EMBO | COB Workshop "Trans-Scale Biology using exotic non-model organisms"

Organizers	Shuji Shigenobu (NIBB) Annika Guse (Ludwig-Maximilians-Universität München, DE)
Venue	Okazaki Conference Center, Okazaki, Japan
Date	July 25 – 27, 2023
Link	Official Website　（https://meetings.embo.org/event/23-trans-scale-bio）
Poster

【About the Workshop】
Recent technical innovations such as genome editing, next-generation sequencing, single-cell omics, modern imaging technologies are transforming today’s biology. The new technologies allow us to study ANY organisms at ANY levels from molecular to a group of individuals, which has been especially difficult for exotic non-model organisms until recently. Such exotic organisms facilitate exciting new questions that can be asked for the first time, or facilitate unprecedented ability to explore long-standing fundamental questions in life sciences. Also, these new technologies promote our understanding of the organisms of interest at a wide range of scales from molecular, cellular, organ, individual even to interactions between species (e.g. symbiosis and sociality), which we term "Trans-Scale Biology"

Nevertheless, establishing new models is still a big challenge. In this EMBO | Company of Biologists Workshop, we invite researchers who are pioneering new biology using exotic non-model organisms. While some issues such as breeding methods are specific to each model system, many issues including the development of genome editing and imaging protocol, genomic resources are common problems. We hope researchers can exchange useful information across the species and disciplines.

This EMBO | Company of Biologists Workshop will be held in Okazaki, Japan on the initiative of National Institute for Basic Biology (NIBB). Since NIBB is the institute serving as a center of excellence in cooperation with other universities and research organizations in Japan, we aim to nurture the scientific community of Japanese and European scientists by leveraging the framework of the EMBO|Company of Biologists Workshop.

【Report】
Recent technical innovations such as genome editing, next-generation sequencing, single-cell omics, and modern imaging technologies are transforming today’s biology. The new technologies allow us to study ANY organisms at ANY levels from molecular to a group of individuals, which has been especially difficult for exotic non-model organisms until recently. Such exotic organisms facilitate exciting new questions that can be asked for the first time, or facilitate unprecedented ability to explore long-standing fundamental questions in life sciences. Also, these new technologies promote our understanding of the organisms of interest at a wide range of scales from molecular, cellular, organ, individual even to interactions between species (e.g. symbiosis and sociality), which we term "Trans-Scale Biology". In this EMBO | Company of Biologists Workshop, researchers who actively utilize non-model organisms to explore new research areas gathered to share a diverse range of techniques, including genome editing, advanced bioimaging, and the development of genome resources, across the species and disciplines.
 
This three-day workshop was held at the Okazaki Conference Center and was attended by a total of 89 participants, including 12 from Europe, 3 from the U.S., and 74 from Asia (including 70 from Japan). We had 21 invited talks (including one keynote each from Japan and Europe) and 52 poster presentations (8 of which were selected as short talks) across six sessions. They showcased research using a diverse group of organisms such as sponges, kleptochloroplast sea slugs, seahorses, axolotl, carnivorous plants, parasitic plants, green hydras, anemones, aphids, marine annelids, shrimp, fireflies, and chironomids. Research topics also varied widely from development, regeneration, aging, symbiosis and parasitism, and bioluminescence, etc. In addition, there were special sessions focusing on advanced methods concerning genome editing using CRISPR/Cas9 and single cell omics. Moreover, two 25-minute group discussions allowed participants to engage in lively discussions that extended beyond the allotted time, leading to new ideas and collaborations.
 
The high level of satisfaction shown in the questionnaire after the workshop indicates that this workshop was a great success in embodying “Trans-Scale Biology” and for sharing this concept widely. We would like to hold the workshop again to further develop this concept and deepen the international research community in the future.

 

 

Day 1 | 25 July 2023
9:00	Registration
9:30-9:45	Opening Remarks
	Shuji Shigenobu (NIBB, JP)
Session: Emerging models of marine organisms
Chair: Annika Guse (LMU Munchen, DE)
9:45-10:15	Morphogenesis in which cells act as construction workers to manipulate materials: Spiculous skeleton construction of sponges
	Noriko Funayama (Kyoto University, JP)
10:15-10:45	Kleptoplastic sea slug: Non-self chloroplast acquisition and absence of horizontal gene transfer
	Taro Maeda (Keio University, JP)
11:15-11:30	Single cell RNA sequencing gives clues for the developmental genetic basis of syngnathid’s edentulism
	Hope M. Healey (University of Oregon, US) (Poster #03)
10:45-11:15	Orphan gene expressed in flame cone cells uniquely found in seahorse epithelium
	Mari Kawaguchi (Sophia University, JP)
11:30-11:45	On the origin of appetite: GLWamide in jellyfish represents an ancestral satiety neuropeptide
	Vladimiros Thoma (Tohoku University, JP) (Poster #08)
11:45-13:00	Lunch with Poster Viewing
Session: Emerging models for regeneration and aging
Chair: Kiyokazu Agata (NIBB, JP)
13:00-13:30	Axolotl as a molecular genetic system for studying regeneration
	Elly Tanaka (IMP, AT)
13:30-13:45	Tenascin-C-enriched regeneration-specific extracellular matrix guarantees superior muscle regeneration in Ambystoma mexicanum
	Ayaka Ohashi (Okayama University, JP) (Poster #14)
13:45-14:15	Sexual development in schistosomes
	James J. Collins (UT Southwestern Medical Center, US)
14:15-14:45	Resistance to aging and carcinogenesis in the naked mole-rat: Insights from the regulation of cellular senescence and cell death
	Kyoko Miura (Kumamoto University, JP)
14:45-15:00	Break
Session: New model plants
Chair: Satoko Yoshida (NAIST, JP) and Takashi Goto (NIBB, JP)
15:00-15:30	Exploring biological questions by establishing new model plants: the moss Physcomitrium patens, the sensitive plant Mimosa pudica, the Venus flytrap Dionaea muscipula, the Albany pitcher plant Cephalotus follicularis, and the sundew Drosera rotundifolia
	Mitsuyasu Hasebe (NIBB, JP)
15:30-16:00	Genetic regulation of 3-dimensional growth in plants
	Laura Moody (Oxford University, UK)
16:00-16:30	Molecular basis for tomato resistance to the parasitic plant Cuscuta
	Neelima Sinha (UC Davis, US)
16:30-17:00	Molecular basis of the haustorium formation in the root parasitic plants in Orobanchaceae
	Satoko Yoshida (NAIST, JP)
17:00-17:15	Investigating the role of MADS-box protein binding In the evolution of seeds and flowers
	Derry Carr (The University of Birmingham, UK) (Poster #26)
17:15-17:30	Break
Poster Session (Odd numbers)
Chair: Miyo T. Morita (NIBB, JP)
17:30-18:00	Poster Flash Talks
18:00-19:00	Poster Session
19:00-20:00	Dinner
Day 2 | 26 July 2023
9:00	Registraion
Keynote
Chair: Shuji Shigenobu (NIBB, JP)
9:30-10:30	Experimental evolution of insect-microbe mutualistic symbiosis
	Takema Fukatsu (AIST, JP)
10:30-10:45	Break
Session: New symbiosis models
Chair: Mayuko Hamada (Okayama University, JP) and Tomonari Nozaki (NIBB, JP)
10:45-11:15	Adaptation to the environment through symbiosis - a model systems' approach
	Annika Guse (LMU Munchen, DE)
11:15-11:45	Diversified photosymbiotic systems in animals: Insights from the symbiosis of green hydra
	Mayuko Hamada (Okayama University, JP)
11:45-12:15	Hologenomics of aphids: an integrative view of the insect and symbionts
	Shuji Shigenobu (NIBB, JP)
12:15-12:30	Group Photo
12:30-13:30	Lunch with Poster viewing
Keynote
Chair: Annika Guse (LMU Munchen, DE)
13:30-14:30	Bridging scales in micro- and macroevolution: the marine annelid Platynereis dumerilii
	Detlev Arendt (EMBL, DE)
14:30-14:45	Break
Session: New technologies to develop emerging model organisms
Chair: Shuji Shigenobu (NIBB, JP)
14:45-15:15	DIPA-CRISPR: Insect gene editing made easy
	Takaaki Daimon (Kyoto University, JP)
15:15-15:45	Two-photon holographic microscope and 3D fluorescence imaging
	Osamu Matoba (Kobe University, JP)
15:45-16:00	Stem cells lineage reconstruction in the adult planarian using single cell transcriptomics
	Sophie Peron (Oxford Brookes University, UK) (Poster #38)
16:00-16:15	Beyond cholesterol: de novo phytosterol synthesis In animals
	Dolma Michellod (MPI for Marine Microbiology, DE) (Poster #42)
16:15-16:30	Break
Group Discussion
16:30-16:55	Theme 1:Omics
	Facilitator: Shuji Shigenobu (NIBB, JP)
	Theme 2: Genome Editing
	Facilitator: Satoshi Ansai (Kyoto University, JP) and Taro Nakamura (NIBB, JP)
	Theme 3: Bioimaging
	Facilitator: Annika Guse (LMU Munchen, DE)
16:55-17:05	Participants Reshuffling
17:05-17:30	Theme 1:Omics
	Facilitator: Shuji Shigenobu (NIBB, JP)
	Theme 2: Genome Editing
	Facilitator: Satoshi Ansai (Kyoto University, JP) and Taro Nakamura (NIBB, JP)
	Theme 3: Bioimaging
	Facilitator: Annika Guse (LMU Munchen, DE)
17:30-17:40	Break
Poster Session (Even numbers)
Chair: Miyo T. Morita (NIBB, JP)
17:40-18:10	Poster Flash Talks
18:10-19:10	Poster Session
19:10-20:00	Dinner
Day 3 | 27 July 2023
9:00	Registration
Session: Emerging model arthropods
Chair: Taro Nakamura (NIBB, JP)
9:30-10:00	Exploring the genetic basis of horn development of the Japanese rhinoceros beetle, Trypoxylus dichotomus
	Teruyuki Niimi (NIBB, JP)
10:00-10:15	A multi-partner symbiotic system in the eusocial aphid Ceratovacuna japonica
	Shunta Yorimoto (NIBB, JP) (Poster #32)
10:15-10:45	Parhyale hawaiensis: a crustacean model for epithelial morphogenesis, limb development and wood digestion
	Anastasios Pavlopoulos (FORTH, GR)
10:45-11:00	Break
11:00-11:15	A 5' UTR-overlapping lncRNA controls environmental sex determination in the freshwater crustacean Daphnia magna
	Yasuhiko Kato (Osaka University, JP) (Poster #47)
11:15-11:45	Heike firefly sheds the light on the evolution of bioluminescent properties
	Yuichi Oba (Chubu University, JP)
11:45-12:15	X-midge: origin and mechanisms of anhydrobiosis at the single-cell level.
	Oleg Gusev (Juntendo University, JP / Kazan Federal University, RU)
12:15-12:25	Closing Remarks
	Annika Guse (LMU Munchen, DE)
Excursion (Short trip to Japanese historical sites in Okazaki City)
Afternoon	Excursion

Please find the list of poster presentations here.