scholarly journals Gene expression patterns are correlated with genomic and genic structure in soybean

Genome ◽  
2011 ◽  
Vol 54 (1) ◽  
pp. 10-18 ◽  
Author(s):  
Jenna L. Woody ◽  
Andrew J. Severin ◽  
Yung-Tsi Bolon ◽  
Bindu Joseph ◽  
Brian W. Diers ◽  
...  
Keyword(s):  
Gene Expression ◽  
Sequence Data ◽  
Expression Patterns ◽  
Nucleotide Composition ◽  
Physical Parameters ◽  
Expression Levels ◽  
Noncoding Regions ◽  
Expression Breadth ◽  
Gene Expression Levels

Studies have indicated that exon and intron size and intergenic distance are correlated with gene expression levels and expression breadth. Previous reports on these correlations in plants and animals have been conflicting. In this study, next-generation sequence data, which has been shown to be more sensitive than previous expression profiling technologies, were generated and analyzed from 14 tissues. Our results revealed a novel dichotomy. At the low expression level, an increase in expression breadth correlated with an increase in transcript size because of an increase in the number of exons and introns. No significant changes in intron or exon sizes were noted. Conversely, genes expressed at the intermediate to high expression levels displayed a decrease in transcript size as their expression breadth increased. This was due to smaller exons, with no significant change in the number of exons. Taking advantage of the known gene space of soybean, we evaluated the positioning of genes and found significant clustering of similarly expressed genes. Identifying the correlations between the physical parameters of individual genes could lead to uncovering the role of regulation owing to nucleotide composition, which might have potential impacts in discerning the role of the noncoding regions.

Correlation of messenger RNA expression patterns of ERCC1, TS, EGFR, and VEGFR2 with KRAS and BRAF mutational status in advanced colorectal cancer: Implications for targeted therapies.

2013 ◽  
Vol 31 (4_suppl) ◽  
pp. 383-383
Author(s):  
Martin K. H. Maus ◽  
Craig Stephens ◽  
Stephanie H. Astrow ◽  
Peter Philipp Grimminger ◽  
Dongyun Yang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Colorectal Cancer ◽  
Mrna Expression ◽  
Advanced Colorectal Cancer ◽  
Expression Patterns ◽  
Mrna Levels ◽  
Expression Levels ◽  
Mutational Status ◽  
Mrna Expression Levels ◽  
Gene Expression Levels

383 Background: Gene expression levels of ERCC1, TS, EGFR and VEGFR2 may have predictive value for the personalized use of standard chemotherapeutics as well as agents targeting the EGFR and VEGF pathways and the efficacy of EGFR directed monoclonal antibodies like panitumumab and cetuximab has been confirmed to be dependent on wt KRAS and wt BRAF in patients with advanced colorectal cancer. We investigated the correlations between KRAS/BRAF mutational status and the mRNA expression levels of these genes. Methods: Formalin-fixed paraffin-embedded tumor specimens from 600 patients with advanced colorectal adenocarcinoma were microdissected and DNA and RNA was extracted. Specifically designed primers and probes were used to detect 7 different base substitutions in codon 12 and 13 of KRAS, V600E mutations in BRAF and the expression levels of ERCC1, TS, EGFR and VEGFR2 by RT-PCR. Results: Mt KRAS tumors had significantly lower TS and EGFR gene expression levels compared with wt KRAS (p<0,001), whereas mt BRAF tumors showed significantly increased TS and EGFR mRNA levels compared to wt BRAF (p<0,001). Mt BRAF tumors showed significantly higher mRNA levels than mt KRAS tumors (p<0,001). ERCC1 and VEGFR2 mRNA levels were significantly down-regulated in mt KRAS specimen (p<0,001), but showed no significant correlation with BRAF mutational status. Conclusions: KRAS and BRAF mutations are associated with opposite mRNA expression levels for TS and EGFR. Recently, resistance to BRAF inhibition in mt BRAF colorectal tumors has been shown in preclinical models to be associated with up-regulation of EGFR. Our data suggests that BRAF mutants are associated with high EGFR levels at the time of diagnosis, and not necessarily part of an acquired mechanism of resistance. Significantly lower mRNA expression levels of VEGFR2 in mt KRAS tumors may explain lower response to angiogenesis inhibition seen in the TML study.

scholarly journals Influence of Insulin-Like Growth Factor 1 Gene Expression in Women with Breast Cancer: A Systematic Review

2020 ◽  
Author(s):  
Danylo Rafhael Costa-Silva ◽  
Francisco Adelton Alves-Ribeiro ◽  
Maria da Conceição Barros-Oliveira ◽  
Larysse Cardoso Campos-Verdes ◽  
Renato de Oliveira Pereira ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Gene Expression ◽  
Systematic Review ◽  
Growth Factor ◽  
Expression Patterns ◽  
Insulin Like Growth Factor ◽  
Expression Levels ◽  
Cancer Support ◽  
Increased Risk ◽  
Gene Expression Levels

Abstract Background: Breast cancer, the leading cause of cancer death among women worldwide, one of the major risk factors for breast cancer is genetic changes. Changes in the expression levels of the insulin-like growth factor 1 (IGF-1) gene have been associated with increased risk and aggressiveness of breast cancer. The IGF-1 gene encodes the IGF-1 peptide that is present in most human tissues, as in the normal and neoplastic mammary gland. Here, we conducted a systematic review to investigate the influence of IGF-1 gene expression levels in women with breast cancer.Methods: PubMed, Scopus, and Web of Science databases were searched for relevant studies published between February 2 and May 15, 2019, using inclusion and exclusion criteria in accordance with PRISMA guidelines. We analyzed the studies to find association between IGF-1gene expression and breast cancer.Results: A growing number of studies in women with breast cancer support, with controversial results, the influence of IGF-1 gene expression levels on clinical-pathological factors, disease-free survival, overall survival, and resistance to tamoxifen.Conclusions: Therefore, the elucidation of IGF-1 gene expression patterns through further studies may enable the characterization of women at high risk for breast cancer, as well as the development of effective prognostic and therapeutic strategies.

scholarly journals The Effect of Eight Weeks of Training on Positive and Negative Slopes with Royal Jelly Consumption on MGMT and ATPase Gene Expression Levels in the Hippocampus Tissue of Trimethyltin-Induced Alzheimer’s Rats

2021 ◽  
Vol In Press (In Press) ◽  
Author(s):  
Zahra Giti ◽  
Abdolali Banaeifar ◽  
Sajad Arshadi ◽  
Mohammad Ali Azarbayjani
Keyword(s):  
Gene Expression ◽  
Royal Jelly ◽  
Interactive Effect ◽  
Negative Slope ◽  
Common Disease ◽  
Positive Slope ◽  
Expression Levels ◽  
Atpase Gene ◽  
Gene Expression Levels

Background: Alzheimer’s disease (AD) is a common disease in the elderly that is associated with impaired metabolism and biology of the hippocampus. Although the role of exercise and natural antioxidants in improving the disease has been reported, the role of muscle contraction-related physical activity along with royal jelly (RJ) consumption is not yet well understood. Objectives: This study aimed to investigate the effect of eight weeks of training on positive slope (ETPS) and negative slope (ETNS) with royal jelly (RJ) consumption on O-6-methylguanine DNA methyltransferase (MGMT) and ATPase gene expression levels in the hippocampus tissue of trimethyltin (TMT)-induced AD rats. Methods: In this experimental trial, 36 male Sprague-Dawley AD rats (induced with 8 mg/kg TMT) were divided into (1) control + normal saline/royal jelly solvent) (Sh); (2) ETPS; (3) ETNS; (4) ETPS + RJ; (5) ETNS + RJ, and (6) RJ groups. Six rats were placed in the healthy control (HC) group. Then the training groups trained on ( + 15 and -15) slopes for eight weeks, five sessions per week, and each session lasted 60 minutes at a speed of 16 m/min. The royal jelly (RJ) groups received 100 mg/kg royal jelly per day by intraperitoneal injection. Results: ETNS, ETPS, ETPS + RJ, and ETNS + RJ increased MGMT gene expression (P ≥ 0.05). ETPS and ETPS + RJ also increased ATPase gene expression (P ≥ 0.05). However, RJ had no significant effect on increasing MGMT and ATPase gene expression in the hippocampus tissue of AD rats (P ≥ 0.05). Conclusions: It seems that the improvement of DNA damage markers and energy levels depends on the type of contraction. Although training on positive and negative slopes with royal jelly consumption has an interactive effect on DNA repair markers, training on a positive slope and royal jelly consumption has an interactive effect on ATPase gene expression.

scholarly journals Reference gene selection for qRT-PCR analyses of luffa (Luffa cylindrica) plants under abiotic stress conditions

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Min-dong Chen ◽  
Bin Wang ◽  
Yong-ping Li ◽  
Mei-juan Zeng ◽  
Jian-ting Liu ◽  
...  
Keyword(s):  
Gene Expression ◽  
Reference Gene ◽  
Reference Genes ◽  
Gene Selection ◽  
Expression Patterns ◽  
Suitable Reference Gene ◽  
Expression Levels ◽  
Qrt Pcr ◽  
Suitable Reference ◽  
Gene Expression Levels

AbstractSelecting suitable internal reference genes is an important prerequisite for the application of quantitative real-time PCR (qRT-PCR). However, no systematic studies have been conducted on reference genes in luffa. In this study, seven reference genes were selected, and their expression levels in luffa plants exposed to various simulated abiotic stresses [i.e., cold, drought, heat, salt, H2O2, and abscisic acid (ABA) treatments] were analyzed by qRT-PCR. The stability of the reference gene expression levels was validated using the geNorm, NormFinder, BestKeeper, and RefFinder algorithms. The results indicated that EF-1α was the most stably expressed and suitable reference gene overall and for the heat, cold, and ABA treatments. Additionally, UBQ expression was stable following the salt treatment, whereas TUB was identified as a suitable reference gene for H2O2 and drought treatments. The reliability of the selected reference genes was verified by analyzing the expression of copper/zinc superoxide dismutase (Cu/Zn-SOD) gene in luffa. When the most unstable reference genes were used for data normalizations, the resulting expression patterns had obvious biases when compared with the expression patterns for the most ideal reference genes used alone or combined. These results will be conducive to more accurate quantification of gene expression levels in luffa.

scholarly journals Low Zip 4 gene expression levels in RPMI - 8226 and ARH - 77 cell lines support the possible role of zip 4 transporter protein in plasma cell tumorogenesis

2013 ◽  
Vol 35 (1) ◽  
pp. 9-13
Author(s):  
Zehra Dilşad Çoban ◽  
Deniz Torun ◽  
Ferit Avcu ◽  
Ali Uğur Ural ◽  
Erhan Parıltay ◽  
...  
Keyword(s):  
Gene Expression ◽  
Cell Lines ◽  
Plasma Cell ◽  
Expression Levels ◽  
Transporter Protein ◽  
Rpmi 8226 ◽  
Gene Expression Levels

IL-10 deficiency protects hamsters from Leptospira infection

2021 ◽  
Author(s):  
Xufeng Xie ◽  
Tianbao Lv ◽  
Dianjun Wu ◽  
Haozhe Shi ◽  
Shilei Zhang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Survival Rate ◽  
Zoonotic Disease ◽  
Protective Effects ◽  
Subclinical Infection ◽  
Expression Levels ◽  
Tnf Α ◽  
Gene Expression Levels

Leptospirosis is a globally spread zoonotic disease with outcomes ranging from subclinical infection to fatal Weil syndrome. In addition to antibiotics, some immune activators have shown protective effects against leptospirosis. However, the unclear relationship between Leptospira and cytokines, has limited the development of antileptospiral immunomodulators. In this study, the particular role of IL-10 in leptospirosis was explored by using IL-10 defective (IL-10 -/- ) hamsters. After Leptospira infection, an improved survival rate, reduced leptospiral burden and alleviation of organ lesions were found in IL-10 -/- hamsters compared with WT hamsters. In addition, the gene expression levels of IL-1β, IL-6 and TNF-α and the NO level were higher in IL-10 -/- hamsters than in WT hamsters. Our results indicate that IL-10 deficiency protects hamsters from Leptospira infection.

Abstract 12423: Normoxic Therapy Attenuated Oxidative Stress Related mRNA Gene Expressions in a Post-Cardiac Arrest Rat Model

Circulation ◽  
2021 ◽  
Vol 144 (Suppl_2) ◽  
Author(s):  
Tomoaki Aoki ◽  
Koichiro Shinozaki ◽  
Yu Okuma ◽  
Kei Hayashida ◽  
Ryosuke Takegawa ◽  
...  
Keyword(s):  
Oxidative Stress ◽  
Gene Expression ◽  
Cardiac Arrest ◽  
Signaling Pathways ◽  
Expression Patterns ◽  
Expression Levels ◽  
Mrna Gene ◽  
The Brain ◽  
Mrna Gene Expression ◽  
Gene Expression Levels

Objective: We recently reported that post-resuscitation normoxic therapy attenuates oxidative stress in multiple organs and improves post-cardiac arrest (CA) organ injury, oxygen metabolism, and survival. Yet, detailed mechanisms of gene expression patterns and signaling pathways mitigated by normoxic therapy have not been elucidated. Therefore, we assessed post-resuscitation normoxic therapy-modified gene expression of oxidative stress-related signaling molecules. Methods: Rats were resuscitated from 10 minutes of asphyxial CA and divided into 2 groups: those that inhaled 100% supplemental O 2 (CA-FIO2 1.0) and those that inhaled 30% supplemental O 2 (CA-FIO2 0.3). Control groups were also prepared for comparison (control-FIO2 1.0, control-FIO2 0.3). At 2 hours after resuscitation, brain and heart tissues were collected, and mRNA purifications followed by real-time PCR measurements were performed to compare gene expression of hyperoxia-induced inflammatory and apoptosis-related signaling pathways amongst these groups. Results: In the brain, relative IL-1 beta mRNA gene expression levels, which represent inflammatory signaling pathways, increased post-CA (8.1±2.3 in CA-FIO2 1.0 and 1.0±0.4 in control-FIO2 0.3, p<0.05), but were significantly attenuated by normoxic therapy (2.3±0.2 in CA-FIO2 0.3, p<0.05). Likewise, normoxic therapy significantly reduced oxidative stress-induced inflammatory (NFKB1, TGFB1, MAPK14, TRAF6) and apoptosis-related (BAX, EGF) mRNA gene expression levels in the brain, whereas no statistical differences were detected in the heart. Conclusions: Post-CA normoxic therapy significantly attenuated the gene expression of oxidative stress-induced inflammation and apoptosis in the brain, while there were no remarkable changes in the heart. Therefore, it is inferred that the heart is more tolerant to hyperoxic injury compared to the brain.

scholarly journals Differential Expression of MicroRNAs in Silent and Functioning Corticotroph Tumors

2020 ◽  
Vol 9 (6) ◽  
pp. 1838
Author(s):  
Araceli García-Martínez ◽  
Antonio C. Fuentes-Fayos ◽  
Carmen Fajardo ◽  
Cristina Lamas ◽  
Rosa Cámara ◽  
...  
Keyword(s):  
Gene Expression ◽  
Transcription Factor ◽  
Transcription Factors ◽  
Potential Role ◽  
Therapeutic Option ◽  
Pharmacological Treatments ◽  
Expression Levels ◽  
Qrt Pcr ◽  
Gene Expression Levels

The potential role of miRNAs in the silencing mechanisms of pituitary neuroendocrine tumors (PitNETs) has not been addressed. The aim of the present study was to evaluate the expression levels and the potential associated role of some miRNAs, pathways, and transcription factors in the silencing mechanisms of corticotroph tumors (CTs). Accordingly, the expression of miR-375, miR-383, miR-488, miR-200a and miR-103; of PKA, MAP3K8, MEK, MAPK3, NGFIB, NURR1, PITX1, and STAT3 were analyzed via qRT-PCR in 23 silent and 24 functioning CTs. miR-200a and miR-103 showed significantly higher expression in silent than in functioning CTs, even after eliminating the bias of tumor size, therefore enabling the differentiation between the two variants. Additionally, miR-383 correlated negatively with TBX19 in silent CTs, a transcription factor related with the processing of POMC that can participate in the silencing mechanisms of CTs. Finally, the gene expression levels of miR-488, miR-200a, and miR-103 were significantly higher in macroadenomas (functioning and silent) than in microadenomas. The evidence from this study indicates that miRNAs could be involved in the pathophysiology of CTs. The translational implications of these findings suggest that pharmacological treatments specifically targeting these miRNAs could become a promising therapeutic option for these patients.

scholarly journals Association of the Adipokines Chemerin, Apelin, Vaspin and Omentin and Their Functional Genetic Variants with Rheumatoid Arthritis

2021 ◽  
Vol 11 (10) ◽  
pp. 976
Author(s):  
Alaa S. Wahba ◽  
Maha E. Ibrahim ◽  
Dina M. Abo-elmatty ◽  
Eman T. Mehanna
Keyword(s):  
Rheumatoid Arthritis ◽  
Gene Expression ◽  
Genetic Variants ◽  
Serum Levels ◽  
Expression Levels ◽  
Protein Levels ◽  
Egyptian Patients ◽  
Gene Expression Levels ◽  
Increased Susceptibility

Adipokines were shown to exert crucial roles in rheumatic diseases. This study aimed to assess the role of chemerin, apelin, vaspin, and omentin adipokines and their genetic variants rs17173608, rs2235306, rs2236242, and rs2274907, respectively, in rheumatoid arthritis (RA) pathogenesis in Egyptian patients. A total of 150 RA patients and 150 healthy individuals were recruited. Blood samples were collected and used for genotyping. Serum was separated and used for expression analysis by quantitative PCR, and various biochemical markers determination by ELISA. Serum protein levels of chemerin and vaspin, as well as their gene expression levels were higher, while those of apelin and omentin were lower in RA patients and were associated with most of RA clinical and laboratory characteristics. G allele of chemerin rs17173608, T allele of vaspin rs2236242, and T allele of omentin rs2274907 were more frequent in RA patients. Serum levels and gene expression levels of chemerin in GG genotype carriers and vaspin in TT genotype group were significantly higher, while those of omentin in TT genotype carriers were significantly lower than RA patients with other genotypes. There was no association between apelin rs2235306 and RA. Chemerin rs17173608, vaspin rs2236242, and omentin rs2274907 polymorphisms were associated with increased susceptibility to RA.

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