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Sample records for annulatus bm86 ortholog

  1. Vaccination with recombinant Boophilus annulatus Bm86 ortholog protein, Ba86, protects cattle against B. annulatus and B. microplus infestations

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    Jongejan Frans

    2009-03-01

    Full Text Available Abstract Background The cattle ticks, Boophilus spp., affect cattle production in tropical and subtropical regions of the world. Tick vaccines constitute a cost-effective and environmentally friendly alternative to tick control. The recombinant B. microplus Bm86 protective antigen has been shown to protect cattle against tick infestations. Recently, the gene coding for B. annulatus Bm86 ortholog, Ba86, was cloned and the recombinant protein was secreted and purified from the yeast Pichia pastoris. Results Recombinant Ba86 (Israel strain was used to immunize cattle to test its efficacy for the control of B. annulatus (Mercedes, Texas, USA strain and B. microplus (Susceptible, Mexico strain infestations. Bm86 (Gavac and Mozambique strain and adjuvant/saline were used as positive and negative controls, respectively. Vaccination with Ba86 reduced tick infestations (71% and 40%, weight (8% and 15%, oviposition (22% and 5% and egg fertility (25% and 50% for B. annulatus and B. microplus, respectively. The efficacy of both Ba86 and Bm86 was higher for B. annulatus than for B. microplus. The efficacy of Ba86 was higher for B. annulatus (83.0% than for B. microplus (71.5%. The efficacy of Bm86 (Gavac; 85.2% but not Bm86 (Mozambique strain; 70.4% was higher than that of Ba86 (71.5% on B. microplus. However, the efficacy of Bm86 (both Gavac and Mozambique strain; 99.6% was higher than that of Ba86 (83.0% on B. annulatus. Conclusion These experiments showed the efficacy of recombinant Ba86 for the control of B. annulatus and B. microplus infestations in cattle and suggested that physiological differences between B. microplus and B. annulatus and those encoded in the sequence of Bm86 orthologs may be responsible for the differences in susceptibility of these tick species to Bm86 vaccines.

  2. Vaccination with recombinant Boophilus annulatus Bm86 ortholog protein, Ba86, protects cattle against B. annulatus and B. microplus infestations

    OpenAIRE

    Jongejan Frans; Naranjo Victoria; Almazán Consuelo; Canales Mario; de la Fuente José

    2009-01-01

    Abstract Background The cattle ticks, Boophilus spp., affect cattle production in tropical and subtropical regions of the world. Tick vaccines constitute a cost-effective and environmentally friendly alternative to tick control. The recombinant B. microplus Bm86 protective antigen has been shown to protect cattle against tick infestations. Recently, the gene coding for B. annulatus Bm86 ortholog, Ba86, was cloned and the recombinant protein was secreted and purified from the yeast Pichia past...

  3. Expression of recombinant Rhipicephalus (Boophilus microplus, R. annulatus and R. decoloratus Bm86 orthologs as secreted proteins in Pichia pastoris

    Directory of Open Access Journals (Sweden)

    Jongejan Frans

    2008-02-01

    Full Text Available Abstract Background Rhipicephalus (Boophilus spp. ticks economically impact on cattle production in Africa and other tropical and subtropical regions of the world. Tick vaccines constitute a cost-effective and environmentally friendly alternative to tick control. The R. microplus Bm86 protective antigen has been produced by recombinant DNA technology and shown to protect cattle against tick infestations. Results In this study, the genes for Bm86 (R. microplus, Ba86 (R. annulatus and Bd86 (R. decoloratus were cloned and characterized from African or Asian tick strains and the recombinant proteins were secreted and purified from P. pastoris. The secretion of recombinant Bm86 ortholog proteins in P. pastoris allowed for a simple purification process rendering a final product with high recovery (35–42% and purity (80–85% and likely to result in a more reproducible conformation closely resembling the native protein. Rabbit immunization experiments with recombinant proteins showed immune cross-reactivity between Bm86 ortholog proteins. Conclusion These experiments support the development and testing of vaccines containing recombinant Bm86, Ba86 and Bd86 secreted in P. pastoris for the control of tick infestations in Africa.

  4. Expression of recombinant Rhipicephalus (Boophilus) microplus, R. annulatus and R. decoloratus Bm86 orthologs as secreted proteins in Pichia pastoris

    OpenAIRE

    Jongejan Frans; Hope Michelle; Nijhof Ard M; Naranjo Victoria; de la Lastra José; Canales Mario; de la Fuente José

    2008-01-01

    Abstract Background Rhipicephalus (Boophilus) spp. ticks economically impact on cattle production in Africa and other tropical and subtropical regions of the world. Tick vaccines constitute a cost-effective and environmentally friendly alternative to tick control. The R. microplus Bm86 protective antigen has been produced by recombinant DNA technology and shown to protect cattle against tick infestations. Results In this study, the genes for Bm86 (R. microplus), Ba86 (R. annulatus) and Bd86 (...

  5. Immunity against Boophilus annulatus induced by the Bm86 (Tick-GARD) vaccine.

    Science.gov (United States)

    Pipano, Eugene; Alekceev, Eugene; Galker, Felicia; Fish, Lea; Samish, Michael; Shkap, Varda

    2003-01-01

    Friesian cattle were immunized with two inoculations of anti-tick Bm86 (Tick-GARD) vaccine and were challenged 30 or 90 d later with Boophilus annulatus larvae derived from 1.2 g of eggs. No nymphs or adult ticks were found on the immunized cattle during four weeks after challenge. Repeated infestations (2 to 4) with larvae on three other calves during a period of 160 and 390 d after the immunization did not result in development of nymphal and adult stages. In control, non-immunized cattle infested with corresponding batches of larvae 1380 to 4653 replete adult female ticks were collected. Larvae issued from Babesia bovis-infected female ticks transmitted the infection to Bm86-immunized cattle, but the progeny of B. bigemina-infected females did not. Since B. bigemina is transmitted exclusively by nymphal stages of Bo. annulatus these results support the observation that immunity induced by Bm86 affects the larval stage of this tick. PMID:14580066

  6. Lesser protein degradation machinery correlates with higher BM86 tick vaccine efficacy in Rhipicephalus annulatus when compared to Rhipicephalus microplus.

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    Popara, Marina; Villar, Margarita; Mateos-Hernández, Lourdes; de Mera, Isabel G Fernández; Marina, Anabel; del Valle, Mercedes; Almazán, Consuelo; Domingos, Ana; de la Fuente, José

    2013-10-01

    Infestations with cattle ticks, Rhipicephalus (Boophilus) microplus and Rhipicephalus annulatus, economically impact cattle production in tropical and subtropical regions of the world. Vaccines containing the recombinant R. microplus BM86 gut antigen were developed and commercialized to induce an immunological protection in cattle against tick infestations. These vaccines demonstrated that tick control by vaccination is cost-effective, reduces environmental contamination and prevents the selection of drug resistant ticks that result from repeated acaricide applications. The protection elicited by BM86-containing vaccines against tick infestations is mediated by a collaborative action between the complement system and IgG antibodies. The efficacy of the vaccination with BM86 and other tick antigens is always higher for R. annulatus than against R. microplus, suggesting that tick genetic and/or physiological factors may affect tick vaccine efficacy. These factors may be related to BM86 protein levels or tick physiological processes such as feeding and protein degradation that could result in more efficient antibody-antigen interactions and vaccine efficacy. To test this hypothesis, we compared the proteome in R. annulatus and R. microplus female ticks after feeding on BM86-vaccinated and control cattle. The results showed that cattle proteins were under represented in R. annulatus when compared to R. microplus, suggesting that R. annulatus ticks ingested less blood, a difference that increased when feeding on vaccinated cattle, probably reflecting the effect of antibody-BM86 interactions on this process. The results also showed that tick protein degradation machinery was under represented in R. annulatus when compared to R. microplus. BM86 mRNA and protein levels were similar in both tick species, suggesting that lesser protease activity in R. annulatus results in more efficient antibody-antigen interactions and higher vaccine efficacy. These results have important

  7. Protection against Boophilus annulatus infestations in cattle vaccinated with the B. microplus Bm86-containing vaccine Gavac. off.

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    Fragoso, H; Rad, P H; Ortiz, M; Rodríguez, M; Redondo, M; Herrera, L; de la Fuente, J

    1998-12-01

    Tick infestations by Boophilus spp. constitute a major problem for the cattle industry in tropical and subtropical areas of the world. The use of traditional control methods has been only partially successful and tick infestations remain a serious problem. Recently, the gut antigen Bm86 was isolated from B. microplus. Recombinant preparations of this antigen have been used in vaccines for the control of B. microplus infestations. However, in several regions of the world, B. microplus coexists with other Boophilus species, mainly B. annulatus and B. decoloratus. Therefore, there is a need for the simultaneous control of infestations by different Boophilus species. To test the capacity of the P. pastoris-derived Bm86 antigen preparation (Gavac, Heber Biotec S.A., Havana) to control B. annulatus infestations, controlled experiments were conducted in Mexico and Iran. Cattle were vaccinated with Gavac or not vaccinated and then artificially infested with B. annulatus larvae. The results showed for the first time a high protection efficacy (> 99.9%) of Gavac in the control of B. annulatus infestations. These results support the application of Bm86-containing vaccines for the control of Boophilus spp. infestations. PMID:9796055

  8. Vaccine Efficacy of Bm86 Ortholog of H. a. anatolicum, rHaa86 Expressed in Prokaryotic Expression System

    OpenAIRE

    Azhahianambi, P.; D. D. Ray; Pallab Chaudhuri; Rohita Gupta; Srikanta Ghosh

    2010-01-01

    The use of tick vaccine in controlling ticks and tick borne diseases has been proved effective in integrated tick management format. For the control of H. a. anatolicum, Bm86 ortholog of H. a. anatolicum was cloned and expressed as fusion protein in E. coli as E. coli-pETHaa86. The molecular weight of the rHaa86 was 97 kDa with a 19 kDa fusion tag of thioredoxin protein. The expressed protein was characterized immunologically and vaccine efficacy was evaluated. After 120 hours of challenge, o...

  9. Vaccine Efficacy of Bm86 Ortholog of H. a. anatolicum, rHaa86 Expressed in Prokaryotic Expression System

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    P. Azhahianambi

    2009-01-01

    Full Text Available The use of tick vaccine in controlling ticks and tick borne diseases has been proved effective in integrated tick management format. For the control of H. a. anatolicum, Bm86 ortholog of H. a. anatolicum was cloned and expressed as fusion protein in E. coli as E. coli-pETHaa86. The molecular weight of the rHaa86 was 97 kDa with a 19 kDa fusion tag of thioredoxin protein. The expressed protein was characterized immunologically and vaccine efficacy was evaluated. After 120 hours of challenge, only 26% tick could successfully fed on immunized animals. Besides significant reduction in feeding percentages, a significant reduction of 49.6 mg; P<.01 in the weight of fed females in comparison to the females fed on control animals was recorded. Following oviposition, a significant reduction of 68.1 mg; P<.05 in the egg masses of ticks fed on immunized animals in comparison to the ticks fed on control animals was noted. The reduction of number of females, mean weight of eggs, adult females and efficacy of immunogen were 73.8%, 31.3%, 15.8%, and 82.3%, respectively. The results indicated the possibility of development of rHaa86 based vaccine as a component of integrated control of tick species.

  10. Vaccine Efficacy of Bm86 Ortholog of H. a. anatolicum, rHaa86 Expressed in Prokaryotic Expression System.

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    Azhahianambi, P; Ray, D D; Chaudhuri, Pallab; Gupta, Rohita; Ghosh, Srikanta

    2009-01-01

    The use of tick vaccine in controlling ticks and tick borne diseases has been proved effective in integrated tick management format. For the control of H. a. anatolicum, Bm86 ortholog of H. a. anatolicum was cloned and expressed as fusion protein in E. coli as E. coli-pETHaa86. The molecular weight of the rHaa86 was 97 kDa with a 19 kDa fusion tag of thioredoxin protein. The expressed protein was characterized immunologically and vaccine efficacy was evaluated. After 120 hours of challenge, only 26% tick could successfully fed on immunized animals. Besides significant reduction in feeding percentages, a significant reduction of 49.6 mg; P < .01 in the weight of fed females in comparison to the females fed on control animals was recorded. Following oviposition, a significant reduction of 68.1 mg; P < .05 in the egg masses of ticks fed on immunized animals in comparison to the ticks fed on control animals was noted. The reduction of number of females, mean weight of eggs, adult females and efficacy of immunogen were 73.8%, 31.3%, 15.8%, and 82.3%, respectively. The results indicated the possibility of development of rHaa86 based vaccine as a component of integrated control of tick species. PMID:20721331

  11. Molecular characterization of Bm86 gene orthologs from Hyalomma excavatum, Hyalomma dromedarii and Hyalomma marginatum marginatum and comparison with a vaccine candidate from Hyalomma scupense.

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    Ben Said, Mourad; Galai, Yousr; Mhadhbi, Moez; Jedidi, Mohamed; de la Fuente, José; Darghouth, Mohamed Aziz

    2012-11-23

    The ixodid ticks from the Hyalomma genus are important pests of livestock, having major medical and veterinary significance in Northern Africa. Beside their direct pathogenic effects, these species are vectors of important diseases of livestock and in some instances of zoonoses. Anti-tick vaccines developed in Australia and Cuba based on the concealed antigen Bm86 have variable efficacy against H. anatolicum and H. dromedarii. This variation in vaccine efficacy could be explained by the variability in protein sequence between the recombinant Bm86 vaccine and Bm86 orthologs expressed in different Hyalomma species. Bm86 orthologs from three Hyalomma tick species were amplified in two overlapping fragments and sequenced. The rate of identity of the amino acid sequence of Hm86, He86 and Hdr86, the orthologs of Bm86, respectively, in H. marginatum marginatum, H. excavatum and H. dromedarii, with the Bm86 proteins from Rhipicephalus microplus (Australia, Argentina and Mozambique) ranged between 60 and 66%. The obtained amino-acid sequences of Hmm86, He86 and Hdr86 were compared with the Hd86-A1 sequence from H. scupense used as an experimental vaccine. The results showed an identity of 91, 88 and 87% for Hmm86, He86 and Hdr86, respectively. A specific program has been used to predict B cells epitopes sites. The comparison of antigenic sites between Hd86-A1 and Hm86/Hdr86/He86 revealed a diversity affecting 4, 8 and 12 antigenic peptides out of a total of 28 antigenic peptides, respectively. When the Bm86 orthologs amplification protocol adopted in this study was applied to H. excavatum, two alleles named He86p2a1 and He86p2a2 were detected in this species. This is the first time that two different alleles of Bm86 gene are recorded in the same tick specimen. He86p2a1 and He86p2a2 showed an amino acid identity of 92%. When He86p2a1 and He86p2a2 were compared to the corresponding sequence of Hd86-A1 protein, an identity of 86.4 and 91.0% was recorded, respectively. When

  12. Hd86, the Bm86 tick protein ortholog in Hyalomma scupense (syn. H. detritum): expression in Pichia pastoris and analysis of nucleotides and amino acids sequences variations prior to vaccination trials.

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    Ben Said, Mourad; Galai, Yousr; Canales, Mario; Nijhof, Ard Menzo; Mhadhbi, Moez; Jedidi, Mohamed; de la Fuente, José; Darghouth, Mohamed Aziz

    2012-02-10

    The genus Hyalomma includes the most frequent tick species infesting livestock in North Africa, one of these species, Hyalomma scupense (syn. H. detritum) is particularly important due to its role in the transmission of tropical theileriosis to cattle (Theileria annulata infection). We have cloned and characterized the orthologs of the Bm86 gene from H. scupense strains collected over Tunisia in 2006 and 2009. The recombinant protein rHd86 was expressed in Pichia pastoris for vaccination purpose using a transcript from the 2006 strain. The rHd86 was then purified from the yeast culture supernatant by a filtration and a size exclusion process. It was recognized by specific anti-Bm86 antisera. An important extent of inter-specific diversity ranging from 35 to 40% was recorded between Hd86 and Bm86/Bm95 proteins whilst a very limited level of intra-specific diversity (1.7%) occurred between the Hd86 vaccine candidate protein and its homologues from H. scupense strains collected in 2009. These results emphasise the need for assessing the efficacy against H. scupense and others important cattle Hyalomma species in Tunisia of our Hd86 vaccine candidate alongside with a Bm86 vaccine. PMID:21871736

  13. Bm86 midgut protein sequence variation in South Texas cattle fever ticks

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    Kammlah Diane M

    2010-11-01

    Full Text Available Abstract Background Cattle fever ticks, Rhipicephalus (Boophilus microplus and R. (B. annulatus, vector bovine and equine babesiosis, and have significantly expanded beyond the permanent quarantine zone established in South Texas. Currently, there are no vaccines approved for use within the United States for controlling these vectors. Vaccines developed in Australia and Cuba based on the midgut antigen Bm86 have variable efficacy against cattle fever ticks. A possible explanation for this variation in vaccine efficacy is amino acid sequence divergence between the recombinant Bm86 vaccine component and native Bm86 expressed in ticks from different geographical regions of the world. Results There was 91.8% amino acid sequence identity in Bm86 among R. microplus and R. annulatus sequenced from South Texas infestations. When South Texas isolates were compared to the Australian Yeerongpilly and Cuban Camcord vaccine strains, there was 89.8% and 90.0% identity, respectively. Most of the sequence divergence was focused in one region of the protein, amino acids 206-298. Hydrophilicity profiles revealed that two short regions of Bm86 (amino acids 206-210 and 560-570 appear to be more hydrophilic in South Texas isolates compared to vaccine strains. Only one amino acid difference was found between South Texas and vaccine strains within two previously described B-cell epitopes. A total of 4 amino acid differences were observed within three peptides previously shown to induce protective immune responses in cattle. Conclusions Sequence differences between South Texas isolates and Yeerongpilly and Camcord strains are spread throughout the entire Bm86 sequence, suggesting that geographic variation does exist. Differences within previously described B-cell epitopes between South Texas isolates and vaccine strains are minimal; however, short regions of hydrophilic amino acids found unique to South Texas isolates suggest that additional unique surface exposed

  14. Bm86 midgut protein sequence variation in South Texas cattle fever ticks

    OpenAIRE

    Kammlah Diane M; Kappmeyer Lowell S; Davey Ronald B; Freeman Jeanne M; Olafson Pia U

    2010-01-01

    Abstract Background Cattle fever ticks, Rhipicephalus (Boophilus) microplus and R. (B.) annulatus, vector bovine and equine babesiosis, and have significantly expanded beyond the permanent quarantine zone established in South Texas. Currently, there are no vaccines approved for use within the United States for controlling these vectors. Vaccines developed in Australia and Cuba based on the midgut antigen Bm86 have variable efficacy against cattle fever ticks. A possible explanation for this v...

  15. Efficacy of Rhipicephalus (Boophilus) microplus Bm86 against Hyalomma dromedarii and Amblyomma cajennense tick infestations in camels and cattle.

    Science.gov (United States)

    Rodríguez-Valle, Manuel; Taoufik, Amar; Valdés, Mario; Montero, Carlos; Ibrahin, Hassan; Hassan, Shawgi Mohammed; Jongejan, Frans; de la Fuente, Jose

    2012-05-14

    The recombinant Bm86-based tick vaccines have shown their efficacy for the control of cattle ticks, Rhipicephalus (Boophilus) microplus and R. annulatus infestations. However, cattle ticks often co-exist with multi-host ticks such as Hyalomma and Amblyomma species, thus requiring the control of multiple tick infestations for cattle and other hosts. Vaccination trials using a R. microplus recombinant Bm86-based vaccine were conducted in cattle and camels against Hyalomma dromedarii and in cattle against Amblyomma cajennense immature and adult ticks. The results showed an 89% reduction in the number of H. dromedarii nymphs engorging on vaccinated cattle, and a further 32% reduction in the weight of the surviving adult ticks. In vaccinated camels, a reduction of 27% and 31% of tick engorgement and egg mass weight, respectively was shown, while egg hatching was reduced by 39%. However, cattle vaccination with Bm86 did not have an effect on A. cajennense tick infestations. These results showed that Bm86 vaccines are effective against R. microplus and other tick species but improved vaccines containing new antigens are required to control multiple tick infestations. PMID:22446633

  16. Bm86 homologues and novel ATAQ proteins with multiple epidermal growth factor (EGF)-like domains from hard and soft ticks☆

    Science.gov (United States)

    Nijhof, Ard M.; Balk, Jesper A.; Postigo, Milagros; Rhebergen, Anne Marie; Taoufik, Amar; Jongejan, Frans

    2010-01-01

    Tick control on livestock relies principally on the use of acaricides but the development of acaricide resistance and concerns for environmental pollution underscore the need for alternative control methods, for instance through the use of anti-tick vaccines. Two commercial vaccines based on the recombinant Bm86 protein from Rhipicephalus (Boophilus) microplus ticks were developed. Partial protection of the Bm86 vaccine against other Rhipicephalus (Boophilus) and Hyalomma tick species suggests that the efficacy of a Bm86-based vaccine may be enhanced when based on the orthologous recombinant Bm86 antigen. We therefore identified and analysed the Bm86 homologues from species representing the main argasid and ixodid tick genera, including two from the prostriate Ixodes ricinus tick species. A novel protein from metastriate ticks with multiple epidermal growth factor (EGF)-like domains which is structurally related to Bm86 was identified by using a 3′ rapid amplification of cDNA ends (3′-RACE) method with a degenerate primer based on a highly conserved region of Bm86 and its orthologues. This second protein was named ATAQ after a part of its signature peptide. Quantitative reverse transcriptase-PCR showed that ATAQ proteins are expressed in both midguts and Malpighian tubules, in contrast to Bm86 orthologues which are expressed exclusively in tick midguts. Furthermore, expression of this protein over the life stages of R. microplus and Rhipicephalus appendiculatus was more continuous compared with Bm86. Although a highly effective vaccine antigen, gene silencing of Bm86 by RNA interference (RNAi) produced only a weak phenotype. Similarly the RNAi phenotype of Rhipicephalus evertsi evertsi females in which the expression of Ree86, ReeATAQ or a combination of both genes was silenced by RNAi did not differ from a mock-injected control group. The vaccine potential of ATAQ proteins against tick infestations is yet to be evaluated. PMID:20647015

  17. Bm86 homologues and novel ATAQ proteins with multiple epidermal growth factor (EGF)-like domains from hard and soft ticks.

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    Nijhof, Ard M; Balk, Jesper A; Postigo, Milagros; Rhebergen, Anne Marie; Taoufik, Amar; Jongejan, Frans

    2010-12-01

    Tick control on livestock relies principally on the use of acaricides but the development of acaricide resistance and concerns for environmental pollution underscore the need for alternative control methods, for instance through the use of anti-tick vaccines. Two commercial vaccines based on the recombinant Bm86 protein from Rhipicephalus (Boophilus) microplus ticks were developed. Partial protection of the Bm86 vaccine against other Rhipicephalus (Boophilus) and Hyalomma tick species suggests that the efficacy of a Bm86-based vaccine may be enhanced when based on the orthologous recombinant Bm86 antigen. We therefore identified and analysed the Bm86 homologues from species representing the main argasid and ixodid tick genera, including two from the prostriate Ixodes ricinus tick species. A novel protein from metastriate ticks with multiple epidermal growth factor (EGF)-like domains which is structurally related to Bm86 was identified by using a 3' rapid amplification of cDNA ends (3'-RACE) method with a degenerate primer based on a highly conserved region of Bm86 and its orthologues. This second protein was named ATAQ after a part of its signature peptide. Quantitative reverse transcriptase-PCR showed that ATAQ proteins are expressed in both midguts and Malpighian tubules, in contrast to Bm86 orthologues which are expressed exclusively in tick midguts. Furthermore, expression of this protein over the life stages of R. microplus and Rhipicephalus appendiculatus was more continuous compared with Bm86. Although a highly effective vaccine antigen, gene silencing of Bm86 by RNA interference (RNAi) produced only a weak phenotype. Similarly the RNAi phenotype of Rhipicephalus evertsi evertsi females in which the expression of Ree86, ReeATAQ or a combination of both genes was silenced by RNAi did not differ from a mock-injected control group. The vaccine potential of ATAQ proteins against tick infestations is yet to be evaluated. PMID:20647015

  18. Comparison of predicted binders in Rhipicephalus (Boophilus) microplus intestine protein variants Bm86 Campo Grande strain, Bm86 and Bm95.

    Science.gov (United States)

    Andreotti, Renato; Pedroso, Marisela S; Caetano, Alexandre R; Martins, Natália F

    2008-01-01

    This paper reports the sequence analysis of Bm86 Campo Grande strain comparing it with Bm86 and Bm95 antigens from the preparations TickGardPLUS and Gavac, respectively. The PCR product was cloned into pMOSBlue and sequenced. The secondary structure prediction tool PSIPRED was used to calculate alpha helices and beta strand contents of the predicted polypeptide. The hydrophobicity profile was calculated using the algorithms from the Hopp and Woods method, in addition to identification of potential MHC class-I binding regions in the antigens. Pair-wise alignment revealed that the similarity between Bm86 Campo Grande strain and Bm86 is 0.2% higher than that between Bm86 Campo Grande strain and Bm95 antigens. The identities were 96.5% and 96.3% respectively. Major suggestive differences in hydrophobicity were predicted among the sequences in two specific regions. PMID:18823577

  19. Vaccination against ticks (Boophilus spp.): the experience with the Bm86-based vaccine Gavac.

    Science.gov (United States)

    de la Fuente, J; Rodríguez, M; Montero, C; Redondo, M; García-García, J C; Méndez, L; Serrano, E; Valdés, M; Enríquez, A; Canales, M; Ramos, E; Boué, O; Machado, H; Lleonart, R

    1999-11-01

    The control of tick infestations and the transmission of tick-borne diseases remain a challenge for the cattle industry in tropical and subtropical areas of the world. Traditional control methods have been only partially successful and the parasites continue to result in significant losses for the cattle industry. Recently, vaccines containing the recombinant B. microplus gut antigen Bm86 have been developed. Our vaccine formulation (Gavac, Heber Biotec S.A., Havana, Cuba) has been registered and is commercially available in Cuba, Colombia, Dominican Republic, Brazil and Mexico. In controlled pen trials, Gavac has been effective for the control of artificial infestations of B. annulatus, B. decoloratus and chemical-sensitive and resistant B. microplus strains from Australia, Africa, America and Iran. In controlled field trials in Cuba, Brazil, Argentina and Mexico, Gavac has shown a 55-100% efficacy in the control of B. microplus infestations in grazing cattle 12-36 weeks after the first vaccination. Field trials under production conditions have been conducted in Cuba, Colombia, Brazil and Mexico in pure and cross-bred cattle herds. The application of Gavac has increased the time between acaricide treatments by an average of 32 /-21 days (P = 0.0005) resulting in important savings for the cattle industry. In Cuba, a cost-effectiveness analysis was conducted in more than 260000 animals. The cost-effectiveness analysis showed a 60% reduction in the number of acaricide treatments, together with the control of tick infestations and transmission of babesiosis, which resulted in savings of 23.4 dollars animal(-1) year (-1). These results clearly demonstrate the advantage of vaccination and support the application of Gavac for the control of Boophilus spp. infestations. PMID:10596754

  20. [Prokaryotic expression of Bm86 gene of Boophilus microplus and optimization of the expression condition].

    Science.gov (United States)

    Ma, Mi-Ling; Guan, Gui-Quan; Li, You-Quan; Liu, Ai-Hong; Ren, Qiao-Yun; Niu, Qing-Li; Yin, Hong; Luo, Jian-Xun

    2009-12-01

    A pair of specific primers was designed based on the reported Bm86 gene of Boophilus microplus,the Bm86 gene was cloned by PCR using the plasmid pMD18-T-Bm86 as templates, and subcloned into the prokaryotic plasmid pGEX-4T-1. The recombined plasmid was transformed into E. coli BL21(DE3) and followed by expression of the protein induced by different concentration of IPTG for different time. SDS-PAGE showed that the recombinant plasmid pGEX-4T-1/Bm86 expressed a fusion protein Bm86-GST (Mr 94 000) after being induced with IPTG. High level expression of Bm86-GST was found at 1 mmol/L IPTG condition a fter incubation for 8 h at 37 degree C, and the expression level of the recombinant Bm86-GST reached up to 29% of total E coli proteins Western-blotting analysis showed that the recombinant Bm86-GST was recognized by the rabbit anti-B. microplus positive serum. PMID:20232640

  1. Biochemical characterization of the recombinant Boophilus microplus Bm86 antigen expressed by transformed Pichia pastoris cells.

    Science.gov (United States)

    Montesino, R; Cremata, J; Rodríguez, M; Besada, V; Falcón, V; de la Fuente, J

    1996-02-01

    In the present paper we report the biochemical characteristics of the recombinant tick (Boophilus microplus) gut antigen Bm86 that previously has been cloned, expressed and recovered at high levels in the methylotrophic yeast Pichia pastoris. The results demonstrate that rBm86 had a modification at position 92 (Thr replaced by Ile) and aggregated, forming particles ranging between 17 and 40 nm. The rBm86 was N-glycosylated, having at least two non-glycosylated sequons (Asn-329 and Asn-363) and a ratio of only 0.4/65 (free Cys/total Cys)/mol of protein. PMID:8867893

  2. Bovine immunoprotection against Rhipicephalus (Boophilus) microplus with recombinant Bm86-Campo Grande antigen.

    Science.gov (United States)

    Cunha, Rodrigo Casquero; Pérez de León, Adalberto Angel; Leite, Fábio Pereira Leivas; Pinto, Luciano da Silva; Dos Santos Júnior, Alceu Gonçalves; Andreotti, Renato

    2012-01-01

    The southern cattle fever tick, Rhipicephalus (Boophilus) microplus, is no doubt the most economically important ectoparasite of cattle globally. The inappropriate use of chemical acaricides has driven the evolution of resistance in populations of R. (B.) microplus. Anti-tick vaccines represent a technology that can be combined with acaricides in integrated control programs to mitigate the impact of R. (B.) microplus. The recombinant form of Bm86 antigen from the Campo Grande (rBm86-CG) strain of R. (B.) microplus was produced using the Pichiapastoris expression system to test its ability to immunoprotect cattle against tick infestation. Secretion of rBm86-CG by P. pastoris through the bioprocess reported here simplified purification of the antigen. A specific humoral immune response was detected by ELISA in vaccinated cattle. Immunoblot results revealed that polyclonal antibodies from vaccinated cattle recognized a protein in larval extracts with a molecular weight corresponding to Bm86. The rBm86-CG antigen showed 31% efficacy against the Campo Grande strain of R. (B.) microplus infesting vaccinated cattle. The rBm86-CG is an antigen that could be used in a polyvalent vaccine as part of an integrated program for the control of R. (B.) microplus in the region that includes Mato Grosso do Sul. PMID:23070436

  3. Comparison of predicted binders in Rhipicephalus (Boophilus microplus intestine protein variants BM86 Campo Grande strain, BM86 and BM95 Comparação da previsão de ligação das variantes de proteína de intestino de Rhipicephalus (Boophilus microplus Bm86 cepa Campo Grande, Bm86 e Bm95

    Directory of Open Access Journals (Sweden)

    Renato Andreotti

    2008-06-01

    Full Text Available This paper reports the sequence analysis of Bm86 Campo Grande strain comparing it with Bm86 and Bm95 antigens from the preparations TickGardPLUS and GavacTM, respectively. The PCR product was cloned into pMOSBlue and sequenced. The secondary structure prediction tool PSIPRED was used to calculate alpha helices and beta strand contents of the predicted polypeptide. The hydrophobicity profile was calculated using the algorithms from the Hopp and Woods method, in addition to identification of potential MHC class-I binding regions in the antigens. Pair-wise alignment revealed that the similarity between Bm86 Campo Grande strain and Bm86 is 0.2% higher than that between Bm86 Campo Grande strain and Bm95 antigens. The identities were 96.5% and 96.3% respectively. Major suggestive differences in hydrophobicity were predicted among the sequences in two specific regions.O objetivo deste estudo foi analisar a seqüência de Bm86 cepa Campo Grande comparando-a com os antígenos Bm86 e Bm95 das preparações TickGardPLUS e GavacTM, respectivamente. O produto de PCR foi clonado em PMOSBlue e seqüenciado. Para calcular os conteúdos de alfa-hélice e fita beta do polipeptídio previsto, foi utilizada a ferramenta de prognóstico de estrutura secundária PSIPRED. O perfil de hidrofobicidade foi calculado usando os algoritmos de Hopp e Woods, além da identificação das possíveis regiões de ligação com MHC classe I nos antígenos. O alinhamento "pair-wise" revelou que a similaridade entre Bm86 cepa Campo Grande e Bm86 é 0,2% maior que aquela entre Bm86 cepa Campo Grande e Bm95. As identidades foram de 96,5% e 96,3%, respectivamente. Com relação à hidrofobicidade, os resultados sugerem que a maior diferença entre as seqüências está localizada em duas regiões específicas.

  4. Vaccination against Bm86 Homologues in Rabbits Does Not Impair Ixodes ricinus Feeding or Oviposition.

    Directory of Open Access Journals (Sweden)

    Jeroen Coumou

    Full Text Available Human tick-borne diseases that are transmitted by Ixodes ricinus, such as Lyme borreliosis and tick borne encephalitis, are on the rise in Europe. Diminishing I. ricinus populations in nature can reduce tick exposure to humans, and one way to do so is by developing an anti-vector vaccine against tick antigens. Currently, there is only one anti-vector vaccine available against ticks, which is a veterinary vaccine based on the tick antigen Bm86 in the gut of Rhipicephalus microplus. Bm86 vaccine formulations cause a reduction in the number of Rhipicephalus microplus ticks that successfully feed, i.e. lower engorgement weights and a decrease in the number of oviposited eggs. Furthermore, Bm86 vaccines reduce transmission of bovine Babesia spp. Previously two conserved Bm86 homologues in I. ricinus ticks, designated as Ir86-1 and Ir86-2, were described. Here we investigated the effect of a vaccine against recombinant Ir86-1, Ir86-2 or a combination of both on Ixodes ricinus feeding. Recombinant Ixodes ricinus Bm86 homologues were expressed in a Drosophila expression system and rabbits were immunized with rIr86-1, rIr86-2, a combination of both or ovalbumin as a control. Each animal was infested with 50 female adults and 50 male adults Ixodes ricinus and tick mortality, engorgement weights and egg mass were analyzed. Although serum IgG titers against rIr86 proteins were elicited, no effect was found on tick feeding between the rIr86 vaccinated animals and ovalbumin vaccinated animals. We conclude that vaccination against Bm86 homologues in Ixodes ricinus is not an effective approach to control Ixodes ricinus populations, despite the clear effects of Bm86 vaccination against Rhipicephalus microplus.

  5. Vaccination against Bm86 Homologues in Rabbits Does Not Impair Ixodes ricinus Feeding or Oviposition.

    Science.gov (United States)

    Coumou, Jeroen; Wagemakers, Alex; Trentelman, Jos J; Nijhof, Ard M; Hovius, Joppe W

    2014-01-01

    Human tick-borne diseases that are transmitted by Ixodes ricinus, such as Lyme borreliosis and tick borne encephalitis, are on the rise in Europe. Diminishing I. ricinus populations in nature can reduce tick exposure to humans, and one way to do so is by developing an anti-vector vaccine against tick antigens. Currently, there is only one anti-vector vaccine available against ticks, which is a veterinary vaccine based on the tick antigen Bm86 in the gut of Rhipicephalus microplus. Bm86 vaccine formulations cause a reduction in the number of Rhipicephalus microplus ticks that successfully feed, i.e. lower engorgement weights and a decrease in the number of oviposited eggs. Furthermore, Bm86 vaccines reduce transmission of bovine Babesia spp. Previously two conserved Bm86 homologues in I. ricinus ticks, designated as Ir86-1 and Ir86-2, were described. Here we investigated the effect of a vaccine against recombinant Ir86-1, Ir86-2 or a combination of both on Ixodes ricinus feeding. Recombinant Ixodes ricinus Bm86 homologues were expressed in a Drosophila expression system and rabbits were immunized with rIr86-1, rIr86-2, a combination of both or ovalbumin as a control. Each animal was infested with 50 female adults and 50 male adults Ixodes ricinus and tick mortality, engorgement weights and egg mass were analyzed. Although serum IgG titers against rIr86 proteins were elicited, no effect was found on tick feeding between the rIr86 vaccinated animals and ovalbumin vaccinated animals. We conclude that vaccination against Bm86 homologues in Ixodes ricinus is not an effective approach to control Ixodes ricinus populations, despite the clear effects of Bm86 vaccination against Rhipicephalus microplus. PMID:25919587

  6. Variation among Bm86 sequences in Rhipicephalus (Boophilus) microplus ticks collected from cattle across Thailand.

    Science.gov (United States)

    Kaewmongkol, S; Kaewmongkol, G; Inthong, N; Lakkitjaroen, N; Sirinarumitr, T; Berry, C M; Jonsson, N N; Stich, R W; Jittapalapong, S

    2015-06-01

    Anti-tick vaccines based on recombinant homologues Bm86 and Bm95 have become a more cost-effective and sustainable alternative to chemical pesticides commonly used to control the cattle tick, Rhipicephalus (Boophilus) microplus. However, Bm86 polymorphism among geographically separate ticks is reportedly associated with reduced effectiveness of these vaccines. The purpose of this study was to investigate the variation of Bm86 among cattle ticks collected from Northern, Northeastern, Central and Southern areas across Thailand. Bm86 cDNA and deduced amino acid sequences representing 29 female tick midgut samples were 95.6-97.0 and 91.5-93.5 % identical to the nucleotide and amino acid reference sequences, respectively, of the Australian Yeerongpilly vaccine strain. Multiple sequence analyses of these Bm86 variants indicated geographical relationships and polymorphism among Thai cattle ticks. Two larger groups of cattle tick strains were discernable based on this phylogenetic analysis of Bm86, a Thai group and a Latin American group. Thai female and male cattle ticks (50 pairs) were also subjected to detailed morphological characterization to confirm their identity. The majority of female ticks had morphological features consistent with those described for R. (B.) microplus, whereas, curiously, the majority of male ticks were more consistent with the recently re-instated R. (B.) australis. A number of these ticks had features consistent with both species. Further investigations are warranted to test the efficacies of rBm86-based vaccines to homologous and heterologous challenge infestations with Thai tick strains and for in-depth study of the phylogeny of Thai cattle ticks. PMID:25777941

  7. Rhipicephalus (Boophilus) microplus: expression and characterization of Bm86-CG in Pichia pastoris.

    Science.gov (United States)

    Cunha, Rodrigo Casquero; Andreotti, Renato; Leite, Fábio Pereira Leivas

    2011-01-01

    The cattle tick Rhipicephalus (Boophilus) microplus is responsible for great economic losses. It is mainly controlled chemically, with limitations regarding development of resistance to the chemicals. Vaccines may help control this parasite, thereby reducing tick pesticide use. In this light, we performed subcloning of the gene of the protein Bm86-GC, the homologue protein that currently forms the basis of vaccines (Gavac(TM) and TickGard(PLUS)) that have been developed against cattle ticks. The subcloning was done in the pPIC9 expression vector, for transformation in the yeast Pichia pastoris. This protein was characterized by expression of the recombinant Mut+ strain, which expressed greater quantities of protein. The expressed protein (rBm86-CG) was recognized in the Western-blot assay using anti-Gavac, anti-TickGard, anti-larval extract and anti-rBm86-CG polyclonal sera. The serum produced in cattle vaccinated with the antigen CG rBm86 presented high antibody titers and recognized the native protein. The rBm86-GC has potential relevance as an immunogen for vaccine formulation against cattle ticks. PMID:21722483

  8. Immunisation with recombinant proteins subolesin and Bm86 for the control of Dermanyssus gallinae in poultry.

    Science.gov (United States)

    Harrington, David; Canales, Mario; de la Fuente, José; de Luna, Carlos; Robinson, Karen; Guy, Jonathan; Sparagano, Olivier

    2009-06-19

    Dermanyssus gallinae has a worldwide distribution and is considered to be the most serious and economically significant ectoparasite affecting egg-laying poultry in Europe. Recombinant Bm86 and subolesin proteins derived from Boophilus microplus ticks and Aedes albopictus mosquitoes were used to immunise poultry in an attempt to control D. gallinaein vitro. Immunisation with subolesin and Bm86 stimulated different profiles of IgY response, whilst Bm86 but not subolesin was recognized by IgY on western blots. Orthologues for Bm86 were not found in D. gallinae by PCR, but a 150 bp fragment aligned with mammalian akirin 1 and a 300 bp fragment aligned with Amblyomma hebraeum were amplified by subolesin PCR. D. gallinae mortality after feeding was 35.1% higher (P=0.009) in the Subolesin group and 23% higher (not significant) in the Bm86 compared to the Control group. Thus it can be concluded that immunisation with recombinant subolesin can stimulate a protective response in laying hens against D. gallinae. PMID:19501789

  9. 微小牛蜱Bm86基因的真核表达%Eukaryotic expression of Bm86 gene of Boophilus microplus in Pichia pastoris

    Institute of Scientific and Technical Information of China (English)

    李文卉; 任巧云; 罗建勋; 殷宏; 关贵全; 马米玲; 刘志杰; 刘爱红; 党志胜; 高金亮

    2005-01-01

    采用RT-PCR技术从微小牛蜱饥饿幼蜱破解物中扩增到Bm86基因,将其与巴斯德毕赤酵母分泌型表达载体pPIC9K重组构建了重组表达载体pPIC9K-Bm86,测序正确后将其用SacⅠ内切酶线性化后采用电穿孔法转化巴斯德毕赤酵母菌GS115,经G418抗性筛选高拷贝重组菌株后用甲醇诱导表达,SDS-PAGE和Western-blotting分析结果表明,诱导表达的培养上清液中表达出具有反应活性的68 ku重组Bm86蛋白,目的蛋白约占培养上清液中蛋白总量的32%以上,诱导96 h目的蛋白的表达量为0.36 mg/mL.

  10. Vaccination against Bm86 Homologues in Rabbits Does Not Impair Ixodes ricinus Feeding or Oviposition

    OpenAIRE

    Jeroen Coumou; Alex Wagemakers; Trentelman, Jos J.; Nijhof, Ard M; Hovius, Joppe W.

    2015-01-01

    Human tick-borne diseases that are transmitted by Ixodes ricinus, such as Lyme borreliosis and tick borne encephalitis, are on the rise in Europe. Diminishing I. ricinus populations in nature can reduce tick exposure to humans, and one way to do so is by developing an anti-vector vaccine against tick antigens. Currently, there is only one anti-vector vaccine available against ticks, which is a veterinary vaccine based on the tick antigen Bm86 in the gut of Rhipicephalus microplus. Bm86 vaccin...

  11. Comparison of predicted binders in Rhipicephalus (Boophilus) microplus intestine protein variants BM86 Campo Grande strain, BM86 and BM95 Comparação da previsão de ligação das variantes de proteína de intestino de Rhipicephalus (Boophilus) microplus Bm86 cepa Campo Grande, Bm86 e Bm95

    OpenAIRE

    Renato Andreotti; Marisela S. Pedroso; Caetano, Alexandre R; Natália F. Martins

    2008-01-01

    This paper reports the sequence analysis of Bm86 Campo Grande strain comparing it with Bm86 and Bm95 antigens from the preparations TickGardPLUS and GavacTM, respectively. The PCR product was cloned into pMOSBlue and sequenced. The secondary structure prediction tool PSIPRED was used to calculate alpha helices and beta strand contents of the predicted polypeptide. The hydrophobicity profile was calculated using the algorithms from the Hopp and Woods method, in addition to identification of po...

  12. Polymorphism of the bm86 gene in South American strains of the cattle tick Boophilus microplus.

    Science.gov (United States)

    Sossai, Sidimar; Peconick, Ana P; Sales-Junior, Policarpo A; Marcelino, Francismar C; Vargas, Marlene I; Neves, Elisangela S; Patarroyo, Joaquín H

    2005-01-01

    Thirty Boophilus microplus strains from various geographic regions of Brazil, Argentina, Uruguay, Venezuela and Colombia were analyzed for the bm86 and bm95 gene. A fragment of cDNA of 794 base pairs of the parasite larvae, included between nucleotides 278-1071s, was amplified and cloned on the pGEM-T vector. Two random clones were sequenced for each population and the nucleotides 278-1071 and predicted amino acid sequences compared with the bm86 and bm95 genes. Variations from 1.76 to 3.65% were detected in the nucleotides sequence when compared with the homologous sequence of the bm86 gene and a 3.4-6.08% in the homologous amino acid sequence of the Bm86 protein. When the sequences obtained were compared with the bm95 gene, variations from 0.50 to 3.15% were detected. Variations from 1.14 to 4.56% were detected for the Bm95 protein homologous sequences in the deduced amino acid sequence. Only five of the 30 strains analyzed presented two different types of alleles expressed and the two alleles of the Alegre population and allele 1 of the Betim population were the most divergent of all those analyzed. PMID:16323051

  13. Adjuvant and immunostimulating properties of the recombinant Bm86 protein expressed in Pichia pastoris.

    Science.gov (United States)

    García-García, J C; Soto, A; Nigro, F; Mazza, M; Joglar, M; Hechevarría, M; Lamberti, J; de la Fuente, J

    1998-01-01

    The cattle tick Boophilus microplus has remained a latent problem to the cattle industry. The recombinant vaccine GAVAC against the cattle tick has proved its efficacy and, conveniently, combined with the use of chemicals could be the solution to this problem. As this vaccine is based in the recombinant concealed antigen Bm86, it has to be given periodically to the animal to maintain an adequate level of antibodies. Some other commercially available vaccines for cattle also have to be given periodically, which creates the possibility of combining vaccines for cattle. In an attempt to evaluate the possible interactions of the Bm86 with other vaccine antigens, a potent stimulatory effect was demonstrated of the recombinant Bm86 on the humoral immune response to the recombinant Hepatitis B surface antigen in mice, and to the inactivated Infectious Bovine Rhinothraqueitis virus in cattle. These results make the Bm86 antigen expressed in Pichia pastoris a good candidate for combining vaccines for cattle because of its dual role, immunogen and adjuvant. PMID:9682358

  14. Molecular characterization of Rhipicephalus (Boophilus) microplus Bm86 homologue from Haemaphysalis longicornis ticks.

    Science.gov (United States)

    Liao, Min; Zhou, Jinlin; Hatta, Takeshi; Umemiya, Rika; Miyoshi, Takeharu; Tsuji, Naotoshi; Xuan, Xuenan; Fujisaki, Kozo

    2007-05-15

    One sequence in the EST database of a midgut cDNA library prepared from semi-engorged female Haemaphysalis longicornis ticks has been found to be a homologue of the Bm86 gene of Rhipicephalus (Boophilus) microplus ticks. The full-length sequence containing a 1785 bp open reading fragment (ORF) was obtained and designated as the Hl86 gene. The predicted amino acid sequence of the Hl86 gene shows a 37% identity to the Bm86 gene. Hl86 is predicted to be a GPI-anchored membrane-bound glycoprotein with a 19-amino acid signal sequence and a 22-amino acid hydrophobic region adjacent to the carboxyl terminus. The most important feature that Hl86 has in common with Bm86 is the repeated pattern of 6 cysteine residues forming epidermal growth factor (EGF)-like domains. RT-PCR analysis showed that Hl86 mRNA transcripts are expressed in all the life cycles of H. longicornis, and the expression was found in the midgut of the adult tick. The Hl86 was expressed in Escherichia coli as a gene10 fusion protein. Mouse anti-recombinant Hl86 serum recognized an 86 kDa protein band in the midgut lysate of semi-engorged ticks in Western blot analysis and showed a strong reaction on the luminal surface of midgut cells in an indirect immunofluorescent antibody test (IFAT). Silencing of the Hl86 gene by RNAi led to a significant reduction in the engorged tick body weight. This is the first report of cloning and characterization of the Bm86 homologue in different genera and species of ixodid and argasid ticks since Bm86 was first reported in 1989. PMID:17363170

  15. Sequence variations in the Boophilus microplus Bm86 locus and implications for immunoprotection in cattle vaccinated with this antigen.

    Science.gov (United States)

    García-García, J C; Gonzalez, I L; González, D M; Valdés, M; Méndez, L; Lamberti, J; D'Agostino, B; Citroni, D; Fragoso, H; Ortiz, M; Rodríguez, M; de la Fuente, J

    1999-11-01

    Cattle tick infestations constitute a major problem for the cattle industry in tropical and subtropical regions of the world. Traditional control methods have been only partially successful, hampered by the selection of chemical-resistant tick populations. The Boophilus microplus Bm86 protein was isolated from tick gut epithelial cells and shown to induce a protective response against tick infestations in vaccinated cattle. Vaccine preparations including the recombinant Bm86 are used to control cattle tick infestations in the field as an alternative measure to reduce the losses produced by this ectoparasite. The principle for the immunological control of tick infestations relies on a polyclonal antibody response against the target antigen and, therefore, should be difficult to select for tick-resistant populations. However, sequence variations in the Bm86 locus, among other factors, could affect the effectiveness of Bm86-containing vaccines. In the present study we have addressed this issue, employing data obtained with B. microplus strains from Australia, Mexico, Cuba, Argentina and Venezuela. The results showed a tendency in the inverse correlation between the efficacy of the vaccination with Bm86 and the sequence variations in the Bm86 locus (R2 = 0.7). The mutation fixation index in the Bm86 locus was calculated and shown to be between 0.02 and 0.1 amino acids per year. Possible implications of these findings for the immunoprotection of cattle against tick infestations employing the Bm86 antigen are discussed. PMID:10668863

  16. Sequence variation of Bm86 in cattle fever ticks isolated from outbreaks in south Texas

    Science.gov (United States)

    The prevalence of Rhipicephalus (Boophilus) microplus and Rhipicephalus (Boophilus) annulatus cattle infestations have significantly expanded beyond the original quarantine zone established in south Texas as part of the Cattle Fever Tick Eradication Program. Major obstacles for containment of ticks...

  17. Effect of particulation on the immunogenic and protective properties of the recombinant Bm86 antigen expressed in Pichia pastoris.

    Science.gov (United States)

    García-García, J C; Montero, C; Rodríguez, M; Soto, A; Redondo, M; Valdés, M; Méndez, L; de la Fuente, J

    1998-02-01

    The recombinant Bm86 tick antigen expressed in Pichia pastoris is obtained in a highly particulated form, as a distinguish feature of this expression system. This particulated protein, the active principle of the recombinant vaccine Gavac against the cattle tick, have shown high immunogenic and protective properties, probably associated with its own characteristics. To evaluate the effects of particulation on the properties of Bm86, three groups of calves were immunized with particulated or non-particulated recombinant Bm86 and the anti-Bm86 antibody response determined. Animals were challenged with a controlled tick infestation and the protective capacities of both proteins assessed. Humoral immune response and protection in cattle vaccinated with the particulated antigen were higher. These experiments suggested that particulation of the Bm86 expressed in P. pastoris is an important feature for the protective properties of the antigen in vaccine preparations. PMID:9607058

  18. Cloning of Bm86 gene of Boophilus microplus and construction of recombinant expression vector%微小牛蜱Bm86基因的克隆及真核表达载体的构建

    Institute of Scientific and Technical Information of China (English)

    李文卉; 任巧云; 殷宏; 罗建勋; 刘磊; 党志胜; 高金亮; 关贵全; 刘志杰; 刘爱红; 马米玲

    2005-01-01

    为了克隆微小牛蜱Bm86基因及构建该基因的表达载体,以微小牛蜱饥饿幼蜱的破解物提取的总RNA为模板,参照已发表的微小牛蜱Bm86基因的核苷酸序列,设计了1对引物,采用 RT-PCR技术获得微小牛蜱Bm86基因;将Bm86基因克隆入载体,并进行序列分析,结果证明,克隆的Bm86基因序列与GenBank上登录的Bm86基因序列的同源性达97.4%,而且该序列包含完整的开放阅读框.将该基因克隆入真核表达载体pPIC9K,构建并获得了重组真核表达载体pPIC9K-Bm86.

  19. Immunization of cattle with synthetic peptides derived from the Boophilus microplus gut protein (Bm86).

    Science.gov (United States)

    Patarroyo, J H; Portela, R W; De Castro, R O; Pimentel, J Couto; Guzman, F; Patarroyo, M E; Vargas, M I; Prates, A A; Mendes, M A Dias

    2002-09-25

    Three synthetic peptides (SBm4912, SBm7462 and SBm19733), derived from the Bm86 glycoprotein from Boophilus microplus gut, were constructed and used to immunize cattle from a tick-free area. The immunized animals received three subcutaneous doses of the peptides, with saponin as adjuvant, at 30-day intervals. The immune response was evaluated by IgG elicited against the peptides by the detection of anti-Bm86 specific antibodies in situ and by Western blotting analysis. After tick challenge, reduction in the number, weight and oviposition capacity of engorged females was observed in the tick population that had fed on immunized animals. The results pointed a high efficacy (81.05%) for the SBm7462 synthetic peptide in relation to the others (p<0.01), demonstrating the efficiency of the immune response elicited by synthetic peptides to control the cattle tick B. microplus. PMID:12127414

  20. Vaccination with BM86, subolesin and akirin protective antigens for the control of tick infestations in white tailed deer and red deer.

    Science.gov (United States)

    Carreón, Diana; de la Lastra, José M Pérez; Almazán, Consuelo; Canales, Mario; Ruiz-Fons, Francisco; Boadella, Mariana; Moreno-Cid, Juan A; Villar, Margarita; Gortázar, Christian; Reglero, Manuel; Villarreal, Ricardo; de la Fuente, José

    2012-01-01

    Red deer (Cervus elaphus) and white-tailed deer (Odocoileus virginianus) are hosts for different tick species and tick-borne pathogens and play a role in tick dispersal and maintenance in some regions. These factors stress the importance of controlling tick infestations in deer and several methods such as culling and acaricide treatment have been used. Tick vaccines are a cost-effective alternative for tick control that reduced cattle tick infestations and tick-borne pathogens prevalence while reducing the use of acaricides. Our hypothesis is that vaccination with vector protective antigens can be used for the control of tick infestations in deer. Herein, three experiments were conducted to characterize (1) the antibody response in red deer immunized with recombinant BM86, the antigen included in commercial tick vaccines, (2) the antibody response and control of cattle tick infestations in white-tailed deer immunized with recombinant BM86 or tick subolesin (SUB) and experimentally infested with Rhipicephalus (Boophilus) microplus, and (3) the antibody response and control of Hyalomma spp. and Rhipicephalus spp. field tick infestations in red deer immunized with mosquito akirin (AKR), the SUB ortholog and candidate protective antigen against different tick species and other ectoparasites. The results showed that deer produced an antibody response that correlated with the reduction in tick infestations and was similar to other hosts vaccinated previously with these antigens. The overall vaccine efficacy was similar between BM86 (E=76%) and SUB (E=83%) for the control of R. microplus infestations in white-tailed deer. The field trial in red deer showed a 25-33% (18-40% when only infested deer were considered) reduction in tick infestations, 14-20 weeks after the first immunization. These results demonstrated that vaccination with vector protective antigens could be used as an alternative method for the control of tick infestations in deer to reduce tick populations

  1. Bovine immunoprotection against Rhipicephalus (Boophilus) microplus with recombinant Bm86-Campo Grande antigen Imunoproteção de bovinos contra Rhipicephalus (Boophilus) microplus com antígeno recombinante Bm86-Campo Grande

    OpenAIRE

    Rodrigo Casquero Cunha; Adalberto Angel Pérez de León; Fábio Pereira Leivas Leite; Luciano da Silva Pinto; Alceu Gonçalves dos Santos Júnior; Renato Andreotti

    2012-01-01

    The southern cattle fever tick, Rhipicephalus (Boophilus) microplus, is no doubt the most economically important ectoparasite of cattle globally. The inappropriate use of chemical acaricides has driven the evolution of resistance in populations of R. (B.) microplus. Anti-tick vaccines represent a technology that can be combined with acaricides in integrated control programs to mitigate the impact of R. (B.) microplus. The recombinant form of Bm86 antigen from the Campo Grande (rBm86-CG) strai...

  2. Cloning and expression of Bm86 gene of Boophilus microplus in E.coli%微小牛蜱Bm86基因的克隆与原核表达

    Institute of Scientific and Technical Information of China (English)

    樊瑞泉; 任巧云; 刘爱红; 罗建勋; 杨孝朴; 殷宏; 高金亮; 关贵全; 刘志杰; 党志胜; 马米玲

    2007-01-01

    根据已发表的Bm86基因序列,设计表达型引物,利用RT-PCR技术,从微小牛蜱饥饿幼蜱的研磨物中扩增Bm86基因,将PCR产物连入pGEM-T Easy载体,构建重组克隆载体pGEM-T easy-Bm86.测序分析表明:克隆的微小牛蜱Bm86基因序列与GenBank上登录的Bm86基因的核苷酸和氨基酸序列的同源性分别为97 %和95.6 %.然后对重组克隆载体pGEM-T easy-Bm86进行双酶切,获得带有粘性末端的Bm86基因片段,并将此片段定向亚克隆入原核表达载体pGEX-4T-1,构建重组原核表达载体pGEX-4T-1-Bm86,将其转化到BL21宿主菌中,用IPTG进行诱导表达.SDS-PAGE检测表明表达产物为分子量为88Ku的融合蛋白,目的蛋白约占蛋白总量的39 %,表达量约为1.08mg/mL.Western blot分析表明此表达产物能被兔抗微小牛蜱阳性血清所识别.

  3. Comparative vaccination of cattle against Boophilus microplus with recombinant antigen Bm86 alone or in combination with recombinant Bm91.

    Science.gov (United States)

    Willadsen, P; Smith, D; Cobon, G; McKenna, R V

    1996-05-01

    Cattle were vaccinated either with a single recombinant tick antigen, Bm86 or with a combination of two recombinant antigens, Bm86 and Bm91 from the tick Boophilus microplus. In three experiments, the responses of cattle to subsequent challenge with the tick were assessed. The addition of the Bm91 antigen enhanced the efficacy of the vaccination over that with Bm86 alone to a statistically significant degree. Moreover, co-vaccination with two antigens did not impair the response of cattle to the Bm86 antigen. Finally, responses of individual cattle to the two antigens were independent. All of these results may be relevant to the increase in efficacy expected from a dual antigen vaccine. PMID:9229376

  4. Partial sequencing of Bm86 gene for studying the phylogeny of an Indian isolate of Rhipicephalus(Boophilus) microplus tick

    OpenAIRE

    Anbarasi, P.; Latha, B. R.; Dhinakar Raj, G.; Sreekumar, C.; Senthuran, S.

    2013-01-01

    Tick gut glycoprotein, designated as Bm86, found on the luminal surface of the plasma membrane of gut epithelial cells of Boophilus microplus, which is a concealed antigen, has been used as vaccine candidate molecule for immunization against ticks. To better understand the molecular diversity of Bm86 gene in ticks, a portion of the cDNA was sequenced from an Indian isolate of B. microplus. Comparison of nucleotide sequence revealed that Indian isolate had 97 % homology (18 polymorphisms) with...

  5. Rhipicephalus (Boophilus microplus: expression and characterization of Bm86-CG in Pichia pastoris Rhipicephalus (Boophilus microplus: expressão e caracterização da Bm86-CG em Pichia pastoris

    Directory of Open Access Journals (Sweden)

    Rodrigo Casquero Cunha

    2011-06-01

    Full Text Available The cattle tick Rhipicephalus (Boophilus microplus is responsible for great economic losses. It is mainly controlled chemically, with limitations regarding development of resistance to the chemicals. Vaccines may help control this parasite, thereby reducing tick pesticide use. In this light, we performed subcloning of the gene of the protein Bm86-GC, the homologue protein that currently forms the basis of vaccines (GavacTM and TickGardPLUS that have been developed against cattle ticks. The subcloning was done in the pPIC9 expression vector, for transformation in the yeast Pichia pastoris. This protein was characterized by expression of the recombinant Mut+ strain, which expressed greater quantities of protein. The expressed protein (rBm86-CG was recognized in the Western-blot assay using anti-Gavac, anti-TickGard, anti-larval extract and anti-rBm86-CG polyclonal sera. The serum produced in cattle vaccinated with the antigen CG rBm86 presented high antibody titers and recognized the native protein. The rBm86-GC has potential relevance as an immunogen for vaccine formulation against cattle ticks.O carrapato-do-boi Rhipicephalus (Boophilus microplus é responsável por grandes perdas econômicas. Seu controle é principalmente químico e apresenta limitações quanto ao desenvolvimento de resistência aos princípios ativos. As vacinas podem auxiliar no controle deste parasita diminuindo as aplicações de carrapaticidas. Considerando isso, foi realizada a subclonagem do gene da proteína Bm86-CG, proteína homologa a que atualmente é a base das vacinas desenvolvidas (GavacTM e TickGardPLUS contra o carrapato-do-boi, no vetor de expressão pPIC9, para ser transformado em levedura, Pichia pastoris. Esta proteína foi caracterizada pela expressão da cepa recombinante Mut+ que expressou maior quantidade de proteína. A proteína expressa, rBm86-CG, foi reconhecida no ensaio de Western-blot pelos soros policlonais anti-Gavac, anti-TickGard, anti

  6. Bm86 midgut protein sequence variation in south Texas cattle fever ticks

    Science.gov (United States)

    Cattle fever ticks, Rhipicephalus (Boophilus) microplus and R. (B.) annulatus, vector bovine and equine babesiosis, and have significantly expanded beyond the permanent quarantine zone established in South Texas. Currently, there are no vaccines approved for use within the United States for controll...

  7. Control of Boophilus microplus populations in grazing cattle vaccinated with a recombinant Bm86 antigen preparation.

    Science.gov (United States)

    Rodríguez, M; Penichet, M L; Mouris, A E; Labarta, V; Luaces, L L; Rubiera, R; Cordovés, C; Sánchez, P A; Ramos, E; Soto, A

    1995-04-01

    Current methods for the control of cattle tick Boophilus microplus infestations are not effective and the parasite remains a serious problem for the cattle industry in tropical and subtropical areas. Recently, we developed a vaccine against B. microplus employing a recombinant Bm86 (rBm86) antigen preparation (Gavac, Heber Biotec) and it was shown to induce a protective response in vaccinated animals under controlled conditions. Here we show that, under field conditions in grazing cattle, the vaccine is able to control B. microplus populations. Two parasite-free farms were employed for the study. In the first farm, animals were vaccinated with the recombinant vaccine, while, in the second, animals received a saline injection in adjuvant. After immunization, animals were artificially infected and the infestation rate was recorded. Over the 33 weeks of the experiment, the infestation rate was lower in the vaccinated group compared with the control group. At the end of the experiment it was necessary to use chemicals in the control farm after serious losses in production and animals. PMID:7660571

  8. Bm86 antigen induces a protective immune response against Boophilus microplus following DNA and protein vaccination in sheep.

    Science.gov (United States)

    De Rose, R; McKenna, R V; Cobon, G; Tennent, J; Zakrzewski, H; Gale, K; Wood, P R; Scheerlinck, J P; Willadsen, P

    1999-11-30

    Vaccination of sheep with a plasmid bearing the full length gene for the tick antigen Bm86 either alone or co-administered with plasmid carrying the ovine genes for the cytokines, granulocyte and macrophage colony stimulating factor (GM-CSF) or interleukin (IL)-1beta induced a relatively low level of protection against subsequent tick infestation. This tick damage reached statistical significance only for the groups which were vaccinated with plasmid encoding for Bm86, co-administered with plasmid encoding for ovine GM-CSF. Antibody titres measured against Bm86 were also low in all groups injected with the Bm86 DNA vaccine. Antibody production and anti-tick effect were significantly less than that achieved by two vaccinations with recombinant Bm86 protein. In all cases only a low level of antigen-specific stimulation of peripheral blood lymphocytes was recorded, as measured either by the incorporation of tritiated thymidine or the release of IFN-gamma. Injection of DNA encoding for Bm86, either alone or with co-administered cytokine genes, did however prime for a strong subsequent antibody response following a single injection of recombinant Bm86 protein in adjuvant. Antibody production nevertheless appeared to be slightly less effective than following two vaccinations with recombinant protein. The persistence of antibody following vaccination was the same regardless of the method of primary sensitization. In all cases the half-life of the antibody response was approximately 40-50 days indicating that, in contrast to results reported in mice, DNA vaccination in sheep did not result in sustained antibody production. PMID:10587297

  9. On Paradoxurus annulatus, Wagner

    NARCIS (Netherlands)

    Jentink, F.A.

    1886-01-01

    In »die Säugethiere Schreber’s, Supplementband II” we find on p. 353 the following description of a new Paradoxurus by J. E. Wagner: P. annulatus Wagn. Der geringelte Roller. P. supra. e nigro fulvoque mixtus, subtus e ferrugineo lutescens, cauda nigro-annulata, auriculis dense pilosis.

  10. Bovine immunoprotection against Rhipicephalus (Boophilus microplus with recombinant Bm86-Campo Grande antigen Imunoproteção de bovinos contra Rhipicephalus (Boophilus microplus com antígeno recombinante Bm86-Campo Grande

    Directory of Open Access Journals (Sweden)

    Rodrigo Casquero Cunha

    2012-09-01

    Full Text Available The southern cattle fever tick, Rhipicephalus (Boophilus microplus, is no doubt the most economically important ectoparasite of cattle globally. The inappropriate use of chemical acaricides has driven the evolution of resistance in populations of R. (B. microplus. Anti-tick vaccines represent a technology that can be combined with acaricides in integrated control programs to mitigate the impact of R. (B. microplus. The recombinant form of Bm86 antigen from the Campo Grande (rBm86-CG strain of R. (B. microplus was produced using the Pichiapastoris expression system to test its ability to immunoprotect cattle against tick infestation. Secretion of rBm86-CG by P. pastoris through the bioprocess reported here simplified purification of the antigen. A specific humoral immune response was detected by ELISA in vaccinated cattle. Immunoblot results revealed that polyclonal antibodies from vaccinated cattle recognized a protein in larval extracts with a molecular weight corresponding to Bm86. The rBm86-CG antigen showed 31% efficacy against the Campo Grande strain of R. (B. microplus infesting vaccinated cattle. The rBm86-CG is an antigen that could be used in a polyvalent vaccine as part of an integrated program for the control of R. (B. microplus in the region that includes Mato Grosso do Sul.O carrapato Rhipicephalus (Boophilus microplus é, sem dúvidas, o ectoparasito economicamente mais importante para o gado a nível mundial. A utilização inadequada de acaricidas tem impulsionado a evolução da resistência em populações de R. (B. microplus. Vacinas contra o carrapato representam uma tecnologia que pode ser combinada com acaricidas em programas de controle integrado para diminuir o impacto de R. (B. microplus. A forma recombinante da Bm86 da cepa Campo Grande (rBm86-CG de R. (B. microplus foi produzido utilizando o sistema de expressão em Pichia pastoris para testar sua capacidade de imunoproteção ao gado contra a infestação de

  11. Exploring the use of an anti-tick vaccine as a tool for the integrated eradication of the cattle fever tick, Rhipicephalus (Boophilus) annulatus.

    Science.gov (United States)

    Miller, Robert; Estrada-Peña, Agustín; Almazán, Consuelo; Allen, Andrew; Jory, Lauren; Yeater, Kathleen; Messenger, Matthew; Ellis, Dee; Pérez de León, Adalberto A

    2012-08-17

    Bovine babesiosis, also known as cattle fever, is a tick-borne protozoal disease foreign to the United States. It was eradicated by eliminating the vector species, Rhipicephalus (Boophilus) annulatus and Rhipicephalus (Boophilus) microplus, through the efforts of the Cattle Fever Tick Eradication Program (CFTEP), with the exception of a permanent quarantine zone (PQZ) in south Texas along the border with Mexico. Keeping the U.S. free of cattle fever ticks in a sustainable manner is a critical national agricultural biosecurity issue. The efficacy of a Bm86-based anti-tick vaccine commercialized outside of the U.S. was evaluated against a strain of R. annulatus originated from an outbreak in Texas. Vaccination controlled 99.9 and 91.4% of the ticks 8 weeks and 5.5 months after the initial vaccination, respectively. Computer modeling of habitat suitability within the PQZ typically at risk of re-infestation with R. annulatus from Mexico predicted that at a level of control greater than 40%, eradication would be maintained indefinitely. Efficacy and computer modeling data indicate that the integration of vaccination using a Bm86-based anti-tick vaccine with standard eradication practices within the northwestern half of the PQZ could incentivize producers to maintain cattle on pasture thereby avoiding the need to vacate infested premises. Implementing this epidemiologically proactive strategy offers the opportunity to prevent R. annulatus outbreaks in the U.S., which would represent a significant shift in the way the CFTEP operates. PMID:22687762

  12. 新疆南疆微小牛蜱Bm86基因及其编码蛋白剖析%Analysis of Bm86 Gene and its Encoding Protein of Rhipicephalus microplus in South Xinjiang

    Institute of Scientific and Technical Information of China (English)

    刘永宏; 赵丽

    2014-01-01

    为了能高效表达理想的微小牛蜱抗原,本研究对新疆生产建设兵团塔里木畜牧科技重点实验室已获得的Bm86基因(Bm86 Tarim)进行遗传进化分析,并对其编码蛋白进行生物学信息分析.结果显示本研究获得的新疆南疆微小牛蜱Bm86Tarim序列与已登录的所有国外Bm86基因完整阅读框序列的核苷酸和氨基酸同源性分别为95.9%~98.6%和93.8%~97.8%,差异极小;遗传进化树分析结果显示本研究毒株与已登录多数毒株在同一分支内;生物学信息预测结果显示该蛋白不稳定,不溶性的概率为93.26%,有4个潜在糖基化位点.本试验结果为后续Bm86基因表达、免疫抗原制备和抗微小牛蜱疫苗的研制奠定基础.

  13. Performance of two Bm86 antigen vaccin formulation against tick using crossbreed bovines in stall test.

    Science.gov (United States)

    Andreotti, Renato

    2006-01-01

    Cattle tick control remains a serious problem for cattle farms in Brazil due to the limited success achieved with chemicals. In Brazil, the use of vaccines for tick control associated with the use of chemicals and pasture rotation may open possibilities for integrated control. However, it is important to know whether regional Boophilus microplus strains are sensitive to antibodies produced by the available antigens: antigen preparations Gavac™ and TickGard(PLUS). The aim of this research was to evaluate the performance of two Bm86 antigen vaccine formulation against tick using crossbred bovines in stall test antigen against a regional B. microplus strain. The experiment was carried out in central Brazil (20 degrees 27'S, 54 degrees 37'W). A trial was conducted in stall conditions on crossbred cattle under controlled infestation. Two groups of 16 animals each, homogeneous in weight and sex, were vaccinated with Gavac™ or TickGard(PLUS), two groups of eight animals as control. Challenge was performed on three alternate days, with 5,000 larvae each time, beginning 21 days after the second injection. The antibody response was measured by ELISA and vaccinated animals presented immune response considering IgG levels. The results showed 49.2% and 46.4% protection efficacy for Gavac™ and TickGard(PLUS), respectively. PMID:16978472

  14. Molecular characterization of HAO3, the homologue of the Bm86 tick vaccine antigen, from the Iranian isolate of Hyalomma anatolicum anatolicum.

    Science.gov (United States)

    Ebrahimi, Seyyed Mahmoud; Paykari, Habib; Memarnejadian, Arash

    2013-12-01

    Hyalomma anatolicum anatolicum tick is widely distributed in many parts of Iran and while the commercial vaccines based on the application of midgut-derived recombinant Bm86 antigen are used for its control, limited information about the efficiency of this vaccination in Iran is available. Herein, with the final aim of evaluation of Bm86-based heterologous vaccination, as the primary step the Bm86 homologue of the H. a. anatolicum (Hao3) from an Iranian isolate was characterized and compared with the commercialized Bm86 and other Bm86 homologoue sequences available in GenBank. Our in silico predictions resulted in the identification of seven epidermal growth factor (EGF)-like domains, one hydrophobic transmembrane region, one leader sequence and several glycosylation sites within the structure of both Hao3 and Bm86 proteins, which suggested the pattern of extracellular membrane-bound glycoproteins with the role of regulation in cell growth for both proteins. Moreover, while the nucleotide and amino acid sequences corresponding to Bm86 homologue showed a high level of conservation among the Iranian isolates (Hao3, Hao3-1 and Hao3-2, more than 99%), the Hao3 amino acid sequence had a homology of around 89%, 64% and 65% with that of Indian, Australian and Argentinean isolates, respectively. This indicated a considerable variation between commercial Bm86 antigen and H. a. anatolicum Bm86-like protein of Iranian and Indian isolates. Taking together, these results imply that the efficiency of commercial Bm86-based vaccine against the Iranian H. a. anatolicum may be under the question and indicates the value of the development of Hao3-based recombinant vaccines and further planning for their in vivo evaluation. PMID:20599993

  15. Rhipicephalus (Boophilus) microplus: expression and characterization of Bm86-CG in Pichia pastoris Rhipicephalus (Boophilus) microplus: expressão e caracterização da Bm86-CG em Pichia pastoris

    OpenAIRE

    Rodrigo Casquero Cunha; Renato Andreotti; Fábio Pereira Leivas Leite

    2011-01-01

    The cattle tick Rhipicephalus (Boophilus) microplus is responsible for great economic losses. It is mainly controlled chemically, with limitations regarding development of resistance to the chemicals. Vaccines may help control this parasite, thereby reducing tick pesticide use. In this light, we performed subcloning of the gene of the protein Bm86-GC, the homologue protein that currently forms the basis of vaccines (GavacTM and TickGardPLUS) that have been developed against cattle ticks. The ...

  16. Partial sequencing of Bm86 gene for studying the phylogeny of an Indian isolate of Rhipicephalus (Boophilus) microplus tick.

    Science.gov (United States)

    Anbarasi, P; Latha, B R; Dhinakar Raj, G; Sreekumar, C; Senthuran, S

    2014-09-01

    Tick gut glycoprotein, designated as Bm86, found on the luminal surface of the plasma membrane of gut epithelial cells of Boophilus microplus, which is a concealed antigen, has been used as vaccine candidate molecule for immunization against ticks. To better understand the molecular diversity of Bm86 gene in ticks, a portion of the cDNA was sequenced from an Indian isolate of B. microplus. Comparison of nucleotide sequence revealed that Indian isolate had 97 % homology (18 polymorphisms) with that of the Australian isolate and 96 % homology (20 polymorphisms) with that of the Cuban vaccine strain. Further, the Indian isolate differed from the Cuban vaccine isolate at 7 amino acid loci, including 5 substitutions (at residues 88, 94, 175, 176 and 177) and 2 deletions (at 183 and 184). However, protein prediction studies did not show any difference in the putative antigenic epitopes of the protein expressed. PMID:25035581

  17. The Rhipicephalus (Boophilus microplus Bm86 gene plays a critical role in the fitness of ticks fed on cattle during acute Babesia bovis infection

    Directory of Open Access Journals (Sweden)

    Knowles Donald P

    2010-11-01

    Full Text Available Abstract Background Rhipicephalus (Boophilus microplus is an economically important tick of cattle involved in the transmission of Babesia bovis, the etiological agent of bovine babesiosis. Commercial anti-tick vaccines based on the R. microplus Bm86 glycoprotein have shown some effect in controlling tick infestation; however their efficacy as a stand-alone solution for tick control has been questioned. Understanding the role of the Bm86 gene product in tick biology is critical to identifying additional methods to utilize Bm86 to reduce R. microplus infestation and babesia transmission. Additionally, the role played by Bm86 in R. microplus fitness during B. bovis infection is unknown. Results Here we describe in two independent experiments that RNA interference-mediated silencing of Bm86 decreased the fitness of R. microplus females fed on cattle during acute B. bovis infection. Notably, Bm86 silencing decreased the number and survival of engorged females, and decreased the weight of egg masses. However, gene silencing had no significant effect on the efficiency of transovarial transmission of B. bovis from surviving female ticks to their larval offspring. The results also show that Bm86 is expressed, in addition to gut cells, in larvae, nymphs, adult males and ovaries of partially engorged adult R. microplus females, and its expression was significantly down-regulated in ovaries of ticks fed on B. bovis-infected cattle. Conclusion The R. microplus Bm86 gene plays a critical role during tick feeding and after repletion during blood digestion in ticks fed on cattle during acute B. bovis infection. Therefore, the data indirectly support the rationale for using Bm86-based vaccines, perhaps in combination with acaricides, to control tick infestation particularly in B. bovis endemic areas.

  18. Identification of a synthetic peptide inducing cross-reactive antibodies binding to Rhipicephalus (Boophilus) decoloratus, Rhipicephalus (Boophilus) microplus, Hyalomma anatolicum anatolicum and Rhipicephalus appendiculatus BM86 homologues.

    Science.gov (United States)

    Kopp, Nadja; Diaz, Diana; Amacker, Mario; Odongo, David O; Beier, Konstantin; Nitsch, Cordula; Bishop, Richard P; Daubenberger, Claudia A

    2009-12-10

    The BM86 antigen, originally identified in Rhipicephalus (Boophilus) microplus, is the basis of the only commercialized anti-tick vaccine. The long-term goal of our study is to improve BM86 based vaccines by induction of high levels of tick gut binding antibodies that are also cross-reactive with a range of BM86 homologues expressed in other important tick species. Here we have used a BD86 derived synthetic peptide, BD86-3, to raise a series of mouse monoclonal antibodies. One of these mAbs, named 12.1, recognized BM86 homologues in immuno-histochemical analyses in four out of five tick species including R. (B.) microplus, Rhipicephalus (Boophilus) decoloratus, Hyalomma anatolicum anatolicum and Rhipicephalus appendiculatus. Our results indicate that broadly cross-reactive tick gut binding antibodies can be induced after immunization with a synthetic peptide derived from the protein BD86. PMID:19808026

  19. The Rhipicephalus (Boophilus) microplus Bm86 gene plays a critical role in the fitness of ticks fed on cattle during acute Babesia bovis infection

    OpenAIRE

    Knowles Donald P; Ueti Massaro W; Bastos Reginaldo G; Scoles Glen A

    2010-01-01

    Abstract Background Rhipicephalus (Boophilus) microplus is an economically important tick of cattle involved in the transmission of Babesia bovis, the etiological agent of bovine babesiosis. Commercial anti-tick vaccines based on the R. microplus Bm86 glycoprotein have shown some effect in controlling tick infestation; however their efficacy as a stand-alone solution for tick control has been questioned. Understanding the role of the Bm86 gene product in tick biology is critical to identifyin...

  20. Bm86 homologues and novel ATAQ proteins with multiple epidermal growth factor (EGF)-like domains from hard and soft ticks ☆

    OpenAIRE

    Nijhof, Ard M; Balk, Jesper A.; Postigo, Milagros; Rhebergen, Anne Marie; Taoufik, Amar; Jongejan, Frans

    2010-01-01

    Tick control on livestock relies principally on the use of acaricides but the development of acaricide resistance and concerns for environmental pollution underscore the need for alternative control methods, for instance through the use of anti-tick vaccines. Two commercial vaccines based on the recombinant Bm86 protein from Rhipicephalus (Boophilus) microplus ticks were developed. Partial protection of the Bm86 vaccine against other Rhipicephalus (Boophilus) and Hyalomma tick species suggest...

  1. 新疆南疆地区微小牛蜱 Bm86基因克隆及鉴定

    Institute of Scientific and Technical Information of China (English)

    代艳艳; 廖秋萍; 贾桂珍; 周桐; 罗福江; 周玉琴; 王帅; 赵丽; 刘永宏

    2015-01-01

    为了克隆及鉴定新疆南疆地区微小牛蜱Bm86基因,参照GenBank登录的微小牛蜱Bm86基因序列,设计了可以扩增Bm86基因完整阅读框架的引物,对微小牛蜱进行总RNA提取、RT-PCR、克隆、测序、序列分析。结果表明,获得的Bm86基因长1953 bp,与GenBank中登录号为M29321、HQ014398的微小牛蜱Bm86基因核苷酸同源性分别为99%、97%,且为一个完整的开放阅读框架。本研究获得的微小牛蜱Bm86基因,为获得基因工程疫苗的候选抗原及中国抗微小牛蜱疫苗制备奠定了基础。

  2. A theoretical analysis of codon adaptation index of the Boophilus microplus bm86 gene directed to the optimization of a DNA vaccine.

    Science.gov (United States)

    Ruiz, Lina María; Armengol, Gemma; Habeych, Edwin; Orduz, Sergio

    2006-04-21

    DNA vaccines utilize host cell molecules for gene transcription and translation to proteins, and the interspecific difference of codon usage is one of the major obstacles for effective induction of specific and strong immune response. In an attempt to improve codon usage effects of DNA vaccine on protein expression, a quantitative study was conducted to clarify the relationship of codon usage in the tick gene bm86 and its potential expression in bovine cells. The calculated relative synonymous codon usage (RSCU) and codon adaptation index (CAI) values of bm86 from Boophilus microplus and a set of 14 highly expressed genes from Bos taurus indicated that some codons utilized frequently in bm86 are rarely used in B. taurus genes and vice versa. The different translational efficiencies obtained suggested that after DNA vaccination using the wild bm86 gene, the protein Bm86 would be expressed in bovines, but it would not be the optimum sequence. However, using the codon-optimized bm86 gene to bovines, whose sequence was theoretically designed, would probably improve the level of the immune response generated against ticks. PMID:16171828

  3. Evidence for the utility of the Bm86 antigen from Boophilus microplus in vaccination against other tick species.

    Science.gov (United States)

    de Vos, S; Zeinstra, L; Taoufik, O; Willadsen, P; Jongejan, F

    2001-01-01

    The Bm86 antigen, as originally identified in Boophilus microplus, is the basis of commercial tick vaccines against this tick species. The potential for using this antigen or homologues of the antigen in vaccination against other tick species has been assessed. We have conducted vaccine trials in cattle using the B. microplus-derived recombinant Bm86 vaccine (TickGARD) using pairs of vaccinated calves and control calves. These were infested with B. microplus and Boophilus decoloratus larvae simultaneously. For both species, the numbers of engorged female adult ticks, their weight and egg-laying capacity were all reduced, leading to a reduction in reproductive capacity of 74% for B. microplus and 70% for B. decoloratus. Hyalomma anatolicum anatolicum ticks were fed both as immatures as well as adults on vaccinated calves and non-vaccinated controls. There was an overall 50% reduction in the total weight of nymphs engorging on vaccinated calves, and a suggestion of a subsequent effect on feeding adults. For Hyalomma dromedarii there was a 95% reduction in the number of nymphs engorging and a further 55% reduction in weight of those ticks surviving. Rhipicephalus appendiculatus and Amblyomma variegatum ticks were fed simultaneously both as immatures and subsequently as adults. There was no evidence for a significant vaccination effect. Finally, the amino acid sequence of a Bm86 homologue found in H. a. anatolicum unequivocally demonstrated the conservation of this molecule in this species. Our strategy for the development of multivalent anti-tick vaccines is discussed in relation to these findings. PMID:11523920

  4. Selection of reference genes for quantitative RT-PCR studies in Rhipicephalus (Boophilus microplus and Rhipicephalus appendiculatus ticks and determination of the expression profile of Bm86

    Directory of Open Access Journals (Sweden)

    Jongejan Frans

    2009-12-01

    Full Text Available Abstract Background For accurate and reliable gene expression analysis, normalization of gene expression data against reference genes is essential. In most studies on ticks where (semi-quantitative RT-PCR is employed, normalization occurs with a single reference gene, usually β-actin, without validation of its presumed expression stability. The first goal of this study was to evaluate the expression stability of commonly used reference genes in Rhipicephalus appendiculatus and Rhipicephalus (Boophilus microplus ticks. To demonstrate the usefulness of these results, an unresolved issue in tick vaccine development was examined. Commercial vaccines against R. microplus were developed based on the recombinant antigen Bm86, but despite a high degree of sequence homology, these vaccines are not effective against R. appendiculatus. In fact, Bm86-based vaccines give better protection against some tick species with lower Bm86 sequence homology. One possible explanation is the variation in Bm86 expression levels between R. microplus and R. appendiculatus. The most stable reference genes were therefore used for normalization of the Bm86 expression profile in all life stages of both species to examine whether antigen abundance plays a role in Bm86 vaccine susceptibility. Results The transcription levels of nine potential reference genes: β-actin (ACTB, β-tubulin (BTUB, elongation factor 1α (ELF1A, glyceraldehyde 3-phosphate dehydrogenase (GAPDH, glutathione S-transferase (GST, H3 histone family 3A (H3F3A, cyclophilin (PPIA, ribosomal protein L4 (RPL4 and TATA box binding protein (TBP were measured in all life stages of R. microplus and R. appendiculatus. ELF1A was found to be the most stable expressed gene in both species following analysis by both geNorm and Normfinder software applications, GST showed the least stability. The expression profile of Bm86 in R. appendiculatus and R. microplus revealed a more continuous Bm86 antigen abundance in R

  5. Immune response in mice and cattle after immunization with a Boophilus microplus DNA vaccine containing bm86 gene.

    Science.gov (United States)

    Ruiz, Lina María; Orduz, Sergio; López, Elkin D; Guzmán, Fanny; Patarroyo, Manuel E; Armengol, Gemma

    2007-03-15

    Plasmid pBMC2 encoding antigen Bm86 from a Colombian strain of cattle tick Boophilus microplus, was used for DNA-mediated immunization of BALB/c mice, employing doses of 10 and 50microg, delivered by intradermic and intramuscular routes. Anti-Bm86 antibody levels were significantly higher compared to control mice treated with PBS. In the evaluation of immunoglobulin isotypes, significant levels of IgG2a and IgG2b were observed in mice immunized with 50microg of pBMC2. Measurement of interleukine (IL) levels (IL-4, IL-5, IL-12(p40)) and interferon-gamma (IFN-gamma) in the sera of mice immunized with pBMC2 indicated high levels of IL-4 and IL-5, although there were also significant levels of IFN-gamma. Mice immunized with pBMC2 showed antigen-specific stimulation of splenocytes according to the incorporation of bromodeoxyuridine and IFN-gamma secretion. In all trials, mice injected intramuscularly with 50microg of pBMC2 presented the highest immune response. Moreover, cattle immunized with this DNA vaccine showed antibody production significantly different to the negative control. In conclusion, these results suggest the potential of DNA immunization with pBMC2 to induce humoral and cellular immune responses against B. microplus. PMID:17055651

  6. Control of Boophilus microplus ticks in cattle calves by immunization with a recombinant Bm86 glucoprotein antigen preparation.

    Science.gov (United States)

    Khalaf-Allah, S S

    1999-06-01

    Forty Egyptian native cattle calves of 4-6 months old randomly allocated into two groups of twenty animals each were used to assess the effect of immunization of animals with a recombinant Bm86 antigen derived from Boophilus microplus ticks on induction of immunity that could protect calves during tick season. The immunization protocol involved two injections administered intramuscularly, the first was applied with complete Freund's adjuvant and the second was given with incomplete Freund's adjuvant two months later. Control calves were given saline plus adjuvant. Immunization reduced the number of adult ticks developing from a subsequent challenge infestation by 78% in immunized calves. Vaccination also, significantly reduced the weight of adult ticks in immunized calves (30.51%). The results of skin delayed hypersensitivity reaction revealed that the diameter of sites injected with the recombinant Bm86 antigen was significantly larger in immunized calves than those in controls. Analysis of the immune response indicated that there was a significant increase in the level of IgG and IgA antibodies in serum of immunized calves and protection from reinfestation was correlated with the levels of circulating antibodies. PMID:10422372

  7. 新疆南疆微小牛蜱Bm86/Bm91双基因原核表达载体的构建%Construction of Prokaryotic Expression Vector of Bm86 and Bm91 Dual Genes of Boophilus microplus in South Xinjiang

    Institute of Scientific and Technical Information of China (English)

    代艳艳; 赵丽; 周桐; 罗福江; 周玉琴; 王帅; 刘永宏

    2014-01-01

    为构建微小牛蜱Bm86和Bm91双基因原核表达载体,以新疆生产建设兵团塔里木畜牧科技重点实验室获得的Bm86和Bm91克隆基因阳性菌或质粒DNA为模板,参照GenBank登录的微小牛蜱Bm86和Bm91基因序列和所用载体序列,设计可以扩增Bm86和Bm91基因完整阅读框架的引物,然后对新疆南疆微小牛蜱Bm86和Bm91基因进行PCR扩增、纯化、酶切后连接,构建双基因重组质粒pET-32a-Bm并鉴定.结果显示,成功构建Bm86和Bm91双基因重组质粒pET-32a-Bm,经测序鉴定和初始获得的Bm86和Bm91基因序列一致,未发生变异.

  8. Efficacy of the Bm86 antigen against immature instars and adults of the dog tick Rhipicephalus sanguineus (Latreille, 1806) (Acari: Ixodidae).

    Science.gov (United States)

    Perez-Perez, D; Bechara, G H; Machado, R Z; Andrade, G M; Del Vecchio, R E M; Pedroso, M S; Hernández, M V; Farnós, O

    2010-02-10

    The Bm86 antigen has been used to control ticks of the Boophilus genera in integrated programs that also include the use of acaricides. Because of recent phylogenetic studies have lead to the inclusion of all Boophilus species within the Rhipicephalus genera, we aimed to investigate the efficacy of the Bm86 antigen on the biotic potential of Rhipicephalus sanguineus. Domestic dogs were vaccinated with Bm86 and challenged with the three instars of R. sanguineus. Male and female mongrel dogs were divided into two groups of four animals each, comprising non-vaccinated and vaccinated animals. Immunized dogs were given two doses of an experimental formulation containing 50mug of recombinant Bm86, at 21 days interval while the other group was given placebo, consisting of the same preparation without Bm86. Each dog was challenged 21 days after the last dose with 250 larvae, 100 nymphs and 55 adults (25 females and 30 males) released inside feeding chambers (one per instar) glued to their shaved flank. The effect of the vaccination was evaluated by determining biological parameters of ticks including the yield rates of larvae, nymphs and adult females. Adult females engorged weight, egg mass weight, efficiency rate of conversion to eggs (ERCE) and hatchability. In addition, sera were collected from dogs at 0, 21, 36, 45 and 75 days after the vaccination and used for the detection of specific antibodies by ELISA. Collection rates of larvae, nymphs and adult females fed on vaccinated dogs were significantly (pBm86. We concluded that the Bm86 antigen used as a vaccine for dogs reduced the viability and biotic potential of the R. sanguineus. PMID:19836894

  9. The evaluation of yeast derivatives as adjuvants for the immune response to the Bm86 antigen in cattle

    Directory of Open Access Journals (Sweden)

    Machado Héctor

    2001-05-01

    Full Text Available Abstract Background The Gavac™ vaccine against the cattle tick Boophilus microplus has proven its efficacy in a large number of controlled and field experiments. However, this vaccine could be further improved by searching for new alternative adjuvants that would induce a stronger long-lasting immune response. We conducted several experiments to assay the adjuvant effect of fractions of the recombinant yeast Pichia pastoris in mouse and cattle models. In previous experiments, the combination of the yeast membrane with saponin was the most effective formulation in stimulating the humoral immune response in mice, eliciting a response higher than Montanide 888. The response was predominantly of the IgG1 isotype. Here, we evaluated the response in cattle and compared the results with that obtained in mice. Results Bm86 on the membrane of P. pastoris plus saponin produced high antibody titers in cattle, though the protection level against tick infestations was lower when compared to Gavac™, probably due to a decrease in the IgG1/IgG2 ratio. The predictive value of the mouse model was studied through correlation analysis between the isotype levels in mice and the efficacy of formulations in cattle. Good correlation was established between the level of antibodies in mice and cattle, and between the amount of anti -Bm86 IgG1 in mice and the degree of protection in cattle. Conclusion Mouse model have the potential to predict immunogenicity and efficacy of formulations in cattle. These results also support the use of the yeast expression system for recombinant vaccine formulations, enabling the prediction of more cost - effective formulations.

  10. Control of ticks resistant to immunization with Bm86 in cattle vaccinated with the recombinant antigen Bm95 isolated from the cattle tick, Boophilus microplus.

    Science.gov (United States)

    García-García, J C; Montero, C; Redondo, M; Vargas, M; Canales, M; Boue, O; Rodríguez, M; Joglar, M; Machado, H; González, I L; Valdés, M; Méndez, L; de la Fuente, J

    2000-04-28

    The recombinant Bm86-containing vaccine Gavac(TM) against the cattle tick Boophilus microplus has proved its efficacy in a number of experiments, especially when combined with acaricides in an integrated manner. However, tick isolates such as the Argentinean strain A, show low susceptibility to this vaccine. In this paper we report on the isolation of the Bm95 gene from the B. microplus strain A, which was cloned and expressed in the yeast Pichia pastoris producing a glycosylated and particulated recombinant protein. This new antigen was effective against different tick strains in a pen trial, including the B. microplus strain A, resistant to vaccination with Bm86. A Bm95-based vaccine was used to protect cattle against tick infestations under production conditions, lowering the number of ticks on vaccinated animals and, therefore, reducing the frequency of acaricide treatments. The Bm95 antigen from strain A was able to protect against infestations with Bm86-sensitive and Bm86-resistant tick strains, thus suggesting that Bm95 could be a more universal antigen to protect cattle against infestations by B. microplus strains from different geographical areas. PMID:10717348

  11. Vaccination of cattle with TickGARD induces cross-reactive antibodies binding to conserved linear peptides of Bm86 homologues in Boophilus decoloratus.

    Science.gov (United States)

    Odongo, David; Kamau, Lucy; Skilton, Robert; Mwaura, Stephen; Nitsch, Cordula; Musoke, Anthony; Taracha, Evans; Daubenberger, Claudia; Bishop, Richard

    2007-01-26

    Vaccines based on recombinant Bm86 gut antigen from Boophilus microplus are a useful component of integrated control strategies against B. microplus infestations of cattle. The capacity of such vaccines to control heterologous infestations by two African tick species was investigated. The mean weight of engorged female ticks and mean egg mass per tick were significantly reduced in B. decoloratus infestations, but there was no effect of the vaccine against adult Rhipicephalus appendiculatus. We cloned, sequenced and expressed two Bm86 homologues (Bd86) from B. decoloratus. Amino acid sequence identity between Bd86 homologues (Bd86-1 and Bd86-2) and Bm86 was 86% and 85%, respectively, compared to 93% identity between the variants. Native Bd86 protein in B. decoloratus tick mid-gut sections and recombinant Bd86-1 reacted strongly with sera from TickGARD vaccinated cattle. TickGARD can therefore protect against a heterologous tick species with multiple antigen sequences. Epitope mapping using sera from TickGARD-vaccinated cattle identified two linear peptides conserved between the Bd86 homologues and Bm86. These epitopes represent candidate synthetic peptide vaccines for control of Boophilus spp. and the pathogens transmitted by these tick vectors. PMID:17070625

  12. Two initial vaccinations with the Bm86-based Gavacplus vaccine against Rhipicephalus (Boophilus microplus induce similar reproductive suppression to three initial vaccinations under production conditions

    Directory of Open Access Journals (Sweden)

    Fernández Erlinda

    2010-09-01

    Full Text Available Abstract Background The cattle tick, Rhipicephalus (Boophilus microplus, affects livestock production in many regions of the world. Up to now, the widespread use of chemical acaricides has led to the selection of acaricide-resistant ticks and to environmental contamination. Gavacplus is a subunit vaccine based on the recombinant Bm86 tick antigen expressed in yeast, capable to control infestations of R. microplus under controlled and production conditions. The vaccine constitutes the core element of broad control programs against this ectoparasite, in which acquired immunity in cattle to Bm86 is combined with a rational use of acaricides. At present, the conventional vaccine scheme consists of three doses that should be administered at weeks 0, 4 and 7, followed by a booster every six months. Results In this study we assayed a reduction in the number of the initial doses of Gavacplus, evaluated the time course and the level of bovine anti-Bm86 antibodies elicited, and analyzed the vaccine effect on ticks engorging on immunized cattle under production conditions. Following three different immunization schemes, the bovines developed a strong and specific immune response characterized by elevated anti-Bm86 IgG titers. A reduction in the weight of engorging female ticks, in the weight of the eggs laid and also in R. microplus viable eggs percentage was obtained by using only two doses of Gavacplus administered at weeks 0 and 4, followed by a booster six months later. This reduction did not differ from the results obtained on ticks engorging on cattle immunized at weeks 0, 4 and 7. It was also demonstrated that anti-Bm86 antibody titers over 1:640, measured in bovines immunized at weeks 0 and 4, were sufficient to affect weight and reproductive potential of female ticks as compared with ticks engorging on unvaccinated animals. In addition, no statistically significant differences were detected in the average weight of eggs laid by ticks engorged on

  13. Differential transcription of two highly divergent gut-expressed Bm86 antigen gene homologues in the tick Rhipicephalus appendiculatus (Acari: Ixodida).

    Science.gov (United States)

    Kamau, L; Skilton, R A; Odongo, D O; Mwaura, S; Githaka, N; Kanduma, E; Obura, M; Kabiru, E; Orago, A; Musoke, A; Bishop, R P

    2011-02-01

    The transcriptional control of gene expression is not well documented in the Arthropoda. We describe transcriptional analysis of two exceptionally divergent homologues (Ra86) of the Bm86 gut antigen from Rhipicephalus appendiculatus. Bm86 forms the basis of a commercial vaccine for the control of Rhipicephalus (Boophilus) microplus. The R. appendiculatus Ra86 proteins contain 654 and 693 amino acids, with only 80% amino acid sequence identity. Reverse-transcription PCR of gut cDNA showed transcription of only one genotype in individual female ticks. PCR amplification of 3' untranslated sequences from genomic DNA indicated that both variants could be encoded within a single genome. When both variants were present, one of the two Ra86 genotypes was transcriptionally dominant. PMID:20854482

  14. Two initial vaccinations with the Bm86-based Gavacplus vaccine against Rhipicephalus (Boophilus) microplus induce similar reproductive suppression to three initial vaccinations under production conditions

    OpenAIRE

    Fernández Erlinda; Suárez Marisela; Lleonart Ricardo; Méndez Luis; Rodríguez Elsa; Machado Héctor; Joglar Marisdania; Alfonso Aymé; Valdés Mario; Pérez Danny; Sánchez Dunia; Montero Carlos; Vargas Milagros; Estrada Mario P; Rodríguez-Mallón Alina

    2010-01-01

    Abstract Background The cattle tick, Rhipicephalus (Boophilus) microplus, affects livestock production in many regions of the world. Up to now, the widespread use of chemical acaricides has led to the selection of acaricide-resistant ticks and to environmental contamination. Gavacplus is a subunit vaccine based on the recombinant Bm86 tick antigen expressed in yeast, capable to control infestations of R. microplus under controlled and production conditions. The vaccine constitutes the core el...

  15. [Molecular analysis of the antigenic sequence (SBm7462®) from Bm86 of the Rhipicephalus (Boophilus) microplus and similarity with Rhipicephalus sanguineus and Hyalomma anatolicum anatolicum].

    Science.gov (United States)

    Peconick, Ana P; Sossai, Sidimar; Medeiros, Carla L; Carvalho, Gabriel D; Vargas, Marlene I; Patarroyo, Joaquín H

    2008-09-01

    The vaccination represents optimum method evaluated with effective cost to prevent economic losses and to increase the duration and quality of life of the production animals. . Diverse vaccines are produced from the intestinal protein Bm86 of the Rhipicephalus. (B.) microplus. The knowledge of the conservation of the gene bm86 is very important to evaluate the vaccine efficiency and the possibility of reaction crossed between different species of ticks. Samples of R. (B.) microplus come from different localities had been sequenced. The analyses of multiple alignments of the sequences had been made through the BioEdit program 7.0.5.3 version and the verification of polymorphism for visual inspection. In this work the alignment of all was become fulfilled sequences using itself BLAST in the search for similarity. Similarity was observed enters the sequenced fragments of R. (B.) microplus with the sequence of the protein Rs86 de Rhipicephalus sanguineus and with protein HA98 of the tick Hyalomma anatolicum anatolicum. The results give molecular support to synthetic the vaccine use based in the gene bm86 (SBm7462®) to be used in different species of ticks. PMID:20059809

  16. Thinning of Apple Fruits with Foliar Fertilizers Goëmar BM 86 E and Goëmar Folical

    Directory of Open Access Journals (Sweden)

    Milutin Misimovic

    2014-02-01

    Full Text Available Normal 0 21 false false false sr-Latn-BA X-NONE X-NONE MicrosoftInternetExplorer4 /* Style Definitions */ table.MsoNormalTable {mso-style-name:"Table Normal"; mso-tstyle-rowband-size:0; mso-tstyle-colband-size:0; mso-style-noshow:yes; mso-style-priority:99; mso-style-qformat:yes; mso-style-parent:""; mso-padding-alt:0cm 5.4pt 0cm 5.4pt; mso-para-margin:0cm; mso-para-margin-bottom:.0001pt; mso-pagination:widow-orphan; font-size:11.0pt; font-family:"Calibri","sans-serif"; mso-ascii-font-family:Calibri; mso-ascii-theme-font:minor-latin; mso-fareast-font-family:"Times New Roman"; mso-fareast-theme-font:minor-fareast; mso-hansi-font-family:Calibri; mso-hansi-theme-font:minor-latin; mso-bidi-font-family:"Times New Roman"; mso-bidi-theme-font:minor-bidi;} Thinning is a regular pomotechnical measure, which is performed by using different chemicals that cause fruit drop in intensive apple orchards. It is common that some apple cultivars overbear, giving small fruits of poor quality. Effects of chemical thinners of apple fruits are as follows: higher productiveness in the next vegetation period, higher percentage of first class apples and the lesser fruit drop before harvest and so on. Hormonal thinners that are currently being used in the surrounding countries are not allowed in our country because of their ecotoxicological characteristics. These products are not applicable in the concept of integral fruit production. The aim of this study was to investigate the impact of natural foliar fertilizer GOEMAR BM 86 E and GOEMAR FOLICAL on apple fruit thinning, and thus on the quantity and quality of harvested fruits. In this paper, four cultivars of apples are included: ‚Golden Delicious‘, ‚Granny Smith‘, ‚Braeburn‘ and ‚Idared‘. In treated trees, these natural fertilizers caused increased fruit drop in relation to the control. Results showed higher sugar content in treated fruits in relation to untreated control fruits. Further research

  17. Cloning, expression and immunoprotective efficacy of rHaa86, the homologue of the Bm86 tick vaccine antigen, from Hyalomma anatolicum anatolicum.

    Science.gov (United States)

    Azhahianambi, P; De La Fuente, J; Suryanarayana, V V S; Ghosh, S

    2009-03-01

    The Bm86 homologue of Hyalomma anatolicum anatolicum Izatnagar isolate was cloned and expressed in methylotropic yeast Pichia pastoris as intracellular, glycosylated and particulated form. It was named as rHaa86, the first recombinant protein of H. a. anatolicum. Seven epidermal growth factor-like domains predicted in Haa86 were structurally similar with that of its Bm86 counterpart. The identity between the corresponding EGF like domains of Bm86 and Haa86 were ranging from 51.3% to 78.3%. The molecular weight of the rHaa86 was 120-140 kDa, with possible 50-70 kDa glycosylation. The purified rHaa86 was characterized immunologically and evaluated for its immunoprotective potential against homologous challenge infestation in three groups of cross-bred calves. The immediate rejection percentage of females of H. a. anatolicum was 36 5%, 12.4% and 10.1% fed on immunized (group 1), adjuvant control (group 2) and untreated control (group 3) calves, respectively. The percent rejection of female ticks fed on immunized calves was 24.1% and 26.4% higher than for the ticks fed on control groups 2 and 3, respectively (P < 0.05). The reduction of number of females, mean weight of eggs, adult females and efficacy of immunogen were 58.0%, 9.0%, 5.0% and 61.6%, respectively. The mean reproductive index of females fed on group 1 calves was significantly lower (P < 0.05) than the females fed on the control groups and 44% reduction in the number of engorged larvae was recorded from the group 1 calves. The data demonstrated that rHaa86 antigen based vaccine could serve as one of the effective components in the integrated control of H. a. anatolicum. PMID:19222782

  18. Gene silencing of the tick protective antigens, Bm86, Bm91 and subolesin, in the one-host tick Boophilus microplus by RNA interference

    OpenAIRE

    Nijhof, A. M.; Taoufik, A.; de la Fuente, M.R.; Kocan, K M; de Vries, E; Jongejan, F

    2007-01-01

    The use of RNA interference (RNAi) to assess gene function has been demonstrated in several three-host tick species but adaptation of RNAi to the one-host tick, Boophilus microplus, has not been reported. We evaluated the application of RNAi in B. microplus and the effect of gene silencing on three tick-protective antigens: Bm86, Bm91 and subolesin. Gene-specific double-stranded (dsRNA) was injected into two tick stages, freshly molted unfed and engorged females, and specific gene silencing w...

  19. Evaluation of antibodies production against Borrelia burgdorferi in cattle submitted to rBm86 protein Boophilus microplus tick immunization and associated challenges influence Avaliação da produção de anticorpos anti Borrelia burgdorferi em bovinos submetidos à imunização com proteína rBm86 de carrapato Boophilus microplus e influência dos desafios associados

    OpenAIRE

    Márcia Mayumi Ishikawa; Adivaldo Henrique Fonseca; Natalino Hajime Yoshinari; Ana Luiza Alves Rosa Osório

    2003-01-01

    IgG antibodies production against Borrelia burgdorferi in immunized cattle with rBm86 protein from Boophilus microplus was evaluated as well as the influence of the association between immunizations and stress through indirect ELISA test during one year. In the present study there was no influence of the isolated challenged used on the production of IgG antibodies against B. burgdorferi. The rBm86 immunogen did not cause significant oscillation in the production of IgG antibodies against B. b...

  20. Gene silencing of the tick protective antigens, Bm86, Bm91 and subolesin, in the one-host tick Boophilus microplus by RNA interference.

    Science.gov (United States)

    Nijhof, Ard M; Taoufik, Amar; de la Fuente, José; Kocan, Katherine M; de Vries, Erik; Jongejan, Frans

    2007-05-01

    The use of RNA interference (RNAi) to assess gene function has been demonstrated in several three-host tick species but adaptation of RNAi to the one-host tick, Boophilus microplus, has not been reported. We evaluated the application of RNAi in B. microplus and the effect of gene silencing on three tick-protective antigens: Bm86, Bm91 and subolesin. Gene-specific double-stranded (dsRNA) was injected into two tick stages, freshly molted unfed and engorged females, and specific gene silencing was confirmed by real time PCR. Gene silencing occurred in injected unfed females after they were allowed to feed. Injection of dsRNA into engorged females caused gene silencing in the subsequently oviposited eggs and larvae that hatched from these eggs, but not in adults that developed from these larvae. dsRNA injected into engorged females could be detected by quantitative real-time RT-PCR in eggs 14 days from the beginning of oviposition, demonstrating that unprocessed dsRNA was incorporated in the eggs. Eggs produced by engorged females injected with subolesin dsRNA were abnormal, suggesting that subolesin may play a role in embryonic development. The injection of dsRNA into engorged females to obtain gene-specific silencing in eggs and larvae is a novel method which can be used to study gene function in tick embryogenesis. PMID:17196597

  1. Evaluation of antibodies production against Borrelia burgdorferi in cattle submitted to rBm86 protein Boophilus microplus tick immunization and associated challenges influence Avaliação da produção de anticorpos anti Borrelia burgdorferi em bovinos submetidos à imunização com proteína rBm86 de carrapato Boophilus microplus e influência dos desafios associados

    Directory of Open Access Journals (Sweden)

    Márcia Mayumi Ishikawa

    2003-11-01

    Full Text Available IgG antibodies production against Borrelia burgdorferi in immunized cattle with rBm86 protein from Boophilus microplus was evaluated as well as the influence of the association between immunizations and stress through indirect ELISA test during one year. In the present study there was no influence of the isolated challenged used on the production of IgG antibodies against B. burgdorferi. The rBm86 immunogen did not cause significant oscillation in the production of IgG antibodies against B. burgdorferi capable to interfere in the serological results for Lyme Borreliosis in cattle. This study demonstrated the possibility of transitory changes in the production of antibodies after the association of vaccine stimuli and stress, emphasizing the necessity of serological studies combined with epidemiological and management data.Avaliou-se a produção de anticorpos da classe Ig-G anti Borrelia burgdorferi em bovinos imunizados com proteína recombinante Bm86 de Boophilus microplus, assim como a influência de imunizações e estresse associados por meio do teste ELISA indireto no período de um ano. Não houve interferência na produção de anticorpos IgG anti B. burgdorferi pelos desafios utilizados isoladamente no presente estudo. O imunógeno rBm86 não causou oscilações significantes na produção de anticorpos IgG anti B. burgdorferi capazes de interferir nos resultados sorológicos para Borreliose de Lyme em bovinos. O estudo demonstrou a possibilidade de alterações transitórias na produção de anticorpos após estímulos vacinais e de estresse associados, ressaltando a necessidade de estudos sorológicos em conjunto a dados epidemiológicos e de manejo.

  2. Acaricidal effect of Cassia fistula Linn. leaf ethanolic extract against Rhipicephlaus (Boophilus) annulatus.

    Science.gov (United States)

    Sunil, A R; Amithamol, K K; Juliet, S; Nair, S N; Ajithkumar, K G; Soorya, V C; Divya, T M; Jyothymol, G; Ghosh, S; Ravindran, R

    2013-06-01

    The present study evaluates the acaricidal properties of crude ethanolic extract of Cassia fistula leaves for controlling Rhipicephalus (Boophilus) annulatus based on adult immersion test (AIT). The percentage of adult mortality, inhibition of fecundity and hatching of ova laid were studied at different concentrations of the extract ranging from 50 to 100 mg / ml. The results were compared using one-way ANOVA. The extract produced complete inhibition of hatching of eggs at concentrations above 80 mg / ml of the extract. Mortality of adult engorged female ticks and inhibition of fecundity were concentration dependent. The LC50 value of extract against R. (B.) annulatus was 97.1 mg / ml.

  3. First report of pyrethroid resistance in Rhipicephalus (Boophilus) annulatus larvae (Say, 1821) from Iran.

    Science.gov (United States)

    Ziapour, Seyyed Payman; Kheiri, Sadegh; Asgarian, Fatemeh; Fazeli-Dinan, Mahmoud; Yazdi, Fariborz; Mohammadpour, Reza Ali; Aarabi, Mohsen; Enayati, Ahmadali

    2016-04-01

    Rhipicephalus (Boophilus) annulatus is one of the most important hard ticks parasitizing cattle in northern Iran. The aim of this study was to evaluate pyrethroid resistance levels of this species from Nur County, northern Iran. The hard ticks were collected through a multistage cluster randomized sampling method from the study area and fully engorged female R. (B.) annulatus were reared in a controlled insectary until they produced larvae for bioassay. Seventeen populations of the hard ticks were bioassayed with cypermethrin and 12 populations with lambda-cyhalothrin using a modified larval packet test (LPT). Biochemical assays to measure the contents/activity of different enzyme groups including mixed function oxidases (MFOs), glutathione S-transferases (GSTs) and general esterases were performed. Population 75 showed a resistance ratio of 4.05 with cypermethrin when compared with the most susceptible field population 66 at the LC50 level. With lambda-cyhalothrin the resistance ratio based on LC50 was 3.67 when compared with the susceptible population. The results of biochemical assays demonstrated significantly elevated levels of GSTs and esterases in populations tested compared with the heterozygous susceptible filed population and a correlation coefficient of these enzymes was found in association to lambda-cyhalothrin resistance. Based on the results, pyrethroid acaricides may operationally fail to control R. (B.) annulatus in North of Iran. This study is the first document of pyrethroid resistance in R. (B.) annulatus populations from Iran. PMID:26772446

  4. First report of pyrethroid resistance in Rhipicephalus (Boophilus) annulatus larvae (Say, 1821) from Iran.

    Science.gov (United States)

    Ziapour, Seyyed Payman; Kheiri, Sadegh; Asgarian, Fatemeh; Fazeli-Dinan, Mahmoud; Yazdi, Fariborz; Mohammadpour, Reza Ali; Aarabi, Mohsen; Enayati, Ahmadali

    2016-04-01

    Rhipicephalus (Boophilus) annulatus is one of the most important hard ticks parasitizing cattle in northern Iran. The aim of this study was to evaluate pyrethroid resistance levels of this species from Nur County, northern Iran. The hard ticks were collected through a multistage cluster randomized sampling method from the study area and fully engorged female R. (B.) annulatus were reared in a controlled insectary until they produced larvae for bioassay. Seventeen populations of the hard ticks were bioassayed with cypermethrin and 12 populations with lambda-cyhalothrin using a modified larval packet test (LPT). Biochemical assays to measure the contents/activity of different enzyme groups including mixed function oxidases (MFOs), glutathione S-transferases (GSTs) and general esterases were performed. Population 75 showed a resistance ratio of 4.05 with cypermethrin when compared with the most susceptible field population 66 at the LC50 level. With lambda-cyhalothrin the resistance ratio based on LC50 was 3.67 when compared with the susceptible population. The results of biochemical assays demonstrated significantly elevated levels of GSTs and esterases in populations tested compared with the heterozygous susceptible filed population and a correlation coefficient of these enzymes was found in association to lambda-cyhalothrin resistance. Based on the results, pyrethroid acaricides may operationally fail to control R. (B.) annulatus in North of Iran. This study is the first document of pyrethroid resistance in R. (B.) annulatus populations from Iran.

  5. Histoarchitecture of the Ovary of Rhipicephalus (Boophilus annulatus during Pre- and Postengorgement Period

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    Sreelekha Kanapadinchareveetil

    2015-01-01

    Full Text Available The present communication describes the detailed day wise study of histological changes of the ovary of Rhipicephalus (Boophilus annulatus in the postengorgement period together with the systematic classification of their oocytes. The ovary of R. (B. annulatus is panoistic type with an asynchronous development of oocytes. All the stages (II, III, IV, and V of oocytes except stage I were similar to R. (B. microplus. The stage I oocytes showed basophilia, which was not reported earlier in other species of ticks. Day wise changes were in the form of presence of oogonia in partially fed and day one engorged adults, considerable degeneration of oocytes on day two, emergence of new wave of oocytes on day three, presence of mature oocytes up to day eight, and complete degeneration of ovarian tissue from day eight onwards. The degenerative changes in the ovary appeared initially in the oocytes followed by germinal epithelium.

  6. Laboratory evaluation of Mesocyclops annulatus (Wierzejski, 1892 (Copepoda: Cyclopidea as a predator of container-breeding mosquitoes in Argentina

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    María V Micieli

    2002-09-01

    Full Text Available In laboratory bioassays we tested the predatory capacity of the copepod Mesocyclops annulatus on Aedes aegypti and Culex pipiens larvae. A single adult female of M. annulatus caused 51.6% and 52.3% mortality of 50 first instar larvae of Ae. aegypti and Cx. pipiens respectively, in a 72 h test period. When alternative food was added to the containers, mortality rates declined to 16% and 10.3% for Ae. aegypti and Cx. pipiens respectively. When 50 first instar larvae of each of the two mosquito species tested were placed together with a single adult female of M. annulatus, mortality rates were 75.5% for Ae. aegypti larvae and 23.5% for Cx. pipiens larvae in a three day test period. Different density of adult females of M. annulatus ranged from 5 to 25 females produced mortality rates of Ae. aegypti first instar larvae from 50% to 100% respectively. When a single adult female of M. annulatus was exposed to an increasing number of first-instar Ae. aegypti larvae ranging from 10 to 100, 100% mortality was recorded from 1 to 25 larvae, then mortality declined to 30% with 100 larvae. The average larvae killed per 24 h period by a single copepod were 29.

  7. High resolution predictive mapping of Rhipicephalus microplus and R. annulatus in south Texas after vaccination with the anti-tick vaccine Gavac

    Science.gov (United States)

    Conventional anti-tick vaccines based on the tick gut antigen Bm86 exist commercially (TickGARD and Gavac) and could serve as an alternative to the use of acaricides to eradicate ticks, but their level of efficacy against R. microplus is too low for eradication if used alone. Therefore, the current ...

  8. Acaricidal effect of Pelargonium roseum and Eucalyptus globulus essential oils against adult stage of Rhipicephalus (Boophilus) annulatus in vitro.

    Science.gov (United States)

    Pirali-Kheirabadi, Khodadad; Razzaghi-Abyaneh, Mehdi; Halajian, Ali

    2009-06-10

    In a laboratory trial, in west-central Iran, the acaricidal effects of the essential oils (EOs) prepared from two medicinal plants, i.e. Pelargonium roseum and Eucalyptus globulus on the adult stage of Rhipicephalus (Boophilus) annulatus were evaluated. For this purpose, the engorged females of R. (B) annulatus were exposed to two-fold serial dilutions of oils (0.31-5.0%) using a "dipping method" in vitro. The engorged ticks were immersed in different plant dilutions (eight per dilution) for 1min then each replicate was incubated in separate petri dishes at 26 degrees C and 80% relative humidity. The mortality rate for adult ticks exposed to different dilutions of P. roseum and E. globulus EO's showed a dose-dependent decrease. It was however significant only for the 2.5% and 5.0% dilutions of P. roseum EO, when compared to the non-treated control (P<0.05). The mass of produced eggs in adult female ticks exposed to both P. roseum and E. globulus EOs had decreased dose-dependently. It was significant for only 2.5% and 5.0% dilutions of P. roseum EO, comparing the non-treated control (P<0.05). The highest decrease in egg laying was reported for ticks treated with 5% dilutions of P. roseum (87.5%) and E. globosus (25%) (P<0.05). This is the first report that details the acaricidal activity of EO's obtained from P. roseum and E. globosus against R. (B) annulatus. The results show that both plants, particularly P. Roseum can be considered as potential candidates for biocontrol of R. (B) annulatus in the field.

  9. Capillariid nematodes in Brazilian turkeys, Meleagris gallopavo (Galliformes, Phasianidae: pathology induced by Baruscapillaria obsignata and Eucoleus annulatus (Trichinelloidea, Capillariidae

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    Roberto Magalhães Pinto

    2008-05-01

    Full Text Available The pathology induced in turkeys (Meleagris gallopavo by two capillariid nematodes, Baruscapillaria obsignata and Eucoleus annulatus is described together with data on prevalences, mean infection and range of worm burdens. B. obsignata occurred with a prevalence of 72.5% in the 40 examined hosts in a range of 2-461 nematodes and a mean intensity of 68.6, whereas E. annulatus was present in 2.5% of the animals, with a total amount of five recovered parasites. Gross lesions were not observed in the parasitized birds. Lesions due to B. obsignata mainly consisted of the thickening of intestinal villi with a mild mixed inflammatory infiltrate with the presence of mononuclear cells and heterophils. The lesions induced by E. annulatus were represented by foci of inflammatory infiltrate with heterophils in the crop epithelium and esophagus of a single infected female. These are the first pathological findings related to the presence of capillariid worms in turkeys to be reported in Brazil so far. Capillaria anatis, although present, was not pathogenic to the investigated turkeys.

  10. Capillariid nematodes in Brazilian turkeys, Meleagris gallopavo (Galliformes, Phasianidae): pathology induced by Baruscapillaria obsignata and Eucoleus annulatus (Trichinelloidea, Capillariidae).

    Science.gov (United States)

    Pinto, Roberto Magalhães; Brener, Beatriz; Tortelly, Rogério; Menezes, Rodrigo Caldas; Muniz-Pereira, Luís Cláudio

    2008-05-01

    The pathology induced in turkeys (Meleagris gallopavo) by two capillariid nematodes, Baruscapillaria obsignata and Eucoleus annulatus is described together with data on prevalences, mean infection and range of worm burdens. B. obsignata occurred with a prevalence of 72.5% in the 40 examined hosts in a range of 2-461 nematodes and a mean intensity of 68.6, whereas E. annulatus was present in 2.5% of the animals, with a total amount of five recovered parasites. Gross lesions were not observed in the parasitized birds. Lesions due to B. obsignata mainly consisted of the thickening of intestinal villi with a mild mixed inflammatory infiltrate with the presence of mononuclear cells and heterophils. The lesions induced by E. annulatus were represented by foci of inflammatory infiltrate with heterophils in the crop epithelium and esophagus of a single infected female. These are the first pathological findings related to the presence of capillariid worms in turkeys to be reported in Brazil so far. Capillaria anatis, although present, was not pathogenic to the investigated turkeys.

  11. Some Aspects of the Reproductive Biology of Female Rhipicephalus annulatus (Say, 1821 in the Laboratory

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    Nkegbe Emmanuel

    2011-12-01

    Full Text Available Ticks are very important in the livestock industry. They are agents of disease causing organisms in addition to the harm they cause to the hide of livestock. A study of some reproductive characteristics of Rhipicephalus annulatus in the laboratory through colony culture showed that between 3140 to 5338 eggs (p<0.05 were laid by each engorged female, of an average weight of 103 to 175 mg (p<0.05. The required number of days for hatching of eggs was found to be 24 to 30 days (p<0.05. Percentage survival of eggs to adult female was highest at 6.1% and as low as 0.57%. Despite the large number of eggs laid, very few larvae survived to the adult stage even in the laboratory where biotic and abiotic factors were controlled to the advantage of the ticks. This showed that in the wild where both biotic and abiotic conditions are very unstable, survivability would be very minimal. We concluded that as much as possible, control strategy be geared towards the destruction of the adult females as possible.

  12. Developmental stages and fecundity of Lepeophtheirus simplex (Copepoda: Caligidae) parasitic on bullseye puffer fish (Sphoeroides annulatus).

    Science.gov (United States)

    Neptali Morales-Serna, Francisco; Rivas-Salas, Ana Ines; Gomez, Samuel; Fajer-Avila, Emma Josefina

    2015-01-01

    Lepeophtheirus simplex Ho, Gómez et Fajer-Avila, 2001 is a parasite of Sphoeroides annulatus (Jenyns), an economically important fish species, with potential for aquaculture, in northwestern Mexico. The goal of this study was to describe the developmental stages under experimental conditions and seasonal fecundity of this parasite on wild fish. There are two naupliar, one copepodid, two chalimus and two pre-adult stages preceding the adult of L. simplex. The results support previous findings, which point out that the life cycle of the caligid copepods includes only six post-naupliar stages. The generation time from egg extrusion to adult for L. simplex was approximately 10 days at 22 °C. The body length of the ovigerous females ranged between 2.2 and 4.1 mm, and its fecundity between 12 and 36 eggs per string. Fecundity was negatively correlated with the egg size and positively correlated with the egg string length. Our data did not reveal significant differences in fecundity among sampling months, but ovigerous females were significantly larger in March (when water temperature was 22 °C) than in June and July (when water temperature was 30 °C). To some extent, our fecundity results contrast with those found in species of sea lice from higher latitudes. Undoubtedly, biological information on different species of sea lice from different environmental conditions will enhance our understanding of their infection strategies and will be valuable, given the increasing interest in marine fish farming in Mexico. PMID:25960548

  13. Acaricidal Activity of Petroleum Ether Extract of Leaves of Tetrastigma leucostaphylum (Dennst. Alston against Rhipicephalus (Boophilus annulatus

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    T. P. Adarsh Krishna

    2014-01-01

    Full Text Available The acaricidal activity of the petroleum ether extract of leaves of Tetrastigma leucostaphylum (Dennst. Alston (family: Vitaceae against Rhipicephalus (Boophilus annulatus was assessed using adult immersion test (AIT. The per cent of adult mortality, inhibition of fecundity, and blocking of hatching of eggs were studied at different concentrations. The extract at 10% concentration showed 88.96% inhibition of fecundity, 58.32% of adult tick mortality, and 50% inhibition of hatching. Peak mortality rate was observed after day 5 of treatment. Mortality of engorged female ticks, inhibition of fecundity, and hatching of eggs were concentration dependent. The LC50 value of the extract against R. (B. annulatus was 10.46%. The HPTLC profiling of the petroleum ether extract revealed the presence of at least seven polyvalent components. In the petroleum ether extract, nicotine was identified as one of the components up to a concentration of 5.4%. However, nicotine did not reveal any acaricidal activity up to 20000 ppm (2%. Coconut oil, used as diluent for dissolving the extract, did not reveal any acaricidal effects. The results are indicative of the involvement of synergistic or additive action of the bioactive components in the tick mortality and inhibition of the oviposition.

  14. Seasonality of parasitic copepods on bullseye puffer, Sphoeroides annulatus (Pisces: Tetraodontidae), from the northwestern coast of Mexico.

    Science.gov (United States)

    Morales-Serna, Francisco Neptalí; Rubio-Godoy, Miguel; Gómez, Samuel

    2011-08-01

    Seasonal occurrence of parasitic copepods in wild bullseye puffer, Sphoeroides annulatus (Pisces: Tetraodontidae), was analyzed in conjunction with variation of biotic and abiotic factors. Eleven samples were taken between February 2007 and February 2008 in Santa María La Reforma lagoon (northwestern coast of México). In total, 337 fish was examined; 5 parasitic copepod species were observed, including Acantholochus zairae , Caligus serratus , Lepeophtheirus simplex , Pseudochondracanthus diceraus , and Parabrachiella sp. The most common species were L. simplex , P. diceraus, and C. serratus (overall prevalence, 59, 53, and 35%, respectively), which significantly varied in prevalence and mean intensity between sampling months. A seasonal pattern was only observed for L. simplex, with higher infection levels in the warmest month than in the coldest month. Statistical analyses indicated that the intensity of L. simplex was positively correlated with water temperature. There were no significant differences in prevalence and intensity of infection among female and male hosts. At the component community level, species richness ranged between 4 and 5 during most of the study period, and no seasonality was observed in the number of individuals, Shannon diversity index, evenness index, or the Berger-Parker dominance index. At the infracommunity level, 4 descriptors used (mean species richness, mean number of individuals, mean Brillouin's diversity index, and mean Berger-Parker index) varied significantly between sampling months, but no seasonality was observed, except for a slight increase in the number of individuals during the warmest month. A significant positive association was detected between number of individuals and water temperature and between host size and both species richness and number of individuals. This is the first account of the ecology of these 5 parasitic copepods. Although no significant association was detected between fish condition factor and the

  15. Effect of surfactants on Ra-sHSPI - A small heat shock protein from the cattle tick Rhipicephalus annulatus

    Science.gov (United States)

    Siddiqi, Mohammad Khursheed; Shahein, Yasser E.; Hussein, Nahla; Khan, Rizwan H.

    2016-09-01

    Electrostatic interaction plays an important role in protein aggregation phenomenon. In this study, we have checked the effect of anionic - Sodium Dodecyl Sulfate (SDS) and cationic-Cetyltrimethyl Ammonium Bromide (CTAB) surfactant on aggregation behavior of Ra-sHSPI, a small heat shock protein purified from Rhipicephalus annulatus tick. To monitor the effect of these surfactants, we have employed several spectroscopic methods such as Rayleigh light scattering measurements, ANS (8-Anilinonaphthalene-1-sulfonic acid) fluorescence measurements, ThT (Thioflavin T) binding assays, Far-UV CD (Circular Dichroism) and dynamic light scattering measurements. In the presence of anionic surfactant-SDS, Ra-sHSPI forms amyloid fibrils, in contrast, no amyloid formation was observed in presence of cationic surfactant at low pH. Enhancement of ANS fluorescence intensity confirms the exposition of more hydrophobic patches during aggregation. ThT binding assay confirms the amyloid fibrillar nature of the SDS induced Ra-sHSPI aggregates and supported by PASTA 2.0 (prediction of amyloid structural aggregation) software. This study demonstrates the crucial role of charge during amyloid fibril formation at low pH in Ra-sHSPI.

  16. Standardized benchmarking in the quest for orthologs

    DEFF Research Database (Denmark)

    Altenhoff, Adrian M; Boeckmann, Brigitte; Capella-Gutierrez, Salvador;

    2016-01-01

    Achieving high accuracy in orthology inference is essential for many comparative, evolutionary and functional genomic analyses, yet the true evolutionary history of genes is generally unknown and orthologs are used for very different applications across phyla, requiring different precision......-recall trade-offs. As a result, it is difficult to assess the performance of orthology inference methods. Here, we present a community effort to establish standards and an automated web-based service to facilitate orthology benchmarking. Using this service, we characterize 15 well-established inference methods...... and resources on a battery of 20 different benchmarks. Standardized benchmarking provides a way for users to identify the most effective methods for the problem at hand, sets a minimum requirement for new tools and resources, and guides the development of more accurate orthology inference methods....

  17. Standardized benchmarking in the quest for orthologs.

    Science.gov (United States)

    Altenhoff, Adrian M; Boeckmann, Brigitte; Capella-Gutierrez, Salvador; Dalquen, Daniel A; DeLuca, Todd; Forslund, Kristoffer; Huerta-Cepas, Jaime; Linard, Benjamin; Pereira, Cécile; Pryszcz, Leszek P; Schreiber, Fabian; da Silva, Alan Sousa; Szklarczyk, Damian; Train, Clément-Marie; Bork, Peer; Lecompte, Odile; von Mering, Christian; Xenarios, Ioannis; Sjölander, Kimmen; Jensen, Lars Juhl; Martin, Maria J; Muffato, Matthieu; Gabaldón, Toni; Lewis, Suzanna E; Thomas, Paul D; Sonnhammer, Erik; Dessimoz, Christophe

    2016-05-01

    Achieving high accuracy in orthology inference is essential for many comparative, evolutionary and functional genomic analyses, yet the true evolutionary history of genes is generally unknown and orthologs are used for very different applications across phyla, requiring different precision-recall trade-offs. As a result, it is difficult to assess the performance of orthology inference methods. Here, we present a community effort to establish standards and an automated web-based service to facilitate orthology benchmarking. Using this service, we characterize 15 well-established inference methods and resources on a battery of 20 different benchmarks. Standardized benchmarking provides a way for users to identify the most effective methods for the problem at hand, sets a minimum requirement for new tools and resources, and guides the development of more accurate orthology inference methods. PMID:27043882

  18. Effect of UV radiation on the genetic inactivation of sperm of the bullseye puffer Sphoeroides annulatus (Jenyns, 1842); Efecto de la radiacion UV en la inactivacion genetica del esperma de botete diana Sphoeroides annulatus (Jenyns, 1842)

    Energy Technology Data Exchange (ETDEWEB)

    Arias-Rodriguez, Lenin; Rodriguez-Ibarra, Luz Estela; Del Valle-Pignataro, Gabriela [Laboratorio de Genetica, Centro de Investigacion en Alimentacion y Desarrollo, A. C., Sinaloa (Mexico)

    2004-09-15

    Genetic (DNA) inactivation of fish sperm with ultraviolet irradiation is generally accompanied by a paradoxical effect on survival rates (Hertwig effect). In the present study, sperm samples from ten males bullseye puffer fish (Sphoeroides annulatus) were diluted 1:50 using Cortland's extender solution and used to test the effect of nine ultraviolet doses (0.2-1.0 J cm{sup -}2 ) on motility time in seconds, motility index, and embryo survival rate after fertilizing eggs from five bullseye puffer females. Motility time of sperm irradiated with 0.2-0.9 J cm{sup -}2 were not statistically different from the controls, but sperm irradiated with a dosage of 1.0 J cm{sup -}2 dosage had significant lower motility time. Motility indices (MI) allowed for the statistical differentiation of four groups in relation to their response to different radiation doses: the first had high MI, and included the controls and 0.2-0.3 J cm{sup -}2 treatments; the second had lower MI and included the 0.4-0.7 J cm{sup -}2 treatments; the third showed recovery of MI and included the 0.8-0.9 J cm{sup -}2 treatments; and the fourth showed the lowest MI with the 1.0 J cm{sup -}2 treatment. Embryo survival was highest for the controls and 0.2 J cm{sup -}2 treatment, decreasing in the 0.3-0.4 J cm{sup -}2 treatments, increasing again in the 0.5-0.8 J cm{sup -}2 treatments, until reaching lowest survival in the 0.9-1.0 J cm{sup -}2 treatments. These results indicate that the best ultraviolet dosage to achieve genetic inactivation of sperm of this species is close to 0.7 J cm{sup -}2, a dosage in which fish fry showed typical haploid syndrome characteristics. [Spanish] La inactivacion genetica (ADN) del esperma de peces se realiza mediante luz ultravioleta que, en irradiaciones crecientes, genera efectos paradojicos (efecto Hertwig) en los porcentajes de supervivencia. En este trabajo se diluyeron muestras de semen provenientes de diez machos de botete diana (Sphoeroides annulatus) en solucion

  19. Assessment of orthologous splicing isoforms in human and mouse orthologous genes

    Directory of Open Access Journals (Sweden)

    Horner David S

    2010-10-01

    Full Text Available Abstract Background Recent discoveries have highlighted the fact that alternative splicing and alternative transcripts are the rule, rather than the exception, in metazoan genes. Since multiple transcript and protein variants expressed by the same gene are, by definition, structurally distinct and need not to be functionally equivalent, the concept of gene orthology should be extended to the transcript level in order to describe evolutionary relationships between structurally similar transcript variants. In other words, the identification of true orthology relationships between gene products now should progress beyond primary sequence and "splicing orthology", consisting in ancestrally shared exon-intron structures, is required to define orthologous isoforms at transcript level. Results As a starting step in this direction, in this work we performed a large scale human- mouse gene comparison with a twofold goal: first, to assess if and to which extent traditional gene annotations such as RefSeq capture genuine splicing orthology; second, to provide a more detailed annotation and quantification of true human-mouse orthologous transcripts defined as transcripts of orthologous genes exhibiting the same splicing patterns. Conclusions We observed an identical exon/intron structure for 32% of human and mouse orthologous genes. This figure increases to 87% using less stringent criteria for gene structure similarity, thus implying that for about 13% of the human RefSeq annotated genes (and about 25% of the corresponding transcripts we could not identify any mouse transcript showing sufficient similarity to be confidently assigned as a splicing ortholog. Our data suggest that current gene and transcript data may still be rather incomplete - with several splicing variants still unknown. The observation that alternative splicing produces large numbers of alternative transcripts and proteins, some of them conserved across species and others truly species

  20. Assessment of bovine immunoprotecion against Rhipicephalus microplus using Bm86-CG antigen expressed in Pichia pastoris

    Science.gov (United States)

    The cattle tick Rhipicephalus microplus is a major pest of cattle in tropical and subtropical parts of the world. In addition to direct effects associated with its obligate parasitic way of life, R. microplus also transmits the pathogens that cause bovine babesiosis and anaplasmosis. Commercially ...

  1. Identifying single copy orthologs in Metazoa.

    Directory of Open Access Journals (Sweden)

    Christopher J Creevey

    2011-12-01

    Full Text Available The identification of single copy (1-to-1 orthologs in any group of organisms is important for functional classification and phylogenetic studies. The Metazoa are no exception, but only recently has there been a wide-enough distribution of taxa with sufficiently high quality sequenced genomes to gain confidence in the wide-spread single copy status of a gene.Here, we present a phylogenetic approach for identifying overlooked single copy orthologs from multigene families and apply it to the Metazoa. Using 18 sequenced metazoan genomes of high quality we identified a robust set of 1,126 orthologous groups that have been retained in single copy since the last common ancestor of Metazoa. We found that the use of the phylogenetic procedure increased the number of single copy orthologs found by over a third more than standard taxon-count approaches. The orthologs represented a wide range of functional categories, expression profiles and levels of divergence.To demonstrate the value of our set of single copy orthologs, we used them to assess the completeness of 24 currently published metazoan genomes and 62 EST datasets. We found that the annotated genes in published genomes vary in coverage from 79% (Ciona intestinalis to 99.8% (human with an average of 92%, suggesting a value for the underlying error rate in genome annotation, and a strategy for identifying single copy orthologs in larger datasets. In contrast, the vast majority of EST datasets with no corresponding genome sequence available are largely under-sampled and probably do not accurately represent the actual genomic complement of the organisms from which they are derived.

  2. A New Orthology Assessment Method for Phylogenomic Data: Unrooted Phylogenetic Orthology.

    Science.gov (United States)

    Ballesteros, Jesús A; Hormiga, Gustavo

    2016-08-01

    Current sequencing technologies are making available unprecedented amounts of genetic data for a large variety of species including nonmodel organisms. Although many phylogenomic surveys spend considerable time finding orthologs from the wealth of sequence data, these results do not transcend the original study and after being processed for specific phylogenetic purposes these orthologs do not become stable orthology hypotheses. We describe a procedure to detect and document the phylogenetic distribution of orthologs allowing researchers to use this information to guide selection of loci best suited to test specific evolutionary questions. At the core of this pipeline is a new phylogenetic orthology method that is neither affected by the position of the root nor requires explicit assignment of outgroups. We discuss the properties of this new orthology assessment method and exemplify its utility for phylogenomics using a small insects dataset. In addition, we exemplify the pipeline to identify and document stable orthologs for the group of orb-weaving spiders (Araneoidea) using RNAseq data. The scripts used in this study, along with sample files and additional documentation, are available at https://github.com/ballesterus/UPhO. PMID:27189539

  3. Zebrafish orthologs of human muscular dystrophy genes

    OpenAIRE

    Zon Leonard I; Zhou Yi; Pusack Timothy J; Beltre Rosanna; Vogel Emily D; Guyon Jeffrey R; Steffen Leta S; Kunkel Louis M

    2007-01-01

    Abstract Background Human muscular dystrophies are a heterogeneous group of genetic disorders which cause decreased muscle strength and often result in premature death. There is no known cure for muscular dystrophy, nor have all causative genes been identified. Recent work in the small vertebrate zebrafish Danio rerio suggests that mutation or misregulation of zebrafish dystrophy orthologs can also cause muscular degeneration phenotypes in fish. To aid in the identification of new causative g...

  4. Immunological control of ticks through vaccination with Boophilus microplus gut antigens.

    Science.gov (United States)

    De La Fuente, J; Rodríguez, M; García-García, J C

    2000-01-01

    The control of tick infestations and the transmission of tick-borne diseases remain a challenge for the scientific community. Traditional control methods have been only partially successful. Recently, vaccination with recombinant Boophilus microplus gut antigens has been shown to control tick infestations. Our Bm86-containing vaccine formulation (Gavac) has been effective for the control of artificial infestations of B. annulatus, B. decoloratus, and chemically sensitive and resistant B. microplus strains from Australia, Africa, America, and Iran. Preliminary results with Hyalomma spp. and Rhipicephalus spp. suggest partial cross protection. In field trials, vaccination with Gavac controlled B. microplus and B. annulatus infestations and reduced the transmission of babesiosis, resulting in important savings for the cattle industry. Different degrees of susceptibility to the vaccination with Bm86 and sequence variations in the Bm86 locus have been reported. The Bm95 antigen was isolated from the Argentinean Bm86-resistant B. microplus strain A. A Bm95-based vaccine was used to protect cattle against tick infestations under production conditions with similar results to that obtained with Gavac. The Bm95 antigen from strain A was able to protect against infestations with Bm86-sensitive and Bm86-resistant tick strains, thus suggesting that Bm95 could be a more universal antigen in protecting cattle against infestations by B. microplus strains from different geographical areas. These results clearly demonstrate the advantage and possibilities for the immunological control of ticks. PMID:11193686

  5. Population structure and reproductive aspects of puffer fish Sphoeroides annulatus (Jenyns, 1842 (Osteichthyes: Tetraodontidae, landed in Teacapán, Sinaloa, Mexico

    Directory of Open Access Journals (Sweden)

    María Candelaria Valdez-Pineda

    2014-03-01

    Full Text Available The puffer fish Sphoeroides annulatus is an important target species for the artisanal fishing fleets of NW Mexico. To obtain information on population structure of the local stock, we determined the total length and total weight (TL and TW ranges, sex ratio and reproductive stages of 745 specimens of this species, landed from May 2010 to April 2011 in Teacapán, Sinaloa, NW Mexico. TL ranged from 15 to 40 cm and TW from 100 to 1600 g. There were no differences between mean TL (27.41 ± 4.14 cm and TW (534.5 ± 226.0 g of males and females respectively. Sex ratio was not significantly different (χ2 = 0.03, P > 0.05 from 1F:1M. The length-weight relationship for both sexes was TW = 0.044TL2.815, R² = 0.895. The value of the slope b was significantly lower than 3 (P < 0.05, and indicated negative allometric growth. The distribution of maturity stages indicated one main reproductive period from June to September and one less intense, from November to December for females, and in December for males. Size at first maturity (L50% of females was 26.52 cm and that of males was 27.41 cm.

  6. Multiple nuclear ortholog next generation sequencing phylogeny of Daucus

    Science.gov (United States)

    Next generation sequencing is helping to solve the data insufficiency problem hindering well-resolved dominant gene phylogenies. We used Roche 454 technology to obtain DNA sequences from 93 nuclear orthologs, dispersed throughout all linkage groups of Daucus. Of these 93 orthologs, ten were designed...

  7. Effects of season, sex and body size on the feeding ecology of turtle-headed sea snakes ( Emydocephalus annulatus) on IndoPacific inshore coral reefs

    Science.gov (United States)

    Goiran, C.; Dubey, S.; Shine, R.

    2013-06-01

    In terrestrial snakes, many cases of intraspecific shifts in dietary habits as a function of predator sex and body size are driven by gape limitation and hence are most common in species that feed on relatively large prey and exhibit a wide body-size range. Our data on sea snakes reveal an alternative mechanism for intraspecific niche partitioning, based on sex-specific seasonal anorexia induced by reproductive activities. Turtle-headed sea snakes ( Emydocephalus annulatus) on coral reefs in the New Caledonian Lagoon feed entirely on the eggs of demersal-spawning fishes. DNA sequence data (cytochrome b gene) on eggs that we palpated from stomachs of 37 snakes showed that despite this ontogenetic stage specialization, the prey comes from a taxonomically diverse array of species including damselfish (41 % of samples, at least 5 species), blennies (41 %, 4 species) and gobies (19 %, 5 species). The composition of snake diets shifted seasonally (with damselfish dominating in winter but not summer), presumably reflecting seasonality of fish reproduction. That seasonal shift affects male and female snakes differently, because reproduction is incompatible with foraging. Adult female sea snakes ceased feeding when they became heavily distended with developing embryos in late summer, and males ceased feeding while they were mate searching in winter. The sex divergence in foraging habits may be amplified by sexual size dimorphism; females grow larger than males, and larger snakes (of both sexes) feed more on damselfish (which often lay their eggs in exposed sites) than on blennies and gobies (whose eggs are hidden within narrow crevices). Specific features of reproductive biology of coral reef fish (seasonality and nest type) have generated intraspecific niche partitioning in these sea snakes, by mechanisms different from those that apply to terrestrial snakes.

  8. The effect of orthology and coregulation on detecting regulatory motifs.

    Directory of Open Access Journals (Sweden)

    Valerie Storms

    Full Text Available BACKGROUND: Computational de novo discovery of transcription factor binding sites is still a challenging problem. The growing number of sequenced genomes allows integrating orthology evidence with coregulation information when searching for motifs. Moreover, the more advanced motif detection algorithms explicitly model the phylogenetic relatedness between the orthologous input sequences and thus should be well adapted towards using orthologous information. In this study, we evaluated the conditions under which complementing coregulation with orthologous information improves motif detection for the class of probabilistic motif detection algorithms with an explicit evolutionary model. METHODOLOGY: We designed datasets (real and synthetic covering different degrees of coregulation and orthologous information to test how well Phylogibbs and Phylogenetic sampler, as representatives of the motif detection algorithms with evolutionary model performed as compared to MEME, a more classical motif detection algorithm that treats orthologs independently. RESULTS AND CONCLUSIONS: Under certain conditions detecting motifs in the combined coregulation-orthology space is indeed more efficient than using each space separately, but this is not always the case. Moreover, the difference in success rate between the advanced algorithms and MEME is still marginal. The success rate of motif detection depends on the complex interplay between the added information and the specificities of the applied algorithms. Insights in this relation provide information useful to both developers and users. All benchmark datasets are available at http://homes.esat.kuleuven.be/~kmarchal/Supplementary_Storms_Valerie_PlosONE.

  9. 微小牛蜱Bm86基因的原核表达与表达条件的优化%Prokaryotic Expression of Bm86 Gene of Boophilus microplus and Optimization of the Expression Condition

    Institute of Scientific and Technical Information of China (English)

    马米玲; 关贵全; 李有全; 刘爱红; 任巧云; 牛庆丽; 殷宏; 罗建勋

    2009-01-01

    根据微小牛蜱Bin86基因序列设计引物,在重组质粒pMD18-T-Bin86中克隆,并将其定向亚克隆入原核表达载体pGEX-4T-1,转化至大肠埃希菌BL21(DE3)株,用不同浓度异丙基-β-D-硫代半乳糖苷(IPTG)在不同时间进行诱导表达.十二烷基硫酸钠-聚丙烯酰胺凝胶电泳(SDS-PAGE)检测结果表明,37℃条件下经1 mmol/L IPTG诱导8 h后,目的 重组蛋白表达量最大,表达相对分子质量(Mr)约为94000的包涵体蛋白,与预期大小一致,目的 蛋白约占蛋白总量的29%.蛋白质印迹(Western blotting)分析表明,该重组蛋白可被兔抗微小牛蜱全蜱阳性血清所识别.

  10. Combinatorial Approaches to Accurate Identification of Orthologous Genes

    OpenAIRE

    Shi, Guanqun

    2011-01-01

    The accurate identification of orthologous genes across different species is a critical and challenging problem in comparative genomics and has a wide spectrum of biological applications including gene function inference, evolutionary studies and systems biology. During the past several years, many methods have been proposed for ortholog assignment based on sequence similarity, phylogenetic approaches, synteny information, and genome rearrangement. Although these methods share many commonly a...

  11. Assessing performance of orthology detection strategies applied to eukaryotic genomes.

    Directory of Open Access Journals (Sweden)

    Feng Chen

    Full Text Available Orthology detection is critically important for accurate functional annotation, and has been widely used to facilitate studies on comparative and evolutionary genomics. Although various methods are now available, there has been no comprehensive analysis of performance, due to the lack of a genomic-scale 'gold standard' orthology dataset. Even in the absence of such datasets, the comparison of results from alternative methodologies contains useful information, as agreement enhances confidence and disagreement indicates possible errors. Latent Class Analysis (LCA is a statistical technique that can exploit this information to reasonably infer sensitivities and specificities, and is applied here to evaluate the performance of various orthology detection methods on a eukaryotic dataset. Overall, we observe a trade-off between sensitivity and specificity in orthology detection, with BLAST-based methods characterized by high sensitivity, and tree-based methods by high specificity. Two algorithms exhibit the best overall balance, with both sensitivity and specificity>80%: INPARANOID identifies orthologs across two species while OrthoMCL clusters orthologs from multiple species. Among methods that permit clustering of ortholog groups spanning multiple genomes, the (automated OrthoMCL algorithm exhibits better within-group consistency with respect to protein function and domain architecture than the (manually curated KOG database, and the homolog clustering algorithm TribeMCL as well. By way of using LCA, we are also able to comprehensively assess similarities and statistical dependence between various strategies, and evaluate the effects of parameter settings on performance. In summary, we present a comprehensive evaluation of orthology detection on a divergent set of eukaryotic genomes, thus providing insights and guides for method selection, tuning and development for different applications. Many biological questions have been addressed by multiple

  12. Update History of This Database - PGDBj - Ortholog DB | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available h archive site is opened. 2012/08/01 PGDBj Ortholog DB ( http://pgdbj.jp/ortholog-db.html ) is opened. Jooml...[ Credits ] BLAST Search Image Search Home About Archive Update History Contact us PGD...Bj - Ortholog DB Update History of This Database Date Update contents 2014/05/12 PGDBj Ortholog DB Englis...ate History of This Database Site Policy | Contact Us Update History of This Database - PGDBj - Ortholog DB | LSDB Archive ...

  13. Evolution of orthologous tandemly arrayed gene clusters

    Directory of Open Access Journals (Sweden)

    Bertrand Denis

    2011-10-01

    Full Text Available Abstract Background Tandemly Arrayed Gene (TAG clusters are groups of paralogous genes that are found adjacent on a chromosome. TAGs represent an important repertoire of genes in eukaryotes. In addition to tandem duplication events, TAG clusters are affected during their evolution by other mechanisms, such as inversion and deletion events, that affect the order and orientation of genes. The DILTAG algorithm developed in 1 makes it possible to infer a set of optimal evolutionary histories explaining the evolution of a single TAG cluster, from an ancestral single gene, through tandem duplications (simple or multiple, direct or inverted, deletions and inversion events. Results We present a general methodology, which is an extension of DILTAG, for the study of the evolutionary history of a set of orthologous TAG clusters in multiple species. In addition to the speciation events reflected by the phylogenetic tree of the considered species, the evolutionary events that are taken into account are simple or multiple tandem duplications, direct or inverted, simple or multiple deletions, and inversions. We analysed the performance of our algorithm on simulated data sets and we applied it to the protocadherin gene clusters of human, chimpanzee, mouse and rat. Conclusions Our results obtained on simulated data sets showed a good performance in inferring the total number and size distribution of duplication events. A limitation of the algorithm is however in dealing with multiple gene deletions, as the algorithm is highly exponential in this case, and becomes quickly intractable.

  14. Efficacy of rHaa86, an orthologue of Bm86, against challenge infestations of Hyalomma anatolicum anatolicum.

    Science.gov (United States)

    Jeyabal, L; Azhahianambi, P; Susitha, K; Ray, D D; Chaudhuri, P; Vanlahmuaka; Ghosh, S

    2010-04-01

    In an attempt to develop vaccine against Hyalomma anatolicum anatolicum, the protective efficacy of rHaa86 was evaluated against experimental challenge infestations of homologous tick species and lethal dose of Theileria annulata. Following challenge, a significant difference of 20.9% (P < 0.01) in the dropping per cent of ticks fed on immunized and control animals was recorded. A statistically significant reduction of 49.6 mg (P < 0.01) in the weight of ticks fed on immunized animals in comparison with control was noted. The ticks dropped from immunized animals laid fewer eggs and a reduction of 68.1 mg (P < 0.05) in comparison with the ticks fed on control animals was noted. The DT%, DO%, DR% and E% were calculated as 73.8, 31.3, 15.8 and 82.3% respectively. In all the calves fever (rectal temperature

  15. Thinning of Apple Fruits with Foliar Fertilizers Goëmar BM 86 E and Goëmar Folical

    OpenAIRE

    Milutin Misimović; Dragana Vukojević; Nada Zavišić; Jasmina Simić

    2014-01-01

    Thinning is a regular pomotechnical measure, which is performed by using different chemicals that cause fruit drop in intensive apple orchards. It is common that some apple cultivars overbear, giving small fruits of poor quality. Effects of chemical thinners of apple fruits are as follows: higher productiveness in the next vegetation period, higher percentage of first class apples and the lesser fruit drop before harvest and so on. Hormonal thinners that are currently being used in th...

  16. Simulation of control strategies for the cattle tick Boophilus microplus employing vaccination with a recombinant Bm86 antigen preparation.

    Science.gov (United States)

    Labarta, V; Rodríguez, M; Penichet, M; Lleonart, R; Luaces, L L; de la Fuente, J

    1996-05-01

    Current strategies for the control of the cattle tick Boophilus microplus include the use of chemicals as the principal control method. These methods, however, have met with partially successful results. The recent development of immunological methods for the control of the cattle tick has opened new possibilities for the design of control strategies. Employing the results obtained by us in experiments testing the effect of vaccination with the recombinant vaccine, Gavac (Heber Biotec S.A.), on tick populations, we have developed a model to evaluate, through a computer program, the efficacy of the vaccine as a control method. The action of the vaccine on the control of tick populations was simulated and the specific serum antibody titers required to decrease the tick population in the field were calculated. The specific serum antibody titer required to decrease the tick population in the field after the first vaccination scheme was found to be > or = 57,200 and the antibody titer required to maintain this effect when the vaccine is already acting and after successive revaccinations was found to be > or = 27,500. Considerations about revaccination schemes and combination between vaccination and acaricide treatments as possible control strategies are discussed. PMID:8792587

  17. The evaluation of yeast derivatives as adjuvants for the immune response to the Bm86 antigen in cattle

    OpenAIRE

    Machado Héctor; Montero Carlos; Rodríguez Valle Manuel; Joglar Marisdania

    2001-01-01

    Abstract Background The Gavac™ vaccine against the cattle tick Boophilus microplus has proven its efficacy in a large number of controlled and field experiments. However, this vaccine could be further improved by searching for new alternative adjuvants that would induce a stronger long-lasting immune response. We conducted several experiments to assay the adjuvant effect of fractions of the recombinant yeast Pichia pastoris in mouse and cattle models. In previous experiments, the combination ...

  18. OMA 2011: orthology inference among 1000 complete genomes.

    Science.gov (United States)

    Altenhoff, Adrian M; Schneider, Adrian; Gonnet, Gaston H; Dessimoz, Christophe

    2011-01-01

    OMA (Orthologous MAtrix) is a database that identifies orthologs among publicly available, complete genomes. Initiated in 2004, the project is at its 11th release. It now includes 1000 genomes, making it one of the largest resources of its kind. Here, we describe recent developments in terms of species covered; the algorithmic pipeline--in particular regarding the treatment of alternative splicing, and new features of the web (OMA Browser) and programming interface (SOAP API). In the second part, we review the various representations provided by OMA and their typical applications. The database is publicly accessible at http://omabrowser.org.

  19. Toward community standards in the quest for orthologs.

    NARCIS (Netherlands)

    Dessimoz, C.; Gabaldon, T.; Roos, D.S.; Sonnhammer, E.L.; Herrero, J.; Szklarczyk, R.J.

    2012-01-01

    The identification of orthologs-genes pairs descended from a common ancestor through speciation, rather than duplication-has emerged as an essential component of many bioinformatics applications, ranging from the annotation of new genomes to experimental target prioritization. Yet, the development a

  20. Orthology between genomes of Brachypodium, wheat and rice

    Directory of Open Access Journals (Sweden)

    Balyan Harindra S

    2009-05-01

    Full Text Available Abstract Background In the past, rice genome served as a good model for studies involving comparative genomics of grass species. More recently, however, Brachypodium distachyon genome has emerged as a better model system for genomes of temperate cereals including wheat. During the present study, Brachypodium EST contigs were utilized to resolve orthologous relationships among the genomes of Brachypodium, wheat and rice. Findings Comparative sequence analysis of 3,818 Brachypodium EST (bEST contigs and 3,792 physically mapped wheat EST (wEST contigs revealed that as many as 449 bEST contigs were orthologous to 1,154 wEST loci that were bin-mapped on all the 21 wheat chromosomes. Similarly 743 bEST contigs were orthologous to specific rice genome sequences distributed on all the 12 rice chromosomes. As many as 183 bEST contigs were orthologous to both wheat and rice genome sequences, which harbored as many as 17 SSRs conserved across the three species. Primers developed for 12 of these 17 conserved SSRs were used for a wet-lab experiment, which resolved relatively high level of conservation among the genomes of Brachypodium, wheat and rice. Conclusion The present study confirmed that Brachypodium is a better model than rice for analysis of the genomes of temperate cereals like wheat and barley. The whole genome sequence of Brachypodium, which should become available in the near future, will further facilitate greatly the studies involving comparative genomics of cereals.

  1. Factors affecting the concordance between orthologous gene trees and species tree in bacteria

    Directory of Open Access Journals (Sweden)

    González Víctor

    2008-10-01

    Full Text Available Abstract Background As originally defined, orthologous genes implied a reflection of the history of the species. In recent years, many studies have examined the concordance between orthologous gene trees and species trees in bacteria. These studies have produced contradictory results that may have been influenced by orthologous gene misidentification and artefactual phylogenetic reconstructions. Here, using a method that allows the detection and exclusion of false positives during identification of orthologous genes, we address the question of whether putative orthologous genes within bacteria really reflect the history of the species. Results We identified a set of 370 orthologous genes from the bacterial order Rhizobiales. Although manifesting strong vertical signal, almost every orthologous gene had a distinct phylogeny, and the most common topology among the orthologous gene trees did not correspond with the best estimate of the species tree. However, each orthologous gene tree shared an average of 70% of its bipartitions with the best estimate of the species tree. Stochastic error related to gene size affected the concordance between the best estimated of the species tree and the orthologous gene trees, although this effect was weak and distributed unevenly among the functional categories. The nodes showing the greatest discordance were those defined by the shortest internal branches in the best estimated of the species tree. Moreover, a clear bias was evident with respect to the function of the orthologous genes, and the degree of divergence among the orthologous genes appeared to be related to their functional classification. Conclusion Orthologous genes do not reflect the history of the species when taken as individual markers, but they do when taken as a whole. Stochastic error affected the concordance of orthologous genes with the species tree, albeit weakly. We conclude that two important biological causes of discordance among

  2. Orthologs of macrophage migration inhibitory factor from parasitic nematodes

    Science.gov (United States)

    Vermeire, Jon J.; Cho, Yoonsang; Lolis, Elias; Bucala, Richard; Cappello, Michael

    2013-01-01

    Chronic helminth infections are associated with modulation of host cellular immune responses, presumably to prolong parasite survival within the mammalian host. This phenomenon is attributed, at least in part, to the elaboration of parasite molecules, including orthologs of host cytokines and receptors, at the host–parasite interface. This review describes recent progress in the characterization of macrophage migration inhibitory factor (MIF) orthologs from parasitic nematodes. The roles of these molecules in parasite developmental biology and pathogenesis are discussed. Further knowledge of the species-specific activities and three-dimensional structures of human and parasitic nematode MIF molecules should make them ideal targets for drug- and/or vaccine-based strategies aimed at nematode disease control. PMID:18603473

  3. Retrotranspositions in orthologous regions of closely related grass species

    Directory of Open Access Journals (Sweden)

    Swigoňová Zuzana

    2006-08-01

    Full Text Available Abstract Background Retrotransposons are commonly occurring eukaryotic transposable elements (TEs. Among these, long terminal repeat (LTR retrotransposons are the most abundant TEs and can comprise 50–90% of the genome in higher plants. By comparing the orthologous chromosomal regions of closely related species, the effects of TEs on the evolution of plant genomes can be studied in detail. Results Here, we compared the composition and organization of TEs within five orthologous chromosomal regions among three grass species: maize, sorghum, and rice. We identified a total of 132 full or fragmented LTR retrotransposons in these regions. As a percentage of the total cumulative sequence in each species, LTR retrotransposons occupy 45.1% of the maize, 21.1% of the rice, and 3.7% of the sorghum regions. The most common elements in the maize retrotransposon-rich regions are the copia-like retrotransposons with 39% and the gypsy-like retrotransposons with 37%. Using the contiguous sequence of the orthologous regions, we detected 108 retrotransposons with intact target duplication sites and both LTR termini. Here, we show that 74% of these elements inserted into their host genome less than 1 million years ago and that many retroelements expanded in size by the insertion of other sequences. These inserts were predominantly other retroelements, however, several of them were also fragmented genes. Unforeseen was the finding of intact genes embedded within LTR retrotransposons. Conclusion Although the abundance of retroelements between maize and rice is consistent with their different genome sizes of 2,364 and 389 Mb respectively, the content of retrotransposons in sorghum (790 Mb is surprisingly low. In all three species, retrotransposition is a very recent activity relative to their speciation. While it was known that genes re-insert into non-orthologous positions of plant genomes, they appear to re-insert also within retrotransposons, potentially

  4. Molecular analysis of Boophilus spp. (Acari: Ixodidae) tick strains.

    Science.gov (United States)

    Fuente, J; García-García, J C; González, D M; Izquierdo, G; Ochagavia, M E

    2000-10-01

    Boophilus spp. (Acari: Ixodidae) parasitize cattle and other farm and wild animals in tropical and subtropical regions of the world. Ticks belonging to the genus Boophilus have undergone evolutionary processes associated with habitat adaptation following biogeographical separation, resulting in strains with marked morphological differences. We have characterized at the molecular level B. microplus strains from Latin America and Australia, employing sequences derived from the bm86 coding region, an intron located within the bm86 gene, and DNA short tandem repeats (STR). A B. annulatus strain was employed for comparison. The results indicated that variation within the bm86 coding region is higher between B. microplus strains than between some B. microplus strains and B. annulatus. The sequence of the intron was not informative for phylogenetic analysis, varying among individuals of the same strain. Two STRs were identified in B. microplus (STRs BmM1 and BmM2) and one in B. annulatus (STR Ba1). Southern hybridization experiments with STRs BmM1 and BmM2 as a probe revealed the prevalence of dispersed moderately repeated DNA in the genome of B. microplus. The analysis of polymorphism at STR locus BmM1 evidenced differences within and between populations of B. microplus. These results support at the molecular level the existing differences between B. microplus strains and suggest tools to characterize these populations. PMID:10962158

  5. Characterization of the ovine ortholog of secretory leukoprotease inhibitor.

    Science.gov (United States)

    Brown, Thomas I; Mistry, Rohit; Gray, Robert; Imrie, Margaret; Collie, David D; Sallenave, Jean-Michel

    2005-08-01

    There is great interest in the use of the sheep as a model for the investigation of inflammation in the lung. The serine antiproteases secretory leukoprotease inhibitor (SLPI) and elafin are important "alarm antiproteases" in the lung and have potentially important roles in the innate immune response. SLPI was first characterized in man and subsequently in murine, porcine, and rat tissues. Here we present the first data concerning the gene and cDNA sequence encoding for the ovine ortholog of SLPI, a protein of 132 amino acids with 66% sequence identity at the amino acid level with human SLPI. A 24-amino-acid signal sequence signifies that, like the other mammalian orthologs, ovine SLPI is a secreted protein. Tissue distribution of expression is demonstrated by reverse transcription polymerase chain reaction (RT-PCR) and shows features similar to SLPI expression in other mammals, specifically at mucosal surfaces such as the upper respiratory and intestinal tracts, and also the skin, liver, and kidney. This distribution lends credence to SLPI having important roles in innate immunity. We have also cloned the ovine SLPI cDNA into an expression vector and expressed the ovine SLPI protein in vitro. This has enabled us to demonstrate that ovine SLPI is correctly processed (Western blot analysis and SELDI-TOF mass spectrometry analysis) and has biological antihuman neutrophil elastase activity. In summary, the ovine ortholog of SLPI shows similarities to other members of the SLPI family and has all the features of a modulator of innate immunity. PMID:16180144

  6. DoOP: Databases of Orthologous Promoters, collections of clusters of orthologous upstream sequences from chordates and plants

    OpenAIRE

    Barta, Endre; Sebestyén, Endre; Pálfy, Tamás B.; Tóth, Gábor; Ortutay, Csaba P.; Patthy, László

    2004-01-01

    DoOP (http://doop.abc.hu/) is a database of eukaryotic promoter sequences (upstream regions) aiming to facilitate the recognition of regulatory sites conserved between species. The annotated first exons of human and Arabidopsis thaliana genes were used as queries in BLAST searches to collect the most closely related orthologous first exon sequences from Chordata and Viridiplantae species. Up to 3000 bp DNA segments upstream from these first exons constitute the clusters in the chordate and pl...

  7. Cluster (Cyanobacteria) - PGDBj - Ortholog DB | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available [ Credits ] BLAST Search Image Search Home About Archive Update History Contact us PGD...es among the amino acid sequences. An amino acid sequence belongs to only one cluster in a taxon. Data file File name: pgd...bj_ortholog_db_cyanobacteria_cluster.zip File URL: ftp://ftp.biosciencedbc.jp/archive/pgd...bj-ortholog-db/LATEST/pgdbj_ortholog_db_cyanobacteria_cluster.zip File size: 9.6 MB Si...mple search URL http://togodb.biosciencedbc.jp/togodb/view/pgdbj_ortholog_db_cyanobacteria_cluster#en Data a

  8. Cluster (Viridiplantae) - PGDBj - Ortholog DB | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available [ Credits ] BLAST Search Image Search Home About Archive Update History Contact us PGD...mong the amino acid sequences. An amino acid sequence belongs to only one cluster in a taxon. Data file File name: pgd...bj_ortholog_db_viridiplantae_cluster.zip File URL: ftp://ftp.biosciencedbc.jp/archive/pgd...bj-ortholog-db/LATEST/pgdbj_ortholog_db_viridiplantae_cluster.zip File size: 15.6 MB Simpl...e search URL http://togodb.biosciencedbc.jp/togodb/view/pgdbj_ortholog_db_viridiplantae_cluster#en Data acqu

  9. Taxon (Cyanobacteria) - PGDBj - Ortholog DB | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available [ Credits ] BLAST Search Image Search Home About Archive Update History Contact us PGD...ntents Phylogenetic relationships among the recursively generated clusters in Cluster (Cyanobacteria). Data file File name: pgd...bj_ortholog_db_cyanobacteria_taxon.zip File URL: ftp://ftp.bio...sciencedbc.jp/archive/pgdbj-ortholog-db/LATEST/pgdbj_ortholog_db_cyanobacteria_taxon.zip File size: 4.3 KB S...imple search URL http://togodb.biosciencedbc.jp/togodb/view/pgdbj_ortholog_db_cyanobacteria_taxon#en Data ac

  10. Taxon (Viridiplantae) - PGDBj - Ortholog DB | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available [ Credits ] BLAST Search Image Search Home About Archive Update History Contact us PGD...ntents Phylogenetic relationships among the recursively generated clusters in Cluster (Viridiplantae). Data file File name: pgd...bj_ortholog_db_viridiplantae_taxon.zip File URL: ftp://ftp.bio...sciencedbc.jp/archive/pgdbj-ortholog-db/LATEST/pgdbj_ortholog_db_viridiplantae_taxon.zip File size: 2.3 KB S...imple search URL http://togodb.biosciencedbc.jp/togodb/view/pgdbj_ortholog_db_viridiplantae_taxon#en Data ac

  11. Protein (Cyanobacteria) - PGDBj - Ortholog DB | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available [ Credits ] BLAST Search Image Search Home About Archive Update History Contact us PGD... The IDs of clusters that the amino acid sequences belong to in each taxon are indicated. Data file File name: pgd...bj_ortholog_db_cyanobacteria_protein.zip File URL: ftp://ftp.biosciencedbc.jp/archive/pgdbj-ortholog-db/LATEST/pgd...ch URL http://togodb.biosciencedbc.jp/togodb/view/pgdbj_ortholog_db_cyanobacteria_protein#en Data acquisitio...ase Database Description Download License Update History of This Database Site Policy | Contact Us Protein (Cyanobacteria) - PGDBj - Ortholog DB | LSDB Archive ...

  12. Efficacy of Hyalomma scupense (Hd86) antigen against Hyalomma excavatum and H. scupense tick infestations in cattle.

    Science.gov (United States)

    Galaï, Yousr; Canales, Mario; Ben Saïd, Mourad; Gharbi, Mohamed; Mhadhbi, Moez; Jedidi, Mohamed; de La Fuente, José; Darghouth, Mohamed-Aziz

    2012-11-19

    The Rhipicephalus microplus recombinant Bm86-based tick vaccines have shown their efficacy for the control of several Hyalomma cattle ticks genera, namely H. dromedarii and H. anatolicum. However, H. scupense species, the most important tick in North Africa has never been studied. Vaccination trials using either a recombinant Bm86-based vaccine or a recombinant Hd86-based vaccine (the Bm86 ortholog in H. scupense) were conducted in cattle against immature and adult H. scupense ticks and adult H. excavatum ticks. The results showed a 59.19% reduction in the number of scupense nymphs engorging on Hd86 vaccinated cattle. However, cattle vaccination with Bm86 or Hd86 did not have an effect on H. scupense or H. excavatum adult ticks infestations. These results showed that Hd86 vaccines are selectively effective against H. scupense immature instars and emphasize on an integrated anti-tick vaccine control in North Africa. PMID:23036501

  13. Human and mouse mitochondrial orthologs of bacterial ClpX

    DEFF Research Database (Denmark)

    Corydon, T J; Wilsbech, M; Jespersgaard, C;

    2000-01-01

    We have determined the cDNA sequence and exon/intron structure of the human CLPX gene encoding a human ortholog of the E. coli ClpX chaperone and protease subunit. The CLPX gene comprises 14 exons and encodes a 633-amino acid-long precursor polypeptide. The polypeptide contains an N-terminal puta......We have determined the cDNA sequence and exon/intron structure of the human CLPX gene encoding a human ortholog of the E. coli ClpX chaperone and protease subunit. The CLPX gene comprises 14 exons and encodes a 633-amino acid-long precursor polypeptide. The polypeptide contains an N......-terminal putative mitochondrial transit peptide, and expression of a full-length ClpX cDNA tagged at its C-terminus (Myc-His) shows that the polypeptide is transported into mitochondria. FISH analysis localized the CLPX gene to human Chromosome (Chr) 15q22.1-22.32. This localization was refined by radiation hybrid...... variability between mouse ClpX cDNAs from different strains. Alignment of the human and mouse ClpX amino acid sequences with ClpX sequences from other organisms shows that they display the typical modular organization of domains with one AAA(+) domain common to a large group of ATPases and several other...

  14. An integrative approach to ortholog prediction for disease-focused and other functional studies

    Directory of Open Access Journals (Sweden)

    Perrimon Norbert

    2011-08-01

    Full Text Available Abstract Background Mapping of orthologous genes among species serves an important role in functional genomics by allowing researchers to develop hypotheses about gene function in one species based on what is known about the functions of orthologs in other species. Several tools for predicting orthologous gene relationships are available. However, these tools can give different results and identification of predicted orthologs is not always straightforward. Results We report a simple but effective tool, the Drosophila RNAi Screening Center Integrative Ortholog Prediction Tool (DIOPT; http://www.flyrnai.org/diopt, for rapid identification of orthologs. DIOPT integrates existing approaches, facilitating rapid identification of orthologs among human, mouse, zebrafish, C. elegans, Drosophila, and S. cerevisiae. As compared to individual tools, DIOPT shows increased sensitivity with only a modest decrease in specificity. Moreover, the flexibility built into the DIOPT graphical user interface allows researchers with different goals to appropriately 'cast a wide net' or limit results to highest confidence predictions. DIOPT also displays protein and domain alignments, including percent amino acid identity, for predicted ortholog pairs. This helps users identify the most appropriate matches among multiple possible orthologs. To facilitate using model organisms for functional analysis of human disease-associated genes, we used DIOPT to predict high-confidence orthologs of disease genes in Online Mendelian Inheritance in Man (OMIM and genes in genome-wide association study (GWAS data sets. The results are accessible through the DIOPT diseases and traits query tool (DIOPT-DIST; http://www.flyrnai.org/diopt-dist. Conclusions DIOPT and DIOPT-DIST are useful resources for researchers working with model organisms, especially those who are interested in exploiting model organisms such as Drosophila to study the functions of human disease genes.

  15. Split-alignment of genomes finds orthologies more accurately.

    Science.gov (United States)

    Frith, Martin C; Kawaguchi, Risa

    2015-01-01

    We present a new pair-wise genome alignment method, based on a simple concept of finding an optimal set of local alignments. It gains accuracy by not masking repeats, and by using a statistical model to quantify the (un)ambiguity of each alignment part. Compared to previous animal genome alignments, it aligns thousands of locations differently and with much higher similarity, strongly suggesting that the previous alignments are non-orthologous. The previous methods suffer from an overly-strong assumption of long un-rearranged blocks. The new alignments should help find interesting and unusual features, such as fast-evolving elements and micro-rearrangements, which are confounded by alignment errors. PMID:25994148

  16. Functional characterization in Caenorhabditis elegans of transmembrane worm-human orthologs

    Directory of Open Access Journals (Sweden)

    Baillie David L

    2004-11-01

    Full Text Available Abstract Background The complete genome sequences for human and the nematode Caenorhabditis elegans offer an opportunity to learn more about human gene function through functional characterization of orthologs in the worm. Based on a previous genome-wide analysis of worm-human orthologous transmembrane proteins, we selected seventeen genes to explore experimentally in C. elegans. These genes were selected on the basis that they all have high confidence candidate human orthologs and that their function is unknown. We first analyzed their phylogeny, membrane topology and domain organization. Then gene functions were studied experimentally in the worm by using RNA interference and transcriptional gfp reporter gene fusions. Results The experiments gave functional insights for twelve of the genes studied. For example, C36B1.12, the worm ortholog of three presenilin-like genes, was almost exclusively expressed in head neurons, suggesting an ancient conserved role important to neuronal function. We propose a new transmembrane topology for the presenilin-like protein family. sft-4, the worm ortholog of surfeit locus gene Surf-4, proved to be an essential gene required for development during the larval stages of the worm. R155.1, whose human ortholog is entirely uncharacterized, was implicated in body size control and other developmental processes. Conclusions By combining bioinformatics and C. elegans experiments on orthologs, we provide functional insights on twelve previously uncharacterized human genes.

  17. Construction of an ortholog database using the semantic web technology for integrative analysis of genomic data.

    Science.gov (United States)

    Chiba, Hirokazu; Nishide, Hiroyo; Uchiyama, Ikuo

    2015-01-01

    Recently, various types of biological data, including genomic sequences, have been rapidly accumulating. To discover biological knowledge from such growing heterogeneous data, a flexible framework for data integration is necessary. Ortholog information is a central resource for interlinking corresponding genes among different organisms, and the Semantic Web provides a key technology for the flexible integration of heterogeneous data. We have constructed an ortholog database using the Semantic Web technology, aiming at the integration of numerous genomic data and various types of biological information. To formalize the structure of the ortholog information in the Semantic Web, we have constructed the Ortholog Ontology (OrthO). While the OrthO is a compact ontology for general use, it is designed to be extended to the description of database-specific concepts. On the basis of OrthO, we described the ortholog information from our Microbial Genome Database for Comparative Analysis (MBGD) in the form of Resource Description Framework (RDF) and made it available through the SPARQL endpoint, which accepts arbitrary queries specified by users. In this framework based on the OrthO, the biological data of different organisms can be integrated using the ortholog information as a hub. Besides, the ortholog information from different data sources can be compared with each other using the OrthO as a shared ontology. Here we show some examples demonstrating that the ortholog information described in RDF can be used to link various biological data such as taxonomy information and Gene Ontology. Thus, the ortholog database using the Semantic Web technology can contribute to biological knowledge discovery through integrative data analysis.

  18. Construction of an ortholog database using the semantic web technology for integrative analysis of genomic data.

    Directory of Open Access Journals (Sweden)

    Hirokazu Chiba

    Full Text Available Recently, various types of biological data, including genomic sequences, have been rapidly accumulating. To discover biological knowledge from such growing heterogeneous data, a flexible framework for data integration is necessary. Ortholog information is a central resource for interlinking corresponding genes among different organisms, and the Semantic Web provides a key technology for the flexible integration of heterogeneous data. We have constructed an ortholog database using the Semantic Web technology, aiming at the integration of numerous genomic data and various types of biological information. To formalize the structure of the ortholog information in the Semantic Web, we have constructed the Ortholog Ontology (OrthO. While the OrthO is a compact ontology for general use, it is designed to be extended to the description of database-specific concepts. On the basis of OrthO, we described the ortholog information from our Microbial Genome Database for Comparative Analysis (MBGD in the form of Resource Description Framework (RDF and made it available through the SPARQL endpoint, which accepts arbitrary queries specified by users. In this framework based on the OrthO, the biological data of different organisms can be integrated using the ortholog information as a hub. Besides, the ortholog information from different data sources can be compared with each other using the OrthO as a shared ontology. Here we show some examples demonstrating that the ortholog information described in RDF can be used to link various biological data such as taxonomy information and Gene Ontology. Thus, the ortholog database using the Semantic Web technology can contribute to biological knowledge discovery through integrative data analysis.

  19. Construction of an ortholog database using the semantic web technology for integrative analysis of genomic data.

    Science.gov (United States)

    Chiba, Hirokazu; Nishide, Hiroyo; Uchiyama, Ikuo

    2015-01-01

    Recently, various types of biological data, including genomic sequences, have been rapidly accumulating. To discover biological knowledge from such growing heterogeneous data, a flexible framework for data integration is necessary. Ortholog information is a central resource for interlinking corresponding genes among different organisms, and the Semantic Web provides a key technology for the flexible integration of heterogeneous data. We have constructed an ortholog database using the Semantic Web technology, aiming at the integration of numerous genomic data and various types of biological information. To formalize the structure of the ortholog information in the Semantic Web, we have constructed the Ortholog Ontology (OrthO). While the OrthO is a compact ontology for general use, it is designed to be extended to the description of database-specific concepts. On the basis of OrthO, we described the ortholog information from our Microbial Genome Database for Comparative Analysis (MBGD) in the form of Resource Description Framework (RDF) and made it available through the SPARQL endpoint, which accepts arbitrary queries specified by users. In this framework based on the OrthO, the biological data of different organisms can be integrated using the ortholog information as a hub. Besides, the ortholog information from different data sources can be compared with each other using the OrthO as a shared ontology. Here we show some examples demonstrating that the ortholog information described in RDF can be used to link various biological data such as taxonomy information and Gene Ontology. Thus, the ortholog database using the Semantic Web technology can contribute to biological knowledge discovery through integrative data analysis. PMID:25875762

  20. Download - PGDBj - Ortholog DB | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available [ Credits ] BLAST Search Image Search Home About Archive Update History Contact us PGD... name File Simple search and download 1 README README_e.html - 2 Protein (Viridiplantae) pgdbj_ortholog_db_v...iridiplantae_protein.zip (85 MB) Simple search and download 3 Cluster (Viridiplantae) pgdbj_ortholog_db_viri...diplantae_cluster.zip (15.6 MB) Simple search and download 4 Taxon (Viridiplantae) pgd...bj_ortholog_db_viridiplantae_taxon.zip (2.3 KB) Simple search and download 5 Protein (Cyanobacteria) pgd

  1. Database Description - PGDBj - Ortholog DB | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available [ Credits ] BLAST Search Image Search Home About Archive Update History Contact us PGD...Bj - Ortholog DB Database Description General information of database Database name PGDBj - Ortholog DB A...ivergence of gene function based on syntenic relationships among species. PGDBj Ortholog DB is a database th...plantae (green plants) and 111 species of Cyanobacteria (blue-green algae). Features and manner of utilization of database PGD...cies and taxa. By connecting entries of multiple plant genome databases to this database, PGD

  2. Protein (Viridiplantae) - PGDBj - Ortholog DB | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available [ Credits ] BLAST Search Image Search Home About Archive Update History Contact us PGD... IDs of clusters that the amino acid sequences belong to in each taxon are indicated. Data file File name: pgd...bj_ortholog_db_viridiplantae_protein.zip File URL: ftp://ftp.biosciencedbc.jp/archive/pgdbj-ortholog-db/LATEST/pgd...RL http://togodb.biosciencedbc.jp/togodb/view/pgdbj_ortholog_db_viridiplantae_protein#en Data acquisition me...BI GI number of Amino Acid sequence RefSeq ID NCBI Reference Sequence ID Cluster (Kingdom) Cluster ID (rank: Kingd

  3. Amphioxus (Branchiostoma floridae has orthologs of vertebrate odorant receptors

    Directory of Open Access Journals (Sweden)

    Taylor John S

    2009-10-01

    Full Text Available Abstract Background A common feature of chemosensory systems is the involvement of G protein-coupled receptors (GPCRs in the detection of environmental stimuli. Several lineages of GPCRs are involved in vertebrate olfaction, including trace amine-associated receptors, type 1 and 2 vomeronasal receptors and odorant receptors (ORs. Gene duplication and gene loss in different vertebrate lineages have lead to an enormous amount of variation in OR gene repertoire among species; some fish have fewer than 100 OR genes, while some mammals possess more than 1000. Fascinating features of the vertebrate olfactory system include allelic exclusion, where each olfactory neuron expresses only a single OR gene, and axonal guidance where neurons expressing the same receptor project axons to common glomerulae. By identifying homologous ORs in vertebrate and in non-vertebrate chordates, we hope to expose ancestral features of the chordate olfactory system that will help us to better understand the evolution of the receptors themselves and of the cellular components of the olfactory system. Results We have identified 50 full-length and 11 partial ORs in Branchiostoma floridae. No ORs were identified in Ciona intestinalis. Phylogenetic analysis places the B. floridae OR genes in a monophyletic clade with the vertebrate ORs. The majority of OR genes in amphioxus are intronless and many are also tandemly arrayed in the genome. By exposing conserved amino acid motifs and testing the ability of those motifs to discriminate between ORs and non-OR GPCRs, we identified three OR-specific amino acid motifs common in cephalochordate, fish and mammalian and ORs. Conclusion Here, we show that amphioxus has orthologs of vertebrate ORs. This conclusion demonstrates that the receptors, and perhaps other components of vertebrate olfaction, evolved at least 550 million years ago. We have also identified highly conserved amino acid motifs that may be important for maintaining

  4. Selection of reference genes for quantitative RT-PCR studies in Rhipicephalus (Boophilus) microplus and Rhipicephalus appendiculatus ticks and determination of the expression profile of Bm86

    OpenAIRE

    Jongejan Frans; Postigo Milagros; Balk Jesper A; Nijhof Ard M

    2009-01-01

    Abstract Background For accurate and reliable gene expression analysis, normalization of gene expression data against reference genes is essential. In most studies on ticks where (semi-)quantitative RT-PCR is employed, normalization occurs with a single reference gene, usually β-actin, without validation of its presumed expression stability. The first goal of this study was to evaluate the expression stability of commonly used reference genes in Rhipicephalus appendiculatus and Rhipicephalus ...

  5. Comment on "Tequila, a neurotrypsin ortholog, regulates long-term memory formation in Drosophila".

    Science.gov (United States)

    Sonderegger, Peter; Patthy, Laszlo

    2007-06-22

    Didelot et al. (Reports, 11 August 2006, p. 851) claimed that Drosophila Tequila (Teq) and human neurotrypsin are orthologs and concluded that deficient long-term memory after Teq inactivation indicates that neurotrypsin plays its essential role for human cognitive functions through a similar mechanism. Our analyses suggest that Teq and neurotrypsin are not orthologous, leading us to question their equivalent roles in higher brain function.

  6. Parallel Construction of Orthologous Sequence-Ready Clone Contig Maps in Multiple Species

    OpenAIRE

    Thomas, James W; Prasad, Arjun B.; Summers, Tyrone J.; Lee-Lin, Shih-Queen; Maduro, Valerie V.B.; Idol, Jacquelyn R.; Ryan, Joseph F.; Pamela J Thomas; McDowell, Jennifer C.; Green, Eric D.

    2002-01-01

    Comparison is a fundamental tool for analyzing DNA sequence. Interspecies sequence comparison is particularly powerful for inferring genome function and is based on the simple premise that conserved sequences are likely to be important. Thus, the comparison of a genomic sequence with its orthologous counterpart from another species is increasingly becoming an integral component of genome analysis. In ideal situations, such comparisons are performed with orthologous sequences from multiple spe...

  7. The Princeton Protein Orthology Database (P-POD): A Comparative Genomics Analysis Tool for Biologists

    OpenAIRE

    Sven Heinicke; Livstone, Michael S.; Charles Lu; Rose Oughtred; Fan Kang; Angiuoli, Samuel V; Owen White; David Botstein; Kara Dolinski

    2007-01-01

    Many biological databases that provide comparative genomics information and tools are now available on the internet. While certainly quite useful, to our knowledge none of the existing databases combine results from multiple comparative genomics methods with manually curated information from the literature. Here we describe the Princeton Protein Orthology Database (P-POD, http://ortholog.princeton.edu), a user-friendly database system that allows users to find and visualize the phylogenetic r...

  8. Construction of an Ortholog Database Using the Semantic Web Technology for Integrative Analysis of Genomic Data

    OpenAIRE

    Hirokazu Chiba; Hiroyo Nishide; Ikuo Uchiyama

    2015-01-01

    Recently, various types of biological data, including genomic sequences, have been rapidly accumulating. To discover biological knowledge from such growing heterogeneous data, a flexible framework for data integration is necessary. Ortholog information is a central resource for interlinking corresponding genes among different organisms, and the Semantic Web provides a key technology for the flexible integration of heterogeneous data. We have constructed an ortholog database using the Semantic...

  9. Orthologous transcription factors in bacteria have different functions and regulate different genes.

    Directory of Open Access Journals (Sweden)

    Morgan N Price

    2007-09-01

    Full Text Available Transcription factors (TFs form large paralogous gene families and have complex evolutionary histories. Here, we ask whether putative orthologs of TFs, from bidirectional best BLAST hits (BBHs, are evolutionary orthologs with conserved functions. We show that BBHs of TFs from distantly related bacteria are usually not evolutionary orthologs. Furthermore, the false orthologs usually respond to different signals and regulate distinct pathways, while the few BBHs that are evolutionary orthologs do have conserved functions. To test the conservation of regulatory interactions, we analyze expression patterns. We find that regulatory relationships between TFs and their regulated genes are usually not conserved for BBHs in Escherichia coli K12 and Bacillus subtilis. Even in the much more closely related bacteria Vibrio cholerae and Shewanella oneidensis MR-1, predicting regulation from E. coli BBHs has high error rates. Using gene-regulon correlations, we identify genes whose expression pattern differs between E. coli and S. oneidensis. Using literature searches and sequence analysis, we show that these changes in expression patterns reflect changes in gene regulation, even for evolutionary orthologs. We conclude that the evolution of bacterial regulation should be analyzed with phylogenetic trees, rather than BBHs, and that bacterial regulatory networks evolve more rapidly than previously thought.

  10. The plant Apolipoprotein D ortholog protects Arabidopsis against oxidative stress

    Directory of Open Access Journals (Sweden)

    Houde Mario

    2008-07-01

    Full Text Available Abstract Background Lipocalins are a large and diverse family of small, mostly extracellular proteins implicated in many important functions. This family has been studied in bacteria, invertebrate and vertebrate animals but little is known about these proteins in plants. We recently reported the identification and molecular characterization of the first true lipocalins from plants, including the Apolipoprotein D ortholog AtTIL identified in the plant model Arabidopsis thaliana. This study aimed to determine its physiological role in planta. Results Our results demonstrate that the AtTIL lipocalin is involved in modulating tolerance to oxidative stress. AtTIL knock-out plants are very sensitive to sudden drops in temperature and paraquat treatment, and dark-grown plants die shortly after transfer to light. These plants accumulate a high level of hydrogen peroxide and other ROS, which causes an oxidative stress that is associated with a reduction in hypocotyl growth and sensitivity to light. Complementation of the knock-out plants with the AtTIL cDNA restores the normal phenotype. On the other hand, overexpression enhances tolerance to stress caused by freezing, paraquat and light. Moreover, this overexpression delays flowering and maintains leaf greenness. Microarray analyses identified several differentially-regulated genes encoding components of oxidative stress and energy balance. Conclusion This study provides the first functional evidence that a plant lipocalin is involved in modulating tolerance to oxidative stress. These findings are in agreement with recently published data showing that overexpression of ApoD enhances tolerance to oxidative stress and increases life span in mice and Drosophila. Together, the three papers strongly support a similar function of lipocalins in these evolutionary-distant species.

  11. MSOAR 2.0: Incorporating tandem duplications into ortholog assignment based on genome rearrangement

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    Zhang Liqing

    2010-01-01

    Full Text Available Abstract Background Ortholog assignment is a critical and fundamental problem in comparative genomics, since orthologs are considered to be functional counterparts in different species and can be used to infer molecular functions of one species from those of other species. MSOAR is a recently developed high-throughput system for assigning one-to-one orthologs between closely related species on a genome scale. It attempts to reconstruct the evolutionary history of input genomes in terms of genome rearrangement and gene duplication events. It assumes that a gene duplication event inserts a duplicated gene into the genome of interest at a random location (i.e., the random duplication model. However, in practice, biologists believe that genes are often duplicated by tandem duplications, where a duplicated gene is located next to the original copy (i.e., the tandem duplication model. Results In this paper, we develop MSOAR 2.0, an improved system for one-to-one ortholog assignment. For a pair of input genomes, the system first focuses on the tandemly duplicated genes of each genome and tries to identify among them those that were duplicated after the speciation (i.e., the so-called inparalogs, using a simple phylogenetic tree reconciliation method. For each such set of tandemly duplicated inparalogs, all but one gene will be deleted from the concerned genome (because they cannot possibly appear in any one-to-one ortholog pairs, and MSOAR is invoked. Using both simulated and real data experiments, we show that MSOAR 2.0 is able to achieve a better sensitivity and specificity than MSOAR. In comparison with the well-known genome-scale ortholog assignment tool InParanoid, Ensembl ortholog database, and the orthology information extracted from the well-known whole-genome multiple alignment program MultiZ, MSOAR 2.0 shows the highest sensitivity. Although the specificity of MSOAR 2.0 is slightly worse than that of InParanoid in the real data experiments

  12. An Effective Big Data Supervised Imbalanced Classification Approach for Ortholog Detection in Related Yeast Species

    Directory of Open Access Journals (Sweden)

    Deborah Galpert

    2015-01-01

    Full Text Available Orthology detection requires more effective scaling algorithms. In this paper, a set of gene pair features based on similarity measures (alignment scores, sequence length, gene membership to conserved regions, and physicochemical profiles are combined in a supervised pairwise ortholog detection approach to improve effectiveness considering low ortholog ratios in relation to the possible pairwise comparison between two genomes. In this scenario, big data supervised classifiers managing imbalance between ortholog and nonortholog pair classes allow for an effective scaling solution built from two genomes and extended to other genome pairs. The supervised approach was compared with RBH, RSD, and OMA algorithms by using the following yeast genome pairs: Saccharomyces cerevisiae-Kluyveromyces lactis, Saccharomyces cerevisiae-Candida glabrata, and Saccharomyces cerevisiae-Schizosaccharomyces pombe as benchmark datasets. Because of the large amount of imbalanced data, the building and testing of the supervised model were only possible by using big data supervised classifiers managing imbalance. Evaluation metrics taking low ortholog ratios into account were applied. From the effectiveness perspective, MapReduce Random Oversampling combined with Spark SVM outperformed RBH, RSD, and OMA, probably because of the consideration of gene pair features beyond alignment similarities combined with the advances in big data supervised classification.

  13. Patterns of nucleotides that flank substitutions in human orthologous genes

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    Huang Zhuoran

    2010-07-01

    Full Text Available Abstract Background Sequence context is an important aspect of base mutagenesis, and three-base periodicity is an intrinsic property of coding sequences. However, how three-base periodicity is influenced in the vicinity of substitutions is still unclear. The effect of context on mutagenesis should be revealed in the usage of nucleotides that flank substitutions. Relative entropy (also known as Kullback-Leibler divergence is useful for finding unusual patterns in biological sequences. Results Using relative entropy, we visualized the periodic patterns in the context of substitutions in human orthologous genes. Neighbouring patterns differed both among substitution categories and within a category that occurred at three codon positions. Transition tended to occur in periodic sequences relative to transversion. Periodic signals were stronger in a set of flanking sequences of substitutions that occurred at the third-codon positions than in those that occurred at the first- or second-codon positions. To determine how the three-base periodicity was affected near the substitution sites, we fitted a sine model to the values of the relative entropy. A sine of period equal to 3 is a good approximation for the three-base periodicity at sites not in close vicinity to some substitutions. These periods were interrupted near the substitution site and then reappeared away from substitutions. A comparative analysis between the native and codon-shuffled datasets suggested that the codon usage frequency was not the sole origin of the three-base periodicity, implying that the native order of codons also played an important role in this periodicity. Synonymous codon shuffling revealed that synonymous codon usage bias was one of the factors responsible for the observed three-base periodicity. Conclusions Our results offer an efficient way to illustrate unusual periodic patterns in the context of substitutions and provide further insight into the origin of three

  14. Identification and characterization of Rhipicephalus (Boophilus) microplus candidate protective antigens for the control of cattle tick infestations.

    Science.gov (United States)

    Almazán, Consuelo; Lagunes, Rodolfo; Villar, Margarita; Canales, Mario; Rosario-Cruz, Rodrigo; Jongejan, Frans; de la Fuente, José

    2010-01-01

    The cattle ticks, Rhipicephalus (Boophilus) spp., affect cattle production in tropical and subtropical regions of the world. Tick vaccines constitute a cost-effective and environmentally friendly alternative to tick control. The recombinant Rhipicephalus microplus Bm86 antigen has been shown to protect cattle against tick infestations. However, variable efficacy of Bm86-based vaccines against geographic tick strains has encouraged the research for additional tick-protective antigens. Herein, we describe the analysis of R. microplus glutathione-S transferase, ubiquitin (UBQ), selenoprotein W, elongation factor-1 alpha, and subolesin (SUB) complementary DNAs (cDNAs) by RNA interference (RNAi) in R. microplus and Rhipicephalus annulatus. Candidate protective antigens were selected for vaccination experiments based on the effect of gene knockdown on tick mortality, feeding, and fertility. Two cDNA clones encoding for UBQ and SUB were used for cattle vaccination and infestation with R. microplus and R. annulatus. Control groups were immunized with recombinant Bm86 or adjuvant/saline. The highest vaccine efficacy for the control of tick infestations was obtained for Bm86. Although with low immunogenic response, the results with the SUB vaccine encourage further investigations on the use of recombinant subolesin alone or in combination with other antigens for the control of cattle tick infestations. The UBQ peptide showed low immunogenicity, and the results of the vaccination trial were inconclusive to assess the protective efficacy of this antigen. These experiments showed that RNAi could be used for the selection of candidate tick-protective antigens. However, vaccination trials are necessary to evaluate the effect of recombinant antigens in the control of tick infestations, a process that requires efficient recombinant protein production and formulation systems. PMID:19943063

  15. Expression Pattern Similarities Support the Prediction of Orthologs Retaining Common Functions after Gene Duplication Events1[OPEN

    Science.gov (United States)

    Haberer, Georg; Panda, Arup; Das Laha, Shayani; Ghosh, Tapas Chandra; Schäffner, Anton R.

    2016-01-01

    The identification of functionally equivalent, orthologous genes (functional orthologs) across genomes is necessary for accurate transfer of experimental knowledge from well-characterized organisms to others. This frequently relies on automated, coding sequence-based approaches such as OrthoMCL, Inparanoid, and KOG, which usually work well for one-to-one homologous states. However, this strategy does not reliably work for plants due to the occurrence of extensive gene/genome duplication. Frequently, for one query gene, multiple orthologous genes are predicted in the other genome, and it is not clear a priori from sequence comparison and similarity which one preserves the ancestral function. We have studied 11 organ-dependent and stress-induced gene expression patterns of 286 Arabidopsis lyrata duplicated gene groups and compared them with the respective Arabidopsis (Arabidopsis thaliana) genes to predict putative expressologs and nonexpressologs based on gene expression similarity. Promoter sequence divergence as an additional tool to substantiate functional orthology only partially overlapped with expressolog classification. By cloning eight A. lyrata homologs and complementing them in the respective four Arabidopsis loss-of-function mutants, we experimentally proved that predicted expressologs are indeed functional orthologs, while nonexpressologs or nonfunctionalized orthologs are not. Our study demonstrates that even a small set of gene expression data in addition to sequence homologies are instrumental in the assignment of functional orthologs in the presence of multiple orthologs. PMID:27303025

  16. OrthoVenn: a web server for genome wide comparison and annotation of orthologous clusters across multiple species

    Science.gov (United States)

    Genome wide analysis of orthologous clusters is an important component of comparative genomics studies. Identifying the overlap among orthologous clusters can enable us to elucidate the function and evolution of proteins across multiple species. Here, we report a web platform named OrthoVenn that i...

  17. RIO: Analyzing proteomes by automated phylogenomics using resampled inference of orthologs

    Directory of Open Access Journals (Sweden)

    Eddy Sean R

    2002-05-01

    Full Text Available Abstract Background When analyzing protein sequences using sequence similarity searches, orthologous sequences (that diverged by speciation are more reliable predictors of a new protein's function than paralogous sequences (that diverged by gene duplication. The utility of phylogenetic information in high-throughput genome annotation ("phylogenomics" is widely recognized, but existing approaches are either manual or not explicitly based on phylogenetic trees. Results Here we present RIO (Resampled Inference of Orthologs, a procedure for automated phylogenomics using explicit phylogenetic inference. RIO analyses are performed over bootstrap resampled phylogenetic trees to estimate the reliability of orthology assignments. We also introduce supplementary concepts that are helpful for functional inference. RIO has been implemented as Perl pipeline connecting several C and Java programs. It is available at http://www.genetics.wustl.edu/eddy/forester/. A web server is at http://www.rio.wustl.edu/. RIO was tested on the Arabidopsis thaliana and Caenorhabditis elegans proteomes. Conclusion The RIO procedure is particularly useful for the automated detection of first representatives of novel protein subfamilies. We also describe how some orthologies can be misleading for functional inference.

  18. Systematic Comparisons of Orthologous Selenocysteine Methyltransferase and Homocysteine Methyltransferase Genes from Seven Monocots Species

    Directory of Open Access Journals (Sweden)

    De-yong ZHAO

    2015-06-01

    Full Text Available Identifying and manipulating genes underlying selenium metabolism could be helpful for increasing selenium content in crop grain, which is an important way to overcome diseases resulted from selenium deficiency. A reciprocal smallest distance algorithm (RSD approach was applied using two experimentally confirmed Homocysteine S-Methyltransferases genes (HMT1 and HMT2 and a putative Selenocysteine Methyltransferase (SMT from dicots plant Arabidopsis thaliana, to explore their orthologs in seven sequenced diploid monocot species: Oryza sativa, Zea mays, Sorghum bicolor, Brachypodium distachyon, Hordeum vulgare, Aegilops tauschii (the D-genome donor of common wheat and Triticum urartu (the A-genome donor of common wheat. HMT1 was apparently diverged from HMT2 and most of SMT orthologs were the same with that of HMT2 in this study, leading to the hypothesis that SMT and HMT originate from one common ancestor gene. Identifying orthologs provide candidates for further experimental confirmation; also it could be helpful in designing primers to clone SMT or HMT orthologs in other crops.

  19. Assessing the evolutionary rate of positional orthologous genes in prokaryotes using synteny data

    Directory of Open Access Journals (Sweden)

    Lespinet Olivier

    2007-11-01

    Full Text Available Abstract Background Comparison of completely sequenced microbial genomes has revealed how fluid these genomes are. Detecting synteny blocks requires reliable methods to determining the orthologs among the whole set of homologs detected by exhaustive comparisons between each pair of completely sequenced genomes. This is a complex and difficult problem in the field of comparative genomics but will help to better understand the way prokaryotic genomes are evolving. Results We have developed a suite of programs that automate three essential steps to study conservation of gene order, and validated them with a set of 107 bacteria and archaea that cover the majority of the prokaryotic taxonomic space. We identified the whole set of shared homologs between two or more species and computed the evolutionary distance separating each pair of homologs. We applied two strategies to extract from the set of homologs a collection of valid orthologs shared by at least two genomes. The first computes the Reciprocal Smallest Distance (RSD using the PAM distances separating pairs of homologs. The second method groups homologs in families and reconstructs each family's evolutionary tree, distinguishing bona fide orthologs as well as paralogs created after the last speciation event. Although the phylogenetic tree method often succeeds where RSD fails, the reverse could occasionally be true. Accordingly, we used the data obtained with either methods or their intersection to number the orthologs that are adjacent in for each pair of genomes, the Positional Orthologous Genes (POGs, and to further study their properties. Once all these synteny blocks have been detected, we showed that POGs are subject to more evolutionary constraints than orthologs outside synteny groups, whichever the taxonomic distance separating the compared organisms. Conclusion The suite of programs described in this paper allows a reliable detection of orthologs and is useful for evaluating gene

  20. Multicopper oxidase-1 orthologs from diverse insect species have ascorbate oxidase activity.

    Science.gov (United States)

    Peng, Zeyu; Dittmer, Neal T; Lang, Minglin; Brummett, Lisa M; Braun, Caroline L; Davis, Lawrence C; Kanost, Michael R; Gorman, Maureen J

    2015-04-01

    Members of the multicopper oxidase (MCO) family of enzymes can be classified by their substrate specificity; for example, ferroxidases oxidize ferrous iron, ascorbate oxidases oxidize ascorbate, and laccases oxidize aromatic substrates such as diphenols. Our previous work on an insect multicopper oxidase, MCO1, suggested that it may function as a ferroxidase. This hypothesis was based on three lines of evidence: RNAi-mediated knock down of Drosophila melanogaster MCO1 (DmMCO1) affects iron homeostasis, DmMCO1 has ferroxidase activity, and DmMCO1 has predicted iron binding residues. In our current study, we expanded our focus to include MCO1 from Anopheles gambiae, Tribolium castaneum, and Manduca sexta. We verified that MCO1 orthologs have similar expression profiles, and that the MCO1 protein is located on the basal surface of cells where it is positioned to oxidize substrates in the hemolymph. In addition, we determined that RNAi-mediated knock down of MCO1 in A. gambiae affects iron homeostasis. To further characterize the enzymatic activity of MCO1 orthologs, we purified recombinant MCO1 from all four insect species and performed kinetic analyses using ferrous iron, ascorbate and two diphenols as substrates. We found that all of the MCO1 orthologs are much better at oxidizing ascorbate than they are at oxidizing ferrous iron or diphenols. This result is surprising because ascorbate oxidases are thought to be specific to plants and fungi. An analysis of three predicted iron binding residues in DmMCO1 revealed that they are not required for ferroxidase or laccase activity, but two of the residues (His374 and Asp380) influence oxidation of ascorbate. These two residues are conserved in MCO1 orthologs from insects and crustaceans; therefore, they are likely to be important for MCO1 function. The results of this study suggest that MCO1 orthologs function as ascorbate oxidases and influence iron homeostasis through an unknown mechanism. PMID:25701385

  1. Orthology inference in nonmodel organisms using transcriptomes and low-coverage genomes: improving accuracy and matrix occupancy for phylogenomics.

    Science.gov (United States)

    Yang, Ya; Smith, Stephen A

    2014-11-01

    Orthology inference is central to phylogenomic analyses. Phylogenomic data sets commonly include transcriptomes and low-coverage genomes that are incomplete and contain errors and isoforms. These properties can severely violate the underlying assumptions of orthology inference with existing heuristics. We present a procedure that uses phylogenies for both homology and orthology assignment. The procedure first uses similarity scores to infer putative homologs that are then aligned, constructed into phylogenies, and pruned of spurious branches caused by deep paralogs, misassembly, frameshifts, or recombination. These final homologs are then used to identify orthologs. We explore four alternative tree-based orthology inference approaches, of which two are new. These accommodate gene and genome duplications as well as gene tree discordance. We demonstrate these methods in three published data sets including the grape family, Hymenoptera, and millipedes with divergence times ranging from approximately 100 to over 400 Ma. The procedure significantly increased the completeness and accuracy of the inferred homologs and orthologs. We also found that data sets that are more recently diverged and/or include more high-coverage genomes had more complete sets of orthologs. To explicitly evaluate sources of conflicting phylogenetic signals, we applied serial jackknife analyses of gene regions keeping each locus intact. The methods described here can scale to over 100 taxa. They have been implemented in python with independent scripts for each step, making it easy to modify or incorporate them into existing pipelines. All scripts are available from https://bitbucket.org/yangya/phylogenomic_dataset_construction. PMID:25158799

  2. MBGD update 2015: microbial genome database for flexible ortholog analysis utilizing a diverse set of genomic data.

    Science.gov (United States)

    Uchiyama, Ikuo; Mihara, Motohiro; Nishide, Hiroyo; Chiba, Hirokazu

    2015-01-01

    The microbial genome database for comparative analysis (MBGD) (available at http://mbgd.genome.ad.jp/) is a comprehensive ortholog database for flexible comparative analysis of microbial genomes, where the users are allowed to create an ortholog table among any specified set of organisms. Because of the rapid increase in microbial genome data owing to the next-generation sequencing technology, it becomes increasingly challenging to maintain high-quality orthology relationships while allowing the users to incorporate the latest genomic data available into an analysis. Because many of the recently accumulating genomic data are draft genome sequences for which some complete genome sequences of the same or closely related species are available, MBGD now stores draft genome data and allows the users to incorporate them into a user-specific ortholog database using the MyMBGD functionality. In this function, draft genome data are incorporated into an existing ortholog table created only from the complete genome data in an incremental manner to prevent low-quality draft data from affecting clustering results. In addition, to provide high-quality orthology relationships, the standard ortholog table containing all the representative genomes, which is first created by the rapid classification program DomClust, is now refined using DomRefine, a recently developed program for improving domain-level clustering using multiple sequence alignment information. PMID:25398900

  3. 9 CFR 72.1 - Ticks [Boophilus annulatus (Margaropus annulatus), Boophilus microplus, or Rhipicephalus evertsi...

    Science.gov (United States)

    2010-01-01

    ... POULTRY) AND ANIMAL PRODUCTS TEXAS (SPLENETIC) FEVER IN CATTLE § 72.1 Ticks ; interstate movement of... 9 Animals and Animal Products 1 2010-01-01 2010-01-01 false Ticks ; interstate movement of infested or exposed animals prohibited. 72.1 Section 72.1 Animals and Animal Products ANIMAL AND...

  4. Conserved repertoire of orthologous vomeronasal type 1 receptor genes in ruminant species

    Directory of Open Access Journals (Sweden)

    Okamura Hiroaki

    2009-09-01

    Full Text Available Abstract Background In mammals, pheromones play an important role in social and innate reproductive behavior within species. In rodents, vomeronasal receptor type 1 (V1R, which is specifically expressed in the vomeronasal organ, is thought to detect pheromones. The V1R gene repertoire differs dramatically between mammalian species, and the presence of species-specific V1R subfamilies in mouse and rat suggests that V1R plays a profound role in species-specific recognition of pheromones. In ruminants, however, the molecular mechanism(s for pheromone perception is not well understood. Interestingly, goat male pheromone, which can induce out-of-season ovulation in anestrous females, causes the same pheromone response in sheep, and vice versa, suggesting that there may be mechanisms for detecting "inter-species" pheromones among ruminant species. Results We isolated 23 goat and 21 sheep intact V1R genes based on sequence similarity with 32 cow V1R genes in the cow genome database. We found that all of the goat and sheep V1R genes have orthologs in their cross-species counterparts among these three ruminant species and that the sequence identity of V1R orthologous pairs among these ruminants is much higher than that of mouse-rat V1R orthologous pairs. Furthermore, all goat V1Rs examined thus far are expressed not only in the vomeronasal organ but also in the main olfactory epithelium. Conclusion Our results suggest that, compared with rodents, the repertoire of orthologous V1R genes is remarkably conserved among the ruminants cow, sheep and goat. We predict that these orthologous V1Rs can detect the same or closely related chemical compound(s within each orthologous set/pair. Furthermore, all identified goat V1Rs are expressed in the vomeronasal organ and the main olfactory epithelium, suggesting that V1R-mediated ligand information can be detected and processed by both the main and accessory olfactory systems. The fact that ruminant and rodent V1Rs

  5. Investigation of tissue-specific human orthologous alternative splice events in pig

    DEFF Research Database (Denmark)

    Hillig, Ann-Britt Nygaard; Jørgensen, Claus Bøttcher; Salicio, Susanna Cirera;

    2010-01-01

    Alternative splicing of pre-mRNA can contribute to differences between tissues or cells either by regulating gene expression or creating proteins with various functions encoded by one gene. The number of investigated alternative splice events in pig has so far been limited. In this study we have...... investigated alternative splice events detected in humans, in orthologous pig genes. A total of 17 genes with predicted exon skipping events were selected for further studies. The splice events for the selected genes were experimentally verified using real-time quantitative PCR analysis (qPCR) with splice......-specific primers in 19 different tissues. The same splice variants as reported in humans were detected in 15 orthologous pig genes, however, the expression pattern predicted in the in silico analyses was only experimentally verified in a few cases. The results support the findings that splice events resulting...

  6. Characterization of the Drosophila ortholog of the human Usher Syndrome type 1G protein sans.

    Directory of Open Access Journals (Sweden)

    Fabio Demontis

    Full Text Available BACKGROUND: The Usher syndrome (USH is the most frequent deaf-blindness hereditary disease in humans. Deafness is attributed to the disorganization of stereocilia in the inner ear. USH1, the most severe subtype, is associated with mutations in genes encoding myosin VIIa, harmonin, cadherin 23, protocadherin 15, and sans. Myosin VIIa, harmonin, cadherin 23, and protocadherin 15 physically interact in vitro and localize to stereocilia tips in vivo, indicating that they form functional complexes. Sans, in contrast, localizes to vesicle-like structures beneath the apical membrane of stereocilia-displaying hair cells. How mutations in sans result in deafness and blindness is not well understood. Orthologs of myosin VIIa and protocadherin 15 have been identified in Drosophila melanogaster and their genetic analysis has identified essential roles in auditory perception and microvilli morphogenesis, respectively. PRINCIPAL FINDINGS: Here, we have identified and characterized the Drosophila ortholog of human sans. Drosophila Sans is expressed in tubular organs of the embryo, in lens-secreting cone cells of the adult eye, and in microvilli-displaying follicle cells during oogenesis. Sans mutants are viable, fertile, and mutant follicle cells appear to form microvilli, indicating that Sans is dispensable for fly development and microvilli morphogenesis in the follicle epithelium. In follicle cells, Sans protein localizes, similar to its vertebrate ortholog, to intracellular punctate structures, which we have identified as early endosomes associated with the syntaxin Avalanche. CONCLUSIONS: Our work is consistent with an evolutionary conserved function of Sans in vesicle trafficking. Furthermore it provides a significant basis for further understanding of the role of this Usher syndrome ortholog in development and disease.

  7. cis-Regulatory and Protein Evolution in Orthologous and Duplicate Genes

    OpenAIRE

    Castillo-Davis, Cristian I.; Hartl, Daniel L.; Achaz, Guillaume

    2004-01-01

    The relationship between protein and regulatory sequence evolution is a central question in molecular evolution. It is currently not known to what extent changes in gene expression are coupled with the evolution of protein coding sequences, or whether these changes differ among orthologs (species homologs) and paralogs (duplicate genes). Here, we develop a method to measure the extent of functionally relevant cis-regulatory sequence change in homologous genes, and validate it using microarray...

  8. Conserved Quantitative Stability/Flexibility Relationships (QSFR) in an Orthologous RNase H Pair

    OpenAIRE

    Livesay, Dennis R.; Jacobs, Donald J.

    2006-01-01

    Many reports qualitatively describe conserved stability and flexibility profiles across protein families, but biophysical modeling schemes have not been available to robustly quantify both. Here we investigate an orthologous RNase H pair by using a minimal distance constraint model (DCM). The DCM is an all atom microscopic model that accurately reproduces heat capacity measurements, and is unique in its ability to harmoniously calculate thermodynamic stability and flexibility in practical com...

  9. Identification and Functional Analysis of Three MAX2 Orthologs in Chrysanthemum

    Institute of Scientific and Technical Information of China (English)

    Lili Dong; Abdurazak Ishak; Jing Yu; Ruiyan Zhao; Liangjun Zhao

    2013-01-01

    MORE AXILLARY BRANCHING 2 (MAX2),initially identified in Arabidopsis thaliana,is a key regulatory gene in strigolactone signal transduction.Three orthologs of MAX2 were cloned from Dendranthema grandiflorum (DgMAX2a,b,and c).Each of the genes has an open reading frame of 2,049 bp and encodes 682 amino acid proteins.The predicted amino acid sequences of the three DgMAX2s are most closely related to the MAX2 orthologs identified in petunia (PhMAX2A and PhMAX2B),and display the highest amino acid sequence similarity with PhMAX2A compared to other MAX2s.Expression analysis revealed that DgMAX2s are predominantly expressed in the stem and axillary buds.On a cellular level,we localized the DgMAX2a::GFP fusion protein to the nucleus in onion epidermal cells,which is consistent with the nuclear localization of MAX2 in Arabidopsis.The chrysanthemum DgMAX2a is able to restore the max2-1 mutant branching to wild-type (WT) Arabidopsis,suggesting that it is a functional MAX2 ortholog.These results suggest that DgMAX2s may be candidate genes for reducing the shoot branching of chrysanthemum.

  10. OrthoDB v8: update of the hierarchical catalog of orthologs and the underlying free software.

    Science.gov (United States)

    Kriventseva, Evgenia V; Tegenfeldt, Fredrik; Petty, Tom J; Waterhouse, Robert M; Simão, Felipe A; Pozdnyakov, Igor A; Ioannidis, Panagiotis; Zdobnov, Evgeny M

    2015-01-01

    Orthology, refining the concept of homology, is the cornerstone of evolutionary comparative studies. With the ever-increasing availability of genomic data, inference of orthology has become instrumental for generating hypotheses about gene functions crucial to many studies. This update of the OrthoDB hierarchical catalog of orthologs (http://www.orthodb.org) covers 3027 complete genomes, including the most comprehensive set of 87 arthropods, 61 vertebrates, 227 fungi and 2627 bacteria (sampling the most complete and representative genomes from over 11,000 available). In addition to the most extensive integration of functional annotations from UniProt, InterPro, GO, OMIM, model organism phenotypes and COG functional categories, OrthoDB uniquely provides evolutionary annotations including rates of ortholog sequence divergence, copy-number profiles, sibling groups and gene architectures. We re-designed the entirety of the OrthoDB website from the underlying technology to the user interface, enabling the user to specify species of interest and to select the relevant orthology level by the NCBI taxonomy. The text searches allow use of complex logic with various identifiers of genes, proteins, domains, ontologies or annotation keywords and phrases. Gene copy-number profiles can also be queried. This release comes with the freely available underlying ortholog clustering pipeline (http://www.orthodb.org/software).

  11. Characterization of AtSTOP1 orthologous genes in tobacco and other plant species.

    Science.gov (United States)

    Ohyama, Yoshinao; Ito, Hiroki; Kobayashi, Yuriko; Ikka, Takashi; Morita, Akio; Kobayashi, Masatomo; Imaizumi, Ryujiro; Aoki, Toshio; Komatsu, Kenji; Sakata, Yoichi; Iuchi, Satoshi; Koyama, Hiroyuki

    2013-08-01

    Aluminum (Al) and proton (H⁺) tolerances are essential traits for plants to adapt to acid soil environments. In Arabidopsis (Arabidopsis thaliana), these tolerances are mediated by a zinc-finger transcription factor, SENSITIVE TO PROTON RHIZOTOXICITY1 (AtSTOP1), which regulates the transcription of multiple genes critical for tolerance to both stressors. Here, the functions of orthologous proteins (STOP1-like proteins) in other plant species were characterized by reverse genetics analyses and in planta complementation assays. RNA interference of a gene for NtSTOP1 repressed Al and H⁺ tolerances of tobacco (Nicotiana tabacum) roots. Tobacco roots released citrate in response to Al, concomitant with the up-regulated transcription of an ortholog of an Al tolerance gene encoding a citrate-transporting multidrug and toxic compound extrusion protein. The RNA interference repression of NtSTOP1 blocked this process and also repressed the transcription of another orthologous gene for Al tolerance, ALUMINUM SENSITIVE3, which encodes a prokaryote-type transporter. These results demonstrated that NtSTOP1 regulates Al tolerance in tobacco through the transcriptional regulation of these genes. The in planta complementation assays revealed that other plant species, including woody plants, a legume, and a moss (Physcomitrella patens), possess functional STOP1-like proteins that can activate several H⁺ and Al-tolerance genes in Arabidopsis. Knocking out the gene encoding the STOP1-like protein decreased the Al tolerance of P. patens. Together, our results strongly suggest that transcriptional regulation by STOP1-like proteins is evolutionarily conserved among land plants and that it confers the ability to survive in acid soils through the transcriptional regulation of Al- and H⁺-tolerance genes.

  12. Systematic discovery of unannotated genes in 11 yeast species using a database of orthologous genomic segments

    LENUS (Irish Health Repository)

    OhEigeartaigh, Sean S

    2011-07-26

    Abstract Background In standard BLAST searches, no information other than the sequences of the query and the database entries is considered. However, in situations where two genes from different species have only borderline similarity in a BLAST search, the discovery that the genes are located within a region of conserved gene order (synteny) can provide additional evidence that they are orthologs. Thus, for interpreting borderline search results, it would be useful to know whether the syntenic context of a database hit is similar to that of the query. This principle has often been used in investigations of particular genes or genomic regions, but to our knowledge it has never been implemented systematically. Results We made use of the synteny information contained in the Yeast Gene Order Browser database for 11 yeast species to carry out a systematic search for protein-coding genes that were overlooked in the original annotations of one or more yeast genomes but which are syntenic with their orthologs. Such genes tend to have been overlooked because they are short, highly divergent, or contain introns. The key features of our software - called SearchDOGS - are that the database entries are classified into sets of genomic segments that are already known to be orthologous, and that very weak BLAST hits are retained for further analysis if their genomic location is similar to that of the query. Using SearchDOGS we identified 595 additional protein-coding genes among the 11 yeast species, including two new genes in Saccharomyces cerevisiae. We found additional genes for the mating pheromone a-factor in six species including Kluyveromyces lactis. Conclusions SearchDOGS has proven highly successful for identifying overlooked genes in the yeast genomes. We anticipate that our approach can be adapted for study of further groups of species, such as bacterial genomes. More generally, the concept of doing sequence similarity searches against databases to which external

  13. The impact of gene duplication, insertion, deletion, lateral gene transfer and sequencing error on orthology inference: a simulation study.

    Science.gov (United States)

    Dalquen, Daniel A; Altenhoff, Adrian M; Gonnet, Gaston H; Dessimoz, Christophe

    2013-01-01

    The identification of orthologous genes, a prerequisite for numerous analyses in comparative and functional genomics, is commonly performed computationally from protein sequences. Several previous studies have compared the accuracy of orthology inference methods, but simulated data has not typically been considered in cross-method assessment studies. Yet, while dependent on model assumptions, simulation-based benchmarking offers unique advantages: contrary to empirical data, all aspects of simulated data are known with certainty. Furthermore, the flexibility of simulation makes it possible to investigate performance factors in isolation of one another.Here, we use simulated data to dissect the performance of six methods for orthology inference available as standalone software packages (Inparanoid, OMA, OrthoInspector, OrthoMCL, QuartetS, SPIMAP) as well as two generic approaches (bidirectional best hit and reciprocal smallest distance). We investigate the impact of various evolutionary forces (gene duplication, insertion, deletion, and lateral gene transfer) and technological artefacts (ambiguous sequences) on orthology inference. We show that while gene duplication/loss and insertion/deletion are well handled by most methods (albeit for different trade-offs of precision and recall), lateral gene transfer disrupts all methods. As for ambiguous sequences, which might result from poor sequencing, assembly, or genome annotation, we show that they affect alignment score-based orthology methods more strongly than their distance-based counterparts.

  14. Comparative sequence analysis of the Ghd7 orthologous regions revealed movement of Ghd7 in the grass genomes.

    Directory of Open Access Journals (Sweden)

    Lu Yang

    Full Text Available Ghd7 is an important rice gene that has a major effect on several agronomic traits, including yield. To reveal the origin of Ghd7 and sequence evolution of this locus, we performed a comparative sequence analysis of the Ghd7 orthologous regions from ten diploid Oryza species, Brachypodium distachyon, sorghum and maize. Sequence analysis demonstrated high gene collinearity across the genus Oryza and a disruption of collinearity among non-Oryza species. In particular, Ghd7 was not present in orthologous positions except in Oryza species. The Ghd7 regions were found to have low gene densities and high contents of repetitive elements, and that the sizes of orthologous regions varied tremendously. The large transposable element contents resulted in a high frequency of pseudogenization and gene movement events surrounding the Ghd7 loci. Annotation information and cytological experiments have indicated that Ghd7 is a heterochromatic gene. Ghd7 orthologs were identified in B. distachyon, sorghum and maize by phylogenetic analysis; however, the positions of orthologous genes differed dramatically as a consequence of gene movements in grasses. Rather, we identified sequence remnants of gene movement of Ghd7 mediated by illegitimate recombination in the B. distachyon genome.

  15. Genomic analysis of NAC transcription factors in banana (Musa acuminata) and definition of NAC orthologous groups for monocots and dicots.

    Science.gov (United States)

    Cenci, Albero; Guignon, Valentin; Roux, Nicolas; Rouard, Mathieu

    2014-05-01

    Identifying the molecular mechanisms underlying tolerance to abiotic stresses is important in crop breeding. A comprehensive understanding of the gene families associated with drought tolerance is therefore highly relevant. NAC transcription factors form a large plant-specific gene family involved in the regulation of tissue development and responses to biotic and abiotic stresses. The main goal of this study was to set up a framework of orthologous groups determined by an expert sequence comparison of NAC genes from both monocots and dicots. In order to clarify the orthologous relationships among NAC genes of different species, we performed an in-depth comparative study of four divergent taxa, in dicots and monocots, whose genomes have already been completely sequenced: Arabidopsis thaliana, Vitis vinifera, Musa acuminata and Oryza sativa. Due to independent evolution, NAC copy number is highly variable in these plant genomes. Based on an expert NAC sequence comparison, we propose forty orthologous groups of NAC sequences that were probably derived from an ancestor gene present in the most recent common ancestor of dicots and monocots. These orthologous groups provide a curated resource for large-scale protein sequence annotation of NAC transcription factors. The established orthology relationships also provide a useful reference for NAC function studies in newly sequenced genomes such as M. acuminata and other plant species.

  16. License - PGDBj - Ortholog DB | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available PGDBj - Ortholog DB License License to Use This Database Last updated : 2014/04/04 You may use this database...se terms regarding the use of this database and the requirements you must follow in using this database.... The license for this database is specified in the Creative Commons Attribution-Share... Alike 2.1 Japan . If you use data from this database, please be sure attribute this database as follows: PG...re . With regard to this database, you are licensed to: freely access part or whole of this database, and ac

  17. Molecular cloning and characterization of the human RNase κ, an ortholog of Cc RNase

    OpenAIRE

    Economopoulou, Marie-angela I.; Fragoulis, Emmanouel G.; Sideris, Diamantis C.

    2007-01-01

    A novel protein family, designated hereafter as RNase κ (kappa) family, has been recently introduced with the characterization of the specific Cc RNase, isolated from the insect Ceratitis capitata. The human ortholog of this family consists of 98 amino acids and shares > 98% identity with its mammalian counterparts. This RNase is encoded by a single-copy gene found to be expressed in a wide spectrum of normal and cancer tissues. The cDNA of the human ribonuclease has been isolated and subclon...

  18. New Insights on Eggplant/Tomato/Pepper Synteny and Identification of Eggplant and Pepper Orthologous QTL.

    Science.gov (United States)

    Rinaldi, Riccardo; Van Deynze, Allen; Portis, Ezio; Rotino, Giuseppe L; Toppino, Laura; Hill, Theresa; Ashrafi, Hamid; Barchi, Lorenzo; Lanteri, Sergio

    2016-01-01

    Eggplant, pepper, and tomato are the most exploited berry-producing vegetables within the Solanaceae family. Their genomes differ in size, but each has 12 chromosomes which have undergone rearrangements causing a redistribution of loci. The genome sequences of all three species are available but differ in coverage, assembly quality and percentage of anchorage. Determining their syntenic relationship and QTL orthology will contribute to exploit genomic resources and genetic data for key agronomic traits. The syntenic analysis between tomato and pepper based on the alignment of 34,727 tomato CDS to the pepper genome sequence, identified 19,734 unique hits. The resulting synteny map confirmed the 14 inversions and 10 translocations previously documented, but also highlighted 3 new translocations and 4 major new inversions. Furthermore, each of the 12 chromosomes exhibited a number of rearrangements involving small regions of 0.5-0.7 Mbp. Due to high fragmentation of the publicly available eggplant genome sequence, physical localization of most eggplant QTL was not possible, thus, we compared the organization of the eggplant genetic map with the genome sequence of both tomato and pepper. The eggplant/tomato syntenic map confirmed all the 10 translocations but only 9 of the 14 known inversions; on the other hand, a newly detected inversion was recognized while another one was not confirmed. The eggplant/pepper syntenic map confirmed 10 translocations and 8 inversions already detected and suggested a putative new translocation. In order to perform the assessment of eggplant and pepper QTL orthology, the eggplant and pepper sequence-based markers located in their respective genetic map were aligned onto the pepper genome. GBrowse in pepper was used as reference platform for QTL positioning. A set of 151 pepper QTL were located as well as 212 eggplant QTL, including 76 major QTL (PVE ≥ 10%) affecting key agronomic traits. Most were confirmed to cluster in orthologous

  19. New Insights on Eggplant/Tomato/Pepper Synteny and Identification of Eggplant and Pepper Orthologous QTL

    Directory of Open Access Journals (Sweden)

    Riccardo Rinaldi

    2016-07-01

    Full Text Available Eggplant, pepper and tomato are the most exploited berry-producing vegetables within the Solanaceae family. Their genomes differ in size, but each has 12 chromosomes which have undergone rearrangements causing a redistribution of loci. The genome sequences of all three species are available but differ in coverage, assembly quality and percentage of anchorage.Determining their syntenic relationship and QTL orthology will contribute to exploit genomic resources and genetic data for key agronomic traits.The syntenic analysis between tomato and pepper based on the alignment of 34,727 tomato CDS to the pepper genome sequence, identified 19,734 unique hits. The resulting synteny map confirmed the 14 inversions and 10 translocations previously documented, but also highlighted 3 new translocations and 4 major new inversions. Furthermore, each of the 12 chromosomes exhibited a number of rearrangements involving small regions of 0.5-0.7 Mbp.Due to high fragmentation of the publicly available eggplant genome sequence, physical localization of most eggplant QTL was not possible, thus, we compared the organization of the eggplant genetic map with the genome sequence of both tomato and pepper. The eggplant/tomato syntenic map confirmed all the 10 translocations but only 9 of the 14 known inversions; on the other hand, a newly detected inversion was recognized while another one was not confirmed. The eggplant/pepper syntenic map confirmed 10 translocations and 8 inversions already detected and suggested a putative new translocation.In order to perform the assessment of eggplant and pepper QTL orthology, the eggplant and pepper sequence-based markers located in their respective genetic map were aligned onto the pepper genome. GBrowse in pepper was used as reference platform for QTL positioning. A set of 151 pepper QTL were located as well as 212 eggplant QTL, including 76 major QTL (PVE ≥ 10% affecting key agronomic traits. Most were confirmed to cluster in

  20. Versatile roles of CspA orthologs in complement inactivation of serum-resistant Lyme disease spirochetes.

    Science.gov (United States)

    Hammerschmidt, Claudia; Koenigs, Arno; Siegel, Corinna; Hallström, Teresia; Skerka, Christine; Wallich, Reinhard; Zipfel, Peter F; Kraiczy, Peter

    2014-01-01

    CspA of the Lyme disease spirochete Borrelia burgdorferi represents a key molecule in immune evasion, protecting borrelial cells from complement-mediated killing. As previous studies focused almost exclusively on CspA of B. burgdorferi, here we investigate the different binding capacities of CspA orthologs of Borrelia burgdorferi, B. afzelii, and B. spielmanii for complement regulator factor H and plasminogen and their ability to inhibit complement activation by either binding these host-derived plasma proteins or independently by direct interaction with components involved in formation of the lethal, pore-like terminal complement complex. To further examine their function in serum resistance in vivo, a serum-sensitive B. garinii strain was used to generate spirochetes, ectopically producing functional CspA orthologs. Irrespective of their species origin, all three CspA orthologs impart resistance to complement-mediated killing when produced in a serum-sensitive B. garinii surrogate strain. To analyze the inhibitory effect on complement activation and to assess the potential to inactivate C3b by binding of factor H and plasminogen, recombinant CspA orthologs were also investigated. All three CspA orthologs simultaneously bound factor H and plasminogen but differed in regard to their capacity to inactivate C3b via bound plasmin(ogen) and inhibit formation of the terminal complement complex. CspA of B. afzelii binds plasmin(ogen) and inhibits the terminal complement complex more efficiently than CspA of B. burgdorferi and B. spielmanii. Taken together, CspA orthologs of serum-resistant Lyme disease spirochetes act as multifunctional evasion molecules that inhibit complement on two central activation levels, C3b generation and assembly of the terminal complement complex.

  1. A combined approach exploring gene function based on Worm-Human Orthology

    Directory of Open Access Journals (Sweden)

    Johnsen Robert

    2005-05-01

    Full Text Available Abstract Background Many aspects of the nematode Caenorhabditis elegans biology are conserved between invertebrates and vertebrates establishing this particular organism as an excellent genetic model. Because of its small size, large populations and self-fertilization of the hermaphrodite, functional predictions carried out by genetic modifications as well as RNAi screens, can be rapidly tested. Results In order to explore the function of a set of C. elegans genes of unknown function, as well as their potential functional roles in the human genome, we performed a phylogenetic analysis to select the most probable worm orthologs. A total of 13 C. elegans genes were subjected to down- regulation via RNAi and characterization of expression profiles using GFP strains. Previously unknown distinct expression patterns were observed for four of the analyzed genes, as well as four visible RNAi phenotypes. In addition, subcellular protein over-expression profiles of the human orthologs for seven out of the thirteen genes using human cells were also analyzed. Conclusion By combining a whole-organism approach using C. elegans with complementary experimental work done on human cell lines, this analysis extends currently available information on the selected set of genes.

  2. The Cyclin-Dependent Kinase Ortholog pUL97 of Human Cytomegalovirus Interacts with Cyclins

    Directory of Open Access Journals (Sweden)

    Laura Graf

    2013-12-01

    Full Text Available The human cytomegalovirus (HCMV-encoded protein kinase, pUL97, is considered a cyclin-dependent kinase (CDK ortholog, due to shared structural and functional characteristics. The primary mechanism of CDK activation is binding to corresponding cyclins, including cyclin T1, which is the usual regulatory cofactor of CDK9. This study provides evidence of direct interaction between pUL97 and cyclin T1 using yeast two-hybrid and co-immunoprecipitation analyses. Confocal immunofluorescence revealed partial colocalization of pUL97 with cyclin T1 in subnuclear compartments, most pronounced in viral replication centres. The distribution patterns of pUL97 and cyclin T1 were independent of HCMV strain and host cell type. The sequence domain of pUL97 responsible for the interaction with cyclin T1 was between amino acids 231–280. Additional co-immunoprecipitation analyses showed cyclin B1 and cyclin A as further pUL97 interaction partners. Investigation of the pUL97-cyclin T1 interaction in an ATP consumption assay strongly suggested phosphorylation of pUL97 by the CDK9/cyclin T1 complex in a substrate concentration-dependent manner. This is the first demonstration of interaction between a herpesviral CDK ortholog and cellular cyclins.

  3. Cloning and characterization of a FLORICAULA/LEAFY ortholog, PFL, in polygamous papaya

    Institute of Scientific and Technical Information of China (English)

    Qingyi YU; Paul H. MOORE; Henrik H. ALBERT; Adrienne H.K. ROADER; Ray MING

    2005-01-01

    The homologous genes FLORICAULA (FLO) in Antirrhinum and LEAFY (LFY) in Arabidopsis are known to regulate the initiation of flowering in these two distantly related plant species. These genes are necessary also for the expression of downstream genes that control floral organ identity. We used Arabidopsis LFY cDNA as a probe to clone and sequence a papaya ortholog of LFY, PFL. It encodes a protein that shares 61% identity with the Arabidopsis LFY gene and 71% identity with the LFYhomologs of the two woody tree species: California sycamore (Platanus racemosa) and black cottonwood (Populus trichocarpa). Despite the high sequence similarity within two conserved regions, the N-terminal proline-rich motif in papaya PFL differs from other members in the family. This difference may not affect the gene function of papaya PFL, since an equally divergent but a functional LFY ortholog NEEDLY of Pinus radiata has been reported. Genomic and BAC Southern analyses indicated that there is only one copy of PFL in the papaya genome. In situ hybridization experiments demonstrated that PFL is expressed at a relatively low level in leaf primordia,but it is expressed at a high level in the floral meristem. Quantitative PCR analyses revealed that PFL was expressed in flower buds of all three sex types - male, female, and hermaphrodite with marginal difference between hermaphrodite and unisexual flowers. These data suggest that PFL may play a similar role as LFY in flower development and has limited effect on sex differentiation in papaya.

  4. Development and bin mapping of a Rosaceae Conserved Ortholog Set (COS of markers

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    Kozik Alex

    2009-01-01

    Full Text Available Abstract Background Detailed comparative genome analyses within the economically important Rosaceae family have not been conducted. This is largely due to the lack of conserved gene-based molecular markers that are transferable among the important crop genera within the family [e.g. Malus (apple, Fragaria (strawberry, and Prunus (peach, cherry, apricot and almond]. The lack of molecular markers and comparative whole genome sequence analysis for this family severely hampers crop improvement efforts as well as QTL confirmation and validation studies. Results We identified a set of 3,818 rosaceaous unigenes comprised of two or more ESTs that correspond to single copy Arabidopsis genes. From this Rosaceae Conserved Orthologous Set (RosCOS, 1039 were selected from which 857 were used for the development of intron-flanking primers and allele amplification. This led to successful amplification and subsequent mapping of 613 RosCOS onto the Prunus TxE reference map resulting in a genome-wide coverage of 0.67 to 1.06 gene-based markers per cM per linkage group. Furthermore, the RosCOS primers showed amplification success rates from 23 to 100% across the family indicating that a substantial part of the RosCOS primers can be directly employed in other less studied rosaceaous crops. Comparisons of the genetic map positions of the RosCOS with the physical locations of the orthologs in the Populus trichocarpa genome identified regions of colinearity between the genomes of Prunus-Rosaceae and Populus-Salicaceae. Conclusion Conserved orthologous genes are extremely useful for the analysis of genome evolution among closely and distantly related species. The results presented in this study demonstrate the considerable potential of the mapped Prunus RosCOS for genome-wide marker employment and comparative whole genome studies within the Rosaceae family. Moreover, these markers will also function as useful anchor points for the genome sequencing efforts currently

  5. eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences

    DEFF Research Database (Denmark)

    Huerta-Cepas, Jaime; Szklarczyk, Damian; Forslund, Kristoffer;

    2016-01-01

    eggNOG is a public resource that provides Orthologous Groups (OGs) of proteins at different taxonomic levels, each with integrated and summarized functional annotations. Developments since the latest public release include changes to the algorithm for creating OGs across taxonomic levels, making ...

  6. Unresolved orthology and peculiar coding sequence properties of lamprey genes: the KCNA gene family as test case

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    Kuraku Shigehiro

    2011-06-01

    Full Text Available Abstract Background In understanding the evolutionary process of vertebrates, cyclostomes (hagfishes and lamprey occupy crucial positions. Resolving molecular phylogenetic relationships of cyclostome genes with gnathostomes (jawed vertebrates genes is indispensable in deciphering both the species tree and gene trees. However, molecular phylogenetic analyses, especially those including lamprey genes, have produced highly discordant results between gene families. To efficiently scrutinize this problem using partial genome assemblies of early vertebrates, we focused on the potassium voltage-gated channel, shaker-related (KCNA family, whose members are mostly single-exon. Results Seven sea lamprey KCNA genes as well as six elephant shark genes were identified, and their orthologies to bony vertebrate subgroups were assessed. In contrast to robustly supported orthology of the elephant shark genes to gnathostome subgroups, clear orthology of any sea lamprey gene could not be established. Notably, sea lamprey KCNA sequences displayed unique codon usage pattern and amino acid composition, probably associated with exceptionally high GC-content in their coding regions. This lamprey-specific property of coding sequences was also observed generally for genes outside this gene family. Conclusions Our results suggest that secondary modifications of sequence properties unique to the lamprey lineage may be one of the factors preventing robust orthology assessments of lamprey genes, which deserves further genome-wide validation. The lamprey lineage-specific alteration of protein-coding sequence properties needs to be taken into consideration in tackling the key questions about early vertebrate evolution.

  7. Mycoplasma hyopneumoniae and Mycoplasma flocculare differential domains from orthologous surface proteins induce distinct cellular immune responses in mice.

    Science.gov (United States)

    Leal, Fernanda Munhoz Dos Anjos; Virginio, Veridiana Gomes; Martello, Carolina Lumertz; Paes, Jéssica Andrade; Borges, Thiago J; Jaeger, Natália; Bonorino, Cristina; Ferreira, Henrique Bunselmeyer

    2016-07-15

    Mycoplasma hyopneumoniae and Mycoplasma flocculare are two genetically close species found in the swine respiratory tract. Despite their similarities, while M. hyopneumoniae is the causative agent of porcine enzootic pneumonia, M. flocculare is a commensal bacterium. Genomic and transcriptional comparative analyses so far failed to explain the difference in pathogenicity between these two species. We then hypothesized that such difference might be, at least in part, explained by amino acid sequence and immunological or functional differences between ortholog surface proteins. In line with that, it was verified that approximately 85% of the ortholog surface proteins from M. hyopneumoniae 7448 and M. flocculare present one or more differential domains. To experimentally assess possible immunological implications of this kind of difference, the extracellular differential domains from one pair of orthologous surface proteins (MHP7448_0612, from M. hyopneumoniae, and MF_00357, from M. flocculare) were expressed in E. coli and used to immunize mice. The recombinant polypeptides (rMHP61267-169 and rMF35767-196, respectively) induced distinct cellular immune responses. While, rMHP61267-169 induced both Th1 and Th2 responses, rMF35767-196 induced just an early pro-inflammatory response. These results indicate that immunological properties determined by differential domains in orthologous surface protein might play a role in pathogenicity, contributing to elicit specific and differential immune responses against each species. PMID:27283856

  8. The Drosophila ortholog of TMEM18 regulates insulin and glucagon-like signaling.

    Science.gov (United States)

    Wiemerslage, Lyle; Gohel, Priya A; Maestri, Giulia; Hilmarsson, Torfi G; Mickael, Michel; Fredriksson, Robert; Williams, Michael J; Schiöth, Helgi B

    2016-06-01

    Transmembrane protein 18 (TMEM18) is an ill-described, obesity-related gene, but few studies have explored its molecular function. We found single-nucleotide polymorphism data, suggesting that TMEM18 may be involved in the regulation/physiology of metabolic syndrome based on associations with insulin, homeostatic model assessment-β (HOMAβ), triglycerides, and blood sugar. We then found an ortholog in the Drosophila genome, knocked down Drosophila Tmem18 specifically in insulin-producing cells, and tested for its effects on metabolic function. Our results suggest that TMEM18 affects substrate levels through insulin and glucagon signaling, and its downregulation induces a metabolic state resembling type 2 diabetes. This work is the first to experimentally describe the metabolic consequences of TMEM18 knockdown, and further supports its association with obesity. PMID:27029472

  9. Orthologous and Paralogous AmpD Peptidoglycan Amidases from Gram-Negative Bacteria

    Science.gov (United States)

    Rivera, Ivanna; Molina, Rafael; Lee, Mijoon; Mobashery, Shahriar

    2016-01-01

    Cell wall recycling and β-lactam antibiotic resistance are linked in Enterobacteriaceae and in Pseudomonas aeruginosa. This process involves a large number of murolytic enzymes, among them a cytoplasmic peptidoglycan amidase AmpD, which plays an essential role by cleaving the peptide stem from key intermediates en route to the β-lactamase production (a resistance mechanism) and cell wall recycling. Uniquely, P. aeruginosa has two additional paralogues of AmpD, designated AmpDh2 and AmpDh3, which are periplasmic enzymes. Despite the fact that AmpDh2 and AmpDh3 share a common motif for their respective catalytic domains, they are each comprised of multidomain architectures and exhibit distinct oligomerization properties. We review herein the structural and biochemical properties of orthologous and paralogous AmpD proteins and discuss their implication in cell wall recycling and antibiotic resistance processes. PMID:27326855

  10. Expression and in vitro properties of guinea pig IL-5: Comparison to human and murine orthologs

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    Clay W Scott

    2000-01-01

    Full Text Available Interleukin-5 (IL-5 is a key mediator of eosinophilic inflammation. The biological role of this cytokine in an allergic airway inflammatory response has been widely demonstrated in guinea pigs, yet the interaction of guinea pig IL-5 (gpIL-5 with its receptor has not been studied. Experiments were performed to quantitate the interaction of gpIL-5 with gpIL-5r and to compare this affinity with that of hIL-5 and mIL-5 and their cognate receptors. The cross-species affinity and agonist efficacy were evaluated to see if gpIL-5r had a restricted species reactivity (as is the case with mIL-5r or did not distinguish between IL-5 orthologs (similar to hIL-5r. gpIL-5 was cloned using mRNA isolated from cells obtained by bronchoalveolar lavage. Recombinant gpIL-5 was expressed in T.ni insect cells and purified from spent media. Binding assays were performed using insect cells expressing hIL-5rαβ or gpIL-5rαβ1 as previously described (Cytokine, 12:858–866, 2000 or using B13 cells which express mIL-5r. The agonist potency and efficacy properties of each IL-5 ortholog were evaluated by quantitating the proliferative response of hum an TF-1 cells and murine B13 cells. gpIL-5 bound with high affinity to recombinant gpIL-5r as demonstrated by displacing [125I]hIL-5 (Ki = 160 pM. gpIL-5 also bound to hIL-5r with high affinity (Ki = 750 pM. hIL-5 and mIL-5 showed similar, high-affinity binding profiles to both gpIL-5r and hIL-5r. In contrast, gpIL-5 and hIL5 did not bind to the mIL-5r as demonstrated by an inability to displace [125I]mIL-5, even at 1000-fold molar excess. These differences in affinity for IL-5r orthologs correlated with bioassay results: human TF1 cells showed roughly com parable proliferative responses to guinea pig, hum an and murine IL-5 whereas murine B13 cells showed a strong preference for murine over guinea pig and human IL-5(EC50 = 1.9, 2200 and 720 pM, respectively. Recombinant gpIL-5 binds to the gpIL-5r with high affinity, similar

  11. Suiformes orthologous satellite DNAs as a hallmark of Pecari tajacu and Tayassu pecari (Tayassuidae) evolutionary rearrangements.

    Science.gov (United States)

    Adega, Filomena; Chaves, Raquel; Guedes-Pinto, Henrique

    2008-12-01

    In a broad general way, eukaryotic satellite DNA sequences are characterized by a highly dynamic molecular behavior due to concerted evolution that leads to rapid change between repeat sequences of different species, achieved by amplification of new variants during speciation or by gradual sequence evolution due to the accumulation of nucleotide substitutions. There are, although exceptions for this almost universal rule. We isolated variants from both the Mc1 and Ac2 pig (Sus scrofa, Suidae) satellite DNA families from the genomes of two Tayassuidae members: Pecari tajacu and Tayassu pecari, which have highly derived karyotypes. The presence of these sequences in both families' genomes (Suidae and Tayassuidae) implies their existence in a common ancestor, what confers to the variants the status of orthology and the approximate age of, at least 40 million years. While at the molecular composition level these orthologous sequences are highly homologous, cross-species physical mapping revealed a completely different chromosomal location in Suidae versus Tayassuidae families, most probably, reflecting the high level of divergence and chromosomes evolution pathways after radiation of each family. Detailed comparative analysis of the satellites assignment on the peccary's chromosomes revealed its co-localization with homologous evolutionary breakpoints in both species, suggesting their involvement in the rearrangement events. The complex behavior of the repeats evolution in the pig/peccaries genomes is here clearly illustrated. These sequences are molecularly preserved for a considerable period of time and display slow rates of sequence change, but show a dynamic motion behavior throughout the peccary's genomes that accompanied the great architectonic reorganization of Tayassuidae chromosomes during evolution.

  12. Drug target prediction and prioritization: using orthology to predict essentiality in parasite genomes

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    Hall Ross S

    2010-04-01

    Full Text Available Abstract Background New drug targets are urgently needed for parasites of socio-economic importance. Genes that are essential for parasite survival are highly desirable targets, but information on these genes is lacking, as gene knockouts or knockdowns are difficult to perform in many species of parasites. We examined the applicability of large-scale essentiality information from four model eukaryotes, Caenorhabditis elegans, Drosophila melanogaster, Mus musculus and Saccharomyces cerevisiae, to discover essential genes in each of their genomes. Parasite genes that lack orthologues in their host are desirable as selective targets, so we also examined prediction of essential genes within this subset. Results Cross-species analyses showed that the evolutionary conservation of genes and the presence of essential orthologues are each strong predictors of essentiality in eukaryotes. Absence of paralogues was also found to be a general predictor of increased relative essentiality. By combining several orthology and essentiality criteria one can select gene sets with up to a five-fold enrichment in essential genes compared with a random selection. We show how quantitative application of such criteria can be used to predict a ranked list of potential drug targets from Ancylostoma caninum and Haemonchus contortus - two blood-feeding strongylid nematodes, for which there are presently limited sequence data but no functional genomic tools. Conclusions The present study demonstrates the utility of using orthology information from multiple, diverse eukaryotes to predict essential genes. The data also emphasize the challenge of identifying essential genes among those in a parasite that are absent from its host.

  13. The fission yeast MTREC and EJC orthologs ensure the maturation of meiotic transcripts during meiosis.

    Science.gov (United States)

    Marayati, Bahjat Fadi; Hoskins, Victoria; Boger, Robert W; Tucker, James F; Fishman, Emily S; Bray, Andrew S; Zhang, Ke

    2016-09-01

    Meiosis is a highly regulated process by which genetic information is transmitted through sexual reproduction. It encompasses unique mechanisms that do not occur in vegetative cells, producing a distinct, well-regulated meiotic transcriptome. During vegetative growth, many meiotic genes are constitutively transcribed, but most of the resulting mRNAs are rapidly eliminated by the Mmi1-MTREC (Mtl1-Red1 core) complex. While Mmi1-MTREC targets premature meiotic RNAs for degradation by the nuclear 3'-5' exoribonuclease exosome during mitotic growth, its role in meiotic gene expression during meiosis is not known. Here, we report that Red5, an essential MTREC component, interacts with pFal1, an ortholog of eukaryotic translation initiation factor eIF4aIII in the fission yeast Schizosaccharomyces pombe In mammals, together with MAGO (Mnh1), Rnps1, and Y14, elF4AIII (pFal1) forms the core of the exon junction complex (EJC), which is essential for transcriptional surveillance and localization of mature mRNAs. In fission yeast, two EJC orthologs, pFal1 and Mnh1, are functionally connected with MTREC, specifically in the process of meiotic gene expression during meiosis. Although pFal1 interacts with Mnh1, Y14, and Rnps1, its association with Mnh1 is not disrupted upon loss of Y14 or Rnps1. Mutations of Red1, Red5, pFal1, or Mnh1 produce severe meiotic defects; the abundance of meiotic transcripts during meiosis decreases; and mRNA maturation processes such as splicing are impaired. Since studying meiosis in mammalian germline cells is difficult, our findings in fission yeast may help to define the general mechanisms involved in accurate meiotic gene expression in higher eukaryotes. PMID:27365210

  14. The fission yeast MTREC and EJC orthologs ensure the maturation of meiotic transcripts during meiosis

    Science.gov (United States)

    Marayati, Bahjat Fadi; Hoskins, Victoria; Boger, Robert W.; Tucker, James F.; Fishman, Emily S.; Bray, Andrew S.; Zhang, Ke

    2016-01-01

    Meiosis is a highly regulated process by which genetic information is transmitted through sexual reproduction. It encompasses unique mechanisms that do not occur in vegetative cells, producing a distinct, well-regulated meiotic transcriptome. During vegetative growth, many meiotic genes are constitutively transcribed, but most of the resulting mRNAs are rapidly eliminated by the Mmi1-MTREC (Mtl1-Red1 core) complex. While Mmi1-MTREC targets premature meiotic RNAs for degradation by the nuclear 3′–5′ exoribonuclease exosome during mitotic growth, its role in meiotic gene expression during meiosis is not known. Here, we report that Red5, an essential MTREC component, interacts with pFal1, an ortholog of eukaryotic translation initiation factor eIF4aIII in the fission yeast Schizosaccharomyces pombe. In mammals, together with MAGO (Mnh1), Rnps1, and Y14, elF4AIII (pFal1) forms the core of the exon junction complex (EJC), which is essential for transcriptional surveillance and localization of mature mRNAs. In fission yeast, two EJC orthologs, pFal1 and Mnh1, are functionally connected with MTREC, specifically in the process of meiotic gene expression during meiosis. Although pFal1 interacts with Mnh1, Y14, and Rnps1, its association with Mnh1 is not disrupted upon loss of Y14 or Rnps1. Mutations of Red1, Red5, pFal1, or Mnh1 produce severe meiotic defects; the abundance of meiotic transcripts during meiosis decreases; and mRNA maturation processes such as splicing are impaired. Since studying meiosis in mammalian germline cells is difficult, our findings in fission yeast may help to define the general mechanisms involved in accurate meiotic gene expression in higher eukaryotes. PMID:27365210

  15. Trypanosomatid RACK1 orthologs show functional differences associated with translation despite similar roles in Leishmania pathogenesis.

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    Kohelia Choudhury

    Full Text Available RACK1 proteins belong to the eukaryote WD40-repeat protein family and function as spatial regulators of multiple cellular events, including signaling pathways, the cell cycle and translation. For this latter role, structural and genetic studies indicate that RACK1 associates with the ribosome through two conserved positively charged amino acids in its first WD40 domain. Unlike RACK1s, including Trypanosoma brucei RACK1 (TbRACK1, only one of these two positively-charged residues is conserved in the first WD40 domain of the Leishmania major RACK1 ortholog, LACK. We compared virulence-attenuated LACK single copy (LACK/- L. major, with L. major expressing either two LACK copies (LACK/LACK, or one copy each of LACK and TbRACK1 (LACK/TbRACK1, to evaluate the function of these structurally distinct RACK1 orthologs with respect to translation, viability at host temperatures and pathogenesis. Our results indicate that although the ribosome-binding residues are not fully conserved in LACK, both LACK and TbRACK1 co-sedimented with monosomes and polysomes in LACK/LACK and LACK/TbRACK1 L. major, respectively. LACK/LACK and LACK/TbRACK1 strains differed in their sensitivity to translation inhibitors implying that minor sequence differences between the RACK1 proteins can alter their functional properties. While biochemically distinguishable, both LACK/LACK and LACK/TbRACK1 lines were more tolerant of elevated temperatures, resistant to translation inhibitors, and displayed robust pathogenesis in vivo, contrasting to LACK/- parasites.

  16. Effect of vaccination with a recombinant Bm86 antigen preparation on natural infestations of Boophilus microplus in grazing dairy and beef pure and cross-bred cattle in Brazil.

    Science.gov (United States)

    Rodríguez, M; Massard, C L; da Fonseca, A H; Ramos, N F; Machado, H; Labarta, V; de la Fuente, J

    1995-12-01

    Current methods for the control of the cattle tick Boophilus microplus infestations are not effective and the parasite remains a serious problem for the cattle industry in tropical and sub-tropical areas. Recent advances have introduced the possibility for the immunological control of the parasite through the use of recombinant vaccines. Recently, it was shown that the recombinant vaccine Gavac (Heber Biotec S.A.) is able to control B. microplus populations in artificially infected grazing dairy cattle in Cuba. To assay the effect of the vaccine on a different B. microplus strain and under different ecological conditions, we conducted a trial in Brazil on grazing dairy and beef pure and cross-bred cattle under natural infestation conditions. A farm in the northeast of the state of Sao Paulo was selected and two groups of animals per breed were included in the experiment and were maintained grazing on separate but similar pastures. For each breed, one group was vaccinated with the vaccine Gavac and the second group was not vaccinated and was employed as a control. In vaccinated cattle, during 36 weeks of experiment, the average infestation rate was maintained below 78 ticks per animal while average infestation peaks (mean +/- S.E.) of 144 +/- 44 ticks per animal (for dairy cross-bred cattle) and 195 +/- 42 ticks per animal (for beef cross-bred cattle) were recorded in the control groups. Tick infestation rates showed statistical significant differences (p = 0.04) between both experimental groups throughout the experiment. These results clearly showed, as in the Cuban study, that the vaccine controlled tick numbers in successive generations in the field. PMID:8701597

  17. Orthologous genes identified by transcriptome sequencing in the spider genus Stegodyphus

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    Mattila Tiina M

    2012-02-01

    Full Text Available Abstract Background The evolution of sociality in spiders involves a transition from an outcrossing to a highly inbreeding mating system, a shift to a female biased sex ratio, and an increase in the reproductive skew among individuals. Taken together, these features are expected to result in a strong reduction in the effective population size. Such a decline in effective population size is expected to affect population genetic and molecular evolutionary processes, resulting in reduced genetic diversity and relaxed selective constraint across the genome. In the genus Stegodyphus, permanent sociality and regular inbreeding has evolved independently three times from periodic-social (outcrossing ancestors. This genus is therefore an ideal model for comparative studies of the molecular evolutionary and population genetic consequences of the transition to a regularly inbreeding mating system. However, no genetic resources are available for this genus. Results We present the analysis of high throughput transcriptome sequencing of three Stegodyphus species. Two of these are periodic-social (Stegodyphus lineatus and S.tentoriicola and one is permanently social (S. mimosarum. From non-normalized cDNA libraries, we obtained on average 7,000 putative uni-genes for each species. Three-way orthology, as predicted from reciprocal BLAST, identified 1,792 genes that could be used for cross-species comparison. Open reading frames (ORFs could be deduced from 1,345 of the three-way alignments. Preliminary molecular analyses suggest a five- to ten-fold reduction in heterozygosity in the social S. mimosarum compared with the periodic-social species. Furthermore, an increased ratio of non-synonymous to synonymous polymorphisms in the social species indicated relaxed efficiency of selection. However, there was no sign of relaxed selection on the phylogenetic branch leading to S. mimosarum. Conclusions The 1,792 three-way ortholog genes identified in this study provide

  18. Yeast Gis2 and its human ortholog CNBP are novel components of stress-induced RNP granules.

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    Marta Rojas

    Full Text Available Although a CCTG expansion in the gene encoding the zinc knuckle protein CNBP causes a common form of muscular dystrophy, the function of both human CNBP and its putative budding yeast ortholog Gis2 remain poorly understood. Here we report the protein interactions of Gis2 and the subcellular locations of both Gis2 and CNBP. We found that Gis2 exhibits RNA-dependent interactions with two proteins involved in mRNA recognition, the poly(A binding protein and the translation initiation factor eIF4G. We show that Gis2 is a component of two large RNA-protein granules, processing bodies and stress granules, which contain translationally repressed mRNAs. Consistent with a functional ortholog, CNBP also associates with the poly(A binding protein and accumulates in stress granules during arsenite treatment of human cells. These results implicate both Gis2 and CNBP in mRNA handling during stress.

  19. Construction and analysis of tag single nucleotide polymorphism maps for six human-mouse orthologous candidate genes in type 1 diabetes

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    Savage David A

    2005-02-01

    Full Text Available Abstract Background One strategy to help identify susceptibility genes for complex, multifactorial diseases is to map disease loci in a representative animal model of the disorder. The nonobese diabetic (NOD mouse is a model for human type 1 diabetes. Linkage and congenic strain analyses have identified several NOD mouse Idd (insulin dependent diabetes loci, which have been mapped to small chromosome intervals, for which the orthologous regions in the human genome can be identified. Here, we have conducted re-sequencing and association analysis of six orthologous genes identified in NOD Idd loci: NRAMP1/SLC11A1 (orthologous to Nramp1/Slc11a1 in Idd5.2, FRAP1 (orthologous to Frap1 in Idd9.2, 4-1BB/CD137/TNFRSF9 (orthologous to 4-1bb/Cd137/Tnrfrsf9 in Idd9.3, CD101/IGSF2 (orthologous to Cd101/Igsf2 in Idd10, B2M (orthologous to B2m in Idd13 and VAV3 (orthologous to Vav3 in Idd18. Results Re-sequencing of a total of 110 kb of DNA from 32 or 96 type 1 diabetes cases yielded 220 single nucleotide polymorphisms (SNPs. Sixty-five SNPs, including 54 informative tag SNPs, and a microsatellite were selected and genotyped in up to 1,632 type 1 diabetes families and 1,709 cases and 1,829 controls. Conclusion None of the candidate regions showed evidence of association with type 1 diabetes (P values > 0.2, indicating that common variation in these key candidate genes does not play a major role in type 1 diabetes susceptibility in the European ancestry populations studied.

  20. Hot spots in cold adaptation: Localized increases in conformational flexibility in lactate dehydrogenase A4 orthologs of Antarctic notothenioid fishes

    OpenAIRE

    Fields, Peter A.; Somero, George N.

    1998-01-01

    To elucidate mechanisms of enzymatic adaptation to extreme cold, we determined kinetic properties, thermal stabilities, and deduced amino acid sequences of lactate dehydrogenase A4 (A4-LDH) from nine Antarctic (−1.86 to 1°C) and three South American (4 to 10°C) notothenioid teleosts. Higher Michaelis–Menten constants (Km) and catalytic rate constants (kcat) distinguish orthologs of Antarctic from those of South American species, but no relationship exists between adaptation temperature and th...

  1. Trappin ovine molecule (TOM), the ovine ortholog of elafin, is an acute phase reactant in the lung

    OpenAIRE

    Brown, Thomas I; Mistry, Rohit; Collie, D David; Tate, Steven; Sallenave, Jean-Michel

    2004-01-01

    As large animal models continue to play an important role in translating lung-directed therapeutic strategies from laboratory animals to humans, there is an increasing interest in the analysis of endogenous regulators of inflammation at both a genomic and a therapeutic level. To this end, we have sought to characterize the ovine ortholog of elafin, an important regulator of inflammation in humans. We have isolated both the elafin cDNA and gene, which have a similar structure to other species'...

  2. Identification and characterization of orthologs of AtNHX5 and AtNHX6 in Brassica napus

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    Brett Andrew Ford

    2012-09-01

    Full Text Available Improving crop species by breeding for salt tolerance or introducing salt tolerant traits is one method of increasing crop yields in saline affected areas. The model plant species Arabidopsis thaliana has been extensively studied and there is substantial information available about the function and importance of many genes and proteins involved in salt tolerance. The identification and characterization of A. thaliana orthologs in species such as Brassica napus (oilseed rape can prove difficult due to the significant genomic changes that have occurred since their divergence approximately 20 million years ago. The recently released B. rapa genome provides an excellent resource for comparative studies of Arabidopsis and the cultivated Brassica species, and facilitates the identification of Brassica species orthologs which may be of agronomic importance. Sodium hydrogen antiporter (NHX proteins transport a sodium or potassium ion in exchange for a hydrogen ion in the other direction across a membrane. In A. thaliana there are eight members of the NHX family designated AtNHX1-8 that can be sub-divided into three clades (plasma membrane (PM, intracellular class I (IC-I and intracellular class II (IC-II based on their subcellular localization. In plants, many NHX proteins are primary determinants of salt tolerance and act by transporting Na+ out of the cytosol where it would otherwise accumulate to toxic levels. Significant work has been done analyzing both PM and IC-I clade members role in salt tolerance in a variety of plant species but relatively little analysis has been described for the IC-II clade. Here we describe the identification of B. napus orthologs of AtNHX5 and AtNHX6, using the Brassica rapa genome sequence, macro- and micro-synteny analysis, comparative expression and promoter motif analysis, and highlight the value of these multiple approaches for identifying true orthologs in closely related species with multiple paralogs.

  3. Trappin ovine molecule (TOM), the ovine ortholog of elafin, is an acute phase reactant in the lung.

    Science.gov (United States)

    Brown, Thomas I; Mistry, Rohit; Collie, D David; Tate, Steven; Sallenave, Jean-Michel

    2004-09-16

    As large animal models continue to play an important role in translating lung-directed therapeutic strategies from laboratory animals to humans, there is an increasing interest in the analysis of endogenous regulators of inflammation at both a genomic and a therapeutic level. To this end, we have sought to characterize the ovine ortholog of elafin, an important regulator of inflammation in humans. We have isolated both the elafin cDNA and gene, which have a similar structure to other species' orthologs. Interestingly, we have isolated two alleles for ovine elafin, which contain a very high number of transglutamination repeats, thought to be important in binding elafin to the interstitium. The mainly mucosal mRNA distribution for ovine elafin suggests that ovine elafin may, like its human ortholog, have functions in innate immunity. This is supported by analysis of elafin and the related protein secretory leukocyte protease inhibitor (SLPI) in ovine bronchoalveolar fluid in response to locally administered lipopolysaccharide and confirmation of them acting as "alarm" antiproteases. We have also cloned the ovine elafin cDNA into an adenoviral vector and have demonstrated correct processing of the secreted protein as well as biological activity. Overexpression of ovine elafin in a lung-derived epithelial cell line has a protective effect against the enzymes human neutrophil and porcine pancreatic elastase. The identification of the ovine elafin gene and its translated protein are important in developing practical strategies aimed at regulating inflammation in the large mammalian lung. PMID:15292488

  4. Inhibition of Aβ42 oligomerization in yeast by a PICALM ortholog and certain FDA approved drugs

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    Sei-Kyoung Park

    2016-01-01

    Full Text Available The formation of small Aβ42 oligomers has been implicated as a toxic species in Alzheimer disease (AD. In strong support of this hypothesis we found that overexpression of Yap1802, the yeast ortholog of the human AD risk factor, phosphatidylinositol binding clathrin assembly protein (PICALM, reduced oligomerization of Aβ42 fused to a reporter in yeast. Thus we used the Aβ42-reporter system to identify drugs that could be developed into therapies that prevent or arrest AD. From a screen of 1,200 FDA approved drugs and drug-like small compounds we identified 7 drugs that reduce Aβ42 oligomerization in yeast: 3 antipsychotics (bromperidol, haloperidol and azaperone, 2 anesthetics (pramoxine HCl and dyclonine HCl, tamoxifen citrate, and minocycline HCl. Also, all 7 drugs caused Aβ42 to be less toxic to PC12 cells and to relieve toxicity of another yeast AD model in which Aβ42 aggregates targeted to the secretory pathway are toxic. Our results identify drugs that inhibit Aβ42 oligomers from forming in yeast. It remains to be determined if these drugs inhibit Aβ42 oligomerization in mammals and could be developed as a therapeutic treatment for AD.

  5. Identification of novel human damage response proteins targeted through yeast orthology.

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    J Peter Svensson

    Full Text Available Studies in Saccharomyces cerevisiae show that many proteins influence cellular survival upon exposure to DNA damaging agents. We hypothesized that human orthologs of these S. cerevisiae proteins would also be required for cellular survival after treatment with DNA damaging agents. For this purpose, human homologs of S. cerevisiae proteins were identified and mapped onto the human protein-protein interaction network. The resulting human network was highly modular and a series of selection rules were implemented to identify 45 candidates for human toxicity-modulating proteins. The corresponding transcripts were targeted by RNA interference in human cells. The cell lines with depleted target expression were challenged with three DNA damaging agents: the alkylating agents MMS and 4-NQO, and the oxidizing agent t-BuOOH. A comparison of the survival revealed that the majority (74% of proteins conferred either sensitivity or resistance. The identified human toxicity-modulating proteins represent a variety of biological functions: autophagy, chromatin modifications, RNA and protein metabolism, and telomere maintenance. Further studies revealed that MMS-induced autophagy increase the survival of cells treated with DNA damaging agents. In summary, we show that damage recovery proteins in humans can be identified through homology to S. cerevisiae and that many of the same pathways are represented among the toxicity modulators.

  6. Deletion of Serpina1a, a murine α1-antitrypsin ortholog, results in embryonic lethality.

    Science.gov (United States)

    Wang, Dongmei; Wang, Weimin; Dawkins, Paul; Paterson, Trevor; Kalsheker, Noor; Sallenave, Jean-Michel; Houghton, A McGarry

    2011-06-01

    Chronic obstructive pulmonary disease (COPD) is the fourth leading cause of death in the United States Approximately 1% to 2% of COPD patients suffer from α(1)-antitrypsin (A1AT) deficiency, the major inheritable predisposition to COPD/emphysema. To further study the role of A1AT deficiency in the pathogenesis of COPD/emphysema, the authors attempted to generate null-mutant mice for Serpina1a, 1 of 2 A1AT orthologs in mice. Here the authors show that targeted deletion of Serpina1a results in embryonic lethality prior to 8.5 days post conception (dpc). The results are surprising given that A1AT-null humans exist and therefore do not require this gene product for normal development. The Serpina1 gene cluster is substantially different between mouse and man. Through gene duplication, mice have 3 to 5 (depending on the strain) highly homologous proteinase inhibiting (Pi) genes, 2 of which inhibit neutrophil elastase. Despite the abundance of Pi genes in mice, Serpina1a serves a critical, nonredundant function during early mouse development. A1AT-deficient mice have been highly sought after to study emphysema, cancer, and liver disease, and as a model to perfect gene replacement therapy. These results highlight important differences between human and murine serpins and point to the difficulty inherent to using gene-targeted mice to study this common human genetic disease. PMID:21574874

  7. Monitoring autophagic flux using Ref(2)P, the Drosophila p62 ortholog.

    Science.gov (United States)

    DeVorkin, Lindsay; Gorski, Sharon M

    2014-09-02

    Human p62, also known as Sequestome-1 (SQSTM1), is a multifunctional scaffold protein that contains many domains, including a Phox/Bem1P (PB1) multimerization domain, an ubiquitin-associated (UBA) domain, and a light chain 3 (LC3) recognition sequence. p62 binds ubiquitinated proteins and targets them for degradation by the proteasome. In addition, p62 directly binds LC3; this may serve as a mechanism to deliver ubiquitinated proteins for degradation by autophagy. During this process, p62 itself is degraded. The inhibition of autophagy leads to the accumulation of p62, indicating that it can be used as a marker of autophagic flux. Ref(2)P (refractory to sigma P), the Drosophila ortholog of p62, is also required for the formation of ubiquitinated protein aggregates. Ref(2)P contains a putative LC3-interacting region, and genetic inhibition of autophagy in Drosophila leads to the accumulation of Ref(2)P protein levels. Thus, like p62, Ref(2)P may serve as a marker of autophagic flux. Here we provide two procedures to examine Ref(2)P protein levels in Drosophila ovaries.

  8. No Distinction of Orthology/Paralogy between Human and Chimpanzee Rh Blood Group Genes.

    Science.gov (United States)

    Kitano, Takashi; Kim, Choong-Gon; Blancher, Antoine; Saitou, Naruya

    2016-03-01

    On human (Homo sapiens) chromosome 1, there is a tandem duplication encompassing Rh blood group genes (Hosa_RHD and Hosa_RHCE). This duplication occurred in the common ancestor of humans, chimpanzees (Pan troglodytes), and gorillas, after splitting from their common ancestor with orangutans. Although several studies have been conducted on ape Rh blood group genes, the clear genome structures of the gene clusters remain unknown. Here, we determined the genome structure of the gene cluster of chimpanzee Rh genes by sequencing five BAC (Bacterial Artificial Chromosome) clones derived from chimpanzees. We characterized three complete loci (Patr_RHα, Patr_RHβ, and Patr_RHγ). In the Patr_RHβ locus, a short version of the gene, which lacked the middle part containing exons 4-8, was observed. The Patr_RHα and Patr_RHβ genes were located on the locations corresponding to Hosa_RHD and Hosa_RHCE, respectively, and Patr_RHγ was in the immediate vicinity of Patr_RHβ. Sequence comparisons revealed high sequence similarity between Patr_RHβ and Hosa_RHCE, while the chimpanzee Rh gene closest to Hosa_RHD was not Patr_RHα but rather Patr_RHγ. The results suggest that rearrangements and gene conversions frequently occurred between these genes and that the classic orthology/paralogy dichotomy no longer holds between human and chimpanzee Rh blood group genes. PMID:26872772

  9. Identification and functional characterization of the AGO1 ortholog in maize.

    Science.gov (United States)

    Xu, Dongdong; Yang, Hailong; Zou, Cheng; Li, Wen-Xue; Xu, Yunbi; Xie, Chuanxiao

    2016-08-01

    Eukaryotic Argonaute proteins play primary roles in miRNA and siRNA pathways that are essential for numerous developmental and biological processes. However, the functional roles of the four ZmAGO1 genes have not yet been characterized in maize (Zea mays L.). In the present study, ZmAGO1a was identified from four putative ZmAGO1 genes for further characterization. Complementation of the Arabidopsis ago1-27 mutant with ZmAGO1a indicated that constitutive overexpression of ZmAGO1a could restore the smaller rosette, serrated leaves, later flowering and maturation, lower seed set, and darker green leaves at late stages of the mutant to the wild-type phenotype. The expression profiles of ZmAGO1a under five different abiotic stresses indicated that ZmAGO1a shares expression patterns similar to those of Argonaute genes in rice, Arabidopsis, and wheat. Further, variation in ZmAGO1a alleles among diverse maize germplasm that resulted in several amino acid changes revealed genetic diversity at this locus. The present data suggest that ZmAGO1a might be an important AGO1 ortholog in maize. The results presented provide further insight into the function of ZmAGO1a. PMID:26848539

  10. Behavioral analysis of the huntingtin-associated protein 1 ortholog trak-1 in Caenorhabditis elegans.

    Science.gov (United States)

    Norflus, Fran; Bu, Jingnan; Guyton, Evon; Gutekunst, Claire-Anne

    2016-09-01

    The precise role of huntingtin-associated protein 1 (HAP1) is not known, but studies have shown that it is important for early development and survival. A Caenorhabditis elegans ortholog of HAP1, T27A3.1 (also called trak-1), has been found and is expressed in a subset of neurons. Potential behavioral functions of three knockout lines of T27A3.1 were examined. From its suspected role in mice we hypothesize that T27A3.1 might be involved in egg hatching and early growth, mechanosensation, chemosensation, sensitivity to osmolarity, and synaptic transmission. Our studies show that the knockout worms are significantly different from the wild-type (WT) worms only in the synaptic transmission test, which was measured by adding aldicarb, an acetylcholinesterase inhibitor. The change in function was determined by measuring the number of worms paralyzed. However, when the T27A3.1 worms were tested for egg hatching and early growth, mechanosensation, chemosensation, and sensitivity to osmolarity, there were no significant differences between the knockout and WT worms. © 2016 Wiley Periodicals, Inc. PMID:27319755

  11. Inference of gene-phenotype associations via protein-protein interaction and orthology.

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    Panwen Wang

    Full Text Available One of the fundamental goals of genetics is to understand gene functions and their associated phenotypes. To achieve this goal, in this study we developed a computational algorithm that uses orthology and protein-protein interaction information to infer gene-phenotype associations for multiple species. Furthermore, we developed a web server that provides genome-wide phenotype inference for six species: fly, human, mouse, worm, yeast, and zebrafish. We evaluated our inference method by comparing the inferred results with known gene-phenotype associations. The high Area Under the Curve values suggest a significant performance of our method. By applying our method to two human representative diseases, Type 2 Diabetes and Breast Cancer, we demonstrated that our method is able to identify related Gene Ontology terms and Kyoto Encyclopedia of Genes and Genomes pathways. The web server can be used to infer functions and putative phenotypes of a gene along with the candidate genes of a phenotype, and thus aids in disease candidate gene discovery. Our web server is available at http://jjwanglab.org/PhenoPPIOrth.

  12. A Leishmania Ortholog of Macrophage Migration Inhibitory Factor Modulates Host Macrophage Responses

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    Kamir,D.; Zierow, S.; Leng, L.; Cho, Y.; Diaz, Y.; Griffith, J.; McDonald, C.; Merk, M.; Mitchell, R.; et al

    2008-01-01

    Parasitic organisms have evolved specialized strategies to evade immune defense mechanisms. We describe herein an ortholog of the cytokine, macrophage migration inhibitory factor (MIF), which is produced by the obligate intracellular parasite, Leishmania major. The Leishmania MIF protein, Lm1740MIF, shows significant structural homology with human MIF as revealed by a high-resolution x-ray crystal structure (1.03 A). Differences between the two proteins in the N-terminal tautomerization site are evident, and we provide evidence for the selective, species-specific inhibition of MIF by small-molecule antagonists that target this site. Lm1740MIF shows significant binding interaction with the MIF receptor, CD74 (K(d) = 2.9 x 10(-8) M). Like its mammalian counterpart, Lm1740MIF induces ERK1/2 MAP kinase activation in a CD74-dependent manner and inhibits the activation-induced apoptosis of macrophages. The ability of Lm1740MIF to inhibit apoptosis may facilitate the persistence of Leishmania within the macrophage and contribute to its evasion from immune destruction.

  13. Computational Identification of the Paralogs and Orthologs of Human Cytochrome P450 Superfamily and the Implication in Drug Discovery

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    Shu-Ting Pan

    2016-06-01

    Full Text Available The human cytochrome P450 (CYP superfamily consisting of 57 functional genes is the most important group of Phase I drug metabolizing enzymes that oxidize a large number of xenobiotics and endogenous compounds, including therapeutic drugs and environmental toxicants. The CYP superfamily has been shown to expand itself through gene duplication, and some of them become pseudogenes due to gene mutations. Orthologs and paralogs are homologous genes resulting from speciation or duplication, respectively. To explore the evolutionary and functional relationships of human CYPs, we conducted this bioinformatic study to identify their corresponding paralogs, homologs, and orthologs. The functional implications and implications in drug discovery and evolutionary biology were then discussed. GeneCards and Ensembl were used to identify the paralogs of human CYPs. We have used a panel of online databases to identify the orthologs of human CYP genes: NCBI, Ensembl Compara, GeneCards, OMA (“Orthologous MAtrix” Browser, PATHER, TreeFam, EggNOG, and Roundup. The results show that each human CYP has various numbers of paralogs and orthologs using GeneCards and Ensembl. For example, the paralogs of CYP2A6 include CYP2A7, 2A13, 2B6, 2C8, 2C9, 2C18, 2C19, 2D6, 2E1, 2F1, 2J2, 2R1, 2S1, 2U1, and 2W1; CYP11A1 has 6 paralogs including CYP11B1, 11B2, 24A1, 27A1, 27B1, and 27C1; CYP51A1 has only three paralogs: CYP26A1, 26B1, and 26C1; while CYP20A1 has no paralog. The majority of human CYPs are well conserved from plants, amphibians, fishes, or mammals to humans due to their important functions in physiology and xenobiotic disposition. The data from different approaches are also cross-validated and validated when experimental data are available. These findings facilitate our understanding of the evolutionary relationships and functional implications of the human CYP superfamily in drug discovery.

  14. Gene cloning, expression and characterization of avian cathelicidin orthologs, Cc-CATHs, from Coturnix coturnix.

    Science.gov (United States)

    Feng, Feifei; Chen, Chen; Zhu, Wenjuan; He, Weiyu; Guang, Huijuan; Li, Zheng; Wang, Duo; Liu, Jingze; Chen, Ming; Wang, Yipeng; Yu, Haining

    2011-05-01

    Cathelicidins comprise a family of antimicrobial peptides sharing a highly conserved cathelin domain, which play a central role in the early innate host defense against infection. In the present study, we report three novel avian cathelicidin orthologs cloned from a constructed spleen cDNA library of Coturnix coturnix, using a nested-PCR-based cloning strategy. Three coding sequences containing ORFs of 447, 465 and 456 bp encode three mature antimicrobial peptides (named Cc-CATH1, 2 and 3) of 26, 32 and 29 amino acid residues, respectively. Phylogenetic analysis indicated that precursors of Cc-CATHs are significantly conserved with known avian cathelicidins. Synthetic Cc-CATH2 and 3 displayed broad and potent antimicrobial activity against most of the 41 strains of bacteria and fungi tested, especially the clinically isolated drug-resistant strains, with minimum inhibitory concentration values in the range 0.3-2.5 μm for most strains with or without the presence of 100 mm NaCl. Cc-CATH2 and 3 showed considerable reduction of cytotoxic activity compared to other avian cathelicidins, with average IC(50) values of 20.18 and 17.16 μm, respectively. They also exerted a negligible hemolytic activity against human erythrocytes, lysing only 3.6% of erythrocytes at a dose up to 100 μg·mL(-1) . As expected, the recombinant Cc-CATH2 (rCc-CATH2) also showed potent bactericidal activity. All these features of Cc-CATHs encourage further studies aiming to estimate their therapeutic potential as drug leads, as well as coping with current widespread antibiotic resistance, especially the new prevalent and dangerous 'superbug' that is resistant to almost all antibiotics. PMID:21375690

  15. Cloning of zebrafish Mustn1 orthologs and their expression during early development.

    Science.gov (United States)

    Camarata, Troy; Vasilyev, Aleksandr; Hadjiargyrou, Michael

    2016-11-15

    Mustn1 is a small nuclear protein that is involved in the development and regeneration of the musculoskeletal system. Previous work established a role for Mustn1 in myogenic and chondrogenic differentiation. In addition, recent evidence suggests a potential role for Mustn1 in cilia function in zebrafish. A detailed study of Mustn1 expression has yet to be conducted in zebrafish. As such, we report herein the cloning of the zebrafish Mustn1 orthologs, mustn1a and mustn1b, and their expression during zebrafish embryonic and larval development. Results indicate a 44% nucleotide identity between the two paralogs. Phylogenetic analysis further confirmed that the Mustn1a and 1b predicted proteins were highly related to other vertebrate members of the Mustn1 protein family. Whole mount in situ hybridization revealed expression of both mustn1a and 1b at the 7-somite stage through 72hpf in structures such as Kupffer's vesicle, segmental mesoderm, head structures, and otic vesicle. Additionally, in 5day old larva, mustn1a and 1b expression is detected in the neurocranium, otic capsule, and the gut. Although both were expressed in the neurocranium, mustn1a was localized in the hypophyseal fenestra whereas mustn1b was found near the posterior basicapsular commissure. mustn1b also displayed expression in the ceratohyal and ceratobranchial elements of the pharyngeal skeleton. These expression patterns were verified temporally by q-PCR analysis. Taken together, we conclude that Mustn1 expression is conserved in vertebrates and that the variations in expression of the two zebrafish paralogs suggest different modes of molecular regulation. PMID:27565701

  16. The complexity of vesicle transport factors in plants examined by orthology search.

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    Puneet Paul

    Full Text Available Vesicle transport is a central process to ensure protein and lipid distribution in eukaryotic cells. The current knowledge on the molecular components and mechanisms of this process is majorly based on studies in Saccharomyces cerevisiae and Arabidopsis thaliana, which revealed 240 different proteinaceous factors either experimentally proven or predicted to be involved in vesicle transport. In here, we performed an orthologue search using two different algorithms to identify the components of the secretory pathway in yeast and 14 plant genomes by using the 'core-set' of 240 factors as bait. We identified 4021 orthologues and (co-orthologues in the discussed plant species accounting for components of COP-II, COP-I, Clathrin Coated Vesicles, Retromers and ESCRTs, Rab GTPases, Tethering factors and SNAREs. In plants, we observed a significantly higher number of (co-orthologues than yeast, while only 8 tethering factors from yeast seem to be absent in the analyzed plant genomes. To link the identified (co-orthologues to vesicle transport, the domain architecture of the proteins from yeast, genetic model plant A. thaliana and agriculturally relevant crop Solanum lycopersicum has been inspected. For the orthologous groups containing (co-orthologues from yeast, A. thaliana and S. lycopersicum, we observed the same domain architecture for 79% (416/527 of the (co-orthologues, which documents a very high conservation of this process. Further, publically available tissue-specific expression profiles for a subset of (co-orthologues found in A. thaliana and S. lycopersicum suggest that some (co-orthologues are involved in tissue-specific functions. Inspection of localization of the (co-orthologues based on available proteome data or localization predictions lead to the assignment of plastid- as well as mitochondrial localized (co-orthologues of vesicle transport factors and the relevance of this is discussed.

  17. Subtractive hybridization identifies chick-cripto, a novel EGF-CFC ortholog expressed during gastrulation, neurulation and early cardiogenesis.

    Science.gov (United States)

    Colas, J F; Schoenwolf, G C

    2000-09-19

    EGF-CFC genes encode a novel class of extracellular, membrane-associated proteins that notably play an important role during vertebrate gastrulation. Whereas the two cysteine-rich domains that characterize these proteins, namely the extracellular EGF-like and the CFC domain, are known to be encoded by two evolutionarily conserved exons, it is generally assumed, based on weak primary sequence identity, that the remaining parts of the protein differ among vertebrates, suggesting that known members of the EGF-CFC family do not represent true orthologs. Here, by characterizing the full cDNA and genomic sequences of a new EGF-CFC gene in chick, and by comparing them with their counterparts in human (CRIPTO), mouse (cripto and cryptic), Xenopus (FRL-1) and zebrafish (one-eyed pinhead), we show that all EGF-CFC genes share an identical genomic organization over the entire coding region. Not only are the central two exons (coding for the EGF-like and CFC motifs) conserved, but also conserved are the total number of exons, their size, their intron phase and their correlation with discrete protein modules, in particular those modules that allow the EGF-CFC motif to become membrane-associated. Therefore, despite apparent divergence between their 5' and 3'-terminal exons, all known CRIPTO-related genes are structurally orthologous. We named this novel ortholog in bird, chick-cripto. We report the mRNA distribution of chick-cripto, which begins in the epiblast of the gastrula, with a pattern similar to EGF-CFC genes of other vertebrates.

  18. From zebrafish heart jogging genes to mouse and human orthologs: using Gene Ontology to investigate mammalian heart development.

    Science.gov (United States)

    Khodiyar, Varsha K; Howe, Doug; Talmud, Philippa J; Breckenridge, Ross; Lovering, Ruth C

    2013-01-01

    For the majority of organs in developing vertebrate embryos, left-right asymmetry is controlled by a ciliated region; the left-right organizer node in the mouse and human, and the Kuppfer's vesicle in the zebrafish. In the zebrafish, laterality cues from the Kuppfer's vesicle determine asymmetry in the developing heart, the direction of 'heart jogging' and the direction of 'heart looping'.  'Heart jogging' is the term given to the process by which the symmetrical zebrafish heart tube is displaced relative to the dorsal midline, with a leftward 'jog'. Heart jogging is not considered to occur in mammals, although a leftward shift of the developing mouse caudal heart does occur prior to looping, which may be analogous to zebrafish heart jogging. Previous studies have characterized 30 genes involved in zebrafish heart jogging, the majority of which have well defined orthologs in mouse and human and many of these orthologs have been associated with early mammalian heart development.    We undertook manual curation of a specific set of genes associated with heart development and we describe the use of Gene Ontology term enrichment analyses to examine the cellular processes associated with heart jogging.  We found that the human, mouse and zebrafish 'heart jogging orthologs' are involved in similar organ developmental processes across the three species, such as heart, kidney and nervous system development, as well as more specific cellular processes such as cilium development and function. The results of these analyses are consistent with a role for cilia in the determination of left-right asymmetry of many internal organs, in addition to their known role in zebrafish heart jogging.    This study highlights the importance of model organisms in the study of human heart development, and emphasises both the conservation and divergence of developmental processes across vertebrates, as well as the limitations of this approach. PMID:24627794

  19. Identification of Putative Ortholog Gene Blocks Involved in Gestant and Lactating Mammary Gland Development: A Rodent Cross-Species Microarray Transcriptomics Approach

    Science.gov (United States)

    Rodríguez-Cruz, Maricela; Coral-Vázquez, Ramón M.; Hernández-Stengele, Gabriel; Sánchez, Raúl; Salazar, Emmanuel; Sanchez-Muñoz, Fausto; Encarnación-Guevara, Sergio; Ramírez-Salcedo, Jorge

    2013-01-01

    The mammary gland (MG) undergoes functional and metabolic changes during the transition from pregnancy to lactation, possibly by regulation of conserved genes. The objective was to elucidate orthologous genes, chromosome clusters and putative conserved transcriptional modules during MG development. We analyzed expression of 22,000 transcripts using murine microarrays and RNA samples of MG from virgin, pregnant, and lactating rats by cross-species hybridization. We identified 521 transcripts differentially expressed; upregulated in early (78%) and midpregnancy (89%) and early lactation (64%), but downregulated in mid-lactation (61%). Putative orthologous genes were identified. We mapped the altered genes to orthologous chromosomal locations in human and mouse. Eighteen sets of conserved genes associated with key cellular functions were revealed and conserved transcription factor binding site search entailed possible coregulation among all eight block sets of genes. This study demonstrates that the use of heterologous array hybridization for screening of orthologous gene expression from rat revealed sets of conserved genes arranged in chromosomal order implicated in signaling pathways and functional ontology. Results demonstrate the utilization power of comparative genomics and prove the feasibility of using rodent microarrays to identification of putative coexpressed orthologous genes involved in the control of human mammary gland development. PMID:24288657

  20. Identifying the activation motif in the N-terminal of rainbow trout and zebrafish melanocortin-2 receptor accessory protein 1 (MRAP1) orthologs.

    Science.gov (United States)

    Dores, Robert M; Liang, Liang; Hollmann, Rebecca E; Sandhu, Navdeep; Vijayan, Mathilakath M

    2016-08-01

    The activation of mammalian melanocortin-2 receptor (MC2R) orthologs is dependent on a four-amino acid activation motif (LDYL/I) located in the N-terminal of mammalian MRAP1 (melanocortin-2 receptor accessory protein). Previous alanine substitution analysis had shown that the Y residue in this motif appears to be the most important for mediating the activation of mammalian MC2R orthologs. Similar, but not identical amino acid motifs were detected in rainbow trout MRAP1 (YDYL) and zebrafish MRAP1 (YDYV). To determine the importance of these residues in the putative activation motifs, rainbow trout and zebrafish MRAP1 orthologs were individually co-expressed in CHO cells with rainbow trout MC2R, and the activation of this receptor with either the wild-type MRAP1 ortholog or alanine-substituted analogs of the two teleost MRAP1s was analyzed. Alanine substitutions at all four amino acid positions in rainbow trout MRAP1 blocked activation of the rainbow trout MC2R. Single alanine substitutions of the D and Y residues in rainbow trout and zebrafish MRAP1 indicate that these two residues play a significant role in the activation of rainbow trout MC2R. These observations indicate that there are subtle differences in the way that teleost and mammalian MRAPs are involved in the activation of their corresponding MC2R orthologs. PMID:26752246

  1. Comparative analysis of function and interaction of transcription factors in nematodes: Extensive conservation of orthology coupled to rapid sequence evolution

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    Singh Rama S

    2008-08-01

    Full Text Available Abstract Background Much of the morphological diversity in eukaryotes results from differential regulation of gene expression in which transcription factors (TFs play a central role. The nematode Caenorhabditis elegans is an established model organism for the study of the roles of TFs in controlling the spatiotemporal pattern of gene expression. Using the fully sequenced genomes of three Caenorhabditid nematode species as well as genome information from additional more distantly related organisms (fruit fly, mouse, and human we sought to identify orthologous TFs and characterized their patterns of evolution. Results We identified 988 TF genes in C. elegans, and inferred corresponding sets in C. briggsae and C. remanei, containing 995 and 1093 TF genes, respectively. Analysis of the three gene sets revealed 652 3-way reciprocal 'best hit' orthologs (nematode TF set, approximately half of which are zinc finger (ZF-C2H2 and ZF-C4/NHR types and HOX family members. Examination of the TF genes in C. elegans and C. briggsae identified the presence of significant tandem clustering on chromosome V, the majority of which belong to ZF-C4/NHR family. We also found evidence for lineage-specific duplications and rapid evolution of many of the TF genes in the two species. A search of the TFs conserved among nematodes in Drosophila melanogaster, Mus musculus and Homo sapiens revealed 150 reciprocal orthologs, many of which are associated with important biological processes and human diseases. Finally, a comparison of the sequence, gene interactions and function indicates that nematode TFs conserved across phyla exhibit significantly more interactions and are enriched in genes with annotated mutant phenotypes compared to those that lack orthologs in other species. Conclusion Our study represents the first comprehensive genome-wide analysis of TFs across three nematode species and other organisms. The findings indicate substantial conservation of transcription

  2. Identification and complete sequencing of novel human transcripts through the use of mouse orthologs and testis cDNA sequences

    DEFF Research Database (Denmark)

    Ferreira, Elisa N; Pires, Lilian C; Parmigiani, Raphael B;

    2004-01-01

    The correct identification of all human genes, and their derived transcripts, has not yet been achieved, and it remains one of the major aims of the worldwide genomics community. Computational programs suggest the existence of 30,000 to 40,000 human genes. However, definitive gene identification...... can only be achieved by experimental approaches. We used two distinct methodologies, one based on the alignment of mouse orthologous sequences to the human genome, and another based on the construction of a high-quality human testis cDNA library, in an attempt to identify new human transcripts within...

  3. Chemically engineering ligand selectivity at the free fatty acid receptor 2 based on pharmacological variation between species orthologs

    DEFF Research Database (Denmark)

    Hudson, Brian D; Christiansen, Elisabeth; Tikhonova, Irina G;

    2012-01-01

    When it is difficult to develop selective ligands within a family of related G-protein-coupled receptors (GPCRs), chemically engineered receptors activated solely by synthetic ligands (RASSLs) are useful alternatives for probing receptor function. In the present work, we explored whether a RASSL...... on this receptor and demonstrates that exploitation of pharmacological variation between species orthologs is a powerful method to generate novel chemically engineered GPCRs.-Hudson, B. D., Christiansen, E., Tikhonova, I. G., Grundmann, M., Kostenis, E., Adams, D. R., Ulven, T., Milligan, G. Chemically engineering...

  4. Systemic acquired resistance in soybean is regulated by two proteins, Orthologous to Arabidopsis NPR1

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    Sandhu Devinder

    2009-08-01

    Full Text Available Abstract Background Systemic acquired resistance (SAR is induced in non-inoculated leaves following infection with certain pathogenic strains. SAR is effective against many pathogens. Salicylic acid (SA is a signaling molecule of the SAR pathway. The development of SAR is associated with the induction of pathogenesis related (PR genes. Arabidopsis non-expressor of PR1 (NPR1 is a regulatory gene of the SA signal pathway 123. SAR in soybean was first reported following infection with Colletotrichum trancatum that causes anthracnose disease. We investigated if SAR in soybean is regulated by a pathway, similar to the one characterized in Arabidopsis. Results Pathogenesis-related gene GmPR1 is induced following treatment of soybean plants with the SAR inducer, 2,6-dichloroisonicotinic acid (INA or infection with the oomycete pathogen, Phytophthora sojae. In P. sojae-infected plants, SAR was induced against the bacterial pathogen, Pseudomonas syringae pv. glycinea. Soybean GmNPR1-1 and GmNPR1-2 genes showed high identities to Arabidopsis NPR1. They showed similar expression patterns among the organs, studied in this investigation. GmNPR1-1 and GmNPR1-2 are the only soybean homologues of NPR1and are located in homoeologous regions. In GmNPR1-1 and GmNPR1-2 transformed Arabidopsis npr1-1 mutant plants, SAR markers: (i PR-1 was induced following INA treatment and (ii BGL2 following infection with Pseudomonas syringae pv. tomato (Pst, and SAR was induced following Pst infection. Of the five cysteine residues, Cys82, Cys150, Cys155, Cys160, and Cys216 involved in oligomer-monomer transition in NPR1, Cys216 in GmNPR1-1 and GmNPR1-2 proteins was substituted to Ser and Leu, respectively. Conclusion Complementation analyses in Arabidopsis npr1-1 mutants revealed that homoeologous GmNPR1-1 and GmNPR1-2 genes are orthologous to Arabidopsis NPR1. Therefore, SAR pathway in soybean is most likely regulated by GmNPR1 genes. Substitution of Cys216 residue, essential

  5. A search of Brassica SI-involved orthologs in buckwheat leads to novel buckwheat sequence identification: MLPK possibly involved in SI response

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    Banović Bojana

    2010-01-01

    Full Text Available Self-incompatibility (SI systems, gamethophytic (GSI and sporophytic (SSI, prevent self-pollination in angiosperms. Buckwheat displays heteromorphic SSI, with pollination allowed only between different flower morphs - thrum and pin. The physiology of thrum and pin morph SI responses are entirely different, resembling homomorphic Brassica SSI and Prunus GSI responses, respectively. Considering angiosperm species may share ancestral SI genes, we examined the presence of Brassica and Prunus SI-involved gene orthologs in the buckwheat genome. We did not find evidence of SRK, SLG and SP11 Brassica or S-RNase and SFB Prunus orthologs in the buckwheat genome, but we found a Brassica MLPK ortholog. We report the partial nucleotide sequence of the buckwheat MLPK and discuss the possible implications of this finding.

  6. ATGC: a database of orthologous genes from closely related prokaryotic genomes and a research platform for microevolution of prokaryotes

    Energy Technology Data Exchange (ETDEWEB)

    Novichkov, Pavel S.; Ratnere, Igor; Wolf, Yuri I.; Koonin, Eugene V.; Dubchak, Inna

    2009-07-23

    The database of Alignable Tight Genomic Clusters (ATGCs) consists of closely related genomes of archaea and bacteria, and is a resource for research into prokaryotic microevolution. Construction of a data set with appropriate characteristics is a major hurdle for this type of studies. With the current rate of genome sequencing, it is difficult to follow the progress of the field and to determine which of the available genome sets meet the requirements of a given research project, in particular, with respect to the minimum and maximum levels of similarity between the included genomes. Additionally, extraction of specific content, such as genomic alignments or families of orthologs, from a selected set of genomes is a complicated and time-consuming process. The database addresses these problems by providing an intuitive and efficient web interface to browse precomputed ATGCs, select appropriate ones and access ATGC-derived data such as multiple alignments of orthologous proteins, matrices of pairwise intergenomic distances based on genome-wide analysis of synonymous and nonsynonymous substitution rates and others. The ATGC database will be regularly updated following new releases of the NCBI RefSeq. The database is hosted by the Genomics Division at Lawrence Berkeley National laboratory and is publicly available at http://atgc.lbl.gov.

  7. TaWRKY68 responses to biotic stresses are revealed by the orthologous genes from major cereals

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    Bo Ding

    2014-01-01

    Full Text Available WRKY transcription factors have been extensively characterized in the past 20 years, but in wheat, studies onWRKY genes and their function are lagging behind many other species. To explore the function of wheat WRKY genes, we identified a TaWRKY68 gene from a common wheat cultivar. It encodes a protein comprising 313 amino acids which harbors 19 conserved motifs or active sites. Gene expression patterns were determined by analyzing microarray data of TaWRKY68 in wheat and of orthologous genes from maize, rice and barley using Genevestigator. TaWRKY68 orthologs were identified and clustered using DELTA-BLAST and COBALT programs available at NCBI. The results showed that these genes, which are expressed in all tissues tested, had relatively higher levels in the roots and were up-regulated in response to biotic stresses. Bioinformatics results were confirmed by RT-PCR experiments using wheat plants infected by Agrobacterium tumefaciens and Blumeria graminis, or treated with Deoxynivalenol, a Fusarium graminearum-induced mycotoxin in wheat or barley. In summary,TaWRKY68 functions differ during plant developmental stages and might be representing a hub gene function in wheat responses to various biotic stresses. It was also found that including data from major cereal genes in the bioinformatics analysis gave more accurate and comprehensive predictions of wheat gene functions.

  8. ANCAC: amino acid, nucleotide, and codon analysis of COGs – a tool for sequence bias analysis in microbial orthologs

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    Meiler Arno

    2012-09-01

    Full Text Available Abstract Background The COG database is the most popular collection of orthologous proteins from many different completely sequenced microbial genomes. Per definition, a cluster of orthologous groups (COG within this database exclusively contains proteins that most likely achieve the same cellular function. Recently, the COG database was extended by assigning to every protein both the corresponding amino acid and its encoding nucleotide sequence resulting in the NUCOCOG database. This extended version of the COG database is a valuable resource connecting sequence features with the functionality of the respective proteins. Results Here we present ANCAC, a web tool and MySQL database for the analysis of amino acid, nucleotide, and codon frequencies in COGs on the basis of freely definable phylogenetic patterns. We demonstrate the usefulness of ANCAC by analyzing amino acid frequencies, codon usage, and GC-content in a species- or function-specific context. With respect to amino acids we, at least in part, confirm the cognate bias hypothesis by using ANCAC’s NUCOCOG dataset as the largest one available for that purpose thus far. Conclusions Using the NUCOCOG datasets, ANCAC connects taxonomic, amino acid, and nucleotide sequence information with the functional classification via COGs and provides a GUI for flexible mining for sequence-bias. Thereby, to our knowledge, it is the only tool for the analysis of sequence composition in the light of physiological roles and phylogenetic context without requirement of substantial programming-skills.

  9. Orthologs of Human Disease Associated Genes and RNAi Analysis of Silencing Insulin Receptor Gene in Bombyx mori

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    Zan Zhang

    2014-10-01

    Full Text Available The silkworm, Bombyx mori L., is an important economic insect that has been domesticated for thousands of years to produce silk. It is our great interest to investigate the possibility of developing the B. mori as human disease model. We searched the orthologs of human disease associated genes in the B. mori by bi-directional best hits of BLAST and confirmed by searching the OrthoDB. In total, 5006 genes corresponding to 1612 kinds of human diseases had orthologs in the B. mori, among which, there are 25 genes associated with diabetes mellitus. Of these, we selected the insulin receptor gene of the B. mori (Bm-INSR to study its expression in different tissues and at different developmental stages and tissues. Quantitative PCR showed that Bm-INSR was highly expressed in the Malpighian tubules but expressed at low levels in the testis. It was highly expressed in the 3rd and 4th instar larvae, and adult. We knocked down Bm-INSR expression using RNA interference. The abundance of Bm-INSR transcripts were dramatically reduced to ~4% of the control level at 6 days after dsRNA injection and the RNAi-treated B. mori individuals showed apparent growth inhibition and malformation such as abnormal body color in black, which is the typical symptom of diabetic patients. Our results demonstrate that B. mori has potential use as an animal model for diabetic mellitus research.

  10. Frequent and recent retrotransposition of orthologous genes plays a role in the evolution of sperm glycolytic enzymes

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    de Villena Fernando

    2010-05-01

    Full Text Available Abstract Background The central metabolic pathway of glycolysis converts glucose to pyruvate, with the net production of 2 ATP and 2 NADH per glucose molecule. Each of the ten reactions in this pathway is typically catalyzed by multiple isozymes encoded by a multigene family. Several isozymes in this pathway are expressed only during spermatogenesis, and gene targeting studies indicate that they are essential for sperm function and male fertility in mouse. At least three of the novel glycolytic isozymes are encoded by retrogenes (Pgk2, Aldoart1, and Aldoart2. Their restricted expression profile suggests that retrotransposition may play a significant role in the evolution of sperm glycolytic enzymes. Results We conducted a comprehensive genomic analysis of glycolytic enzymes in the human and mouse genomes and identified several intronless copies for all enzymes in the pathway, except Pfk. Within each gene family, a single orthologous gene was typically retrotransposed frequently and independently in both species. Several retroposed sequences maintained open reading frames (ORFs and/or provided evidence of alternatively spliced exons. We analyzed expression of sequences with ORFs and Gpi1 transcript in mouse spermatogenic cells. Conclusions Our analysis detected frequent, recent, and lineage-specific retrotransposition of orthologous glycolytic enzymes in the human and mouse genomes. Retrotransposition events are associated with LINE/LTR and genomic integration is random. We found evidence for the alternative splicing of parent genes. Many retroposed sequences have maintained ORFs, suggesting a functional role for these genes.

  11. Functional evolution of a multigene family: orthologous and paralogous pheromone receptor genes in the turnip moth, Agrotis segetum.

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    Dan-Dan Zhang

    Full Text Available Lepidopteran pheromone receptors (PRs, for which orthologies are evident among closely related species, provide an intriguing example of gene family evolution in terms of how new functions may arise. However, only a limited number of PRs have been functionally characterized so far and thus evolutionary scenarios suffer from elements of speculation. In this study we investigated the turnip moth Agrotis segetum, in which female moths produce a mixture of chemically related pheromone components that elicit specific responses from receptor cells on male antennae. We cloned nine A. segetum PR genes and the Orco gene by degenerate primer based RT-PCR. The nine PR genes, named as AsegOR1 and AsegOR3-10, fall into four distinct orthologous clusters of known lepidopteran PRs, of which one contains six paralogues. The paralogues are under relaxed selective pressure, contrasting with the purifying selection on other clusters. We identified the receptors AsegOR9, AsegOR4 and AsegOR5, specific for the respective homologous pheromone components (Z-5-decenyl, (Z-7-dodecenyl and (Z-9-tetradecenyl acetates, by two-electrode voltage clamp recording from Xenopus laevis oocytes co-expressing Orco and each PR candidate. These receptors occur in three different orthologous clusters. We also found that the six paralogues with high sequence similarity vary dramatically in ligand selectivity and sensitivity. Different from AsegOR9, AsegOR6 showed a relatively large response to the behavioural antagonist (Z-5-decenol, and a small response to (Z-5-decenyl acetate. AsegOR1 was broadly tuned, but most responsive to (Z-5-decenyl acetate, (Z-7-dodecenyl acetate and the behavioural antagonist (Z-8-dodecenyl acetate. AsegOR8 and AsegOR7, which differ from AsegOR6 and AsegOR1 by 7 and 10 aa respectively, showed much lower sensitivities. AsegOR10 showed only small responses to all the tested compounds. These results suggest that new receptors arise through gene duplication, and

  12. Loss-of-function mutations in the C9ORF72 mouse ortholog cause fatal autoimmune disease.

    Science.gov (United States)

    Burberry, Aaron; Suzuki, Naoki; Wang, Jin-Yuan; Moccia, Rob; Mordes, Daniel A; Stewart, Morag H; Suzuki-Uematsu, Satomi; Ghosh, Sulagna; Singh, Ajay; Merkle, Florian T; Koszka, Kathryn; Li, Quan-Zhen; Zon, Leonard; Rossi, Derrick J; Trowbridge, Jennifer J; Notarangelo, Luigi D; Eggan, Kevin

    2016-07-13

    C9ORF72 mutations are found in a significant fraction of patients suffering from amyotrophic lateral sclerosis and frontotemporal dementia, yet the function of the C9ORF72 gene product remains poorly understood. We show that mice harboring loss-of-function mutations in the ortholog of C9ORF72 develop splenomegaly, neutrophilia, thrombocytopenia, increased expression of inflammatory cytokines, and severe autoimmunity, ultimately leading to a high mortality rate. Transplantation of mutant mouse bone marrow into wild-type recipients was sufficient to recapitulate the phenotypes observed in the mutant animals, including autoimmunity and premature mortality. Reciprocally, transplantation of wild-type mouse bone marrow into mutant mice improved their phenotype. We conclude that C9ORF72 serves an important function within the hematopoietic system to restrict inflammation and the development of autoimmunity. PMID:27412785

  13. Critical role of the virus-encoded microRNA-155 ortholog in the induction of Marek's disease lymphomas.

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    Yuguang Zhao

    2011-02-01

    Full Text Available Notwithstanding the well-characterised roles of a number of oncogenes in neoplastic transformation, microRNAs (miRNAs are increasingly implicated in several human cancers. Discovery of miRNAs in several oncogenic herpesviruses such as KSHV has further highlighted the potential of virus-encoded miRNAs to contribute to their oncogenic capabilities. Nevertheless, despite the identification of several possible cancer-related genes as their targets, the direct in vivo role of virus-encoded miRNAs in neoplastic diseases such as those induced by KSHV is difficult to demonstrate in the absence of suitable models. However, excellent natural disease models of rapid-onset Marek's disease (MD lymphomas in chickens allow examination of the oncogenic potential of virus-encoded miRNAs. Using viruses modified by reverse genetics of the infectious BAC clone of the oncogenic RB-1B strain of MDV, we show that the deletion of the six-miRNA cluster 1 from the viral genome abolished the oncogenicity of the virus. This loss of oncogenicity appeared to be primarily due to the single miRNA within the cluster, miR-M4, the ortholog of cellular miR-155, since its deletion or a 2-nucleotide mutation within its seed region was sufficient to inhibit the induction of lymphomas. The definitive role of this miR-155 ortholog in oncogenicity was further confirmed by the rescue of oncogenic phenotype by revertant viruses that expressed either the miR-M4 or the cellular homolog gga-miR-155. This is the first demonstration of the direct in vivo role of a virus-encoded miRNA in inducing tumors in a natural infection model. Furthermore, the use of viruses deleted in miRNAs as effective vaccines against virulent MDV challenge, enables the prospects of generating genetically defined attenuated vaccines.

  14. A novel firmicute protein family related to the actinobacterial resuscitation-promoting factors by non-orthologous domain displacement

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    Finan Christopher L

    2005-03-01

    Full Text Available Abstract Background In Micrococcus luteus growth and resuscitation from starvation-induced dormancy is controlled by the production of a secreted growth factor. This autocrine resuscitation-promoting factor (Rpf is the founder member of a family of proteins found throughout and confined to the actinobacteria (high G + C Gram-positive bacteria. The aim of this work was to search for and characterise a cognate gene family in the firmicutes (low G + C Gram-positive bacteria and obtain information about how they may control bacterial growth and resuscitation. Results In silico analysis of the accessory domains of the Rpf proteins permitted their classification into several subfamilies. The RpfB subfamily is related to a group of firmicute proteins of unknown function, represented by YabE of Bacillus subtilis. The actinobacterial RpfB and firmicute YabE proteins have very similar domain structures and genomic contexts, except that in YabE, the actinobacterial Rpf domain is replaced by another domain, which we have called Sps. Although totally unrelated in both sequence and secondary structure, the Rpf and Sps domains fulfil the same function. We propose that these proteins have undergone "non-orthologous domain displacement", a phenomenon akin to "non-orthologous gene displacement" that has been described previously. Proteins containing the Sps domain are widely distributed throughout the firmicutes and they too fall into a number of distinct subfamilies. Comparative analysis of the accessory domains in the Rpf and Sps proteins, together with their weak similarity to lytic transglycosylases, provide clear evidence that they are muralytic enzymes. Conclusions The results indicate that the firmicute Sps proteins and the actinobacterial Rpf proteins are cognate and that they control bacterial culturability via enzymatic modification of the bacterial cell envelope.

  15. Predicting protein-protein interactions in Arabidopsis thaliana through integration of orthology, gene ontology and co-expression

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    Vandepoele Klaas

    2009-06-01

    Full Text Available Abstract Background Large-scale identification of the interrelationships between different components of the cell, such as the interactions between proteins, has recently gained great interest. However, unraveling large-scale protein-protein interaction maps is laborious and expensive. Moreover, assessing the reliability of the interactions can be cumbersome. Results In this study, we have developed a computational method that exploits the existing knowledge on protein-protein interactions in diverse species through orthologous relations on the one hand, and functional association data on the other hand to predict and filter protein-protein interactions in Arabidopsis thaliana. A highly reliable set of protein-protein interactions is predicted through this integrative approach making use of existing protein-protein interaction data from yeast, human, C. elegans and D. melanogaster. Localization, biological process, and co-expression data are used as powerful indicators for protein-protein interactions. The functional repertoire of the identified interactome reveals interactions between proteins functioning in well-conserved as well as plant-specific biological processes. We observe that although common mechanisms (e.g. actin polymerization and components (e.g. ARPs, actin-related proteins exist between different lineages, they are active in specific processes such as growth, cancer metastasis and trichome development in yeast, human and Arabidopsis, respectively. Conclusion We conclude that the integration of orthology with functional association data is adequate to predict protein-protein interactions. Through this approach, a high number of novel protein-protein interactions with diverse biological roles is discovered. Overall, we have predicted a reliable set of protein-protein interactions suitable for further computational as well as experimental analyses.

  16. Patterns of sequence divergence and evolution of the S orthologous regions between Asian and African cultivated rice species.

    Science.gov (United States)

    Guyot, Romain; Garavito, Andrea; Gavory, Frédérick; Samain, Sylvie; Tohme, Joe; Ghesquière, Alain; Lorieux, Mathias

    2011-01-01

    A strong postzygotic reproductive barrier separates the recently diverged Asian and African cultivated rice species, Oryza sativa and O. glaberrima. Recently a model of genetic incompatibilities between three adjacent loci: S(1)A, S(1) and S(1)B (called together the S(1) regions) interacting epistatically, was postulated to cause the allelic elimination of female gametes in interspecific hybrids. Two candidate factors for the S(1) locus (including a putative F-box gene) were proposed, but candidates for S(1)A and S(1)B remained undetermined. Here, to better understand the basis of the evolution of regions involved in reproductive isolation, we studied the genic and structural changes accumulated in the S(1) regions between orthologous sequences. First, we established an 813 kb genomic sequence in O. glaberrima, covering completely the S(1)A, S(1) and the majority of the S(1)B regions, and compared it with the orthologous regions of O. sativa. An overall strong structural conservation was observed, with the exception of three isolated regions of disturbed collinearity: (1) a local invasion of transposable elements around a putative F-box gene within S(1), (2) the multiple duplication and subsequent divergence of the same F-box gene within S(1)A, (3) an interspecific chromosomal inversion in S(1)B, which restricts recombination in our O. sativa×O. glaberrima crosses. Beside these few structural variations, a uniform conservative pattern of coding sequence divergence was found all along the S(1) regions. Hence, the S(1) regions have undergone no drastic variation in their recent divergence and evolution between O. sativa and O. glaberrima, suggesting that a small accumulation of genic changes, following a Bateson-Dobzhansky-Muller (BDM) model, might be involved in the establishment of the sterility barrier. In this context, genetic incompatibilities involving the duplicated F-box genes as putative candidates, and a possible strengthening step involving the

  17. Patterns of Sequence Divergence and Evolution of the S1 Orthologous Regions between Asian and African Cultivated Rice Species

    Science.gov (United States)

    Gavory, Frédérick; Samain, Sylvie; Tohme, Joe; Ghesquière, Alain; Lorieux, Mathias

    2011-01-01

    A strong postzygotic reproductive barrier separates the recently diverged Asian and African cultivated rice species, Oryza sativa and O. glaberrima. Recently a model of genetic incompatibilities between three adjacent loci: S1A, S1 and S1B (called together the S1 regions) interacting epistatically, was postulated to cause the allelic elimination of female gametes in interspecific hybrids. Two candidate factors for the S1 locus (including a putative F-box gene) were proposed, but candidates for S1A and S1B remained undetermined. Here, to better understand the basis of the evolution of regions involved in reproductive isolation, we studied the genic and structural changes accumulated in the S1 regions between orthologous sequences. First, we established an 813 kb genomic sequence in O. glaberrima, covering completely the S1A, S1 and the majority of the S1B regions, and compared it with the orthologous regions of O. sativa. An overall strong structural conservation was observed, with the exception of three isolated regions of disturbed collinearity: (1) a local invasion of transposable elements around a putative F-box gene within S1, (2) the multiple duplication and subsequent divergence of the same F-box gene within S1A, (3) an interspecific chromosomal inversion in S1B, which restricts recombination in our O. sativa×O. glaberrima crosses. Beside these few structural variations, a uniform conservative pattern of coding sequence divergence was found all along the S1 regions. Hence, the S1 regions have undergone no drastic variation in their recent divergence and evolution between O. sativa and O. glaberrima, suggesting that a small accumulation of genic changes, following a Bateson-Dobzhansky-Muller (BDM) model, might be involved in the establishment of the sterility barrier. In this context, genetic incompatibilities involving the duplicated F-box genes as putative candidates, and a possible strengthening step involving the chromosomal inversion might participate to

  18. Patterns of sequence divergence and evolution of the S orthologous regions between Asian and African cultivated rice species.

    Directory of Open Access Journals (Sweden)

    Romain Guyot

    Full Text Available A strong postzygotic reproductive barrier separates the recently diverged Asian and African cultivated rice species, Oryza sativa and O. glaberrima. Recently a model of genetic incompatibilities between three adjacent loci: S(1A, S(1 and S(1B (called together the S(1 regions interacting epistatically, was postulated to cause the allelic elimination of female gametes in interspecific hybrids. Two candidate factors for the S(1 locus (including a putative F-box gene were proposed, but candidates for S(1A and S(1B remained undetermined. Here, to better understand the basis of the evolution of regions involved in reproductive isolation, we studied the genic and structural changes accumulated in the S(1 regions between orthologous sequences. First, we established an 813 kb genomic sequence in O. glaberrima, covering completely the S(1A, S(1 and the majority of the S(1B regions, and compared it with the orthologous regions of O. sativa. An overall strong structural conservation was observed, with the exception of three isolated regions of disturbed collinearity: (1 a local invasion of transposable elements around a putative F-box gene within S(1, (2 the multiple duplication and subsequent divergence of the same F-box gene within S(1A, (3 an interspecific chromosomal inversion in S(1B, which restricts recombination in our O. sativa×O. glaberrima crosses. Beside these few structural variations, a uniform conservative pattern of coding sequence divergence was found all along the S(1 regions. Hence, the S(1 regions have undergone no drastic variation in their recent divergence and evolution between O. sativa and O. glaberrima, suggesting that a small accumulation of genic changes, following a Bateson-Dobzhansky-Muller (BDM model, might be involved in the establishment of the sterility barrier. In this context, genetic incompatibilities involving the duplicated F-box genes as putative candidates, and a possible strengthening step involving the chromosomal

  19. SymGRASS: a database of sugarcane orthologous genes involved in arbuscular mycorrhiza and root nodule symbiosis

    Science.gov (United States)

    2013-01-01

    Background The rationale for gathering information from plants procuring nitrogen through symbiotic interactions controlled by a common genetic program for a sustainable biofuel production is the high energy demanding application of synthetic nitrogen fertilizers. We curated sequence information publicly available for the biofuel plant sugarcane, performed an analysis of the common SYM pathway known to control symbiosis in other plants, and provide results, sequences and literature links as an online database. Methods Sugarcane sequences and informations were downloaded from the nucEST database, cleaned and trimmed with seqclean, assembled with TGICL plus translating mapping method, and annotated. The annotation is based on BLAST searches against a local formatted plant Uniprot90 generated with CD-HIT for functional assignment, rpsBLAST to CDD database for conserved domain analysis, and BLAST search to sorghum's for Gene Ontology (GO) assignment. Gene expression was normalized according the Unigene standard, presented as ESTs/100 kb. Protein sequences known in the SYM pathway were used as queries to search the SymGRASS sequence database. Additionally, antimicrobial peptides described in the PhytAMP database served as queries to retrieve and generate expression profiles of these defense genes in the libraries compared to the libraries obtained under symbiotic interactions. Results We describe the SymGRASS, a database of sugarcane orthologous genes involved in arbuscular mycorrhiza (AM) and root nodule (RN) symbiosis. The database aggregates knowledge about sequences, tissues, organ, developmental stages and experimental conditions, and provides annotation and level of gene expression for sugarcane transcripts and SYM orthologous genes in sugarcane through a web interface. Several candidate genes were found for all nodes in the pathway, and interestingly a set of symbiosis specific genes was found. Conclusions The knowledge integrated in SymGRASS may guide studies on

  20. Characterization of structural and free energy properties of promoters associated with Primary and Operon TSS in Helicobacter pylori genome and their orthologs

    Indian Academy of Sciences (India)

    Aditya Kumar; Manju Bansal

    2012-07-01

    Promoter regions in the genomes of all domains of life show similar trends in several structural properties such as stability, bendability, curvature, etc. In current study we analysed the stability and bendability of various classes of promoter regions (based on the recent identification of different classes of transcription start sites) of Helicobacter pylori 26695 strain. It is found that primary TSS and operon-associated TSS promoters show significantly strong features in their promoter regions. DNA free-energy-based promoter prediction tool PromPredict was used to annotate promoters of different classes, and very high recall values (∼80%) are obtained for primary TSS. Orthologous genes from other strains of H. pylori show conservation of structural properties in promoter regions as well as coding regions. PromPredict annotates promoters of orthologous genes with very high recall and precision.

  1. Set Domain-Dependent Regulation of Transcriptional Silencing and Growth Control by SUV39H1, a Mammalian Ortholog of Drosophila Su(var)3-9

    OpenAIRE

    Firestein, Ron; Cui, Xiangmin; Huie, Phil; Cleary, Michael L.

    2000-01-01

    Mammalian SET domain-containing proteins define a distinctive class of chromatin-associated factors that are targets for growth control signals and oncogenic activation. SUV39H1, a mammalian ortholog of Drosophila Su(var)3-9, contains both SET and chromo domains, signature motifs for proteins that contribute to epigenetic control of gene expression through effects on the regional organization of chromatin structure. In this report we demonstrate that SUV39H1 represses transcription in a trans...

  2. Lack of Benefit of Early Intervention with Dietary Flax and Fish Oil and Soy Protein in Orthologous Rodent Models of Human Hereditary Polycystic Kidney Disease

    Science.gov (United States)

    Monirujjaman, Md; Gabbs, Melissa

    2016-01-01

    Rationale for dietary advice in polycystic kidney disease (PKD) is based in part on animal studies that have examined non-orthologous models with progressive development of cystic disease. Since no model completely mimics human PKD, the purpose of the current studies was to examine the effects of dietary soy protein (compared to casein) or oils enriched in omega-3 fatty acids (fish or flax oil compared to soy oil) on early disease progression in two orthologous models of PKD. The models studied were Pkd2WS25/- mice as a model of autosomal dominant PKD, and PCK rats as a model of autosomal recessive PKD. After 13 weeks of feeding, dietary fish (but not flax) oil resulted in larger kidneys and greater kidney water content in female Pkd2WS25/- compared to control mice. After 12 weeks of feeding male PCK compared to control rats, both fish and flax compared to soy oil resulted in enlarged kidneys and livers, greater kidney water content and higher kidney cyst area in diseased rats. Dietary soy protein compared to casein had no effects in Pkd2WS25/- compared to control mice. In PCK rats, kidney and liver histology were not improved, but lower proteinuria and higher urine pH suggest that soy protein could be beneficial in the long term. Therefore, in contrast to studies in non-orthologous models during the progressive development phase, these studies in orthologous PKD models do not support dietary advice to increase soy protein or oils enriched in omega-3 oils in early PKD. PMID:27213553

  3. A role in immunity for Arabidopsis cysteine protease RD21, the ortholog of the tomato immune protease C14.

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    Takayuki Shindo

    Full Text Available Secreted papain-like Cys proteases are important players in plant immunity. We previously reported that the C14 protease of tomato is targeted by cystatin-like EPIC proteins that are secreted by the oomycete pathogen Phytophthora infestans (Pinf during infection. C14 has been under diversifying selection in wild potato species coevolving with Pinf and reduced C14 levels result in enhanced susceptibility for Pinf. Here, we investigated the role C14-EPIC-like interactions in the natural pathosystem of Arabidopsis with the oomycete pathogen Hyaloperonospora arabidopsidis (Hpa. In contrast to the Pinf-solanaceae pathosystem, the C14 orthologous protease of Arabidopsis, RD21, does not evolve under diversifying selection in Arabidopsis, and rd21 null mutants do not show phenotypes upon compatible and incompatible Hpa interactions, despite the evident lack of a major leaf protease. Hpa isolates express highly conserved EPIC-like proteins during infections, but it is unknown if these HpaEPICs can inhibit RD21 and one of these HpaEPICs even lacks the canonical cystatin motifs. The rd21 mutants are unaffected in compatible and incompatible interactions with Pseudomonas syringae pv. tomato, but are significantly more susceptible for the necrotrophic fungal pathogen Botrytis cinerea, demonstrating that RD21 provides immunity to a necrotrophic pathogen.

  4. Serine- and threonine/valine-dependent activation of PDK and Tor orthologs converge on Sch9 to promote aging.

    Science.gov (United States)

    Mirisola, Mario G; Taormina, Giusi; Fabrizio, Paola; Wei, Min; Hu, Jia; Longo, Valter D

    2014-02-01

    Dietary restriction extends longevity in organisms ranging from bacteria to mice and protects primates from a variety of diseases, but the contribution of each dietary component to aging is poorly understood. Here we demonstrate that glucose and specific amino acids promote stress sensitization and aging through the differential activation of the Ras/cAMP/PKA, PKH1/2 and Tor/S6K pathways. Whereas glucose sensitized cells through a Ras-dependent mechanism, threonine and valine promoted cellular sensitization and aging primarily by activating the Tor/S6K pathway and serine promoted sensitization via PDK1 orthologs Pkh1/2. Serine, threonine and valine activated a signaling network in which Sch9 integrates TORC1 and Pkh signaling via phosphorylation of threonines 570 and 737 and promoted intracellular relocalization and transcriptional inhibition of the stress resistance protein kinase Rim15. Because of the conserved pro-aging role of nutrient and growth signaling pathways in higher eukaryotes, these results raise the possibility that similar mechanisms contribute to aging in mammals.

  5. The ABCs of eye color in Tribolium castaneum: orthologs of the Drosophila white, scarlet, and brown Genes.

    Science.gov (United States)

    Grubbs, Nathaniel; Haas, Sue; Beeman, Richard W; Lorenzen, Marcé D

    2015-03-01

    In Drosophila melanogaster, each of the three paralogous ABC transporters, White, Scarlet and Brown, is required for normal pigmentation of the compound eye. We have cloned the three orthologous genes from the beetle Tribolium castaneum. Conceptual translations of Tribolium white (Tcw), scarlet (Tcst), and brown (Tcbw) are 51, 48, and 32% identical to their respective Drosophila counterparts. We have identified loss-of-eye-pigment strains that bear mutations in Tcw and Tcst: the Tcw gene in the ivory (i) strain carries a single-base transversion, which leads to an E → D amino-acid substitution in the highly conserved Walker B motif, while the Tcst gene in the pearl (p) strain has a deletion resulting in incorporation of a premature stop codon. In light of these findings, the mutant strains i and p are herein renamed white(ivory) (w(i)) and scarlet(pearl) (st(p)), respectively. In addition, RNA inhibition of Tcw and Tcst recapitulates the mutant phenotypes, confirming the roles of these genes in normal eye pigmentation, while RNA interference of Tcbw provides further evidence that it has no role in eye pigmentation in Tribolium. We also consider the evolutionary implications of our findings.

  6. Serine- and threonine/valine-dependent activation of PDK and Tor orthologs converge on Sch9 to promote aging.

    Directory of Open Access Journals (Sweden)

    Mario G Mirisola

    2014-02-01

    Full Text Available Dietary restriction extends longevity in organisms ranging from bacteria to mice and protects primates from a variety of diseases, but the contribution of each dietary component to aging is poorly understood. Here we demonstrate that glucose and specific amino acids promote stress sensitization and aging through the differential activation of the Ras/cAMP/PKA, PKH1/2 and Tor/S6K pathways. Whereas glucose sensitized cells through a Ras-dependent mechanism, threonine and valine promoted cellular sensitization and aging primarily by activating the Tor/S6K pathway and serine promoted sensitization via PDK1 orthologs Pkh1/2. Serine, threonine and valine activated a signaling network in which Sch9 integrates TORC1 and Pkh signaling via phosphorylation of threonines 570 and 737 and promoted intracellular relocalization and transcriptional inhibition of the stress resistance protein kinase Rim15. Because of the conserved pro-aging role of nutrient and growth signaling pathways in higher eukaryotes, these results raise the possibility that similar mechanisms contribute to aging in mammals.

  7. Serine- and threonine/valine-dependent activation of PDK and Tor orthologs converge on Sch9 to promote aging.

    Science.gov (United States)

    Mirisola, Mario G; Taormina, Giusi; Fabrizio, Paola; Wei, Min; Hu, Jia; Longo, Valter D

    2014-02-01

    Dietary restriction extends longevity in organisms ranging from bacteria to mice and protects primates from a variety of diseases, but the contribution of each dietary component to aging is poorly understood. Here we demonstrate that glucose and specific amino acids promote stress sensitization and aging through the differential activation of the Ras/cAMP/PKA, PKH1/2 and Tor/S6K pathways. Whereas glucose sensitized cells through a Ras-dependent mechanism, threonine and valine promoted cellular sensitization and aging primarily by activating the Tor/S6K pathway and serine promoted sensitization via PDK1 orthologs Pkh1/2. Serine, threonine and valine activated a signaling network in which Sch9 integrates TORC1 and Pkh signaling via phosphorylation of threonines 570 and 737 and promoted intracellular relocalization and transcriptional inhibition of the stress resistance protein kinase Rim15. Because of the conserved pro-aging role of nutrient and growth signaling pathways in higher eukaryotes, these results raise the possibility that similar mechanisms contribute to aging in mammals. PMID:24516402

  8. Makorin ortholog LEP-2 regulates LIN-28 stability to promote the juvenile-to-adult transition in Caenorhabditis elegans.

    Science.gov (United States)

    Herrera, R Antonio; Kiontke, Karin; Fitch, David H A

    2016-03-01

    The heterochronic genes lin-28, let-7 and lin-41 regulate fundamental developmental transitions in animals, such as stemness versus differentiation and juvenile versus adult states. We identify a new heterochronic gene, lep-2, in Caenorhabditis elegans. Mutations in lep-2 cause a delay in the juvenile-to-adult transition, with adult males retaining pointed, juvenile tail tips, and displaying defective sexual behaviors. In both sexes, lep-2 mutants fail to cease molting or produce an adult cuticle. We find that LEP-2 post-translationally regulates LIN-28 by promoting LIN-28 protein degradation. lep-2 encodes the sole C. elegans ortholog of the Makorin (Mkrn) family of proteins. Like lin-28 and other heterochronic pathway members, vertebrate Mkrns are involved in developmental switches, including the timing of pubertal onset in humans. Based on shared roles, conservation and the interaction between lep-2 and lin-28 shown here, we propose that Mkrns, together with other heterochronic genes, constitute an evolutionarily ancient conserved module regulating switches in development.

  9. Variation in the flowering time orthologs BrFLC and BrSOC1 in a natural population of Brassica rapa.

    Science.gov (United States)

    Franks, Steven J; Perez-Sweeney, Beatriz; Strahl, Maya; Nowogrodzki, Anna; Weber, Jennifer J; Lalchan, Rebecca; Jordan, Kevin P; Litt, Amy

    2015-01-01

    Understanding the genetic basis of natural phenotypic variation is of great importance, particularly since selection can act on this variation to cause evolution. We examined expression and allelic variation in candidate flowering time loci in Brassica rapa plants derived from a natural population and showing a broad range in the timing of first flowering. The loci of interest were orthologs of the Arabidopsis genes FLC and SOC1 (BrFLC and BrSOC1, respectively), which in Arabidopsis play a central role in the flowering time regulatory network, with FLC repressing and SOC1 promoting flowering. In B. rapa, there are four copies of FLC and three of SOC1. Plants were grown in controlled conditions in the lab. Comparisons were made between plants that flowered the earliest and latest, with the difference in average flowering time between these groups ∼30 days. As expected, we found that total expression of BrSOC1 paralogs was significantly greater in early than in late flowering plants. Paralog-specific primers showed that expression was greater in early flowering plants in the BrSOC1 paralogs Br004928, Br00393 and Br009324, although the difference was not significant in Br009324. Thus expression of at least 2 of the 3 BrSOC1 orthologs is consistent with their predicted role in flowering time in this natural population. Sequences of the promoter regions of the BrSOC1 orthologs were variable, but there was no association between allelic variation at these loci and flowering time variation. For the BrFLC orthologs, expression varied over time, but did not differ between the early and late flowering plants. The coding regions, promoter regions and introns of these genes were generally invariant. Thus the BrFLC orthologs do not appear to influence flowering time in this population. Overall, the results suggest that even for a trait like flowering time that is controlled by a very well described genetic regulatory network, understanding the underlying genetic basis of

  10. DNA microarray data integration by ortholog gene analysis reveals potential molecular mechanisms of estrogen-dependent growth of human uterine fibroids

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    Shou Jianyong

    2007-04-01

    Full Text Available Abstract Background Uterine fibroids or leiomyoma are a common benign smooth muscle tumor. The tumor growth is well known to be estrogen-dependent. However, the molecular mechanisms of its estrogen-dependency is not well understood. Methods Differentially expressed genes in human uterine fibroids were either retrieved from published papers or from our own statistical analysis of downloaded array data. Probes for the same genes on different Affymetrix chips were mapped based on probe comparison information provided by Affymetrix. Genes identified by two or three array studies were submitted for ortholog analysis. Human and rat ortholog genes were identified by using ortholog gene databases, HomoloGene and TOGA and were confirmed by synteny analysis with MultiContigView tool in the Ensembl genome browser. Results By integrated analysis of three recently published DNA microarray studies with human tissue, thirty-eight genes were found to be differentially expressed in the same direction in fibroid compared to adjacent uterine myometrium by at least two research groups. Among these genes, twelve with rat orthologs were identified as estrogen-regulated from our array study investigating uterine expression in ovariectomized rats treated with estrogen. Functional and pathway analyses of the twelve genes suggested multiple molecular mechanisms for estrogen-dependent cell survival and tumor growth. Firstly, estrogen increased expression of the anti-apoptotic PCP4 gene and suppressed the expression of growth inhibitory receptors PTGER3 and TGFBR2. Secondly, estrogen may antagonize PPARγ signaling, thought to inhibit fibroid growth and survival, at two points in the PPAR pathway: 1 through increased ANXA1 gene expression which can inhibit phospholipase A2 activity and in turn decrease arachidonic acid synthesis, and 2 by decreasing L-PGDS expression which would reduce synthesis of PGJ2, an endogenous ligand for PPARγ. Lastly, estrogen affects retinoic

  11. Both STING and MAVS fish orthologs contribute to the induction of interferon mediated by RIG-I.

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    Stéphane Biacchesi

    Full Text Available Viral infections are detected in most cases by the host innate immune system through pattern-recognition receptors (PRR, the sensors for pathogen-associated molecular patterns (PAMPs, which induce the production of cytokines, such as type I interferons (IFN. Recent identification in mammalian and teleost fish of cytoplasmic viral RNA sensors, RIG-I-like receptors (RLRs, and their mitochondrial adaptor: the mitochondrial antiviral signaling (MAVS protein, also called IPS-1, highlight their important role in the induction of IFN at the early stage of a virus infection. More recently, an endoplasmic reticulum (ER adaptor: the stimulator of interferon genes (STING protein, also called MITA, ERIS and MPYS, has been shown to play a pivotal role in response to both non-self-cytosolic RNA and dsDNA. In this study, we cloned STING cDNAs from zebrafish and showed that it was an ortholog to mammalian STING. We demonstrated that overexpression of this ER protein in fish cells led to a constitutive induction of IFN and interferon-stimulated genes (ISGs. STING-overexpressing cells were almost fully protected against RNA virus infection with a strong inhibition of both DNA and RNA virus replication. In addition, we found that together with MAVS, STING was an important player in the RIG-I IFN-inducing pathway. This report provides the demonstration that teleost fish possess a functional RLR pathway in which MAVS and STING are downstream signaling molecules of RIG-I. The Sequences presented in this article have been submitted to GenBank under accession numbers: Zebrafish STING (HE856619; EPC STING (HE856620; EPC IRF3 (HE856621; EPC IFN promoter (HE856618.

  12. Saccharomyces cerevisiae Bat1 and Bat2 aminotransferases have functionally diverged from the ancestral-like Kluyveromyces lactis orthologous enzyme.

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    Maritrini Colón

    Full Text Available BACKGROUND: Gene duplication is a key evolutionary mechanism providing material for the generation of genes with new or modified functions. The fate of duplicated gene copies has been amply discussed and several models have been put forward to account for duplicate conservation. The specialization model considers that duplication of a bifunctional ancestral gene could result in the preservation of both copies through subfunctionalization, resulting in the distribution of the two ancestral functions between the gene duplicates. Here we investigate whether the presumed bifunctional character displayed by the single branched chain amino acid aminotransferase present in K. lactis has been distributed in the two paralogous genes present in S. cerevisiae, and whether this conservation has impacted S. cerevisiae metabolism. PRINCIPAL FINDINGS: Our results show that the KlBat1 orthologous BCAT is a bifunctional enzyme, which participates in the biosynthesis and catabolism of branched chain aminoacids (BCAAs. This dual role has been distributed in S. cerevisiae Bat1 and Bat2 paralogous proteins, supporting the specialization model posed to explain the evolution of gene duplications. BAT1 is highly expressed under biosynthetic conditions, while BAT2 expression is highest under catabolic conditions. Bat1 and Bat2 differential relocalization has favored their physiological function, since biosynthetic precursors are generated in the mitochondria (Bat1, while catabolic substrates are accumulated in the cytosol (Bat2. Under respiratory conditions, in the presence of ammonium and BCAAs the bat1Δ bat2Δ double mutant shows impaired growth, indicating that Bat1 and Bat2 could play redundant roles. In K. lactis wild type growth is independent of BCAA degradation, since a Klbat1Δ mutant grows under this condition. CONCLUSIONS: Our study shows that BAT1 and BAT2 differential expression and subcellular relocalization has resulted in the distribution of the

  13. Fermitins, the orthologs of mammalian Kindlins, regulate the development of a functional cardiac syncytium in Drosophila melanogaster.

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    James H Catterson

    Full Text Available The vertebrate Kindlins are an evolutionarily conserved family of proteins critical for integrin signalling and cell adhesion. Kindlin-2 (KIND2 is associated with intercalated discs in mice, suggesting a role in cardiac syncytium development; however, deficiency of Kind2 leads to embryonic lethality. Morpholino knock-down of Kind2 in zebrafish has a pleiotropic effect on development that includes the heart. It therefore remains unclear whether cardiomyocyte Kind2 expression is required for cardiomyocyte junction formation and the development of normal cardiac function. To address this question, the expression of Fermitin 1 and Fermitin 2 (Fit1, Fit2, the two Drosophila orthologs of Kind2, was silenced in Drosophila cardiomyocytes. Heart development was assessed in adult flies by immunological methods and videomicroscopy. Silencing both Fit1 and Fit2 led to a severe cardiomyopathy characterised by the failure of cardiomyocytes to develop as a functional syncytium and loss of synchrony between cardiomyocytes. A null allele of Fit1 was generated but this had no impact on the heart. Similarly, the silencing of Fit2 failed to affect heart function. In contrast, the silencing of Fit2 in the cardiomyocytes of Fit1 null flies disrupted syncytium development, leading to severe cardiomyopathy. The data definitively demonstrate a role for Fermitins in the development of a functional cardiac syncytium in Drosophila. The findings also show that the Fermitins can functionally compensate for each other in order to control syncytium development. These findings support the concept that abnormalities in cardiomyocyte KIND2 expression or function may contribute to cardiomyopathies in humans.

  14. New species of Ehrlichia isolated from Rhipicephalus (Boophilus microplus shows an ortholog of the E. canis major immunogenic glycoprotein gp36 with a new sequence of tandem repeats

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    Cruz Alejandro Cabezas

    2012-12-01

    Full Text Available Abstract Background Ehrlichia species are the etiological agents of emerging and life-threatening tick-borne human zoonoses that inflict serious and fatal infections in companion animals and livestock. The aim of this paper was to phylogeneticaly characterise a new species of Ehrlichia isolated from Rhipicephalus (Boophilus microplus from Minas Gerais, Brazil. Methods The agent was isolated from the hemolymph of Rhipicephalus (B. microplus engorged females that had been collected from naturally infested cattle in a farm in the state of Minas Gerais, Brazil. This agent was then established and cultured in IDE8 tick cells. The molecular and phylogenetic analysis was based on 16S rRNA, groEL, dsb, gltA and gp36 genes. We used the maximum likelihood method to construct the phylogenetic trees. Results The phylogenetic trees based on 16S rRNA, groEL, dsb and gltA showed that the Ehrlichia spp isolated in this study falls in a clade separated from any previously reported Ehrlichia spp. The molecular analysis of the ortholog of gp36, the major immunoreactive glycoproteins in E. canis and ortholog of the E. chaffeensis gp47, showed a unique tandem repeat of 9 amino acids (VPAASGDAQ when compared with those reported for E. canis, E. chaffeensis and the related mucin-like protein in E. ruminantium. Conclusions Based on the molecular and phylogenetic analysis of the 16S rRNA, groEL, dsb and gltA genes we concluded that this tick-derived microorganism isolated in Brazil is a new species, named E. mineirensis (UFMG-EV, with predicted novel antigenic properties in the gp36 ortholog glycoprotein. Further studies on this new Ehrlichia spp should address questions about its transmissibility by ticks and its pathogenicity for mammalian hosts.

  15. Cloning and Function Characteristic of GhDWF 4,an Ortholog of Arabidopsis DWF 4 from Upland Cotton (Gossypium hirsutum L.)

    Institute of Scientific and Technical Information of China (English)

    HU Ming-yu; LUO Ming; TAN Kun-ling; XIAO Zhong-yi; PEI Yan

    2008-01-01

    @@ As one of the longest cells characterized in plant kingdom,cotton fibers were regarded as an ideal material for studying plant cell growth and development.In recent years,several reports revealed that brassinosteroids (BRs) play an important role in the growth and development of cotton fiber.To further investigate the effect of BRs on fiber cell development and illuminate the mechanism of BRs action,we cloned GhDWF4,an ortholog of Arabidopsis DWF4 from upland cotton (Gossypium hirsuturn L.).

  16. The Structure of YqeH: AN AtNOS1/AtNOA1 ORTHOLOG THAT COUPLES GTP HYDROLYSIS TO MOLECULAR RECOGNITION*S⃞

    OpenAIRE

    Sudhamsu, Jawahar; Lee, Gyu In; Klessig, Daniel F; Crane, Brian R.

    2008-01-01

    AtNOS1/AtNOA1 was identified as a nitric oxide-generating enzyme in plants, but that function has recently been questioned. To resolve issues surrounding AtNOA1 activity, we report the biochemical properties and a 2.36 Å resolution crystal structure of a bacterial AtNOA1 ortholog (YqeH). Geobacillus YqeH fused to a putative AtNOA1 leader peptide complements growth and morphological defects of Atnoa1 mutant plants. YqeH does not synthesize nitric oxide from l-arginine b...

  17. eggNOG v2.0: extending the evolutionary genealogy of genes with enhanced non-supervised orthologous groups, species and functional annotations

    DEFF Research Database (Denmark)

    Muller, J; Szklarczyk, D; Julien, P;

    2010-01-01

    of the tree of life; in addition to the species groups included in our first release (i.e. fungi, metazoa, insects, vertebrates and mammals), we have now constructed OGs for archaea, fishes, rodents and primates. We automatically annotate the non-supervised orthologous groups (NOGs) with functional...... descriptions, protein domains, and functional categories as defined initially for the COG/KOG database. In-depth analysis is facilitated by precomputed high-quality multiple sequence alignments and maximum-likelihood trees for each of the available OGs. Altogether, eggNOG covers 2,242 035 proteins (built from...

  18. Identification and characterization of the Non-race specific Disease Resistance 1 (NDR1 orthologous protein in coffee

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    Mongrand Sébastien

    2011-10-01

    Full Text Available Abstract Background Leaf rust, which is caused by the fungus Hemileia vastatrix (Pucciniales, is a devastating disease that affects coffee plants (Coffea arabica L.. Disadvantages that are associated with currently developed phytoprotection approaches have recently led to the search for alternative strategies. These include genetic manipulations that constitutively activate disease resistance signaling pathways. However, molecular actors of such pathways still remain unknown in C. arabica. In this study, we have isolated and characterized the coffee NDR1 gene, whose Arabidopsis ortholog is a well-known master regulator of the hypersensitive response that is dependent on coiled-coil type R-proteins. Results Two highly homologous cDNAs coding for putative NDR1 proteins were identified and cloned from leaves of coffee plants. One of the candidate coding sequences was then expressed in the Arabidopsis knock-out null mutant ndr1-1. Upon a challenge with a specific strain of the bacterium Pseudomonas syringae (DC3000::AvrRpt2, analysis of both macroscopic symptoms and in planta microbial growth showed that the coffee cDNA was able to restore the resistance phenotype in the mutant genetic background. Thus, the cDNA was dubbed CaNDR1a (standing for Coffea arabica Non-race specific Disease Resistance 1a. Finally, biochemical and microscopy data were obtained that strongly suggest the mechanistic conservation of the NDR1-driven function within coffee and Arabidopsis plants. Using a transient expression system, it was indeed shown that the CaNDR1a protein, like its Arabidopsis counterpart, is localized to the plasma membrane, where it is possibly tethered by means of a GPI anchor. Conclusions Our data provide molecular and genetic evidence for the identification of a novel functional NDR1 homolog in plants. As a key regulator initiating hypersensitive signalling pathways, CaNDR1 gene(s might be target(s of choice for manipulating the coffee innate immune

  19. An ortholog of farA of Aspergillus nidulans is implicated in the transcriptional activation of genes involved in fatty acid utilization in the yeast Yarrowia lipolytica

    Energy Technology Data Exchange (ETDEWEB)

    Poopanitpan, Napapol; Kobayashi, Satoshi; Fukuda, Ryouichi; Horiuchi, Hiroyuki [Department of Biotechnology, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657 (Japan); Ohta, Akinori, E-mail: aaohta@mail.ecc.u-tokyo.ac.jp [Department of Biotechnology, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657 (Japan)

    2010-11-26

    Research highlights: {yields} POR1 is a Yarrowia lipolytica ortholog of farA involved in fatty acid response in A. nidulans. {yields} Deletion of POR1 caused growth defects on fatty acids. {yields} {Delta}por1 strain exhibited defects in the induction of genes involved in fatty acid utilization. -- Abstract: The yeast Yarrowia lipolytica effectively utilizes hydrophobic substrates such as fatty acids and n-alkanes. To identify a gene(s) regulating fatty acid utilization in Y. lipolytica, we first studied homologous genes to OAF1 and PIP2 of Saccharomyces cerevisiae, but their disruption did not change growth on oleic acid at all. We next characterized a Y. lipolytica gene, POR1 (primary oleate regulator 1), an ortholog of farA encoding a transcriptional activator that regulates fatty acid utilization in Aspergillus nidulans. The deletion mutant of POR1 was defective in the growth on various fatty acids, but not on glucose, glycerol, or n-hexadecane. It exhibited slight defect on n-decane. The transcriptional induction of genes involved in {beta}-oxidation and peroxisome proliferation by oleate was distinctly diminished in the {Delta}por1 strains. These data suggest that POR1 encodes a transcriptional activator widely regulating fatty acid metabolism in Y. lipolytica.

  20. Characterization of gana-1, a Caenorhabditis elegans gene encoding a single ortholog of vertebrate α-galactosidase and α-N-acetylgalactosaminidase

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    Kostrouchová Marta

    2005-01-01

    Full Text Available Abstract Background Human α-galactosidase A (α-GAL and α-N-acetylgalactosaminidase (α-NAGA are presumed to share a common ancestor. Deficiencies of these enzymes cause two well-characterized human lysosomal storage disorders (LSD – Fabry (α-GAL deficiency and Schindler (α-NAGA deficiency diseases. Caenorhabditis elegans was previously shown to be a relevant model organism for several late endosomal/lysosomal membrane proteins associated with LSDs. The aim of this study was to identify and characterize C. elegans orthologs to both human lysosomal luminal proteins α-GAL and α-NAGA. Results BlastP searches for orthologs of human α-GAL and α-NAGA revealed a single C. elegans gene (R07B7.11 with homology to both human genes (α-galactosidase and α-N-acetylgalactosaminidase – gana-1. We cloned and sequenced the complete gana-1 cDNA and elucidated the gene organization. Phylogenetic analyses and homology modeling of GANA-1 based on the 3D structure of chicken α-NAGA, rice α-GAL and human α-GAL suggest a close evolutionary relationship of GANA-1 to both human α-GAL and α-NAGA. Both α-GAL and α-NAGA enzymatic activities were detected in C. elegans mixed culture homogenates. However, α-GAL activity on an artificial substrate was completely inhibited by the α-NAGA inhibitor, N-acetyl-D-galactosamine. A GANA-1::GFP fusion protein expressed from a transgene, containing the complete gana-1 coding region and 3 kb of its hypothetical promoter, was not detectable under the standard laboratory conditions. The GFP signal was observed solely in a vesicular compartment of coelomocytes of the animals treated with Concanamycin A (CON A or NH4Cl, agents that increase the pH of the cellular acidic compartment. Immunofluorescence detection of the fusion protein using polyclonal anti-GFP antibody showed a broader and coarsely granular cytoplasmic expression pattern in body wall muscle cells, intestinal cells, and a vesicular compartment of

  1. Expression conservation within the circadian clock of a monocot: natural variation at barley Ppd-H1 affects circadian expression of flowering time genes, but not clock orthologs

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    Campoli Chiara

    2012-06-01

    Full Text Available Abstract Background The circadian clock is an endogenous mechanism that coordinates biological processes with daily changes in the environment. In plants, circadian rhythms contribute to both agricultural productivity and evolutionary fitness. In barley, the photoperiod response regulator and flowering-time gene Ppd-H1 is orthologous to the Arabidopsis core-clock gene PRR7. However, relatively little is known about the role of Ppd-H1 and other components of the circadian clock in temperate crop species. In this study, we identified barley clock orthologs and tested the effects of natural genetic variation at Ppd-H1 on diurnal and circadian expression of clock and output genes from the photoperiod-response pathway. Results Barley clock orthologs HvCCA1, HvGI, HvPRR1, HvPRR37 (Ppd-H1, HvPRR73, HvPRR59 and HvPRR95 showed a high level of sequence similarity and conservation of diurnal and circadian expression patterns, when compared to Arabidopsis. The natural mutation at Ppd-H1 did not affect diurnal or circadian cycling of barley clock genes. However, the Ppd-H1 mutant was found to be arrhythmic under free-running conditions for the photoperiod-response genes HvCO1, HvCO2, and the MADS-box transcription factor and vernalization responsive gene Vrn-H1. Conclusion We suggest that the described eudicot clock is largely conserved in the monocot barley. However, genetic differentiation within gene families and differences in the function of Ppd-H1 suggest evolutionary modification in the angiosperm clock. Our data indicates that natural variation at Ppd-H1 does not affect the expression level of clock genes, but controls photoperiodic output genes. Circadian control of Vrn-H1 in barley suggests that this vernalization responsive gene is also controlled by the photoperiod-response pathway. Structural and functional characterization of the barley circadian clock will set the basis for future studies of the adaptive significance of the circadian clock in

  2. Two Poplar Glycosyltransferase Genes, PdGATL1.1 and PdGATL1.2, Are Functional Orthologs to PARVUS/AtGATL 1 in Arabidopsis

    Institute of Scientific and Technical Information of China (English)

    Yingzhen Kong; Gongke Zhou; Utku Avci; Xiaogang Gu; Chelsea Jones; Yanbin Yin; Ying Xu; Michael G. Hahn

    2009-01-01

    Several genes in Arabidopsis, including PARVUS/AtGATL1, have been implicated in xylan synthesis. However, the biosynthesis of xylan in woody plants, where this polysaccharide is a major component of wood, is poorly understood. Here, we characterize two Populus genes, PdGATL1.1 and PdGATL1.2, the closest orthologs to the Arabidopsis PARVUS/GATL 1 gene, with respect to their gene expression in poplar, their sub-cellular localization, and their ability to complement the parvus mutation in Arabidopsis. Overexpression of the two poplar genes in the parvus mutant rescued most of the defects caused by the parvus mutation, including morphological changes, collapsed xylem, and altered cell wall mono-saccharide composition. Quantitative RT-PCR showed that PdGATL1.1 is expressed most strongly in developing xylem of poplar. In contrast, PdGATL1.2 is expressed much more uniformly in leaf, shoot tip, cortex, phloem, and xylem, and the transcript level of PdGATL1.2 is much lower than that of PdGATL1.1 in all tissues examined. Sub-cellular localization experi-ments showed that these two proteins are localized to both ER and Golgi in comparison with marker proteins resident to these sub-cellular compartments. Our data indicate that PdGATLI.1 and PdGATL1.2 are functional orthologs of PARVUS/ GATL1 and can play a role in xylan synthesis, but may also have role(s) in the synthesis of other wall polymers.

  3. A functional EDS1 ortholog is differentially regulated in powdery mildew resistant and susceptible grapevines and complements an Arabidopsis eds1 mutant.

    Science.gov (United States)

    Gao, Fei; Shu, Xiaomei; Ali, Mohammad Babar; Howard, Susanne; Li, Nan; Winterhagen, Patrick; Qiu, Wenping; Gassmann, Walter

    2010-04-01

    Vitis vinifera (grapevine) is the most economically important deciduous fruit crop, but cultivated grapevine varieties lack adequate innate immunity to a range of devastating diseases. To identify genetic resources for grapevine innate immunity and understand pathogen defense pathways in a woody perennial plant, we focus in this study on orthologs of the central Arabidopsis thaliana defense regulator ENHANCED DISEASE SUSCEPTIBILITY1 (EDS1). The family of EDS1-like genes is expanded in grapevine, and members of this family were previously found to be constitutively upregulated in the resistant variety 'Norton' of the North American grapevine species Vitis aestivalis, while they were induced by Erysiphe necator, the causal agent of grapevine powdery mildew (PM), in the susceptible V. vinifera variety 'Cabernet Sauvignon'. Here, we determine the responsiveness of individual EDS1-like genes in grapevine to PM and salicylic acid, and find that EDS1-like paralogs are differentially regulated in 'Cabernet Sauvignon', while two are constitutively upregulated in 'Norton'. Sequencing of VvEDS1 and VaEDS1 cDNA and genomic clones revealed high conservation in the protein-encoding sequence and some divergence of the promoter sequence in the two grapevine varieties. Complementation of the Arabidopsis eds1-1 mutant showed that the EDS1-like gene with highest predicted amino acid sequence similarity to AtEDS1 from either grapevine varieties is a functional ortholog of AtEDS1. Together, our analyses show that differential susceptibility to PM is correlated with differences in EDS1 expression, not differences in EDS1 function, between resistant 'Norton' and susceptible 'Cabernet Sauvignon'.

  4. Two maize END-1 orthologs, BETL9 and BETL9like, are transcribed in a non-overlapping spatial pattern on the outer surface of the developing endosperm

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    Joaquín eRoyo

    2014-05-01

    Full Text Available In the course of a project aimed to isolate transfer cells-specific genes in maize endosperm we have identified the BETL9 gene. BETL9 encodes for a small protein very similar in sequence to the product of the barley transfer cell-specific gene end-1. Both BETL9 and END-1 proteins are lipid transfer proteins, but their function is currently unknown. In situ hybridization analysis confirms that the BETL9 gene is exclusively transcribed in the basal endosperm transfer cell layer during seed development since 10 days after pollination. However, immunolocalization data indicates that the BETL9 protein accumulates in the maternal placento-chalaza cells located just beside the transfer cell layer. This suggests that the BETL9 protein should be transported to the maternal side to exert its, still unknown, function. In addition, we have identified a second maize gene very similar in sequence to BETL9 and we have named it BETL9like. In situ hybridization shows that BETL9like is also specifically transcribed in the developing maize endosperm within the same time frame that BETL9, but in this case it is exclusively expressed in the aleurone cell layer. Consequently, the BETL9 and BETL9like genes are transcribed in a non-overlapping pattern on the outer surface of the maize endosperm. The BETL9 and BETL9like promoter sequences, fused to the GUS reporter gen, accurately reflected the expression pattern observed for the genes in maize. Finally, we have identified in the Arabidopsis genome a set of four genes orthologous to BETL9 and BETL9like and analysed the activity of their promoters in Arabidopsis transgenic plants carrying fusions of their promoter sequences to the GUS reporter. As in the case of the maize genes, the Arabidopsis orthologs showed highly complementary expression patterns.

  5. Transcriptional activity and nuclear localization of Cabut, the Drosophila ortholog of vertebrate TGF-β-inducible early-response gene (TIEG proteins.

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    Yaiza Belacortu

    Full Text Available BACKGROUND: Cabut (Cbt is a C(2H(2-class zinc finger transcription factor involved in embryonic dorsal closure, epithelial regeneration and other developmental processes in Drosophila melanogaster. Cbt orthologs have been identified in other Drosophila species and insects as well as in vertebrates. Indeed, Cbt is the Drosophila ortholog of the group of vertebrate proteins encoded by the TGF-ß-inducible early-response genes (TIEGs, which belong to Sp1-like/Krüppel-like family of transcription factors. Several functional domains involved in transcriptional control and subcellular localization have been identified in the vertebrate TIEGs. However, little is known of whether these domains and functions are also conserved in the Cbt protein. METHODOLOGY/PRINCIPAL FINDINGS: To determine the transcriptional regulatory activity of the Drosophila Cbt protein, we performed Gal4-based luciferase assays in S2 cells and showed that Cbt is a transcriptional repressor and able to regulate its own expression. Truncated forms of Cbt were then generated to identify its functional domains. This analysis revealed a sequence similar to the mSin3A-interacting repressor domain found in vertebrate TIEGs, although located in a different part of the Cbt protein. Using β-Galactosidase and eGFP fusion proteins, we also showed that Cbt contains the bipartite nuclear localization signal (NLS previously identified in TIEG proteins, although it is non-functional in insect cells. Instead, a monopartite NLS, located at the amino terminus of the protein and conserved across insects, is functional in Drosophila S2 and Spodoptera exigua Sec301 cells. Last but not least, genetic interaction and immunohistochemical assays suggested that Cbt nuclear import is mediated by Importin-α2. CONCLUSIONS/SIGNIFICANCE: Our results constitute the first characterization of the molecular mechanisms of Cbt-mediated transcriptional control as well as of Cbt nuclear import, and demonstrate the

  6. Rescue of Drosophila Melanogaster l(2)35Aa lethality is only mediated by polypeptide GalNAc-transferase pgant35A, but not by the evolutionary conserved human ortholog GalNAc-transferase-T11

    DEFF Research Database (Denmark)

    Bennett, Eric P; Chen, Ya-Wen; Schwientek, Tilo;

    2010-01-01

    conserved family of genes encoding polypeptide GalNAc-transferases. Phylogenetic and functional analyses have proposed that subfamilies of orthologous GalNAc-transferase genes are conserved in species, suggesting that they serve distinct functions in vivo. Based on sequence alignments, pgant35A and human......)35Aa lethality. By use of genetic "domain swapping" experiments we demonstrate, that lack of rescue was not caused by inappropriate sub-cellular targeting of functionally active GalNAc-T11. Collectively our results show, that fly embryogenesis specifically requires functional pgant35A......, and that the presence of this gene product during fly embryogenesis is functionally distinct from other Drosophila GalNAc-transferase isoforms and from the proposed human ortholog GALNT11....

  7. Rescue of Drosophila Melanogaster l(2)35Aa lethality is only mediated by polypeptide GalNAc-transferase pgant35A, but not by the evolutionary conserved human ortholog GalNAc-transferase-T11.

    Science.gov (United States)

    Bennett, Eric P; Chen, Ya-Wen; Schwientek, Tilo; Mandel, Ulla; Schjoldager, Katrine ter-Borch Gram; Cohen, Stephen M; Clausen, Henrik

    2010-05-01

    The Drosophila l(2)35Aa gene encodes a UDP-N-acetylgalactosamine: Polypeptide N-acetylgalactosaminyltransferase, essential for embryogenesis and development (J. Biol. Chem. 277, 22623-22638; J. Biol. Chem. 277, 22616-22). l(2)35Aa, also known as pgant35A, is a member of a large evolutionarily conserved family of genes encoding polypeptide GalNAc-transferases. Phylogenetic and functional analyses have proposed that subfamilies of orthologous GalNAc-transferase genes are conserved in species, suggesting that they serve distinct functions in vivo. Based on sequence alignments, pgant35A and human GALNT11 are thought to belong to a distinct subfamily. Recent in vitro studies have shown that pgant35A and pgant7, encoding enzymes from different subfamilies, prefer different acceptor substrates, whereas the orthologous pgant35A and human GALNT11 gene products possess, 1) conserved substrate preferences and 2) similar acceptor site preferences in vitro. In line with the in vitro pgant7 studies, we show that l(2)35Aa lethality is not rescued by ectopic pgant7 expression. Remarkably and in contrast to this observation, the human pgant35A ortholog, GALNT11, was shown not to support rescue of the l(2)35Aa lethality. By use of genetic "domain swapping" experiments we demonstrate, that lack of rescue was not caused by inappropriate sub-cellular targeting of functionally active GalNAc-T11. Collectively our results show, that fly embryogenesis specifically requires functional pgant35A, and that the presence of this gene product during fly embryogenesis is functionally distinct from other Drosophila GalNAc-transferase isoforms and from the proposed human ortholog GALNT11.

  8. The structure of YqeH: An AtNOS1/AtNOA1 ortholog that couples GTP hydrolysis to molecular recognition

    Energy Technology Data Exchange (ETDEWEB)

    Sudhamsu, J.; Lee, G.I.; Klessig, D.F.; Crane, B.R. (Cornell); (Boyce)

    2009-03-27

    AtNOS1/AtNOA1 was identified as a nitric oxide-generating enzyme in plants, but that function has recently been questioned. To resolve issues surrounding AtNOA1 activity, we report the biochemical properties and a 2.36 {angstrom} resolution crystal structure of a bacterial AtNOA1 ortholog (YqeH). Geobacillus YqeH fused to a putative AtNOA1 leader peptide complements growth and morphological defects of Atnoa1 mutant plants. YqeH does not synthesize nitric oxide from L-arginine but rather hydrolyzes GTP. The YqeH structure reveals a circularly permuted GTPase domain and an unusual C-terminal {beta}-domain. A small N-terminal domain, disordered in the structure, binds zinc. Structural homology among the C-terminal domain, the RNA-binding regulator TRAP, and the hypoxia factor pVHL define a recognition module for peptides and nucleic acids. TRAP residues important for RNA binding are conserved by the YqeH C-terminal domain, whose positioning is coupled to GTP hydrolysis. YqeH and AtNOA1 probably act as G-proteins that regulate nucleic acid recognition and not as nitric-oxide synthases.

  9. X-ray crystallographic studies of the extracellular domain of the first plant ATP receptor, DORN1, and the orthologous protein from Camelina sativa

    Energy Technology Data Exchange (ETDEWEB)

    Li, Zhijie; Chakraborty, Sayan; Xu, Guozhou (NCSU)

    2016-10-26

    Does not respond to nucleotides 1 (DORN1) has recently been identified as the first membrane-integral plant ATP receptor, which is required for ATP-induced calcium response, mitogen-activated protein kinase activation and defense responses inArabidopsis thaliana. In order to understand DORN1-mediated ATP sensing and signal transduction, crystallization and preliminary X-ray studies were conducted on the extracellular domain of DORN1 (atDORN1-ECD) and that of an orthologous protein,Camelina sativalectin receptor kinase I.9 (csLecRK-I.9-ECD or csI.9-ECD). A variety of deglycosylation strategies were employed to optimize the glycosylated recombinant atDORN1-ECD for crystallization. In addition, the glycosylated csI.9-ECD protein was crystallized at 291 K. X-ray diffraction data were collected at 4.6 Å resolution from a single crystal. The crystal belonged to space groupC222 orC2221, with unit-cell parametersa= 94.7,b= 191.5,c= 302.8 Å. These preliminary studies have laid the foundation for structural determination of the DORN1 and I.9 receptor proteins, which will lead to a better understanding of the perception and function of extracellular ATP in plants.

  10. Inhibition of human high-affinity copper importer Ctr1 orthologous in the nervous system of Drosophila ameliorates Aβ42-induced Alzheimer's disease-like symptoms.

    Science.gov (United States)

    Lang, Minglin; Fan, Qiangwang; Wang, Lei; Zheng, Yajun; Xiao, Guiran; Wang, Xiaoxi; Wang, Wei; Zhong, Yi; Zhou, Bing

    2013-11-01

    Disruption of copper homeostasis has been implicated in Alzheimer's disease (AD) during the last 2 decades; however, whether copper is a friend or a foe is controversial. Within a genetically tractable Drosophila AD model, we manipulated the expression of human high-affinity copper importer orthologous in Drosophila to explore the in vivo roles of copper ions in the development of AD. We found that inhibition of Ctr1C expression by RNAi in Aβ-expressing flies significantly reduced copper accumulation in the brains of the flies as well as ameliorating neurodegeneration, enhancing climbing ability, and prolonging lifespan. Interestingly, Ctr1C inhibition led to a significant increase in higher-molecular-weight Aβ42 forms in brain lysates, whereas it was accompanied by a trend of decreased expression of amyloid-β degradation proteases (including NEP1-3 and IDE) with age and reduced Cu-Aβ interaction-induced oxidative stress in Ctr1C RNAi flies. Similar results were obtained from inhibiting another copper importer Ctr1B and overexpressing a copper exporter DmATP7 in the nervous system of AD flies. These results imply that copper may play a causative role in developing AD, as either Aβ oligomers or aggregates were less toxic in a reduced copper environment or one with less copper binding. Early manipulation of brain copper uptake can have a great effect on Aβ pathology.

  11. Efficient Generation of Gene-Modified Pigs Harboring Precise Orthologous Human Mutation via CRISPR/Cas9-Induced Homology-Directed Repair in Zygotes.

    Science.gov (United States)

    Zhou, Xiaoyang; Wang, Lulu; Du, Yinan; Xie, Fei; Li, Liang; Liu, Yu; Liu, Chuanhong; Wang, Shiqiang; Zhang, Shibing; Huang, Xingxu; Wang, Yong; Wei, Hong

    2016-01-01

    Precise genetic mutation of model animals is highly valuable for functional investigation of human mutations. Clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated 9 (Cas9)-induced homology-directed repair (HDR) is usually used for precise genetic mutation, being limited by the relatively low efficiency compared with that of non-homologous end joining (NHEJ). Although inhibition of NHEJ was shown to enhance HDR-derived mutation, in this work, without inhibition of NHEJ, we first generated gene-modified pigs harboring precise orthologous human mutation (Sox10 c.A325>T) via CRISPR/Cas9-induced HDR in zygotes using single-strand oligo DNA (ssODN) as template with an efficiency as high as 80%, indicating that pig zygotes exhibited high activities of HDR relative to NHEJ and were highly amendable to genetic mutation via CIRSPR/Cas9-induced HDR. Besides, we found a higher concentration of ssODN remarkably reduced HDR-derived mutation in pig zygotes, suggesting a possible balance for optimal HDR-derived mutation in zygotes between the excessive accessibility to HDR templates and the activities of HDR relative to NHEJ which appeared to be negatively correlated to ssODN concentration. In addition, the HDR-derived mutation, as well as those from NHEJ, extensively integrated into various tissues including gonad of founder pig without detected off-targeting, suggesting CRISPR/Cas9-induced HDR in zygotes is a reliable approach for precise genetic mutation in pigs.

  12. Virus-encoded miR-155 ortholog is an important potential regulator but not essential for the development of lymphomas induced by very virulent Marek's disease virus.

    Science.gov (United States)

    Yu, Zu-Hua; Teng, Man; Sun, Ai-Jun; Yu, Le-Le; Hu, Bo; Qu, Liang-Hu; Ding, Ke; Cheng, Xiang-Chao; Liu, Ju-Xiong; Cui, Zhi-Zhong; Zhang, Gai-Ping; Luo, Jun

    2014-01-01

    The microRNA (miRNA) mdv1-miR-M4, a functional miR-155 ortholog encoded by oncogenic Marek's disease virus (MDV), has previously been suggested to be involved in MDV pathogenesis. Using the technique of bacterial artificial chromosome mutagenesis, we have presently evaluated the potential role of mdv1-miR-M4 in the oncogenesis of the very virulent (vv) MDV strain GX0101. Unexpectedly, deletions of the Meq-cluster or mdv1-miR-M4 alone from the viral genome strongly decreased rather than abolished its oncogenicity. Compared to GX0101, mortalities of mutants GXΔmiR-M4 and GXΔMeq-miRs were reduced from 100% to 18% and 4%, coupled with the gross tumor incidence reduction from 28% to 22% and 8%, respectively. Our data suggests that the mdv1-miR-M4 is possibly an important regulator in the development of Marek's disease (MD) lymphomas but is not essential for the oncogenicity of vvMDV. In addition, some of the other Meq-clustered miRNAs may also play potentially critical roles in vvMDV induction of lymphomas. PMID:24314636

  13. Identification of single-copy orthologous genes between Physalis and Solanum lycopersicum and analysis of genetic diversity in Physalis using molecular markers.

    Science.gov (United States)

    Wei, Jingli; Hu, Xiaorong; Yang, Jingjing; Yang, Wencai

    2012-01-01

    The genus Physalis includes a number of commercially important edible and ornamental species. Its high nutritional value and potential medicinal properties leads to the increased commercial interest in the products of this genus worldwide. However, lack of molecular markers prevents the detailed study of genetics and phylogeny in Physalis, which limits the progress of breeding. In the present study, we compared the DNA sequences between Physalis and tomato, and attempted to analyze genetic diversity in Physalis using tomato markers. Blasting 23180 DNA sequences derived from Physalis against the International Tomato Annotation Group (ITAG) Release2.3 Predicted CDS (SL2.40) discovered 3356 single-copy orthologous genes between them. A total of 38 accessions from at least six species of Physalis were subjected to genetic diversity analysis using 97 tomato markers and 25 SSR markers derived from P. peruviana. Majority (73.2%) of tomato markers could amplify DNA fragments from at least one accession of Physalis. Diversity in Physalis at molecular level was also detected. The average Nei's genetic distance between accessions was 0.3806 with a range of 0.2865 to 0.7091. These results indicated Physalis and tomato had similarity at both molecular marker and DNA sequence levels. Therefore, the molecular markers developed in tomato can be used in genetic study in Physalis. PMID:23166835

  14. Deletion of the Ustilago maydis ortholog of the Aspergillus sporulation regulator medA affects mating and virulence through pheromone response.

    Science.gov (United States)

    Chacko, Nadia; Gold, Scott

    2012-06-01

    Mating of compatible haploid cells of Ustilago maydis is essential for infection and disease development in the host. For mating and subsequent filamentous growth and pathogenicity, the transcription factor, prf1 is necessary. Prf1 is in turn regulated by the cAMP and MAPK pathways and other regulators like rop1 and hap1. Here we describe the identification of another putative Prf1 regulator, med1, the ortholog of the Aspergillus nidulans medusa (medA) transcription factor and show that it is required for mating and full virulence in U. maydis. med1 deletion mutants show both pre- and post-mating defects and are unresponsive to external pheromone. The expression of prf1 is down-regulated in Δmed1 compared to the wild type, suggesting that med1 is upstream of prf1. Additionally, indicative of a role in secondary metabolism regulation, deletion of the med1 gene de-represses the production of glycolipids in U. maydis.

  15. A novel DFNA36 mutation in TMC1 orthologous to the Beethoven (Bth mouse associated with autosomal dominant hearing loss in a Chinese family.

    Directory of Open Access Journals (Sweden)

    Yali Zhao

    Full Text Available Mutations in the transmembrane channel-like gene 1 (TMC1 can cause both DFNA36 and DFNB7/11 hearing loss. More than thirty DFNB7/11 mutations have been reported, but only three DFNA36 mutations were reported previously. In this study, we found a large Chinese family with 222 family members showing post-lingual, progressive sensorineural hearing loss which were consistent with DFNA36 hearing loss. Auditory brainstem response (ABR test of the youngest patient showed a special result with nearly normal threshold but prolonged latency, decreased amplitude, and the abnormal waveform morphology. Exome sequencing of the proband found four candidate variants in known hearing loss genes. Sanger sequencing in all family members found a novel variant c.1253T>A (p.M418K in TMC1 at DFNA36 that co-segregated with the phenotype. This mutation in TMC1 is orthologous to the mutation found in the hearing loss mouse model named Bth ten years ago. In another 51 Chinese autosomal dominant hearing loss families, we screened the segments containing the dominant mutations of TMC1 and no functional variants were found. TMC1 is expressed in the hair cells in inner ear. Given the already known roles of TMC1 in the mechanotransduction in the cochlea and its expression in inner ear, our results may provide an interesting perspective into its function in inner ear.

  16. A role for the yeast CLIP170 ortholog, the plus-end-tracking protein Bik1, and the Rho1 GTPase in Snc1 trafficking

    Science.gov (United States)

    Loeillet, Sophie; Kurzawa, Laetitia; Denarier, Eric; Aubry, Laurence

    2016-01-01

    ABSTRACT The diversity of microtubule functions is dependent on the status of tubulin C-termini. To address the physiological role of the C-terminal aromatic residue of α-tubulin, a tub1-Glu yeast strain expressing an α-tubulin devoid of its C-terminal amino acid was used to perform a genome-wide-lethality screen. The identified synthetic lethal genes suggested links with endocytosis and related processes. In the tub1-Glu strain, the routing of the v-SNARE Snc1 was strongly impaired, with a loss of its polarized distribution in the bud, and Abp1, an actin patch or endocytic marker, developed comet-tail structures. Snc1 trafficking required dynamic microtubules but not dynein and kinesin motors. Interestingly, deletion of the microtubule plus-end-tracking protein Bik1 (a CLIP170 ortholog), which is preferentially recruited to the C-terminal residue of α-tubulin, similarly resulted in Snc1 trafficking defects. Finally, constitutively active Rho1 rescued both Bik1 localization at the microtubule plus-ends in tub1-Glu strain and a correct Snc1 trafficking in a Bik1-dependent manner. Our results provide the first evidence for a role of microtubule plus-ends in membrane cargo trafficking in yeast, through Rho1- and Bik1-dependent mechanisms, and highlight the importance of the C-terminal α-tubulin amino acid in this process. PMID:27466378

  17. The Caenorhabditis elegans iodotyrosine deiodinase ortholog SUP-18 functions through a conserved channel SC-box to regulate the muscle two-pore domain potassium channel SUP-9.

    Directory of Open Access Journals (Sweden)

    Ignacio Perez de la Cruz

    2014-02-01

    Full Text Available Loss-of-function mutations in the Caenorhabditis elegans gene sup-18 suppress the defects in muscle contraction conferred by a gain-of-function mutation in SUP-10, a presumptive regulatory subunit of the SUP-9 two-pore domain K(+ channel associated with muscle membranes. We cloned sup-18 and found that it encodes the C. elegans ortholog of mammalian iodotyrosine deiodinase (IYD, an NADH oxidase/flavin reductase that functions in iodine recycling and is important for the biosynthesis of thyroid hormones that regulate metabolism. The FMN-binding site of mammalian IYD is conserved in SUP-18, which appears to require catalytic activity to function. Genetic analyses suggest that SUP-10 can function with SUP-18 to activate SUP-9 through a pathway that is independent of the presumptive SUP-9 regulatory subunit UNC-93. We identified a novel evolutionarily conserved serine-cysteine-rich region in the C-terminal cytoplasmic domain of SUP-9 required for its specific activation by SUP-10 and SUP-18 but not by UNC-93. Since two-pore domain K(+ channels regulate the resting membrane potentials of numerous cell types, we suggest that the SUP-18 IYD regulates the activity of the SUP-9 channel using NADH as a coenzyme and thus couples the metabolic state of muscle cells to muscle membrane excitability.

  18. Functional and spatial analysis of C. elegans SYG-1 and SYG-2, orthologs of the Neph/nephrin cell adhesion module directing selective synaptogenesis.

    Directory of Open Access Journals (Sweden)

    Nicola Wanner

    Full Text Available The assembly of specific synaptic connections represents a prime example of cellular recognition. Members of the Ig superfamily are among the most ancient proteins represented in the genomes of both mammalian and invertebrate organisms, where they constitute a trans-synaptic adhesion system. The correct connectivity patterns of the highly conserved immunoglobulin superfamily proteins nephrin and Neph1 are crucial for the assembly of functional neuronal circuits and the formation of the kidney slit diaphragm, a synapse-like structure forming the filtration barrier. Here, we utilize the nematode C. elegans model for studying the requirements of synaptic specificity mediated by nephrin-Neph proteins. In C. elegans, the nephrin/Neph1 orthologs SYG-2 and SYG-1 form intercellular contacts strictly in trans between epithelial guidepost cells and neurons specifying the localization of synapses. We demonstrate a functional conservation between mammalian nephrin and SYG-2. Expression of nephrin effectively compensated loss of syg-2 function in C. elegans and restored defective synaptic connectivity further establishing the C. elegans system as a valuable model for slit diaphragm proteins. Next, we investigated the effect of SYG-1 and SYG-2 trans homodimerization respectively. Strikingly, synapse assembly could be induced by homophilic SYG-1 but not SYG-2 binding indicating a critical role of SYG-1 intracellular signalling for morphogenetic events and pointing toward the dynamic and stochastic nature of extra- and intracellular nephrin-Neph interactions to generate reproducible patterns of synaptic connectivity.

  19. Identification of single-copy orthologous genes between Physalis and Solanum lycopersicum and analysis of genetic diversity in Physalis using molecular markers.

    Directory of Open Access Journals (Sweden)

    Jingli Wei

    Full Text Available The genus Physalis includes a number of commercially important edible and ornamental species. Its high nutritional value and potential medicinal properties leads to the increased commercial interest in the products of this genus worldwide. However, lack of molecular markers prevents the detailed study of genetics and phylogeny in Physalis, which limits the progress of breeding. In the present study, we compared the DNA sequences between Physalis and tomato, and attempted to analyze genetic diversity in Physalis using tomato markers. Blasting 23180 DNA sequences derived from Physalis against the International Tomato Annotation Group (ITAG Release2.3 Predicted CDS (SL2.40 discovered 3356 single-copy orthologous genes between them. A total of 38 accessions from at least six species of Physalis were subjected to genetic diversity analysis using 97 tomato markers and 25 SSR markers derived from P. peruviana. Majority (73.2% of tomato markers could amplify DNA fragments from at least one accession of Physalis. Diversity in Physalis at molecular level was also detected. The average Nei's genetic distance between accessions was 0.3806 with a range of 0.2865 to 0.7091. These results indicated Physalis and tomato had similarity at both molecular marker and DNA sequence levels. Therefore, the molecular markers developed in tomato can be used in genetic study in Physalis.

  20. Arabidopsis semidwarfs evolved from independent mutations in GA20ox1, ortholog to green revolution dwarf alleles in rice and barley.

    Science.gov (United States)

    Barboza, Luis; Effgen, Sigi; Alonso-Blanco, Carlos; Kooke, Rik; Keurentjes, Joost J B; Koornneef, Maarten; Alcázar, Rubén

    2013-09-24

    Understanding the genetic bases of natural variation for developmental and stress-related traits is a major goal of current plant biology. Variation in plant hormone levels and signaling might underlie such phenotypic variation occurring even within the same species. Here we report the genetic and molecular basis of semidwarf individuals found in natural Arabidopsis thaliana populations. Allelism tests demonstrate that independent loss-of-function mutations at GA locus 5 (GA5), which encodes gibberellin 20-oxidase 1 (GA20ox1) involved in the last steps of gibberellin biosynthesis, are found in different populations from southern, western, and northern Europe; central Asia; and Japan. Sequencing of GA5 identified 21 different loss-of-function alleles causing semidwarfness without any obvious general tradeoff affecting plant performance traits. GA5 shows signatures of purifying selection, whereas GA5 loss-of-function alleles can also exhibit patterns of positive selection in specific populations as shown by Fay and Wu's H statistics. These results suggest that antagonistic pleiotropy might underlie the occurrence of GA5 loss-of-function mutations in nature. Furthermore, because GA5 is the ortholog of rice SD1 and barley Sdw1/Denso green revolution genes, this study illustrates the occurrence of conserved adaptive evolution between wild A.thaliana and domesticated plants. PMID:24023067

  1. Insights into the origin of nematode chemosensory GPCRs: putative orthologs of the Srw family are found across several phyla of protostomes.

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    Arunkumar Krishnan

    Full Text Available Nematode chemosensory GPCRs in Caenorhabditis elegans (NemChRs are classified into 19 gene families, and are initially thought to have split from the ancestral Rhodopsin family of GPCRs. However, earlier studies have shown that among all 19 NemChR gene families, only the srw family has a clear sequence relationship to the ancestral Rhodopsin GPCR family. Yet, the phylogenetic relationships between the srw family of NemChRs and the Rhodopsin subfamilies are not fully understood. Also, a widespread search was not previously performed to check for the presence of putative srw family-like sequences or the other 18 NemChR families in several new protostome species outside the nematode lineage. In this study, we have investigated for the presence of 19 NemChR families across 26 eukaryotic species, covering basal eukaryotic branches and provide the first evidence that the srw family of NemChRs is indeed present across several phyla of protostomes. We could identify 29 putative orthologs of the srw family in insects (15 genes, molluscs (11 genes and Schistosoma mansoni (3 genes. Furthermore, using HMM-HMM profile based comparisons and phylogenetic analysis we show that among all Rhodopsin subfamilies, the peptide and SOG (somatostatin/opioid/galanin subfamilies are phylogenetically the closest relatives to the srw family of NemChRs. Taken together, we demonstrate that the srw family split from the large Rhodopsin family, possibly from the peptide and/or SOG subfamilies, well before the split of the nematode lineage, somewhere close to the divergence of the common ancestor of protostomes. Our analysis also suggests that the srsx family of NemChRs shares a clear sequence homology with the Rhodopsin subfamilies, as well as with few of the vertebrate olfactory receptors. Overall, this study provides further insights into the evolutionary events that shaped the GPCR chemosensory system in protostome species.

  2. The role of the RACK1 ortholog Cpc2p in modulating pheromone-induced cell cycle arrest in fission yeast.

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    Magdalena Mos

    Full Text Available The detection and amplification of extracellular signals requires the involvement of multiple protein components. In mammalian cells the receptor of activated C kinase (RACK1 is an important scaffolding protein for signal transduction networks. Further, it also performs a critical function in regulating the cell cycle by modulating the G1/S transition. Many eukaryotic cells express RACK1 orthologs, with one example being Cpc2p in the fission yeast Schizosaccharomyces pombe. In contrast to RACK1, Cpc2p has been described to positively regulate, at the ribosomal level, cells entry into M phase. In addition, Cpc2p controls the stress response pathways through an interaction with Msa2p, and sexual development by modulating Ran1p/Pat1p. Here we describe investigations into the role, which Cpc2p performs in controlling the G protein-mediated mating response pathway. Despite structural similarity to Gβ-like subunits, Cpc2p appears not to function at the G protein level. However, upon pheromone stimulation, cells overexpressing Cpc2p display substantial cell morphology defects, disorientation of septum formation and a significantly protracted G1 arrest. Cpc2p has the potential to function at multiple positions within the pheromone response pathway. We provide a mechanistic interpretation of this novel data by linking Cpc2p function, during the mating response, with its previous described interactions with Ran1p/Pat1p. We suggest that overexpressing Cpc2p prolongs the stimulated state of pheromone-induced cells by increasing ste11 gene expression. These data indicate that Cpc2p regulates the pheromone-induced cell cycle arrest in fission yeast by delaying cells entry into S phase.

  3. A motif-based search in bacterial genomes identifies the ortholog of the small RNA Yfr1 in all lineages of cyanobacteria

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    Axmann Ilka M

    2007-10-01

    Full Text Available Abstract Background Non-coding RNAs (ncRNA are regulators of gene expression in all domains of life. They control growth and differentiation, virulence, motility and various stress responses. The identification of ncRNAs can be a tedious process due to the heterogeneous nature of this molecule class and the missing sequence similarity of orthologs, even among closely related species. The small ncRNA Yfr1 has previously been found in the Prochlorococcus/Synechococcus group of marine cyanobacteria. Results Here we show that screening available genome sequences based on an RNA motif and followed by experimental analysis works successfully in detecting this RNA in all lineages of cyanobacteria. Yfr1 is an abundant ncRNA between 54 and 69 nt in size that is ubiquitous for cyanobacteria except for two low light-adapted strains of Prochlorococcus, MIT 9211 and SS120, in which it must have been lost secondarily. Yfr1 consists of two predicted stem-loop elements separated by an unpaired sequence of 16–20 nucleotides containing the ultraconserved undecanucleotide 5'-ACUCCUCACAC-3'. Conclusion Starting with an ncRNA previously found in a narrow group of cyanobacteria only, we show here the highly specific and sensitive identification of its homologs within all lineages of cyanobacteria, whereas it was not detected within the genome sequences of E. coli and of 7 other eubacteria belonging to the alpha-proteobacteria, chlorobiaceae and spirochaete. The integration of RNA motif prediction into computational pipelines for the detection of ncRNAs in bacteria appears as a promising step to improve the quality of such predictions.

  4. The C. elegans Chp/Wrch Ortholog CHW-1 Contributes to LIN-18/Ryk and LIN-17/Frizzled Signaling in Cell Polarity.

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    Ambrose R Kidd

    Full Text Available Wnt signaling controls various aspects of developmental and cell biology, as well as contributing to certain cancers. Expression of the human Rho family small GTPase Wrch/RhoU is regulated by Wnt signaling, and Wrch and its paralog Chp/RhoV are both implicated in oncogenic transformation and regulation of cytoskeletal dynamics. We performed developmental genetic analysis of the single Caenorhabditis elegans ortholog of Chp and Wrch, CHW-1. Using a transgenic assay of the distal tip cell migration, we found that wild-type CHW-1 is likely to be partially constitutively active and that we can alter ectopic CHW-1-dependent migration phenotypes with mutations predicted to increase or decrease intrinsic GTP hydrolysis rate. The vulval P7.p polarity decision balances multiple antagonistic Wnt signals, and also uses different types of Wnt signaling. Previously described cooperative Wnt receptors LIN-17/Frizzled and LIN-18/Ryk orient P7.p posteriorly, with LIN-17/Fz contributing approximately two-thirds of polarizing activity. CHW-1 deletion appears to equalize the contributions of these two receptors. We hypothesize that CHW-1 increases LIN-17/Fz activity at the expense of LIN-18/Ryk, thus making the contribution of these signals unequal. For P7.p to polarize correctly and form a proper vulva, LIN-17/Fz and LIN-18/Ryk antagonize other Wnt transmembrane systems VANG-1/VanGogh and CAM-1/Ror. Our genetic data suggest that LIN-17/Fz represses both VANG-1/VanGogh and CAM-1/Ror, while LIN-18/Ryk represses only VANG-1. These data expand our knowledge of a sophisticated signaling network to control P7.p polarity, and suggests that CHW-1 can alter ligand gradients or receptor priorities in the system.

  5. The C. elegans Chp/Wrch Ortholog CHW-1 Contributes to LIN-18/Ryk and LIN-17/Frizzled Signaling in Cell Polarity.

    Science.gov (United States)

    Kidd, Ambrose R; Muñiz-Medina, Vanessa; Der, Channing J; Cox, Adrienne D; Reiner, David J

    2015-01-01

    Wnt signaling controls various aspects of developmental and cell biology, as well as contributing to certain cancers. Expression of the human Rho family small GTPase Wrch/RhoU is regulated by Wnt signaling, and Wrch and its paralog Chp/RhoV are both implicated in oncogenic transformation and regulation of cytoskeletal dynamics. We performed developmental genetic analysis of the single Caenorhabditis elegans ortholog of Chp and Wrch, CHW-1. Using a transgenic assay of the distal tip cell migration, we found that wild-type CHW-1 is likely to be partially constitutively active and that we can alter ectopic CHW-1-dependent migration phenotypes with mutations predicted to increase or decrease intrinsic GTP hydrolysis rate. The vulval P7.p polarity decision balances multiple antagonistic Wnt signals, and also uses different types of Wnt signaling. Previously described cooperative Wnt receptors LIN-17/Frizzled and LIN-18/Ryk orient P7.p posteriorly, with LIN-17/Fz contributing approximately two-thirds of polarizing activity. CHW-1 deletion appears to equalize the contributions of these two receptors. We hypothesize that CHW-1 increases LIN-17/Fz activity at the expense of LIN-18/Ryk, thus making the contribution of these signals unequal. For P7.p to polarize correctly and form a proper vulva, LIN-17/Fz and LIN-18/Ryk antagonize other Wnt transmembrane systems VANG-1/VanGogh and CAM-1/Ror. Our genetic data suggest that LIN-17/Fz represses both VANG-1/VanGogh and CAM-1/Ror, while LIN-18/Ryk represses only VANG-1. These data expand our knowledge of a sophisticated signaling network to control P7.p polarity, and suggests that CHW-1 can alter ligand gradients or receptor priorities in the system. PMID:26208319

  6. Caenorhabditis elegans AGXT-1 is a mitochondrial and temperature-adapted ortholog of peroxisomal human AGT1: New insights into between-species divergence in glyoxylate metabolism.

    Science.gov (United States)

    Mesa-Torres, Noel; Calvo, Ana C; Oppici, Elisa; Titelbaum, Nicholas; Montioli, Riccardo; Miranda-Vizuete, Antonio; Cellini, Barbara; Salido, Eduardo; Pey, Angel L

    2016-09-01

    In humans, glyoxylate is an intermediary product of metabolism, whose concentration is finely balanced. Mutations in peroxisomal alanine:glyoxylate aminotransferase (hAGT1) cause primary hyperoxaluria type 1 (PH1), which results in glyoxylate accumulation that is converted to toxic oxalate. In contrast, glyoxylate is used by the nematode Caenorhabditis elegans through a glyoxylate cycle to by-pass the decarboxylation steps of the tricarboxylic acid cycle and thus contributing to energy production and gluconeogenesis from stored lipids. To investigate the differences in glyoxylate metabolism between humans and C. elegans and to determine whether the nematode might be a suitable model for PH1, we have characterized here the predicted nematode ortholog of hAGT1 (AGXT-1) and compared its molecular properties with those of the human enzyme. Both enzymes form active PLP-dependent dimers with high specificity towards alanine and glyoxylate, and display similar three-dimensional structures. Interestingly, AGXT-1 shows 5-fold higher activity towards the alanine/glyoxylate pair than hAGT1. Thermal and chemical stability of AGXT-1 is lower than that of hAGT1, suggesting temperature-adaptation of the nematode enzyme linked to the lower optimal growth temperature of C. elegans. Remarkably, in vivo experiments demonstrate the mitochondrial localization of AGXT-1 in contrast to the peroxisomal compartmentalization of hAGT1. Our results support the view that the different glyoxylate metabolism in the nematode is associated with the divergent molecular properties and subcellular localization of the alanine:glyoxylate aminotransferase activity.

  7. Endo-(1,4-β-Glucanase gene families in the grasses: temporal and spatial Co-transcription of orthologous genes1

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    Buchanan Margaret

    2012-12-01

    Full Text Available Abstract Background Endo-(1,4-β-glucanase (cellulase glycosyl hydrolase GH9 enzymes have been implicated in several aspects of cell wall metabolism in higher plants, including cellulose biosynthesis and degradation, modification of other wall polysaccharides that contain contiguous (1,4-β-glucosyl residues, and wall loosening during cell elongation. Results The endo-(1,4-β-glucanase gene families from barley (Hordeum vulgare, maize (Zea mays, sorghum (Sorghum bicolor, rice (Oryza sativa and Brachypodium (Brachypodium distachyon range in size from 23 to 29 members. Phylogenetic analyses show variations in clade structure between the grasses and Arabidopsis, and indicate differential gene loss and gain during evolution. Map positions and comparative studies of gene structures allow orthologous genes in the five species to be identified and synteny between the grasses is found to be high. It is also possible to differentiate between homoeologues resulting from ancient polyploidizations of the maize genome. Transcript analyses using microarray, massively parallel signature sequencing and quantitative PCR data for barley, rice and maize indicate that certain members of the endo-(1,4-β-glucanase gene family are transcribed across a wide range of tissues, while others are specifically transcribed in particular tissues. There are strong correlations between transcript levels of several members of the endo-(1,4-β-glucanase family and the data suggest that evolutionary conservation of transcription exists between orthologues across the grass family. There are also strong correlations between certain members of the endo-(1,4-β-glucanase family and other genes known to be involved in cell wall loosening and cell expansion, such as expansins and xyloglucan endotransglycosylases. Conclusions The identification of these groups of genes will now allow us to test hypotheses regarding their functions and joint participation in wall synthesis, re

  8. Identification of functionally important residues of the silkmoth pheromone biosynthesis-activating neuropeptide receptor, an insect ortholog of the vertebrate neuromedin U receptor.

    Science.gov (United States)

    Kawai, Takeshi; Katayama, Yukie; Guo, Linjun; Liu, Desheng; Suzuki, Tatsuya; Hayakawa, Kou; Lee, Jae Min; Nagamine, Toshihiro; Hull, J Joe; Matsumoto, Shogo; Nagasawa, Hiromichi; Tanokura, Masaru; Nagata, Koji

    2014-07-01

    The biosynthesis of sex pheromone components in many lepidopteran insects is regulated by the interaction between pheromone biosynthesis-activating neuropeptide (PBAN) and the PBAN receptor (PBANR), a class A G-protein-coupled receptor. To identify functionally important amino acid residues in the silkmoth PBANR, a series of 27 alanine substitutions was generated using a PBANR chimera C-terminally fused with enhanced GFP. The PBANR mutants were expressed in Sf9 insect cells, and their ability to bind and be activated by a core PBAN fragment (C10PBAN(R2K)) was monitored. Among the 27 mutants, 23 localized to the cell surface of transfected Sf9 cells, whereas the other four remained intracellular. Reduced binding relative to wild type was observed with 17 mutants, and decreased Ca(2+) mobilization responses were observed with 12 mutants. Ala substitution of Glu-95, Glu-120, Asn-124, Val-195, Phe-276, Trp-280, Phe-283, Arg-287, Tyr-307, Thr-311, and Phe-319 affected both binding and Ca(2+) mobilization. The most pronounced effects were observed with the E120A mutation. A molecular model of PBANR indicated that the functionally important PBANR residues map to the 2nd, 3rd, 6th, and 7th transmembrane helices, implying that the same general region of class A G-protein-coupled receptors recognizes both peptidic and nonpeptidic ligands. Docking simulations suggest similar ligand-receptor recognition interactions for PBAN-PBANR and the orthologous vertebrate pair, neuromedin U (NMU) and NMU receptor (NMUR). The simulations highlight the importance of two glutamate residues, Glu-95 and Glu-120, in silkmoth PBANR and Glu-117 and Glu-142 in human NMUR1, in the recognition of the most functionally critical region of the ligands, the C-terminal residue and amide. PMID:24847080

  9. The Salmonella enterica PhoP directly activates the horizontally acquired SPI-2 gene sseL and is functionally different from a S. bongori ortholog.

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    Ohad Gal-Mor

    Full Text Available To establish a successful infection within the host, a pathogen must closely regulate multiple virulence traits to ensure their accurate temporal and spatial expression. As a highly adapted intracellular pathogen, Salmonella enterica has acquired during its evolution various virulence genes via numerous lateral transfer events, including the acquisition of the Salmonella Pathogenicity Island 2 (SPI-2 and its associated effectors. Beneficial use of horizontally acquired genes requires that their expression is effectively coordinated with the already existing virulence programs and the regulatory set-up in the bacterium. As an example for such a mechanism, we show here that the ancestral PhoPQ system of Salmonella enterica is able to regulate directly the SPI-2 effector gene sseL (encoding a secreted deubiquitinase in an SsrB-independent manner and that PhoP plays a part in a feed-forward regulatory loop, which fine-tunes the cellular level of SseL. Additionally, we demonstrate the presence of conserved cis regulatory elements in the promoter region of sseL and show direct binding of purified PhoP to this region. Interestingly, in contrast to the S. enterica PhoP, an ortholog regulator from a S. bongori SARC 12 strain was found to be impaired in promoting transcription of sseL and other genes from the PhoP regulon. These findings have led to the identification of a previously uncharacterized residue in the DNA-binding domain of PhoP, which is required for the transcriptional activation of PhoP regulated genes in Salmonella spp. Collectively our data demonstrate an interesting interface between the acquired SsrB regulon and the ancestral PhoPQ regulatory circuit, provide novel insights into the function of PhoP, and highlight a mechanism of regulatory integration of horizontally acquired genes into the virulence network of Salmonella enterica.

  10. AtbHLH29 of Arabidopsis thaliana is a functional ortholog of tomato FER involved in controlling iron acquisition in strategy I plants

    Institute of Scientific and Technical Information of China (English)

    You Xi YUAN; Juan ZHANG; Dao Wen WANG; Hong Qing LING

    2005-01-01

    AtbHLH29 of Arabidopsis, encoding a bHLH protein, reveals a high similarity to the tomato FER which is proposed as a transcriptional regulator involved in controlling the iron deficiency responses and the iron uptake in tomato. For identification of its biological functions, AtbHLH29 was introduced into the genome of the tomato FER mutant T3238fer mediated by Agrobacterium tumefaciencs. Transgenic plants were regenerated and the stable integration of AtbHLH29 into their genomes was confirmed by Southern hybridization. Molecular analysis demonstrated that expression of the exogenous AtbHLH29 of Arabidopsis in roots of the FER mutant T3238fer enabled to complement the defect functions of FER. The transgenic plants regained the ability to activate the whole iron deficiency responses and showed normal growth as the wild type under iron-limiting stress. Our transformation data demonstrate that AtbHLH29 is a functional ortholog of the tomato FER and can completely replace FER in controlling the effective iron acquisition in tomato.Except of iron, FER protein was directly or indirectly involved in manganese homeostasis due to that loss functions of FER in T3238fer resulted in strong reduction of Mn content in leaves and the defect function on Mn accumulation in leaves was complemented by expression of AtbHLH29 in the transgenic plants. Identification of the similar biological functions of FER and AtbHLH29, which isolated from two systematically wide-diverged "strategy I" plants, suggests that FER might be a universal gene presented in all strategy I plants in controlling effective iron acquisition system in roots.

  11. Characterization of ferritin 2 for the control of tick infestations.

    Science.gov (United States)

    Hajdusek, Ondrej; Almazán, Consuelo; Loosova, Gabriela; Villar, Margarita; Canales, Mario; Grubhoffer, Libor; Kopacek, Petr; de la Fuente, José

    2010-04-01

    Ixodes ricinus is one the most abundant tick species in Europe and these ticks transmit pathogens causing human and animal diseases. The cattle ticks, Rhipicephalus (Boophilus) spp., affect cattle production in tropical and subtropical regions of the world. Development of vaccines directed against tick proteins may reduce tick infestations and the transmission of tick-borne pathogens. However, a limiting step in tick vaccine development has been the identification of tick protective antigens. Herein, the tick iron metabolism pathway was targeted in an effort to identify new tick protective antigens. Recombinant I. ricinus (IrFER2) and Rhipicephalus microplus (RmFER2) ferritin 2 proteins were expressed in Escherichia coli and used to immunize rabbits and cattle, respectively. Vaccination with IrFER2 reduced I. ricinus tick numbers, weight and fertility in rabbits with an overall vaccine efficacy (E) of 98%. Control of cattle tick, R. microplus and Rhipicephalus annulatus infestations was obtained in vaccinated cattle with overall E of 64% and 72%, respectively. Notably, the efficacy of the RmFER2 vaccine was similar to that obtained with Bm86 against R. microplus. These collective results demonstrated the feasibility of using ferritin 2 to develop vaccines for the control of tick infestations. PMID:20171306

  12. Control of tick infestations in cattle vaccinated with bacterial membranes containing surface-exposed tick protective antigens.

    Science.gov (United States)

    Almazán, Consuelo; Moreno-Cantú, Orlando; Moreno-Cid, Juan A; Galindo, Ruth C; Canales, Mario; Villar, Margarita; de la Fuente, José

    2012-01-01

    Vaccines containing the Rhipicephalus (Boophilus) microplus BM86 and BM95 antigens protect cattle against tick infestations. Tick subolesin (SUB), elongation factor 1a (EF1a) and ubiquitin (UBQ) are new candidate protective antigens for the control of cattle tick infestations. Previous studies showed that R. microplus BM95 immunogenic peptides fused to the Anaplasma marginale major surface protein (MSP) 1a N-terminal region (BM95-MSP1a) for presentation on the Escherichia coli membrane were protective against R. microplus infestations in rabbits. In this study, we extended these results by expressing SUB-MSP1a, EF1a-MSP1a and UBQ-MSP1a fusion proteins on the E. coli membrane using this system and demonstrating that bacterial membranes containing the chimeric proteins BM95-MSP1a and SUB-MSP1a were protective (>60% vaccine efficacy) against experimental R. microplus and Rhipicephalus annulatus infestations in cattle. This system provides a novel, simple and cost-effective approach for the production of tick protective antigens by surface display of antigenic protein chimera on the E. coli membrane and demonstrates the possibility of using recombinant bacterial membrane fractions in vaccine preparations to protect cattle against tick infestations. PMID:22085549

  13. Candida albicans AGE3, the ortholog of the S. cerevisiae ARF-GAP-encoding gene GCS1, is required for hyphal growth and drug resistance.

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    Thomas Lettner

    Full Text Available BACKGROUND: Hyphal growth and multidrug resistance of C. albicans are important features for virulence and antifungal therapy of this pathogenic fungus. METHODOLOGY/PRINCIPAL FINDINGS: Here we show by phenotypic complementation analysis that the C. albicans gene AGE3 is the functional ortholog of the yeast ARF-GAP-encoding gene GCS1. The finding that the gene is required for efficient endocytosis points to an important functional role of Age3p in endosomal compartments. Most C. albicans age3Delta mutant cells which grew as cell clusters under yeast growth conditions showed defects in filamentation under different hyphal growth conditions and were almost completely disabled for invasive filamentous growth. Under hyphal growth conditions only a fraction of age3Delta cells shows a wild-type-like polarization pattern of the actin cytoskeleton and lipid rafts. Moreover, age3Delta cells were highly susceptible to several unrelated toxic compounds including antifungal azole drugs. Irrespective of the AGE3 genotype, C-terminal fusions of GFP to the drug efflux pumps Cdr1p and Mdr1p were predominantly localized in the plasma membrane. Moreover, the plasma membranes of wild-type and age3Delta mutant cells contained similar amounts of Cdr1p, Cdr2p and Mdr1p. CONCLUSIONS/SIGNIFICANCE: The results indicate that the defect in sustaining filament elongation is probably caused by the failure of age3Delta cells to polarize the actin cytoskeleton and possibly of inefficient endocytosis. The high susceptibility of age3Delta cells to azoles is not caused by inefficient transport of efflux pumps to the cell membrane. A possible role of a vacuolar defect of age3Delta cells in drug susceptibility is proposed and discussed. In conclusion, our study shows that the ARF-GAP Age3p is required for hyphal growth which is an important virulence factor of C. albicans and essential for detoxification of azole drugs which are routinely used for antifungal therapy. Thus, it

  14. miR-1279, miR-548j, miR-548m, and miR-548d-5p Binding Sites in CDSs of Paralogous and Orthologous PTPN12, MSH6, and ZEB1 Genes

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    Anatoliy T. Ivashchenko

    2013-01-01

    Full Text Available Only PTPN12, MSH6, and ZEB1 have significant miR-1279 binding sites among paralogous genes of human tyrosine phosphatase family, DNA mismatch repair family, and zinc finger family, respectively. All miRNA binding sites are located within CDSs of studied mRNAs. Nucleotide sequences of hsa-miR-1279 binding sites with mRNAs of human PTPN12, MSH6, and ZEB1 genes encode TKEQYE, EGSSDE, and GEKPYE oligopeptides, respectively. The conservation of miRNA binding sites encoding oligopeptides has been revealed. MRNAs of many paralogs of zinc finger gene family have from 1 to 12 binding sites coding the same GEKPYE hexapeptide. MRNAs of PTPN12, MSH6, and ZEB1 orthologous genes from different animal species have binding sites for hsa-miR-1279 which consist of homologous oligonucleotides encoding similar human oligopeptides TKEQYE, EGSSDE, and GEKPYE. MiR-548j, miR-548m, and miR-548d-5p have homologous binding sites in the mRNA of PTPN12 orthologous genes which encode PRTRSC, TEATDI, and STASAT oligopeptides, respectively. All regions of miRNA are important for binding with the mRNA.

  15. From zebrafish heart jogging genes to mouse and human orthologs: using Gene Ontology to investigate mammalian heart development. [v2; ref status: indexed, http://f1000r.es/2ys

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    Varsha K Khodiyar

    2014-02-01

    Full Text Available For the majority of organs in developing vertebrate embryos, left-right asymmetry is controlled by a ciliated region; the left-right organizer node in the mouse and human, and the Kuppfer’s vesicle in the zebrafish. In the zebrafish, laterality cues from the Kuppfer’s vesicle determine asymmetry in the developing heart, the direction of ‘heart jogging’ and the direction of ‘heart looping’.  ‘Heart jogging’ is the term given to the process by which the symmetrical zebrafish heart tube is displaced relative to the dorsal midline, with a leftward ‘jog’. Heart jogging is not considered to occur in mammals, although a leftward shift of the developing mouse caudal heart does occur prior to looping, which may be analogous to zebrafish heart jogging. Previous studies have characterized 30 genes involved in zebrafish heart jogging, the majority of which have well defined orthologs in mouse and human and many of these orthologs have been associated with early mammalian heart development.    We undertook manual curation of a specific set of genes associated with heart development and we describe the use of Gene Ontology term enrichment analyses to examine the cellular processes associated with heart jogging.  We found that the human, mouse and zebrafish ‘heart jogging orthologs’ are involved in similar organ developmental processes across the three species, such as heart, kidney and nervous system development, as well as more specific cellular processes such as cilium development and function. The results of these analyses are consistent with a role for cilia in the determination of left-right asymmetry of many internal organs, in addition to their known role in zebrafish heart jogging.    This study highlights the importance of model organisms in the study of human heart development, and emphasises both the conservation and divergence of developmental processes across vertebrates, as well as the limitations of this approach.

  16. From zebrafish heart jogging genes to mouse and human orthologs: using Gene Ontology to investigate mammalian heart development. [v1; ref status: indexed, http://f1000r.es/28b

    Directory of Open Access Journals (Sweden)

    Varsha K Khodiyar

    2013-11-01

    Full Text Available For the majority of organs in developing vertebrate embryos, left-right asymmetry is controlled by a ciliated region; the left-right organizer node in the mouse and human, and the Kuppfer’s vesicle in the zebrafish. In the zebrafish, laterality cues from the Kuppfer’s vesicle determine asymmetry in the developing heart, the direction of ‘heart jogging’ and the direction of ‘heart looping’.  ‘Heart jogging’ is the term given to the process by which the symmetrical zebrafish heart tube is displaced relative to the dorsal midline, with a leftward ‘jog’. Heart jogging is not considered to occur in mammals, although a leftward shift of the developing mouse caudal heart does occur prior to looping, which may be analogous to zebrafish heart jogging. Previous studies have characterized 30 genes involved in zebrafish heart jogging, the majority of which have well defined orthologs in mouse and human and many of these orthologs have been associated with early mammalian heart development.    We undertook manual curation of a specific set of genes associated with heart development and we describe the use of Gene Ontology term enrichment analyses to examine the cellular processes associated with heart jogging.  We found that the human, mouse and zebrafish ‘heart jogging orthologs’ are involved in similar organ developmental processes across the three species, such as heart, kidney and nervous system development, as well as more specific cellular processes such as cilium development and function. The results of these analyses are consistent with a role for cilia in the determination of left-right asymmetry of many internal organs, in addition to their known role in zebrafish heart jogging.    This study highlights the importance of model organisms in the study of human heart development, and emphasises both the conservation and divergence of developmental processes across vertebrates, as well as the limitations of this approach.

  17. Proteomic characterization of the small subunit of Chlamydomonas reinhardtii chloroplast ribosome: identification of a novel S1 domain-containing protein and unusually large orthologs of bacterial S2, S3, and S5.

    Science.gov (United States)

    Yamaguchi, Kenichi; Prieto, Susana; Beligni, María Verónica; Haynes, Paul A; McDonald, W Hayes; Yates, John R; Mayfield, Stephen P

    2002-11-01

    To understand how chloroplast mRNAs are translated into functional proteins, a detailed understanding of all of the components of chloroplast translation is needed. To this end, we performed a proteomic analysis of the plastid ribosomal proteins in the small subunit of the chloroplast ribosome from the green alga Chlamydomonas reinhardtii. Twenty proteins were identified, including orthologs of Escherichia coli S1, S2, S3, S4, S5, S6, S7, S9, S10, S12, S13, S14, S15, S16, S17, S18, S19, S20, and S21 and a homolog of spinach plastid-specific ribosomal protein-3 (PSRP-3). In addition, a novel S1 domain-containing protein, PSRP-7, was identified. Among the identified proteins, S2 (57 kD), S3 (76 kD), and S5 (84 kD) are prominently larger than their E. coli or spinach counterparts, containing N-terminal extensions (S2 and S5) or insertion sequence (S3). Structural predictions based on the crystal structure of the bacterial 30S subunit suggest that the additional domains of S2, S3, and S5 are located adjacent to each other on the solvent side near the binding site of the S1 protein. These additional domains may interact with the S1 protein and PSRP-7 to function in aspects of mRNA recognition and translation initiation that are unique to the Chlamydomonas chloroplast.

  18. Structures of PHR Domains from Mus musculus Phr1 (Mycbp2) Explain the Loss-of-Function Mutation (Gly1092 → Glu) of the C. elegans Ortholog RPM-1

    Energy Technology Data Exchange (ETDEWEB)

    Sampathkumar, Parthasarathy; Ozyurt, Sinem A.; Miller, Stacy A.; Bain, Kevin T.; Rutter, Marc E.; Gheyi, Tarun; Abrams, Benjamin; Wang, Yingchun; Atwell, Shane; Luz, John G.; Thompson, Devon A.; Wasserman, Stephen R.; Emtage, J. Spencer; Park, Eun Chan; Rongo, Christopher; Jin, Yishi; Klemke, Richard L.; Sauder, J. Michael; Burley, Stephen K. (Rutgers); (UCSC); (Lilly); (UCSD)

    2010-11-15

    PHR [PAM (protein associated with Myc)-HIW (Highwire)-RPM-1 (regulator of presynaptic morphology 1)] proteins are conserved, large multi-domain E3 ubiquitin ligases with modular architecture. PHR proteins presynaptically control synaptic growth and axon guidance and postsynaptically regulate endocytosis of glutamate receptors. Dysfunction of neuronal ubiquitin-mediated proteasomal degradation is implicated in various neurodegenerative diseases. PHR proteins are characterized by the presence of two PHR domains near the N-terminus, which are essential for proper localization and function. Structures of both the first and second PHR domains of Mus musculus (mouse) Phr1 (MYC binding protein 2, Mycbp2) have been determined, revealing a novel {beta} sandwich fold composed of 11 antiparallel {beta}-strands. Conserved loops decorate the apical side of the first PHR domain (MmPHR1), yielding a distinct conserved surface feature. The surface of the second PHR domain (MmPHR2), in contrast, lacks significant conservation. Importantly, the structure of MmPHR1 provides insights into a loss-of-function mutation, Gly1092 {yields} Glu, observed in the Caenorhabditis elegans ortholog RPM-1.

  19. Hd86 mRNA expression profile in Hyalomma scupense life stages, could it contribute to explain anti-tick vaccine effect discrepancy between adult and immature instars?

    Science.gov (United States)

    Ben Said, Mourad; Galaï, Yousr; Ben Ahmed, Melika; Gharbi, Mohamed; de la Fuente, José; Jedidi, Mohamed; Darghouth, Mohamed Aziz

    2013-11-15

    Bm86 midgut protein has been used in order to control ticks of the Hyalomma genus. Previous studies demonstrated the inefficacity of this antigen in the control of Hyalomma scupense, whereas recombinant Hd86 antigen, the Bm86 ortholog in H. scupense produced in Pichia pastoris, was protective against larval H. scupense tick stage infestations but ineffective in the control of the adult stage. One possible explanation for this result is the variation in Hd86 expression levels between these two developmental stages. To test this hypothesis, Hd86 mRNA levels were characterized in H. scupense developmental stages. The expression profile of Hd86 demonstrated a significant variation between tick life stages and showed a significant reduction in the number of transcripts during feeding and, particularly after molting to adults. The most interesting result was noted after molting of engorged nymphs in unfed adults where the expression levels decreased significantly by 12.78 (10.77-17.39) (p<0.001) and 9.25 (5.77-15.72)-fold (p<0.001) in unfed males and unfed females, respectively. Comparing unfed nymphs to unfed adult ticks, the Hd86 expression levels decreased by 13.82 (5.39-24.45) (p=0.035) and 9.93 (2.87-22.08)-fold (p=0.038) in males and females respectively. Lower Hd86 mRNA levels in adult ticks should result in lower protein levels and thus less antibody-antigen interactions necessary for vaccine efficacy in ticks fed on vaccinated animals. Thus, the observed differences in Hd86 expression profile between immature and adult stages might explain, in part, the discrepancy of the Hd86 vaccine efficacy against these two life stages of H. scupense. PMID:24029714

  20. Analysis of genomic DNA of DcACS1, a 1-aminocyclopropane-1-carboxylate synthase gene, expressed in senescing petals of carnation (Dianthus caryophyllus) and its orthologous genes in D. superbus var. longicalycinus.

    Science.gov (United States)

    Harada, Taro; Murakoshi, Yuino; Torii, Yuka; Tanase, Koji; Onozaki, Takashi; Morita, Shigeto; Masumura, Takehiro; Satoh, Shigeru

    2011-04-01

    Carnation (Dianthus caryophyllus) flowers exhibit climacteric ethylene production followed by petal wilting, a senescence symptom. DcACS1, which encodes 1-aminocyclopropane-1-carboxylate synthase (ACS), is a gene involved in this phenomenon. We determined the genomic DNA structure of DcACS1 by genomic PCR. In the genome of 'Light Pink Barbara', we found two distinct nucleotide sequences: one corresponding to the gene previously shown as DcACS1, designated here as DcACS1a, and the other novel one designated as DcACS1b. It was revealed that both DcACS1a and DcACS1b have five exons and four introns. These two genes had almost identical nucleotide sequences in exons, but not in some introns and 3'-UTR. Analysis of transcript accumulation revealed that DcACS1b is expressed in senescing petals as well as DcACS1a. Genomic PCR analysis of 32 carnation cultivars showed that most cultivars have only DcACS1a and some have both DcACS1a and DcACS1b. Moreover, we found two DcACS1 orthologous genes with different nucleotide sequences from D. superbus var. longicalycinus, and designated them as DsuACS1a and DsuACS1b. Petals of D. superbus var. longicalycinus produced ethylene in response to exogenous ethylene, accompanying accumulation of DsuACS1 transcripts. These data suggest that climacteric ethylene production in flowers was genetically established before the cultivation of carnation.

  1. ASYMMETRIC-LEAVES2 and an ortholog of eukaryotic NudC domain proteins repress expression of AUXIN-RESPONSE-FACTOR and class 1 KNOX homeobox genes for development of flat symmetric leaves in Arabidopsis

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    Nanako Ishibashi

    2012-01-01

    Leaf primordia form around the shoot apical meristem, which consists of indeterminate stem cells. Upon initiation of leaf development, adaxial-abaxial patterning is crucial for appropriate lateral expansion, via cellular proliferation, and the formation of flat symmetric leaves. Many genes that specify such patterning have been identified, but regulation by upstream factors of the expression of relevant effector genes remains poorly understood. In Arabidopsis thaliana, ASYMMETRIC LEAVES2 (AS2 and AS1 play important roles in repressing transcription of class 1 KNOTTED1-like homeobox (KNOX genes and leaf abaxial-determinant effector genes. We report here a mutation, designated enhancer of asymmetric leaves2 and asymmetric leaves1 (eal, that is associated with efficient generation of abaxialized filamentous leaves on the as2 or as1 background. Levels of transcripts of many abaxial-determinant genes, including ETTIN (ETT/AUXIN RESPONSE FACTOR3 (ARF3, and all four class 1 KNOX genes were markedly elevated in as2 eal shoot apices. Rudimentary patterning in as2 eal leaves was suppressed by the ett mutation. EAL encodes BOBBER1 (BOB1, an Arabidopsis ortholog of eukaryotic NudC domain proteins. BOB1 was expressed in plant tissues with division potential and bob1 mutations resulted in lowered levels of transcripts of some cell-cycle genes and decreased rates of cell division in shoot and root apices. Coordinated cellular proliferation, supported by BOB1, and repression of all class 1 KNOX genes, ETT/ARF3 by AS2 (AS1 and BOB1 might be critical for repression of the indeterminate state and of aberrant abaxialization in the presumptive adaxial domain of leaf primordia, which might ensure the formation of flat symmetric leaves.

  2. The Mammalian Orthologs of Drosophila Lgd, CC2D1A and CC2D1B, Function in the Endocytic Pathway, but Their Individual Loss of Function Does Not Affect Notch Signalling.

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    Nadja Drusenheimer

    2015-12-01

    Full Text Available CC2D1A and CC2D1B belong to the evolutionary conserved Lgd protein family with members in all multi-cellular animals. Several functions such as centrosomal cleavage, involvement in signalling pathways, immune response and synapse maturation have been described for CC2D1A. Moreover, the Drosophila melanogaster ortholog Lgd was shown to be involved in the endosomal trafficking of the Notch receptor and other transmembrane receptors and physically interacts with the ESCRT-III component Shrub/CHMP4. To determine if this function is conserved in mammals we generated and characterized Cc2d1a and Cc2d1b conditional knockout mice. While Cc2d1b deficient mice displayed no obvious phenotype, we found that Cc2d1a deficient mice as well as conditional mutants that lack CC2D1A only in the nervous system die shortly after birth due to respiratory distress. This finding confirms the suspicion that the breathing defect is caused by the central nervous system. However, an involvement in centrosomal function could not be confirmed in Cc2d1a deficient MEF cells. To analyse an influence on Notch signalling, we generated intestine specific Cc2d1a mutant mice. These mice did not display any alterations in goblet cell number, proliferating cell number or expression of the Notch reporter Hes1-emGFP, suggesting that CC2D1A is not required for Notch signalling. However, our EM analysis revealed that the average size of endosomes of Cc2d1a mutant cells, but not Cc2d1b mutant cells, is increased, indicating a defect in endosomal morphogenesis. We could show that CC2D1A and its interaction partner CHMP4B are localised on endosomes in MEF cells, when the activity of the endosomal protein VPS4 is reduced. This indicates that CC2D1A cycles between the cytosol and the endosomal membrane. Additionally, in rescue experiments in D. melanogaster, CC2D1A and CC2D1B were able to functionally replace Lgd. Altogether our data suggest a functional conservation of the Lgd protein family

  3. Protein (Cyanobacteria): 260653 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available e protein Arthrospira sp. PCC 8005 MSGVGLGYSMSGVGMSGVGLGVTESGVGLGYSMSGVGMSGVGLGVTESGVGLGYSMSGVGMSGVGLGVTESGVGLGYSMSGVGMSGVGLGYSMS...GVGMSGVGLGVTESGVGLGYSMSGVGMSGVGLGVTESGSALGYSMSGVGMSGVGMGYSMSGVGMTESGSALGYSMSGVGMSGVGMGYSMSGVGMTESGSALGYSMS...GVGMSGVGMGYSMSGVGMTESGSALSYSMSGVGMSGVGMAERMSGIGFTMSGSALGYSMSGI

  4. Protein (Cyanobacteria): 108117 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available rotein MC7420_8002 Coleofasciculus chthonoplastes PCC 7420 MARLYRMGRRWILLTSIKDSSMSIKHSSMSIKHSSASIKHSSASTKHSSMSIKHSSASTKHSSMS...IKHSSASIKHSSMSIKHSSASIKHSSASIKHSSVSIKHSSVSIKHSSASIKHSSMSIKHSSAMNQAQAFIRINLSQNPCQFWFTAIQWKHSLNRGIF ...

  5. Protein (Cyanobacteria): 260655 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available n factor-like protein, partial Arthrospira maxima CS-328 LGVTESGVGLGYSMSGVGMSGVGLGVTESGVGLGYSMSGVGMSGVGLGVTESGVGLGYSMSGVGMSGVGLGYSMS...GVGMSGVGLGVTESGVGLGYSMSGVGMSGVGLGVTESGSALGYSMSGVGMSGVGMGYSMSGVGMTESGSALGYSMSGVGMSGVGMGYSMSGVGMTESGSALGYSMS...GVGMSGVGMGYSMSGVGMTESGSALSYSMSGVGMSGVGMAERMSGIGFTMSGSALGYSMS

  6. Protein (Viridiplantae): 159482410 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 899 ribosome biogenesis pescadillo-like protein Chlamydomonas reinhardtii MAGKKLKKGKSGNAAQYITRTQAVRKLQLRLSEF...XP_001699264.1 33090:20893 3041:6297 3166:6990 3042:6990 3051:6899 3052:6899 3055:6

  7. Protein (Viridiplantae): 168039319 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available AVDKMEVVLSSMQAVGIPINTMALHALIMAYSRAGTYDRLAKTMEVVKDAGWMLQPATYNILISEYGKVGYLDKMEQAFREMMNASVKPSFETFQYMINAYEAADNETQVDRILDLMRKAGCEPKSNAVWTDDKVFSEKVRW ... ...NTLISMYSRMGATEEMKKIFLDCTEAEFVPDRHTYNALIWGYMRAGQLNEMEVTFNELQAKKFNADVITYNALIIGYARAN

  8. Protein (Cyanobacteria): 170031 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available EGQGAIGCIILGAALGAAIGLGLAVGIAQWFILRSIVSRSQWWILASVLGWCGIFFTLIVMLYTAIPVPGSPEFGQPIIAQLPLAGRAIAQVTLAGALMGLFQWLILRSSVRQSWCWIPAHALIMLLAALGVLILGYNIGGLPGMGIFIMIFSPIYAVLSGSLLDWLVKHSRNPVTT ...

  9. Protein (Viridiplantae): 356575200 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available YSDASTMLRIDGNARETAAAMLQIHALIMSLSYARIEIKTAQSLESWSGGVLVMVSGSVQVKDYSRRRKFMQTFFLAPQEK...77 3847:377 PREDICTED: uncharacterized protein LOC100817177 Glycine max MATPFPIPVTAAQVGTYFVGQYYQVLQSQPEFVHQF

  10. Protein (Viridiplantae): 303278618 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 564608:3894 predicted protein Micromonas pusilla CCMP1545 MSQPTMLMSPALYCQRGSNRGVAPQKSRRNAYRAFPAGASAMRSAHPMGS...PTSASIAALAFSSCFTAGANFSFPGRSSSKRIDPFSPPFPVAASNVPASRIASAMRSSTDAVTYFSMIGMQYPAYTVCALSAAATGISSTAFSE ...

  11. Protein (Cyanobacteria): 354536 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available tical protein glr0419 Gloeobacter violaceus PCC 7421 MDGSYSAESNVQDQMQQCIDLCLKAHDLCLASAMRRIELGGEAAGLAPVRLLLDCAELCQTHANLMSRRSEYHARLSPICAAVCEQVAAHSEMAGDDPQFQACAEACRRAGESCQKMTYADSSLGATV ...

  12. Protein (Cyanobacteria): 197732 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available ZP_01083417.1 1117:3837 1118:1190 1129:258 69042:4 ABC-type transport system involved in resistance to organ...icsolvents ATPase component Synechococcus sp. WH 5701 MNHSPPIAPDGPVLELDGVGMRWGSNIVL

  13. Protein (Cyanobacteria): 205740 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available r protein) Oscillatoria sp. PCC 6506 MNNELLHSQFNATAVEFDPFASGEILVTAPATEAQKEIWLSVQMGDEANCAFNESQSLRLRGPLNLEILRS...SFQAIVQRHEALRTTLSADGSTLCITESLNLEIPLIDLSALSEQERKIQLAQLRRQAVEQPFNLEHGPLLRVQIIKLQAEEHLAIITAHHIICDGWSWGVFIPDLGAI

  14. Protein (Cyanobacteria): 21396 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available QSREDYEAMLQEKAEPVLQEWMQRCITESLLTPRAVYGYFPAARDGNTLRVFDADGTRELGFFELPRQRSGNRYCIADFFNDLDAEGRPKDVLPMQAVTMGQKASVVA...MDAKRSDNWTNNKGFLADAPQGVGLDEEGTTSENAEETSTSASDAPAADLPPVSSDRSDAVPAEAAPVPPFLGSAVITEVDIDITEVFHYLDRNALFAGQWMLRKTKE

  15. Protein (Cyanobacteria): 69941 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available l regulator Rivularia sp. PCC 7116 MNSLKNKPLDPVNHAGFLIWQVANNWEKQINNELKEFGLNQAEYFHLVSLFWLLENQEEVTQTEIARFADTIPMNTSKIMTKFEKKGLITRVAGSDSRSKSLCITESGEQIAIQATARLSRLSEQFFDKDDDNNFLNYLKYLKTK ...

  16. Protein (Viridiplantae): 224143651 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 9 3694:4809 predicted protein Populus trichocarpa MRGSKAHSKECKKKASAQRHARRGKRGLKGARRGKRGLKGALEEESEGSKARSKRTAR...AQRHARRGKRGLKGTLEEKRGLKGALEEESEGSKARLKRSEGSKARSKGESEGSKAPSKGESEGSKARSKGSEGSKAPSKGESEGSKARSKGSEGSKARSKGESEGSKARSKGSEDSKARSKRKGSAQRHSKRKASAHRHSNRKPRA ...

  17. Protein (Viridiplantae): 224161003 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 9 3694:4809 predicted protein Populus trichocarpa MRARRRARKNGRAQRRSKKKGRAQRRSKGESEGSKARSKGESEGSKARSKGESEGSKARSKGSEGSKARSKGENEGSKARSKGESEGSKARSKGSEGSKARSKGESEGSKARSKGSEGSKARSKGESEG ...

  18. Protein (Viridiplantae): 224077122 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 9 3694:4809 predicted protein Populus trichocarpa MRARRRARKNVRAQRRSKRKGRAQRRARREARAQRRARREKAGSKARSKGGSEGSKARSKGSEGSKARSKGESEGSK...ARLKGESEGSKARSKGSEGSKARSKGSEGSKARSKGESEGSKARSNGSEGSKARSKGESEGSKARSKGSEGSKARSKGSEGSK...ARSKGESEGSKARSNGSEGSKARSKGESEAQRRARREARAQRRARREARAQRRARREKARAQRRARMEARAQRRARREKARAQRRARREKRGLKGALEWKRGLKGALEGRKRGLKGRSNEKQGLKSAPKEIRA ...

  19. Protein (Viridiplantae): 224088256 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 9 3694:4809 predicted protein Populus trichocarpa MEGRAQRRSKGGEGSKARSKGESEGSKARSKGSEGSKARSKGESEGSKARSNGSEGSKARSKGGEGSKARSKGESEGSK...ARSKGESEGSKARSKGESEGSKARSNGSEGSKARSKGESEGSKARSNGSEGSKARSKGESEGSKARSKGSEGSKARSKGERRGLKGALEGKSKCSEALEEEIKCSKTLEEKQGLKGAPKEIRA ...

  20. Protein (Cyanobacteria): 96882 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available ent protein kinase II, association-domain Arthrospira sp. PCC 8005 MIKKLFCSTLSASFLAATMSGCAPVAETGEVACAEVTEAEI...ZP_09781165.1 1117:1835 1150:12908 35823:2083 376219:1678 Calcium/calmodulin depend

  1. Protein (Cyanobacteria): 352975 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available ciation-domain protein Synechococcus sp. CB0205 MAFSERDQEILRLNQAMLNSVASGDWQAYSAVCAD...ZP_07970261.1 1117:14446 1118:14646 1129:7054 232363:890 Calcium/calmodulin dependent protein kinase II asso

  2. Protein (Viridiplantae): 356556652 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available rectional sugar transporter SWEET2-like Glycine max MSLFGAYSICEVGKDAAGVAGNIFAFGLFVS...24:4295 3398:4295 71240:107 91827:107 71275:973 91835:854 72025:570 3803:570 3814:570 163735:1332 3846:1332 3847:1332 PREDICTED: bidi

  3. Protein (Viridiplantae): 356554726 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available rectional sugar transporter SWEET2-like Glycine max MSLFSAYSICEVGKDAAGVTGNIFAFGLFVP...24:4295 3398:4295 71240:107 91827:107 71275:973 91835:854 72025:570 3803:570 3814:570 163735:1332 3846:1332 3847:1332 PREDICTED: bidi

  4. Protein (Viridiplantae): 357130727 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available ectional sugar transporter SWEET6a-like Brachypodium distachyon MTEQRFPQNGNTSVPAGNS...24:4295 3398:4295 4447:4380 4734:4380 38820:4380 4479:4380 359160:3487 147368:3422 147385:3422 15367:3422 15368:3422 PREDICTED: bidir

  5. Protein (Viridiplantae): 356573875 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available rectional sugar transporter SWEET17-like Glycine max MMQTYVLENIKIKKHGSTEDFLSLPYICTL...24:4295 3398:4295 71240:107 91827:107 71275:973 91835:854 72025:570 3803:570 3814:570 163735:1332 3846:1332 3847:1332 PREDICTED: bidi

  6. Protein (Viridiplantae): 356509295 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available rectional sugar transporter SWEET3-like Glycine max MAETIRLGVAVLGNAASVALYAAPMVTFRRV...24:4295 3398:4295 71240:107 91827:107 71275:973 91835:854 72025:570 3803:570 3814:570 163735:1332 3846:1332 3847:1332 PREDICTED: bidi

  7. Protein (Viridiplantae): 356544144 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available rectional sugar transporter SWEET2-like Glycine max MSLFAAFSICKVAKDAAGVAGNVFAFGLFVS...24:4295 3398:4295 71240:107 91827:107 71275:973 91835:854 72025:570 3803:570 3814:570 163735:1332 3846:1332 3847:1332 PREDICTED: bidi

  8. Protein (Viridiplantae): 356554435 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available rectional sugar transporter NEC1-like Glycine max MVSFSDHELVLIFGLLGNIVSFMVFLAPLSNFY...24:4295 3398:4295 71240:107 91827:107 71275:973 91835:854 72025:570 3803:570 3814:570 163735:1332 3846:1332 3847:1332 PREDICTED: bidi

  9. Protein (Viridiplantae): 357135133 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available ectional sugar transporter SWEET2a-like Brachypodium distachyon MASLGLPGVSSYHDLCCYG...24:4295 3398:4295 4447:4380 4734:4380 38820:4380 4479:4380 359160:3487 147368:3422 147385:3422 15367:3422 15368:3422 PREDICTED: bidir

  10. Protein (Viridiplantae): 356524569 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available rectional sugar transporter N3-like Glycine max MVITHHTLAFTFGMLGNVISFLVFLAPVPTFYRIY...24:4295 3398:4295 71240:107 91827:107 71275:973 91835:854 72025:570 3803:570 3814:570 163735:1332 3846:1332 3847:1332 PREDICTED: bidi

  11. Protein (Viridiplantae): 356513594 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available rectional sugar transporter SWEET5-like Glycine max MVDTGAIRTVIGVIGNVISFCLFMSPVPTFI...24:4295 3398:4295 71240:107 91827:107 71275:973 91835:854 72025:570 3803:570 3814:570 163735:1332 3846:1332 3847:1332 PREDICTED: bidi

  12. Protein (Cyanobacteria): 319556 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available cal protein Cha6605_6427 Chamaesiphon minutus PCC 6605 MGGDGFPPDRNHFSRAFSTSFNNMTFKRTQAEPLSCQCNIRLTPSEMEELKDAASVAGITVSTYIRQRALGRRVAANTDMTTIRELRRIGGLLKHIHNESGGAYSQLTADTLIEIQKAIVSIGNGL ...

  13. Protein (Cyanobacteria): 243777 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available occus sp. JA-3-3Ab MATPFSWPYRTPGIPDSAFERIPGIPMSPREVRVLVLSQLRLGEDHCLWDIGAGTGTIAIEAAILCPRARVIAIERDAEVVSLIESNCE...KFGLNNVQVIQGTAPDCLHQLSPPPDRICIEGGHPLREILEASWNHLKPNGRIVATTNSLEGLYGLSAGLAAVRAHHVEVIQSAVNRLEHRGRSQLLLPLDPTFVLSGEKSS ...

  14. Protein (Cyanobacteria): 170237 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 8802_4468 Cyanothece sp. PCC 8802 MNFDFPSPISPDSSKQQELSPKKLNPSRIRDHLANERTYLAWMRTAVGLMGFGVVILRIRAFQPPSIPGPGFGWKLGLIFAGVGLLTVLLSTVQYFIVRRDIEEDTYEPPDRWVILFSLTIALLGSGIIYFVSTSSFDLVDIIM ...

  15. Protein (Cyanobacteria): 320772 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available MC7420_6233 Coleofasciculus chthonoplastes PCC 7420 MIRHTSNNTTKPALPHHQTTKSILIFHAIARQSSTPSCRGGFRNSIITHTANKTTKPALSPPPDR...EIYPNFQAIARQSSTPSCRGGFRNSIITHTANKTTKPALSPPPDREIYPNFQAIAHQSSTPSCRGGFRDSIITHTANKTTKPALSPPPDREIYPNFQAI

  16. Protein (Cyanobacteria): 69702 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available osphatase Oscillatoria sp. PCC 6506 MNHLIKQADLADRIICDSAGTGGYHVGNPPDRRMAIAASKRELELRGSARKFQRSDFENFDLILAMDKDNYQDILSLDPHGKYRDKVRLMCEFCQKYDLREVPDPYYGGPEGFDRVIDLLWDACEGLLEYVTKEKLIFNS ...

  17. Protein (Cyanobacteria): 438681 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 8 Synechococcus sp. JA-2-3B'a(2-13) MNDLLFEPTSERPSLAEIRRLSPAALAYLGDAIYELHVRRQRLFPPDRLERYHQQVVRRVRGSAQAKLLLALLPHLNPEEQEIVRWGRNGCGRPPRHLPLADYQNASGLETVLGYLYLANPERLRHILALTDVLAETLGEWEG ...

  18. Protein (Cyanobacteria): 69717 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available osine phosphatase Moorea producens 3L MNHLIAQANLSDQIVCDSAGTSSYHIGSPPDRRMTAAAKRRGIILQGKARQFNRSDLEEFDLILAMDQQNYEDIISLDPAGKYKDKVRLMCDFASHHTERSVPDPYYGGPEGFNKVIDLLLDACEGLLEHVVDNYTKTRQN ...

  19. Protein (Cyanobacteria): 197706 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available porter Synechococcus sp. WH 5701 MWLRLDSASRLKPPFTPAPLPPDRQLPEGYDTLEGERGYQLSGGQRQRISLARAILRKPELLILDEATSALDSQSEHLVQQAIERFARKHTVLVIAHRPSTVVHPDLICVMDQGRIVERGHHGELLARDGLYADLWKKQVRHDHGL ...

  20. Protein (Cyanobacteria): 170238 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 01_4405 Cyanothece sp. PCC 8801 MNFDFPSPISPDSSKQQELSRKKLNPSRIRDHLANERTYLAWMRTAVGLMGFGVVILRIRAFQPPSIPGPGFGWKLGLIFAGVGLLTVLLSTVQYFIVRRDIEEDTYEPPDRWVILFSLAIALLGSGIIYFVSTSSFDLVDIIM ...

  1. Protein (Cyanobacteria): 313833 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available ELVGSPLPDTVPSTISEAAIETKIDEILEKKLSNHLPDNVPSIVESIILDKLPSMILEYLPSDLMARIENMERLLRLQQSASIADHSPIPTGEPYPLPPSPPDRPAIE...AVTPEVSPSPLVTDAIASIDGTVEGGNGDIFPDSPPDRPAIASSAKKGLTDSELARELGIDKSNITRWKQKGRPTQKYENWELRGRFWYEKD ...

  2. Protein (Viridiplantae): 225431324 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available RPPDSRIPFEFCYDMSPGENTSLIPSMSLTMKGGSQFPVYDPIIIISSQSELIYCMAVVRSAELNIIGQNFMTGYRIIFDR...GLEKISVPSILSKEGFTADSFSMCFGPDGIGRISFGDKGSPDQEETPFNLNALHPTYNITVTQVRVGTTLIDLDFTALFDSGTSFTYLVDPIYTNVLKSFHSQAQDSR

  3. Protein (Cyanobacteria): 22493 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available FIRWMAALTITVGVFIVSISENPPTSKPITSALEHRTKSWFKRSMFFLLPLSFSLPKIWLFAVIIAFADGFGDIFNAKGMKQIGAVKLGSLPEMLQIGQKIITNHWIIQGITCQTLSFLSFVSALSWADISFVRPATALTYVISLLGAYFILKERIELGRLIGIVVVGIGILIITLDPSMSL ...

  4. Protein (Viridiplantae): 303290558 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available NTMGWIDKAGYGLLLHALEALAIDVVLVVDHEKLHAELSRDLRGKKIKVWKLQKSGGVVERTPEFRRRSRDARVREYFYGPLGDLSPHSQTLEFGKVSIFKIGAGPSAPRSALPIGQESSADPLRVSTVAPSM...SLLNAVLGVSHGKTQAELLSSNVAGFIFVTDVDVANGRFTYLTPCPGELPSRNLIAGTLKWIETR ...

  5. Protein (Viridiplantae): 359473770 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available HHSRSASATGISNIKRTQNFAAKAAAQRLAQVMASQTADDDEDDEDDDLGFRYSAPPPPAFSRTVNSGKPAVPASRVTRSPSPGLGRNFVEETPSVRSTSAGRPSM...SLNAIPLVSPSRAPLRTPVPIPPIEPPNRQKEKRFSSNVGHFNPKDTGDQREASALRDEVDMLQEENENILDKLRLEEERCKD

  6. Protein (Cyanobacteria): 123908 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available RQWQSEHREIEMGDRYQAVLQEKVPSMSLAELGKITTEMVARFQACYQQSLRLPDGVKDMLEFWHGRVRLGVVSNFYIQGWPTELLESFGLRSYFDFVVDSAACGWRK...genase-like hydrolase Acaryochloris marina MBIC11017 MTLDWIFFDCFNTLIDDFDQTGEELALLPVYSLPAEVGLYTSAAEFRQHYHAWRN

  7. Protein (Viridiplantae): 359494619 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 024:2019 3398:2019 71240:1909 91827:1909 71275:3358 91834:6442 403667:6442 3602:6442 3603:6442 29760:6442 PREDICTED: protein strawber...ry notch-like Vitis vinifera MGQPSVPPPLTPPAPPLMGGGGGGGCQVRCAGCRMILTVGAGLTEFVCPTCQLP

  8. Protein (Viridiplantae): 255074015 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available RKLAASDSESDSDSDSDSDSGDEPAAKKAKTAPASSDSSSDSDSSSSDSDSDSGEKKEDENKEPAKPAKSESSSATSSDSDSSDSDSDSDSDSKPPAEEEKKDEPVAAVKADSSSSSDSDSS...SSDSDSDSDSGEKKEEEKAEVKKADSSDSDSSDSDSSSSDSDSDEKEEEKKDEPKAEVKADSSSSSS...SSSSSSDSDSDSDSDEKEEEKKEEKAEVKKADSSDSDSSSSDSDSDSDSDSDSGEKKEEEKAEVKKADSSSSSSSSDSDSDSDSDSDEKEEEKKDDEPKAEVKADSSS...SSSSSDSDSDSDSDSDSKPAAKTMEDKKDDSSSSDSDSDSSSSDSESEEKKEEEKAEVKADSSSSSDSDSSSSDSDSDSDEKEEEKKDDDKMDVEDAKADSSSSSSSS...SSSDSDDDSDSETEPVKMDADAAVAKPESSSSDSDSDSGSDSDSDSDSKPTAMDVDEKQEEAKAAASSDSDSSDSDSDSDSSDSDSGEKDDAPAVKPAEAKADSS

  9. Protein (Cyanobacteria): 7963 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available chococcus sp. CB0101 MELLPIRPAGAMNKTLVPPQDPSSRQWYLVDAENQTLGRLASEVASVLRGKNNPNFAPHIDAGDFVVVINAEKVKVSGNKFTEKVYRRHSGRPGGMKTESFAALQARIPERIIEKAVKGMLPHNALGRQLFRKLKVYKGAEHPHAAQQPQALALDPAASAQ ...

  10. Protein (Cyanobacteria): 229199 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available _3623 Cyanothece sp. PCC 7424 MAIQQITDNNINDYTLQISDNNILWTNQDPNTFITALYLYNGSQTIEIDRDELSTTLGLSGNNVVWKTPLGRNTYNENLYLYNGS...EIIQIDSNNHYDWVRISGDNVVWSASDGTDNEIYLYNGSQTLQLTNNDINDINPLISGNNIVWSSYDANNNYEIFFYNGSQVIQITNNNIGDFNPEISGNNIAWSGYVNGNSEVFFYNGS...ETIQLTNNDIDDYSPQISGNNIAWSTPNKEIYLYNGSQIIQLANNYNNDLSLKFSGDNLVWSGNDGNDNEIYFYNGS...EVIQLSNNNIDDRVSQISGNTVLWVSDDGTDKNVYFYNGSQVIQLTNNNIDNYSDSDYPKLSGNYIVWAASDGTDNEIYLADTREFASLNQAP

  11. Protein (Viridiplantae): 255568373 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 024:2425 3398:2425 71240:505 91827:505 71275:3061 91835:898 3646:5804 3977:4530 235629:4530 235880:4530 3987:4530 3988:4530 (iso)euge...nol O-methyltransferase, putative Ricinus communis MESTMLTKLIQAQAHIWNHIFNFINSMSLKSA

  12. Protein (Viridiplantae): 255568375 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 024:2425 3398:2425 71240:505 91827:505 71275:3061 91835:898 3646:5804 3977:4530 235629:4530 235880:4530 3987:4530 3988:4530 (iso)euge...nol O-methyltransferase, putative Ricinus communis MADAKHAAVELLQAQAHIWNHMFNFINSMSLK

  13. Protein (Viridiplantae): 356527579 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 24:2780 3398:2780 71240:414 91827:414 71275:1623 91835:562 72025:981 3803:981 3814:981 163735:1038 3846:1038 3847:1038 PREDICTED: ran...dom slug protein 5-like Glycine max METVRTREGAIAKDTTETELTKIPLLRATVETLHPSSKEEDDFMIRR

  14. Protein (Viridiplantae): 356508874 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 24:2780 3398:2780 71240:414 91827:414 71275:1623 91835:562 72025:981 3803:981 3814:981 163735:1038 3846:1038 3847:1038 PREDICTED: ran...dom slug protein 5-like Glycine max MEGVSPEPLRSELDSKSKHDTAKEDDDALKDSTEAEVTKIRLMRAFV

  15. Protein (Viridiplantae): 297852830 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available QSAPSSYFSSFGESIEEFLDRPTSPETERILSGFLQTTDTSNNVDSFLHHTFNSDGTEKKPPEVKTEEDETEIPVTVTTME...972:1358 basic helix-loop-helix family protein Arabidopsis lyrata subsp. lyrata MESEFQQHHFLLHDHQHQRPRNSGLIRY

  16. Protein (Viridiplantae): 168006546 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available patens subsp. patens MHHEDEIGFRENVAAMAATTKKQLLLTYTYLIVYKDVLSKGTRSYQDNKHTALLERKWLILHRPPPLQYTKKNNNNFKQRPPHPEPRHLHYVRAGSTKMALNHPNDEPWVKSENHSVKPETERDAIGRWTVRWEDKIYTGLWLHFEHKNYGFPTGGKK ...

  17. Protein (Viridiplantae): 226501650 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 2772 uncharacterized protein LOC100273695 Zea mays MIEAYLRANKMFVDKHEPETERVFSSYLELDLSEVEPCVSGPKRPHDRVPLKEMKSDWHACLDNEVGFKGYAVPKEQQGKVVKFNFHGRPAEIKHGSVVLAAICSSTNTSNPSFMIGAGLVEESMRIGP ...

  18. Protein (Cyanobacteria): 256132 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available IVGAFVQMVTEGEIHRALGNQQRQRQIANLTDHTIICGFGRMGQVLAKQLKQSGLPFSIIDNQPSQVAIAEELGYLAHCGDATREEQLQMLGVMRAKTLATVLPEDAT...NVFITLTARELNSRLTILARGEIPETERKLRLAGADQVILPLTVGAVQMADLITQSNRRDFLNRPDERGFLNDLLASVEVQ

  19. Protein (Cyanobacteria): 212762 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available LGSESEWNILVSKLQQFLKALFIHEALDSQILIELVNRIYYLNPAESKTNRHLNSSLDISNNYPVGFQELKSDESTQEISESPQKQIESEQAANNSQNDSESSNYQPLANSNNKSPIAVLLLDAENIILNPET...ERFLETVCNFPIQVKVAFANWYRKGKLDTELHMRNYDLIHVPSGKDNADGKMIAFG

  20. Protein (Cyanobacteria): 435835 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available CP_0098 Synechocystis sp. PCC 6803 substr. PCC-P MASTPIQSEARTDLEPSFVIPLVLLFGAIPIFFLQMWVGLAIAVFGVFLMVQTAIIKLSFTATALEVYRGSKLIRSFPYTEWQNWRIFWEPAPILFYFKEVKSIHFLPIIFDPGTLKACLERHCPLQSLRAE ...

  1. Protein (Cyanobacteria): 435916 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available hetical protein Cal6303_0562 Calothrix sp. PCC 6303 MPPLSVTTVELKPSYNIPLVLVIAGIPLIFFQPWIGSAIALFGLFLMFQTVNIRLIFTPTALDVYRKDTLIRSFPYQEWENWRIFWNPVPILFYFKEVKSIHFLPIIFDPKTLKTCLEERCPRK ...

  2. Protein (Cyanobacteria): 435829 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 3658 Cyanothece sp. ATCC 51142 MSCSIQIPALSMTSVTPPNVNQQTIELAPSYNIPIILILMAIATLLIQPWVSLPLALFGLFLLLQTVTIRLQFTATALDVYRSDQRIRSFPYSEWQNWKIFWQPIPILFYFKEVNSIHFLPIIFDPQTLNVCLERFCNFDKMEEMG ...

  3. Protein (Cyanobacteria): 435852 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available rotein Cyan10605_0702 Cyanobacterium aponinum PCC 10605 MNSTTLTSETIELTPRYNLPIFIIILGVALSLVQMFVGIITILFGFFLLIQANIIKLKFTPKALEVYRQQNKIREFPYTDWQNWAIFWQPVPILFYFKEVKSIHFLPIIFDPITLKKCLEKYYPLS ...

  4. Protein (Cyanobacteria): 435833 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available I_0098 Synechocystis sp. PCC 6803 substr. GT-I MASTPIQSEARTDLEPSFVIPLVLLFGAIPIFFLQMWVGLAIAVFGVFLMVQTAIIKLSFTATALEVYRGSKLIRSFPYTEWQNWRIFWEPAPILFYFKEVKSIHFLPIIFDPGTLKACLERHCPLQSLRAE ...

  5. Protein (Cyanobacteria): 354868 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available ICYGVAGNSCYIVLEWLEIGRGDSKASEEMGRKLAQMHKKSLSEKFGWDMNNTIGSTPQINTWTDDWVEFWTKHRLGYQFELGKRRGGSFPQASELLNAIPELLAGHEVQPSLVHGDLWGGNAGFTVDGEPII...FDPATYFGDREVDIAMTEVFGGFSTAFYQGYNEVFPLDHGYEKRKTLYNLYHILNHFNLFGGGYGSQANGMIGRILSNK ...

  6. Protein (Cyanobacteria): 435834 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available CN_0098 Synechocystis sp. PCC 6803 substr. PCC-N MASTPIQSEARTDLEPSFVIPLVLLFGAIPIFFLQMWVGLAIAVFGVFLMVQTAIIKLSFTATALEVYRGSKLIRSFPYTEWQNWRIFWEPAPILFYFKEVKSIHFLPIIFDPGTLKACLERHCPLQSLRAE ...

  7. Protein (Viridiplantae): 115473185 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 5677 39947:5677 Os07g0599600 Oryza sativa Japonica Group MVFKKNAMSSSVLFLAALLLLSSSSMSSAARWLEEEYPPHPTVPELPKPEVPPHPAVPELPKHEEPPHP...VVPELPKHEEPPHPVVPELPKPELPPHPVVPELPKHEEPPHPAVVPELPKHEEPPHPAVVPEFPKHEEPPHPAVPELPHPAVPEIPHP...AVPELPKHEEPPHPVVPELPKPEVPHAAVPELPKPELPPHPAVPELPKHEEPPHPVVPELPKHEEPPHPVVPELPKPEEPHHPEVPEHEQPPKPESHYPEVPMAKP ...

  8. Protein (Viridiplantae): 255577163 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available :6554 3988:6554 hypothetical protein RCOM_0753050 Ricinus communis MQLGNAFIAILLILILFCISIDFSVASAGLKQNFTIVISQSPWLKNVTENLPHP...VSPFNCGSCGNKCPWGVLCVYGMCGYAEPWPPWPHPHPHPHPHPHPHPHPHPHPHPHPHPHPHPPPKPPKPWPHRPPQSPPKPIKPWPHHPPKADHEPSQSAMGPSY ...

  9. Protein (Viridiplantae): 225463067 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 9 58024:7609 3398:7609 71240:9051 91827:9051 71275:11363 91834:5297 403667:5297 3602:5297 3603:5297 29760:5297 PREDICTED: NEDD8 ultim...ate buster 1 Vitis vinifera MEKLKIAGAWSGVLELELQVWTVSMLREEVAKRASCGPESINLIWSGKLLKDENL

  10. Protein (Cyanobacteria): 50412 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available GFSPPEMHLPNHPDTLFEYVKALKECGYRWLMVQEHSVENLDGSGLSGDQKYVPNRLVARNSRGETVSIVALIKTQGSDTKLVAQMQPYYEALGRGKQPVGNHHIP...ACVTQIADGENGGVMMNEFPPAYEQATRKMAENGGKSGTVAINGTEYLELLEAAGVQESDFPAIQAIQQHKIWQRVNPDSPSH

  11. Protein (Cyanobacteria): 189042 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available n MAE_13150 Microcystis aeruginosa NIES-843 MFELSDLKQTRVYQEALAEGEKQGLERGLQEGLERGLERGLERGLERGLERGLERGLERGLERGLERGLERGLQEGKRLVVENLLRVRFGELDPEIQAIISRILQLSPEEFTPLLLHCSKQELLKRFPPEKSRGN ...

  12. Protein (Viridiplantae): 242070245 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available HEGDDGELWLWTEMMDAVVPVGSRFMCWVDYSRGFLVCDTVREYLHDSIDDGAADETTVWMVKINTRSKALLSVFRSDNEDYDAKDLLPVKLDG ... ...ADTSDYFLYEAGAGRRRPPSLSLLPGCYIPMQYQYQFPTATPMARELSVWNATGILRRGDGEVLVAQLETPPPLNGAPCKTAELCVLRLRPGGHDHHDWVLKRVPIVH

  13. Protein (Viridiplantae): 357497337 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 163742:19360 3877:19360 3880:19360 hypothetical protein MTR_6g029290 Medicago truncatula MVERDTRDGFMCWSFENVNNGSGVGWRSSLLQCKMLGPPPSISTIVNHLKSNISHISFAWKIAAAILTPTSSPMVPDDQPVSGDNFCKIT ...

  14. Protein (Viridiplantae): 302855606 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 68:667 hypothetical protein VOLCADRAFT_100718 Volvox carteri f. nagariensis MRIALYEACTAFIPTRKRVLKRASNCATKRALNPAADCTLNCMSNCAIRAMRI...ALYEARTAFIPTRKRVLKRASNCATKRALNPAADCTLNCMSNCAIRAMRIALYEACTAFIRGSAF ...

  15. Protein (Viridiplantae): 356515098 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available PQSEDPNMVHPQSEDQNMAQPLMEDENTALPQLEDENTAQPQLEDENTAQLQGSSKLEDENTAQPQVTSRSEEGNTAQPQMSSRSEEGNTAQPQMSSRSEEGNTAQPQ...DQNMVQTEVGSGLEDGNKAQPRGEDQNMAQTQEGSRLEDENTAQPPGEDHNLAQTQVNSRLEDGDMAQPQLDDQNMVQPQSEDQNMAQSQSEDHIMAQPQSEDQNMAQ

  16. Protein (Cyanobacteria): 528 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available al protein P9303_04231 Prochlorococcus marinus str. MIT 9303 MATRSLISLYALLATSAVITQSAEAAVYSQPNACNPIEANIQGIRNGS...WSLFLRPNNIIFGENDQARSWKNGSGKSWKNGSSSGKWKNGSGKNWKNSSGWRNGGWRNGSSGKWKNGSGGFLNW ...

  17. Protein (Viridiplantae): 226492042 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 24:2811 3398:2811 4447:698 4734:698 38820:698 4479:698 147370:502 147369:502 147429:502 4575:418 4577:418 protein held out wings...LGPRGHSLKRVEATTGCRVFIRGKGSVKDPVKEEQLKGRPGYEHLGDPTHILIEAELPADVIDARLAQAQEILEELLKPVDESQDNVKRQQLRELAMLNSVYREDSPHQNGSASPFSNGGTKQ ...

  18. Protein (Cyanobacteria): 417077 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available ADAANAIAELRTKYPALAIRPVEAPPPWADWVATLKVVDWVPLHRYRLKRYDGSSFVDVPDAEETGFYELYEEGSQQQHALFYDRQHNAWYSAEWYSLRFLALTHLAPKNLSVSYDPNAQELSIPISQRWPLAYERYLVMQSGCLPRYNRTTEELIYQNIAPTVWQVIGEQLPFFDLEK ...

  19. Protein (Viridiplantae): 159479054 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 96 hypothetical protein CHLREDRAFT_120274, partial Chlamydomonas reinhardtii PPGCRCSSAPPGCRCSSAPPGCRCSSAPPGCRCSSAPPGCRCSSAPPGCRCSSAPP...GCRCSSAPPGCRCSSAPPGCRCSSAPPGCRCSSAPPGCRCSSAPPGCRCSSAPPGCRCS ...

  20. Protein (Viridiplantae): 302846807 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 6811 3068:6811 hypothetical protein VOLCADRAFT_37529, partial Volvox carteri f. nagariensis PGPPHIYLRRTAPPGPPHIYLRRTAPPGPPHIYLRRTAPP...GPPHIYLRRTAPPGPPHIYLRRTAPPGPPHIYLRRTAPPGPPHIYLRRTAPPGPPHIYLRRTAPPGPPHIHLRRTAPPGPCPP ...

  1. Protein (Viridiplantae): 302829264 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available KLRGDRFVGLRGGRQILLAMDDQPNAAPLPTAPSPLFAAHQPAGLSQSKTPSPPLPRPPGNPQPYNPDQMPTPAQPPVQSPAPPVQSPAPPVQSPAPPVQSPAPPVQSPAPPVQSPAPPVQSPAPPVQSPAPP...VQSPAPPVQSPAPPVQSPAPPVQSPAPPVQSPAPPVQSPAPPVQSPAPPVQSPAPPVQSPAPPVQSPAPP...VQSPTPPSPSELMGSSCPDAQAFLDLHNLYRARHQAPPLRWNNNLAIAATAYAQQLADNDCALKHSGVRDAGENLLSQQSFPKPDNTCTLAARG

  2. Protein (Viridiplantae): 302830432 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 2914 3068:2914 hypothetical protein VOLCADRAFT_56324, partial Volvox carteri f. nagariensis CMIASCTMIAPCTVSPCTIASCTIASCTIAPCTIAPCT...IALCMIAPCTIAPCTIAPCTVALVRLPLYDCPFYGCTLYGCPCTIAPCTIAPFTIAPCTMVAPCTIALCMIALLYDCPFHDCPLYDCTLHDCPCTIAPCTVAPCTIALV ...

  3. Protein (Viridiplantae): 226504466 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available AASGGDPWLSRHGDLRRVFLAGDSAGGNIVHNVAMMAAASGPRVEGAVLLHAGFGGKEPVHGEAPASVALMERLWGVVCPGATDGVDDPWVNPLAAVAPPRPSLRDMPCERVLVCGAELDSLLPRDRAYYEALAASGWGGTVEWFESKGQDHVFFLFKPDCGESVALIDRLVAFFAAN ...

  4. Protein (Viridiplantae): 302840219 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 5423 3068:5423 hypothetical protein VOLCADRAFT_117895, partial Volvox carteri f. nagariensis MARRGSAPSTAAVGPRVASGPR...PDAALVRREAEEAAAAPPSRHGLAAGSVNARAAQPFSGLFNTFGSGGGAAGGGGGGRPNGGSGTAAAASGPRRITSGRPGSGRGPQLLPPGGDHSSTSTAGGGPPS ...

  5. Protein (Viridiplantae): 226507314 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available ASGGDPWLSRHGDLRRVFLAGDSAGGNIVHNVAMMAAASGPRVEGAVLLHAGFGGKEPVDGEAPASVALMERLWGVVCPGATDGVDDPRVNPLAAAAPPRPSLRDMPCERVLVCGAELDSLLPRDRAYYEALAASGWSGTVEWFESQGQDHVFFLFKPDCGESVALMDRLVAFFAAN ...

  6. Protein (Viridiplantae): 357437461 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available tioning 1A Medicago truncatula MKEEIHNNPSENKTKVSKFSDQNQPPKLQTTKTTNPNNNNHSKPRLWGAHIV...36 3398:436 71240:66 91827:66 71275:1826 91835:7886 72025:8391 3803:8391 3814:8391 163742:99 3877:99 3880:99 Chloroplast unusual posi

  7. Protein (Viridiplantae): 303277825 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available XP_003058206.1 33090:2376 3041:1616 1035538:518 13792:518 38832:2208 38833:3670 564608:3670 nucleosome posit...ioning protein Micromonas pusilla CCMP1545 MDPMSNAPAGAPTSMDGWGSIVAAASPPAKRERDDDAADP

  8. Protein (Viridiplantae): 356524346 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available NKGKASKSHPTKQHTAYHAQTTSQNPPCASQPTNSMEGAHSPARTSDVSPPPSMKGVRSPCTSQPTNSDAGRADRSFASLETQRNEAKPILYLDGQGFLPSRSAANGIGDILKKNFTDPWPSWKKIPISTRNSLFEEFLSTFG ... ...HLAEMTSQIPPCVSSHAISHPTDPPARTSDVIPPPSIQGVQSPCTSQPKNPDAGCTLDMASEKRTALRTKFVRQKVAEKDT...46:2504 3847:2504 PREDICTED: uncharacterized protein LOC100776972 Glycine max MAPKRKRQMAVRDQNKGKAFKSHPTIQLAR

  9. Protein (Viridiplantae): 308800396 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available med protein product Ostreococcus tauri MTCVGNLDENMQVQDDDSRPARDKAKANFAQKAARKALERQEKDRLSARSASVLARFSSIRHLRISSYQLVPARTSWSILFTHTINTFGHSAGTYQYADTYQEIPDTHFKQSYQQSGQPRTGGWTFSSRAVIRVWLRGSP ...

  10. Protein (Viridiplantae): 293336748 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 575:7472 4577:7472 uncharacterized protein LOC100383091 Zea mays MNTPGHGAQRTCGGACISSTNSKIFGRQTAAESSPARTSTHGETFRYESVDYGDEPTVPDPATLQRTGAAANTQLPYRHRNSCPGAIPVRLPNPATQGAPWLGPQKQLLQA ...

  11. Protein (Viridiplantae): 168050221 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available omitrella patens subsp. patens MSYNTVLTLLHSNPLLFPAKGRQMPRIIGINQGYISGFALVRVSCFWVVNASQLPGLSSTNYCTCLDSCLPAQSFLL...HCHEKRAIILNLMLDCHRLRAIYPARTSLFRRLRVMVADTMTRPRCRKGCIQAIDYRSWGPMALVSLLPECGDRKETGEEIEFLEGIECSQYCCFDWGHGSFRYVDRNNGRSASLGLRLMK ...

  12. Protein (Viridiplantae): 351720716 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 6 3847:3116 uncharacterized protein LOC100527152 Glycine max MARSLVMIHPLPSISHIGFTVMSLMVCAIALLMCASHSRKWPKWISCYAFVEEPVIEFNNEAVINTCDERQEDGSLWQKNILMGGKCQLPDFSGVIIYDSDGNIVNPARTSPPLLTWK ...

  13. Protein (Cyanobacteria): 73947 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available barrel domain protein Calothrix sp. PCC 7507 MDIKRSGSQPSAKGQAEYFTGTVRVDPLFEAHDPARTSGASVTFEPAARTAWHTHPLGQTLIVTAGCGLIQRWGGAIEEIRPGDAIWISPSEKHWHGATATTSITHIAIQEWLDGKPVDWLEHVSDEQYEGIP ...

  14. Protein (Viridiplantae): 168040746 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available GGTMFPEGAEGYVQKLEKHIPFGTSAIRTALDLGCGVASFGAYLLDKEVLTMSVAPRDSYKAQIQFALERGLPAFVGMLGTQRLPFPASSFDLIHCSRCRISFSSFNGSYFIEMDR...PVPGPNTLGTIYDRGLLGVFHDWQVLTSLFCFLIPFSTYPRTYDLLHVSSVEALTTSQNRYLSVPSLCSLAEIMVEMDRILRPKGTVIIRDTPAMLARVSKVANGIQWNYEIFDGEPGATDRILIATKQFWKAEIAEPQ ...

  15. Protein (Viridiplantae): 302755490 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available EQYIPLSDGQIRTALDAGCGVASFGAYMLRKDVLTMSFAPRDSHKAQIQFALERGIPAFVAMLGTQKLPFPAFSYDLVHCSRCLIHFSAYNGSYMIEMDRLLRPGGFF...IGVLHDWCEAFSTYPRTYDFIHVSNMQSFTTQASTSCSLVDVMLEMDRILRPQGTILVRDTTKMVEKISKIAYALQWTTEVLTTEGGVLGKERLFVATKPFHT ...

  16. Protein (Cyanobacteria): 20524 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 375DRAFT_4878 Leptolyngbya sp. PCC 7375 MELYERIEQIIVTFRPAFSRNATFGWFVLLLWGALLTTQPPAVTSYLNALGLGAEYYHQALHWFHSSGYEMDRVCRRWGRWLSHQTDGYRLKGHRVYVGDGIKVSKEGRKMPGLKACIKSPITSVNQNGYGGIILVRWAF ...

  17. Protein (Viridiplantae): 302821216 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available ENQIQFALERGIPALVAALGTKRLPYPSRSFDAVHCSRCRVDWHEDGGILLREMDRILRPGGFFIYSAPPAYRKDKDFPEVWNILTNITESLCWKLIARHVQTAVWRK...ALLLQNNPVWIMNVVPSESSNTLNVVYGRGLVGTLHSWCESFSSYPRSYDLLHAYRVMSLYPGRKGCQIEDIMLEMDRLLRPNALAIFQDSSPAVQRILELAPRFLWVARVHRILEKDEQLLICSKKFWIVDV ...

  18. Protein (Viridiplantae): 225433261 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 8 PREDICTED: mitochondrial import receptor subunit TOM22 homolog 2 Vitis vinifera MAGGSSDSKSNSGLVSRISNSISGSGIMFHGKRAASDAAYVTKKLLRSTGKAAWIAGTTFVILVVPLIIEMDREQQLNDLDLQQATLLGTTPLPARN ...

  19. Protein (Cyanobacteria): 316244 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available _3027 Synechocystis sp. PCC 6803 MLKLAGKKASALTCKKTKAKIGILEMDRQWYQSVKRFLCPSFEISAINFQDILFNNVDVGEYHSILVGCGIKYESIDISATLDLVTIIKKLSAKPPALLLITDCADSQITVQARSYLPQIDGVFAKDHDLALLLKVMKIIAKQKYFK ...

  20. Protein (Cyanobacteria): 42724 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available anothece sp. PCC 7425 MAITRWEPFRRIERWEPLREMETLRREMDRLFDRMIPFGDGEEGLLAFTPSVEMEETDEAINLRLEIPGMDPKDLDIQVSEESVSIRGERKSESRTEEQGTIRSEFRYGKFQRIIPLPAHIQTDQVKAENRQGVLHLILPKAEEERRKVVKVQID ...

  1. Protein (Viridiplantae): 302766834 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available LEQYIPLSDGQIRTALDAGCGVASFGAYMLRKDVLTMSFAPRDSHKAQIQFALERGIPAFVAMLGTQKLPFPAFSYDLVHCSRCLIHFSAYNGSYMIEMDRLLRPGGF...LIGVLHDWCEAFSTYPRTYDFIHVSNMQSFTTQASTSCSLVDVMLEMDRILRPQGTILVRDTTKMVEKISKIAYALQWTTEVLTTEGGVLGKERLFVATKPFHT ...

  2. Protein (Cyanobacteria): 319568 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available al protein Cha6605_1253 Chamaesiphon minutus PCC 6605 MTTSAAVRQKLVEALSLDLVGPDATADYHYQDEIISQSPSKWYLTGFLVPYEASVQDRSGDTADEGLEIDAPTSKSSED...ENTPETASARKALFPSSIGLSFLISDKTTSLDLEVYWGDYQPLKPDGIENKAKTDRWQRQRQLQRLTVTINDSTKPVTLDVPH

  3. Protein (Viridiplantae): 357168326 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 2 3398:112 4447:10886 4734:10886 38820:10886 4479:10886 359160:6892 147368:7145 147385:7145 15367:7145 15368:7145 PREDICTED: craniofa...cial development protein 2-like Brachypodium distachyon MKPKRISLGRNPLSDAPYRNPGVVSNG

  4. Protein (Viridiplantae): 357132051 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 15368:4872 PREDICTED: craniofacial development protein 1-like Brachypodium distachyon MASRSSASEAGGSGAKVVAAD...58024:4234 3398:4234 4447:6074 4734:6074 38820:6074 4479:6074 359160:4801 147368:4872 147385:4872 15367:4872

  5. Protein (Cyanobacteria): 341533 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available otein P9215_03981 Prochlorococcus marinus str. MIT 9215 MWSKIRLTIYGTTAIAGILWPFYFIIQFINLVRNGNIQGTFIDIGNAFFDDAWITPTSGFISADTAILLIAIFVFYAAEGKRLKLRFWGIYFPLTFIISLAFSFGAFMFIRELEINKELNETD ...

  6. Protein (Cyanobacteria): 99176 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available ILTPLPGIGINFDIVESRGPMIDPPIRSVEQIEKLHPLEPAESLPFIREILQTLRQEVGDRSTVLGFVGAPWTLAAYAIEGKSSKDYTVIKGMAFSEPAMLHQFLSKL...VDWTVDMAEARARLGSKVGVQGNIDPCVLFGSKDFIRERILETIRKAGNKGHILNLGHGVLQNTPEENVAFFFKTAKQADKLLS ...

  7. Protein (Cyanobacteria): 462892 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available I7407_2252 Geitlerinema sp. PCC 7407 MRFKLLVSGLVTAAAIALSGTGAEAQTLMRTGLMRNVLVDALANRSTVFSSGVLADLETDENFGGDYQQIFDYASGILNDYTVVDRGGVFPENAGIPRDRQLPRTDVVYTVFTLDNGNELFLYRSPLEDTARYFIRESVPFGG ...

  8. Protein (Viridiplantae): 15230093 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available VCRRDLFVGKFEVCGENNSSSNLSFIRENNSSANLKIYSSAKKRFVREIYSSAKKRFVEEIYSSANLRFVGENNSSANLSFIGQNNLSANLSFIRE...NNSSANLSSFLAIVSQTCEGNIRRKVCDGIASWSCSFGEIYSSKKRFVREIYSSAKKRFVGEIYSSANLRFVGENNLSANLSFIRENNLSANL...02:4271 uncharacterized protein Arabidopsis thaliana MTYTQFPRNCLANVRGKYSSQNLRRNSELVMFPRRDLFVGEEEVCRRDLFVGEEE

  9. Protein (Cyanobacteria): 440743 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available ocystis aeruginosa PCC 9809 MTTSPESQFLQALEMCQSLSNLTAQFSSIPCRIIEILSDISQEPRVLYSLLIKYSREVDSALVALDIYAKSADNWRVKDRDKTCSLGFGVKDHCTILSCLLNFGKRPFSFISYTGNFASEAIIFELLKDWKNLDIAPFFEEKMQEFIREAKIA ...

  10. Protein (Viridiplantae): 167999346 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 5 3214:7255 114656:7255 3215:7255 3216:7255 3217:7255 3218:7255 145481:7255 predicted protein Physcomitrella patens subsp. patens MAD...REIRDGHLHGYKVLSSQKPHELQHAPVAIADITRAKHPRHTTSNHSPTLQLSYPLRIQDSPKKAMQPRSSSQLKTGKTPLQLSGEMPNIIERGSIMWQGKLAVRAVSDISMPRLAVSLAHKALMVCMDEVFTNNYR ...

  11. Protein (Viridiplantae): 168051496 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available :614 114656:614 3215:614 3216:614 3217:614 3218:614 145481:614 predicted protein, partial Physcomitrella patens subsp. patens TSLTSLN...LSGCLSLITLPNELGNFTSLTSLNLSGCWKLISLPNELGNLTSLSSLNLVECWKLTSLPNELGNLTSLTSLNLSGCWNGFLNL...TSLPNELGNLTSLTSLSISEYWELTSLPNEFGNLTSLTSLNLSWCSRLTSLSNNLGNLTSLASLSLSRCSNLTSLPNELGNLTSLTSLN...LSGCLSLITLPNELGNFTSLTSLNLSGCWKLISLPNELGNLTSLTSLNLSGCLSLTSLPNELGNLTSLTSLNLSGCLSLITLPNELGNFTSLTSLNLSGCWKLISLPNELDNLTSLSSLNLVECWKLTSLPNELGNLTSLTSLNLSGCWKLTSLPNELDNLTSFTSLNLSGC ...

  12. Protein (Viridiplantae): 168042943 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available ens subsp. patens LNLRDCSRLTSLPNELGNLSSLTTLNMSKCRSLASLPNELGNLTSLTSLNLSGCWELTSLPNELGNLTSLTSLNLCDCSRLTSLPNELGN...LTSLTSLDMSKCPYLTSLPNELGNLASLTSLNLSGCWKLTSLPNELGNLTSLAFLNLCDCSRLTSLPNELGNLTTLTSLNISGCLKLTSLPNELGNLTSLTSLN...LSRCWKLISLPNELGNLISLTSLNLSGCWELTSLPNDLNNLTSLVSLNLFECPSLIILPNELGNLTTLTSLNISECLKLTSLPNELGNLTSLTSLN...LSGCWDLTSLPNELGNMTTLTSLNISGCQKLTSLPNELGNLTTLTSLNISRCQKLTSLPNELGNLTSLTSINLCDCSRLKSLPNELSNLTTLTSSNISGCLKLTSLPNELGNLISLISLN...LSGCWELTSLRNELGNLTSLTSLNISGCQKLTSLPNELGNLTSLTSINLRHCSRLKSLPNELGNLTSLTSLNISGCWELTSLPNELGNLTSLISLNLSRCWELTSLPNKLSNLTSLTS ...

  13. Protein (Cyanobacteria): 321356 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available ein MC7420_5364 Coleofasciculus chthonoplastes PCC 7420 MPQRLSARFTIQSLNPPLQFTLLTHQPLHSHQLFLKKGRVLPQTLSARFTIKSLN...PPLQFTLLSHHPLHSHQLFLKKGRVLPQRLSARFTIQSLNPPLQFALLSHHPLHSHQLFLKKGRVLPQRLSARFTIQSLNPPLQITLFSHQPLHSHQLFLKKGRVLPQRLSARFTIQSLN...PPLQITLFSHQPLHSHQLFLKKGRVLPQTLSARFTIKSLNPPRQITLFSHQPLHSHQLFLKKGRVLPQTLSARFTIKSLN...PPLQFALLSHHPLHSHQLFLKKGRVLPQTLSARFTIQSLNPPLQFTLLTHQPLHSHQLFLKKGRVLPQTLSARFTIQSLNPPLQITLLSHQPLH

  14. Protein (Viridiplantae): 168043922 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available ens subsp. patens TSLTSLHISQCHELRSLPNELGNLVSLTSLNLVNCWKLTSLPKELVNLTSLTSLNLSGFWEVTLLPNELGNLTSLTSLEISGCSKLTSLPNKLGNLTSLTSLN...LSGNSSLTSLPNEMGNLTSLTSLNLKRCSNLTSLPNELGNLASLTSLKLSRCSSLKSLPIELSNLTSL...PSLSLSGCWKLTSLPNELGNLTSLTSLNLSGCSNLTSLPNELGNLTSLTSLKLRRCSNLTSLPNEFGNLASLTSLNLDGWKNLTSLPKVLVNLTSLTSLNLSRCSSLTSLPNELGNLASLTSLN...LSGCWRLRSLPNELGNLTSLTSLHISKCWELTSLPNELGNLTSLILLNLSECSNLTSLPNELCNLTSLISLDLSGCSNLTSMPNELHNITSLTSLNINE ...

  15. Protein (Viridiplantae): 159486336 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 7735 hypothetical protein CHLREDRAFT_107425, partial Chlamydomonas reinhardtii MASNIVFCSLNLASSSVFCLLNLASSFVFCSLNLASSLAFCSLN...LASSFVFCSLNLASSLAFCSLNLASSFVFCSLNLASSFVFCSLNLASNKLFCSLNLASNIVFCSLNLASSLVISTA ...

  16. Protein (Cyanobacteria): 322756 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available ber protein (repeat/shaft region) Coleofasciculus chthonoplastes PCC 7420 MSLNPPLQLSLNPPLQLSLNLALQLSLNPPLQLSLNLALQLSLNPPLQLSLNLALQLSLNLALQLSLNPPLQLSLNLALQLSLNPPLQLSLNLASTIVPKPGFYNCP ...

  17. Protein (Cyanobacteria): 321355 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available ein MC7420_5449 Coleofasciculus chthonoplastes PCC 7420 MWASAHQRNADTTNVKYTFNLNQGRVLPQTLSVRFTIKSLNPPLQITLFSHQ...LLHSHQLFLKKGRVLPQRLSARFTIQSLNPPLQITLFSHQLLHSHQRPFNSYLKKGRVLPQRLSARFTIKSLNPPLQFALLSHHPLHSHQLFLKKGRVLPQTLSARFTIKSLN...PPLQFTLLTHQPLHSHQLFLKKGRVLPQTVSAIFSIKSLNPPLQFTLLTHQPLHSHQLFLKKGRVLPQTLSARFTIKSLNPPLQITLFSHQPLHSHQRPIQLIP ...

  18. Protein (Cyanobacteria): 321354 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available ein MC7420_5443 Coleofasciculus chthonoplastes PCC 7420 MPQTLSTIFSIQSLNPPLQITLFSHQPLHSHQLFLKKGRVLPQTLSARFTIKSLN...PPLQFTLLSHHPLHSHQLFLKKGRVLPQTLSARFTIKSLNPPLQITLFSHQPLHSHQLFLKKGRVLPQTLSARFTIQSLNPPLQITLLSHQPLHSHQRPIQLIP ...

  19. Protein (Cyanobacteria): 327034 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available n SPLC1_S201560 Arthrospira platensis C1 MSSLDSCWVSLNLTNKFVLGFTQPTFWVSLNLTNKFVLGFTQPTFWVSLNLTNKFVLGFTQPTFWVSLNPTNKFVLGFTQPTFWVSLN...PTNKFVLGFTQPTFWVSLNPTNKFVLGFTQPTFWVSLNPTNKFVLGFTQPTFWVSLNLTNKFVLGFTQPTFWVSLNLTNKFVLGFTQPTFWVSLNLTNKFVLGFTQPTFWVSLNLTNKFYL ...

  20. Protein (Viridiplantae): 168015435 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available ial Physcomitrella patens subsp. patens NNNNFNQSFIKSLNNNNFNQSFIKSLNNNNFNQSFIKSLNNNNFNQSFIKSLNNNNFNQSFIKSLNNNNFNQSFIKSLNNNNFNQSFIKSLN...NNNFNQSFIKSLNNNNFNQSFIKSLNNNNFNQSFIKSLNNNNFNQSFIKSLNNNNFNQSSNV ...

  1. Protein (Viridiplantae): 159490560 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 7735 hypothetical protein CHLREDRAFT_110145, partial Chlamydomonas reinhardtii MASNIVFCSLNLASSSVFCLLNLASSFVFCSLNLASSLAFCSLN...LASSFVFCSLNLASSLAFCSLNLASSFVFCSLNLASSFVFCSLNLASNKLFCSLNLASNIVFCSLNLASSLVISTA ...

  2. Protein (Viridiplantae): 159486781 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available XP_001701416.1 33090:11327 3041:3848 3166:6911 3042:6911 3051:6800 3052:6800 3055:6800 gln-glu non-discrimin...atory tRNA synthetase Chlamydomonas reinhardtii MSATLTFWDRNPPYAAVALARLANVPVAATHDPKA

  3. Protein (Viridiplantae): 302856447 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 068:309 hypothetical protein VOLCADRAFT_71439, partial Volvox carteri f. nagariensis MLADRICSQIAYGTCLQTVYACIMQMHAHMYNISH...ISYIAYRILHIAYRILHIAYRISHIAYCILHIAYCISHIPYRCIWHIAYCILHIAYCISHIAYCISHIAYCILHIAYCISHIAY ...

  4. Protein (Viridiplantae): 302842451 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 068:309 hypothetical protein VOLCADRAFT_93481 Volvox carteri f. nagariensis MRICITYRISYIAYRILHIAYRILHIAYRILHIAYCISHIAYCISH...IAYCILHIAYCILHIAYRILHIAYCISHIAAYGISHITYRISHIANCMHIAAYRISLHIAAYCISHIHICIYAHI ...

  5. Protein (Viridiplantae): 302842580 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 068:309 hypothetical protein VOLCADRAFT_62920, partial Volvox carteri f. nagariensis CILHIAYCILHIAYCILHIAYCILHIAYRILHIAYRISHIAYCISH...IAYCISHIACRISHIAYCISHIAYRILHIPYRCIWHIAYHIPHIAYRKLHAYRCISHIAAYRCILHIAYTYMHICTYTKHKT ...

  6. Protein (Viridiplantae): 302857466 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 068:309 hypothetical protein VOLCADRAFT_71945 Volvox carteri f. nagariensis MRICLHIAYVCISHIAYRICACLHIAISHIIHIAYRILPIAYCISHIAYCISH...IAYCILHIAYCISHIAYRISHIAYCISHIAYCISHIAYCILHIAYCILHIAYCILHIAYCILHIAYCILHIAYCILHIAYCILHIAAYGILHIAYAYRSQHSIA ...

  7. Protein (Viridiplantae): 302837846 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 068:309 hypothetical protein VOLCADRAFT_90903 Volvox carteri f. nagariensis MQMHIVYCISHIAYCILHIAYRILHIAYCISHIAYRILHIAYCILHIAYCISH...VAYCISHIPYRCIWHIARISHTAYRIPQITYRCISHIAAYRCILHITYTYMYIYAHI ...

  8. Protein (Viridiplantae): 302855806 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 068:309 hypothetical protein VOLCADRAFT_35996, partial Volvox carteri f. nagariensis HIAYCISHIAYCISHIAYCISHIAYCILHIAYCISH...IAYCVSHIAYRILHIAYRILHIAYRILHIAYCILHIAYCILHIAYRISHIAYCISHPYRCIWHIAY ...

  9. Protein (Viridiplantae): 302837844 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 068:309 hypothetical protein VOLCADRAFT_60268, partial Volvox carteri f. nagariensis CILHIAYCILHIAYCILHIAYCILHIAYCILHIAYCISHIAYRISH...ITYRILHIAYCISHIAYCISHIAYRISHIPYPISHIPYHCIWHIAYHIPHIAYRKLHIAAYRISLHIAAYCISHIHICIYAHNET ...

  10. Protein (Viridiplantae): 302848645 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 068:309 hypothetical protein VOLCADRAFT_96833 Volvox carteri f. nagariensis MRICITYRTYRILHIAYCILHIAYCILHIAYRISHIAYCISHIAYRISHIAAYGISH...IAYCISHIAYRISHIAYRILHIAYCILHIAYRISHIPYRCIWHIAYHIPHIAHRKLHIAAYRISLHIAPYCISHIHICIYAHI ...

  11. Protein (Viridiplantae): 302855635 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 068:309 hypothetical protein VOLCADRAFT_100737 Volvox carteri f. nagariensis MYNISHIVYCISHIAYCISHIAYRISHIAYRILHIAYCISHIAYCISHIAYCISH...IAYRISHIPYRCTISLHMAYRISHTARISHIANCISLHIAYCILHIAYCISHIAYPISLHHIAAYGISHITYRTHIAYRKLHIAAYRISLHIAAYCISHIHICIYAHI ...

  12. Protein (Viridiplantae): 302853005 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 068:309 hypothetical protein VOLCADRAFT_99209 Volvox carteri f. nagariensis MQMHAHTYNISHIVYCISHIAYCISHIAYRISHIAYRISH...IVYRVSHIAYRILHIAYCILHIAYCILHIAYCILHIAYCILHIAYCILHIAYRISHIAAYMAYRISHTAYRISQIAYRCISHIAAYRCILHITYMHIIYAHI ...

  13. Protein (Viridiplantae): 357441081 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available :4956 3880:4956 PGPS/D12 Medicago truncatula MNIFGRSSPPKWSAKLCGCGENPGTCLITCCLPCITFGQIAEVVDEGRSSCAMQGCVYGLLMTITCHWLYSCLYREKLRAKYGLPAEPCCDCCVHFCCDACALCQEHAELKARGFNPSKGWIGPPHAPPRMPPTMFR ...

  14. Protein (Cyanobacteria): 12372 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 01 Synechocystis sp. PCC 6803 substr. GT-I MPLNREEIIQTLKERGLRVTPQRYGVYANLLQRRDHPSAEQLLFDLNQAAPTSSQATVYSSLKALQSVGLIREVLLEEGVCRYDANVEPHHHFCCRHCGAIEDVDWEELPAVDLGKLRVGLKAERYEITVHGVCENCGD ...

  15. Protein (Cyanobacteria): 12515 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available lator, Fur family Calothrix sp. PCC 7507 MQHQANAIVQTLKSKGLRVTPQRFAVYANLLSRTDHPTVDQILTELNKDFPVSSQATIYSSLQALREVGLVREVLLEEGVCRYDANVGPHHHFCCCQCGAIEDITWDTFEYIQLQSLRPGLRGKTYEVTVQGICDRCDPE ...

  16. Protein (Viridiplantae): 159491002 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available hypothetical protein CHLREDRAFT_127770 Chlamydomonas reinhardtii MFPGMPAGPGGPGGAGAFDFSALQSALNDPSIKQMAEQIANDPSFKEIAKQMQESFGAMMGGMP...PPGGAPGGDARAAGALPGGMPGMPGMPGMPGMPAGMPGMPGMPGMPGMPGMPGGMPGGMPGMMPGMMPPGFDPSKYMEAMQGMFQNP

  17. Protein (Viridiplantae): 302849879 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available VGRFMAFDRHMNLVLGDSEEFRRLPPKKGKSEEEREERRVLGLVLLRGEEIISLTIEGPPPNEEMRTDRSQVAPGGPGVARAVGRGMPAAAPGQAPAGLAGPARGVGG...PAPGMMMPRPQVSAPPVPRPGPPTPGVPPPRPGMAPPGMPPPGMPPPRPGMPPPPGMGPPGMMPPPGGMPPPGMPPRPGMPPPGMPPPGMPPPGMP...PPRPGMMPPPGMPPPGMPPPGMPPGMMPPGMGPPGMPPRPGMPPPGMPPPGMPPPGMPPGMRPPGQ ...

  18. Protein (Cyanobacteria): 471778 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available VQFLVLSNSGAPLSLEENRTVTVPVAARAGGLTIPGGALLVGRFERTGEASGALNIESLVIGQNVYAVRATSTPIPGLLRRTGTATPRYPGREASGTLFEAGGDLLGIPVHSRQARAATSLLGALFGAAAPPAPERSTGTLAASLEPMQTLGVQFLGEVDFDSPIAQLPNGPADLNGSW ...

  19. Protein (Viridiplantae): 168030478 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available ens subsp. patens MRPDPPAPERSGFFSGKMLQRTLHNSRITILCGVVTILVLRGTIGSGVDKTHFLDLTLDMDDIPDVEWDPSVPFTLGPTITNWDEQRAKW...14:9016 114656:9016 3215:9016 3216:9016 3217:9016 3218:9016 145481:9016 predicted protein Physcomitrella pat

  20. Protein (Viridiplantae): 145354199 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available DDDDAEGLRVENGETMDAFLTRHGLSASLRAAVTYALALQTRADCAAATALEDLKVYILSVAKYGPQTGACLIPVYGAGDIPQAFCRVGAVDGATYVLRQGVRELDASTTISAAISTGGQEIRARKFIVPAPE...RSSGPLLVHAVCILDAPLVAEYGQMLVVFPPLSAADAQTAVIRALQVGSHTGCCPEGKYLLYLSTVVDDVNVDPYAGLNAALD

  1. Protein (Cyanobacteria): 109031 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available LQSHSRANVARGLEILDNTLDLGRKRSLLIVLDRRSTLEKLQSLSDLVTYEPMTPSDRLRYLMDRQHFLSDWGLACCFHLAYRARWSIPAEQTLACLSHPIGFVREAVLSYLSMASPRTLREILPMMANDPNRLVAHQVARLMQEMGISAPGANAASSPRSPAPERSTSTMQFRPT ...

  2. Protein (Cyanobacteria): 175822 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available agen triple helix repeat-containing protein 'Nostoc azollae' 0708 MRLIEDGEDGEDGEDGEDGEDGEDGEDGEDGEDGEDGEDGEDGGEIFLMPYALCPMPYALCPMPYALCPMPYALCPMPYALCPMPYAQNQDFSHPNRESSVKLFSSVAPKP ...

  3. Protein (Viridiplantae): 302831698 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available XP_002947414.1 33090:15635 3041:4416 3166:3916 3042:3916 3065:3289 3066:3289 3067:3289 3068:3289 iron-nutrit...ion responsive ZIP family transporter Volvox carteri f. nagariensis MAGGCQGISAGRLGV

  4. Protein (Viridiplantae): 226493496 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available :3745 4577:3745 maltose excess protein 1-like Zea mays MSSPSVASLRLPMLPASPPLSRRAIAGVTPSAAAPRALLLQPLAPKALAAYHQ...402 58024:15402 3398:15402 4447:7759 4734:7759 38820:7759 4479:7759 147370:7480 147369:7480 147429:7480 4575

  5. Protein (Viridiplantae): 18418329 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 58024:15402 3398:15402 71240:8796 91827:8796 71275:11084 91836:6080 3699:6080 3700:6080 980083:6080 3701:6080 3702:6263 Maltose exce...ss protein 1 Arabidopsis thaliana MEGKAIATSLGGDRVLIFPCSPRSSFVFTSRLSSLPLKRASIGGAVSCS

  6. Protein (Cyanobacteria): 80731 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available function DUF29 Dactylococcopsis salina PCC 8305 MQTHQVSNQPQLYDQDYYLWLKKTQEQLATGNFSALDVANLIEELADMGKSEKRAVESN...LTILIMHLLKYQYQPQKRSNSWLFTIREHRRRLEKLFKDSPSLKRYFNEVLNECYQDARELAAAETGLPLEMFPTQTPFTTENILNPAFLPSTNDDNNSNI ...

  7. Protein (Cyanobacteria): 311090 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available tein Chro_5799 Chroococcidiopsis thermalis PCC 7203 MKIEKQKKNNRVTVRFNDRDYTEVKKKAKKSNTTVAEYIERSALRRELPTPPTINQVLVYQNLGKARELTFTIRNTCKLYGDRTVPTTEIMSLLEAMENHIQAAGMEAYGLGKIRTNIETATKNKEEVA ...

  8. Protein (Cyanobacteria): 236201 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available otein tlr1675 Thermosynechococcus elongatus BP-1 MRQSLSMTRLATGCPMRQLNFLMIFVIGLGLVLFSIQNTEPVSIKFFEGKVIQAPLCIELIIAMGIGAVFAWVFNVWVQVQRLFTIRVEMEARDEQIAHLEQDVERYKAALEEQQRLLPSVSSASTEK ...

  9. Protein (Cyanobacteria): 322998 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available in Tery_4629 Trichodesmium erythraeum IMS101 MLYDKQQKKSLCNKYFPKLLTVHLEDKATEIYLQKFIYRNLSTDIYLQKFIYRHLSTDIYLQKFIYRHLSTDIYLQTFIYRNLSTD...IYLQKFIYRNLSTEIYLQTFIYRNLSTEIYLQTFIYRHLSIEIYLQKFIYRHLSTDIYLQKFIYRHLSTDIYLQTFIYRHLSTEI

  10. Protein (Viridiplantae): 297720699 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available SASAGASADVGTDVGTDAGASADSRTSASTSTSTSADAGADVGTDVSSDASASSSADSRTSASASTSTSADASADVRTDVSTD...AGASASADSCASASASTSADARTSASTDVSTDANASSSADAGADASTNASADLRTNASTDLRTDASTSANADASTDLRTDASTSANADASTNLRTDASTDVRTNASACSNAGASTDLRTDASTD...LRTYASADASTDAGASANADVSSDASADASASASTSASASTGAGAGAAVQAEAGLAGDADVGLDGRRVVAEQQKQRQHRHAQHRRPHLAGPRRHRRCFLLRRIGSFIELGLLLQS ...

  11. Protein (Viridiplantae): 357480181 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available :6556 3398:6556 71240:5452 91827:5452 71275:3181 91835:20007 72025:9590 3803:9590 3814:9590 163742:17625 3877:17625 3880:17625 Temper...ature-induced lipocalin Medicago truncatula MAHYLYSVLFCYVLPCIYLFLPVLQHAMGEPEVVKGVDL

  12. Protein (Viridiplantae): 357492761 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available :6556 3398:6556 71240:5452 91827:5452 71275:3181 91835:20007 72025:9590 3803:9590 3814:9590 163742:17625 3877:17625 3880:17625 Temper...ature-induced lipocalin Medicago truncatula MKVTKTDSYDYYKVRKLVRNIFMNKIVLNKLKGYPKRIKDFIVVMDRWRKCYMVEGDGRNPRRRWWQKRCTCKQTHLDDESYNKLVQKTKDDGYDATKLHKTPQSKPPPQ ...

  13. Protein (Viridiplantae): 357480173 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available :6556 3398:6556 71240:5452 91827:5452 71275:3181 91835:20007 72025:9590 3803:9590 3814:9590 163742:17625 3877:17625 3880:17625 Temper...ature-induced lipocalin Medicago truncatula MGNTVGKDKEVVKGVDLERYMGRWYEIASFPSFFQPKNG

  14. Protein (Cyanobacteria): 260028 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available ARSAKVQRLEEILEEVIEAGDRALLFTQFAEWGHLLKAHLEQRWKQPVPFLYGNTSKAERQAMVDRFQEDPRGPQLFLLSLKAGGVGLNLTRASHVFHIDRWWNPAVENQATDRAYRIGQQNRVMVHKFITSGSVEERIDRMIKEKSKLAEDIVGSGEDWLGGMDVSQLKDLVTLSED ...

  15. Protein (Viridiplantae): 357442357 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 3137 3880:13137 hypothetical protein MTR_1g087730 Medicago truncatula MEGYGYGSDHGSFGSERRIEIVSGRSYGFSQSYYVGRSESTGEVTRASHDGAAPVAKPWSFNDAATKRRKRIARYKVYAVEGKVKATFRNGIRWIKHTCSRIVHGY ...

  16. Protein (Cyanobacteria): 36700 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available otein CWATWH0003_4348b3, partial Crocosphaera watsonii WH 0003 YMGWRSRFATDPEVVSKTRASHTQLAPWVFLFVALGYTGGVLSLVMQNHDLLSSGHFWTGTGALGLMAVSAITPFIGFGGEKKEAYRAFHAYLGAVVAIVFIAHGILGLKLGLSL ...

  17. Protein (Cyanobacteria): 260023 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available ARSAKVQRLEEILEEVIEAGDRALLFTQFAEWGLLLQAHLQKRWRQEVPFLYGSTSKTERQAMVDRFQEDPRGPQLFLLSLKAGGVGLNLTRASHVFHIDRWWNPAVENQATDRAYRIGQQNRVMVHKFITSGSVEEKVDRMIREKSKLAEEIVGSGEDWLGGLDVGQLKDLVALEE ...

  18. Protein (Cyanobacteria): 207811 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available bya sp. PCC 7375 MVAPITISPATRNDIPLLFELVMALAEYEDLAHEVSGAPEDLEKYLFGDSPKAHAIVARIDGAPAGFALYFFNFSTFLMKPGIYLEDLFVLPGYRRRGIGTAIFQYLAQTALAKGCGRFEWSVLDWNQPAIDFYRSKGAVMLNDWRTCRVAGIALEELATSEQ ...

  19. Protein (Cyanobacteria): 173276 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available QKALALTELRCTFEGRSLVPDVAVFEWSRIPTDGNGEIANRFESYPDWIIEILSPDQSPNRVINKIIFCINQGTKLGWFIDPNDKSVMVFQPNRLPEVKYDTDILPVLDVLGNCQVNAADIFSWLKVK ... ...rotein Ava_0761 Anabaena variabilis ATCC 29413 MTLSTQVSFHPSLDEFLKLPETKPASEYIDGRIYQKPMPQGKHSILQTRLSSNINQVGEPQ

  20. Protein (Cyanobacteria): 436078 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available photosystem I PsaK protein (subunit X) Prochlorococcus marinus subsp. pastoris str. CCMP1986 MLTTLFAAAAAPATFEWSPKCAIVMIACNVFAYAIARATIRKPNEGFEIPNSQFFGGLSHASVVGANCLGHIFGIGAILGLASRGVL ...

  1. Protein (Viridiplantae): 302822432 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available endorffii ILELGCGNSRMSEDMYQDGFTDITATDLSPVAVESKRWRCFDLNYGIKVLVADIMDMPFKDASFDIVIEKGVMDVLFVDSGSPWDPEPQTRARVDVTL...KEVHRVLGANGPHFRRPFFEASGFEWSMEYSTFGDSFHYYFYTLRKVVSFLPGQTFKHSNIVLPGNGQKGFASRLDGNHKH ...

  2. Protein (Cyanobacteria): 255110 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available ZP_09780818.1 1117:4705 1150:1851 35823:76 376219:316 cyclopropane fatty acyl phospholipid synthase (unsatur...ated-phospholipid methyltransferase) Arthrospira sp. PCC 8005 MSIRKAAMKSTLNQQIQQFYD

  3. Protein (Viridiplantae): 356546122 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available HDFERLSTPKIVEARDVLLQKLGERKNLQAGEPENPRTVDTYQEGREDRGTESISFEQNQILTEVTNAVEGLEVDDTVSTEKWLEDTDIDASSLASCTKLQQEEDVSFSDLEDDRSYSSDKLSGYREAHDIRGSSPEGATSDWVRLRESSERDGRKKVIRLKGKDSEDESNDWLTVDDFN ...

  4. Protein (Viridiplantae): 168044488 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available ens subsp. patens MTRCTSLISLPNEIANLSSLEELYLNGCSSLKSLPNELANLSNLRRLDLRYCSSLTSLPNELANLSSLKELDLSSCSSLRRLPNELENLSSLIRLDL...SGCSSLISLPNELRNLSSLEELDLSHCSSLINLPNELANLSSLTRLVLSGCSSLTSLPNELENLSSLEELRLNNCSSLTSLPNKLRNLSSLEELDL...SHCSSLTNLPNELANLSSLTRLDLSGCSSLTSLPNELTNLSSLTRLDLSGCSSLTSLPNELTNLSSLTRLDLSGCSSLTSLPNELTNLSSLTRLDL...SGCSSLTSLPNELENLSFLEELGLNHCSSLTSLPNELTNLSSLTRLDLSGCSSLTSLPNELTNLSSLTRLDLSGCSSLTSLPNELANISSLTTLYLRG...CSSLRSLPNESVHISSLTILYFHGYVSLTSLLNELVNLSSLMTLDLNGCSSLKSLPNELTNFTSLTILDLSGRLSLTSLPNEFTNLSSLKELVLSHCSSLTSLPNELTNLSSLKELDLSSCSSLRSLPNELANLSSLTRLDL ...

  5. Protein (Cyanobacteria): 71748 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available othetical protein gll1203 Gloeobacter violaceus PCC 7421 MERLSFLALAAIAAGVIQVPAAMARPTAIERSAFNSRVRDAVVSRWRIPLVERTTTVDVTARWDLQAPMVLLVLLWWAAPGTGTRGLAAGRSALRDNGRAVLVGTPTYGKGAIQQDYTCPIAPG ...

  6. Protein (Viridiplantae): 302846369 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 56 3068:1056 hypothetical protein VOLCADRAFT_65200, partial Volvox carteri f. nagariensis RWAAPEVLTGGPPSEAGDVWSFGVTCWEIFANGAEPYASLSNAQVALALRAGYRLDRPRGCPLELWELILQCWSEDPSVRPTFTSIAETL ...

  7. Protein (Cyanobacteria): 377866 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available MARENKEELDYYFVVVSAAGCVADWAAPRAKATEIVAINSMYSGKFSGQTPKIKKINLVQVKDEKRKLLVEETKEKLAFATLMGSQSTYTQQTCQNFKQFQHALKLKGYEETVY ... ...an7822_4541 Cyanothece sp. PCC 7822 MTKLTIGLGAVILGIGLWGCSNVSNQMTPPMTQVTVQICGEQLVRNKIEEDCLSNTGVYWGEVTEKDIKLVG

  8. Protein (Viridiplantae): 302850746 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 3068:957 hypothetical protein VOLCADRAFT_36129, partial Volvox carteri f. nagariensis VLTGGLGTYQWAAPEVLAHQRYSEKADVYSFGIVLWECLTRKLPYEGMTAVQAALGVVTHGLRPDIPRVTPHDVADLVRACWAAVPEQRPSFAQI ...

  9. Protein (Cyanobacteria): 449752 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available otein MAE_27120 Microcystis aeruginosa NIES-843 MLAKPIMGLGFVNVWLTGIGVIGGVPIRVIAFKTLTAAKPRPANSPVGVPTNPVVVPGVRVGLVVPHEPAVAFPPTAIILAAWAAPAKLRAATLAAIATVPVASCLEMLVIILSRLLREHLTYAISNYT ...

  10. Protein (Cyanobacteria): 456819 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available o7375DRAFT_0719 Leptolyngbya sp. PCC 7375 MQLSPVHAFETPPGLESAYQQVLSDWSAPLLPAEIPFEFTGVETSSSASHHLLSIDINEFQTVAIAAGEGSKRIDTLSSEPVQQIALNNQVVGYFLPAGETDEEPPELSFLIEEINYYVGGWAAPDDLIAIANSMIDNQ ...

  11. Protein (Viridiplantae): 159489270 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available TLWLWRPRVQAGQGAGGGAAGTAAAAPGGGGGAGAGHAARPPATNRRQSGASNSSADTVAPLRPTAVHQAAAAAVAASGPAAAPSVSVSGGNGSSAAPGRRTGGGVSG...DVDAVGWVAVWVVAKANWQTVQAQTPVQSPAALRQVVLLFMRPPCLHRRVQAGQGAGGGAAGAAAAALGGGGGAGAGHAARPPATNRRQSGASNSTDGSEGPTGAGREAAGASRACGGIWRRRGRG ...

  12. Protein (Viridiplantae): 224138406 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available SGLQPWFGLRADMDALPIQEMVEWEHKSKNNGKMHACGHDAHVTMLLGAAKLLERMKDELKGTVKLVFQPGEESYGGAYHMLKEGALDNFQGIFGLHVAPEIPVGTVDSRPGPMLAASGRFIATIKGKGGHAA...RPQDTRDPVVAASFAILALQQIVSRETDPLDARVVSVGFVEAGQAGNVIPETVRFGGSIRSMTTEGLVSLQQRVMQIVEMQAA

  13. Protein (Viridiplantae): 115434654 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 4527:2250 4530:2250 39947:2250 Os01g0159500 Oryza sativa Japonica Group MGKAASMRVALVSVVLVGLILVSTAHAARPEKLPAVVSPSIAPAVAEVVDAAINAVDLLAGFQKPPGARLPPPGGTAVTGGNRGNRAKPRQIYKSKFEFKNSGKPRGLTR ...

  14. Protein (Viridiplantae): 159467908 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available EQAADDSSTLTAVPVVEGAGDIIPSHPLPEDTERTVSALGWLPPVQVLTEAPEPGAWCFTAPLWGNPLLTPSPAAASGEQEEEDSGSDGETAVEPVPAGVARRTQGRG...LDYRHRTLRACARLVTIGDLVRAHAARPPAAAAVDWEGWLRDYLAPSDGRRRRRGPTLAALQGLVGDIPPSWWSAAQAHAA

  15. Protein (Cyanobacteria): 229984 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available LNNSTISGNYATNEGGGIFNVSGTINISNSTISGNYAMSLISGGGGINNFFGTINISNSTISGNYASDSAGGIYNGAGTINIS...QQVVNISGLTITQGNSSGNGGGIENIENLTLSNSTVSGNLAGGFSGGIFNGGNLTLSKSTVSGNSATNGGGIFNVGGTTSI...DENDGIGVGGISLREALGAIADGGTITFADSIANGTIILNGTELVINKSVTIDGDTDNITVSGNNNSGVFNIDDGDINIQQVVNISGLTITKGRTNFGGGIDNRENLT...SNSTVSGNSITYSAGGIGNWGGTINISNSTVSSNSAGLNGGGIFNLAGTTNISSSIISGNSATSGDEVYSNSGTVTADNNNLFGNSSQSNSDAFVNFTSGANDINATT

  16. Protein (Cyanobacteria): 254399 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available QAEALPYANGTFSGVLCTLAIHHFNTLVPAFKEIYRVLSHGCFVLFTATPEQMSKYWLVEYFPEAMRKSAEQMPRLEEVRNALNQAGFNSIDIEVYSVSKNLQDLFLYSGKHRPELYLDSNVRSGISTFALLASRDEITTGCQRLAADIECGMITKIIKKYDHAQGDYLFLIANKIN ...

  17. Protein (Viridiplantae): 302830706 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 98 3068:2998 hypothetical protein VOLCADRAFT_103166 Volvox carteri f. nagariensis MSHHQSLAAGHARVLANSSLTCSRFVRGRRVCHQTQPTSLRCRHQLDRFAL...LASANEPITSASNGAVLDKRSGRMTYKPLSYGEMVNDAVDSVVSAIGDNLKWLEVEFPALPTNVDGYKGSSDLFIDSNTQLAL

  18. Protein (Cyanobacteria): 266185 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available IRFLLDEILKSFSENTLVKDKKPVLIIKGLENSIGLDEYPPILQNLNFVRDAFSHQVPYPILFCLPSSTTTRFAKFAPDFWAWKSGIFKFRSLPEAERSQIAFPTLSL...LQKLGDLYRKKKYGERAENLELAIAAYKLSLEVYTRDAFPYEWARTQNNLGIAYSDRIRGERAENLELAIAAYRQSLEVRTRDAFPVEWARTQNNLGIAYSDRIRGGRAENLELAIAAYRQSLEVRTRDAFP...VEWAMTQNNLGTAYSDRILGDRAENLELAIAAYYQSLEVRTRAAFPVEWARTQNNLGNAYSDRILGERAENLELAIAAYRHSLEVLTRNAFP...YEWATTQNNLGIAYRSRILGERAENLELAIAAYRHSLEVRTRDAFPEDWARTQNNLGIAYRSRILGERAENLELAIAALNQSLEVLTRDAFP...EDWARTQNNLGTAYSDRILGDRAENLELAIAAYKLSLEVYTRDAFPYEWAGTQNNLGNAYSDRILGDRAENLELAIAALNQSLEVYTRDAFP

  19. Protein (Cyanobacteria): 266255 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available PIFQKYQDQLDLEFTETLTEWFHSQLALNAIITNKDLARIWGNFVIDIWRFPLDFDFAEIVALWFHSQPNLNKIRKNKDLARNLNNFAIDIQQFPLGSRANNLEIAIAAYQAALKVYTRTAFP...EDWARTQNNLAVAYRDRIKGERANNIEEAIRYHQAALEVFTRTAFPEDWARTQNNLGIAYSDRIKG...ERADNMEEAIRCYQAALEVFTPTAFPEDCARTQNNLGEVYRNRIQGERADNIEEAIPYYQAALEVFTCTAFPQYWATTQMNLGSAYLYRIRGERADNIEEAITALQVALEVFTRTAFP...QYWAMTQGNLGNAYWSCIRGERADNIEEAIRCYQAALEVYTRTAFPEDWARTQMNLGNAYCNRIKGERADNIEEAIPYYQTALEVFTRTAFPEDWART...QMNLGNAYCNRIKGERADNIEEAIPYYQTALEVFTRTAFPEDWARTQMNLGNAYCNRIKGERADNIEEAIPYLQAALEVYTRTAFP

  20. Protein (Cyanobacteria): 266190 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available QVVNIEEYQEFLLEVLQAEYESDDPTVVYPILERRQYLLDDTFAQLLQQYARNVFSQRKAEEVAVIAGVIQNLCIDIKNFPLGSRANNLEIAITGYQTLLEVYTRDAFP...EKWAMTKNNLGIAYSDRILGERGDNLEKAIAAYNLSLEVYTPTAFPYEWARTQNNLGGAYNDRILGGRAENLEFAIVAYNLSLEVYTRKAFP...EDWARSQNNLGEAYRNRILGEKADNIELGITALNQSLEVRTREAFPEEWARTQNNLGLAYSDRILGERAENLELAIVAYNLSLEVYTREAFPEDWA...RSQNNLGLAYSDRILGGRAENLELAIAAYNRSLEVYTREAFPEKWAGTQNNLGNAYLYRILGERRLNLELAIAAYKLSLEVYTRDAFPYEWARSQNNLGNAYLYRILG...ERAENLELAIVAYNLSLEVYTREAFPEDWARSQNNLGLAYSDRILGGRADNLELAIAAYKLSLEVYTREAFPEKWAGTQNN

  1. Protein (Viridiplantae): 302817905 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available PLPSCNENPFRHSKPAVADDQGSSAAPPPHPAFPGFGNFPPFFPGAIPPTANKVAPPPHPAFPGFGSFPPFFPGAFPPVDHSTASKVAPPPHSAFPGLGWNFPPFVPGAFP...PVDHSTAFKVAPPPHPGFGYPLKPAPHGSNKAAPPPFANSPPSFPGAFPPHPSSSKPGSAPPTHGSHSTQAPPPFHGTKKHHHP ...

  2. Protein (Cyanobacteria): 465646 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available othetical protein N9414_12533 Nodularia spumigena CCY9414 MGSGAFPDFGGDLVSPSENSLLITEMGSGAFPDFGGDLVSPSENSLLITEMGSGAFP...DFGGDLVSPSENSLLITEIGSLAFPDAGGDLVSPPENSLLITEIGSGAFPGAGGDLVSASENSLLITEIGSGAFPGAGGDLVSPSENSLLITEIGSGAFP ...

  3. Protein (Viridiplantae): 302770641 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available IARPWPFYSAGPFFFQPPEPLPSCNENPFRHPKPAVADDQGSSAAPPPHPAFPGFGNFPPFFPGAIPPTANKVAPPPHPAFPGFGSFPPFFPGAFP...PVDHSTASKVAPPPHSAFPGLGWNFPPFVPGAFPPVDHSTAFKMAPPPHPGFGYPLKPAPHGSNKAAPPPHSTPFPGFANSPPSFPGAFPPHPSSSKPGSAPPTHGSHSTQAPPPFHGTKKHHHP ...

  4. Protein (Viridiplantae): 115439729 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available VTYSFEHNHSATVPRAQNRQAAPQKPKAQACSPPEPVVEVEPEETHQYGVTAGPATGGGGGAAAIEVRDEFRWLYDVVSVPATSTSPSDIDAADEMQLYDQPMFFGGAVVGTAALLPDEFGDVGGLGGEGLGEEEALFEGLGELPECAMVFRRRAGDGLEMGGGVKIEQPAESTAMT ...

  5. Protein (Viridiplantae): 357112985 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 58024:7047 3398:7047 4447:4465 4734:4465 38820:4465 4479:4465 359160:2518 147368:2334 147385:2334 15367:2334... 15368:2334 PREDICTED: josephin-like protein-like Brachypodium distachyon MEPGAKSEANQNEEGSGAVGSSGGSSKVYHERQR

  6. Protein (Viridiplantae): 15235180 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available protein Arabidopsis thaliana MMVLYCGRKLLVVLMVTAFVFSGSAEAWSWSWGSGQSGSNGGWGWRSGNSGGSSGSGSGGSDSNSGGSSWGWGWSSDGTDTNWGWGSSSGSNHS...SGTGSTHNGHSSGSNHSSATGSTHNGHTSTGSNHSSGNGSRHNGYSSGSNHSSSTGSNHSSSTGSTHNNHSSGSNHSSILGSTHKNHS...SGSNHSSIVGSTHNNHSSGSNHSSITGSTHNHTAPIPAGRKIAVTVWKNGYGYTEWTAKHAPFYVSDVLVFKYNNDDQTQSKTKHR

  7. Protein (Viridiplantae): 225436803 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 478 58024:14478 3398:14478 71240:8172 91827:8172 71275:10399 91834:3545 403667:3545 3602:3545 3603:3545 29760:3545 PREDICTED: classic...al arabinogalactan protein 26-like Vitis vinifera MAAIWSLIAVFMVFITIHSSVAFPYQLKLQTST

  8. Protein (Viridiplantae): 224114153 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available redicted protein Populus trichocarpa MENRGRMGHLSPMIHAIAICLVATSVVAYEPYYYKSPPPPSQSPPPPYHYSSPPPPKKSPPPPYHYTSPPPPKKSPPPPYHYSSPPPPKKS...PPPPYHYSSPPPPKKSPPPPYHYSSPPPPKKSPPPPYHYSSPPPPKKSPPPPYHYSSPPPPKKSPPPPYHYSSPPPPKKS...PPPPYHYSSPPPPKKSPPPPYHYTSPPPPKKSPPPPYHYSSPPPPKKSPPPPYHYTSPPPPKKSPPPPYHYSSPPPPKKSPPPPYHYSSPPPPKKSPPPPYHYSSPPPPKKSPPPPYHYSSPPPPKKSPPPPYHYTSPPPP ...

  9. Protein (Cyanobacteria): 324054 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 472DRAFT_2939 Cyanothece sp. ATCC 51472 MKISLIFLTLPLLFLITLLSSCNRSDFSNSIKSQSLIKQNNSQNSINLNQTCTNKKVGYQVNYPQDWQ...TNSGNVMNDCQVFDPTYAKVPEQTESISKAIYLRVEENAPFDLISQENVGEQHLSKQTLTIDSYQAVAVESKSTGRAMLPKGQRNYSYIVDLGDRTLIATTYDVPDNNYAKNKQILDSMLKTIEFNNNELK ...

  10. Protein (Cyanobacteria): 303920 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available TGGSVPSPSTGNYVVFVNSSSQALLDIMRTIDPSVGFLNFEGRTVITLGTFTGATEAKQRLQQFQALGITGFAKDTVDGRLIPSLELPSPFANTPQPIPTTYNRGYYLAIPSFGQDVPALTSVLTRFDLQGGQVQSRSLPLGNFVVVGPYAQSSQLNTVLQTLRKAGLQTVRIYFGG ...

  11. Protein (Viridiplantae): 145355221 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 436017:4609 distinct from photosynthetic electron transfer catalyst, CYC6, partial Ostreococcus lucimarinus CCE9901 RDLERNGVATKEDISNLIERGKGKMPGYGESCAPKGACTFGARLDAEEIDALATYVLDRAAVDW ...

  12. Protein (Viridiplantae): 18395518 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available QTGLMGKSLIEFQSNKGDVLPAHKFGNHDVVVLKLNKSDLGSSPLAQGVVYRLKDSSITVVFDEVPEEGLNTSLRLEKLAN...VDNIVERLVPHKVKLVRVGHPARLLPQVLDSALDAQVLKGDNSGLANDIRKEMKALNGKLLKAKDKNTRRLIQKELRTLGKEERKRQQLAVSDVIKNADVILTTLTGA

  13. Protein (Viridiplantae): 18402126 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available RRVLLETLASQLPPQTIRFSSKLESIQSNANGDTLLQLKDGTRFLANIVIGCDGIRSKVATWMGFSEPKYVGYCAFRGLGFFPNGQPFQQKVNYIFGRGLRAGYVPVS...ATKVYWFITFNSPSLGPQMMDPAILRKEAKELVSTWPEDLQNLIDLTPDEAISRTPLADRWLWPGIAPSASKGRVVLVGDAWHPMTPNLGQGACCALEDSVLLANKLASAINGGTESVEGAMESYRSERWSQVFRLTVLANLVGKLLQSDNPLVCSVRDNIVSAMGKSSRTNDGTHKL ...

  14. Protein (Viridiplantae): 18394621 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available tetraspanin11 Arabidopsis thaliana MFRVSNFMVGLANTLVMLVGASAIGYSIYMFVHQGVTDCESAIRIPLLTTGLILFLVSLLGVIGSCFKENLA...SQIADAFYHKNLSPIQSGCCKPPSDCNFEFRNATFWIPPSKNETAVAENGDCGTWSNVQTELCFNCNACKAGVLANIREKWRNLLVFNICLLILLITVYSCGCCARRNNRTARKSDSV ...

  15. Protein (Viridiplantae): 15228000 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available GVLPMFAVVFIGYWAYGSSTSPYLLNNVNGPLWVKALANISAILQSVISLHIFASPTYEYMDTKFGIKGNPLALKNLLFRIMARGGYIAVSTLLSALLPFLGDFMSLTGAVSTFPLTFILANHMYYKAKNNKLNTLQKLCHWLNVVFFSLMSVAAAIAALRLIALDSKNFHVFADL ...

  16. Protein (Viridiplantae): 15236089 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available e 43 Arabidopsis thaliana MSVSIPVLMKRLCLYNSLSLFLFHLFPSPSLALSFSVELNLLKAQMVWANAKMRLALSLVTVFFGISLANLEVGFYSNTCPQ...AESIVKRVVSGAALSDPNLPAILLRLHFHDCFVEGCDGSILVNNGAISEKNAFGHEGVRGFEIVEAVKAELEAACPGVVSCSDIVALAARDAISLAN

  17. Protein (Viridiplantae): 15221544 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 1-aminocyclopropane-1-carboxylate oxidase-2 Arabidopsis thaliana MESTKIAPSFDRASELKAFDETKTGVKGLVDSGISKIPRIFHHSSVELAN...PDLTFGTSKHSDGSFLTVLLPDNIEGLQVCREGYWFDVPHVPGALIINIGDLLQLITNDKFISLKHRVLANRATRARVSVACFFHTHVKPNPRVYGPIKELVSEENPPKYRETTIRDYATYFNGKGLGGTSALLDFKV ...

  18. Protein (Viridiplantae): 42571955 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available YINSTMPKLSGLCSLNFSASESLIQTTSHNCWTVFAPLLANVMCCPQLDATLTIILGKASKETGLLALNRTQSKHCLSDLE...QILVGKGASGQLNKICSIHSSNLTSSSCPVINVDEFESTVDTAKLLLACEKIDPVKECCEEACQNAILDAATNISLKASETLTDNSDRINDCKNVVNRWLATKLDPSRVKETLRGLAN

  19. Protein (Viridiplantae): 357508099 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available ERSDRYHDRSSSERSDSYQERSSVEKADHDRYHDRSSSERSDRYHDKSTSERSDCYEKRSSAEKADRDYDHDKSPSERSDR...YRVKCSSERSDRYHKRSSAEKADHNRYHDRSSSERSDRYHDRSSSERSGRYQERSSVEKADHDRYHDRSSSERSDRFHDKSTSERSDRYKKRSSAEKADRDYDHDKSPSERSDHYRVKCSSERSDRYQDRSSTEREHSNRSSTKSDKHSRKRKERDESSRRWEKFSRYSPDED ...

  20. Protein (Viridiplantae): 302767038 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available oellendorffii APNVYTYNTVMSALCKAGRLDQAHRLFGVMLASDSTPPNAITYRALIHGLCLKMELERAVLLLDAVYFKLSWLVPATYLIIRFKACHERGNLRA...PDIYTYNILFEGLSRHGLWRFAYKLLPRMNQDGVLPDAVTFNSLINGLVEDNRYHRAVTLIQEMVSRGCDPNAITYTILLKWLARNARADECVELFQRLLDRKLAPNV...YTYNTVMSALCKAGRLDQAHRLFGVMLASDCTPPNAITYRALIHGLCLKMELERAVLLLDAMAKRDCAPDVACYGTIVAAFCKQGRIDEAFELLERMPFAGDKVMFRTLVRALCK ...