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  1. The pioneering ancestor of land plants that conquered terrestrial habitats around 500 million years ago had to face dramatic stresses including UV radiation, desiccation, and microbial attack. This drove a num...

    Authors: Giovanni Emiliani, Marco Fondi, Renato Fani and Simonetta Gribaldo
    Citation: Biology Direct 2009 4:7
    Content type: Research Published on:

  2. Quorum sensing (QS) is a form of gene regulation based on cell-density that depends on inter-cellular communication. While there are a variety of models for bacterial colony morphology, there is little work li...

    Authors: Sergiu Netotea, Iris Bertani, Laura Steindler, Ádám Kerényi, Vittorio Venturi and Sándor Pongor
    Citation: Biology Direct 2009 4:6
    Content type: Research Published on:

  3. β-catenin is a dual function adhesion/transcriptional co-activator protein, and both functions are critical for normal tissue homeostasis. Since the transcriptional functions of β-catenin are more often implic...

    Authors: Meghan T Maher, Annette S Flozak, Alyssa M Hartsell, Susan Russell, Rohinee Beri, Ofra N Peled and Cara J Gottardi
    Citation: Biology Direct 2009 4:5
    Content type: Research Published on:

  7. Staphylococcus aureus is a major human pathogen responsible for a variety of nosocomial and community-acquired infections. Recent reports show that the prevalence of Methicillin-Resistant S. aureus (MRSA) infecti...

    Authors: Jean-Marc Rolain, Patrice François, David Hernandez, Fadi Bittar, Hervé Richet, Ghislain Fournous, Yves Mattenberger, Emmanuelle Bosdure, Nathalie Stremler, Jean-Christophe Dubus, Jacques Sarles, Martine Reynaud-Gaubert, Stephanie Boniface, Jacques Schrenzel and Didier Raoult
    Citation: Biology Direct 2009 4:1
    Content type: Research Published on:

  8. DNA topoisomerase IB (TopoIB) was thought for a long time to be a eukaryotic specific enzyme. A shorter version was then found in viruses and later on in several bacteria, but not in archaea. Here, we show tha...

    Authors: Céline Brochier-Armanet, Simonetta Gribaldo and Patrick Forterre
    Citation: Biology Direct 2008 3:54
    Content type: Discovery notes Published on:

  12. Within the bilaterians, the appearance and evolution of vertebrates is accompanied by enormous changes in anatomical, morphological and developmental features. This evolution of increased complexity has been a...

    Authors: Amir Ali Abbasi
    Citation: Biology Direct 2008 3:50
    Content type: Hypothesis Published on:

  14. Maelstrom (MAEL) plays a crucial role in a recently-discovered piRNA pathway; however its specific function remains unknown. Here a novel MAEL-specific domain characterized by a set of conserved residues (Glu-...

    Authors: Dapeng Zhang, Huiling Xiong, Jufang Shan, Xuhua Xia and Vance L Trudeau
    Citation: Biology Direct 2008 3:48
    Content type: Discovery notes Published on:

  15. The nature of size fluctuations is crucial in forecasting future population persistence, independently of whether the variability stems from external forces or from the dynamics of the population renewal proce...

    Authors: Cino Pertoldi, Lars A Bach and Volker Loeschcke
    Citation: Biology Direct 2008 3:47
    Content type: Hypothesis Published on:

  20. 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
    Content type: Hypothesis Published on:

  21. 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
    Content type: Discovery notes Published on:

  22. 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
    Content type: Research Published on:

  23. 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
    Content type: Discovery notes Published on:

  24. 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
    Content type: Research Published on:

  28. 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
    Content type: Research Published on:

  29. 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
    Content type: Research Published on:

  32. 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
    Content type: Discovery notes Published on:

  34. 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
    Content type: Research Published on:

  35. 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
    Content type: Research Published on:

  36. 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:

  39. 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:

  43. 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:

  44. 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:

  46. 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:

  49. 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:
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Biology Direct

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