Biology subjects

Bando, Y.

Publications and source records attributed to Bando, Y..

7 recordsLinked to original sources

bioRxiv2026

RnR-ExM: Robust Non-rigid Registration Challenge for Expansion Microscopy Volumes

Expansion Microscopy (ExM) enables nanoscale imaging of biological samples while preserving structural and molecular details. The Robust Non-rigid Registration Challenge for ExM (RnR-ExM) was launched to benchmark 3D registration algorithms on real-world ExM datasets. The challenge released 24 pairs of high-resolution 3D volumes from zebrafish, mouse, and C.~elegans, deliberately selected for their difficulty with standard alignment methods. To evaluate performance, we provided curated segmentation masks of nuclei and blood vessels as landmarks for half of the dataset. To encourage learning-based approaches, we released code for generating synthetic training data reflecting the deformation and appearance of the unlabeled pairs. By submission, 168 participants registered, with six teams submitting results by the deadline; the top three were invited to present at ISBI 2023. Accurate registration of ExM volumes is essential for downstream biological analyses such as multiplexed molecular mapping and cell-type-specific structural profiling. In this paper, we detail the methods and results of these top teams, highlighting current capabilities and future directions for 3D registration in ExM. All datasets and code are available at https://rnr-exm.grand-challenge.org/

neuroscience↗

bioRxiv2025

Integrated Antibody and DIA Based Plasma Proteomics Uncover Temporal Host Responses to SARS CoV 2 Infection

This is a single-case longitudinal study in which we monitored antibody responses and plasma proteome dynamics over a 310-day period in a single individual who underwent COVID-19 vaccination and SARS-CoV-2 infection. To evaluate COVID-19 antibody responses, human plasma samples collected over 310 days (August 18, 2021, to June 22, 2022) were analyzed by DIA-LC-MS/MS proteomics. This led to the acquisition of a quantitative protein profile and allowed validation of the temporal behavior of expressed proteins within the samples. A total of 1,502 proteins were identified from the plasma samples. Before vaccination, after the first dose, after the second dose, and during the period after contracting the novel coronavirus, protein quantification values during each event interval were compared. Despite minimal changes before and after COVID-19 vaccination, notable proteins exhibiting distinct high-expression and low-expression patterns were identified after SARS-CoV-2 infection.

molecular biology↗

bioRxiv2023

Deep proteome analysis of time-series human plasma samples applied to Covid-19 antibody test

For the purpose of Covid-19 antibody testing, the human plasma samples acquired over a period of 310 days from August 18, 2021, to June 22, 2022, were subjected to DIA LC-MS proteome analysis. This process led to the acquisition of a quantitative protein profile and allowed for the validation of the temporal behavior of expressed proteins within the samples. A total of 1502 proteins were identified from the plasma samples. Before vaccination, after the first dose, after the second dose, and during the period after contracting the novel coronavirus, protein quantification values during each event interval were compared. Despite minimal changes observed before and after Covid-19 vaccination, notable proteins exhibiting distinct high-expression and low-expression patterns were identified after contracting the novel coronavirus infection.

molecular biology↗

bioRxiv2022

Expansion Sequencing of RNA Barcoded Neurons in the Mammalian Brain: Progress and Implications for Molecularly Annotated Connectomics

Mapping and molecularly annotating mammalian neural circuits is challenging due to the inability to uniquely label cells while also resolving subcellular features such as synaptic proteins or fine cellular processes. We argue that an ideal technology for connectomics would have the following characteristics: the capacity for robust distance-independent labeling, synaptic resolution, molecular interrogation, and scalable computational methods. The recent development of high-diversity cellular barcoding with RNA has provided a way to overcome the labeling limitations associated with spectral dyes, however performing all-optical circuit mapping has not been demonstrated because no method exists to image barcodes throughout cells at synaptic-resolution. Here we show ExBarSeq, an integrated method combining in situ sequencing of RNA barcodes, immunostaining, and Expansion Microscopy coupled with an end-to-end software pipeline that automatically extracts barcode identities from large imaging datasets without data processing bottlenecks. As a proof of concept, we applied ExBarSeq to thick tissue sections from mice virally infected with MAPseq viral vectors and demonstrated the extraction of 50 barcoded cells in the visual cortex as well as cell morphologies uncovered via immunostaining. The current work demonstrates high resolution multiplexing of exogenous barcodes and endogenous synaptic proteins and outlines a roadmap for molecularly annotated connectomics at a brain-wide scale.

neuroscience↗

bioRxiv2021

Orfamide-A-mediated bacterial-algal interactions involve specific Ca2+ signalling pathways

The antagonistic bacterium Pseudomonas protegens secretes the cyclic lipopeptide orfamide A, which triggers a Ca2+ signal, causing the deflagellation of the green microalga Chlamydomonas reinhardtii. By investigating targeted synthetic orfamide A variants and inhibitors, we found that at least two Ca2+-signalling pathways and TRP channels are involved in this response.

microbiology↗

bioRxiv2020

Expansion Sequencing: Spatially Precise In Situ Transcriptomics in Intact Biological Systems

AbstractMethods for highly multiplexed RNA imaging are limited in spatial resolution, and thus in their ability to localize transcripts to nanoscale and subcellular compartments. We adapt expansion microscopy, which physically expands biological specimens, for long-read untargeted and targeted in situ RNA sequencing. We applied untargeted expansion sequencing (ExSeq) to mouse brain, yielding readout of thousands of genes, including splice variants and novel transcripts. Targeted ExSeq yielded nanoscale-resolution maps of RNAs throughout dendrites and spines in neurons of the mouse hippocampus, revealing patterns across multiple cell types; layer-specific cell types across mouse visual cortex; and the organization and position-dependent states of tumor and immune cells in a human metastatic breast cancer biopsy. Thus ExSeq enables highly multiplexed mapping of RNAs, from nanoscale to system scale. One Sentence SummaryIn situ sequencing of physically expanded specimens enables multiplexed mapping of RNAs at nanoscale, subcellular resolution.

genomics↗

bioRxiv2017

Three-Dimensional Two-Photon Optogenetics And Imaging Of Neural Circuits In Vivo

We demonstrate a holographic system for simultaneous three-dimensional (3D) two-photon stimulation and imaging of neural activity in the mouse neocortex in vivo with cellular resolution. Dual two-photon excitation paths are implemented with independent 3D targeting for calcium imaging and precision optogenetics. We validate the usefulness of the microscope by photoactivating local pools of interneurons in awake mice visual cortex in 3D, which suppress the nearby pyramidal neurons response to visual stimuli.

neuroscience↗