Showing papers by "Jessore University of Science & Technology published in 2020"

Genome-wide analysis of SARS-CoV-2 virus strains circulating worldwide implicates heterogeneity.

Abstract: Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), a novel evolutionary divergent RNA virus, is responsible for the present devastating COVID-19 pandemic To explore the genomic signatures, we comprehensively analyzed 2,492 complete and/or near-complete genome sequences of SARS-CoV-2 strains reported from across the globe to the GISAID database up to 30 March 2020 Genome-wide annotations revealed 1,516 nucleotide-level variations at different positions throughout the entire genome of SARS-CoV-2 Moreover, nucleotide (nt) deletion analysis found twelve deletion sites throughout the genome other than previously reported deletions at coding sequence of the ORF8 (open reading frame), spike, and ORF7a proteins, specifically in polyprotein ORF1ab (n = 9), ORF10 (n = 1), and 3´-UTR (n = 2) Evidence from the systematic gene-level mutational and protein profile analyses revealed a large number of amino acid (aa) substitutions (n = 744), demonstrating the viral proteins heterogeneous Notably, residues of receptor-binding domain (RBD) showing crucial interactions with angiotensin-converting enzyme 2 (ACE2) and cross-reacting neutralizing antibody were found to be conserved among the analyzed virus strains, except for replacement of lysine with arginine at 378th position of the cryptic epitope of a Shanghai isolate, hCoV-19/Shanghai/SH0007/2020 (EPI_ISL_416320) Furthermore, our results of the preliminary epidemiological data on SARS-CoV-2 infections revealed that frequency of aa mutations were relatively higher in the SARS-CoV-2 genome sequences of Europe (4307%) followed by Asia (3809%), and North America (2964%) while case fatality rates remained higher in the European temperate countries, such as Italy, Spain, Netherlands, France, England and Belgium Thus, the present method of genome annotation employed at this early pandemic stage could be a promising tool for monitoring and tracking the continuously evolving pandemic situation, the associated genetic variants, and their implications for the development of effective control and prophylaxis strategies

Ligand based sustainable composite material for sensitive nickel(II) capturing in aqueous media

Abstract: Organic ligand based sustainable composite material was prepared for the detection and removal of nickel (Ni(II)) ion from contaminated water. The ligand was anchored based on the building-block approach. The carrier silica and ligand embedded composite material were characterized systematically. The detection and removal of Ni(II) ion operation was evaluated according to the solution pH, reaction time, detection limit, initial Ni(II) concentration and diverse co-existing metal ions. The detection limit of Ni(II) ion by the proposed composite material was 0.41 μg L−1. The detection and removal of Ni(II) ion was significantly influenced by the solution pH. However, the neutral pH 7.0 was chosen for sensitive and selective detection and removal of Ni(II) ion. The co-existing diverse metal ions were not interfered during the detection and removal of Ni(II) ion because of the high affinity of Ni(II) ion to composite material at the optimum experimental conditions. The Langmuir adsorption isotherm model was selected based on the materials morphology and applied to validate the adsorption isotherms according to the homogeneous ordered frameworks. The adsorption capacity was 199.19 mg g−1 as expected due to the high surface area of material. The adsorbed Ni(II) ion was completely eluted from the composite material with the eluent of 0.50 M HCl and the regenerated material was used in several cycles without deterioration in its initial performances. Therefore, it is expected to that the Facile composite material may hold huge potentials in applications and may be scaled up for commercial applications, including environmental detection and removal of Ni(II) ion.

Knowledge, attitudes, and fear of COVID-19 during the Rapid Rise Period in Bangladesh

Abstract: The study aims to determine the level of Knowledge, Attitude, and Practice (KAP) related to COVID-19 preventive health habits and perception of fear towards COVID-19 in subjects living in Bangladesh. Design: Prospective, cross-sectional survey of (n = 2157) male and female subjects, 13–88 years of age, living in Bangladesh. Methods: Ethical approval and trial registration were obtained before the commencement of the study. Subjects who volunteered to participate and signed the informed consent were enrolled in the study and completed the structured questionnaire on KAP and Fear of COVID-19 scale (FCV-19S). Results: Twenty-eight percent (28.69%) of subjects reported one or more COVID-19 symptoms, and 21.4% of subjects reported one or more co-morbidities. Knowledge scores were slightly higher in males (8.75± 1.58) than females (8.66± 1.70). Knowledge was significantly correlated with age (p < .005), an education level (p < .001), attitude (p < .001), and urban location (p < .001). Knowledge scores showed an inverse correlation with fear scores (p < .001). Eighty-three percent (83.7%) of subjects with COVID-19 symptoms reported wearing a mask in public, and 75.4% of subjects reported staying away from crowded places. Subjects with one or more symptoms reported higher fear compared to subjects without (18.73± 4.6; 18.45± 5.1). Conclusion: Bangladeshis reported a high prevalence of self-isolation, positive preventive health behaviors related to COVID-19, and moderate to high fear levels. Higher knowledge and Practice were found in males, higher education levels, older age, and urban location. Fear of COVID-19 was more prevalent in female and elderly subjects. A positive attitude was reported for the majority of subjects, reflecting the belief that COVID-19 was controllable and containable.

Epitope-based chimeric peptide vaccine design against S, M and e proteins of SARS-CoV-2, the etiologic agent of COVID-19 pandemic: An in silico approach

Abstract: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the etiologic agent of the ongoing pandemic of coronavirus disease 2019 (COVID-19), a public health emergency of international concerns declared by the World Health Organization (WHO). An immuno-informatics approach along with comparative genomics was applied to design a multi-epitope-based peptide vaccine against SARS-CoV-2 combining the antigenic epitopes of the S, M, and E proteins. The tertiary structure was predicted, refined and validated using advanced bioinformatics tools. The candidate vaccine showed an average of ≥90.0% world population coverage for different ethnic groups. Molecular docking and dynamics simulation of the chimeric vaccine with the immune receptors (TLR3 and TLR4) predicted efficient binding. Immune simulation predicted significant primary immune response with increased IgM and secondary immune response with high levels of both IgG1 and IgG2. It also increased the proliferation of T-helper cells and cytotoxic T-cells along with the increased IFN-γ and IL-2 cytokines. The codon optimization and mRNA secondary structure prediction revealed that the chimera is suitable for high-level expression and cloning. Overall, the constructed recombinant chimeric vaccine candidate demonstrated significant potential and can be considered for clinical validation to fight against this global threat, COVID-19.

Designing a multi-epitope vaccine against SARS-CoV-2: an immunoinformatics approach.

Abstract: Ongoing COVID-19 outbreak has raised a drastic challenge to global public health security. Most of the patients with COVID-19 suffer from mild flu-like illnesses such as cold and fever; however, fe...

Knowledge, Attitudes, and Fear of COVID-19 during the Rapid Rise Period in Bangladesh

Abstract: Objectives To determine the level of Knowledge, Attitude, and Practice (KAP) related to COVID-19 preventive health habits and perception of Fear towards COVID-19 in subjects living in Bangladesh Design Prospective, cross-sectional survey of (n= 2157) male and female subjects, 13-90 years of age, living in Bangladesh Methods Ethical Approval and Trial registration were obtained prior to the commencement of the study Subjects who volunteered to participate and signed the informed consent were enrolled in the study and completed the “Fear of COVID-19 Scale” (FCS) Results Twenty-eight percent (2869%) of subjects reported one or more COVID-19 symptoms and 214% of subjects reported one or more comorbidities Knowledge scores were slightly higher in males (875± 158) than females (866± 170) Knowledge was significantly correlated with age (p Conclusions Overall, Bangladeshis reported a high prevalence of self-isolation, positive preventive health behaviors related to COVID-19, and moderate to high fear levels Higher Knowledge and Practice were found in males, higher education levels, older age, and urban location “Fear” of COVID-19 was more prevalent in female and elderly subjects Positive “Attitude” was reported for the majority of subjects, reflecting the belief that COVID-19 was controllable and containable Ethical approval Ethical permission obtained from the Institutional review board (BPA-IPRR/IRB/29/03/2020/021) of Institute of Physiotherapy, Rehabilitation, and Research (IPRR), the academic organization of the Bangladesh Physiotherapy Association WHO Trial registry The trial registration obtained prospectively from a primary trial registry of WHO (CTRI/2020/04/024413) Data Availability The data are available regarding this study and can be viewed upon request

Human health risk assessment of elevated and variable iron and manganese intake with arsenic-safe groundwater in Jashore, Bangladesh.

Abstract: Groundwater through hand-operated tubewell (a type of water well) tapping is the main source of drinking water in Bangladesh. This study investigated iron and manganese concentration in groundwater across Jashore district-one of the worst arsenic contaminated area in Bangladesh. One working tubewell that had been tested previously for arsenic and marked safe (green) was selected from each unions of the district. Results revealed that approximately 73% and 87% of groundwater samples exceeded the limits for iron and manganese in Bangladesh drinking water, respectively. Additionally, spatial distribution of iron and manganese indicate that only 5% of the total surface area of groundwater is covered by safe level of iron and manganese. Human health risk due to ingestion of iron and manganese through drinking water was evaluated using hazard quotients (HQ) for adults and children. The result of the health risk assessment revealed that the non-carcinogenic health risks due to ingestion of iron (HQ up to 1.446 for adults and 0.590 for children) and manganese (HQ up to 2.459 for adults and 1.004 for children) contaminated groundwater are much higher among adults than children. On the basis of occurrences, spatial distribution and health risk assessment results, the area can be categorized as a high-risk zone for iron and manganese-related problems and needs special attention in order to protect public health of local residents.

Ultrathin Assembles of Porous Array for Enhanced H 2 Evolution.

Abstract: Since the complexity of photocatalyst synthesis process and high cost of noble cocatalyst leftovers a major hurdle to producing hydrogen (H2) from water, a noble metal-free Ni-Si/MgO photocatalyst was realized for the first time to generate H2 effectively under illumination with visible light. The catalyst was produced by means of simple one-pot solid reaction using self-designed metal reactor. The physiochemical properties of photocatalyst were identified by XRD, FESEM, HRTEM, EDX, UV-visible, XPS, GC and PL. The photocatalytic activities of Ni-Si/MgO photocatalyst at different nickel concentrations were evaluated without adjusting pH, applied voltage, sacrificial agent or electron donor. The ultrathin-nanosheet with hierarchically porous structure of catalyst was found to exhibit higher photocatalytic H2 production than hexagonal nanorods structured catalyst, which suggests that the randomly branched nanosheets are more active surface to increase the light-harvesting efficiency due to its short electron diffusion path. The catalyst exhibited remarkable performance reaching up to 714 µmolh-1 which is higher among the predominant semiconductor catalyst. The results demonstrated that the photocatalytic reaction irradiated under visible light illumination through the production of hydrogen and hydroxyl radicals on metals. The outcome indicates an important step forward one-pot facile approach to prepare noble ultrathin photocatalyst for hydrogen production from water.

Plasmonic Temperature Sensor Using D-shaped Photonic Crystal Fiber

Abstract: Simple structure and high sensitivity with a broad detection range are highly desirable for temperature sensor. This work presents a highly sensitive plasmonic sensor based on D-shaped photonic crystal fiber (PCF) in the near infrared region (900-1900 nm) for temperature measurement. The proposed sensor is designed by finite element method (FEM) based simulation tool and sensing properties are investigated by means of wavelength interrogation method (WIM). To support the surface plasmon oscillation, 45 nm gold film is deposited on the flat portion of the D-shaped PCF which consists of pure silica. Benzene is used as the temperature sensitive material that offers large propagation loss (PL) peak shift. Simulation outcome shows that the maximum possible sensitivity of 110 nm/°C in the temperature range from 10 °C to 70 °C. To our knowledge, the achieved sensitivity is the highest for temperature sensing in the existing literature. In addition, the proposed sensor exhibits the maximum figure of merit (FOM) of 5.5 /°C, resolution of 9.09 × 10–4 °C, and excellent fitting characteristics of PL peak wavelengths. Moreover, low PL of the proposed sensor helps to extend the sensor length up to few centimeters. Such excellent results and wider temperature range make sure that the proposed sensor can be an appropriate choice for temperature measurement even in the remote sensing application.

Formulation of a Hybrid Nanofertilizer for Slow and Sustainable Release of Micronutrients.

Abstract: In this work, we have proposed a new formulation of a hybrid nanofertilizer (HNF) for slow and sustainable release of nutrients into soil and water. Urea-modified hydroxyapatite was synthesized, wh...

Greener and sustainable production of bioethylene from bioethanol: current status, opportunities and perspectives

Abstract: Abstract The economic value of bioethylene produced from bioethanol dehydration is remarkable due to its extensive usage in the petrochemical industry. Bioethylene is produced through several routes, such as steam cracking of hydrocarbons from fossil fuel and dehydration of bioethanol, which can be produced through fermentation processes using renewable substrates such as glucose and starch. The rise in oil prices, environmental issues due to toxic emissions caused by the combustion of fossil fuel and depletion of fossil fuel resources have led a demand for an alternative pathway to produce green ethylene. One of the abundant alternative renewable sources for bioethanol production is biomass. Bioethanol produced from biomass is alleged to be a competitive alternative to bioethylene production as it is environmentally friendly and economical. In recent years, many studies have investigated catalysts and new reaction engineering pathways to enhance the bioethylene yield and to lower reaction temperature to drive the technology toward economic feasibility and practicality. This paper critically reviews bioethylene production from bioethanol in the presence of different catalysts, reaction conditions and reactor technologies to achieve a higher yield and selectivity of ethylene. Techno-economic and environmental assessments are performed to further development and commercialization. Finally, key issues and perspectives that require utmost attention to facilitate global penetration of technology are highlighted.

Graphene-Coated Optical Fiber SPR Biosensor for BRCA1 and BRCA2 Breast Cancer Biomarker Detection: a Numerical Design-Based Analysis

Abstract: This paper provides a simple hybrid design and numerical analysis of the graphene-coated fiber-optic surface plasmon resonance (SPR) biosensor for breast cancer gene-1 early onset (BRCA1) and breast cancer gene-2 early onset (BRCA2) genetic breast cancer detection. Two specific mutations named 916delTT and 6174delT in the BRCA1 and BRCA2 are selected for numerical detection of breast cancer. This sensor is based on the technique of the attenuated total reflection (ATR) method to detect deoxyribonucleic acid (DNA) hybridization along with individual point mutations in BRCA1 and BRCA2 genes. We have numerically shown that momentous changes present in the SPR angle (minimum: 135% more) and surface resonance frequency (SRF) (minimum: 136% more) for probe DNA with various concentrations of target DNA corresponding to a mutation of the BRCA1 and BRCA2 genes. The variation of the SPR angle and SRF for mismatched DNA strands is quite negligible, whereas that for complementary DNA strands is considerable, which is essential for proper detection of genetic biomarkers (916delTT and 6174delT) for early breast cancer. At last, the effect of electric field distribution in inserting graphene layer is analyzed incorporating the finite difference time domain (FDTD) technique by using Lumerical FDTD solution commercial software. To the best of our knowledge, this is the first demonstration of such a highly efficient biosensor for detecting BRCA1 and BRCA2 breast cancer. Therefore, the proposed biosensor opens a new window toward the detection of breast cancers.

Biocompatible Ionic Liquid Surfactant-Based Microemulsion as a Potential Carrier for Sparingly Soluble Drugs

Abstract: Developing a universal drug delivery vehicle of sparingly soluble drugs remains a challenge, with surface-active ionic liquid (SAIL)-based ionic liquid-in-oil (IL/O) microemulsions (MEs) being the ...

Inhibitory effects of probiotic potential lactic acid bacteria isolated from kimchi against Listeria monocytogenes biofilm on lettuce, stainless-steel surfaces, and MBEC™ biofilm device

Abstract: Probiotics show great promise as alternative and environmentally friendly candidates to control microbial pathogens. Here, six isolated lactic acid bacteria (LAB) were chosen based on their anti-listerial activity. Anti-listerial LAB isolates were identified by 16S rRNA gene sequencing. The anti-listerial activities of these isolates were evaluated by Listeria monocytogenes biofilm inhibition assays on stainless-steel coupons (SS), lettuce, and a minimum biofilm eradication concentration (MBEC™) biofilm device. Results revealed that following co-culture with LAB for 24 h, L. monocytogenes biofilm cells were inhibited by up to 2.17 log CFU/cm2, 1.62 log CFU/cm2, and 1.09 log CFU/peg on SS, lettuce, and MBEC™, respectively. Although these LAB bacteria suppressed L. monocytogenes biofilm formation on both surfaces, the inhibitory effect on lettuce surfaces was lower than that on SS. These results support the potential use of LAB strains to inhibit biofilm formation by pathogenic bacteria on vegetable products and in the food industry, without associated risk to consumers.

Insights Into the Resistome of Bovine Clinical Mastitis Microbiome, a Key Factor in Disease Complication

Abstract: Bovine clinical mastitis (CM) is one of the most prevalent diseases caused by a wide range of resident microbes. The emergence of antimicrobial resistance in CM bacteria is well-known, however, the genomic resistance composition (the resistome) at the microbiome-level is not well characterized. In this study, we applied whole metagenome sequencing (WMS) to characterize the resistome of the CM microbiome, focusing on antibiotics and metals resistance, biofilm formation (BF), and quorum sensing (QS) along with in vitro resistance assays of six selected pathogens isolated from the same CM samples. The WMS generated an average of 21.13 million reads (post-processing) from 25 CM samples that mapped to 519 bacterial strains, of which 30.06% were previously unreported. We found a significant (P = 0.001) association between the resistomes and microbiome composition with no association with cattle breed, despite significant differences in microbiome diversity among breeds. The in vitro investigation determined that 76.2% of six selected pathogens considered "biofilm formers" actually formed biofilms and were also highly resistant to tetracycline, doxycycline, nalidixic acid, ampicillin, and chloramphenicol and remained sensitive to metals (Cr, Co, Ni, Cu, Zn) at varying concentrations. We also found bacterial flagellar movement and chemotaxis, regulation and cell signaling, and oxidative stress to be significantly associated with the pathophysiology of CM. Thus, identifying CM microbiomes, and analyzing their resistomes and genomic potentials will help improve the optimization of therapeutic schemes involving antibiotics and/or metals usage in the prevention and control of bovine CM.

Impacts of energy decentralization viewed through the lens of the energy cultures framework: Solar home systems in the developing economies

Abstract: A large and growing body of literature has investigated diverse impacts of solar power technologies, in particular, solar home systems (SHS) in the developing economies. These studies evaluated either the social or economic impacts of solar photovoltaic (PV) technology adoption, often both, as a socio-economic analysis. A few other studies investigated the environmental impacts only. On the other hand, some studies considered the drivers and barriers of this technology adoption. However, studies considering all these factors – impacts, drivers, barriers – together to derive an overall picture of solar electricity deployment as a part of energy decentralization rarely occur in the literature. This study has taken into account this gap in the literature and tried to analyze all the factors together through the lens of the energy cultures framework (ECF) and provide insights into the interplay that exists between these factors. The ECF revealed that the drivers of SHS adoption are dominated by the ‘cognitive norms’ of the adopters. In contrast, the significant barriers belong to the ‘material culture’ of the people. This study further indicates the policy implications of energy decentralization. These findings might be a useful source of information for energy policymakers towards formulating a sustainable national electricity generation plan for developing economies to meet the United Nations sustainable development goals.

Combination of QSAR, molecular docking, molecular dynamic simulation and MM-PBSA: analogues of lopinavir and favipiravir as potential drug candidates against COVID-19.

Abstract: Pandemic COVID-19 infections have spread throughout the world. There is no effective treatment against this disease. Viral RNA-dependent RNA polymerase (RdRp) catalyzes the replication of RNA from ...

Highly sensitive photonic crystal fiber salinity sensor based on Sagnac interferometer

Abstract: For a sensor, high sensitivity, structural simplicity, and longevity are highly desired for measurement of salinity in seawater. This work proposed an ultrahigh sensitive photonic crystal fiber (PCF) salinity sensor based on the sagnac interferometer (SI). The propagation characteristics of the proposed PCF are analyzed by the finite element method (FEM). The achieved sensitivity reaches up to 37,500 nm/RIU and 7.5 nm/% in the salinity range from 0% to 100%. The maximum resolutions of 2.66 × 10−06 RIU and 1.33 × 10−02% are achieved with high linearity of 0.9924 for 2.20 cm length of the proposed PCF. Owing to such excellent results, this proposed sensor offers the potential to measure the salinity of seawater.