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  1. Understanding the origin of protein synthesis has been notoriously difficult. We have taken as a starting premise Wolf and Koonin's view that "evolution of the translation system is envisaged to occur in a com...

    Authors: Harold S Bernhardt and Warren P Tate

    Citation: Biology Direct 2010 5:16

    Content type: Hypothesis

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  2. The mechanism by which the arthropod Oskar and vertebrate TDRD5/TDRD7 proteins nucleate or organize structurally related ribonucleoprotein (RNP) complexes, the polar granule and nuage, is poorly understood. Us...

    Authors: Vivek Anantharaman, Dapeng Zhang and L Aravind

    Citation: Biology Direct 2010 5:13

    Content type: Discovery notes

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  3. Attempts to engage the scientific community to annotate biological data (such as protein/gene function) stored in databases have not been overly successful. There are several hypotheses on why this has not bee...

    Authors: Raja Mazumder, Darren A Natale, Jessica Anne Ecalnir Julio, Lai-Su Yeh and Cathy H Wu

    Citation: Biology Direct 2010 5:12

    Content type: Opinion

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  4. The success of invertebrates throughout evolution is an excellent illustration of the efficiency of their defence strategies. Caenorhabditis elegans has proven to be an appropriate model for transcriptome studies...

    Authors: Annelies Bogaerts, Isabel Beets, Liesbet Temmerman, Liliane Schoofs and Peter Verleyen

    Citation: Biology Direct 2010 5:11

    Content type: Research

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  5. The Z-curve is a three dimensional representation of DNA sequences proposed over a decade ago and has been extensively applied to sequence segmentation, horizontal gene transfer detection, and sequence analysi...

    Authors: Eran Elhaik, Dan Graur and Krešimir Josić

    Citation: Biology Direct 2010 5:10

    Content type: Research

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  6. The transcription factor FOXP3 is essential for the development and function of CD4+CD25hiFOXP3+ regulatory T (Treg) cells, but also expressed in activated human helper T cells without acquisition of a regulatory...

    Authors: Michael Probst-Kepper and Jan Buer

    Citation: Biology Direct 2010 5:8

    Content type: Comment

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  7. 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

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  8. 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

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  9. 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

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  10. 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:

  11. 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

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  12. 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:

  13. 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

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  14. 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

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  15. 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

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  16. 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

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  17. 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:

  18. 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

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  19. 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:

  20. 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

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  21. 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

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  22. 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:

  23. 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:

  24. 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:

  25. 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:

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