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  1. The mechanism underlying autoimmune diabetes has been difficult to define. There is a strong genetic contribution and numerous studies associate the major histocompatibility complex, especially the class II re...

    Authors: Christian S Parry and Bernard R Brooks
    Citation: Biology Direct 2008 3:42
  2. Transposable elements may acquire unrelated gene fragments into their sequences in a process called transduplication. Transduplication of protein-coding genes is common in plants, but is unknown of in animals....

    Authors: Noa Sela, Adi Stern, Wojciech Makalowski, Tal Pupko and Gil Ast
    Citation: Biology Direct 2008 3:41
  3. Proteins show a broad range of evolutionary rates. Understanding the factors that are responsible for the characteristic rate of evolution of a given protein arguably is one of the major goals of evolutionary ...

    Authors: Maxim Y Wolf, Yuri I Wolf and Eugene V Koonin
    Citation: Biology Direct 2008 3:40
  4. Using sequence profile methods and structural comparisons we characterize a previously unknown family of nucleic acid polymerases in a group of mobile elements from genomes of diverse bacteria, an algal plasti...

    Authors: Lakshminarayan M Iyer, Saraswathi Abhiman and L Aravind
    Citation: Biology Direct 2008 3:39
  5. The Codon Adaptation Index (CAI) was first developed to measure the synonymous codon usage bias for a DNA or RNA sequence. The CAI quantifies the similarity between the synonymous codon usage of a gene and the...

    Authors: Pere Puigbò, Ignacio G Bravo and Santiago Garcia-Vallve
    Citation: Biology Direct 2008 3:38
  6. Upon repeated or chronic antigen stimulation, activated T cells undergo a T cell receptor (TCR)-triggered propriocidal cell death important for governing the intensity of immune responses. This is thought to b...

    Authors: Andrew L Snow, João B Oliveira, Lixin Zheng, Janet K Dale, Thomas A Fleisher and Michael J Lenardo
    Citation: Biology Direct 2008 3:34
  7. The simplest conceivable example of evolving systems is RNA molecules that can replicate themselves. Since replication produces a new RNA strand complementary to a template, all templates would eventually beco...

    Authors: Nobuto Takeuchi, Laura Salazar, Anthony M Poole and Paulien Hogeweg
    Citation: Biology Direct 2008 3:33
  8. The GT dinucleotide in the first two intron positions is the most conserved element of the U2 donor splice signals. However, in a small fraction of donor sites, GT is replaced by GC. A substantial enrichment o...

    Authors: Alexander Churbanov, Stephen Winters-Hilt, Eugene V Koonin and Igor B Rogozin
    Citation: Biology Direct 2008 3:30
  9. Members of the green fluorescent protein (GFP) family share sequence similarity and the 11-stranded β-barrel fold. Fluorescence or bright coloration, observed in many members of this family, is enabled by the ...

    Authors: Diana Baumann, Malcolm Cook, Limei Ma, Arcady Mushegian, Erik Sanders, Joel Schwartz and C Ron Yu
    Citation: Biology Direct 2008 3:28
  10. Current experimental techniques, especially those applying liquid chromatography mass spectrometry, have made high-throughput proteomic studies possible. The increase in throughput however also raises concerns...

    Authors: Gelio Alves, Aleksey Y Ogurtsov, Siwei Kwok, Wells W Wu, Guanghui Wang, Rong-Fong Shen and Yi-Kuo Yu
    Citation: Biology Direct 2008 3:27
  11. 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
  12. 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
  13. 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
  14. 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
  15. 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
  16. 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
  17. 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
  18. 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
  19. 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
  20. 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
  21. 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
  22. 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
  23. 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
  24. 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
  25. 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

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