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Laurent Kamel, Michelle Keller-Pearson, Christophe Roux, Jean-Michel Ané
I. II. III. IV. V. References SUMMARY: Arbuscular mycorrhizal (AM) fungi associate with the vast majority of land plants, providing mutual nutritional benefits and protecting hosts against biotic and abiotic stresses. Significant progress was made recently in our understanding of the genomic organization, the obligate requirements, and the sexual nature of these fungi through the release and subsequent mining of genome sequences. Genomic and genetic approaches also improved our understanding of the signal repertoire used by AM fungi and their plant hosts to recognize each other for the initiation and maintenance of this association...
October 25, 2016: New Phytologist
Ying Chen, Shuyan Cao, Pingping Xu, Wei Han, Tiankai Shan, Jingying Pan, Weiwei Lin, Xue Chen, Xiaodong Wang
BACKGROUND Results from DNA microarray experiments have shown that the expression of miR-34s undergoes significant changes following spinal cord injury (SCI). The present study was designed to detect changes in the expression of miR-34s and its target genes during the acute and sub-acute stages of SCI. MATERIAL AND METHODS Luxol fast blue (LFB) staining for myelin was used to observe the differences in the general morphology of the spinal cord after SCI in a contusion model in rats. qPCR was carried out to determine the expression variation of miR-34s and its target genes during the acute and sub-acute stages of SCI...
October 25, 2016: Medical Science Monitor: International Medical Journal of Experimental and Clinical Research
Dingwei Zhang, Zhangjun Li, Yanfei Zhang, Chen Tu, Jia Huo, Yan Liu
Alterations in the levels and functions of microRNAs (miRs) have been associated with carcinogenesis. In this study, we investigated the role and underlying mechanism of miR-4262 in the proliferation of human cutaneous malignant melanoma (CMM) cells. The expression levels of miR-4262 were significantly upregulated in cancerous tissues compared with those in matched adjacent normal tissues from 110 CMM patients. miR-4262 was also regulated in five types of CMM cell lines, displaying an opposite expression pattern to that of Kruppel-like 6 (KLF6), a proven tumor suppressor in several cancers other than CMM...
October 21, 2016: Oncology Reports
Timothy R Valentic, David R Jackson, Sean F Brady, Shiou-Chuan Sheryl Tsai
Arixanthomycins are pentangular polyphenols (PP) with potent antiproliferative activities that were discovered through the heterologous expression of environmental DNA-derived gene clusters. The biosynthesis of arixanthomycin and other PPs is unusual, because it requires several novel type II polyketide synthase (PKS) enzymes for its complete maturation. Most type II PKSs contain a ketoreductase (KR) that mediates the C7-C12 first ring cyclization and C9-reduction. In contrast, based on previous studies of product analysis and genome mining, the arixanthomycin (ARX) gene cluster like harbors a C11-reducing ketoreductase (ARX 27), a C9-C14 first-ring aromatase/cyclase (ARX 19), and an unprecedented C-17 and C-19 reducing KR (ARX 21)...
October 25, 2016: ACS Chemical Biology
Miguel Jesus Nunes Ramos, João Lucas Coito, Joana Fino, Jorge Cunha, Helena Silva, Patrícia Gomes de Almeida, Maria Manuela Ribeiro Costa, Sara Amâncio, Octávio S Paulo, Margarida Rocheta
RNA-seq of Vitis during early stages of bud development, in male, female and hermaphrodite flowers, identified new loci outside of annotated gene models, suggesting their involvement in sex establishment. The molecular mechanisms responsible for flower sex specification remain unclear for most plant species. In the case of V. vinifera ssp. vinifera, it is not fully understood what determines hermaphroditism in the domesticated subspecies and male or female flowers in wild dioecious relatives (Vitis vinifera ssp...
October 24, 2016: Plant Molecular Biology
Kusum Mehla, Jayashree Ramana
Campylobacter jejuni remains a major cause of human gastroenteritis with estimated annual incidence rate of 450 million infections worldwide. C. jejuni is a major burden to public health in both socioeconomically developing and industrialized nations. Virulence determinants involved in C. jejuni pathogenesis are multifactorial in nature and not yet fully understood. Despite the completion of the first C. jejuni genome project in 2000, there are currently no vaccines in the market against this pathogen. Traditional vaccinology approach is an arduous and time extensive task...
October 24, 2016: Functional & Integrative Genomics
Rintaro Saito, Anaïs Rocanin-Arjo, Young-Hyun You, Manjula Darshi, Benjamin Van Espen, Satoshi Miyamoto, Jessica Pham, Minya Pu, Simone Romoli, Loki Natarajan, Wenjun Ju, Matthias Kretzler, Robert Nelson, Keiichiro Ono, Dana Thomasova, Shrikant R Mulay, Trey Ideker, Vivette D'Agati, Ergin Beyret, Juan Carlos Izpisua Belmonte, Hans Joachim Anders, Kumar Sharma
To derive new insights in diabetic complications, we integrated publicly available human protein-protein interaction (PPI) networks with global metabolic networks using metabolomic data from patients with diabetic nephropathy. We focused on the participating proteins in the network that were computationally predicted to connect the urine metabolites. MDM2 had the highest significant number of PPI connections. As validation, significant downregulation of MDM2 gene expression was found in both glomerular and tubulointerstitial compartments of kidney biopsy tissue from 2 independent cohorts of patients with diabetic nephropathy...
October 20, 2016: JCI Insight
Andrea Orellana-Manzano, Miguel G O'Ryan, Anne J Lagomarcino, Sergio George, Mindy S Muñoz, Nora Mamani, Carolina A Serrano, Paul R Harris, Octavio Ramilo, Asunción Mejías, Juan P Torres, Yalda Lucero, Andrew F G Quest
Background:Helicobacter pylori infects half of the world's population and causes gastric cancer in a subset of infected adults. Previous blood microarray findings showed that apparently healthy children, persistently infected with H. pylori have differential gene expression compared to age-matched, non-infected children. SLC5A8, a cancer suppressor gene with decreased expression among infected children, was chosen for further study based on bioinformatics analysis. Methods: A pilot study was conducted using specific qRT-PCR amplification of SLC5A8 in blood samples from H...
2016: Frontiers in Cellular and Infection Microbiology
Christian Montes, Fabiola Altimira, Hayron Canchignia, Álvaro Castro, Evelyn Sánchez, María Miccono, Eduardo Tapia, Álvaro Sequeida, Jorge Valdés, Paz Tapia, Carolina González, Humberto Prieto
A new plant commensal Pseudomonas veronii isolate (strain R4) was identified from a Xiphinema index biocontrol screen. Isolated from grapevine roots from vineyards in central Chile, the strain R4 exhibited a slower yet equivalently effective nematicide activity as the well-characterized P. protegens CHA0. Whole genome sequencing of strain R4 and comparative analysis among the available Pseudomonas spp. genomes allowed for the identification of gene clusters that encode putative extracellular proteases and lipase synthesis and secretion systems, which are proposed to mediate-at least in part-the observed nematicidal activity...
2016: Standards in Genomic Sciences
Leila Sabrina Ullmann, Ramiro das Neves Dias-Neto, Didier Quevedo Cagnini, Ricardo Seiti Yamatogi, Jose Paes Oliveira-Filho, Viviane Nemer, Rodrigo Hidalgo Friciello Teixeira, Alexander Welker Biondo, João Pessoa Araújo
BACKGROUND: Mycobacterium is an important zoonotic agent with companion, livestock and wildlife animals reportedly playing a role as reservoirs. Although its association with reptiles has been described, the disease cycle remains to be fully established, particularly in snakes. Accordingly, this study aimed to report the occurrence of mycobacteriosis with clinical pneumonia in one exotic python snake (Python molurus) and one native green snake (Philodryas olfersii) from the Sorocaba Zoo, São Paulo state, Brazil...
2016: Journal of Venomous Animals and Toxins Including Tropical Diseases
Jullien M Flynn, Frédéric J J Chain, Daniel J Schoen, Melania E Cristescu
Understanding the rates, spectra, and fitness effects of spontaneous mutations is fundamental to answering key questions in evolution, molecular biology, disease genetics and conservation biology. To estimate mutation rates and evaluate the effect of selection on new mutations, we propagated mutation accumulation (MA) lines of Daphnia pulex for more than 82 generations and maintained a non-MA population under conditions where selection could act. Both experiments were started with the same obligate asexual progenitor clone...
October 24, 2016: Molecular Biology and Evolution
Yi An, Jiawei Wang, Chen Li, André Leier, Tatiana Marquez-Lago, Jonathan Wilksch, Yang Zhang, Geoffrey I Webb, Jiangning Song, Trevor Lithgow
Bacterial effector proteins secreted by various protein secretion systems play crucial roles in host-pathogen interactions. In this context, computational tools capable of accurately predicting effector proteins of the various types of bacterial secretion systems are highly desirable. Existing computational approaches use different machine learning (ML) techniques and heterogeneous features derived from protein sequences and/or structural information. These predictors differ not only in terms of the used ML methods but also with respect to the used curated data sets, the features selection and their prediction performance...
October 24, 2016: Briefings in Bioinformatics
Chunjin Li, Lu Chen, Yun Zhao, Shuxiong Chen, Lulu Fu, Yanwen Jiang, Shan Gao, Zhuo Liu, Fengge Wang, Xiaoling Zhu, Jiahui Rao, Jing Zhang, Xu Zhou
Polycystic ovary syndrome (PCOS) causes female subfertility with ovarian disorders and may be associated with increased rate of early-pregnancy failure. Rat PCOS models were established using letrozole to understand the uterine pathogenesis of PCOS. The differential expression of microRNAs (miRNAs) was observed in rat uterus with PCOS. After estrous cycles were disrupted, significantly abnormal ovarian morphology and hormone level were observed in rats with PCOS. A total of 148 miRNAs differentially expressed were identified in the uterus from the letrozole-induced rat model compared with the control...
October 21, 2016: Gene
Hai-Jing Yu, Hua Deng, Jian Ma, Shu-Jun Huang, Jian-Min Yang, Yan-Fen Huang, Xiao-Ping Mu, Liang Zhang, Qi Wang
BACKGROUND: Granulomatous mastitis (GM) is a chronic inflammatory breast lesion and its etiology remains incompletely defined. Although mounting evidence suggests the involvement of Corynebacterium in GM, there has been no systematic study of GM bacteriology using -omics technology. METHODS: The bacterial diversity and relative abundances in breast abscesses from 19 women with GM were investigated using 16S rDNA metagenomic sequencing and Sanger sequencing. A quantitative PCR (qPCR) assay was also developed to identify C...
October 21, 2016: International Journal of Infectious Diseases: IJID
Richard Lindqvist, Filip Mundt, Jonathan D Gilthorpe, Silke Wölfel, Nelson O Gekara, Andrea Kröger, Anna K Överby
BACKGROUND: Neurotropic flaviviruses such as tick-borne encephalitis virus (TBEV), Japanese encephalitis virus (JEV), West Nile virus (WNV), and Zika virus (ZIKV) are causative agents of severe brain-related diseases including meningitis, encephalitis, and microcephaly. We have previously shown that local type I interferon response within the central nervous system (CNS) is involved in the protection of mice against tick-borne flavivirus infection. However, the cells responsible for mounting this protective response are not defined...
October 24, 2016: Journal of Neuroinflammation
Jason Roszik, Lauren E Haydu, Kenneth R Hess, Junna Oba, Aron Y Joon, Alan E Siroy, Tatiana V Karpinets, Francesco C Stingo, Veera Baladandayuthapani, Michael T Tetzlaff, Jennifer A Wargo, Ken Chen, Marie-Andrée Forget, Cara L Haymaker, Jie Qing Chen, Funda Meric-Bernstam, Agda K Eterovic, Kenna R Shaw, Gordon B Mills, Jeffrey E Gershenwald, Laszlo G Radvanyi, Patrick Hwu, P Andrew Futreal, Don L Gibbons, Alexander J Lazar, Chantale Bernatchez, Michael A Davies, Scott E Woodman
BACKGROUND: While clinical outcomes following immunotherapy have shown an association with tumor mutation load using whole exome sequencing (WES), its clinical applicability is currently limited by cost and bioinformatics requirements. METHODS: We developed a method to accurately derive the predicted total mutation load (PTML) within individual tumors from a small set of genes that can be used in clinical next generation sequencing (NGS) panels. PTML was derived from the actual total mutation load (ATML) of 575 distinct melanoma and lung cancer samples and validated using independent melanoma (n = 312) and lung cancer (n = 217) cohorts...
October 25, 2016: BMC Medicine
Arif Uddin, Monisha Nath Choudhury, Supriyo Chakraborty
The mitochondrially encoded NADH:ubiquinone oxidoreductase core subunit 1 (MT-ND1) gene is a subunit of the respiratory chain complex I and involved in the first step of the electron transport chain of oxidative phosphorylation (OXPHOS). To understand the pattern of compositional properties, codon usage and expression level of mitochondrial ND1 genes in pisces, aves, and mammals, we used bioinformatic approaches as no work was reported earlier. In this study, a perl script was used for calculating nucleotide contents and different codon usage bias parameters...
October 24, 2016: Mitochondrial DNA. Part A. DNA Mapping, Sequencing, and Analysis
Qi Zhang, Zhongduo Wang, Feng Hou, Rachel Harding, Xinyi Huang, Aiping Dong, John R Walker, Yufeng Tong
BACKGROUND: Seven in absentia homologs (SIAHs) comprise a family of highly conserved E3 ubiquitin ligases that play an important role in regulating signalling pathways in tumorigenesis, including the DNA damage repair and hypoxia response pathways. SIAH1 and SIAH2 have been found to function as a tumour repressor and a proto-oncogene, respectively, despite the high sequence identity of their substrate binding domains (SBDs). Ubiquitin-specific protease USP19 is a deubiquitinase that forms a complex with SIAHs and counteracts the ligase function...
October 21, 2016: Biochimica et Biophysica Acta
Suli Huang, Ziquan Lv, Yi Guo, Lu Li, Yanwei Zhang, Li Zhou, Binyao Yang, Shuang Wu, Ying Zhang, Changhui Xie, Shanshan Li, Jinquan Cheng
Circulating microRNAs (miRNAs) are emerging as novel disease biomarkers. Using a miRNA microarray, we previously showed that the whole blood level of let-7e-5p was significantly higher in ischemic stroke patients than in control subjects. However, the association between let-7e-5p expression and the occurrence of ischemic stroke remains unknown. In this study, we validated the expression levels of let-7e-5p in two case-control populations using miRNA TaqMan assays and further investigated the potential targets of let-7e-5p...
2016: PloS One
Hui Feng, Yalei Wang, Jiaojiao Su, Hongwei Liang, Chen-Yu Zhang, Xi Chen, Weiyan Yao
OBJECTIVES: ErbB3 (HER3) has been associated with pancreatic cancer progression, but little is known about its regulatory mechanisms. We investigated whether microRNAs (miRNAs) regulate levels of ErbB3 in pancreatic cancer cells. METHODS: We used bioinformatic analyses to search for miRNAs that can potentially target ERBB3. Furthermore, the biological consequences of the targeting of ERBB3 by miR-148a were examined by cell proliferation and migration assays in vitro...
October 2016: Pancreas
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