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https://www.readbyqxmd.com/read/28092693/pathogenic-streptococcus-strains-employ-novel-escape-strategy-to-inhibit-bacteriostatic-effect-mediated-by-mammalian-peptidoglycan-recognition-protein
#1
Jing Wang, Youjun Feng, Changjun Wang, Swaminath Srinivas, Chen Chen, Hui Liao, Elaine He, Shibo Jiang, Jiaqi Tang
Pathogenic streptococcal species are responsible for some of the most lethal and prevalent animal and human infections. Previous reports have identified a candidate pathogenicity island (PAI) in two highly virulent clinical isolates of Streptococcus suis type 2 (SS2), a causative agent of high-mortality streptococcal toxic shock syndrome (STSS). This PAI contains a Type-IVC secretion system C subgroup (Type-IVC secretion system) that is involved in the secretion of unknown pathogenic effectors that are responsible for STSS caused by highly virulent strains of SS2...
January 16, 2017: Cellular Microbiology
https://www.readbyqxmd.com/read/28092684/biallelic-mutations-in-the-3-exonuclease-toe1-cause-pontocerebellar-hypoplasia-and-uncover-a-role-in-snrna-processing
#2
Rea M Lardelli, Ashleigh E Schaffer, Veerle R C Eggens, Maha S Zaki, Stephanie Grainger, Shashank Sathe, Eric L Van Nostrand, Zinayida Schlachetzki, Basak Rosti, Naiara Akizu, Eric Scott, Jennifer L Silhavy, Laura Dean Heckman, Rasim Ozgur Rosti, Esra Dikoglu, Anne Gregor, Alicia Guemez-Gamboa, Damir Musaev, Rohit Mande, Ari Widjaja, Tim L Shaw, Sebastian Markmiller, Isaac Marin-Valencia, Justin H Davies, Linda de Meirleir, Hulya Kayserili, Umut Altunoglu, Mary Louise Freckmann, Linda Warwick, David Chitayat, Susan Blaser, Ahmet Okay Çağlayan, Kaya Bilguvar, Huseyin Per, Christina Fagerberg, Henrik T Christesen, Maria Kibaek, Kimberly A Aldinger, David Manchester, Naomichi Matsumoto, Kazuhiro Muramatsu, Hirotomo Saitsu, Masaaki Shiina, Kazuhiro Ogata, Nicola Foulds, William B Dobyns, Neil C Chi, David Traver, Luigina Spaccini, Stefania Maria Bova, Stacey B Gabriel, Murat Gunel, Enza Maria Valente, Marie-Cecile Nassogne, Eric J Bennett, Gene W Yeo, Frank Baas, Jens Lykke-Andersen, Joseph G Gleeson
Deadenylases are best known for degrading the poly(A) tail during mRNA decay. The deadenylase family has expanded throughout evolution and, in mammals, consists of 12 Mg(2+)-dependent 3'-end RNases with substrate specificity that is mostly unknown. Pontocerebellar hypoplasia type 7 (PCH7) is a unique recessive syndrome characterized by neurodegeneration and ambiguous genitalia. We studied 12 human families with PCH7, uncovering biallelic, loss-of-function mutations in TOE1, which encodes an unconventional deadenylase...
January 16, 2017: Nature Genetics
https://www.readbyqxmd.com/read/28091882/identification-of-some-main-streptococcus-iniae-associated-proteins-relationship
#3
Fatima El Aamri, José Ángel Guillén, Daniel Padilla, Félix Acosta, Fernando Real
The surface-associated proteins play a key role in bacterial physiology and pathogenesis, and are the major targets in the development of new vaccines. These proteins contribute to the adaptation of bacteria to different hosts and environments. To study differences at the genomic level, we first sequenced the whole genome of Streptococcus iniae from fish (IUSA-1 strain) and compared it to Streptococcus iniae from human (9117 strain), revealing a high similitude between both strains. To gain further insights into host- and environment-specific differences, we then studied proteins in silico and by High Performance Liquid Chromatography...
January 14, 2017: Veterinary Research Communications
https://www.readbyqxmd.com/read/28091623/comparative-genomics-of-canine-isolated-leishmania-leishmania-amazonensis-from-an-endemic-focus-of-visceral-leishmaniasis-in-governador-valadares-southeastern-brazil
#4
Hugo O Valdivia, Laila V Almeida, Bruno M Roatt, João Luís Reis-Cunha, Agnes Antônia Sampaio Pereira, Celia Gontijo, Ricardo Toshio Fujiwara, Alexandre B Reis, Mandy J Sanders, James A Cotton, Daniella C Bartholomeu
Leishmaniasis is a highly diverse group of diseases caused by kinetoplastid of the genus Leishmania. These parasites are taxonomically diverse, with human pathogenic species separated into two subgenera according to their development site inside the alimentary tract of the sand fly insect vector. The disease encompasses a variable spectrum of clinical manifestations with tegumentary or visceral symptoms. Among the causative species in Brazil, Leishmania (Leishmania) amazonensis is an important etiological agent of human cutaneous leishmaniasis that accounts for more than 8% of all cases in endemic regions...
January 16, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28091388/blood-meal-identification-of-the-mosquito-diptera-culicidae-specimens-belong-to-culex-pipiens-complex-that-were-collected-from-kayseri-province
#5
Seval Korkmaz, Alparslan Yıldırım, Önder Düzlü, Arif Çiloğlu, Zuhal Önder, Abdullah İnci
OBJECTIVE: This study aimed to determine the host preferences in blood meal of specimens belonging to Culex pipiens complex. METHODS: A total of 1284 female mosquitos were morphologically examined, and genomic DNA isolations were individually performed on 376 (28.4%) specimens that were determined to be Cx. pipiens complex. PCR was performed with primers to specifically amplify the avian and mammalian mitochondrial cytochrome b (mt-cytb) gene region. Amplicons were cloned, and the obtained plasmids were sequenced to determine host species...
December 2016: Türkiye Parazitolojii Dergisi
https://www.readbyqxmd.com/read/28090760/expression-patterns-of-cardiac-aging-in-drosophila
#6
Leah Cannon, Alexander C Zambon, Anthony Cammarato, Zhi Zhang, Georg Vogler, Matthew Munoz, Erika Taylor, Jérôme Cartry, Sanford I Bernstein, Simon Melov, Rolf Bodmer
Aging causes cardiac dysfunction, often leading to heart failure and death. The molecular basis of age-associated changes in cardiac structure and function is largely unknown. The fruit fly, Drosophila melanogaster, is well-suited to investigate the genetics of cardiac aging. Flies age rapidly over the course of weeks, benefit from many tools to easily manipulate their genome, and their heart has significant genetic and phenotypic similarities to the human heart. Here, we performed a cardiac-specific gene expression study on aging Drosophila and carried out a comparative meta-analysis with published rodent data...
February 2017: Aging Cell
https://www.readbyqxmd.com/read/28090699/modelling-irf8-deficient-human-hematopoiesis-and-dendritic-cell-development-with-engineered-ips-cells
#7
Stephanie Sontag, Malrun Förster, Jie Qin, Paul Wanek, Saskia Mitzka, Herdit M Schüler, Steffen Koschmieder, Stefan Rose-John, Kristin Seré, Martin Zenke
Human induced pluripotent stem (iPS) cells can differentiate into cells of all three germ layers, including hematopoietic stem cells and their progeny. Interferon regulatory factor 8 (IRF8) is a transcription factor, which acts in hematopoiesis as lineage determining factor for myeloid cells, including dendritic cells (DC). Autosomal recessive or dominant IRF8 mutations occurring in patients cause severe monocytic and DC immunodeficiency. To study IRF8 in human hematopoiesis we generated human IRF8-/- iPS cells and IRF8-/- embryonic stem (ES) cells using RNA guided CRISPR/Cas9n genome editing...
January 16, 2017: Stem Cells
https://www.readbyqxmd.com/read/28090592/the-first-genome-sequences-of-human-bocaviruses-from-vietnam
#8
Tran Tan Thanh, Hoang Minh Tu Van, Nguyen Thi Thu Hong, Le Nguyen Truc Nhu, Nguyen To Anh, Ha Manh Tuan, Ho Van Hien, Nguyen Manh Tuong, Trinh Trung Kien, Truong Huu Khanh, Le Nguyen Thanh Nhan, Nguyen Thanh Hung, Nguyen Van Vinh Chau, Guy Thwaites, H Rogier van Doorn, Le Van Tan
As part of an ongoing effort to generate complete genome sequences of hand, foot and mouth disease-causing enteroviruses directly from clinical specimens, two complete coding sequences and two partial genomic sequences of human bocavirus 1 (n=3) and 2 (n=1) were co-amplified and sequenced, representing the first genome sequences of human bocaviruses from Vietnam. The sequences may aid future study aiming at understanding the evolution of the pathogen.
November 16, 2016: Wellcome Open Res
https://www.readbyqxmd.com/read/28090586/holliday-junction-trap-shows-how-cells-use-recombination-and-a-junction-guardian-role-of-recq-helicase
#9
Jun Xia, Li-Tzu Chen, Qian Mei, Chien-Hui Ma, Jennifer A Halliday, Hsin-Yu Lin, David Magnan, John P Pribis, Devon M Fitzgerald, Holly M Hamilton, Megan Richters, Ralf B Nehring, Xi Shen, Lei Li, David Bates, P J Hastings, Christophe Herman, Makkuni Jayaram, Susan M Rosenberg
DNA repair by homologous recombination (HR) underpins cell survival and fuels genome instability, cancer, and evolution. However, the main kinds and sources of DNA damage repaired by HR in somatic cells and the roles of important HR proteins remain elusive. We present engineered proteins that trap, map, and quantify Holliday junctions (HJs), a central DNA intermediate in HR, based on catalytically deficient mutant RuvC protein of Escherichia coli. We use RuvCDefGFP (RDG) to map genomic footprints of HR at defined DNA breaks in E...
November 2016: Science Advances
https://www.readbyqxmd.com/read/28090239/the-screening-and-ranking-algorithm-for-change-points-detection-in-multiple-samples
#10
Chi Song, Xiaoyi Min, Heping Zhang
The chromosome copy number variation (CNV) is the deviation of genomic regions from their normal copy number states, which may associate with many human diseases. Current genetic studies usually collect hundreds to thousands of samples to study the association between CNV and diseases. CNVs can be called by detecting the change-points in mean for sequences of array-based intensity measurements. Although multiple samples are of interest, the majority of the available CNV calling methods are single sample based...
December 2016: Annals of Applied Statistics
https://www.readbyqxmd.com/read/28089818/notochordal-cell-derived-conditioned-medium-nccm-protects-human-nucleus-pulposus-cells-from-stress-induced-apoptosis
#11
Arne Mehrkens, Ajay Matta, M Zia Karim, Sarah Kim, Michael G Fehlings, Stefan Schaeren, W Mark Erwin
BACKGROUND CONTEXT: Degenerative Disc Disease (DDD) remains without an effective therapy and presents a costly burden to society. PURPOSE: Based upon prior reports concerning the effects of notochordal cell conditioned medium (NCCM) upon disc cells, we performed a proof of principle study to determine whether NCCM could reduce cytotoxic stress induced apoptosis in human disc nucleus pulpous (NP) cells. STUDY DESIGN/SETTING: 'in vitro' fundamental/basic science study METHODS: NP cells derived from 15 patients undergoing spinal surgery were treated with interleukin 1β (IL-1β) and Fas ligand (FasL) or etoposide in the presence of NCCM...
January 9, 2017: Spine Journal: Official Journal of the North American Spine Society
https://www.readbyqxmd.com/read/28089755/biodistribution-and-retention-of-locally-administered-human-mesenchymal-stromal-cells-quantitative-polymerase-chain-reaction-based-detection-of-human-dna-in-murine-organs
#12
Michael Creane, Linda Howard, Timothy O'Brien, Cynthia M Coleman
BACKGROUND: Determining the distributive fate and retention of a cell therapy product after administration is an essential part of characterizing it's biosafety profile. Therefore, regulatory guidelines stipulate that biodistribution assays are a requirement prior to advancing a cell therapy to the clinic. Here the development of a highly sensitive quantitative polymerase chain reaction (qPCR)-based method of tracking the biodistribution and retention of human mesenchymal stromal cells (hMSCs) in mice, rats or rabbits is described...
January 12, 2017: Cytotherapy
https://www.readbyqxmd.com/read/28089486/molecular-genetics-of-human-obesity-a-comprehensive-review
#13
Rajan Kumar Singh, Permendra Kumar, Kulandaivelu Mahalingam
Obesity and its related health complications is a major problem worldwide. Hypothalamus and their signalling molecules play a critical role in the intervening and coordination with energy balance and homeostasis. Genetic factors play a crucial role in determining an individual's predisposition to the weight gain and being obese. In the past few years, several genetic variants were identified as monogenic forms of human obesity having success over common polygenic forms. In the context of molecular genetics, genome-wide association studies (GWAS) approach and their findings signified a number of genetic variants predisposing to obesity...
January 12, 2017: Comptes Rendus Biologies
https://www.readbyqxmd.com/read/28089356/insertions-and-deletions-target-lineage-defining-genes-in-human-cancers
#14
Marcin Imielinski, Guangwu Guo, Matthew Meyerson
Certain cell types function as factories, secreting large quantities of one or more proteins that are central to the physiology of the respective organ. Examples include surfactant proteins in lung alveoli, albumin in liver parenchyma, and lipase in the stomach lining. Whole-genome sequencing analysis of lung adenocarcinomas revealed noncoding somatic mutational hotspots near VMP1/MIR21 and indel hotspots in surfactant protein genes (SFTPA1, SFTPB, and SFTPC). Extrapolation to other solid cancers demonstrated highly recurrent and tumor-type-specific indel hotspots targeting the noncoding regions of highly expressed genes defining certain secretory cellular lineages: albumin (ALB) in liver carcinoma, gastric lipase (LIPF) in stomach carcinoma, and thyroglobulin (TG) in thyroid carcinoma...
January 11, 2017: Cell
https://www.readbyqxmd.com/read/28089252/practical-approaches-for-whole-genome-sequence-analysis-of-heart-and-blood-related-traits
#15
Alanna C Morrison, Zhuoyi Huang, Bing Yu, Ginger Metcalf, Xiaoming Liu, Christie Ballantyne, Josef Coresh, Fuli Yu, Donna Muzny, Elena Feofanova, Navin Rustagi, Richard Gibbs, Eric Boerwinkle
Whole-genome sequencing (WGS) allows for a comprehensive view of the sequence of the human genome. We present and apply integrated methodologic steps for interrogating WGS data to characterize the genetic architecture of 10 heart- and blood-related traits in a sample of 1,860 African Americans. In order to evaluate the contribution of regulatory and non-protein coding regions of the genome, we conducted aggregate tests of rare variation across the entire genomic landscape using a sliding window, complemented by an annotation-based assessment of the genome using predefined regulatory elements and within the first intron of all genes...
January 5, 2017: American Journal of Human Genetics
https://www.readbyqxmd.com/read/28089213/a-genome-wide-profiling-of-brain-dna-hydroxymethylation-in-alzheimer-s-disease
#16
Jinying Zhao, Yun Zhu, Jingyun Yang, Lin Li, Hao Wu, Philip L De Jager, Peng Jin, David A Bennett
INTRODUCTION: DNA methylation is a key epigenetic mechanism in brain aging and Alzheimer's disease (AD). The newly discovered 5-hydroxymethylcytosine mediates DNA demethylation, is highly abundant in the brain, and is dynamically regulated by life experiences. However, little is known about its genome-wide patterns and potential role in AD. METHODS: Using a genome-wide capture followed by high-throughput sequencing, we studied the genome-wide distribution of 5-hydroxymethylcytosine at specific genomic loci in human AD brain and identified differentially hydroxymethylated regions (DhMRs) associated with AD pathology...
January 6, 2017: Alzheimer's & Dementia: the Journal of the Alzheimer's Association
https://www.readbyqxmd.com/read/28088694/metabolic-network-modeling-with-model-organisms
#17
REVIEW
L Safak Yilmaz, Albertha Jm Walhout
Flux balance analysis (FBA) with genome-scale metabolic network models (GSMNM) allows systems level predictions of metabolism in a variety of organisms. Different types of predictions with different accuracy levels can be made depending on the applied experimental constraints ranging from measurement of exchange fluxes to the integration of gene expression data. Metabolic network modeling with model organisms has pioneered method development in this field. In addition, model organism GSMNMs are useful for basic understanding of metabolism, and in the case of animal models, for the study of metabolic human diseases...
January 12, 2017: Current Opinion in Chemical Biology
https://www.readbyqxmd.com/read/28088541/secretory-pathway-optimization-of-cho-producer-cells-by-co-engineering-of-the-mitosrna-1978-target-genes-cers2-and-tbc1d20
#18
Lisa A Pieper, Michaela Strotbek, Till Wenger, Martin Gamer, Monilola A Olayioye, Angelika Hausser
Chinese Hamster Ovary (CHO) cells are the most commonly used host for the production of biopharmaceuticals. Although transcription and translation engineering strategies have been employed to generate high-producer cell clones, the secretory pathway still remains a bottleneck in cellular productivity. In this study we show that ectopic expression of a human mitochondrial genome-encoded small RNA (mitosRNA-1978) in an IgG expressing CHO cell line strongly improved specific productivity by functioning in a microRNA-like fashion...
January 11, 2017: Metabolic Engineering
https://www.readbyqxmd.com/read/28088539/the-dna-damage-response-of-c-elegans-affected-by-gravity-sensing-and-radiosensitivity-during-the-shenzhou-8-spaceflight
#19
Ying Gao, Dan Xu, Lei Zhao, Yeqing Sun
Space radiation and microgravity are recognized as primary and inevitable risk factors for humans traveling in space, but the reports regarding their synergistic effects remain inconclusive and vary across studies due to differences in the environmental conditions and intrinsic biological sensitivity. Thus, we studied the synergistic effects on transcriptional changes in the global genome and DNA damage response (DDR) by using dys-1 mutant and ced-1 mutant of C. elegans, which respectively presented microgravity-insensitivity and radiosensitivity when exposure to spaceflight condition (SF) and space radiation (SR)...
January 7, 2017: Mutation Research
https://www.readbyqxmd.com/read/28088524/possible-roles-of-the-transcription-factor-nrf1-nfe2l1-in-neural-homeostasis-by-regulating-the-gene-expression-of-deubiquitinating-enzymes
#20
Hiroaki Taniguchi, Shota Okamuro, Misaki Kohji, Tsuyoshi Waku, Kaori Kubo, Atsushi Hatanaka, Yimeng Sun, A M Masudul Azad Chowdhury, Akiyoshi Fukamizu, Akira Kobayashi
The transcription factor Nrf1 (NFE2L1) maintains protein homeostasis (proteostasis) by regulating the gene expression of proteasome subunits in response to proteasome inhibition. The deletion of the Nrf1 gene in neural stem/progenitor cells causes severe neurodegeneration due to the accumulation of ubiquitinated proteins in Purkinje cells and motor neurons (Nrf1 NKO mice). However, the molecular mechanisms governing this neurodegenerative process remain unclear. We demonstrate herein that the loss of Nrf1 leads to the reduced gene expression of the deubiquitinating enzymes (DUBs) but not proteasome subunits in Nrf1 NKO mice between P7 and P18...
January 11, 2017: Biochemical and Biophysical Research Communications
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