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https://www.readbyqxmd.com/read/29045840/clonal-heterogeneity-influences-the-fate-of-new-adaptive-mutations
#1
Ignacio Vázquez-García, Francisco Salinas, Jing Li, Andrej Fischer, Benjamin Barré, Johan Hallin, Anders Bergström, Elisa Alonso-Perez, Jonas Warringer, Ville Mustonen, Gianni Liti
The joint contribution of pre-existing and de novo genetic variation to clonal adaptation is poorly understood but essential to designing successful antimicrobial or cancer therapies. To address this, we evolve genetically diverse populations of budding yeast, S. cerevisiae, consisting of diploid cells with unique haplotype combinations. We study the asexual evolution of these populations under selective inhibition with chemotherapeutic drugs by time-resolved whole-genome sequencing and phenotyping. All populations undergo clonal expansions driven by de novo mutations but remain genetically and phenotypically diverse...
October 17, 2017: Cell Reports
https://www.readbyqxmd.com/read/29045605/diagnostics-for-yaws-eradication-insights-from-direct-next-generation-sequencing-of-cutaneous-strains-of-treponema-pallidum
#2
Michael Marks, Maria Fookes, Josef Wagner, Robert Butcher, Rosanna Ghinai, Oliver Sokana, Yaw-Adu Sarkodie, Sheila A Lukehart, Anthony W Solomon, David C W Mabey, Nicholas Thomson
Background: Yaws-like chronic ulcers can be caused by Treponema pallidum subsp. pertenue, Haemophilus ducreyi, or other still-undefined bacteria. To permit accurate evaluation of yaws elimination efforts programmatic use of molecular diagnostics is required. The accuracy and sensitivity of current tools remains unclear because our understanding of T. pallidum diversity is limited by the low number of sequenced genomes. Methods: We tested samples from patients with suspected yaws collected in previous studies in the Solomon Islands and Ghana...
October 16, 2017: Clinical Infectious Diseases: An Official Publication of the Infectious Diseases Society of America
https://www.readbyqxmd.com/read/29045591/sage2-parallel-human-genome-assembly
#3
Michael Molnar, Ehsan Haghshenas, Lucian Ilie
Summary: De novo genome assembly of next-generation sequencing data is a fundamental problem in bioinformatics. There are many programs that assemble small genomes, but very few can assemble whole human genomes. We present a new algorithm for parallel overlap graph construction that is capable of assembling human genomes and improves upon the current state-of-the-art in genome assembly. Availability: SAGE2 is written in C ++ and OpenMP and is freely available at github...
October 13, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29045549/emerging-treatment-paradigms-in-brain-metastasis-in-non-small-cell-lung-cancer-an-overview-of-the-current-landscape-and-challenges-ahead
#4
D Ulahannan, J Khalifa, C Faivre-Finn, S M Lee
Advances in the last decade in genomic profiling and the identification of druggable targets amenable to biological agents, has transformed the management and survival of a subgroup of patients with brain metastasis in non-small cell lung cancer. In parallel, clinicians have re-evaluated the role of whole brain radiotherapy in selected patients with brain metastases to reduce neurocognitive toxicity. Continual progress in this understudied field is required: optimisation of the sequence of schedules for therapies in patients with brain metastases of differing genomic profiles, focusing on new strategies to overcome mechanisms of biological resistance and increasing drug penetrability into the central nervous system...
October 17, 2017: Annals of Oncology: Official Journal of the European Society for Medical Oncology
https://www.readbyqxmd.com/read/29045504/molecular-tumor-boards-current-practice-and-future-needs
#5
D L van der Velden, C M L van Herpen, H W M van Laarhoven, E F Smit, H J M Groen, S M Willems, P M Nederlof, M H G Langenberg, E Cuppen, S Sleijfer, N Steeghs, E E Voest
Background: due to rapid technical advances, steeply declining sequencing costs, and the ever-increasing number of targeted therapies, it can be expected that extensive tumor sequencing such as Whole Exome- and -Genome Sequencing will soon be applied in standard care. Clinicians will thus be confronted with increasingly complex genetic information and multiple test-platforms to choose from. General medical training, meanwhile, can hardly keep up with the pace of innovation. Consequently, there is a rapidly growing gap between clinical knowledge and genetic potential in cancer care...
September 27, 2017: Annals of Oncology: Official Journal of the European Society for Medical Oncology
https://www.readbyqxmd.com/read/29045390/the-dynamics-of-molecular-evolution-over-60-000-generations
#6
Benjamin H Good, Michael J McDonald, Jeffrey E Barrick, Richard E Lenski, Michael M Desai
The outcomes of evolution are determined by a stochastic dynamical process that governs how mutations arise and spread through a population. However, it is difficult to observe these dynamics directly over long periods and across entire genomes. Here we analyse the dynamics of molecular evolution in twelve experimental populations of Escherichia coli, using whole-genome metagenomic sequencing at five hundred-generation intervals through sixty thousand generations. Although the rate of fitness gain declines over time, molecular evolution is characterized by signatures of rapid adaptation throughout the duration of the experiment, with multiple beneficial variants simultaneously competing for dominance in each population...
October 18, 2017: Nature
https://www.readbyqxmd.com/read/29044765/a-novel-inborn-error-of-the-coenzyme-q10-biosynthesis-pathway-cerebellar-ataxia-and-static-encephalomyopathy-due-to-coq5-c-methyltransferase-deficiency
#7
May Christine V Malicdan, Thierry Vilboux, Bruria Ben-Zeev, Jennifer Guo, Aviva Eliyahu, Ben Pode-Shakked, Amir Dori, Sravan Kakani, Settara C Chandrasekharappa, Carlos Ferreira, Natalia Shelestovich, Dina Marek-Yagel, Hadass Pri-Chen, Ilan Blatt, John E Niederhuber, Langping He, Camilo Toro, Robert W Taylor, John Deeken, Tal Yardeni, Douglas C Wallace, William A Gahl, Yair Anikster
Primary coenzyme Q10 (CoQ10 ; MIM# 607426) deficiencies are an emerging group of inherited mitochondrial disorders with heterogonous clinical phenotypes. Over a dozen genes are involved in the biosynthesis of CoQ10 , and mutations in several of these are associated with human disease. However, mutations in COQ5 (MIM# 616359), catalyzing the only C-methylation in the CoQ10 synthetic pathway, have not been implicated in human disease. Here, we report three female siblings of Iraqi-Jewish descent, who had varying degrees of cerebellar ataxia, encephalopathy, generalized tonic-clonic seizures and cognitive disability...
October 16, 2017: Human Mutation
https://www.readbyqxmd.com/read/29044609/phenomics-allows-identification-of-genomic-regions-affecting-maize-stomatal-conductance-with-conditional-effects-of-water-deficit-and-evaporative-demand
#8
Santiago Alvarez Prado, Llorenç Cabrera-Bosquet, Antonin Grau, Aude Coupel-Ledru, Emilie J Millet, Claude Welcker, François Tardieu
Stomatal conductance is central for the trades-off between hydraulics and photosynthesis. We aimed at deciphering its genetic control and that of its responses to evaporative demand and water deficit, a nearly impossible task with gas exchanges measurements. Whole-plant stomatal conductance was estimated via inversion of the Penman Monteith equation from data of transpiration and plant architecture collected in a phenotyping platform. We have analyzed jointly four experiments with contrasting environmental conditions imposed to a panel of 254 maize hybrids...
October 17, 2017: Plant, Cell & Environment
https://www.readbyqxmd.com/read/29044471/analysis-and-annotation-of-whole-genome-or-whole-exome-sequencing-derived-variants-for-clinical-diagnosis
#9
Elizabeth A Worthey
Over the last 10 years, next-generation sequencing (NGS) has transformed genomic research through substantial advances in technology and reduction in the cost of sequencing, and also in the systems required for analysis of these large volumes of data. This technology is now being used as a standard molecular diagnostic test in some clinical settings. The advances in sequencing have come so rapidly that the major bottleneck in identification of causal variants is no longer the sequencing or analysis (given access to appropriate tools), but rather clinical interpretation...
October 18, 2017: Current Protocols in Human Genetics
https://www.readbyqxmd.com/read/29044436/preterm-infant-associated-clostridium-tertium-clostridium-cadaveris-and-clostridium-paraputrificum-strains-genomic-and-evolutionary-insights
#10
Raymond Kiu, Shabhonam Caim, Cristina Alcon-Giner, Gusztav Belteki, Paul Clarke, Derek Pickard, Gordon Dougan, Lindsay J Hall
Clostridium species (particularly Clostridium difficile, Clostridium botulinum, Clostridium tetani and Clostridium perfringens) are associated with a range of human and animal diseases. Several other species including Clostridium tertium, Clostridium cadaveris, and Clostridium paraputrificum have also been linked with sporadic human infections, however there is very limited, or in some cases, no genomic information publicly available. Thus, we isolated one C. tertium strain, one C. cadaveris strain and three C...
October 1, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/29044423/cultured-bovine-embryo-biopsy-conserves-methylation-marks-from-original-embryo
#11
Noelia Fonseca Balvís, Soledad Garcia-Martinez, Serafín Pérez-Cerezales, Elena Ivanova, Isabel Gomez-Redondo, Meriem Hamdi, Dimitrios Rizos, Pilar Coy, Gavin Kelsey, Alfonso Gutierrez-Adan
A major limitation of embryo epigenotyping by chromatin immunoprecipitation analysis is the reduced amount of sample available from an embryo biopsy. We developed an in vitro system to expand trophectoderm cells from an embryo biopsy to overcome this limitation. This work analyzes whether expanded trophectoderm (EX) is representative of the trophectoderm (TE) methylation or adaptation to culture has altered its epigenome. We took a small biopsy from the trophectoderm (30-40 cells) of in vitro produced bovine-hatched blastocysts and cultured it on fibronectin-treated plates until we obtained ∼4 × 104 cells...
August 1, 2017: Biology of Reproduction
https://www.readbyqxmd.com/read/29044373/antimicrobial-resistance-a-one-health-perspective
#12
Laura H Kahn
Introduction: Worsening antimicrobial resistance (AMR) threatens the practice of modern human and veterinary medicine. For decades, medicine and agriculture have blamed each other for the rise of resistant microbes. Widespread use and misuse of antibiotics in both medicine and agriculture have increased the prevalence and expression of resistance genes. VRE: The rise of vancomycin-resistant Enterococcus faecium (VRE) in the European Union (EU) led to the ban of avoparcin, an antibiotic that is chemically related to vancomycin...
June 1, 2017: Transactions of the Royal Society of Tropical Medicine and Hygiene
https://www.readbyqxmd.com/read/29044207/demographic-history-and-biologically-relevant-genetic-variation-of-native-mexicans-inferred-from-whole-genome-sequencing
#13
Sandra Romero-Hidalgo, Adrián Ochoa-Leyva, Alejandro Garcíarrubio, Victor Acuña-Alonzo, Erika Antúnez-Argüelles, Martha Balcazar-Quintero, Rodrigo Barquera-Lozano, Alessandra Carnevale, Fernanda Cornejo-Granados, Juan Carlos Fernández-López, Rodrigo García-Herrera, Humberto García-Ortíz, Ángeles Granados-Silvestre, Julio Granados, Fernando Guerrero-Romero, Enrique Hernández-Lemus, Paola León-Mimila, Gastón Macín-Pérez, Angélica Martínez-Hernández, Marta Menjivar, Enrique Morett, Lorena Orozco, Guadalupe Ortíz-López, Fernando Pérez-Villatoro, Javier Rivera-Morales, Fernando Riveros-McKay, Marisela Villalobos-Comparán, Hugo Villamil-Ramírez, Teresa Villarreal-Molina, Samuel Canizales-Quinteros, Xavier Soberón
Understanding the genetic structure of Native American populations is important to clarify their diversity, demographic history, and to identify genetic factors relevant for biomedical traits. Here, we show a demographic history reconstruction from 12 Native American whole genomes belonging to six distinct ethnic groups representing the three main described genetic clusters of Mexico (Northern, Southern, and Maya). Effective population size estimates of all Native American groups remained below 2,000 individuals for up to 10,000 years ago...
October 18, 2017: Nature Communications
https://www.readbyqxmd.com/read/29043951/verrucosispora-endophytica-sp-nov-isolated-from-the-root-of-wild-orchid-grosourdya-appendiculata-blume-rchb-f
#14
Wipaporn Ngaemthao, Tawanmol Pujchakarn, Suwanee Chunhametha, Chanwit Suriyachadkun
A novel endophytic filamentous bacterium strain A-T 7972(T), was isolated from wild orchid Grosourdya appendiculata (Blume) Rchb.f. collected in Thailand. The bacterium developed single non-motile spores with warty surface on substrate mycelia. The taxonomic position was described using a polyphasic approach. The 16S rRNA gene sequence and phylogenetic analysis indicated that strain A-T 7972(T) belonged to the genus Verrucosispora and shared the highest sequence similarity with V. lutea YIM 013(T) (98.71 %) and V...
October 18, 2017: International Journal of Systematic and Evolutionary Microbiology
https://www.readbyqxmd.com/read/29043620/inserting-site-specific-dna-lesions-into-whole-genomes
#15
Vincent Pagès, Robert P Fuchs
Here, we describe a methodology that allows the insertion of site-specific DNA lesions into genomes in living cells. The technique involves the integration of a plasmid containing a site-specific lesion engineered in vitro into a precise location in the genome via the site-specific recombination reaction from phage lambda. The notion of DNA lesion is not restricted to chemically modified nucleotides but also refers to unusual DNA structures. This method will be instrumental to study qualitatively and quantitatively the genetic consequences of site-specific lesions in vivo; moreover, it does also allow analyzing the molecular structure of stalled replication forks at well-defined locations...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29042801/investigating-a-rare-methicillin-resistant-staphylococcus-aureus-strain-first-description-of-genome-sequencing-and-molecular-characterization-of-cc15-mrsa
#16
Abiola C Senok, Ali M Somily, Peter Slickers, Muhabat A Raji, Ghada Garaween, Atef Shibl, Stefan Monecke, Ralf Ehricht
PURPOSE: Methicillin resistant Staphylococcus aureus CC15 strains (CC15-MRSA) have only been sporadically described in literature. This study was carried out to describe the genetic make-up for this rare MRSA strain. METHODS: Four CC15-MRSA isolates collected in Riyadh, Saudi Arabia, between 2013 and 2014 were studied. Two isolates were from clinical infection and 2 from retail meat products. Whole genome sequencing was carried out using Illumina HiSeq2500 genome analyzer...
2017: Infection and Drug Resistance
https://www.readbyqxmd.com/read/29042633/catsper1-promoter-is-bidirectional-and-regulates-the-expression-of-a-novel-lncrna
#17
Salma E Jiménez-Badillo, Norma Oviedo, Christian Hernández-Guzmán, Lorenza González-Mariscal, Javier Hernández-Sánchez
The Catsper1 gene, whose expression is restricted to male germ cells, has great importance in reproductive biology because of its function in sperm motility and fertilization. We previously reported that the promoter of this gene has transcriptional activity in either direction in a heterologous system. In the present study, we found that the Catsper1 promoter has in vitro transcriptional activity in either orientation in GC-1 spg mouse spermatogonial cells. The results also showed that this promoter regulates the expression of a new divergent Catsper1 gene named Catsper1au (Catsper1 antisense upstream transcript)...
October 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29042411/a-horizontally-transferred-autonomous-helitron-became-a-full-polydnavirus-segment-in-cotesia-vestalis
#18
Pedro Heringer, Guilherme B Dias, Gustavo C S Kuhn
Bracoviruses associate symbiotically with thousands of parasitoid wasp species in the family Braconidae, working as virulence gene vectors, and allowing the development of wasp larvae within hosts. These viruses are composed by multiple DNA circles that are packaged into infective particles and injected together with wasp's eggs during parasitization. One of the viral segments of Cotesia vestalis bracovirus contains a gene that has been previously described as a helicase of unknown origin. Here we demonstrate that this gene is a Rep/Helicase from an intact Helitron transposable element that covers the viral segment almost entirely...
October 17, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/29041973/the-establishment-and-application-of-preimplantation-genetic-haplotyping-in-embryo-diagnosis-for-reciprocal-and-robertsonian-translocation-carriers
#19
Shuo Zhang, Caixia Lei, Junping Wu, Jing Zhou, Haiyan Sun, Jing Fu, Yijuan Sun, Xiaoxi Sun, Daru Lu, Yueping Zhang
BACKGROUND: Preimplantation genetic diagnosis (PGD) is now widely used to select embryos free of chromosomal copy number variations (CNV) from chromosome balanced translocation carriers. However, it remains a difficulty to distinguish in embryos between balanced and structurally normal chromosomes efficiently. METHODS: For this purpose, genome wide preimplantation genetic haplotyping (PGH) analysis was utilized based on single nucleotide polymorphism (SNP) microarray...
October 17, 2017: BMC Medical Genomics
https://www.readbyqxmd.com/read/29041789/epidemiological-studies-based-on-multi-locus-sequence-typing-genotype-of-methicillin-susceptible-i-staphylococcus-aureus-i-isolated-from-camel-s-milk
#20
Alsagher O Ali, Hassan Y A H Mahmoud
One hundred milk samples were collected from camel's milk for the isolation of Staphylococcus aureus. Thirty-one isolates were S. aureus, 45 were other forms of staphylococci and 24 represented other bacteria. Five isolates from S. aureus were methicillin resistant S. aureus (MRSA) and 26 samples were methicillin susceptible S. aureus (MSSA). The whole genome sequence of S. aureus was annotated and visualised by rapid annotation using subsystem technology (RAST) which is a fully-automated service for annotating complete or nearly complete bacterial genomes...
September 22, 2017: Onderstepoort Journal of Veterinary Research
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