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https://www.readbyqxmd.com/read/28092920/evolutionary-genomics-of-the-cold-adapted-diatom-fragilariopsis-cylindrus
#1
Thomas Mock, Robert P Otillar, Jan Strauss, Mark McMullan, Pirita Paajanen, Jeremy Schmutz, Asaf Salamov, Remo Sanges, Andrew Toseland, Ben J Ward, Andrew E Allen, Christopher L Dupont, Stephan Frickenhaus, Florian Maumus, Alaguraj Veluchamy, Taoyang Wu, Kerrie W Barry, Angela Falciatore, Maria I Ferrante, Antonio E Fortunato, Gernot Glöckner, Ansgar Gruber, Rachel Hipkin, Michael G Janech, Peter G Kroth, Florian Leese, Erika A Lindquist, Barbara R Lyon, Joel Martin, Christoph Mayer, Micaela Parker, Hadi Quesneville, James A Raymond, Christiane Uhlig, Ruben E Valas, Klaus U Valentin, Alexandra Z Worden, E Virginia Armbrust, Matthew D Clark, Chris Bowler, Beverley R Green, Vincent Moulton, Cock van Oosterhout, Igor V Grigoriev
The Southern Ocean houses a diverse and productive community of organisms. Unicellular eukaryotic diatoms are the main primary producers in this environment, where photosynthesis is limited by low concentrations of dissolved iron and large seasonal fluctuations in light, temperature and the extent of sea ice. How diatoms have adapted to this extreme environment is largely unknown. Here we present insights into the genome evolution of a cold-adapted diatom from the Southern Ocean, Fragilariopsis cylindrus, based on a comparison with temperate diatoms...
January 16, 2017: Nature
https://www.readbyqxmd.com/read/28092796/global-open-data-management-in-metabolomics
#2
REVIEW
Kenneth Haug, Reza M Salek, Christoph Steinbeck
Chemical Biology employs chemical synthesis, analytical chemistry and other tools to study biological systems. Recent advances in both molecular biology such as next generation sequencing (NGS) have led to unprecedented insights towards the evolution of organisms' biochemical repertoires. Because of the specific data sharing culture in Genomics, genomes from all kingdoms of life become readily available for further analysis by other researchers. While the genome expresses the potential of an organism to adapt to external influences, the Metabolome presents a molecular phenotype that allows us to asses the external influences under which an organism exists and develops in a dynamic way...
January 13, 2017: Current Opinion in Chemical Biology
https://www.readbyqxmd.com/read/28092686/epigenomic-reprogramming-during-pancreatic-cancer-progression-links-anabolic-glucose-metabolism-to-distant-metastasis
#3
Oliver G McDonald, Xin Li, Tyler Saunders, Rakel Tryggvadottir, Samantha J Mentch, Marc O Warmoes, Anna E Word, Alessandro Carrer, Tal H Salz, Sonoko Natsume, Kimberly M Stauffer, Alvin Makohon-Moore, Yi Zhong, Hao Wu, Kathryn E Wellen, Jason W Locasale, Christine A Iacobuzio-Donahue, Andrew P Feinberg
During the progression of pancreatic ductal adenocarcinoma (PDAC), heterogeneous subclonal populations emerge that drive primary tumor growth, regional spread, distant metastasis, and patient death. However, the genetics of metastases largely reflects that of the primary tumor in untreated patients, and PDAC driver mutations are shared by all subclones. This raises the possibility that an epigenetic process might operate during metastasis. Here we report large-scale reprogramming of chromatin modifications during the natural evolution of distant metastasis...
January 16, 2017: Nature Genetics
https://www.readbyqxmd.com/read/28092684/biallelic-mutations-in-the-3-exonuclease-toe1-cause-pontocerebellar-hypoplasia-and-uncover-a-role-in-snrna-processing
#4
Rea M Lardelli, Ashleigh E Schaffer, Veerle R C Eggens, Maha S Zaki, Stephanie Grainger, Shashank Sathe, Eric L Van Nostrand, Zinayida Schlachetzki, Basak Rosti, Naiara Akizu, Eric Scott, Jennifer L Silhavy, Laura Dean Heckman, Rasim Ozgur Rosti, Esra Dikoglu, Anne Gregor, Alicia Guemez-Gamboa, Damir Musaev, Rohit Mande, Ari Widjaja, Tim L Shaw, Sebastian Markmiller, Isaac Marin-Valencia, Justin H Davies, Linda de Meirleir, Hulya Kayserili, Umut Altunoglu, Mary Louise Freckmann, Linda Warwick, David Chitayat, Susan Blaser, Ahmet Okay Çağlayan, Kaya Bilguvar, Huseyin Per, Christina Fagerberg, Henrik T Christesen, Maria Kibaek, Kimberly A Aldinger, David Manchester, Naomichi Matsumoto, Kazuhiro Muramatsu, Hirotomo Saitsu, Masaaki Shiina, Kazuhiro Ogata, Nicola Foulds, William B Dobyns, Neil C Chi, David Traver, Luigina Spaccini, Stefania Maria Bova, Stacey B Gabriel, Murat Gunel, Enza Maria Valente, Marie-Cecile Nassogne, Eric J Bennett, Gene W Yeo, Frank Baas, Jens Lykke-Andersen, Joseph G Gleeson
Deadenylases are best known for degrading the poly(A) tail during mRNA decay. The deadenylase family has expanded throughout evolution and, in mammals, consists of 12 Mg(2+)-dependent 3'-end RNases with substrate specificity that is mostly unknown. Pontocerebellar hypoplasia type 7 (PCH7) is a unique recessive syndrome characterized by neurodegeneration and ambiguous genitalia. We studied 12 human families with PCH7, uncovering biallelic, loss-of-function mutations in TOE1, which encodes an unconventional deadenylase...
January 16, 2017: Nature Genetics
https://www.readbyqxmd.com/read/28092027/classification-and-lineage-tracing-of-sh2-domains-throughout-eukaryotes
#5
Bernard A Liu
Today there exists a rapidly expanding number of sequenced genomes. Cataloging protein interaction domains such as the Src Homology 2 (SH2) domain across these various genomes can be accomplished with ease due to existing algorithms and predictions models. An evolutionary analysis of SH2 domains provides a step towards understanding how SH2 proteins integrated with existing signaling networks to position phosphotyrosine signaling as a crucial driver of robust cellular communication networks in metazoans. However organizing and tracing SH2 domain across organisms and understanding their evolutionary trajectory remains a challenge...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28091548/genome-analysis-of-a-zygomycete-fungus-choanephora-cucurbitarum-elucidates-necrotrophic-features-including-bacterial-genes-related-to-plant-colonization
#6
Byoungnam Min, Ji-Hyun Park, Hongjae Park, Hyeon-Dong Shin, In-Geol Choi
A zygomycete fungus, Choanephora cucurbitarum is a plant pathogen that causes blossom rot in cucurbits and other plants. Here we report the genome sequence of Choanephora cucurbitarum KUS-F28377 isolated from squash. The assembled genome has a size of 29.1 Mbp and 11,977 protein-coding genes. The genome analysis indicated that C. cucurbitarum may employ a plant pathogenic mechanism similar to that of bacterial plant pathogens. The genome contained 11 genes with a Streptomyces subtilisin inhibitor-like domain, which plays an important role in the defense against plant immunity...
January 16, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28091414/acute-myeloid-leukemia-advancements-in-diagnosis-and-treatment
#7
REVIEW
Meng-Ge Yu, Hu-Yong Zheng
OBJECTIVE: Leukemia is the most common pediatric malignancy and a major cause of morbidity and mortality in children. Among all subtypes, a lack of consensus exists regarding the diagnosis and treatment of acute myeloid leukemia (AML). Patient survival rates have remained modest for the past three decades in AML. Recently, targeted therapy has emerged as a promising treatment. DATA SOURCES: We searched the PubMed database for recently published research papers on diagnostic development, target therapy, and other novel therapies of AML...
2017: Chinese Medical Journal
https://www.readbyqxmd.com/read/28090592/the-first-genome-sequences-of-human-bocaviruses-from-vietnam
#8
Tran Tan Thanh, Hoang Minh Tu Van, Nguyen Thi Thu Hong, Le Nguyen Truc Nhu, Nguyen To Anh, Ha Manh Tuan, Ho Van Hien, Nguyen Manh Tuong, Trinh Trung Kien, Truong Huu Khanh, Le Nguyen Thanh Nhan, Nguyen Thanh Hung, Nguyen Van Vinh Chau, Guy Thwaites, H Rogier van Doorn, Le Van Tan
As part of an ongoing effort to generate complete genome sequences of hand, foot and mouth disease-causing enteroviruses directly from clinical specimens, two complete coding sequences and two partial genomic sequences of human bocavirus 1 (n=3) and 2 (n=1) were co-amplified and sequenced, representing the first genome sequences of human bocaviruses from Vietnam. The sequences may aid future study aiming at understanding the evolution of the pathogen.
November 16, 2016: Wellcome Open Res
https://www.readbyqxmd.com/read/28090586/holliday-junction-trap-shows-how-cells-use-recombination-and-a-junction-guardian-role-of-recq-helicase
#9
Jun Xia, Li-Tzu Chen, Qian Mei, Chien-Hui Ma, Jennifer A Halliday, Hsin-Yu Lin, David Magnan, John P Pribis, Devon M Fitzgerald, Holly M Hamilton, Megan Richters, Ralf B Nehring, Xi Shen, Lei Li, David Bates, P J Hastings, Christophe Herman, Makkuni Jayaram, Susan M Rosenberg
DNA repair by homologous recombination (HR) underpins cell survival and fuels genome instability, cancer, and evolution. However, the main kinds and sources of DNA damage repaired by HR in somatic cells and the roles of important HR proteins remain elusive. We present engineered proteins that trap, map, and quantify Holliday junctions (HJs), a central DNA intermediate in HR, based on catalytically deficient mutant RuvC protein of Escherichia coli. We use RuvCDefGFP (RDG) to map genomic footprints of HR at defined DNA breaks in E...
November 2016: Science Advances
https://www.readbyqxmd.com/read/28090077/clinical-and-biological-insights-from-viral-genome-sequencing
#10
Charlotte J Houldcroft, Mathew A Beale, Judith Breuer
Whole-genome sequencing (WGS) of pathogens is becoming increasingly important not only for basic research but also for clinical science and practice. In virology, WGS is important for the development of novel treatments and vaccines, and for increasing the power of molecular epidemiology and evolutionary genomics. In this Opinion article, we suggest that WGS of viruses in a clinical setting will become increasingly important for patient care. We give an overview of different WGS methods that are used in virology and summarize their advantages and disadvantages...
January 16, 2017: Nature Reviews. Microbiology
https://www.readbyqxmd.com/read/28089933/hfb7-a-novel-orphan-hydrophobin-of-the-harzianum-and-virens-clades-of-trichoderma-is-involved-in-response-to-biotic-and-abiotic-stresses
#11
Agnes Przylucka, Gunseli Bayram Akcapinar, Komal Chenthamara, Feng Cai, Marica Grujuc, Juriy Karpenko, Miriam Livoi, Qirong Shen, Christian P Kubicek, Irina S Druzhinina
Hydrophobins are small secreted cysteine-rich proteins exclusively found in fungi. They are able to self-assemble in single molecular layers at hydrophobic-hydrophilic interfaces and can therefore be directly involved in establishment of fungi in their habitat. The genomes of filamentous mycotrophic fungi Trichoderma encode a rich diversity of hydrophobins, which are divided in several groups based on their structure and evolution. Here we describe a new member of class II hydrophobins, HFB7, that has a taxonomically restricted occurrence in Harzianum and Virens clades of Trichoderma...
January 12, 2017: Fungal Genetics and Biology: FG & B
https://www.readbyqxmd.com/read/28089793/eggshell-palaeogenomics-palaeognath-evolutionary-history-revealed-through-ancient-nuclear-and-mitochondrial-dna-from-madagascan-elephant-bird-aepyornis-sp-eggshell
#12
Alicia Grealy, Matthew Phillips, Gifford Miller, M Thomas P Gilbert, Jean-Marie Rouillard, David Lambert, Michael Bunce, James Haile
Palaeognaths, the sister group of all other living birds (neognaths), were once considered to be vicariant relics from the breakup of the Gondwanan supercontinent. However, recent molecular studies instead argue for dispersal of volant ancestors across marine barriers. Resolving this debate hinges upon accurately reconstructing their evolutionary relationships and dating their divergences, which often relies on phylogenetic information from extinct relatives and nuclear genomes. Mitogenomes from the extinct elephant birds of Madagascar have helped inform the palaeognath phylogeny; however, nuclear information has remained unavailable...
January 9, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/28089512/paleozoic-nymphal-wing-pads-support-dual-model-of-insect-wing-origins
#13
Jakub Prokop, Martina Pecharová, André Nel, Thomas Hörnschemeyer, Ewa Krzemińska, Wiesław Krzemiński, Michael S Engel
The appearance of wings in insects, early in their evolution [1], has been one of the more critical innovations contributing to their extraordinary diversity. Despite the conspicuousness and importance of wings, the origin of these structures has been difficult to resolve and represented one of the "abominable mysteries" in evolutionary biology [2]. More than a century of debate has boiled the matter down to two competing alternatives-one of wings representing an extension of the thoracic notum, the other stating that they are appendicular derivations from the lateral body wall...
January 9, 2017: Current Biology: CB
https://www.readbyqxmd.com/read/28089430/high-variability-of-expression-profiles-of-homeologous-genes-for-wnt-hh-notch-and-hippo-signaling-pathways-in-xenopus-laevis
#14
Tatsuo Michiue, Takayoshi Yamamoto, Yuuri Yasuoka, Toshiyasu Goto, Takafumi Ikeda, Kei Nagura, Takuya Nakayama, Masanori Taira, Tsutomu Kinoshita
Cell signaling pathways, such as Wnt, Hedgehog (Hh), Notch, and Hippo, are essential for embryogenesis, organogenesis, and tissue homeostasis. In this study, we analyzed 415 genes involved in these pathways in the allotetraploid frog, Xenopus laevis. Most genes are retained in two subgenomes called L and S (193 homeologous gene pairs and 29 singletons). This conservation rate of homeologs is much higher than that of all genes in the X. laevis genome (86.9% vs 60.2%). Among singletons, 24 genes are retained in the L subgenome, a rate similar to the average for all genes (82...
January 12, 2017: Developmental Biology
https://www.readbyqxmd.com/read/28088192/nucleotide-diversity-inflation-as-a-genome-wide-response-to-experimental-lifespan-extension-in-drosophila-melanogaster
#15
Pawel Michalak, Lin Kang, Pernille M Sarup, Mads F Schou, Volker Loeschcke
BACKGROUND: Evolutionary theory predicts that antagonistically selected alleles, such as those with divergent pleiotropic effects in early and late life, may often reach intermediate population frequencies due to balancing selection, an elusive process when sought out empirically. Alternatively, genetic diversity may increase as a result of positive frequency-dependent selection and genetic purging in bottlenecked populations. RESULTS: While experimental evolution systems with directional phenotypic selection typically result in at least local heterozygosity loss, we report that selection for increased lifespan in Drosophila melanogaster leads to an extensive genome-wide increase of nucleotide diversity in the selected lines compared to replicate control lines, pronounced in regions with no or low recombination, such as chromosome 4 and centromere neighborhoods...
January 14, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28087931/evolution-of-cell-autonomous-effector-mechanisms-in-macrophages-versus-non-immune-cells
#16
Ryan G Gaudet, Clinton J Bradfield, John D MacMicking
Specialized adaptations for killing microbes are synonymous with phagocytic cells including macrophages, monocytes, inflammatory neutrophils, and eosinophils. Recent genome sequencing of extant species, however, reveals that analogous antimicrobial machineries exist in certain non-immune cells and also within species that ostensibly lack a well-defined immune system. Here we probe the evolutionary record for clues about the ancient and diverse phylogenetic origins of macrophage killing mechanisms and how some of their properties are shared with cells outside the traditional bounds of immunity in higher vertebrates such as mammals...
December 2016: Microbiology Spectrum
https://www.readbyqxmd.com/read/28087779/genomics-of-parallel-experimental-evolution-in-drosophila
#17
J L Graves, K L Hertweck, M A Phillips, M V Han, L G Cabral, T T Barter, L F Greer, M K Burke, L D Mueller, M R Rose
What are the genomic foundations of adaptation in sexual populations? We address this question using fitness-character and whole-genome sequence data from 30 Drosophila laboratory populations. These 30 populations are part of a nearly forty-year laboratory radiation featuring three selection regimes, each shared by ten populations for up to 837 generations, with moderately large effective population sizes. Each of three sets of ten populations that shared a selection regime consist of five populations that have long been maintained under that selection regime, paired with five populations that had only recently been subjected to that selection regime...
January 12, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28087778/no-evidence-for-phylostratigraphic-bias-impacting-inferences-on-patterns-of-gene-emergence-and-evolution
#18
Tomislav Domazet-Lošo, Anne-Ruxandra Carvunis, M Mar Albà, Martin Sebastijan Šestak, Robert Bakarić, Rafik Neme, Diethard Tautz
Phylostratigraphy is a computational framework for dating the emergence of DNA and protein sequences in a phylogeny. It has been extensively applied to make inferences on patterns of genome evolution, including patterns of disease gene evolution, ontogeny and de novo gene origination. Phylostratigraphy typically relies on BLAST searches along a species tree, but new simulation studies have raised concerns about the ability of BLAST to detect remote homologues and its impact on phylostratigraphic inferences...
January 12, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28087776/seed-plant-specific-gene-lineages-involved-in-carpel-development
#19
Kai C Pfannebecker, Matthias Lange, Oliver Rupp, Annette Becker
Evolutionary innovations are important drivers of speciation and some are the defining characters of entire phyla. One such major innovation is the carpel, the unifying character and most complex plant organ, composed of many clearly distinct tissue types to ensure reproductive success. The origin of the carpel is unknown, but many components of the gene regulatory network (GRN) governing carpel development and their genetic interactions are known from the core eudicot Arabidopsis thaliana To unravel the evolution of the carpel GRN and to discriminate between "early" and "late" steps in carpel evolution we calculated thorough phylogeny reconstructions based on sequenced genomes...
January 12, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28087772/possible-roles-of-new-mutations-shared-by-asian-and-american-zika-viruses
#20
Shozo Yokoyama, William T Starmer
Originating in Africa, the Zika virus (ZIKV) has spread to Asia, Pacific Islands and now to the Americas and beyond. Since the first isolation in 1947, ZIKV strains have been sampled at various times in the last 69 years, but this history has not been reflected in studying the patterns of mutation accumulation in their genomes. Implementing the viral history, we show that the ZIKV ancestor appeared sometime in 1930-1945 and, at that point, its mutation rate was probably less than 0.2 x 10(-3)/nucleotide site/year and subsequently increased significantly in most of its descendants...
January 12, 2017: Molecular Biology and Evolution
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