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https://www.readbyqxmd.com/read/29334678/genome-evolution-analysis-of-recurrent-testicular-malignant-mesothelioma-by-whole-genome-sequencing
#1
Shigeng Zhang, Qi Zhang, Qing Sun, Jinlong Tang, Jimin Chen, Na Ji, Yichun Zheng, Francia Fang, Wanjun Lei, Pengpeng Li, Nan Zhang
BACKGROUND/AIMS: Malignant mesothelioma of the tunica vaginalis testis is a rare and lethal disease. The genomic characteristics and genetic changes of tumor cells during the progression of this disease are unknown. METHODS: we performed whole-genome sequencing of four successive tumor samples derived from surgery and a blood sample in a single patient. RESULTS: All tumors were found to have significant C-to-T and T-to-C mutations, and amplification of copy number in chromosomes 1 and 12 were notified in all tumor samples...
January 15, 2018: Cellular Physiology and Biochemistry
https://www.readbyqxmd.com/read/29334409/climate-driven-mitochondrial-selection-a-test-in-australian-songbirds
#2
Annika Mae Lamb, Han Ming Gan, Chris Greening, Leo Joseph, Yin Peng Lee, Alejandra Morán-Ordóñez, Paul Sunnucks, Alexandra Pavlova
Diversifying selection between populations that inhabit different environments can promote lineage divergence within species and ultimately drive speciation. The mitochondrial genome (mitogenome) encodes essential proteins of the oxidative phosphorylation (OXPHOS) system and can be a strong target for climate-driven selection (i.e. associated with inhabiting different climates). We investigated whether Pleistocene climate changes drove mitochondrial selection and evolution within Australian birds. First, using phylogeographic analyses of the mitochondrial ND2 gene for 17 songbird species, we identified mitochondrial clades (mitolineages)...
January 15, 2018: Molecular Ecology
https://www.readbyqxmd.com/read/29331971/a-study-protocol-for-a-non-randomised-comparison-trial-evaluating-the-feasibility-and-effectiveness-of-a-mobile-cognitive-behavioural-programme-with-integrated-coaching-for-anxious-adults-in-primary-care
#3
Eva Szigethy, Francis Solano, Meredith Wallace, Dina L Perry, Lauren Morrell, Kathryn Scott, Megan Jones Bell, Megan Oser
INTRODUCTION: Generalised anxiety disorder (GAD) and subclinical GAD are highly prevalent in primary care. Unmanaged anxiety worsens quality of life in patients seen in primary care practices and leads to increased medical utilisation and costs. Programmes that teach patients cognitive-behavioural therapy (CBT) techniques have been shown to improve anxiety and to prevent the evolution of anxiety symptoms to disorders, but access and engagement have hampered integration of CBT into medical settings...
January 13, 2018: BMJ Open
https://www.readbyqxmd.com/read/29330556/evolution-of-the-phosphatidylcholine-biosynthesis-pathways-in-green-algae-combinatorial-diversity-of-methyltransferases
#4
Takashi Hirashima, Masakazu Toyoshima, Takashi Moriyama, Naoki Sato
Phosphatidylcholine (PC) is one of the most common phospholipids in eukaryotes, although some green algae such as Chlamydomonas reinhardtii are known to lack PC. Recently, we detected PC in four species in the genus Chlamydomonas: C. applanata NIES-2202, C. asymmetrica NIES-2207, C. debaryana NIES-2212, and C. sphaeroides NIES-2242. To reveal the PC biosynthesis pathways in green algae and the evolutionary scenario involved in their diversity, we analyzed the PC biosynthesis genes in these four algae using draft genome sequences...
January 12, 2018: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/29329546/whole-genome-sequencing-of-genotype-vi-newcastle-disease-viruses-from-formalin-fixed-paraffin-embedded-tissues-from-wild-pigeons-reveals-continuous-evolution-and-previously-unrecognized-genetic-diversity-in-the-u-s
#5
Ying He, Tonya L Taylor, Kiril M Dimitrov, Salman L Butt, James B Stanton, Iryna V Goraichuk, Heather Fenton, Rebecca Poulson, Jian Zhang, Corrie C Brown, Hon S Ip, Marcos Isidoro-Ayza, Claudio L Afonso
BACKGROUND: Newcastle disease viruses (NDV) are highly contagious and cause disease in both wild birds and poultry. A pigeon-adapted variant of genotype VI NDV, often termed pigeon paramyxovirus 1, is commonly isolated from columbids in the United States and worldwide. Complete genomic characterization of these genotype VI viruses circulating in wild columbids in the United States is limited, and due to the genetic variability of the virus, failure of rapid diagnostic detection has been reported...
January 12, 2018: Virology Journal
https://www.readbyqxmd.com/read/29325926/the-study-of-the-inhibitory-effect-of-calcium-oxalate-monohydrate-s-crystallization-by-two-medicinal-and-aromatic-plants-ammi-visnaga-and-punica-granatum
#6
R Kachkoul, T Sqalli Houssaini, Y Miyah, M Mohim, R El Habbani, A Lahrichi
INTRODUCTION: Urinary lithiasis is a recurrent disease defined by the presence of calculi in the urinary tract. Most urinary calculi have as a major component calcium oxalate which occurs mainly in two crystalline forms: Calcium oxalate monohydrate (whewellite) and calcium oxalate dihydrate (weddellite). The target behind, this work is to study the inhibiting effect of the calcium oxalate's crystallization by the extract of the Ammi visnaga and the Punica granatum. METHODS: The inhibition of crystallization has been studied in vitro with both the absence and the presence of the different concentrations of the extracts of the two plants...
January 8, 2018: Progrès en Urologie
https://www.readbyqxmd.com/read/29325895/the-vertebrate-limb-an-evolving-complex-of-self-organizing-systems
#7
REVIEW
Stuart A Newman, Tilmann Glimm, Ramray Bhat
The paired appendages (fins or limbs) of jawed vertebrates contain an endoskeleton consisting of nodules, bars and, in some groups, plates of cartilage, or bone arising from replacement of cartilaginous templates. The generation of the endoskeletal elements occurs by processes involving production and diffusion of morphogens, with, variously, positive and negative feedback circuits, adhesion, and receptor dynamics with similarities to the mechanism for chemical pattern formation proposed by Alan Turing. This review presents a unified interpretation of the evolution and functioning of these mechanisms...
January 8, 2018: Progress in Biophysics and Molecular Biology
https://www.readbyqxmd.com/read/29325872/structure-and-function-of-a-highly-active-bile-salt-hydrolase-bsh-from-enterococcus-faecalis-and-post-translational-processing-of-bsh-enzymes
#8
Deepak Chand, Priyabrata Panigrahi, Nishant Kumar Varshney, Sureshkumar Ramasamy, C G Suresh
Bile Salt Hydrolase (BSH), a member of Cholylglycine hydrolase family, catalyses the de-conjugation of bile acids and is evolutionarily related to penicillin V acylase (PVA) that hydrolyses a different substrate such as penicillin V. We report the three-dimensional structure of a BSH enzyme from the Gram-positive bacteria Enterococcus faecalis (EfBSH) which has manifold higher hydrolase activity compared to other known BSHs and displays unique allosteric catalytic property. The structural analysis revealed reduced secondary structure content compared to other known BSH structures, particularly devoid of an anti-parallel β-sheet in the assembly loop and part of a β-strand is converted to increase the length of a substrate binding loop 2...
January 8, 2018: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/29325077/integrating-restriction-site-associated-dna-sequencing-rad-seq-with-morphological-cladistic-analysis-clarifies-evolutionary-relationships-among-major-species-groups-of-bee-orchids
#9
Richard M Bateman, Gábor Sramkó, Ovidiu Paun
Background and Aims: Bee orchids (Ophrys) have become the most popular model system for studying reproduction via insect-mediated pseudo-copulation and for exploring the consequent, putatively adaptive, evolutionary radiations. However, despite intensive past research, both the phylogenetic structure and species diversity within the genus remain highly contentious. Here, we integrate next-generation sequencing and morphological cladistic techniques to clarify the phylogeny of the genus...
January 9, 2018: Annals of Botany
https://www.readbyqxmd.com/read/29324969/apobec-mutagenesis-in-drug-resistance-and-immune-escape-in-hiv-and-cancer-evolution
#10
S Venkatesan, R Rosenthal, N Kanu, N McGranahan, J Bartek, S A Quezada, J Hare, R S Harris, C Swanton
The APOBEC mutational signature has only recently been detected in a multitude of cancers through next-generation sequencing. In contrast, APOBEC has been a focus of virology research for over a decade. Many lessons learnt regarding APOBEC within virology are likely to be applicable to cancer. In this review, we explore the parallels between the role of APOBEC enzymes in HIV and cancer evolution. We discuss data supporting the role of APOBEC mutagenesis in creating HIV genome heterogeneity, drug resistance, and immune escape variants...
January 8, 2018: Annals of Oncology: Official Journal of the European Society for Medical Oncology
https://www.readbyqxmd.com/read/29323115/wet-dry-cycles-enable-the-parallel-origin-of-canonical-and-non-canonical-nucleosides-by-continuous-synthesis
#11
Sidney Becker, Christina Schneider, Hidenori Okamura, Antony Crisp, Tynchtyk Amatov, Milan Dejmek, Thomas Carell
The molecules of life were created by a continuous physicochemical process on an early Earth. In this hadean environment, chemical transformations were driven by fluctuations of the naturally given physical parameters established for example by wet-dry cycles. These conditions might have allowed for the formation of (self)-replicating RNA as the fundamental biopolymer during chemical evolution. The question of how a complex multistep chemical synthesis of RNA building blocks was possible in such an environment remains unanswered...
January 11, 2018: Nature Communications
https://www.readbyqxmd.com/read/29321241/evolution-of-the-shut-off-steps-of-vertebrate-phototransduction
#12
Trevor D Lamb, Hardip R Patel, Aaron Chuah, David M Hunt
Different isoforms of the genes involved in phototransduction are expressed in vertebrate rod and cone photoreceptors, providing a unique example of parallel evolution via gene duplication. In this study, we determine the molecular phylogeny of the proteins underlying the shut-off steps of phototransduction in the agnathan and jawed vertebrate lineages. For the G-protein receptor kinases (GRKs), the GRK1 and GRK7 divisions arose prior to the divergence of tunicates, with further expansion during the two rounds of whole-genome duplication (2R); subsequently, jawed and agnathan vertebrates retained different subsets of three isoforms of GRK...
January 2018: Open Biology
https://www.readbyqxmd.com/read/29316123/from-designing-the-molecules-of-life-to-designing-life-future-applications-derived-from-advances-in-dna-technologies
#13
Richie E Kohman, Aditya M Kunjapur, Eriona Hysolli, Yu Wang, George M Church
Since the elucidation of its structure, DNA has been at the forefront of biological research. In the past half century, an explosion of DNA-based technology development has occurred with the most rapid advances being made for DNA sequencing. In parallel, dramatic improvements have also been made in the synthesis and editing of DNA from the oligonucleotide to the genome scale. In this Review, we will summarize four different subfields relating to DNA technologies following this trajectory of smaller to larger scale...
January 9, 2018: Angewandte Chemie
https://www.readbyqxmd.com/read/29315904/the-effects-of-ageing-on-mouse-muscle-microstructure-a-comparative-study-of-time-dependent-diffusion-mri-and-histological-assessment
#14
Paola Porcari, Matt G Hall, Chris A Clark, Elizabeth Greally, Volker Straub, Andrew M Blamire
The investigation of age-related changes in muscle microstructure between developmental and healthy adult mice may help us to understand the clinical features of early-onset muscle diseases, such as Duchenne muscular dystrophy. We investigated the evolution of mouse hind-limb muscle microstructure using diffusion imaging of in vivo and in vitro samples from both actively growing and mature mice. Mean apparent diffusion coefficients (ADCs) of the gastrocnemius and tibialis anterior muscles were determined as a function of diffusion time (Δ), age (7...
January 9, 2018: NMR in Biomedicine
https://www.readbyqxmd.com/read/29311648/auditory-opportunity-and-visual-constraint-enabled-the-evolution-of-echolocation-in-bats
#15
Jeneni Thiagavel, Clément Cechetto, Sharlene E Santana, Lasse Jakobsen, Eric J Warrant, John M Ratcliffe
Substantial evidence now supports the hypothesis that the common ancestor of bats was nocturnal and capable of both powered flight and laryngeal echolocation. This scenario entails a parallel sensory and biomechanical transition from a nonvolant, vision-reliant mammal to one capable of sonar and flight. Here we consider anatomical constraints and opportunities that led to a sonar rather than vision-based solution. We show that bats' common ancestor had eyes too small to allow for successful aerial hawking of flying insects at night, but an auditory brain design sufficient to afford echolocation...
January 8, 2018: Nature Communications
https://www.readbyqxmd.com/read/29309586/cytosolic-hsc20-integrates-de-novo-iron-sulfur-cluster-biogenesis-with-the-ciao1-mediated-transfer-to-recipients
#16
Ki Soon Kim, Nunziata Maio, Anamika Singh, Tracey A Rouault
Iron sulfur (Fe-S) clusters are cofactors in hundreds of proteins involved in multiple cellular processes, including mitochondrial respiration, the maintenance of genome stability, ribosome biogenesis and translation. Fe-S cluster biogenesis is performed by multiple enzymes that are highly conserved throughout evolution, and mutations in numerous biogenesis factors are now recognized to cause a wide range of previously uncategorized rare human diseases. Recently, a complex formed of components of the cytoplasmic Fe-S cluster assembly (CIA) machinery, consisting of CIAO1, FAM96B and MMS19, was found to deliver Fe-S clusters to a subset of proteins involved in DNA metabolism, but it was unclear how this complex acquired its fully synthesized Fe-S clusters, since Fe-S clusters have been alleged to be assembled de novo solely in the mitochondrial matrix...
January 3, 2018: Human Molecular Genetics
https://www.readbyqxmd.com/read/29309203/microbeam-evolution-from-single-cell-irradiation-to-preclinical-studies
#17
Mihaela Ghita, Cristian Fernandez-Palomo, Hisanori Fukunaga, Pil M Fredericia, Giuseppe Schettino, Elke Bräuer-Krisch, Karl T Butterworth, Stephen J McMahon, Kevin M Prise
PURPOSE: This review follows the development of microbeam technology from the early days of single cell irradiations, to investigations of specific cellular mechanisms and to the development of new treatment modalities in vivo. A number of microbeam applications are discussed with a focus on preclinical modalities and translation towards clinical application. CONCLUSIONS: The development of radiation microbeams has been a valuable tool for the exploration of fundamental radiobiological response mechanisms...
January 8, 2018: International Journal of Radiation Biology
https://www.readbyqxmd.com/read/29305767/finite-element-modeling-to-analyze-teer-values-across-silicon-nanomembranes
#18
Tejas S Khire, Barrett J Nehilla, Jirachai Getpreecharsawas, Maria E Gracheva, Richard E Waugh, James L McGrath
Silicon nanomembranes are ultrathin, highly permeable, optically transparent and biocompatible substrates for the construction of barrier tissue models. Trans-epithelial/endothelial electrical resistance (TEER) is often used as a non-invasive, sensitive and quantitative technique to assess barrier function. The current study characterizes the electrical behavior of devices featuring silicon nanomembranes to facilitate their application in TEER studies. In conventional practice with commercial systems, raw resistance values are multiplied by the area of the membrane supporting cell growth to normalize TEER measurements...
January 5, 2018: Biomedical Microdevices
https://www.readbyqxmd.com/read/29305244/light-in-the-darkness-new-perspective-on-lanternfish-relationships-and-classification-using-genomic-and-morphological-data
#19
Rene P Martin, Emily E Olson, Matthew G Girard, Wm Leo Smith, Matthew P Davis
Massive parallel sequencing allows scientists to gather DNA sequences composed of millions of base pairs that can be combined into large datasets and analyzed to infer organismal relationships at a genome-wide scale in non-model organisms. Although the use of these large datasets is becoming more widespread, little to no work has been done in estimating phylogenetic relationships using UCEs in deep-sea fishes. Among deep-sea animals, the 257 species of lanternfishes (Myctophiformes) are among the most important open-ocean lineages, representing half of all mesopelagic vertebrate biomass...
January 2, 2018: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/29298932/island-and-lake-like-parallel-adaptive-radiations-replicated-in-rivers
#20
Edward D Burress, Lubomír Piálek, Jorge R Casciotta, Adriana Almirón, Milton Tan, Jonathan W Armbruster, Oldřich Říčan
Parallel adaptive radiations have arisen following the colonization of islands by lizards and lakes by fishes. In these classic examples, parallel adaptive radiation is a response to the ecological opportunities afforded by the colonization of novel ecosystems and similar adaptive landscapes that favour the evolution of similar suites of ecomorphs, despite independent evolutionary histories. Here, we demonstrate that parallel adaptive radiations of cichlid fishes arose in South American rivers. Speciation-assembled communities of pike cichlids (Crenicichla) have independently diversified into similar suites of novel ecomorphs in the Uruguay and Paraná Rivers, including crevice feeders, periphyton grazers and molluscivores...
January 10, 2018: Proceedings. Biological Sciences
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