Genomes and Genes
Summary: The parts of a GENOME sequence that are involved with the different functions or properties of genomes as a whole as opposed to those of individual GENES.
- Garcia S, McArthur E, Pellicer J, Sanderson S, Vallès J, Garnatje T. A molecular phylogenetic approach to western North America endemic Artemisia and allies (Asteraceae): untangling the sagebrushes. Am J Bot. 2011;98:638-53 pubmed publisher..The position of the circumboreal and other North American species suggests that subgenus Artemisia is the ancestral stock for the New World endemics, including those native to South America. ..
- Zhang S, Xu J, Wei C. Sequence periodic pattern of HERV LTRs: a matrix simulation algorithm. J Biosci. 2012;37:19-24 pubmed..These conservative nucleotide base positions represent critical binding sites of regulatory LTRs, and may be indicative of conserved regulatory mechanisms in LRT-participating regulatory networks. ..
- Mendez Rios J, Martens C, Bruno D, Porcella S, Zheng Z, Moss B. Genome sequence of erythromelalgia-related poxvirus identifies it as an ectromelia virus strain. PLoS ONE. 2012;7:e34604 pubmed publisher..Small DNA deletions in the Naval genome that are absent from ERPV may suggest that the sequenced strain of Naval was not the immediate progenitor of ERPV...
- Walsh D, Doolittle W. The real 'domains' of life. Curr Biol. 2005;15:R237-40 pubmed
- Ullmann A, Lima C, Guerrero F, Piesman J, Black W. Genome size and organization in the blacklegged tick, Ixodes scapularis and the Southern cattle tick, Boophilus microplus. Insect Mol Biol. 2005;14:217-22 pubmed..Genome size and organization in the three tick species so far examined are distinct from other arthropods in having a greater proportion of MR, a lower proportion of unique and HR DNA of very low sequence complexity. ..
- Qi J, Guo A, Cui P, Chen Y, Mustafa R, Ba X, et al. Comparative geno-plasticity analysis of Mycoplasma bovis HB0801 (Chinese isolate). PLoS ONE. 2012;7:e38239 pubmed publisher..05). Compared to Hubei-1, a total of 122 SNP loci were disclosed in HB0801. In conclusion, although genomic plasticity was thought to be an evolutionary advantage, it did not apparently affect virulence of M. bovis strains in cattle...
- Shen J, Dushoff J, Bewick A, Chain F, Evans B. Genomic dynamics of transposable elements in the western clawed frog (Silurana tropicalis). Genome Biol Evol. 2013;5:998-1009 pubmed publisher..Taken together, these results identify factors that sculpt heterogeneity in TE distribution in S. tropicalis and illustrate that genomic dynamics differ markedly among TE classes and between TE and non-TE repeats. ..
- Stanyon R, Stone G, Garcia M, Froenicke L. Reciprocal chromosome painting shows that squirrels, unlike murid rodents, have a highly conserved genome organization. Genomics. 2003;82:245-9 pubmed..Apparently, few derived translocations characterize the evolutionary origin of the rodents. One association (10p/1qter) may be a cladistic marker for the cohort Glires, linking rodents and lagomorphs. ..
- Correia F, Plummer A, Paster B, Dewhirst F. Genome size of human oral Treponema species by pulsed-field gel electrophoresis. Oral Microbiol Immunol. 2004;19:129-31 pubmed..2 to 2.5 Mbp. The genome sizes of these strains are 20-25% smaller than Treponema denticola strains, which have genome sizes of approximately 2.8-3.0 Mbp. ..
- Henmi M. [Genomic organization and promoter analysis of mouse apoptosis signal-regulating kinase 2 (ASK 2)]. Kokubyo Gakkai Zasshi. 2003;70:9-18 pubmed..Interestingly, the 5'-flanking region of the promoter possessed a strong suppressive element. These results suggest that expression of ASK 2 is regulated by multiple mechanisms. ..
- Chen K, Chen L, Fan X, Wallis J, Ding L, Weinstock G. TIGRA: a targeted iterative graph routing assembler for breakpoint assembly. Genome Res. 2014;24:310-7 pubmed publisher..TIGRA has been applied in the 1000 Genomes Project and other projects and is freely available for academic use. ..
- Flores M, Morales L, Gonzaga Jauregui C, Domínguez Vidaña R, Zepeda C, Yáñez O, et al. Recurrent DNA inversion rearrangements in the human genome. Proc Natl Acad Sci U S A. 2007;104:6099-106 pubmed..The relevance of our results in regard to human genomic variation is discussed. ..
- Zheng J, Liu G, Liu S. Phylogenetically clustering of rhizobia by genome structure: application to unclassified Rhizobium. J Environ Sci (China). 2006;18:530-6 pubmed
- ..In most of these cases, it is unclear to what extent a function is related to transcription per se or to the RNA products. ..
- Huitema E, Bos J, Tian M, Win J, Waugh M, Kamoun S. Linking sequence to phenotype in Phytophthora-plant interactions. Trends Microbiol. 2004;12:193-200 pubmed
- Henics T, Nagy E. [Antigenome technology: rapid and comprehensive identification and validation of antigens as putative components in vaccines against bacterial pathogens]. Orv Hetil. 2005;146:2209-14 pubmed..Using the antigenome technology, novel protective antigens had been discovered from several important human pathogens. ..
- James T, Sun S, Li W, Heitman J, Kuo H, Lee Y, et al. Polyporales genomes reveal the genetic architecture underlying tetrapolar and bipolar mating systems. Mycologia. 2013;105:1374-90 pubmed publisher..The data are consistent with multiple origins of bipolarity within the Agaricomycetes and Polyporales, although the alternative hypothesis that tetrapolarity and bipolarity are reversible states needs better testing. ..
- Gbadegesin M. Transposable elements in the genomes: parasites, junks or drivers of evolution?. Afr J Med Med Sci. 2012;41 Suppl:13-25 pubmed..It also describes some adverse effects of TEs as agents of genomic instability and diseases such as cancers, and the genetic regulations of their activities. ..
- Sassi M, Bebeacua C, Drancourt M, Cambillau C. The first structure of a mycobacteriophage, the Mycobacterium abscessus subsp. bolletii phage Araucaria. J Virol. 2013;87:8099-109 pubmed publisher..All together, these results suggest that Araucaria may infect its mycobacterial host using a mechanism involving adhesion to cell wall saccharides and protein, a feature that remains to be further explored. ..
- Glukhov A, Krutilina A, Shlyapnikov M, Severinov K, Lavysh D, Kochetkov V, et al. Genomic analysis of Pseudomonas putida phage tf with localized single-strand DNA interruptions. PLoS ONE. 2012;7:e51163 pubmed publisher..Although localized nicks were previously found only in the DNA of T5-like and phiKMV-like phages, it seems increasingly likely that this enigmatic structural feature is common to various other bacteriophages...
- Ammayappan A, Kurath G, Thompson T, Vakharia V. A reverse genetics system for the Great Lakes strain of viral hemorrhagic septicemia virus: the NV gene is required for pathogenicity. Mar Biotechnol (NY). 2011;13:672-83 pubmed publisher..This system will facilitate studies of VHSV replication, virulence, and production of viral vectored vaccines. ..
- Lunyak V. Boundaries. Boundaries...Boundaries???. Curr Opin Cell Biol. 2008;20:281-7 pubmed publisher..Rule 19 (a) (Boundaries)"Before the toss, the umpires shall agree the boundary of the field of play with both captains. The boundary shall, if possible, be marked along its whole length" Rules of Cricket...
- Wolc A, Arango J, Jankowski T, Settar P, Fulton J, O Sullivan N, et al. Pedigree and genomic analyses of feed consumption and residual feed intake in laying hens. Poult Sci. 2013;92:2270-5 pubmed publisher..These results indicate that genomic selection can be used to improve feed efficiency in layers. ..
- Porta M. The genome sequence is a jazz score. Int J Epidemiol. 2003;32:29-31 pubmed
- Dong Q, Wilkerson M, Brendel V. Tracembler--software for in-silico chromosome walking in unassembled genomes. BMC Bioinformatics. 2007;8:151 pubmed..A web server hosting Tracembler is provided at http://www.plantgdb.org/tool/tracembler/, and the software is also freely available from the authors for local installations. ..
- Loots G, Ovcharenko I. ECRbase: database of evolutionary conserved regions, promoters, and transcription factor binding sites in vertebrate genomes. Bioinformatics. 2007;23:122-4 pubmed..ECRbase currently includes human, rhesus macaque, dog, opossum, rat, mouse, chicken, frog, zebrafish and fugu genomes. It is freely accessible at http://ecrbase.dcode.org. ..
- Keeling P, Fast N, Law J, Williams B, Slamovits C. Comparative genomics of microsporidia. Folia Parasitol (Praha). 2005;52:8-14 pubmed
- Maronpot R. Regulatory forum opinion piece: the role of the toxicologic pathologist in the postgenomic era: challenges and opportunities. Toxicol Pathol. 2012;40:1082-6 pubmed..advice do we also give to the experienced bench pathologist confronted with emerging technologies each accompanied by a bewildering array of techno-jargon so that he or she can remain effective as a toxicologic pathology practitioner? ..
- Hong S, Kim D. Computational characterization of chromatin domain boundary-associated genomic elements. Nucleic Acids Res. 2017;45:10403-10414 pubmed publisher..We propose a structural model of TAD boundaries based on these findings that provides a basis for studying the mechanism of chromatin structure formation and gene regulation...
- Desmaze C, Soria J, Freulet Marrière M, Mathieu N, Sabatier L. Telomere-driven genomic instability in cancer cells. Cancer Lett. 2003;194:173-82 pubmed..All of the aberrations that occur prior to, during or after activation of a telomere maintenance mechanism promote the development of cancer. ..
- Wenick A, Hobert O. Genomic cis-regulatory architecture and trans-acting regulators of a single interneuron-specific gene battery in C. elegans. Dev Cell. 2004;6:757-70 pubmed..The identity of these homeodomain targets provides novel insights into the biology of the AIY interneuron. ..
- Jabbari K, Bernardi G. Cytosine methylation and CpG, TpG (CpA) and TpA frequencies. Gene. 2004;333:143-9 pubmed..The implications of these results are discussed. ..
- McClelland M, Sanderson K, Clifton S, Latreille P, Porwollik S, Sabo A, et al. Comparison of genome degradation in Paratyphi A and Typhi, human-restricted serovars of Salmonella enterica that cause typhoid. Nat Genet. 2004;36:1268-74 pubmed..Loss of function also occurs by mutation in different genes in the same pathway (e.g., in chemotaxis and in the production of fimbriae)...
- Ogilvie L, Caplin J, Dedi C, Diston D, Cheek E, Bowler L, et al. Comparative (meta)genomic analysis and ecological profiling of human gut-specific bacteriophage ?B124-14. PLoS ONE. 2012;7:e35053 pubmed publisher..This not only verified the human gut-specific nature of both phage, but also indicated that these phage populate a distinct and unexplored ecological landscape within the human gut microbiome. ..
- Mizoguchi H, Mori H, Fujio T. Escherichia coli minimum genome factory. Biotechnol Appl Biochem. 2007;46:157-67 pubmed..coli metabolic networks. The data sets from the functional genomics will be used to improve design of an E. coli MGF. The present minireview summarizes the progress of the E. coli MGF project and overviews related research. ..
- Jacques N, Sacerdot C, Derkaoui M, Dujon B, Ozier Kalogeropoulos O, Casaregola S. Population polymorphism of nuclear mitochondrial DNA insertions reveals widespread diploidy associated with loss of heterozygosity in Debaryomyces hansenii. Eukaryot Cell. 2010;9:449-59 pubmed publisher..hansenii is phylogenetically related, we observed a differential loss of heterozygosity in the diploid strains, which can explain some of the large genetic diversity found in D. hansenii over the years. ..
- Mao F, Su Z, Olman V, Dam P, Liu Z, Xu Y. Mapping of orthologous genes in the context of biological pathways: An application of integer programming. Proc Natl Acad Sci U S A. 2006;103:129-34 pubmed..We conclude that using genomic structure information as constraints could greatly improve the pathway-mapping accuracy over methods that use sequence-similarity information alone. ..
- Brunkhorst A, Neuman T, Hall A, Arenas E, Bartfai T, Hermanson O, et al. Novel isoforms of the TFIID subunit TAF4 modulate nuclear receptor-mediated transcriptional activity. Biochem Biophys Res Commun. 2004;325:574-9 pubmed..Our results indicate an additional level of complexity in TAF4-mediated regulation of transcription and suggest context-specific roles for these new TAF4 isoforms in transcriptional regulation in vivo. ..
- Liu G, Zhou L, Gu C. Complete sequence and gene organization of the mitochondrial genome of scaly-sided merganser (Mergus squamatus) and phylogeny of some Anatidae species. Mol Biol Rep. 2012;39:2139-45 pubmed publisher..The results are different from the present classification, and we support Lophodytes cucullatus and Mergullus albellus to be members of the genus Mergus. ..
- Hosono M, Sugawara S, Tatsuta T, Hikita T, Kominami J, Nakamura Tsuruta S, et al. Domain composition of rhamnose-binding lectin from shishamo smelt eggs and its carbohydrate-binding profiles. Fish Physiol Biochem. 2013;39:1619-30 pubmed publisher..The domain composition of these RBLs and an analytical environment such as the "cluster effect" of a ligand might influence the binding between RBL and sugar chains. ..
- Liu J, Liu H, Zhang X, Gao P, Wang J, Hu Z. Identification and characterization of P15RS, a novel P15(INK4b) related gene on G1/S progression. Biochem Biophys Res Commun. 2002;299:880-5 pubmed..Expressing antisense P15RS in MLIK6 cells can up-regulate the expression of cyclinD1 and cyclinE. These data indicate that P15RS may act as a negative regulator in G(1) phase. ..
- Witherspoon D, Xing J, Zhang Y, Watkins W, Batzer M, Jorde L. Mobile element scanning (ME-Scan) by targeted high-throughput sequencing. BMC Genomics. 2010;11:410 pubmed publisher..In light of recent improvements to high-throughput sequencing technology, it should be possible to employ ME-Scan to genotype insertions of almost any mobile element family in many individuals from any species. ..
- Rich S, Bowden D, Haffner S, Norris J, Saad M, Mitchell B, et al. A genome scan for fasting insulin and fasting glucose identifies a quantitative trait locus on chromosome 17p: the insulin resistance atherosclerosis study (IRAS) family study. Diabetes. 2005;54:290-5 pubmed..Identifying genes in these regions should provide insight into the nature of genetic factors regulating plasma glucose and insulin concentrations. ..
- Santos F, Meyerdierks A, Peña A, Rossello Mora R, Amann R, Antón J. Metagenomic approach to the study of halophages: the environmental halophage 1. Environ Microbiol. 2007;9:1711-23 pubmed..Forty open reading frames have been predicted, including genes that putatively code for proteins involved in DNA replication (ribonucleotide reductases, thymidylate kinase) normally found in lytic viruses...
- Ferini Strambi L, Bonati M, Oldani A, Aridon P, Zucconi M, Casari G. Genetics in restless legs syndrome. Sleep Med. 2004;5:301-4 pubmed..However, the efforts toward the identification of RLS genes must continue in order to obtain a better characterization of the syndrome and to identify new therapeutic strategies. ..
- Phillips R. Adaptive evolution or genetic drift? Does genome complexity produce organismal complexity?. Heredity (Edinb). 2004;93:122-3 pubmed