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Genetic evolution

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https://www.readbyqxmd.com/read/29228309/prp8-intein-in-dermatophytes-evolution-and-species-identification
#1
Hans Garcia Garces, Raquel Theodoro Cordeiro, E Bagagli
Dermatophytes are keratinophilic fungi belonging to the family Arthrodermataceae. Despite having a monophyletic origin, its systematics has always been complex and controversial. Sequencing of nuclear ribosomal ITS and D1/D2 rDNA has been proposed as an efficient tool for identifying species in this group of fungi, while multilocus analyses have been used for phylogenetic species recognition. However, the search for new markers, with sequence and size variation, which enable species identification in only one polymerase chain reaction (PCR) step, is very attractive...
December 8, 2017: Medical Mycology: Official Publication of the International Society for Human and Animal Mycology
https://www.readbyqxmd.com/read/29228281/the-intriguing-evolution-of-effect-sizes-in-biomedical-research-over-time-smaller-but-more-often-statistically-significant
#2
Paul Monsarrat, Jean-Noel Vergnes
Background: In medicine, effect sizes (ESs) allow the effects of independent variables (including risk/protective factors, or treatment interventions) on dependent variables (e.g., health outcomes) to be quantified. Given that many public health decisions and health care policies are based on ES estimates, it is important to assess how ESs are used in the biomedical literature and to investigate potential trends in their reporting over time. Results: Through a big data approach, the text mining process automatically extracted 814 120 ESs from 13 322 754 PubMed abstracts...
December 6, 2017: GigaScience
https://www.readbyqxmd.com/read/29228267/the-effects-of-sex-biased-gene-expression-and-x-linkage-on-rates-of-sequence-evolution-in-drosophila
#3
José Luis Campos, Keira Johnston, Brian Charlesworth
A faster rate of adaptive evolution of X-linked genes compared with autosomal genes (the faster-X effect) can be caused by the fixation of recessive or partially recessive advantageous mutations. This effect should be largest for advantageous mutations that affect only male fitness, and least for mutations that affect only female fitness. We tested these predictions in Drosophila melanogaster by using coding and functionally significant non-coding sequences of genes with different levels of sex-biased expression...
December 8, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/29228229/variable-plasmid-fitness-effects-and-mobile-genetic-element-dynamics-across-pseudomonas-species
#4
Anastasia Kottara, James P J Hall, Ellie Harrison, Michael A Brockhurst
Mobile genetic elements (MGE) such as plasmids and transposons mobilise genes within and between species, playing a crucial role in bacterial evolution via horizontal gene transfer (HGT). Currently we lack data on variation in MGE dynamics across bacterial host species. We tracked the dynamics of a large conjugative plasmid, pQBR103, and its Tn5042 mercury resistance transposon, in five diverse Pseudomonas species in environments with and without mercury selection. Plasmid fitness effects and stability varied extensively between host species and environments, as did the propensity for chromosomal capture of the Tn5042 mercury resistance transposon associated with loss of the plasmid...
December 4, 2017: FEMS Microbiology Ecology
https://www.readbyqxmd.com/read/29228218/nonhuman-primate-models-and-understanding-the-pathogenesis-of-hiv-infection-and-aids
#5
Ronald S Veazey, Andrew A Lackner
Research using nonhuman primates (NHPs) as models for human immunodeficiency virus (HIV) infection and acquired immunodeficiency syndrome (AIDS) has resulted in tremendous achievements not only in the prevention and treatment of HIV, but also in biomedical research more broadly. Once considered a death sentence, HIV infection is now fairly well controlled with combination antiretroviral treatments, almost all of which were first tested for efficacy and safety in nonhuman primates or other laboratory animals...
December 8, 2017: ILAR Journal
https://www.readbyqxmd.com/read/29226181/a-bioreactor-method-to-generate-high-titer-genetically-stable-clinical-isolate-human-cytomegalovirus
#6
Victoria R Saykally, Luke I Rast, Jeff Sasaki, Seung-Yong Jung, Cynthia Bolovan-Fritts, Leor S Weinberger
Human cytomegalovirus (HCMV) infection is a major cause of morbidity and mortality in transplant patients and a leading cause of congenital birth defects (Saint Louis, 2016). Vaccination and therapeutic studies often require scalable cell culture production of wild type virus, represented by clinical isolates. Obtaining sufficient stocks of wild-type clinical HCMV is often labor intensive and inefficient due to low yield and genetic loss, presenting a barrier to studies of clinical isolates. Here we report a bioreactor method based on continuous infection, where retinal pigment epithelial (ARPE-19) cells adhered to microcarrier beads are infected in a bioreactor and used to produce high-titers of clinical isolate HCMV that maintain genetic integrity of key viral tropism factors and the viral genome...
November 5, 2017: Bio-protocol
https://www.readbyqxmd.com/read/29226035/molecular-evolution-of-virulence-genes-and-non-virulence-genes-in-clinical-natural-and-artificial-environmental-legionella-pneumophila-isolates
#7
Xiao-Yong Zhan, Qing-Yi Zhu
Background: L. pneumophila is the main causative agent of Legionnaires' disease. Free-living amoeba in natural aquatic environments is the reservoir and shelter for L. pneumophila. From natural water sources, L. pneumophila can colonize artificial environments such as cooling towers and hot-water systems, and then spread in aerosols, infecting the susceptible person. Therefore, molecular phylogeny and genetic variability of L. pneumophila from different sources (natural water, artificial water, and human lung tissue) might be distinct because of the selection pressure in different environments...
2017: PeerJ
https://www.readbyqxmd.com/read/29225770/sex-determination-mode-does-not-affect-body-or-genital-development-of-the-central-bearded-dragon-pogona-vitticeps
#8
Sarah L Whiteley, Clare E Holleley, Wendy A Ruscoe, Meghan Castelli, Darryl L Whitehead, Juan Lei, Arthur Georges, Vera Weisbecker
Background: The development of male- or female-specific phenotypes in squamates is typically controlled by either temperature-dependent sex determination (TSD) or chromosome-based genetic sex determination (GSD). However, while sex determination is a major switch in individual phenotypic development, it is unknownhow evolutionary transitions between GSD and TSD might impact on the evolution of squamate phenotypes, particularly the fast-evolving and diverse genitalia. Here, we take the unique opportunity of studying the impact of both sex determination mechanisms on the embryological development of the central bearded dragon (Pogona vitticeps)...
2017: EvoDevo
https://www.readbyqxmd.com/read/29225610/horizontal-gene-transfer-contributes-to-plant-evolution-the-case-of-agrobacterium-t-dnas
#9
REVIEW
Dora G Quispe-Huamanquispe, Godelieve Gheysen, Jan F Kreuze
Horizontal gene transfer (HGT) can be defined as the acquisition of genetic material from another organism without being its offspring. HGT is common in the microbial world including archaea and bacteria, where HGT mechanisms are widely understood and recognized as an important force in evolution. In eukaryotes, HGT now appears to occur more frequently than originally thought. Many studies are currently detecting novel HGT events among distinct lineages using next-generation sequencing. Most examples to date include gene transfers from bacterial donors to recipient organisms including fungi, plants, and animals...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/29225287/lysogenisation-of-shiga-toxin-encoding-bacteriophage-represses-cell-motility
#10
Shoichi Mitsunaka, Naoki Sudo, Yasuhiko Sekine
Bacteriophages are genetic elements that play key roles in the evolution and diversification of bacterial genomes. The Shiga toxin (Stx)-encoding phage plays an important role in the horizontal transfer of the stx gene. However, the influence of the Stx phage integration on the physiological properties and gene expression pattern of the host have not been clearly resolved. In this study, we constructed the Sp5 lysogen through lysogenisation of E. coli K-12 by Sp5, an Stx2 phage in enterohaemorrhagic E. coli (EHEC) O157:H7 Sakai, and examined the effect of the resulting lysogen on cell motility under various growth conditions...
December 8, 2017: Journal of General and Applied Microbiology
https://www.readbyqxmd.com/read/29223477/immuno-oncology-from-the-perspective-of-somatic-evolution
#11
REVIEW
Santiago González, Nadezda Volkova, Philip Beer, Moritz Gerstung
The past years have witnessed significant success for cancer immunotherapies that activate a patient's immune system against their cancer cells. At the same time our understanding of the genetic changes driving tumor evolution have progressed dramatically. The study of cancer genomes has shown that tumors are best understood as cell populations governed by the rules of evolution, leading to the emergence and spread of cell lineages with pathogenic mutations. Moreover, somatic evolution can explain the acquisition of mutations conferring drug resistance in the ever-lasting battle for reaching even fitter cell states...
December 6, 2017: Seminars in Cancer Biology
https://www.readbyqxmd.com/read/29223357/phylogenomic-detection-and-functional-prediction-of-genes-potentially-important-for-plant-meiosis
#12
Luoyan Zhang, Hongzhi Kong, Hong Ma, Ji Yang
Meiosis is a specialized type of cell division necessary for sexual reproduction in eukaryotes. A better understanding of the cytological procedures of meiosis has been achieved by comprehensive cytogenetic studies in plants, while the genetic mechanisms regulating meiotic progression remain incompletely understood. The increasing accumulation of complete genome sequences and large-scale gene expression datasets has provided a powerful resource for phylogenomic inference and unsupervised identification of genes involved in plant meiosis...
December 6, 2017: Gene
https://www.readbyqxmd.com/read/29222702/molecular-insights-into-the-non-recombining-nature-of-the-spinach-male-determining-region
#13
Tomohiro Kudoh, Mitsuhiko Takahashi, Takayuki Osabe, Atsushi Toyoda, Hideki Hirakawa, Yutaka Suzuki, Nobuko Ohmido, Yasuyuki Onodera
Spinach (Spinacia oleracea L.) is a dioecious plant with male heterogametic sex determination and homomorphic sex chromosomes (XY). The dioecism is utilized for producing commercial hybrid seeds, and hence understanding the molecular-genetic basis of the species' sex determining locus is an important issue for spinach breeding. In this study, seven dominant DNA markers were shown to completely co-segregate with the male-determining gene in segregating spinach populations comprising > 1500 plants. In addition, these seven dominant DNA markers were completely associated with the male-determining gene in over 100 spinach germplasm accessions and cultivars...
December 8, 2017: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/29222441/robust-rna-based-in-situ-mutation-detection-delineates-colorectal-cancer-subclonal-evolution
#14
Ann-Marie Baker, Weini Huang, Xiao-Ming Mindy Wang, Marnix Jansen, Xiao-Jun Ma, Jeffrey Kim, Courtney M Anderson, Xingyong Wu, Liuliu Pan, Nan Su, Yuling Luo, Enric Domingo, Timon Heide, Andrea Sottoriva, Annabelle Lewis, Andrew D Beggs, Nicholas A Wright, Manuel Rodriguez-Justo, Emily Park, Ian Tomlinson, Trevor A Graham
Intra-tumor heterogeneity (ITH) is a major underlying cause of therapy resistance and disease recurrence, and is a read-out of tumor growth. Current genetic ITH analysis methods do not preserve spatial context and may not detect rare subclones. Here, we address these shortfalls by developing and validating BaseScope-a novel mutation-specific RNA in situ hybridization assay. We target common point mutations in the BRAF, KRAS and PIK3CA oncogenes in archival colorectal cancer samples to precisely map the spatial and morphological context of mutant subclones...
December 8, 2017: Nature Communications
https://www.readbyqxmd.com/read/29222311/role-of-the-microenvironment-across-histological-subtypes-of-nhl
#15
REVIEW
Karin Tarte
Recent progress in next-generation sequencing strategies has revealed the genetic landscape of B-cell non-Hodgkin lymphoma, but the tumor microenvironment is increasingly recognized as crucial to sustaining malignant B-cell survival and growth, subclonal evolution, and drug resistance. The tumor niche is made up of a dynamic and organized network of strongly heterogeneous immune and stromal cell subsets characterized by specific phenotypic, transcriptomic, and functional features. Nonmalignant cell recruitment and plasticity are dictated by lymphoma B cells, which convert their surrounding microenvironment into a supportive niche...
December 8, 2017: Hematology—the Education Program of the American Society of Hematology
https://www.readbyqxmd.com/read/29222300/emerging-options-in-multiple-myeloma-targeted-immune-and-epigenetic-therapies
#16
REVIEW
Shaji Kumar
Considerable progress has been made in the treatment of multiple myeloma in the past decade with median survival for the disease improving significantly. This has come through a combination of better understanding of the disease biology and coordinated research into new treatment approaches including better supportive care. However, patients eventually become refractory to available treatments and succumb to the disease, highlighting the need to develop new treatment approaches. The genetic heterogeneity in the disease and clonal evolution under treatment pressure underlie the development of resistance, underscoring the need to develop more effective therapies that can eradicate the disease at initial treatment as well as the need for new classes of drugs with varying mechanisms of action...
December 8, 2017: Hematology—the Education Program of the American Society of Hematology
https://www.readbyqxmd.com/read/29222170/imprecision-and-dna-break-repair-biased-towards-incompatible-end-joining-in-leukemia
#17
Franz Josef Gassner, Maria Schubert, Stefan Rebhandl, Karina Spandl, Nadja Zaborsky, Kemal Catakovic, Stephanie Blaimer, Daniel Hebenstreit, Richard Greil, Roland Geisberger
Cancer is a genetic disease caused by mutations and chromosomal abnormalities which contribute to uncontrolled cell growth. In addition, cancer cells can rapidly respond to conventional and targeted therapies by accumulating novel and often specific genetic lesions leading to acquired drug resistance and relapsing disease. In chronic lymphocytic leukemia (CLL), however, diverse chromosomal aberrations often occur. In many cases, improper repair of DNA double strand breaks (DSBs) is a major source for genomic abnormalities...
December 8, 2017: Molecular Cancer Research: MCR
https://www.readbyqxmd.com/read/29220506/a-molecular-portrait-of-de-novo-genes-in-yeasts
#18
Nikolaos N Vakirlis, Alex S Hebert, Dana A Opulente, Guillaume Achaz, Chris Todd Hittinger, Gilles Fischer, Joshua J Coon, Ingrid Lafontaine
New genes, with novel protein functions, can evolve "from scratch" out of intergenic sequences. These de novo genes can integrate the cell's genetic network and drive important phenotypic innovations. Therefore, identifying de novo genes and understanding how the transition from noncoding to coding occurs are key problems in evolutionary biology. However, identifying de novo genes is a difficult task, hampered by the presence of remote homologs, fast evolving sequences and erroneously annotated protein coding genes...
December 6, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/29220486/transcriptome-signatures-of-selection-drift-introgression-and-gene-duplication-in-the-evolution-of-an-extremophile-endemic-plant
#19
Angela K Hawkins, Elyssa R Garza, Valerie A Dietz, Oscar J Hernandez, W Daryl Hawkins, A Millie Burrell, Alan E Pepper
Plants on serpentine soils provide extreme examples of adaptation to environment, and thus offer excellent models for the study of evolution at the molecular and genomic level. Serpentine outcrops are derived from ultramafic rock and have extremely low levels of essential plant nutrients (e.g. N, P, K, Ca), as well as toxic levels of heavy metals (e.g. Ni, Cr, Co) and low moisture availability. These outcrops provide habitat to a number of endemic plant species, including the annual mustard Caulanthus amplexicaulis var...
December 6, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/29220374/a-blaoxa-181-harbouring-multi-resistant-st147-klebsiella-pneumoniae-isolate-from-pakistan-that-represent-an-intermediate-stage-towards-pan-drug-resistance
#20
Fouzia Nahid, Rabaab Zahra, Linus Sandegren
Carbapenem resistant Klebsiella pneumoniae (CR-KP) infections are an ever-increasing global issue, especially in the Indian subcontinent. Here we report genetic insight into a blaOXA-181 harbouring Klebsiella pneumoniae, belonging to the pandemic lineage ST147, that represents an intermediate stage towards pan-drug resistance. The CR-KP isolate DA48896 was isolated from a patient from Pakistan and was susceptible only to tigecycline and colistin. It harboured blaOXA-181 and was assigned to sequence type ST147...
2017: PloS One
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