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		Discovery notes Lateral transfer of tetrahymenol-synthesizing genes has allowed multiple diverse eukaryote lineages to independently adapt to environments without oxygen Kiyotaka Takishita, Yoshito Chikaraishi, Michelle M Leger, Eunsoo Kim, Akinori Yabuki, Naohiko Ohkouchi, Andrew J Roger Biology Direct 2012, 7:5 (1 February 2012) Abstract \| Provisional PDF \| Editor’s summary Tetrahymanol functions as a surrogate of sterol in eukaryotes inhabiting oxygen-poor environments, and genes encoding the tetrahymanol synthesizing enzyme have been laterally transferred among several phylogenetically diverged eukaryotes.
		Hypothesis Primordial soup or vinaigrette: did the RNA world evolve at acidic pH? Harold S Bernhardt, Warren P Tate Biology Direct 2012, 7:4 (20 January 2012) Abstract \| Provisional PDF \| PubMed \| Editor’s summary The greater stability of key RNA bonds at acidic pH, such as link the phosphodiester backbone and between amino acids and tRNA, suggests the RNA world evolved in acidic conditions.
		Research IgG3 deficiency extends lifespan and attenuates progression of glomerulonephritis in MRL/lpr mice Neil S Greenspan, Myro A Lu, Jacob W Shipley, Xuedong Ding, Qing Li, Dilara Sultana, Maria Kollaros, John R Schreiber, Pingfu Fu, Chaim Putterman, Steven N Emancipator Biology Direct 2012, 7:3 (16 January 2012) Abstract \| Provisional PDF \| PubMed \| Editor’s summary In MRL/lpr mice, which spontaneously develop autoimmune glomerulonephritis like that in systemic lupus erythematosus, genetic elimination of IgG3 antibody production diminishes renal pathology and extends lifespan.
		Research On the Molecular Mechanism of GC Content Variation among Eubacterial Genomes Hao Wu, Zhang Zhang, Songnian Hu, Jun Yu Biology Direct 2012, 7:2 (10 January 2012) Abstract \| Provisional PDF \| PubMed \| Editor’s summary New large-scale comparative genome analyses provided further evidences indicating that polymerases involved in either replication or repair pathways underlie the GC content variability in eubacteria.
		Research Evolution before genes Vera Vasas, Chrisantha Fernando, Mauro Santos, Stuart Kauffman, Eors Szathmary Biology Direct 2012, 7:1 (5 January 2012) Abstract \| Provisional PDF \| PubMed
		Research CRISPR loci reveal networks of gene exchange in archaea Avital Brodt, Mor N Lurie-Weinberger, Uri Gophna Biology Direct 2011, 6:65 (21 December 2011) Abstract \| Provisional PDF \| PubMed
		Research Accurate State Estimation from Uncertain Data and Models: An Application of Data Assimilation to Mathematical Models of Human Brain Tumors Eric J Kostelich, Yang Kuang, Joshua M McDaniel, Nina Z Moore, Nikolay L Martirosyan, Mark C Preul Biology Direct 2011, 6:64 (21 December 2011) Abstract \| Provisional PDF \| PubMed \| Editor’s summary State estimation schemes, employed operationally for weather forecasting, can be applied in principle to make useful short-term predictions of the growth and spread of malignant tumors in individual patient cases.
		Research Purine biosynthesis in archaea: variations on a theme Anne M Brown, Samantha L Hoopes, Robert H White, Catherine A Sarisky Biology Direct 2011, 6:63 (14 December 2011) Abstract \| Full text \| PDF \| PubMed
		Research The existence of species rests on a metastable equilibrium between inbreeding and outbreeding. Etienne Joly Biology Direct 2011, 6:62 (9 December 2011) Abstract \| Provisional PDF \| PubMed \| Editor’s summary A model whereby new species arise by budding from the ancestral stock rather than by splitting into separate populations, with advantageous recessive phenotypes promoting the direct selection of reproductive barriers.
		Research Transcription factor binding sites are highly enriched within microRNA precursor sequences Jittima Piriyapongsa, I King Jordan, Andrew B Conley, Tom Ronan, Neil R Smalheiser Biology Direct 2011, 6:61 (2 December 2011) Abstract \| Full text \| PDF \| PubMed
		Research On universal common ancestry, sequence similarity, and phylogenetic structure: The sins of P-values and the virtues of Bayesian evidence Douglas L Theobald Biology Direct 2011, 6:60 (24 November 2011) Abstract \| Provisional PDF \| PubMed \| Editor’s summary Douglas Theobald, in response to recent criticisms, provides evidence to further support his claim that Darwin's hypothesis that all life on earth has a universal common ancestor has been formally confirmed by a homology independent statistic test.
		Research Extensive intron gain in the ancestor of placental mammals Dušan Kordiš Biology Direct 2011, 6:59 (23 November 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Phylogenomic analysis of domesticated genes provides evidence for numerous intron gains in the ancestor of placental mammals and demonstrates that adequate taxon sampling is crucial for reconstructing intron evolution.
		Review Molecular musings in microbial ecology and evolution Rebecca J Case, Yan Boucher Biology Direct 2011, 6:58 (10 November 2011) Abstract \| Full text \| PDF \| PubMed
		Research Not all transmembrane helices are born equal: Towards the extension of the sequence homology concept to membrane proteins Wing-Cheong Wong, Sebastian Maurer-Stroh, Frank Eisenhaber Biology Direct 2011, 6:57 (25 October 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Transmembrane helices can be either complex (possibly common ancestry) or simple (likely of convergent evolution); the latter should be excluded from similarity searches to avoid false assignments of protein homology.
		Hypothesis Probable presence of an ubiquitous cryptic mitochondrial gene on the antisense strand of the cytochrome oxidase I gene Eric Faure, Luis Delaye, Sandra Tribolo, Anthony Levasseur, Hervé Seligmann, Roxane-Marie Barthélémy Biology Direct 2011, 6:56 (24 October 2011) Abstract \| Full text \| PDF \| PubMed
		Research The rhizome of Reclinomonas americana, Homo sapiens, Pediculus humanus and Saccharomyces cerevisiae mitochondria Kalliopi Georgiades, Didier Raoult Biology Direct 2011, 6:55 (20 October 2011) Abstract \| Full text \| PDF \| PubMed
		Discovery notes Phylogenetic analysis reveals wide distribution of globin X Jasmin Dröge, Wojciech Makałowski Biology Direct 2011, 6:54 (17 October 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Phylogenetic analysis and comparative genomics reveal wide distribution of globin X in vertebrates and its invertebrate orthologs confirming its ancient origin.
		Research A network-based approach to classify the three domains of life Laurin AJ Mueller, Karl G Kugler, Michael Netzer, Armin Graber, Matthias Dehmer Biology Direct 2011, 6:53 (13 October 2011) Abstract \| Full text \| PDF \| PubMed
		Discovery notes Xenorhodopsins, an enigmatic new class of microbial rhodopsins horizontally transferred between archaea and bacteria Juan A Ugalde, Sheila Podell, Priya Narasingarao, Eric E Allen Biology Direct 2011, 6:52 (10 October 2011) Abstract \| Full text \| PDF \| PubMed
		Research Fish the ChIPs: a pipeline for automated genomic annotation of ChIP-Seq data Iros Barozzi, Alberto Termanini, Saverio Minucci, Gioacchino Natoli Biology Direct 2011, 6:51 (6 October 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Fish the ChIPs is a computational pipeline for complete ChIP-Seq data analysis of unlimited samples; it can be run on any Unix machine while providing a graphic interface for Mac.
		Research Evolution of vacuolar proton pyrophosphatase domains and volutin granules: clues into the early evolutionary origin of the acidocalcisome Manfredo J Seufferheld, Kyung Kim, James Whitfield, Alejandro Valerio, Gustavo Caetano-Anollés Biology Direct 2011, 6:50 (5 October 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The universality of volutin granules and presence of the vacuolar pyrophosphatase in the three superkingdoms of life reveals that the acidocalcisomes may have originated in the Last Universal Common Ancestor.
		Research Structural analysis of hubs in human NR-RTK network Mouna Choura, Ahmed Rebaï Biology Direct 2011, 6:49 (5 October 2011) Abstract \| Full text \| PDF \| PubMed
		Research Sequence variability of Rhizobiales orthologs and relationship with physico-chemical characteristics of proteins Humberto Peralta, Gabriela Guerrero, Alejandro Aguilar, Jaime Mora Biology Direct 2011, 6:48 (4 October 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Diversification of orthologous genes provokes specific physico-chemical changes in proteins of related species, revealing particular trends required to perform their functional roles in the adaptation to niche and intra-cellular conditions.
		Research Biased gene transfer and its implications for the concept of lineage Cheryl P Andam, J Peter Gogarten Biology Direct 2011, 6:47 (23 September 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Evolutionary histories of three aminoacyl-tRNA synthetases show that the concept of organismal lineage in the prokaryotic world is defined by vertical inheritance and horizontal gene transfer biased towards close relatives.
		Research A mathematical model for targeting chemicals to tissues by exploiting complex degradation Bruce S Gardiner, Lihai Zhang, David W Smith, Peter Pivonka, Alan J Grodzinsky Biology Direct 2011, 6:46 (22 September 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A mathematical model describing the co-diffusion of binding partners into a tissue is presented, elucidating a general method for targeting a chemical to a tissue.

	All
		Discovery notes Lateral transfer of tetrahymenol-synthesizing genes has allowed multiple diverse eukaryote lineages to independently adapt to environments without oxygen Kiyotaka Takishita, Yoshito Chikaraishi, Michelle M Leger, Eunsoo Kim, Akinori Yabuki, Naohiko Ohkouchi, Andrew J Roger Biology Direct 2012, 7:5 (1 February 2012) Abstract \| Provisional PDF \| Editor’s summary Tetrahymanol functions as a surrogate of sterol in eukaryotes inhabiting oxygen-poor environments, and genes encoding the tetrahymanol synthesizing enzyme have been laterally transferred among several phylogenetically diverged eukaryotes.
		Hypothesis Primordial soup or vinaigrette: did the RNA world evolve at acidic pH? Harold S Bernhardt, Warren P Tate Biology Direct 2012, 7:4 (20 January 2012) Abstract \| Provisional PDF \| PubMed \| Editor’s summary The greater stability of key RNA bonds at acidic pH, such as link the phosphodiester backbone and between amino acids and tRNA, suggests the RNA world evolved in acidic conditions.
		Research IgG3 deficiency extends lifespan and attenuates progression of glomerulonephritis in MRL/lpr mice Neil S Greenspan, Myro A Lu, Jacob W Shipley, Xuedong Ding, Qing Li, Dilara Sultana, Maria Kollaros, John R Schreiber, Pingfu Fu, Chaim Putterman, Steven N Emancipator Biology Direct 2012, 7:3 (16 January 2012) Abstract \| Provisional PDF \| PubMed \| Editor’s summary In MRL/lpr mice, which spontaneously develop autoimmune glomerulonephritis like that in systemic lupus erythematosus, genetic elimination of IgG3 antibody production diminishes renal pathology and extends lifespan.
		Research On the Molecular Mechanism of GC Content Variation among Eubacterial Genomes Hao Wu, Zhang Zhang, Songnian Hu, Jun Yu Biology Direct 2012, 7:2 (10 January 2012) Abstract \| Provisional PDF \| PubMed \| Editor’s summary New large-scale comparative genome analyses provided further evidences indicating that polymerases involved in either replication or repair pathways underlie the GC content variability in eubacteria.
		Research Evolution before genes Vera Vasas, Chrisantha Fernando, Mauro Santos, Stuart Kauffman, Eors Szathmary Biology Direct 2012, 7:1 (5 January 2012) Abstract \| Provisional PDF \| PubMed
		Research CRISPR loci reveal networks of gene exchange in archaea Avital Brodt, Mor N Lurie-Weinberger, Uri Gophna Biology Direct 2011, 6:65 (21 December 2011) Abstract \| Provisional PDF \| PubMed
		Research Accurate State Estimation from Uncertain Data and Models: An Application of Data Assimilation to Mathematical Models of Human Brain Tumors Eric J Kostelich, Yang Kuang, Joshua M McDaniel, Nina Z Moore, Nikolay L Martirosyan, Mark C Preul Biology Direct 2011, 6:64 (21 December 2011) Abstract \| Provisional PDF \| PubMed \| Editor’s summary State estimation schemes, employed operationally for weather forecasting, can be applied in principle to make useful short-term predictions of the growth and spread of malignant tumors in individual patient cases.
		Research Purine biosynthesis in archaea: variations on a theme Anne M Brown, Samantha L Hoopes, Robert H White, Catherine A Sarisky Biology Direct 2011, 6:63 (14 December 2011) Abstract \| Full text \| PDF \| PubMed
		Research The existence of species rests on a metastable equilibrium between inbreeding and outbreeding. Etienne Joly Biology Direct 2011, 6:62 (9 December 2011) Abstract \| Provisional PDF \| PubMed \| Editor’s summary A model whereby new species arise by budding from the ancestral stock rather than by splitting into separate populations, with advantageous recessive phenotypes promoting the direct selection of reproductive barriers.
		Research Transcription factor binding sites are highly enriched within microRNA precursor sequences Jittima Piriyapongsa, I King Jordan, Andrew B Conley, Tom Ronan, Neil R Smalheiser Biology Direct 2011, 6:61 (2 December 2011) Abstract \| Full text \| PDF \| PubMed
		Research On universal common ancestry, sequence similarity, and phylogenetic structure: The sins of P-values and the virtues of Bayesian evidence Douglas L Theobald Biology Direct 2011, 6:60 (24 November 2011) Abstract \| Provisional PDF \| PubMed \| Editor’s summary Douglas Theobald, in response to recent criticisms, provides evidence to further support his claim that Darwin's hypothesis that all life on earth has a universal common ancestor has been formally confirmed by a homology independent statistic test.
		Research Extensive intron gain in the ancestor of placental mammals Dušan Kordiš Biology Direct 2011, 6:59 (23 November 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Phylogenomic analysis of domesticated genes provides evidence for numerous intron gains in the ancestor of placental mammals and demonstrates that adequate taxon sampling is crucial for reconstructing intron evolution.
		Review Molecular musings in microbial ecology and evolution Rebecca J Case, Yan Boucher Biology Direct 2011, 6:58 (10 November 2011) Abstract \| Full text \| PDF \| PubMed
		Research Not all transmembrane helices are born equal: Towards the extension of the sequence homology concept to membrane proteins Wing-Cheong Wong, Sebastian Maurer-Stroh, Frank Eisenhaber Biology Direct 2011, 6:57 (25 October 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Transmembrane helices can be either complex (possibly common ancestry) or simple (likely of convergent evolution); the latter should be excluded from similarity searches to avoid false assignments of protein homology.
		Hypothesis Probable presence of an ubiquitous cryptic mitochondrial gene on the antisense strand of the cytochrome oxidase I gene Eric Faure, Luis Delaye, Sandra Tribolo, Anthony Levasseur, Hervé Seligmann, Roxane-Marie Barthélémy Biology Direct 2011, 6:56 (24 October 2011) Abstract \| Full text \| PDF \| PubMed
		Research The rhizome of Reclinomonas americana, Homo sapiens, Pediculus humanus and Saccharomyces cerevisiae mitochondria Kalliopi Georgiades, Didier Raoult Biology Direct 2011, 6:55 (20 October 2011) Abstract \| Full text \| PDF \| PubMed
		Discovery notes Phylogenetic analysis reveals wide distribution of globin X Jasmin Dröge, Wojciech Makałowski Biology Direct 2011, 6:54 (17 October 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Phylogenetic analysis and comparative genomics reveal wide distribution of globin X in vertebrates and its invertebrate orthologs confirming its ancient origin.
		Research A network-based approach to classify the three domains of life Laurin AJ Mueller, Karl G Kugler, Michael Netzer, Armin Graber, Matthias Dehmer Biology Direct 2011, 6:53 (13 October 2011) Abstract \| Full text \| PDF \| PubMed
		Discovery notes Xenorhodopsins, an enigmatic new class of microbial rhodopsins horizontally transferred between archaea and bacteria Juan A Ugalde, Sheila Podell, Priya Narasingarao, Eric E Allen Biology Direct 2011, 6:52 (10 October 2011) Abstract \| Full text \| PDF \| PubMed
		Research Fish the ChIPs: a pipeline for automated genomic annotation of ChIP-Seq data Iros Barozzi, Alberto Termanini, Saverio Minucci, Gioacchino Natoli Biology Direct 2011, 6:51 (6 October 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Fish the ChIPs is a computational pipeline for complete ChIP-Seq data analysis of unlimited samples; it can be run on any Unix machine while providing a graphic interface for Mac.
		Research Evolution of vacuolar proton pyrophosphatase domains and volutin granules: clues into the early evolutionary origin of the acidocalcisome Manfredo J Seufferheld, Kyung Kim, James Whitfield, Alejandro Valerio, Gustavo Caetano-Anollés Biology Direct 2011, 6:50 (5 October 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The universality of volutin granules and presence of the vacuolar pyrophosphatase in the three superkingdoms of life reveals that the acidocalcisomes may have originated in the Last Universal Common Ancestor.
		Research Structural analysis of hubs in human NR-RTK network Mouna Choura, Ahmed Rebaï Biology Direct 2011, 6:49 (5 October 2011) Abstract \| Full text \| PDF \| PubMed
		Research Sequence variability of Rhizobiales orthologs and relationship with physico-chemical characteristics of proteins Humberto Peralta, Gabriela Guerrero, Alejandro Aguilar, Jaime Mora Biology Direct 2011, 6:48 (4 October 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Diversification of orthologous genes provokes specific physico-chemical changes in proteins of related species, revealing particular trends required to perform their functional roles in the adaptation to niche and intra-cellular conditions.
		Research Biased gene transfer and its implications for the concept of lineage Cheryl P Andam, J Peter Gogarten Biology Direct 2011, 6:47 (23 September 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Evolutionary histories of three aminoacyl-tRNA synthetases show that the concept of organismal lineage in the prokaryotic world is defined by vertical inheritance and horizontal gene transfer biased towards close relatives.
		Research A mathematical model for targeting chemicals to tissues by exploiting complex degradation Bruce S Gardiner, Lihai Zhang, David W Smith, Peter Pivonka, Alan J Grodzinsky Biology Direct 2011, 6:46 (22 September 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A mathematical model describing the co-diffusion of binding partners into a tissue is presented, elucidating a general method for targeting a chemical to a tissue.