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https://www.readbyqxmd.com/read/27896729/identifying-optimal-models-of-evolution
#1
Lars S Jermiin, Vivek Jayaswal, Faisal M Ababneh, John Robinson
Most phylogenetic methods are model-based and depend on models of evolution designed to approximate the evolutionary processes. Several methods have been developed to identify suitable models of evolution for phylogenetic analysis of alignments of nucleotide or amino acid sequences and some of these methods are now firmly embedded in the phylogenetic protocol. However, in a disturbingly large number of cases, it appears that these models were used without acknowledgement of their inherent shortcomings. In this chapter, we discuss the problem of model selection and show how some of the inherent shortcomings may be identified and overcome...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27890800/metabolic-responses-of-haliotis-diversicolor-to-vibrio-parahaemolyticus-infection
#2
Jie Lu, Yanyan Shi, Shuhui Cai, Jianghua Feng
Vibrio parahemolyticus is a devastating bacterial pathogen that often causes outbreak of vibriosis in abalone Haliotis diversicolor. Elucidation of metabolic mechanisms of abalones in responding to V. parahemolyticus infection is essential for controlling the epidemic. In this work, (1)H NMR-based metabolomic techniques along with correlation and network analyses are used to investigate characteristic metabolites, as well as corresponding disturbed pathways in hepatopancreas and gill of H. diversicolor after V...
November 24, 2016: Fish & Shellfish Immunology
https://www.readbyqxmd.com/read/27888132/vitamin-e-deficiency-depressed-fish-growth-disease-resistance-and-the-immunity-and-structural-integrity-of-immune-organs-in-grass-carp-ctenopharyngodon-idella-referring-to-nf-%C3%AE%C2%BAb-tor-and-nrf2-signaling
#3
Jia-Hong Pan, Lin Feng, Wei-Dan Jiang, Pei Wu, Sheng-Yao Kuang, Ling Tang, Yong-An Zhang, Xiao-Qiu Zhou, Yang Liu
This study investigated the effects of dietary vitamin E on growth, disease resistance and the immunity and structural integrity of head kidney, spleen and skin in grass carp (Ctenopharyngodon idella). The fish were fed six diets containing graded levels of vitamin E (0, 45, 90, 135, 180 and 225 mg/kg diet) for 10 weeks. Subsequently, a challenge test was conducted by injection of Aeromonas hydrophila. The results showed that compared with optimal vitamin E supplementation, vitamin E deficiency caused depressed growth, poor survival rates and increased skin lesion morbidity in grass carp...
November 22, 2016: Fish & Shellfish Immunology
https://www.readbyqxmd.com/read/27882682/prevalence-of-equine-hepacivirus-infections-in-france-and-evidence-for-two-viral-subtypes-circulating-worldwide
#4
S Pronost, E Hue, C Fortier, M Foursin, G Fortier, F Desbrosse, F A Rey, P-H Pitel, E Richard, B Saunier
Like hepatitis C virus (HCV) in humans, the newly identified equine hepacivirus (NPHV) displays a predominating liver tropism that may evolve into chronic infections. The genomes of the two viruses share several organizational and functional features and are phylogenetically closest amongst the Hepacivirus genus. A limited amount of data is available regarding the spread of hepacivirus infections in horses. In this study, we asked whether in a more representative sample the prevalence and distribution of NPHV infections in France would resemble that reported so far in other countries...
November 24, 2016: Transboundary and Emerging Diseases
https://www.readbyqxmd.com/read/27866847/detection-of-trans-fatty-acids-by-high-performance-liquid-chromatography-coupled-with-in-tube-solid-phase-microextraction-using-hydrophobic-polymeric-monolith
#5
Fangling Wu, Jiabin Wang, Qi Zhao, Nan Jiang, Xucong Lin, Zenghong Xie, Jianhua Li, Qiqing Zhang
Based on in-tube solid-phase microextraction (in-tube SPME) using a hydrophobic poly (octadecyl methacrylate-co-ethylene dimethacrylate) [poly (OMA-co-EDMA)] monolith, a simple high performance liquid chromatography (HPLC) method has been developed for detection of trans-fatty acids (TFAs) as their fatty acid methyl esters (FAMEs). The poly (OMA-co-EDMA) monolithic column with high hydrophobicity was specially prepared for simultaneous microextraction, pre-separation and purification for the analytes. The pre-separation selectivity, the extraction efficiency, and the purification effect for FAMEs were investigated respectively...
November 10, 2016: Journal of Chromatography. B, Analytical Technologies in the Biomedical and Life Sciences
https://www.readbyqxmd.com/read/27863254/acute-exposure-to-high-environmental-ammonia-hea-triggers-the-emersion-response-in-the-green-shore-crab
#6
Alex M Zimmer, Chris M Wood
The physiological effects of high environmental ammonia (HEA) exposure have been well documented in many aquatic species. In particular, it has recently been demonstrated that exposure to ammonia in fish leads to a similar hyperventilatory response as observed during exposure to hypoxia. In littoral crabs, such as the green crab (Carcinus maenas), exposure to severe hypoxia triggers an emersion response whereby crabs escape hypoxia to breathe air. We hypothesized that exposure to HEA in green crabs would lead to a similar behavioural response which is specific to ammonia...
November 15, 2016: Comparative Biochemistry and Physiology. Part A, Molecular & Integrative Physiology
https://www.readbyqxmd.com/read/27848965/sulfheme-formation-during-homocysteine-s-oxygenation-by-catalase-in-cancers-and-neurodegenerative-diseases
#7
Dominique Padovani, Assia Hessani, Francine T Castillo, Géraldine Liot, Mireille Andriamihaja, Annaïg Lan, Camilla Pilati, François Blachier, Suvajit Sen, Erwan Galardon, Isabelle Artaud
Accumulating evidence suggests that abnormal levels of homocysteine are associated with vascular dysfunctions, cancer cell proliferation and various neurodegenerative diseases. With respect to the latter, a perturbation of transition metal homeostasis and an inhibition of catalase bioactivity have been reported. Herein, we report on some of the molecular bases for the cellular toxicity of homocysteine and demonstrate that it induces the formation of sulfcatalase, an irreversible inactive state of the enzyme, without the intervention of hydrogen sulfide...
November 16, 2016: Nature Communications
https://www.readbyqxmd.com/read/27834920/dietary-strategies-implicated-in-the-prevention-and-treatment-of-metabolic-syndrome
#8
REVIEW
Rocio de la Iglesia, Viviana Loria-Kohen, Maria Angeles Zulet, Jose Alfredo Martinez, Guillermo Reglero, Ana Ramirez de Molina
Metabolic syndrome (MetS) is established as the combination of central obesity and different metabolic disturbances, such as insulin resistance, hypertension and dyslipidemia. This cluster of factors affects approximately 10%-50% of adults worldwide and the prevalence has been increasing in epidemic proportions over the last years. Thus, dietary strategies to treat this heterogenic disease are under continuous study. In this sense, diets based on negative-energy-balance, the Mediterranean dietary pattern, n-3 fatty acids, total antioxidant capacity and meal frequency have been suggested as effective approaches to treat MetS...
November 10, 2016: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/27825399/fluctuations-in-metabolite-content-in-the-liver-of-magnesium-deficient-rats
#9
Mei Shigematsu, Ryosuke Nakagawa, Shozo Tomonaga, Masayuki Funaba, Tohru Matsui
Mg deficiency induces various metabolic disturbances including glucose metabolism in the liver. However, no comprehensive information is currently available on the metabolic pathways affected by Mg deficiency. The present study examined metabolite content in the liver of Mg-deficient rats using a metabolomic analysis. In this study, 4-week-old, male Sprague-Dawley rats were fed a control diet or a Mg-deficient diet for 8 weeks. The metabolomic analysis identified 105 metabolites in the liver, and significant differences were observed in the hepatic contents for thirty-three metabolites between the two groups...
November 9, 2016: British Journal of Nutrition
https://www.readbyqxmd.com/read/27816519/cognitive-decline-in-type-2-diabetic-db-db-mice-may-be-associated-with-brain-region-specific-metabolic-disorders
#10
Hong Zheng, Yongquan Zheng, Liangcai Zhao, Minjiang Chen, Guanghui Bai, Yongsheng Hu, Wenyi Hu, Zhihan Yan, Hongchang Gao
Type 2 diabetes has been associated with cognitive decline, but its metabolic mechanism remains unclear. In the present study, we attempted to investigate brain region-specific metabolic changes in db/db mice with cognitive decline and explore the potential metabolic mechanism linking type 2 diabetes and cognitive decline. We analyzed the metabolic changes in seven brain regions of two types of mice (wild-type mice and db/db mice with cognitive decline) using a (1)H NMR-based metabolomic approach. Then, a mixed-model analysis was used to evaluate the effects of mice type, brain region, and their interaction on metabolic changes...
November 3, 2016: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/27801804/human-lactobacillus-strains-from-the-intestine-can-suppress-ige-mediated-degranulation-of-rat-basophilic-leukaemia-rbl-2h3-cells
#11
Gaku Harata, Fang He, Kyoko Takahashi, Akira Hosono, Kenji Miyazawa, Kazutoyo Yoda, Masaru Hiramatsu, Shuichi Kaminogawa
Mast cells play a critical role in immunoglobulin E (IgE)-mediated allergic diseases, and the degranulation of mast cells is important in the pathogenesis of these diseases. A disturbance of the intestinal microflora, especially of endogenous lactic acid bacteria, might be a contributing factor for IgE-mediated allergic diseases. Additional knowledge regarding the interaction of human intestinal Lactobacilli with mast cells is still necessary. Twenty-three strains of Lactobacilli, including commercial and reference strains and strains from the human intestine, were tested for their ability to regulate degranulation of cells from rat basophilic leukemia RBL-2H3 cells (RBL-2H3) in vitro based on a β-hexosaminidase release assay...
October 27, 2016: Microorganisms
https://www.readbyqxmd.com/read/27784637/screening-and-verifying-endometrial-carcinoma-diagnostic-biomarkers-based-on-a-urine-metabolomic-profiling-study-using-uplc-q-tof-ms
#12
Xidong Shao, Ke Wang, Xinyu Liu, Caiyun Gu, Pengjie Zhang, Jiabin Xie, Wenxin Liu, Lu Sun, Tong Chen, Yubo Li
BACKGROUND: Endometrial carcinoma (EOC) is a gynecological disease with one of the highest worldwide incidences. Due to the lack of typical clinical symptoms and limited sensitive screening methods used to diagnose endometrial carcinoma, the disease is easily neglected before patients are aware of its presence. Therefore, EOC results in serious impacts on women's lives and health. We screened diagnostic biomarkers of EOC with a noninvasive method that compared healthy individuals and endometrial hyperplasia (EOH) patients...
October 23, 2016: Clinica Chimica Acta; International Journal of Clinical Chemistry
https://www.readbyqxmd.com/read/27780848/sucrose-non-fermenting-related-kinase-enzyme-mediated-rho-associated-kinase-signaling-is-responsible-for-cardiac-function
#13
Stephanie M Cossette, Vijesh J Bhute, Xiaoping Bao, Leanne M Harmann, Mark A Horswill, Indranil Sinha, Adam Gastonguay, Shabnam Pooya, Michelle Bordas, Suresh N Kumar, Shama P Mirza, Sean Palecek, Jennifer Strande, Ramani Ramchandran
BACKGROUND: -Cardiac metabolism is critical for the functioning of the heart, and disturbance in this homeostasis is likely to influence cardiac disorders or cardiomyopathy. Our lab has previously shown that sucrose non-fermenting related kinase (SNRK) enzyme, which belongs to the AMP-activated kinase (AMPK) family, was essential for cardiac metabolism in mammals. Snrk global homozygous knockout (KO) mice die at postnatal day 0, and conditional deletion of Snrk in cardiomyocytes (Snrk cmcKO) leads to cardiac failure, and death by 8-10 months...
October 25, 2016: Circulation. Cardiovascular Genetics
https://www.readbyqxmd.com/read/27777693/comparison-of-end-tidal-carbon-dioxide-and-arterial-blood-bicarbonate-levels-in-patients-with-metabolic-acidosis-referred-to-emergency-medicine
#14
Ali Taghizadieh, Mahboub Pouraghaei, Payman Moharamzadeh, Alireza Ala, Farzad Rahmani, Karim Basiri Sofiani
Introduction: The routine and gold standard method to diagnose of acid - base disturbance is arterial blood gas (ABG) sampling. Capnography could be used to measure the end-tidal carbon dioxide (ETCO2) levels and ETco2 has a close correlation with the PaCo2. The aim of this study was comparison the ETco2 and arterial blood bicarbonate levels in patients with metabolic acidosis. Methods: In a descriptive-analytical study that performed in Emergency Department of Emam Reza Medical Research and Training Hospital of Tabriz on patients with metabolic acidosis, ETco2 level and blood bicarbonate levels in 262 patients were evaluated...
2016: Journal of Cardiovascular and Thoracic Research
https://www.readbyqxmd.com/read/27776194/rna-seq-based-analysis-of-differential-gene-expression-associated-with-hepatitis-c-virus-infection-in-a-cell-culture
#15
Anna Hojka-Osinska, Lucyna Budzko, Agnieszka Zmienko, Agnieszka Rybarczyk, Patrick Maillard, Agata Budkowska, Marek Figlerowicz, Paulina Jackowiak
Hepatitis C virus (HCV) infection is one of the major causes of chronic liver diseases. Unfortunately, the mechanisms of HCV infection-induced liver injury and host-virus interactions are still not well recognized. To better understand these processes we determined the changes in the host gene expression that occur during HCV infection of Huh-7.5 cells. As a result, we identified genes that may contribute to the immune and metabolic cellular responses to infection. Pathway enrichment analysis indicated that HCV induced an increased expression of genes involved in mitogen-activated protein kinases signaling, adipocytokine signaling, cell cycle and nitrogen metabolism...
October 25, 2016: Acta Biochimica Polonica
https://www.readbyqxmd.com/read/27775848/metabolic-profiling-of-fatty-liver-in-young-and-middle-aged-adults-cross-sectional-and-prospective-analyses-of-the-young-finns-study
#16
Jari E Kaikkonen, Peter Würtz, Emmi Suomela, Miia Lehtovirta, Antti J Kangas, Antti Jula, Vera Mikkilä, Jorma S A Viikari, Markus Juonala, Tapani Rönnemaa, Nina Hutri-Kähönen, Mika Kähönen, Terho Lehtimäki, Pasi Soininen, Mika Ala-Korpela, Olli T Raitakari
: Non-alcoholic fatty liver is associated with obesity-related metabolic disturbances, but little is known about the metabolic perturbations preceding fatty liver disease. We performed comprehensive metabolic profiling to assess how circulating metabolites, such as lipoprotein lipids, fatty acids, amino acids and glycolysis-related metabolites, reflect the presence of and future risk for fatty liver in young adults. Sixty-eight lipids and metabolites were quantified by nuclear magnetic resonance metabolomics in the population-based Young Finns Study from serum collected in 2001 (n=1,575), 2007 (n=1,509) and 2011 (n=2,002)...
October 24, 2016: Hepatology: Official Journal of the American Association for the Study of Liver Diseases
https://www.readbyqxmd.com/read/27774805/-fructose-and-fructose-intolerance
#17
György Miklós Buzás
Although fructose was discovered in 1794, it was realised in recent decades only that its malabsorption can lead to intestinal symptoms while its excessive consumption induces metabolic disturbances. Fructose is a monosaccharide found naturally in most fruits and vegetables. Dietary intake of fructose has gradually increased in the past decades, especially because of the consumption of high fructose corn syrup. With its 16.4 kg/year consumption, Hungary ranks secondly after the United States. Fructose is absorbed in the small intestine by facilitated transport mediated by glucose transporter proteins-2 and -5, and arrives in the liver cells...
October 2016: Orvosi Hetilap
https://www.readbyqxmd.com/read/27760991/identification-of-a-regulation-network-in-response-to-cadmium-toxicity-using-blood-clam-tegillarca-granosa-as-model
#18
Yongbo Bao, Xiao Liu, Weiwei Zhang, Jianping Cao, Wei Li, Chenghua Li, Zhihua Lin
Clam, a filter-feeding lamellibranch mollusk, is capable to accumulate high levels of trace metals and has therefore become a model for investigation the mechanism of heavy metal toxification. In this study, the effects of cadmium were characterized in the gills of Tegillarca granosa during a 96-hour exposure course using integrated metabolomic and proteomic approaches. Neurotoxicity and disturbances in energy metabolism were implicated according to the metabolic responses after Cd exposure, and eventually affected the osmotic function of gill tissue...
October 20, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27755574/nestedness-in-arbuscular-mycorrhizal-fungal-communities-along-soil-ph-gradients-in-early-primary-succession-acid-tolerant-fungi-are-ph-generalists
#19
Ai Kawahara, Gi-Hong An, Sachie Miyakawa, Jun Sonoda, Tatsuhiro Ezawa
Soil acidity is a major constraint on plant productivity. Arbuscular mycorrhizal (AM) fungi support plant colonization in acidic soil, but soil acidity also constrains fungal growth and diversity. Fungi in extreme environments generally evolve towards specialists, suggesting that AM fungi in acidic soil are acidic-soil specialists. In our previous surveys, however, some AM fungi detected in strongly acidic soils could also be detected in a soil with moderate pH, which raised a hypothesis that the fungi in acidic soils are pH generalists...
2016: PloS One
https://www.readbyqxmd.com/read/27752032/starvation-ketoacidosis-as-a-cause-of-unexplained-metabolic-acidosis-in-the-perioperative-period
#20
Monique Mostert, Anthony Bonavia
BACKGROUND Besides providing anesthesia for surgery, the anesthesiologist's role is to optimize the patient for surgery and for post-surgical recovery. This involves timely identification and treatment of medical comorbidities and abnormal laboratory values that could complicate the patient's perioperative course. There are several potential causes of anion and non-anion gap metabolic acidosis in surgical patients, most of which could profoundly affect a patient's surgical outcome. Thus, the presence of an acute acid-base disturbance requires a thorough workup, the results of which will influence the patient's anesthetic management...
October 18, 2016: American Journal of Case Reports
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