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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 8 of 10

  1. Heat-shock proteins of the 70 kDa family (Hsp70s) are essential chaperones required for key cellular functions. In eukaryotes, four subfamilies can be distinguished according to their function and localisation...

    Authors: Sascha Krenek, Martin Schlegel and Thomas U Berendonk
    Citation: BMC Evolutionary Biology 2013 13:49
  2. Parasitic plants, represented by several thousand species of angiosperms, use modified structures known as haustoria to tap into photosynthetic host plants and extract nutrients and water. As a result of their...

    Authors: Yeting Zhang, Monica Fernandez-Aparicio, Eric K Wafula, Malay Das, Yuannian Jiao, Norman J Wickett, Loren A Honaas, Paula E Ralph, Martin F Wojciechowski, Michael P Timko, John I Yoder, James H Westwood and Claude W dePamphilis
    Citation: BMC Evolutionary Biology 2013 13:48
  3. Proteins are composed of a combination of discrete, well-defined, sequence domains, associated with specific functions that have arisen at different times during evolutionary history. The emergence of novel do...

    Authors: Macarena Toll-Riera and M Mar Albà
    Citation: BMC Evolutionary Biology 2013 13:47
  4. Increasing genome data show that introns, a hallmark of eukaryotes, already existed at a high density in the last common ancestor of extant eukaryotes. However, intron content is highly variable among species....

    Authors: Jean-Luc Da Lage, Manfred Binder, Aurélie Hua-Van, Štefan Janeček and Didier Casane
    Citation: BMC Evolutionary Biology 2013 13:40
  5. The acquisition of complex transcriptional regulatory abilities and epigenetic machinery facilitated the transition of the ancestor of apicomplexans from a free-living organism to an obligate parasite. The abi...

    Authors: Sandeep P Kishore, John W Stiller and Kirk W Deitsch
    Citation: BMC Evolutionary Biology 2013 13:37
  6. Hair is one of the main distinguishing characteristics of mammals and it has many important biological functions. Cetaceans originated from terrestrial mammals and they have evolved a series of adaptations to ...

    Authors: Zhuo Chen, Zhengfei Wang, Shixia Xu, Kaiya Zhou and Guang Yang
    Citation: BMC Evolutionary Biology 2013 13:34
  7. Ribonucleotide reductase (RNR), the enzyme responsible for the formation of deoxyribonucleotides from ribonucleotides, is found in all domains of life and many viral genomes. RNRs are also amongst the most abu...

    Authors: Bhakti Dwivedi, Bingjie Xue, Daniel Lundin, Robert A Edwards and Mya Breitbart
    Citation: BMC Evolutionary Biology 2013 13:33
  8. Inherited Copy Number Variants (CNVs) can modulate the expression levels of individual genes. However, little is known about how CNVs alter biological pathways and how this varies across different populations....

    Authors: Maria Poptsova, Samprit Banerjee, Omer Gokcumen, Mark A Rubin and Francesca Demichelis
    Citation: BMC Evolutionary Biology 2013 13:19
  9. Proteomes of thermophilic prokaryotes have been instrumental in structural biology and successfully exploited in biotechnology, however many proteins required for eukaryotic cell function are absent from bacte...

    Authors: Vera van Noort, Bettina Bradatsch, Manimozhiyan Arumugam, Stefan Amlacher, Gert Bange, Chris Creevey, Sebastian Falk, Daniel R Mende, Irmgard Sinning, Ed Hurt and Peer Bork
    Citation: BMC Evolutionary Biology 2013 13:7
  10. Every year the human population encounters epidemic outbreaks of influenza, and history reveals recurring pandemics that have had devastating consequences. The current work focuses on the development of a robu...

    Authors: Victoria Svinti, James A Cotton and James O McInerney
    Citation: BMC Evolutionary Biology 2013 13:1
  11. Theories of ageing predict a trade-off between metabolism, reproduction, and maintenance. Species with low investment in early reproduction are thus expected to be able to evolve more efficient maintenance and...

    Authors: Angela Pauliny, Kjell Larsson and Donald Blomqvist
    Citation: BMC Evolutionary Biology 2012 12:257
  12. Toll-like receptors (Tlrs) are major molecular pattern recognition receptors of the innate immune system. Atlantic cod (Gadus morhua) is the first vertebrate known to have lost most of the mammalian Tlr orthologu...

    Authors: Arvind YM Sundaram, Viswanath Kiron, Joaquín Dopazo and Jorge MO Fernandes
    Citation: BMC Evolutionary Biology 2012 12:256
  13. Gene duplications have been proposed to be the main mechanism involved in genome evolution and in acquisition of new functions. Polydnaviruses (PDVs), symbiotic viruses associated with parasitoid wasps, are id...

    Authors: Céline Serbielle, Stéphane Dupas, Elfie Perdereau, François Héricourt, Catherine Dupuy, Elisabeth Huguet and Jean-Michel Drezen
    Citation: BMC Evolutionary Biology 2012 12:253
  14. Single-stranded (ss) DNA viruses in the family Geminiviridae are proving to be very useful in real-time evolution studies. The high mutation rate of geminiviruses and other ssDNA viruses is somewhat mysterious in...

    Authors: Adérito L Monjane, Daniel Pande, Francisco Lakay, Dionne N Shepherd, Eric van der Walt, Pierre Lefeuvre, Jean-Michel Lett, Arvind Varsani, Edward P Rybicki and Darren P Martin
    Citation: BMC Evolutionary Biology 2012 12:252
  15. Marine fish, such as the Atlantic herring (Clupea harengus), often show a low degree of differentiation over large geographical regions. Despite strong environmental gradients (salinity and temperature) in the Ba...

    Authors: Amber GF Teacher, Carl André, Juha Merilä and Christopher W Wheat
    Citation: BMC Evolutionary Biology 2012 12:248
  16. Horizontal gene transfer (HGT) is considered to be a major force driving the evolutionary history of prokaryotes. HGT is widespread in prokaryotes, contributing to the genomic repertoire of prokaryotic organis...

    Authors: Phuong Thi Le, Hemalatha Golaconda Ramulu, Laurent Guijarro, Julien Paganini, Philippe Gouret, Olivier Chabrol, Dider Raoult and Pierre Pontarotti
    Citation: BMC Evolutionary Biology 2012 12:243
  17. HIV-1 derives from multiple independent transfers of simian immunodeficiency virus (SIV) strains from chimpanzees to human populations. We hypothesized that human populations in west central Africa may have be...

    Authors: Kai Zhao, Yasuko Ishida, Taras K Oleksyk, Cheryl A Winkler and Alfred L Roca
    Citation: BMC Evolutionary Biology 2012 12:237
  18. Somatostatin and its related neuroendocrine peptides have a wide variety of physiological functions that are mediated by five somatostatin receptors with gene names SSTR1-5 in mammals. To resolve their evolution ...

    Authors: Daniel Ocampo Daza, Görel Sundström, Christina A Bergqvist and Dan Larhammar
    Citation: BMC Evolutionary Biology 2012 12:231
  19. The broadly accepted pattern of rapid evolution of reproductive genes is primarily based on studies of animal systems, although several examples of rapidly evolving genes involved in reproduction are found in ...

    Authors: Kristiina Nygren, Andreas Wallberg, Nicklas Samils, Jason E Stajich, Jeffrey P Townsend, Magnus Karlsson and Hanna Johannesson
    Citation: BMC Evolutionary Biology 2012 12:229
  20. In 2004, we discovered an atypical protein in metagenomic data from marine thaumarchaeotal species. This protein, referred as DnaJ-Fer, is composed of a J domain fused to a Ferredoxin (Fer) domain. Surprisingl...

    Authors: Céline Petitjean, David Moreira, Purificación López-García and Céline Brochier-Armanet
    Citation: BMC Evolutionary Biology 2012 12:226
  21. Plant parasitic nematodes are unusual Metazoans as they are equipped with genes that allow for symbiont-independent degradation of plant cell walls. Among the cell wall-degrading enzymes, glycoside hydrolase f...

    Authors: Katarzyna Rybarczyk-Mydłowska, Hazel Ruvimbo Maboreke, Hanny van Megen, Sven van den Elsen, Paul Mooyman, Geert Smant, Jaap Bakker and Johannes Helder
    Citation: BMC Evolutionary Biology 2012 12:221
  22. The sequencing of the genome of the pea aphid Acyrthosiphon pisum revealed an unusual expansion of the miRNA machinery, with two argonaute-1, two dicer-1 and four pasha gene copies. In this report, we have undert...

    Authors: Benjamín Ortiz-Rivas, Stéphanie Jaubert-Possamai, Sylvie Tanguy, Jean-Pierre Gauthier, Denis Tagu and Rispe Claude
    Citation: BMC Evolutionary Biology 2012 12:216
  23. In the Calvin cycle of eubacteria, the dephosphorylations of both fructose-1, 6-bisphosphate (FBP) and sedoheptulose-1, 7-bisphosphate (SBP) are catalyzed by the same bifunctional enzyme: fructose-1, 6-bisphos...

    Authors: Yong-Hai Jiang, De-Yong Wang and Jian-Fan Wen
    Citation: BMC Evolutionary Biology 2012 12:208
  24. The exponential growth of the number of fully sequenced genomes at varying taxonomic closeness allows one to characterize transcriptional regulation using comparative-genomics analysis instead of time-consumin...

    Authors: Olga V Tsoy, Mikhail A Pyatnitskiy, Marat D Kazanov and Mikhail S Gelfand
    Citation: BMC Evolutionary Biology 2012 12:200
  25. The maintenance of biological systems requires plasticity and robustness. The function of the ecdysone receptor, a heterodimer composed of the nuclear receptors ECR (NR1H1) and USP (NR2B4), was maintained in i...

    Authors: Arnaud Chaumot, Jean-Luc Da Lage, Oscar Maestro, David Martin, Thomas Iwema, Frederic Brunet, Xavier Belles, Vincent Laudet and François Bonneton
    Citation: BMC Evolutionary Biology 2012 12:199
  26. Among multigene families, ribosomal RNA (rRNA) genes are the most frequently studied and have been explored as cytogenetic markers to study the evolutionary history of karyotypes among animals and plants. In t...

    Authors: Rafael T Nakajima, Diogo C Cabral-de-Mello, Guilherme T Valente, Paulo C Venere and Cesar Martins
    Citation: BMC Evolutionary Biology 2012 12:198
  27. Calpains are Ca2+-dependent cysteine proteases that participate in a range of crucial cellular processes. Dysfunction of these enzymes may cause, for instance, life-threatening diseases in humans, the loss of sex...

    Authors: Sen Zhao, Zhe Liang, Viktor Demko, Robert Wilson, Wenche Johansen, Odd-Arne Olsen and Kamran Shalchian-Tabrizi
    Citation: BMC Evolutionary Biology 2012 12:193
  28. Proteins evolve at disparate rates, as a result of the action of different types and strengths of evolutionary forces. An open question in evolutionary biology is what factors are responsible for this variabil...

    Authors: David Alvarez-Ponce
    Citation: BMC Evolutionary Biology 2012 12:192
  29. Type II antifreeze protein (AFP) from the rainbow smelt, Osmerus mordax, is a calcium-dependent C-type lectin homolog, similar to the AFPs from herring and sea raven. While C-type lectins are ubiquitous, type II ...

    Authors: Laurie A Graham, Jieying Li, William S Davidson and Peter L Davies
    Citation: BMC Evolutionary Biology 2012 12:190
  30. The large Glycoside Hydrolase family 5 (GH5) groups together a wide range of enzymes acting on β-linked oligo- and polysaccharides, and glycoconjugates from a large spectrum of organisms. The long and complex ...

    Authors: Henrik Aspeborg, Pedro M Coutinho, Yang Wang, Harry Brumer III and Bernard Henrissat
    Citation: BMC Evolutionary Biology 2012 12:186
  31. Small nucleolar (sno)RNAs are required for posttranscriptional processing and modification of ribosomal, spliceosomal and messenger RNAs. Their presence in both eukaryotes and archaea indicates that snoRNAs ar...

    Authors: Marc P Hoeppner and Anthony M Poole
    Citation: BMC Evolutionary Biology 2012 12:183
  32. The Escherichia coli species contains a variety of commensal and pathogenic strains, and its intraspecific diversity is extraordinarily high. With the availability of an increasing number of E. coli strain genome...

    Authors: Yan Zhang and Kui Lin
    Citation: BMC Evolutionary Biology 2012 12:174
  33. The basic helix-loop-helix (bHLH) transcription factors and their homologs form a superfamily that plays essential roles in transcriptional networks of multiple developmental processes. bHLH family members hav...

    Authors: Ake Liu, Yong Wang, Chunwang Dang, Debao Zhang, Huifang Song, Qin Yao and Keping Chen
    Citation: BMC Evolutionary Biology 2012 12:165
  34. The amount of transcription factor binding sites (TFBS) in an organism’s genome positively correlates with the complexity of the regulatory network of the organism. However, the manner by which TFBS arise and ...

    Authors: Troy Ruths and Luay Nakhleh
    Citation: BMC Evolutionary Biology 2012 12:159
  35. The discovery of giant viruses with genome and physical size comparable to cellular organisms, remnants of protein translation machinery and virus-specific parasites (virophages) have raised intriguing questio...

    Authors: Arshan Nasir, Kyung Mo Kim and Gustavo Caetano-Anolles
    Citation: BMC Evolutionary Biology 2012 12:156
  36. Short chain dehydrogenases/reductases (SDR) are NAD(P)(H)-dependent oxidoreductases with a highly conserved 3D structure and of an early origin, which has allowed them to diverge into several families and enzy...

    Authors: Agustín Sola-Carvajal, María I García-García, Francisco García-Carmona and Álvaro Sánchez-Ferrer
    Citation: BMC Evolutionary Biology 2012 12:147
  37. The highly improved cognitive function is the most significant change in human evolutionary history. Recently, several large-scale studies reported the evolutionary roles of DNA methylation; however, the role ...

    Authors: Jinkai Wang, Xiangyu Cao, Yanfeng Zhang and Bing Su
    Citation: BMC Evolutionary Biology 2012 12:144
  38. Proteins of the mammalian PYHIN (IFI200/HIN-200) family are involved in defence against infection through recognition of foreign DNA. The family member absent in melanoma 2 (AIM2) binds cytosolic DNA via its H...

    Authors: Jasmyn A Cridland, Eva Z Curley, Michelle N Wykes, Kate Schroder, Matthew J Sweet, Tara L Roberts, Mark A Ragan, Karin S Kassahn and Katryn J Stacey
    Citation: BMC Evolutionary Biology 2012 12:140
  39. The glucosinolate-myrosinase system is an activated chemical defense system found in plants of the Brassicales order. Glucosinolates are stored separately from their hydrolytic enzymes, the myrosinases, in pla...

    Authors: Jennifer C Kuchernig, Meike Burow and Ute Wittstock
    Citation: BMC Evolutionary Biology 2012 12:127
  40. Despite recent progress in studies of the evolution of protein function, the questions what were the first functional protein domains and what were their basic building blocks remain unresolved. Previously, we...

    Authors: Alexander Goncearenco and Igor N Berezovsky
    Citation: BMC Evolutionary Biology 2012 12:75
  41. The entire evolutionary history of life can be studied using myriad sequences generated by genomic research. This includes the appearance of the first cells and of superkingdoms Archaea, Bacteria, and Eukarya....

    Authors: Kyung Mo Kim and Gustavo Caetano-Anollés
    Citation: BMC Evolutionary Biology 2012 12:13
  42. Comparative genomics can inform us about the processes of mutation and selection across diverse taxa. Among seed plants, gymnosperms have been lacking in genomic comparisons. Recent EST and full-length cDNA co...

    Authors: Emmanuel Buschiazzo, Carol Ritland, Jörg Bohlmann and Kermit Ritland
    Citation: BMC Evolutionary Biology 2012 12:8
  43. Elucidating the selective and neutral forces underlying molecular evolution is fundamental to understanding the genetic basis of adaptation. Plants have evolved a suite of adaptive responses to cope with varia...

    Authors: Lino Ometto, Mingai Li, Luisa Bresadola and Claudio Varotto
    Citation: BMC Evolutionary Biology 2012 12:7
  44. Protein domains are the structural, functional and evolutionary units of the protein. Protein domain architectures are the linear arrangements of domain(s) in individual proteins. Although the evolutionary his...

    Authors: Xue-Cheng Zhang, Zheng Wang, Xinyan Zhang, Mi Ha Le, Jianguo Sun, Dong Xu, Jianlin Cheng and Gary Stacey
    Citation: BMC Evolutionary Biology 2012 12:6

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