Positive and negative control of the Antennapediapromoter P2

Development ◽  
1991 ◽  
Vol 113 (Supplement_1) ◽  
pp. 177-185 ◽  
Author(s):  
George R. Riley ◽  
Erik M. Jorgensen ◽  
Robert K. Baker ◽  
Richard L. Garber
Keyword(s):  
Expression Patterns ◽  
Negative Control ◽  
Segmentation Genes ◽  
Active Gene ◽  
Inhibitory Drug

To understand the nature of the regulatory signals impinging on the second promoter of the Antennapedia gene (Antp P2), analysis of its expression in mutants and in inhibitory drug injected embryos has been carried out. The maternally-active gene osk is identified as one of two general repressors of P2 which prevent Antp transcription until division cycle 14. Products of the zygotically-active segmentation genes ftz, hb, Kr, gt and kni then act as activators or repressors of Antp P2 in a combinatorial fashion. The timing of these events, and their positive versus negative nature, is critical for generating the expression patterns normal for Antp.

174 EPIDERMAL GROWTH FACTORS AND CALBINDIN-D9k GENE EXPRESSIONS DURING PREGANCY IN THE PORCINE UTERUS

2008 ◽  
Vol 20 (1) ◽  
pp. 167
Author(s):  
Y.-J. Kim ◽  
E.-M. Jung ◽  
G.-S. Lee ◽  
S.-H. Hyun ◽  
E.-B. Jeung
Keyword(s):  
Growth Factors ◽  
Growth Factor ◽  
Transforming Growth Factor ◽  
Expression Patterns ◽  
Negative Control ◽  
Heparin Binding ◽  
Gene Expressions ◽  
Calbindin D9k ◽  
Genes Encoding ◽  
Epidermal Growth

To stably maintain pregnancy, several genes are expressed in the uterus. In particular, the endometrial expression of genes encoding growth factors appears to play a key role in maternal–fetal communication. Previous studies have characterized the endometrial expression kinetics of the genes encoding epidermal growth factor (EGF), its receptor (EGFR), transforming growth factor-alpha (TGF-α), amphiregulin (Areg), heparin-binding (Hb) EGF, and calbindin-D9k (CaBP-9k) in the pig during implantation. Here, we further characterized the expression patterns of these molecules during the entire porcine pregnancy. Porcine (n = 3 per PD) were collected at pregnancy days (PD) 12, 15, 30, 60, 90, and 110 and subjected to semi-quantitative RT-PCR. The data were analyzed with a nonparametric one-way analysis of variance using the Kruskal-Wallis test, followed by Dunnett's test for multiple comparisons to the negative control. EGF and EGFR showed similar expression patterns, being highly expressed around implantation time and then disappearing. TGF-α and Areg expression levels rose steadily until they peaked at PD30, after which they gradually decreased to PD12 levels. The Areg mRNA expression pattern was confirmed by real-time PCR, and similar Areg protein expression patterns were observed. Immunohistochemical analysis of PD60 uteri revealed Areg in the glandular and luminal epithelial cells. Hb-EGF was steadily expressed throughout the entire pregnancy while CaBP-9k was expressed strongly on PD12, and then declined sharply in PD15 before recovering slightly for the remainder of the pregnancy. Thus, the EGF family may play a key role during implantation in pigs. In addition, CaBP-9k may help maintain uterine quiescence during pregnancy by sequestering cytoplasmic Ca2+.

scholarly journals Sex differences in gene expression patterns associated with the APOE4 allele

F1000Research ◽  
2019 ◽  
Vol 8 ◽  
pp. 387
Author(s):  
Michelle Hsu ◽  
Mehek Dedhia ◽  
Wim Crusio ◽  
Anna Delprato
Keyword(s):  
Gene Expression ◽  
Sex Differences ◽  
Age Of Onset ◽  
Late Onset ◽  
Expression Patterns ◽  
Differential Expression Analysis ◽  
Negative Control ◽  
Gene Expression Patterns ◽  
Dependent Manner ◽  
Examine Gene Expression

Background: The APOE gene encodes apolipoprotein ε (ApoE), a protein that associates with lipids to form lipoproteins that package and traffic cholesterol and lipids through the bloodstream. There are at least three different alleles of the APOE gene: APOE2, APOE3, and APOE4. The APOE4 allele increases an individual's risk for developing late-onset Alzheimer disease (AD) in a dose-dependent manner. Sex differences have been reported for AD susceptibility, age of onset, and symptom progression, with females being more affected than males. Methods: In this study, we use a systems biology approach to examine gene expression patterns in the brains of aged female and male individuals who are positive for the APOE4 allele in order to identify possible sex-related differences that may be relevant to AD. Results: Based on correlation analysis, we identified a large number of genes with an expression pattern similar to that of APOE in APOE4-positive individuals. The number of these genes was much higher in APOE4-positive females than in APOE4-positive males, who in turn had more of such genes than APOE4-negative control groups. Conclusions: Profiling of these genes using Gene Ontology (GO) term classification, pathway enrichment, and differential expression analysis supports the idea of a transcriptional role of APOE with respect to sex differences and AD.

scholarly journals Sex differences in gene expression patterns associated with the APOE4 allele

F1000Research ◽  
2019 ◽  
Vol 8 ◽  
pp. 387 ◽  
Author(s):  
Michelle Hsu ◽  
Mehek Dedhia ◽  
Wim E Crusio ◽  
Anna Delprato
Keyword(s):  
Gene Expression ◽  
Sex Differences ◽  
Age Of Onset ◽  
Late Onset ◽  
Brain Area ◽  
Expression Patterns ◽  
Differential Expression Analysis ◽  
Negative Control ◽  
Gene Expression Patterns ◽  
Dependent Manner

Background: The APOE gene encodes apolipoprotein ε (ApoE), a protein that associates with lipids to form lipoproteins that package and traffic cholesterol and lipids through the bloodstream. There are at least three different alleles of the APOE gene: APOE2, APOE3, and APOE4. The APOE4 allele increases an individual's risk for developing late-onset Alzheimer disease (AD) in a dose-dependent manner. Sex differences have been reported for AD susceptibility, age of onset, and symptom progression, with females being more affected than males. Methods: In this study, we use a systems biology approach to examine gene expression patterns in the brains of aged female and male individuals who are positive for the APOE4 allele in order to identify possible sex-related differences that may be relevant to AD. Results: Based on correlation analysis, we identified a large number of genes with an expression pattern similar to that of APOE in APOE4-positive individuals. The number of these genes was much higher in APOE4-positive females than in APOE4-positive males, who in turn had more of such genes than APOE4-negative control groups. Our findings also indicate a significant sex* genotype interaction for the CNTNAP2 gene, a member of the neurexin family and a significant interaction for brain area*sex* genotype for PSEN2, a risk factor gene for AD.  Conclusions: Profiling of these genes using Gene Ontology (GO) term classification, pathway enrichment, and differential expression analysis supports the idea of a transcriptional role of APOE with respect to sex differences and AD.

scholarly journals Genome-wide characterization and expression analysis of PP2CA family members in response to ABA and osmotic stress in Gossypium

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e7105 ◽  
Author(s):  
Tingting Lu ◽  
Gaofeng Zhang ◽  
Yibin Wang ◽  
Shibin He ◽  
Lirong Sun ◽  
...  
Keyword(s):  
Osmotic Stress ◽  
Expression Patterns ◽  
Family Members ◽  
Purifying Selection ◽  
Gene Families ◽  
Negative Control ◽  
Genome Wide ◽  
Control Growth ◽  
Cotton Species ◽  
Aba Receptors

Clade A type 2C protein phosphatases (PP2CAs), as central regulators of abscisic acid (ABA) signaling, negative control growth, development and responses to multiple stresses in plants. PP2CA gene families have been characterized at genome-wide levels in several diploid plants like Arabidopsis and rice. However, the information about genome organization, phylogenesis and putative functions of PP2CAs in Gossypium is lacking. Here, PP2CA family members were comprehensively analyzed in four Gossypium species including the diploid progenitor Gossypium arboreum, G. raimondii and the tetraploid G. hirsutum and G. barbadense, and 14, 13, 27, and 23 PP2CA genes were identified in the genomic sequences of these plants, respectively. Analysis results showed that most Gossypium PP2CAs were highly conserved in chromosomal locations, structures, and phylogeny among the four cotton species. Segmental duplication might play important roles in the formation of the PP2CAs, and most PP2CAs may be under purifying selection in Gossypium during evolution. The majority of the PP2CAs were expressed specifically in diverse tissues, and highly expressed in flowers in G. hirsutum. The GhPP2CAs displayed diverse expression patterns in responding to ABA and osmotic stress. Yeast-two hybrid assays revealed that many GhPP2CAs were capable of interaction with the cotton ABA receptors pyrabactin resistance1/PYR1-like/regulatory components of ABA receptors (PYR1/PYL/RCAR) GhPYL2-2D (Gh_D08G2587), GhPYL6-2A (Gh_A06G1418), and GhPYL9-2A (Gh_A11G0870) in the presence and/or absence of ABA. These results gave a comprehensive view of the Gossypium PP2CAs and are valuable for further studying the functions of PP2CAs in Gossypium.

scholarly journals Registration of the expression patterns of Drosophila segmentation genes by two independent methods

2001 ◽  
Vol 17 (1) ◽  
pp. 3-12 ◽  
Author(s):  
E. Myasnikova ◽  
A. Samsonova ◽  
K. Kozlov ◽  
M. Samsonova ◽  
J. Reinitz
Keyword(s):  
Expression Patterns ◽  
Segmentation Genes

34 Multi-step antibody validation for the geomx® digital spatial profiler

2020 ◽  
Vol 8 (Suppl 3) ◽  
pp. A35-A35
Author(s):  
Alyssa Rosenbloom ◽  
Jenny Cronin ◽  
Shilah Bonnett
Keyword(s):  
Protein Expression ◽  
Limit Of Detection ◽  
False Positive Rate ◽  
Expression Patterns ◽  
Negative Control ◽  
False Positives ◽  
List Type ◽  
Validation Process ◽  
Tissue Slices ◽  
Antibody Validation

BackgroundUnderstanding protein expression patterns within tissue compartments is imperative to investigating a range of biological questions. Historically, low plex immunohistochemical (IHC) approaches have been employed to assess the spatial heterogeneity of protein expression in tissue slices, but these techniques are of limited utility due to the challenge of measuring multiple targets in parallel. Compounding this limitation is the necessity of validating all antibodies which is resource intensive. Antibodies with poor quality have led to wasted time and resources, including false positives and non-reproducible results.1 2 Here we review the antibody validation process for the GeoMx® Digital Spatial Profiler (DSP) which enables investigation of high-plex, validated, spatially resolved protein targets from a single slide mounted formalin-fixed paraffin-embedded (FFPE) or fresh frozen sample. The robust validation process is in line with recent suggestions for antibody validation from SITC.3MethodsUnconjugated and oligo-conjugated antibodies are screened by IHC to assess staining sensitivity, patterns, and more importantly ensure that the oligo-conjugation has not adversely affected antibody performance. Upon approval by a pathologist, the antibodies are incorporated into a core or module and further validated using the GeoMx DSP. Using FFPE cell pellet arrays (CPAs) containing positive and negative control pellets, we assess the specificity as defined as a lack of signal in negative control pellets and a robust signal in positive control pellets. Antibodies with robust signals are then screened on tissue microarrays (TMAs) composed of healthy and diseased tissues to ensure that they will perform as expected in real samples and yield sufficient signal over background. Finally, after antibodies pass functional validation, we assess the performance of antibodies within panels of antibodies that will be commercialized.ResultsIn total, approximately 60% of off-the-shelf antibodies tested for use in GeoMx assays pass the entire validation process and are put into commercial assays. Passing requirements include exhibiting a maximum positive signal divided by the limit of detection, plus two standard deviations (SD) that is greater than or equal to 5 in both CPAs and TMAs for individual antibodies; such a threshold gives a false positive rate of less than 10%.ConclusionsUnvalidated or poorly validated antibodies can result in false positives and non-reproducible results. Following the robust validation process outlined here, approximately 40% of off-the-shelf antibodies are removed from panels, underscoring the importance of antibody validation prior to incorporating new antibodies into experiments.ReferencesTaussig MJ, Fonseca C, and Trimmer JS. Antibody validation: a view from the mountains. N Biotechnol. 2018; 45:1–8.Bordeaux J, Welsh AW, Agarwal S, Killiam E, Baquero MT, Hanna JA, Anagnostou VK, Rimm DL. Antibody validation. Biotechniques 2010;48(3):197–209.Taube, et al. The Society for Immunotherapy of Cancer statement on best practices for multiplex immunohistochemistry (IHC) and immunofluorescence (IF) staining and validation. J Immunother Cancer 2020;8(1):e000155.

scholarly journals Up-Regulating ERIC by CRISPR-dCas9-VPR Inhibits Cell Proliferation and Invasion and Promotes Apoptosis in Human Bladder Cancer

2021 ◽  
Vol 8 ◽  
Author(s):  
Jiangeng Yang ◽  
An Xia ◽  
Huajie Zhang ◽  
Qi Liu ◽  
Hongke You ◽  
...  
Keyword(s):  
Cell Proliferation ◽  
Bladder Cancer ◽  
Urothelial Carcinoma ◽  
Cell Lines ◽  
Expression Patterns ◽  
Regulation Of Gene Expression ◽  
Negative Control Group ◽  
Negative Control ◽  
Control Group ◽  
Bladder Urothelial Carcinoma

LncRNAs are defined as non-coding RNAs that are longer than 200 nucleotides in length. The previous studys has shown that lncRNAs played important roles in the regulation of gene expression and were essential in mammalian development and disease processes. Inspired by the observation that lncRNAs are aberrantly expressed in tumors, we extracted RNA from Bladder urothelial carcinoma and matched histologically normal urothelium from each patient and bladder carcinoma cell lines. Then, we reversed transcribed them into cDNA.Last, we investigated the expression patterns of ERIC by the fluorescence quantitative PCR in bladder cancer tissues and cell lines. CRISPR-dCas9-VPR targeting ERIC plasmid was transfected into T24 and 5637 cells, and cells were classified into two groups: negative control (NC) and ERIC overexpression group. MTT assay, transwell assay, and flow cytometry were performed to examine changes in cell proliferation, invasiveness, and apoptosis. We found that the expression of ERIC was down-regulated in bladder urothelial carcinoma compared to matched histologically normal urotheliam. The differences of the expression of this gene were large in the bladder cancer lines. Compared with the negative control group, the ERIC overexpression group showed significantly decreased cell proliferation rate (t = 7.583, p = 0.002; t = 3.283, p = 0.03) and invasiveness (t = 11.538, p < 0.001; t = 8.205, p = 0.01); and increased apoptotic rate (t = −34.083, p < 0.001; t = −14.316, p < 0.001). Our study lays a foundation for further study of its pathogenic mechanism in bladder cancer.

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