AFOB Newsletter

Greetings AFOB community,

It is a great pleasure to introduce our team on the AFOB community. The Biochemical Engineering Laboratory (Kumada Group) in the Department of Molecular Chemistry at Kyoto Institute of Technology is conducting engineering research to maximize the potential of biomolecules, including antibodies, using original and unique approaches, and to contribute to the establishment of a healthy and safe society. Our research group focuses on development of next generation of biomolecular recognition reagents for more precise and selective affinity separation of biomolecules that has been considerably important in the fields of industrial biopharmaceutical production as well as sensitive immunological tests. We have particularly studied immobilization of antibodies and their fragments onto the surfaces of a variety of materials utilizing our original “Materials-Binding Peptides (MBPs)”. MBPs that are preferentially adsorbed on the target surfaces with strong binding affinity can be identified and isolated from our original protein/peptide resources and can be introduced at the terminal regions of target proteins such as single-chain variable fragments (scFvs) and single-domain antibodies (VHHs).

The MBP-fused scFv antibodies that we are developing are much smaller in molecular size than the conventional antibodies and can be densely immobilized on the surface of materials by strong binding affinity of MBPs. This adhesion region, namely MBPs can physically link the antibody itself to the surface of the substrate material. This technology is very unique and has many advantages and possibilities. In order to achieve the perfect immobilization of antibodies, it is also necessary to take on the great challenges of protein/peptide engineering, surface chemistry and materials science. Combination of our original technologies with the other distinguished technologies will create economical and precise biorecognition surface that will be highly useful for the purpose described above.

Our research group very welcomes graduate students and researchers to achieve the goals together, and we are looking forward to exchanging ideas, enhancing technologies and contributing health science with you in near future.

References

• Y. Kumada*, R. Tanibata, K. Yamamoto, H. Noguchi, A. Angelini, J. Horiuchi, Development and characterization of a latex turbidimetric immunoassay using rabbit anti-CRP single-chain Fv antibodies, Journal of Immunological Methods, in press
• Y. Kumada*, H. M. Rakotondravao, Y. Hasegawa, Y. Iwashita, H. Okura, S. Uchimura, J. Horiuchi, Strategies for selection and identification of rabbit single-chain Fv antibodies as ligand in affinity chromatography, Journal of Bioscience and Bioengineering, 134, 233-239 (2022)
• H. M. Rakotondravao, R. Takahashi, T. Takai, Y. Sakoda, J. Horiuchi, Y. Kumada*, Control of accessible surface area and height equivalent to a theoretical plate by grafted dextran during anion-exchange chromatography of therapeutic proteins, Journal of Chemical Engineering of Japan, 55, 267-274 (2022)
• J. Blazeck, C. S. Karamitros, K. Ford, C. Somody, A. Qerqez, K. Murray, N. T. Burkholder, N. Marshall, A. Sivakumar, W. C. Lu, B. Tan, C. Lamb, Y. Tanno, M. Y. Siddiqui, N. Ashoura, S. Coma, X. M. Z., K. McGovern, Y. Kumada, Y. J. Zhang, M. Manfredi, K. A. Johnson, S. D’Arcy, E. Stone, G. Georgiou, Bypassing evolutionary dead-ends and switching the rate-limiting step of a human immunotherapeutic enzyme, Nature Catalysis, 5, 952-967 (2022)
• Y. Kumada*, Y. Hasegawa, J. Horiuchi, Efficient and robust isolation of rabbit scFv antibodies using antigen-coupled multilamellar vesicles, Journal of Bioscience and Bioengineering, 131, 299-304 (2021)
• Y. Kumada*, Y. Miyamura, R. Tanibata, K. Takahashi, S. Ogasawara, F. Gondaira, J. Horiuchi, Design and site-directed immobilization of single-chain Fv antibody to polystyrene latex beads via material-binding peptides and application to latex turbidimetric assay, Journal of Bioscience and Bioengineering, 131, 84-89 (2021)
• Y. Kumada*, Y. Miyamura, R. Tanibata, K. Takahashi, S. Ogasawara, F. Gondaira, J. Horiuchi, Design and site-directed immobilization of single-chain Fv antibody to polystyrene latex beads via material-binding peptides and application to latex turbidimetric assay, Journal of Bioscience and Bioengineering, 131, 84-89 (2021)






Laboratory members

Greetings AFOB community,

My lab, Enzyme and Fermentation Biotechnology Laboratory, focuses on the indirect mechanism of PGPR (plant growth promoting rhizobacteria) for controlling plant diseases that are caused by various phytopathogenic fungi. Plants serve as the cornerstone of our global food supply, providing sustenance and nourishment to billions of people worldwide. However, the very foundation of this critical food chain is under constant threat from phytopathogenic fungi. Irish famine and Bengal famine were two of the major catastrophic events people had to deal with, and the main culprit behind these two famines were the phytopathogenic fungi. These phytopathogenic fungi have the potential to reduce crop yield by 40-90%. Chemical pesticides utilization as a means to mitigate plant diseases has given rise to a spectrum of adverse conditions, impacting both human well-being and the environment. In response to these challenges, our lab tries to explores the biocontrol potential of PGPR, offering a sustainable and environmentally friendly alternative.

Our studies involve the use of PGPR isolates: Achromobacter xylosoxidans, Bacillus aryabhattai MS3 epi, B. aryabhattai B8W22 endo, Enterobacter cloacae and Stenotrophomonas pavanii, reported earlier (1), against phytopathogenic fungi which were isolated from diseased plants such as rice, barley, mustard and wheat. We conducted a dual culture assay using both whole-cell and cell-free supernatant from PGPR and the co-culture assay for in vitro inhibition testing. Growth inhibition of isolated fungi was observed by all tested PGPR. Now, we aim to stretch the work under in vivo conditions, i.e., greenhouse trials followed by field trials. Utilization of this biocontrol agents could be the way forward to achieve the SDG (Sustainable Development Goals) goal of zero hunger, improve crop production in a commercially viable manner.

• Ref: 1 Jhuma TA, Rafeya J, Sultana S, Rahman MT, and Karim MM. 2021. Isolation of endophytic salt-tolerant plant growth-promoting rhizobacteria from Oryza sativa and evaluation of their plant growth-promoting traits under salinity stress condition. Frontiers in Sustainable Food System, 5, 250. https://www.frontiersin.org/articles/10.3389/fsufs.2021.687531/full

Hello, AFOB community!

The Fermentation and Enzyme Biotechnology Laboratory at the University of Dhaka is actively engaged in research across four key areas:

1. PGPR (Plant Growth-Promoting Rhizobacteria),
2. Fish Probiotics,
3. Neglected Tropical Diseases (NTD), and
4. Commercial Enzyme Production.

My specific focus here in this laboratory is on development of a molecular diagnostic (MDx) on lymphatic filariasis (LF), an NTD in Bangladesh. Lymphatic filariasis is a chronic parasitic disease transmitted by mosquitoes, and it ranks as the second leading cause of permanent deformities and disabilities worldwide. Once the filarial parasite is introduced into the human body through a mosquito bite, it takes up residence within the lymphatic nodes and vessels. Over the course of several years following the initial infection, the parasite disrupts lymphatic vessels, leading to the gradual onset of symptoms such as lymphedema, scrotal swelling, and even elephantiasis. As the patient remains asymptomatic for over a long period of time, say 10-15 years, owing to the longer incubation period of the agent, Wuchereria bancrofti, an effective diagnosis and treatment of the disease especially in the childhood age can greatly reduce the risk of permanent disability.

The development of a rapid and reliable molecular diagnostic system for LF holds the key to significantly reduce the morbidity of the disease. Our team is working on the designing of a suitable set of primer pairs for RT-PCR with a view to quantitatively estimate the disease burden on the affected individuals, studying the nature and characteristics of the circulatory agent in this geographic region, and sensitivity of the agent to the drugs already in operation for Mass Drug Administration (MDA). We hope the developed MDx could address the elimination program of LF from Bangladesh, thereby achieving one of the goals of SDGs.

Greetings AFOB community,

It’s a great pleasure to introduce my lab to the AFOB community. My lab, Clinical Microbiology Laboratory, focuses on phenotypic and genotypic characterization of multidrug-resistant Gram-negative bacteria isolated from clinical samples. Gram-negative bacteria are mostly responsible for multidrug-resistant infections in the community and hospital settings in Bangladesh. Prior investigations indicate a growing trend in the emergence of multidrug-resistance, rendering the management of these infections progressively challenging over time. Regular monitoring of pathogens and their AMR trends in clinical samples is crucial to keep track on the changing AMR landscape as well as to improve patient outcomes. So, our lab aims to conduct characterization of Gram-negative bacteria retrieved from clinical samples by phenotypic and genotypic techniques.

Our study includes the isolation of different Gram-negative bacteria from different clinical samples and their subsequent phenotypic and genotypic characterization. For phenotypic characterization, their antibiotic sensitivity and biofilm formation ability were tested by disc diffusion assay and microtiter plate assay respectively. Carbapenemase production potential was tested by Modified Hodge test for all the isolates that were carbapenem-resistant phenotypically. For genotypic analysis, Ribosomal DNA Restriction Analysis (ARDRA) and polymerase Chain Reaction (PCR) were performed to characterize microbial diversity and for molecular identification. Also, the underlying mechanism of fluoroquinolone resistance was assessed. Thus, our study provides an overview on the current status of antimicrobial resistance in clinically important Gram-negative bacteria and can serve as a basis for taking effective measures to control MDR infections. In the future, whole genome sequencing of the isolates will help in further understanding of the resistance mechanisms and origin of isolates. In addition, further research on alternative antimicrobial strategies including bacteriophages, bacteriocins, anti-biofilm agents can be done to control the evolution and transmission of such ESKAPE pathogens in clinical and environmental settings.