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Eukaryote microbial genomics

This section covers the structure and function of genomes of single-celled parasites, yeasts, fungi and viruses.

Page 14 of 14

  1. Rhizopus oryzae is a zygomycete filamentous fungus, well-known as a saprobe ubiquitous in soil and as a pathogenic/spoilage fungus, causing Rhizopus rot and mucomycoses.

    Authors: Evy Battaglia, Isabelle Benoit, Joost van den Brink, Ad Wiebenga, Pedro M Coutinho, Bernard Henrissat and Ronald P de Vries

    Citation: BMC Genomics 2011 12:38

    Content type: Research article

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  2. Streptococcus dysgalactiae subsp. equisimilis (SDSE) causes invasive streptococcal infections, including streptococcal toxic shock syndrome (STSS), as does Lancefield group A Streptococcus pyogenes (GAS). We sequ...

    Authors: Yumi Shimomura, Kayo Okumura, Somay Yamagata Murayama, Junji Yagi, Kimiko Ubukata, Teruo Kirikae and Tohru Miyoshi-Akiyama

    Citation: BMC Genomics 2011 12:17

    Content type: Research article

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  3. Escherichia coli is a model prokaryote, an important pathogen, and a key organism for industrial biotechnology. E. coli W (ATCC 9637), one of four strains designated as safe for laboratory purposes, has not been ...

    Authors: Colin T Archer, Jihyun F Kim, Haeyoung Jeong, Jin Hwan Park, Claudia E Vickers, Sang Yup Lee and Lars K Nielsen

    Citation: BMC Genomics 2011 12:9

    Content type: Research article

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  4. Corynebacterium pseudotuberculosis is generally regarded as an important animal pathogen that rarely infects humans. Clinical strains are occasionally recovered from human cases of lymphadenitis, such as C. pseud...

    Authors: Eva Trost, Lisa Ott, Jessica Schneider, Jasmin Schröder, Sebastian Jaenicke, Alexander Goesmann, Peter Husemann, Jens Stoye, Fernanda Alves Dorella, Flavia Souza Rocha, Siomar de Castro Soares, Vívian D'Afonseca, Anderson Miyoshi, Jeronimo Ruiz, Artur Silva, Vasco Azevedo…

    Citation: BMC Genomics 2010 11:728

    Content type: Research article

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  5. The need for rapid and efficient microbial cell factory design and construction are possible through the enabling technology, metabolic engineering, which is now being facilitated by systems biology approaches...

    Authors: José Manuel Otero, Wanwipa Vongsangnak, Mohammad A Asadollahi, Roberto Olivares-Hernandes, Jérôme Maury, Laurent Farinelli, Loïc Barlocher, Magne Østerås, Michel Schalk, Anthony Clark and Jens Nielsen

    Citation: BMC Genomics 2010 11:723

    Content type: Research article

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  6. Although the importance and widespread occurrence of iron limitation in the contemporary ocean is well documented, we still know relatively little about genetic adaptation of phytoplankton to these environment...

    Authors: Markus Lommer, Alexandra-Sophie Roy, Markus Schilhabel, Stefan Schreiber, Philip Rosenstiel and Julie LaRoche

    Citation: BMC Genomics 2010 11:718

    Content type: Research article

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  7. The pattern-forming bacterium Paenibacillus vortex is notable for its advanced social behavior, which is reflected in development of colonies with highly intricate architectures. Prior to this study, only two oth...

    Authors: Alexandra Sirota-Madi, Tsviya Olender, Yael Helman, Colin Ingham, Ina Brainis, Dalit Roth, Efrat Hagi, Leonid Brodsky, Dena Leshkowitz, Vladimir Galatenko, Vladimir Nikolaev, Raja C Mugasimangalam, Sharron Bransburg-Zabary, David L Gutnick, Doron Lancet and Eshel Ben-Jacob

    Citation: BMC Genomics 2010 11:710

    Content type: Research article

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  8. Comparative analysis of gene expression among serotypes within a species can provide valuable information on important differences between related genomes. For the pig lung pathogen Actinobacillus pleuropneumonia...

    Authors: Kirstine Klitgaard, Carsten Friis, Øystein Angen and Mette Boye

    Citation: BMC Genomics 2010 11:698

    Content type: Research article

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  9. Saccharomyces cerevisiae myosin type II-deficient (myo1 Δ) strains remain viable and divide, despite the absence of a cytokinetic ring, by activation of the PKC1-dependent cell wall integrity pathway (CWIP). Sinc...

    Authors: Marielis E Rivera-Ruiz, José F Rodríguez-Quiñones, Pearl Akamine and José R Rodríguez-Medina

    Citation: BMC Genomics 2010 11:690

    Content type: Research article

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  10. The bacterial genus Listeria contains pathogenic and non-pathogenic species, including the pathogens L. monocytogenes and L. ivanovii, both of which carry homologous virulence gene clusters such as the prfA clust...

    Authors: Henk C den Bakker, Craig A Cummings, Vania Ferreira, Paolo Vatta, Renato H Orsi, Lovorka Degoricija, Melissa Barker, Olga Petrauskene, Manohar R Furtado and Martin Wiedmann

    Citation: BMC Genomics 2010 11:688

    Content type: Research article

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  11. Whilst being closely related to the model actinomycete Streptomyces coelicolor A3(2), S. lividans 66 differs from it in several significant and phenotypically observable ways, including antibiotic production. Pre...

    Authors: Richard A Lewis, Emma Laing, Nicholas Allenby, Giselda Bucca, Volker Brenner, Marcus Harrison, Andrzej M Kierzek and Colin P Smith

    Citation: BMC Genomics 2010 11:682

    Content type: Research article

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  12. Succinate is produced petrochemically from maleic anhydride to satisfy a small specialty chemical market. If succinate could be produced fermentatively at a price competitive with that of maleic anhydride, tho...

    Authors: James B McKinlay, Maris Laivenieks, Bryan D Schindler, Anastasia A McKinlay, Shivakumara Siddaramappa, Jean F Challacombe, Stephen R Lowry, Alicia Clum, Alla L Lapidus, Kirk B Burkhart, Victoria Harkins and Claire Vieille

    Citation: BMC Genomics 2010 11:680

    Content type: Research article

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  13. Adherent and invasive Escherichia coli (AIEC) are commonly found in ileal lesions of Crohn's Disease (CD) patients, where they adhere to intestinal epithelial cells and invade into and survive in epithelial cells...

    Authors: John HE Nash, Andre Villegas, Andrew M Kropinski, Renan Aguilar-Valenzuela, Paulina Konczy, Mariola Mascarenhas, Kim Ziebell, Alfredo G Torres, Mohamed A Karmali and Brian K Coombes

    Citation: BMC Genomics 2010 11:667

    Content type: Research article

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  14. Repeat-induced point mutation (RIP) is a fungal genome defence mechanism guarding against transposon invasion. RIP mutates the sequence of repeated DNA and over time renders the affected regions unrecognisable...

    Authors: James K Hane and Richard P Oliver

    Citation: BMC Genomics 2010 11:655

    Content type: Research article

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  15. In Lactic Acid Bacteria (LAB), the extracellular and surface-associated proteins can be involved in processes such as cell wall metabolism, degradation and uptake of nutrients, communication and binding to sub...

    Authors: Miaomiao Zhou, Daniel Theunissen, Michiel Wels and Roland J Siezen

    Citation: BMC Genomics 2010 11:651

    Content type: Research article

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  16. Phytophthora infestans is the most devastating pathogen of potato and a model organism for the oomycetes. It exhibits high evolutionary potential and rapidly adapts to host plants. The P. infestans genome experie...

    Authors: Sylvain Raffaele, Joe Win, Liliana M Cano and Sophien Kamoun

    Citation: BMC Genomics 2010 11:637

    Content type: Research article

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  17. Microarrays are invaluable tools for genome interrogation, SNP detection, and expression analysis, among other applications. Such broad capabilities would be of value to many pathogen research communities, alt...

    Authors: Amit Bahl, Paul H Davis, Michael Behnke, Florence Dzierszinski, Manjunatha Jagalur, Feng Chen, Dhanasekaran Shanmugam, Michael W White, David Kulp and David S Roos

    Citation: BMC Genomics 2010 11:603

    Content type: Research article

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  18. The bacterium Pseudomonas aeruginosa is capable of three types of motilities: swimming, twitching and swarming. The latter is characterized by a fast and coordinated group movement over a semi-solid surface resul...

    Authors: Julien Tremblay and Eric Déziel

    Citation: BMC Genomics 2010 11:587

    Content type: Research article

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  19. The onset of antibiotics production in Streptomyces species is co-ordinated with differentiation events. An understanding of the genetic circuits that regulate these coupled biological phenomena is essential to d...

    Authors: Marlene Castro-Melchor, Salim Charaniya, George Karypis, Eriko Takano and Wei-Shou Hu

    Citation: BMC Genomics 2010 11:578

    Content type: Research article

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  20. Elevated parasite biomass in the human red blood cells can lead to increased malaria morbidity. The genes and mechanisms regulating growth and development of Plasmodium falciparum through its erythrocytic cycle a...

    Authors: Heather B Reilly Ayala, Mark A Wacker, Geoffrey Siwo and Michael T Ferdig

    Citation: BMC Genomics 2010 11:577

    Content type: Research article

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  21. The human pathogen Listeria monocytogenes resides and proliferates within the cytoplasm of epithelial cells. While the virulence factors essentially contributing to this step of the infection cycle are well chara...

    Authors: Kristina Schauer, Gernot Geginat, Chunguang Liang, Werner Goebel, Thomas Dandekar and Thilo M Fuchs

    Citation: BMC Genomics 2010 11:573

    Content type: Research article

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  22. Flexible genomes facilitate bacterial evolution and are classically organized into polymorphic strain-specific segments called regions of genomic plasticity (RGPs). Using a new web tool, RGPFinder, we investigate...

    Authors: Jean-Claude Ogier, Alexandra Calteau, Steve Forst, Heidi Goodrich-Blair, David Roche, Zoé Rouy, Garret Suen, Robert Zumbihl, Alain Givaudan, Patrick Tailliez, Claudine Médigue and Sophie Gaudriault

    Citation: BMC Genomics 2010 11:568

    Content type: Research article

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  23. Mycobacterium avium subsp. paratuberculosis (MAP) persistently infects intestines and mesenteric lymph nodes leading to a prolonged subclinical disease. The MAP genome sequence was published in 2005, yet its tran...

    Authors: Harish K Janagama, Elise A Lamont, Sajan George, John P Bannantine, Wayne W Xu, Zheng J Tu, Scott J Wells, Jeremy Schefers and Srinand Sreevatsan

    Citation: BMC Genomics 2010 11:561

    Content type: Research article

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  24. Clostridium sticklandii belongs to a cluster of non-pathogenic proteolytic clostridia which utilize amino acids as carbon and energy sources. Isolated by T.C. Stadtman in 1954, it has been generally regarded as a...

    Authors: Nuria Fonknechten, Sébastien Chaussonnerie, Sabine Tricot, Aurélie Lajus, Jan R Andreesen, Nadia Perchat, Eric Pelletier, Michel Gouyvenoux, Valérie Barbe, Marcel Salanoubat, Denis Le Paslier, Jean Weissenbach, Georges N Cohen and Annett Kreimeyer

    Citation: BMC Genomics 2010 11:555

    Content type: Research article

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  25. Giardia intestinalis is a protozoan parasite that causes diarrhea in a wide range of mammalian species. To further understand the genetic diversity between the Giardia intestinalis species, we have performed geno...

    Authors: Jon Jerlström-Hultqvist, Oscar Franzén, Johan Ankarklev, Feifei Xu, Eva Nohýnková, Jan O Andersson, Staffan G Svärd and Björn Andersson

    Citation: BMC Genomics 2010 11:543

    Content type: Research article

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  26. Grosmannia clavigera is a bark beetle-vectored fungal pathogen of pines that causes wood discoloration and may kill trees by disrupting nutrient and water transport. Trees respond to attacks from beetles and asso...

    Authors: Uljana Hesse-Orce, Scott DiGuistini, Christopher I Keeling, Ye Wang, Maria Li, Hannah Henderson, T Roderick Docking, Nancy Y Liao, Gordon Robertson, Robert A Holt, Steven JM Jones, Jörg Bohlmann and Colette Breuil

    Citation: BMC Genomics 2010 11:536

    Content type: Research article

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  27. Efforts using computational algorithms towards the enumeration of the full set of miRNAs of an organism have been limited by strong reliance on arguments of precursor conservation and feature similarity. Howev...

    Authors: Nuno D Mendes, Ana T Freitas, Ana T Vasconcelos and Marie-France Sagot

    Citation: BMC Genomics 2010 11:529

    Content type: Methodology article

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  28. Enzymes involved in carbohydrate metabolism include Carbohydrate esterases (CE), Glycoside hydrolases (GH), Glycosyl transferases (GT), and Polysaccharide lyases (PL), commonly referred to as carbohydrate-acti...

    Authors: Manuel D Ospina-Giraldo, John G Griffith, Emma W Laird and Christina Mingora

    Citation: BMC Genomics 2010 11:525

    Content type: Research article

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  29. Pseudomonas fluorescens is a genetically and physiologically diverse species of bacteria present in many habitats and in association with plants. This species of bacteria produces a large array of secondary metab...

    Authors: Jeffrey A Kimbrel, Scott A Givan, Anne B Halgren, Allison L Creason, Dallice I Mills, Gary M Banowetz, Donald J Armstrong and Jeff H Chang

    Citation: BMC Genomics 2010 11:522

    Content type: Research article

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  30. Vibrio vulnificus is the leading cause of reported death from consumption of seafood in the United States. Despite several decades of research on molecular pathogenesis, much remains to be learned about the mecha...

    Authors: Paul A Gulig, Valérie de Crécy-Lagard, Anita C Wright, Brandon Walts, Marina Telonis-Scott and Lauren M McIntyre

    Citation: BMC Genomics 2010 11:512

    Content type: Research article

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  31. Classical and quantitative linkage analyses of genetic crosses have traditionally been used to map genes of interest, such as those conferring chloroquine or quinine resistance in malaria parasites. Next-gener...

    Authors: Paul Hunt, Axel Martinelli, Katarzyna Modrzynska, Sofia Borges, Alison Creasey, Louise Rodrigues, Dario Beraldi, Laurence Loewe, Richard Fawcett, Sujai Kumar, Marian Thomson, Urmi Trivedi, Thomas D Otto, Arnab Pain, Mark Blaxter and Pedro Cravo

    Citation: BMC Genomics 2010 11:499

    Content type: Research article

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  32. Out-of-frame stop codons (OSCs) occur naturally in coding sequences of all organisms, providing a mechanism of early termination of translation in incorrect reading frame so that the metabolic cost associated ...

    Authors: Herman Tse, James J Cai, Hoi-Wah Tsoi, Esther PT Lam and Kwok-Yung Yuen

    Citation: BMC Genomics 2010 11:491

    Content type: Research article

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  33. Geobacter species in a phylogenetic cluster known as subsurface clade 1 are often the predominant microorganisms in subsurface environments in which Fe(III) reduction is the primary electron-accepting process. Ge...

    Authors: Muktak Aklujkar, Nelson D Young, Dawn Holmes, Milind Chavan, Carla Risso, Hajnalka E Kiss, Cliff S Han, Miriam L Land and Derek R Lovley

    Citation: BMC Genomics 2010 11:490

    Content type: Research article

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  34. Bacterial vaginosis (BV) is an ecological disorder of the vaginal microbiota that affects millions of women annually, and is associated with numerous adverse health outcomes including pre-term birth and the ac...

    Authors: Zongxin Ling, Jianming Kong, Fang Liu, Haibin Zhu, Xiaoyi Chen, Yuezhu Wang, Lanjuan Li, Karen E Nelson, Yaxian Xia and Charlie Xiang

    Citation: BMC Genomics 2010 11:488

    Content type: Research article

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  35. Systems biology and functional genomics require genome-wide datasets and resources. Complete sets of cloned open reading frames (ORFs) have been made for about a dozen bacterial species and allow researchers t...

    Authors: Seesandra V Rajagopala, Natsuko Yamamoto, Adrienne E Zweifel, Tomoko Nakamichi, Hsi-Kuang Huang, Jorge David Mendez-Rios, Jonathan Franca-Koh, Meher Preethi Boorgula, Kazutoshi Fujita, Ken-ichirou Suzuki, James C Hu, Barry L Wanner, Hirotada Mori and Peter Uetz

    Citation: BMC Genomics 2010 11:470

    Content type: Research article

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