keyword
MENU ▼
Read by QxMD icon Read
search

Core genome

keyword
https://www.readbyqxmd.com/read/28442399/the-genome-sequence-of-agrotis-segetum-granulovirus-isolate-agsegv-da-reveals-a-new-betabaculovirus-species-of-a-slow-killing-granulovirus
#1
Gianpiero Gueli Alletti, Marina Eigenbrod, Eric B Carstens, Regina G Kleespies, Johannes A Jehle
The European isolate Agrotis segetum granulovirus DA (AgseGV-DA) is a slow killing, type I granulovirus due to low dose-mortality responses within seven days post infection and a tissue tropism of infection restricted solely to the fat body of infected Agrotis segetum host larvae. The genome of AgseGV-DA was completely sequenced and compared to the whole genome sequences of the Chinese isolates AgseGV-XJ and AgseGV-L1. All three isolates share highly conserved genomes. The AgseGV-DA genome is 131,557 bp in length and encodes for 149 putative open reading frames, including 37 baculovirus core genes and the per os infectivity factor ac110...
April 22, 2017: Journal of Invertebrate Pathology
https://www.readbyqxmd.com/read/28442219/virulence-potential-of-staphylococcus-aureus-isolates-from-buruli-ulcer-patients
#2
Nana Ama Amissah, Monika A Chlebowicz, Anthony Ablordey, Caitlin S Tetteh, Isaac Prah, Tjip S van der Werf, Alex W Friedrich, Jan Maarten van Dijl, Ymkje Stienstra, John W Rossen
Buruli ulcer (BU) is a necrotizing infection of the skin and subcutaneous tissue caused by Mycobacterium ulcerans. BU wounds may also be colonized with other microorganisms including Staphylococcus aureus. This study aimed to characterize the virulence factors of S. aureus isolated from BU patients. Previously sequenced genomes of 21 S. aureus isolates from BU patients were screened for the presence of virulence genes. The results show that all S. aureus isolates harbored on their core genomes genes for known virulence factors like α-hemolysin, and the α- and β-phenol soluble modulins...
April 19, 2017: International Journal of Medical Microbiology: IJMM
https://www.readbyqxmd.com/read/28439475/transcriptomic-resources-for-an-endemic-neotropical-plant-lineage-gesneriaceae
#3
Martha L Serrano-Serrano, Anna Marcionetti, Mathieu Perret, Nicolas Salamin
PREMISE OF THE STUDY: Despite the extensive phenotypic variation that characterizes the Gesneriaceae family, there is a lack of genomic resources to investigate the molecular basis of their diversity. We developed and compared the transcriptomes for two species of the Neotropical lineage of the Gesneriaceae. METHODS AND RESULTS: Illumina sequencing and de novo assembly of floral and leaf samples were used to generate multigene sequence data for Sinningia eumorpha and S...
April 2017: Applications in Plant Sciences
https://www.readbyqxmd.com/read/28438632/molecular-diagnostic-development-for-two-begomovirus-betasatellite-complexes-undergoing-diversification-a-case-study
#4
Judith K Brown, Muhammad Zia Ur-Rehman, Sofia Avelar, N Chingandu, Usman Hameed, Saleem Haider, Muhammad Ilyas
At least five begomoviral species that cause leaf curl disease of cotton have emerged recently in Asia and Africa, reducing fiber quality and yield. The potential for the spread of these viruses to other cotton-vegetable growing regions throughout the world is extensive, owing to routine, global transport of alternative hosts of the leaf curl viruses, especially ornamentals. The research reported here describes the design and validation of polymerase chain reaction (PCR) primers undertaken to facilitate molecular detection of the two most-prevalent leaf curl-associated begomovirus-betasatellite complexes in the Indian Subcontinent and Africa, the Cotton leaf curl Kokhran virus-Burewala strain and Cotton leaf curl Gezira virus, endemic to Asia and Africa, respectively...
April 21, 2017: Virus Research
https://www.readbyqxmd.com/read/28437468/role-of-cleavage-at-the-core-e1-junction-of-hepatitis-c-virus-polyprotein-in-viral-morphogenesis
#5
Véronique Pène, Matthieu Lemasson, Francis Harper, Gérard Pierron, Arielle R Rosenberg
In hepatitis C virus (HCV) polyprotein sequence, core protein terminates with E1 envelope signal peptide. Cleavage by signal peptidase (SP) separates E1 from the complete form of core protein, anchored in the endoplasmic reticulum (ER) membrane by the signal peptide. Subsequent cleavage of the signal peptide by signal-peptide peptidase (SPP) releases the mature form of core protein, which preferentially relocates to lipid droplets. Both of these cleavages are required for the HCV infectious cycle, supporting the idea that HCV assembly begins at the surface of lipid droplets, yet SPP-catalyzed cleavage is dispensable for initiation of budding in the ER...
2017: PloS One
https://www.readbyqxmd.com/read/28434945/prognostic-biomarker-identification-through-integrating-the-gene-signatures-of-hepatocellular-carcinoma-properties
#6
Jialin Cai, Bin Li, Yan Zhu, Xuqian Fang, Mingyu Zhu, Mingjie Wang, Shupeng Liu, Xiaoqing Jiang, Jianming Zheng, XinXin Zhang, Peizhan Chen
Many molecular classification and prognostic gene signatures for hepatocellular carcinoma (HCC) patients have been established based on genome-wide gene expression profiling; however, their generalizability is unclear. Herein, we systematically assessed the prognostic effects of these gene signatures and identified valuable prognostic biomarkers by integrating these gene signatures. With two independent HCC datasets (GSE14520, N=242 and GSE54236, N=78), 30 published gene signatures were evaluated, and 11 were significantly associated with the overall survival (OS) of postoperative HCC patients in both datasets...
April 12, 2017: EBioMedicine
https://www.readbyqxmd.com/read/28432356/a-role-of-human-rnase-p-subunits-rpp29-and-rpp21-in-homology-directed-repair-of-double-strand-breaks
#7
Enas R Abu-Zhayia, Hanan Khoury-Haddad, Noga Guttmann-Raviv, Raphael Serruya, Nayef Jarrous, Nabieh Ayoub
DNA damage response (DDR) is needed to repair damaged DNA for genomic integrity preservation. Defective DDR causes accumulation of deleterious mutations and DNA lesions that can lead to genomic instabilities and carcinogenesis. Identifying new players in the DDR, therefore, is essential to advance the understanding of the molecular mechanisms by which cells keep their genetic material intact. Here, we show that the core protein subunits Rpp29 and Rpp21 of human RNase P complex are implicated in DDR. We demonstrate that Rpp29 and Rpp21 depletion impairs double-strand break (DSB) repair by homology-directed repair (HDR), but has no deleterious effect on the integrity of non-homologous end joining...
April 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28431857/modeling-human-infertility-with-pluripotent-stem-cells
#8
Di Chen, Joanna J Gell, Yu Tao, Enrique Sosa, Amander T Clark
Human fertility is dependent upon the correct establishment and differentiation of the germline. This is because no other cell type in the body is capable of passing a genome and epigenome from parent to child. Terminally differentiated germline cells in the adult testis and ovary are called gametes. However, the initial specification of germline cells occurs in the embryo around the time of gastrulation. Most of our knowledge regarding the cell and molecular events that govern human germline specification involves extrapolating scientific principles from model organisms, most notably the mouse...
April 13, 2017: Stem Cell Research
https://www.readbyqxmd.com/read/28431284/mitovirus-uga-trp-codon-usage-parallels-that-of-host-mitochondria
#9
Max L Nibert
Mitoviruses replicate in mitochondria of their host fungi. They have small RNA genomes that encompass a single ORF encoding the viral RdRp. Since UGA codons encode Trp in fungal mitochondria, the RdRp ORF of a typical mitovirus includes multiple UGA codons. In some mitoviruses, however, the ORF has no such codons, suggesting that these particular viruses may be under selective pressure to exclude them. In this report, new evidence is presented that host fungi whose mitoviruses have no or few UGA codons are distinctive in also having no or few UGA codons in their core mitochondrial genes...
April 18, 2017: Virology
https://www.readbyqxmd.com/read/28430982/evidence-of-nuclei-encoded-spliceosome-mediating-splicing-of-mitochondrial-rna
#10
Roberto H Herai, Priscilla D Negraes, Alysson R Muotri
Mitochondria are thought to have originated as free-living prokaryotes. Mitochondria organelles have small circular genomes with substantial structural (absence of histones and introns) and genetic similarity to bacteria. Contrary to the prevailing concept of intronless mitochondria, here we present evidences that mitochondrial RNA transcripts (mtRNA) are not limited to policystronic molecules, but also processed as nuclei-like transcripts that are differentially spliced and expressed in a cell-type specific manner...
April 19, 2017: Human Molecular Genetics
https://www.readbyqxmd.com/read/28430818/comparative-genomics-of-burkholderia-multivorans-a-ubiquitous-pathogen-with-a-highly-conserved-genomic-structure
#11
Charlotte Peeters, Vaughn S Cooper, Philip J Hatcher, Bart Verheyde, Aurélien Carlier, Peter Vandamme
The natural environment serves as a reservoir of opportunistic pathogens. A well-established method for studying the epidemiology of such opportunists is multilocus sequence typing, which in many cases has defined strains predisposed to causing infection. Burkholderia multivorans is an important pathogen in people with cystic fibrosis (CF) and its epidemiology suggests that strains are acquired from non-human sources such as the natural environment. This raises the central question of whether the isolation source (CF or environment) or the multilocus sequence type (ST) of B...
2017: PloS One
https://www.readbyqxmd.com/read/28430577/synthetic-lethal-interaction-between-the-tumour-suppressor-stag2-and-its-paralog-stag1
#12
Lorena Benedetti, Matteo Cereda, LeeAnn Monteverde, Nikita Desai, Francesca D Ciccarelli
Cohesin is a multi-protein complex that tethers sister chromatids during mitosis and mediates DNA repair, genome compartmentalisation and regulation of gene expression. Cohesin subunits frequently acquire cancer loss-of-function alterations and act as tumour suppressors in several tumour types. This has led to increased interest in cohesin as potential target in anti-cancer therapy. Here we show that the loss-of-function of STAG2, a core component of cohesin and an emerging tumour suppressor, leads to synthetic dependency of mutated cancer cells on its paralog STAG1...
April 5, 2017: Oncotarget
https://www.readbyqxmd.com/read/28428793/transcriptomics-targeted-metabolomics-and-gene-expression-of-blackberry-leaves-and-fruits-indicate-flavonoid-metabolic-flux-from-leaf-to-red-fruit
#13
Enrique Gutierrez, Ana García-Villaraco, José A Lucas, Ana Gradillas, F Javier Gutierrez-Mañero, Beatriz Ramos-Solano
Blackberries (Rubus spp.) are among the high added value food products relevant for human health due to the increasing evidence of the beneficial effects of polyphenols, which are very abundant in these fruits. Interestingly, these compounds also play a role on plant physiology, being especially relevant their role in plant defense against biotic and abiotic stress. Hence, we hypothesize that since blackberry fruits have high amounts of flavonols and anthocyanins, leaves would also have high amounts of these compounds, and can be studied as a source of active molecules; furthermore, leaf synthesis would support their high contents in fruits...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28428776/mapping-and-identification-of-antifungal-peptides-in-the-putative-antifungal-protein-afpb-from-the-filamentous-fungus-penicillium-digitatum
#14
Sandra Garrigues, Mónica Gandía, Attila Borics, Florentine Marx, Paloma Manzanares, Jose F Marcos
Antifungal proteins (AFPs) from Ascomycetes are small cysteine-rich proteins that are abundantly secreted and show antifungal activity against non-producer fungi. A gene coding for a class B AFP (AfpB) was previously identified in the genome of the plant pathogen Penicillium digitatum. However, previous attempts to detect the AfpB protein were not successful despite the high expression of the corresponding afpB gene. In this work, the structure of the putative AfpB was modeled. Based on this model, four synthetic cysteine-containing peptides, PAF109, PAF112, PAF118, and PAF119, were designed and their antimicrobial activity was tested and characterized...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28428554/network-assisted-analysis-of-gwas-data-identifies-a-functionally-relevant-gene-module-for-childhood-onset-asthma
#15
Y Liu, M Brossard, C Sarnowski, A Vaysse, M Moffatt, P Margaritte-Jeannin, F Llinares-López, M H Dizier, M Lathrop, W Cookson, E Bouzigon, F Demenais
The number of genetic factors associated with asthma remains limited. To identify new genes with an undetected individual effect but collectively influencing asthma risk, we conducted a network-assisted analysis that integrates outcomes of genome-wide association studies (GWAS) and protein-protein interaction networks. We used two GWAS datasets, each consisting of the results of a meta-analysis of nine childhood-onset asthma GWASs (5,924 and 6,043 subjects, respectively). We developed a novel method to compute gene-level P-values (fastCGP), and proposed a parallel dense-module search and cross-selection strategy to identify an asthma-associated gene module...
April 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28426720/a-new-model-mimicking-persistent-hbv-e-antigen-negative-infection-using-covalently-closed-circular-dna-in-immunocompetent-mice
#16
Lei Wang, Min Cao, Qing Lu Wei, Zhong Hua Zhao, Qin Xiang, Hui Juan Wang, Hua Tang Zhang, Guo Qi Lai
Despite the availability of an effective vaccine, hepatitis B virus (HBV) infection remains a major health problem. HBV e antigen (HBeAg)-negative strains have become prevalent. Previously, no animal model mimicked the clinical course of HBeAg-negative HBV infection. To establish an HBeAg-negative HBV infection model, the 3.2-kb full-length genome of HBeAg-negative HBV was cloned from a clinical sample and then circularized to form covalently closed circular (cccDNA). The resulting cccDNA was introduced into the liver of C57BL/6J mice through hydrodynamic injection...
2017: PloS One
https://www.readbyqxmd.com/read/28425915/competition-between-histone-and-transcription-factor-binding-regulates-the-onset-of-transcription-in-zebrafish-embryos
#17
Shai R Joseph, Máté Pálfy, Lennart Hilbert, Mukesh Kumar, Jens Karschau, Vasily Zaburdaev, Andrej Shevchenko, Nadine L Vastenhouw
Upon fertilization, the genome of animal embryos remains transcriptionally inactive until the maternal-to-zygotic transition. At this time, the embryo takes control of its development and transcription begins. How the onset of zygotic transcription is regulated remains unclear. Here, we show that a dynamic competition for DNA binding between nucleosome-forming histones and transcription factors regulates zebrafish genome activation. Taking a quantitative approach, we found that the concentration of non-DNA bound core histones sets the time for the onset of transcription...
April 20, 2017: ELife
https://www.readbyqxmd.com/read/28424731/identification-of-tify-family-genes-and-analysis-of-their-expression-profiles-in-response-to-phytohormone-treatments-and-melampsora-larici-populina-infection-in-poplar
#18
Wenxiu Xia, Hongyan Yu, Pei Cao, Jie Luo, Nian Wang
The TIFY domain contains approximately 36 conserved amino acids that form the core motif TIF[F/Y]XG, and they were reported to play important roles in plant growth, tissue development and defense regulation. Moreover, more and more evidence has shown that some members of the TIFY gene family perform their functions by modulating plant hormone signaling pathways. Poplar trees are found worldwide, and they comprise approximately 30 species. Benefit from the importance of poplar and its advanced platform, this tree is considered to be the model perennial plant...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28423718/itraq-based-quantitative-proteomic-analysis-of-yamanaka-factors-reprogrammed-breast-cancer-cells
#19
Kun Wang, Zhiyan Shan, Lian Duan, Tiantian Gong, Feng Liu, Yue Zhang, Zhendong Wang, Jingling Shen, Lei Lei
Cancer cells had been developed to be reprogrammed into embryonic stem like cells by induced pluripotent stem cells (iPSCs) technology, however, the tumor differentiation/dedifferentiation mechanisms had not yet been analyzed on a genome-wide scale. Here, we inserted the four stem cell transcription factor genes OCT4, SOX2, C-MYC and KLF4 into MCF cells (MCFs), represented a female breast cancer cell type, and obtained iPSCs (Mcfips) in about 3 weeks. By using the LC MS/MS iTRAQ technology, we analyzed the proteomic changes between MCFs and Mcfips...
March 11, 2017: Oncotarget
https://www.readbyqxmd.com/read/28423671/genome-wide-dna-methylation-analysis-reveals-molecular-subtypes-of-pancreatic-cancer
#20
Nitish Kumar Mishra, Chittibabu Guda
Pancreatic cancer (PC) is the fourth leading cause of cancer deaths in the United States with a five-year patient survival rate of only 6%. Early detection and treatment of this disease is hampered due to lack of reliable diagnostic and prognostic markers. Recent studies have shown that dynamic changes in the global DNA methylation and gene expression patterns play key roles in the PC development; hence, provide valuable insights for better understanding the initiation and progression of PC. In the current study, we used DNA methylation, gene expression, copy number, mutational and clinical data from pancreatic patients...
March 7, 2017: Oncotarget
keyword
keyword
31169
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"