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lipid modification and sequencing

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https://www.readbyqxmd.com/read/27930681/transcriptomic-changes-in-liver-of-young-bulls-caused-by-diets-low-in-mineral-and-protein-contents-and-supplemented-with-n-3-fatty-acids-and-conjugated-linoleic-acid
#1
Sara Pegolo, Alessio Cecchinato, Núria Mach, Massimiliano Babbucci, Marianna Pauletto, Luca Bargelloni, Stefano Schiavon, Giovanni Bittante
The aim of the present study was to identify transcriptional modifications and regulatory networks accounting for physiological and metabolic responses to specific nutrients in the liver of young Belgian Blue × Holstein bulls using RNA-sequencing. A larger trial has been carried out in which animals were fed with different diets: 1] a conventional diet; 2] a low-protein/low-mineral diet (low-impact diet) and 3] a diet enriched in n-3 fatty acids (FAs), conjugated linoleic acid (CLA) and vitamin E (nutraceutical diet)...
2016: PloS One
https://www.readbyqxmd.com/read/27899336/complete-genome-sequence-of-stenotrophomonas-sp-kacc-91585-an-efficient-bacterium-for-unsaturated-fatty-acid-hydration
#2
Kyoung-Rok Kim, Woo-Ri Kang, Deok-Kun Oh
Hydroxy fatty acids (HFAs) such as 10-hydroxystearic acid (10-HSA) and 10-hydroxy-12(Z)-octadecenoic acid (10-HOD), which are similar to ricinoleic acid, are important starting materials and intermediates for the industrial manufacture of many commodities. Stenotrophomonas sp. KACC 91585, which was isolated from lake sediment, is an efficient bacterium for unsaturated fatty acid hydration that produces 10-HSA and 10-HOD from oleic acid and linoleic acid, respectively, with high conversion rates. The complete genome of this strain is 4,541,729bp with 63...
November 27, 2016: Journal of Biotechnology
https://www.readbyqxmd.com/read/27870114/the-molecular-genetics-of-autosomal-recessive-nonsyndromic-intellectual-disability-a-mutational-continuum-and-future-recommendations
#3
REVIEW
Muzammil Ahmad Khan, Saadullah Khan, Christian Windpassinger, Muhammad Badar, Zafar Nawaz, Ramzi M Mohammad
Intellectual disability (ID) is a clinical manifestation of the central nervous system without any major dysmorphologies of the brain. Biologically it affects learning capabilities, memory, and cognitive functioning. The basic defining features of ID are characterized by IQ<70, age of onset before 18 years, and impairment of at least two of the adaptive skills. Clinically it is classified in a syndromic (with additional abnormalities) and a nonsyndromic form (with only cognitive impairment). The study of nonsyndromic intellectual disability (NSID) can best explain the pathophysiology of cognition, intelligence and memory...
November 2016: Annals of Human Genetics
https://www.readbyqxmd.com/read/27867388/transcriptomic-changes-of-drought-tolerant-and-sensitive-banana-cultivars-exposed-to-drought-stress
#4
Muthusamy Muthusamy, Subbaraya Uma, Suthanthiram Backiyarani, Marimuthu Somasundaram Saraswathi, Arumugam Chandrasekar
In banana, drought responsive gene expression profiles of drought-tolerant and sensitive genotypes remain largely unexplored. In this research, the transcriptome of drought-tolerant banana cultivar (Saba, ABB genome) and sensitive cultivar (Grand Naine, AAA genome) was monitored using mRNA-Seq under control and drought stress condition. A total of 162.36 million reads from tolerant and 126.58 million reads from sensitive libraries were produced and mapped onto the Musa acuminata genome sequence and assembled into 23,096 and 23,079 unigenes...
2016: Frontiers in Plant Science
https://www.readbyqxmd.com/read/27860427/the-role-of-adipoq-methylation-in-experimental-non-alcoholic-fatty-liver-disease
#5
Wen Ji Chen, Bing Cai, Hui Ting Chen, Chuang Yu Cao, Yan Lei Du, Yu Yuan Li, Yu Qiang Nie, Yong Jian Zhou
AIM: To investigate the role of adiponectin gene (ADIPOQ) DNA methylation and curcumin in the intervention of non-alcoholic fatty liver disease (NAFLD). METHODS: Twenty-four Sprague-Dawley (SD) rats were divided into three groups: normal, NAFLD and curcumin groups. The genetic and epigenetic features of each rat were tested. RT-PCR and western blot were used to quantify the ADIPOQ mRNA and protein level respectively. Bisulfite sequencing PCR (BSP) was used to detect the extent of methylation in rat livers...
November 9, 2016: Journal of Digestive Diseases
https://www.readbyqxmd.com/read/27858497/high-fat-diet-and-exercise-lead-to-a-disrupted-and-pathogenic-dna-methylome-in-mouse-liver
#6
Dan Zhou, Ryan A Hlady, Marissa J Schafer, Thomas A White, Chen Liu, Jeong-Hyeon Choi, Jordan D Miller, Lewis R Roberts, Nathan K LeBrasseur, Keith D Robertson
High-fat diet consumption and sedentary life style elevates risk for obesity, non-alcoholic fatty liver disease, and cancer. Exercise training conveys health benefits in populations with or without these chronic conditions. Diet and exercise regulate gene expression by mediating epigenetic mechanisms in many tissues; however, such effects are poorly documented in the liver, a central metabolic organ. To dissect the consequences of diet and exercise on the liver epigenome, we measured DNA methylation, using reduced representation bisulfite sequencing, and transcription, using RNA-seq, in mice maintained on a fast food diet with sedentary lifestyle or exercise, compared to control diet with and without exercise...
November 18, 2016: Epigenetics: Official Journal of the DNA Methylation Society
https://www.readbyqxmd.com/read/27806444/engineering-specific-chemical-modification-sites-into-a-collagen-like-protein-from-streptococcus-pyogenes
#7
Violet Stoichevska, Yong Y Peng, Aditya V Vashi, Jerome A Werkmeister, Geoff J Dumsday, John A M Ramshaw
Recombinant bacterial collagens provide a new opportunity for safe biomedical materials. They are readily expressed in E. coli in good yield and can be readily purified by simple approaches. However, recombinant proteins are limited in that direct secondary modification during expression is generally not easily achieved. Thus, inclusion of unusual amino acids, cyclic peptides, sugars, lipids and other complex functions generally needs to be achieved chemically after synthesis and extraction. In the present study we have illustrated that bacterial collagens that have had their sequences modified to include cysteine residue(s), which are not normally present in bacterial collagen-like sequences, enable a range of specific chemical modification reactions to be produced...
November 2, 2016: Journal of Biomedical Materials Research. Part A
https://www.readbyqxmd.com/read/27706605/in-silico-characterization-of-1-2-diacylglycerol-cholinephosphotransferase-and-lysophospha-tidylcholine-acyltransferase-genes-in-glycine-max-l-merrill
#8
C S Sousa, B A Barros, D Barh, P Ghosh, V Azevedo, E G Barros, M A Moreira
The enzymes 1,2-diacylglycerol cholinephosphotrans-ferase (CPT) and lysophosphatidylcholine acyltransferase (LPCAT) are important in lipid metabolism in soybean seeds. Thus, understand-ing the genes that encode these enzymes may enable their modification and aid the improvement of soybean oil quality. In soybean, the genes encoding these enzymes have not been completely described; there-fore, this study aimed to identify, characterize, and analyze the in silico expression of these genes in soybean. We identified two gene models encoding CPT and two gene models encoding LPCAT, one of which presented an alternative transcript...
August 26, 2016: Genetics and Molecular Research: GMR
https://www.readbyqxmd.com/read/27697616/lipid-metabolism-in-rhodnius-prolixus-lessons-from-the-genome
#9
David Majerowicz, Gustavo M Calderón-Fernández, Michele Alves-Bezerra, Iron F De Paula, Lívia S Cardoso, M Patricia Juárez, Georgia C Atella, Katia C Gondim
The kissing bug Rhodnius prolixus is both an important vector of Chagas' disease and an interesting model for investigation into the field of physiology, including lipid metabolism. The publication of this insect genome will bring a huge amount of new molecular biology data to be used in future experiments. Although this work represents a promising scenario, a preliminary analysis of the sequence data is necessary to identify and annotate the genes involved in lipid metabolism. Here, we used bioinformatics tools and gene expression analysis to explore genes from different genes families and pathways, including genes for fat breakdown, as lipases and phospholipases, and enzymes from β-oxidation, fatty acid metabolism, and acyl-CoA and glycerolipid synthesis...
September 30, 2016: Gene
https://www.readbyqxmd.com/read/27695101/transcriptome-dynamics-during-maize-endosperm-development
#10
Jianzhou Qu, Chuang Ma, Jiaojiao Feng, Shutu Xu, Lei Wang, Feifei Li, Yibo Li, Renhe Zhang, Xinghua Zhang, Jiquan Xue, Dongwei Guo
The endosperm is a major organ of the seed that plays vital roles in determining seed weight and quality. However, genome-wide transcriptome patterns throughout maize endosperm development have not been comprehensively investigated to date. Accordingly, we performed a high-throughput RNA sequencing (RNA-seq) analysis of the maize endosperm transcriptome at 5, 10, 15 and 20 days after pollination (DAP). We found that more than 11,000 protein-coding genes underwent alternative splicing (AS) events during the four developmental stages studied...
2016: PloS One
https://www.readbyqxmd.com/read/27682829/transcriptome-analysis-of-the-response-to-nacl-in-suaeda-maritima-provides-an-insight-into-salt-tolerance-mechanisms-in-halophytes
#11
Sachin Ashruba Gharat, Shaifaly Parmar, Subodh Tambat, Madavan Vasudevan, Birendra Prasad Shaw
Although salt tolerance is a feature representative of halophytes, most studies on this topic in plants have been conducted on glycophytes. Transcriptome profiles are also available for only a limited number of halophytes. Hence, the present study was conducted to understand the molecular basis of salt tolerance through the transcriptome profiling of the halophyte Suaeda maritima, which is an emerging plant model for research on salt tolerance. Illumina sequencing revealed 72,588 clustered transcripts, including 27,434 that were annotated using BLASTX...
2016: PloS One
https://www.readbyqxmd.com/read/27672697/chemical-synthesis-of-peptides-containing-site-specific-advanced-glycation-endproducts
#12
Harveen Kaur, Meder Kamalov, Margaret A Brimble
In nature, proteins, lipids, and nucleic acids can nonenzymatically react with sugars and sugar degradation products to give rise to a diverse range of modifications, known as advanced glycation endproducts (AGEs). These AGEs typically occur at lysine and arginine residues of long-lived proteins, such as collagen, and can modify the structure and function of the native protein. AGEs accumulate during the normal aging process, and AGE formation is dramatically accelerated with diabetes. AGEs have also been implicated in a wide range of debilitating conditions including cardiovascular, renal failure, and neurodegenerative diseases...
October 18, 2016: Accounts of Chemical Research
https://www.readbyqxmd.com/read/27669744/de-novo-transcriptomic-analysis-of-chlorella-sorokiniana-reveals-differential-genes-expression-in-photosynthetic-carbon-fixation-and-lipid-production
#13
Lin Li, Guoqiang Zhang, Qinhong Wang
BACKGROUND: Microalgae, which can absorb carbon dioxide and then transform it into lipid, are promising candidates to produce renewable energy, especially biodiesel. The paucity of genomic information, however, limits the development of genome-based genetic modification to improve lipid production in many microalgae. Here, we describe the de novo sequencing, transcriptome assembly, annotation and differential expression analysis for Chlorella sorokiniana cultivated in different conditions to reveal the change of genes expression associated with lipid accumulation and photosynthetic carbon fixation...
September 26, 2016: BMC Microbiology
https://www.readbyqxmd.com/read/27594860/comparative-transcriptome-analysis-of-primary-roots-of-brassica-napus-seedlings-with-extremely-different-primary-root-lengths-using-rna-sequencing
#14
Xiaoling Dun, Zhangsheng Tao, Jie Wang, Xinfa Wang, Guihua Liu, Hanzhong Wang
Primary root (PR) development is a crucial developmental process that is essential for plant survival. The elucidation of the PR transcriptome provides insight into the genetic mechanism controlling PR development in crops. In this study, we performed a comparative transcriptome analysis to investigate the genome-wide gene expression profiles of the seedling PRs of four Brassica napus genotypes that were divided into two groups, short group (D43 and D61), and long group (D69 and D72), according to their extremely different primary root lengths (PRLs)...
2016: Frontiers in Plant Science
https://www.readbyqxmd.com/read/27497512/lipases-from-the-genus-rhizopus-characteristics-expression-protein-engineering-and-application
#15
REVIEW
Xiao-Wei Yu, Yan Xu, Rong Xiao
Lipases are versatile catalysts that hydrolyze ester bonds of water-insoluble glycerides or carry out reversible reactions at the water/lipid interface. The remarkable characteristics of lipases from the genus Rhizopus are their high sn-1,3-positional specificity, enantioselectivity and activity in nonaqueous media, which make them one of the most desirable enzymes for many applications, including lipid modification and biodiesel and chiral organic compound synthesis. sn-1,3-Position-specific Rhizopus lipases are particularly useful for the production of structured triacylglycerols...
August 4, 2016: Progress in Lipid Research
https://www.readbyqxmd.com/read/27476530/common-disease-signatures-from-gene-expression-analysis-in-huntington-s-disease-human-blood-and-brain
#16
Eleni Mina, Willeke van Roon-Mom, Kristina Hettne, Erik van Zwet, Jelle Goeman, Christian Neri, Peter A C 't Hoen, Barend Mons, Marco Roos
BACKGROUND: Huntington's disease (HD) is a devastating brain disorder with no effective treatment or cure available. The scarcity of brain tissue makes it hard to study changes in the brain and impossible to perform longitudinal studies. However, peripheral pathology in HD suggests that it is possible to study the disease using peripheral tissue as a monitoring tool for disease progression and/or efficacy of novel therapies. In this study, we investigated if blood can be used to monitor disease severity and progression in brain...
2016: Orphanet Journal of Rare Diseases
https://www.readbyqxmd.com/read/27446030/sterol-synthesis-in-diverse-bacteria
#17
Jeremy H Wei, Xinchi Yin, Paula V Welander
Sterols are essential components of eukaryotic cells whose biosynthesis and function has been studied extensively. Sterols are also recognized as the diagenetic precursors of steranes preserved in sedimentary rocks where they can function as geological proxies for eukaryotic organisms and/or aerobic metabolisms and environments. However, production of these lipids is not restricted to the eukaryotic domain as a few bacterial species also synthesize sterols. Phylogenomic studies have identified genes encoding homologs of sterol biosynthesis proteins in the genomes of several additional species, indicating that sterol production may be more widespread in the bacterial domain than previously thought...
2016: Frontiers in Microbiology
https://www.readbyqxmd.com/read/27411307/a-machine-learning-approach-for-predicting-palmitoylation-sites-from-integrated-sequence-based-features
#18
Liqi Li, Qifa Luo, Weidong Xiao, Jinhui Li, Shiwen Zhou, Yongsheng Li, Xiaoqi Zheng, Hua Yang
Palmitoylation is the covalent attachment of lipids to amino acid residues in proteins. As an important form of protein posttranslational modification, it increases the hydrophobicity of proteins, which contributes to the protein transportation, organelle localization, and functions, therefore plays an important role in a variety of cell biological processes. Identification of palmitoylation sites is necessary for understanding protein-protein interaction, protein stability, and activity. Since conventional experimental techniques to determine palmitoylation sites in proteins are both labor intensive and costly, a fast and accurate computational approach to predict palmitoylation sites from protein sequences is in urgent need...
June 14, 2016: Journal of Bioinformatics and Computational Biology
https://www.readbyqxmd.com/read/27407169/protein-lysine-methylation-by-seven-%C3%AE-strand-methyltransferases
#19
REVIEW
Pål Ø Falnes, Magnus E Jakobsson, Erna Davydova, Angela Ho, Jędrzej Małecki
Methylation of biomolecules is a frequent biochemical reaction within the cell, and a plethora of highly specific methyltransferases (MTases) catalyse the transfer of a methyl group from S-adenosylmethionine (AdoMet) to various substrates. The posttranslational methylation of lysine residues, catalysed by numerous lysine (K)-specific protein MTases (KMTs), is a very common and important protein modification, which recently has been subject to intense studies, particularly in the case of histone proteins. The majority of KMTs belong to a class of MTases that share a defining 'SET domain', and these enzymes mostly target lysines in the flexible tails of histones...
July 15, 2016: Biochemical Journal
https://www.readbyqxmd.com/read/27376274/age-specific-lipid-and-fatty-acid-profiles-of-atlantic-salmon-juveniles-in-the-varzuga-river
#20
Svetlana A Murzina, Zinaida A Nefedova, Svetlana N Pekkoeva, Alexey E Veselov, Denis A Efremov, Nina N Nemova
The age-specific lipid and fatty acid profiles of juvenile Atlantic salmon at different ages (0+, 1+, and 2+ years) after hatching from nests located in the mainstream of a large Arctic River, the Varzuga River, and resettling to the favorable Sobachji shoal in autumn before overwinter are herein presented. The contemporary methods of the lipid analysis were used: thin layer chromatography and gas chromatography. The results show that the stability of the regulation of important functions in developing organisms is maintained through structural alterations in lipids...
2016: International Journal of Molecular Sciences
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