scholarly journals Same same but different: Cluster architecture variation in five ‘Pinot Noir’ clonal selection lines correlates with differential expression of three transcription factors and further growth related genes

2020 ◽  
Author(s):  
Robert Richter ◽  
Susanne Rossmann ◽  
Doreen Gabriel ◽  
Reinhard Töpfer ◽  
Klaus Theres ◽  
...  
Keyword(s):  
Gene Expression ◽  
Transcription Factor ◽  
Differential Gene Expression ◽  
Fungal Infections ◽  
Clonal Selection ◽  
Pinot Noir ◽  
Cellular Growth ◽  
Wine Production ◽  
Cluster Architecture ◽  
Differential Gene

AbstractGrapevine (Vitis vinifera L.) is an economically important crop that needs to comply with high quality standards for fruit, juice and wine production. Intense plant protection is required to avoid losses caused by fungal infections. Grapevine cultivars with loose cluster architecture enable to reduce protective chemical treatments due to their enhanced resilience against fungal infections such as Botrytis cinerea induced grey mold. A recent study identified transcription factor gene VvGRF4 as determinant of inflorescence structure in exemplary samples of loose and compact quasi-isogenic ‘Pinot Noir’ clones. Here, we extended the analysis to 12 differently clustered ‘Pinot Noir’ clones originating from five different clonal selection programs. Differential gene expression of these clones was studied in three different locations over three seasons in demonstrative vineyards. Two phenotypically contrasting clones were grown at all three locations and served for standardization of downstream analyses. Differential gene expression data were correlated to the phenotypic variation of cluster architecture sub-traits. A consistent differential gene expression of VvGRF4 in relation to loose clusters was verified over the different environments and in the extended set of ‘Pinot Noir’ clones. In addition, 14 more genes with consistent expression differences between loosely and compactly clustered clones independent from season and location were identified. These genes show annotations related to cellular growth, cell wall extension, cell division and auxin metabolism. They include two more transcription factor genes.

scholarly journals Differential expression of transcription factor- and further growth-related genes correlates with contrasting cluster architecture in Vitis vinifera ‘Pinot Noir’ and Vitis spp. genotypes

2020 ◽  
Vol 133 (12) ◽  
pp. 3249-3272
Author(s):  
Robert Richter ◽  
Susanne Rossmann ◽  
Doreen Gabriel ◽  
Reinhard Töpfer ◽  
Klaus Theres ◽  
...  
Keyword(s):  
Gene Expression ◽  
Transcription Factor ◽  
Vitis Vinifera ◽  
Differential Expression ◽  
Fungal Infections ◽  
Clonal Selection ◽  
Interspecific Cross ◽  
Pinot Noir ◽  
Wine Production ◽  
Cluster Architecture

Abstract Grapevine (Vitis vinifera L.) is an economically important crop that needs to comply with high quality standards for fruit, juice and wine production. Intense plant protection is required to avoid fungal damage. Grapevine cultivars with loose cluster architecture enable reducing protective treatments due to their enhanced resilience against fungal infections, such as Botrytis cinerea-induced gray mold. A recent study identified transcription factor gene VvGRF4 as determinant of pedicel length, an important component of cluster architecture, in samples of two loose and two compact quasi-isogenic ‘Pinot Noir’ clones. Here, we extended the analysis to 12 differently clustered ‘Pinot Noir’ clones from five diverse clonal selection programs. Differential gene expression of these clones was studied in three different locations over three seasons. Two phenotypically opposite clones were grown at all three locations and served for standardization. Data were correlated with the phenotypic variation of cluster architecture sub-traits. A set of 14 genes with consistent expression differences between loosely and compactly clustered clones—independent from season and location—was newly identified. These genes have annotations related to cellular growth, cell division and auxin metabolism and include two more transcription factor genes, PRE6 and SEP1-like. The differential expression of VvGRF4 in relation to loose clusters was exclusively found in ‘Pinot Noir’ clones. Gene expression studies were further broadened to phenotypically contrasting F1 individuals of an interspecific cross and OIV reference varieties of loose cluster architecture. This investigation confirmed PRE6 and six growth-related genes to show differential expression related to cluster architecture over genetically divergent backgrounds.

Early genetic responses in rat vascular tissue after simulated diving

2012 ◽  
Vol 44 (24) ◽  
pp. 1201-1207 ◽  
Author(s):  
Ingrid Eftedal ◽  
Arve Jørgensen ◽  
Ragnhild Røsbjørgen ◽  
Arnar Flatberg ◽  
Alf O. Brubakk
Keyword(s):  
Gene Expression ◽  
Transcription Factor ◽  
Plasminogen Activator ◽  
Differential Gene Expression ◽  
Vascular Function ◽  
Plasminogen Activator Inhibitor ◽  
Fine Tuning ◽  
Plasminogen Activator Inhibitor 1 ◽  
Differential Gene ◽  
Activator Inhibitor

Diving causes a transient reduction of vascular function, but the mechanisms behind this are largely unknown. The aim of this study was therefore to analyze genetic reactions that may be involved in acute changes of vascular function in divers. Rats were exposed to 709 kPa of hyperbaric air (149 kPa Po2) for 50 min followed by postdive monitoring of vascular bubble formation and full genome microarray analysis of the aorta from diving rats ( n = 8) and unexposed controls ( n = 9). Upregulation of 23 genes was observed 1 h after simulated diving. The differential gene expression was characteristic of cellular responses to oxidative stress, with functions of upregulated genes including activation and fine-tuning of stress-responsive transcription, cytokine/cytokine receptor signaling, molecular chaperoning, and coagulation. By qRT-PCR, we verified increased transcription of neuron-derived orphan receptor-1 ( Nr4a3), plasminogen activator inhibitor 1 ( Serpine1), cytokine TWEAK receptor FN14 ( Tnfrsf12a), transcription factor class E basic helix-loop-helix protein 40 ( Bhlhe40), and adrenomedullin ( Adm). Hypoxia-inducible transcription factor HIF1 subunit HIF1-α was stabilized in the aorta 1 h after diving, and after 4 h there was a fivefold increase in total protein levels of the procoagulant plasminogen activator inhibitor 1 (PAI1) in blood plasma from diving rats. The study did not have sufficient power for individual assessment of effects of hyperoxia and decompression-induced bubbles on postdive gene expression. However, differential gene expression in rats without venous bubbles was similar to that of all the diving rats, indicating that elevated Po2 instigated the observed genetic reactions.

scholarly journals EDGEdb: a transcription factor-DNA Interaction database for the analysis of C. elegans differential gene expression

BMC Genomics ◽  
2007 ◽  
Vol 8 (1) ◽  
Author(s):  
M Inmaculada Barrasa ◽  
Philippe Vaglio ◽  
Fabien Cavasino ◽  
Laurent Jacotot ◽  
Albertha JM Walhout
Keyword(s):  
Gene Expression ◽  
Transcription Factor ◽  
Differential Gene Expression ◽  
Dna Interaction ◽  
C Elegans ◽  
Interaction Database ◽  
Differential Gene

Differential Gene Expression Patterns and Interaction Networks in BCR/ABL Positive and Negative Adult Acute Lymphoblastic Leukemias.

Blood ◽  
2006 ◽  
Vol 108 (11) ◽  
pp. 1836-1836
Author(s):  
Dejan Juric ◽  
Norman J. Lacayo ◽  
Meghan C. Ramsey ◽  
Janis Racevskis ◽  
Peter H. Wiernik ◽  
...  
Keyword(s):  
Gene Expression ◽  
Differential Gene Expression ◽  
Expression Profiles ◽  
Lymphoblastic Leukemia ◽  
Expression Patterns ◽  
Cellular Growth ◽  
Interaction Networks ◽  
Pcr Analysis ◽  
Interaction Patterns ◽  
Differential Gene

Abstract BCR/ABL is associated with an unfavorable prognosis in adults with acute lymphoblastic leukemia (ALL). We used DNA microarrays to identify gene expression profiles and molecular interaction networks related to BCR/ABL status and clinical outcome in a set of 54 adult ALL specimens from the MRC UKALL XII/ECOG E2993 intergroup study (21 p185BCR/ABL- and 16 p210BCR/ABL-positive and 17 BCR/ABL negative). In order to avoid biases associated with commonly used sample amplification procedures, we have implemented an indirect two-step labeling protocol based on signal amplification by use of dendrimer technology. Using a two-class, non-parametric t-test and a false discovery rate cutoff of 5%, we identified 271 genes (including GAB1, CIITA, XBP1, CD83, SERPINB9, PTP4A3, NOV, LOX, CTNND1, BAALC and RAB21) as differentially expressed in BCR/ABL positive ALL compared with BCR/ABL negative ALL. They separate these two classes of adult ALL with an overall accuracy of 93% and are enriched for three highly relevant biological functions: Cellular Growth and Proliferation (57 genes, p = 0.004–0.044), Cell Death (49 genes, p = 0.0007–0.049), and Hematological System Development and Function (40 genes, p = 0.00004–0.049). Network analysis demonstrated complex interaction patterns of these genes, and identified FYN and IL15 as the hubs of the top-scoring network. We confirmed these findings by both qRT-PCR analysis of the initial set of samples and by cross-platform validation in an independent cohort of 128 adult ALL specimens. In addition, within the BCR/ABL positive subgroup, we identified 14 clones found to be over-expressed (TSPAN16, ADAMTSL4) or under-expressed (PILRB, STS-1, SPRY1) in p185BCR-ABL- relative to p210BCR-ABL-ALL. In a nearest-centroid classification, these clones correctly predict the BCR/ABL subtype with a cross-validated prediction accuracy of 95%. No differential gene expression was detected among Rho family GTPases and their known interaction partners. Finally, we constructed a gene expression- and interaction-based outcome predictor consisting of 27 genes (including GRB2, GAB1, GLI1, IRS1, RUNX2 and SPP1), which strongly correlated with overall survival in BCR/ABL positive adult ALL (p=0.0001), independently of other clinical parameters such as age (p=0.25) and white blood cell count at presentation (p = 0.003). These findings may be useful for developing novel therapeutic targets and prognostic markers in adult ALL.

scholarly journals Alterations in gene expression in the spinal cord of mice lacking Nfix

2020 ◽  
Vol 13 (1) ◽  
Author(s):  
Elise Matuzelski ◽  
Alexandra Essebier ◽  
Lachlan Harris ◽  
Richard M. Gronostajski ◽  
Tracey J. Harvey ◽  
...  
Keyword(s):  
Gene Expression ◽  
Spinal Cord ◽  
Transcription Factor ◽  
Differential Gene Expression ◽  
Cell Biology ◽  
Wild Type ◽  
Spinal Cord Development ◽  
Differential Gene ◽  
Developing Mouse Brain

Abstract Objective Nuclear Factor One X (NFIX) is a transcription factor expressed by neural stem cells within the developing mouse brain and spinal cord. In order to characterise the pathways by which NFIX may regulate neural stem cell biology within the developing mouse spinal cord, we performed an microarray-based transcriptomic analysis of the spinal cord of embryonic day (E)14.5 Nfix−/− mice in comparison to wild-type controls. Data description Using microarray and differential gene expression analyses, we were able to identify differentially expressed genes in the spinal cords of E14.5 Nfix−/− mice compared to wild-type controls. We performed microarray-based sequencing on spinal cords from n = 3 E14.5 Nfix−/− mice and n = 3 E14.5 Nfix+/+ mice. Differential gene expression analysis, using a false discovery rate (FDR) p-value of p < 0.05, and a fold change cut-off for differential expression of >  ± 1.5, revealed 1351 differentially regulated genes in the spinal cord of Nfix−/− mice. Of these, 828 were upregulated, and 523 were downregulated. This resource provides a tool to interrogate the role of this transcription factor in spinal cord development.

scholarly journals Transcriptome Profiling and Differential Gene Expression in Canine Microdissected Anagen and Telogen Hair Follicles and Interfollicular Epidermis

Genes ◽  
2020 ◽  
Vol 11 (8) ◽  
pp. 884
Author(s):  
Dominique J. Wiener ◽  
Kátia R. Groch ◽  
Magdalena A.T. Brunner ◽  
Tosso Leeb ◽  
Vidhya Jagannathan ◽  
...  
Keyword(s):  
Gene Expression ◽  
Differential Gene Expression ◽  
Transcriptome Profiling ◽  
Structure And Function ◽  
Hair Follicles ◽  
Cellular Growth ◽  
Genes Encoding ◽  
Interfollicular Epidermis ◽  
Differential Gene ◽  
And Function

The transcriptome profile and differential gene expression in telogen and late anagen microdissected hair follicles and the interfollicular epidermis of healthy dogs was investigated by using RNAseq. The genes with the highest expression levels in each group were identified and genes known from studies in other species to be associated with structure and function of hair follicles and epidermis were evaluated. Transcriptome profiling revealed that late anagen follicles expressed mainly keratins and telogen follicles expressed GSN and KRT15. The interfollicular epidermis expressed predominately genes encoding for proteins associated with differentiation. All sample groups express genes encoding for proteins involved in cellular growth and signal transduction. The expression pattern of skin-associated genes in dogs is similar to humans. Differences in expression compared to mice and humans include BMP2 expression mainly in telogen and high KRT17 expression in the interfollicular epidermis of dogs. Our data provide the basis for the investigation of the structure and function of canine skin or skin disease and support the use of dogs as a model for human cutaneous disease by assigning gene expression to specific tissue states.

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