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  1. The virus-host arms race is a major theater for evolutionary innovation. Archaea and bacteria have evolved diverse, elaborate antivirus defense systems that function on two general principles: i) immune system...

    Authors: Kira S Makarova, Vivek Anantharaman, L Aravind and Eugene V Koonin
    Citation: Biology Direct 2012 7:40
  2. Members of the Arabidopsis LSH1 and Oryza G1 (ALOG) family of proteins have been shown to function as key developmental regulators in land plants. However, their precise mode of action remains unclear. Using sens...

    Authors: Lakshminarayan M Iyer and L Aravind
    Citation: Biology Direct 2012 7:39
  3. Cellular life with complex metabolism probably evolved during the reign of RNA, when it served as both information carrier and enzyme. Jensen proposed that enzymes of primordial cells possessed broad specifici...

    Authors: András Szilágyi, Ádám Kun and Eörs Szathmáry
    Citation: Biology Direct 2012 7:38
  4. The dramatic reduction in the cost of sequencing has allowed many researchers to join in the effort of sequencing and annotating prokaryotic genomes. Annotation methods vary considerably and may fail to identi...

    Authors: Derrick E Wood, Henry Lin, Ami Levy-Moonshine, Rajiswari Swaminathan, Yi-Chien Chang, Brian P Anton, Lais Osmani, Martin Steffen, Simon Kasif and Steven L Salzberg
    Citation: Biology Direct 2012 7:37
  5. Mammalian genomes are repositories of repetitive DNA sequences derived from transposable elements (TEs). Typically, TEs generate multiple, mostly inactive copies of themselves, commonly known as repetitive fam...

    Authors: Jerzy Jurka, Weidong Bao, Kenji K Kojima, Oleksiy Kohany and Matthew G Yurka
    Citation: Biology Direct 2012 7:36
  6. Viruses with large genomes encode numerous proteins that do not directly participate in virus biogenesis but rather modify key functional systems of infected cells. We report that a distinct group of giant vir...

    Authors: Natalya Yutin and Eugene V Koonin
    Citation: Biology Direct 2012 7:34
  7. The availability of over 3000 published genome sequences has enabled the use of comparative genomic approaches to drive the biological function discovery process. Classically, one used to link gene with functi...

    Authors: Valérie de Crécy-Lagard, Farhad Forouhar, Céline Brochier-Armanet, Liang Tong and John F Hunt
    Citation: Biology Direct 2012 7:32
  8. The evolution and genomic stop codon frequencies have not been rigorously studied with the exception of coding of non-canonical amino acids. Here we study the rate of evolution and frequency distribution of st...

    Authors: Inna S Povolotskaya, Fyodor A Kondrashov, Alice Ledda and Peter K Vlasov
    Citation: Biology Direct 2012 7:30
  9. Acid Mine Drainages (AMDs) are extreme environments characterized by very acid conditions and heavy metal contaminations. In these ecosystems, the bacterial diversity is considered to be low. Previous culture-...

    Authors: François Delavat, Marie-Claire Lett and Didier Lièvremont
    Citation: Biology Direct 2012 7:28
  10. Prions are agents of analog, protein conformation-based inheritance that can confer beneficial phenotypes to cells, especially under stress. Combined with genetic variation, prion-mediated inheritance can be c...

    Authors: Eugene V Koonin
    Citation: Biology Direct 2012 7:27
  11. In previous work, we introduced a concept, a mathematical model and its computer realization that describe the interaction between bacterial and phage type RNA polymerases, protein factors, DNA and RNA seconda...

    Authors: Vassily A Lyubetsky, Oleg A Zverkov, Sergey A Pirogov, Lev I Rubanov and Alexandr V Seliverstov
    Citation: Biology Direct 2012 7:26
  12. 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
  13. 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
  14. 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
  15. 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
  16. 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
  17. 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
  18. 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
  19. 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
  20. 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
  21. 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
  22. 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
  23. 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
  24. 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
  25. 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
  26. 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
  27. 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
  28. 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
  29. 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
  30. 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
  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
  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
  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

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