Dynamic readers for 5-(hydroxy)methylcytosine and its oxidized derivatives.

Tet proteins oxidize 5-methylcytosine (mC) to generate 5-hydroxymethyl (hmC), 5-formyl (fC), and 5-carboxylcytosine (caC). The exact function of these oxidative cytosine bases remains elusive. We applied quantitative mass-spectrometry-based proteomics to identify readers for mC and hmC in mouse embryonic stem cells (mESC), neuronal progenitor cells (NPC), and adult mouse brain tissue. Readers for these modifications are only partially overlapping, and some readers, such as Rfx proteins, display strong specificity. Interactions are dynamic during differentiation, as for example evidenced by the mESC-specific binding of Klf4 to mC and the NPC-specific binding of Uhrf2 to hmC, suggesting specific biological roles for mC and hmC. Oxidized derivatives of mC recruit distinct transcription regulators as well as a large number of DNA repair proteins in mouse ES cells, implicating the DNA damage response as a major player in active DNA demethylation.

Insights to antimicrobial resistance: heavy metals can inhibit antibiotic resistance in bacteria isolated from wastewater.

The alarming upsurge in the co-existence of heavy metal and antibiotic resistance may have a devastating impact on humans, animals, and the environment. Four metal-resistant bacteria were isolated from hospital effluents and industrial drain. Heavy metal resistance and antimicrobial resistance were examined in the isolates followed by identification through 16S rRNA gene sequencing. Delftia tsuruhatensis strain FK-01 and Carnobacterium inhibens strain FK-02 tolerated arsenic with maximal tolerated concentration (MTC) of 30 mM and 10 mM, respectively. Staphylococcus hominis strain FK-04 tolerated copper up to 4 mM and lead-resistant Raoultella ornithinolytica strain FK-05 exhibited tolerance to 1 mM lead. The growth kinetics of bacteria were monitored in the presence of metals and the following antibiotics, tetracycline, chloramphenicol, and kanamycin. The presence of arsenate significantly enhanced tetracycline resistance in C. inhibens. Heavy metal-induced antibiotic resistance was also observed in S. hominis and R. ornithinolytica, against chloramphenicol and tetracycline respectively. D. tsuruhatensis showed resistance to kanamycin but when grown in the presence of arsenic and kanamycin, bacteria lost resistance to the antibiotic. Therefore, it is suggested that the novel arsenate-resistant strain Delftia tsuruhatensis FK-01 has a unique ability to inhibit antimicrobial resistance that can be harnessed in bioremediation.

Structural basis of nucleic acid binding by Nicotiana tabacum glycine-rich RNA-binding protein: implications for its RNA chaperone function.

Glycine-rich RNA-binding proteins (GR-RBPs) are involved in cold shock response of plants as RNA chaperones facilitating mRNA transport, splicing and translation. GR-RBPs are bipartite proteins containing a RNA recognition motif (RRM) followed by a glycine-rich region. Here, we studied the structural basis of nucleic acid binding of full-length Nicotiana tabacum GR-RBP1. NMR studies of NtGR-RBP1 show that the glycine-rich domain, while intrinsically disordered, is responsible for mediating self-association by transient interactions with its RRM domain (NtRRM). Both NtGR-RBP1 and NtRRM bind specifically and with low micromolar affinity to RNA and single-stranded DNA. The solution structure of NtRRM shows that it is a canonical RRM domain. A HADDOCK model of the NtRRM-RNA complex, based on NMR chemical shift and NOE data, shows that nucleic acid binding results from a combination of stacking and electrostatic interactions with conserved RRM residues. Finally, DNA melting experiments demonstrate that NtGR-RBP1 is more efficient in melting CTG containing nucleic acids than isolated NtRRM. Together, our study supports the model that self-association of GR-RBPs by the glycine-rich region results in cooperative unfolding of non-native substrate structures, thereby enhancing its chaperone function.

A common missense variant rs874881 of PADI4 gene and rheumatoid arthritis: Genetic association study and in-silico analysis.

The peptidylarginine-deiminase 4 (PADI4) is involved in the post-translational catalytic conversion of arginine into citrulline. The autoantibodies including anti-citrullinated protein antibodies (ACPAs) produced in response to hypercitrullinated proteins are a hallmark of rheumatoid arthritis (RA) autoimmunity. Therefore, the role of a missense variant rs874881 (Gly112Ala) of PADI4 in RA susceptibility was analyzed, along with in-silico analysis of structural and functional impacts of this substitution. We did a case-control association study and in-silico analysis. For the case-control study, confirmed RA cases and healthy controls were recruited. Genotyping for rs874881 (n = 750) was performed through polymerase chain reaction-restriction fragment length polymorphism. Multivariate logistic regression analysis was employed to determine association. The in-silico analysis was carried out through HOPE, VarMap, MutationAssessor, MutPred2, SIFT, PolyPhen, CADD, REVEL and MetaLR. In the case-control study, the rs874881 exhibited a strong association with increased RA susceptibility (G vs C odds ratio = 3.85, 95 % confidence interval = 2.81-5.27). Interaction analysis revealed significant interaction of genotype with smoking and gender (p < 0.05). Significant results (p < 0.05) were also obtained in stratified analysis by presence/absence of comorbidities and radiographic damage. According to in-silico pathogenicity prediction analysis, this Gly112Ala substitution does not exert a major effect on protein structure and function including its enzymatic activity. We report a significant association of PADI4 rs874881 with overall RA susceptibility. To our knowledge, this is the first study to do the interaction and stratified analyses on the PADI4 rs874881 in RA. Similar detailed studies should also be performed in other populations.

The positive impact of social media on health behavior towards the COVID-19 pandemic in Bangladesh: A web-based cross-sectional study.

BACKGROUND: Health information has a profound impact on developing awareness and ultimately preventing the burden of coronavirus disease-2019 (COVID-19) pandemic, but study in Bangladesh is lacking. AIMS: Therefore, this study was conducted to investigate the impact of information from social media and television in developing health awareness among people amid the COVID-19 pandemic. METHODS: Data was collected during December 10, 2020 to February 10, 2021 from 1808 people. Data was collected by using questionnaire about information source and their impact on COVID-19 related health measures. Pearson's correlation analyses was conducted. RESULTS: Female (52%, 937 of 1808) was the most prevalent sex and the mean age was 24 ± 3.9 years. Most of the social media users were students (63%, 1131 of 1808). Social media (53%, 959 of 1808) and television (44%, 800 of 1808) were the most popular sources and Facebook (66.5%, 1203 of 1808) was the most common source of getting health information. About 87% people received health information on social media and television. Users of social media had about 3 times more likelihood to follow the health rules. About 80% participants who used social media followed the health measures after 0-28 days of getting the information. The strongest correlation was found between social distancing and the information on television (r = 0.943). CONCLUSION: Strong correlation of health information was present among the participants in building awareness about taking preventive measures. This is the first study to describe the positive influence of information amid COVID-19 in Bangladesh.

Prevalence and impact of comorbidities on disease prognosis among patients with COVID-19 in Bangladesh: A nationwide study amid the second wave.

BACKGROUND: Socio-demographics and comorbidities are involved in determining the severity and fatality in patients with COVID-19 suggested by studies in various countries, but study in Bangladesh is insufficient. AIMS: We designed the study to evaluate the association of sociodemographic and comorbidities with the prognosis of adverse health outcomes in patients with COVID-19 in Bangladesh. METHODS: A multivariate retrospective cohort study was conducted on data from 966 RT-PCR positive patients from eight divisions during December 13, 2020, to February 13, 2021. Variables included sociodemographic, comorbidities, symptoms, Charlson comorbidity index (CCI) and access to health facilities. Major outcome was fatality. Secondary outcomes included hospitalization, duration of hospital stay, requirement of mechanical ventilation and severity. RESULTS: Male (65.8%, 636 of 966) was predominant and mean age was 39.8 ± 12.6 years. Fever (79%), dry cough (55%), and loss of test/smell (51%) were frequent and 74% patients had >3 symptoms. Fatality was recorded in 10.5% patients. Comorbidities were found in 44% patients. Hypertension (21.5%) diabetes (14.6%), and cardiovascular diseases (11.3%) were most prevalent. Age >60 years (OR: 4.83, 95% CI: 2.45-6.49), and CCI >3 (OR: 5.48, 95% CI: 3.95-7.24) were predictors of hospitalizations. CCI >4 (aOR: 3.41, 95% CI: 2.57-6.09) was predictor of severity. Age >60 years (aOR: 3.77, 95% CI: 1.07-6.34), >3 symptoms (aOR: 2.14, 95% CI: 0.97-4.91) and CCI >3 vs. CCI <3 (aOR: 5.23, 95% CI: 3.77-8.09) were independently associated with fatality. CONCLUSIONS: Increased age, >3 symptoms, increasing comorbidities, higher CCI were associated with increased hospitalization, severity and fatality in patients with COVID-19.

Validation of the Recent Life Changes Questionnaire (RLCQ) for stress measurement among adults residing in urban communities in Pakistan.

BACKGROUND: Recent Life Changes Questionnaire (RLCQ) developed by Richard Rahe has enabled quantification of stress by analyzing life events. The overall aim of the study was to create a reliable version of the Rahe's RLCQ for measuring stress in individuals living in developing countries and assess its validity. This paper discusses criterion validation of the adapted RLCQ in urban communities in Pakistan. METHODS: This is a criterion validation study. Four urban communities of Karachi, Pakistan were selected for the study in which households were randomly chosen. Two data collectors were assigned to administer the adapted RLCQ to eligible participants after obtaining written informed consent. Following this interaction, two psychologists interviewed the same participants with a diagnostic gold standard of Mini International Neuropsychiatric Interview (MINI) which is utilized in usual practice within Pakistan to confirm the presence of stress related mental disorders such as Depression, Anxiety, Dysthymia, Suicide, Phobia, OCD, Panic Disorder, PTSD, Drug abuse and dependence, Alcohol abuse and dependence, Eating Disorders and Antisocial Personality Disorder to validate the accuracy of the adapted RLCQ. We generated the ROC curves for the adapted RLCQ with suggested cut-offs, and analyzed the sensitivity and specificity of the adapted RLCQ. RESULTS: The area under the receiver operating characteristic curve (ROC) of common mental disorders such as depression and anxiety was 0.64, where sensitivity was 66%, specificity was 56% and the corresponding cut off from the adapted RLCQ was 750. Individuals scoring ≥750 were classified as high stress and vice versa. In contrast, the area under the ROC curve for serious mental disorder and adverse outcomes such as suicide, bipolar and dysthymia was 0.75, where sensitivity was 72% and specificity was 60% at the cut off of 800 on the adapted RLCQ. Individuals scoring ≥800 were classified as high stress and vice versa. The rate of agreement between the two psychologists was 94.32% (Kappa = 0.84). CONCLUSION: The adapted and validated RLCQ characterizes common mental disorders such as depression and anxiety with moderate accuracy and severe mental disorders such as suicide, bipolar and dysthymia with high accuracy. TRIAL REGISTRATION: Clinicaltrials.gov NCT02356263 . Registered January 28, 2015. (Observational Study Only).

Ectopic Expression of Plant RNA Chaperone Offering Multiple Stress Tolerance in E. coli.

Members of the plant glycine-rich RNA-binding proteins (GR-RBPs) family have been reported in flowering, development, circadian rhythms, biotic and abiotic stresses. Particularly, GR-RBPs are reported to function as RNA chaperones, promoting growth and acclimation during cold shock. It is indispensable to further question the efficacy and mechanism of GR-RBPs under various environmental strains. Monitoring the expression of stress-regulated proteins under stress conditions has been a beneficial strategy to study their functional roles. In an effort to elucidate the NtGR-RBP1 function, stress markers such as salinity, drought, low temperature and heat stresses were studied. The NtGR-RBP1 gene was expressed in E. coli followed by the exposure to stress conditions. Recombinant E. coli expressing NtGR-RBP1 were more tolerant to stresses, e.g., salinity, drought, cold and heat shock. Recombinants exhibited higher growth rates compared to control in spot assays. The tolerance was further confirmed by monitoring the growth in liquid culture assays. Cells expressing NtGR-RBP1 under salt (500 mM NaCl), drought (20% PEG), cold (4 and 20 °C) and heat stresses (50 °C) had enhanced growing ability and better endurance. Our study supports the notion that the protective role of NtGR-RBP1 may contribute to growth and survival during diverse environmental stresses.