Genomes and Genes
Experts and Doctors on dna sequence analysis in Helsinki, Uusimaa, Finland
Locale: Helsinki, Uusimaa, Finland
Topic: dna sequence analysis
- Bomberg M, Timonen S. Distribution of cren- and euryarchaeota in scots pine mycorrhizospheres and boreal forest humus. Microb Ecol. 2007;54:406-16 pubmed..Most compartments with fungal components contained euryarchaeotal 16S rRNA gene sequences, whereas a high diversity of crenarchaeotal sequences and no euryarchaeotal sequences were found in forest humus outside mycorrhizospheres...
- Audzijonyte A, Daneliya M, Mugue N, Väinölä R. Phylogeny of Paramysis (Crustacea: Mysida) and the origin of Ponto-Caspian endemic diversity: resolving power from nuclear protein-coding genes. Mol Phylogenet Evol. 2008;46:738-59 pubmed publisher..The two nuclear protein-coding genes had more congruent rates of evolution, and were about 10-15 times slower than the mitochondrial COI gene...
- Blomqvist S, Savolainen C, Laine P, Hirttiö P, Lamminsalo E, Penttilä E, et al. Characterization of a highly evolved vaccine-derived poliovirus type 3 isolated from sewage in Estonia. J Virol. 2004;78:4876-83 pubmed..In spite of the apparent transmission potential, no evidence was obtained for circulation of the virus in the Estonian population. ..
- Berg K, Lyra C, Sivonen K, Paulin L, Suomalainen S, Tuomi P, et al. High diversity of cultivable heterotrophic bacteria in association with cyanobacterial water blooms. ISME J. 2009;3:314-25 pubmed publisher..The isolated strains provide a large group of bacteria that could be used in assessing and controlling the harmful effects of cyanobacteria. ..
- Ibrahem S, Salmenlinna S, Lyytikainen O, Vaara M, Vuopio Varkila J. Molecular characterization of methicillin-resistant Staphylococcus epidermidis strains from bacteraemic patients. Clin Microbiol Infect. 2008;14:1020-7 pubmed publisher..In conclusion, the MRSE strains were genetically related to each other (ST2) but their SCCmec complexes were unique combinations of elements previously recognized among SCCmec types III and IV. ..
- Saarela J, Laine M, Oinonen C, von Schantz C, Jalanko A, Rouvinen J, et al. Molecular pathogenesis of a disease: structural consequences of aspartylglucosaminuria mutations. Hum Mol Genet. 2001;10:983-95 pubmed..Depending on their effects on the AGA polypeptide the mutations can be categorized as mild, moderate or severe. These data contribute to the expanding body of knowledge pertaining to molecular pathogenesis of AGU. ..
- Liitsola K, Holm K, Bobkov A, Pokrovsky V, Smolskaya T, Leinikki P, et al. An AB recombinant and its parental HIV type 1 strains in the area of the former Soviet Union: low requirements for sequence identity in recombination. UNAIDS Virus Isolation Network. AIDS Res Hum Retroviruses. 2000;16:1047-53 pubmed..This suggests that only short stretches of absolute sequence identity may be needed for efficient RNA recombination between HIV-1 subtypes. ..
- Suppola J, Kolho E, Salmenlinna S, Tarkka E, Vuopio Varkila J, Vaara M. vanA and vanB incorporate into an endemic ampicillin-resistant vancomycin-sensitive Enterococcus faecium strain: effect on interpretation of clonality. J Clin Microbiol. 1999;37:3934-9 pubmed..None of the differences was specific to or determinative for any of the groups. Our material suggests that vanA and vanB incorporate into an endemic ampicillin-resistant VSE strain. ..
- Kivistö R, Linros J, Rossi M, Rautelin H, Hänninen M. Characterization of multiple Helicobacter bizzozeronii isolates from a Finnish patient with severe dyspeptic symptoms and chronic active gastritis. Helicobacter. 2010;15:58-66 pubmed publisher..heilmannii"-infected patients in PCR-based screening studies. The relevance of H. bizzozeronii and other potentially zoonotic gastric Helicobacter spp. in human disease remains to be determined. ..
- Suutari M, Majaneva M, Fewer D, Voirin B, Aiello A, Friedl T, et al. Molecular evidence for a diverse green algal community growing in the hair of sloths and a specific association with Trichophilus welckeri (Chlorophyta, Ulvophyceae). BMC Evol Biol. 2010;10:86 pubmed publisher..However, this phenomenon has not been explored in any detail and there is little evidence to substantiate this widely held opinion...
- Riento K, Jantti J, Jansson S, Hielm S, Lehtonen E, Ehnholm C, et al. A sec1-related vesicle-transport protein that is expressed predominantly in epithelial cells. Eur J Biochem. 1996;239:638-46 pubmed
- Pietil M, Roine E, Paulin L, Kalkkinen N, Bamford D. An ssDNA virus infecting archaea: a new lineage of viruses with a membrane envelope. Mol Microbiol. 2009;72:307-19 pubmed publisher..HRPV-1 virion may represent commonly used virion architecture, and it seems that structure-based virus lineages may be extended to non-icosahedral viruses...
- Varvio S, Iso Touru T, Kantanen J, Viitala S, Tapio I, Mäki Tanila A, et al. Molecular anatomy of the cytoplasmic domain of bovine growth hormone receptor, a quantitative trait locus. Proc Biol Sci. 2008;275:1525-34 pubmed publisher..Alternative explanations for the persistent polymorphism include balancing selection, hitch-hiking, pleiotropic or sexually antagonistic fitness effects or relaxed functional constraints. ..
- Nousiainen H, Kestila M, Pakkasjärvi N, Honkala H, Kuure S, Tallila J, et al. Mutations in mRNA export mediator GLE1 result in a fetal motoneuron disease. Nat Genet. 2008;40:155-7 pubmed publisher..Our finding of mutated GLE1 exposes a common pathway connecting the genes implicated in LCCS1, LCCS2 and LCCS3 and elucidates mRNA processing as a critical molecular mechanism in motoneuron development and maturation. ..
- Kankainen M, Löytynoja A. MATLIGN: a motif clustering, comparison and matching tool. BMC Bioinformatics. 2007;8:189 pubmed..A web-server is available at http://ekhidna.biocenter.helsinki.fi/poxo/matlign. ..
- Wei G, Badis G, Berger M, Kivioja T, Palin K, Enge M, et al. Genome-wide analysis of ETS-family DNA-binding in vitro and in vivo. EMBO J. 2010;29:2147-60 pubmed publisher..The results indicate that even relatively small differences in in vitro binding specificity of a TF contribute to site selectivity in vivo. ..
- Suokko A, Savijoki K, Malinen E, Palva A, Varmanen P. Characterization of a mobile clpL gene from Lactobacillus rhamnosus. Appl Environ Microbiol. 2005;71:2061-9 pubmed publisher..rhamnosus strains suggest that the L. rhamnosus E-97800 has acquired the clpL2 gene via horizontal transfer. No change in the stress tolerance of the ClpL2-deficient derivative of E-97800 compared to the parental strain was observed...
- Nemirov K, Henttonen H, Vaheri A, Plyusnin A. Phylogenetic evidence for host switching in the evolution of hantaviruses carried by Apodemus mice. Virus Res. 2002;90:207-15 pubmed..5 MYA). Taken together with other proposed cases of host switching, our observations suggest that these events might not be exceptional in the hantavirus evolution...
- Antikainen J, Kuparinen V, Lähteenmäki K, Korhonen T. Enolases from Gram-positive bacterial pathogens and commensal lactobacilli share functional similarity in virulence-associated traits. FEMS Immunol Med Microbiol. 2007;51:526-34 pubmed..The individual enolases showed varying efficiencies in these functions. In particular, highly and equally effective interactions with plasminogen and laminin were seen with lactobacillar and staphylococcal enolases. ..
- Tang J, Hanage W, Fraser C, Corander J. Identifying currents in the gene pool for bacterial populations using an integrative approach. PLoS Comput Biol. 2009;5:e1000455 pubmed publisher..The statistical tools introduced here are freely available in BAPS 5.2 software, which can be downloaded from http://web.abo.fi/fak/mnf/mate/jc/software/baps.html...
- Blomqvist S, Savolainen Kopra C, Paananen A, El Bassioni L, El Maamoon Nasr E, Firstova L, et al. Recurrent isolation of poliovirus 3 strains with chimeric capsid protein Vp1 suggests a recombination hot-spot site in Vp1. Virus Res. 2010;151:246-51 pubmed publisher..Our results suggest that there exists a PV3/PV2 recombination hot-spot site in the 3' partial region of the VP1 capsid protein and that the recombination may occur within weeks or a few months after the administration of OPV...
- Galand P, Fritze H, Yrjälä K. Microsite-dependent changes in methanogenic populations in a boreal oligotrophic fen. Environ Microbiol. 2003;5:1133-43 pubmed..Novel methanogenic sequences were found at both sites at both depths. Vegetation characterizing the microsites probably influences the microbial communities in the layers of the fen where methane is produced...
- M nnist R, Kivel H, Paulin L, Bamford D, Bamford J. The complete genome sequence of PM2, the first lipid-containing bacterial virus To Be isolated. Virology. 1999;262:355-63 pubmed publisher..2-kb sequence that is similar to the maintenance region of a plasmid found in a marine Pseudoalteromonas sp. strain A28...
- Ahokas K, Lohi J, Lohi H, Elomaa O, Karjalainen Lindsberg M, Kere J, et al. Matrix metalloproteinase-21, the human orthologue for XMMP, is expressed during fetal development and in cancer. Gene. 2002;301:31-41 pubmed..MMP-21 protein can also be detected in malignancies such as ovarian and colon carcinomas by immunohistochemical staining. Our findings suggest that MMP-21 functions in embryogenesis and tumor progression. ..
- Pussinen P, Olkkonen V, Jauhiainen M, Ehnholm C. Molecular cloning and functional expression of cDNA encoding the pig plasma phospholipid transfer protein. J Lipid Res. 1997;38:1473-81 pubmed..This study forms the basis for future work on the structure-function relationships in pig PLTP. ..
- Korhonen J, Martinmäki P, Pizzi C, Rastas P, Ukkonen E. MOODS: fast search for position weight matrix matches in DNA sequences. Bioinformatics. 2009;25:3181-2 pubmed publisher..The package with documentation and examples of usage is available at http://www.cs.helsinki.fi/group/pssmfind. The source code is also available under the terms of a GNU General Public License (GPL). ..
- Ranta S, Zhang Y, Ross B, Lonka L, Takkunen E, Messer A, et al. The neuronal ceroid lipofuscinoses in human EPMR and mnd mutant mice are associated with mutations in CLN8. Nat Genet. 1999;23:233-6 pubmed..Our data demonstrate that mutations in these orthologous genes underlie NCL phenotypes in human and mouse, and represent the first description of the molecular basis of a naturally occurring animal model for NCL. ..
- Jansen G, Savolainen R, Vepsalainen K. Phylogeny, divergence-time estimation, biogeography and social parasite-host relationships of the Holarctic ant genus Myrmica (Hymenoptera: Formicidae). Mol Phylogenet Evol. 2010;56:294-304 pubmed publisher..The oldest inquiline, Myrmica karavajevi, was estimated at 17 Ma, the youngest species M. hirsuta at 0.8 Ma, whereas the microgyne of M.rubra is an intraspecific inquiline. ..
- Torniainen S, Parker M, Holmberg V, Lahtela E, Dandara C, Jarvela I. Screening of variants for lactase persistence/non-persistence in populations from South Africa and Ghana. BMC Genet. 2009;10:31 pubmed publisher..Further studies are needed to confirm the possible relationship of the novel substitutions to the lactase persistence trait. ..
- Hoglund P, Haila S, Socha J, Tomaszewski L, Saarialho Kere U, Karjalainen Lindsberg M, et al. Mutations of the Down-regulated in adenoma (DRA) gene cause congenital chloride diarrhoea. Nat Genet. 1996;14:316-9 pubmed..We conclude that DRA is an intestinal anion transport molecule that causes chloride diarrhoea when mutated. ..
- Tynkkynen S, Buist G, Kunji E, Kok J, Poolman B, Venema G, et al. Genetic and biochemical characterization of the oligopeptide transport system of Lactococcus lactis. J Bacteriol. 1993;175:7523-32 pubmed..The OppA-deficient mutant was unable to transport Leu-enkephalin. Growth experiments with pasteurized milk revealed that transport of oligopeptides forms an essential part of the proteolytic system in lactococci...
- Tyynismaa H, Ylikallio E, Patel M, Molnar M, Haller R, Suomalainen A. A heterozygous truncating mutation in RRM2B causes autosomal-dominant progressive external ophthalmoplegia with multiple mtDNA deletions. Am J Hum Genet. 2009;85:290-5 pubmed publisher..We conclude that dominant-negative or gain-of-function mutations in RRM2B are a cause of multiple mtDNA deletions and adPEO. ..
- Ekman A, Niku M, Liljavirta J, Iivanainen A. Bos taurus genome sequence reveals the assortment of immunoglobulin and surrogate light chain genes in domestic cattle. BMC Immunol. 2009;10:22 pubmed publisher..The heavy chains probably contribute more to recombinational immunoglobulin repertoire diversity than the light chains but the heavy chain locus could not be annotated from the version 3.1 of Bos taurus genome. ..
- Wheat C. Rapidly developing functional genomics in ecological model systems via 454 transcriptome sequencing. Genetica. 2010;138:433-51 pubmed publisher..How to use species with genomic resources to inform study of those without is also discussed. In closing, some of the drawbacks of 454 sequencing are presented along with future prospects of this technology. ..
- Luoma P, Melberg A, Rinne J, Kaukonen J, Nupponen N, Chalmers R, et al. Parkinsonism, premature menopause, and mitochondrial DNA polymerase gamma mutations: clinical and molecular genetic study. Lancet. 2004;364:875-82 pubmed..We aimed to analyse the gene sequence of POLG in patients with progressive external ophthalmoplegia and their healthy relatives...
- Lappalainen M, Paavola Sakki P, Halme L, Turunen U, Helio T, Farkkila M, et al. Screening of tumor necrosis factor receptor-associated factor 6 as a candidate gene for inflammatory bowel disease. Scand J Gastroenterol. 2006;41:424-9 pubmed
- Tuuminen T, Heinäsmäki T, Kerttula T. First report of bacteremia by Asaia bogorensis, in a patient with a history of intravenous-drug abuse. J Clin Microbiol. 2006;44:3048-50 pubmed..bogorensis was identified by sequencing the 16S rRNA gene. The isolate was exceptionally resistant to almost all antibiotics that are routinely tested for gram-negative rods but was susceptible to netilmicin, gentamicin, and doxycycline...
- Paananen A, Ylipaasto P, Rieder E, Hovi T, Galama J, Roivainen M. Molecular and biological analysis of echovirus 9 strain isolated from a diabetic child. J Med Virol. 2003;69:529-37 pubmed..However, only isolate DM was clearly cytolytic for beta-cells. The infectious clones that were made allow further investigations of the molecular features responsible for the diabetogenicity of the isolate DM...
- Happonen L, Redder P, Peng X, Reigstad L, Prangishvili D, Butcher S. Familial relationships in hyperthermo- and acidophilic archaeal viruses. J Virol. 2010;84:4747-54 pubmed publisher..A combination of genomic and proteomic analyses revealed important new insights into the structural organization of these viruses and added to our limited knowledge of archaeal virus life cycles and host-cell interactions...
- Koivu T, Laitinen S, Riento K, Olkkonen V. Sequence of a human cDNA encoding Cab45, a Ca2+-binding protein with six EF-hand motifs. DNA Seq. 1997;7:217-20 pubmed..1996), J. Cell Biol. 133, 257-268], displaying 87% aa and 83% nt identity with this sequence. The mRNA for human Cab45 is detected ubiquitously in tissue Northern blots. ..
- Chang W, Schulman A. BARE retrotransposons produce multiple groups of rarely polyadenylated transcripts from two differentially regulated promoters. Plant J. 2008;56:40-50 pubmed publisher..Only about 15% of BARE transcripts are polyadenylated. The data suggest that distinct subfamilies of transcripts may play independent roles in providing the proteins and replication templates for the BARE retrotransposon life cycle. ..
- Hannila Handelberg T, Kontula K, Tikkanen I, Tikkanen T, Fyhrquist F, Helin K, et al. Common variants of the beta and gamma subunits of the epithelial sodium channel and their relation to plasma renin and aldosterone levels in essential hypertension. BMC Med Genet. 2005;6:4 pubmed..Patients with the variant alleles showed an increased urinary potassium excretion rate in relation to their renin levels. ..