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https://www.readbyqxmd.com/read/29346560/aggregation-and-travelling-wave-dynamics-in-a-two-population-model-of-cancer-cell-growth-and-invasion
#1
Vasiliki Bitsouni, Dumitru Trucu, Mark A J Chaplain, Raluca Eftimie
Cells adhere to each other and to the extracellular matrix (ECM) through protein molecules on the surface of the cells. The breaking and forming of adhesive bonds, a process critical in cancer invasion and metastasis, can be influenced by the mutation of cancer cells. In this paper, we develop a nonlocal mathematical model describing cancer cell invasion and movement as a result of integrin-controlled cell-cell adhesion and cell-matrix adhesion, for two cancer cell populations with different levels of mutation...
January 15, 2018: Mathematical Medicine and Biology: a Journal of the IMA
https://www.readbyqxmd.com/read/29345308/positive-size-speed-relationships-in-gametes-and-vegetative-cells-of-chlamydomonas-reinhardtii-implications-for-the-evolution-of-sperm
#2
Catherine E Seed, Joseph L Tomkins
It is commonly held that differences in gametes of the two sexes (anisogamy) evolved from ancestors whose gametes were similar in size and behaviour (isogamy). Underlying many hypotheses explaining anisogamy are assumed relationships between cell size and speed in the ancestral isogamous population. Using the isogamous alga Chlamydomonas reinhardtii, we explored size-speed distributions in vegetative and gamete cells of ten cell lines, and clonal data from within two cell lines. We applied an independent speed selection approach to gamete populations of C...
January 18, 2018: Evolution; International Journal of Organic Evolution
https://www.readbyqxmd.com/read/29343437/memory-b-cells-that-cross-react-with-group-1-and-group-2-influenza-a-viruses-are-abundant-in-adult-human-repertoires
#3
Kevin R McCarthy, Akiko Watanabe, Masayuki Kuraoka, Khoi T Do, Charles E McGee, Gregory D Sempowski, Thomas B Kepler, Aaron G Schmidt, Garnett Kelsoe, Stephen C Harrison
Human B cell antigen-receptor (BCR) repertoires reflect repeated exposures to evolving influenza viruses; new exposures update the previously generated B cell memory (Bmem) population. Despite structural similarity of hemagglutinins (HAs) from the two groups of influenza A viruses, cross-reacting antibodies (Abs) are uncommon. We analyzed Bmem compartments in three unrelated, adult donors and found frequent cross-group BCRs, both HA-head directed and non-head directed. Members of a clonal lineage from one donor had a BCR structure similar to that of a previously described Ab, encoded by different gene segments...
January 16, 2018: Immunity
https://www.readbyqxmd.com/read/29342233/quantumclone-clonal-assessment-of-functional-mutations-in-cancer-based-on-a-genotype-aware-method-for-clonal-reconstruction
#4
Paul Deveau, Leo Colmet Daage, Derek Oldridge, Virginie Bernard, Angela Bellini, Mathieu Chicard, Nathalie Clement, Eve Lapouble, Valerie Combaret, Anne Boland, Vincent Meyer, Jean-Francois Deleuze, Isabelle Janoueix-Lerosey, Emmanuel Barillot, Olivier Delattre, John Maris, Gudrun Schleiermacher, Valentina Boeva
Motivation: In cancer, clonal evolution is assessed based on information coming from single nucleotide variants and copy number alterations. Nonetheless, existing methods often fail to accurately combine information from both sources to truthfully reconstruct clonal populations in a given tumor sample or in a set of tumor samples coming from the same patient. Moreover, previously published methods detect clones from a single set of variants. As a result, compromises have to be done between stringent variant filtering (reducing dispersion in variant allele frequency estimates, VAFs) and using all biologically relevant variants...
January 12, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29340211/differences-in-adaptive-dynamics-determine-the-success-of-virus-variants-that-propagate-together
#5
María Arribas, Jacobo Aguirre, Susanna Manrubia, Ester Lázaro
Virus fitness is a complex parameter that results from the interaction of virus-specific characters (e.g. intracellular growth rate, adsorption rate, virion extracellular stability, and tolerance to mutations) with others that depend on the underlying fitness landscape and the internal structure of the whole population. Individual mutants usually have lower fitness values than the complex population from which they come from. When they are propagated and allowed to attain large population sizes for a sufficiently long time, they approach mutation-selection equilibrium with the concomitant fitness gains...
January 2018: Virus Evolution
https://www.readbyqxmd.com/read/29339446/ontogeny-of-human-mucosal-associated-invariant-t-cells-and-related-t-cell-subsets
#6
Ghada Ben Youssef, Marie Tourret, Marion Salou, Liana Ghazarian, Véronique Houdouin, Stanislas Mondot, Yvonne Mburu, Marion Lambert, Saba Azarnoush, Jean-Sébastien Diana, Anne-Laure Virlouvet, Michel Peuchmaur, Thomas Schmitz, Jean-Hugues Dalle, Olivier Lantz, Valérie Biran, Sophie Caillat-Zucman
Mucosal-associated invariant T (MAIT) cells are semi-invariant Vα7.2+ CD161highCD4- T cells that recognize microbial riboflavin precursor derivatives such as 5-OP-RU presented by MR1. Human MAIT cells are abundant in adult blood, but there are very few in cord blood. We longitudinally studied Vα7.2+ CD161high T cell and related subset levels in infancy and after cord blood transplantation. We show that Vα7.2+ and Vα7.2- CD161high T cells are generated early during gestation and likely share a common prenatal developmental program...
January 16, 2018: Journal of Experimental Medicine
https://www.readbyqxmd.com/read/29338034/clonal-growth-strategy-diversity-and-structure-a-spatiotemporal-response-to-sedimentation-in-tropical-cyperus-papyrus-swamps
#7
Addisie Geremew, Iris Stiers, Tim Sierens, Alemayehu Kefalew, Ludwig Triest
Land degradation and soil erosion in the upper catchments of tropical lakes fringed by papyrus vegetation can result in a sediment load gradient from land to lakeward. Understanding the dynamics of clonal modules (ramets and genets) and growth strategies of plants on such a gradient in both space and time is critical for exploring a species adaptation and processes regulating population structure and differentiation. We assessed the spatial and temporal dynamics in clonal growth, diversity, and structure of an emergent macrophyte, Cyperus papyrus (papyrus), in response to two contrasting sedimentation regimes by combining morphological traits and genotype data using 20 microsatellite markers...
2018: PloS One
https://www.readbyqxmd.com/read/29335635/the-emergence-of-metabolic-heterogeneity-and-diverse-growth-responses-in-isogenic-bacterial-cells
#8
Emrah Şimşek, Minsu Kim
Microorganisms adapt to frequent environmental changes through population diversification. Previous studies demonstrated phenotypic diversity in a clonal population and its important effects on microbial ecology. However, the dynamic changes of phenotypic composition have rarely been characterized. Also, cellular variations and environmental factors responsible for phenotypic diversity remain poorly understood. Here, we studied phenotypic diversity driven by metabolic heterogeneity. We characterized metabolic activities and growth kinetics of starved Escherichia coli cells subject to nutrient upshift at single-cell resolution...
January 15, 2018: ISME Journal
https://www.readbyqxmd.com/read/29328552/changes-in-chromosome-counts-and-patterns-in-cho-cell-lines-upon-generation-of-recombinant-cell-lines-and-subcloning
#9
Sabine Vcelar, Michael Melcher, Norbert Auer, Astrid Hrdina, Anja Puklowski, Friedrich Leisch, Vaibhav Jadhav, Till Wenger, Martina Baumann, Nicole Borth
Chinese hamster ovary cells are the number one production system for therapeutic proteins. A pre-requirement for their use in industrial production of biopharmaceuticals is to be clonal, thus originating from a single cell in order to be phenotypically and genomically identical. In the present study it was evaluated whether standard procedures, such as the generation of a recombinant cell line in combination with selection for a specific and stable phenotype (expression of the recombinant product) or subcloning have any impact on karyotype stability or homogeneity in CHO cells...
January 12, 2018: Biotechnology Journal
https://www.readbyqxmd.com/read/29327728/diverse-modes-of-clonal-evolution-in-hbv-related-hepatocellular-carcinoma-revealed-by-single-cell-genome-sequencing
#10
Meng Duan, Junfeng Hao, Sijia Cui, Daniel L Worthley, Shu Zhang, Zhichao Wang, Jieyi Shi, Longzi Liu, Xiaoying Wang, Aiwu Ke, Ya Cao, Ruibin Xi, Xiaoming Zhang, Jian Zhou, Jia Fan, Chong Li, Qiang Gao
Hepatocellular carcinoma (HCC) is a cancer of substantial morphologic, genetic and phenotypic diversity. Yet we do not understand the relationship between intratumor heterogeneity and the associated morphologic/histological characteristics of the tumor. Using single-cell whole-genome sequencing to profile 96 tumor cells (30-36 each) and 15 normal liver cells (5 each), collected from three male patients with HBV-associated HCC, we confirmed that copy number variations occur early in hepatocarcinogenesis but thereafter remain relatively stable throughout tumor progression...
January 12, 2018: Cell Research
https://www.readbyqxmd.com/read/29326010/genomics-of-corynebacterium-striatum-an-emerging-multi-drug-resistant-pathogen-of-immunocompromised-patients
#11
Kathleen Nudel, Xiaomin Zhao, Sankha Basu, Xiaoxi Dong, Maria Hoffmann, Michael Feldgarden, Marc Allard, Michael Klompas, Lynn Bry
OBJECTIVES: Corynebacterium striatum is an emerging multi-drug resistant (MDR) pathogen of immunocompromised and chronically ill patients. The objective of these studies was to provide a detailed genomic analysis of disease causing C. striatum and determine the genomic drivers of resistance and resistance-gene transmission. METHODS: A multi-institutional and prospective pathogen genomics program flagged seven MDR C. striatum infections occurring close in time, and specifically in immunocompromised patients with underlying respiratory diseases...
January 8, 2018: Clinical Microbiology and Infection
https://www.readbyqxmd.com/read/29325057/tumor-purity-quantification-by-clonal-dna-methylation-signatures
#12
Matteo Benelli, Dario Romagnoli, Francesca Demichelis
Motivation: Controlling for tumor purity in molecular analyses is essential to allow for reliable genomic aberration calls, for inter-sample comparison and to monitor heterogeneity of cancer cell populations. In genome wide screening studies, the assessment of tumor purity is typically performed by means of computational methods that exploit somatic copy number aberrations (SCNAs). Results: We present a strategy, called PAMES (Purity Assessment from clonal MEthylation Sites), which uses the methylation level of a few dozen, highly clonal, tumor type specific CpG sites to estimate the purity of tumor samples, without the need of a matched benign control...
January 8, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29323290/clonal-analysis-of-lineage-fate-in-native-haematopoiesis
#13
Alejo E Rodriguez-Fraticelli, Samuel L Wolock, Caleb S Weinreb, Riccardo Panero, Sachin H Patel, Maja Jankovic, Jianlong Sun, Raffaele A Calogero, Allon M Klein, Fernando D Camargo
Haematopoiesis, the process of mature blood and immune cell production, is functionally organized as a hierarchy, with self-renewing haematopoietic stem cells and multipotent progenitor cells sitting at the very top. Multiple models have been proposed as to what the earliest lineage choices are in these primitive haematopoietic compartments, the cellular intermediates, and the resulting lineage trees that emerge from them. Given that the bulk of studies addressing lineage outcomes have been performed in the context of haematopoietic transplantation, current models of lineage branching are more likely to represent roadmaps of lineage potential than native fate...
January 11, 2018: Nature
https://www.readbyqxmd.com/read/29321869/imitating-the-cost-of-males-a-hypothesis-for-coexistence-of-all-female-sperm-dependent-species-and-their-sexual-host
#14
Christelle Leung, Bernard Angers
All-female sperm-dependent species are particular asexual organisms that must coexist with a closely related sexual host for reproduction. However, demographic advantages of asexual over sexual species that have to produce male individuals could lead both to extinction. The unresolved question of their coexistence still challenges and fascinates evolutionary biologists. As an alternative hypothesis, we propose those asexual organisms are afflicted by a demographic cost analogous to the production of males to prevent exclusion of the host...
January 2018: Ecology and Evolution
https://www.readbyqxmd.com/read/29318912/population-genetics-of-verticillium-dahliae-in-iran-based-on-microsatellite-and-snp-markers
#15
Vahideh Rafiei, Ziaeddin Banihashemi, Laura S Bautista-Jalon, María Del Mar Jiménez-Gasco, Gillian Turgeon, Michael G Milgroom
Verticillium dahliae is a plant pathogenic fungus that reproduces asexually and its population structure is highly clonal. In the present study, 78 V. dahliae isolates from Iran were genotyped for mating type, SNPs and microsatellites to assign them to clonal lineages and to determine population genetic structure in Iran. The mating type of all isolates was MAT1-2. Based on neighbor-joining analysis and minimum spanning networks constructed from SNPs and microsatellite genotypes, all but four isolates were assigned to lineage 2B824; four isolates were assigned to lineage 4B...
January 10, 2018: Phytopathology
https://www.readbyqxmd.com/read/29316828/hodgkin-s-lymphoma-and-its-association-with-ebv-and-hiv-infection
#16
Ravnit Grewal, Alexandra Irimie, Nasheen Naidoo, Nooroudien Mohamed, Bobe Petrushev, Manogari Chetty, Ciprian Tomuleasa, Emmanuel-Akinola Abayomi
Hodgkin's lymphoma (HL) constitutes a clonal expansion of what appears to be malignant B cells. Viruses are involved in its pathogenesis, such as the Epstein-Barr virus (EBV) and human immunodeficiency virus (HIV). Since these viral infections have been shown to play key roles in the pathogenesis of HL, countries with a prevalence of HIV and EBV represent interesting population targets to study the pathogenesis of HL, linking the evolution of the disease with viral infections. Usually, patients present with late stage disease often involving the bone marrow at the time of diagnosis...
January 9, 2018: Critical Reviews in Clinical Laboratory Sciences
https://www.readbyqxmd.com/read/29312820/resistance-strategies-of-phragmites-australis-common-reed-to-pb-pollution-in-flood-and-drought-conditions
#17
Na Zhang, Jinwei Zhang, Zhiqiang Li, Jing Chen, Zhenhua Zhang, Chunsheng Mu
Resistance strategies of clonal organs, and parent and offspring shoots of Phragmites australis (common reed) to heavy metal pollution in soils are not well known. To clarify the tolerance or resistance strategies in reeds, we conducted a pot experiment with five levels of Pb concentration (0∼4,500 mg kg-1) in flood and drought conditions. Lead toxicity had no inhibitory effect on the number of offspring shoots in flood environment; however, biomass accumulation, and photosynthetic and clonal growth parameters were inhibited in both water environment...
2018: PeerJ
https://www.readbyqxmd.com/read/29305512/molecular-epidemiology-of-dairy-cattle-associated-escherichia-coli-carrying-blactx-m-genes-in-washington-state
#18
Josephine A Afema, Sara Ahmed, Thomas E Besser, Lisa P Jones, William M Sischo, Margaret A Davis
An increase in prevalence of commensal Escherichia coli carrying blaCTX-M genes among dairy cattle was observed between 2008 and 2012 in Washington State. To study the molecular epidemiology of this change, we selected 126 blaCTX-M-positive and 126 blaCTX-M-negative isolates for multi-locus sequence typing (MLST) and antibiotic resistance phenotyping from E. coli obtained during a previous study. For 99 isolates we also determined the blaCTX-M alleles using PCR and sequencing and identified the replicon types of blaCTX-M carrying plasmids...
January 5, 2018: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/29304868/further-characterization-of-adult-sheep-ovarian-stem-cells-and-their-involvement-in-neo-oogenesis-and-follicle-assembly
#19
Hiren Patel, Deepa Bhartiya, Seema Parte
BACKGROUND: Stem cells in the ovary comprise of two distinct populations including very small embryonic-like stem cells (VSELs) and slightly bigger progenitors termed ovarian stem cells (OSCs). They are lodged in ovary surface epithelium (OSE) and are expected to undergo neo-oogenesis and primordial follicle (PF) assembly in adult ovaries. The ovarian stem cells express follicle stimulating hormone (FSH) receptors and are directly activated by FSH resulting in formation of germ cell nests (GCN) in vitro...
January 5, 2018: Journal of Ovarian Research
https://www.readbyqxmd.com/read/29298653/synthesis-and-biological-evaluation-of-novel-triazoles-linked-7-hydroxycoumarin-as-potent-cytotoxic-agents
#20
Aashiq Hussain, Mushtaq A Qurishi, Abid Hamid, S Koul
Cancer is regarded as second leading cause of death worldwide. Therefore, there is a high demand for the discovery, development and improvement of novel anti-cancer agents which could efficiently prevent proliferative pathways and clonal expansion of cells. In view of this, a new series of bioactive scaffolds viz triazoles linked 7-hydroxycoumarin (1) were synthesized using click chemistry approach. All the synthesized compounds were screened for cytotoxicity against a panel of seven different human cancer cell lines viz...
December 29, 2017: Anti-cancer Agents in Medicinal Chemistry
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