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  1. The evolution of complex molecular traits such as disulphide bridges often requires multiple mutations. The intermediate steps in such evolutionary trajectories are likely to be selectively neutral or deleteri...

    Authors: Dion J Whitehead, Claus O Wilke, David Vernazobres and Erich Bornberg-Bauer
    Citation: Biology Direct 2008 3:18
  2. The origin and early evolution of the active site of the ribosome can be elucidated through an analysis of the ribosomal proteins' taxonomic block structures and their RNA interactions. Comparison between the ...

    Authors: Temple F Smith, Jung C Lee, Robin R Gutell and Hyman Hartman
    Citation: Biology Direct 2008 3:16
  3. The F- and V-type ATPases are rotary molecular machines that couple translocation of protons or sodium ions across the membrane to the synthesis or hydrolysis of ATP. Both the F-type (found in most bacteria an...

    Authors: Armen Y Mulkidjanian, Michael Y Galperin, Kira S Makarova, Yuri I Wolf and Eugene V Koonin
    Citation: Biology Direct 2008 3:13
  4. The evolution of complexity is among the most important questions in biology. The evolution of complexity is often observed as the increase of genetic information or that of the organizational complexity of a ...

    Authors: Nobuto Takeuchi and Paulien Hogeweg
    Citation: Biology Direct 2008 3:11
  5. We analyzed the chicken (Gallus gallus) genome sequence to search for previously uncharacterized endogenous retrovirus (ERV) sequences using ab initio and combined evidence approaches. We discovered 11 novel fami...

    Authors: Ahsan Huda, Nalini Polavarapu, I King Jordan and John F McDonald
    Citation: Biology Direct 2008 3:9
  6. Rare genomic changes (RGCs) that are thought to comprise derived shared characters of individual clades are becoming an increasingly important class of markers in genome-wide phylogenetic studies. Recently, we...

    Authors: Igor B Rogozin, Karen Thomson, Miklós Csürös, Liran Carmel and Eugene V Koonin
    Citation: Biology Direct 2008 3:7
  7. CD4+CD25+Foxp3+ regulatory T (Treg) cells are believed to play an important role in suppressing autoimmunity and maintaining peripheral tolerance. How their survival is regulated in the periphery is less clear. H...

    Authors: Pushpa Pandiyan and Michael J Lenardo
    Citation: Biology Direct 2008 3:6
  8. Molecular chaperones help to restore the native states of proteins after their destabilization by external stress. It has been proposed that another function of chaperones is to maintain the activity of protei...

    Authors: Katarzyna Tomala and Ryszard Korona
    Citation: Biology Direct 2008 3:5
  9. Intracellular vesicle traffic that enables delivery of proteins between the endoplasmic reticulum, Golgi and various endosomal subcompartments is one of the hallmarks of the eukaryotic cell. Its evolutionary h...

    Authors: Mircea Podar, Mark A Wall, Kira S Makarova and Eugene V Koonin
    Citation: Biology Direct 2008 3:2
  10. Although most of the key components of the transcription apparatus, and in particular, RNA polymerase (RNAP) subunits, are conserved between archaea and eukaryotes, no archaeal homologs of the small RPB8 subun...

    Authors: Eugene V Koonin, Kira S Makarova and James G Elkins
    Citation: Biology Direct 2007 2:38
  11. All standard methods for cDNA cloning are affected by a potential inability to effectively clone the 5' region of mRNA. The aim of this work was to estimate mRNA open reading frame (ORF) 5' region sequence com...

    Authors: Flavia Frabetti, Raffaella Casadei, Luca Lenzi, Silvia Canaider, Lorenza Vitale, Federica Facchin, Paolo Carinci, Maria Zannotti and Pierluigi Strippoli
    Citation: Biology Direct 2007 2:34
  12. An evolutionary classification of genes from sequenced genomes that distinguishes between orthologs and paralogs is indispensable for genome annotation and evolutionary reconstruction. Shortly after multiple g...

    Authors: Kira S Makarova, Alexander V Sorokin, Pavel S Novichkov, Yuri I Wolf and Eugene V Koonin
    Citation: Biology Direct 2007 2:33
  13. Transposable element (TE) sequences, once thought to be merely selfish or parasitic members of the genomic community, have been shown to contribute a wide variety of functional sequences to their host genomes....

    Authors: Jittima Piriyapongsa, Mark T Rutledge, Sanil Patel, Mark Borodovsky and I King Jordan
    Citation: Biology Direct 2007 2:31
  14. The last third of the 20th Century featured an accumulation of research findings that severely challenged the assumptions of the "Modern Synthesis" which provided the foundations for most biological research duri...

    Authors: Michael R Rose and Todd H Oakley
    Citation: Biology Direct 2007 2:30
  15. This work was undertaken in response to a recently published paper by Okoniewski and Miller (BMC Bioinformatics 2006, 7: Article 276). The authors of that paper came to the conclusion that the process of multiple...

    Authors: Lev Klebanov, Linlin Chen and Andrei Yakovlev
    Citation: Biology Direct 2007 2:28
  16. One objective of metagenomics is to reconstruct information about specific uncultured organisms from fragmentary environmental DNA sequences. We used the genome of an isolate of the marine alphaproteobacterium...

    Authors: Larry J Wilhelm, H James Tripp, Scott A Givan, Daniel P Smith and Stephen J Giovannoni
    Citation: Biology Direct 2007 2:27
  17. The key to mass-spectrometry-based proteomics is peptide identification, which relies on software analysis of tandem mass spectra. Although each search engine has its strength, combining the strengths of vario...

    Authors: Gelio Alves, Aleksey Y Ogurtsov, Wells W Wu, Guanghui Wang, Rong-Fong Shen and Yi-Kuo Yu
    Citation: Biology Direct 2007 2:26
  18. The standard genetic code table has a distinctly non-random structure, with similar amino acids often encoded by codons series that differ by a single nucleotide substitution, typically, in the third or the fi...

    Authors: Artem S Novozhilov, Yuri I Wolf and Eugene V Koonin
    Citation: Biology Direct 2007 2:24
  19. Recent comparative genomic studies claim local syntenic gene-interleaving relationships in Ashbya gossypii and Kluyveromyces waltii are compelling evidence for an ancient whole-genome duplication event in Sacchar...

    Authors: Nicolas Martin, Elizabeth A Ruedi, Richard LeDuc, Feng-Jie Sun and Gustavo Caetano-Anollés
    Citation: Biology Direct 2007 2:23
  20. Independently evolving lineages mostly accumulate different changes, which leads to their gradual divergence. However, parallel accumulation of identical changes is also common, especially in traits with only ...

    Authors: Georgii A Bazykin, Fyodor A Kondrashov, Michael Brudno, Alexander Poliakov, Inna Dubchak and Alexey S Kondrashov
    Citation: Biology Direct 2007 2:20
  21. The origin of the translation system is, arguably, the central and the hardest problem in the study of the origin of life, and one of the hardest in all evolutionary biology. The problem has a clear catch-22 a...

    Authors: Yuri I Wolf and Eugene V Koonin
    Citation: Biology Direct 2007 2:14
  22. Both mechanistic features and recent correlative findings suggest a potential role for protein kinase C-beta (PKC-β) in tumor pathogenesis, particularly in B-cell malignancies. To evaluate the role of this gen...

    Authors: Shuyu Li, Mark Phong, Michael Lahn, Leslie Brail, Susan Sutton, Boris K Lin, Donald Thornton and Birong Liao
    Citation: Biology Direct 2007 2:8

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