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  1. 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:

  3. 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:

  4. The current analysis of transposon elements (TE) in Drosophila melanogaster at Evolution Canyon, (EC), Israel, is based on data and analysis done by our collaborators (Drs. J. Gonzalez, J. Martinez and W. Makalow...

    Authors: Avigdor Beiles, Shmuel Raz, Yuval Ben-Abu and Eviatar Nevo

    Citation: Biology Direct 2015 10:58

    Content type: Research

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  5. 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

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  7. Genomic studies have greatly expanded our knowledge of structural non-coding RNAs (ncRNAs). These RNAs fold into characteristic secondary structures and perform specific-structure dependent biological function...

    Authors: Avinash Achar and Pål Sætrom

    Citation: Biology Direct 2015 10:61

    Content type: Review

    Published on:

  9. While hundreds of genes have been implicated already in the etiology of schizophrenia, the exact cause is not known or the disease is considered multigenic in origin. Recent discoveries of new types of RNAs an...

    Authors: Vadim Gumerov and Hedi Hegyi

    Citation: Biology Direct 2015 10:59

    Content type: Research

    Published on:

  11. The interaction between the ribosome and the endoplasmic reticulum-located Sec61 protein translocon is mediated through an arginine residue of Sec61α, which is conserved in all prokaryotic and eukaryotic ortho...

    Authors: Abhishek Sinha, Atrayee Ray, Sandipan Ganguly, Shubhra Ghosh Dastidar and Srimonti Sarkar

    Citation: Biology Direct 2015 10:56

    Content type: Discovery notes

    Published on:

  12. Various methods are currently used to define species and are based on the phylogenetic marker 16S ribosomal RNA gene sequence, DNA-DNA hybridization and DNA GC content. However, these are restricted genetic to...

    Authors: Aurélia Caputo, Vicky Merhej, Kalliopi Georgiades, Pierre-Edouard Fournier, Olivier Croce, Catherine Robert and Didier Raoult

    Citation: Biology Direct 2015 10:55

    Content type: Research

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  17. γ-glutamyltranspeptidase (GGT) is a bi-substrate enzyme conserved in all three domains of life. It catalyzes the cleavage and transfer of γ-glutamyl moiety of glutathione to either water (hydrolysis) or substr...

    Authors: Ved Vrat Verma, Rani Gupta and Manisha Goel

    Citation: Biology Direct 2015 10:49

    Content type: Research

    Published on:

  20. Oligonucleotide microarrays belong to the basic tools of molecular biology and allow for simultaneous assessment of the expression level of thousands of genes. Analysis of microarray data is however very compl...

    Authors: Roman Jaksik, Marta Iwanaszko, Joanna Rzeszowska-Wolny and Marek Kimmel

    Citation: Biology Direct 2015 10:46

    Content type: Review

    Published on:

  21. Resolution of the link between micro- and macroevolution calls for comparing both processes on the same deterministic landscape, such as genomic, metabolic or fitness networks. We apply this perspective to the...

    Authors: Alexander V. Badyaev, Erin S. Morrison, Virginia Belloni and Michael J. Sanderson

    Citation: Biology Direct 2015 10:45

    Content type: Research

    Published on:

  22. Spodoptera is an important polyphagous agricultural insect pest in the tropical world. The genomic details are limited to understand the pest biology at molecular level. In the present...

    Authors: Pavan Kumar Kakumani, Rohit Shukla, Vivek N. Todur, Pawan Malhotra, Sunil K. Mukherjee and Raj K. Bhatnagar

    Citation: Biology Direct 2015 10:44

    Content type: Discovery notes

    Published on:

  23. High-throughput technologies, such as next-generation sequencing, have turned molecular biology into a data-intensive discipline, requiring bioinformaticians to use high-performance computing resources and car...

    Authors: Ola Spjuth, Erik Bongcam-Rudloff, Guillermo Carrasco Hernández, Lukas Forer, Mario Giovacchini, Roman Valls Guimera, Aleksi Kallio, Eija Korpelainen, Maciej M Kańduła, Milko Krachunov, David P Kreil, Ognyan Kulev, Paweł P. Łabaj, Samuel Lampa, Luca Pireddu, Sebastian Schönherr…

    Citation: Biology Direct 2015 10:43

    Content type: Review

    Published on:

  24. Stoichiometric imbalances in macromolecular complexes can lead to altered function. Such imbalances stem from under- or over-expression of a subunit of a complex consequent to a deletion, duplication or regula...

    Authors: Reiner A. Veitia and James A. Birchler

    Citation: Biology Direct 2015 10:42

    Content type: Research

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  25. Antibiotic resistance is a major biomedical problem upon which public health systems demand solutions to construe the dynamics and epidemiological risk of resistant bacteria in anthropogenically-altered enviro...

    Authors: Marcelino Campos, Carlos Llorens, José M. Sempere, Ricardo Futami, Irene Rodriguez, Purificación Carrasco, Rafael Capilla, Amparo Latorre, Teresa M. Coque, Andres Moya and Fernando Baquero

    Citation: Biology Direct 2015 10:41

    Content type: Research

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  27. Annotation transfer for function and structure within the sequence homology concept essentially requires protein sequence similarity for the secondary structural blocks forming the fold of a protein. A simplis...

    Authors: Wing-Cheong Wong, Choon-Kong Yap, Birgit Eisenhaber and Frank Eisenhaber

    Citation: Biology Direct 2015 10:39

    Content type: Research

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  28. In the post-genomic era where sequences are being determined at a rapid rate, we are highly reliant on computational methods for their tentative biochemical characterization. The Pfam database currently contai...

    Authors: Richa Mudgal, Sankaran Sandhya, Nagasuma Chandra and Narayanaswamy Srinivasan

    Citation: Biology Direct 2015 10:38

    Content type: Research

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  29. Mounting evidence indicates that our planet might experience runaway effects associated to rising temperatures and ecosystem overexploitation, leading to catastrophic shifts on short time scales. Remediation s...

    Authors: Ricard V. Solé, Raúl Montañez and Salva Duran-Nebreda

    Citation: Biology Direct 2015 10:37

    Content type: Hypothesis

    Published on:

  32. “Which came first, the Chicken or the Egg?” We suggest this question is not a paradox. The Modern Synthesis envisions speciation through genetic changes in germ cells via random mutations, an “Egg first” scena...

    Authors: Yitzhak Pilpel and Oded Rechavi

    Citation: Biology Direct 2015 10:34

    Content type: Comment

    Published on:

  33. Origin of life research has been slow to advance not only because of its complex evolutionary nature (Franklin Harold: In Search of Cell History, 2014) but also because of the lack of agreement on fundamental ...

    Authors: Jan Spitzer, Gary J. Pielak and Bert Poolman

    Citation: Biology Direct 2015 10:33

    Content type: Review

    Published on:

  34. The ever-increasing expanse of online bioinformatics data is enabling new ways to, not only explore the visualization of these data, but also to apply novel mathematical methods to extract meaningful informati...

    Authors: Sebastian Benzekry, Jack A. Tuszynski, Edward A. Rietman and Giannoula Lakka Klement

    Citation: Biology Direct 2015 10:32

    Content type: Research

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  35. Transmembrane proteins have important roles in cells, as they are involved in energy production, signal transduction, cell-cell interaction, cell-cell communication and more. In human cells, they are frequentl...

    Authors: László Dobson, István Reményi and Gábor E. Tusnády

    Citation: Biology Direct 2015 10:31

    Content type: Research

    Published on:

  37. Binding of cytochrome c, released from the damaged mitochondria, to the apoptotic protease activating factor 1 (Apaf-1) is a key event in the apoptotic signaling cascade. The binding triggers a major domain rearr...

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

    Citation: Biology Direct 2015 10:29

    Content type: Research

    Published on:

  38. In this study, we identified 19 intron losses, including 11 precise intron losses (PILs), six imprecise intron losses (IILs), one de-exonization, and one exon deletion in tomato and potato, and 17 IILs in Arabido...

    Authors: Ming-Yue Ma, Tao Zhu, Xue-Nan Li, Xin-Ran Lan, Heng-Yuan Liu, Yu-Fei Yang and Deng-Ke Niu

    Citation: Biology Direct 2015 10:24

    Content type: Discovery notes

    Published on:

  39. Lignin plays an important role in plant structural support and water transport, and is considered one of the hallmarks of land plants. The recent discovery of lignin or its precursors in various algae has rais...

    Authors: Leen Labeeuw, Patrick T Martone, Yan Boucher and Rebecca J Case

    Citation: Biology Direct 2015 10:23

    Content type: Research

    Published on:

  41. Deciphering the origin of uniquely eukaryotic features of sub-cellular systems, such as the translation apparatus, is critical in reconstructing eukaryogenesis. One such feature is the highly conserved, but po...

    Authors: A Maxwell Burroughs, Dapeng Zhang and L Aravind

    Citation: Biology Direct 2015 10:21

    Content type: Discovery notes

    Published on:

  43. Search of metagenomics sequence databases for homologs of virophage capsid proteins resulted in the discovery of a new family of virophages in the sheep rumen metagenome. The genomes of the rumen virophages (R...

    Authors: Natalya Yutin, Vladimir V Kapitonov and Eugene V Koonin

    Citation: Biology Direct 2015 10:19

    Content type: Discovery notes

    Published on:

  44. Co-regulation of gene expression has been known for many years, and studied widely both globally and for individual genes. Nevertheless, most analyses concerned transcriptional control, which in case of physic...

    Authors: Marlena Siwiak and Piotr Zielenkiewicz

    Citation: Biology Direct 2015 10:18

    Content type: Research

    Published on:

  45. RNA viruses rapidly accumulate genetic variation, which can give rise to synthetic lethal (SL) and deleterious (SD) mutations. Synthetic lethal mutations (non-lethal when alone but lethal when combined in one ...

    Authors: Michel Petitjean, Anne Badel, Reiner A Veitia and Anne Vanet

    Citation: Biology Direct 2015 10:17

    Content type: Research

    Published on:

  46. Members of the alphavirus supergroup include human pathogens such as chikungunya virus, hepatitis E virus and rubella virus. They encode a capping enzyme with methyltransferase-guanylyltransferase (MTase-GTase...

    Authors: Tero Ahola and David G Karlin

    Citation: Biology Direct 2015 10:16

    Content type: Research

    Published on:

  47. Non-small cell lung cancer (NSCLC) is the predominant histological type of lung cancer, accounting for up to 85% of cases. Disease stage is commonly used to determine adjuvant treatment eligibility of NSCLC pa...

    Authors: Suyan Tian, Chi Wang and Ming-Wen An

    Citation: Biology Direct 2015 10:15

    Content type: Research

    Published on:

  48. CD4+ T cells are key regulators of the adaptive immune system and can be divided into T helper (Th) cells and regulatory T (Treg) cells. During an immune response Th cells mature from a naive state into one of se...

    Authors: Michael JT Stubbington, Bidesh Mahata, Valentine Svensson, Andrew Deonarine, Jesper K Nissen, Alexander G Betz and Sarah A Teichmann

    Citation: Biology Direct 2015 10:14

    Content type: Research

    Published on:

  49. Only a small fraction of bacteria and archaea that are identifiable by metagenomics can be grown on standard media. Recent efforts on deep metagenomics sequencing, single-cell genomics and the use of specializ...

    Authors: Isabelle Pagnier, Natalya Yutin, Olivier Croce, Kira S Makarova, Yuri I Wolf, Samia Benamar, Didier Raoult, Eugene V Koonin and Bernard La Scola

    Citation: Biology Direct 2015 10:13

    Content type: Research

    Published on:

  50. Plant viruses of the recently recognized family Amalgaviridae have monopartite double-stranded (ds) RNA genomes and encode two proteins: an RNA-dependent RNA polymerase (RdRp) and a putative capsid protein (CP). ...

    Authors: Mart Krupovic, Valerian V Dolja and Eugene V Koonin

    Citation: Biology Direct 2015 10:12

    Content type: Discovery notes

    Published on:

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