Sample records for citrobacter rodentium genome

  1. Citrobacter rodentium is an unstable pathogen showing evidence of significant genomic flux.

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    Nicola K Petty


    Full Text Available Citrobacter rodentium is a natural mouse pathogen that causes attaching and effacing (A/E lesions. It shares a common virulence strategy with the clinically significant human A/E pathogens enteropathogenic E. coli (EPEC and enterohaemorrhagic E. coli (EHEC and is widely used to model this route of pathogenesis. We previously reported the complete genome sequence of C. rodentium ICC168, where we found that the genome displayed many characteristics of a newly evolved pathogen. In this study, through PFGE, sequencing of isolates showing variation, whole genome transcriptome analysis and examination of the mobile genetic elements, we found that, consistent with our previous hypothesis, the genome of C. rodentium is unstable as a result of repeat-mediated, large-scale genome recombination and because of active transposition of mobile genetic elements such as the prophages. We sequenced an additional C. rodentium strain, EX-33, to reveal that the reference strain ICC168 is representative of the species and that most of the inactivating mutations were common to both isolates and likely to have occurred early on in the evolution of this pathogen. We draw parallels with the evolution of other bacterial pathogens and conclude that C. rodentium is a recently evolved pathogen that may have emerged alongside the development of inbred mice as a model for human disease.

  2. Citrobacter rodentium: infection, inflammation and the microbiota. (United States)

    Collins, James W; Keeney, Kristie M; Crepin, Valerie F; Rathinam, Vijay A K; Fitzgerald, Katherine A; Finlay, B Brett; Frankel, Gad


    Citrobacter rodentium is a mucosal pathogen of mice that shares several pathogenic mechanisms with enteropathogenic Escherichia coli (EPEC) and enterohaemorrhagic E. coli (EHEC), which are two clinically important human gastrointestinal pathogens. Thus, C. rodentium has long been used as a model to understand the molecular basis of EPEC and EHEC infection in vivo. In this Review, we discuss recent studies in which C. rodentium has been used to study mucosal immunology, including the deregulation of intestinal inflammatory responses during bacteria-induced colitis and the role of the intestinal microbiota in mediating resistance to colonization by enteric pathogens. These insights should help to elucidate the roles of mucosal inflammatory responses and the microbiota in the virulence of enteric pathogens.

  3. Citrobacter rodentium mouse model of bacterial infection. (United States)

    Crepin, Valerie F; Collins, James W; Habibzay, Maryam; Frankel, Gad


    Infection of mice with Citrobacter rodentium is a robust model to study bacterial pathogenesis, mucosal immunology, the health benefits of probiotics and the role of the microbiota during infection. C. rodentium was first isolated by Barthold from an outbreak of mouse diarrhea in Yale University in 1972 and was 'rediscovered' by Falkow and Schauer in 1993. Since then the use of the model has proliferated, and it is now the gold standard for studying virulence of the closely related human pathogens enteropathogenic and enterohemorrhagic Escherichia coli (EPEC and EHEC, respectively). Here we provide a detailed protocol for various applications of the model, including bacterial growth, site-directed mutagenesis, mouse inoculation (from cultured cells and after cohabitation), monitoring of bacterial colonization, tissue extraction and analysis, immune responses, probiotic treatment and microbiota analysis. The main protocol, from mouse infection to clearance and analysis of tissues and host responses, takes ∼5 weeks to complete.

  4. Genome-wide analysis of the Pho regulon in a pstCA mutant of Citrobacter rodentium.

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    Catherine Cheng

    Full Text Available The phosphate-specific transport operon, pstSCAB-phoU, of Gram-negative bacteria is an essential part of the Pho regulon. Its key roles are to encode a high-affinity inorganic phosphate transport system and to prevent activation of PhoB in phosphate-rich environments. In general, mutations in pstSCAB-phoU lead to the constitutive expression of the Pho regulon. Previously, we constructed a pstCA deletion mutant of Citrobacter rodentium and found it to be attenuated for virulence in mice, its natural host. This attenuation was dependent on PhoB or PhoB-regulated gene(s because a phoB mutation restored virulence for mice to the pstCA mutant. To investigate how downstream genes may contribute to the virulence of C. rodentium, we used microarray analysis to investigate global gene expression of C. rodentium strain ICC169 and its isogenic pstCA mutant when grown in phosphate-rich medium. Overall 323 genes of the pstCA mutant were differentially expressed by at least 1.5-fold compared to the wild-type C. rodentium. Of these 145 were up-regulated and 178 were down-regulated. Differentially expressed genes included some involved in phosphate homoeostasis, cellular metabolism and protein metabolism. A large number of genes involved in stress responses and of unknown function were also differentially expressed, as were some virulence-associated genes. Up-regulated virulence-associated genes in the pstCA mutant included that for DegP, a serine protease, which appeared to be directly regulated by PhoB. Down-regulated genes included those for the production of the urease, flagella, NleG8 (a type III-secreted protein and the tad focus (which encodes type IVb pili in Yersinia enterocolitica. Infection studies using C57/BL6 mice showed that DegP and NleG8 play a role in bacterial virulence. Overall, our study provides evidence that Pho is a global regulator of gene expression in C. rodentium and indicates the presence of at least two previously unrecognized

  5. Virulence factors enhance Citrobacter rodentium expansion through aerobic respiration. (United States)

    Lopez, Christopher A; Miller, Brittany M; Rivera-Chávez, Fabian; Velazquez, Eric M; Byndloss, Mariana X; Chávez-Arroyo, Alfredo; Lokken, Kristen L; Tsolis, Renée M; Winter, Sebastian E; Bäumler, Andreas J


    Citrobacter rodentium uses a type III secretion system (T3SS) to induce colonic crypt hyperplasia in mice, thereby gaining an edge during its competition with the gut microbiota through an unknown mechanism. Here, we show that by triggering colonic crypt hyperplasia, the C. rodentium T3SS induced an excessive expansion of undifferentiated Ki67-positive epithelial cells, which increased oxygenation of the mucosal surface and drove an aerobic C. rodentium expansion in the colon. Treatment of mice with the γ-secretase inhibitor dibenzazepine to diminish Notch-driven colonic crypt hyperplasia curtailed the fitness advantage conferred by aerobic respiration during C. rodentium infection. We conclude that C. rodentium uses its T3SS to induce histopathological lesions that generate an intestinal microenvironment in which growth of the pathogen is fueled by aerobic respiration.

  6. Fermented dairy products modulate Citrobacter rodentium-induced colonic hyperplasia. (United States)

    Collins, James W; Chervaux, Christian; Raymond, Benoit; Derrien, Muriel; Brazeilles, Rémi; Kosta, Artemis; Chambaud, Isabelle; Crepin, Valerie F; Frankel, Gad


    We evaluated the protective effects of fermented dairy products (FDPs) in an infection model, using the mouse pathogen Citrobacter rodentium (CR). Treatment of mice with FDP formulas A, B, and C or a control product did not affect CR colonization, organ specificity, or attaching and effacing lesion formation. Fermented dairy product A (FDP-A), but neither the supernatant from FDP-A nor β-irradiated (IR) FDP-A, caused a significant reduction in colonic crypt hyperplasia and CR-associated pathology. Profiling the gut microbiota revealed that IR-FDP-A promoted higher levels of phylotypes belonging to Alcaligenaceae and a decrease in Lachnospiraceae (Ruminococcus) during CR infection. Conversely, FDP-A prevented a decrease in Ruminococcus and increased Turicibacteraceae (Turicibacter). Importantly, loss of Ruminococcus and Turicibacter has been associated with susceptibility to dextran sodium sulfate-induced colitis. Our results demonstrate that viable bacteria in FDP-A reduced CR-induced colonic crypt hyperplasia and prevented the loss of key bacterial genera that may contribute to disease pathology.

  7. Long-term selenium deficiency increases the pathogenicity of a Citrobacter rodentium infection in mice (United States)

    Citrobacter rodentium is a mouse pathogen that causes infectious colitis and shares characteristics with human enteropathogenic (EPEC) and enterohemorrhagic (EHEC) Escherichia coli, including the ability to cause attaching and effacing lesions in the colon, and serves as a useful model to study the ...

  8. Hypervirulent- host-associated Citrobacter rodentium cells have poor acid tolerance (United States)

    Enhanced virulence or infectivity after passage through a mammalian host has been reported for a number of enteric food-borne pathogens. Citrobacter rodentium is a mouse pathogen that mimics many aspects of enterohemorrhagic E. coli infection of humans and serves as a useful model for studying viru...

  9. Citrobacter rodentium-induced colitis: A robust model to study mucosal immune responses in the gut. (United States)

    Koroleva, Ekaterina P; Halperin, Sydney; Gubernatorova, Ekaterina O; Macho-Fernandez, Elise; Spencer, Cody M; Tumanov, Alexei V


    Citrobacter rodentium is a natural mouse pathogen which reproducibly infects mice and causes intestinal disease. The C. rodentium model of infection is very useful for investigating host-pathogen immune interactions in the gut, and can also be used to understand the pathogenesis of several important human intestinal disorders, including Crohn's disease, ulcerative colitis, dysbiosis and colon tumorigenesis. Both innate and adaptive immune responses play a critical role in protection against C. rodentium. Here, we summarize the role of immune components in protection against C. rodentium and describe techniques for the analysis of innate and adaptive mucosal immune responses, including setting up the infection, analysis of colonic hyperplasia and bacterial dissemination, evaluation of antibody responses, and purification and analysis of intestinal epithelial and lymphoid cells.

  10. Hypervirulent-host-associated Citrobacter rodentium cells have poor acid tolerance. (United States)

    Smith, Allen; Bhagwat, Arvind A


    Enhanced virulence or infectivity after passage through a mammalian host has been reported for a number of enteric food-borne pathogens. Citrobacter rodentium is a mouse pathogen that mimics many aspects of enterohemorrhagic Escherichia coli infection of humans and serves as a useful model for studying virulence mechanisms. Emergence of a hyperinfectious state after passage through mouse gastrointestinal tract was reported for C. rodentium. We wanted to investigate if increased acid tolerance could explain hypervirulence status of C. rodentium. Although we were able to observe hyperinfectious state of C. rodentium upon host passage, the cells were extremely acid sensitive. Growth under mildly acidic conditions (LB-MES, pH 5.5) induced acid tolerance of C. rodentium, but did not improve the organism's ability to establish infection. Growth under anaerobic environment on fecal components also did not induce hyperinfectious state. Thus, contrary to conventional anticipation, hypervirulent C. rodentium cells were found to be acid sensitive thereby revealing limitations of the role of mouse gastric acidity by itself in elucidating the hypervirulent phenotype.

  11. Development of a real-time PCR assay for quantification of Citrobacter rodentium. (United States)

    Sagaidak, Sofia; Taibi, Amel; Wen, Bijun; Comelli, Elena M


    Molecular tools to quantify Citrobacter rodentium are not available. We developed a quantitative PCR assay targeting the espB gene. This assay is specific, has a linearity range of about 6.7×10(1) to 6.7×10(6)cells/PCR reaction (92% efficiency) and a detection limit of about 10(4)cells/g wet feces.

  12. Stressor exposure has prolonged effects on colonic microbial community structure in Citrobacter rodentium-challenged mice (United States)

    Galley, Jeffrey D.; Mackos, Amy R.; Varaljay, Vanessa A.; Bailey, Michael T.


    Stressor exposure significantly affects the colonic mucosa-associated microbiota, and exacerbates Citrobacter rodentium-induced inflammation, effects that can be attenuated with probiotic Lactobacillus reuteri. This study assessed the structure of the colonic mucosa-associated microbiota in mice exposed to a social stressor (called social disruption), as well as non-stressed control mice, during challenge with the colonic pathogen C. rodentium. Mice were exposed to the social stressor or home cage control conditions for six consecutive days and all mice were challenged with C. rodentium immediately following the first exposure to the stressor. In addition, mice received probiotic L. reuteri, or vehicle as a control, via oral gavage following each stressor exposure. The stressor-exposed mice had significant differences in microbial community composition compared to non-stressed control mice. This difference was first evident following the six-cycle exposure to the stressor, on Day 6 post-C. rodentium challenge, and persisted for up to 19 days after stressor termination. Mice exposed to the stressor had different microbial community composition regardless of whether they were treated with L. reuteri or treated with vehicle as a control. These data indicate that stressor exposure affects the colonic microbiota during challenge with C. rodentium, and that these effects are long-lasting and not attenuated by probiotic L. reuteri. PMID:28344333

  13. The Serine Protease Autotransporter Pic Modulates Citrobacter rodentium Pathogenesis and Its Innate Recognition by the Host. (United States)

    Bhullar, Kirandeep; Zarepour, Maryam; Yu, Hongbing; Yang, Hong; Croxen, Matthew; Stahl, Martin; Finlay, B Brett; Turvey, Stuart E; Vallance, Bruce A


    Bacterial pathogens produce a number of autotransporters that possess diverse functions. These include the family of serine protease autotransporters of Enterobacteriaceae (SPATEs) produced by enteric pathogens such as Shigella flexneri and enteroaggregative Escherichia coli. Of these SPATEs, one termed "protein involved in colonization," or Pic, has been shown to possess mucinase activity in vitro, but to date, its role in in vivo enteric pathogenesis is unknown. Testing a pic null (ΔpicC) mutant in Citrobacter rodentium, a natural mouse pathogen, found that the C. rodentium ΔpicC strain was impaired in its ability to degrade mucin in vitro compared to the wild type. Upon infection of mice, the ΔpicC mutant exhibited a hypervirulent phenotype with dramatically heavier pathogen burdens found in intestinal crypts. ΔpicC mutant-infected mice suffered greater barrier disruption and more severe colitis and weight loss, necessitating their euthanization between 10 and 14 days postinfection. Notably, the virulence of the ΔpicC mutant was normalized when the picC gene was restored; however, a PicC point mutant causing loss of mucinase activity did not replicate the ΔpicC phenotype. Exploring other aspects of PicC function, the ΔpicC mutant was found to aggregate to higher levels in vivo than wild-type C. rodentium. Moreover, unlike the wild type, the C. rodentium ΔpicC mutant had a red, dry, and rough (RDAR) morphology in vitro and showed increased activation of the innate receptor Toll-like receptor 2 (TLR2). Interestingly, the C. rodentium ΔpicC mutant caused a degree of pathology similar to that of wild-type C. rodentium when infecting TLR2-deficient mice, showing that despite its mucinase activity, PicC's major role in vivo may be to limit C. rodentium's stimulation of the host's innate immune system.

  14. The CpxRA two-component system is essential for Citrobacter rodentium virulence. (United States)

    Thomassin, Jenny-Lee; Giannakopoulou, Natalia; Zhu, Lei; Gross, Jeremy; Salmon, Kristiana; Leclerc, Jean-Mathieu; Daigle, France; Le Moual, Hervé; Gruenheid, Samantha


    Citrobacter rodentium is a murine intestinal pathogen used as a model for the foodborne human pathogens enterohemorrhagic Escherichia coli and enteropathogenic E. coli. During infection, these pathogens use two-component signal transduction systems to detect and adapt to changing environmental conditions. In E. coli, the CpxRA two-component signal transduction system responds to envelope stress by modulating the expression of a myriad of genes. Quantitative real-time PCR showed that cpxRA was expressed in the colon of C57BL/6J mice infected with C. rodentium. To determine whether CpxRA plays a role during C. rodentium infection, a cpxRA deletion strain was generated and found to have a colonization defect during infection. This defect was independent of an altered growth rate or a defective type III secretion system, and single-copy chromosomal complementation of cpxRA restored virulence. The C. rodentium strains were then tested in C3H/HeJ mice, a lethal intestinal infection model. Mice infected with the ΔcpxRA strain survived infection, whereas mice infected with the wild-type or complemented strains succumbed to infection. Furthermore, we found that the cpxRA expression level was higher during early infection than at a later time point. Taken together, these data demonstrate that the CpxRA two-component signal transduction system is essential for the in vivo virulence of C. rodentium. In addition, these data suggest that fine-tuned cpxRA expression is important for infection. This is the first study that identifies a C. rodentium two-component transduction system required for pathogenesis. This study further indicates that CpxRA is an interesting target for therapeutics against enteric pathogens.

  15. Evolutionary adaptation of an AraC-like regulatory protein in Citrobacter rodentium and Escherichia species. (United States)

    Tan, Aimee; Petty, Nicola K; Hocking, Dianna; Bennett-Wood, Vicki; Wakefield, Matthew; Praszkier, Judyta; Tauschek, Marija; Yang, Ji; Robins-Browne, Roy


    The evolution of pathogenic bacteria is a multifaceted and complex process, which is strongly influenced by the horizontal acquisition of genetic elements and their subsequent expression in their new hosts. A well-studied example is the RegA regulon of the enteric pathogen Citrobacter rodentium. The RegA regulatory protein is a member of the AraC/XylS superfamily, which coordinates the expression of a gene repertoire that is necessary for full pathogenicity of this murine pathogen. Upon stimulation by an exogenous, gut-associated signal, namely, bicarbonate ions, RegA activates the expression of a series of genes, including virulence factors, such as autotransporters, fimbriae, a dispersin-like protein, and the grlRA operon on the locus of enterocyte effacement pathogenicity island. Interestingly, the genes encoding RegA homologues are distributed across the genus Escherichia, encompassing pathogenic and nonpathogenic subtypes. In this study, we carried out a series of bioinformatic, transcriptional, and functional analyses of the RegA regulons of these bacteria. Our results demonstrated that regA has been horizontally transferred to Escherichia spp. and C. rodentium. Comparative studies of two RegA homologues, namely, those from C. rodentium and E. coli SMS-3-5, a multiresistant environmental strain of E. coli, showed that the two regulators acted similarly in vitro but differed in terms of their abilities to activate the virulence of C. rodentium in vivo, which evidently was due to their differential activation of grlRA. Our data indicate that RegA from C. rodentium has strain-specific adaptations that facilitate infection of its murine host. These findings shed new light on the development of virulence by C. rodentium and on the evolution of virulence-regulatory genes of bacterial pathogens in general.

  16. Tir Triggers Expression of CXCL1 in Enterocytes and Neutrophil Recruitment during Citrobacter rodentium Infection. (United States)

    Crepin, Valerie F; Habibzay, Maryam; Glegola-Madejska, Izabela; Guenot, Marianne; Collins, James W; Frankel, Gad


    The hallmarks of enteropathogenic Escherichia coli (EPEC) infection are formation of attaching and effacing (A/E) lesions on mucosal surfaces and actin-rich pedestals on cultured cells, both of which are dependent on the type III secretion system effector Tir. Following translocation into cultured cells and clustering by intimin, Tir Y474 is phosphorylated, leading to recruitment of Nck, activation of N-WASP, and actin polymerization via the Arp2/3 complex. A secondary, weak, actin polymerization pathway is triggered via an NPY motif (Y454). Importantly, Y454 and Y474 play no role in A/E lesion formation on mucosal surfaces following infection with the EPEC-like mouse pathogen Citrobacter rodentium. In this study, we investigated the roles of Tir segments located upstream of Y451 and downstream of Y471 in C. rodentium colonization and A/E lesion formation. We also tested the role that Tir residues Y451 and Y471 play in host immune responses to C. rodentium infection. We found that deletion of amino acids 382 to 462 or 478 to 547 had no impact on the ability of Tir to mediate A/E lesion formation, although deletion of amino acids 478 to 547 affected Tir translocation. Examination of enterocytes isolated from infected mice revealed that a C. rodentium strain expressing Tir_Y451A/Y471A recruited significantly fewer neutrophils to the colon and triggered less colonic hyperplasia on day 14 postinfection than the wild-type strain. Consistently, enterocytes isolated from mice infected with C. rodentium expressing Tir_Y451A/Y471A expressed significantly less CXCL1. These result show that Tir-induced actin remodeling plays a direct role in modulation of immune responses to C. rodentium infection.

  17. Dietary Chitosan Supplementation Increases Microbial Diversity and Attenuates the Severity of Citrobacter rodentium Infection in Mice (United States)

    Wang, Hongbing; Xiong, Xia; Tan, Bie; Al-Dhabi, Naif Abdullah; Fang, Jun


    C57BL/6 mice were tested in order to investigate the effects of dietary chitosan (COS) supplements on intestinal microflora and resistance to Citrobacter rodentium infection. The findings reveal that, after consuming a 300 mg/kg COS diet for 14 days, microflora became more diverse as a result of the supplement. Mice receiving COS exhibited an increase in the percentage of Bacteroidetes phylum and a decrease in the percentage of Firmicutes phylum. After Citrobacter rodentium infection, the histopathology scores indicated that COS feeding resulted in less severe colitis. IL-6 and TNF-α were significantly lower in colon from COS-feeding mice than those in the control group. Furthermore, mice in COS group were also found to experience inhibited activation of nuclear factor-kappa B (NF-κB) in the colonic tissue. Overall, the findings revealed that adding 300 mg/kg COS to the diet changed the composition of the intestinal microflora of mice, resulting in suppressed NF-κB activation and less production of TNF-α and IL-6; and these changes led to better control of inflammation and resolution of infection with C. rodentium. PMID:27761062

  18. Dietary Chitosan Supplementation Increases Microbial Diversity and Attenuates the Severity of Citrobacter rodentium Infection in Mice

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    Guiping Guan


    Full Text Available C57BL/6 mice were tested in order to investigate the effects of dietary chitosan (COS supplements on intestinal microflora and resistance to Citrobacter rodentium infection. The findings reveal that, after consuming a 300 mg/kg COS diet for 14 days, microflora became more diverse as a result of the supplement. Mice receiving COS exhibited an increase in the percentage of Bacteroidetes phylum and a decrease in the percentage of Firmicutes phylum. After Citrobacter rodentium infection, the histopathology scores indicated that COS feeding resulted in less severe colitis. IL-6 and TNF-α were significantly lower in colon from COS-feeding mice than those in the control group. Furthermore, mice in COS group were also found to experience inhibited activation of nuclear factor-kappa B (NF-κB in the colonic tissue. Overall, the findings revealed that adding 300 mg/kg COS to the diet changed the composition of the intestinal microflora of mice, resulting in suppressed NF-κB activation and less production of TNF-α and IL-6; and these changes led to better control of inflammation and resolution of infection with C. rodentium.

  19. The cell surface receptor Slamf6 modulates innate immune responses during Citrobacter rodentium-induced colitis. (United States)

    van Driel, Boaz; Wang, Guoxing; Liao, Gongxian; Halibozek, Peter J; Keszei, Marton; O'Keeffe, Michael S; Bhan, Atul K; Wang, Ninghai; Terhorst, Cox


    The homophilic cell surface receptors CD150 (Slamf1) and CD352 (Slamf6) are known to modulate adaptive immune responses. Although the Th17 response was enhanced in Slamf6(-/-) C57BL/6 mice upon oral infection with Citrobacter rodentium, the pathologic consequences are indistinguishable from an infection of wild-type C57BL/6 mice. Using a reporter-based binding assay, we show that Slamf6 can engage structures on the outer cell membrane of several Gram(-) bacteria. Therefore, we examined whether Slamf6, like Slamf1, is also involved in innate responses to bacteria and regulates peripheral inflammation by assessing the outcome of C. rodentium infections in Rag(-/-) mice. Surprisingly, the pathology and immune responses in the lamina propria of C. rodentium-infected Slamf6(-/-) Rag(-/-) mice were markedly reduced as compared with those of Rag(-/-) mice. Infiltration of inflammatory phagocytes into the lamina propria was consistently lower in Slamf6(-/-) Rag(-/-) mice than in Rag(-/-) animals. Concomitant with the reduced systemic translocation of the bacteria was an enhanced production of IL-22, suggesting that Slamf6 suppresses a mucosal protective program. Furthermore, administering a mAb (330) that inhibits bacterial interactions with Slamf6 to Rag(-/-) mice ameliorated the infection compared with a control antibody. We conclude that Slamf6-mediated interactions of colonic innate immune cells with specific Gram(-) bacteria reduce mucosal protection and enhance inflammation, contributing to lethal colitis that is caused by C. rodentium infections in Rag(-/-) mice.

  20. Selective enrichment of commensal gut bacteria protects against Citrobacter rodentium-induced colitis. (United States)

    Vong, Linda; Pinnell, Lee J; Määttänen, Pekka; Yeung, C William; Lurz, Eberhard; Sherman, Philip M


    The intestinal microbiota plays a key role in shaping the host immune system. Perturbation of gut microbial composition, termed dysbiosis, is associated with an increased susceptibility to intestinal pathogens and is a hallmark of a number of inflammatory, metabolic, and infectious diseases. The prospect of mining the commensal gut microbiota for bacterial strains that can impact immune function represents an attractive strategy to counteract dysbiosis and resulting disease. In this study, we show that selective enrichment of commensal gut lactobacilli protects against the murine pathogen Citrobacter rodentium, a well-characterized model of enteropathogenic and enterohemorrhagic Escherichia coli infection. The lactobacilli-enriched bacterial culture prevented the expansion of Gammaproteobacteria and Actinobacteria and was associated with improved indexes of epithelial barrier function (dextran flux), transmissible crypt hyperplasia, and tissue inflammatory cytokine levels. Moreover, cultivation of gut bacteria from Citrobacter rodentium-infected mice reveals the differential capacity of bacterial subsets to mobilize neutrophil oxidative burst and initiate the formation of weblike neutrophil extracellular traps. Our findings highlight the beneficial effects of a lactobacilli-enriched commensal gut microenvironment and, in the context of an intestinal barrier breach, the ability of neutrophils to immobilize both commensal and pathogenic bacteria.

  1. The pathogenicity of an enteric Citrobacter rodentium infection is enhanced by deficiencies in the antioxidants selenium and vitamin E (United States)

    Citrobacter rodentium is a mouse pathogen that shares many characteristics with human enteropathogenic (EPEC) and enterohemorrhagic (EHEC) Escherichia coli, the causative agents for human disease, and serves as a useful model to study immunity to these organisms. In this study, the effect of a doub...

  2. Influence of NleH effector expression, host genetics, and inflammation on Citrobacter rodentium colonization of mice. (United States)

    Feuerbacher, Leigh Ann; Hardwidge, Philip R


    The Escherichia coli NleH1 and NleH2 virulence proteins differentially regulate host transcription of innate immunity genes. The mouse pathogen Citrobacter rodentium encodes one NleH protein, which functions equivalently to E. coli NleH1. We examined the impact of host genetics and intestinal inflammation on the contribution of NleH to C. rodentium colonization of mice differing in LPS responsiveness. NleH expression was detrimental to C. rodentium in C57BL/10ScNJ mice, which do not mount LPS-induced inflammatory responses. This phenotype was reversed if inflammation was induced by chemical means. C. rodentium that expressed both E. coli NleH1 and NleH2 was hypervirulent in C3H/HeJ mice.

  3. Investigation of Host and Pathogen Contributions to Infectious Colitis Using the Citrobacter rodentium Mouse Model of Infection. (United States)

    Bosman, Else S; Chan, Justin M; Bhullar, Kirandeep; Vallance, Bruce A


    Citrobacter rodentium is used as a model organism to study enteric bacterial infections in mice. Infection occurs via the oral-fecal route and results in the pathogen forming attaching and effacing lesions on infected epithelial cells. Moreover, infection leads to a subsequent host-mediated form of colitis. C. rodentium infection is thus an excellent model to study infectious colitis in vivo, while the ability to genetically manipulate C. rodentium virulence genes provides the opportunity to develop clear insights into the pathogenesis of this and related infectious microbes. This chapter outlines the basic techniques involved in setting up a C. rodentium infection in mice and several different methodologies to assess the severity of the infection.

  4. Rac2-deficiency leads to exacerbated and protracted colitis in response to Citrobacter rodentium infection.

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    Ramzi Fattouh

    Full Text Available Recent genetic-based studies have implicated a number of immune-related genes in the pathogenesis of inflammatory bowel disease (IBD. Our recent genetic studies showed that RAC2 is associated with human IBD; however, its role in disease pathogenesis is unclear. Given Rac2's importance in various fundamental immune cell processes, we investigated whether a defect in Rac2 may impair host immune responses in the intestine and promote disease in the context of an infection-based (Citrobacter rodentium model of colitis. In response to infection, Rac2(-/- mice showed i worsened clinical symptoms (days 13-18, ii increased crypt hyperplasia at days 11 and 22 (a time when crypt hyperplasia was largely resolved in wild-type mice; WT, and iii marked mononuclear cell infiltration characterized by higher numbers of T (CD3(+ cells (day 22, compared to WT-infected mice. Moreover, splenocytes harvested from infected Rac2(-/- mice and stimulated in vitro with C. rodentium lysate produced considerably higher levels of interferon-γ and interleukin-17A. The augmented responses observed in Rac2(-/- mice did not appear to stem from Rac2's role in NADPH oxidase-driven reactive oxygen species production as no differences in crypt hyperplasia, nor inflammation, were observed in infected NOX2(-/- mice compared to WT. Collectively, our findings demonstrate that Rac2(-/- mice develop more severe disease when subjected to a C. rodentium-induced model of infectious colitis, and suggest that impaired Rac2 function may promote the development of IBD in humans.

  5. Psidium guajava leaf extract prevents intestinal colonization of Citrobacter rodentium in the mouse model

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    Pooja Gupta


    Full Text Available Diarrheal diseases are the second highest cause of mortality of children under 5 years worldwide. There is a continuous search for developing a cost-effective treatment for diarrhea as the present ones are facing challenges. Medicinal plants can be explored further as an alternative treatment for diarrhea. Psidium guajava leaves have been used as an antidiarrheal globally. Citrobacter rodentium, a common mouse pathogen, is known to mimic the pathogenecity of enteropathogenic and enterohemorrhagic E. coli. It can thus present an effective model to study infectious diarrhea. In the present study, the P. guajava leaf extract was tested for its efficacy in treating infectious diarrhea using a C. rodentium mouse model. The mice in the test group (treated with P. guajava leaf extract showed quicker clearance of infection as compared with the control group. The bacterial load in the fecal sample of the mice in the test group was high on Day 4 as compared with that in the control group, suggesting a flush out of the bacteria. In the test group, 6/7 (85.71% mice showed clearance of infection by Day 19. The control group continued to show infection till Day 29. P. guajava leaf extract thus has the potential for use in the treatment of infectious diarrhea.

  6. A balanced IL-1β activity is required for host response to Citrobacter rodentium infection.

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    Misagh Alipour

    Full Text Available Microbial sensing plays essential roles in the innate immune response to pathogens. In particular, NLRP3 forms a multiprotein inflammasome complex responsible for the maturation of interleukin (IL-1β. Our aim was to delineate the role of the NLRP3 inflammasome in macrophages, and the contribution of IL-1β to the host defense against Citrobacter rodentium acute infection in mice. Nlrp3(-/- and background C57BL/6 (WT mice were infected by orogastric gavage, received IL-1β (0.5 µg/mouse; ip on 0, 2, and 4 days post-infection (DPI, and assessed on 6 and 10 DPI. Infected Nlrp3(-/- mice developed severe colitis; IL-1β treatments reduced colonization, abrogated dissemination of bacteria to mesenteric lymph nodes, and protected epithelial integrity of infected Nlrp3(-/- mice. In contrast, IL-1β treatments of WT mice had an opposite effect with increased penetration of bacteria and barrier disruption. Microscopy showed reduced damage in Nlrp3(-/- mice, and increased severity of disease in WT mice with IL-1β treatments, in particular on 10 DPI. Secretion of some pro-inflammatory plasma cytokines was dissipated in Nlrp3(-/- compared to WT mice. IL-1β treatments elevated macrophage infiltration into infected crypts in Nlrp3(-/- mice, suggesting that IL-1β may improve macrophage function, as exogenous administration of IL-1β increased phagocytosis of C. rodentium by peritoneal Nlrp3(-/- macrophages in vitro. As well, the exogenous administration of IL-1β to WT peritoneal macrophages damaged the epithelial barrier of C. rodentium-infected polarized CMT-93 cells. Treatment of Nlrp3(-/- mice with IL-1β seems to confer protection against C. rodentium infection by reducing colonization, protecting epithelial integrity, and improving macrophage activity, while extraneous IL-1β appeared to be detrimental to WT mice. Together, these findings highlight the importance of balanced cytokine responses as IL-1β improved bacterial clearance in Nlrp3(-/- mice

  7. Polarizing the T helper 17 response in Citrobacter rodentium infection via expression of resistin-like molecule α. (United States)

    Chen, Gang; Chan, Alexander J; Chung, Josiah I; Jang, Jessica C; Osborne, Lisa C; Nair, Meera G


    Citrobacter rodentium infection is a murine model of pathogenic Escherichia coli infection that allows investigation of the cellular and molecular mechanisms involved in host-protective immunity and bacterial-induced intestinal inflammation. We recently demonstrated that following C. rodentium infection, the absence of Resistin-Like Molecule (RELM) α resulted in attenuated Th17 cell responses and reduced intestinal inflammation with minimal effects on bacterial clearance. In this addendum, we investigated the cytokine modulatory effects of RELMα and RELMα expression in the intestinal mucosa following C. rodentium infection. We show that in addition to promoting Th17 cytokine responses, RELMα inhibits Th2 cytokine expression and Th2-cytokine effector macrophage responses in the C. rodentium-infected colons. Second, utilizing reporter C. rodentium, we examined RELMα expression and macrophage recruitment at the host pathogen interface. We observed infection-induced macrophage infiltration and RELMα expression by intestinal epithelial cells. The influence of infection-induced RELMα on macrophage recruitment in the intestine is discussed.

  8. Role of class 1 serine protease autotransporter in the pathogenesis of Citrobacter rodentium colitis. (United States)

    Vijayakumar, Vidhya; Santiago, Araceli; Smith, Rachel; Smith, Mark; Robins-Browne, Roy M; Nataro, James P; Ruiz-Perez, Fernando


    A growing family of virulence factors called serine protease autotransporters of Enterobacteriaceae (SPATEs) are secreted by Shigella, Salmonella, and Escherichia coli pathotypes. SPATEs are subdivided into class 1 and class 2 based on structural features and phylogenetics. Class 1 SPATEs induce cytopathic effects in numerous epithelial cell lines, and several have been shown to cleave the cytoskeletal protein spectrin in vitro. However, to date the in vivo role of class 1 SPATEs in enteric pathogenesis is unknown. Citrobacter rodentium, a natural mouse pathogen, has recently been shown to harbor class 1 and class 2 SPATEs. To better understand the contribution of class 1 SPATEs in enteric infection, we constructed a class 1 SPATE null mutant (Δcrc1) in C. rodentium. Upon infection of C57BL/6 mice, the Δcrc1 mutant exhibited a hypervirulent, hyperinflammatory phenotype compared with its parent, accompanied by greater weight loss and a trend toward increased mortality in young mice; the effect was reversed when the crc1 gene was restored. Using flow cytometry, we observed increased infiltration of T cells, B cells, and neutrophils into the lamina propria of the distal colon in mice fed the Δcrc1 mutant, starting as early as 5 days after infection. No significant difference in epithelial cytotoxicity was observed. Reverse transcription-PCR (RT-PCR) analysis of distal colonic tissue on day 10 postinfection showed significant increases in mRNA encoding cytokines interleukin-6 (IL-6), tumor necrosis factor alpha (TNF-α), gamma interferon (IFN-γ), IL-1β, and inducible nitric oxide synthase (iNOS) but not in mRNA encoding IL-17, IL-4, or IL-10 in the Δcrc1 mutant-infected mice. Our data suggest a previously unsuspected role for class 1 SPATEs in enteric infection.

  9. Immunological mechanisms involved in probiotic-mediated protection against Citrobacter rodentium-induced colitis. (United States)

    Jiang, Y; Yang, G; Meng, F; Yang, W; Hu, J; Ye, L; Shi, C; Wang, C


    Inflammatory bowel disease is a group of chronic, incurable inflammatory disorders of the gastrointestinal tract that cause severe diarrhoea, intestinal inflammation, pain, fatigue and weight loss. In this study, we first developed a model of Citrobacter rodentium-induced colitis and then evaluated the protective effects of selected probiotics on inflammation. The results showed that administration of a combination of probiotics including Lactobacillus rhamnosus ATCC 53103, Lactobacillus acidophilus ATCC 4356 and Lactobacillus plantarum A significantly increased the production of CD11c(+) dendritic cells in the spleen (3.62% vs phosphate buffered saline (PBS)-treated control, P<0.01) and mesenteric lymph nodes (MLNs). In addition, the presence of probiotics significantly up-regulated the development of CD4(+)/CD25(+)/Foxp3(+) regulatory T cells in MLNs by approximately 2.07% compared to the effect observed in the PBS-treated control (P<0.01) and down-regulated the expression of inflammatory cytokines, including interleukin-17, tumour necrosis factor-α and interferon-γ, by 0.11, 0.11 and 0.15%, respectively, compared to the effect observed in the PBS-treated control (P<0.01).These effects conferred protection against colitis, as shown by histopathological analyses.

  10. Understanding the host-adapted state of Citrobacter rodentium by transcriptomic analysis. (United States)

    Smith, Allen D; Yan, Xianghe; Chen, Celine; Dawson, Harry D; Bhagwat, Arvind A


    Citrobacter rodentium (Cr) is a mouse pathogen that mimics many aspects of enteropathogenic Escherichia coli infections including producing attaching and effacing (A/E) lesions. Host-adapted (HA) Cr cells that are shed at the peak of infection have been reported to be hyper-infective. The exact mechanism underlying this phenomenon has remained elusive since the pathogen loses its HA 'status' immediately upon subculturing in laboratory media. We sequenced the entire transcriptome of Cr directly from the feces of infected mice and analyzed the gene expression pattern. We observed that the entire transcriptional machinery as well as several transcriptional regulators to be differentially expressed when compared with the transcriptome of cells grown on laboratory media. Major adhesion and effector genes, tir and eae, were highly expressed in HA along with many genes located on all five loci of enterocyte effacement regions (LEE 1-5). Notable absent among the HA expressed genes were 19 fimbrial operons and non-fimbrial adhesions and several non-LEE encoded effectors. These results demonstrate that host-adapted Cr has a unique transcriptome that is associated with increased host transmission.

  11. Inflammasome Activation by ATP Enhances Citrobacter rodentium Clearance through ROS Generation

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    Michael Bording-Jorgensen


    Full Text Available Background: Nod-like receptor family, pyrin domain containing 3 (NLRP3 is an important cytosolic sensor of cellular stress and infection. Once activated, NLRP3 forms a multiprotein complex (inflammasome that triggers the maturation and secretion of interleukin (IL-1β and IL-18. We aimed to define the consequences of NLRP3 induction, utilizing exogenous adenosine triphosphate (ATP as an inflammasome activator, to determine if inflammasome activation increases macrophage killing of Citrobacter rodentium and define mechanisms. Methods: Bacterial survival was measured using a gentamicin protection assay. Inflammasome activation or inhibition in mouse J774A.1 macrophages were assessed by measuring IL-1β; cytokines and reactive oxygen species (ROS were measured by ELISA and DCFDA, respectively. Results: Activation of the inflammasome increased bacterial killing by macrophages and its inhibition attenuated this effect with no impact on phagocytosis or cell death. Furthermore, inflammasome activation suppressed pro-inflammatory cytokines during infection, possibly due to more effective bacterial killing. While the infection increased ROS production, this effect was reduced by inflammasome inhibitors, indicating that ROS is inflammasome-dependent. ROS inhibitors increased bacterial survival in the presence of ATP, suggesting that inflammasome-induced bacterial killing is mediated, at least in part, by ROS activity. Conclusion: Improving inflammasome activity during infection may increase bacterial clearance by macrophages and reduce subsequent microbe-induced inflammation.

  12. IL-23-mediated mononuclear phagocyte crosstalk protects mice from Citrobacter rodentium-induced colon immunopathology. (United States)

    Aychek, Tegest; Mildner, Alexander; Yona, Simon; Kim, Ki-Wook; Lampl, Nardy; Reich-Zeliger, Shlomit; Boon, Louis; Yogev, Nir; Waisman, Ari; Cua, Daniel J; Jung, Steffen


    Gut homeostasis and mucosal immune defense rely on the differential contributions of dendritic cells (DC) and macrophages. Here we show that colonic CX3CR1(+) mononuclear phagocytes are critical inducers of the innate response to Citrobacter rodentium infection. Specifically, the absence of IL-23 expression in macrophages or CD11b(+) DC results in the impairment of IL-22 production and in acute lethality. Highlighting immunopathology as a death cause, infected animals are rescued by the neutralization of IL-12 or IFNγ. Moreover, mice are also protected when the CD103(+) CD11b(-) DC compartment is rendered deficient for IL-12 production. We show that IL-12 production by colonic CD103(+) CD11b(-) DC is repressed by IL-23. Collectively, in addition to its role in inducing IL-22 production, macrophage-derived or CD103(-) CD11b(+) DC-derived IL-23 is required to negatively control the otherwise deleterious production of IL-12 by CD103(+) CD11b(-) DC. Impairment of this critical mononuclear phagocyte crosstalk results in the generation of IFNγ-producing former TH17 cells and fatal immunopathology.

  13. Dysbiosis caused by vitamin D receptor deficiency confers colonization resistance to Citrobacter rodentium through modulation of innate lymphoid cells. (United States)

    Chen, J; Waddell, A; Lin, Y-D; Cantorna, M T


    Vitamin D receptor (VDR) knockout (KO) mice had fewer Citrobacter rodentium in the feces than wild-type (WT) mice and the kinetics of clearance was faster in VDR KO than WT mice. VDR KO mice had more interleukin-22 (IL-22)-producing innate lymphoid cells (ILCs) and more antibacterial peptides than WT mice. The increased ILCs in the VDR KO mice was a cell-autonomous effect of VDR deficiency on ILC frequencies. Bone marrow (BM) transplantation from VDR KO mice into WT resulted in higher ILCs and colonization resistance of the WT mice. Disruption of the gut microbiota using antibiotics in VDR KO mice reversed colonization resistance to C. rodentium infection. Confirming the role of the microbiota in the colonization resistance of VDR KO mice, transfer of the VDR KO microbiota to WT germ-free mice resulted in colonization resistance. Once colonization resistance was overcome, VDR KO mice had increased susceptibility to C. rodentium. VDR expression is a regulator of ILC frequencies, IL-22, dysbiosis, and C. rodentium susceptibility.

  14. Dietary vitamin D3 deficiency alters intestinal mucosal defense and increases susceptibility to Citrobacter rodentium-induced colitis. (United States)

    Ryz, Natasha R; Lochner, Arion; Bhullar, Kirandeep; Ma, Caixia; Huang, Tina; Bhinder, Ganive; Bosman, Else; Wu, Xiujuan; Innis, Sheila M; Jacobson, Kevan; Vallance, Bruce A


    Vitamin D deficiency affects more that 1 billion people worldwide. Although thought to increase risk of bacterial infections, the importance of vitamin D on host defense against intestinal bacterial pathogens is currently unclear since injection of the active form of vitamin D, 1,25(OH)2D3, increased susceptibility to the enteric bacterial pathogen Citrobacter rodentium by suppressing key immune/inflammatory factors. To further characterize the role of vitamin D during bacteria-induced colitis, we fed weanling mice either vitamin D3-deficient or vitamin D3-sufficient diets for 5 wk and then challenged them with C. rodentium. Vitamin D3-deficient mice lost significantly more body weight, carried higher C. rodentium burdens, and developed worsened histological damage. Vitamin D3-deficient mice also suffered greater bacterial translocation to extra-intestinal tissues, including mesenteric lymph nodes, spleen, and liver. Intestinal tissues of infected vitamin D3-deficient mice displayed increased inflammatory cell infiltrates as well as significantly higher gene transcript levels of inflammatory mediators TNF-α, IL-1β, IL-6, TGF-β, IL-17A, and IL-17F as well as the antimicrobial peptide REG3γ. Notably, these exaggerated inflammatory responses accelerated the loss of commensal microbes and were associated with an impaired ability to detoxify bacterial lipopolysaccharide. Overall, these studies show that dietary-induced vitamin D deficiency exacerbates intestinal inflammatory responses to infection, also impairing host defense.

  15. CXCL9 contributes to antimicrobial protection of the gut during citrobacter rodentium infection independent of chemokine-receptor signaling.

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    Sarah A Reid-Yu


    Full Text Available Chemokines have been shown to be effective bactericidal molecules against a variety of bacteria and fungi in vitro. These direct antimicrobial effects are independent of their chemotactic activities involving immunological receptors. However, the direct biological role that these proteins may play in host defense, particularly against intestinal pathogens, is poorly understood. Here, we show that CXCL9, an ELR- chemokine, exhibits direct antimicrobial activity against Citrobacter rodentium, an attaching/effacing pathogen that infects the gut mucosa. Inhibition of this antimicrobial activity in vivo using anti-CXCL9 antibodies increases host susceptibility to C. rodentium infection with pronounced bacterial penetration into crypts, increased bacterial load, and worsened tissue pathology. Using Rag1(-/- mice and CXCR3(-/- mice, we demonstrate that the role for CXCL9 in protecting the gut mucosa is independent of an adaptive response or its immunological receptor, CXCR3. Finally, we provide evidence that phagocytes function in tandem with NK cells for robust CXCL9 responses to C. rodentium. These findings identify a novel role for the immune cell-derived CXCL9 chemokine in directing a protective antimicrobial response in the intestinal mucosa.

  16. CXCL9 contributes to antimicrobial protection of the gut during citrobacter rodentium infection independent of chemokine-receptor signaling. (United States)

    Reid-Yu, Sarah A; Tuinema, Brian R; Small, Cherrie N; Xing, Lydia; Coombes, Brian K


    Chemokines have been shown to be effective bactericidal molecules against a variety of bacteria and fungi in vitro. These direct antimicrobial effects are independent of their chemotactic activities involving immunological receptors. However, the direct biological role that these proteins may play in host defense, particularly against intestinal pathogens, is poorly understood. Here, we show that CXCL9, an ELR- chemokine, exhibits direct antimicrobial activity against Citrobacter rodentium, an attaching/effacing pathogen that infects the gut mucosa. Inhibition of this antimicrobial activity in vivo using anti-CXCL9 antibodies increases host susceptibility to C. rodentium infection with pronounced bacterial penetration into crypts, increased bacterial load, and worsened tissue pathology. Using Rag1(-/-) mice and CXCR3(-/-) mice, we demonstrate that the role for CXCL9 in protecting the gut mucosa is independent of an adaptive response or its immunological receptor, CXCR3. Finally, we provide evidence that phagocytes function in tandem with NK cells for robust CXCL9 responses to C. rodentium. These findings identify a novel role for the immune cell-derived CXCL9 chemokine in directing a protective antimicrobial response in the intestinal mucosa.

  17. The Probiotic Lactobacillus Prevents Citrobacter rodentium-Induced Murine Colitis in a TLR2-Dependent Manner. (United States)

    Ryu, Seung-Hyun; Park, Jong-Hyung; Choi, Soo-Young; Jeon, Hee-Yeon; Park, Jin-Il; Kim, Jun-Young; Ham, Seung-Hoon; Choi, Yang-Kyu


    The main objective of this study was to investigate whether Lactobacillus rhamnosus GG (LGG) ameliorated the effects of Citrobactor rodentium infection in Toll-like receptor 2 (TLR2) knockout (KO) and TLR4 KO mice, as well as in wild-type C57BL/6 (B6) mice. TLR2 KO, TLR4 KO, and B6 mice were divided into three groups per each strain. Each group had an uninfected control group (n = 5), C. rodentium-infected group (n = 8), and LGG-pretreated C. rodentium-infected group (n = 8). The survival rate of B6 mice infected with C. rodentium was higher when pretreated with LGG. Pretreatment with LGG ameliorated C. rodentium-induced mucosal hyperplasia in B6 and TLR4 KO mice. However, in C-rodentium-infected TLR2 KO mice, mucosal hyperplasia persisted, regardless of pretreatment with LGG. In addition, LGG-pretreated B6 and TLR4 KO mice showed a decrease in spleen weight and downregulation of tumor necrosis factor alpha, interferon gamma, and monocyte chemotactic protein 1 mRNA expression compared with the non-pretreated group. In contrast, such changes were not observed in TLR2 KO mice, regardless of pretreatment with LGG. From the above results, we conclude that pretreatment with LGG ameliorates C. rodentium-induced colitis in B6 and TLR4 KO mice, but not in TLR2 KO mice. Therefore, LGG protects mice from C. rodentium-induced colitis in a TLR2-dependent manner.

  18. Interleukin-7 produced by intestinal epithelial cells in response to Citrobacter rodentium infection plays a major role in innate immunity against this pathogen. (United States)

    Zhang, Wei; Du, Jiang-Yuan; Yu, Qing; Jin, Jun-O


    Interleukin-7 (IL-7) engages multiple mechanisms to overcome chronic viral infections, but the role of IL-7 in bacterial infections, especially enteric bacterial infections, remains unclear. Here we characterized the previously unexplored role of IL-7 in the innate immune response to the attaching and effacing bacterium Citrobacter rodentium. C. rodentium infection induced IL-7 production from intestinal epithelial cells (IECs). IL-7 production from IECs in response to C. rodentium was dependent on gamma interferon (IFN-γ)-producing NK1.1(+) cells and IL-12. Treatment with anti-IL-7Rα antibody during C. rodentium infection resulted in a higher bacterial burden, enhanced intestinal damage, and greater weight loss and mortality than observed with the control IgG treatment. IEC-produced IL-7 was only essential for protective immunity against C. rodentium during the first 6 days after infection. An impaired bacterial clearance upon IL-7Rα blockade was associated with a significant decrease in macrophage accumulation and activation in the colon. Moreover, C. rodentium-induced expansion and activation of intestinal CD4(+) lymphoid tissue inducer (LTi) cells was completely abrogated by IL-7Rα blockade. Collectively, these data demonstrate that IL-7 is produced by IECs in response to C. rodentium infection and plays a critical role in the protective immunity against this intestinal attaching and effacing bacterium.

  19. The inhibition of COPII trafficking is important for intestinal epithelial tight junction disruption during enteropathogenic Escherichia coli and Citrobacter rodentium infection. (United States)

    Thanabalasuriar, Ajitha; Kim, Jinoh; Gruenheid, Samantha


    Enterohemorrhagic Escherichia coli (EHEC) and enteropathogenic E. coli (EPEC) are bacterial pathogens that cause severe illnesses in humans. Citrobacter rodentium is a related mouse pathogen that serves as a small animal model for EPEC and EHEC infections. EPEC, EHEC and C. rodentium translocate bacterial virulence proteins directly into host intestinal cells via a type III secretion system (T3SS). Non-LEE-encoded effector A (NleA) is a T3SS effector that is common to EPEC, EHEC and C. rodentium. NleA interacts with and inhibits the mammalian COPII complex, impairing cellular secretion; this interaction is required for bacterial virulence. Although diarrhea is a hallmark of EPEC, EHEC and C. rodentium infections, the underlying mechanisms are not well characterized. One of the essential functions of the intestine is to maintain a barrier between the lumen and submucosa. Tight junctions seal the space between adjacent epithelial cells creating this barrier. Consequently, it is thought that the disruption of intestinal epithelial tight junctions by EPEC, EHEC, and C. rodentium could result in a loss of barrier function. In this study, we demonstrate that NleA mediated COPII inhibition is required for EPEC- and C. rodentium-mediated disruption of tight junction proteins and increases in fecal water content.

  20. Promoter swapping unveils the role of the Citrobacter rodentium CTS1 type VI secretion system in interbacterial competition. (United States)

    Gueguen, Erwan; Cascales, Eric


    The type VI secretion system (T6SS) is a versatile secretion machine dedicated to various functions in Gram-negative bacteria, including virulence toward eukaryotic cells and antibacterial activity. Activity of T6SS might be followed in vitro by the release of two proteins, Hcp and VgrG, in the culture supernatant. Citrobacter rodentium, a rodent pathogen, harbors two T6SS gene clusters, cts1 and cts2. Reporter fusion and Hcp release assays suggested that the CTS1 T6SS was not produced or not active. The cts1 locus is composed of two divergent operons. We therefore developed a new vector allowing us to swap the two divergent endogenous promoters by P(tac) and P(BAD) using the λ red recombination technology. Artificial induction of both promoters demonstrated that the CTS1 T6SS is functional as shown by the Hcp release assay and confers on C. rodentium a growth advantage in antibacterial competition experiments with Escherichia coli.

  1. Properdin provides protection from Citrobacter rodentium-induced intestinal inflammation in a C5a/IL-6-dependent manner. (United States)

    Jain, Umang; Cao, Qi; Thomas, Nikhil A; Woodruff, Trent M; Schwaeble, Wilhelm J; Stover, Cordula M; Stadnyk, Andrew W


    Citrobacter rodentium is an attaching and effacing mouse pathogen that models enteropathogenic and enterohemorrhagic Escherichia coli in humans. The complement system is an important innate defense mechanism; however, only scant information is available about the role of complement proteins during enteric infections. In this study, we examined the impact of the lack of properdin, a positive regulator of complement, in C. rodentium-induced colitis. Following infection, properdin knockout (P(KO)) mice had increased diarrhea and exacerbated inflammation combined with defective epithelial cell-derived IL-6 and greater numbers of colonizing bacteria. The defect in the mucosal response was reversed by administering exogenous properdin to P(KO) mice. Then, using in vitro and in vivo approaches, we show that the mechanism behind the exacerbated inflammation of P(KO) mice is due to a failure to increase local C5a levels. We show that C5a directly stimulates IL-6 production from colonic epithelial cells and that inhibiting C5a in infected wild-type mice resulted in defective epithelial IL-6 production and exacerbated inflammation. These outcomes position properdin early in the response to an infectious challenge in the colon, leading to complement activation and C5a, which in turn provides protection through IL-6 expression by the epithelium. Our results unveil a previously unappreciated mechanism of intestinal homeostasis involving complement, C5a, and IL-6 during bacteria-triggered epithelial injury.

  2. Dietary oils modify the host immune response and colonic tissue damage following Citrobacter rodentium infection in mice. (United States)

    Hekmatdoost, Azita; Wu, Xiujuan; Morampudi, Vijay; Innis, Sheila M; Jacobson, Kevan


    Inflammatory bowel disease is an intestinal inflammatory disorder of multifactorial origin, in which diets that favor high n-6 and low n-3 fatty acids have been implicated. The present study addressed whether dietary n-6 and n-3 fatty acids alter colonic mucosal response to Citrobacter rodentium (C. rodentium) infection. Mice were fed diets identical except for fatty acids, with an energy percentage of 15% 18:2n-6 and <0.06% 18:3n-3, 4.2% 18:2n-6 and 1.9% 18:3n-3, or 1.44% 20:5n-3, 4.9% 22:6n-3, 0.32% 18:2n-6, and 0.12% 18:3n-3 from safflower, canola, or fish oil, respectively for 3 wk before infection. Dietary oils had no effect on colonic C. rodentium growth but altered colon 20:4n-6/(20:5n-3+22:6n-3) with 9.40 ± 0.06, 1.94 ± 0.08, and 0.32 ± 0.03% in colon phosphatidylcholine and 3.82 ± 0.18, 1.14 ± 0.02, and 0.30 ± 0.02% in phosphatidylethanolamine of mice fed safflower, canola, or fish oil, respectively. At 10 days postinfection, histological damage, F4/80-positive macrophages, and myeloperoxidase-positive neutrophils in colonic mucosa were higher in infected mice fed safflower than fish oil. Colon gene transcripts for macrophage inflammatory protein 2, keratinocyte cytokine, and monocyte chemoattractant protein 1 expression were significantly higher in infected mice fed safflower than canola or fish oil; IFN-γ, IL-6, and IL-17A expression were significantly elevated in mice fed safflower rather than fish oil; and IL-10 was significantly higher in mice fed fish oil rather than canola or safflower oil. This study demonstrates that oils high in 18:2n-6 with minimal n-3 fatty acids exacerbate mucosal immune response, whereas oils high in n-3 fatty acids attenuate mucosal immune response to C. rodentium. These studies implicate dietary oils as environmental modifiers of intestinal inflammation in response to infection.

  3. R-Spondins Are Expressed by the Intestinal Stroma and are Differentially Regulated during Citrobacter rodentium- and DSS-Induced Colitis in Mice. (United States)

    Kang, Eugene; Yousefi, Mitra; Gruenheid, Samantha


    The R-spondin family of proteins has recently been described as secreted enhancers of β-catenin activation through the canonical Wnt signaling pathway. We previously reported that Rspo2 is a major determinant of susceptibility to Citrobacter rodentium-mediated colitis in mice and recent genome-wide association studies have revealed RSPO3 as a candidate Crohn's disease-specific inflammatory bowel disease susceptibility gene in humans. However, there is little information on the endogenous expression and cellular source of R-spondins in the colon at steady state and during intestinal inflammation. RNA sequencing and qRT-PCR were used to assess the expression of R-spondins at steady state and in two mouse models of colonic inflammation. The cellular source of R-spondins was assessed in specific colonic cell populations isolated by cell sorting. Data mining from publicly available datasets was used to assess the expression of R-spondins in the human colon. At steady state, colonic expression of R-spondins was found to be exclusive to non-epithelial CD45- lamina propria cells, and Rspo3/RSPO3 was the most highly expressed R-spondin in both mouse and human colon. R-spondin expression was found to be highly dynamic and differentially regulated during C. rodentium infection and dextran sodium sulfate (DSS) colitis, with notably high levels of Rspo3 expression during DSS colitis, and high levels of Rspo2 expression during C. rodentium infection, specifically in susceptible mice. Our data are consistent with the hypothesis that in the colon, R-spondins are expressed by subepithelial stromal cells, and that Rspo3/RSPO3 is the family member most implicated in colonic homeostasis. The differential regulation of the R-spondins in different models of intestinal inflammation indicate they respond to specific pathogenic and inflammatory signals that differ in the two models and provides further evidence that this family of proteins plays a key role in linking intestinal

  4. IL-4 Protects the Mitochondria Against TNFα and IFNγ Induced Insult During Clearance of Infection with Citrobacter rodentium and Escherichia coli. (United States)

    Maiti, Arpan K; Sharba, Sinan; Navabi, Nazanin; Forsman, Huamei; Fernandez, Harvey R; Lindén, Sara K


    Citrobacter rodentium is a murine pathogen that serves as a model for enteropathogenic Escherichia coli. C. rodentium infection reduced the quantity and activity of mitochondrial respiratory complexes I and IV, as well as phosphorylation capacity, mitochondrial transmembrane potential and ATP generation at day 10, 14 and 19 post infection. Cytokine mRNA quantification showed increased levels of IFNγ, TNFα, IL-4, IL-6, and IL-12 during infection. The effects of adding these cytokines, C. rodentium and E. coli were hence elucidated using an in vitro colonic mucosa. Both infection and TNFα, individually and combined with IFNγ, decreased complex I and IV enzyme levels and mitochondrial function. However, IL-4 reversed these effects, and IL-6 protected against loss of complex IV. Both in vivo and in vitro, the dysfunction appeared caused by nitric oxide-generation, and was alleviated by an antioxidant targeting mitochondria. IFNγ -/- mice, containing a similar pathogen burden but higher IL-4 and IL-6, displayed no loss of any of the four complexes. Thus, the cytokine environment appears to be a more important determinant of mitochondrial function than direct actions of the pathogen. As IFNγ and TNFα levels increase during clearance of infection, the concomitant increase in IL-4 and IL-6 protects mitochondrial function.

  5. Draft Genome Sequence of the Type Species of the Genus Citrobacter, Citrobacter freundii MTCC 1658


    Kumar, Shailesh; Kaur, Chandandeep; Kimura, Kazuyuki; Takeo, Masahiro; Raghava, Gajendra Pal Singh; Mayilraj, Shanmugam


    We report the 5.0-Mb genome sequence of the type species of the genus Citrobacter, Citrobacter freundii strain MTCC 1658, isolated from canal water. This draft genome sequence of C. freundii strain MTCC 1658T consists of 5,001,265 bp with a G+C content of 51.61%, 4,691 protein-coding genes, 70 tRNAs, and 10 rRNAs.

  6. The in vitro and in vivo effects of constitutive light expression on a bioluminescent strain of the mouse enteropathogen Citrobacter rodentium

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    Hannah M. Read


    Full Text Available Bioluminescent reporter genes, such as those from fireflies and bacteria, let researchers use light production as a non-invasive and non-destructive surrogate measure of microbial numbers in a wide variety of environments. As bioluminescence needs microbial metabolites, tagging microorganisms with luciferases means only live metabolically active cells are detected. Despite the wide use of bioluminescent reporter genes, very little is known about the impact of continuous (also called constitutive light expression on tagged bacteria. We have previously made a bioluminescent strain of Citrobacter rodentium, a bacterium which infects laboratory mice in a similar way to how enteropathogenic Escherichia coli (EPEC and enterohaemorrhagic E. coli (EHEC infect humans. In this study, we compared the growth of the bioluminescent C. rodentium strain ICC180 with its non-bioluminescent parent (strain ICC169 in a wide variety of environments. To understand more about the metabolic burden of expressing light, we also compared the growth profiles of the two strains under approximately 2,000 different conditions. We found that constitutive light expression in ICC180 was near-neutral in almost every non-toxic environment tested. However, we also found that the non-bioluminescent parent strain has a competitive advantage over ICC180 during infection of adult mice, although this was not enough for ICC180 to be completely outcompeted. In conclusion, our data suggest that constitutive light expression is not metabolically costly to C. rodentium and supports the view that bioluminescent versions of microbes can be used as a substitute for their non-bioluminescent parents to study bacterial behaviour in a wide variety of environments.

  7. Streptococcus pneumoniae-induced pneumonia and Citrobacter rodentium-induced gut infection differentially alter vitamin A concentrations in the lung and liver of mice. (United States)

    Restori, Katherine H; McDaniel, Kaitlin L; Wray, Amanda E; Cantorna, Margherita T; Ross, A Catharine


    In the developing world, vitamin A (VA) deficiency is endemic in populations that are also at great risk of morbidity and mortality because of pneumococcal pneumonia and enteric infections. To better understand how lung and gastrointestinal pathogens affect VA status, we assessed VA concentrations in serum, lung, and liver during an invasive pneumonia infection induced by Streptococcus pneumoniae serotype 3, and a noninvasive gut infection induced by Citrobacter rodentium, in vitamin A-adequate (VAA) and vitamin A-deficient (VAD) mice. For pneumonia infection, mice were immunized with pneumococcal polysaccharide serotype 3 (PPS3), or not (infected-control), 5 d prior to intranasal inoculation with S. pneumoniae. Two days post-inoculation, immunization was protective against systemic infection regardless of VA status as PPS3 immunization decreased bacteremia compared with infected-control mice (P pneumonia had less effect on VA status than gastrointestinal infection, predominantly owing to reduced hepatic VA storage at the peak of gut infection.

  8. Social stress-enhanced severity of Citrobacter rodentium-induced colitis is CCL2-dependent and attenuated by probiotic Lactobacillus reuteri. (United States)

    Mackos, A R; Galley, J D; Eubank, T D; Easterling, R S; Parry, N M; Fox, J G; Lyte, M; Bailey, M T


    Psychological stressors are known to affect colonic diseases but the mechanisms by which this occurs, and whether probiotics can prevent stressor effects, are not understood. Because inflammatory monocytes that traffic into the colon can exacerbate colitis, we tested whether CCL2, a chemokine involved in monocyte recruitment, was necessary for stressor-induced exacerbation of infectious colitis. Mice were exposed to a social disruption stressor that entails repeated social defeat. During stressor exposure, mice were orally challenged with Citrobacter rodentium to induce a colonic inflammatory response. Exposure to the stressor during challenge resulted in significantly higher colonic pathogen levels, translocation to the spleen, increases in colonic macrophages, and increases in inflammatory cytokines and chemokines. The stressor-enhanced severity of C. rodentium-induced colitis was not evident in CCL2(-/-) mice, indicating the effects of the stressor are CCL2-dependent. In addition, we tested whether probiotic intervention could attenuate stressor-enhanced infectious colitis by reducing monocyte/macrophage accumulation. Treating mice with probiotic Lactobacillus reuteri reduced CCL2 mRNA levels in the colon and attenuated stressor-enhanced infectious colitis. These data demonstrate that probiotic L. reuteri can prevent the exacerbating effects of stressor exposure on pathogen-induced colitis, and suggest that one mechanism by which this occurs is through downregulation of the chemokine CCL2.

  9. Transcriptional frameshifting rescues Citrobacter rodentium type VI secretion by the production of two length variants from the prematurely interrupted tssM gene. (United States)

    Gueguen, Erwan; Wills, Norma M; Atkins, John F; Cascales, Eric


    The Type VI secretion system (T6SS) mediates toxin delivery into both eukaryotic and prokaryotic cells. It is composed of a cytoplasmic structure resembling the tail of contractile bacteriophages anchored to the cell envelope through a membrane complex composed of the TssL and TssM inner membrane proteins and of the TssJ outer membrane lipoprotein. The C-terminal domain of TssM is required for its interaction with TssJ, and for the function of the T6SS. In Citrobacter rodentium, the tssM1 gene does not encode the C-terminal domain. However, the stop codon is preceded by a run of 11 consecutive adenosines. In this study, we demonstrate that this poly-A tract is a transcriptional slippery site that induces the incorporation of additional adenosines, leading to frameshifting, and hence the production of two TssM1 variants, including a full-length canonical protein. We show that both forms of TssM1, and the ratio between these two forms, are required for the function of the T6SS in C. rodentium. Finally, we demonstrate that the tssM gene associated with the Yersinia pseudotuberculosis T6SS-3 gene cluster is also subjected to transcriptional frameshifting.

  10. Interleukin-1 (IL-1) signaling in intestinal stromal cells controls KC/ CXCL1 secretion, which correlates with recruitment of IL-22- secreting neutrophils at early stages of Citrobacter rodentium infection. (United States)

    Lee, Yong-Soo; Yang, Hyungjun; Yang, Jin-Young; Kim, Yeji; Lee, Su-Hyun; Kim, Ji Heui; Jang, Yong Ju; Vallance, Bruce A; Kweon, Mi-Na


    Attaching and effacing pathogens, including enterohemorrhagic Escherichia coli in humans and Citrobacter rodentium in mice, raise serious public health concerns. Here we demonstrate that interleukin-1 receptor (IL-1R) signaling is indispensable for protection against C. rodentium infection in mice. Four days after infection with C. rodentium, there were significantly fewer neutrophils (CD11b+ Ly6C+ Ly6G+) in the colons of IL-1R−/− mice than in wild-type mice. Levels of mRNA and protein of KC/CXCL1 were also significantly reduced in colon homogenates of infected IL-1R−/− mice relative to wild-type mice. Of note, infiltrated CD11b+ Ly6C+ Ly6G+ neutrophils were the main source of IL-22 secretion after C. rodentium infection. Interestingly, intestinal stromal cells isolated from IL-1R−/− mice secreted lower levels of KC/CXCL1 than stromal cells from wild-type mice during C. rodentium infection. Similar effects were found when mouse intestinal stromal cells and human nasal polyp stromal cells were treated with IL-1R antagonists (i.e., anakinra) in vitro. These results suggest that IL-1 signaling plays a pivotal role in activating mucosal stromal cells to secrete KC/CXCL1, which is essential for infiltration of IL-22-secreting neutrophils upon bacterial infection.

  11. Citrobacter rodentium NleB Protein Inhibits Tumor Necrosis Factor (TNF) Receptor-associated Factor 3 (TRAF3) Ubiquitination to Reduce Host Type I Interferon Production. (United States)

    Gao, Xiaofei; Pham, Thanh H; Feuerbacher, Leigh Ann; Chen, Kangming; Hays, Michael P; Singh, Gyanendra; Rueter, Christian; Hurtado-Guerrero, Ramon; Hardwidge, Philip R


    Interferon signaling plays important roles in both intestinal homeostasis and in the host response to pathogen infection. The extent to which bacterial pathogens inhibit this host pathway is an understudied area of investigation. We characterized Citrobacter rodentium strains bearing deletions in individual type III secretion system effector genes to determine whether this pathogen inhibits the host type I IFN response and which effector is responsible. The NleB effector limited host IFN-β production by inhibiting Lys(63)-linked ubiquitination of TNF receptor-associated factor 3 (TRAF3). Inhibition was dependent on the glycosyltransferase activity of NleB. GAPDH, a target of NleB during infection, bound to TRAF3 and was required for maximal TRAF3 ubiquitination. NleB glycosyltransferase activity inhibited GAPDH-TRAF3 binding, resulting in reduced TRAF3 ubiquitination. Collectively, our data reveal important interplay between GAPDH and TRAF3 and suggest a mechanism by which the NleB effector inhibits type I IFN signaling.

  12. Genome sequence of Citrobacter sp. strain A1, a dye-degrading bacterium. (United States)

    Chan, Giek Far; Gan, Han Ming; Rashid, Noor Aini Abdul


    Citrobacter sp. strain A1, isolated from a sewage oxidation pond, is a facultative aerobe and mesophilic dye-degrading bacterium. This organism degrades azo dyes efficiently via azo reduction and desulfonation, followed by the successive biotransformation of dye intermediates under an aerobic environment. Here we report the draft genome sequence of Citrobacter sp. A1.

  13. Complete genome sequence of novel carbon monoxide oxidizing bacteria Citrobacter amalonaticus Y19, assembled de novo. (United States)

    Ainala, Satish Kumar; Seol, Eunhee; Park, Sunghoon


    We report here the complete genome sequence of Citrobacter amalonaticus Y19 isolated from an anaerobic digester. PacBio single-molecule real-time (SMRT) sequencing was employed, resulting in a single scaffold of 5.58Mb. The sequence of a mega plasmid of 291Kb size is also presented.

  14. Draft Genome Sequence of Citrobacter freundii Strain A47, Resistant to the Mycotoxin Deoxynivalenol (United States)

    Zhou, Ting; Lepp, Dion; Pauls, K. P.


    ABSTRACT Here, we present the draft genome sequence of Citrobacter freundii strain A47 with a length of 4,878,242 bp, which contains 4,357 putative protein coding genes, including 270 unique genes. This work is expected to assist in obtaining novel gene(s) that code for deoxynivalenol (DON) de-epoxidation enzyme(s). PMID:28302773

  15. Phylogeny and Comparative Genomics Unveil Independent Diversification Trajectories of qnrB and Genetic Platforms within Particular Citrobacter Species. (United States)

    Ribeiro, Teresa G; Novais, Ângela; Branquinho, Raquel; Machado, Elisabete; Peixe, Luísa


    To gain insights into the diversification trajectories of qnrB genes, a phylogenetic and comparative genomics analysis of these genes and their surrounding genetic sequences was performed. For this purpose, Citrobacter sp. isolates (n = 21) and genome or plasmid sequences (n = 56) available in public databases harboring complete or truncated qnrB genes were analyzed. Citrobacter species identification was performed by phylogenetic analysis of different genotypic markers. The clonal relatedness among isolates, the location of qnrB genes, and the genetic surroundings of qnrB genes were investigated by pulsed-field gel electrophoresis (PFGE), S1-/I-CeuI-PFGE and hybridization, and PCR mapping and sequencing, respectively. Identification of Citrobacter isolates was achieved using leuS and recN gene sequences, and isolates characterized in this study were diverse and harbored chromosomal qnrB genes. Phylogenetic analysis of all known qnrB genes revealed seven main clusters and two branches, with most of them included in two clusters. Specific platforms (comprising pspF and sapA and varying in synteny and/or identity of other genes and intergenic regions) were associated with each one of these qnrB clusters, and the reliable identification of all Citrobacter isolates revealed that each platform evolved in different recognizable (Citrobacter freundii, C. braakii, C. werkmanii, and C. pasteurii) and putatively new species. A high identity was observed between some of the platforms identified in the chromosome of Citrobacter spp. and in different plasmids of Enterobacteriaceae. Our data corroborate Citrobacter as the origin of qnrB and further suggest divergent evolution of closely related qnrB genes/platforms in particular Citrobacter spp., which were delineated using particular genotypic markers.

  16. Characterization and genome sequencing of a Citrobacter freundii phage CfP1 harboring a lysin active against multidrug-resistant isolates. (United States)

    Oliveira, Hugo; Pinto, Graça; Oliveira, Ana; Oliveira, Carla; Faustino, Maria Alberta; Briers, Yves; Domingues, Lucília; Azeredo, Joana


    Citrobacter spp., although frequently ignored, is emerging as an important nosocomial bacterium able to cause various superficial and systemic life-threatening infections. Considered to be hard-to-treat bacterium due to its pattern of high antibiotic resistance, it is important to develop effective measures for early and efficient therapy. In this study, the first myovirus (vB_CfrM_CfP1) lytic for Citrobacter freundii was microbiologically and genomically characterized. Its morphology, activity spectrum, burst size, and biophysical stability spectrum were determined. CfP1 specifically infects C. freundii, has broad host range (>85 %; 21 strains tested), a burst size of 45 PFU/cell, and is very stable under different temperatures (-20 to 50 °C) and pH (3 to 11) values. CfP1 demonstrated to be highly virulent against multidrug-resistant clinical isolates up to 12 antibiotics, including penicillins, cephalosporins, carbapenems, and fluroquinoles. Genomically, CfP1 has a dsDNA molecule with 180,219 bp with average GC content of 43.1 % and codes for 273 CDSs. The genome architecture is organized into function-specific gene clusters typical for tailed phages, sharing 46 to 94 % nucleotide identity to other Citrobacter phages. The lysin gene encoding a predicted D-Ala-D-Ala carboxypeptidase was also cloned and expressed in Escherichia coli and its activity evaluated in terms of pH, ionic strength, and temperature. The lysine optimum activity was reached at 20 mM HEPES, pH 7 at 37 °C, and was able to significantly reduce all C. freundii (>2 logs) as well as Citrobacter koseri (>4 logs) strains tested. Interestingly, the antimicrobial activity of this enzyme was performed without the need of pretreatment with outer membrane-destabilizing agents. These results indicate that CfP1 lysin is a good candidate to control problematic Citrobacter infections, for which current antibiotics are no longer effective.

  17. Unraveling the dha cluster in Citrobacter werkmanii: comparative genomic analysis of bacterial 1,3-propanediol biosynthesis clusters. (United States)

    Maervoet, Veerle E T; De Maeseneire, Sofie L; Soetaert, Wim K; De Mey, Marjan


    In natural 1,3-propanediol (PDO) producing microorganisms such as Klebsiella pneumoniae, Citrobacter freundii and Clostridium sp., the genes coding for PDO producing enzymes are grouped in a dha cluster. This article describes the dha cluster of a novel candidate for PDO production, Citrobacter werkmanii DSM17579 and compares the cluster to the currently known PDO clusters of Enterobacteriaceae and Clostridiaceae. Moreover, we attribute a putative function to two previously unannotated ORFs, OrfW and OrfY, both in C. freundii and in C. werkmanii: both proteins might form a complex and support the glycerol dehydratase by converting cob(I)alamin to the glycerol dehydratase cofactor coenzyme B12. Unraveling this biosynthesis cluster revealed high homology between the deduced amino acid sequence of the open reading frames of C. werkmanii DSM17579 and those of C. freundii DSM30040 and K. pneumoniae MGH78578, i.e., 96 and 87.5 % identity, respectively. On the other hand, major differences between the clusters have also been discovered. For example, only one dihydroxyacetone kinase (DHAK) is present in the dha cluster of C. werkmanii DSM17579, while two DHAK enzymes are present in the cluster of K. pneumoniae MGH78578 and Clostridium butyricum VPI1718.

  18. Multilocus sequence analysis of the genus Citrobacter and description of Citrobacter pasteurii sp. nov. (United States)

    Clermont, Dominique; Motreff, Laurence; Passet, Virginie; Fernandez, José-Carlos; Bizet, Chantal; Brisse, Sylvain


    Strains originating from various sources and classified as members of the genus Citrobacter within the family Enterobacteriaceae were characterized by sequencing internal portions of genes rpoB, fusA, pyrG and leuS, 16S rRNA gene sequencing, average nucleotide identity (ANI) of genomic sequences and biochemical tests. Phylogenetic analysis based on the four housekeeping genes showed that the 11 species of the genus Citrobacter with validly published names are well demarcated. Strains CIP 55.13(T) and CIP 55.9 formed a distinct branch associated with Citrobacter youngae. The ANI between CIP 55.9 and CIP 55.13(T) was 99.19%, whereas it was 94.75% between CIP 55.13(T) and strain CIP 105016(T) of the species C. youngae, the most closely related species. Biochemical characteristics consolidated the fact that the two isolates represent a separate species, for which the name Citrobacter pasteurii sp. nov. is proposed. The type strain is CIP 55.13(T) ( =DSM 28879(T) =Na 1a(T)).

  19. Endocarditis Due to Citrobacter Freundii


    Reyes, Cesar V.; Folwarkiw, Oksana


    The etiologic association of acute bacterial endocarditis with the Citrobacter species has been rare, although it is one of the opportunistic organisms that afflicts the elderly, neonates, the debilitated and immunocompromised. We report a case of endocarditis due to Citrobacter freundii.

  20. A Genomic Island in Salmonella enterica ssp. salamae provides new insights on the genealogy of the locus of enterocyte effacement. (United States)

    Chandry, P Scott; Gladman, Simon; Moore, Sean C; Seemann, Torsten; Crandall, Keith A; Fegan, Narelle


    The genomic island encoding the locus of enterocyte effacement (LEE) is an important virulence factor of the human pathogenic Escherichia coli. LEE typically encodes a type III secretion system (T3SS) and secreted effectors capable of forming attaching and effacing lesions. Although prominent in the pathogenic E. coli such as serotype O157:H7, LEE has also been detected in Citrobacter rodentium, E. albertii, and although not confirmed, it is likely to also be in Shigella boydii. Previous phylogenetic analysis of LEE indicated the genomic island was evolving through stepwise acquisition of various components. This study describes a new LEE region from two strains of Salmonella enterica subspecies salamae serovar Sofia along with a phylogenetic analysis of LEE that provides new insights into the likely evolution of this genomic island. The Salmonella LEE contains 36 of the 41 genes typically observed in LEE within a genomic island of 49, 371 bp that encodes a total of 54 genes. A phylogenetic analysis was performed on the entire T3SS and four T3SS genes (escF, escJ, escN, and escV) to elucidate the genealogy of LEE. Phylogenetic analysis inferred that the previously known LEE islands are members of a single lineage distinct from the new Salmonella LEE lineage. The previously known lineage of LEE diverged between islands found in Citrobacter and those in Escherichia and Shigella. Although recombination and horizontal gene transfer are important factors in the genealogy of most genomic islands, the phylogeny of the T3SS of LEE can be interpreted with a bifurcating tree. It seems likely that the LEE island entered the Enterobacteriaceae through horizontal gene transfer as a single unit, rather than as separate subsections, which was then subjected to the forces of both mutational change and recombination.

  1. A Genomic Island in Salmonella enterica ssp. salamae provides new insights on the genealogy of the locus of enterocyte effacement.

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    P Scott Chandry

    Full Text Available The genomic island encoding the locus of enterocyte effacement (LEE is an important virulence factor of the human pathogenic Escherichia coli. LEE typically encodes a type III secretion system (T3SS and secreted effectors capable of forming attaching and effacing lesions. Although prominent in the pathogenic E. coli such as serotype O157:H7, LEE has also been detected in Citrobacter rodentium, E. albertii, and although not confirmed, it is likely to also be in Shigella boydii. Previous phylogenetic analysis of LEE indicated the genomic island was evolving through stepwise acquisition of various components. This study describes a new LEE region from two strains of Salmonella enterica subspecies salamae serovar Sofia along with a phylogenetic analysis of LEE that provides new insights into the likely evolution of this genomic island. The Salmonella LEE contains 36 of the 41 genes typically observed in LEE within a genomic island of 49, 371 bp that encodes a total of 54 genes. A phylogenetic analysis was performed on the entire T3SS and four T3SS genes (escF, escJ, escN, and escV to elucidate the genealogy of LEE. Phylogenetic analysis inferred that the previously known LEE islands are members of a single lineage distinct from the new Salmonella LEE lineage. The previously known lineage of LEE diverged between islands found in Citrobacter and those in Escherichia and Shigella. Although recombination and horizontal gene transfer are important factors in the genealogy of most genomic islands, the phylogeny of the T3SS of LEE can be interpreted with a bifurcating tree. It seems likely that the LEE island entered the Enterobacteriaceae through horizontal gene transfer as a single unit, rather than as separate subsections, which was then subjected to the forces of both mutational change and recombination.

  2. Genetic characterization of atypical Citrobacter freundii. (United States)

    Delgado, Gabriela; Souza, Valeria; Morales, Rosario; Cerritos, René; González-González, Andrea; Méndez, José Luis; Vázquez, Virginia; Cravioto, Alejandro


    The ability of a bacterial population to survive in different niches, as well as in stressful and rapidly changing environmental conditions, depends greatly on its genetic content. To survive such fluctuating conditions, bacteria have evolved different mechanisms to modulate phenotypic variations and related strategies to produce high levels of genetic diversity. Laboratories working in microbiological diagnosis have shown that Citrobacter freundii is very versatile in its colony morphology, as well as in its biochemical, antigenic and pathogenic behaviours. This phenotypic versatility has made C. freundii difficult to identify and it is frequently confused with both Salmonella enterica and Escherichia coli. In order to determine the genomic events and to explain the mechanisms involved in this plasticity, six C. freundii isolates were selected from a phenotypic variation study. An I-CeuI genomic cleavage map was created and eight housekeeping genes, including 16S rRNA, were sequenced. In general, the results showed a range of both phenotypes and genotypes among the isolates with some revealing a greater similarity to C. freundii and some to S. enterica, while others were identified as phenotypic and genotypic intermediary states between the two species. The occurrence of these events in natural populations may have important implications for genomic diversification in bacterial evolution, especially when considering bacterial species boundaries. In addition, such events may have a profound impact on medical science in terms of treatment, course and outcomes of infectious diseases, evading the immune response, and understanding host-pathogen interactions.

  3. Citrobacter bitternis sp. nov. isolated from bitterns. (United States)

    Ko, Kwan Soo; Choi, Ji-Young; Kim, Joo; Park, Myoung Kyu


    In this study, we reported two gram-negative bacteria that were isolated from bitterns, designated as SKKU-TP7(T) and SKKU-TP20, representing a novel species of Citrobacter. Based on the 16S rRNA gene sequences, the two strains were found to be closely related and showed the highest pairwise similarity with Citrobacter farmeri CDC 2992-81(T) (97.1-97.3 %) and other Citrobacter species. Cellular fatty acid analysis revealed that the profiles of strains SKKU-TP7(T) and SKKU-TP20 were similar to those of related species of Citrobacter. The major cellular fatty acids were C16:0 (31.5 %), summed feature 3 (C16:1 ω7c, C16:1 ω6c, 19.7 %), summed feature 8 (C18:1 ω7c, C18:1 ω6c, 11.9 %), C17:0 cyclo (10.7 %), and summed feature 2 (C12:0 aldehyde/unknown 10928, 9.5 %). Although the strains could utilize sucrose and raffinose as a carbon source, they did not produce ornithine decarboxylase and urease. The biochemical and genotypic characteristics indicate that strains SKKU-TP7(T) and SKKU-TP20 represent a novel species of Citrobacter, for which the name Citrobacter bitterns sp. nov. is proposed. The type strain is SKKU-TP7(T) (=KCTC 42139(T) = JCM 30009(T)).

  4. Pathogenicity of Helicobacter rodentium in A/JCr and SCID mice. (United States)

    Myles, Matthew H; Livingston, Robert S; Franklin, Craig L


    Helicobacter rodentium was first recognized as a potential pathogen when it was isolated, along with Helicobacter bilis, from a colony of scid/Trp53 knockout mice with diarrhea. Clinical disease in these mice was more severe than that previously reported in mice infected with H. bilis alone, thus suggesting that H. rodentium contributed to the pathogenesis of enteritis. The purpose of the study reported here was to address two questions: is H. rodentium pathogenic in mice, and when co-infection with a pathogenic helicobacter occurs, does H. rodentium augment disease? To this end, A/JCr and C.B-17/IcrCrl-scidBr mice were inoculated with H. rodentium and/or H. hepaticus. Twelve weeks after inoculation, mice were euthanized. The cecum and liver were evaluated microscopically for evidence of disease. Cecal interferon-inducible protein 10 (IP-10), macrophage inflammatory protein 1alpha (MIP-1alpha), interleukin 10 (IL-10), and interferon gamma (IFN-gamma) mRNA values were measured as an indicator of mucosal immune response. Hepatic lesions were not identified in mice mono-infected with H. rodentium; likewise, cecal lesion scores were not significantly different from those of uninfected controls. With the exception of an increased IL-10 mRNA value in SCID mice, mean immune-related gene expression in H. rodentium mono-infected and uninfected control mice was not significantly different. In contrast, all mice infected with H. hepaticus developed moderate to severe hepatitis, significant increase in cecal lesion scores, and increased immune-related gene expression. The C.B-17/IcrCrl-scidBr mice co-infected with H. hepaticus and H. rodentium had liquid cecal contents and low terminal body weight. Further, compared with mice infected with H. hepaticus alone, co-infection was associated with significant increases of IL-10, MIP-1alpha, and IP-10 mRNA values in C.B-17/IcrCrl-scidBr and IFN-gamma and MIP-1alpha mRNA values in A/JCr mice. These results suggested that H. rodentium

  5. Identification of Novel Host Interactors of Effectors Secreted by Salmonella and Citrobacter

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    Sontag, Ryan L.; Nakayasu, Ernesto S.; Brown, Roslyn N.; Niemann, George S.; Sydor, Michael A.; Sanchez, Octavio; Ansong, Charles; Lu, Shao-Yeh; Choi, Hyungwon; Valleau, Dylan; Weitz, Karl K.; Savchenko, Alexei; Cambronne, Eric D.; Adkins, Joshua N.; McFall-Ngai, Margaret J.


    Many pathogenic bacteria of the familyEnterobacteriaceaeuse type III secretion systems to inject virulence proteins, termed “effectors,” into the host cell cytosol. Although host-cellular activities of several effectors have been demonstrated, the function and host-targeted pathways of most of the effectors identified to date are largely undetermined. To gain insight into host proteins targeted by bacterial effectors, we performed coaffinity purification of host proteins from cell lysates using recombinant effectors from theEnterobacteriaceaeintracellular pathogensSalmonella entericaserovar Typhimurium andCitrobacter rodentium. We identified 54 high-confidence host interactors for theSalmonellaeffectors GogA, GtgA, GtgE, SpvC, SrfH, SseL, SspH1, and SssB collectively and 21 interactors for theCitrobactereffectors EspT, NleA, NleG1, and NleK. We biochemically validated the interaction between the SrfHSalmonellaprotein and the extracellular signal-regulated kinase 2 (ERK2) host protein kinase, which revealed a role for this effector in regulating phosphorylation levels of this enzyme, which plays a central role in signal transduction.

    IMPORTANCEDuring infection, pathogenic bacteria face an adverse environment of factors driven by both cellular and humoral defense mechanisms. To help evade the immune response and ultimately proliferate inside the host, many bacteria evolved specialized secretion systems to deliver effector proteins directly into host cells. Translocated effector proteins function to subvert host defense mechanisms. Numerous pathogenic bacteria use a specialized secretion system called type III secretion to deliver effectors into the host cell cytosol. Here, we identified 75 new host targets ofSalmonellaandCitrobactereffectors, which will help elucidate their mechanisms of

  6. Characterization of a virulent bacteriophage LK1 specific for Citrobacter freundii isolated from sewage water. (United States)

    Chaudhry, Waqas Nasir; Haq, Irshad Ul; Andleeb, Saadia; Qadri, Ishtiaq


    Citrobacter freundii is a worldwide emerging nosocomial pathogen with escalating incidence of multidrug resistance. Citrobacter freundii exists in natural environment, especially in health care settings and is difficult to eradicate. Phage therapy is considered as an alternative way of controlling bacterial infections and contaminations. In this study, we have described isolation and characterization of a virulent bacteriophage LK1 capable of specifically infecting Citrobacter freundii. A virulent bacteriophage LK1, specific for Citrobacter freundii was isolated from sewage water sample. TEM showed that phage Lk1 has an icosahedral head 70 nm in diameter and short tail of 17 nm, and can be classified as a member of the Podoviridae family. Restriction analysis indicated that phage LK1 was a dsDNA virus with an approximate genome size of 20-23 kb. Proteomic pattern generated by SDS PAGE using purified LK1 phage particles, revealed three major and six minor protein bands with molecular weight ranging from 25 to 80 kDa. Adsorption rate of LK1 relative to the host bacterium was also determined which showed significant improvement in adsorption with the addition of CaCl2 . In a single step growth experiment, LK1 exhibited a latent period of 24 min and burst size of 801 particle/cell. Moreover, pH and thermal stability of phage LK1 demonstrated a pH range of 5.0-6.0 and phage viability decreased to 0% at 65 °C. When LK1 was used to infect six other clinically isolated pathogenic strains, it showed relatively narrow host range. LK1 was capable of eliciting efficient lysis of Citrobacter freundii, revealing its potential as a non-toxic sanitizer for controlling Citrobacter freundii infection and contamination in both hospital and other public environments.

  7. Optimum management of Citrobacter koseri infection. (United States)

    Deveci, Aydin; Coban, Ahmet Yilmaz


    Low virulent Citrobacter koseri can cause life threatening infections. Neonates and other immunocompromised patients are particularly susceptible to infection from C. koseri. Any infection due to C. koseri mandates antimicrobial therapy based on the sensitivity of the pathogen microorganism. Various types of antibiotics, including aminoglycosides carbapenems, cephalosporins, chloramphenicol and quinolones, are used for the treatment of C. koseri infections. The rational choice of antimicrobial therapy for Citrobacter infections is a challenge for clinicians because there is a sustained increase in antibacterial resistance. We reviewed antimicrobial agents used for C. koseri infections in this review.

  8. 21 CFR 866.3125 - Citrobacter spp. serological reagents. (United States)


    ... isolates derived from clinical specimens. The identification aids in the diagnosis of disease caused by bacteria belonging to the genus Citrobacter and provides epidemiological information on diseases caused...



    Dhanya; Sevitha


    BACKGROUND & OBJECTIVES: Citrobacter species have emerged as important nosocomial pathogens . The infections caused by this organism include UTI , wound infection , Neonatal sepsis , pulmonary infection , brain abscess , meningitis . The organism is recovered from a variety of clinical specimen incl uding pus , urine , sputum . Antibiotic resistance is on rise among the Citrobacter spp . The present study w...

  10. In vitro susceptibility of Citrobacter species to various antimicrobial agents.


    Samonis, G.; Ho, D H; Gooch, G F; Rolston, K V; Bodey, G P


    The in vitro activities of 16 antimicrobial agents against 14 clinical isolates of Citrobacter diversus and 27 isolates of Citrobacter freundii were studied. C. freundii isolates were more resistant, being susceptible only to amikacin, netilmicin, gentamicin, imipenem, ciprofloxacin, and enoxacin. C. diversus isolates were susceptible to many more of the agents tested.

  11. Citrobacter koseri septicaemia in a holstein calf. (United States)

    Komine, M; Massa, A; Moon, L; Mullaney, T


    A 4-day-old male Holstein calf with dull mentation, nystagmus and blindness was humanely destroyed and subject to necropsy examination. Gross lesions included severe suppurative meningitis characterized by diffuse cloudy thickening of the meninges, bilateral hypopyon and fibrinosuppurative polyarthritis affecting the hocks. Citrobacter koseri was isolated from the meninges, ocular fluid, synovial fluid, spleen and small intestine. Microscopically, there was neutrophilic and histiocytic meningitis with intralesional bacilli, endophthalmitis, neutrophilic splenitis and multiple renal microabscesses. Failure of passive transfer of colostrum was confirmed. This appears to be the first characterization of septicaemia in a calf caused by C. koseri, with lesions comparable with those described in human neonates.

  12. Characterization of Five Podoviridae Phages Infecting Citrobacter freundii. (United States)

    Hamdi, Sana; Rousseau, Geneviève M; Labrie, Simon J; Kourda, Rim S; Tremblay, Denise M; Moineau, Sylvain; Slama, Karim B


    Citrobacter freundii causes opportunistic infections in humans and animals, which are becoming difficult to treat due to increased antibiotic resistance. The aim of this study was to explore phages as potential antimicrobial agents against this opportunistic pathogen. We isolated and characterized five new virulent phages, SH1, SH2, SH3, SH4, and SH5 from sewage samples in Tunisia. Morphological and genomic analyses revealed that the five C. freundii phages belong to the Caudovirales order, Podoviridae family, and Autographivirinae subfamily. Their linear double-stranded DNA genomes range from 39,158 to 39,832 bp and are terminally redundant with direct repeats between 183 and 242 bp. The five genomes share the same organization as coliphage T7. Based on genomic comparisons and on the phylogeny of the DNA polymerases, we assigned the five phages to the T7virus genus but separated them into two different groups. Phages SH1 and SH2 are very similar to previously characterized phages phiYeO3-12 and phiSG-JL2, infecting, respectively, Yersinia enterocolitica and Salmonella enterica, as well as sharing more than 80% identity with most genes of coliphage T7. Phages SH3, SH4, and SH5 are very similar to phages K1F and Dev2, infecting, respectively, Escherichia coli and Cronobacter turicensis. Several structural proteins of phages SH1, SH3, and SH4 were detected by mass spectrometry. The five phages were also stable from pH 5 to 10. No genes coding for known virulence factors or integrases were found, suggesting that the five isolated phages could be good candidates for therapeutic applications to prevent or treat C. freundii infections. In addition, this study increases our knowledge about the evolutionary relationships within the T7virus genus.

  13. Native Valve Endocarditis Due to Citrobacter Chronic Prostatitis (United States)

    Lum, Corey; Bolger, Dennis; Bello, Erlaine


    Introduction: Citrobacter koseri is a gram-negative bacillus that rarely causes infection in immunocompetent hosts and typically is associated with urinary or respiratory tract infections. Rarely will Citrobacter be a cause of infective endocarditis. Case Report: We present a case of a 77-year-old man with no known immunocompromising conditions who was hospitalized for infective aortic endocarditis due to Citrobacter koseri originating from a chronically infected prostate. Unusually, he also developed a C. koseri diskitis and phlegmon, which, along with the aortic vegetations, increased in size despite appropriate antibiotics. The patient thus met indications for aortic valve replacement and had improved appearance of lesions in follow-up imaging.

  14. Brain abscess caused by Citrobacter koseri infection in an adult. (United States)

    Liu, Heng-Wei; Chang, Chih-Ju; Hsieh, Cheng-Ta


    Citrobacter koseri is a gram-negative bacillus that causes mostly meningitis and brain abscesses in neonates and infants. However, brain abscess caused by Citrobacter koseri infection in an adult is extremely rare, and only 2 cases have been described. Here, we reported a 73-year-old male presenting with a 3-week headache. A history of diabetes mellitus was noted. The images revealed a brain abscess in the left frontal lobe and pus culture confirmed the growth of Citrobacter koseri. The clinical symptoms improved completely postoperatively.

  15. A case of emphysematous pyelonephritis induced by Citrobacter freundii infection

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    Youichi Yanagawa


    Full Text Available A 79-year-old female with diabetes mellitus had general fatigue, a high fever and vomiting. A CT revealed acute emphysematous pyelonephritis (EPN. A nephrectomy was performed on the 2 nd hospital day. The results of the blood culture showed the presence of Citrobacter freundii infection. The patient′s post-operative course was uneventful. This case is the second reported case of EPN induced by Citrobacter freundii. Bacteremia induced by Citrobacter freundii infection typically results in a high mortality rate. In this case, the early diagnosis of the EPN using CT and immediate medical treatment, including urgent elective nephrectomy, were key to the favorable outcome.

  16. Citrobacter koseri folliculitis of the face. (United States)

    Raia, D D; Barbareschi, M; Veraldi, S


    We report a case of severe Citrobacter koseri folliculitis of the face in a boy with acne. A 15-year-old boy affected by acne was admitted because of a rash located on the face. Dermatological examination revealed two large plaques, with numerous pustules, eschars and crusts, located bilaterally and symmetrically on the cheeks. Three bacteriological examinations were positive for C. koseri. The patient was successfully treated with i.m. ceftriaxone. C. koseri is a Gram-negative, aerobic, mobile, nonsporulating bacillus belonging to the Enterobacteriaceae family. It can cause meningitis, central nervous system abscess and sepsis, almost exclusively in infants and immunocompromised hosts. Respiratory tract and urinary infections have been reported in elderly people. Furthermore, rare cases of skin infections have been described.

  17. Musculoskeletal infections associated with Citrobacter koseri. (United States)

    Kwaees, T A; Hakim, Z; Weerasinghe, C; Dunkow, P


    Introduction Citrobacter koseri is a well known cause of central nervous system infections in the paediatric setting. Musculoskeletal infections caused by C koseri are rare, with only 14 previously reported cases. We present the first recorded case of C koseri induced septic arthritis of the knee along with a review of the literature. Methods A search of the PubMed, Embase(®) and Google Scholar™ databases was undertaken. Only complete or near complete cases were reviewed. Findings Fourteen musculoskeletal infections were identified. Of these, five were associated with an operative procedure and five involved a septic joint. Surgical treatment was required in the majority of cases and cure was achieved in all cases following prolonged antibiotic use. Conclusions C koseri associated musculoskeletal infections may complicate primary orthopaedic procedures. The organism can present aggressively and can be difficult to identify microbiologically. It is sensitive to newer generation beta-lactams, cephalosporin-based antibiotics and timely surgery.

  18. [Transpon Tn5 mutagenesis in Citrobacter]. (United States)

    Wang, A Q; Yin, P; Chen, X Z


    When E. coli 1830/PJB4JI mating with four Citrobacter strains all were Kanamycin resistant, but a majority of KanrGens transconjugants were obtained from C-3-1. Among 3000 KanrGens 21 were auxotrophs, these are Lys-(1), Ura-(1), Arg-(2), Iso-(2), His-(2), Met-(1), Phe-(1), Tyr-(1), Ser-(1), Thr-(1), Leu-(3), Pro-(1), Ade-(3), Lac-(1), PJB4JI plasmid DNA were detected in parent strain E. coli 1830, but not in auxotrophs strains which carrying Tn5 induced mutations. Twenty auxotrophs chromosome DNA were hybridized with Tn5 DNA labeled with 32P respectively, all auxotrophs has positive reaction. Therefore, we concluded from genetic and physical data that auxotrophs resulted from Tn5 transposition from PJB4JI into C-3-1 chromosome.

  19. Biochemical Identification of Citrobacter Species Defined by DNA Hybridization and Description of Citrobacter gillenii sp. nov. (Formerly Citrobacter Genomospecies 10) and Citrobacter murliniae sp. nov. (Formerly Citrobacter Genomospecies 11)


    Brenner, Don J.; O’Hara, Caroline M.; Grimont, Patrick A. D.; Janda, J. Michael; Falsen, Enevold; Aldova, Eva; Ageron, Elisabeth; Schindler, Jiri; Abbott, Sharon L.; Steigerwalt, Arnold G.


    Recent work describing six named species and two unnamed genomospecies within Citrobacter has enlarged the genus to 11 species. DNA relatedness and phenotypic tests were used to determine how well these species can be identified. One hundred thirty-six strains were identified to species level by DNA relatedness and then identified phenotypically in a blinded fashion. By using conventional tests, 119 of the 136 strains (88%) were correctly identified to species level. Three additional strains ...

  20. Quorum sensing activity of Citrobacter amalonaticus L8A, a bacterium isolated from dental plaque. (United States)

    Goh, Share-Yuan; Khan, Saad Ahmed; Tee, Kok Keng; Abu Kasim, Noor Hayaty; Yin, Wai-Fong; Chan, Kok-Gan


    Cell-cell communication is also known as quorum sensing (QS) that happens in the bacterial cells with the aim to regulate their genes expression in response to increased cell density. In this study, a bacterium (L8A) isolated from dental plaque biofilm was identified as Citrobacter amalonaticus by matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry (MS). Its N-acylhomoserine-lactone (AHL) production was screened by using two types of AHL biosensors namely Chromobacterium violaceum CV026 and Escherichia coli [pSB401]. Citrobacter amalonaticus strain L8A was identified and confirmed producing numerous types of AHL namely N-butyryl-L-homoserine lactone (C4-HSL), N-hexanoyl-L-homoserine lactone (C6-HSL), N-octanoyl-L-homoserine lactone (C8-HSL) and N-hexadecanoyl-L-homoserine lactone (C16-HSL). We performed the whole genome sequence analysis of this oral isolate where its genome sequence reveals the presence of QS signal synthase gene and our work will pave the ways to study the function of the related QS genes in this bacterium.

  1. Characterization of phiCFP-1, a virulent bacteriophage specific for Citrobacter freundii. (United States)

    Zhao, Xiangna; Huang, Simo; Zhao, Jiangtao; He, Xiaoming; Li, Erna; Li, Huan; Liu, Wei; Zou, Dayang; Wei, Xiao; Wang, Xuesong; Dong, Derong; Yang, Zhan; Yan, Xiabei; Shen, Zhiqiang; Yuan, Jing


    Citrobacter freundii, a Gram-negative bacterium, causes many opportunistic infections. Bacteriophage phiCFP-1 was isolated and characterized by its ability to lyse the multidrug-resistant clinical C. freundii strain P10159. Transmission electron microscopy showed that the phage has an icosahedral head and a short tail, making it a Podoviridae family member. In a single-step growth experiment, phiCFP-1 exhibited an eclipse period of 20 min and a burst size of 100 particles per cell. Its genome assembled as a circular molecule when genomic sequencing was completed. However, based on genome content and organization, it was categorized as a classic T7-related phage, and such phages are known to have linear genomes with direct terminal repeats. With the quick and simple method established herein, the 38,625-bp linear double-stranded DNA with 229-bp direct terminal repeats was accurately identified. The genome contained 43 putative open reading frames and no tRNA genes. Using a proteomics-based approach, seven viral and two host proteins from purified phiCFP-1 particles were identified. Comparative genomics and recombination analyzes revealed close genetic relatedness among phiCFP-1, phiYeO3-12/vB_YenP_AP5 (from Yersinia enterocolitica O3), and phiSG-JL2 (from Salmonella enterica).

  2. Pneumorachis associated with multiorgan infection due to Citrobacter koseri. (United States)

    Yamamoto, Norihisa; Takegawa, Ryosuke; Seki, Masafumi; Takahashi, Kyosuke; Tahara, Kenichi; Hirose, Tomoya; Hamaguchi, Shigeto; Irisawa, Taro; Matsumoto, Naoya; Shimazu, Takeshi; Tomono, Kazunori


    Pneumorachis rarely occurs after spreading from a contiguous site of infection or after a traumatic event. We describe an adult patient who developed sepsis and a renal abscess due to Citrobacter koseri, and computed tomographic imaging identified gas within the entire spinal canal as well as an iliopsoas abscess. This patient recovered from pneumorachis caused by disseminated infection.

  3. Citrobacter amalonaticus human urinary tract infections, Marseille, France


    Garcia,V.; C. Abat; V. Moal; J.-M. Rolain


    Citrobacter amalonaticus is a bacterium that has rarely been reported as a human pathogen. Here we report four cases of C. amalonaticus infections occurring in patients hospitalized in Marseille, France, and review all cases described in the published literature.

  4. Citrobacter freundii induced endocarditis in a yearling colt. (United States)

    Guidi, Eleonora E A; Thomas, Aurélie; Cadoré, Jean-Luc; Smith, Agnès Benamou


    Endocarditis is a rare pathology in horses and the clinical signs can be misleading. We describe the clinical, echocardiographic, and pathological features of Citrobacter freundii induced bacterial endocarditis in a horse. This bacterium has never been reported before as an agent of vegetative endocarditis in the horse.

  5. Citrobacter amalonaticus human urinary tract infections, Marseille, France (United States)

    Garcia, V.; Abat, C.; Moal, V.; Rolain, J.-M.


    Citrobacter amalonaticus is a bacterium that has rarely been reported as a human pathogen. Here we report four cases of C. amalonaticus infections occurring in patients hospitalized in Marseille, France, and review all cases described in the published literature. PMID:26958347

  6. Citrobacter amalonaticus human urinary tract infections, Marseille, France. (United States)

    Garcia, V; Abat, C; Moal, V; Rolain, J-M


    Citrobacter amalonaticus is a bacterium that has rarely been reported as a human pathogen. Here we report four cases of C. amalonaticus infections occurring in patients hospitalized in Marseille, France, and review all cases described in the published literature.

  7. Phosphatase production and activity in Citrobacter freundii and a naturally occurring, heavy-metal-accumulating Citrobacter sp. (United States)

    Montgomery, D M; Dean, A C; Wiffen, P; Macaskie, L E


    The ability of a naturally occurring Citrobacter sp. to accumulate cadmium has been attributed to cellular precipitation of CdHPO4, utilizing HPO4(2-) liberated via the activity of an overproduced, Cd-resistant acid-type phosphatase. Phosphatase production and heavy metal accumulation by batch cultures of this strain (N14) and a phosphatase-deficient mutant were compared with two reference strains of Citrobacter freundii. Only strain N14 expressed a high level of acid phosphatase and accumulated lanthanum and uranyl ion enzymically. Acid phosphatase is regulated via carbon-starvation; although the C. freundii strains overexpressed phosphatase activity in carbon-limiting continuous culture, this was approximately 20-fold less than the activity of strain N14 grown similarly. Citrobacter strain N14 was originally isolated from a metal-contaminated soil environment; phosphatase overproduction and metal accumulation were postulated as a detoxification mechanism. However, application of Cd-stress, and enrichment for Cd-resistant C. freundii ('training'), reduced the phosphatase activity of this organism by about 50% as compared to Cd-unstressed cultures. The acid phosphatase of C. freundii and Citrobacter N14 had a similar pattern of resistance to some diagnostic reagents. The enzyme of the latter is similar to the PhoN acid phosphatase of Salmonella typhimurium described by other workers; the results are discussed with respect to the known phosphatases of the enterobacteria.

  8. Community-Acquired Pneumonia and Empyema Caused by Citrobacter koseri in an Immunocompetent Patient


    Miguel Angel Ariza-Prota; Ana Pando-Sandoval; Marta García-Clemente; Ramón Fernández; Pere Casan


    Citrobacter species, belonging to the family Enterobacteriaceae, are environmental organisms commonly found in soil, water, and the intestinal tracts of animals and humans. Citrobacter koseri is known to be an uncommon but serious cause of both sporadic and epidemic septicemia and meningitis in neonates and young infants. Most cases reported have occurred in immunocompromised hosts. The infections caused by Citrobacter are difficult to treat with usual broad spectrum antibiotics owing to rapi...

  9. Characterization of qnrB-like genes in Citrobacter species of the American Type Culture Collection. (United States)

    Saga, Tomoo; Sabtcheva, Stefana; Mitsutake, Kotaro; Ishii, Yoshikazu; Tateda, Kazuhiro; Yamaguchi, Keizo; Kaku, Mitsuo


    Among five American Type Culture Collection (ATCC) Citrobacter strains, qnrB60 in Citrobacter freundii ATCC 6879, an isolate from the preantibiotic era, and qnrB61 in Citrobacter braakii ATCC 51113(T), a type strain belonging to the C. freundii complex, were identified. Meanwhile, a truncated qnrB-like pseudogene was identified in C. freundii ATCC 8090(T) and ATCC 43864. No qnrB-like sequence was found in Citrobacter koseri ATCC 27028(T). These findings underscore the close relationship between this species and qnrB.

  10. Neonatal Citrobacter koseri Meningitis: Report of Four Cases


    Joana Rodrigues; Dalila Rocha; Fátima Santos; Anabela João


    Citrobacter koseri is a rare cause of neonatal meningitis with predisposal for brain abscesses, and therefore responsible for high mortality and serious neurologic sequelae in this age group. We present the evolution and outcome of four cases of C. koseri meningitis. One of them developed brain abscesses and another one died. The cases show the bacteria's propensity for serious brain damage, despite early and adequate treatment, and the high risk of long-term neurologic complications in survi...

  11. Citrobacter koseri Pneumonia As Initial Presentation of Underlying Pulmonary Adenocarcinoma


    Kelly Pennington; Martin Van Zyl; Patricio Escalante


    Citrobacter koseri is a motile, gram-negative rod traditionally known to cause infection in individuals with significant comorbidities and immunocompromised status. While most cases represent nosocomial infections, rarely community-acquired infections have been reported. We present a previously healthy man in his 60s with C. koseri pneumonia who was subsequently found to have underlying pulmonary adenocarcinoma, illustrating the need for further investigation for immunodeficiency and/or intra...

  12. Citrobacter koseri Pneumonia As Initial Presentation of Underlying Pulmonary Adenocarcinoma (United States)

    Pennington, Kelly; Van Zyl, Martin; Escalante, Patricio


    Citrobacter koseri is a motile, gram-negative rod traditionally known to cause infection in individuals with significant comorbidities and immunocompromised status. While most cases represent nosocomial infections, rarely community-acquired infections have been reported. We present a previously healthy man in his 60s with C. koseri pneumonia who was subsequently found to have underlying pulmonary adenocarcinoma, illustrating the need for further investigation for immunodeficiency and/or intrapulmonary pathology.

  13. Characterization of a virulent bacteriophage LK1 specific for Citrobacter freundii isolated from sewage water

    NARCIS (Netherlands)

    Chaudhry, Waqas Nasir; Ul Haq, Irshad; Andleeb, Saadia; Qadri, Ishtiaq


    Citrobacter freundii is a worldwide emerging nosocomial pathogen with escalating incidence of multidrug resistance. Citrobacter freundii exists in natural environment, especially in health care settings and is difficult to eradicate. Phage therapy is considered as an alternative way of controlling b

  14. Structural and serological studies on the O-antigen show that Citrobacter youngae PCM1505 must be classified to a new Citrobacter O-serogroup. (United States)

    Katzenellenbogen, Ewa; Kocharova, Nina A; Górska-Frączek, Sabina; Gamian, Andrzej; Shashkov, Alexander S; Knirel, Yuriy A


    The O-polysaccharide obtained by mild acid hydrolysis of the lipopolysaccharide of Citrobacter youngae PCM1505 was studied by sugar and methylation analyses along with 1D and 2D (1)H and (13)C NMR spectroscopies. The following structure of the tetrasaccharide repeating unit of the polysaccharide was established: [Formula: see text]. Structural and serological data obtained earlier and in this work show that the strain studied is a candidate to a new Citrobacter O-serogroup.

  15. Citrobacter freundii brain abscess in a preterm infant: a case report and literature review. (United States)

    Plakkal, Nishad; Soraisham, Amuchou Singh; Amin, Harish


    Intracranial abscesses are serious conditions but uncommon in preterm neonates. Citrobacter species are an uncommon cause of bacterial meningitis in neonates, but are associated with brain abscesses in a majority of cases. We report a preterm infant who developed Citrobacter freundii meningitis with brain abscess, who was successfully treated with antibiotics and surgical drainage. The infant had normal neurological outcome at follow-up. We report this case to highlight the importance of serial neuroimaging in the diagnosis of cerebral abscess in infants with Citrobacter meningitis.

  16. Acute death associated with Citrobacter freundii infection in an African elephant (Loxodonta africana). (United States)

    Ortega, Joaquín; Corpa, Juan M; Orden, José A; Blanco, Jorge; Carbonell, María D; Gerique, Amalia C; Latimer, Erin; Hayward, Gary S; Roemmelt, Andreas; Kraemer, Thomas; Romey, Aurore; Kassimi, Labib B; Casares, Miguel


    A 21-year-old male African elephant (Loxodonta africana) died suddenly with no previous medical history. Grossly, there were severe multifocal epicardial and endocardial hemorrhages of the atria and ventricles, hydropericardium, multifocal pleural hemorrhages, and severe pulmonary congestion and edema. Histologically, there was fibrinoid vasculitis and thrombosis in the heart and lung and myocardial necrosis. Citrobacter freundii was isolated in abundance in pure culture from liver and heart samples. Low levels of multiples types of elephant endotheliotropic herpesvirus (EEHV-6, EEHV-2B, and EEHV-3A) were detected in spleen samples, but not in heart samples. The levels of EEHV DNA found were much lower than those usually associated with acute EEHV hemorrhagic disease, and many other genomic loci that would normally be found in such cases were evidently below the level of detection. Therefore, these findings are unlikely to indicate lethal EEHV disease. Polymerase chain reaction for encephalomyocarditis virus (EMCV) and toxicology for oleander (Nerium oleander) were negative. Stress, resulting from recent transport, and antimicrobial therapy may have contributed to the death of this animal.

  17. Glycerol assimilation and production of 1,3-propanediol by Citrobacter amalonaticus Y19. (United States)

    Ainala, Satish Kumar; Ashok, Somasundar; Ko, Yeounjoo; Park, Sunghoon


    Citrobacter amalonaticus Y19 (Y19) was isolated because of its ability for carbon monoxide-dependent hydrogen production (water-gas shift reaction). This paper reports the assimilation of glycerol and the production of 1,3-propanediol (1,3-PDO) by Y19. Genome sequencing revealed that Y19 contained the genes for the utilization of glycerol and 1,2-propanediol (pdu operon) along with those for the synthesis of coenzyme B12 (cob operon). On the other hand, it did not possess the genes for the fermentative metabolism of glycerol of Klebsiella pneumoniae, which consists of both the oxidative (dhaD and dhaK) and reductive (dhaB and dhaT) pathways. In shake-flask cultivation under aerobic conditions, Y19 could grow well with glycerol as the sole carbon source and produced 1,3-PDO. The level of 1,3-PDO production was improved when vitamin B12 was added to the culture medium under aerobic conditions. Under anaerobic conditions, cell growth and 1,3-PDO production on glycerol was also possible, but only when an exogenous electron acceptor, such as nitrate or fumarate, was added. This is the first report of the glycerol metabolism and 1,3-PDO production by C. amalonaticus Y19.

  18. Community-Acquired Pneumonia and Empyema Caused by Citrobacter koseri in an Immunocompetent Patient

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    Miguel Angel Ariza-Prota


    Full Text Available Citrobacter species, belonging to the family Enterobacteriaceae, are environmental organisms commonly found in soil, water, and the intestinal tracts of animals and humans. Citrobacter koseri is known to be an uncommon but serious cause of both sporadic and epidemic septicemia and meningitis in neonates and young infants. Most cases reported have occurred in immunocompromised hosts. The infections caused by Citrobacter are difficult to treat with usual broad spectrum antibiotics owing to rapid generation of mutants and have been associated with high death rates in the past. We believe this is the first case described in the literature of a community-acquired pneumonia and empyema caused by Citrobacter koseri in an immunocompetent adult patient.

  19. Anti-microbial resistance profile of Citrobacter species in a tertiary care hospital of southern India

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    Basavaraj C Metri


    Full Text Available Background: Recently, the isolation of this pathogen in hospital settings is increasing and multidrug-resistant strains are emerging; these strains present a challenge for clinician and the clinical microbiologist because of their increased occurrence in nosocomial infection. The current study was done to find out the antibiotic sensitivity pattern of Citrobacter species from various clinical specimens. Materials and Methods: Samples were collected from patients in accordance with standard protocols. Citrobacter species were identified by conventional biochemical tests. Antibiotic susceptibility of the isolates was done by disc diffusion method according to National Committee for Clinical Laboratory Standards (NCCLS recommendations. Results: Out of 563 isolates of Citrobacter, majority were from pus (48.1%, followed by urine (24.3%, sputum (20.3%, body fluids (05.2%, blood (02.1%. C. koseri was the predominant species [391 (70%] isolated. Infection was nosocomialy acquired in 493 (87.4% patients. The mean age was 39.5 years. Anti-biograms of Citrobacter isolates revealed that effective agent against Citrobacter isolates was imipenem (91.8% sensitive, followed by piperacillin/tazobactam (58.3% and amikacin (53.4%. Conclusion: Citrobacter isolates resistant to multiple anti-microbial agents have emerged, including strains resistant to imipenem, making it an emerging nosocomial pathogen. Therefore, the results of this study suggest that surveillance of anti-microbial resistance in Citrobacter is necessary. Antibiotic policy should be formulated in the hospital. Depending on the antibiotic sensitivity pattern of the Citrobacter isolates, antibiotics should be used, and proper infection control measures should be strictly followed to prevent spread of this pathogen.

  20. Fulminant citrobacter meningitis with multiple periventricular abscesses in a three-month-old infant

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    P. Anoop


    Full Text Available Citrobacter, a Gram-negative enteric bacillus, is a rare cause of septicemia and meningitis, seldom reported beyond the neonatal period. It is characterized by a fulminant clinical course and a high incidence of complications, including brain abscesses. We studied a three-month-old infant with Citrobacter meningitis, who developed acute communicating hydrocephalus and multiple periventricular brain abscesses while on treatment. The patient died, despite intensive antibiotic treatment directed towards the causative organism, C. diversus.

  1. Citrobacter europaeus sp. nov., isolated from water and human faecal samples. (United States)

    Ribeiro, Teresa G; Clermont, Dominique; Branquinho, Raquel; Machado, Elisabete; Peixe, Luísa; Brisse, Sylvain


    Strains 97/79T and A121, recovered respectively from human faeces and well water, were compared to currently known species of the genus Citrobacter using genotypic and phenotypic approaches. Multilocus sequence analysis based on housekeeping genes fusA, leuS, pyrG, rpoB and recN, showed that the two strains formed a distinct phylogenetic lineage within the genus Citrobacter. Average nucleotide identity (ANI) between strains 97/79T and A121 was 99.2 %, whereas ANI values of strain 97/79T with the type strains of closely related species of the genus Citrobacter, C. werkmanii, C. braakii, C. freundii, C. youngae and C. pasteurii, were all below 93.0 %. The ability to metabolize different compounds also discriminated strains 97/79T and A121 from other species of the genus Citrobacter. Based on these results, strains 97/79T and A121 represent a novel species of the genus Citrobacter, for which the name Citrobacter europaeus sp. nov. is proposed, with strain 97/79T (=CIP 106467T=DSM 103031T) as the type strain. The DNA G+C content of strain 97/79T is 52.0 %.



    Priyadarshini; Kasukurthy Leela; Rajendran


    BACKGROUND Genus Citrobacter is one of the aerobic Gram negative non-sporing bacilli, from the Enterobacteriaceae family. Citrobacter koseri and Citrobacter freundii are the commonest species implicated in infections. It is emerging as an important nosocomial pathogen. It is associated with high mortality and morbidity rate. They are often resistant to routinely used antibiotics. Emerging drug resistance is a therapeutic concern for clinicians worldwide, thus isolation and ant...

  3. Genome Sequences of 12 Bacterial Isolates Obtained from the Urine of Pregnant Women (United States)

    Weimer, Cory M.; Deitzler, Grace E.; Robinson, Lloyd S.; Park, SoEun; Hallsworth-Pepin, Kymberlie; Wollam, Aye; Mitreva, Makedonka


    The presence of bacteria in urine can pose significant risks during pregnancy. However, there are few reference genome strains for many common urinary bacteria. We isolated 12 urinary strains of Streptococcus, Staphylococcus, Citrobacter, Gardnerella, and Lactobacillus. These strains and their genomes are now available to the research community. PMID:27688327

  4. Production and properties of alpha-amylase from Citrobacter species

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    Ebuta N. Etim-Osowo


    Full Text Available Amylase production by Citrobacter sp. isolated from potato was optimized in batch culture studies under shake flask conditions. Effects and interactions of best sources and levels of carbon and nitrogen estimated by 4 x 5 and 4 x 4 factorial experimental arrangements were significant (P < 0.01 on amylase production. Optimal alpha-amylase yield was obtained in a medium containing sorghum flour (2.0 % w/v and a mixture of (NH42SO4 + soybean meal (1.5% w/v with an initial medium pH of 8.0. Under optimum conditions, amylase yield was maximal (0.499 U/ml after 60h incubation at room temperature (28oC ± 2oC. Characterization studies showed that the enzyme had maximum activity at 60oC, retained 100% of its original activities at 60oC for 2h, was maximally active at pH 7.0 and retained 100% of original activities at pH 9.0 for 2h. Enzyme activity was stimulated by urea, Mg2+, Ca2+ and Zn2+ but inhibited by Hg2+.

  5. Multidrug resistant citrobacter: an unusual cause of liver abscess. (United States)

    Kumar, Prabhat; Ghosh, Soumik; Rath, Deepak; Gadpayle, A K


    Liver abscesses are infectious, space occupying lesions in the liver, the two most common abscesses being pyogenic and amoebic. A pyogenic liver abscess (PLA) is a rare condition with a reported incidence of 20 per 100 000 hospital admissions in the western population. The right lobe of the liver is the most common site in both types of liver abscess. Clinical presentation is elusive with complaints of fever, right upper quadrant pain in the abdomen and hepatomegaly with or without jaundice. The aetiology of PLA has changed in the past few decades and may be of biliary, portal, arterial or traumatic origin, but many cases are still cryptogenic. The most common organisms causing PLA are Gram-negative aerobes, especially Escherichia coli and Klebsiella pneumoniae. Studies have shown a high degree of antimicrobial susceptibility of isolated organism resulting in an overall lower mortality in PLA. Here, we present a case of PLA caused by multidrug-resistant Citrobacter freundii, which is an unusual organism to be isolated.

  6. Genome Sequences of Nine Gram-Negative Vaginal Bacterial Isolates (United States)

    Deitzler, Grace E.; Ruiz, Maria J.; Lu, Wendy; Weimer, Cory; Park, SoEun; Robinson, Lloyd S.; Hallsworth-Pepin, Kymberlie; Wollam, Aye; Mitreva, Makedonka


    The vagina is home to a wide variety of bacteria that have great potential to impact human health. Here, we announce reference strains (now available through BEI Resources) and draft genome sequences for 9 Gram-negative vaginal isolates from the taxa Citrobacter, Klebsiella, Fusobacterium, Proteus, and Prevotella. PMID:27688330


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    Full Text Available BACKGROUND Genus Citrobacter is one of the aerobic Gram negative non-sporing bacilli, from the Enterobacteriaceae family. Citrobacter koseri and Citrobacter freundii are the commonest species implicated in infections. It is emerging as an important nosocomial pathogen. It is associated with high mortality and morbidity rate. They are often resistant to routinely used antibiotics. Emerging drug resistance is a therapeutic concern for clinicians worldwide, thus isolation and antibiotic sensitivity of Citrobacter is critically needed. OBJECTIVES Identification of Citrobacter species and antibiotic sensitivity pattern with AmpC and ESBL Detection. METHODS Prospective study was done from June 2014 to March 2015. The samples were collected from patients attending VIMS and RC. The samples were processed and identified by standard protocol. Citrobacter isolates were tested for antibiotic sensitivity by Kirby-Bauer disc diffusion method as per clinical and standard institute guidelines. Detection of AmpC by Cephamycin Hodge test using Cefoxitin 30 μg with ATCC strains of Escherichia coli 25922 was done. ESBL detection was done by Ceftazidime (30 μg and Ceftazidime/clavulanic acid (30 μg/10 μg and Cefotaxime (30 ug Cefotaxime/clavulanic acid (30 ug/10 ug. RESULTS Out of 5695 Gram negative isolates identified, 690 were Citrobacter isolates. Citrobacter koseri 398 (62.5% and Citrobacter freundii 292 (37.5% were the commonest species isolated. The antibiogram as per CLSI Guidelines showed resistance to Fluoroquinolones, Cephalosporins and beta lactamase inhibitors. Carbapenems were found to be sensitive. The resistance to beta lactamase inhibitors increased with the presence of AmpC beta lactamase (76% and ESBL (50%. CONCLUSION Citrobacter species are emerging as an important nosocomial pathogen. Citrobacter koseri and Citrobacter freundii were the commonest species isolated. Antibiogram showing an increase in resistance among the beta lactamase

  8. Utilization of aminoaromatic acids by a methanogenic enrichment culture and by a novel Citrobacter freundii strain

    NARCIS (Netherlands)

    Savelieva, O.; Kotova, I.; Roelofsen, W.; Stams, A.J.M.; Netrusov, A.


    Following incubation of mesophilic methanogenic floccular sludge from a lab-scale upflow anaerobic sludge bed reactor used to treat cattle manure wastewater, a stable 5-aminosalicylate-degrading enrichment culture was obtained. Subsequently, a Citrobacter freundii strain, WA1, was isolated from the

  9. Clonal origin of aminoglycoside-resistant Citrobacter freundii isolates in a Danish county

    DEFF Research Database (Denmark)

    Norskov-Lauritsen, N.; Sandvang, Dorthe; Hedegaard, J.;


    During 1997, attention was drawn to an increased frequency of aminoglycoside-resistant Citrobacter freundii in a Danish county, when a total of 24 resistant C. freundii isolates was detected. In this study, 15 such isolates were typed by pulsed-field gel electrophoresis, riboprinting and partial...

  10. Favorable outcome in cerebral abscesses caused by Citrobacter koseri in a newborn infant


    Sarah Algubaisi; Christoph Bührer; Ulrich-Wilhelm Thomale; Birgit Spors


    The treatment of brain abscesses in newborn infants is controversial. We report on a 6-week-old infant with multiple brain abscesses caused by Citrobacter koseri that resolved after treatment with combined surgical drainage and intravenous therapy with meropenem and fosfomycin.

  11. Distribution of chitin/chitosan-like bioflocculant-producing potential in the genus Citrobacter. (United States)

    Kimura, Kazuyuki; Inoue, Takuya; Kato, Dai-Ichiro; Negoro, Seiji; Ike, Michihiko; Takeo, Masahiro


    Some strains belonging to the genera Citrobacter and Enterobacter have been reported to produce chitin/chitosan-like bioflocculants (BFs) from acetate. In this study, to investigate the distribution of the BF-producing potential in the genus Citrobacter and to screen stably and highly BF-producing strains, we obtained 36 Citrobacter strains from different culture collection centers, which were distributed among seven species in the genus, and tested for the flocculating activities of their culture supernatants using a kaolin suspension method. As a result, 21 strains belonging to C. freundii (17 strains in 23 strains tested), C. braakii (two in two), C. youngae (one in one), and C. werkmanii (one in two) showed flocculating activity, but this ability was limited to cells grown on acetate. Gas chromatography/mass spectrometry (GC/MS) analysis of the hydrolysates from the BFs of five selected strains indicated that they consisted of glucosamine and/or N-acetylglucosamine, such as the chitin/chitosan-like BF (BF04) produced by Citrobacter sp. TKF04 (Fujita et al. J Biosci Bioeng 89: 40-46, 2000). Gel filtration chromatography using a high-performance liquid chromatography system revealed that the molecular weight ranges of these BFs varied, but the average sizes were all above 1.66 × 10⁶Da.

  12. Complete Nucleotide Sequence of a Citrobacter freundii Plasmid Carrying KPC-2 in a Unique Genetic Environment (United States)

    Yao, Yancheng; Imirzalioglu, Can; Hain, Torsten; Kaase, Martin; Gatermann, Soeren; Exner, Martin; Mielke, Martin; Hauri, Anja; Dragneva, Yolanta; Bill, Rita; Wendt, Constanze; Wirtz, Angela; Chakraborty, Trinad


    The complete and annotated nucleotide sequence of a 54,036-bp plasmid harboring a blaKPC-2 gene that is clonally present in Citrobacter isolates from different species is presented. The plasmid belongs to incompatibility group N (IncN) and harbors the class A carbapenemase KPC-2 in a unique genetic environment. PMID:25395635

  13. Citrobacter freundii septicemia in a stranded newborn Cuvier's beaked whale (Ziphius cavirostris). (United States)

    Fernández, Antonio; Vela, Ana Isabel; Andrada, Marisa; Herraez, Pedro; Díaz-Delgado, Josue; Domínguez, Lucas; Arbelo, Manuel


    Citrobacter freundii, a gram-negative enterobacterium, may cause fatal septicemia in humans and animals. Its potential pathogenic role in cetaceans (bottlenose dolphins and beluga whales) has been hypothesized. Here we describe fatal C. freundii septicemia in a stranded newborn Cuvier's beaked whale (Ziphius cavirostris).

  14. Bacteremia due to Citrobacter braakii: A case report and literature review. (United States)

    Hirai, Jun; Uechi, Kohei; Hagihara, Mao; Sakanashi, Daisuke; Kinjo, Takeshi; Haranaga, Shusaku; Fujita, Jiro


    Among the Citrobacter genus, the most commonly isolated bacteria from human specimens are Citrobacter freundii and Citrobacter koseri, and previous cases of infection due to Citrobacter braakii have been rarely reported. We present a case of bacteremia due to C. braakii in a 38-year-old woman with cervical cancer. She was admitted to our hospital with complaints of a fever, chills, and nausea. Blood culture results showed gram-negative bacilli identified as C. braakii via matrix-assisted laser desorption/ionization time-of-flight mass spectrometry analysis, although biochemical testing findings were suggestive of C. freundii. Since a rare pathogen was detected in the present case and the results of additional biochemical studies were suggestive of both C. braakii and Citrobacter farmeri, genetic analysis was conducted. Finally, the gram-negative bacilli were confirmed as C. braakii, a member of the C. freundii complex since 1993, by 16S ribosomal RNA gene sequencing analysis. The gastrointestinal tract was considered the portal of entry, because the patient had a rectal fistula and other cultures such as urine and vaginal discharge incubated species other than C. braakii. The patient recovered after receiving treatment with ciprofloxacin for 14 days. The epidemiology and clinical characteristics of C. braakii infection are still unknown because of the limitations in accurate identification by using currently available commercial biochemical testing and previously, only 6 cases of C. braakii infection have been reported. Physicians should focus on this species, because it causes community-acquired infections, although further studies are needed to clarify the clinical characteristics of C. braakii infections.


    Institute of Scientific and Technical Information of China (English)

    张莉; 李文; 肖正华; 王云霞; 夏仕文


    以在L-酪氨酸诱导下高效表达酪氨酸酚解酶的菌株Citrobacter freundii48003-3的休止细胞为生物催化剂,以邻苯二酚、丙酮酸钠、醋酸铵为前体,选择性合成L-DOPA.研究了反应温度、pH和前体浓度等对合成L-DOPA的影响.最优反应条件下,反应12h,L-DOPA的量可达到9.5g/L.

  16. Phosphatase-mediated heavy metal accumulation by a Citrobacter sp. and related enterobacteria. (United States)

    Macaskie, L E; Bonthrone, K M; Rouch, D A


    A Citrobacter sp. was reported previously to accumulate heavy metals as cell-bound heavy metal phosphates. Metal uptake is mediated by the activity of a periplasmic acid-type phosphatase that liberates inorganic phosphate to provide the precipitant ligand for heavy metals presented to the cells. Amino acid sequencing of peptide fragments of the purified enzyme revealed significant homology to the phoN product (acid phosphatase) of some other enterobacteria. These organisms, together with Klebsiella pneumoniae, previously reported to produce acid phosphatase, were tested for their ability to remove uranium and lanthanum from challenge solutions supplemented with phosphatase substrate. The coupling of phosphate liberation to metal bioaccumulation was limited to the metal accumulating Citrobacter sp.; therefore the participation of species-specific additional factors in metal bioaccumulation was suggested.

  17. Identification and phylogeny of Enterobacter sakazakii relative to Enterobacter and Citrobacter species

    DEFF Research Database (Denmark)

    Iversen, Carol; Waddington, Michael; On, Stephen L.W.;


    The phylogenetic relationships of Enterobacter sakazakii strains were investigated using 16S ribosomal DNA (rDNA) and hsp60 sequencing. Each analysis distributed E. sakazakii strains among four clusters, indicating substantial taxonomic heterogeneity. The E. sakazakii type strain 16S rDNA sequenc...... was 97.8% similar to that of Citrobacter koseri but 97.0% similar to that of Enterobacter cloacae....

  18. Morphological alterations on Citrobacter freundii bacteria induced by erythrosine dye and laser light. (United States)

    Silva, Josmary R; Cardoso, Gleidson; Maciel, Rafael R G; de Souza, Nara C


    The effect of the laser irradiation (532 nm) on films prepared from Citrobacter freundii mixed with erythrosine dye was investigated by using atomic force microscopy. It was observed that morphological changes of bacterial surfaces after irradiations, which were attributed to cellular damage of the outer membranes, are a result of a photodynamic effect. The results suggested that the combination of erythrosine and laser light at 532 nm could be a candidate to a photodynamic therapy against C. freundii.

  19. Emergence of Citrobacter freundii carrying IMP-8 metallo-β-lactamase in Germany (United States)

    Peter, S; Wolz, C; Kaase, M; Marschal, M; Schulte, B; Vogel, W; Autenrieth, I; Willmann, M


    Metallo-β-lactamases (MBLs) in Enterobacteriaceae are an increasing problem worldwide. This report describes the isolation of Citrobacter freundii carrying IMP-8 MBL from three patients during the period from March 2012 until March 2013 in Germany. The blaIMP-8 enzyme is predominantly found in Asia, where IMP-8 has spread to various enterobacterial species causing serious infections. To our best knowledge, this is the first report of blaIMP-8 habouring Enterobacteriaceae in Europe. PMID:25356340

  20. Emergence of Citrobacter freundii carrying IMP-8 metallo-β-lactamase in Germany

    Directory of Open Access Journals (Sweden)

    S. Peter


    Full Text Available Metallo-β-lactamases (MBLs in Enterobacteriaceae are an increasing problem worldwide. This report describes the isolation of Citrobacter freundii carrying IMP-8 MBL from three patients during the period from March 2012 until March 2013 in Germany. The blaIMP-8 enzyme is predominantly found in Asia, where IMP-8 has spread to various enterobacterial species causing serious infections. To our best knowledge, this is the first report of blaIMP-8 habouring Enterobacteriaceae in Europe.

  1. Sulfate reduction and copper precipitation by a Citrobacter sp. isolated from a mining area

    Energy Technology Data Exchange (ETDEWEB)

    Qiu Rongliang, E-mail: [School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510275 (China)] [Guangdong Provincial Key Laboratory for Environmental Pollution Control and Remediation Technology, Guangzhou 510275 (China); Zhao Benliang; Liu Jinling [School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510275 (China); Huang, Xiongfei [School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510275 (China)] [Guangdong Provincial Key Laboratory for Environmental Pollution Control and Remediation Technology, Guangzhou 510275 (China); Li, Qingfei [School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510275 (China); Brewer, Eric [Viridian Environmental LLC, VA 22207 (United States); Wang, Shizhong; Shi, Ning [School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510275 (China)


    A strain of sulfate-reducing bacteria, designated strain 'DBM', was isolated from sediments of a mining area. Phylogenetic analysis of the 16S rRNA gene sequence of the isolate revealed that it was related to members of the genus Citrobacter, with C. AzoR-4, C. freundii, C. braakii and C. werkmanii being the most closely related species (sequence similarity up to 98%). Few studies have been done on sulfate reduction ability in Citrobacter. Electron microscopy studies showed that the morphology of the strain DBM was rod-shaped. Strain DBM reduced 10 mM of sulfate completely to sulfide within 7 d, and it recovered its sulfate reduction ability after 7 d of aerobic growth. Furthermore, strain DBM effectively precipitated 0.40 mM copper during its growth. Elemental composition of the resulting microbial precipitate was studied using electro-dispersive X-ray spectroscopy, and it was found that the ratio of S:Cu was 1.07. The result was consistent with the formation of copper sulfide. Heavy metal precipitation by Citrobacter sp. strain DBM was a phenomenon that may be useful in the bioremediation of acid mine drainage.

  2. Biosorption of lead, cadmium, and zinc by Citrobacter strain MCM B-181: Characterization studies

    Energy Technology Data Exchange (ETDEWEB)

    Puranik, P.R.; Paknikar, K.M. [Agharkar Research Inst., Pune (India). Div. of Microbial Sciences


    The biosorption process for removal of lead, cadmium, and zinc by Citrobacter strain MCM B-181, a laboratory isolate, was characterized. Effects of environmental factors and growth conditions on metal uptake capacity were studied. Pretreatment of biomass with chemical agents increased cadmium sorption efficiency; however, there was no significant enhancement in lead and zinc sorption capacity. Metal sorption by Citrobacter strain MCM B-181 was found to be influenced by the pH of the solution, initial metal concentration, biomass concentration, and type of growth medium. The metal sorption process was not affected by the age of the culture or change in temperature. Equilibrium metal sorption was found to fit the Langmuir adsorption model. Kinetic studies showed that metal uptake by Citrobacter strain MCm B-181 was a fast process, requiring < 20 min to achieve > 90% adsorption efficiency. The presence of cations reduced lead, zinc, and cadmium sorption to the extent of 11.8%, 84.3%, and 33.4%, respectively. When biomass was exposed to multimetal solutions, metals were adsorbed in the order Co{sup 2+} < Ni{sup 2+} < Cd{sup 2+} < Cu{sup 2+}, Zn{sup 2+} < Pb{sup 2+}. A new mathematical model used for batch kinetic studies was found to be highly useful in prediction of experimentally obtained metal concentration profiles as a function of time.


    Institute of Scientific and Technical Information of China (English)

    彭丽花; 任源; 邓留杰; 张小璇; 韦朝海


    考察了在不同温度、pH值、摇床转速、氮源等环境和营养条件下,间甲酚降解菌Citrobacter farmeri对降解速率和降解过程中反应液的TOC值、紫外吸收及酶活的变化.结果表明,Citrobacter farmeri 降解间甲酚的最适温度为35℃,培养基初始pH值为6.5-8.0,摇床转速为170 r·min-1,无机氮比有机氮和氨态氮比硝态氮更利于Citrobacter farmeri/对间甲酚的降解;当间甲酚初始浓度低于375mg·l-1时,Citrobacter farmerifarmeri降解间甲酚符合零级动力学方程;间甲酚初始浓度约为60 mg·I-1时约4 h完全降解,TOC的去除率8 h内可达到77%,之后几乎不变;Citrobacter farmeri 可完全降解约600 mg·l-1的间甲酚,表现出高效与强耐受能力的结合.对酶活的测定发现,儿茶酚1,2-双加氧酶有明显增大,初步判断Citrobacter farmeri以邻位裂解的途径对间甲酚进行降解.

  4. Exoelectrogenic bacterium phylogenetically related to Citrobacter freundii, isolated from anodic biofilm of a microbial fuel cell. (United States)

    Huang, Jianjian; Zhu, Nengwu; Cao, Yanlan; Peng, Yue; Wu, Pingxiao; Dong, Wenhao


    An electrogenic bacterium, named Citrobacter freundii Z7, was isolated from the anodic biofilm of microbial fuel cell (MFC) inoculated with aerobic sewage sludge. Cyclic voltammetry (CV) analysis exhibited that the strain Z7 had relatively high electrochemical activity. When the strain Z7 was inoculated into MFC, the maximum power density can reach 204.5 mW/m(2) using citrate as electron donor. Series of substrates including glucose, glycerol, lactose, sucrose, and rhammose could be utilized to generate power. CV tests and the addition of anode solution as well as AQDS experiments indicated that the strain Z7 might transfer electrons indirectly via secreted mediators.

  5. Ureolytic Citrobacter freundii infection of the urine as a cause of dissolution of cystine renal calculi. (United States)

    Gutierrez Millet, V; Praga, M; Miranda, B; Bello, I; Ruilope, L; Diaz Gonzalez, R; Leyva, O; Alcazar, J M; Barrientos, A; Rodicio, J L


    We report a case of cystinuria with staghorn renal lithiasis in a solitary right kidney and chronic renal failure. Right nephropyelolithotomy was performed and although 29 renal calculi were extracted many stones remained in situ. A permanent nephrostomy was left in the kidney. Several months later the urine was infected chronically with a ureolytic Citrobacter freundii bacteria and urinary pH oscillated between 8.0 and 9.2. Spontaneous dissolution of the cystine calculi was observed and many tiny fragments of cystine were expulsed through the nephrostomy, following which renal function improved. Despite the conditions favoring struvite calculi, formation did not occur.

  6. [Septic shock following platelet transfusion contaminated with Citrobacter koseri in a child with postchemotherapy febrile neutropenia]. (United States)

    Tichit, R; Saumet, L; Marchandin, H; Haouy, S; Latry, P; Sirvent, N


    The bacterial transfusion risk is currently the greatest infectious risk of blood transfusion. We report the case of a child with postchemotherapy febrile neutropenia who presented septic shock following platelet transfusion contaminated with Citrobacter koseri. The life-threatening development could have been avoided by strict compliance with good clinical practice. The stability of mortality rates due to adverse effects of bacterial proliferation during platelet transfusions in France since 1994 calls for optimization of all preventive measures throughout the transfusion chain and perfect knowledge of transfusion rules by medical staff and care givers.

  7. Syntheses of L-tyrosine-related amino acids by tyrosine phenol-lyase of Citrobacter intermedius. (United States)

    Nagasawa, T; Utagawa, T; Goto, J; Kim, C J; Tani, Y; Kumagai, H; Yamada, H


    Degradation of tyrosine to phenol, pyruvate and ammonia by tyrosine phenol-lyase from Citrobacter intermedius (formerly named Escherichia intermedia) is readily reversible at high concentrations of pyruvate and ammonia. Spectrophotometric studies indicate that ammonia is the first substrate which interacts with bound pyridoxal 5'-phosphate. Kinetic results show that pyruvate is the second substrate bound, hence phenol must be the third. When an appropriate phenol derivative is substituted for phenol, the corresponding tyrosine analogue can be synthesized. 3-Fluoro-, 2-fluoro-, 3-chloro-, 2-chloro-, 3-bromo-, 2-bromo-, 2-iodo-, 3-methyl-, 2-methyl- and 2-methoxy-L-tyrosines have been synthesized by this reaction. By using various phenol derivatives or tyrosine analogues as substrates, the substrate specificity of tyrosine phenol-lyase is investigated and the situation of its active site is discussed.

  8. Decolorization of textile plant effluent by Citrobacter sp. strain KCTC 18061P. (United States)

    Jang, Moon-Sun; Jung, Byung-Gil; Sung, Nak-Chang; Lee, Young-Choon


    Citrobacter sp. strain KCTC 18061P was found to be able to decolorize textile plant effluent containing different types of reactive dyes. Effects of physico-chemical parameters, such as aeration, nitrogen source, glucose and effluent concentrations on the color removal of real dye effluent by this strain were investigated. The observed changes in the visible spectra indicated color removal by the absorption of dye to cells during incubation with the strain. This strain showed higher decolorization ability under aerobic than static culture conditions. With 1% glucose, this strain removed 70% of effluent color within 5 days. Decolorization was not significantly dependent on the nitrogen sources tested. Chemical oxygen demand (COD) and biological oxygen demand (BOD) were decreased in proportion to incubation times, and their removal rates were about 35% and 50%, respectively, at 7 days of culture.

  9. Isolation,Identification and Antibiotics Susceptibility Test of Citrobacter freundii from Procambarus clarkia

    Institute of Scientific and Technical Information of China (English)

    Chen; Honglian; Song; Guangtong; He; Jixiang; Hou; Guanjun; Wang; Yongjie


    This experiment was conducted to clarify species and drug resistance of pathogen from the diseased Procambarus clarkia. Pathogenic bacteria from hepatopancreas of the diseased P. clarkia were examined using conventional methods,and then were isolated. The further tests and analysis of the isolated strain were developed,including the regression experiment to P. clarkia,the morphology,physiological and biochemical characteristics,sequence analysis of their 16 S rRNA and gyr B genes,and the susceptibility test to antibiotics. Large colonies with similar morphology and color were obtained. Strain X120523 was identified as Citrobacter freundii,proved to have strong pathogenicity,and was susceptible to quinolones and aminoglycosides.

  10. 微生物燃料电池中一株产电菌Citrobacter freundii的分离及特性研究%ISOLATION AND CHARACTERIZATION OF EXOELECTROGENIC BACTERIUM Citrobacter freundii LY-3 FROM MICROBIAL FUEL CELL

    Institute of Scientific and Technical Information of China (English)

    李颖; 孙永明; 孔晓英; 李连华; 李东; 袁振宏


    An exoelectrogenic bacterium LY-3 was isolated from microbial fuel cell. According to its phenotypic, physiological and biochemical characteristics as well as the phylogenetic analysis based on the sequence of 16S rDNA, it was identified as Citrobacter sp. and shared the highest similarities to C. freundi. So we named it as C. freundi LY-3. Cyclic voltammetry experiment showed that strain LY-3 is electrochemical activity. The C. freundi LY-3 is inoculated into the anode chamber of two-chamber MFC and the maximal voltage output was 0. 43 V with 2. 0g/L beef extract as the fuel. The maximal power density is 98. 2mW/m2.%通过形态、生理生化特性及系统进化分析表明,从微生物燃料电池中分离出的产电菌株LY-3与弗氏柠檬酸杆菌(Citrobacter freundii)最相近,将其命名为Citrobacter freundii LY-3.循环伏安扫描显示,该菌株具有电化学活性,在微生物燃料电池中,以牛肉膏为燃料产生的最大电压为0.43V,最大功率密度为98.2mW/m2.

  11. Identification, cloning and heterologous expression of active [NiFe]-hydrogenase 2 from Citrobacter sp. SG in Escherichia coli. (United States)

    Maier, Johannes A H; Ragozin, Sergey; Jeltsch, Albert


    Hydrogen (H2) is a potential alternative energy carrier which only produces water and heat upon combustion. Today, industrial hydrogen production mainly uses thermochemical processes based on fossil fuels or electrolysis of water. Therefore, biotechnological approaches to produce H2 from biomass are an interesting alternative. We introduce here a novel direct hydrogen measurement system using a semiconducting device specific for hydrogen detection. Using this device, a bacterium producing considerable amounts of hydrogen under aerobic cultivation was isolated and identified by 16S ribosomal DNA sequencing as Citrobacter sp. The enzyme responsible for the observed hydrogenase activity was partially purified by 3 chromatographic purification steps and could be identified by peptide mass fingerprinting to be a type 2 [NiFe]-hydrogenase. Expression of the [NiFe]-hydrogenase 2 containing operon from Citrobacter sp. SG in Escherichia coli allowed recombinant hydrogen production. The [NiFe]-hydrogenase 2 identified here may be useful for biotechnological hydrogen production. We speculate that the expression of the hydrogenase in Citrobacter may be an adaptation to growth in acidic conditions.

  12. O2-stable membrane-bound [NiFe]hydrogenase from a newly isolated Citrobacter sp. S-77. (United States)

    Eguchi, Shigenobu; Yoon, Ki-Seok; Ogo, Seiji


    Hydrogenases are of great interest due to their potential use in H(2)-based technology. However, most hydrogenases are highly sensitive to O(2), which have been the major bottleneck in hydrogenase studies. Here we report an O(2)-stable membrane-bound [NiFe]hydrogenase (MBH) purified from a newly isolated strain, S-77. According to the 16S rRNA gene sequence and phylogenetic analysis of the strain S-77, it belongs to the genus of Citrobacter. In vitro experiments using the cytoplasmic membrane of strain S-77 suggested that a cytochrome b acts as the physiological electron acceptor of the MBH. The purified MBH was composed of a dimer of heterodimers, consisting of two distinct subunits with the molecular weights of 58.5 and 38.5 kDa. The enzyme showed a specific activity for H(2)-oxidation of 661 U/mg, which is 35-fold greater than that for H(2)-production of 18.7 U/mg. Notably, the MBH showed a remarkable O(2)-stability, maintaining almost 95% of its original activity even after incubation for 30 h in air at 4°C. These results suggest that the O(2)-stable MBH may play an important role in the H(2)-metabolic pathway under the aerobic conditions of Citrobacter sp. S-77. This is the first report of the purification and biochemical characterization of an O(2)-stable MBH from the genus of Citrobacter.

  13. Reduction of azo dyes by flavin reductase from Citrobacter freundii A1

    Directory of Open Access Journals (Sweden)

    Mohd Firdaus Abdul-Wahab


    Full Text Available Citrobacter freundii A1 isolated from a sewage treatment facility was demonstrated to be able to effectively decolorize azo dyes as pure and mixed culture. This study reports on the investigation on the enzymatic systems involved. An assay performed suggested the possible involvement of flavin reductase (Fre as an azo reductase. A heterologouslyexpressed recombinant Fre from C. freundii A1 was used to investigate its involvement in the azo reduction process. Three model dyes were used, namely Acid Red 27 (AR27, Direct Blue 15 (DB15 and Reactive Black 5 (RB5. AR27 was found to be reduced the fastest by Fre, followed by RB5, and lastly DB15. Redox mediators nicotinamide adenine dinucleotide (NADH and riboflavin enhance the reduction, suggesting the redox activity of the enzyme. The rate and extent of reduction of the model dyes correlate well with the reduction potentials (Ep. The data presented here strongly suggest that Fre is one of the enzymes responsible for azo reduction in C. freundii A1, acting via an oxidation-reduction reaction.

  14. Impact of cold plasma on Citrobacter freundii in apple juice: inactivation kinetics and mechanisms. (United States)

    Surowsky, Björn; Fröhling, Antje; Gottschalk, Nathalie; Schlüter, Oliver; Knorr, Dietrich


    Various studies have shown that cold plasma is capable of inactivating microorganisms located on a variety of food surfaces, food packaging materials and process equipment under atmospheric pressure conditions; however, less attention has been paid to the impact of cold plasma on microorganisms in liquid foodstuffs. The present study investigates cold plasma's ability to inactivate Citrobacter freundii in apple juice. Optical emission spectroscopy (OES) and temperature measurements were performed to characterise the plasma source. The plasma-related impact on microbial loads was evaluated by traditional plate count methods, while morphological changes were determined using scanning electron microscopy (SEM). Physiological property changes were obtained through flow cytometric measurements (membrane integrity, esterase activity and membrane potential). In addition, mathematical modelling was performed in order to achieve a reliable prediction of microbial inactivation and to establish the basis for possible industrial implementation. C. freundii loads in apple juice were reduced by about 5 log cycles after a plasma exposure of 480s using argon and 0.1% oxygen plus a subsequent storage time of 24h. The results indicate that a direct contact between bacterial cells and plasma is not necessary for achieving successful inactivation. The plasma-generated compounds in the liquid, such as H2O2 and most likely hydroperoxy radicals, are particularly responsible for microbial inactivation.

  15. Effect of surfactant on phenanthrene metabolic kinetics by Citrobacter sp. SA01. (United States)

    Li, Feng; Zhu, Lizhong; Zhang, Dong


    To attain a better understanding of the effects of surfactants on the metabolic kinetics of hydrophobic organic compounds, the biodegradation of phenanthrene by Citrobacter sp. SA01 was investigated in a batch experiment containing Tween 80, sodium dodecyl benzene sulfonate and liquid mineral salt medium. The Monod model was modified to effectively describe the partition, phenanthrene biodegradation and biopolymer production. The results showed that Tween 80 and sodium dodecyl benzene sulfonate (each at 50mg/L) enhanced phenanthrene metabolism and poly-β-hydroxybutyrate production as indicated by the increasing amounts of intermediates (by 17.2% to 47.9%), and percentages of poly-β-hydroxybutyrate (by 107.3% and 33.1%) within the cell dry weight when compared to their absence. The modified Monod model was capable of predicting microbial growth, phenanthrene depletion and biopolymer production. Furthermore, the Monod kinetic coefficients were largely determined by the surfactant-enhanced partition, suggesting that partitioning is a critical process in surfactant-enhanced bioremediation of hydrophobic organic compounds.

  16. Biohydrogen production by dark fermentation of glycerol using Enterobacter and Citrobacter Sp. (United States)

    Maru, Biniam T; Constanti, Magda; Stchigel, Alberto M; Medina, Francesc; Sueiras, Jesus E


    Glycerol is an attractive substrate for biohydrogen production because, in theory, it can produce 3 mol of hydrogen per mol of glycerol. Moreover, glycerol is produced in substantial amounts as a byproduct of producing biodiesel, the demand for which has increased in recent years. Therefore, hydrogen production from glycerol was studied by dark fermentation using three strains of bacteria: namely, Enterobacter spH1, Enterobacter spH2, and Citrobacter freundii H3 and a mixture thereof (1:1:1). It was found that, when an initial concentration of 20 g/L of glycerol was used, all three strains and their mixture produced substantial amounts of hydrogen ranging from 2400 to 3500 mL/L, being highest for C. freundii H3 (3547 mL/L) and Enterobacter spH1 (3506 mL/L). The main nongaseous fermentation products were ethanol and acetate, albeit in different ratios. For Enterobacter spH1, Enterobacter spH2, C. freundii H3, and the mixture (1:1:1), the ethanol yields (in mol EtOH/mol glycerol consumed) were 0.96, 0.67, 0.31, and 0.66, respectively. Compared to the individual strains, the mixture (1:1:1) did not show a significantly higher hydrogen level, indicating that there was no synergistic effect. Enterobacter spH1 was selected for further investigation because of its higher yield of hydrogen and ethanol.

  17. Proteome responses of Citrobacter werkmanii BF-6 planktonic cells and biofilms to calcium chloride. (United States)

    Zhou, Gang; Shi, Qing-shan; Huang, Xiao-mo; Xie, Xiao-bao


    Calcium ions are well-known as intracellular second messengers that also have an important extracellular structural role for bacteria. Recently, we found that denser biofilms were formed by Citrobacter werkmanii BF-6 in the presence of 400 mM Ca(2+) than that of 12.5mM Ca(2+). Therefore, we employed two-dimensional (2-D) electrophoresis methods to investigate the proteome profiles of planktonic cells and biofilms in BF-6 under different concentrations of Ca(2+). Meanwhile, BF-6 biofilm architecture was also visualized with confocal laser scanning microscopy (CLSM). The results demonstrated that BF-6 biofilms formed at the bottom of microtiter plates when grown in the presence of 400 mM Ca(2+). A total of 151 proteins from planktonic cells and biofilms after exposure of BF-6 cells to 12.5 and 400 mM Ca(2+) were successfully identified. Different gene ontology (GO) and KEGG pathways were categorized and enriched for the above proteins. Growth in the presence of 400 mM Ca(2+) induced more complex signal pathways in BF-6 than 12.5mM Ca(2+). In addition, the biofilm architectures were also affected by Ca(2+). Our results show two different modes of biofilm enhancement for C. werkmanii in the presence of excess Ca(2+) and provide a preliminary expression of these differences based on proteomic assays.

  18. Engineered Citrobacter freundii methionine γ-lyase effectively produces antimicrobial thiosulfinates. (United States)

    Morozova, Elena A; Kulikova, Vitalia V; Rodionov, Alexei N; Revtovich, Svetlana V; Anufrieva, Natalya V; Demidkina, Tatyana V


    Antimicrobial activity of thiosulfinates in situ produced by mixtures of Citrobacter freundii methionine γ-lyase (MGL) with new substrates, l-methionine and S-(alkyl/allyl)-l-cysteine sulfoxides has been recently demonstrated (Anufrieva et al., 2015). This opens a way to the rational design of a new biotechnologically relevant antimicrobial drug producer. To increase the efficiency of the enzyme toward sulfoxides, the mutant forms of MGL, with the replacements of active site cysteine 115 with alanine (C115A MGL) and histidine (C115H MGL) were obtained. The replacement of cysteine 115 by histidine results in the loss of activity of the mutant enzyme in the γ-elimination reaction of physiological substrate, whereas the activity in the β-elimination reaction of characteristic substrates persists. However, the catalytic efficiency of C115H MGL in the β-elimination reaction of S-substituted l-cysteine sulfoxides is increased by about an order of magnitude compared to the wild type MGL. The antibacterial activity of C115H MGL mixtures with a number of sulfoxides was assessed against Gram-positive and Gram-negative bacteria. The bacteriostatic effect was more pronounced against Gram-positive than against Gram-negative bacteria, while antibacterial potential proved to be quite similar. Thus, the mutant enzyme C115H MGL is an effective catalyst, in particular, for decomposition of sulfoxides and the pharmacological couples of the mutant form with sulfoxides might be new antimicrobial agents.

  19. Hydrogen production by a new chemoheterotrophic bacterium Citrobacter sp. Y19

    Energy Technology Data Exchange (ETDEWEB)

    Jung, G.Y. [Pusan National Univ. (Korea). Inst. for Environmental Technology and Industry; Kim, J.R.; Park, J.Y. [Pusan National Univ. (Korea). Dept. of Chemical Engineering; Park, S. [Pusan National Univ. (Korea). Inst. for Environmental Technology and Industry; Pusan National Univ. (Korea). Dept. of Chemical Engineering


    A newly isolated Citrobacter sp. Y19 grows on organic carbons aerobically and produces hydrogen from carbon monoxide (CO) and water when transferred to anaerobic conditions. Hydrogen production capability of Y19 was studied in serum-bottle and bioreactor cultures. Optimal cell growth was observed at pH 5-8, temperature of 30-40 {sup o} C, oxygen partial pressure of 0.2-0.4 atm. Induction of hydrogen production activity could be carried out efficiently under 20% (v/v) CO when the culture was removed to anaerobic conditions at 12 h. Optimal conditions for hydrogen production were 30-40{sup o} C and pH 5.5-7.5. The maximum hydrogen production activity was observed as 27.1 mmol/gcellh, which was about three times higher than that of Rhodospirillium rubrum. In bioreactor experiments, a stable hydrogen production along with a high activity of 20 mmolH{sub 2}gcellh was observed during the continuous operation of 68 h. (author)

  20. Study on biosorption kinetics and thermodynamics of uranium by Citrobacter freudii

    Energy Technology Data Exchange (ETDEWEB)

    Xie Shuibo [Department of Environment Science and Engineering, Tsinghua University, Beijing 100084 (China) and School of Urban Construction, University of South China, Hengyang, Hunan 421001 (China)], E-mail:; Yang Jing [School of Urban Construction, University of South China, Hengyang, Hunan 421001 (China); Chen Chao; Zhang Xiaojian [Department of Environment Science and Engineering, Tsinghua University, Beijing 100084 (China); Wang Qingliang; Zhang Chun [School of Urban Construction, University of South China, Hengyang, Hunan 421001 (China)


    Biosorption has been developed as an effective and economic method to treat wastewater containing low concentrations of metal pollutants. In this study, a bacterium, Citrobacter freudii, was used as a biosorbent to adsorb uranium ions. The thermodynamics and kinetics of this adsorption, as well as its mechanism, were investigated. The results indicated that the biosorption rate could be better described by a pseudo 2nd-order model than a pseudo 1st-order model. The adsorption of U (VI) proceeded very rapidly in the first 30 min and subsequently slowed down continuously for a long period. The biosorption isotherm of uranium by C. freudii could be described well by the Langmuir or Freundlich isotherm, and the latter was better. The thermodynamics parameters, {delta}H{sup o}, {delta}G{sup o}, and {delta}S{sup o} were calculated according to the results of the experiment, which showed this biosorption as being endothermic and spontaneous. The authors investigated the active sites of bacteria for biosorption and the results proved that carboxyl in the cell wall played an important role in biosorption.

  1. Metabolic-flux analysis of hydrogen production pathway in Citrobacter amalonaticus Y19

    Energy Technology Data Exchange (ETDEWEB)

    Oh, You-Kwan; Kim, Mi-Sun [Bioenergy Research Center, Korea Institute of Energy Research, Daejeon 305-343 (Korea); Kim, Heung-Joo; Park, Sunghoon [Department of Chemical and Biochemical Engineering and Institute for Environmental Technology and Industry, Pusan National University, Busan 609-735 (Korea); Ryu, Dewey D.Y. [Biochemical Engineering Program, Department of Chemical Engineering and Material Science, University of California, Davis, CA 95616 (United States)


    For the newly isolated chemoheterotrophic bacterium Citrobacter amalonaticus Y19, anaerobic glucose metabolism and hydrogen (H{sub 2}) production pathway were studied using batch cultivation and an in silico metabolic-flux analysis. Batch cultivation was conducted under varying initial glucose concentration between 1.5 and 9.5 g/L with quantitative measurement of major metabolites to obtain accurate carbon material balance. The metabolic flux of Y19 was analyzed using a metabolic-pathway model which was constructed from 81 biochemical reactions. The linear optimization program MetaFluxNet was employed for the analysis. When the specific growth rate of cells was chosen as an objective function, the model described the batch culture characteristics of Ci. amalonaticus Y19 reasonably well. When the specific H{sub 2} production rate was selected as an objective function, on the other hand, the achievable maximal H{sub 2} production yield (8.7molH{sub 2}/mol glucose) and the metabolic pathway enabling the high H{sub 2} yield were identified. The pathway involved non-native NAD(P)-linked hydrogenase and H{sub 2} production from NAD(P)H which were supplied at a high rate from glucose degradation through the pentose phosphate pathway. (author)

  2. Studies of polypropylene membrane fouling during microfiltration of broth with Citrobacter freundii bacteria

    Directory of Open Access Journals (Sweden)

    Gryta Marek


    Full Text Available In this work a fouling study of polypropylene membranes used for microfiltration of glycerol solutions fermented by Citrobacter freundii bacteria was presented. The permeate free of C. freundii bacteria and having a turbidity in the range of 0.72–1.46 NTU was obtained. However, the initial permeate flux (100–110 L/m2h at 30 kPa of transmembrane pressure was decreased 3–5 fold during 2–3 h of process duration. The performed scanning electron microscope observations confirmed that the filtered bacteria and suspensions present in the broth formed a cake layer on the membrane surface. A method of periodical module rinsing was used for restriction of the fouling influence on a flux decline. Rinsing with water removed most of the bacteria from the membrane surface, but did not permit to restore the initial permeate flux. It was confirmed that the irreversible fouling was dominated during broth filtration. The formed deposit was removed using a 1 wt% solution of sodium hydroxide as a rinsing solution.

  3. The Type VI Secretion System Modulates Flagellar Gene Expression and Secretion in Citrobacter freundii and Contributes to Adhesion and Cytotoxicity to Host Cells. (United States)

    Liu, Liyun; Hao, Shuai; Lan, Ruiting; Wang, Guangxia; Xiao, Di; Sun, Hui; Xu, Jianguo


    The type VI secretion system (T6SS) as a virulence factor-releasing system contributes to virulence development of various pathogens and is often activated upon contact with target cells. Citrobacter freundii strain CF74 has a complete T6SS genomic island (GI) that contains clpV, hcp-2, and vgr T6SS genes. We constructed clpV, hcp-2, vgr, and T6SS GI deletion mutants in CF74 and analyzed their effects on the transcriptome overall and, specifically, on the flagellar system at the levels of transcription and translation. Deletion of the T6SS GI affected the transcription of 84 genes, with 15 and 69 genes exhibiting higher and lower levels of transcription, respectively. Members of the cell motility class of downregulated genes of the CF74ΔT6SS mutant were mainly flagellar genes, including effector proteins, chaperones, and regulators. Moreover, the production and secretion of FliC were also decreased in clpV, hcp-2, vgr, or T6SS GI deletion mutants in CF74 and were restored upon complementation. In swimming motility assays, the mutant strains were found to be less motile than the wild type, and motility was restored by complementation. The mutant strains were defective in adhesion to HEp-2 cells and were restored partially upon complementation. Further, the CF74ΔT6SS, CF74ΔclpV, and CF74Δhcp-2 mutants induced lower cytotoxicity to HEp-2 cells than the wild type. These results suggested that the T6SS GI in CF74 regulates the flagellar system, enhances motility, is involved in adherence to host cells, and induces cytotoxicity to host cells. Thus, the T6SS plays a wide-ranging role in C. freundii.

  4. Kinetics study on decolorization of Reactive Red KN-3B by Citrobacter sp. CK3%Citrobacter sp. CK3对活性红KN-3B的脱色反应动力学研究

    Institute of Scientific and Technical Information of China (English)

    赖正; 熊小京; 郑天凌; 林光辉; 张章堂


    采用脱色菌Citrobacter sp. CK3,以活性红KN-3B染料为处理对象,在厌氧批式反应条件下,系统考察了pH值,温度和染料浓度对脱色反应速度的影响;通过动力学模拟及反应过程中染料的UV-Vis扫描图分析,探讨了脱色反应机理。结果表明:Citrobacter sp. CK3对活性红KN-3B的脱色反应的适宜pH为7~9;脱色反应速度在温度为32℃时达到最大。染料初浓度从57 mg/L逐渐增大到458 mg/L时脱色率逐渐降低。脱色过程中染料的偶氮键发生断裂,脱色反应符合二级反应动力学。%The kinetic modeling and mechanism with which Citrobacter sp. CK3 removed the textile dye, C.I. Reactive Red 180, from aqueous solution was investigated using different parameters, such as initial dye concentration,pH and temperature. In anaerobic batch experiments, the decolorization efficiency decreased with increase in initial dye concentration. The high decolorization rate was observed at pH of 7 -9 and temperature of 32C. The decolorization followed a second order kinetic model. The UV-Vis spectra analysis revealed that the decolorization process was azo bond cleaved reaction.

  5. NDM-1-Producing Citrobacter freundii, Escherichia coli, and Acinetobacter baumannii Identified from a Single Patient in China. (United States)

    Huang, Ying-Min; Zhong, Lan-Lan; Zhang, Xue-Fei; Hu, Hang-Tong; Li, Yu-Qi; Yang, Xiao-Rong; Feng, Lian-Qiang; Huang, Xi; Tian, Guo-Bao


    We identified New Delhi metallo-β-lactamase (NDM-1)-producing Citrobacter freundii GB032, Escherichia coli GB102, and Acinetobacter baumannii GB661 in urine and stool samples from a single patient in China. Plasmid profiling and Southern blotting indicated that blaNDM-1 from GB032 and that from GB102 were likely located on the same plasmid, while blaNDM-1 from GB661 was located on a very large (>400-kb) plasmid. This case underscores the broad host range of blaNDM-1 and its potential to spread between members of the family Enterobacteriaceae and A. baumannii.

  6. Polymeric and compositional properties of novel extracellular microbial polyglucosamine biopolymer from new strain of citrobacter sp. BL-4. (United States)

    Kim, Lin-Su; Hong, Soo-Jung; Son, Mi-Kyung; Lee, Yong-Hyun


    A novel polyglucosamine polymer, PGB-2, was produced extracellularly from a new strain Citrobacter sp. BL-4 using pH-stat fed batch cultivation. It was composed of 97.3% glucosamine and 2.7% rhamnose; its average molecular weight, solubility in 2% acetic acid and viscosity were 20 kDa, 5 g l(-1) and 2.9 cps, respectively. FT-IR and 1H NMR spectra of PGB-2 revealed a close identity with chitosan from crab shells.

  7. 1,3-Propanediol production by Escherichia coli using genes from Citrobacter freundii atcc 8090. (United States)

    Przystałowska, Hanna; Zeyland, Joanna; Kośmider, Alicja; Szalata, Marlena; Słomski, Ryszard; Lipiński, Daniel


    Compared with chemical synthesis, fermentation has the advantage of mass production at low cost, and has been used in the production of various industrial chemicals. As a valuable organic compound, 1,3-propanediol (1,3-PDO) has numerous applications in the production of polymers, lubricants, cosmetics and medicines. Here, conversion of glycerol (a renewable substrate and waste from biodiesel production) to 1,3-PDO by E. coli bacterial strain carrying altered glycerol metabolic pathway was investigated. Two gene constructs containing the 1,3-PDO operon from Citrobacter freundii (pCF1 and pCF2) were used to transform the bacteria. The pCF1 gene expression construct contained dhaBCE genes encoding the three subunits of glycerol dehydratase, dhaF encoding the large subunit of the glycerol dehydratase reactivation factor and dhaG encoding the small subunit of the glycerol dehydratase reactivating factor. The pCF2 gene expression construct contained the dhaT gene encoding the 1,3-propanediol dehydrogenase. Expression of the genes cloned in the above constructs was under regulation of the T7lac promoter. RT-PCR, SDS-PAGE analyses and functional tests confirmed that 1,3-PDO synthesis pathway genes were expressed at the RNA and protein levels, and worked flawlessly in the heterologous host. In a batch flask culture, in a short time applied just to identify the 1,3-PDO in a preliminary study, the recombinant E. coli bacteria produced 1.53 g/L of 1,3-PDO, using 21.2 g/L of glycerol in 72 h. In the Sartorius Biostat B Plus reactor, they produced 11.7 g/L of 1,3-PDO using 24.2 g/L of glycerol, attaining an efficiency of 0.58 [mol1,3-PDO/molglycerol].

  8. Fermentative biohydrogen production by a new chemoheterotrophic bacterium Citrobacter sp. Y19

    Energy Technology Data Exchange (ETDEWEB)

    Youkwan Oh; Sunghoon Park [Changjeon Univ., Pusan (Korea). Dept. of Chemical Engineering; Pusan National Univ. (Korea). Inst. for Environmental Technology and Industry; Eunhee Seol [Changjeon Univ., Pusan (Korea). Dept. of Chemical Engineering; Jung Rae Kim [Pusan National Univ. (Korea). Inst. for Environmental Technology and Industry


    A newly isolated Citrobacter sp. Y19 for CO-dependent H{sub 2} production was studied for its capability of fermentative H{sub 2} production in batch cultivation. When glucose was used as carbon source, the pH of the culture medium significantly decreased as fermentation proceeded and H{sub 2} production was seriously inhibited. The use of fortified phosphate at 60-180 mM alleviated this inhibition. By increasing culture temperatures (25-36{sup o}C), faster cell growth and higher initial H{sub 2} production rates were observed but final H{sub 2} production and yield were almost constant irrespective of temperature. Optimal specific H{sub 2} production activity was observed at 36{sup o}C and pH 6-7. The increase of glucose concentration (1-20 g/l) in the culture medium resulted in higher H{sub 2} production, but the yield of H{sub 2} production (mol H{sub 2}/mol glucose) gradually decreased with increasing glucose concentration. Carbon mass balance showed that, in addition to cell mass, ethanol, acetate and CO{sub 2} were the major fermentation products and comprised more than 70% of the carbon consumed. The maximal H{sub 2} yield and H{sub 2} production rate were estimated to be 2.49 mol H{sub 2}/mol glucose and 32.3 mmol H{sub 2}/gcellh, respectively. The overall performance of Y19 in fermentative H{sub 2} production is quite similar to that of most H{sub 2}-producing bacteria previously studied, especially to that of Rhodopseudomonas palustris P4, and this indicates that the attempt to find an outstanding bacterial strain for fermentative H{sub 2} production might be very difficult if not impossible. (author)

  9. The role of active site tyrosine 58 in Citrobacter freundii methionine γ-lyase. (United States)

    Anufrieva, Natalya V; Faleev, Nicolai G; Morozova, Elena A; Bazhulina, Natalia P; Revtovich, Svetlana V; Timofeev, Vladimir P; Tkachev, Yaroslav V; Nikulin, Alexei D; Demidkina, Tatyana V


    In the spatial structure of methionine γ-lyase (MGL, EC from Citrobacter freundii, Tyr58 is located at H-bonding distance to the oxygen atom of the phosphate "handle" of pyridoxal 5'-phosphate (PLP). It was replaced for phenylalanine by site-directed mutagenesis. The X-ray structure of the mutant enzyme was determined at 1.96Å resolution. Comparison of spatial structures and absorption spectra of wild-type and mutant holoenzymes demonstrated that the replacement did not result in essential changes of the conformation of the active site Tyr58Phe MGL. The Kd value of PLP for Tyr58Phe MGL proved to be comparable to the Kd value for the wild-type enzyme. The replacement led to a decrease of catalytic efficiencies in both γ- and β-elimination reactions of about two orders of magnitude as compared to those for the wild-type enzyme. The rates of exchange of C-α- and C-β- protons of inhibitors in D2O catalyzed by the mutant form are comparable with those for the wild-type enzyme. Spectral data on the complexes of the mutant form with the substrates and inhibitors showed that the replacement led to a change of rate the limiting step of the physiological reaction. The results allowed us to conclude that Tyr58 is involved in an optimal positioning of the active site Lys210 at some stages of γ- and β-elimination reactions. This article is part of a Special Issue entitled: Cofactor-dependent proteins: evolution, chemical diversity and bio-applications.

  10. Microbial degradation of Paclitaxel using Citrobacter amalonaticus Rashtia isolated from pharmaceutical wastewater: kinetic and thermodynamic study. (United States)

    Zamani, Hojjatolah; Grakoee, Seyed Reza; Rakhshaee, Roohan


    Paclitaxel is a highly toxic anticancer agent which is used in a wide range against ovarian, breast, lung, and prostate cancers. Paclitaxel is manufactured recently in the north of Iran which may lead to the introduction of the drug into the environment via pharmaceutical wastewater. To our knowledge, Paclitaxel degradation is currently performed using physicochemical methods and biological degradation of Paclitaxel has not been reported. In this study, a Paclitaxel degrading bacterium was isolated from pharmaceutical wastewater for the first time. The bacterium was identified using biochemical and molecular assays and its Paclitaxel degradation potential was evaluated using High Performance Liquid Chromatography (HPLC). In addition, kinetic and thermodynamic study of Paclitaxel degradation at different experimental conditions was performed. A Citrobacter species named as C. amalonaticus Rashtia able to degrade and utilize Paclitaxel as the sole carbon source was isolated. The isolated strain tolerated high level concentration of Paclitaxel (0.4 mg/mL) in liquid culture media and was able to degrade spillage-level concentrations of the drug (0.01-0.1 mg/mL) with 87-93 % efficacy under aerobic condition. Kinetic and thermodynamic study at different pHs (4.0, 7.0 and 10.0) and temperatures (285, 295 and 310 K) revealed that Paclitaxel degradation is a non-spontaneous process and the highest rate constant was observed in the basic condition and at the highest temperature. The ΔG values at 285, 295 and 310 K were determined 103.3, 105.9 and 109.9 kJ/mol, respectively. In addition, The ΔH and activation energy (Ea) of the process were determined +28.7 kJ/mol and +30.87 kJ/mol, respectively.

  11. Profile of Citrobacter freundii ST2, a Multi-acyl-homoserine Lactone Producer Associated with Marine Dinoflagellates. (United States)

    Huang, Xinqi; Gao, Yan; Ma, Zhiping; Lin, Guanghui; Cai, Zhonghua; Zhou, Jin


    Marine algae provide a unique niche termed the phycosphere for microorganism inhabitation. The phycosphere environment is an important niche for mutualistic and competitive interactions between algae and bacteria. Quorum sensing (QS) serves as a gene regulatory system in the microbial biosphere that allows bacteria to sense the population density with signaling molecules, such as acyl-homoserine lactone (AHL), and adapt their physiological activities to their surroundings. Understanding the QS system is important to elucidate the interactions between algal-associated microbial communities in the phycosphere condition. In this study, we isolated an epidermal bacterium (ST2) from the marine dinoflagellate Scrippsiella trochoidea and evaluated its AHL production profile. Strain ST2 was classified as a member of the genus Citrobacter closely related to Citrobacter freundii by 16S rRNA gene sequence analysis. Thin-layer chromatography revealed that C. freundii ST2 secreted three active AHL compounds into the culture supernatant. Specific compounds, such as N-butyryl-L-homoserine lactone (C4-AHL), N-octanoyl-DL-homoserine lactone (C8-AHL), and N-decanoyl-DL-homoserine lactone (C10-AHL), were identified by high-resolution tandem mass spectrometry. Carbon metabolic profiling with Biolog EcoPlate™ indicated that C. freundii ST2 was widely used as a carbon source and preferred carbohydrates, amino acids, and carboxylic acids as carbon substrates. Our results demonstrated that C. freundii ST2 is a multi-AHL producer that participates in the phycosphere carbon cycle.

  12. Species identification of strains belonging to genus Citrobacter using the biochemical method and MALDI-TOF mass spectrometry. (United States)

    Kolínská, Renáta; Spanělová, Petra; Dřevínek, Michal; Hrabák, Jaroslav; Zemličková, Helena


    Strains of genus Citrobacter (152 isolates from 1950 to 1988 deposited in the Czech National Collection of Type Cultures, Prague) were re-classified using biological and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) methods. One-hundred thirty-six strains (ca. 90 %) were identified to the species level using the biological method with evaluation by Farmer matrix. MALDI-TOF MS exhibited better identification capability, the data being more compact; the method was unambiguously successful in typing 145 (95 %) strains. Comparison of the results of identification by the two methods revealed differences (for 12 samples) in identified species which, considering all biochemical and/or MS characteristics, could be attributed to the natural variability of strains and close relation of the misidentified species (all of them belonged to the Citrobacter freundii complex). Taking into account all the above data, both methods can be considered reliable; however, the MALDI-TOF MS exhibits higher accuracy, efficiency, and rapidity.

  13. Effects of nutritional and environmental conditions on planktonic growth and biofilm formation of Citrobacter werkmanii BF-6. (United States)

    Zhou, Gang; Li, Long-jie; Shi, Qing-shan; Ouyang, You-sheng; Chen, Yi-ben; Hu, Wen-feng


    Citrobacter sp. is a cause of significant opportunistic nosocomial infection and is frequently found in human and animal feces, soil, and sewage water, and even in industrial waste or putrefaction. Biofilm formation is an important virulence trait of Citrobacter sp. pathogens but the process and characteristics of this formation are unclear. Therefore, we employed in vitro assays to study the nutritional and environmental parameters that might influence biofilm formation of C. werkmanii BF-6 using 96-well microtiter plates. In addition, we detected the relative transcript levels of biofilm formation genes by RT-PCR. Our results indicated that the capacity of C. werkmanii BF-6 to form biofilms was affected by culture temperature, media, time, pH, and the osmotic agents glucose, sucrose, NaCl, and KCl. Confocal laser scanning microscopy results illustrated that the structure of biofilms and extracellular polysaccharide was influenced by 100 mM NaCl or 100 mM KCl. In addition, nine biofilm formation genes (bsmA, bssR, bssS, csgD, csgE, csgF, mrkA, mrkB, and mrkE) were found to contribute to planktonic and biofilm growth. Our data suggest that biofilm formation by C. werkmanii BF-6 is affected by nutritional and environmental factors, which could pave the way to the prevention and elimination of biofilm formation using proper strategies.

  14. Improved purification, crystallization and crystallographic study of Hyd-2-type [NiFe]-hydrogenase from Citrobacter sp. S-77. (United States)

    Muhd Noor, Noor Dina; Nishikawa, Koji; Nishihara, Hirofumi; Yoon, Ki Seok; Ogo, Seiji; Higuchi, Yoshiki


    The purification procedure of Hyd-2-type [NiFe]-hydrogenase from Citrobacter sp. S-77 was improved by applying treatment with trypsin before chromatography. Purified protein samples both with and without trypsin treatment were successfully crystallized using the sitting-drop vapour-diffusion method with polyethylene glycol as a precipitant. Both crystals belonged to space group P21, with unit-cell parameters a = 63.90, b = 118.89, c = 96.70 Å, β = 100.61° for the protein subjected to trypsin treatment and a = 65.38, b = 121.45, c = 98.63 Å, β = 102.29° for the sample not treated with trypsin. The crystal obtained from the trypsin-treated protein diffracted to 1.60 Å resolution, which is considerably better than the 2.00 Å resolution obtained without trypsin treatment. The [NiFe]-hydrogenase from Citrobacter sp. S-77 retained catalytic activity with some amount of O2, indicating that it has clear O2 tolerance.

  15. 枸橼酸杆菌医院感染特点及耐药性检测%Nosocomial infection and antibiotic resistance surveillance of citrobacter

    Institute of Scientific and Technical Information of China (English)

    刘红梅; 姜玉昌


    Objective To investigate the distribution and antibiotic resistance of citrobacter for anti-infection therapy .Methods The citrobacter were identified by Walk-Away-40 according to《National Guide to Clinical Laboratory Procedures》 .Kirby-Bauer(K-B ) were used for drug sensitive test and WHONET5.4 for statistics .Results We isolated 172 strains of citrobacteT .Of which C .freundii was major (70.3%) ,then Citrobacter am alonaticus (14.0%) and Citrobacter diversus (5.2%).In 172 strains of citrobacte which came mainly from respiratoy tract (67 .4%) and urogenital tract was the next(22.1% ).The infected ward were neurology ward (29.1%) ,respiratoy ward(27.9%)nephrology ward (16.9%)and oncology ward(11.0%).Drug sensitive test showed higher resistance rate in 172 strains of citrobacter to ampicillin ,cefazolin and Cefoxitin were above 87% ,while to amikacin ,imipenem and sulperazone were lower 20% .Conclusion C .freundii was the common citrobacter in nosocomial infection and came mainly from respiratory tract.Citrobacter produced multi-β-lactam ase resistance .Imipenem ,sulperazone and amikacin have higher antibacterial activities to citrobacte.%目的 了解枸橼酸杆菌在医院感染中的分布特点及耐药特性,为临床抗感染治疗提供依据.方法 细菌分离培养按进行;采用WalkAway-40全自动细菌鉴定仪对临床分离菌株进行菌种鉴定;采用K-B法进行药敏试验,用WHONET5.4软件进行统计分析.结果 共分离枸橼酸杆菌属细菌172株,其中弗劳地枸橼酸杆菌最多,占70.3%,其次为丙二酸盐阴性枸橼酸杆菌和异型枸橼酸杆菌,分别占14.0%和5.2%,172株枸橼酸杆菌的感染部位以呼吸道最多(67.4%),其次为泌尿生殖道(22.1%);病区分布主要为神经内科病房、呼吸内科病房、肾内科病房和肿瘤病房,分别占29.1%、27.9%、16.9%和11.0%;药敏结果显示,172株枸橼酸杆菌对氨苄西林、头孢唑啉、头孢

  16. Morphological Evolution during the Formation of Carbonate Spherulite in Citrobacter freundii Culture%Citrobacter freundii作用下球状碳酸盐矿物的形态演化过程研究

    Institute of Scientific and Technical Information of China (English)

    马恒; 李福春; 苏宁; 李学林


    不少微生物都具有形成球状碳酸盐矿物的能力.对形成过程的动态跟踪研究是了解球状碳酸盐矿物形成机理的关键.利用光学显微镜和电子显微镜对Citrobacter freundii作用下球状碳酸盐矿物的形成过程进行了跟踪研究.结果表明,纳米晶体在有机物质的包裹下逐渐聚集.最终生长为具有辐射状内部结构和菱形表面纹理的球状构造.在球状构造形成之前,矿物集合体经历了花形、哑铃形、花菜形、纺锤形以及类似于十字形的多种过渡形态.对最初、过渡和最终形态进行总结,有助于理解微生物作用下的球状碳酸盐矿物形成机理,为识别微生物活动在沉积环境中遗留的痕迹提供更多有用的信息.以往的研究极少涉及Citrobacter freundii诱导碳酸盐矿物的形成.研究结果将丰富微生物促进球状碳酸盐矿化的研究内容.

  17. Development of a Rapid and Accurate Identification Method for Citrobacter Species Isolated from Pork Products Using a Matrix-Assisted Laser-Desorption Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF MS). (United States)

    Kwak, Hye-Lim; Han, Sun-Kyung; Park, Sunghoon; Park, Si Hong; Shim, Jae-Yong; Oh, Mihwa; Ricke, Steven C; Kim, Hae-Yeong


    Previous detection methods for Citrobacter are considered time consuming and laborious. In this study, we have developed a rapid and accurate detection method for Citrobacter species in pork products, using matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) mass spectrometry (MS). A total of 35 Citrobacter strains were isolated from 30 pork products and identified by both MALDI-TOF MS and 16S rRNA gene sequencing approaches. All isolates were identified to the species level by the MALDI-TOF MS, while 16S rRNA gene sequencing results could not discriminate them clearly. These results confirmed that MALDI-TOF MS is a more accurate and rapid detection method for the identification of Citrobacter species.

  18. [NiFe]Hydrogenase from Citrobacter sp. S-77 surpasses platinum as an electrode for H2 oxidation reaction. (United States)

    Matsumoto, Takahiro; Eguchi, Shigenobu; Nakai, Hidetaka; Hibino, Takashi; Yoon, Ki-Seok; Ogo, Seiji


    Reported herein is an electrode for dihydrogen (H2) oxidation, and it is based on [NiFe]Hydrogenase from Citrobacter sp. S-77 ([NiFe]S77). It has a 637 times higher mass activity than Pt (calculated based on 1 mg of [NiFe]S77 or Pt) at 50 mV in a hydrogen half-cell. The [NiFe]S77 electrode is also stable in air and, unlike Pt, can be recovered 100 % after poisoning by carbon monoxide. Following characterization of the [NiFe]S77 electrode, a fuel cell comprising a [NiFe]S77 anode and Pt cathode was constructed and shown to have a a higher power density than that achievable by Pt.

  19. Molecular cloning, co-expression, and characterization of glycerol dehydratase and 1,3-propanediol dehydrogenase from Citrobacter freundii. (United States)

    Qi, Xianghui; Deng, Wenying; Wang, Fei; Guo, Qi; Chen, Huayou; Wang, Liang; He, Xiang; Huang, Ribo


    1,3-Propanediol (1,3-PD), an important material for chemical industry, is biologically synthesized by glycerol dehydratase (GDHt) and 1,3-propanediol dehydrogenase (PDOR). In present study, the dhaBCE and dhaT genes encoding glycerol dehydratase and 1,3-propanediol dehydrogenase respectively were cloned from Citrobacter freundii and co-expressed in E. coli. Sequence analysis revealed that the cloned genes were 85 and 77 % identical to corresponding gene of C. freundii DSM 30040 (GenBank No. U09771), respectively. The over-expressed recombinant enzymes were purified by nickel-chelate chromatography combined with gel filtration, and recombinant GDHt and PDOR were characterized by activity assay, kinetic analysis, pH, and temperature optimization. This research may form a basis for the future work on biological synthesis of 1,3-PD.

  20. Malachite green bioremoval by a newly isolated strain Citrobacter sedlakii RI11; enhancement of the treatment by biosurfactant addition. (United States)

    Mnif, Inès; Fendri, Raouia; Ghribi, Dhouha


    Citrobacter sedlackii RI11, isolated from acclimated textile effluent after selective enrichment on synthetic dyes, was assessed for malachite green (MG) biotreatment potency. Results indicate that this bacterium has potential for use in effective treatment of MG contaminated wastewaters under shaking conditions at neutral and alkaline pH value, characteristic of typical textile effluents. Also, the newly isolated strain can tolerate higher doses of dye and decolorize up to 1,000 mg/l of dye. When used as microbial surfactant to enhance MG biodecolorization, Bacillus subtilis SPB1-derived lipopeptide accelerated the decolorization rate and maximized the decolorization efficiency at an optimal concentration of biosurfactant of about 0.075%. Studies ensured that MG removal by this strain could be due to biodegradation and/or adsorption. Results on germination potencies of different seeds using the treated dyes under different conditions favor the use of SPB1 biosurfactant for the treatment of MG.

  1. Citrobacter amalonaticus Phytase on the Cell Surface of Pichia pastoris Exhibits High pH Stability as a Promising Potential Feed Supplement


    Cheng Li; Ying Lin; Yuanyuan Huang; Xiaoxiao Liu; Shuli Liang


    Phytase expressed and anchored on the cell surface of Pichia pastoris avoids the expensive and time-consuming steps of protein purification and separation. Furthermore, yeast cells with anchored phytase can be used as a whole-cell biocatalyst. In this study, the phytase gene of Citrobacter amalonaticus was fused with the Pichia pastoris glycosylphosphatidylinositol (GPI)-anchored glycoprotein homologue GCW61. Phytase exposed on the cell surface exhibits a high activity of 6413.5 U/g, with an ...

  2. Urinary Tract Infection Caused by Citrobacter koseri in a Patient With Spina Bifida, an Ileal Conduit and Renal Caluli Progressing to Peri-nephric Abscess and Empyema. (United States)

    Stewart, Zachary E; Shaker, Mohammed; Baxter, J David


    Urological problems are common in spina bifida and are often treated with urinary diversions. Spina bifida and ileal conduits put patients at increased risk for ascending urinary tract infections. Here we present a novel case of a Citrobacter koseri urinary tract infection complicated by a perinephric abscess with pleural extension. To our knowledge, no case of an ascending C. koseri UTI progressing to peri-nephric abscess and empyema by direct extension exists in the literature.

  3. Novel genetic environment of the plasmid-mediated KPC-3 gene detected in Escherichia coli and Citrobacter freundii isolates from China


    Li, G.; Wei, Q; Wang, Y.; Du, X.; Zhao, Y.; Jiang, X.


    The imipenem and meropenem-resistant strains Citrobacter freundii HS70 and Escherichia coli HS510 were isolated from patients in Shanghai, China. By isoelectric focusing, PCR amplification and sequencing, these strains were each found to produce four β-lactamases: TEM-1, KPC-3, SHV-7 and CTX-M-14. A conjugation experiment and plasmid restriction digestion revealed that the bla KPC-3 gene was located on the same plasmid in both isolates. Bidirectional primer walking sequencing showed that the ...

  4. Molybdenum-containing membrane-bound formate dehydrogenase isolated from Citrobacter sp. S-77 having high stability against oxygen, pH, and temperature. (United States)

    Nguyen, Nga T; Yatabe, Takeshi; Yoon, Ki-Seok; Ogo, Seiji


    Membrane-bound formate dehydrogenase (FDH) was purified to homogeneity from a facultative anaerobic bacterium Citrobacter sp. S-77. The FDH from Citrobacter sp. S-77 (FDHS77) was a monomer with molecular mass of approximately 150 kDa. On SDS-PAGE, the purified FDHS77 showed as three different protein bands with molecular mass of approximately 95, 87, and 32 kDa, respectively. Based on the N-terminal amino acid sequence analysis, the sequence alignments observed for the 87 kDa protein band were identical to that of the large subunit of 95 kDa, indicating that the purified FDHS77 consisted of two subunits; a 95 kDa large subunit and a 32 kDa small subunit. The purified FDHS77 in this purification did not contain a heme b subunit, but the FDHS77 showed significant activity for formate oxidation, determined by the Vmax of 30.4 U/mg using benzyl viologen as an electron acceptor. The EPR and ICP-MS spectra indicate that the FDHS77 is a molybdenum-containing enzyme, displaying a remarkable O2-stability along with thermostability and pH resistance. This is the first report of the purification and characterization of a FDH from Citrobacter species.

  5. CXCR2-dependent mucosal neutrophil influx protects against colitis-associated diarrhea caused by an attaching/effacing lesion-forming bacterial pathogen. (United States)

    Spehlmann, Martina E; Dann, Sara M; Hruz, Petr; Hanson, Elaine; McCole, Declan F; Eckmann, Lars


    Enteropathogenic Escherichia coli (EPEC) is a major cause of diarrheal disease in young children, yet symptoms and duration are highly variable for unknown reasons. Citrobacter rodentium, a murine model pathogen that shares important functional features with EPEC, colonizes mice in colon and cecum and causes inflammation, but typically little or no diarrhea. We conducted genome-wide microarray studies to define mechanisms of host defense and disease in C. rodentium infection. A significant fraction of the genes most highly induced in the colon by infection encoded CXC chemokines, particularly CXCL1/2/5 and CXCL9/10, which are ligands for the chemokine receptors CXCR2 and CXCR3, respectively. CD11b(+) dendritic cells were the major producers of CXCL1, CXCL5, and CXCL9, while CXCL2 was mainly induced in macrophages. Infection of gene-targeted mice revealed that CXCR3 had a significant but modest role in defense against C. rodentium, whereas CXCR2 had a major and indispensable function. CXCR2 was required for normal mucosal influx of neutrophils, which act as direct antibacterial effectors. Moreover, CXCR2 loss led to severe diarrhea and failure to express critical components of normal ion and fluid transport, including ATPase beta(2)-subunit, CFTR, and DRA. The antidiarrheal functions were unique to CXCR2, since other immune defects leading to increased bacterial load and inflammation did not cause diarrhea. Thus, CXCR2-dependent processes, particularly mucosal neutrophil influx, not only contribute to host defense against C. rodentium, but provide protection against infection-associated diarrhea.

  6. Surfactant-modified fatty acid composition of Citrobacter sp. SA01 and its effect on phenanthrene transmembrane transport. (United States)

    Li, Feng; Zhu, Lizhong


    The effects of the surfactants, Tween 80 and sodium dodecyl benzene sulfonate (SDBS) on a membrane's fatty acid composition and the transmembrane transport of phenanthrene were investigated. The results indicated that both surfactants could modify the composition of fatty acids of Citrobacter sp. Strain SA01 cells, 50 mg L(-1) of both surfactants changed the composition of the fatty acids the most, increasing the amount of unsaturated fatty acids. The comparison of fatty acid profiles with diphenylhexatriene fluorescence anisotropy, a probe for plasma membrane fluidity, suggested that an increased amount of unsaturated fatty acids corresponded to greater membrane fluidity. In addition, increased unsaturated fatty acids promoted phenanthrene to partition from the extracellular matrix to cell debris, which increased reverse partitioning from the cell debris to the cytochylema. The results of this study were expected in that the addition of a surfactant is a simple and effective method for accelerating the rate-limiting step of transmembrane transport of hydrophobic organic compounds (HOCs) in bioremediation.

  7. Conversion of glycerol to 1,3-propanediol by Citrobacter freundii and Hafnia alvei - newly isolated strains from the Enterobacteriaceae. (United States)

    Drożdżyńska, Agnieszka; Pawlicka, Joanna; Kubiak, Piotr; Kośmider, Alicja; Pranke, Dorota; Olejnik-Schmidt, Agnieszka; Czaczyk, Katarzyna


    In this study, nearly 4000 bacterial strains from the family of Enterobacteriaceae isolated from different environments were screened for ability to convert glycerol to 1,3-propanediol (1,3-PD). The aim of the research was to isolate 1,3-PD producers from the natural environment, identify and characterize the best isolates. Three selective media were tested to usefulness in the isolation of bacteria from the family Enterobacteriaceae. Only, 28% of examined isolates could synthesize 1,3-PD from glycerol. 1,3-PD producing bacteria were identified by API 20E tests and 16S rRNA sequences to be Klebsiella pneumoniae, Klebsiella oxytoca, Citrobacter freundii and Hafnia alvei. It is the first time, when the fermentation glycerol to 1,3-PD by H. alvei was investigated. The selected strains (C. freundii AD119 and H. alvei AD27) were analyzed on a bioreactor scale under constant pH value 7.0 at temperature of 30°C and 37°C. After 40h in batch fermentation, H. alvei AD27 produced 11.3g/L of 1,3-PD at 37°C. For C. freundii AD119, the best results were obtained at temperature of 30°C. After 24h of fermentation, the 1,3-PD concentration reached above 23 g/L of 1,3-PD.

  8. Biochemical characterization of a bifunctional acetaldehyde-alcohol dehydrogenase purified from a facultative anaerobic bacterium Citrobacter sp. S-77. (United States)

    Tsuji, Kohsei; Yoon, Ki-Seok; Ogo, Seiji


    Acetaldehyde-alcohol dehydrogenase (ADHE) is a bifunctional enzyme consisting of two domains of an N-terminal acetaldehyde dehydrogenase (ALDH) and a C-terminal alcohol dehydrogenase (ADH). The enzyme is known to be important in the cellular alcohol metabolism. However, the role of coenzyme A-acylating ADHE responsible for ethanol production from acetyl-CoA remains uncertain. Here, we present the purification and biochemical characterization of an ADHE from Citrobacter sp. S-77 (ADHE(S77)). Interestingly, the ADHE(S77) was unable to be solubilized from membrane with detergents either 1% Triton X-100 or 1% Sulfobetaine 3-12. However, the enzyme was easily dissociated from membrane by high-salt buffers containing either 1.0 M NaCl or (NH(4))(2)SO(4) without detergents. The molecular weight of a native protein was estimated as approximately 400 kDa, consisting of four identical subunits of 96.3 kDa. Based on the specific activity and kinetic analysis, the ADHES77 tended to have catalytic reaction towards acetaldehyde elimination rather than acetaldehyde formation. Our experimental observation suggests that the ADHES77 may play a pivotal role in modulating intracellular acetaldehyde concentration.

  9. Alliin is a suicide substrate of Citrobacter freundii methionine γ-lyase: structural bases of inactivation of the enzyme. (United States)

    Morozova, Elena A; Revtovich, Svetlana V; Anufrieva, Natalya V; Kulikova, Vitalia V; Nikulin, Alexey D; Demidkina, Tatyana V


    The interaction of Citrobacter freundii methionine γ-lyase (MGL) and the mutant form in which Cys115 is replaced by Ala (MGL C115A) with the nonprotein amino acid (2R)-2-amino-3-[(S)-prop-2-enylsulfinyl]propanoic acid (alliin) was investigated. It was found that MGL catalyzes the β-elimination reaction of alliin to form 2-propenethiosulfinate (allicin), pyruvate and ammonia. The β-elimination reaction of alliin is followed by the inactivation and modification of SH groups of the wild-type and mutant enzymes. Three-dimensional structures of inactivated wild-type MGL (iMGL wild type) and a C115A mutant form (iMGL C115A) were determined at 1.85 and 1.45 Å resolution and allowed the identification of the SH groups that were oxidized by allicin. On this basis, the mechanism of the inactivation of MGL by alliin, a new suicide substrate of MGL, is proposed.

  10. Genetic characteristics of blaNDM-1-positive plasmid in Citrobacter freundii isolate separated from a clinical infectious patient. (United States)

    Du, Xiao-Xing; Wang, Jian-Feng; Fu, Ying; Zhao, Feng; Chen, Yan; Wang, Hai-Ping; Yu, Yun-Song


    This study reports an infectious case involving an (NDM-1)-producing Citrobacter freundii and further explored the potential threat of the bla(NDM-1) gene by analysing the characteristics of the (NDM-1)-encoding plasmid sequence. A bla(NDM-1)-positive C. freundii with high resistance to carbapenems was separated from a clinical patient suffering from a urinary tract infection. S1 nuclease-based plasmid analysis followed by Southern blot hybridization, a conjugation experiment and electrotransformation confirmed that the bla(NDM-1) gene was located on a plasmid. High-throughput sequencing of the bla(NDM-1)-positive plasmid (pCFNDM-CN) showed that it was a 54 kb IncX-type plasmid and contained a backbone region and a variable region with two β-lactamase genes (bla(NDM-1) and bla(SHV-12)). The NDM-1 composite transposon in the variable region was surrounded by IS26 and IS5-truncated ISAba125, and shared a high sequence similarity to the bla(NDM-1) surrounding structure in Acinetobacter spp. Our research suggested that the NDM-1 composite transposon might play an essential role in mobilization of the bla(NDM-1) gene from Acinetobacter spp. to Enterobacteriaceae.

  11. Diarrhea-associated biofilm formed by enteroaggregative Escherichia coli and aggregative Citrobacter freundii: a consortium mediated by putative F pili

    Directory of Open Access Journals (Sweden)

    Araújo Ana CG


    Full Text Available Abstract Background Enteroaggregative Escherichia coli (EAEC are enteropathogenic strains identified by the aggregative adhesion (AA pattern that share the capability to form biofilms. Citrobacter freundii is classically considered as an indigenous intestinal species that is sporadically associated with diarrhea. Results During an epidemiologic study focusing on infantile diarrhea, aggregative C. freundii (EACF and EAEC strains were concomitantly recovered from a severe case of mucous diarrhea. Thereby, the occurrence of synergic events involving these strains was investigated. Coinfection of HeLa cells with EACF and EAEC strains showed an 8-fold increase in the overall bacterial adhesion compared with single infections (P traA were capable of forming bacterial aggregates only in the presence of EACF. Scanning electronic microscopy analyses revealed that bacterial aggregates as well as enhanced biofilms formed by EACF and traA-positive EAEC were mediated by non-bundle forming, flexible pili. Moreover, mixed biofilms formed by EACF and traA-positive EAEC strains were significantly reduced using nonlethal concentration of zinc, a specific inhibitor of F pili. In addition, EAEC strains isolated from diarrheic children frequently produced single biofilms sensitive to zinc. Conclusions Putative F pili expressed by EAEC strains boosted mixed biofilm formation when in the presence of aggregative C. freundii.

  12. 柠檬酸杆菌吸附重金属铀的试验研究%Study on Adsorption of Heavy Metal Uranium by Citrobacter freundii

    Institute of Scientific and Technical Information of China (English)



    Citrobacter freundii was used to adsorb heavy metal uranium. The influence of pH, strain concentration and initial concentration of uranium on the adsorption of uranium were investigated. The results show that the adsorption efficiency of uranium by Citrobacter freundii increases with the in-crease of pH at the beginning of the adsorption and reaches its maximum at pH of 6 then decreases. The adsorption efficiency increases with the increase of strain concentration, while the adsorption capacity de-creases. The adsorption capacity increases with the increase of the initial concentration of uranium while the adsorption efficiency decreases. The adsorption process of uranium by Citrobacter freundii is in ac-cordance with Langmuir and Freundlich isotherms, and the fitting result of Freundlich isotherm is better.%采用弗氏柠檬酸杆菌吸附重金属铀,考察了pH、菌体浓度和铀离子浓度对吸附效果的影响.结果表明,弗氏柠檬酸杆菌对铀的吸附一开始随pH的增大而增大,当pH值为6时吸附率达到最大,而后降低;吸附率随菌体浓度的增加而增大,吸附量则相反;吸附量随铀起始浓度的增加而增大,而吸附率则降低;吸附过程符合Langmuir和Freundlich等温吸附方程,且后者的拟合效果较前者好.

  13. Complete sequence of the IncT-type plasmid pT-OXA-181 carrying the blaOXA-181 carbapenemase gene from Citrobacter freundii. (United States)

    Villa, Laura; Carattoli, Alessandra; Nordmann, Patrice; Carta, Claudio; Poirel, Laurent


    The gene encoding the carbapenemase OXA-181 (an OXA-48 variant) was identified from a Citrobacter freundii isolate coproducing NDM-1. The whole sequence of plasmid pT-OXA-181 bearing the blaOXA-181 gene was determined and revealed a 84-kb mobilizable but non-self-conjugative IncT-type plasmid. It totally differs from the 7.6-kb ColE-type and blaOXA-181-bearing plasmid recently identified in a Klebsiella pneumoniae isolate. However, in both plasmids, insertion sequence ISEcp1 might have played a role in acquisition of the blaOXA-181 gene.

  14. Degradation characteristics of m-cresol by Citrobacterfarmeri%Citrobacter farmeri降解间甲酚的特性分析

    Institute of Scientific and Technical Information of China (English)

    彭丽花; 董佳


    从某焦化厂废水好氧生物处理的污泥中分离出一株能以间甲酚为唯一碳源、能源生长代谢的菌株Citrobacter farmeri.考察了间甲酚在不同初始浓度下Citrobacter farmeri细菌生长动力学,4种等浓度酚类物质的降解先后顺序,分别添加共基质葡萄糖和蛋白胨对低浓度和高浓度间甲酚降解的影响,以及在添加共基质葡萄糖时Citrobacter farmeri降解高浓度间甲酚过程中产生的酶活.结果表明,当间甲酚初始质量浓度低于375 mg/L时,Citrobacter farmeri菌株生长符合一级动力学方程;Citrobacter farmeri降解4种酚类物质的降解顺序依次为苯酚>邻甲酚>间甲酚>萘酚;外加葡萄糖或蛋白胨对质量浓度低于375 mg/L的间甲酚的降解没有影响,但对高于375mg/L的间甲酚降解有明显的促进作用,在最佳葡萄糖添加量为800 mg/L或最佳蛋白胨添加量为640 mg/L时,缩短降解时间分别为30 h和29 h;对酶活的测定发现儿茶酚1,2-双加氧酶和儿茶酚2,3-双加氧酶有明显增大,初步判断Citrobacter farmeri以邻位和间位裂解的途径对间甲酚进行降解.%A bacterium named Citrobacterfarmeri, which utilizes m-cresol as the sole source of carbon and energy, was isolated from the sludge in the aerobic biological wastewater treatment system of a coking plant. The effects of the Citrobacter farmeri bacteria growth kinetics of m-cresol with various initial concentrations, the degradation sequence of the four kinds of phenols with the same concentration, and the separate addition of glucose or peptone on degradation of m-cresol with low or high concentration were studied. The key enzyme activity related to the ring-cleaving during the high-concentration m-cresol degradation by Citrobacter farmeri was measured to analyze the metabolic pathway when added glucose as co-substrate. The results showed that, the Citrobacter farmeri bacterium growth could be described by first-order dynamic equation

  15. Characterization of chromosomal qnrB and ampC alleles in Citrobacter freundii isolates from different origins. (United States)

    Liao, Xiaoping; Fang, Liangxing; Li, Liang; Sun, Jian; Li, Xingping; Chen, Muya; Deng, Hui; Yang, Qiu'e; Li, Xue; Liu, Yahong


    The association of ESBLs (extended-spectrum beta-lactamases)/pAmpCs (plasmid-mediated AmpC β-lactamases) with PMQR (plasmid mediated quinolone resistance) in gram-negative bacteria has been of great concern. The present study was performed to characterize the diversity, gene location, genetic context, and evolution of ampC and qnrB alleles in isolates of Citrobacter freundii. Fifteen isolates of C. freundii were identified from a total of 788 isolates of Enterobacteriaceae derived from humans, animals, animal food products, and the environment between 2010 and 2012. Co-existence of qnrB/ΔqnrB with ampC was detected in all C. freundii isolates. Both ampC and qnrB genes were found to be located on the chromosome, but were distantly separated on the chromosome. Seven and six novel alleles were discovered for the 10 ampC and qnrB variants detected in this study, respectively. Phylogenetic analysis showed that the new alleles differed a little from the variants of ampC/qnrB previously described in this genus. The genetic context surrounding ampC genes was AmpR-AmpC-Blc-SugE. However, five different genetic contexts surrounding qnrB/ΔqnrB genes were observed, but they occurred in all cases between the pspF and sapA genes. Additionally, cloning experiments showed that the regions containing different qnrB alleles, even with different genetic contexts, contributed to the reduction of quinolone susceptibility. Our results showed that the chromosomal ampC and qnrB alleles are closely related to C. freundii. However, unlike ampC, qnrB alleles seemed to be related to the genetic contexts surrounding them. The evolution of these two genes in C. freundii isolates might be through different pathways.

  16. Fermentative hydrogen production by Clostridium butyricum CWBI1009 and Citrobacter freundii CWBI952 in pure and mixed cultures

    Directory of Open Access Journals (Sweden)

    Beckers, L.


    Full Text Available This paper investigates the biohydrogen production by two mesophilic strains, a strict anaerobe (Clostridium butyricum CWBI1009 and a facultative anaerobe (Citrobacter freundii CWBI952. They were cultured in pure and mixed cultures in serum bottles with five different carbon sources. The hydrogen yields of pure C. freundii cultures ranged from 0.09 molH2.molhexose-1 (with sucrose to 0.24 molH2.molhexose-1 (with glucose. Higher yields were obtained by the pure cultures of Cl. butyricum ranging from 0.44 molH2.molhexose-1 (with sucrose to 0.69 molH2.molhexose-1 (with lactose. This strain also fermented starch whereas C. freundii did not. However, it consumed the other substrates faster and produced hydrogen earlier than Cl. butyricum. This ability has been used to promote the growth conditions of Cl. butyricum in co-culture with C. freundii, since Cl. butyricum is extremely sensitive to the presence of oxygen which strongly inhibits H2 production. This approach could avoid the addition of any expensive reducing agents in the culture media such as L-cysteine since C. freundii consumes the residual oxygen. Thereafter, co-cultures with glucose and starch were investigated: hydrogen yields decreased from 0.53 molH2.molhexose-1 for pure Cl. butyricum cultures to 0.38 molH2.molhexose-1 for mixed culture with glucose but slightly increased with starch (respectively 0.69 and 0.73 molH2.molhexose-1. After 48 h of fermentation, metabolites analysis confirmed with microbial observation, revealed that the cell concentration of C. freundii dramatically decreased or was strongly inhibited by the development of Cl. butyricum.

  17. Cancer genomics

    DEFF Research Database (Denmark)

    Norrild, Bodil; Guldberg, Per; Ralfkiær, Elisabeth Methner


    Almost all cells in the human body contain a complete copy of the genome with an estimated number of 25,000 genes. The sequences of these genes make up about three percent of the genome and comprise the inherited set of genetic information. The genome also contains information that determines whe...

  18. Use of WGS data for investigation of a long-term NDM-1-producing Citrobacter freundii outbreak and secondary in vivo spread of blaNDM-1 to Escherichia coli, Klebsiella pneumoniae and Klebsiella oxytoca

    DEFF Research Database (Denmark)

    Hammerum, Anette M; Hansen, Frank; Linde Nielsen, Hans


    Objectives An outbreak of NDM-1-producing Citrobacter freundii and possible secondary in vivo spread of blaNDM-1 to other Enterobacteriaceae were investigated. Methods From October 2012 to March 2015, meropenem-resistant Enterobacteriaceae were detected in 45 samples from seven patients at Aalbor...

  19. 潜在致病性的弗氏枸橼酸杆菌的筛查%Screening of potential pathogenic Citrobacter freundii

    Institute of Scientific and Technical Information of China (English)

    刘丽云; 夏胜利; 孙晖


    目的 筛查具有潜在致病性的弗氏枸橼酸杆菌.方法 对从河南省睢县分离到的36株弗氏枸橼酸杆菌进行黏附HEp-2细胞的检测,以及与HEp-2细胞(MOI:100)作用10 h后的乳酸脱氢酶(LDH)释放情况分析.同时比较弗氏枸橼酸杆菌CF74(Citrobacter freundii 74)、CF72(Citrobacter freundii 72)、肠聚集性大肠埃希菌(EnteroaggregativeE.coli,EAEC)、肠致病性大肠埃希菌(Enteropathogenic E.coli,EPEC)2348/69和HB101的黏附和细胞毒性差异.结果 16株弗氏枸橼酸杆菌几乎没有黏附性,黏附指数<1;18株弗氏枸橼酸杆菌具有中等强度的黏附性,黏附指数<100;2株弗氏枸橼酸杆菌CF74和CF65(Citrobacter freundii 65)具有强的黏附性.与HEp-2细胞作用10 h后,除了CF74(24.4%),其余的35株弗氏枸橼酸杆菌具有低的LDH释放量,LDH释放量与阴性对照HB101 (5.02%)相似.说明除了CF74,其余的弗氏枸橼酸杆菌不具有细胞毒性.CF74具有和EAEC042一样的聚集性黏附类型,并且CF74引起的LDH释放率明显高于CF72、2348/69和HB101(P<0.01)而低于EAEC17-2.结论 作为潜在的致病菌,CF74具有强的黏附性和细胞毒性.

  20. 弗劳地枸橼酸杆菌引起的猕猴腹泻%Identification of Citrobacter freundii Caused Diarrhea in Rhesus Monkey

    Institute of Scientific and Technical Information of China (English)

    周勤; 郭光远


    对从腹泻猕猴脓血便中分离的一株细菌,经ATB细菌分析仪,选用ID32E肠杆菌测试条鉴定为弗劳地枸橼酸杆菌(Citrobacter freundii),id%=99.9.用K-B纸片法做药敏试验,结果表明,该菌对诺氟沙星、环丙沙星、头孢噻肟、头孢曲松、头孢他定、氯霉素敏感.对庆大霉素、头孢拉定、痢特灵等十几种抗生素耐药.总之,在做腹泻病猴粪便培养时,应重视弗劳地枸橼酸菌的检测.

  1. Isolation and Screening of a native Citrobacter sp. with high nicotine-tolerant and its application as a biocatalyst for biodegradation of nicotine

    Directory of Open Access Journals (Sweden)

    Morahem Ashengroph


    Full Text Available Introduction: Nicotine is a toxic plant alkaloid and it has been designated as hazardous by the United States Environmental Protection Agency (USEPA since 1994. The present work was directed to screen nicotine resistant bacteria, that is used as biocatalyst in the biodegradation of nicotine from contaminated sites. Materials and methods: Collected soil samples from 12 tobacco farms were selected as target sites for sampling. Enrichment nicotine-degrading bacteria were performed in minimal salt media containing nicotine as the sole carbon and nitrogen sources. Agar dilution plate method was performed for determining intrinsic tolerance of bacterial isolates to nicotine. Phenotypic characterization and phylogenetic analysis were used to identify the selected bacterial isolate able to degrade nicotine. To determine the optimal conditions for the bio-removal of nicotine, the effects of initial nicotine concentration, incubation time and the addition of carbon and nitrogen sources in the selected strain were tested. The quantification of residual nicotine in the culture media was measured by high performance liquid chromatography (HPLC. Results: Among 20 bacterial isolates for degradation of nicotine, the strain TPS2 showed a high level of resistance and degradation efficiency. Results of phenotypic identification and phylogenetic analysis showed the native strain TPS2 belongs to the Citrobacter sp. strain TPS2 (GeneBank accession no. KM110046. According to the results of de-nicotination experiment, the native strain TPS2 is able to remove 100% of nicotine with an initial concentration 2.5 g/l in the presence of 2.5 g/l fructose. Discussion and conclusion: The results showed that the screened Citrobacter sp. was suitable candidate for degradation of nicotine from wastewater and sites that contaminated with nicotine. It is seemed by using of the microbial biocatalyst the ecosystem contamination of toxic nicotine can be decreased. The present work is

  2. Box counting method in recording, processing and evaluation of genomic signals

    Directory of Open Access Journals (Sweden)

    Martin Valla*


    Full Text Available Fractals are geometrical shapes with noninteger dimension andinvariance against change of scale factor. For each geometricalshape, a single parameter - dimension - can be calculated. Forcalculation, Box Counting Method (BCM was chosen.Determination of dimension on one level of resolution is notsufficient, it is necessary to subsequently process it and determine multifractal coefficient. Aim of our interest consists in analysis of images obtained from a linear sequence of DNA code. For analysis itself, sequences of Homo sapiens and Citrobacter youngae were chosen. Results of calculation are fractal coefficients derived from dimensions of generated structures. This result enables to introduce criterion for sequences determination. Graphical outputs may bealso represented as multidimensional alternative transformation of linearly recorded genomic signal. Algorithms were developed in computational environment MATLAB. Data were downloaded from a public database EMBL (ESI and GenBank (NCBI.

  3. Veggies and Intact Grains a Day Keep the Pathogens Away. (United States)

    Gazzaniga, Francesca S; Kasper, Dennis L


    In this issue of Cell, Desai et al. compare how dietary fiber affects the gut microbiota and susceptibility to disease. They find that a fiber-free diet promotes mucus-degrading bacteria and susceptibility to Citrobacter rodentium infection.

  4. Listeria Genomics (United States)

    Cabanes, Didier; Sousa, Sandra; Cossart, Pascale

    The opportunistic intracellular foodborne pathogen Listeria monocytogenes has become a paradigm for the study of host-pathogen interactions and bacterial adaptation to mammalian hosts. Analysis of L. monocytogenes infection has provided considerable insight into how bacteria invade cells, move intracellularly, and disseminate in tissues, as well as tools to address fundamental processes in cell biology. Moreover, the vast amount of knowledge that has been gathered through in-depth comparative genomic analyses and in vivo studies makes L. monocytogenes one of the most well-studied bacterial pathogens. This chapter provides an overview of progress in the exploration of genomic, transcriptomic, and proteomic data in Listeria spp. to understand genome evolution and diversity, as well as physiological aspects of metabolism used by bacteria when growing in diverse environments, in particular in infected hosts.

  5. Marine genomics

    DEFF Research Database (Denmark)

    Oliveira Ribeiro, Ângela Maria; Foote, Andrew D.; Kupczok, Anne


    Marine ecosystems occupy 71% of the surface of our planet, yet we know little about their diversity. Although the inventory of species is continually increasing, as registered by the Census of Marine Life program, only about 10% of the estimated two million marine species are known. This lag......-throughput sequencing approaches have been helping to improve our knowledge of marine biodiversity, from the rich microbial biota that forms the base of the tree of life to a wealth of plant and animal species. In this review, we present an overview of the applications of genomics to the study of marine life, from...... evolutionary biology of non-model organisms to species of commercial relevance for fishing, aquaculture and biomedicine. Instead of providing an exhaustive list of available genomic data, we rather set to present contextualized examples that best represent the current status of the field of marine genomics....

  6. Ancient genomics

    DEFF Research Database (Denmark)

    Der Sarkissian, Clio; Allentoft, Morten Erik; Avila Arcos, Maria del Carmen


    by increasing the number of sequence reads to billions effectively means that contamination issues that have haunted aDNA research for decades, particularly in human studies, can now be efficiently and confidently quantified. At present, whole genomes have been sequenced from ancient anatomically modern humans......, archaic hominins, ancient pathogens and megafaunal species. Those have revealed important functional and phenotypic information, as well as unexpected adaptation, migration and admixture patterns. As such, the field of aDNA has entered the new era of genomics and has provided valuable information when...

  7. Genome Sequencing

    DEFF Research Database (Denmark)

    Sato, Shusei; Andersen, Stig Uggerhøj


    The current Lotus japonicus reference genome sequence is based on a hybrid assembly of Sanger TAC/BAC, Sanger shotgun and Illumina shotgun sequencing data generated from the Miyakojima-MG20 accession. It covers nearly all expressed L. japonicus genes and has been annotated mainly based on transcr......The current Lotus japonicus reference genome sequence is based on a hybrid assembly of Sanger TAC/BAC, Sanger shotgun and Illumina shotgun sequencing data generated from the Miyakojima-MG20 accession. It covers nearly all expressed L. japonicus genes and has been annotated mainly based...

  8. Identification of Citrobacter freundii from Ornamental Carp ( Cyprinus carpio L. )%锦鲤弗氏柠檬酸杆菌的鉴定

    Institute of Scientific and Technical Information of China (English)

    陈翠珍; 房海; 葛慕湘; 王秀云


    对从病死锦鲤(cyprinuscarpioL.)肝组织中分离的2株菌(编号:HC050630B-1,HC050630B-2)进行了形态特征、主要理化特性、对健康鲤鱼的致病作用、药物敏感性等方面的检验;同时测定了HCOS0630B-1株菌的16SrRNA基因序列,构建了系统发育树。结果表明,2株被检菌为弗氏柠檬酸杆菌(Citrobacter加吼蒯),对健康鲤鱼有致病作用;所测菌株的16SrRNA基因序列长度1458bp,在GenBank中登录号为EF669481,该菌株16SrRNA基因序列与GenBank数据库中柠檬酸杆菌属细菌的16SrRNA基因序列同源性在99%;药敏试验结果显示,对供试的头孢噻肟等21种药物呈现高度敏感或敏感,对头孢唑啉等5种呈低度敏感,对四环素等11种耐药。%Two strains ( HC050630B-1 ,HC050630B-2) isolated from the liver of diseased ( or dead) ornamen- tal carp were examined,including their morphological characteristics,physiological and biochemical character- istics ,pathogenicity to healthy carp and antibiotic sensitivity. In addition,the 16S rRNA gene of HC050630B-1 were sequenced,and molecular phylogenetic tree was constructed. The results showed that the two examined strains were identified as Citrobacter freundii, and had strong pathogenicity to healthy carp. The length of the 16S rRNA gene sequence of examined strain is 1 458 bp. Its database accession numbers in NCBI is EF669481 ,and the similarity of the 16S rRNA gene sequence of examined strain with the 16S rRNA gene of Citrobacter from GenBank database is 99%. The antibiotic sensitivity using 37 antimicrobial agents showed that isolates were high sensitive or sensitive to 21 agents including cefotaxime, slight sensitive to 5 agents including cefazolin, and resistant to 11 agents including tetrecycline.

  9. Cephalopod genomics

    DEFF Research Database (Denmark)

    Albertin, Caroline B.; Bonnaud, Laure; Brown, C. Titus


    The Cephalopod Sequencing Consortium (CephSeq Consortium) was established at a NESCent Catalysis Group Meeting, ``Paths to Cephalopod Genomics-Strategies, Choices, Organization,'' held in Durham, North Carolina, USA on May 24-27, 2012. Twenty-eight participants representing nine countries (Austri...

  10. Ancient genomics

    DEFF Research Database (Denmark)

    Der Sarkissian, Clio; Allentoft, Morten Erik; Avila Arcos, Maria del Carmen;


    , archaic hominins, ancient pathogens and megafaunal species. Those have revealed important functional and phenotypic information, as well as unexpected adaptation, migration and admixture patterns. As such, the field of aDNA has entered the new era of genomics and has provided valuable information when...

  11. Discovery of a Bacterial Glycoside Hydrolase Family 3 (GH3) β-Glucosidase with Myrosinase Activity from a Citrobacter Strain Isolated from Soil. (United States)

    Albaser, Abdulhadi; Kazana, Eleanna; Bennett, Mark H; Cebeci, Fatma; Luang-In, Vijitra; Spanu, Pietro D; Rossiter, John T


    A Citrobacter strain (WYE1) was isolated from a UK soil by enrichment using the glucosinolate sinigrin as sole carbon source. The enzyme myrosinase was purified using a combination of ion exchange and gel filtration to give a pure protein of approximately 66 kDa. The N-terminal amino acid and internal peptide sequence of the purified protein were determined and used to identify the gene, which, based on InterPro sequence analysis, belongs to the family GH3, contains a signal peptide, and is a periplasmic protein with a predicted molecular mass of 71.8 kDa. A preliminary characterization was carried out using protein extracts from cell-free preparations. The apparent KM and Vmax were 0.46 mM and 4.91 mmol dm(-3) min(-1) mg(-1), respectively, with sinigrin as substrate. The optimum temperature and pH for enzyme activity were 25 °C and 6.0, respectively. The enzyme was marginally activated with ascorbate by a factor of 1.67.

  12. Enhanced 1,3-propanediol production by a newly isolated Citrobacter freundii strain cultivated on biodiesel-derived waste glycerol through sterile and non-sterile bioprocesses. (United States)

    Metsoviti, Maria; Zeng, An-Ping; Koutinas, Apostolis A; Papanikolaou, Seraphim


    The production of 1,3-propanediol (PD) by a newly isolated Citrobacter freundii strain [FMCC-B 294 (VK-19)] was investigated. Different grades of biodiesel-derived glycerol were employed. Slightly lower PD biosynthesis was observed in batch experiments only when crude glycerol from waste-cooking oil trans-esterification was utilized and only at elevated initial substrate concentrations employed. Batch bioreactor cultures revealed the capability of the strain to tolerate elevated amounts of substrate (glycerol up to 170 g/L) and produce quantities of PD in such high substrate concentrations. Nevertheless, maximum PD quantities (45.9 g/L) were achieved at lower initial glycerol concentrations (∼100 g/L) employed, suggesting some inhibition exerted due to the increased initial substrate concentrations. In order to improve PD production, a fed-batch fermentation was carried out and 68.1g/L of PD were produced (the highest PD quantity achieved by C. freundii strains so far) with yield per glycerol consumed ∼0.40 g/g and volumetric productivity 0.79 g/L/h. Aiming to perform a more economical and eco-friendlier procedure, batch and fed-batch fermentations under completely non-sterile conditions were carried out. During non-sterilized fed-batch process, 176 g/L of raw glycerol were converted to 66.3g/L of PD, suggesting the potentiality of the non-sterile fermentation by C. freundii FMCC-B 294.

  13. Complex integrons containing qnrB4-ampC (bla(DHA-1)) in plasmids of multidrug-resistant Citrobacter freundii from wastewater. (United States)

    Yim, Grace; Kwong, Waldan; Davies, Julian; Miao, Vivian


    Microbial populations in wastewater treatment plants (WWTPs) are increasingly being recognized as environmental reservoirs of antibiotic resistance genes. PCR amplicons for plasmid-mediated quinolone resistance determinants qnrA, qnrB, and qnrS were recorded in samples from a WWTP in Vancouver, British Columbia. Six strains of ciprofloxacin-resistant Citrobacter freundii were isolated and found to carry mutations in gyrA and parC, as well as multiple plasmid-borne resistance genes, collectively including qnrB; aac(6')-Ib-cr; β-lactamase-encoding genes from molecular classes A (blaTEM-1), C (ampC), D (blaOXA-1, blaOXA-10); and genes for resistance to 5 other types of antibiotics. In 3 strains, large (>60 kb) plasmids carried qnrB4 and ampC as part of a complex integron in a 14 kb arrangement that has been reported worldwide but, until recently, only among pathogenic strains of Klebsiella. Analysis of single-nucleotide polymorphisms in the qnrB4-ampC regions infers 2 introductions into the WWTP environment. These results suggest recent passage of plasmid-borne fluoroquinolone and β-lactam resistance genes from pathogens to bacteria that may be indigenous inhabitants of WWTPs, thus contributing to an environmental pool of antibiotic resistance.

  14. Citrobacter amalonaticus phytase on the cell surface of Pichia pastoris exhibits high pH stability as a promising potential feed supplement. (United States)

    Li, Cheng; Lin, Ying; Huang, Yuanyuan; Liu, Xiaoxiao; Liang, Shuli


    Phytase expressed and anchored on the cell surface of Pichia pastoris avoids the expensive and time-consuming steps of protein purification and separation. Furthermore, yeast cells with anchored phytase can be used as a whole-cell biocatalyst. In this study, the phytase gene of Citrobacter amalonaticus was fused with the Pichia pastoris glycosylphosphatidylinositol (GPI)-anchored glycoprotein homologue GCW61. Phytase exposed on the cell surface exhibits a high activity of 6413.5 U/g, with an optimal temperature of 60°C. In contrast to secreted phytase, which has an optimal pH of 5.0, phytase presented on the cell surface is characterized by an optimal pH of 3.0. Moreover, our data demonstrate that phytase anchored on the cell surface exhibits higher pH stability than its secreted counterpart. Interestingly, our in vitro digestion experiments demonstrate that phytase attached to the cell surface is a more efficient enzyme than secreted phytase.

  15. Effect of surfactant-induced cell surface modifications on electron transport system and catechol 1,2-dioxygenase activities and phenanthrene biodegradation by Citrobacter sp. SA01. (United States)

    Li, Feng; Zhu, Lizhong


    In order to better understand how surfactants affect biodegradation of hydrophobic organic compounds (HOCs), Tween 80 and sodium dodecyl benzene sulfonate (SDBS), were selected to investigate effects on cell surface hydrophobicity (CSH), electron transport system (ETS) activities and phenanthrene biodegradation by Citrobacter sp. SA01. Tween 80 and SDBS increased CSH by 19.8-25.2%, ETS activities by 352.1-376.0μmol/gmin, catechol 1,2-dioxygenase (C12) activities by 50.8-52.7U/L, and phenanthrene biodegradation by 8.9-17.2% separately in the presence of 50mg/L of surfactants as compared to in their absence. Lipopolysaccharide (LPS) release was 334.7μg/mg in the presence of both surfactants whereas in their absence only 8.6-44.4μg/mg of LPS was released. Thus, enhanced LPS release probably increased ETS and C12 activities as well as phenanthrene biodegradation by increasing CSH. The results demonstrate that surfactant-enhanced CSH provides a simple, yet effective strategy for field applications of surfactant-enhanced bioremediation of HOCs.

  16. 花鳗鲡病原菌弗氏柠檬酸杆菌的鉴定%Identification of Pathogenic Citrobacter freundii Isolated from Anguilla marmorata

    Institute of Scientific and Technical Information of China (English)

    杨方园; 关瑞章; 李忠琴; 于海振; 李秋云


    首次报道了从养殖花鳗鲡(Anguilla marmorata)肝脏中分离得到优势菌株AMRB6,经人工腹腔注射感染健康花鳗鲡试验,结果证实该菌有致病作用,其半数致死量LD50为3.2×107 CFU/mL.结合菌体形态特征、常规生理生化鉴定和Biolog自动微生物鉴定系统鉴定,以及16S rRNA序列扩增结果,表明该菌为弗氏柠檬酸杆菌(Citrobacter freundii).30种药物药敏试验结果表明,该菌株对左氧氟沙星、诺氟沙星、庆大霉素、卡那霉素等14种药物高度敏感.

  17. Novel genetic environment of the plasmid-mediated KPC-3 gene detected in Escherichia coli and Citrobacter freundii isolates from China. (United States)

    Li, G; Wei, Q; Wang, Y; Du, X; Zhao, Y; Jiang, X


    The imipenem and meropenem-resistant strains Citrobacter freundii HS70 and Escherichia coli HS510 were isolated from patients in Shanghai, China. By isoelectric focusing, PCR amplification and sequencing, these strains were each found to produce four β-lactamases: TEM-1, KPC-3, SHV-7 and CTX-M-14. A conjugation experiment and plasmid restriction digestion revealed that the bla (KPC-3) gene was located on the same plasmid in both isolates. Bidirectional primer walking sequencing showed that the nucleotide sequence surrounding the 3.8 kb bla(KPC-3) contained a 671-bp insertion similar to that previously characterized in China. The insertion was located between the promoter and the coding region of the bla(KPC-3) gene. Susceptibility testing performed on recombinant strains carrying the bla(KPC-3) gene with or without the insertion revealed that minimum inhibitory concentrations of imipenem, meropenem, cefepime, and cefotaxime for E. coli EMU-KPC3 (without insertion) were four times higher than that of E. coli EKPC3 (with insertion). The 671 bp insertion reduced bla(KPC-3) expression significantly. Taken together, these results suggest that KPC-3-producing C. freundii and E. coli have begun to emerge in our hospital.

  18. Kinetic Parameters and Cytotoxic Activity of Recombinant Methionine γ-Lyase from Clostridium tetani, Clostridium sporogenes, Porphyromonas gingivalis and Citrobacter freundii. (United States)

    Morozova, E A; Kulikova, V V; Yashin, D V; Anufrieva, N V; Anisimova, N Y; Revtovich, S V; Kotlov, M I; Belyi, Y F; Pokrovsky, V S; Demidkina, T V


    The steady-state kinetic parameters of pyridoxal 5'-phosphate-dependent recombinant methionine γ -lyase from three pathogenic bacteria, Clostridium tetani, Clostridium sporogenes, and Porphyromonas gingivalis, were determined in β- and γ-elimination reactions. The enzyme from C. sporogenes is characterized by the highest catalytic efficiency in the γ-elimination reaction of L-methionine. It was demonstrated that the enzyme from these three sources exists as a tetramer. The N-terminal poly-histidine fragment of three recombinant enzymes influences their catalytic activity and facilitates the aggregation of monomers to yield dimeric forms under denaturing conditions. The cytotoxicity of methionine γ-lyase from C. sporogenes and C. tetani in comparison with Citrobacter freundii was evaluated using K562, PC-3, LnCap, MCF7, SKOV-3, and L5178y tumor cell lines. K562 (IC50=0.4-1.3 U/ml), PC-3 (IC50=0.1-0.4 U/ml), and MCF7 (IC50=0.04-3.2 U/ml) turned out to be the most sensitive cell lines.

  19. Evaluative profiling of arsenic sensing and regulatory systems in the human microbiome project genomes. (United States)

    Isokpehi, Raphael D; Udensi, Udensi K; Simmons, Shaneka S; Hollman, Antoinesha L; Cain, Antia E; Olofinsae, Samson A; Hassan, Oluwabukola A; Kashim, Zainab A; Enejoh, Ojochenemi A; Fasesan, Deborah E; Nashiru, Oyekanmi


    The influence of environmental chemicals including arsenic, a type 1 carcinogen, on the composition and function of the human-associated microbiota is of significance in human health and disease. We have developed a suite of bioinformatics and visual analytics methods to evaluate the availability (presence or absence) and abundance of functional annotations in a microbial genome for seven Pfam protein families: As(III)-responsive transcriptional repressor (ArsR), anion-transporting ATPase (ArsA), arsenical pump membrane protein (ArsB), arsenate reductase (ArsC), arsenical resistance operon transacting repressor (ArsD), water/glycerol transport protein (aquaporins), and universal stress protein (USP). These genes encode function for sensing and/or regulating arsenic content in the bacterial cell. The evaluative profiling strategy was applied to 3,274 genomes from which 62 genomes from 18 genera were identified to contain genes for the seven protein families. Our list included 12 genomes in the Human Microbiome Project (HMP) from the following genera: Citrobacter, Escherichia, Lactobacillus, Providencia, Rhodococcus, and Staphylococcus. Gene neighborhood analysis of the arsenic resistance operon in the genome of Bacteroides thetaiotaomicron VPI-5482, a human gut symbiont, revealed the adjacent arrangement of genes for arsenite binding/transfer (ArsD) and cytochrome c biosynthesis (DsbD_2). Visual analytics facilitated evaluation of protein annotations in 367 genomes in the phylum Bacteroidetes identified multiple genomes in which genes for ArsD and DsbD_2 were adjacently arranged. Cytochrome c, produced by a posttranslational process, consists of heme-containing proteins important for cellular energy production and signaling. Further research is desired to elucidate arsenic resistance and arsenic-mediated cellular energy production in the Bacteroidetes.

  20. The function genomics study

    Institute of Scientific and Technical Information of China (English)


    @@ Genomics is a biology term appeared ten years ago, used to describe the researches of genomic mapping, sequencing, and structure analysis, etc. Genomics, the first journal for publishing papers on genomics research was born in 1986. In the past decade, the concept of genomics has been widely accepted by scientists who are engaging in biology research. Meanwhile, the research scope of genomics has been extended continuously, from simple gene mapping and sequencing to function genomics study. To reflect the change, genomics is divided into two parts now, the structure genomics and the function genomics.

  1. Visualization for genomics: the Microbial Genome Viewer.

    NARCIS (Netherlands)

    Kerkhoven, R.; Enckevort, F.H.J. van; Boekhorst, J.; Molenaar, D.; Siezen, R.J.


    SUMMARY: A Web-based visualization tool, the Microbial Genome Viewer, is presented that allows the user to combine complex genomic data in a highly interactive way. This Web tool enables the interactive generation of chromosome wheels and linear genome maps from genome annotation data stored in a My

  2. 一株大凉疣螈肠道弗氏柠檬酸杆菌的分离及其药敏试验%Isolation and Susceptibility Test of an Intestinal Citrobacter freundii from Tylototriton taliangensis

    Institute of Scientific and Technical Information of China (English)

    李蓓; 邹立扣; 罗燕


    首次从大凉疣螈(Tylototritoa taliangemsis)肠道分离获得弗氏柠稼酸杆菌(Citrobacter freundii),利用分子生物学方法对其16S rDNA进行了扩增测序,并与GenBank中已有的有关序列进行比较,进行了系统发育分析.测序结果表明,16S rDNA与GenBank中序列同源率在98%~99%,分离的菌株与GU126681(C.freundii MRB0903)处于同一分支中;序列同源性及系统发育树表明,此菌为弗氏柠檬酸杆菌;药敏试验表明.弗氏柠檬酸杆菌对氨苄西林及头孢噻吩中介,对其余药物均敏感.%A Citrobacter freundii was isolated from the intestinal tact of Tylototriton taliangensis ,and its 16S rDNA was amplified and sequenced by the molecular biology method,and then the 16S rDNA was compared with other sequences in Genbank to conduct a phylogenetic analysis. The results indicated that the 16S rDNA sequence of Citrobacter freundii showed 98% -99% homogeny with those in the GenBank.and belonged to the same branch with GU126681 (C.freundii MRB0903). As shown by the sequence homology and phylogenetic tree,the bacterium was C. Freun-dii,which was medium sensitive to ampicillin and cephalothin,and sensitive to other biotics.

  3. Optimization of culture conditions for biological hydrogen production by Citrobacter freundii CWBI952 in batch, sequenced-batch and semicontinuous operating mode

    Energy Technology Data Exchange (ETDEWEB)

    Hamilton, Christopher; Hiligsmann, Serge; Beckers, Laurent; Masset, Julien; Thonart, Philippe [Walloon Centre of Industrial Biology, Bd du Rectorat, 29, B.40 - P.70, B-4000 Liege (Belgium); Wilmotte, Annick [Center for Protein Engineering, Institute of Chemistry, B.6-P.14, B-4000 Liege (Belgium)


    Investigations were carried out to determine the effect of the pH, the nitrogen source, iron and the dilution rate (h{sup -1}) on fermentative hydrogen production from glucose by the newly isolated strain Citrobacter freundii CWBI952. The hydrogen production rate (HPR), hydrogen yield, biomass and soluble metabolites were monitored at 30 C in 100 mL serum bottles and in a 2.3 L bioreactor operated in batch, sequenced-batch and semicontinuous mode. The results indicate that hydrogen production activity, formate biosynthesis and glucose intake rates are very sensitive to the culture pH, and that additional formate bioconversion and production of hydrogen with lower biomass yields can be obtained at pH 5.9. In a further series of cultures casein peptone was replaced by (NH{sub 4}){sub 2}SO{sub 4}, a low cost alternative nitrogen source. The ammonia-based substitute was found to be suitable for H{sub 2} production when a concentration of 0.045 g/L FeSO{sub 4} was provided. Optimal overall performances (ca. an HPR of 33.2 mL H{sub 2}/L h and a yield of 0.83mol{sub H{sub 2}}/mol{sub glucose}) were obtained in the semicontinuous culture applying the previously optimized parameters for pH, nitrogen, and iron with a dilution rate of 0.012 h{sup -1} and degassing of biogas by N{sub 2} at a 28 mL/min flow rate. (author)

  4. Characterization of KPC-2-producing Escherichia coli, Citrobacter freundii, Enterobacter cloacae, Enterobacter aerogenes, and Klebsiella oxytoca isolates from a Chinese Hospital. (United States)

    Luo, Yanping; Yang, Jiyong; Ye, Liyan; Guo, Lin; Zhao, Qiang; Chen, Rong; Chen, Yong; Han, Xuelin; Zhao, Jingya; Tian, Shuguang; Han, Li


    Twelve nonduplicated KPC-2-producing enterobacterial isolates, including three Escherichia coli, two Citrobacter freundii, two Enterobacter cloacae, four Enterobacter aerogenes, and one Klebsiella oxytoca, were collected from various clinical samples within 18 months (March 2011 to September 2012). Two of the 12 patients died from infections caused by KPC-2-producing pathogens, while the rest of the patients with KPC-2-producing pathogens improved or were cured. The majority of the clinical isolates exhibited a high-level of resistance to oxyimino-cephalosporins and carbapenems, and possessed self-transferable bla(KPC-2)-carrying plasmids with sizes ranging from 20 to 120 kb. Most isolates carried bla(CTX-M) and plasmid-mediated quinolone resistance genes, while some isolates produced 16S rRNA methylases (ArmA or RmtB). The genetic environment of bla(KPC-2) of most clinical strains was consistent with the genetic structure surrounding bla(KPC-2) on the plasmid pKP048, which contains an integration structure of a Tn3-based transposon and partial Tn4401 segment. Inserted fragments (truncated bla(TEM)) were detected upstream of the bla(KPC-2) gene for two E. aerogenes strains. In conclusion, the enterobacterial isolates exhibited sporadic emergence and did not arise by clonal spread at our hospital. The outcome of infections caused by KPC-producing enterobacterial isolates and their mortality were closely associated with the baseline condition of patients. The spread of bla(KPC-2) gene between different enterobacterial species in China was mainly mediated by horizontal transfer of the Tn3-based transposons and not the bla(KPC-2)-carrying plasmids.

  5. Cloning, expression and characterization of a cold-adapted endo-1, 4-β-glucanase from Citrobacter farmeri A1, a symbiotic bacterium of Reticulitermes labralis

    Directory of Open Access Journals (Sweden)

    Xi Bai


    Full Text Available Background Many biotechnological and industrial applications can benefit from cold-adapted EglCs through increased efficiency of catalytic processes at low temperature. In our previous study, Citrobacter farmeri A1 which was isolated from a wood-inhabiting termite Reticulitermes labralis could secrete a cold-adapted EglC. However, its EglC was difficult to purify for enzymatic properties detection because of its low activity (0.8 U/ml. The objective of the present study was to clone and express the C. farmeri EglC gene in Escherichia coli to improve production level and determine the enzymatic properties of the recombinant enzyme. Methods The EglC gene was cloned from C. farmeri A1 by thermal asymmetric interlaced PCR. EglC was transformed into vector pET22b and functionally expressed in E. coli. The recombination protein EglC22b was purified for properties detection. Results SDS-PAGE revealed that the molecular mass of the recombinant endoglucanase was approximately 42 kDa. The activity of the E. coli pET22b-EglC crude extract was 9.5 U/ml. Additionally, it was active at pH 6.5–8.0 with an optimum pH of 7.0. The recombinant enzyme had an optimal temperature of 30–40 °C and exhibited >50% relative activity even at 5 °C, whereas it lost approximately 90% of its activity after incubation at 60 °C for 30 min. Its activity was enhanced by Co2+ and Fe3+, but inhibited by Cd2+, Zn2+, Li+, Triton X-100, DMSO, acetonitrile, Tween 80, SDS, and EDTA. Conclusion These biochemical properties indicate that the recombinant enzyme is a cold-adapted endoglucanase that can be used for various industrial applications.

  6. Plant Genome Duplication Database. (United States)

    Lee, Tae-Ho; Kim, Junah; Robertson, Jon S; Paterson, Andrew H


    Genome duplication, widespread in flowering plants, is a driving force in evolution. Genome alignments between/within genomes facilitate identification of homologous regions and individual genes to investigate evolutionary consequences of genome duplication. PGDD (the Plant Genome Duplication Database), a public web service database, provides intra- or interplant genome alignment information. At present, PGDD contains information for 47 plants whose genome sequences have been released. Here, we describe methods for identification and estimation of dates of genome duplication and speciation by functions of PGDD.The database is freely available at

  7. Rodent malaria parasites : genome organization & comparative genomics

    NARCIS (Netherlands)

    Kooij, Taco W.A.


    The aim of the studies described in this thesis was to investigate the genome organization of rodent malaria parasites (RMPs) and compare the organization and gene content of the genomes of RMPs and the human malaria parasite P. falciparum. The release of the complete genome sequence of P. falciparu

  8. 156株弗氏柠檬酸杆菌感染的分布与耐药性分析%Distribution and drug resistance of 156 strains of citrobacter freundii

    Institute of Scientific and Technical Information of China (English)



    OBJECTIVE To understand the distribution and drug resistance of citrobacter freundii, to provide a reasonable basis for clinicians to use anti-infective therapy. METHODS Totally 156 strains of Citrobacter freundii from patients from Oct 2008 to May 2010 were analyzed, the component ratio and the isolation rate from various department were calculated by referring to the National Clinical Laboratory Operation Rules, as well as the drug sensitivity testing was performed by K-B methods. RESULTS Of 156 strains of isolated citrobacter freundii, the isolates from department of respiratory medicine accounted for 39.1%, from department of neurology 15.4 %,from intensive care unit was 12.2% ; the main clinical specimens were collected from the sputum, the liquor purisand the urine, accounting for 60. 3%, 21. 2% and 7. 1%, respectively. Of 447 strains of detected pathogenic bacteria, there were 156 strains of citrobacter freundii, accounting for 34.9%; drug resistance rates of CFR to ampicillin and cefazolin were 100. 0% and 91.0%, which could cause multiple sites infection. CONCLUSION Hospital should attach importance to the monitoring and the controlling of multidrug-resistant citrobacter freundii and prevent the outbreak and epidemic of nosocomial infections.%目的 了解医院临床标本分离的弗氏柠檬酸杆菌(CFR)检出分布规律及耐药性特点,为临床医师合理抗感染治疗提供依据.方法 回顾性分析2008年1月-2010年5月,住院患者送检标本中分离的156株CFR,计算其构成比、科室分离率,鉴定按进行;药物敏感性试验采用CLSI推荐的K-B法.结果 分离的156株CFR中,呼吸内科检出占39.1%,神经内科占15.4%,综合ICU占12.2%;主要标本来源于痰液、脓液、尿液,分别占总数的60.3%、21.2%、7.1%;病原菌检出447株,检出CFR 156株,占34.9%;CFR对氨苄西林、头孢唑林的耐药性较强,耐药率分别为100.0%、91.0%,可引起多部位感染.结论应重视对多药

  9. Funding Opportunity: Genomic Data Centers (United States)

    Funding Opportunity CCG, Funding Opportunity Center for Cancer Genomics, CCG, Center for Cancer Genomics, CCG RFA, Center for cancer genomics rfa, genomic data analysis network, genomic data analysis network centers,

  10. Ontology for Genome Comparison and Genomic Rearrangements

    Directory of Open Access Journals (Sweden)

    Anil Wipat


    Full Text Available We present an ontology for describing genomes, genome comparisons, their evolution and biological function. This ontology will support the development of novel genome comparison algorithms and aid the community in discussing genomic evolution. It provides a framework for communication about comparative genomics, and a basis upon which further automated analysis can be built. The nomenclature defined by the ontology will foster clearer communication between biologists, and also standardize terms used by data publishers in the results of analysis programs. The overriding aim of this ontology is the facilitation of consistent annotation of genomes through computational methods, rather than human annotators. To this end, the ontology includes definitions that support computer analysis and automated transfer of annotations between genomes, rather than relying upon human mediation.

  11. Genome Mapping in Plant Comparative Genomics. (United States)

    Chaney, Lindsay; Sharp, Aaron R; Evans, Carrie R; Udall, Joshua A


    Genome mapping produces fingerprints of DNA sequences to construct a physical map of the whole genome. It provides contiguous, long-range information that complements and, in some cases, replaces sequencing data. Recent advances in genome-mapping technology will better allow researchers to detect large (>1kbp) structural variations between plant genomes. Some molecular and informatics complications need to be overcome for this novel technology to achieve its full utility. This technology will be useful for understanding phenotype responses due to DNA rearrangements and will yield insights into genome evolution, particularly in polyploids. In this review, we outline recent advances in genome-mapping technology, including the processes required for data collection and analysis, and applications in plant comparative genomics.

  12. Enabling functional genomics with genome engineering. (United States)

    Hilton, Isaac B; Gersbach, Charles A


    Advances in genome engineering technologies have made the precise control over genome sequence and regulation possible across a variety of disciplines. These tools can expand our understanding of fundamental biological processes and create new opportunities for therapeutic designs. The rapid evolution of these methods has also catalyzed a new era of genomics that includes multiple approaches to functionally characterize and manipulate the regulation of genomic information. Here, we review the recent advances of the most widely adopted genome engineering platforms and their application to functional genomics. This includes engineered zinc finger proteins, TALEs/TALENs, and the CRISPR/Cas9 system as nucleases for genome editing, transcription factors for epigenome editing, and other emerging applications. We also present current and potential future applications of these tools, as well as their current limitations and areas for future advances.

  13. Characterization of extended-spectrum β-lactamase (ESBL)-producing Klebsiella, Enterobacter, and Citrobacter obtained in environmental samples of a Tunisian hospital. (United States)

    Dziri, Raoudha; Klibi, Naouel; Alonso, Carla Andrea; Said, Leila Ben; Bellaaj, Ridha; Slama, Karim Ben; Boudabous, Abdellatif; Torres, Carmen


    The assessment of the hospital environment as a reservoir of ESBL-producing Enterobacteriaceae in Tunisian hospitals is scarcely analyzed, except for Escherichia coli. The aim of this study was to evaluate the presence of ESBL-producing non-E. coli Enterobacteriaceae (ESBL-EbNoEc) in 300 samples of abiotic surfaces and the hands of patients and staff of a Tunisian Hospital, and to characterize the ESBL genes of the recovered isolates. ESBL-EbNoEc were recovered in 28 of 300 (9.3%) analyzed samples and were identified as Klebsiella pneumoniae (n= 11), Enterobacter cloacae (n=11), Citrobacter freundii (n=4) and Klebsiella oxytoca (n=2). The bla genes identified by PCR and sequencing among the strains were as follows: 11 K.pneumoniae strains [blaCTX-M-15+ blaTEM-1+ blaSHV-11 (n=6); blaCTX-M-15+ blaTEM-1+ blaSHV-28 (n=3); blaCTX-M-15+ blaTEM-1+ blaSHV-1 (n=2)], 11 E. cloacae strains [blaCTX-M-15 (n=6); blaCTX-M-15+ blaTEM-1b (n=2); blaCTX-M-15+ blaTEM-1b+ blaOXA-1 (n=1);blaCTX-M-15+ blaOXA-1 (n=1);blaSHV-12 (n=1)], 4 C. freundii strains [blaCTX-M-15] and 2 K. oxytoca strains [blaCTX-M-15 (n=1); blaSHV-12 (n=1)]. The ISEcp1 and orf477 sequences were identified upstream and downstream of the blaCTX-M-15 gene, respectively, in 3 K. pneumoniae and 3 E. cloacae isolates. The PFGE analysis demonstrated three unrelated pulsotypes in K. pneumoniae strains and five pulsotypes in E. cloacae. The uncontrolled dissemination of ESBL-producing bacteria, even in the hospital environment, has become a real problem and new strategies and hygienic rules are needed to stop this bacterial dissemination.

  14. An Analysis of the Effects of Vancomycin and/or Vancomycin-Resistant Citrobacter freundii Exposure on the Microbial Community Structure in Soil. (United States)

    Cycoń, Mariusz; Borymski, Sławomir; Orlewska, Kamila; Wąsik, Tomasz J; Piotrowska-Seget, Zofia


    The occurrence of antibiotics and antibiotic resistance genes in the environment has become a subject of growing concern. The extensive use of vancomycin and other pharmaceuticals may alter the biodiversity of soil microbial communities and select antibiotic-resistant bacteria. Therefore, the purpose of the study was to evaluate the impact of vancomycin and/or vancomycin-resistant Citrobacter freundii on soil microbial communities using the denaturing gradient gel electrophoresis (DGGE) and the phospholipid fatty acid (PLFA) approaches. The experiment had a completely randomized block design with the following treatments: control soil (C), soil with vancomycin (1 mg/kg soil-VA1), soil with vancomycin (10 mg/kg soil-VA10), soil with C. freundii (Cit), soil with vancomycin (1 mg/kg soil) and C. freundii (VA1+Cit), and soil with vancomycin (10 mg/kg soil) and C. freundii (VA10+Cit). A bacterial strain resistant to vancomycin was isolated from raw sewage collected from the municipal sewage treatment plant. The obtained results indicated that the antibiotic and/or the bacterial strain exerted a selective pressure that resulted in qualitative and quantitative changes in the population of soil microorganisms. However, a multivariate analysis showed that the genetic and structural diversity of the soil microbial community was primarily affected by the incubation time and to a lesser extent by the antibiotic and introduced bacteria. DGGE analysis clearly showed that certain species within the bacterial community were sensitive to vancomycin as was evidenced by a decrease in the values of S (richness) and H (Shannon-Wiener) indices. Moreover, a PLFA method-based analysis revealed alterations in the structure of the soil microbial community as indicated by changes in the biomass of the PLFA biomarkers specific for Gram-positive and Gram-negative bacteria as well as fungi. The changes observed in the community of soil microorganisms may decrease the rate of microbial

  15. 中华绒螯蟹病原弗氏柠檬酸杆菌的鉴定%Identification of Citrobacter freundii isolated from crab (Eriocheir sinensis)

    Institute of Scientific and Technical Information of China (English)

    陈翠珍; 张晓君; 房海; 巩元芳; 葛慕湘


    目的对从一起自然发病的病(死)中华绒螯蟹(Eriocheir sinensis H.Milne-Edwards)肝胰腺中,所分离做纯培养的6株(HQ010516B-1至HQ010516B-6)菌,进行在主要生物学性状、感染试验的致病作用、对抗菌类药物的敏感性等方面的检验,旨在明确分离菌的种类、病原学意义及耐药特征等.方法在发病情况及主要病变检验的基础上,以6只病(死)蟹的肝胰腺为材料做细菌分离与纯培养,对纯培养菌做形态特征、理化特性、16S rRNA基因序列测定及系统发育学分析等方面较系统的鉴定,主要依据(1994)并结合系统发育特征做菌种归类判定;以3×108CFU/ml的菌悬液,对健康蟹做感染试验,测定相应的致病作用;用琼脂扩散(K-B)法做对常用抗菌类药物的敏感性测定,以抑菌圈直径作为敏感与耐药的判定指标.结果分离做纯培养的6株菌为同种的弗氏柠檬酸杆菌(Citrobacter freundii),对供试健康蟹有致病性,对供试37种抗菌类药物中的头孢噻肟等22种药物呈敏感或高度敏感、对四环素等5种呈低度敏感、对青霉素G等10种耐药.结论所检出的弗氏柠檬酸杆菌,构成了所检中华绒螯蟹病例的病原菌之一,对供试抗菌类药物未表现出敏感与耐药的明显株间差异性.

  16. Exploring Other Genomes: Bacteria. (United States)

    Flannery, Maura C.


    Points out the importance of genomes other than the human genome project and provides information on the identified bacterial genomes Pseudomonas aeuroginosa, Leprosy, Cholera, Meningitis, Tuberculosis, Bubonic Plague, and plant pathogens. Considers the computer's use in genome studies. (Contains 14 references.) (YDS)


    Directory of Open Access Journals (Sweden)

    Ignacio Briceño Balcázar


    Full Text Available Until the twilight of the 20th century, genetics was a branch of medicine applied to diseases of rare occurrence. The advent of the human genome sequence and the possibility of studying it at affordable costs for patients and healthcare institutions, has permitted its application in high-priority diseases like cancer, cardiovascular disease, diabetes, and Alzheimer’s, among others.There is great potential in predictive and preventive medicine, through studying polymorphic genetic variants associated to risks for different diseases. Currently, clinical laboratories offer studies of over 30,000 variants associated with susceptibilities, to which individuals can access without much difficulty because a medical prescription is not required. These exams permit conducting a specific plan of preventive medicine. For example, upon the possibility of finding a deleterious mutation in the BRCA1 and BRCA2 genes, the patient can prevent the breast cancer by mastectomy or chemoprophylaxis and in the presence of polymorphisms associated to cardiovascular risk preventive action may be undertaken through changes in life style (diet, exercise, etc..Legal aspects are also present in this new conception of medicine. For example, currently there is legislation for medications to indicate on their labels the different responses such medication can offer regarding the genetic variants of the patients, given that similar doses may provoke adverse reactions in an individual, while for another such dosage may be insufficient. This scenario would allow verifying the polymorphisms of drug response prior to administering medications like anticoagulants, hyperlipidemia treatments, or chemotherapy, among others.We must specially mention recessive diseases, produced by the presence of two alleles of a mutated gene, which are inherited from the mother, as well as the father. By studying the mutations, we may learn if a couple is at risk of bearing children with the disease

  18. Genomic Medicine

    Directory of Open Access Journals (Sweden)

    Ignacio Briceño Balcázar


    Full Text Available Until the twilight of the 20th century, genetics was a branch of medicine applied to diseases of rare occurrence.  The advent of the human genome sequence and the possibility of studying it at affordable costs for patients and healthcare institutions, has permitted its application in high-priority diseases like cancer, cardiovascular disease, diabetes, and Alzheimer’s, among others. There is great potential in predictive and preventive medicine, through studying polymorphic genetic variants associated to risks for different diseases. Currently, clinical laboratories offer studies of over 30,000 variants associated with susceptibilities, to which individuals can access without much difficulty because a medical prescription is not required. These exams permit conducting a specific plan of preventive medicine.  For example, upon the possibility of finding a deleterious mutation in the BRCA1 and BRCA2 genes, the patient can prevent the breast cancer by mastectomy or chemoprophylaxis and in the presence of polymorphisms associated to cardiovascular risk preventive action may be undertaken through changes in life style (diet, exercise, etc.. Legal aspects are also present in this new conception of medicine.  For example, currently there is legislation for medications to indicate on their labels the different responses such medication can offer regarding the genetic variants of the patients, given that similar doses may provoke adverse reactions in an individual, while for another such dosage may be insufficient. This scenario would allow verifying the polymorphisms of drug response prior to administering medications like anticoagulants, hyperlipidemia treatments, or chemotherapy, among others. We must specially mention recessive diseases, produced by the presence of two alleles of a mutated gene, which are inherited from the mother, as well as the father. By studying the mutations, we may learn if a couple is at risk of bearing children with the

  19. Between Two Fern Genomes


    Sessa, Emily B.; Banks, Jo; Michael S Barker; Der, Joshua P; Duffy, Aaron M; Graham, Sean W.; Hasebe, Mitsuyasu; Langdale, Jane; Li, Fay-Wei; Marchant, D; Kathleen M. Pryer; Rothfels, Carl J.; Roux, Stanley J.; Salmi, Mari L; Sigel, Erin M.


    Ferns are the only major lineage of vascular plants not represented by a sequenced nuclear genome. This lack of genome sequence information significantly impedes our ability to understand and reconstruct genome evolution not only in ferns, but across all land plants. Azolla and Ceratopteris are ideal and complementary candidates to be the first ferns to have their nuclear genomes sequenced. They differ dramatically in genome size, life history, and habit, and thus represent the immense divers...

  20. Genomes and evolutionary genomics of animals

    Institute of Scientific and Technical Information of China (English)

    Luting SONG; Wen WANG


    Alongside recent advances and booming applications of DNA sequencing technologies,a great number of complete genome sequences for animal species are available to researchers.Hundreds of animals have been involved in whole genome sequencing,and at least 87 non-human animal species' complete or draft genome sequences have been published since 1998.Based on these technological advances and the subsequent accumulation of large quantity of genomic data,evolutionary genomics has become one of the most rapidly advancing disciplines in biology.Scientists now can perform a number of comparative and evolutionary genomic studies for animals,to identify conserved genes or other functional elements among species,genomic elements that confer animals their own specific characteristics and new phenotypes for adaptation.This review deals with the current genomic and evolutionary research on non-human animals,and displays a comprehensive landscape of genomes and the evolutionary genomics of non-human animals.It is very helpful to a better understanding of the biology and evolution of the myriad forms within the animal kingdom [Current Zoology 59 (1):87-98,2013].

  1. Genome Maps, a new generation genome browser. (United States)

    Medina, Ignacio; Salavert, Francisco; Sanchez, Rubén; de Maria, Alejandro; Alonso, Roberto; Escobar, Pablo; Bleda, Marta; Dopazo, Joaquín


    Genome browsers have gained importance as more genomes and related genomic information become available. However, the increase of information brought about by new generation sequencing technologies is, at the same time, causing a subtle but continuous decrease in the efficiency of conventional genome browsers. Here, we present Genome Maps, a genome browser that implements an innovative model of data transfer and management. The program uses highly efficient technologies from the new HTML5 standard, such as scalable vector graphics, that optimize workloads at both server and client sides and ensure future scalability. Thus, data management and representation are entirely carried out by the browser, without the need of any Java Applet, Flash or other plug-in technology installation. Relevant biological data on genes, transcripts, exons, regulatory features, single-nucleotide polymorphisms, karyotype and so forth, are imported from web services and are available as tracks. In addition, several DAS servers are already included in Genome Maps. As a novelty, this web-based genome browser allows the local upload of huge genomic data files (e.g. VCF or BAM) that can be dynamically visualized in real time at the client side, thus facilitating the management of medical data affected by privacy restrictions. Finally, Genome Maps can easily be integrated in any web application by including only a few lines of code. Genome Maps is an open source collaborative initiative available in the GitHub repository ( Genome Maps is available at:

  2. Genome Maps, a new generation genome browser (United States)

    Medina, Ignacio; Salavert, Francisco; Sanchez, Rubén; de Maria, Alejandro; Alonso, Roberto; Escobar, Pablo; Bleda, Marta; Dopazo, Joaquín


    Genome browsers have gained importance as more genomes and related genomic information become available. However, the increase of information brought about by new generation sequencing technologies is, at the same time, causing a subtle but continuous decrease in the efficiency of conventional genome browsers. Here, we present Genome Maps, a genome browser that implements an innovative model of data transfer and management. The program uses highly efficient technologies from the new HTML5 standard, such as scalable vector graphics, that optimize workloads at both server and client sides and ensure future scalability. Thus, data management and representation are entirely carried out by the browser, without the need of any Java Applet, Flash or other plug-in technology installation. Relevant biological data on genes, transcripts, exons, regulatory features, single-nucleotide polymorphisms, karyotype and so forth, are imported from web services and are available as tracks. In addition, several DAS servers are already included in Genome Maps. As a novelty, this web-based genome browser allows the local upload of huge genomic data files (e.g. VCF or BAM) that can be dynamically visualized in real time at the client side, thus facilitating the management of medical data affected by privacy restrictions. Finally, Genome Maps can easily be integrated in any web application by including only a few lines of code. Genome Maps is an open source collaborative initiative available in the GitHub repository ( Genome Maps is available at: PMID:23748955

  3. Genomic Encyclopedia of Fungi

    Energy Technology Data Exchange (ETDEWEB)

    Grigoriev, Igor


    Genomes of fungi relevant to energy and environment are in focus of the Fungal Genomic Program at the US Department of Energy Joint Genome Institute (JGI). Its key project, the Genomics Encyclopedia of Fungi, targets fungi related to plant health (symbionts, pathogens, and biocontrol agents) and biorefinery processes (cellulose degradation, sugar fermentation, industrial hosts), and explores fungal diversity by means of genome sequencing and analysis. Over 150 fungal genomes have been sequenced by JGI to date and released through MycoCosm (, a fungal web-portal, which integrates sequence and functional data with genome analysis tools for user community. Sequence analysis supported by functional genomics leads to developing parts list for complex systems ranging from ecosystems of biofuel crops to biorefineries. Recent examples of such parts suggested by comparative genomics and functional analysis in these areas are presented here.

  4. JGI Fungal Genomics Program

    Energy Technology Data Exchange (ETDEWEB)

    Grigoriev, Igor V.


    Genomes of energy and environment fungi are in focus of the Fungal Genomic Program at the US Department of Energy Joint Genome Institute (JGI). Its key project, the Genomics Encyclopedia of Fungi, targets fungi related to plant health (symbionts, pathogens, and biocontrol agents) and biorefinery processes (cellulose degradation, sugar fermentation, industrial hosts), and explores fungal diversity by means of genome sequencing and analysis. Over 50 fungal genomes have been sequenced by JGI to date and released through MycoCosm (, a fungal web-portal, which integrates sequence and functional data with genome analysis tools for user community. Sequence analysis supported by functional genomics leads to developing parts list for complex systems ranging from ecosystems of biofuel crops to biorefineries. Recent examples of such 'parts' suggested by comparative genomics and functional analysis in these areas are presented here

  5. Gene cloning and expression of glycerol dehydratase from Citrobacter freundii in Escherichia coli%弗氏柠檬酸菌甘油脱水酶基因在大肠杆菌中的克隆和表达

    Institute of Scientific and Technical Information of China (English)

    齐向辉; 朱绮霞; 韦宇拓; 黄鲲; 黄日波


    以弗氏柠檬酸菌(Citrobacter freundii)基因组DNA为模板,通过PCR得到甘油脱水酶(glycerol dehydratase)基因dhaB、dhaC、dhaE,克隆到表达载体pSE380上,得到重组质粒pSE-dhaBCE.将此重组质粒转化到E.coliJM109中,重组菌株SDS-PAGE结果显示有明显的61kD、22kD、16kD三条特异性蛋白条带出现.重组菌株经诱导表达,酶活力为11.59U/mL.

  6. Purification and properties of Citrobacter freundii phytase%弗氏柠檬酸杆菌植酸酶的分离纯化及其酶学性质研究

    Institute of Scientific and Technical Information of China (English)

    罗会颖; 石鹏君; 李江; 王亚茹; 姚斌; 黄火青; 袁铁铮; 柏映国


    从弗氏柠檬酸杆菌(Citrobacter freundii)中分离纯化了一种植酸酶并进行了酶学性质研究,其反应最适pH为4.0~4.5,最适温度为40℃,在37℃下以植酸钠为底物的Km值为0.85nmol/L,Vmax为0.53IU/(mg·min),具有较好的抗胰蛋白酶的能力.酶蛋白的分子量大小约为45kDa,成熟酶蛋白N端序列为QCAPEGYQLQQVLMM.

  7. Isolation and identification of Citrobacter freundii from Cherax quadricarinatus%红螯螯虾弗氏柠檬酸杆菌病病原的分离与鉴定

    Institute of Scientific and Technical Information of China (English)

    沈锦玉; 顾志敏; 潘晓艺; 周保中; 尹文林; 曹铮


    从濒死的红螯螯虾(Cherax quadricarinatus)的肝胰脏中分离得到可疑病菌L1和L2,经细菌学鉴定2株细菌均为弗氏柠檬酸杆菌(Citrobacter freundii);经人工感染试验证实L1和L2均导致健康虾发病死亡,其LD50分别为2.2×105CFU/ind、7×105CFU/ind;2株细菌对14种药物的敏感性相似,对9种抗生素敏感,对5种抗生素有抗性.从中筛选出有效药物,应用于生产中取得了较好效果.

  8. Investigation of a foodborne disease outbreak caused by Citrobacter freundii%一起弗氏柠檬酸杆菌所致食源性疾病调查

    Institute of Scientific and Technical Information of China (English)

    闫革彬; 隋吉林; 芦丹; 刘重程; 王涛


    本文用描述性流行病学分析方法,对一起集体聚餐所致食源性疾病进行分析,根据流行病学调查资料、病例临床特点和实验室检验结果,证实该起食源性疾病由食用受弗氏柠檬酸杆菌污染的食品所致.%Descriptive epidemiological analysis was conducted on a food borne disease outbreak after a mass dinner, and laboratory detection was performed to understand the etiology of the disease. According to the epidemiological survey and laboratory detection results, the outbreak was identified to be caused by the food contaminated with Citrobacter freundii.

  9. 弗氏柠檬酸杆菌随机扩增多态性DNA法基因分型%Genotyping of Citrobacter freundii by Randomly Amplified Polymorphic DNA Technique

    Institute of Scientific and Technical Information of China (English)

    叶明亮; 黄象艳; 吕波; 侯晓琦; 李银太


    目的建立弗氏柠檬酸杆菌(Citrobacter freundii)随机扩增多态性DNA(RAPD)法基因分型图谱. 方法以优化的反应体系及单一随机引物L8,对临床分离的116株C.freundii进行RAPD分析,并按指纹图上DNA条带数及片段大小绘制基因分型图谱. 结果 116株临床分离C.freundii共得78种RAPD型. 结论 RAPD法可将C.freundii分型78种.

  10. Genomic Data Commons | Office of Cancer Genomics (United States)

    The NCI’s Center for Cancer Genomics launches the Genomic Data Commons (GDC), a unified data sharing platform for the cancer research community. The mission of the GDC is to enable data sharing across the entire cancer research community, to ultimately support precision medicine in oncology.

  11. Directed genome engineering for genome optimization. (United States)

    D'Halluin, Kathleen; Ruiter, Rene


    The ability to develop nucleases with tailor-made activities for targeted DNA double-strand break induction at will at any desired position in the genome has been a major breakthrough to make targeted genome optimization feasible in plants. The development of site specific nucleases for precise genome modification has expanded the repertoire of tools for the development and optimization of traits, already including mutation breeding, molecular breeding and transgenesis.Through directed genome engineering technology, the huge amount of information provided by genomics and systems biology can now more effectively be used for the creation of plants with improved or new traits, and for the dissection of gene functions. Although still in an early phase of deployment, its utility has been demonstrated for engineering disease resistance, herbicide tolerance, altered metabolite profiles, and for molecular trait stacking to allow linked transmission of transgenes. In this article, we will briefly review the different approaches for directed genome engineering with the emphasis on double strand break (DSB)-mediated engineering to-wards genome optimization for crop improvement and towards the acceleration of functional genomics.

  12. Comparative Genome Analysis and Genome Evolution

    NARCIS (Netherlands)

    Snel, Berend


    This thesis described a collection of bioinformatic analyses on complete genome sequence data. We have studied the evolution of gene content and find that vertical inheritance dominates over horizontal gene trasnfer, even to the extent that we can use the gene content to make genome phylogenies. Usi

  13. Isolation, identification and antibiotics susceptibility test of Citrobacter freundii from Procambarus clarkii%克氏原螯虾弗氏柠檬酸杆菌的分离鉴定与药敏试验

    Institute of Scientific and Technical Information of China (English)

    陈红莲; 宋光同; 何吉祥; 侯冠军; 王永杰


    为确定引起养殖克氏原螯虾( Procambarus clarkii)患病的病原种类及耐药情况,从患病克氏原螯虾肝胰腺取样进行常规细菌学检查,对分离株进行回归感染试验、形态观察、生理生化特性检测、16S rRNA和gyrB基因分析及药敏试验。结果显示:从患病克氏原螯虾肝胰腺分离到大量菌落形态和色泽一致的细菌,代表菌株X120523为弗氏柠檬酸杆菌( Citrobacter freundii),具有较强致病性,对20种抗生素中的喹诺酮类和氨基糖苷类抗生素敏感。%This experiment was conducted to clarify species and drug resistance of pathogen from the diseased Procambarus clarkia.Pathogenic bacteria from hepatopancreas of the diseased Procambarus clarkia were examined using conventional methods and isolated.The further tests and analysis of the isolated strain were developed , including the regression experi-ment to Procambarus clarkii, the morphology, physiological and biochemical characteristics , sequence analysis of their 16S rRNA and gyrB genes , and the susceptibility test to antibiotics.Large colonies with similar morphology and color were obtained.Strain X120523 was identified as Citrobacter freundii, proved to have strong pathogenicity , and susceptible to quinolones and aminoglycosides.

  14. Genomic Data Commons launches (United States)

    The Genomic Data Commons (GDC), a unified data system that promotes sharing of genomic and clinical data between researchers, launched today with a visit from Vice President Joe Biden to the operations center at the University of Chicago.

  15. Rat Genome Database (RGD) (United States)

    U.S. Department of Health & Human Services — The Rat Genome Database (RGD) is a collaborative effort between leading research institutions involved in rat genetic and genomic research to collect, consolidate,...

  16. National Human Genome Research Institute (United States)

    ... the Director Organization Reports & Publications Español The National Human Genome Research Institute conducts genetic and genomic research, funds ... Landscape Social Media Videos Image Gallery Fact Sheets Human Genome Project Clinical Studies Genomic Careers DNA Day Calendar ...

  17. Genomic Prediction in Barley

    DEFF Research Database (Denmark)

    Edriss, Vahid; Cericola, Fabio; Jensen, Jens D;

    Genomic prediction uses markers (SNPs) across the whole genome to predict individual breeding values at an early growth stage potentially before large scale phenotyping. One of the applications of genomic prediction in plant breeding is to identify the best individual candidate lines to contribut...

  18. Genomic Prediction in Barley

    DEFF Research Database (Denmark)

    Edriss, Vahid; Cericola, Fabio; Jensen, Jens D;


    Genomic prediction uses markers (SNPs) across the whole genome to predict individual breeding values at an early growth stage potentially before large scale phenotyping. One of the applications of genomic prediction in plant breeding is to identify the best individual candidate lines to contribut...

  19. Chicken's Genome Decoded

    Institute of Scientific and Technical Information of China (English)


    @@ After completing the work on mapping chicken genome sequence and chicken genome variation in early March, 2004, two international research consortiums have made significant progress in reading the maps, shedding new light on the studies into the first bird as well as the first agricultural animal that has its genome sequenced and analyzed in the world.

  20. [Genomics and functional genomics in microbiology]. (United States)

    Encarnación-Guevara, Sergio


    Functional genomics is changing our understanding of biology and changing our approach to biological research. It brings about concerted, high-throughput genetics with analyses of gene transcripts, proteins, and metabolites to answer the ultimate question posed by all genome-sequencing projects: what is the biological function of each and every gene? Functional genomics is stimulating a change in the research paradigm away from the analysis of single genes, proteins, or metabolites towards the analysis of each of these parameters on a global scale. By identifying and measuring several, if not the entire, molecular group of actors that take part in a given biological process, functional genomics offers the panorama of obtaining a truly holistic representation of life. Functional genomics methods are defined by high-throughput methods which are, not necessarily hypothesis-dependent. They offer insights into mRNA expression, protein expression, protein localization, and protein interactions and may cast light on the flow of information within signaling pathways. At its beginning, biology involved observing nature and experimenting on its isolated parts. Genomic research now generates new types of complex observational data derived from nature. This review describes the tools that are currently being used for functional genomics work and considers the impact that this new discipline on microbiology research.

  1. Genomic taxonomy of vibrios

    DEFF Research Database (Denmark)

    Thompson, Cristiane C.; Vicente, Ana Carolina P.; Souza, Rangel C.


    . RESULTS: We have generated four new genome sequences of three Vibrio species, i.e., V. alginolyticus 40B, V. harveyi-like 1DA3, and V. mimicus strains VM573 and VM603, and present a broad analyses of these genomes along with other sequenced Vibrio species. The genome atlas and pangenome plots provide...... a tantalizing image of the genomic differences that occur between closely related sister species, e.g. V. cholerae and V. mimicus. The vibrio pangenome contains around 26504 genes. The V. cholerae core genome and pangenome consist of 1520 and 6923 genes, respectively. Pangenomes might allow different strains...

  2. A genome blogger manifesto

    Directory of Open Access Journals (Sweden)

    Corpas Manuel


    Full Text Available Abstract Cheap prices for genomic testing have revolutionized consumers’ access to personal genomics. Exploration of personal genomes poses significant challenges for customers wishing to learn beyond provider customer reports. A vibrant community has spontaneously appeared blogging experiences and data as a way to learn about their personal genomes. No set of values has publicly been described to date encapsulating ideals and code of conduct for this community. Here I present a first attempt to address this vacuum based on my own personal experiences as genome blogger.

  3. UCSC genome browser tutorial. (United States)

    Zweig, Ann S; Karolchik, Donna; Kuhn, Robert M; Haussler, David; Kent, W James


    The University of California Santa Cruz (UCSC) Genome Bioinformatics website consists of a suite of free, open-source, on-line tools that can be used to browse, analyze, and query genomic data. These tools are available to anyone who has an Internet browser and an interest in genomics. The website provides a quick and easy-to-use visual display of genomic data. It places annotation tracks beneath genome coordinate positions, allowing rapid visual correlation of different types of information. Many of the annotation tracks are submitted by scientists worldwide; the others are computed by the UCSC Genome Bioinformatics group from publicly available sequence data. It also allows users to upload and display their own experimental results or annotation sets by creating a custom track. The suite of tools, downloadable data files, and links to documentation and other information can be found at

  4. Whole-exome/genome sequencing and genomics. (United States)

    Grody, Wayne W; Thompson, Barry H; Hudgins, Louanne


    As medical genetics has progressed from a descriptive entity to one focused on the functional relationship between genes and clinical disorders, emphasis has been placed on genomics. Genomics, a subelement of genetics, is the study of the genome, the sum total of all the genes of an organism. The human genome, which is contained in the 23 pairs of nuclear chromosomes and in the mitochondrial DNA of each cell, comprises >6 billion nucleotides of genetic code. There are some 23,000 protein-coding genes, a surprisingly small fraction of the total genetic material, with the remainder composed of noncoding DNA, regulatory sequences, and introns. The Human Genome Project, launched in 1990, produced a draft of the genome in 2001 and then a finished sequence in 2003, on the 50th anniversary of the initial publication of Watson and Crick's paper on the double-helical structure of DNA. Since then, this mass of genetic information has been translated at an ever-increasing pace into useable knowledge applicable to clinical medicine. The recent advent of massively parallel DNA sequencing (also known as shotgun, high-throughput, and next-generation sequencing) has brought whole-genome analysis into the clinic for the first time, and most of the current applications are directed at children with congenital conditions that are undiagnosable by using standard genetic tests for single-gene disorders. Thus, pediatricians must become familiar with this technology, what it can and cannot offer, and its technical and ethical challenges. Here, we address the concepts of human genomic analysis and its clinical applicability for primary care providers.

  5. Genome evolution of Oryza

    Directory of Open Access Journals (Sweden)

    Tieyan Liu


    Full Text Available The genus Oryza is composed of approximately 24 species. Wild species of Oryza contain a largely untapped resource of agronomically important genes. As an increasing number of genomes of wild rice species have been or will be sequenced, Oryza is becoming a model system for plant comparative, functional and evolutionary genomics studies. Comparative analyses of large genomic regions and whole-genome sequences have revealed molecular mechanisms involved in genome size variation, gene movement, genome evolution of polyploids, transition of euchromatin to heterochromatin and centromere evolution in the genus Oryza. Transposon activity and removal of transposable elements by unequal recombination or illegitimate recombination are two important factors contributing to expansion or contraction of Oryza genomes. Double-strand break repair mediated gene movement, especially non-homologous end joining, is an important source of non-colinear genes. Transition of euchromatin to heterochromatin is accompanied by transposable element amplification, segmental and tandem duplication of genic segments, and acquisition of heterochromatic genes from other genomic locations. Comparative analyses of multiple genomes dramatically improve the precision and sensitivity of evolutionary inference than single-genome analyses can provide. Further investigations on the impact of structural variation, lineage-specific genes and evolution of agriculturally important genes on phenotype diversity and adaptation in the genus Oryza should facilitate molecular breeding and genetic improvement of rice.

  6. Bioinformatics decoding the genome

    CERN Document Server

    CERN. Geneva; Deutsch, Sam; Michielin, Olivier; Thomas, Arthur; Descombes, Patrick


    Extracting the fundamental genomic sequence from the DNA From Genome to Sequence : Biology in the early 21st century has been radically transformed by the availability of the full genome sequences of an ever increasing number of life forms, from bacteria to major crop plants and to humans. The lecture will concentrate on the computational challenges associated with the production, storage and analysis of genome sequence data, with an emphasis on mammalian genomes. The quality and usability of genome sequences is increasingly conditioned by the careful integration of strategies for data collection and computational analysis, from the construction of maps and libraries to the assembly of raw data into sequence contigs and chromosome-sized scaffolds. Once the sequence is assembled, a major challenge is the mapping of biologically relevant information onto this sequence: promoters, introns and exons of protein-encoding genes, regulatory elements, functional RNAs, pseudogenes, transposons, etc. The methodological ...

  7. State of cat genomics. (United States)

    O'Brien, Stephen J; Johnson, Warren; Driscoll, Carlos; Pontius, Joan; Pecon-Slattery, Jill; Menotti-Raymond, Marilyn


    Our knowledge of cat family biology was recently expanded to include a genomics perspective with the completion of a draft whole genome sequence of an Abyssinian cat. The utility of the new genome information has been demonstrated by applications ranging from disease gene discovery and comparative genomics to species conservation. Patterns of genomic organization among cats and inbred domestic cat breeds have illuminated our view of domestication, revealing linkage disequilibrium tracks consequent of breed formation, defining chromosome exchanges that punctuated major lineages of mammals and suggesting ancestral continental migration events that led to 37 modern species of Felidae. We review these recent advances here. As the genome resources develop, the cat is poised to make a major contribution to many areas in genetics and biology.

  8. Causes of genome instability

    DEFF Research Database (Denmark)

    Langie, Sabine A S; Koppen, Gudrun; Desaulniers, Daniel;


    chemicals present in our modern society could contribute to carcinogenesis by indirectly affecting genome stability. The selected chemicals with their mechanisms of action proposed to indirectly contribute to genome instability are: heavy metals (DNA repair, epigenetic modification, DNA damage signaling...... function, chromosome segregation, telomere length). The purpose of this review is to describe the crucial aspects of genome instability, to outline the ways in which environmental chemicals can affect this cancer hallmark and to identify candidate chemicals for further study. The overall aim is to make......Genome instability is a prerequisite for the development of cancer. It occurs when genome maintenance systems fail to safeguard the genome's integrity, whether as a consequence of inherited defects or induced via exposure to environmental agents (chemicals, biological agents and radiation). Thus...

  9. Genomics of oral bacteria. (United States)

    Duncan, Margaret J


    Advances in bacterial genetics came with the discovery of the genetic code, followed by the development of recombinant DNA technologies. Now the field is undergoing a new revolution because of investigators' ability to sequence and assemble complete bacterial genomes. Over 200 genome projects have been completed or are in progress, and the oral microbiology research community has benefited through projects for oral bacteria and their non-oral-pathogen relatives. This review describes features of several oral bacterial genomes, and emphasizes the themes of species relationships, comparative genomics, and lateral gene transfer. Genomics is having a broad impact on basic research in microbial pathogenesis, and will lead to new approaches in clinical research and therapeutics. The oral microbiota is a unique community especially suited for new challenges to sequence the metagenomes of microbial consortia, and the genomes of uncultivable bacteria.

  10. Reference Based Genome Compression

    CERN Document Server

    Chern, Bobbie; Manolakos, Alexandros; No, Albert; Venkat, Kartik; Weissman, Tsachy


    DNA sequencing technology has advanced to a point where storage is becoming the central bottleneck in the acquisition and mining of more data. Large amounts of data are vital for genomics research, and generic compression tools, while viable, cannot offer the same savings as approaches tuned to inherent biological properties. We propose an algorithm to compress a target genome given a known reference genome. The proposed algorithm first generates a mapping from the reference to the target genome, and then compresses this mapping with an entropy coder. As an illustration of the performance: applying our algorithm to James Watson's genome with hg18 as a reference, we are able to reduce the 2991 megabyte (MB) genome down to 6.99 MB, while Gzip compresses it to 834.8 MB.

  11. Querying genomic databases

    Energy Technology Data Exchange (ETDEWEB)

    Baehr, A.; Hagstrom, R.; Joerg, D.; Overbeek, R.


    A natural-language interface has been developed that retrieves genomic information by using a simple subset of English. The interface spares the biologist from the task of learning database-specific query languages and computer programming. Currently, the interface deals with the E. coli genome. It can, however, be readily extended and shows promise as a means of easy access to other sequenced genomic databases as well.

  12. Malaria Genome Sequencing Project (United States)


    facts have stimulated efforts to develop an international, coordinated strategy for malaria research and control . Development of new drugs and...Interpolated Markov models for facilitate the development of new drugs and vaccines, the genome eukaryotic gene finding. Genomics 59, 24-31 (1999). of...Gardner, M. I. & Tettelin, H. Interpolated Markov models for facilitate the development of new drugs and vaccines, the genome eukaryotic gene finding

  13. Reference Based Genome Compression


    Chern, Bobbie; Ochoa, Idoia; Manolakos, Alexandros; No, Albert; Venkat, Kartik; Weissman, Tsachy


    DNA sequencing technology has advanced to a point where storage is becoming the central bottleneck in the acquisition and mining of more data. Large amounts of data are vital for genomics research, and generic compression tools, while viable, cannot offer the same savings as approaches tuned to inherent biological properties. We propose an algorithm to compress a target genome given a known reference genome. The proposed algorithm first generates a mapping from the reference to the target gen...

  14. [Landscape and ecological genomics]. (United States)

    Tetushkin, E Ia


    Landscape genomics is the modern version of landscape genetics, a discipline that arose approximately 10 years ago as a combination of population genetics, landscape ecology, and spatial statistics. It studies the effects of environmental variables on gene flow and other microevolutionary processes that determine genetic connectivity and variations in populations. In contrast to population genetics, it operates at the level of individual specimens rather than at the level of population samples. Another important difference between landscape genetics and genomics and population genetics is that, in the former, the analysis of gene flow and local adaptations takes quantitative account of landforms and features of the matrix, i.e., hostile spaces that separate species habitats. Landscape genomics is a part of population ecogenomics, which, along with community genomics, is a major part of ecological genomics. One of the principal purposes of landscape genomics is the identification and differentiation of various genome-wide and locus-specific effects. The approaches and computation tools developed for combined analysis of genomic and landscape variables make it possible to detect adaptation-related genome fragments, which facilitates the planning of conservation efforts and the prediction of species' fate in response to expected changes in the environment.

  15. Between two fern genomes. (United States)

    Sessa, Emily B; Banks, Jo Ann; Barker, Michael S; Der, Joshua P; Duffy, Aaron M; Graham, Sean W; Hasebe, Mitsuyasu; Langdale, Jane; Li, Fay-Wei; Marchant, D Blaine; Pryer, Kathleen M; Rothfels, Carl J; Roux, Stanley J; Salmi, Mari L; Sigel, Erin M; Soltis, Douglas E; Soltis, Pamela S; Stevenson, Dennis W; Wolf, Paul G


    Ferns are the only major lineage of vascular plants not represented by a sequenced nuclear genome. This lack of genome sequence information significantly impedes our ability to understand and reconstruct genome evolution not only in ferns, but across all land plants. Azolla and Ceratopteris are ideal and complementary candidates to be the first ferns to have their nuclear genomes sequenced. They differ dramatically in genome size, life history, and habit, and thus represent the immense diversity of extant ferns. Together, this pair of genomes will facilitate myriad large-scale comparative analyses across ferns and all land plants. Here we review the unique biological characteristics of ferns and describe a number of outstanding questions in plant biology that will benefit from the addition of ferns to the set of taxa with sequenced nuclear genomes. We explain why the fern clade is pivotal for understanding genome evolution across land plants, and we provide a rationale for how knowledge of fern genomes will enable progress in research beyond the ferns themselves.

  16. Fungal Genomics Program

    Energy Technology Data Exchange (ETDEWEB)

    Grigoriev, Igor


    The JGI Fungal Genomics Program aims to scale up sequencing and analysis of fungal genomes to explore the diversity of fungi important for energy and the environment, and to promote functional studies on a system level. Combining new sequencing technologies and comparative genomics tools, JGI is now leading the world in fungal genome sequencing and analysis. Over 120 sequenced fungal genomes with analytical tools are available via MycoCosm (, a web-portal for fungal biologists. Our model of interacting with user communities, unique among other sequencing centers, helps organize these communities, improves genome annotation and analysis work, and facilitates new larger-scale genomic projects. This resulted in 20 high-profile papers published in 2011 alone and contributing to the Genomics Encyclopedia of Fungi, which targets fungi related to plant health (symbionts, pathogens, and biocontrol agents) and biorefinery processes (cellulose degradation, sugar fermentation, industrial hosts). Our next grand challenges include larger scale exploration of fungal diversity (1000 fungal genomes), developing molecular tools for DOE-relevant model organisms, and analysis of complex systems and metagenomes.

  17. Genomic Database Searching. (United States)

    Hutchins, James R A


    The availability of reference genome sequences for virtually all species under active research has revolutionized biology. Analyses of genomic variations in many organisms have provided insights into phenotypic traits, evolution and disease, and are transforming medicine. All genomic data from publicly funded projects are freely available in Internet-based databases, for download or searching via genome browsers such as Ensembl, Vega, NCBI's Map Viewer, and the UCSC Genome Browser. These online tools generate interactive graphical outputs of relevant chromosomal regions, showing genes, transcripts, and other genomic landmarks, and epigenetic features mapped by projects such as ENCODE.This chapter provides a broad overview of the major genomic databases and browsers, and describes various approaches and the latest resources for searching them. Methods are provided for identifying genomic locus and sequence information using gene names or codes, identifiers for DNA and RNA molecules and proteins; also from karyotype bands, chromosomal coordinates, sequences, motifs, and matrix-based patterns. Approaches are also described for batch retrieval of genomic information, performing more complex queries, and analyzing larger sets of experimental data, for example from next-generation sequencing projects.

  18. Genomics of Clostridium tetani. (United States)

    Brüggemann, Holger; Brzuszkiewicz, Elzbieta; Chapeton-Montes, Diana; Plourde, Lucile; Speck, Denis; Popoff, Michel R


    Genomic information about Clostridium tetani, the causative agent of the tetanus disease, is scarce. The genome of strain E88, a strain used in vaccine production, was sequenced about 10 years ago. One additional genome (strain 12124569) has recently been released. Here we report three new genomes of C. tetani and describe major differences among all five C. tetani genomes. They all harbor tetanus-toxin-encoding plasmids that contain highly conserved genes for TeNT (tetanus toxin), TetR (transcriptional regulator of TeNT) and ColT (collagenase), but substantially differ in other plasmid regions. The chromosomes share a large core genome that contains about 85% of all genes of a given chromosome. The non-core chromosome comprises mainly prophage-like genomic regions and genes encoding environmental interaction and defense functions (e.g. surface proteins, restriction-modification systems, toxin-antitoxin systems, CRISPR/Cas systems) and other fitness functions (e.g. transport systems, metabolic activities). This new genome information will help to assess the level of genome plasticity of the species C. tetani and provide the basis for detailed comparative studies.

  19. 产CMY型AmpC酶费劳地枸橼酸杆菌的分子学特性研究%Study on molecule characteristics of a novel CMY-type AmpC β-Lactamase from Citrobacter freundii

    Institute of Scientific and Technical Information of China (English)

    张晓坤; 徐韫健; 廖伟娇; 张东梅; 张丽梅


    目的 对产CMY型AmpC酶费劳地枸橼酸杆菌进行耐药表型及分子学特性进行研究,探讨研制新的酶抑制剂.方法 对临床分离的两株费劳地枸橼酸杆菌所产CMY型AmpC酶用纸片扩散法、三相水解试验进行耐药表型检测,以该菌总基因组DNA和质粒DNA为模板进行PCR扩增、序列分析、质粒接合试验、构建重组表达载体及AmpC酶检测.结果 两株菌株对青霉素类、头孢菌素类、喹诺酮类、氨基糖苷类抗生素均表现为耐药,对呋喃类和碳青霉烯类表现为敏感;三相水解试验结果显示该菌能水解头孢西丁;PCR扩增出大小为1 146 bp的基因片段,与GenBank上多种CMY亚型的基因序列同源性为97%;质粒接合试验证实质粒上含CMY基因,为可转移质粒.结论 两株菌株所产CMY型AmpC酶为新的CMY型头孢菌素酶,它介导了该菌对青霉素类、头孢菌素类、喹诺酮类等抗生素耐药,其耐药性能水平传播.%Objective To investigate the antibiotic phenotype and moleculelogy characteristics of novel CMY-type AmpC β-Lactamase from Citrobacter freundii,in order to triturate homologue enzyme inhibitors. Methods Slip diffusion method and three-phase hydrolyses test were used to analyze antibiotic phenotype of novel CMY-type AmpC β-Lactamase from Citrobacter freundii that was detached from clinic.The DNA and plasmid of CMY-type AmpCβ-Lactamase from Citrobacter freundii Strain was amplified by PCR、sequence analysis.Plasmid Conjugation tests、construction recombinant expression vector and AmpC induce tests. Results Two strains were resistant to penicillins , cephalosporin, quinolone, aminoglycoside , and susceptible to nitrofuran , carbapenem , The results of three-dimension test showed, AmpCβ-Lactamase from DNA Strain and recombinant strain could hydrolyz cefoxitin,The 1 l46bp DNA fragment of CMY-type AmpC β-Lactamase encoding gene sequence shared 97% amino acid identity with CMY-type AmpC β-Lactamase that

  20. MIPS plant genome information resources. (United States)

    Spannagl, Manuel; Haberer, Georg; Ernst, Rebecca; Schoof, Heiko; Mayer, Klaus F X


    The Munich Institute for Protein Sequences (MIPS) has been involved in maintaining plant genome databases since the Arabidopsis thaliana genome project. Genome databases and analysis resources have focused on individual genomes and aim to provide flexible and maintainable data sets for model plant genomes as a backbone against which experimental data, for example from high-throughput functional genomics, can be organized and evaluated. In addition, model genomes also form a scaffold for comparative genomics, and much can be learned from genome-wide evolutionary studies.

  1. Activation of intestinal epithelial Stat3 orchestrates tissue defense during gastrointestinal infection.

    Directory of Open Access Journals (Sweden)

    Nadine Wittkopf

    Full Text Available Gastrointestinal infections with EHEC and EPEC are responsible for outbreaks of diarrheal diseases and represent a global health problem. Innate first-line-defense mechanisms such as production of mucus and antimicrobial peptides by intestinal epithelial cells are of utmost importance for host control of gastrointestinal infections. For the first time, we directly demonstrate a critical role for Stat3 activation in intestinal epithelial cells upon infection of mice with Citrobacter rodentium - a murine pathogen that mimics human infections with attaching and effacing Escherichia coli. C. rodentium induced transcription of IL-6 and IL-22 in gut samples of mice and was associated with activation of the transcription factor Stat3 in intestinal epithelial cells. C. rodentium infection induced expression of several antimicrobial peptides such as RegIIIγ and Pla2g2a in the intestine which was critically dependent on Stat3 activation. Consequently, mice with specific deletion of Stat3 in intestinal epithelial cells showed increased susceptibility to C. rodentium infection as indicated by high bacterial load, severe gut inflammation, pronounced intestinal epithelial cell death and dissemination of bacteria to distant organs. Together, our data implicate an essential role for Stat3 activation in intestinal epithelial cells during C. rodentium infection. Stat3 concerts the host response to bacterial infection by controlling bacterial growth and suppression of apoptosis to maintain intestinal epithelial barrier function.

  2. Brief Guide to Genomics: DNA, Genes and Genomes (United States)

    ... Breve guía de genómica A Brief Guide to Genomics DNA, Genes and Genomes Deoxyribonucleic acid (DNA) is ... genetic basis for health and disease. Implications of Genomics for Medical Science Virtually every human ailment has ...

  3. Isolation and identification of Citrobacter sedlakii from Palea steindachneri and its antibiotic sensitivity%山瑞鳖塞氏柠檬酸杆菌的分离鉴定及药物敏感性研究

    Institute of Scientific and Technical Information of China (English)

    韦信贤; 童桂香; 黎小正; 吴祥庆; 庞燕飞


    从患致死性传染病的山瑞鳖(Palea steindachneri)组织中分离到一株细菌(YL090422),对该菌形态、生理生化特征及致病性进行分析,并用BIOLOG自动微生物鉴定系统及16S rDNA序列分析对其进行了鉴定.结果显示:该菌具有较强的致病性,且为发酵型革兰氏阴性短杆菌,无芽胞及荚膜;具有对葡萄糖、精氨酸双水解酶、鸟氨酸脱羧酶、脲酶、西蒙氏柠檬酸盐、丙二酸盐、卫茅醇、吲哚、动力等反应呈阳性,对氧化酶、赖氨酸脱羧酶、苯丙氨酸脱氨酶、V-P反应等呈阴性的特点.BIOLOG自动微生物鉴定系统显示该菌为塞氏柠檬酸杆菌(Citrobacter sedlakii).16S rDNA序列分析得到1条长度为1464bp的核苷酸序列(GenBank登录号为GU726186),并显示该分离株与塞氏柠檬酸杆菌(C.sedlakii)的同源性达99.9%,且在系统发育树上与C.sedlakii聚为一支.鉴定结果确认菌株YL090422为塞氏柠檬酸杆菌(Citrobacter sedlakii).药敏试验结果显示:该菌对供试16种抗菌药物中的阿米卡星等3种药物敏感,对头孢哌酮等3种药物中度敏感,对氨苄青霉素等10种抗生素均存在不同程度的耐药.

  4. Isolation and Identification of Citrobacter freundii and Its PCR-SSCP Analysis%弗氏柠檬酸杆菌的分离鉴定与PCR-SSCP分析

    Institute of Scientific and Technical Information of China (English)

    胡秀彩; 王艺; 吕爱军


    摘要利用营养琼脂、MaC培养基从草鱼肠道中分离到3株细菌,暂时编号为TC-1、TC-2和TC-3,通过形态学观察、生理生化特征、药敏试验、动物试验、构建系统发育进化树及PCR-SSCP分析等系统鉴定,结果表明3株菌株均为弗氏柠檬酸杆菌(Citrobacter freundii),其中TC-2菌株对小鼠、斑马鱼有致病性;3株菌均对头孢噻肟、头孢曲松、洛美沙星、诺氟沙星等多种药物敏感;系统发育分析表明,3株弗氏柠檬酸杆菌16S rDNA序列与DSM 30039模式株同源性分别为99.59%、99.47%和99.53%,且位于系统发育树的同一分支;进一步采用V3区PCR-SSCP分析结果显示弗氏柠檬酸杆菌SSCP图谱中菌株间带型存在差异.%The bacteria were isolated from intestine in grass carp ( Ctenopharyngodon idellus ) using nutrient agar and MaC medium, designated temporarily as TC-1, TC-2 and TC-3, and identified with morphological observation, physiological and biochemical characteristics, drug sensitive test, animal test, established phylogcnctic tree, as well as PCR-SSCP analysis. The results showed that all 3 strains were Citrobacter freundii (Cf). Animal tests showed that TC-2 strain was lethal to mice and zebrafish, respectively. Drug sensitivity test analysis revealed that 3 strains were sensitivity to cefotaxime, ceftriaxone, lomefloxacin, norfloxacin, and many others. The phylogenetic analysis showed that 16S rDNA sequence of the 3 strains had homoiogy to the typical strain DSM 30039 at 99. 59% , 99. 47% and 99.53% respectively, and they located on the same branch of the phylogenelic tree. Further analysis results adopting V3 region of PCR-SSCP showed there were differences among SSCP atlases of Cf strains.

  5. Isolation and identification of multidrug resistant Citrobacter freundii from diseased soft -shelled turtle, Pelodiscus sinensis%一株多重耐药中华鳖源弗氏柠檬酸杆菌的分离鉴定

    Institute of Scientific and Technical Information of China (English)

    毛烁君; 斯广杰; 任晓金; 石婷婷; 章烨; 王卓瑞; 章晓栋


    从患典型鳃腺炎病中华鳖(Pelodiscus sinensis)肝脏和腹水处进行细菌接种,分离获得一株细菌。综合菌落形态,16 S rRNA 序列进化分析和 API 细菌生化鉴定系统判定,所得菌株为弗氏柠檬酸杆菌(Citrobacter freundii)(SX43)。动物回归实验显示,分离株对小鼠的半数致死量(LD50)为106.5 CFU,显示该菌株具有较强的致病性,可从实验幼鳖体内再次分离到相同的病原菌。常用药物的抗菌敏感性测定显示,菌株 SX43对头孢哌酮、头孢曲松、头孢呋辛、复方新诺明、氯霉素高度敏感。%One bacteria was isolated from liver and ascites of diseased soft- shelled turtles( Pelodiscus sinensis) suffered with parotitis, on the colony morphology, Gram’s staining, API ID32E bacterial biochemical identification system and se-quence analysis of 16S rRNA gene, the isolate bacteria was identified as Citrobacter freundii, named SX43.Healthy soft -shelled turtles (Pelodiscus sinensis) were used for experimental infection with bacterial suspension, the same bacterium could be recovered.Isolate SX43 was demonstrated virulence potential in mouse models, with the median lethal dose (LD50 ) in mice at 10 6.5 CFU.The susceptibility test to antibiotics demonstrated that the bacterial strain SX43 was suscepti-ble to cefoperazone, rocephin, cefuroxim, co -trimoxazole, chloramphenicol.

  6. Bacterial Adrenergic Sensors Regulate Virulence of Enteric Pathogens in the Gut

    Directory of Open Access Journals (Sweden)

    Cristiano G. Moreira


    Full Text Available Enteric pathogens such as enterohemorrhagic Escherichia coli (EHEC and Citrobacter rodentium, which is largely used as a surrogate EHEC model for murine infections, are exposed to several host neurotransmitters in the gut. An important chemical exchange within the gut involves the neurotransmitters epinephrine and/or norepinephrine, extensively reported to increase virulence gene expression in EHEC, acting through two bacterial adrenergic sensors: QseC and QseE. However, EHEC is unable to establish itself and cause its hallmark lesions, attaching and effacing (AE lesions, on murine enterocytes. To address the role of these neurotransmitters during enteric infection, we employed C. rodentium. Both EHEC and C. rodentium harbor the locus of enterocyte effacement (LEE that is necessary for AE lesion formation. Here we show that expression of the LEE, as well as that of other virulence genes in C. rodentium, is also activated by epinephrine and/or norepinephrine. Both QseC and QseE are required for LEE gene activation in C. rodentium, and the qseC and qseE mutants are attenuated for murine infection. C. rodentium has a decreased ability to colonize dopamine β-hydroxylase knockout (Dbh−/− mice, which do not produce epinephrine and norepinephrine. Both adrenergic sensors are required for C. rodentium to sense these neurotransmitters and activate the LEE genes during infection. These data indicate that epinephrine and norepinephrine are sensed by bacterial adrenergic receptors during enteric infection to promote activation of their virulence repertoire. This is the first report of the role of these neurotransmitters during mammalian gastrointestinal (GI infection by a noninvasive pathogen.

  7. Breeding-assisted genomics. (United States)

    Poland, Jesse


    The revolution of inexpensive sequencing has ushered in an unprecedented age of genomics. The promise of using this technology to accelerate plant breeding is being realized with a vision of genomics-assisted breeding that will lead to rapid genetic gain for expensive and difficult traits. The reality is now that robust phenotypic data is an increasing limiting resource to complement the current wealth of genomic information. While genomics has been hailed as the discipline to fundamentally change the scope of plant breeding, a more symbiotic relationship is likely to emerge. In the context of developing and evaluating large populations needed for functional genomics, none excel in this area more than plant breeders. While genetic studies have long relied on dedicated, well-structured populations, the resources dedicated to these populations in the context of readily available, inexpensive genotyping is making this philosophy less tractable relative to directly focusing functional genomics on material in breeding programs. Through shifting effort for basic genomic studies from dedicated structured populations, to capturing the entire scope of genetic determinants in breeding lines, we can move towards not only furthering our understanding of functional genomics in plants, but also rapidly improving crops for increased food security, availability and nutrition.

  8. Safeguarding genome integrity

    DEFF Research Database (Denmark)

    Sørensen, Claus Storgaard; Syljuåsen, Randi G


    Mechanisms that preserve genome integrity are highly important during the normal life cycle of human cells. Loss of genome protective mechanisms can lead to the development of diseases such as cancer. Checkpoint kinases function in the cellular surveillance pathways that help cells to cope with D...

  9. Unlocking the bovine genome

    Directory of Open Access Journals (Sweden)

    Worley Kim C


    Full Text Available Abstract The draft genome sequence of cattle (Bos taurus has now been analyzed by the Bovine Genome Sequencing and Analysis Consortium and the Bovine HapMap Consortium, which together represent an extensive collaboration involving more than 300 scientists from 25 different countries.

  10. Estimation of genome length

    Institute of Scientific and Technical Information of China (English)


    The genome length is a fundamental feature of a species. This note outlined the general concept and estimation method of the physical and genetic length. Some formulae for estimating the genetic length were derived in detail. As examples, the genome genetic length of Pinus pinaster Ait. and the genetic length of chromosome Ⅵ of Oryza sativa L. were estimated from partial linkage data.

  11. Ensembl Genomes 2013

    DEFF Research Database (Denmark)

    Kersey, Paul Julian; Allen, James E; Christensen, Mikkel


    genomes, and now includes the genomes of over 9000 bacteria. Specific extensions to the web and programmatic interfaces have been developed to support users in navigating these large data sets. Looking forward, analytic tools to allow targeted selection of data for visualization and download are likely...

  12. Genomic understanding of dinoflagellates. (United States)

    Lin, Senjie


    The phylum of dinoflagellates is characterized by many unusual and interesting genomic and physiological features, the imprint of which, in its immense genome, remains elusive. Much novel understanding has been achieved in the last decade on various aspects of dinoflagellate biology, but most remarkably about the structure, expression pattern and epigenetic modification of protein-coding genes in the nuclear and organellar genomes. Major findings include: 1) the great diversity of dinoflagellates, especially at the base of the dinoflagellate tree of life; 2) mini-circularization of the genomes of typical dinoflagellate plastids (with three membranes, chlorophylls a, c1 and c2, and carotenoid peridinin), the scrambled mitochondrial genome and the extensive mRNA editing occurring in both systems; 3) ubiquitous spliced leader trans-splicing of nuclear-encoded mRNA and demonstrated potential as a novel tool for studying dinoflagellate transcriptomes in mixed cultures and natural assemblages; 4) existence and expression of histones and other nucleosomal proteins; 5) a ribosomal protein set expected of typical eukaryotes; 6) genetic potential of non-photosynthetic solar energy utilization via proton-pump rhodopsin; 7) gene candidates in the toxin synthesis pathways; and 8) evidence of a highly redundant, high gene number and highly recombined genome. Despite this progress, much more work awaits genome-wide transcriptome and whole genome sequencing in order to unfold the molecular mechanisms underlying the numerous mysterious attributes of dinoflagellates.

  13. Phytozome Comparative Plant Genomics Portal

    Energy Technology Data Exchange (ETDEWEB)

    Goodstein, David; Batra, Sajeev; Carlson, Joseph; Hayes, Richard; Phillips, Jeremy; Shu, Shengqiang; Schmutz, Jeremy; Rokhsar, Daniel


    The Dept. of Energy Joint Genome Institute is a genomics user facility supporting DOE mission science in the areas of Bioenergy, Carbon Cycling, and Biogeochemistry. The Plant Program at the JGI applies genomic, analytical, computational and informatics platforms and methods to: 1. Understand and accelerate the improvement (domestication) of bioenergy crops 2. Characterize and moderate plant response to climate change 3. Use comparative genomics to identify constrained elements and infer gene function 4. Build high quality genomic resource platforms of JGI Plant Flagship genomes for functional and experimental work 5. Expand functional genomic resources for Plant Flagship genomes

  14. 乌翅真鲨弗氏柠檬酸杆菌的分离与鉴定%Isolation and Identification of Pathogenic Bacterium Citrobacter Freundii from Blacktip Reef Shark Carcharhinus melanopterus

    Institute of Scientific and Technical Information of China (English)

    卢君辉; 孙佳佳; 董世龙; 任硕


    为确定引起乌翅真鲨(Carcharhinus melanopterus)患病的病原种类及耐药情况,用常规方法从患病乌翅真鲨内脏取样分离得到的1株优势菌,通过回归感染试验确定该菌株的致病性,通过经典生理生化分析、API 20E细菌快速鉴定系统、16S rDNA序列分析对其进行鉴定,确定该株致病菌为弗氏柠檬酸杆菌(Citrobacter freundii).药敏试验结果表明:该菌株对左氧氟沙星、头孢曲松钠、四环素、链霉素和庆大霉素等敏感.

  15. Mechanism of resistance to β-lactam antibiotics in Citrobacter%枸橼酸杆菌对β-内酰胺类抗生素的耐药机制

    Institute of Scientific and Technical Information of China (English)

    余燕; 徐建国; 熊衍文; 叶长芸



  16. 枸橼酸杆菌中质粒介导喹诺酮耐药基因的检测%Study of plasmid-mediated quinolone resistance determinants in Citrobacter freundii

    Institute of Scientific and Technical Information of China (English)

    邵宜波; 李旭; 胡立芬; 谢琴秀


    目的 了解枸橼酸杆菌中质粒介导喹诺酮耐药(PMQR)基因的分布,以期发现新型PMQR基因.测定临床分离的PMQR基因阳性枸橼酸杆菌对临床常用抗菌药物的敏感性.方法 收集安徽医科大学第一附属医院检验科2009年临床分离的枸橼酸杆菌,PCR扩增qnr、aac(6′)-Ib-cr和qepA基因,产物纯化测序,测序结果在GenBank上比对并行转移接合实验.对收集的PMQR基因阳性枸橼酸杆菌及其接合子,采用琼脂对倍稀释法进行临床常用抗菌药物的药物敏感试验.结果 收集的枸橼酸杆菌共31株,8株菌株扩增出qnr,qnr基因阳性率为25.8%;其中6株扩增出qnrB.4株qnr阳性菌株的qnr基因转移接合成功.在qnr阳性的枸橼酸杆菌中,测序发现1种PMQR基因新亚型,命名为qnrB24.所有qnr阳性临床菌株对喹诺酮类药物的耐药率为87.5%,对头孢噻肟、阿米卡星、头孢他啶、头孢吡肟和庆大霉素的耐药率分别为75.0%、7.5%、62.5%、37.5%和87.5%,所有qnr阳性菌株对亚胺培南耐药表型为敏感.喹诺酮类药物对qnr阳性的接合子最低抑菌浓度升高10~23倍,敏感性下降.结论 安徽地区枸橼酸杆菌中qnr基因型的检出率较高,以qnrB基因型为主,qnr阳性枸橼酸杆菌对常用抗菌药物耐药性较高.%Objectives This study was conducted to detect and analyze the presence of plasmidmediated quinolone resistance (PMQR) determinants [qnr,aac-(6′)-Ib-cr and qepA] among clinical isolates of Citrobacter freundii strains isolated from patients in Anhui,China,and to understand the susceptibility of PMQR positive strains to commonly used antimicrobial agents.Methods During the year 2009,31 Citrobacter strains were collected from the First Affiliated Hospital of Anhui Medical University.Polymerase chain reaction (PCR) was used to detect PMQR genes.Amplicons were purified,sequenced and compared with data from the GenBank.Conjugation experiments were conducted to

  17. Isolation and algicidal characteristics of Citrobacter sp.strain N10%柠檬酸杆菌 N10的分离及其溶藻特性

    Institute of Scientific and Technical Information of China (English)

    孙朋飞; 卢丽玲; 王冠; 赵宇华


    Summary In recent decades,harmful algal blooms(HABs),which are natural phenomena that occur across all the world, have posed threats to decrease dissolved oxygen and have had a negative effect on fisheries, aquaculture,drinking water,tourism and human health.It is increasingly urgent to develop useful strategies for predicting and reducing the negative impacts of HABs.Actually,many methods have been devoted to controlling HABs,including copper sulfate,hydrogen peroxide,ozonization,ultrasonication,collection of algae from water surface using nets,iron powder and magnets,centrifugal separation,or ultraviolet radiation.As an effective and environment friendly strategy to control harmful algal bloom outbreaks,biologic control methods such as using algicidal bacteria against M.aeruginosa have been more and more attractive.It has been demonstrated that algicidal bacteria could serve as potential ways in reducing the impacts of HABs. In this study,a Citrobacter sp.N10 with algicidal activity against the toxic algae M.aeruginosa was isolated and identified from a lake of Zhejiang University using liquid infection technology and 1 6S rDNA sequence analysis.The growth and algicidal characters of Citrobacter sp.N10 were then studied in order to offer some useful information for HABs controlling. The results showed that the bacterium was gram-negative and its colonies were smooth, convex, low moisture,translucent or opaque and gray,and its colony surfaces were glossy.Sequence analysis of 1 6S rDNA demonstrated that strain N10 belonged to Citrobacter sp.When inoculation time was 2 to 12 h,N10 grew in logarithmic-growth period,and when inoculation time was beyond 12 h,N10 was in stationary phase.Strain N10 showed a high lysis of M.aeruginosa with an algicidal rate of 86.55% within 24 h.The algicidal rate of N10 increased with increasing incubation time and reached 97.08% within 72 h.pH value had the most significant effect on the growth of strain N10,followed by Na

  18. NCBI viral genomes resource. (United States)

    Brister, J Rodney; Ako-Adjei, Danso; Bao, Yiming; Blinkova, Olga


    Recent technological innovations have ignited an explosion in virus genome sequencing that promises to fundamentally alter our understanding of viral biology and profoundly impact public health policy. Yet, any potential benefits from the billowing cloud of next generation sequence data hinge upon well implemented reference resources that facilitate the identification of sequences, aid in the assembly of sequence reads and provide reference annotation sources. The NCBI Viral Genomes Resource is a reference resource designed to bring order to this sequence shockwave and improve usability of viral sequence data. The resource can be accessed at and catalogs all publicly available virus genome sequences and curates reference genome sequences. As the number of genome sequences has grown, so too have the difficulties in annotating and maintaining reference sequences. The rapid expansion of the viral sequence universe has forced a recalibration of the data model to better provide extant sequence representation and enhanced reference sequence products to serve the needs of the various viral communities. This, in turn, has placed increased emphasis on leveraging the knowledge of individual scientific communities to identify important viral sequences and develop well annotated reference virus genome sets.

  19. Genomic taxonomy of vibrios

    Directory of Open Access Journals (Sweden)

    Iida Tetsuya


    Full Text Available Abstract Background Vibrio taxonomy has been based on a polyphasic approach. In this study, we retrieve useful taxonomic information (i.e. data that can be used to distinguish different taxonomic levels, such as species and genera from 32 genome sequences of different vibrio species. We use a variety of tools to explore the taxonomic relationship between the sequenced genomes, including Multilocus Sequence Analysis (MLSA, supertrees, Average Amino Acid Identity (AAI, genomic signatures, and Genome BLAST atlases. Our aim is to analyse the usefulness of these tools for species identification in vibrios. Results We have generated four new genome sequences of three Vibrio species, i.e., V. alginolyticus 40B, V. harveyi-like 1DA3, and V. mimicus strains VM573 and VM603, and present a broad analyses of these genomes along with other sequenced Vibrio species. The genome atlas and pangenome plots provide a tantalizing image of the genomic differences that occur between closely related sister species, e.g. V. cholerae and V. mimicus. The vibrio pangenome contains around 26504 genes. The V. cholerae core genome and pangenome consist of 1520 and 6923 genes, respectively. Pangenomes might allow different strains of V. cholerae to occupy different niches. MLSA and supertree analyses resulted in a similar phylogenetic picture, with a clear distinction of four groups (Vibrio core group, V. cholerae-V. mimicus, Aliivibrio spp., and Photobacterium spp.. A Vibrio species is defined as a group of strains that share > 95% DNA identity in MLSA and supertree analysis, > 96% AAI, ≤ 10 genome signature dissimilarity, and > 61% proteome identity. Strains of the same species and species of the same genus will form monophyletic groups on the basis of MLSA and supertree. Conclusion The combination of different analytical and bioinformatics tools will enable the most accurate species identification through genomic computational analysis. This endeavour will culminate in

  20. Human Genome Project

    Energy Technology Data Exchange (ETDEWEB)

    Block, S. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Cornwall, J. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Dally, W. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Dyson, F. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Fortson, N. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Joyce, G. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Kimble, H. J. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Lewis, N. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Max, C. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Prince, T. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Schwitters, R. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Weinberger, P. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Woodin, W. H. [The MITRE Corporation, McLean, VA (US). JASON Program Office


    The study reviews Department of Energy supported aspects of the United States Human Genome Project, the joint National Institutes of Health/Department of Energy program to characterize all human genetic material, to discover the set of human genes, and to render them accessible for further biological study. The study concentrates on issues of technology, quality assurance/control, and informatics relevant to current effort on the genome project and needs beyond it. Recommendations are presented on areas of the genome program that are of particular interest to and supported by the Department of Energy.

  1. Human Genome Program

    Energy Technology Data Exchange (ETDEWEB)


    The DOE Human Genome program has grown tremendously, as shown by the marked increase in the number of genome-funded projects since the last workshop held in 1991. The abstracts in this book describe the genome research of DOE-funded grantees and contractors and invited guests, and all projects are represented at the workshop by posters. The 3-day meeting includes plenary sessions on ethical, legal, and social issues pertaining to the availability of genetic data; sequencing techniques, informatics support; and chromosome and cDNA mapping and sequencing.

  2. Genomic signal processing

    CERN Document Server

    Shmulevich, Ilya


    Genomic signal processing (GSP) can be defined as the analysis, processing, and use of genomic signals to gain biological knowledge, and the translation of that knowledge into systems-based applications that can be used to diagnose and treat genetic diseases. Situated at the crossroads of engineering, biology, mathematics, statistics, and computer science, GSP requires the development of both nonlinear dynamical models that adequately represent genomic regulation, and diagnostic and therapeutic tools based on these models. This book facilitates these developments by providing rigorous mathema

  3. Center for Cancer Genomics | Office of Cancer Genomics (United States)

    The Center for Cancer Genomics (CCG) was established to unify the National Cancer Institute's activities in cancer genomics, with the goal of advancing genomics research and translating findings into the clinic to improve the precise diagnosis and treatment of cancers. In addition to promoting genomic sequencing approach

  4. Genomic libraries: I. Construction and screening of fosmid genomic libraries. (United States)

    Quail, Mike A; Matthews, Lucy; Sims, Sarah; Lloyd, Christine; Beasley, Helen; Baxter, Simon W


    Large insert genome libraries have been a core resource required to sequence genomes, analyze haplotypes, and aid gene discovery. While next generation sequencing technologies are revolutionizing the field of genomics, traditional genome libraries will still be required for accurate genome assembly. Their utility is also being extended to functional studies for understanding DNA regulatory elements. Here, we present a detailed method for constructing genomic fosmid libraries, testing for common contaminants, gridding the library to nylon membranes, then hybridizing the library membranes with a radiolabeled probe to identify corresponding genomic clones. While this chapter focuses on fosmid libraries, many of these steps can also be applied to bacterial artificial chromosome libraries.

  5. Mouse Genome Informatics (MGI) (United States)

    U.S. Department of Health & Human Services — MGI is the international database resource for the laboratory mouse, providing integrated genetic, genomic, and biological data to facilitate the study of human...

  6. Epidemiology & Genomics Research Program (United States)

    The Epidemiology and Genomics Research Program, in the National Cancer Institute's Division of Cancer Control and Population Sciences, funds research in human populations to understand the determinants of cancer occurrence and outcomes.

  7. Yeast genome sequencing:

    DEFF Research Database (Denmark)

    Piskur, Jure; Langkjær, Rikke Breinhold


    For decades, unicellular yeasts have been general models to help understand the eukaryotic cell and also our own biology. Recently, over a dozen yeast genomes have been sequenced, providing the basis to resolve several complex biological questions. Analysis of the novel sequence data has shown...... of closely related species helps in gene annotation and to answer how many genes there really are within the genomes. Analysis of non-coding regions among closely related species has provided an example of how to determine novel gene regulatory sequences, which were previously difficult to analyse because...... they are short and degenerate and occupy different positions. Comparative genomics helps to understand the origin of yeasts and points out crucial molecular events in yeast evolutionary history, such as whole-genome duplication and horizontal gene transfer(s). In addition, the accumulating sequence data provide...

  8. The Lotus japonicus genome

    DEFF Research Database (Denmark)

    This book provides insights into some of the key achievements made in the study of Lotus japonicus (birdsfoot trefoil), as well as a timely overview of topics that are pertinent for future developments in legume genomics. Key topics covered include endosymbiosis, development, hormone regulation......, carbon/nitrogen and secondary metabolism, as well as advances made in high-throughput genomic and genetic approaches. Research focusing on model plants has underpinned the recent growth in plant genomics and genetics and provided a basis for investigations of major crop species. In the legume family...... Fabaceae, groundbreaking genetic and genomic research has established a significant body of knowledge on Lotus japonicus, which was adopted as a model species more than 20 years ago. The diverse nature of legumes means that such research has a wide potential and agricultural impact, for example...

  9. Lophotrochozoan mitochondrial genomes

    Energy Technology Data Exchange (ETDEWEB)

    Valles, Yvonne; Boore, Jeffrey L.


    Progress in both molecular techniques and phylogeneticmethods has challenged many of the interpretations of traditionaltaxonomy. One example is in the recognition of the animal superphylumLophotrochozoa (annelids, mollusks, echiurans, platyhelminthes,brachiopods, and other phyla), although the relationships within thisgroup and the inclusion of some phyla remain uncertain. While much ofthis progress in phylogenetic reconstruction has been based on comparingsingle gene sequences, we are beginning to see the potential of comparinglarge-scale features of genomes, such as the relative order of genes.Even though tremendous progress is being made on the sequencedetermination of whole nuclear genomes, the dataset of choice forgenome-level characters for many animals across a broad taxonomic rangeremains mitochondrial genomes. We review here what is known aboutmitochondrial genomes of the lophotrochozoans and discuss the promisethat this dataset will enable insight into theirrelationships.

  10. The genomics of adaptation. (United States)

    Radwan, Jacek; Babik, Wiesław


    The amount and nature of genetic variation available to natural selection affect the rate, course and outcome of evolution. Consequently, the study of the genetic basis of adaptive evolutionary change has occupied biologists for decades, but progress has been hampered by the lack of resolution and the absence of a genome-level perspective. Technological advances in recent years should now allow us to answer many long-standing questions about the nature of adaptation. The data gathered so far are beginning to challenge some widespread views of the way in which natural selection operates at the genomic level. Papers in this Special Feature of Proceedings of the Royal Society B illustrate various aspects of the broad field of adaptation genomics. This introductory article sets up a context and, on the basis of a few selected examples, discusses how genomic data can advance our understanding of the process of adaptation.

  11. Mouse genome database 2016. (United States)

    Bult, Carol J; Eppig, Janan T; Blake, Judith A; Kadin, James A; Richardson, Joel E


    The Mouse Genome Database (MGD; is the primary community model organism database for the laboratory mouse and serves as the source for key biological reference data related to mouse genes, gene functions, phenotypes and disease models with a strong emphasis on the relationship of these data to human biology and disease. As the cost of genome-scale sequencing continues to decrease and new technologies for genome editing become widely adopted, the laboratory mouse is more important than ever as a model system for understanding the biological significance of human genetic variation and for advancing the basic research needed to support the emergence of genome-guided precision medicine. Recent enhancements to MGD include new graphical summaries of biological annotations for mouse genes, support for mobile access to the database, tools to support the annotation and analysis of sets of genes, and expanded support for comparative biology through the expansion of homology data.

  12. Whole-Genome Sequence Assembly for Mammalian Genomes: Arachne 2


    Jaffe, David B.; Butler, Jonathan; Gnerre, Sante; Mauceli, Evan; Lindblad-Toh, Kerstin; Jill P. Mesirov; Michael C Zody; Lander, Eric S.


    We previously described the whole-genome assembly program Arachne, presenting assemblies of simulated data for small to mid-sized genomes. Here we describe algorithmic adaptations to the program, allowing for assembly of mammalian-size genomes, and also improving the assembly of smaller genomes. Three principal changes were simultaneously made and applied to the assembly of the mouse genome, during a six-month period of development: (1) Supercontigs (scaffolds) were iteratively broken and rej...

  13. An Introduction to Genome Annotation. (United States)

    Campbell, Michael S; Yandell, Mark


    Genome projects have evolved from large international undertakings to tractable endeavors for a single lab. Accurate genome annotation is critical for successful genomic, genetic, and molecular biology experiments. These annotations can be generated using a number of approaches and available software tools. This unit describes methods for genome annotation and a number of software tools commonly used in gene annotation.

  14. Decoding the human genome

    CERN Document Server

    CERN. Geneva. Audiovisual Unit; Antonerakis, S E


    Decoding the Human genome is a very up-to-date topic, raising several questions besides purely scientific, in view of the two competing teams (public and private), the ethics of using the results, and the fact that the project went apparently faster and easier than expected. The lecture series will address the following chapters: Scientific basis and challenges. Ethical and social aspects of genomics.

  15. Molluscan Evolutionary Genomics

    Energy Technology Data Exchange (ETDEWEB)

    Simison, W. Brian; Boore, Jeffrey L.


    In the last 20 years there have been dramatic advances in techniques of high-throughput DNA sequencing, most recently accelerated by the Human Genome Project, a program that has determined the three billion base pair code on which we are based. Now this tremendous capability is being directed at other genome targets that are being sampled across the broad range of life. This opens up opportunities as never before for evolutionary and organismal biologists to address questions of both processes and patterns of organismal change. We stand at the dawn of a new 'modern synthesis' period, paralleling that of the early 20th century when the fledgling field of genetics first identified the underlying basis for Darwin's theory. We must now unite the efforts of systematists, paleontologists, mathematicians, computer programmers, molecular biologists, developmental biologists, and others in the pursuit of discovering what genomics can teach us about the diversity of life. Genome-level sampling for mollusks to date has mostly been limited to mitochondrial genomes and it is likely that these will continue to provide the best targets for broad phylogenetic sampling in the near future. However, we are just beginning to see an inroad into complete nuclear genome sequencing, with several mollusks and other eutrochozoans having been selected for work about to begin. Here, we provide an overview of the state of molluscan mitochondrial genomics, highlight a few of the discoveries from this research, outline the promise of broadening this dataset, describe upcoming projects to sequence whole mollusk nuclear genomes, and challenge the community to prepare for making the best use of these data.

  16. How the genome folds (United States)

    Lieberman Aiden, Erez


    I describe Hi-C, a novel technology for probing the three-dimensional architecture of whole genomes by coupling proximity-based ligation with massively parallel sequencing. Working with collaborators at the Broad Institute and UMass Medical School, we used Hi-C to construct spatial proximity maps of the human genome at a resolution of 1Mb. These maps confirm the presence of chromosome territories and the spatial proximity of small, gene-rich chromosomes. We identified an additional level of genome organization that is characterized by the spatial segregation of open and closed chromatin to form two genome-wide compartments. At the megabase scale, the chromatin conformation is consistent with a fractal globule, a knot-free conformation that enables maximally dense packing while preserving the ability to easily fold and unfold any genomic locus. The fractal globule is distinct from the more commonly used globular equilibrium model. Our results demonstrate the power of Hi-C to map the dynamic conformations of whole genomes.

  17. Human Genome Annotation (United States)

    Gerstein, Mark

    A central problem for 21st century science is annotating the human genome and making this annotation useful for the interpretation of personal genomes. My talk will focus on annotating the 99% of the genome that does not code for canonical genes, concentrating on intergenic features such as structural variants (SVs), pseudogenes (protein fossils), binding sites, and novel transcribed RNAs (ncRNAs). In particular, I will describe how we identify regulatory sites and variable blocks (SVs) based on processing next-generation sequencing experiments. I will further explain how we cluster together groups of sites to create larger annotations. Next, I will discuss a comprehensive pseudogene identification pipeline, which has enabled us to identify >10K pseudogenes in the genome and analyze their distribution with respect to age, protein family, and chromosomal location. Throughout, I will try to introduce some of the computational algorithms and approaches that are required for genome annotation. Much of this work has been carried out in the framework of the ENCODE, modENCODE, and 1000 genomes projects.

  18. Human social genomics.

    Directory of Open Access Journals (Sweden)

    Steven W Cole


    Full Text Available A growing literature in human social genomics has begun to analyze how everyday life circumstances influence human gene expression. Social-environmental conditions such as urbanity, low socioeconomic status, social isolation, social threat, and low or unstable social status have been found to associate with differential expression of hundreds of gene transcripts in leukocytes and diseased tissues such as metastatic cancers. In leukocytes, diverse types of social adversity evoke a common conserved transcriptional response to adversity (CTRA characterized by increased expression of proinflammatory genes and decreased expression of genes involved in innate antiviral responses and antibody synthesis. Mechanistic analyses have mapped the neural "social signal transduction" pathways that stimulate CTRA gene expression in response to social threat and may contribute to social gradients in health. Research has also begun to analyze the functional genomics of optimal health and thriving. Two emerging opportunities now stand to revolutionize our understanding of the everyday life of the human genome: network genomics analyses examining how systems-level capabilities emerge from groups of individual socially sensitive genomes and near-real-time transcriptional biofeedback to empirically optimize individual well-being in the context of the unique genetic, geographic, historical, developmental, and social contexts that jointly shape the transcriptional realization of our innate human genomic potential for thriving.

  19. Evolution of small prokaryotic genomes


    Martínez-Cano, David J.; Reyes-Prieto, Mariana; Martínez-Romero, Esperanza; Partida-Martínez, Laila P.; Latorre, Amparo; Moya, Andrés; Delaye, Luis


    As revealed by genome sequencing, the biology of prokaryotes with reduced genomes is strikingly diverse. These include free-living prokaryotes with ∼800 genes as well as endosymbiotic bacteria with as few as ∼140 genes. Comparative genomics is revealing the evolutionary mechanisms that led to these small genomes. In the case of free-living prokaryotes, natural selection directly favored genome reduction, while in the case of endosymbiotic prokaryotes neutral processes played a more prominent ...

  20. Evolution of small prokaryotic genomes


    David José Martínez-Cano; Mariana eReyes-Prieto; Esperanza eMartinez-Romero; Laila Pamela Partida-Martinez; Amparo eLatorre; Andres eMoya; Luis eDelaye


    As revealed by genome sequencing, the biology of prokaryotes with reduced genomes is strikingly diverse. These include free-living prokaryotes with ~800 genes as well as endosymbiotic bacteria with as few as ~140 genes. Comparative genomics is revealing the evolutionary mechanisms that led to these small genomes. In the case of free-living prokaryotes, natural selection directly favored genome reduction, while in the case of endosymbiotic prokaryotes neutral processes played a more prominent ...

  1. A Review on Genomics APIs

    Directory of Open Access Journals (Sweden)

    Rajeswari Swaminathan


    Full Text Available The constant improvement and falling prices of whole human genome Next Generation Sequencing (NGS has resulted in rapid adoption of genomic information at both clinics and research institutions. Considered together, the complexity of genomics data, due to its large volume and diversity along with the need for genomic data sharing, has resulted in the creation of Application Programming Interface (API for secure, modular, interoperable access to genomic data from different applications, platforms, and even organizations. The Genomics APIs are a set of special protocols that assist software developers in dealing with multiple genomic data sources for building seamless, interoperable applications leading to the advancement of both genomic and clinical research. These APIs help define a standard for retrieval of genomic data from multiple sources as well as to better package genomic information for integration with Electronic Health Records. This review covers three currently available Genomics APIs: a Google Genomics, b SMART Genomics, and c 23andMe. The functionalities, reference implementations (if available and authentication protocols of each API are reviewed. A comparative analysis of the different features across the three APIs is provided in the Discussion section. Though Genomics APIs are still under active development and have yet to reach widespread adoption, they hold the promise to make building of complicated genomics applications easier with downstream constructive effects on healthcare.

  2. Screening of Lipase-Producing Bacteria and Conditions Optimization of Lipase Production by Citrobacter sp.%产脂肪酶菌株筛选及柠檬酸杆菌产酶条件优化

    Institute of Scientific and Technical Information of China (English)

    张晶晶; 刘金峰; 牟伯中; 杨世忠


    Lipase can catalyze hydrolysis of triglyceride into fatty acids and glycerol,and has been widely applied in industries,and to obtain lipase-producing microorganisms is the basis of the study. A novel lipase-producing microbe was isolated from lipid-contaminated soil samples using plate-screening method. It was purified and identified as Citrobacter sp. through 16S rRNA sequence analysis. The enzyme production condition was optimized by single factor experiment. The optimum culture condition in a liter medium was 2. 0(g/ L,the same below)of soluble starch,1. 0 KH2 PO4 ,2. 2 K2 HPO4 ·3H2 O,1. 0(NH4 )2 SO4 ,0. 1 MgSO4 ·7H2 O,2. 0 beef extract,olive oil 10. 0 mL,pH 7. 5 and 15 mL of inoculum,culture for 43 h at 37 °C in shaker. The obtained enzymatic activity was 384 U/ mL at the highest,and it was 13-fold of that before the optimization. This strain could be used to produce lipase.%脂肪酶可以催化甘油三酯水解成脂肪酸和甘油,已广泛应用在工业领域,而获得产酶微生物是研究的基础。采用油脂平板法筛选出1株脂肪酶产生菌。经16S rRNA 序列分析可知,该菌株属于柠檬酸杆菌(Citrobacter werkman and Gillen)。单因素试验对其进行产酶条件优化,优化后产酶条件(g/ L):淀粉2.0,KH2 PO41.0,K2 HPO4·3H2 O 2.2,(NH4)2 SO41.0,MgSO4·7H2 O 0.1,牛肉膏2.0,橄榄油10.0 mL,pH 7.5,每升接种量为15 mL,37℃培养43 h。获得最大酶活为384 U/ mL,是优化前的13倍。可以利用该菌制备脂肪酶。

  3. 产AmpC酶弗劳地枸橼酸杆菌的耐药基因研究%Study on resistance gene of AmpC β-lactamase in Citrobacter freundii

    Institute of Scientific and Technical Information of China (English)

    曾红莲; 赵东明; 徐韫健; 张晓坤


    Aim To investigate the drug resistance gene of AmpC β-Lactamase from ten Citrobacter freundii.Methods -lactamases of ten strains was extracted by ultrasonic crushing,and AmpC -lactamases was tested with Cefoxitin in three dimensional test,the genotype of AmpC were amplified by multiple PCR and PCR products were sequenced subsequently. Drug sensitivity of ten strains were determined. Results There were 4 strains positive in three-dimensional test.The genotype of β-lactamases were not detected in CMY-G1 (1/10),CMY-G2 (2/10),FOX (1/10),CIT(2/10),ACT,DHA and MOX genes in ten strains. The 1 146bp DNA fragment of CMY-type AmpC β-Lactamase gene sequence shared 99 % amino acid identity with blaCMY that already appeared in Guangzhou. The resistant strains overexpressing AmpC β-lactamases were multi-drug resistant. Conclusion The surveillance of overexpressing AmpC β-lactamases in Citrobacter freundii should be emphasized so as to choose effective antibiotic for dealing with AmpC β-lactamases producing strains.%目的 对广州医学院第一附属医院临床分离的10株弗劳地枸橼酸杆菌进行AmpC酶的耐药基因研究.方法 用超声破碎法提取10株菌的β-内酰胺酶粗提物,进行三维试验;提取10株细菌的总DNA,PCR扩增CMY-G1、CMY-G2、FOX、ACT、DHA、MOX、CIT耐药基因并进行测序;对菌株进行MIC药物敏感试验.结果 三维试验阳性的有4株,β-内酰胺酶基因的检出率:CMY-G1(1/10)、CMY-G2(2/10)、FOX(1/10)、CIT(2/10),ACT、DHA和MOX未检出;CMY基因经全序列测定得到1 146bp的基因片段,与广州地区报道的CMY基因有99%同源;AmpC酶阳性的菌株茵呈多重耐药现象.结论 加强菌弗劳地枸橼酸杆菌产AmpC酶的监测,以选择合适的抗生素应对产酶株.

  4. Correlation between integron and drug-resistance in clinical isolates of Citrobacter freundii%弗氏柠檬酸杆菌临床分离株整合子与耐药相关性的研究

    Institute of Scientific and Technical Information of China (English)

    俞燕; 魏取好; 王卫忠


    目的 了解临床分离弗氏柠檬酸杆菌中整合子的分布,分析整合子与细菌耐药性的关系.方法 选取2011年7月至2013年2月非重复分离自浙江省人民医院就诊患者临床样本中的37株弗氏柠檬酸杆菌,用聚合酶链反应(PCR)检测菌株第Ⅰ、Ⅱ、Ⅲ类整合子.抗生素药敏试验采用微量肉汤稀释法.结果 37株弗氏柠檬酸杆菌中,有14株(37.8%)检测到第Ⅰ类整合子,未检出第Ⅱ类和第Ⅲ类整合子.对15种常用抗生素的耐药性检测显示,第Ⅰ类整合子阳性菌株对复方磺胺甲(噁)唑及环丙沙星的耐药率高于第Ⅰ类整合子阴性菌株(P均<0.05);对其他抗生素的耐药性,第Ⅰ类整合子阳性和阴性菌株间差异无统计学意义(P均>0.05).结论 第Ⅰ类整合子在弗氏柠檬酸杆菌中分布普遍.第Ⅰ类整合子与复方磺胺甲(噁)唑及环丙沙星的耐药性密切相关.%Objective To investigate the distribution of integrons in clinical Citrobacterfreundii strains and analyze the relationship between integrons and antibiotic resistance.Methods A total of 37 non-repeated clinical isolates of Citrobacter freundii from Zhejiang Provincial People's Hospital were selected from July 2011 to February 2013.The types of the interons(intIl、intI2、intI3) were identified by PCR and the drug-sensitivity tests were carried out by broth dilution method.Results Among 37 non-repeated isolates of Citrobacter freundii,intIl was detected in 14 isolates (37.8 %),intI2 and intI3 genes were not detected.After drug-resistance test of 15 common used antibiotics,the intI1-positive strains showed higher resistant rates of trimethoprim-sulfamethoxazole and ciprofloxacin than the intIl-negative strains (P all < 0.05).For resistance rates of the other antibiotics,there was no difference between theintIl-positive and intIl-negative strains(P all > 0.05).Conclusions In this study,the class Ⅰ integron is extensively found in clinical isolates

  5. 患病大鲵中弗氏柠檬酸杆菌的分离与鉴定%Isolation and identification of Citrobacter freundii from diseased giant salamander, Andrias davidianus

    Institute of Scientific and Technical Information of China (English)

    高正勇; 曾令兵; 孟彦; 刘小玲; 张波


    [目的]确定导致大鲵(Andrias davidianus)细菌性感染死亡的病原.[方法]从大鲵肝脏中分离细菌,通过Biolog微生物自动鉴定系统及分子生物学方法对纯培养的细菌进行鉴定,再用大鲵和鲫鱼分别进行人工感染试验,以确定分离菌的致病性,同时对分离到的病原菌进行药物敏感试验.[结果]从患病大鲵肝脏中分离到一株致病菌JZ01,经人工感染健康大鲵,可复制与自然发病相同的症状,且从人工感染病鲵体内再次分离到相同的病原菌.该致病菌对健康鲫鱼也有致病性.经Biolog微生物自动鉴定系统的鉴定,以及进一步的16S rDNA基因序列和系统发育分析都表明,此致病菌为弗氏柠檬酸杆菌.药物敏感性试验表明,该菌株对氨曲南、头孢三嗪、先锋噻肟等9种药物高度敏感.[结论]弗氏柠檬酸杆菌是大鲵的一种致病菌.本文在国内外首次报道了该菌对大鲵具有致病性.%[ Objective ] To determine the pathogenic bacterium infecting giant salamander ( Andrias davidianus ) . [ Methods] Bacterium was isolated from the liver of diseased Chinese giant salamander and identified by the Biolog Microbial Identification System and molecular biology method. Healthy Chinese giant salamander and crucian carp were used for experimental infection with bacterial suspension. [Results] A bacterial strain JZO1 was isolated and identified from diseased giant salamander. Infection with the bacterial suspension to healthy giant salamander could reproduce the diseased symptoms as occurred naturally and the same bacterium could be recovered from these infected giant salamanders. The isolated bacterium also has certain pathogenicity to crucian carp. Identification by the Biolog Microbial Identification System, and further 16S rDNA sequence and phylogenetic analysis demonstrated that the bacterium isolated from diseased giant salamander was Citrobacter freundii. The susceptibility test to antibiotics

  6. Translational genomics for plant breeding with the genome sequence explosion. (United States)

    Kang, Yang Jae; Lee, Taeyoung; Lee, Jayern; Shim, Sangrea; Jeong, Haneul; Satyawan, Dani; Kim, Moon Young; Lee, Suk-Ha


    The use of next-generation sequencers and advanced genotyping technologies has propelled the field of plant genomics in model crops and plants and enhanced the discovery of hidden bridges between genotypes and phenotypes. The newly generated reference sequences of unstudied minor plants can be annotated by the knowledge of model plants via translational genomics approaches. Here, we reviewed the strategies of translational genomics and suggested perspectives on the current databases of genomic resources and the database structures of translated information on the new genome. As a draft picture of phenotypic annotation, translational genomics on newly sequenced plants will provide valuable assistance for breeders and researchers who are interested in genetic studies.

  7. Genomes to Proteomes

    Energy Technology Data Exchange (ETDEWEB)

    Panisko, Ellen A. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Grigoriev, Igor [USDOE Joint Genome Inst., Walnut Creek, CA (United States); Daly, Don S. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Webb-Robertson, Bobbie-Jo [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Baker, Scott E. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States)


    Biologists are awash with genomic sequence data. In large part, this is due to the rapid acceleration in the generation of DNA sequence that occurred as public and private research institutes raced to sequence the human genome. In parallel with the large human genome effort, mostly smaller genomes of other important model organisms were sequenced. Projects following on these initial efforts have made use of technological advances and the DNA sequencing infrastructure that was built for the human and other organism genome projects. As a result, the genome sequences of many organisms are available in high quality draft form. While in many ways this is good news, there are limitations to the biological insights that can be gleaned from DNA sequences alone; genome sequences offer only a bird's eye view of the biological processes endemic to an organism or community. Fortunately, the genome sequences now being produced at such a high rate can serve as the foundation for other global experimental platforms such as proteomics. Proteomic methods offer a snapshot of the proteins present at a point in time for a given biological sample. Current global proteomics methods combine enzymatic digestion, separations, mass spectrometry and database searching for peptide identification. One key aspect of proteomics is the prediction of peptide sequences from mass spectrometry data. Global proteomic analysis uses computational matching of experimental mass spectra with predicted spectra based on databases of gene models that are often generated computationally. Thus, the quality of gene models predicted from a genome sequence is crucial in the generation of high quality peptide identifications. Once peptides are identified they can be assigned to their parent protein. Proteins identified as expressed in a given experiment are most useful when compared to other expressed proteins in a larger biological context or biochemical pathway. In this chapter we will discuss the automatic

  8. Genomic Feature Models

    DEFF Research Database (Denmark)

    Sørensen, Peter; Edwards, Stefan McKinnon; Rohde, Palle Duun

    Whole-genome sequences and multiple trait phenotypes from large numbers of individuals will soon be available in many populations. Well established statistical modeling approaches enable the genetic analyses of complex trait phenotypes while accounting for a variety of additive and non-additive g......Whole-genome sequences and multiple trait phenotypes from large numbers of individuals will soon be available in many populations. Well established statistical modeling approaches enable the genetic analyses of complex trait phenotypes while accounting for a variety of additive and non......-additive genetic mechanisms. These modeling approaches have proven to be highly useful to determine population genetic parameters as well as prediction of genetic risk or value. We present a series of statistical modelling approaches that use prior biological information for evaluating the collective action...... of sets of genetic variants. We have applied these approaches to whole genome sequences and a complex trait phenotype resistance to starvation collected on inbred lines from the Drosophila Genome Reference Panel population. We identified a number of genomic features classification schemes (e.g. prior QTL...

  9. Secondary metabolites extracted from marine sponge associated Comamonas testosteroni and Citrobacter freundii as potential antimicrobials against MDR pathogens and hypothetical leads for VP40 matrix protein of Ebola virus: an in vitro and in silico investigation. (United States)

    Skariyachan, Sinosh; Acharya, Archana B; Subramaniyan, Saumya; Babu, Sumangala; Kulkarni, Shruthi; Narayanappa, Rajeswari


    The current study explores therapeutic potential of metabolites extracted from marine sponge (Cliona sp.)-associated bacteria against MDR pathogens and predicts the binding prospective of probable lead molecules against VP40 target of Ebola virus. The metabolite-producing bacteria were characterized by agar overlay assay and as per the protocols in Bergey's manual of determinative bacteriology. The antibacterial activities of extracted metabolites were tested against clinical pathogens by well-diffusion assay. The selected metabolite producers were characterized by 16S rDNA sequencing. Chemical screening and Fourier Transform Infrared (FTIR) analysis for selected compounds were performed. The probable lead molecules present in the metabolites were hypothesized based on proximate analysis, FTIR data, and literature survey. The drug-like properties and binding potential of lead molecules against VP40 target of Ebola virus were hypothesized by computational virtual screening and molecular docking. The current study demonstrated that clear zones around bacterial colonies in agar overlay assay. Antibiotic sensitivity profiling demonstrated that the clinical isolates were multi-drug resistant, however; most of them showed sensitivity to secondary metabolites (MIC-15 μl/well). The proximate and FTIR analysis suggested that probable metabolites belonged to alkaloids with O-H, C-H, C=O, and N-H groups. 16S rDNA characterization of selected metabolite producers demonstrated that 96% and 99% sequence identity to Comamonas testosteroni and Citrobacter freundii, respectively. The docking studies suggested that molecules such as Gymnastatin, Sorbicillactone, Marizomib, and Daryamide can designed as probable lead candidates against VP40 target of Ebola virus.

  10. Detection of an IncA/C plasmid encoding VIM-4 and CMY-4 β-lactamases in Klebsiella oxytoca and Citrobacter koseri from an inpatient in a cardiac rehabilitation unit. (United States)

    Caltagirone, Mariasofia; Bitar, Ibrahim; Piazza, Aurora; Spalla, Melissa; Nucleo, Elisabetta; Navarra, Antonella; Migliavacca, Roberta


    A 62-year-old patient was transferred to the cardiac rehabilitation unit of the I.R.C.C.S. Fondazione S. Maugeri after undergoing a heart transplantation at the Acute Care Hospital I.R.C.C.S. S. Matteo of Pavia. On 1 August 2013 and during hospitalization in the rehabilitation unit, Klebsiella oxytoca and Citrobacter koseri clinical isolates were simultaneously recovered from the patient's preputial swab. Both the K. oxytoca and C. koseri strains were carbapenem- resistant by MicroScan System (Beckman Coulter). Carbapenem-resistant K. pneumoniae had previously been reported in the same rehabilitation facility. The aim of the study was to identify the carbapenem resistance mechanisms among the enterobacterial species recovered. Phenotypic screening tests useful to detect the β-lactamases/carbapenemases were performed. Carbapenem MICs were obtained by Etest. AmpC and MBL encoding genes were identified by PCR and sequencing. Conjugation assays and plasmid characterization were performed. Both of the K. oxytoca and C. koseri isolates were multi drug resistant, showing resistance to amoxicillin-clavulanic acid, three generation cephalosporins, ertapenem (K. oxytoca MIC, >32 mg/L; C. koseri MIC, 4 mg/L), imipenem (K. oxytoca MIC, 4 mg/L; C. koseri MIC, 12 mg/L), thrimethoprim sulphamethoxazole and gentamicin. Susceptibility was retained to fluoroquinolones, colistin and tigecycline. Molecular characterization confirmed the co-presence of blaCMY-4 and blaVIM-4 determinants in a 150 Kb transferable plasmid of IncA/C group. This case is the first detection in Italy of the K. oxytoca and C. koseri clinical isolates co-producing the CMY-4 and VIM-4 enzymes.

  11. Genomic dairy cattle breeding

    DEFF Research Database (Denmark)

    Mark, Thomas; Sandøe, Peter


    The aim of this paper is to discuss the potential consequences of modern dairy cattle breeding for the welfare of dairy cows. The paper focuses on so-called genomic selection, which deploys thousands of genetic markers to estimate breeding values. The discussion should help to structure...... the thoughts of breeders and other stakeholders on how to best make use of genomic breeding in the future. Intensive breeding has played a major role in securing dramatic increases in milk yield since the Second World War. Until recently, the main focus in dairy cattle breeding was on production traits......, unfavourable genetic trends for metabolic, reproductive, claw and leg diseases indicate that these attempts have been insufficient. Today, novel genome-wide sequencing techniques are revolutionising dairy cattle breeding; these enable genetic changes to occur at least twice as rapidly as previously. While...

  12. Genomics and drug discovery. (United States)

    Haseltine, W A


    Genomics, the systematic study of all the genes of an organism, offers a new and much-needed source of systematic productivity for the pharmaceutical industry. The isolation of the majority of human genes in their most useful form is leading to the creation of new drugs based on human proteins, antibodies, peptides, and genes. Human Genome Sciences, Inc, was the first company to use the systematic, genomics approach to discovering drugs, and we have placed 4 of these in clinical trials. Two are described: repifermin (keratinocyte growth factor-2, KGF-2) for wound healing and treatment of mucositis caused by cancer therapy, and B lymphocyte stimulator (BLyS) for stimulation of the immune system. An anti-BLyS antibody drug is in advanced preclinical development for treatment of autoimmune diseases.

  13. Genomics of Salmonella Species (United States)

    Canals, Rocio; McClelland, Michael; Santiviago, Carlos A.; Andrews-Polymenis, Helene

    Progress in the study of Salmonella survival, colonization, and virulence has increased rapidly with the advent of complete genome sequencing and higher capacity assays for transcriptomic and proteomic analysis. Although many of these techniques have yet to be used to directly assay Salmonella growth on foods, these assays are currently in use to determine Salmonella factors necessary for growth in animal models including livestock animals and in in vitro conditions that mimic many different environments. As sequencing of the Salmonella genome and microarray analysis have revolutionized genomics and transcriptomics of salmonellae over the last decade, so are new high-throughput sequencing technologies currently accelerating the pace of our studies and allowing us to approach complex problems that were not previously experimentally tractable.

  14. Screening of genomic libraries. (United States)

    Novelli, Valdenice M; Cristofani-Yaly, Mariângela; Bastianel, Marinês; Palmieri, Dario A; Machado, Marcos A


    Microsatellites, or simple sequence repeats (SSRs), have proven to be an important molecular marker in plant genetics and breeding research. The main strategies to obtain these markers can be through genomic DNA and from expressed sequence tags (ESTs) from mRNA/cDNA libraries. Genetic studies using microsatellite markers have increased rapidly because they can be highly polymorphic, codominant markers and they show heterozygous conserved sequences. Here, we describe a methodology to obtain microsatellite using the enrichment library of DNA genomic sequences. This method is highly efficient to development microsatellite markers especially in plants that do not have available ESTs or genome databases. This methodology has been used to enrich SSR marker libraries in Citrus spp., an important tool to genotype germplasm, to select zygotic hybrids, and to saturate genetic maps in breeding programs.

  15. Domestication and plant genomes. (United States)

    Tang, Haibao; Sezen, Uzay; Paterson, Andrew H


    The techniques of plant improvement have been evolving with the advancement of technology, progressing from crop domestication by Neolithic humans to scientific plant breeding, and now including DNA-based genotyping and genetic engineering. Archeological findings have shown that early human ancestors often unintentionally selected for and finally fixed a few major domestication traits over time. Recent advancement of molecular and genomic tools has enabled scientists to pinpoint changes to specific chromosomal regions and genetic loci that are responsible for dramatic morphological and other transitions that distinguish crops from their wild progenitors. Extensive studies in a multitude of additional crop species, facilitated by rapid progress in sequencing and resequencing(s) of crop genomes, will further our understanding of the genomic impact from both the unusual population history of cultivated plants and millennia of human selection.

  16. Genomics of Preterm Birth (United States)

    Swaggart, Kayleigh A.; Pavlicev, Mihaela; Muglia, Louis J.


    The molecular mechanisms controlling human birth timing at term, or resulting in preterm birth, have been the focus of considerable investigation, but limited insights have been gained over the past 50 years. In part, these processes have remained elusive because of divergence in reproductive strategies and physiology shown by model organisms, making extrapolation to humans uncertain. Here, we summarize the evolution of progesterone signaling and variation in pregnancy maintenance and termination. We use this comparative physiology to support the hypothesis that selective pressure on genomic loci involved in the timing of parturition have shaped human birth timing, and that these loci can be identified with comparative genomic strategies. Previous limitations imposed by divergence of mechanisms provide an important new opportunity to elucidate fundamental pathways of parturition control through increasing availability of sequenced genomes and associated reproductive physiology characteristics across diverse organisms. PMID:25646385

  17. Improving pan-genome annotation using whole genome multiple alignment

    Directory of Open Access Journals (Sweden)

    Salzberg Steven L


    Full Text Available Abstract Background Rapid annotation and comparisons of genomes from multiple isolates (pan-genomes is becoming commonplace due to advances in sequencing technology. Genome annotations can contain inconsistencies and errors that hinder comparative analysis even within a single species. Tools are needed to compare and improve annotation quality across sets of closely related genomes. Results We introduce a new tool, Mugsy-Annotator, that identifies orthologs and evaluates annotation quality in prokaryotic genomes using whole genome multiple alignment. Mugsy-Annotator identifies anomalies in annotated gene structures, including inconsistently located translation initiation sites and disrupted genes due to draft genome sequencing or pseudogenes. An evaluation of species pan-genomes using the tool indicates that such anomalies are common, especially at translation initiation sites. Mugsy-Annotator reports alternate annotations that improve consistency and are candidates for further review. Conclusions Whole genome multiple alignment can be used to efficiently identify orthologs and annotation problem areas in a bacterial pan-genome. Comparisons of annotated gene structures within a species may show more variation than is actually present in the genome, indicating errors in genome annotation. Our new tool Mugsy-Annotator assists re-annotation efforts by highlighting edits that improve annotation consistency.

  18. Exploring functional elements and genomic variation in the noncoding genome

    NARCIS (Netherlands)

    van Heesch, S.A.A.C.


    Gene expression regulation is a delicate process that depends on multiple aspects including genome structure and transcription factor binding to DNA elements. The majority of our genome consists of noncoding DNA, which was shown to be crucial in providing the correct context for genome function. Alt

  19. On genomics, kin, and privacy. (United States)

    Telenti, Amalio; Ayday, Erman; Hubaux, Jean Pierre


    The storage of greater numbers of exomes or genomes raises the question of loss of privacy for the individual and for families if genomic data are not properly protected. Access to genome data may result from a personal decision to disclose, or from gaps in protection. In either case, revealing genome data has consequences beyond the individual, as it compromises the privacy of family members. Increasing availability of genome data linked or linkable to metadata through online social networks and services adds one additional layer of complexity to the protection of genome privacy.  The field of computer science and information technology offers solutions to secure genomic data so that individuals, medical personnel or researchers can access only the subset of genomic information required for healthcare or dedicated studies.

  20. Illuminating the Druggable Genome (IDG) (United States)

    Federal Laboratory Consortium — Results from the Human Genome Project revealed that the human genome contains 20,000 to 25,000 genes. A gene contains (encodes) the information that each cell uses...

  1. The Nostoc punctiforme Genome

    Energy Technology Data Exchange (ETDEWEB)

    John C. Meeks


    Nostoc punctiforme is a filamentous cyanobacterium with extensive phenotypic characteristics and a relatively large genome, approaching 10 Mb. The phenotypic characteristics include a photoautotrophic, diazotrophic mode of growth, but N. punctiforme is also facultatively heterotrophic; its vegetative cells have multiple development alternatives, including terminal differentiation into nitrogen-fixing heterocysts and transient differentiation into spore-like akinetes or motile filaments called hormogonia; and N. punctiforme has broad symbiotic competence with fungi and terrestrial plants, including bryophytes, gymnosperms and an angiosperm. The shotgun-sequencing phase of the N. punctiforme strain ATCC 29133 genome has been completed by the Joint Genome Institute. Annotation of an 8.9 Mb database yielded 7432 open reading frames, 45% of which encode proteins with known or probable known function and 29% of which are unique to N. punctiforme. Comparative analysis of the sequence indicates a genome that is highly plastic and in a state of flux, with numerous insertion sequences and multilocus repeats, as well as genes encoding transposases and DNA modification enzymes. The sequence also reveals the presence of genes encoding putative proteins that collectively define almost all characteristics of cyanobacteria as a group. N. punctiforme has an extensive potential to sense and respond to environmental signals as reflected by the presence of more than 400 genes encoding sensor protein kinases, response regulators and other transcriptional factors. The signal transduction systems and any of the large number of unique genes may play essential roles in the cell differentiation and symbiotic interaction properties of N. punctiforme.

  2. The tomato genome (United States)

    The tomato genome sequence was undertaken at a time when state-of-the-art sequencing methodologies were undergoing a transition to co-called next generation methodologies. The result was an international consortium undertaking a strategy merging both old and new approaches. Because biologists were...

  3. Better chocolate through genomics (United States)

    Theobroma cacao, the cacao or chocolate tree, is a tropical understory tree whose seeds are used to make chocolate. And like any important crop, cacao is the subject of much research. On September 15, 2010, scientists publicly released a preliminary sequence of the cacao genome--which contains all o...

  4. RIKEN mouse genome encyclopedia. (United States)

    Hayashizaki, Yoshihide


    We have been working to establish the comprehensive mouse full-length cDNA collection and sequence database to cover as many genes as we can, named Riken mouse genome encyclopedia. Recently we are constructing higher-level annotation (Functional ANnoTation Of Mouse cDNA; FANTOM) not only with homology search based annotation but also with expression data profile, mapping information and protein-protein database. More than 1,000,000 clones prepared from 163 tissues were end-sequenced to classify into 159,789 clusters and 60,770 representative clones were fully sequenced. As a conclusion, the 60,770 sequences contained 33,409 unique. The next generation of life science is clearly based on all of the genome information and resources. Based on our cDNA clones we developed the additional system to explore gene function. We developed cDNA microarray system to print all of these cDNA clones, protein-protein interaction screening system, protein-DNA interaction screening system and so on. The integrated database of all the information is very useful not only for analysis of gene transcriptional network and for the connection of gene to phenotype to facilitate positional candidate approach. In this talk, the prospect of the application of these genome resourced should be discussed. More information is available at the web page:

  5. Genetics, genomics and fertility (United States)

    In order to enhance the sustainability of dairy businesses, new management tools are needed to increase the fertility of dairy cattle. Genomic selection has been successfully used by AI studs to screen potential sires and significantly decrease the generation interval of bulls. Buoyed by the success...

  6. Poster: the macaque genome. (United States)


    The rhesus macaque (Macaca mulatta) facilitates an extraordinary range of biomedical and basic research, and the publication of the genome only makes it a more powerful model for studies of human disease; moreover, the macaque's position relative to humans and chimpanzees affords the opportunity to learn about the processes that have shaped the last 25 million years of primate evolution. To allow users to explore these themes of the macaque genome, Science has created a special interactive version of the poster published in the print edition of the 13 April 2007 issue. The interactive version includes additional text and exploration, as well as embedded video featuring seven scientists discussing the importance of the macaque and its genome sequence in studies of biomedicine and evolution. We have also created an accompanying teaching resource, including a lesson plan aimed at teachers of advanced high school life science students, for exploring what a comparison of the macaque and human genomes can tell us about human biology and evolution. These items are free to all site visitors.

  7. The Genomic Standards Consortium

    DEFF Research Database (Denmark)

    Field, Dawn; Amaral-Zettler, Linda; Cochrane, Guy;


    A vast and rich body of information has grown up as a result of the world's enthusiasm for 'omics technologies. Finding ways to describe and make available this information that maximise its usefulness has become a major effort across the 'omics world. At the heart of this effort is the Genomic S...

  8. The Genome Atlas Resource

    DEFF Research Database (Denmark)

    Azam Qureshi, Matloob; Rotenberg, Eva; Stærfeldt, Hans Henrik;


    with scripts and algorithms developed in a variety of programming languages at the Centre for Biological Sequence Analysis in order to create a three-tier software application for genome analysis. The results are made available via a web interface developed in Java, PHP and Perl CGI. User...

  9. Genome stability in Caenorhabditis elegans

    NARCIS (Netherlands)

    Haaften, G.W. van


    Genome stability is closely linked to cancer. Most, if not all tumor cells show some form of genome instability, mutations can range from single point mutations to gross chromosomal rearrangements and aneuploidy. Genome instability is believed to be the driving force behind tumorigenesis. In order t

  10. The UCSC genome browser database

    DEFF Research Database (Denmark)

    Kuhn, R M; Karolchik, D; Zweig, A S


    The University of California, Santa Cruz Genome Browser Database contains, as of September 2006, sequence and annotation data for the genomes of 13 vertebrate and 19 invertebrate species. The Genome Browser displays a wide variety of annotations at all scales from the single nucleotide level up t...

  11. The UCSC Genome Browser Database

    DEFF Research Database (Denmark)

    Hinrichs, A S; Karolchik, D; Baertsch, R


    The University of California Santa Cruz Genome Browser Database (GBD) contains sequence and annotation data for the genomes of about a dozen vertebrate species and several major model organisms. Genome annotations typically include assembly data, sequence composition, genes and gene predictions, ...

  12. Implementing genomics and pharmacogenomics in the clinic: The National Human Genome Research Institute's genomic medicine portfolio. (United States)

    Manolio, Teri A


    Increasing knowledge about the influence of genetic variation on human health and growing availability of reliable, cost-effective genetic testing have spurred the implementation of genomic medicine in the clinic. As defined by the National Human Genome Research Institute (NHGRI), genomic medicine uses an individual's genetic information in his or her clinical care, and has begun to be applied effectively in areas such as cancer genomics, pharmacogenomics, and rare and undiagnosed diseases. In 2011 NHGRI published its strategic vision for the future of genomic research, including an ambitious research agenda to facilitate and promote the implementation of genomic medicine. To realize this agenda, NHGRI is consulting and facilitating collaborations with the external research community through a series of "Genomic Medicine Meetings," under the guidance and leadership of the National Advisory Council on Human Genome Research. These meetings have identified and begun to address significant obstacles to implementation, such as lack of evidence of efficacy, limited availability of genomics expertise and testing, lack of standards, and difficulties in integrating genomic results into electronic medical records. The six research and dissemination initiatives comprising NHGRI's genomic research portfolio are designed to speed the evaluation and incorporation, where appropriate, of genomic technologies and findings into routine clinical care. Actual adoption of successful approaches in clinical care will depend upon the willingness, interest, and energy of professional societies, practitioners, patients, and payers to promote their responsible use and share their experiences in doing so.

  13. The perennial ryegrass GenomeZipper: targeted use of genome resources for comparative grass genomics. (United States)

    Pfeifer, Matthias; Martis, Mihaela; Asp, Torben; Mayer, Klaus F X; Lübberstedt, Thomas; Byrne, Stephen; Frei, Ursula; Studer, Bruno


    Whole-genome sequences established for model and major crop species constitute a key resource for advanced genomic research. For outbreeding forage and turf grass species like ryegrasses (Lolium spp.), such resources have yet to be developed. Here, we present a model of the perennial ryegrass (Lolium perenne) genome on the basis of conserved synteny to barley (Hordeum vulgare) and the model grass genome Brachypodium (Brachypodium distachyon) as well as rice (Oryza sativa) and sorghum (Sorghum bicolor). A transcriptome-based genetic linkage map of perennial ryegrass served as a scaffold to establish the chromosomal arrangement of syntenic genes from model grass species. This scaffold revealed a high degree of synteny and macrocollinearity and was then utilized to anchor a collection of perennial ryegrass genes in silico to their predicted genome positions. This resulted in the unambiguous assignment of 3,315 out of 8,876 previously unmapped genes to the respective chromosomes. In total, the GenomeZipper incorporates 4,035 conserved grass gene loci, which were used for the first genome-wide sequence divergence analysis between perennial ryegrass, barley, Brachypodium, rice, and sorghum. The perennial ryegrass GenomeZipper is an ordered, information-rich genome scaffold, facilitating map-based cloning and genome assembly in perennial ryegrass and closely related Poaceae species. It also represents a milestone in describing synteny between perennial ryegrass and fully sequenced model grass genomes, thereby increasing our understanding of genome organization and evolution in the most important temperate forage and turf grass species.

  14. Microbial Genomics Research in China

    Institute of Scientific and Technical Information of China (English)



    Microorganisms, including phage/virus, were initial targets and tools for developing DNA sequencing technology. Microbial genomic study was started as a model system for the Human Genome Project (HGP) and it did successfully supported the HGP, particularly with respect to BAC contig construction and large-scale shotgun sequencing and assembly. Microbial genomics study has become the fastest developed genomics discipline along with HGP, taking the advantage of the organisms' highly diversified physiology, extremely long history of evolution, close relationship with human/environment,as well as relatively small genome sizes and simple systems for functional analysis.

  15. Microbial Genomics Research in China

    Institute of Scientific and Technical Information of China (English)

    ZHAO Guo-ping


    @@ Microorganisms, including phage/virus, were initial targets and tools for developing DNA sequencing technology. Microbial genomic study was started as a model system for the Human Genome Project (HGP) and it did successfully supported the HGP, particularly with respect to BAC contig construction and large-scale shotgun sequencing and assembly. Microbial genomics study has become the fastest developed genomics discipline along with HGP, taking the advantage of the organisms' highly diversified physiology, extremely long history of evolution, close relationship with human/environment,as well as relatively small genome sizes and simple systems for functional analysis.

  16. Nongenetic functions of the genome. (United States)

    Bustin, Michael; Misteli, Tom


    The primary function of the genome is to store, propagate, and express the genetic information that gives rise to a cell's architectural and functional machinery. However, the genome is also a major structural component of the cell. Besides its genetic roles, the genome affects cellular functions by nongenetic means through its physical and structural properties, particularly by exerting mechanical forces and by serving as a scaffold for binding of cellular components. Major cellular processes affected by nongenetic functions of the genome include establishment of nuclear structure, signal transduction, mechanoresponses, cell migration, and vision in nocturnal animals. We discuss the concept, mechanisms, and implications of nongenetic functions of the genome.

  17. Genomics and the immune system. (United States)

    Pipkin, Matthew E; Monticelli, Silvia


    While the hereditary information encoded in the Watson-Crick base pairing of genomes is largely static within a given individual, access to this information is controlled by dynamic mechanisms. The human genome is pervasively transcribed, but the roles played by the majority of the non-protein-coding genome sequences are still largely unknown. In this review we focus on insights to gene transcriptional regulation by placing special emphasis on genome-wide approaches, and on how non-coding RNAs, which derive from global transcription of the genome, in turn control gene expression. We review recent progress in the field with highlights on the immune system.

  18. Informational laws of genome structures (United States)

    Bonnici, Vincenzo; Manca, Vincenzo


    In recent years, the analysis of genomes by means of strings of length k occurring in the genomes, called k-mers, has provided important insights into the basic mechanisms and design principles of genome structures. In the present study, we focus on the proper choice of the value of k for applying information theoretic concepts that express intrinsic aspects of genomes. The value k = lg2(n), where n is the genome length, is determined to be the best choice in the definition of some genomic informational indexes that are studied and computed for seventy genomes. These indexes, which are based on information entropies and on suitable comparisons with random genomes, suggest five informational laws, to which all of the considered genomes obey. Moreover, an informational genome complexity measure is proposed, which is a generalized logistic map that balances entropic and anti-entropic components of genomes and is related to their evolutionary dynamics. Finally, applications to computational synthetic biology are briefly outlined.

  19. Evolution of small prokaryotic genomes

    Directory of Open Access Journals (Sweden)

    David José Martínez-Cano


    Full Text Available As revealed by genome sequencing, the biology of prokaryotes with reduced genomes is strikingly diverse. These include free-living prokaryotes with ~800 genes as well as endosymbiotic bacteria with as few as ~140 genes. Comparative genomics is revealing the evolutionary mechanisms that led to these small genomes. In the case of free-living prokaryotes, natural selection directly favored genome reduction, while in the case of endosymbiotic prokaryotes neutral processes played a more prominent role. However, new experimental data suggest that selective processes may be at operation as well for endosymbiotic prokaryotes at least during the first stages of genome reduction. Endosymbiotic prokaryotes have evolved diverse strategies for living with reduced gene sets inside a host-defined medium. These include utilization of host-encoded functions (some of them coded by genes acquired by gene transfer from the endosymbiont and/or other bacteria; metabolic complementation between co-symbionts; and forming consortiums with other bacteria within the host. Recent genome sequencing projects of intracellular mutualistic bacteria showed that previously believed universal evolutionary trends like reduced G+C content and conservation of genome synteny are not always present in highly reduced genomes. Finally, the simplified molecular machinery of some of these organisms with small genomes may be used to aid in the design of artificial minimal cells. Here we review recent genomic discoveries of the biology of prokaryotes endowed with small gene sets and discuss the evolutionary mechanisms that have been proposed to explain their peculiar nature.

  20. Toward genome-enabled mycology. (United States)

    Hibbett, David S; Stajich, Jason E; Spatafora, Joseph W


    Genome-enabled mycology is a rapidly expanding field that is characterized by the pervasive use of genome-scale data and associated computational tools in all aspects of fungal biology. Genome-enabled mycology is integrative and often requires teams of researchers with diverse skills in organismal mycology, bioinformatics and molecular biology. This issue of Mycologia presents the first complete fungal genomes in the history of the journal, reflecting the ongoing transformation of mycology into a genome-enabled science. Here, we consider the prospects for genome-enabled mycology and the technical and social challenges that will need to be overcome to grow the database of complete fungal genomes and enable all fungal biologists to make use of the new data.

  1. Precision genome editing

    DEFF Research Database (Denmark)

    Steentoft, Catharina; Bennett, Eric P; Schjoldager, Katrine Ter-Borch Gram


    Precise and stable gene editing in mammalian cell lines has until recently been hampered by the lack of efficient targeting methods. While different gene silencing strategies have had tremendous impact on many biological fields, they have generally not been applied with wide success in the field...... of glycobiology, primarily due to their low efficiencies, with resultant failure to impose substantial phenotypic consequences upon the final glycosylation products. Here, we review novel nuclease-based precision genome editing techniques enabling efficient and stable gene editing, including gene disruption...... by introducing single or double-stranded breaks at a defined genomic sequence. We here compare and contrast the different techniques and summarize their current applications, highlighting cases from the field of glycobiology as well as pointing to future opportunities. The emerging potential of precision gene...

  2. Marine Bacterial Genomics

    DEFF Research Database (Denmark)

    Machado, Henrique

    microorganisms to be used as cell factories for production. Therefore exploitation of new microbial niches and use of different strategies is an opportunity to boost discoveries. Even though scientists have started to explore several habitats other than the terrestrial ones, the marine environment stands out...... as a hitherto under-explored niche. This thesis work uses high-throughput sequencing technologies on a collection of marine bacteria established during the Galathea 3 expedition, with the purpose of unraveling new biodiversity and new bioactivities. Several tools were used for genomic analysis in order...... to better understand the potential harbored in marine bacteria. The work presented makes use of whole genome sequencing of marine bacteria to prove that the genetic repertoire for secondary metabolite production harbored in these bacteria is far larger than anticipated; to identify and develop a new...

  3. The Genomic Standards Consortium.

    Directory of Open Access Journals (Sweden)

    Dawn Field


    Full Text Available A vast and rich body of information has grown up as a result of the world's enthusiasm for 'omics technologies. Finding ways to describe and make available this information that maximise its usefulness has become a major effort across the 'omics world. At the heart of this effort is the Genomic Standards Consortium (GSC, an open-membership organization that drives community-based standardization activities, Here we provide a short history of the GSC, provide an overview of its range of current activities, and make a call for the scientific community to join forces to improve the quality and quantity of contextual information about our public collections of genomes, metagenomes, and marker gene sequences.

  4. Genome size analyses of Pucciniales reveal the largest fungal genomes

    Directory of Open Access Journals (Sweden)

    Silvia eTavares


    Full Text Available Rust fungi (Basidiomycota, Pucciniales are biotrophic plant pathogens which exhibit diverse complexities in their life cycles and host ranges. The completion of genome sequencing of a few rust fungi has revealed the occurrence of large genomes. Sequencing efforts for other rust fungi have been hampered by uncertainty concerning their genome sizes. Flow cytometry was recently applied to estimate the genome size of a few rust fungi, and confirmed the occurrence of large genomes in this order (averaging 151.5 Mbp, while the average for Basidiomycota was 49.9 Mbp and was 37.7 Mbp for all fungi. In this work, we have used an innovative and simple approach to simultaneously isolate nuclei from the rust and its host plant in order to estimate the genome size of 30 rust species by flow cytometry. Genome sizes varied over 10-fold, from 70 to 893 Mbp, with an average genome size value of 380.2 Mbp. Compared to the genome sizes of over 1,800 fungi, Gymnosporangium confusum possesses the largest fungal genome ever reported (893.2 Mbp. Moreover, even the smallest rust genome determined in this study is larger than the vast majority of fungal genomes (94 %. The average genome size of the Pucciniales is now of 305.5 Mbp, while the average Basidiomycota genome size has shifted to 70.4 Mbp and the average for all fungi reached 44.2 Mbp. Despite the fact that no correlation could be drawn between the genome sizes, the phylogenomics or the life cycle of rust fungi, it is interesting to note that rusts with Fabaceae hosts present genomes clearly larger than those with Poaceae hosts. Although this study comprises only a small fraction of the more than 7,000 rust species described, it seems already evident that the Pucciniales represent a group where genome size expansion could be a common characteristic. This is in sharp contrast to sister taxa, placing this order in a relevant position in fungal genomics research.

  5. Microarray Genomic Systems Development (United States)


    proteins, and lipids were pelleted at 10,000 x g for 5 minutes, and the supernatant was collected. DNA pellet was precipitated from the DNAzol by...For hybridization to the microarray, 3.5 ml of hybridization buffer, made with 10% (w/v) Dextran sulphate (EMD Chemicals, Gibbstown, NJ), 1 M...microarray system. Genome Biology, 3(9): 1-16. DRDC Suffield CR 2009-145 15 List of symbols/abbreviations/acronyms/initialisms APS Ammonium

  6. The Giardia lamblia genome. (United States)

    Adam, R D


    Giardia lamblia is a protozoan parasite of humans and other mammals that is thought to be one of the most primitive extant eukaryotic organisms. Although distinctly eukaryotic, it is notable for its lack of mitochondria, nucleoli, and perixosomes. It has been suggested that Giardia spp. are pre-mitochondriate organisms, but the identification of genes in G. lamblia thought to be of mitochondrial origin has generated controversy regarding that designation. Giardi lamblia trophozoites have two nuclei that are identical in all ways that have been studied. They are polyploid with at least four, and perhaps eight or more, copies of each of five chromosomes per organism and have an estimated genome complexity of 1.2x10(7)bp of DNA, and GC content of 46%. There is evidence for recombination at the telomeres of some of the chromosomes, and multiple size variants of single chromosomes have been identified within cloned isolates. However, the internal regions of the chromosomes demonstrate no evidence of recombination. For example, there is no evidence for control of vsp gene expression by DNA recombination, and no evidence for rapid mutation in the vsp genes. Single pass sequences of approximately 9% of the G. lamblia genome have already been obtained. An ongoing genome project plans to obtain approximately 95% of the genome by a random approach, as well as a complete physical map using a bacterial artificial chromosome library. The results will facilitate a better understanding of the biology of Giardia spp. as well as their phylogenetic relationship to other primitive organisms.

  7. Genomic landscape of liposarcoma. (United States)

    Kanojia, Deepika; Nagata, Yasunobu; Garg, Manoj; Lee, Dhong Hyun; Sato, Aiko; Yoshida, Kenichi; Sato, Yusuke; Sanada, Masashi; Mayakonda, Anand; Bartenhagen, Christoph; Klein, Hans-Ulrich; Doan, Ngan B; Said, Jonathan W; Mohith, S; Gunasekar, Swetha; Shiraishi, Yuichi; Chiba, Kenichi; Tanaka, Hiroko; Miyano, Satoru; Myklebost, Ola; Yang, Henry; Dugas, Martin; Meza-Zepeda, Leonardo A; Silberman, Allan W; Forscher, Charles; Tyner, Jeffrey W; Ogawa, Seishi; Koeffler, H Phillip


    Liposarcoma (LPS) is the most common type of soft tissue sarcoma accounting for 20% of all adult sarcomas. Due to absence of clinically effective treatment options in inoperable situations and resistance to chemotherapeutics, a critical need exists to identify novel therapeutic targets. We analyzed LPS genomic landscape using SNP arrays, whole exome sequencing and targeted exome sequencing to uncover the genomic information for development of specific anti-cancer targets. SNP array analysis indicated known amplified genes (MDM2, CDK4, HMGA2) and important novel genes (UAP1, MIR557, LAMA4, CPM, IGF2, ERBB3, IGF1R). Carboxypeptidase M (CPM), recurrently amplified gene in well-differentiated/de-differentiated LPS was noted as a putative oncogene involved in the EGFR pathway. Notable deletions were found at chromosome 1p (RUNX3, ARID1A), chromosome 11q (ATM, CHEK1) and chromosome 13q14.2 (MIR15A, MIR16-1). Significantly and recurrently mutated genes (false discovery rate < 0.05) included PLEC (27%), MXRA5 (21%), FAT3 (24%), NF1 (20%), MDC1 (10%), TP53 (7%) and CHEK2 (6%). Further, in vitro and in vivo functional studies provided evidence for the tumor suppressor role for Neurofibromin 1 (NF1) gene in different subtypes of LPS. Pathway analysis of recurrent mutations demonstrated signaling through MAPK, JAK-STAT, Wnt, ErbB, axon guidance, apoptosis, DNA damage repair and cell cycle pathways were involved in liposarcomagenesis. Interestingly, we also found mutational and copy number heterogeneity within a primary LPS tumor signifying the importance of multi-region sequencing for cancer-genome guided therapy. In summary, these findings provide insight into the genomic complexity of LPS and highlight potential druggable pathways for targeted therapeutic approach.

  8. Personalized genomic medicine with a patchwork, partially owned genome. (United States)

    Mason, Christopher E; Seringhaus, Michael R; Sattler de Sousa e Brito, Clara


    "His book was known as the Book of Sand, because neither the book nor the sand have any beginning or end." - Jorge Luis BorgesThe human genome is a three billion-letter recipe for the genesis of a human being, directing development from a single-celled embryo to the trillions of adult cells. Since the sequencing of the human genome was announced in 2001, researchers have an increased ability to discern the genetic basis for diseases. This reference genome has opened the door to genomic medicine, aimed at detecting and understanding all genetic variations of the human genome that contribute to the manifestation and progression of disease. The overarching vision of genomic (or "personalized") medicine is to custom-tailor each treatment for maximum effectiveness in an individual patient. Detecting the variation in a patient's deoxyribonucleic acid (DNA), ribonucleic acid (RNA), and protein structures is no longer an insurmountable hurdle. Today, the challenge for genomic medicine lies in contextualizing those myriad genetic variations in terms of their functional consequences for a person's health and development throughout life and in terms of that patient's susceptibility to disease and differential clinical responses to medication. Additionally, several recent developments have complicated our understanding of the nominal human genome and, thereby, altered the progression of genomic medicine. In this brief review, we shall focus on these developments and examine how they are changing our understanding of our genome.

  9. eGenomics: Cataloguing Our Complete Genome Collection III

    Directory of Open Access Journals (Sweden)

    Dawn Field


    Full Text Available This meeting report summarizes the proceedings of the “eGenomics: Cataloguing our Complete Genome Collection III” workshop held September 11–13, 2006, at the National Institute for Environmental eScience (NIEeS, Cambridge, United Kingdom. This 3rd workshop of the Genomic Standards Consortium was divided into two parts. The first half of the three-day workshop was dedicated to reviewing the genomic diversity of our current and future genome and metagenome collection, and exploring linkages to a series of existing projects through formal presentations. The second half was dedicated to strategic discussions. Outcomes of the workshop include a revised “Minimum Information about a Genome Sequence” (MIGS specification (v1.1, consensus on a variety of features to be added to the Genome Catalogue (GCat, agreement by several researchers to adopt MIGS for imminent genome publications, and an agreement by the EBI and NCBI to input their genome collections into GCat for the purpose of quantifying the amount of optional data already available (e.g., for geographic location coordinates and working towards a single, global list of all public genomes and metagenomes.

  10. Mapping the human genome

    Energy Technology Data Exchange (ETDEWEB)

    Cantor, Charles R.


    The following pages aim to lay a foundation for understanding the excitement surrounding the ''human genome project,'' as well as to convey a flavor of the ongoing efforts and plans at the Human Genome Center at the Lawrence Berkeley Laboratory. Our own work, of course, is only part of a broad international effort that will dramatically enhance our understanding of human molecular genetics before the end of this century. In this country, the bulk of the effort will be carried out under the auspices of the Department of Energy and the National Institutes of Health, but significant contributions have already been made both by nonprofit private foundations and by private corporation. The respective roles of the DOE and the NIH are being coordinated by an inter-agency committee, the aims of which are to emphasize the strengths of each agency, to facilitate cooperation, and to avoid unnecessary duplication of effort. The NIH, for example, will continue its crucial work in medical genetics and in mapping the genomes of nonhuman species. The DOE, on the other hand, has unique experience in managing large projects, and its national laboratories are repositories of expertise in physics, engineering, and computer science, as well as the life sciences. The tools and techniques the project will ultimately rely on are thus likely to be developed in multidisciplinary efforts at laboratories like LBL. Accordingly, we at LBL take great pride in this enterprise -- an enterprise that will eventually transform our understanding of ourselves.

  11. Mucin dynamics in intestinal bacterial infection.

    Directory of Open Access Journals (Sweden)

    Sara K Lindén

    Full Text Available BACKGROUND: Bacterial gastroenteritis causes morbidity and mortality in humans worldwide. Murine Citrobacter rodentium infection is a model for gastroenteritis caused by the human pathogens enteropathogenic Escherichia coli and enterohaemorrhagic E. coli. Mucin glycoproteins are the main component of the first barrier that bacteria encounter in the intestinal tract. METHODOLOGY/PRINCIPAL FINDINGS: Using Immunohistochemistry, we investigated intestinal expression of mucins (Alcian blue/PAS, Muc1, Muc2, Muc4, Muc5AC, Muc13 and Muc3/17 in healthy and C. rodentium infected mice. The majority of the C. rodentium infected mice developed systemic infection and colitis in the mid and distal colon by day 12. C. rodentium bound to the major secreted mucin, Muc2, in vitro, and high numbers of bacteria were found in secreted MUC2 in infected animals in vivo, indicating that mucins may limit bacterial access to the epithelial surface. In the small intestine, caecum and proximal colon, the mucin expression was similar in infected and non-infected animals. In the distal colonic epithelium, all secreted and cell surface mucins decreased with the exception of the Muc1 cell surface mucin which increased after infection (p<0.05. Similarly, during human infection Salmonella St Paul, Campylobacter jejuni and Clostridium difficile induced MUC1 in the colon. CONCLUSION: Major changes in both the cell-surface and secreted mucins occur in response to intestinal infection.

  12. Whole-genome sequencing for comparative genomics and de novo genome assembly. (United States)

    Benjak, Andrej; Sala, Claudia; Hartkoorn, Ruben C


    Next-generation sequencing technologies for whole-genome sequencing of mycobacteria are rapidly becoming an attractive alternative to more traditional sequencing methods. In particular this technology is proving useful for genome-wide identification of mutations in mycobacteria (comparative genomics) as well as for de novo assembly of whole genomes. Next-generation sequencing however generates a vast quantity of data that can only be transformed into a usable and comprehensible form using bioinformatics. Here we describe the methodology one would use to prepare libraries for whole-genome sequencing, and the basic bioinformatics to identify mutations in a genome following Illumina HiSeq or MiSeq sequencing, as well as de novo genome assembly following sequencing using Pacific Biosciences (PacBio).

  13. Integrated genome browser: visual analytics platform for genomics



    Motivation: Genome browsers that support fast navigation through vast datasets and provide interactive visual analytics functions can help scientists achieve deeper insight into biological systems. Toward this end, we developed Integrated Genome Browser (IGB), a highly configurable, interactive and fast open source desktop genome browser. Results: Here we describe multiple updates to IGB, including all-new capabilities to display and interact with data from high-throughput sequencing experime...

  14. Genome-wide association and genomic selection in animal breeding. (United States)

    Hayes, Ben; Goddard, Mike


    Results from genome-wide association studies in livestock, and humans, has lead to the conclusion that the effect of individual quantitative trait loci (QTL) on complex traits, such as yield, are likely to be small; therefore, a large number of QTL are necessary to explain genetic variation in these traits. Given this genetic architecture, gains from marker-assisted selection (MAS) programs using only a small number of DNA markers to trace a limited number of QTL is likely to be small. This has lead to the development of alternative technology for using the available dense single nucleotide polymorphism (SNP) information, called genomic selection. Genomic selection uses a genome-wide panel of dense markers so that all QTL are likely to be in linkage disequilibrium with at least one SNP. The genomic breeding values are predicted to be the sum of the effect of these SNPs across the entire genome. In dairy cattle breeding, the accuracy of genomic estimated breeding values (GEBV) that can be achieved and the fact that these are available early in life have lead to rapid adoption of the technology. Here, we discuss the design of experiments necessary to achieve accurate prediction of GEBV in future generations in terms of the number of markers necessary and the size of the reference population where marker effects are estimated. We also present a simple method for implementing genomic selection using a genomic relationship matrix. Future challenges discussed include using whole genome sequence data to improve the accuracy of genomic selection and management of inbreeding through genomic relationships.

  15. Genomic Data Commons and Genomic Cloud Pilots - Google Hangout (United States)

    Join us for a live, moderated discussion about two NCI efforts to expand access to cancer genomics data: the Genomic Data Commons and Genomic Cloud Pilots. NCI subject matters experts will include Louis M. Staudt, M.D., Ph.D., Director Center for Cancer Genomics, Warren Kibbe, Ph.D., Director, NCI Center for Biomedical Informatics and Information Technology, and moderated by Anthony Kerlavage, Ph.D., Chief, Cancer Informatics Branch, Center for Biomedical Informatics and Information Technology. We welcome your questions before and during the Hangout on Twitter using the hashtag #AskNCI.

  16. Big Data: Astronomical or Genomical? (United States)

    Stephens, Zachary D; Lee, Skylar Y; Faghri, Faraz; Campbell, Roy H; Zhai, Chengxiang; Efron, Miles J; Iyer, Ravishankar; Schatz, Michael C; Sinha, Saurabh; Robinson, Gene E


    Genomics is a Big Data science and is going to get much bigger, very soon, but it is not known whether the needs of genomics will exceed other Big Data domains. Projecting to the year 2025, we compared genomics with three other major generators of Big Data: astronomy, YouTube, and Twitter. Our estimates show that genomics is a "four-headed beast"--it is either on par with or the most demanding of the domains analyzed here in terms of data acquisition, storage, distribution, and analysis. We discuss aspects of new technologies that will need to be developed to rise up and meet the computational challenges that genomics poses for the near future. Now is the time for concerted, community-wide planning for the "genomical" challenges of the next decade.

  17. Domestication genomics: evidence from animals. (United States)

    Wang, Guo-Dong; Xie, Hai-Bing; Peng, Min-Sheng; Irwin, David; Zhang, Ya-Ping


    Animal domestication has far-reaching significance for human society. The sequenced genomes of domesticated animals provide critical resources for understanding the genetic basis of domestication. Various genomic analyses have shed a new light on the mechanism of artificial selection and have allowed the mapping of genes involved in important domestication traits. Here, we summarize the published genomes of domesticated animals that have been generated over the past decade, as well as their origins, from a phylogenomic point of view. This review provides a general description of the genomic features encountered under a two-stage domestication process. We also introduce recent findings for domestication traits based on results from genome-wide association studies and selective-sweep scans for artificially selected genomic regions. Particular attention is paid to issues relating to the costs of domestication and the convergent evolution of genes between domesticated animals and humans.

  18. Big Data: Astronomical or Genomical?

    Directory of Open Access Journals (Sweden)

    Zachary D Stephens


    Full Text Available Genomics is a Big Data science and is going to get much bigger, very soon, but it is not known whether the needs of genomics will exceed other Big Data domains. Projecting to the year 2025, we compared genomics with three other major generators of Big Data: astronomy, YouTube, and Twitter. Our estimates show that genomics is a "four-headed beast"--it is either on par with or the most demanding of the domains analyzed here in terms of data acquisition, storage, distribution, and analysis. We discuss aspects of new technologies that will need to be developed to rise up and meet the computational challenges that genomics poses for the near future. Now is the time for concerted, community-wide planning for the "genomical" challenges of the next decade.

  19. Programs | Office of Cancer Genomics (United States)

    OCG facilitates cancer genomics research through a series of highly-focused programs. These programs generate and disseminate genomic data for use by the cancer research community. OCG programs also promote advances in technology-based infrastructure and create valuable experimental reagents and tools. OCG programs encourage collaboration by interconnecting with other genomics and cancer projects in order to accelerate translation of findings into the clinic. Below are OCG’s current, completed, and initiated programs:

  20. Vaccinology in the genome era


    Rinaudo, C. Daniela; Telford, John L.; Rappuoli, Rino; Seib, Kate L.


    Vaccination has played a significant role in controlling and eliminating life-threatening infectious diseases throughout the world, and yet currently licensed vaccines represent only the tip of the iceberg in terms of controlling human pathogens. However, as we discuss in this Review, the arrival of the genome era has revolutionized vaccine development and catalyzed a shift from conventional culture-based approaches to genome-based vaccinology. The availability of complete bacterial genomes h...

  1. The genome editing revolution

    DEFF Research Database (Denmark)

    Stella, Stefano; Montoya, Guillermo


    the previously available DNA binding templates, zinc fingers and meganucleases. Recently, the area experimented a quantum leap because of the introduction of the clustered regularly interspaced short palindromic repeats (CRISPR)-associated protein (Cas) system (clustered regularly interspaced short palindromic...... sequence). This ribonucleoprotein complex protects bacteria from invading DNAs, and it was adapted to be used in genome editing. The CRISPR ribonucleic acid (RNA) molecule guides to the specific DNA site the Cas9 nuclease to cleave the DNA target. Two years and more than 1000 publications later, the CRISPR...

  2. Bacterial genome reengineering. (United States)

    Zhou, Jindan; Rudd, Kenneth E


    The web application PrimerPair at generates large sets of paired DNA sequences surrounding- all protein and RNA genes of Escherichia coli K-12. Many DNA fragments, which these primers amplify, can be used to implement a genome reengineering strategy using complementary in vitro cloning and in vivo recombineering. The integration of a primer design tool with a model organism database increases the level of quality control. Computer-assisted design of gene primer pairs relies upon having highly accurate genomic DNA sequence information that exactly matches the DNA of the cells being used in the laboratory to ensure predictable DNA hybridizations. It is equally crucial to have confidence that the predicted start codons define the locations of genes accurately. Annotations in the EcoGene database are queried by PrimerPair to eliminate pseudogenes, IS elements, and other problematic genes before the design process starts. These projects progressively familiarize users with the EcoGene content, scope, and application interfaces that are useful for genome reengineering projects. The first protocol leads to the design of a pair of primer sequences that were used to clone and express a single gene. The N-terminal protein sequence was experimentally verified and the protein was detected in the periplasm. This is followed by instructions to design PCR primer pairs for cloning gene fragments encoding 50 periplasmic proteins without their signal peptides. The design process begins with the user simply designating one pair of forward and reverse primer endpoint positions relative to all start and stop codon positions. The gene name, genomic coordinates, and primer DNA sequences are reported to the user. When making chromosomal deletions, the integrity of the provisional primer design is checked to see whether it will generate any unwanted double deletions with adjacent genes. The bad designs are recalculated and replacement primers are provided alongside the

  3. Organizational heterogeneity of vertebrate genomes.

    Directory of Open Access Journals (Sweden)

    Svetlana Frenkel

    Full Text Available Genomes of higher eukaryotes are mosaics of segments with various structural, functional, and evolutionary properties. The availability of whole-genome sequences allows the investigation of their structure as "texts" using different statistical and computational methods. One such method, referred to as Compositional Spectra (CS analysis, is based on scoring the occurrences of fixed-length oligonucleotides (k-mers in the target DNA sequence. CS analysis allows generating species- or region-specific characteristics of the genome, regardless of their length and the presence of coding DNA. In this study, we consider the heterogeneity of vertebrate genomes as a joint effect of regional variation in sequence organization superimposed on the differences in nucleotide composition. We estimated compositional and organizational heterogeneity of genome and chromosome sequences separately and found that both heterogeneity types vary widely among genomes as well as among chromosomes in all investigated taxonomic groups. The high correspondence of heterogeneity scores obtained on three genome fractions, coding, repetitive, and the remaining part of the noncoding DNA (the genome dark matter--GDM allows the assumption that CS-heterogeneity may have functional relevance to genome regulation. Of special interest for such interpretation is the fact that natural GDM sequences display the highest deviation from the corresponding reshuffled sequences.

  4. Advances in yeast genome engineering. (United States)

    David, Florian; Siewers, Verena


    Genome engineering based on homologous recombination has been applied to yeast for many years. However, the growing importance of yeast as a cell factory in metabolic engineering and chassis in synthetic biology demands methods for fast and efficient introduction of multiple targeted changes such as gene knockouts and introduction of multistep metabolic pathways. In this review, we summarize recent improvements of existing genome engineering methods, the development of novel techniques, for example for advanced genome redesign and evolution, and the importance of endonucleases as genome engineering tools.

  5. Preemptive public policy for genomics. (United States)

    Carlson, Rick J


    To many, genomics is merely exploitable technology for the leviathan of biotechnology. This is both shallow and short sighted. Genomics is applied knowledge based on profound and evolving science about how living things develop, how healthy or sick we are, and what our future will be like. In health care, genomics technologies are disruptive yet potentially cost-effective because they enable primary prevention, the antidote to runaway costs and declining productivity. The challenges to integration are great, however, and many bioethical and social-policy implications are alarming. Because it is poorly understood today, we must debate genomics vigorously if we are to act wisely. Public policy must lead.

  6. Comparative genomics of Lactobacillus and other LAB

    DEFF Research Database (Denmark)

    Wassenaar, Trudy M.; Lukjancenko, Oksana


    The genomes of 66 LABs, belonging to five different genera, were compared for genome size and gene content. The analyzed genomes included 37 Lactobacillus genomes of 17 species, six Lactococcus lactis genomes, four Leuconostoc genomes of three species, six Streptococcus genomes of two species...... that of the others, with the two Streptococcus species having the shortest genomes. The widest distribution in genome content was observed for Lactobacillus. The number of tRNA and rRNA gene copies varied considerably, with exceptional high numbers observed for Lb. delbrueckii, while these numbers were relatively...

  7. Genome Update: alignment of bacterial chromosomes

    DEFF Research Database (Denmark)

    Ussery, David; Jensen, Mette; Poulsen, Tine Rugh;


    There are four new microbial genomes listed in this month's Genome Update, three belonging to Gram-positive bacteria and one belonging to an archaeon that lives at pH 0; all of these genomes are listed in Table 1⇓. The method of genome comparison this month is that of genome alignment and, as an ...

  8. Genomics of human longevity. (United States)

    Slagboom, P E; Beekman, M; Passtoors, W M; Deelen, J; Vaarhorst, A A M; Boer, J M; van den Akker, E B; van Heemst, D; de Craen, A J M; Maier, A B; Rozing, M; Mooijaart, S P; Heijmans, B T; Westendorp, R G J


    In animal models, single-gene mutations in genes involved in insulin/IGF and target of rapamycin signalling pathways extend lifespan to a considerable extent. The genetic, genomic and epigenetic influences on human longevity are expected to be much more complex. Strikingly however, beneficial metabolic and cellular features of long-lived families resemble those in animals for whom the lifespan is extended by applying genetic manipulation and, especially, dietary restriction. Candidate gene studies in humans support the notion that human orthologues from longevity genes identified in lower species do contribute to longevity but that the influence of the genetic variants involved is small. Here we discuss how an integration of novel study designs, labour-intensive biobanking, deep phenotyping and genomic research may provide insights into the mechanisms that drive human longevity and healthy ageing, beyond the associations usually provided by molecular and genetic epidemiology. Although prospective studies of humans from the cradle to the grave have never been performed, it is feasible to extract life histories from different cohorts jointly covering the molecular changes that occur with age from early development all the way up to the age at death. By the integration of research in different study cohorts, and with research in animal models, biological research into human longevity is thus making considerable progress.

  9. Genomic prediction using QTL derived from whole genome sequence data

    DEFF Research Database (Denmark)

    Brøndum, Rasmus Froberg; Su, Guosheng; Janss, Luc

    This study investigated the gain in accuracy of genomic prediction when a small number of significant variants from single marker analysis based on whole genome sequence data were added to the regular 54k SNP data. Analyses were performed for Nordic Holstein and Danish Jersey animals, using eithe...

  10. Insights into structural variations and genome rearrangements in prokaryotic genomes. (United States)

    Periwal, Vinita; Scaria, Vinod


    Structural variations (SVs) are genomic rearrangements that affect fairly large fragments of DNA. Most of the SVs such as inversions, deletions and translocations have been largely studied in context of genetic diseases in eukaryotes. However, recent studies demonstrate that genome rearrangements can also have profound impact on prokaryotic genomes, leading to altered cell phenotype. In contrast to single-nucleotide variations, SVs provide a much deeper insight into organization of bacterial genomes at a much better resolution. SVs can confer change in gene copy number, creation of new genes, altered gene expression and many other functional consequences. High-throughput technologies have now made it possible to explore SVs at a much refined resolution in bacterial genomes. Through this review, we aim to highlight the importance of the less explored field of SVs in prokaryotic genomes and their impact. We also discuss its potential applicability in the emerging fields of synthetic biology and genome engineering where targeted SVs could serve to create sophisticated and accurate genome editing.

  11. Comparative genomics reveals insights into avian genome evolution and adaptation

    DEFF Research Database (Denmark)

    Zhang, Guojie; Li, Cai; Li, Qiye


    Birds are the most species-rich class of tetrapod vertebrates and have wide relevance across many research fields. We explored bird macroevolution using full genomes from 48 avian species representing all major extant clades. The avian genome is principally characterized by its constrained size, ...

  12. Parasite Genome Projects and the Trypanosoma cruzi Genome Initiative

    Directory of Open Access Journals (Sweden)

    Wim Degrave


    Full Text Available Since the start of the human genome project, a great number of genome projects on other "model" organism have been initiated, some of them already completed. Several initiatives have also been started on parasite genomes, mainly through support from WHO/TDR, involving North-South and South-South collaborations, and great hopes are vested in that these initiatives will lead to new tools for disease control and prevention, as well as to the establishment of genomic research technology in developing countries. The Trypanosoma cruzi genome project, using the clone CL-Brener as starting point, has made considerable progress through the concerted action of more than 20 laboratories, most of them in the South. A brief overview of the current state of the project is given

  13. A Taste of Algal Genomes from the Joint Genome Institute

    Energy Technology Data Exchange (ETDEWEB)

    Kuo, Alan; Grigoriev, Igor


    Algae play profound roles in aquatic food chains and the carbon cycle, can impose health and economic costs through toxic blooms, provide models for the study of symbiosis, photosynthesis, and eukaryotic evolution, and are candidate sources for bio-fuels; all of these research areas are part of the mission of DOE's Joint Genome Institute (JGI). To date JGI has sequenced, assembled, annotated, and released to the public the genomes of 18 species and strains of algae, sampling almost all of the major clades of photosynthetic eukaryotes. With more algal genomes currently undergoing analysis, JGI continues its commitment to driving forward basic and applied algal science. Among these ongoing projects are the pan-genome of the dominant coccolithophore Emiliania huxleyi, the interrelationships between the 4 genomes in the nucleomorph-containing Bigelowiella natans and Guillardia theta, and the search for symbiosis genes of lichens.

  14. OryzaGenome: Genome Diversity Database of Wild Oryza Species

    KAUST Repository

    Ohyanagi, Hajime


    The species in the genus Oryza, encompassing nine genome types and 23 species, are a rich genetic resource and may have applications in deeper genomic analyses aiming to understand the evolution of plant genomes. With the advancement of next-generation sequencing (NGS) technology, a flood of Oryza species reference genomes and genomic variation information has become available in recent years. This genomic information, combined with the comprehensive phenotypic information that we are accumulating in our Oryzabase, can serve as an excellent genotype-phenotype association resource for analyzing rice functional and structural evolution, and the associated diversity of the Oryza genus. Here we integrate our previous and future phenotypic/habitat information and newly determined genotype information into a united repository, named OryzaGenome, providing the variant information with hyperlinks to Oryzabase. The current version of OryzaGenome includes genotype information of 446 O. rufipogon accessions derived by imputation and of 17 accessions derived by imputation-free deep sequencing. Two variant viewers are implemented: SNP Viewer as a conventional genome browser interface and Variant Table as a textbased browser for precise inspection of each variant one by one. Portable VCF (variant call format) file or tabdelimited file download is also available. Following these SNP (single nucleotide polymorphism) data, reference pseudomolecules/ scaffolds/contigs and genome-wide variation information for almost all of the closely and distantly related wild Oryza species from the NIG Wild Rice Collection will be available in future releases. All of the resources can be accessed through

  15. OryzaGenome: Genome Diversity Database of Wild Oryza Species. (United States)

    Ohyanagi, Hajime; Ebata, Toshinobu; Huang, Xuehui; Gong, Hao; Fujita, Masahiro; Mochizuki, Takako; Toyoda, Atsushi; Fujiyama, Asao; Kaminuma, Eli; Nakamura, Yasukazu; Feng, Qi; Wang, Zi-Xuan; Han, Bin; Kurata, Nori


    The species in the genus Oryza, encompassing nine genome types and 23 species, are a rich genetic resource and may have applications in deeper genomic analyses aiming to understand the evolution of plant genomes. With the advancement of next-generation sequencing (NGS) technology, a flood of Oryza species reference genomes and genomic variation information has become available in recent years. This genomic information, combined with the comprehensive phenotypic information that we are accumulating in our Oryzabase, can serve as an excellent genotype-phenotype association resource for analyzing rice functional and structural evolution, and the associated diversity of the Oryza genus. Here we integrate our previous and future phenotypic/habitat information and newly determined genotype information into a united repository, named OryzaGenome, providing the variant information with hyperlinks to Oryzabase. The current version of OryzaGenome includes genotype information of 446 O. rufipogon accessions derived by imputation and of 17 accessions derived by imputation-free deep sequencing. Two variant viewers are implemented: SNP Viewer as a conventional genome browser interface and Variant Table as a text-based browser for precise inspection of each variant one by one. Portable VCF (variant call format) file or tab-delimited file download is also available. Following these SNP (single nucleotide polymorphism) data, reference pseudomolecules/scaffolds/contigs and genome-wide variation information for almost all of the closely and distantly related wild Oryza species from the NIG Wild Rice Collection will be available in future releases. All of the resources can be accessed through

  16. 132株弗劳地枸橼酸杆菌致重症患者医院感染的原因与耐药性分析%Analysis of the etiology and drug resistance of hospital infection in critically ill patients caused by 132 Citrobacter freundii

    Institute of Scientific and Technical Information of China (English)



    Objective To analysis of the causes and drug resistance characteristics in ICU patients with Citrobacter freundii hos‐pital infections ,for the future of clinical treatment and prevention of Citrobacter freundii infection provides the basis .Methods Col‐lected our hospitals from December 2011 to November 2014 clinical samples of ICU patients ,conventional isolation and culture of bacteria ,K‐B disk diffusion susceptibility test ,using Whonet5 .6 software analysis processing tentative data .Results Isolated from Critically ill patients Citrobacter freundii lower respiratory tract ,accounted for 64 .4% ;ESBLs producing high ,accounted for 35 .6% ;susceptibility testing showed the bacteria to imipenem ,meropenem ,nitrofurantoin ,kanamycin ,amikacin ,cefoperazone/sul‐bactam and piperacillin/tazobactam were more sensitive ,drug resistance rates were 3 .8% ,4 .5% ,8 .3% ,9 .1% ,17 .4% ,18 .1% and 22 .7% ,the rest of antimicrobial drug resistance rates more than 25 .0% .Conclusion Citrobacter freundii caused critically ill pa‐tients hospital infection have become increasingly serious ,lower respiratory tract was the main site of infection ,the bacteria used in the clinic for cephalosporin ,quinolones ,aminoglycosides and a variety of internal β‐lactam antibiotics were highly resistant ,clinicians should strengthen monitoring of drug resistance ,to reduce the resistant strains produced and spread within the hospital .%目的:分析该院重症监护病房患者弗劳地枸橼酸杆菌医院感染的原因和耐药特点,为今后的临床治疗和预防弗劳地枸橼酸杆菌感染提供依据。方法收集该院2011年12月至2014年11月重症监护病房患者的临床标本,常规分离培养细菌,K‐B纸片法进行药敏试验,利用WHONET 5.6软件分析处理实验数据。结果从重症患者分离的弗劳地枸橼酸杆菌以下呼吸道为主,占64.4%;产ESBLs高,达35.6%;药敏试验表明该菌对亚胺培南、

  17. Optimization of fermentation conditions for violacein production by recombinant Citrobacter freundii%重组柠檬酸杆菌合成紫色杆菌素的工艺条件优化

    Institute of Scientific and Technical Information of China (English)

    张瑞萍; 蒋培霞; 李春; 邢新会


    以L-色氨酸为前体物,对弗氏柠檬酸杆菌(Citrobacter freundii)基因工程菌株生产紫色杆菌素的工艺条件进行了优化.通过单因素实验研究了培养基种类、培养温度、碳源、溶氧、种子液的状态、接种量、诱导时机、诱导剂的浓度及初始pH对细胞生长和紫色杆菌素产量的影响,通过正交实验研究了这些因素中可能存在交互作用的4个因素(种子液OD660、接种量、诱导时机、诱导剂浓度)的影响主次,确定了这些因素、水平的最佳搭配方案.结果表明,重组柠檬酸杆菌合成紫色杆菌素的最优培养条件为:种子液培养至OD660=3.6时,以3 %的接种量接种于以甘油为碳源、初始pH为6.5的磷酸盐发酵培养基E2(25 μg·ml-1卡那霉素),先在37℃、200 r·min-1下培养至OD660=1.4,然后加入0.5 μl·ml-1的诱导剂正辛烷,同时转入20℃,在150 r·min-1下诱导培养31 h.在此最优条件下,紫色杆菌素粗提物(紫色杆菌素及脱氧紫色杆菌素的混合物)产量可达1.809 g·L-1,比优化前(0.514 g·L-1)提高了252%,是目前国际上其他研究小组报道的最高摇瓶产量(0.43 g·L-1)的4.2倍.质粒稳定性实验结果表明重组柠檬酸杆菌在抗生素选择压力条件下具有良好的遗传稳定性.


    Institute of Scientific and Technical Information of China (English)

    张静; 李进; 王开强; 孟小然


    A strain of Citrobacter freundii with sulfate-reducing function was isolated from the sludge at the bottom of cooling tower in a power plant using reclaimed water.Scanning electron microscopy(SEM) and energy dispersive spectrometry(EDS) were employed to investigate the characteristics of the biofilm formed on the surface of HSn70-1A and BFe30-1-1 in reclaimed water.The results show that the characteristics of biofilm-forming for HSn70-1A was better than BFe30-1-1.In biofilm the contents of C,O and other inorganic elements were relatively high,while the contents of matrix elements significantly decreased.The components of extracellular polymer substances(EPS)in the bio-film formed on the surface of copper alloy at the different time were analyzed.Differences in the ratio of polysaccharide to protein revealed that the 3rd day and 7th day were two critical periods for the formation of biofilm.During these two periods,EPS from HSn70-1A showed better hydrophobic properties than EPS from BFe30-1-1,which made HSn70-1A more resistant to microorganism corrosion.%从使用再生水的某电厂冷却塔粘泥中分离出一株具有硫酸盐还原功能的弗氏柠檬酸杆菌.利用扫描电子显微镜(SEM)和能谱仪(EDS)对再生水中HSn70-1A和BFe30-1-1两种合金表面弗氏柠檬酸杆菌生物膜结构和成分进行表征,结果表明HSn70-1A成膜特性好于BFe30-1-1,两种合金表面生物膜中C、O等无机元素含量较大、基体金属元素含量下降较为明显.对不同时刻合金表面生物膜胞外聚合物(EPS)组分进行分析,多糖与蛋白质含量之比揭示出,在第3天和第7天两个关键期EPS的疏水性能对微生物膜的致密性和完整性产生重要影响,实验结果表明在两个关键期内HSn70-1A显示较好的疏水性能,使其比BFe30-1-1表现出较强的耐微生物腐蚀性能.

  19. The promise of insect genomics

    DEFF Research Database (Denmark)

    Grimmelikhuijzen, Cornelis J P; Cazzamali, Giuseppe; Williamson, Michael


    Insects are the largest animal group in the world and are ecologically and economically extremely important. This importance of insects is reflected by the existence of currently 24 insect genome projects. Our perspective discusses the state-of-the-art of these genome projects and the impacts tha...

  20. Cocoa/Cotton Comparative Genomics (United States)

    With genome sequence from two members of the Malvaceae family recently made available, we are exploring syntenic relationships, gene content, and evolutionary trajectories between the cacao and cotton genomes. An assembly of cacao (Theobroma cacao) using Illumina and 454 sequence technology yielded ...

  1. Genomic medicine: too great expectations? (United States)

    O'Rourke, P P


    As advances in genomic medicine have captured the interest and enthusiasm of the public, an unintended consequence has been the creation of unrealistic expectations. Because these expectations may have a negative impact on individuals as well as genomics in general, it is important that they be understood and confronted.

  2. Integrating genome assemblies with MAIA

    NARCIS (Netherlands)

    Nijkamp, J.F.; Winterbach, W.; Van den Broek, M.; Daran, J.M.; Reinders, M.J.T.; De Ridder, D.


    De novo assembly of a eukaryotic genome with next-generation sequencing data is still a challenging task. Over the past few years several assemblers have been developed, often suitable for one specific type of sequencing data. The number of known genomes is expanding rapidly, therefore it becomes po

  3. Bioinformatics for plant genome annotation

    NARCIS (Netherlands)

    Fiers, M.W.E.J.


    Large amounts of genome sequence data are available and much more will become available in the near future. A DNA sequence alone has, however, limited use. Genome annotation is required to assign biological interpretation to the DNA sequence. This thesis describ

  4. Plant cytogenetics in genome databases (United States)

    Cytogenetic maps provide an integrated representation of genetic and cytological information that can be used to enhance genome and chromosome research. As genome analysis technologies become more affordable, the density of markers on cytogenetic maps increases, making these resources more useful a...

  5. The UCSC Genome Browser Database

    DEFF Research Database (Denmark)

    Karolchik, D; Kuhn, R M; Baertsch, R


    The University of California, Santa Cruz, Genome Browser Database (GBD) provides integrated sequence and annotation data for a large collection of vertebrate and model organism genomes. Seventeen new assemblies have been added to the database in the past year, for a total coverage of 19 vertebrat...

  6. Comparative genomic hybridization: practical guidelines.

    NARCIS (Netherlands)

    Jeuken, J.W.M.; Sprenger, S.H.; Wesseling, P.


    Comparative genomic hybridization (CGH) is a technique used to identify copy number changes throughout a genome. Until now, hundreds of CGH studies have been published reporting chromosomal imbalances in a large variety of human neoplasms. Additionally, technical improvements of specific steps in a

  7. Fueling Future with Algal Genomics

    Energy Technology Data Exchange (ETDEWEB)

    Grigoriev, Igor


    Algae constitute a major component of fundamental eukaryotic diversity, play profound roles in the carbon cycle, and are prominent candidates for biofuel production. The US Department of Energy Joint Genome Institute (JGI) is leading the world in algal genome sequencing ( and contributes of the algal genome projects worldwide (GOLD database, 2012). The sequenced algal genomes offer catalogs of genes, networks, and pathways. The sequenced first of its kind genomes of a haptophyte E.huxleyii, chlorarachniophyte B.natans, and cryptophyte G.theta fill the gaps in the eukaryotic tree of life and carry unique genes and pathways as well as molecular fossils of secondary endosymbiosis. Natural adaptation to conditions critical for industrial production is encoded in algal genomes, for example, growth of A.anophagefferens at very high cell densities during the harmful algae blooms or a global distribution across diverse environments of E.huxleyii, able to live on sparse nutrients due to its expanded pan-genome. Communications and signaling pathways can be derived from simple symbiotic systems like lichens or complex marine algae metagenomes. Collectively these datasets derived from algal genomics contribute to building a comprehensive parts list essential for algal biofuel development.

  8. Genome editing in cardiovascular diseases. (United States)

    Strong, Alanna; Musunuru, Kiran


    Genome-editing tools, which include zinc finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), and clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated 9 (Cas9) systems, have emerged as an invaluable technology to achieve somatic and germline genomic manipulation in cells and model organisms for multiple applications, including the creation of knockout alleles, introducing desired mutations into genomic DNA, and inserting novel transgenes. Genome editing is being rapidly adopted into all fields of biomedical research, including the cardiovascular field, where it has facilitated a greater understanding of lipid metabolism, electrophysiology, cardiomyopathies, and other cardiovascular disorders, has helped to create a wider variety of cellular and animal models, and has opened the door to a new class of therapies. In this Review, we discuss the applications of genome-editing technology throughout cardiovascular disease research and the prospect of in vivo genome-editing therapies in the future. We also describe some of the existing limitations of genome-editing tools that will need to be addressed if cardiovascular genome editing is to achieve its full scientific and therapeutic potential.

  9. International genomic evaluation methods for dairy cattle (United States)

    Background Genomic evaluations are rapidly replacing traditional evaluation systems used for dairy cattle selection. Economies of scale in genomics promote cooperation across country borders. Genomic information can be transferred across countries using simple conversion equations, by modifying mult...

  10. Genomic Heritability: What Is It?

    DEFF Research Database (Denmark)

    de los Campos, Gustavo; Sorensen, Daniel; Gianola, Daniel


    of phenotypic variance that can be explained by regression on molecular markers. This is so even though some of the assumptions commonly adopted for data analysis are at odds with important quantitative genetic concepts. In this article we develop theory that leads to a precise definition of parameters arising...... in high dimensional genomic regressions; we focus on the so-called genomic heritability: the proportion of variance of a trait that can be explained (in the population) by a linear regression on a set of markers. We propose a definition of this parameter that is framed within the classical quantitative...... genetics theory and show that the genomic heritability and the trait heritability parameters are equal only when all causal variants are typed. Further, we discuss how the genomic variance and genomic heritability, defined as quantitative genetic parameters, relate to parameters of statistical models...

  11. Genomics in Neurological Disorders

    Institute of Scientific and Technical Information of China (English)

    Guangchun Han; Jiya Sun; Jiajia Wang; Zhouxian Bai; Fuhai Song; Hongxing Lei


    Neurological disorders comprise a variety of complex diseases in the central nervous system, which can be roughly classified as neurodegenerative diseases and psychiatric disorders. The basic and translational research of neurological disorders has been hindered by the difficulty in accessing the pathological center (i.e., the brain) in live patients. The rapid advancement of sequencing and array technologies has made it possible to investigate the disease mechanism and biomarkers from a systems perspective. In this review, recent progresses in the discovery of novel risk genes, treatment targets and peripheral biomarkers employing genomic technologies will be dis-cussed. Our major focus will be on two of the most heavily investigated neurological disorders, namely Alzheimer’s disease and autism spectrum disorder.

  12. The Video Genome

    CERN Document Server

    Bronstein, Alexander M; Kimmel, Ron


    Fast evolution of Internet technologies has led to an explosive growth of video data available in the public domain and created unprecedented challenges in the analysis, organization, management, and control of such content. The problems encountered in video analysis such as identifying a video in a large database (e.g. detecting pirated content in YouTube), putting together video fragments, finding similarities and common ancestry between different versions of a video, have analogous counterpart problems in genetic research and analysis of DNA and protein sequences. In this paper, we exploit the analogy between genetic sequences and videos and propose an approach to video analysis motivated by genomic research. Representing video information as video DNA sequences and applying bioinformatic algorithms allows to search, match, and compare videos in large-scale databases. We show an application for content-based metadata mapping between versions of annotated video.

  13. Genomics of sex determination. (United States)

    Zhang, Jisen; Boualem, Adnane; Bendahmane, Abdelhafid; Ming, Ray


    Sex determination is a major switch in the evolutionary history of angiosperm, resulting 11% monoecious and dioecious species. The genomic sequences of papaya sex chromosomes unveiled the molecular basis of recombination suppression in the sex determination region, and candidate genes for sex determination. Identification and analyses of sex determination genes in cucurbits and maize demonstrated conservation of sex determination mechanism in one lineage and divergence between the two systems. Epigenetic control and hormonal influence of sex determination were elucidated in both plants and animals. Intensive investigation of potential sex determination genes in model species will improve our understanding of sex determination gene network. Such network will in turn accelerate the identification of sex determination genes in dioecious species with sex chromosomes, which are burdensome due to no recombination in sex determining regions. The sex determination genes in dioecious species are crucial for understanding the origin of dioecy and sex chromosomes, particularly in their early stage of evolution.

  14. Sequencing the maize genome. (United States)

    Martienssen, Robert A; Rabinowicz, Pablo D; O'Shaughnessy, Andrew; McCombie, W Richard


    Sequencing of complex genomes can be accomplished by enriching shotgun libraries for genes. In maize, gene-enrichment by copy-number normalization (high C(0)t) and methylation filtration (MF) have been used to generate up to two-fold coverage of the gene-space with less than 1 million sequencing reads. Simulations using sequenced bacterial artificial chromosome (BAC) clones predict that 5x coverage of gene-rich regions, accompanied by less than 1x coverage of subclones from BAC contigs, will generate high-quality mapped sequence that meets the needs of geneticists while accommodating unusually high levels of structural polymorphism. By sequencing several inbred strains, we propose a strategy for capturing this polymorphism to investigate hybrid vigor or heterosis.

  15. The South Asian genome.

    Directory of Open Access Journals (Sweden)

    John C Chambers

    Full Text Available The genetic sequence variation of people from the Indian subcontinent who comprise one-quarter of the world's population, is not well described. We carried out whole genome sequencing of 168 South Asians, along with whole-exome sequencing of 147 South Asians to provide deeper characterisation of coding regions. We identify 12,962,155 autosomal sequence variants, including 2,946,861 new SNPs and 312,738 novel indels. This catalogue of SNPs and indels amongst South Asians provides the first comprehensive map of genetic variation in this major human population, and reveals evidence for selective pressures on genes involved in skin biology, metabolism, infection and immunity. Our results will accelerate the search for the genetic variants underlying susceptibility to disorders such as type-2 diabetes and cardiovascular disease which are highly prevalent amongst South Asians.

  16. Privacy in the Genomic Era (United States)



    Genome sequencing technology has advanced at a rapid pace and it is now possible to generate highly-detailed genotypes inexpensively. The collection and analysis of such data has the potential to support various applications, including personalized medical services. While the benefits of the genomics revolution are trumpeted by the biomedical community, the increased availability of such data has major implications for personal privacy; notably because the genome has certain essential features, which include (but are not limited to) (i) an association with traits and certain diseases, (ii) identification capability (e.g., forensics), and (iii) revelation of family relationships. Moreover, direct-to-consumer DNA testing increases the likelihood that genome data will be made available in less regulated environments, such as the Internet and for-profit companies. The problem of genome data privacy thus resides at the crossroads of computer science, medicine, and public policy. While the computer scientists have addressed data privacy for various data types, there has been less attention dedicated to genomic data. Thus, the goal of this paper is to provide a systematization of knowledge for the computer science community. In doing so, we address some of the (sometimes erroneous) beliefs of this field and we report on a survey we conducted about genome data privacy with biomedical specialists. Then, after characterizing the genome privacy problem, we review the state-of-the-art regarding privacy attacks on genomic data and strategies for mitigating such attacks, as well as contextualizing these attacks from the perspective of medicine and public policy. This paper concludes with an enumeration of the challenges for genome data privacy and presents a framework to systematize the analysis of threats and the design of countermeasures as the field moves forward. PMID:26640318

  17. The UCSC Archaeal Genome Browser: 2012 update


    Chan, Patricia P.; Holmes, Andrew D.; Smith, Andrew M.; Tran, Danny; Lowe, Todd M.


    The UCSC Archaeal Genome Browser ( offers a graphical web-based resource for exploration and discovery within archaeal and other selected microbial genomes. By bringing together existing gene annotations, gene expression data, multiple-genome alignments, pre-computed sequence comparisons and other specialized analysis tracks, the genome browser is a powerful aggregator of varied genomic information. The genome browser environment maintains the current look-and-feel of ...

  18. Microbiology in the post-genomic era. (United States)

    Medini, Duccio; Serruto, Davide; Parkhill, Julian; Relman, David A; Donati, Claudio; Moxon, Richard; Falkow, Stanley; Rappuoli, Rino


    Genomics has revolutionized every aspect of microbiology. Now, 13 years after the first bacterial genome was sequenced, it is important to pause and consider what has changed in microbiology research as a consequence of genomics. In this article, we review the evolving field of bacterial typing and the genomic technologies that enable comparative analysis of multiple genomes and the metagenomes of complex microbial environments, and address the implications of the genomic era for the future of microbiology.

  19. Wheat Landrace Genome Diversity. (United States)

    Wingen, Luzie U; West, Claire; Leverington-Waite, Michelle; Collier, Sarah; Orford, Simon; Goram, Richard; Yang, Cai-Yun; King, Julie; Allen, Alexandra M; Burridge, Amanda; Edwards, Keith J; Griffiths, Simon


    Understanding the genomic complexity of bread wheat (Triticum aestivum L.) is a cornerstone in the quest to unravel the processes of domestication and the following adaptation of domesticated wheat to a wide variety of environments across the globe. Additionally, it is of importance for future improvement of the crop, particularly in the light of climate change. Focussing on the adaptation after domestication, a nested association mapping (NAM) panel of 60 segregating bi-parental populations were developed mainly involving landrace accessions from the core set of the Watkins hexaploid wheat collection optimized for genetic diversity (WINGEN et al. 2014). A modern spring elite variety, 'Paragon,' was used as common reference parent. Genetic maps were constructed following identical rules to make them comparable. In total, 1,611 linkage groups were identified, based on recombination from an estimated 126,300 crossover events over the whole NAM panel. A consensus map, named landrace consensus map (LRC) was constructed and contained 2,498 genetic loci. These newly developed genetics tools were used to investigate the rules underlying genome fluidity or rigidity, e.g. by comparing at marker distances and marker orders. In general, marker order was highly correlated, which provides support for strong synteny between bread wheat accessions. However, many exceptional cases of incongruent linkage groups and increased marker distances were also found. Segregation distortion was detected for many markers, sometimes as hot-spots present in different populations. Furthermore, evidence for translocations in at least 36 of the maps was found. These translocations fell, in general, into many different translocation classes, but a few translocation classes were found in several accessions, the most frequent one being the well known T5B:7B translocation. Loci involved in recombination rate, which is an interesting trait for plant breeding, were identified by QTL analyses using the

  20. Human myoblast genome therapy

    Institute of Scientific and Technical Information of China (English)

    Peter K Law; Leo A Bockeria; Choong-Chin Liew; Danlin M Law; Ping Lu; Eugene KW Sim; Khawja H Haider; Lei Ye; Xun Li; Margarita N Vakhromeeva; Ilia I Berishvili


    Human Myoblast Genome Therapy (HMGT) is a platform technology of cell transplantation, nuclear transfer, and tissue engineering. Unlike stem cells, myoblasts are differentiated, immature cells destined to become muscles. Myoblasts cultured from satellite cells of adult muscle biopsies survive, develop, and function to revitalize degenerative muscles upon transplantation. Injection injury activates regeneration of host myofibers that fuse with the engrafted myoblasts, sharing their nuclei in a common gene pool of the syncytium. Thus, through nuclear transfer and complementation, the normal human genome can be transferred into muscles of patients with genetic disorders to achieve phenotype repair or disease prevention. Myoblasts are safe and efficient gene transfer vehicles endogenous to muscles that constitute 50% of body weight. Results of over 280 HMGT procedures on Duchenne Muscular Dystrophy (DMD) subjects in the past 15 years demonstrated absolute safety. Myoblast-injected DMD muscles showed improved histology.Strength increase at 18 months post-operatively averaged 123%. In another application of HMGT on ischemic cardiomyopathy, the first human myoblast transfer into porcine myocardium revealed that it was safe and effective. Clinical trials on approximately 220 severe cardiomyopathy patients in 15 countries showed a <10% mortality. Most subjects received autologous cells implanted on the epicardial surface during coronory artery bypass graft, or injected on the endomyocardial surface percutaneously through guiding catheters. Significant increases in left ventricular ejection fraction, wall thickness, and wall motion have been reported, with reduction in perfusion defective areas, angina, and shortness of breath. As a new modality of treatment for disease in the skeletal muscle or myocardium, HMGT emerged as safe and effective. Large randomized multi-center trials are under way to confirm these preliminary results. The future of HMGT is bright and exciting

  1. Genomic SELEX: a discovery tool for genomic aptamers. (United States)

    Zimmermann, Bob; Bilusic, Ivana; Lorenz, Christina; Schroeder, Renée


    Genomic SELEX is a discovery tool for genomic aptamers, which are genomically encoded functional domains in nucleic acid molecules that recognize and bind specific ligands. When combined with genomic libraries and using RNA-binding proteins as baits, Genomic SELEX used with high-throughput sequencing enables the discovery of genomic RNA aptamers and the identification of RNA-protein interaction networks. Here we describe how to construct and analyze genomic libraries, how to choose baits for selections, how to perform the selection procedure and finally how to analyze the enriched sequences derived from deep sequencing. As a control procedure, we recommend performing a "Neutral" SELEX experiment in parallel to the selection, omitting the selection step. This control experiment provides a background signal for comparison with the positively selected pool. We also recommend deep sequencing the initial library in order to facilitate the final in silico analysis of enrichment with respect to the initial levels. Counter selection procedures, using modified or inactive baits, allow strengthening the binding specificity of the winning selected sequences.

  2. Plantagora: modeling whole genome sequencing and assembly of plant genomes.

    Directory of Open Access Journals (Sweden)

    Roger Barthelson

    Full Text Available BACKGROUND: Genomics studies are being revolutionized by the next generation sequencing technologies, which have made whole genome sequencing much more accessible to the average researcher. Whole genome sequencing with the new technologies is a developing art that, despite the large volumes of data that can be produced, may still fail to provide a clear and thorough map of a genome. The Plantagora project was conceived to address specifically the gap between having the technical tools for genome sequencing and knowing precisely the best way to use them. METHODOLOGY/PRINCIPAL FINDINGS: For Plantagora, a platform was created for generating simulated reads from several different plant genomes of different sizes. The resulting read files mimicked either 454 or Illumina reads, with varying paired end spacing. Thousands of datasets of reads were created, most derived from our primary model genome, rice chromosome one. All reads were assembled with different software assemblers, including Newbler, Abyss, and SOAPdenovo, and the resulting assemblies were evaluated by an extensive battery of metrics chosen for these studies. The metrics included both statistics of the assembly sequences and fidelity-related measures derived by alignment of the assemblies to the original genome source for the reads. The results were presented in a website, which includes a data graphing tool, all created to help the user compare rapidly the feasibility and effectiveness of different sequencing and assembly strategies prior to testing an approach in the lab. Some of our own conclusions regarding the different strategies were also recorded on the website. CONCLUSIONS/SIGNIFICANCE: Plantagora provides a substantial body of information for comparing different approaches to sequencing a plant genome, and some conclusions regarding some of the specific approaches. Plantagora also provides a platform of metrics and tools for studying the process of sequencing and assembly

  3. Inheritance of the yeast mitochondrial genome

    DEFF Research Database (Denmark)

    Piskur, Jure


    Mitochondrion, extrachromosomal genetics, intergenic sequences, genome size, mitochondrial DNA, petite mutation, yeast......Mitochondrion, extrachromosomal genetics, intergenic sequences, genome size, mitochondrial DNA, petite mutation, yeast...

  4. Genome Annotation Transfer Utility (GATU: rapid annotation of viral genomes using a closely related reference genome

    Directory of Open Access Journals (Sweden)

    Upton Chris


    Full Text Available Abstract Background Since DNA sequencing has become easier and cheaper, an increasing number of closely related viral genomes have been sequenced. However, many of these have been deposited in GenBank without annotations, severely limiting their value to researchers. While maintaining comprehensive genomic databases for a set of virus families at the Viral Bioinformatics Resource Center and Viral Bioinformatics – Canada, we found that researchers were unnecessarily spending time annotating viral genomes that were close relatives of already annotated viruses. We have therefore designed and implemented a novel tool, Genome Annotation Transfer Utility (GATU, to transfer annotations from a previously annotated reference genome to a new target genome, thereby greatly reducing this laborious task. Results GATU transfers annotations from a reference genome to a closely related target genome, while still giving the user final control over which annotations should be included. GATU also detects open reading frames present in the target but not the reference genome and provides the user with a variety of bioinformatics tools to quickly determine if these ORFs should also be included in the annotation. After this process is complete, GATU saves the newly annotated genome as a GenBank, EMBL or XML-format file. The software is coded in Java and runs on a variety of computer platforms. Its user-friendly Graphical User Interface is specifically designed for users trained in the biological sciences. Conclusion GATU greatly simplifies the initial stages of genome annotation by using a closely related genome as a reference. It is not intended to be a gene prediction tool or a "complete" annotation system, but we have found that it significantly reduces the time required for annotation of genes and mature peptides as well as helping to standardize gene names between related organisms by transferring reference genome

  5. The genome of Eucalyptus grandis

    Energy Technology Data Exchange (ETDEWEB)

    Myburg, Alexander A.; Grattapaglia, Dario; Tuskan, Gerald A.; Hellsten, Uffe; Hayes, Richard D.; Grimwood, Jane; Jenkins, Jerry; Lindquist, Erika; Tice, Hope; Bauer, Diane; Goodstein, David M.; Dubchak, Inna; Poliakov, Alexandre; Mizrachi, Eshchar; Kullan, Anand R. K.; Hussey, Steven G.; Pinard, Desre; van der Merwe, Karen; Singh, Pooja; van Jaarsveld, Ida; Silva-Junior, Orzenil B.; Togawa, Roberto C.; Pappas, Marilia R.; Faria, Danielle A.; Sansaloni, Carolina P.; Petroli, Cesar D.; Yang, Xiaohan; Ranjan, Priya; Tschaplinski, Timothy J.; Ye, Chu-Yu; Li, Ting; Sterck, Lieven; Vanneste, Kevin; Murat, Florent; Soler, Marçal; Clemente, Hélène San; Saidi, Naijib; Cassan-Wang, Hua; Dunand, Christophe; Hefer, Charles A.; Bornberg-Bauer, Erich; Kersting, Anna R.; Vining, Kelly; Amarasinghe, Vindhya; Ranik, Martin; Naithani, Sushma; Elser, Justin; Boyd, Alexander E.; Liston, Aaron; Spatafora, Joseph W.; Dharmwardhana, Palitha; Raja, Rajani; Sullivan, Christopher; Romanel, Elisson; Alves-Ferreira, Marcio; Külheim, Carsten; Foley, William; Carocha, Victor; Paiva, Jorge; Kudrna, David; Brommonschenkel, Sergio H.; Pasquali, Giancarlo; Byrne, Margaret; Rigault, Philippe; Tibbits, Josquin; Spokevicius, Antanas; Jones, Rebecca C.; Steane, Dorothy A.; Vaillancourt, René E.; Potts, Brad M.; Joubert, Fourie; Barry, Kerrie; Pappas, Georgios J.; Strauss, Steven H.; Jaiswal, Pankaj; Grima-Pettenati, Jacqueline; Salse, Jérôme; Van de Peer, Yves; Rokhsar, Daniel S.; Schmutz, Jeremy


    Eucalypts are the world s most widely planted hardwood trees. Their broad adaptability, rich species diversity, fast growth and superior multipurpose wood, have made them a global renewable resource of fiber and energy that mitigates human pressures on natural forests. We sequenced and assembled >94% of the 640 Mbp genome of Eucalyptus grandis into its 11 chromosomes. A set of 36,376 protein coding genes were predicted revealing that 34% occur in tandem duplications, the largest proportion found thus far in any plant genome. Eucalypts also show the highest diversity of genes for plant specialized metabolism that act as chemical defence against biotic agents and provide unique pharmaceutical oils. Resequencing of a set of inbred tree genomes revealed regions of strongly conserved heterozygosity, likely hotspots of inbreeding depression. The resequenced genome of the sister species E. globulus underscored the high inter-specific genome colinearity despite substantial genome size variation in the genus. The genome of E. grandis is the first reference for the early diverging Rosid order Myrtales and is placed here basal to the Eurosids. This resource expands knowledge on the unique biology of large woody perennials and provides a powerful tool to accelerate comparative biology, breeding and biotechnology.

  6. Functional genomics of intracellular bacteria. (United States)

    de Barsy, Marie; Greub, Gilbert


    During the genomic era, a large amount of whole-genome sequences accumulated, which identified many hypothetical proteins of unknown function. Rapidly, functional genomics, which is the research domain that assign a function to a given gene product, has thus been developed. Functional genomics of intracellular pathogenic bacteria exhibit specific peculiarities due to the fastidious growth of most of these intracellular micro-organisms, due to the close interaction with the host cell, due to the risk of contamination of experiments with host cell proteins and, for some strict intracellular bacteria such as Chlamydia, due to the absence of simple genetic system to manipulate the bacterial genome. To identify virulence factors of intracellular pathogenic bacteria, functional genomics often rely on bioinformatic analyses compared with model organisms such as Escherichia coli and Bacillus subtilis. The use of heterologous expression is another common approach. Given the intracellular lifestyle and the many effectors that are used by the intracellular bacteria to corrupt host cell functions, functional genomics is also often targeting the identification of new effectors such as those of the T4SS of Brucella and Legionella.

  7. Components of Adenovirus Genome Packaging (United States)

    Ahi, Yadvinder S.; Mittal, Suresh K.


    Adenoviruses (AdVs) are icosahedral viruses with double-stranded DNA (dsDNA) genomes. Genome packaging in AdV is thought to be similar to that seen in dsDNA containing icosahedral bacteriophages and herpesviruses. Specific recognition of the AdV genome is mediated by a packaging domain located close to the left end of the viral genome and is mediated by the viral packaging machinery. Our understanding of the role of various components of the viral packaging machinery in AdV genome packaging has greatly advanced in recent years. Characterization of empty capsids assembled in the absence of one or more components involved in packaging, identification of the unique vertex, and demonstration of the role of IVa2, the putative packaging ATPase, in genome packaging have provided compelling evidence that AdVs follow a sequential assembly pathway. This review provides a detailed discussion on the functions of the various viral and cellular factors involved in AdV genome packaging. We conclude by briefly discussing the roles of the empty capsids, assembly intermediates, scaffolding proteins, portal vertex and DNA encapsidating enzymes in AdV assembly and packaging. PMID:27721809

  8. [Genome editing of industrial microorganism]. (United States)

    Zhu, Linjiang; Li, Qi


    Genome editing is defined as highly-effective and precise modification of cellular genome in a large scale. In recent years, such genome-editing methods have been rapidly developed in the field of industrial strain improvement. The quickly-updating methods thoroughly change the old mode of inefficient genetic modification, which is "one modification, one selection marker, and one target site". Highly-effective modification mode in genome editing have been developed including simultaneous modification of multiplex genes, highly-effective insertion, replacement, and deletion of target genes in the genome scale, cut-paste of a large DNA fragment. These new tools for microbial genome editing will certainly be applied widely, and increase the efficiency of industrial strain improvement, and promote the revolution of traditional fermentation industry and rapid development of novel industrial biotechnology like production of biofuel and biomaterial. The technological principle of these genome-editing methods and their applications were summarized in this review, which can benefit engineering and construction of industrial microorganism.

  9. Genome size variation in the genus Avena. (United States)

    Yan, Honghai; Martin, Sara L; Bekele, Wubishet A; Latta, Robert G; Diederichsen, Axel; Peng, Yuanying; Tinker, Nicholas A


    Genome size is an indicator of evolutionary distance and a metric for genome characterization. Here, we report accurate estimates of genome size in 99 accessions from 26 species of Avena. We demonstrate that the average genome size of C genome diploid species (2C = 10.26 pg) is 15% larger than that of A genome species (2C = 8.95 pg), and that this difference likely accounts for a progression of size among tetraploid species, where AB genome configuration had similar genome sizes (average 2C = 25.74 pg). Genome size was mostly consistent within species and in general agreement with current information about evolutionary distance among species. Results also suggest that most of the polyploid species in Avena have experienced genome downsizing in relation to their diploid progenitors. Genome size measurements could provide additional quality control for species identification in germplasm collections, especially in cases where diploid and polyploid species have similar morphology.

  10. The bonobo genome compared with the chimpanzee and human genomes. (United States)

    Prüfer, Kay; Munch, Kasper; Hellmann, Ines; Akagi, Keiko; Miller, Jason R; Walenz, Brian; Koren, Sergey; Sutton, Granger; Kodira, Chinnappa; Winer, Roger; Knight, James R; Mullikin, James C; Meader, Stephen J; Ponting, Chris P; Lunter, Gerton; Higashino, Saneyuki; Hobolth, Asger; Dutheil, Julien; Karakoç, Emre; Alkan, Can; Sajjadian, Saba; Catacchio, Claudia Rita; Ventura, Mario; Marques-Bonet, Tomas; Eichler, Evan E; André, Claudine; Atencia, Rebeca; Mugisha, Lawrence; Junhold, Jörg; Patterson, Nick; Siebauer, Michael; Good, Jeffrey M; Fischer, Anne; Ptak, Susan E; Lachmann, Michael; Symer, David E; Mailund, Thomas; Schierup, Mikkel H; Andrés, Aida M; Kelso, Janet; Pääbo, Svante


    Two African apes are the closest living relatives of humans: the chimpanzee (Pan troglodytes) and the bonobo (Pan paniscus). Although they are similar in many respects, bonobos and chimpanzees differ strikingly in key social and sexual behaviours, and for some of these traits they show more similarity with humans than with each other. Here we report the sequencing and assembly of the bonobo genome to study its evolutionary relationship with the chimpanzee and human genomes. We find that more than three per cent of the human genome is more closely related to either the bonobo or the chimpanzee genome than these are to each other. These regions allow various aspects of the ancestry of the two ape species to be reconstructed. In addition, many of the regions that overlap genes may eventually help us understand the genetic basis of phenotypes that humans share with one of the two apes to the exclusion of the other.

  11. The bonobo genome compared with the chimpanzee and human genomes (United States)

    Prüfer, Kay; Munch, Kasper; Hellmann, Ines; Akagi, Keiko; Miller, Jason R.; Walenz, Brian; Koren, Sergey; Sutton, Granger; Kodira, Chinnappa; Winer, Roger; Knight, James R.; Mullikin, James C.; Meader, Stephen J.; Ponting, Chris P.; Lunter, Gerton; Higashino, Saneyuki; Hobolth, Asger; Dutheil, Julien; Karakoç, Emre; Alkan, Can; Sajjadian, Saba; Catacchio, Claudia Rita; Ventura, Mario; Marques-Bonet, Tomas; Eichler, Evan E.; André, Claudine; Atencia, Rebeca; Mugisha, Lawrence; Junhold, Jörg; Patterson, Nick; Siebauer, Michael; Good, Jeffrey M.; Fischer, Anne; Ptak, Susan E.; Lachmann, Michael; Symer, David E.; Mailund, Thomas; Schierup, Mikkel H.; Andrés, Aida M.; Kelso, Janet; Pääbo, Svante


    Two African apes are the closest living relatives of humans: the chimpanzee (Pan troglodytes) and the bonobo (Pan paniscus). Although they are similar in many respects, bonobos and chimpanzees differ strikingly in key social and sexual behaviours1–4, and for some of these traits they show more similarity with humans than with each other. Here we report the sequencing and assembly of the bonobo genome to study its evolutionary relationship with the chimpanzee and human genomes. We find that more than three per cent of the human genome is more closely related to either the bonobo or the chimpanzee genome than these are to each other. These regions allow various aspects of the ancestry of the two ape species to be reconstructed. In addition, many of the regions that overlap genes may eventually help us understand the genetic basis of phenotypes that humans share with one of the two apes to the exclusion of the other. PMID:22722832

  12. Recurring genomic breaks in independent lineages support genomic fragility

    Directory of Open Access Journals (Sweden)

    Hannenhalli Sridhar


    Full Text Available Abstract Background Recent findings indicate that evolutionary breaks in the genome are not randomly distributed, and that certain regions, so-called fragile regions, are predisposed to breakages. Previous approaches to the study of genomic fragility have examined the distribution of breaks, as well as the coincidence of breaks with segmental duplications and repeats, within a single species. In contrast, we investigate whether this regional fragility is an inherent genomic characteristic and is thus conserved over multiple independent lineages. Results We do this by quantifying the extent to which certain genomic regions are disrupted repeatedly in independent lineages. Our investigation, based on Human, Chimp, Mouse, Rat, Dog and Chicken, suggests that the propensity of a chromosomal region to break is significantly correlated among independent lineages, even when covariates are considered. Furthermore, the fragile regions are enriched for segmental duplications. Conclusion Based on a novel methodology, our work provides additional support for the existence of fragile regions.

  13. Genome Modeling System: A Knowledge Management Platform for Genomics.

    Directory of Open Access Journals (Sweden)

    Malachi Griffith


    Full Text Available In this work, we present the Genome Modeling System (GMS, an analysis information management system capable of executing automated genome analysis pipelines at a massive scale. The GMS framework provides detailed tracking of samples and data coupled with reliable and repeatable analysis pipelines. The GMS also serves as a platform for bioinformatics development, allowing a large team to collaborate on data analysis, or an individual researcher to leverage the work of others effectively within its data management system. Rather than separating ad-hoc analysis from rigorous, reproducible pipelines, the GMS promotes systematic integration between the two. As a demonstration of the GMS, we performed an integrated analysis of whole genome, exome and transcriptome sequencing data from a breast cancer cell line (HCC1395 and matched lymphoblastoid line (HCC1395BL. These data are available for users to test the software, complete tutorials and develop novel GMS pipeline configurations. The GMS is available at

  14. Radiation Induced Genomic Instability

    Energy Technology Data Exchange (ETDEWEB)

    Morgan, William F.


    Radiation induced genomic instability can be observed in the progeny of irradiated cells multiple generations after irradiation of parental cells. The phenotype is well established both in vivo (Morgan 2003) and in vitro (Morgan 2003), and may be critical in radiation carcinogenesis (Little 2000, Huang et al. 2003). Instability can be induced by both the deposition of energy in irradiated cells as well as by signals transmitted by irradiated (targeted) cells to non-irradiated (non-targeted) cells (Kadhim et al. 1992, Lorimore et al. 1998). Thus both targeted and non-targeted cells can pass on the legacy of radiation to their progeny. However the radiation induced events and cellular processes that respond to both targeted and non-targeted radiation effects that lead to the unstable phenotype remain elusive. The cell system we have used to study radiation induced genomic instability utilizes human hamster GM10115 cells. These cells have a single copy of human chromosome 4 in a background of hamster chromosomes. Instability is evaluated in the clonal progeny of irradiated cells and a clone is considered unstable if it contains three or more metaphase sub-populations involving unique rearrangements of the human chromosome (Marder and Morgan 1993). Many of these unstable clones have been maintained in culture for many years and have been extensively characterized. As initially described by Clutton et al., (Clutton et al. 1996) many of our unstable clones exhibit persistently elevated levels of reactive oxygen species (Limoli et al. 2003), which appear to be due dysfunctional mitochondria (Kim et al. 2006, Kim et al. 2006). Interestingly, but perhaps not surprisingly, our unstable clones do not demonstrate a “mutator phenotype” (Limoli et al. 1997), but they do continue to rearrange their genomes for many years. The limiting factor with this system is the target – the human chromosome. While some clones demonstrate amplification of this chromosome and thus lend

  15. Human genome. 1993 Program report

    Energy Technology Data Exchange (ETDEWEB)


    The purpose of this report is to update the Human Genome 1991-92 Program Report and provide new information on the DOE genome program to researchers, program managers, other government agencies, and the interested public. This FY 1993 supplement includes abstracts of 60 new or renewed projects and listings of 112 continuing and 28 completed projects. These two reports, taken together, present the most complete published view of the DOE Human Genome Program through FY 1993. Research is progressing rapidly toward 15-year goals of mapping and sequencing the DNA of each of the 24 different human chromosomes.

  16. Capturing prokaryotic dark matter genomes. (United States)

    Gasc, Cyrielle; Ribière, Céline; Parisot, Nicolas; Beugnot, Réjane; Defois, Clémence; Petit-Biderre, Corinne; Boucher, Delphine; Peyretaillade, Eric; Peyret, Pierre


    Prokaryotes are the most diverse and abundant cellular life forms on Earth. Most of them, identified by indirect molecular approaches, belong to microbial dark matter. The advent of metagenomic and single-cell genomic approaches has highlighted the metabolic capabilities of numerous members of this dark matter through genome reconstruction. Thus, linking functions back to the species has revolutionized our understanding of how ecosystem function is sustained by the microbial world. This review will present discoveries acquired through the illumination of prokaryotic dark matter genomes by these innovative approaches.

  17. [Targeted genome modifications using TALEN]. (United States)

    Dupret, Barbara; Angrand, Pierre-Olivier


    Precise modifications of genomes have been one of the biggest goals in the fields of biotechnology and biomedical research. Recent discovery of TALE (transcription activator-like effectors) and the engineering of customized TALEN (transcription activator-like effector nucleases) allowed rapid genome editing in a variety of cell types and different model organisms. TALEN are molecular scissors used to induce a wide range of specific and efficient genomic modifications. TALEN promise to have profound impacts on biological and medical research over the coming years.

  18. The Materials Genome Project (United States)

    Aourag, H.


    In the past, the search for new and improved materials was characterized mostly by the use of empirical, trial- and-error methods. This picture of materials science has been changing as the knowledge and understanding of fundamental processes governing a material's properties and performance (namely, composition, structure, history, and environment) have increased. In a number of cases, it is now possible to predict a material's properties before it has even been manufactured thus greatly reducing the time spent on testing and development. The objective of modern materials science is to tailor a material (starting with its chemical composition, constituent phases, and microstructure) in order to obtain a desired set of properties suitable for a given application. In the short term, the traditional "empirical" methods for developing new materials will be complemented to a greater degree by theoretical predictions. In some areas, computer simulation is already used by industry to weed out costly or improbable synthesis routes. Can novel materials with optimized properties be designed by computers? Advances in modelling methods at the atomic level coupled with rapid increases in computer capabilities over the last decade have led scientists to answer this question with a resounding "yes'. The ability to design new materials from quantum mechanical principles with computers is currently one of the fastest growing and most exciting areas of theoretical research in the world. The methods allow scientists to evaluate and prescreen new materials "in silico" (in vitro), rather than through time consuming experimentation. The Materials Genome Project is to pursue the theory of large scale modeling as well as powerful methods to construct new materials, with optimized properties. Indeed, it is the intimate synergy between our ability to predict accurately from quantum theory how atoms can be assembled to form new materials and our capacity to synthesize novel materials atom

  19. Genomics, environmental genomics and the issue of microbial species. (United States)

    Ward, D M; Cohan, F M; Bhaya, D; Heidelberg, J F; Kühl, M; Grossman, A


    A microbial species concept is crucial for interpreting the variation detected by genomics and environmental genomics among cultivated microorganisms and within natural microbial populations. Comparative genomic analyses of prokaryotic species as they are presently described and named have led to the provocative idea that prokaryotes may not form species as we think about them for plants and animals. There are good reasons to doubt whether presently recognized prokaryotic species are truly species. To achieve a better understanding of microbial species, we believe it is necessary to (i) re-evaluate traditional approaches in light of evolutionary and ecological theory, (ii) consider that different microbial species may have evolved in different ways and (iii) integrate genomic, metagenomic and genome-wide expression approaches with ecological and evolutionary theory. Here, we outline how we are using genomic methods to (i) identify ecologically distinct populations (ecotypes) predicted by theory to be species-like fundamental units of microbial communities, and (ii) test their species-like character through in situ distribution and gene expression studies. By comparing metagenomic sequences obtained from well-studied hot spring cyanobacterial mats with genomic sequences of two cultivated cyanobacterial ecotypes, closely related to predominant native populations, we can conduct in situ population genetics studies that identify putative ecotypes and functional genes that determine the ecotypes' ecological distinctness. If individuals within microbial communities are found to be grouped into ecologically distinct, species-like populations, knowing about such populations should guide us to a better understanding of how genomic variation is linked to community function.

  20. Challenges in Whole-Genome Annotation of Pyrosequenced Eukaryotic Genomes

    Energy Technology Data Exchange (ETDEWEB)

    Kuo, Alan; Grigoriev, Igor


    Pyrosequencing technologies such as 454/Roche and Solexa/Illumina vastly lower the cost of nucleotide sequencing compared to the traditional Sanger method, and thus promise to greatly expand the number of sequenced eukaryotic genomes. However, the new technologies also bring new challenges such as shorter reads and new kinds and higher rates of sequencing errors, which complicate genome assembly and gene prediction. At JGI we are deploying 454 technology for the sequencing and assembly of ever-larger eukaryotic genomes. Here we describe our first whole-genome annotation of a purely 454-sequenced fungal genome that is larger than a yeast (>30 Mbp). The pezizomycotine (filamentous ascomycote) Aspergillus carbonarius belongs to the Aspergillus section Nigri species complex, members of which are significant as platforms for bioenergy and bioindustrial technology, as members of soil microbial communities and players in the global carbon cycle, and as agricultural toxigens. Application of a modified version of the standard JGI Annotation Pipeline has so far predicted ~;;10k genes. ~;;12percent of these preliminary annotations suffer a potential frameshift error, which is somewhat higher than the ~;;9percent rate in the Sanger-sequenced and conventionally assembled and annotated genome of fellow Aspergillus section Nigri member A. niger. Also,>90percent of A. niger genes have potential homologs in the A. carbonarius preliminary annotation. Weconclude, and with further annotation and comparative analysis expect to confirm, that 454 sequencing strategies provide a promising substrate for annotation of modestly sized eukaryotic genomes. We will also present results of annotation of a number of other pyrosequenced fungal genomes of bioenergy interest.

  1. Identification of genomic sites for CRISPR/Cas9-based genome editing in the Vitis vinifera genome (United States)

    CRISPR/Cas9 has been recently demonstrated as an effective and popular genome editing tool for modifying genomes of human, animals, microorganisms, and plants. Success of such genome editing is highly dependent on the availability of suitable target sites in the genomes to be edited. Many specific t...

  2. The Global Cancer Genomics Consortium: interfacing genomics and cancer medicine. (United States)


    The Global Cancer Genomics Consortium (GCGC) is an international collaborative platform that amalgamates cancer biologists, cutting-edge genomics, and high-throughput expertise with medical oncologists and surgical oncologists; they address the most important translational questions that are central to cancer research and treatment. The annual GCGC symposium was held at the Advanced Centre for Treatment Research and Education in Cancer, Mumbai, India, from November 9 to 11, 2011. The symposium showcased international next-generation sequencing efforts that explore cancer-specific transcriptomic changes, single-nucleotide polymorphism, and copy number variations in various types of cancers, as well as the structural genomics approach to develop new therapeutic targets and chemical probes. From the spectrum of studies presented at the symposium, it is evident that the translation of emerging cancer genomics knowledge into clinical applications can only be achieved through the integration of multidisciplinary expertise. In summary, the GCGC symposium provided practical knowledge on structural and cancer genomics approaches, as well as an exclusive platform for focused cancer genomics endeavors.

  3. The CGView Server: a comparative genomics tool for circular genomes. (United States)

    Grant, Jason R; Stothard, Paul


    The CGView Server generates graphical maps of circular genomes that show sequence features, base composition plots, analysis results and sequence similarity plots. Sequences can be supplied in raw, FASTA, GenBank or EMBL format. Additional feature or analysis information can be submitted in the form of GFF (General Feature Format) files. The server uses BLAST to compare the primary sequence to up to three comparison genomes or sequence sets. The BLAST results and feature information are converted to a graphical map showing the entire sequence, or an expanded and more detailed view of a region of interest. Several options are included to control which types of features are displayed and how the features are drawn. The CGView Server can be used to visualize features associated with any bacterial, plasmid, chloroplast or mitochondrial genome, and can aid in the identification of conserved genome segments, instances of horizontal gene transfer, and differences in gene copy number. Because a collection of sequences can be used in place of a comparison genome, maps can also be used to visualize regions of a known genome covered by newly obtained sequence reads. The CGView Server can be accessed at

  4. Genomic Datasets for Cancer Research (United States)

    A variety of datasets from genome-wide association studies of cancer and other genotype-phenotype studies, including sequencing and molecular diagnostic assays, are available to approved investigators through the Extramural National Cancer Institute Data Access Committee.

  5. Collaborators | Office of Cancer Genomics (United States)

    The TARGET initiative is jointly managed within the National Cancer Institute (NCI) by the Office of Cancer Genomics (OCG)Opens in a New Tab and the Cancer Therapy Evaluation Program (CTEP)Opens in a New Tab.

  6. Genomic understanding of glioblastoma expanded (United States)

    Glioblastoma multiforme (GBM) was the first cancer type to be systematically studied by TCGA in 2008. In a new, complementary report, TCGA experts examined more than 590 GBM samples--the largest to date utilizing genomic characterization techniques and ne

  7. Genomic Resources for Cancer Epidemiology (United States)

    This page provides links to research resources, complied by the Epidemiology and Genomics Research Program, that may be of interest to genetic epidemiologists conducting cancer research, but is not exhaustive.

  8. Gene finding in novel genomes

    Directory of Open Access Journals (Sweden)

    Korf Ian


    Full Text Available Abstract Background Computational gene prediction continues to be an important problem, especially for genomes with little experimental data. Results I introduce the SNAP gene finder which has been designed to be easily adaptable to a variety of genomes. In novel genomes without an appropriate gene finder, I demonstrate that employing a foreign gene finder can produce highly inaccurate results, and that the most compatible parameters may not come from the nearest phylogenetic neighbor. I find that foreign gene finders are more usefully employed to bootstrap parameter estimation and that the resulting parameters can be highly accurate. Conclusion Since gene prediction is sensitive to species-specific parameters, every genome needs a dedicated gene finder.

  9. Genome engineering in human cells. (United States)

    Song, Minjung; Kim, Young-Hoon; Kim, Jin-Soo; Kim, Hyongbum


    Genome editing in human cells is of great value in research, medicine, and biotechnology. Programmable nucleases including zinc-finger nucleases, transcription activator-like effector nucleases, and RNA-guided engineered nucleases recognize a specific target sequence and make a double-strand break at that site, which can result in gene disruption, gene insertion, gene correction, or chromosomal rearrangements. The target sequence complexities of these programmable nucleases are higher than 3.2 mega base pairs, the size of the haploid human genome. Here, we briefly introduce the structure of the human genome and the characteristics of each programmable nuclease, and review their applications in human cells including pluripotent stem cells. In addition, we discuss various delivery methods for nucleases, programmable nickases, and enrichment of gene-edited human cells, all of which facilitate efficient and precise genome editing in human cells.

  10. Structural variations in pig genomes

    NARCIS (Netherlands)

    Paudel, Y.


    Abstract Paudel, Y. (2015). Structural variations in pig genomes. PhD thesis, Wageningen University, the Netherlands Structural variations are chromosomal rearrangements such as insertions-deletions (INDELs), duplications, inversions, translocations, and copy number variations (CNVs

  11. Genomics and Health Impact Update (United States)

    ... Publications Birth Defects/ Child Health Cancer Cardiovascular Diseases Chronic Disease Ethics, Policy and Law Genomics in Practice Newborn Screening Pharmacogenomics Reproductive Health Tools/ Databases AMD Clips News Concepts/ Comments Pathogenicity/ Antimicrobial Resistance Epidemiology/ ...

  12. Empowering marine science through genomics

    NARCIS (Netherlands)

    Volckaert, F.A M J; Barbier, M.; Canario, A; Olsen, J.L.; Wesnigk, J; Clark, M; Boyen, C


    Marine scientists in Europe summarize their successes with genome technologies in the marine sciences and make a plea for a concerted international effort to raise greater public education for support. (C) 2008 Elsevier B.V. All rights reserved.

  13. International network of cancer genome projects

    NARCIS (Netherlands)

    Hudson, Thomas J.; Anderson, Warwick; Aretz, Axel; Barker, Anna D.; Bell, Cindy; Bernabe, Rosa R.; Bhan, M. K.; Calvo, Fabien; Eerola, Iiro; Gerhard, Daniela S.; Guttmacher, Alan; Guyer, Mark; Hemsley, Fiona M.; Jennings, Jennifer L.; Kerr, David; Klatt, Peter; Kolar, Patrik; Kusuda, Jun; Lane, David P.; Laplace, Frank; Lu, Youyong; Nettekoven, Gerd; Ozenberger, Brad; Peterson, Jane; Rao, T. S.; Remacle, Jacques; Schafer, Alan J.; Shibata, Tatsuhiro; Stratton, Michael R.; Vockley, Joseph G.; Watanabe, Koichi; Yang, Huanming; Yuen, Matthew M. F.; Knoppers, M.; Bobrow, Martin; Cambon-Thomsen, Anne; Dressler, Lynn G.; Dyke, Stephanie O. M.; Joly, Yann; Kato, Kazuto; Kennedy, Karen L.; Nicolas, Pilar; Parker, Michael J.; Rial-Sebbag, Emmanuelle; Romeo-Casabona, Carlos M.; Shaw, Kenna M.; Wallace, Susan; Wiesner, Georgia L.; Zeps, Nikolajs; Lichter, Peter; Biankin, Andrew V.; Chabannon, Christian; Chin, Lynda; Clement, Bruno; de Alava, Enrique; Degos, Francoise; Ferguson, Martin L.; Geary, Peter; Hayes, D. Neil; Johns, Amber L.; Nakagawa, Hidewaki; Penny, Robert; Piris, Miguel A.; Sarin, Rajiv; Scarpa, Aldo; Shibata, Tatsuhiro; van de Vijver, Marc; Futreal, P. Andrew; Aburatani, Hiroyuki; Bayes, Monica; Bowtell, David D. L.; Campbell, Peter J.; Estivill, Xavier; Grimmond, Sean M.; Gut, Ivo; Hirst, Martin; Lopez-Otin, Carlos; Majumder, Partha; Marra, Marco; Nakagawa, Hidewaki; Ning, Zemin; Puente, Xose S.; Ruan, Yijun; Shibata, Tatsuhiro; Stratton, Michael R.; Stunnenberg, Hendrik G.; Swerdlow, Harold; Velculescu, Victor E.; Wilson, Richard K.; Xue, Hong H.; Yang, Liu; Spellman, Paul T.; Bader, Gary D.; Boutros, Paul C.; Campbell, Peter J.; Flicek, Paul; Getz, Gad; Guigo, Roderic; Guo, Guangwu; Haussler, David; Heath, Simon; Hubbard, Tim J.; Jiang, Tao; Jones, Steven M.; Li, Qibin; Lopez-Bigas, Nuria; Luo, Ruibang; Pearson, John V.; Puente, Xose S.; Quesada, Victor; Raphael, Benjamin J.; Sander, Chris; Shibata, Tatsuhiro; Speed, Terence P.; Stuart, Joshua M.; Teague, Jon W.; Totoki, Yasushi; Tsunoda, Tatsuhiko; Valencia, Alfonso; Wheeler, David A.; Wu, Honglong; Zhao, Shancen; Zhou, Guangyu; Stein, Lincoln D.; Guigo, Roderic; Hubbard, Tim J.; Joly, Yann; Jones, Steven M.; Lathrop, Mark; Lopez-Bigas, Nuria; Ouellette, B. F. Francis; Spellman, Paul T.; Teague, Jon W.; Thomas, Gilles; Valencia, Alfonso; Yoshida, Teruhiko; Kennedy, Karen L.; Axton, Myles; Dyke, Stephanie O. M.; Futreal, P. Andrew; Gunter, Chris; Guyer, Mark; McPherson, John D.; Miller, Linda J.; Ozenberger, Brad; Kasprzyk, Arek; Zhang, Junjun; Haider, Syed A.; Wang, Jianxin; Yung, Christina K.; Cross, Anthony; Liang, Yong; Gnaneshan, Saravanamuttu; Guberman, Jonathan; Hsu, Jack; Bobrow, Martin; Chalmers, Don R. C.; Hasel, Karl W.; Joly, Yann; Kaan, Terry S. H.; Kennedy, Karen L.; Knoppers, Bartha M.; Lowrance, William W.; Masui, Tohru; Nicolas, Pilar; Rial-Sebbag, Emmanuelle; Rodriguez, Laura Lyman; Vergely, Catherine; Yoshida, Teruhiko; Grimmond, Sean M.; Biankin, Andrew V.; Bowtell, David D. L.; Cloonan, Nicole; Defazio, Anna; Eshleman, James R.; Etemadmoghadam, Dariush; Gardiner, Brooke A.; Kench, James G.; Scarpa, Aldo; Sutherland, Robert L.; Tempero, Margaret A.; Waddell, Nicola J.; Wilson, Peter J.; Gallinger, Steve; Tsao, Ming-Sound; Shaw, Patricia A.; Petersen, Gloria M.; Mukhopadhyay, Debabrata; Chin, Lynda; DePinho, Ronald A.; Thayer, Sarah; Muthuswamy, Lakshmi; Shazand, Kamran; Beck, Timothy; Sam, Michelle; Timms, Lee; Ballin, Vanessa; Lu, Youyong; Ji, Jiafu; Zhang, Xiuqing; Chen, Feng; Hu, Xueda; Zhou, Guangyu; Yang, Qi; Tian, Geng; Zhang, Lianhai; Xing, Xiaofang; Li, Xianghong; Zhu, Zhenggang; Yu, Yingyan; Yu, Jun; Yang, Huanming; Lathrop, Mark; Tost, Joerg; Brennan, Paul; Holcatova, Ivana; Zaridze, David; Brazma, Alvis; Egevad, Lars; Prokhortchouk, Egor; Banks, Rosamonde Elizabeth; Uhlen, Mathias; Cambon-Thomsen, Anne; Viksna, Juris; Ponten, Fredrik; Skryabin, Konstantin; Stratton, Michael R.; Futreal, P. Andrew; Birney, Ewan; Borg, Ake; Borresen-Dale, Anne-Lise; Caldas, Carlos; Foekens, John A.; Martin, Sancha; Reis-Filho, Jorge S.; Richardson, Andrea L.; Sotiriou, Christos; Stunnenberg, Hendrik G.; Thomas, Gilles; van de Vijver, Marc; van't Veer, Laura; Birnbaum, Daniel; Blanche, Helene; Boucher, Pascal; Boyault, Sandrine; Chabannon, Christian; Gut, Ivo; Masson-Jacquemier, Jocelyne D.; Lathrop, Mark; Pauporte, Iris; Pivot, Xavier; Vincent-Salomon, Anne; Tabone, Eric; Theillet, Charles; Thomas, Gilles; Tost, Joerg; Treilleux, Isabelle; Bioulac-Sage, Paulette; Clement, Bruno; Decaens, Thomas; Degos, Francoise; Franco, Dominique; Gut, Ivo; Gut, Marta; Heath, Simon; Lathrop, Mark; Samuel, Didier; Thomas, Gilles; Zucman-Rossi, Jessica; Lichter, Peter; Eils, Roland; Brors, Benedikt; Korbel, Jan O.; Korshunov, Andrey; Landgraf, Pablo; Lehrach, Hans; Pfister, Stefan; Radlwimmer, Bernhard; Reifenberger, Guido; Taylor, Michael D.; von Kalle, Christof; Majumder, Partha P.; Sarin, Rajiv; Scarpa, Aldo; Pederzoli, Paolo; Lawlor, Rita T.; Delledonne, Massimo; Bardelli, Alberto; Biankin, Andrew V.; Grimmond, Sean M.; Gress, Thomas; Klimstra, David; Zamboni, Giuseppe; Shibata, Tatsuhiro; Nakamura, Yusuke; Nakagawa, Hidewaki; Kusuda, Jun; Tsunoda, Tatsuhiko; Miyano, Satoru; Aburatani, Hiroyuki; Kato, Kazuto; Fujimoto, Akihiro; Yoshida, Teruhiko; Campo, Elias; Lopez-Otin, Carlos; Estivill, Xavier; Guigo, Roderic; de Sanjose, Silvia; Piris, Miguel A.; Montserrat, Emili; Gonzalez-Diaz, Marcos; Puente, Xose S.; Jares, Pedro; Valencia, Alfonso; Himmelbaue, Heinz; Quesada, Victor; Bea, Silvia; Stratton, Michael R.; Futreal, P. Andrew; Campbell, Peter J.; Vincent-Salomon, Anne; Richardson, Andrea L.; Reis-Filho, Jorge S.; van de Vijver, Marc; Thomas, Gilles; Masson-Jacquemier, Jocelyne D.; Aparicio, Samuel; Borg, Ake; Borresen-Dale, Anne-Lise; Caldas, Carlos; Foekens, John A.; Stunnenberg, Hendrik G.; van't Veer, Laura; Easton, Douglas F.; Spellman, Paul T.; Martin, Sancha; Chin, Lynda; Collins, Francis S.; Compton, Carolyn C.; Ferguson, Martin L.; Getz, Gad; Gunter, Chris; Guyer, Mark; Hayes, D. Neil; Lander, Eric S.; Ozenberger, Brad; Penny, Robert; Peterson, Jane; Sander, Chris; Speed, Terence P.; Spellman, Paul T.; Wheeler, David A.; Wilson, Richard K.; Chin, Lynda; Knoppers, Bartha M.; Lander, Eric S.; Lichter, Peter; Stratton, Michael R.; Bobrow, Martin; Burke, Wylie; Collins, Francis S.; DePinho, Ronald A.; Easton, Douglas F.; Futreal, P. Andrew; Green, Anthony R.; Guyer, Mark; Hamilton, Stanley R.; Hubbard, Tim J.; Kallioniemi, Olli P.; Kennedy, Karen L.; Ley, Timothy J.; Liu, Edison T.; Lu, Youyong; Majumder, Partha; Marra, Marco; Ozenberger, Brad; Peterson, Jane; Schafer, Alan J.; Spellman, Paul T.; Stunnenberg, Hendrik G.; Wainwright, Brandon J.; Wilson, Richard K.; Yang, Huanming


    The International Cancer Genome Consortium (ICGC) was launched to coordinate large-scale cancer genome studies in tumours from 50 different cancer types and/or subtypes that are of clinical and societal importance across the globe. Systematic studies of more than 25,000 cancer genomes at the genomic

  14. Draft Genome Sequence of Lactobacillus rhamnosus 2166.


    Karlyshev, Andrey V.; Melnikov, Vyacheslav G.; Kosarev, Igor V.; Abramov, Vyacheslav M.


    In this report, we present a draft sequence of the genome of Lactobacillus rhamnosus strain 2166, a potential novel probiotic. Genome annotation and read mapping onto a reference genome of L. rhamnosus strain GG allowed for the identification of the differences and similarities in the genomic contents and gene arrangements of these strains.

  15. Genomic Aspects of Research Involving Polyploid Plants

    Energy Technology Data Exchange (ETDEWEB)

    Yang, Xiaohan [ORNL; Ye, Chuyu [ORNL; Tschaplinski, Timothy J [ORNL; Wullschleger, Stan D [ORNL; Tuskan, Gerald A [ORNL


    Almost all extant plant species have spontaneously doubled their genomes at least once in their evolutionary histories, resulting in polyploidy which provided a rich genomic resource for evolutionary processes. Moreover, superior polyploid clones have been created during the process of crop domestication. Polyploid plants generated by evolutionary processes and/or crop domestication have been the intentional or serendipitous focus of research dealing with the dynamics and consequences of genome evolution. One of the new trends in genomics research is to create synthetic polyploid plants which provide materials for studying the initial genomic changes/responses immediately after polyploid formation. Polyploid plants are also used in functional genomics research to study gene expression in a complex genomic background. In this review, we summarize the recent progress in genomics research involving ancient, young, and synthetic polyploid plants, with a focus on genome size evolution, genomics diversity, genomic rearrangement, genetic and epigenetic changes in duplicated genes, gene discovery, and comparative genomics. Implications on plant sciences including evolution, functional genomics, and plant breeding are presented. It is anticipated that polyploids will be a regular subject of genomics research in the foreseeable future as the rapid advances in DNA sequencing technology create unprecedented opportunities for discovering and monitoring genomic and transcriptomic changes in polyploid plants. The fast accumulation of knowledge on polyploid formation, maintenance, and divergence at whole-genome and subgenome levels will not only help plant biologists understand how plants have evolved and diversified, but also assist plant breeders in designing new strategies for crop improvement.

  16. Application of bioinformatics in cardiovascular genomics

    NARCIS (Netherlands)

    Tragante Do O, V.


    Genetic research made a remarkable progress in the past 20 years, with the Human Genome Project, which sequenced an entire genome; the HapMap project, that identified common genetic variation in hundreds of genomes from different populations; and the 1000 Genomes project, which identified common and

  17. 2004 Structural, Function and Evolutionary Genomics

    Energy Technology Data Exchange (ETDEWEB)

    Douglas L. Brutlag Nancy Ryan Gray


    This Gordon conference will cover the areas of structural, functional and evolutionary genomics. It will take a systematic approach to genomics, examining the evolution of proteins, protein functional sites, protein-protein interactions, regulatory networks, and metabolic networks. Emphasis will be placed on what we can learn from comparative genomics and entire genomes and proteomes.

  18. Contact | Office of Cancer Genomics (United States)

    For more information about the Office of Cancer Genomics, please contact: Office of Cancer Genomics National Cancer Institute 31 Center Drive, 10A07 Bethesda, Maryland 20892-2580 Phone: (301) 451-8027 Fax: (301) 480-4368 Email: *Please note that this site will not function properly in Internet Explorer unless you completely turn off the Compatibility View*

  19. Genomic heritability: what is it?

    Directory of Open Access Journals (Sweden)

    Gustavo de Los Campos


    Full Text Available Whole-genome regression methods are being increasingly used for the analysis and prediction of complex traits and diseases. In human genetics, these methods are commonly used for inferences about genetic parameters, such as the amount of genetic variance among individuals or the proportion of phenotypic variance that can be explained by regression on molecular markers. This is so even though some of the assumptions commonly adopted for data analysis are at odds with important quantitative genetic concepts. In this article we develop theory that leads to a precise definition of parameters arising in high dimensional genomic regressions; we focus on the so-called genomic heritability: the proportion of variance of a trait that can be explained (in the population by a linear regression on a set of markers. We propose a definition of this parameter that is framed within the classical quantitative genetics theory and show that the genomic heritability and the trait heritability parameters are equal only when all causal variants are typed. Further, we discuss how the genomic variance and genomic heritability, defined as quantitative genetic parameters, relate to parameters of statistical models commonly used for inferences, and indicate potential inferential problems that are assessed further using simulations. When a large proportion of the markers used in the analysis are in LE with QTL the likelihood function can be misspecified. This can induce a sizable finite-sample bias and, possibly, lack of consistency of likelihood (or Bayesian estimates. This situation can be encountered if the individuals in the sample are distantly related and linkage disequilibrium spans over short regions. This bias does not negate the use of whole-genome regression models as predictive machines; however, our results indicate that caution is needed when using marker-based regressions for inferences about population parameters such as the genomic heritability.

  20. Plague in the genomic area. (United States)

    Drancourt, M


    With plague being not only a subject of interest for historians, but still a disease of public health concern in several countries, mainly in Africa, there were hopes that analyses of the Yersinia pestis genomes would put an end to this deadly epidemic pathogen. Genomics revealed that Y. pestis isolates evolved from Yersinia pseudotuberculosis in Central Asia some millennia ago, after the acquisition of two Y. pestis-specific plasmids balanced genomic reduction parallel with the expansion of insertion sequences, illustrating the modern concept that, except for the acquisition of plasmid-borne toxin-encoding genes, the increased virulence of Y. pestis resulted from gene loss rather than gene acquisition. The telluric persistence of Y. pestis reminds us of this close relationship, and matters in terms of plague epidemiology. Whereas biotype Orientalis isolates spread worldwide, the Antiqua and Medievalis isolates showed more limited expansion. In addition to animal ectoparasites, human ectoparasites such as the body louse may have participated in this expansion and in devastating historical epidemics. The recent analysis of a Black Death genome indicated that it was more closely related to the Orientalis branch than to the Medievalis branch. Modern Y. pestis isolates grossly exhibit the same gene content, but still undergo micro-evolution in geographically limited areas by differing in the genome architecture, owing to inversions near insertion sequences and the stabilization of the YpfPhi prophage in Orientalis biotype isolates. Genomics have provided several new molecular tools for the genotyping and phylogeographical tracing of isolates and description of plague foci. However, genomics and post-genomics approaches have not yet provided new tools for the prevention, diagnosis and management of plague patients and the plague epidemics still raging in some sub-Saharan countries.

  1. Genomic methods take the plunge

    DEFF Research Database (Denmark)

    Cammen, Kristina M.; Andrews, Kimberly R.; Carroll, Emma L.


    The dramatic increase in the application of genomic techniques to non-model organisms (NMOs) over the past decade has yielded numerous valuable contributions to evolutionary biology and ecology, many of which would not have been possible with traditional genetic markers. We review this recent...... of fitness, demography, and population structure. Here we review the primary options for generating genomic data, introduce several emerging techniques, and discuss the suitability of each approach for different applications in the study of NMOs....

  2. Probability landscapes for integrative genomics

    Directory of Open Access Journals (Sweden)

    Benecke Arndt


    Full Text Available Abstract Background The comprehension of the gene regulatory code in eukaryotes is one of the major challenges of systems biology, and is a requirement for the development of novel therapeutic strategies for multifactorial diseases. Its bi-fold degeneration precludes brute force and statistical approaches based on the genomic sequence alone. Rather, recursive integration of systematic, whole-genome experimental data with advanced statistical regulatory sequence predictions needs to be developed. Such experimental approaches as well as the prediction tools are only starting to become available and increasing numbers of genome sequences and empirical sequence annotations are under continual discovery-driven change. Furthermore, given the complexity of the question, a decade(s long multi-laboratory effort needs to be envisioned. These constraints need to be considered in the creation of a framework that can pave a road to successful comprehension of the gene regulatory code. Results We introduce here a concept for such a framework, based entirely on systematic annotation in terms of probability profiles of genomic sequence using any type of relevant experimental and theoretical information and subsequent cross-correlation analysis in hypothesis-driven model building and testing. Conclusion Probability landscapes, which include as reference set the probabilistic representation of the genomic sequence, can be used efficiently to discover and analyze correlations amongst initially heterogeneous and un-relatable descriptions and genome-wide measurements. Furthermore, this structure is usable as a support for automatically generating and testing hypotheses for alternative gene regulatory grammars and the evaluation of those through statistical analysis of the high-dimensional correlations between genomic sequence, sequence annotations, and experimental data. Finally, this structure provides a concrete and tangible basis for attempting to formulate a

  3. Genome Exploitation and Bioinformatics Tools (United States)

    de Jong, Anne; van Heel, Auke J.; Kuipers, Oscar P.

    Bioinformatic tools can greatly improve the efficiency of bacteriocin screening efforts by limiting the amount of strains. Different classes of bacteriocins can be detected in genomes by looking at different features. Finding small bacteriocins can be especially challenging due to low homology and because small open reading frames (ORFs) are often omitted from annotations. In this chapter, several bioinformatic tools/strategies to identify bacteriocins in genomes are discussed.

  4. Gender And The Human Genome

    Directory of Open Access Journals (Sweden)

    Chadwick Ruth


    Full Text Available Gender issues arise in relation to the human genome across a number of dimensions: the level of attention given to the nuclear genome as opposed to the mitochondrial; the level of basic scientific research; decision-making in the clinic related to both reproductive decision-making on the one hand, and diagnostic and predictive testing on the other; and wider societal implications. Feminist bioethics offers a useful perspective for addressing these issues.

  5. Genom-undersøgelser

    DEFF Research Database (Denmark)

    Mark, Edith


    Genom-undersøgelser bør anvendes varsomt, da de kan kompromittere den undersøgtes ret til ikke-viden, til selvbestemmelse og til privatliv. Myndighederne bør ikke forhindre borgere i at købe genom-undersøgelser hos private udbydere, uanset at testens sundhedsmæssige værdi kan være tvivlsom, men...... bør derudover sikre tilstrækkelig regulering • Såfremt genom-undersøgelser anvendes i forskning, bør forsøgspersoner ikke tilbydes tilbagemelding om fund af genetiske risikofaktorer • Såfremt genom-undersøgelser anvendes i diagnostik bør patienters ønsker om tilbagemelding af tilfældighedsfund aftales......, før undersøgelse igangsættes. Omfanget af tilbagemelding bør aftales i fællesskab mellem patient og læge • Genom-undersøgelser bør i både offentlig og privat regi være ledsaget af fyldestgørende og uvildig rådgivning og information • Information, rådgivning, henvisning og opfølgning på genom...

  6. The dynamic genome of Hydra (United States)

    Chapman, Jarrod A.; Kirkness, Ewen F.; Simakov, Oleg; Hampson, Steven E.; Mitros, Therese; Weinmaier, Therese; Rattei, Thomas; Balasubramanian, Prakash G.; Borman, Jon; Busam, Dana; Disbennett, Kathryn; Pfannkoch, Cynthia; Sumin, Nadezhda; Sutton, Granger G.; Viswanathan, Lakshmi Devi; Walenz, Brian; Goodstein, David M.; Hellsten, Uffe; Kawashima, Takeshi; Prochnik, Simon E.; Putnam, Nicholas H.; Shu, Shengquiang; Blumberg, Bruce; Dana, Catherine E.; Gee, Lydia; Kibler, Dennis F.; Law, Lee; Lindgens, Dirk; Martinez, Daniel E.; Peng, Jisong; Wigge, Philip A.; Bertulat, Bianca; Guder, Corina; Nakamura, Yukio; Ozbek, Suat; Watanabe, Hiroshi; Khalturin, Konstantin; Hemmrich, Georg; Franke, André; Augustin, René; Fraune, Sebastian; Hayakawa, Eisuke; Hayakawa, Shiho; Hirose, Mamiko; Hwang, Jung Shan; Ikeo, Kazuho; Nishimiya-Fujisawa, Chiemi; Ogura, Atshushi; Takahashi, Toshio; Steinmetz, Patrick R. H.; Zhang, Xiaoming; Aufschnaiter, Roland; Eder, Marie-Kristin; Gorny, Anne-Kathrin; Salvenmoser, Willi; Heimberg, Alysha M.; Wheeler, Benjamin M.; Peterson, Kevin J.; Böttger, Angelika; Tischler, Patrick; Wolf, Alexander; Gojobori, Takashi; Remington, Karin A.; Strausberg, Robert L.; Venter, J. Craig; Technau, Ulrich; Hobmayer, Bert; Bosch, Thomas C. G.; Holstein, Thomas W.; Fujisawa, Toshitaka; Bode, Hans R.; David, Charles N.; Rokhsar, Daniel S.; Steele, Robert E.


    The freshwater cnidarian Hydra was first described in 17021 and has been the object of study for 300 years. Experimental studies of Hydra between 1736 and 1744 culminated in the discovery of asexual reproduction of an animal by budding, the first description of regeneration in an animal, and successful transplantation of tissue between animals2. Today, Hydra is an important model for studies of axial patterning3, stem cell biology4 and regeneration5. Here we report the genome of Hydra magnipapillata and compare it to the genomes of the anthozoan Nematostella vectensis6 and other animals. The Hydra genome has been shaped by bursts of transposable element expansion, horizontal gene transfer, trans-splicing, and simplification of gene structure and gene content that parallel simplification of the Hydra life cycle. We also report the sequence of the genome of a novel bacterium stably associated with H. magnipapillata. Comparisons of the Hydra genome to the genomes of other animals shed light on the evolution of epithelia, contractile tissues, developmentally regulated transcription factors, the Spemann–Mangold organizer, pluripotency genes and the neuromuscular junction. PMID:20228792

  7. Comparative genomics of Helicobacter pylori

    Institute of Scientific and Technical Information of China (English)

    Quan-Jiang Dong; Qing Wang; Ying-Nin Xin; Ni Li; Shi-Ying Xuan


    Genomic sequences have been determined for a number of strains of Helicobacter pylori (H pylori) and related bacteria.With the development of microarray analysis and the wide use of subtractive hybridization techniques,comparative studies have been carried out with respect to the interstrain differences between H pylori and inter-species differences in the genome of related bacteria.It was found that the core genome of H pylori constitutes 1111 genes that are determinants of the species properties.A great pool of auxillary genes are mainly from the categories of cag pathogenicity islands,outer membrane proteins,restriction-modification system and hypothetical proteins of unknown function.Persistence of H pylori in the human stomach leads to the diversification of the genome.Comparative genomics suggest that a host jump has occurs from humans to felines.Candidate genes specific for the development of the gastric diseases were identified.With the aid of proteomics,population genetics and other molecular methods,future comparative genomic studies would dramatically promote our understanding of the evolution,pathogenesis and microbiology of H pylori.

  8. Genomics and marine microbial ecology. (United States)

    Pedrós-Alió, Carlos


    Genomics has brought about a revolution in all fields of biology. Before the development of microbial ecology in the 1970s, microbes were not even considered in marine ecological studies. Today we know that half of the total primary production of the planet must be credited to microorganisms. This and other discoveries have changed dramatically the perspective and the focus of marine microbial ecology. The application of genomics-based approaches has provided new challenges and has allowed the discovery of novel functions, an appreciation of the great diversity of microorganisms, and the introduction of controversial ideas regarding the concepts of species, genome, and niche. Nevertheless, thorough knowledge of the traditional disciplines of biology is necessary to explore the possibilities arising from these new insights. This work reviews the different genomic techniques that can be applied to marine microbial ecology, including both sequencing of the complete genomes of microorganisms and metagenomics, which, in turn, can be complemented with the study of mRNAs (transcriptomics) and proteins (proteomics). The example of proteorhodopsin illustrates the type of information that can be gained from these approaches. A genomics perspective constitutes a map that will allow microbiologists to focus their research on potentially more productive aspects.

  9. Value of a newly sequenced bacterial genome

    DEFF Research Database (Denmark)

    Barbosa, Eudes; Aburjaile, Flavia F; Ramos, Rommel Tj;


    Next-generation sequencing (NGS) technologies have made high-throughput sequencing available to medium- and small-size laboratories, culminating in a tidal wave of genomic information. The quantity of sequenced bacterial genomes has not only brought excitement to the field of genomics but also...... in an exponential increase in draft (partial data) genome deposits in public databases. If no further interests are expressed for a particular bacterial genome, it is more likely that the sequencing of its genome will be limited to a draft stage, and the painstaking tasks of completing the sequencing of its genome...

  10. Genomic medicine implementation: learning by example. (United States)

    Williams, Marc S


    Genomic Medicine is beginning to emerge into clinical practice. The National Human Genome Research Institute's Genomic Medicine Working Group consists of organizations that have begun to implement some aspect of genomic medicine (e.g., family history, systematic implementation of Mendelian disease program, pharmacogenomics, whole exome/genome sequencing). This article concisely reviews the working group and provides a broader context for the articles in the special issue including an assessment of anticipated provider needs and ethical, legal, and social issues relevant to the implementation of genomic medicine. The challenges of implementation of innovation in clinical practice and the potential value of genomic medicine are discussed.

  11. The integrated microbial genome resource of analysis. (United States)

    Checcucci, Alice; Mengoni, Alessio


    Integrated Microbial Genomes and Metagenomes (IMG) is a biocomputational system that allows to provide information and support for annotation and comparative analysis of microbial genomes and metagenomes. IMG has been developed by the US Department of Energy (DOE)-Joint Genome Institute (JGI). IMG platform contains both draft and complete genomes, sequenced by Joint Genome Institute and other public and available genomes. Genomes of strains belonging to Archaea, Bacteria, and Eukarya domains are present as well as those of viruses and plasmids. Here, we provide some essential features of IMG system and case study for pangenome analysis.

  12. The fishes of Genome 10K

    KAUST Repository

    Bernardi, Giacomo


    The Genome 10K project aims to sequence the genomes of 10,000 vertebrates, representing approximately one genome for each vertebrate genus. Since fishes (cartilaginous fishes, ray-finned fishes and lobe-finned fishes) represent more than 50% of extant vertebrates, it is planned to target 4,000 fish genomes. At present, nearly 60 fish genomes are being sequenced at various public funded labs, and under a Genome 10K and BGI pilot project. An additional 100 fishes have been identified for sequencing in the next phase of Genome 10K project. © 2012 Elsevier B.V.

  13. Genome size and genome evolution in diploid Triticeae species. (United States)

    Eilam, T; Anikster, Y; Millet, E; Manisterski, J; Sagi-Assif, O; Feldman, M


    One of the intriguing issues concerning the dynamics of plant genomes is the occurrence of intraspecific variation in nuclear DNA amount. The aim of this work was to assess the ranges of intraspecific, interspecific, and intergeneric variation in nuclear DNA content of diploid species of the tribe Triticeae (Poaceae) and to examine the relation between life form or habitat and genome size. Altogether, 438 plants representing 272 lines that belong to 22 species were analyzed. Nuclear DNA content was estimated by flow cytometry. Very small intraspecific variation in DNA amount was found between lines of Triticeae diploid species collected from different habitats or between different morphs. In contrast to the constancy in nuclear DNA amount at the intraspecific level, there are significant differences in genome size between the various diploid species. Within the genus Aegilops, the 1C DNA amount ranged from 4.84 pg in A. caudata to 7.52 pg in A. sharonensis; among genera, the 1C DNA amount ranged from 4.18 pg in Heteranthelium piliferum to 9.45 pg in Secale montanum. No evidence was found for a smaller genome size in annual, self-pollinating species relative to perennial, cross-pollinating ones. Diploids that grow in the southern part of the group's distribution have larger genomes than those growing in other parts of the distribution. The contrast between the low variation at the intraspecific level and the high variation at the interspecific one suggests that changes in genome size originated in close temporal proximity to the speciation event, i.e., before, during, or immediately after it. The possible effects of sudden changes in genome size on speciation processes are discussed.

  14. Genomics and museum specimens. (United States)

    Nachman, Michael W


    Nearly 25 years ago, Allan Wilson and colleagues isolated DNA sequences from museum specimens of kangaroo rats (Dipodomys panamintinus) and compared these sequences with those from freshly collected animals (Thomas et al. 1990). The museum specimens had been collected up to 78 years earlier, so the two samples provided a direct temporal comparison of patterns of genetic variation. This was not the first time DNA sequences had been isolated from preserved material, but it was the first time it had been carried out with a population sample. Population geneticists often try to make inferences about the influence of historical processes such as selection, drift, mutation and migration on patterns of genetic variation in the present. The work of Wilson and colleagues was important in part because it suggested a way in which population geneticists could actually study genetic change in natural populations through time, much the same way that experimentalists can do with artificial populations in the laboratory. Indeed, the work of Thomas et al. (1990) spawned dozens of studies in which museum specimens were used to compare historical and present-day genetic diversity (reviewed in Wandeler et al. 2007). All of these studies, however, were limited by the same fundamental problem: old DNA is degraded into short fragments. As a consequence, these studies mostly involved PCR amplification of short templates, usually short stretches of mitochondrial DNA or microsatellites. In this issue, Bi et al. (2013) report a breakthrough that should open the door to studies of genomic variation in museum specimens. They used target enrichment (exon capture) and next-generation (Illumina) sequencing to compare patterns of genetic variation in historic and present-day population samples of alpine chipmunks (Tamias alpinus) (Fig. 1). The historic samples came from specimens collected in 1915, so the temporal span of this comparison is nearly 100 years.

  15. The Genomic Code: Genome Evolution and Potential Applications

    KAUST Repository

    Bernardi, Giorgio


    The genome of metazoans is organized according to a genomic code which comprises three laws: 1) Compositional correlations hold between contiguous coding and non-coding sequences, as well as among the three codon positions of protein-coding genes; these correlations are the consequence of the fact that the genomes under consideration consist of fairly homogeneous, long (≥200Kb) sequences, the isochores; 2) Although isochores are defined on the basis of purely compositional properties, GC levels of isochores are correlated with all tested structural and functional properties of the genome; 3) GC levels of isochores are correlated with chromosome architecture from interphase to metaphase; in the case of interphase the correlation concerns isochores and the three-dimensional “topological associated domains” (TADs); in the case of mitotic chromosomes, the correlation concerns isochores and chromosomal bands. Finally, the genomic code is the fourth and last pillar of molecular biology, the first three pillars being 1) the double helix structure of DNA; 2) the regulation of gene expression in prokaryotes; and 3) the genetic code.

  16. GIPSy: Genomic island prediction software. (United States)

    Soares, Siomar C; Geyik, Hakan; Ramos, Rommel T J; de Sá, Pablo H C G; Barbosa, Eudes G V; Baumbach, Jan; Figueiredo, Henrique C P; Miyoshi, Anderson; Tauch, Andreas; Silva, Artur; Azevedo, Vasco


    Bacteria are highly diverse organisms that are able to adapt to a broad range of environments and hosts due to their high genomic plasticity. Horizontal gene transfer plays a pivotal role in this genome plasticity and in evolution by leaps through the incorporation of large blocks of genome sequences, ordinarily known as genomic islands (GEIs). GEIs may harbor genes encoding virulence, metabolism, antibiotic resistance and symbiosis-related functions, namely pathogenicity islands (PAIs), metabolic islands (MIs), resistance islands (RIs) and symbiotic islands (SIs). Although many software for the prediction of GEIs exist, they only focus on PAI prediction and present other limitations, such as complicated installation and inconvenient user interfaces. Here, we present GIPSy, the genomic island prediction software, a standalone and user-friendly software for the prediction of GEIs, built on our previously developed pathogenicity island prediction software (PIPS). We also present four application cases in which we crosslink data from literature to PAIs, MIs, RIs and SIs predicted by GIPSy. Briefly, GIPSy correctly predicted the following previously described GEIs: 13 PAIs larger than 30kb in Escherichia coli CFT073; 1 MI for Burkholderia pseudomallei K96243, which seems to be a miscellaneous island; 1 RI of Acinetobacter baumannii AYE, named AbaR1; and, 1 SI of Mesorhizobium loti MAFF303099 presenting a mosaic structure. GIPSy is the first life-style-specific genomic island prediction software to perform analyses of PAIs, MIs, RIs and SIs, opening a door for a better understanding of bacterial genome plasticity and the adaptation to new traits.

  17. Genomic Treasure Troves: Complet Genome Sequencing of Herbarium and Insect Museum Specimens

    NARCIS (Netherlands)

    Staats, M.; Erkens, R.H.J.; Vossenberg, van de B.; Wieringa, J.J.; Kraaijeveld, K.; Stielow, B.; Geml, J.; Richardson, J.E.; Bakker, F.T.


    Unlocking the vast genomic diversity stored in natural history collections would create unprecedented opportunities for genome-scale evolutionary, phylogenetic, domestication and population genomic studies. Many researchers have been discouraged from using historical specimens in molecular studies b

  18. Human Genome Education Program

    Energy Technology Data Exchange (ETDEWEB)

    Richard Myers; Lane Conn


    The funds from the DOE Human Genome Program, for the project period 2/1/96 through 1/31/98, have provided major support for the curriculum development and field testing efforts for two high school level instructional units: Unit 1, ''Exploring Genetic Conditions: Genes, Culture and Choices''; and Unit 2, ''DNA Snapshots: Peaking at Your DNA''. In the original proposal, they requested DOE support for the partial salary and benefits of a Field Test Coordinator position to: (1) complete the field testing and revision of two high school curriculum units, and (2) initiate the education of teachers using these units. During the project period of this two-year DOE grant, a part-time Field-Test Coordinator was hired (Ms. Geraldine Horsma) and significant progress has been made in both of the original proposal objectives. Field testing for Unit 1 has occurred in over 12 schools (local and non-local sites with diverse student populations). Field testing for Unit 2 has occurred in over 15 schools (local and non-local sites) and will continue in 12-15 schools during the 96-97 school year. For both curricula, field-test sites and site teachers were selected for their interest in genetics education and in hands-on science education. Many of the site teachers had no previous experience with HGEP or the unit under development. Both of these first-year biology curriculum units, which contain genetics, biotechnology, societal, ethical and cultural issues related to HGP, are being implemented in many local and non-local schools (SF Bay Area, Southern California, Nebraska, Hawaii, and Texas) and in programs for teachers. These units will reach over 10,000 students in the SF Bay Area and continues to receive support from local corporate and private philanthropic organizations. Although HGEP unit development is nearing completion for both units, data is still being gathered and analyzed on unit effectiveness and student learning. The final field

  19. Molecular characterization of encoding plasmid-mediated ESBLs and AmpC β-lactamases genes in Citrobacter freundii%质粒介导产ESBLs与AmpCβ-内酰胺酶基因弗氏柠檬酸杆菌的研究

    Institute of Scientific and Technical Information of China (English)

    陈坚; 余方友


    OBJECTIVE To investigate the resistant mechanism of Citrobacter freundii which coexisted with ESBLs and AmpC genes. METHODS A multi-resistant Citrobacter freundii was isolated from hospital by VITEK-60 system. The detection of ESBLs was performed by the CLSI-recommended confirmatory test, Cefoxitin three-dimentional test was presented to identify AmpC β-lactamases, the mimimal inhibitative concentration (MIC) was determined by E-test. Polymerase chain reaction(PCR) and sequencing were carried out for analyzing the encoding genes of β-lactamases. Conjugation study was performed to determine whether resistant genes were likely transferred by plasmid. RESULTS The isolate was highly resistant to ceftazidime (MICs,96 jug/ml), cefotaxime (MlCs,96 μg/ml), cefoxitin(MICs.256 μg/ml) , aztreonam(MICs, 192 fig/ml) , ampicillin(MICs,>256 μg/ml) and sinomin compositea(MICs,>32 fig/ml). The clinical isolate produced AmpCs and ESBLs. The presence of blacrx-M-3 and blaCMY-2 of clinical isolate were identified by PCR and sequenced. Those genes of clinical isolate could be transferred to Escherichia coli J53 through conjugation. CONCLUSION Citrobacter freundii carries ESBLs and AmpC β-lactamases genes synchronously, which were mediated by plasmid.%目的 研究一株同时产ESBLs和AmpC β-内酰胺酶弗氏柠檬酸杆菌(CFR)的耐药机制.方法 2008年1月从临床尿液标本中分离出多药耐药弗氏柠檬酸杆菌1株,采用双纸片扩散法检测产ESBLs,头孢西丁三维试验检测AmpC酶,E-test法测定抗菌药物最低抑菌浓度(MIC),聚合酶链反应(PCR)检测产ESBss和AmpC酶基因,DNA测序决定基因型;接合试验测定耐药基因的转移性.结果 临床分离出一株同时产ESBLs和AmpCβ-内酰胺酶的多药耐药弗氏柠檬酸杆菌,对头孢他啶、头孢噻肟、头孢西丁、氨曲南、氨苄西林、磺胺甲噁唑/甲氧苄啶的MIC分别为96、96、256、192、>256、>32 μg/ml,PCR扩增及测序

  20. Allele coding in genomic evaluation

    Directory of Open Access Journals (Sweden)

    Christensen Ole F


    Full Text Available Abstract Background Genomic data are used in animal breeding to assist genetic evaluation. Several models to estimate genomic breeding values have been studied. In general, two approaches have been used. One approach estimates the marker effects first and then, genomic breeding values are obtained by summing marker effects. In the second approach, genomic breeding values are estimated directly using an equivalent model with a genomic relationship matrix. Allele coding is the method chosen to assign values to the regression coefficients in the statistical model. A common allele coding is zero for the homozygous genotype of the first allele, one for the heterozygote, and two for the homozygous genotype for the other allele. Another common allele coding changes these regression coefficients by subtracting a value from each marker such that the mean of regression coefficients is zero within each marker. We call this centered allele coding. This study considered effects of different allele coding methods on inference. Both marker-based and equivalent models were considered, and restricted maximum likelihood and Bayesian methods were used in inference. Results Theoretical derivations showed that parameter estimates and estimated marker effects in marker-based models are the same irrespective of the allele coding, provided that the model has a fixed general mean. For the equivalent models, the same results hold, even though different allele coding methods lead to different genomic relationship matrices. Calculated genomic breeding values are independent of allele coding when the estimate of the general mean is included into the values. Reliabilities of estimated genomic breeding values calculated using elements of the inverse of the coefficient matrix depend on the allele coding because different allele coding methods imply different models. Finally, allele coding affects the mixing of Markov chain Monte Carlo algorithms, with the centered coding being

  1. AcCNET (Accessory Genome Constellation Network): comparative genomics software for accessory genome analysis using bipartite networks. (United States)

    Lanza, Val F; Baquero, Fernando; de la Cruz, Fernando; Coque, Teresa M


    AcCNET (Accessory genome Constellation Network) is a Perl application that aims to compare accessory genomes of a large number of genomic units, both at qualitative and quantitative levels. Using the proteomes extracted from the analysed genomes, AcCNET creates a bipartite network compatible with standard network analysis platforms. AcCNET allows merging phylogenetic and functional information about the concerned genomes, thus improving the capability of current methods of network analysis. The AcCNET bipartite network opens a new perspective to explore the pangenome of bacterial species, focusing on the accessory genome behind the idiosyncrasy of a particular strain and/or population.

  2. Pseudomonas genomes: diverse and adaptable. (United States)

    Silby, Mark W; Winstanley, Craig; Godfrey, Scott A C; Levy, Stuart B; Jackson, Robert W


    Members of the genus Pseudomonas inhabit a wide variety of environments, which is reflected in their versatile metabolic capacity and broad potential for adaptation to fluctuating environmental conditions. Here, we examine and compare the genomes of a range of Pseudomonas spp. encompassing plant, insect and human pathogens, and environmental saprophytes. In addition to a large number of allelic differences of common genes that confer regulatory and metabolic flexibility, genome analysis suggests that many other factors contribute to the diversity and adaptability of Pseudomonas spp. Horizontal gene transfer has impacted the capability of pathogenic Pseudomonas spp. in terms of disease severity (Pseudomonas aeruginosa) and specificity (Pseudomonas syringae). Genome rearrangements likely contribute to adaptation, and a considerable complement of unique genes undoubtedly contributes to strain- and species-specific activities by as yet unknown mechanisms. Because of the lack of conserved phenotypic differences, the classification of the genus has long been contentious. DNA hybridization and genome-based analyses show close relationships among members of P. aeruginosa, but that isolates within the Pseudomonas fluorescens and P. syringae species are less closely related and may constitute different species. Collectively, genome sequences of Pseudomonas spp. have provided insights into pathogenesis and the genetic basis for diversity and adaptation.

  3. The genome of Chenopodium quinoa. (United States)

    Jarvis, David E; Ho, Yung Shwen; Lightfoot, Damien J; Schmöckel, Sandra M; Li, Bo; Borm, Theo J A; Ohyanagi, Hajime; Mineta, Katsuhiko; Michell, Craig T; Saber, Noha; Kharbatia, Najeh M; Rupper, Ryan R; Sharp, Aaron R; Dally, Nadine; Boughton, Berin A; Woo, Yong H; Gao, Ge; Schijlen, Elio G W M; Guo, Xiujie; Momin, Afaque A; Negrão, Sónia; Al-Babili, Salim; Gehring, Christoph; Roessner, Ute; Jung, Christian; Murphy, Kevin; Arold, Stefan T; Gojobori, Takashi; Linden, C Gerard van der; van Loo, Eibertus N; Jellen, Eric N; Maughan, Peter J; Tester, Mark


    Chenopodium quinoa (quinoa) is a highly nutritious grain identified as an important crop to improve world food security. Unfortunately, few resources are available to facilitate its genetic improvement. Here we report the assembly of a high-quality, chromosome-scale reference genome sequence for quinoa, which was produced using single-molecule real-time sequencing in combination with optical, chromosome-contact and genetic maps. We also report the sequencing of two diploids from the ancestral gene pools of quinoa, which enables the identification of sub-genomes in quinoa, and reduced-coverage genome sequences for 22 other samples of the allotetraploid goosefoot complex. The genome sequence facilitated the identification of the transcription factor likely to control the production of anti-nutritional triterpenoid saponins found in quinoa seeds, including a mutation that appears to cause alternative splicing and a premature stop codon in sweet quinoa strains. These genomic resources are an important first step towards the genetic improvement of quinoa.

  4. The genome of Chenopodium quinoa

    KAUST Repository

    Jarvis, David E.


    Chenopodium quinoa (quinoa) is a highly nutritious grain identified as an important crop to improve world food security. Unfortunately, few resources are available to facilitate its genetic improvement. Here we report the assembly of a high-quality, chromosome-scale reference genome sequence for quinoa, which was produced using single-molecule real-time sequencing in combination with optical, chromosome-contact and genetic maps. We also report the sequencing of two diploids from the ancestral gene pools of quinoa, which enables the identification of sub-genomes in quinoa, and reduced-coverage genome sequences for 22 other samples of the allotetraploid goosefoot complex. The genome sequence facilitated the identification of the transcription factor likely to control the production of anti-nutritional triterpenoid saponins found in quinoa seeds, including a mutation that appears to cause alternative splicing and a premature stop codon in sweet quinoa strains. These genomic resources are an important first step towards the genetic improvement of quinoa.

  5. NCBI prokaryotic genome annotation pipeline. (United States)

    Tatusova, Tatiana; DiCuccio, Michael; Badretdin, Azat; Chetvernin, Vyacheslav; Nawrocki, Eric P; Zaslavsky, Leonid; Lomsadze, Alexandre; Pruitt, Kim D; Borodovsky, Mark; Ostell, James


    Recent technological advances have opened unprecedented opportunities for large-scale sequencing and analysis of populations of pathogenic species in disease outbreaks, as well as for large-scale diversity studies aimed at expanding our knowledge across the whole domain of prokaryotes. To meet the challenge of timely interpretation of structure, function and meaning of this vast genetic information, a comprehensive approach to automatic genome annotation is critically needed. In collaboration with Georgia Tech, NCBI has developed a new approach to genome annotation that combines alignment based methods with methods of predicting protein-coding and RNA genes and other functional elements directly from sequence. A new gene finding tool, GeneMarkS+, uses the combined evidence of protein and RNA placement by homology as an initial map of annotation to generate and modify ab initio gene predictions across the whole genome. Thus, the new NCBI's Prokaryotic Genome Annotation Pipeline (PGAP) relies more on sequence similarity when confident comparative data are available, while it relies more on statistical predictions in the absence of external evidence. The pipeline provides a framework for generation and analysis of annotation on the full breadth of prokaryotic taxonomy. For additional information on PGAP see and the NCBI Handbook,

  6. Evolutionary engineering by genome shuffling. (United States)

    Biot-Pelletier, Damien; Martin, Vincent J J


    An upsurge in the bioeconomy drives the need for engineering microorganisms with increasingly complex phenotypes. Gains in productivity of industrial microbes depend on the development of improved strains. Classical strain improvement programmes for the generation, screening and isolation of such mutant strains have existed for several decades. An alternative to traditional strain improvement methods, genome shuffling, allows the directed evolution of whole organisms via recursive recombination at the genome level. This review deals chiefly with the technical aspects of genome shuffling. It first presents the diversity of organisms and phenotypes typically evolved using this technology and then reviews available sources of genetic diversity and recombination methodologies. Analysis of the literature reveals that genome shuffling has so far been restricted to microorganisms, both prokaryotes and eukaryotes, with an overepresentation of antibiotics- and biofuel-producing microbes. Mutagenesis is the main source of genetic diversity, with few studies adopting alternative strategies. Recombination is usually done by protoplast fusion or sexual recombination, again with few exceptions. For both diversity and recombination, prospective methods that have not yet been used are also presented. Finally, the potential of genome shuffling for gaining insight into the genetic basis of complex phenotypes is also discussed.

  7. Accelerated genome engineering through multiplexing. (United States)

    Bao, Zehua; Cobb, Ryan E; Zhao, Huimin


    Throughout the biological sciences, the past 15 years have seen a push toward the analysis and engineering of biological systems at the organism level. Given the complexity of even the simplest organisms, though, to elicit a phenotype of interest often requires genotypic manipulation of several loci. By traditional means, sequential editing of genomic targets requires a significant investment of time and labor, as the desired editing event typically occurs at a very low frequency against an overwhelming unedited background. In recent years, the development of a suite of new techniques has greatly increased editing efficiency, opening up the possibility for multiple editing events to occur in parallel. Termed as multiplexed genome engineering, this approach to genome editing has greatly expanded the scope of possible genome manipulations in diverse hosts, ranging from bacteria to human cells. The enabling technologies for multiplexed genome engineering include oligonucleotide-based and nuclease-based methodologies, and their application has led to the great breadth of successful examples described in this review. While many technical challenges remain, there also exists a multiplicity of opportunities in this rapidly expanding field.

  8. How good is our genome? (United States)

    Weill, Jean-Claude; Radman, Miroslav


    Our genome has evolved to perpetuate itself through the maintenance of the species via an uninterrupted chain of reproductive somas. Accordingly, evolution is not concerned with diseases occurring after the soma's reproductive stage. Following Richard Dawkins, we would like to reassert that we indeed live as disposable somas, slaves of our germline genome, but could soon start rebelling against such slavery. Cancer and its relation to the TP53 gene may offer a paradigmatic example. The observation that the latency period in cancer can be prolonged in mice by increasing the number of TP53 genes in their genome, suggests that sooner or later we will have to address the question of heritable disease avoidance via the manipulation of the human germline.

  9. Genome engineering in Vibrio cholerae

    DEFF Research Database (Denmark)

    Val, Marie-Eve; Skovgaard, Ole; Ducos-Galand, Magaly


    importance in public health, Vibrio cholerae, the causative agent of cholera, has become a preferred model to study bacteria with multipartite genomes. However, most in vivo studies in V. cholerae have been hampered by its genome architecture, as it is difficult to give phenotypes to a specific chromosome....... This difficulty was surmounted using a unique and powerful strategy based on massive rearrangement of prokaryotic genomes. We developed a site-specific recombination-based engineering tool, which allows targeted, oriented, and reciprocal DNA exchanges. Using this genetic tool, we obtained a panel of V. cholerae...... in V. cholerae and the general question concerning bacteria carrying circular chromosomes--by looking at the effect of chromosome size on topological issues. In this article, we show that Dam, RctB, and ParA2/ParB2 are strictly essential for chrII origin maintenance, and we formally demonstrate...

  10. Bioprospecting in the genomic age. (United States)

    Hicks, Michael A; Prather, Kristala L J


    The genomic revolution promises great advances in the search for useful biocatalysts. Function-based metagenomic approaches have identified several enzymes with properties that make them useful candidates for a variety of bioprocesses. As DNA sequencing costs continue to decline, the volume of genomic data, along with their corresponding predicted protein sequences, will continue to increase dramatically, necessitating new approaches to leverage this information for gene-based bioprospecting efforts. Additionally, as new functions are discovered and correlated with this sequence information, the knowledge of the often complex relationship between a protein's sequence and function will improve. This in turn will lead to better gene-based bioprospecting approaches and facilitate the tailoring of desired properties through protein engineering projects. In this chapter, we discuss a number of recent advances in bioprospecting within the context of the genomic age.

  11. Fungal genomics beyond Saccharomyces cerevisiae?

    DEFF Research Database (Denmark)

    Hofmann, Gerald; Mcintyre, Mhairi; Nielsen, Jens


    Fungi are used extensively in both fundamental research and industrial applications. Saccharomyces cerevisiae has been the model organism for fungal research for many years, particularly in functional genomics. However, considering the diversity within the fungal kingdom, it is obvious that the a......Fungi are used extensively in both fundamental research and industrial applications. Saccharomyces cerevisiae has been the model organism for fungal research for many years, particularly in functional genomics. However, considering the diversity within the fungal kingdom, it is obvious...... that the application of the existing methods of genome, transcriptome, proteome and metabolome analysis to other fungi has enormous potential, especially for the production of food and food ingredients. The developments in the past year demonstrate that we have only just started to exploit this potential....

  12. Enhancer Identification through Comparative Genomics

    Energy Technology Data Exchange (ETDEWEB)

    Visel, Axel; Bristow, James; Pennacchio, Len A.


    With the availability of genomic sequence from numerousvertebrates, a paradigm shift has occurred in the identification ofdistant-acting gene regulatory elements. In contrast to traditionalgene-centric studies in which investigators randomly scanned genomicfragments that flank genes of interest in functional assays, the modernapproach begins electronically with publicly available comparativesequence datasets that provide investigators with prioritized lists ofputative functional sequences based on their evolutionary conservation.However, although a large number of tools and resources are nowavailable, application of comparative genomic approaches remains far fromtrivial. In particular, it requires users to dynamically consider thespecies and methods for comparison depending on the specific biologicalquestion under investigation. While there is currently no single generalrule to this end, it is clear that when applied appropriately,comparative genomic approaches exponentially increase our power ingenerating biological hypotheses for subsequent experimentaltesting.

  13. The genome of Theobroma cacao. (United States)

    Argout, Xavier; Salse, Jerome; Aury, Jean-Marc; Guiltinan, Mark J; Droc, Gaetan; Gouzy, Jerome; Allegre, Mathilde; Chaparro, Cristian; Legavre, Thierry; Maximova, Siela N; Abrouk, Michael; Murat, Florent; Fouet, Olivier; Poulain, Julie; Ruiz, Manuel; Roguet, Yolande; Rodier-Goud, Maguy; Barbosa-Neto, Jose Fernandes; Sabot, Francois; Kudrna, Dave; Ammiraju, Jetty Siva S; Schuster, Stephan C; Carlson, John E; Sallet, Erika; Schiex, Thomas; Dievart, Anne; Kramer, Melissa; Gelley, Laura; Shi, Zi; Bérard, Aurélie; Viot, Christopher; Boccara, Michel; Risterucci, Ange Marie; Guignon, Valentin; Sabau, Xavier; Axtell, Michael J; Ma, Zhaorong; Zhang, Yufan; Brown, Spencer; Bourge, Mickael; Golser, Wolfgang; Song, Xiang; Clement, Didier; Rivallan, Ronan; Tahi, Mathias; Akaza, Joseph Moroh; Pitollat, Bertrand; Gramacho, Karina; D'Hont, Angélique; Brunel, Dominique; Infante, Diogenes; Kebe, Ismael; Costet, Pierre; Wing, Rod; McCombie, W Richard; Guiderdoni, Emmanuel; Quetier, Francis; Panaud, Olivier; Wincker, Patrick; Bocs, Stephanie; Lanaud, Claire


    We sequenced and assembled the draft genome of Theobroma cacao, an economically important tropical-fruit tree crop that is the source of chocolate. This assembly corresponds to 76% of the estimated genome size and contains almost all previously described genes, with 82% of these genes anchored on the 10 T. cacao chromosomes. Analysis of this sequence information highlighted specific expansion of some gene families during evolution, for example, flavonoid-related genes. It also provides a major source of candidate genes for T. cacao improvement. Based on the inferred paleohistory of the T. cacao genome, we propose an evolutionary scenario whereby the ten T. cacao chromosomes were shaped from an ancestor through eleven chromosome fusions.

  14. Genomics of Escherichia and Shigella (United States)

    Perna, Nicole T.

    The laboratory workhorse Escherichia coli K-12 is among the most intensively studied living organisms on earth, and this single strain serves as the model system behind much of our understanding of prokaryotic molecular biology. Dense genome sequencing and recent insightful comparative analyses are making the species E. coli, as a whole, an emerging system for studying prokaryotic population genetics and the relationship between system-scale, or genome-scale, molecular evolution and complex traits like host range and pathogenic potential. Genomic perspective has revealed a coherent but dynamic species united by intraspecific gene flow via homologous lateral or horizontal transfer and differentiated by content flux mediated by acquisition of DNA segments from interspecies transfers.

  15. Mitochondrial genomes of parasitic flatworms. (United States)

    Le, Thanh H; Blair, David; McManus, Donald P


    Complete or near-complete mitochondrial genomes are now available for 11 species or strains of parasitic flatworms belonging to the Trematoda and the Cestoda. The organization of these genomes is not strikingly different from those of other eumetazoans, although one gene (atp8) commonly found in other phyla is absent from flatworms. The gene order in most flatworms has similarities to those seen in higher protostomes such as annelids. However, the gene order has been drastically altered in Schistosoma mansoni, which obscures this possible relationship. Among the sequenced taxa, base composition varies considerably, creating potential difficulties for phylogeny reconstruction. Long non-coding regions are present in all taxa, but these vary in length from only a few hundred to approximately 10000 nucleotides. Among Schistosoma spp., the long non-coding regions are rich in repeats and length variation among individuals is known. Data from mitochondrial genomes are valuable for studies on species identification, phylogenies and biogeography.

  16. : a database of ciliate genome rearrangements. (United States)

    Burns, Jonathan; Kukushkin, Denys; Lindblad, Kelsi; Chen, Xiao; Jonoska, Nataša; Landweber, Laura F


    Ciliated protists exhibit nuclear dimorphism through the presence of somatic macronuclei (MAC) and germline micronuclei (MIC). In some ciliates, DNA from precursor segments in the MIC genome rearranges to form transcriptionally active genes in the mature MAC genome, making these ciliates model organisms to study the process of somatic genome rearrangement. Similar broad scale, somatic rearrangement events occur in many eukaryotic cells and tumors. The ( is a database of genome recombination and rearrangement annotations, and it provides tools for visualization and comparative analysis of precursor and product genomes. The database currently contains annotations for two completely sequenced ciliate genomes: Oxytricha trifallax and Tetrahymena thermophila.

  17. A physical map of the human genome

    Energy Technology Data Exchange (ETDEWEB)

    McPherson, J.D.; Marra, M.; Hillier, L.; Waterston, R.H.; Chinwalla, A.; Wallis, J.; Sekhon, M.; Wylie, K.; Mardis, E.R.; Wilson, R.K.; Fulton, R.; Kucaba, T.A.; Wagner-McPherson, C.; Barbazuk, W.B.; Gregory, S.G.; Humphray, S.J.; French, L.; Evans, R.S.; Bethel, G.; Whittaker, A.; Holden, J.L.; McCann, O.T.; Dunham, A.; Soderlund, C.; Scott, C.E.; Bentley, D.R.; Schuler, G.; Chen, H.-C.; Jang, W.; Green, E.D.; Idol, J.R.; Maduro, V.V. Braden; Montgomery, K.T.; Lee, E.; Miller, A.; Emerling, S.; Kucherlapati; Gibbs, R.; Scherer, S.; Gorrell, J.H.; Sodergren, E.; Clerc-Blankenburg, K.; Tabor, P.; Naylor, S.; Garcia, D.; de Jong, P.J.; Catanese, J.J.; Nowak, N.; Osoegawa, K.; Qin, S.; Rowen, L.; Madan, A.; Dors, M.; Hood, L.; Trask, B.; Friedman, C.; Massa, H.; Cheung, V.G.; Kirsch, I.R.; Reid, T.; Yonescu, R.; Weissenbach, J.; Bruls, T.; Heilig, R.; Branscomb, E.; Olsen, A.; Doggett, N.; Cheng, J.F.; Hawkins, T.; Myers, R.M.; Shang, J.; Ramirez, L.; Schmutz, J.; Velasquez, O.; Dixon, K.; Stone, N.E.; Cox, D.R.; Haussler, D.; Kent, W.J.; Furey, T.; Rogic, S.; Kennedy, S.; Jones, S.; Rosenthal, A.; Wen, G.; Schilhabel, M.; Gloeckner, G.; Nyakatura, G.; Siebert, R.; Schlegelberger, B.; Korenberg, J.; Chen, X.N.; Fujiyama, A.; Hattori, M.; Toyoda, A.; Yada, T.; Park, H.S.; Sakaki, Y.; Shimizu, N.; Asakawa, S.; Kawasaki, K.; Sasaki, T.; Shintani, A.; Shimizu, A.; Shibuya, K.; Kudoh, J.; Minoshima, S.; Ramser, J.; Seranski, P.; Hoff, C.; Poustka, A.; Reinhardt, R.; Lehrach, H.


    The human genome is by far the largest genome to be sequenced, and its size and complexity present many challenges for sequence assembly. The International Human Genome Sequencing Consortium constructed a map of the whole genome to enable the selection of clones for sequencing and for the accurate assembly of the genome sequence. Here we report the construction of the whole-genome bacterial artificial chromosome (BAC) map and its integration with previous landmark maps and information from mapping efforts focused on specific chromosomal regions. We also describe the integration of sequence data with the map.

  18. Comparison of 61 Sequenced Escherichia coli Genomes

    DEFF Research Database (Denmark)

    Lukjancenko, Oksana; Wassenaar, T. M.; Ussery, David


    MLST was performed, many of the various strains appear jumbled and less well resolved. The predicted pan-genome comprises 15,741 gene families, and only 993 (6%) of the families are represented in every genome, comprising the core genome. The variable or 'accessory' genes thus make up more than 90......% of the pan-genome and about 80% of a typical genome; some of these variable genes tend to be co-localized on genomic islands. The diversity within the species E. coli, and the overlap in gene content between this and related species, suggests a continuum rather than sharp species borders in this group...

  19. Genomics and the origin of species. (United States)

    Seehausen, Ole; Butlin, Roger K; Keller, Irene; Wagner, Catherine E; Boughman, Janette W; Hohenlohe, Paul A; Peichel, Catherine L; Saetre, Glenn-Peter; Bank, Claudia; Brännström, Ake; Brelsford, Alan; Clarkson, Chris S; Eroukhmanoff, Fabrice; Feder, Jeffrey L; Fischer, Martin C; Foote, Andrew D; Franchini, Paolo; Jiggins, Chris D; Jones, Felicity C; Lindholm, Anna K; Lucek, Kay; Maan, Martine E; Marques, David A; Martin, Simon H; Matthews, Blake; Meier, Joana I; Möst, Markus; Nachman, Michael W; Nonaka, Etsuko; Rennison, Diana J; Schwarzer, Julia; Watson, Eric T; Westram, Anja M; Widmer, Alex


    Speciation is a fundamental evolutionary process, the knowledge of which is crucial for understanding the origins of biodiversity. Genomic approaches are an increasingly important aspect of this research field. We review current understanding of genome-wide effects of accumulating reproductive isolation and of genomic properties that influence the process of speciation. Building on this work, we identify emergent trends and gaps in our understanding, propose new approaches to more fully integrate genomics into speciation research, translate speciation theory into hypotheses that are testable using genomic tools and provide an integrative definition of the field of speciation genomics.

  20. Difluoromethylornithine is a novel inhibitor of Helicobacter pylori growth, CagA translocation, and interleukin-8 induction.

    Directory of Open Access Journals (Sweden)

    Daniel P Barry

    Full Text Available Helicobacter pylori infects half the world's population, and carriage is lifelong without antibiotic therapy. Current regimens prescribed to prevent infection-associated diseases such as gastroduodenal ulcers and gastric cancer can be thwarted by antibiotic resistance. We reported that administration of 1% D,L-α-difluoromethylornithine (DFMO to mice infected with H. pylori reduces gastritis and colonization, which we attributed to enhanced host immune response due to inhibition of macrophage ornithine decarboxylase (ODC, the rate-limiting enzyme in polyamine biosynthesis. Although no ODC has been identified in any H. pylori genome, we sought to determine if DFMO has direct effects on the bacterium. We found that DFMO significantly reduced the growth rate of H. pylori in a polyamine-independent manner. Two other gram-negative pathogens possessing ODC, Escherichia coli and Citrobacter rodentium, were resistant to the DFMO effect. The effect of DFMO on H. pylori required continuous exposure to the drug and was reversible when removed, with recovery of growth rate in vitro and the ability to colonize mice. H. pylori exposed to DFMO were significantly shorter in length than those untreated and they contained greater internal levels of ATP, suggesting severe effects on bacterial metabolism. DFMO inhibited expression of the H. pylori virulence factor cytotoxin associated gene A, and its translocation and phosphorylation in gastric epithelial cells, which was associated with a reduction in interleukin-8 expression. These findings suggest that DFMO has effects on H. pylori that may contribute to its effectiveness in reducing gastritis and colonization and may be a useful addition to anti-H. pylori therapies.

  1. Difluoromethylornithine Is a Novel Inhibitor of Helicobacter pylori Growth, CagA Translocation, and Interleukin-8 Induction (United States)

    Barry, Daniel P.; Asim, Mohammad; Leiman, David A.; de Sablet, Thibaut; Singh, Kshipra; Casero, Robert A.; Chaturvedi, Rupesh; Wilson, Keith T.


    Helicobacter pylori infects half the world's population, and carriage is lifelong without antibiotic therapy. Current regimens prescribed to prevent infection-associated diseases such as gastroduodenal ulcers and gastric cancer can be thwarted by antibiotic resistance. We reported that administration of 1% d,l-α-difluoromethylornithine (DFMO) to mice infected with H. pylori reduces gastritis and colonization, which we attributed to enhanced host immune response due to inhibition of macrophage ornithine decarboxylase (ODC), the rate-limiting enzyme in polyamine biosynthesis. Although no ODC has been identified in any H. pylori genome, we sought to determine if DFMO has direct effects on the bacterium. We found that DFMO significantly reduced the growth rate of H. pylori in a polyamine-independent manner. Two other Gram-negative pathogens possessing ODC, Escherichia coli and Citrobacter rodentium, were resistant to the DFMO effect. The effect of DFMO on H. pylori required continuous exposure to the drug and was reversible when removed, with recovery of growth rate in vitro and the ability to colonize mice. H. pylori exposed to DFMO were significantly shorter in length than those untreated and they contained greater internal levels of ATP, suggesting severe effects on bacterial metabolism. DFMO inhibited expression of the H. pylori virulence factor cytotoxin associated gene A, and its translocation and phosphorylation in gastric epithelial cells, which was associated with a reduction in interleukin-8 expression. These findings suggest that DFMO has effects on H. pylori that may contribute to its effectiveness in reducing gastritis and colonization and may be a useful addition to anti-H. pylori therapies. PMID:21386987

  2. Translating genomics in cancer care. (United States)

    Bombard, Yvonne; Bach, Peter B; Offit, Kenneth


    There is increasing enthusiasm for genomics and its promise in advancing personalized medicine. Genomic information has been used to personalize health care for decades, spanning the fields of cardiovascular disease, infectious disease, endocrinology, metabolic medicine, and hematology. However, oncology has often been the first test bed for the clinical translation of genomics for diagnostic, prognostic, and therapeutic applications. Notable hereditary cancer examples include testing for mutations in BRCA1 or BRCA2 in unaffected women to identify those at significantly elevated risk for developing breast and ovarian cancers, and screening patients with newly diagnosed colorectal cancer for mutations in 4 mismatch repair genes to reduce morbidity and mortality in their relatives. Somatic genomic testing is also increasingly used in oncology, with gene expression profiling of breast tumors and EGFR testing to predict treatment response representing commonly used examples. Health technology assessment provides a rigorous means to inform clinical and policy decision-making through systematic assessment of the evidentiary base, along with precepts of clinical effectiveness, cost-effectiveness, and consideration of risks and benefits for health care delivery and society. Although this evaluation is a fundamental step in the translation of any new therapeutic, procedure, or diagnostic test into clinical care, emerging developments may threaten this standard. These include "direct to consumer" genomic risk assessment services and the challenges posed by incidental results generated from next-generation sequencing (NGS) technologies. This article presents a review of the evidentiary standards and knowledge base supporting the translation of key cancer genomic technologies along the continuum of validity, utility, cost-effectiveness, health service impacts, and ethical and societal issues, and offers future research considerations to guide the responsible introduction of

  3. Biocommunication and natural genome editing

    Institute of Scientific and Technical Information of China (English)

    Guenther; Witzany


    The biocommunicative approach investigates communication processes within and among cells,tissues,organs and organisms as sign-mediated interactions,and nucleotide sequences as code,i.e.language-like text,which follows in parallel three kinds of rules:combinatorial (syntactic),context-sensitive(pragmatic),and contentspecific(semantic).Natural genome editing from a bio-communicative perspective is competent agent-driven generation and integration of meaningful nucleotide sequences into pre-existing genomic content arrangements and the ability to(re-)combine and(re-)regulate them according to context-dependent(i.e.adaptational) purposes of the host organism.

  4. How retrotransposons shape genome regulation. (United States)

    Mita, Paolo; Boeke, Jef D


    Retrotransposons are mutagenic units able to move within the genome. Despite many defenses deployed by the host to suppress potentially harmful activities of retrotransposons, these genetic units have found ways to meld with normal cellular functions through processes of exaptation and domestication. The same host mechanisms targeting transposon mobility allow for expansion and rewiring of gene regulatory networks on an evolutionary time scale. Recent works demonstrating retrotransposon activity during development, cell differentiation and neurogenesis shed new light on unexpected activities of transposable elements. Moreover, new technological advances illuminated subtler nuances of the complex relationship between retrotransposons and the host genome, clarifying the role of retroelements in evolution, development and impact on human disease.

  5. Genome editing comes of age. (United States)

    Kim, Jin-Soo


    Genome editing harnesses programmable nucleases to cut and paste genetic information in a targeted manner in living cells and organisms. Here, I review the development of programmable nucleases, including zinc finger nucleases (ZFNs), TAL (transcription-activator-like) effector nucleases (TALENs) and CRISPR (cluster of regularly interspaced palindromic repeats)-Cas9 (CRISPR-associated protein 9) RNA-guided endonucleases (RGENs). I specifically highlight the key advances that set the foundation for the rapid and widespread implementation of CRISPR-Cas9 genome editing approaches that has revolutionized the field.

  6. Engineering Relative Compression of Genomes

    CERN Document Server

    Grabowski, Szymon


    Technology progress in DNA sequencing boosts the genomic database growth at faster and faster rate. Compression, accompanied with random access capabilities, is the key to maintain those huge amounts of data. In this paper we present an LZ77-style compression scheme for relative compression of multiple genomes of the same species. While the solution bears similarity to known algorithms, it offers significantly higher compression ratios at compression speed over a order of magnitude greater. One of the new successful ideas is augmenting the reference sequence with phrases from the other sequences, making more LZ-matches available.

  7. Delivery technologies for genome editing. (United States)

    Yin, Hao; Kauffman, Kevin J; Anderson, Daniel G


    With the recent development of CRISPR technology, it is becoming increasingly easy to engineer the genome. Genome-editing systems based on CRISPR, as well as transcription activator-like effector nucleases (TALENs) and zinc-finger nucleases (ZFNs), are becoming valuable tools for biomedical research, drug discovery and development, and even gene therapy. However, for each of these systems to effectively enter cells of interest and perform their function, efficient and safe delivery technologies are needed. This Review discusses the principles of biomacromolecule delivery and gene editing, examines recent advances and challenges in non-viral and viral delivery methods, and highlights the status of related clinical trials.

  8. Genomic profiling of breast cancer. (United States)

    Pandey, Anjita; Singh, Alok Kumar; Maurya, Sanjeev Kumar; Rai, Rajani; Tewari, Mallika; Kumar, Mohan; Shukla, Hari S


    Genome study provides significant changes in the advancement of molecular diagnosis and treatment in Breast cancer. Several recent critical advances and high-throughput techniques identified the genomic trouble and dramatically accelerated the pace of research in preventing and curing this malignancy. Tumor-suppressor genes, proto-oncogenes, DNA-repair genes, carcinogen-metabolism genes are critically involved in progression of breast cancer. We reviewed imperative finding in breast genetics, ongoing work to segregate further susceptible genes, and preliminary studies on molecular profiling.

  9. Cancer Genome Anatomy Project | Office of Cancer Genomics (United States)

    The National Cancer Institute (NCI) Cancer Genome Anatomy Project (CGAP) is an online resource designed to provide the research community access to biological tissue characterization data. Request a free copy of the CGAP Website Virtual Tour CD from

  10. Translational Genomics of Onion: Challenges of an Enormous Nuclear Genome (United States)

    The use of high throughput DNA sequencing to address important production constraints has been termed “translational genomics”. Classical breeding of onion (Allium cepa) is expensive and slow due to a long generation time and the high costs of crossing with insects. Translational genomics should r...

  11. A genome wide dosage suppressor network reveals genomic robustness (United States)

    Patra, Biranchi; Kon, Yoshiko; Yadav, Gitanjali; Sevold, Anthony W.; Frumkin, Jesse P.; Vallabhajosyula, Ravishankar R.; Hintze, Arend; Østman, Bjørn; Schossau, Jory; Bhan, Ashish; Marzolf, Bruz; Tamashiro, Jenna K.; Kaur, Amardeep; Baliga, Nitin S.; Grayhack, Elizabeth J.; Adami, Christoph; Galas, David J.; Raval, Alpan; Phizicky, Eric M.; Ray, Animesh


    Genomic robustness is the extent to which an organism has evolved to withstand the effects of deleterious mutations. We explored the extent of genomic robustness in budding yeast by genome wide dosage suppressor analysis of 53 conditional lethal mutations in cell division cycle and RNA synthesis related genes, revealing 660 suppressor interactions of which 642 are novel. This collection has several distinctive features, including high co-occurrence of mutant-suppressor pairs within protein modules, highly correlated functions between the pairs and higher diversity of functions among the co-suppressors than previously observed. Dosage suppression of essential genes encoding RNA polymerase subunits and chromosome cohesion complex suggests a surprising degree of functional plasticity of macromolecular complexes, and the existence of numerous degenerate pathways for circumventing the effects of potentially lethal mutations. These results imply that organisms and cancer are likely able to exploit the genomic robustness properties, due the persistence of cryptic gene and pathway functions, to generate variation and adapt to selective pressures. PMID:27899637

  12. Genome update: the 1000th genome - a cautionary tale

    DEFF Research Database (Denmark)

    Lagesen, Karin; Ussery, David; Wassenaar, Gertrude Maria


    for a variety of logistical reasons, including differences in format and loading errors, such as those caused by file transfer protocol interruptions. This means that the 1000th genome will be different in the various databases. Some of the data on the highly accessed web pages are inaccurate, leading to false...

  13. Cancer Genome Anatomy Project (CGAP) | Office of Cancer Genomics (United States)

    CGAP generated a wide range of genomics data on cancerous cells that are accessible through easy-to-use online tools. Researchers, educators, and students can find "in silico" answers to biological questions through the CGAP website. Request a free copy of the CGAP Website Virtual Tour CD from to learn how to navigate the website.

  14. Human and mouse genome analysis using array comparative genomic hybridization

    NARCIS (Netherlands)

    Snijders, Antoine Maria


    Almost all human cancers as well as developmental abnormalities are characterized by the presence of genetic alterations, most of which target a gene or a particular genomic locus resulting in altered gene expression and ultimately an altered phenotype. Different types of genetic alterations include

  15. Burkholderia pseudomallei genome plasticity associated with genomic island variation

    Directory of Open Access Journals (Sweden)

    Currie Bart J


    Full Text Available Abstract Background Burkholderia pseudomallei is a soil-dwelling saprophyte and the cause of melioidosis. Horizontal gene transfer contributes to the genetic diversity of this pathogen and may be an important determinant of virulence potential. The genome contains genomic island (GI regions that encode a broad array of functions. Although there is some evidence for the variable distribution of genomic islands in B. pseudomallei isolates, little is known about the extent of variation between related strains or their association with disease or environmental survival. Results Five islands from B. pseudomallei strain K96243 were chosen as representatives of different types of genomic islands present in this strain, and their presence investigated in other B. pseudomallei. In silico analysis of 10 B. pseudomallei genome sequences provided evidence for the variable presence of these regions, together with micro-evolutionary changes that generate GI diversity. The diversity of GIs in 186 isolates from NE Thailand (83 environmental and 103 clinical isolates was investigated using multiplex PCR screening. The proportion of all isolates positive by PCR ranged from 12% for a prophage-like island (GI 9, to 76% for a metabolic island (GI 16. The presence of each of the five GIs did not differ between environmental and disease-associated isolates (p > 0.05 for all five islands. The cumulative number of GIs per isolate for the 186 isolates ranged from 0 to 5 (median 2, IQR 1 to 3. The distribution of cumulative GI number did not differ between environmental and disease-associated isolates (p = 0.27. The presence of GIs was defined for the three largest clones in this collection (each defined as a single sequence type, ST, by multilocus sequence typing; these were ST 70 (n = 15 isolates, ST 54 (n = 11, and ST 167 (n = 9. The rapid loss and/or acquisition of gene islands was observed within individual clones. Comparisons were drawn between isolates obtained

  16. Genome Size Dynamics and Evolution in Monocots

    Directory of Open Access Journals (Sweden)

    Ilia J. Leitch


    Full Text Available Monocot genomic diversity includes striking variation at many levels. This paper compares various genomic characters (e.g., range of chromosome numbers and ploidy levels, occurrence of endopolyploidy, GC content, chromosome packaging and organization, genome size between monocots and the remaining angiosperms to discern just how distinctive monocot genomes are. One of the most notable features of monocots is their wide range and diversity of genome sizes, including the species with the largest genome so far reported in plants. This genomic character is analysed in greater detail, within a phylogenetic context. By surveying available genome size and chromosome data it is apparent that different monocot orders follow distinctive modes of genome size and chromosome evolution. Further insights into genome size-evolution and dynamics were obtained using statistical modelling approaches to reconstruct the ancestral genome size at key nodes across the monocot phylogenetic tree. Such approaches reveal that while the ancestral genome size of all monocots was small (1C=1.9 pg, there have been several major increases and decreases during monocot evolution. In addition, notable increases in the rates of genome size-evolution were found in Asparagales and Poales compared with other monocot lineages.

  17. Fungal genome sequencing: basic biology to biotechnology. (United States)

    Sharma, Krishna Kant


    The genome sequences provide a first glimpse into the genomic basis of the biological diversity of filamentous fungi and yeast. The genome sequence of the budding yeast, Saccharomyces cerevisiae, with a small genome size, unicellular growth, and rich history of genetic and molecular analyses was a milestone of early genomics in the 1990s. The subsequent completion of fission yeast, Schizosaccharomyces pombe and genetic model, Neurospora crassa initiated a revolution in the genomics of the fungal kingdom. In due course of time, a substantial number of fungal genomes have been sequenced and publicly released, representing the widest sampling of genomes from any eukaryotic kingdom. An ambitious genome-sequencing program provides a wealth of data on metabolic diversity within the fungal kingdom, thereby enhancing research into medical science, agriculture science, ecology, bioremediation, bioenergy, and the biotechnology industry. Fungal genomics have higher potential to positively affect human health, environmental health, and the planet's stored energy. With a significant increase in sequenced fungal genomes, the known diversity of genes encoding organic acids, antibiotics, enzymes, and their pathways has increased exponentially. Currently, over a hundred fungal genome sequences are publicly available; however, no inclusive review has been published. This review is an initiative to address the significance of the fungal genome-sequencing program and provides the road map for basic and applied research.

  18. An Exploration into Fern Genome Space. (United States)

    Wolf, Paul G; Sessa, Emily B; Marchant, Daniel Blaine; Li, Fay-Wei; Rothfels, Carl J; Sigel, Erin M; Gitzendanner, Matthew A; Visger, Clayton J; Banks, Jo Ann; Soltis, Douglas E; Soltis, Pamela S; Pryer, Kathleen M; Der, Joshua P


    Ferns are one of the few remaining major clades of land plants for which a complete genome sequence is lacking. Knowledge of genome space in ferns will enable broad-scale comparative analyses of land plant genes and genomes, provide insights into genome evolution across green plants, and shed light on genetic and genomic features that characterize ferns, such as their high chromosome numbers and large genome sizes. As part of an initial exploration into fern genome space, we used a whole genome shotgun sequencing approach to obtain low-density coverage (∼0.4X to 2X) for six fern species from the Polypodiales (Ceratopteris, Pteridium, Polypodium, Cystopteris), Cyatheales (Plagiogyria), and Gleicheniales (Dipteris). We explore these data to characterize the proportion of the nuclear genome represented by repetitive sequences (including DNA transposons, retrotransposons, ribosomal DNA, and simple repeats) and protein-coding genes, and to extract chloroplast and mitochondrial genome sequences. Such initial sweeps of fern genomes can provide information useful for selecting a promising candidate fern species for whole genome sequencing. We also describe variation of genomic traits across our sample and highlight some differences and similarities in repeat structure between ferns and seed plants.

  19. Advancing Eucalyptus Genomics: Cytogenomics Reveals Conservation of Eucalyptus Genomes (United States)

    Ribeiro, Teresa; Barrela, Ricardo M.; Bergès, Hélène; Marques, Cristina; Loureiro, João; Morais-Cecílio, Leonor; Paiva, Jorge A. P.


    The genus Eucalyptus encloses several species with high ecological and economic value, being the subgenus Symphyomyrtus one of the most important. Species such as E. grandis and E. globulus are well characterized at the molecular level but knowledge regarding genome and chromosome organization is very scarce. Here we characterized and compared the karyotypes of three economically important species, E. grandis, E. globulus, and E. calmadulensis, and three with ecological relevance, E. pulverulenta, E. cornuta, and E. occidentalis, through an integrative approach including genome size estimation, fluorochrome banding, rDNA FISH, and BAC landing comprising genes involved in lignin biosynthesis. All karyotypes show a high degree of conservation with pericentromeric 35S and 5S rDNA loci in the first and third pairs, respectively. GC-rich heterochromatin was restricted to the 35S rDNA locus while the AT-rich heterochromatin pattern was species-specific. The slight differences in karyotype formulas and distribution of AT-rich heterochromatin, along with genome sizes estimations, support the idea of Eucalyptus genome evolution by local expansions of heterochromatin clusters. The unusual co-localization of both rDNA with AT-rich heterochromatin was attributed mainly to the presence of silent transposable elements in those loci. The cinnamoyl CoA reductase gene (CCR1) previously assessed to linkage group 10 (LG10) was clearly localized distally at the long arm of chromosome 9 establishing an unexpected correlation between the cytogenetic chromosome 9 and the LG10. Our work is novel and contributes to the understanding of Eucalyptus genome organization which is essential to develop successful advanced breeding strategies for this genus. PMID:27148332

  20. Genome Sequences of Eight Morphologically Diverse Alphaproteobacteria▿


    Brown, Pamela J.B.; Kysela, David T.; Buechlein, Aaron; Hemmerich, Chris; Brun, Yves V


    The Alphaproteobacteriacomprise morphologically diverse bacteria, including many species of stalked bacteria. Here we announce the genome sequences of eight alphaproteobacteria, including the first genome sequences of species belonging to the genera Asticcacaulis, Hirschia, Hyphomicrobium, and Rhodomicrobium.