The receptor-binding domain (RBD) of SARS-CoV-2 spike (S) protein plays a vital role in binding and internalization through the alpha-helix (AH) of human angiotensin-converting enzyme 2 (hACE2). ...Thus, it is a potential target for designing and developing antiviral agents. Inhibition of RBD activity of the S protein may be achieved by blocking RBD interaction with hACE2. In this context, inhibitors with large contact surface area are preferable as they can form a potentially stable complex with RBD of S protein and would not allow RBD to come in contact with hACE2. Peptides represent excellent features as potential anti-RBD agents due to better efficacy, safety, and tolerability in humans compared to that of small molecules. The present study has selected 645 antiviral peptides known to inhibit various viruses and computationally screened them against the RBD of SARS-CoV-2 S protein. In primary screening, 27 out of 645 peptides exhibited higher affinity for the RBD of S protein compared to that of AH of the hACE2 receptor. Subsequently, AVP1795 appeared as the most promising candidate that could inhibit hACE2 recognition by SARS-CoV 2 as was predicted by the molecular dynamics simulation. The critical residues in RBD found for protein-peptide interactions are TYR 489, GLY 485, TYR 505, and GLU 484. Peptide-protein interactions were substantially influenced by hydrogen bonding and hydrophobic interactions. This comprehensive computational screening may provide a guideline to design the most effective peptides targeting the spike protein, which could be studied further in vitro and in vivo for assessing their anti-SARS CoV-2 activity.
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•Antiviral peptides can be a promising therapeutic strategy to inhibit SARS-CoV-2.•645 antiviral peptides were screened against RBD of the spike protein of SARS-CoV-2.•150 ns molecular dynamics simulation has been performed for peptide-protein complexes.•Two promising peptides were found which show significant binding and interactions with RBD of SARS CoV-2.
This study investigated microplastics (MPs) in commercial sea salts from Bangladesh. The presence of MPs in the 18 sea salt bands was 100 %, where the mean MPs abundance was 471.67 MPs/kg, ranging ...between 300 and 670 MPs/kg. The maximum number of MPs in the 300-1500 μm size class was significantly higher than the 1500-3000 μm and 3000-5000 μm size class. The most dominant color was black. Fibers and foams were the dominant shapes. The highest number of MPs was 41 %, obtained from coarse salt grains. Four types of polymers were mainly identified from the analyzed samples: PP, PE, PET, and PA. The mean polymer risk index value among these sea salts was 539 to 1257. The findings of this study can be helpful for consumers, salt industries, and policymakers to be aware of or reduce MP contamination levels in sea salts during production and consumption.
As online group buying (OGB) businesses increasingly face strong competition, understanding the beliefs, attitudes, and behaviors of their customers is critical. Hence, the purpose of this study is ...to understand why customers choose one OGB vendor over others. By extending the transaction cost economics (TCE) theory, we explain OGB customers’ purchase behavior. We conducted a two-stage online survey. The first survey (T
1
) captured the perceptions of the respondents before making a purchase (i.e., purchase intention and its antecedents, namely unpredictability, trust, customizability, and frequency of OGB use
)
. In the second stage (T
2
), we collected responses from the participants of the first study who committed at least one purchase in the last month. The second survey collected responses about the frequency of OGB use, purchase behavior, and online customer review (OCR). Data were analyzed with partial-least-square-based structural equation modelling technique (PLS-SEM). Results suggest that unpredictability, trust, and customizability influence purchase intention and are influenced by the frequency of OGB use. In addition, customizability decreases unpredictability. Finally, in seeking an answer to how to convert potential customers into actual customers, we found that OCR is a moderator of the relationship between purchase intention and purchase behavior. The findings from the longitudinal study extend TCE theory in electronic markets by capturing the OGB dynamics (i.e., antecedents and effects), the mediating effects (i.e., purchase intention) and the moderating effect (i.e., OCR) in a robust nomological relationship.
Coronavirus disease 19 (COVID-19)-caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-has spread rapidly around the world. The global shortage of equipment and health care ...professionals, diagnostic cost, and difficulty in collecting nasopharyngeal swabs (NPSs) necessitate the use of an alternative specimen type for SARS-CoV-2 diagnosis. In this study, we investigated the use of saliva as an alternative specimen type for SARS-CoV-2 detection. Participants presenting COVID-19 symptoms and their contacts were enrolled at the COVID-19 Screening Unit of Dhaka Hospital of the International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), from July to November 2020. Paired NPS and saliva specimens were collected from each participant. Reverse transcription-quantitative PCR (RT-qPCR) was performed to detect SARS-CoV-2. Of the 596 suspected COVID-19-positive participants, 231 (38.7%) were detected as COVID-19 positive by RT-qPCR from at least 1 specimen type. Among the positive cases, 184 (79.6%) patients were identified to be positive for SARS-CoV-2 based on NPS and saliva samples, whereas 45 (19.65%) patients were positive for SARS-CoV-2 based on NPS samples but negative for SARS-CoV-2 based on the saliva samples. Two (0.5%) patients were positive for SARS-CoV-2 based on saliva samples but negative for SARS-CoV-2 based on NPS samples. The sensitivity and specificity of the saliva samples were 80.3% and 99.4%, respectively. SARS-CoV-2 detection was higher in saliva (85.1%) among the patients who visited the clinic after 1 to 5 days of symptom onset. A lower median cycle threshold (
) value indicated a higher SARS-CoV-2 viral load in NPS than that in saliva for target genes among the positive specimens. The study findings suggest that saliva can be used accurately for diagnosis of SARS-CoV-2 early after symptom onset in clinical and community settings.
As the COVID-19 pandemic erupted, the WHO recommended the use of nasopharyngeal or throat swabs for the detection of SARS-CoV-2 etiology of COVID-19. The collection of NPS causes discomfort because of its invasive collection procedure. There are considerable risks to health care workers during the collection of these specimens. Therefore, an alternative, noninvasive, reliable, and self-collected specimen was explored in this study. This study investigated the feasibility and suitability of saliva versus NPS for the detection of SARS-CoV-2. Here, we showed that the sensitivity of saliva specimens was 80.35%, which meets the WHO criteria. Saliva is an easy-to-get, convenient, and low-cost specimen that yields better results if it is collected within the first 5 days of symptom onset. Our study findings suggest that saliva can be used in low-resource countries, community settings, and vulnerable groups, such as children and elderly people.
This study determined the influence of different cooking procedures on the removal of toxic elements (TEs) including arsenic (As), cadmium (Cd), and lead (Pb) along with other nutrient elements from ...different commercially available rice brands sold in Bangladeshi markets. We observed 33%, 35%, and 27% average removal of As, Cd, and Pb accordingly from rice when cooked with a rice to water ratio of 1:6 after washing 5 times. We also found a significant reduction in essential elements: Zn (17%), Cu (10%), Mn (22%), Se (49%), and Mo (22%), when rice cooking was performed as in traditional practice. Daily dietary intakes were found to be between 0.36 and 1.67 µg/kgbw for As, 0.06 and 1.15 µg/kgbw for Cd, and 0.04 and 0.17 µg/kgbw for Pb when rice was cooked by the rice cooker method (rice:water 1:2), while in the traditional method (rice:water 1:6) daily intake rates ranged from 0.23 to 1.3 µg/kgbw for As, 0.04 to 0.88 µg/kgbw for Cd, and 0.03 to 0.15 µg/kgbw for Pb for adults. The HQ and ILCR for As, Cd, and Pb revealed that there is a possibility of noncarcinogenic and carcinogenic risk for As but no appreciable risk for Cd and Pb from consumption of rice.
Background: Rifampicin resistance (RR) is a key indicator of multidrug-resistant tuberculosis (MDR-TB) and 95% of the RR is associated with the mutation in the 81-bp rifampicin resistance determining ...region (RRDR) of the rpoB gene of Mycobacterium tuberculosis complex (MTBC). The Xpert MTB/RIF (Xpert) assay uses five overlapping molecular beacon probes (A-E) complementary to RRDR region that detect MTBC and mutations associated with RR. The objective of the study was to investigate the distribution and frequency of mutations detected by Xpert assay among Beijing and non-Beijing RR-TB isolates. Methods: A total of 205 randomly selected RR-TB specimens detected by Xpert assay were included in this study. A portion of specimens was further subjected to culture, MTBDRplus test and the positive culture isolates were genotyped by spoligotyping. Results: We found that the most frequent mutation occurred at probe E (S531L) binding region in both Beijing and non-Beijing isolates (61.9% and 66.9%, respectively). The Beijing family had higher mutation rates than non-Beijing (19.0% vs 12.4%) at probe B (D516V) while the non-Beijing family had higher mutations at probe D (H526D or H526Y) than the Beijing (13.2% vs 10.7%) family. Mutations at probes A and C were less common in both Beijing and non-Beijing isolates. There was no significant difference (P=0.36) in the occurrence of mutations at different probes between Beijing and non-Beijing isolates. Conclusions: The study results revealed that the most frequent mutation occurs in the region of probe E and the least common mutations at probe A and C among both Beijing and non-Beijing RR-TB cases. This first insight into the probe mutation variation and frequencies among the RR-TB cases in Bangladesh forms the baseline information for further investigation. Keywords: Mycobacterium tuberculosis, rifampicin resistant, GeneXpert, probe mutations, spoligotyping
Although the number of multidrug-resistant (MDR) tuberculosis (TB) cases is high overall, a major gap exists in our understanding of the molecular characteristics and transmission dynamics of the MDR ...Mycobacterium tuberculosis isolates circulating in Bangladesh. The present study aims to characterize the MDR-TB isolates of Bangladesh and to investigate the mode of transmission. A total of 544 MDR-TB isolates were obtained from a nationwide drug-resistant TB surveillance study conducted between October 2011 and March 2017 covering all geographic divisions of Bangladesh. The isolates were characterized using TbD1 deletion analysis, spoligotyping, and mycobacterial interspersed repetitive-unit-variable-number tandem-repeat (MIRU-VNTR) typing. Deletion analysis showed that 440 (80.9%) isolates were the modern type, while the remainder were the ancestral type. The largest circulating lineage was the Beijing type, comprising 208 isolates (38.2%), followed by T, EAI, and LAM with 93 (17.1%), 58 (10.7%), and 52 (9.5%) isolates, respectively. Combined MIRU-VNTR and spoligotyping analysis demonstrated that the majority of the clustered isolates were of the Beijing and T1 lineages. The overall rate of recent transmission was estimated at 33.8%. In conclusion, the MDR M. tuberculosis isolates circulating in Bangladesh are mostly of the modern virulent type. The Beijing and T lineages are the predominant types and most of the transmission of MDR-TB can be attributed to them. The findings also suggest that, along with the remarkable transmission, the emergence of MDR-TB in Bangladesh is largely due to acquired resistance. Rapid and accurate diagnosis and successful treatment will be crucial for controlling MDR-TB in Bangladesh.
Multidrug-resistant TB is considered to be the major threat to tuberculosis control activities worldwide, including in Bangladesh. Despite the fact that the number of MDR-TB cases is high, a major gap exists in our understanding of the molecular epidemiology of the MDR-TB isolates in Bangladesh. In our study, we characterized and classified the MDR-TB isolates circulating in Bangladesh and investigated their mode of transmission. Our results demonstrated that the MDR M. tuberculosis isolates circulating in Bangladesh are mostly of the modern virulent type. The Beijing and T lineages are the predominant types and are implicated in the majority of MDR-TB transmission. Our findings reveal that, along with the remarkable transmission, the emergence of MDR-TB in Bangladesh is largely due to acquired resistance, which may be due to nonadherence to treatment or inadequate treatment of TB patients. Rapid diagnosis and adherence to an appropriate treatment regimen are therefore crucial to controlling MDR-TB in Bangladesh.
Arsenic exposure affects Formula: see text people worldwide, including Formula: see text in Bangladesh. Arsenic exposure increases the risk of cancer and other chronic diseases, and one potential ...mechanism of arsenic toxicity is epigenetic dysregulation.
We assessed associations between arsenic exposure and genome-wide DNA methylation measured at baseline among 396 Bangladeshi adults participating in the Health Effects of Arsenic Longitudinal Study (HEALS) who were exposed by drinking naturally contaminated well water.
Methylation in whole blood DNA was measured at Formula: see text using the Illumina InfiniumMethylationEPIC (EPIC) array. To assess associations between arsenic exposure and CpG methylation, we used linear regression models adjusted for covariates and surrogate variables (SVs) (capturing unknown technical and biologic factors). We attempted replication and conducted a meta-analysis using an independent dataset of Formula: see text from 400 Bangladeshi individuals with arsenical skin lesions.
We identified 34 CpGs associated with Formula: see text creatinine-adjusted urinary arsenic Formula: see text. Sixteen of these CpGs annotated to the Formula: see text array, and 10 associations were replicated (Formula: see text). The top two CpGs annotated upstream of the ABR gene (cg01912040, cg10003262 ). All urinary arsenic-associated CpGs were also associated with arsenic concentration measured in drinking water (Formula: see text). Meta-analysis (Formula: see text samples) identified 221 urinary arsenic-associated CpGs (Formula: see text). The arsenic-associated CpGs from the meta-analysis were enriched in non-CpG islands and shores (Formula: see text) and depleted in promoter regions (Formula: see text). Among the arsenic-associated CpGs (Formula: see text), we observed significant enrichment of genes annotating to the reactive oxygen species pathway, inflammatory response, and tumor necrosis factor Formula: see text (Formula: see text) signaling via nuclear factor kappa-B (Formula: see text) hallmarks (Formula: see text).
The novel and replicable associations between arsenic exposure and DNA methylation at specific CpGs observed in this work suggest that epigenetic alterations should be further investigated as potential mediators in arsenic toxicity and as biomarkers of exposure and effect in exposed populations. https://doi.org/10.1289/EHP3849.
Abstract
The Institute of Epidemiology, Disease Control and Research (IEDCR) conducts active, case-based national antimicrobial resistance (AMR) surveillance in Bangladesh. The Capturing Data on ...Antimicrobial Resistance Patterns and Trends in Use in Regions of Asia (CAPTURA) project accessed aggregated retrospective data from non-IEDCR study sites and 9 IEDCR sites to understand the pattern and extent of AMR and to use analyzed data to guide ongoing and future national AMR surveillance in both public and private laboratories. Record-keeping practices, data completeness, quality control, and antimicrobial susceptibility test practices were investigated in all laboratories participating in case-based IEDCR surveillance and laboratory-based CAPTURA sites. All 9 IEDCR laboratories recorded detailed case-based data (n = 16 816) in electronic format for a priority subset of processed laboratory samples. In contrast, most CAPTURA sites (n = 18/33 54.5%) used handwritten registers to store data. The CAPTURA sites were characterized by fewer recorded variables (such as patient demographics, clinical history, and laboratory findings) with 1 020 197 individual data, less integration of patient records with the laboratory information system, and nonuniform practice of data recording; however, data were collected from all available clinical samples. The analyses conducted on AMR data collected by IEDCR and CAPTURA in Bangladesh provide current data collection status and highlight opportunities to improve ongoing data collection to strengthen current AMR surveillance system initiatives. We recommend a tailored approach to conduct AMR surveillance in high-burden, resource-limited settings.
In this study we collected and explored retrospective antimicrobial resistance data from microbiology laboratories across Bangladesh and compared with those from active case-based surveillance carried out by the national surveillance network to inform policy.
Wetland resource governance is a critical issue in Bangladesh, where the rural communities depend on natural resources and cause over-exploitation of natural resources. Purposive exploitation of ...wetland resources in Bangladesh is a result of the top-down approach. In response to centralized resources management system, community-based co-management emerged mainly to ensure the sustainability of natural resources through benefiting the local communities. Based on our study in Tanguar Haor, a unique wetland ecosystem in the northeastern region of Bangladesh, co-management approach can promote greater participation of the local community in resource management but establishing such governance arrangements take time depending on the potential of community organizations. As the study revealed, the Initiative of establishing co-management is still a challenge in Tanguar Haor, where there is a high dependency on resources given the socio-economic conditions. Also, the ineffectiveness of the existing community organization, largely due to a lack of leadership at the local level, is an obstacle to governing this wetland. Therefore, the findings of this study broadly highlight the necessity for strengthening the community organization through a collaborative process. In line with the commitment of government as well as its realization at the community level, the need for responsible, legitimate and effective roles of the community people including leaders has been further urged towards sustainable management of the wetland resources.
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