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Hui Ling Lee, Haosheng Shen, In Young Hwang, Hua Ling, Wen Shan Yew, Yung Seng Lee, Matthew Wook Chang
Microbial communities and their collective genomes form the gut microbiome, of which bacteria are the major contributor. Through their secreted metabolites, bacteria interact with the host, influencing human health and physiology. Perturbation of the microbiota and metabolome has been associated with various diseases and metabolic conditions. As knowledge on fundamental host-microbiome interactions and genetic engineering tools becomes readily available, targeted manipulation of the gut microbiome for therapeutic applications gains favourable attention...
July 12, 2018: Genes
Xia Guo, Xue Jiang, Jing Xu, Xiongwen Quan, Min Wu, Han Zhang
Due to the complexity of the pathological mechanisms of neurodegenerative diseases, traditional differentially-expressed gene selection methods cannot detect disease-associated genes accurately. Recent studies have shown that consensus-guided unsupervised feature selection (CGUFS) performs well in feature selection for identifying disease-associated genes. Since the random initialization of the feature selection matrix in CGUFS results in instability of the final disease-associated gene set, for the purposes of this study we proposed an ensemble method based on CGUFS-namely, ensemble consensus-guided unsupervised feature selection (ECGUFS) in order to further improve the accuracy of disease-associated genes and the stability of feature gene sets...
July 12, 2018: Genes
Jesus Rolando Delgado-Balderas, Maria Lourdes Garza-Rodriguez, Gabriela Sofia Gomez-Macias, Alvaro Barboza-Quintana, Oralia Barboza-Quintana, Ricardo M Cerda-Flores, Ivett Miranda-Maldonado, Hugo Mauricio Vazquez-Garcia, Lezmes Dionicio Valdez-Chapa, Mauro Antonio-Macedo, Michael Dean, Hugo A Barrera-Saldaña
Gynecologic cancers are among the leading causes of death worldwide, ovarian cancer being the one with the highest mortality rate. Olaparib is a targeted therapy used in patients presenting mutations in BRCA1 and BRCA2 genes. The aim of this study was to describe BRCA1 and BRCA2 gene variants in Mexican patients with ovarian cancer. Sequencing of BRCA1 and BRCA2 genes from tumors of 50 Mexican patients with ovarian cancer was made in a retrospective, non-randomized, and exploratory study. We found genetic variants in 48 of 50 cases...
July 11, 2018: Genes
Briardo Llorente, Thomas C Williams, Hugh D Goold
The interest in human space journeys to distant planets and moons has been re-ignited in recent times and there are ongoing plans for sending the first manned missions to Mars in the near future. In addition to generating oxygen, fixing carbon, and recycling waste and water, plants could play a critical role in producing food and biomass feedstock for the microbial manufacture of materials, chemicals, and medicines in long-term interplanetary outposts. However, because life on Earth evolved under the conditions of the terrestrial biosphere, plants will not perform optimally in different planetary habitats...
July 10, 2018: Genes
Nia Oetiker, Rodrigo Norambuena, Cristóbal Martínez-Bussenius, Claudio A Navarro, Fernando Amaya, Sergio A Álvarez, Alberto Paradela, Carlos A Jerez
Acidithiobacillus ferrooxidans resists extremely high concentrations of copper. Strain ATCC 53993 is much more resistant to the metal compared with strain ATCC 23270, possibly due to the presence of a genomic island in the former one. The global response of strain ATCC 53993 to copper was analyzed using iTRAQ (isobaric tag for relative and absolute quantitation) quantitative proteomics. Sixty-seven proteins changed their levels of synthesis in the presence of the metal. On addition of CusCBA efflux system proteins, increased levels of other envelope proteins, such as a putative periplasmic glucan biosynthesis protein (MdoG) involved in the osmoregulated synthesis of glucans and a putative antigen O polymerase (Wzy), were seen in the presence of copper...
July 10, 2018: Genes
Thomas Blankers, Kevin P Oh, Kerry L Shaw
Mating behavior divergence can make significant contributions to reproductive isolation and speciation in various biogeographic contexts. However, whether the genetic architecture underlying mating behavior divergence is related to the biogeographic history and the tempo and mode of speciation remains poorly understood. Here, we use quantitative trait locus (QTL) mapping to infer the number, distribution, and effect size of mating song rhythm variations in the crickets Laupala eukolea and Laupala cerasina , which occur on different islands (Maui and Hawaii)...
July 10, 2018: Genes
Jingwen Yu, Pengyao Ping, Lei Wang, Linai Kuang, Xueyong Li, Zhelun Wu
An increasing number of studies have indicated that long-non-coding RNAs (lncRNAs) play crucial roles in biological processes, complex disease diagnoses, prognoses, and treatments. However, experimentally validated associations between lncRNAs and diseases are still very limited. Recently, computational models have been developed to discover potential associations between lncRNAs and diseases by integrating multiple heterogeneous biological data; this has become a hot topic in biological research. In this article, we constructed a global tripartite network by integrating a variety of biological information including miRNA⁻disease, miRNA⁻lncRNA, and lncRNA⁻disease associations and interactions...
July 8, 2018: Genes
Natalie Gugala, Joe Lemire, Kate Chatfield-Reed, Ying Yan, Gordon Chua, Raymond J Turner
It is essential to understand the mechanisms by which a toxicant is capable of poisoning the bacterial cell. The mechanism of action of many biocides and toxins, including numerous ubiquitous compounds, is not fully understood. For example, despite the widespread clinical and commercial use of silver (Ag), the mechanisms describing how this metal poisons bacterial cells remains incomplete. To advance our understanding surrounding the antimicrobial action of Ag, we performed a chemical genetic screen of a mutant library of Escherichia coli —the Keio collection, in order to identify Ag sensitive or resistant deletion strains...
July 6, 2018: Genes
Elena Knops, Saleta Sierra, Prabhav Kalaghatgi, Eva Heger, Rolf Kaiser, Olga V Kalinina
Hepatitis C virus (HCV) causes a major health burden and can be effectively treated by direct-acting antivirals (DAAs). The non-structural protein 5A (NS5A), which plays a role in the viral genome replication, is one of the DAAs’ targets. Resistance-associated viruses (RAVs) harbouring NS5A resistance-associated mutations (RAMs) have been described at baseline and after therapy failure. A mutation from glutamine to arginine at position 30 (Q30R) is a characteristic RAM for the HCV sub/genotype (GT) 1a, but arginine corresponds to the wild type in the GT-1b; still, GT-1b strains are susceptible to NS5A-inhibitors...
July 6, 2018: Genes
Linlin Xing, Maozu Guo, Xiaoyan Liu, Chunyu Wang, Lei Zhang
The explosion of genomic data provides new opportunities to improve the task of gene regulatory network reconstruction. Because of its inherent probability character, the Bayesian network is one of the most promising methods. However, excessive computation time and the requirements of a large number of biological samples reduce its effectiveness and application to gene regulatory network reconstruction. In this paper, Flooding-Pruning Hill-Climbing algorithm (FPHC) is proposed as a novel hybrid method based on Bayesian networks for gene regulatory networks reconstruction...
July 6, 2018: Genes
Hugh Douglas Goold, Philip Wright, Deborah Hailstones
Rapid expansion in the emerging field of synthetic biology has to date mainly focused on the microbial sciences and human health. However, the zeitgeist is that synthetic biology will also shortly deliver major outcomes for agriculture. The primary industries of agriculture, fisheries and forestry, face significant and global challenges; addressing them will be assisted by the sector’s strong history of early adoption of transformative innovation, such as the genetic technologies that underlie synthetic biology...
July 6, 2018: Genes
Roy S K Walker, Isak S Pretorius
Engineered yeast are an important production platform for the biosynthesis of high-value compounds with medical applications. Recent years have witnessed several new developments in this area, largely spurred by advances in the field of synthetic biology and the elucidation of natural metabolic pathways. This minireview presents an overview of synthetic biology applications for the heterologous biosynthesis of biopharmaceuticals in yeast and demonstrates the power and potential of yeast cell factories by highlighting several recent examples...
July 6, 2018: Genes
Ethan J Andersen, Shaukat Ali, Emmanuel Byamukama, Yang Yen, Madhav P Nepal
Plants have developed a complex defense system against diverse pests and pathogens. Once pathogens overcome mechanical barriers to infection, plant receptors initiate signaling pathways driving the expression of defense response genes. Plant immune systems rely on their ability to recognize enemy molecules, carry out signal transduction, and respond defensively through pathways involving many genes and their products. Pathogens actively attempt to evade and interfere with response pathways, selecting for a decentralized, multicomponent immune system...
July 4, 2018: Genes
Kristina B V Døssing, Christina Kjær, Jonas Vikeså, Tina Binderup, Ulrich Knigge, Michael D Culler, Andreas Kjær, Birgitte Federspiel, Lennart Friis-Hansen
Somatostatin (SST) analogues are used to control the proliferation and symptoms of neuroendocrine tumors (NETs). MicroRNAs (miRNA) are small non-coding RNAs that modulate posttranscriptional gene expression. We wanted to characterize the miRNAs operating under the control of SST to elucidate to what extent they mediate STT actions. NCI-H727 carcinoid cell line was treated with either a chimeric SST/dopamine analogue; a SST or dopamine analogue for proliferation assays and for identifying differentially expressed miRNAs using miRNA microarray...
July 4, 2018: Genes
Anna Bratus-Neuenschwander, Francesc Castro-Giner, Mojca Frank-Bertoncelj, Sirisha Aluri, Sandro F Fucentese, Ralph Schlapbach, Haiko Sprott
Joint pain causes significant morbidity in osteoarthritis (OA). The aetiology of joint pain in OA is not well understood. The synovial membrane as an innervated joint structure represents a potential source of peripheral pain in OA. Here we analyse, using a hypothesis-free next generation RNA sequencing, the differences in protein-coding and non-coding transcriptomes in knee synovial tissues from OA patients with high knee pain ( n = 5) compared with OA patients with low knee pain ( n = 5), as evaluated by visual analogue scale (VAS)...
July 4, 2018: Genes
Yueyuan Xu, Xiaolong Qi, Mingyang Hu, Ruiyi Lin, Ye Hou, Zhangxu Wang, Huanhuan Zhou, Yunxia Zhao, Yu Luan, Shuhong Zhao, Xinyun Li
Feed efficiency (FE) is one of the main factors that determine the production costs in the pig industry. In this study, RNA Sequencing (RNA-seq) was applied to identify genes and long intergenic non-coding RNAs (lincRNAs) that are differentially expressed (DE) in the adipose tissues of Yorkshire pigs with extremely high and low FE. In total, 147 annotated genes and 18 lincRNAs were identified as DE between high- and low-FE pigs. Seventeen DE lincRNAs were significantly correlated with 112 DE annotated genes at the transcriptional level...
July 4, 2018: Genes
Qiansi Chen, Meng Li, Chen Wang, Zefeng Li, Jiayang Xu, Qingxia Zheng, Pingping Liu, Huina Zhou
Maca ( Lepidium meyenii Walp.) is a traditional Andean crop with great potential for various sanitarian and medical functions, which is attracting increased research attention. The majority of previous Maca studies were focused on biochemistry and pharmacodynamics, while the genetic basis of its unique characteristics lagged due to a lack of genome information. The authors perform gas chromatography-mass spectrometry (GC/MS) analysis in the hypocotyls of three Maca ecotypes and identify 79 compounds. Among them, 62 compounds have distinct profiles among Maca ecotypes...
July 3, 2018: Genes
Kun Wu, Xiao-Ying Tan, Yi-Huan Xu, Guang-Hui Chen, Mei-Qin Zhuo
We characterized the promoters of target genes of the signal transducer and activator of transcription 3, STAT3 (carnitine palmitoyltransferase I, CPT Iα1b , acetyl-CoA carboxylase alpha, ACCα ; fatty acid synthase, FAS ; and peroxisome proliferator-activated receptor gamma, PPARγ ) in a teleost Pelteobagrus fulvidraco . Binding sites of STAT3 were predicted on these promoters, indicating that STAT3 probably mediated their transcriptional activities. Leptin had no effect on the activity of ACCα and PPARγ promoters, but increased CPT Iα1b promoter activity and decreased FAS promoter activity...
July 3, 2018: Genes
Xiao Li, Youbo Zhu, Huifang Zhang, Guangjun Ma, Guofang Wu, Aoqi Xiang, Xin'E Shi, Gong She Yang, Shiduo Sun
The microRNA (miR)-17 family is widely expressed in mammalian tissues and play important roles in various physiological and pathological processes. Here, the functions of miR-106a-5p, a member of miR-17 family, were explored during myogenic differentiation in C2C12 cell line. First, miR-106a-5p was found to be relatively lower expressed in two-month skeletal muscle tissues and gradually decreased upon myogenic stimuli. Forced expression of miR-106a-5p significantly reduced the differentiation index, fusion index as well as the expression of myogenic markers (MyoD, MyoG, MyHC, Myomixer, Myomarker)...
July 2, 2018: Genes
Mafalda Cavalheiro, Pedro Pais, Mónica Galocha, Miguel C Teixeira
Fungal infections caused by Candida , Aspergillus , and Cryptococcus species are an increasing problem worldwide, associated with very high mortality rates. The successful prevalence of these human pathogens is due to their ability to thrive in stressful host niche colonization sites, to tolerate host immune system-induced stress, and to resist antifungal drugs. This review focuses on the key role played by multidrug resistance (MDR) transporters, belonging to the ATP-binding cassette (ABC), and the major facilitator superfamilies (MFS), in mediating fungal resistance to pathogenesis-related stresses...
July 2, 2018: Genes
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