Genomes and Genes
Summary: Genes that are located on the MITOCHONDRIAL DNA. Mitochondrial inheritance is often referred to as maternal inheritance but should be differentiated from maternal inheritance that is transmitted chromosomally.
- Li L, Wang B, Liu Y, Qiu Y. The complete mitochondrial genome sequence of the hornwort Megaceros aenigmaticus shows a mixed mode of conservative yet dynamic evolution in early land plant mitochondrial genomes. J Mol Evol. 2009;68:665-78 pubmed publisher..Overall, this genome and those of other 2 bryophytes show that mitochondrial genomes in early land plants, unlike their seed plant counterparts, exhibit a mixed mode of conservative yet dynamic evolution. ..
- De Filippis E, Alvarez G, Berria R, Cusi K, Everman S, Meyer C, et al. Insulin-resistant muscle is exercise resistant: evidence for reduced response of nuclear-encoded mitochondrial genes to exercise. Am J Physiol Endocrinol Metab. 2008;294:E607-14 pubmed publisher..of peroxisome proliferator-activated receptor-gamma coactivator-1alpha (PGC-1alpha) and nuclear-encoded mitochondrial genes. This deficit could be due to decreased physical activity or a decreased response of gene expression to ..
- Dole S, Jordal B, Cognato A. Polyphyly of Xylosandrus Reitter inferred from nuclear and mitochondrial genes (Coleoptera: Curculionidae: Scolytinae). Mol Phylogenet Evol. 2010;54:773-82 pubmed publisher..Since the taxon sample available for molecular work represents only a fraction of Xylosandrus species, a complete revision that combines molecular and morphological data in a total evidence approach is recommended for the genus. ..
- Cui P, Liu H, Lin Q, Ding F, Zhuo G, Hu S, et al. A complete mitochondrial genome of wheat (Triticum aestivum cv. Chinese Yumai), and fast evolving mitochondrial genes in higher plants. J Genet. 2009;88:299-307 pubmed
- Mower J. The PREP suite: predictive RNA editors for plant mitochondrial genes, chloroplast genes and user-defined alignments. Nucleic Acids Res. 2009;37:W253-9 pubmed publisher..The PREP suite provides predictive RNA editors for plant mitochondrial genes (PREP-Mt), for chloroplast genes (PREP-Cp), and for alignments submitted by the user (PREP-Aln)...
- Espregueira Themudo G, Wielstra B, Arntzen J. Multiple nuclear and mitochondrial genes resolve the branching order of a rapid radiation of crested newts (Triturus arntzenii) (corrected). Mol Phylogenet Evol. 2009;52:321-8 pubmed publisher..Results show a previously undetected basal dichotomy between T. karelinii and the other four species and a deep differentiation of T. karelinii in two lineages, here raised to full species status...
- Strübing U, Lucius R, Hoerauf A, Pfarr K. Mitochondrial genes for heme-dependent respiratory chain complexes are up-regulated after depletion of Wolbachia from filarial nematodes. Int J Parasitol. 2010;40:1193-202 pubmed publisher..Our results support targeting the Wolbachia heme synthesis pathway for the discovery of new anti-filarial drugs...
- Martherus R, Sluiter W, Timmer E, VanHerle S, Smeets H, Ayoubi T. Functional annotation of heart enriched mitochondrial genes GBAS and CHCHD10 through guilt by association. Biochem Biophys Res Commun. 2010;402:203-8 pubmed publisher..We predicted both genes to be involved in oxidative phosphorylation. Through in vitro experiments using gene-knockdown we could indeed confirm this and furthermore we asserted CHCHD10 to play a role in complex IV activity. ..
- Schoenfeld R, Wong A, Silva J, Li M, Itoh A, Horiuchi M, et al. Oligodendroglial differentiation induces mitochondrial genes and inhibition of mitochondrial function represses oligodendroglial differentiation. Mitochondrion. 2010;10:143-50 pubmed publisher..Cholesterol, myelin and mitochondrial genes were significantly increased with oligodendroglial differentiation...
- Curole J, Meyer E, Manahan D, Hedgecock D. Unequal and genotype-dependent expression of mitochondrial genes in larvae of the pacific oyster Crassostrea gigas. Biol Bull. 2010;218:122-31 pubmed..Differences in mitochondrial gene expression could provide a biochemical index for the metabolic basis of genetically determined differences in larval growth. ..
- Lakra W, Goswami M, Gopalakrishnan A. Molecular identification and phylogenetic relationships of seven Indian Sciaenids (Pisces: Perciformes, Sciaenidae) based on 16S rRNA and cytochrome c oxidase subunit I mitochondrial genes. Mol Biol Rep. 2009;36:831-9 pubmed publisherThe partial sequences of 16S rRNA and cytochrome c oxidase subunit I (COI) mitochondrial genes were analyzed for species identification and phylogenetic relationships among the commercially important Indian sciaenids (Otolithes cuvieri, ..
- Hao W, Palmer J. Fine-scale mergers of chloroplast and mitochondrial genes create functional, transcompartmentally chimeric mitochondrial genes. Proc Natl Acad Sci U S A. 2009;106:16728-33 pubmed publisher..All characterized chloroplast integrants exist apart from native mitochondrial genes, and only a few, involving chloroplast tRNA genes that have functionally supplanted their mitochondrial ..
- Li J, Che J, Murphy R, Zhao H, Zhao E, Rao D, et al. New insights to the molecular phylogenetics and generic assessment in the Rhacophoridae (Amphibia: Anura) based on five nuclear and three mitochondrial genes, with comments on the evolution of reproduction. Mol Phylogenet Evol. 2009;53:509-22 pubmed publisher..Analyses of the nuclear and mitochondrial genes supported the following results: (1) Genus Liuixalus formed the sister group of all other rhacophorines...
- Ahmed V, Chandra V, Sudhakaran R, Kumar S, Sarathi M, Babu V, et al. Development and characterization of cell lines derived from rohu, Labeo rohita (Hamilton), and catla, Catla catla (Hamilton). J Fish Dis. 2009;32:211-8 pubmed publisher..The cell lines were further characterized by immunocytochemistry using confocal laser scanning microscopy. ..
- Aubry K, Statham M, Sacks B, Perrine J, Wisely S. Phylogeography of the North American red fox: vicariance in Pleistocene forest refugia. Mol Ecol. 2009;18:2668-86 pubmed publisher..The montane lineage, which includes endangered populations, may be ecologically and evolutionarily distinct...
- Poulton J, Hirano M, Spinazzola A, Arenas Hernandez M, Jardel C, Lombes A, et al. Collated mutations in mitochondrial DNA (mtDNA) depletion syndrome (excluding the mitochondrial gamma polymerase, POLG1). Biochim Biophys Acta. 2009;1792:1109-12 pubmed publisher..We have included genes known to cause mtDNA depletion, excluding POLG1, because of the existing database (http://tools.niehs.nih.gov/polg/). We have also excluded mutations in C10orf2 associated with dominant adult onset disorders. ..
- Tachibana M, Sparman M, Sritanaudomchai H, Ma H, Clepper L, Woodward J, et al. Mitochondrial gene replacement in primate offspring and embryonic stem cells. Nature. 2009;461:367-72 pubmed publisher..This approach may offer a reproductive option to prevent mtDNA disease transmission in affected families. ..
- Patterson J, Gaunt M. Phylogenetic multi-locus codon models and molecular clocks reveal the monophyly of haematophagous reduviid bugs and their evolution at the formation of South America. Mol Phylogenet Evol. 2010;56:608-21 pubmed publisher..The placement of the enigmatic tribe Bolboderini as an ingroup to the Triatominae monophyly, confirms the 95MYA node as the most ancient in the subfamily...
- Curado S, Ober E, Walsh S, Cortes Hernandez P, Verkade H, Koehler C, et al. The mitochondrial import gene tomm22 is specifically required for hepatocyte survival and provides a liver regeneration model. Dis Model Mech. 2010;3:486-95 pubmed publisher..We used this regeneration model to analyze the signaling commonalities between hepatocyte development and regeneration. ..
- Cho H, Eda M, Nishida S, Yasukochi Y, Chong J, Koike H. Tandem duplication of mitochondrial DNA in the black-faced spoonbill, Platalea minor. Genes Genet Syst. 2009;84:297-305 pubmed
- Moiseeva O, Bourdeau V, Roux A, Deschênes Simard X, Ferbeyre G. Mitochondrial dysfunction contributes to oncogene-induced senescence. Mol Cell Biol. 2009;29:4495-507 pubmed publisher..Taking these results together, this work suggests that mitochondrial dysfunction is an effector pathway of oncogene-induced senescence. ..
- Shiflett A, Johnson P. Mitochondrion-related organelles in eukaryotic protists. Annu Rev Microbiol. 2010;64:409-29 pubmed publisher..This review examines the metabolism and biogenesis of these organelles in divergent unicellular microbes, with a focus on parasitic protists. ..
- Maslov D. Complete set of mitochondrial pan-edited mRNAs in Leishmania mexicana amazonensis LV78. Mol Biochem Parasitol. 2010;173:107-14 pubmed publisher..This property differs drastically from the other Leishmania species which lost some or all of the G1-G5 mRNA editing ability in culture. ..
- Chandak P, Radovic B, Aflaki E, Kolb D, Buchebner M, Fröhlich E, et al. Efficient phagocytosis requires triacylglycerol hydrolysis by adipose triglyceride lipase. J Biol Chem. 2010;285:20192-201 pubmed publisher..This novel mechanism links ATGL-mediated lipolysis to macrophage function in host defense and opens the way to explore possible roles of ATGL in immune response, inflammation, and atherosclerosis. ..
- Forgacs A, Burgoon L, Lynn S, LaPres J, Zacharewski T. Effects of TCDD on the expression of nuclear encoded mitochondrial genes. Toxicol Appl Pharmacol. 2010;246:58-65 pubmed publisher..This high-throughput approach suggests that TCDD alters the expression of genes associated with mitochondrial function which may contribute to TCDD-elicited mitochondrial toxicity. ..
- Phayuhasena S, Colgan D, Kuvangkadilok C, Pramual P, Baimai V. Phylogenetic relationships among the black fly species (Diptera: Simuliidae) of Thailand based on multiple gene sequences. Genetica. 2010;138:633-48 pubmed publisher..Data were collected from three mitochondrial genes (COI, ND4 and 16S rRNA) and two segments of the nuclear 28S ribosomal RNA (the D1 to D2 and the D4 ..
- McKay B, Zink R. The causes of mitochondrial DNA gene tree paraphyly in birds. Mol Phylogenet Evol. 2010;54:647-50 pubmed publisher..We ultimately conclude that, far from a hindrance, mtDNA is generally a useful tool that should continue to facilitate delimitation of avian species. ..
- Minge M, Silberman J, Orr R, Cavalier Smith T, Shalchian Tabrizi K, Burki F, et al. Evolutionary position of breviate amoebae and the primary eukaryote divergence. Proc Biol Sci. 2009;276:597-604 pubmed publisher..Furthermore, mitochondrial genes among the Breviata ESTs demonstrate that Breviata probably contains a modified anaerobic mitochondrion...
- Sinha R, Pathak A, Mohan V, Babu S, Pal A, Khare D, et al. Evidence of a bigenomic regulation of mitochondrial gene expression by thyroid hormone during rat brain development. Biochem Biophys Res Commun. 2010;397:548-52 pubmed publisher..These results thus indicate an integrated nuclear-mitochondrial cross talk in regulation of mitochondrial transcription by TH during brain development. ..
- HAJDUK S, Ochsenreiter T. RNA editing in kinetoplastids. RNA Biol. 2010;7:229-36 pubmed..Sequences within gRNAs define the position and extend of mRNA editing. Both mRNAs and gRNAs are encoded by mitochondrial genes in the kinetoplast DNA (kDNA), which consists of thousands of small circular DNA molecules, called ..
- Hirayama M, Mukai T, Miya M, Murata Y, Sekiya Y, Yamashita T, et al. Intraspecific variation in the mitochondrial genome among local populations of Medaka Oryzias latipes. Gene. 2010;457:13-24 pubmed publisher..This study revealed that the repeated sequences in the mtDNA CR might function for mtDNA gene expression and that the number of tandem repeats in Medaka mtDNA is likely related to adaptation to a harsh habitat. ..
- Outlaw D, Ricklefs R. Comparative gene evolution in haemosporidian (apicomplexa) parasites of birds and mammals. Mol Biol Evol. 2010;27:537-42 pubmed publisher..The high d(N)/d(S) ratio in the cyt b branch separating avian and mammalian parasites and a mammal-parasite codon bias suggest that adaptive evolution has distinguished mammal and bird parasites...
- Carling M, Lovette I, Brumfield R. Historical divergence and gene flow: coalescent analyses of mitochondrial, autosomal and sex-linked loci in Passerina buntings. Evolution. 2010;64:1762-72 pubmed publisher..These results are consistent with the low fitness of female avian hybrids under Haldane's rule and demonstrate that sex-linked loci likely are important in the initial generation of reproductive isolation, not just its maintenance. ..
- Timpe E, Graham S, Bonett R. Phylogeography of the Brownback Salamander reveals patterns of local endemism in Southern Appalachian springs. Mol Phylogenet Evol. 2009;52:368-76 pubmed publisher..The distribution of these lineages is coincident with the distribution of other endemic spring-dwelling vertebrates, and suggests that this region may be a relictual habitat for an unexpected diversity of unrecognized endemics. ..
- Ohshima I, Yoshizawa K. Differential introgression causes genealogical discordance in host races of Acrocercops transecta (Insecta: Lepidoptera). Mol Ecol. 2010;19:2106-19 pubmed publisher..We tested this hypothesis by combining phylogenetic analyses with coalescent simulations, focusing on mitochondrial genes (COI and ND5) and the nuclear Tpi, Per and Ldh genes located on the Z-chromosome...
- Temperley R, Richter R, Dennerlein S, Lightowlers R, Chrzanowska Lightowlers Z. Hungry codons promote frameshifting in human mitochondrial ribosomes. Science. 2010;327:301 pubmed publisher..By using a sequence-specific endoribonuclease, we show that the rare arginine codons, presumably in association with other cis elements, promote frameshifting in human mitoribosomes. ..
- Baranowska I, Jäderlund K, Nennesmo I, Holmqvist E, Heidrich N, Larsson N, et al. Sensory ataxic neuropathy in golden retriever dogs is caused by a deletion in the mitochondrial tRNATyr gene. PLoS Genet. 2009;5:e1000499 pubmed publisher..Altogether, these results provide conclusive evidence that the deletion in the mitochondrial tRNA(Tyr) gene is the causative mutation for SAN. ..
- Boothby M, McGee K, Tomlinson J, Gathercole L, McTernan P, Shojaee Moradie F, et al. Adipocyte differentiation, mitochondrial gene expression and fat distribution: differences between zidovudine and tenofovir after 6 months. Antivir Ther. 2009;14:1089-100 pubmed publisher..We compared the expression of several key adipocyte genes in HIV-infected patients randomized to antiretroviral regimens containing zidovudine (AZT) or tenofovir disoproxil fumarate (TDF)...
- Zhu H, Wang S, Liu L, Chen R, Wang L, Gong X, et al. Genetic variants in mitochondrial tRNA genes are associated with essential hypertension in a Chinese Han population. Clin Chim Acta. 2009;410:64-9 pubmed publisher..0010) and A4263G (P=0.0001) decreased as compared to the average level of control cell lines. Variants located in mitochondrial tRNA genes may have biologic plausibility to implicate in the pathogenesis of Chinese essential hypertension. ..
- Das S, Sen S, Chakraborty A, Chakraborti P, Maiti M, Basu A, et al. An unedited 1.1 kb mitochondrial orfB gene transcript in the wild abortive cytoplasmic male sterility (WA-CMS) system of Oryza sativa L. subsp. indica. BMC Plant Biol. 2010;10:39 pubmed publisher..A new point of departure to dissect the mechanisms governing the CMS-WA system in rice has been identified, which can be applied to further harness the opportunities afforded by hybrid vigor in rice...
- Wu X, Wang L, Chen S, Zan R, Xiao H, Zhang Y. The complete mitochondrial genomes of two species from Sinocyclocheilus (Cypriniformes: Cyprinidae) and a phylogenetic analysis within Cyprininae. Mol Biol Rep. 2010;37:2163-71 pubmed publisher..The two Sinocyclocheilus species fall within the Cyprinion-Onychostoma lineage, including Cyprinus, Carassius, and Procypris, rather than among the Barbinae, as previously suggested on morphological grounds. ..
- Pook C, Joger U, Stümpel N, Wüster W. When continents collide: phylogeny, historical biogeography and systematics of the medically important viper genus Echis (Squamata: Serpentes: Viperidae). Mol Phylogenet Evol. 2009;53:792-807 pubmed publisher..jogeri, for the presence of unsuspected genetic diversity within the E. pyramidum complex in eastern Africa, and for the conspecificity of E. carinatus and E. multisquamatus. The status of E. leucogaster remains to be confirmed...
- Jung P, Schacherer J, Souciet J, Potier S, Wincker P, De Montigny J. The complete mitochondrial genome of the yeast Pichia sorbitophila. FEMS Yeast Res. 2009;9:903-10 pubmed publisher..Although the mitochondrial genome of P. sorbitophila contains the same core of mitochondrial genes observed in the ascomycetous yeasts, those coding for the RNAse P and the ribosomal protein VAR1p are ..
- Charlat S, Duplouy A, Hornett E, Dyson E, Davies N, Roderick G, et al. The joint evolutionary histories of Wolbachia and mitochondria in Hypolimnas bolina. BMC Evol Biol. 2009;9:64 pubmed publisher..In contrast, the sharing of haplotypes between wBol2-infected and uninfected individuals indicates that this strain is not perfectly transmitted and/or shows a significant level of horizontal transmission. ..
- Katsumura T, Oda S, Mano S, Suguro N, Watanabe K, Mitani H, et al. Genetic differentiation among local populations of medaka fish (Oryzias latipes) evaluated through grid- and deme-based sampling. Gene. 2009;443:170-7 pubmed publisher..This could be a basis of strategy to use medaka as a vertebrate model animal for comparative population genomics. ..
- Pons J, Ribera I, Bertranpetit J, Balke M. Nucleotide substitution rates for the full set of mitochondrial protein-coding genes in Coleoptera. Mol Phylogenet Evol. 2010;56:796-807 pubmed publisher..In contrast, nad5, nad4 and nad2 perform better, as they exhibit more homogeneous rates among codon positions. ..
- Grill A, Amori G, Aloise G, Lisi I, Tosi G, Wauters L, et al. Molecular phylogeography of European Sciurus vulgaris: refuge within refugia?. Mol Ecol. 2009;18:2687-99 pubmed publisher..Calabrian mtDNA probably diverged in an ice age contraction and remained isolated from the neighbouring squirrel populations until very recent times...
- Kitahara M, Cairns S, Stolarski J, Blair D, Miller D. A comprehensive phylogenetic analysis of the Scleractinia (Cnidaria, Anthozoa) based on mitochondrial CO1 sequence data. PLoS ONE. 2010;5:e11490 pubmed publisher..Deep-sea corals are likely to be critical to understanding anthozoan evolution and the origins of the Scleractinia. ..