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clonal population

Paul J Planet, Apurva Narechania, Liang Chen, Barun Mathema, Sam Boundy, Gordon Archer, Barry Kreiswirth
A deluge of whole-genome sequencing has begun to give insights into the patterns and processes of microbial evolution, but genome sequences have accrued in a haphazard manner, with biased sampling of natural variation that is driven largely by medical and epidemiological priorities. For instance, there is a strong bias for sequencing epidemic lineages of methicillin-resistant Staphylococcus aureus (MRSA) over sensitive isolates (methicillin-sensitive S. aureus: MSSA). As more diverse genomes are sequenced the emerging picture is of a highly subdivided species with a handful of relatively clonal groups (complexes) that, at any given moment, dominate in particular geographical regions...
October 14, 2016: Trends in Microbiology
Olga De Castro, Antonietta Di Maio, Mirko Di Febbraro, Gennaro Imparato, Michele Innangi, Errol Véla, Bruno Menale
The Mediterranean coastline is a dynamic and complex system which owes its complexity to its past and present vicissitudes, e.g. complex tectonic history, climatic fluctuations, and prolonged coexistence with human activities. A plant species that is widespread in this habitat is the sea daffodil, Pancratium maritimum (Amaryllidaceae), which is a perennial clonal geophyte of the coastal sands of the Mediterranean and neighbouring areas, well adapted to the stressful conditions of sand dune environments. In this study, an integrated approach was used, combining genetic and environmental data with a niche modelling approach, aimed to investigate: (1) the effect of climate change on the geographic range of this species at different times {past (last inter-glacial, LIG; and last glacial maximum, LGM), present (CURR), near-future (FUT)} and (2) the possible influence of environmental variables on the genetic structure of this species in the current period...
2016: PloS One
Gerd Horneff, Ariane Klein, Prasad T Oommen, Anton Hospach, Ivan Foeldvari, Isa Feddersen, Kirsten Minden
OBJECTIVES: While tumour necrosis factor (TNF)-α-inhibitor treatment improved outcome of juvenile idiopathic arthritis (JIA) management markedly, concerns have been raised about an association of TNF-α-inhibitor treatment and an increased risk for malignancies especially lymphoma. METHODS: Cases of suspected malignancies documented in the German Biker Registry are reviewed in detail. RESULTS: Until Dec 31, 2015, 3695 JIA patients were prospectively followed with a total of more than 13,198 observation years...
September 8, 2016: Clinical and Experimental Rheumatology
A Egli, H Schmid, E Kuenzli, A Widmer, M Battegay, H Plagge, R Frei, Rita Achermann, M Weisser
OBJECTIVE: In this study we aimed to analyse the association between use of daptomycin and MICs of daptomycin in E. faecium bacteremia. METHODS: We prospectively enrolled patients aged ≥18 years with E. faecium bacteremia hospitalized at the University Hospital Basel from 2008-2014. We determined daptomycin minimal inhibitory concentrations (MICs) by Etests and used pulsed field gel electrophoresis to determine clonal relatedness. We recorded the defined daily dosages of daptomycin (DDDs) per 100 patient days (PDs) and clinical data from charts...
October 13, 2016: Clinical Microbiology and Infection
Liang Xu, Zhen-Feng Zhou
Physiological integration can enhance the performance of clonal plants in aquatic and terrestrial heterogeneous habitats and associated ecotones. Similar to nutrients, pollutants may be transported among connected ramets via physiological integration. Few studies have examined the expansion of amphibious clonal plants from terrestrial to aquatic environments, particularly when the local water supply is polluted with heavy metals. A greenhouse experiment was conducted using the amphibious plant Alternanthera philoxeroides to determine whether Cu can spread among clonal plants and examine the corresponding effects of this pollution on the expansion of clonal plants in aquatic-terrestrial ecotones...
2016: PloS One
Dinh Minh Tran, André Clément-Demange, Marine Déon, Dominique Garcia, Vincent Le Guen, Anne Clément-Vidal, Mouman Soumahoro, Aurélien Masson, Philippe Label, Mau Tuy Le, Valérie Pujade-Renaud
An indirect phenotyping method was developed in order to estimate the susceptibility of rubber tree clonal varieties to Corynespora Leaf Fall (CLF) disease caused by the ascomycete Corynespora cassiicola. This method consists in quantifying the impact of fungal exudates on detached leaves by measuring the induced electrolyte leakage (EL%). The tested exudates were either crude culture filtrates from diverse C. cassiicola isolates or the purified cassiicolin (Cas1), a small secreted effector protein produced by the aggressive isolate CCP...
2016: PloS One
Thomas Stiehl, Christoph Lutz, Anna Marciniak-Czochra
BACKGROUND: Leukemias are malignant proliferative disorders of the blood forming system. Sequencing studies demonstrate that the leukemic cell population consists of multiple clones. The genetic relationship between the different clones, referred to as the clonal hierarchy, shows high interindividual variability. So far, the source of this heterogeneity and its clinical relevance remain unknown. We propose a mathematical model to study the emergence and evolution of clonal heterogeneity in acute leukemias...
October 12, 2016: Biology Direct
Wei Li, Yingpeng Guo, Aixiang Zhang, Huaigu Chen
Sharp eyespot on wheat is caused by Rhizoctonia cerealis anastomosis group D subgroup I (AG-DI) and is an economically important stem-base disease of wheat in temperate regions worldwide. However, the understanding about the field population structure of R. cerealis is limited. In this study, the genetic structure of four wheat-infecting populations in China was investigated using six microsatellite markers characterized from the transcriptome data of R. cerealis AG-DI. A total of 173 unique genotypes were identified among 235 fungal isolates...
October 11, 2016: Phytopathology
Tejaswini Kulkarni, Chihiro Aikawa, Takashi Nozawa, Kazunori Murase, Fumito Maruyama, Ichiro Nakagawa
BACKGROUND: Group A Streptococcus (GAS; Streptococcus pyogenes) causes a range of mild to severe infections in humans. It can also colonize healthy persons asymptomatically. Therefore, it is important to study GAS carriage in healthy populations, as carriage of it might lead to subsequent disease manifestation, clonal spread in the community, and/or diversification of the organism. Throat swab culture is the gold standard method for GAS detection. Advanced culture-independent methods provide rapid and efficient detection of microorganisms directly from clinical samples...
October 11, 2016: BMC Microbiology
Mindy L Richlen, Oliver Zielinski, Lars Holinde, Urban Tillmann, Allan Cembella, Yihua Lyu, Donald M Anderson
The bloom-forming dinoflagellate Alexandrium fundyense has been extensively studied due its toxin-producing capabilities and consequent impacts to human health and economies. This study investigated the prevalence of resting cysts of A. fundyense in western Greenland and Iceland to assess the historical presence and magnitude of bloom populations in the region, and to characterize environmental conditions during summer, when bloom development may occur. Analysis of sediments collected from these locations showed that Alexandrium cysts were present at low to moderate densities in most areas surveyed, with highest densities observed in western Iceland...
2016: Marine Ecology Progress Series
Steven R Wiley, Vanitha S Raman
Adjuvants in vaccine formulations are designed to enhance immune responses against a target antigen or pathogen. The ability of these vaccines to induce activation and differentiation of mature naïve B cells to produce pathogen-specific antibodies (immunoglobulins; Ig) helps guarantee long-lived humoral immunity. This process involves clonal expansion of antigen-specific B cells, genomic rearrangement of Ig heavy (IgH) and light (IgL) loci, somatic hypermutation (SHM), and clonal selection for affinity-matured antibody, resulting in a vast but directed repertoire of B cells expressing highly specific antibody proteins...
2017: Methods in Molecular Biology
Surya Paudel, Beatrix Stessl, Claudia Hess, Angelika Zloch, Michael Hess
BACKGROUND: Various information about the genetic diversity of Escherichia coli isolates from chickens are available but a detailed epidemiological investigation based upon isolates obtained from interrelated pullet and layer flocks is still missing. Therefore, in the course of a longitudinal epidemiological study on pullets and layers, 144 E. coli isolates from chickens with or without pathological lesions of the reproductive tract were serotyped and genotyped with pulsed-field gel electrophoresis (PFGE)...
October 7, 2016: BMC Veterinary Research
Jasmine Chong, Chelsea Caya, Simon Lévesque, Caroline Quach
CONTEXT: NICUs in the province of Québec have seen an increase in hVICoNS, detected in the clinical laboratory. OBJECTIVE: To investigate the clinical relevance of hVICoNS on the course of infection, and to determine the prevalence of hVICoNS sepsis in the NICU. METHODS: We searched MEDLINE, EMBASE, and PubMed from 1 January 1980 to 1 July 2016. Both observational and interventional studies were considered eligible if they provided data on hVICoNS in the NICU population...
2016: PloS One
Cristina Rodriguez, Bernard Taminiau, Nicolas Korsak, Véronique Avesani, Johan Van Broeck, Philippe Brach, Michel Delmée, Georges Daube
BACKGROUND: Increasing age, several co-morbidities, environmental contamination, antibiotic exposure and other intestinal perturbations appear to be the greatest risk factors for C. difficile infection (CDI). Therefore, elderly care home residents are considered particularly vulnerable to the infection. The main objective of this study was to evaluate and follow the prevalence of C. difficile in 23 elderly care home residents weekly during a 4-month period. A C. difficile microbiological detection scheme was performed along with an overall microbial biodiversity study of the faeces content by 16S rRNA gene analysis...
October 1, 2016: BMC Microbiology
Sebastiaan J van Hal, Camilla L C Ip, M Azim Ansari, Daniel J Wilson, Bjorn A Espedido, Slade O Jensen, Rory Bowden
Enterococcus faecium, a major cause of hospital-acquired infections, remains problematic because of its propensity to acquire resistance to vancomycin, which currently is considered first-line therapy. Here, we assess the evolution and resistance acquisition dynamics of E. faecium in a clinical context using a series of 132 bloodstream infection isolates from a single hospital. All isolates, of which 49 (37 %) were vancomycin-resistant, underwent whole-genome sequencing. E. faecium was found to be subject to high rates of recombination with little evidence of sequence importation from outside the local E...
January 19, 2016: Microbial Genomics
Christian Mayer, Rachel C Bandler, Gord Fishell
This Matters Arising Response paper addresses the Sultan et al. (2016) Matters Arising paper, published concurrently in Neuron. Clonally related excitatory neurons maintain a coherent relationship following their specification and migration. Whether cortical interneurons behave similarly is a fundamental question in developmental neuroscience. In Mayer et al. (2015), we reported that sibling interneurons disperse over several millimeters, across functional and anatomical boundaries. This finding demonstrated that clonality is not predictive of an interneuron's ultimate circuit specificity...
October 5, 2016: Neuron
Khadeejah T Sultan, Zhi Han, Xin-Jun Zhang, Anjin Xianyu, Zhizhong Li, Kun Huang, Song-Hai Shi
Progenitor cells in the medial ganglionic eminence (MGE) and preoptic area (PoA) give rise to GABAergic inhibitory interneurons that are distributed in the forebrain, largely in the cortex, hippocampus, and striatum. Two previous studies suggest that clonally related interneurons originating from individual MGE/PoA progenitors frequently form local clusters in the cortex. However, Mayer et al. and Harwell et al. recently argued that MGE/PoA-derived interneuron clones disperse widely and populate different forebrain structures...
October 5, 2016: Neuron
Fabian Lorenzo-Diaz, Cris Fernández-Lopez, Pierre-Emmanuel Douarre, Adrian Baez-Ortega, Carlos Flores, Philippe Glaser, Manuel Espinosa
Streptococcus agalactiae or Group B Streptococcus (GBS) are opportunistic bacteria that can cause lethal sepsis in children and immuno-compromised patients. Their genome is a reservoir of mobile genetic elements that can be horizontally transferred. Among them, integrative and conjugative elements (ICEs) and the smaller integrative and mobilizable elements (IMEs) primarily reside in the bacterial chromosome, yet have the ability to be transferred between cells by conjugation. ICEs and IMEs are therefore a source of genetic variability that participates in the spread of antibiotic resistance...
October 2016: Open Biology
F Cui, B Yuan
Here, we applied a two-stage clonal expansion model of morphological (cell-size) evolution to a long-term evolution experiment with Escherichia coli. Using this model, we derived the incidence function of the appearance of cell-size stability, the waiting time until this morphological stability, and the conditional and unconditional probabilities of morphological stability. After assessing the parameter values, we verified that the calculated waiting time was consistent with the experimental results, demonstrating the effectiveness of the two-stage model...
August 30, 2016: Genetics and Molecular Research: GMR
Laura Clusa, Alba Ardura, Fiona Gower, Laura Miralles, Valentina Tsartsianidou, Anastasija Zaiko, Eva Garcia-Vazquez
Potamopyrgus antipodarum (New Zealand mud snail) is a prosobranch mollusk native to New Zealand with a wide invasive distribution range. Its non-indigenous populations are reported from Australia, Asia, Europe and North America. Being an extremely tolerant species, Potamopyrgus is capable to survive in a great range of salinity and temperature conditions, which explains its high invasiveness and successful spread outside the native range. Here we report the first finding of Potamopyrgus antipodarum in a basin of the Cantabrian corridor in North Iberia (Bay of Biscay, Spain)...
2016: PloS One
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