Main Menu (Mobile)- Block

Main Menu - Block

janelia7_blocks-janelia7_fake_breadcrumb | block
Koyama Lab / Publications
custom | custom

Filter

facetapi-Q2b17qCsTdECvJIqZJgYMaGsr8vANl1n | block

Associated Lab

facetapi-W9JlIB1X0bjs93n1Alu3wHJQTTgDCBGe | block
facetapi-PV5lg7xuz68EAY8eakJzrcmwtdGEnxR0 | block
facetapi-021SKYQnqXW6ODq5W5dPAFEDBaEJubhN | block
general_search_page-panel_pane_1 | views_panes

3843 Publications

Showing 61-70 of 3843 results
01/11/24 | Bridging gaps in traditional research training with iBiology Courses.
Schnoes AM, Green NH, Nguyen TA, Vale RD, Goodwin SS, Behrman SL
PLoS Biology. 2024 Jan 11;22(1):e3002458. doi: 10.1371/journal.pbio.3002458

iBiology Courses provide trainees with just-in-time learning resources to become effective researchers. These courses can help scientists build core research skills, plan their research projects and careers, and learn from scientists with diverse backgrounds.

View Publication Page
01/11/24 | Epigenetic priming of embryonic lineages in the mammalian epiblast
Miquel Sendra , Katie McDole , Daniel Jimenez-Carretero , Juan de Dios Hourcade , Susana Temiño , Léo Guignard , Philipp J Keller , Fátima Sánchez-Cabo , Jorge N. Domínguez , Miguel Torres
bioRxiv. 2024 Jan 11:. doi: 10.1101/2024.01.11.575188

Understanding the diversification of mammalian cell lineages is an essential to embryonic development, organ regeneration and tissue engineering. Shortly after implantation in the uterus, the pluripotent cells of the mammalian epiblast generate the three germ layers: ectoderm, mesoderm and endoderm1. Although clonal analyses suggest early specification of epiblast cells towards particular cell lineages24, single-cell transcriptomes do not identify lineage-specific markers in the epiblast511 and thus, the molecular regulation of such specification remains unknow. Here, we studied the epigenetic landscape of single epiblast cells, which revealed lineage priming towards endoderm, ectoderm or mesoderm. Unexpectedly, epiblast cells with mesodermal priming show a strong signature for the endothelial/endocardial fate, suggesting early specification of this lineage aside from other mesoderm. Through clonal analysis and live imaging, we show that endothelial precursors show early lineage divergence from the rest of mesodermal derivatives. In particular, cardiomyocytes and endocardial cells show limited lineage relationship, despite being temporally and spatially co-recruited during gastrulation. Furthermore, analysing the live tracks of single cells through unsupervised classification of cell migratory activity, we found early behavioral divergence of endothelial precursors shortly after the onset of mesoderm migration towards the cardiogenic area. These results provide a new model for the phenotypically silent specification of mammalian cell lineages in pluripotent cells of the epiblast and modify current knowledge on the sequence and timing of cardiovascular lineages diversification.

View Publication Page
01/11/24 | Prediction of Cellular Identities from Trajectory and Cell Fate Information
Baiyang Dai , Jiamin Yang , Hari Shroff , Patrick La Riviere
arXiv. 2024 Jan 11:. doi: 10.48550/arXiv.2401.06182

Determining cell identities in imaging sequences is an important yet challenging task. The conventional method for cell identification is via cell tracking, which is complex and can be time-consuming. In this study, we propose an innovative approach to cell identification during early C. elegans embryogenesis using machine learning. We employed random forest, MLP, and LSTM models, and tested cell classification accuracy on 3D time-lapse confocal datasets spanning the first 4 hours of embryogenesis. By leveraging a small number of spatial-temporal features of individual cells, including cell trajectory and cell fate information, our models achieve an accuracy of over 90%, even with limited data. We also determine the most important feature contributions and can interpret these features in the context of biological knowledge. Our research demonstrates the success of predicting cell identities in 4D imaging sequences directly from simple spatio-temporal features.

View Publication Page
01/10/24 | Believing is seeing - the deceptive influence of bias in quantitative microscopy.
Lee RM, Eisenman LR, Khuon S, Aaron JS, Chew T
Journal of Cell Science. 2024 Jan 10;137(1):. doi: 10.1242/jcs.261567

The visual allure of microscopy makes it an intuitively powerful research tool. Intuition, however, can easily obscure or distort the reality of the information contained in an image. Common cognitive biases, combined with institutional pressures that reward positive research results, can quickly skew a microscopy project towards upholding, rather than rigorously challenging, a hypothesis. The impact of these biases on a variety of research topics is well known. What might be less appreciated are the many forms in which bias can permeate a microscopy experiment. Even well-intentioned researchers are susceptible to bias, which must therefore be actively recognized to be mitigated. Importantly, although image quantification has increasingly become an expectation, ostensibly to confront subtle biases, it is not a guarantee against bias and cannot alone shield an experiment from cognitive distortions. Here, we provide illustrative examples of the insidiously pervasive nature of bias in microscopy experiments - from initial experimental design to image acquisition, analysis and data interpretation. We then provide suggestions that can serve as guard rails against bias.

View Publication Page
01/10/24 | Song Torrent: A modular, open-source 96-chamber audio and video recording apparatus with optogenetic activation and inactivation capabilities for Drosophila
Steve Sawtelle , Lakshmi Narayan , Yun Ding , Elizabeth Kim , Emily L. Behrman , Joshua L. Lillvis , Takashi Kawase , David L. Stern
bioRxiv. 2024 Jan 10:. doi: 10.1101/2024.01.09.574712

Background

  • Many Drosophila species use acoustic communication during courtship and studies of these communication systems have provided insight into neurobiology, behavioral ecology, ethology, and evolution.

  • Recording Drosophila courtship sounds and associated behavior is challenging, especially at high throughput, and previously designed devices are relatively expensive and complex to assemble.

Results

  • We present construction plans for a modular system utilizing mostly off-the-shelf, relatively inexpensive components that provides simultaneous high-resolution audio and video recording of 96 isolated or paired Drosophila individuals.

  • We provide open-source control software to record audio and video.

  • We designed high intensity LED arrays that can be used to perform optogenetic activation and inactivation of labelled neurons.

  • The basic design can be modified to facilitate novel study designs or to record insects larger than Drosophila.

  • Fewer than 96 microphones can be used in the system if the full array is not required or to reduce costs.

Implications

  • Our hardware design and software provide an improved platform for reliable and comparatively inexpensive high-throughput recording of Drosophila courtship acoustic and visual behavior and perhaps for recording acoustic signals of other small animals.

View Publication Page
01/09/24 | Direct measurement of dynamic attractant gradients reveals breakdown of the Patlak-Keller-Segel chemotaxis model
Trung V. Phan , Henry H. Mattingly , Lam Vo , Jonathan S. Marvin , Loren L. Looger , Thierry Emonet
Proceedings of the National Academy of Sciences. 2024 Jan 09:. doi: 10.1073/pnas.230925112

Chemotactic bacteria not only navigate chemical gradients, but also shape their environments by consuming and secreting attractants. Investigating how these processes influence the dynamics of bacterial populations has been challenging because of a lack of experimental methods for measuring spatial profiles of chemoattractants in real time. Here, we use a fluorescent sensor for aspartate to directly measure bacterially generated chemoattractant gradients during collective migration. Our measurements show that the standard Patlak-Keller-Segel model for collective chemotactic bacterial migration breaks down at high cell densities. To address this, we propose modifications to the model that consider the impact of cell density on bacterial chemotaxis and attractant consumption. With these changes, the model explains our experimental data across all cell densities, offering new insight into chemotactic dynamics. Our findings highlight the significance of considering cell density effects on bacterial behavior, and the potential for fluorescent metabolite sensors to shed light on the complex emergent dynamics of bacterial communities.

View Publication Page
01/05/24 | Homeodomain proteins hierarchically specify neuronal diversity and synaptic connectivity
Chundi Xu , Tyler B. Ramos , Ed M. Rogers , Michael B. Reiser , Chris Q. Doe
eLife. 2024 Jan 05:. doi: 10.7554/eLife.90133

The brain generates diverse neuron types which express unique homeodomain transcription factors (TFs) and assemble into precise neural circuits. Yet a mechanistic framework is lacking for how homeodomain TFs specify both neuronal fate and synaptic connectivity. We use Drosophila lamina neurons (L1-L5) to show the homeodomain TF Brain-specific homeobox (Bsh) is initiated in lamina precursor cells (LPCs) where it specifies L4/L5 fate and suppresses homeodomain TF Zfh1 to prevent L1/L3 fate. Subsequently, Bsh activates the homeodomain TF Apterous (Ap) in L4 in a feedforward loop to express the synapse recognition molecule DIP-β, in part by Bsh direct binding a DIP-β intron. Thus, homeodomain TFs function hierarchically: primary homeodomain TF (Bsh) first specifies neuronal fate, and subsequently acts with secondary homeodomain TF (Ap) to activate DIP-β, thereby generating precise synaptic connectivity. We speculate that hierarchical homeodomain TF function may represent a general principle for coordinating neuronal fate specification and circuit assembly.

View Publication Page
01/04/24 | Petascale pipeline for precise alignment of images from serial section electron microscopy.
Popovych S, Macrina T, Kemnitz N, Castro M, Nehoran B, Jia Z, Bae JA, Mitchell E, Mu S, Trautman ET, Saalfeld S, Li K, Seung HS
Nature Communications. 2024 Jan 04;15(1):289. doi: 10.1038/s41467-023-44354-0

The reconstruction of neural circuits from serial section electron microscopy (ssEM) images is being accelerated by automatic image segmentation methods. Segmentation accuracy is often limited by the preceding step of aligning 2D section images to create a 3D image stack. Precise and robust alignment in the presence of image artifacts is challenging, especially as datasets are attaining the petascale. We present a computational pipeline for aligning ssEM images with several key elements. Self-supervised convolutional nets are trained via metric learning to encode and align image pairs, and they are used to initialize iterative fine-tuning of alignment. A procedure called vector voting increases robustness to image artifacts or missing image data. For speedup the series is divided into blocks that are distributed to computational workers for alignment. The blocks are aligned to each other by composing transformations with decay, which achieves a global alignment without resorting to a time-consuming global optimization. We apply our pipeline to a whole fly brain dataset, and show improved accuracy relative to prior state of the art. We also demonstrate that our pipeline scales to a cubic millimeter of mouse visual cortex. Our pipeline is publicly available through two open source Python packages.

View Publication Page
01/02/24 | Cutting through stress.
Jasper LA, Wang MC
Nature Metabolism. 2024 Jan 02:. doi: 10.1038/s42255-023-00946-0
01/01/24 | Image processing tools for petabyte-scale light sheet microscopy data.
Xiongtao Ruan , Matthew Mueller , Gaoxiang Liu , Frederik Görlitz , Tian-Ming Fu , Daniel E. Milkie , Joshua Lillvis , Alison Killilea , Eric Betzig , Srigokul Upadhyayula
bioRxiv. 2024 Jan 01:. doi: 10.1101/2023.12.31.573734

Light sheet microscopy is a powerful technique for visualizing dynamic biological processes in 3D. Studying large specimens or recording time series with high spatial and temporal resolution generates large datasets, often exceeding terabytes and potentially reaching petabytes in size. Handling these massive datasets is challenging for conventional data processing tools with their memory and performance limitations. To overcome these issues, we developed LLSM5DTools, a software solution specifically designed for the efficient management of petabyte-scale light sheet microscopy data. This toolkit, optimized for memory and per-formance, features fast image readers and writers, efficient geometric transformations, high-performance Richardson-Lucy deconvolution, and scalable Zarr-based stitching. These advancements enable LLSM5DTools to perform over ten times faster than current state-of-the-art methods, facilitating real-time processing of large datasets and opening new avenues for biological discoveries in large-scale imaging experiments.

View Publication Page