for removing HMs and dyes from water, while supporting effective management solid waste.

PHDcleav: a SVM based method for predicting human Dicer cleavage sites using sequence and secondary structure of miRNA precursors.

BACKGROUND: Dicer, an RNase III enzyme, plays a vital role in the processing of pre-miRNAs for generating the miRNAs. The structural and sequence features on pre-miRNA which can facilitate position and efficiency of cleavage are not well known. A precise cleavage by Dicer is crucial because an inaccurate processing can produce miRNA with different seed regions which can alter the repertoire of target genes. RESULTS: In this study, a novel method has been developed to predict Dicer cleavage sites on pre-miRNAs using Support Vector Machine. We used the dataset of experimentally validated human miRNA hairpins from miRBase, and extracted fourteen nucleotides around Dicer cleavage sites. We developed number of models using various types of features and achieved maximum accuracy of 66% using binary profile of nucleotide sequence taken from 5p arm of hairpin. The prediction performance of Dicer cleavage site improved significantly from 66% to 86% when we integrated secondary structure information. This indicates that secondary structure plays an important role in the selection of cleavage site. All models were trained and tested on 555 experimentally validated cleavage sites and evaluated using 5-fold cross validation technique. In addition, the performance was also evaluated on an independent testing dataset that achieved an accuracy of ~82%. CONCLUSION: Based on this study, we developed a webserver PHDcleav (http://www.imtech.res.in/raghava/phdcleav/) to predict Dicer cleavage sites in pre-miRNA. This tool can be used to investigate functional consequences of genetic variations/SNPs in miRNA on Dicer cleavage site, and gene silencing. Moreover, it would also be useful in the discovery of miRNAs in human genome and design of Dicer specific pre-miRNAs for potent gene silencing.

Survey of culture, goldengate assay, universal biosensor assay, and 16S rRNA Gene sequencing as alternative methods of bacterial pathogen detection.

Cultivation-based assays combined with PCR or enzyme-linked immunosorbent assay (ELISA)-based methods for finding virulence factors are standard methods for detecting bacterial pathogens in stools; however, with emerging molecular technologies, new methods have become available. The aim of this study was to compare four distinct detection technologies for the identification of pathogens in stools from children under 5 years of age in The Gambia, Mali, Kenya, and Bangladesh. The children were identified, using currently accepted clinical protocols, as either controls or cases with moderate to severe diarrhea. A total of 3,610 stool samples were tested by established clinical culture techniques: 3,179 DNA samples by the Universal Biosensor assay (Ibis Biosciences, Inc.), 1,466 DNA samples by the GoldenGate assay (Illumina), and 1,006 DNA samples by sequencing of 16S rRNA genes. Each method detected different proportions of samples testing positive for each of seven enteric pathogens, enteroaggregative Escherichia coli (EAEC), enterotoxigenic E. coli (ETEC), enteropathogenic E. coli (EPEC), Shigella spp., Campylobacter jejuni, Salmonella enterica, and Aeromonas spp. The comparisons among detection methods included the frequency of positive stool samples and kappa values for making pairwise comparisons. Overall, the standard culture methods detected Shigella spp., EPEC, ETEC, and EAEC in smaller proportions of the samples than either of the methods based on detection of the virulence genes from DNA in whole stools. The GoldenGate method revealed the greatest agreement with the other methods. The agreement among methods was higher in cases than in controls. The new molecular technologies have a high potential for highly sensitive identification of bacterial diarrheal pathogens.

Effects of examination-induced stress on memory and blood pressure.

Stress has been defined in many ways as a state of psychological arousal that results when the external demand is beyond what one can cope with. Stress is caused by various factors called stressors. Medical students are subjected to different kinds of stressors, such as pressure of academics with obligation to succeed, an uncertain future and difficulties of integrating into the system and different teaching protocols, which may affect their learning ability and performance. Stress has a great impact on brain mainly in the form of impaired memory and on cardiovascular function in the form of increased heart rate and blood pressure. The study was planned to assess the effects of examination induced stress on memory and blood pressure. The study was longitudinal in nature conducted at Department of Physiology, Santosh Medical College, Ghaziabad, India. Initially 100 subjects were selected from 17-24 years of age group then all the subjects were divided into two groups of 'slow-learners' and 'fast-learners' based upon their past academic performances. Readings were taken at two stages of academic year, 05 months before pre-prof examination and 03 days before pre-prof examination. Blood Pressure were measured and the memory assessments were done by using 10 subtests of PGI memory scale. We found a significant increase in stress level 3 days before the examination, compared to 5 months before the examination which in turn affected both blood pressure and memory functions. But, slow-learners were affected more compared to fast-learners.

Bacterial profile, antimicrobial resistance, and molecular detection of ESBL and quinolone resistance gene of uropathogens causing urinary tract infection in the southeastern part of Bangladesh.

Humans frequently contract urinary tract infections (UTIs), which can be brought on by uropathogens (UPs) that are multi-drug resistant. Treatment for UTIs brought on by pathogenic UPs that produce extended-spectrum lactamases (ESBLs) is more costly and potentially fatal. As a result, the objective of this study was to use culture, biochemical, and 16S rRNA sequencing to identify and characterize UPs isolated from outpatients in Noakhali, Bangladesh, who had symptoms of UTIs. ESBL gene identification and quinolone resistance gene typing were then performed on the isolates using polymerase chain reaction (PCR). Throughout the trial's 8-month duration, 152 (76%) of 200 urine samples were positive for the presence of UPs. The overall number of UPs recovered was 210, with 39 individuals having multiple UPs present in their samples. Among all of the isolates, Escherichia coli (45.24%, 95/210; 95% confidence interval (CI): 35.15-57.60%), Enterobacter spp. (24.76%, 52/210; CI: 19.15-35.77%), Klebsiella spp. (20.95%; 44/210; CI: 15.15-30.20%), and Providencia spp. (9.05%; 19/210; CI: 4.95-19.25%) were the four most prevalent bacteria found in the isolates. The UPs displayed a very high level of resistance to piperacillin 96.92% (126/130), ampicillin 90% (117/130), nalidixic acid 77.69% (101/130), cefazolin 70% (91/130), amoxicillin 50% (55/130), cefazolin 42.31% (55/130), nitrofurantoin 43.08% (56/130), and ciprofloxacin 33.08% (43/130), whereas resistance to netilmicin (3.85%), amikacin (4.62%), and imipenem (9.23%) was low. Individually, every species of E. coli and Providencia spp. showed greater ampicillin, amikacin, cefazolin, cefazolin, and nalidixic acid resistance than the others. The bivariate results indicate several antibiotic pairings, and isolates had meaningful associations. All MDR isolates were subjected to PCR, which revealed that blaCTX-M-15 genes predominated among the isolates, followed by the blaTEM class (37%). Isolates also had the qnrS, aac-6´-Ib-cr, and gyrA genes. The findings provide worrying indications of a major expansion of MDR isolates in the study locations, particularly the epidemiological balCTX-M 15, with the potential for the transmission of multi-drug-resistant UP strains in the population.

Efficient SABRE-SHEATH Hyperpolarization of Potent Branched-Chain-Amino-Acid Metabolic Probe [1-13C]ketoisocaproate.

Efficient 13C hyperpolarization of ketoisocaproate is demonstrated in natural isotopic abundance and [1-13C]enriched forms via SABRE-SHEATH (Signal Amplification By Reversible Exchange in SHield Enables Alignment Transfer to Heteronuclei). Parahydrogen, as the source of nuclear spin order, and ketoisocaproate undergo simultaneous chemical exchange with an Ir-IMes-based hexacoordinate complex in CD3OD. SABRE-SHEATH enables spontaneous polarization transfer from parahydrogen-derived hydrides to the 13C nucleus of transiently bound ketoisocaproate. 13C polarization values of up to 18% are achieved at the 1-13C site in 1 min in the liquid state at 30 mM substrate concentration. The efficient polarization build-up becomes possible due to favorable relaxation dynamics. Specifically, the exponential build-up time constant (14.3 ± 0.6 s) is substantially lower than the corresponding polarization decay time constant (22.8 ± 1.2 s) at the optimum polarization transfer field (0.4 microtesla) and temperature (10 °C). The experiments with natural abundance ketoisocaproate revealed polarization level on the 13C-2 site of less than 1%-i.e., one order of magnitude lower than that of the 1-13C site-which is only partially due to more-efficient relaxation dynamics in sub-microtesla fields. We rationalize the overall much lower 13C-2 polarization efficiency in part by less favorable catalyst-binding dynamics of the C-2 site. Pilot SABRE experiments at pH 4.0 (acidified sample) versus pH 6.1 (unaltered sodium [1-13C]ketoisocaproate) reveal substantial modulation of SABRE-SHEATH processes by pH, warranting future systematic pH titration studies of ketoisocaproate, as well as other structurally similar ketocarboxylate motifs including pyruvate and alpha-ketoglutarate, with the overarching goal of maximizing 13C polarization levels in these potent molecular probes. Finally, we also report on the pilot post-mortem use of HP [1-13C]ketoisocaproate in a euthanized mouse, demonstrating that SABRE-hyperpolarized 13C contrast agents hold promise for future metabolic studies.

Effects of halotolerant rhizobacteria on rice seedlings under salinity stress.

Avirulent halotolerant plant growth-promoting rhizobacteria (HPGPR) located on the roots' periphery can reduce abiotic stressors (such as salinity and drought), enhance plant productivity. Salinity poses a significant challenge for growing agricultural products, like rice, in the coastal regions. It is crucial to enhance production because of limited arable land and the high growth rate of the population. This study targeted to identify HPGPR from legume root nodules and assessed their effects on rice plants experiencing salt stress in coastal regions of Bangladesh. Based on the culture morphology, biochemical, salt, pH, and temperature tolerance traits, sixteen bacteria were isolated from the root nodules of leguminous plants (Common bean, Yardlong bean, Dhaincha, and Shameplant). All the bacterial strains can tolerate 3 % salt concentration, and capable to survive at the highest 45 °C temperature and pH 11 (without isolate 1). Three preeminent bacteria, Agrobacterium tumefaciens (B1), Bacillus subtilis (B2), and Lysinibacillus fusiformis (B3) were specified through morpho-biochemical and molecular (16S rRNA gene sequence) exploration for inoculation. To assess the plant growth-promoting activities, germination tests are applied where bacterial inoculation increased germination in saline and non-saline conditions. Control group (C) showed 89.47 % and bacterial treated groups (C + B1, C + B2, and C + B3) 95 %, 90 %, and 75 % germination after 2 days of inoculation. In (1 % NaCl) saline condition control group revealed 40 % whereas three groups with bacteria showed 60 %, 40 %, and 70 % germination after 3 days, which increased 70 %, 90 %, 85 %, and 95 % respectively after 4 days of inoculation. The HPGPR significantly improved plant development metrics such as root length, shoot length, fresh and arid biomass yield, chlorophyll content, etc. Our results suggest that the salt-resistant bacteria (Halotolerant) have a great potential role in recuperating plant growth and would be cost-effective as a bio-inoculant in saline conditions to be used as a prospective bio-fertilizer for rice production. These findings indicate that the HPGPR has a substantially promising function in reviving plant development in an eco-friendly manner.

Evaluation of antibacterial activity, in-vitro cytotoxicity and catalytic activity of biologically synthesized silver nanoparticles using leaf extracts of Leea macrophylla.

Nanotechnology has become a cutting-edge field of research that has emerged as an interdisciplinary research area and contributes to almost every field of science. With the increasing demand for sustainable greener products, attention has recently been focused on green nanotechnology. This study manifested the aptitude of Leea macrophylla (LM) leaf extract, fortified with phytochemicals, to biosynthesize silver nanoparticles (AgNPs) for the first time. As soon as the AgNPs were biosynthesized, they immediately changed color, and the distinctive surface plasmon resonance (SPR) occurred at 420 nm in the Ultraviolet-Visible spectrum, proving that the biosynthesis had been successful. Fourier Transform Infrared Spectroscopy (FTIR) was used to examine the phytochemicals present in the LM leaf extract, those are accountable for the formation and stabilization of AgNPs. The Transmission Electron Microscope (TEM) revealed the formation of quasi spherical silver nanoparticles with an average diameter of 22.77 nm. Synthesized nanoparticles were further characterized by X-ray diffraction (XRD), Field Emission Scanning Electron microscope (FESEM), Energy Dispersive X-ray (EDX), Dynamic Light Scattering (DLS) and Thermogravimetric analysis (TGA). The production of AgNPs with high metal content from LM leaf extract exhibited encouraging results. The LM leaf extract mediated silver nanoparticles evinced significant antibacterial and catalytic activities. The cytotoxicity effects of biosynthesized AgNPs were tested on brine shrimps.

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

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.

In Silico Functional Characterization of a Hypothetical Protein From Pasteurella Multocida Reveals a Novel S-Adenosylmethionine-Dependent Methyltransferase Activity.

Genomes may now be sequenced in a matter of weeks, leading to an influx of "hypothetical" proteins (HP) whose activities remain a mystery in GenBank. The information included inside these genes has quickly grown in prominence. Thus, we selected to look closely at the structure and function of an HP (AFF25514.1; 246 residues) from Pasteurella multocida (PM) subsp. multocida str. HN06. Possible insights into bacterial adaptation to new environments and metabolic changes might be gained by studying the functions of this protein. The PM HN06 2293 gene encodes an alkaline cytoplasmic protein with a molecular weight of 28352.60 Da, an isoelectric point (pI) of 9.18, and an overall average hydropathicity of around -0.565. One of its functional domains, tRNA (adenine (37)-N6)-methyltransferase TrmO, is a S-adenosylmethionine (SAM)-dependent methyltransferase (MTase), suggesting that it belongs to the Class VIII SAM-dependent MTase family. The tertiary structures represented by HHpred and I-TASSER models were found to be flawless. We predicted the model's active site using the Computed Atlas of Surface Topography of Proteins (CASTp) and FTSite servers, and then displayed it in 3 dimensional (3D) using PyMOL and BIOVIA Discovery Studio. Based on molecular docking (MD) results, we know that HP interacts with SAM and S-adenosylhomocysteine (SAH), 2 crucial metabolites in the tRNA methylation process, with binding affinities of 7.4 and 7.5 kcal/mol, respectively. Molecular dynamic simulations (MDS) of the docked complex, which included only modest structural adjustments, corroborated the strong binding affinity of SAM and SAH to the HP. Evidence for HP's possible role as an SAM-dependent MTase was therefore given by the findings of Multiple sequence alignment (MSA), MD, and molecular dynamic modeling. These in silico data suggest that the investigated HP might be used as a useful adjunct in the investigation of Pasteurella infections and the development of drugs to treat zoonotic pasteurellosis.

Genome-wide study of globally distributed respiratory syncytial virus (RSV) strains implicates diversification utilizing phylodynamics and mutational analysis.

Respiratory syncytial virus (RSV) is a common respiratory pathogen that causes mild cold-like symptoms and severe lower respiratory tract infections, causing hospitalizations in children, the elderly and immunocompromised individuals. Due to genetic variability, this virus causes life-threatening pneumonia and bronchiolitis in young infants. Thus, we examined 3600 whole genome sequences submitted to GISAID by 31 December 2022 to examine the genetic variability of RSV. While RSVA and RSVB coexist throughout RSV seasons, RSVA is more prevalent, fatal, and epidemic-prone in several countries, including the United States, the United Kingdom, Australia, and China. Additionally, the virus's attachment glycoprotein and fusion protein were highly mutated, with RSVA having higher Shannon entropy than RSVB. The genetic makeup of these viruses contributes significantly to their prevalence and epidemic potential. Several strain-specific SNPs co-occurred with specific haplotypes of RSVA and RSVB, followed by different haplotypes of the viruses. RSVA and RSVB have the highest linkage probability at loci T12844A/T3483C and G13959T/C2198T, respectively. The results indicate that specific haplotypes and SNPs may significantly affect their spread. Overall, this analysis presents a promising strategy for tracking the evolving epidemic situation and genetic variants of RSV, which could aid in developing effective control, prophylactic, and treatment strategies.