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https://www.readbyqxmd.com/read/28340398/proteomics-analysis-of-maize-zea-mays-l-grain-based-on-itraq-reveals-molecular-mechanisms-of-poor-grain-filling-in-inferior-grains
#1
Tao Yu, Geng Li, Peng Liu, Shuting Dong, Jiwang Zhang, Bin Zhao
In maize, inferior grains (IG) located on the upper part of the ear have poor grain filling process compared to superior grains (SG) located on the middle and lower parts of the ear. This difference limits satisfactory yield and quality; however, the underlying molecular mechanisms remain unknown. Here, using the isobaric tag for relative and absolute quantification (iTRAQ) technology, the proteomes of IG and SG during early and middle grain filling stages were investigated. In total, 4720 proteins were identified in maize grain and 305 differentially accumulated proteins (DiAPs) were detected between IG and SG...
March 11, 2017: Plant Physiology and Biochemistry: PPB
https://www.readbyqxmd.com/read/28340140/lipidomic-profiling-of-endometrial-fluid-in-women-with-ovarian-endometriosis
#2
Francisco Domínguez, Marcos Ferrando, Patricia Díaz-Gimeno, Fernando Quintana, Gemma Fernández, Inés Castells, Carlos Simón
The proteomic content of the endometrial fluid from patients with endometriosis has been investigated, but the lipidomic profile has not been analyzed yet in detail. This study is a comparative untargeted lipidomic analysis of human endometrial fluid obtained from thirty-five patients (12 endometriosis and 23 controls). Global differential lipidomic profile was analyzed in both groups by ultrahigh performance liquid chromatography (UPLC) coupled to mass spectrometry (MS). 123 out of the 457 metabolites identified in the endometrial fluid were found to be significantly differentially expressed between ovarian endometriosis versus controls...
March 18, 2017: Biology of Reproduction
https://www.readbyqxmd.com/read/28339978/ozone-sensitive-arabidopsis-mutants-with-deficiencies-in-photorespiratory-enzymes
#3
Shoko Saji, Srinivas Bathula, Akihiro Kubo, Masanori Tamaoki, Mitsuko Aono, Tomoharu Sano, Kazuo Tobe, Stefan Timm, Hermann Bauwe, Nobuyoshi Nakajima, Hikaru Saji
An ozone-sensitive mutant was isolated from T-DNA-tagged lines of Arabidopsis thaliana. The T-DNA was inserted at a locus on chromosome 3, where two genes encoding glycolate oxidases, GOX1 and GOX2, peroxisomal enzymes involved in photorespiration, reside contiguously. The amounts of the mutant's foliar transcripts for these genes were reduced, and glycolate oxidase activity was approximately 60% of that of the wild-type plants. No difference in growth and appearance was observed between the mutant and the wild-type plants under normal conditions with ambient air under a light intensity of 100 µmol photons m-2 s-1...
February 21, 2017: Plant & Cell Physiology
https://www.readbyqxmd.com/read/28339747/deep-learning-for-pharmacovigilance-recurrent-neural-network-architectures-for-labeling-adverse-drug-reactions-in-twitter-posts
#4
Anne Cocos, Alexander G Fiks, Aaron J Masino
Objective: Social media is an important pharmacovigilance data source for adverse drug reaction (ADR) identification. Human review of social media data is infeasible due to data quantity, thus natural language processing techniques are necessary. Social media includes informal vocabulary and irregular grammar, which challenge natural language processing methods. Our objective is to develop a scalable, deep-learning approach that exceeds state-of-the-art ADR detection performance in social media...
February 22, 2017: Journal of the American Medical Informatics Association: JAMIA
https://www.readbyqxmd.com/read/28339303/development-of-rap-tag-a-novel-tagging-system-for-protein-detection-and-purification
#5
Yuki Fujii, Mika K Kaneko, Satoshi Ogasawara, Shinji Yamada, Miyuki Yanaka, Takuro Nakamura, Noriko Saidoh, Kanae Yoshida, Ryusuke Honma, Yukinari Kato
Affinity tag systems, possessing high affinity and specificity, are useful for protein detection and purification. The most suitable tag for a particular purpose should be selected from many available affinity tag systems. In this study, we developed a novel affinity tag called the "RAP tag" system, which comprises a mouse antirat podoplanin monoclonal antibody (clone PMab-2) and the RAP tag (DMVNPGLEDRIE). This system is useful not only for protein detection in Western blotting, flow cytometry, and sandwich enzyme-linked immunosorbent assay, but also for protein purification...
March 24, 2017: Monoclonal Antibodies in Immunodiagnosis and Immunotherapy
https://www.readbyqxmd.com/read/28334762/missense-uros-mutations-causing-congenital-erythropoietic-porphyria-reduce-uros-homeostasis-that-can-be-rescued-by-proteasome-inhibition
#6
Jean-Marc Blouin, Ganeko Bernardo-Seisdedos, Emma Sasso, Julie Esteve, Cécile Ged, Magalie Lalanne, Arantza Sanz-Parra, Pedro Urquiza, Hubert de Verneuil, Oscar Millet, Emmanuel Richard
Congenital erythropoietic porphyria (CEP) is an inborn error of heme biosynthesis characterized by uroporphyrinogen III synthase (UROS) deficiency resulting in deleterious porphyrin accumulation in blood cells responsible for hemolytic anemia and cutaneous photosensitivity. We analyzed here the molecular basis of UROS impairment associated with twenty nine UROS missense mutations actually described in CEP patients. Using a computational and biophysical joint approach we predicted that most disease-causing mutations would affect UROS folding and stability...
February 21, 2017: Human Molecular Genetics
https://www.readbyqxmd.com/read/28334711/quantitative-proteomics-analysis-of-ischemia-reperfusion-injury-modulated-proteins-in-cardiac-microvascular-endothelial-cells-and-the-protective-role-of-tongxinluo
#7
Qing Li, He-He Cui, Yue-Jin Yang, Xiang-Dong Li, Gui-Hao Chen, Xia-Qiu Tian, Chen Jin, Qiu-Ting Dong, Pei-Sen Huang, Jun Xu
BACKGROUND: The protection of endothelial cells (ECs) against reperfusion injury has received little attention. In this study, we used Tandem Mass Tag (TMT) labeling proteomics to investigate the modulated proteins in an in vitro model of cardiac microvascular endothelial cells (CMECs) subjected to ischemia/reperfusion (I/R) injury and their alteration by traditional Chinese medicine Tongxinluo (TXL). METHODS: Human CMECs were subjected to 2 h of hypoxia followed by 2 h of reoxygenation with different concentrations of TXL Protein expression profiles of CMECs were determined using tandem mass spectrometry...
March 24, 2017: Cellular Physiology and Biochemistry
https://www.readbyqxmd.com/read/28334342/tagging-snp-set-selection-with-maximum-information-based-on-linkage-disequilibrium-structure-in-genome-wide-association-studies
#8
Shudong Wang, Sicheng He, Fayou Yuan, Xinjie Zhu
Motivation: Effective tagging single-nucleotide polymorphism (SNP)-set selection is crucial to SNP-set analysis in genome-wide association studies (GWAS). Most of the existing tagging SNP-set selection methods cannot make full use of the information hidden in common or rare variants associated diseases. It is noticed that some SNPs have overlapping genetic information owing to linkage disequilibrium (LD) structure between SNPs. Therefore, when testing the association between SNPs and disease susceptibility, it is sufficient to elect the representative SNPs (called tag SNP-set or tagSNP-set) with maximum information...
March 16, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28334306/peptidemapper-efficient-and-versatile-amino-acid-sequence-and-tag-mapping
#9
Dominik Kopczynski, Harald Barsnes, Pål R Njølstad, Albert Sickmann, Marc Vaudel, Robert Ahrends
Summary: The mapping of amino acid sequences is an essential task in bioinformatics. Notably, the mapping of peptide sequences on a proteome is required for the post-processing of proteomics results. However, this step can quickly become a bottleneck when working with extensive numbers of peptides or large protein sequence databases. Here, we present PeptideMapper, a novel amino acid sequence mapper for both peptide sequences and de novo sequencing identification results. By taking advantage of the latest advances in pattern matching, PeptideMapper achieves unprecedented performance (i...
March 2, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28334162/biparental-transmission-of-verminephrobacter-symbionts-in-the-earthworm-aporrectodea-tuberculata-lumbricidae
#10
Laura-Carlota Paz, Andreas Schramm, Marie Braad Lund
Most lumbricid earthworms harbor species-specific Verminephrobacter symbionts in their excretory organs (nephridia). These symbionts are vertically transmitted via the cocoon, where they colonize the embryos. Despite cospeciation for >100 million years with their hosts, Verminephrobacter lack genome reduction and AT bias typical of evolutionary old, vertically transmitted symbionts, caused by recurring bottlenecks. We hypothesized that biparental symbiont transmission into the cocoon enabled genetic mixing and relieved the bottleneck, and tested biparental transmission experimentally for V...
February 23, 2017: FEMS Microbiology Ecology
https://www.readbyqxmd.com/read/28333953/involvement-of-%C3%AE-and-%C3%AE-actin-isoforms-in-actin-cytoskeleton-organization-and-migration-abilities-of-bleb-forming-human-colon-cancer-cells
#11
Aleksandra Simiczyjew, Antonina Joanna Mazur, Ewelina Dratkiewicz, Dorota Nowak
Amoeboid movement is characteristic for rounded cells, which do not form strong adhesion contacts with the ECM and use blebs as migratory protrusions. It is well known that actin is the main component of mature forms of these structures, but the exact role fulfilled by non-muscle actin isoforms β- and γ- in bleb formation and migration of these cells is still not fully understood. The aim of this study was to establish the role of β- and γ-actin in migration of bleb-forming cancer cells using isoform-specific antibodies and expression of fluorescently tagged actin isoforms...
2017: PloS One
https://www.readbyqxmd.com/read/28333398/dietary-cholesterol-interacts-with-srebf1-to-modulate-obesity-in-chinese-children
#12
Shixiu Zhang, Xinying Lin, Henry Lynn, Guifa Xu, Jun Li, Changfeng Zhao, Mingmei Li
SCOPE: Sterol Regulatory Element Binding Protein 1 Gene (SREBF1) is an important candidate gene for obesity that could be affected by cholesterol. Different SREBF1 gene variants may have distinct responses to cholesterol, leading to different risks for obesity and obesity-related metabolic traits. Thus, we performed a gene-by-diet correlation analysis to test whether SREBF1 gene variation modulate the relationship between cholesterol and obesity. METHODS AND RESULTS: A total of 642 school-aged children in Jinan, China, were selected by stratified cluster nested sampling...
March 23, 2017: Molecular Nutrition & Food Research
https://www.readbyqxmd.com/read/28332766/the-effects-of-center-volume-on-mortality-in-pediatric-heart-transplantation-the-rest-of-the-story
#13
EDITORIAL
C E Canter
Paul Harvey was an American radio commentator in the latter part of the twentieth century. He would present vignettes and would finish them with the tag line "now you know the rest of the story". In this issue Rana, et al (1) have analyzed the effects of center transplant volume on outcomes with pediatric heart transplantation. Instead of focusing on outcomes after transplantation, their primary aim was to analyze center volume effects on waitlist mortality- the rest of the story. This article is protected by copyright...
March 23, 2017: American Journal of Transplantation
https://www.readbyqxmd.com/read/28332302/protein-bodies-how-the-er-deals-with-high-accumulation-of-recombinant-proteins
#14
Reza Saberianfar, Rima Menassa
Protein bodies (PBs) are highly specialized protein storage organelles in cereal seeds. PB formation in seeds initiates in the endoplasmic reticulum (ER), and depending on the plant species, PBs remain in the ER or find their way out of the ER, bypass the Golgi and end up in protein storage vacuoles (PSVs) (Khan et al., 2012). Protein bodies have been ectopically induced in leaves by producing high amounts of ER-retrieved recombinant proteins, usually by fusing them to protein tags such as Zera(®) , elastin-like polypeptide (ELP) and hydrophobin-I (HFBI)...
March 23, 2017: Plant Biotechnology Journal
https://www.readbyqxmd.com/read/28332258/n-terminal-chemical-protein-labeling-using-the-naturally-split-gos-terl-intein
#15
Anne-Lena Bachmann, Henning D Mootz
Chemoselective and regioselective chemical protein labeling is of great importance, yet no current technique is sufficiently general and simple to perform. Protein trans-splicing by split inteins can be used to ligate short tags with chemical labels to either the N or the C terminus of a protein. The CysTag approach exploits split intein fragments without a cysteine fused with such a short tag containing a single cysteine that is easily amenable to selective modification using classical cysteine bioconjugation...
March 23, 2017: Journal of Peptide Science: An Official Publication of the European Peptide Society
https://www.readbyqxmd.com/read/28332185/mechanism-of-prolactin-inhibition-of-mir-135b-via-methylation-in-goat-mammary-epithelial-cells
#16
Zhi Chen, Jun Luo, ChangHui Zhang, Yue Ma, Shuang Sun, Tianyin Zhang, Juan J Loor
Prolactin is an important endocrine activator of lactogenesis. This study investigated the function and mechanism of miR-135b in the enhancement of lactation by prolactin in goat mammary epithelial tissue. We utilized S-Poly (T) sequencing to evaluate changes in gene regulation in the goat mammary gland after incubation with 2.5 ug/ml prolactin and 2.5 ug/ml IGF-1 by examining highly expressed miRNAs during early-lactation and late-lactation. The results illustrated that miR-135b is highly expressed in the goat mammary gland during early-lactation and late-lactation, and also after treatment with 2...
March 23, 2017: Journal of Cellular Physiology
https://www.readbyqxmd.com/read/28332043/high-arachidonic-acid-levels-in-the-tissues-of-herbivorous-fish-species-siganus-fuscescens-calotomus-japonicus-and-kyphosus-bigibbus
#17
Asada Jiarpinijnun, Soottawat Benjakul, Akasith Pornphatdetaudom, Junichiro Shibata, Emiko Okazaki, Kazufumi Osako
The lipid and fatty acid compositions in the various organs (muscle, liver, other viscera) and stomach contents of three common herbivorous fish species in Japan, Siganus fuscescens, Calotomus japonicus and Kyphosus bigibbus, were examined to explore the stable 20:4n-6 (arachidonic acid, ARA) sources. Triacylglycerol (TAG), phosphatidylethanolamine (PtdEtn), and phosphatidylcholine (PtdCho) were the dominant lipid classes, while the major FA contents were 16:0, 18:1n-9, 16:1n-7, 14:0, 18:0, 18:1n-7, and some PUFA, including ARA, 20:5n-3 (eicosapentaenoic acid, EPA), 22:5n-3 (docosapentaenoic acid, DPA), and 22:6n-3 (docosahexaenoic acid, DHA)...
March 22, 2017: Lipids
https://www.readbyqxmd.com/read/28332019/comparative-tissue-transcriptomics-highlights-dynamic-differences-among-tissues-but-conserved-metabolic-transcript-prioritization-in-preparation-for-arousal-from-torpor
#18
Lori K Bogren, Katharine R Grabek, Gregory S Barsh, Sandra L Martin
During the hibernation season, 13-lined ground squirrels spend days to weeks in torpor with body temperatures near freezing then spontaneously rewarm. The molecular drivers of the drastic physiological changes that orchestrate and permit torpor are not well understood. Although transcription effectively ceases at the low body temperatures of torpor, previous work has demonstrated that some transcripts are protected from bulk degradation in brown adipose tissue (BAT), consistent with the importance of their protein products for metabolic heat generation during arousal from torpor...
March 23, 2017: Journal of Comparative Physiology. B, Biochemical, Systemic, and Environmental Physiology
https://www.readbyqxmd.com/read/28331958/nucleic-acid-sensing-with-enzyme-dna-binding-protein-conjugates-cascade-and-simple-dna-nanostructures
#19
Gülsen Betül Aktas, Vasso Skouridou, Lluis Masip
A versatile and universal DNA sensing platform is presented based on enzyme-DNA binding protein tags conjugates and simple DNA nanostructures. Two enzyme conjugates were thus prepared, with horseradish peroxidase linked to the dimeric single-chain bacteriophage Cro repressor protein (HRP-scCro) and glucose oxidase linked to the dimeric headpiece domain of Escherichia coli LacI repressor protein (GOx-dHP), and used in conjunction with a hybrid ssDNA-dsDNA detection probe. This probe served as a simple DNA nanostructure allowing first for target recognition through its target-complementary single-stranded DNA (ssDNA) part and then for signal generation after conjugate binding on the double-stranded DNA (dsDNA) containing the specific binding sites for the dHP and scCro DNA binding proteins...
March 22, 2017: Analytical and Bioanalytical Chemistry
https://www.readbyqxmd.com/read/28331545/metabolic-engineering-of-saccharomyces-cerevisiae-to-produce-a-reduced-viscosity-oil-from-lignocellulose
#20
Tam N T Tran, Rebecca J Breuer, Ragothaman Avanasi Narasimhan, Lucas S Parreiras, Yaoping Zhang, Trey K Sato, Timothy P Durrett
BACKGROUND: Acetyl-triacylglycerols (acetyl-TAGs) are unusual triacylglycerol (TAG) molecules that contain an sn-3 acetate group. Compared to typical triacylglycerol molecules (here referred to as long chain TAGs; lcTAGs), acetyl-TAGs possess reduced viscosity and improved cold temperature properties, which may allow direct use as a drop-in diesel fuel. Their different chemical and physical properties also make acetyl-TAGs useful for other applications such as lubricants and plasticizers...
2017: Biotechnology for Biofuels
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