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Commentaries Lateral gene transfer between prokaryotes and multicellular eukaryotes: ongoing and significant? Vera ID Ros and Gregory DD Hurst PMCID: PMC2687425 Phylo-evo-devo: combining phylogenetics with evolutionary developmental biology Alessandro Minelli PMCID: PMC2707371 Correspondence Magnetic resonance imaging (MRI) has failed to distinguish between smaller gut regions and larger haemal sinuses in sea urchins (Echinodermata: Echinoidea) Nicholas D Holland and Michael T Ghiselin PMCID: PMC2729296 Methodology Articles Factors necessary to produce basoapical polarity in human glandular epithelium formed in conventional and high-throughput three-dimensional culture: example of the breast epithelium Cedric Plachot, Lesley S Chaboub, Hibret A Adissu, Lei Wang, Albert Urazaev, Jennifer Sturgis, Elikplimi K Asem, and Sophie A Lelièvre PMCID: PMC2784453 Fluorescence resonance energy transfer (FRET)-based subcellular visualization of pathogen-induced host receptor signaling Alexander Buntru, Timo Zimmermann, and Christof R Hauck PMCID: PMC2788528 Research Articles Microarray and cDNA sequence analysis of transcription during nerve-dependent limb regeneration James R Monaghan, Leonard G Epp, Srikrishna Putta, Robert B Page, John A Walker, Chris K Beachy, Wei Zhu, Gerald M Pao, Inder M Verma, Tony Hunter, Susan V Bryant, David M Gardiner, Tim T Harkins, and S Randal Voss PMCID: PMC2630914 Host-symbiont co-speciation and reductive genome evolution in gut symbiotic bacteria of acanthosomatid stinkbugs Yoshitomo Kikuchi, Takahiro Hosokawa, Naruo Nikoh, Xian-Ying Meng, Yoichi Kamagata, and Takema Fukatsu PMCID: PMC2637841 Assigning strains to bacterial species via the internet Cynthia J Bishop, David M Aanensen, Gregory E Jordan, Mogens Kilian, William P Hanage, and Brian G Spratt PMCID: PMC2636762 Conditional embryonic lethality to improve the sterile insect technique in Ceratitis capitata (Diptera: Tephritidae) Marc F Schetelig, Carlos Caceres, Antigone Zacharopoulou, Gerald Franz, and Ernst A Wimmer PMCID: PMC2662800 Eukaryotic protein production in designed storage organelles Margarita Torrent, Blanca Llompart, Sabine Lasserre-Ramassamy, Immaculada Llop-Tous, Miriam Bastida, Pau Marzabal, Ann Westerholm-Parvinen, Markku Saloheimo, Peter B Heifetz, and M Dolors Ludevid PMCID: PMC2637842 Evolution and diversity of Rickettsia bacteria Lucy A Weinert, John H Werren, Alexandre Aebi, Graham N Stone, and Francis M Jiggins PMCID: PMC2662801 A large new subset of TRIM genes highly diversified by duplication and positive selection in teleost fish Lieke M van der Aa, Jean-Pierre Levraud, Malika Yahmi, Emilie Lauret, Valérie Briolat, Philippe Herbomel, Abdenour Benmansour, and Pierre Boudinot PMCID: PMC2657112 Indexing TNF-α gene expression using a gene-targeted reporter cell line Ziying Yan, Diana Lei-Butters, John F Engelhardt, and Gregory H Leno PMCID: PMC2657777 Double fossilization in eukaryotic microorganisms from Lower Cretaceous amber Ana Martín-González, Jacek Wierzchos, Juan-Carlos Gutiérrez, Jesús Alonso, and Carmen Ascaso PMCID: PMC2649901 Concerted evolution of male and female display traits in the European corn borer, Ostrinia nubilalis Jean-Marc Lassance and Christer Löfstedt PMCID: PMC2671483 Contributions of gut bacteria to Bacillus thuringiensis-induced mortality vary across a range of Lepidoptera Nichole A Broderick, Courtney J Robinson, Matthew D McMahon, Jonathan Holt, Jo Handelsman, and Kenneth F Raffa PMCID: PMC2653032 Aphids acquired symbiotic genes via lateral gene transfer Naruo Nikoh and Atsushi Nakabachi PMCID: PMC2662799 The relative ages of ectomycorrhizal mushrooms and their plant hosts estimated using Bayesian relaxed molecular clock analyses David S Hibbett and P Brandon Matheny PMCID: PMC2660285 Defining behavioral and molecular differences between summer and migratory monarch butterflies Haisun Zhu, Robert J Gegear, Amy Casselman, Sriramana Kanginakudru, and Steven M Reppert PMCID: PMC2681450 Remarkable convergent evolution in specialized parasitic Thecostraca (Crustacea) Marcos Pérez-Losada, Jens T Høeg, and Keith A Crandall PMCID: PMC2678073 Immunomodulatory parasites and toll-like receptor-mediated tumour necrosis factor alpha responsiveness in wild mammals Joseph A Jackson, Ida M Friberg, Luke Bolch, Ann Lowe, Catriona Ralli, Philip D Harris, Jerzy M Behnke, and Janette E Bradley PMCID: PMC2685781 The calcium-sensing receptor regulates parathyroid hormone gene expression in transfected HEK293 cells Hillel Galitzer, Vardit Lavi-Moshayoff, Morris Nechama, Tomer Meir, Justin Silver, and Tally Naveh-Many PMCID: PMC2681451 Genomic expression dominance in allopolyploids Ryan A Rapp, Joshua A Udall, and Jonathan F Wendel PMCID: PMC2684529 F-actin-based extensions of the head cyst cell adhere to the maturing spermatids to maintain them in a tight bundle and prevent their premature release in Drosophila testis Bela S Desai, Seema Shirolikar, and Krishanu Ray PMCID: PMC2683793 Specific retention of the protostome-specific PsGEF may parallel with the evolution of mushroom bodies in insect and lophotrochozoan brains Nozomu Higuchi, Keigo Kohno, and Tatsuhiko Kadowaki PMCID: PMC2684095 Single molecule resolution of the antimicrobial action of quantum dot-labeled sushi peptide on live bacteria Sebastian Leptihn, Jia Yi Har, Jianzhu Chen, Bow Ho, Thorsten Wohland, and Jeak Ling Ding PMCID: PMC2685782 Noisy splicing, more than expression regulation, explains why some exons are subject to nonsense-mediated mRNA decay Zhenguo Zhang, Dedong Xin, Ping Wang, Li Zhou, Landian Hu, Xiangyin Kong, and Laurence D Hurst PMCID: PMC2697156 The cAMP-HMGA1-RBP4 system: a novel biochemical pathway for modulating glucose homeostasis Eusebio Chiefari, Francesco Paonessa, Stefania Iiritano, Ilaria Le Pera, Dario Palmieri, Giuseppe Brunetti, Angelo Lupo, Vittorio Colantuoni, Daniela Foti, Elio Gulletta, Giovambattista De Sarro, Alfredo Fusco, and Antonio Brunetti PMCID: PMC2698822 AP-2α regulates migration of GN-11 neurons via a specific genetic programme involving the Axl receptor tyrosine kinase Francesca Orso, Richard Jäger, Raffaele Adolfo Calogero, Hubert Schorle, Piero Sismondi, Michele De Bortoli, and Daniela Taverna PMCID: PMC2700071 Heterologous cross-seeding mimics cross-species prion conversion in a yeast model Namitha Vishveshwara and Susan W Liebman PMCID: PMC2694167 A single muscle moves a crustacean limb joint rhythmically by acting against a spring containing resilin Malcolm Burrows PMCID: PMC2694168 Candidate chemoreceptor subfamilies differentially expressed in the chemosensory organs of the mollusc Aplysia Scott F Cummins, Dirk Erpenbeck, Zhihua Zou, Charles Claudianos, Leonid L Moroz, Gregg T Nagle, and Bernard M Degnan PMCID: PMC2700072 Mutations in many genes affect aggressive behavior in Drosophila melanogaster Alexis C Edwards, Liesbeth Zwarts, Akihiko Yamamoto, Patrick Callaerts, and Trudy FC Mackay PMCID: PMC2707370 Early calcium increase triggers the formation of olfactory long-term memory in honeybees Emmanuel Perisse, Valérie Raymond-Delpech, Isabelle Néant, Yukihisa Matsumoto, Catherine Leclerc, Marc Moreau, and Jean-Christophe Sandoz PMCID: PMC2713209 Hibernation-like state induced by an opioid peptide protects against experimental stroke Cesar V Borlongan, Teruo Hayashi, Peter R Oeltgen, Tsung-Ping Su, and Yun Wang PMCID: PMC2708132 Microbial modification of host long-distance dispersal capacity Sara L Goodacre, Oliver Y Martin, Dries Bonte, Linda Hutchings, Chris Woolley, Kamal Ibrahim, CF George Thomas, and Godfrey M Hewitt PMCID: PMC2706808 Coordination of opposing sex-specific and core muscle groups regulates male tail posture during Caenorhabditis elegans male mating behavior Allyson J Whittaker and Paul W Sternberg PMCID: PMC2715377 Single-copy nuclear genes resolve the phylogeny of the holometabolous insects Brian M Wiegmann, Michelle D Trautwein, Jung-Wook Kim, Brian K Cassel, Matthew A Bertone, Shaun L Winterton, and David K Yeates PMCID: PMC2709105 Effect of hydroxyurea on the promoter occupancy profiles of tumor suppressor p53 and p73 Vera Huang, Xin Lu, Yong Jiang, and Jean YJ Wang PMCID: PMC2711048 Erythropoietin improves operant conditioning and stability of cognitive performance in mice Ahmed El-Kordi, Konstantin Radyushkin, and Hannelore Ehrenreich PMCID: PMC2715378 Expression of the peroxisome proliferator activated receptor γ gene is repressed by DNA methylation in visceral adipose tissue of mouse models of diabetes Katsunori Fujiki, Fumi Kano, Kunio Shiota, and Masayuki Murata PMCID: PMC2715379 Proliferation of Ty3/gypsy-like retrotransposons in hybrid sunflower taxa inferred from phylogenetic data Mark C Ungerer, Suzanne C Strakosh, and Kaitlin M Stimpson PMCID: PMC2715380 Remodeling of the chromatin structure of the facioscapulohumeral muscular dystrophy (FSHD) locus and upregulation of FSHD-related gene 1 (FRG1) expression during human myogenic differentiation Beatrice Bodega, Gabriella Di Capua Ramirez, Florian Grasser, Stefania Cheli, Silvia Brunelli, Marina Mora, Raffaella Meneveri, Anna Marozzi, Stefan Mueller, Elena Battaglioli, and Enrico Ginelli PMCID: PMC2719609 Ontogeny and phylogeny: molecular signatures of selection, constraint, and temporal pleiotropy in the development of Drosophila Carlo G Artieri, Wilfried Haerty, and Rama S Singh PMCID: PMC2722573 Features of the ancestral bilaterian inferred from Platynereis dumerilii ParaHox genes Jerome HL Hui, Florian Raible, Natalia Korchagina, Nicolas Dray, Sylvie Samain, Ghislaine Magdelenat, Claire Jubin, Béatrice Segurens, Guillaume Balavoine, Detlev Arendt, and David EK Ferrier PMCID: PMC2723086 A Dictyostelium chalone uses G proteins to regulate proliferation Deenadayalan Bakthavatsalam, Jonathan M Choe, Nana E Hanson, and Richard H Gomer PMCID: PMC2726123 TBP2 is a substitute for TBP in Xenopus oocyte transcription Waseem Akhtar and Gert Jan C Veenstra PMCID: PMC2731028 Roles of octopaminergic and dopaminergic neurons in appetitive and aversive memory recall in an insect Makoto Mizunami, Sae Unoki, Yasuhiro Mori, Daisuke Hirashima, Ai Hatano, and Yukihisa Matsumoto PMCID: PMC2729297 Evidence for inhibition of cholinesterases in insect and mammalian nervous systems by the insect repellent deet Vincent Corbel, Maria Stankiewicz, Cédric Pennetier, Didier Fournier, Jure Stojan, Emmanuelle Girard, Mitko Dimitrov, Jordi Molgó, Jean-Marc Hougard, and Bruno Lapied PMCID: PMC2739159 Selective entrainment of the Drosophila circadian clock to daily gradients in environmental temperature Jake Currie, Tadahiro Goda, and Herman Wijnen PMCID: PMC2745372 Mapping the human membrane proteome: a majority of the human membrane proteins can be classified according to function and evolutionary origin Markus Sällman Almén, Karl JV Nordström, Robert Fredriksson, and Helgi B Schiöth PMCID: PMC2739160 Two mycoheterotrophic orchids from Thailand tropical dipterocarpacean forests associate with a broad diversity of ectomycorrhizal fungi Mélanie Roy, Santi Watthana, Anna Stier, Franck Richard, Suyanee Vessabutr, and Marc-André Selosse PMCID: PMC2745373 Connexin channels and phospholipids: association and modulation Darren Locke and Andrew L Harris PMCID: PMC2733891 Control of chicken CR1 retrotransposons is independent of Dicer-mediated RNA interference pathway Sung-Hun Lee, Preethi Eldi, Soo-Young Cho, and Danny Rangasamy PMCID: PMC2734521 Antibiotic treatment leads to the elimination of Wolbachia endosymbionts and sterility in the diplodiploid collembolan Folsomia candida Nathan Pike and Rachel Kingcombe PMCID: PMC2739161 δ-Opioid receptor activation attenuates oxidative injury in the ischemic rat brain Yilin Yang, Xiwei Xia, Yi Zhang, Qiang Wang, Lu Li, Guanghua Luo, and Ying Xia PMCID: PMC2754429 Golgi localisation of GMAP210 requires two distinct cis-membrane binding
mechanisms Jesus Cardenas, Sabrina Rivero, Bruno Goud, Michel Bornens, and Rosa M Rios PMCID: PMC2744908 Phylogeographic analysis reveals association of tick-borne pathogen, Anaplasma marginale, MSP1a sequences with ecological traits affecting tick vector performance Agustín Estrada-Peña, Victoria Naranjo, Karina Acevedo-Whitehouse, Atilio J Mangold, Katherine M Kocan, and José de la Fuente PMCID: PMC2741432 Light-dependent roles of the G-protein α subunit GNA1 of Hypocrea jecorina (anamorph Trichoderma reesei) Christian Seibel, Gabriela Gremel, Roberto do Nascimento Silva, André Schuster, Christian P Kubicek, and Monika Schmoll PMCID: PMC2749820 Receptor oligomerization and beyond: a case study in bone morphogenetic proteins Kai Heinecke, Axel Seher, Werner Schmitz, Thomas D Mueller, Walter Sebald, and Joachim Nickel PMCID: PMC2749821 Genetic determinants of mate recognition in Brachionus manjavacas (Rotifera) Terry W Snell, Tonya L Shearer, Hilary A Smith, Julia Kubanek, Kristin E Gribble, and David B Mark Welch PMCID: PMC2746195 Genes encoding novel secreted and transmembrane proteins are temporally and spatially regulated during Drosophila melanogaster embryogenesis Alejandro Zúñiga, Christian Hödar, Patricia Hanna, Freddy Ibáñez, Pablo Moreno, Rodrigo Pulgar, Luis Pastenes, Mauricio González, and Verónica Cambiazo PMCID: PMC2761875 scribble mutants promote aPKC and JNK-dependent epithelial neoplasia independently of Crumbs Gregory R Leong, Karen R Goulding, Nancy Amin, Helena E Richardson, and Anthony M Brumby PMCID: PMC2760524 c-Myc affects mRNA translation, cell proliferation and progenitor cell function in the mammary gland Tina Stoelzle, Patrick Schwarb, Andreas Trumpp, and Nancy E Hynes PMCID: PMC2761394 Dual control by a single gene of secondary sexual characters and mating preferences in medaka Shoji Fukamachi, Masato Kinoshita, Kouichi Aizawa, Shoji Oda, Axel Meyer, and Hiroshi Mitani PMCID: PMC2761876 Coordinated spatial and temporal expression of Hox genes during embryogenesis in the acoel Convolutriloba longifissura Andreas Hejnol and Mark Q Martindale PMCID: PMC2761877 Recombination and insertion events involving the botulinum neurotoxin complex genes in Clostridium botulinum types A, B, E and F and Clostridium butyricum type E strains Karen K Hill, Gary Xie, Brian T Foley, Theresa J Smith, Amy C Munk, David Bruce, Leonard A Smith, Thomas S Brettin, and John C Detter PMCID: PMC2764570 Retinoic acid enhances skeletal muscle progenitor formation and bypasses inhibition by bone morphogenetic protein 4 but not dominant negative β-catenin Karen AM Kennedy, Tammy Porter, Virja Mehta, Scott D Ryan, Feodor Price, Vian Peshdary, Christina Karamboulas, Josée Savage, Thomas A Drysdale, Shun-Cheng Li, Steffany AL Bennett, and Ilona S Skerjanc PMCID: PMC2764571 TonB-dependent transporters and their occurrence in cyanobacteria Oliver Mirus, Sascha Strauss, Kerstin Nicolaisen, Arndt von Haeseler, and Enrico Schleiff PMCID: PMC2771747 Evidence for the adaptation of protein pH-dependence to subcellular pH Pedro Chan and Jim Warwicker PMCID: PMC2770037 Genetical genomic determinants of alcohol consumption in rats and humans Boris Tabakoff, Laura Saba, Morton Printz, Pam Flodman, Colin Hodgkinson, David Goldman, George Koob, Heather N Richardson, Katerina Kechris, Richard L Bell, Norbert Hübner, Matthias Heinig, Michal Pravenec, Jonathan Mangion, Lucie Legault, Maurice Dongier, Katherine M Conigrave, John B Whitfield, John Saunders, Bridget Grant, Paula L Hoffman, and WHO/ISBRA Study on State and Trait Markers of Alcoholism PMCID: PMC2777866 The scent of supercolonies: the discovery, synthesis and behavioural verification of ant colony recognition cues Miriam Brandt, Ellen van Wilgenburg, Robert Sulc, Kenneth J Shea, and Neil D Tsutsui PMCID: PMC2775022 Massively parallel tag sequencing reveals the complexity of anaerobic marine protistan communities Thorsten Stoeck, Anke Behnke, Richard Christen, Linda Amaral-Zettler, Maria J Rodriguez-Mora, Andrei Chistoserdov, William Orsi, and Virginia P Edgcomb PMCID: PMC2777867 A genome-wide synthetic dosage lethality screen reveals multiple pathways that require the functioning of ubiquitin-binding proteins Rad23 and Dsk2 Chang Liu, Dewald van Dyk, Yue Li, Brenda Andrews, and Hai Rao PMCID: PMC2777868 Research article Large-scale insertional mutagenesis of a coleopteran stored grain pest, the red flour beetle Tribolium castaneum, identifies embryonic lethal mutations and enhancer traps Jochen Trauner, Johannes Schinko, Marcé D Lorenzen, Teresa D Shippy, Ernst A Wimmer, Richard W Beeman, Martin Klingler, Gregor Bucher, and Susan J Brown PMCID: PMC2779179 A remarkable diversity of bone-eating worms (Osedax; Siboglinidae; Annelida) Robert C Vrijenhoek, Shannon B Johnson, and Greg W Rouse PMCID: PMC2780999 Predominant membrane localization is an essential feature of the bacterial signal recognition particle receptor Miryana Mircheva, Diana Boy, Benjamin Weiche, Friederike Hucke, Peter Graumann, and Hans-Georg Koch PMCID: PMC2780400 Phylogeographic reconstruction of a bacterial species with high levels of lateral gene transfer Talima Pearson, Philip Giffard, Stephen Beckstrom-Sternberg, Raymond Auerbach, Heidie Hornstra, Apichai Tuanyok, Erin P Price, Mindy B Glass, Benjamin Leadem, James S Beckstrom-Sternberg, Gerard J Allan, Jeffrey T Foster, David M Wagner, Richard T Okinaka, Siew Hoon Sim, Ofori Pearson, Zaining Wu, Jean Chang, Rajinder Kaul, Alex R Hoffmaster, Thomas S Brettin, Richard A Robison, Mark Mayo, Jay E Gee, Patrick Tan, Bart J Currie, and Paul Keim PMCID: PMC2784454 Environmentally-acquired bacteria influence microbial diversity and natural innate immune responses at gut surfaces Imke E Mulder, Bettina Schmidt, Christopher R Stokes, Marie Lewis, Mick Bailey, Rustam I Aminov, James I Prosser, Bhupinder P Gill, John R Pluske, Claus-Dieter Mayer, Corran C Musk, and Denise Kelly PMCID: PMC2785767 Mapping cortical hubs in tinnitus Winfried Schlee, Nadia Mueller, Thomas Hartmann, Julian Keil, Isabel Lorenz, and Nathan Weisz PMCID: PMC2787501 Have giant lobelias evolved several times independently? Life form shifts and historical biogeography of the cosmopolitan and highly diverse subfamily Lobelioideae (Campanulaceae) Alexandre Antonelli PMCID: PMC2789055 Proteomic analysis of blastema formation in regenerating axolotl limbs Nandini Rao, Deepali Jhamb, Derek J Milner, Bingbing Li, Fengyu Song, Mu Wang, S Randal Voss, Mathew Palakal, Michael W King, Behnaz Saranjami, Holly LD Nye, Jo Ann Cameron, and David L Stocum PMCID: PMC2794268 Increasing phylogenetic resolution at low taxonomic levels using massively parallel sequencing of chloroplast genomes Matthew Parks, Richard Cronn, and Aaron Liston PMCID: PMC2793254 Profound human/mouse differences in alpha-dystrobrevin isoforms: a novel syntrophin-binding site and promoter missing in mouse and rat Sabrina V Böhm, Panayiotis Constantinou, Sipin Tan, Hong Jin, and Roland G Roberts PMCID: PMC2796648 Other Issues: Journal List
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