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  2. Divergence of two independently evolving sequences that originated from a common ancestor can be described by two parameters, the asymptotic level of divergence E and the rate r at which this level of divergence ...

    Authors: Alexey S Kondrashov, Inna S Povolotskaya, Dmitry N Ivankov and Fyodor A Kondrashov
    Citation: Biology Direct 2010 5:5
    Content type: Research Published on:

  3. In several studies, secondary structures of ribosomal genes have been used to improve the quality of phylogenetic reconstructions. An extensive evaluation of the benefits of secondary structure, however, is la...

    Authors: Alexander Keller, Frank Förster, Tobias Müller, Thomas Dandekar, Jörg Schultz and Matthias Wolf
    Citation: Biology Direct 2010 5:4
    Content type: Research Published on:

  4. The bacterial elongation factor P (EF-P) is strictly conserved in bacteria and essential for protein synthesis. It is homologous to the eukaryotic translation initiation factor 5A (eIF5A). A highly conserved e...

    Authors: Marc Bailly and Valérie de Crécy-Lagard
    Citation: Biology Direct 2010 5:3
    Content type: Hypothesis Published on:

  6. Eukaryotic extracellular matrices such as proteoglycans, sclerotinized structures, mucus, external tests, capsules, cell walls and waxes contain highly modified proteins, glycans and other composite biopolymer...

    Authors: Vivek Anantharaman and L Aravind
    Citation: Biology Direct 2010 5:1
    Content type: Discovery notes Published on:

  8. Ribonucleotide reductase is the main control point of dNTP production. It has two subunits, R1, and R2 or p53R2. R1 has 5 possible catalytic site states (empty or filled with 1 of 4 NDPs), 5 possible s-site state...

    Authors: Tomas Radivoyevitch
    Citation: Biology Direct 2009 4:50
    Content type: Research Published on:

  10. A total of 929 polymorphic SNPs in EB (out of 54, 000 SNPs screened using a BovineSNP50 Illumina Genotyping BeadChip), and 1, 524 and 1, 403 polymorphic SNPs in WB and PB, respectively, were analysed. EB, WB a...

    Authors: Cino Pertoldi, Małgorzata Tokarska, Jan M Wójcik, Ditte Demontis, Volker Loeschcke, Vivi R Gregersen, David Coltman, Gregory A Wilson, Ettore Randi, Michael M Hansen and Christian Bendixen
    Citation: Biology Direct 2009 4:48
    Content type: Discovery notes Published on:

  11. The γδ T cells serve as early immune defense against certain encountered microbes. Only a few γδ T cell-recognized ligands from microbial antigens have been identified so far and the mechanisms by which γδ T c...

    Authors: Yongchun Cui, Lei Kang, Lianxian Cui and Wei He
    Citation: Biology Direct 2009 4:47
    Content type: Research Published on:

  12. Sequence related families of genes and proteins are common in bacterial genomes. In Escherichia coli they constitute over half of the genome. The presence of families and superfamilies of proteins suggest a hi...

    Authors: Margrethe H Serres, Alastair RW Kerr, Thomas J McCormack and Monica Riley
    Citation: Biology Direct 2009 4:46
    Content type: Research Published on:

  15. It is well-known that Charles Darwin sketched abstract trees of relationship in his 1837 notebook, and depicted a tree in the Origin of Species (1859). Here I attempt to place Darwin's trees in historical context...

    Authors: Mark A Ragan
    Citation: Biology Direct 2009 4:43
    Content type: Review Published on:

  16. The year 2009 is the 200th anniversary of the publication of Jean-Bapteste Lamarck's Philosophie Zoologique and the 150th anniversary of Charles Darwin's On the Origin of Species. Lamarck believed that evolution ...

    Authors: Eugene V Koonin and Yuri I Wolf
    Citation: Biology Direct 2009 4:42
    Content type: Opinion Published on:

  18. CD4+CD25+ regulatory T (Treg) cells develop in the thymus and can suppress T cell proliferation, modulated by Foxp3 and cytokines; however, the relevance of CD44 in Treg cell development is less clear. To address...

    Authors: Tie Liu, Lynn Soong, Gang Liu, Rolf König and Ashok K Chopra
    Citation: Biology Direct 2009 4:40
    Content type: Research Published on:

  19. One of the hallmarks of eukaryotic information processing is the co-existence of 3 distinct, multi-subunit RNA polymerase complexes that are dedicated to the transcription of specific classes of coding or non-...

    Authors: Fabian Blombach, Kira S Makarova, Jeannette Marrero, Bettina Siebers, Eugene V Koonin and John van der Oost
    Citation: Biology Direct 2009 4:39
    Content type: Discovery notes Published on:

  21. We have previously shown that deviations from the average transcription profile of a group of functionally related genes are not only heritable, but also demonstrate specific patterns associated with age, gend...

    Authors: Johannes WIM Simons
    Citation: Biology Direct 2009 4:37
    Content type: Research Published on:

  24. The concept of a tree of life is prevalent in the evolutionary literature. It stems from attempting to obtain a grand unified natural system that reflects a recurrent process of species and lineage splittings ...

    Authors: Eric Bapteste, Maureen A O'Malley, Robert G Beiko, Marc Ereshefsky, J Peter Gogarten, Laura Franklin-Hall, François-Joseph Lapointe, John Dupré, Tal Dagan, Yan Boucher and William Martin
    Citation: Biology Direct 2009 4:34
    Content type: Review Published on:

  27. Multipotent adult germ-line stem cells (maGSCs) represent a new pluripotent cell type that can be derived without genetic manipulation from spermatogonial stem cells (SSCs) present in adult testis. Similarly t...

    Authors: Ralf Dressel, Kaomei Guan, Jessica Nolte, Leslie Elsner, Sebastian Monecke, Karim Nayernia, Gerd Hasenfuss and Wolfgang Engel
    Citation: Biology Direct 2009 4:31
    Content type: Research Published on:

  29. In eukaryotes, RNA interference (RNAi) is a major mechanism of defense against viruses and transposable elements as well of regulating translation of endogenous mRNAs. The RNAi systems recognize the target RNA...

    Authors: Kira S Makarova, Yuri I Wolf, John van der Oost and Eugene V Koonin
    Citation: Biology Direct 2009 4:29
    Content type: Hypothesis Published on:

  31. The accompanying article (A.Y. Mulkidjanian, Biology Direct 4:26) puts forward a detailed hypothesis on the role of zinc sulfide (ZnS) in the origin of life on Earth. The hypothesis suggests that life emerged wit...

    Authors: Armen Y Mulkidjanian and Michael Y Galperin
    Citation: Biology Direct 2009 4:27
    Content type: Research Published on:

  32. The complexity of the problem of the origin of life has spawned a large number of possible evolutionary scenarios. Their number, however, can be dramatically reduced by the simultaneous consideration of variou...

    Authors: Armen Y Mulkidjanian
    Citation: Biology Direct 2009 4:26
    Content type: Hypothesis Published on:

  33. The Anabaena sensory rhodopsin transducer (ASRT) is a small protein that has been claimed to function as a signaling molecule downstream of the cyanobacterial sensory rhodopsin. However, orthologs of ASRT have be...

    Authors: Robson F De Souza, Lakshminarayan M Iyer and L Aravind
    Citation: Biology Direct 2009 4:25
    Content type: Discovery notes Published on:

  34. The transcription machineries of Archaea and eukaryotes are similar in many aspects, but little is understood about archaeal chromatin and its role in transcription. Here, we describe the identification in hyp...

    Authors: Jan-Peter Daniels, Steven Kelly, Bill Wickstead and Keith Gull
    Citation: Biology Direct 2009 4:24
    Content type: Discovery notes Published on:

  37. Previous studies have revealed a wide-spread occurence of the partial and complete genomes of the reverse-transcribing pararetroviruses in the nuclear genomes of herbaceous plants. Although the absence of the ...

    Authors: Christophe Bertsch, Monique Beuve, Valerian V Dolja, Marion Wirth, Frédérique Pelsy, Etienne Herrbach and Olivier Lemaire
    Citation: Biology Direct 2009 4:21
    Content type: Hypothesis Published on:

  39. The prokaryotic toxin-antitoxin systems (TAS, also referred to as TA loci) are widespread, mobile two-gene modules that can be viewed as selfish genetic elements because they evolved mechanisms to become addic...

    Authors: Kira S Makarova, Yuri I Wolf and Eugene V Koonin
    Citation: Biology Direct 2009 4:19
    Content type: Research Published on:

  40. In this work, we study the consequences of sequence variations of the "2009 H1N1" (swine or Mexican flu) influenza A virus strain neuraminidase for drug treatment and vaccination. We find that it is phylogenet...

    Authors: Sebastian Maurer-Stroh, Jianmin Ma, Raphael Tze Chuen Lee, Fernanda L Sirota and Frank Eisenhaber
    Citation: Biology Direct 2009 4:18
    Content type: Discovery notes Published on:

  47. Evolution of DNA polymerases, the key enzymes of DNA replication and repair, is central to any reconstruction of the history of cellular life. However, the details of the evolutionary relationships between DNA...

    Authors: Tahir H Tahirov, Kira S Makarova, Igor B Rogozin, Youri I Pavlov and Eugene V Koonin
    Citation: Biology Direct 2009 4:11
    Content type: Research Published on:

  49. Phagocytosis, that is, engulfment of large particles by eukaryotic cells, is found in diverse organisms and is often thought to be central to the very origin of the eukaryotic cell, in particular, for the acqu...

    Authors: Natalya Yutin, Maxim Y Wolf, Yuri I Wolf and Eugene V Koonin
    Citation: Biology Direct 2009 4:9
    Content type: Research Published on:

  50. The fatty acids of anaerobic ammonium oxidizing (anammox) bacteria contain linearly concatenated cyclobutane moieties, so far unique to biology. These moieties are under high ring strain and are synthesised by...

    Authors: Jayne E Rattray, Marc Strous, Huub JM Op den Camp, Stefan Schouten, Mike SM Jetten and Jaap S Sinninghe Damsté
    Citation: Biology Direct 2009 4:8
    Content type: Research Published on:
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Biology Direct

ISSN: 1745-6150

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