Kedar Narayan
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View article: MIFA: Metadata, Incentives, Formats and Accessibility guidelines to improve the reuse of AI datasets for bioimage analysis
MIFA: Metadata, Incentives, Formats and Accessibility guidelines to improve the reuse of AI datasets for bioimage analysis Open
Artificial intelligence (AI) methods are powerful tools for biological image analysis and processing. High-quality annotated images are key to training and developing new algorithms, but access to such data is often hindered by the lack of…
View article: Functionally Essential and Structurally Diverse: Insights into the zebrafish Left-Right Organizer’s Cilia via Optogenetic IFT88 Perturbation and Volume Electron Microscopy
Functionally Essential and Structurally Diverse: Insights into the zebrafish Left-Right Organizer’s Cilia via Optogenetic IFT88 Perturbation and Volume Electron Microscopy Open
In the zebrafish left-right organizer (LRO), the Kupffer’s Vesicle (KV), cilia extend from all cells into the fluid-filled lumen, but their structural diversity and contribution to morphogenesis remain incompletely defined. We hypothesized…
View article: A simple liquid 3D cell culture paradigm models oxidative mitochondrial metabolism of epithelial breast cancer cells with relevance for lung metastases
A simple liquid 3D cell culture paradigm models oxidative mitochondrial metabolism of epithelial breast cancer cells with relevance for lung metastases Open
Three-dimensional (3D) cell culture systems have emerged as powerful tools for modeling tumor biology in ex vivo settings. However, the diverse array of available 3D culture methods presents challenges in selecting the most appropriate mod…
View article: Characterization of membrane structures regulating primary ciliogenesis by quantitative isotropic ultrastructure imaging
Characterization of membrane structures regulating primary ciliogenesis by quantitative isotropic ultrastructure imaging Open
The trafficking, docking, and fusion of membrane vesicles at the mother centriole (MC) are required to construct the primary cilium. Here, we determined the three-dimensional (3D) membrane ultrastructures, and associated proteins, involved…
View article: CDK2 inhibition produces a persistent population of polyploid cancer cells
CDK2 inhibition produces a persistent population of polyploid cancer cells Open
Aneuploidy, a cancer hallmark, drives chromosomal instability, drug resistance, and clinically aggressive tumors. Cyclin-dependent kinase 2 (CDK2) antagonism with independent inhibitors or CDK2 knockdown triggered anaphase catastrophe. Thi…
View article: 3D nanoscale architecture of the respiratory epithelium reveals motile cilia-rootlets-mitochondria axis of communication
3D nanoscale architecture of the respiratory epithelium reveals motile cilia-rootlets-mitochondria axis of communication Open
A major frontier in single cell biology is decoding how transcriptional states result in cellular-level architectural changes, ultimately driving function. A remarkable example of this cellular remodelling program is the differentiation of…
View article: Coordination of force-generating actin-based modules stabilizes and remodels membranes in vivo
Coordination of force-generating actin-based modules stabilizes and remodels membranes in vivo Open
Membrane remodeling drives a broad spectrum of cellular functions, and it is regulated through mechanical forces exerted on the membrane by cytoplasmic complexes. Here, we investigate how actin filaments dynamically tune their structure to…
View article: The axillary lymphoid organ - an external, experimentally accessible immune organ in the zebrafish
The axillary lymphoid organ - an external, experimentally accessible immune organ in the zebrafish Open
Lymph nodes and other secondary lymphoid organs play critical roles in immune surveillance and immune activation in mammals, but the deep internal locations of these organs make it challenging to image and study them in living animals. Her…
View article: HypoRiPPAtlas as an Atlas of hypothetical natural products for mass spectrometry database search
HypoRiPPAtlas as an Atlas of hypothetical natural products for mass spectrometry database search Open
Recent analyses of public microbial genomes have found over a million biosynthetic gene clusters, the natural products of the majority of which remain unknown. Additionally, GNPS harbors billions of mass spectra of natural products without…
View article: A spatial map of hepatic mitochondria uncovers functional heterogeneity shaped by nutrient-sensing signaling
A spatial map of hepatic mitochondria uncovers functional heterogeneity shaped by nutrient-sensing signaling Open
In the liver, mitochondria are exposed to different concentrations of nutrients due to their spatial positioning across the periportal and pericentral axis. How the mitochondria sense and integrate these signals to respond and maintain hom…
View article: Enabling Global Image Data Sharing in the Life Sciences
Enabling Global Image Data Sharing in the Life Sciences Open
Coordinated collaboration is essential to realize the added value of and infrastructure requirements for global image data sharing in the life sciences. In this White Paper, we take a first step at presenting some of the most common use ca…
View article: Spatial and Temporal Coordination of Force-generating Actin-based Modules Drives Membrane Remodeling<i>In Vivo</i>
Spatial and Temporal Coordination of Force-generating Actin-based Modules Drives Membrane Remodeling<i>In Vivo</i> Open
Summary Membrane remodeling drives a broad spectrum of cellular functions, and it is regulated through mechanical forces exerted on the membrane by cytoplasmic complexes. Here, we investigate how actin filaments dynamically tune their stru…
View article: CDK2 inhibition disorders centrosome stoichiometry and alters cellular outcomes in aneuploid cancer cells
CDK2 inhibition disorders centrosome stoichiometry and alters cellular outcomes in aneuploid cancer cells Open
Cyclin-dependent Kinase 2 (CDK2) inhibition prevents supernumerary centrosome clustering. This causes multipolarity, anaphase catastrophe and apoptotic death of aneuploid cancers. This study elucidated how CDK2 antagonism affected centroso…
View article: MIFA: Metadata, Incentives, Formats, and Accessibility guidelines to improve the reuse of AI datasets for bioimage analysis
MIFA: Metadata, Incentives, Formats, and Accessibility guidelines to improve the reuse of AI datasets for bioimage analysis Open
Artificial Intelligence methods are powerful tools for biological image analysis and processing. High-quality annotated images are key to training and developing new methods, but access to such data is often hindered by the lack of standar…
View article: Centrosome amplification and aneuploidy driven by the HIV-1-induced Vpr•VprBP•Plk4 complex in CD4+ T cells
Centrosome amplification and aneuploidy driven by the HIV-1-induced Vpr•VprBP•Plk4 complex in CD4+ T cells Open
HIV-1 infection elevates the risk of developing various cancers, including T-cell lymphoma. Whether HIV-1-encoded proteins directly contribute to oncogenesis remains unknown. We observed that approximately 1–5% of CD4+ T cells from the blo…
View article: A spatial map of hepatic mitochondria uncovers functional heterogeneity shaped by nutrient-sensing signaling
A spatial map of hepatic mitochondria uncovers functional heterogeneity shaped by nutrient-sensing signaling Open
In the liver, mitochondria are exposed to different concentrations of nutrients due to their spatial positioning across the periportal (PP) and pericentral (PC) axis. How these mitochondria sense and integrate these signals to respond and …
View article: Non‐specific and specific <scp>DNA</scp> binding modes of bacterial histone, <scp>HU</scp>, separately regulate distinct physiological processes through different mechanisms
Non‐specific and specific <span>DNA</span> binding modes of bacterial histone, <span>HU</span>, separately regulate distinct physiological processes through different mechanisms Open
The histone‐like protein HU plays a diverse role in bacterial physiology from the maintenance of chromosome structure to the regulation of gene transcription. HU binds DNA in a sequence‐non‐specific manner via two distinct binding modes: (…
View article: Delivery of ceramide phosphoethanolamine lipids to the cleavage furrow through the endocytic pathway is essential for male meiotic cytokinesis
Delivery of ceramide phosphoethanolamine lipids to the cleavage furrow through the endocytic pathway is essential for male meiotic cytokinesis Open
Cell division, wherein 1 cell divides into 2 daughter cells, is fundamental to all living organisms. Cytokinesis, the final step in cell division, begins with the formation of an actomyosin contractile ring, positioned midway between the s…
View article: Intracellular connections between basal bodies promote the coordinated behavior of motile cilia
Intracellular connections between basal bodies promote the coordinated behavior of motile cilia Open
Whether intracellular connections between basal bodies control ciliary behavior in multiciliated cells is investigated. Using a Tetrahymena live cell immobilization technique to quantify ciliary dynamics, it is shown that inter-BB connecti…
View article: A versatile enhanced freeze-substitution protocol for volume electron microscopy
A versatile enhanced freeze-substitution protocol for volume electron microscopy Open
Volume electron microscopy, a powerful approach to generate large three-dimensional cell and tissue volumes at electron microscopy resolutions, is rapidly becoming a routine tool for understanding fundamental and applied biological questio…
View article: Intracellular connections between basal bodies promote the coordinated behavior of motile cilia
Intracellular connections between basal bodies promote the coordinated behavior of motile cilia Open
Summary Hydrodynamic flow produced by multi-ciliated cells is critical for fluid circulation and cell motility. Hundreds of cilia beat with metachronal synchrony for fluid flow. Cilia-driven fluid flow produces extracellular hydrodynamic f…