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  1 / 15844 MEDLINE  
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PMID:29220443
Autor:Rosikiewicz W; Kabza M; Kosinski JG; Ciomborowska-Basheer J; Kubiak MR; Makalowska I
Endereço:Department of Integrative Genomics, Institute of Anthropology, Faculty of Biology, Adam Mickiewicz University in Poznan, Umultowska 89, 61-614, Poznan, Poland.
Título:RetrogeneDB-a database of plant and animal retrocopies.
Fonte:Database (Oxford); 2017, 2017 Jan 01.
ISSN:1758-0463
País de publicação:England
Idioma:eng
Resumo:Database URL: http://yeti.amu.edu.pl/retrogenedb. Secondary database URL: http://rhesus.amu.edu.pl/retrogenedb.
Tipo de publicação: JOURNAL ARTICLE
Nome de substância:63231-63-0 (RNA)


  2 / 15844 MEDLINE  
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PMID:28741379
Autor:Choi JW; Um JH; Cho JH; Lee HJ
Endereço:1 Department of Microbiology and Immunology, Kyungpook National University School of Dentistry, Daegu 41940, Korea.
Título:Tiny RNAs and their voyage via extracellular vesicles: Secretion of bacterial small RNA and eukaryotic microRNA.
Fonte:Exp Biol Med (Maywood); 242(15):1475-1481, 2017 09.
ISSN:1535-3699
País de publicação:England
Idioma:eng
Resumo:MicroRNAs are small non-coding RNAs that bind to the 3'-untranslated region of target mRNAs and have transcriptional or translational inhibitory function in eukaryotes. Before microRNAs were widely known, bacterial non-coding small RNAs around 50-200 nt in length were discovered whose mechanism of action resembled that of microRNAs. Recently, RNAs that are of similar size to or smaller than microRNAs have been discovered in bacteria and indeed, this class of small RNAs have been found throughout all domains of life. Moreover, recent findings suggest that these tiny RNAs can be released via extracellular vesicles (such as exosomes in eukaryotes and outer membrane vesicles in bacteria), which in turn heralds a new field of research, interkingdom communication. This review discusses two similar classes of small RNAs in evolutionarily distinct eukaryotes and bacteria. In addition to their biogenesis and regulation, we discuss small RNA vehicles and their secretion. Impact statement The possible endogenous functions of small RNAs such as regulatory small RNAs in bacteria and microRNAs in eukaryotes have been extensively studied since they were first discovered. However, their powerful functions should not be seen as limited to their cells of origin. Recently, several papers have demonstrated that small RNAs function as signaling molecules between cells. This is possible because small RNAs can be shuttled around after being incorporated into environmentally protective extracellular vesicles. It is now clearly plausible that secreted small RNAs can regulate other types of cells through biofluids. Given their "common molecule" status, the role of small RNAs in mediating bacteria-human crosstalk is an emerging and competitive area of genetic research. This review provides insight into the function of small RNAs in intercellular and even interkingdom communication.
Tipo de publicação: JOURNAL ARTICLE; REVIEW; RESEARCH SUPPORT, NON-U.S. GOV'T
Nome de substância:0 (RNA, Bacterial); 0 (RNA, Small Untranslated)


  3 / 15844 MEDLINE  
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PMID:29371626
Autor:Carradec Q; Pelletier E; Da Silva C; Alberti A; Seeleuthner Y; Blanc-Mathieu R; Lima-Mendez G; Rocha F; Tirichine L; Labadie K; Kirilovsky A; Bertrand A; Engelen S; Madoui MA; Méheust R; Poulain J; Romac S; Richter DJ; Yoshikawa G; Dimier C; Kandels-Lewis S; Picheral M; Searson S; Jaillon O; Aury JM; Karsenti E; Sullivan MB; Sunagawa S; Bork P; Not F; Hingamp P; Raes J; Guidi L; Ogata H; de Vargas C; Iudicone D; Bowler C; Wincker P; Tara Oceans Coordinators
Endereço:CEA - Institut de Biologie François Jacob, Genoscope, Evry, 91057, France.
Título:A global ocean atlas of eukaryotic genes.
Fonte:Nat Commun; 9(1):373, 2018 01 25.
ISSN:2041-1723
País de publicação:England
Idioma:eng
Resumo:While our knowledge about the roles of microbes and viruses in the ocean has increased tremendously due to recent advances in genomics and metagenomics, research on marine microbial eukaryotes and zooplankton has benefited much less from these new technologies because of their larger genomes, their enormous diversity, and largely unexplored physiologies. Here, we use a metatranscriptomics approach to capture expressed genes in open ocean Tara Oceans stations across four organismal size fractions. The individual sequence reads cluster into 116 million unigenes representing the largest reference collection of eukaryotic transcripts from any single biome. The catalog is used to unveil functions expressed by eukaryotic marine plankton, and to assess their functional biogeography. Almost half of the sequences have no similarity with known proteins, and a great number belong to new gene families with a restricted distribution in the ocean. Overall, the resource provides the foundations for exploring the roles of marine eukaryotes in ocean ecology and biogeochemistry.
Tipo de publicação: JOURNAL ARTICLE; RESEARCH SUPPORT, NON-U.S. GOV'T


  4 / 15844 MEDLINE  
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PMID:28460059
Autor:Nevers Y; Prasad MK; Poidevin L; Chennen K; Allot A; Kress A; Ripp R; Thompson JD; Dollfus H; Poch O; Lecompte O
Endereço:Complex Systems and Translational Bioinformatics, ICube UMR 7357, Université de Strasbourg, Fédération de Médecine Translationnelle, Strasbourg, France.
Título:Insights into Ciliary Genes and Evolution from Multi-Level Phylogenetic Profiling.
Fonte:Mol Biol Evol; 34(8):2016-2034, 2017 Aug 01.
ISSN:1537-1719
País de publicação:United States
Idioma:eng
Resumo:Cilia (flagella) are important eukaryotic organelles, present in the Last Eukaryotic Common Ancestor, and are involved in cell motility and integration of extracellular signals. Ciliary dysfunction causes a class of genetic diseases, known as ciliopathies, however current knowledge of the underlying mechanisms is still limited and a better characterization of genes is needed. As cilia have been lost independently several times during evolution and they are subject to important functional variation between species, ciliary genes can be investigated through comparative genomics. We performed phylogenetic profiling by predicting orthologs of human protein-coding genes in 100 eukaryotic species. The analysis integrated three independent methods to predict a consensus set of 274 ciliary genes, including 87 new promising candidates. A fine-grained analysis of the phylogenetic profiles allowed a partitioning of ciliary genes into modules with distinct evolutionary histories and ciliary functions (assembly, movement, centriole, etc.) and thus propagation of potential annotations to previously undocumented genes. The cilia/basal body localization was experimentally confirmed for five of these previously unannotated proteins (LRRC23, LRRC34, TEX9, WDR27, and BIVM), validating the relevance of our approach. Furthermore, our multi-level analysis sheds light on the core gene sets retained in gamete-only flagellates or Ecdysozoa for instance. By combining gene-centric and species-oriented analyses, this work reveals new ciliary and ciliopathy gene candidates and provides clues about the evolution of ciliary processes in the eukaryotic domain. Additionally, the positive and negative reference gene sets and the phylogenetic profile of human genes constructed during this study can be exploited in future work.
Tipo de publicação: JOURNAL ARTICLE


  5 / 15844 MEDLINE  
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PMID:27779617
Autor:Lopes Dos Santos A; Gourvil P; Tragin M; Noël MH; Decelle J; Romac S; Vaulot D
Endereço:Sorbonne Universités, UPMC Université Paris 06, CNRS, UMR 7144 Station Biologique de Roscoff, Roscoff, France.
Título:Diversity and oceanic distribution of prasinophytes clade VII, the dominant group of green algae in oceanic waters.
Fonte:ISME J; 11(2):512-528, 2017 02.
ISSN:1751-7370
País de publicação:England
Idioma:eng
Resumo:Prasinophytes clade VII is a group of pico/nano-planktonic green algae (division Chlorophyta) for which numerous ribosomal RNA (rRNA) sequences have been retrieved from the marine environment in the last 15 years. A large number of strains have also been isolated but have not yet received a formal taxonomic description. A phylogenetic analysis of available strains using both the nuclear 18S and plastidial 16S rRNA genes demonstrates that this group composes at least 10 different clades: A1-A7 and B1-B3. Analysis of sequences from the variable V9 region of the 18S rRNA gene collected during the Tara Oceans expedition and in the frame of the Ocean Sampling Day consortium reveal that clade VII is the dominant Chlorophyta group in oceanic waters, replacing Mamiellophyceae, which have this role in coastal waters. At some location, prasinophytes clade VII can even be the dominant photosynthetic eukaryote representing up to 80% of photosynthetic metabarcodes overall. B1 and A4 are the overall dominant clades and different clades seem to occupy distinct niches, for example, A6 is dominant in surface Mediterranean Sea waters, whereas A4 extend to high temperate latitudes. Our work demonstrates that prasinophytes clade VII constitute a highly diversified group, which is a key component of phytoplankton in open oceanic waters but has been neglected in the conceptualization of marine microbial diversity and carbon cycle.
Tipo de publicação: JOURNAL ARTICLE; RESEARCH SUPPORT, NON-U.S. GOV'T
Nome de substância:0 (DNA, Ribosomal)


  6 / 15844 MEDLINE  
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PMID:28449025
Autor:Lozano-Fernandez J; Dos Reis M; Donoghue PCJ; Pisani D
Endereço:School of Earth Sciences, Life Sciences Building, University of Bristol, United Kingdom.
Título:RelTime Rates Collapse to a Strict Clock When Estimating the Timeline of Animal Diversification.
Fonte:Genome Biol Evol; 9(5):1320-1328, 2017 May 01.
ISSN:1759-6653
País de publicação:England
Idioma:eng
Resumo:Establishing an accurate timescale for the history of life is crucial to understand evolutionary processes. For this purpose, relaxed molecular clock models implemented in a Bayesian MCMC framework are generally used. However, these methods are time consuming. RelTime, a non-Bayesian method implementing a fast, ad hoc, algorithm for relative dating, was developed to overcome the computational inefficiencies of Bayesian software. RelTime was recently used to investigate the timing of origin of animals, yielding results consistent with early strict clock studies from the 1980s and 1990s, estimating metazoans to have a Mesoproterozoic origin-over a billion years ago. RelTime results are unexpected and disagree with the largest majority of modern, relaxed, Bayesian molecular clock analyses, which suggest animals originated in the Tonian-Cryogenian (less that 850 million years ago). Here, we demonstrate that RelTime-inferred divergence times for the origin of animals are spurious, a consequence of the inability of RelTime to relax the clock along the internal branches of the animal phylogeny. RelTime-inferred divergence times are comparable to strict-clock estimates because they are essentially inferred under a strict clock. Our results warn us of the danger of using ad hoc algorithms making implicit assumptions about rate changes along a tree. Our study roundly rejects a Mesoproterozoic origin of animals; metazoans emerged in the Tonian-Cryogenian, and diversified in the Ediacaran, in the immediate prelude to the routine fossilization of animals in the Cambrian associated with the emergence of readily preserved skeletons.
Tipo de publicação: JOURNAL ARTICLE


  7 / 15844 MEDLINE  
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PMID:29283231
Autor:Mustafin RN; Khusnutdinova EK
Título:The Role of Transposable Elements in Ontogenesis.
Fonte:Usp Fiziol Nauk; 47(3):70-96, 2016 Jul-Sep.
ISSN:0301-1798
País de publicação:Russia (Federation)
Idioma:rus
Resumo:The article describes the role of transposable elements in the ontogenesis of eukaryotes. Adaptive and controlled transposition of mobile elements occurs at different stages of development of an organism, causing dramatic changes in the regulation of gene expression, representing a cascade of reactions inherited genome evolutionary fixed at the species level. At this cascade of reactions involved regulatory system of tissue-specific expression of proteins splice variants in connection with the role of adaptive genes mosaic structure to numerous transpositions and the interconnectedness of mechanisms their evolutionary stabilization. Important role in the transposition of mobile elements and their interaction with groups of genes play epigenetic mechanisms - DNA methylation, histone modification, the expression of non-coding RNA. The genome structures responsible for the epigenetic regulation can have a transposons origin. In contrast to the previously established hypotheses on transpositions of mobile elements in the ontogenesis as a chaotic process, causing the destabilization of genotype, with a modern viewpoint, this mechanism has a species-specific patterns, formed evolutionarily. Mechanisms of the evolutionary transformation of genomes by natural selection create a relatively stable complex regulatory epigenetic characteristics of transpositions in the process of individual development, acting among individuals of the same species. The stability of the complex genomic information regulation in ontogenesis provides a specific set of transposons. Changing this regulation set transposons can cause fatal for the development of events. Dysregulation of transposons, not involved in the developmental restructuring, can give the inheritance of these changes. The aging process is a consequence of the evolutionary relationship of species-specific features of the regulation of mobile elements in ontogenesis, aimed at continuity and continuous increase in living matter for maximum adaptability. In the overall scheme of ontogenetic development process can be described as a way to implement the established evolutionary genomic information in time by means of gradually stabilized complex interaction of regulators of transpositions of mobile elements of the genome with a differentiated pattern of gene expression and regulation of splicing variants of their products. These transpositions vary with each cell division, especially by implementing the expression of sets of genes, the products of which affect the nature of the further transposition and change of regulation in the subsequent stages of development of an organism.
Tipo de publicação: JOURNAL ARTICLE; REVIEW
Nome de substância:0 (DNA Transposable Elements); 0 (Histones); 0 (RNA, Untranslated)


  8 / 15844 MEDLINE  
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PMID:29232693
Autor:Rai SK; Sangesland M; Lee M; Esnault C; Cui Y; Chatterjee AG; Levin HL
Endereço:Section on Eukaryotic Transposable Elements, Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health (NIH), Bethesda, Maryland, United States of America.
Título:Host factors that promote retrotransposon integration are similar in distantly related eukaryotes.
Fonte:PLoS Genet; 13(12):e1006775, 2017 12.
ISSN:1553-7404
País de publicação:United States
Idioma:eng
Resumo:Retroviruses and Long Terminal Repeat (LTR)-retrotransposons have distinct patterns of integration sites. The oncogenic potential of retrovirus-based vectors used in gene therapy is dependent on the selection of integration sites associated with promoters. The LTR-retrotransposon Tf1 of Schizosaccharomyces pombe is studied as a model for oncogenic retroviruses because it integrates into the promoters of stress response genes. Although integrases (INs) encoded by retroviruses and LTR-retrotransposons are responsible for catalyzing the insertion of cDNA into the host genome, it is thought that distinct host factors are required for the efficiency and specificity of integration. We tested this hypothesis with a genome-wide screen of host factors that promote Tf1 integration. By combining an assay for transposition with a genetic assay that measures cDNA recombination we could identify factors that contribute differentially to integration. We utilized this assay to test a collection of 3,004 S. pombe strains with single gene deletions. Using these screens and immunoblot measures of Tf1 proteins, we identified a total of 61 genes that promote integration. The candidate integration factors participate in a range of processes including nuclear transport, transcription, mRNA processing, vesicle transport, chromatin structure and DNA repair. Two candidates, Rhp18 and the NineTeen complex were tested in two-hybrid assays and were found to interact with Tf1 IN. Surprisingly, a number of pathways we identified were found previously to promote integration of the LTR-retrotransposons Ty1 and Ty3 in Saccharomyces cerevisiae, indicating the contribution of host factors to integration are common in distantly related organisms. The DNA repair factors are of particular interest because they may identify the pathways that repair the single stranded gaps flanking the sites of strand transfer following integration of LTR retroelements.
Tipo de publicação: JOURNAL ARTICLE; RESEARCH SUPPORT, N.I.H., EXTRAMURAL
Nome de substância:0 (Integration Host Factors); 0 (Retroelements); 0 (Saccharomyces cerevisiae Proteins); 0 (Spp382 protein, S cerevisiae); EC 2.3.2.27 (Rhp18 protein, S pombe); EC 2.3.2.27 (Ubiquitin-Protein Ligases); EC 2.7.7.- (Integrases); EC 2.7.7.49 (RNA-Directed DNA Polymerase); EC 2.7.7.49 (reverse transcriptase Ty3, S cerevisiae)


  9 / 15844 MEDLINE  
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PMID:28455334
Autor:Núñez A; Amo de Paz G; Ferencova Z; Rastrojo A; Guantes R; García AM; Alcamí A; Gutiérrez-Bustillo AM; Moreno DA
Endereço:Escuela Técnica Superior de Ingenieros Industriales, Universidad Politécnica de Madrid (ETSII-UPM), Madrid, Spain.
Título:Validation of the Hirst-Type Spore Trap for Simultaneous Monitoring of Prokaryotic and Eukaryotic Biodiversities in Urban Air Samples by Next-Generation Sequencing.
Fonte:Appl Environ Microbiol; 83(13), 2017 Jul 01.
ISSN:1098-5336
País de publicação:United States
Idioma:eng
Resumo:Pollen, fungi, and bacteria are the main microscopic biological entities present in outdoor air, causing allergy symptoms and disease transmission and having a significant role in atmosphere dynamics. Despite their relevance, a method for monitoring simultaneously these biological particles in metropolitan environments has not yet been developed. Here, we assessed the use of the Hirst-type spore trap to characterize the global airborne biota by high-throughput DNA sequencing, selecting regions of the 16S rRNA gene and internal transcribed spacer for the taxonomic assignment. We showed that aerobiological communities are well represented by this approach. The operational taxonomic units (OTUs) of two traps working synchronically compiled >87% of the total relative abundance for bacterial diversity collected in each sampler, >89% for fungi, and >97% for pollen. We found a good correspondence between traditional characterization by microscopy and genetic identification, obtaining more-accurate taxonomic assignments and detecting a greater diversity using the latter. We also demonstrated that DNA sequencing accurately detects differences in biodiversity between samples. We concluded that high-throughput DNA sequencing applied to aerobiological samples obtained with Hirst spore traps provides reliable results and can be easily implemented for monitoring prokaryotic and eukaryotic entities present in the air of urban areas. Detection, monitoring, and characterization of the wide diversity of biological entities present in the air are difficult tasks that require time and expertise in different disciplines. We have evaluated the use of the Hirst spore trap (an instrument broadly employed in aerobiological studies) to detect and identify these organisms by DNA-based analyses. Our results showed a consistent collection of DNA and a good concordance with traditional methods for identification, suggesting that these devices can be used as a tool for continuous monitoring of the airborne biodiversity, improving taxonomic resolution and characterization together. They are also suitable for acquiring novel DNA amplicon-based information in order to gain a better understanding of the biological particles present in a scarcely known environment such as the air.
Tipo de publicação: JOURNAL ARTICLE; VALIDATION STUDIES


  10 / 15844 MEDLINE  
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PMID:29185664
Autor:Staley ZR; Rohr JR; Senkbeil JK; Harwood VJ
Título:Agrochemicals indirectly increase survival of E. coli O157:H7 and indicator bacteria by reducing ecosystem services.
Fonte:Ecol Appl; 24(8):1945-53, 2014.
ISSN:1051-0761
País de publicação:United States
Idioma:eng
Resumo:Storm water and agricultural runoff frequently contain agrochemicals, fecal indicator bacteria (FIB), and zoonotic pathogens. Entry of such contaminants into aquatic ecosystems may affect ecology and human health. This study tested the hypothesis that the herbicide atrazine and the fungicide chlorothalonil indirectly affect the survival of FIB (Escherichia coli and Enterococcus faecalis) and a pathogen (E. coli O157:H7) by altering densities of protozoan predators or by altering competition from autochthonous bacteria. Streptomycin-resistant E. coli, En. faecalis, and E. coli O157:H7 were added to microcosms composed of Florida river water containing natural protozoan and bacterial populations. FIB, pathogen, and protozoan densities were monitored over six days. Known metabolic inhibitors, cycloheximide and streptomycin, were used to inhibit autochthonous protozoa or bacteria, respectively. The inhibitors made it possible to isolate the effects of predation or competition on survival of allochthonous bacteria, and each treatment increased the survival of FIB and pathogens. Chlorothalonil's effect was similar to that of cycloheximide, significantly reducing protozoan densities and elevating densities of FIB and pathogens relative to the control. Atrazine treatment did not affect protozoan densities, but, through an effect on competition, resulted in significantly greater densities of En. faecalis and E. coli O157:H7. Hence, by reducing predaceous protozoa and bacterial competitors that facilitate purifying water bodies of FIBs and human pathogens, chlorothalonil and atrazine indirectly diminished an ecosystem service of fresh water.
Tipo de publicação: JOURNAL ARTICLE; RESEARCH SUPPORT, U.S. GOV'T, NON-P.H.S.
Nome de substância:0 (Agrochemicals); 0 (Antifungal Agents); 0 (Fungicides, Industrial); 0 (Herbicides); 0 (Nitriles); 0 (Water Pollutants, Chemical); 98600C0908 (Cycloheximide); J718M71A7A (tetrachloroisophthalonitrile); QJA9M5H4IM (Atrazine)



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