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https://www.readbyqxmd.com/read/28087939/dendritic-cells-in-the-immune-system-history-lineages-tissues-tolerance-and-immunity
#1
Jonathan M Austyn
The aim of this review is to provide a coherent framework for understanding dendritic cells (DCs). It has seven sections. The introduction provides an overview of the immune system and essential concepts, particularly for the nonspecialist reader. Next, the "History" section outlines the early evolution of ideas about DCs and highlights some sources of confusion that still exist today. The "Lineages" section then focuses on five different populations of DCs: two subsets of "classical" DCs, plasmacytoid DCs, monocyte-derived DCs, and Langerhans cells...
December 2016: Microbiology Spectrum
https://www.readbyqxmd.com/read/28077674/population-structure-of-japanese-extraintestinal-pathogenic-escherichia-coli-and-its-relationship-with-antimicrobial-resistance
#2
Yasufumi Matsumura, Taro Noguchi, Michio Tanaka, Toru Kanahashi, Masaki Yamamoto, Miki Nagao, Shunji Takakura, Satoshi Ichiyama
OBJECTIVES: To define the population structure of extraintestinal pathogenic Escherichia coli (ExPEC) in Japan and its relationship with antimicrobial resistance and the major resistance mechanisms for fluoroquinolones and β-lactams, we designed a multicentre prospective study. METHODS: A total of 329 ExPEC isolates were collected at 10 Japanese acute-care hospitals during December 2014. We defined the clonal groups of ExPEC by fumC and fimH sequencing (CH typing)...
January 10, 2017: Journal of Antimicrobial Chemotherapy
https://www.readbyqxmd.com/read/28074843/sexy-males-and-sexless-females-the-origin-of-triploid-apomicts
#3
P Muralidhar, D Haig
Apomixis and polyploidy are closely associated in angiosperms, but the evolutionary reason for this association is unknown. Taraxacum officinale, the common dandelion, exists both as diploid sexuals and triploid apomicts. Here, in the context of T. officinale, we provide a model of the evolution of triploid apomicts from diploid sexuals. We posit an apomictic allele that arrests female meiosis in diploids, so that the plant produces diploid egg cells that can develop without fertilization, but haploid pollen...
January 11, 2017: Heredity
https://www.readbyqxmd.com/read/28069394/catch-my-drift-making-sense-of-genomic-intra-tumour-heterogeneity
#4
Andrea Sottoriva, Chris P Barnes, Trevor A Graham
The cancer genome is shaped by three components of the evolutionary process: mutation, selection and drift. While many studies have focused on the first two of these evolutionary components, the role of drift in cancer evolution has received little attention. Drift occurs when all individuals in the population have the same likelihood of producing surviving offspring, and so by definition a drifting population is one that is evolving neutrally. Here we focus on how neutral evolution is manifested in the cancer genome...
January 6, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28068781/complex-subtype-diversity-of-hiv-1-among-drug-users-in-major-kenyan-cities
#5
Kamini Gounder, Micah Oyaro, Nagavelli Padayachi, Thando Mbali Zulu, Tulio de Oliveira, John Wylie, Thumbi Ndung'u
Drug users are increasingly recognized as a key population driving HIV spread in sub-Saharan Africa. To determine HIV-1 subtypes circulating in this population group and explore possible geographic differences, we analyzed HIV-1 sequences among drug users from Nairobi, Mombasa and Kisumu in Kenya. We sequenced gag and env from 55 drug users. Subtype analysis from 220 gag clonal sequences from 54/55 participants (median=4/participant) showed that 44.4% were A, 16.7% were C, 3.7% were D and 35.2% were intersubtype recombinants...
January 9, 2017: AIDS Research and Human Retroviruses
https://www.readbyqxmd.com/read/28068559/the-ageing-genome-clonal-mosaicism-and-chronic-disease
#6
REVIEW
Mitchell J Machiela, Stephen J Chanock
Clonal mosaicism arises when a postzygotic mutational event is detectable in subpopulations of cells as an alternative genotype while not present in the germline genome. Although described in a subset of pediatric disorders, new genomic technologies have detected higher than anticipated frequencies of clonal mosaicism in adult population studies, stimulating investigation as to how clonal mosaicism could contribute to chronic human diseases, such as cancer, diabetes and neurodegenerative disorders. It has also been postulated to be an important mechanism for functional cellular diversity, including the brain...
January 6, 2017: Current Opinion in Genetics & Development
https://www.readbyqxmd.com/read/28068406/superclone-expansion-long-distance-clonal-dispersal-and-local-genetic-structuring-in-the-coral-pocillopora-damicornis-type-%C3%AE-in-reunion-island-south-western-indian-ocean
#7
Pauline Gélin, Cécile Fauvelot, Vincent Mehn, Sophie Bureau, Héloïse Rouzé, Hélène Magalon
The scleractinian coral Pocillopora damicornis type β is known to present a mixed reproduction mode: through sexual reproduction, new genotypes are created, while asexual reproduction insures their propagation. In order to investigate the relative proportion of each reproduction mode in P. damicornis type β populations from Reunion Island, Indian Ocean, clonal propagation along the west coast was assessed through four sampling sites with increasing geographical distance between sites. Coral colonies were sampled either exhaustively, randomly or haphazardly within each site, and genotypic diversity was assessed using 13 microsatellite loci over a total of 510 P...
2017: PloS One
https://www.readbyqxmd.com/read/28068316/scalable-whole-genome-single-cell-library-preparation-without-preamplification
#8
Hans Zahn, Adi Steif, Emma Laks, Peter Eirew, Michael VanInsberghe, Sohrab P Shah, Samuel Aparicio, Carl L Hansen
Single-cell genomics is critical for understanding cellular heterogeneity in cancer, but existing library preparation methods are expensive, require sample preamplification and introduce coverage bias. Here we describe direct library preparation (DLP), a robust, scalable, and high-fidelity method that uses nanoliter-volume transposition reactions for single-cell whole-genome library preparation without preamplification. We examined 782 cells from cell lines and triple-negative breast xenograft tumors. Low-depth sequencing, compared with existing methods, revealed greater coverage uniformity and more reliable detection of copy-number alterations...
January 9, 2017: Nature Methods
https://www.readbyqxmd.com/read/28067900/donor-cd19-car-t-cells-exert-potent-graft-versus-lymphoma-activity-with-diminished-graft-versus-host-activity
#9
Arnab Ghosh, Melody Smith, Scott E James, Marco L Davila, Enrico Velardi, Kimon V Argyropoulos, Gertrude Gunset, Fabiana Perna, Fabiana M Kreines, Emily R Levy, Sophie Lieberman, Hillary V Jay, Andrea Z Tuckett, Johannes L Zakrzewski, Lisa Tan, Lauren F Young, Kate Takvorian, Jarrod A Dudakov, Robert R Jenq, Alan M Hanash, Ana Carolina F Motta, George F Murphy, Chen Liu, Andrea Schietinger, Michel Sadelain, Marcel R M van den Brink
Allogeneic hematopoietic stem cell transplantation (allo-HSCT) is a potentially curative therapy for hematological malignancies. However, graft-versus-host disease (GVHD) and relapse after allo-HSCT remain major impediments to the success of allo-HSCT. Chimeric antigen receptors (CARs) direct tumor cell recognition of adoptively transferred T cells. CD19 is an attractive CAR target, which is expressed in most B cell malignancies, as well as in healthy B cells. Clinical trials using autologous CD19-targeted T cells have shown remarkable promise in various B cell malignancies...
January 9, 2017: Nature Medicine
https://www.readbyqxmd.com/read/28065889/antimicrobial-resistance-in-staphylococcus-pseudintermedius-and-the-molecular-epidemiology-of-methicillin-resistant-s-pseudintermedius-in-small-animals-in-finland
#10
Thomas Grönthal, Marjut Eklund, Katariina Thomson, Heli Piiparinen, Tarja Sironen, Merja Rantala
OBJECTIVES: To investigate antimicrobial susceptibility in Staphylococcus pseudintermedius and the occurrence of methicillin-resistant S. pseudintermedius (MRSP), to explore the molecular structure of the MRSP population and to analyse risk factors for MRSP. METHODS: Susceptibility data for clinical S. pseudintermedius isolates in 2011-15 were analysed using WHONET. All MRSP isolates in 2010-14 (n = 362) were typed using PFGE. Representative isolates (n = 87) of clusters were analysed using MLST and staphylococcal cassette chromosome mec (SCCmec) typing...
January 8, 2017: Journal of Antimicrobial Chemotherapy
https://www.readbyqxmd.com/read/28062695/the-clonal-invariant-nkt-cell-repertoire-in-people-with-type-1-diabetes-is-characterized-by-a-loss-of-clones-expressing-high-affinity-tcrs
#11
Anna S Tocheva, Salah Mansour, Tristan G H Holt, Samuel Jones, Andrew Chancellor, Joseph P Sanderson, Efrem Eren, Tim J Elliott, Richard I G Holt, Stephan D Gadola
Invariant NKT (iNKT) cells in healthy people express iNKT-TCRs with widely varying affinities for CD1d, suggesting different roles for high- and low-affinity iNKT clones in immune regulation. However, the functional implications of this heterogeneity have not yet been determined. Functionally aberrant iNKT responses have been previously demonstrated in different autoimmune diseases, including human type 1 diabetes, but their relationship to changes in the iNKT clonal repertoire have not been addressed. In this study, we directly compared the clonal iNKT repertoire of people with recent onset type 1 diabetes and age- and gender-matched healthy controls with regard to iNKT-TCR affinity and cytokine production...
January 6, 2017: Journal of Immunology: Official Journal of the American Association of Immunologists
https://www.readbyqxmd.com/read/28059958/future-technologies-for-monitoring-hiv-drug-resistance-and-cure
#12
Urvi M Parikh, Kevin McCormick, Gert van Zyl, John W Mellors
PURPOSE OF REVIEW: Sensitive, scalable and affordable assays are critically needed for monitoring the success of interventions for preventing, treating and attempting to cure HIV infection. This review evaluates current and emerging technologies that are applicable for both surveillance of HIV drug resistance (HIVDR) and characterization of HIV reservoirs that persist despite antiretroviral therapy and are obstacles to curing HIV infection. RECENT FINDINGS: Next-generation sequencing (NGS) has the potential to be adapted into high-throughput, cost-efficient approaches for HIVDR surveillance and monitoring during continued scale-up of antiretroviral therapy and rollout of preexposure prophylaxis...
January 5, 2017: Current Opinion in HIV and AIDS
https://www.readbyqxmd.com/read/28059107/single-cell-time-lapse-analysis-reveals-that-podoplanin-enhances-cell-survival-and-colony-formation-capacity-of-squamous-cell-carcinoma-cells
#13
Tomoyuki Miyashita, Youichi Higuchi, Motohiro Kojima, Atsushi Ochiai, Genichiro Ishii
Tumor initiating cells (TICs) are characterized by high clonal expansion capacity. We previously reported that podoplanin is a TIC-specific marker for the human squamous cell carcinoma cell line A431. The aim of this study is to explore the molecular mechanism underlying the high clonal expansion potential of podoplanin-positive A431cells using Fucci imaging. Single podoplanin-positive cells created large colonies at a significantly higher frequency than single podoplanin-negative cells, whereas no difference was observed between the two types of cells with respect to cell cycle status...
January 6, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28057731/extremely-low-genomic-diversity-of-rickettsia-japonica-distributed-in-japan
#14
Arzuba Akter, Tadasuke Ooka, Yasuhiro Gotoh, Seigo Yamamoto, Hiromi Fujita, Fumio Terasoma, Kouji Kida, Masakatsu Taira, Fumiko Nakadouzono, Mutsuyo Gokuden, Manabu Hirano, Mamoru Miyashiro, Kouichi Inari, Yukie Shimazu, Kenji Tabara, Atsushi Toyoda, Dai Yoshimura, Takehiko Itoh, Tomokazu Kitano, Mitsuhiko P Sato, Keisuke Katsura, Shakhinur Islam Mondal, Yoshitoshi Ogura, Shuji Ando, Tetsuya Hayashi
Rickettsiae are obligate intracellular bacteria that have small genomes as a result of reductive evolution. Many Rickettsia species of the spotted fever group (SFG) cause tick-borne diseases known as "spotted fevers." The life cycle of SFG rickettsiae is closely associated with that of the tick, which is generally thought to act as a bacterial vector and reservoir that maintains the bacterium through transstadial and transovarial transmission. Each SFG member is thought to have adapted to a specific tick species, thus restricting the bacterial distribution to a relatively limited geographic region...
January 4, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28053211/optical-screening-for-rapid-antimicrobial-susceptibility-testing-and-for-observation-of-phenotypic-diversity-among-the-genetically-clonal-species-bacillus-anthracis
#15
Heather P McLaughlin, Amy S Gargis, Pierre Michel, David Sue, Linda M Weigel
: During high-impact events involving Bacillus anthracis, such as the Amerithrax incident of 2001 or the anthrax outbreaks in Russia and Sweden in 2016, critical decisions to reduce morbidity and mortality include rapid selection and distribution of effective antimicrobial agents for treatment and post-exposure prophylaxis. Detection of antimicrobial resistance currently relies on a conventional broth microdilution (BMD) method that requires a 16 - 20 hour incubation time for B. anthracis Advances in high-resolution optical screening offer a new technology to more rapidly evaluate antimicrobial susceptibility and to simultaneously assess growth characteristics of an isolate...
January 4, 2017: Journal of Clinical Microbiology
https://www.readbyqxmd.com/read/28052487/the-coexistence-of-generalist-and-specialist-clonal-lineages-in-natural-populations-of-the-irish-famine-pathogen-phytophthora-infestans-explains-local-adaptation-to-potato-and-tomato
#16
Alexander Kröner, Romain Mabon, Roselyne Corbière, Josselin Montarry, Didier Andrivon
Phytophthora infestans, causing late blight on Solanaceae, is a serious threat to potato and tomato crops worldwide. P. infestans populations sampled on either potato or tomato differ in genotypes and pathogenicity, suggesting niche exclusion in the field. We hypothesized that such niche separation can reflect differential host exploitation by different P. infestans genotypes. We thus compared genotypes and phenotypes in 21 isolates sampled on potato (n = 11) or tomato (n = 10). Typing at 12 microsatellite loci assigned potato isolates to the 13_A2, 6_A1 and 1_A1 lineages, and tomato isolates to the 23_A1, 2_A1 and unclassified multi-locus genotypes...
January 4, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28052104/insertional-mutagenesis-by-crispr-cas9-ribonucleoprotein-gene-editing-in-cells-targeted-for-point-mutation-repair-directed-by-short-single-stranded-dna-oligonucleotides
#17
Natalia Rivera-Torres, Kelly Banas, Pawel Bialk, Kevin M Bloh, Eric B Kmiec
CRISPR/Cas9 and single-stranded DNA oligonucleotides (ssODNs) have been used to direct the repair of a single base mutation in human genes. Here, we examine a method designed to increase the precision of RNA guided genome editing in human cells by utilizing a CRISPR/Cas9 ribonucleoprotein (RNP) complex to initiate DNA cleavage. The RNP is assembled in vitro and induces a double stranded break at a specific site surrounding the mutant base designated for correction by the ssODN. We use an integrated mutant eGFP gene, bearing a single base change rendering the expressed protein nonfunctional, as a single copy target in HCT 116 cells...
2017: PloS One
https://www.readbyqxmd.com/read/28050271/evolution-of-tumor-clones-in-adult-acute-lymphoblastic-leukemia
#18
S Yu Smirnova, Yu V Sidorova, N V Ryzhikova, K A Sychevskaya, E N Parovichnikova, A B Sudarikov
Clonal instability of a tumor cell population in acute lymphoblastic leukemia (ALL) may complicate the monitoring of a minimal residual disease (MRD) by means of patient-specific targets identified at the disease onset. Most of the data concerning the possible instability of rearranged clonal TCR and IG genes during disease recurrence were obtained for ALL in children. The appropriate features of adult ALL, which are known to differ from those of childhood ALL in certain biological characteristics and prognosis, remain insufficiently studied...
October 2016: Acta Naturae
https://www.readbyqxmd.com/read/28049849/cd4-t-cell-cytokines-synergize-to-induce-proliferation-of-malignant-and-nonmalignant-innate-intraepithelial-lymphocytes
#19
Yvonne M C Kooy-Winkelaar, Dagmar Bouwer, George M C Janssen, Allan Thompson, Martijn H Brugman, Frederike Schmitz, Arnoud H de Ru, Tom van Gils, Gerd Bouma, Jon J van Rood, Peter A van Veelen, M Luisa Mearin, Chris J Mulder, Frits Koning, Jeroen van Bergen
Refractory celiac disease type II (RCDII) is a severe complication of celiac disease (CD) characterized by the presence of an enlarged clonal population of innate intraepithelial lymphocytes (IELs) lacking classical B-, T-, and natural killer (NK)-cell lineage markers (Lin(-)IELs) in the duodenum. In ∼50% of patients with RCDII, these Lin(-)IELs develop into a lymphoma for which no effective treatment is available. Current evidence indicates that the survival and expansion of these malignant Lin(-)IELs is driven by epithelial cell-derived IL-15...
January 3, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28043818/molecular-noise-can-minimize-the-collective-sensitivity-of-a-clonal-heterogeneous-cell-population
#20
Marzo Forment, Guillermo Rodrigo
It is now widely accepted that molecular noise, rather than be always detrimental, introduces in many circumstances the required boost to reach fundamental cellular activities or strategies otherwise unattainable. In threshold-like genetic systems, molecular noise serves to generate heterogeneous responses in a clonal population, also in a tissue, due to cell-to-cell variability. Here, we derived a mathematical framework from which we could study in detail this effect. We focused on a minimal decision-making gene circuit implemented as a transcriptional positive-feedback loop...
December 31, 2016: Journal of Theoretical Biology
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