1,723,813 research outputs found
Intracellular Calcium Carbonate Biomineralization in Cyanothece sp. PCC 7425 : Genetic Approaches to Uncover the Function of CcyA
No full textCyanobacteria are Gram-negative photosynthetic bacteria that historically have been linked to bacterial carbonate biomineralization, a process involving the precipitation of carbonate minerals made thermodynamically possible by metabolically active bacteria. The recent discovery of intracellular calcium carbonate formation in cyanobacteria has raised numerous questions about the mechanisms underlying cyanobacterial biomineralization. Traditionally believed to occur exclusively extracellularly, this process has now been observed intracellularly in specific cyanobacterial strains. This project aimed to investigate the function of ccyA, a candidate marker gene for intracellular calcium carbonate formation (iACC), in Cyanothece sp. PCC 7425 through overexpression, deletion, and repression. The overexpression experiments of ccyA indicated a potential link between pH changes in growth media and Ca2+ uptake in Cyanothece sp. PCC 7425. While overexpression did not impact growth, it increased extracellular pH, usually an indicator for extracellular biomineralization. However, whether the changes in pH and Ca2+ uptake affected the formation of intracellular calcium carbonate granules remains to be investigated. For deletion, the modern CRISPR/Cas12a system successfully deleted two CAX genes used as technical controls in Cyanothece sp. PCC 7425, establishing the system as a valid method for genomic modification. However, complete chromosome segregation of ccyA deletion was not achieved, indicating that ccyA might be crucial for Cyanothece sp. PCC 7425 survival. Partially segregated mutants obtained can still offer valuable information on ccyA and intracellular biomineralization in future experiments. For repression, a CRISPR/dCas12a (CRISPRi) system was utilized. Experiments aimed at repressing nblA, a reporter gene, in Cyanothece sp. PCC 7425, did not produce a noticeable phenotype, likely due to physiological differences in Cyanothece sp. PCC 7425 as compared to model cyanobacteria used in previous research with nblA as a reporter. It could also be due to limitations in the inducibility of the CRISPRi system, with Cyanothece sp. PCC 7425 lacking the ability to import the inducer, IPTG. Overall, this study provides a foundation for further exploration into the role of ccyA in intracellular biomineralization and offers insights into optimizing genetic tools for studying gene function in Cyanothece sp. PCC 7425.
Intracellular calcium carbonate biomineralization in sp. PCC 7425: Genetic approaches to uncover the function of CcyA
No full textRapport de MasterEncadrant : Franck Chauvat (CEA Paris-Saclay) ; Examinateurs : Pia Lindberg; Peter KassonCyanobacteria are Gram-negative photosynthetic bacteria that historically have been linked tobacterial carbonate biomineralization, a process involving the precipitation of carbonateminerals made thermodynamically possible by metabolically active bacteria. The recentdiscovery of intracellular calcium carbonate formation in cyanobacteria has raised numerousquestions about the mechanisms underlying cyanobacterial biomineralization. Traditionallybelieved to occur exclusively extracellularly, this process has now been observed intracellularlyin specific cyanobacterial strains.This project aimed to investigate the function of ccyA, a candidate marker gene for intracellularcalcium carbonate formation (iACC), in Cyanothece sp. PCC 7425 through overexpression,deletion, and repression. The overexpression experiments of ccyA indicated a potential linkbetween pH changes in growth media and Ca2+ uptake in Cyanothece sp. PCC 7425. Whileoverexpression did not impact growth, it increased extracellular pH, usually an indicator forextracellular biomineralization. However, whether the changes in pH and Ca2+ uptake affectedthe formation of intracellular calcium carbonate granules remains to be investigated.For deletion, the modern CRISPR/Cas12a system successfully deleted two CAX genes used astechnical controls in Cyanothece sp. PCC 7425, establishing the system as a valid method forgenomic modification. However, complete chromosome segregation of ccyA deletion was notachieved, indicating that ccyA might be crucial for Cyanothece sp. PCC 7425 survival. Partiallysegregated mutants obtained can still offer valuable information on ccyA and intracellularbiomineralization in future experiments.For repression, a CRISPR/dCas12a (CRISPRi) system was utilized. Experiments aimed atrepressing nblA, a reporter gene, in Cyanothece sp. PCC 7425, did not produce a noticeablephenotype, likely due to physiological differences in Cyanothece sp. PCC 7425 as compared tomodel cyanobacteria used in previous research with nblA as a reporter. It could also be due tolimitations in the inducibility of the CRISPRi system, with Cyanothece sp. PCC 7425 lacking theability to import the inducer, IPTG.Overall, this study provides a foundation for further exploration into the role of ccyA inintracellular biomineralization and offers insights into optimizing genetic tools for studying genefunction in Cyanothece sp. PCC 742
Intracellular Calcium Carbonate Biomineralization in Cyanothece sp. PCC 7425 : Genetic Approaches to Uncover the Function of CcyA
No full textCyanobacteria are Gram-negative photosynthetic bacteria that historically have been linked to bacterial carbonate biomineralization, a process involving the precipitation of carbonate minerals made thermodynamically possible by metabolically active bacteria. The recent discovery of intracellular calcium carbonate formation in cyanobacteria has raised numerous questions about the mechanisms underlying cyanobacterial biomineralization. Traditionally believed to occur exclusively extracellularly, this process has now been observed intracellularly in specific cyanobacterial strains. This project aimed to investigate the function of ccyA, a candidate marker gene for intracellular calcium carbonate formation (iACC), in Cyanothece sp. PCC 7425 through overexpression, deletion, and repression. The overexpression experiments of ccyA indicated a potential link between pH changes in growth media and Ca2+ uptake in Cyanothece sp. PCC 7425. While overexpression did not impact growth, it increased extracellular pH, usually an indicator for extracellular biomineralization. However, whether the changes in pH and Ca2+ uptake affected the formation of intracellular calcium carbonate granules remains to be investigated. For deletion, the modern CRISPR/Cas12a system successfully deleted two CAX genes used as technical controls in Cyanothece sp. PCC 7425, establishing the system as a valid method for genomic modification. However, complete chromosome segregation of ccyA deletion was not achieved, indicating that ccyA might be crucial for Cyanothece sp. PCC 7425 survival. Partially segregated mutants obtained can still offer valuable information on ccyA and intracellular biomineralization in future experiments. For repression, a CRISPR/dCas12a (CRISPRi) system was utilized. Experiments aimed at repressing nblA, a reporter gene, in Cyanothece sp. PCC 7425, did not produce a noticeable phenotype, likely due to physiological differences in Cyanothece sp. PCC 7425 as compared to model cyanobacteria used in previous research with nblA as a reporter. It could also be due to limitations in the inducibility of the CRISPRi system, with Cyanothece sp. PCC 7425 lacking the ability to import the inducer, IPTG. Overall, this study provides a foundation for further exploration into the role of ccyA in intracellular biomineralization and offers insights into optimizing genetic tools for studying gene function in Cyanothece sp. PCC 7425.
Going Beyond Counting First Authors in Author Co-citation Analysis
No full textThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Variations on the Author
No full text“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
Appropriate Similarity Measures for Author Cocitation Analysis
No full textWe provide a number of new insights into the methodological discussion about author cocitation analysis. We first argue that the use of the Pearson correlation for measuring the similarity between authors’ cocitation profiles is not very satisfactory. We then discuss what kind of similarity measures may be used as an alternative to the Pearson correlation. We consider three similarity measures in particular. One is the well-known cosine. The other two similarity measures have not been used before in the bibliometric literature. Finally, we show by means of an example that our findings have a high practical relevance.information science;Pearson correlation;cosine;similarity measure;author cocitation analysis
Dispelling the Myths Behind First-author Citation Counts
No full textWe conducted a full-scale evaluative citation analysis study of scholars in the XML research field to explore just how different from each other author rankings resulting from different citation counting methods actually are, and to demonstrate the capability of emerging data and tools on the Web in supporting more realistic citation counting methods. Our results contest some common arguments for the continued
use of first-author citation counts in the evaluation of scholars, such as high correlations between author rankings by first-author citation counts and other citation
counting methods, and high costs of using more realistic citation counting methods that are not well-supported by the ISI databases. It is argued that increasingly available digital full text research papers make it possible for citation analysis studies to go beyond what the ISI databases have directly supported and to employ more
sophisticated methods
A Genetic Toolbox for the New Model Cyanobacterium Cyanothece PCC 7425: A Case Study for the Photosynthetic Production of Limonene
No full textInternational audienceCyanobacteria, the largest phylum of prokaryotes, perform oxygenic photosynthesis and are regarded as the ancestors of the plant chloroplast and the purveyors of the oxygen and biomass that shaped the biosphere. Nowadays, cyanobacteria are attracting a growing interest in being able to use solar energy, H2O, CO2 and minerals to produce biotechnologically interesting chemicals. This often requires the introduction and expression of heterologous genes encoding the enzymes that are not present in natural cyanobacteria. However, only a handful of model strains with a well-established genetic system are being studied so far, leaving the vast biodiversity of cyanobacteria poorly understood and exploited. In this study, we focused on the robust unicellular cyanobacterium Cyanothece PCC 7425 that has many interesting attributes, such as large cell size; capacity to fix atmospheric nitrogen (under anaerobiosis) and to grow not only on nitrate but also on urea (a frequent pollutant) as the sole nitrogen source; capacity to form CO2-sequestrating intracellular calcium carbonate granules and to produce various biotechnologically interesting products. We demonstrate for the first time that RSF1010-derived plasmid vectors can be used for promoter analysis, as well as constitutive or temperature-controlled overproduction of proteins and analysis of their sub-cellular localization in Cyanothece PCC 7425. These findings are important because no gene manipulation system had been developed for Cyanothece PCC 7425, yet, handicapping its potential to serve as a model host. Furthermore, using this toolbox, we engineered Cyanothece PCC 7425 to produce the high-value terpene, limonene which has applications in biofuels, bioplastics, cosmetics, food and pharmaceutical industries. This is the first report of the engineering of a Cyanothece strain for the production of a chemical and the first demonstration that terpene can be produced by an engineered cyanobacterium growing on urea as the sole nitrogen source
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