107 Insights from roe deer oocyte transcriptome across embryonic diapause

2019 ◽  
Vol 31 (1) ◽  
pp. 179
Author(s):  
S. M. Bernal-Ulloa ◽  
V. A. van der Weijden ◽  
J. T. Bick ◽  
A. B. Rüegg ◽  
B. Drews ◽  
...  
Keyword(s):  
Gene Ontology ◽  
False Discovery Rate ◽  
Roe Deer ◽  
Expression Profiles ◽  
Polar Body ◽  
Morphological Characteristics ◽  
Reduction Process ◽  
Immature Oocytes ◽  
Developmental Arrest ◽  
False Discovery

Embryonic developmental arrest, known as diapause, has been reported in more than 130 species. However, its mechanisms are still not completely understood. In the roe deer, the only known ungulate that exhibits this phenomenon, diapause lasts for approximately 5 months, starting after the rut period in mid-July to early August and ending with embryo elongation and implantation in December/January. Little is known regarding oocyte characteristics during this period. Here, we analysed the roe deer oocyte transcriptome as a model to understand diapause effects on oocyte features during embryonic developmental arrest and reactivation. During regular hunting, immature oocytes were obtained by ovary slicing from diapause and nondiapause stages, and classified according to morphological characteristics. Only oocytes with >2 layers of compact cumulus cells and cytoplasm from 30 hunted females were used for analyses. Immature oocytes were denuded and snap frozen. Additional oocytes were cultured in maturation medium for 20-24h. Matured oocytes with a present polar body were snap frozen. Two pools of 10 immature and mature oocytes for both diapause and nondiapause stages were included (at least 4 donors/pool). Oocyte pools were processed using the Smart-seq 2 single-cell protocol (Illumina Inc., San Diego, CA, USA) for full-length cDNA and library preparation. We performed RNA-seq on an Illumina sequencer. The obtained Fastq files were clipped and analysed with a locally installed version of the Galaxy platform. Sequences were mapped against the roe deer transcriptome (unpublished data) and annotated against human and bovine transcripts. Differentially expressed genes (DEG; false discovery rate <1%) were identified using EdgeR (https://bioconductor.org/packages/release/bioc/html/edgeR.html) in immature (IMM) and mature (M) oocytes from diapause (D) and nondiapause (ND) stages. Additionally, to evaluate the effects of maturation on oocyte transcript abundancy, DEG between IMM and M oocytes for D and ND were identified. Multidimensional scaling resulted in clustering according to oocyte types. Gene ontology terms for biological processes were assigned using ToppCluster tools. A total of 23066, 23022, 22438, and 22532 transcripts were detected for IMM D, M D, IMM ND and M ND oocytes, respectively. Using false discovery rate filtering, we found 333 and 288 DEG in immature and mature oocytes, respectively. Furthermore, maturation changed the oocyte expression profiles during D (2233 DEG) and ND periods (2589 DEG). Gene ontology classification revealed that most of the DEG in immature oocytes were involved in macromolecule catabolic process and oxidation-reduction process. For mature oocytes, DEG were mostly related to regulation of chromosome condensation and ER and Golgi vesicle-mediated transport. Additionally, the top 20 DEG from IMM D v. M D oocytes were related to mRNA splicing, mRNA metabolic process, and mRNA processing. These processes were not identified in the top 20 DEG from IMM ND v. M ND oocytes. These preliminary results suggest that oocyte transcriptome analysis could disclose new pathways implicated in oocyte competence and embryonic developmental arrest and activation stages.

scholarly journals Gene expression profiles of bovine caruncular and intercaruncular endometrium at implantation

2009 ◽  
Vol 39 (1) ◽  
pp. 14-27 ◽  
Author(s):  
Nadéra Mansouri-Attia ◽  
Julie Aubert ◽  
Pierrette Reinaud ◽  
Corinne Giraud-Delville ◽  
Géraldine Taghouti ◽  
...  
Keyword(s):  
False Discovery Rate ◽  
Cellular Localization ◽  
Target Genes ◽  
Expression Profiles ◽  
Primary Cultures ◽  
Gene Expression Profiles ◽  
Oligonucleotide Array ◽  
Endometrial Cells ◽  
False Discovery ◽  
The Impact

At implantation the endometrium undergoes modifications necessary for its physical interactions with the trophoblast as well as the development of the conceptus. We aim to identify endometrial factors and pathways essential for a successful implantation in the caruncular (C) and the intercaruncular (IC) areas in cattle. Using a 13,257-element bovine oligonucleotide array, we established expression profiles at day 20 of the estrous cycle or pregnancy (implantation), revealing 446 and 1,295 differentially expressed genes (DEG) in C and IC areas, respectively (false discovery rate = 0.08). The impact of the conceptus was higher on the immune response function in C but more prominent on the regulation of metabolism function in IC. The C vs. IC direct comparison revealed 1,177 and 453 DEG in cyclic and pregnant animals respectively (false discovery rate = 0.05), with a major impact of the conceptus on metabolism and cell adhesion. We selected 15 genes including C11ORF34, CXCL12, CXCR4, PLAC8, SCARA5, and NPY and confirmed their differential expression by quantitative RT-PCR. The cellular localization was analyzed by in situ hybridization and, upon pregnancy, showed gene-specific patterns of cell distribution, including a high level of expression in the luminal epithelium for C11ORF34 and MX1. Using primary cultures of bovine endometrial cells, we identified PTN, PLAC8, and CXCL12 as interferon-τ (IFNT) target genes and MSX1 and CXCR7 as IFNT-regulated genes, whereas C11ORF34 was not an IFNT-regulated gene. Our transcriptomic data provide novel molecular insights accounting for the biological functions related to the C or IC endometrial areas and may contribute to the identification of potential biomarkers for normal and perturbed early pregnancy.

scholarly journals Comparison of gene expression in the red imported fire ant (Solenopsis invicta) under different temperature conditions

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Mohammad Vatanparast ◽  
Robert T. Puckett ◽  
Deuk-Soo Choi ◽  
Youngjin Park
Keyword(s):  
Gene Expression ◽  
Gene Ontology ◽  
High Temperature ◽  
Temperature Stress ◽  
Solenopsis Invicta ◽  
Expression Profiles ◽  
Fire Ant ◽  
Molecular Response ◽  
Red Imported Fire Ant ◽  
Imported Fire Ant

AbstractThe red imported fire ant (RIFA), Solenopsis invicta Buren is native to South America and is known as a global problematic invasive species. This study focused on the molecular response of RIFA by comparing gene expression profiles after exposing ants to low (10 °C) and high (40 °C) temperature stress and comparing them to untreated controls (30 °C). A total of 99,085 unigenes (the clustered non-redundant transcripts that are filtered from the longest assembled contigs) were obtained, of which 19,154 were annotated with gene descriptions, gene ontology terms, and metabolic pathways. 86 gene ontology (GO) functional sub-groups and 23 EggNOG terms resulted. Differentially expressed genes (DEGs) with log2FC ≥ 10 were screened and were compared at different temperatures. We found 203, 48, and 66 specific DEGs co-regulated at 10, 20, and 40 °C. Comparing transcriptome profiles for differential gene expression resulted in various DE genes, including cytochrome P450, NADH dehydrogenase subunit 1, cuticle protein and heat shock protein (HSP), which have previously been reported to be involved in cold and high temperature resistance. GO analysis revealed that antioxidant activity is up-regulated under high temperature stress. We verified the RNA-seq data by qPCR on 20 up- and down-regulated DEGs. These findings provide a basis for future understanding of the adaptation mechanisms of RIFA and the molecular mechanisms underlying the response to low and high temperatures.

scholarly journals False Discovery Rate in Linkage and Association Genome Screens for Complex Disorders

Genetics ◽  
2003 ◽  
Vol 164 (2) ◽  
pp. 829-833
Author(s):  
Chiara Sabatti ◽  
Susan Service ◽  
Nelson Freimer
Keyword(s):  
Gene Mapping ◽  
False Discovery Rate ◽  
Disease Gene ◽  
Susceptibility Genes ◽  
Complex Disorders ◽  
Disease Gene Mapping ◽  
False Discovery ◽  
Simple Step ◽  
Multiple Comparison Procedure ◽  
Step Down

Abstract We explore the implications of the false discovery rate (FDR) controlling procedure in disease gene mapping. With the aid of simulations, we show how, under models commonly used, the simple step-down procedure introduced by Benjamini and Hochberg controls the FDR for the dependent tests on which linkage and association genome screens are based. This adaptive multiple comparison procedure may offer an important tool for mapping susceptibility genes for complex diseases.

scholarly journals P14.21 Tehila Kaisman-Elbaz MD/PhD

2019 ◽  
Vol 21 (Supplement_3) ◽  
pp. iii71-iii71
Author(s):  
T Kaisman-Elbaz ◽  
Y Elbaz ◽  
V Merkin ◽  
L Dym ◽  
A Noy ◽  
...  
Keyword(s):  
Overall Survival ◽  
Multivariate Analysis ◽  
False Discovery Rate ◽  
Medical Center ◽  
Tumor Resection ◽  
Multiple Hypothesis Testing ◽  
Hemoglobin Level ◽  
Distribution Width ◽  
False Discovery ◽  
Dismal Prognosis

Abstract BACKGROUND Glioblastoma is known for its dismal prognosis though its dependency on patients’ readily available RBCs parameters defining the patient’s anemic status such as hemoglobin level and Red blood cells distribution Width (RDW) is not fully established. Several works demonstrated a connection between low hemoglobin level or high RDW values to overall glioblastoma patient’s survival, but in other works, a clear connection was not found. This study addresses this unclarity. MATERIAL AND METHODS In this work, 170 glioblastoma patients, diagnosed and treated in Soroka University Medical Center (SUMC) in the last 12 years were retrospectively inspected for their survival dependency on pre-operative RBCs parameters using multivariate analysis followed by false discovery rate procedure due to the multiple hypothesis testing. A survival stratification tree and Kaplan-Meier survival curves that indicate the patient’s prognosis according to these parameters were prepared. RESULTS Beside KPS>70 and tumor resection supplemented by oncological treatment, age<70 (HR=0.4, 95% CI 0.24–0.65), low hemoglobin level (HR=1.79, 95% CI 1.06–2.99) and RDW<14% (HR=0.57, 95% CI 0.37–0.88) were found to be prognostic to patients’ overall survival in multivariate analysis, accounting for false discovery rate of less than 5%. CONCLUSION A survival stratification highlighted a non-anemic subgroup of nearly 30% of the cohort’s patients whose median overall survival was 21.1 months (95% CI 16.2–27.2) - higher than the average Stupp protocol overall median survival of about 15 months. A discussion on the beneficial or detrimental effect of RBCs parameters on glioblastoma prognosis and its possible causes is given.

scholarly journals Associations Between Genetically Predicted Protein Levels and COVID-19 Severity

2020 ◽  
Vol 223 (1) ◽  
pp. 19-22
Author(s):  
Jingjing Zhu ◽  
Chong Wu ◽  
Lang Wu
Keyword(s):  
False Discovery Rate ◽  
Drug Repurposing ◽  
Bonferroni Correction ◽  
Host Genetics ◽  
Protein Levels ◽  
False Discovery

Abstract It is critical to identify potential causal targets for SARS-CoV-2, which may guide drug repurposing options. We assessed the associations between genetically predicted protein levels and COVID-19 severity. Leveraging data from the COVID-19 Host Genetics Initiative comparing 6492 hospitalized COVID-19 patients and 1 012 809 controls, we identified 18 proteins with genetically predicted levels to be associated with COVID-19 severity at a false discovery rate of &lt;0.05, including 12 that showed an association even after Bonferroni correction. Of the 18 proteins, 6 showed positive associations and 12 showed inverse associations. In conclusion, we identified 18 candidate proteins for COVID-19 severity.

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