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  1. 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:

  2. 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:

  3. 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:

  4. 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:

  5. 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:

  6. 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:

  7. 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:

  8. 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:

  9. 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:

  10. 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:

  11. 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:

  12. 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:

  13. 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:

  14. 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:

  15. 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:

  16. 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:

  17. 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:

  18. 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:

  19. 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:

  20. 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:

  21. 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:

  22. 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:

  23. 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:

  24. 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:

  25. 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:

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