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Amino acids

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https://www.readbyqxmd.com/read/28109201/genetic-analyses-of-the-fusion-protein-genes-in-human-parainfluenza-virus-types-1-and-3-among-patients-with-acute-respiratory-infections-in-eastern-japan-from-2011-to-2015
#1
Rika Tsutsui, Hiroyuki Tsukagoshi, Koo Nagasawa, Masaki Takahashi, Yuki Matsushima, Akihide Ryo, Makoto Kuroda, Hideki Takami, Hirokazu Kimura
PURPOSE: To genetically explorer the fusion protein gene (F) in human parainfluenza virus type 1 (HPIV1) and type 3 (HPIV3) strains, we analyzed them in the patients with acute respiratory infections (ARI) in Eastern Japan from 2011 to 2015. METHODOLOGY: We constructed phylogenetic trees based on the HPIV and HPIV3 F gene using the maximum likelihood method and conducted p-distance, and selective pressure analyses. We also predicted the linear epitopes of the protein in the prototype strains...
January 20, 2017: Journal of Medical Microbiology
https://www.readbyqxmd.com/read/28109156/-cloning-and-sequence-analysis-of-variable-region-genes-of-mouse-anti-human-s100a9-monoclonal-antibody
#2
Min Yan, Danyang Mi, Xiangdong Sun, Zhenqiang Zhang, Huahui Zeng, Wendi Liu
Objective To clone and analyze variable region gene sequences of mouse monoclonal antibody against human S100A9 (anti-human S100A9 mAb). Methods Total RNA was extracted from the hybridoma cell line (IID4B10) secreting mouse anti-human S100A9 mAb. Furthermore, the heavy chain variable region (VH) and light chain variable region (VL) genes were amplified using reverse transcription-polymerase chain reaction (RT-PCR). After the cloning and sequencing of the VH and VL genes, the sequence analyses were performed by BLAST program...
February 2017: Xi Bao Yu Fen Zi Mian Yi Xue za Zhi, Chinese Journal of Cellular and Molecular Immunology
https://www.readbyqxmd.com/read/28109042/expression-and-characterization-of-a-codon-optimized-blood-coagulation-factor-viii
#3
S A Shestopal, J-J Hao, E Karnaukhova, Y Liang, M V Ovanesov, M Lin, J H Kurasawa, T K Lee, J H McVey, A G Sarafanov
BACKGROUND: Production of recombinant factor VIII (FVIII) is challenging due to its low expression. It was previously shown that codon-optimization of a B domain-deleted FVIII (BDD-FVIII) cDNA resulted in increased protein expression. However, it is well-recognized that synonymous mutations may affect the protein structure and function. OBJECTIVES: To compare biochemical properties of a BDD-FVIII expressed from codon-optimized (CO) and the wild-type (WT) cDNAs. METHODS: Each variant of the BDD-FVIII was expressed in several independent CHO cell lines, generated using a lentiviral platform...
January 21, 2017: Journal of Thrombosis and Haemostasis: JTH
https://www.readbyqxmd.com/read/28108917/quantitative-proteomics-analysis-reveals-the-tolerance-of-mirabilis-jalapa-l-to-petroleum-contamination
#4
Shuisen Chen, Hui Ma, Zhifu Guo, Yaping Feng, Jingwei Lin, Menghua Zhang, Ming Zhong
Petroleum is not only an important energy resource but is also a major soil pollutant. To gain better insight into the adaptability mechanism of Mirabilis jalapa to petroleum-contaminated soil, the protein profiles of M. jalapa root were investigated using label-free quantitative proteomics technique. After exposing to petroleum-contaminated soil for 24 h, 34 proteins significantly changed their protein abundance and most of the proteins increased in protein abundance (91.18%). Combined with gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses as well as data from previous studies, our results revealed that M...
January 20, 2017: Environmental Science and Pollution Research International
https://www.readbyqxmd.com/read/28108862/effects-of-chromium-methionine-supplementation-with-different-sources-of-zinc-on-growth-performance-carcass-traits-meat-quality-serum-metabolites-endocrine-parameters-and-the-antioxidant-status-in-growing-finishing-pigs
#5
Xiao Xu, Li Liu, Shen-Fei Long, Xiang-Shu Piao, Terry L Ward, Fei Ji
This experiment was conducted to evaluate the effects of chromium methionine with/without zinc sulfate or zinc amino acid complex on the growth performance, carcass traits, meat quality, serum parameters, endocrine parameters, and antioxidant status of growing-finishing pigs. A total of 180 (32.0 ± 1.7 kg body weight, BW) crossbred pigs (Duroc × Landrace × Yorkshire) were used in a completely randomized design with three dietary treatments and 10 replicates per treatment (five pens of barrows and five pens of gilts with six pigs per replicate)...
January 21, 2017: Biological Trace Element Research
https://www.readbyqxmd.com/read/28108804/antigenic-and-genotypic-characterization-of-rabies-virus-isolated-from-bats-mammalia-chiroptera-from-municipalities-in-s%C3%A3-o-paulo-state-southeastern-brazil
#6
Benedito Donizete Menozzi, Rafael de Novaes Oliveira, Laís Moraes Paiz, Virgínia Bodelão Richini-Pereira, Helio Langoni
Bats have aroused growing attention in the public health sphere because they are considered the main reservoir of rabies virus (RABV) in the Americas, in places where canine rabies is under control. Antigenic and genetic studies of RABV isolates have been used to describe the epidemiological profile of rabies and to identify possible hosts/reservoirs for different epidemiological cycles. This study describes the antigenic and genotypic characterization of 19 RABV isolates from central nervous system samples of non-hematophagous bats (Mammalia: Chiroptera)...
January 20, 2017: Archives of Virology
https://www.readbyqxmd.com/read/28108803/the-genome-sequence-of-a-novel-rna-virus-in-adelphocoris-suturalis
#7
Xinlian Li, Pengjun Xu, Xianming Yang, He Yuan, Lizhen Chen, Yanhui Lu
The complete genome of a novel virus found in Adelphocoris suturalis was determined by RNA-seq and named Adelphocoris suturalis-associated virus 1 (ASV1). ASV1 has a single-stranded RNA genome of 10,845 nucleotides in length and contains five putative open reading frames (ORFs). ORF1 encodes a polypeptide of 2592 amino acids (aa) and contains four conserved domains: a viral RNA methyltransferase domain, an FtsJ-like methyltransferase domain, a viral RNA helicase domain and an RNA-dependent RNA polymerase domain...
January 20, 2017: Archives of Virology
https://www.readbyqxmd.com/read/28108753/release-of-free-amino-acids-upon-oxidation-of-peptides-and-proteins-by-hydroxyl-radicals
#8
Fobang Liu, Senchao Lai, Haijie Tong, Pascale S J Lakey, Manabu Shiraiwa, Michael G Weller, Ulrich Pöschl, Christopher J Kampf
Hydroxyl radical-induced oxidation of proteins and peptides can lead to the cleavage of the peptide, leading to a release of fragments. Here, we used high-performance liquid chromatography tandem mass spectrometry (HPLC-MS/MS) and pre-column online ortho-phthalaldehyde (OPA) derivatization-based amino acid analysis by HPLC with diode array detection and fluorescence detection to identify and quantify free amino acids released upon oxidation of proteins and peptides by hydroxyl radicals. Bovine serum albumin (BSA), ovalbumin (OVA) as model proteins, and synthetic tripeptides (comprised of varying compositions of the amino acids Gly, Ala, Ser, and Met) were used for reactions with hydroxyl radicals, which were generated by the Fenton reaction of iron ions and hydrogen peroxide...
January 20, 2017: Analytical and Bioanalytical Chemistry
https://www.readbyqxmd.com/read/28108603/glucagon-and-amino-acids-are-linked-in-a-mutual-feedback-cycle-the-liver-%C3%AE-cell-axis
#9
Jens J Holst, Nicolai J Wewer Albrechtsen, Jens Pedersen, Filip K Knop
Glucagon is usually viewed as an important counterregulatory hormone in glucose metabolism, with actions opposing those of insulin. Evidence exists that shows glucagon is important for minute-to-minute regulation of postprandial hepatic glucose production, although conditions of glucagon excess or deficiency do not cause changes compatible with this view. In patients with glucagon-producing tumors (glucagonomas), the most conspicuous signs are skin lesions (necrolytic migratory erythema), while in subjects with inactivating mutations of the glucagon receptor, pancreatic swelling may be the first sign; neither condition is necessarily associated with disturbed glucose metabolism...
February 2017: Diabetes
https://www.readbyqxmd.com/read/28108520/rna-binding-specificity-landscape-of-the-pentatricopeptide-repeat-protein-ppr10
#10
Rafael G Miranda, Margarita Rojas, Michael P Montgomery, Kyle P Gribbin, Alice Barkan
Pentatricopeptide repeat (PPR) proteins comprise a large family of helical repeat proteins that influence gene expression in mitochondria and chloroplasts. PPR tracts can bind RNA via a modular one repeat-one nucleotide mechanism in which the nucleotide is specified by the identities of several amino acids in each repeat. This mode of recognition, the so-called PPR code, offers opportunities for the prediction of native PPR binding sites and the design of proteins to bind specified RNAs. However, a deep understanding of the parameters that dictate the affinity and specificity of PPR-RNA interactions is necessary to realize these goals...
January 20, 2017: RNA
https://www.readbyqxmd.com/read/28108400/overexpression-of-a-three-gene-conidial-pigment-biosynthetic-pathway-in-aspergillus-nidulans-reveals-the-first-nrps-known-to-acetylate-tryptophan
#11
Calvin T Sung, Shu-Lin Chang, Ruth Entwistle, Green Ahn, Tzu-Shyang Lin, Vessela Petrova, Hsu-Hua Yeh, Mike B Praseuth, Yi-Ming Chiang, Berl R Oakley, Clay C C Wang
Fungal nonribosomal peptide synthetases (NRPSs) are megasynthetases that produce cyclic and acyclic peptides. In Aspergillus nidulans, the NRPS ivoA (AN10576) has been associated with the biosynthesis of grey-brown conidiophore pigments. Another gene, ivoB (AN0231), has been demonstrated to be an N-acetyl-6-hydroxytryptophan oxidase that putatively acts downstream of IvoA. A third gene, ivoC, has also been predicted to be involved in pigment biosynthesis based on publicly available genomic and transcriptomic information...
January 17, 2017: Fungal Genetics and Biology: FG & B
https://www.readbyqxmd.com/read/28108384/molecular-features-of-the-l-type-amino-acid-transporter-2-determine-different-import-and-export-profiles-for-thyroid-hormones-and-amino-acids
#12
Katrin M Hinz, Dominik Neef, Claudia Rutz, Jens Furkert, Josef Köhrle, Ralf Schülein, Gerd Krause
The L-type amino acid transporter 2 (LAT2) imports amino acids (AA) and also certain thyroid hormones (TH), e.g. 3,3'-T2 and T3, but not rT3 and T4. We utilized LAT2 mutations (Y130A, N133S, F242W) that increase 3,3'-T2 import and focus here on import and export capacity for AA, T4, T3, BCH and derivatives thereof to delineate molecular features. Transport studies and analysis of competitive inhibition of import by radiolabelled TH and AA were performed in Xenopus laevis oocytes. Only Y130A, a pocket widening mutation, enabled import for T4 and increased it for T3...
January 17, 2017: Molecular and Cellular Endocrinology
https://www.readbyqxmd.com/read/28108366/functional-analysis-of-a-tyrosinase-gene-involved-in-early-larval-shell-biogenesis-in-crassostrea-angulata-and-its-response-to-ocean-acidification
#13
Bingye Yang, Fei Pu, Lingling Li, Weiwei You, Caihuan Ke, Danqing Feng
The formation of the primary shell is a vital process in marine bivalves. Ocean acidification largely influences shell formation. It has been reported that enzymes involved in phenol oxidation, such as tyrosinase and phenoloxidases, participate in the formation of the periostracum. In the present study, we cloned a tyrosinase gene from Crassostrea angulata named Ca-tyrA1, and its potential function in early larval shell biogenesis was investigated. The Ca-tyrA1 gene has a full-length cDNA of 2430bp in size, with an open reading frame of 1896bp in size, which encodes a 631-amino acid protein that includes a 24-amino acid putative signal peptide...
January 17, 2017: Comparative Biochemistry and Physiology. Part B, Biochemistry & Molecular Biology
https://www.readbyqxmd.com/read/28108341/molecular-cloning-genomic-structure-polymorphism-analysis-and-recombinant-expression-of-a-%C3%AE-1-antitrypsin-like-gene-from-swamp-eel-monopterus-albus
#14
Wei Li, Quanhe Wang, Shaobin Li, Ao Jiang, Wenxiu Sun
Alpha-1-antitrypsin (AAT) is a highly polymorphic glycoprotein antiprotease, involved in the regulation of human immune response. Beyond some genomic characterization and a few protein characterizations, the function of teleost AAT remains uncertain. In this study we cloned an AAT-like gene from a swamp eel liver identifying four exons and three introns, and the full-length cDNA. The elucidated swamp eel AAT amino acid sequence showed high homology with known AATs from other teleosts. The swamp eel AAT was examined both in ten healthy tissues and in four bacterially-stimulated tissues resulting in up-regulation of swamp eel AAT at different times...
January 17, 2017: Fish & Shellfish Immunology
https://www.readbyqxmd.com/read/28108305/efficient-dynamic-programming-algorithm-with-prior-knowledge-for-protein-%C3%AE-strand-alignment
#15
Mostafa Sabzekar, Mahmoud Naghibzadeh, Javad Sadri
One of the main tasks towards the prediction of protein β-sheet structure is to predict the native alignment of β-strands. The alignment of two β-strands defines similar regions that may reflect functional, structural, or evolutionary relationships between them. Therefore, any improvement in β-strands alignment not only reduces the computational search space but also improves β-sheet structure prediction accuracy. To define the alignment scores, previous studies utilized predicted residue-residue contacts (contact maps)...
January 17, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28108278/comparison-of-the-redox-chemistry-of-sulfur-and-selenium-containing-analogs-of-uracil
#16
N Connor Payne, Andrew Geissler, Aileen Button, Alexandru R Sasuclark, Alayne L Schroll, Erik L Ruggles, Vadim N Gladyshev, Robert J Hondal
Selenium is present in proteins in the form of selenocysteine, where this amino acid serves catalytic oxidoreductase functions. The use of selenocysteine in nature is strongly associated with redox catalysis. However, selenium is also found in a 2-selenouridine moiety at the wobble position of tRNA(Glu), tRNA(Gln) and tRNA(Lys). It is thought that the modifications of the wobble position of the tRNA improves the selectivity of the codon-anticodon pair as a result of the physico-chemical changes that result from substitution of sulfur and selenium for oxygen...
January 17, 2017: Free Radical Biology & Medicine
https://www.readbyqxmd.com/read/28108177/discriminating-between-adaptive-and-carcinogenic-liver-hypertrophy-in-rat-studies-using-logistic-ridge-regression-analysis-of-toxicogenomic-data-the-mode-of-action-and-predictive-models
#17
Shujie Liu, Taisuke Kawamoto, Osamu Morita, Kouichi Yoshinari, Hiroshi Honda
Chemical exposure often results in liver hypertrophy in animal tests, characterized by increased liver weight, hepatocellular hypertrophy, and/or cell proliferation. While most of these changes are considered adaptive responses, there is concern that they may be associated with carcinogenesis. In this study, we have employed a toxicogenomic approach using a logistic ridge regression model to identify genes responsible for liver hypertrophy and hypertrophic hepatocarcinogenesis and to develop a predictive model for assessing hypertrophy-inducing compounds...
January 17, 2017: Toxicology and Applied Pharmacology
https://www.readbyqxmd.com/read/28108158/evolutionary-plasticity-of-plasma-membrane-interaction-in-drepp-family-proteins
#18
Stanislav Vosolsobě, Jan Petrášek, Kateřina Schwarzerová
The plant-specific DREPP protein family comprises proteins that were shown to regulate the actin and microtubular cytoskeleton in a calcium-dependent manner. Our phylogenetic analysis showed that DREPPs first appeared in ferns and that DREPPs have a rapid and plastic evolutionary history in plants. Arabidopsis DREPP paralogues called AtMDP25/PCaP1 and AtMAP18/PCaP2 are N-myristoylated, which has been reported as a key factor in plasma membrane localization. Here we show that N-myristoylation is neither conserved nor ancestral for the DREPP family...
January 17, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28108094/metabolic-profiling-identification-of-metabolites-formed-in-mediterranean-mussels-mytilus-galloprovincialis-after-diclofenac-exposure
#19
Bénilde Bonnefille, Lauren Arpin-Pont, Elena Gomez, Hélène Fenet, Frédérique Courant
Despite the growing concern on the presence of pharmaceutically active compounds in the environment, few studies have been conducted on their metabolism in marine organisms. In this study, a non-targeted strategy based on the generation of chemical profiles generated by liquid chromatography combined with high resolution mass spectrometry was used to highlight metabolite production by the Mediterranean mussel (Mytilus galloprovincialis) after diclofenac exposure. This method allowed revealing the production of 13 metabolites in mussel tissues...
January 17, 2017: Science of the Total Environment
https://www.readbyqxmd.com/read/28107990/combined-use-of-peptide-ion-and-normalized-delta-scores-to-evaluate-milk-authenticity-by-ion-trap-based-proteomics-coupled-with-error-tolerant-searching
#20
Donatella Nardiello, Anna Natale, Carmen Palermo, Maurizio Quinto, Diego Centonze
A fundamental issue in proteomics is the peptide identification by database searching and the assessment of the goodness of fit between experimental and theoretical data. Despite the different number of ways to measure the quality of search results, the definition of a scoring criterion is still highly desirable in ion-trap based proteomics. Indeed, in order to fully take advantage of a low resolution MS/MS dataset, it is essential to strike a balance between greater information capture and reduced number of incorrect peptide assignments...
March 1, 2017: Talanta
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