scholarly journals Spatio-temporal dynamics of gene expression of the Edn1-Dlx5/6 pathway during development of the lower jaw

genesis ◽  
2010 ◽  
Vol 48 (6) ◽  
pp. 262-373 ◽  
Author(s):  
Maxence Vieux-Rochas ◽  
Stefano Mantero ◽  
Eglantine Heude ◽  
Ottavia Barbieri ◽  
Simonetta Astigiano ◽  
...  
Keyword(s):  
Gene Expression ◽  
Temporal Dynamics ◽  
Lower Jaw ◽  
Spatio Temporal

scholarly journals A sensitive mNeonGreen reporter system to measure transcriptional dynamics in Drosophila development

2020 ◽  
Vol 3 (1) ◽  
Author(s):  
Stefano Ceolin ◽  
Monika Hanf ◽  
Marta Bozek ◽  
Andrea Ennio Storti ◽  
Nicolas Gompel ◽  
...  
Keyword(s):  
Gene Expression ◽  
Fluorescent Protein ◽  
Temporal Dynamics ◽  
Reconstruction Algorithm ◽  
Detection Sensitivity ◽  
Axis Formation ◽  
Reporter System ◽  
Enhancer Activity ◽  
Spatio Temporal ◽  
Pioneer Transcription Factor

AbstractThe gene regulatory network governing anterior–posterior axis formation in Drosophila is a well-established paradigm to study transcription in developmental biology. The rapid temporal dynamics of gene expression during early stages of development, however, are difficult to track with standard techniques. We optimized the bright and fast-maturing fluorescent protein mNeonGreen as a real-time, quantitative reporter of enhancer expression. We derive enhancer activity from the reporter fluorescence dynamics with high spatial and temporal resolution, using a robust reconstruction algorithm. By comparing our results with data obtained with the established MS2-MCP system, we demonstrate the higher detection sensitivity of our reporter. We used the reporter to quantify the activity of variants of a simple synthetic enhancer, and observe increased activity upon reduction of enhancer–promoter distance or addition of binding sites for the pioneer transcription factor Zelda. Our reporter system constitutes a powerful tool to study spatio-temporal gene expression dynamics in live embryos.

Spatio-temporal dynamics in global rice gene expression ( Oryza sativa  L.) in response to high ammonium stress

2017 ◽  
Vol 212 ◽  
pp. 94-104 ◽  
Author(s):  
Li Sun ◽  
Dongwei Di ◽  
Guangjie Li ◽  
Herbert J. Kronzucker ◽  
Weiming Shi
Keyword(s):  
Gene Expression ◽  
Oryza Sativa ◽  
Temporal Dynamics ◽  
Oryza Sativa L ◽  
Rice Gene ◽  
Spatio Temporal ◽  
Ammonium Stress

scholarly journals Modeling Spatio-temporal Dynamics of Chromatin Marks

2017 ◽  
Author(s):  
Petko Fiziev ◽  
Jason Ernst
Keyword(s):  
Gene Expression ◽  
Time Course ◽  
Temporal Dynamics ◽  
Spatial Dynamics ◽  
Computational Method ◽  
Time Points ◽  
Signal Density ◽  
Spatial Changes ◽  
Spatio Temporal ◽  
Over Time

ABSTRACTTo model spatial changes of chromatin mark peaks over time we developed and applied ChromTime, a computational method that predicts regions for which peaks either expand or contract significantly or hold steady between time points. Predicted expanding and contracting peaks can mark regulatory regions associated with transcription factor binding and gene expression changes. Spatial dynamics of peaks provided information about gene expression changes beyond localized signal density changes. ChromTime detected asymmetric expansions and contractions, which for some marks associated with the direction of transcription. ChromTime facilitates the analysis of time course chromatin data in a range of biological systems.

scholarly journals A cell cycle-coordinated nuclear compartment for Polymerase II transcription encompasses the earliest gene expression before global genome activation

2018 ◽  
Author(s):  
Yavor Hadzhiev ◽  
Haseeb K. Qureshi ◽  
Lucy Wheatley ◽  
Ledean Cooper ◽  
Aleksandra Jasiulewicz ◽  
...  
Keyword(s):  
Gene Expression ◽  
Temporal Dynamics ◽  
Nuclear Compartment ◽  
Cell Cycles ◽  
Regulatory Architecture ◽  
4D Imaging ◽  
Zygotic Gene ◽  
A Cell ◽  
Spatio Temporal ◽  
Genome Activation

AbstractMost metazoan embryos commence development with rapid cleavages without zygotic gene expression and their genome activation is delayed until the mid-blastula transition (MBT). However, a set of genes escape global repression during the extremely fast cell cycles, which lack gap phases and their transcription is activated before the MBT. Here we describe the formation and the spatio-temporal dynamics of a distinct transcription compartment, which encompasses the earliest detectable transcription during the first wave of genome activation. Simultaneous 4D imaging of expression of pri-miR430 and zinc finger genes by a novel, native transcription imaging approach reveals a pair of shared transcription compartments regulated by homolog chromosome organisation. These nuclear compartments carry the majority of nascent RNAs and transcriptionally active Polymerase II, are depleted of compact chromatin and represent the main sites for detectable transcription before MBT. We demonstrate that transcription occurs in the S-phase of the cleavage cycles and that the gradual slowing of these cell cycles are permissive to transcription before global genome activation. We propose that the demonstrated transcription compartment is part of the regulatory architecture of nucleus organisation, and provides a transcriptionally competent, supporting environment to facilitate early escape from the general nuclear repression before global genome activation.

scholarly journals Large field of view-spatially resolved transcriptomics at nanoscale resolution

2021 ◽  
Author(s):  
Ao Chen ◽  
Sha Liao ◽  
Mengnan Cheng ◽  
Kailong Ma ◽  
Liang Wu ◽  
...  
Keyword(s):  
Gene Expression ◽  
Temporal Dynamics ◽  
Capture Rate ◽  
Large Field ◽  
Major Advance ◽  
Widespread Application ◽  
Spatially Resolved ◽  
Sample Throughput ◽  
Spatio Temporal

ABSTRACTHigh-throughput profiling of in situ gene expression represents a major advance towards the systematic understanding of tissue complexity. Applied with enough capture area and high sample throughput it will help to define the spatio-temporal dynamics of gene expression in tissues and organisms. Yet, current technologies have considerable bottlenecks that limit widespread application. Here, we have combined DNA nanoball (DNB) patterned array chips and in situ RNA capture to develop Stereo-seq (Spatio-Temporal Enhanced REsolution Omics-sequencing). This approach allows high sample throughput transcriptomic profiling of histological sections at unprecedented (nanoscale) resolution with areas expandable to centimeter scale, high sensitivity and homogenous capture rate. As proof of principle, we applied Stereo-seq to the adult mouse brain and sagittal sections of E11.5 and E16.5 mouse embryos. Thanks to its unique features and amenability to additional modifications, Stereo-seq can pave the way for the systematic spatially resolved-omics characterization of tissues and organisms.

scholarly journals Transcriptional Regulators and Human-Specific/Primate-Specific Genes in Neocortical Neurogenesis

2020 ◽  
Vol 21 (13) ◽  
pp. 4614 ◽  
Author(s):  
Samir Vaid ◽  
Wieland B. Huttner
Keyword(s):  
Gene Expression ◽  
Cognitive Abilities ◽  
Temporal Dynamics ◽  
De Novo ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Transcriptional Regulators ◽  
New Genes ◽  
Recent Part ◽  
Spatio Temporal

During development, starting from a pool of pluripotent stem cells, tissue-specific genetic programs help to shape and develop functional organs. To understand the development of an organ and its disorders, it is important to understand the spatio-temporal dynamics of the gene expression profiles that occur during its development. Modifications in existing genes, the de-novo appearance of new genes, or, occasionally, even the loss of genes, can greatly affect the gene expression profile of any given tissue and contribute to the evolution of organs or of parts of organs. The neocortex is evolutionarily the most recent part of the brain, it is unique to mammals, and is the seat of our higher cognitive abilities. Progenitors that give rise to this tissue undergo sequential waves of differentiation to produce the complete sets of neurons and glial cells that make up a functional neocortex. We will review herein our understanding of the transcriptional regulators that control the neural precursor cells (NPCs) during the generation of the most abundant class of neocortical neurons, the glutametergic neurons. In addition, we will discuss the roles of recently-identified human- and primate-specific genes in promoting neurogenesis, leading to neocortical expansion.

Nonlinear Spatio-Temporal Dynamics and Chaos in Semiconductors

2001 ◽  
Author(s):  
Eckehard Schöll
Keyword(s):  
Temporal Dynamics ◽  
Spatio Temporal

Spatio-temporal dynamics of ascidian larval recruitment and colony abundance in a non-indigenous Newfoundland population

2017 ◽  
Vol 585 ◽  
pp. 99-112 ◽  
Author(s):  
KCK Ma ◽  
D Deibel ◽  
JB Lowen ◽  
CH McKenzie
Keyword(s):  
Temporal Dynamics ◽  
Larval Recruitment ◽  
Spatio Temporal

Spatial and temporal dynamics of Pacific capelin Mallotus catervarius in the Gulf of Alaska: implications for ecosystem-based fisheries management

2020 ◽  
Vol 637 ◽  
pp. 117-140 ◽  
Author(s):  
DW McGowan ◽  
ED Goldstein ◽  
ML Arimitsu ◽  
AL Deary ◽  
O Ormseth ◽  
...  
Keyword(s):  
Temporal Dynamics ◽  
Marine Ecosystem ◽  
Gulf Of Alaska ◽  
Data Series ◽  
Limited Information ◽  
Important Species ◽  
Multiple Data ◽  
Spatial And Temporal Dynamics ◽  
Spawning Areas ◽  
Spatio Temporal

Pacific capelin Mallotus catervarius are planktivorous small pelagic fish that serve an intermediate trophic role in marine food webs. Due to the lack of a directed fishery or monitoring of capelin in the Northeast Pacific, limited information is available on their distribution and abundance, and how spatio-temporal fluctuations in capelin density affect their availability as prey. To provide information on life history, spatial patterns, and population dynamics of capelin in the Gulf of Alaska (GOA), we modeled distributions of spawning habitat and larval dispersal, and synthesized spatially indexed data from multiple independent sources from 1996 to 2016. Potential capelin spawning areas were broadly distributed across the GOA. Models of larval drift show the GOA’s advective circulation patterns disperse capelin larvae over the continental shelf and upper slope, indicating potential connections between spawning areas and observed offshore distributions that are influenced by the location and timing of spawning. Spatial overlap in composite distributions of larval and age-1+ fish was used to identify core areas where capelin consistently occur and concentrate. Capelin primarily occupy shelf waters near the Kodiak Archipelago, and are patchily distributed across the GOA shelf and inshore waters. Interannual variations in abundance along with spatio-temporal differences in density indicate that the availability of capelin to predators and monitoring surveys is highly variable in the GOA. We demonstrate that the limitations of individual data series can be compensated for by integrating multiple data sources to monitor fluctuations in distributions and abundance trends of an ecologically important species across a large marine ecosystem.

Sign in / Sign up

Export Citation Format

Share Document