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Genome evolution and evolutionary systems biology

Section edited by Maria Anisimova, Arndt von Haeseler and David Liberles

This section considers studies on genome evolution and systems biology approaches to determining evolutionary processes.

Page 10 of 10

  1. Evidence for historical, demographic and selective factors affecting enzyme evolution can be obtained by examining nucleotide sequence variation in candidate genes such as Lactate dehydrogenase (Ldh). Two closely...

    Authors: Teresa J Crease, Robin Floyd, Melania E Cristescu and David Innes
    Citation: BMC Evolutionary Biology 2011 11:212
    Content type: Research article Published on:

  2. Histone variants alter the composition of nucleosomes and play crucial roles in transcription, chromosome segregation, DNA repair, and sperm compaction. Modification of metazoan histone variant lineages occurs...

    Authors: Alexandra Moosmann, Coen Campsteijn, Pascal WTC Jansen, Carole Nasrallah, Martina Raasholm, Henk G Stunnenberg and Eric M Thompson
    Citation: BMC Evolutionary Biology 2011 11:208
    Content type: Research article Published on:

  4. Pathogens have represented an important selective force during the adaptation of modern human populations to changing social and other environmental conditions. The evolution of the immune system has therefore...

    Authors: Ferran Casals, Martin Sikora, Hafid Laayouni, Ludovica Montanucci, Aura Muntasell, Ross Lazarus, Francesc Calafell, Philip Awadalla, Mihai G Netea and Jaume Bertranpetit
    Citation: BMC Evolutionary Biology 2011 11:202
    Content type: Research article Published on:

  5. Since the discovery of the Malta fever agent, Brucella melitensis, in the 19th century, six terrestrial mammal-associated Brucella species were recognized over the next century. More recently the number of novel

    Authors: Stéphane Audic, Magali Lescot, Jean-Michel Claverie, Axel Cloeckaert and Michel S Zygmunt
    Citation: BMC Evolutionary Biology 2011 11:200
    Content type: Research article Published on:

  8. Domain or gene fusion analysis is a bioinformatics method for detecting gene fusions in one organism by comparing its genome to that of other organisms. The occurrence of gene fusions suggests that the two ori...

    Authors: Dimitris Dimitriadis, V Lila Koumandou, Philip Trimpalis and Sophia Kossida
    Citation: BMC Evolutionary Biology 2011 11:193
    Content type: Research article Published on:

  9. Small insertions and deletions ("indels" with size ≦ 100 bp) whose lengths are not multiples of three (non-3n) are strongly constrained and depleted in protein-coding sequences. Such a constraint has never bee...

    Authors: Chun-Hsi Chen, Ben-Yang Liao and Feng-Chi Chen
    Citation: BMC Evolutionary Biology 2011 11:192
    Content type: Research article Published on:

  11. The Erythrinidae fish family is characterized by a large variation with respect to diploid chromosome numbers and sex-determining systems among its species, including two multiple X1X2Y sex systems in Hoplias mal...

    Authors: Marcelo B Cioffi, Antonio Sánchez, Juan A Marchal, Nadezda Kosyakova, Thomas Liehr, Vladimir Trifonov and Luiz AC Bertollo
    Citation: BMC Evolutionary Biology 2011 11:186
    Content type: Research article Published on:

  12. Escherichia coli is one of the best studied organisms in all of biology, but its phylogenetic structure has been difficult to resolve with current data and analytical techniques. We analyzed single nucleotide pol...

    Authors: Shana R Leopold, Stanley A Sawyer, Thomas S Whittam and Phillip I Tarr
    Citation: BMC Evolutionary Biology 2011 11:183
    Content type: Research article Published on:

  13. Several susceptibility genetic variants for autoimmune diseases have been identified. A subset of these polymorphisms displays an opposite risk profile in different autoimmune conditions. This observation open...

    Authors: Rachele Cagliani, Stefania Riva, Uberto Pozzoli, Matteo Fumagalli, Giacomo P Comi, Nereo Bresolin, Mario Clerici and Manuela Sironi
    Citation: BMC Evolutionary Biology 2011 11:171
    Content type: Research article Published on:

  14. Genome wide analysis of variation within a species can reveal the evolution of fundamental biological processes such as mutation, recombination, and natural selection. We compare genome wide sequence differenc...

    Authors: Eleanne Solorzano, Kazufusa Okamoto, Pushpa Datla, Way Sung, RD Bergeron and WK Thomas
    Citation: BMC Evolutionary Biology 2011 11:168
    Content type: Research article Published on:

  15. Chloroplasts and mitochondria evolved from the endosymbionts of once free-living eubacteria, and they transferred most of their genes to the host nuclear genome during evolution. The mechanisms used by plants ...

    Authors: Jie Wang, Yu Wang, Zhuo Wang, Lei Liu, Xin-Guang Zhu and Xiaotu Ma
    Citation: BMC Evolutionary Biology 2011 11:161
    Content type: Research article Published on:

  16. Glyceraldehyde-3-phosphate dehydrogenase (GAPD) catalyses one of the glycolytic reactions and is also involved in a number of non-glycolytic processes, such as endocytosis, DNA excision repair, and induction o...

    Authors: Mikhail L Kuravsky, Vladimir V Aleshin, Dmitrij Frishman and Vladimir I Muronetz
    Citation: BMC Evolutionary Biology 2011 11:160
    Content type: Research article Published on:

  17. We have recently discovered that the two tryptophans of human β2-microglobulin have distinctive roles within the structure and function of the protein. Deeply buried in the core, Trp95 is essential for folding...

    Authors: Sara Raimondi, Nicola Barbarini, Palma Mangione, Gennaro Esposito, Stefano Ricagno, Martino Bolognesi, Irene Zorzoli, Loredana Marchese, Cristina Soria, Riccardo Bellazzi, Maria Monti, Monica Stoppini, Mario Stefanelli, Paolo Magni and Vittorio Bellotti
    Citation: BMC Evolutionary Biology 2011 11:159
    Content type: Research article Published on:

  18. Long terminal repeat (LTR) retrotransposons are a widespread kind of transposable element present in eukaryotic genomes. They are a major factor in genome evolution due to their ability to create large scale m...

    Authors: Nicole de la Chaux and Andreas Wagner
    Citation: BMC Evolutionary Biology 2011 11:154
    Content type: Research article Published on:

  19. Divergence of transcription factor binding sites is considered to be an important source of regulatory evolution. The associations between transcription factor binding sites and phenotypic diversity have been ...

    Authors: Krishna BS Swamy, Wen-Yi Chu, Chun-Yi Wang, Huai-Kuang Tsai and Daryi Wang
    Citation: BMC Evolutionary Biology 2011 11:150
    Content type: Research article Published on:

  20. The Toll-like receptors represent a large superfamily of type I transmembrane glycoproteins, some common to a wide range of species and others are more restricted in their distribution. Most members of the Tol...

    Authors: Yinhua Huang, Nicholas D Temperley, Liming Ren, Jacqueline Smith, Ning Li and David W Burt
    Citation: BMC Evolutionary Biology 2011 11:149
    Content type: Research article Published on:

  21. Cellular ATP levels are generated by glucose-stimulated mitochondrial metabolism and determine metabolic responses, such as glucose-stimulated insulin secretion (GSIS) from the β-cells of pancreatic islets. We...

    Authors: Chrysanthi Ainali, Michelle Simon, Shiri Freilich, Octavio Espinosa, Lee Hazelwood, Sophia Tsoka, Christos A Ouzounis and John M Hancock
    Citation: BMC Evolutionary Biology 2011 11:142
    Content type: Research article Published on:

  22. Microinversions are cytologically undetectable inversions of DNA sequences that accumulate slowly in genomes. Like many other rare genomic changes (RGCs), microinversions are thought to be virtually homoplasy-...

    Authors: Edward L Braun, Rebecca T Kimball, Kin-Lan Han, Naomi R Iuhasz-Velez, Amber J Bonilla, Jena L Chojnowski, Jordan V Smith, Rauri CK Bowie, Michael J Braun, Shannon J Hackett, John Harshman, Christopher J Huddleston, Ben D Marks, Kathleen J Miglia, William S Moore, Sushma Reddy…
    Citation: BMC Evolutionary Biology 2011 11:141
    Content type: Research article Published on:

  24. Porcine endogenous retroviruses (PERVs) represent remnants of an exogenous form that have become integrated in the domestic pig (Sus scrofa) genome. Although they are usually inactive, the capacity of γ1 ERVs to ...

    Authors: Fabrícia F Nascimento, Jaime Gongora, Michael Charleston, Michael Tristem, Stewart Lowden and Chris Moran
    Citation: BMC Evolutionary Biology 2011 11:139
    Content type: Research article Published on:

  25. The Hemichordata comprises solitary-living Enteropneusta and colonial-living Pterobranchia, sharing morphological features with both Chordata and Echinodermata. Despite their key role for understanding deutero...

    Authors: Marleen Perseke, Joerg Hetmank, Matthias Bernt, Peter F Stadler, Martin Schlegel and Detlef Bernhard
    Citation: BMC Evolutionary Biology 2011 11:134
    Content type: Research article Published on:

  26. Stearoyl-CoA desaturases (SCDs) are key enzymes involved in de novo monounsaturated fatty acid synthesis. They catalyze the desaturation of saturated fatty acyl-CoA substrates at the delta-9 position, generating ...

    Authors: L Filipe C Castro, Jonathan M Wilson, Odete Gonçalves, Susana Galante-Oliveira, Eduardo Rocha and Isabel Cunha
    Citation: BMC Evolutionary Biology 2011 11:132
    Content type: Research article Published on:

  27. The wheat tribe Triticeae (Poaceae) is a diverse group of grasses representing a textbook example of reticulate evolution. Apart from globally important grain crops, there are also wild grasses which are of gr...

    Authors: Václav Mahelka, David Kopecký and Ladislava Paštová
    Citation: BMC Evolutionary Biology 2011 11:127
    Content type: Research article Published on:

  28. Recent advances in comparative genomics have considerably improved our knowledge of the evolution of mammalian karyotype architecture. One of the breakthroughs was the preferential localization of evolutionary...

    Authors: Benoîte Cazaux, Josette Catalan, Frédéric Veyrunes, Emmanuel JP Douzery and Janice Britton-Davidian
    Citation: BMC Evolutionary Biology 2011 11:124
    Content type: Research article Published on:

  29. Hybridization and polyploidy are potent forces that have regularly stimulated plant evolution and adaptation. Dactylorhiza majalis s.s., D. traunsteineri s.l. and D. ebudensis are three allopolyploid species of a...

    Authors: Ovidiu Paun, Richard M Bateman, Michael F Fay, Javier A Luna, Justin Moat, Mikael Hedrén and Mark W Chase
    Citation: BMC Evolutionary Biology 2011 11:113
    Content type: Research article Published on:

  30. Major intrinsic proteins (MIPs) also named aquaporins form channels facilitating the passive transport of water and other small polar molecules across membranes. MIPs are particularly abundant and diverse in t...

    Authors: Hanna I Anderberg, Jonas Ã…H Danielson and Urban Johanson
    Citation: BMC Evolutionary Biology 2011 11:110
    Content type: Research article Published on:

  31. Species generally have a fixed number of chromosomes in the cell nuclei while between-species differences are common and often pronounced. These differences could have evolved through multiple speciation event...

    Authors: Vladimir A Lukhtanov, Vlad Dincă, Gerard Talavera and Roger Vila
    Citation: BMC Evolutionary Biology 2011 11:109
    Content type: Research article Published on:

  32. The SLC11A1/Nramp1 and SLC11A2/Nramp2 genes belong to the SLC11/Nramp family of transmembrane divalent metal transporters, with SLC11A1 being associated with resistance to pathogens and SLC11A2 involved in intest...

    Authors: João V Neves, Jonathan M Wilson, Heiner Kuhl, Richard Reinhardt, L Filipe C Castro and Pedro NS Rodrigues
    Citation: BMC Evolutionary Biology 2011 11:106
    Content type: Research article Published on:

  33. Euglenophytes are a group of photosynthetic flagellates possessing a plastid derived from a green algal endosymbiont, which was incorporated into an ancestral host cell via secondary endosymbiosis. However, th...

    Authors: Shinichiro Maruyama, Toshinobu Suzaki, Andreas PM Weber, John M Archibald and Hisayoshi Nozaki
    Citation: BMC Evolutionary Biology 2011 11:105
    Content type: Research article Published on:

  35. A gene's position in regulatory, protein interaction or metabolic networks can be predictive of the strength of purifying selection acting on it, but these relationships are neither universal nor invariably st...

    Authors: Corey M Hudson and Gavin C Conant
    Citation: BMC Evolutionary Biology 2011 11:89
    Content type: Research article Published on:

  36. Urea amidolyase breaks down urea into ammonia and carbon dioxide in a two-step process, while another enzyme, urease, does this in a one step-process. Urea amidolyase has been found only in some fungal species...

    Authors: Pooja K Strope, Kenneth W Nickerson, Steven D Harris and Etsuko N Moriyama
    Citation: BMC Evolutionary Biology 2011 11:80
    Content type: Research article Published on:

  37. Polyploidy has long been recognized as playing an important role in plant evolution. In flowering plants, the major route of polyploidization is suggested to be sexual through gametes with somatic chromosome n...

    Authors: Riccardo Aiese Cigliano, Walter Sanseverino, Gaetana Cremona, Federica M Consiglio and Clara Conicella
    Citation: BMC Evolutionary Biology 2011 11:78
    Content type: Research article Published on:

  38. Previously, we described the heat shock response in dipteran species belonging to the family Stratiomyidae that develop in thermally and chemically contrasting habitats including highly aggressive ones. Althou...

    Authors: David G Garbuz, Irina A Yushenova, Olga G Zatsepina, Andrey A Przhiboro, Brian R Bettencourt and Michael B Evgen'ev
    Citation: BMC Evolutionary Biology 2011 11:74
    Content type: Research article Published on:

  39. Genes involved in post-mating processes of multiple mating organisms are known to evolve rapidly due to coevolution driven by sexual conflict among male-female interacting proteins. In the malaria mosquito Anophe...

    Authors: Emiliano Mancini, Federica Tammaro, Francesco Baldini, Allegra Via, Domenico Raimondo, Phillip George, Paolo Audisio, Igor V Sharakhov, Anna Tramontano, Flaminia Catteruccia and Alessandra della Torre
    Citation: BMC Evolutionary Biology 2011 11:72
    Content type: Research article Published on:

  40. The Immunoglobulin heavy chain (IgH) 3' Regulatory Region (3'RR), located at the 3' of the constant alpha gene, plays a crucial role in immunoglobulin production. In humans, there are 2 copies of the 3'RR, eac...

    Authors: Pietro D'Addabbo, Moira Scascitelli, Vincenzo Giambra, Mariano Rocchi and Domenico Frezza
    Citation: BMC Evolutionary Biology 2011 11:71
    Content type: Research article Published on:

  41. Ammonium is one of the major forms in which nitrogen is available for plant growth. OsAMT1;1 is a high-affinity ammonium transporter in rice (Oryza sativa L.), responsible for ammonium uptake at low nitrogen conc...

    Authors: Zehong Ding, Chongrong Wang, Sheng Chen and Sibin Yu
    Citation: BMC Evolutionary Biology 2011 11:61
    Content type: Research article Published on:

  43. Two component systems (TCS) are signal transduction pathways which typically consist of a sensor histidine kinase (HK) and a response regulator (RR). In this study, we have analyzed the evolution of TCS of the...

    Authors: Manuel Zúñiga, Ciara Luna Gómez-Escoín and Fernando González-Candelas
    Citation: BMC Evolutionary Biology 2011 11:34
    Content type: Research article Published on:

  45. Corticosteroid receptors include mineralocorticoid (MR) and glucocorticoid (GR) receptors. Teleost fishes have a single MR and duplicate GRs that show variable sensitivities to mineralocorticoids and glucocort...

    Authors: Adam S Arterbery, Daniel J Fergus, Elizabeth A Fogarty, John Mayberry, David L Deitcher, W Lee Kraus and Andrew H Bass
    Citation: BMC Evolutionary Biology 2011 11:14
    Content type: Research article Published on:

  46. Ribonucleotide reduction is the only de novo pathway for synthesis of deoxyribonucleotides, the building blocks of DNA. The reaction is catalysed by ribonucleotide reductases (RNRs), an ancient enzyme family comp...

    Authors: Daniel Lundin, Simonetta Gribaldo, Eduard Torrents, Britt-Marie Sjöberg and Anthony M Poole
    Citation: BMC Evolutionary Biology 2010 10:383
    Content type: Research article Published on:
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