WorldWideScience

Sample records for blm ortholog sgs1

  1. Processing of homologous recombination repair intermediates by the Sgs1-Top3-Rmi1 and Mus81-Mms4 complexes

    DEFF Research Database (Denmark)

    Hickson, Ian D; Mankouri, Hocine W

    2011-01-01

    Homologous recombination repair (HRR) is an evolutionarily conserved cellular process that is important for the maintenance of genome stability during S phase. Inactivation of the Saccharomyces cerevisiae Sgs1-Top3-Rmi1 complex leads to the accumulation of unprocessed, X-shaped HRR intermediates (X...... structures) following replicative stress. Further characterization of these X structures may reveal why loss of BLM (the human Sgs1 ortholog) leads to the human cancer predisposition disorder, Bloom syndrome. In two recent complementary studies, we examined the nature of the X structures arising in yeast strains...... lacking Sgs1, Top3 or Rmi1 by identifying which proteins could process these structures in vivo. We revealed that the unprocessed X structures that accumulate in these strains could be resolved by the ectopic overexpression of two different Holliday junction (HJ) resolvases, and that the endogenous Mus81...

  2. Differential genetic interactions between Sgs1, DNA-damage checkpoint components and DNA repair factors in the maintenance of chromosome stability

    Directory of Open Access Journals (Sweden)

    Doerfler Lillian

    2011-10-01

    Full Text Available Abstract Background Genome instability is associated with human cancers and chromosome breakage syndromes, including Bloom's syndrome, caused by inactivation of BLM helicase. Numerous mutations that lead to genome instability are known, yet how they interact genetically is poorly understood. Results We show that spontaneous translocations that arise by nonallelic homologous recombination in DNA-damage-checkpoint-defective yeast lacking the BLM-related Sgs1 helicase (sgs1Δ mec3Δ are inhibited if cells lack Mec1/ATR kinase. Tel1/ATM, in contrast, acts as a suppressor independently of Mec3 and Sgs1. Translocations are also inhibited in cells lacking Dun1 kinase, but not in cells defective in a parallel checkpoint branch defined by Chk1 kinase. While we had previously shown that RAD51 deletion did not inhibit translocation formation, RAD59 deletion led to inhibition comparable to the rad52Δ mutation. A candidate screen of other DNA metabolic factors identified Exo1 as a strong suppressor of chromosomal rearrangements in the sgs1Δ mutant, becoming even more important for chromosomal stability upon MEC3 deletion. We determined that the C-terminal third of Exo1, harboring mismatch repair protein binding sites and phosphorylation sites, is dispensable for Exo1's roles in chromosomal rearrangement suppression, mutation avoidance and resistance to DNA-damaging agents. Conclusions Our findings suggest that translocations between related genes can form by Rad59-dependent, Rad51-independent homologous recombination, which is independently suppressed by Sgs1, Tel1, Mec3 and Exo1 but promoted by Dun1 and the telomerase-inhibitor Mec1. We propose a model for the functional interaction between mitotic recombination and the DNA-damage checkpoint in the suppression of chromosomal rearrangements in sgs1Δ cells.

  3. Rmi1 stimulates decatenation of double Holliday junctions during dissolution by Sgs1-Top3

    DEFF Research Database (Denmark)

    Cejka, Petr; Plank, Jody L; Bachrati, Csanad Z;

    2010-01-01

    A double Holliday junction (dHJ) is a central intermediate of homologous recombination that can be processed to yield crossover or non-crossover recombination products. To preserve genomic integrity, cells possess mechanisms to avoid crossing over. We show that Saccharomyces cerevisiae Sgs1 and Top......3 proteins are sufficient to migrate and disentangle a dHJ to produce exclusively non-crossover recombination products, in a reaction termed "dissolution." We show that Rmi1 stimulates dHJ dissolution at low Sgs1-Top3 protein concentrations, although it has no effect on the initial rate of Holliday...

  4. Recombination-mediated lengthening of terminal telomeric repeats requires the Sgs1 DNA helicase

    OpenAIRE

    Cohen, Haim; Sinclair, David A.

    2001-01-01

    The Saccharomyces cerevisiae SGS1 gene encodes a RecQ-like DNA helicase, human homologues of which are implicated in the genetic instability disorders, Bloom syndrome (BS), Rothmund-Thomson syndrome (RTS), and Werner syndrome (WS). Telomerase-negative yeast cells can recover from senescence via two recombinational telomere elongation pathways. The “type I” pathway generates telomeres with large blocks of telomeric and subtelomeric sequences and short terminal repea...

  5. Holliday junction-containing DNA structures persist in cells lacking Sgs1 or Top3 following exposure to DNA damage

    DEFF Research Database (Denmark)

    Mankouri, Hocine W; Ashton, Thomas M; Hickson, Ian D

    2011-01-01

    The Sgs1-Rmi1-Top3 "dissolvasome" is required for the maintenance of genome stability and has been implicated in the processing of various types of DNA structures arising during DNA replication. Previous investigations have revealed that unprocessed (X-shaped) homologous recombination repair (HRR......) intermediates persist when S-phase is perturbed by using methyl methanesulfonate (MMS) in Saccharomyces cerevisiae cells with impaired Sgs1 or Top3. However, the precise nature of these persistent DNA structures remains poorly characterized. Here, we report that ectopic expression of either of two heterologous...... to RusA or GEN1(1-527), demonstrating specificity of these HJ resolvases for MMS-induced X-structures in vivo. These data suggest that the X-structures persisting in cells with impaired Sgs1 or Top3 contain HJs. Furthermore, we demonstrate that Sgs1 directly promotes X-structure removal, because the...

  6. Shu proteins promote the formation of homologous recombination intermediates that are processed by Sgs1-Rmi1-Top3

    DEFF Research Database (Denmark)

    Mankouri, Hocine W; Ngo, Hien-Ping; Hickson, Ian D

    2007-01-01

    CSM2, PSY3, SHU1, and SHU2 (collectively referred to as the SHU genes) were identified in Saccharomyces cerevisiae as four genes in the same epistasis group that suppress various sgs1 and top3 mutant phenotypes when mutated. Although the SHU genes have been implicated in homologous recombination...... formation of MMS-induced HRR intermediates (X-molecules) arising during replication in sgs1 cells, mutation of SHU genes attenuated the level of these structures. Similar findings were also observed in shu1 cells in which Rmi1 or Top3 function was impaired. We propose a model in which the Shu proteins act...... in HRR to promote the formation of HRR intermediates that are processed by the Sgs1-Rmi1-Top3 complex....

  7. Esc2 and Sgs1 act in functionally distinct branches of the homologous recombination repair pathway in Saccharomyces cerevisiae

    DEFF Research Database (Denmark)

    Mankouri, Hocine W; Ngo, Hien-Ping; Hickson, Ian D

    2009-01-01

    Esc2 is a member of the RENi family of SUMO-like domain proteins and is implicated in gene silencing in Saccharomyces cerevisiae. Here, we identify a dual role for Esc2 during S-phase in mediating both intra-S-phase DNA damage checkpoint signaling and preventing the accumulation of Rad51-dependen......, and sgs1esc2 cells attempt to undergo mitosis with unprocessed HRR intermediates. We propose a model whereby Esc2 acts in an Mph1-dependent process, separately from Sgs1, to influence the repair/tolerance of MMS-induced lesions during S-phase....

  8. Sgs1 and Exo1 suppress targeted chromosome duplication during ends-in and ends-out gene targeting.

    Science.gov (United States)

    Štafa, Anamarija; Miklenić, Marina; Zunar, Bojan; Lisnić, Berislav; Symington, Lorraine S; Svetec, Ivan-Krešimir

    2014-10-01

    Gene targeting is extremely efficient in the yeast Saccharomyces cerevisiae. It is performed by transformation with a linear, non-replicative DNA fragment carrying a selectable marker and containing ends homologous to the particular locus in a genome. However, even in S. cerevisiae, transformation can result in unwanted (aberrant) integration events, the frequency and spectra of which are quite different for ends-out and ends-in transformation assays. It has been observed that gene replacement (ends-out gene targeting) can result in illegitimate integration, integration of the transforming DNA fragment next to the target sequence and duplication of a targeted chromosome. By contrast, plasmid integration (ends-in gene targeting) is often associated with multiple targeted integration events but illegitimate integration is extremely rare and a targeted chromosome duplication has not been reported. Here we systematically investigated the influence of design of the ends-out assay on the success of targeted genetic modification. We have determined transformation efficiency, fidelity of gene targeting and spectra of all aberrant events in several ends-out gene targeting assays designed to insert, delete or replace a particular sequence in the targeted region of the yeast genome. Furthermore, we have demonstrated for the first time that targeted chromosome duplications occur even during ends-in gene targeting. Most importantly, the whole chromosome duplication is POL32 dependent pointing to break-induced replication (BIR) as the underlying mechanism. Moreover, the occurrence of duplication of the targeted chromosome was strikingly increased in the exo1Δ sgs1Δ double mutant but not in the respective single mutants demonstrating that the Exo1 and Sgs1 proteins independently suppress whole chromosome duplication during gene targeting. PMID:25089886

  9. A Rad53 Independent Function of Rad9 Becomes Crucial for Genome Maintenance in the Absence of the RecQ Helicase Sgs1

    DEFF Research Database (Denmark)

    Nielsen, Ida; Bentsen, Iben Bach; Andersen, Anni Hangaard;

    2013-01-01

    The conserved family of RecQ DNA helicases consists of caretaker tumour suppressors, that defend genome integrity by acting on several pathways of DNA repair that maintain genome stability. In budding yeast, Sgs1 is the sole RecQ helicase and it has been implicated in checkpoint responses......, replisome stability and dissolution of double Holliday junctions during homologous recombination. In this study we investigate a possible genetic interaction between SGS1 and RAD9 in the cellular response to methyl methane sulphonate (MMS) induced damage and compare this with the genetic interaction between...... SGS1 and RAD24. The Rad9 protein, an adaptor for effector kinase activation, plays well-characterized roles in the DNA damage checkpoint response, whereas Rad24 is characterized as a sensor protein also in the DNA damage checkpoint response. Here we unveil novel insights into the cellular response to...

  10. Survival and growth of yeast without telomere capping by Cdc13 in the absence of Sgs1, Exo1, and Rad9.

    Directory of Open Access Journals (Sweden)

    Hien-Ping Ngo

    2010-08-01

    Full Text Available Maintenance of telomere capping is absolutely essential to the survival of eukaryotic cells. Telomere capping proteins, such as Cdc13 and POT1, are essential for the viability of budding yeast and mammalian cells, respectively. Here we identify, for the first time, three genetic modifications that allow budding yeast cells to survive without telomere capping by Cdc13. We found that simultaneous inactivation of Sgs1, Exo1, and Rad9, three DNA damage response (DDR proteins, is sufficient to allow cell division in the absence of Cdc13. Quantitative amplification of ssDNA (QAOS was used to show that the RecQ helicase Sgs1 plays an important role in the resection of uncapped telomeres, especially in the absence of checkpoint protein Rad9. Strikingly, simultaneous deletion of SGS1 and the nuclease EXO1, further reduces resection at uncapped telomeres and together with deletion of RAD9 permits cell survival without CDC13. Pulsed-field gel electrophoresis studies show that cdc13-1 rad9Delta sgs1Delta exo1Delta strains can maintain linear chromosomes despite the absence of telomere capping by Cdc13. However, with continued passage, the telomeres of such strains eventually become short and are maintained by recombination-based mechanisms. Remarkably, cdc13Delta rad9Delta sgs1Delta exo1Delta strains, lacking any Cdc13 gene product, are viable and can grow indefinitely. Our work has uncovered a critical role for RecQ helicases in limiting the division of cells with uncapped telomeres, and this may provide one explanation for increased tumorigenesis in human diseases associated with mutations of RecQ helicases. Our results reveal the plasticity of the telomere cap and indicate that the essential role of telomere capping is to counteract specific aspects of the DDR.

  11. Rmi1, a member of the Sgs1–Top3 complex in budding yeast, contributes to sister chromatid cohesion

    OpenAIRE

    Lai, Mong Sing; Seki, Masayuki; Ui, Ayako; Enomoto, Takemi

    2007-01-01

    The Saccharomyces cerevisiae RecQ-mediated genome instability (Rmi1) protein was recently identified as the third member of the slow growth suppressor 1–DNA topoisomerase III (Sgs1–Top3) complex, which is required for maintaining genomic stability. Here, we show that cells lacking RMI1 have a mitotic delay, which is partly dependent on the spindle checkpoint, and are sensitive to the microtubule depolymerizing agent benomyl. We show that rmi1 and top3 single mutants are defective in sister ch...

  12. A transient α-helical molecular recognition element in the disordered N-terminus of the Sgs1 helicase is critical for chromosome stability and binding of Top3/Rmi1.

    Science.gov (United States)

    Kennedy, Jessica A; Daughdrill, Gary W; Schmidt, Kristina H

    2013-12-01

    The RecQ-like DNA helicase family is essential for the maintenance of genome stability in all organisms. Sgs1, a member of this family in Saccharomyces cerevisiae, regulates early and late steps of double-strand break repair by homologous recombination. Using nuclear magnetic resonance spectroscopy, we show that the N-terminal 125 residues of Sgs1 are disordered and contain a transient α-helix that extends from residue 25 to 38. Based on the residue-specific knowledge of transient secondary structure, we designed proline mutations to disrupt this α-helix and observed hypersensitivity to DNA damaging agents and increased frequency of genome rearrangements. In vitro binding assays show that the defects of the proline mutants are the result of impaired binding of Top3 and Rmi1 to Sgs1. Extending mutagenesis N-terminally revealed a second functionally critical region that spans residues 9-17. Depending on the position of the proline substitution in the helix functional impairment of Sgs1 function varied, gradually increasing from the C- to the N-terminus. The multiscale approach we used to interrogate structure/function relationships in the long disordered N-terminal segment of Sgs1 allowed us to precisely define a functionally critical region and should be generally applicable to other disordered proteins. PMID:24038467

  13. Regulation of BLM Nucleolar Localization

    Science.gov (United States)

    Tangeman, Larissa; McIlhatton, Michael A.; Grierson, Patrick; Groden, Joanna; Acharya, Samir

    2016-01-01

    Defects in coordinated ribosomal RNA (rRNA) transcription in the nucleolus cause cellular and organismal growth deficiencies. Bloom’s syndrome, an autosomal recessive human disorder caused by mutated recQ-like helicase BLM, presents with growth defects suggestive of underlying defects in rRNA transcription. Our previous studies showed that BLM facilitates rRNA transcription and interacts with RNA polymerase I and topoisomerase I (TOP1) in the nucleolus. The mechanisms regulating localization of BLM to the nucleolus are unknown. In this study, we identify the TOP1-interaction region of BLM by co-immunoprecipitation of in vitro transcribed and translated BLM segments and show that this region includes the highly conserved nuclear localization sequence (NLS) of BLM. Biochemical and nucleolar co-localization studies using site-specific mutants show that two serines within the NLS (S1342 and S1345) are critical for nucleolar localization of BLM but do not affect the functional interaction of BLM with TOP1. Mutagenesis of both serines to aspartic acid (phospho-mimetic), but not alanine (phospho-dead), results in approximately 80% reduction in nucleolar localization of BLM while retaining the biochemical functions and nuclear localization of BLM. Our studies suggest a role for this region in regulating nucleolar localization of BLM via modification of the two serines within the NLS. PMID:27657136

  14. BLM Scale Fixing in Event Shape Distributions

    CERN Document Server

    Gehrmann, Thomas; Monni, Pier Francesco

    2014-01-01

    We study the application of the Brodsky-Lepage-Mackenzie (BLM) scale setting prescription to event shape distributions in electron-positron collisions. The renormalization scale is set dynamically according to the BLM method. We study NLO predictions and we discuss extensions of the prescription to NNLO.

  15. DNA double strand break repair in mammalian cells: role of MRE11 and BLM proteins at the initiation of Non Homologous End Joining (NHEJ)

    International Nuclear Information System (INIS)

    DNA double strand breaks (DSBs) are highly cytotoxic lesions, which can lead to genetic rearrangements. Two pathways are responsible for repairing these lesions: homologous recombination (HR) and non homologous end joining (NHEJ). In our laboratory, an intrachromosomal substrate has been established in order to measure the efficiency and the fidelity of NHEJ in living cells (Guirouilh-Barbat 2004). This approach led us to identify a KU-independent alternative pathway, which uses micro homologies in the proximity of the junction to accomplish repair - the alternative NHEJ (Guirouilh-Barbat 2004, Guirouilh-Barbat et Rass 2007). The goal of my thesis consisted in identifying and characterising major actors of this pathway. In the absence of KU, alternative NHEJ would be initiated by ssDNA resection of damaged ends. We showed that the nuclease activity of MRE11 is necessary for this mechanism. MRE11 overexpression leads to a two fold stimulation of NHEJ efficiency, while the extinction of MRE11 by siRNA results in a two fold decrease. Our results demonstrate that the proteins RAD50 and CtIP act in the same pathway as MRE11. Moreover, in cells deficient for XRCC4, MIRIN - an inhibitor of the MRN complex - leads to a decrease in repair efficiency, implicating MRE11 in alternative NHEJ. We also showed that MRE11 can act in an ATM-dependent and independent manner (Rass et Grabarz Nat Struct Mol Biol 2009). The initiation of break resection needs to be pursued by a more extensive degradation of DNA, which is accomplished in yeast by the proteins Exo1 and Sgs1/Dna2. In human cells, in vitro studies have recently proposed a similar model of a two-step break resection. We chose to elucidate the role of one of the human homologs of Sgs1 - the RecQ helicase BLM - in the resection process. Our experiments show, that he absence of BLM decreases the efficiency of end joining by NHEJ, accompanied by an increase in error-prone events, especially long-range deletions (≥200 nt). This

  16. Data acquisition system for BLM at NSRL

    Science.gov (United States)

    Gong, Guanghua; Li, Yuxiong; Cui, Yonggang; Li, Juexin; Li, Weiming; Shao, Beibei

    2003-06-01

    A Beam Loss Monitoring (BLM) System has been built up for the 800 MeV storage ring in National Synchrotron Radiation Laboratory. It has helped to resolve some problems about beam lifetime. This paper introduces the data acquisition system of BLM. It has a counter whose counting rate is higher than 10 MHz. Furthermore, this counter is a free running one that will never lose any pulse when it is being read or written. This DAQ system is composed of 14 front-ends and a console connected via CAN bus. The intensity, distribution and time information of the beam loss can be offered by this system. This BLM system is helpful for machine study and operation.

  17. Luminosity monitoring and calibration of BLM

    Institute of Scientific and Technical Information of China (English)

    薛镇; 蔡啸; 俞伯祥; 方建; 孙希磊; 石峰; 王志刚; 交正华; 孙丽君; 刘宏邦; 章爱武; 许咨宗; 王晓东; 汪晓莲; 胡涛; 王至勇; 傅成栋; 鄢文标; 吕军光; 周莉

    2011-01-01

    The BEPC II Luminosity Monitor (BLM) monitors relative luminosity per bunch. The counting rates of gamma photons, which are proportional to the luminosities from the BLM at the center of mass system energy of the φ(3770) resonance, are obtained with a sta

  18. Classification of the LHC BLM Ionization Chamber

    CERN Document Server

    Stockner, M; Fabjan, Christian Wolfgang; Holzer, E B; Kramer, Daniel

    2008-01-01

    The LHC beam loss monitoring (BLM) system must prevent the super conducting magnets from quenching and protect the machine components from damage. The main monitor type is an ionization chamber. About 4000 of them will be installed around the ring. The lost beam particles initiate hadronic showers through the magnets and other machine components. These shower particles are measured by the monitors installed on the outside of the accelerator equipment. For the calibration of the BLM system the signal response of the ionization chamber is simulated in GEANT4 for all relevant particle types and energies (keV to TeV range). For validation, the simulations are compared to measurements using protons, neutrons, photons and mixed radiation fields at various energies and intensities. This paper will focus on the signal response of the ionization chamber to various particle types and energies including space charge effects at high ionization densities.

  19. Commissioning and optimization of the LHC BLM System

    CERN Document Server

    Holzer, E B; Effinger, E; Emery, J; Hajdu, C F; Jackson, S; Kurfurst, C; Marsili, A; Misiowiec, M; Nebot Del Busto, E; Nordt, A; Roderick, C; Sapinski, M; Zamantzas, C; Grishin, V

    2011-01-01

    Due to rapid progress with the LHC commissioning in 2010, set-up beam intensities were soon surpassed and damage potential was reached. One of the key systems for machine protection is the beam loss monitoring (BLM) system. Around 4000 monitors are installed at likely or critical loss locations. Each monitor has 384 associated beam abort thresholds (12 integrated loss durations from 40 μs to 84 s for 32 energy intervals). A single integrated loss over threshold on a single monitor aborts the beam. Simulations of deposited energy, critical energy deposition for damage or quench and BLM signal response backedup by control measurements determined the initial threshold settings. The commissioning and optimization of the BLM system is presented. Test procedures were used to verify the machine protection functionalities. Accidental magnet quenches were used to fine-tune threshold settings. The most significant changes to the BLM system during the 2010 run concern the injection, the collimation and the beam dump re...

  20. Number of New Leases Issued During Fiscal Year by BLM

    Data.gov (United States)

    Bureau of Land Management, Department of the Interior — This table contains the total number of new leases, by state, issued by the BLM during each fiscal year. Leases issued over the course of a fiscal year may or may...

  1. 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....

  2. 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

  3. Prototype of linac BLM at NSRL

    Science.gov (United States)

    Zeng, Ming; Li, Yuxiong; Gong, Guanghua; Li, Juexin; Shao, Beibei; Zhao, Zhengguo

    2007-08-01

    A prototype of the Beam Loss Monitoring (BLM) System for the linac and transportation line has been built up in National Synchrotron Radiation Laboratory. Different from the storage ring, the radiation field around linac and transportation line have a duty factor of 10 -6 and a dose rate of hundreds Gy/h. The Monte-Carlo calculation gave the dose, flux, energy and direction distributions of the radiation field. According to the simulation result, the proper type of detector was chosen and the installation positions were selected accordingly. The widely used ionization chamber is not suitable to give accurate and real-time information of beam loss due to its large dimension and slow respond speed. Several PIN silicon diode-based detectors were designed and tested, and a charge-balanced integrating amplifier circuit was applied to read out the charge. A distributed data acquisition system based on embedded Ethernet technology was implemented in the prototype, which can offer a web server from the microcontroller. From preliminary tests, this new prototype was proved to be sensitive to the change of the linac status, and is a useful tool for monitoring and adjusting machine parameters. Further analyses are required to achieve a more accurate measurement of the beam loss.

  4. 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

  5. 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.

  6. Handling of BLM abort thresholds in the LHC

    CERN Document Server

    Nebot Del Busto, E; Holzer, EB; Zamantzas, C; Kruk, G; Nordt, A; Sapinski, M; Nemcic, M; Orecka, A; Jackson, S; Roderick, C; Skaugen, A

    2011-01-01

    The Beam Loss Monitoring system (BLM) for the LHC consists of about 3600 Ionization Chambers (IC) located around the ring. Its main purpose is to request a beam abort when the measured losses exceed a certain threshold. The BLM detectors integrate the measured signals in 12 different time intervals (running from 40us to 83.8s) enabling for a different set of abort thresholds depending on the duration of the beam loss. Furthermore, 32 energy levels running from 450GeV to 7TeV account for the fact that the energy density of a particle shower increases with the energy of the primary particle, i.e. the beam energy. Thus, a set of ! 3600 × 12 × 32 = 1.3 · 106 thresholds must be handled. These thresholds are highly critical for the safety of the machine and depend to a large part on human judgment, which cannot be replaced by automatic test procedures. The BLM team has defined well established procedures to compute, set and check new BLM thresholds, in order to avoid and/or find non-conformities due to manipulat...

  7. 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

  8. 78 FR 29379 - BLM Director's Response to the Appeal by the Governors of Utah and Wyoming of the BLM Assistant...

    Science.gov (United States)

    2013-05-20

    ...) for Allocation of Oil Shale and Tar Sands Resources on Lands Administered by the Bureau of Land... for Allocation of Oil Shale and Tar Sands Resources on Lands Administered by the BLM in Colorado, Utah... telecommunications device for the deaf (TDD) may call the Federal Information Relay Service (FIRS) at...

  9. Theoretical analysis of BLM system for HLS II

    CERN Document Server

    Yukai, Chen; Lijuan, He; Weimin, Li

    2014-01-01

    Hefei Light Source (HLS) is being upgraded to HLS II. Its emittance will be much lower than before, therefore the Touschek scattering will increase significantly and become the dominant factor of beam loss. So it is necessary to build a new beam loss monitoring (BLM) system differed from the old one to obtain the quantity and position information of lost electrons. This information is useful in the commissioning, troubleshooting and beam lifetime studying for HLS II. This paper analyzes the distribution features of different kinds of lost electrons, introduces the new machine's operation parameters and discusses the way to choose proper monitoring positions. Base on these comprehensive analysis, a new BLM system for HLS II is proposed.

  10. Theoretical analysis of BLM system for HLS II

    Science.gov (United States)

    Chen, Yu-Kai; Li, Yu-Xiong; Li, Wei-Min; He, Li-Juan

    2015-01-01

    Hefei Light Source (HLS) is being upgraded to HLS II. Its emittance will be much lower than before, therefore the Touschek scattering will increase significantly and become the dominant factor of beam loss. So it is necessary to build a new beam loss monitoring (BLM) system that, in contrast to the old one, is able to obtain the quantity and position information of lost electrons. This information is useful in the commissioning, troubleshooting, and beam lifetime studying for HLS II. This paper analyzes the distribution features of different kinds of lost electrons, introduces the operation parameters of the new machine and discusses how to choose proper monitoring positions. Based on these comprehensive analyses, a new BLM system for HLS II is proposed.

  11. On the BLM optimal renormalization scale setting for semihard processes

    CERN Document Server

    Caporale, Francesco; Murdaca, Beatrice; Papa, Alessandro

    2015-01-01

    The BFKL approach for the investigation of semihard processes is plagued by large next-to-leading corrections, both in the kernel of the universal BFKL Green's function and in the process-dependent impact factors, as well as by large uncertainties in the renormalization scale setting. All that calls for some optimization procedure of the perturbative series. In this respect, one of the most common methods is the Brodsky-Lepage-Mackenzie (BLM) one, that eliminates the renormalization scale ambiguity by absorbing the non-conformal $\\beta_0$-terms into the running coupling. In this paper, we apply BLM scale setting procedure directly to the amplitudes (cross sections) of several semihard processes. We show that, due to the presence of $\\beta_0$-terms in the next-to-leading expressions for the impact factors, the optimal renormalization scale is not universal, but depends both on the energy and on the type of process in question.

  12. Is the BLM system ready to go to higher intensities?

    CERN Document Server

    Sapinski, M; Dehning, B; Effinger, E; Emery, J; Goddard, B; Guerrero, A; Grishin, S; Holzer, E; Jackson, S; Kurfuerst, C; Lechner, A; Marsili, A; Misiowiec, M; Nebot, E; Nordt, A; Priebe, A; Roderick, C; Schmidt, R; Verweij, A; Wenninger, J; Zamantzas, C; Zimmermann, F

    2011-01-01

    The higher beam intensities will enhance the effects of the beam losses observed during 2010 run. In particular beam losses due to so called UFO events are discussed, but also other beam loss phenomena like luminosity losses, injection losses and the leakage from the collimation system are considered. The current understanding of the quench limits reflected in the BLM thresholds on the cold magnets is presented. The thresholds for possible increased beam energy are reviewed.

  13. BLM has early and late functions in homologous recombination repair in mouse embryonic stem cells

    DEFF Research Database (Denmark)

    Chu, W K; Hanada, K; Kanaar, R;

    2010-01-01

    ' roles, such as dissolution of double Holliday junctions. However, most of the evidence for these putative roles comes from in vitro biochemical data. In this study, we report the characterization of mouse embryonic stem cells with disruption of Blm and/or Rad54 genes. We show that Blm has roles both...... in Rad54(-/-) cells rescued their mitomycin C (MMC) sensitivity, and decreased both the level of DNA damage and cell cycle perturbation induced by MMC, suggesting an early role for Blm. Our data are consistent with Blm having at least two roles in HR repair in mammalian cells....

  14. 75 FR 34152 - Notice of Public Meeting, BLM Alaska Resource Advisory Council

    Science.gov (United States)

    2010-06-16

    ... attend and need special assistance, such as sign language interpretation, transportation, or other reasonable accommodations, should contact the BLM. Dated: June 9, 2010. Julia Dougan, Acting State...

  15. 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...

  16. Transcriptomic and Protein Expression Analysis Reveals Clinicopathological Significance of Bloom Syndrome Helicase (BLM) in Breast Cancer.

    Science.gov (United States)

    Arora, Arvind; Abdel-Fatah, Tarek M A; Agarwal, Devika; Doherty, Rachel; Moseley, Paul M; Aleskandarany, Mohammed A; Green, Andrew R; Ball, Graham; Alshareeda, Alaa T; Rakha, Emad A; Chan, Stephen Y T; Ellis, Ian O; Madhusudan, Srinivasan

    2015-04-01

    Bloom syndrome helicase (BLM) has key roles in homologous recombination repair, telomere maintenance, and DNA replication. Germ-line mutations in the BLM gene causes Bloom syndrome, a rare disorder characterized by premature aging and predisposition to multiple cancers, including breast cancer. The clinicopathologic significance of BLM in sporadic breast cancers is unknown. We investigated BLM mRNA expression in the Molecular Taxonomy of Breast Cancer International Consortium cohort (n = 1,950) and validated in an external dataset of 2,413 tumors. BLM protein level was evaluated in the Nottingham Tenovus series comprising 1,650 breast tumors. BLM mRNA overexpression was significantly associated with high histologic grade, larger tumor size, estrogen receptor-negative (ER(-)), progesterone receptor-negative (PR(-)), and triple-negative phenotypes (ps < 0.0001). BLM mRNA overexpression was also linked to aggressive molecular phenotypes, including PAM50.Her2 (P < 0.0001), PAM50.Basal (P < 0.0001), and PAM50.LumB (P < 0.0001) and Genufu subtype (ER(+)/Her2(-)/high proliferation; P < 0.0001). PAM50.LumA tumors and Genufu subtype (ER(+)/Her2(-)/low proliferation) were more likely to express low levels of BLM mRNA (ps < 0.0001). Integrative molecular clusters (intClust) intClust.1 (P < 0.0001), intClust.5 (P < 0.0001), intClust.9 (P < 0.0001), and intClust.10 (P < 0.0001) were also more likely in tumors with high BLM mRNA expression. BLM mRNA overexpression was associated with poor breast cancer-specific survival (BCSS; ps < 0.000001). At the protein level, altered subcellular localization with high cytoplasmic BLM and low nuclear BLM was linked to aggressive phenotypes. In multivariate analysis, BLM mRNA and BLM protein levels independently influenced BCSS. This is the first and the largest study to provide evidence that BLM is a promising biomarker in breast cancer. PMID:25673821

  17. Collaborating functions of BLM and DNA topoisomerase I in regulating human rDNA transcription

    Energy Technology Data Exchange (ETDEWEB)

    Grierson, Patrick M. [Department of Microbiology, Immunology and Medical Genetics, The Ohio State University College of Medicine, Columbus, OH 43210 (United States); Acharya, Samir, E-mail: samir.acharya@osumc.edu [Department of Microbiology, Immunology and Medical Genetics, The Ohio State University College of Medicine, Columbus, OH 43210 (United States); Groden, Joanna [Department of Microbiology, Immunology and Medical Genetics, The Ohio State University College of Medicine, Columbus, OH 43210 (United States)

    2013-03-15

    Bloom's syndrome (BS) is an inherited disorder caused by loss of function of the recQ-like BLM helicase. It is characterized clinically by severe growth retardation and cancer predisposition. BLM localizes to PML nuclear bodies and to the nucleolus; its deficiency results in increased intra- and inter-chromosomal recombination, including hyper-recombination of rDNA repeats. Our previous work has shown that BLM facilitates RNA polymerase I-mediated rRNA transcription in the nucleolus (Grierson et al., 2012 [18]). This study uses protein co-immunoprecipitation and in vitro transcription/translation (IVTT) to identify a direct interaction of DNA topoisomerase I with the C-terminus of BLM in the nucleolus. In vitro helicase assays demonstrate that DNA topoisomerase I stimulates BLM helicase activity on a nucleolar-relevant RNA:DNA hybrid, but has an insignificant effect on BLM helicase activity on a control DNA:DNA duplex substrate. Reciprocally, BLM enhances the DNA relaxation activity of DNA topoisomerase I on supercoiled DNA substrates. Our study suggests that BLM and DNA topoisomerase I function coordinately to modulate RNA:DNA hybrid formation as well as relaxation of DNA supercoils in the context of nucleolar transcription.

  18. Completing the Calculation of BLM corrections to B -> Xs gamma

    OpenAIRE

    Misiak, Mikolaj; Poradzinski, Michal

    2010-01-01

    Perturbative O(alpha_s^2) corrections to BR(B -> Xs gamma) in the BLM approximation receive contributions from two-, three- and four-body final states. While all the two-body results are well established by now, the other ones have remained incomplete for several years. Here, we calculate the last contribution that has been missing to date, namely the one originating from interference of the current-current and gluonic dipole operators (K_18^{(2)beta_0} and K_{28}^{(2)beta_0}). Moreover, we c...

  19. Association of BLM and BRCA1 during Telomere Maintenance in ALT Cells.

    Directory of Open Access Journals (Sweden)

    Samir Acharya

    Full Text Available Fifteen percent of tumors utilize recombination-based alternative lengthening of telomeres (ALT to maintain telomeres. The mechanisms underlying ALT are unclear but involve several proteins involved in homologous recombination including the BLM helicase, mutated in Bloom's syndrome, and the BRCA1 tumor suppressor. Cells deficient in either BLM or BRCA1 have phenotypes consistent with telomere dysfunction. Although BLM associates with numerous DNA damage repair proteins including BRCA1 during DNA repair, the functional consequences of BLM-BRCA1 association in telomere maintenance are not completely understood. Our earlier work showed the involvement of BRCA1 in different mechanisms of ALT, and telomere shortening upon loss of BLM in ALT cells. In order to delineate their roles in telomere maintenance, we studied their association in telomere metabolism in cells using ALT. This work shows that BLM and BRCA1 co-localize with RAD50 at telomeres during S- and G2-phases of the cell cycle in immortalized human cells using ALT but not in cells using telomerase to maintain telomeres. Co-immunoprecipitation of BRCA1 and BLM is enhanced in ALT cells at G2. Furthermore, BRCA1 and BLM interact with RAD50 predominantly in S- and G2-phases, respectively. Biochemical assays demonstrate that full-length BRCA1 increases the unwinding rate of BLM three-fold in assays using a DNA substrate that models a forked structure composed of telomeric repeats. Our results suggest that BRCA1 participates in ALT through its interactions with RAD50 and BLM.

  20. A Blm-Recql5 partnership in replication stress response

    Institute of Scientific and Technical Information of China (English)

    Xincheng Lu; Hua Lou; Guangbin Luo

    2011-01-01

    Deficiencies in DNA damage response and repair not only can result in genome instability and cancer predisposition, but also can render the cancer cells intrinsically more vulnerable to certain types of DNA damage insults. Particularly, replication stress is both a hallmark of human cancers and a common instigator for genome instability and cell death. Here, we review our work based on the genetic knockout studies on Blm and Recql5, two members of the mammalian RecQ helicase family. These studies have uncovered a unique partnership between these two helicases in the implementation of proper mitigation strategies under different circumstances to promote DNA replication and cell survival and suppress genome instability and cancer. In particular, current studies have revealed the presence of a novel Recql5/RECQL5-dependent mechanism for suppressing replication fork collapse in response to global replication fork stalling following exposure to camptothecin (CPT), a topoisomerase I inhibitor, and a potent inhibitor of DNA replication. The unique partnership between Blm and Recql5 in coping with the challenge imposed by replication stress is discussed. In addition, given that irinotecan and topotecan, two CPT derivatives, are currently used in clinic for treating human cancer patients with very promising results, the potential implication of the new findings from these studies in anticancer treatments is also discussed.

  1. 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...

  2. 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.

  3. Meiotic and Mitotic Phenotypes Conferred by the blm1-1 Mutation in Saccharomyces cerevisiae and MSH4 Suppression of the Bleomycin Hypersusceptibility

    Directory of Open Access Journals (Sweden)

    Carol Wood Moore

    2003-01-01

    Full Text Available Abstract: Oxidative damage can lead to a number of diseases, and can be fatal. The blm1-1 mutation of Saccharomyces cerevisiae confers hypersusceptibility to lethal effects of the oxidative, anticancer and antifungal agent, bleomycin. For the current report, additional defects conferred by the mutation in meiosis and mitosis were investigated. The viability of spores produced during meiosis by homozygous normal BLM1/BLM1, heterozygous BLM1/blm1-1, and homozygous mutant blm1-1/blm1-1 diploid strains was studied and compared. Approximately 88% of the tetrads derived from homozygous blm1-1/blm1-1 mutant diploid cells only produced one or two viable spores. In contrast, just one tetrad among all BLM1/BLM1 and BLM1/blm1-1 tetrads only produced one or two viable spores. Rather, 94% of BLM1/BLM1 tetrads and 100% of BLM1/blm1-1 tetrads produced asci with four or three viable spores. Thus, at least one copy of the BLM1 gene is essential for the production of four viable spores after meiosis. During mitotic growth, mutant blm1-1 strains grew at reduced rates and produced cells with high frequencies of unusual morphologies compared to wild-type strains. These results indicated BLM1 is also essential for normal mitotic growth. We also investigated the suppression by the MSH4 gene, a meiosis-specific MutS homolog, of the bleomycin hypersusceptibility of blm1-1 mutant cells, and the relationship of MSH4 to BLM1. We screened a genomic library, and isolated the MSH4 gene on the basis of its ability to suppress lethal effects of bleomycin in blm1-1 cells. However, genetic mapping studies indicated that BLM1 and MSH4 are not the same gene. The possibility that chromosomal nondisjunction could be the basis for the inability of blm1-1/blm1-1 mutant cells to produce four viable spores after meiosis is discussed.

  4. Number of Drilling Permits Approved by Fiscal Year on Federal Lands by BLM

    Data.gov (United States)

    Bureau of Land Management, Department of the Interior — This table contains the total number of Applications for Permit to Drill (APDs) by state approved by the BLM each fiscal year. Oil and gas operators may not begin...

  5. 2012 Oregon Department of Interior, Bureau of Land Management (BLM) Lidar: Panther Creek Study Area

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — The Oregon Department of Interior, Bureau of Land Management (BLM) contracted with Watershed Sciences, Inc. to collect high resolution topographic LiDAR data for...

  6. BLM/OCS South Texas Outer Continental Shelf (STOCS) Project Sediment Data

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — The South Texas Outer Continental Shelf Project (STOCS) conducted by the University of Texas and the USGS with funding from BLM/NOAA. The USGS produced geochemical...

  7. 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...

  8. 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

  9. 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 ...

  10. The SMC-5/6 Complex and the HIM-6 (BLM Helicase Synergistically Promote Meiotic Recombination Intermediate Processing and Chromosome Maturation during Caenorhabditis elegans Meiosis.

    Directory of Open Access Journals (Sweden)

    Ye Hong

    2016-03-01

    Full Text Available Meiotic recombination is essential for the repair of programmed double strand breaks (DSBs to generate crossovers (COs during meiosis. The efficient processing of meiotic recombination intermediates not only needs various resolvases but also requires proper meiotic chromosome structure. The Smc5/6 complex belongs to the structural maintenance of chromosome (SMC family and is closely related to cohesin and condensin. Although the Smc5/6 complex has been implicated in the processing of recombination intermediates during meiosis, it is not known how Smc5/6 controls meiotic DSB repair. Here, using Caenorhabditis elegans we show that the SMC-5/6 complex acts synergistically with HIM-6, an ortholog of the human Bloom syndrome helicase (BLM during meiotic recombination. The concerted action of the SMC-5/6 complex and HIM-6 is important for processing recombination intermediates, CO regulation and bivalent maturation. Careful examination of meiotic chromosomal morphology reveals an accumulation of inter-chromosomal bridges in smc-5; him-6 double mutants, leading to compromised chromosome segregation during meiotic cell divisions. Interestingly, we found that the lethality of smc-5; him-6 can be rescued by loss of the conserved BRCA1 ortholog BRC-1. Furthermore, the combined deletion of smc-5 and him-6 leads to an irregular distribution of condensin and to chromosome decondensation defects reminiscent of condensin depletion. Lethality conferred by condensin depletion can also be rescued by BRC-1 depletion. Our results suggest that SMC-5/6 and HIM-6 can synergistically regulate recombination intermediate metabolism and suppress ectopic recombination by controlling chromosome architecture during meiosis.

  11. The SMC-5/6 Complex and the HIM-6 (BLM) Helicase Synergistically Promote Meiotic Recombination Intermediate Processing and Chromosome Maturation during Caenorhabditis elegans Meiosis

    Science.gov (United States)

    Hong, Ye; Sonneville, Remi; Agostinho, Ana; Meier, Bettina; Wang, Bin; Blow, J. Julian; Gartner, Anton

    2016-01-01

    Meiotic recombination is essential for the repair of programmed double strand breaks (DSBs) to generate crossovers (COs) during meiosis. The efficient processing of meiotic recombination intermediates not only needs various resolvases but also requires proper meiotic chromosome structure. The Smc5/6 complex belongs to the structural maintenance of chromosome (SMC) family and is closely related to cohesin and condensin. Although the Smc5/6 complex has been implicated in the processing of recombination intermediates during meiosis, it is not known how Smc5/6 controls meiotic DSB repair. Here, using Caenorhabditis elegans we show that the SMC-5/6 complex acts synergistically with HIM-6, an ortholog of the human Bloom syndrome helicase (BLM) during meiotic recombination. The concerted action of the SMC-5/6 complex and HIM-6 is important for processing recombination intermediates, CO regulation and bivalent maturation. Careful examination of meiotic chromosomal morphology reveals an accumulation of inter-chromosomal bridges in smc-5; him-6 double mutants, leading to compromised chromosome segregation during meiotic cell divisions. Interestingly, we found that the lethality of smc-5; him-6 can be rescued by loss of the conserved BRCA1 ortholog BRC-1. Furthermore, the combined deletion of smc-5 and him-6 leads to an irregular distribution of condensin and to chromosome decondensation defects reminiscent of condensin depletion. Lethality conferred by condensin depletion can also be rescued by BRC-1 depletion. Our results suggest that SMC-5/6 and HIM-6 can synergistically regulate recombination intermediate metabolism and suppress ectopic recombination by controlling chromosome architecture during meiosis. PMID:27010650

  12. The SMC-5/6 Complex and the HIM-6 (BLM) Helicase Synergistically Promote Meiotic Recombination Intermediate Processing and Chromosome Maturation during Caenorhabditis elegans Meiosis.

    Science.gov (United States)

    Hong, Ye; Sonneville, Remi; Agostinho, Ana; Meier, Bettina; Wang, Bin; Blow, J Julian; Gartner, Anton

    2016-03-01

    Meiotic recombination is essential for the repair of programmed double strand breaks (DSBs) to generate crossovers (COs) during meiosis. The efficient processing of meiotic recombination intermediates not only needs various resolvases but also requires proper meiotic chromosome structure. The Smc5/6 complex belongs to the structural maintenance of chromosome (SMC) family and is closely related to cohesin and condensin. Although the Smc5/6 complex has been implicated in the processing of recombination intermediates during meiosis, it is not known how Smc5/6 controls meiotic DSB repair. Here, using Caenorhabditis elegans we show that the SMC-5/6 complex acts synergistically with HIM-6, an ortholog of the human Bloom syndrome helicase (BLM) during meiotic recombination. The concerted action of the SMC-5/6 complex and HIM-6 is important for processing recombination intermediates, CO regulation and bivalent maturation. Careful examination of meiotic chromosomal morphology reveals an accumulation of inter-chromosomal bridges in smc-5; him-6 double mutants, leading to compromised chromosome segregation during meiotic cell divisions. Interestingly, we found that the lethality of smc-5; him-6 can be rescued by loss of the conserved BRCA1 ortholog BRC-1. Furthermore, the combined deletion of smc-5 and him-6 leads to an irregular distribution of condensin and to chromosome decondensation defects reminiscent of condensin depletion. Lethality conferred by condensin depletion can also be rescued by BRC-1 depletion. Our results suggest that SMC-5/6 and HIM-6 can synergistically regulate recombination intermediate metabolism and suppress ectopic recombination by controlling chromosome architecture during meiosis.

  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. Structural mechanisms of human RecQ helicases WRN and BLM

    Directory of Open Access Journals (Sweden)

    Ken eKitano

    2014-10-01

    Full Text Available The RecQ family DNA helicases WRN (Werner syndrome protein and BLM (Bloom syndrome protein play a key role in protecting the genome against deleterious changes. In humans, mutations in these proteins lead to rare genetic diseases associated with cancer predisposition and accelerated aging. WRN and BLM are distinguished from other helicases by possessing signature tandem domains toward the C terminus, referred to as the RecQ C-terminal (RQC and helicase-and-ribonuclease D-C-terminal (HRDC domains. Although the precise function of the HRDC domain remains unclear, the previous crystal structure of a WRN RQC-DNA complex visualized a central role for the RQC domain in recognizing, binding and unwinding DNA at branch points. In particular, a prominent hairpin structure (the β-wing within the RQC winged-helix motif acts as a scalpel to induce the unpairing of a Watson-Crick base pair at the DNA duplex terminus. A similar RQC-DNA interaction was also observed in the recent crystal structure of a BLM-DNA complex. I review the latest structures of WRN and BLM, and then provide a docking simulation of BLM with a Holliday junction. The model offers an explanation for the efficient branch migration activity of the RecQ family toward recombination and repair intermediates.

  15. BLM realization for ${\\mathcal U}_{\\mathbb Z}(\\hat{\\frak{gl}}_n)$

    OpenAIRE

    Fu, Qiang

    2012-01-01

    In 1990, Beilinson-Lusztig-MacPherson (BLM) discovered a realization \\cite[5.7]{BLM} for quantum $\\frak{gl}_n$ via a geometric setting of quantum Schur algebras. We will generailze their result to the classical affine case. More precisely, we first use Ringel-Hall algebras to construct an integral form ${\\mathcal U}_{\\mathbb Z}(\\hat{\\frak{gl}}_n)$ of ${\\mathcal U}(\\hat{\\frak{gl}}_n)$, where ${\\mathcal U}(\\hat{\\frak{gl}}_n)$ is the universal enveloping algebra of the loop algebra $\\hat{\\frak{g...

  16. 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.

  17. 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

  18. 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.

  19. 25 CFR 225.4 - Authority and responsibility of the Bureau of Land Management (BLM).

    Science.gov (United States)

    2010-04-01

    ... Agreements: Unproven Areas, 43 CFR part 3260—Geothermal Resources Operations, 43 CFR part 3280—Geothermal... Management (BLM). 225.4 Section 225.4 Indians BUREAU OF INDIAN AFFAIRS, DEPARTMENT OF THE INTERIOR ENERGY AND MINERALS OIL AND GAS, GEOTHERMAL, AND SOLID MINERALS AGREEMENTS General § 225.4 Authority...

  20. 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

  1. 2012 U.S. Department of Interior, Bureau of Land Management (BLM) Lidar: Panther Creek Study Area

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — The U.S. Department of Interior, Bureau of Land Management (BLM) contracted with Watershed Sciences, Inc. to collect high resolution topographic LiDAR data for...

  2. Road and Street Centerlines, BLM Horse Valley, Published in 2007, 1:24000 (1in=2000ft) scale, Iron County.

    Data.gov (United States)

    NSGIC GIS Inventory (aka Ramona) — , published at 1:24000 (1in=2000ft) scale, was produced all or in part from Other information as of 2007. It is described as 'BLM Horse Valley'. The extent of these...

  3. 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

  4. 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

  5. Experimental inhibition of nitric oxide increases Plasmodium relictum (lineage SGS1) parasitaemia.

    Science.gov (United States)

    Bichet, Coraline; Cornet, Stéphane; Larcombe, Stephen; Sorci, Gabriele

    2012-12-01

    Malaria is a widespread vector-borne disease infecting a wide range of terrestrial vertebrates including reptiles, birds and mammals. In addition to being one of the most deadly infectious diseases for humans, malaria is a threat to wildlife. The host immune system represents the main defence against malaria parasites. Identifying the immune effectors involved in malaria resistance has therefore become a major focus of research. However, this has mostly involved humans and animal models (rodents) and how the immune system regulates malaria progression in non-model organisms has been largely ignored. The aim of the present study was to investigate the role of nitric oxide (NO) as an immune effector contributing to the control of the acute phase of infection with the avian malaria agent Plasmodium relictum. We used experimental infections of domestic canaries in conjunction with the inhibition of the enzyme inducible nitric oxide synthase (iNOS) to assess the protective function of NO during the infection, and the physiological costs paid by the host in the absence of an effective NO response. Our results show that birds treated with the iNOS inhibitor suffered from a higher parasitaemia, but did not pay a higher cost of infection (anaemia). While these findings confirm that NO contributes to the resistance to avian malaria during the acute phase of the infection, they also suggest that parasitaemia and costs of infection can be decoupled.

  6. 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

  7. Measurements and Simulations of Ionization Chamber Signals in Mixed Radiation Fields for the LHC BLM System

    CERN Document Server

    Dehning, B; Ferioli, G; Holzer, EB; Stockner, M

    2006-01-01

    The LHC beam loss monitoring (BLM) system must prevent the super conducting magnets from quenching and protect the machine components from damage. The main monitor type is an ionization chamber. About 4000 of them will be installed around the ring. The lost beam particles initiate hadronic showers through the magnets, which are measured by the monitors installed outside of the cryostat around each quadrupole magnet. They probe the far transverse tail of the hadronic shower. The specification for the BLM system includes a factor of two absolute precision on the prediction of the quench levels. To reach this accuracy a number of simulations are being combined to calibrate the monitor signals. To validate the monitor calibration the simulations are compared with test measurements. This paper will focus on the simulated prediction of the development of the hadronic shower tails and the signal response of ionization chambers to various particle types and energies. Test measurements have been performed at CERN and ...

  8. 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...

  9. The roles of WRN and BLM RecQ helicases in the Alternative Lengthening of Telomeres

    OpenAIRE

    Mendez-Bermudez, Aaron; Hidalgo-Bravo, Alberto; Cotton, Victoria E.; Gravani, Athanasia; Jeyapalan, Jennie N.; Royle, Nicola J.

    2012-01-01

    Approximately 10% of all cancers, but a higher proportion of sarcomas, use the recombination-based alternative lengthening of telomeres (ALT) to maintain telomeres. Two RecQ helicase genes, BLM and WRN, play important roles in homologous recombination repair and they have been implicated in telomeric recombination activity, but their precise roles in ALT are unclear. Using analysis of sequence variation present in human telomeres, we found that a WRN– ALT+ cell line lacks the class of complex...

  10. The generalized BLM approach to fix scale-dependence in QCD: the current status of investigations

    CERN Document Server

    Kataev, A L

    2014-01-01

    I present a brief review of the generalized Brodsky-Lepage-McKenzie (BLM) approaches to fix the scale-dependence of the renormalization group (RG) invariant quantities in QCD. At first, these approaches are based on the expansions of the coefficients of the perturbative series for the RG-invariant quantities in the products of the coefficients $\\beta_i$ of the QCD $\\beta$-function, which are evaluated in the MS-like schemes. As a next step all $\\beta_i$-dependent terms are absorbed into the BLM-type scale(s) of the powers of the QCD couplings. The difference between two existing formulations of the above mentioned generalizations based on the seBLM approach and the Principle of Maximal Conformality (PMC) are clarified in the case of the Bjorken polarized deep-inelastic scattering sum rule. Using the conformal symmetry-based relations for the non-singlet coefficient functions of the Adler D-function and of Bjorken polarized deep-inelastic scattering sum rules $C^{\\rm Bjp}_{\\rm NS}(a_s)$ the $\\beta_i$-dependent...

  11. Measurements and simulations of the BLM response to a radiation field inside the CERF target area

    CERN Document Server

    Lebbos, E; Dehning, B; Effinger, E; Ferrari, A; Kramer, D; Nordt, A; Roeed, K; Roesler, S; Sapinski, M; Vlachoudis, V

    2010-01-01

    The CERN-EU high-energy reference field (CERF) facility is installed in one of the secondary beam lines (H6) of the Super Proton Synchrotron (SPS), in the North Experimental Area at CERN. This facility is used as a reference for testing, inter-comparing and calibrating passive and active instruments. In May 2009, the SPS provided a mixed hadron beam (protons, pions and kaons) during a few days, in order to perform several measurements with different devices such as the Radiation Protection Monitor used for residual dose rates due to Induced Radioactivity in the LHC (PMI), the Secondary Emission Monitor used for high beam losses (SEM), the Radiation Monitor for electronics (RadMon), and the Beam Loss Monitor for the LHC (BLM). This report focuses on the measurements of the BLM response during this year’s operation at CERF. The measurements evaluate the sensitivity of the BLM signal to the particle energy spectrum, with special attention to the contribution coming from thermal neutrons. For this purpose, meas...

  12. 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

  13. 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

  14. 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

  15. 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

  16. 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 ...

  17. BlmB and TlmB provide resistance to the bleomycin family of antitumor antibiotics by N-acetylating metal-free bleomycin, tallysomycin, phleomycin, and zorbamycin.

    Science.gov (United States)

    Coughlin, Jane M; Rudolf, Jeffrey D; Wendt-Pienkowski, Evelyn; Wang, Liyan; Unsin, Claudia; Galm, Ute; Yang, Dong; Tao, Meifeng; Shen, Ben

    2014-11-11

    The bleomycin (BLM) family of glycopeptide-derived antitumor antibiotics consists of BLMs, tallysomycins (TLMs), phleomycins (PLMs), and zorbamycin (ZBM). The self-resistant elements BlmB and TlmB, discovered from the BLM- and TLM-producing organisms Streptomyces verticillus ATCC15003 and Streptoalloteichus hindustanus E465-94 ATCC31158, respectively, are N-acetyltransferases that provide resistance to the producers by disrupting the metal-binding domain of the antibiotics required for activity. Although each member of the BLM family of antibiotics possesses a conserved metal-binding domain, the structural differences between each member, namely, the bithiazole moiety and C-terminal amine of BLMs, have been suggested to instill substrate specificity within BlmB. Here we report that BlmB and TlmB readily accept and acetylate BLMs, TLMs, PLMs, and ZBM in vitro but only in the metal-free forms. Kinetic analysis of BlmB and TlmB reveals there is no strong preference or rate enhancement for specific substrates, indicating that the structural differences between each member of the BLM family play a negligible role in substrate recognition, binding, or catalysis. Intriguingly, the zbm gene cluster from Streptomyces flavoviridis ATCC21892 does not contain an N-acetyltransferase, yet ZBM is readily acetylated by BlmB and TlmB. We subsequently established that S. flavoviridis lacks the homologue of BlmB and TlmB, and ZbmA, the ZBM-binding protein, alone is sufficient to provide ZBM resistance. We further confirmed that BlmB can indeed confer resistance to ZBM in vivo in S. flavoviridis, introduction of which into wild-type S. flavoviridis further increases the level of resistance.

  18. 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...

  19. A Role for BLM in Double-Strand Break Repair Pathway Choice: Prevention of CtIP/Mre11-Mediated Alternative Nonhomologous End-Joining

    DEFF Research Database (Denmark)

    Grabarz, Anastazja; Guirouilh-Barbat, Josée; Barascu, Aurelia;

    2013-01-01

    represses A-EJ in an epistatic manner with 53BP1 and RIF1 and is required for ionizing-radiation-induced 53BP1 focus assembly. Conversely, in the absence of 53BP1 or RIF1, BLM promotes formation of A-EJ long deletions, consistent with a role for BLM in DSB end resection. These data highlight a dual role...

  20. A novel frameshift mutation in BLM gene associated with high sister chromatid exchanges (SCE) in heterozygous family members.

    Science.gov (United States)

    Ben Salah, Ghada; Hadj Salem, Ikhlas; Masmoudi, Abderrahmen; Kallabi, Fakhri; Turki, Hamida; Fakhfakh, Faiza; Ayadi, Hamadi; Kamoun, Hassen

    2014-11-01

    The Bloom syndrome (BS) is an autosomic recessive disorder comprising a wide range of abnormalities, including stunted growth, immunodeficiency, sun sensitivity and increased frequency of various types of cancer. Bloom syndrome cells display a high level of genetic instability, including a 10-fold increase in the sister chromatid exchanges (SCE) level. Bloom syndrome arises through mutations in both alleles of the BLM gene, which was identified as a member of the RecQ helicase family. In this study, we screened a Tunisian family with three BS patients. Cytogenetic analysis showed several chromosomal aberrations, and an approximately 14-fold elevated SCE frequency in BS cells. A significant increase in SCE frequency was observed in some family members but not reaching the BS patients values, leading to suggest that this could be due to the heterozygous profile. Microsatellite genotyping using four fluorescent dye-labeled microsatellite markers revealed evidence of linkage to BLM locus and the healthy members, sharing higher SCE frequency, showed heterozygous haplotypes as expected. Additionally, the direct BLM gene sequencing identified a novel homozygous frameshift mutation c.3617-3619delAA (p.K1207fsX9) in BS patients and a heterozygous BLM mutation in the family members with higher SCE frequency. Our findings suggest that this latter mutation likely leads to a reduced BLM activity explaining the homologous recombination repair defect and, therefore, the increase in SCE. Based on the present data, the screening of this mutation could contribute to the rapid diagnosis of BS. The genetic confirmation of the mutation in BLM gene provides crucial information for genetic counseling and prenatal diagnosis.

  1. 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.

  2. Drill baby drill: An analysis of how energy development displaced ranching's dominance over the BLM's subgovernment policymaking environment

    Science.gov (United States)

    Forbis, Robert Earl, Jr.

    Academic literature analyzing the Bureau of Land Management (BLM) land-use subgovernment stops at the Taylor Grazing Act and concludes that the historical development of administering grazing on public lands led to the capture of the BLM by ranching interests. Using a two-pronged methodological approach of process tracing and elite interviews this dissertation seeks to advance our collective knowledge of subgovernment theory by (a) clarifying the impact executive decision-making has on subgovernments and (b) identifying the conditions under which strategically competitive behavior between two competing subgovernment actors occurs. The dissertation seeks to update the literature by explaining what has caused the BLM to shift from a rancher-dominated agency to an energy dominated agency by identifying conditions under which subgovernment actors strategically respond to a political conflict. The research poses two questions: (1) how have executive actions disrupted an existing balance of power in a so-called "strong corner" of an entrenched subgovernment system and (2) what happens when conflict and competition break out between allied members of the system? Analysis indicates that as the BLM responded to Executive actions emphasizing domestic energy production, a conflict emerged between traditional allies: ranching and energy. Triggered by the unintended consequence of awakening long-dormant legislation, split-estate energy development---where property rights are severed between private surface and federal mineral estates---expanded across the West. In turn, this expansion helped establish the conditions for conflict and in doing so disrupted the balance of power between large public resource use interests in the relatively stable land-use subgovernment of the BLM. Indicative of energy's emerging dominance of the BLM's subgovernment, split-estate energy development led ranching interests to seek the protection of their Western state legislatures. This shift in

  3. An economic analysis of alternative fertility control and associated management techniques for three BLM wild horse herds

    Science.gov (United States)

    Bartholow, John M.

    2004-01-01

    Contemporary cost projections were computed for several alternative strategies that could be used by BLM to manage three wild horse populations. The alternatives included existing gather and selective removal methods, combined with potential contraceptive applications of varying duration and other potentially useful management techniques. Costs were projected for a 20-year economic life using the Jenkins wild horse population model and cost estimates from BLM that reflect state-by-state per horse removal, adoption, long-term holding, and contraceptive application expenses. Important findings include: Application of currently available 2-year contraceptives appears capable of reducing variable operating costs for wild horse populations by about 21% on average.

  4. 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

  5. A Low-Noise Transimpedance Amplifier for BLM-Based Ion Channel Recording

    Science.gov (United States)

    Crescentini, Marco; Bennati, Marco; Saha, Shimul Chandra; Ivica, Josip; de Planque, Maurits; Morgan, Hywel; Tartagni, Marco

    2016-01-01

    High-throughput screening (HTS) using ion channel recording is a powerful drug discovery technique in pharmacology. Ion channel recording with planar bilayer lipid membranes (BLM) is scalable and has very high sensitivity. A HTS system based on BLM ion channel recording faces three main challenges: (i) design of scalable microfluidic devices; (ii) design of compact ultra-low-noise transimpedance amplifiers able to detect currents in the pA range with bandwidth >10 kHz; (iii) design of compact, robust and scalable systems that integrate these two elements. This paper presents a low-noise transimpedance amplifier with integrated A/D conversion realized in CMOS 0.35 μm technology. The CMOS amplifier acquires currents in the range ±200 pA and ±20 nA, with 100 kHz bandwidth while dissipating 41 mW. An integrated digital offset compensation loop balances any voltage offsets from Ag/AgCl electrodes. The measured open-input input-referred noise current is as low as 4 fA/√Hz at ±200 pA range. The current amplifier is embedded in an integrated platform, together with a microfluidic device, for current recording from ion channels. Gramicidin-A, α-haemolysin and KcsA potassium channels have been used to prove both the platform and the current-to-digital converter. PMID:27213382

  6. Analysis of fast losses in the LHC with the BLM system

    CERN Document Server

    Nebot, E; Holzer, E; Dehning, B; Nordt, A; Sapinski, M; Emery, J; Zamantzas, C; Effinger, E; Marsili, A; Wenninger, J; Baer, T; Schmidt, R; Yang, Z; Zimmerman, F; Fuster, N

    2011-01-01

    About 3600 Ionization Chambers are located around the LHC ring to detect beam losses that could damage the equipment or quench superconducting magnets. The Beam Loss Monitors (BLMs) integrate the losses in 12 different time intervals (from 40 us to 83.8 s) allowing for different abort thresholds depending on the duration of the loss and the beam energy. The signals are also recorded in a database at 1 Hz for offline analysis. During the 2010 run, a limiting factor in the machine availability were sudden losses appearing around the ring on the ms time scale and detected exclusively by the BLM system. It is believed that such losses originate from dust particles falling into the beam, or being attracted by its strong electromagnetic field. This document describes some of the properties of these ”Unidentified Falling Objects” (UFOs) putting special emphasis on their dependence on beam parameters (energy, intensity, etc). The subsequent modification of the BLM beam abort thresholds for the 2011 run that were ...

  7. A Low-Noise Transimpedance Amplifier for BLM-Based Ion Channel Recording

    Directory of Open Access Journals (Sweden)

    Marco Crescentini

    2016-05-01

    Full Text Available High-throughput screening (HTS using ion channel recording is a powerful drug discovery technique in pharmacology. Ion channel recording with planar bilayer lipid membranes (BLM is scalable and has very high sensitivity. A HTS system based on BLM ion channel recording faces three main challenges: (i design of scalable microfluidic devices; (ii design of compact ultra-low-noise transimpedance amplifiers able to detect currents in the pA range with bandwidth >10 kHz; (iii design of compact, robust and scalable systems that integrate these two elements. This paper presents a low-noise transimpedance amplifier with integrated A/D conversion realized in CMOS 0.35 μm technology. The CMOS amplifier acquires currents in the range ±200 pA and ±20 nA, with 100 kHz bandwidth while dissipating 41 mW. An integrated digital offset compensation loop balances any voltage offsets from Ag/AgCl electrodes. The measured open-input input-referred noise current is as low as 4 fA/√Hz at ±200 pA range. The current amplifier is embedded in an integrated platform, together with a microfluidic device, for current recording from ion channels. Gramicidin-A, α-haemolysin and KcsA potassium channels have been used to prove both the platform and the current-to-digital converter.

  8. A Low-Noise Transimpedance Amplifier for BLM-Based Ion Channel Recording.

    Science.gov (United States)

    Crescentini, Marco; Bennati, Marco; Saha, Shimul Chandra; Ivica, Josip; de Planque, Maurits; Morgan, Hywel; Tartagni, Marco

    2016-01-01

    High-throughput screening (HTS) using ion channel recording is a powerful drug discovery technique in pharmacology. Ion channel recording with planar bilayer lipid membranes (BLM) is scalable and has very high sensitivity. A HTS system based on BLM ion channel recording faces three main challenges: (i) design of scalable microfluidic devices; (ii) design of compact ultra-low-noise transimpedance amplifiers able to detect currents in the pA range with bandwidth >10 kHz; (iii) design of compact, robust and scalable systems that integrate these two elements. This paper presents a low-noise transimpedance amplifier with integrated A/D conversion realized in CMOS 0.35 μm technology. The CMOS amplifier acquires currents in the range ±200 pA and ±20 nA, with 100 kHz bandwidth while dissipating 41 mW. An integrated digital offset compensation loop balances any voltage offsets from Ag/AgCl electrodes. The measured open-input input-referred noise current is as low as 4 fA/√Hz at ±200 pA range. The current amplifier is embedded in an integrated platform, together with a microfluidic device, for current recording from ion channels. Gramicidin-A, α-haemolysin and KcsA potassium channels have been used to prove both the platform and the current-to-digital converter. PMID:27213382

  9. Very High Radiation Detector for the LHC BLM System Based on Secondary Electron Emission

    CERN Document Server

    Dehning, B; Holzer, EB; Kramer, D

    2007-01-01

    Beam Loss Monitoring (BLM) system plays a vital role in the active protection of the LHC accelerators elements. It should provide the number of particles lost from the primary hadron beam by measuring the radiation field induced by their interaction with matter surrounding the beam pipe. The LHC BLM system will use ionization chambers as standard detectors but in the areas where very high dose rates are expected, the Secondary Emission Monitor (SEM) chambers will be employed because of their high linearity, low sensitivity and fast response. The SEM needs a high vacuum for proper operation and has to be functional for up to 20 years, therefore all the components were designed according to the UHV requirements and a getter pump was included. The SEM electrodes are made of Ti because of its Secondary Emission Yield (SEY) stability. The sensitivity of the SEM was modeled in Geant4 via the Photo-Absorption Ionization module together with custom parameterization of the very low energy secondary electron production...

  10. 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.

  11. 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.

  12. 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.

  13. 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

  14. 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

  15. 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

  16. 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

  17. Regulation of gene expression by the BLM helicase correlates with the presence of G-quadruplex DNA motifs

    DEFF Research Database (Denmark)

    Nguyen, Giang Huong; Tang, Weiliang; Robles, Ana I;

    2014-01-01

    dysfunction, and other features observed in Bloom syndrome individuals. BLM binds to G-quadruplex (G4) DNA, and G4 motifs were enriched at transcription start sites (TSS) and especially within first introns (false discovery rate ≤ 0.001) of differentially expressed mRNAs in Bloom syndrome compared with normal...

  18. 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

  19. Tables of co-located geothermal-resource sites and BLM Wilderness Study Areas

    Energy Technology Data Exchange (ETDEWEB)

    Foley, D.; Dorscher, M.

    1982-11-01

    Matched pairs of known geothermal wells and springs with BLM proposed Wilderness Study Areas (WSAs) were identified by inspection of WSA and Geothermal resource maps for the states of Arizona, California, Colorado, Idaho, Montana, Nevada, New Mexico, Oregon, Utah, Washington and Wyoming. A total of 3952 matches, for geothermal sites within 25 miles of a WSA, were identified. Of these, only 71 (1.8%) of the geothermal sites are within one mile of a WSA, and only an additional 100 (2.5%) are within one to three miles. Approximately three-fourths of the matches are at distances greater than ten miles. Only 12 of the geothermal sites within one mile of a WSA have surface temperatures reported above 50/sup 0/C. It thus appears that the geothermal potential of WSAs overall is minimal, but that evaluation of geothermal resources should be considered in more detail for some areas prior to their designation as Wilderness.

  20. 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.

  1. 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...

  2. 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...

  3. 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...

  4. 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.

  5. 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.

  6. Blm-s, a BH3-Only Protein Enriched in Postmitotic Immature Neurons, Is Transcriptionally Upregulated by p53 during DNA Damage

    Directory of Open Access Journals (Sweden)

    Wei-Wen Liu

    2014-10-01

    Full Text Available Programmed cell death is a pivotal process that regulates neuronal number during development. Key regulators of this process are members of the BCL-2 family. Using mRNA differential display, we identified a Bcl-2 family gene, Blm-s (Bcl-2-like molecule, short form, enriched in postmitotic neurons of the developing cerebral cortex. BLM-s functions as a BH3-only apoptosis sensitizer/derepressor and causes BAX-dependent mitochondria-mediated apoptosis by selectively binding to prosurvival BCL-2 or MCL-1. When challenged with γ-irradiation that produces DNA double-strand breaks (DSBs, Blm-s is transcriptionally upregulated in postmitotic immature neurons with concurrently increased apoptosis. RNAi-mediated depletion of Blm-s protects immature neurons from irradiation-induced apoptosis. Furthermore, Blm-s is a direct target gene of p53 and AP1 via the ataxia telangiectasia mutated (ATM- and c-Jun N-terminal kinase (JNK-signaling pathways activated by DSBs. Thus, BLM-s is likely an apoptosis sensor activated by DSBs accumulating in postmitotic immature neurons.

  7. CSNS束流损失监控(BLM)系统电离室的改进%Improved Design and Construction of the Lonization Chamber for CSNS Beam Loss Monitor (BLM) System

    Institute of Scientific and Technical Information of China (English)

    赵中亮; 陈昌; 徐美杭; 田建民; 阮向东; 韩晨霞; 陈元柏; 徐韬光; 陆双桐

    2011-01-01

    Improved design and construction of the ionization chamber (IC) for CSNS and PA beam loss monitor (BLM) system is reported. The good plateau( ≥2 000 V) and the measurement range up to 3.6 × 105rad/h are obtained in the improved ionization chamber. All of these show us the performances of the improved ionization chamber can be satisfied for CSNS BLM application.%报道了中国散裂中子源工程(CSNS)和强流质子加速器(PA)柬流损失监控(BLM)系统的电离室的改进.对改进后的电离室测量得到,电离室有良好的坪特性(坪长≥2 000 V),测量的辐照剂量范围到3.6×10 5rad/h,高压加到3500 V仍能稳定工作.测量的结果表明电离室探头性能已能满足CSNS和PA对束流损失监控的性能需求.

  8. Genetic variation in the NBS1, MRE11, RAD50 and BLM genes and susceptibility to non-Hodgkin lymphoma

    OpenAIRE

    Gascoyne Randy D; Connors Joseph M; Gallagher Richard P; Lai Agnes S; Leach Stephen; MacArthur Amy C; Schuetz Johanna M; Spinelli John J; Brooks-Wilson Angela R

    2009-01-01

    Abstract Background Translocations are hallmarks of non-Hodgkin lymphoma (NHL) genomes. Because lymphoid cell development processes require the creation and repair of double stranded breaks, it is not surprising that disruption of this type of DNA repair can cause cancer. The members of the MRE11-RAD50-NBS1 (MRN) complex and BLM have central roles in maintenance of DNA integrity. Severe mutations in any of these genes cause genetic disorders, some of which are characterized by increased risk ...

  9. Design and construction of the first prototype ionization chamber for CSNS and PA beam loss monitor (BLM) system

    Institute of Scientific and Technical Information of China (English)

    XU Mei-Hang; TIAN Jian-Min; CHEN Chang; CHEN Yuan-Bo; XU Tao-Guang; LU Shuang-Tong

    2009-01-01

    Design and construction of the first prototype ionization chamber for CSNS and Proton Accelerator (PA) beam loss monitor (BLM) system is reported. The low leakage current (<0.1 pA), good plateau (≈800 V) and linearity range up to 200 Roentgen/h axe obtained in the first prototype. All of these give us good experience for further improving the ionization chamber construction.

  10. R2E-related MD: slow controlled losses for RadMon/BLM cross-checks

    CERN Document Server

    Calviani, M; Spiezia, G; Sapinski, M; Priebe, A; Nordt, A; Pojer, M; CERN. Geneva. ATS Department

    2011-01-01

    The purpose of the dedicated R2E MD has been to evaluate the R factor (i.e. the ratio between the thermal neutron fluence and the high energy hadron fluence (>20MeV) for various tunnel locations, to measure the HEH radiation level gradient along the MBC dipole and on the MQ, to check the ratio the BLM measured dose and RadMon SEU counts and to study the dose gradient between the standard BLM beam axis location and at the level of the equipment location. Within the R2E Mitigation Project, these accurate measurement and cross-check of the mentioned parameters are of great importance for the evaluation and interpretation of the R2E-related radiation levels, as well as for the evaluation of the failure cross-section of specific equipment (i.e. QPS ISO150). In addition, a short part of the MD has been devoted to the comparison of BLM signals generated by loss directed inwards and outwards with respect to the LHC ring.

  11. Virtual Screening and Molecular Docking Study of Bloom’s Syndrome Protein (BLM for Finding Potential Lead Drug Candidate

    Directory of Open Access Journals (Sweden)

    Manoj Kumar Verma

    2014-06-01

    Full Text Available Increased levels of locus-specific mutations within the BLM result in development of Bloom Syndrome and patients are found to be immune deficient. HRDC domain amino acid Lys1270 is presumably to play role in mediating interactions with DNA. Single point mutation of Lys1270 (K1270V reduces the potency of Double Holliday junction (DHJ DNA unwinding so BLM lead to its functional loss. Quadruplex formation have role in immunoglobulin heavy chain switching and inhibiting RecQ helicases activity in-vitro in BLM. Variety of G-Quadruplex ligands are employed by molecular docking for arriving at lead compound identification. The scoring function of docking results describes protein-ligand interaction and it conjointly instructed that docking of ligand at mutational binding site shows some repressing function to make potential lead drug molecule. So as to know the elaborated purposeful functional mechanism of protein and to relate impact of mutation with function and activity; dock screening, hit identification and lead optimization facilitate in design of lead drug compound.

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

    Directory of Open Access Journals (Sweden)

    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

  13. 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.

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

    Directory of Open Access Journals (Sweden)

    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

  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. Chromosomal instability associated with a novel BLM frameshift mutation (c.1980-1982delAA) in two unrelated Tunisian families with Bloom syndrome.

    Science.gov (United States)

    Ben Salah, G; Salem, I Hadj; Masmoudi, A; Ben Rhouma, B; Turki, H; Fakhfakh, F; Ayadi, H; Kamoun, H

    2014-10-01

    The Bloom syndrome (BS) is an autosomal recessive disorder associated with dwarfism, immunodeficiency, reduced fertility and cancer risk. BS cells show genomic instability, particularly an hyper exchange between the sister chromatids due to a defective processing of the DNA replication intermediates. It is caused by mutations in the BLM gene which encodes a member of the RecQ family of DExH box DNA helicases. In this study, we reported cytogenetic, BLM linkage and mutational analyses for two affected Tunisian families. The Cytogenetic parameters were performed by chromosomal aberration (CA) and sister chromatid exchange (SCE) assays and results showed a significant increase in mean frequency of CA and SCE in BS cells. BLM linkage performed by microsatellite genotyping revealed homozygous haplotypes for the BS patients, evidence of linkage to BLM gene. Mutational analysis by direct DNA sequencing revealed a novel frameshift mutation (c.1980-1982delAA) in exon 8 of BLM gene, resulting in a truncated protein (p.Lys662fsX5). The truncated protein could explain genomic instability and its related symptoms in the BS patients. The screening of this mutation is useful for BS diagnosis confirmation in Tunisian families.

  18. A Role for BLM in Double-Strand Break Repair Pathway Choice: Prevention of CtIP/Mre11-Mediated Alternative Nonhomologous End-Joining

    Directory of Open Access Journals (Sweden)

    Anastazja Grabarz

    2013-10-01

    Full Text Available The choice of the appropriate double-strand break (DSB repair pathway is essential for the maintenance of genomic stability. Here, we show that the Bloom syndrome gene product, BLM, counteracts CtIP/MRE11-dependent long-range deletions (>200 bp generated by alternative end-joining (A-EJ. BLM represses A-EJ in an epistatic manner with 53BP1 and RIF1 and is required for ionizing-radiation-induced 53BP1 focus assembly. Conversely, in the absence of 53BP1 or RIF1, BLM promotes formation of A-EJ long deletions, consistent with a role for BLM in DSB end resection. These data highlight a dual role for BLM that influences the DSB repair pathway choice: (1 protection against CtIP/MRE11 long-range deletions associated with A-EJ and (2 promotion of DNA resection. These antagonist roles can be regulated, according to cell-cycle stage, by interacting partners such as 53BP1 and TopIII, to avoid unscheduled resection that might jeopardize genome integrity.

  19. 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.

  20. 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.

  1. 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

  2. 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

  3. 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

  4. 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

  5. The radiation hardness of silica optical fiber used in the LED-fiber monitor of BLM and BESIII EMC

    International Nuclear Information System (INIS)

    LED-fiber system has been used to monitor BLM and BESIII EMC. A radiation hard silica optical fiber is essential for its stability and reliability. Three types of silica optical fibers, silicone-clad silica optical fiber with high OH- content (SeCS), silica-clad silica optical fiber with low OH- content (SCSL) and silica-clad silica opical fiber with high OH- content (SCSH) were studied. In the experiment, 12 groups of fiber samples were irradiated by 60Co and 3 groups of fiber samples were irradiated by BEPCII background radiation. Radiation hardness: the radiation hardness of SCSH is best and meets the radiation hardness requirement for LED-fiber monitor of BLM and BESIII EMC. The transmission of SeCS and SCSH decreased to around 80% under the 60Co-irradiation of 5 Gy and 10 Gy, respectively. The radiation hardness of SeCS is worst because of its silicone cladding. Recovery characteristics: 60Co-irradiated by the same doses, there were both more annealable and more permanent color centers formed in SeCS than SCSL, and for the same kind of fibers, as long as the irradiated doses are under a certain amount (for example, less than 5 Gy for SeCS), the higher the doses, both the more annealable and the more permanent color centers are formed.

  6. Human DNA2 possesses a cryptic DNA unwinding activity that functionally integrates with BLM or WRN helicases

    Science.gov (United States)

    Pinto, Cosimo; Kasaciunaite, Kristina; Seidel, Ralf; Cejka, Petr

    2016-01-01

    Human DNA2 (hDNA2) contains both a helicase and a nuclease domain within the same polypeptide. The nuclease of hDNA2 is involved in a variety of DNA metabolic processes. Little is known about the role of the hDNA2 helicase. Using bulk and single-molecule approaches, we show that hDNA2 is a processive helicase capable of unwinding kilobases of dsDNA in length. The nuclease activity prevents the engagement of the helicase by competing for the same substrate, hence prominent DNA unwinding by hDNA2 alone can only be observed using the nuclease-deficient variant. We show that the helicase of hDNA2 functionally integrates with BLM or WRN helicases to promote dsDNA degradation by forming a heterodimeric molecular machine. This collectively suggests that the hDNA2 motor promotes the enzyme's capacity to degrade dsDNA in conjunction with BLM or WRN and thus promote the repair of broken DNA. DOI: http://dx.doi.org/10.7554/eLife.18574.001 PMID:27612385

  7. 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

  8. 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...

  9. 78 FR 65356 - Notice of Mailing/Street Address Change for the BLM-Utah West Desert District and Salt Lake Field...

    Science.gov (United States)

    2013-10-31

    ... and Salt Lake Field Offices AGENCY: Bureau of Land Management, Interior. ACTION: Notice. SUMMARY: The mailing/street address for the Bureau of Land Management (BLM), West Desert District and Salt Lake Field Offices will be changing from 2370 South 2300 West, Salt Lake City, UT 84119-2022, to 2370 South...

  10. 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.

  11. 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...

  12. 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...

  13. 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.

  14. 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).

  15. Geochemical investigations and interim recommendations for priority abandoned mine sites, BLM lands, upper Animas River watershed, San Juan County, Colorado

    Science.gov (United States)

    Nash, J. Thomas

    1999-01-01

    Field observations, sampling of mine dumps and mine drainage waters, and laboratory studies of dump materials have been made at mining areas deemed to be on public lands administered by the U. S. Bureau of Land Management (BLM) in the Upper Animas River watershed. Results of chemical analyses of dump materials, leachates of those materials, and surface waters draining mines or dumps provide indications of where acid is generated or consumed, and metal concentrations below mines or dumps. Information on sites previously identified as needing reclamation is reviewed and available geochemical information is used to rank 26 sites into four classes of priority for reclamation. Although there are more than a thousand mining sites (productive mines and prospects) on BLM lands in the Upper Animas River watershed study area, the majority are very small (less than about 70 cubic yards of dump material), are more than 2 miles from a major stream, or so inaccessible as to prohibit reclamation. In the summers of 1997 and 1998 approximately 200 sites were observed and more than 100 of these that appeared to have the potential to geochemically impact the watershed were examined more carefully and sampled. Building upon the prior work of the BLM and associated agencies, this work attempted to identify the most significant sources of mine-related contamination and to rank those sites as to priority for reclamation. These most significant mining areas have been examined within a geologic framework and were evaluated by multiple criteria, including tendency to generate acid and release toxic metals, observed damage to vegetation, potential to release metals based on leach tests, and likelihood of transport into streams of the watershed. No single measurable parameter, such as metal concentration, can be used to rank the sites. Rather, subjective estimates are required to evaluate combinations or interactions among several parameters. The most subjective estimate, while ranking

  16. Mre11 and Blm-Dependent Formation of ALT-Like Telomeres in Ku-Deficient Ustilago maydis.

    Directory of Open Access Journals (Sweden)

    Eun Young Yu

    2015-10-01

    Full Text Available A subset of human cancer cells uses a specialized, aberrant recombination pathway known as ALT to maintain telomeres, which in these cells are characterized by complex aberrations including length heterogeneity, high levels of unpaired C-strand, and accumulation of extra-chromosomal telomere repeats (ECTR. These phenotypes have not been recapitulated in any standard budding or fission yeast mutant. We found that eliminating Ku70 or Ku80 in the yeast-like fungus Ustilago maydis results initially in all the characteristic telomere aberrations of ALT cancer cells, including C-circles, a highly specific marker of ALT. Subsequently the ku mutants experience permanent G2 cell cycle arrest, accompanied by loss of telomere repeats from chromosome ends and even more drastic accumulation of very short ECTRs (vsECTRs. The deletion of atr1 or chk1 rescued the lethality of the ku mutant, and "trapped" the telomere aberrations in the early ALT-like stage. Telomere abnormalities are telomerase-independent, but dramatically suppressed by deletion of mre11 or blm, suggesting major roles for these factors in the induction of the ALT pathway. In contrast, removal of other DNA damage response and repair factors such as Rad51 has disparate effects on the ALT phenotypes, suggesting that these factors process ALT intermediates or products. Notably, the antagonism of Ku and Mre11 in the induction of ALT is reminiscent of their roles in DSB resection, in which Blm is also known to play a key role. We suggest that an aberrant resection reaction may constitute an early trigger for ALT telomeres, and that the outcomes of ALT are distinct from DSB because of the unique telomere nucleoprotein structure.

  17. Mre11 and Blm-Dependent Formation of ALT-Like Telomeres in Ku-Deficient Ustilago maydis.

    Science.gov (United States)

    Yu, Eun Young; Pérez-Martín, José; Holloman, William K; Lue, Neal F

    2015-10-01

    A subset of human cancer cells uses a specialized, aberrant recombination pathway known as ALT to maintain telomeres, which in these cells are characterized by complex aberrations including length heterogeneity, high levels of unpaired C-strand, and accumulation of extra-chromosomal telomere repeats (ECTR). These phenotypes have not been recapitulated in any standard budding or fission yeast mutant. We found that eliminating Ku70 or Ku80 in the yeast-like fungus Ustilago maydis results initially in all the characteristic telomere aberrations of ALT cancer cells, including C-circles, a highly specific marker of ALT. Subsequently the ku mutants experience permanent G2 cell cycle arrest, accompanied by loss of telomere repeats from chromosome ends and even more drastic accumulation of very short ECTRs (vsECTRs). The deletion of atr1 or chk1 rescued the lethality of the ku mutant, and "trapped" the telomere aberrations in the early ALT-like stage. Telomere abnormalities are telomerase-independent, but dramatically suppressed by deletion of mre11 or blm, suggesting major roles for these factors in the induction of the ALT pathway. In contrast, removal of other DNA damage response and repair factors such as Rad51 has disparate effects on the ALT phenotypes, suggesting that these factors process ALT intermediates or products. Notably, the antagonism of Ku and Mre11 in the induction of ALT is reminiscent of their roles in DSB resection, in which Blm is also known to play a key role. We suggest that an aberrant resection reaction may constitute an early trigger for ALT telomeres, and that the outcomes of ALT are distinct from DSB because of the unique telomere nucleoprotein structure.

  18. 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.

  19. 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

  20. 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.

  1. 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.

  2. 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.

  3. 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

  4. 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...

  5. 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

  6. 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

  7. In-vitro rescue and recovery studies of human melanoma (BLM) cell growth, adhesion and migration functions after treatment with progesterone

    OpenAIRE

    Leder, Douglas C; Brown, Jason R; Ramaraj, Pandurangan

    2015-01-01

    Treatment of human melanoma (BLM) cells for 48 hrs with progesterone resulted in a significant inhibition of cell growth. The mechanism of growth inhibition was due to autophagy and this action of progesterone was not mediated through progesterone receptor. As cells were floating during treatment, adhesion assay was performed, which showed complete loss of adhesion. When cells were allowed to recover after treatment by culturing in growth medium without progesterone, there was recovery in cel...

  8. Assessment Fargas and BLM Models for Identification of Erosion Degree and Critical Sediment Sources (Case Study: Aghbolagh Drainage Basin, Hashtrood City

    Directory of Open Access Journals (Sweden)

    Naser Abdi

    2014-08-01

    Full Text Available The identification of the different areas in drainage basin (as a natural planning unit for occurring the sedimentation and its severity in different phases of basic studies has been always one of the most important purposes of the natural resources experts. For achieving to this purpose some experimental models has been presented that Some of them have high efficiency and others have weaknesses. Fargas and BLM models are used in this research and they are run in Aghbolagh drainage basin in Hashtrood town, East Azarbayjan province with 7.8 km2 area. Fargas model includes only two factors, the rock type erosivity and drainage density in the every rock unit, whereas BLM model includes seven factors; the surface erosion, the litter cover, the rock cover on the surface, the affection of destruction on the surface, the surface rill erosion, the affection of the sedimentation due to the water flow and the amplification of gully erosion. The objective of this research is the handling of these two models for different phases of basic studies in the study area. The results of two models showed, in Fargas model 3.67% area of the basin has high erosion, 14.26% area of the basin has severe erosion and 81.04% has very severe erosion and in BLM model 42.97% area of the basin has moderate erosion and 24.93% has high erosion, therefore 52.85% of the study area in Fargas and BLM models has concurrence in the erosion severity.

  9. Analyses of hydrocarbons in BLM sediment intercalibration sample from Santa Barbara basin and spiked with API South Louisiana crude oil. A preliminary report

    Energy Technology Data Exchange (ETDEWEB)

    Farrington, J W; Tripp, B W; Sass, J

    1977-01-01

    A preliminary report is made of a BLM intercalibration sediment sample from the Santa Barbara basin spiked with South Louisiana crude oil. The two subsamples reported were analyzed by a procedure described in the appendix for which a separate abstract was written. Because of the high oil content of the sediment the usual thin layer chromatography procedure resulted in an overloaded plate. An appendix was indexed separately. (JSR)

  10. 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.

  11. 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.

  12. 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.

  13. 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.

  14. Roles of Werner syndrome protein in protection of genome integrity

    DEFF Research Database (Denmark)

    Rossi, Marie L; Ghosh, Avik K; Bohr, Vilhelm A

    2010-01-01

    Werner syndrome protein (WRN) is one of a family of five human RecQ helicases implicated in the maintenance of genome stability. The conserved RecQ family also includes RecQ1, Bloom syndrome protein (BLM), RecQ4, and RecQ5 in humans, as well as Sgs1 in Saccharomyces cerevisiae, Rqh1 in Schizosacc...

  15. Total Glucosides of Danggui Buxue Tang Attenuate BLM-Induced Pulmonary Fibrosis via Regulating Oxidative Stress by Inhibiting NOX4

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    Ping Zhao

    2015-01-01

    Full Text Available Pulmonary fibrosis (PF is a serious chronic lung disease with unknown pathogenesis. Researches have confirmed that oxidative stress which is regulated by NADPH oxidase-4 (NOX4, a main source of reactive oxygen species (ROS, is an important molecular mechanism underlying PF. Previous studies showed that total glucosides of Danggui Buxue Tang (DBTG, an extract from a classical traditional Chinese herbal formula, Danggui Buxue Tang (DBT, attenuated bleomycin-induced PF in rats. However, the mechanisms of DBTG are still not clear. We hypothesize that DBTG attenuates PF through regulating the level of oxidative stress by inhibiting NOX4. And we found that fibrosis indexes hydroxyproline (HYP and type I collagen (Col-I were lower in DBTG groups compared with the model group. In addition, the expression of transforming growth factor-β1 (TGF-β1 and expression of alpha smooth muscle actin (α-SMA were also much more decreased than the model group. For oxidative stress indicators, DBTG blunted the decrease of superoxide dismutase (SOD activity, total antioxidant capacity (T-AOC, and the increase in malondialdehyde (MDA, 8-iso-prostaglandin in lung homogenates. Treatment with DBTG restrained the expression of NOX4 compared to the model group. Present study confirms that DBTG inhibits BLM-induced PF by modulating the level of oxidative stress via suppressing NOX4.

  16. Genetic variation in the NBS1, MRE11, RAD50 and BLM genes and susceptibility to non-Hodgkin lymphoma

    Directory of Open Access Journals (Sweden)

    Gascoyne Randy D

    2009-11-01

    Full Text Available Abstract Background Translocations are hallmarks of non-Hodgkin lymphoma (NHL genomes. Because lymphoid cell development processes require the creation and repair of double stranded breaks, it is not surprising that disruption of this type of DNA repair can cause cancer. The members of the MRE11-RAD50-NBS1 (MRN complex and BLM have central roles in maintenance of DNA integrity. Severe mutations in any of these genes cause genetic disorders, some of which are characterized by increased risk of lymphoma. Methods We surveyed the genetic variation in these genes in constitutional DNA of NHL patients by means of gene re-sequencing, then conducted genetic association tests for susceptibility to NHL in a population-based collection of 797 NHL cases and 793 controls. Results 114 SNPs were discovered in our sequenced samples, 61% of which were novel and not previously reported in dbSNP. Although four variants, two in RAD50 and two in NBS1, showed association results suggestive of an effect on NHL, they were not significant after correction for multiple tests. Conclusion These results suggest an influence of RAD50 and NBS1 on susceptibility to diffuse large B-cell lymphoma and marginal zone lymphoma. Larger association and functional studies could confirm such a role.

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

    Directory of Open Access Journals (Sweden)

    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

  18. 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 ...

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

    Directory of Open Access Journals (Sweden)

    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.

  20. 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

  1. 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

  2. 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

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

    Directory of Open Access Journals (Sweden)

    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

  4. 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.

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

    Directory of Open Access Journals (Sweden)

    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.

  6. 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

  7. 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

  8. 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.

  9. 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

  10. 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.

  11. 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.

  12. 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...

  13. 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'...

  14. 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...

  15. 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.

  16. 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

  17. 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.

  18. 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.

  19. 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

  20. 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.

  1. 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

  2. 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

  3. 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

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

    Directory of Open Access Journals (Sweden)

    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.

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

    Energy Technology Data Exchange (ETDEWEB)

    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.

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

    Directory of Open Access Journals (Sweden)

    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.

  7. BLM Solar Energy Zones

    Data.gov (United States)

    Bureau of Land Management, Department of the Interior — Priority development areas for utility-scale solar energy facilities as identified in the Solar PEIS Record of Decision. An additional Solar Energy Zone identified...

  8. 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

  9. 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

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

    Directory of Open Access Journals (Sweden)

    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.

  11. Landscape Measures of Rangeland Condition in the BLM Owyhee Pilot Project: Shrub Canopy Mapping, Vegetation Classification, and Detection of Anomalous Land Areas

    Energy Technology Data Exchange (ETDEWEB)

    Tagestad, Jerry D.; Downs, Janelle L.

    2007-12-28

    In 2006, the BLM tasked PNNL to collaborate in research being conducted under the Owyhee Uplands Pilot Project to assess rangeland condition. The objective of this effort was to provide Owyhee Uplands Pilot Project with a sophisticated suite of data and tools to assist in evaluating the health and condition of the Owyhee Uplands study area. We focused on three technical areas. The first involved enhancing existing algorithms to estimate shrub canopy cover in the Lower Reynolds Creek Watershed. The second task involved developing and applying a strategy to assess and compare three vegetation map products for the Idaho portion of the Owyhee study area. The third task developed techniques and data that can be used to identify areas exhibiting anomalous rangeland conditions (for example exotic plants or excessive bare soil exposure). This report documents the methods used, results obtained, and conclusions drawn.

  12. 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.

  13. 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

  14. pH modulates transport rates of manganese and cadmium in the green alga Chlamydomonas reinhardtii through non-competitive interactions: Implications for an algal BLM

    International Nuclear Information System (INIS)

    The influence of pH on short-term uptake of manganese and cadmium by the green alga Chlamydomonas reinhardtii was studied to better understand the nature of proton interactions with metal membrane transporters. Manganese and cadmium internalization fluxes (Jint) were measured over a wide range of free metal ion concentrations from 1 x 10-10 to 4 x 10-4 M at several pH values (Mn: 5.0, 6.5 and 8.0; Cd: 5.0 and 6.5). For both metals, first-order biological internalization kinetics were observed but the maximum transport flux (Jmax) decreased when pH decreased, in contradiction with the Biotic Ligand Model (BLM). This result suggested a non-competitive inhibition of metal uptake by the H+-ion. A Michaelis-Menten type inhibition model considering proton and calcium competition was tested. The metal biotic ligand stability constants and the stability constants for competitive binding of Ca2+ and H+ with the metal transporters were calculated: for manganese, KMn = 104.20 and KCa = 103.71; for cadmium, KCd = 104.19 and KCa = 104.76; for both metal transport systems, KH was not a significant parameter. Furthermore, metal uptake was not significantly influenced by the pH of the antecedent growth medium, suggesting that increases in metal fluxes as the pH is raised are caused by conformational changes of the surface transport proteins rather than by the synthesis of additional transport sites. Our results demonstrate that the BLM in its present state does not properly describe the true influence of pH on manganese and cadmium uptake by algae and that a non-competitive inhibition component must be integrated

  15. 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

  16. 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

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

    Directory of Open Access Journals (Sweden)

    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

  18. 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...

  19. 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...

  20. 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...

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

    Directory of Open Access Journals (Sweden)

    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

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

    Directory of Open Access Journals (Sweden)

    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.

  3. 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.

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

    Directory of Open Access Journals (Sweden)

    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.

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

    Directory of Open Access Journals (Sweden)

    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.

  6. 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.

  7. 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.

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

    Directory of Open Access Journals (Sweden)

    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.

  9. 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

  10. 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

  11. 用于CSNS和PA束流损失监控(BLM)系统的电离室设计参数的优化%Optimization of Design and Parameters of the Ionization Chamber for CSNS and PA Beam Loss Monitor (BLM) System

    Institute of Scientific and Technical Information of China (English)

    田建民; 陈昌; 徐美杭; 陈元柏; 徐韬光; 阮向东; 陆双桐

    2010-01-01

    运用GEANT4蒙特卡洛模拟程序包,对用于中国散裂中子源(CSNS)和质子加速器(PA)束流损失监控系统(BLM)的γ电离室探头进行模拟研究,由模拟计算给出优化的电离室设计参数.工作气体选用1个大气压的氩气;内、外电极用无缝不锈钢管代替镍管,它们的分别为0.1和0.15 mm;屏蔽外壳亦选用1 mm厚度的不锈钢.按照以上参数制成的电离室模型用放射源测试,性能良好.

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

    Directory of Open Access Journals (Sweden)

    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.

  13. 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.

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

    Directory of Open Access Journals (Sweden)

    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.

  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.

    Directory of Open Access Journals (Sweden)

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

    Directory of Open Access Journals (Sweden)

    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.

    Science.gov (United States)

    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. 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

  12. 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

  13. Combinatorial regulation of meiotic holliday junction resolution in C. elegans by HIM-6 (BLM helicase, SLX-4, and the SLX-1, MUS-81 and XPF-1 nucleases.

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    Ana Agostinho

    Full Text Available Holliday junctions (HJs are cruciform DNA structures that are created during recombination events. It is a matter of considerable importance to determine the resolvase(s that promote resolution of these structures. We previously reported that C. elegans GEN-1 is a symmetrically cleaving HJ resolving enzyme required for recombinational repair, but we could not find an overt role in meiotic recombination. Here we identify C. elegans proteins involved in resolving meiotic HJs. We found no evidence for a redundant meiotic function of GEN-1. In contrast, we discovered two redundant HJ resolution pathways likely coordinated by the SLX-4 scaffold protein and also involving the HIM-6/BLM helicase. SLX-4 associates with the SLX-1, MUS-81 and XPF-1 nucleases and has been implicated in meiotic recombination in C. elegans. We found that C. elegans [mus-81; xpf-1], [slx-1; xpf-1], [mus-81; him-6] and [slx-1; him-6] double mutants showed a similar reduction in survival rates as slx-4. Analysis of meiotic diakinesis chromosomes revealed a distinct phenotype in these double mutants. Instead of wild-type bivalent chromosomes, pairs of "univalents" linked by chromatin bridges occur. These linkages depend on the conserved meiosis-specific transesterase SPO-11 and can be restored by ionizing radiation, suggesting that they represent unresolved meiotic HJs. This suggests the existence of two major resolvase activities, one provided by XPF-1 and HIM-6, the other by SLX-1 and MUS-81. In all double mutants crossover (CO recombination is reduced but not abolished, indicative of further redundancy in meiotic HJ resolution. Real time imaging revealed extensive chromatin bridges during the first meiotic division that appear to be eventually resolved in meiosis II, suggesting back-up resolution activities acting at or after anaphase I. We also show that in HJ resolution mutants, the restructuring of chromosome arms distal and proximal to the CO still occurs, suggesting that

  14. 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.

  15. 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

  16. 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.

  17. 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.

  18. 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.).

  19. 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...

  20. 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...

  1. 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

  2. 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.

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

    Science.gov (United States)

    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

  4. 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

  5. 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

  6. 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.

  7. 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'.

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

    Directory of Open Access Journals (Sweden)

    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.

  9. 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

  10. 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....

  11. 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.

  12. 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.

  13. 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.

  14. 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.

  15. 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.

  16. 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

  17. 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

  18. 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.

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

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    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.

  20. 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

  1. 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.

  2. 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.

  3. 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.

  4. 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

  5. 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.

  6. 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.

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

    Directory of Open Access Journals (Sweden)

    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.

  8. 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.

  9. 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

  10. 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.

  11. 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

  12. 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

  13. 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.

  14. 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.

  15. 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

  16. Characterization of a highly conserved binding site of Mlh1 required for exonuclease I-dependent mismatch repair

    DEFF Research Database (Denmark)

    Dherin, Claudine; Gueneau, Emeric; Francin, Mathilde;

    2009-01-01

    Mlh1 is an essential factor of mismatch repair (MMR) and meiotic recombination. It interacts through its C-terminal region with MutL homologs and proteins involved in DNA repair and replication. In this study, we identified the site of yeast Mlh1 critical for the interaction with Exo1, Ntg2...... protein box. Direct and specific interactions between yeast Mlh1 and peptides derived from Exo1, Ntg2, and Sgs1 and between human MLH1 and peptide derived from EXO1 and BLM were measured with K(d) values ranging from 8.1 to 17.4 microM. In Saccharomyces cerevisiae, a mutant of Mlh1 targeted at site S2......, and Sgs1 proteins, designated as site S2 by reference to the Mlh1/Pms1 heterodimerization site S1. We show that site S2 is also involved in the interaction between human MLH1 and EXO1 or BLM. Binding at this site involves a common motif on Mlh1 partners that we called the MIP-box for the Mlh1 interacting...

  17. 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.

  18. Effects of Dragons Blood on Interstitial Over -repairing and TGFβ1 mRNA Expression in the Lung Tissue of BLM -lung- injury rat%龙血竭对大鼠肺损伤间质过度修复及其TGFβ1 mRNA表达的影响

    Institute of Scientific and Technical Information of China (English)

    杨礼腾; 刘欣; 程德云; 方洵; 穆茂; 胡晓波; 聂莉

    2012-01-01

    目的:探讨龙血竭(LXJ)对博莱霉素肺损伤大鼠肺间质过度修复及其TGFβ1mRNA表达的调控作用.方法:60只健康SD大鼠,随机分为生理盐水组(NS)、博莱霉素肺损伤组(BLM)及龙血竭组(LXJ),每组20只,再分成两亚组,每亚组10只,通过博莱霉素一次性气管内滴入复制肺损伤修复大鼠模型,并在肺损伤修复过程中予龙血竭灌胃干预,分别于14和28天取大鼠肺组织,运用组织芯片,进行HE、胶原纤维染色及免疫组化分别定量肺内炎性细胞数、胶原蛋白、Ⅰ型胶原,用实时荧光定量RT -PCR技术定量转化生长因子beta( TGFβ1)mRNA的表达.结果:龙血竭对两时相肺组织的炎症程度和胶原(IOD分别从0.5492±0.2105和0.9578±0.3756降至0.2749±0.1592和0.3181±0.1210)及28天的Ⅰ型胶原过度沉积(IOD从0.9348±0.3774降至0.5045±0.2796)皆有明显抑制作用(P<0.05),对两时相TGFβ1 mRNA表达(从0.0219±0.0110和0.0170±0.0157分别1降至0.0083±0.0024和0.0062±0.0051)有明显下调的作用(P<0.05).结论:龙血竭具有抑制炎症性肺损伤促进修复,并可通过抑制胶原尤其是Ⅰ型胶原的过度沉积而调控肺损伤肺间质过度修复之作用,后者可能主要与下调肺组织TGFβ1mRNA的表达有关.%Objectives:To investigate the effects of the Dragons Blood (LXJ) on interstitial over - repairing and transform growth factor betal(TGFβ1 )mRNA expression in the lung tissue of bleomycin( BLM) - lung - injury rat. Methods; 60 healthy Sprague - Dawley rats were randomly divided into the NS group ( NS) ,the BLM - lung - injury group ( BLM) and the Dragons Blood group ( LXJ) ,every group had 20 rats and were suhdivided into two subgroups by 14 days and 28 days courses,each subgroup had 10 rats. BLM -lung-injury rat models were established by blemycin -induced by way of once -dripping into trachea and prevented and treated with the Dragons Blood by primed -stomach,at day 14 and day 28 respectively,the rats

  19. 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

    Directory of Open Access Journals (Sweden)

    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.

  20. 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.

  1. 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.

  2. 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.

  3. 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.

    Science.gov (United States)

    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

  4. 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.

  5. 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

    Directory of Open Access Journals (Sweden)

    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.

  6. DNA End Resection:Facts and Mechanisms

    Institute of Scientific and Technical Information of China (English)

    Ting Liu; a Jun Huang; b

    2016-01-01

    DNA double-strand breaks (DSBs), which arise following exposure to a number of endogenous and exogenous agents, can be repaired by either the homologous recombination (HR) or non-homologous end-joining (NHEJ) pathways in eukaryotic cells. A vital step in HR repair is DNA end resection, which generates a long 30 single-stranded DNA (ssDNA) tail that can invade the homologous DNA strand. The generation of 30 ssDNA is not only essential for HR repair, but also promotes activation of the ataxia telangiectasia and Rad3-related protein (ATR). Multiple fac-tors, including the MRN/X complex, C-terminal-binding protein interacting protein (CtIP)/Sae2, exonuclease 1 (EXO1), Bloom syndrome protein (BLM)/Sgs1, DNA2 nuclease/helicase, and several chromatin remodelers, cooperate to complete the process of end resection. Here we review the basic machinery involved in DNA end resection in eukaryotic cells.

  7. 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.

    Directory of Open Access Journals (Sweden)

    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

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

    Lifescience Database Archive (English)

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

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

    Lifescience Database Archive (English)

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

  10. 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

  11. 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

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

    Lifescience Database Archive (English)

    Full Text Available AVDKMEVVLSSMQAVGIPINTMALHALIMAYSRAGTYDRLAKTMEVVKDAGWMLQPATYNILISEYGKVGYLDKMEQAFREMMNASVKPSFETFQYMINAYEAADNETQVDRILDLMRKAGCEPKSNAVWTDDKVFSEKVRW ... ...NTLISMYSRMGATEEMKKIFLDCTEAEFVPDRHTYNALIWGYMRAGQLNEMEVTFNELQAKKFNADVITYNALIIGYARAN

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

    Lifescience Database Archive (English)

    Full Text Available EGQGAIGCIILGAALGAAIGLGLAVGIAQWFILRSIVSRSQWWILASVLGWCGIFFTLIVMLYTAIPVPGSPEFGQPIIAQLPLAGRAIAQVTLAGALMGLFQWLILRSSVRQSWCWIPAHALIMLLAALGVLILGYNIGGLPGMGIFIMIFSPIYAVLSGSLLDWLVKHSRNPVTT ...

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

    Lifescience Database Archive (English)

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

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

    Lifescience Database Archive (English)

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

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

    Lifescience Database Archive (English)

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

  17. 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

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

    Lifescience Database Archive (English)

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

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

    Lifescience Database Archive (English)

    Full Text Available QSREDYEAMLQEKAEPVLQEWMQRCITESLLTPRAVYGYFPAARDGNTLRVFDADGTRELGFFELPRQRSGNRYCIADFFNDLDAEGRPKDVLPMQAVTMGQKASVVA...MDAKRSDNWTNNKGFLADAPQGVGLDEEGTTSENAEETSTSASDAPAADLPPVSSDRSDAVPAEAAPVPPFLGSAVITEVDIDITEVFHYLDRNALFAGQWMLRKTKE

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

    Lifescience Database Archive (English)

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

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

    Lifescience Database Archive (English)

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

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

    Lifescience Database Archive (English)

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

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

    Lifescience Database Archive (English)

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

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

    Lifescience Database Archive (English)

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

  5. 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

  6. 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

  7. 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

  8. 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

  9. 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

  10. 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

  11. 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

  12. 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

  13. 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

  14. 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

  15. 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

  16. 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

  17. Protein (Cyanobacteria): 319556 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available cal protein Cha6605_6427 Chamaesiphon minutus PCC 6605 MGGDGFPPDRNHFSRAFSTSFNNMTFKRTQAEPLSCQCNIRLTPSEMEELKDAASVAGITVSTYIRQRALGRRVAANTDMTTIRELRRIGGLLKHIHNESGGAYSQLTADTLIEIQKAIVSIGNGL ...

  18. Protein (Cyanobacteria): 243777 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available occus sp. JA-3-3Ab MATPFSWPYRTPGIPDSAFERIPGIPMSPREVRVLVLSQLRLGEDHCLWDIGAGTGTIAIEAAILCPRARVIAIERDAEVVSLIESNCE...KFGLNNVQVIQGTAPDCLHQLSPPPDRICIEGGHPLREILEASWNHLKPNGRIVATTNSLEGLYGLSAGLAAVRAHHVEVIQSAVNRLEHRGRSQLLLPLDPTFVLSGEKSS ...

  19. Protein (Cyanobacteria): 170237 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 8802_4468 Cyanothece sp. PCC 8802 MNFDFPSPISPDSSKQQELSPKKLNPSRIRDHLANERTYLAWMRTAVGLMGFGVVILRIRAFQPPSIPGPGFGWKLGLIFAGVGLLTVLLSTVQYFIVRRDIEEDTYEPPDRWVILFSLTIALLGSGIIYFVSTSSFDLVDIIM ...

  20. Protein (Cyanobacteria): 320772 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available MC7420_6233 Coleofasciculus chthonoplastes PCC 7420 MIRHTSNNTTKPALPHHQTTKSILIFHAIARQSSTPSCRGGFRNSIITHTANKTTKPALSPPPDR...EIYPNFQAIARQSSTPSCRGGFRNSIITHTANKTTKPALSPPPDREIYPNFQAIAHQSSTPSCRGGFRDSIITHTANKTTKPALSPPPDREIYPNFQAI

  1. Protein (Cyanobacteria): 69702 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available osphatase Oscillatoria sp. PCC 6506 MNHLIKQADLADRIICDSAGTGGYHVGNPPDRRMAIAASKRELELRGSARKFQRSDFENFDLILAMDKDNYQDILSLDPHGKYRDKVRLMCEFCQKYDLREVPDPYYGGPEGFDRVIDLLWDACEGLLEYVTKEKLIFNS ...

  2. Protein (Cyanobacteria): 438681 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 8 Synechococcus sp. JA-2-3B'a(2-13) MNDLLFEPTSERPSLAEIRRLSPAALAYLGDAIYELHVRRQRLFPPDRLERYHQQVVRRVRGSAQAKLLLALLPHLNPEEQEIVRWGRNGCGRPPRHLPLADYQNASGLETVLGYLYLANPERLRHILALTDVLAETLGEWEG ...

  3. Protein (Cyanobacteria): 69717 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available osine phosphatase Moorea producens 3L MNHLIAQANLSDQIVCDSAGTSSYHIGSPPDRRMTAAAKRRGIILQGKARQFNRSDLEEFDLILAMDQQNYEDIISLDPAGKYKDKVRLMCDFASHHTERSVPDPYYGGPEGFNKVIDLLLDACEGLLEHVVDNYTKTRQN ...

  4. Protein (Cyanobacteria): 197706 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available porter Synechococcus sp. WH 5701 MWLRLDSASRLKPPFTPAPLPPDRQLPEGYDTLEGERGYQLSGGQRQRISLARAILRKPELLILDEATSALDSQSEHLVQQAIERFARKHTVLVIAHRPSTVVHPDLICVMDQGRIVERGHHGELLARDGLYADLWKKQVRHDHGL ...

  5. Protein (Cyanobacteria): 170238 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 01_4405 Cyanothece sp. PCC 8801 MNFDFPSPISPDSSKQQELSRKKLNPSRIRDHLANERTYLAWMRTAVGLMGFGVVILRIRAFQPPSIPGPGFGWKLGLIFAGVGLLTVLLSTVQYFIVRRDIEEDTYEPPDRWVILFSLAIALLGSGIIYFVSTSSFDLVDIIM ...

  6. Protein (Cyanobacteria): 313833 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available ELVGSPLPDTVPSTISEAAIETKIDEILEKKLSNHLPDNVPSIVESIILDKLPSMILEYLPSDLMARIENMERLLRLQQSASIADHSPIPTGEPYPLPPSPPDRPAIE...AVTPEVSPSPLVTDAIASIDGTVEGGNGDIFPDSPPDRPAIASSAKKGLTDSELARELGIDKSNITRWKQKGRPTQKYENWELRGRFWYEKD ...

  7. Protein (Viridiplantae): 225431324 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available RPPDSRIPFEFCYDMSPGENTSLIPSMSLTMKGGSQFPVYDPIIIISSQSELIYCMAVVRSAELNIIGQNFMTGYRIIFDR...GLEKISVPSILSKEGFTADSFSMCFGPDGIGRISFGDKGSPDQEETPFNLNALHPTYNITVTQVRVGTTLIDLDFTALFDSGTSFTYLVDPIYTNVLKSFHSQAQDSR

  8. Protein (Cyanobacteria): 22493 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available FIRWMAALTITVGVFIVSISENPPTSKPITSALEHRTKSWFKRSMFFLLPLSFSLPKIWLFAVIIAFADGFGDIFNAKGMKQIGAVKLGSLPEMLQIGQKIITNHWIIQGITCQTLSFLSFVSALSWADISFVRPATALTYVISLLGAYFILKERIELGRLIGIVVVGIGILIITLDPSMSL ...

  9. Protein (Viridiplantae): 303290558 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available NTMGWIDKAGYGLLLHALEALAIDVVLVVDHEKLHAELSRDLRGKKIKVWKLQKSGGVVERTPEFRRRSRDARVREYFYGPLGDLSPHSQTLEFGKVSIFKIGAGPSAPRSALPIGQESSADPLRVSTVAPSM...SLLNAVLGVSHGKTQAELLSSNVAGFIFVTDVDVANGRFTYLTPCPGELPSRNLIAGTLKWIETR ...

  10. Protein (Viridiplantae): 359473770 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available HHSRSASATGISNIKRTQNFAAKAAAQRLAQVMASQTADDDEDDEDDDLGFRYSAPPPPAFSRTVNSGKPAVPASRVTRSPSPGLGRNFVEETPSVRSTSAGRPSM...SLNAIPLVSPSRAPLRTPVPIPPIEPPNRQKEKRFSSNVGHFNPKDTGDQREASALRDEVDMLQEENENILDKLRLEEERCKD

  11. Protein (Cyanobacteria): 123908 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available RQWQSEHREIEMGDRYQAVLQEKVPSMSLAELGKITTEMVARFQACYQQSLRLPDGVKDMLEFWHGRVRLGVVSNFYIQGWPTELLESFGLRSYFDFVVDSAACGWRK...genase-like hydrolase Acaryochloris marina MBIC11017 MTLDWIFFDCFNTLIDDFDQTGEELALLPVYSLPAEVGLYTSAAEFRQHYHAWRN

  12. 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

  13. Protein (Viridiplantae): 255074015 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available RKLAASDSESDSDSDSDSDSGDEPAAKKAKTAPASSDSSSDSDSSSSDSDSDSGEKKEDENKEPAKPAKSESSSATSSDSDSSDSDSDSDSDSKPPAEEEKKDEPVAAVKADSSSSSDSDSS...SSDSDSDSDSGEKKEEEKAEVKKADSSDSDSSDSDSSSSDSDSDEKEEEKKDEPKAEVKADSSSSSS...SSSSSSDSDSDSDSDEKEEEKKEEKAEVKKADSSDSDSSSSDSDSDSDSDSDSGEKKEEEKAEVKKADSSSSSSSSDSDSDSDSDSDEKEEEKKDDEPKAEVKADSSS...SSSSSDSDSDSDSDSDSKPAAKTMEDKKDDSSSSDSDSDSSSSDSESEEKKEEEKAEVKADSSSSSDSDSSSSDSDSDSDEKEEEKKDDDKMDVEDAKADSSSSSSSS...SSSDSDDDSDSETEPVKMDADAAVAKPESSSSDSDSDSGSDSDSDSDSKPTAMDVDEKQEEAKAAASSDSDSSDSDSDSDSSDSDSGEKDDAPAVKPAEAKADSS

  14. Protein (Cyanobacteria): 7963 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available chococcus sp. CB0101 MELLPIRPAGAMNKTLVPPQDPSSRQWYLVDAENQTLGRLASEVASVLRGKNNPNFAPHIDAGDFVVVINAEKVKVSGNKFTEKVYRRHSGRPGGMKTESFAALQARIPERIIEKAVKGMLPHNALGRQLFRKLKVYKGAEHPHAAQQPQALALDPAASAQ ...

  15. Protein (Cyanobacteria): 229199 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available _3623 Cyanothece sp. PCC 7424 MAIQQITDNNINDYTLQISDNNILWTNQDPNTFITALYLYNGSQTIEIDRDELSTTLGLSGNNVVWKTPLGRNTYNENLYLYNGS...EIIQIDSNNHYDWVRISGDNVVWSASDGTDNEIYLYNGSQTLQLTNNDINDINPLISGNNIVWSSYDANNNYEIFFYNGSQVIQITNNNIGDFNPEISGNNIAWSGYVNGNSEVFFYNGS...ETIQLTNNDIDDYSPQISGNNIAWSTPNKEIYLYNGSQIIQLANNYNNDLSLKFSGDNLVWSGNDGNDNEIYFYNGS...EVIQLSNNNIDDRVSQISGNTVLWVSDDGTDKNVYFYNGSQVIQLTNNNIDNYSDSDYPKLSGNYIVWAASDGTDNEIYLADTREFASLNQAP

  16. 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

  17. 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

  18. 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

  19. 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

  20. 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

  1. Protein (Viridiplantae): 168006546 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available patens subsp. patens MHHEDEIGFRENVAAMAATTKKQLLLTYTYLIVYKDVLSKGTRSYQDNKHTALLERKWLILHRPPPLQYTKKNNNNFKQRPPHPEPRHLHYVRAGSTKMALNHPNDEPWVKSENHSVKPETERDAIGRWTVRWEDKIYTGLWLHFEHKNYGFPTGGKK ...

  2. Protein (Viridiplantae): 226501650 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 2772 uncharacterized protein LOC100273695 Zea mays MIEAYLRANKMFVDKHEPETERVFSSYLELDLSEVEPCVSGPKRPHDRVPLKEMKSDWHACLDNEVGFKGYAVPKEQQGKVVKFNFHGRPAEIKHGSVVLAAICSSTNTSNPSFMIGAGLVEESMRIGP ...

  3. Protein (Cyanobacteria): 256132 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available IVGAFVQMVTEGEIHRALGNQQRQRQIANLTDHTIICGFGRMGQVLAKQLKQSGLPFSIIDNQPSQVAIAEELGYLAHCGDATREEQLQMLGVMRAKTLATVLPEDAT...NVFITLTARELNSRLTILARGEIPETERKLRLAGADQVILPLTVGAVQMADLITQSNRRDFLNRPDERGFLNDLLASVEVQ

  4. Protein (Cyanobacteria): 212762 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available LGSESEWNILVSKLQQFLKALFIHEALDSQILIELVNRIYYLNPAESKTNRHLNSSLDISNNYPVGFQELKSDESTQEISESPQKQIESEQAANNSQNDSESSNYQPLANSNNKSPIAVLLLDAENIILNPET...ERFLETVCNFPIQVKVAFANWYRKGKLDTELHMRNYDLIHVPSGKDNADGKMIAFG

  5. Protein (Cyanobacteria): 435835 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available CP_0098 Synechocystis sp. PCC 6803 substr. PCC-P MASTPIQSEARTDLEPSFVIPLVLLFGAIPIFFLQMWVGLAIAVFGVFLMVQTAIIKLSFTATALEVYRGSKLIRSFPYTEWQNWRIFWEPAPILFYFKEVKSIHFLPIIFDPGTLKACLERHCPLQSLRAE ...

  6. Protein (Cyanobacteria): 435916 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available hetical protein Cal6303_0562 Calothrix sp. PCC 6303 MPPLSVTTVELKPSYNIPLVLVIAGIPLIFFQPWIGSAIALFGLFLMFQTVNIRLIFTPTALDVYRKDTLIRSFPYQEWENWRIFWNPVPILFYFKEVKSIHFLPIIFDPKTLKTCLEERCPRK ...

  7. Protein (Cyanobacteria): 435829 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 3658 Cyanothece sp. ATCC 51142 MSCSIQIPALSMTSVTPPNVNQQTIELAPSYNIPIILILMAIATLLIQPWVSLPLALFGLFLLLQTVTIRLQFTATALDVYRSDQRIRSFPYSEWQNWKIFWQPIPILFYFKEVNSIHFLPIIFDPQTLNVCLERFCNFDKMEEMG ...

  8. Protein (Cyanobacteria): 435852 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available rotein Cyan10605_0702 Cyanobacterium aponinum PCC 10605 MNSTTLTSETIELTPRYNLPIFIIILGVALSLVQMFVGIITILFGFFLLIQANIIKLKFTPKALEVYRQQNKIREFPYTDWQNWAIFWQPVPILFYFKEVKSIHFLPIIFDPITLKKCLEKYYPLS ...

  9. Protein (Cyanobacteria): 435833 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available I_0098 Synechocystis sp. PCC 6803 substr. GT-I MASTPIQSEARTDLEPSFVIPLVLLFGAIPIFFLQMWVGLAIAVFGVFLMVQTAIIKLSFTATALEVYRGSKLIRSFPYTEWQNWRIFWEPAPILFYFKEVKSIHFLPIIFDPGTLKACLERHCPLQSLRAE ...

  10. Protein (Cyanobacteria): 354868 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available ICYGVAGNSCYIVLEWLEIGRGDSKASEEMGRKLAQMHKKSLSEKFGWDMNNTIGSTPQINTWTDDWVEFWTKHRLGYQFELGKRRGGSFPQASELLNAIPELLAGHEVQPSLVHGDLWGGNAGFTVDGEPII...FDPATYFGDREVDIAMTEVFGGFSTAFYQGYNEVFPLDHGYEKRKTLYNLYHILNHFNLFGGGYGSQANGMIGRILSNK ...

  11. Protein (Cyanobacteria): 435834 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available CN_0098 Synechocystis sp. PCC 6803 substr. PCC-N MASTPIQSEARTDLEPSFVIPLVLLFGAIPIFFLQMWVGLAIAVFGVFLMVQTAIIKLSFTATALEVYRGSKLIRSFPYTEWQNWRIFWEPAPILFYFKEVKSIHFLPIIFDPGTLKACLERHCPLQSLRAE ...

  12. Protein (Viridiplantae): 115473185 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 5677 39947:5677 Os07g0599600 Oryza sativa Japonica Group MVFKKNAMSSSVLFLAALLLLSSSSMSSAARWLEEEYPPHPTVPELPKPEVPPHPAVPELPKHEEPPHP...VVPELPKHEEPPHPVVPELPKPELPPHPVVPELPKHEEPPHPAVVPELPKHEEPPHPAVVPEFPKHEEPPHPAVPELPHPAVPEIPHP...AVPELPKHEEPPHPVVPELPKPEVPHAAVPELPKPELPPHPAVPELPKHEEPPHPVVPELPKHEEPPHPVVPELPKPEEPHHPEVPEHEQPPKPESHYPEVPMAKP ...

  13. Protein (Viridiplantae): 255577163 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available :6554 3988:6554 hypothetical protein RCOM_0753050 Ricinus communis MQLGNAFIAILLILILFCISIDFSVASAGLKQNFTIVISQSPWLKNVTENLPHP...VSPFNCGSCGNKCPWGVLCVYGMCGYAEPWPPWPHPHPHPHPHPHPHPHPHPHPHPHPHPHPHPPPKPPKPWPHRPPQSPPKPIKPWPHHPPKADHEPSQSAMGPSY ...

  14. 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

  15. Protein (Cyanobacteria): 50412 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available GFSPPEMHLPNHPDTLFEYVKALKECGYRWLMVQEHSVENLDGSGLSGDQKYVPNRLVARNSRGETVSIVALIKTQGSDTKLVAQMQPYYEALGRGKQPVGNHHIP...ACVTQIADGENGGVMMNEFPPAYEQATRKMAENGGKSGTVAINGTEYLELLEAAGVQESDFPAIQAIQQHKIWQRVNPDSPSH

  16. Protein (Cyanobacteria): 189042 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available n MAE_13150 Microcystis aeruginosa NIES-843 MFELSDLKQTRVYQEALAEGEKQGLERGLQEGLERGLERGLERGLERGLERGLERGLERGLERGLERGLERGLQEGKRLVVENLLRVRFGELDPEIQAIISRILQLSPEEFTPLLLHCSKQELLKRFPPEKSRGN ...

  17. Protein (Viridiplantae): 242070245 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available HEGDDGELWLWTEMMDAVVPVGSRFMCWVDYSRGFLVCDTVREYLHDSIDDGAADETTVWMVKINTRSKALLSVFRSDNEDYDAKDLLPVKLDG ... ...ADTSDYFLYEAGAGRRRPPSLSLLPGCYIPMQYQYQFPTATPMARELSVWNATGILRRGDGEVLVAQLETPPPLNGAPCKTAELCVLRLRPGGHDHHDWVLKRVPIVH

  18. 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 ...

  19. 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 ...

  20. Protein (Viridiplantae): 356515098 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available PQSEDPNMVHPQSEDQNMAQPLMEDENTALPQLEDENTAQPQLEDENTAQLQGSSKLEDENTAQPQVTSRSEEGNTAQPQMSSRSEEGNTAQPQMSSRSEEGNTAQPQ...DQNMVQTEVGSGLEDGNKAQPRGEDQNMAQTQEGSRLEDENTAQPPGEDHNLAQTQVNSRLEDGDMAQPQLDDQNMVQPQSEDQNMAQSQSEDHIMAQPQSEDQNMAQ

  1. Protein (Cyanobacteria): 528 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available al protein P9303_04231 Prochlorococcus marinus str. MIT 9303 MATRSLISLYALLATSAVITQSAEAAVYSQPNACNPIEANIQGIRNGS...WSLFLRPNNIIFGENDQARSWKNGSGKSWKNGSSSGKWKNGSGKNWKNSSGWRNGGWRNGSSGKWKNGSGGFLNW ...

  2. 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 ...

  3. Protein (Cyanobacteria): 417077 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available ADAANAIAELRTKYPALAIRPVEAPPPWADWVATLKVVDWVPLHRYRLKRYDGSSFVDVPDAEETGFYELYEEGSQQQHALFYDRQHNAWYSAEWYSLRFLALTHLAPKNLSVSYDPNAQELSIPISQRWPLAYERYLVMQSGCLPRYNRTTEELIYQNIAPTVWQVIGEQLPFFDLEK ...

  4. Protein (Viridiplantae): 159479054 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 96 hypothetical protein CHLREDRAFT_120274, partial Chlamydomonas reinhardtii PPGCRCSSAPPGCRCSSAPPGCRCSSAPPGCRCSSAPPGCRCSSAPPGCRCSSAPP...GCRCSSAPPGCRCSSAPPGCRCSSAPPGCRCSSAPPGCRCSSAPPGCRCSSAPPGCRCS ...

  5. 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 ...

  6. Protein (Viridiplantae): 302829264 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available KLRGDRFVGLRGGRQILLAMDDQPNAAPLPTAPSPLFAAHQPAGLSQSKTPSPPLPRPPGNPQPYNPDQMPTPAQPPVQSPAPPVQSPAPPVQSPAPPVQSPAPPVQSPAPPVQSPAPPVQSPAPPVQSPAPP...VQSPAPPVQSPAPPVQSPAPPVQSPAPPVQSPAPPVQSPAPPVQSPAPPVQSPAPPVQSPAPPVQSPAPP...VQSPTPPSPSELMGSSCPDAQAFLDLHNLYRARHQAPPLRWNNNLAIAATAYAQQLADNDCALKHSGVRDAGENLLSQQSFPKPDNTCTLAARG

  7. 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 ...

  8. Protein (Viridiplantae): 226504466 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available AASGGDPWLSRHGDLRRVFLAGDSAGGNIVHNVAMMAAASGPRVEGAVLLHAGFGGKEPVHGEAPASVALMERLWGVVCPGATDGVDDPWVNPLAAVAPPRPSLRDMPCERVLVCGAELDSLLPRDRAYYEALAASGWGGTVEWFESKGQDHVFFLFKPDCGESVALIDRLVAFFAAN ...

  9. 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 ...

  10. Protein (Viridiplantae): 226507314 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available ASGGDPWLSRHGDLRRVFLAGDSAGGNIVHNVAMMAAASGPRVEGAVLLHAGFGGKEPVDGEAPASVALMERLWGVVCPGATDGVDDPRVNPLAAAAPPRPSLRDMPCERVLVCGAELDSLLPRDRAYYEALAASGWSGTVEWFESQGQDHVFFLFKPDCGESVALMDRLVAFFAAN ...

  11. 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

  12. 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

  13. 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

  14. Protein (Viridiplantae): 308800396 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available med protein product Ostreococcus tauri MTCVGNLDENMQVQDDDSRPARDKAKANFAQKAARKALERQEKDRLSARSASVLARFSSIRHLRISSYQLVPARTSWSILFTHTINTFGHSAGTYQYADTYQEIPDTHFKQSYQQSGQPRTGGWTFSSRAVIRVWLRGSP ...

  15. Protein (Viridiplantae): 293336748 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 575:7472 4577:7472 uncharacterized protein LOC100383091 Zea mays MNTPGHGAQRTCGGACISSTNSKIFGRQTAAESSPARTSTHGETFRYESVDYGDEPTVPDPATLQRTGAAANTQLPYRHRNSCPGAIPVRLPNPATQGAPWLGPQKQLLQA ...

  16. Protein (Viridiplantae): 168050221 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available omitrella patens subsp. patens MSYNTVLTLLHSNPLLFPAKGRQMPRIIGINQGYISGFALVRVSCFWVVNASQLPGLSSTNYCTCLDSCLPAQSFLL...HCHEKRAIILNLMLDCHRLRAIYPARTSLFRRLRVMVADTMTRPRCRKGCIQAIDYRSWGPMALVSLLPECGDRKETGEEIEFLEGIECSQYCCFDWGHGSFRYVDRNNGRSASLGLRLMK ...

  17. Protein (Viridiplantae): 351720716 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 6 3847:3116 uncharacterized protein LOC100527152 Glycine max MARSLVMIHPLPSISHIGFTVMSLMVCAIALLMCASHSRKWPKWISCYAFVEEPVIEFNNEAVINTCDERQEDGSLWQKNILMGGKCQLPDFSGVIIYDSDGNIVNPARTSPPLLTWK ...

  18. Protein (Cyanobacteria): 73947 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available barrel domain protein Calothrix sp. PCC 7507 MDIKRSGSQPSAKGQAEYFTGTVRVDPLFEAHDPARTSGASVTFEPAARTAWHTHPLGQTLIVTAGCGLIQRWGGAIEEIRPGDAIWISPSEKHWHGATATTSITHIAIQEWLDGKPVDWLEHVSDEQYEGIP ...

  19. Protein (Viridiplantae): 168040746 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available GGTMFPEGAEGYVQKLEKHIPFGTSAIRTALDLGCGVASFGAYLLDKEVLTMSVAPRDSYKAQIQFALERGLPAFVGMLGTQRLPFPASSFDLIHCSRCRISFSSFNGSYFIEMDR...PVPGPNTLGTIYDRGLLGVFHDWQVLTSLFCFLIPFSTYPRTYDLLHVSSVEALTTSQNRYLSVPSLCSLAEIMVEMDRILRPKGTVIIRDTPAMLARVSKVANGIQWNYEIFDGEPGATDRILIATKQFWKAEIAEPQ ...

  20. Protein (Viridiplantae): 302755490 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available EQYIPLSDGQIRTALDAGCGVASFGAYMLRKDVLTMSFAPRDSHKAQIQFALERGIPAFVAMLGTQKLPFPAFSYDLVHCSRCLIHFSAYNGSYMIEMDRLLRPGGFF...IGVLHDWCEAFSTYPRTYDFIHVSNMQSFTTQASTSCSLVDVMLEMDRILRPQGTILVRDTTKMVEKISKIAYALQWTTEVLTTEGGVLGKERLFVATKPFHT ...

  1. Protein (Cyanobacteria): 20524 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 375DRAFT_4878 Leptolyngbya sp. PCC 7375 MELYERIEQIIVTFRPAFSRNATFGWFVLLLWGALLTTQPPAVTSYLNALGLGAEYYHQALHWFHSSGYEMDRVCRRWGRWLSHQTDGYRLKGHRVYVGDGIKVSKEGRKMPGLKACIKSPITSVNQNGYGGIILVRWAF ...

  2. Protein (Viridiplantae): 302821216 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available ENQIQFALERGIPALVAALGTKRLPYPSRSFDAVHCSRCRVDWHEDGGILLREMDRILRPGGFFIYSAPPAYRKDKDFPEVWNILTNITESLCWKLIARHVQTAVWRK...ALLLQNNPVWIMNVVPSESSNTLNVVYGRGLVGTLHSWCESFSSYPRSYDLLHAYRVMSLYPGRKGCQIEDIMLEMDRLLRPNALAIFQDSSPAVQRILELAPRFLWVARVHRILEKDEQLLICSKKFWIVDV ...

  3. 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 ...

  4. Protein (Cyanobacteria): 316244 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available _3027 Synechocystis sp. PCC 6803 MLKLAGKKASALTCKKTKAKIGILEMDRQWYQSVKRFLCPSFEISAINFQDILFNNVDVGEYHSILVGCGIKYESIDISATLDLVTIIKKLSAKPPALLLITDCADSQITVQARSYLPQIDGVFAKDHDLALLLKVMKIIAKQKYFK ...

  5. Protein (Cyanobacteria): 42724 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available anothece sp. PCC 7425 MAITRWEPFRRIERWEPLREMETLRREMDRLFDRMIPFGDGEEGLLAFTPSVEMEETDEAINLRLEIPGMDPKDLDIQVSEESVSIRGERKSESRTEEQGTIRSEFRYGKFQRIIPLPAHIQTDQVKAENRQGVLHLILPKAEEERRKVVKVQID ...

  6. Protein (Viridiplantae): 302766834 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available LEQYIPLSDGQIRTALDAGCGVASFGAYMLRKDVLTMSFAPRDSHKAQIQFALERGIPAFVAMLGTQKLPFPAFSYDLVHCSRCLIHFSAYNGSYMIEMDRLLRPGGF...LIGVLHDWCEAFSTYPRTYDFIHVSNMQSFTTQASTSCSLVDVMLEMDRILRPQGTILVRDTTKMVEKISKIAYALQWTTEVLTTEGGVLGKERLFVATKPFHT ...

  7. Protein (Cyanobacteria): 319568 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available al protein Cha6605_1253 Chamaesiphon minutus PCC 6605 MTTSAAVRQKLVEALSLDLVGPDATADYHYQDEIISQSPSKWYLTGFLVPYEASVQDRSGDTADEGLEIDAPTSKSSED...ENTPETASARKALFPSSIGLSFLISDKTTSLDLEVYWGDYQPLKPDGIENKAKTDRWQRQRQLQRLTVTINDSTKPVTLDVPH

  8. 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

  9. 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

  10. Protein (Cyanobacteria): 341533 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available otein P9215_03981 Prochlorococcus marinus str. MIT 9215 MWSKIRLTIYGTTAIAGILWPFYFIIQFINLVRNGNIQGTFIDIGNAFFDDAWITPTSGFISADTAILLIAIFVFYAAEGKRLKLRFWGIYFPLTFIISLAFSFGAFMFIRELEINKELNETD ...

  11. Protein (Cyanobacteria): 99176 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available ILTPLPGIGINFDIVESRGPMIDPPIRSVEQIEKLHPLEPAESLPFIREILQTLRQEVGDRSTVLGFVGAPWTLAAYAIEGKSSKDYTVIKGMAFSEPAMLHQFLSKL...VDWTVDMAEARARLGSKVGVQGNIDPCVLFGSKDFIRERILETIRKAGNKGHILNLGHGVLQNTPEENVAFFFKTAKQADKLLS ...

  12. Protein (Cyanobacteria): 462892 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available I7407_2252 Geitlerinema sp. PCC 7407 MRFKLLVSGLVTAAAIALSGTGAEAQTLMRTGLMRNVLVDALANRSTVFSSGVLADLETDENFGGDYQQIFDYASGILNDYTVVDRGGVFPENAGIPRDRQLPRTDVVYTVFTLDNGNELFLYRSPLEDTARYFIRESVPFGG ...

  13. Protein (Viridiplantae): 15230093 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available VCRRDLFVGKFEVCGENNSSSNLSFIRENNSSANLKIYSSAKKRFVREIYSSAKKRFVEEIYSSANLRFVGENNSSANLSFIGQNNLSANLSFIRE...NNSSANLSSFLAIVSQTCEGNIRRKVCDGIASWSCSFGEIYSSKKRFVREIYSSAKKRFVGEIYSSANLRFVGENNLSANLSFIRENNLSANL...02:4271 uncharacterized protein Arabidopsis thaliana MTYTQFPRNCLANVRGKYSSQNLRRNSELVMFPRRDLFVGEEEVCRRDLFVGEEE

  14. Protein (Cyanobacteria): 440743 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available ocystis aeruginosa PCC 9809 MTTSPESQFLQALEMCQSLSNLTAQFSSIPCRIIEILSDISQEPRVLYSLLIKYSREVDSALVALDIYAKSADNWRVKDRDKTCSLGFGVKDHCTILSCLLNFGKRPFSFISYTGNFASEAIIFELLKDWKNLDIAPFFEEKMQEFIREAKIA ...

  15. 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 ...

  16. 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 ...

  17. Protein (Viridiplantae): 168042943 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available ens subsp. patens LNLRDCSRLTSLPNELGNLSSLTTLNMSKCRSLASLPNELGNLTSLTSLNLSGCWELTSLPNELGNLTSLTSLNLCDCSRLTSLPNELGN...LTSLTSLDMSKCPYLTSLPNELGNLASLTSLNLSGCWKLTSLPNELGNLTSLAFLNLCDCSRLTSLPNELGNLTTLTSLNISGCLKLTSLPNELGNLTSLTSLN...LSRCWKLISLPNELGNLISLTSLNLSGCWELTSLPNDLNNLTSLVSLNLFECPSLIILPNELGNLTTLTSLNISECLKLTSLPNELGNLTSLTSLN...LSGCWDLTSLPNELGNMTTLTSLNISGCQKLTSLPNELGNLTTLTSLNISRCQKLTSLPNELGNLTSLTSINLCDCSRLKSLPNELSNLTTLTSSNISGCLKLTSLPNELGNLISLISLN...LSGCWELTSLRNELGNLTSLTSLNISGCQKLTSLPNELGNLTSLTSINLRHCSRLKSLPNELGNLTSLTSLNISGCWELTSLPNELGNLTSLISLNLSRCWELTSLPNKLSNLTSLTS ...

  18. Protein (Cyanobacteria): 321356 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available ein MC7420_5364 Coleofasciculus chthonoplastes PCC 7420 MPQRLSARFTIQSLNPPLQFTLLTHQPLHSHQLFLKKGRVLPQTLSARFTIKSLN...PPLQFTLLSHHPLHSHQLFLKKGRVLPQRLSARFTIQSLNPPLQFALLSHHPLHSHQLFLKKGRVLPQRLSARFTIQSLNPPLQITLFSHQPLHSHQLFLKKGRVLPQRLSARFTIQSLN...PPLQITLFSHQPLHSHQLFLKKGRVLPQTLSARFTIKSLNPPRQITLFSHQPLHSHQLFLKKGRVLPQTLSARFTIKSLN...PPLQFALLSHHPLHSHQLFLKKGRVLPQTLSARFTIQSLNPPLQFTLLTHQPLHSHQLFLKKGRVLPQTLSARFTIQSLNPPLQITLLSHQPLH

  19. Protein (Viridiplantae): 168043922 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available ens subsp. patens TSLTSLHISQCHELRSLPNELGNLVSLTSLNLVNCWKLTSLPKELVNLTSLTSLNLSGFWEVTLLPNELGNLTSLTSLEISGCSKLTSLPNKLGNLTSLTSLN...LSGNSSLTSLPNEMGNLTSLTSLNLKRCSNLTSLPNELGNLASLTSLKLSRCSSLKSLPIELSNLTSL...PSLSLSGCWKLTSLPNELGNLTSLTSLNLSGCSNLTSLPNELGNLTSLTSLKLRRCSNLTSLPNEFGNLASLTSLNLDGWKNLTSLPKVLVNLTSLTSLNLSRCSSLTSLPNELGNLASLTSLN...LSGCWRLRSLPNELGNLTSLTSLHISKCWELTSLPNELGNLTSLILLNLSECSNLTSLPNELCNLTSLISLDLSGCSNLTSMPNELHNITSLTSLNINE ...

  20. Protein (Viridiplantae): 159486336 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 7735 hypothetical protein CHLREDRAFT_107425, partial Chlamydomonas reinhardtii MASNIVFCSLNLASSSVFCLLNLASSFVFCSLNLASSLAFCSLN...LASSFVFCSLNLASSLAFCSLNLASSFVFCSLNLASSFVFCSLNLASNKLFCSLNLASNIVFCSLNLASSLVISTA ...

  1. Protein (Cyanobacteria): 322756 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available ber protein (repeat/shaft region) Coleofasciculus chthonoplastes PCC 7420 MSLNPPLQLSLNPPLQLSLNLALQLSLNPPLQLSLNLALQLSLNPPLQLSLNLALQLSLNLALQLSLNPPLQLSLNLALQLSLNPPLQLSLNLASTIVPKPGFYNCP ...

  2. Protein (Cyanobacteria): 321355 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available ein MC7420_5449 Coleofasciculus chthonoplastes PCC 7420 MWASAHQRNADTTNVKYTFNLNQGRVLPQTLSVRFTIKSLNPPLQITLFSHQ...LLHSHQLFLKKGRVLPQRLSARFTIQSLNPPLQITLFSHQLLHSHQRPFNSYLKKGRVLPQRLSARFTIKSLNPPLQFALLSHHPLHSHQLFLKKGRVLPQTLSARFTIKSLN...PPLQFTLLTHQPLHSHQLFLKKGRVLPQTVSAIFSIKSLNPPLQFTLLTHQPLHSHQLFLKKGRVLPQTLSARFTIKSLNPPLQITLFSHQPLHSHQRPIQLIP ...

  3. Protein (Cyanobacteria): 321354 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available ein MC7420_5443 Coleofasciculus chthonoplastes PCC 7420 MPQTLSTIFSIQSLNPPLQITLFSHQPLHSHQLFLKKGRVLPQTLSARFTIKSLN...PPLQFTLLSHHPLHSHQLFLKKGRVLPQTLSARFTIKSLNPPLQITLFSHQPLHSHQLFLKKGRVLPQTLSARFTIQSLNPPLQITLLSHQPLHSHQRPIQLIP ...

  4. Protein (Cyanobacteria): 327034 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available n SPLC1_S201560 Arthrospira platensis C1 MSSLDSCWVSLNLTNKFVLGFTQPTFWVSLNLTNKFVLGFTQPTFWVSLNLTNKFVLGFTQPTFWVSLNPTNKFVLGFTQPTFWVSLN...PTNKFVLGFTQPTFWVSLNPTNKFVLGFTQPTFWVSLNPTNKFVLGFTQPTFWVSLNLTNKFVLGFTQPTFWVSLNLTNKFVLGFTQPTFWVSLNLTNKFVLGFTQPTFWVSLNLTNKFYL ...

  5. Protein (Viridiplantae): 168015435 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available ial Physcomitrella patens subsp. patens NNNNFNQSFIKSLNNNNFNQSFIKSLNNNNFNQSFIKSLNNNNFNQSFIKSLNNNNFNQSFIKSLNNNNFNQSFIKSLNNNNFNQSFIKSLN...NNNFNQSFIKSLNNNNFNQSFIKSLNNNNFNQSFIKSLNNNNFNQSFIKSLNNNNFNQSSNV ...

  6. Protein (Viridiplantae): 159490560 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 7735 hypothetical protein CHLREDRAFT_110145, partial Chlamydomonas reinhardtii MASNIVFCSLNLASSSVFCLLNLASSFVFCSLNLASSLAFCSLN...LASSFVFCSLNLASSLAFCSLNLASSFVFCSLNLASSFVFCSLNLASNKLFCSLNLASNIVFCSLNLASSLVISTA ...

  7. 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

  8. 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 ...

  9. 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 ...

  10. 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 ...

  11. 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 ...

  12. 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 ...

  13. 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 ...

  14. 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 ...

  15. 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 ...

  16. 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 ...

  17. 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 ...

  18. Protein (Viridiplantae): 357441081 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available :4956 3880:4956 PGPS/D12 Medicago truncatula MNIFGRSSPPKWSAKLCGCGENPGTCLITCCLPCITFGQIAEVVDEGRSSCAMQGCVYGLLMTITCHWLYSCLYREKLRAKYGLPAEPCCDCCVHFCCDACALCQEHAELKARGFNPSKGWIGPPHAPPRMPPTMFR ...

  19. Protein (Cyanobacteria): 12372 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 01 Synechocystis sp. PCC 6803 substr. GT-I MPLNREEIIQTLKERGLRVTPQRYGVYANLLQRRDHPSAEQLLFDLNQAAPTSSQATVYSSLKALQSVGLIREVLLEEGVCRYDANVEPHHHFCCRHCGAIEDVDWEELPAVDLGKLRVGLKAERYEITVHGVCENCGD ...

  20. Protein (Cyanobacteria): 12515 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available lator, Fur family Calothrix sp. PCC 7507 MQHQANAIVQTLKSKGLRVTPQRFAVYANLLSRTDHPTVDQILTELNKDFPVSSQATIYSSLQALREVGLVREVLLEEGVCRYDANVGPHHHFCCCQCGAIEDITWDTFEYIQLQSLRPGLRGKTYEVTVQGICDRCDPE ...

  1. Protein (Viridiplantae): 159491002 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available hypothetical protein CHLREDRAFT_127770 Chlamydomonas reinhardtii MFPGMPAGPGGPGGAGAFDFSALQSALNDPSIKQMAEQIANDPSFKEIAKQMQESFGAMMGGMP...PPGGAPGGDARAAGALPGGMPGMPGMPGMPGMPAGMPGMPGMPGMPGMPGMPGGMPGGMPGMMPGMMPPGFDPSKYMEAMQGMFQNP

  2. Protein (Viridiplantae): 302849879 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available VGRFMAFDRHMNLVLGDSEEFRRLPPKKGKSEEEREERRVLGLVLLRGEEIISLTIEGPPPNEEMRTDRSQVAPGGPGVARAVGRGMPAAAPGQAPAGLAGPARGVGG...PAPGMMMPRPQVSAPPVPRPGPPTPGVPPPRPGMAPPGMPPPGMPPPRPGMPPPPGMGPPGMMPPPGGMPPPGMPPRPGMPPPGMPPPGMPPPGMP...PPRPGMMPPPGMPPPGMPPPGMPPGMMPPGMGPPGMPPRPGMPPPGMPPPGMPPPGMPPGMRPPGQ ...

  3. Protein (Cyanobacteria): 471778 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available VQFLVLSNSGAPLSLEENRTVTVPVAARAGGLTIPGGALLVGRFERTGEASGALNIESLVIGQNVYAVRATSTPIPGLLRRTGTATPRYPGREASGTLFEAGGDLLGIPVHSRQARAATSLLGALFGAAAPPAPERSTGTLAASLEPMQTLGVQFLGEVDFDSPIAQLPNGPADLNGSW ...

  4. 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

  5. Protein (Viridiplantae): 145354199 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available DDDDAEGLRVENGETMDAFLTRHGLSASLRAAVTYALALQTRADCAAATALEDLKVYILSVAKYGPQTGACLIPVYGAGDIPQAFCRVGAVDGATYVLRQGVRELDASTTISAAISTGGQEIRARKFIVPAPE...RSSGPLLVHAVCILDAPLVAEYGQMLVVFPPLSAADAQTAVIRALQVGSHTGCCPEGKYLLYLSTVVDDVNVDPYAGLNAALD

  6. Protein (Cyanobacteria): 109031 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available LQSHSRANVARGLEILDNTLDLGRKRSLLIVLDRRSTLEKLQSLSDLVTYEPMTPSDRLRYLMDRQHFLSDWGLACCFHLAYRARWSIPAEQTLACLSHPIGFVREAVLSYLSMASPRTLREILPMMANDPNRLVAHQVARLMQEMGISAPGANAASSPRSPAPERSTSTMQFRPT ...

  7. Protein (Cyanobacteria): 175822 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available agen triple helix repeat-containing protein 'Nostoc azollae' 0708 MRLIEDGEDGEDGEDGEDGEDGEDGEDGEDGEDGEDGEDGEDGGEIFLMPYALCPMPYALCPMPYALCPMPYALCPMPYALCPMPYAQNQDFSHPNRESSVKLFSSVAPKP ...

  8. 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

  9. 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

  10. 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

  11. Protein (Cyanobacteria): 80731 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available function DUF29 Dactylococcopsis salina PCC 8305 MQTHQVSNQPQLYDQDYYLWLKKTQEQLATGNFSALDVANLIEELADMGKSEKRAVESN...LTILIMHLLKYQYQPQKRSNSWLFTIREHRRRLEKLFKDSPSLKRYFNEVLNECYQDARELAAAETGLPLEMFPTQTPFTTENILNPAFLPSTNDDNNSNI ...

  12. Protein (Cyanobacteria): 311090 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available tein Chro_5799 Chroococcidiopsis thermalis PCC 7203 MKIEKQKKNNRVTVRFNDRDYTEVKKKAKKSNTTVAEYIERSALRRELPTPPTINQVLVYQNLGKARELTFTIRNTCKLYGDRTVPTTEIMSLLEAMENHIQAAGMEAYGLGKIRTNIETATKNKEEVA ...

  13. Protein (Cyanobacteria): 236201 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available otein tlr1675 Thermosynechococcus elongatus BP-1 MRQSLSMTRLATGCPMRQLNFLMIFVIGLGLVLFSIQNTEPVSIKFFEGKVIQAPLCIELIIAMGIGAVFAWVFNVWVQVQRLFTIRVEMEARDEQIAHLEQDVERYKAALEEQQRLLPSVSSASTEK ...

  14. Protein (Cyanobacteria): 322998 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available in Tery_4629 Trichodesmium erythraeum IMS101 MLYDKQQKKSLCNKYFPKLLTVHLEDKATEIYLQKFIYRNLSTDIYLQKFIYRHLSTDIYLQKFIYRHLSTDIYLQTFIYRNLSTD...IYLQKFIYRNLSTEIYLQTFIYRNLSTEIYLQTFIYRHLSIEIYLQKFIYRHLSTDIYLQKFIYRHLSTDIYLQTFIYRHLSTEI

  15. Protein (Viridiplantae): 297720699 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available SASAGASADVGTDVGTDAGASADSRTSASTSTSTSADAGADVGTDVSSDASASSSADSRTSASASTSTSADASADVRTDVSTD...AGASASADSCASASASTSADARTSASTDVSTDANASSSADAGADASTNASADLRTNASTDLRTDASTSANADASTDLRTDASTSANADASTNLRTDASTDVRTNASACSNAGASTDLRTDASTD...LRTYASADASTDAGASANADVSSDASADASASASTSASASTGAGAGAAVQAEAGLAGDADVGLDGRRVVAEQQKQRQHRHAQHRRPHLAGPRRHRRCFLLRRIGSFIELGLLLQS ...

  16. 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

  17. 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 ...

  18. 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

  19. Protein (Cyanobacteria): 260028 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available ARSAKVQRLEEILEEVIEAGDRALLFTQFAEWGHLLKAHLEQRWKQPVPFLYGNTSKAERQAMVDRFQEDPRGPQLFLLSLKAGGVGLNLTRASHVFHIDRWWNPAVENQATDRAYRIGQQNRVMVHKFITSGSVEERIDRMIKEKSKLAEDIVGSGEDWLGGMDVSQLKDLVTLSED ...

  20. Protein (Viridiplantae): 357442357 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 3137 3880:13137 hypothetical protein MTR_1g087730 Medicago truncatula MEGYGYGSDHGSFGSERRIEIVSGRSYGFSQSYYVGRSESTGEVTRASHDGAAPVAKPWSFNDAATKRRKRIARYKVYAVEGKVKATFRNGIRWIKHTCSRIVHGY ...

  1. Protein (Cyanobacteria): 36700 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available otein CWATWH0003_4348b3, partial Crocosphaera watsonii WH 0003 YMGWRSRFATDPEVVSKTRASHTQLAPWVFLFVALGYTGGVLSLVMQNHDLLSSGHFWTGTGALGLMAVSAITPFIGFGGEKKEAYRAFHAYLGAVVAIVFIAHGILGLKLGLSL ...

  2. Protein (Cyanobacteria): 260023 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available ARSAKVQRLEEILEEVIEAGDRALLFTQFAEWGLLLQAHLQKRWRQEVPFLYGSTSKTERQAMVDRFQEDPRGPQLFLLSLKAGGVGLNLTRASHVFHIDRWWNPAVENQATDRAYRIGQQNRVMVHKFITSGSVEEKVDRMIREKSKLAEEIVGSGEDWLGGLDVGQLKDLVALEE ...

  3. Protein (Cyanobacteria): 207811 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available bya sp. PCC 7375 MVAPITISPATRNDIPLLFELVMALAEYEDLAHEVSGAPEDLEKYLFGDSPKAHAIVARIDGAPAGFALYFFNFSTFLMKPGIYLEDLFVLPGYRRRGIGTAIFQYLAQTALAKGCGRFEWSVLDWNQPAIDFYRSKGAVMLNDWRTCRVAGIALEELATSEQ ...

  4. Protein (Cyanobacteria): 173276 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available QKALALTELRCTFEGRSLVPDVAVFEWSRIPTDGNGEIANRFESYPDWIIEILSPDQSPNRVINKIIFCINQGTKLGWFIDPNDKSVMVFQPNRLPEVKYDTDILPVLDVLGNCQVNAADIFSWLKVK ... ...rotein Ava_0761 Anabaena variabilis ATCC 29413 MTLSTQVSFHPSLDEFLKLPETKPASEYIDGRIYQKPMPQGKHSILQTRLSSNINQVGEPQ

  5. 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 ...

  6. Protein (Viridiplantae): 302822432 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available endorffii ILELGCGNSRMSEDMYQDGFTDITATDLSPVAVESKRWRCFDLNYGIKVLVADIMDMPFKDASFDIVIEKGVMDVLFVDSGSPWDPEPQTRARVDVTL...KEVHRVLGANGPHFRRPFFEASGFEWSMEYSTFGDSFHYYFYTLRKVVSFLPGQTFKHSNIVLPGNGQKGFASRLDGNHKH ...

  7. 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

  8. Protein (Viridiplantae): 356546122 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available HDFERLSTPKIVEARDVLLQKLGERKNLQAGEPENPRTVDTYQEGREDRGTESISFEQNQILTEVTNAVEGLEVDDTVSTEKWLEDTDIDASSLASCTKLQQEEDVSFSDLEDDRSYSSDKLSGYREAHDIRGSSPEGATSDWVRLRESSERDGRKKVIRLKGKDSEDESNDWLTVDDFN ...

  9. Protein (Viridiplantae): 168044488 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available ens subsp. patens MTRCTSLISLPNEIANLSSLEELYLNGCSSLKSLPNELANLSNLRRLDLRYCSSLTSLPNELANLSSLKELDLSSCSSLRRLPNELENLSSLIRLDL...SGCSSLISLPNELRNLSSLEELDLSHCSSLINLPNELANLSSLTRLVLSGCSSLTSLPNELENLSSLEELRLNNCSSLTSLPNKLRNLSSLEELDL...SHCSSLTNLPNELANLSSLTRLDLSGCSSLTSLPNELTNLSSLTRLDLSGCSSLTSLPNELTNLSSLTRLDLSGCSSLTSLPNELTNLSSLTRLDL...SGCSSLTSLPNELENLSFLEELGLNHCSSLTSLPNELTNLSSLTRLDLSGCSSLTSLPNELTNLSSLTRLDLSGCSSLTSLPNELANISSLTTLYLRG...CSSLRSLPNESVHISSLTILYFHGYVSLTSLLNELVNLSSLMTLDLNGCSSLKSLPNELTNFTSLTILDLSGRLSLTSLPNEFTNLSSLKELVLSHCSSLTSLPNELTNLSSLKELDLSSCSSLRSLPNELANLSSLTRLDL ...

  10. Protein (Cyanobacteria): 71748 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available othetical protein gll1203 Gloeobacter violaceus PCC 7421 MERLSFLALAAIAAGVIQVPAAMARPTAIERSAFNSRVRDAVVSRWRIPLVERTTTVDVTARWDLQAPMVLLVLLWWAAPGTGTRGLAAGRSALRDNGRAVLVGTPTYGKGAIQQDYTCPIAPG ...

  11. 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 ...

  12. Protein (Cyanobacteria): 377866 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available MARENKEELDYYFVVVSAAGCVADWAAPRAKATEIVAINSMYSGKFSGQTPKIKKINLVQVKDEKRKLLVEETKEKLAFATLMGSQSTYTQQTCQNFKQFQHALKLKGYEETVY ... ...an7822_4541 Cyanothece sp. PCC 7822 MTKLTIGLGAVILGIGLWGCSNVSNQMTPPMTQVTVQICGEQLVRNKIEEDCLSNTGVYWGEVTEKDIKLVG

  13. 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 ...

  14. Protein (Cyanobacteria): 449752 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available otein MAE_27120 Microcystis aeruginosa NIES-843 MLAKPIMGLGFVNVWLTGIGVIGGVPIRVIAFKTLTAAKPRPANSPVGVPTNPVVVPGVRVGLVVPHEPAVAFPPTAIILAAWAAPAKLRAATLAAIATVPVASCLEMLVIILSRLLREHLTYAISNYT ...

  15. Protein (Cyanobacteria): 456819 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available o7375DRAFT_0719 Leptolyngbya sp. PCC 7375 MQLSPVHAFETPPGLESAYQQVLSDWSAPLLPAEIPFEFTGVETSSSASHHLLSIDINEFQTVAIAAGEGSKRIDTLSSEPVQQIALNNQVVGYFLPAGETDEEPPELSFLIEEINYYVGGWAAPDDLIAIANSMIDNQ ...

  16. Protein (Viridiplantae): 159489270 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available TLWLWRPRVQAGQGAGGGAAGTAAAAPGGGGGAGAGHAARPPATNRRQSGASNSSADTVAPLRPTAVHQAAAAAVAASGPAAAPSVSVSGGNGSSAAPGRRTGGGVSG...DVDAVGWVAVWVVAKANWQTVQAQTPVQSPAALRQVVLLFMRPPCLHRRVQAGQGAGGGAAGAAAAALGGGGGAGAGHAARPPATNRRQSGASNSTDGSEGPTGAGREAAGASRACGGIWRRRGRG ...

  17. Protein (Viridiplantae): 224138406 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available SGLQPWFGLRADMDALPIQEMVEWEHKSKNNGKMHACGHDAHVTMLLGAAKLLERMKDELKGTVKLVFQPGEESYGGAYHMLKEGALDNFQGIFGLHVAPEIPVGTVDSRPGPMLAASGRFIATIKGKGGHAA...RPQDTRDPVVAASFAILALQQIVSRETDPLDARVVSVGFVEAGQAGNVIPETVRFGGSIRSMTTEGLVSLQQRVMQIVEMQAA

  18. 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 ...

  19. Protein (Viridiplantae): 159467908 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available EQAADDSSTLTAVPVVEGAGDIIPSHPLPEDTERTVSALGWLPPVQVLTEAPEPGAWCFTAPLWGNPLLTPSPAAASGEQEEEDSGSDGETAVEPVPAGVARRTQGRG...LDYRHRTLRACARLVTIGDLVRAHAARPPAAAAVDWEGWLRDYLAPSDGRRRRRGPTLAALQGLVGDIPPSWWSAAQAHAA

  20. Protein (Cyanobacteria): 229984 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available LNNSTISGNYATNEGGGIFNVSGTINISNSTISGNYAMSLISGGGGINNFFGTINISNSTISGNYASDSAGGIYNGAGTINIS...QQVVNISGLTITQGNSSGNGGGIENIENLTLSNSTVSGNLAGGFSGGIFNGGNLTLSKSTVSGNSATNGGGIFNVGGTTSI...DENDGIGVGGISLREALGAIADGGTITFADSIANGTIILNGTELVINKSVTIDGDTDNITVSGNNNSGVFNIDDGDINIQQVVNISGLTITKGRTNFGGGIDNRENLT...SNSTVSGNSITYSAGGIGNWGGTINISNSTVSSNSAGLNGGGIFNLAGTTNISSSIISGNSATSGDEVYSNSGTVTADNNNLFGNSSQSNSDAFVNFTSGANDINATT

  1. Protein (Cyanobacteria): 254399 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available QAEALPYANGTFSGVLCTLAIHHFNTLVPAFKEIYRVLSHGCFVLFTATPEQMSKYWLVEYFPEAMRKSAEQMPRLEEVRNALNQAGFNSIDIEVYSVSKNLQDLFLYSGKHRPELYLDSNVRSGISTFALLASRDEITTGCQRLAADIECGMITKIIKKYDHAQGDYLFLIANKIN ...

  2. 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

  3. Protein (Cyanobacteria): 266185 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available IRFLLDEILKSFSENTLVKDKKPVLIIKGLENSIGLDEYPPILQNLNFVRDAFSHQVPYPILFCLPSSTTTRFAKFAPDFWAWKSGIFKFRSLPEAERSQIAFPTLSL...LQKLGDLYRKKKYGERAENLELAIAAYKLSLEVYTRDAFPYEWARTQNNLGIAYSDRIRGERAENLELAIAAYRQSLEVRTRDAFPVEWARTQNNLGIAYSDRIRGGRAENLELAIAAYRQSLEVRTRDAFP...VEWAMTQNNLGTAYSDRILGDRAENLELAIAAYYQSLEVRTRAAFPVEWARTQNNLGNAYSDRILGERAENLELAIAAYRHSLEVLTRNAFP...YEWATTQNNLGIAYRSRILGERAENLELAIAAYRHSLEVRTRDAFPEDWARTQNNLGIAYRSRILGERAENLELAIAALNQSLEVLTRDAFP...EDWARTQNNLGTAYSDRILGDRAENLELAIAAYKLSLEVYTRDAFPYEWAGTQNNLGNAYSDRILGDRAENLELAIAALNQSLEVYTRDAFP

  4. Protein (Cyanobacteria): 266255 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available PIFQKYQDQLDLEFTETLTEWFHSQLALNAIITNKDLARIWGNFVIDIWRFPLDFDFAEIVALWFHSQPNLNKIRKNKDLARNLNNFAIDIQQFPLGSRANNLEIAIAAYQAALKVYTRTAFP...EDWARTQNNLAVAYRDRIKGERANNIEEAIRYHQAALEVFTRTAFPEDWARTQNNLGIAYSDRIKG...ERADNMEEAIRCYQAALEVFTPTAFPEDCARTQNNLGEVYRNRIQGERADNIEEAIPYYQAALEVFTCTAFPQYWATTQMNLGSAYLYRIRGERADNIEEAITALQVALEVFTRTAFP...QYWAMTQGNLGNAYWSCIRGERADNIEEAIRCYQAALEVYTRTAFPEDWARTQMNLGNAYCNRIKGERADNIEEAIPYYQTALEVFTRTAFPEDWART...QMNLGNAYCNRIKGERADNIEEAIPYYQTALEVFTRTAFPEDWARTQMNLGNAYCNRIKGERADNIEEAIPYLQAALEVYTRTAFP

  5. Protein (Cyanobacteria): 266190 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available QVVNIEEYQEFLLEVLQAEYESDDPTVVYPILERRQYLLDDTFAQLLQQYARNVFSQRKAEEVAVIAGVIQNLCIDIKNFPLGSRANNLEIAITGYQTLLEVYTRDAFP...EKWAMTKNNLGIAYSDRILGERGDNLEKAIAAYNLSLEVYTPTAFPYEWARTQNNLGGAYNDRILGGRAENLEFAIVAYNLSLEVYTRKAFP...EDWARSQNNLGEAYRNRILGEKADNIELGITALNQSLEVRTREAFPEEWARTQNNLGLAYSDRILGERAENLELAIVAYNLSLEVYTREAFPEDWA...RSQNNLGLAYSDRILGGRAENLELAIAAYNRSLEVYTREAFPEKWAGTQNNLGNAYLYRILGERRLNLELAIAAYKLSLEVYTRDAFPYEWARSQNNLGNAYLYRILG...ERAENLELAIVAYNLSLEVYTREAFPEDWARSQNNLGLAYSDRILGGRADNLELAIAAYKLSLEVYTREAFPEKWAGTQNN

  6. Protein (Viridiplantae): 302817905 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available PLPSCNENPFRHSKPAVADDQGSSAAPPPHPAFPGFGNFPPFFPGAIPPTANKVAPPPHPAFPGFGSFPPFFPGAFPPVDHSTASKVAPPPHSAFPGLGWNFPPFVPGAFP...PVDHSTAFKVAPPPHPGFGYPLKPAPHGSNKAAPPPFANSPPSFPGAFPPHPSSSKPGSAPPTHGSHSTQAPPPFHGTKKHHHP ...

  7. Protein (Cyanobacteria): 465646 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available othetical protein N9414_12533 Nodularia spumigena CCY9414 MGSGAFPDFGGDLVSPSENSLLITEMGSGAFPDFGGDLVSPSENSLLITEMGSGAFP...DFGGDLVSPSENSLLITEIGSLAFPDAGGDLVSPPENSLLITEIGSGAFPGAGGDLVSASENSLLITEIGSGAFPGAGGDLVSPSENSLLITEIGSGAFP ...

  8. Protein (Viridiplantae): 302770641 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available IARPWPFYSAGPFFFQPPEPLPSCNENPFRHPKPAVADDQGSSAAPPPHPAFPGFGNFPPFFPGAIPPTANKVAPPPHPAFPGFGSFPPFFPGAFP...PVDHSTASKVAPPPHSAFPGLGWNFPPFVPGAFPPVDHSTAFKMAPPPHPGFGYPLKPAPHGSNKAAPPPHSTPFPGFANSPPSFPGAFPPHPSSSKPGSAPPTHGSHSTQAPPPFHGTKKHHHP ...

  9. Protein (Viridiplantae): 115439729 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available VTYSFEHNHSATVPRAQNRQAAPQKPKAQACSPPEPVVEVEPEETHQYGVTAGPATGGGGGAAAIEVRDEFRWLYDVVSVPATSTSPSDIDAADEMQLYDQPMFFGGAVVGTAALLPDEFGDVGGLGGEGLGEEEALFEGLGELPECAMVFRRRAGDGLEMGGGVKIEQPAESTAMT ...

  10. 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

  11. Protein (Viridiplantae): 15235180 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available protein Arabidopsis thaliana MMVLYCGRKLLVVLMVTAFVFSGSAEAWSWSWGSGQSGSNGGWGWRSGNSGGSSGSGSGGSDSNSGGSSWGWGWSSDGTDTNWGWGSSSGSNHS...SGTGSTHNGHSSGSNHSSATGSTHNGHTSTGSNHSSGNGSRHNGYSSGSNHSSSTGSNHSSSTGSTHNNHSSGSNHSSILGSTHKNHS...SGSNHSSIVGSTHNNHSSGSNHSSITGSTHNHTAPIPAGRKIAVTVWKNGYGYTEWTAKHAPFYVSDVLVFKYNNDDQTQSKTKHR

  12. 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

  13. Protein (Viridiplantae): 224114153 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available redicted protein Populus trichocarpa MENRGRMGHLSPMIHAIAICLVATSVVAYEPYYYKSPPPPSQSPPPPYHYSSPPPPKKSPPPPYHYTSPPPPKKSPPPPYHYSSPPPPKKS...PPPPYHYSSPPPPKKSPPPPYHYSSPPPPKKSPPPPYHYSSPPPPKKSPPPPYHYSSPPPPKKSPPPPYHYSSPPPPKKS...PPPPYHYSSPPPPKKSPPPPYHYTSPPPPKKSPPPPYHYSSPPPPKKSPPPPYHYTSPPPPKKSPPPPYHYSSPPPPKKSPPPPYHYSSPPPPKKSPPPPYHYSSPPPPKKSPPPPYHYSSPPPPKKSPPPPYHYTSPPPP ...

  14. Protein (Cyanobacteria): 324054 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 472DRAFT_2939 Cyanothece sp. ATCC 51472 MKISLIFLTLPLLFLITLLSSCNRSDFSNSIKSQSLIKQNNSQNSINLNQTCTNKKVGYQVNYPQDWQ...TNSGNVMNDCQVFDPTYAKVPEQTESISKAIYLRVEENAPFDLISQENVGEQHLSKQTLTIDSYQAVAVESKSTGRAMLPKGQRNYSYIVDLGDRTLIATTYDVPDNNYAKNKQILDSMLKTIEFNNNELK ...

  15. Protein (Cyanobacteria): 303920 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available TGGSVPSPSTGNYVVFVNSSSQALLDIMRTIDPSVGFLNFEGRTVITLGTFTGATEAKQRLQQFQALGITGFAKDTVDGRLIPSLELPSPFANTPQPIPTTYNRGYYLAIPSFGQDVPALTSVLTRFDLQGGQVQSRSLPLGNFVVVGPYAQSSQLNTVLQTLRKAGLQTVRIYFGG ...

  16. 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 ...

  17. Protein (Viridiplantae): 18395518 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available QTGLMGKSLIEFQSNKGDVLPAHKFGNHDVVVLKLNKSDLGSSPLAQGVVYRLKDSSITVVFDEVPEEGLNTSLRLEKLAN...VDNIVERLVPHKVKLVRVGHPARLLPQVLDSALDAQVLKGDNSGLANDIRKEMKALNGKLLKAKDKNTRRLIQKELRTLGKEERKRQQLAVSDVIKNADVILTTLTGA

  18. Protein (Viridiplantae): 18402126 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available RRVLLETLASQLPPQTIRFSSKLESIQSNANGDTLLQLKDGTRFLANIVIGCDGIRSKVATWMGFSEPKYVGYCAFRGLGFFPNGQPFQQKVNYIFGRGLRAGYVPVS...ATKVYWFITFNSPSLGPQMMDPAILRKEAKELVSTWPEDLQNLIDLTPDEAISRTPLADRWLWPGIAPSASKGRVVLVGDAWHPMTPNLGQGACCALEDSVLLANKLASAINGGTESVEGAMESYRSERWSQVFRLTVLANLVGKLLQSDNPLVCSVRDNIVSAMGKSSRTNDGTHKL ...

  19. Protein (Viridiplantae): 18394621 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available tetraspanin11 Arabidopsis thaliana MFRVSNFMVGLANTLVMLVGASAIGYSIYMFVHQGVTDCESAIRIPLLTTGLILFLVSLLGVIGSCFKENLA...SQIADAFYHKNLSPIQSGCCKPPSDCNFEFRNATFWIPPSKNETAVAENGDCGTWSNVQTELCFNCNACKAGVLANIREKWRNLLVFNICLLILLITVYSCGCCARRNNRTARKSDSV ...

  20. Protein (Viridiplantae): 15228000 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available GVLPMFAVVFIGYWAYGSSTSPYLLNNVNGPLWVKALANISAILQSVISLHIFASPTYEYMDTKFGIKGNPLALKNLLFRIMARGGYIAVSTLLSALLPFLGDFMSLTGAVSTFPLTFILANHMYYKAKNNKLNTLQKLCHWLNVVFFSLMSVAAAIAALRLIALDSKNFHVFADL ...

  1. Protein (Viridiplantae): 15236089 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available e 43 Arabidopsis thaliana MSVSIPVLMKRLCLYNSLSLFLFHLFPSPSLALSFSVELNLLKAQMVWANAKMRLALSLVTVFFGISLANLEVGFYSNTCPQ...AESIVKRVVSGAALSDPNLPAILLRLHFHDCFVEGCDGSILVNNGAISEKNAFGHEGVRGFEIVEAVKAELEAACPGVVSCSDIVALAARDAISLAN

  2. Protein (Viridiplantae): 15221544 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 1-aminocyclopropane-1-carboxylate oxidase-2 Arabidopsis thaliana MESTKIAPSFDRASELKAFDETKTGVKGLVDSGISKIPRIFHHSSVELAN...PDLTFGTSKHSDGSFLTVLLPDNIEGLQVCREGYWFDVPHVPGALIINIGDLLQLITNDKFISLKHRVLANRATRARVSVACFFHTHVKPNPRVYGPIKELVSEENPPKYRETTIRDYATYFNGKGLGGTSALLDFKV ...

  3. Protein (Viridiplantae): 42571955 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available YINSTMPKLSGLCSLNFSASESLIQTTSHNCWTVFAPLLANVMCCPQLDATLTIILGKASKETGLLALNRTQSKHCLSDLE...QILVGKGASGQLNKICSIHSSNLTSSSCPVINVDEFESTVDTAKLLLACEKIDPVKECCEEACQNAILDAATNISLKASETLTDNSDRINDCKNVVNRWLATKLDPSRVKETLRGLAN

  4. Protein (Viridiplantae): 357508099 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available ERSDRYHDRSSSERSDSYQERSSVEKADHDRYHDRSSSERSDRYHDKSTSERSDCYEKRSSAEKADRDYDHDKSPSERSDR...YRVKCSSERSDRYHKRSSAEKADHNRYHDRSSSERSDRYHDRSSSERSGRYQERSSVEKADHDRYHDRSSSERSDRFHDKSTSERSDRYKKRSSAEKADRDYDHDKSPSERSDHYRVKCSSERSDRYQDRSSTEREHSNRSSTKSDKHSRKRKERDESSRRWEKFSRYSPDED ...

  5. Protein (Viridiplantae): 302767038 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available oellendorffii APNVYTYNTVMSALCKAGRLDQAHRLFGVMLASDSTPPNAITYRALIHGLCLKMELERAVLLLDAVYFKLSWLVPATYLIIRFKACHERGNLRA...PDIYTYNILFEGLSRHGLWRFAYKLLPRMNQDGVLPDAVTFNSLINGLVEDNRYHRAVTLIQEMVSRGCDPNAITYTILLKWLARNARADECVELFQRLLDRKLAPNV...YTYNTVMSALCKAGRLDQAHRLFGVMLASDCTPPNAITYRALIHGLCLKMELERAVLLLDAMAKRDCAPDVACYGTIVAAFCKQGRIDEAFELLERMPFAGDKVMFRTLVRALCK ...

  6. Protein (Cyanobacteria): 74944 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available in tlr1014 Thermosynechococcus elongatus BP-1 MCSVGLLLVPALLPYSLAQTSPRTDVIAPWEITTYARVVLEIEPIRQKYYRQAQAAFQGQVPSNACFGMNPQHIPSGLEAICASYGWEAIQVLKKYNMSLEQFNAITLRAQQDSTLSRRIQAEMLRLQQP ...

  7. Protein (Cyanobacteria): 330427 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available eaction center Psb27 protein Acaryochloris sp. CCMEE 5410 MFLTGCSLLSPETLLSGDYQQDTIYVIDNLSNAITLPDDDPNKAENQAAAGALISEYVSRYRRKPKLAGSASFMTMATALNGLAGHYNSYPNRPLPQRLKDRLEQEFKQAKIALKRENAA ...

  8. Protein (Viridiplantae): 302755288 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available AKHCTSVVTYNSLVLGFLKARRLKRGIKVFTRMARTGPSPDIYTYNILFEGLSRHGLWRFAYKLLPRMNQDGVLPDVVTFNSLINGLVEDNRYHRAVTLIQEMVSRGCDPNAIT...YTILLKWLARNARTDECVELFQRLLDRKLAPNVYTYNTVMSALCKAGRLDQAHRLFGVMLASDCTPPNAITYRALIHGLCLKMELERAVLLLDAMAKRGCAPDVACYGTIVAAFCKQGRIDEAFELLERMPFAGDKVMFRTLVRALCKLQLRSFSEQISCDEI ...

  9. Protein (Cyanobacteria): 104400 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available sphoprotein Arthrospira maxima CS-328 MDVNAITSHDSPSIQRLSETSDSVDVNAIASDDSPIQRLPETSDSVGVNNAIASHDSPSIQRVSETSDSV...EDISNAIASHDSPIQRLPETSDSGDVNNAIASHDSPIQRLSETSDSSPIQRLSETSDSGDVNNAIASHDSSIQRLPKTSDSVGVNNAIASHDSPSIQRVSETSDSVEDISNAIT

  10. Protein (Viridiplantae): 303282257 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available KVYGVLSDADKRRVYDETGRFDDADGLSDEKFNSLYEYYRGIYKQVTEEDIESFELEYRGGDEEKKDLLEAYEKFAGNMSKVFMWVMCSEEAVDSHRFADVVDAAVDARESKRYPAFTSWAAKIRKKPAPKDPLKPRPKKKKKAASAGGGGEGDLMAIIQARQNARAAAADDLFARLEEKYG ...

  11. Protein (Viridiplantae): 297819616 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 53 81972:1953 predicted protein Arabidopsis lyrata subsp. lyrata MMIMEEEDQNECNSVGSFYVKVNMEGVPIGRKIDLLSLNGYHDLITTLDYMFNASILYQNLLYYVSLRPKLMAIKNCENRAEEEEMCSEKSHVLTYADKEGDWMMVGDVPWE ...

  12. Protein (Cyanobacteria): 307558 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available LADGHHIAADQVVVACGIWSDLLLAPLGLSPKLEIWPMLWAHYTVDPSLADRYPQWFCFQRERGDDGGLYYGFPVLSRTAD...GRPRIKAGIDWAPKELRVAEPNAMCSEPPARLVELLDSFLFNELDGVQERVETVMSPYSMASDVNFVLDRLSPKLSLFAGGSGQAFKFAPLVGDSLARLACGESPAVDLSCWGHQREAVRA ...

  13. Protein (Viridiplantae): 308803120 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available SDPEKRAAYDKTGSVEDAELASEEFRTLYEYYRSLYKEVTKEDVEAFEKEYRGSEEERRDVLECYAKYEGDMAKVFAWVMCSEESEDSHRFADLVDAAIETEEVKSTSVYQKWAKDIRKRKAPKDPLGARREKKGGKSKKGEDAADLFALIQRKNAMRADQADAMFADLEAKYAKPKKAKR ...

  14. Protein (Viridiplantae): 356567582 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 6:985 3847:985 PREDICTED: probable xyloglucan endotransglucosylase/hydrolase protein 8-like Glycine max MNNINDYAESLFQMCSENGAGPERDELDFEFLGNKIGEPYLIQTNVYKNGTRGRKMRHMLWFDPTEDCHTYSIQQELE ...

  15. Protein (Cyanobacteria): 130081 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available n all1672 Nostoc sp. PCC 7120 MFKILFDSDLILDAVMNRTELAEDVRTLLENLHPSIRLYLTDVGLQKVSTYTYCLKNSQIPEIIVDWLQEQIQICPIDQGLLQKARYSPLRDFESAVELACINHYQLNAIVTNKPEDFIVTAHPLCVWSFADLWLRVNLESQLQATIHS ...

  16. Protein (Viridiplantae): 15224369 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available ne/histidine-rich C1 domain-containing protein Arabidopsis thaliana MAAKPTALGRPTVAPGHQLRLVFKGPEQTHQNRRMCDICDESAEGLYYQCKPCGFDVHPLC...GYINQENNKKTTKMSSSRPEQLVVQHFTHIHPLTKVDGYGEFTCDGCKTYGFGKTYRCTRCDYNLHDHCATCPSTLATFMHPQHELRLVFRGPEHTHQNKRMCDICDESAEGLYYQCEPCGFDVHPLC

  17. Protein (Viridiplantae): 255583123 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 024:1655 3398:1655 71240:1733 91827:1733 71275:3201 91835:1833 3646:1211 3977:764 235629:764 235880:764 3987:764 3988:764 Osmotic avo...idance abnormal protein, putative Ricinus communis MEVETSSLNTPRSIKTCMDTSFISKVRVIVRV

  18. Protein (Viridiplantae): 168014930 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available ens subsp. patens MANMMCNKHLDGEPSNIQANDEDITKEEVSNSKGVLHHDRSSVVLHYGIASLGGDWLTPLLPRPHPTIRANLVDLYFIRPNNFALDMYCL...VSVTLIKYRSTRLALTAGCGVGSDGDCIIAKGVEYVTNIQNNLNIEFYYQILNDKLFCSLEYYKLDIDDVIFYQNNNPKHTSKLAKACLEDLELKDHLKHQLNMKSMEASGMIELCERVEKELEDIT ...

  19. Protein (Cyanobacteria): 303632 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available otein APPUASWS_01688, partial Arthrospira platensis str. Paraca FYDPLQCEFEKNFILVWEDITPSLLIENENMLSLFKVLNRKNSR...ITISSQTPGTNMIFNAFALKVINSIHPLWTFWELNELKRRMFPIWFKKRETMTSEEYRGNHFELNELSDIEDITLDKLSSQLEIFWRNLDNCNQYSKAKKLLQKHKKD

  20. Protein (Cyanobacteria): 452378 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 06_28576 Lyngbya sp. PCC 8106 MGLSCLMNQIINAFPSPTRLTGLMHPTERLMGLSCLMNQIINAFPSPTRLTGLMHPTERLMGLSCLMNQIINAFPSPTRLTGLMHPTERLMGLSC...LMNQMINAFPSPTRLTGLMHPTERLMGLSCLMNQIINAFPSPTRLTGLMHPTDLLTPK ...