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https://www.readbyqxmd.com/read/28645204/when-homoplasy-is-not-homoplasy-dissecting-trait-evolution-by-contrasting-composite-and-reductive-coding
#1
Alejandro Torres-Montúfar, Thomas Borsch, Helga Ochoterena
The conceptualization and coding of characters is a difficult issue in phylogenetic systematics, no matter which inference method is used when reconstructing phylogenetic trees or if the characters are just mapped onto a specific tree. Complex characters are groups of features that can be divided into simpler hierarchical characters (reductive coding), although the implied hierarchical relational information may change depending on the type of coding (composite vs reductive). Up to now, there is no common agreement to either code characters as complex or simple...
June 22, 2017: Systematic Biology
https://www.readbyqxmd.com/read/28644561/the-redox-sensitive-module-of-cyclophilin-20-3-2-cysteine-peroxiredoxin-and-cysteine-synthase-integrates-sulfur-metabolism-and-oxylipin-signaling-in-the-high-light-acclimation-response
#2
Sara M Müller, Shanshan Wang, Wilena Telman, Michael Liebthal, Helena Schnitzer, Andrea Viehhauser, Carsten Sticht, Carolina Delatorre, Markus Wirtz, Rüdiger Hell, Karl-Josef Dietz
The integration of redox- and reactive oxygen species-dependent signaling and metabolic activities are fundamental to plant acclimation to biotic and abiotic stresses. Previous data suggest the existence of a dynamically interacting module in the chloroplast stroma consisting of cyclophilin 20-3 (Cyp20-3), O-acetylserine(thiol)lyase B (OASTL-B), 2-cysteine peroxiredoxins A/B (2-CysPrx) and serine acetyltransferase 2;1 (SERAT2;1). The functionality of this COPS module is influenced by redox stimuli and oxophytodienoic acid (OPDA) which is the precursor for jasmonic acid...
June 23, 2017: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/28644509/comparative-transcriptomic-analysis-of-two-important-life-stages-of-angiostrongylus-cantonensis-fifth-stage-larvae-and-female-adults
#3
Liang Yu, Binbin Cao, Ying Long, Meks Tukayo, Chonglv Feng, Wenzhen Fang, Damin Luo
The mechanisms involved in the fast growth of Angiostrongylus cantonensis from fifth-stage larvae (L5) to female adults and how L5 breaks through the blood-brain barrier in a permissive host remain unclear. In this work, we compared the transcriptomes of these two life stages to identify the main factors involved in the rapid growth and transition to adulthood. RNA samples from the two stages were sequenced and assembled de novo. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analyses of 1,346 differentially expressed genes between L5 and female adults was then undertaken...
April 2017: Genetics and Molecular Biology
https://www.readbyqxmd.com/read/28642771/transcriptomic-analysis-of-avocado-hass-persea-americana-mill-in-the-interaction-system-fruit-chitosan-colletotrichum
#4
Luis-Ángel Xoca-Orozco, Esther Angélica Cuellar-Torres, Sandra González-Morales, Porfirio Gutiérrez-Martínez, Ulises López-García, Luis Herrera-Estrella, Julio Vega-Arreguín, Alejandra Chacón-López
Avocado (Persea americana) is one of the most important crops in Mexico as it is the main producer, consumer, and exporter of avocado fruit in the world. However, successful avocado commercialization is often reduced by large postharvest losses due to Colletotrichum sp., the causal agent of anthracnose. Chitosan is known to have a direct antifungal effect and acts also as an elicitor capable of stimulating a defense response in plants. However, there is little information regarding the genes that are either activated or repressed in fruits treated with chitosan...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28642749/rna-seq-reveals-enhanced-sugar-metabolism-in-streptococcus-mutans-co-cultured-with-candida-albicans-within-mixed-species-biofilms
#5
Jinzhi He, Dongyeop Kim, Xuedong Zhou, Sang-Joon Ahn, Robert A Burne, Vincent P Richards, Hyun Koo
Early childhood caries (ECC), which can lead to rampant tooth-decay that is painful and costly to treat, is one of the most prevalent infectious diseases affecting children worldwide. Previous studies support that interactions between Streptococcus mutans and Candida albicans are associated with the pathogenesis of ECC. The presence of Candida enhances S. mutans growth, fitness and accumulation within biofilms in vitro, although the molecular basis for these behaviors is undefined. Using an established co-cultivation biofilm model and RNA-Seq, we investigated how C...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28641485/microarray-based-gene-expression-analysis-for-veterinary-pathologists-a-review
#6
Barbara B Raddatz, Ingo Spitzbarth, Katja A Matheis, Arno Kalkuhl, Ulrich Deschl, Wolfgang Baumgärtner, Reiner Ulrich
High-throughput, genome-wide transcriptome analysis is now commonly used in all fields of life science research and is on the cusp of medical and veterinary diagnostic application. Transcriptomic methods such as microarrays and next-generation sequencing generate enormous amounts of data. The pathogenetic expertise acquired from understanding of general pathology provides veterinary pathologists with a profound background, which is essential in translating transcriptomic data into meaningful biological knowledge, thereby leading to a better understanding of underlying disease mechanisms...
January 1, 2017: Veterinary Pathology
https://www.readbyqxmd.com/read/28641268/newgoa-predicting-new-go-annotations-of-proteins-by-bi-random-walks-on-a-hybrid-graph
#7
Guoxian Yu, Guangyuan Fu, Jun Wang, Yingwen Zhao
A remaining key challenge of modern biology is annotating the functional roles of proteins. Various computational models have been proposed for this challenge. Most of them assume the annotations of annotated proteins are complete. But in fact, many of them are incomplete. We proposed a method called NewGOA to predict new Gene Ontology (GO) annotations for incompletely annotated proteins and for completely un-annotated ones. NewGOA employs a hybrid graph, composed of two types of nodes (proteins and GO terms), to encode interactions between proteins, hierarchical relationships between terms and available annotations of proteins...
June 15, 2017: IEEE/ACM Transactions on Computational Biology and Bioinformatics
https://www.readbyqxmd.com/read/28641008/hypoxia-induced-changes-in-the-fibroblast-secretome-exosome-and-whole-cell-proteome-using-cultured-cardiac-derived-cells-isolated-from-neonatal-mice
#8
Jake Cosme, Hongbo Guo, Sina Hadipour-Lakmehsari, Andrew Emili, Anthony O Gramolini
Cardiac fibroblasts (CF) represent a major subpopulation of cells in the developing and adult heart. Cardiomyocyte (CM) and CF intercellular communication occurs through paracrine interactions and modulate myocyte development and stress response. Detailed proteomic analysis of the CF secretome in normal and stressed conditions may offer insights into the role of CF in heart development and disease. Primary neonatal mouse CF were isolated and cultured for 24h in 21% (normoxic) or 2% (hypoxic) O2. Conditioned media was separated to obtain EXO and EXO-depleted secretome fractions...
June 22, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28640079/a-genome-wide-association-scan-of-biological-processes-involved-in-oral-lichen-planus-and-oral-squamous-cell-carcinoma
#9
Qiaozhen Yang, Beiyun Xu, Hongying Sun, Xiaxia Wang, Jie Zhang, Xuedi Yu, Xiaojuan Ma
BACKGROUND: In this study, the molecular mechanisms underlying malignant transformation from oral lichen planus (OLP) to oral squamous cell carcinoma (OSCC) were examined. METHODS: High-throughput sequencing of long noncoding RNAs (lncRNAs) and mRNAs of normal subjects and patients with OLP and OSCC was conducted. RNA-seq reads were mapped, lncRNA and mRNA transcripts were assembled, and expression levels were estimated. The targets of lncRNAs were predicted. Finally, Gene Ontology (GO) and pathway enrichment analyses of differentially expressed genes (DEGs) and lncRNA targets were performed...
June 2017: Medicine (Baltimore)
https://www.readbyqxmd.com/read/28640074/bioinformatics-analysis-of-key-genes-and-pathways-for-hepatocellular-carcinoma-transformed-from-cirrhosis
#10
Bosheng He, Jianbing Yin, Shenchu Gong, Jinhua Gu, Jing Xiao, Weixiang Shi, Wenbin Ding, Ying He
OBJECTIVE: We aimed to identify some pivotal genes and pathways for hepatocellular carcinoma (HCC) transformation from cirrhosis and explore potential targets for treatment of the disease. METHODS: The GSE17548 microarray data were downloaded from Gene Expression Omnibus database, and 37 samples (20 cirrhosis and 17 HCC samples) were used for analysis. The differentially expressed genes (DEGs) in HCC tissues were compared with those in cirrhosis tissues and analyzed using the limma package...
June 2017: Medicine (Baltimore)
https://www.readbyqxmd.com/read/28639574/mir-551b-5p-contributes-to-pathogenesis-of-vein-graft-failure-via-upregulating-early-growth-response-1-expression
#11
Ran Dong, Kui Zhang, Yue-Li Wang, Feng Zhang, Jian Cao, Ju-Bing Zheng, Hong-Jia Zhang
BACKGROUND: Vein graft failure (VGF) is a serious complication of coronary artery bypass graft, although the mechanism remains unclear. The study aimed to investigate the effects of microRNAs (miRNAs) on the endothelial dysfunction involved in VGF. METHODS: Human umbilical vein endothelial cells (HUVECs) were subjected to mechanical stretch stimulation to induce endothelial dysfunction. Genome-wide transcriptome profiling was performed using the Human miRNA OneArray® V4 (PhalanxBio Inc...
July 5, 2017: Chinese Medical Journal
https://www.readbyqxmd.com/read/28639573/a-transcriptomic-analysis-of-physiological-significance-of-hypoxia-inducible-factor-1%C3%AE-in-myogenesis-and-carbohydrate-metabolism-of-genioglossus-in-mice
#12
Tong Hao, Yue-Hua Liu, Yuan-Yuan Li, Yun Lu, Hong-Yi Xu
BACKGROUND: Chronic intermittent hypoxia is the most remarkable feature of obstructive sleep apnea/hypopnea syndrome and it can induce the change of hypoxia-inducible factor-1α (HIF-1α) expression and contractile properties in the genioglossus. To clarify the role of HIF-1α in contractile properties of the genioglossus, this study generated and compared high-throughput RNA-sequencing data from genioglossus between HIF-1α conditional knockout (KO) mice and littermate wild-type (WT) mice...
July 5, 2017: Chinese Medical Journal
https://www.readbyqxmd.com/read/28637587/comparative-study-on-secretome-and-transmembranome-of-immature-and-mature-metacestodes-of-echinococcus-multilocularis
#13
Fuqiang Huang, Zhisheng Dang, Haoji Zhang, Kinpei Yagi, Kyeongsoon Kim, Magona Joseph, Wenjun Pu, Yuzaburo Oku
Alveolar echinococcosis (AE) is a worldwide zoonosis caused by E. multilocularis. Humans become infected through oral ingestion of the eggs. Host of E. multilocularis produces immune responses that help to either reject and/or limit the growth of this parasite, and in response the parasite produces molecules against this immune attack. This study identifies candidate key molecules in the early infection phase and the chronic stage of the parasite infestation, through comparison of gene expression of 4- and 16-week metacestodes...
May 12, 2017: Veterinary Parasitology
https://www.readbyqxmd.com/read/28637447/differential-gene-expression-at-different-stages-of-mesocarp-development-in-high-and-low-yielding-oil-palm
#14
Yick Ching Wong, Huey Fang Teh, Katharina Mebus, Tony Eng Keong Ooi, Qi Bin Kwong, Ka Loo Koo, Chuang Kee Ong, Sean Mayes, Fook Tim Chew, David R Appleton, Harikrishna Kulaveerasingam
BACKGROUND: The oil yield trait of oil palm is expected to involve multiple genes, environmental influences and interactions. Many of the underlying mechanisms that contribute to oil yield are still poorly understood. In this study, we used a microarray approach to study the gene expression profiles of mesocarp tissue at different developmental stages, comparing genetically related high- and low- oil yielding palms to identify genes that contributed to the higher oil-yielding palm and might contribute to the wider genetic improvement of oil palm breeding populations...
June 21, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28637421/a-novel-pathway-based-distance-score-enhances-assessment-of-disease-heterogeneity-in-gene-expression
#15
Xiting Yan, Anqi Liang, Jose Gomez, Lauren Cohn, Hongyu Zhao, Geoffrey L Chupp
BACKGROUND: Distance based unsupervised clustering of gene expression data is commonly used to identify heterogeneity in biologic samples. However, high noise levels in gene expression data and relatively high correlation between genes are often encountered, so traditional distances such as Euclidean distance may not be effective at discriminating the biological differences between samples. An alternative method to examine disease phenotypes is to use pre-defined biological pathways. These pathways have been shown to be perturbed in different ways in different subjects who have similar clinical features...
June 20, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28637233/identification-of-exosomal-muscle-specific-mirnas-in-serum-of-myotonic-dystrophy-patients-relating-to-muscle-disease-progress
#16
Andrie Koutsoulidou, Marinos Photiades, Tassos C Kyriakides, Kristia Georgiou, Marianna Prokopi, Konstantinos Kapnisis, Anna Lusakowska, Marianna Nearchou, Yiolanda Christou, George K Papadimas, Andreas Anayiotos, Kyriakos Kyriakou, Evangelia Kararizou, Eleni Zamba Papanicolaou, Leonidas A Phylactou
Myotonic dystrophy type 1 (DM1) is the most common form of adult-onset muscular dystrophy, which is characterised by progressive muscle wasting and the discovery of reliable blood-based biomarkers could be useful for the disease progress monitoring. There have been some reports showing that the presence of specific miRNAs in blood correlate with DM1. In one of these, our group identified four muscle-specific miRNAs, miR-1, miR-133a, miR-133b and miR-206, which correlated with the progression of muscle wasting observed in DM1 patients...
June 16, 2017: Human Molecular Genetics
https://www.readbyqxmd.com/read/28636987/combination-of-calr-and-pdia3-is-a-potential-prognostic-biomarker-for-non-small-cell-lung-cancer
#17
Ke Wang, Hao Li, Ruo Chen, Yang Zhang, Xiu-Xuan Sun, Wan Huang, Huijie Bian, Zhi-Nan Chen
Proteomic-based approaches for biomarker discovery are promising strategies used in cancer research. In this study, we performed quantitative proteomic analysis on 16 paired samples of non-small cell lung cancer (NSCLC) and adjacent non-tumor lung tissues using label-free quantitative proteomics and liquid chromatography-tandem mass spectrometry/mass spectrometry (LC-MS/MS) to identify differentially expressed proteins. A total of 91 proteins were differentially expressed in NSCLC compared with adjacent non-tumor lung tissues among 4047 identified proteins (fold change > 1...
June 16, 2017: Oncotarget
https://www.readbyqxmd.com/read/28635590/imbalance-between-innate-antiviral-and-pro-inflammatory-immune-responses-may-contribute-to-different-outcomes-involving-low-and-highly-pathogenic-avian-influenza-h5n3-infections-in-chickens
#18
John Pasick, Sandra Diederich, Yohannes Berhane, Carissa Embury-Hyatt, Wanhong Xu
In order to gain further insight into the early virus-host interactions associated with highly pathogenic avian influenza virus infections in chickens, genome-wide expression profiling of chicken lung and brain was carried out at 24 and 72 h post-inoculation (h p.i.). For this purpose two recombinant H5N3 viruses were utilized, each possessing a polybasic HA0 cleavage site but differing in pathogenicity. The original rH5N3 P0 virus, which has a low-pathogenic phenotype, was passaged six times through chickens to give rise to the derivative rH5N3 P6 virus, which is highly pathogenic (Diederich S, Berhane Y, Embury-Hyatt C, Hisanaga T, Handel K et al...
June 21, 2017: Journal of General Virology
https://www.readbyqxmd.com/read/28635589/regulation-of-escherichia-coli-pathogenesis-by-alternative-sigma-factor-n
#19
James T Riordan, Avishek Mitra
σ(N) (also σ(54)) is an alternative sigma factor subunit of the RNA polymerase complex that regulates the expression of genes from many different ontological groups. It is broadly conserved in the Eubacteria with major roles in nitrogen metabolism, membrane biogenesis, and motility. σ(N) is encoded as the first gene of a five-gene operon including rpoN (σ(N)), ptsN, hpf, rapZ, and npr that has been genetically retained among species of Escherichia, Shigella, and Salmonella. In an increasing number of bacteria, σ(N) has been implicated in the control of genes essential to pathogenic behavior, including those involved in adherence, secretion, immune subversion, biofilm formation, toxin production, and resistance to both antimicrobials and biological stressors...
June 2017: EcoSal Plus
https://www.readbyqxmd.com/read/28634367/proteomic-analysis-reveals-large-amounts-of-decomposition-enzymes-and-major-metabolic-pathways-involved-in-algicidal-process-of-trametes-versicolor-f21a
#20
Xueyan Gao, Congyan Wang, Wei Dai, Shenrong Ren, Fang Tao, Xingbing He, Guomin Han, Wei Wang
A recent algicidal mode indicates that fungal mycelia can wrap and eliminate almost all co-cultivated algal cells within a short time span. However, the underlying molecular mechanism is rarely understood. We applied proteomic analysis to investigate the algicidal process of Trametes versicolor F21a and identified 3,754 fungal proteins. Of these, 30 fungal enzymes with endo- or exoglycosidase activities such as β-1,3-glucanase, α-galactosidase, α-glucosidase, alginate lyase and chondroitin lyase were significantly up-regulated...
June 20, 2017: Scientific Reports
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