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https://www.readbyqxmd.com/read/28340380/the-origin-and-evolution-of-the-term-clone
#1
David P Steensma
In biology, the term "clone" is most widely used to designate genetically identical cells or organisms that are asexually descended from a common progenitor. The concept of clonality in hematology-oncology has received much attention in recent years, as the advent of next-generation sequencing platforms has provided new tools for detection of clonal populations in patients, and experiments on primary cells have provided fascinating new insights into the clonal architecture of human malignancies. The term "clone" is used more loosely by the general public to mean any close or identical copy...
March 4, 2017: Leukemia Research
https://www.readbyqxmd.com/read/28338786/recombination-mediated-host-adaptation-by-avian-staphylococcus-aureus
#2
Susan Murray, Ben Pascoe, Guillaume Méric, Leonardos Mageiros, Koji Yahara, Matthew D Hitchings, Yasmin Friedmann, Thomas S Wilkinson, Fraser J Gormley, Dietrich Mack, James E Bray, Sarah Lamble, Rory Bowden, Keith A Jolley, Martin C J Maiden, Sarah Wendlandt, Stefan Schwarz, Jukka Corander, J Ross Fitzgerald, Samuel K Sheppard
Staphylococcus aureus are globally disseminated among farmed chickens causing skeletal muscle infections, dermatitis and septicaemia. The emergence of poultry-associated lineages has involved zoonotic transmission from humans to chickens but questions remain about the specific adaptations that promote proliferation of chicken pathogens. We characterised genetic variation in a population of genome-sequenced S. aureus isolates of poultry and human origin. Genealogical analysis identified a dominant poultry-associated sequence cluster within the CC5 clonal complex...
February 28, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28335715/cytotype-coexistence-in-the-field-cannot-be-explained-by-inter-cytotype-hybridization-alone-linking-experiments-and-computer-simulations-in-the-sexual-species-pilosella-echioides-asteraceae
#3
Jindřich Chrtek, Tomáš Herben, Radka Rosenbaumová, Zuzana Münzbergová, Zuzana Dočkalová, Jaroslav Zahradníček, Jana Krejčíková, Pavel Trávníček
BACKGROUND: Processes driving ploidal diversity at the population level are virtually unknown. Their identification should use a combination of large-scale screening of ploidy levels in the field, pairwise crossing experiments and mathematical modelling linking these two types of data. We applied this approach to determine the drivers of frequencies of coexisting cytotypes in mixed-ploidy field populations of the fully sexual plant species Pilosella echioides. We examined fecundity and ploidal diversity in seeds from all possible pairwise crosses among 2x, 3x and 4x plants...
March 23, 2017: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/28334409/siapopr-a-computational-method-to-simulate-evolutionary-branching-trees-for-analysis-of-tumor-clonal-evolution
#4
Thomas O McDonald, Franziska Michor
Summary: SIApopr (Simulating Infinite-Allele populations) is an R package to simulate homogeneous and inhomogeneous stochastic branching processes under a very flexible set of assumptions using the speed of C ++. The software simulates clonal evolution with the emergence of driver and passenger mutations under the infinite-allele assumption. The software is an application of the Gillespie Stochastic Simulation Algorithm expanded to a large number of cell types and scenarios, with the intention of allowing users to easily modify existing models or create their own...
March 16, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28334141/distribution-of-antimicrobial-resistance-determinants-virulence-associated-factors-and-crispr-loci-in-isolates-of-enterococcus-faecalis-from-various-settings-and-genetic-lineages
#5
Iwona Gawryszewska, Katarzyna Malinowska, Alicja Kuch, Dorota Chrobak-Chmiel, Lucja Laniewska-Trokenheim, Waleria Hryniewicz, Ewa Sadowy
Enterococcus faecalis represents an important factor of hospital-associated infections (HAIs). The knowledge on its evolution from a commensal to an opportunistic pathogen is still limited, thus we performed a study to characterize distribution of factors that may contribute to this adaptation. Using a collection obtained from various settings (hospitalized patients, community carriers, animals, fresh food, sewage, water) we investigated differences in antimicrobial susceptibility, distribution of antimicrobial resistance genes, virulence-associated determinants and phenotypes, and CRISPR loci in the context of the clonal relatedness of isolates...
March 1, 2017: Pathogens and Disease
https://www.readbyqxmd.com/read/28333351/ecological-impact-of-ciprofloxacin-on-commensal-enterococci-in-healthy-volunteers
#6
Victoire de Lastours, Elena Maugy, Vincent Mathy, Françoise Chau, Benjamin Rossi, François Guérin, Vincent Cattoir, Bruno Fantin
Background: The ecological impact of ciprofloxacin on commensal enterococci is unknown. Methods: Forty-eight healthy volunteers received ciprofloxacin from day (D) 0 to D14; stools were collected on D7, D14 and D42. Fluoroquinolone-susceptible and -resistant enterococci (FQ-SE and FQ-RE) were detected and quantified by culture, and identified by MALDI-TOF MS. The relative abundance of FQ-RE over FQ-SE was determined. The genetic basis of fluoroquinolone resistance was deciphered by partial sequencing of gyrA and parC genes...
March 4, 2017: Journal of Antimicrobial Chemotherapy
https://www.readbyqxmd.com/read/28333347/polymyxin-resistant-carbapenem-resistant-acinetobacter-baumannii-is-eradicated-by-a-triple-combination-of-agents-that-lack-individual-activity
#7
Justin R Lenhard, Visanu Thamlikitkul, Fernanda P Silveira, Samira M Garonzik, Xun Tao, Alan Forrest, Beom Soo Shin, Keith S Kaye, Jürgen B Bulitta, Roger L Nation, Jian Li, Brian T Tsuji
Objectives: The emergence of polymyxin resistance threatens to leave clinicians with few options for combatting drug-resistant Acinetobacter baumannii . The objectives of the current investigation were to define the in vitro emergence of polymyxin resistance and identify a combination regimen capable of eradicating A. baumannii with no apparent drug susceptibilities. Methods: Two clonally related, paired, A. baumannii isolates collected from a critically ill patient who developed colistin resistance while receiving colistin methanesulfonate in a clinical population pharmacokinetic study were evaluated: an A...
February 28, 2017: Journal of Antimicrobial Chemotherapy
https://www.readbyqxmd.com/read/28333298/occurrence-and-molecular-characteristics-of-esbl-ampc-producing-escherichia-coli-in-faecal-samples-from-horses-in-an-equine-clinic
#8
Ilias Apostolakos, Eelco Franz, Angela H A M van Hoek, Alice Florijn, Christiaan Veenman, Marianne M Sloet-van Oldruitenborgh-Oosterbaan, Cindy Dierikx, Engeline van Duijkeren
Objectives: To investigate the occurrence and characteristics of ESBL/AmpC-producing Escherichia coli in faecal samples from horses at one equine clinic in the Netherlands. Methods: A total of 91 horses, including residents and patients, were sampled. ESBL/AmpC-producing E. coli were identified by a combination disc diffusion test. Phylogenetic groups and MLST were determined. ESBL/AmpC genes were analysed using PCR and sequencing. Plasmids were characterized by transformation and PCR-based replicon typing...
March 13, 2017: Journal of Antimicrobial Chemotherapy
https://www.readbyqxmd.com/read/28332468/regenerative-medicine-shedding-light-into-the-link-between-aging-and-cancer
#9
Fabio Marongiu, Maria Paola Serra, Maura Fanti, Erika Cadoni, Monica Serra, Ezio Laconi
The evidence linking aging and cancer is overwhelming. Findings emerging from the field of regenerative medicine reinforce the notion that aging and cancer are profoundly interrelated in their pathogenetic pathways. We discuss evidence to indicate that age-associated alterations in the tissue microenvironment contribute to the emergence of a neoplastic-prone tissue landscape, which is able to support the selective growth of pre-neoplastic cell populations. Interestingly, tissue contexts that are able to select for the growth of pre-neoplastic cells, including the aged liver microenvironment, are also supportive for the clonal expansion of normal, homotypic, transplanted cells...
March 2, 2017: Cell Transplantation
https://www.readbyqxmd.com/read/28330290/successful-cloning-of-an-adult-breeding-boar-from-the-novel-chinese-guike-no-1-swine-specialized-strain
#10
Jun-Yu Nie, Xiang-Xing Zhu, Bing-Kun Xie, Su-Qun Nong, Qing-Yan Ma, Hui-Yan Xu, Xiao-Gan Yang, Yang-Qing Lu, Ke-Huan Lu, Yu-Ying Liao, Sheng-Sheng Lu
Somatic cloning, also known as somatic cell nuclear transfer (SCNT), is a promising technology which has been expected to rapidly extend the population of elaborately selected breeding boars with superior production performance. Chinese Guike No. 1 pig breed is a novel swine specialized strain incorporated with the pedigree background of Duroc and Chinese Luchuan pig breeds, thus inherits an excellent production performance. The present study was conducted to establish somatic cloning procedures of adult breeding boars from the Chinese Guike No...
December 2016: 3 Biotech
https://www.readbyqxmd.com/read/28330243/micropropagation-and-validation-of-genetic-and-biochemical-fidelity-among-regenerants-of-nothapodytes-nimmoniana-graham-mabb-employing-issr-markers-and-hplc
#11
Lokesh Prakash, Sushil Kumar Middha, Sudipta Kumar Mohanty, Mallappa Kumara Swamy
An in vitro protocol has been established for clonal propagation of Nothapodytes nimmoniana which is an important source of Camptothecin (CPT). Elite source was identified based on the chemical potency to accumulate the optimum level of CPT. Different types and concentrations of plant growth regulators were used to study their effect on inducing multiple shoots from the explants regenerated from embryos of N. nimmoniana. Of these, a combination of N6-benzyladenine (0.2 mg L(-1)) and Indole-3-butyric acid (IBA) (0...
December 2016: 3 Biotech
https://www.readbyqxmd.com/read/28329763/the-allosteric-inhibitor-abl001-enables-dual-targeting-of-bcr-abl1
#12
Andrew A Wylie, Joseph Schoepfer, Wolfgang Jahnke, Sandra W Cowan-Jacob, Alice Loo, Pascal Furet, Andreas L Marzinzik, Xavier Pelle, Jerry Donovan, Wenjing Zhu, Silvia Buonamici, A Quamrul Hassan, Franco Lombardo, Varsha Iyer, Michael Palmer, Giuliano Berellini, Stephanie Dodd, Sanjeev Thohan, Hans Bitter, Susan Branford, David M Ross, Timothy P Hughes, Lilli Petruzzelli, K Gary Vanasse, Markus Warmuth, Francesco Hofmann, Nicholas J Keen, William R Sellers
Chronic myeloid leukaemia (CML) is driven by the activity of the BCR-ABL1 fusion oncoprotein. ABL1 kinase inhibitors have improved the clinical outcomes for patients with CML, with over 80% of patients treated with imatinib surviving for more than 10 years. Second-generation ABL1 kinase inhibitors induce more potent molecular responses in both previously untreated and imatinib-resistant patients with CML. Studies in patients with chronic-phase CML have shown that around 50% of patients who achieve and maintain undetectable BCR-ABL1 transcript levels for at least 2 years remain disease-free after the withdrawal of treatment...
March 22, 2017: Nature
https://www.readbyqxmd.com/read/28328934/proviruses-with-identical-sequences-comprise-a-large-fraction-of-the-replication-competent-hiv-reservoir
#13
John K Bui, Michele D Sobolewski, Brandon F Keele, Jonathan Spindler, Andrew Musick, Ann Wiegand, Brian T Luke, Wei Shao, Stephen H Hughes, John M Coffin, Mary F Kearney, John W Mellors
The major obstacle to curing HIV infection is the persistence of cells with intact proviruses that can produce replication-competent virus. This HIV reservoir is believed to exist primarily in CD4+ T-cells and is stable despite years of suppressive antiretroviral therapy. A potential mechanism for HIV persistence is clonal expansion of infected cells, but how often such clones carry replication-competent proviruses has been controversial. Here, we used single-genome sequencing to probe for identical HIV sequence matches among viruses recovered in different viral outgrowth cultures and between the sequences of outgrowth viruses and proviral or intracellular HIV RNA sequences in uncultured blood mononuclear cells from eight donors on suppressive ART with diverse proviral populations...
March 22, 2017: PLoS Pathogens
https://www.readbyqxmd.com/read/28327938/targeting-the-fibroblast-growth-factor-receptor-2-in-gastric-cancer-promise-or-pitfall
#14
C Hierro, M Alsina, M Sánchez, V Serra, J Rodon, J Tabernero
Gastric cancer is the third leading cause of death from cancer worldwide. Systemic chemotherapy remains the mainstay therapeutic option for this poor prognosis cancer. Trastuzumab, the epidermal growth factor receptor 2 (ERBB2 or HER2)-antibody, is the only biological agent approved for the molecularly-selected population of HER2-positive gastric cancer patients. Over the last decade, several groups have been working for deepening into the molecular characterization of gastric cancer, shedding some light into the heterogeneity of this tumour...
March 7, 2017: Annals of Oncology: Official Journal of the European Society for Medical Oncology
https://www.readbyqxmd.com/read/28327256/origin-and-distribution-of-sporothrix-globosa-causing-sapronoses-in-asia
#15
Tarek A A Moussa, Naif M S Kadasa, Hassan S Al Zahrani, Sarah Abdallah Ahmed, Peiying Feng, Albertus H G Gerrits van den Ende, Yu Zhang, Rui Kano, Fuqiu Li, Shanshan Li, Yang Song, Bilin Dong, Luana Rossato, Somayeh Dolatabadi, Sybren de Hoog
PURPOSE: The aim of the study was to evaluate the main sources and epidemiological patterns and speculate on the evolutionary origin of Sporothrix globosa in Asia. METHODOLOGY: Case and case series literature on sporotrichosis in Asia from January 2007 onwards were reviewed using meta-analysis. Phylogenetic analysis of relevant S. globosa was carried out on the basis of concatenated sequences of ITS, TEF3 and CAL. A haplotype network of CAL sequences of 281 Sporothrix isolates was analysed to determine the population structure of S...
March 23, 2017: Journal of Medical Microbiology
https://www.readbyqxmd.com/read/28325372/is-predominant-clonal-evolution-a-common-evolutionary-adaptation-to-parasitism-in-pathogenic-parasitic-protozoa-fungi-bacteria-and-viruses
#16
M Tibayrenc, F J Ayala
We propose that predominant clonal evolution (PCE) in microbial pathogens be defined as restrained recombination on an evolutionary scale, with genetic exchange scarce enough to not break the prevalent pattern of clonal population structure. The main features of PCE are (1) strong linkage disequilibrium, (2) the widespread occurrence of stable genetic clusters blurred by occasional bouts of genetic exchange ('near-clades'), (3) the existence of a "clonality threshold", beyond which recombination is efficiently countered by PCE, and near-clades irreversibly diverge...
2017: Advances in Parasitology
https://www.readbyqxmd.com/read/28323864/population-genetic-structure-of-eelgrass-zostera-marina-on-the-korean-coast-current-status-and-conservation-implications-for-future-management
#17
Jae Hwan Kim, Ji Hyoun Kang, Ji Eun Jang, Sun Kyeong Choi, Min Ji Kim, Sang Rul Park, Hyuk Je Lee
Seagrasses provide numerous ecosystem services for coastal and estuarine environments, such as nursery functions, erosion protection, pollution filtration, and carbon sequestration. Zostera marina (common name "eelgrass") is one of the seagrass bed-forming species distributed widely in the northern hemisphere, including the Korean Peninsula. Recently, however, there has been a drastic decline in the population size of Z. marina worldwide, including Korea. We examined the current population genetic status of this species on the southern coast of Korea by estimating the levels of genetic diversity and genetic structure of 10 geographic populations using eight nuclear microsatellite markers...
2017: PloS One
https://www.readbyqxmd.com/read/28319730/deconstructing-the-germinal-center-one-cell-at-a-time
#18
REVIEW
Chad R Dufaud, Louise J McHeyzer-Williams, Michael G McHeyzer-Williams
Successful vaccination relies on driving the immune response towards high specificity, affinity and longevity. Germinal centers facilitate the evolution of antigen-specific B cells by iterative rounds of diversification, selection, and differentiation to memory and plasma cells. Experimental evidence points to B cell receptor affinity and amount of antigen presented to follicular helper T cells as main drivers of clonal evolution. Concurrent studies suggest that modifiers of cognate contact, temporal mechanisms, and stochastic factors can also shape diversity and influence differentiation to memory and plasma cells, but molecular pathways driving these selection decisions are unresolved...
March 17, 2017: Current Opinion in Immunology
https://www.readbyqxmd.com/read/28317291/intravascular-t-cell-lymphoma-a-rare-poorly-characterized-entity-with-cytotoxic-phenotype
#19
Tara L Sharma, Gabrielle A Yeaney, Payam Soltanzadeh, Yuebing Li, Claudiu V Cotta
Intravascular T-cell lymphomas are rare, poorly characterized lesions. We discuss the clinical, radiologic and especially the laboratory characteristics of a lesion which presented in a 62-year-old woman with a history of progressive CNS abnormalities. Throughout the course of the disease, radiologic findings consisted mainly of multifocal mixed areas of ischemia and vasogenic edema involving cortical and subcortical regions. A brain biopsy identified an abnormal T-cell population confined to lumens of vessels...
March 20, 2017: Neuropathology: Official Journal of the Japanese Society of Neuropathology
https://www.readbyqxmd.com/read/28315400/multicolor-flow-cytometry-and-multi-gene-next-generation-sequencing-are-complementary-and-highly-predictive-for-relapse-in-acute-myeloid-leukemia-following-allogeneic-transplant
#20
Bartlomiej M Getta, Sean M Devlin, Ross L Levine, Maria E Arcila, Abhinita S Mohanty, Ahmet Zehir, Martin S Tallman, Sergio A Giralt, Mikhail Roshal
Minimal Residual disease (MRD) in acute myeloid leukemia (AML) is typically measured using multi-parameter flow cytometry (MFC). Detection of leukemia mutations using multi-gene next generation sequencing (NGS) can potentially be used to measure residual disease. We used a targeted 28-gene NGS panel to detect mutations and different-from-normal 10-colour MFC to measure MRD in AML patients before allogeneic hematopoietic stem cell transplant (HCT). Residual disease was defined when any abnormal blast population was detected using MFC and when any leukemia allele was detected with a variant allele frequency (VAF) ≥5% using NGS...
March 14, 2017: Biology of Blood and Marrow Transplantation
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