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  3. Molecular markers based on gene expression profiles have been used in experimental and clinical settings to distinguish cancerous tumors in stage, grade, survival time, metastasis, and drug sensitivity. Howeve...

    Authors: Shinuk Kim, Mark Kon and Charles DeLisi
    Citation: Biology Direct 2012 7:21
    Content type: Research Published on:

  6. Proteinaceous toxins are observed across all levels of inter-organismal and intra-genomic conflicts. These include recently discovered prokaryotic polymorphic toxin systems implicated in intra-specific conflic...

    Authors: Dapeng Zhang, Robson F de Souza, Vivek Anantharaman, Lakshminarayan M Iyer and L Aravind
    Citation: Biology Direct 2012 7:18
    Content type: Research Published on:

  7. Viruses are known to be the most abundant organisms on earth, yet little is known about their collective origin and evolutionary history. With exceptionally high rates of genetic mutation and mosaicism, it is ...

    Authors: Geoffrey S Diemer and Kenneth M Stedman
    Citation: Biology Direct 2012 7:13
    Content type: Research Published on:

  8. Single nucleotide polymorphisms (SNPs) are the most abundant type of genetic variation in eukaryotic genomes and have recently become the marker of choice in a wide variety of ecological and evolutionary studi...

    Authors: Jinzhuang Dou, Xiqiang Zhao, Xiaoteng Fu, Wenqian Jiao, Nannan Wang, Lingling Zhang, Xiaoli Hu, Shi Wang and Zhenmin Bao
    Citation: Biology Direct 2012 7:17
    Content type: Research Published on:

  10. MicroRNAs (miRNAs) are endogenous small non-coding RNAs of about 20–24 nt, known to play key roles in post-transcriptional gene regulation, that can be coded either by intergenic or intragenic loci. Intragenic...

    Authors: Moreno Colaiacovo, Antonella Lamontanara, Letizia Bernardo, Renzo Alberici, Cristina Crosatti, Lorenzo Giusti, Luigi Cattivelli and Primetta Faccioli
    Citation: Biology Direct 2012 7:15
    Content type: Discovery notes Published on:

  11. mtRF1 is a vertebrate mitochondrial protein with an unknown function that arose from a duplication of the mitochondrial release factor mtRF1a. To elucidate the function of mtRF1, we determined the positions th...

    Authors: Martijn A Huynen, Isabel Duarte, Zofia M A Chrzanowska-Lightowlers and Sander B Nabuurs
    Citation: Biology Direct 2012 7:14
    Content type: Research Published on:

  12. BLAST is a commonly-used software package for comparing a query sequence to a database of known sequences; in this study, we focus on protein sequences. Position-specific-iterated BLAST (PSI-BLAST) iteratively...

    Authors: Grzegorz M Boratyn, Alejandro A Schäffer, Richa Agarwala, Stephen F Altschul, David J Lipman and Thomas L Madden
    Citation: Biology Direct 2012 7:12
    Content type: Research Published on:

  13. Evolution of exon-intron structure of eukaryotic genes has been a matter of long-standing, intensive debate. The introns-early concept, later rebranded ‘introns first’ held that protein-coding genes were inter...

    Authors: Igor B Rogozin, Liran Carmel, Miklos Csuros and Eugene V Koonin
    Citation: Biology Direct 2012 7:11
    Content type: Review Published on:

  14. Tubulins are a family of GTPases that are key components of the cytoskeleton in all eukaryotes and are distantly related to the FtsZ GTPase that is involved in cell division in most bacteria and many archaea. ...

    Authors: Natalya Yutin and Eugene V Koonin
    Citation: Biology Direct 2012 7:10
    Content type: Discovery notes Published on:

  15. Injuries to articular cartilage result in the development of lesions that form on the surface of the cartilage. Such lesions are associated with articular cartilage degeneration and osteoarthritis. The typical...

    Authors: Jason M Graham, Bruce P Ayati, Lei Ding, Prem S Ramakrishnan and James A Martin
    Citation: Biology Direct 2012 7:9
    Content type: Research Published on:

  17. In eukaryotes, the CMG (CDC45, MCM, GINS) complex containing the replicative helicase MCM is a key player in DNA replication. Archaeal homologs of the eukaryotic MCM and GINS proteins have been identified but ...

    Authors: Kira S Makarova, Eugene V Koonin and Zvi Kelman
    Citation: Biology Direct 2012 7:7
    Content type: Research Published on:

  19. Sterols are key components of eukaryotic cellular membranes that are synthesized by multi-enzyme pathways that require molecular oxygen. Because prokaryotes fundamentally lack sterols, it is unclear how the va...

    Authors: Kiyotaka Takishita, Yoshito Chikaraishi, Michelle M Leger, Eunsoo Kim, Akinori Yabuki, Naohiko Ohkouchi and Andrew J Roger
    Citation: Biology Direct 2012 7:5
    Content type: Discovery notes Published on:

  21. Antibodies of the IgG3 subclass have been implicated in the pathogenesis of the spontaneous glomerulonephritis observed in mice of the MRL/MpJ-Tnfrsf6lpr (MRL/lpr) inbred strain which have been widely studied as ...

    Authors: Neil S Greenspan, Myro A Lu, Jacob W Shipley, Xuedong Ding, Qing Li, Dilara Sultana, Maria Kollaros, John R Schreiber, Pingfu Fu, Chaim Putterman and Steven N Emancipator
    Citation: Biology Direct 2012 7:3
    Content type: Research Published on:

  23. Our current understanding of evolution is so tightly linked to template-dependent replication of DNA and RNA molecules that the old idea from Oparin of a self-reproducing 'garbage bag' ('coacervate') of chemic...

    Authors: Vera Vasas, Chrisantha Fernando, Mauro Santos, Stuart Kauffman and Eörs Szathmáry
    Citation: Biology Direct 2012 7:1
    Content type: Research Published on:

  24. CRISPR (Clustered, Regularly, Interspaced, Short, Palindromic Repeats) loci provide prokaryotes with an adaptive immunity against viruses and other mobile genetic elements. CRISPR arrays can be transcribed and...

    Authors: Avital Brodt, Mor N Lurie-Weinberger and Uri Gophna
    Citation: Biology Direct 2011 6:65
    Content type: Research Published on:

  25. Data assimilation refers to methods for updating the state vector (initial condition) of a complex spatiotemporal model (such as a numerical weather model) by combining new observations with one or more prior ...

    Authors: Eric J Kostelich, Yang Kuang, Joshua M McDaniel, Nina Z Moore, Nikolay L Martirosyan and Mark C Preul
    Citation: Biology Direct 2011 6:64
    Content type: Research Published on:

  26. The ability to perform de novo biosynthesis of purines is present in organisms in all three domains of life, reflecting the essentiality of these molecules to life. Although the pathway is quite similar in eukary...

    Authors: Anne M Brown, Samantha L Hoopes, Robert H White and Catherine A Sarisky
    Citation: Biology Direct 2011 6:63
    Content type: Research Published on:

  27. Speciation corresponds to the progressive establishment of reproductive barriers between groups of individuals derived from an ancestral stock. Since Darwin did not believe that reproductive barriers could be ...

    Authors: Etienne Joly
    Citation: Biology Direct 2011 6:62
    Content type: Research Published on:

  28. Transcription factors are thought to regulate the transcription of microRNA genes in a manner similar to that of protein-coding genes; that is, by binding to conventional transcription factor binding site DNA ...

    Authors: Jittima Piriyapongsa, I King Jordan, Andrew B Conley, Tom Ronan and Neil R Smalheiser
    Citation: Biology Direct 2011 6:61
    Content type: Research Published on:

  31. A few major discoveries have influenced how ecologists and evolutionists study microbes. Here, in the format of an interview, we answer questions that directly relate to how these discoveries are perceived in ...

    Authors: Rebecca J Case and Yan Boucher
    Citation: Biology Direct 2011 6:58
    Content type: Review Published on:

  32. Sequence homology considerations widely used to transfer functional annotation to uncharacterized protein sequences require special precautions in the case of non-globular sequence segments including membrane-...

    Authors: Wing-Cheong Wong, Sebastian Maurer-Stroh and Frank Eisenhaber
    Citation: Biology Direct 2011 6:57
    Content type: Research Published on:

  33. Mitochondria mediate most of the energy production that occurs in the majority of eukaryotic organisms. These subcellular organelles contain a genome that differs from the nuclear genome and is referred to as ...

    Authors: Eric Faure, Luis Delaye, Sandra Tribolo, Anthony Levasseur, Hervé Seligmann and Roxane-Marie Barthélémy
    Citation: Biology Direct 2011 6:56
    Content type: Hypothesis Published on:

  35. The vertebrate globin gene repertoire consists of seven members that differ in terms of structure, function and phyletic distribution. While hemoglobin, myoglobin, cytoglobin, and neuroglobin are present in al...

    Authors: Jasmin Dröge and Wojciech Makałowski
    Citation: Biology Direct 2011 6:54
    Content type: Discovery notes Published on:

  36. Identifying group-specific characteristics in metabolic networks can provide better insight into evolutionary developments. Here, we present an approach to classify the three domains of life using topological ...

    Authors: Laurin AJ Mueller, Karl G Kugler, Michael Netzer, Armin Graber and Matthias Dehmer
    Citation: Biology Direct 2011 6:53
    Content type: Research Published on:

  37. Based on unique, coherent properties of phylogenetic analysis, key amino acid substitutions and structural modeling, we have identified a new class of unusual microbial rhodopsins related to the Anabaena senso...

    Authors: Juan A Ugalde, Sheila Podell, Priya Narasingarao and Eric E Allen
    Citation: Biology Direct 2011 6:52
    Content type: Discovery notes Published on:

  39. Volutin granules appear to be universally distributed and are morphologically and chemically identical to acidocalcisomes, which are electron-dense granular organelles rich in calcium and phosphate, whose func...

    Authors: Manfredo J Seufferheld, Kyung Mo Kim, James Whitfield, Alejandro Valerio and Gustavo Caetano-Anollés
    Citation: Biology Direct 2011 6:50
    Content type: Research Published on:

  40. Currently a huge amount of protein-protein interaction data is available therefore extracting meaningful ones are a challenging task. In a protein-protein interaction network, hubs are considered as key protei...

    Authors: Mouna Choura and Ahmed Rebaï
    Citation: Biology Direct 2011 6:49
    Content type: Research Published on:

  41. Chromosomal orthologs can reveal the shared ancestral gene set and their evolutionary trends. Additionally, physico-chemical properties of encoded proteins could provide information about functional adaptation...

    Authors: Humberto Peralta, Gabriela Guerrero, Alejandro Aguilar and Jaime Mora
    Citation: Biology Direct 2011 6:48
    Content type: Research Published on:

  43. In many biological and therapeutic contexts, it is highly desirable to target a chemical specifically to a particular tissue where it exerts its biological effect. In this paper, we present a simple, generic, ...

    Authors: Bruce S Gardiner, Lihai Zhang, David W Smith, Peter Pivonka and Alan J Grodzinsky
    Citation: Biology Direct 2011 6:46
    Content type: Research Published on:

  44. Phylogenetic reconstruction using DNA and protein sequences has allowed the reconstruction of evolutionary histories encompassing all life. We present and discuss a means to incorporate much of this rich narra...

    Authors: David Williams, Gregory P Fournier, Pascal Lapierre, Kristen S Swithers, Anna G Green, Cheryl P Andam and J Peter Gogarten
    Citation: Biology Direct 2011 6:45
    Content type: Review Published on:

  48. It is becoming increasingly difficult to reconcile the observed extent of horizontal gene transfers with the central metaphor of a great tree uniting all evolving entities on the planet. In this manuscript we ...

    Authors: James O McInerney, Davide Pisani, Eric Bapteste and Mary J O'Connell
    Citation: Biology Direct 2011 6:41
    Content type: Hypothesis Published on:

  50. We introduce several forest-based and network-based methods for exploring microbial evolution, and apply them to the study of thousands of genes from 30 strains of E. coli. This case study illustrates how additio...

    Authors: Julie Beauregard-Racine, Cédric Bicep, Klaus Schliep, Philippe Lopez, François-Joseph Lapointe and Eric Bapteste
    Citation: Biology Direct 2011 6:39
    Content type: Research Published on:
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Biology Direct

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