Saifullah, Ph.D.

SAIFULLAH, Ph.D.

Address: New uposhahar, Jashore sadar, Jashore-7408, Bangladesh. 

Email: d.saifullah@just.edu.bd

Office Address

Lecturer

Department of Genetic Engineering and Technology

Jashore University of Science and Technology (JUST)

Jashore-7408, Bangladesh.

Profile: https://just.edu.bd/t/gebt-dr-saifullah 

E-mail: d.saifullah@just.edu.bd

Research Experience

JSPS Postdoctoral Fellow (October 2022 to 2023)

Institute: Department of Molecular Therapy, National Center of Neurology and Psychiatry (NCNP), Kodaira City, Tokyo 187-8502, Japan

Research topic:

●   Development of RNA therapy for neuromuscular diseases including Duchenne Muscular Dystrophy.

●   Supervisor: Yoshitsugu Aoki, MD, Ph.D., NCNP.

●   Research fund: Grant-in-Aid for JSPS Fellows from the Japan Society for the Promotion of Science (JSPS) [PI: Yoshitsugu Aoki, MD, Ph.D.; Co-PI: Saifullah, Ph.D.].

Postdoctoral Research Fellow (October 2021 to September 2022)

Institute: Department of Molecular Therapy, National Center of Neurology and Psychiatry (NCNP), Kodaira City, Tokyo 187-8502, Japan.

Research topic:

●       Molecular mechanism of muscle impairment and development of gene therapy for SOD1 positive Amyotrophic Lateral Sclerosis.

●       Supervisor: Yoshitsugu Aoki, MD, Ph.D., NCNP.

●       Research fund: Grant-in-Aid for Scientific Research from the Japan Society for the Promotion of Science (JSPS) [PI: Yoshitsugu Aoki, MD, Ph.D., NCNP].

Ph.D. Research (October 2018 to September 2021)

University: Area of Bioscience and Biotechnology, Japan Advanced Institute of Science and Technology (JAIST), Nomi City, Ishikawa 923-1292, Japan.

Research topic:

●     Optimized the CRISPR-Cas13a activity and functionality using luciferase transcript (FLuc) as a target transcript.

●     Developed new therapeutic strategy for ALK-positive lung cancer using the CRISPR-Cas13a system.

●     Inspected ALK as a prognostic biomarker using integrative bioinformatics.

●     Supervisor: Professor Dr. Toshifumi Tsukahara, JAIST.

●     Research fund: Grant-in-Aid for Scientific Research from the Japan Society for the Promotion of Science (JSPS) (Grant ID: 17H02204 and 18K19288) [PI: Professor Dr. Toshifumi Tsukahara, JAIST].

Masters Research (October 2016 to September 2018)

University: Area of Bioscience and Biotechnology, JAIST.

Research topic:

●   Demonstrated an economical DNA chip that can evaluate more than 1,000 Single Nucleotide Polymorphisms (SNPs) at a cost of less than $10 per chip.

●   Investigated novel Single Nucleotide Polymorphism (SNP) using SNP-RFLP method in human cells.  

●   Supervisor: Professor Dr. Toshifumi Tsukahara, JAIST.

●   Research fund: Grant-in-Aid for Scientific Research from the Japan Society for the Promotion of Science (JSPS) (Grant ID: 26670167 and 17H02204) [PI: Professor Dr. Toshifumi Tsukahara, JAIST].

Undergraduate Research (March 2015 to October 2015)

University: Department of Genetic Engineering & Biotechnology, Jashore University of Science and Technology (JUST), Jashore-7408, Bangladesh.

Research topic:

●   Conducted a survey from street food vendors and evaluated quality of the foods in the laboratory.

●   Supervisor: Assistant Professor Biplab Kumar Dash, JUST.

Education

Ph.D. in Materials Science (Major: Bioscience and Biotechnology) (September 2021)

♦      University: Japan Advanced Institute of Science and Technology (JAIST), Nomi City, Ishikawa 923-1292, Japan.

♦   Dissertation: A programmable RNA knockdown using CRISPR-Cas13 ribonuclease toward gene therapy.

♦      Supervisor: Professor Dr. Toshifumi Tsukahara, JAIST.

♦      Results: 90% marks in Dissertation.

Master of Science in Bioscience and Biotechnology (September 2018)

♦      University: Japan Advanced Institute of Science and Technology (JAIST), Japan.

♦   Thesis: Proposing a probes-on-carrier based oligo-DNA microarray method for SNPs detection.

♦      Secured CGPA 3.96 out of 4.00 scale.

♦      Obtained Excellent Student Award.

♦      Supervisor: Professor Dr. Toshifumi Tsukahara, JAIST.

Bachelor of Science in Genetic Engineering and Biotechnology, (November 2015)

♦  University: Jashore University of Science and Technology (JUST), Jashore-7408, Bangladesh.

♦    Thesis: Analysis of Food Hygiene Knowledge of Street Food Vendors and Microbiological Quality of Fuska and Jhalmuri in Jashore Town.

♦      Graduated with CGPA 3.65 out of 4.00 scale (Position: Third).

♦      Supervisor: Biplab Kumar Dash, JUST.

Training 

Ph.D. Research Student (August 2019 to October 2019; Two months)

Institute: Department of Molecular Therapy, National Center for Neurology and Psychiatry (NCNP), Kodaira City, Tokyo 187-8502, Japan.

Research topic:

●   Knockdown of Mvp gene and elucidation of its association in muscle cell proliferation, differentiation, apoptosis, and autophagy.

●     Techniques I learned: lentivirus production and transduction, myoblast culture and isolation, proliferation and apoptosis assays. 

●      Supervisor: Yoshitsugu Aoki, MD, Ph.D., NCNP.

Masters Student (December 2017 to April 2018; Six months)

University: JAIST, Japan.

Research topic:

●   Inspected in vivo protein crystallization which was mimic to check the disease-relevant protein’s structural analysis.

●     Techniques I learned: Gene cloning, human cell culture, transfection, inverted microscope analysis, and in-vivo protein crystal formation. 

●   PI: Associate Professor Dr. Hidekazu Tsutsui, JAIST.

Undergraduate Student (June 20 to 25, 2015; Five days)

Institute: National Institute of Biotechnology (NIB), Savar, Dhaka, Bangladesh.

Training topic:

●   Hands-on training in DNA extraction and quantification, Tissue culture, microbial culture, basic bioinformatics tools, and intellectual property rights

Teaching Portfolio

• Conducted Cell Biology, Developmental Biology, Medical Biotechnology, and Molecular Genetics in undergratuage level and Bioinformatics in molecular biology in Masters of Science level in the department of Genetic Engineering and Biotechnology at JUST (June 2023-Present).

List of Publication

(a) Research Article (peer-reviewed)

1. Saifullah & Tsukahara T., 2022. Integrated analysis of ALK higher expression in human cancer and downregulation in LUAD using RNA molecular scissors. Clinical and Translational Oncology–Springer (Q2, IF 3.4), 24(9):1785-1799. (PMID: 35486222).

[Contribution: I performed all of the laboratory work, wrote the first draft of the manuscript, and was the primary author of the paper]

2. Saifullah, Motohashi N., Tsukahara T., Aoki Y., 2022. Development of therapeutic RNA manipulation for muscular dystrophy. Frontiers in Genome Editing (Q1, IF 4.9), 4:863651. (PMCID: PMC9127466) (Invited Review Article).

[Contribution: I wrote the first draft of the manuscript and was the primary author of the paper]

3. Saifullah & Tsukahara T., 2022. Integrated analysis of clinical consequence and associated gene of ALK expression in ALK-positive human cancer. Heliyon–CellPress (Q1, IF 3.77), 8(7): e09878. (PMCID: PMC9293659).

[Contribution: I carried out all of the laboratory work, wrote the first draft of the manuscript, and was the first author of the paper]

4. Saifullah, Sakari M., Suzuki T., Yano S., Tsukahara T., 2020. Effective RNA knockdown using CRISPR-Cas13a and molecular targeting of the EML4-ALK transcript in H3122 lung cancer cells. Int. J. Mol. Sci. (Q1, IF 5.1) 21(23):8904. (PMCID: PMC7727695) (Selected as Top Download Papers in 2020-2021).

[Contribution: I carried out all of the laboratory work, wrote the first draft of the manuscript, and was the primary author of the paper]

5. Saifullah, Fuke S., Nagasawa H., Tsukahara T., 2019. Single nucleotide recognition using a probes-on-carrier DNA chip. BioTechniques (Q2, IF 2.74), 66(2):73-78. (PMID: 30744407).

[Contribution: I did co-work in the laboratory experiment, wrote the first draft of the manuscript, and was the first author of the paper]

6. Saifullah & Tsukahara T., 2018. Genotyping of single nucleotide polymorphisms using the SNP-RFLP method. BioScience Trends (Q1, IF 5.5), 12(3):240-246. (PMID: 30012914).

[Contribution: I performed all of the laboratory work, wrote the first draft of the manuscript, and was the primary author of the paper]

7.  Abdullah-Al-Mamun M., Saifullah, Rahman S.M.K., 2017. Assessment of Probiotic Properties of Isolated Lactic Acid Bacteria from Human Milk Sample. Advances in Bioresearch. (DOI: 10.15515/abr.0976-4585.8.6.140146).

[I partly wrote, formatted, and edited the manuscript, and was the second author of the paper].

8. Rifat-Al-Naser, Saifullah, Abdullah-Al-Mamun M., Hossain M.S., Arifuzzaman M., Saikot F.K., 2016. Probiotic Properties Profiling of Isolated Lactic Acid Bacteria from the Intestine of Channa punctata. Microbiology Research Journal International (DOI: 10.9734/mrji/2016/v17i45181)

[I co-prepared manuscript draft, formatted, edited, and was the second author of the paper].

(b) Abstract publication (peer-reviewed)

9. Saifullah, Sakari M., Suzuki T., Tsukahara T., 2022. RNA-guided CRISPR-Cas protein downregulates the oncogenic driver ALK expression in human lung cancer cell. European Journal of Human Genetics–Nature publishing group (Q1, IF 5.35);30 (Suppl 1):88-608. (PMID: 35393538).

10. Saifullah, Sakari M., Suzuki T., Yano S., Tsukahara T., July 2021. The CRISPR-Cas13a gene-editing system underlies a potential therapeutic strategy for EML4-ALK-positive lung cancer cells. Annals of Oncology–Elsevier (Q1, IF 56.7). 32: p. S347. (DOI: https://doi.org/10.1016/j.annonc.2021.05.737).

11. Saifullah, Shiratori M., Motohashi N., Uyeda A., Muramatsu R., Aoki Y., 2022. Elucidation of the molecular mechanism for skeletal muscle degeneration in Amyotrophic Lateral Sclerosis. The 8th Annual Meeting of Japan Muscle Society (JMS), The University of Tokyo, Japan (Poster ID: P-33).

12. Saifullah, Sakari M., Tsukahara T., 2020. Programmable RNA knockdown using CRISPR-Cas13a and therapeutic target for ALK-rearranged lung cancer. The 43rd Annual Meeting of the Molecular Biology Society of Japan (MBSJ) (Online ID: 2P-0069).

13.  Saifullah, Sakari M., Tsukahara T., 2019. Application of CRISPR-Cas13 machinery in disease treatment. The 42nd Annual Meeting of the MBSJ, Kyushu, Japan (Poster ID: 1P-0517).

14. Saifullah, Fuke S., Nagasawa H., Tsukahara T., 2018. Proposing a probes-on-carrier based oligo-DNA microarray method for SNPs detection. Japan-India Symposium on Materials Science 2018. JAIST, Japan (Poster).

15.  Saifullah, Akter S., Roy C.K., Dash B.K., 2015. Analysis of Common Food Safety Practices of Street Food Vendors and Microbiological Quality of Some Street Vended Foods in Jessore Town. Organizer: Bangladesh Society of Microbiologists (BSM) and Dept. of Microbiology, Dhaka University, Bangladesh.

Experimental Skills

Skills in Molecular & cellular biology: Mouse satellite cell isolation, Fusion indexing, Aneural AChR clustering analysis, CRISPR-Cas13a, qPCR, siRNA knockdown, shRNA knockdown, DNA/RNA extraction, RT-PCR, Recombinant DNA engineering, Cloning, Transfection using chemical methods and electroporation, DNA sequencing by Sanger method, Protein purification, Western Blot, Immunocytochemistry, Gel electrophoresis: Agarose, PAGE, SDS-PAGE, ELISA assay, MTT assay, Click-IT EdU cell proliferation assay, TUNNEL assay, Fluorescence microscopy, Confocal microscopy, SNP-RFLP, DNA Microarray, Cell-line culture (6-year experience): HEK293T, HeLa, H3122, H2228, C2C12, H2kmdx52 cells, mouse tail fibroblast, mouse primary myoblasts, and Bacteria culture.

Skills in Bioinformatics: RNA Seq data analysis using Galaxy tool, LC/MS proteomics data analysis, Gene Set Enrichment Analysis (GSEA), Cancer biomarker analysis, Primer design, and Molecular Docking (Intermediate level). 

Awards and Achievements

• Awarded JSPS Postdoctoral Fellowship standard program-2022–provided by the Japan Society for the Promotion of Science (JSPS).

•  Granted the Grant-in-Aid for JSPS Fellows (2.4 million yen) for research expenses from the Japan Society for the Promotion of Science (JSPS) as Co-PI, 2022.

•  Obtained JAIST foundation grant 2021 for attending the ESHG conference.

• Achieved JAIST Research grant 2020 for attending the JSMO 2021 annual meeting.

•  Received the Ministry of Education, Culture, Sports, Science and Technology (MEXT) Scholarship for Doctoral research program–(Oct. 2018 - Sep. 2021).

• Obtained the Ministry of Education, Culture, Sports, Science and Technology (MEXT) Scholarship for Master of Science program– (Oct. 2016 - Sep, 2018).

• Awarded Excellent Student Award in Masters of Science – 2018 (received from the president of JAIST).

•  Granted the Dutch-Bangla Bank Foundation (DBBF) Scholarship for Bachelor of Science program (from July 2011 to June 2015).

Society Affiliation

●       Member of Japan Muscle Society (JMS) (August 2022–Present)

●       Member of Molecular Biology Society of Japan (MBSJ) (Jan. 2019–Present)

●       Member of Bangladesh Association of Biotechnology Graduate (BABG) (2014–present)

●       American Society of Microbiology (ASM) (Outreach member) (2014–present)

Miscellaneous

●       Writing skills: I have written six complete research articles (See publication list) and three theses (PhD, MS, & BSc).

●       Software: GraphPad Prism, EndNote, Origin, Illustrator, Microsoft office, and Photoshop.

●       Language:

●       Bangla (Native)

●       English (Business level)

●       Japanese (Basic level)

●       Arabic (Basic level)

Referees

1.   Yoshitsugu Aoki, MD, Ph.D.

Director, Department of Molecular Therapy, National Institute of Neuroscience, National Center of Neurology and Psychiatry (NCNP), Kodaira City, Tokyo 187-8502, Japan.

Relationship: Postdoc Supervisor.

E-mail: tsugu56@ncnp.go.jp 

2.    Professor Dr. Toshifumi Tsukahara

Vice-president, Japan Advanced Institute of Science and Technology (JAIST), 1-1 Asahidai, Nomi City, Ishikawa 923-1292, Japan (www.jaist.ac.jp).

Professor, Area of Bioscience and Biotechnology, School of Materials Science, JAIST, Japan. Tel. +81-761-51-1640. Fax. +81-761-51-1149.

Relationship: Masters and Ph.D. Supervisor.

E-mail: tukahara@jaist.ac.jp 

3.    Biplab Kumar Dash

Assisstant Professor, Department of Genetic Engineering and Biotechnology (GEBT), Jashore University of Science and Technology (JUST), Jashore-7408, Bangladesh.

Relationship: B.Sc. Thesis supervisor.

E-mail: bk.dash.gebt@just.edu.bd  ( Or, biplab.iu@gmail.com)