A5080159006- Genetics, Aging, and Longevity in Model Organisms
- Pluripotent Stem Cells Research
- Developmental Biology and Gene Regulation
- Gene Regulatory Network Analysis
- RNA Research and Splicing
- Reproductive Biology and Fertility
- Planarian Biology and Electrostimulation
- CRISPR and Genetic Engineering
- Markov Chains and Monte Carlo Methods
- RNA and protein synthesis mechanisms
- Genomics and Rare Diseases
- Circadian rhythm and melatonin
- Cellular Mechanics and Interactions
- Genomics and Chromatin Dynamics
- Congenital heart defects research
- Single-cell and spatial transcriptomics
- HIV/AIDS drug development and treatment
- Gaussian Processes and Bayesian Inference
- Algorithms and Data Compression
- Topic Modeling
- Biochemical and Molecular Research
- Spaceflight effects on biology
- RNA modifications and cancer
- Enzyme Structure and Function
- Advanced Fluorescence Microscopy Techniques
University of California, Irvine
2010-2024
Institut de Biologie Intégrative de la Cellule
2020
Université Paris-Saclay
2020
Technologies pour la Santé
2020
CEA Paris-Saclay
2020
Commissariat à l'Énergie Atomique et aux Énergies Alternatives
2020
Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement
2020
Centre National de la Recherche Scientifique
2002-2020
Howard Hughes Medical Institute
2008-2010
University of Wisconsin–Madison
2007-2008
We describe a label-free imaging method to monitor stem-cell metabolism that discriminates different states of stem cells as they differentiate in living tissues. In this we use intrinsic fluorescence biomarkers and the phasor approach lifetime microscopy conjunction with image segmentation, which introduce concept cell phasor. live tissues are able identify fluorophores, such collagen, retinol, retinoic acid, porphyrin, flavins, free bound NADH. have exploited detect trend metabolite...
Controls of stem cell maintenance and early differentiation are known in several systems. However, the progression from self-renewal to overt signs is a poorly understood but important problem biology. The Caenorhabditis elegans germ line provides genetically defined model for studying that progression. In this system, single-celled mesenchymal niche, distal tip (DTC), employs GLP-1/Notch signaling an RNA regulatory network balance within “mitotic region,” which continuously self-renews...
Abstract Increasing volumes of biomedical data are amassing in databases. Large-scale analyses these have wide-ranging applications biology and medicine. Such require tools to characterize process entries at scale. However, existing tools, mainly centered on extracting predefined fields, often fail comprehensively database or correct evident errors—a task humans can easily perform. These also lack the ability reason like domain experts, hindering their robustness analytical depth. Recent...
The oscillations of the somitogenesis clock are linked to fundamental process vertebrate embryo segmentation, yet little is known about their generation. In zebrafish, it has been proposed that Her proteins repress transcription own mRNA. However, in its simplest form, this model incompatible with fact morpholino knockdown can impair expression Simple self-repression models also do not account for spatiotemporal pattern gene expression, waves shrinking as they propagate. Here we study...
A critical event in mammalian embryo development is construction of an inner cell mass surrounded by a trophoectoderm (a shell cells that later form extraembryonic structures). We utilize multi-scale, stochastic modeling to investigate the design principles responsible for robust establishment these structures. This investigation makes three predictions, each supported our quantitative imaging. First, stochasticity expression genes promotes plasticity and has role accurately organizing...
Self-renewing organs often experience a decline in function the course of aging. It is unclear whether chronological age or external factors control this decline, it driven by stem cell self-renewal—for example, because cycling cells exhaust their replicative capacity and become senescent. Here we assay relationship between senescence Caenorhabditis elegans reproductive system, defining as progressive "reproductive capacity," i.e. number progeny that can be produced until cessation...
Stem cells niches are increasingly recognized as dynamic environments that play a key role in transducing signals allow an organism to exert control on its stem cells. Live imaging of cell their vivo setting is thus high interest dissect controls. Here we report new microfluidic design highly amenable dissemination biology laboratories have no microfluidics expertise. This has allowed us perform the first time lapse C. elegans germline niche. Our results show this niche strikingly dynamic,...
Stem cells are thought to play a critical role in minimizing the accumulation of mutations, but it is not clear which strategies they follow fulfill that performance objective. Slow cycling stem provides simple strategy can minimize cell pedigree depth and thereby replication-dependent mutations. Although power this was recognized early on, quantitative assessment whether how employed by biological systems missing.Here we address problem using self-renewing organ - C. elegans gonad whose...
Analysis of single cells in their native environment is a powerful method to address key questions developmental systems biology. Confocal microscopy imaging intact tissues, followed by automatic image segmentation, provides means conduct cytometric studies while at the same time preserving crucial information about spatial organization tissue and morphological features cells. This technique rapidly evolving but still not widespread use among research groups that do specialize development,...
Abstract Background The mouse anterior visceral endoderm (AVE) and the chick hypoblast are thought to have homologous roles in early stages of neural induction primitive streak formation. In mouse, many regulatory elements directing gene expression AVE been identified. However, there is no technique introduce DNA into that would enable a comparison their activity this has hampered direct regulation extraembryonic endoderm. Results Here we describe new method hypoblast, using...
We have cloned genes encoding three enzymes of the de novo pyrimidine pathway using genomic DNA from Plasmodium falciparum and sequence information Malarial Genome Project. Genes dihydroorotase (reaction 3), orotate phosphoribosyltransferase 5), OMP decarboxylase 6) been into plasmid pET 3a or 3d with a thrombin cleavable 9xHis tag at C-terminus were expressed in Escherichia coli. To overcome toxicity malarial when E. coli, unusual codon usage gene, hybrid plasmid, pMICO, was constructed...
Cyclodipeptide synthases (CDPSs) use two aminoacyl-tRNAs (AA-tRNAs) to catalyse cyclodipeptide formation in a ping-pong mechanism. Despite intense studies of these enzymes past years, the tRNA regions substrates required for CDPS activity are poorly documented, mainly because limitations. First, previously studied CDPSs identical AA-tRNAs produce homocyclodipeptides, thus preventing discriminative study binding substrates. Second, range analogues that can be aminoacylated by aminoacyl-tRNA...
Assaying in vivo accrual of DNA damage and mutations by stem cells pinpointing sources would further our understanding aging carcinogenesis. Two main hurdles must be overcome. First, mutation rates are orders magnitude lower than raw sequencing error rates. Second, vastly outnumbered differentiated cells, which have a higher rate—quantification cell is thus best performed from small, well-defined populations. Here we report detection technique, based on the “duplex sequencing” principle,...
Large language models (LLMs) leverage factual knowledge from pretraining. Yet this remains incomplete and sometimes challenging to retrieve-especially in scientific domains not extensively covered pretraining datasets where information is still evolving. Here, we focus on genomics bioinformatics. We confirm expand upon issues with plain ChatGPT functioning as a bioinformatics assistant. Poor data retrieval hallucination lead err, do incorrect sequence manipulations. To address this, propose...