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Essential amino acids

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https://www.readbyqxmd.com/read/28101932/amino-acid-profiling-of-zinc-resistant-prostate-cancer-cell-lines-associations-with-cancer-progression
#1
Monika Kratochvilova, Martina Raudenska, Zbynek Heger, Lukas Richtera, Natalia Cernei, Vojtech Adam, Petr Babula, Marie Novakova, Michal Masarik, Jaromir Gumulec
BACKGROUND: Failure in intracellular zinc accumulation is a key process in prostate carcinogenesis. Nevertheless, epidemiological studies of zinc administration have provided contradicting results. In order to examine the impact of the artificial intracellular increase of zinc(II) ions on prostate cancer metabolism, PNT1A, 22Rv1, and PC-3 prostatic cell lines-depicting different stages of cancer progression-and their zinc-resistant counterparts were used. To determine "benign" and "malignant" metabolic profiles, amino acid patterns, gene expression, and antioxidant capacity of these cell lines were assessed...
January 19, 2017: Prostate
https://www.readbyqxmd.com/read/28100782/triphosphate-re-orientation-of-the-incoming-nucleotide-as-a-fidelity-checkpoint-in-viral-rna-dependent-rna-polymerases
#2
Xiaorong Yang, Xinran Liu, Derek M Musser, Ibrahim M Moustafa, Jamie J Arnold, Craig E Cameron, David D Boehr
The nucleotide incorporation fidelity of the viral RNA-dependent RNA polymerase (RdRp) is important for maintaining functional genetic information, but at the same time for generating sufficient genetic diversity to escape the bottlenecks of the host's anti-viral response. We have previously shown that the structural dynamics of the motif-D loop is closely related to nucleotide discrimination. Previous studies have also suggested that there is a re-orientation of the triphosphate of the incoming nucleotide, which is essential prior to nucleophilic attack from the primer RNA 3'-hydroxyl...
January 18, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28100770/control-of-amino-acid-homeostasis-by-a-ubiquitin-ligase-coactivator-protein-complex
#3
Damian Guerra, Sonia M Chapiro, Réjane Pratelli, Shi Yu, Weitao Jia, Julie Leary, Guillaume Pilot, Judy Callis
Intercellular amino acid transport is essential for the growth of all multicellular organisms, and its dysregulation is implicated in developmental disorders. By an unknown mechanism, amino acid efflux is stimulated in plants by over-expression of a membrane-localized protein (GLUTAMINE DUMPER 1, GDU1) that requires a ubiquitin ligase (LOSS OF GDU 2, LOG2). Here we further explore the physiological consequences of the interaction between these two proteins. LOG2 ubiquitin ligase activity is necessary for GDU1-dependent tolerance to exogenous amino acids, and LOG2 self-ubiquitination was markedly stimulated by the GDU1 cytosolic domain, suggesting that GDU1 functions as an adaptor or coactivator of amino acid exporter(s)...
January 18, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28100609/sterol-binding-by-the-tombusviral-replication-proteins-is-essential-for-replication-in-yeast-and-plants
#4
Kai Xu, Peter D Nagy
: Membranous structures derived from various organelles are important for replication of plus-stranded RNA viruses. Although the important roles of co-opted host proteins in RNA virus replication have been appreciated for a decade, the equally important functions of cellular lipids in virus replication are gaining full attention only recently. Previous works with Tomato bushy stunt tombusvirus (TBSV) in model host yeast have revealed essential roles for phosphatidylethanolamine and sterols in viral replication...
January 18, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28100316/optimizing-nutrition-of-the-preterm-infant
#5
William W Jr Hay
The goal of nutrition of the preterm infant is to meet the growth rate of the healthy fetus of the same gestational age and to produce the same body composition of the healthy fetus in terms of organ growth, tissue components, and cell number and structure. Nutritional quantity and quality are fundamental for normal growth and development of preterm infants, including neurodevelopmental outcomes. Failure to provide the necessary amounts of all of the essential nutrients has produced not only growth failure, but also increased morbidity and less than optimal neurodevelopment...
January 2017: Zhongguo Dang Dai Er Ke za Zhi, Chinese Journal of Contemporary Pediatrics
https://www.readbyqxmd.com/read/28099515/polymorphisms-and-mutational-covariation-associated-with-death-in-a-prospective-cohort-of-hiv-aids-patients-receiving-long-term-art-in-china
#6
Pengtao Liu, Yi Feng, Jianjun Wu, Suian Tian, Bin Su, Zhe Wang, Lingjie Liao, Hui Xing, Yinghui You, Yiming Shao, Yuhua Ruan
BACKGROUND: HIV drug resistance is associated with faster clinical progression of AIDS. However, the effect of significant polymorphisms and mutational covariation on mortality among HIV/AIDS patients receiving long-term antiretroviral therapy (ART), have rarely been studied. METHODS: In this prospective cohort study from December 2003 to December 2014, we present a new computational modelling approach based on bioinformatics-based models and several statistical methods to elucidate the molecular mechanisms involved in the acquisition of polymorphisms and mutations on death in HIV/AIDS patients receiving long-term ART in China...
2017: PloS One
https://www.readbyqxmd.com/read/28099419/genomic-deletion-of-malic-enzyme-2-confers-collateral-lethality-in-pancreatic-cancer
#7
Prasenjit Dey, Joelle Baddour, Florian Muller, Chia Chin Wu, Huamin Wang, Wen-Ting Liao, Zangdao Lan, Alina Chen, Tony Gutschner, Yaan Kang, Jason Fleming, Nikunj Satani, Di Zhao, Abhinav Achreja, Lifeng Yang, Jiyoon Lee, Edward Chang, Giannicola Genovese, Andrea Viale, Haoqiang Ying, Giulio Draetta, Anirban Maitra, Y Alan Wang, Deepak Nagrath, Ronald A DePinho
The genome of pancreatic ductal adenocarcinoma (PDAC) frequently contains deletions of tumour suppressor gene loci, most notably SMAD4, which is homozygously deleted in nearly one-third of cases. As loss of neighbouring housekeeping genes can confer collateral lethality, we sought to determine whether loss of the metabolic gene malic enzyme 2 (ME2) in the SMAD4 locus would create cancer-specific metabolic vulnerability upon targeting of its paralogous isoform ME3. The mitochondrial malic enzymes (ME2 and ME3) are oxidative decarboxylases that catalyse the conversion of malate to pyruvate and are essential for NADPH regeneration and reactive oxygen species homeostasis...
January 18, 2017: Nature
https://www.readbyqxmd.com/read/28096492/identification-of-glutaminyl-cyclase-genes-involved-in-pyroglutamate-modification-of-fungal-lignocellulolytic-enzymes
#8
Vincent W Wu, Craig M Dana, Anthony T Iavarone, Douglas S Clark, N Louise Glass
: The breakdown of plant biomass to simple sugars is essential for the production of second-generation biofuels and high-value bioproducts. Currently, enzymes produced from filamentous fungi are used for deconstructing plant cell wall polysaccharides into fermentable sugars for biorefinery applications. A post-translational N-terminal pyroglutamate modification observed in some of these enzymes occurs when N-terminal glutamine or glutamate is cyclized to form a five-membered ring. This modification has been shown to confer resistance to thermal denaturation for CBH-1 and EG-1 cellulases...
January 17, 2017: MBio
https://www.readbyqxmd.com/read/28096377/comparative-genomics-reveals-convergent-evolution-between-the-bamboo-eating-giant-and-red-pandas
#9
Yibo Hu, Qi Wu, Shuai Ma, Tianxiao Ma, Lei Shan, Xiao Wang, Yonggang Nie, Zemin Ning, Li Yan, Yunfang Xiu, Fuwen Wei
Phenotypic convergence between distantly related taxa often mirrors adaptation to similar selective pressures and may be driven by genetic convergence. The giant panda (Ailuropoda melanoleuca) and red panda (Ailurus fulgens) belong to different families in the order Carnivora, but both have evolved a specialized bamboo diet and adaptive pseudothumb, representing a classic model of convergent evolution. However, the genetic bases of these morphological and physiological convergences remain unknown. Through de novo sequencing the red panda genome and improving the giant panda genome assembly with added data, we identified genomic signatures of convergent evolution...
January 17, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28095303/gd-dtpa-induced-dynamic-metabonomic-changes-in-rat-biofluids
#10
Chuanling Wan, Youyang Zhan, Rong Xue, Yijie Wu, Xiaojing Li, Fengkui Pei
OBJECTIVES: The purposes of this study were (1) to detect the dynamic metabonomic changes induced by gadopentetate dimeglumine (Gd-DTPA) and (2) to investigate the potential metabolic disturbances associated with the pathogenesis of nephrogenic systemic fibrosis (NSF) at the early stage. METHODS: A nuclear magnetic resonance (NMR)-based metabolomics approach was used to investigate the urinary and serum metabolic changes induced by a single tail vein injection of Gd-DTPA (dosed at 2 and 5mmol/kg body weight) in rats...
January 14, 2017: Magnetic Resonance Imaging
https://www.readbyqxmd.com/read/28095274/protein-intake-and-breast-cancer-survival-in-the-nurses-health-study
#11
Michelle D Holmes, Jun Wang, Susan E Hankinson, Rulla M Tamimi, Wendy E Chen
Purpose Greater protein intake has been associated with better breast cancer survival in several prospective studies, including among 1,982 women in the Nurses' Health Study. We proposed to extend this previous finding. We hypothesized that protein, essential amino acid, branched-chain amino acid, and leucine intakes are associated with improved survival and that these associations are stronger in tumors expressing insulin receptor (IR). Patients and Methods We included 6,348 women diagnosed with stage I to III breast cancer between 1976 and 2004...
January 20, 2017: Journal of Clinical Oncology: Official Journal of the American Society of Clinical Oncology
https://www.readbyqxmd.com/read/28094221/synthesis-biological-evaluation-and-molecular-docking-analysis-of-2-phenyl-benzofuran-3-carboxamide-derivatives-as-potential-inhibitors-of-staphylococcus-aureus-sortase-a
#12
Wan He, Yong Zhang, Jian Bao, Xinxian Deng, Jennifer Batara, Shawn Casey, Qiuyuan Guo, Faqin Jiang, Lei Fu
In Gram-positive bacteria, Sortase A (Srt A) is a critical cysteine transpeptidase that is responsible for recognizing and assembling surface virulence proteins through the recognition of a LPXTG (leucine, proline, X, threonine, and glycine, where X is any amino acid) signal. Mutants lacking genes for Srt A attenuate infections without affecting microbial viability. Here a series of 2-phenyl-benzofuran-3-carboxamide derivatives were synthesized and identified as potent Srt A inhibitors. Activity assays revealed that multiple compounds exhibited excellent inhibitory activity against Srt A compared with known Sortase A inhibitor pHMB (IC50=130μM)...
December 25, 2016: Bioorganic & Medicinal Chemistry
https://www.readbyqxmd.com/read/28093073/application-of-meta-omics-techniques-to-understand-greenhouse-gas-emissions-originating-from-ruminal-metabolism
#13
REVIEW
Robert J Wallace, Timothy J Snelling, Christine A McCartney, Ilma Tapio, Francesco Strozzi
Methane emissions from ruminal fermentation contribute significantly to total anthropological greenhouse gas (GHG) emissions. New meta-omics technologies are beginning to revolutionise our understanding of the rumen microbial community structure, metabolic potential and metabolic activity. Here we explore these developments in relation to GHG emissions. Microbial rumen community analyses based on small subunit ribosomal RNA sequence analysis are not yet predictive of methane emissions from individual animals or treatments...
January 16, 2017: Genetics, Selection, Evolution: GSE
https://www.readbyqxmd.com/read/28092150/issues-in-nutrition-dietary-supplements
#14
Margaret E Thompson, Mary Barth Noel
The majority of American adults report use of one or more dietary supplements every day or occasionally. The Dietary Supplement Health and Education Act of 1994 defines dietary supplements and regulates their manufacture and distribution. One of the most commonly used supplements is vitamin D. Measurement of serum levels of vitamin D must be undertaken with the caveats that different laboratories define normal levels differently, and that there is rarely a clinical correlation with the actual level. Patients should understand that supplements should not be used to excess, as there are toxicities and other adverse effects associated with most of them...
January 2017: FP Essentials
https://www.readbyqxmd.com/read/28091608/binding-of-n-methylscopolamine-to-the-extracellular-domain-of-muscarinic-acetylcholine-receptors
#15
Jan Jakubík, Alena Randáková, Pavel Zimčík, Esam E El-Fakahany, Vladimír Doležal
Interaction of orthosteric ligands with extracellular domain was described at several aminergic G protein-coupled receptors, including muscarinic acetylcholine receptors. The orthosteric antagonists quinuclidinyl benzilate (QNB) and N-methylscopolamine (NMS) bind to the binding pocket of the muscarinic acetylcholine receptor formed by transmembrane α-helices. We show that high concentrations of either QNB or NMS slow down dissociation of their radiolabeled species from all five subtypes of muscarinic acetylcholine receptors, suggesting allosteric binding...
January 16, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28091567/quantifying-the-relative-contributions-of-different-solute-carriers-to-aggregate-substrate-transport
#16
Mehdi Taslimifar, Lalita Oparija, Francois Verrey, Vartan Kurtcuoglu, Ufuk Olgac, Victoria Makrides
Determining the contributions of different transporter species to overall cellular transport is fundamental for understanding the physiological regulation of solutes. We calculated the relative activities of Solute Carrier (SLC) transporters using the Michaelis-Menten equation and global fitting to estimate the normalized maximum transport rate for each transporter (Vmax). Data input were the normalized measured uptake of the essential neutral amino acid (AA) L-leucine (Leu) from concentration-dependence assays performed using Xenopus laevis oocytes...
January 16, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28089725/high-concentration-of-branched-chain-amino-acids-promotes-oxidative-stress-inflammation-and-migration-of-human-peripheral-blood-mononuclear-cells-via-mtorc1-activation
#17
Olha Zhenyukh, Esther Civantos, Marta Ruiz-Ortega, María Soledad Sánchez, Clotilde Vázquez, Concepción Peiró, Jesús Egido, Sebastián Mas
Leucine, isoleucine and valine are essential aminoacids termed branched-chain amino acids (BCAA) due to its aliphatic side-chain. In several pathological and physiological conditions increased BCAA plasma concentrations have been described. Elevated BCAA levels predict insulin resistance development. Moreover, BCAA levels higher than 2mmol/L are neurotoxic by inducing microglial activation in maple syrup urine disease. However, there are no studies about the direct effects of BCAA in circulating cells. We have explored whether BCAA could promote oxidative stress and pro-inflammatory status in peripheral blood mononuclear cells (PBMCs) obtained from healthy donors...
January 12, 2017: Free Radical Biology & Medicine
https://www.readbyqxmd.com/read/28088476/a-chimeric-protein-of-abrin-and-abrus-precatorius-agglutinin-that-neutralizes-abrin-mediated-lethality-in-mice
#18
Vinita Tiwari, Shradha Bagaria, Anjali A Karande
Abrin, a type II ribosome inactivating protein from the Abrus precatorius plant, is extremely toxic. It has been shown to be 75 times more potent than its infamous sister toxin, ricin and their potential use in bio-warfare is a cause of major concern. Although several vaccine candidates are under clinical trials for ricin, none are available against abrin. The present study proposes a chimeric protein, comprising of 1-123 amino acids taken from the A chain of abrin and 124-175 amino acids from Abrus precatorius agglutinin A chain, as a vaccine candidate against abrin intoxication...
January 11, 2017: Toxicon: Official Journal of the International Society on Toxinology
https://www.readbyqxmd.com/read/28088356/advancing-the-prediction-accuracy-of-protein-protein-interactions-by-utilizing-evolutionary-information-from-position-specific-scoring-matrix-and-ensemble-classifier
#19
Lei Wang, Zhu-Hong You, Shi-Xiong Xia, Feng Liu, Xing Chen, Xin Yan, Yong Zhou
Protein-Protein Interactions (PPIs) are essential to most biological processes and play a critical role in most cellular functions. With the development of high-throughput biological techniques and in silico methods, a large number of PPI data have been generated for various organisms, but many problems remain unsolved. These factors promoted the development of the in silico methods based on machine learning to predict PPIs. In this study, we propose a novel method by combining ensemble Rotation Forest (RF) classifier and Discrete Cosine Transform (DCT) algorithm to predict the interactions among proteins...
January 11, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28087294/bioactive-metabolites-of-docosahexaenoic-acid
#20
REVIEW
Ondrej Kuda
Docosahexaenoic acid (DHA) is an essential fatty acid that is recognized as a beneficial dietary constituent and as a source of the anti-inflammatory specialized proresolving mediators (SPM): resolvins, protectins and maresins. Apart from SPMs, other metabolites of DHA also exert potent biological effects. This article summarizes current knowledge on the metabolic pathways involved in generation of DHA metabolites. Over 70 biologically active metabolites have been described, but are often discussed separately within specific research areas...
January 10, 2017: Biochimie
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