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Sarah E Calvo, Olivier Julien, Karl R Clauser, Hongying Shen, Kimberli J Kamer, James A Wells, Vamsi K Mootha
The majority of mitochondrial proteins are encoded in the nuclear genome, translated in the cytoplasm, and directed to the mitochondria by a N-terminal presequence that is cleaved upon import. Recently, N-proteome catalogs have been generated for mitochondria from yeast and from human U937 cells. Here we applied the subtiligase method to determine N-termini for 327 proteins in mitochondria isolated from mouse liver and kidney. Comparative analysis between mitochondrial N-termini from mouse, human, and yeast proteins shows that while presequences are poorly conserved at the sequence level, other presequence properties are extremely conserved including a length of ~20-60aa, a net charge between +3 to +6, and the presence of stabilizing amino acids at the N-termini of mature proteins that follows the N-end rule from bacteria...
January 25, 2017: Molecular & Cellular Proteomics: MCP
Binglei Shen, Qiqi Pan, Yuwei Yang, Yan Gao, Xin Liu, Wei Li, Yunsheng Han, Xue Yuan, Yongli Qu, Zhihui Zhao
MicroRNAs (miRNAs) are small noncoding RNA molecules that involve in various biological functions by regulating the expressions of target genes. In recent years, many researchers have demonstrated that miR-224 played an important role in regulating lipid metabolism. Therefore, in this study, the target genes of miR-224 were verified and the regulatory role of miR-224 was confirmed in lipid metabolism. In this study, bioinformatics methods were used for primarily predicting the target gene of miR-224 and dual-luciferase reporter system was used for further verify the relationship between miR-224 and its target gene...
January 2017: DNA and Cell Biology
Go Tajima, Keiichi Hara, Miyuki Tsumura, Reiko Kagawa, Satoshi Okada, Nobuo Sakura, Ikue Hata, Yosuke Shigematsu, Masao Kobayashi
BACKGROUND: Medium-chain acyl-CoA dehydrogenase (MCAD) deficiency is a representative disorder of fatty acid oxidation and is one of the most prevalent inborn errors of metabolism among Caucasian populations. In Japan, however, it was as late as 2000 when the first patient was found, and enzymatic and genetic evaluation of MCAD deficiency began. METHODS: We measured octanoyl-CoA dehydrogenase activity in lymphocytes of symptomatic children and newborn screening (NBS)-positive subjects who showed elevated levels of C8-acylcarnitine in blood...
December 2016: Molecular Genetics and Metabolism
Ibrahim Tanyalcin, Katrien Stouffs, Dorien Daneels, Carla Al Assaf, Willy Lissens, Anna Jansen, Alexander Gheldof
BACKGROUND: Predict whether a mutation is deleterious based on the custom 3D model of a protein. RESULTS: We have developed MODICT, a mutation prediction tool which is based on per residue RMSD (root mean square deviation) values of superimposed 3D protein models. Our mathematical algorithm was tested for 42 described mutations in multiple genes including renin (REN), beta-tubulin (TUBB2B), biotinidase (BTD), sphingomyelin phosphodiesterase-1 (SMPD1), phenylalanine hydroxylase (PAH) and medium chain Acyl-Coa dehydrogenase (ACADM)...
October 19, 2016: BMC Bioinformatics
Jian-Qiang Tan, Da-Yu Chen, Zhe-Tao Li, Ji-Wei Huang, Ti-Zhen Yan, Ren Cai
Medium- and short-chain acyl-CoA dehydrogenase deficiency is a disorder of fatty acid β-oxidation. Gene mutation prevents medium- and short-chain fatty acids from entry into mitochondria for oxidation, which leads to multiple organ dysfunction. In this study, serum acylcarnitines and the organic acid profile in urea were analyzed in two children whose clinical symptoms were hypoglycemia and metabolic acidosis. Moreover, gene mutations in the two children and their parents were evaluated. One of the patients was a 3-day-old male who was admitted to the hospital due to neonatal asphyxia, sucking weakness, and sleepiness...
October 2016: Zhongguo Dang Dai Er Ke za Zhi, Chinese Journal of Contemporary Pediatrics
Patrick Vancura, Tanja Wolloscheck, Kenkichi Baba, Gianluca Tosini, P Michael Iuvone, Rainer Spessert
The energy metabolism of the retina might comply with daily changes in energy demand and is impaired in diabetic retinopathy-one of the most common causes of blindness in Europe and the USA. The aim of this study was to investigate putative adaptation of energy metabolism in healthy and diabetic retina. Hence expression analysis of metabolic pathway genes was performed using quantitative polymerase chain reaction, semi-quantitative western blot and immunohistochemistry. Transcriptional profiling of key enzymes of energy metabolism identified transcripts of mitochondrial fatty acid β-oxidation enzymes, i...
2016: PloS One
Yuzhi Jia, Hsiang-Chun Chang, Matthew J Schipma, Jing Liu, Varsha Shete, Ning Liu, Tatsuya Sato, Edward B Thorp, Philip M Barger, Yi-Jun Zhu, Navin Viswakarma, Yashpal S Kanwar, Hossein Ardehali, Bayar Thimmapaya, Janardan K Reddy
Mediator, an evolutionarily conserved multi-protein complex consisting of about 30 subunits, is a key component of the polymerase II mediated gene transcription. Germline deletion of the Mediator subunit 1 (Med1) of the Mediator in mice results in mid-gestational embryonic lethality with developmental impairment of multiple organs including heart. Here we show that cardiomyocyte-specific deletion of Med1 in mice (csMed1-/-) during late gestational and early postnatal development by intercrossing Med1fl/fl mice to α-MyHC-Cre transgenic mice results in lethality within 10 days after weaning due to dilated cardiomyopathy-related ventricular dilation and heart failure...
2016: PloS One
Kristi Bentler, Shaohui Zhai, Sara A Elsbecker, Georgianne L Arnold, Barbara K Burton, Jerry Vockley, Cynthia A Cameron, Sally J Hiner, Mathew J Edick, Susan A Berry
INTRODUCTION: There is limited understanding of relationships between genotype, phenotype and other conditions contributing to health in neonates with medium-chain acyl-coenzyme A dehydrogenase deficiency (MCADD) identified through newborn screening. METHODS: Retrospective analysis of comprehensive data from a cohort of 221 newborn-screened subjects identified as affected with MCADD in the Inborn Errors of Metabolism - Information System (IBEM-IS), a long term follow-up database of the Inborn Errors of Metabolism Collaborative, was performed...
September 2016: Molecular Genetics and Metabolism
Alekhya Narravula, Kathryn B Garber, S Hussain Askree, Madhuri Hegde, Patricia L Hall
PURPOSE: As exome and genome sequencing using high-throughput sequencing technologies move rapidly into the diagnostic process, laboratories and clinicians need to develop a strategy for dealing with uncertain findings. A commitment must be made to minimize these findings, and all parties may need to make adjustments to their processes. The information required to reclassify these variants is often available but not communicated to all relevant parties. METHODS: To illustrate these issues, we focused on three well-characterized monogenic, metabolic disorders included in newborn screens: classic galactosemia, caused by GALT variants; phenylketonuria, caused by PAH variants; and medium-chain acyl-CoA dehydrogenase (MCAD) deficiency, caused by ACADM variants...
June 16, 2016: Genetics in Medicine: Official Journal of the American College of Medical Genetics
Mien-Cheng Chen, Jen-Ping Chang, Yu-Sheng Lin, Kuo-Li Pan, Wan-Chun Ho, Wen-Hao Liu, Tzu-Hao Chang, Yao-Kuang Huang, Chih-Yuan Fang, Chien-Jen Chen
BACKGROUND: Differentially expressed genes in the left atria of mitral regurgitation (MR) pigs have been linked to peroxisome proliferator-activated receptor (PPAR) signaling pathway in the KEGG pathway. However, specific genes of the PPAR signaling pathway in the left atria of MR patients have never been explored. METHODS: This study enrolled 15 MR patients with heart failure, 7 patients with aortic valve disease and heart failure, and 6 normal controls. We used PCR assay (84 genes) for PPAR pathway and quantitative RT-PCR to study specific genes of the PPAR pathway in the left atria...
2016: Journal of Translational Medicine
Jiangfei Cheng, Suping Lv, Shangfei Nie, Jing Liu, Shoufang Tong, Ning Kang, Yanyan Xiao, Qiaoxiang Dong, Changjiang Huang, Dongren Yang
Perfluorooctane sulfonate (PFOS), one persistent organic pollutant, has been widely detected in the environment, wildlife and human. Currently few studies have documented the effects of chronic PFOS exposure on lipid metabolism, especially in aquatic organisms. The underlying mechanisms of hepatotoxicity induced by chronic PFOS exposure are still largely unknown. The present study defined the effects of chronic exposure to low level of PFOS on lipid metabolism using zebrafish as a model system. Our findings revealed a severe hepatic steatosis in the liver of males treated with 0...
July 2016: Aquatic Toxicology
Mingda Han, Alexei V Evsikov, Lifeng Zhang, Rosana Lastra-Vicente, Kersti K Linask
Embryonic exposures can increase the risk of congenital cardiac birth defects and adult disease. The present study identifies the predominant pathways modulated by an acute embryonic mouse exposure during gastrulation to lithium or homocysteine that induces cardiac defects. High dose periconceptional folate supplementation normalized development. Microarray bioinformatic analysis of gene expression demonstrated that primarily lipid metabolism is altered after the acute exposures. The lipid-related modulation demonstrated a gender bias with male embryos showing greater number of lipid-related Gene Ontology biological processes altered than in female embryos...
June 2016: Reproductive Toxicology
Keiichi Hara, Go Tajima, Satoshi Okada, Miyuki Tsumura, Reiko Kagawa, Kenichiro Shirao, Yoshinori Ohno, Shin'ichiro Yasunaga, Motoaki Ohtsubo, Ikue Hata, Nobuo Sakura, Yosuke Shigematsu, Yoshihiro Takihara, Masao Kobayashi
BACKGROUND: Since the first case was detected in 2000, there has been a remarkable increase in Japanese patients diagnosed with medium-chain acyl-CoA dehydrogenase (MCAD) deficiency. Genetic analysis has revealed a spectrum of mutations that is quite different from those observed in Caucasian populations. In 2014, Japan initiated nationwide newborn screening (NBS) for MCAD using tandem mass spectrometry (MS/MS). It is an urgent issue to assess the risk of acute metabolic decompensation from the respective novel mutations found thus far...
May 2016: Molecular Genetics and Metabolism
Tahnee Sente, An M Van Berendoncks, Erik Fransen, Christiaan J Vrints, Vicky Y Hoymans
Skeletal muscle metabolic changes are common in patients with chronic heart failure (HF). Previously, we demonstrated a functional skeletal muscle adiponectin resistance in HF patients with reduced left ventricular ejection fraction (HFrEF). We aimed to examine the impact of adiponectin receptor 1 (AdipoR1) deficiency and TNF-α treatment on adiponectin signaling, proliferative capacity, myogenic differentiation, and mitochondrial biogenesis in primary human skeletal muscle cells. Primary cultures of myoblasts and myotubes were initiated from the musculus vastus lateralis of 10 HFrEF patients (left ventricular ejection fraction; 31...
May 1, 2016: American Journal of Physiology. Heart and Circulatory Physiology
Y Zhi, Z Cao, Q H Li, X L Li, Y Sun, T Zhang, Q Zhang
Previous studies have used microarray technology to explore gene expression differences between the atrium and the ventricle. However, selection criteria for the differentially expressed genes (DEGs) based only on either the fold change or the P value in these studies. Here, we aim to further identify the DEGs by setting a P value threshold of <0.05 and a fold change of >2, which may yield more specific gene expression differences between the atrium and the ventricle. Gene expression profiling of the atrial appendages and the ventricular free walls in 13 normal male Sprague Dawley rats were obtained from the Gene Expression Omnibus data base (accession No...
January 29, 2016: Genetics and Molecular Research: GMR
Teri-Louise North, Yoav Ben-Shlomo, Cyrus Cooper, Ian J Deary, John Gallacher, Mika Kivimaki, Meena Kumari, Richard M Martin, Alison Pattie, Avan Aihie Sayer, John M Starr, Andrew Wong, Diana Kuh, Santiago Rodriguez, Ian N M Day
BACKGROUND: Several recessive Mendelian disorders are common in Europeans, including cystic fibrosis (CFTR), medium-chain-acyl-Co-A-dehydrogenase deficiency (ACADM), phenylketonuria (PAH) and alpha 1-antitrypsin deficiency (SERPINA1). METHODS: In a multicohort study of >19,000 older individuals, we investigated the relevant phenotypes in heterozygotes for these genes: lung function (forced expiratory volume in 1 second (FEV1), forced vital capacity (FVC)) for CFTR and SERPINA1; cognitive measures for ACADM and PAH; and physical capability for ACADM, PAH and SERPINA1...
April 2016: Journal of Medical Genetics
Holli M Drendel, Jason E Pike, Katherine Schumacher, Karen Ouyang, Jing Wang, Mary Stuy, Stephen Dlouhy, Shaochun Bai
Medium-chain acyl-CoA dehydrogenase deficiency (MCADD) is an autosomal recessive disorder that leads to a defect in fatty acid oxidation. ACADM is the only candidate gene causing MCAD deficiency. A single nucleotide change, c.985A>G, occurring at exon 11 of the ACADM gene, is the most prevalent mutation. In this study, we report a Caucasian family with multiple MCADD individuals. DNA sequence analysis of the ACADM gene performed in this family revealed that two family members showing mild MCADD symptoms share the same novel change in exon 11, c...
2015: Case Reports in Genetics
Xiaoli Xu, Zhaorong Shi, Jiale Hu, Bo Yuan, Huimin Huang, Hongmei Fang, Xiangyi Yin, Niuyan Nie, Xiaoyue Sheng
The aim of the present study was to identify the potential target biomarkers associated with burn sepsis using microarray. GSE1781 was downloaded from Gene Expression Omnibus and included a collective of three biological replicates for each of the three conditions: Sham‑Sham, Sham‑cecal ligation and puncture (CLP) and Burn‑CLP. Subsequently, limma was applied to screen the differentially expressed genes (DEGs). Additionally, functional annotations were predicted by pathway enrichment. Furthermore, the transcription factors were screened according to the transcriptional regulation from patterns to profiles database...
December 2015: International Journal of Molecular Medicine
Yanqing Liu, Yueqiu Wang, Nailong Yang, Suning Wu, Yanhua Lv, Lili Xu
Postmenopausal osteoporosis (PO) is a common disease in females >50 years of age worldwide and is becoming an increasing burden to society. The present study aimed to assess the molecular mechanism of PO using bioinformatic methods. The gene expression data from patients with PO and normal controls were downloaded from the ArrayExpress database provided by European Bioinformatics Institute. Following the screening of the differentially expressed genes (DEGs) using the Limma package in R language, Kyoto Encyclopedia of Genes and Genomes pathways enrichment analysis was performed using the Database for Annotation, Visualization and Integrated Discovery online tools...
November 2015: Molecular Medicine Reports
Sarah C Grünert, A Wehrle, P Villavicencio-Lorini, E Lausch, B Vetter, K O Schwab, S Tucci, U Spiekerkoetter
BACKGROUND: Medium-chain acyl-CoA dehydrogenase (MCAD) deficiency is the most common disorder of mitochondrial fatty acid β-oxidation and a target disease of newborn screening in many countries. CASE PRESENTATION: We report on two siblings with mild MCAD deficiency associated with a novel splice site mutation in the ACADM gene. The younger sibling was detected by newborn screening, while the older sister was missed, but diagnosed later on by genetic family testing...
2015: BMC Medical Genetics
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