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  1. The PVC super-phylum gathers bacteria from seven phyla (Planctomycetes, Verrucomicrobiae, Chlamydiae, Lentisphaera, Poribacteria, OP3, WWE2) presenting different lifestyles, cell plans and environments. Planctomy...

    Authors: Sandrine Pinos, Pierre Pontarotti, Didier Raoult, Jean Pierre Baudoin and Isabelle Pagnier

    Citation: Biology Direct 2016 11:38

    Content type: Research

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  2. Retroposition, one of the processes of copying the genetic material, is an important RNA-mediated mechanism leading to the emergence of new genes. Because the transcription controlling segments are usually not...

    Authors: Marcin Jąkalski, Kazutaka Takeshita, Mathieu Deblieck, Kanako O. Koyanagi, Izabela Makałowska, Hidemi Watanabe and Wojciech Makałowski

    Citation: Biology Direct 2016 11:35

    Content type: Research

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  3. Eukaryogenesis, a major transition in evolution of life, originated from the symbiogenic fusion of an archaea with a metabolically versatile bacterium. By general consensus, the latter organism belonged to α p...

    Authors: Mauro Degli Esposti, Diego Cortez, Luis Lozano, Simon Rasmussen, Henrik Bjørn Nielsen and Esperanza Martinez Romero

    Citation: Biology Direct 2016 11:34

    Content type: Discovery notes

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  4. While commonly assumed in the biochemistry community that the control of metabolic pathways is thought to be critical to cellular function, it is unclear if metabolic pathways generally have evolutionarily sta...

    Authors: Alena Orlenko, Ashley I. Teufel, Peter B. Chi and David A. Liberles

    Citation: Biology Direct 2016 11:31

    Content type: Research

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  5. Histone lysine methyltransferases (HKMTs), catalyze mono-, di- and trimethylation of lysine residues, resulting in a regulatory pattern that controls gene expression. Their involvement in many different cellul...

    Authors: Tamas Lazar, Eva Schad, Beata Szabo, Tamas Horvath, Attila Meszaros, Peter Tompa and Agnes Tantos

    Citation: Biology Direct 2016 11:30

    Content type: Discovery notes

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  6. Evolutionary relationship between class III nucleotide cyclases and an uncharacterized set of bacterial proteins from Actinobacteria, Bacteroidetes and Proteobacteria has been recognized and analyzed. Detailed...

    Authors: Gayatri Ramakrishnan, Abha Jain, Nagasuma Chandra and Narayanaswamy Srinivasan

    Citation: Biology Direct 2016 11:27

    Content type: Discovery notes

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  7. Viruses are the simplest replicating units, characterized by a limited number of coding genes and an exceptionally high rate of overlapping genes. We sought a unified evolutionary explanation that accounts for...

    Authors: Nadav Brandes and Michal Linial

    Citation: Biology Direct 2016 11:26

    Content type: Research

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  8. Viral capsid assembly involves the oligomerization of the capsid nucleoprotein (NP), which is an essential step in viral replication and may represent a potential antiviral target. An in vitro transcription-tr...

    Authors: Sean Broce, Lisa Hensley, Tomoharu Sato, Joshua Lehrer-Graiwer, Christian Essrich, Katie J. Edwards, Jacqueline Pajda, Christopher J. Davis, Rami Bhadresh, Clarence R. Hurt, Beverly Freeman, Vishwanath R. Lingappa, Colm A. Kelleher and Marcela V. Karpuj

    Citation: Biology Direct 2016 11:25

    Content type: Research

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  9. Recent advances in sequencing technologies enable the large-scale identification of genes that are affected by various genetic alterations in cancer. However, understanding tumor development requires insights ...

    Authors: Bálint Mészáros, András Zeke, Attila Reményi, István Simon and Zsuzsanna Dosztányi

    Citation: Biology Direct 2016 11:23

    Content type: Research

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  10. The family of D cyclins has a fundamental role in cell cycle progression, but its members (D1, D2, D3) are believed to have redundant functions. However, there is some evidence that contradicts the notion of m...

    Authors: Miguel Chaves-Ferreira, Gerald Krenn, Florence Vasseur, Aleksandr Barinov, Pedro Gonçalves, Orly Azogui, Ana Cumano, Zhi Li, Sandra Pellegrini, Benedita Rocha and Diego Laderach

    Citation: Biology Direct 2016 11:21

    Content type: Research

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  11. Short leader genes usually do not encode stable proteins, although their importance in expression control of bacterial genomes is widely accepted. Such genes are often involved in the control of attenuation re...

    Authors: Semen A. Korolev, Oleg A. Zverkov, Alexandr V. Seliverstov and Vassily A. Lyubetsky

    Citation: Biology Direct 2016 11:20

    Content type: Discovery notes

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  12. In the recent years, sequence-specific nucleases such as ZFNs, TALENs, and CRISPR/Cas9 have revolutionzed the fields of animal genome editing and transgenesis. However, these new techniques require microinject...

    Authors: Masahiro Sato, Masato Ohtsuka, Satoshi Watanabe and Channabasavaiah B. Gurumurthy

    Citation: Biology Direct 2016 11:16

    Content type: Review

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  13. The discovery of the viroid in 1971, which initiated the third major expansion of the biosphere towards smaller living entities—after discovery of the “subvisual” microorganisms in 1675 and that of the “submic...

    Authors: Theodor O. Diener

    Citation: Biology Direct 2016 11:15

    Content type: Hypothesis

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  14. The hypothalamic-pituitary-adrenal (HPA) axis is a neuroendocrine system that regulates numerous physiological processes. Disruptions in the activity of the HPA axis are correlated with stress-related diseases...

    Authors: Lae U. Kim, Maria R. D’Orsogna and Tom Chou

    Citation: Biology Direct 2016 11:13

    Content type: Research

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  15. Antiangiogenic agents have been recently added to the oncological armamentarium with bevacizumab probably being the most popular representative in current clinical practice. The elucidation of the mode of acti...

    Authors: Katerina D. Argyri, Dimitra D. Dionysiou, Fay D. Misichroni and Georgios S. Stamatakos

    Citation: Biology Direct 2016 11:12

    Content type: Research

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  16. CpG dinucleotides are extensively underrepresented in mammalian genomes. It is widely accepted that genome-wide CpG depletion is predominantly caused by an elevated CpG > TpG mutation rate due to frequent cyto...

    Authors: Alexander Y. Panchin, Vsevolod J. Makeev and Yulia A. Medvedeva

    Citation: Biology Direct 2016 11:11

    Content type: Research

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  17. Genotyping by re-sequencing has become a standard approach to estimate single nucleotide polymorphism (SNP) diversity, haplotype structure and the biodiversity and has been defined as an efficient approach to ...

    Authors: Salvatore Camiolo, Gaurav Sablok and Andrea Porceddu

    Citation: Biology Direct 2016 11:8

    Content type: Application note

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  18. Translation of nucleotides into a numeric form has been approached in many ways and has allowed researchers to investigate the properties of protein-coding sequences and noncoding sequences. Typically, more pr...

    Authors: Tonya Woods, Thanawadee Preeprem, Kichun Lee, Woojin Chang and Brani Vidakovic

    Citation: Biology Direct 2016 11:6

    Content type: Research

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  19. The cilium (flagellum) is a complex cellular structure inherited from the last eukaryotic common ancestor (LECA). A large number of ciliary proteins have been characterized in a few model organisms, but their ...

    Authors: Marek Eliáš, Vladimír Klimeš, Romain Derelle, Romana Petrželková and Jan Tachezy

    Citation: Biology Direct 2016 11:5

    Content type: Research

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  20. Next-generation sequencing (NGS) enables the recovery of pathogen genomes from clinical samples without the need for culturing. Depletion of host/microbiota components (e.g., ribosomal RNA and poly-A RNA) and ...

    Authors: Dingchen Li, Zongwei Li, Zhe Zhou, Zhen Li, Xinyan Qu, Peisong Xu, Pingkun Zhou, Xiaochen Bo and Ming Ni

    Citation: Biology Direct 2016 11:3

    Content type: Discovery notes

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  21. The length of a protein sequence is largely determined by its function. In certain species, it may be also affected by additional factors, such as growth temperature or acidity. In 2002, it was shown that in t...

    Authors: Tatiana V. Tatarinova, Inna Lysnyansky, Yuri V. Nikolsky and Alexander Bolshoy

    Citation: Biology Direct 2016 11:2

    Content type: Research

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  22. It is widely believed that the treatment of glioblastomas (GBM) could benefit from oncolytic virus therapy. Clinical research has shown that Vesicular Stomatitis Virus (VSV) has strong oncolytic properties. In...

    Authors: Victor Lopez de Rioja, Neus Isern and Joaquim Fort

    Citation: Biology Direct 2016 11:1

    Content type: Research

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  23. In the past, many methods have been developed for peptide tertiary structure prediction but they are limited to peptides having natural amino acids. This study describes a method PEPstrMOD, which is an updated...

    Authors: Sandeep Singh, Harinder Singh, Abhishek Tuknait, Kumardeep Chaudhary, Balvinder Singh, S. Kumaran and Gajendra P. S. Raghava

    Citation: Biology Direct 2015 10:73

    Content type: Research

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  24. The structure and organisation of ecological interactions within an ecosystem is modified by the evolution and coevolution of the individual species it contains. Understanding how historical conditions have sh...

    Authors: Daniel A. Power, Richard A. Watson, Eörs Szathmáry, Rob Mills, Simon T. Powers, C. Patrick Doncaster and BłaŻej Czapp

    Citation: Biology Direct 2015 10:69

    Content type: Research

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    The Erratum to this article has been published in Biology Direct 2016 11:29

  25. Many proteins of viruses infecting hyperthermophilic Crenarchaeota have no detectable homologs in current databases, hampering our understanding of viral evolution. We used sensitive database search methods an...

    Authors: Mart Krupovic, Virginija Cvirkaite-Krupovic, David Prangishvili and Eugene V. Koonin

    Citation: Biology Direct 2015 10:65

    Content type: Discovery notes

    Published on:

  26. Microbial rhodopsins and G-protein coupled receptors (GPCRs, which include animal rhodopsins) are two distinct (super) families of heptahelical (7TM) membrane proteins that share obvious structural similaritie...

    Authors: Daria N. Shalaeva, Michael Y. Galperin and Armen Y. Mulkidjanian

    Citation: Biology Direct 2015 10:63

    Content type: Discovery notes

    Published on:

  27. Transposable elements (TEs) play an important role in genome function and evolution. It has been shown that TEs are a considerable source of adaptive changes in the genome of Drosophila melanogaster. Specifically...

    Authors: Josefa González, Jose Martínez and Wojciech Makalowski

    Citation: Biology Direct 2015 10:50

    Content type: Research

    Published on:

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