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Seminars & Workshops 

"FRONTIERS in Rhizosphere Research"
Date: November 20th, 2018
Time: 10:30-17:00
Venue: Main Lecture Hall, RIKEN Yokohama Campus
Language: English


Thank you very much for your attendance for “FRONTIERS in Rhizosphere Research”! Nine young researchers were invited from inside and outside of Japan to present their research. High-level discussions took place and new ideas and advanced technology were introduced during the event. We hope that this event gave an opportunity to build and deepen connections with others.
Speakers and Titles:
-Stephane Hacquard “Microbial Interkingdom Interactions in Roots Promote 
-Yasunori Ichihashi “Soil solarization-induced organic nitrogen increase agricultural crop yield"
-Arno Germond “Toward predicting gene expression and metabolism from label free spectral imaging”
-Hirokazu Toju "Core microbiomes for designing sustainable ecosystems”
-Ruben Garrido-Oter “Association studies of plant-associated microbial genomes"
-Shuta Asai “Field-Patho-Genomics−for establishment of soil diagnostics−”
-Ryohei Thomas Nakano “Ternaryinteraction assays revealed modular traits of root microbiota that dictate host growth and immune status”
-Masahito Hosokawa “Obtaining high-quality draft genomes from uncultured microbesby single-cell genome sequencing with droplet microfluidics”
-Yuji Ishigaki “Rhizosphere interactions regulate secondary metabolite production of root-associated microbes"
Host: Ken Shirasu, Group Director of Plant Immunity Research Group
Program(PDF File)
Group Photo Host:Ken Shirasu, Group Director of Plant Immunity Research Group Dr. Stephane Hacquard Discussion Time1 Dr. Yasunori Ichihashi Dr. Arno Germond Discussion Time2 Dr. Hirokazu Toju Discussion Time3 Dr. Ruben Garrido-Oter Discussion Time4 Dr. Shuta Asai Coffee Break 1 Coffee Break 2 Coffee Break 3 Coffee Break 4 Coffee Break 5 Dr. Ryohei Thomas Nakano Discussion Time5 Dr. Masahito Hosokawa Discussion Time6 Dr. Yuji Ishigaki Discussion Time7

iSYM Seminar@RIKEN Yokohama
Photo of Dr. Shigehiro Kuraku
Date: December 19th, 2018
Time: 10:30-11:30
Venue: E717/719, East Research Building, RIKEN Yokohama Campus
Language: English
Speaker:  Dr. Shigehiro Kuraku, Laboratory for Phyloinformatics, RIKEN BDR in Kobe
Title: Challenges in genomic studies of non-laboratory species: lessons from sharks
Advancement of DNA sequencing technologies has enhanced the potential of in-depth genome analysis on diverse species through de novo sequencing. However, the success of such projects targeting non-laboratory species largely depends on other strategic factors, including deliberate sampling, preparation of unbiased libraries, appropriate sequencing design and assembly, and researchers’ biological sense for data interpretation. Each of these factors requires decision-making, which cannot usually be evidenced by own prior experience, due to resource-demanding nature of sequencing and computation. This seminar will cover speaker’s recent experience in shark genome analysis (Hara et al., 2018. Nat. Ecol. Evol. 2: 1761-1771), with a special emphasis on technical and strategic aspects of de novo genome sequencing projects. Application of the prevailing method for chromosome-scale genome scaffolding based on Hi-C will also be discussed herein.
Host: Dr. Ken Shirasu, Plant Immunity Research Group, CSRS
iSYM Seminars@RIKEN Yokohama
Date: December 13th, 2018
Time: 13:00-14:00, 14:00-15:00
Venue: Main Lecture Hall, RIKEN Yokohama Campus
Language: English
Dr. Martin J. Blaser
Dr. Martin J. Blaser, New York University Langone Medical Center, USA
Title: The role of the early life microbiome in host metabolic and immunologic development
A central feature of mammalian development across an evolutionary timeframe is the high fidelity intergenerational transfer of resident microbes. Yet the microbiome of young animals, crucial in the early life window of development, has limited resilience, and is vulnerable to perturbation. We have shown that early life antibiotic exposures can alter microbiota development with both metabolic and immunological consequences. We have extended these studies to both include the prior generation, and to more fully examine both antibiotic and dietary effects. Network models best explain microbiota dynamics, with linkages to phenotypes. In total, our work highlights the importance of early events in shaping the microbiome of developing animals, with effects that may extend to successive generations.
Dr.Maria Gloria Dominguez-Bello
Dr. Maria Gloria Dominguez-Bello, Principle Investigator, Rutgers University, USA
Title: Developmental effects of impaired perinatal microbial colonization

The microbiota is transmitted vertically, within species and throughout generations.In mammals, exposure to live microbes occurs at the time of labor. Different body sites of the baby reshape the primordial source of maternal vaginal/perineal microbiota, and these microbes play a role in healthy development of each organ. Bypassing the birth canal at birth (such as in C-section), and early exposure to antibiotics, have been associated with increased incidence of immune and metabolic disorders (asthma, T1D, allergies, obesity). Urban lifestyle is rich in antimicrobial practices, and has been associated with decrease in the human microbiota diversity. If the degraded the human microbiota, result of modern practices (some of them needed, such as medical interventions), is a factor fostering modern diseases, we will need restoration approaches to arrest and prevent the current trend in urban diseases. More research is needed to determine lost microbes and their functions and evolutionary history, to be used in the restorative medicine of the future.
Host: Dr. Hiroshi Ohno, Laboratory for Intestinal Ecosystem, IMS

iSYM Seminar@RIKEN Yokohama
Photo of Dr. Youssef Belkhadir
Date: December 5th, 2018
Time: 14:00-15:00
Venue: E717/719, East Research Building, RIKEN Yokohama Campus
Language: English
Speaker:  Dr. Youssef Belkhadir, Gregor Mendel Institute of Molecular Plant Biology
TitleMolecular logic in large-scale ligand-receptor interaction networks
In plants genomes, an expanded family of cell-surface receptor kinases (RKs) transduce either ‘self’ or ‘non‐self’ signals into changes in nuclear gene expression. Plant RKs are typically characterized by an extracellular domain, and in most cases, a functional intracellular kinase domain. Extracellular domains (ECDs) can modulate the activity of signaling competent RKs complexes by controlling ligand specificity and by recruiting appropriate signaling partners.  There is very limited knowledge on the global interaction network ECDs can establish in their resting or ligand-activated functioning modes. I will present collaborative efforts aimed at discovering novel ligands ad ECD interactions in the RKs repertoire of Arabidopsis.
Host: Dr. Ken Shirasu, Plant Immunity Research Group, CSRS
Dr. Youssef Belkhadir Seminar photo

RIKEN International Symposium"Frontiers in Integrated Symbiology"
Date: June 4th, 2018
Time: 10:00-17:00
Venue: Small Hall, Tower Hall Funabori, Tokyo
Language: English


On June 4th 2018, or first symposium was held at Tower Hall Funabori. This time we invited nine speakers from RIKEN and other institutions. Each speaker gave us an interesting talk related to biology of symbiosis, or symbiology. It was a unique opportunity to hear various symbiological systems at a time. For example, we heard the most recent findings in human-microbe, mouse-microbe, fish-microbe, insect-microbe, and plant-microbe interactions. In addition, we also heard organelle integration originated from symbiological interactions. Question time was lively and 5 min wasn't enough at all! Also, coffee time was a great opportunity to meet new people from different fields of research.  Thank you everyone for coming to the symposium. We look forward to the next iSYM event!
Host: iSYM, RIKEN, Japan Symbiosis Society
Program(PDF File)
Dr.Ken Shirasu Dr.Jun Kikuchi Closing Remarks by Shigeo Koyasu, Executive Director RIKEN Question Time1 Prof.Tomoyoshi Nozaki Prof.Ifor Williams Prof.Kiwamu Minamisawa Dr.Moriya Ohkuma Question Time2 Dr.Wataru Suda Dr.Hiroshi Ohno Prof.Neil Mabbott Question Time3

IMS Seminar @RIKEN Yokohama
Date: June 11th, 2018
Time: 15:00-16:00
Venue: C214/220, 2nd floor, Central Research Building, RIKEN Yokohama Campus
Language: English
Speaker: Dr. Mahesh S. Desai, Group Leader, Department of Infection and Immunity, Luxembourg Institute of Health
TitleDiet-driven interactions of the gut microbiome with the intestinal mucus barrier
The functional interactions of the human gut microbiome with its host are largely driven by diet, yet the underlying mechanisms have remained poorly understood. By employing a gnotobiotic mouse model containing a synthetic human gut microbiota composed of 14 commensal bacteria—we recently showed that a dietary fiber-deprived microbiota degrades the colonic mucus layer, which is the first line of defense against invading microorganisms. Furthermore, a fiber-deprived, mucus-eroding microbiota enhances
susceptibility to the enteric pathogen Citrobacter rodentium (Desai et al.Cell (2016), 167, 1339–1353). Our follow-up experiments indicate that such deterioration of the colonic mucus barrier is associated with the immunological changes observed in inflammatory bowel disease. In the face of changing Western diets, our results suggest that dietary therapeutics, including nextgeneration prebiotics, could be utilized to modulate the the gut barrier alterations and to reduce the incidence of colitis.
Host: Dr. Hiroshi Ohno, Laboratory for Intestinal Ecosystem, IMS

iSYM Innovation Seminar @RIKEN Yokohama
Photo of Dr.Jonas Korlach
Date: March 15th, 2018
Time: 13:00 - 14:00
Venue: E717/719, East Research Building, RIKEN Yokohama Campus
Language: English
Speaker: Dr. Jonas Korlach, Chief Scientific Officer, PacBio
Title: Latest Capabilities & Future Directions of Long-read PacBio Sequencing
While short-read Next-Generation Sequencing (NGS) has brought about tremendous insights into biology, challenges have remained to characterize many important features of genomes, transcriptomes and epigenomes. Dr. Korlach will describe the latest capabilities and applications of long-read PacBio sequencing on the new Sequel System, including the areas of:
-        Efficient and cost-effective de novo assembly of complete bacterial genomes, and simultaneous characterization of their epigenomes
-        Full-length bacterial RNA sequencing
-        High-resolution 16S and shotgun metagenomics
-        Eukaryotic whole-genome sequencing and structural genetic variation detection
-        Single-cell transcriptomics
Dr. Korlach will also give an outlook on the roadmap of further throughput increases and resulting applications for the Sequel System.
Host: Dr. Sachiko Masuda, Plant Immunity Research Group, CSRS
Dr.Jonas Korlach seminar photo
iSYM Internal Seminar Series @RIKEN Yokohama
Photo of Dr.Arno Germond
Date: February 22nd, 2018
Time: 14:00 - 14:40
Venue: Room C218/220, Central Research Building, RIKEN Yokohama Campus
Language: English
Speaker: Dr. Arno Germond, Laboratory for Comprehensive Bioimaging, RIKEN QBiC
Title: Predicting gene expression from label-free Raman spectroscopy
Raman spectroscopy is a label free microscopy technique that provides a chemical signature of the considered entity. When used on single-cells, spectral images can be reconstructed to visualize the distribution of the molecular compounds present in cells (Lipids, Proteins, Cytochrome, Nucleic Acids.). Spectral information provides a unique phenotype of the measured entity, which have proven useful to classify and discriminate cell type or cell state of single living cells with a high accuracy. In the past 3 years, I have been developing the Raman platform of QBIC, from the measurement methodology to the analysis pipeline, and proved its efficiency and utility to classify and discriminate samples of both chemical liquids and cells, such as E. coli and human iPS cells. Despite the relatively low sensitivity and temporal resolution of Raman spectroscopy, our laboratory demonstrated that Raman spectroscopy is a useful tool to monitor the change in cell-state (such as differentiation or reprogramming) over time.
However, in most cases, spectral data cannot be easily interpreted in a straightforward or biologically-relevant manner. Gene expression, on the other hand, provide a much more informative layer of informative about the biological system. My hypothesis was that these two layers of high-dimensional information are linked through the complex network of the cell.  Today I report about my most recent research which aims at linking the Raman spectral information to the transcriptomic data. Using a multivariate statistical model, and a simple biological model (namely, various mutant cell lines of E. coli), I show that the prediction of the transcriptome from Raman spectral data is possible. The model showed excellent performances and some accurate prediction of 2613 genes. Results showed that the worst predicted genes by the model were also the genes that showed mutations in their respective cell lines, which tend to support the proposed hypothesis. Then, by applying a network analysis, we highlighted the “strongest” pairs of Raman wavelengths and gene expression, which are the best pairs explained by the model. These nodes can provide useful information to decipher the unique relation between Raman spectra and gene expression. Now, I would like to apply this method on the microbiota cell lines to see how good we could predict the gene expression of cell lines from label-free fast measurements. I strongly encourage people interested in this technique of classification/discrimination to come forward for a collaboration to answers problematics relating to the study of symbiosis.
Host: Dr. Ken Shirasu, Plant Immunity Research Group, CSRS
Dr.Arno Germond seminar photo

iSYM Seminar @RIKEN Yokohama
Date: December 14th, 2017
Time: 14:00 - 15:00
Venue: Room E717/719, East Research Building, RIKEN Yokohama Campus
Language: English
Speaker: Prof. Scott C. Peck 
Biochemistry Department, University of Missouri, USA
TitleNew Insights into the Basis of Innate Immunity in Plants
Plants perceive potential pathogens by recognizing pathogen-associated molecular patterns (PAMPs) through plasma membrane (PM) receptors. Recognition of flg22, a 22 amino acid PAMP derived from the bacterial flagellum, by the receptor-like kinase FLS2 induces defense signaling responses and contributes to innate immunity by restricting bacterial invasion. We have developed quantitative phosphoproteomic technology to identify novel Arabidopsis proteins that are rapidly phosphorylated following PAMP treatments, and using reverse genetics, we have defined functions for a number of these candidates in innate immune responses.
Plant recognition of potential bacterial pathogens initiates the rapid deployment of defenses, thereby preventing colonization. Much of what is known about plant resistance against bacteria involves production of and response(s) to salicylic acid (SA). However, SA-independent mechanisms of resistance are known to exist but have been poorly defined. We found that the enhanced resistance of the MAP kinase phosphatase 1 (mkp1) mutant in Arabidopsis is genetically independent of SA production and signaling, providing possible insights into SA-independent mechanisms. We previously reported that resistance in mkp1involves the restriction of plant chemical signals used by virulent bacteria to induce of their type III secretion system (TTSS), and we also reported that this mechanism appears to be shared with PAMP-triggered immunity (PTI; Anderson et al., 2014). Because PTI, like the resistance in mkp1, previously has been found to be independent of SA, we examined if – and confirmed that – PTI restriction of effector delivery was also independent of SA. These results provide a simple explanation of a mode of SA-independent resistance that can be rapidly activated before SA production is initiated. Anderson et al (2014) Decreased abundance of type III secretion system-inducing signals in Arabidopsis mkp1 enhances resistance against Pseudomonas syringae. PNAS 111:6846-6851.
Host: Dr. Ken Shirasu, Plant Immunity Research Group, CSRS

Prof.Scott Peck seminar photo
iSYM Seminar @RIKEN Yokohama
Photo of Prof. Heidi H Kong
Date: November 10th, 2017
Time: 11:00 - 12:00
Venue: Conference Room, 6F North Research Building, RIKEN Yokohama Campus
Language: English
Speaker:  Heidi H. Kong, M.D., M.H.Sc
Head, Cutaneous Microbiome and Inflammation Section, Adjunct Investigator, National Cancer Institute (NCI), Dermatology Branch
Title: The microbiome in healthy skin and atopic dermatitis
The varied topography of human skin offers a unique opportunity to study the body’s microenvironments and the functional and taxonomic composition of microbial communities. The general accessibility of skin also enables longitudinal clinical studies throughout the course of disease. Metagenomic analyses of diverse body sites in healthy humans have defined the skin microbiome as shaped by the local biogeography, yet marked by strong individuality. Additionally, strain-level variation of dominant species was heterogeneous and multiphyletic in healthy adults. Re-sampling months and years later revealed that despite the skin’s exposure to the external environment, the bacterial, fungal, and viral communities were largely stable over time. Strain and single nucleotide variant level analysis showed that individuals maintain, rather than reacquire prevalent microbes from the environment. Longitudinal stability of skin microbial communities informs clinical studies exploring alterations observed in disease states, such as the inflammatory skin disorder atopic dermatitis (commonly known as eczema). We are integrating shotgun metagenomic sequencing, culturing, and animal models to improve our understanding of atopic dermatitis. 
Host: Masayuki Amagai, M.D., Ph.D, Laboratory for Skin Homeostasis, IMS
iSYM Seminar @RIKEN Yokohama
Photo of Dr. Henrik Stotz
Date: October 24th, 2017
Time: 15:00 - 16:00
Venue: Room E717/719, East Research Building, RIKEN Yokohama Campus
Language: English
SpeakerDr. Henrik Stotz
School of Life and Medical Sciences, University of Hertfordshire, UK
Effector-triggered defence against apoplastic fungal pathogens of oilseed rape
Apoplastic fungal pathogens cause annual crop losses in the order of tens of billions of dollars each year.  At the University of Hertfordshire, we work on the two most important oilseed rape diseases in the UK, phoma stem canker and light leaf spot caused by Leptosphaeria spp. and Pyrenopeziza brassicae, respectively.  We hypothesise that receptors with extracellular leucine-rich repeat (eLRR) domains are responsible for R gene-mediated resistance against these apoplastic fungal pathogens.  We introduced the term effector-triggered defence to better describe resistance against pathogens that colonise the extracellular space of plant tissues. 
Sequenced oilseed rape (Brassica napus) genomes were used to identify eLRR genes and to determine their contribution to resistance against different classes of oilseed rape pathogens.  Efforts are underway to better understand temperature sensitivity of phoma stem canker resistance.  Evidence has been obtained that specific effectors of L. maculans suppress host defence responses.  Analysis of RNAseq data suggests cellular processes that are involved in host susceptibility to or resistance against L. maculans.  A better molecular understanding of effector-triggered defence will help plant breeders in more effectively managing disease losses caused by these fungal pathogens.
Host: Dr. Ken Shirasu, Plant Immunity Research Group, CSRS
Dr.Henrik Stotz Seminar photo
iSYM 1st Innovation Seminar @RIKEN Yokohama
Date: October 5th, 2017
Photo of Dr Derek Bartlem

Time: 10:30 - 11:30
Venue: Room 214/216, Central Research Building, RIKEN Yokohama Campus
Language: English
Speaker: Dr. Derek Bartlem
Head of Research USA, KWS Gateway Research Center, USA
KWS – a different kind of plant breeding company with research institutes in US and Europe.
This seminar will provide an introduction to an international plant breeding company that was first established over 160 years ago.  KWS is based in Germany and present in over 70 countries.  In addition to strong biotech research activities in Germany, the KWS Gateway Research Center was recently established as KWS’ North America plant biotech research facility in St. Louis, USA.  There is a strong focus on innovative research and new product development in KWS, and a very unique culture that provides a positive environment for scientists coming from both industry and academic backgrounds.  This seminar is focused towards academic researchers to explain the history and focus of KWS, and to encourage dialogue with you on potential opportunities for collaborating together.
Host: Dr. Ken Shirasu, Plant Immunity Research Group, CSRS
Dr.Derek Bartlem seminar photo

iSYM Seminar Series @RIKEN Yokohama
Date: September 29th, 2017
Time: 10:00 - 15:00
Venue: Room 214/216, Central Research Building, RIKEN Yokohama Campus
Language: English
10:00 - 10:45
Brad Day, Professor & Associate Chair for Research
Department of Plant, Soil and Microbial Sciences, Michigan State University, USA
"The plant guard cell as a paradigm for the analysis of immunity and pathogen virulence"
10:45 - 11:30 
Gregg A. Howe, MSU Foundation Professor, 
Department of Energy-Plant Research Laboratory; Department of Biochemistry and Molecular Biology; Plant Resilience Institute, Michigan State University, USA
 "Modularity in Jasmonate Signaling for Multi-stress Tolerance”  

(Lunch Break)

13:30 - 14:15    
Michael Thomashow, MSU Foundation Professor,  
Department of Energy-Plant Research Laboratory; Department of Plant, Soil and Microbial Sciences; Plant Resilience Institute, Michigan State University, USA
"Regulation of Freezing Tolerance and Salicylic Acid-Mediated Immunity by Arabidopsis CAMTA Transcription Factors”

14:15 - 15:00    
David B. Lowry, Assistant Professor, 
Department of Plant Biology, Michigan State University, USA
"The Genetic and Physiological Basis of Adaptation to Divergent Habitats" 
Host: Dr. Ken Shirasu, Plant Immunity Research Group, CSRS
CSRS Yokohama Seminar Series Organizer:
Dr. Keiko Sugimoto, Dr. Mitsunori Seo, and Dr. Makoto Hayashi

Prof. Brad Day seminar photo
Prof. Gregg A Howe seminar photo

iSYM Seminar @CSRS Yokohama
Date: August 30th, 2017
Time: 15:00 - 16:00
Venue: Room 717/719, East Research Building, RIKEN Yokohama Campus
Language: English
Dr. Ryoji Shinya
Senior Assistant with tenure (Principal Investigator)
Department of Agriculture, Meiji University
Bursaphelenchus okinawaensis: an emerging genetic model for plant-parasitic nematodes
Nematodes have successfully adapted to nearly every ecological niche and developed various unique morphological and ecological traits. In particular, the economically relevant plant-parasitic nematodes are diverged from free-living nematodes including the model organism Caenorhabditis elegans, and have highly specialized characteristics such as parasitism, morphology, and sexual traits. Unfortunately, most of the genetic techniques and tools developed in C. elegans research are not directly applicable to the plant-parasitic nematodes due to these differences. Therefore, little is known about the genes controlling such plant-parasitic nematode-specific functions. Recently, a genetically tractable system with the hermaphroditic nematode Bursaphelenchus okinawaensis is being developed to solve this problem. This seminar will introduce this emerging genetically tractable system for the study of plant-parasitic nematodes and explain how it works using the study of sex determination mechanisms as an example.
Host: Dr. Yasuhiro Kadota, Plant Immunity Research Group, CSRS

Dr. Ryoji Shinya seminar photo

iSYM "Biology of Symbiosis" Workshop
Dates: August 21st - 22nd, 2017
Place: RIKEN Yokohama Campus, Main Office Building, Lecture Hall (Koryuto Hall)
Language: English
The program of "Biology of Symbiosis" Workshop

Photo of Biology of Symbiosis workshop


Photo of Biology of Symbiosis workshop question time


Photo of Biology of Symbiosis Workshop group photo


 RIKEN Seminar 
Microbial fermentation products shape host immune system through epigenetic modifications 
Prof. Koji Hase(Division of Biochemistry, Faculty of Pharmaceutical Science, Keio University) 
Date: Tuesday, June 27, 2017 17:00-18:00 
Language: English 
Venue: Main Office Bldg. (Koryu-to)Hall, Yokohama Campus
※Live telecast from Wako
 <Wako: 408 Seminar Room, Chemical Biology Bldg.> 
<Kobe: N701-703 Seminar Room, Building A>   
<Tsukuba: Moriwaki Hall> 
HostHiroshi Ohno, M.D., Ph.D, Laboratory for Intestinal Ecosystem, IMS
 Seminar Poster

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