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  1. Article: Molecular genetics of surfactin and its effects on different sub-populations of

    Rahman, Faisal Bin / Sarkar, Bishajit / Moni, Ripa / Rahman, Mohammad Shahedur

    Biotechnology reports (Amsterdam, Netherlands)

    2021  Volume 32, Page(s) e00686

    Abstract: Surfactin is a biosurfactant produced ... ...

    Abstract Surfactin is a biosurfactant produced by
    Language English
    Publishing date 2021-10-26
    Publishing country Netherlands
    Document type Journal Article ; Review
    ZDB-ID 2801018-8
    ISSN 2215-017X
    ISSN 2215-017X
    DOI 10.1016/j.btre.2021.e00686
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: In silico

    Moin, Abu Tayab / Sarkar, Bishajit / Ullah, Md Asad / Araf, Yusha / Ahmed, Nafisa / Rudra, Bashudev

    Biochemistry and biophysics reports

    2021  Volume 27, Page(s) 101074

    Abstract: Epithelial cell adhesion molecule (EpCAM) is a transmembrane glycoprotein which is involved in cell signaling, proliferation, maturation, and movement, all of which are crucial for the proper development of cells and tissues. Cleavage of the EpCAM ... ...

    Abstract Epithelial cell adhesion molecule (EpCAM) is a transmembrane glycoprotein which is involved in cell signaling, proliferation, maturation, and movement, all of which are crucial for the proper development of cells and tissues. Cleavage of the EpCAM protein leads to the up-regulation of c-myc, e-fabp, and cyclins A and E which promote tumorigenesis.
    Language English
    Publishing date 2021-07-19
    Publishing country Netherlands
    Document type Journal Article
    ZDB-ID 2831046-9
    ISSN 2405-5808 ; 2405-5808
    ISSN (online) 2405-5808
    ISSN 2405-5808
    DOI 10.1016/j.bbrep.2021.101074
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  3. Article ; Online: A systematic and reverse vaccinology approach to design novel subunit vaccines against Dengue virus type-1 (DENV-1) and human Papillomavirus-16 (HPV-16)

    Bishajit Sarkar / Md Asad Ullah / Yusha Araf

    Informatics in Medicine Unlocked, Vol 19, Iss , Pp 100343- (2020)

    2020  

    Abstract: Currently, dengue fever and human cervical cancer are two of the most dangerous diseases around the world. Dengue fever is caused by four serotypes of dengue virus (DENV)- 1, 2, 3 and 4 and most of the human cervical cancer cases are found to be caused ... ...

    Abstract Currently, dengue fever and human cervical cancer are two of the most dangerous diseases around the world. Dengue fever is caused by four serotypes of dengue virus (DENV)- 1, 2, 3 and 4 and most of the human cervical cancer cases are found to be caused by human papillomavirus type-16 (HPV-16). In this study, potential epitope-based subunit vaccines were designed using numerous tools of reverse vaccinology, targeting the DENV-1 envelope protein E and HPV-16 major capsid protein L1. Reverse vaccinology is a genome-based approach of vaccine designing, identifying potential antigenic epitopes of a pathogen. After obtaining the target protein sequences, their antigenicity and physicochemical properties were determined. Thereafter, the possible T cell and B cell epitopes were predicted and after analyzing their antigenicity, allergenicity, toxicity, and conservancy, as well as docking results (docked with MHC class-I and class-II alleles), the best epitopes were selected for vaccine construction. Thereafter, two best vaccine constructs (one for each of the virus) were selected for further analysis based on analyzing the docking results (docked with various MHC alleles and TLR molecules) of the initially constructed six vaccines. The molecular dynamics simulation of the two selected docked complexes with the two best vaccines showed quite satisfactory results. Finally, after codon adaptation, the vaccine constructs were inserted into the pET-19b plasmid vector for E. coli strain K12 using an in silico cloning approach. However, more in vitro and in vivo studies might be required on the suggested vaccines for their proper validation.
    Keywords Vaccine ; Dengue ; Human papillomavirus ; Molecular docking ; Antigenicity ; Vaccinology ; Computer applications to medicine. Medical informatics ; R858-859.7
    Subject code 572
    Language English
    Publishing date 2020-01-01T00:00:00Z
    Publisher Elsevier
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  4. Article ; Online: Prediction of biomarker signatures and therapeutic agents from blood sample against Pancreatic Ductal Adenocarcinoma (PDAC)

    Md Asad Ullah / Bishajit Sarkar / Fayza Akter

    Informatics in Medicine Unlocked, Vol 19, Iss , Pp 100346- (2020)

    A network-based study

    2020  

    Abstract: Pancreatic Ductal Adenocarcinoma (PDAC) is a form of pancreatic cancer with poor prognosis and rising incidence. Difficulties in the early detection and aggressive biological nature of this disease are responsible for most of the therapeutic failures. In ...

    Abstract Pancreatic Ductal Adenocarcinoma (PDAC) is a form of pancreatic cancer with poor prognosis and rising incidence. Difficulties in the early detection and aggressive biological nature of this disease are responsible for most of the therapeutic failures. In this study, publicly available microarray expression data of full RNA from the peripheral blood of PDAC patients has been utilized via a network-based approach in order to identify potential non-invasive biomarkers and drug targets for early diagnosis and treatment of PDAC. Analysis of differentially expressed genes revealed their predominant involvement in the translational process, apoptotic process, protein phosphorylation, immune response, ATP binding, protein binding, and signal transduction. Moreover, CREBBP, MAPK14, MAPK1, SMAD3, UBC, MAGOH, HSP90AB1, RPL23A, ACTB and STAT3 were identified as the best proteome signatures, GATA2, FOXC1, PPARG, E2F1, HINFP, USF2, MEF2A, FOXL1, YY1 and NFIC were identified as the best transcriptional regulatory signatures, and hsa-miR-93, hsa-miR-16, hsa-miR-195, hsa-miR-424, hsa-miR-506, hsa-miR-124, hsa-miR-590-3p, hsa-miR-1, hsa-miR-497 and hsa-miR-9 were identified as the best post-transcriptional regulatory signatures in PDAC patients. Analysis of drug-gene interactions revealed Anisomycin, Azactidine, Arsenic trioxide, Bortezomib, Ulixertinib, and some other molecules as probable candidate molecules which may reverse the PDAC condition.
    Keywords Adenocarcinoma ; Biomarkers ; Cancer ; Pancreatic ; PDAC ; Treatment ; Computer applications to medicine. Medical informatics ; R858-859.7
    Subject code 500
    Language English
    Publishing date 2020-01-01T00:00:00Z
    Publisher Elsevier
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  5. Article ; Online: Exploiting the reverse vaccinology approach to design novel subunit vaccines against Ebola virus.

    Ullah, Md Asad / Sarkar, Bishajit / Islam, Syed Sajidul

    Immunobiology

    2020  Volume 225, Issue 3, Page(s) 151949

    Abstract: Ebola virus is a highly pathogenic RNA virus that causes the Ebola haemorrhagic fever in human. This virus is considered as one of the dangerous viruses in the world with very high mortality rate. To date, no epitope-based subunit vaccine has yet been ... ...

    Abstract Ebola virus is a highly pathogenic RNA virus that causes the Ebola haemorrhagic fever in human. This virus is considered as one of the dangerous viruses in the world with very high mortality rate. To date, no epitope-based subunit vaccine has yet been discovered to fight against Ebola although the outbreaks of this deadly virus took many lives in the past. In this study, approaches of reverse vaccinology were utilized in combination with different tools of immunoinformatics to design subunit vaccines against Ebola virus strain Mayinga-76. Three potential antigenic proteins of this virus i.e., matrix protein VP40, envelope glycoprotein and nucleoprotein were selected to construct the subunit vaccine. The MHC class-I, MHC class-II and B-cell epitopes were determined initially and after some robust analysis i.e., antigenicity, allergenicity, toxicity, conservancy and molecular docking study, EV-1, EV-2 and EV-3 were constructed as three potential vaccine constructs. These vaccine constructs are also expected to be effective on few other strains of Ebola virus since the highly conserved epitopes were used for vaccine construction. Thereafter, molecular docking study was conducted on these vaccines and EV-1 emerged as the best vaccine construct. Afterward, molecular dynamics simulation study revealed the good performances and stability of the intended vaccine protein. Finally, codon adaptation and in silico cloning were carried out to design a possible plasmid (pET-19b plasmid vector was used) for large scale production of the EV-1 vaccine. However, further in vitro and in vivo studies might be required on the predicted vaccines for final validation.
    MeSH term(s) Antigens, Viral/chemistry ; Antigens, Viral/immunology ; Computational Biology/methods ; Ebola Vaccines/immunology ; Ebolavirus/classification ; Ebolavirus/immunology ; Epitopes/chemistry ; Epitopes/immunology ; Genetic Engineering ; Hemorrhagic Fever, Ebola/prevention & control ; Humans ; Models, Molecular ; Reproducibility of Results ; Structure-Activity Relationship ; Vaccines, Subunit/immunology ; Vaccinology/methods
    Chemical Substances Antigens, Viral ; Ebola Vaccines ; Epitopes ; Vaccines, Subunit
    Language English
    Publishing date 2020-05-01
    Publishing country Netherlands
    Document type Journal Article
    ZDB-ID 563292-4
    ISSN 1878-3279 ; 0171-2985
    ISSN (online) 1878-3279
    ISSN 0171-2985
    DOI 10.1016/j.imbio.2020.151949
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    In stock of ZB MED Cologne/Königswinter

    Ud II Zs.32: Show issues Location:
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  6. Article: Age and gender-related differences in quality of life of Bangladeshi patients with Down Syndrome: A cross-sectional study.

    Islam, Nafisa Nawal / Sumit, Ahmed Faisal / Chowdhury, Md Mottakin / Ullah, Md Asad / Araf, Yusha / Sarkar, Bishajit / Gozal, David

    Heliyon

    2022  Volume 8, Issue 1, Page(s) e08777

    Abstract: Currently available screening instruments for evaluation of individuals with intellectual disabilities do not capture all the complications associated with Down Syndrome (DS). Here, we examined age and gender-specific variability revolving around major ... ...

    Abstract Currently available screening instruments for evaluation of individuals with intellectual disabilities do not capture all the complications associated with Down Syndrome (DS). Here, we examined age and gender-specific variability revolving around major challenges related to ophthalmologic and auditory health, social integration, daily life, and behavioral problems in 468 (age: 2-84 years) individuals with DS living in all eight divisions of Bangladesh. More than half of the children presented with significant difficulty in walking or other targeted movements compared with 37.9% of adolescents (
    Language English
    Publishing date 2022-01-19
    Publishing country England
    Document type Journal Article
    ZDB-ID 2835763-2
    ISSN 2405-8440
    ISSN 2405-8440
    DOI 10.1016/j.heliyon.2022.e08777
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  7. Article: Engineering a novel subunit vaccine against SARS-CoV-2 by exploring immunoinformatics approach.

    Sarkar, Bishajit / Ullah, Md Asad / Araf, Yusha / Rahman, Mohammad Shahedur

    Informatics in medicine unlocked

    2020  Volume 21, Page(s) 100478

    Abstract: As the number of infections and deaths caused by the recent COVID-19 pandemic is increasing dramatically day-by-day, scientists are rushing towards developing possible countermeasures to fight the deadly virus, SARS-CoV-2. Although many efforts have ... ...

    Abstract As the number of infections and deaths caused by the recent COVID-19 pandemic is increasing dramatically day-by-day, scientists are rushing towards developing possible countermeasures to fight the deadly virus, SARS-CoV-2. Although many efforts have already been put forward for developing potential vaccines; however, most of them are proved to possess negative consequences. Therefore, in this study, immunoinformatics methods were exploited to design a novel epitope-based subunit vaccine against the SARS-CoV-2, targeting four essential proteins of the virus i.e., spike glycoprotein, nucleocapsid phosphoprotein, membrane glycoprotein, and envelope protein. The highly antigenic, non-allergenic, non-toxic, non-human homolog, and 100% conserved (across other isolates from different regions of the world) epitopes were used for constructing the vaccine. In total, fourteen CTL epitopes and eighteen HTL epitopes were used to construct the vaccine. Thereafter, several
    Keywords covid19
    Language English
    Publishing date 2020-11-11
    Publishing country England
    Document type Journal Article
    ISSN 2352-9148
    ISSN 2352-9148
    DOI 10.1016/j.imu.2020.100478
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  8. Article ; Online: Blueprint of epitope-based multivalent and multipathogenic vaccines: targeted against the dengue and zika viruses.

    Sarkar, Bishajit / Ullah, Md Asad / Araf, Yusha / Das, Sowmen / Hosen, Mohammad Jakir

    Journal of biomolecular structure & dynamics

    2020  Volume 39, Issue 18, Page(s) 6882–6902

    Abstract: Both dengue virus (DENV) and zika virus (ZIKV) belong to the highly ... ...

    Abstract Both dengue virus (DENV) and zika virus (ZIKV) belong to the highly infectious
    MeSH term(s) Animals ; Dengue/prevention & control ; Dengue Virus ; Epitopes, B-Lymphocyte ; Molecular Docking Simulation ; Vaccines ; Zika Virus ; Zika Virus Infection/prevention & control
    Chemical Substances Epitopes, B-Lymphocyte ; Vaccines
    Language English
    Publishing date 2020-08-08
    Publishing country England
    Document type Journal Article
    ZDB-ID 49157-3
    ISSN 1538-0254 ; 0739-1102
    ISSN (online) 1538-0254
    ISSN 0739-1102
    DOI 10.1080/07391102.2020.1804456
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    In stock of ZB MED Cologne/Königswinter

    Zs.A 2093: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (1.OG)
    ab Jg. 2022: Lesesaal (EG)

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  9. Article ; Online: Engineering a Novel Subunit Vaccine against SARS-CoV-2 by Exploring Immunoformatics Approach

    Sarkar, Bishajit / Ullah, Md. Asad / Araf, Yusha / Rahman, Mohammad Shahedur

    Informatics in Medicine Unlocked

    2020  , Page(s) 100478

    Keywords covid19
    Language English
    Publisher Elsevier BV
    Publishing country us
    Document type Article ; Online
    ISSN 2352-9148
    DOI 10.1016/j.imu.2020.100478
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  10. Article ; Online: Genome Sequences of Two Novel Coronavirus (SARS-CoV-2) Isolates from Dhaka, Bangladesh.

    Matin, M Abdul / Nahid, Abdullah Al / Sarkar, Bishajit / Ullah, M Asad / Araf, Yusha / Adnan, Nihad / Islam, Rashedul / Rahman, Mohammad Shahedur

    Microbiology resource announcements

    2021  Volume 10, Issue 27, Page(s) e0051121

    Abstract: This study reports the genome sequences of two severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) strains detected in the nasopharyngeal swab specimens of two coronavirus disease 2019 (COVID-19) patients from Dhaka, Bangladesh. ...

    Abstract This study reports the genome sequences of two severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) strains detected in the nasopharyngeal swab specimens of two coronavirus disease 2019 (COVID-19) patients from Dhaka, Bangladesh.
    Language English
    Publishing date 2021-07-08
    Publishing country United States
    Document type Journal Article
    ISSN 2576-098X
    ISSN (online) 2576-098X
    DOI 10.1128/MRA.00511-21
    Database MEDical Literature Analysis and Retrieval System OnLINE

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