Genomes and Genes
Experts and Doctors on molecular evolution in Denmark
Topic: molecular evolution
- Dutheil J, Boussau B. Non-homogeneous models of sequence evolution in the Bio++ suite of libraries and programs. BMC Evol Biol. 2008;8:255 pubmed publisher..We furthermore illustrate the use of such general models for parametric bootstrapping, using tests of non-homogeneity applied to an already published ribosomal RNA data set. ..
- Groth C, Petersen R, Piskur J. Diversity in organization and the origin of gene orders in the mitochondrial DNA molecules of the genus Saccharomyces. Mol Biol Evol. 2000;17:1833-41 pubmed..While within the sensu stricto group transposition has been a predominant mechanism for the creation of novel gene orders, the sensu lato yeasts could have used both transposition- and inversion-based mechanisms. ..
- Seemann S, Gorodkin J, Backofen R. Unifying evolutionary and thermodynamic information for RNA folding of multiple alignments. Nucleic Acids Res. 2008;36:6355-62 pubmed publisher..Our implementation, PETfold, was tested on a set of 46 well-curated Rfam families and its performance compared favorably to that of Pfold and RNAalifold. ..
- Pedersen J, Meyer I, Forsberg R, Simmonds P, Hein J. A comparative method for finding and folding RNA secondary structures within protein-coding regions. Nucleic Acids Res. 2004;32:4925-36 pubmed..When scanning the entire genomes of HCV and polio virus for structure elements, RNA-DECODER's results indicate a markedly higher specificity than MFOLD, PFOLD and RNAALIFOLD. ..
- Laessøe T, Hansen K. Truffle trouble: what happened to the Tuberales?. Mycol Res. 2007;111:1075-99 pubmed..The value of the number of nuclei in mature ascospores as a delimiting family character is evaluated and found to be more variable than generally assumed. ..
- Brinkmann N, Wanninger A. Neurogenesis suggests independent evolution of opercula in serpulid polychaetes. BMC Evol Biol. 2009;9:270 pubmed publisher..In addition, our data on Spirorbis neurogenesis provide a novel set of characters that highlight the developmental plasticity of the segmented annelid nervous system. ..
- Nyborg J. Possible evolution of factors involved in protein biosynthesis. Acta Biochim Pol. 1998;45:883-94 pubmed..This observation has initiated much speculation on the evolution of all factors involved in protein synthesis, as well as on the details of the ribosomal function in one part of elongation. ..
- Goetze E. Elongation factor 1-alpha in marine copepods (Calanoida: Eucalanidae): phylogenetic utility and unique intron structure. Mol Phylogenet Evol. 2006;40:880-6 pubmed
- Samuelsen C, Baraznenok V, Khorosjutina O, Spahr H, Kieselbach T, Holmberg S, et al. TRAP230/ARC240 and TRAP240/ARC250 Mediator subunits are functionally conserved through evolution. Proc Natl Acad Sci U S A. 2003;100:6422-7 pubmed..Apparently Srb8/TRAP230/ARC240, Srb9/TRAP240/ARC250, Srb10, and Srb11 constitute a conserved Mediator submodule, which is involved in negative regulation of transcription in all eukaryotes. ..
- Knudsen B, Miyamoto M, Laipis P, Silverman D. Using evolutionary rates to investigate protein functional divergence and conservation. A case study of the carbonic anhydrases. Genetics. 2003;164:1261-9 pubmed..As illustrated by the CAs, these LRTs, in combination with other biological evidence, offer a powerful and cost-effective approach for testing hypotheses, making predictions, and designing experiments in protein functional studies. ..
- Rosendahl S, McGee P, Morton J. Lack of global population genetic differentiation in the arbuscular mycorrhizal fungus Glomus mosseae suggests a recent range expansion which may have coincided with the spread of agriculture. Mol Ecol. 2009;18:4316-29 pubmed publisher..The results of this study suggest that speciation and the range expansion happened much later than continental spread and that human activity may have had a major impact on the dispersal and the population structure of the fungus. ..
- Larsen K, Hedegaard C, Bertelsen M, Bendixen C. Threonine 53 in alpha-synuclein is conserved in long-living non-primate animals. Biochem Biophys Res Commun. 2009;387:602-5 pubmed publisher..In all these investigated species the 53Thr is found. We conclude that 53Thr is not a molecular adaptation for long-living animals to minimize the risk of developing PD...
- Vorup Jensen T, Jensenius J, Thiel S. MASP-2, the C3 convertase generating protease of the MBLectin complement activating pathway. Immunobiology. 1998;199:348-57 pubmed..Phylogenetic analysis indicates that MASP-2 is closer to C1r and C1s than is MASP-1, but no particular association between MASP-2 and the C4 cleaving enzyme, C1s, can be deduced from sequence comparison. ..
- Olsen J, Christensen H, Aarestrup F. Diversity and evolution of blaZ from Staphylococcus aureus and coagulase-negative staphylococci. J Antimicrob Chemother. 2006;57:450-60 pubmed publisher..Results indicated a separate evolution for plasmid- and chromosomally-encoded blaZ. Although a common gene pool seems to exist among staphylococci, exchange of blaZ between strains and species is judged to be an extremely rare event...
- Agerbirk N, Warwick S, Hansen P, Olsen C. Sinapis phylogeny and evolution of glucosinolates and specific nitrile degrading enzymes. Phytochemistry. 2008;69:2937-49 pubmed publisher..NMR data for desulfated homosinalbin, 9-methylsulphonylnonylglucosinolate, 3-methylpentylglucosinolate and related glucosinolates are reported, and a facultative connection between sinalbin and specific nitrilases is suggested...
- Lara E, Heger T, Ekelund F, Lamentowicz M, Mitchell E. Ribosomal RNA genes challenge the monophyly of the Hyalospheniidae (Amoebozoa: Arcellinida). Protist. 2008;159:165-76 pubmed..g. N. penardiana var. minor). Finally our results suggest that the genera Hyalosphenia and Nebela are paraphyletic, and that Porosia bigibbosa branches inside the main Nebela clade. ..
- Honore B, Vorum H. The CREC family, a novel family of multiple EF-hand, low-affinity Ca(2+)-binding proteins localised to the secretory pathway of mammalian cells. FEBS Lett. 2000;466:11-8 pubmed
- Nielsen F, Nielsen J, Christiansen J. A family of IGF-II mRNA binding proteins (IMP) involved in RNA trafficking. Scand J Clin Lab Invest Suppl. 2001;234:93-9 pubmed..The identification of developmentally expressed zipcode-binding proteins indicates that RNA trafficking participates in processes such as cell-growth and migration during embryogenesis. ..
- Hansen M, Nielsen J, Retelska D, Larsen N, Leffers H. A shared promoter region suggests a common ancestor for the human VCX/Y, SPANX, and CSAG gene families and the murine CYPT family. Mol Reprod Dev. 2008;75:219-29 pubmed..Finally, we present evidence that VCX/Y and SPANX may be paralogs with a similar protein structure consisting of C terminal acidic repeats of variable lengths. ..
- Larsen J, Kuhnert P, Frey J, Christensen H, Bisgaard M, Olsen J. Analysis of gene order data supports vertical inheritance of the leukotoxin operon and genome rearrangements in the 5' flanking region in genus Mannheimia. BMC Evol Biol. 2007;7:184 pubmed..We have tested the hypothesis that vertical inheritance of the leukotoxin (lktCABD) operon has occurred from the last common ancestor of genus Mannheimia to any ancestor of the diverging subclades by exploring gene order data...
- Torralba S, Sojat J, Hartmann R. 2'-5' oligoadenylate synthetase shares active site architecture with the archaeal CCA-adding enzyme. Cell Mol Life Sci. 2008;65:2613-20 pubmed publisher..Our findings also have profound implications for our understanding of the evolutionary origin of the OAS enzymes and suggest that the OAS proteins diverged from a common 3'-specific ancestor at the beginning of metazoan evolution. ..
- Lykke Andersen J, Garrett R. RNA-protein interactions of an archaeal homotetrameric splicing endoribonuclease with an exceptional evolutionary history. EMBO J. 1997;16:6290-300 pubmed publisher..jannaschii enzyme consists of two isologously associated dimers, each similar to one H.volcanii monomer and each consisting of two monomers, where one face of monomer 1 and the opposite face of monomer 2 are involved in RNA binding...
- Schwientek T, Bennett E, Flores C, Thacker J, Hollmann M, Reis C, et al. Functional conservation of subfamilies of putative UDP-N-acetylgalactosamine:polypeptide N-acetylgalactosaminyltransferases in Drosophila, Caenorhabditis elegans, and mammals. One subfamily composed of l(2)35Aa is essential in Drosophila. J Biol Chem. 2002;277:22623-38 pubmed
- Sørensen H, Hedegaard J, Sperling Petersen H, Mortensen K. Remarkable conservation of translation initiation factors: IF1/eIF1A and IF2/eIF5B are universally distributed phylogenetic markers. IUBMB Life. 2001;51:321-7 pubmed..Because of these two application levels, IF1/eIF1A-IF2/eIF5B is a phylogenetic "dual level" marker. ..
- Gojkovic Z, Rislund L, Andersen B, Sandrini M, Cook P, Schnackerz K, et al. Dihydropyrimidine amidohydrolases and dihydroorotases share the same origin and several enzymatic properties. Nucleic Acids Res. 2003;31:1683-92 pubmed..Therefore, only a few modifications might have been necessary during evolution to convert the unspecialized enzyme into anabolic and catabolic ones. ..
- Vesth T, Wassenaar T, Hallin P, Snipen L, Lagesen K, Ussery D. On the origins of a Vibrio species. Microb Ecol. 2010;59:1-13 pubmed publisher..We are able to identify a number of genes that are conserved in, and unique to, V. cholerae. Some of these genes may be crucial to the niche adaptation of this species...
- Carter A. Evolution of the placenta and fetal membranes seen in the light of molecular phylogenetics. Placenta. 2001;22:800-7 pubmed..Therefore, future comparative studies should strive to include species such as the rock hyrax and the armadillo...
- Norman A, Hansen L, Sørensen S. Conjugative plasmids: vessels of the communal gene pool. Philos Trans R Soc Lond B Biol Sci. 2009;364:2275-89 pubmed publisher..This communal pool provides the prokaryotes with an important mechanistic framework for obtaining adaptability and functional diversity that alleviates the need for large genomes of specialized 'private genes'. ..
- Gorodkin J, Hofacker I, Torarinsson E, Yao Z, Havgaard J, Ruzzo W. De novo prediction of structured RNAs from genomic sequences. Trends Biotechnol. 2010;28:9-19 pubmed publisher..This paper surveys recent computational advances in this difficult arena, which have enabled genome-scale prediction of cross-species conserved RNA elements. These predictions suggest that a wealth of these elements indeed exist. ..
- Hansen K, Stafflinger E, Schneider M, Hauser F, Cazzamali G, Williamson M, et al. Discovery of a novel insect neuropeptide signaling system closely related to the insect adipokinetic hormone and corazonin hormonal systems. J Biol Chem. 2010;285:10736-47 pubmed publisher..In particular, this frequent loss of hormonal systems is unique for arthropods compared with vertebrates. ..
- Hansen K, Hauser F, Cazzamali G, Williamson M, Grimmelikhuijzen C. Cloning and characterization of the adipokinetic hormone receptor from the cockroach Periplaneta americana. Biochem Biophys Res Commun. 2006;343:638-43 pubmed publisher..This paper describes the first AKH receptor from a hemimetabolous insect...
- Lohmann G, Shimoda Y, Nielsen M, J rgensen F, Grossmann C, Sandal N, et al. Evolution and regulation of the Lotus japonicus LysM receptor gene family. Mol Plant Microbe Interact. 2010;23:510-21 pubmed publisher..In a detailed expression analysis, we found several Lotus Lys genes regulated not only during the symbiotic association with Mesorhizobium loti but also in response to chitin treatment...
- Salomonsen J, Sørensen M, Marston D, Rogers S, Collen T, van Hateren A, et al. Two CD1 genes map to the chicken MHC, indicating that CD1 genes are ancient and likely to have been present in the primordial MHC. Proc Natl Acad Sci U S A. 2005;102:8668-73 pubmed..The unexpected location of these genes in the chicken MHC suggests the CD1 system was present in the primordial MHC and is thus approximately 600 million years old. ..
- Bøttger P, Pedersen L. Evolutionary and experimental analyses of inorganic phosphate transporter PiT family reveals two related signature sequences harboring highly conserved aspartic acids critical for sodium-dependent phosphate transport function of human PiT2. FEBS J. 2005;272:3060-74 pubmed..The present data are in agreement with a possible role of the signature sequences in translocation of cations. ..
- Singh R, Nielsen A, Johansen M, Jørgensen A. Genetic polymorphism and sequence evolution of an alternatively spliced exon of the glial fibrillary acidic protein gene, GFAP. Genomics. 2003;82:185-93 pubmed..Threonine represents a potential phosphorylation site, and positive selection of that effect could explain the high allele frequency. ..
- Larsen J, Pedersen A, Davies R, Kuhnert P, Frey J, Christensen H, et al. Evolution of the leukotoxin promoter in genus Mannheimia. BMC Evol Biol. 2009;9:121 pubmed publisher..We also consider how the evolution of the leukotoxin operon fits with the evolution and maintenance of virulence...
- Langkjaer R, Cliften P, Johnston M, Piskur J. Yeast genome duplication was followed by asynchronous differentiation of duplicated genes. Nature. 2003;421:848-52 pubmed..Further evolution of each duplicated gene pair-such as specialization or differentiation of the two copies, or deletion of a single copy--has taken place independently throughout the evolution of these species. ..
- Burton M, Rose T, Faergeman N, Knudsen J. Evolution of the acyl-CoA binding protein (ACBP). Biochem J. 2005;392:299-307 pubmed..The appearance of ACBP very early on in evolution points towards a fundamental role of ACBP in acyl-CoA metabolism, including ceramide synthesis and in signalling. ..
- Gerdes K, Gultyaev A, Franch T, Pedersen K, Mikkelsen N. Antisense RNA-regulated programmed cell death. Annu Rev Genet. 1997;31:1-31 pubmed..The complex phylogenetic relationships of the plasmid- and chromosome-encoded systems are also presented and discussed. ..
- Jespersen H, Kjaersgård I, Ostergaard L, Welinder K. From sequence analysis of three novel ascorbate peroxidases from Arabidopsis thaliana to structure, function and evolution of seven types of ascorbate peroxidase. Biochem J. 1997;326 ( Pt 2):305-10 pubmed..The data support the hypothesis that present-day peroxidases evolved by an early gene duplication event. ..
- Willerslev E, Gilbert M, Binladen J, Ho S, Campos P, Ratan A, et al. Analysis of complete mitochondrial genomes from extinct and extant rhinoceroses reveals lack of phylogenetic resolution. BMC Evol Biol. 2009;9:95 pubmed publisher..One notable example concerns the rhinoceroses, a group for which several contradictory phylogenies were proposed on the basis of morphology, then apparently resolved using mitochondrial DNA fragments...
- Hansen M, Meier K, Mensberg K. Identifying footprints of selection in stocked brown trout populations: a spatio-temporal approach. Mol Ecol. 2010;19:1787-800 pubmed publisher..To our knowledge, this is the first study demonstrating footprints of selection in wild salmonid populations subject to spawning intrusion by farmed fish...
- Stukenbrock E, McDonald B. Population genetics of fungal and oomycete effectors involved in gene-for-gene interactions. Mol Plant Microbe Interact. 2009;22:371-80 pubmed publisher..Under this scenario, the optimal number of R genes in a plant genome may be determined by the relative abundance of necrotrophic and biotrophic pathogens in the plant's environment. ..
- Klein J, Hussain M, Ahmad M, Normann P, Afzal M, Alexandersen S. Genetic characterisation of the recent foot-and-mouth disease virus subtype A/IRN/2005. Virol J. 2007;4:122 pubmed
- Piskur J, Sandrini M, Knecht W, Munch Petersen B. Animal deoxyribonucleoside kinases: 'forward' and 'retrograde' evolution of their substrate specificity. FEBS Lett. 2004;560:3-6 pubmed..Thereafter, insects lost all but one kinase, dNK (EC 220.127.116.11), which subsequently, through remodelling of a limited number of amino acid residues, gained a broad substrate specificity. ..
- She Q, Shen B, Chen L. Archaeal integrases and mechanisms of gene capture. Biochem Soc Trans. 2004;32:222-6 pubmed..Thus we infer that site-specific integration constitutes an important mechanism for horizontal gene transfer and genome evolution...
- Patil K, Rocha I, Forster J, Nielsen J. Evolutionary programming as a platform for in silico metabolic engineering. BMC Bioinformatics. 2005;6:308 pubmed
- Kjeldbjerg A, Villesen P, Aagaard L, Pedersen F. Gene conversion and purifying selection of a placenta-specific ERV-V envelope gene during simian evolution. BMC Evol Biol. 2008;8:266 pubmed publisher..Together with the placenta-specific expression of the human and baboon ENVV1 and ENVV2 envelope genes, these data provide strong evidence of a beneficial role for the host. ..
- Kilian M, Poulsen K, Lomholt H. Evolution of the paralogous hap and iga genes in Haemophilus influenzae: evidence for a conserved hap pseudogene associated with microcolony formation in the recently diverged Haemophilus aegyptius and H. influenzae biogroup aegyptius. Mol Microbiol. 2002;46:1367-80 pubmed..aegyptius and H. influenzae biogroup aegyptius occurred subsequent to this genetic event. The loss of Hap protein expression may be one of the genetic events that facilitated exploitation of the conjunctivae as a new niche...
- Siegismund H. Disparity in population differentiation of sex-linked and autosomal variation in sibling species of the Jaera albifrons (Isopoda) complex. J Hered. 2002;93:432-9 pubmed..The results are attributed to introgression with a higher rate for autosomes than for sex chromosomes...
- Nielsen A, Jørgensen A. Structural and functional characterization of the zebrafish gene for glial fibrillary acidic protein, GFAP. Gene. 2003;310:123-32 pubmed..This indicates that a change of functionally core residues in GFAP is a prerequisite for the disease phenotype to develop and the initial steps in the pathogenesis may thus be modeled in zebrafish. ..
- Jensen H, Rourke I, M ller M, J nson L, Johnsen A. Identification and distribution of CCK-related peptides and mRNAs in the rainbow trout, Oncorhynchus mykiss. Biochim Biophys Acta. 2001;1517:190-201 pubmed..The last was dominating and had the sequence ASGPGPSHKIKDRDYLGWMDF(.)NH2. All isolated peptides were fully sulfated. The trout is the first species in which three different CCK-like cDNAs have been identified...
- Justesen J, Hartmann R, Kjeldgaard N. Gene structure and function of the 2'-5'-oligoadenylate synthetase family. Cell Mol Life Sci. 2000;57:1593-612 pubmed..Alignments of the human 2'-5'-oligoadenylate synthetase sequences with non-human 2'-5'-oligoadenylate synthetase sequences suggest that the exon structure and several amino acid sequence motifs have been conserved during evolution. ..
- Rukov J, Irimia M, Mørk S, Lund V, Vinther J, Arctander P. High qualitative and quantitative conservation of alternative splicing in Caenorhabditis elegans and Caenorhabditis briggsae. Mol Biol Evol. 2007;24:909-17 pubmed..Moreover, our results indicate that AS contributes little to transcript variation in Caenorhabditis genes and that gene duplication may be the major evolutionary mechanism for the origin of novel transcripts in these 2 species. ..
- Nielsen E, Hemmer Hansen J, Poulsen N, Loeschcke V, Moen T, Johansen T, et al. Genomic signatures of local directional selection in a high gene flow marine organism; the Atlantic cod (Gadus morhua). BMC Evol Biol. 2009;9:276 pubmed publisher..We investigated variation in 98 gene-associated single nucleotide polymorphisms (SNPs) for evidence of selection in local populations of Atlantic cod (Gadus morhua L.) across the species distribution...
- Villesen P, Aagaard L, Wiuf C, Pedersen F. Identification of endogenous retroviral reading frames in the human genome. Retrovirology. 2004;1:32 pubmed..All data are publicly available through a database at http://www.retrosearch.dk. ..
- Schauser L, Wieloch W, Stougaard J. Evolution of NIN-like proteins in Arabidopsis, rice, and Lotus japonicus. J Mol Evol. 2005;60:229-37 pubmed publisher..Thus, the origin of this putative DNA binding region seems to predate the fungus-plant divide...
- Secher T, Lenz C, Cazzamali G, S rensen G, Williamson M, Hansen G, et al. Molecular cloning of a functional allatostatin gut/brain receptor and an allatostatin preprohormone from the silkworm Bombyx mori. J Biol Chem. 2001;276:47052-60 pubmed publisher..To our knowledge, this is the first report on the molecular cloning and functional expression of an insect gut/brain peptide hormone receptor...
- Hansen K, Ibarra P, Thon G. Evolutionary-conserved telomere-linked helicase genes of fission yeast are repressed by silencing factors, RNAi components and the telomere-binding protein Taz1. Nucleic Acids Res. 2006;34:78-88 pubmed..The tlh genes are found in the subtelomeric regions of several other fungi raising the intriguing possibility of conserved regulation and function. ..