This seminar will be led by Dr. Itoshi Nikaido, who will speak on the following topics. Illumina will also provide information on our latest new products, including PIPseq, an instrument-free single-cell solution scheduled for release in 2025.
Single-cell RNA sequencing (scRNA-seq) has been widely applied in various research fields for the analysis of cell type identification, lineage inference, and cell-cell interactions. With advancements in experimental methods, scRNA-seq has been evolving toward higher precision, larger scale, and multi-modal capabilities.
Meanwhile, the advent of ChatGPT has drawn attention to large-scale generative AI models (foundation models) that can handle multiple tasks within a single AI framework. Foundation models are expected to have applications beyond natural language processing, extending to scientific data, and omics fields have already seen the emergence of such AI models. Given that foundation models require vast amounts of training data, they are well-suited to large-scale data generated by scRNA-seq.
In this presentation, I will introduce recent technological advancements in scRNA-seq methods that enable large-scale data production, such as PIP-seq, which operates without specialized equipment, and the highly sensitive Quartz-Seq2. Furthermore, I will discuss the applications of generative AI to scRNA-seq data.

Extracellular vesicles (EVs), including exosomes, play an important role as communication tools between cells and are involved in various diseases such as cancer, inflammatory diseases, and neurological diseases. The properties of EVs and their inclusions (nucleic acids, proteins, lipids, etc.) differ depending on the tissues and cells that secrete them, and attempts are being made to use EVs and their inclusions in body fluid samples as biomarkers to diagnose diseases. In this seminar, we will introduce examples of analysis of tissue-specific EVs in blood samples under the title of “Characterization of extracellular vesicle subpopulations from tissues in blood”.

TBA

Chemical modification of biomolecules by synthetic probes is a powerful technique for creating useful molecular tools for biological research. For example, the selective attachment of fluorescent dyes to target proteins in cells or living animals allows various applications such as bioimaging, interaction detection, and activity regulation of proteins. In addition, direct functionalization of metabolites not directly encoded by genes, such as lipids, with synthetic probes enables dynamic analysis that cannot be achieved by conventional molecular biology-based techniques and genetic engineering. In this talk, I will introduce our recent works on in situ modification for biomolecules imaging with Zeiss microscopy and their applications in proteomics and genomics.

As a pioneer in molecular biology research reagents and genome analysis services, Takara Bio has focused on the field of next-generation sequencing (NGS) analysis, particularly in the genome and transcriptome of small samples, providing high-performance NGS library preparation reagents and other omics research solutions.
In this seminar, we will review the basics and advancements of NGS technology, introduce NGS analysis reagents and services for the rapidly advancing field of multi-omics analysis in recent years, and present new systems that strongly support single-cell analysis.
<Main Topics:>
- Advances in omics analysis technology utilizing modern sequencers that have evolved to ultra-high performance
- Takara Bio’s NGS library preparation kits that enable the analysis of ultra-small samples
- Shasta Single Cell System: A system that enables full-length analysis for single-cell preparation

Immune checkpoint inhibitors have significantly improved outcomes of patients with various cancer types, revolutionizing cancer treatment. However, response rates to such therapies are rather limited, and thus, there persists a need to decipher the complex biology of immune checkpoints to enhance therapeutic efficacy as well as to prevent immune-related adverse events.

QIAGEN Ingenuity Pathway Analysis (IPA) supports the interpretation of your omics data by utilizing a high-quality knowledge base and a large amount of omics data from past research. This time, we will focus on the very hot field of chimeric antigen receptor (CAR) T cell therapy. CAR-T cell therapy is a promising treatment that aims to cure recurrent and refractory cancers, but the disease group in which it can provide sustained efficacy is still limited. Currently, research is being conducted to change the function of CAR-T cells. In order to make rational modifications to T cells, it is important to narrow down the process of finding key molecules related to functional decline such as terminal differentiation and exhaustion of T cells from comprehensive gene expression data such as RNA sequencing. By using IPA to search for upstream regulatory molecules that cause the comprehensive changes in RNA abundance, it may be possible to apply it to the rational improvement and development of CAR-T cells. In this presentation, we will introduce specific examples of CAR-T cell modifications that the presenter's group is promoting based on IPA interpretation.

Automation of biomeasurement has developed rapidly in recent years, and many measurement methods that previously relied on craftsmanship have been automated, making it possible to acquire large-scale and highly reproducible data.
In this presentation, we will use the automation of digital biomeasurement as an example to introduce the automation of biomeasurement using a custom dispensing equipment, which can be easily and quickly implemented in academia.

We will introduce the support activities of four platforms that support the research of researchers in the field of life science who have obtained MEXT KAKENHI.

There has been growing interest in artificially manipulating cellular functions, particularly through synthetic molecules in chemical biology and light-responsive proteins in optogenetics. Related with these technologies, the presenter developed ""Photochromic CID Technology"" (CID: Chemically Induced Dimerization). This technology employs synthetic compounds that exhibit photochromism—a property where color or shape changes in response to light—to rapidly and reversibly control the dimerization of universal tag-fused proteins in cells, enabling precise manipulation of various intracellular phenomena. In the seminar, he will present several applications, such as regulation of intracellular signal transduction and protein assembly.
References：
1. T. Mashita et al., ChemBioChem 2019, 20, 1382.
2. T. Mashita et al., Nat. Chem. Biol. 2024, https://doi.org/10.1038/s41589-024-01654-w

Long-read sequencer can read nucleic acid sequences over 100 kb, facilitating the determination of sequences in repetitive genomic regions and full-length mRNA sequences that were difficult to analyze with short-read sequencing. Additionally, hybridization capture using complementary probes is useful for deep sequencing of target regions and reducing sequencing costs. This seminar will introduce the technological developments for targeted long-read analysis combining long-read sequencing and hybridization capture.

Recent technological innovations in in situ hybridization (ISH) have enabled highly sensitive detection at the single-copy level of mRNA and the simultaneous detection of multiple genes. However, many problems remain to be solved, such as cost barriers and the inability to optimize the signal-to-noise ratio of staining signals due to autofluorescence derived from tissue samples.
Dr. Yosuke Tsuneoka, Toho University Faculty of Medicine, has developed a new fluorescent ISH method based on the in situ hybridization chain reaction (isHCR) method. This new isHCR method is a revolutionary ISH method that has many advantages by using short hairpin DNAs. Furthermore, the fluorescence quenching system based on the principle of photobleaching, also developed by Dr. Tsuneoka, can be applied simultaneously to analyze gene expression with higher signal-noise ratio.
In this seminar, Dr. Tsuneoka will introduce this new isHCR and present the latest results of his research.
Even those who are not interested in gene expression analysis will enjoy this seminar. Please join us!

The FDA Modernization Act 2.0 has been enacted, promoting the international use of human-derived cultured cells for compound evaluation in chemical assessments and drug development. New Approach Methods (NAMs), which aim to avoid the use of laboratory animals and provide information on the toxicity and risk assessment of chemicals, are being actively adopted. In this context, the Organization for Economic Co-operation and Development (OECD) has proposed 17 in vitro assays for developmental neurotoxicity assessment of chemicals. In this luncheon seminar, I would like to introduce the utilization of NAMs in the nervous system for compound evaluation, including pharmaceuticals, as well as the use of Microphysiological Systems (MPS). Additionally, I will present data and international trends related to the use of human-derived central nervous system, peripheral nervous system, and brain organoids.

In recent years, various approaches utilizing machine learning for protein function analysis and design have become possible, leading to many new insights. However, to screen the vast number of candidate sequences proposed by machine learning and obtain useful sequences, it is essential to establish a system for preparing large amounts of DNA sequences and expressing, evaluating, and analyzing them. In this seminar, we are honored to welcome Dr. Kotaro Tsuboyama from the Institute of Industrial Science, Lecturer of the University of Tokyo, who will introduce cutting-edge case studies, along with an introduction to high-throughput screening-optimized synthetic DNA tools provided by Twist Bioscience.

Until now, the conventional procedure for 3D observation of cells has been to first label cells with fluorescenc and then create sectioning images using a confocal microscope, but there have been concerns about artifacts on cells caused by fluorescent labeling and phototoxicity caused by fluorescent excitation.
The label-free 3D imaging technology introduced in this seminar, as the name suggests, enables 3D observation without the need of fluorescent labeling. In addition, its extremely low phototoxicity makes it ideal for long time time-lapse observation of living cells. Recently, various cell analysis techniques have been developed using AI technology. In this seminar, we will introduce some of these AI analysis technologies as well.

Social collaboration program "Integrated Molecular Structure Analysis Laboratory" in the University of Tokyo is promoting joint research related to molecular structure analysis through industry-academia collaboration. The program has established an open innovation base called "FS CREATION" in Mitsui Link Lab Kashiwanoha 1, a rental lab in Kashiwanoha smart city. At this base, we are conducting joint research with companies in a wide range of fields related to molecular structure analysis, such as pharmaceuticals, agrochemicals, herbal medicines, food, and chemical manufacturing, while accurately grasping the needs of the industrial world, with the aim of implementing the results in society. This seminar will introduce the results of the research from both an academic and industrial perspective, focusing on the collaboration with Shimadzu Corporation.

Mitochondria, essential for respiratory energy production, are dynamics organelles, move in cytoplasm with active membrane fusion and fission. The dynamics of mitochondrial membrane and genome have important roles in the maintenance and quality control of mitochondrial and cellular functions. In this seminar, we are honored to have Professor Naotada Ishihara from the Department of Biological Sciences, Graduate School of Science, Osaka University. He will present the progress of research on mitochondrial dynamics.

SSBD is a public repository and database for sharing bioimaging data, established and maintained since 2013 with support from the NBDC Database Integration Coordination Program. SSBD is a core repository/database in the global ecosystem of public repositories and database systems for bioimaging data, including those in Europe and the United States, and promotes data sharing both domestically and internationally. In this seminar, we will introduce the status of global sharing of bioimaging data, the procedures for registering data in SSBD, and future prospects. SSBD will continue to contribute to the broader research community by enhancing data findability and reusability.