The 24th Academic Exchange Seminar
BetweenShanghai Jiao Tong University
And
Osaka University
General Opening Session
Date:
Time:

November 29th, 2022
CST13:00～13:30 / JST14:00～14:30 (online)

13:00 (JST14:00)
Opening words by moderator:
Dai Yanjun Professor, Shanghai Jiao Tong University
13:02 (JST14:02) Opening remarks:
HUANG Zhen, Dean of College of Smart Energy Former Vice President,
Shanghai Jiao Tong University, Academician of the Chinese Academy of Engineering
13:07 (JST14:07)
Opening remarks:
KAWAHARA Genta, Vice President, Osaka University
13:12 (JST14:12)
Brief explanation of collaboration in each field:
Materials Science (OU), Joining & Welding (SJTU)
Information Sciences (OU), Naval Architecture & Ocean Engineering (SJTU)
Industrial Biotechnology (OU), Chemistry (SJTU),
Combustion Engineering (OU),Smart City Studies (SJTU)
13:25 (JST14:25)
Closing words by moderator / Group photo
Dai Yanjun, Professor, Shanghai Jiao Tong University

Date: November 29, Tuesday, 2022
Time:

CST15:00～17:30 / JST16:00～18:30“4th Industrial Biotechnology Symposium”

Industrial Biotechnology

Co-organizer: Industrial Biotechnology Division, Institute for Open and Transdisciplinary Research
Initiatives, OTRI, Osaka U.
Zoom address https://zoom.us/j/93415620551
Meeting ID: 934 1562 0551 PW: 452565

Opening remarks Prof. Takeshi Omasa (Grad Sch of Eng and OTRI, Osaka U)
CST 15:00-16:20 (JST 16:00-17:20)
20 min Presentation, including Discussion
15:00-15:20 (JST 16:00-16:20) Chairperson: Prof. Takeshi Omasa
Professor Susumu Uchiyama(Department of Biotechnology, Graduate School of Engineering, Osaka University)"Biophysical characterizations of AAV vectors for gene therapy"
15:20-15:40 (JST 16:20-16:40) Chairperson: Prof. Linquan Bai
Professor Fei Tao(Shanghai Jiao Tong University)"Carbon-negative synthetic biology: biomanufacture of biodegradable plastics"

1

15:40-16:00 (JST 16:40-17:00) Chairperson: Prof. Takeshi Omasa
Associate Professor Masaru Kojima(Department of Materials Engineering Science, Graduate School of Engineering Science,
Osaka University)"Measuring the mechanical properties of cell using a two-fingered microhand system"
16:00-16:20 (JST 17:00-17:20) Chairperson: Prof. Linquan Bai
Tenure-track Associate Professor Rui Qing
(Department of Bioengineering, School of Life Sciences and Biotechnology, Shanghai Jiao
Tong University)"QTY code: the membrane protein solubilization tool and its applications"

CST 16:20-18:20 (JST 17:20-18:20) Student session (Zoom: breakout room 1 and 2)
6min Presentation, 3min Discussion
Chairperson: Associate Prof. Chen-Guang Liu, Associate Prof. HiroyaTomita
Room 1 : Associate Prof. HiroyaTomita

Room 2: Associate Prof. Chen-Guang Liu

16:20-16:30 (JST 17:20-17:30)
Soichiro Ikuta"In situ visualization of glutamate decarboxylase
activity in germinating plant seed using mass
microscope"
16:30-16:40 (JST 17:30-17:40)
Rui Wang"Lipid turnover and SQUAMOSA promoter-binding
proteins mediate variation in fatty acid desaturation
under early nitrogen deprivation revealed by lipidomic
and transcriptomic analyses in Chlorella pyrenoidosa "16:40-16:50 (JST 17:40-17:50)
Shunsuke Ito"Metabolic engineering of Solanum species for
efficient production of useful steroidal compounds"
16:50-17:00 (JST 17:50-18:00)
Kaikai Tian
"Synergistic effect of fibrous structure and stiffness ofdesigner protein hydrogels on bone marrowmesenchymal stem cell behaviors"
17:00-17:10 (JST 18:00-18:10)
Kai Torng Ang"Effect of methylglyoxal on growth maintenance ofhuman mesenchymal stem cells"
17:10-17:20 (JST 18:10-18:20)
Ru-Xiang Deng"Characterization of the lomofungin biosynthetic genecluster from Streptomyces lomondensis S015"
17:20-17:30 (JST 18:20-18:30)
Ryo Otsuka"Activation of cryptic Streptomyces secondary
metabolism by site-directed mutagenesis of ribosomal
RNA gene"

16:20-16:30 (JST 17:20-17:30)
Yiqun Huang"Community-integrated
multi-omics
faciliates
screening and isolation of the organohalide
dehalogenation microorganism"
16:30-16:40 (JST 17:30-17:40)
Chukwuebuka Maxwell Ononugbo"Engineering the β-sandwich domain 1 of athermostable protease for improved soluble expression
for novel target binding"
16:40-16:50 (JST 17:40-17:50)
Kai Jiang"Expanding the chemical diversity of fasamycin via
genome mining and biocatalysis"
16:50-17:00 (JST 17:50-18:00)
Kulachatr Panyawechamontri"The transient expression in Nicotiana benthamiana of
human acid sphingomyelinase for enzyme replacement
therapy"
17:00-17:10 (JST 18:00-18:10)
Ayturk Ali"Identification of sucrose utilization genes foransamitocin over-production from Actinosynnema
pretiosum"
17:10-17:20 (JST 18:10-18:20)
Ayano Hara
"Development of CRISPR/dCas9-VPR transcriptional
activation system in D. magna"
17:20-17:30 (JST 18:20-18:30)
Tian-Jie Ao"Cascade utilization of carbon resource in corn stover
to produce renewable energy products"

Closing remarks: Prof. Linquan Bai

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The 24th Academic Exchange Seminar
Between Shanghai Jiao Tong University and Osaka University

Presentation Title: Biophysical characterizations of AAV vectors forgene therapy
Keywords：Gene Therapy, Virus Vector, Adeno Associated Virus, Mass
Spectrometry
Name: Susumu Uchiyama
Affiliation and position:
Department of Biotechnology, Graduate School of Engineering, Osaka
University
Short biography and publications (up to three)Prof. Dr. Uchiyama is a biophysical chemist with over 25 years of experiences in studying solution biophysics ofproteins and protein complexes, by using various kinds of biophysical methods. His research interest includes
development of characterization methods and formulation for therapeutic proteins and virus vectors. Container
closure system for biopharmaceuticals and vectors with better quality and more safety is also in his research scope.
Recent years he is leading a Japan national project for the development of characterization and quality control ofvirus vectors for gene therapy. He has published more than 250 peer-reviewed papers including AAV
characterizations and reviews. He serves on the Editorial Advisory Boards for Journal of Pharmaceutical Sciences.
1) Yoneda S, Torisu T, Uchiyama S. Development of syringes and vials for delivery of biologics: current challenges
and innovative solutions. Expert Opin Drug Deliv. 18, 459-470 (2021).
2) Uchiyama S., Noda M., and Krayukhina E. Sedimentation velocity analytical ultracentrifugation forcharacterization of therapeutic antibodies. Biophy. Rev. 10, 259-269 (2018).
3) Uchiyama, S. Liquid formulation for antibody drugs. Biochim Biophys Acta. 1844, 2041-2052 (2014).

Abstract
Adeno-associated virus (AAV) vector is one of the most frequently used viral vector platforms used in gene therapies.
As the scalable production of AAV vector is developed and the number of clinical trials is increased, more detailed
and accurate characterizations of AAV vector are required. Unlike biopharmaceuticals, a certain number of species
with similar properties to authentic AAV full particle are inevitably included in AAV product even after all purification
processes. The difficulty of AAV characterizations originates not only from that AAV is composed of proteins andnucleic acid but also sample amount that can be subjected to biophysical analysis is limited. We have beendeveloped several analytical methods for AAVs. For example, the confirmation of primary structure is performed byliquid chromatography mass spectrometry (LC-MS) and the ratio of VP proteins can be accurately determined by
the combination approach using capillary electrophoresis CE-SDS and LC-MS. In this presentation, status and future
perspectives of biophysical characterizations of AAV vectors will be introduced.
[Reference] Oyama H, Ishii K, Maruno T, Torisu T, Uchiyama S. Characterization of Adeno-Associated Virus Capsid
Proteins with Two Types of VP3-Related Components by Capillary Gel Electrophoresis and Mass Spectrometry.
Hum. Gene Ther. 32, 1403-1416 (2021).

As of Nov. 6, 2022

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The 24th Academic Exchange Seminar
Between Shanghai Jiao Tong University and Osaka University

Presentation
Title:
Carbon-negativesynthetic
biology:biomanufacture of biodegradable plastics
Keywords: synthetic biology, carbon capture, biodegradable
plastic, cyanobacteria
Name: Fei Tao
Affiliation and position:
Shanghai Jiao Tong University, Professor
Short biography and publications (up to three)
Fei Tao was born in Anhui Province of China in 1983. He went to Shandong University to study and obtaineda Bachelor's degree in pharmacy (2004) and a Doctoral degree in microbiology (2009). After that, he joined
Shanghai Jiao Tong University and has worked till now. From 2013 to 2014, he was a postdoctoral researcher
at the Massachusetts Institute of Technology. His current main interests include synthetic biology, metabolic
science, and biosensors.
1. Tan, C., Xu, P. & Tao, F.*, 2022 Carbon-negative synthetic biology: challenges and emerging trends ofcyanobacterial technology. Trends Biotechnol. 40, 1488-1502.
2. Tan, C., Tao, F.* & Xu, P.*, 2022 Direct carbon capture for the production of high-performance biodegradable
plastics by cyanobacterial cell factories. Green Chem., 24, 4470-4483.
3. Liu, H., Ni, J., Xu, P., Tao, F.*, 2018. Enhancing light-driven 1,3-propanediol production by using naturalcompartmentalization of differentiated cells. ACS Synth. Biol., 7, 2436-2446.
Abstract
Carbon emissions since the Industrial Revolution have significantly changed the Earth's climate, causing
more serious environmental problems such as extreme weather. Synthetic biology is an emerging advanced
technology. Taking advantage of it, people are expected to develop new and advanced green carbon-capture
technologies to achieve carbon reduction. Plastic pollution is another serious environmental problem faced byhumanity. Deleting and using degradable plastics is considered the ultimate solution for plastic pollution. In thisreport, we will present and discuss our research work in the production of degradable plastics using synthetic
biotechnology. First, we will explore the basic concepts and scope of carbon-negative manufacturing and lightdriven synthetic biology. We then will discuss the links between plastic pollution, degradable plastics, andsustainable production. Afterward, we use experiments as research work to explore the realization of carbonnegative production of degradable plastics. Finally, we will propose our prospects for the future of carbonnegative manufacturing of materials.

As of Nov. 29, 2022

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The 24th Academic Exchange Seminar
Between Shanghai Jiao Tong University and Osaka University

Presentation Title: Measuring the mechanical properties of cell using a
two-fingered microhand system
Keywords ： Micromanipulation, Cell stiffness, Force measurement,
Mechanobiology of single cells
Name: Masaru Kojima
Affiliation and position:
Department of Materials Engineering Science, Graduate School ofEngineering Science, Osaka University, Associate professor
Short biography and publications (up to three)
Masaru Kojima received his Ph.D. from Nagoya Univ. in 2006. He had been Research Fellow with the
Department of Biology, Nagoya Univ. from 2006, Assistant Professor on GCOE with the Department of MicroNano Systems Engineering, Nagoya Univ. from 2008, Assistant Professor in Department of Systems
Innovation, Osaka Univ. from 2012, Assistant Professor in Department of Materials Engineering Science,
Osaka Univ. from 2019. His research interests include development of microrobotic system for biologicalapplication, integration of robotics and biomaterials engineering for tissue regeneration and bio-robotics.
1) Kawakami M., Kojima M. et al., Automated Microhand System for Measuring Cell Stiffness By Using Two Plate
End-Effectors, IEEE Robotics and Automation Letters 7(2), 2385-2390 (2022).
2) Mubarok W., Nakahata M., Kojima M., Sakai S., Nematode surface functionalization with hydrogel sheaths
tailored in situ, Materials today. Bio 15, 100328-100328 (2022).
3) Hidaka M., Kojima M., Nakahata M., Sakai S., Visible light-curable chitosan ink for extrusion-based and vat
polymerization-based 3d bioprintings, Polymers 13(9), 1382 (2021).

Abstract
In vivo, cells are constantly exposed to various stimuli, and these stimuli play an important role in determining thefate of cells. Therefore, there is a increasing demand to establish techniques for manipulating the environment
around cells and tissues, in addition to measuring their characteristics. In particular, various techniques have been
proposed to measure specific cellular responses to various external stimuli and to realize unprecedented analysis.
In this background, we have developed a compact microhand system that can approach cells dexterously andrapidly. Furthermore, based on this microhand technology, we also developed a new end-effector that can measure
the stiffness of cells and small tissues. We are still developing the system and realizing a variety of stimulation, suchas chemical and thermal stimulation, in addition to force stimulation. In this seminar, we introduce a microhand
system that enables the application of multimodal stimuli such as force stimulation as well as local chemical
stimulation, and report an actual example of application of force stimulation response measurement to cell
evaluation.

As of Nov. 11, 2022

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The 24th Academic Exchange Seminar
Between Shanghai Jiao Tong University and Osaka University

Presentation Title: QTY code: the membrane protein solubilization
tool and its applications
Keywords：membrane proteins, protein design, GPCR, therapeutics,
biosensing
Name:

Rui Qing

Affiliation and position:
Tenure-track associate professor, Department of Bioengineering,
School of Life Sciences and Biotechnology, Shanghai Jiao Tong
University.
Short biography and publications (up to three)
Rui Qing earned his Ph.D. degree in Materials Science and worked on advanced battery technology at
University of Florida, received postdoctoral training in Media Lab and was a research scientist at Koch
Institute for Integrative Cancer Research at MIT. Dr. Qing has a multi-disciplinary scientific background inboth material science and molecular biology. He co-developed with Dr. Shuguang Zhang the QTY code formembrane protein solubilization, and expanded its application in therapeutics and biosensing. His current
research focus is to advance the design methodology of membrane proteins and the molecular level
integration in bioelectronics, so as to address the societal challenges in human health and sustainability.
1. R. Qing, et al., 2022, Protein design: From the aspect of water solubility, Chemical Reviews, (issue cover).
2. R. Qing, et al., 2020, Non-full-length water-soluble CXCR4QTY and CCR5QTY chemokine receptors:
implication for overlooked truncated but functional membrane receptors, iScience, 23-12: 101670.
7. R. Qing, et al., 2019, QTY code designed thermostable and water-soluble chimeric chemokine receptors
with tunable ligand affinity, Proceedings of the National Academy of Sciences, 116-51: 25668-25676.
Abstract
Membrane proteins comprise about 30% of the open reading frames in the genomes of higher eukaryotes
and represent indispensable sets of biological functions that make up over 60% of therapeutic targets for
drugs. Yet large-scale synthesis, characterization and utilization of these functional molecules lag far behindsoluble proteins as they are difficult to overexpress and tend to aggregate in aqueous conditions due tomolecules’ hydrophobicity, especially for multi-pass TM proteins like GPCRs (G-protein couple receptor).
Traditional means to stabilize the protein for their study requires arduous, non-transferrable efforts that are
expensive and time-consuming, while limit their use beyond lab benches.
Here we devise a simple tool named QTY code to regulate the solubility of these hydrophobic receptors,
by pairwise amino acid substitution in the transmembrane region. Over 10 membrane receptors weresuccessfully solubilized, expressed and experimentally verified for ligand binding functions. The functionalsoluble variants of membrane receptors enable further biomedical use as 1), antibody-like decoy receptors
for immunoregulation in vivo; 2) specific and sensitive probes in affinity-based biomimetic sensing platform
with designated diagnostics purposes. Our approach not only enables the readily design of membraneproteins for functional and mechanistic study, but also produce a novel type of bio-nanomaterials that was
not previously not attainable.
As of Nov. 29, 2022

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The 24th Academic Exchange Seminar
Between Shanghai Jiao Tong University and Osaka University

Presentation Title:

In situ visualization of glutamate decarboxylase activity ingerminating plant seed using mass microscope

Keywords：mass microscope, glutamate decarboxylase, enzymatic activity
Photo
Name:

Soichiro Ikuta

Affiliation and position:
Department of Biotechnology, Osaka University 3rd year PhD student
Abstract

Visualizing the distribution of enzymes is vital for understanding physiologicalphenomena. Recently, mass spectrometry imaging (MSI)-based enzyme histochemistry has
been developed as a novel method to visualize the localization of enzymatic activity. It can beapplied to enzyme histochemistry as it detects products from the supplied substrate using
enzymes present on the tissue sections. However, enzyme histochemistry using MSI has notbeen applied to plant tissue samples.
Glutamate decarboxylase (GAD, EC:4.1.1.15) is an enzyme that catalyzes thedecarboxylation reaction of L-glutamic acid to produce γ-aminobutyric acid(GABA). GABA
biosynthesis is important both in the field of food chemistry and plant physiology. Therefore, theobjective of this study was to develop a method to visualize the localization of GAD enzyme
activity in germinating legume seeds using enzyme histochemistry with MSI. To achieve thisobjective, conversion by GAD enzyme was confirmed on the sections, and then the enzymatic
reaction parameters were optimized to visualize the localization of GAD activity on germinatedsoybean seed sections using MSI. Subsequently, the results were evaluated using liquid
chromatography-mass spectrometry (LC/MS) analysis. In addition, tissue-specific localization of
GAD activity was further investigated in detail. Finally, the applicability of this method was verified
using germinated alfalfa seeds. As a result, GAD activity in legume seeds was successfully
visualized using MSI. This report is the first example of an MSI-based enzyme histochemistry
technique applied to plant samples.
As of Nov.29, 2022

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The 24th Academic Exchange Seminar
Between Shanghai Jiao Tong University and Osaka University

Presentation Title: Lipid turnover and SQUAMOSA promoter-binding proteins
mediate variation in fatty acid desaturation under early nitrogen deprivation revealed bylipidomic and transcriptomic analyses in Chlorella pyrenoidosa

Keywords: microalgae, nitrogen deprivation, fatty acid desaturation, lipid turnover
Name: Rui Wang
Affiliation and position:
School of Life Sciences and Biotechnology, Shanghai Jiao Tong University
Ph.D. candidate
Short biography and publications (up to three)
Rui Wang is a Ph.D. candidate at Shanghai Jiao Tong University. His research focuses on fatty aciddesaturation of microalgae affected by availability of nitrogen. He applied lipidomic, transcriptomic analyses,
and functional characterization to identify key transcription factors in determining fatty acid desaturation.
Publications:
Wang R and Miao X (2022) Lipid turnover and SQUAMOSA promoter-binding proteins mediate variation in
fatty acid desaturation under early nitrogen deprivation revealed by lipidomic and transcriptomic analyses
in Chlorella pyrenoidosa. Front. Plant Sci. 13:987354. doi: 10.3389/fpls.2022.987354

Abstract
Nitrogen deprivation induces variations in fatty acid desaturation in microalgae, which determines theperformance of biodiesel and the nutritional value of bioproducts. However, the detailed scenario and theunderlying regulatory mechanism remain unclear. In this study, we attempt to outline these scenario andmechanisms by performing biochemical, lipidomic, and transcriptomic analyses in Chlorella pyrenoidosa andfunctional characterization of transcription factors in Yarrowia lipolytica. We found that early nitrogendeprivation dramatically reduced fatty acid desaturation without increasing lipid content. The contents ofpalmitic acid (16:0) and oleic acid (18:1) dramatically increased to 2.14 and 2.87 times that of nitrogen
repletion on the second day, respectively. Lipidomic analysis showed the transfer of polyunsaturated fatty
acids from phospholipids and glycolipids to triacylglycerols, and an increase in lipid species with 16:0 or 18:1
under nitrogen deprivation conditions. Upregulated stearoyl-ACP desaturase and oleyl-ACP thioesterase
promoted the synthesis of 18:1, but restricted acetyl-CoA supply revealed that it was the intensive lipid
turnover instead of an attenuated Kennedy pathway that played an important role in the variation in fatty acidcomposition under early nitrogen deprivation. Finally, two differentially expressed SQUAMOSA promoterbinding proteins (SBPs) were heterologously expressed in Y. lipolytica, demonstrating their role in promoting
the accumulation of total fatty acid and the reduction in fatty acid desaturation. These results revealed the
crucial role of lipid turnover and SBPs in determining fatty acid desaturation under early nitrogen deprivation,
opening new avenues for the metabolic engineering of fatty acid desaturation in microalgae.
As of Nov. 29, 2022

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The 24th Academic Exchange Seminar
Between Shanghai Jiao Tong University and Osaka University

Presentation Title: Metabolic engineering of Solanum species for
efficient production of useful steroidal compounds
Keywords：metabolic engineering, potato, Solanum, yamogenin
Photo
Name:

ITO Shunsuke

Affiliation and position:
Department of Biotechnology, Graduate School of Engineering, Osaka
University, Osaka, Japan. Master’s student.
Abstract
Yamogenin is one of useful compounds that show avariety of biological activities and synthesized in yam
plants (Dioscorea spp.). However, Yam-based efficient
production is difficult because it takes 4 to 5 years togrow and limited growing environment. Our laboratory
has revealed that CYP88B1 knockout potato
accumulates steroidal saponins (SSs), Protoneodioscin
and 25-epi-Indioside D instead of toxic steroid Fig. 1 Biosynthetic pathway of SSs and SGAs
glycoalkaloids (SGAs), α-solanine and α-chaconine. These SSs can be converted to Yamogenin byhydrolysis (Fig. 1). In this study, I aim to enhance productivity of protoneodioscin and 25-epi-Indioside D intissue culture of CYP88B1 knockout potato.
I induced microtuber formation in plastic-bag-culture (Fig. 2). To test the effect oflight on SS production in microtubers, harvested microtubers were incubated under
different light conditions for 7 days, however, there was no significant changes in
the contents of SS among examined condition. I also studied the effect of methyl
jasmonate (MeJA) on the formation of microtubers and SS contents. As a result,
100 μM MeJA treatment during microtuber induction significantly increased the SScontents and the number of microtuber. These reults indicate that tissue culture of Fig. 2 Microtuber
potato microtubers is effective for the production useful SS. In the future, further genetic modification andoptimization of culture conditions could lead to higher productivity of those SS.
As of November 16th, 2022

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The 24th Academic Exchange Seminar
Between Shanghai Jiao Tong University and Osaka University

Presentation Title: Synergistic effect of fibrous structure and stiffnessof designer protein hydrogels on bone marrow mesenchymal stem cell
behaviors
Keywords: Protein hydrogels, fibrous structure, stiffness, bone marrowmesenchymal stem cell
Name:

Kaikai Tian

Affiliation and position: State Key Laboratory of Microbial Metabolism,
Joint International Research Laboratory of Metabolic andDevelopmental Sciences, and School of Life Sciences andBiotechnology, Shanghai Jiao Tong University, PhD candidate.
Short biography and publications (up to three)
Kai-Kai Tian received his BS and MS degree from Yantai University and Dalian University of Technology,
respectively. Now, he is studying for the PhD degree at Shanghai Jiao Tong University. His research is focused on
design and fabrication of protein polymer-based hydrogels for tissue engineering.
Publications:
1. Tian KK, Huang SC, Xia XX, Qian ZG. Fibrous Structure and Stiffness of Designer Protein Hydrogels Synergize
to Regulate Endothelial Differentiation of Bone Marrow Mesenchymal Stem Cells. Biomacromolecules, 2022, 23(4):1777-1788.
2. Huang SC, Fan RX, Tian KK, Xia XX, Qian ZG. Controllable Fibrillization Reinforces Genetically Engineered
Rubberlike Protein Hydrogels. Biomacromolecules, 2021, 22(2): 961-970.

Abstract
Stiffness and fibrous structure provided by native extracellular matrix have been proven as important cues inregulating cell fates. However, an understanding of how stiffness and fibrous structure synergize to regulate cell
behaviors remains a challenge due to the inherent difficulties in making hydrogels with well-defined compositions,
tunable stiffness and structures. Here, we fabricate two series of fibrous and porous hydrogels based on engineered
resilin-silk-like and resilin-like protein polymers with similar stiffness.These two series of hydrogels were utilized as
two-dimensional culture platforms for BMSCs to explore the effects of stiffness and fibrous structure on their
proliferation and endothelial differentiation. For both hydrogel series, increasing compression modulus from about
8.5 to 23 kPa consistently promoted cell proliferation and endothelial differentiation. Nonetheless, the promoting
effects were more pronounced on the fibrous gels than their porous counterparts at all three stiffness levels, which
may be attributed to the differences in promoting the activation of transcription cofactor Yes-associated protein(YAP). Then, it was found that the stiffness signal activated YAP via spreading of focal adhesions and cytoskeleton,
whereas fibrous structure reinforced YAP activation by promoting the maturation of focal adhesions and associatedF-actin alignment. Therefore, our results clarify the synergistic effect of stiffness and fibrous structure on stem cell
behaviors and may guide the fabrication of designer proteinaceous matrices toward tissue engineering.

As of Nov. 29, 2022

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The 24th Academic Exchange Seminar
Between Shanghai Jiao Tong University and Osaka University

Presentation Title: Effect of methylglyoxal on growth maintenance ofhuman mesenchymal stem cells
Keywords ： Human mesenchymal stem cells; Extracellular matrix;
Growth behavior; Methylglyoxal
Name: Kai Torng ANG
Affiliation and position:
Department of Biotechnology, Graduate School of Engineering, Osaka
University, Ph.D. student
Abstract
In order to apply human mesenchymal stem cells (hMSCs) for practical uses in regenerative medicine,
culture strategies for producing a sufficient quantity of cells with stable quality are required. During the
expansion culture of hMSCs, local cell density exponentially increases in the culture vessel along with changes
in cell behaviors, causing cell contact inhibition and restricting cell proliferation. Previous studies on stem cellproliferation have reported that secretion and structural changes of the extracellular matrix (ECM) are importantfor maintaining cell proliferative potential. In this study, we investigated the proliferative effect of hMSCs using
methylglyoxal (MG), a precursor of advanced glycation end products which is capable of modifying ECM
structure.
hMSCs were seeded at a seeding density of 3.0 × 103 cells/cm2 and cultured for 144 h. At t = 48 h, hMSCs
were exposed to MG at 0.125 nM for 24 hours, and MG was removed from the culture at t = 72 h. In cells
without MG exposure, the apparent specific growth rate μapp (h–1) increased to (2.05 ± 0.3) × 10-2 h-1 in theearly phase of culture (t = 48-72 h), while the apparent specific growth rate decreased to (0.89 ± 0.04) × 10-2
h-1 in the late phase of culture (t = 72-144 h). On the other hand, the apparent specific growth rate of cells with
MG exposure in the late phase of culture was (1.50 ± 0.1) × 10-2 h-1, confirming the maintenance of apparent
specific growth rate of cells throughout the culture. The assembly and structural changes of the ECM main
components, fibronectin and collagen type I after MG exposure and withdrawal (t = 72 h and 144 h) were
examined by immunofluorescence staining. We confirmed that MG exposure disrupted fibronectin andcollagen fibril formation and it prevented its deposition in the ECM, however it did not influence fibronectin andcollagen type I secretion. These results suggest that MG could reform ECM and the reconstruction of thescaffold environment leads to the maintenance of cell proliferative capacity, indicating a new potential inestablishing an expansion culture system.
As of Nov 29, 2021

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The 24th Academic Exchange Seminar
Between Shanghai Jiao Tong University and Osaka University

Presentation Title: Characterization of the lomofungin biosynthetic genecluster from Streptomyces lomondensis S015

Keywords: natural phenazines, biosynthetic pathway, cluster refactoring
Name:

Ru-Xiang Deng

Affiliation and position:
School of Life Sciences and Biotechnology, Shanghai Jiao Tong University
PhD student
Short biography and publications (up to three)
Ru-Xiang Deng received the BS degree from Shandong University in 2017. He began as a master student(2017-2020) under the supervision of Professor Wei Wang at Shanghai Jiao Tong University. He continued
studying for his PhD degree with Professor Xue-Hong Zhang at Shanghai Jiao Tong University. His researchinterests are metabolic engineering of Streptomyces for the production of secondary metabolites, microbial
fermentation and identification of novel natural compounds.
Publications:
Deng RX, Zhang Z, Li HL, Wang W, Hu HB, Zhang XH. Identification of a Novel Bioactive Phenazine Derivativeand Regulation of phoP on Its Production in Streptomyces lomondensis S015. J Agric Food Chem. 2021
Jan 27;69(3):974-981.
Li HL, Deng RX, Wang W, Liu KQ, Hu HB, Huang XQ, Zhang XH. Biosynthesis and Characterization ofMedium-Chain-Length Polyhydroxyalkanoate with an Enriched 3-Hydroxydodecanoate Monomer from a
Pseudomonas chlororaphis Cell Factory. J Agric Food Chem. 2021 Apr 7;69(13):3895-3903.
Abstract
Natural phenazines are a class of multifunctional secondary metabolites that play an important role in the
biocontrol of various pathogens. Lomofungin is a highly substituted phenazine derivative that exhibit significant
bioactivities against several tumor cell lines and can be employed for the construction of biosensor. However,the biosynthetic pathway of lomofungin has not been fully understood. In this study, we firstly analyzed theputative gene cluster and proposed a possible biosynthetic pathway. Then, the intact gene cluster was
identified by heterogeneous expression combined with gene cluster refactoring. The function of modification
enzymes was further verified by combinatorial expression percursor genes with modification enzymes.
Specifically, SAM-dependent methyltransferase Lomo11 catalyzed the methylation of carboxyl group at C-1
position. Acyl-CoA dehydrogenase Lomo9 was responsible for the hydroxylation of the phenazine ring at
positions 4 and 9. Finally, lomofungin biosynthetic pathway was revised and extended. This study provided
valuable reference for the identification of phenazine biosynthetic pathways and discovery of phenazine
modification enzymes.

As of Nov. 29, 2022

12

The 24th Academic Exchange Seminar
Between Shanghai Jiao Tong University and Osaka University

Presentation Title: Activation of cryptic Streptomyces secondary
metabolism by site-directed mutagenesis of ribosomal RNA gene
Keywords ： Base-editing;Anti-Shine-Dalgarno
sequence;
Actinomycetes
Name:

OTSUKA Ryo

Affiliation and position:
Department of Biotechnology, Graduate School of Engineering, Osaka
University, Osaka, Japan. Master’s student.
Abstract

Streptomyces spp. produce a wide variety of bioactive compounds as secondary metabolites. However,most of the genes for the biosynthesis of secondary metabolites remain “cryptic”. Activation of these
cryptic secondary metabolism may lead to the discovery of new bioactive compounds. Ribosomal
mutagenesis is a technique to activate cryptic secondary metabolism in actinomycetes. The introductionof drug-resistant mutations into the ribosome has enabled the discovery of new bioactive compounds.
Here, we used Target-AID, a genome editing tool that replaces cytosines with thymines in target
sequences, to introduce mutations in anti-Shine-Dalgarno (anti-SD) sequences and activate cryptic
Streptomyces secondary metabolism. In the transformants of Streptomyces coelicolor A3(2), the cytosine
residues of anti-SD sequence of the rrnF gene were replaced by thymine residues. Mutant strain #1
produced more actinorhodin and undecylprodigiosin than the wild-type strain, while no such differenceswere observed in mutant strain #2, #3 and the wild-type strain. These results suggest that secondary
metabolism might be changed in the mutant strain #1.

As of November 14, 2022

13

The 24th Academic Exchange Seminar
Between Shanghai Jiao Tong University and Osaka University

Presentation Title: Community-integrated multi-omics faciliates
screening and isolation of the organohalide dehalogenation
microorganism
Keywords ： Microbial community, Wastewater, Metagenome
assembled genome, Organohalide dehalogenation
Name: Yiqun Huang
Affiliation and position:
School of Life Sciences and Biotechnology ,Shanghai Jiao Tong
University
PhD student
Short biography and publications (up to three)
Short biography:
Yiqun Huang, using bioinformatics and molecular biology tools to investigate the environmental microbiome,
Is focusing on the functional genes, metabolic pathways, and bacteria resources of the polluted environment
microbial community (e.g., chemical plant wastewater).
Publications:
1. Huang Y，Wen L，Zhang L. et al. Community-integrated multi-omics faciliates screening and isolation of
the organohalide dehalogenation microorganism. The innovation. (pre-accpected).
2. Wen L+, Huang Y+, Wang W. et al. A novel Diaphorobacter sp. strain isolated from saponification wastewatershows highly efficient phenanthrene degradation. Environmental Research. 214, 114047. (2022).
3. Hu H, Wang M, Huang Y. et al. Guided by the principles of microbiome engineering: Accomplishments andperspectives for environmental use. mLife.12043 (2022)
Abstract
A variety of anthropogenic organohalide contaminants generated from industry are released into theenvironment, and thus cause serious pollution that endangers human health. In the present study, weinvestigated the microbial community composition of industrial saponification wastewater using 16S rDNA
sequencing, providing genomic insights of potential organohalide dehalogenation bacteria (OHDBs) by wholemetagenome sequencing. We also explored yet-to-culture OHDBs involved in the microbial community.
Microbial diversity analysis reveals that Proteobacteria and Patescibacteria phyla dominate microbiome
abundance of the wastewater. In addition, a total of six bacterial groups (Rhizobiales, Rhodobacteraceae,
Rhodospirillales, Flavobạcteriales, Micrococcales, and Saccharimonadales) were enriched in the key
organohalide removal module. Ninety-four metagenome-assembled genomes (MAGs) were reconstructedfrom Proteobacteria, Bacteroidota, Patescibacteria, and Actinobacteria, and 105 dehalogenase genes within
42 MAGs were identified, suggesting that the potential for hydrolytic organohalide dehalogenation is present
in the microbial community. Subsequently, we characterized the organohalide dehalogenation of an isolated
OHDB, Microbacterium sp. J1-1, which shows the dehalogenation activities of chloropropanol,
dichloropropanol, and epichlorohydrin. This study provides a community-integrated multi-omics approach tocollect functional OHDBs for industrial organohalide dehalogenation.
As of Nov. 29, 2022

14

The 24th Academic Exchange Seminar
Between Shanghai Jiao Tong University and Osaka University

Presentation Title: Engineering the β-sandwich domain 1 ofa thermostable protease for improved soluble expression for
novel target binding.
Keywords：SD1, target binding, E. coli, soluble expression,
stability, rational design.
Name: Chukwuebuka Maxwell Ononugbo
Affiliation and position: Department of Biotechnology,
Graduate School of Engineering, Osaka University, Japan.
PhD student (Omasa laboratory).
Short biography and publications (up to three)

Chukwuebuka Maxwell Ononugbo earned a bachelor’s and master’s degree in Microbiology
from the Department of Microbiology, Faculty of Biological Sciences, University of Nigeria,
Nsukka. He also received a master’s degree in Biotechnology from the Department of
Biotechnology, Graduate school of Engineering, Osaka University, Japan. He is currently a PhD
student under the supervision of Prof. Takeshi Omasa and Prof. Yuichi Koga (Omasa
laboratory), in the same program at Osaka University, with a bias in Molecular Biotechnology
and Protein Engineering. His research interests include improving protein structure/function for
novel target binding for applications in biomedicine and research.
Abstract

Over the years, the concept of target binding has been exploited significantly indiagnostics/therapeutics, medicine, and research. This field is dominated by monoclonal
antibodies, as the most common biopharmaceuticals. However, this biologic faces several
drawbacks, including large size, limited tissue penetration and high cost of production. These
led to the extension of this concept to alternative protein frameworks leveraging their small size,
stability, and expression in E. coli. The β-sandwich domain 1 of a thermostable proteaseIslandisin (SD1) provides a suitable framework, including exposed surface loops that could
generate binding to several targets. A small-sized protein that folds like the variable domain of
immunoglobulin with its hydrophobic core built by several hydrophobic residues, providing
stability to the protein. It is expressible in E. coli, but most of the protein aggregates andaccumulates in inclusion bodies. A limiting factor for binding applications. Therefore, in thisstudy, SD1 surfaces were re-engineered to augment their net charge, reversibility of unfolding
and generally reduce its aggregation. We identified the aggregation-prone regions (APRs), andthe effect of aggregation gatekeeper residues on the protein stability was in silico analyzed. We
also explored mutations within the core residues to improve the thermodynamic stability of themutant(s). All mutants were confirmed soluble on SDS-PAGE and purified by affinity
chromatography for further characterization. In conclusion, we could reduce the aggregation of
SD1 and improve its soluble expression in E. coli by rational design. This study adds to thewealth of knowledge for understanding protein physicochemical properties and improvement
strategies. The result of this study shows the possibility of the amenability of SD1 to novel target
binding.
As of 9th November, 2022

15

The 24th Academic Exchange Seminar
Between Shanghai Jiao Tong University and Osaka University

Presentation Title: Expanding the Chemical Diversity of Fasamycin
Via Genome Mining and Biocatalysis
Keywords: genome mining, biocatalysis, halogenase
Name:

Kai Jiang

Affiliation and position: School of Life Sciences and Biotechnology,
Shanghai Jiao Tong University, Ph.D. candidate

Short biography and publications (up to three)
Kai Jiang is currently a PhD student at Shanghai Jiao Tong University. He received his MS degree under thesupervision of Professor Xudong Qu from Wuhan University in 2021. His research interest focuses onbiosynthesis of the scaffold formation in the type II polyketide ABX and fasamycin.
Publications:
1. Jiang K, Yan X, Deng Z, Lei C, Qu X. Expanding the Chemical Diversity of Fasamycin Via Genome Mining
and Biocatalysis. J Nat Prod. 2022 Apr 22;85(4):943-950.
Abstract
The rapid increase in multidrug-resistant pathogens has posed a great threat to global public health.
Discovery of novel antibiotics with a mode of action that differs from those in current clinical use is therefore
an urgent need. In this study, we activated the silenced microbial biosynthetic pathways throughoverexpression of the phosphopantetheinyl transferase (PPtase). PPtase is responsible forphosphopantetheinylation of the carrier proteins (CPs), which is a key step in the biosynthesis of polyketides(PKs), nonribosomal peptides (NRPs), fatty acids (FAs), lysine, and tetrahydrofolate. It has been demonstrated
as able to activate both of the phosphopantetheinylation-dependent and -independent biosynthetic pathways.
To discover bioactive secondary metabolites based on our developed PPtase strategy, we herein reported theidentification of three new and four known fasamycin congeners from the Pptase-activated chemical
constituents of Streptomyces kanamyceticus. By treating the fasamycin derivatives with two halogenases
Abx(−)H and FasVsk, we generated additional five new and one known fasamycins. A few of the analogues
demonstrated significantly improved antimicrobial activity. The C29-methyl and C-2/C-22-halogen substitutions
were revealed to be important for the bioactivity. Herein, we report the details of the genome mining,
biocatalysis, structural elucidation, and antibacterial activities of these new antimicrobial products. This study
increases the chemical diversity of bioactive fasamycin derivatives and provides useful halogenation tools forengineering their scaffolds.

As of Nov. 29, 2022

16

The 24th Academic Exchange Seminar
Between Shanghai Jiao Tong University and Osaka University

Presentation Title: The transient expression in Nicotiana benthamianaof human acid sphingomyelinase for enzyme replacement therapy.
Keywords：Acid sphingomyelinase; Agroinfiltration; Nicotiana benthamiana
Name:

Kulachatr Panyawechamontri

Affiliation and position:
Ph.D. student, Laboratory of Applied Microbiology, Department of
Biotechnology, Graduate School of Engineering, Osaka University.
Abstract
Acid sphingomyelinase (ASM) converts sphingomyelin into phosphocholine and ceramide. Hereditary mutations of
ASM result in the lysosomal storage disease called Niemann-Pick disease. Currently, enzyme replacement therapy(ERT) is considered as a new clinical trial for treating patients with Niemann-Pick disease type B. Plant-based
expression system is an attractive and alternative system for recombinant protein production, because it enables
post-translational modifications, and are safe from contamination by human pathogens. In this study, recombinanthuman ASM was produced in Nicotiana benthamiana as a functional protein using the Agrobacterium-mediatedtransient expression system. Moreover, ASM was successfully produced as a plasma membrane protein. Crude
proteins were extracted from the infiltrated leaves using the revised microcentrifuge method. In addition, coexpression with p19 enhanced the production, resulted in showing the highest ASM activity in 6 days post-infiltration
with the enzyme activity of 238.6 Units/mg total soluble protein. This study developed an alternative plantexpression system of recombinant ASM production in N. benthamiana whole plant that might be applied to otherapplications in the future. However, ASM purification method in plant is necessary to improve the purity of ASM.

As of Nov 29, 2021

17

The 24th Academic Exchange Seminar
Between Shanghai Jiao Tong University and Osaka University

Presentation Title: Identification of sucrose utilization genes foransamitocin over-production from Actinosynnema pretiosum
Keywords: Carbon utilization, Sucrose hydrolase activity, Proteomic
analysis, Ansamitocin
Name: Ayturk·Ali
Affiliation and position: Master candidate at Shanghai Jiao Tong
University. (Supervisor: Prof. Linquan Bai)

Short biography and publications (up to three)
Ayturk·Ali is a master candidate at Shanghai Jiao Tong University. Her main research interest is the mechanism of
sucrose utilization in Actinosynnema pretiosum. Guided by sucrose hydrolysis activity of fractionations of intracellular or
extracellular proteins, she identified sucrose hydrolase proteins from Actinosynnema pretiosum and illustrated theunderlying molecular mechanism for the ansamitocin over-production effect of sucrose supplementation.

Abstract
Sucrose, the most abundant disaccharide in nature, is a common carbon and energy source for the industrial
biotechnology. However, sucrose is mostly used for pellet morphology control and rarely as a carbon source for antibiotic
production in actinobacteria. Given the limited studies on the mechanism of sucrose utilization in actinobacteria, weinvestigated sucrose utilization by Actinosynnema pretiosum ATCC 31280 and illustrated the mechanism for effect ofsucrose supplementation on the production of secondary metabolite ansamitocin P-3 (AP-3), a member of microbial
maytansinoids with potential antitumor activity. The result showed that Actinosynnema pretiosum ATCC 31280 efficiently
utilizes sucrose as the sole carbon source, and the optimal concentration of sucrose is 70 g/L with a 79.3% titerimprovement of AP-3. Sucrose hydrolysis activity guided fractionation and subsequent proteomic analysis identified 1
intracellular and 2 extracellular sucrose utilization proteins in Actinosynnma pretiosum ATCC 31280. We also geneticallyengineered the identified sucrose utilization genes, and achieved a 36.9% titer improvement of AP-3 and a 44.3% decreaseof residual sucrose in the medium. Our work elucidated the sucrose utilization mechanism and provided a new strategy fornatural product over-production in actinobacteria.

As of Nov. 29, 2022
1

18

The 24th Academic Exchange Seminar
Between Shanghai Jiao Tong University and Osaka University

Presentation
Title:Developmentof
CRISPR/dCas9-VPR
transcriptional activation system in D. magna
Keywords：genetic engineering, CRISPR, transgenic
Photo
Name:

Ayano Hara

Affiliation and position:
Bioenvironmental Science Laboratory, Department of Biotechnology,
Graduate School of Engineering, Osaka University.
Abstract
The crustacean Daphnia magna is a model organism for environmental and toxicological studies. In response
to environmental stimuli, they are known to switch phenotypes variously. To understand these mechanisms at
the genomic level, useful tools of loss-of-function (LOF) studies were established. On the other hand, gain-offunction (GOF) techniques still have some problems, so there are limitations to genetic analysis in D. magna.
In this study, we aimed to develop CRISPR/dCas9 VPR system that activates the expression of the target genefrom the endogenous genomic locus. We constructed a plasmid expressing dCas9-VPR protein ubiquitously
and designed gRNA, which targets to activate green fluorescence protein (GFP) expression in transgenic line.
Next, we injected the plasmid and gRNA into the embryo and found that GFP expression was activated by
CRISPR/dCas9-VPR system. Now we are trying to generate transgenic D. magna, which expresses dCas9VPR protein in their whole body. For the knock-in experiment, I optimized the promoter region and added afluorescent protein gene as a reporter in the donor plasmid. This study might accelerate to reveal of the genetic
function of D. magna.

As of 16st November, 2022

19

The 24th Academic Exchange Seminar
Between Shanghai Jiao Tong University and Osaka University

Presentation Title: Cascade utilization of carbon resource in cornstover to produce renewable energy products
Keywords: cascade utilization, corn stover, ethanol, methane ，microalgae
Name: Tian-Jie Ao
Affiliation and position:
Affiliation: State Key Laboratory of Microbial Metabolism, Joint
International Research Laboratory of Metabolic and Developmental
Sciences, and School of Life Sciences and Biotechnology, Shanghai
Jiao Tong University
Position: Ph.D. candidate
Short biography and publications (up to three)
Short biography:
Tian-Jie Ao is a Ph.D. candidate at Shanghai Jiao Tong University. His research interests are focused on
biomass resources and biorefinery, organic waste re-utilization, and wastewater treatment.
Publications
Ao, T., Li, K., Mehmood, M.A., Zhao, X.-Q., Bai, F.-W., Boopathy, R., Liu, C.-G., 2022. Process optimization
for acidic deep eutectic solvent pretreatment of corn stover to enhance enzymatic saccharification. Biomass
Conversion and Biorefinery.
Ao, T., Chen, L., Chen, Y., Liu, X., Wan, L., Li, D., 2021. The screening of early warning indicators and microbialcommunity of chicken manure thermophilic digestion at high organic loading rate. Energy 224, 120201.
Ao, T., Chen, L., Zhou, P., Liu, X.F., Li, D., 2021. The role of oxidation-reduction potential as an early warning
indicator, and a microbial instability mechanism in a pilot-scale anaerobic mesophilic digestion of chicken
manure. Renewable Energy 179, 223-232.
Abstract
Corn stover (CS) is the most widely distributed agricultural residue in China, which can be utilized as thefeedstock for cellulosic ethanol production. Nonetheless, nearly half of the carbon resource in the CS will be
released into the atmosphere in the form of CO2 during the cellulosic ethanol fermentation process. Besides,
the residual vinasse still contains a certain amount of carbon-based compounds derived from CS that cannot
be utilized in the cellulosic ethanol fermentative process, which finally results in the loss of carbon resourcesin CS. Here we proposed an effective scheme via cascade utilization of carbon resources in corn stover toachieve the improvement of carbon utilization from 40% to 75%. CS was first effectively pretreated by deep
eutectic solvent (DES) to deconstruct the refractory structure of CS. Second, the pretreated CS was selected
as the substrate for ethanol fermentation by the genetically engineered Saccharomyces cerevisiae that can
assimilate mixed sugar simultaneously. Third, the residual vinasse from the ethanol production process was
utilized by combining microbial electrolysis cell (MEC) with anaerobic digestion (AD) to transfer the organic
waste to methane to achieve the carbon resource re-utilization and clean energy production, simultaneously.
Finally, the released CO2 from the ethanol fermentative process and the digestate from the MEC-AD process
were collected as the substrates for self-flocculating microalgae cultivation to achieve the cascade utilizationof carbon resources in CS.
As of Nov. 29, 2022

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