scholarly journals Correlation of mRNA Expression and Protein Abundance Affected by Multiple Sequence Features Related to Translational Efficiency inDesulfovibrio vulgaris: A Quantitative Analysis

Genetics ◽  
2006 ◽  
Vol 174 (4) ◽  
pp. 2229-2243 ◽  
Author(s):  
Lei Nie ◽  
Gang Wu ◽  
Weiwen Zhang
Keyword(s):  
Quantitative Analysis ◽  
Mrna Expression ◽  
Translational Efficiency ◽  
Protein Abundance ◽  
Multiple Sequence ◽  
Sequence Features

scholarly journals PredNTS: Improved and Robust Prediction of Nitrotyrosine Sites by Integrating Multiple Sequence Features

2021 ◽  
Vol 22 (5) ◽  
pp. 2704
Author(s):  
Andi Nur Nilamyani ◽  
Firda Nurul Auliah ◽  
Mohammad Ali Moni ◽  
Watshara Shoombuatong ◽  
Md Mehedi Hasan ◽  
...  
Keyword(s):  
Machine Learning ◽  
Random Forest ◽  
Web Application ◽  
Computational Prediction ◽  
Vital Role ◽  
Machine Learning Algorithms ◽  
Recursive Feature Elimination ◽  
Post Translational Modification ◽  
Multiple Sequence ◽  
Sequence Features

Nitrotyrosine, which is generated by numerous reactive nitrogen species, is a type of protein post-translational modification. Identification of site-specific nitration modification on tyrosine is a prerequisite to understanding the molecular function of nitrated proteins. Thanks to the progress of machine learning, computational prediction can play a vital role before the biological experimentation. Herein, we developed a computational predictor PredNTS by integrating multiple sequence features including K-mer, composition of k-spaced amino acid pairs (CKSAAP), AAindex, and binary encoding schemes. The important features were selected by the recursive feature elimination approach using a random forest classifier. Finally, we linearly combined the successive random forest (RF) probability scores generated by the different, single encoding-employing RF models. The resultant PredNTS predictor achieved an area under a curve (AUC) of 0.910 using five-fold cross validation. It outperformed the existing predictors on a comprehensive and independent dataset. Furthermore, we investigated several machine learning algorithms to demonstrate the superiority of the employed RF algorithm. The PredNTS is a useful computational resource for the prediction of nitrotyrosine sites. The web-application with the curated datasets of the PredNTS is publicly available.

scholarly journals Effect of thyroid hormone on the postnatal renal expression of NHE8

2008 ◽  
Vol 294 (1) ◽  
pp. F198-F204 ◽  
Author(s):  
Jyothsna Gattineni ◽  
David Sas ◽  
Amit Dagan ◽  
Vangipuram Dwarakanath ◽  
Michel Baum
Keyword(s):  
Thyroid Hormone ◽  
Mrna Expression ◽  
Rat Kidney ◽  
Surface Expression ◽  
Protein Abundance ◽  
Adult Rats ◽  
Dependent Rate ◽  
Normal Rat ◽  
Acid Load ◽  
Actin Protein

We previously demonstrated that there are developmental changes in proximal tubule Na+/H+ exchanger (NHE) activity. There is a maturational increase in postnatal brush-border membrane (BBM) vesicle NHE3 protein abundance and decrease in NHE8 protein abundance. The purpose of this study was to determine whether thyroid hormone plays a role in the rat renal maturational isoform switch from NHE8 to NHE3 and whether thyroid hormone regulates NHE8. Administration of thyroid hormone to neonatal rats, before the normal postnatal increase in serum thyroid hormone levels at 3 wk of age, resulted in a premature increase in NHE3/β-actin BBM protein abundance and mRNA abundance. Thyroid hormone also caused a premature decrease in BBM NHE8/β-actin protein abundance, whereas there was no change in mRNA expression (standardized to 28s). Rats made hypothyroid from birth were studied at 28 days, after the normal maturational increase in thyroid hormone. In these hypothyroid adult rats, the maturational increase in BBM NHE3 protein abundance and NHE3 mRNA expression was prevented. In contrast, the developmental decrease in BBM NHE8 protein abundance was prevented in hypothyroid adults, but mRNA expression was unchanged in hypothyroid rats. To determine whether the effect of thyroid hormone was due to a direct epithelial effect, we studied normal rat kidney cells in culture. We recently showed that this cell line expresses NHE8, but does not express NHE3. Thyroid hormone caused a decrease in surface expression of NHE8, determined by biotinylation, but total cellular abundance remained unchanged. NHE8 activity, measured as the sodium-dependent rate of intracellular pH recovery from an acid load, was less with thyroid treatment than control. In conclusion, thyroid hormone plays a potential role in the developmental isoform change from NHE8 to NHE3 and decreases NHE8 activity.

Regulation of AQP6 mRNA and protein expression in rats in response to altered acid-base or water balance

2000 ◽  
Vol 279 (6) ◽  
pp. F1014-F1026 ◽  
Author(s):  
Dominique Promeneur ◽  
Tae-Hwan Kwon ◽  
Masato Yasui ◽  
Gheun-Ho Kim ◽  
Jørgen Frøkiær ◽  
...  
Keyword(s):  
Water Balance ◽  
Mrna Expression ◽  
Water Intake ◽  
Collecting Duct ◽  
Free Access ◽  
Protein Abundance ◽  
Acid Base ◽  
Urine Ph ◽  
Daily Water Intake ◽  
Acid Load

In the rat, aquaporin-6 (AQP6) is mainly localized in intercalated cells (ICs) in collecting ducts, where it is exclusively associated with intracellular vesicles. In this study, we examined whether AQP6 protein and mRNA expression were regulated in the inner medulla or inner stripe of the outer medulla. Rats treated with dietary alkali or acid load for 7 days with a fixed daily water intake revealed appropriate changes in urine pH but unchanged urine output. AQP6 protein and mRNA abundance were increased in alkali-loaded rats (187 ± 18 and 151 ± 17% of control, respectively), whereas no changes were observed in acid-loaded rats. Immunohistochemistry revealed increased IC AQP6 labeling in alkali-loaded rats but not in acid-loaded rats. In contrast, administration of NH4Cl in the drinking water for 2 wk (free access to water) revealed a significant increase in AQP6 protein abundance (194 ± 9% of control), but this was associated with increased water intake. Combined, this suggests that AQP6 expression was not affected by acid loading per se but rather was in response to changes in water intake. Consistent with this, water loading for 48 h was associated with increased AQP6 protein abundance, compared with thirsted rats. Moreover, rats with lithium-induced nephrogenic diabetes insipidus had a threefold increase in both AQP6 protein and mRNA expression. Overall, these results suggest that AQP6 expression in collecting duct ICs is regulated by altered acid/alkali load or water balance. Thus AQP6 may contribute to maintenance of acid-base homeostasis and water balance.

Quantitative Analysis of Cytokine mRNA Expression in Hearts from Patients with Nonischemic Dilated Cardiomyopathy (DCM)

2003 ◽  
Vol 18 ◽  
pp. S101-S108 ◽  
Author(s):  
Akira Ukimura ◽  
Fumio Terasaki ◽  
Shigekazu Fujioka ◽  
Hirofumi Deguchi ◽  
Yasushi Kitaura ◽  
...  
Keyword(s):  
Quantitative Analysis ◽  
Dilated Cardiomyopathy ◽  
Mrna Expression ◽  
Cytokine Mrna ◽  
Cytokine Mrna Expression ◽  
Nonischemic Dilated Cardiomyopathy

scholarly journals Multidimensional quantitative analysis of mRNA expression within intact vertebrate embryos

Development ◽  
2018 ◽  
Vol 145 (1) ◽  
pp. dev156869 ◽  
Author(s):  
Vikas Trivedi ◽  
Harry M. T. Choi ◽  
Scott E. Fraser ◽  
Niles A. Pierce
Keyword(s):  
Quantitative Analysis ◽  
Mrna Expression ◽  
Vertebrate Embryos

scholarly journals Modulation of Mucin (MUC2, MUC5AC and MUC5B) mRNA Expression and Protein Production and Secretion in Caco-2/HT29-MTX Co-Cultures Following Exposure to Individual and Combined Aflatoxin M1 and Ochratoxin A

Toxins ◽  
2019 ◽  
Vol 11 (2) ◽  
pp. 132 ◽  
Author(s):  
Xin Huang ◽  
Yanan Gao ◽  
Songli Li ◽  
Chenqing Wu ◽  
Jiaqi Wang ◽  
...  
Keyword(s):  
Cell Viability ◽  
Mrna Expression ◽  
Ochratoxin A ◽  
Protein Production ◽  
Interactive Effects ◽  
Intestinal Cell ◽  
Aflatoxin M1 ◽  
Protein Abundance ◽  
Mucin Production ◽  
Intestinal Mucin

Aflatoxin M1 (AFM1) and ochratoxin A (OTA), which widely coexist in milk, may pose a serious threat to human health. Mucin is a major component of the intestinal mucus layer, which plays an important role in maintaining intestinal mucosal homeostasis. However, the effect of mycotoxins AFM1 and OTA on intestinal mucin production is still not clear. This study aimed to investigate individual and interactive effects of mycotoxins AFM1 and OTA on the intestinal barrier and the mRNA expression of intestinal mucin (MUC2, MUC5AC and MUC5B) and on protein production in Caco-2/HT29-MTX cultures after 48 h of exposure. Our results show that individual mycotoxins and their mixtures significantly reduced intestinal cell viability and transepithelial electrical resistance (TEER) values, as well as significantly altered intestinal mucin mRNA expression and protein abundance. Moreover, OTA showed toxicity similar to AFM1 in cell viability and TEER value at the same concentration. When the two mycotoxins acted in combination, the synergistic effects observed in the assessment of cell viability and protein abundance in all mono- and co-cultures. In general, this study provides evidence that AFM1 and OTA can damage the intestine, and it contributes to optimized maximum permissible limits of mycotoxins in milk.

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