Confirmed Speakers and Distinguished Guests
[by Alphabetical Order]
Dr. Pei-Lin Cheng 鄭珮琳 博士
Assistant Research Fellow, Institute of Biomedical Sciences, Academia Sinica
Keywords: proteasome transport, neuronal morphogenesis, axon biology, brain mimetic platform
Dr. Pei-Lin Cheng is a cell biologist and neuroscientist. She received a Ph.D degree at NYMU, mentored by Dr. Yan-Hwa Wu Lee from 1999-2004 for exploring roles of TGF-beta signaling pathway in hepatitis C virus infection. Then she researched neuronal polarization with Dr. Mu-Ming Poo at UC Berkeley from 2006-2011. After that, she joined the IMB, Academia Sinica, in 2011. Dr. Cheng’s research was aimed at determining: 1) how were the distribution and function of proteasomes developmentally regulated, and 2) what molecular mechanism(s) governed timely neurite initiation and neuron maturation on soft tissue environments. The strength of her lab has been the ability to implement novel platforms to address these questions.
● Title: Mutually Exclusive AIS- and Ecm29-mediated Proteasomal Distribution Modulates Excitatory GABA Responses in the Developing Brain
Neuronal GABAergic responses switch from excitatory to inhibitory at an early postnatal period in rodents. The timing of this switch is controlled by intracellular Cl-concentrations, but factors determining local levels of cation–chloride cotransporters remain elusive. Here,we report that local abundance of the chloride importer NKCC1 and timely emergence of GABAergic inhibition are modulated by proteasome distribution, which is mediated through mutually exclusive interaction of proteasomes with the adaptor Ecm29 and the axon initial segment (AIS). Mechanistically, both the Ecm29 N-terminal domain and an intact AIS structure are required for transport and retention of proteasomes in the AIS region. In mice, Ecm29 knockout (KO) neuron alters NKCC1 infiltration of the AIS region, with increased NKCC1 expression correlates with the delayed GABAergic response switch. Phenotypically, Ecm29 KO mice showed increased firing frequency of action potentials at early postnatal ages, impaired juvenile social interactions, and higher susceptibility to chemically-induced convulsive seizures. Finally, Ecm29 KO neurons exhibited altered AIS structural plasticity, namely hyperexcitability arising from proteasome inhibition, a phenotype rescued by ectopic Ecm29 expression or NKCC1 inhibition. Together, our findings support the idea that neuronal maturation requires regulation of proteasomal distribution controlled by Ecm29/AIS.
Dr. Sheau-Yann Shieh 謝小燕 博士
Research Fellow, Institute of Biomedical Sciences, Academia Sinica
Keywords: cell cycle check-points, DNA damage response, DNA repair, cancer cell signaling
Born in Taiwan; B.S., Department of Plant Pathology, National Taiwan University; M.S., Graduate Institute of Biochemical Science, National Taiwan University; Ph.D., Department of Cell Biology, Baylor College of Medicine, Houston, Texas, USA; post-doctoral research, Department of Biological Sciences, Columbia University, New York, New York, USA
● Title: CHK2-dependent regulation of PARP1 in oxidative DNA damage response
Poly(ADP-ribose) polymerase 1 (PARP1) is a DNA damage sensor, which upon activation, recruits downstream proteins by poly(ADP-ribosyl)ation (PARylation). However, it remains largely unclear how PARP1 activity is regulated. Interestingly, the data obtained through this study revealed that PARP1 was co-immunoprecipitated with checkpoint kinase 2 (CHK2), and the interaction was increased after oxidative DNA damage. Moreover, CHK2 depletion resulted in a reduction in overall PARylation. To further explore the functional relationship between PARP1 and CHK2, this study employed H2O2 to induce an oxidative DNA damage response in cells. Here, we showed that CHK2 and PARP1 interact in vitro and in vivo through the CHK2 SCD domain and the PARP1 BRCT domain. Furthermore, CHK2 stimulates the PARylation activity of PARP1 through CHK2-dependent phosphorylation. Consequently, the impaired repair associated with PARP1 depletion could be rescued by re-expression of wild-type PARP1 and the phospho-mimic but not the phospho-deficient mutant. Mechanistically, we showed that CHK2-dependent phosphorylation of PARP1 not only regulates its cellular localization but also promotes its catalytic activity and its interaction with XRCC1. These findings indicate that CHK2 exerts a multifaceted impact on PARP1 in response to oxidative stress to facilitate DNA repair and to maintain cell survival.
Dr. Che-Ming (Jack) Hu 胡哲銘 博士
Assistant Research Fellow, Institute of Biomedical Sciences, Academia Sinica
Keywords: artificial antigen presenting cells, personalized cancer vaccine, vaccine nanotechnology
Dr. Che-Ming Jack Hu received his B.S. in Biomedical Engineering from UC Berkeley in 2005 and Ph.D. in Bioengineering from UC San Diego in 2011. He is passionate about the interfacial dynamics between nanomaterials and biological components with a strong interest in therapeutic, immunomodulatory, and biomimetic materials. Jack Hu currently serves as the principal investigator at the Laboratory of Medicinal and Vaccine Nanotechnology, which focuses on manipulating nano-bio interface and developing novel nanoparticles for therapeutics and vaccine applications. He has published 50 scientific papers with several landmark publications in Nature and Nature Nanotechnology. Dr. Hu’s laboratory is presently working on macromolecule delivery and vaccine development. Dr. Hu received the prestigious Academia Sinica Career Development Award and the Excellence in Creativity Award for Young Scholar, which support his continuing passion in nanomedicine research.
● Title: Bioinspired Materials Engineering for Immune Modulation
Immuno-engineering has benefited significantly from materials research in the last decade, and development of virus- and cell-mimicking particles have gained growing interest for modulating immune responses for vaccination and other therapeutic applications. We herein demonstrate the use of synthetic materials such as polymers and hydrogels for constructing novel virus-like nanoparticles and artificial antigen presentation cells for stimulating the immune system. These bioinspired immunomodulatory systems have been applied for antiviral vaccination and anticancer immunotherapy, and they exhibit multiple attributes and performance comparable to their natural counterparts. The virus-like nanoparticles and artificial cells provide synthetically flexible platforms for further design modifications towards precise immune modulation.
Dr. Pui-Yan Kwok 郭沛恩 博士 (Keynote)
Director, Institute of Biomedical Sciences, Academia Sinica
Keywords: human genetics, genome analysis, precision medicine
Dr. Kwok received his AB (Chemistry), MS (Human Biology), MD, and PhD (Organic Chemistry) degrees from the University of Chicago. After residency/fellowship training in Dermatology and Genetics at Washington University in St. Louis, he joined its faculty in 1993. Since 2002, he is the Henry Bachrach Distinguished Professor at UCSF. In 2017, he also became a Distinguished Research Fellow and the Director of the Institute of Biomedical Sciences at the Academia Sinica in Taiwan. Dr. Kwok’s research focuses on developing tools and strategies to study the human genome and the role of human variation in common diseases. In July 2018, he launched the Taiwan Precision Medicine Initiative, a 3-year pilot study to obtain genetic profiles of 1 million people and bring genetics into clinical practice in the context of risk prediction for common diseases. Dr. Kwok is an Academician of the Academia Sinica and the recipient of the 2017 Distinguished Service Award from the University of Chicago Pritzker School of Medicine.
● Title: Genome Assembly and Analysis with Single Molecule Technologies
Most sequencing projects to-date are based on short-read massively parallel approaches followed by aligning the sequencing reads to a genome reference. However, the human reference genome is just a haplotype among many in the human population so a significant amount of unique sequences found in other populations are missing in the reference. Furthermore, structural variations are not captured in short-read sequencing data so this important class of variations are not studied adequately. The same is true in the sequencing of other organisms. Using single molecule approaches, such as the Bionano Genomics optical mapping and the 10x Genomics “Linked-Read” technologies, we performed deep whole genome sequencing and de novo assembly on the Komodo dragon and almost 200 humans from diverse populations. The de novo genome assembly of the Komodo dragon showed evidence of positive selection in pathways related to muscle energy metabolism, cardiovascular homeostasis, and thrombosis. We also found species-specific expansions of a chemoreceptor gene family related to pheromone and kairomone sensing. In addition to identifying numerous breakpoint-resolved Non-reference Unique Insertions (NUIs) that are not described in the human genome reference, we also observed distinct structural variation patterns in multiple populations. The human genome assemblies of this study represent an initial set of human reference genomes that incorporates a comprehensive list of alternative haplotypes to depict the complete spectrum of genetic diversity across populations.
Dr. Kay-Hooi Khoo 邱繼輝 博士
Acting Director, Institute of Biological Chemistry, Academia Sinica
Keywords: mass spectrometry, protein glycosylation, glycomics, glycoproteomics, glycobiology, proteomics, post-translational modifications
Dr. Khoo received his B.Sc. (1989) and Ph.D. in Biochemistry (1992) from Imperial College, London, UK. He then stayed at Imperial College as a Wellcome Trust Prize Postdoctoral Fellow for another year before moving to Colorado State University as a Heiser Fellow for Research in Leprosy and Tuberculosis and worked there for another 2 years. He started his independent research career as Associate Research Fellow at the Institute of Biological Chemistry, Academia Sinica, Taiwan in 1996, served as Associate Director from 2012 to 2017, and Acting Director since then. He is currently an Editorial Board member of Glycobiology, Glycoconjugate J, and Molecular and Cellular Proteomics; council member of Taiwan Proteomics Society; co-founder and Steering Committee member of Taiwan GlycoForum; and oversees the running of GlycoNet@Academia Sinica. Dr. Khoo is the author and co-author of over 200 publications. He received the 2018 ASBMB/MCP Lectureship award for contribution to the emerging fields of glycomcis and glycoproteomics.
Dr. Paola Laurino
Assistant Professor, Protein Engineering and Evolution Unit, OIST
Keywords: Enzymes, cofactor engineering, Biocatalysis, Last Universal Common Ancestor , Directed evolution, phylogenetic analysis, gene duplication
Nucleoside-based cofactors are presumed to have preceded proteins. The Rossmann fold is one of the most ancient and functionally diverse protein folds. We analyzed an omnipresent Rossmann ribose binding interaction and identified a canonical motif, defined by unique geometry. This motif is uniquely found in Rossmann enzymes that use different cofactors. Overall, these data indicate the divergence of several major Rossmann-fold enzyme classes from a common pre-Last Universal Common Ancestor (LUCA).
While we were studying how Rossmann fold enzyme binding ribose based cofactor evolves, the adenosine mode of binding attracted our attention. Based on this observation we started our cofactor engineering studies to remodel the catalytic site for a new cofactor. Our approach may provide a powerful tool to study the cellular roles of cofactor binding enzymes in cell.
Dr. Tsung-Lin Li 李宗璘 博士
Associate Research Fellow, Genomics Research Center, Academia Sinica
Keywords: glycopeptide antibiotics, pathway engineering, synthetic biology, structural/mechanistic enzymology
Dr. Li received his Ph.D. in Chemistry at the University of Cambridge, UK, under supervision of the late Prof. Jonathan Spencer. He developed an interest in the biosynthesis of natural products during his postdoctoral training with Profs. Jonathan Spencer and Peter Leadlay in Departments of Chemistry and Biochemistry at the same university. He joined the National Taiwan Ocean University in 2004, where he initiated his current studies on the biosynthesis of clinically important antibiotics teicoplanin, albofungin, mannopeptimycin streptosthricin, etc. In 2007, he moved to Genomics Research Center, Academia Sinica, where he expanded his research dimension by integrating biophysics, such as X-ray crystallography, and synthetic biology to gain insights into enzyme reactivities/mechanisms and expand their utilizations. Of these practices, his team is able to create biologically effective unnatural natural products.
● Title: Lipoglycopeptide reprogrammed with the N-Acyl-Glc pharmacophore at an unnatural position acquires broad-spectrum antimicrobial activities against drug-resistant pathogens
Lipoglycopeptide antibiotics, teicoplanin or A40926, feature an aliphatic acyl side chain on glucosamine (Glm) at residue 4 (r4). They are more potent than vancomycin against Gram-(+) drug-resistant pathogens, e.g. MRSA. To extend their therapeutic effectiveness on drug-resistant pathogens, e.g. VRSA, the biosynthetic pathway of N-acyl Glc was redirected to enable the pharmacophore relocation from r4 to r6 of Tei pseudoaglycone, which remains a synthetic challenge. On the basis of two crystal structures, Orf2* and Orf11*, two new regio-selective biocatalysts Orf2*T (a triple-mutation mutant S98A/V121A/F193Y) and Orf11*S (a single-mutation mutant W163A) were evolved, allowing them to act on GlcNAc at r6. New Tei analogs thereby made show marked antimicrobial activity effectively against MRSA/VRSA by two orders of magnitude better than teicoplanin/vancomycin. The lipid side chain of the Tei analogs further armed with a terminal mono-/di-guanidino group extends the antimicrobial specificity from Gram-(+) to Gram-(-), comparable to that of kanamycin.In addition to low toxicity/high safety, the developed Tei analogs exhibit new modes of action as a result of re-sensitization of VRSA and Acinetobacter baumannii. Importantly, the redirected biosynthetic route bodes well a large-scale production of selected r6,Tei congeners in an environment-friendly synthetic biology approach.
Dr. Hsiao-Ching Lin 林曉青 博士
Assistant Research Fellow, Institute of Biological Chemistry, Academia Sinica
Keywords: natural products, biosynthesis, biocatalysts
Hsiao-Ching Lin obtained her PhD in 2011 from Department of Pharmaceutical Science, School of Pharmacy, National Taiwan University. Her graduate research focused on exploration and characterization of bioactive natural products with pharmaceutical potential from natural sources mainly from plants. She moved to University of California, Los Angeles, in 2012, for a postdoctoral position to study the biosynthesis of fungal secondary metabolites with Professor Yi Tang. In 2015, she started her own research group and appointed as an assistant research fellow at Institute of Biological Chemistry, Academia Sinica, Taiwan. Her research interests are in natural product biosynthesis and the discovery of new enzyme biocatalysts.
● Title: Biosynthesis of bioactive fungal natural products: the discovery of new enzymes synthesizing isoprenoids
Nature uses enzymes that display diverse chemical catalytic power. Enzymes catalyze a variety of chemical reactions efficiently and generate a large number of natural products from primary metabolites as building blocks through biosynthetic pathways. The application of Nature’s chemical tools, enzymes/biocatalysts, provides many advantages in green chemistry such as the reduction of the use of hazardous substances and reacting under ambient temperature without high energy consumption.Isoprenoids are natural products (NPs) containing isoprene units and are widely found in different kingdom from bacteria to plants. However, only a limited number of enzymes are known to be involved in the biosynthesis of this class of NPs compared to other classes of NPs such as polyketides which are better understood. We here present the identification and characterization of the biosynthetic gene clusters of NPs belong to both isoprene-containing alkaloids and terpenoids, then elucidated the pathways with target gene inactivation, heterologous reconstitution, and biochemical characterization. These findings not only provide insights into specific enzymes but also demonstrate the potential for synthesizing natural products.
Dr. Todd Lowary
Incoming Director, Institute of Biological Chemistry, Academia Sinica
Keywords: bacterial glycans, synthesis, ologosaccharides, carbohydrate-protein interactions
Todd Lowary received his B.A. in Chemistry from the University of Montana and his Ph.D. in organic chemistry under the supervision of Professor Ole Hindsgaul at the University of Alberta. Subsequent postdoctoral appointments were with Professor David Bundle (University of Alberta) and Dr. Morten Meldal (Carlsberg Laboratory, Copenhagen, Denmark). In 1996, he started a position in the Department of Chemistry at The Ohio State University as an Assistant Professor and in 2002 was promoted to Associate Professor with tenure. He returned to the University of Alberta in 2003, where he is the R. U. Lemieux Professor Carbohydrate Chemistry and a Tier 1 Canada Research Chair. He currently serves as the Scientific Director of the Canadian Glycomics Network (GlycoNet). GlycoNet is a pan-Canadian network connecting all Canadian glycoscience researchers with a mission to identify novel solutions to unmet medical needs. In July 2019, he will become the Director of the Institute of Biological Chemistry at Academia Sinica.
Dr. James Liao 廖俊智 院長
President, Academia Sinica
Keywords: metabolic engineering, synthetic biology, systems biology, bioenergy
Dr. James C. Liao, President, Academia Sinica, is a pioneer in Metabolic Engineering, Synthetic Biology, and Systems Biology. He received his BS degree from National Taiwan University and PhD from University of Wisconsin-Madison. After working as a research scientist at Eastman Kodak Company, Rochester, NY, he started his academic career at Texas A&M University in 1990 and moved to UCLA in 1997. He received numerous awards and recognitions, including the Presidential Green Chemistry Challenge Award (2010), the White House “Champion of Change” for innovations in renewable energy (2012), the ENI Renewable Energy Prize bestowed by the President of Italy in 2013, and the 2014 National Academy of Sciences Award for the Industrial Application of Science. He is a Member of the National Academy of Engineering, National Academy of Sciences, and Academician of Academia Sinica in Taiwan.
Dr. Shiro Maeda 前田 士郎 博士
Chair Professor of Advanced Genomic Medicine, University of the Ryukyus
Keywords: Genome-wide association study, Single nucleotide polymorphism, Type 2 diabetes, Diabetic nephropathy (kidney disease), Genetic susceptibility, Okinawa Bioinformation Bank
●Title: The Okinawa Bio-Information Bank Project towards future precision medicine
After completion of the human genome project, development of single nucleotide polymorphism (SNP) typing technology and collation of information regarding linkage disequilibrium in the human genome have facilitated genome-wide association studies (GWAS) for investigating genes associated with disease susceptibility across the entire human genome. Until now, several hundreds of genetic loci have been identified and confirmed as susceptibility to individual common diseases, such as type 2 diabetes, through GWAS in different ethnic groups. However, integration of these information accounts for less than 20 % of the disease heritability, and thus most of the heritability of common diseases remain to be identified. Peoples living in Okinawa have been shown to have a unique genetic background, which is clearly different from those for peoples living in Japan main islands. Since it has been reported that GWAS using populations having unique genetic backgrounds is useful, even if its sample size is not so large, to identify strong susceptibility variants, i.e. TBC1D4 variant for type 2 diabetes in Greenlandic Inuit, genetic studies in Okinawa may provide additional useful information for susceptibility to several common diseases. To perform a genetic study using Okinawa populations, we have started an Okinawa Bio-information Bank Project, which aims to establish a bio-resource consists of genomic DNA, plasma and clinical information from ~20,0000 participants living in Okinawa. In this symposium, I would like to introduce a recent progress of genetic study for Okinawa populations.
Dr. Alexander (Sasha) Mikheyev
Associate Professor, Ecology and Evolution Unit, OIST
Keywords: coevolution, invasive species, genomics, parasitism, social insects
Sasha (Alexander) Mikheyev holds joint appointments at the Australian National University and the Okinawa Institute of Science and Technology in Japan. His research focuses on evolutionary genomics, in particular using geographic and historical samples to infer microevolutionary processes. His current work aims to understand selection exerted on and by parasites and diseases, using honey bees and their parasitic mites as models.
●Title: Coevolution while you wait: the arms race between honey bees and ectoparasitic Varroa mites
Novel diseases and pathogens force populations to adapt or face potential extinction. Likewise, parasites must evolve to reach a fitness optimum on their new host. Despite the ubiquity of this adversarial coevolutionary relationship, how it takes place at the genomic level remains poorly understood, particularly in natural environments. Honey bee and parasitic Varroa mites provide an excellent model system for this process. At least two Varroa species have repeatedly switched from a closely related bee to the western honey bee over the past century, and have become major drivers of global bee population declines. Because bees are agriculturally important, excellent records and collections of their parasites exist, and their rapid generation time allows for direct measurements of evolutionary change. Our lab has focused on understanding how bees evolve to Varroa, and we have recently started to focus on how the parasite adapts to the bee.
In particular, we took advantage of unique decade-long data sets from two wild honey bee populations in the U.S., to reconstruct evolution of tolerance to a novel parasite, the Varroa mite. After a host switch in the early 20th century, Varroa started a worldwide pandemic, which led to widespread honey bee colony collapses, though some populations are known to have evolved certain level of tolerance. The study populations simultaneously suffered massive Varroa-induced mortality in 1996, but stabilized within two years. Using sequenced and phased genomes of 465 specimens, we inferred the strength of selection acting on every polymorphic gene in naive and adapted populations. Despite massive gene flow from Africanized bees during the same time frame, selection acted primarily on standing genetic variation, with immigrant alleles playing only a minor role. Remarkably, gene-wise changes were strongly correlated across the separate populations, indicating parallel selective responses to Varroa.
For Varroa, we have recently sequenced its genome, producing chromosome-level scaffolds. We have re-sequenced samples collected from its native range, from both original and switched hosts to understand the mechanisms underlying host switches. It appears that host switches cause massive reproductive isolation between the Varroa populations adapted to original and switched hosts, despite sympatry and multiple opportunities come into contact. We are also in the process of sampling Varroa worldwide to understand post host-switch selection operating on this species. Genome-scale data provide a comprehensive view of how new parasites emerge, and how they spread, which is particularly relevant in Australia, the only continent that is still Varroa-free.
Dr. Hidetohi Saze 佐瀨 英俊 博士
Associate Professor, Plant Epigenetics Unit, OIST
Keywords: Epigenetics, DNA methylation, histone modifications, Transposable elements, Plant
●Title: Epigenetic regulation of intragenic transposons and gene transcription in plants
●Abstract: Genomes of higher eukaryotes contain a large number of transposable elements (TEs), that are often silenced by epigenetic mechanisms, such as histone modifications and DNA methylation. Although TE silencing adversely affects expression of nearby genes, recent studies revealed the presence of intragenic TEs marked by repressive epigenetic marks within transcriptionally permissive chromatin environments. However, molecular mechanism underlying the regulation of intragenic TEs and their potential impacts on gene expression are still poorly understood. We analyzed genome-wide distribution and epigenetic regulation of intragenic TEs in Arabidopsis thaliana, and revealed that the repressive chromatin state of intragenic TEs is critical for proper transcription and splicing of associated genes. Our study provides new insights into how intragenic TEs affect the transcriptional landscape of the A. thaliana genome, and suggests the importance of epigenetic mechanisms for regulation of TEs within transcriptional gene units.
Dr. Nori Satoh 佐藤 矩行 博士 (Keynote)
Professor, Marine Genomics Unit, OIST
Keywords: Comparative genomics, Evolutionary Developmental Biology, Ascidians, Chordates, Corals, Dinoflagellates, COTS, Marine invertebrates
●Title: Biodiversity in the Marine Genomes
Approximately 1.5 million species of animals have been described on the Earth. They are categorized into 34-36 phyla; most of them are marine species. Namely, the sea is the place of animal diversity. A genome contains all the genetic information of a given organism; it provides basis for studying every field of animal diversity. My interest is genomic basis of animal evolution and diversity. Taking advantages of DNA and RNA sequencing facilities at OIST, my Unit of Marine Genomics has decoded genomes of several marine metazoans, including ascidian, amphioxus, acorn worms, starfish, mollusc, brachiopod, phoronid, nemertini, mesozoa, acoel, and corals. Of them, I wish to discuss two topics; one is related to the origin and evolution of chordates and the other coral reef biology.
Chordates consist of three taxa, cephalochordates (amphioxus), urochordates (ascidians) and vertebrates. Chordates originated from a common ancestor of deuterostomes, shared with echinoderms (starfish) and hemichordates (acorn worms). Decoded genomes of the five deuterostome taxa therefore provide us information how we can interpret the origin and evolution of chordates with newly-obtained genomic information.
Although coral reefs occupy less than 0.1% of all marine habitats, they are estimated to harbor around one-third of all described marine species. Their productivity supports around one-quarter of marine fisheries. Declines in coral abundance and wholesale loss of reef habitats are one of the most pressing environmental issues of our time. OIST or Okinawa is a place suitable for studying coral reef biology, and decoded genomes of corals, dinoflagellates, and crown-of thorns starfish give us hints for future studies of coral reef biology.
Dr. Hsiung-Lin Tu 涂熊林 博士
Assistant Research Fellow, Institute of Chemistry, Academia Sinica
Keywords: membrane assay, valve microfluidics, single cell analysis, membrane signaling reactions
Hsiung-Lin Tu is currently an assistant research fellow at Institute of Chemistry Academia Sinica in Taiwan. Hsiung-Lin received his B.S. from National Chiao Tung University and M.S. from National Taiwan University; following that he received his PhD in Chemistry from University of California Berkeley (USA) in 2013. After 3 years post-doc training in ETH Zurich and University of Chicago, he joined Academia Sinica in August 2017. His research interest and expertise includes (1) development and application of interdisciplinary tools and methods for biomedical and materials research, (2) study of cell signaling dynamics at single molecule and single cell level and (3) investigation of materials-cell interaction to learn better design principle for biomaterials.
● Title: Towards quantiative study of biological systems
Cells use an array of sophisticated chemical and physical reactions to organize and elicit proper cellular responses upon environmental changes. Regulated cell signaling is critical for the maintenance of normal biologicalfunctions; many dysregulated signaling reactions are found in diseases such as cancer. Over past years, ample knowledge regarding bio-molecules and their roles in various signaling pathways has been characterized and studied extensively. But in most cases relevant parameters were obtained using ensemble measurements, thus masking the molecular/cellular heterogeneities. Many recent high-resolution (i.e. single molecule and single cell) studies showed that both molecular and cellular heterogeneity actually plays beneficial role for underlying biological systems. In light of these findings, we were interested in designing experiments that can directly measure both the mean and variations embedded in biological systems, in order to get more holistic understanding of cellular processes. In the presentation, I will discuss the development of analytical platforms for quantitative biology studies both in a reconstituted assay and in live cells. I will share the development of microfluidics for the cultivation and time-varying stimulation (sequential and combinatorial) of embryonic neural stem cells (NSCs) for extended period of time on-chip. And based such measurements, we identified interesting cellular logic rules during NSCsfate decision. Moreover, I will also discuss the application of membrane assays and dynamical input perturbations for the high-resolution mechanistic interrogation of MAPK (Ras-SOS-ERK)and immune (TNF-NFkappaB) signaling pathway respectively.
Dr. Yohei Yokobayashi 横林 洋平 博士
Associate Professor, Nucleic Acid Chemistry and Engineering Unit, OIST
Keywords: RNA, ribozyme, riboswitch, aptamer, artificial cells, RNA synthetic biology, gene therapy
●Title: Engineering RNA gene switches
RNA can transfer genetic information (mRNA, tRNA), regulate gene expression (microRNA), catalyze chemical reactions (ribozyme), and recognize specific molecules (aptamer, riboswitch). These diverse biological functions of RNA inspire us to desing and engineer synthetic RNA devices with sophisticated functions. We have focused on engineering synthetic gene switches based on RNA (riboswitches) that control gene expression in response to chemical signals. Our efforts to engineer and apply synthetic riboswitches that function in artificial cells, bacteria, and mammalian cells will be discussed.
Dr. Ye Zhang
Assistant Professor, Bioinspired Soft Matter Unit, OIST
Keywords: peptide synthesis, molecular assembly, mechanobiology, nanomedicine
●Title: Regulate Hippo Signalling via Lipid-raft-targeted Molecular Assembly for Ovarian Cancer Treatment
Hippo signalling pathway controls multiple cellular functions that are central to tumorigenesis. Its importance in cancer cell proliferation and metastasis has been well recognized. Here we created polypyridyl ruthenium comjugated peptide complex for lipid-raft-targeted molecular assembly. Via hydrolyzation by ovarian cancer biomarker, glycosylphatidylinositol-anchored placental alkaline phosphatase (ALPP), molecules assemble into nanostructures adhere to lipid rafts restricting their dynamics and spatial distributions. Through actin cytoskeleton, the regulation of lipid rafts stimulates Hippo signalling pathway deactivating the core oncogene YAP in cancer cells suppressing cancer cell migration and inducing cancer cell apoptosis.
[by Alphabetical Order]
Dr. Han-Wen Huang (AS) 黃漢文 博士
Post-Doctoral Fellow, Genomics Research Center, Academia Sinica
Keywords: BCMA, APRIL, BAFF, plasma cell, survival, N-glycosylation
I majored in Life Science in National Chung-Hsing University and received master and phD degrees from Institute of Microbiology and Immunology of National Yang-Ming University. My first research topic, also my master thesis, was investigation of the signaling molecules in the signaling cascade of the chemokine receptors on T cells under the supervision of Prof. Fang Liao in Institute of Biomedical Science of Academia Sinica. Then I joined Prof. Chi-Huey Wong’s lab in Genomic Research Center of Academia Sinica to study the glycobiology and pursued phD degree with help from Prof. Kuo-I Lin, whose expertise is B cell immunology. Therefore, my phD thesis, study of the sialylated and fucosylated proteins in plasma cells, was related to these two fields. After research and development substitute military services, I am doing postdoctoral fellow job to continue my project in Prof. Chi-Huey Wong’s lab.
●Title: B-Cell Maturation Antigen is modified by a single N-glycan that modulates surface expression and cleavage
B cell maturation antigen (BCMA), which belongs to a tumor necrosis factor receptor (TNFR) family, is required for the survival of plasmablasts and plasma cells in normal physiological condition. In some tumor cells or inflammatory accessory cells, the expression of BCMA also can be detected. Through binding to its ligands, trimerization of BCMA activates downstream signaling cascade and provides survival signaling for the reacted cells. In our study, we unexpectedly identified BCMA as a glycoprotein with a single N-glycosylation site with an aid of sugar alkynyl probes coupled with mass spectrometry. Afterwards, this novel finding was further proved by mutating the identified glycosite and the change of mobility in SDS-PAGE after PNGase F hydrolysis, changing the previous thought that BCMA was a non-glycosylated protein. We observed that ectopically expressed glycosylation site-mutated BCMA (BCMA-N42A) exhibited lower surface expression than wild type (WT) BCMA. By treating cells with cycloheximide (CHX) to inhibit protein synthesis, we observed that surface BCMA in BCMA-N42A-expressing cells or PNGase F-treated BCMA-WT-expressing cells was significantly decreased. The reduced expression of non-glycosylated BCMA was linked with the increased generation of soluble BCMA in the culture medium. Furthermore, mass spectrometry analysis showed the soluble BCMA was extracellular domain alone without glycosylation. Consistently, increased surface BCMA was detected in both WT BCMA and BCMA-N42A-expressing cells after treating cells with inhibitors that block the cleavage of BCMA from membrane. To our surprise, almost increased BCMA was almost non-glycosylated. These results imply that the N-glycan of BCMA is required for the retention of BMCA on cell surface.
Dr. Shang-Te Danny Hsu (AS) 徐尚德 博士
Associate Research Fellow, Institute of Biological Chemistry, Academia Sinica
Keywords: NMR spectroscopy, hydrogen-deuterium exchange/chemical croslinking mass spectrometry, cryoEM, SAXS
Danny Hsu obtained his Ph.D. from the Bijvoet Center for Biomolecular Research, Utrecht University, the Netherlands, specializing in structural analysis of lantibiotics recognition of bacterial cell wall precursor, Lipid II. He was awarded a Netherlands Ramsay Memorial Fellowship and a Human Frontier Science Program (HFSP) fellowship to study co-translational protein folding on the ribosome in Chris Dobson’s group at Cambridge University, where he also worked with Shankar Balasubramanian to study the structure-function relationship of DNA/RNA G-quadruplexes. He was awarded a HFSP Career Development Award to study the folding and functions of topologically knotted proteins. His recently demonstrated that protein knots confer superior mechanostabilities, and successfully untied protein knots while maintaining their structures through protein engineering. He currently serves as the President of the Taiwan Magnetic Resonance Society, Director of the IBC Protein Structure and Biophysics Facility, and Co-Principle Investigator of the Academia Sinica cryoEM Center.
●Title: 3.3 Å Cryo-EM Structure of Feline Infectious Peritonitis Virus Spike Protein with Unique Domain Architecture and Camouflaging Glycans
Feline infectious peritonitis virus (FIPV) is an alphacoronavirus that causes near 100% mortality rate and virtually no effective interventions. The molecular basis of the pathogenesis remains poorly understood due to the difficulties of viral isolation. We report here the 3.3 Å cryo-EM structure of the serotype I FIPV spike (S) glycoprotein and reveal that the S1 subunit, which is responsible for host receptor binding, adopts an unprecedented propeller-like conformation and N terminal lectin-like Domains that preferentially binds to core-1 sialyolated glycans. The conserved S2 subunit also shares similar domain organization with other coronaviruses. Through cryo-EM and mass spectrometry, we profiled the chemical structures and visualized the densely distributed N-linked glycans that shield most of the protein surface. Our results shed light on the underlying molecular pathogenesis of serotype I FIPV, which can serve as a blueprint for therapeutics developments.
Dr. Huei-Mien Ke (AS) 柯惠棉 博士
Post-Doctoral Fellow, Biodiversity Research Center, Academia Sinica
Keywords: Genomics, Evolution, Vibrio, Basidiomycetes, Bioluminescence
Dr. Ke received her PhD in molecular genomics from the Academia Sinica and NCTU joint program in 2017. She worked on genomics of microbes in the field of microbial ecology for her postdoctoral fellowship in the Isheng Jason Tsai’s Lab. She interested in the evolution of microorganisms in their environmental niches from a molecular perspective. First, she employed comparative genomics to predict gene functions, identify the core-conserved genes from a group of species, and identify lineage-specific genes. She mainly focused on Vibrio species which are widely present in aquatic environments and some are human or aquatic animal pathogens. Second, she investigated the evolution and mechanism of fungal bioluminescence by using comparative genomics and transcriptomics. Third, she focused on making discovery in ecology issues by applying genomics tools but with lower costs. She attempted and optimized Nanopore and chromosome conformation capture (Hi-C) sequencing techniques in genome sequencing and RNA-seq.
●Title: Transcriptome analysis reveals molecular profiles associated with evolution of fungal bioluminescence
Bioluminescence is a visible light produced by oxidation of luciferin by luciferase enzymes. It is ubiquitously present in many species ranging from marine bacteria to terrestrial fungi, earthworm, and firefly. Currently more than 78 fungal species are known to display bioluminescence. Although the underlying chemical reaction in all bioluminescent species are believed to involve a luciferin and a luciferase enzyme were recently discovered, its regulation and ecological role remains elusive. To further understand the global view of expression profile of bioluminescence and its evolution, comparative transcriptomics and comparative genomics were conducted. Five species belonging to Mycena genus including four bioluminescent species and one nonbioluminescent species were selected for genome sequencing. In these four bioluminescent fungi, differential expression genes were either identified from comparison between higher and lower bioluminescent mycelium in the same species or identified from the correlation between bioluminescent intensity of tissues and gene expression levels. Our results reveal that that all bioluminescent fungi shared common ancestry. Three gene families including luciferase (luz), hispidin-3-hydroxylase (H3H), and fatty acid desaturase were up-regulated according to the intersect of up-regulated genes among four bioluminescent species. The gene luz is absent in the nonbioluminescent species. There are 6-30 paralogues of h3h in the four bioluminescent fungi but with different gene expression levels. These systematically understanding will further unravel the roles of fungi in ecological niches and evolution in the bioluminescence of Mycena fungi in general.
Dr. Reina Komiya (OIST) 小宮 怜奈 博士
Science and Technology Associate, Science and Technology Group, OIST
JST PRESTO Researcher
Keywords: long non-coding RNA, small RNAs, microRNA, reproduction, rice
Phased small interfering RNAs (phasiRNAs), which are generated from long RNA precursors at intervals of 21- to 26-nucleotides (nt), have been identified in animals and plants. In the family Poaceae, numerous 21-nt phasiRNAs are expressed from the premeiotic to the early meiotic stage, and subsequently, 24-nt phasiRNAs are expressed during the meiotic stage. In the biogenesis of both types of reproductive phasiRNAs, precursors of long intergenic non-coding RNAs (lincRNAs), which contain consensus sequences complementary to 22-nt miR2118/miR2775, are cleaved within the miRNA targeting site. These miRNA cleavages induce dsRNA synthesis from cleaved RNAs and dsRNAs are processed by DICER-LIKE proteins (DCLs) into 21-/24-nt phasiRNAs (Komiya et al., 2014; Komiya 2017). However, the function of lincRNAs, microRNA2118 (miR2118) and numerous number of phasiRNAs remain unknown. miR2118 triggering the 21nt phasiRNA biogenesis are conserved in gymnosperms, dicots, and monocots. There are 18 miR2118 family members in rice genome. A gene targeting analysis suggests that miR2118 family members regulate early reproduction. In this symposium, we will introduce the function of miR2118 through phasiRNA production in the reproductive development in rice.
Dr. Chih-Horng Kuo (AS) 郭志鴻 博士
Associate Research Fellow, Institute of Plant and Microbial Biology, Academia Sinica
Keywords: Genome, transcriptome, molecular evolution, symbiont, Mollicutes, Spiroplasma, phytoplasma, Agrobacterium
In microbial evolution, the development of a host-dependent lifestyle often has profound effects on the genome architecture. To better understand the evolutionary processes involved, as well as the functional consequences of changes in the gene content, our research group utilize genomics tools to conduct comparative analyses among bacteria with different ecological niches. In recent years, our major study systems include two genera within the class Mollicutes. The genus Spiroplasma contains species that are commensals, pathogens, or mutualists of diverse arthropod hosts. Our comparative genomics work revealed that the patterns of genome evolution varied widely among different clades within this genus, and horizontal gene transfer appeared to be a recurrent theme that is linked to the evolutionary transitions between different ecological niches. The second genus, ‘Candidatus Phytoplasma’, contains uncultivated bacteria that are all insect-transmitted plant pathogens. These phloem-restricted endosymbionts can systematically reprogram the development of their plant hosts by effectors. Notable symptoms of infection include phyllody (i.e., abnormal development of flower parts into leafy structure), witches’-broom (i.e., extensive proliferation of auxiliary shoots), and stunting (i.e., small flowers and leaves). We found that phytoplasma effector genes are often associated with potential mobile units on the chromosome, and these mobile genetic elements may facilitate gene flow between divergent lineages. Taken together, our findings suggested that the genome evolution of these symbionts are far more dynamic than previously thought. To further improve our understanding of these bacteria, our on-going work aims to functionally screen and characterize key genes that are linked to their adaptation.
Dr. Chien-Yu Lin (AS) 林建宇 博士
Post-Doctoral Fellow, Institute of Biomedical Sciences, Academia Sinica
Keywords: sialic acid, sialylation, dopamine receptor (D2R), adenosine receptor (A2AR), adenylyl cyclase (AC5)
Sialic acids are typically added to the end of glycoconjugates by sialyltransferases. Among the five ST8 α-N-acetyl-neuraminide α-2,8-sialyltransferases (ST8SIA) existing in adult brains, ST8SIA2 is a schizophrenia-associated gene. However, the in vivo substrates and physiological functions of most sialyltransferases are currently unknown. The ST8SIA3 is enriched in the striatum. Here, we showed that ablation of St8sia3 in mice (St8sia3-KO) led to fewer disialylated and trisialylated terminal glycotopes in the striatum of St8sia3-KO mice. Moreover, the apparent sizes of several striatum-enriched G-protein-coupled receptors (GPCRs) (including the adenosine A2A receptor (A2AR) and dopamine D1/D2 receptors (D1R and D2R)) were smaller in St8sia3-KO mice than in WT mice. A sialidase treatment removed the differences in the sizes of these molecules between St8sia3-KO and WT mice, confirming the involvement of sialylation. Expression of ST8SIA3 in the striatum of St8sia3-KO mice using adeno-associated viruses normalized the sizes of these proteins, demonstrating a direct role of ST8SIA3. The lack of ST8SIA3-mediated sialylation altered the distribution of these proteins in lipid rafts and the interaction between D2R and A2AR. Locomotor activity assays revealed altered pharmacological responses of St8sia3-KO mice to drugs targeting these receptors and verified that a greater population of D2R formed heteromers with A2AR in the striatum of St8sia3-KO mice. Since the A2AR-D2R heteromer is an important drug target for several basal ganglia diseases (such as schizophrenia and Parkinson’s disease), the present study not only reveals a crucial role for ST8SIA3 in striatal functions but also provides a new drug target for basal ganglia diseases.
Dr. Yao-Cheng Lin (AS) 林耀正 博士
Assistant Research Fellow, Agricultural Biotechnology Research Center, Academia Sinica
Keywords: bioinformatics, comparative genomics, systems biology, plant genetics, genome evolution
Cauliflower curd is a specialized floral organ with high economical values in agricultural production. It is known that multiple parts of the plant including shoot apical meristem, inflorescent meristem and leaves can sense environment stimulus and affect the floral development. However, the detail molecular mechanisms underlying the regulation of curd development is still largely unknown. In this study, cauliflower curds and the corresponding leaf samples were collected in five developmental stages under long day condition. Each sample with three biological replicates were sequenced by Illumina paired-end reads. The gene expression was quantified by KALLISTO. To increase the accuracy of gene expression analysis, genes with CPM (count per million) less than 1 and the median absolute deviation less than 0.7 were removed. Based on the “guilt by association” principle, genes with similar spatial expression profiles (coexpression) are assumed to share similar biological functions, forming a neighborhood network of potential partners. A total to 70 coexpression modules were constructed by weighted correlation network analysis (WGCNA). Combining inter-sample normalization approach where gene expression were further normalized between samples, 15 and 18 modules were identified corresponding with curd and leave development, respectively. Further analysis will be performed to prioritize candidate genes to reveal hidden regulatory networks in curd development.
Dalmira Merzhakupova (OIST)
Ph.D. Student, Protein Engineering and Evolution Unit, OIST
Keywords: protein-protein interactions (PPI), protein co-evolution, EGF,EGFR
Protein-protein interactions (PPI) is a driving force for the regulation of many biological processes. The elucidation of key residues important for PPI network should provide new insights not only into structures and functions of molecules but also about proteins co-evolution within biological systems. In recent years different computational methods have been emerging to tackle this problem. However, no single method can provide a structural information on a broad scale analysis of homologous proteins to predict not only functional association but physical binding and enable to decipher residues significant for a protein evolution. In our research, we developed a bioinformatics-based experimental approach to study the evolution of EGF-EGRF ligand receptor binding system. As a result, this novel method let us to analyze and characterize EGF residues conserved in evolution and homology for structure and function, respectively. According to the analysis it was possible to identify positions which appear to be essential for binding to the receptor.
Experimentally we generated EGF mutants to study the importance of the above identified positions for the EGFR binding. We determined binding affinity of EGF (Kd≈1 uM) mutants to EGFR through isothermal titration calorimetry (ITC). Mutant N32R showed stronger affinity (Kd≈600 nM) in comparison to WT EGF while other mutants were comparable to EGF. Finally, EGF mutants were tested for cell proliferation assay and variants with three times fold higher affinity showed inhibition of cell growth in normal skin fibroblasts. Overall, this approach will be useful to identify important residues for ligand-protein interactions within biological systems.
Dr. Matin Miryeganeh (OIST)
Post-Doctoral Fellow, Plant Epigenetics Unit, OIST
Mangroves are salt tolerant trees that grow in coastal saline water in tropics and subtropics and are adapted to harsh conditions with high salinity, extreme tides, strong winds, high temperatures, and anaerobic wetlands. They have developed specific morphological and physiological characteristics, such as breathing and support roots, salt-excreting leaves, and viviparous seedlings. Mangrove communities show gradual phenotypic changes in forest structure such as tree height and biomass that usually decrease due to increasing stress factors along the tidal gradients. We have set the study site in a mangrove forest located along the estuary of a river and coastal area of Pacific Ocean in Okinawa-Japan. This forest is consisted mainly of three mangrove species from the family Rhizophoraceae, and show highly developed morphological adaptations to extreme conditions. We are investigating how methylation variation is distributed among individuals from different habitats in different level of stress, and how this variation is correlated with their morphological differences and gene expression. To produce a high-quality reference genome, we generated a de novo assembly of representative mangrove species. We have done a complementary detailed de novo annotation of genes based on RNA sequencing data. Gene expression analysis identified remarkable genomic characteristics that are conserved within each group but differ among them and annotations of Gene Ontology, revealed differences in the transcriptome profiles among the two populations.
Dr. Charles Plessy (OIST)
Staff Scientist, Genomics and Regulatory Systems Unit, OIST
Keywords: Genome, transcriptome, systems biology, bioinformatics, open data, programming, Linux systems
Oikopleura dioica is a globally distributed marine animal that distinguishes itself in the animal reign by extreme features such as a very short life cycle (5 days), a quick cell cycle (down to 7 minutes), a small number of chromosomes (3 pairs) and a very compact genome (70 Megabases). Yet, it is evolutionarily closer to human than are model organisms such as yeast, nematodes or fruit flies, for instance, as it belongs to the chordate phylum it has features common with vertebrate embryonic development, such as a dorsal nerve cord, or the formation of a muscular tail supported by a notochord. Using the Nanopore sequencing technology, our unit produced a chromosomal assembly of O. dioica’s compact genome. Here, I will present this genome assembly and how we use it to explore the genomic variations found in wild populations. In light of these findings, I will then discuss what this animal might teach us about the constraints, or lack of constraints, for encoding the genetic information necessary for building multi-cellular animals that are the closest invertebrates to humans, and the opportunities and challenges that O. dioica may provide as a model for systems biology.
Dr. Dharmodharan Venugopal (OIST)
Post-Doctoral Fellow, Nucleic Acid Chemistry and Engineering Unit, OIST
Keywords: Ribozyme, Riboswitch, Photocaged guanine, Aptazyme, Gene regulation
Riboswitches are RNA gene regulatory elements embedded in the untranslated region of an mRNA. Riboswitches contain an aptamer domain that specifically binds a ligand and an associated regulatory sequence. Synthetic riboswitches that respond to various small molecules (ligands) have been constructed that function in mammalian cells. These riboswitches can also be controlled by light using photocaged ligands allowing finer spatial and temporal control of gene expression. However, photocaged aptamer ligands that function in living cells are highly limited. To expand the limited toolbox for optochemical regulation of riboswitches in cells, we synthesized a novel photocaged guanine (pc-G) and used it to control gene expression in both mammalian cells and in E. coli using light.