Correction: An immunoinformatics and extended molecular dynamics approach for designing a polyvalent vaccine against multiple strains of Human T-lymphotropic virus (HTLV).

[This corrects the article DOI: 10.1371/journal.pone.0287416.].

An immunoinformatics and extended molecular dynamics approach for designing a polyvalent vaccine against multiple strains of Human T-lymphotropic virus (HTLV).

Human T-lymphotropic virus (HTLV), a group of retroviruses belonging to the oncovirus family, has long been associated with various inflammatory and immunosuppressive disorders. At present, there is no approved vaccine capable of effectively combating all the highly pathogenic strains of HTLV that makes this group of viruses a potential threat to human health. To combat the devastating impact of any potential future outbreak caused by this virus group, our study employed a reverse vaccinology approach to design a novel polyvalent vaccine targeting the highly virulent subtypes of HTLV. Moreover, we comprehensively analyzed the molecular interactions between the designed vaccine and corresponding Toll-like receptors (TLRs), providing valuable insights for future research on preventing and managing HTLV-related diseases and any possible outbreaks. The vaccine was designed by focusing on the envelope glycoprotein gp62, a crucial protein involved in the infectious process and immune mechanisms of HTLV inside the human body. Epitope mapping identified T cell and B cell epitopes with low binding energies, ensuring their immunogenicity and safety. Linkers and adjuvants were incorporated to enhance the vaccine's stability, antigenicity, and immunogenicity. Initially, two vaccine constructs were formulated, and among them, vaccine construct-2 exhibited superior solubility and structural stability. Molecular docking analyses also revealed strong binding affinity between the vaccine construct-2 and both targeted TLR2 and TLR4. Molecular dynamics simulations demonstrated enhanced stability, compactness, and consistent hydrogen bonding within TLR-vaccine complexes, suggesting a strong binding affinity. The stability of the complexes was further corroborated by contact, free energy, structure, and MM-PBSA analyses. Consequently, our research proposes a vaccine targeting multiple HTLV subtypes, offering valuable insights into the molecular interactions between the vaccine and TLRs. These findings should contribute to developing effective preventive and treatment approaches against HTLV-related diseases and preventing possible outbreaks. However, future research should focus on in-depth validation through experimental studies to confirm the interactions identified in silico and to evaluate the vaccine's efficacy in relevant animal models and, eventually, in clinical trials.

Risk factors and actionable molecular signatures in COVID-19-associated lung adenocarcinoma and lung squamous cell carcinoma patients.

The molecular mechanism of the pathological impact of COVID-19 in lung cancer patients remains poorly understood to date. In this study, we used differential gene expression pattern analysis to try to figure out the possible disease mechanism of COVID-19 and its associated risk factors in patients with the two most common types of non-small-cell lung cancer, namely, lung adenocarcinoma and lung squamous cell carcinoma. We also used network-based approaches to identify potential diagnostic and molecular targets for COVID-19-infected lung cancer patients. Our study showed that lung cancer and COVID-19 patients share 36 genes that are expressed differently and in common. Most of these genes are expressed in lung tissues and are mostly involved in the pathogenesis of different respiratory tract diseases. Additionally, we also found that COVID-19 may affect the expression of several cancer-associated genes in lung cancer patients, such as the oncogenes JUN, TNC, and POU2AF1. Moreover, our findings suggest that COVID-19 may predispose lung cancer patients to other diseases like acute liver failure and respiratory distress syndrome. Additionally, our findings, in concert with published literature, suggest that molecular signatures, such as hsa-mir-93-5p, CCNB2, IRF1, CD163, and different immune cell-based approaches could help both diagnose and treat this group of patients. Altogether, the scientific findings of this study will help formulate appropriate management measures and guide the development of diagnostic and therapeutic measures for COVID-19-infected lung cancer patients.

Evaluation of growth and some unexplored bioactivities of bioreactor grown adventitious root culture of ginseng (Panax ginseng C.A. Meyer).

The purpose of the present study was to evaluate the growth potential and some rarely reported bioactivities (antioxidant, thrombolytic, anticoagulant, and anthelmintic) of Panax ginseng C.A. Meyer adventitious roots. To demonstrate the growth, shake flask and laboratory-scale bioreactor cultures have been employed. The obtained biomass was dried and extracted with water, ethanol, and methanol. The growth ratio (12.62 ± 1.03) observed in the bioreactor was significantly higher than in the shake flask culture. The presence of 10 different phytochemical classes, including carbohydrates, saponins, glycosides, and terpenoids were detected in qualitative estimation. Significant quantities of phenolics, flavonoids, proteins, and tannins were determined. Dose-dependent antioxidant activities were observed, and the IC50 values of methanolic and ethanolic extracts were very similar to the standard. The highest (29.26 ± 5.31%) thrombolytic potential was shown by the methanolic extract. The ethanolic extract significantly extended the coagulation times up to 2.5 fold. The highest anthelmintic properties in terms of paralyzing (2.21 ± 0.31 min) and killing (3.69 ± 0.41 min) of the parasitic worms were displayed by the aqueous extract. The in vitro root growth implies the commercial feasibility of ginseng production in Bangladesh and the demonstration of potential bioactivities strengthens medicinal implications and also offering new research areas.

Influence on attitudes and lifestyle due to lockdown amidst COVID-19 pandemic: a perception-based analysis among Bangladeshi residents.

BACKGROUND: Countrywide lockdown or stay-at-home order has been implemented to slow down the transmission of emergent coronavirus. However, the influence on attitudes and lifestyle due to lockdown amidst the coronavirus disease 2019 (COVID-19) pandemic has been poorly understood. The present study aimed to investigate the influence on attitudes and lifestyle due to lockdown amidst the COVID-19 pandemic among Bangladeshi residents. METHODS: A cross-sectional survey carried out involving 1635 community dwellers across eight divisions in Bangladesh conducted from April 15, 2020 to May 10, 2020. A structured questionnaire incorporating socio-demographic, attitudes towards lockdown and adverse lifestyle amidst lockdown measures was employed to collect data using the Google Forms. Multiple regression analyses were executed to determine the associated factors of positive attitudes towards lockdown and adverse lifestyle. RESULTS: The mean scores of attitudes towards lockdown were 67.9 (SD = 8.4) out of 85 with an overall correct rate (positive attitudes) of 79.9%; whereas the mean scores of adverse lifestyle amidst lockdown were 16.1 (SD = 4.8) out of 34 with an overall rate of 47.4%. The factors associated with more positive attitudes towards lockdown included being female, divorced, higher educated, and students. Conversely, being male, having no formal education, and rural residence were associated factors of adverse lifestyle amidst the COVID-19 pandemic. CONCLUSIONS: The findings reflect how the COVID-19 lockdown has preciously impacted the attitudes, and lifestyle of Bangladeshi citizens, which will contribute to promoting appropriate measures during a subsequent zonal or complete lockdown.

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.

ESBL Producing Escherichia coli in Faecal Sludge Treatment Plants: An Invisible Threat to Public Health in Rohingya Camps, Cox's Bazar, Bangladesh.

Introduction: Human faecal sludge contains diverse harmful microorganisms, making it hazardous to the environment and public health if it is discharged untreated. Faecal sludge is one of the major sources of E. coli that can produce extended-spectrum ß-lactamases (ESBLs). Objective: This study aimed to investigate the prevalence and molecular characterization of ESBL-producing E. coli in faecal sludge samples collected from faecal sludge treatment plants (FSTPs) in Rohingya camps, Bangladesh. Methods: ESBL producing E. coli were screened by cultural as well as molecular methods and further characterized for their major ESBL genes, plasmid profiles, pathotypes, antibiotic resistance patterns, conjugation ability, and genetic similarity. Results: Of 296 isolates, 180 were phenotypically positive for ESBL. All the isolates, except one, contained at least one ESBL gene that was tested (blaCTX-M-1, blaCTX-M-2, blaCTX-M-8, blaCTX-M-9, blaCTX-M-15, blaCTX-M-25, blaTEM , and blaSHV ). From plasmid profiling, it was observed that plasmids of 1-211 MDa were found in 84% (151/180) of the isolates. Besides, 13% (24/180) of the isolates possessed diarrhoeagenic virulence genes. From the remaining isolates, around 51% (79/156) harbored at least one virulence gene that is associated with the extraintestinal pathogenicity of E. coli. Moreover, 4% (3/156) of the isolates were detected to be potential extraintestinal pathogenic E. coli (ExPEC) strains. Additionally, all the diarrhoeagenic and ExPEC strains showed resistance to three or more antibiotic groups which indicate their multidrug-resistant potential. ERIC-PCR differentiated these pathogenic isolates into seven clusters. In addition to this, 16 out of 35 tested isolates transferred plasmids of 32-112 MDa to E. coli J53 recipient strain. Conclusion: The present study implies that the faecal sludge samples examined here could be a potential origin for spreading MDR pathogenic ESBL-producing E. coli. The exposure of Rohingya individuals, living in overcrowded camps, to these organisms poses a severe threat to their health.

A comprehensive in silico exploration of pharmacological properties, bioactivities and COX-2 inhibitory potential of eleutheroside B from Eleutherococcus senticosus (Rupr. & Maxim.) Maxim.

Eleutherococcus senticosus (Rupr. & Maxim.) Maxim., popularly known as 'Siberian ginseng', is an important medicinal plant. Pharmacologically active compounds of this plant are called eleutherosides and among them, eleutheroside B is the most prevalent. The E. senticosus has been reported to have many medicinal properties however; very few studies are reported to understand the medicinal properties of eleutheroside B. Consequently, in the present study various computational tools have been used to predict the drug-likeness, bioactivities, and pharmacokinetic properties of eleutheroside B. Besides, the inhibitory potential of eleutheroside B has been investigated against cyclooxygenase 2 (COX-2) enzyme. This study suggests that eleutheroside B is a drug-like compound with bioactivity score (-0.08 to 0.38), having satisfactory pharmacokinetic values. Metabolism and toxicities were further studied using FAME3, GLORY, pred-hERG and Endocrine Disruptome tools. No severe toxicities (Ames, hepatotoxicity, cardiotoxicity, skin sensitization) were predicted. Rat acute toxicity, ecotoxicity and cell line cytotoxicity were evaluated based on GUSAR and CLC-pred. The compound has been predicted as non-toxic (class 5), non-hERG inhibitor and less likely to cause adverse drug interactions. Molecular docking against COX-2 enzyme revealed strong hydrogen bonds (SER530, TYR355, LEU352, SER353, VAL349, TYR385, MET522) and hydrophobic interaction (LEU352) with eleutheroside B. The docking score (-6.97 kcal/mol) suggested that this molecule can be utilized as an anti-inflammatory agent as well as a potential anticancer drug in the future. Hence, this is a comprehensive integrated in silico approach to establish the anti-inflammatory mechanism of eleutheroside B in the background of its potential in future drug development.Communicated by Ramaswamy H. Sarma.

A comprehensive multi-directional exploration of phytochemicals and bioactivities of flower extracts from Delonix regia (Bojer ex Hook.) Raf., Cassia fistula L. and Lagerstroemia speciosa L.

Delonix regia (Bojer ex Hook.) Raf., Cassia fistula L. and Lagerstroemia speciosa L. are three ornamental plants that produce colorful flowers. The present study aimed to evaluate the phytochemicals and bioactivities of methanolic extracts of flowers from Delonix regia (DrFME), Cassia fistula (CfFME), and Lagerstroemia speciosa (LsFME). The presence of ten different chemical classes in varying degrees was confirmed while qualitatively screened. During quantitative determination, LsFME possesses the highest amount of total phenolic (418.0 mg/g), flavonoid (50.8 mg/g), and tannin (256.3 mg/g) contents. The extracts showed excellent antioxidant capacity in a concentration-dependent manner with the lowest IC50 value (41.51 µg/mL) displayed by LsFME. LsFME paralyzed the experimental worms at 2.95 min and killed at 3.96 min. DrFME was found to be more effective in thrombolytic (35.5% clot lysis) and anticoagulant activities. Negligible hemolytic activity (IC50 > 200 µg/mL) found for all extracts which suggest their less potential toxicity. The in vivo experiments revealed that the CfFME has the highest analgesic (64.34% pain inhibition) activity while LsFME has the highest antidiarrheal (70.27% inhibition) and antihyperglycemic (46.94% inhibition) activities at 400 mg/kg of body weight doses. This study has shown the presence of phytochemicals and potential bioactivities which indicates the possibility of these flowers to be used as a source of phytochemicals as well as safe and effective natural medicine.

Structure to function analysis with antigenic characterization of a hypothetical protein,HPAG1_0576 from Helicobacter pylori HPAG1.

Helicobacter pylori, a unique gastric pathogen causing chronic inflammation in the gastric mucosa with a possibility to develop gastric cancer has one-third of its proteins still uncharacterized. In this study, a hypothetical protein (HP) namely HPAG1_0576 from H. pylori HPAG1 was chosen for detailed computational analysis of its structural, functional and epitopic properties. The primary, secondary and 3D structure/model of the selected HP was constructed. Then refinement and structure validation were done, which indicated a good quality of the newly constructed model. ProFunc and STRING suggested that HPAG1_0576 shares 98% identity with a carcinogenic factor, TNF-α inducing protein (Tip-α ) of H. pylori. IEDB immunoinformatics tool predicted VLMLQACTCPNTSQRNS from position 19-35 as most potential B-cell linear epitope and SFLKSKQL from position 5-12 as most potent conformational epitope. Alternatively, FALVRARGF and FLCGLGVLM were predicted as most immunogenic CD8+ and CD4+ T-cell epitopes respectively. At the same time findings of IFN epitope tool suggests that, HPAG1_0576 had a great potential to evoke interferon-gamma (IFN-γ) mediated immune response. However, this experiment is a primary approach for in silico vaccine designing from a HP, findings of this study will provide significant insights in further investigations and will assist in identifying new drug targets/vaccine candidates.

Overexpression of the alfalfa DnaJ-like protein (MsDJLP) gene enhances tolerance to chilling and heat stresses in transgenic tobacco plants.

Heat shock proteins (HSPs) are generally considered as important molecular chaperones; they are known to perform critical functions in plant development and abiotic stress response processes. In this study, we examined the role of a HSP, the Medicago sativa DnaJ-like protein (MsDJLP), in alfalfa and its potential application for the development of abiotic stress tolerance in plants. We found that expression of the MsDJLP gene was induced by chilling (4 °C) and heat (42 °C), but not by cadmium (500 µM) or arsenic (500 µM) stresses. We then cloned the MsDJLP gene downstream of the strong constitutive CaMV 35S promoter and transformed it into tobacco plants. Ectopic expression of MsDJLP conferred enhanced tolerance to both chilling and heat stresses in transgenic tobacco plants. Under chilling stress, the transgenic tobacco plants showed lower H2O2 accumulation and electrolyte leakage (EL) activity, and better photosystem II efficiency than wild-type (WT) plants, indicating that photoinhibition was less severe in transgenic compared to WT plants. Following heat treatment, the transgenic plants showed better relative chlorophyll and water contents, and lower malondialdehyde accumulation than WT plants. Our study provides evidence for a pivotal role of MsDJLP for chilling and heat stress tolerance in transgenic tobacco plants.

Pilot-scale culture of somatic embryos of Eleutherococcus senticosus in airlift bioreactors for the production of eleutherosides.

PURPOSE OF WORK: To establish pilot scale bioreactor cultures of somatic embryos of Siberian ginseng for the production of biomass and eleutherosides. Somatic embryos of Eleutherococcus senticosus were cultured in airlift bioreactors using Murashige and Skoog medium with 30 g sucrose l(-1) for the production of biomass and eleutherosides. Various parameters including the type of bioreactor, aeration volume, and inoculum density were optimized for 3 l capacity bioreactors. Balloon-type airlift bioreactors, utilizing a variable aeration volume of 0.1-0.3 vvm and an inoculum of 5 g l(-1), were suitable for biomass and eleutheroside production. In 500 l balloon-type airlift bioreactors, 11.3 g dry biomass l(-1), 220 µg eleutheroside B l(-1), 413 µg eleutheroside E l(-1), and 262 µg eleutheroside E1 l(-1) were produced.

Ubiquitin promoter-terminator cassette promotes genetically stable expression of the taste-modifying protein miraculin in transgenic lettuce.

Lettuce is a commercially important leafy vegetable that is cultivated worldwide, and it is also a target crop for plant factories. In this study, lettuce was selected as an alternative platform for recombinant miraculin production because of its fast growth, agronomic value, and wide availability. The taste-modifying protein miraculin is a glycoprotein extracted from the red berries of the West African native shrub Richadella dulcifica. Because of its limited natural availability, many attempts have been made to produce this protein in suitable alternative hosts. We produced transgenic lettuce with miraculin gene driven either by the ubiquitin promoter/terminator cassette from lettuce or a 35S promoter/nos terminator cassette. Miraculin gene expression and miraculin accumulation in both cassettes were compared by quantitative real-time PCR analysis, Western blotting, and enzyme-linked immunosorbent assay. The expression level of the miraculin gene and protein in transgenic lettuce was higher and more genetically stable in the ubiquitin promoter/terminator cassette than in the 35S promoter/nos terminator cassette. These results demonstrated that the ubiquitin promoter/terminator cassette is an efficient platform for the genetically stable expression of the miraculin protein in lettuce and hence this platform is of benefit for recombinant miraculin production on a commercial scale.

Methyl jasmonate induced overproduction of eleutherosides in somatic embryos of Eleutherococcus senticosus cultured in bioreactors

This study was concentrated on the production of eleutherosides and chlorogenic acid in embryogenic suspension cultures of Eleutherococcus senticosus by exposing them to different concentrations (50-400 µM) of methyl jasmonate (MJ) during the culture period. In the bioreactor cultures, eleutheroside content increased significantly by elicitation of MJ, however, the fresh weight, dry weight and growth ratio of embryos was strongly inhibited by increasing MJ concentrations. The highest total eleutheroside (7.3 fold increment) and chlorogenic acid (3.9 fold increment) yield was obtained with 200 µM MJ treatment. There was 1.4, 3.4 and 14.9 fold increase in the eleutheroside B, E, and E1 production respectively with such elicitation treatment. These results suggest that MJ elicitation is beneficial for eleutheroside accumulation in the embryogenic cell suspension cultures.