scholarly journals An atlas of the Norway spruce needle seasonal transcriptome

2021 ◽  
Author(s):  
Pushan Bag ◽  
Jenna Lihavainen ◽  
Nicolas Delhomme ◽  
Thomas Riquelme ◽  
Kathryn M Robinson ◽  
...  
Keyword(s):  
Gene Expression ◽  
Norway Spruce ◽  
Cellular Functions ◽  
Developmental Program ◽  
Tentative Model ◽  
Visualization Tools ◽  
Global Transcriptome ◽  
Spruce Needles ◽  
Comprehensive Characterization

Boreal conifers possess a tremendous ability to survive and remain evergreen during harsh winter conditions and resume growth during summer. This is enabled by coordinated regulation of major cellular functions at the level of gene expression, metabolism, and physiology. Here we present a comprehensive characterization of the annual changes in the global transcriptome of Norway spruce needles as a resource to understand needle development and acclimation processes throughout the year. In young, growing needles (May 15 to June 30), cell walls, organelles etc. were formed, and this developmental program heavily influenced the transcriptome, explained by over represented Gene Ontology (GO) categories. Later changes in gene expression were smaller but four phases were recognized: summer (July-August), autumn (September-October), winter (November-February) and spring (March-April), where over represented GO categories demonstrated how the needles acclimated to the various seasons. Changes in the seasonal global transcriptome profile were accompanied by differential expression of members of the major transcription factor families. We present a tentative model of how cellular activities are regulated over the year in needles of Norway spruce, which demonstrates the value of mining this dataset, accessible in ConGenIE together with advanced visualization tools.

scholarly journals Comprehensive Characterization of Multitissue Expression Landscape, Co-Expression Networks and Positive Selection in Pikeperch

Cells ◽  
2021 ◽  
Vol 10 (9) ◽  
pp. 2289
Author(s):  
Julien Alban Nguinkal ◽  
Marieke Verleih ◽  
Lidia de los Ríos-Pérez ◽  
Ronald Marco Brunner ◽  
Arne Sahm ◽  
...  
Keyword(s):  
Gene Expression ◽  
Positive Selection ◽  
Tissue Specificity ◽  
Fish Family ◽  
Physiological Functions ◽  
Tissue Specific ◽  
Network Analyses ◽  
Network Modules ◽  
Comprehensive Characterization

Promising efforts are ongoing to extend genomics resources for pikeperch (Sander lucioperca), a species of high interest for the sustainable European aquaculture sector. Although previous work, including reference genome assembly, transcriptome sequence, and single-nucleotide polymorphism genotyping, added a great wealth of genomic tools, a comprehensive characterization of gene expression across major tissues in pikeperch still remains an unmet research need. Here, we used deep RNA-Sequencing of ten vital tissues collected in eight animals to build a high-confident and annotated trancriptome atlas, to detect the tissue-specificity of gene expression and co-expression network modules, and to investigate genome-wide selective signatures in the Percidae fish family. Pathway enrichment and protein–protein interaction network analyses were performed to characterize the unique biological functions of tissue-specific genes and co-expression modules. We detected strong functional correlations and similarities of tissues with respect to their expression patterns—but also significant differences in the complexity and composition of their transcriptomes. Moreover, functional analyses revealed that tissue-specific genes essentially play key roles in the specific physiological functions of the respective tissues. Identified network modules were also functionally coherent with tissues’ main physiological functions. Although tissue specificity was not associated with positive selection, several genes under selection were found to be involved in hypoxia, immunity, and gene regulation processes, that are crucial for fish adaption and welfare. Overall, these new resources and insights will not only enhance the understanding of mechanisms of organ biology in pikeperch, but also complement the amount of genomic resources for this commercial species.

scholarly journals Image based annotation of Chemogenomic Libraries for Phenotypic Screening

2022 ◽  
Author(s):  
Amelie Tjaden ◽  
Apirat Chaikuad ◽  
Eric Kowarz ◽  
Rolf Marschalek ◽  
Stefan Knapp ◽  
...  
Keyword(s):  
Small Molecules ◽  
Cellular Responses ◽  
Chemical Probes ◽  
Cellular Functions ◽  
Single Experiment ◽  
Cell Functions ◽  
Specific Effects ◽  
Apoptosis And Necrosis ◽  
Comprehensive Characterization

Phenotypical screening is a widely used approach in drug discovery for the identification of small molecules with cellular activities. However, functional annotation of identified hits often poses a challenge. The development of small molecules with narrow or exclusive target selectivity such as chemical probes and chemogenomic (CG) libraries, greatly diminishes this challenge, but non-specific effects caused by compound toxicity or interference with basic cellular functions still poses a problem to associate phenotypic readouts with molecular targets. Hence, each compound should ideally be comprehensively characterized regarding its effects on general cell functions. Here, we report an optimized live-cell multiplexed assay that classifies cells based on nuclear morphology, presenting an excellent indicator for cellular responses such as early apoptosis and necrosis. This basic readout in combination with the detection of other general cell damaging activities of small molecules such as changes in cytoskeletal morphology, cell cycle and mitochondrial health provides a comprehensive time-dependent characterization of the effect of small molecules on cellular health in a single experiment. The developed high-content assay offers multi-dimensional comprehensive characterization that can be used to delineate generic effects regarding cell functions and cell viability, allowing an assessment of compound suitability for subsequent detailed phenotypic and mechanistic studies.

scholarly journals Inferring spatially transient gene expression pattern from spatial transcriptomic studies

2020 ◽  
Author(s):  
Jan Kueckelhaus ◽  
Jasmin von Ehr ◽  
Vidhya M. Ravi ◽  
Paulina Will ◽  
Kevin Joseph ◽  
...  
Keyword(s):  
Gene Expression ◽  
Spatial Organization ◽  
Transient Gene Expression ◽  
Gene Expression Pattern ◽  
Spatially Resolved ◽  
Regional Adaptation ◽  
Spatial Trajectories ◽  
Comprehensive Characterization ◽  
Transcriptomic Studies

AbstractSpatial transcriptomic is a technology to provide deep transcriptomic profiling by preserving the spatial organization. Here, we present a framework for SPAtial Transcriptomic Analysis (SPATA, https://themilolab.github.io/SPATA), to provide a comprehensive characterization of spatially resolved gene expression, regional adaptation of transcriptional programs and transient dynamics along spatial trajectories.

Sign in / Sign up

Export Citation Format

Share Document