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Abstract Yellow fever outbreaks are prevalent, particularly in endemic regions. Given the lack of an established treatment for this disease, significant attention has been directed toward managing this arbovirus. In response, we developed a multiepitope vaccine designed to elicit an immune response, utilizing advanced immunoinformatic and molecular modeling techniques. To achieve this, we predicted B- and T-cell epitopes using the sequences from all structural (E, prM, and C) and nonstructural proteins of 196 YFV strains. Through comprehensive analysis, we identified 10 cytotoxic T-lymphocyte (CTL) and 5T-helper (Th) epitopes that exhibited overlap with B-lymphocyte epitopes. These epitopes were further evaluated for their affinity to a wide range of human leukocyte antigen system alleles and were rigorously tested for antigenicity, immunogenicity, allergenicity, toxicity, and conservation. These epitopes were linked to an adjuvant ( $$\beta$$ β -defensin) and to each other using ligands, resulting in a vaccine sequence with appropriate physicochemical properties. The 3D structure of this sequence was created, improved, and quality checked; then it was anchored to the Toll-like receptor. Molecular Dynamics and Quantum Mechanics/Molecular Mechanics simulations were employed to enhance the accuracy of docking calculations, with the QM portion of the simulations carried out utilizing the density functional theory formalism. Moreover, the inoculation model was able to provide an optimal codon sequence that was inserted into the pET-28a( +) vector for in silico cloning and could even stimulate highly relevant humoral and cellular immunological responses. Overall, these results suggest that the designed multi-epitope vaccine can serve as prophylaxis against the yellow fever virus.

Background: Frontonasal dysplasia type-2(FND2), a rare phenotypically variable and heterogeneous developmental anomaly resulting from mutation of the ALX4 gene, is primarily characterized by malformation of the skull and facial skeleton. This study was designed to showcase a clinical, imaging, and genetic analysis of FND2 in a consanguineous family of Bangladeshi origin. Methodology: Clinical imaging and whole genome sequencing of mother, father and patient was done by using Nextera DNA flex library preparation kit (Illumina, USA) using Novaseq 6000 next generation sequencer to find out ALX4 mutation which causes FND2 in patient. Result: We report the clinical as well as molecular findings in an 8-year-old girl with FND2. The child presented with various characteristic features of skull and facial anomalies associated with FND 2 along with numerous other features many of which have not been described in previous literature. The parents also showed some key clinical, radiological, and genetic features of FND 2. The whole genome sequencing (WGS) revealed homozygosity for a 793C-T transition in the ALX4 gene, which resulted in premature termination at codon 265 (p.Arg265Ter). Both of her parents were heterozygous carriers of ALX4 mutation. Conclusions: This is the first report that associates clinical, imaging, and genomics analyses in a Bangladeshi patient for better understanding the disease FND2. These results will facilitate diagnosis and genetic counseling of the future FND2 patients.

Abstract Quantitative reverse transcriptase polymerase chain reaction (qRT-PCR) is the gold standard method for SARS-CoV-2 detection, and several qRT-PCR kits have been established targeting different genes of the virus. Due to the high mutation rate of these genes, false negative results arise thus complicating the interpretation of the diagnosis and increasing the need of alternative targets. In this study, an alternative approach for the detection of SARS-CoV-2 viral RNA targeting the membrane (M) gene of the virus using qRT-PCR was described. Performance evaluation of this newly developed in-house assay against commercial qRT-PCR kits was done using clinical oropharyngeal specimens of COVID-19 positive patients. The limit of detection was determined using successive dilutions of known copies of SARS-CoV-2 pseudovirus. The M gene based assay was able to detect a minimum of 100 copies of virus/mL indicating its capacity to detect low viral load. The assay showed comparable accuracy, sensitivity and specificity with commercially available kits while detecting all the variants efficiently. The study concluded that the in-house M gene based assay might be an effective alternative for the currently available commercial qRT-PCR kits.

Abstract Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), the causative agent of COVID -19, is constantly evolving, requiring continuous genomic surveillance. In this study, we used whole-genome sequencing to investigate the genetic epidemiology of SARS-CoV-2 in Bangladesh, with particular emphasis on identifying dominant variants and associated mutations. We used high-throughput next-generation sequencing (NGS) to obtain DNA sequences from COVID-19 patient samples and compared these sequences to the Wuhan SARS-CoV-2 reference genome using the Global Initiative for Sharing All Influenza Data (GISAID). Our phylogenetic and mutational analyzes revealed that the majority (88%) of the samples belonged to the pangolin lineage B.1.1.25, whereas the remaining 11% were assigned to the parental lineage B.1.1. Two main mutations, D614G and P681R, were identified in the spike protein sequences of the samples. The D614G mutation, which is the most common, decreases S1 domain flexibility, whereas the P681R mutation may increase the severity of viral infections by increasing the binding affinity between the spike protein and the ACE2 receptor. We employed molecular modeling techniques, including protein modeling, molecular docking, and quantum mechanics/molecular mechanics (QM/MM) geometry optimization, to build and validate three-dimensional models of the S_D614G-ACE2 and S_P681R-ACE2 complexes from the predominant strains. The description of the binding mode and intermolecular contacts of the referenced systems suggests that the P681R mutation may be associated with increased viral pathogenicity in Bangladeshi patients due to enhanced electrostatic interactions between the mutant spike protein and the human ACE2 receptor, underscoring the importance of continuous genomic surveillance in the fight against COVID -19. Finally, the binding profile of the S_D614G-ACE2 and S_P681R-ACE2 complexes offer valuable insights to deeply understand the binding site characteristics that could help to develop antiviral therapeutics that inhibit protein–protein interactions between SARS-CoV-2 spike protein and human ACE2 receptor.

Abstract Background The next-generation sequencing (NGS) technology facilitates in-depth study of host-pathogen metatranscriptome. We, therefore, implicated phylodynamic and transcriptomic approaches through NGS technology to know/understand the dengue virus (DENV) origin and host response with dengue fever. Methods In this study, blood serum RNA was extracted from 21 dengue patients and 3 healthy individuals. Total transcriptomic data were analyzed for phylogenetic, phylodynamic, differential express gene (DEG), and gene ontology (GO) using respective bioinformatics tools. Results The viral genome sequence revealed dengue viral genome size ranges 10647 to 10707 nucleotide. Phylogenetic and phylodynamic analysis showed that the 2021 epidemic isolates were DENV-3 genotype-I and maintained as a new clade in compared to 2019 epidemic. Transcriptome analysis showed a total of 2686 genes were DEG in dengue patients compared to control with a q-value

The goal of this study was to evaluate the antibacterial and cytotoxic effects of both the in vitro and in vivo plant part extracts of the medicinal plant Gynura procumbens. An effective protocol for regeneration and callus formation was developed using nodal segments and regenerated leaf explants, respectively. The highest fresh and dry weight calli were produced after four weeks of culture on Murashige and Skoog (MS) medium containing 2.0 mg/L BAP and 2.0 mg/L NAA, while the most shoots were produced on MS medium containing 1.0 mg/L BAP and 0.5 mg/L IAA. The in vitro shoots developed roots on MS media with 0.1 mg/L IBA. The antibacterial activity of extracts against various bacteria was examined to determine their significance (p

Abstract Background Streptococcus pneumoniae (SPN) is the agent responsible for causing respiratory diseases, including pneumonia, which causes severe health hazards and child deaths globally. Antibiotics are used to treat SPN as a first-line treatment, but nowadays, SPN is showing resistance to several antibiotics. A vaccine can overcome this global problem by preventing this deadly pathogen. The conventional methods of wet-laboratory vaccine design and development are an intense, lengthy, and costly procedure. In contrast, epitope-based in silico vaccine designing can save time, money, and energy. In this study, pneumococcal surface protein A (PspA), one of the major virulence factors of SPN, is used to design a multi-epitope vaccine. Methods For designing the vaccine, the sequence of PspA was retrieved, and then, phylogenetic analysis was performed. Several CTL epitopes, HTL epitopes, and LBL epitopes of PspA were all predicted by using several bioinformatics tools. After checking the antigenicity, allergenicity, and toxicity scores, the best epitopes were selected for the vaccine construction, and then, physicochemical and immunological properties were analyzed. Subsequently, vaccine 3D structure prediction, refinement, and validation were performed. Molecular docking, molecular dynamic simulation, and immune simulation were performed to ensure the binding between HLA and TLR4. Finally, codon adaptation and in silico cloning were performed to transfer into a suitable vector. Results The constructed multi-epitope vaccine showed a strong binding affinity with the receptor molecule TLR4. Analysis of molecular dynamic simulation, C-immune simulation, codon adaptation, and in silico cloning validated that our designed vaccine is a suitable candidate against SPN. Conclusion The in silico analysis has proven the vaccine as an alternative medication to combat against S. pneumoniae. The designated vaccine can be further tested in the wet lab, and a novel vaccine can be developed.

Abstract The impact of SARS-CoV-2 infection on the nasopharyngeal microbiome has not been well characterised. We sequenced genetic material extracted from nasopharyngeal swabs of SARS-CoV-2-positive individuals who were asymptomatic (n = 14), had mild (n = 64) or severe symptoms (n = 11), as well as from SARS-CoV-2-negative individuals who had never-been infected (n = 5) or had recovered from infection (n = 7). Using robust filters, we identified 1345 taxa with approximately 0.1% or greater read abundance. Overall, the severe cohort microbiome was least diverse. Bacterial pathogens were found in all cohorts, but fungal species identifications were rare. Few taxa were common between cohorts suggesting a limited human nasopharynx core microbiome. Genes encoding resistance mechanisms to 10 antimicrobial classes (> 25% sequence coverages, 315 genes, 63 non-redundant) were identified, with β-lactam resistance genes near ubiquitous. Patients infected with SARS-CoV-2 (asymptomatic and mild) had a greater incidence of antibiotic resistance genes and a greater microbial burden than the SARS-CoV-2-negative individuals. This should be considered when deciding how to treat COVID-19 related bacterial infections.

In the healthcare sector, the production of bioactive silver nanoparticles (AgNPs) with antimicrobial properties is of great importance. In this study, a novel bacterial strain, Paenibacillus sp. MAHUQ-63, was identified as a potential candidate for facile and rapid biosynthesis of AgNPs. The synthesized AgNPs were used to control the growth of human pathogens, Salmonella Enteritidis and Candida albicans. The bacterial culture supernatant was used to synthesize the nanoparticles (NPs). Field emission transmission electron microscope examination showed spherical-shaped NPs with 15–55 nm in size. Fourier transform-infrared analysis identified various functional groups. The synthesized AgNPs demonstrated remarkable activity against S. Enteritidis and C. albicans. The zones of inhibition for 100 µl (0.5 mg ml−1) of AgNPs against S. Enteritidis and C. albicans were 18.0 ± 1.0 and 19.5 ± 1.3 mm, respectively. The minimum inhibitory concentrations were 25.0 and 12.5 µg ml−1 against S. Enteritidis and C. albicans, respectively. Additionally, the minimum bactericidal concentrations were 25.0 µg ml−1 against both pathogenic microbes. The field emission scanning electron microscopy analysis showed that the treatment of AgNPs caused morphological and structural damage to both S. Enteritidis and C. albicans. Therefore, these AgNPs can be used as a new and effective antimicrobial agent.

Abstract Background Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of the ongoing coronavirus disease 2019 (COVID-19) pandemic which has brought a great challenge to public health. After the first emergence of novel coronavirus SARS-CoV-2 in the city of Wuhan, China, in December 2019. As of March 2020, SARS-CoV-2 was first reported in Bangladesh and since then the country has experienced a steady rise in infections, resulting in 13,355,191 cases and 29,024 deaths as of 27 February 2022. Bioinformatics techniques are used to predict B cell and T cell epitopes from the new SARS-CoV-2 spike glycoprotein in order to build a unique multiple epitope vaccine. The immunogenicity, antigenicity scores, and toxicity of these epitopes were evaluated and chosen based on their capacity to elicit an immune response. Result The best multi-epitope of the possible immunogenic property was created by combining epitopes. EAAAK, AAY, and GPGPG linkers were used to connect the epitopes. In several computer-based immune response analyses, this vaccine design was found to be efficient, as well as having high population coverage. Conclusion This research is entirely reliant on the development of epitope-based vaccines, and these in silico findings would represent a major step forward in the development of a vaccine that might eradicate SARS-CoV-2 in Bangladeshi patients.

Abstract Acute myeloid leukemia (AML) is a malignant disease of immature myeloid cells and the most prevalent acute leukemia among adults. The oncogenic homo-tetrameric fusion protein RUNX1/ETO results from the chromosomal translocation t(8;21) and is found in AML patients. The nervy homology region 2 (NHR2) domain of ETO mediates tetramerization; this oligomerization is essential for oncogenic activity. Previously, we identified the first-in-class small-molecule inhibitor of NHR2 tetramer formation, 7.44, which was shown to specifically interfere with NHR2, restore gene expression down-regulated by RUNX1/ETO, inhibit the proliferation of RUNX1/ETO-depending SKNO-1 cells, and reduce the RUNX1/ETO-related tumor growth in a mouse model. However, no biophysical and structural characterization of 7.44 binding to the NHR2 domain has been reported. Likewise, the compound has not been characterized as to physicochemical, pharmacokinetic, and toxicological properties. Here, we characterize the interaction between the NHR2 domain of RUNX1/ETO and 7.44 by biophysical assays and show that 7.44 interferes with NHR2 tetramer stability and leads to an increase in the dimer population of NHR2. The affinity of 7.44 with respect to binding to NHR2 is K lig = 3.75 ± 1.22 µM. By NMR spectroscopy combined with molecular dynamics simulations, we show that 7.44 binds with both heteroaromatic moieties to NHR2 and interacts with or leads to conformational changes in the N-termini of the NHR2 tetramer. Finally, we demonstrate that 7.44 has favorable physicochemical, pharmacokinetic, and toxicological properties. Together with biochemical, cellular, and in vivo assessments, the results reveal 7.44 as a lead for further optimization towards targeted therapy of t(8;21) AML.

Abstract A commercial plant probiotic product was developed employing Bacillus subtilis CW-S in submerged fermentation. The effects of molasses and urea on cell growth were investigated with the goal of low-cost manufacturing. Plackett–Burman and Central-Composite Design (CCD) were utilized to optimize production parameters to maximize productivity. The stability of the formulated product and its efficacy in cultivating minituber in aeroponics and industrial-grade potatoes in the field were assessed. The results showed that the medium BS10 (molasses and urea) produced satisfactory cell density (7.19 × 108 CFU/mL) as compared to the control (1.51 × 107 CFU/mL) and BS1-BS9 (expensive) media (1.84 × 107–1.37 × 109 CFU/mL). According to validated CCD results, optimized parameters fitted well in pilot (300 L; 2.05 × 109 CFU/mL) and industrial (3000 L; 2.01 × 109 CFU/mL) bioreactors, resulting in a two-fold increase in cell concentration over laboratory (9.84 × 108 CFU/mL) bioreactors. In aeroponics, CW-S produced excellent results, with a significant increase in the quantity and weight of minitubers and the survival rate of transplanted plantlets. In a field test, the yield of industrial-grade (> 55 mm) potatoes was increased with a reduction in fertilizer dose. Overall, the findings suggest that CW-S can be produced commercially utilizing the newly developed media and optimized conditions, making plant probiotics more cost-effective and accessible to farmers for crop cultivation, particularly in aeroponic minituber and industrial-grade potato production.

Abstract Background Burkholderia pseudomallei is an infectious agent causing severe disease melioidosis resulting in pneumonia, fever, and acute septicemia in humans. B. pseudomallei show resistance to drugs. No such FDA-approved vaccine is available against B. pseudomallei, and treatment is limited to therapy. Therefore, the scientific study was designed to develop a vaccine for B. pseudomallei. The protein sequence of B. pseudomallei was retrieved from NCBI. B-cell and T-cell epitopes were identified and further screened for allergenicity, antigenicity docking, and simulation. Results Here, in this study, in silico approach was applied to design a multi-epitope subunit vaccine peptide consisting of linear B-cell and T-cell epitopes of proteins considered to be potential novel vaccine candidates. Peptide epitopes were joined by adjuvant and EAAAK, CPGPG, and AAY linkers. This constructed vaccine was subjected to in silico immune simulations by C-ImmSim. The protein construct was cloned into PET28a (+) vector for expression study in Escherichia coli using SnapGene. Conclusion The designed multi-epitope vaccine was analyzed for its physicochemical, structural, and immunological characteristics, and it was found to be antigenic, soluble, stable, nonallergenic, and have a high affinity to its target receptor. The immune simulation studies were carried out on the C-ImmSim showing increased production of cellular and humoral responses indicating that the constructed vaccine proved effective and able to provoke humoral and cell-mediated response immune responses. In silico study could be a breakthrough in designing effective vaccines to eradicate B. pseudomallei globally.

In recent years, biosynthesized zinc oxide nanoparticles (ZnONPs) have gained tremendous attention because of their safe and non-toxic nature and distinctive biomedical applications. A diverse range of microbes (bacteria, fungi and yeast) and various parts (leaf, root, fruit, flower, peel, stem, etc.) of plants have been exploited for the facile, rapid, cost-effective and non-toxic synthesis of ZnONPs. Plant extracts, microbial biomass or culture supernatant contain various biomolecules including enzymes, amino acids, proteins, vitamins, alkaloids, flavonoids, etc., which serve as reducing, capping and stabilizing agents during the biosynthesis of ZnONPs. The biosynthesized ZnONPs are generally characterized using UV-VIS spectroscopy, TEM, SEM, EDX, XRD, FTIR, etc. Antibiotic resistance is a serious problem for global public health. Due to mutation, shifting environmental circumstances and excessive drug use, the number of multidrug-resistant pathogenic microbes is continuously rising. To solve this issue, novel, safe and effective antimicrobial agents are needed urgently. Biosynthesized ZnONPs could be novel and effective antimicrobial agents because of their safe and non-toxic nature and powerful antimicrobial characteristics. It is proven that biosynthesized ZnONPs have strong antimicrobial activity against various pathogenic microorganisms including multidrug-resistant bacteria. The possible antimicrobial mechanisms of ZnONPs are the generation of reactive oxygen species, physical interactions, disruption of the cell walls and cell membranes, damage to DNA, enzyme inactivation, protein denaturation, ribosomal destabilization and mitochondrial dysfunction. In this review, the biosynthesis of ZnONPs using microbes and plants and their characterization have been reviewed comprehensively. Also, the antimicrobial applications and mechanisms of biosynthesized ZnONPs against various pathogenic microorganisms have been highlighted.

mRNA vaccines are a new class of vaccine that can induce potent and specific immune responses against various pathogens. However, the design of mRNA vaccines requires the identification and optimization of suitable antigens, which can be challenging and time consuming. Reverse vaccinology is a computational approach that can accelerate the discovery and development of mRNA vaccines by using genomic and proteomic data of the target pathogen. In this article, we review the advances of reverse vaccinology for mRNA vaccine design against SARS-CoV-2, the causative agent of COVID-19. We describe the steps of reverse vaccinology and compare the in silico tools used by different studies to design mRNA vaccines against SARS-CoV-2. We also discuss the challenges and limitations of reverse vaccinology and suggest future directions for its improvement. We conclude that reverse vaccinology is a promising and powerful approach to designing mRNA vaccines against SARS-CoV-2 and other emerging pathogens.

We previously reported that SARS-CoV-2 infection reduces human nasopharyngeal commensal microbiomes (bacteria, archaea and commensal respiratory viruses) with inclusion of pathobionts. This study aimed to assess the possible changes in the abundance and diversity of resident mycobiome in the nasopharyngeal tract (NT) of humans due to SARS-CoV-2 infections. Twenty-two (n = 22) nasopharyngeal swab samples (including COVID-19 = 8, Recovered = 7, and Healthy = 7) were collected for RNA-sequencing followed by taxonomic profiling of mycobiome. Our analyses indicate that SARS-CoV-2 infection significantly increased (p < 0.05, Wilcoxon test) the population and diversity of fungi in the NT with inclusion of a high proportion of opportunistic pathogens. We detected 863 fungal species including 533, 445, and 188 species in COVID-19, Recovered, and Healthy individuals, respectively that indicate a distinct mycobiome dysbiosis due to the SARS-CoV-2 infection. Remarkably, 37% of the fungal species were exclusively associated with SARS-CoV-2 infection, where S. cerevisiae (88.62%) and Phaffia rhodozyma (10.30%) were two top abundant species. Likewise, Recovered humans NT samples were predominated by Aspergillus penicillioides (36.64%), A. keveii (23.36%), A. oryzae (10.05%) and A. pseudoglaucus (4.42%). Conversely, Nannochloropsis oceanica (47.93%), Saccharomyces pastorianus (34.42%), and S. cerevisiae (2.80%) were the top abundant fungal species in Healthy controls nasal swabs. Importantly, 16% commensal fungal species found in the Healthy controls were not detected in either COVID-19 patients or when they were cured from COVID-19 (Recovered). We also detected several altered metabolic pathways correlated with the dysbiosis of fungal mycobiota in COVID-19 patients. Our results suggest that SARS-CoV-2 infection causes significant dysbiosis of mycobiome and related metabolic functions possibly play a determining role in the progression of SARS-CoV-2 pathogenesis. These findings might be helpful for developing mycobiome-based diagnostics, and also devising appropriate therapeutic regimens including antifungal drugs for prevention and control of concurrent fungal coinfections in COVID-19 patients.

The COVID-19 pandemic, caused by SARS-CoV-2, has globally affected both human health and economy. Several variants with a high potential for reinfection and the ability to evade immunity were detected shortly after the initial reported case of COVID-19. A total of 30 mutations in the spike protein (S) have been reported in the SARS-CoV-2 (BA.2) variant in India and South Africa, while half of these mutations are in the receptor-binding domain and have spread rapidly throughout the world. Drug repurposing offers potential advantages over the discovery of novel drugs, and one is that it can be delivered quickly without lengthy assessments and time-consuming clinical trials. In this study, computational drug design, such as pharmacophore-based virtual screening and MD simulation has been concentrated, in order to find a novel small molecular inhibitor that prevents hACE2 from binding to the receptor binding domain (RBD). three medicinal compound databases: North-East African, North African, and East African were screened and carried out a multi-step screening approach that identified three compounds, which are thymoquinol 2-O-beta-glucopyranoside (C1), lanneaflavonol (C2), and naringenin-4′-methoxy-7-O-Alpha-L-rhamnoside (C3), with excellent anti-viral properties against the RBD of the omicron variant. Furthermore, PAIN assay interference, computation bioactivity prediction, binding free energy, and dissociation constant were used to validate the top hits, which indicated good antiviral activity. The three compounds that were found may be useful against COVID-19, though more research is required. These findings could aid the development of novel therapeutic drugs against the emerging Omicron variant of SARS-CoV-2.

Introduction: This study aimed to evaluate new Staphylococcus aureus β-lactamase inhibitors from medicinal plants Rosmarinus officinalis, Ocimum basilicum, Eucalyptus globulus, and Thymus vulgaris by molecular docking analysis. Methods: The three-dimensional (3D) structures of phytochemical compounds were obtained from the PubChem database. The 3D structure of the β-lactamase was procured from Protein Data Bank. In silico absorption, distribution, metabolism, excretion, and toxicity (ADMET) analysis was performed using SwissADME online server to evaluate the drug likeliness of the phytochemicals. AutoDock was used for docking analysis to see the best binding energy and inhibition potential of the beta-lactamase enzyme. Results: ADMET values of all tested phytochemicals showed positive results and were within the recommended ranges, confirming that the plants can be taken as candidates for the detection of new drugs. Based on the docking results, the inhibitory potential of the studied compounds was different. The results showed that in E. globulus, the carvotanacetone compound with a binding energy equivalent to −6.54 kcal/mol was the most effective constituent against β-lactamase enzyme. Among the compounds analyzed in R. officinalis and T. vulgaris, the α-terpineol with an energy equivalent to −6.32 kcal per mole was the most effective constituent against β-lactamase enzyme. Also, in the O. basilicum, the 3,7-dimethyloct-1,5-dien-3,7-diol with an energy equivalent to −6.43 kcal per mole was the most effective constituent against β-lactamase enzyme. Conclusion: E. globulus was found to have promising inhibitory properties and might be used along with antibiotics against S. aureus that produces β-lactamase. Further in vitro or in vivo experiment are needed to confirm the obtained results.

We previously reported that SARS-CoV-2 infection reduces human nasopharyngeal commensal microbiomes (bacteria, archaea and commensal respiratory viruses) with inclusion of pathobionts. This study aimed to assess the possible changes in the abundance and diversity of resident mycobiome in the nasopharyngeal tract (NT) of humans due to SARS-CoV-2 infections. Twenty-two (n = 22) nasopharyngeal swab samples (including COVID-19 = 8, Recovered = 7, and Healthy = 7) were collected for RNA-sequencing followed by taxonomic profiling of mycobiome. Our analyses indicate that SARS-CoV-2 infection significantly increased (p < 0.05, Wilcoxon test) the population and diversity of fungi in the NT with inclusion of a high proportion of opportunistic pathogens. We detected 863 fungal species including 533, 445, and 188 species in COVID-19, Recovered, and Healthy individuals, respectively that indicate a distinct mycobiome dysbiosis due to the SARS-CoV-2 infection. Remarkably, 37% of the fungal species were exclusively associated with SARS-CoV-2 infection, where S. cerevisiae (88.62%) and Phaffia rhodozyma (10.30%) were two top abundant species. Likewise, Recovered humans NT samples were predominated by Aspergillus penicillioides (36.64%), A. keveii (23.36%), A. oryzae (10.05%) and A. pseudoglaucus (4.42%). Conversely, Nannochloropsis oceanica (47.93%), Saccharomyces pastorianus (34.42%), and S. cerevisiae (2.80%) were the top abundant fungal species in Healthy controls nasal swabs. Importantly, 16% commensal fungal species found in the Healthy controls were not detected in either COVID-19 patients or when they were cured from COVID-19 (Recovered). We also detected several altered metabolic pathways correlated with the dysbiosis of fungal mycobiota in COVID-19 patients. Our results suggest that SARS-CoV-2 infection causes significant dysbiosis of mycobiome and related metabolic functions possibly play a determining role in the progression of SARS-CoV-2 pathogenesis. These findings might be helpful for developing mycobiome-based diagnostics, and also devising appropriate therapeutic regimens including antifungal drugs for prevention and control of concurrent fungal coinfections in COVID-19 patients.

Abstract The microbiota of the nasopharyngeal tract (NT) play a role in host immunity against respiratory infectious diseases. However, scant information is available on interactions of SARS-CoV-2 with the nasopharyngeal microbiome. This study characterizes the effects of SARS-CoV-2 infection on human nasopharyngeal microbiomes and their relevant metabolic functions. Twenty-two (n = 22) nasopharyngeal swab samples (including COVID-19 patients = 8, recovered humans = 7, and healthy people = 7) were collected, and underwent to RNAseq-based metagenomic investigation. Our RNAseq data mapped to 2281 bacterial species (including 1477, 919 and 676 in healthy, COVID-19 and recovered metagenomes, respectively) indicating a distinct microbiome dysbiosis. The COVID-19 and recovered samples included 67% and 77% opportunistic bacterial species, respectively compared to healthy controls. Notably, 79% commensal bacterial species found in healthy controls were not detected in COVID-19 and recovered people. Similar dysbiosis was also found in viral and archaeal fraction of the nasopharyngeal microbiomes. We also detected several altered metabolic pathways and functional genes in the progression and pathophysiology of COVID-19. The nasopharyngeal microbiome dysbiosis and their genomic features determined by our RNAseq analyses shed light on early interactions of SARS-CoV-2 with the nasopharyngeal resident microbiota that might be helpful for developing microbiome-based diagnostics and therapeutics for this novel pandemic disease.

The COVID-19 pandemic, caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), has created an urgent global situation. Therefore, it is necessary to identify the differentially expressed genes (DEGs) in COVID-19 patients to understand disease pathogenesis and the genetic factor(s) responsible for inter-individual variability and disease comorbidities. The pandemic continues to spread worldwide, despite intense efforts to develop multiple vaccines and therapeutic options against COVID-19. However, the precise role of SARS-CoV-2 in the pathophysiology of the nasopharyngeal tract (NT) is still unfathomable. This study utilized machine learning approaches to analyze 22 RNA-seq data from COVID-19 patients (n = 8), recovered individuals (n = 7), and healthy individuals (n = 7) to find disease-related differentially expressed genes (DEGs). We compared dysregulated DEGs to detect critical pathways and gene ontology (GO) connected to COVID-19 comorbidities. We found 1960 and 153 DEG signatures in COVID-19 patients and recovered individuals compared to healthy controls. In COVID-19 patients, the DEG–miRNA, and DEG–transcription factors (TFs) interactions network analysis revealed that E2F1, MAX, EGR1, YY1, and SRF were the highly expressed TFs, whereas hsa-miR-19b, hsa-miR-495, hsa-miR-340, hsa-miR-101, and hsa-miR-19a were the overexpressed miRNAs. Three chemical agents (Valproic Acid, Alfatoxin B1, and Cyclosporine) were abundant in COVID-19 patients and recovered individuals. Mental retardation, mental deficit, intellectual disability, muscle hypotonia, micrognathism, and cleft palate were the significant diseases associated with COVID-19 by sharing DEGs. Finally, the detected DEGs mediated by TFs and miRNA expression indicated that SARS-CoV-2 infection might contribute to various comorbidities. Our results provide the common DEGs between COVID-19 patients and recovered humans, which suggests some crucial insights into the complex interplay between COVID-19 progression and the recovery stage, and offer some suggestions on therapeutic target identification in COVID-19 caused by the SARS-CoV-2.

Abstract Objective The major objective of the study was to sequence the whole genome of four Bangladeshi individuals and identify variants that are known to be associated with functional changes or disease states. We also carried out an ontology analysis to identify the functions and pathways most likely to be affected by these variants. Results We identified around 900,000 common variants and close to 5 million unique ones in all four of the individuals. This included over 11,500 variants that caused nonsynonymous changes in proteins. Heart function associated pathways were heavily implicated by the ontology analysis; corroborating previous studies that claimed the Bangladeshi population as highly susceptible to heart disorders. Two variants were found that have been previously identified as pathogenic factors in familial hypercholesteremia and structural disorders of the heart. Other pathogenic variants we found were associated with pseudoxanthoma elasticum, cancer progression, polyagglutinable erythrocyte syndrome, preeclampsia, and others.

The present study highlights the biological synthesis of silver nanoparticles (AgNPs) using Sphingobium sp. MAH-11 and also their antibacterial mechanisms against drug-resistant pathogenic microorganisms. The nanoparticle synthesis method used in this study was reliable, facile, rapid, cost-effective and ecofriendly. The AgNPs exhibited the highest absorbance at 423 nm. The TEM image expressed spherical shape of AgNPs and the size of synthesized AgNPs was 7–22 nm. The selected area diffraction (SAED) pattern and XRD spectrum revealed the crystalline structure of AgNPs. The results of FTIR analysis disclosed the functional groups responsible for the reduction of silver ion to metal nanoparticles. The biosynthesized AgNPs showed strong anti-microbial activity against drug-resistant pathogenic microorganisms. Moreover, Escherichia coli and Staphylococcus aureus were used to explore the antibacterial mechanisms of biosynthesized AgNPs. Minimal inhibitory concentrations (MICs) of E. coli and S. aureus were 6.25 μg/mL and 50 μg/mL, respectively and minimum bactericidal concentrations (MBCs) of E. coli and S. aureus were 25 μg/mL and 100 μg/mL, respectively. Results exhibited that biosynthesized AgNPs caused morphological changes and injured the membrane integrity of strains E. coli and S. aureus. The AgNPs synthesized by Sphingobium sp. MAH-11 may serve as a potent antimicrobial agent for many therapeutic applications.

In this study, we report one-pot, single step synthesis of silver nanoparticles stabilized by using arbutin. The concentration of reducing agent (NaBH4) used in the preparation was kept at double, and arbutin was used as a stabilizing agent. The confirmation of prepared silver nanoparticles was done by color change and UV-Vis surface plasmon resonance peak at 435 nm in UV-Vis spectrum. Size dispersion of nanoparticles was carried out by Dynamic Light Scattering (DLS) and surface charge on nanoparticles. Stability was analyzed by Zeta potential. A strong negative charge indicated that nanoparticles are well stabilized throughout the solution. Morphology and 3D topographic images were obtained by Atomic Force Microscopy (AFM). The crystalline nature of nanoparticles was elucidated by X-ray diffraction analysis. The size and morphology of solid, well-grinded nanoparticles was proceeded by Scanning Electron Microscopy (SEM). The catalytic activities of nanoparticles were carried out against methylene blue, methyl orange, safranin, and eosin. The results demonstrated that synthesized silver nanoparticles commenced the degradation reaction of dyes mentioned. Prepared silver nanoparticles are found to have adequate catalytic activity, as it can be comprehended in time-dependent UV-Vis spectrums of dyes after treating them with AgNPs.

Biosynthesized metal nanoparticles, especially silver and gold nanoparticles, and their conjugates with biopolymers have immense potential in various fields of science due to their enormous applications, including biomedical applications. Polymeric nanoparticles are particles of small sizes from 1 nm to 1000 nm. Among different polymeric nanoparticles, chitosan-coated silver and gold nanoparticles have gained significant interest from researchers due to their various biomedical applications, such as anti-cancer, antibacterial, antiviral, antifungal, anti-inflammatory technologies, as well as targeted drug delivery, etc. Multidrug-resistant pathogenic bacteria have become a serious threat to public health day by day. Novel, effective, and safe antibacterial agents are required to control these multidrug-resistant pathogenic microorganisms. Chitosan-coated silver and gold nanoparticles could be effective and safe agents for controlling these pathogens. It is proven that both chitosan and silver or gold nanoparticles have strong antibacterial activity. By the conjugation of biopolymer chitosan with silver or gold nanoparticles, the stability and antibacterial efficacy against multidrug-resistant pathogenic bacteria will be increased significantly, as well as their toxicity in humans being decreased. In recent years, chitosan-coated silver and gold nanoparticles have been increasingly investigated due to their potential applications in nanomedicine. This review discusses the biologically facile, rapid, and ecofriendly synthesis of chitosan-coated silver and gold nanoparticles; their characterization; and potential antibacterial applications against multidrug-resistant pathogenic bacteria.

The present study aimed to suggest a simple and environmentally friendly biosynthesis method of silver nanoparticles (AgNPs) using the strain Bacillus sonorensis MAHUQ-74 isolated from kimchi. Antibacterial activity and mechanisms of AgNPs against antibiotic-resistant pathogenic strains of Escherichia coli O157:H7 were investigated. The strain MAHUQ-74 had 99.93% relatedness to the B. sonorensis NBRC 101234T strain. The biosynthesized AgNPs had a strong surface plasmon resonance (SPR) peak at 430 nm. The transmission electron microscope (TEM) image shows the spherical shape and size of the synthesized AgNPs is 13 to 50 nm. XRD analysis and SAED pattern revealed the crystal structure of biosynthesized AgNPs. Fourier transform infrared spectroscopy (FTIR) data showed various functional groups associated with the reduction of silver ions to AgNPs. The resultant AgNPs showed strong antibacterial activity against nine E. coli O157:H7 pathogens. Minimum inhibitory concentration (MIC) values of the AgNPs synthesized by strain MAHUQ-74 were 3.12 μg/mL for eight E. coli O157:H7 strains and 12.5 μg/mL for strain E. coli ATCC 25922. Minimum bactericidal concentrations (MBCs) were 25 μg/mL for E. coli O157:H7 ATCC 35150, E. coli O157:H7 ATCC 43895, E. coli O157:H7 ATCC 43890, E. coli O157:H7 ATCC 43889, and E. coli ATCC 25922; and 50 μg/mL for E. coli O157:H7 2257, E. coli O157: NM 3204-92, E. coli O157:H7 8624 and E. coli O157:H7 ATCC 43894. FE-SEM analysis demonstrated that the probiotic-mediated synthesized AgNPs produced structural and morphological changes and destroyed the membrane integrity of pathogenic E. coli O157:H7. Therefore, AgNPs synthesized by strain MAHUQ-74 may be potential antibacterial agents for the control of antibiotic-resistant pathogenic strains of E. coli O157:H7.

Green synthesis of silver nanoparticles (AgNPs) using biological resources is the most facile, economical, rapid, and environmentally friendly method that mitigates the drawbacks of chemical and physical methods. Various biological resources such as plants and their different parts, bacteria, fungi, algae, etc. could be utilized for the green synthesis of bioactive AgNPs. In recent years, several green approaches for non-toxic, rapid, and facile synthesis of AgNPs using biological resources have been reported. Plant extract contains various biomolecules, including flavonoids, terpenoids, alkaloids, phenolic compounds, and vitamins that act as reducing and capping agents during the biosynthesis process. Similarly, microorganisms produce different primary and secondary metabolites that play a crucial role as reducing and capping agents during synthesis. Biosynthesized AgNPs have gained significant attention from the researchers because of their potential applications in different fields of biomedical science. The widest application of AgNPs is their bactericidal activity. Due to the emergence of multidrug-resistant microorganisms, researchers are exploring the therapeutic abilities of AgNPs as potential antibacterial agents. Already, various reports have suggested that biosynthesized AgNPs have exhibited significant antibacterial action against numerous human pathogens. Because of their small size and large surface area, AgNPs have the ability to easily penetrate bacterial cell walls, damage cell membranes, produce reactive oxygen species, and interfere with DNA replication as well as protein synthesis, and result in cell death. This paper provides an overview of the green, facile, and rapid synthesis of AgNPs using biological resources and antibacterial use of biosynthesized AgNPs, highlighting their antibacterial mechanisms.

The present study highlights the biosynthesis of silver nanoparticles (AgNPs) using culture supernatant of Massilia sp. MAHUQ-52 as well as the antimicrobial application of synthesized AgNPs against multi-drug resistant pathogenic Klebsiella pneumoniae and Salmonella Enteritidis. Well-defined AgNPs formation occurred from the reaction mixture of cell-free supernatant and silver nitrate (AgNO3) solution within 48 h of incubation. UV-visible spectroscopy analysis showed a strong peak at 435 nm, which corresponds to the surface plasmon resonance of AgNPs. The synthesized AgNPs were characterized by FE-TEM, EDX, XRD, DLS and FT-IR. From FE-TEM analysis, it was found that most of the particles were spherical shape, and the size of synthesized nanoparticles (NPs) was 15–55 nm. EDX spectrum revealed a strong silver signal at 3 keV. XRD analysis determined the crystalline, pure, face-centered cubic AgNPs. FT-IR analysis identified various functional molecules that may be involved with the synthesis and stabilization of AgNPs. The antimicrobial activity of Massilia sp. MAHUQ-52 mediated synthesized AgNPs was determined using the disk diffusion method against K. pneumoniae and S. Enteritidis. Biosynthesized AgNPs showed strong antimicrobial activity against both K. pneumoniae and S. Enteritidis. The MICs of synthesized AgNPs against K. pneumoniae and S. Enteritidis were 12.5 and 25.0 μg/mL, respectively. The MBC of biosynthesized AgNPs against both pathogens was 50.0 μg/mL. From FE-SEM analysis, it was found that the AgNPs-treated cells showed morphological changes with irregular and damaged cell walls that culminated in cell death.

The present study describes the isolation and characterization of novel bacterial species Arthrobacter bangladeshi sp. nov., applied for the green synthesis of AgNPs, and investigates its antibacterial efficacy against drug-resistant pathogenic Salmonella Typhimurium and Yersinia enterocolitica. Novel strain MAHUQ-56T is Gram-positive, aerobic, non-motile, and rod-shaped. Colonies were spherical and milky white. The strain showed positive activity for catalase and nitrate reductase, and the hydrolysis of starch, L-tyrosine, casein, and Tween 20. On the basis of the 16S rRNA gene sequence, strain MAHUQ-56T belongs to the Arthrobacter genus and is most closely related to Arthrobacter pokkalii P3B162T (98.6%). Arthrobacter bangladeshi MAHUQ-56T has a genome 4,566,112 bp long (26 contigs) with 4125 protein-coding genes, 51 tRNA and 6 rRNA genes. The culture supernatant of Arthrobacter bangladeshi MAHUQ-56T was used for the easy and green synthesis of AgNPs. Synthesized AgNPs were characterized by UV–vis spectroscopy, FE-TEM, XRD, DLS, and FT-IR. Synthesized AgNPs were spherical and 12–50 nm in size. FT-IR analysis revealed various biomolecules that may be involved in the synthesis process. Synthesized AgNPs showed strong antibacterial activity against multidrug-resistant pathogenic S. typhimurium and Y. enterocolitica. MIC values of the synthesized AgNPs against S. typhimurium and Y. enterocolitica were 6.2 and 3.1 ug/mL, respectively. The MBC of synthesized AgNPs for both pathogens was 12.5 ug/mL. FE-SEM analysis revealed the morphological and structural alterations, and damage of pathogens treated by AgNPs. These changes might disturb normal cellular functions, which ultimately leads to the death of cells.

In the present study, silver nanoparticles (AgNPs), biosynthesized using culture supernatant of bacterial strain Paenarthrobacter nicotinovorans MAHUQ-43, were characterized and their antimicrobial activity was investigated against both Gram-positive Bacillus cereus and Gram-negative bacteria Pseudomonas aeruginosa. Bacterial-mediated synthesized AgNPs were characterized by UV-Visible (UV-Vis) spectrophotometer, field emission-transmission electron microscopy (FE-TEM), energy dispersive X-ray (EDX), X-ray diffraction (XRD), Fourier transform infrared (FTIR) spectroscopy, and dynamic light scattering (DLS) analysis. The UV-Vis spectral analysis showed the absorption maxima at 466 nm which assured the synthesis of AgNPs. The FE-TEM analysis revealed the spherical shape of nanoparticles with the size range from 13 to 27 nm. The EDX and XRD analysis ensured the crystalline nature of biosynthesized AgNPs. The FTIR analysis revealed the involvement of different biomolecules for the synthesis of AgNPs as reducing and capping agents. The bacterial-mediated synthesized AgNPs inhibited the growth of pathogenic strains B. cereus and P. aeruginosa and developed a clear zone of inhibition (ZOI). The MIC and MBC for both pathogens were 12.5 µg/mL and 25 µg/mL, respectively. Moreover, field emission scanning electron microscopy analysis revealed that the synthesized AgNPs can destroy the outer membrane and alter the cell morphology of treated pathogens, leading to the death of cells. This study concludes the eco-friendly, facile and rapid synthesis of AgNPs using P. nicotinovorans MAHUQ-43 and synthesized AgNPs showed excellent antimicrobial activity against both Gram-positive and Gram-negative pathogens.

It is essential to develop and discover alternative eco-friendly antibacterial agents due to the emergence of multi-drug-resistant microorganisms. In this study, we isolated and characterized a novel bacterium named Terrabacter humi MAHUQ-38T, utilized for the eco-friendly synthesis of silver nanoparticles (AgNPs) and the synthesized AgNPs were used to control multi-drug-resistant microorganisms. The novel strain was Gram stain positive, strictly aerobic, milky white colored, rod shaped and non-motile. The optimal growth temperature, pH and NaCl concentration were 30 °C, 6.5 and 0%, respectively. Based on 16S rRNA gene sequence, strain MAHUQ-38T belongs to the genus Terrabacter and is most closely related to several Terrabacter type strains (98.2%–98.8%). Terrabacter humi MAHUQ-38T had a genome of 5,156,829 bp long (19 contigs) with 4555 protein-coding genes, 48 tRNA and 5 rRNA genes. The culture supernatant of strain MAHUQ-38T was used for the eco-friendly and facile synthesis of AgNPs. The transmission electron microscopy (TEM) image showed the spherical shape of AgNPs with a size of 6 to 24 nm, and the Fourier transform infrared (FTIR) analysis revealed the functional groups responsible for the synthesis of AgNPs. The synthesized AgNPs exhibited strong anti-bacterial activity against multi-drug-resistant pathogens, Escherichia coli and Pseudomonas aeruginosa. Minimal inhibitory/bactericidal concentrations against E. coli and P. aeruginosa were 6.25/50 and 12.5/50 μg/mL, respectively. The AgNPs altered the cell morphology and damaged the cell membrane of pathogens. This study encourages the use of Terrabacter humi for the ecofriendly synthesis of AgNPs to control multi-drug-resistant microorganisms.