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https://www.readbyqxmd.com/read/28207813/interacting-networks-of-resistance-virulence-and-core-machinery-genes-identified-by-genome-wide-epistasis-analysis
#1
Marcin J Skwark, Nicholas J Croucher, Santeri Puranen, Claire Chewapreecha, Maiju Pesonen, Ying Ying Xu, Paul Turner, Simon R Harris, Stephen B Beres, James M Musser, Julian Parkhill, Stephen D Bentley, Erik Aurell, Jukka Corander
Recent advances in the scale and diversity of population genomic datasets for bacteria now provide the potential for genome-wide patterns of co-evolution to be studied at the resolution of individual bases. Here we describe a new statistical method, genomeDCA, which uses recent advances in computational structural biology to identify the polymorphic loci under the strongest co-evolutionary pressures. We apply genomeDCA to two large population data sets representing the major human pathogens Streptococcus pneumoniae (pneumococcus) and Streptococcus pyogenes (group A Streptococcus)...
February 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28207406/degeneration-recognizing-clonal-selection-algorithm-for-multimodal-optimization
#2
Nan Xu, Yongsheng Ding, Lihong Ren, Kuangrong Hao
In this paper, a computing speed improvement for the clonal selection algorithm (CSA) is proposed based on a degeneration recognizing (DR) method. The degeneration recognizing clonal selection algorithm (DR-CSA) is designed for solving complex engineering multimodal optimization problems. On each iteration of CSA, there is a large amount of eliminated solutions which are usually neglected. But these solutions do contain the knowledge of the nonoptimal area. By storing and utilizing these data, the DR-CSA is aimed to identify part of the new population as degenerated and eliminate them before the evaluation operation, so that a number of evaluation times can be avoided...
February 9, 2017: IEEE Transactions on Cybernetics
https://www.readbyqxmd.com/read/28206693/plasmid-and-clonal-interference-during-post-horizontal-gene-transfer-evolution
#3
S Bedhomme, D Perez Pantoja, I G Bravo
Plasmids are nucleic acid molecules that can drive their own replication in a living cell. They can be transmitted horizontally and can thrive in the host cell to high copy numbers. Plasmid replication and gene expression consume cellular resources and cells carrying plasmids incur fitness costs. But many plasmids carry genes that can be beneficial under certain conditions, allowing the cell to endure in the presence of antibiotics, toxins, competitors or parasites. Horizontal transfer of plasmid-encoded genes can thus instantaneously confer differential adaptation to local or transient selection conditions...
February 16, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28203307/epigenetic-strategies-to-reverse-drug-resistance-in-heterogeneous-multiple-myeloma
#4
REVIEW
Mark E Issa, Farnaz Sedigheh Takhsha, Chandra Sekhar Chirumamilla, Claudina Perez-Novo, Wim Vanden Berghe, Muriel Cuendet
Multiple myeloma (MM) is a hematological malignancy, which remains incurable because most patients eventually relapse or become refractory to current treatments. Due to heterogeneity within the cancer cell microenvironment, cancer cell populations employ a dynamic survival strategy to chemotherapeutic treatments, which frequently results in a rapid acquisition of therapy resistance. Besides resistance-conferring genetic alterations within a tumor cell population selected during drug treatment, recent findings also reveal non-mutational mechanisms of drug resistance, involving a small population of "cancer stem cells" (CSCs) which are intrinsically more refractory to the effects of a variety of anticancer drugs...
2017: Clinical Epigenetics
https://www.readbyqxmd.com/read/28202626/cancer-cells-exhibit-clonal-diversity-in-phenotypic-plasticity
#5
Robert Austin Mathis, Ethan S Sokol, Piyush B Gupta
Phenotypic heterogeneity in cancers is associated with invasive progression and drug resistance. This heterogeneity arises in part from the ability of cancer cells to switch between phenotypic states, but the dynamics of this cellular plasticity remain poorly understood. Here we apply DNA barcodes to quantify and track phenotypic plasticity across hundreds of clones in a population of cancer cells exhibiting epithelial or mesenchymal differentiation phenotypes. We find that the epithelial-to-mesenchymal cell ratio is highly variable across the different clones in cancer cell populations, but remains stable for many generations within the progeny of any single clone-with a heritability of 0...
February 2017: Open Biology
https://www.readbyqxmd.com/read/28199659/mating-system-and-genetic-structure-across-all-known-populations-of-dyckia-brevifolia-a-clonal-endemic-and-endangered-rheophyte-bromeliad
#6
Juliana Marcia Rogalski, Ademir Reis, Marcelo Rogalski, Tiago Montagna, Maurício Sedrez Dos Reis
No abstract text is available yet for this article.
February 12, 2017: Journal of Heredity
https://www.readbyqxmd.com/read/28199329/correction-mlst-based-population-genetic-analysis-in-a-global-context-reveals-clonality-amongst-cryptococcus-neoformans-var-grubii-vni-isolates-from-hiv-patients-in-southeastern-brazil
#7
(no author information available yet)
[This corrects the article DOI: 10.1371/journal.pntd.0005223.].
February 2017: PLoS Neglected Tropical Diseases
https://www.readbyqxmd.com/read/28197208/molecular-mutations-and-their-cooccurrences-in-cytogenetically-normal-acute-myeloid-leukemia
#8
REVIEW
Mengning Wang, Chuanwei Yang, Le Zhang, Dale G Schaar
Adult acute myeloid leukemia (AML) clinically is a disparate disease that requires intensive treatments ranging from chemotherapy alone to allogeneic hematopoietic cell transplantation (allo-HCT). Historically, cytogenetic analysis has been a useful prognostic tool to classify patients into favorable, intermediate, and unfavorable prognostic risk groups. However, the intermediate-risk group, consisting predominantly of cytogenetically normal AML (CN-AML), itself exhibits diverse clinical outcomes and requires further characterization to allow for more optimal treatment decision-making...
2017: Stem Cells International
https://www.readbyqxmd.com/read/28195089/immunogenetics-of-chronic-lymphocytic-leukemia
#9
Nikhil Patkar, Nikhil Rabade, Pratibha Amare Kadam, Falguni Mishra, Aditi Muranjan, Prashant Tembhare, Shruti Chaudhary, Swapnali Joshi, Hasmukh Jain, Uma Dangi, Bhausaheb Bagal, Navin Khattry, Hari Menon, Sumeet Gujral, Manju Sengar, P G Subramanian
INTRODUCTION: Cytogenetic aberrations as well as presence of IGVH mutations are the underlying reason for clinical heterogeneity in Chronic Lymphocytic Leukemia (CLL). The presence of IGVH mutations as well as the predominant gene usage shows geographical variations. However, there is no study from India addressing immunogenetics of CLL. In a first Indian study we document the immunogenetics of CLL in a large tertiary hospital. METHODS: We analyzed IGVH mutation status, VH gene usage, cytogenetic abnormalities using FISH, immunophenotyping data and correlated them with standard clinical variables in 84 patients of CLL...
January 2017: Indian Journal of Pathology & Microbiology
https://www.readbyqxmd.com/read/28192371/somatic-mutations-in-telomerase-promoter-counterbalance-germline-loss-of-function-mutations
#10
Lindley Maryoung, Yangbo Yue, Ashley Young, Chad A Newton, Cindy Barba, Nicolai S C van Oers, Richard C Wang, Christine Kim Garcia
Germline coding mutations in different telomere-related genes have been linked to autosomal-dominant familial pulmonary fibrosis. Individuals with these inherited mutations demonstrate incomplete penetrance of clinical phenotypes affecting the lung, blood, liver, skin, and other organs. Here, we describe the somatic acquisition of promoter mutations in telomerase reverse transcriptase (TERT) in blood leukocytes of approximately 5% of individuals with inherited loss-of-function coding mutations in TERT or poly(A)-specific ribonuclease (PARN), another gene linked to telomerase function...
February 13, 2017: Journal of Clinical Investigation
https://www.readbyqxmd.com/read/28191880/single-cell-gene-expression-using-multiplex-rt-qpcr-to-characterize-heterogeneity-of-rare-lymphoid-populations
#11
Thibaut Perchet, Sylvestre Chea, Milena Hasan, Ana Cumano, Rachel Golub
Gene expression heterogeneity is an interesting feature to investigate in lymphoid populations. Gene expression in these cells varies during cell activation, stress, or stimulation. Single-cell multiplex gene expression enables the simultaneous assessment of tens of genes(1)(,)(2)(,)(3). At the single-cell level, multiplex gene expression determines population heterogeneity(4)(,)(5). It allows for the distinction of population heterogeneity by determining both the probable mix of diverse precursor stages among mature cells and also the diversity of cell responses to stimuli...
January 19, 2017: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/28188692/bioreactor-scale-up-and-protein-product-quality-characterization-of-piggybac-transposon-derived-cho-pools
#12
Yashas Rajendra, Sowmya Balasubramanian, Robert B Peery, James R Swartling, Neil A McCracken, Dawn L Norris, Christopher C Frye, Gavin C Barnard
Chinese hamster ovary (CHO) cells remain the most popular host for the production of biopharmaceutical drugs, particularly monoclonal antibodies (mAbs), bispecific antibodies and Fc-fusion proteins. Creating and characterizing the stable CHO clonally-derived cell lines (CDCLs) needed to manufacture these therapeutic proteins is a lengthy and laborious process. Therefore, CHO pools have increasingly been used to rapidly produce protein to support and enable preclinical drug development. We recently described the generation of CHO pools yielding mAb titers as high as 7...
February 11, 2017: Biotechnology Progress
https://www.readbyqxmd.com/read/28188662/population-genetics-of-reef-coral-endosymbionts-symbiodinium-dinophyceae
#13
D J Thornhill, E J Howells, D C Wham, T D Steury, S R Santos
Symbiodinium is a diverse genus of unicellular dinoflagellate symbionts associating with various marine protists and invertebrates. Although the broad-scale diversity and phylogenetics of the Symbiodinium complex is well established, there have been surprisingly few data on fine-scale population structure and biogeography of these dinoflagellates. Yet population level processes contribute strongly to the biology of Symbiodinium, including how anthropogenic-driven global climate change impacts these symbionts and their host associations...
February 11, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28188180/a-population-genomics-approach-to-assessing-the-genetic-basis-of-within-host-microevolution-underlying-recurrent-cryptococcal-meningitis-infection
#14
Johanna Rhodes, Mathew A Beale, Mathieu Vanhove, Joseph N Jarvis, Shichina Kannambath, John A Simpson, Anthea Ryan, Graeme Meintjes, Thomas S Harrison, Matthew C Fisher, Tihana Bicanic
Recurrence of meningitis due to Cryptococcus neoformans after treatment causes substantial mortality in HIV/AIDS patients across sub-Saharan Africa. In order to determine whether recurrence occurred due to relapse of the original infecting isolate or reinfection with a different isolate weeks or months after initial treatment, we used whole-genome sequencing to assess the genetic basis of infection in 17 HIV-infected individuals with recurrent cryptococcal meningitis. Comparisons revealed a clonal relationship for 15 pairs of isolates recovered before and after recurrence showing relapse of the original infection...
February 10, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28177186/characterization-of-enterococcus-faecalis-isolated-from-the-cloaca-of-fancy-breeds-and-confined-chickens
#15
Steffen Lynge Jørgensen, Louise Ladefoged Poulsen, Lotte Thorndal, Amir Atabak Ronaghinia, Magne Bisgaard, Henrik Christensen
AIMS: The aim was to investigate the intestinal community of E. faecalis from healthy confined non-industrialized chicken. METHODS AND RESULTS: A total of 206 E. faecalis isolates were collected from cloacal swabs. The prevalence of E. faecalis from two confined flocks, were 83% and 96%, while only 44% and 13% in two fancy breeder flocks. A total of 204 isolates were characterized by pulsed-field-gel-electrophoresis (PFGE) where 40 strains were selected for multi locus sequence typing (MLST)...
February 8, 2017: Journal of Applied Microbiology
https://www.readbyqxmd.com/read/28176811/intestinal-cancer-stem-cells-marked-by-bmi1-or-lgr5-expression-contribute-to-tumor-propagation-via-clonal-expansion
#16
Hirotsugu Yanai, Naho Atsumi, Toshihiro Tanaka, Naohiro Nakamura, Yoshihiro Komai, Taichi Omachi, Kiyomichi Tanaka, Kazuhiko Ishigaki, Kazuho Saiga, Haruyuki Ohsugi, Yoko Tokuyama, Yuki Imahashi, Shuichi Ohe, Hiroko Hisha, Naoko Yoshida, Keiki Kumano, Masanori Kon, Hiroo Ueno
Although the existence of cancer stem cells in intestine tumors has been suggested, direct evidence has not been yet provided. Here, we showed, using the multicolor lineage-tracing method and mouse models of intestinal adenocarcinoma and adenoma that Bmi1- or Lgr5- positive tumorigenic cells clonally expanded in proliferating tumors. At tumor initiation and during tumor propagation in the colon, the descendants of Lgr5-positive cells clonally proliferated to form clusters. Clonal analysis using ubiquitous multicolor lineage tracing revealed that colon tumors derived from Lgr5-positive cells were monoclonal in origin but eventually merged with neighboring tumors, producing polyclonal tumors at the later stage...
February 8, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28174566/application-of-a-dot-blot-hybridization-platform-to-assess-streptococcus-uberis-population-structure-in-dairy-herds
#17
Pedro Albuquerque, Niza Ribeiro, Alexandre Almeida, Irena Panschin, Afonso Porfirio, Marta Vales, Francisca Diniz, Helena Madeira, Fernando Tavares
Streptococcus uberis is considered one of the most important pathogens associated with bovine mastitis. While traditionally acknowledged as an environmental pathogen, S. uberis has been shown to adopt a contagious epidemiological pattern in several dairy herds. Since different control strategies are employed depending on the mode of transmission, in-depth studies of S. uberis populations are essential to determine the best practices to control this pathogen. In this work, we optimized and validated a dot blot platform, combined with automatic image analysis, to rapidly assess the population structure of infective S...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28170182/primary-salivary-human-stem-progenitor-cells-undergo-microenvironment-driven-acinar-like-differentiation-in-hyaluronate-hydrogel-culture
#18
Padma Pradeepa Srinivasan, Vaishali N Patel, Shuang Liu, Daniel A Harrington, Matthew P Hoffman, Xinqiao Jia, Robert L Witt, Mary C Farach-Carson, Swati Pradhan-Bhatt
Radiotherapy for head and neck cancer often has undesirable effects on salivary glands that lead to xerostomia or severe dry mouth, which can increase oral infections. Our goal is to engineer functional, three-dimensional (3D) salivary gland neotissue for autologous implantation to provide permanent relief. An immediate need exists to obtain autologous adult progenitor cells as the use of embryonic and induced pluripotent stem cells potentially pose serious risks such as teratogenicity and immunogenic rejection...
January 2017: Stem Cells Translational Medicine
https://www.readbyqxmd.com/read/28168700/progenitor-genotyping-reveals-a-complex-clonal-architecture-in-a-subset-of-calr-mutated-myeloproliferative-neoplasms
#19
Sarah Martin, Casey M Wright, Linda M Scott
The identification of acquired CALR mutations in patients with essential thrombocythaemia (ET) or myelofibrosis (MF) has meant that disease-initiating mutations can now be detected in about 90% of all patients with a myeloproliferative neoplasm (MPN). Here, we show that only those CALR mutations that cause a +1 frameshift, thereby altering the carboxy-terminus of calreticulin, promote cytokine independence in vitro; in-frame deletions were not functional, and are unlikely to be the pathogenetic mutation underlying some MPN cases...
February 7, 2017: British Journal of Haematology
https://www.readbyqxmd.com/read/28168221/global-population-genetic-analysis-of-aspergillus-fumigatus
#20
Eta Ebasi Ashu, Ferry Hagen, Anuradha Chowdhary, Jacques F Meis, Jianping Xu
Aspergillus fumigatus is a ubiquitous opportunistic fungal pathogen capable of causing invasive aspergillosis, a globally distributed disease with a mortality rate of up to 90% in high-risk populations. Effective control and prevention of this disease require a thorough understanding of its epidemiology. However, despite significant efforts, the global molecular epidemiology of A. fumigatus remains poorly understood. In this study, we analyzed 2,026 A. fumigatus isolates from 13 countries in four continents using nine highly polymorphic microsatellite markers...
January 2017: MSphere
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