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Sample records for chlamydomonas annotation jamboree

  1. MEETING: Chlamydomonas Annotation Jamboree - October 2003

    Energy Technology Data Exchange (ETDEWEB)

    Grossman, Arthur R

    2007-04-13

    Shotgun sequencing of the nuclear genome of Chlamydomonas reinhardtii (Chlamydomonas throughout) was performed at an approximate 10X coverage by JGI. Roughly half of the genome is now contained on 26 scaffolds, all of which are at least 1.6 Mb, and the coverage of the genome is ~95%. There are now over 200,000 cDNA sequence reads that we have generated as part of the Chlamydomonas genome project (Grossman, 2003; Shrager et al., 2003; Grossman et al. 2007; Merchant et al., 2007); other sequences have also been generated by the Kasuza sequence group (Asamizu et al., 1999; Asamizu et al., 2000) or individual laboratories that have focused on specific genes. Shrager et al. (2003) placed the reads into distinct contigs (an assemblage of reads with overlapping nucleotide sequences), and contigs that group together as part of the same genes have been designated ACEs (assembly of contigs generated from EST information). All of the reads have also been mapped to the Chlamydomonas nuclear genome and the cDNAs and their corresponding genomic sequences have been reassembled, and the resulting assemblage is called an ACEG (an Assembly of contiguous EST sequences supported by genomic sequence) (Jain et al., 2007). Most of the unique genes or ACEGs are also represented by gene models that have been generated by the Joint Genome Institute (JGI, Walnut Creek, CA). These gene models have been placed onto the DNA scaffolds and are presented as a track on the Chlamydomonas genome browser associated with the genome portal (http://genome.jgi-psf.org/Chlre3/Chlre3.home.html). Ultimately, the meeting grant awarded by DOE has helped enormously in the development of an annotation pipeline (a set of guidelines used in the annotation of genes) and resulted in high quality annotation of over 4,000 genes; the annotators were from both Europe and the USA. Some of the people who led the annotation initiative were Arthur Grossman, Olivier Vallon, and Sabeeha Merchant (with many individual

  2. National Boy Scout Jamboree

    Science.gov (United States)

    1989-01-01

    This video looks at a NASA sponsored exhibit at the National Boy Scout Jamboree in Fredricksburg, VA. Boy Scouts are shown interacting with NASA researchers and astronauts and touring mockups of Space Station Freedom and Apollo 11. NASA's program to encourage the researchers of tomorrow is detailed.

  3. Genome-wide functional annotation and structural verification of metabolic ORFeome of Chlamydomonas reinhardtii

    Directory of Open Access Journals (Sweden)

    Fan Changyu

    2011-06-01

    Full Text Available Abstract Background Recent advances in the field of metabolic engineering have been expedited by the availability of genome sequences and metabolic modelling approaches. The complete sequencing of the C. reinhardtii genome has made this unicellular alga a good candidate for metabolic engineering studies; however, the annotation of the relevant genes has not been validated and the much-needed metabolic ORFeome is currently unavailable. We describe our efforts on the functional annotation of the ORF models released by the Joint Genome Institute (JGI, prediction of their subcellular localizations, and experimental verification of their structural annotation at the genome scale. Results We assigned enzymatic functions to the translated JGI ORF models of C. reinhardtii by reciprocal BLAST searches of the putative proteome against the UniProt and AraCyc enzyme databases. The best match for each translated ORF was identified and the EC numbers were transferred onto the ORF models. Enzymatic functional assignment was extended to the paralogs of the ORFs by clustering ORFs using BLASTCLUST. In total, we assigned 911 enzymatic functions, including 886 EC numbers, to 1,427 transcripts. We further annotated the enzymatic ORFs by prediction of their subcellular localization. The majority of the ORFs are predicted to be compartmentalized in the cytosol and chloroplast. We verified the structure of the metabolism-related ORF models by reverse transcription-PCR of the functionally annotated ORFs. Following amplification and cloning, we carried out 454FLX and Sanger sequencing of the ORFs. Based on alignment of the 454FLX reads to the ORF predicted sequences, we obtained more than 90% coverage for more than 80% of the ORFs. In total, 1,087 ORF models were verified by 454 and Sanger sequencing methods. We obtained expression evidence for 98% of the metabolic ORFs in the algal cells grown under constant light in the presence of acetate. Conclusions We functionally

  4. Japanin Jamboree 2015 - Suomen joukkueen onnistumiset ja kehittämisen kohteet

    OpenAIRE

    Tapaninen, Emma

    2016-01-01

    Japanissa järjestettiin kesällä 2015 kansainvälinen Jamboree-partioleiri, johon osallistui Suomesta noin 970 hengen joukkue. Joukkueen johtoryhmä asetti Jamboree-projektille erilaisia tavoitteita. Tämän opinnäytetyön tavoitteena oli selvittää joukkueen laajennetun johtoryhmän näkökulmasta, saavutettiinko kyseiset tavoitteet, missä onnistuttiin ja mitä kehitettävää jäi seuraavalle Jamboree-leirille. Työn teoriaosuus käsittelee tapahtuman järjestämistä. Siinä käydään läpi tapahtuman määritelmä ...

  5. DDBJ in collaboration with mass-sequencing teams on annotation

    OpenAIRE

    Tateno, Y; Saitou, N; Okubo, K; Sugawara, H.; Gojobori, T

    2004-01-01

    In the past year, we at DDBJ (DNA Data Bank of Japan; http://www.ddbj.nig.ac.jp) collected and released 1 066 084 entries or 718 072 425 bases including the whole chromosome 22 of chimpanzee, the whole-genome shotgun sequences of silkworm and various others. On the other hand, we hosted workshops for human full-length cDNA annotation and participated in jamborees of mouse full-length cDNA annotation. The annotated data are made public at DDBJ. We are also in collaboration with a RIKEN team to...

  6. Algal functional annotation tool

    Energy Technology Data Exchange (ETDEWEB)

    Lopez, D. [UCLA; Casero, D. [UCLA; Cokus, S. J. [UCLA; Merchant, S. S. [UCLA; Pellegrini, M. [UCLA

    2012-07-01

    The Algal Functional Annotation Tool is a web-based comprehensive analysis suite integrating annotation data from several pathway, ontology, and protein family databases. The current version provides annotation for the model alga Chlamydomonas reinhardtii, and in the future will include additional genomes. The site allows users to interpret large gene lists by identifying associated functional terms, and their enrichment. Additionally, expression data for several experimental conditions were compiled and analyzed to provide an expression-based enrichment search. A tool to search for functionally-related genes based on gene expression across these conditions is also provided. Other features include dynamic visualization of genes on KEGG pathway maps and batch gene identifier conversion.

  7. Algal functional annotation tool

    Energy Technology Data Exchange (ETDEWEB)

    2012-07-12

    Abstract BACKGROUND: Progress in genome sequencing is proceeding at an exponential pace, and several new algal genomes are becoming available every year. One of the challenges facing the community is the association of protein sequences encoded in the genomes with biological function. While most genome assembly projects generate annotations for predicted protein sequences, they are usually limited and integrate functional terms from a limited number of databases. Another challenge is the use of annotations to interpret large lists of 'interesting' genes generated by genome-scale datasets. Previously, these gene lists had to be analyzed across several independent biological databases, often on a gene-by-gene basis. In contrast, several annotation databases, such as DAVID, integrate data from multiple functional databases and reveal underlying biological themes of large gene lists. While several such databases have been constructed for animals, none is currently available for the study of algae. Due to renewed interest in algae as potential sources of biofuels and the emergence of multiple algal genome sequences, a significant need has arisen for such a database to process the growing compendiums of algal genomic data. DESCRIPTION: The Algal Functional Annotation Tool is a web-based comprehensive analysis suite integrating annotation data from several pathway, ontology, and protein family databases. The current version provides annotation for the model alga Chlamydomonas reinhardtii, and in the future will include additional genomes. The site allows users to interpret large gene lists by identifying associated functional terms, and their enrichment. Additionally, expression data for several experimental conditions were compiled and analyzed to provide an expression-based enrichment search. A tool to search for functionally-related genes based on gene expression across these conditions is also provided. Other features include dynamic visualization of genes

  8. Patching Holes in the Chlamydomonas Genome.

    Science.gov (United States)

    Tulin, Frej; Cross, Frederick R

    2016-01-01

    The Chlamydomonas genome has been sequenced, assembled, and annotated to produce a rich resource for genetics and molecular biology in this well-studied model organism. However, the current reference genome contains ∼1000 blocks of unknown sequence ('N-islands'), which are frequently placed in introns of annotated gene models. We developed a strategy to search for previously unknown exons hidden within such blocks, and determine the sequence, and exon/intron boundaries, of such exons. These methods are based on assembly and alignment of short cDNA and genomic DNA reads, completely independent of prior reference assembly or annotation. Our evidence indicates that a substantial proportion of the annotated intronic N-islands contain hidden exons. For most of these, our algorithm recovers full exonic sequence with associated splice junctions and exon-adjacent intronic sequence. These new exons represent de novo sequence generally present nowhere in the assembled genome, and the added sequence improves evolutionary conservation of the predicted encoded peptides. PMID:27175017

  9. Annotated English

    CERN Document Server

    Hernandez-Orallo, Jose

    2010-01-01

    This document presents Annotated English, a system of diacritical symbols which turns English pronunciation into a precise and unambiguous process. The annotations are defined and located in such a way that the original English text is not altered (not even a letter), thus allowing for a consistent reading and learning of the English language with and without annotations. The annotations are based on a set of general rules that make the frequency of annotations not dramatically high. This makes the reader easily associate annotations with exceptions, and makes it possible to shape, internalise and consolidate some rules for the English language which otherwise are weakened by the enormous amount of exceptions in English pronunciation. The advantages of this annotation system are manifold. Any existing text can be annotated without a significant increase in size. This means that we can get an annotated version of any document or book with the same number of pages and fontsize. Since no letter is affected, the ...

  10. High quality metabolomic data for Chlamydomonas reinhardtii

    Directory of Open Access Journals (Sweden)

    Fiehn Oliver

    2008-04-01

    Full Text Available Abstract The green eukaryote alga Chlamydomonas reinhardtii is a unicellular model to study control of metabolism in a photosynthetic organism. We here present method improvements for metabolite profiling based on GC-TOF mass spectrometry focusing on three parameters: quenching and cell disruption, extract solvent composition and metabolite annotation. These improvements facilitate using smaller cell numbers and hence, smaller culture volumes which enable faster and more precise sampling techniques that eventually lead to a higher number of samples that can be processed, e.g. for time course experiments. Quenching of metabolism was achieved by mixing 1 ml of culture to 1 ml of -70°C cold 70% methanol. After centrifugation, cells were lyophilized and disrupted by milling using 2-6E6 lyophilized cells, around 500-fold less than previously reported. Glass beads were compared to metal balls for milling, and five different extraction solvents were tested. Additionally, all peaks were annotated in an automated way using the GC-TOF database BinBase instead of manual investigation of a single reference chromatogram. Median precision of analysis was used to decide for the eventual procedure which was applied to a proof-of-principle study of time dependent changes of metabolism under standard conditions.

  11. Annotated Answer Set Programming

    OpenAIRE

    Straccia, Umberto

    2005-01-01

    We present Annotated Answer Set Programming, that extends the ex pressive power of disjunctive logic programming with annotation terms, taken from the generalized annotated logic programming framework.

  12. Annotated Videography.

    Science.gov (United States)

    United States Holocaust Memorial Museum, Washington, DC.

    This annotated list of 43 videotapes recommended for classroom use addresses various themes for teaching about the Holocaust, including: (1) overviews of the Holocaust; (2) life before the Holocaust; (3) propaganda; (4) racism, anti-Semitism; (5) "enemies of the state"; (6) ghettos; (7) camps; (8) genocide; (9) rescue; (10) resistance; (11)…

  13. Construction and evaluation of a whole genome microarray of Chlamydomonas reinhardtii

    Directory of Open Access Journals (Sweden)

    Toepel Jörg

    2011-11-01

    Full Text Available Abstract Background Chlamydomonas reinhardtii is widely accepted as a model organism regarding photosynthesis, circadian rhythm, cell mobility, phototaxis, and biotechnology. The complete annotation of the genome allows transcriptomic studies, however a new microarray platform was needed. Based on the completed annotation of Chlamydomonas reinhardtii a new microarray on an Agilent platform was designed using an extended JGI 3.1 genome data set which included 15000 transcript models. Results In total 44000 probes were determined (3 independent probes per transcript model covering 93% of the transcriptome. Alignment studies with the recently published AUGUSTUS 10.2 annotation confirmed 11000 transcript models resulting in a very good coverage of 70% of the transcriptome (17000. Following the estimation of 10000 predicted genes in Chlamydomonas reinhardtii our new microarray, nevertheless, covers the expected genome by 90-95%. Conclusions To demonstrate the capabilities of the new microarray, we analyzed transcript levels for cultures grown under nitrogen as well as sulfate limitation, and compared the results with recently published microarray and RNA-seq data. We could thereby confirm previous results derived from data on nutrient-starvation induced gene expression of a group of genes related to protein transport and adaptation of the metabolism as well as genes related to efficient light harvesting, light energy distribution and photosynthetic electron transport.

  14. Chlamydomonas: A Model Green Plant.

    Science.gov (United States)

    Sheffield, E.

    1985-01-01

    Discusses the instructional potential of Chlamydomonas in providing a basis for a range of experimental investigations to illustrate basic biological phenomena. Describes the use of this algae genus in studies of population growth, photosynthesis, and mating behavior. Procedures for laboratory exercises are included. (ML)

  15. Modeling Loosely Annotated Images with Imagined Annotations

    CERN Document Server

    Tang, Hong; Chen, Yunhao

    2008-01-01

    In this paper, we present an approach to learning latent semantic analysis models from loosely annotated images for automatic image annotation and indexing. The given annotation in training images is loose due to: (1) ambiguous correspondences between visual features and annotated keywords; (2) incomplete lists of annotated keywords. The second reason motivates us to enrich the incomplete annotation in a simple way before learning topic models. In particular, some imagined keywords are poured into the incomplete annotation through measuring similarity between keywords. Then, both given and imagined annotations are used to learning probabilistic topic models for automatically annotating new images. We conduct experiments on a typical Corel dataset of images and loose annotations, and compare the proposed method with state-of-the-art discrete annotation methods (using a set of discrete blobs to represent an image). The proposed method improves word-driven probability Latent Semantic Analysis (PLSA-words) up to ...

  16. 13th International Conference on Chlamydomonas

    Energy Technology Data Exchange (ETDEWEB)

    Silflow, Carolyn D. [University of Minnesota

    2014-03-11

    The 13th International Conference on Chlamydomonas (EMBO Workshop on the Cell and Molecular Biology of Chlamydomonas) was held May 27 to June 1, 2008 in Hyeres, France. The conference was the biennial meeting for all researchers studying the green algal systems Chlamydomonas and Volvox. The conference brought together approximately 200 investigators from around the world (North America, Asia, Europe and Australia) representing different fields and disciplines (cell biology, genetics, biochemistry, biophysics, plant physiology, genomics). It provided an opportunity for investigators from different countries to share methodologies and to discuss recent results with a focus on the Chlamydomonas experimental system.

  17. Iron economy in Chlamydomonas reinhardtii

    Science.gov (United States)

    Glaesener, Anne G.; Merchant, Sabeeha S.; Blaby-Haas, Crysten E.

    2013-01-01

    While research on iron nutrition in plants has largely focused on iron-uptake pathways, photosynthetic microbes such as the unicellular green alga Chlamydomonas reinhardtii provide excellent experimental systems for understanding iron metabolism at the subcellular level. Several paradigms in iron homeostasis have been established in this alga, including photosystem remodeling in the chloroplast and preferential retention of some pathways and key iron-dependent proteins in response to suboptimal iron supply. This review presents our current understanding of iron homeostasis in Chlamydomonas, with specific attention on characterized responses to changes in iron supply, like iron-deficiency. An overview of frequently used methods for the investigation of iron-responsive gene expression, physiology and metabolism is also provided, including preparation of media, the effect of cell size, cell density and strain choice on quantitative measurements and methods for the determination of metal content and assessing the effect of iron supply on photosynthetic performance. PMID:24032036

  18. Selenoprotein-Transgenic Chlamydomonas reinhardtii

    OpenAIRE

    Jiazuan Ni; Zhangli Hu; Jing Tian; Qintang Hou; Qiong Liu; Shi Qiu

    2013-01-01

    Selenium (Se) deficiency is associated with the occurrence of many diseases. However, excessive Se supplementation, especially with inorganic Se, can result in toxicity. Selenoproteins are the major forms of Se in vivo to exert its biological function. Expression of those selenoproteins, especially with the application of a newly developed system, is thus very important for studying the mechanism of Se in nutrition. The use of Chlamydomonas reinhardtii (C. reinhardtii) as a biological vector ...

  19. Annotated bibliography

    International Nuclear Information System (INIS)

    Under a cooperative agreement with the U.S. Department of Energy's Office of Science and Technology, Waste Policy Institute (WPI) is conducting a five-year research project to develop a research-based approach for integrating communication products in stakeholder involvement related to innovative technology. As part of the research, WPI developed this annotated bibliography which contains almost 100 citations of articles/books/resources involving topics related to communication and public involvement aspects of deploying innovative cleanup technology. To compile the bibliography, WPI performed on-line literature searches (e.g., Dialog, International Association of Business Communicators Public Relations Society of America, Chemical Manufacturers Association, etc.), consulted past years proceedings of major environmental waste cleanup conferences (e.g., Waste Management), networked with professional colleagues and DOE sites to gather reports or case studies, and received input during the August 1996 Research Design Team meeting held to discuss the project's research methodology. Articles were selected for annotation based upon their perceived usefulness to the broad range of public involvement and communication practitioners

  20. The basal bodies of Chlamydomonas reinhardtii

    OpenAIRE

    Dutcher, Susan K.; O’Toole, Eileen T.

    2016-01-01

    The unicellular green alga, Chlamydomonas reinhardtii, is a biflagellated cell that can swim or glide. C. reinhardtii cells are amenable to genetic, biochemical, proteomic, and microscopic analysis of its basal bodies. The basal bodies contain triplet microtubules and a well-ordered transition zone. Both the mother and daughter basal bodies assemble flagella. Many of the proteins found in other basal body-containing organisms are present in the Chlamydomonas genome, and mutants in these genes...

  1. ChlamyCyc: an integrative systems biology database and web-portal for Chlamydomonas reinhardtii

    Directory of Open Access Journals (Sweden)

    Kempa Stefan

    2009-05-01

    Full Text Available Abstract Background The unicellular green alga Chlamydomonas reinhardtii is an important eukaryotic model organism for the study of photosynthesis and plant growth. In the era of modern high-throughput technologies there is an imperative need to integrate large-scale data sets from high-throughput experimental techniques using computational methods and database resources to provide comprehensive information about the molecular and cellular organization of a single organism. Results In the framework of the German Systems Biology initiative GoFORSYS, a pathway database and web-portal for Chlamydomonas (ChlamyCyc was established, which currently features about 250 metabolic pathways with associated genes, enzymes, and compound information. ChlamyCyc was assembled using an integrative approach combining the recently published genome sequence, bioinformatics methods, and experimental data from metabolomics and proteomics experiments. We analyzed and integrated a combination of primary and secondary database resources, such as existing genome annotations from JGI, EST collections, orthology information, and MapMan classification. Conclusion ChlamyCyc provides a curated and integrated systems biology repository that will enable and assist in systematic studies of fundamental cellular processes in Chlamydomonas. The ChlamyCyc database and web-portal is freely available under http://chlamycyc.mpimp-golm.mpg.de.

  2. Interlinking Multimedia Annotations

    OpenAIRE

    Li, Yunjia; Wald, Mike; Wills, Gary

    2011-01-01

    With the fast growth of multimedia sharing and annotating applications on the Web, there is an increasing research interests in semantic annotations of multimedia. However, applying linked data principles in multimedia annotations is a relatively new topic, especially when annotations are related to media fragments. This paper, therefore, discusses this problem and further breaks it down into three fundamental sub-questions: 1) choosing media fragment URIs 2) Dereferencing media fragment URIs...

  3. The basal bodies of Chlamydomonas reinhardtii.

    Science.gov (United States)

    Dutcher, Susan K; O'Toole, Eileen T

    2016-01-01

    The unicellular green alga, Chlamydomonas reinhardtii, is a biflagellated cell that can swim or glide. C. reinhardtii cells are amenable to genetic, biochemical, proteomic, and microscopic analysis of its basal bodies. The basal bodies contain triplet microtubules and a well-ordered transition zone. Both the mother and daughter basal bodies assemble flagella. Many of the proteins found in other basal body-containing organisms are present in the Chlamydomonas genome, and mutants in these genes affect the assembly of basal bodies. Electron microscopic analysis shows that basal body duplication is site-specific and this may be important for the proper duplication and spatial organization of these organelles. Chlamydomonas is an excellent model for the study of basal bodies as well as the transition zone. PMID:27252853

  4. Photomixing of chlamydomonas rheinhardtii suspensions

    Science.gov (United States)

    Dervaux, Julien; Capellazzi Resta, Marina; Abou, Bérengère; Brunet, Philippe

    2014-11-01

    Chlamydomonas rheinhardtii is a fast swimming unicellular alga able to bias its swimming direction in gradients of light intensity, an ability know as phototaxis. We have investigated experimentally both the swimming behavior of individual cells and the macroscopic response of shallow suspensions of these micro-organisms in response to a localized light source. At low light intensity, algae exhibit positive phototaxis and accumulate beneath the excitation light. In weakly concentrated thin layers, the balance between phototaxis and cell motility results in steady symmetrical patterns compatible with a purely diffusive model using effective diffusion coefficients extracted from the analysis of individual cell trajectories. However, at higher cell density and layer depth, collective effects induce convective flows around the light source. These flows disturb the cell concentration patterns which spread and may then becomes unstable. Using large passive tracer particles, we have characterized the velocity fields associated with this forced bioconvection and their dependence on the cell density and layer depth. By tuning the light distribution, this mechanism of photo-bioconvection allows a fine control over the local fluid flows, and thus the mixing efficiency, in algal suspensions.

  5. Selenoprotein-Transgenic Chlamydomonas reinhardtii

    Directory of Open Access Journals (Sweden)

    Jiazuan Ni

    2013-02-01

    Full Text Available Selenium (Se deficiency is associated with the occurrence of many diseases. However, excessive Se supplementation, especially with inorganic Se, can result in toxicity. Selenoproteins are the major forms of Se in vivo to exert its biological function. Expression of those selenoproteins, especially with the application of a newly developed system, is thus very important for studying the mechanism of Se in nutrition. The use of Chlamydomonas reinhardtii (C. reinhardtii as a biological vector to express an heterogeneous protein is still at the initial stages of development. In order to investigate the possibility of using this system to express selenoproteins, human 15-KDa selenoprotein (Sep15, a small but widely distributed selenoprotein in mammals, was chosen for the expression platform test. Apart from the wild-type human Sep15 gene fragment, two Sep15 recombinants were constructed containing Sep15 open reading frame (ORF and the selenocysteine insertion sequence (SECIS element from either human Sep15 or C. reinhardtii selenoprotein W1, a highly expressed selenoprotein in this alga. Those Sep15-containing plasmids were transformed into C. reinhardtii CC-849 cells. Results showed that Sep15 fragments were successfully inserted into the nuclear genome and expressed Sep15 protein in the cells. The transgenic and wild-type algae demonstrated similar growth curves in low Se culture medium. To our knowledge, this is the first report on expressing human selenoprotein in green alga.

  6. A steering mechanism for phototaxis in Chlamydomonas

    CERN Document Server

    Bennett, Rachel R

    2014-01-01

    Chlamydomonas shows both positive and negative phototaxis. It has a single eyespot near its equator and as the cell rotates during forward motion the light signal received by the eyespot varies. We use a simple mechanical model of Chlamydomonas that couples the flagellar beat pattern to the light intensity at the eyespot to demonstrate a mechanism for phototactic steering that is consistent with observations. The direction of phototaxis is controlled by a parameter in our model and the steering mechanism is robust to noise. Our model shows switching between directed phototaxis when the light is on and run-and-tumble behaviour in the dark.

  7. Annotations for Intersection Typechecking

    Directory of Open Access Journals (Sweden)

    Joshua Dunfield

    2013-07-01

    Full Text Available In functional programming languages, the classic form of annotation is a single type constraint on a term. Intersection types add complications: a single term may have to be checked several times against different types, in different contexts, requiring annotation with several types. Moreover, it is useful (in some systems, necessary to indicate the context in which each such type is to be used. This paper explores the technical design space of annotations in systems with intersection types. Earlier work (Dunfield and Pfenning 2004 introduced contextual typing annotations, which we now tease apart into more elementary mechanisms: a "right hand" annotation (the standard form, a "left hand" annotation (the context in which a right-hand annotation is to be used, a merge that allows for multiple annotations, and an existential binder for index variables. The most novel element is the left-hand annotation, which guards terms (and right-hand annotations with a judgment that must follow from the current context.

  8. Annotated Stack Trees

    OpenAIRE

    Hague, Matthew; Penelle, Vincent

    2015-01-01

    Annotated pushdown automata provide an automaton model of higher-order recursion schemes, which may in turn be used to model higher-order programs for the purposes of verification. We study Ground Annotated Stack Tree Rewrite Systems -- a tree rewrite system where each node is labelled by the configuration of an annotated pushdown automaton. This allows the modelling of fork and join constructs in higher-order programs and is a generalisation of higher-order stack trees recently introduced by...

  9. Lipidomic Analysis of Chlamydomonas reinhardtii under Nitrogen and Sulfur Deprivation.

    Directory of Open Access Journals (Sweden)

    Dawei Yang

    Full Text Available Chlamydomonas reinhardtii accumulates lipids under complete nutrient starvation conditions while overall growth in biomass stops. In order to better understand biochemical changes under nutrient deprivation that maintain production of algal biomass, we used a lipidomic assay for analyzing the temporal regulation of the composition of complex lipids in C. reinhardtii in response to nitrogen and sulfur deprivation. Using a chip-based nanoelectrospray direct infusion into an ion trap mass spectrometer, we measured a diversity of lipid species reported for C. reinhardtii, including PG phosphatidylglycerols, PI Phosphatidylinositols, MGDG monogalactosyldiacylglycerols, DGDG digalactosyldiacylglycerols, SQDG sulfoquinovosyldiacylglycerols, DGTS homoserine ether lipids and TAG triacylglycerols. Individual lipid species were annotated by matching mass precursors and MS/MS fragmentations to the in-house LipidBlast mass spectral database and MS2Analyzer. Multivariate statistics showed a clear impact on overall lipidomic phenotypes on both the temporal and the nutrition stress level. Homoserine-lipids were found up-regulated at late growth time points and higher cell density, while triacyclglycerols showed opposite regulation of unsaturated and saturated fatty acyl chains under nutritional deprivation.

  10. Computing human image annotation.

    Science.gov (United States)

    Channin, David S; Mongkolwat, Pattanasak; Kleper, Vladimir; Rubin, Daniel L

    2009-01-01

    An image annotation is the explanatory or descriptive information about the pixel data of an image that is generated by a human (or machine) observer. An image markup is the graphical symbols placed over the image to depict an annotation. In the majority of current, clinical and research imaging practice, markup is captured in proprietary formats and annotations are referenced only in free text radiology reports. This makes these annotations difficult to query, retrieve and compute upon, hampering their integration into other data mining and analysis efforts. This paper describes the National Cancer Institute's Cancer Biomedical Informatics Grid's (caBIG) Annotation and Image Markup (AIM) project, focusing on how to use AIM to query for annotations. The AIM project delivers an information model for image annotation and markup. The model uses controlled terminologies for important concepts. All of the classes and attributes of the model have been harmonized with the other models and common data elements in use at the National Cancer Institute. The project also delivers XML schemata necessary to instantiate AIMs in XML as well as a software application for translating AIM XML into DICOM S/R and HL7 CDA. Large collections of AIM annotations can be built and then queried as Grid or Web services. Using the tools of the AIM project, image annotations and their markup can be captured and stored in human and machine readable formats. This enables the inclusion of human image observation and inference as part of larger data mining and analysis activities. PMID:19964202

  11. Personnalisation de Syst\\`emes OLAP Annot\\'es

    CERN Document Server

    Jerbi, Houssem; Ravat, Franck; Teste, Olivier

    2010-01-01

    This paper deals with personalization of annotated OLAP systems. Data constellation is extended to support annotations and user preferences. Annotations reflect the decision-maker experience whereas user preferences enable users to focus on the most interesting data. User preferences allow annotated contextual recommendations helping the decision-maker during his/her multidimensional navigations.

  12. A steering mechanism for phototaxis in Chlamydomonas

    Science.gov (United States)

    Bennett, Rachel; Golestanian, Ramin

    2015-03-01

    Chlamydomonas shows both positive and negative phototaxis. It has a single eyespot near its equator and as the cell rotates during forward motion the light signal received by the eyespot varies. We use a simple mechanical model of Chlamydomonas that couples the flagellar beat pattern to the light intensity at the eyespot to demonstrate a mechanism for phototactic steering that is consistent with observations. The direction of phototaxis is controlled by a parameter in our model and the steering mechanism is robust to noise. In the dark, our model shows emergent run-and-tumble behavior and we see switching between directed phototaxis and run-and-tumble when we switch the light on and off.

  13. Inheritance of chloroplast DNA in Chlamydomonas reinhardtii

    OpenAIRE

    Grant, David M; Nicholas W. Gillham; Boynton, John E.

    1980-01-01

    Two symmetrically located deletions of approximately 100 base pairs each have been identified in chloroplast DNA of Chlamydomonas reinhardtii. Although present in a mutant strain that requires acetate for growth, both deletions have been shown to be distinct from the nonphotosynthetic phenotype of this strain. These physical markers in the chloroplast genome and maternally inherited genetic markers showed strict cotransmission in reciprocal crosses. Thus, our results are consistent with the l...

  14. Chlamydomonas sajao nov. sp. (Chlorophyta, Volvocales)

    Science.gov (United States)

    Lewin, Ralph A.

    1984-06-01

    A new species of Chlamydomonas, namely, C. sajao nov. sp. of the Volvocales, Chlorophyta was isolated from a duckweed growing near a ricefield in the vicinity of Guangzhou, China. This interesting unicellular green alga, similar to C. mexicana from Mexico, secretes quantities of extracellular mucilaginous polysaccharides, and may be employed in improving soil quality. The new species resembles C. waldenburgensis Moewus in most characteristics but differs in three important features.

  15. Creating Annotation Tools with the Annotation Graph Toolkit

    OpenAIRE

    Maeda, Kazuaki; Bird, Steven; Ma, Xiaoyi; Lee, Haejoong

    2002-01-01

    The Annotation Graph Toolkit is a collection of software supporting the development of annotation tools based on the annotation graph model. The toolkit includes application programming interfaces for manipulating annotation graph data and for importing data from other formats. There are interfaces for the scripting languages Tcl and Python, a database interface, specialized graphical user interfaces for a variety of annotation tasks, and several sample applications. This paper describes all ...

  16. On Anomalies in Annotation Systems

    CERN Document Server

    Brust, Matthias R

    2007-01-01

    Today's computer-based annotation systems implement a wide range of functionalities that often go beyond those available in traditional paper-and-pencil annotations. Conceptually, annotation systems are based on thoroughly investigated psycho-sociological and pedagogical learning theories. They offer a huge diversity of annotation types that can be placed in textual as well as in multimedia format. Additionally, annotations can be published or shared with a group of interested parties via well-organized repositories. Although highly sophisticated annotation systems exist both conceptually as well as technologically, we still observe that their acceptance is somewhat limited. In this paper, we argue that nowadays annotation systems suffer from several fundamental problems that are inherent in the traditional paper-and-pencil annotation paradigm. As a solution, we propose to shift the annotation paradigm for the implementation of annotation system.

  17. Semantic annotation of mutable data.

    Directory of Open Access Journals (Sweden)

    Robert A Morris

    Full Text Available Electronic annotation of scientific data is very similar to annotation of documents. Both types of annotation amplify the original object, add related knowledge to it, and dispute or support assertions in it. In each case, annotation is a framework for discourse about the original object, and, in each case, an annotation needs to clearly identify its scope and its own terminology. However, electronic annotation of data differs from annotation of documents: the content of the annotations, including expectations and supporting evidence, is more often shared among members of networks. Any consequent actions taken by the holders of the annotated data could be shared as well. But even those current annotation systems that admit data as their subject often make it difficult or impossible to annotate at fine-enough granularity to use the results in this way for data quality control. We address these kinds of issues by offering simple extensions to an existing annotation ontology and describe how the results support an interest-based distribution of annotations. We are using the result to design and deploy a platform that supports annotation services overlaid on networks of distributed data, with particular application to data quality control. Our initial instance supports a set of natural science collection metadata services. An important application is the support for data quality control and provision of missing data. A previous proof of concept demonstrated such use based on data annotations modeled with XML-Schema.

  18. [An experiment with Chlamydomonas reinhardtii on the Kosmos-2044 biosatellite].

    Science.gov (United States)

    Gavrilova, O V; Gabova, A V; Goriainova, L N; Filatova, E V

    1992-01-01

    Space experiment with Chlamydomonas reinhardtii demonstrated that the microgravity effects were noted in Chlamydomonas at both cellular and population levels: in space the cell size is increased, stage of active growth of the culture is extended, it contains the juvenile vegetative motile cells in greater quantities. Ultrastructural analysis indicated that in microgravity the changes in shape, structure and distribution of intracellular organelles and in volume ratio of organelles and cytoplasma are absent. Chlamydomonas data are in line with the results of the Infusoria and Chlorella experiments. PMID:1307032

  19. Collaborative Movie Annotation

    Science.gov (United States)

    Zad, Damon Daylamani; Agius, Harry

    In this paper, we focus on metadata for self-created movies like those found on YouTube and Google Video, the duration of which are increasing in line with falling upload restrictions. While simple tags may have been sufficient for most purposes for traditionally very short video footage that contains a relatively small amount of semantic content, this is not the case for movies of longer duration which embody more intricate semantics. Creating metadata is a time-consuming process that takes a great deal of individual effort; however, this effort can be greatly reduced by harnessing the power of Web 2.0 communities to create, update and maintain it. Consequently, we consider the annotation of movies within Web 2.0 environments, such that users create and share that metadata collaboratively and propose an architecture for collaborative movie annotation. This architecture arises from the results of an empirical experiment where metadata creation tools, YouTube and an MPEG-7 modelling tool, were used by users to create movie metadata. The next section discusses related work in the areas of collaborative retrieval and tagging. Then, we describe the experiments that were undertaken on a sample of 50 users. Next, the results are presented which provide some insight into how users interact with existing tools and systems for annotating movies. Based on these results, the paper then develops an architecture for collaborative movie annotation.

  20. Annotated bibliography traceability

    NARCIS (Netherlands)

    Narain, G.

    2006-01-01

    This annotated bibliography contains summaries of articles and chapters of books, which are relevant to traceability. After each summary there is a part about the relevancy of the paper for the LEI project. The aim of the LEI-project is to gain insight in several aspects of traceability in order to

  1. Annotation: The Savant Syndrome

    Science.gov (United States)

    Heaton, Pamela; Wallace, Gregory L.

    2004-01-01

    Background: Whilst interest has focused on the origin and nature of the savant syndrome for over a century, it is only within the past two decades that empirical group studies have been carried out. Methods: The following annotation briefly reviews relevant research and also attempts to address outstanding issues in this research area.…

  2. Paternal inheritance of mitochondria in Chlamydomonas.

    Science.gov (United States)

    Nakamura, Soichi

    2010-03-01

    To analyze mitochondrial DNA (mtDNA)inheritance, differences in mtDNA between Chlamydomonas reinhardtii and Chlamydomonas smithii, respiration deficiency and antibiotic resistance were used to distinguish mtDNA origins. The analyses indicated paternal inheritance. However, these experiments raised questions regarding whether paternal inheritance occurred normally.Mitochondrial nucleoids were observed in living zygotes from mating until 3 days after mating and then until progeny formation. However, selective disappearance of nucleoids was not observed. Subsequently, experimental serial backcrosses between the two strains demonstrated strict paternal inheritance. The fate of mt+ and mt- mtDNA was followed using the differences in mtDNA between the two strains. The slow elimination of mt+ mtDNA through zygote maturation in darkness was observed, and later the disappearance of mt+ mtDNA was observed at the beginning of meiosis. To explain the different fates of mtDNA, methylation status was investigated; however, no methylation was detected. Variously constructed diploid cells showed biparental inheritance. Thus, when the mating process occurs normally, paternal inheritance occurs. Mutations disrupting mtDNA inheritance have not yet been isolated. Mutations that disrupt maternal inheritance of chloroplast DNA (cpDNA) do not disrupt inheritance of mtDNA. The genes responsible for mtDNA inheritance are different from those of chloroplasts. PMID:20069335

  3. Vegetative and gametic flagellum membranes of Chlamydomonas reinhardtii

    OpenAIRE

    Sikorski, Aleksander F

    2015-01-01

    Differences were demonstrated in the composition, electrophoretic patterns of polypeptide chains and neutral sugar composition between vegetative and gametic flagellum membranes of two strains (89 and 90) of Chlamydomonas reinhardtii.

  4. Vegetative and gametic flagellum membranes of Chlamydomonas reinhardtii

    Directory of Open Access Journals (Sweden)

    Aleksander F. Sikorski

    2015-05-01

    Full Text Available Differences were demonstrated in the composition, electrophoretic patterns of polypeptide chains and neutral sugar composition between vegetative and gametic flagellum membranes of two strains (89 and 90 of Chlamydomonas reinhardtii.

  5. Introduction of exogenous DNA into Chlamydomonas reinhardtii by electroporation.

    OpenAIRE

    Brown, L. E.; Sprecher, S L; Keller, L R

    1991-01-01

    The fate of exogenous DNA introduced into Chlamydomonas reinhardtii by electroporation was analyzed. With single and double electrical pulses, plasmids as large as 14 kb were introduced into cells with and without intact cell walls. Within hours after introduction, exogenous plasmid DNA was associated with nuclei isolated from cells; several weeks after introduction, exogenous DNA was stably integrated into the Chlamydomonas genome. These studies establish electroporation as a method for intr...

  6. Identification of an NADP/thioredoxin system in Chlamydomonas reinhardtii

    Science.gov (United States)

    Huppe, H. C.; Picaud, A.; Buchanan, B. B.; Miginiac-Maslow, M.

    1991-01-01

    The protein components of the NADP/thioredoxin system, NADP-thioredoxin reductase (NTR) and thioredoxin h, have been purified and characterized from the green alga, Chlamydomonas reinhardtii. The analysis of this system confirms that photoautotrophic Chlamydomonas cells resemble leaves in having both an NADP- and ferrodoxin-linked thioredoxin redox system. Chlamydomonas thioredoxin h, which is smaller on sodium dodecyl sulfate-polyacrylamide gel electrophoresis than thioredoxin m from the same source, cross-reacted with antisera to thioredoxin h from spinach (Spinacia oleracea L.) and wheat germ (Triticum vulgaris L.) but not with antisera to m or f thioredoxins. In these properties, the thioredoxin h resembled a thioredoxin from Chlamydomonas, designated Ch1, whose sequence was reported recently (P. Decottignies et al., 1991, Eur. J. Biochem. 198, 505-512). The differential reactivity of thioredoxin h with antisera was used to demonstrate that thioredoxin h is enriched outside the chloroplast. The NTR was purified from Chlamydomonas using thioredoxin h from the same source. Similar to its counterpart from other organisms, Chlamydomonas NTR had a subunit size of approx. 36 kDa and was specific for NADPH. Chlamydomonas NTR effectively reduced thioredoxin h from the same source but showed little activity with the other thioredoxins tested, including spinach thioredoxin h and Escherichia coli thioredoxin. Comparison of the reduction of Chlamydomonas thioredoxins m and h by each of the endogenous thioredoxin reductases, NTR and ferredoxin-thioredoxin reductase, revealed a differential specificity of each enzyme for thioredoxin. Thus, NTR showed increased activity with thioredoxin h and ferredoxin-thioredoxin reductase with thioredoxins m and f.

  7. A brief introduction to the model microswimmer {\\it Chlamydomonas reinhardtii}

    CERN Document Server

    Jeanneret, Raphaël; Polin, Marco

    2016-01-01

    The unicellular biflagellate green alga {\\it Chlamydomonas reinhardtii} has been an important model system in biology for decades, and in recent years it has started to attract growing attention also within the biophysics community. Here we provide a concise review of some of the aspects of {\\it Chlamydomonas} biology and biophysics most immediately relevant to physicists that might be interested in starting to work with this versatile microorganism.

  8. A homologue of the defender against the apoptotic death gene (dad1) in UV-exposed Chlamydomonas cells is downregulated with the onset of programmed cell death

    Indian Academy of Sciences (India)

    Swati Moharikar; Jacinta S D’souza; Basuthkar J Rao

    2007-03-01

    We report here the isolation of a homologue of the potential anti-apoptotic gene, defender against apoptotic death (dad1) from Chlamydomonas reinhardtii cells. Using polymerase chain reaction (PCR), we investigated its expression in the execution process of programmed cell death (PCD) in UV-C exposed dying C. reinhardtii cells. Reverse-transcriptase (RT)-PCR showed that C. reinhardtii dad1 amplification was drastically reduced in UV-C exposed dying C. reinhardtii cells. We connect the downregulation of dad1 with the upregulation of apoptosis protease activating factor-1 (APAF-1) and the physiological changes that occur in C. reinhardtii cells upon exposure to 12 J/m2 UV-C in order to show a reciprocal relationship between proapoptotic and inhibitor of apoptosis factors. The temporal changes indicate a correlation between the onset of cell death and dad1 downregulation. The sequence of the PCR product of the cDNA encoding the dad1 homologue was aligned with the annotated dad1 (C_20215) from the Chlamydomonas database (http://genome.jgi-psf.org:8080/annotator/servlet/jgi.annotation.Annotation?pDb=chlre2); Annotation?pDb=chlre2); this sequence was found to show 100% identity, both at the nucleotide and amino acid level. The 327 bp transcript showed an open reading frame of 87 amino acid residues. The deduced amino acid sequence of the putative C. reinhardtii DAD1 homologue showed 54% identity with Oryza sativa, 56% identity with Drosophila melanogaster, 66% identity with Xenopus laevis, and 64% identity with Homo sapiens, Sus scrofa, Gallus gallus, Rattus norvegicus and Mus musculus.

  9. Functional annotation and ENU

    OpenAIRE

    Gunn, Teresa M.

    2012-01-01

    Functional annotation of every gene in the mouse genome is a herculean task that requires a multifaceted approach. Many large-scale initiatives are contributing to this undertaking. The International Knockout Mouse Consortium (IKMC) plans to mutate every protein-coding gene, using a combination of gene trapping and gene targeting in embryonic stem cells. Many other groups are performing using the chemical mutagen ethylnitrosourea (ENU) or transpon-based systems to induce mutations, screening ...

  10. Studies on flagellar shortening in Chlamydomonas reinhardtii

    International Nuclear Information System (INIS)

    Flagellar shortening of Chlamydomonas reinhardtii was promoted by sodium chloride, pyrophosphate (sodium, potassium and ammonium salts), EDTA and EGTA, succinate, citrate and oxalate (sodium salts), caffeine and aminophylline. Removal of calcium from the medium potentiated the effects of these agents in inducing shortening. Investigations of the release of phosphorylated compounds to the medium during pyrophosphate-induced flagellar shortening of cells pre-labelled with 32P, revealed an as yet unidentified 32P-labelled compound with distinct chromatographic properties. Chromatography and electrophoresis indicates that it is a small, highly polar molecule with a high charge to mass ratio, containing thermo- and acid-labile phosphate linkages. Investigations showed of the release of 35S-labelled protein to the medium from cells pre-labelled with 35S-sulfate showed that flagellated cells released two prominent polypeptides which comigrated with α- and β-flagellar tubulin on SDS polyacrylamide gel electrophoresis, while deflagellated cells did not

  11. Cilia and ciliopathies: From Chlamydomonas and beyond

    Institute of Scientific and Technical Information of China (English)

    PAN JunMin

    2008-01-01

    The biological function of motile cilia/flagella has long been recognized. The non-motile primary cilium, once regarded as a vestigial organelle;however, has been found recently to play unexpected roles in mammalian physiology and development. Defects in cilia have profound impact on human health. Diseases related to cilia, collectively called ciliopathies include male infertility, primary cilia dyskinesia, renal cyst formation, blindness, polydactyly, obesity, hypertension, and even mental retardation. Our current understanding of cilia and ciliopathies has been fueled by basic research employing various model organisms including Chlamydomonas, a unicellular green alga. This review article provides a general introduction to the cell biology of cilia and an overview of various cilia-relateddiseases.

  12. A photorespiratory mutant of Chlamydomonas reinhardtii

    International Nuclear Information System (INIS)

    A mutant strain of Chlamydomonas reinhardtii, designated 18-7F, has been isolated and characterized. 18-7F requires a high CO2 concentration for photoautrophic growth in spite of the apparent induction of a functional CO2 concentrating mechanism in air-adapted cells. In 2% O2 the photosynthetic characteristics of 18-7F and wild type are similar. In 21% O2, photosynthetic O2 evolution is severely inhibited in the mutant by preillumination in limiting CO2, although the apparent photosynthetic affinity for inorganic carbon is similar in preilluminated cells and in cells incubated in the dark prior to O2 evolution measurements. Net CO2 uptake is also inhibited when the cells are exposed to air (21% O2, 0.035% CO2, balance N2) for longer than a few minutes. [14C]Phosphoglycolate accumulates within 5 minutes of photosynthetic 14CO2 fixation in cells of 18-7F. Phosphoglycolate does not accumulate in wild type. Phosphoglycolate phosphatase activity in extracts from air-adapted cells of 18-7F is 10 to 20% of that in wild-type Chlamydomonas. The activity of phosphoglycolate phosphatase in heterozygous diploids is intermediate between that of homozygous mutant and wild-type diploids. It was concluded that the high-CO2 requiring phenotype in 18-7F results from a phosphoglycolate phosphatase deficiency. Genetic analyses indicate that this deficiency results from a single-gene, nuclear mutation. We have named the locus pgp-1

  13. Toxicity of PAMAM dendrimers to Chlamydomonas reinhardtii

    International Nuclear Information System (INIS)

    In recent decades, a new class of polymeric materials, PAMAM dendrimers, has attracted marked interest owing to their unique nanoscopic architecture and their hopeful perspectives in nanomedicine and therapeutics. However, the potential release of dendrimers into the aquatic environment raises the issue about their toxicity on aquatic organisms. Our investigation sought to estimate the toxicity of cationic PAMAM dendrimers on the green alga, Chlamydomonas reinhardtii. Algal cultures were exposed to different concentrations (0.3-10 mg L-1) of low dendrimer generations (G2, G4 and G5) for 72 h. Potential adverse effects on Chlamydomonas were assessed using esterase activity (cell viability), photosynthetic O2 evolution, pigments content and chlorophyll a fluorescence transient. According to the median inhibitory concentration (IC50) appraised from esterase activity, toxicity on cell viability decreased with dendrimer generation number (2, 3 and 5 mg L-1 for G2, G4 and G5 dendrimers, respectively). Moreover, the three generations of dendrimers did not induce the same changes in the photosynthetic metabolism of the green alga. O2 evolution was stimulated in cultures exposed to the lowest generations tested (i.e. G2 and G4) whereas no significant effects were observed with G5. In addition, total chlorophyll content was increased after G2 treatment at 2.5 mg L-1. Finally, G2 and G4 had positive effects on photosystem II (PSII): the amount of active PSII reaction centers, the primary charge separation and the electron transport between QA and QB were all increased inducing activation of the photosynthetic electron transport chain. These changes resulted in stimulation of full photosynthetic performance.

  14. Tying Down Loose Ends in the Chlamydomonas Genome: Functional Significance of Abundant Upstream Open Reading Frames

    Directory of Open Access Journals (Sweden)

    Frederick R. Cross

    2016-02-01

    Full Text Available The Chlamydomonas genome has been sequenced, assembled, and annotated to produce a rich resource for genetics and molecular biology in this well-studied model organism. The annotated genome is very rich in open reading frames upstream of the annotated coding sequence (‘uORFs’: almost three quarters of the assigned transcripts have at least one uORF, and frequently more than one. This is problematic with respect to the standard ‘scanning’ model for eukaryotic translation initiation. These uORFs can be grouped into three classes: class 1, initiating in-frame with the coding sequence (CDS (thus providing a potential in-frame N-terminal extension; class 2, initiating in the 5′ untranslated sequences (5UT and terminating out-of-frame in the CDS; and class 3, initiating and terminating within the 5UT. Multiple bioinformatics criteria (including analysis of Kozak consensus sequence agreement and BLASTP comparisons to the closely related Volvox genome, and statistical comparison to cds and to random sequence controls indicate that of ∼4000 class 1 uORFs, approximately half are likely in vivo translation initiation sites. The proposed resulting N-terminal extensions in many cases will sharply alter the predicted biochemical properties of the encoded proteins. These results suggest significant modifications in ∼2000 of the ∼20,000 transcript models with respect to translation initiation and encoded peptides. In contrast, class 2 uORFs may be subject to purifying selection, and the existent ones (surviving selection are likely inefficiently translated. Class 3 uORFs are found in more than half of transcripts, frequently multiple times per transcript; however, they are remarkably similar to random sequence expectations with respect to size, number, and composition, and therefore may in most cases be selectively neutral.

  15. Predicting word sense annotation agreement

    DEFF Research Database (Denmark)

    Martinez Alonso, Hector; Johannsen, Anders Trærup; Lopez de Lacalle, Oier;

    2015-01-01

    High agreement is a common objective when annotating data for word senses. However, a number of factors make perfect agreement impossible, e.g. the limitations of the sense inventories, the difficulty of the examples or the interpretation preferences of the annotations. Estimating potential...... agreement is thus a relevant task to supplement the evaluation of sense annotations. In this article we propose two methods to predict agreement on word-annotation instances. We experiment with a continuous representation and a three-way discretization of observed agreement. In spite of the difficulty of...

  16. The Ensembl gene annotation system.

    Science.gov (United States)

    Aken, Bronwen L; Ayling, Sarah; Barrell, Daniel; Clarke, Laura; Curwen, Valery; Fairley, Susan; Fernandez Banet, Julio; Billis, Konstantinos; García Girón, Carlos; Hourlier, Thibaut; Howe, Kevin; Kähäri, Andreas; Kokocinski, Felix; Martin, Fergal J; Murphy, Daniel N; Nag, Rishi; Ruffier, Magali; Schuster, Michael; Tang, Y Amy; Vogel, Jan-Hinnerk; White, Simon; Zadissa, Amonida; Flicek, Paul; Searle, Stephen M J

    2016-01-01

    The Ensembl gene annotation system has been used to annotate over 70 different vertebrate species across a wide range of genome projects. Furthermore, it generates the automatic alignment-based annotation for the human and mouse GENCODE gene sets. The system is based on the alignment of biological sequences, including cDNAs, proteins and RNA-seq reads, to the target genome in order to construct candidate transcript models. Careful assessment and filtering of these candidate transcripts ultimately leads to the final gene set, which is made available on the Ensembl website. Here, we describe the annotation process in detail.Database URL: http://www.ensembl.org/index.html. PMID:27337980

  17. Heat shock induced change in protein ubiquitination in Chlamydomonas

    International Nuclear Information System (INIS)

    Ubiquitin was purified from pea (Pisum sativum L.) and its antibody was produced. Western blot analysis showed that the antibody cross-reacted with ubiquitins from a green alga Chlamydomonas reinhardtii, a brown alga Laminaria angustata and a red alga Porphyridium cruentum but not with ubiquitin from a blue-green alga Synechococcus sp. In Chlamydomonas, the antibody also reacted with some ubiquitinated proteins including 28- and 31-kDa polypeptides. The isoelectric points of Chlamydomonas ubiquitin and the 28- and 31-kDa ubiquitinated proteins were 8.0, 8.9 and 10.3, respectively. The ubiquitinated proteins, including the 28- and 31-kDa polypeptides were detected after in vitro ATP-dependent ubiquitination of Chlamydomonas cell extract with l25I-labeled bovine ubiquitin. Heat treatment of Chlamydomonas cells (>40°C) caused drastic increase of ubiquitinated proteins with high mol wt (>60kDa), and coordinated redistribution or decrease of other ubiquitinated proteins and free ubiquitin. Quantitative analysis revealed that the 28- and 31-kDa ubiquitinated proteins showed different responses against heat stress, i.e. the former being more sensitive than the latter. (author)

  18. Algal Functional Annotation Tool: a web-based analysis suite to functionally interpret large gene lists using integrated annotation and expression data

    Directory of Open Access Journals (Sweden)

    Merchant Sabeeha S

    2011-07-01

    Full Text Available Abstract Background Progress in genome sequencing is proceeding at an exponential pace, and several new algal genomes are becoming available every year. One of the challenges facing the community is the association of protein sequences encoded in the genomes with biological function. While most genome assembly projects generate annotations for predicted protein sequences, they are usually limited and integrate functional terms from a limited number of databases. Another challenge is the use of annotations to interpret large lists of 'interesting' genes generated by genome-scale datasets. Previously, these gene lists had to be analyzed across several independent biological databases, often on a gene-by-gene basis. In contrast, several annotation databases, such as DAVID, integrate data from multiple functional databases and reveal underlying biological themes of large gene lists. While several such databases have been constructed for animals, none is currently available for the study of algae. Due to renewed interest in algae as potential sources of biofuels and the emergence of multiple algal genome sequences, a significant need has arisen for such a database to process the growing compendiums of algal genomic data. Description The Algal Functional Annotation Tool is a web-based comprehensive analysis suite integrating annotation data from several pathway, ontology, and protein family databases. The current version provides annotation for the model alga Chlamydomonas reinhardtii, and in the future will include additional genomes. The site allows users to interpret large gene lists by identifying associated functional terms, and their enrichment. Additionally, expression data for several experimental conditions were compiled and analyzed to provide an expression-based enrichment search. A tool to search for functionally-related genes based on gene expression across these conditions is also provided. Other features include dynamic visualization of

  19. Swimming of Chlamydomonas reinhardtii in weakly elastic fluids

    Science.gov (United States)

    Yang, Jing; Gollub, Jerry; Arratia, Paulo

    2012-11-01

    The swimming behavior of the algae Chlamydomonas reinhardtii in weakly elastic fluids is investigated in experiments using microscopy and tracking methods. The effects of fluid viscosity and elasticity on the swimming speed, flagellar shape, beating frequency, and efficiency are examined. Here, the fluid viscosity is varied using water and sucrose solutions, while fluid elasticity is introduced by adding flexible polymer CMC (carboxymethyl cellulose) to the buffer solution. Swimming experiments are performed in a thin-film apparatus equipped with a microscope and high-speed camera. We find that even small amounts of fluid elasticity can have a significant effect on the swimming kinematics and dynamics of Chlamydomonas because of the relatively high beating frequency of its flagella (50-60 Hz). For example, the Chlamydomonas swimming speed is hindered by fluid elasticity compared to Newtonian fluids. In addition, the algae swimming speed decreases as the fluid elasticity is increased. This research is supported by the NSF through grant DMR-1104705.

  20. Collective dynamics of social annotation

    CERN Document Server

    Cattuto, Ciro; Baldassarri, Andrea; Schehr, G; Loreto, Vittorio

    2009-01-01

    The enormous increase of popularity and use of the WWW has led in the recent years to important changes in the ways people communicate. An interesting example of this fact is provided by the now very popular social annotation systems, through which users annotate resources (such as web pages or digital photographs) with text keywords dubbed tags. Understanding the rich emerging structures resulting from the uncoordinated actions of users calls for an interdisciplinary effort. In particular concepts borrowed from statistical physics, such as random walks, and the complex networks framework, can effectively contribute to the mathematical modeling of social annotation systems. Here we show that the process of social annotation can be seen as a collective but uncoordinated exploration of an underlying semantic space, pictured as a graph, through a series of random walks. This modeling framework reproduces several aspects, so far unexplained, of social annotation, among which the peculiar growth of the size of the...

  1. Temperature-sensitive rubisco mutant of Chlamydomonas

    International Nuclear Information System (INIS)

    The Chlamydomonas reinhardtii mutant 68-4PP is a temperature-sensitive mutant that lacks photosynthetic ability at 350C, but is able to grow photosynthetically at 250C. Genetic analysis indicated that 68-4PP is a chloroplast mutant that is allelic with known Rubisco large-subunit structural-gene mutants, implying that 68-4PP also resulted from a mutation in the large-subunit gene. The 68-4PP mutant has about 35% of the wild-type level of Rubisco holoenzyme and carboxylase activity when grown at 250C, but it has less than 10% of normal holoenzyme and carboxylase activity when grown at 350C. However, [35S]-sulfate pulse labeling showed that Rubisco subunits were synthesized at normal rates at both temperatures. More significantly, the ratio of carboxylase activity in the absence and presence of oxygen at a limiting CO2 concentration (6.6 μM) was about 2.2 for the mutant enzyme, as compared to about 3.0 for the wild-type enzyme. The decreased ratio of the mutant enzyme is maternally inherited, indicating that this reduced oxygen sensitivity results from a mutation in chloroplast DNA. The authors have recently cloned the 68-4PP Rubisco large-subunit gene, and DNA sequencing is in progress

  2. Annotation of Regular Polysemy

    DEFF Research Database (Denmark)

    Martinez Alonso, Hector

    Regular polysemy has received a lot of attention from the theory of lexical semantics and from computational linguistics. However, there is no consensus on how to represent the sense of underspecified examples at the token level, namely when annotating or disambiguating senses of metonymic words...... like “London” (Location/Organization) or “cup” (Container/Content). The goal of this dissertation is to assess whether metonymic sense underspecification justifies incorporating a third sense into our sense inventories, thereby treating the underspecified sense as independent from the literal and...... metonymic. We have conducted an analysis in English, Danish and Spanish. Later on, we have tried to replicate the human judgments by means of unsupervised and semi-supervised sense prediction. The automatic sense-prediction systems have been unable to find empiric evidence for the underspecified sense, even...

  3. Analysis of Axonemal Assembly During Ciliary Regeneration in Chlamydomonas.

    Science.gov (United States)

    Hunter, Emily L; Sale, Winfield S; Alford, Lea M

    2016-01-01

    Chlamydomonas reinhardtii is an outstanding model genetic organism for study of assembly of cilia. Here, methods are described for synchronization of ciliary regeneration in Chlamydomonas to analyze the sequence in which ciliary proteins assemble. In addition, the methods described allow analysis of the mechanisms involved in regulation of ciliary length, the proteins required for ciliary assembly, and the temporal expression of genes encoding ciliary proteins. Ultimately, these methods can contribute to discovery of conserved genes that when defective lead to abnormal ciliary assembly and human disease. PMID:27514926

  4. Gene Ontology annotations and resources.

    Science.gov (United States)

    Blake, J A; Dolan, M; Drabkin, H; Hill, D P; Li, Ni; Sitnikov, D; Bridges, S; Burgess, S; Buza, T; McCarthy, F; Peddinti, D; Pillai, L; Carbon, S; Dietze, H; Ireland, A; Lewis, S E; Mungall, C J; Gaudet, P; Chrisholm, R L; Fey, P; Kibbe, W A; Basu, S; Siegele, D A; McIntosh, B K; Renfro, D P; Zweifel, A E; Hu, J C; Brown, N H; Tweedie, S; Alam-Faruque, Y; Apweiler, R; Auchinchloss, A; Axelsen, K; Bely, B; Blatter, M -C; Bonilla, C; Bouguerleret, L; Boutet, E; Breuza, L; Bridge, A; Chan, W M; Chavali, G; Coudert, E; Dimmer, E; Estreicher, A; Famiglietti, L; Feuermann, M; Gos, A; Gruaz-Gumowski, N; Hieta, R; Hinz, C; Hulo, C; Huntley, R; James, J; Jungo, F; Keller, G; Laiho, K; Legge, D; Lemercier, P; Lieberherr, D; Magrane, M; Martin, M J; Masson, P; Mutowo-Muellenet, P; O'Donovan, C; Pedruzzi, I; Pichler, K; Poggioli, D; Porras Millán, P; Poux, S; Rivoire, C; Roechert, B; Sawford, T; Schneider, M; Stutz, A; Sundaram, S; Tognolli, M; Xenarios, I; Foulgar, R; Lomax, J; Roncaglia, P; Khodiyar, V K; Lovering, R C; Talmud, P J; Chibucos, M; Giglio, M Gwinn; Chang, H -Y; Hunter, S; McAnulla, C; Mitchell, A; Sangrador, A; Stephan, R; Harris, M A; Oliver, S G; Rutherford, K; Wood, V; Bahler, J; Lock, A; Kersey, P J; McDowall, D M; Staines, D M; Dwinell, M; Shimoyama, M; Laulederkind, S; Hayman, T; Wang, S -J; Petri, V; Lowry, T; D'Eustachio, P; Matthews, L; Balakrishnan, R; Binkley, G; Cherry, J M; Costanzo, M C; Dwight, S S; Engel, S R; Fisk, D G; Hitz, B C; Hong, E L; Karra, K; Miyasato, S R; Nash, R S; Park, J; Skrzypek, M S; Weng, S; Wong, E D; Berardini, T Z; Huala, E; Mi, H; Thomas, P D; Chan, J; Kishore, R; Sternberg, P; Van Auken, K; Howe, D; Westerfield, M

    2013-01-01

    The Gene Ontology (GO) Consortium (GOC, http://www.geneontology.org) is a community-based bioinformatics resource that classifies gene product function through the use of structured, controlled vocabularies. Over the past year, the GOC has implemented several processes to increase the quantity, quality and specificity of GO annotations. First, the number of manual, literature-based annotations has grown at an increasing rate. Second, as a result of a new 'phylogenetic annotation' process, manually reviewed, homology-based annotations are becoming available for a broad range of species. Third, the quality of GO annotations has been improved through a streamlined process for, and automated quality checks of, GO annotations deposited by different annotation groups. Fourth, the consistency and correctness of the ontology itself has increased by using automated reasoning tools. Finally, the GO has been expanded not only to cover new areas of biology through focused interaction with experts, but also to capture greater specificity in all areas of the ontology using tools for adding new combinatorial terms. The GOC works closely with other ontology developers to support integrated use of terminologies. The GOC supports its user community through the use of e-mail lists, social media and web-based resources. PMID:23161678

  5. Estudio del metabolismo del glicolato en celulas de Chlamydomonas reinhardtii

    OpenAIRE

    Borrero Rubio, José Antonio

    1994-01-01

    En este trabajo pretendemos contribuir a los actuales conocimientos sobre el metabolismo del glicolato en Chlamydomonas reinhardtii desde tres aproximaciones:1. Por una parte , analizar las actividades enzimáticas implicadas en la biosíntesis y oxidación

  6. Dissecting the molecular mechanisms of intraflagellar transport in Chlamydomonas

    DEFF Research Database (Denmark)

    Pedersen, L. B.; Geimer, S.; Rosenbaum, J. L.

    2006-01-01

    the IFT system have been identified and characterized, but the mechanisms by which these different components are coordinated and regulated at the flagellar base and tip are unclear. Results Using a variety of Chlamydomonas mutants, we confirm that cDynein1b requires kinesin-2 for transport toward the...

  7. Manganese encrustation of zygospores of a chlamydomonas (chlorophyta: volvocales).

    Science.gov (United States)

    Schulz-Baldes, M; Lewin, R A

    1975-06-13

    In media containing normal trace-element supplements, but not in manganese-deficient media, zygospores of a new species of Chlamydomonas (isolated from soil) become encrusted with a dark brown mineral coating. Staining with benzidine indicates that the encrustation is rich in manganese. This has been confirmed by x-ray analysis in combination with a scanning electron microscope. PMID:17798436

  8. Model of carbon dioxide assimilation in Chlamydomonas reinhardii

    Energy Technology Data Exchange (ETDEWEB)

    Spalding, M.H.; Portis, A.R. Jr.

    1985-01-01

    A simple model of photosynthetic CO/sub 2/ assimilation in Chlamydomonas has been developed in order to evaluate whether a CO/sub 2/-concentrating system could explain the photosynthetic characteristics of this alga (high apparent affinity for CO/sub 2/, low photorespiration, little O/sub 2/ inhibition of photosynthesis, and low CO/sub 2/ compensation concentration). Similarly, the model was developed to evaluate whether the proposed defects in the CO/sub 2/-concentrating system of two Chlamydomonas mutants were consistent with their observed photosynthetic characteristics. The model treats a Chlamydomonas cell as a single compartment with two carbon inputs: passive diffusion of CO/sub 2/, and active transport of HCO/sub 3//sup -/. Internal inorganic carbon was considered to have two potential fates: assimilation to fixed carbon via ribulose 1,5-bisphosphate carboxylase-oxygenase or exiting the cell by either passive CO/sub 2/ diffusion or reversal of HCO/sub 3//sup -/ transport. Published values for kinetic parameters were used where possible. The model accurately reproduced the CO/sub 2/-response curves of photosynthesis for wild-type Chlamydomonas, the two mutants defective in the CO/sub 2/-concentrating system, and a double mutant constructed by crossing these two mutants. The model also predicts steady-state internal inorganic-carbon concentrations in reasonable agreement with measured values in all four cases. Carbon dioxide compensation concentrations for wild-type Chlamydomonas were accurately predicted by the model and those predicted for the mutants were in qualitative agreement with measured values. The model also allowed calculation of approximate energy costs of the CO/sub 2/-concentrating system. These calculations indicate that the system may be no more energy-costly than CO/sub 4/ photosynthesis. 38 references, 4 figures, 4 tables.

  9. UV-B Perception and Acclimation in Chlamydomonas reinhardtii.

    Science.gov (United States)

    Tilbrook, Kimberley; Dubois, Marine; Crocco, Carlos D; Yin, Ruohe; Chappuis, Richard; Allorent, Guillaume; Schmid-Siegert, Emanuel; Goldschmidt-Clermont, Michel; Ulm, Roman

    2016-04-01

    Plants perceive UV-B, an intrinsic component of sunlight, via a signaling pathway that is mediated by the photoreceptor UV RESISTANCE LOCUS8 (UVR8) and induces UV-B acclimation. To test whether similar UV-B perception mechanisms exist in the evolutionarily distant green alga Chlamydomonas reinhardtii, we identified Chlamydomonas orthologs of UVR8 and the key signaling factor CONSTITUTIVELY PHOTOMORPHOGENIC1 (COP1). Cr-UVR8 shares sequence and structural similarity to Arabidopsis thaliana UVR8, has conserved tryptophan residues for UV-B photoreception, monomerizes upon UV-B exposure, and interacts with Cr-COP1 in a UV-B-dependent manner. Moreover, Cr-UVR8 can interact with At-COP1 and complement the Arabidopsis uvr8 mutant, demonstrating that it is a functional UV-B photoreceptor. Chlamydomonas shows apparent UV-B acclimation in colony survival and photosynthetic efficiency assays. UV-B exposure, at low levels that induce acclimation, led to broad changes in the Chlamydomonas transcriptome, including in genes related to photosynthesis. Impaired UV-B-induced activation in the Cr-COP1 mutant hit1 indicates that UVR8-COP1 signaling induces transcriptome changes in response to UV-B. Also, hit1 mutants are impaired in UV-B acclimation. Chlamydomonas UV-B acclimation preserved the photosystem II core proteins D1 and D2 under UV-B stress, which mitigated UV-B-induced photoinhibition. These findings highlight the early evolution of UVR8 photoreceptor signaling in the green lineage to induce UV-B acclimation and protection. PMID:27020958

  10. NCBI prokaryotic genome annotation pipeline.

    Science.gov (United States)

    Tatusova, Tatiana; DiCuccio, Michael; Badretdin, Azat; Chetvernin, Vyacheslav; Nawrocki, Eric P; Zaslavsky, Leonid; Lomsadze, Alexandre; Pruitt, Kim D; Borodovsky, Mark; Ostell, James

    2016-08-19

    Recent technological advances have opened unprecedented opportunities for large-scale sequencing and analysis of populations of pathogenic species in disease outbreaks, as well as for large-scale diversity studies aimed at expanding our knowledge across the whole domain of prokaryotes. To meet the challenge of timely interpretation of structure, function and meaning of this vast genetic information, a comprehensive approach to automatic genome annotation is critically needed. In collaboration with Georgia Tech, NCBI has developed a new approach to genome annotation that combines alignment based methods with methods of predicting protein-coding and RNA genes and other functional elements directly from sequence. A new gene finding tool, GeneMarkS+, uses the combined evidence of protein and RNA placement by homology as an initial map of annotation to generate and modify ab initio gene predictions across the whole genome. Thus, the new NCBI's Prokaryotic Genome Annotation Pipeline (PGAP) relies more on sequence similarity when confident comparative data are available, while it relies more on statistical predictions in the absence of external evidence. The pipeline provides a framework for generation and analysis of annotation on the full breadth of prokaryotic taxonomy. For additional information on PGAP see https://www.ncbi.nlm.nih.gov/genome/annotation_prok/ and the NCBI Handbook, https://www.ncbi.nlm.nih.gov/books/NBK174280/. PMID:27342282

  11. Developing molecular tools for Chlamydomonas reinhardtii

    Science.gov (United States)

    Noor-Mohammadi, Samaneh

    Microalgae have garnered increasing interest over the years for their ability to produce compounds ranging from biofuels to neutraceuticals. A main focus of researchers has been to use microalgae as a natural bioreactor for the production of valuable and complex compounds. Recombinant protein expression in the chloroplasts of green algae has recently become more routine; however, the heterologous expression of multiple proteins or complete biosynthetic pathways remains a significant challenge. To take full advantage of these organisms' natural abilities, sophisticated molecular tools are needed to be able to introduce and functionally express multiple gene biosynthetic pathways in its genome. To achieve the above objective, we have sought to establish a method to construct, integrate and express multigene operons in the chloroplast and nuclear genome of the model microalgae Chlamydomonas reinhardtii. Here we show that a modified DNA Assembler approach can be used to rapidly assemble multiple-gene biosynthetic pathways in yeast and then integrate these assembled pathways at a site-specific location in the chloroplast, or by random integration in the nuclear genome of C. reinhardtii. As a proof of concept, this method was used to successfully integrate and functionally express up to three reporter proteins (AphA6, AadA, and GFP) in the chloroplast of C. reinhardtii and up to three reporter proteins (Ble, AphVIII, and GFP) in its nuclear genome. An analysis of the relative gene expression of the engineered strains showed significant differences in the mRNA expression levels of the reporter genes and thus highlights the importance of proper promoter/untranslated-region selection when constructing a target pathway. In addition, this work focuses on expressing the cofactor regeneration enzyme phosphite dehydrogenase (PTDH) in the chloroplast and nuclear genomes of C. reinhardtii. The PTDH enzyme converts phosphite into phosphate and NAD(P)+ into NAD(P)H. The reduced

  12. Collective dynamics of social annotation.

    Science.gov (United States)

    Cattuto, Ciro; Barrat, Alain; Baldassarri, Andrea; Schehr, Gregory; Loreto, Vittorio

    2009-06-30

    The enormous increase of popularity and use of the worldwide web has led in the recent years to important changes in the ways people communicate. An interesting example of this fact is provided by the now very popular social annotation systems, through which users annotate resources (such as web pages or digital photographs) with keywords known as "tags." Understanding the rich emergent structures resulting from the uncoordinated actions of users calls for an interdisciplinary effort. In particular concepts borrowed from statistical physics, such as random walks (RWs), and complex networks theory, can effectively contribute to the mathematical modeling of social annotation systems. Here, we show that the process of social annotation can be seen as a collective but uncoordinated exploration of an underlying semantic space, pictured as a graph, through a series of RWs. This modeling framework reproduces several aspects, thus far unexplained, of social annotation, among which are the peculiar growth of the size of the vocabulary used by the community and its complex network structure that represents an externalization of semantic structures grounded in cognition and that are typically hard to access. PMID:19506244

  13. SENTIMENT ANALYSIS OF DOCUMENT BASED ON ANNOTATION

    Directory of Open Access Journals (Sweden)

    Archana Shukla

    2011-11-01

    Full Text Available I present a tool which tells the quality of document or its usefulness based on annotations. Annotation mayinclude comments, notes, observation, highlights, underline, explanation, question or help etc. commentsare used for evaluative purpose while others are used for summarization or for expansion also. Furtherthese comments may be on another annotation. Such annotations are referred as meta-annotation. Allannotation may not get equal weightage. My tool considered highlights, underline as well as comments toinfer the collective sentiment of annotators. Collective sentiments of annotators are classified as positive,negative, objectivity. My tool computes collective sentiment of annotations in two manners. It counts all theannotation present on the documents as well as it also computes sentiment scores of all annotation whichincludes comments to obtain the collective sentiments about the document or to judge the quality ofdocument. I demonstrate the use of tool on research paper.

  14. Vcfanno: fast, flexible annotation of genetic variants.

    Science.gov (United States)

    Pedersen, Brent S; Layer, Ryan M; Quinlan, Aaron R

    2016-01-01

    The integration of genome annotations is critical to the identification of genetic variants that are relevant to studies of disease or other traits. However, comprehensive variant annotation with diverse file formats is difficult with existing methods. Here we describe vcfanno, which flexibly extracts and summarizes attributes from multiple annotation files and integrates the annotations within the INFO column of the original VCF file. By leveraging a parallel "chromosome sweeping" algorithm, we demonstrate substantial performance gains by annotating ~85,000 variants per second with 50 attributes from 17 commonly used genome annotation resources. Vcfanno is available at https://github.com/brentp/vcfanno under the MIT license. PMID:27250555

  15. The Chlamydomonas cell wall: characterization of the wall framework

    OpenAIRE

    1985-01-01

    The cell wall of the biflagellate alga Chlamydomonas reinhardtii is a multilayered, extracellular matrix composed of carbohydrates and 20-25 polypeptides. To learn more about the forces responsible for the integrity of this cellulose-deficient cell wall, we have begun studies to identify and characterize the framework of the wall and to determine the effects of the cell wall-degrading enzyme, lysin, on framework structure and protein composition. In these studies we used walls released into t...

  16. Lipidomic Analysis of Chlamydomonas reinhardtii under Nitrogen and Sulfur Deprivation

    OpenAIRE

    Dawei Yang; Donghui Song; Tobias Kind; Yan Ma; Jens Hoefkens; Oliver Fiehn

    2015-01-01

    Chlamydomonas reinhardtii accumulates lipids under complete nutrient starvation conditions while overall growth in biomass stops. In order to better understand biochemical changes under nutrient deprivation that maintain production of algal biomass, we used a lipidomic assay for analyzing the temporal regulation of the composition of complex lipids in C. reinhardtii in response to nitrogen and sulfur deprivation. Using a chip-based nanoelectrospray direct infusion into an ion trap mass spectr...

  17. High-efficiency transformation of Chlamydomonas reinhardtii by electroporation.

    OpenAIRE

    Shimogawara, K; Fujiwara, S.; Grossman, A; Usuda, H

    1998-01-01

    We have established a high-efficiency method for transforming the unicellular, green alga Chlamydomonas reinhardtii by electroporation. Electroporation of strains CC3395 and CC425, cell wall-less mutants devoid of argininosuccinate lyase (encoded by ARG7), in the presence of the plasmid pJD67 (which contains ARG7) was used to optimize conditions for the introduction of exogenous DNA. The conditions that were varied included osmolarity, temperature, concentration of exogenous DNA, voltage and ...

  18. Green algae Chlamydomonas reinhardtii possess endogenous sialylated N-glycans

    OpenAIRE

    Mamedov, Tarlan; Yusibov, Vidadi

    2011-01-01

    Green algae have a great potential as biofactories for the production of proteins. Chlamydomonas reinhardtii, a representative of eukaryotic microalgae, has been extensively used as a model organism to study light-induced gene expression, chloroplast biogenesis, photosynthesis, light perception, cell–cell recognition, and cell cycle control. However, little is known about the glycosylation machinery and N-linked glycan structures of green algae. In this study, we performed mass spectrometry a...

  19. Induction and Characterization of Mitochondrial DNA Mutants in Chlamydomonas Reinhardtii

    OpenAIRE

    Matagne, René-Fernand; Michel-Wolwertz, M.R.; Munaut, Carine; Duyckaerts, Claire; Sluse, Francis

    1989-01-01

    In addition to lethal minute colony mutations which correspond to loss of mitochondrial DNA, acriflavin induces in Chlamydomonas reinhardtii a low percentage of cells that grow in the light but do not divide under heterotrophic conditions. Two such obligate photoautotrophic mutants were shown to lack the cyanide-sensitive cytochrome pathway of the respiration and to have a reduced cytochrome c oxidase activity. In crosses to wild type, the mutations are transmitted almost exclusively from the...

  20. Mechanosensitive physiology of chlamydomonas reinhardtii under direct membrane distortion

    OpenAIRE

    Seul Ki Min; Gwang Heum Yoon; Jung Hyun Joo; Sang Jun Sim; Hwa Sung Shin

    2014-01-01

    Cellular membrane distortion invokes variations in cellular physiology. However, lack of an appropriate system to control the stress and facilitate molecular analyses has hampered progress of relevant studies. In this study, a microfluidic system that finely manipulates membrane distortion of Chlamydomonas reinhardtii (C. reinhardtii) was developed. The device facilitated a first-time demonstration that directs membrane distortion invokes variations in deflagellation, cell cycle, and lipid me...

  1. TETX: a novel nuclear selection marker for Chlamydomonas reinhardtii transformation

    OpenAIRE

    Garcia-Echauri, Sergio A; Cardineau, Guy A.

    2015-01-01

    Background Transformation of microalgae to obtain recombinant proteins, lipids or metabolites of economic value is of growing interest due to low costs associated with culture growth and scaling up. At present there are only three stable nuclear selection markers for the transformation of Chlamydomonas reinhardtii, which is the most commonly transformed microalgae, specifically: the aminoglycoside phosphotransferaseses aph7and aphVIII and the phleomycin resistance ble gene. As several microal...

  2. Transformace ptDNA \\kur{Chlamydomonas reinhardtii}

    OpenAIRE

    Husáková, Jana

    2011-01-01

    The aim of this master thesis was to test and compare two available methods of genetic transformation (biolistics, electroporation) of the plastid genome of green algae Chlamydomonas reinhardtii. For biolistic transformation a wide range of experimental parameters which generally influence ptDNA transformation efficiency was optimized: physiological condition of acceptor cells, type and size of microparticles, pressure of propulsion gas (helium), length of projectile trajectory, transformatio...

  3. An optimized, chemically regulated gene expression system for Chlamydomonas.

    Directory of Open Access Journals (Sweden)

    Paola Ferrante

    Full Text Available BACKGROUND: Chlamydomonas reinhardtii is a model system for algal and cell biology and is used for biotechnological applications, such as molecular farming or biological hydrogen production. The Chlamydomonas metal-responsive CYC6 promoter is repressed by copper and induced by nickel ions. However, induction by nickel is weak in some strains, poorly reversible by chelating agents like EDTA, and causes, at high concentrations, toxicity side effects on Chlamydomonas growth. Removal of these bottlenecks will encourage the wide use of this promoter as a chemically regulated gene expression system. METHODOLOGY: Using a codon-optimized Renilla luciferase as a reporter gene, we explored several strategies to improve the strength and reversibility of CYC6 promoter induction. Use of the first intron of the RBCS2 gene or of a modified TAP medium increases the strength of CYC6 induction up to 20-fold. In the modified medium, induction is also obtained after addition of specific copper chelators, like TETA. At low concentrations (up to 10 microM TETA is a more efficient inducer than Ni, which becomes a very efficient inducer at higher concentrations (50 microM. Neither TETA nor Ni show toxicity effects at the concentrations used. Unlike induction by Ni, induction by TETA is completely reversible by micromolar copper concentrations, thus resulting in a transient "wave" in luciferase activity, which can be repeated in subsequent growth cycles. CONCLUSIONS: We have worked out a chemically regulated gene expression system that can be finely tuned to produce temporally controlled "waves" in gene expression. The use of cassettes containing the CYC6 promoter, and of modified growth media, is a reliable and economically sustainable system for the temporally controlled expression of foreign genes in Chlamydomonas.

  4. Relevance of nutrient media composition for hydrogen production in Chlamydomonas.

    Science.gov (United States)

    Gonzalez-Ballester, David; Jurado-Oller, Jose Luis; Fernandez, Emilio

    2015-09-01

    Microalgae are capable of biological H2 photoproduction from water, solar energy, and a variety of organic substrates. Acclimation responses to different nutrient regimes finely control photosynthetic activity and can influence H2 production. Hence, nutrient stresses are an interesting scenario to study H2 production in photosynthetic organisms. In this review, we mainly focus on the H2-production mechanisms in Chlamydomonas reinhardtii and the physiological relevance of the nutrient media composition when producing H2. PMID:25952745

  5. Characterizing the Anaerobic Response of Chlamydomonas reinhardtii by Quantitative Proteomics

    OpenAIRE

    Terashima, Mia; Specht, Michael; Naumann, Bianca; Hippler, Michael

    2010-01-01

    The versatile metabolism of the green alga Chlamydomonas reinhardtii is reflected in its complex response to anaerobic conditions. The anaerobic response is also remarkable in the context of renewable energy because C. reinhardtii is able to produce hydrogen under anaerobic conditions. To identify proteins involved during anaerobic acclimation as well as to localize proteins and pathways to the powerhouses of the cell, chloroplasts and mitochondria from C. reinhardtii in aerobic and anaerobic...

  6. Molecular Map of the Chlamydomonas reinhardtii Nuclear Genome

    OpenAIRE

    Kathir, Pushpa; LaVoie, Matthew; Brazelton, William J.; Haas, Nancy A.; Lefebvre, Paul A.; Silflow, Carolyn D.

    2003-01-01

    We have prepared a molecular map of the Chlamydomonas reinhardtii genome anchored to the genetic map. The map consists of 264 markers, including sequence-tagged sites (STS), scored by use of PCR and agarose gel electrophoresis, and restriction fragment length polymorphism markers, scored by use of Southern blot hybridization. All molecular markers tested map to one of the 17 known linkage groups of C. reinhardtii. The map covers approximately 1,000 centimorgans (cM). Any position on the C. re...

  7. New thioredoxin targets in the unicellular photosynthetic eukaryote Chlamydomonas reinhardtii

    OpenAIRE

    Lemaire, Stéphane D.; Guillon, Blanche; Le Maréchal, Pierre; Keryer, Eliane; Miginiac-Maslow, Myroslawa; Decottignies, Paulette

    2004-01-01

    Proteomics were used to identify the proteins from the eukaryotic unicellular green alga Chlamydomonas reinhardtii that can be reduced by thioredoxin. These proteins were retained specifically on a thioredoxin affinity column made of a monocysteinic thioredoxin mutant able to form mixed disulfides with its targets. Of a total of 55 identified targets, 29 had been found previously in higher plants or Synechocystis, but 26 were new targets. Biochemical tests were performed on three of them, sho...

  8. D-lactate metabolism in the alga, Chlamydomonas Reinhardtii

    International Nuclear Information System (INIS)

    [14C]D-lactate rapidly accumulates in Chlamydomonas cells under anaerobic conditions from the sugar-phosphate pools which are labeled during photosynthesis with 14CO2. A soluble D-lactate dehydrogenase (30 μmol NADH oxidized/h/mg Chl), which functions only in the direction of pyruvate reduction, has been partially purified and characterized. The D-lactate is reoxidized in Chlamydomonas by a mitochondrial membrane-bound dehydrogenase. This enzyme is known in the plant literature as glycolate dehydrogenase, an enzyme of the oxidative photosynthetic carbon (C2) cycle. This dehydrogenase may be linked to the mitochondrial electron transport chain, although the direct electron acceptor is unknown. Therefore, D-lactate accumulation may be, in part, due to the shut down of electron transport during anaerobiosis. In vivo chase experiments have shown that the D-lactate turns over rapidly when algal cells, which have been grown with air levels of CO2 (0.04%), are returned to aerobic conditions in the light. Such turnover is not observed in cells which had been grown with 1 to 5% CO2. Cells grown with high CO2 have lower levels of glycolate dehydrogenase activity. They are currently using mutants of Chlamydomonas deficient in mitochondrial respiration to study the role of D-lactate oxidation in these algae

  9. Characterization of new radioresistant strains of Chlamydomonas reinhardtii

    International Nuclear Information System (INIS)

    The purpose of this work is to investigate 4 new mutant strains of Chlamydomonas reinhardtii induced in respect to their radioresistance at different levels: cellular, molecular and biochemical. A comparison between radioresistance of the strains, DNA-ssb repair activity and pigment contents (chl 'a', chl 'b' and carotenoids) is made. Strain 137C(+) and mutant strains GK-1(+), GK-2(+), GK-3(+), and AKK-9-9(-) are used. The radioresistance has been assessed according to colony forming ability of the strains after irradiation with gamma rays (60C0, I=12.4 rads-1 doses 10, 50, 100, 150, 200 and 250 Gy). The data obtained reveal that there is a relationship between radioresistance, DNA-ssb repair efficiency and plastid pigment content in the tested Chlamydomonas reinhardtii strains. This relationship is most pronounced in strain AK-9-9 which displays the highest level of radioresistance. On the basis of data obtained the authors propose mutant strain AK-9-9 to be included in the existing collection of mutant strains of Chlamydomonas reinhardtii

  10. Tools for regulated gene expression in the chloroplast of Chlamydomonas.

    Science.gov (United States)

    Rochaix, Jean-David; Surzycki, Raymond; Ramundo, Silvia

    2014-01-01

    The green unicellular alga Chlamydomonas reinhardtii has emerged as a very attractive model system for chloroplast genetic engineering. Algae can be transformed readily at the chloroplast level through bombardment of cells with a gene gun, and transformants can be selected using antibiotic resistance or phototrophic growth. An inducible chloroplast gene expression system could be very useful for several reasons. First, it could be used to elucidate the function of essential chloroplast genes required for cell growth and survival. Second, it could be very helpful for expressing proteins which are toxic to the algal cells. Third, it would allow for the reversible depletion of photosynthetic complexes thus making it possible to study their biogenesis in a controlled fashion. Fourth, it opens promising possibilities for hydrogen production in Chlamydomonas. Here we describe an inducible/repressible chloroplast gene expression system in Chlamydomonas in which the copper-regulated Cyc6 promoter drives the expression of the nuclear Nac2 gene encoding a protein which is targeted to the chloroplast where it acts specifically on the chloroplast psbD 5'-untranslated region and is required for the stable accumulation of the psbD mRNA and photosystem II. The system can be used for any chloroplast gene or transgene by placing it under the control of the psbD 5'-untranslated region. PMID:24599871

  11. Activation of Autophagy by Metals in Chlamydomonas reinhardtii.

    Science.gov (United States)

    Pérez-Martín, Marta; Blaby-Haas, Crysten E; Pérez-Pérez, María Esther; Andrés-Garrido, Ascensión; Blaby, Ian K; Merchant, Sabeeha S; Crespo, José L

    2015-09-01

    Autophagy is an intracellular self-degradation pathway by which eukaryotic cells recycle their own material in response to specific stress conditions. Exposure to high concentrations of metals causes cell damage, although the effect of metal stress on autophagy has not been explored in photosynthetic organisms. In this study, we investigated the effect of metal excess on autophagy in the model unicellular green alga Chlamydomonas reinhardtii. We show in cells treated with nickel an upregulation of ATG8 that is independent of CRR1, a global regulator of copper signaling in Chlamydomonas. A similar effect on ATG8 was observed with copper and cobalt but not with cadmium or mercury ions. Transcriptome sequencing data revealed an increase in the abundance of the protein degradation machinery, including that responsible for autophagy, and a substantial overlap of that increased abundance with the hydrogen peroxide response in cells treated with nickel ions. Thus, our results indicate that metal stress triggers autophagy in Chlamydomonas and suggest that excess nickel may cause oxidative damage, which in turn activates degradative pathways, including autophagy, to clear impaired components and recover cellular homeostasis. PMID:26163317

  12. Nucleated assembly of Chlamydomonas and Volvox cell walls.

    Science.gov (United States)

    Adair, W S; Steinmetz, S A; Mattson, D M; Goodenough, U W; Heuser, J E

    1987-11-01

    The Chlamydomonas reinhardtii cell wall is made up of hydroxyproline-rich glycoproteins, arranged in five distinct layers. The W6 (crystalline) layer contains three major glycoproteins (GP1, GP2, GP3), selectively extractable with chaotropic agents, that self-assemble into crystals in vitro. A system to study W6 assembly in a quantitative fashion was developed that employs perchlorate-extracted Chlamydomonas cells as nucleating agents. Wall reconstitution by biotinylated W6 monomers was monitored by FITC-streptavidin fluorescence and quick-freeze/deep-etch electron microscopy. Optimal reconstitution was obtained at monomer concentrations (0.2-0.3 mg/ml) well below those required for nonnucleated assembly. Assembly occurred from multiple nucleation sites, and faithfully reflected the structure of the intact W6 layer. Specificity of nucleated assembly was demonstrated using two cell-wall mutants (cw-2 and cw-15); neither served as a substrate for assembly of wild-type monomers. In addition, W6 sublayers were assembled from purified components: GP2 and GP3 coassembled to form the inner (W6A) sublayer; this then served as a substrate for self-assembly of GP1 into the outer (W6B) sublayer. Finally, evolutionary relationships between C. reinhardtii and two additional members of the Volvocales (Chlamydomonas eugametos and Volvox carteri) were explored by performing interspecific reconstitutions. Hybrid walls were obtained between C. reinhardtii and Volvox but not with C. eugametos, confirming taxonomic assignments based on structural criteria. PMID:3680387

  13. Actin is required for IFT regulation in Chlamydomonas reinhardtii.

    Science.gov (United States)

    Avasthi, Prachee; Onishi, Masayuki; Karpiak, Joel; Yamamoto, Ryosuke; Mackinder, Luke; Jonikas, Martin C; Sale, Winfield S; Shoichet, Brian; Pringle, John R; Marshall, Wallace F

    2014-09-01

    Assembly of cilia and flagella requires intraflagellar transport (IFT), a highly regulated kinesin-based transport system that moves cargo from the basal body to the tip of flagella [1]. The recruitment of IFT components to basal bodies is a function of flagellar length, with increased recruitment in rapidly growing short flagella [2]. The molecular pathways regulating IFT are largely a mystery. Because actin network disruption leads to changes in ciliary length and number, actin has been proposed to have a role in ciliary assembly. However, the mechanisms involved are unknown. In Chlamydomonas reinhardtii, conventional actin is found in both the cell body and the inner dynein arm complexes within flagella [3, 4]. Previous work showed that treating Chlamydomonas cells with the actin-depolymerizing compound cytochalasin D resulted in reversible flagellar shortening [5], but how actin is related to flagellar length or assembly remains unknown. Here we utilize small-molecule inhibitors and genetic mutants to analyze the role of actin dynamics in flagellar assembly in Chlamydomonas reinhardtii. We demonstrate that actin plays a role in IFT recruitment to basal bodies during flagellar elongation and that when actin is perturbed, the normal dependence of IFT recruitment on flagellar length is lost. We also find that actin is required for sufficient entry of IFT material into flagella during assembly. These same effects are recapitulated with a myosin inhibitor, suggesting that actin may act via myosin in a pathway by which flagellar assembly is regulated by flagellar length. PMID:25155506

  14. Meeting Report: Synthetic Biology Jamboree for Undergraduates

    Science.gov (United States)

    Campbell, A. Malcolm

    2005-01-01

    The field of synthetic biology (the name is derived from an analogy to synthetic chemistry) has recognized itself as a "field" only since about 2002. Synthetic biology has gotten some high-profile attention recently, but most people are not aware the field even exists. Synthetic biologists apply engineering principles to genomic circuits to…

  15. Systems Theory and Communication. Annotated Bibliography.

    Science.gov (United States)

    Covington, William G., Jr.

    This annotated bibliography presents annotations of 31 books and journal articles dealing with systems theory and its relation to organizational communication, marketing, information theory, and cybernetics. Materials were published between 1963 and 1992 and are listed alphabetically by author. (RS)

  16. International Standard for a Linguistic Annotation Framework

    CERN Document Server

    Romary, Laurent

    2004-01-01

    This paper describes the Linguistic Annotation Framework under development within ISO TC37 SC4 WG1. The Linguistic Annotation Framework is intended to serve as a basis for harmonizing existing language resources as well as developing new ones.

  17. Annotated Bibliography, Grades K-6.

    Science.gov (United States)

    Massachusetts Dept. of Education, Boston. Bureau of Nutrition Education and School Food Services.

    This annotated bibliography on nutrition is for the use of teachers at the elementary grade level. It contains a list of books suitable for reading about nutrition and foods for pupils from kindergarten through the sixth grade. Films and audiovisual presentations for classroom use are also listed. The names and addresses from which these materials…

  18. All-trans retinal constitutes the functional chromophore in Chlamydomonas rhodopsin

    OpenAIRE

    Hegemann, P.; Gärtner, W; R. Uhl

    1991-01-01

    Orientation of the green alga Chlamydomonas in light (phototaxis and stop responses) is controlled by a visual system with a rhodopsin as the functional photoreceptor. Here, we present evidence that in Chlamydomonas wild-type cells all-trans retinal is the predominant isomer and that it is present in amounts similar to that of the rhodopsin itself.

  19. The NIT1 Promoter Allows Inducible and Reversible Silencing of Centrin in Chlamydomonas reinhardtii

    OpenAIRE

    Koblenz, Bettina; Lechtreck, Karl-Ferdinand

    2005-01-01

    An inverted repeat corresponding to parts of the centrin gene of Chlamydomonas reinhardtii was placed downstream of the NIT1 promoter, which is induced by ammonium starvation. After induction, transformants developed centrin deficiency as assayed by immunofluorescence, Western blotting, and Northern blotting. The effect was reversible, demonstrating that the NIT1 promoter allowed controlled RNA interference in Chlamydomonas reinhardtii.

  20. Concept annotation in the CRAFT corpus

    OpenAIRE

    Bada Michael; Eckert Miriam; Evans Donald; Garcia Kristin; Shipley Krista; Sitnikov Dmitry; Baumgartner William A; Cohen K; Verspoor Karin; Blake Judith A; Hunter Lawrence E

    2012-01-01

    Abstract Background Manually annotated corpora are critical for the training and evaluation of automated methods to identify concepts in biomedical text. Results This paper presents the concept annotations of the Colorado Richly Annotated Full-Text (CRAFT) Corpus, a collection of 97 full-length, open-access biomedical journal articles that have been annotated both semantically and syntactically to serve as a research resource for the biomedical natural-language-processing (NLP) community. CRA...

  1. Annotating images by mining image search results

    NARCIS (Netherlands)

    X.J. Wang; L. Zhang; X. Li; W.Y. Ma

    2008-01-01

    Although it has been studied for years by the computer vision and machine learning communities, image annotation is still far from practical. In this paper, we propose a novel attempt at model-free image annotation, which is a data-driven approach that annotates images by mining their search results

  2. Eight questions about semantic web annotations

    OpenAIRE

    Euzenat, Jérôme

    2002-01-01

    Improving information retrieval is annotation¹s central goal. However, without sufficient planning, annotation - especially when running a robot and attaching automatically extracted content - risks producing incoherent information. The author recommends answering eight questions before you annotate. He provides a practical application of this approach, and discusses applying the questions to other systems.

  3. Annotation and Classification of Argumentative Writing Revisions

    Science.gov (United States)

    Zhang, Fan; Litman, Diane

    2015-01-01

    This paper explores the annotation and classification of students' revision behaviors in argumentative writing. A sentence-level revision schema is proposed to capture why and how students make revisions. Based on the proposed schema, a small corpus of student essays and revisions was annotated. Studies show that manual annotation is reliable with…

  4. Genome re-annotation: a wiki solution?

    OpenAIRE

    Salzberg, Steven L.

    2007-01-01

    The annotation of most genomes becomes outdated over time, owing in part to our ever-improving knowledge of genomes and in part to improvements in bioinformatics software. Unfortunately, annotation is rarely if ever updated and resources to support routine reannotation are scarce. Wiki software, which would allow many scientists to edit each genome's annotation, offers one possible solution.

  5. Evidence for transcription of three genes with characteristics of hydrogenases in the green alga Chlamydomonas noctigama

    Energy Technology Data Exchange (ETDEWEB)

    Skjaanes, Kari [Bioforsk, Fr. A. Dahls vei 20, N-1432 Aas (Norway); Department of Photochemistry and Molecular Science, The Aangstroem Laboratories, Uppsala University, Box 523, SE-751 20 Uppsala (Sweden); Pinto, Fernando Lopes; Lindblad, Peter [Department of Photochemistry and Molecular Science, The Aangstroem Laboratories, Uppsala University, Box 523, SE-751 20 Uppsala (Sweden)

    2010-02-15

    Some green algae have shown the ability to produce hydrogen under anaerobic conditions. The production of hydrogen in green algae is catalyzed by hydrogenases, which are small monomeric enzymes with high conversion efficiency and high oxygen sensitivity. Most green algae analyzed to date where hydrogenase genes are detected, have been shown to contain two distinct hydrogenases. However, very little is known about which functions the two different enzymes represent. There are also many unknowns within the mechanisms behind hydrogen production as to the roles hydrogenases play under different conditions, and consequently also about the potential for optimization of a hydrogen production process which could be found in this respect. This study focuses on the possibility for the presence of more than two hydrogenases in a single green alga. A large number of degenerate primers were designed and used to produce 3'-RACE products, which in turn were used to design gene specific primers used for PCR and 5'-RACE reactions. The sequences were aligned with known algal hydrogenases to identify products which had homology to these. Products where homology was identified were then explored further. A high number of clones from each band were sequenced to identify products with similar lengths which would not show up as separate bands on a gel. Sequences found to have homology with algal hydrogenases were translated into putative amino acid sequences and analyzed further to obtain detailed information about the presence of specific amino acids with known functions in the enzyme. This information was used to evaluate the likelihood of these transcripts coding for true hydrogenases, versus hydrogenase-like or narf-like proteins. We here present evidence showing that Chlamydomonas noctigama is able to transcribe three genes which share a significant number of characteristics with other known algal FeFe-hydrogenases. The three genes have been annotated HYDA1, HYDA2 and HYDA

  6. Experimental Definition and Validation of Protein Coding Transcripts in Chlamydomonas reinhardtii

    Energy Technology Data Exchange (ETDEWEB)

    Kourosh Salehi-Ashtiani; Jason A. Papin

    2012-01-13

    Algal fuel sources promise unsurpassed yields in a carbon neutral manner that minimizes resource competition between agriculture and fuel crops. Many challenges must be addressed before algal biofuels can be accepted as a component of the fossil fuel replacement strategy. One significant challenge is that the cost of algal fuel production must become competitive with existing fuel alternatives. Algal biofuel production presents the opportunity to fine-tune microbial metabolic machinery for an optimal blend of biomass constituents and desired fuel molecules. Genome-scale model-driven algal metabolic design promises to facilitate both goals by directing the utilization of metabolites in the complex, interconnected metabolic networks to optimize production of the compounds of interest. Using Chlamydomonas reinhardtii as a model, we developed a systems-level methodology bridging metabolic network reconstruction with annotation and experimental verification of enzyme encoding open reading frames. We reconstructed a genome-scale metabolic network for this alga and devised a novel light-modeling approach that enables quantitative growth prediction for a given light source, resolving wavelength and photon flux. We experimentally verified transcripts accounted for in the network and physiologically validated model function through simulation and generation of new experimental growth data, providing high confidence in network contents and predictive applications. The network offers insight into algal metabolism and potential for genetic engineering and efficient light source design, a pioneering resource for studying light-driven metabolism and quantitative systems biology. Our approach to generate a predictive metabolic model integrated with cloned open reading frames, provides a cost-effective platform to generate metabolic engineering resources. While the generated resources are specific to algal systems, the approach that we have developed is not specific to algae and

  7. Werkzeuge zur Annotation diachroner Korpora

    OpenAIRE

    Burghardt, Manuel; Wolff, Christian

    2009-01-01

    Wir diskutieren zunächst die Problematik der (syntaktischen) Annotation diachroner Korpora und stellen anschließend eine Evaluationsstudie vor, bei der mehr als 50 Annotationswerkzeuge und -frameworks vor dem Hintergrund eines funktionalen und software-ergonomischen Anforderungsprofils nach dem Qualitätsmodell von ISO/IEC 9126-1:2001 (Software engineering – Product quality – Part 1: Quality model) und ISO/IEC 25000:2005 (Software Engineering – Software product Quality Requirements and Evaluat...

  8. Effective viscosity of non-gravitactic Chlamydomonas Reinhardtii microswimmer suspensions

    Science.gov (United States)

    Mussler, Matthias; Rafaï, Salima; Peyla, Philippe; Wagner, Christian

    2013-03-01

    Active microswimmers are known to affect the macroscopic viscosity of suspensions in a more complex manner than passive particles. For puller-like microswimmers an increase in the viscosity has been observed. It has been suggested that the persistence of the orientation of the microswimmers hinders the rotation that is normally caused by the vorticity. It was previously shown that some sorts of algae are bottom-heavy swimmers, i.e., their centre of mass is not located in the centre of the body. In this way, the algae affect the vorticity of the flow when they are perpendicularly oriented to the axis of gravity. This orientation of gravity to vorticity is given in a rheometer that is equipped with a cone-plate geometry. Here we present measurements of the viscosity both in a cone-plate and a Taylor-Couette cell. The two set-ups yielded the same increase in viscosity although the axis of gravitation in the Taylor-Couette cell is parallel to the direction of vorticity. In a complementary experiment we tested the orientation of the direction of swimming through microscopic observation of single Chlamydomonas reinhardtii and could not identify a preferred orientation, i.e., our specific strain of Chlamydomonas reinhardtii are not bottom-heavy swimmers. We thus conclude that bottom heaviness is not a prerequisite for the increase of viscosity and that the effect of gravity on the rheology of our strain of Chlamydomonas reinhardtii is negligible. This finding reopens the question of whether the origin of persistence in the orientation of cells is actually responsible for the increased viscosity of the suspension.

  9. Synthesizing and salvaging NAD: lessons learned from Chlamydomonas reinhardtii.

    Directory of Open Access Journals (Sweden)

    Huawen Lin

    2010-09-01

    Full Text Available The essential coenzyme nicotinamide adenine dinucleotide (NAD+ plays important roles in metabolic reactions and cell regulation in all organisms. Bacteria, fungi, plants, and animals use different pathways to synthesize NAD+. Our molecular and genetic data demonstrate that in the unicellular green alga Chlamydomonas NAD+ is synthesized from aspartate (de novo synthesis, as in plants, or nicotinamide, as in mammals (salvage synthesis. The de novo pathway requires five different enzymes: L-aspartate oxidase (ASO, quinolinate synthetase (QS, quinolate phosphoribosyltransferase (QPT, nicotinate/nicotinamide mononucleotide adenylyltransferase (NMNAT, and NAD+ synthetase (NS. Sequence similarity searches, gene isolation and sequencing of mutant loci indicate that mutations in each enzyme result in a nicotinamide-requiring mutant phenotype in the previously isolated nic mutants. We rescued the mutant phenotype by the introduction of BAC DNA (nic2-1 and nic13-1 or plasmids with cloned genes (nic1-1 and nic15-1 into the mutants. NMNAT, which is also in the de novo pathway, and nicotinamide phosphoribosyltransferase (NAMPT constitute the nicotinamide-dependent salvage pathway. A mutation in NAMPT (npt1-1 has no obvious growth defect and is not nicotinamide-dependent. However, double mutant strains with the npt1-1 mutation and any of the nic mutations are inviable. When the de novo pathway is inactive, the salvage pathway is essential to Chlamydomonas for the synthesis of NAD+. A homolog of the human SIRT6-like gene, SRT2, is upregulated in the NS mutant, which shows a longer vegetative life span than wild-type cells. Our results suggest that Chlamydomonas is an excellent model system to study NAD+ metabolism and cell longevity.

  10. Genetic Analysis of Mating Locus Linked Mutations in CHLAMYDOMONAS REINHARDII

    OpenAIRE

    Galloway, R. E.; Goodenough, U. W.

    1985-01-01

    The mating-type (mt) locus of Chlamydomonas reinhardii has been analyzed using four mutant strains (imp-1, imp-10, imp-11 and imp-12). All have been shown, or are shown here, to carry mutations linked to either the plus (mt+) or the minus (mt-) locus, and their behavior in complementation tests has allowed us to define several distinct functions for each locus. Specifically, we propose that the mt+ locus contains the following genes or regulatory elements: a locus designated sfu, which is n...

  11. Flagellar force production during regeneration in Chlamydomonas reinhardtii

    Science.gov (United States)

    Yukich, John N.; Clodfelter, Catherine; Bernd, Karen K.

    2009-11-01

    Several respiratory, digestive, and reproductive disorders originate with motional dysfunction of cilia and flagella. The usefulness of cilia and flagella is understood, but the internal mechanism for creating their breast stroke-like motion is not. This study reports on standardization of calibration, trapping and cell movement recording methods. Our techniques permit us to measure the flagellar swimming force of Chlamydomonas during flagella regeneration. We find that as flagella length increases, the flagellar force is maximized after 50% of full length is achieved except for a significant dip at 75% of full length. These results raise many questions regarding the flagella infrastructure.

  12. Chlamydomonas reinhardtii selenocysteine tRNA[Ser]Sec

    OpenAIRE

    RAO, MAHADEV; CARLSON, Bradley A.; Novoselov, Sergey V.; Weeks, Donald P.; Vadim N Gladyshev; Dolph L Hatfield

    2003-01-01

    Eukaryotic selenocysteine (Sec) protein insertion machinery was thought to be restricted to animals, but the occurrence of both Sec-containing proteins and the Sec insertion system was recently found in Chlamydomonas reinhardtii, a member of the plant kingdom. Herein, we used RT-PCR to determine the sequence of C. reinhardtii Sec tRNA[Ser]Sec, the first non-animal eukaryotic Sec tRNA[Ser]Sec sequence. Like its animal counterpart, it is 90 nucleotides in length, is aminoacylated with serine by...

  13. The vacuum ultraviolet irradiation of green inicellular alga chlamydomonas reinbardtii

    International Nuclear Information System (INIS)

    The action of vacuum ultraviolet (Ar, 120-130 nm) irradiation of green alga Chlamydomonas reinhardtii was investigated. The high frequency discharge in Ar as a source of vacuum ultraviolet radiation was used. The registration of cell destruction by microscopic observation and photography was realized. The dependence of cells survival rate was compared with those by UV-B and UV-C irradiation. It was shown that most efficiency of cell's destruction by vacuum ultraviolet irradiation was realized. This work was carring out according with project proposed for vacuum ultraviolet support. 21 refs., 6 figs.,

  14. Reverse genetics in Chlamydomonas: a platform for isolating insertional mutants

    Directory of Open Access Journals (Sweden)

    de Montaigu Amaury

    2011-07-01

    Full Text Available Abstract A method was developed to identify insertional mutants of Chlamydomonas reinhardtii disrupted for selected target genes. The approach relies on the generation of thousands of transformants followed by PCR-based screenings that allow for identification of strains harboring the introduced marker gene within specific genes of interest. Our results highlight the strengths and limitations of two independent screens that differed in the nature of the marker DNA used (PCR-amplified fragment containing the plasmid-free marker versus entire linearized plasmid with the marker and in the strategies used to maintain and store transformants.

  15. Genome-wide analysis of alternative splicing in Chlamydomonas reinhardtii

    Directory of Open Access Journals (Sweden)

    Thomas Julie

    2010-02-01

    Full Text Available Abstract Background Genome-wide computational analysis of alternative splicing (AS in several flowering plants has revealed that pre-mRNAs from about 30% of genes undergo AS. Chlamydomonas, a simple unicellular green alga, is part of the lineage that includes land plants. However, it diverged from land plants about one billion years ago. Hence, it serves as a good model system to study alternative splicing in early photosynthetic eukaryotes, to obtain insights into the evolution of this process in plants, and to compare splicing in simple unicellular photosynthetic and non-photosynthetic eukaryotes. We performed a global analysis of alternative splicing in Chlamydomonas reinhardtii using its recently completed genome sequence and all available ESTs and cDNAs. Results Our analysis of AS using BLAT and a modified version of the Sircah tool revealed AS of 498 transcriptional units with 611 events, representing about 3% of the total number of genes. As in land plants, intron retention is the most prevalent form of AS. Retained introns and skipped exons tend to be shorter than their counterparts in constitutively spliced genes. The splice site signals in all types of AS events are weaker than those in constitutively spliced genes. Furthermore, in alternatively spliced genes, the prevalent splice form has a stronger splice site signal than the non-prevalent form. Analysis of constitutively spliced introns revealed an over-abundance of motifs with simple repetitive elements in comparison to introns involved in intron retention. In almost all cases, AS results in a truncated ORF, leading to a coding sequence that is around 50% shorter than the prevalent splice form. Using RT-PCR we verified AS of two genes and show that they produce more isoforms than indicated by EST data. All cDNA/EST alignments and splice graphs are provided in a website at http://combi.cs.colostate.edu/as/chlamy. Conclusions The extent of AS in Chlamydomonas that we observed is much

  16. Cell response of Chlamydomonas actinochloris culture to repeated microwave irradiation

    Directory of Open Access Journals (Sweden)

    OLESIA O. GRYGORIEVA

    2015-05-01

    Full Text Available Abstract. Grygorieva OO, Berezovsjka MA, Dacenko OI. 2015. Cell response of Chlamydomonas actinochloris culture to repeated microwave irradiation. Nusantara Bioscience 7: 38-42. Two cultures of Chlamydomonas actinochloris Deason et Bold in the lag-phase were exposed to the microwave irradiation. One of them (culture 1 was not treated beforehand, whereas the other (culture 2 was irradiated by microwaves 2 years earlier. The measurement of cell quantity as well as measurement of change of intensities and spectra of cultures photoluminescence (PL in the range of chlorophyll a emission was regularly conducted during the cell cultures development. Cell concentration of culture 1 exposed to the microwave irradiation for the first time has quickly restored while cell concentration of culture 2 which was irradiated repeatedly has fallen significantly. The following increasing of cell concentration of culture 2 is negligible. Cell concentration reaches the steady-state level that is about a half of the cell concentration of control culture. Initially the PL efficiency of cells of both cultures decreases noticeable as a result of irradiation. Then there is the monotonic increase to the values which are significantly higher than the corresponding values in the control cultures. The ratio of the intensities at the maxima of the main emission bands of chlorophyll for control samples of both cultures remained approximately at the same level. At the same time effect of irradiation on the cell PL spectrum appears as a temporary reduction of this magnitude.

  17. Bioenergetics of growth and lipid production in Chlamydomonas reinhardtii

    International Nuclear Information System (INIS)

    The study of thermodynamic aspects of the lipid, e.g., raw material for biodiesel, production in microalgae is important, as the non-lipid producing biological activities of the algal cultivation consume part of the solar energy captured during photosynthesis in expense of the exergetic efficiency of the lipid production process. The cultivation of Chlamydomonas reinhardtii (a unicellular biflagellate fresh-water microalga) is modeled as a three-step chemical mechanism representing growth, respiration, and lipid production. Further, the comprehensive thermodynamic analysis of these mechanisms is presented. The cumulative degree of perfection of the cellular proliferation, after excluding the lipid synthesis, fluctuates with no trend around 0.52 ± 0.19. The exergy analysis has indicated that C. reinhardtii prefers to maximize the lipid production when it is difficult to generate new cells. Under batch production of algal biomass, the highest heat and exergy loss per unit biomass production are accountable under the most favorable biological growth conditions, whereas the highest exergetic efficiency of the lipid production accounted under the least favorable growth conditions, which is in line with the previous studies. - Highlights: • Biomass, lipid production and respiration modeled as three-step chemical reaction. • CDP (cumulative degree of perfection) is calculated based on the model. • The CDP of the algae, after excluding the lipids, is about 0.52 ± 0.19. • Chlamydomonas reinhardtii maximized lipid production when it was difficult to grow

  18. Glucose respiration in the intact chloroplast of Chlamydomonas reinhardtii

    International Nuclear Information System (INIS)

    Chloroplastic respiration was monitored by measuring 14CO2 from 14C glucose in the darkened Chlamydomonas reinhardtii F-60 chloroplast, The patterns of 14CO2 evolution from labeled glucose in the absence and presence of the inhibitors iodoacetamide, glycolate-2-phosphate, and phosphoenolypyruvate were those expected from the oxidative pentose phosphate cycle and glycolysis. The Km for glucose was 56 micromolar and for MgATP was 200 micromolar. Release of 14CO2 was inhibited by phloretin and inorganic phosphate. Comparing the inhibition of CO2 evolution generated by pH 7.5 with respect to pH 8.2 (optimum) in chloroplasts given C-1, C-2, and C-6 labeled glucose indicated that a suboptimum pH affects the recycling of the pentose phosphate intermediates to a greater extent than CO2 evolution from C-1 of glucose. Respiratory inhibition by pH 7.5 in the darkened chloroplast was alleviated by NH4Cl and KCl (stromal alkalating agents), iodoacetamide (an inhibitor of glyceraldehyde 3-phosphate dehydrogenase), or phosphoenolypyruvate (an inhibitor of phosphofructokinase). It is concluded that the site which primarily mediates respiration in the darkened Chlamydomonas chloroplast is the fructose-1,6-bisphosphatase/phosphofructokinase junction. The respiratory pathways described here can account for the total oxidation of a hexose to Co2 and for interactions between carbohydrate metabolism and the oxyhydrogen reaction in algal cells adapted to a hydrogen metabolism

  19. Potassium fluxes in Chlamydomonas reinhardtii. II. Compartmental analysis

    International Nuclear Information System (INIS)

    42K+ and 86Rb+ were used to determine the subcellular distribution of potassium in Chlamydomonas reinhardtii by compartmental analysis. In both wild type and a mutant strain, three distinct compartments (referred to as I, II, and III) were apparent. Using 42K+, we found that these had half-lives for K+ exchange of 1.07 min, 12.8 min, and 2.9 h, respectively, in wild-type cells and 0.93 min, 14.7 min, and 9.8 h, respectively, for the mutants. Half-lives were not significantly different when 86Rb+ was used to trace K+. Compartments I and II probably correspond to the cell wall and cytoplasm, respectively. Based on the lack of a large central vacuole in Chlamydomonas, the effect of a dark pretreatment on the kinetic properties of compartment III and the similarity between the [K+] of compartment III and that of isolated chloroplasts, this slowly exchanging compartment was identified as the chloroplast. Growth of wild-type cells at 100 micromolars (instead of 10 mM K+) caused no change of cytoplasmic [K+] but reduced chloroplast [K+] very substantially. The mutants failed to grow at 100 micromolars K+

  20. A role for the membrane in regulating Chlamydomonas flagellar length.

    Directory of Open Access Journals (Sweden)

    William Dentler

    Full Text Available Flagellar assembly requires coordination between the assembly of axonemal proteins and the assembly of the flagellar membrane and membrane proteins. Fully grown steady-state Chlamydomonas flagella release flagellar vesicles from their tips and failure to resupply membrane should affect flagellar length. To study vesicle release, plasma and flagellar membrane surface proteins were vectorially pulse-labeled and flagella and vesicles were analyzed for biotinylated proteins. Based on the quantity of biotinylated proteins in purified vesicles, steady-state flagella appeared to shed a minimum of 16% of their surface membrane per hour, equivalent to a complete flagellar membrane being released every 6 hrs or less. Brefeldin-A destroyed Chlamydomonas Golgi, inhibited the secretory pathway, inhibited flagellar regeneration, and induced full-length flagella to disassemble within 6 hrs, consistent with flagellar disassembly being induced by a failure to resupply membrane. In contrast to membrane lipids, a pool of biotinylatable membrane proteins was identified that was sufficient to resupply flagella as they released vesicles for 6 hrs in the absence of protein synthesis and to support one and nearly two regenerations of flagella following amputation. These studies reveal the importance of the secretory pathway to assemble and maintain full-length flagella.

  1. Metabolism of acyl-lipids in Chlamydomonas reinhardtii.

    Science.gov (United States)

    Li-Beisson, Yonghua; Beisson, Fred; Riekhof, Wayne

    2015-05-01

    Microalgae are emerging platforms for production of a suite of compounds targeting several markets, including food, nutraceuticals, green chemicals, and biofuels. Many of these products, such as biodiesel or polyunsaturated fatty acids (PUFAs), derive from lipid metabolism. A general picture of lipid metabolism in microalgae has been deduced from well characterized pathways of fungi and land plants, but recent advances in molecular and genetic analyses of microalgae have uncovered unique features, pointing out the necessity to study lipid metabolism in microalgae themselves. In the past 10 years, in addition to its traditional role as a model for photosynthetic and flagellar motility processes, Chlamydomonas reinhardtii has emerged as a model organism to study lipid metabolism in green microalgae. Here, after summarizing data on total fatty acid composition, distribution of acyl-lipid classes, and major acyl-lipid molecular species found in C. reinhardtii, we review the current knowledge on the known or putative steps for fatty acid synthesis, glycerolipid desaturation and assembly, membrane lipid turnover, and oil remobilization. A list of characterized or putative enzymes for the major steps of acyl-lipid metabolism in C. reinhardtii is included, and subcellular localizations and phenotypes of associated mutants are discussed. Biogenesis and composition of Chlamydomonas lipid droplets and the potential importance of lipolytic processes in increasing cellular oil content are also highlighted. PMID:25660108

  2. Omics data management and annotation.

    Science.gov (United States)

    Harel, Arye; Dalah, Irina; Pietrokovski, Shmuel; Safran, Marilyn; Lancet, Doron

    2011-01-01

    Technological Omics breakthroughs, including next generation sequencing, bring avalanches of data which need to undergo effective data management to ensure integrity, security, and maximal knowledge-gleaning. Data management system requirements include flexible input formats, diverse data entry mechanisms and views, user friendliness, attention to standards, hardware and software platform definition, as well as robustness. Relevant solutions elaborated by the scientific community include Laboratory Information Management Systems (LIMS) and standardization protocols facilitating data sharing and managing. In project planning, special consideration has to be made when choosing relevant Omics annotation sources, since many of them overlap and require sophisticated integration heuristics. The data modeling step defines and categorizes the data into objects (e.g., genes, articles, disorders) and creates an application flow. A data storage/warehouse mechanism must be selected, such as file-based systems and relational databases, the latter typically used for larger projects. Omics project life cycle considerations must include the definition and deployment of new versions, incorporating either full or partial updates. Finally, quality assurance (QA) procedures must validate data and feature integrity, as well as system performance expectations. We illustrate these data management principles with examples from the life cycle of the GeneCards Omics project (http://www.genecards.org), a comprehensive, widely used compendium of annotative information about human genes. For example, the GeneCards infrastructure has recently been changed from text files to a relational database, enabling better organization and views of the growing data. Omics data handling benefits from the wealth of Web-based information, the vast amount of public domain software, increasingly affordable hardware, and effective use of data management and annotation principles as outlined in this chapter

  3. Project Aloha:indexing, highlighting and annotation

    OpenAIRE

    Fallahkhair, Sanaz; Kennedy, Ian

    2010-01-01

    Lifelong learning requires many skills that are often not taught or are poorly taught. Such skills include speed reading, critical analysis, creative thinking, active reading and even a “little” skill like annotation. There are many ways that readers annotate. A short classification of some ways that reader may annotate includes underlining, using coloured highlighters, interlinear notes, marginal notes, and disassociated notes. This paper presents an investigation into the use of a tool for ...

  4. Automatic Multilevel Medical Image Annotation and Retrieval

    OpenAIRE

    Mueen, A.; Zainuddin, R.; Baba, M. Sapiyan

    2007-01-01

    Image retrieval at the semantic level mostly depends on image annotation or image classification. Image annotation performance largely depends on three issues: (1) automatic image feature extraction; (2) a semantic image concept modeling; (3) algorithm for semantic image annotation. To address first issue, multilevel features are extracted to construct the feature vector, which represents the contents of the image. To address second issue, domain-dependent concept hierarchy is constructed for...

  5. Knowledge Annotation maknig implicit knowledge explicit

    CERN Document Server

    Dingli, Alexiei

    2011-01-01

    Did you ever read something on a book, felt the need to comment, took up a pencil and scribbled something on the books' text'? If you did, you just annotated a book. But that process has now become something fundamental and revolutionary in these days of computing. Annotation is all about adding further information to text, pictures, movies and even to physical objects. In practice, anything which can be identified either virtually or physically can be annotated. In this book, we will delve into what makes annotations, and analyse their significance for the future evolutions of the web. We wil

  6. Estimating the annotation error rate of curated GO database sequence annotations

    Directory of Open Access Journals (Sweden)

    Brown Alfred L

    2007-05-01

    Full Text Available Abstract Background Annotations that describe the function of sequences are enormously important to researchers during laboratory investigations and when making computational inferences. However, there has been little investigation into the data quality of sequence function annotations. Here we have developed a new method of estimating the error rate of curated sequence annotations, and applied this to the Gene Ontology (GO sequence database (GOSeqLite. This method involved artificially adding errors to sequence annotations at known rates, and used regression to model the impact on the precision of annotations based on BLAST matched sequences. Results We estimated the error rate of curated GO sequence annotations in the GOSeqLite database (March 2006 at between 28% and 30%. Annotations made without use of sequence similarity based methods (non-ISS had an estimated error rate of between 13% and 18%. Annotations made with the use of sequence similarity methodology (ISS had an estimated error rate of 49%. Conclusion While the overall error rate is reasonably low, it would be prudent to treat all ISS annotations with caution. Electronic annotators that use ISS annotations as the basis of predictions are likely to have higher false prediction rates, and for this reason designers of these systems should consider avoiding ISS annotations where possible. Electronic annotators that use ISS annotations to make predictions should be viewed sceptically. We recommend that curators thoroughly review ISS annotations before accepting them as valid. Overall, users of curated sequence annotations from the GO database should feel assured that they are using a comparatively high quality source of information.

  7. Evidences of oxidative stress during hydrogen photoproduction in sulfur-deprived cultures of Chlamydomonas reinhardtii

    Czech Academy of Sciences Publication Activity Database

    Sáens, M. E.; Bišová, Kateřina; Touloupakis, E.; Faraloni, C.; Dario Di Marzio, W.; Torzillo, G.

    2015-01-01

    Roč. 40, č. 30 (2015), s. 10410-10417. ISSN 0360-3199 Institutional support: RVO:61388971 Keywords : Oxidative stress * Chlamydomonas reinhardtii * H-2 production Subject RIV: EE - Microbiology, Virology Impact factor: 3.313, year: 2014

  8. The Chlamydomonas genome reveals the evolution of key animal and plant functions

    Czech Academy of Sciences Publication Activity Database

    Merchant, S.S.; Prochnik, S. E.; Bišová, Kateřina

    2007-01-01

    Roč. 318, - (2007), s. 245-251. ISSN 0036-8075 Institutional research plan: CEZ:AV0Z50200510 Keywords : chlamydomonas reinhardtii * alga * eukaryotic cell Subject RIV: EE - Microbiology, Virology Impact factor: 26.372, year: 2007

  9. Is the cell division cycle gated by a circadian clock? The case of Chlamydomonas reinhardtii

    OpenAIRE

    1995-01-01

    Circadian oscillators are known to regulate the timing of cell division in many organisms. In the case of Chlamydomonas reinhardtii, however, this conclusion has been challenged by several investigators. We have reexamined this issue and find that the division behavior of Chlamydomonas meets all the criteria for circadian rhythmicity: persistence of a cell division rhythm (a) with a period of approximately 24 h under free-running conditions, (b) that is temperature compensated, and (c) which ...

  10. The Chlamydomonas Genome Reveals the Evolution of Key Animal and Plant Functions

    OpenAIRE

    Merchant, Sabeeha S; Prochnik, Simon E; Vallon, Olivier; Harris, Elizabeth H.; Karpowicz, Steven J.; Witman, George B.; Terry, Astrid; Salamov, Asaf; Fritz-Laylin, Lillian K.; Maréchal-Drouard, Laurence; Marshall, Wallace F.; Qu, Liang-Hu; Nelson, David R.; Sanderfoot, Anton A.; Spalding, Martin H

    2007-01-01

    Chlamydomonas reinhardtii is a unicellular green alga whose lineage diverged from land plants over 1 billion years ago. It is a model system for studying chloroplast-based photosynthesis, as well as the structure, assembly, and function of eukaryotic flagella (cilia), which were inherited from the common ancestor of plants and animals, but lost in land plants. We sequenced the ∼120-megabase nuclear genome of Chlamydomonas and performed comparative phylogenomic analyses, identifying genes enco...

  11. Distinct Mechanisms Regulating Gene Expression Coexist within the Fermentative Pathways in Chlamydomonas reinhardtii

    OpenAIRE

    Larisa Angela Swirsky Whitney; Giacomo Novi; Pierdomenico Perata; Elena Loreti

    2012-01-01

    Under dark anoxia, the unicellular green algae Chlamydomonas reinhardtii may produce hydrogen by means of its hydrogenase enzymes, in particular HYD1, using reductants derived from the degradation of intercellular carbon stores. Other enzymes belonging to the fermentative pathways compete for the same reductants. A complete understanding of the mechanisms determining the activation of one pathway rather than another will help us engineer Chlamydomonas for fermentative metabolite production, ...

  12. Azolla filiculoides Nitrogenase Activity Decrease Induced by Inoculation with Chlamydomonas sp. †

    OpenAIRE

    Habte, Mitiku

    1986-01-01

    Experiments were conducted to determine the influence of Chlamydomonas sp. on nitrogen fixation (C2H2 → C2H4) in Azolla filiculoides and on the nitrogen fixation and growth of free-living Anabaena azollae 2B organisms. Inoculation of azolla medium with Chlamydomonas sp. was associated with decreased nitrogenase activity in A. filiculoides and with increases in the density of a fungal population identified as Acremonium sp. Subsequent inoculation of azolla medium with this fungus was also acco...

  13. Development of a forward genetic screen to isolate oil mutants in the green microalga Chlamydomonas reinhardtii

    OpenAIRE

    Cagnon, Caroline; Mirabella, Boris; Nguyen, Hoa Mai; Beyly-Adriano, Audrey; Bouvet, Séverine; Cuiné, Stéphan; Beisson, Fred; Peltier, Gilles; Li-Beisson, Yonghua

    2013-01-01

    Background Oils produced by microalgae are precursors to biodiesel. To achieve a profitable production of biodiesel from microalgae, identification of factors governing oil synthesis and turnover is desirable. The green microalga Chlamydomonas reinhardtii is amenable to genetic analyses and has recently emerged as a model to study oil metabolism. However, a detailed method to isolate various types of oil mutants that is adapted to Chlamydomonas has not been reported. Results We describe here ...

  14. A new method to identify flanking sequence tags in chlamydomonas using 3’-RACE

    OpenAIRE

    Meslet-Cladière Laurence; Vallon Olivier

    2012-01-01

    Abstract Background The green alga Chlamydomonas reinhardtii, although a premier model organism in biology, still lacks extensive insertion mutant libraries with well-identified Flanking Sequence Tags (FSTs). Rapid and efficient methods are needed for FST retrieval. Results Here, we present a novel method to identify FSTs in insertional mutants of Chlamydomonas. Transformants can be obtained with a resistance cassette lacking a 3’ untranslated region (UTR), suggesting that the RNA that is pro...

  15. Chloroplast lipid transfer processes in Chlamydomonas reinhardtii involving a TRIGALACTOSYLDIACYLGLYCEROL 2 (TGD2) orthologue.

    Science.gov (United States)

    Warakanont, Jaruswan; Tsai, Chia-Hong; Michel, Elena J S; Murphy, George R; Hsueh, Peter Y; Roston, Rebecca L; Sears, Barbara B; Benning, Christoph

    2015-12-01

    In plants, lipids of the photosynthetic membrane are synthesized by parallel pathways associated with the endoplasmic reticulum (ER) and the chloroplast envelope membranes. Lipids derived from the two pathways are distinguished by their acyl-constituents. Following this plant paradigm, the prevalent acyl composition of chloroplast lipids suggests that Chlamydomonas reinhardtii (Chlamydomonas) does not use the ER pathway; however, the Chlamydomonas genome encodes presumed plant orthologues of a chloroplast lipid transporter consisting of TGD (TRIGALACTOSYLDIACYLGLYCEROL) proteins that are required for ER-to-chloroplast lipid trafficking in plants. To resolve this conundrum, we identified a mutant of Chlamydomonas deleted in the TGD2 gene and characterized the respective protein, CrTGD2. Notably, the viability of the mutant was reduced, showing the importance of CrTGD2. Galactoglycerolipid metabolism was altered in the tgd2 mutant with monogalactosyldiacylglycerol (MGDG) synthase activity being strongly stimulated. We hypothesize this to be a result of phosphatidic acid accumulation in the chloroplast outer envelope membrane, the location of MGDG synthase in Chlamydomonas. Concomitantly, increased conversion of MGDG into triacylglycerol (TAG) was observed. This TAG accumulated in lipid droplets in the tgd2 mutant under normal growth conditions. Labeling kinetics indicate that Chlamydomonas can import lipid precursors from the ER, a process that is impaired in the tgd2 mutant. PMID:26496373

  16. Biofiksasi CO2 Oleh Mikroalga Chlamydomonas sp dalam Photobioreaktor Tubular

    Directory of Open Access Journals (Sweden)

    Hadiyanto Hadiyanto

    2014-05-01

    Full Text Available Mikroalga memiliki potensi dalam membiofiksasi CO2 dan dapat dimanfaatkan untuk mengurangi kadar CO2 dalam gas pencemar. Pertumbuhan mikroalga sangat dipengaruhi oleh konsentrasi gas CO2 di dalam gas pencemar. Tujuan penelitian ini adalah untuk mengeetahui kemampuan mikroalga Chlamydomonas sp yang dikultivasi dalam photobioreaktor tubular dalam penyerapan gas CO2 serta untuk mengetahui konsentrasi maksimum gas CO2 dalam umpan untuk memproduksi biomasa mikroalga yang optimal. Percobaan dilakukan dnegan memvariasi laju alir dari 0.03 -0.071 L/menit dan konsentrasi CO2 dalam umpan 10-30%. Hasil penelitian menunjukkan bahwa biomasa mikroalga dapat diproduksi dengan maksimal dengan konsentrasi gas CO2 20% dengan laju alir 0.07 L/min. Semakin tinggi laju alir maka produksi biomasa alga semakin besar. Kecepatan pertumbuhan alga maksimum terjadi pada 0.31 /hari. Pada konsentrasi gas CO2 30%, terjadi substrate inhibition yang disebabkan carbon dalam bentuk ion bicarbonate tidak dapat dikonsumsi lagi di dalam kultur alga. Kata kunci : Mikroalga, chlamydomonas sp, biofiksasi CO2, biogas Abstract Microalgae have a potential for CO2 biofixation and therefore can be used to reduce the CO2 concentration in the gas pollutants. Moreover, microalgae growth is strongly affected by the concentration of CO2 in the exhaust gas pollutants. The objective of this research was to investigate the ability of microalgae Chlamydomonas sp which was cultivated in a tubular photobioreactor for CO2 absorption as well as to determine the maximum concentration of CO2 in the feed gas to obtain optimum microalgae biomass. The experiments were performed by varying the gas flow rate of 0.03 -0.071 L / min and the concentration of CO2 in the feed of 10-30%. The results showed that the maximum biomass of microalgae can be produced with CO2 concentration of 20% vol with a flow rate of 0.07 L / min. The result also showed that increasing the gas flow rate, the greater of the production of

  17. The surplus value of semantic annotations

    NARCIS (Netherlands)

    M. Marx

    2010-01-01

    We compare the costs of semantic annotation of textual documents to its benefits for information processing tasks. Semantic annotation can improve the performance of retrieval tasks and facilitates an improved search experience through faceted search, focused retrieval, better document summaries, an

  18. Towards an event annotated corpus of Polish

    Directory of Open Access Journals (Sweden)

    Michał Marcińczuk

    2015-12-01

    Full Text Available Towards an event annotated corpus of PolishThe paper presents a typology of events built on the basis of TimeML specification adapted to Polish language. Some changes were introduced to the definition of the event categories and a motivation for event categorization was formulated. The event annotation task is presented on two levels – ontology level (language independent and text mentions (language dependant. The various types of event mentions in Polish text are discussed. A procedure for annotation of event mentions in Polish texts is presented and evaluated. In the evaluation a randomly selected set of documents from the Corpus of Wrocław University of Technology (called KPWr was annotated by two linguists and the annotator agreement was calculated. The evaluation was done in two iterations. After the first evaluation we revised and improved the annotation procedure. The second evaluation showed a significant improvement of the agreement between annotators. The current work was focused on annotation and categorisation of event mentions in text. The future work will be focused on description of event with a set of attributes, arguments and relations.

  19. DIMA – Annotation guidelines for German intonation

    DEFF Research Database (Denmark)

    Kügler, Frank; Smolibocki, Bernadett; Arnold, Denis;

    2015-01-01

    easier since German intonation is currently annotated according to different models. To this end, we aim to provide guidelines that are easy to learn. The guidelines were evaluated running an inter-annotator reliability study on three different speech styles (read speech, monologue and dialogue...

  20. Creating Gaze Annotations in Head Mounted Displays

    DEFF Research Database (Denmark)

    Mardanbeigi, Diako; Qvarfordt, Pernilla

    To facilitate distributed communication in mobile settings, we developed GazeNote for creating and sharing gaze annotations in head mounted displays (HMDs). With gaze annotations it possible to point out objects of interest within an image and add a verbal description. To create an annota- tion, ...

  1. Crowdsourcing and annotating NER for Twitter #drift

    DEFF Research Database (Denmark)

    Fromreide, Hege; Hovy, Dirk; Søgaard, Anders

    2014-01-01

    We present two new NER datasets for Twitter; a manually annotated set of 1,467 tweets (kappa=0.942) and a set of 2,975 expert-corrected, crowdsourced NER annotated tweets from the dataset described in Finin et al. (2010). In our experiments with these datasets, we observe two important points: (a...

  2. Annotation of regular polysemy and underspecification

    DEFF Research Database (Denmark)

    Martínez Alonso, Héctor; Pedersen, Bolette Sandford; Bel, Núria

    2013-01-01

    We present the result of an annotation task on regular polysemy for a series of seman- tic classes or dot types in English, Dan- ish and Spanish. This article describes the annotation process, the results in terms of inter-encoder agreement, and the sense distributions obtained with two methods...

  3. Harnessing Collaborative Annotations on Online Formative Assessments

    Science.gov (United States)

    Lin, Jian-Wei; Lai, Yuan-Cheng

    2013-01-01

    This paper harnesses collaborative annotations by students as learning feedback on online formative assessments to improve the learning achievements of students. Through the developed Web platform, students can conduct formative assessments, collaboratively annotate, and review historical records in a convenient way, while teachers can generate…

  4. Manual Annotation of Translational Equivalence The Blinker Project

    CERN Document Server

    Melamed, I D

    1998-01-01

    Bilingual annotators were paid to link roughly sixteen thousand corresponding words between on-line versions of the Bible in modern French and modern English. These annotations are freely available to the research community from http://www.cis.upenn.edu/~melamed . The annotations can be used for several purposes. First, they can be used as a standard data set for developing and testing translation lexicons and statistical translation models. Second, researchers in lexical semantics will be able to mine the annotations for insights about cross-linguistic lexicalization patterns. Third, the annotations can be used in research into certain recently proposed methods for monolingual word-sense disambiguation. This paper describes the annotated texts, the specially-designed annotation tool, and the strategies employed to increase the consistency of the annotations. The annotation process was repeated five times by different annotators. Inter-annotator agreement rates indicate that the annotations are reasonably rel...

  5. Effect of mutagen combined action on Chlamydomonas reinhardtii cells. II

    International Nuclear Information System (INIS)

    The effect of UV radiation and UV radiation combined with alkylnitrosourea derivatives (N-methyl-N-nitrosourea and N-ethyl-N-nitrosourea) was observed on survival of cells of the algae Chlamydomonas reinhardtii. In particular, single parts were evaluated of the overall lethal effect - dying of cells before division and dying of cells after division. It was found that the combined action of low doses of UV radiation and alkylnitrosoureas result in a pronounced protective effect which manifests itself by a higher frequency of surviving cells than was that effected by the action of alkylnitrosoureas alone. As a result of combined action with higher doses of UV radiation this effect is lost, and the resultant values will come close to the theoretically anticipated values. This gradual transition from a protective to an additive effect mainly manifests itself by changes in the proportion of cells dying before division. (author)

  6. Effect of mutagen combined action on Chlamydomonas Reinhardtii cells. I

    International Nuclear Information System (INIS)

    The effect was investigated of single and combined actions of alkylnitrosourea derivatives (N-methyl-N-nitrosourea and N-ethyl-N-nitrosourea) and UV-radiation on the survival of cells of Chlamydomonas reinhardtii algae in dependence on the sequence of application of mutagens and on the given conditions of cultivation following mutagen activity. In particular, the single phases were investigated of the total lethal effect, i.e., the death of cells before division and their death after division. The most pronounced changes in dependence on the sequence of application of mutagens and on the given conditions of cultivation were noted in cell death before division. In dependence on the sequence of application of mutagens, the effect of the combined action on the survival of cells changed from an additive (alkylnitrosourea + UV-radiation) to a protective effect (UV-radiation + alkylnitrosourea). (author)

  7. Antiphase Synchronization in a Flagellar-Dominance Mutant of Chlamydomonas

    Science.gov (United States)

    Leptos, Kyriacos C.; Wan, Kirsty Y.; Polin, Marco; Tuval, Idan; Pesci, Adriana I.; Goldstein, Raymond E.

    2013-10-01

    Groups of beating flagella or cilia often synchronize so that neighboring filaments have identical frequencies and phases. A prime example is provided by the unicellular biflagellate Chlamydomonas reinhardtii, which typically displays synchronous in-phase beating in a low-Reynolds number version of breaststroke swimming. We report the discovery that ptx1, a flagellar-dominance mutant of C. reinhardtii, can exhibit synchronization in precise antiphase, as in the freestyle swimming stroke. High-speed imaging shows that ptx1 flagella switch stochastically between in-phase and antiphase states, and that the latter has a distinct waveform and significantly higher frequency, both of which are strikingly similar to those found during phase slips that stochastically interrupt in-phase beating of the wild-type. Possible mechanisms underlying these observations are discussed.

  8. Antiphase Synchronization in a Flagellar-Dominance Mutant of Chlamydomonas

    CERN Document Server

    Leptos, Kyriacos C; Polin, Marco; Tuval, Idan; Pesci, Adriana I; Goldstein, Raymond E

    2013-01-01

    Groups of beating flagella or cilia often synchronize so that neighboring filaments have identical frequencies and phases. A prime example is provided by the unicellular biflagellate Chlamydomonas reinhardtii, which typically displays synchronous in-phase beating in a low-Reynolds number version of breaststroke swimming. We report here the discovery that ptx1, a flagellar dominance mutant of C. reinhardtii, can exhibit synchronization in precise antiphase, as in the freestyle swimming stroke. Long-duration high-speed imaging shows that ptx1 flagella switch stochastically between in-phase and antiphase states, and that the latter has a distinct waveform and significantly higher frequency, both of which are strikingly similar to those found during phase slips that stochastically interrupt in-phase beating of the wildtype. Possible mechanisms underlying these observations are discussed.

  9. Cilia and ciliopathies:From Chlamydomonas and beyond

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    The biological function of motile cilia/flagella has long been recognized. The non-motile primary cilium, once regarded as a vestigial organelle, however, has been found recently to play unexpected roles in mammalian physiology and development. Defects in cilia have profound impact on human health. Diseases related to cilia, collectively called ciliopathies include male infertility, primary cilia dyskinesia, renal cyst formation, blindness, polydactyly, obesity, hypertension, and even mental retardation. Our current understanding of cilia and ciliopathies has been fueled by basic research employing various model organisms including Chlamydomonas, a unicellular green alga. This review article provides a general introduction to the cell biology of cilia and an overview of various cilia-related diseases.

  10. Facilitating functional annotation of chicken microarray data

    Directory of Open Access Journals (Sweden)

    Gresham Cathy R

    2009-10-01

    Full Text Available Abstract Background Modeling results from chicken microarray studies is challenging for researchers due to little functional annotation associated with these arrays. The Affymetrix GenChip chicken genome array, one of the biggest arrays that serve as a key research tool for the study of chicken functional genomics, is among the few arrays that link gene products to Gene Ontology (GO. However the GO annotation data presented by Affymetrix is incomplete, for example, they do not show references linked to manually annotated functions. In addition, there is no tool that facilitates microarray researchers to directly retrieve functional annotations for their datasets from the annotated arrays. This costs researchers amount of time in searching multiple GO databases for functional information. Results We have improved the breadth of functional annotations of the gene products associated with probesets on the Affymetrix chicken genome array by 45% and the quality of annotation by 14%. We have also identified the most significant diseases and disorders, different types of genes, and known drug targets represented on Affymetrix chicken genome array. To facilitate functional annotation of other arrays and microarray experimental datasets we developed an Array GO Mapper (AGOM tool to help researchers to quickly retrieve corresponding functional information for their dataset. Conclusion Results from this study will directly facilitate annotation of other chicken arrays and microarray experimental datasets. Researchers will be able to quickly model their microarray dataset into more reliable biological functional information by using AGOM tool. The disease, disorders, gene types and drug targets revealed in the study will allow researchers to learn more about how genes function in complex biological systems and may lead to new drug discovery and development of therapies. The GO annotation data generated will be available for public use via AgBase website and

  11. Concept annotation in the CRAFT corpus

    Directory of Open Access Journals (Sweden)

    Bada Michael

    2012-07-01

    Full Text Available Abstract Background Manually annotated corpora are critical for the training and evaluation of automated methods to identify concepts in biomedical text. Results This paper presents the concept annotations of the Colorado Richly Annotated Full-Text (CRAFT Corpus, a collection of 97 full-length, open-access biomedical journal articles that have been annotated both semantically and syntactically to serve as a research resource for the biomedical natural-language-processing (NLP community. CRAFT identifies all mentions of nearly all concepts from nine prominent biomedical ontologies and terminologies: the Cell Type Ontology, the Chemical Entities of Biological Interest ontology, the NCBI Taxonomy, the Protein Ontology, the Sequence Ontology, the entries of the Entrez Gene database, and the three subontologies of the Gene Ontology. The first public release includes the annotations for 67 of the 97 articles, reserving two sets of 15 articles for future text-mining competitions (after which these too will be released. Concept annotations were created based on a single set of guidelines, which has enabled us to achieve consistently high interannotator agreement. Conclusions As the initial 67-article release contains more than 560,000 tokens (and the full set more than 790,000 tokens, our corpus is among the largest gold-standard annotated biomedical corpora. Unlike most others, the journal articles that comprise the corpus are drawn from diverse biomedical disciplines and are marked up in their entirety. Additionally, with a concept-annotation count of nearly 100,000 in the 67-article subset (and more than 140,000 in the full collection, the scale of conceptual markup is also among the largest of comparable corpora. The concept annotations of the CRAFT Corpus have the potential to significantly advance biomedical text mining by providing a high-quality gold standard for NLP systems. The corpus, annotation guidelines, and other associated resources are

  12. The GOA database: Gene Ontology annotation updates for 2015

    OpenAIRE

    Huntley, Rachael P; Sawford, Tony; Mutowo-Meullenet, Prudence; Shypitsyna, Aleksandra; Bonilla, Carlos; Martin, Maria J.; O'Donovan, Claire

    2014-01-01

    The Gene Ontology Annotation (GOA) resource (http://www.ebi.ac.uk/GOA) provides evidence-based Gene Ontology (GO) annotations to proteins in the UniProt Knowledgebase (UniProtKB). Manual annotations provided by UniProt curators are supplemented by manual and automatic annotations from model organism databases and specialist annotation groups. GOA currently supplies 368 million GO annotations to almost 54 million proteins in more than 480 000 taxonomic groups. The resource now provides annotat...

  13. Effect of selenate on growth and photosynthesis of Chlamydomonas reinhardtii

    International Nuclear Information System (INIS)

    Algal communities play a crucial role in aquatic food webs by facilitating the transfer of dissolved inorganic selenium (both an essential trace element and a toxic compound for a wide variety of organisms) to higher trophic levels. The dominant inorganic chemical species of selenium in freshwaters are selenite (SeO32-) and selenate (SeO42-). At environmental concentrations, selenite is not likely to have direct toxic effects on phytoplankton growth [Morlon, H., Fortin, C., Floriani, M., Adam, C., Garnier-Laplace, J., Boudou, A., 2005a. Toxicity of selenite in the unicellular green alga Chlamydomonas reinharditii: comparison between effects at the population and sub-cellular level. Aquat. Toxicol. 73(1), 65-78]. The effects of selenate, on the other hand, are poorly documented. We studied the effects of selenate on Chlamydomonas reinhardtii growth (a common parameter in phytotoxicity tests). Growth inhibition (96-h IC50) was observed at 4.5 ± 0.2 μM selenate (p < 0.001), an effective concentration which is low compared to environmental concentrations. Growth inhibition at high selenium concentrations may result from impaired photosynthesis. This is why we also studied the effects of selenate on the photosynthetic process (not previously assessed in this species to our knowledge) as well as selenate's effects on cell ultrastructure. The observed ultrastructural damage (chloroplast alterations, loss of appressed domains) confirmed that chloroplasts are important targets in the mechanism of selenium toxicity. Furthermore, the inhibition of photosynthetic electron transport evaluated by chlorophyll fluorescence induction confirmed this hypothesis and demonstrated that selenate disrupts the photosynthetic electron chain. Compared to the classical 'growth inhibition' parameter used in phytotoxicity tests, cell diameter and operational photosynthetic yield were more sensitive and may be convenient tools for selenate toxicity assessment in non-target plants

  14. A Common XML-based Framework for Syntactic Annotations

    CERN Document Server

    Ide, Nancy; Erjavec, Tomaz

    2009-01-01

    It is widely recognized that the proliferation of annotation schemes runs counter to the need to re-use language resources, and that standards for linguistic annotation are becoming increasingly mandatory. To answer this need, we have developed a framework comprised of an abstract model for a variety of different annotation types (e.g., morpho-syntactic tagging, syntactic annotation, co-reference annotation, etc.), which can be instantiated in different ways depending on the annotator's approach and goals. In this paper we provide an overview of the framework, demonstrate its applicability to syntactic annotation, and show how it can contribute to comparative evaluation of parser output and diverse syntactic annotation schemes.

  15. Analysis of sensitive CO2 pathways and genes related to carbon uptake and accumulation in Chlamydomonas reinhardtii through genomic scale modeling and experimental validation

    Directory of Open Access Journals (Sweden)

    Flavia Vischi Winck

    2016-02-01

    Full Text Available The development of microalgae sustainable applications needs better understanding of microalgae biology. Moreover, how cells coordinate their metabolism towards biomass accumulation is not fully understood. In this present study, flux balance analysis (FBA was performed to identify sensitive metabolic pathways of Chlamydomonas reinhardtii under varied CO2 inputs. The metabolic network model of Chlamydomonas was updated based on the genome annotation data and sensitivity analysis revealed CO2 sensitive reactions. Biological experiments were performed with cells cultivated at 0.04% (air, 2.5%, 5%, 8% and 10% CO2 concentration under controlled conditions and cell growth profiles and biomass content were measured. Pigments, lipids, proteins and starch were further quantified for the reference low (0.04% and high (10% CO2 conditions. The expression level of candidate genes of sensitive reactions was measured and validated by quantitative real time qPCR. The sensitive analysis revealed mitochondrial compartment as the major affected by high CO2 levels and glycolysis/gluconeogenesis, glyoxylate and dicarboxylate metabolism among the affected metabolic pathways. Genes coding for glycerate kinase (GLYK, glycine cleavage system, H-protein (GCSH, NAD-dependent malate dehydrogenase (MDH3, low-CO2 inducible protein A (LCIA, carbonic anhydrase 5 (CAH5, E1 component, alpha subunit (PDC3, dual function alcohol dehydrogenase/acetaldehyde dehydrogenase (ADH1 and phosphoglucomutase (GPM2, were defined, among other genes, as sensitive nodes in the metabolic network simulations. These genes were experimentally responsive to the changes in the carbon fluxes in the system. We performed metabolomics analysis using mass spectrometry validating the modulation of carbon dioxide responsive pathways and metabolites. The changes on CO2 levels mostly affected the metabolism of amino acids found in the photorespiration pathway. Our updated metabolic network was compared to

  16. Analysis of Sensitive CO2 Pathways and Genes Related to Carbon Uptake and Accumulation in Chlamydomonas reinhardtii through Genomic Scale Modeling and Experimental Validation.

    Science.gov (United States)

    Winck, Flavia V; Melo, David O Páez; Riaño-Pachón, Diego M; Martins, Marina C M; Caldana, Camila; Barrios, Andrés F González

    2016-01-01

    The development of microalgae sustainable applications needs better understanding of microalgae biology. Moreover, how cells coordinate their metabolism toward biomass accumulation is not fully understood. In this present study, flux balance analysis (FBA) was performed to identify sensitive metabolic pathways of Chlamydomonas reinhardtii under varied CO2 inputs. The metabolic network model of Chlamydomonas was updated based on the genome annotation data and sensitivity analysis revealed CO2 sensitive reactions. Biological experiments were performed with cells cultivated at 0.04% (air), 2.5, 5, 8, and 10% CO2 concentration under controlled conditions and cell growth profiles and biomass content were measured. Pigments, lipids, proteins, and starch were further quantified for the reference low (0.04%) and high (10%) CO2 conditions. The expression level of candidate genes of sensitive reactions was measured and validated by quantitative real time PCR. The sensitive analysis revealed mitochondrial compartment as the major affected by changes on the CO2 concentrations and glycolysis/gluconeogenesis, glyoxylate, and dicarboxylate metabolism among the affected metabolic pathways. Genes coding for glycerate kinase (GLYK), glycine cleavage system, H-protein (GCSH), NAD-dependent malate dehydrogenase (MDH3), low-CO2 inducible protein A (LCIA), carbonic anhydrase 5 (CAH5), E1 component, alpha subunit (PDC3), dual function alcohol dehydrogenase/acetaldehyde dehydrogenase (ADH1), and phosphoglucomutase (GPM2), were defined, among other genes, as sensitive nodes in the metabolic network simulations. These genes were experimentally responsive to the changes in the carbon fluxes in the system. We performed metabolomics analysis using mass spectrometry validating the modulation of carbon dioxide responsive pathways and metabolites. The changes on CO2 levels mostly affected the metabolism of amino acids found in the photorespiration pathway. Our updated metabolic network was

  17. Making web annotations persistent over time

    Energy Technology Data Exchange (ETDEWEB)

    Sanderson, Robert [Los Alamos National Laboratory; Van De Sompel, Herbert [Los Alamos National Laboratory

    2010-01-01

    As Digital Libraries (DL) become more aligned with the web architecture, their functional components need to be fundamentally rethought in terms of URIs and HTTP. Annotation, a core scholarly activity enabled by many DL solutions, exhibits a clearly unacceptable characteristic when existing models are applied to the web: due to the representations of web resources changing over time, an annotation made about a web resource today may no longer be relevant to the representation that is served from that same resource tomorrow. We assume the existence of archived versions of resources, and combine the temporal features of the emerging Open Annotation data model with the capability offered by the Memento framework that allows seamless navigation from the URI of a resource to archived versions of that resource, and arrive at a solution that provides guarantees regarding the persistence of web annotations over time. More specifically, we provide theoretical solutions and proof-of-concept experimental evaluations for two problems: reconstructing an existing annotation so that the correct archived version is displayed for all resources involved in the annotation, and retrieving all annotations that involve a given archived version of a web resource.

  18. Annotating user-defined abstractions for optimization

    Energy Technology Data Exchange (ETDEWEB)

    Quinlan, D; Schordan, M; Vuduc, R; Yi, Q

    2005-12-05

    This paper discusses the features of an annotation language that we believe to be essential for optimizing user-defined abstractions. These features should capture semantics of function, data, and object-oriented abstractions, express abstraction equivalence (e.g., a class represents an array abstraction), and permit extension of traditional compiler optimizations to user-defined abstractions. Our future work will include developing a comprehensive annotation language for describing the semantics of general object-oriented abstractions, as well as automatically verifying and inferring the annotated semantics.

  19. Meteor showers an annotated catalog

    CERN Document Server

    Kronk, Gary W

    2014-01-01

    Meteor showers are among the most spectacular celestial events that may be observed by the naked eye, and have been the object of fascination throughout human history. In “Meteor Showers: An Annotated Catalog,” the interested observer can access detailed research on over 100 annual and periodic meteor streams in order to capitalize on these majestic spectacles. Each meteor shower entry includes details of their discovery, important observations and orbits, and gives a full picture of duration, location in the sky, and expected hourly rates. Armed with a fuller understanding, the amateur observer can better view and appreciate the shower of their choice. The original book, published in 1988, has been updated with over 25 years of research in this new and improved edition. Almost every meteor shower study is expanded, with some original minor showers being dropped while new ones are added. The book also includes breakthroughs in the study of meteor showers, such as accurate predictions of outbursts as well ...

  20. FolksAnnotation: A Semantic Metadata Tool for Annotating Learning Resources Using Folksonomies and Domain Ontologies

    OpenAIRE

    Hend S. Al-Khalifa; Davis, Hugh C.

    2006-01-01

    There are many resources on the Web which are suitable for educational purposes. Unfortunately the task of identifying suitable resources for a particular educational purpose is difficult as they have not typically been annotated with educational metadata. However, many resources have now been annotated in an unstructured manner within contemporary social bookmaking services. This paper describes a novel tool called ‘FolksAnnotation’ that creates annotations with educational semantics from th...

  1. Metabolism of D-lactate and structurally related organic acids in Chlamydomonas reinhardtii

    International Nuclear Information System (INIS)

    During the initial minutes of anaerobiosis, 14C-labeled D-lactate, derived from the photosynthetic sugar phosphate pool, accumulated in the unicellular green alga, Chlamydomonas reinhardtii. The production of the D-isomer of lactate by algae is in contrast to plant and mammalian cells in which L-lactate is formed. After initial lactate formation, Chlamydomonas exhibits a mixed-acid type fermentation, thereby avoiding lactate accumulation and enabling the cells to tolerate extended periods of anaerobiosis. A pyruvate reductase which catalyzes the formation of D-lactate in Chlamydomonas was partially purified and characterized. Lactate produced anaerobically was metabolized only when Chlamydomonas cells were returned to aerobic conditions, and reoxidation of the D-lactate was apparently catalyzed by a mitochondrial membrane-bound dehydrogenase, rather than by the soluble pyruvate reductase. Mutants of Chlamydomonas, deficient in mitochondrial respiration, were used to demonstrate that lactate metabolism was linked to the mitochondrial electron transport chain. In addition, the oxidation of glycolate, a structural analog of lactate, was also linked to mitochondrial electron transport in vivo

  2. Activation of a chloroplast type of fructose bisphosphatase from Chlamydomonas reinhardtii by light-mediated agents

    Science.gov (United States)

    Huppe, H. C.; Buchanan, B. B.

    1989-01-01

    A chloroplast type of fructose-1,6-bisphosphatase, a central regulatory enzyme of photosynthetic carbon metabolism, has been partially purified from Chlamydomonas reinhardtii. Unlike its counterpart from spinach chloroplasts, the algal FBPase showed a strict requirement for a dithiol reductant irrespective of Mg2+ concentration. The enzymes from the two sources resembled each other immunologically, in subunit molecular mass and response to pH. In the presence of dithiothreitol, the pH optimum for both the algal and spinach enzymes shifted from 8.5 to a more physiologic value of 8.0 as the Mg2+ concentration was increased from 1 to 16 mM. At 1 mM Mg2+, a concentration estimated to be close to physiological, the Chlamydomonas FBPase was active only in the presence of reduced thioredoxin and was most active with Chlamydomonas thioredoxin f. Under these conditions, the enzyme showed a pH optimum of 8.0. The data suggest that the Chlamydomonas enzyme resembles its spinach counterpart in most respects, but it has a stricter requirement for reduction and less strict reductant specificity. A comparison of the properties of the FBPases from Chlamydomonas and spinach will be helpful for elucidating the mechanism of the reductive activation of this enzyme.

  3. SASL: A Semantic Annotation System for Literature

    Science.gov (United States)

    Yuan, Pingpeng; Wang, Guoyin; Zhang, Qin; Jin, Hai

    Due to ambiguity, search engines for scientific literatures may not return right search results. One efficient solution to the problems is to automatically annotate literatures and attach the semantic information to them. Generally, semantic annotation requires identifying entities before attaching semantic information to them. However, due to abbreviation and other reasons, it is very difficult to identify entities correctly. The paper presents a Semantic Annotation System for Literature (SASL), which utilizes Wikipedia as knowledge base to annotate literatures. SASL mainly attaches semantic to terminology, academic institutions, conferences, and journals etc. Many of them are usually abbreviations, which induces ambiguity. Here, SASL uses regular expressions to extract the mapping between full name of entities and their abbreviation. Since full names of several entities may map to a single abbreviation, SASL introduces Hidden Markov Model to implement name disambiguation. Finally, the paper presents the experimental results, which confirm SASL a good performance.

  4. Modeling Social Annotation: a Bayesian Approach

    CERN Document Server

    Plangprasopchok, Anon

    2008-01-01

    Collaborative tagging systems, such as del.icio.us, CiteULike, and others, allow users to annotate objects, e.g., Web pages or scientific papers, with descriptive labels called tags. The social annotations, contributed by thousands of users, can potentially be used to infer categorical knowledge, classify documents or recommend new relevant information. Traditional text inference methods do not make best use of socially-generated data, since they do not take into account variations in individual users' perspectives and vocabulary. In a previous work, we introduced a simple probabilistic model that takes interests of individual annotators into account in order to find hidden topics of annotated objects. Unfortunately, our proposed approach had a number of shortcomings, including overfitting, local maxima and the requirement to specify values for some parameters. In this paper we address these shortcomings in two ways. First, we extend the model to a fully Bayesian framework. Second, we describe an infinite ver...

  5. Annotation sémantique par classification

    OpenAIRE

    Toussaint, Yannick; Tenier, Sylvain

    2007-01-01

    Les systèmes actuels d'annotation sémantique exploitent peu les connaissances du domaine et fonctionnent essentiellement du texte vers l'ontologie. Pourtant, il est fréquent qu'un élément dans une page doive être annoté par un concept parce que certains autres éléments de cette même page sont annotés par d'autres concepts. Cet article propose une méthode d'annotation prenant en compte cette dépendance entre concepts, exprimée dans une ontologie sous forme de concepts définis. L'utilisation de...

  6. GRADUATE AND PROFESSIONAL EDUCATION, AN ANNOTATED BIBLIOGRAPHY.

    Science.gov (United States)

    HEISS, ANN M.; AND OTHERS

    THIS ANNOTATED BIBLIOGRAPHY CONTAINS REFERENCES TO GENERAL GRADUATE EDUCATION AND TO EDUCATION FOR THE FOLLOWING PROFESSIONAL FIELDS--ARCHITECTURE, BUSINESS, CLINICAL PSYCHOLOGY, DENTISTRY, ENGINEERING, LAW, LIBRARY SCIENCE, MEDICINE, NURSING, SOCIAL WORK, TEACHING, AND THEOLOGY. (HW)

  7. Services for annotation of biomedical text

    OpenAIRE

    Hakenberg, Jörg

    2008-01-01

    Motivation: Text mining in the biomedical domain in recent years has focused on the development of tools for recognizing named entities and extracting relations. Such research resulted from the need for such tools as basic components for more advanced solutions. Named entity recognition, entity mention normalization, and relationship extraction now have reached a stage where they perform comparably to human annotators (considering inter--annotator agreement, measured in many studies to be aro...

  8. Multimedia Annotations on the Semantic Web

    OpenAIRE

    Stamou, G.; Ossenbruggen, J.R.; Pan, J; Schreiber, A.T.

    2006-01-01

    Multimedia in all forms (images, video, graphics, music, speech) is exploding on the Web. The content needs to be annotated and indexed to enable effective search and retrieval. However, recent standards and best practices for multimedia metadata don't provide semantically rich descriptions of multimedia content. On the other hand, the World Wide Web Consortium's (W3C's) Semantic Web effort has been making great progress in advancing techniques for annotating semantics of Web resources. To br...

  9. Fluid Annotations in a Open World

    DEFF Research Database (Denmark)

    Zellweger, Polle Trescott; Bouvin, Niels Olof; Jehøj, Henning;

    2001-01-01

    Fluid Documents use animated typographical changes to provide a novel and appealing user experience for hypertext browsing and for viewing document annotations in context. This paper describes an effort to broaden the utility of Fluid Documents by using the open hypermedia Arakne Environment to l...... layer fluid annotations and links on top of abitrary HTML pages on the World Wide Web. Changes to both Fluid Documents and Arakne are required....

  10. Learning Object Annotation for Agricultural Learning Repositories

    OpenAIRE

    Ebner, Hannes; Manouselis, Nikos; Palmér, Matthias; Enoksson, Fredrik; Palavitsinis, Nikos; Kastrantas, Kostas; Naeve, Ambjörn

    2009-01-01

    This paper introduces a Web-based tool that has been developed to facilitate learning object annotation in agricultural learning repositories with IEEE LOM-compliant metadata. More specifically, it presents how an application profile of the IEEE LOM standard has been developed for the description of learning objects on organic agriculture and agroecology. Then, it describes the design and prototype development of the Organic.Edunet repository tool: a Web-based for annotating learning objects ...

  11. Instantiation of relations for semantic annotation

    OpenAIRE

    Tenier, Sylvain; Toussaint, Yannick; Napoli, Amedeo; Polanco, Xavier

    2006-01-01

    This paper presents a methodology for the semantic annotation of web pages with individuals of a domain ontology. While most semantic annotation systems can recognize knowledge units, they usually do not establish explicit relations between them. The method presented identifies the individuals which should be related among the whole set of individuals and codes them as role instances within an OWL ontology. This is done by using a correspondence between the tree structure of a web page and th...

  12. Instructions for Temporal Annotation of Scheduling Dialogs

    OpenAIRE

    O'Hara, Tom; Wiebe, Janyce; Payne, Karen

    1997-01-01

    Human annotation of natural language facilitates standardized evaluation of natural language processing systems and supports automated feature extraction. This document consists of instructions for annotating the temporal information in scheduling dialogs, dialogs in which the participants schedule a meeting with one another. Task-oriented dialogs, such as these are, would arise in many useful applications, for instance, automated information providers and automated phone operators. Explicit ...

  13. DIMA – Annotation guidelines for German intonation

    OpenAIRE

    Kügler, Frank; Smolibocki, Bernadett; Arnold, Denis; Baumann, Stefan; Braun, Bettina; Grice, Martine; Jannedy, Stefanie; Michalsky, Jan; Niebuhr, Oliver; Peters, Jörg; Ritter, Simon; Röhr, Christine T.; Schweitzer, Antje; Schweitzer, Katrin; Wagner, Petra

    2015-01-01

    This paper presents newly developed guidelines for prosodic annotation of German as a consensus system agreed upon by German intonologists. The DIMA system is rooted in the framework of autosegmental-metrical phonology. One important goal of the consensus is to make exchanging data between groups easier since German intonation is currently annotated according to different models. To this end, we aim to provide guidelines that are easy to learn. The guidelines were e...

  14. Facilitating functional annotation of chicken microarray data

    OpenAIRE

    Buza, Teresia J; Kumar, Ranjit; Gresham, Cathy R; Burgess, Shane C.; McCarthy, Fiona M

    2009-01-01

    Modeling results from chicken microarray studies is challenging for researchers due to little functional annotation associated with these arrays. The Affymetrix GenChip chicken genome array, one of the biggest arrays that serve as a key research tool for the study of chicken functional genomics, is among the few arrays that link gene products to Gene Ontology (GO). However the GO annotation data presented by Affymetrix is incomplete, for example, they do not show references linked to manually...

  15. Annotating Honorifics Denoting Social Ranking of Referents

    OpenAIRE

    Nariyama, Shigeko; Nakaiwa, Hiromi; Siegel, Melanie

    2011-01-01

    This paper proposes an annotating scheme that encodes honorifics (respectful words). Honorifics are used extensively in Japanese, reflecting the social relationship (e.g. social ranks and age) of the referents. This referential information is vital for resolving zero pronouns and improving machine translation outputs. Annotating honorifics is a complex task that involves identifying a predicate with honorifics, assigning ranks to referents of the predicate, calibrating the ranks, and co...

  16. Related Documents Search Using User Created Annotations

    Directory of Open Access Journals (Sweden)

    Jakub Sevcech

    2013-01-01

    Full Text Available We often use various services for creating bookmarks,tags, highlights and other types of annotations while surf-ing the Internet or when reading electronic documentsas well. These services allows us to create a number oftypes of annotation that we are commonly creating intoprinted documents. Annotations attached to electronicdocuments however can be used for other purposes suchas navigation support, text summarization etc. We pro-posed a method for searching related documents to cur-rently studied document using annotations created by thedocument reader as indicators of user's interest in par-ticular parts of the document. The method is based onspreading activation in text transformed into graph. Forevaluation we created a service called Annota, which al-lows users to insert various types of annotations into webpages and PDF documents displayed in the web browser.We analyzed properties of various types of annotations in-serted by users of Annota into documents. Based on thesewe evaluated our method by simulation and we comparedit against commonly used TF-IDF based method.

  17. JGI Plant Genomics Gene Annotation Pipeline

    Energy Technology Data Exchange (ETDEWEB)

    Shu, Shengqiang; Rokhsar, Dan; Goodstein, David; Hayes, David; Mitros, Therese

    2014-07-14

    Plant genomes vary in size and are highly complex with a high amount of repeats, genome duplication and tandem duplication. Gene encodes a wealth of information useful in studying organism and it is critical to have high quality and stable gene annotation. Thanks to advancement of sequencing technology, many plant species genomes have been sequenced and transcriptomes are also sequenced. To use these vastly large amounts of sequence data to make gene annotation or re-annotation in a timely fashion, an automatic pipeline is needed. JGI plant genomics gene annotation pipeline, called integrated gene call (IGC), is our effort toward this aim with aid of a RNA-seq transcriptome assembly pipeline. It utilizes several gene predictors based on homolog peptides and transcript ORFs. See Methods for detail. Here we present genome annotation of JGI flagship green plants produced by this pipeline plus Arabidopsis and rice except for chlamy which is done by a third party. The genome annotations of these species and others are used in our gene family build pipeline and accessible via JGI Phytozome portal whose URL and front page snapshot are shown below.

  18. An annotation based approach to support design communication

    CERN Document Server

    Hisarciklilar, Onur

    2007-01-01

    The aim of this paper is to propose an approach based on the concept of annotation for supporting design communication. In this paper, we describe a co-operative design case study where we analyse some annotation practices, mainly focused on design minutes recorded during project reviews. We point out specific requirements concerning annotation needs. Based on these requirements, we propose an annotation model, inspired from the Speech Act Theory (SAT) to support communication in a 3D digital environment. We define two types of annotations in the engineering design context, locutionary and illocutionary annotations. The annotations we describe in this paper are materialised by a set of digital artefacts, which have a semantic dimension allowing express/record elements of technical justifications, traces of contradictory debates, etc. In this paper, we first clarify the semantic annotation concept, and we define general properties of annotations in the engineering design context, and the role of annotations in...

  19. The Annotation of RNA Motifs

    Directory of Open Access Journals (Sweden)

    Eric Westhof

    2006-04-01

    Full Text Available The recent deluge of new RNA structures, including complete atomic-resolution views of both subunits of the ribosome, has on the one hand literally overwhelmed our individual abilities to comprehend the diversity of RNA structure, and on the other hand presented us with new opportunities for comprehensive use of RNA sequences for comparative genetic, evolutionary and phylogenetic studies. Two concepts are key to understanding RNA structure: hierarchical organization of global structure and isostericity of local interactions. Global structure changes extremely slowly, as it relies on conserved long-range tertiary interactions. Tertiary RNA–RNA and quaternary RNA–protein interactions are mediated by RNA motifs, defined as recurrent and ordered arrays of non-Watson–Crick base-pairs. A single RNA motif comprises a family of sequences, all of which can fold into the same three-dimensional structure and can mediate the same interaction(s. The chemistry and geometry of base pairing constrain the evolution of motifs in such a way that random mutations that occur within motifs are accepted or rejected insofar as they can mediate a similar ordered array of interactions. The steps involved in the analysis and annotation of RNA motifs in 3D structures are: (a decomposition of each motif into non-Watson–Crick base-pairs; (b geometric classification of each basepair; (c identification of isosteric substitutions for each basepair by comparison to isostericity matrices; (d alignment of homologous sequences using the isostericity matrices to identify corresponding positions in the crystal structure; (e acceptance or rejection of the null hypothesis that the motif is conserved.

  20. GOAnnotator: linking protein GO annotations to evidence text

    OpenAIRE

    Couto, Francisco M.; Silva, Mário J.; Lee, Vivian; Dimmer, Emily; Camon, Evelyn; Apweiler, Rolf; Kirsch, Harald; Rebholz-Schuhmann, Dietrich

    2006-01-01

    Background Annotation of proteins with gene ontology (GO) terms is ongoing work and a complex task. Manual GO annotation is precise and precious, but it is time-consuming. Therefore, instead of curated annotations most of the proteins come with uncurated annotations, which have been generated automatically. Text-mining systems that use literature for automatic annotation have been proposed but they do not satisfy the high quality expectations of curators. Results In this paper we describe an ...

  1. Web Database Query Interface Annotation Based on User Collaboration

    Institute of Scientific and Technical Information of China (English)

    LIU Wei; LIN Can; MENG Xiaofeng

    2006-01-01

    A vision based query interface annotation method is used to relate attributes and form elements in form-based web query interfaces, this method can reach accuracy of 82%.And a user participation method is used to tune the result; user can answer "yes" or "no" for existing annotations, or manually annotate form elements.Mass feedback is added to the annotation algorithm to produce more accurate result.By this approach, query interface annotation can reach a perfect accuracy.

  2. Phase-dependent forcing and synchronization in the three-sphere model of Chlamydomonas

    Science.gov (United States)

    Bennett, Rachel R.; Golestanian, Ramin

    2013-07-01

    The green alga Chlamydomonas swims with synchronized beating of its two flagella, and is experimentally observed to exhibit run-and-tumble behaviour similar to bacteria. Recently, we studied a simple hydrodynamic three-sphere model of Chlamydomonas with a phase-dependent driving force that can produce run-and-tumble behaviour when intrinsic noise is added, due to the nonlinear mechanics of the system. Here, we consider the noiseless case and explore numerically the parameter space in the driving force profiles, which determine whether or not the synchronized state evolves from a given initial condition, as well as the stability of the synchronized state. We find that phase-dependent forcing, or a beat pattern, is necessary for stable synchronization in the geometry we work with. The phase-dependent forcing allows this simple model of Chlamydomonas to produce a rich variety of behaviours.

  3. The Chlamydomonas Genome Reveals the Evolution of Key Animal and Plant Functions

    Energy Technology Data Exchange (ETDEWEB)

    Merchant, Sabeeha S

    2007-04-09

    Chlamydomonas reinhardtii is a unicellular green alga whose lineage diverged from land plants over 1 billion years ago. It is a model system for studying chloroplast-based photosynthesis, as well as the structure, assembly, and function of eukaryotic flagella (cilia), which were inherited from the common ancestor of plants and animals, but lost in land plants. We sequenced the 120-megabase nuclear genome of Chlamydomonas and performed comparative phylogenomic analyses, identifying genes encoding uncharacterized proteins that are likely associated with the function and biogenesis of chloroplasts or eukaryotic flagella. Analyses of the Chlamydomonas genome advance our understanding of the ancestral eukaryotic cell, reveal previously unknown genes associated with photosynthetic and flagellar functions, and establish links between ciliopathy and the composition and function of flagella.

  4. Isolation, growth, ultrastructure, and metal tolerance of the green alga, Chlamydomonas acidophila (Chlorophyta).

    Science.gov (United States)

    Nishikawa, K; Tominaga, N

    2001-12-01

    An acidophilic volvocine flagellate, Chlamydomonas acidophila (Volvocales) that was isolated from an acid lake, Katanuma, in Miyagi prefecture, Japan was studied for growth, ultrastructural characterization, and metal tolerance. Chlamydomonas acidophila is obligately photoautotrophic, and did not grow in the cultures containing acetate or citrate even in the light. The optimum pH for growth was 3.5-4.5. To characterize metal tolerance, the toxic effects of Cd, Co, Cu, and Zn on this alga were also studied. Effective metal concentrations, which limited the growth by 50%, EC50 were measured, after 72 h of static exposure. EC50s were 14.4 microM Cd2+, 81.3 microM Co2+, 141 microM Cu2+, and 1.16 mM Zn2+ for 72 h of exposure. Thus, this alga had stronger tolerance to these metals than other species in the genus Chlamydomonas. PMID:11826960

  5. Phase-dependent forcing and synchronization in the three-sphere model of Chlamydomonas

    International Nuclear Information System (INIS)

    The green alga Chlamydomonas swims with synchronized beating of its two flagella, and is experimentally observed to exhibit run-and-tumble behaviour similar to bacteria. Recently, we studied a simple hydrodynamic three-sphere model of Chlamydomonas with a phase-dependent driving force that can produce run-and-tumble behaviour when intrinsic noise is added, due to the nonlinear mechanics of the system. Here, we consider the noiseless case and explore numerically the parameter space in the driving force profiles, which determine whether or not the synchronized state evolves from a given initial condition, as well as the stability of the synchronized state. We find that phase-dependent forcing, or a beat pattern, is necessary for stable synchronization in the geometry we work with. The phase-dependent forcing allows this simple model of Chlamydomonas to produce a rich variety of behaviours. (paper)

  6. Site-specific basal body duplication in Chlamydomonas.

    Science.gov (United States)

    O'Toole, Eileen T; Dutcher, Susan K

    2014-02-01

    Correct centriole/basal body positioning is required for numerous biological processes, yet how the cell establishes this positioning is poorly understood. Analysis of centriolar/basal body duplication provides a key to understanding basal body positioning and function. Chlamydomonas basal bodies contain structural features that enable specific triplet microtubules to be specified. Electron tomography of cultures enriched in mitotic cells allowed us to follow basal body duplication and identify a specific triplet at which duplication occurs. Probasal bodies elongate in prophase, assemble transitional fibers (TF) and are segregated with a mature basal body near the poles of the mitotic spindle. A ring of nine-singlet microtubules is initiated at metaphase, orthogonal to triplet eight. At telophase/cytokinesis, triplet microtubule blades assemble first at the distal end, rather than at the proximal cartwheel. The cartwheel undergoes significant changes in length during duplication, which provides further support for its scaffolding role. The uni1-1 mutant contains short basal bodies with reduced or absent TF and defective transition zones, suggesting that the UNI1 gene product is important for coordinated probasal body elongation and maturation. We suggest that this site-specific basal body duplication ensures the correct positioning of the basal body to generate landmarks for intracellular patterning in the next generation. PMID:24166861

  7. Isolation and characterization of glutamine synthetase genes in Chlamydomonas reinhardtii.

    Science.gov (United States)

    Chen, Q; Silflow, C D

    1996-11-01

    To elucidate the role of glutamine synthetase (GS) in nitrogen assimilation in the green alga Chlamydomonas reinhardtii we used maize GS1 (the cytosolic form) and GS2 (the chloroplastic form) cDNAs as hybridization probes to isolate C. reinhardtii cDNA clones. The amino acid sequences derived from the C. reinhardtii clones have extensive homology with GS enzymes from higher plants. A putative amino-terminal transit peptide encoded by the GS2 cDNA suggests that the protein localizes to the chloroplast. Genomic DNA blot analysis indicated that GS1 is encoded by a single gene, whereas two genomic fragments hybridized to the GS2 cDNA probe. All GS2 cDNA clones corresponded to only one of the two GS2 genomic sequences. We provide evidence that ammonium, nitrate, and light regulate GS transcript accumulation in green algae. Our results indicate that the level of GS1 transcripts is repressed by ammonium but induced by nitrate. The level of GS2 transcripts is not affected by ammonium or nitrate. Expression of both GS1 and GS2 genes is regulated by light, but perhaps through different mechanisms. Unlike in higher plants, no decreased level of GS2 transcripts was detected when cells were grown under conditions that repress photorespiration. Analysis of GS transcript levels in mutants with defects in the nitrate assimilation pathway show that nitrate assimilation and ammonium assimilation are regulated independently. PMID:8938407

  8. Histones of Chlamydomonas reinhardtii. Synthesis, acetylation, and methylation

    International Nuclear Information System (INIS)

    Histones of the green alga Chlamydomonas reinhardtii were prepared by a new method and fractionated by reversed-phase high-performance liquid chromatography. Acid-urea-Triton gel analysis and tritiated acetate labeling demonstrated high levels of steady-state acetylation for the single histone H3 protein, in contrast to low levels on histones H4 and H2B. Twenty percent of histone H3 is subject to dynamic acetylation with, on average, three acetylated lysine residues per protein molecule. Histone synthesis in light-dark-synchronized cultures was biphasic with pattern differences between two histone H1 variants, between two H2A variants, and between H2B and ubiquitinated H2B. Automated protein sequence analysis of histone H3 demonstrated a site-specific pattern of steady-state acetylation between 7 and 17% at five of the six amino-terminal lysines and of monomethylation between 5 and 81% at five of the eight amino-terminal lysines in a pattern that may limit dynamic acetylation. An algal histone H3 sequence was confirmed by protein sequencing with a since threonine as residue 28 instead of the serine(28)-alanine(29) sequence, present in all other known plant and animal H3 histones

  9. Response of Chlamydomonas reinhardtii to naphthenic acid exposure

    International Nuclear Information System (INIS)

    This study examined the feasibility of using a model organism for the algal bioremediation of oil sands process water (OSPW), a highly toxic mixture of sediments, bitumen, ions, and organic and inorganic compounds. Naphthenic acids (NAs) are a contaminant class of particular concern. Bioremediation techniques may mitigate toxicity of OSPW in general, and NAs in particular. Although most studies on the biodegradation of NAs focus on the role of bacteria, fungi, and emergent macrophytes, studies have indicated that algae may also play a key role through direct degradation, biosequestration, or photosynthetic aeration of waters to promote other biological reactions. Chlamydomonas frigida is of particular interest, but no cultures are currently available. Therefore, this study used C. reinhardtii, a well-characterized model organism, to begin analysis of potential algal bioremediation of OSPW. Cultures of C. reinhardtii were grown heterotrophically in nutrient media spiked with a dilution series of NAs. Culture densities were measured to compile growth curves over time, changes in rate of growth, and survivability. Negative ion electrospray mass spectrometry was used to determine the concentration of NAs in solution in relation to growth rate and culture density. The study determined the tolerance of C. reinhardtii to NAs. A mechanism for this tolerance was then proposed.

  10. Transport and metabolism of glycolic acid by Chlamydomonas reinhardtii

    International Nuclear Information System (INIS)

    In order to understand the excretion of glycolate from Chlamydomonas reinhardtii, the conditions affecting glycolate synthesis and metabolism were investigated. Although glycolate is synthesized only in the light, the metabolism occurs in the light and dark with greater metabolism in the light due to refixation of photorespiratory CO2. The amount of internal glycolate will affect the metabolism of externally added glycolate. When glycolate synthesis exceeds the metabolic capacity, glycolate is excreted from the cell. The transport of glycolate into the cells occurs very rapidly. Equilibrium is achieved at 40C within the time cells are pelleted by the silicone oil centrifugation technique through a layer of [14C] glycolate. Glycolate uptake does not show the same time, temperature and pH dependencies as diffusion of benzoate. Uptake can be inhibited by treatment of cells with N-ethylmaleimide and stimulated in the presence of valino-mycin/KCl. Acetate and lactate are taken up as quickly as glycolate. The hypothesis was made that glycolate is transported by a protein carrier that transports monocarboxylic acids. The equilibrium concentration of glycolate is dependent on the cell density, implying that there may be a large number of transporter sites and that uptake is limited by substrate availability

  11. Carbonic anhydrase activity in isolated chloroplasts of chlamydomonas reinhardtii

    International Nuclear Information System (INIS)

    In a new assay of carbonic anhydrase, NaH14CO3 solution at the bottom of a sealed vessel releases 14CO3 which diffuses to the top of the vessel to be assimilated by actively photosynthesizing Chlamydomonas cells. The assay is initiated by illuminating cells and stopped by turning the light off and killing the cells with acid. Enzyme activity was estimated from acid stable radioactivity above the uncatalyzed background level. With bovine carbonic anhydrase, 1.5 Wilbur Anderson Unit (WAU) can be consistantly measured at 5-6 fold above background. Sonicated whole cells of air adapted wild type (+)gave 741.1 ± 12.4 WAU/mg chl. Intact washed cells of mixotrophically grown wall-less mutant CWD(-) and a high CO2 requiring wall-less double mutant CIA-3/CW15 (-) gave 7.1 ± 1.9 and 2.8 ± 7.8 WAU/mg chl respectively. Chloroplasts isolated from CWD and CIA-3/CW15 and subsequently disrupted gave 64.0 ± 14.7 and 2.8 ± 3.2 WAU/mg chl respectively. Chloroplast sonicate from another wall-less mutant CW15(-) gave activity comparable to CWD. Thus on a chlorophyll basis, enzyme activity in chloroplasts from mixotrophically grown cells is about 1/10th of the level found in air adapted wild type cells. CIA-3 seems to lack this activity

  12. Singlet oxygen production in Chlamydomonas reinhardtii under heat stress.

    Science.gov (United States)

    Prasad, Ankush; Ferretti, Ursula; Sedlářová, Michaela; Pospíšil, Pavel

    2016-01-01

    In the current study, singlet oxygen formation by lipid peroxidation induced by heat stress (40 °C) was studied in vivo in unicellular green alga Chlamydomonas reinhardtii. Primary and secondary oxidation products of lipid peroxidation, hydroperoxide and malondialdehyde, were generated under heat stress as detected using swallow-tailed perylene derivative fluorescence monitored by confocal laser scanning microscopy and high performance liquid chromatography, respectively. Lipid peroxidation was initiated by enzymatic reaction as inhibition of lipoxygenase by catechol and caffeic acid prevented hydroperoxide formation. Ultra-weak photon emission showed formation of electronically excited species such as triplet excited carbonyl, which, upon transfer of excitation energy, leads to the formation of either singlet excited chlorophyll or singlet oxygen. Alternatively, singlet oxygen is formed by direct decomposition of hydroperoxide via Russell mechanisms. Formation of singlet oxygen was evidenced by the nitroxyl radical 2,2,6,6-tetramethylpiperidine-1-oxyl detected by electron paramagnetic resonance spin-trapping spectroscopy and the imaging of green fluorescence of singlet oxygen sensor green detected by confocal laser scanning microscopy. Suppression of singlet oxygen formation by lipoxygenase inhibitors indicates that singlet oxygen may be formed via enzymatic lipid peroxidation initiated by lipoxygenase. PMID:26831215

  13. Identification of the Elusive Pyruvate Reductase of Chlamydomonas reinhardtii Chloroplasts.

    Science.gov (United States)

    Burgess, Steven J; Taha, Hussein; Yeoman, Justin A; Iamshanova, Oksana; Chan, Kher Xing; Boehm, Marko; Behrends, Volker; Bundy, Jacob G; Bialek, Wojciech; Murray, James W; Nixon, Peter J

    2016-01-01

    Under anoxic conditions the green alga Chlamydomonas reinhardtii activates various fermentation pathways leading to the creation of formate, acetate, ethanol and small amounts of other metabolites including d-lactate and hydrogen. Progress has been made in identifying the enzymes involved in these pathways and their subcellular locations; however, the identity of the enzyme involved in reducing pyruvate to d-lactate has remained unclear. Based on sequence comparisons, enzyme activity measurements, X-ray crystallography, biochemical fractionation and analysis of knock-down mutants, we conclude that pyruvate reduction in the chloroplast is catalyzed by a tetrameric NAD(+)-dependent d-lactate dehydrogenase encoded by Cre07.g324550. Its expression during aerobic growth supports a possible function as a 'lactate valve' for the export of lactate to the mitochondrion for oxidation by cytochrome-dependent d-lactate dehydrogenases and by glycolate dehydrogenase. We also present a revised spatial model of fermentation based on our immunochemical detection of the likely pyruvate decarboxylase, PDC3, in the cytoplasm. PMID:26574578

  14. Characterizing the anaerobic response of Chlamydomonas reinhardtii by quantitative proteomics.

    Science.gov (United States)

    Terashima, Mia; Specht, Michael; Naumann, Bianca; Hippler, Michael

    2010-07-01

    The versatile metabolism of the green alga Chlamydomonas reinhardtii is reflected in its complex response to anaerobic conditions. The anaerobic response is also remarkable in the context of renewable energy because C. reinhardtii is able to produce hydrogen under anaerobic conditions. To identify proteins involved during anaerobic acclimation as well as to localize proteins and pathways to the powerhouses of the cell, chloroplasts and mitochondria from C. reinhardtii in aerobic and anaerobic (induced by 8 h of argon bubbling) conditions were isolated and analyzed using comparative proteomics. A total of 2315 proteins were identified. Further analysis based on spectral counting clearly localized 606 of these proteins to the chloroplast, including many proteins of the fermentative metabolism. Comparative quantitative analyses were performed with the chloroplast-localized proteins using stable isotopic labeling of amino acids ([(13)C(6)]arginine/[(12)C(6)]arginine in an arginine auxotrophic strain). The quantitative data confirmed proteins previously characterized as induced at the transcript level as well as identified several new proteins of unknown function induced under anaerobic conditions. These proteins of unknown function provide new candidates for further investigation, which could bring insights for the engineering of hydrogen-producing alga strains. PMID:20190198

  15. Calcium titration of Chlamydomonas reinhardtii centrin and its structural changes

    Science.gov (United States)

    Ocaña, Wanda; Pastrana-Ríos, Belinda

    2014-07-01

    Chlamydomonas reinhardtii centrin is a highly conserved calcium binding protein belonging to the EF-hand superfamily. Centrin, like other calcium binding proteins, changes conformation upon calcium binding. In addition, the calcium binding sites are comprised mainly of aspartates and glutamates which would serve as probes for a calcium binding event. 2D IR correlation spectroscopy has proven to be a valuable technique to determine the differences in the molecular behavior of the EF-hand domains within centrin. Moreover, the differences in affinity for calcium displayed by these domains were correlated to differences in the molecular behavior of these EF-hand domains when compared with each other and the full-length protein. We were able to confirm the nature of the two independent domains within centrin. Furthermore, we established the mechanism of aggregation was self-association due to adsorption of centrin to the ZnSe ATR crystal and estimated the extent of aggregation of the full-length protein.

  16. Expression of human soluble TRAIL in Chlamydomonas reinhardtii chloroplast

    Institute of Scientific and Technical Information of China (English)

    YANG Zongqi; LI yinü; CHEN Feng; LI Dong; ZHANG Zhifang; LIU Yanxin; ZHENG Dexian; WANG Yong; SHEN Guifang

    2006-01-01

    Tumor necrosis factor-related apoptosis-inducing ligand (TRAIL) induces selectively apoptosis in various tumor cells and virus-infected cells, but rarely in normal cells. A chloroplast expression vector, p64TRAIL, containing the cDNA coding for the soluble TRAIL (sTRAIL), was constructed with clpP-trnL-petB-chlL-rpl23-rpl2 as Chlamydomonas reinhardtii plastid homologous recombinant fragments and spectinomycin-resistant aadA gene as a select marker. The plasmid p64TRAIL was transferred into the chloroplast genome of C. reinhardtii by the biolistic method. Three independently transformed lines were obtained by 100 mg/L spectinomycin selection. PCR amplification, Southern blot analysis of the sTRAIL coding region DNA and cultivation cells in the dark all showed that the exogenous DNA had been integrated into chloroplast genome of C. reinhardtii. Western blot analysis showed that human soluble TRAIL was expressed in C. reinhardtii chloroplast. The densitometric analysis of Western blot indicated that the expressed human sTRAIL protein in the chloroplasts of C. reinhardtii accounted for about 0.43%-0.67% of the total soluble proteins.These experimental results demonstrated the possibility of using transgenic chloroplasts of green alga as bioreactors for production of biopharmaceuticals.

  17. LET dependence of survival curve shape in chlamydomonas

    International Nuclear Information System (INIS)

    Chlamydomonas reinhardi, a haploid eukaryotic alga, was grown synchronously. A tandem Van de Graaff accelerator was used to produce protons and deuterons with LET's of 13 to 26 MeV-cm/sup 2//g and /sup 3/He and /sup 4/He nuclei at 71 to 87 MeV-cm/sup 2//g. Low-LET electrons were supplied by a 1.5 MeV electron Van de Graaff machine. The survival curves were fitted to the linear quadratic formula: S = exp(-αD + βD/sup 2/). In contrast to the response of mammalian cells, the first-power coefficient, α, remained at zero, or slightly less than zero, for all LET values up to 26 MeV-cm/sup 2//g. At the higher values it became positive; however, even at the highest stopping power, the curve had an obvious shoulder. The second-power coefficient, β, increased gradually with increasing LET up to 71 MeV-cm/sup 2//g, and rapidly between 71 and 87 MeV-cm/sup 2//g. This suggests that intra-track interactions may be largely responsible for ''sublesions''

  18. The pH tolerance of Chlamydomonas applanata (Volvocales, Chlorophyta).

    Science.gov (United States)

    Visviki, I; Santikul, D

    2000-02-01

    The effects of hydrogen ions on the growth and ultrastructure of Chlamydomonas applanata Pringsheim were examined. This species exhibits wide tolerance growing at pH values ranging from 3.4 to 8.4, with optimum growth obtained at 7.4. Growth is noticeably depressed at pH 4.4 and 3.4. At the ultrastructural level, exposure to pH 4.4 results in a 10% decrease in cell volume of single vegetative cells, an increase in pyrenoidal volume, and reduction of starch reserves. Palmelloid colonies also appear. pH 3.4 induces excessive production of mucilage and leads to the preponderance of palmelloid colonies. Cell death of both colony and single cells is seen, as well as loss of motility and abnormal cell division. Surviving single cells are significantly larger than controls, with thicker cell walls, smaller chloroplasts, and larger vacuome. Such cells entering dormancy ensure the survival of the species in times of stress. PMID:10629274

  19. Annotated chemical patent corpus: a gold standard for text mining.

    Directory of Open Access Journals (Sweden)

    Saber A Akhondi

    Full Text Available Exploring the chemical and biological space covered by patent applications is crucial in early-stage medicinal chemistry activities. Patent analysis can provide understanding of compound prior art, novelty checking, validation of biological assays, and identification of new starting points for chemical exploration. Extracting chemical and biological entities from patents through manual extraction by expert curators can take substantial amount of time and resources. Text mining methods can help to ease this process. To validate the performance of such methods, a manually annotated patent corpus is essential. In this study we have produced a large gold standard chemical patent corpus. We developed annotation guidelines and selected 200 full patents from the World Intellectual Property Organization, United States Patent and Trademark Office, and European Patent Office. The patents were pre-annotated automatically and made available to four independent annotator groups each consisting of two to ten annotators. The annotators marked chemicals in different subclasses, diseases, targets, and modes of action. Spelling mistakes and spurious line break due to optical character recognition errors were also annotated. A subset of 47 patents was annotated by at least three annotator groups, from which harmonized annotations and inter-annotator agreement scores were derived. One group annotated the full set. The patent corpus includes 400,125 annotations for the full set and 36,537 annotations for the harmonized set. All patents and annotated entities are publicly available at www.biosemantics.org.

  20. Stimulation of growth and photosynthetic carbon metabolism in Chlamydomonas reinhardtii with triacontanol

    International Nuclear Information System (INIS)

    Treatment of Chlamydomonas reinhardtii Dangeard cells (-, strain N. 90), cultured at 5% CO2, with 1 to 1000 μg/L triacontanol (TRIA) resulted in a 21% to 35% increase in cell density, 7% to 31% increase in total chlorophyll, and 20% to 100% increase in photosynthetic CO2 assimilation. Chlamydomonas cells responded to a broad range of TRIA concentrations that were at least 10-fold above the optimum concentration for higher plants. Octacosanol inhibited the effect of TRIA on photosynthetic CO2 assimilation. TRIA did not alter glycolate excretion, the CO2 compensation point or sensitivity of photosynthetic CO2 assimilation to O2 in Chlamydomonas. Kinetic analysis of TRIA-treated cells showed that the increase in photosynthetic CO2 assimilation was a result of an increase in the whole-cell apparent Vmax. The activity of RuBP carboxylase/oxygenase was significantly higher in cell lysates from TRIA-treated cells than those from control cells. However, quantification of RuBP carboxylase/oxygenase levels by 14CABP binding did not show increased enzyme levels in TRIA-treated cells. Therefore, there was an increase in the specific activity of RuBP carboxylase/oxygenase extracted from Chlamydomonas cells treated with TRIA. TRIA alone had no effect in vitro on the activity of RuBPcarboxylase/oxygenase purified from spinach (Spinacia oleracea) leaves or from cell lysates of Chlamydomonas. RuBP levels were significantly higher in TRIA-treated cells at high and low CO2. Increased RuBP levels in TRIA-treated Chlamydomonas cells were also observed in the absence of CO2 with atmospheres of N2 and 21% O2

  1. Gene Ontology annotations at SGD: new data sources and annotation methods.

    Science.gov (United States)

    Hong, Eurie L; Balakrishnan, Rama; Dong, Qing; Christie, Karen R; Park, Julie; Binkley, Gail; Costanzo, Maria C; Dwight, Selina S; Engel, Stacia R; Fisk, Dianna G; Hirschman, Jodi E; Hitz, Benjamin C; Krieger, Cynthia J; Livstone, Michael S; Miyasato, Stuart R; Nash, Robert S; Oughtred, Rose; Skrzypek, Marek S; Weng, Shuai; Wong, Edith D; Zhu, Kathy K; Dolinski, Kara; Botstein, David; Cherry, J Michael

    2008-01-01

    The Saccharomyces Genome Database (SGD; http://www.yeastgenome.org/) collects and organizes biological information about the chromosomal features and gene products of the budding yeast Saccharomyces cerevisiae. Although published data from traditional experimental methods are the primary sources of evidence supporting Gene Ontology (GO) annotations for a gene product, high-throughput experiments and computational predictions can also provide valuable insights in the absence of an extensive body of literature. Therefore, GO annotations available at SGD now include high-throughput data as well as computational predictions provided by the GO Annotation Project (GOA UniProt; http://www.ebi.ac.uk/GOA/). Because the annotation method used to assign GO annotations varies by data source, GO resources at SGD have been modified to distinguish data sources and annotation methods. In addition to providing information for genes that have not been experimentally characterized, GO annotations from independent sources can be compared to those made by SGD to help keep the literature-based GO annotations current. PMID:17982175

  2. MPEG-7 based video annotation and browsing

    Science.gov (United States)

    Hoeynck, Michael; Auweiler, Thorsten; Wellhausen, Jens

    2003-11-01

    The huge amount of multimedia data produced worldwide requires annotation in order to enable universal content access and to provide content-based search-and-retrieval functionalities. Since manual video annotation can be time consuming, automatic annotation systems are required. We review recent approaches to content-based indexing and annotation of videos for different kind of sports and describe our approach to automatic annotation of equestrian sports videos. We especially concentrate on MPEG-7 based feature extraction and content description, where we apply different visual descriptors for cut detection. Further, we extract the temporal positions of single obstacles on the course by analyzing MPEG-7 edge information. Having determined single shot positions as well as the visual highlights, the information is jointly stored with meta-textual information in an MPEG-7 description scheme. Based on this information, we generate content summaries which can be utilized in a user-interface in order to provide content-based access to the video stream, but further for media browsing on a streaming server.

  3. Automated analysis and annotation of basketball video

    Science.gov (United States)

    Saur, Drew D.; Tan, Yap-Peng; Kulkarni, Sanjeev R.; Ramadge, Peter J.

    1997-01-01

    Automated analysis and annotation of video sequences are important for digital video libraries, content-based video browsing and data mining projects. A successful video annotation system should provide users with useful video content summary in a reasonable processing time. Given the wide variety of video genres available today, automatically extracting meaningful video content for annotation still remains hard by using current available techniques. However, a wide range video has inherent structure such that some prior knowledge about the video content can be exploited to improve our understanding of the high-level video semantic content. In this paper, we develop tools and techniques for analyzing structured video by using the low-level information available directly from MPEG compressed video. Being able to work directly in the video compressed domain can greatly reduce the processing time and enhance storage efficiency. As a testbed, we have developed a basketball annotation system which combines the low-level information extracted from MPEG stream with the prior knowledge of basketball video structure to provide high level content analysis, annotation and browsing for events such as wide- angle and close-up views, fast breaks, steals, potential shots, number of possessions and possession times. We expect our approach can also be extended to structured video in other domains.

  4. Critical Assessment of Function Annotation Meeting, 2011

    Energy Technology Data Exchange (ETDEWEB)

    Friedberg, Iddo

    2015-01-21

    The Critical Assessment of Function Annotation meeting was held July 14-15, 2011 at the Austria Conference Center in Vienna, Austria. There were 73 registered delegates at the meeting. We thank the DOE for this award. It helped us organize and support a scientific meeting AFP 2011 as a special interest group (SIG) meeting associated with the ISMB 2011 conference. The conference was held in Vienna, Austria, in July 2011. The AFP SIG was held on July 15-16, 2011 (immediately preceding the conference). The meeting consisted of two components, the first being a series of talks (invited and contributed) and discussion sections dedicated to protein function research, with an emphasis on the theory and practice of computational methods utilized in functional annotation. The second component provided a large-scale assessment of computational methods through participation in the Critical Assessment of Functional Annotation (CAFA).

  5. Graph Annotations in Modeling Complex Network Topologies

    CERN Document Server

    Dimitropoulos, Xenofontas; Vahdat, Amin; Riley, George

    2007-01-01

    The coarsest approximation of the structure of a complex network, such as the Internet, is a simple undirected unweighted graph. This approximation, however, loses too much detail. In reality, objects represented by vertices and edges in such a graph possess some non-trivial internal structure that varies across and differentiates among distinct types of links or nodes. In this work, we abstract such additional information as network annotations. We introduce a network topology modeling framework that treats annotations as an extended correlation profile of a network. Assuming we have this profile measured for a given network, we present an algorithm to rescale it in order to construct networks of varying size that still reproduce the original measured annotation profile. Using this methodology, we accurately capture the network properties essential for realistic simulations of network applications and protocols, or any other simulations involving complex network topologies, including modeling and simulation ...

  6. Ultraviolet modification of Chlamydomonas reinhardtii for carbon capture

    Directory of Open Access Journals (Sweden)

    Gopal NS

    2016-04-01

    Full Text Available Nikhil S Gopal,1 K Sudhakar2 1The Lawrenceville School, Lawrenceville, NJ, USA; 2Bioenergy Laboratory, Malauna Azad National Institute of Technology, Bhopal, India Purpose: Carbon dioxide (CO2 levels have been rising rapidly. Algae are single-cell organisms with highly efficient CO2 uptake mechanisms. Algae yield two to ten times more biomass versus terrestrial plants and can grow nearly anywhere. Large scale CO2 sequestration is not yet sustainable due to high amounts of nitrogen (N and phosphate (P needed to grow algae in media. Methods: Mutant strains of Chlamydomonas reinhardtii were created using ultraviolet light (2.2–3 K J/m2 and natural selection using media with 20%–80% lower N and P compared to standard Sueoka's high salt medium. Strains were selected based upon growth in media concentrations varying from 20% to 80% less N/P compared to control. Biomass was compared to wild-type control (CC-125 using direct counts, optical density dry weight, and mean doubling time. Results: Mean doubling time was 20 and 25 hours in the low N and N/P strains, respectively (vs 66 hours in control. Using direct counts, growth rates of mutant strains of low N and N/P cultures were not statistically different from control (P=0.37 and 0.70, respectively. Conclusion: Two new strains of algae, as well as wild-type control, were able to grow while using 20%–40% less N and P. Ultraviolet light-based modification of algae is an inexpensive and alternative option to genetic engineering techniques. This technique might make larger scale biosequestration possible. Keywords: biosequestration, ultraviolet, carbon sequestration, carbon capture, algae

  7. Chloroplast genetics of chlamydomonas. II. Mapping by cosegregation frequency analysis

    International Nuclear Information System (INIS)

    This paper presents segregation and cosegregation data for a set of 15 chloroplast genes of Chlamydomonas, and uses these data to generate a linear map of the chloroplast genome. The data were derived from pedigree analysis of a total of 1596 zoospore clones resulting from 12 crosses in each of which 4 to 7 pairs of chloroplast alleles were segregating. The crosses are a subset of those previously described. By means of pedigree analysis, Type III segregations (nonreciprocal conversion-like events) were distinguished from Type III segregations (reciprocal events). The average frequency of Type II segregation was found to be the same for all 15 genes, indicating randomness of this event with respect to map location. Type III segregations occurred with a different and characteristic frequency for each gene, and were interpreted as a measure of the distance of each gene from the postulated centromere-like attachment point. Cosegregations, involving two or more genes, occurred with frequencies characteristic of the particular genes and much lower than expected for the product of single-gene events, indicating strong positive interference. Pairwise cosegregation frequencies provided unambiguous data for the gene order, confirmed by cosegregation runs of three or more genes. Apparent lengths of cosegregation runs, as fractions of the total map, indicate much longer stretches of gene conversion-like events than have been reported for other genetic systems. Comparisons of cosegregation frequencies in cross 20 after 15'', 30'', and 15'' uv irradiation of the mt+ before mating, indicate little if any consistent effect of this irradiation on segregation events

  8. Photosynthetic H2 metabolism in Chlamydomonas reinhardtii (unicellular green algae).

    Science.gov (United States)

    Melis, Anastasios

    2007-10-01

    Unicellular green algae have the ability to operate in two distinctly different environments (aerobic and anaerobic), and to photosynthetically generate molecular hydrogen (H2). A recently developed metabolic protocol in the green alga Chlamydomonas reinhardtii permitted separation of photosynthetic O2-evolution and carbon accumulation from anaerobic consumption of cellular metabolites and concomitant photosynthetic H2-evolution. The H2 evolution process was induced upon sulfate nutrient deprivation of the cells, which reversibly inhibits photosystem-II and O2-evolution in their chloroplast. In the absence of O2, and in order to generate ATP, green algae resorted to anaerobic photosynthetic metabolism, evolved H2 in the light and consumed endogenous substrate. This study summarizes recent advances on green algal hydrogen metabolism and discusses avenues of research for the further development of this method. Included is the mechanism of a substantial tenfold starch accumulation in the cells, observed promptly upon S-deprivation, and the regulated starch and protein catabolism during the subsequent H2-evolution. Also discussed is the function of a chloroplast envelope-localized sulfate permease, and the photosynthesis-respiration relationship in green algae as potential tools by which to stabilize and enhance H2 metabolism. In addition to potential practical applications of H2, approaches discussed in this work are beginning to address the biochemistry of anaerobic H2 photoproduction, its genes, proteins, regulation, and communication with other metabolic pathways in microalgae. Photosynthetic H2 production by green algae may hold the promise of generating a renewable fuel from nature's most plentiful resources, sunlight and water. The process potentially concerns global warming and the question of energy supply and demand. PMID:17721788

  9. An Annotated Dataset of 14 Meat Images

    DEFF Research Database (Denmark)

    Stegmann, Mikkel Bille

    2002-01-01

    This note describes a dataset consisting of 14 annotated images of meat. Points of correspondence are placed on each image. As such, the dataset can be readily used for building statistical models of shape. Further, format specifications and terms of use are given.......This note describes a dataset consisting of 14 annotated images of meat. Points of correspondence are placed on each image. As such, the dataset can be readily used for building statistical models of shape. Further, format specifications and terms of use are given....

  10. Software for computing and annotating genomic ranges.

    Directory of Open Access Journals (Sweden)

    Michael Lawrence

    Full Text Available We describe Bioconductor infrastructure for representing and computing on annotated genomic ranges and integrating genomic data with the statistical computing features of R and its extensions. At the core of the infrastructure are three packages: IRanges, GenomicRanges, and GenomicFeatures. These packages provide scalable data structures for representing annotated ranges on the genome, with special support for transcript structures, read alignments and coverage vectors. Computational facilities include efficient algorithms for overlap and nearest neighbor detection, coverage calculation and other range operations. This infrastructure directly supports more than 80 other Bioconductor packages, including those for sequence analysis, differential expression analysis and visualization.

  11. Electrophoretic analysis, labeling and isolation of Chlamydomonas reinhardtii flagellum membrane proteins

    OpenAIRE

    Aleksander F. Sikorski

    2015-01-01

    SDS-polyacrylamide electrophoretic patterns of Chlamydomonas flagellum membrane proteins displayad 6 fractions, 3 PAS-positive among them. The surface radiolabeling of the flagellum membrane suggested an outer surface exposure of fraction '5', and internal localization of fractions '4' and '6'. Application of SDS-polyacrylamide gel electrophoresis and radiolabeled membranes allowed to isolate individual membrane polypeptides.

  12. Similar relative mutation rates in the three genetic compartments of Mesostigma and Chlamydomonas.

    Science.gov (United States)

    Hua, Jimeng; Smith, David Roy; Borza, Tudor; Lee, Robert W

    2012-01-01

    Levels of nucleotide substitution at silent sites in organelle versus nuclear DNAs have been used to estimate relative mutation rates among these compartments and explain lineage-specific features of genome evolution. Synonymous substitution divergence values in animals suggest that the rate of mutation in the mitochondrial DNA is 10-50 times higher than that of the nuclear DNA, whereas overall data for most seed plants support relative mutation rates in mitochondrial, plastid, and nuclear DNAs of 1:3:10. Little is known about relative mutation rates in green algae, as substitution rate data is limited to only the mitochondrial and nuclear genomes of the chlorophyte Chlamydomonas. Here, we measure silent-site substitution rates in the plastid DNA of Chlamydomonas and the three genetic compartments of the streptophyte green alga Mesostigma. In contrast to the situation in animals and land plants, our results support similar relative mutation rates among the three genetic compartments of both Chlamydomonas and Mesostigma. These data are discussed in relation to published intra-species genetic diversity data for the three genetic compartments of Chlamydomonas and are ultimately used to address contemporary hypotheses on the organelle genome evolution. To guide future work, we describe evolutionary divergence data of all publically available Mesostigma viride strains and identify, for the first time, three distinct lineages of Mesostigma. PMID:21621456

  13. Nonthermal effect of microwave irradiation on nitrite uptake in Chlamydomonas reinhardtii

    International Nuclear Information System (INIS)

    When cells of the unicellular green alga Chlamydomonas reinhardtii were subjected to microwave irradiation at 2.45 GHz, nitrite uptake kinetics still obeyed the Michaelis-Menten equation, the Km of the process remaining constant, whereas V max increased, which indicates an enhanced nonthermal permeability in irradiated cells. (author)

  14. In Vitro Evolution and Preliminary Characterization of a Cadmium-Resistant Population of Chlamydomonas reinhardtii

    OpenAIRE

    Nagel, Klaus; Voigt, Jürgen

    1989-01-01

    A cadmium-tolerant population of Chlamydomonas reinhardtii was derived from a Cd-sensitive cell wall-deficient strain by long-term selection in liquid culture. A comparison of Cd-sensitive and Cd-tolerant cells revealed that Cd tolerance was due to genetically determined alterations of metabolism rather than to increased efficiency of a detoxification system.

  15. Modifying effect of caffeine on lethality and mutability of Chlamydomonas reinhardii cells following UV irradiation

    International Nuclear Information System (INIS)

    The modifying effect of caffeine was studied using two standard and two UV-sensitive strains of Chlamydomonas reinhardii Dang. Cell survival and mutation frequency was microscopically evaluated on media without caffeine and on media with 1.5 mM of caffeine. The obtained results were indicative of the stimulating effect of caffeine upon survival in all strains. (author)

  16. Electrophoretic analysis, labeling and isolation of Chlamydomonas reinhardtii flagellum membrane proteins

    Directory of Open Access Journals (Sweden)

    Aleksander F. Sikorski

    2015-05-01

    Full Text Available SDS-polyacrylamide electrophoretic patterns of Chlamydomonas flagellum membrane proteins displayad 6 fractions, 3 PAS-positive among them. The surface radiolabeling of the flagellum membrane suggested an outer surface exposure of fraction '5', and internal localization of fractions '4' and '6'. Application of SDS-polyacrylamide gel electrophoresis and radiolabeled membranes allowed to isolate individual membrane polypeptides.

  17. Rapid induction of lipid droplets in Chlamydomonas reinhardtii and Chlorella vulgaris by Brefeldin A.

    Directory of Open Access Journals (Sweden)

    Sangwoo Kim

    Full Text Available Algal lipids are the focus of intensive research because they are potential sources of biodiesel. However, most algae produce neutral lipids only under stress conditions. Here, we report that treatment with Brefeldin A (BFA, a chemical inducer of ER stress, rapidly triggers lipid droplet (LD formation in two different microalgal species, Chlamydomonas reinhardtii and Chlorella vulgaris. LD staining using Nile red revealed that BFA-treated algal cells exhibited many more fluorescent bodies than control cells. Lipid analyses based on thin layer chromatography and gas chromatography revealed that the additional lipids formed upon BFA treatment were mainly triacylglycerols (TAGs. The increase in TAG accumulation was accompanied by a decrease in the betaine lipid diacylglyceryl N,N,N-trimethylhomoserine (DGTS, a major component of the extraplastidic membrane lipids in Chlamydomonas, suggesting that at least some of the TAGs were assembled from the degradation products of membrane lipids. Interestingly, BFA induced TAG accumulation in the Chlamydomonas cells regardless of the presence or absence of an acetate or nitrogen source in the medium. This effect of BFA in Chlamydomonas cells seems to be due to BFA-induced ER stress, as supported by the induction of three homologs of ER stress marker genes by the drug. Together, these results suggest that ER stress rapidly triggers TAG accumulation in two green microalgae, C. reinhardtii and C. vulgaris. A further investigation of the link between ER stress and TAG synthesis may yield an efficient means of producing biofuel from algae.

  18. The cell cycle of Chlamydomonas reinhardtii: the role of the commitment point

    Czech Academy of Sciences Publication Activity Database

    Oldenhof, H.; Zachleder, Vilém; van den Ende, H.

    2007-01-01

    Roč. 52, č. 1 (2007), s. 53-60. ISSN 0015-5632 Institutional research plan: CEZ:AV0Z50200510 Keywords : chlamydomonas reinhardtii * cell cycle * commitment point Subject RIV: EE - Microbiology, Virology Impact factor: 0.989, year: 2007

  19. Azolla filiculoides Nitrogenase Activity Decrease Induced by Inoculation with Chlamydomonas sp. †

    Science.gov (United States)

    Habte, Mitiku

    1986-01-01

    Experiments were conducted to determine the influence of Chlamydomonas sp. on nitrogen fixation (C2H2 → C2H4) in Azolla filiculoides and on the nitrogen fixation and growth of free-living Anabaena azollae 2B organisms. Inoculation of azolla medium with Chlamydomonas sp. was associated with decreased nitrogenase activity in A. filiculoides and with increases in the density of a fungal population identified as Acremonium sp. Subsequent inoculation of azolla medium with this fungus was also accompanied by a significant decrease in nitrogenase activity of A. filiculoides. However, the extent of depression of nitrogenase activity was significantly higher when azolla medium was inoculated with Chlamydomonas sp. than when it was inoculated with Acremonium sp. Inoculation of nitrogen-free Stanier medium with either Acremonium sp. or Chlamydomonas sp. did not adversely affect the growth or nitrogenase activity of free-living A. azollae. Decreased nitrogenase activity in A. filiculoides is apparently related to the adverse influence of the green alga and the fungus on the macrosymbiont. The mechanisms that might be involved are discussed. PMID:16347211

  20. Manipulating the chloroplast genome of Chlamydomonas: Present realities and future prospects

    Energy Technology Data Exchange (ETDEWEB)

    Boynton, J.; Gillham, N.; Hauser, C.; Heifetz, P.; Lers, A.; Newman, S.; Osmond, B.

    1992-12-31

    Biotechnology is being applied in vitro modification and stable reintroduction of chloroplast genes in Chlamydomonas reinhardtii and Nicotiana tabacum by homologous recombination. We are attempting the function analyses of plastid encoded proteins involved in photosynthesis, characterization of sequences which regulate expression of plastid genes at the transcriptional and translational levels, targeted disruption of chloroplast genes and molecular analysis of processes involved in chloroplast recombination.

  1. Characterization and differential expression of microRNAs elicited by sulfur deprivation in Chlamydomonas reinhardtii

    Directory of Open Access Journals (Sweden)

    Shu Longfei

    2012-03-01

    Full Text Available Abstract Background microRNAs (miRNAs have been found to play an essential role in the modulation of numerous biological processes in eukaryotes. Chlamydomonas reinhardtii is an ideal model organism for the study of many metabolic processes including responses to sulfur-deprivation. We used a deep sequencing platform to extensively profile and identify changes in the miRNAs expression that occurred under sulfur-replete and sulfur-deprived conditions. The aim of our research was to characterize the differential expression of Chlamydomonas miRNAs under sulfur-deprived conditions, and subsequently, the target genes of miRNA involved in sulfur-deprivation were further predicted and analyzed. Results By using high-throughput sequencing, we characterized the microRNA transcriptomes under sulphur-replete and sulfur-deprived conditions in Chlamydomonas reinhardtii. We predicted a total of 310 miRNAs which included 85 known miRNAs and 225 novel miRNAs. 13 miRNAs were the specific to the sulfur-deprived conditions. 47 miRNAs showed significantly differential expressions responding to sulfur-deprivation, and most were up-regulated in the small RNA libraries with sulfur-deprivation. Using a web-based integrated system (Web MicroRNAs Designer 3 and combing the former information from a transcriptome of Chlamydomonas reinhardtii, 22 miRNAs and their targets involved in metabolism regulation with sulfur-deprivation were verified. Conclusions Our results indicate that sulfur-deprivation may have a significant influence on small RNA expression patterns, and the differential expressions of miRNAs and interactions between miRNA and its targets might further reveal the molecular mechanism responding to sulfur-deprivation in Chlamydomonas reinhardtii.

  2. Chlamydomonas reinhardtii PsbS Protein Is Functional and Accumulates Rapidly and Transiently under High Light.

    Science.gov (United States)

    Tibiletti, Tania; Auroy, Pascaline; Peltier, Gilles; Caffarri, Stefano

    2016-08-01

    Photosynthetic organisms must respond to excess light in order to avoid photo-oxidative stress. In plants and green algae the fastest response to high light is non-photochemical quenching (NPQ), a process that allows the safe dissipation of the excess energy as heat. This phenomenon is triggered by the low luminal pH generated by photosynthetic electron transport. In vascular plants the main sensor of the low pH is the PsbS protein, while in the green alga Chlamydomonas reinhardtii LhcSR proteins appear to be exclusively responsible for this role. Interestingly, Chlamydomonas also possesses two PsbS genes, but so far the PsbS protein has not been detected and its biological function is unknown. Here, we reinvestigated the kinetics of gene expression and PsbS and LhcSR3 accumulation in Chlamydomonas during high light stress. We found that, unlike LhcSR3, PsbS accumulates very rapidly but only transiently. In order to determine the role of PsbS in NPQ and photoprotection in Chlamydomonas, we generated transplastomic strains expressing the algal or the Arabidopsis psbS gene optimized for plastid expression. Both PsbS proteins showed the ability to increase NPQ in Chlamydomonas wild-type and npq4 (lacking LhcSR3) backgrounds, but no clear photoprotection activity was observed. Quantification of PsbS and LhcSR3 in vivo indicates that PsbS is much less abundant than LhcSR3 during high light stress. Moreover, LhcSR3, unlike PsbS, also accumulates during other stress conditions. The possible role of PsbS in photoprotection is discussed. PMID:27329221

  3. Annotation Method (AM): SE22_AM1 [Metabolonote[Archive

    Lifescience Database Archive (English)

    Full Text Available ether with predicted molecular formulae and putative structures, were provided as metabolite annotations. Comparison with public data...bases was performed. A grading system was introduced to describe the evidence supporting the annotations. ...

  4. Computer systems for annotation of single molecule fragments

    Science.gov (United States)

    Schwartz, David Charles; Severin, Jessica

    2016-07-19

    There are provided computer systems for visualizing and annotating single molecule images. Annotation systems in accordance with this disclosure allow a user to mark and annotate single molecules of interest and their restriction enzyme cut sites thereby determining the restriction fragments of single nucleic acid molecules. The markings and annotations may be automatically generated by the system in certain embodiments and they may be overlaid translucently onto the single molecule images. An image caching system may be implemented in the computer annotation systems to reduce image processing time. The annotation systems include one or more connectors connecting to one or more databases capable of storing single molecule data as well as other biomedical data. Such diverse array of data can be retrieved and used to validate the markings and annotations. The annotation systems may be implemented and deployed over a computer network. They may be ergonomically optimized to facilitate user interactions.

  5. Multicultural Education: A Selected Annotated Bibliography.

    Science.gov (United States)

    Mathieson, Moira B.; Tatis, Rita M.

    This annotated bibliography lists 70 documents dealing with cultural differences and cross-cultural educational problems on the elementary-secondary-collegiate level and does not include material on the economically disadvantaged or inner city problems as such. The first section reports citations drawn from Research in Education and the…

  6. Semantic Annotation to Support Automatic Taxonomy Classification

    DEFF Research Database (Denmark)

    Kim, Sanghee; Ahmed, Saeema; Wallace, Ken

    2006-01-01

    This paper presents a new taxonomy classification method that generates classification criteria from a small number of important sentences identified through semantic annotations, e.g. cause-effect. Rhetorical Structure Theory (RST) is used to discover the semantics (Mann et al. 1988). Specifically...

  7. Reflective Annotations: On Becoming a Scholar

    Science.gov (United States)

    Alexander, Mark; Taylor, Caroline; Greenberger, Scott; Watts, Margie; Balch, Riann

    2012-01-01

    This article presents the authors' reflective annotations on becoming a scholar. This paper begins with a discussion on socialization for teaching, followed by a discussion on socialization for service and sense of belonging. Then, it describes how the doctoral process evolves. Finally, it talks about adult learners who pursue doctoral education.

  8. Annotated Bibliography of EDGE2D Use

    International Nuclear Information System (INIS)

    This annotated bibliography is intended to help EDGE2D users, and particularly new users, find existing published literature that has used EDGE2D. Our idea is that a person can find existing studies which may relate to his intended use, as well as gain ideas about other possible applications by scanning the attached tables

  9. Statistical mechanics of ontology based annotations

    CERN Document Server

    Hoyle, David C

    2016-01-01

    We present a statistical mechanical theory of the process of annotating an object with terms selected from an ontology. The term selection process is formulated as an ideal lattice gas model, but in a highly structured inhomogeneous field. The model enables us to explain patterns recently observed in real-world annotation data sets, in terms of the underlying graph structure of the ontology. By relating the external field strengths to the information content of each node in the ontology graph, the statistical mechanical model also allows us to propose a number of practical metrics for assessing the quality of both the ontology, and the annotations that arise from its use. Using the statistical mechanical formalism we also study an ensemble of ontologies of differing size and complexity; an analysis not readily performed using real data alone. Focusing on regular tree ontology graphs we uncover a rich set of scaling laws describing the growth in the optimal ontology size as the number of objects being annotate...

  10. Statistical mechanics of ontology based annotations

    Science.gov (United States)

    Hoyle, David C.; Brass, Andrew

    2016-01-01

    We present a statistical mechanical theory of the process of annotating an object with terms selected from an ontology. The term selection process is formulated as an ideal lattice gas model, but in a highly structured inhomogeneous field. The model enables us to explain patterns recently observed in real-world annotation data sets, in terms of the underlying graph structure of the ontology. By relating the external field strengths to the information content of each node in the ontology graph, the statistical mechanical model also allows us to propose a number of practical metrics for assessing the quality of both the ontology, and the annotations that arise from its use. Using the statistical mechanical formalism we also study an ensemble of ontologies of differing size and complexity; an analysis not readily performed using real data alone. Focusing on regular tree ontology graphs we uncover a rich set of scaling laws describing the growth in the optimal ontology size as the number of objects being annotated increases. In doing so we provide a further possible measure for assessment of ontologies.

  11. Studies of Scientific Disciplines. An Annotated Bibliography.

    Science.gov (United States)

    Weisz, Diane; Kruytbosch, Carlos

    Provided in this bibliography are annotated lists of social studies of science literature, arranged alphabetically by author in 13 disciplinary areas. These areas include astronomy; general biology; biochemistry and molecular biology; biomedicine; chemistry; earth and space sciences; economics; engineering; mathematics; physics; political science;…

  12. Food Habits: A Selected Annotated Bibliography

    Science.gov (United States)

    Wilson, Christine S.

    1973-01-01

    This is a selective annotated bibliography of material on food habits and factors affecting them, published during the period 1928-1972. References are mainly in English, although a few in European languages are included, and represent information primarily from scholarly and professional journals. Entries are organized by subject and author. (LK)

  13. An Annotated Publications List on Homelessness.

    Science.gov (United States)

    Tutunjian, Beth Ann

    This annotated publications list on homelessness contains citations for 19 publications, most of which deal with problems of alcohol or drug abuse among homeless persons. Citations are listed alphabetically by author and cover the topics of homelessness and alcoholism, drug abuse, public policy, research methodologies, mental illness, alcohol- and…

  14. SNAD: sequence name annotation-based designer

    Directory of Open Access Journals (Sweden)

    Gorbalenya Alexander E

    2009-08-01

    Full Text Available Abstract Background A growing diversity of biological data is tagged with unique identifiers (UIDs associated with polynucleotides and proteins to ensure efficient computer-mediated data storage, maintenance, and processing. These identifiers, which are not informative for most people, are often substituted by biologically meaningful names in various presentations to facilitate utilization and dissemination of sequence-based knowledge. This substitution is commonly done manually that may be a tedious exercise prone to mistakes and omissions. Results Here we introduce SNAD (Sequence Name Annotation-based Designer that mediates automatic conversion of sequence UIDs (associated with multiple alignment or phylogenetic tree, or supplied as plain text list into biologically meaningful names and acronyms. This conversion is directed by precompiled or user-defined templates that exploit wealth of annotation available in cognate entries of external databases. Using examples, we demonstrate how this tool can be used to generate names for practical purposes, particularly in virology. Conclusion A tool for controllable annotation-based conversion of sequence UIDs into biologically meaningful names and acronyms has been developed and placed into service, fostering links between quality of sequence annotation, and efficiency of communication and knowledge dissemination among researchers.

  15. Law in the Classroom. An Annotated Bibliography.

    Science.gov (United States)

    Carsello, Carmen J.

    An annotated bibliography of some 236 items relevant to discussions of school law, from novels to government-published law and court reports. The material is listed alphabetically by author within each document type (books; periodicals; documents; monographs and special reports; law reports; digests; newsletters; dictionaries, directories, and…

  16. Organizational and Intercultural Communication: An Annotated Bibliography.

    Science.gov (United States)

    Constantinides, Helen; St. Amant, Kirk; Kampf, Connie

    2001-01-01

    Presents a 27-item annotated bibliography that overviews theories of organization from the viewpoint of culture, using five themes of organizational research as a framework. Notes that each section introduces specific theories of international, intercultural, or organizational communication, building upon them through a series of related articles,…

  17. Teleconferencing, an annotated bibliography, volume 3

    Science.gov (United States)

    Shervis, K.

    1971-01-01

    In this annotated and indexed listing of works on teleconferencing, emphasis has been placed upon teleconferencing as real-time, two way audio communication with or without visual aids. However, works on the use of television in two-way or multiway nets, data transmission, regional communications networks and on telecommunications in general are also included.

  18. Ontological Annotation with WordNet

    Energy Technology Data Exchange (ETDEWEB)

    Sanfilippo, Antonio P.; Tratz, Stephen C.; Gregory, Michelle L.; Chappell, Alan R.; Whitney, Paul D.; Posse, Christian; Paulson, Patrick R.; Baddeley, Bob; Hohimer, Ryan E.; White, Amanda M.

    2006-06-06

    Semantic Web applications require robust and accurate annotation tools that are capable of automating the assignment of ontological classes to words in naturally occurring text (ontological annotation). Most current ontologies do not include rich lexical databases and are therefore not easily integrated with word sense disambiguation algorithms that are needed to automate ontological annotation. WordNet provides a potentially ideal solution to this problem as it offers a highly structured lexical conceptual representation that has been extensively used to develop word sense disambiguation algorithms. However, WordNet has not been designed as an ontology, and while it can be easily turned into one, the result of doing this would present users with serious practical limitations due to the great number of concepts (synonym sets) it contains. Moreover, mapping WordNet to an existing ontology may be difficult and requires substantial labor. We propose to overcome these limitations by developing an analytical platform that (1) provides a WordNet-based ontology offering a manageable and yet comprehensive set of concept classes, (2) leverages the lexical richness of WordNet to give an extensive characterization of concept class in terms of lexical instances, and (3) integrates a class recognition algorithm that automates the assignment of concept classes to words in naturally occurring text. The ensuing framework makes available an ontological annotation platform that can be effectively integrated with intelligence analysis systems to facilitate evidence marshaling and sustain the creation and validation of inference models.

  19. Automating Ontological Annotation with WordNet

    Energy Technology Data Exchange (ETDEWEB)

    Sanfilippo, Antonio P.; Tratz, Stephen C.; Gregory, Michelle L.; Chappell, Alan R.; Whitney, Paul D.; Posse, Christian; Paulson, Patrick R.; Baddeley, Bob L.; Hohimer, Ryan E.; White, Amanda M.

    2006-01-22

    Semantic Web applications require robust and accurate annotation tools that are capable of automating the assignment of ontological classes to words in naturally occurring text (ontological annotation). Most current ontologies do not include rich lexical databases and are therefore not easily integrated with word sense disambiguation algorithms that are needed to automate ontological annotation. WordNet provides a potentially ideal solution to this problem as it offers a highly structured lexical conceptual representation that has been extensively used to develop word sense disambiguation algorithms. However, WordNet has not been designed as an ontology, and while it can be easily turned into one, the result of doing this would present users with serious practical limitations due to the great number of concepts (synonym sets) it contains. Moreover, mapping WordNet to an existing ontology may be difficult and requires substantial labor. We propose to overcome these limitations by developing an analytical platform that (1) provides a WordNet-based ontology offering a manageable and yet comprehensive set of concept classes, (2) leverages the lexical richness of WordNet to give an extensive characterization of concept class in terms of lexical instances, and (3) integrates a class recognition algorithm that automates the assignment of concept classes to words in naturally occurring text. The ensuing framework makes available an ontological annotation platform that can be effectively integrated with intelligence analysis systems to facilitate evidence marshaling and sustain the creation and validation of inference models.

  20. Kwanzaa: A Selective Annotated Bibliography for Teachers.

    Science.gov (United States)

    Dupree, Sandra K., Comp.; Gillum, Holly A., Comp.

    This annotated bibliography about Kwanzaa, an end-of-the-year holiday that emphasizes an appreciation for the culture of African Americans, aims to provide ready access to information for classroom teachers. Noting that Kwanzaa (celebrated from December 26 to January 1) is an important cultural event, the bibliography states that the festival…

  1. Skin Cancer Education Materials: Selected Annotations.

    Science.gov (United States)

    National Cancer Inst. (NIH), Bethesda, MD.

    This annotated bibliography presents 85 entries on a variety of approaches to cancer education. The entries are grouped under three broad headings, two of which contain smaller sub-divisions. The first heading, Public Education, contains prevention and general information, and non-print materials. The second heading, Professional Education,…

  2. College Students in Transition: An Annotated Bibliography

    Science.gov (United States)

    Foote, Stephanie M., Ed.; Hinkle, Sara M., Ed.; Kranzow, Jeannine, Ed.; Pistilli, Matthew D., Ed.; Miles, LaTonya Rease, Ed.; Simmons, Jannell G., Ed.

    2013-01-01

    The transition from high school to college is an important milestone, but it is only one of many steps in the journey through higher education. This volume is an annotated bibliography of the emerging literature examining the many other transitions students make beyond the first year, including the sophomore year, the transfer experience, and the…

  3. Annotated Bibliography of EDGE2D Use

    Energy Technology Data Exchange (ETDEWEB)

    J.D. Strachan and G. Corrigan

    2005-06-24

    This annotated bibliography is intended to help EDGE2D users, and particularly new users, find existing published literature that has used EDGE2D. Our idea is that a person can find existing studies which may relate to his intended use, as well as gain ideas about other possible applications by scanning the attached tables.

  4. Classes d'annotation pour l'annotation sémantique

    OpenAIRE

    Tenier, Sylvain; Toussaint, Yannick

    2007-01-01

    Les classes d'annotation constituent une méthode d'annotation sémantique de pages web fondée sur les logiques de descriptions. Elles désignent l'annotation à la fois comme processus et comme résultat de ce processus. Cette approche est motivée par un parallèle entre la structure d'une page web et la sémantique qui lui est associée. Ces deux dimensions de structure et de sémantique sont formalisées en OWL-DL, un langage fondé sur les logiques de descriptions. L'annotation est ensuite traitée c...

  5. Carbon allocation and element composition in four Chlamydomonas mutants defective in genes related to the CO2 concentrating mechanism

    Czech Academy of Sciences Publication Activity Database

    Memmola, F.; Mukherjee, B.; Moroney, James V.; Giordano, Mario

    2014-01-01

    Roč. 121, 2-3 (2014), s. 201-211. ISSN 0166-8595 Institutional support: RVO:61388971 Keywords : Chlamydomonas mutants * carbon * carbon dioxide * elemental stoichiometry Subject RIV: EE - Microbiology, Virology Impact factor: 3.502, year: 2014

  6. High-Throughput Genetics Strategies for Identifying New Components of Lipid Metabolism in the Green Alga Chlamydomonas reinhardtii.

    Science.gov (United States)

    Li, Xiaobo; Jonikas, Martin C

    2016-01-01

    Microalgal lipid metabolism is of broad interest because microalgae accumulate large amounts of triacylglycerols (TAGs) that can be used for biodiesel production (Durrett et al Plant J 54(4):593-607, 2008; Hu et al Plant J 54(4):621-639, 2008). Additionally, green algae are close relatives of land plants and serve as models to understand conserved lipid metabolism pathways in the green lineage. The green alga Chlamydomonas reinhardtii (Chlamydomonas hereafter) is a powerful model organism for understanding algal lipid metabolism. Various methods have been used to screen Chlamydomonas mutants for lipid amount or composition, and for identification of the mutated loci in mutants of interest. In this chapter, we summarize the advantages and caveats for each of these methods with a focus on screens for mutants with perturbed TAG content. We also discuss technical opportunities and new tools that are becoming available for screens of mutants altered in TAG content or perturbed in other processes in Chlamydomonas. PMID:27023238

  7. Ontology Learning and Semantic Annotation: a Necessary Symbiosis

    OpenAIRE

    Giovannetti, Emiliano; Marchi, Simone; Montemagni, Simonetta; Bartolini, Roberto

    2008-01-01

    Semantic annotation of text requires the dynamic merging of linguistically structured information and a ?world model?, usually represented as a domain-specific ontology. On the other hand, the process of engineering a domain-ontology through semi-automatic ontology learning system requires the availability of a considerable amount of semantically annotated documents. Facing this bootstrapping paradox requires an incremental process of annotation-acquisition-annotation, whereby domain-specific...

  8. SURFACE: a database of protein surface regions for functional annotation

    OpenAIRE

    Ferrè, Fabrizio; Ausiello, Gabriele; Zanzoni, Andreas; Helmer-Citterich, Manuela

    2004-01-01

    The SURFACE (SUrface Residues and Functions Annotated, Compared and Evaluated, URL http://cbm.bio.uniroma2.it/surface/) database is a repository of annotated and compared protein surface regions. SURFACE contains the results of a large-scale protein annotation and local structural comparison project. A non-redundant set of protein chains is used to build a database of protein surface patches, defined as putative surface functional sites. Each patch is annotated with sequence and structure-der...

  9. A unified representation for morphological, syntactic, semantic, and referential annotations

    OpenAIRE

    Hinrichs, Erhard W.; Kübler, Sandra; Naumann, Karin

    2008-01-01

    This paper reports on the SYN-RA (SYNtax-based Reference Annotation) project, an on-going project of annotating German newspaper texts with referential relations. The project has developed an inventory of anaphoric and coreference relations for German in the context of a unified, XML-based annotation scheme for combining morphological, syntactic, semantic, and anaphoric information. The paper discusses how this unified annotation scheme relates to other formats currently discussed in the lite...

  10. AnnaBot: A Static Verifier for Java Annotation Usage

    OpenAIRE

    Ian Darwin

    2010-01-01

    This paper describes AnnaBot, one of the first tools to verify correct use of Annotation-based metadata in the Java programming language. These Annotations are a standard Java 5 mechanism used to attach metadata to types, methods, or fields without using an external configuration file. A binary representation of the Annotation becomes part of the compiled “.class” file, for inspection by another component or library at runtime. Java Annotations were introduced into the Java language in 2004 a...

  11. BEACON: automated tool for Bacterial GEnome Annotation ComparisON

    KAUST Repository

    Kalkatawi, Manal Matoq Saeed

    2015-08-18

    Background Genome annotation is one way of summarizing the existing knowledge about genomic characteristics of an organism. There has been an increased interest during the last several decades in computer-based structural and functional genome annotation. Many methods for this purpose have been developed for eukaryotes and prokaryotes. Our study focuses on comparison of functional annotations of prokaryotic genomes. To the best of our knowledge there is no fully automated system for detailed comparison of functional genome annotations generated by different annotation methods (AMs). Results The presence of many AMs and development of new ones introduce needs to: a/ compare different annotations for a single genome, and b/ generate annotation by combining individual ones. To address these issues we developed an Automated Tool for Bacterial GEnome Annotation ComparisON (BEACON) that benefits both AM developers and annotation analysers. BEACON provides detailed comparison of gene function annotations of prokaryotic genomes obtained by different AMs and generates extended annotations through combination of individual ones. For the illustration of BEACON’s utility, we provide a comparison analysis of multiple different annotations generated for four genomes and show on these examples that the extended annotation can increase the number of genes annotated by putative functions up to 27 %, while the number of genes without any function assignment is reduced. Conclusions We developed BEACON, a fast tool for an automated and a systematic comparison of different annotations of single genomes. The extended annotation assigns putative functions to many genes with unknown functions. BEACON is available under GNU General Public License version 3.0 and is accessible at: http://www.cbrc.kaust.edu.sa/BEACON/

  12. Automatic annotation of head velocity and acceleration in Anvil

    DEFF Research Database (Denmark)

    Jongejan, Bart

    2012-01-01

    We describe an automatic face tracker plugin for the ANVIL annotation tool. The face tracker produces data for velocity and for acceleration in two dimensions. We compare the annotations generated by the face tracking algorithm with independently made manual annotations for head movements. The...

  13. The conserved plant sterility gene HAP2 functions after attachment of fusogenic membranes in Chlamydomonas and Plasmodium gametes

    OpenAIRE

    Liu, Yanjie; Tewari, Rita; Ning, Jue; Blagborough, Andrew M; Garbom, Sara; Pei, Jimin; Grishin, Nick V.; Steele, Robert E.; Sinden, Robert E.; Snell, William J.; Billker, Oliver

    2008-01-01

    The cellular and molecular mechanisms that underlie species-specific membrane fusion between male and female gametes remain largely unknown. Here, by use of gene discovery methods in the green alga Chlamydomonas, gene disruption in the rodent malaria parasite Plasmodium berghei, and distinctive features of fertilization in both organisms, we report discovery of a mechanism that accounts for a conserved protein required for gamete fusion. A screen for fusion mutants in Chlamydomonas identified...

  14. Model and Interoperability using Meta Data Annotations

    Science.gov (United States)

    David, O.

    2011-12-01

    Software frameworks and architectures are in need for meta data to efficiently support model integration. Modelers have to know the context of a model, often stepping into modeling semantics and auxiliary information usually not provided in a concise structure and universal format, consumable by a range of (modeling) tools. XML often seems the obvious solution for capturing meta data, but its wide adoption to facilitate model interoperability is limited by XML schema fragmentation, complexity, and verbosity outside of a data-automation process. Ontologies seem to overcome those shortcomings, however the practical significance of their use remains to be demonstrated. OMS version 3 took a different approach for meta data representation. The fundamental building block of a modular model in OMS is a software component representing a single physical process, calibration method, or data access approach. Here, programing language features known as Annotations or Attributes were adopted. Within other (non-modeling) frameworks it has been observed that annotations lead to cleaner and leaner application code. Framework-supported model integration, traditionally accomplished using Application Programming Interfaces (API) calls is now achieved using descriptive code annotations. Fully annotated components for various hydrological and Ag-system models now provide information directly for (i) model assembly and building, (ii) data flow analysis for implicit multi-threading or visualization, (iii) automated and comprehensive model documentation of component dependencies, physical data properties, (iv) automated model and component testing, calibration, and optimization, and (v) automated audit-traceability to account for all model resources leading to a particular simulation result. Such a non-invasive methodology leads to models and modeling components with only minimal dependencies on the modeling framework but a strong reference to its originating code. Since models and

  15. Annotations and the Collaborative Digital Library: Effects of an Aligned Annotation Interface on Student Argumentation and Reading Strategies

    Science.gov (United States)

    Wolfe, Joanna

    2008-01-01

    Recent research on annotation interfaces provides provocative evidence that anchored, annotation-based discussion environments may lead to better conversations about a text. However, annotation interfaces raise complicated tradeoffs regarding screen real estate and positioning. It is argued that solving this screen real estate problem requires…

  16. Using Hausdorff Distance for New Medical Image Annotation

    CERN Document Server

    Bouslimi, Riadh

    2012-01-01

    Medical images annotation is most of the time a repetitive hard task. Collecting old similar annotations and assigning them to new medical images may not only enhance the annotation process, but also reduce ambiguity caused by repetitive annotations. The goal of this work is to propose an approach based on Hausdorff distance able to compute similarity between a new medical image and old stored images. User has to choose then one of the similar images and annotations related to the selected one are assigned to the new one.

  17. A Novel Technique to Image Annotation using Neural Network

    Directory of Open Access Journals (Sweden)

    Pankaj Savita

    2013-03-01

    Full Text Available : Automatic annotation of digital pictures is a key technology for managing and retrieving images from large image collection. Traditional image semantics extraction and representation schemes were commonly divided into two categories, namely visual features and text annotations. However, visual feature scheme are difficult to extract and are often semantically inconsistent. On the other hand, the image semantics can be well represented by text annotations. It is also easier to retrieve images according to their annotations. Traditional image annotation techniques are time-consuming and requiring lots of human effort. In this paper we propose Neural Network based a novel approach to the problem of image annotation. These approaches are applied to the Image data set. Our main work is focused on the image annotation by using multilayer perceptron, which exhibits a clear-cut idea on application of multilayer perceptron with special features. MLP Algorithm helps us to discover the concealed relations between image data and annotation data, and annotate image according to such relations. By using this algorithm we can save more memory space, and in case of web applications, transferring of images and download should be fast. This paper reviews 50 image annotation systems using supervised machine learning Techniques to annotate images for image retrieval. Results obtained show that the multi layer perceptron Neural Network classifier outperforms conventional DST Technique.

  18. Automated annotation of microbial proteomes in SWISS-PROT.

    Science.gov (United States)

    Gattiker, Alexandre; Michoud, Karine; Rivoire, Catherine; Auchincloss, Andrea H; Coudert, Elisabeth; Lima, Tania; Kersey, Paul; Pagni, Marco; Sigrist, Christian J A; Lachaize, Corinne; Veuthey, Anne Lise; Gasteiger, Elisabeth; Bairoch, Amos

    2003-02-01

    Large-scale sequencing of prokaryotic genomes demands the automation of certain annotation tasks currently manually performed in the production of the SWISS-PROT protein knowledgebase. The HAMAP project, or 'High-quality Automated and Manual Annotation of microbial Proteomes', aims to integrate manual and automatic annotation methods in order to enhance the speed of the curation process while preserving the quality of the database annotation. Automatic annotation is only applied to entries that belong to manually defined orthologous families and to entries with no identifiable similarities (ORFans). Many checks are enforced in order to prevent the propagation of wrong annotation and to spot problematic cases, which are channelled to manual curation. The results of this annotation are integrated in SWISS-PROT, and a website is provided at http://www.expasy.org/sprot/hamap/. PMID:12798039

  19. A Concept Annotation System for Clinical Records

    CERN Document Server

    Kang, Ning; Afzal, Zubair; Singh, Bharat; Schuemie, Martijn J; van Mulligen, Erik M; Kors, Jan A

    2010-01-01

    Unstructured information comprises a valuable source of data in clinical records. For text mining in clinical records, concept extraction is the first step in finding assertions and relationships. This study presents a system developed for the annotation of medical concepts, including medical problems, tests, and treatments, mentioned in clinical records. The system combines six publicly available named entity recognition system into one framework, and uses a simple voting scheme that allows to tune precision and recall of the system to specific needs. The system provides both a web service interface and a UIMA interface which can be easily used by other systems. The system was tested in the fourth i2b2 challenge and achieved an F-score of 82.1% for the concept exact match task, a score which is among the top-ranking systems. To our knowledge, this is the first publicly available clinical record concept annotation system.

  20. Exploiting Social Annotation for Automatic Resource Discovery

    CERN Document Server

    Plangprasopchok, Anon

    2007-01-01

    Information integration applications, such as mediators or mashups, that require access to information resources currently rely on users manually discovering and integrating them in the application. Manual resource discovery is a slow process, requiring the user to sift through results obtained via keyword-based search. Although search methods have advanced to include evidence from document contents, its metadata and the contents and link structure of the referring pages, they still do not adequately cover information sources -- often called ``the hidden Web''-- that dynamically generate documents in response to a query. The recently popular social bookmarking sites, which allow users to annotate and share metadata about various information sources, provide rich evidence for resource discovery. In this paper, we describe a probabilistic model of the user annotation process in a social bookmarking system del.icio.us. We then use the model to automatically find resources relevant to a particular information dom...

  1. Semantic Annotation: The Mainstay of Semantic Web

    OpenAIRE

    Slimani, Thabet

    2013-01-01

    Given that semantic Web realization is based on the critical mass of metadata accessibility and the representation of data with formal knowledge, it needs to generate metadata that is specific, easy to understand and well-defined. However, semantic annotation of the web documents is the successful way to make the Semantic Web vision a reality. This paper introduces the Semantic Web and its vision (stack layers) with regard to some concept definitions that helps the understanding of semantic a...

  2. About Certain Semantic Annotation in Parallel Corpora

    OpenAIRE

    Violetta Koseska-Toszewa

    2015-01-01

    About Certain Semantic Annotation in Parallel CorporaThe semantic notation analyzed in this works is contained in the second stream of semantic theories presented here – in the direct approach semantics. We used this stream in our work on the Bulgarian-Polish Contrastive Grammar. Our semantic notation distinguishes quantificational meanings of names and predicates, and indicates aspectual and temporal meanings of verbs. It relies on logical scope-based quantification and on the contemporary t...

  3. Improving gene annotation of complete viral genomes

    OpenAIRE

    Mills, Ryan; Rozanov, Michael; Lomsadze, Alexandre; Tatusova, Tatiana; Borodovsky, Mark

    2003-01-01

    Gene annotation in viruses often relies upon similarity search methods. These methods possess high specificity but some genes may be missed, either those unique to a particular genome or those highly divergent from known homologs. To identify potentially missing viral genes we have analyzed all complete viral genomes currently available in GenBank with a specialized and augmented version of the gene finding program GeneMarkS. In particular, by implementing genome-specific self-training protoc...

  4. Html template system using java annotations

    OpenAIRE

    Speck, Peter

    2007-01-01

    The problems that motivate this project are to (1) solve the lack of separation between html templates and java code when using existing template systems (e.g. embedded language or macros), to (2) solve the lack of scoped declaration of macros and java variables inside template loops, and (3) to solve the lack of validation of template macro definitions at compile time to help finding bugs before the web applications are deployed. Annotations are used as metadata format for...

  5. EFFICIENT VIDEO ANNOTATIONS BY AN IMAGE GROUPS

    OpenAIRE

    K . Mahi balan; K . Rajakumari

    2015-01-01

    Searching desirable events in uncontrolled videos is a challenging task. So, researches mainly focus on obtaining concepts from numerous labelled videos. But it is time consuming and labour expensive to collect a large amount of required labelled videos for training event models under various condition. To avoid this problem, we propose to leverage abundant Web images for videos since Web images contain a rich source of information with many events roughly annotated and taken under various co...

  6. Deburring: an annotated bibliography. Volume V

    International Nuclear Information System (INIS)

    An annotated summary of 204 articles and publications on burrs, burr prevention and deburring is presented. Thirty-seven deburring processes are listed. Entries cited include English, Russian, French, Japanese and German language articles. Entries are indexed by deburring processes, author, and language. Indexes also indicate which references discuss equipment and tooling, how to use a process, economics, burr properties, and how to design to minimize burr problems. Research studies are identified as are the materials deburred

  7. Transcriptome Annotation using Tandem SAGE Tags

    OpenAIRE

    Rivals, Eric; Boureux, Anthony; Lejeune, Mireille; Ottones, Florence; Pecharromàn Pérez, Oscar; Tarhio, Jorma; Pierrat, Fabien; Ruffle, Florence; Commes, Thérèse; Marti, Jacques

    2007-01-01

    Analysis of several million expressed gene signatures (tags) revealed an increasing number of different sequences, largely exceeding that of annotated genes in mammalian genomes. Serial Analysis of Gene Expression (SAGE) can reveal new polyadenylated RNAs transcribed from previously unrecognized chromosomal regions. However, conventional SAGE tags are too short to identify unambiguously unique sites in large genomes. Here, we design a novel strategy with tags anchored on two different restric...

  8. The energy balance of the biomass generation of Chlamydomonas acidophila under acidic and neutral conditions and Chlamydomonas reinhardtii; Die Energiebilanz der Biomasseneubildung von Chlamydomonas acidophila unter sauren und neutralen Bedingungen und von Chlamydomonas reinhardtii

    Energy Technology Data Exchange (ETDEWEB)

    Langner, Uwe

    2009-01-16

    In this study the influence of pH < 3 as an extreme environment has been investigated for the eukaryotic green alga Chlamydomonas (C.) acidophila. The limited number of trophic levels, consisting of bacteria, phytoplankton, zooplankton and macrophytes, is a special characteristic of extreme acidic water bodies. C. acidophila was isolated from an extreme acidic mining lake (RL 111) (Bissinger et al. 2000). A special feature of the examined algal species is its wide tolerance range of external pH values from 2 to 7 (Cassin 1874, Gerloff-Elias et al. 2005a). C. acidophila is a dominant species in the acidic mining lakes, it can grow up to chlorophyll maxima of 500 {mu}g L{sup -1} during the summer time (Nixdorf et al. 1998, 2003). The alga can be found elsewhere in extreme acidic water bodies around the world. The hydrochemistry of the acidic mining lakes in the central regions of Germany and Lusatia show clear differences compared to neutral water bodies. Some of the characteristics of acidic mining lakes are high metal and heavy metal (aluminum) concentrations, high ion concentrations, which lead to high conductivity, as well as low phosphate concentrations, ammonium as the only nitrogen source and CO{sub 2} as the only inorganic carbon source. Many eukaryotic microalgae in acidic water bodies including C. acidophila show a neutral cytosolic pH. This is provided by special adaptations of the organisms. Thus, organisms in extreme acidic environments have a positive cell surface charge, a very efficient H{sup +}-ATPase and high internal buffer capacities. These mechanisms work contrary to the proton influx and the acidification of the cytosol and are therefore proof for the physiological impact of osmoregulation by microalgae in extreme acidic environments (Sekler et al.1991, Weiss et al. 1999). Hence, these mechanisms also complicate the access to nutrients for the algal cell. The passive influx of positively charged ions such as potassium or ammonium is reduced by

  9. The microalga Chlamydomonas reinhardtii as a platform for the production of human protein therapeutics

    OpenAIRE

    Rasala, Beth A.; Mayfield, Stephen P.

    2011-01-01

    Microalgae are a diverse group of eukaryotic photosynthetic microorganisms. While microalgae play a crucial role in global carbon fixation and oxygen evolution, these organisms have recently gained much attention for their potential role in biotechnological and industrial applications, such as the production of biofuels. We investigated the potential of the microalga Chlamydomonas reinhardtii to be a platform for the production of human therapeutic proteins. C. reinhardtii is a unicellular fr...

  10. Isolation and genetic analysis of Chlamydomonas reinhardtii strains resistant to cadmium.

    OpenAIRE

    Collard, J. M.; Matagne, R. F.

    1990-01-01

    In Chlamydomonas reinhardtii, cadmium induces reduction of growth, reduction of chlorophyll content, and lethality. The toxicity was higher in a cell wall-deficient strain than in the wild type. By growing the cells on agar medium containing cadmium at concentrations inducing high lethality, stable resistant clones were isolated. The resistance was due to a nuclear mutation (cadAR) which probably preexisted in the wild-type cell population, as suggested by the fluctuation test. A double mutan...

  11. Protocol: methodology for chromatin immunoprecipitation (ChIP) in Chlamydomonas reinhardtii

    OpenAIRE

    Strenkert Daniela; Schmollinger Stefan; Schroda Michael

    2011-01-01

    Abstract We report on a detailed chromatin immunoprecipitation (ChIP) protocol for the unicellular green alga Chlamydomonas reinhardtii. The protocol is suitable for the analysis of nucleosome occupancy, histone modifications and transcription factor binding sites at the level of mononucleosomes for targeted and genome-wide studies. We describe the optimization of conditions for crosslinking, chromatin fragmentation and antibody titer determination and provide recommendations and an example f...

  12. Characterization of Chlamydomonas reinhardtii phosphatidylglycerophosphate synthase in Synechocystis sp. PCC 6803

    OpenAIRE

    Hung, Chun-Hsien; Endo, Kaichiro; Kobayashi, Koichi; Nakamura, Yuki; Wada, Hajime

    2015-01-01

    Phosphatidylglycerol (PG) is an indispensable phospholipid class with photosynthetic function in plants and cyanobacteria. However, its biosynthesis in eukaryotic green microalgae is poorly studied. Here, we report the isolation and characterization of two homologs (CrPGP1 and CrPGP2) of phosphatidylglycerophosphate synthase (PGPS), the rate-limiting enzyme in PG biosynthesis, in Chlamydomonas reinhardtii. Heterologous complementation of Synechocystis sp. PCC 6803 pgsA mutant by CrPGP1 and Cr...

  13. Regulation by Light of Chemotaxis to Nitrite during the Sexual Life Cycle in Chlamydomonas reinhardtii

    OpenAIRE

    Elena Ermilova; Zhanneta Zalutskaya

    2014-01-01

    Nitrite plays an important role in the nitrogen metabolism of most cells, including Chlamydomonas reinhardtii. We have shown that vegetative cells of C. reinhardtii are attracted by nitrite. The Nia1nit2 mutant with defects in genes encoding the nitrate reductase and regulatory protein NIT2 respectively was found to exhibit normal chemotaxis to nitrite. The data suggest that chemotaxis events appear to be specific and independent of those involved in nitrate assimilation. Unlike vegetative ce...

  14. Predicting the physiological role of circadian metabolic regulation in the green alga Chlamydomonas reinhardtii.

    Directory of Open Access Journals (Sweden)

    Sascha Schäuble

    Full Text Available Although the number of reconstructed metabolic networks is steadily growing, experimental data integration into these networks is still challenging. Based on elementary flux mode analysis, we combine sequence information with metabolic pathway analysis and include, as a novel aspect, circadian regulation. While minimizing the need of assumptions, we are able to predict changes in the metabolic state and can hypothesise on the physiological role of circadian control in nitrogen metabolism of the green alga Chlamydomonas reinhardtii.

  15. ChlamyCyc: an integrative systems biology database and web-portal for Chlamydomonas reinhardtii

    OpenAIRE

    Kempa Stefan; Christian Jan-Ole; May Patrick; Walther Dirk

    2009-01-01

    Abstract Background The unicellular green alga Chlamydomonas reinhardtii is an important eukaryotic model organism for the study of photosynthesis and plant growth. In the era of modern high-throughput technologies there is an imperative need to integrate large-scale data sets from high-throughput experimental techniques using computational methods and database resources to provide comprehensive information about the molecular and cellular organization of a single organism. Results In the fra...

  16. A forward genetic approach in Chlamydomonas reinhardtii as a strategy for exploring starch catabolism

    OpenAIRE

    Hande Tunçay; Justin Findinier; Thierry Duchêne; Virginie Cogez; Charlotte Cousin; Gilles Peltier; Ball, Steven G; David Dauvillée

    2013-01-01

    A screen was recently developed to study the mobilization of starch in the unicellular green alga Chlamydomonas reinhardtii. This screen relies on starch synthesis accumulation during nitrogen starvation followed by the supply of nitrogen and the switch to darkness. Hence multiple regulatory networks including those of nutrient starvation, cell cycle control and light to dark transitions are likely to impact the recovery of mutant candidates. In this paper we monitor the specificity of this m...

  17. Rapid Induction of Lipid Droplets in Chlamydomonas reinhardtii and Chlorella vulgaris by Brefeldin A

    OpenAIRE

    Sangwoo Kim; Hanul Kim; Donghwi Ko; Yasuyo Yamaoka; Masumi Otsuru; Maki Kawai-Yamada; Toshiki Ishikawa; Hee-Mock Oh; Ikuo Nishida; Yonghua Li-Beisson; Youngsook Lee

    2013-01-01

    Algal lipids are the focus of intensive research because they are potential sources of biodiesel. However, most algae produce neutral lipids only under stress conditions. Here, we report that treatment with Brefeldin A (BFA), a chemical inducer of ER stress, rapidly triggers lipid droplet (LD) formation in two different microalgal species, Chlamydomonas reinhardtii and Chlorella vulgaris. LD staining using Nile red revealed that BFA-treated algal cells exhibited many more fluorescent bodies t...

  18. UREA TRANSPORT DURING GAMETOGENESIS OF THE UNICELLULAR GREEN ALGA CHLAMYDOMONAS REINHARDTII

    OpenAIRE

    Zalutskaya, Zhanneta; Lapina, Tatyana; Von, Wiren; Ermilova, Elena

    2009-01-01

    Direct urea transport mechanisms are present in Chlamydomonas reinhardtii. Urea uptake system(s) are repressed by ammonium and they can be induced by urea or acetamide in ammonium-starved vegetative cells. Urea transport ability of the alga is altered during gametogenesis. Unlike vegetative cells, mature gametes showed a low urea uptake. Incubation of gametes with urea or acetamide resulted in the increasing of urea uptake ability and the regaining of chemotactic activity. The data suggest a ...

  19. Biochemische und funktionelle Charakterisierung eines anaerob induzierten Ferredoxins aus Chlamydomonas reinhardtii

    OpenAIRE

    Jacobs, Jessica

    2009-01-01

    Im Genom der einzelligen Grünalge Chlamydomonas reinhardtii konnten sechs Gene identifiziert werden, die für (putative) Ferredoxine kodieren. Semiquantitative RT-PCR-Analysen zeigten, dass unter anaeroben Bedingungen nur das Transkript des FDX5-Gens signifikant akkumuliert. Da dies eine vitale Funktion des FDX5-Genproduktes im veränderten Metabolismus anaerober C. reinhardtii Zellen, der durch einen komplexen bakterienartigen Gärungsstoffwechsel und die Produktion von Wasserstoff ...

  20. The Involvement of hybrid cluster protein 4, HCP4, in Anaerobic Metabolism in Chlamydomonas reinhardtii

    OpenAIRE

    Olson, Adam C.; Carter, Clay J

    2016-01-01

    The unicellular green algae Chlamydomonas reinhardtii has long been studied for its unique fermentation pathways and has been evaluated as a candidate organism for biofuel production. Fermentation in C. reinhardtii is facilitated by a network of three predominant pathways producing four major byproducts: formate, ethanol, acetate and hydrogen. Previous microarray studies identified many genes as being highly up-regulated during anaerobiosis. For example, hybrid cluster protein 4 (HCP4) was fo...

  1. Phytotoxicity Evaluation of Type B Trichothecenes Using a Chlamydomonas reinhardtii Model System

    OpenAIRE

    Suzuki, Tadahiro; Iwahashi, Yumiko

    2014-01-01

    Type B trichothecenes, which consist of deoxynivalenol (DON) and nivalenol (NIV) as the major end products, are produced by phytotoxic fungi, such as the Fusarium species, and pollute arable fields across the world. The DON toxicity has been investigated using various types of cell systems or animal bioassays. The evaluation of NIV toxicity, however, has been relatively restricted because of its lower level compared with DON. In this study, the Chlamydomonas reinhardtii testing system, which ...

  2. СHEMOTAXIS OF CHLAMYDOMONAS REINHARDTII TO NITRATE IS CHANGED DURING GAMETOGENESIS

    OpenAIRE

    Ermilova, Elena; Zalutskaya, Zhanneta; Lapina, Tatyana

    2009-01-01

    During sexual differentiation Chlamydomonas reinhardtii changes its chemotactic behavior to nitrate. Unlike vegetative cells and noncompetent pregametes, mature gametes did not show chemotaxis to nitrate. Loss of chemotaxis to nitrate in matingcompetent cells is controlled by gamete-specific genes that are common for both mating-type gametes. Just like gamete formation, the change in chemotaxis mode is controlled by the sequential action of two environmental cues, removal of nitrogen from the...

  3. Successful Transient Expression of Cas9 and Single Guide RNA Genes in Chlamydomonas reinhardtii

    OpenAIRE

    Jiang, Wenzhi; Brueggeman, Andrew J.; Horken, Kempton M.; Plucinak, Thomas M.; Weeks, Donald P.

    2014-01-01

    The clustered regularly interspaced short palindromic repeat (CRISPR)/Cas9 system has become a powerful and precise tool for targeted gene modification (e.g., gene knockout and gene replacement) in numerous eukaryotic organisms. Initial attempts to apply this technology to a model, the single-cell alga, Chlamydomonas reinhardtii, failed to yield cells containing edited genes. To determine if the Cas9 and single guide RNA (sgRNA) genes were functional in C. reinhardtii, we tested the ability o...

  4. Light-Induced Production of An Antibody Fragment and Malaria Vaccine Antigen from Chlamydomonas reinhardtii

    OpenAIRE

    Neera Munjal; Andrea Juliana Garzon-Sanabria; Katelyn Wilson Quinones; James Gregory; Zivko L. Nikolov

    2014-01-01

    The eukaryotic green alga, Chlamydomonas reinhardtii, is a unique expression platform that can efficiently express complex therapeutic proteins. However, demonstrating that therapeutic molecules can be produced in quantifiable levels is essential to establish the potential of the C. reinhardtii expression system. Thus, the objective of this investigation was to determine the process conditions that could maximize C. reinhardtii biomass accumulation and induced-production of the two recombinan...

  5. Sustainability Evaluation of Biodiesel Produced from Microalgae Chlamydomonas sp Grown in Brewery Wastewater

    OpenAIRE

    Mata, Teresa M.; Santos, Janaína; Mendes, Adélio M; Caetano, Nídia S.; Martins, António A.

    2014-01-01

    This study performs a sustainability evaluation of biodiesel from microalga Chlamydomonas sp. grown in 20 % (v/v) of brewery’s wastewater, blended with pentose sugars (xylose, arabinose or ribose resulting from the hydrolysis of brewer’s spent grains (BSG). The life cycle steps considered for the study are: microalgae cultivation, biomass processing and lipids extraction at the brewery site, and its conversion to biodiesel at a dedicated external biofuel’s plant. Three sustainabil...

  6. Chlamydomonas reinhardtii: duration of its cell cycle and phases at growth rates affected by light intensity

    Czech Academy of Sciences Publication Activity Database

    Vítová, Milada; Bišová, Kateřina; Umysová, Dáša; Hlavová, Monika; Kawano, S.; Zachleder, Vilém; Čížková, Mária

    2011-01-01

    Roč. 233, č. 1 (2011), s. 75-86. ISSN 0032-0935 R&D Projects: GA AV ČR IAA500200614; GA ČR GA525/09/0102; GA ČR GA204/09/0111 Institutional research plan: CEZ:AV0Z50200510 Keywords : Cell division timing * Cell cycle phases * Chlamydomonas Subject RIV: EE - Microbiology, Virology Impact factor: 3.000, year: 2011

  7. A rapid, modular and marker-free chloroplast expression system for the green alga Chlamydomonas reinhardtii.

    Science.gov (United States)

    Bertalan, Ivo; Munder, Matthias C; Weiß, Caroline; Kopf, Judith; Fischer, Dirk; Johanningmeier, Udo

    2015-02-10

    In search of alternative expression platforms heterologous protein production in microalgae has gained increasing importance in the last years. Particularly, the chloroplast of the green alga Chlamydomonas reinhardtii has been adopted to successfully express foreign proteins like vaccines and antibodies. However, when compared with other expression systems, the development of the algal chloroplast to a powerful production platform for recombinant proteins is still in its early stages. In an effort to further improve methods for a reliable and rapid generation of transplastomic Chlamydomonas strains we constructed the key plasmid pMM2 containing the psbA gene and a multiple cloning site for foreign gene insertion. The psbA gene allows a marker-free selection procedure using as a recipient the Fud7 strain of Chlamydomonas, which grows on media containing acetate as a carbon source, but is unable to grow photoautotrophically due to the lack of an intact psbA gene. Biolistic transformation of Fud7 with vectors containing this gene restores photoautotrophic growth and thus permits selection in the light on media without carbon sources and antibiotics. The multiple cloning site with a BsaI recognition sequence allows type IIs restriction enzyme-based modular cloning which rapidly generates new gene constructs without sequences, which could influence the expression and characteristics of the foreign protein. In order to demonstrate the feasibility of this approach, a codon optimized version of the gene for the bacterial protein MPT64 has been integrated into the plastome. Several strains with different promoter/UTR combinations show a stable expression of the HA tagged MPT64 protein in Chlamydomonas chloroplasts. PMID:25554634

  8. Relation between hydrogen production and photosynthesis in the green algae Chlamydomonas reinhardtii

    OpenAIRE

    Basu, Alex

    2015-01-01

    The modernized world is over-consuming low-cost energy sources that strongly contributes to pollution and environmental stress. As a consequence, the interest for environmentally friendly alternatives has increased immensely. One such alternative is the use of solar energy and water as a raw material to produce biohydrogen through the process of photosynthetic water splitting. In this work, the relation between H2-production and photosynthesis in the green algae Chlamydomonas reinhardtii was ...

  9. Low oxygen levels contribute to improve photohydrogen production in mixotrophic non-stressed Chlamydomonas cultures

    OpenAIRE

    Jurado-Oller, Jose Luis; Dubini, Alexandra; Galván, Aurora; Fernández, Emilio; González-Ballester, David

    2015-01-01

    Background Currently, hydrogen fuel is derived mainly from fossil fuels, but there is an increasing interest in clean and sustainable technologies for hydrogen production. In this context, the ability of some photosynthetic microorganisms, particularly cyanobacteria and microalgae, to produce hydrogen is a promising alternative for renewable, clean-energy production. Among a diverse array of photosynthetic microorganisms able to produce hydrogen, the green algae Chlamydomonas reinhardtii is t...

  10. The Metabolome of Chlamydomonas reinhardtii following Induction of Anaerobic H2 Production by Sulfur Depletion*

    OpenAIRE

    Timmins, Matthew; Zhou, Wenxu; Rupprecht, Jens; Lim, Lysha; Thomas-Hall, Skye R.; Doebbe, Anja; Kruse, Olaf; Hankamer, Ben; Marx, Ute C.; Smith, Steven M.; Schenk, Peer M.

    2009-01-01

    The metabolome of the model species Chlamydomonas reinhardtii has been analyzed during 120 h of sulfur depletion to induce anaerobic hydrogen (H2) production, using NMR spectroscopy, gas chromatography coupled to mass spectrometry, and TLC. The results indicate that these unicellular green algae consume freshly supplied acetate in the medium to accumulate energy reserves during the first 24 h of sulfur depletion. In addition to the previously reported accumulation of starch, large amounts of ...

  11. CRISPR/Cas9-induced knockout and knock-in mutations in Chlamydomonas reinhardtii

    OpenAIRE

    Sung-Eun Shin; Jong-Min Lim; Hyun Gi Koh; Eun Kyung Kim; Nam Kyu Kang; Seungjib Jeon; Sohee Kwon; Won-Sub Shin; Bongsoo Lee; Kwon Hwangbo; Jungeun Kim; Sung Hyeok Ye; Jae-Young Yun; Hogyun Seo; Hee-Mock Oh

    2016-01-01

    Genome editing is crucial for genetic engineering of organisms for improved traits, particularly in microalgae due to the urgent necessity for the next generation biofuel production. The most advanced CRISPR/Cas9 system is simple, efficient and accurate in some organisms; however, it has proven extremely difficult in microalgae including the model alga Chlamydomonas. We solved this problem by delivering Cas9 ribonucleoproteins (RNPs) comprising the Cas9 protein and sgRNAs to avoid cytotoxicit...

  12. Stress induces the assembly of RNA granules in the chloroplast of Chlamydomonas reinhardtii

    OpenAIRE

    Uniacke, James; Zerges, William

    2008-01-01

    Eukaryotic cells under stress repress translation and localize these messenger RNAs (mRNAs) to cytoplasmic RNA granules. We show that specific stress stimuli induce the assembly of RNA granules in an organelle with bacterial ancestry, the chloroplast of Chlamydomonas reinhardtii. These chloroplast stress granules (cpSGs) form during oxidative stress and disassemble during recovery from stress. Like mammalian stress granules, cpSGs contain poly(A)-binding protein and the small, but not the lar...

  13. Time-Course Global Expression Profiles of Chlamydomonas reinhardtii during Photo-Biological H2 Production

    OpenAIRE

    Anh Vu Nguyen; Joerg Toepel; Steven Burgess; Andreas Uhmeyer; Olga Blifernez; Anja Doebbe; Ben Hankamer; Peter Nixon; Lutz Wobbe; Olaf Kruse

    2011-01-01

    We used a microarray study in order to compare the time course expression profiles of two Chlamydomonas reinhardtii strains, namely the high H₂ producing mutant stm6glc4 and its parental WT strain during H₂ production induced by sulfur starvation. Major cellular reorganizations in photosynthetic apparatus, sulfur and carbon metabolism upon H₂ production were confirmed as common to both strains. More importantly, our results pointed out factors which lead to the higher H₂ production in the mut...

  14. Plectin-like proteins are present in cells of Chlamydomonas eugametos (Volvocales).

    Science.gov (United States)

    Hendrychová, J; Vítová, M; Bisová, K; Wiche, G; Zachleder, V

    2002-01-01

    Using both monoclonal and polyclonal antibodies against mammalian plectin (multifunctional protein cross-linking cytoskeletal structures, mainly intermediate filaments, in mammalian cells), several putative isoforms of plectin-like proteins were found in protein extracts from the green alga Chlamydomonas eugametos (Volvocales). Immunofluorescence and immunoblotting revealed that some of the plectin-like proteins were present in perinuclear region or localized near the cell wall, probably being attached to the cytoplasmic membrane. PMID:12503400

  15. Plectin-like Proteins Are Present in Cells of Chlamydomonas eugametos (Volvocales)

    Czech Academy of Sciences Publication Activity Database

    Hendrychová, Jana; Vítová, Milada; Bišová, Kateřina; Wiche, G.; Zachleder, Vilém

    2002-01-01

    Roč. 47, č. 5 (2002), s. 535-539. ISSN 0015-5632 R&D Projects: GA ČR GA204/97/0576; GA ČR GA204/99/1235; GA ČR GA204/02/1438; GA AV ČR IAC5020012 Institutional research plan: CEZ:AV0Z5020903 Keywords : chlamydomonas eugametos * immunofluorescence Subject RIV: EE - Microbiology, Virology Impact factor: 0.979, year: 2002

  16. Chlamydomonas reinhardtii telomere repeats form unstable structures involving guanine-guanine base pairs.

    OpenAIRE

    Petracek, M E; Berman, J.

    1992-01-01

    Unusual DNA structures involving four guanines in a planar formation (guanine tetrads) are formed by guanine-rich (G-rich) telomere DNA and other G-rich sequences (reviewed in (1)) and may be important in the structure and function of telomeres. These structures result from intrastrand and/or interstrand Hoogsteen base pairs between the guanines. We used the telomeric repeat of Chlamydomonas reinhardtii, TTTTAGGG, which contains 3 guanines and has a long interguanine A + T tract, to determine...

  17. Plastid terminal oxidase 2 (PTOX2) is the major oxidase involved in chlororespiration in Chlamydomonas

    OpenAIRE

    Houille-Vernes, Laura; Rappaport, Fabrice; Wollman, Francis-André; Alric, Jean; Johnson, Xenie

    2011-01-01

    By homology with the unique plastid terminal oxidase (PTOX) found in plants, two genes encoding oxidases have been found in the Chlamydomonas genome, PTOX1 and PTOX2. Here we report the identification of a knockout mutant of PTOX2. Its molecular and functional characterization demonstrates that it encodes the oxidase most predominantly involved in chlororespiration in this algal species. In this mutant, the plastoquinone pool is constitutively reduced under dark-aerobic conditions, resulting ...

  18. Cell adhesion-dependent inactivation of a soluble protein kinase during fertilization in Chlamydomonas.

    OpenAIRE

    Zhang, Y.; Luo, Y.; Emmett, K; Snell, W J

    1996-01-01

    Within seconds after the flagella of mt+ and mt- Chlamydomonas gametes adhere during fertilization, their flagellar adenylyl cyclase is activated several fold and preparation for cell fusion is initiated. Our previous studies indicated that early events in this pathway, including control of adenylyl cyclase, are regulated by phosphorylation and dephosphorylation. Here, we describe a soluble, flagellar protein kinase activity that is regulated by flagellar adhesion. A 48-kDa, soluble flagellar...

  19. Expression and molecular analysis of phbB gene in Chlamydomonas reinhardtii

    Institute of Scientific and Technical Information of China (English)

    WANG Chaogang; HU Zhangli; HU Wei; LEI Anping

    2004-01-01

    The expression vector containing phbB and ble genes was constructed and transformed into cell-walldeficient strain Chlamydomonas reinhardtii CC-849 by the glass-bead method. The transgenic alga was selected and maintained in the TAP agar plates containing 10 μg/mL Zeomycin. Transgenic alga, which could express phbB at the transcriptional level, was obtained and further confirmed with PCR, Southern blot and RT-PCR-DNA hybridization analysis.

  20. Identification and molecular characterization of a novel Chlamydomonas reinhardtii mutant defective in chlorophyll biosynthesis

    Science.gov (United States)

    Mitra, Mautusi

    2013-01-01

    The green micro-alga Chlamydomonas reinhardtii is an elegant model organism to study all aspects of oxygenic photosynthesis. Chlorophyll (Chl) and heme are major tetrapyrroles that play an essential role in energy metabolism in photosynthetic organisms and are synthesized via a common branched tetrapyrrole biosynthetic pathway. One of the enzymes in the pathway is Mg chelatase (MgChel) which inserts Mg 2+ into protoporphyrin IX (PPIX, proto) to form magnesium-protoporphyrin IX (MgPPIX, Mgproto), the first biosynthetic intermediate in the Chl branch. MgChel is a multimeric enzyme that consists of three subunits designated CHLD, CHLI and CHLH. Plants have two isozymes of CHLI (CHLI1 and CHLI2) which are 70%-81% identical in protein sequences. Although the functional role of CHLI1 is well characterized, that of CHLI2 is not. We have isolated a non-photosynthetic light sensitive mutant 5A7 by random DNA insertional mutagenesis that is devoid of any detectable Chl. PCR based analyses show that 5A7 is missing the CHLI1 gene and at least eight additional functionally uncharacterized genes. 5A7 has an intact CHLI2 gene. Complementation with a functional copy of the CHLI1 gene restored Chl biosynthesis, photo-autotrophic growth and light tolerance in 5A7. We have identified the first chli1 (chli1-1) mutant of Chlamydomonas reinhardtii and in green algae. Our results show that in the wild type Chlamydomonas CHLI2 protein amount is lower than that of CHLI1 and the chli1-1 mutant has a drastic reduction in CHLI2 protein levels although it possesses the CHLI2 gene. Our chli1-1 mutant opens up new avenues to explore the functional roles of CHLI1 and CHLI2 in Chl biosynthesis in Chlamydomonas, which has never been studied before. PMID:24555064

  1. Recharacterization of Chlamydomonas reinhardtii and its relatives with new isolates from Japan.

    Science.gov (United States)

    Nakada, Takashi; Shinkawa, Haruka; Ito, Takuro; Tomita, Masaru

    2010-01-01

    Chlamydomonas reinhardtii P. A. Dang. (Volvocales, Chlorophyceae) is one of the most intensely studied algae, and its whole genome was sequenced. Although this species was originally described based on materials from France and is often referred to as a cosmopolitan species, all culture strains available today have been isolated from eastern North America. The distinctions with similar and/or closely related species, such as Chlamydomonas globosa J. Snow and Chlamydomonas orbicularis E. G. Pringsh., are also contentious. In this study, new strains of C. reinhardtii and C. globosa were isolated from Japan and compared with several strains similar to C. reinhardtii. Based on the morphological, genealogical, phylogenetical, and mating studies including the new Japanese strains, the circumscription of C. reinhardtii was clarified. C. reinhardtii was most closely related to C. globosa, and they were shown to be different species. Although C. reinhardtii was similar to C. orbicularis, the authentic strain of C. orbicularis was morphologically distinguishable and phylogenetically distant from C. reinhardtii. Discovery of the Japanese strains of C. reinhardtii supports the cosmopolitan distribution of this species. Based on Japanese strains and/or strains from other countries, emended descriptions of C. reinhardtii, C. globosa, and C. orbicularis are given. PMID:19882207

  2. Distinct Mechanisms Regulating Gene Expression Coexist within the Fermentative Pathways in Chlamydomonas reinhardtii

    Directory of Open Access Journals (Sweden)

    Larisa Angela Swirsky Whitney

    2012-01-01

    Full Text Available Under dark anoxia, the unicellular green algae Chlamydomonas reinhardtii may produce hydrogen by means of its hydrogenase enzymes, in particular HYD1, using reductants derived from the degradation of intercellular carbon stores. Other enzymes belonging to the fermentative pathways compete for the same reductants. A complete understanding of the mechanisms determining the activation of one pathway rather than another will help us engineer Chlamydomonas for fermentative metabolite production, including hydrogen. We examined the expression pattern of the fermentative genes PDC3, LDH1, ADH2, PFL1, and PFR1 in response to day-night cycles, continuous light, continuous darkness, and low or high oxygen availability, which are all conditions that vary on a regular basis in Chlamydomonas' natural environment. We found that all genes except PFL1 show daily fluctuations in expression, and that PFR1 differentiated itself from the others in that it is clearly responsive to low oxygen, where as PDC3, LDH1, and ADH2 are primarily under diurnal regulation. Our results provide evidence that there exist at least three different regulatory mechanisms within the fermentative pathways and suggest that the fermentative pathways are not redundant but rather that availability of a variety of pathways allows for a differential metabolic response to different environmental conditions.

  3. Survival of Human Metallothionein-2 Transplastomic Chlamydomonas reinhardtii to Ultraviolet B Exposure

    Institute of Scientific and Technical Information of China (English)

    Yu-Kun ZHANG; Gui-Fang SHEN; Bing-Gen RU

    2006-01-01

    Solar ultraviolet (UV) radiation has a great influence on green organisms, especially plankton like Chlamydomonas. A human metallothionein-2 gene, which is generally considered to have an anti-radiation function by its coding product, was transferred into the chloroplast genome of Chlamydomonas reinhardtii.To dynamically measure the UV effects on Chlamydomonas cells grown in liquid tris-acetate-phosphate medium, a new method was developed based on the relationship between the chlorophyll content of an algal culture and its absorbance at 570 nm after the 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide assay. In this experiment, both the wild-type and the transplastomic C. reinhardtii cells were cultivated in 96-well microplates containing liquid tris-acetate-phosphate medium in the absence or presence of zinc, copper,cadmium and cysteine. The transgenic C. reinhardtii showed a higher resistance than wild-type to UV-B exposure under all the examined conditions. Metals in the medium had positive impacts on both types of cells,but had significant influence only on the transplastomic cells. However, the high cell viability of the transgenic alga at the end of the 8 h UV-B treatment disappeared after a 20-h recovery culture. Cysteine did not protect cells from UV-B damage, but clearly enhanced the growth of both wild-type and transgenic C.reinhardtii.

  4. Mutants of Chlamydomonas: tools to study thylakoid membrane structure, function and biogenesis.

    Science.gov (United States)

    de Vitry, C; Vallon, O

    1999-06-01

    The unicellular green alga Chlamydomonas reinhardtii is a model system for the study of photosynthesis and chloroplast biogenesis. C. reinhardtii has a photosynthesis apparatus similar to that of higher plants and it grows at rapid rate (generation time about 8 h). It is a facultative phototroph, which allows the isolation of mutants unable to perform photosynthesis and its sexual cycle allows a variety of genetic studies. Transformation of the nucleus and chloroplast genomes is easily performed. Gene transformation occurs mainly by homologous recombination in the chloroplast and heterologous recombination in the nucleus. Mutants are precious tools for studies of thylakoid membrane structure, photosynthetic function and assembly. Photosynthesis mutants affected in the biogenesis of a subunit of a protein complex usually lack the entire complex; this pleiotropic effect has been used in the identification of the other subunits, in the attribution of spectroscopic signals and also as a 'genetic cleaning' process which facilitates both protein complex purification, absorption spectroscopy studies or freeze-fracture analysis. The cytochrome b6f complex is not required for the growth of C. reinhardtii, unlike the case of photosynthetic prokaryotes in which the cytochrome complex is also part of the respiratory chain, and can be uniquely studied in Chlamydomonas by genetic approaches. We describe in greater detail the use of Chlamydomonas mutants in the study of this complex. PMID:10433117

  5. Detection and characterization of phosphatidylcholine in various strains of the genus Chlamydomonas (Volvocales, Chlorophyceae).

    Science.gov (United States)

    Sakurai, Kenta; Mori, Natsumi; Sato, Naoki

    2014-09-01

    The laboratory strains of Chlamydomonas reinhardtii have been reported to contain no phosphatidylcholine (PC), which is considered to be replaced by another zwitterionic lipid, diacylglyceryl-N,N,N-trimethylhomoserine (DGTS). According to the recently published classification, the strains belonged to the subgroup Reinhardtinia. Screening for PC in 13 selected strains of Chlamydomonas in the NIES Algal Collection, which are different in habitats and belong to different phylogenetic subgroups in the genus, revealed the presence of PC in four strains: a strain in the subgroup Polytominia, and three strains in Reinhardtinia. PC was not detected in three other strains of Reinhardtinia analyzed. The presence/absence of PC was not related to the phylogenetic relationship based on 18S rRNA. DGTS was detected in all the strains analyzed. The rare isomer of linolenic acid, 18:3(5,9,12), which has been found in the DGTS of C. reinhardtii, was found in the PC of the two strains and in the DGTS of the five strains. The occurrence of this fatty acid seems limited to a branch of Reinhardtinia. Acquisition and loss of PC in various strains of Chlamydomonas are discussed from the viewpoint of evolution of PC biosynthetic pathway. PMID:24947506

  6. A new method to identify flanking sequence tags in chlamydomonas using 3’-RACE

    Directory of Open Access Journals (Sweden)

    Meslet-Cladière Laurence

    2012-06-01

    Full Text Available Abstract Background The green alga Chlamydomonas reinhardtii, although a premier model organism in biology, still lacks extensive insertion mutant libraries with well-identified Flanking Sequence Tags (FSTs. Rapid and efficient methods are needed for FST retrieval. Results Here, we present a novel method to identify FSTs in insertional mutants of Chlamydomonas. Transformants can be obtained with a resistance cassette lacking a 3’ untranslated region (UTR, suggesting that the RNA that is produced from the resistance marker terminates in the flanking genome when it encounters a cleavage/polyadenylation signal. We have used a robust 3’-RACE method to specifically amplify such chimeric cDNAs. Out of 38 randomly chosen transformants, 27 (71% yielded valid FSTs, of which 23 could be unambiguously mapped to the genome. Eighteen of the mutants lie within a predicted gene. All but two of the intragenic insertions occur in the sense orientation with respect to transcription, suggesting a bias against situations of convergent transcription. Among the 14 insertion sites tested by genomic PCR, 12 could be confirmed. Among these are insertions in genes coding for PSBS3 (possibly involved in non-photochemical quenching, the NimA-related protein kinase CNK2, the mono-dehydroascorbate reductase MDAR1, the phosphoglycerate mutase PGM5 etc.. Conclusion We propose that our 3’-RACE FST method can be used to build large scale FST libraries in Chlamydomonas and other transformable organisms.

  7. The GOA database: gene Ontology annotation updates for 2015.

    Science.gov (United States)

    Huntley, Rachael P; Sawford, Tony; Mutowo-Meullenet, Prudence; Shypitsyna, Aleksandra; Bonilla, Carlos; Martin, Maria J; O'Donovan, Claire

    2015-01-01

    The Gene Ontology Annotation (GOA) resource (http://www.ebi.ac.uk/GOA) provides evidence-based Gene Ontology (GO) annotations to proteins in the UniProt Knowledgebase (UniProtKB). Manual annotations provided by UniProt curators are supplemented by manual and automatic annotations from model organism databases and specialist annotation groups. GOA currently supplies 368 million GO annotations to almost 54 million proteins in more than 480,000 taxonomic groups. The resource now provides annotations to five times the number of proteins it did 4 years ago. As a member of the GO Consortium, we adhere to the most up-to-date Consortium-agreed annotation guidelines via the use of quality control checks that ensures that the GOA resource supplies high-quality functional information to proteins from a wide range of species. Annotations from GOA are freely available and are accessible through a powerful web browser as well as a variety of annotation file formats. PMID:25378336

  8. Gene Ontology annotation of the rice blast fungus, Magnaporthe oryzae

    Directory of Open Access Journals (Sweden)

    Deng Jixin

    2009-02-01

    Full Text Available Abstract Background Magnaporthe oryzae, the causal agent of blast disease of rice, is the most destructive disease of rice worldwide. The genome of this fungal pathogen has been sequenced and an automated annotation has recently been updated to Version 6 http://www.broad.mit.edu/annotation/genome/magnaporthe_grisea/MultiDownloads.html. However, a comprehensive manual curation remains to be performed. Gene Ontology (GO annotation is a valuable means of assigning functional information using standardized vocabulary. We report an overview of the GO annotation for Version 5 of M. oryzae genome assembly. Methods A similarity-based (i.e., computational GO annotation with manual review was conducted, which was then integrated with a literature-based GO annotation with computational assistance. For similarity-based GO annotation a stringent reciprocal best hits method was used to identify similarity between predicted proteins of M. oryzae and GO proteins from multiple organisms with published associations to GO terms. Significant alignment pairs were manually reviewed. Functional assignments were further cross-validated with manually reviewed data, conserved domains, or data determined by wet lab experiments. Additionally, biological appropriateness of the functional assignments was manually checked. Results In total, 6,286 proteins received GO term assignment via the homology-based annotation, including 2,870 hypothetical proteins. Literature-based experimental evidence, such as microarray, MPSS, T-DNA insertion mutation, or gene knockout mutation, resulted in 2,810 proteins being annotated with GO terms. Of these, 1,673 proteins were annotated with new terms developed for Plant-Associated Microbe Gene Ontology (PAMGO. In addition, 67 experiment-determined secreted proteins were annotated with PAMGO terms. Integration of the two data sets resulted in 7,412 proteins (57% being annotated with 1,957 distinct and specific GO terms. Unannotated proteins

  9. An improved ARS2-derived nuclear reporter enhances the efficiency and ease of genetic engineering in Chlamydomonas

    DEFF Research Database (Denmark)

    Specht, Elizabeth A; Nour-Eldin, Hussam Hassan; Hoang, Kevin T D;

    2015-01-01

    The model alga Chlamydomonas reinhardtii has been used to pioneer genetic engineering techniques for high-value protein and biofuel production from algae. To date, most studies of transgenic Chlamydomonas have utilized the chloroplast genome due to its ease of engineering, with a sizeable suite o...... nuclear promoters. This enhanced arylsulfatase reporter construct improves the efficiency and ease of genetic engineering within the Chlamydomonas nuclear genome, with potential application to other algal strains.......The model alga Chlamydomonas reinhardtii has been used to pioneer genetic engineering techniques for high-value protein and biofuel production from algae. To date, most studies of transgenic Chlamydomonas have utilized the chloroplast genome due to its ease of engineering, with a sizeable suite...... of reporters and well-characterized expression constructs. The advanced manipulation of algal nuclear genomes has been hampered by limited strong expression cassettes, and a lack of high-throughput reporters. We have improved upon an endogenous reporter gene - the ARS2 gene encoding an arylsulfatase enzyme...

  10. Viewing a World of Annotations through AnnoVIP

    OpenAIRE

    Karanasos, Konstantinos; Zoupanos, Spyros

    2010-01-01

    The proliferation of electronic content has notably lead to the apparition of large corpora of interrelated structured documents (such as HTML and XML Web pages) and semantic annotations (typically expressed in RDF), which further complement these documents. Documents and annotations may be authored independently by different users or programs. We present AnnoVIP, a peer-to-peer platform, capable of efficiently exploiting a multitude of annotated documents, based on innovative materialized vi...

  11. Search-based Automatic Image Annotation Using Geotagged Community Photos

    OpenAIRE

    Mousselly Sergieh, Hatem

    2014-01-01

    In the Web 2.0 era, platforms for sharing and collaboratively annotating images with keywords, called tags, became very popular. Tags are a powerful means for organizing and retrieving photos. However, manual tagging is time consuming. Recently, the sheer amount of user-tagged photos available on the Web encouraged researchers to explore new techniques for automatic image annotation. The idea is to annotate an unlabeled image by propagating the labels of community photos that are visually sim...

  12. COFECO: composite function annotation enriched by protein complex data

    OpenAIRE

    Sun, Choong-Hyun; Kim, Min-Sung; Han, Youngwoong; Yi, Gwan-Su

    2009-01-01

    COFECO is a web-based tool for a composite annotation of protein complexes, KEGG pathways and Gene Ontology (GO) terms within a class of genes and their orthologs under study. Widely used functional enrichment tools using GO and KEGG pathways create large list of annotations that make it difficult to derive consolidated information and often include over-generalized terms. The interrelationship of annotation terms can be more clearly delineated by integrating the information of physically int...

  13. DIYA: a bacterial annotation pipeline for any genomics lab

    OpenAIRE

    Stewart, Andrew C.; Osborne, Brian; Read, Timothy D

    2009-01-01

    Summary:DIYA (Do-It-Yourself Annotator) is a modular and configurable open source pipeline software, written in Perl, used for the rapid annotation of bacterial genome sequences. The software is currently used to take DNA contigs as input, either in the form of complete genomes or the result of shotgun sequencing, and produce an annotated sequence in Genbank file format as output. Availability: Distribution and source code are available at (https://sourceforge.net/projects/diyg/). Contact: tr...

  14. Barcode Annotations for Medical Image Retrieval: A Preliminary Investigation

    OpenAIRE

    Tizhoosh, Hamid R.

    2015-01-01

    This paper proposes to generate and to use barcodes to annotate medical images and/or their regions of interest such as organs, tumors and tissue types. A multitude of efficient feature-based image retrieval methods already exist that can assign a query image to a certain image class. Visual annotations may help to increase the retrieval accuracy if combined with existing feature-based classification paradigms. Whereas with annotations we usually mean textual descriptions, in this paper barco...

  15. An Extensible, Kinematically-Based Gesture Annotation Scheme

    OpenAIRE

    Martell, Craig H.

    2002-01-01

    Chapter 1 in the book: Advances in Natural Multimodal Dialogue Systems Annotated corpora have played a critical role in speech and natural language research; and, there is an increasing interest in corpora-based research in sign language and gesture as well. We present a non-semantic, geometrically-based annotation scheme, FORM, which allows an annotator to capture the kinematic information in a gesture just from videos of speakers. In addition, FORM stores this gestural in...

  16. Gene Ontology annotation quality analysis in model eukaryotes

    OpenAIRE

    Buza, Teresia J; McCarthy, Fiona M; Wang, Nan; Bridges, Susan M.; Burgess, Shane C.

    2008-01-01

    Functional analysis using the Gene Ontology (GO) is crucial for array analysis, but it is often difficult for researchers to assess the amount and quality of GO annotations associated with different sets of gene products. In many cases the source of the GO annotations and the date the GO annotations were last updated is not apparent, further complicating a researchers’ ability to assess the quality of the GO data provided. Moreover, GO biocurators need to ensure that the GO quality is maintai...

  17. Snap: An Integrated SNP Annotation Platform

    DEFF Research Database (Denmark)

    Li, S.; Ma, L.; Li, H.;

    2007-01-01

    Snap (Single Nucleotide Polymorphism Annotation Platform) is a server designed to comprehensively analyze single genes and relationships between genes basing on SNPs in the human genome. The aim of the platform is to facilitate the study of SNP finding and analysis within the framework of medical...... research. Using a user-friendly web interface, genes can be searched by name, description, position, SNP ID or clone name. Several public databases are integrated, including gene information from Ensembl, protein features from Uniprot/SWISS-PROT, Pfam and DAS-CBS. Gene relationships are fetched from BIND...

  18. Evaluating Modelling Approaches for Medical Image Annotations

    CERN Document Server

    Opitz, Jasmin; Sattler, Ulrike

    2010-01-01

    Information system designers face many challenges w.r.t. selecting appropriate semantic technologies and deciding on a modelling approach for their system. However, there is no clear methodology yet to evaluate "semantically enriched" information systems. In this paper we present a case study on different modelling approaches for annotating medical images and introduce a conceptual framework that can be used to analyse the fitness of information systems and help designers to spot the strengths and weaknesses of various modelling approaches as well as managing trade-offs between modelling effort and their potential benefits.

  19. FINDING GENERIFS VIA GENE ONTOLOGY ANNOTATIONS

    OpenAIRE

    Lu, Zhiyong; Cohen, K Bretonnel; Hunter, Lawrence

    2006-01-01

    A Gene Reference Into Function (GeneRIF) is a concise phrase describing a function of a gene in the Entrez Gene database. Applying techniques from the area of natural language processing known as automatic summarization, it is possible to link the Entrez Gene database, the Gene Ontology, and the biomedical literature. A system was implemented that automatically suggests a sentence from a PubMed/MEDLINE abstract as a candidate GeneRIF by exploiting a gene’s GO annotations along with location f...

  20. A Novel Approach to Semantic and Coreference Annotation at LLNL

    Energy Technology Data Exchange (ETDEWEB)

    Firpo, M

    2005-02-04

    A case is made for the importance of high quality semantic and coreference annotation. The challenges of providing such annotation are described. Asperger's Syndrome is introduced, and the connections are drawn between the needs of text annotation and the abilities of persons with Asperger's Syndrome to meet those needs. Finally, a pilot program is recommended wherein semantic annotation is performed by people with Asperger's Syndrome. The primary points embodied in this paper are as follows: (1) Document annotation is essential to the Natural Language Processing (NLP) projects at Lawrence Livermore National Laboratory (LLNL); (2) LLNL does not currently have a system in place to meet its need for text annotation; (3) Text annotation is challenging for a variety of reasons, many related to its very rote nature; (4) Persons with Asperger's Syndrome are particularly skilled at rote verbal tasks, and behavioral experts agree that they would excel at text annotation; and (6) A pilot study is recommend in which two to three people with Asperger's Syndrome annotate documents and then the quality and throughput of their work is evaluated relative to that of their neuro-typical peers.

  1. Review of actinide-sediment reactions with an annotated bibliography

    Energy Technology Data Exchange (ETDEWEB)

    Ames, L.L.; Rai, D.; Serne, R.J.

    1976-02-10

    The annotated bibliography is divided into sections on chemistry and geochemistry, migration and accumulation, cultural distributions, natural distributions, and bibliographies and annual reviews. (LK)

  2. The UniProt-GO Annotation database in 2011

    Science.gov (United States)

    Dimmer, Emily C.; Huntley, Rachael P.; Alam-Faruque, Yasmin; Sawford, Tony; O'Donovan, Claire; Martin, Maria J.; Bely, Benoit; Browne, Paul; Mun Chan, Wei; Eberhardt, Ruth; Gardner, Michael; Laiho, Kati; Legge, Duncan; Magrane, Michele; Pichler, Klemens; Poggioli, Diego; Sehra, Harminder; Auchincloss, Andrea; Axelsen, Kristian; Blatter, Marie-Claude; Boutet, Emmanuel; Braconi-Quintaje, Silvia; Breuza, Lionel; Bridge, Alan; Coudert, Elizabeth; Estreicher, Anne; Famiglietti, Livia; Ferro-Rojas, Serenella; Feuermann, Marc; Gos, Arnaud; Gruaz-Gumowski, Nadine; Hinz, Ursula; Hulo, Chantal; James, Janet; Jimenez, Silvia; Jungo, Florence; Keller, Guillaume; Lemercier, Phillippe; Lieberherr, Damien; Masson, Patrick; Moinat, Madelaine; Pedruzzi, Ivo; Poux, Sylvain; Rivoire, Catherine; Roechert, Bernd; Schneider, Michael; Stutz, Andre; Sundaram, Shyamala; Tognolli, Michael; Bougueleret, Lydie; Argoud-Puy, Ghislaine; Cusin, Isabelle; Duek- Roggli, Paula; Xenarios, Ioannis; Apweiler, Rolf

    2012-01-01

    The GO annotation dataset provided by the UniProt Consortium (GOA: http://www.ebi.ac.uk/GOA) is a comprehensive set of evidenced-based associations between terms from the Gene Ontology resource and UniProtKB proteins. Currently supplying over 100 million annotations to 11 million proteins in more than 360 000 taxa, this resource has increased 2-fold over the last 2 years and has benefited from a wealth of checks to improve annotation correctness and consistency as well as now supplying a greater information content enabled by GO Consortium annotation format developments. Detailed, manual GO annotations obtained from the curation of peer-reviewed papers are directly contributed by all UniProt curators and supplemented with manual and electronic annotations from 36 model organism and domain-focused scientific resources. The inclusion of high-quality, automatic annotation predictions ensures the UniProt GO annotation dataset supplies functional information to a wide range of proteins, including those from poorly characterized, non-model organism species. UniProt GO annotations are freely available in a range of formats accessible by both file downloads and web-based views. In addition, the introduction of a new, normalized file format in 2010 has made for easier handling of the complete UniProt-GOA data set. PMID:22123736

  3. The UniProt-GO Annotation database in 2011.

    Science.gov (United States)

    Dimmer, Emily C; Huntley, Rachael P; Alam-Faruque, Yasmin; Sawford, Tony; O'Donovan, Claire; Martin, Maria J; Bely, Benoit; Browne, Paul; Mun Chan, Wei; Eberhardt, Ruth; Gardner, Michael; Laiho, Kati; Legge, Duncan; Magrane, Michele; Pichler, Klemens; Poggioli, Diego; Sehra, Harminder; Auchincloss, Andrea; Axelsen, Kristian; Blatter, Marie-Claude; Boutet, Emmanuel; Braconi-Quintaje, Silvia; Breuza, Lionel; Bridge, Alan; Coudert, Elizabeth; Estreicher, Anne; Famiglietti, Livia; Ferro-Rojas, Serenella; Feuermann, Marc; Gos, Arnaud; Gruaz-Gumowski, Nadine; Hinz, Ursula; Hulo, Chantal; James, Janet; Jimenez, Silvia; Jungo, Florence; Keller, Guillaume; Lemercier, Phillippe; Lieberherr, Damien; Masson, Patrick; Moinat, Madelaine; Pedruzzi, Ivo; Poux, Sylvain; Rivoire, Catherine; Roechert, Bernd; Schneider, Michael; Stutz, Andre; Sundaram, Shyamala; Tognolli, Michael; Bougueleret, Lydie; Argoud-Puy, Ghislaine; Cusin, Isabelle; Duek-Roggli, Paula; Xenarios, Ioannis; Apweiler, Rolf

    2012-01-01

    The GO annotation dataset provided by the UniProt Consortium (GOA: http://www.ebi.ac.uk/GOA) is a comprehensive set of evidenced-based associations between terms from the Gene Ontology resource and UniProtKB proteins. Currently supplying over 100 million annotations to 11 million proteins in more than 360,000 taxa, this resource has increased 2-fold over the last 2 years and has benefited from a wealth of checks to improve annotation correctness and consistency as well as now supplying a greater information content enabled by GO Consortium annotation format developments. Detailed, manual GO annotations obtained from the curation of peer-reviewed papers are directly contributed by all UniProt curators and supplemented with manual and electronic annotations from 36 model organism and domain-focused scientific resources. The inclusion of high-quality, automatic annotation predictions ensures the UniProt GO annotation dataset supplies functional information to a wide range of proteins, including those from poorly characterized, non-model organism species. UniProt GO annotations are freely available in a range of formats accessible by both file downloads and web-based views. In addition, the introduction of a new, normalized file format in 2010 has made for easier handling of the complete UniProt-GOA data set. PMID:22123736

  4. Gene Ontology annotation quality analysis in model eukaryotes

    Science.gov (United States)

    Buza, Teresia J.; McCarthy, Fiona M.; Wang, Nan; Bridges, Susan M.; Burgess, Shane C.

    2008-01-01

    Functional analysis using the Gene Ontology (GO) is crucial for array analysis, but it is often difficult for researchers to assess the amount and quality of GO annotations associated with different sets of gene products. In many cases the source of the GO annotations and the date the GO annotations were last updated is not apparent, further complicating a researchers’ ability to assess the quality of the GO data provided. Moreover, GO biocurators need to ensure that the GO quality is maintained and optimal for the functional processes that are most relevant for their research community. We report the GO Annotation Quality (GAQ) score, a quantitative measure of GO quality that includes breadth of GO annotation, the level of detail of annotation and the type of evidence used to make the annotation. As a case study, we apply the GAQ scoring method to a set of diverse eukaryotes and demonstrate how the GAQ score can be used to track changes in GO annotations over time and to assess the quality of GO annotations available for specific biological processes. The GAQ score also allows researchers to quantitatively assess the functional data available for their experimental systems (arrays or databases). PMID:18187504

  5. Introduction to annotated logics foundations for paracomplete and paraconsistent reasoning

    CERN Document Server

    Abe, Jair Minoro; Nakamatsu, Kazumi

    2015-01-01

    This book is written as an introduction to annotated logics. It provides logical foundations for annotated logics, discusses some interesting applications of these logics and also includes the authors' contributions to annotated logics. The central idea of the book is to show how annotated logic can be applied as a tool to solve problems of technology and of applied science. The book will be of interest to pure and applied logicians, philosophers, and computer scientists as a monograph on a kind of paraconsistent logic. But, the layman will also take profit from its reading.

  6. Second Annual NASA Ames Space Science and Astrobiology Jamboree

    Science.gov (United States)

    Dotson, Jessie

    2014-01-01

    The Space Science and Astrobiology Division's researchers are pursuing investigations in a variety of fields, including exoplanets, planetary science, astrobiology, and astrophysics. In addition division personnel support a wide variety of NASA missions. With a wide variety of interesting research going on, distributed among the three branches in at least 5 buildings, it can be difficult to stay abreast of what one's fellow researchers are doing. Our goal in organizing this symposium is to facilitate communication and collaboration among the scientist within the division and to give center management and other ARC researchers and Engineers an opportunity to see what scientific missions work is being done in the division.

  7. Transcriptome annotation using tandem SAGE tags

    Science.gov (United States)

    Rivals, Eric; Boureux, Anthony; Lejeune, Mireille; Ottones, Florence; Pecharromàn Pérez, Oscar; Tarhio, Jorma; Pierrat, Fabien; Ruffle, Florence; Commes, Thérèse; Marti, Jacques

    2007-01-01

    Analysis of several million expressed gene signatures (tags) revealed an increasing number of different sequences, largely exceeding that of annotated genes in mammalian genomes. Serial analysis of gene expression (SAGE) can reveal new Poly(A) RNAs transcribed from previously unrecognized chromosomal regions. However, conventional SAGE tags are too short to identify unambiguously unique sites in large genomes. Here, we design a novel strategy with tags anchored on two different restrictions sites of cDNAs. New transcripts are then tentatively defined by the two SAGE tags in tandem and by the spanning sequence read on the genome between these tagged sites. Having developed a new algorithm to locate these tag-delimited genomic sequences (TDGS), we first validated its capacity to recognize known genes and its ability to reveal new transcripts with two SAGE libraries built in parallel from a single RNA sample. Our algorithm proves fast enough to experiment this strategy at a large scale. We then collected and processed the complete sets of human SAGE tags to predict yet unknown transcripts. A cross-validation with tiling arrays data shows that 47% of these TDGS overlap transcriptional active regions. Our method provides a new and complementary approach for complex transcriptome annotation. PMID:17709346

  8. EFFICIENT VIDEO ANNOTATIONS BY AN IMAGE GROUPS

    Directory of Open Access Journals (Sweden)

    K . Mahi balan

    2015-10-01

    Full Text Available Searching desirable events in uncontrolled videos is a challenging task. So, researches mainly focus on obtaining concepts from numerous labelled videos. But it is time consuming and labour expensive to collect a large amount of required labelled videos for training event models under various condition. To avoid this problem, we propose to leverage abundant Web images for videos since Web images contain a rich source of information with many events roughly annotated and taken under various conditions. However, information from the Web is difficult .so,brute force knowledge transfer of images may hurt the video annotation performance. so, we propose a novel Group-based Domain Adaptation learning framework to leverage different groups of knowledge (source target queried from the Web image search engine to consumer videos (domain target. Different from old methods using multiple source domains of images, our method makes the Web images according to their intrinsic semantic relationships instead of source. Specifically, two different types of groups ( event-specific groups and concept-specific groups are exploited to respectively describe the event-level and concept-level semantic meanings of target-domain videos.

  9. Comparing functional annotation analyses with Catmap

    Directory of Open Access Journals (Sweden)

    Krogh Morten

    2004-12-01

    Full Text Available Abstract Background Ranked gene lists from microarray experiments are usually analysed by assigning significance to predefined gene categories, e.g., based on functional annotations. Tools performing such analyses are often restricted to a category score based on a cutoff in the ranked list and a significance calculation based on random gene permutations as null hypothesis. Results We analysed three publicly available data sets, in each of which samples were divided in two classes and genes ranked according to their correlation to class labels. We developed a program, Catmap (available for download at http://bioinfo.thep.lu.se/Catmap, to compare different scores and null hypotheses in gene category analysis, using Gene Ontology annotations for category definition. When a cutoff-based score was used, results depended strongly on the choice of cutoff, introducing an arbitrariness in the analysis. Comparing results using random gene permutations and random sample permutations, respectively, we found that the assigned significance of a category depended strongly on the choice of null hypothesis. Compared to sample label permutations, gene permutations gave much smaller p-values for large categories with many coexpressed genes. Conclusions In gene category analyses of ranked gene lists, a cutoff independent score is preferable. The choice of null hypothesis is very important; random gene permutations does not work well as an approximation to sample label permutations.

  10. Descartes' fly: the geometry of genomic annotation.

    Science.gov (United States)

    Kim, J

    2001-03-01

    The completion of the Drosophila melanogaster genome marks another significant milestone in the growth of sequence information. But it also contributes to the ever-widening gap between sequence information and biological knowledge. One important approach to reducing this gap is theoretical inference through computational technologies. Many computer programs have been designed to annotate genomic sequence information with biologically relevant information. Here, I suggest that all of these methods have a common structure in which the sequence fragments are "coordinated" by some method of description such as Hidden Markov models. The key to the algorithms lies in constructing the most efficient set of coordinates that allow extrapolation and interpolation from existing knowledge. Efficient extrapolation and interpolation are produced if the sequence fragments acquire a natural geometrical structure in the coordinated description. Finding such a coordinate frame is an inductive problem with no algorithmic solution. The greater part of the problem of genomic annotation lies in biological modeling of the data rather than in algorithmic improvements. PMID:11793243

  11. A Factor Graph Approach to Automated GO Annotation.

    Science.gov (United States)

    Spetale, Flavio E; Tapia, Elizabeth; Krsticevic, Flavia; Roda, Fernando; Bulacio, Pilar

    2016-01-01

    As volume of genomic data grows, computational methods become essential for providing a first glimpse onto gene annotations. Automated Gene Ontology (GO) annotation methods based on hierarchical ensemble classification techniques are particularly interesting when interpretability of annotation results is a main concern. In these methods, raw GO-term predictions computed by base binary classifiers are leveraged by checking the consistency of predefined GO relationships. Both formal leveraging strategies, with main focus on annotation precision, and heuristic alternatives, with main focus on scalability issues, have been described in literature. In this contribution, a factor graph approach to the hierarchical ensemble formulation of the automated GO annotation problem is presented. In this formal framework, a core factor graph is first built based on the GO structure and then enriched to take into account the noisy nature of GO-term predictions. Hence, starting from raw GO-term predictions, an iterative message passing algorithm between nodes of the factor graph is used to compute marginal probabilities of target GO-terms. Evaluations on Saccharomyces cerevisiae, Arabidopsis thaliana and Drosophila melanogaster protein sequences from the GO Molecular Function domain showed significant improvements over competing approaches, even when protein sequences were naively characterized by their physicochemical and secondary structure properties or when loose noisy annotation datasets were considered. Based on these promising results and using Arabidopsis thaliana annotation data, we extend our approach to the identification of most promising molecular function annotations for a set of proteins of unknown function in Solanum lycopersicum. PMID:26771463

  12. Product annotations - KOME | 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 ...ile name: kome_product_annotation.zip File URL: ftp://ftp.biosciencedbc.jp/archiv...ate History of This Database Site Policy | Contact Us Product annotations - KOME | LSDB Archive ...

  13. The GATO gene annotation tool for research laboratories

    Directory of Open Access Journals (Sweden)

    A. Fujita

    2005-11-01

    Full Text Available Large-scale genome projects have generated a rapidly increasing number of DNA sequences. Therefore, development of computational methods to rapidly analyze these sequences is essential for progress in genomic research. Here we present an automatic annotation system for preliminary analysis of DNA sequences. The gene annotation tool (GATO is a Bioinformatics pipeline designed to facilitate routine functional annotation and easy access to annotated genes. It was designed in view of the frequent need of genomic researchers to access data pertaining to a common set of genes. In the GATO system, annotation is generated by querying some of the Web-accessible resources and the information is stored in a local database, which keeps a record of all previous annotation results. GATO may be accessed from everywhere through the internet or may be run locally if a large number of sequences are going to be annotated. It is implemented in PHP and Perl and may be run on any suitable Web server. Usually, installation and application of annotation systems require experience and are time consuming, but GATO is simple and practical, allowing anyone with basic skills in informatics to access it without any special training. GATO can be downloaded at [http://mariwork.iq.usp.br/gato/]. Minimum computer free space required is 2 MB.

  14. The GATO gene annotation tool for research laboratories.

    Science.gov (United States)

    Fujita, A; Massirer, K B; Durham, A M; Ferreira, C E; Sogayar, M C

    2005-11-01

    Large-scale genome projects have generated a rapidly increasing number of DNA sequences. Therefore, development of computational methods to rapidly analyze these sequences is essential for progress in genomic research. Here we present an automatic annotation system for preliminary analysis of DNA sequences. The gene annotation tool (GATO) is a Bioinformatics pipeline designed to facilitate routine functional annotation and easy access to annotated genes. It was designed in view of the frequent need of genomic researchers to access data pertaining to a common set of genes. In the GATO system, annotation is generated by querying some of the Web-accessible resources and the information is stored in a local database, which keeps a record of all previous annotation results. GATO may be accessed from everywhere through the internet or may be run locally if a large number of sequences are going to be annotated. It is implemented in PHP and Perl and may be run on any suitable Web server. Usually, installation and application of annotation systems require experience and are time consuming, but GATO is simple and practical, allowing anyone with basic skills in informatics to access it without any special training. GATO can be downloaded at [http://mariwork.iq.usp.br/gato/]. Minimum computer free space required is 2 MB. PMID:16258624

  15. Behavioral Contributions to "Teaching of Psychology": An Annotated Bibliography

    Science.gov (United States)

    Karsten, A. M.; Carr, J. E.

    2008-01-01

    An annotated bibliography that summarizes behavioral contributions to the journal "Teaching of Psychology" from 1974 to 2006 is provided. A total of 116 articles of potential utility to college-level instructors of behavior analysis and related areas were identified, annotated, and organized into nine categories for ease of accessibility.…

  16. Evaluating techniques for metagenome annotation using simulated sequence data.

    Science.gov (United States)

    Randle-Boggis, Richard J; Helgason, Thorunn; Sapp, Melanie; Ashton, Peter D

    2016-07-01

    The advent of next-generation sequencing has allowed huge amounts of DNA sequence data to be produced, advancing the capabilities of microbial ecosystem studies. The current challenge is to identify from which microorganisms and genes the DNA originated. Several tools and databases are available for annotating DNA sequences. The tools, databases and parameters used can have a significant impact on the results: naïve choice of these factors can result in a false representation of community composition and function. We use a simulated metagenome to show how different parameters affect annotation accuracy by evaluating the sequence annotation performances of MEGAN, MG-RAST, One Codex and Megablast. This simulated metagenome allowed the recovery of known organism and function abundances to be quantitatively evaluated, which is not possible for environmental metagenomes. The performance of each program and database varied, e.g. One Codex correctly annotated many sequences at the genus level, whereas MG-RAST RefSeq produced many false positive annotations. This effect decreased as the taxonomic level investigated increased. Selecting more stringent parameters decreases the annotation sensitivity, but increases precision. Ultimately, there is a trade-off between taxonomic resolution and annotation accuracy. These results should be considered when annotating metagenomes and interpreting results from previous studies. PMID:27162180

  17. Annotating abstract pronominal anaphora in the DAD project

    DEFF Research Database (Denmark)

    Navarretta, Costanza; Olsen, Sussi Anni

    2008-01-01

    extended scheme, which we call the DAD annotation scheme, allows to annotate information about abstract anaphora which is important to investigate their use, see Webber (1988), Gundel et al. (2003), Navarretta (2004) and which can influence their automatic treatment. Intercoder agreement scores obtained by...

  18. Beyond annotations : a proposal for extensible java (XJ).

    OpenAIRE

    Clark, Anthony; Sammut, Paul; Willans, James

    2008-01-01

    Annotations provide a limited way of extending Java in order to tailor the language for specific tasks. This paper describes a proposal for a Java extension which generalises annotations to allow Java to be a platform for developing domain specific languages.

  19. Bioinformatics Assisted Gene Discovery and Annotation of Human Genome

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    As the sequencing stage of human genome project is near the end, the work has begun for discovering novel genes from genome sequences and annotating their biological functions. Here are reviewed current major bioinformatics tools and technologies available for large scale gene discovery and annotation from human genome sequences. Some ideas about possible future development are also provided.

  20. Online Metacognitive Strategies, Hypermedia Annotations, and Motivation on Hypertext Comprehension

    Science.gov (United States)

    Shang, Hui-Fang

    2016-01-01

    This study examined the effect of online metacognitive strategies, hypermedia annotations, and motivation on reading comprehension in a Taiwanese hypertext environment. A path analysis model was proposed based on the assumption that if English as a foreign language learners frequently use online metacognitive strategies and hypermedia annotations,…

  1. Acclimation of Antarctic Chlamydomonas to the sea-ice environment: a transcriptomic analysis.

    Science.gov (United States)

    Liu, Chenlin; Wang, Xiuliang; Wang, Xingna; Sun, Chengjun

    2016-07-01

    The Antarctic green alga Chlamydomonas sp. ICE-L was isolated from sea ice. As a psychrophilic microalga, it can tolerate the environmental stress in the sea-ice brine, such as freezing temperature and high salinity. We performed a transcriptome analysis to identify freezing stress responding genes and explore the extreme environmental acclimation-related strategies. Here, we show that many genes in ICE-L transcriptome that encoding PUFA synthesis enzymes, molecular chaperon proteins, and cell membrane transport proteins have high similarity to the gens from Antarctic bacteria. These ICE-L genes are supposed to be acquired through horizontal gene transfer from its symbiotic microbes in the sea-ice brine. The presence of these genes in both sea-ice microalgae and bacteria indicated the biological processes they involved in are possibly contributing to ICE-L success in sea ice. In addition, the biological pathways were compared between ICE-L and its closely related sister species, Chlamydomonas reinhardtii and Volvox carteri. In ICE-L transcripome, many sequences homologous to the plant or bacteria proteins in the post-transcriptional, post-translational modification, and signal-transduction KEGG pathways, are absent in the nonpsychrophilic green algae. These complex structural components might imply enhanced stress adaptation capacity. At last, differential gene expression analysis at the transcriptome level of ICE-L indicated that genes that associated with post-translational modification, lipid metabolism, and nitrogen metabolism are responding to the freezing treatment. In conclusion, the transcriptome of Chlamydomonas sp. ICE-L is very useful for exploring the mutualistic interaction between microalgae and bacteria in sea ice; and discovering the specific genes and metabolism pathways responding to the freezing acclimation in psychrophilic microalgae. PMID:27161450

  2. Trophic transfer of gold nanoparticles from Euglena gracilis or Chlamydomonas reinhardtii to Daphnia magna

    International Nuclear Information System (INIS)

    Understanding the trophic transfer of nanoparticles (NPs) is important because NPs are small enough to easily penetrate into organisms. In this study, we evaluated the trophic transfer of gold NPs (AuNPs) within the aquatic food chain. We observed AuNPs transfer from 2 species of primary producers (Chlamydomonas reinhardtii or Euglena gracilis) to the primary consumer (Daphnia magna). Also, bioaccumulation of AuNPs in E. gracilis was higher than that in C. reinhardtii. The reasons for the difference in Au accumulation may be the physical structure of these organisms, and the surface area that is available for interaction with NPs. C. reinhardtii has a cell wall that may act as a barrier to the penetration of NPs. The size of E. gracilis is larger than that of C. reinhardtii. This study demonstrates the trophic transfer of AuNPs from a general producer to a consumer in an aquatic environment. - Highlights: • This study evaluated the trophic transfer of AuNPs in an aquatic food chain. • Chlamydomonas reinhardtii and Euglena gracilis were selected as the primary producers. • Daphnia magna was used as the primary consumer. • The bioaccumulation of AuNPs in E. gracilis was higher than that in C. reinhardtii. • AuNPs were transferred from C. reinhardtii and E. gracilis to D. magna. - Gold nanoparticles can transfer from primary producers (Chlamydomonas reinhardtii or Euglena gracilis) to the primary consumer (Daphnia magna) in an aquatic environment

  3. Engineering the chloroplast targeted malarial vaccine antigens in Chlamydomonas starch granules.

    Directory of Open Access Journals (Sweden)

    David Dauvillée

    Full Text Available BACKGROUND: Malaria, an Anopheles-borne parasitic disease, remains a major global health problem causing illness and death that disproportionately affects developing countries. Despite the incidence of malaria, which remains one of the most severe infections of human populations, there is no licensed vaccine against this life-threatening disease. In this context, we decided to explore the expression of Plasmodium vaccine antigens fused to the granule bound starch synthase (GBSS, the major protein associated to the starch matrix in all starch-accumulating plants and algae such as Chlamydomonas reinhardtii. METHODS AND FINDINGS: We describe the development of genetically engineered starch granules containing plasmodial vaccine candidate antigens produced in the unicellular green algae Chlamydomonas reinhardtii. We show that the C-terminal domains of proteins from the rodent Plasmodium species, Plasmodium berghei Apical Major Antigen AMA1, or Major Surface Protein MSP1 fused to the algal granule bound starch synthase (GBSS are efficiently expressed and bound to the polysaccharide matrix. Mice were either immunized intraperitoneally with the engineered starch particles and Freund adjuvant, or fed with the engineered particles co-delivered with the mucosal adjuvant, and challenged intraperitoneally with a lethal inoculum of P. Berghei. Both experimental strategies led to a significantly reduced parasitemia with an extension of life span including complete cure for intraperitoneal delivery as assessed by negative blood thin smears. In the case of the starch bound P. falciparum GBSS-MSP1 fusion protein, the immune sera or purified immunoglobulin G of mice immunized with the corresponding starch strongly inhibited in vitro the intra-erythrocytic asexual development of the most human deadly plasmodial species. CONCLUSION: This novel system paves the way for the production of clinically relevant plasmodial antigens as algal starch-based particles

  4. Semantator: annotating clinical narratives with semantic web ontologies.

    Science.gov (United States)

    Song, Dezhao; Chute, Christopher G; Tao, Cui

    2012-01-01

    To facilitate clinical research, clinical data needs to be stored in a machine processable and understandable way. Manual annotating clinical data is time consuming. Automatic approaches (e.g., Natural Language Processing systems) have been adopted to convert such data into structured formats; however, the quality of such automatically extracted data may not always be satisfying. In this paper, we propose Semantator, a semi-automatic tool for document annotation with Semantic Web ontologies. With a loaded free text document and an ontology, Semantator supports the creation/deletion of ontology instances for any document fragment, linking/disconnecting instances with the properties in the ontology, and also enables automatic annotation by connecting to the NCBO annotator and cTAKES. By representing annotations in Semantic Web standards, Semantator supports reasoning based upon the underlying semantics of the owl:disjointWith and owl:equivalentClass predicates. We present discussions based on user experiences of using Semantator. PMID:22779043

  5. On Semantic Annotation in Clarin-PL Parallel Corpora

    Directory of Open Access Journals (Sweden)

    Violetta Koseska-Toszewa

    2015-12-01

    Full Text Available On Semantic Annotation in Clarin-PL Parallel CorporaIn the article, the authors present a proposal for semantic annotation in Clarin-PL parallel corpora: Polish-Bulgarian-Russian and Polish-Lithuanian ones. Semantic annotation of quantification is a novum in developing sentence level semantics in multilingual parallel corpora. This is why our semantic annotation is manual. The authors hope it will be interesting to IT specialists working on automatic processing of the given natural languages. Semantic annotation defined the way it is defined here will make contrastive studies of natural languages more efficient, which in turn will help verify the results of those studies, and will certainly improve human and machine translations.

  6. Improving microbial genome annotations in an integrated database context.

    Directory of Open Access Journals (Sweden)

    I-Min A Chen

    Full Text Available Effective comparative analysis of microbial genomes requires a consistent and complete view of biological data. Consistency regards the biological coherence of annotations, while completeness regards the extent and coverage of functional characterization for genomes. We have developed tools that allow scientists to assess and improve the consistency and completeness of microbial genome annotations in the context of the Integrated Microbial Genomes (IMG family of systems. All publicly available microbial genomes are characterized in IMG using different functional annotation and pathway resources, thus providing a comprehensive framework for identifying and resolving annotation discrepancies. A rule based system for predicting phenotypes in IMG provides a powerful mechanism for validating functional annotations, whereby the phenotypic traits of an organism are inferred based on the presence of certain metabolic reactions and pathways and compared to experimentally observed phenotypes. The IMG family of systems are available at http://img.jgi.doe.gov/.

  7. Genotyping and annotation of Affymetrix SNP arrays

    DEFF Research Database (Denmark)

    Lamy, Philippe; Andersen, Claus Lindbjerg; Wikman, Friedrik;

    2006-01-01

    In this paper we develop a new method for genotyping Affymetrix single nucleotide polymorphism (SNP) array. The method is based on (i) using multiple arrays at the same time to determine the genotypes and (ii) a model that relates intensities of individual SNPs to each other. The latter point...... allows us to annotate SNPs that have poor performance, either because of poor experimental conditions or because for one of the alleles the probes do not behave in a dose-response manner. Generally, our method agrees well with a method developed by Affymetrix. When both methods make a call they agree in...... 99.25% (using standard settings) of the cases, using a sample of 113 Affymetrix 10k SNP arrays. In the majority of cases where the two methods disagree, our method makes a genotype call, whereas the method by Affymetrix makes a no call, i.e. the genotype of the SNP is not determined. By visualization...

  8. Applied bioinformatics: Genome annotation and transcriptome analysis

    DEFF Research Database (Denmark)

    Gupta, Vikas

    Next generation sequencing (NGS) has revolutionized the field of genomics and its wide range of applications has resulted in the genome-wide analysis of hundreds of species and the development of thousands of computational tools. This thesis represents my work on NGS analysis of four species, Lotus...... japonicus (Lotus), Vaccinium corymbosum (blueberry), Stegodyphus mimosarum (spider) and Trifolium occidentale (clover). From a bioinformatics data analysis perspective, my work can be divided into three parts; genome annotation, small RNA, and gene expression analysis. Lotus is a legume of significant...... agricultural and biological importance. Its capacity to form symbiotic relationships with rhizobia and microrrhizal fungi has fascinated researchers for years. Lotus has a small genome of approximately 470 Mb and a short life cycle of 2 to 3 months, which has made Lotus a model legume plant for many molecular...

  9. A transposon with an unusual arrangement of long terminal repeats in the green alga Chlamydomonas reinhardtii.

    OpenAIRE

    Day, A; Schirmer-Rahire, M; Kuchka, M R; Mayfield, S P; Rochaix, J D

    1988-01-01

    We have isolated a 5.7-kbp dispersed moderately repeated DNA sequence (TOC1) from the mutant OEE1 gene of the Chlamydomonas reinhardtii strain FUD44. The copy number (2 to over 30) and genomic locations of TOC1 elements vary widely in different C. reinhardtii strains. Our standard laboratory photosynthetic strain exhibits a high degree of TOC1 instability during short periods of mitotic growth. TOC1 appears to be a retrotransposon: it contains LTRs and an oligonucleotide stretch that correspo...

  10. Molecular studies of linkage group XIX of Chlamydomonas reinhardtii: evidence against a basal body location

    OpenAIRE

    1991-01-01

    Linkage group XIX (also known as the UNI linkage group) in the green alga, Chlamydomonas reinhardtii, exhibits a number of unusual properties that have lead to the suggestion that it represents a basal body-associated chromosome. To begin a molecular analysis of this linkage group, we have identified DNA sequences from it and used them to determine the copy number of linkage group XIX within the cell. We find that linkage group XIX is present in the same copy number per cell as nuclear linkag...

  11. Effect of temperature and light intensity on growth and photosynthetic activity of Chlamydomonas Reinhardtii

    International Nuclear Information System (INIS)

    The effect of five temperatures (15, 20, 25, 30 and 350C) and two levels of illumination on growth and photosynthetic activity of Chlamydomonas reinhardtii has been studied. The growth of the cultures was evaluated by optical density. Photosynthetic activity has been carried out studying either the assimilation rate of CO2 labelled with C 14 or the oxygen evolution by means of polarographic measurements. The maximum photosynthetic rate has been obtained at 250C for the lower lavel of illumination (2400 lux) and at 350C for the higher one (13200 lux). These results suggest an interacton of temperature and illumination on photosynthetic activity. (author)

  12. Multiple facets of anoxic metabolism and hydrogen production in the unicellular green alga Chlamydomonas reinhardtii.

    Science.gov (United States)

    Grossman, Arthur R; Catalanotti, Claudia; Yang, Wenqiang; Dubini, Alexandra; Magneschi, Leonardo; Subramanian, Venkataramanan; Posewitz, Matthew C; Seibert, Michael

    2011-04-01

    Many microbes in the soil environment experience micro-oxic or anoxic conditions for much of the late afternoon and night, which inhibit or prevent respiratory metabolism. To sustain the production of energy and maintain vital cellular processes during the night, organisms have developed numerous pathways for fermentative metabolism. This review discusses fermentation pathways identified for the soil-dwelling model alga Chlamydomonas reinhardtii, its ability to produce molecular hydrogen under anoxic conditions through the activity of hydrogenases, and the molecular flexibility associated with fermentative metabolism that has only recently been revealed through the analysis of specific mutant strains. PMID:21563367

  13. Ciliary kinematics of Chlamydomonas reinhardtii in Complex Fluids: Role of viscosity

    Science.gov (United States)

    Gopinath, Arvind; Qin, Boyang; Arratia, Paulo

    2014-11-01

    The motility behavior of microorganisms can be significantly affected by the rheology of their fluidic environment. Guided by our experiments on the swimming gait of Chlamydomonas reinhardtii in viscoelastic fluids, we focus on ciliary waveforms in Newtonian fluids and systematically study the effect of increasing viscosity. We find that the beat frequency as well as the wave speed are both strongly influenced by fluid viscosity. Interestingly, ciliary waveforms at low viscosity show a larger influence of the cell body than waveforms at higher viscosity. We use slender body theory and principal component analysis to elucidate the role of fluid viscosity in regulating the kinematics of the swimming process.

  14. Protocol: methodology for chromatin immunoprecipitation (ChIP in Chlamydomonas reinhardtii

    Directory of Open Access Journals (Sweden)

    Strenkert Daniela

    2011-11-01

    Full Text Available Abstract We report on a detailed chromatin immunoprecipitation (ChIP protocol for the unicellular green alga Chlamydomonas reinhardtii. The protocol is suitable for the analysis of nucleosome occupancy, histone modifications and transcription factor binding sites at the level of mononucleosomes for targeted and genome-wide studies. We describe the optimization of conditions for crosslinking, chromatin fragmentation and antibody titer determination and provide recommendations and an example for the normalization of ChIP results as determined by real-time PCR.

  15. Emergent Run-and-Tumble Behavior in a Simple Model of Chlamydomonas with Intrinsic Noise

    Science.gov (United States)

    Bennett, Rachel R.; Golestanian, Ramin

    2013-04-01

    Recent experiments on the green alga Chlamydomonas that swims using synchronized beating of a pair of flagella have revealed that it exhibits a run-and-tumble behavior similar to that of bacteria such as E. coli. Using a simple purely hydrodynamic model that incorporates a stroke cycle and an intrinsic Gaussian white noise, we show that a stochastic run-and-tumble behavior could emerge due to the nonlinearity of the combined synchronization-rotation-translation dynamics. Our study suggests that nonlinear mechanics could be a significant contributing factor to how the trajectories of the microorganism are selected.

  16. Emergent run-and-tumble behavior in a simple model of Chlamydomonas with intrinsic noise.

    Science.gov (United States)

    Bennett, Rachel R; Golestanian, Ramin

    2013-04-01

    Recent experiments on the green alga Chlamydomonas that swims using synchronized beating of a pair of flagella have revealed that it exhibits a run-and-tumble behavior similar to that of bacteria such as E. coli. Using a simple purely hydrodynamic model that incorporates a stroke cycle and an intrinsic Gaussian white noise, we show that a stochastic run-and-tumble behavior could emerge due to the nonlinearity of the combined synchronization-rotation-translation dynamics. Our study suggests that nonlinear mechanics could be a significant contributing factor to how the trajectories of the microorganism are selected. PMID:25167039

  17. Population Dynamics of Chlamydomonas sajao and Its Influence on Soil Aggregate Stabilization in the Field

    OpenAIRE

    Metting, Blaine

    1986-01-01

    Chlamydomonas sajao, a single-celled, eucaryotic microalga, was inoculated onto replicated field plots cropped to corn at two rates (5 × 1011 and 5 × 107 log-phase cells ha−1) to assess colonization, reproduction, and persistence, changes in soil carbohydrate content, and wet stability of 0.92- to 1.68-mm-sized aggregates from the surface 2- to 3-mm soil veneer. The most-probable-number technique and extraction and fluorometric quantification of chlorophyll were used as indices of microalgal ...

  18. Effect of O2:CO2 Ratio on the Primary Metabolism of Chlamydomonas reinhardtii

    OpenAIRE

    Kliphuis, A.M.J.; Martens, D. E.; Janssen, M.G.J.; Wijffels, R.H.

    2011-01-01

    High oxygen:carbon dioxide ratios may have a negative effect on growth and productivity of microalgae. To investigate the effect of O2 and CO2 concentrations and the ratio between these on the metabolism of Chlamydomonas reinhardtii we performed turbidostat experiments at different O2:CO2 ratios. These experiments showed that elevated O2 concentrations and the corresponding increase in the ratio of O2:CO2 common in photobioreactors led to a reduction of growth and biomass yield on light with ...

  19. The GOA database in 2009--an integrated Gene Ontology Annotation resource

    OpenAIRE

    Barrell, D.; Dimmer, E.; Huntley, R. P.; Binns, D.; O Donovan, C.; Apweiler, R.

    2009-01-01

    The Gene Ontology Annotation (GOA) project at the EBI (http://www.ebi.ac.uk/goa) provides high-quality electronic and manual associations (annotations) of Gene Ontology (GO) terms to UniProt Knowledgebase (UniProtKB) entries. Annotations created by the project are collated with annotations from external databases to provide an extensive, publicly available GO annotation resource. Currently covering over 160 000 taxa, with greater than 32 million annotations, GOA remains the largest and most c...

  20. Gene Ontology annotations at SGD: new data sources and annotation methods

    OpenAIRE

    Hong, Eurie L.; Balakrishnan, Rama; Dong, Qing; Christie, Karen R.; Park, Julie; Binkley, Gail; Costanzo, Maria C.; Dwight, Selina S.; Engel, Stacia R.; Fisk, Dianna G.; Hirschman, Jodi E.; Hitz, Benjamin C.; Krieger, Cynthia J.; Livstone, Michael S.; Miyasato, Stuart R.

    2007-01-01

    The Saccharomyces Genome Database (SGD; http://www.yeastgenome.org/) collects and organizes biological information about the chromosomal features and gene products of the budding yeast Saccharomyces cerevisiae. Although published data from traditional experimental methods are the primary sources of evidence supporting Gene Ontology (GO) annotations for a gene product, high-throughput experiments and computational predictions can also provide valuable insights in the absence of an extensive bo...

  1. Semi-automatic conversion of BioProp semantic annotation to PASBio annotation

    OpenAIRE

    Dai Hong-Jie; Tsai Richard; Huang Chi-Hsin; Hsu Wen-Lian

    2008-01-01

    Abstract Background Semantic role labeling (SRL) is an important text analysis technique. In SRL, sentences are represented by one or more predicate-argument structures (PAS). Each PAS is composed of a predicate (verb) and several arguments (noun phrases, adverbial phrases, etc.) with different semantic roles, including main arguments (agent or patient) as well as adjunct arguments (time, manner, or location). PropBank is the most widely used PAS corpus and annotation format in the newswire d...

  2. The Collation of Three Versions of Front Annotations of the Siku Quanshu: Based on 365 Pieces of Front Annotations

    Directory of Open Access Journals (Sweden)

    Wen-Chin Lan

    2015-06-01

    Full Text Available A bibliographic annotation (tiyao提要 is a brief description of the author and content of a book as well as a comment on, or a critique of, the book. The Siku Quanshu Zongmu (四庫全書總目 has long been viewed as a model of the traditional Chinese annotated bibliography and its bibliographic annotations have been praised by many scholars. It is suggested that these annotations can be used as examples for learning how to write bibliographic annotations. The compilation of the Siku Quanshu Zongmu went through three stages: (1 individual draft annotations (分纂稿 written by various scholars, (2 front annotations (書前提要 revised and modified by the officials of the Siku Quanshu Project, and (3 finalized annotations (總目提要 mainly edited and compiled by Ji Yun (紀昀. Initially, the Siku Quanshu had seven written copies and there were seven sets of front annotations. They were housed separately in the seven chambers that Qianlong Emperor (乾隆, r. 1736-1795 built to store the Siku Quanshu. Currently, only three of the seven sets are intact and extant, including Wenyuange (文淵閣, Wensuge (文溯閣, and Wenjinge ( 文津閣. This study attempts to conduct a collation project of the three versions of front annotations. We chose 365 pieces of front annotations from the aforementioned three sets, respectively. The results corroborate that there exist variations and differences among the three sets of front annotations. This paper presents three examples to illustrate how the collation task was done. Since these annotations were transcribed manually, it is quite common to notice that the three sets might use variant forms for the same character. The descriptions of author, title, or number of volumes might be different as well. In particular, the annotation for the same book might be different slightly or significantly among the three sets. This paper is a summary report of the preliminary findings of the collation task

  3. Altered Fermentative Metabolism in Chlamydomonas reinhardtii Mutants Lacking Pyruvate Formate Lyase and Both Pyruvate Formate Lyase and Alcohol Dehydrogenase

    Energy Technology Data Exchange (ETDEWEB)

    Catalanotti, C.; Dubini, A.; Subramanian, V.; Yang, W. Q.; Magneschi, L.; Mus, F.; Seibert, M.; Posewitz, M. C.; Grossman, A. R.

    2012-02-01

    Chlamydomonas reinhardtii, a unicellular green alga, often experiences hypoxic/anoxic soil conditions that activate fermentation metabolism. We isolated three Chlamydomonas mutants disrupted for the pyruvate formate lyase (PFL1) gene; the encoded PFL1 protein catalyzes a major fermentative pathway in wild-type Chlamydomonas cells. When the pfl1 mutants were subjected to dark fermentative conditions, they displayed an increased flux of pyruvate to lactate, elevated pyruvate decarboxylation, ethanol accumulation, diminished pyruvate oxidation by pyruvate ferredoxin oxidoreductase, and lowered H2 production. The pfl1-1 mutant also accumulated high intracellular levels of lactate, succinate, alanine, malate, and fumarate. To further probe the system, we generated a double mutant (pfl1-1 adh1) that is unable to synthesize both formate and ethanol. This strain, like the pfl1 mutants, secreted lactate, but it also exhibited a significant increase in the levels of extracellular glycerol, acetate, and intracellular reduced sugars and a decrease in dark, fermentative H2 production. Whereas wild-type Chlamydomonas fermentation primarily produces formate and ethanol, the double mutant reroutes glycolytic carbon to lactate and glycerol. Although the metabolic adjustments observed in the mutants facilitate NADH reoxidation and sustained glycolysis under dark, anoxic conditions, the observed changes could not have been predicted given our current knowledge of the regulation of fermentation metabolism.

  4. Refactoring the six-gene photosystem II core in the chloroplast of the green algae chlamydomonas reinhardtii

    DEFF Research Database (Denmark)

    Gimpel, Javier A; Nour-Eldin, Hussam Hassan; Scranton, Melissa A;

    2016-01-01

    production, particularly under specific environmental conditions. PSII is a complex multisubunit enzyme with strong interdependence among its components. In this work, we have deleted the six core genes of PSII in the eukaryotic alga Chlamydomonas reinhardtii and refactored them in a single DNA construct...

  5. Stable expression of a bifunctional diterpene synthase in the chloroplast of Chlamydomonas reinhardtii

    DEFF Research Database (Denmark)

    Zedler, Julie A Z; Gangl, Doris; Hamberger, Björn Robert;

    2015-01-01

    Chlamydomonas reinhardtii has been shown to hold significant promise as a production platform for recombinant proteins, but transformation of the nuclear genome is still a non-trivial process due to random gene insertion and frequent silencing. Insertion of transgenes into the chloroplasts is an...

  6. Scoring consensus of multiple ECG annotators by optimal sequence alignment.

    Science.gov (United States)

    Haghpanahi, Masoumeh; Sameni, Reza; Borkholder, David A

    2014-01-01

    Development of ECG delineation algorithms has been an area of intense research in the field of computational cardiology for the past few decades. However, devising evaluation techniques for scoring and/or merging the results of such algorithms, both in the presence or absence of gold standards, still remains as a challenge. This is mainly due to existence of missed or erroneous determination of fiducial points in the results of different annotation algorithms. The discrepancy between different annotators increases when the reference signal includes arrhythmias or significant noise and its morphology deviates from a clean ECG signal. In this work, we propose a new approach to evaluate and compare the results of different annotators under such conditions. Specifically, we use sequence alignment techniques similar to those used in bioinformatics for the alignment of gene sequences. Our approach is based on dynamic programming where adequate mismatch penalties, depending on the type of the fiducial point and the underlying signal, are defined to optimally align the annotation sequences. We also discuss how to extend the algorithm for more than two sequences by using suitable data structures to align multiple annotation sequences with each other. Once the sequences are aligned, different heuristics are devised to evaluate the performance against a gold standard annotation, or to merge the results of multiple annotations when no gold standard exists. PMID:25570339

  7. Fuzzy Emotional Semantic Analysis and Automated Annotation of Scene Images

    Directory of Open Access Journals (Sweden)

    Jianfang Cao

    2015-01-01

    Full Text Available With the advances in electronic and imaging techniques, the production of digital images has rapidly increased, and the extraction and automated annotation of emotional semantics implied by images have become issues that must be urgently addressed. To better simulate human subjectivity and ambiguity for understanding scene images, the current study proposes an emotional semantic annotation method for scene images based on fuzzy set theory. A fuzzy membership degree was calculated to describe the emotional degree of a scene image and was implemented using the Adaboost algorithm and a back-propagation (BP neural network. The automated annotation method was trained and tested using scene images from the SUN Database. The annotation results were then compared with those based on artificial annotation. Our method showed an annotation accuracy rate of 91.2% for basic emotional values and 82.4% after extended emotional values were added, which correspond to increases of 5.5% and 8.9%, respectively, compared with the results from using a single BP neural network algorithm. Furthermore, the retrieval accuracy rate based on our method reached approximately 89%. This study attempts to lay a solid foundation for the automated emotional semantic annotation of more types of images and therefore is of practical significance.

  8. Fuzzy emotional semantic analysis and automated annotation of scene images.

    Science.gov (United States)

    Cao, Jianfang; Chen, Lichao

    2015-01-01

    With the advances in electronic and imaging techniques, the production of digital images has rapidly increased, and the extraction and automated annotation of emotional semantics implied by images have become issues that must be urgently addressed. To better simulate human subjectivity and ambiguity for understanding scene images, the current study proposes an emotional semantic annotation method for scene images based on fuzzy set theory. A fuzzy membership degree was calculated to describe the emotional degree of a scene image and was implemented using the Adaboost algorithm and a back-propagation (BP) neural network. The automated annotation method was trained and tested using scene images from the SUN Database. The annotation results were then compared with those based on artificial annotation. Our method showed an annotation accuracy rate of 91.2% for basic emotional values and 82.4% after extended emotional values were added, which correspond to increases of 5.5% and 8.9%, respectively, compared with the results from using a single BP neural network algorithm. Furthermore, the retrieval accuracy rate based on our method reached approximately 89%. This study attempts to lay a solid foundation for the automated emotional semantic annotation of more types of images and therefore is of practical significance. PMID:25838818

  9. A proteogenomic update to Yersinia: enhancing genome annotation

    Directory of Open Access Journals (Sweden)

    Huang Shih-Ting

    2010-08-01

    Full Text Available Abstract Background Modern biomedical research depends on a complete and accurate proteome. With the widespread adoption of new sequencing technologies, genome sequences are generated at a near exponential rate, diminishing the time and effort that can be invested in genome annotation. The resulting gene set contains numerous errors in even the most basic form of annotation: the primary structure of the proteins. Results The application of experimental proteomics data to genome annotation, called proteogenomics, can quickly and efficiently discover misannotations, yielding a more accurate and complete genome annotation. We present a comprehensive proteogenomic analysis of the plague bacterium, Yersinia pestis KIM. We discover non-annotated genes, correct protein boundaries, remove spuriously annotated ORFs, and make major advances towards accurate identification of signal peptides. Finally, we apply our data to 21 other Yersinia genomes, correcting and enhancing their annotations. Conclusions In total, 141 gene models were altered and have been updated in RefSeq and Genbank, which can be accessed seamlessly through any NCBI tool (e.g. blast or downloaded directly. Along with the improved gene models we discover new, more accurate means of identifying signal peptides in proteomics data.

  10. The caBIG annotation and image Markup project.

    Science.gov (United States)

    Channin, David S; Mongkolwat, Pattanasak; Kleper, Vladimir; Sepukar, Kastubh; Rubin, Daniel L

    2010-04-01

    Image annotation and markup are at the core of medical interpretation in both the clinical and the research setting. Digital medical images are managed with the DICOM standard format. While DICOM contains a large amount of meta-data about whom, where, and how the image was acquired, DICOM says little about the content or meaning of the pixel data. An image annotation is the explanatory or descriptive information about the pixel data of an image that is generated by a human or machine observer. An image markup is the graphical symbols placed over the image to depict an annotation. While DICOM is the standard for medical image acquisition, manipulation, transmission, storage, and display, there are no standards for image annotation and markup. Many systems expect annotation to be reported verbally, while markups are stored in graphical overlays or proprietary formats. This makes it difficult to extract and compute with both of them. The goal of the Annotation and Image Markup (AIM) project is to develop a mechanism, for modeling, capturing, and serializing image annotation and markup data that can be adopted as a standard by the medical imaging community. The AIM project produces both human- and machine-readable artifacts. This paper describes the AIM information model, schemas, software libraries, and tools so as to prepare researchers and developers for their use of AIM. PMID:19294468

  11. Enhanced methane production of Chlorella vulgaris and Chlamydomonas reinhardtii by hydrolytic enzymes addition

    International Nuclear Information System (INIS)

    Highlights: • Methane production of microalgae biomass is hampered by their cell wall. • Pretreatment should be designed in accordance to the microalgae specie. • Fresh Chlamydomonas reinhardtii exhibited high anaerobic biodegradability. • Chlorella vulgaris anaerobic biodegradability was enhanced by 50% using protease pretreatment. - Abstract: The effect of enzymatic hydrolysis on microalgae organic matter solubilisation and methane production was investigated in this study. Even though both biomasses, Chlamydomonas reinhardtii and Chlorella vulgaris, exhibited similar macromolecular distribution, their cell wall composition provided different behaviors. The addition of carbohydrolase (Viscozyme) and protease (Alcalase) resulted in high carbohydrates and protein solubilisation on both biomasses (86–96%). Despite the high carbohydrate solubilisation with the carbohydrolase, methane production was enhanced by 14% for C. vulgaris, while hydrolyzed C. reinhardtii did not show any improvement. The addition of protease to C. reinhardtii increased methane production by 1.17-fold. The low enhancement achieved together with the inherent high biodegradability of this biomass would not justify the cost associated to the enzyme addition. On the other hand, C. vulgaris hydrolyzed with the protease resulted in 86% anaerobic biodegradability compared to 54% of the raw biomass. Therefore, the application of protease prior anaerobic digestion of C. vulgaris could be a promising approach to decrease the energetic input required for cell wall disruption

  12. Experimental Genome-Wide Determination of RNA Polyadenylation in Chlamydomonas reinhardtii.

    Directory of Open Access Journals (Sweden)

    Stephen A Bell

    Full Text Available The polyadenylation of RNA is a near-universal feature of RNA metabolism in eukaryotes. This process has been studied in the model alga Chlamydomonas reinhardtii using low-throughput (gene-by-gene and high-throughput (transcriptome sequencing approaches that recovered poly(A-containing sequence tags which revealed interesting features of this critical process in Chlamydomonas. In this study, RNA polyadenylation has been studied using the so-called Poly(A Tag Sequencing (PAT-Seq approach. Specifically, PAT-Seq was used to study poly(A site choice in cultures grown in four different media types-Tris-Phosphate (TP, Tris-Phosphate-Acetate (TAP, High-Salt (HS, and High-Salt-Acetate (HAS. The results indicate that: 1. As reported before, the motif UGUAA is the primary, and perhaps sole, cis-element that guides mRNA polyadenylation in the nucleus; 2. The scope of alternative polyadenylation events with the potential to change the coding sequences of mRNAs is limited; 3. Changes in poly(A site choice in cultures grown in the different media types are very few in number and do not affect protein-coding potential; 4. Organellar polyadenylation is considerable and affects primarily ribosomal RNAs in the chloroplast and mitochondria; and 5. Organellar RNA polyadenylation is a dynamic process that is affected by the different media types used for cell growth.

  13. Measurement of Lipid Droplet Accumulation Kinetics in Chlamydomonas reinhardtii Using Seoul-Fluor

    Directory of Open Access Journals (Sweden)

    Noo Li Jeon

    2013-10-01

    Full Text Available Alternative energy resources have become an important issue due to the limited stocks of petroleum-based fuel. Microalgae, a source of renewable biodiesel, use solar light to convert CO2 into lipid droplets (LDs. Quantification of LDs in microalgae is required for developing and optimizing algal bioprocess engineering. However, conventional quantification methods are both time and labor-intensive and difficult to apply in high-throughput screening systems. LDs in plant and mammalian cells can be visualized by staining with various fluorescence probes such as the Nile Red, BODIPY, and Seoul-Fluor (SF series. This report describes the optimization of LD staining in Chlamydomonas reinhardtii with SF probes via systematic variations of dye concentration, staining time, temperature, and pH. A protocol for quantitative measurement of accumulation kinetics of LDs in C. reinhardtii was developed using a spectrofluorimeter and the accuracy of LD size measurement was confirmed by transmission electron microscopy (TEM. Our results indicate that our spectrofluorimeter-based measurement approach can monitor kinetics of intracellular LDs (in control and nitrogen-source-starved Chlamydomonas reinhardtii accumulation that has not been possible in the case of conventional imaging-based methods. Our results presented here confirmed that an SF44 can be a powerful tool for in situ monitoring and tracking of intracellular LDs formation.

  14. Biofixation of Carbon dioxide by Chlamydomonas sp. in a Tubular Photobioreactor

    Directory of Open Access Journals (Sweden)

    H Hadiyanto

    2012-02-01

    Full Text Available The biogas production from anaerobic digestion is a potential fuel for power generators application, if biogas can be upgraded to the same standards as fossil natural gas by CO2, H2S, and other non-combustible component removal. Microalgae Chlamydomonas sp. has potency to biofix the carbon dioxide and can be used as an additional food ingredient. The variations of flow rate and carbon dioxide concentration in the process resulting different value of biomass production and carbon dioxide biofixation. Biomass production at 40% carbon dioxide concentration obtained 5.685 gr/dm3 at 10% carbon dioxide concentration obtained 4.892 gr/dm3. The greatest value of carbon dioxide absorption occurs at a 40% concentration amounting to 12.09%. The rate of growth and productivity of microalgae tend to rise in 10% and 20% (%v carbon dioxide concentration, but began started a constant at 30% and 40% (%v carbon dioxide concentration. Biomass production tends to increase in light conditions while a constant in dark conditions. This study used Chlamydomonas sp. as media culture and performed on bubble column and tubular reactor with 6 litres of culture medium at a temperature of 28oC and atmospheric pressure.

  15. Characterization of DNA repair deficient strains of Chlamydomonas reinhardtii generated by insertional mutagenesis.

    Directory of Open Access Journals (Sweden)

    Andrea Plecenikova

    Full Text Available While the mechanisms governing DNA damage response and repair are fundamentally conserved, cross-kingdom comparisons indicate that they differ in many aspects due to differences in life-styles and developmental strategies. In photosynthetic organisms these differences have not been fully explored because gene-discovery approaches are mainly based on homology searches with known DDR/DNA repair proteins. Here we performed a forward genetic screen in the green algae Chlamydomonas reinhardtii to identify genes deficient in DDR/DNA repair. We isolated five insertional mutants that were sensitive to various genotoxic insults and two of them exhibited altered efficiency of transgene integration. To identify genomic regions disrupted in these mutants, we established a novel adaptor-ligation strategy for the efficient recovery of the insertion flanking sites. Four mutants harbored deletions that involved known DNA repair factors, DNA Pol zeta, DNA Pol theta, SAE2/COM1, and two neighbouring genes encoding ERCC1 and RAD17. Deletion in the last mutant spanned two Chlamydomonas-specific genes with unknown function, demonstrating the utility of this approach for discovering novel factors involved in genome maintenance.

  16. Characterization of Hydrocortisone Biometabolites and 18S rRNA Gene in Chlamydomonas reinhardtii Cultures

    Directory of Open Access Journals (Sweden)

    Seyed Bagher Mosavi-Azam

    2008-10-01

    Full Text Available A unicellular microalga, Chlamydomonas reinhardtii, was isolated from rice paddy-field soil and water samples and used in the biotransformation of hydrocortisone (1. This strain has not been previously tested for steroid bioconversion. Fermentation was carried out in BG-11 medium supplemented with 0.05% substrate at 25ºC for 14 days of incubation. The products obtained were chromatographically purified and characterized using spectroscopic methods. 11b,17b-Dihydroxyandrost-4-en-3-one (2, 11b-hydroxyandrost-4-en-3,17-dione (3, 11b,17a,20b,21-tetrahydroxypregn-4-en-3-one (4 and prednisolone (5 were the main products of the bioconversion. The observed bioreaction features were the side chain degradation of the substrate to give compounds 2 and 3 and the 20-ketone reduction and 1,2-dehydrogenation affording compounds 4 and 5, respectively. A time course study showed the accumulation of product 2 from the second day of the fermentation and of compounds 3, 4 and 5 from the third day. All the metabolites reached their maximum concentration in seven days. Microalgal 18S rRNA gene was also amplified by PCR. PCR products were sequenced to confirm their authenticity as 18S rRNA gene of microalgae. The result of PCR blasted with other sequenced microalgae in NCBI showed 100% homology to the 18S small subunit rRNA of two Chlamydomonas reinhardtii spp.

  17. Overexpression of Ferredoxin, PETF, Enhances Tolerance to Heat Stress in Chlamydomonas reinhardtii

    Directory of Open Access Journals (Sweden)

    Li-Fen Huang

    2013-10-01

    Full Text Available Reactive oxygen species (ROS produced by plants in adverse environments can cause damage to organelles and trigger cell death. Removal of excess ROS can be achieved through the ascorbate scavenger pathway to prevent plant cell death. The amount of this scavenger can be regulated by ferredoxin (FDX. Chloroplastic FDXs are electron transfer proteins that perform in distributing photosynthetic reducing power. In this study, we demonstrate that overexpression of the endogenous photosynthetic FDX gene, PETF, in Chlamydomonas reinhardtii could raise the level of reduced ascorbate and diminish H2O2 levels under normal growth conditions. Furthermore, the overexpressing PETF transgenic Chlamydomonas lines produced low levels of H2O2 and exhibited protective effects that were observed through decreased chlorophyll degradation and increased cell survival under heat-stress conditions. The findings of this study suggest that overexpression of PETF can increase the efficiency of ROS scavenging in chloroplasts to confer heat tolerance. The roles of PETF in the downregulation of the ROS level offer a method for potentially improving the tolerance of crops against heat stress.

  18. Proteomic Alterations of Antarctic Ice Microalga Chlamydomonas sp. Under Low-Temperature Stress

    Institute of Scientific and Technical Information of China (English)

    Guang-Feng Kan; Jin-Lai Miao; Cui-Juan Shi; Guang-You Li

    2006-01-01

    Antarctic ice microalga can survive and thrive in cold channels or pores in the Antarctic ice layer. In order to understand the adaptive mechanisms to low temperature, in the present study we compared two-dimensional polyacrylamide gel electrophoresis (2-DE) profiles of normal and low temperature-stressed Antarctic ice microalga Chlamydomonas sp. cells. In addition, new protein spots induced by low temperature were identified with peptide mass fingerprinting based on matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) and database searching. Well-resolved and reproducible 2-DE patterns of both normal and low temperature-stressed cells were acquired. A total of 626 spots was detected in control cells and 652 spots were detected in the corresponding low temperature-stressed cells. A total of 598 spots was matched between normal and stressed cells. Two newly synthesized proteins (a and b) in low temperature-stressed cells were characterized. Protein spot A (53 kDa, pI 6.0) was similar to isopropylmalate/homocitrate/citramalate synthases, which act in the transport and metabolism of amino acids. Protein spot b (25 kDa, pI 8.0) was related to glutathione S-transferase, which functions as a scavenger of active oxygen, free radicals, and noxious metabolites. The present study is valuable for the application of ice microalgae, establishing an ice microalga Chlamydomonas sp. proteome database, and screening molecular biomarkers for further studies.

  19. CRISPR/Cas9-induced knockout and knock-in mutations in Chlamydomonas reinhardtii.

    Science.gov (United States)

    Shin, Sung-Eun; Lim, Jong-Min; Koh, Hyun Gi; Kim, Eun Kyung; Kang, Nam Kyu; Jeon, Seungjib; Kwon, Sohee; Shin, Won-Sub; Lee, Bongsoo; Hwangbo, Kwon; Kim, Jungeun; Ye, Sung Hyeok; Yun, Jae-Young; Seo, Hogyun; Oh, Hee-Mock; Kim, Kyung-Jin; Kim, Jin-Soo; Jeong, Won-Joong; Chang, Yong Keun; Jeong, Byeong-Ryool

    2016-01-01

    Genome editing is crucial for genetic engineering of organisms for improved traits, particularly in microalgae due to the urgent necessity for the next generation biofuel production. The most advanced CRISPR/Cas9 system is simple, efficient and accurate in some organisms; however, it has proven extremely difficult in microalgae including the model alga Chlamydomonas. We solved this problem by delivering Cas9 ribonucleoproteins (RNPs) comprising the Cas9 protein and sgRNAs to avoid cytotoxicity and off-targeting associated with vector-driven expression of Cas9. We obtained CRISPR/Cas9-induced mutations at three loci including MAA7, CpSRP43 and ChlM, and targeted mutagenic efficiency was improved up to 100 fold compared to the first report of transgenic Cas9-induced mutagenesis. Interestingly, we found that unrelated vectors used for the selection purpose were predominantly integrated at the Cas9 cut site, indicative of NHEJ-mediated knock-in events. As expected with Cas9 RNPs, no off-targeting was found in one of the mutagenic screens. In conclusion, we improved the knockout efficiency by using Cas9 RNPs, which opens great opportunities not only for biological research but also industrial applications in Chlamydomonas and other microalgae. Findings of the NHEJ-mediated knock-in events will allow applications of the CRISPR/Cas9 system in microalgae, including "safe harboring" techniques shown in other organisms. PMID:27291619

  20. High-Level Accumulation of Triacylglycerol and Starch in Photoautotrophically Grown Chlamydomonas debaryana NIES-2212.

    Science.gov (United States)

    Toyoshima, Masakazu; Sato, Naoki

    2015-12-01

    Microalgae have the potential to produce triacylglycerol (TAG) and starch, which provide alternative sources of biofuel. A problem in using Chlamydomonas reinhardtii as a model for TAG production has been that this alga lacks phosphatidylcholine (PC), which is thought to be important for TAG synthesis in plants. We found that C. debaryana is one of the rare species of Chlamydomonas having PC. Here we show that this strain, grown under complete photoautotrophic conditions, accumulated TAG and starch up to 20 and 250 pg per cell, respectively, during the stationary phase without nutrient deprivation. Addition of nutrients in this state did not cause loss of TAG, which was found in dilution with fresh medium. The photosynthetically produced TAG contained a high level of monounsaturated fatty acids, which is a preferred property as a material for biodiesel. The oil bodies were present in the cytoplasm, either between the cytoplasmic membrane and the chloroplast or between the chloroplast and the nucleus, whereas the starch granules were present within the chloroplast. Oil bodies were also deposited as a broad layer in the peripheral space of the cytoplasm outside the chloroplast, and might be easily released from the cells by genetic, chemical or mechanical manipulation. These results suggest that C. debaryana is a promising seed organism for developing a good biofuel producer. PMID:26542110

  1. Spontaneous mutations in the ammonium transport gene AMT4 of Chlamydomonas reinhardtii.

    Science.gov (United States)

    Kim, Kwang-Seo; Feild, Eithne; King, Natalie; Yaoi, Takuro; Kustu, Sydney; Inwood, William

    2005-06-01

    Evidence in several microorganisms indicates that Amt proteins are gas channels for NH(3) and CH(3)NH(2), and this has been confirmed structurally. Chlamydomonas reinhardtii has at least four AMT genes, the most reported for a microorganism. Under nitrogen-limiting conditions all AMT genes are transcribed and Chlamydomonas is sensitive to methylammonium toxicity. All 16 spontaneous methylammonium-resistant mutants that we analyzed had defects in accumulation of [(14)C]methylammonium. Genetic crosses indicated that 12 had lesions in a single locus, whereas two each had lesions in other loci. Lesions in different loci were correlated with different degrees of defect in [(14)C]methylammonium uptake. One mutant in the largest class had an insert in the AMT4 gene, and the insert cosegregated with methylammonium resistance in genetic crosses. The other 11 strains in this class also had amt4 lesions, which we characterized at the molecular level. Properties of the amt4 mutants were clearly different from those of rh1 RNAi lines. They indicated that the physiological substrates for Amt and Rh proteins, the only two members of their protein superfamily, are NH(3) and CO(2), respectively. PMID:15802504

  2. Biofixation of Carbon dioxide by Chlamydomonas sp. in a Tubular Photobioreactor

    Directory of Open Access Journals (Sweden)

    H Hadiyanto

    2012-04-01

    Full Text Available The biogas production from anaerobic digestion is a potential fuel for power generators application, if biogas can be upgraded to the same standards as fossil natural gas by CO2, H2S, and other non-combustible component removal. Microalgae Chlamydomonas sp. has potency to biofix the carbon dioxide and can be used as an additional food ingredient. The variations of flow rate and carbon dioxide concentration in the process resulting different value of biomass production and carbon dioxide biofixation. Biomass production at 40% carbon dioxide concentration obtained 5.685 gr/dm3 at 10% carbon dioxide concentration obtained 4.892 gr/dm3. The greatest value of carbon dioxide absorption occurs at a 40% concentration amounting to 12.09%. The rate of growth and productivity of microalgae tend to rise in 10% and 20% (%v carbon dioxide concentration, but began started a constant at 30% and 40% (%v carbon dioxide concentration. Biomass production tends to increase in light conditions while a constant in dark conditions. This study used Chlamydomonas sp. as media culture and performed on bubble column and tubular reactor with 6 litres of culture medium at a temperature of 28oC and atmospheric pressure.

  3. CRISPR/Cas9-induced knockout and knock-in mutations in Chlamydomonas reinhardtii

    Science.gov (United States)

    Shin, Sung-Eun; Lim, Jong-Min; Koh, Hyun Gi; Kim, Eun Kyung; Kang, Nam Kyu; Jeon, Seungjib; Kwon, Sohee; Shin, Won-Sub; Lee, Bongsoo; Hwangbo, Kwon; Kim, Jungeun; Ye, Sung Hyeok; Yun, Jae-Young; Seo, Hogyun; Oh, Hee-Mock; Kim, Kyung-Jin; Kim, Jin-Soo; Jeong, Won-Joong; Chang, Yong Keun; Jeong, Byeong-ryool

    2016-01-01

    Genome editing is crucial for genetic engineering of organisms for improved traits, particularly in microalgae due to the urgent necessity for the next generation biofuel production. The most advanced CRISPR/Cas9 system is simple, efficient and accurate in some organisms; however, it has proven extremely difficult in microalgae including the model alga Chlamydomonas. We solved this problem by delivering Cas9 ribonucleoproteins (RNPs) comprising the Cas9 protein and sgRNAs to avoid cytotoxicity and off-targeting associated with vector-driven expression of Cas9. We obtained CRISPR/Cas9-induced mutations at three loci including MAA7, CpSRP43 and ChlM, and targeted mutagenic efficiency was improved up to 100 fold compared to the first report of transgenic Cas9-induced mutagenesis. Interestingly, we found that unrelated vectors used for the selection purpose were predominantly integrated at the Cas9 cut site, indicative of NHEJ-mediated knock-in events. As expected with Cas9 RNPs, no off-targeting was found in one of the mutagenic screens. In conclusion, we improved the knockout efficiency by using Cas9 RNPs, which opens great opportunities not only for biological research but also industrial applications in Chlamydomonas and other microalgae. Findings of the NHEJ-mediated knock-in events will allow applications of the CRISPR/Cas9 system in microalgae, including “safe harboring” techniques shown in other organisms. PMID:27291619

  4. MimoSA: a system for minimotif annotation

    Directory of Open Access Journals (Sweden)

    Kundeti Vamsi

    2010-06-01

    Full Text Available Abstract Background Minimotifs are short peptide sequences within one protein, which are recognized by other proteins or molecules. While there are now several minimotif databases, they are incomplete. There are reports of many minimotifs in the primary literature, which have yet to be annotated, while entirely novel minimotifs continue to be published on a weekly basis. Our recently proposed function and sequence syntax for minimotifs enables us to build a general tool that will facilitate structured annotation and management of minimotif data from the biomedical literature. Results We have built the MimoSA application for minimotif annotation. The application supports management of the Minimotif Miner database, literature tracking, and annotation of new minimotifs. MimoSA enables the visualization, organization, selection and editing functions of minimotifs and their attributes in the MnM database. For the literature components, Mimosa provides paper status tracking and scoring of papers for annotation through a freely available machine learning approach, which is based on word correlation. The paper scoring algorithm is also available as a separate program, TextMine. Form-driven annotation of minimotif attributes enables entry of new minimotifs into the MnM database. Several supporting features increase the efficiency of annotation. The layered architecture of MimoSA allows for extensibility by separating the functions of paper scoring, minimotif visualization, and database management. MimoSA is readily adaptable to other annotation efforts that manually curate literature into a MySQL database. Conclusions MimoSA is an extensible application that facilitates minimotif annotation and integrates with the Minimotif Miner database. We have built MimoSA as an application that integrates dynamic abstract scoring with a high performance relational model of minimotif syntax. MimoSA's TextMine, an efficient paper-scoring algorithm, can be used to

  5. The UniProt-GO Annotation database in 2011

    OpenAIRE

    Dimmer, E. C.; Huntley, R. P.; Alam-Faruque, Y.; Sawford, T.; O'Donovan, C.; Martin, M. J.; Bely, B.; Browne, P.; Mun Chan, W.; Eberhardt, R.; Gardner, M; Laiho, K; Legge, D.; Magrane, M.; Pichler, K.

    2011-01-01

    The GO annotation dataset provided by the UniProt Consortium (GOA: http://www.ebi.ac.uk/GOA) is a comprehensive set of evidenced-based associations between terms from the Gene Ontology resource and UniProtKB proteins. Currently supplying over 100 million annotations to 11 million proteins in more than 360 000 taxa, this resource has increased 2-fold over the last 2 years and has benefited from a wealth of checks to improve annotation correctness and consistency as well as now supplying a grea...

  6. Formalisation d'annotations produites par des apprenants

    OpenAIRE

    Mille, Dominique

    2005-01-01

    L'objet de cet article est la description d'une formalisation computable des annotations produites par des apprenants, représentée par une ontologie. Cette formalisation explicite la sémantique des annotations grâce à des attributs auxquels le lecteur devrait donner une valeur. Elle contient également les valeurs possibles de ces attributs. L'intérêt d'une telle formalisation est de couvrir toutes les annotations produites par des apprenants, et d'expliciter tout ce qui constitue leur sens, a...

  7. Annotation of the protein coding regions of the equine genome

    DEFF Research Database (Denmark)

    Hestand, Matthew S.; Kalbfleisch, Theodore S.; Coleman, Stephen J.; Zeng, Zheng; Liu, Jinze; Orlando, Ludovic Antoine Alexandre; MacLeod, James N.

    2015-01-01

    Current gene annotation of the horse genome is largely derived from in silico predictions and cross-species alignments. Only a small number of genes are annotated based on equine EST and mRNA sequences. To expand the number of equine genes annotated from equine experimental evidence, we sequenced m...... appear to be small errors in the equine reference genome, since they are also identified as homozygous variants by genomic DNA resequencing of the reference horse. Taken together, we provide a resource of equine mRNA structures and protein coding variants that will enhance equine and cross...

  8. Comparative Omics-Driven Genome Annotation Refinement: Application across Yersiniae

    Energy Technology Data Exchange (ETDEWEB)

    Rutledge, Alexandra C.; Jones, Marcus B.; Chauhan, Sadhana; Purvine, Samuel O.; Sanford, James; Monroe, Matthew E.; Brewer, Heather M.; Payne, Samuel H.; Ansong, Charles; Frank, Bryan C.; Smith, Richard D.; Peterson, Scott; Motin, Vladimir L.; Adkins, Joshua N.

    2012-03-27

    Genome sequencing continues to be a rapidly evolving technology, yet most downstream aspects of genome annotation pipelines remain relatively stable or are even being abandoned. To date, the perceived value of manual curation for genome annotations is not offset by the real cost and time associated with the process. In order to balance the large number of sequences generated, the annotation process is now performed almost exclusively in an automated fashion for most genome sequencing projects. One possible way to reduce errors inherent to automated computational annotations is to apply data from 'omics' measurements (i.e. transcriptional and proteomic) to the un-annotated genome with a proteogenomic-based approach. This approach does require additional experimental and bioinformatics methods to include omics technologies; however, the approach is readily automatable and can benefit from rapid developments occurring in those research domains as well. The annotation process can be improved by experimental validation of transcription and translation and aid in the discovery of annotation errors. Here the concept of annotation refinement has been extended to include a comparative assessment of genomes across closely related species, as is becoming common in sequencing efforts. Transcriptomic and proteomic data derived from three highly similar pathogenic Yersiniae (Y. pestis CO92, Y. pestis pestoides F, and Y. pseudotuberculosis PB1/+) was used to demonstrate a comprehensive comparative omic-based annotation methodology. Peptide and oligo measurements experimentally validated the expression of nearly 40% of each strain's predicted proteome and revealed the identification of 28 novel and 68 previously incorrect protein-coding sequences (e.g., observed frameshifts, extended start sites, and translated pseudogenes) within the three current Yersinia genome annotations. Gene loss is presumed to play a major role in Y. pestis acquiring its niche as a virulent

  9. Function of the chloroplast hydrogenase in the microalga Chlamydomonas: the role of hydrogenase and state transitions during photosynthetic activation in anaerobiosis.

    Directory of Open Access Journals (Sweden)

    Bart Ghysels

    Full Text Available Like a majority of photosynthetic microorganisms, the green unicellular alga Chlamydomonas reinhardtii may encounter O2 deprived conditions on a regular basis. In response to anaerobiosis or in a respiration defective context, the photosynthetic electron transport chain of Chlamydomonas is remodeled by a state transition process to a conformation that favours the photoproduction of ATP at the expense of reductant synthesis. In some unicellular green algae including Chlamydomonas, anoxia also triggers the induction of a chloroplast-located, oxygen sensitive hydrogenase, which accepts electrons from reduced ferredoxin to convert protons into molecular hydrogen. Although microalgal hydrogen evolution has received much interest for its biotechnological potential, its physiological role remains unclear. By using specific Chlamydomonas mutants, we demonstrate that the state transition ability and the hydrogenase function are both critical for induction of photosynthesis in anoxia. These two processes are thus important for survival of the cells when they are transiently placed in an anaerobic environment.

  10. Function of the chloroplast hydrogenase in the microalga Chlamydomonas: the role of hydrogenase and state transitions during photosynthetic activation in anaerobiosis.

    Science.gov (United States)

    Ghysels, Bart; Godaux, Damien; Matagne, René F; Cardol, Pierre; Franck, Fabrice

    2013-01-01

    Like a majority of photosynthetic microorganisms, the green unicellular alga Chlamydomonas reinhardtii may encounter O2 deprived conditions on a regular basis. In response to anaerobiosis or in a respiration defective context, the photosynthetic electron transport chain of Chlamydomonas is remodeled by a state transition process to a conformation that favours the photoproduction of ATP at the expense of reductant synthesis. In some unicellular green algae including Chlamydomonas, anoxia also triggers the induction of a chloroplast-located, oxygen sensitive hydrogenase, which accepts electrons from reduced ferredoxin to convert protons into molecular hydrogen. Although microalgal hydrogen evolution has received much interest for its biotechnological potential, its physiological role remains unclear. By using specific Chlamydomonas mutants, we demonstrate that the state transition ability and the hydrogenase function are both critical for induction of photosynthesis in anoxia. These two processes are thus important for survival of the cells when they are transiently placed in an anaerobic environment. PMID:23717558

  11. System-level network analysis of nitrogen starvation and recovery in Chlamydomonas reinhardtii reveals potential new targets for increased lipid accumulation

    Czech Academy of Sciences Publication Activity Database

    Valledor, Luis; Furuhashi, T.; Recuenco-Muňoz, L.; Wienkoop, S.; Weckwerth, W.

    2014-01-01

    Roč. 7, č. 171 (2014), s. 1-17. ISSN 1754-6834 Institutional support: RVO:67179843 Keywords : chlamydomonas reinhardtii * lipid accumulation * nitrogen Subject RIV: EI - Biotechnology ; Bionics Impact factor: 6.044, year: 2014

  12. Annotation et rature Annotation and Deletion: Outline of a Sociology of Forms

    Directory of Open Access Journals (Sweden)

    Axel Pohn-Weidinger

    2012-05-01

    Full Text Available Ce texte interroge les traces graphiques laissées sur un corpus de formulaires de demande de logement social telles qu’annotations, ratures, biffures et commentaires griffonnés. L’étude de ces traces, laissées en marge des catégories de l’imprimé administratif lors du remplissage, montre le recours au droit comme une opération problématique. Pour les administrés, il s’agit de décrire leur situation de vie de sorte à établir l’éligibilité à un droit, mais bien souvent il est impossible de traduire celle-ci dans les catégories préétablies du formulaire. Les annotations et commentaires laissés sur le formulaire tentent alors d’ouvrir la catégorisation juridique des situations à une prise en compte de la singularité des circonstances de vie du demandeur. Elles montrent le recours au droit comme un accomplissement réflexif, un travail à la fois sur sa propre perception de sa situation et sur celle que l’institution offre à travers le formulaire, et dont la négociation et la mise en œuvre sont au cœur de la production du dossier administratif.This text examines the graphical traces left on a collection of social housing application forms: annotations, erasures, crossed-out words and scribbled-out comments. The study of these traces, left in the margins of the categories on printed administrative forms in the process of being completed, shows the exercising of a right as a problematic operation. Citizens making applications must describe their living situation in a way that will establish their eligibility for a right, but quite often it is impossible to convey this through the form’s predetermined categories. The annotations and comments left on the form attempt to open the legal classification of situations to considering the uniqueness of the applicant’s living circumstances. They show the use of a right as an introspective accomplishment, requiring applicants to work both on their own perception of

  13. Annotated Bibliography of Recent Research Related to Academic Advising

    Science.gov (United States)

    Mottarella, Karen, Comp.

    2011-01-01

    This article presents an annotated bibliography of recent research related to academic advising. It includes research papers that focus on advising and a special section of the "Journal of Career Development" that is devoted to multicultural graduate advising relationships.

  14. Geothermal wetlands: an annotated bibliography of pertinent literature

    Energy Technology Data Exchange (ETDEWEB)

    Stanley, N.E.; Thurow, T.L.; Russell, B.F.; Sullivan, J.F.

    1980-05-01

    This annotated bibliography covers the following topics: algae, wetland ecosystems; institutional aspects; macrophytes - general, production rates, and mineral absorption; trace metal absorption; wetland soils; water quality; and other aspects of marsh ecosystems. (MHR)

  15. OntoELAN: An Ontology-based Linguistic Multimedia Annotator

    CERN Document Server

    Chebotko, Artem; Lu, Shiyong; Fotouhi, Farshad; Aristar, Anthony; Brugman, Hennie; Klassmann, Alexander; Sloetjes, Han; Russel, Albert; Wittenburg, Peter

    2009-01-01

    Despite its scientific, political, and practical value, comprehensive information about human languages, in all their variety and complexity, is not readily obtainable and searchable. One reason is that many language data are collected as audio and video recordings which imposes a challenge to document indexing and retrieval. Annotation of multimedia data provides an opportunity for making the semantics explicit and facilitates the searching of multimedia documents. We have developed OntoELAN, an ontology-based linguistic multimedia annotator that features: (1) support for loading and displaying ontologies specified in OWL; (2) creation of a language profile, which allows a user to choose a subset of terms from an ontology and conveniently rename them if needed; (3) creation of ontological tiers, which can be annotated with profile terms and, therefore, corresponding ontological terms; and (4) saving annotations in the XML format as Multimedia Ontology class instances and, linked to them, class instances of o...

  16. A Machine Learning Based Analytical Framework for Semantic Annotation Requirements

    CERN Document Server

    Hassanzadeh, Hamed; 10.5121/ijwest.2011.2203

    2011-01-01

    The Semantic Web is an extension of the current web in which information is given well-defined meaning. The perspective of Semantic Web is to promote the quality and intelligence of the current web by changing its contents into machine understandable form. Therefore, semantic level information is one of the cornerstones of the Semantic Web. The process of adding semantic metadata to web resources is called Semantic Annotation. There are many obstacles against the Semantic Annotation, such as multilinguality, scalability, and issues which are related to diversity and inconsistency in content of different web pages. Due to the wide range of domains and the dynamic environments that the Semantic Annotation systems must be performed on, the problem of automating annotation process is one of the significant challenges in this domain. To overcome this problem, different machine learning approaches such as supervised learning, unsupervised learning and more recent ones like, semi-supervised learning and active learn...

  17. Hymenoptera Genome Database: integrating genome annotations in HymenopteraMine.

    Science.gov (United States)

    Elsik, Christine G; Tayal, Aditi; Diesh, Colin M; Unni, Deepak R; Emery, Marianne L; Nguyen, Hung N; Hagen, Darren E

    2016-01-01

    We report an update of the Hymenoptera Genome Database (HGD) (http://HymenopteraGenome.org), a model organism database for insect species of the order Hymenoptera (ants, bees and wasps). HGD maintains genomic data for 9 bee species, 10 ant species and 1 wasp, including the versions of genome and annotation data sets published by the genome sequencing consortiums and those provided by NCBI. A new data-mining warehouse, HymenopteraMine, based on the InterMine data warehousing system, integrates the genome data with data from external sources and facilitates cross-species analyses based on orthology. New genome browsers and annotation tools based on JBrowse/WebApollo provide easy genome navigation, and viewing of high throughput sequence data sets and can be used for collaborative genome annotation. All of the genomes and annotation data sets are combined into a single BLAST server that allows users to select and combine sequence data sets to search. PMID:26578564

  18. An Annotated Checklist of the Fishes of Samoa

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — All fishes currently known from the Samoan Islands are listed by their scientific and Samoan names. Species entries are annotated to include the initial Samoan...

  19. Annotation sémantique de pages web

    OpenAIRE

    Tenier, Sylvain; Napoli, Amedeo; Polanco, Xavier; Toussaint, Yannick

    2006-01-01

    Cet article présente un système automatique d'annotation sémantique de pages web. Les systèmes d'annotation automatique existants sont essentiellement syntaxiques, même lorsque les travaux visent à produire une annotation sémantique. La prise en compte d'informations sémantiques sur le domaine pour l'annotation d'un élément dans une page web à partir d'une ontologie suppose d'aborder conjointement deux problèmes : (1) l'identification de la structure syntaxique caractérisant cet élément dans ...

  20. Annotation Method (AM): SE28_AM1 [Metabolonote[Archive

    Lifescience Database Archive (English)

    Full Text Available o compound name or compound category name can assign, predicted molecular formulas are used for the annotati...on. Peaks without predicted molecular formula are assigned as unidentified peak. TogoAnalysisMethodID=TAFT2013A ...

  1. Annotation Method (AM): SE4_AM1 [Metabolonote[Archive

    Lifescience Database Archive (English)

    Full Text Available compound name or compound category name can assign, predicted molecular formulas are used for the annotatio...n. Peaks without predicted molecular formula are assigned as unidentified peak. TogoAnalysisMethodID=TAFT2012A ...

  2. Annotation Method (AM): SE15_AM1 [Metabolonote[Archive

    Lifescience Database Archive (English)

    Full Text Available o compound name or compound category name can assign, predicted molecular formulas are used for the annotati...on. Peaks without predicted molecular formula are assigned as unidentified peak. TogoAnalysisMethodID=TAOT201112 ...

  3. Annotation Method (AM): SE26_AM1 [Metabolonote[Archive

    Lifescience Database Archive (English)

    Full Text Available o compound name or compound category name can assign, predicted molecular formulas are used for the annotati...on. Peaks without predicted molecular formula are assigned as unidentified peak. TogoAnalysisMethodID=TAFT2012A ...

  4. Annotation Method (AM): SE34_AM1 [Metabolonote[Archive

    Lifescience Database Archive (English)

    Full Text Available o compound name or compound category name can assign, predicted molecular formulas are used for the annotati...on. Peaks without predicted molecular formula are assigned as unidentified peak. TogoAnalysisMethodID=TAFT2012A ...

  5. Annotation Method (AM): SE10_AM1 [Metabolonote[Archive

    Lifescience Database Archive (English)

    Full Text Available o compound name or compound category name can assign, predicted molecular formulas are used for the annotati...on. Peaks without predicted molecular formula are assigned as unidentified peak. TogoAnalysisMethodID=TAFT2012A ...

  6. Annotation Method (AM): SE27_AM1 [Metabolonote[Archive

    Lifescience Database Archive (English)

    Full Text Available o compound name or compound category name can assign, predicted molecular formulas are used for the annotati...on. Peaks without predicted molecular formula are assigned as unidentified peak. TogoAnalysisMethodID=TAFT2012A ...

  7. Annotation Method (AM): SE16_AM1 [Metabolonote[Archive

    Lifescience Database Archive (English)

    Full Text Available o compound name or compound category name can assign, predicted molecular formulas are used for the annotati...on. Peaks without predicted molecular formula are assigned as unidentified peak. TogoAnalysisMethodID=TAFT2012A ...

  8. Annotation Method (AM): SE32_AM1 [Metabolonote[Archive

    Lifescience Database Archive (English)

    Full Text Available o compound name or compound category name can assign, predicted molecular formulas are used for the annotati...on. Peaks without predicted molecular formula are assigned as unidentified peak. TogoAnalysisMethodID=TAFT2012A ...

  9. Annotation Method (AM): SE2_AM1 [Metabolonote[Archive

    Lifescience Database Archive (English)

    Full Text Available compound name or compound category name can assign, predicted molecular formulas are used for the annotatio...n. Peaks without predicted molecular formula are assigned as unidentified peak. TogoAnalysisMethodID=TAFT2011A ...

  10. Annotation Method (AM): SE6_AM1 [Metabolonote[Archive

    Lifescience Database Archive (English)

    Full Text Available compound name or compound category name can assign, predicted molecular formulas are used for the annotatio...n. Peaks without predicted molecular formula are assigned as unidentified peak. TogoAnalysisMethodID=TAOT2012A ...

  11. Annotation Method (AM): SE11_AM1 [Metabolonote[Archive

    Lifescience Database Archive (English)

    Full Text Available o compound name or compound category name can assign, predicted molecular formulas are used for the annotati...on. Peaks without predicted molecular formula are assigned as unidentified peak. TogoAnalysisMethodID=TAFT2012A ...

  12. Annotation Method (AM): SE12_AM1 [Metabolonote[Archive

    Lifescience Database Archive (English)

    Full Text Available o compound name or compound category name can assign, predicted molecular formulas are used for the annotati...on. Peaks without predicted molecular formula are assigned as unidentified peak. TogoAnalysisMethodID=TAFT2012A ...

  13. Annotation Method (AM): SE14_AM1 [Metabolonote[Archive

    Lifescience Database Archive (English)

    Full Text Available o compound name or compound category name can assign, predicted molecular formulas are used for the annotati...on. Peaks without predicted molecular formula are assigned as unidentified peak. TogoAnalysisMethodID=TAFT2012A ...

  14. Annotation Method (AM): SE13_AM1 [Metabolonote[Archive

    Lifescience Database Archive (English)

    Full Text Available o compound name or compound category name can assign, predicted molecular formulas are used for the annotati...on. Peaks without predicted molecular formula are assigned as unidentified peak. TogoAnalysisMethodID=TAFT2012A ...

  15. Annotation Method (AM): SE20_AM1 [Metabolonote[Archive

    Lifescience Database Archive (English)

    Full Text Available o compound name or compound category name can assign, predicted molecular formulas are used for the annotati...on. Peaks without predicted molecular formula are assigned as unidentified peak. Terms of chemical category

  16. Annotation Method (AM): SE17_AM1 [Metabolonote[Archive

    Lifescience Database Archive (English)

    Full Text Available o compound name or compound category name can assign, predicted molecular formulas are used for the annotati...on. Peaks without predicted molecular formula are assigned as unidentified peak. TogoAnalysisMethodID=TAFT2012A ...

  17. Annotation Method (AM): SE5_AM1 [Metabolonote[Archive

    Lifescience Database Archive (English)

    Full Text Available compound name or compound category name can assign, predicted molecular formulas are used for the annotatio...n. Peaks without predicted molecular formula are assigned as unidentified peak. TogoAnalysisMethodID=TAFT2012A ...

  18. Annotation Method (AM): SE30_AM1 [Metabolonote[Archive

    Lifescience Database Archive (English)

    Full Text Available o compound name or compound category name can assign, predicted molecular formulas are used for the annotati...on. Peaks without predicted molecular formula are assigned as unidentified peak. TogoAnalysisMethodID=TAFT2012A ...

  19. Annotation Method (AM): SE31_AM1 [Metabolonote[Archive

    Lifescience Database Archive (English)

    Full Text Available o compound name or compound category name can assign, predicted molecular formulas are used for the annotati...on. Peaks without predicted molecular formula are assigned as unidentified peak. TogoAnalysisMethodID=TAFT2012A ...

  20. Annotation Method (AM): SE33_AM1 [Metabolonote[Archive

    Lifescience Database Archive (English)

    Full Text Available o compound name or compound category name can assign, predicted molecular formulas are used for the annotati...on. Peaks without predicted molecular formula are assigned as unidentified peak. TogoAnalysisMethodID=TAFT2012A ...

  1. Annotation Method (AM): SE35_AM1 [Metabolonote[Archive

    Lifescience Database Archive (English)

    Full Text Available o compound name or compound category name can assign, predicted molecular formulas are used for the annotati...on. Peaks without predicted molecular formula are assigned as unidentified peak. TogoAnalysisMethodID=TAFT2012A ...

  2. Annotation Method (AM): SE25_AM1 [Metabolonote[Archive

    Lifescience Database Archive (English)

    Full Text Available o compound name or compound category name can assign, predicted molecular formulas are used for the annotati...on. Peaks without predicted molecular formula are assigned as unidentified peak. TogoAnalysisMethodID=TAFT2012A ...

  3. Annotation Method (AM): SE36_AM1 [Metabolonote[Archive

    Lifescience Database Archive (English)

    Full Text Available o compound name or compound category name can assign, predicted molecular formulas are used for the annotati...on. Peaks without predicted molecular formula are assigned as unidentified peak. TogoAnalysisMethodID=TAFT2012A ...

  4. Annotation Method (AM): SE8_AM1 [Metabolonote[Archive

    Lifescience Database Archive (English)

    Full Text Available compound name or compound category name can assign, predicted molecular formulas are used for the annotatio...n. Peaks without predicted molecular formula are assigned as unidentified peak. TogoAnalysisMethodID=TAFT2012A ...

  5. Annotation Method (AM): SE3_AM1 [Metabolonote[Archive

    Lifescience Database Archive (English)

    Full Text Available compound name or compound category name can assign, predicted molecular formulas are used for the annotatio...n. Peaks without predicted molecular formula are assigned as unidentified peak. TogoAnalysisMethodID=TAFT2011A ...

  6. Annotation Method (AM): SE1_AM1 [Metabolonote[Archive

    Lifescience Database Archive (English)

    Full Text Available compound name or compound category name can assign, predicted molecular formulas are used for the annotatio...n. Peaks without predicted molecular formula are assigned as unidentified peak. TogoAnalysisMethodID=TAFT2011A ...

  7. Annotation Method (AM): SE9_AM1 [Metabolonote[Archive

    Lifescience Database Archive (English)

    Full Text Available compound name or compound category name can assign, predicted molecular formulas are used for the annotatio...n. Peaks without predicted molecular formula are assigned as unidentified peak. TogoAnalysisMethodID=TAFT2012A ...

  8. Annotation Method (AM): SE7_AM1 [Metabolonote[Archive

    Lifescience Database Archive (English)

    Full Text Available compound name or compound category name can assign, predicted molecular formulas are used for the annotatio...n. Peaks without predicted molecular formula are assigned as unidentified peak. TogoAnalysisMethodID=TAOT2012A ...

  9. Annotation Method (AM): SE29_AM1 [Metabolonote[Archive

    Lifescience Database Archive (English)

    Full Text Available o compound name or compound category name can assign, predicted molecular formulas are used for the annotati...on. Peaks without predicted molecular formula are assigned as unidentified peak. TogoAnalysisMethodID=TAFT2013A ...

  10. Creating New Medical Ontologies for Image Annotation A Case Study

    CERN Document Server

    Stanescu, Liana; Brezovan, Marius; Mihai, Cristian Gabriel

    2012-01-01

    Creating New Medical Ontologies for Image Annotation focuses on the problem of the medical images automatic annotation process, which is solved in an original manner by the authors. All the steps of this process are described in detail with algorithms, experiments and results. The original algorithms proposed by authors are compared with other efficient similar algorithms. In addition, the authors treat the problem of creating ontologies in an automatic way, starting from Medical Subject Headings (MESH). They have presented some efficient and relevant annotation models and also the basics of the annotation model used by the proposed system: Cross Media Relevance Models. Based on a text query the system will retrieve the images that contain objects described by the keywords.

  11. Collaborative Semantic Annotation of Images : Ontology-Based Model

    Directory of Open Access Journals (Sweden)

    Damien E. ZOMAHOUN

    2015-12-01

    Full Text Available In the quest for models that could help to represen t the meaning of images, some approaches have used contextual knowledge by building semantic hierarchi es. Others have resorted to the integration of imag es analysis improvement knowledge and images interpret ation using ontologies. The images are often annotated with a set of keywords (or ontologies, w hose relevance remains highly subjective and relate d to only one interpretation (one annotator. However , an image can get many associated semantics because annotators can interpret it differently. Th e purpose of this paper is to propose a collaborati ve annotation system that brings out the meaning of im ages from the different interpretations of annotato rs. The different works carried out in this paper lead to a semantic model of an image, i.e. the different means that a picture may have. This method relies o n the different tools of the Semantic Web, especial ly ontologies.

  12. 06491 Summary -- Digital Historical Corpora- Architecture, Annotation, and Retrieval

    OpenAIRE

    Burnard, Lou; Dobreva, Milena; Fuhr, Norbert; Lüdeling, Anke

    2007-01-01

    The seminar "Digital Historical Corpora" brought together scholars from (historical) linguistics, (historical) philology, computational linguistics and computer science who work with collections of historical texts. The issues that were discussed include digitization, corpus design, corpus architecture, annotation, search, and retrieval.

  13. Descriptive Cataloging: A Selected, Annotated Bibliography, 1984-1985.

    Science.gov (United States)

    Cook, C. Donald; Jones, Ellen

    1986-01-01

    This annotated bibliography of materials published during 1984-1985 on descriptive cataloging covers bibliographic control, Anglo American Cataloging Rules, 2nd edition (AACR2), specific types of materials, authority control, retrospective conversion, management issues, expert systems, and manuals. (EM)

  14. GIFtS: annotation landscape analysis with GeneCards

    Directory of Open Access Journals (Sweden)

    Dalah Irina

    2009-10-01

    Full Text Available Abstract Background Gene annotation is a pivotal component in computational genomics, encompassing prediction of gene function, expression analysis, and sequence scrutiny. Hence, quantitative measures of the annotation landscape constitute a pertinent bioinformatics tool. GeneCards® is a gene-centric compendium of rich annotative information for over 50,000 human gene entries, building upon 68 data sources, including Gene Ontology (GO, pathways, interactions, phenotypes, publications and many more. Results We present the GeneCards Inferred Functionality Score (GIFtS which allows a quantitative assessment of a gene's annotation status, by exploiting the unique wealth and diversity of GeneCards information. The GIFtS tool, linked from the GeneCards home page, facilitates browsing the human genome by searching for the annotation level of a specified gene, retrieving a list of genes within a specified range of GIFtS value, obtaining random genes with a specific GIFtS value, and experimenting with the GIFtS weighting algorithm for a variety of annotation categories. The bimodal shape of the GIFtS distribution suggests a division of the human gene repertoire into two main groups: the high-GIFtS peak consists almost entirely of protein-coding genes; the low-GIFtS peak consists of genes from all of the categories. Cluster analysis of GIFtS annotation vectors provides the classification of gene groups by detailed positioning in the annotation arena. GIFtS also provide measures which enable the evaluation of the databases that serve as GeneCards sources. An inverse correlation is found (for GIFtS>25 between the number of genes annotated by each source, and the average GIFtS value of genes associated with that source. Three typical source prototypes are revealed by their GIFtS distribution: genome-wide sources, sources comprising mainly highly annotated genes, and sources comprising mainly poorly annotated genes. The degree of accumulated knowledge for a

  15. Combined evidence annotation of transposable elements in genome sequences.

    Directory of Open Access Journals (Sweden)

    Hadi Quesneville

    2005-07-01

    Full Text Available Transposable elements (TEs are mobile, repetitive sequences that make up significant fractions of metazoan genomes. Despite their near ubiquity and importance in genome and chromosome biology, most efforts to annotate TEs in genome sequences rely on the results of a single computational program, RepeatMasker. In contrast, recent advances in gene annotation indicate that high-quality gene models can be produced from combining multiple independent sources of computational evidence. To elevate the quality of TE annotations to a level comparable to that of gene models, we have developed a combined evidence-model TE annotation pipeline, analogous to systems used for gene annotation, by integrating results from multiple homology-based and de novo TE identification methods. As proof of principle, we have annotated "TE models" in Drosophila melanogaster Release 4 genomic sequences using the combined computational evidence derived from RepeatMasker, BLASTER, TBLASTX, all-by-all BLASTN, RECON, TE-HMM and the previous Release 3.1 annotation. Our system is designed for use with the Apollo genome annotation tool, allowing automatic results to be curated manually to produce reliable annotations. The euchromatic TE fraction of D. melanogaster is now estimated at 5.3% (cf. 3.86% in Release 3.1, and we found a substantially higher number of TEs (n = 6,013 than previously identified (n = 1,572. Most of the new TEs derive from small fragments of a few hundred nucleotides long and highly abundant families not previously annotated (e.g., INE-1. We also estimated that 518 TE copies (8.6% are inserted into at least one other TE, forming a nest of elements. The pipeline allows rapid and thorough annotation of even the most complex TE models, including highly deleted and/or nested elements such as those often found in heterochromatic sequences. Our pipeline can be easily adapted to other genome sequences, such as those of the D. melanogaster heterochromatin or other

  16. A codon-optimized luciferase from Gaussia princeps facilitates the in vivo monitoring of gene expression in the model alga Chlamydomonas reinhardtii

    OpenAIRE

    N Shao; R. Bock

    2008-01-01

    The unicellular green alga Chlamydomonas reinhardtii has emerged as a superb model species in plant biology. Although the alga is easily transformable, the low efficiency of transgene expression from the Chlamydomonas nuclear genome has severely hampered functional genomics research. For example, poor transgene expression is held responsible for the lack of sensitive reporter genes to monitor gene expression in vivo, analyze subcellular protein localization or study protein–protein interactio...

  17. Semantic annotation of biological concepts interplaying microbial cellular responses

    Directory of Open Access Journals (Sweden)

    Carreira Rafael

    2011-11-01

    Full Text Available Abstract Background Automated extraction systems have become a time saving necessity in Systems Biology. Considerable human effort is needed to model, analyse and simulate biological networks. Thus, one of the challenges posed to Biomedical Text Mining tools is that of learning to recognise a wide variety of biological concepts with different functional roles to assist in these processes. Results Here, we present a novel corpus concerning the integrated cellular responses to nutrient starvation in the model-organism Escherichia coli. Our corpus is a unique resource in that it annotates biomedical concepts that play a functional role in expression, regulation and metabolism. Namely, it includes annotations for genetic information carriers (genes and DNA, RNA molecules, proteins (transcription factors, enzymes and transporters, small metabolites, physiological states and laboratory techniques. The corpus consists of 130 full-text papers with a total of 59043 annotations for 3649 different biomedical concepts; the two dominant classes are genes (highest number of unique concepts and compounds (most frequently annotated concepts, whereas other important cellular concepts such as proteins account for no more than 10% of the annotated concepts. Conclusions To the best of our knowledge, a corpus that details such a wide range of biological concepts has never been presented to the text mining community. The inter-annotator agreement statistics provide evidence of the importance of a consolidated background when dealing with such complex descriptions, the ambiguities naturally arising from the terminology and their impact for modelling purposes. Availability is granted for the full-text corpora of 130 freely accessible documents, the annotation scheme and the annotation guidelines. Also, we include a corpus of 340 abstracts.

  18. Integrative annotation of chromatin elements from ENCODE data

    OpenAIRE

    Hoffman, Michael M.; Ernst, Jason; Wilder, Steven P.; Kundaje, Anshul; Harris, Robert S.; Libbrecht, Max; Giardine, Belinda; Ellenbogen, Paul M.; Bilmes, Jeffrey A.; Birney, Ewan; Hardison, Ross C.; Dunham, Ian; Kellis, Manolis; Noble, William Stafford

    2012-01-01

    The ENCODE Project has generated a wealth of experimental information mapping diverse chromatin properties in several human cell lines. Although each such data track is independently informative toward the annotation of regulatory elements, their interrelations contain much richer information for the systematic annotation of regulatory elements. To uncover these interrelations and to generate an interpretable summary of the massive datasets of the ENCODE Project, we apply unsupervised learnin...

  19. A Non-Null Annotation Inferencer for Java Bytecode

    OpenAIRE

    Hubert, Laurent

    2008-01-01

    We present a non-null annotations inferencer for the Java bytecode language. We previously proposed an analysis to infer non-null annotations and proved it soundness and completeness with respect to a state of the art type system. This paper proposes extensions to our former analysis in order to deal with the Java bytecode language. We have implemented both analyses and compared their behaviour on several benchmarks. The results show a substantial improvement in the precision and, despite bei...

  20. CATMAID: collaborative annotation toolkit for massive amounts of image data

    OpenAIRE

    Saalfeld, Stephan; Cardona, Albert; Hartenstein, Volker; Tomančák, Pavel

    2009-01-01

    Summary: High-resolution, three-dimensional (3D) imaging of large biological specimens generates massive image datasets that are difficult to navigate, annotate and share effectively. Inspired by online mapping applications like GoogleMaps™, we developed a decentralized web interface that allows seamless navigation of arbitrarily large image stacks. Our interface provides means for online, collaborative annotation of the biological image data and seamless sharing of regions of interest by boo...

  1. Classification and Image Annotation for Bridging the Semantic Gap

    OpenAIRE

    Muda, Zurina

    2007-01-01

    The use of digital images is rapidly increasing in digital archives, community databases, as well as on the Web. This creates new challenges for image management and retrieval and promotes the importance of automatic image classification and annotation research. In general current content-based image retrieval methods are still struggling to deal with the semantic gap between low-level visual features and the high-level abstractions perceived by humans. Manual annotation is typically a diffic...

  2. Developing a lexical resource annotated with semantic roles for Portuguese

    OpenAIRE

    Leonardo Zilio; Carlos Ramisch; Maria José Bocorny Finatto

    2014-01-01

    The objectives of this study are as follows: to present a methodology for the development of a lexical resource with semantic information; to compare semantic roles in specialized and non-specialized language; and to observe the semantic role labeling (SRL) made by a group of annotators. Two experiments revolving around SRL in Portuguese were developed: a comparison between data in specialized and non-specialized language corpora; and an annotation evaluation for verifying the agreement among...

  3. Annotation Method (AM): SE40_AM1 [Metabolonote[Archive

    Lifescience Database Archive (English)

    Full Text Available se search. Peaks with no hit to these databases are then selected to secondary sear...ch using EX-HR2 (http://webs2.kazusa.or.jp/mfsearcher/) databases. After the database search processes, each database...SE40_AM1 PowerGet annotation In annotation process, KEGG, KNApSAcK and LipidMAPS are used for primary databa

  4. Comparative omics-driven genome annotation refinement: application across Yersiniae.

    Directory of Open Access Journals (Sweden)

    Alexandra C Schrimpe-Rutledge

    Full Text Available Genome sequencing continues to be a rapidly evolving technology, yet most downstream aspects of genome annotation pipelines remain relatively stable or are even being abandoned. The annotation process is now performed almost exclusively in an automated fashion to balance the large number of sequences generated. One possible way of reducing errors inherent to automated computational annotations is to apply data from omics measurements (i.e. transcriptional and proteomic to the un-annotated genome with a proteogenomic-based approach. Here, the concept of annotation refinement has been extended to include a comparative assessment of genomes across closely related species. Transcriptomic and proteomic data derived from highly similar pathogenic Yersiniae (Y. pestis CO92, Y. pestis Pestoides F, and Y. pseudotuberculosis PB1/+ was used to demonstrate a comprehensive comparative omic-based annotation methodology. Peptide and oligo measurements experimentally validated the expression of nearly 40% of each strain's predicted proteome and revealed the identification of 28 novel and 68 incorrect (i.e., observed frameshifts, extended start sites, and translated pseudogenes protein-coding sequences within the three current genome annotations. Gene loss is presumed to play a major role in Y. pestis acquiring its niche as a virulent pathogen, thus the discovery of many translated pseudogenes, including the insertion-ablated argD, underscores a need for functional analyses to investigate hypotheses related to divergence. Refinements included the discovery of a seemingly essential ribosomal protein, several virulence-associated factors, a transcriptional regulator, and many hypothetical proteins that were missed during annotation.

  5. Computational evaluation of TIS annotation for prokaryotic genomes

    OpenAIRE

    Zhu Huaiqiu; Ju Li-Ning; Zheng Xiaobin; Hu Gang-Qing; She Zhen-Su

    2008-01-01

    Abstract Background Accurate annotation of translation initiation sites (TISs) is essential for understanding the translation initiation mechanism. However, the reliability of TIS annotation in widely used databases such as RefSeq is uncertain due to the lack of experimental benchmarks. Results Based on a homogeneity assumption that gene translation-related signals are uniformly distributed across a genome, we have established a computational method for a large-scale quantitative assessment o...

  6. Automatically Annotated Mapping for Indoor Mobile Robot Applications

    DEFF Research Database (Denmark)

    Özkil, Ali Gürcan; Howard, Thomas J.

    2012-01-01

    This paper presents a new and practical method for mapping and annotating indoor environments for mobile robot use. The method makes use of 2D occupancy grid maps for metric representation, and topology maps to indicate the connectivity of the ‘places-of-interests’ in the environment. Novel use of...... consistent, automatically annotated hybrid metric-topological maps that is needed by mobile service robots....

  7. Experimental Polish-Lithuanian Corpus with the Semantic Annotation Elements

    Directory of Open Access Journals (Sweden)

    Danuta Roszko

    2015-06-01

    Full Text Available Experimental Polish-Lithuanian Corpus with the Semantic Annotation ElementsIn the article the authors present the experimental Polish-Lithuanian corpus (ECorpPL-LT formed for the idea of Polish-Lithuanian theoretical contrastive studies, a Polish-Lithuanian electronic dictionary, and as help for a sworn translator. The semantic annotation being brought into ECorpPL-LT is extremely useful in Polish-Lithuanian contrastive studies, and also proves helpful in translation work.

  8. Wearable cameras for real-time activity annotation

    OpenAIRE

    Zhou, Jiang; Duane, Aaron; Albatal, Rami; Gurrin, Cathal; Johansen, Dag

    2015-01-01

    Google Glass has potential to be a real-time data capture and annotation tool. With professional sports as a use-case, we present a platform which helps a football coach capture and annotate interesting events using Google Glass. In our implementation, an interesting event is indicated by a predefined hand gesture or motion, and our platform can automatically detect these gestures in a video without training any classifier. Three event detectors are examined and our experiment shows that the ...

  9. JAABA: interactive machine learning for automatic annotation of animal behavior

    OpenAIRE

    Kabra, Mayank; Robie, Alice A.; Rivera-Alba, Marta; Branson, Steven; Branson, Kristin

    2013-01-01

    We present a machine learning-based system for automatically computing interpretable, quantitative measures of animal behavior. Through our interactive system, users encode their intuition about behavior by annotating a small set of video frames. These manual labels are converted into classifiers that can automatically annotate behaviors in screen-scale data sets. Our general-purpose system can create a variety of accurate individual and social behavior classifiers for different organisms, in...

  10. Challenges in Whole-Genome Annotation of Pyrosequenced Eukaryotic Genomes

    Energy Technology Data Exchange (ETDEWEB)

    Kuo, Alan; Grigoriev, Igor

    2009-04-17

    Pyrosequencing technologies such as 454/Roche and Solexa/Illumina vastly lower the cost of nucleotide sequencing compared to the traditional Sanger method, and thus promise to greatly expand the number of sequenced eukaryotic genomes. However, the new technologies also bring new challenges such as shorter reads and new kinds and higher rates of sequencing errors, which complicate genome assembly and gene prediction. At JGI we are deploying 454 technology for the sequencing and assembly of ever-larger eukaryotic genomes. Here we describe our first whole-genome annotation of a purely 454-sequenced fungal genome that is larger than a yeast (>30 Mbp). The pezizomycotine (filamentous ascomycote) Aspergillus carbonarius belongs to the Aspergillus section Nigri species complex, members of which are significant as platforms for bioenergy and bioindustrial technology, as members of soil microbial communities and players in the global carbon cycle, and as agricultural toxigens. Application of a modified version of the standard JGI Annotation Pipeline has so far predicted ~;;10k genes. ~;;12percent of these preliminary annotations suffer a potential frameshift error, which is somewhat higher than the ~;;9percent rate in the Sanger-sequenced and conventionally assembled and annotated genome of fellow Aspergillus section Nigri member A. niger. Also,>90percent of A. niger genes have potential homologs in the A. carbonarius preliminary annotation. Weconclude, and with further annotation and comparative analysis expect to confirm, that 454 sequencing strategies provide a promising substrate for annotation of modestly sized eukaryotic genomes. We will also present results of annotation of a number of other pyrosequenced fungal genomes of bioenergy interest.

  11. Experimental Polish-Lithuanian Corpus with the Semantic Annotation Elements

    OpenAIRE

    Danuta Roszko; Roman Roszko

    2015-01-01

    Experimental Polish-Lithuanian Corpus with the Semantic Annotation ElementsIn the article the authors present the experimental Polish-Lithuanian corpus (ECorpPL-LT) formed for the idea of Polish-Lithuanian theoretical contrastive studies, a Polish-Lithuanian electronic dictionary, and as help for a sworn translator. The semantic annotation being brought into ECorpPL-LT is extremely useful in Polish-Lithuanian contrastive studies, and also proves helpful in translation work.

  12. GELATO and SAGE: An Integrated Framework for MS Annotation

    OpenAIRE

    AlJadda, Khalifeh; Ranzinger, Rene; Porterfield, Melody; Weatherly, Brent; Korayem, Mohammed; Miller, John A.; Rasheed, Khaled; Kochut, Krys J; York, William S.

    2015-01-01

    Several algorithms and tools have been developed to (semi) automate the process of glycan identification by interpreting Mass Spectrometric data. However, each has limitations when annotating MSn data with thousands of MS spectra using uncurated public databases. Moreover, the existing tools are not designed to manage MSn data where n > 2. We propose a novel software package to automate the annotation of tandem MS data. This software consists of two major components. The first, is a free, sem...

  13. GENCODE: the reference human genome annotation for The ENCODE Project.

    Science.gov (United States)

    Harrow, Jennifer; Frankish, Adam; Gonzalez, Jose M; Tapanari, Electra; Diekhans, Mark; Kokocinski, Felix; Aken, Bronwen L; Barrell, Daniel; Zadissa, Amonida; Searle, Stephen; Barnes, If; Bignell, Alexandra; Boychenko, Veronika; Hunt, Toby; Kay, Mike; Mukherjee, Gaurab; Rajan, Jeena; Despacio-Reyes, Gloria; Saunders, Gary; Steward, Charles; Harte, Rachel; Lin, Michael; Howald, Cédric; Tanzer, Andrea; Derrien, Thomas; Chrast, Jacqueline; Walters, Nathalie; Balasubramanian, Suganthi; Pei, Baikang; Tress, Michael; Rodriguez, Jose Manuel; Ezkurdia, Iakes; van Baren, Jeltje; Brent, Michael; Haussler, David; Kellis, Manolis; Valencia, Alfonso; Reymond, Alexandre; Gerstein, Mark; Guigó, Roderic; Hubbard, Tim J

    2012-09-01

    The GENCODE Consortium aims to identify all gene features in the human genome using a combination of computational analysis, manual annotation, and experimental validation. Since the first public release of this annotation data set, few new protein-coding loci have been added, yet the number of alternative splicing transcripts annotated has steadily increased. The GENCODE 7 release contains 20,687 protein-coding and 9640 long noncoding RNA loci and has 33,977 coding transcripts not represented in UCSC genes and RefSeq. It also has the most comprehensive annotation of long noncoding RNA (lncRNA) loci publicly available with the predominant transcript form consisting of two exons. We have examined the completeness of the transcript annotation and found that 35% of transcriptional start sites are supported by CAGE clusters and 62% of protein-coding genes have annotated polyA sites. Over one-third of GENCODE protein-coding genes are supported by peptide hits derived from mass spectrometry spectra submitted to Peptide Atlas. New models derived from the Illumina Body Map 2.0 RNA-seq data identify 3689 new loci not currently in GENCODE, of which 3127 consist of two exon models indicating that they are possibly unannotated long noncoding loci. GENCODE 7 is publicly available from gencodegenes.org and via the Ensembl and UCSC Genome Browsers. PMID:22955987

  14. A Machine Learning Based Analytical Framework for Semantic Annotation Requirements

    Directory of Open Access Journals (Sweden)

    Hamed Hassanzadeh

    2011-04-01

    Full Text Available The Semantic Web is an extension of the current web in which information is given well-defined meaning.The perspective of Semantic Web is to promote the quality and intelligence of the current web by changingits contents into machine understandable form. Therefore, semantic level information is one of thecornerstones of the Semantic Web. The process of adding semantic metadata to web resources is calledSemantic Annotation. There are many obstacles against the Semantic Annotation, such as multilinguality,scalability, and issues which are related to diversity and inconsistency in content of different web pages.Due to the wide range of domains and the dynamic environments that the Semantic Annotation systemsmust be performed on, the problem of automating annotation process is one of the significant challenges inthis domain. To overcome this problem, different machine learning approaches such as supervisedlearning, unsupervised learning and more recent ones like, semi-supervised learning and active learninghave been utilized. In this paper we present an inclusive layered classification of Semantic Annotationchallenges and discuss the most important issues in this field. Also, we review and analyze machinelearning applications for solving semantic annotation problems. For this goal, the article tries to closelystudy and categorize related researches for better understanding and to reach a framework that can mapmachine learning techniques into the Semantic Annotation challenges and requirements.

  15. AUTOMATIC ANNOTATION OF QUERY RESULTS FROM DEEP WEB DATABASE

    Directory of Open Access Journals (Sweden)

    Chaitanya Bhosale

    2015-08-01

    Full Text Available In recent years, web database extraction and annotation has received more attention from the database . When search query is submitted to the interface the search result page is generated. Search Result Records (SRRs are the result pages obtained from web database (WDB and these SRRs are used to display the result for each query. Every SRRs contains multiple data units similar to one semantic. These sea rch results can be used in many web applications such as comparison shopping, data integration, metaquerying. But to make these applications successful the search pages are annotated in a meaningful fashion. To reduce human efforts, an automatic annotation approach is used. In which, we first aligns the data units on result records into various groups such that the information in the similar group have same meaning. After this we annotate each and every group in different domains and obtain the final annota tion after aggregating them. In addition, we use New CTVS technique for extraction of QRRs from a query result page, in which we use optional labeling and dynamic tagging for the improvement. Then an annotation wrapper is generated automatically which is u sed for annotation new result records from the same web database

  16. Sulphate, more than a nutrient, protects the microalga Chlamydomonas moewusii from cadmium toxicity

    Energy Technology Data Exchange (ETDEWEB)

    Mera, Roi; Torres, Enrique, E-mail: torres@udc.es; Abalde, Julio

    2014-03-01

    Highlights: • Sulphate effect on cadmium toxicity in the microalga Chlamydomonas moewusii Gerloff. • Cadmium increases the sulphur requirements in Chlamydomonas moewusii. • Kinetic coefficients for sulphate utilization and cadmium effect on them. • Sulphate and cadmium influence on the biosynthesis of low-molecular mass thiols. • Cadmium toxicity reduction by sulphate due to higher biosynthesis of thiols. - Abstract: Sulphur is an essential macroelement that plays important roles in living organisms. The thiol rich sulphur compounds, such as cysteine, γ-Glu–Cys, glutathione and phytochelatins participate in the tolerance mechanisms against cadmium toxicity. Plants, algae, yeasts and most prokaryotes cover their demand for reduced sulphur by reduction of inorganic sulphate. The aim of this study was to investigate, using a bifactorial experimental design, the effect of different sulphate concentrations in the nutrient solution on cadmium toxicity in the freshwater microalga Chlamydomonas moewusii. Cell growth, kinetic parameters of sulphate utilization and intracellular concentrations of low-molecular mass thiol compounds were determined. A mathematical model to describe the growth of this microalga based on the effects of sulphate and cadmium was obtained. An ANOVA revealed an interaction between them, 16% of the effect sizes was explained by this interaction. A higher amount of sulphate in the culture medium allowed a higher cadmium tolerance due to an increase in the thiol compound biosynthesis. The amount of low-molecular mass thiol compounds, mainly phytochelatins, synthesized by this microalga was significantly dependent on the sulphate and cadmium concentrations; the higher phytochelatin content was obtained in cultures with 4 mg Cd/L and 1 mM sulphate. The maximum EC{sub 50} value (based on nominal cadmium concentration) reached for this microalga was 4.46 ± 0.42 mg Cd/L when the sulphate concentration added to the culture medium was also 1 m

  17. Deep Question Answering for protein annotation.

    Science.gov (United States)

    Gobeill, Julien; Gaudinat, Arnaud; Pasche, Emilie; Vishnyakova, Dina; Gaudet, Pascale; Bairoch, Amos; Ruch, Patrick

    2015-01-01

    Biomedical professionals have access to a huge amount of literature, but when they use a search engine, they often have to deal with too many documents to efficiently find the appropriate information in a reasonable time. In this perspective, question-answering (QA) engines are designed to display answers, which were automatically extracted from the retrieved documents. Standard QA engines in literature process a user question, then retrieve relevant documents and finally extract some possible answers out of these documents using various named-entity recognition processes. In our study, we try to answer complex genomics questions, which can be adequately answered only using Gene Ontology (GO) concepts. Such complex answers cannot be found using state-of-the-art dictionary- and redundancy-based QA engines. We compare the effectiveness of two dictionary-based classifiers for extracting correct GO answers from a large set of 100 retrieved abstracts per question. In the same way, we also investigate the power of GOCat, a GO supervised classifier. GOCat exploits the GOA database to propose GO concepts that were annotated by curators for similar abstracts. This approach is called deep QA, as it adds an original classification step, and exploits curated biological data to infer answers, which are not explicitly mentioned in the retrieved documents. We show that for complex answers such as protein functional descriptions, the redundancy phenomenon has a limited effect. Similarly usual dictionary-based approaches are relatively ineffective. In contrast, we demonstrate how existing curated data, beyond information extraction, can be exploited by a supervised classifier, such as GOCat, to massively improve both the quantity and the quality of the answers with a +100% improvement for both recall and precision. Database URL: http://eagl.unige.ch/DeepQA4PA/. PMID:26384372

  18. Enriching a biomedical event corpus with meta-knowledge annotation

    Directory of Open Access Journals (Sweden)

    Thompson Paul

    2011-10-01

    Full Text Available Abstract Background Biomedical papers contain rich information about entities, facts and events of biological relevance. To discover these automatically, we use text mining techniques, which rely on annotated corpora for training. In order to extract protein-protein interactions, genotype-phenotype/gene-disease associations, etc., we rely on event corpora that are annotated with classified, structured representations of important facts and findings contained within text. These provide an important resource for the training of domain-specific information extraction (IE systems, to facilitate semantic-based searching of documents. Correct interpretation of these events is not possible without additional information, e.g., does an event describe a fact, a hypothesis, an experimental result or an analysis of results? How confident is the author about the validity of her analyses? These and other types of information, which we collectively term meta-knowledge, can be derived from the context of the event. Results We have designed an annotation scheme for meta-knowledge enrichment of biomedical event corpora. The scheme is multi-dimensional, in that each event is annotated for 5 different aspects of meta-knowledge that can be derived from the textual context of the event. Textual clues used to determine the values are also annotated. The scheme is intended to be general enough to allow integration with different types of bio-event annotation, whilst being detailed enough to capture important subtleties in the nature of the meta-knowledge expressed in the text. We report here on both the main features of the annotation scheme, as well as its application to the GENIA event corpus (1000 abstracts with 36,858 events. High levels of inter-annotator agreement have been achieved, falling in the range of 0.84-0.93 Kappa. Conclusion By augmenting event annotations with meta-knowledge, more sophisticated IE systems can be trained, which allow interpretative

  19. Membrane-Associated Polypeptides Induced in Chlamydomonas by Limiting CO(2) Concentrations.

    Science.gov (United States)

    Spalding, M H; Jeffrey, M

    1989-01-01

    Chlamydomonas reinhardtii and other unicellular green algae have a high apparent affinity for CO(2), little O(2) inhibition of photosynthesis, and reduced photorespiration. These characteristics result from operation of a CO(2)-concentrating system. The CO(2)-concentrating system involves active inorganic carbon transport and is under environmental control. Cells grown at limiting CO(2) concentrations have inorganic carbon transport activity, but cells grown at 5% CO(2) do not. Four membrane-associated polypeptides (M(r) 19, 21, 35, and 36 kilodaltons) have been identified which either appear or increase in abundance during adaptation to limiting CO(2) concentrations. The appearance of two of the polypeptides occurs over roughly the same time course as the appearance of the CO(2)-concentrating system activity in response to CO(2) limitation. PMID:16666503

  20. Some observations on the carbon dioxide burst in chlorella and chlamydomonas.

    Science.gov (United States)

    Bunt, J S

    1970-02-01

    In the course of mass spectrometer studies with the algae Chlorella and Chlamydomonas, data were obtained which indicate that the CO(2) burst and gulp are sensitive to oxygen. Furthermore, the CO(2) burst was found to be strongly suppressed when wave lengths shorter than 460 nanometers were blocked at intensities adequate to saturate photosynthesis. Under appropriate conditions at 30 degrees , the CO(2) burst was interrupted by a brief CO(2) gulp and the post illumination gulp by a brief burst of CO(2). The post illumination gulp of CO(2) could be induced during illumination by interposition of a filter blocking wave lengths shorter than 460 nanometers. These data are discussed in relation to earlier reports of the phenomenon and briefly as they affect the detection of photorespiration. PMID:16657291

  1. Membrane-associated polypeptides induced in Chlamydomonas by limiting CO sub 2 concentrations

    Energy Technology Data Exchange (ETDEWEB)

    Spalding, M.H.; Jeffrey, M. (Iowa State Univ., Ames (USA))

    1989-01-01

    Chlamydomonas reinhardtii and other unicellular green algae have a high apparent affinity for CO{sub 2}, little O{sub 2} inhibition of photosynthesis, and reduced photorespiration. These characteristics result from operation of a CO{sub 2}-concentrating system. The CO{sub 2}-concentrating system involves active inorganic carbon transport and is under environmental control. Cells grown at limiting CO{sub 2} concentrations have inorganic carbon transport activity, but cells grown at 5% CO{sub 2} do not. Four membrane-associated polypeptides (M{sub r}, 19, 21, 35, and 36 kilodaltons) have been identified which either appear or increase in abundance during adaptation to limiting CO{sub 2} concentrations. The appearance of two of the polypeptides occurs over roughly the same time course as the appearance of the CO{sub 2}-concentrating system activity in response to CO{sub 2} limitation.

  2. Influence of sulphate on the reduction of cadmium toxicity in the microalga Chlamydomonas moewusii.

    Science.gov (United States)

    Mera, Roi; Torres, Enrique; Abalde, Julio

    2016-06-01

    Cadmium is considered as one of the most hazardous metals for living organism and ecosystems. Environmental factors play an important role since they alter the toxicity of metals by varying the bioavailability of these elements for the organisms. The aim of the present study was to investigate, using the freshwater microalga Chlamydomonas moewusii, the existence of an interaction between cadmium and sulphate as a factor that varied the toxicity of this metal. Different cell parameters such as cell growth, content of chlorophylls and biosynthesis of phytochelatins (PCs) were determined. A two-way ANOVA showed that the interaction had a significant effect size of 21% (pcadmium on the growth and on the content of chlorophylls was observed. In addition, the increase of sulphate concentration allowed the biosynthesis of a higher amount of PCs and/or PCs with higher chain length. This higher biosynthesis was responsible for the reduction of the toxic effect of cadmium and explained the interaction. PMID:26963118

  3. A forward genetic approach in Chlamydomonas reinhardtii as a strategy for exploring starch catabolism.

    Directory of Open Access Journals (Sweden)

    Hande Tunçay

    Full Text Available A screen was recently developed to study the mobilization of starch in the unicellular green alga Chlamydomonas reinhardtii. This screen relies on starch synthesis accumulation during nitrogen starvation followed by the supply of nitrogen and the switch to darkness. Hence multiple regulatory networks including those of nutrient starvation, cell cycle control and light to dark transitions are likely to impact the recovery of mutant candidates. In this paper we monitor the specificity of this mutant screen by characterizing the nature of the genes disrupted in the selected mutants. We show that one third of the mutants consisted of strains mutated in genes previously reported to be of paramount importance in starch catabolism such as those encoding β-amylases, the maltose export protein, and branching enzyme I. The other mutants were defective for previously uncharacterized functions some of which are likely to define novel proteins affecting starch mobilization in green algae.

  4. Measurement of swimming force generation during flagella regeneration in Chlamydomonas reinhardtii

    Science.gov (United States)

    Yukich, John N.; Shaban, Mona; Clodfelter, Catherine; Bernd, Karen

    2007-11-01

    The green alga Chlamydomonas reinhardtii has been at the forefront of many studies investigating the establishment and function of flagella in facilitating cellular motility. Previously we reported an intriguing pattern during flagella regeneration in which increases in force do not always correspond with increase in flagella length. That work made direct measurement of maximum flagellar swimming force by measuring the cell's ability to escape from an optical trap (optical tweezers). Here, we report on optimization and automation of the force measurement using power spectral density calibration of the trap and distance of periodic displacement from the trap center. This process yields an average value for the swimming force. The intriguing pattern described for maximum swimming force is also evident in the average swimming force data, suggesting that the phenomenon reflects a change in flagella functionality during regeneration.

  5. Effect of Temperature and light intensity on growth and Photosynthetic Activity of Chlamydomonas reinhard II

    International Nuclear Information System (INIS)

    The effect of five temperatures (15,20,25,30 and 35 degree centigree) and two levels of illumination on growth and photosynthetic activity of Chlamydomonas reinhard II has been studied. The growth of the cultures was evaluated by optical density. Photosynthetic activity has been carried out studying either the assimilation rate of C02 labelled with C-14 or the oxygen evolution by means of polarographic measurements. The maximum photosynthetic rate has been obtained at 25 degree centigree for the lower level of illumination (2400 lux) and at 35 degree centigree for the higher one (13200 lux) and at 35 degree centigree for the higher ono (13200 lux). These results suggest an interaction of temperature and illumination on photosynthetic activity. (Author) 37 refs

  6. A chloroplast pathway for the de novo biosynthesis of triacylglycerol in Chlamydomonas reinhardtii

    Energy Technology Data Exchange (ETDEWEB)

    Fan, J.; Xu, C.; Andre, C.

    2011-06-23

    Neutral lipid metabolism has been extensively studied in yeast, plants and mammals. In contrast, little information is available regarding the biochemical pathway, enzymes and regulatory factors involved in the biosynthesis of triacylglycerol (TAG) in microalgae. In the conventional TAG biosynthetic pathway widely accepted for yeast, plants and mammals, TAG is assembled in the endoplasmic reticulum (ER) from its immediate precursor diacylglycerol (DAG) made by ER-specific acyltransferases, and is deposited exclusively in lipid droplets in the cytosol. Here, we demonstrated that the unicellular microalga Chlamydomonas reinhardtii employs a distinct pathway that uses DAG derived almost exclusively from the chloroplast to produce TAG. This unique TAG biosynthesis pathway is largely dependent on de novo fatty acid synthesis, and the TAG formed in this pathway is stored in lipid droplets in both the chloroplast and the cytosol. These findings have wide implications for understanding TAG biosynthesis and storage and other areas of lipid metabolism in microalgae and other organisms.

  7. Efficient expression of green fluorescent protein (GFP) mediated by a chimeric promoter in Chlamydomonas reinhardtii

    Science.gov (United States)

    Wu, Jinxia; Hu, Zhangli; Wang, Chaogang; Li, Shuangfei; Lei, Anping

    2008-08-01

    To improve the expression efficiency of exogenous genes in Chlamydomonas reinhardtii, a high efficient expression vector was constructed. Green fluorescent protein (GFP) was expressed in C. reinhardtii under the control of promoters: RBCS2 and HSP70A-RBCS2. Efficiency of transformation and expression were compared between two transgenic algae: RBCS2 mediated strain Tran-I and HSP70A-RBCS2 mediated strain Tran-II. Results show that HSP70A-RBCS2 could improve greatly the transformation efficiency by approximately eightfold of RBCS2, and the expression efficiency of GFP in Tran-II was at least double of that in Tran-I. In addition, a threefold increase of GFP in Tran-II was induced by heat shock at 40°C. All of the results demonstrated that HSP70A-RBCS2 was more efficient than RBCS2 in expressing exogenous gene in C. reinhardtii.

  8. ATP Production in Chlamydomonas reinhardtii Flagella by Glycolytic Enzymes

    DEFF Research Database (Denmark)

    Mitchell, Beth F; Pedersen, Lotte B; Feely, Michael;

    2005-01-01

    Eukaryotic cilia and flagella are long, thin organelles, and diffusion from the cytoplasm may not be able to support the high ATP concentrations needed for dynein motor activity. We discovered enzyme activities in the Chlamydomonas reinhardtii flagellum that catalyze three steps of the lower half...... of glycolysis (phosphoglycerate mutase, enolase, and pyruvate kinase). These enzymes can generate one ATP molecule for every substrate molecule consumed. Flagellar fractionation shows that enolase is at least partially associated with the axoneme, whereas phosphoglycerate mutase and pyruvate kinase...... primarily reside in the detergent-soluble (membrane + matrix) compartments. We further show that axonemal enolase is a subunit of the CPC1 central pair complex and that reduced flagellar enolase levels in the cpc1 mutant correlate with the reduced flagellar ATP concentrations and reduced in vivo beat...

  9. Investigating the link between fermentative metabolism and hydrogen production in the unicellular green alga Chlamydomonas reinhardtii

    Energy Technology Data Exchange (ETDEWEB)

    Burgess, S.J.; Nixon, P.J. [Imperial College London (United Kingdom)

    2010-07-01

    In the model green alga Chlamydomonas reinhardtii, the electrons required for hydrogen production can come from both the biophotolysis of water and from the fermentation of carbohydrate reserves. Anoxia leads to the activation of several fermentative pathways, which produce a number of end products including formic, malic and acetic acid along with ethanol, carbon dioxide and hydrogen. It has been proposed that by switching off competing fermentative pathways hydrogen production can be increased. Therefore the aim of this study was to devise an experimental strategy to down-regulate the expression of enzymes thought to control C. reinhardtii's fermentative metabolism. We demonstrate here that it is possible to use artificial microRNA (amiRNA) technology to generate knock-down mutants with reduced expression of pyruvate formate lyase (PFL1), a key fermentative enzyme in C. reinhardtii. This work opens up new possibilities to improve hydrogen yields through metabolic engineering. (orig.)

  10. Structural Insight into the Complex of Ferredoxin and [FeFe] Hydrogenase from Chlamydomonas reinhardtii.

    Science.gov (United States)

    Rumpel, Sigrun; Siebel, Judith F; Diallo, Mamou; Farès, Christophe; Reijerse, Edward J; Lubitz, Wolfgang

    2015-07-27

    The transfer of photosynthetic electrons by the ferredoxin PetF to the [FeFe] hydrogenase HydA1 in the microalga Chlamydomonas reinhardtii is a key step in hydrogen production. Electron delivery requires a specific interaction between PetF and HydA1. However, because of the transient nature of the electron-transfer complex, a crystal structure remains elusive. Therefore, we performed protein-protein docking based on new experimental data from a solution NMR spectroscopy investigation of native and gallium-substituted PetF. This provides valuable information about residues crucial for complex formation and electron transfer. The derived complex model might help to pinpoint residue substitution targets for improved hydrogen production. PMID:26010059

  11. Brownian dynamics and molecular dynamics study of the association between hydrogenase and ferredoxin from Chlamydomonas reinhardtii.

    Science.gov (United States)

    Long, Hai; Chang, Christopher H; King, Paul W; Ghirardi, Maria L; Kim, Kwiseon

    2008-10-01

    The [FeFe] hydrogenase from the green alga Chlamydomonas reinhardtii can catalyze the reduction of protons to hydrogen gas using electrons supplied from photosystem I and transferred via ferredoxin. To better understand the association of the hydrogenase and the ferredoxin, we have simulated the process over multiple timescales. A Brownian dynamics simulation method gave an initial thorough sampling of the rigid-body translational and rotational phase spaces, and the resulting trajectories were used to compute the occupancy and free-energy landscapes. Several important hydrogenase-ferredoxin encounter complexes were identified from this analysis, which were then individually simulated using atomistic molecular dynamics to provide more details of the hydrogenase and ferredoxin interaction. The ferredoxin appeared to form reasonable complexes with the hydrogenase in multiple orientations, some of which were good candidates for inclusion in a transition state ensemble of configurations for electron transfer. PMID:18621810

  12. Dynamic curvature regulation accounts for the symmetric and asymmetric beats of Chlamydomonas flagella

    CERN Document Server

    Sartori, Pablo; Scholich, Andre; Jülicher, Frank; Howard, Jonathon

    2015-01-01

    Axonemal dyneins are the molecular motors responsible for the beating of cilia and flagella. These motors generate sliding forces between adjacent microtubule doublets within the axoneme, the motile cytoskeletal structure inside the flagellum. To create regular, oscillatory beating patterns, the activities of the axonemal dyneins must be coordinated both spatially and temporally. It is thought that coordination is mediated by stresses or strains that build up within the moving axoneme, but it is not known which components of stress or strain are involved, nor how they feed back on the dyneins. To answer this question, we used isolated, reactivate axonemes of the unicellular alga Chlamydomonas as a model system. We derived a theory for beat regulation in a two-dimensional model of the axoneme. We then tested the theory by measuring the beat waveforms of wild type axonemes, which have asymmetric beats, and mutant axonemes, in which the beat is nearly symmetric, using high-precision spatial and temporal imaging....

  13. Recombinant Reconstitution and Purification of the IFT-B Core Complex from Chlamydomonas reinhardtii.

    Science.gov (United States)

    Taschner, Michael; Lorentzen, Esben

    2016-01-01

    Eukaryotic cilia and flagella are assembled and maintained by intraflagellar transport (IFT), the bidirectional transport of proteins between the ciliary base and tip. IFT is mediated by the multi-subunit IFT complex, which simultaneously binds cargo proteins and the ciliary motors. So far 22 subunits of the IFT complex have been identified, but insights into the biochemical architecture and especially the three-dimensional structure of this machinery are only starting to emerge because of difficulties in obtaining homogeneous material suitable for structural analysis. Here, we describe a protocol for the purification and reconstitution of a complex containing nine Chlamydomonas reinhardtii IFT proteins, commonly known as the IFT-B core complex. In our hands, this protocol routinely yields several milligrams of pure complex suitable for structural analysis by X-ray crystallography and single-particle cryo-electron microscopy. PMID:27514916

  14. DNA-free two-gene knockout in Chlamydomonas reinhardtii via CRISPR-Cas9 ribonucleoproteins.

    Science.gov (United States)

    Baek, Kwangryul; Kim, Duk Hyoung; Jeong, Jooyeon; Sim, Sang Jun; Melis, Anastasios; Kim, Jin-Soo; Jin, EonSeon; Bae, Sangsu

    2016-01-01

    Microalgae are versatile organisms capable of converting CO2, H2O, and sunlight into fuel and chemicals for domestic and industrial consumption. Thus, genetic modifications of microalgae for enhancing photosynthetic productivity, and biomass and bio-products generation are crucial for both academic and industrial applications. However, targeted mutagenesis in microalgae with CRISPR-Cas9 is limited. Here we report, a one-step transformation of Chlamydomonas reinhardtii by the DNA-free CRISPR-Cas9 method rather than plasmids that encode Cas9 and guide RNAs. Outcome was the sequential CpFTSY and ZEP two-gene knockout and the generation of a strain constitutively producing zeaxanthin and showing improved photosynthetic productivity. PMID:27466170

  15. Trichloroacetate affects the EPR SignalⅡslow and SignalⅠin the thylakoid of Chlamydomonas reinhardtii

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    One electron paramagnetic resonance (EPR) signal, named SignalⅡslow, originates from the oxidized Tyrosine 160 (YDo) of D2 polypeptide of photosystemⅡ reaction center. After adding high concentration trichloroacetate (TCA) to the Chlamydomonas reinhardtii thylakoid suspension, this signal was abolished in a minute. Treatment of TCA also removes a few of polypeptides, including three extrinsic polypeptides of oxygen-evolving complex, from the thylakoid membrane. Based upon the analysis of the microenvironment around YD with a three-dimensional model, it is indicated that relatively high hydrophobicity of this microenvironment may be the essential prerequisite for TCA to affect YD. It has been observed that TCA treatment also retards the decay of the SignalⅠ, produced by the oxidized reaction center chlorophyll dimer (P700+) of photosys- temⅠ.

  16. Identification and Characterization of a cis-Regulatory Element for Zygotic Gene Expression in Chlamydomonas reinhardtii.

    Science.gov (United States)

    Hamaji, Takashi; Lopez, David; Pellegrini, Matteo; Umen, James

    2016-01-01

    Upon fertilization Chlamydomonas reinhardtii zygotes undergo a program of differentiation into a diploid zygospore that is accompanied by transcription of hundreds of zygote-specific genes. We identified a distinct sequence motif we term a zygotic response element (ZYRE) that is highly enriched in promoter regions of C reinhardtii early zygotic genes. A luciferase reporter assay was used to show that native ZYRE motifs within the promoter of zygotic gene ZYS3 or intron of zygotic gene DMT4 are necessary for zygotic induction. A synthetic luciferase reporter with a minimal promoter was used to show that ZYRE motifs introduced upstream are sufficient to confer zygotic upregulation, and that ZYRE-controlled zygotic transcription is dependent on the homeodomain transcription factor GSP1. We predict that ZYRE motifs will correspond to binding sites for the homeodomain proteins GSP1-GSM1 that heterodimerize and activate zygotic gene expression in early zygotes. PMID:27172209

  17. Cell types and their status in Chlamydomonas-like algae (Chlorophyceae on agar medium culture

    Directory of Open Access Journals (Sweden)

    M.М. Pavlovska

    2014-04-01

    Full Text Available The classification of cell types under agar culture was proposed. Six cell morphotypes were allocated. The statuses were identified depending on the reduction of monade attributes of cells. The variants of transition from one cell morphotype to another under dissolving mucilage were shown. The monade, cocciod, palmeloid and gloeocysta morphotypes approximately equally represented in all clades. The asterococcus and mucogleocysta morphotypes presented only in Reinhardtinia аnd Oogamochlamydinia clades. Any morphotype isn’t typical for all clades of Chlamydomonas-like algae at once. The most of morphotypes numbers (5 from 6 are presented in Reinhardtinia clade. This demonstrates the diversity of the Reinhardtinia clade species. There are only one morphotype presented in Polytominia and Monadinia clades. There are four morphotypes presented in Oogamochlamydinia clade, three – in Moewusinia, two morphotypes – in Chloromonadinia.

  18. Growth of the green algae Chlamydomonas reinhardtii under red and blue lasers

    Science.gov (United States)

    Kuwahara, Sara S.; Cuello, Joel L.; Myhre, Graham; Pau, Stanley

    2011-03-01

    Red and blue lasers, holding promise as an electric light source for photosynthetic systems on account of being true monochromatic, high-power, and having high electrical-conversion efficiency, were employed in growing a green alga, Chlamydomonas reinhardtii. The laser treatments tested included: 655-nm Red; 680-nm Red; 655-nm Red+474-nm Blue and 680-nm Red+474-nm Blue. A white cold cathode lamp with spectral output similar to that of white fluorescent lamp served as control. C. reinhardtii successfully grew and divided under the 655 and 680-nm red lasers as well as under the white-light control. Supplementing either red with blue laser, however, resulted in increased algae cell count that significantly exceeded those under both red lasers and the white-light control on average by 241%.

  19. Efficient expression of green fluorescent protein (GFP) mediated by a chimeric promoter in Chlamydomonas reinhardtii

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    To improve the expression efficiency of exogenous genes in Chlamydomonas reinhardtii, a high efficient expression vector was constructed. Green fluorescent protein (GFP) was expressed in C. Reinhardtii under the control of promoters: RBCS2 and HSP70A-RBCS2. Efficiency of transformation and expression were compared between two transgenic algae: RBCS2 mediated strain Tran-I and HSP70A-RBCS2 mediated strain Tran-II. Results show that HSP70A-RBCS2 could improve greatly the transformation efficiency by approximately eightfold of RBCS2, and the expression efficiency of GFP in Tran-II was at least double of that in Tran-I. In addition, a threefold increase of GFP in Tran-II was induced by heat shock at 40°C. All of the results demonstrated that HSP70A-RBCS2 was more efficient than RBCS2 in expressing exogenous gene in C. Reinhardtii.

  20. Successful expression of heterologous egfp gene in the mitochondria of a photosynthetic eukaryote Chlamydomonas reinhardtii.

    Science.gov (United States)

    Hu, Zhangli; Zhao, Zhonglin; Wu, Zhihua; Fan, Zhun; Chen, Jun; Wu, Jinxia; Li, Jiancheng

    2011-09-01

    The efficient expression of exogenous gene in mitochondria of photosynthetic organism has been an insurmountable problem. In this study, the pBsLPNCG was constructed by inserting the egfp gene into a site between TERMINVREP-Left repeats and the cob gene in a fragment of mitochondrial DNA of Chlamydomonas reinhardtii CC-124 and introduced into the mitochondria of respiratory deficient dum-1 mutation of C. reinhardtii CC-2654. Sequencing and DNA Southern analyses revealed that egfp gene had been integrated into the mitochondrial genome of transgenic algae as expected and no other copy of egfp existed in their nucleic genome. Both the fluorescence detection and Western blot analysis confirmed the presence of eGFP protein in the transgenic algae; it indicated that the egfp gene was successfully expressed in the mitochondria of C. reinhardtii. PMID:21664493

  1. DNA-free two-gene knockout in Chlamydomonas reinhardtii via CRISPR-Cas9 ribonucleoproteins

    Science.gov (United States)

    Baek, Kwangryul; Kim, Duk Hyoung; Jeong, Jooyeon; Sim, Sang Jun; Melis, Anastasios; Kim, Jin-Soo; Jin, EonSeon; Bae, Sangsu

    2016-01-01

    Microalgae are versatile organisms capable of converting CO2, H2O, and sunlight into fuel and chemicals for domestic and industrial consumption. Thus, genetic modifications of microalgae for enhancing photosynthetic productivity, and biomass and bio-products generation are crucial for both academic and industrial applications. However, targeted mutagenesis in microalgae with CRISPR-Cas9 is limited. Here we report, a one-step transformation of Chlamydomonas reinhardtii by the DNA-free CRISPR-Cas9 method rather than plasmids that encode Cas9 and guide RNAs. Outcome was the sequential CpFTSY and ZEP two-gene knockout and the generation of a strain constitutively producing zeaxanthin and showing improved photosynthetic productivity. PMID:27466170

  2. Inhomogeneous distribution of Chlamydomonas in a cylindrical container with a bubble plume

    Directory of Open Access Journals (Sweden)

    Yuki Nonaka

    2016-02-01

    Full Text Available Swimming microalgae show various taxes, such as phototaxis and gravitaxis, which sometimes result in the formation of a cell-rich layer or a patch in a suspension. Despite intensive studies on the effects of shear flow and turbulence on the inhomogeneous distribution of microalgae, the effect of a bubble plume has remained unclear. In this study, we used Chlamydomonas as model microalgae, and investigated the spatial distribution of cells in a cylindrical container with a bubble plume. The results illustrate that cells become inhomogeneously distributed in the suspension due to their motility and photo-responses. A vortical ring distribution was observed below the free surface when the bubble flow rate was sufficiently small. We performed a scaling analysis on the length scale of the vortical ring, which captured the main features of the experimental results. These findings are important in understanding transport phenomena in a microalgae suspension with a bubble plume.

  3. Inhomogeneous distribution of Chlamydomonas in a cylindrical container with a bubble plume

    Science.gov (United States)

    Nonaka, Yuki; Kikuchi, Kenji; Numayama-Tsuruta, Keiko; Kage, Azusa; Ueno, Hironori; Ishikawa, Takuji

    2016-01-01

    ABSTRACT Swimming microalgae show various taxes, such as phototaxis and gravitaxis, which sometimes result in the formation of a cell-rich layer or a patch in a suspension. Despite intensive studies on the effects of shear flow and turbulence on the inhomogeneous distribution of microalgae, the effect of a bubble plume has remained unclear. In this study, we used Chlamydomonas as model microalgae, and investigated the spatial distribution of cells in a cylindrical container with a bubble plume. The results illustrate that cells become inhomogeneously distributed in the suspension due to their motility and photo-responses. A vortical ring distribution was observed below the free surface when the bubble flow rate was sufficiently small. We performed a scaling analysis on the length scale of the vortical ring, which captured the main features of the experimental results. These findings are important in understanding transport phenomena in a microalgae suspension with a bubble plume. PMID:26787679

  4. Critical role of Chlamydomonas reinhardtii ferredoxin-5 in maintaining membrane structure and dark metabolism.

    Science.gov (United States)

    Yang, Wenqiang; Wittkopp, Tyler M; Li, Xiaobo; Warakanont, Jaruswan; Dubini, Alexandra; Catalanotti, Claudia; Kim, Rick G; Nowack, Eva C M; Mackinder, Luke C M; Aksoy, Munevver; Page, Mark Dudley; D'Adamo, Sarah; Saroussi, Shai; Heinnickel, Mark; Johnson, Xenie; Richaud, Pierre; Alric, Jean; Boehm, Marko; Jonikas, Martin C; Benning, Christoph; Merchant, Sabeeha S; Posewitz, Matthew C; Grossman, Arthur R

    2015-12-01

    Photosynthetic microorganisms typically have multiple isoforms of the electron transfer protein ferredoxin, although we know little about their exact functions. Surprisingly, a Chlamydomonas reinhardtii mutant null for the ferredoxin-5 gene (FDX5) completely ceased growth in the dark, with both photosynthetic and respiratory functions severely compromised; growth in the light was unaffected. Thylakoid membranes in dark-maintained fdx5 mutant cells became severely disorganized concomitant with a marked decrease in the ratio of monogalactosyldiacylglycerol to digalactosyldiacylglycerol, major lipids in photosynthetic membranes, and the accumulation of triacylglycerol. Furthermore, FDX5 was shown to physically interact with the fatty acid desaturases CrΔ4FAD and CrFAD6, likely donating electrons for the desaturation of fatty acids that stabilize monogalactosyldiacylglycerol. Our results suggest that in photosynthetic organisms, specific redox reactions sustain dark metabolism, with little impact on daytime growth, likely reflecting the tailoring of electron carriers to unique intracellular metabolic circuits under these two very distinct redox conditions. PMID:26627249

  5. Separate origins of ice-binding proteins in antarctic chlamydomonas species.

    Directory of Open Access Journals (Sweden)

    James A Raymond

    Full Text Available The green alga Chlamydomonas raudensis is an important primary producer in a number of ice-covered lakes and ponds in Antarctica. A C. raudensis isolate (UWO241 from Lake Bonney in the McMurdo Dry Valleys, like many other Antarctic algae, was found to secrete ice-binding proteins (IBPs, which appear to be essential for survival in icy environments. The IBPs of several Antarctic algae (diatoms, a prymesiophyte, and a prasinophyte are similar to each other (here designated as type I IBPs and have been proposed to have bacterial origins. Other IBPs (type II IBPs that bear no resemblance to type I IBPs, have been found in the Antarctic Chlamydomonas sp. CCMP681, a putative snow alga, raising the possibility that chlamydomonad IBPs developed separately from the IBPs of other algae. To test this idea, we obtained the IBP sequences of C. raudensis UWO241 by sequencing the transcriptome. A large number of transcripts revealed no sequences resembling type II IBPs. Instead, many isoforms resembling type I IBPs were found, and these most closely matched a hypothetical protein from the bacterium Stigmatella aurantiaca. The sequences were confirmed to encode IBPs by the activity of a recombinant protein and by the matching of predicted and observed isoelectric points and molecular weights. Furthermore, a mesophilic sister species, C. raudensis SAG49.72, showed no ice-binding activity or PCR products from UWO241 IBP primers. These results confirm that algal IBPs are required for survival in icy habitats and demonstrate that they have diverse origins that are unrelated to the taxonomic positions of the algae. Last, we show that the C. raudensis UWO241 IBPs can change the structure of ice in a way that could increase the survivability of cells trapped in the ice.

  6. Separate origins of ice-binding proteins in antarctic chlamydomonas species.

    Science.gov (United States)

    Raymond, James A; Morgan-Kiss, Rachael

    2013-01-01

    The green alga Chlamydomonas raudensis is an important primary producer in a number of ice-covered lakes and ponds in Antarctica. A C. raudensis isolate (UWO241) from Lake Bonney in the McMurdo Dry Valleys, like many other Antarctic algae, was found to secrete ice-binding proteins (IBPs), which appear to be essential for survival in icy environments. The IBPs of several Antarctic algae (diatoms, a prymesiophyte, and a prasinophyte) are similar to each other (here designated as type I IBPs) and have been proposed to have bacterial origins. Other IBPs (type II IBPs) that bear no resemblance to type I IBPs, have been found in the Antarctic Chlamydomonas sp. CCMP681, a putative snow alga, raising the possibility that chlamydomonad IBPs developed separately from the IBPs of other algae. To test this idea, we obtained the IBP sequences of C. raudensis UWO241 by sequencing the transcriptome. A large number of transcripts revealed no sequences resembling type II IBPs. Instead, many isoforms resembling type I IBPs were found, and these most closely matched a hypothetical protein from the bacterium Stigmatella aurantiaca. The sequences were confirmed to encode IBPs by the activity of a recombinant protein and by the matching of predicted and observed isoelectric points and molecular weights. Furthermore, a mesophilic sister species, C. raudensis SAG49.72, showed no ice-binding activity or PCR products from UWO241 IBP primers. These results confirm that algal IBPs are required for survival in icy habitats and demonstrate that they have diverse origins that are unrelated to the taxonomic positions of the algae. Last, we show that the C. raudensis UWO241 IBPs can change the structure of ice in a way that could increase the survivability of cells trapped in the ice. PMID:23536869

  7. O(2) uptake in the light in chlamydomonas: evidence for persistent mitochondrial respiration.

    Science.gov (United States)

    Peltier, G; Thibault, P

    1985-09-01

    The nature of the process responsible for the stationary O(2) uptake occurring in the light under saturating CO(2) concentration in Chlamydomonas reinhardii has been investigated. For this purpose, a mass spectrometer with a membrane inlet system was used to measure O(2) uptake and evolution in the algal suspension. First, we observed that the O(2) uptake rate was constant (about 0.5 micromoles of O(2) per milligram chlorophyll per minute) during a light to dark transition and was not affected by 3-(3,4-dichlorophenyl)-1,1-dimethylurea. Salicylhydroxamic acid had no effect on O(2) uptake in the dark or in the light, but was found to have the same inhibitory effect either in the dark or in the light when added to cyanide-treated algae. The stimulation of the O(2) uptake rate due to the uncoupling effect of carbonyl cyanide m-chlorophenylhydrazone was about the same in the dark or in the light. From these results, we conclude that mitochondrial respiration is maintained during illumination and therefore is not inhibited by high ATP levels. Another conclusion is that in conditions where photorespiration is absent, no other light-dependent O(2) uptake process occurs. If Mehler reactions are involved, in Chlamydomonas, under conditions where both photosynthetic carbon oxidation and reduction cycles cannot operate (as in cyanide-treated algae), their occurrence in photosynthesizing algae either under saturating CO(2) concentration or at the CO(2) compensation point appears very unlikely. The comparison with the situation previously reported in Scenedesmus (R. J. Radmer and B. Kok 1976 Plant Physiol 58: 336-340) suggests that different O(2) uptake processes might be present in these two algal species. PMID:16664375

  8. A Chlamydomonas-derived Human Papillomavirus 16 E7 vaccine induces specific tumor protection.

    Directory of Open Access Journals (Sweden)

    Olivia C Demurtas

    Full Text Available BACKGROUND: The E7 protein of the Human Papillomavirus (HPV type 16, being involved in malignant cellular transformation, represents a key antigen for developing therapeutic vaccines against HPV-related lesions and cancers. Recombinant production of this vaccine antigen in an active form and in compliance with good manufacturing practices (GMP plays a crucial role for developing effective vaccines. E7-based therapeutic vaccines produced in plants have been shown to be active in tumor regression and protection in pre-clinical models. However, some drawbacks of in whole-plant vaccine production encouraged us to explore the production of the E7-based therapeutic vaccine in Chlamydomonas reinhardtii, an organism easy to grow and transform and fully amenable to GMP guidelines. METHODOLOGY/PRINCIPAL FINDINGS: An expression cassette encoding E7GGG, a mutated, attenuated form of the E7 oncoprotein, alone or as a fusion with affinity tags (His6 or FLAG, under the control of the C. reinhardtii chloroplast psbD 5' UTR and the psbA 3' UTR, was introduced into the C. reinhardtii chloroplast genome by homologous recombination. The protein was mostly soluble and reached 0.12% of total soluble proteins. Affinity purification was optimized and performed for both tagged forms. Induction of specific anti-E7 IgGs and E7-specific T-cell proliferation were detected in C57BL/6 mice vaccinated with total Chlamydomonas extract and with affinity-purified protein. High levels of tumor protection were achieved after challenge with a tumor cell line expressing the E7 protein. CONCLUSIONS: The C. reinhardtii chloroplast is a suitable expression system for the production of the E7GGG protein, in a soluble, immunogenic form. The production in contained and sterile conditions highlights the potential of microalgae as alternative platforms for the production of vaccines for human uses.

  9. A comparison of hydrogen photoproduction by sulfur-deprived Chlamydomonas reinhardtii under different growth conditions.

    Science.gov (United States)

    Kosourov, Sergey; Patrusheva, Elena; Ghirardi, Maria L; Seibert, Michael; Tsygankov, Anatoly

    2007-03-10

    Continuous photoproduction of H(2) by the green alga, Chlamydomonas reinhardtii, is observed after incubating the cultures for about a day in the absence of sulfate and in the presence of acetate. Sulfur deprivation causes the partial and reversible inactivation of photosynthetic O(2) evolution in algae, resulting in the light-induced establishment of anaerobic conditions in sealed photobioreactors, expression of two [FeFe]-hydrogenases in the cells, and H(2) photoproduction for several days. We have previously demonstrated that sulfur-deprived algal cultures can produce H(2) gas in the absence of acetate, when appropriate experimental protocols were used (Tsygankov, A.A., Kosourov, S.N., Tolstygina, I.V., Ghirardi, M.L., Seibert, M., 2006. Hydrogen production by sulfur-deprived Chlamydomonas reinhardtii under photoautotrophic conditions. Int. J. Hydrogen Energy 31, 1574-1584). We now report the use of an automated photobioreactor system to compare the effects of photoautotrophic, photoheterotrophic and photomixotrophic growth conditions on the kinetic parameters associated with the adaptation of the algal cells to sulfur deprivation and H(2) photoproduction. This was done under the experimental conditions outlined in the above reference, including controlled pH. From this comparison we show that both acetate and CO(2) are required for the most rapid inactivation of photosystem II and the highest yield of H(2) gas production. Although, the presence of acetate in the system is not critical for the process, H(2) photoproduction under photoautotrophic conditions can be increased by optimizing the conditions for high starch accumulation. These results suggest ways of engineering algae to improve H(2) production, which in turn may have a positive impact on the economics of applied systems for H(2) production. PMID:17275940

  10. Photo-oxidative stress in a xanthophyll-deficient mutant of Chlamydomonas.

    Science.gov (United States)

    Baroli, Irene; Gutman, Benjamin L; Ledford, Heidi K; Shin, Jai W; Chin, Brian L; Havaux, Michel; Niyogi, Krishna K

    2004-02-20

    When there is an imbalance between the light energy absorbed by a photosynthetic organism and that which can be utilized in photosynthesis, photo-oxidative stress can damage pigments, proteins, lipids, and nucleic acids. In this work we compared the wild type and a xanthophyll-deficient mutant of Chlamydomonas reinhardtii in their response to high amounts of light. Wild-type Chlamydomonas cells were able to acclimate to high amounts of light following transfer from low light conditions. In contrast, the npq1 lor1 double mutant, which lacks protective xanthophylls (zeaxanthin and lutein) in the chloroplast, progressively lost viability and photosynthetic capacity along with destruction of thylakoid membrane protein-pigment complexes and accumulation of reactive oxygen species and membrane lipid peroxides. Loss of viability was partially rescued by lowered oxygen tension, suggesting that the high sensitivity of the mutant to light stress is caused by the production of reactive oxygen species in the chloroplast. Cell death was not prevented by the addition of an organic carbon source to the growth medium, demonstrating that the photo-oxidative damage can target other essential chloroplast processes besides photosynthesis. From the differential sensitivity of the mutant to exogenously added pro-oxidants, we infer that the reactive oxygen species produced during light stress in npq1 lor1 may be singlet oxygen and/or superoxide but not hydrogen peroxide. The bleaching phenotype of npq1 lor1 was not due to enhanced photodamage to photosystem II but rather to a less localized phenomenon of accumulation of photo-oxidation products in chloroplast membranes. PMID:14665619

  11. Survival and proliferation characteristics of the microalga Chlamydomonas sp. ICE-L after hypergravitational stress pretreatment

    Science.gov (United States)

    Gao, Zhengquan; Li, Demao; Meng, Chunxiao; Xu, Dong; Zhang, Xiaowen; Ye, Naihao

    2013-09-01

    Seeking extraterrestrial life, transferring between planets, even migrating to other planets attracts more and more attention of public and scientists. However, to make it clear for the ability to survive the forces studies is prerequisite to enable the speculations by natural means. Gravity is a critical force involved in all the life on Earth and, possibly, others planets. Organisms have been grown in microgravity habitats and in centrifuges to characterize the biological response to a range of gravitational forces and radiation levels in space and on Earth. However, little is known about the profiles of eukaryotic life under conditions of hyperacceleration attributable to extreme gravities. In this study, a eukaryotic extremophile, the Antarctic green microalga Chlamydomonas sp. ICE-L, showed amazing proliferation capacity during and after hypergravitational stress for 30 min to 48 h at 110,200, 423,400, and 670,800g. These extreme gravities also had profound effects on viability, reproduction rate, photosynthesis efficiency, and gene transcriptional expression of this microalga. Most notably, all three supergravities efficiently stimulated algal cell division, but the greater the centrifugal force and the longer the duration of treatment, the lower the viable rate and breeding potential of samples in the following incubation. These results illustrated Chlamydomonas sp. ICE-L is a useful eukaryotic model system candidate for space research. Further studies could provide new insight into the physical limits of life and its evolution and enhance the possibility for interstellar space travel and the quest for extraterrestrial life according to panspermia theory. Also, it indicated that life come from the outer space is not always prokaryotes but may be eukaryotes.

  12. Construction of an annotated corpus to support biomedical information extraction

    Directory of Open Access Journals (Sweden)

    McNaught John

    2009-10-01

    Full Text Available Abstract Background Information Extraction (IE is a component of text mining that facilitates knowledge discovery by automatically locating instances of interesting biomedical events from huge document collections. As events are usually centred on verbs and nominalised verbs, understanding the syntactic and semantic behaviour of these words is highly important. Corpora annotated with information concerning this behaviour can constitute a valuable resource in the training of IE components and resources. Results We have defined a new scheme for annotating sentence-bound gene regulation events, centred on both verbs and nominalised verbs. For each event instance, all participants (arguments in the same sentence are identified and assigned a semantic role from a rich set of 13 roles tailored to biomedical research articles, together with a biological concept type linked to the Gene Regulation Ontology. To our knowledge, our scheme is unique within the biomedical field in terms of the range of event arguments identified. Using the scheme, we have created the Gene Regulation Event Corpus (GREC, consisting of 240 MEDLINE abstracts, in which events relating to gene regulation and expression have been annotated by biologists. A novel method of evaluating various different facets of the annotation task showed that average inter-annotator agreement rates fall within the range of 66% - 90%. Conclusion The GREC is a unique resource within the biomedical field, in that it annotates not only core relationships between entities, but also a range of other important details about these relationships, e.g., location, temporal, manner and environmental conditions. As such, it is specifically designed to support bio-specific tool and resource development. It has already been used to acquire semantic frames for inclusion within the BioLexicon (a lexical, terminological resource to aid biomedical text mining. Initial experiments have also shown that the corpus may

  13. ASAP: Amplification, sequencing & annotation of plastomes

    Directory of Open Access Journals (Sweden)

    Folta Kevin M

    2005-12-01

    Full Text Available Abstract Background Availability of DNA sequence information is vital for pursuing structural, functional and comparative genomics studies in plastids. Traditionally, the first step in mining the valuable information within a chloroplast genome requires sequencing a chloroplast plasmid library or BAC clones. These activities involve complicated preparatory procedures like chloroplast DNA isolation or identification of the appropriate BAC clones to be sequenced. Rolling circle amplification (RCA is being used currently to amplify the chloroplast genome from purified chloroplast DNA and the resulting products are sheared and cloned prior to sequencing. Herein we present a universal high-throughput, rapid PCR-based technique to amplify, sequence and assemble plastid genome sequence from diverse species in a short time and at reasonable cost from total plant DNA, using the large inverted repeat region from strawberry and peach as proof of concept. The method exploits the highly conserved coding regions or intergenic regions of plastid genes. Using an informatics approach, chloroplast DNA sequence information from 5 available eudicot plastomes was aligned to identify the most conserved regions. Cognate primer pairs were then designed to generate ~1 – 1.2 kb overlapping amplicons from the inverted repeat region in 14 diverse genera. Results 100% coverage of the inverted repeat region was obtained from Arabidopsis, tobacco, orange, strawberry, peach, lettuce, tomato and Amaranthus. Over 80% coverage was obtained from distant species, including Ginkgo, loblolly pine and Equisetum. Sequence from the inverted repeat region of strawberry and peach plastome was obtained, annotated and analyzed. Additionally, a polymorphic region identified from gel electrophoresis was sequenced from tomato and Amaranthus. Sequence analysis revealed large deletions in these species relative to tobacco plastome thus exhibiting the utility of this method for structural and

  14. Temperature dependence of photosynthesis and thylakoid lipid composition in the red snow alga Chlamydomonas cf. nivalis (Chlorophyceae).

    Science.gov (United States)

    Lukeš, Martin; Procházková, Lenka; Shmidt, Volha; Nedbalová, Linda; Kaftan, David

    2014-08-01

    Here, we report an effect of short acclimation to a wide span of temperatures on photosynthetic electron transfer, lipid and fatty acid composition in the snow alga Chlamydomonas cf. nivalis. The growth and oxygen evolution capacity were low at 2 °C yet progressively enhanced at 10 °C and were significantly higher at temperatures from 5 to 15 °C in comparison with the mesophilic control Chlamydomonas reinhardtii. In search of the molecular mechanisms responsible for the adaptation of photosynthesis to low temperatures, we have found unprecedented high rates of QA to QB electron transfer. The thermodynamics of the process revealed the existence of an increased structural flexibility that we explain with the amino acid changes in the D1 protein combined with the physico-chemical characteristics of the thylakoid membrane composed of > 80% negatively charged phosphatidylglycerol. PMID:24698015

  15. Photoregulation of fructose and glucose respiration in the intact chloroplasts of Chlamydomonas reinhardtii F-60 and spinach

    International Nuclear Information System (INIS)

    The photoregulation of chloroplastic respiration was studied by monitoring in darkness and in light the release of 14CO2 from whole chloroplasts of Chlamydomonas reinhardtii F-60 and spinach (Spinacia oleracea L.) supplied externally with [14C]glucose and [14C]fructose, respectively. CO2 release was inhibited more than 90% in both chloroplasts by a light intensity of 4 W m-2. Oxidants, oxaloacetate in Chlamydomonas, nitrite in spinach, and phenazine methosulfate in both chloroplasts, reversed the inhibition. The onset of the photoinhibitory effect on CO2 release was relatively rapid compared to the restoration of CO2 release following illumination. In both darkened chloroplasts, dithiothreitol inhibited release. Of the four enzymes (fructokinase, phosphoglucose isomerase, glucose-6-P dehydrogenase, and gluconate-6-P dehydrogenase) in the pathway catalyzing the release of CO2 from fructose, only glucose-6-P dehydrogenase was deactivated by light and by dithiothreitol. 33 refs., 3 figs., 4 tabs

  16. Effective and Efficient Multi-Facet Web Image Annotation

    Institute of Scientific and Technical Information of China (English)

    Jia Chen; Yi-He Zhu; Hao-Fen Wang; Wei Jin; Yong Yu

    2012-01-01

    The vast amount of images available on the Web request for an effective and efficient search service to help users find relevant images.The prevalent way is to provide a keyword interface for users to submit queries.However,the amount of images without any tags or annotations are beyond the reach of manual efforts.To overcome this,automatic image annotation techniques emerge,which are generally a process of selecting a suitable set of tags for a given image without user intervention.However,there are three main challenges with respect to Web-scale image annotation:scalability,noiseresistance and diversity.Scalability has a twofold meaning:first an automatic image annotation system should be scalable with respect to billions of images on the Web; second it should be able to automatically identify several relevant tags among a huge tag set for a given image within seconds or even faster.Noise-resistance means that the system should be robust enough against typos and ambiguous terms used in tags.Diversity represents that image content may include both scenes and objects,which are further described by multiple different image features constituting different facets in annotation.In this paper,we propose a unified framework to tackle the above three challenges for automatic Web image annotation.It mainly involves two components:tag candidate retrieval and multi-facet annotation.In the former content-based indexing and concept-based codebook are leveraged to solve scalability and noise-resistance issues.In the latter the joint feature map has been designed to describe different facets of tags in annotations and the relations between these facets.Tag graph is adopted to represent tags in the entire annotation and the structured learning technique is employed to construct a learning model on top of the tag graph based on the generated joint feature map.Millions of images from Flickr are used in our evaluation.Experimental results show that we have achieved 33% performance

  17. Annotations of Mexican bullfighting videos for semantic index

    Science.gov (United States)

    Montoya Obeso, Abraham; Oropesa Morales, Lester Arturo; Fernando Vázquez, Luis; Cocolán Almeda, Sara Ivonne; Stoian, Andrei; García Vázquez, Mireya Saraí; Zamudio Fuentes, Luis Miguel; Montiel Perez, Jesús Yalja; de la O Torres, Saul; Ramírez Acosta, Alejandro Alvaro

    2015-09-01

    The video annotation is important for web indexing and browsing systems. Indeed, in order to evaluate the performance of video query and mining techniques, databases with concept annotations are required. Therefore, it is necessary generate a database with a semantic indexing that represents the digital content of the Mexican bullfighting atmosphere. This paper proposes a scheme to make complex annotations in a video in the frame of multimedia search engine project. Each video is partitioned using our segmentation algorithm that creates shots of different length and different number of frames. In order to make complex annotations about the video, we use ELAN software. The annotations are done in two steps: First, we take note about the whole content in each shot. Second, we describe the actions as parameters of the camera like direction, position and deepness. As a consequence, we obtain a more complete descriptor of every action. In both cases we use the concepts of the TRECVid 2014 dataset. We also propose new concepts. This methodology allows to generate a database with the necessary information to create descriptors and algorithms capable to detect actions to automatically index and classify new bullfighting multimedia content.

  18. APPRIS: annotation of principal and alternative splice isoforms.

    Science.gov (United States)

    Rodriguez, Jose Manuel; Maietta, Paolo; Ezkurdia, Iakes; Pietrelli, Alessandro; Wesselink, Jan-Jaap; Lopez, Gonzalo; Valencia, Alfonso; Tress, Michael L

    2013-01-01

    Here, we present APPRIS (http://appris.bioinfo.cnio.es), a database that houses annotations of human splice isoforms. APPRIS has been designed to provide value to manual annotations of the human genome by adding reliable protein structural and functional data and information from cross-species conservation. The visual representation of the annotations provided by APPRIS for each gene allows annotators and researchers alike to easily identify functional changes brought about by splicing events. In addition to collecting, integrating and analyzing reliable predictions of the effect of splicing events, APPRIS also selects a single reference sequence for each gene, here termed the principal isoform, based on the annotations of structure, function and conservation for each transcript. APPRIS identifies a principal isoform for 85% of the protein-coding genes in the GENCODE 7 release for ENSEMBL. Analysis of the APPRIS data shows that at least 70% of the alternative (non-principal) variants would lose important functional or structural information relative to the principal isoform. PMID:23161672

  19. Incorporating Feature-Based Annotations into Automatically Generated Knowledge Representations

    Science.gov (United States)

    Lumb, L. I.; Lederman, J. I.; Aldridge, K. D.

    2006-12-01

    Earth Science Markup Language (ESML) is efficient and effective in representing scientific data in an XML- based formalism. However, features of the data being represented are not accounted for in ESML. Such features might derive from events (e.g., a gap in data collection due to instrument servicing), identifications (e.g., a scientifically interesting area/volume in an image), or some other source. In order to account for features in an ESML context, we consider them from the perspective of annotation, i.e., the addition of information to existing documents without changing the originals. Although it is possible to extend ESML to incorporate feature-based annotations internally (e.g., by extending the XML schema for ESML), there are a number of complicating factors that we identify. Rather than pursuing the ESML-extension approach, we focus on an external representation for feature-based annotations via XML Pointer Language (XPointer). In previous work (Lumb &Aldridge, HPCS 2006, IEEE, doi:10.1109/HPCS.2006.26), we have shown that it is possible to extract relationships from ESML-based representations, and capture the results in the Resource Description Format (RDF). Thus we explore and report on this same requirement for XPointer-based annotations of ESML representations. As in our past efforts, the Global Geodynamics Project (GGP) allows us to illustrate with a real-world example this approach for introducing annotations into automatically generated knowledge representations.

  20. Annotating Simplices with a Homology Basis and Its Applications

    CERN Document Server

    Busaryev, Oleksiy; Chen, Chao; Dey, Tamal K; Wang, Yusu

    2011-01-01

    Let $K$ be a simplicial complex and $g$ the rank of its $p$-th homology group $H_p(K)$ defined with $Z_2$ coefficients. We show that we can compute a basis $H$ of $H_p(K)$ and annotate each $p$-simplex of $K$ with a binary vector of length $g$ with the following property: the annotations, summed over all $p$-simplices in any $p$-cycle $z$, provide the coordinate vector of the homology class $[z]$ in the basis $H$. The basis and the annotations for all simplices can be computed in $O(n^{\\omega})$ time, where $n$ is the size of $K$ and $\\omega<2.376$ is a quantity so that two $n\\times n$ matrices can be multiplied in $O(n^{\\omega})$ time. The pre-computation of annotations permits answering queries about the independence or the triviality of $p$-cycles efficiently. Using annotations of edges in 2-complexes, we derive better algorithms for computing optimal basis and optimal homologous cycles in 1-dimensional homology. Specifically, for computing an optimal basis of $H_1(K)$, we improve the time complexity kn...