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Article ; Online: Performance of F1 progenies developed through crosses between Brassica carinata A. Braun A(♀) and Brassica rapa L (♂)

Goswami, Barna / Momtaz, Nasima / Hoque, M. I. / Sarker, R. H.

Genet Resour Crop Evol. 2022 Dec., v. 69, no. 8 p.2745-2753

2022

Abstract: The present investigation was aimed to study the performance of F₁ progenies of crosses between Brassica carinata A. Braun and Brassica rapa L. considering their morphological characters, agronomic traits and yield attributes. Increased vegetative growth ...

Abstract	The present investigation was aimed to study the performance of F₁ progenies of crosses between Brassica carinata A. Braun and Brassica rapa L. considering their morphological characters, agronomic traits and yield attributes. Increased vegetative growth in F1 progenies over their parents was observed. F₁ progeny exhibited wider ranges of variations compared to the female parents for all characters studied. F₁ progenies had taller plants and larger flowers than the female parent B. carinata. Average pollen fertility in the F₁ progeny was lower than female parent. F₁ progeny from the cross of Brassica carinata × Brassica rapa var.BAU M.91 had comparatively higher percentages of pollen fertility as well as siliqua setting. Number of seeds per siliqua were found to be lower than their female parent. Mean seed weight per plant in the F₁ progenies was lower than the parents. Days to flowering in the F₁ progenies were in between the parents and closer to the B. rapa parent. F₁ progeny from the cross of Brassica carinata × Brassica rapa var. BAU M.91 were found to be promising considering morphological characters, agronomic traits, pollen fertility, yield attributes like percentage of fully developed seed, seed weight etc. These F₁ progenies could be evaluated in the subsequent generations to select the stable and desirable Brassica breeding lines for the development of synthetic hexaploid (AABBCC) Brassica with traits of economic importance.
Keywords	Brassica carinata ; Brassica rapa ; females ; hexaploidy ; pollen ; progeny ; seed weight ; vegetative growth
Language	English
Dates of publication	2022-12
Size	p. 2745-2753.
Publishing place	Springer Netherlands
Document type	Article ; Online
ZDB-ID	1134125-7
ISSN	0925-9864
ISSN	0925-9864
DOI	10.1007/s10722-022-01395-6
Database	NAL-Catalogue (AGRICOLA)

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Article: Assessment of antibacterial activity and cytotoxic effects of

Saha, Sanchita / Al Amin, G M / Khan, Md Salim / Goswami, Barna / Afroz, Farhana / Habib, Md Ahashan / Akter, Shahina / Banu, Tanjina Akhtar

Heliyon

2023 Volume 9, Issue 12, Page(s) e22954

Abstract: The goal of this study was to evaluate the antibacterial and cytotoxic effects of both ... ...

Abstract	The goal of this study was to evaluate the antibacterial and cytotoxic effects of both the
Language	English
Publishing date	2023-11-28
Publishing country	England
Document type	Journal Article
ZDB-ID	2835763-2
ISSN	2405-8440
ISSN	2405-8440
DOI	10.1016/j.heliyon.2023.e22954
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Article ; Online: SARS-CoV-2 testing and its role in understanding the evolving landscape of the pandemic in Bangladesh.

Azam, Shafiul / Sayem, Mohammed / Khan, Salim / Martini, Catherine / Sarkar, Murshed Hasan / Akter, Shahina / Goswami, Barna / Sinha, Sylvana Q / Husain, Zaheed

Journal of biosciences

2023 Volume 48

Abstract: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is readily transmitted from person to person. We evaluated the emerging landscape of SARS-CoV-2 variants in Bangladesh from a retrospective study of nasopharyngeal swabs collected from 130 SARS- ...

Abstract	Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is readily transmitted from person to person. We evaluated the emerging landscape of SARS-CoV-2 variants in Bangladesh from a retrospective study of nasopharyngeal swabs collected from 130 SARS-CoV-2-positive cases randomly selected over 6 months. Mutation analysis of whole-genome sequencing of 130 SARS-CoV-2 variants revealed 528 unique coding mutations, of which 102 were deletions, 6 were premature stop codons, and the remaining were substitutions. The most common mutation in the cohort was ORF1b:P314L, with a frequency of 98.5%. A total of 132 unique coding mutations were observed in the spike protein gene. Fourteen mutations were mapped to the spike protein receptor binding domain (RBD). These mutations increase the affinity between the spike protein and its human receptor, angiotensin converting enzyme 2 (ACE2), thereby increasing SARS-CoV-2 transmissibility. This study will help understand the SARS-CoV-2 virus and ultimately aid in monitoring and combatting the COVID-19 pandemic by furthering research on appropriate therapies. Analysis of age revealed closer association of the Delta variant with older populations and of the Omicron variant with younger populations. This may have important implications on how we monitor infections, distribute vaccines, and treat patients based on their ages.
MeSH term(s)	Humans ; SARS-CoV-2/genetics ; COVID-19/diagnosis ; COVID-19/epidemiology ; Pandemics ; Bangladesh/epidemiology ; COVID-19 Testing ; Retrospective Studies ; Spike Glycoprotein, Coronavirus/genetics ; Mutation ; Protein Binding
Chemical Substances	Spike Glycoprotein, Coronavirus ; spike protein, SARS-CoV-2
Language	English
Publishing date	2023-12-13
Publishing country	India
Document type	Journal Article
ZDB-ID	756157-x
ISSN	0973-7138 ; 0250-5991
ISSN (online)	0973-7138
ISSN	0250-5991
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Article: Antimicrobial Potential of Coriandrum Sativum, Lactuca Sativa and Mentha Spicata against Antibiotic Resistant Microorganisms

Afrin, Sadia / Goswami, Barna / Rahman, Saidur / Bhuiyan, Mohammad Nazrul Islam / Shamima, Kazi Asma Ahmed / Nandi, Nemai Chandra

Journal of herbs, spices & medicinal plants. 2022 Apr. 03, v. 28, no. 2

2022

Abstract: The antimicrobial properties of Coriandrum sativum, Lactuca sativa, and Mentha spicata were examined using Kirby-Bauer disk diffusion technique. Among the solvents used for extraction, methanol, acetone, and n-hexane extracts were effective against ... ...

Abstract	The antimicrobial properties of Coriandrum sativum, Lactuca sativa, and Mentha spicata were examined using Kirby-Bauer disk diffusion technique. Among the solvents used for extraction, methanol, acetone, and n-hexane extracts were effective against antibiotic resistant microbes. The highest inhibition zone (17.0 ± 0.5 mm) was noted for the methanol extract of C. sativum against Bacillus cereus and the lowest zone of inhibition (7.0 ± 0.7 mm) was observed for the aqueous extract of M. spicata against E. coli. Methanol extracts from the three plants inhibited mycelial growth of tested fungi particularly for Aspergillus sp. and Penicillium sp.. The methanol extract of these plants had minimum inhibitory concentration (MIC), minimum bactericidal concentration (MBC), and minimum fungicidal concentration (MFC) values ranging from 200 to 400 mg mL⁻¹, 300 to 500 mg mL⁻¹, and 400 to 500 mg mL⁻¹, respectively.
Keywords	Aspergillus ; Bacillus cereus ; Coriandrum sativum ; Escherichia coli ; Lactuca sativa ; Mentha spicata ; Penicillium ; acetone ; antibiotic resistance ; hexane ; methanol ; minimum inhibitory concentration ; mycelium
Language	English
Dates of publication	2022-0403
Size	p. 193-205.
Publishing place	Taylor & Francis
Document type	Article
ZDB-ID	1122804-0
ISSN	1540-3580 ; 1049-6475
ISSN (online)	1540-3580
ISSN	1049-6475
DOI	10.1080/10496475.2022.2040684
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Article: Computational design of medicinal compounds to inhibit RBD-hACE2 interaction in the Omicron variant: unveiling a vulnerable target site.

Shahab, Muhammad / Akter, Shahina / Sarkar, Md Murshed Hasan / Banu, Tanjina Akhtar / Goswami, Barna / Chowdhury, Sanjana Fatema / Naser, Showti Raheel / Habib, Md Ahashan / Shaikh, Aftab Ali / Saki, Morteza / Zheng, Guojun / Khan, Md Salim

Informatics in medicine unlocked

2023 Volume 40, Page(s) 101281

Abstract: 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. ... ...

Abstract	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.
Language	English
Publishing date	2023-05-25
Publishing country	England
Document type	Journal Article
ISSN	2352-9148
ISSN	2352-9148
DOI	10.1016/j.imu.2023.101281
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Article ; Online: In silico design of an epitope-based vaccine against PspC in Streptococcus pneumoniae using reverse vaccinology.

Nahian, Md / Shahab, Muhammad / Mazumder, Lincon / Oliveira, Jonas Ivan Nobre / Banu, Tanjina Akhtar / Sarkar, Murshed Hasan / Goswami, Barna / Habib, Ahashan / Begum, Shamima / Akter, Shahina

Journal, genetic engineering & biotechnology

2023 Volume 21, Issue 1, Page(s) 166

Abstract: Background: Streptococcus pneumoniae is a major pathogen that poses a significant hazard to global health, causing a variety of infections including pneumonia, meningitis, and sepsis. The emergence of antibiotic-resistant strains has increased the ... ...

Abstract	Background: Streptococcus pneumoniae is a major pathogen that poses a significant hazard to global health, causing a variety of infections including pneumonia, meningitis, and sepsis. The emergence of antibiotic-resistant strains has increased the difficulty of conventional antibiotic treatment, highlighting the need for alternative therapies such as multi-epitope vaccines. In this study, immunoinformatics algorithms were used to identify potential vaccine candidates based on the extracellular immunogenic protein Pneumococcal surface protein C (PspC). Method: The protein sequence of PspC was retrieved from NCBI for the development of the multi-epitope vaccine (MEV), and potential B cell and T cell epitopes were identified. Linkers including EAAAK, AAY, and CPGPG were used to connect the epitopes. Through molecular docking, molecular dynamics, and immunological simulation, the affinity between MEV and Toll-like receptors was determined. After cloning the MEV construct into the PET28a ( +) vector, SnapGene was used to achieve expression in Escherichia coli. Result: The constructed MEV was discovered to be stable, non-allergenic, and antigenic. Microscopic interactions between ligand and receptor are confirmed by molecular docking and molecular dynamics simulation. The use of an in-silico cloning approach guarantees the optimal expression and translation efficiency of the vaccine within an expression vector. Conclusion: Our study demonstrates the potential of in silico approaches for designing effective multi-epitope vaccines against S. pneumoniae. The designated vaccine exhibits the required physicochemical, structural, and immunological characteristics of a successful vaccine against SPN. However, laboratory validation is required to confirm the safety and immunogenicity of the proposed vaccine design.
Language	English
Publishing date	2023-12-12
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	2637420-1
ISSN	2090-5920 ; 1687-157X ; 2090-5920
ISSN (online)	2090-5920
ISSN	1687-157X ; 2090-5920
DOI	10.1186/s43141-023-00604-8
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Article ; Online: Transcriptome analysis reveals increased abundance and diversity of opportunistic fungal pathogens in nasopharyngeal tract of COVID-19 patients.

Hoque, M Nazmul / Rahman, M Shaminur / Sarkar, Md Murshed Hasan / Habib, Md Ahashan / Akter, Shahina / Banu, Tanjina Akhtar / Goswami, Barna / Jahan, Iffat / Hossain, M Anwar / Khan, M Salim / Islam, Tofazzal

PloS one

2023 Volume 18, Issue 1, Page(s) e0278134

Abstract: 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 ... ...

Abstract	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.
MeSH term(s)	Humans ; COVID-19 ; Saccharomyces cerevisiae/genetics ; SARS-CoV-2/genetics ; Dysbiosis ; Nasopharynx ; Gene Expression Profiling
Language	English
Publishing date	2023-01-19
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2267670-3
ISSN	1932-6203 ; 1932-6203
ISSN (online)	1932-6203
ISSN	1932-6203
DOI	10.1371/journal.pone.0278134
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Article ; Online: Spike protein mutations and structural insights of pangolin lineage B.1.1.25 with implications for viral pathogenicity and ACE2 binding affinity.

Akter, Shahina / Oliveira, Jonas Ivan Nobre / Barton, Carl / Sarkar, Murshed Hasan / Shahab, Muhammad / Banu, Tanjina Akhtar / Goswami, Barna / Osman, Eshrar / Uzzaman, Mohammad Samir / Nafisa, Tasnim / Molla, Maruf Ahmed / Yeasmin, Mahmuda / Farzana, Maisha / Habib, Ahashan / Shaikh, Aftab Ali / Khan, Salim

Scientific reports

2023 Volume 13, Issue 1, Page(s) 13146

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 ... ...

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.
MeSH term(s)	Animals ; Humans ; Angiotensin-Converting Enzyme 2/genetics ; Angiotensin-Converting Enzyme 2/metabolism ; COVID-19 ; Molecular Docking Simulation ; Molecular Dynamics Simulation ; Mutation ; Pangolins/metabolism ; Phylogeny ; Protein Binding ; SARS-CoV-2/genetics ; SARS-CoV-2/metabolism ; Spike Glycoprotein, Coronavirus/metabolism ; Virulence
Chemical Substances	Angiotensin-Converting Enzyme 2 (EC 3.4.17.23) ; Spike Glycoprotein, Coronavirus ; spike protein, SARS-CoV-2 ; ACE2 protein, human (EC 3.4.17.23)
Language	English
Publishing date	2023-08-12
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-023-40005-y
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Article ; Online: Comparative phylogenetic analysis and transcriptomic profiling of Dengue (DENV-3 genotype I) outbreak in 2021 in Bangladesh.

Sarkar, Md Murshed Hasan / Rahman, M Shaminur / Islam, M Rafiul / Rahman, Arafat / Islam, Md Shariful / Banu, Tanjina Akhtar / Akter, Shahina / Goswami, Barna / Jahan, Iffat / Habib, Md Ahashan / Uddin, Mohammad Mohi / Mia, Md Zakaria / Miah, Md Ibrahim / Shaikh, Aftab Ali / Khan, Md Salim

Virology journal

2023 Volume 20, Issue 1, Page(s) 127

MeSH term(s)	Humans ; Phylogeny ; Bangladesh/epidemiology ; Transcriptome ; Dengue/epidemiology ; Disease Outbreaks ; Genotype ; Serogroup
Language	English
Publishing date	2023-06-19
Publishing country	England
Document type	Journal Article
ZDB-ID	2160640-7
ISSN	1743-422X ; 1743-422X
ISSN (online)	1743-422X
ISSN	1743-422X
DOI	10.1186/s12985-023-02030-1
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Article ; Online: Correction to: Comparative phylogenetic analysis and transcriptomic profiling of dengue (DENV-3 genotype I) outbreak in 2021 in Bangladesh.

Sarkar, Md Murshed Hasan / Rahman, M Shaminur / Rafiul, M / Rahman, Arafat / Islam, Md Shariful / Banu, Tanjina Akhtar / Akter, Shahina / Goswami, Barna / Jahan, Iffat / Habib, Md Ahashan / Uddin, Mohammad Mohi / Mia, Md Zakaria / Miah, Md Ibrahim / Shaikh, Md Aftab Ali / Khan, Md Salim

Virology journal

2023 Volume 20, Issue 1, Page(s) 184

Language	English
Publishing date	2023-08-18
Publishing country	England
Document type	Published Erratum
ZDB-ID	2160640-7
ISSN	1743-422X ; 1743-422X
ISSN (online)	1743-422X
ISSN	1743-422X
DOI	10.1186/s12985-023-02151-7
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