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  1. The phylum Verrucomicrobia is a widespread but poorly characterized bacterial clade. Although cultivation-independent approaches detect representatives of this phylum in a wide range of environments, including so...

    Authors: Shaobin Hou, Kira S Makarova, Jimmy HW Saw, Pavel Senin, Benjamin V Ly, Zhemin Zhou, Yan Ren, Jianmei Wang, Michael Y Galperin, Marina V Omelchenko, Yuri I Wolf, Natalya Yutin, Eugene V Koonin, Matthew B Stott, Bruce W Mountain, Michelle A Crowe…

    Citation: Biology Direct 2008 3:26

    Content type: Research

    Published on:

  2. The original spotted array technology with competitive hybridization of two experimental samples and measuring relative expression levels is increasingly displaced by more accurate platforms that allow determi...

    Authors: Wing-Cheong Wong, Marie Loh and Frank Eisenhaber

    Citation: Biology Direct 2008 3:23

    Content type: Research

    Published on:

  3. We report that the positions of minor, U12 introns are conserved in orthologous genes from human and Arabidopsis to an even greater extent than the positions of the major, U2 introns. The U12 introns, especially,...

    Authors: Malay Kumar Basu, Wojciech Makalowski, Igor B Rogozin and Eugene V Koonin

    Citation: Biology Direct 2008 3:19

    Content type: Discovery notes

    Published on:

  4. 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

    Content type: Research

    Published on:

  5. 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

    Content type: Research

    Published on:

  6. 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

    Content type: Research

    Published on:

  7. 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

    Content type: Research

    Published on:

  8. 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

    Content type: Discovery notes

    Published on:

  9. 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

    Content type: Research

    Published on:

  10. 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

    Content type: Research

    Published on:

  11. 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

    Content type: Review

    Published on:

  12. 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

    Content type: Discovery notes

    Published on:

  13. 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

    Content type: Discovery notes

    Published on:

  14. 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

    Content type: Research

    Published on:

  15. 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

    Content type: Research

    Published on:

  16. 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

    Content type: Research

    Published on:

  17. 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

    Content type: Review

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  18. 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

    Content type: Research

    Published on:

  19. 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

    Content type: Research

    Published on:

  20. 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

    Content type: Research

    Published on:

  21. 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

    Content type: Research

    Published on:

  22. 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

    Content type: Research

    Published on:

  23. 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

    Content type: Research

    Published on:

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