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		Research article Phylogenomics supports microsporidia as the earliest diverging clade of sequenced fungi. Salvador Capella-Gutierrez, Marina Marcet-Houben, Toni Gabaldon BMC Biology 2012, 10:47 (31 May 2012) Abstract \| Provisional PDF \| Editor’s summary The evolutionary history of the parasitic microsporidia has always been hard to pin down, and although they are now established as fungi their precise position is still debated. A rigorous analysis of five recently-released genomes supports their positioning as a sister taxon to the rest of the fungal clade.
		Research article Comprehensive microarray-based analysis for stage-specific larval camouflage pattern-associated genes in the swallowtail butterfly, Papilio xuthus Ryo Futahashi, Hiroko Shirataki, Takanori Narita, Kazuei Mita, Haruhiko Fujiwara BMC Biology 2012, 10:46 (31 May 2012) Abstract \| Provisional PDF
		Research article Monoaminergic modulation of photoreception in ascidian: Evidence for a proto-hypothalamo-retinal territory Florian Razy-Krajka, Euan Brown, Takeo Horie, Jacques Callebert, Yasunori Sasakura, Jean-Stephane Joly, Takehiro Kusakabe, Philippe Vernier BMC Biology 2012, 10:45 (29 May 2012) Abstract \| Provisional PDF \| PubMed \| Editor’s summary A string of remarkable similarities between dopamine-synthesizing cells that modulate the photic responses of ascidian larvae, and amacrine cells of the vertebrate retina, suggests a common evolutionary origin from ancestral cells in the photoreceptive field of the anterior neural tube of chordates.
		Research article MAVS ubiquitination by the E3 ligase TRIM25 and degradation by the proteasome is involved in type I Interferon production after activation of the antiviral RIG-I-Like receptors Celine Castanier, Naima Zemirli, Alain Portier, Dominique Garcin, Nicolas Bidere, Aime Vazquez, Damien Arnoult BMC Biology 2012, 10:44 (24 May 2012) Abstract \| Provisional PDF \| PubMed \| Editor’s summary A number of proteins are now known to sense viral infection in cells and signal antiviral responses. Studies by Damien Arnoult and colleagues suggest that the interferon response involves the sequential assembly and proteasomal dissolution of a signalling complex at the mitochondrial surface.
		Commentary Constrained evolution drives limited influenza diversity Paul G Thomas, Tomer Hertz BMC Biology 2012, 10:43 (21 May 2012) Abstract \| Full text \| PDF \| PubMed
		Question and Answer Q&A: 'Toxic' effects of sugar: should we be afraid of fructose? Luc Tappy BMC Biology 2012, 10:42 (21 May 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Before the colonial era of sugar plantations we consumed, on average, about 15-fold less fructose than we do today. Luc Tappy explains, in question and answer format, the special features of fructose metabolism and discusses the evidence that high fructose intake has contributed to the current epidemic of obesity and metabolic disease.
		Comment Mending walls Gregory A Petsko BMC Biology 2012, 10:41 (11 May 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The real topic of Gregory Petsko's Comment in our Metabolism diet and disease series is not, despite its title, mending walls, but patterns of comorbidity that argue for cross-disciplinary research: obesity and cancer are linked, for example, but apparently not if you are also schizophrenic.
		Research article Macondo crude oil from the Deepwater Horizon oil spill disrupts specific developmental processes during zebrafish embryogenesis T Yvanka de Soysa, Allison Ulrich, Timo Friedrich, Danielle Pite, Shannon L Compton, Deborah Ok, Rebecca L Bernardos, Gerald B Downes, Shizuka Hsieh, Rachael Stein, M Caterina Lagdameo, Katherine Halvorsen, Lydia-Rose Kesich, Michael JF Barresi BMC Biology 2012, 10:40 (4 May 2012) Abstract \| Full text \| PDF \| PubMed
		Commentary A never ending race for new and improved fluorescent proteins Alexander M Jones, David W Ehrhardt, Wolf B Frommer BMC Biology 2012, 10:39 (3 May 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Visualizing proteins in plants requires stable expression of fluorescent proteins, with brightness able to overcome the autofluorescence of chlorophyll. Wolf Frommer and colleagues provide a broad overview of what makes an optimal fluorophore and evaluate the virtues of a novel orange fluorescent protein described recently in BMC Biotechnology.
		Research article Canalization of the evolutionary trajectory of the human influenza virus Trevor Bedford, Andrew Rambaut, Mercedes Pascual BMC Biology 2012, 10:38 (30 April 2012) Abstract \| Provisional PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The influenza virus evolves rapidly, but this doesn't usually lead to a genetically diverse population as one might expect. A new model suggests how short-term selection to avoid human immune responses could cause this long-term lack of diversity.
		Research article BMP2 and mechanical loading cooperatively regulate immediate early signalling events in the BMP pathway Jessica Kopf, Ansgar Petersen, Georg N Duda, Petra Knaus BMC Biology 2012, 10:37 (30 April 2012) Abstract \| Full text \| PDF \| PubMed
		Research article UBXN7 docks on neddylated cullin complexes using its UIM motif and causes HIF1α accumulation Susanne Bandau, Axel Knebel, Zoe O Gage, Nicola T Wood, Gabriela Alexandru BMC Biology 2012, 10:36 (26 April 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary p97 is a AAA+ ATPase that extracts proteins from membranes and protein complexes for ubiquitin-dependent degradation. Gabriela Alexandru and colleagues suggest how its interaction with the ubiquitinating complex CUL2 may regulate HIF1alpha degradation in normoxia.
		Opinion Evolving a photosynthetic organelle Takuro Nakayama, John M Archibald BMC Biology 2012, 10:35 (24 April 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The photosynthetic chromatophore of the amoeba Paulinella has a recent origin - at least in evolutionary terms. Nakayama and Archibald discuss how this makes it an ideal model for studying how photosynthetic organelles arise and evolve.
		Review Clamp loader ATPases and the evolution of DNA replication machinery Brian A Kelch, Debora L Makino, Mike O'Donnell, John Kuriyan BMC Biology 2012, 10:34 (20 April 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The speed of DNA replication depends on the sliding clamp which encircles the DNA and holds the polymerase in place. Mike O'Donnell, John Kuriyan and colleagues review the growing understanding of the conformational rearrangements whereby the clamp loader opens the clamp and screws it on to the DNA throughout DNA synthesis.
		Correction Correction: Polyploidization increases meiotic recombination frequency in Arabidopsis Ales Pecinka, Wei Fang, Marc Rehmsmeier, Avraham A Levy, Ortrun Mittelsten Scheid BMC Biology 2012, 10:33 (18 April 2012) Abstract \| Full text \| PDF \| PubMed
		Correspondence Response to Wang and Luo Marc Rehmsmeier BMC Biology 2012, 10:32 (18 April 2012) Abstract \| Provisional PDF \| PubMed \| Cited on BioMed Central
		Correspondence Answer to Wang and Luo, "Polyploidization increases meiotic recombination frequency in Arabidopsis: a close look at statistical modelling and data analysis" Ales Pecinka, Avraham Levy, Ortrun Mittelsten Scheid BMC Biology 2012, 10:31 (18 April 2012) Abstract \| Full text \| PDF \| PubMed
		Correspondence Polyploidization increases meiotic recombination frequency in Arabidopsis: a close look at statistical modeling and data analysis Lin Wang, Zewei Luo BMC Biology 2012, 10:30 (18 April 2012) Abstract \| Full text \| PDF \| PubMed
		Methodology article Advances in establishment and analysis of three-dimensional tumor spheroid-based functional assays for target validation and drug evaluation Maria Vinci, Sharon Gowan, Frances Boxall, Lisa Patterson, Miriam Zimmermann, William Court, Cara Lomas, Marta Mendiola, David Hardisson, Suzanne A Eccles BMC Biology 2012, 10:29 (22 March 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A high throughput method to assay for the growth, invasiveness and angiogenic activity of tumor cells grown in 3-dimensions is validated by testing known cancer drugs, and offers a tool-kit for testing new ones.
		Methodology article Real-time determination of intracellular oxygen in bacteria using a genetically encoded FRET-based biosensor Janko Potzkei, Martin Kunze, Thomas Drepper, Thomas Gensch, Karl-Erich Jaeger, Jochen Büchs BMC Biology 2012, 10:28 (22 March 2012) Abstract \| Full text \| PDF \| PubMed
		Commentary Regulation of G protein-coupled receptors by palmitoylation and cholesterol Alan D Goddard, Anthony Watts BMC Biology 2012, 10:27 (19 March 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The lipid membrane environment influences G-protein coupled receptor signaling. Alan Goddard and Anthony Watts comment on recent data in BMC Cell Biology where a functional, dimerised mu-opioid receptor (OPRM1) complex forms only with palmitate and cholesterol.
		Research article Astrocytes convert network excitation to tonic inhibition of neurons László Héja, Gabriella Nyitrai, Orsolya Kékesi, Árpád Dobolyi, Pál Szabó, Richárd Fiáth, István Ulbert, Borbála Pál-Szenthe, Miklós Palkovits, Julianna Kardos BMC Biology 2012, 10:26 (15 March 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary By mopping up excess glutamate released by excited neurons, and coupling this to export of endogenously synthesized GABA, astrocytes provide an adjustable and local feedback inhibition of network excitation.
		Review Signaling-mediated control of ubiquitin ligases in endocytosis Simona Polo BMC Biology 2012, 10:25 (15 March 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Simona Polo reviews the role of ubiquitination in the regulation of signaling by endocytosis, drawing parallels with the regulation of signalling pathways by phoshorylation.
		Review Following Ariadne's thread: a new perspective on RBR ubiquitin ligases Dawn M Wenzel, Rachel E Klevit BMC Biology 2012, 10:24 (15 March 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The RING-between-RING (RBR) ubiquitin ligases were assumed on the basis of their homologous RING domains to assemble ubiquitin chains by the same mechanism.
		Review Generation and physiological roles of linear ubiquitin chains Henning Walczak, Kazuhiro Iwai, Ivan Dikic BMC Biology 2012, 10:23 (15 March 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Henning Walczak, Kazuhiro Iwai and Ivan Dikic explain what is known of the assembly of linear ubiquitin chains, and discuss the evidence for their role in the regulation of inflammatory immune responses.

	All
		Research article Phylogenomics supports microsporidia as the earliest diverging clade of sequenced fungi. Salvador Capella-Gutierrez, Marina Marcet-Houben, Toni Gabaldon BMC Biology 2012, 10:47 (31 May 2012) Abstract \| Provisional PDF \| Editor’s summary The evolutionary history of the parasitic microsporidia has always been hard to pin down, and although they are now established as fungi their precise position is still debated. A rigorous analysis of five recently-released genomes supports their positioning as a sister taxon to the rest of the fungal clade.
		Research article Comprehensive microarray-based analysis for stage-specific larval camouflage pattern-associated genes in the swallowtail butterfly, Papilio xuthus Ryo Futahashi, Hiroko Shirataki, Takanori Narita, Kazuei Mita, Haruhiko Fujiwara BMC Biology 2012, 10:46 (31 May 2012) Abstract \| Provisional PDF
		Research article Monoaminergic modulation of photoreception in ascidian: Evidence for a proto-hypothalamo-retinal territory Florian Razy-Krajka, Euan Brown, Takeo Horie, Jacques Callebert, Yasunori Sasakura, Jean-Stephane Joly, Takehiro Kusakabe, Philippe Vernier BMC Biology 2012, 10:45 (29 May 2012) Abstract \| Provisional PDF \| PubMed \| Editor’s summary A string of remarkable similarities between dopamine-synthesizing cells that modulate the photic responses of ascidian larvae, and amacrine cells of the vertebrate retina, suggests a common evolutionary origin from ancestral cells in the photoreceptive field of the anterior neural tube of chordates.
		Research article MAVS ubiquitination by the E3 ligase TRIM25 and degradation by the proteasome is involved in type I Interferon production after activation of the antiviral RIG-I-Like receptors Celine Castanier, Naima Zemirli, Alain Portier, Dominique Garcin, Nicolas Bidere, Aime Vazquez, Damien Arnoult BMC Biology 2012, 10:44 (24 May 2012) Abstract \| Provisional PDF \| PubMed \| Editor’s summary A number of proteins are now known to sense viral infection in cells and signal antiviral responses. Studies by Damien Arnoult and colleagues suggest that the interferon response involves the sequential assembly and proteasomal dissolution of a signalling complex at the mitochondrial surface.
		Commentary Constrained evolution drives limited influenza diversity Paul G Thomas, Tomer Hertz BMC Biology 2012, 10:43 (21 May 2012) Abstract \| Full text \| PDF \| PubMed
		Question and Answer Q&A: 'Toxic' effects of sugar: should we be afraid of fructose? Luc Tappy BMC Biology 2012, 10:42 (21 May 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Before the colonial era of sugar plantations we consumed, on average, about 15-fold less fructose than we do today. Luc Tappy explains, in question and answer format, the special features of fructose metabolism and discusses the evidence that high fructose intake has contributed to the current epidemic of obesity and metabolic disease.
		Comment Mending walls Gregory A Petsko BMC Biology 2012, 10:41 (11 May 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The real topic of Gregory Petsko's Comment in our Metabolism diet and disease series is not, despite its title, mending walls, but patterns of comorbidity that argue for cross-disciplinary research: obesity and cancer are linked, for example, but apparently not if you are also schizophrenic.
		Research article Macondo crude oil from the Deepwater Horizon oil spill disrupts specific developmental processes during zebrafish embryogenesis T Yvanka de Soysa, Allison Ulrich, Timo Friedrich, Danielle Pite, Shannon L Compton, Deborah Ok, Rebecca L Bernardos, Gerald B Downes, Shizuka Hsieh, Rachael Stein, M Caterina Lagdameo, Katherine Halvorsen, Lydia-Rose Kesich, Michael JF Barresi BMC Biology 2012, 10:40 (4 May 2012) Abstract \| Full text \| PDF \| PubMed
		Commentary A never ending race for new and improved fluorescent proteins Alexander M Jones, David W Ehrhardt, Wolf B Frommer BMC Biology 2012, 10:39 (3 May 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Visualizing proteins in plants requires stable expression of fluorescent proteins, with brightness able to overcome the autofluorescence of chlorophyll. Wolf Frommer and colleagues provide a broad overview of what makes an optimal fluorophore and evaluate the virtues of a novel orange fluorescent protein described recently in BMC Biotechnology.
		Research article Canalization of the evolutionary trajectory of the human influenza virus Trevor Bedford, Andrew Rambaut, Mercedes Pascual BMC Biology 2012, 10:38 (30 April 2012) Abstract \| Provisional PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The influenza virus evolves rapidly, but this doesn't usually lead to a genetically diverse population as one might expect. A new model suggests how short-term selection to avoid human immune responses could cause this long-term lack of diversity.
		Research article BMP2 and mechanical loading cooperatively regulate immediate early signalling events in the BMP pathway Jessica Kopf, Ansgar Petersen, Georg N Duda, Petra Knaus BMC Biology 2012, 10:37 (30 April 2012) Abstract \| Full text \| PDF \| PubMed
		Research article UBXN7 docks on neddylated cullin complexes using its UIM motif and causes HIF1α accumulation Susanne Bandau, Axel Knebel, Zoe O Gage, Nicola T Wood, Gabriela Alexandru BMC Biology 2012, 10:36 (26 April 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary p97 is a AAA+ ATPase that extracts proteins from membranes and protein complexes for ubiquitin-dependent degradation. Gabriela Alexandru and colleagues suggest how its interaction with the ubiquitinating complex CUL2 may regulate HIF1alpha degradation in normoxia.
		Opinion Evolving a photosynthetic organelle Takuro Nakayama, John M Archibald BMC Biology 2012, 10:35 (24 April 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The photosynthetic chromatophore of the amoeba Paulinella has a recent origin - at least in evolutionary terms. Nakayama and Archibald discuss how this makes it an ideal model for studying how photosynthetic organelles arise and evolve.
		Review Clamp loader ATPases and the evolution of DNA replication machinery Brian A Kelch, Debora L Makino, Mike O'Donnell, John Kuriyan BMC Biology 2012, 10:34 (20 April 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The speed of DNA replication depends on the sliding clamp which encircles the DNA and holds the polymerase in place. Mike O'Donnell, John Kuriyan and colleagues review the growing understanding of the conformational rearrangements whereby the clamp loader opens the clamp and screws it on to the DNA throughout DNA synthesis.
		Correction Correction: Polyploidization increases meiotic recombination frequency in Arabidopsis Ales Pecinka, Wei Fang, Marc Rehmsmeier, Avraham A Levy, Ortrun Mittelsten Scheid BMC Biology 2012, 10:33 (18 April 2012) Abstract \| Full text \| PDF \| PubMed
		Correspondence Response to Wang and Luo Marc Rehmsmeier BMC Biology 2012, 10:32 (18 April 2012) Abstract \| Provisional PDF \| PubMed \| Cited on BioMed Central
		Correspondence Answer to Wang and Luo, "Polyploidization increases meiotic recombination frequency in Arabidopsis: a close look at statistical modelling and data analysis" Ales Pecinka, Avraham Levy, Ortrun Mittelsten Scheid BMC Biology 2012, 10:31 (18 April 2012) Abstract \| Full text \| PDF \| PubMed
		Correspondence Polyploidization increases meiotic recombination frequency in Arabidopsis: a close look at statistical modeling and data analysis Lin Wang, Zewei Luo BMC Biology 2012, 10:30 (18 April 2012) Abstract \| Full text \| PDF \| PubMed
		Methodology article Advances in establishment and analysis of three-dimensional tumor spheroid-based functional assays for target validation and drug evaluation Maria Vinci, Sharon Gowan, Frances Boxall, Lisa Patterson, Miriam Zimmermann, William Court, Cara Lomas, Marta Mendiola, David Hardisson, Suzanne A Eccles BMC Biology 2012, 10:29 (22 March 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A high throughput method to assay for the growth, invasiveness and angiogenic activity of tumor cells grown in 3-dimensions is validated by testing known cancer drugs, and offers a tool-kit for testing new ones.
		Methodology article Real-time determination of intracellular oxygen in bacteria using a genetically encoded FRET-based biosensor Janko Potzkei, Martin Kunze, Thomas Drepper, Thomas Gensch, Karl-Erich Jaeger, Jochen Büchs BMC Biology 2012, 10:28 (22 March 2012) Abstract \| Full text \| PDF \| PubMed
		Commentary Regulation of G protein-coupled receptors by palmitoylation and cholesterol Alan D Goddard, Anthony Watts BMC Biology 2012, 10:27 (19 March 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The lipid membrane environment influences G-protein coupled receptor signaling. Alan Goddard and Anthony Watts comment on recent data in BMC Cell Biology where a functional, dimerised mu-opioid receptor (OPRM1) complex forms only with palmitate and cholesterol.
		Research article Astrocytes convert network excitation to tonic inhibition of neurons László Héja, Gabriella Nyitrai, Orsolya Kékesi, Árpád Dobolyi, Pál Szabó, Richárd Fiáth, István Ulbert, Borbála Pál-Szenthe, Miklós Palkovits, Julianna Kardos BMC Biology 2012, 10:26 (15 March 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary By mopping up excess glutamate released by excited neurons, and coupling this to export of endogenously synthesized GABA, astrocytes provide an adjustable and local feedback inhibition of network excitation.
		Review Signaling-mediated control of ubiquitin ligases in endocytosis Simona Polo BMC Biology 2012, 10:25 (15 March 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Simona Polo reviews the role of ubiquitination in the regulation of signaling by endocytosis, drawing parallels with the regulation of signalling pathways by phoshorylation.
		Review Following Ariadne's thread: a new perspective on RBR ubiquitin ligases Dawn M Wenzel, Rachel E Klevit BMC Biology 2012, 10:24 (15 March 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The RING-between-RING (RBR) ubiquitin ligases were assumed on the basis of their homologous RING domains to assemble ubiquitin chains by the same mechanism.
		Review Generation and physiological roles of linear ubiquitin chains Henning Walczak, Kazuhiro Iwai, Ivan Dikic BMC Biology 2012, 10:23 (15 March 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Henning Walczak, Kazuhiro Iwai and Ivan Dikic explain what is known of the assembly of linear ubiquitin chains, and discuss the evidence for their role in the regulation of inflammatory immune responses.