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  • 1
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 1987-10-02
    Description: Overall, each of the program packages performed their tasks satisfactorily. For analyses where there was a well-defined answer, such as a search for a restriction site, there were few significant differences between the program sets. However, for tasks in which a degree of flexibility is desirable, such as homology or similarity determinations and database searches, DNASTAR consistently afforded the user more options in conducting the required analysis than did the other two packages. However, for laboratories where sequence analysis is not a major effort and the expense of a full sequence analysis workstation cannot be justified, MicroGenie and IBI-Pustell offer a satisfactory alternative. MicroGenie is a polished program system. Many may find that its user interface is more "user friendly" than the standard menu-driven interfaces. Its system of filing sequences under individual passwords facilitates use by more than one person. MicroGenie uses a hardware device for software protection that occupies a card slot in the computer on which it is used. Although I am sympathetic to the problem of software piracy, I feel that a less drastic solution is in order for a program likely to be sharing limited computer space with other software packages. The IBI-Pustell package performs the required analysis functions as accurately and quickly as MicroGenie but it lacks the clearness and ease of use. The menu system seems disjointed, and new or infrequent users often find themselves at apparent "dead-end menus" where the only clear alternative is to restart the entire program package. It is suggested from published accounts that the user interface is going to be upgraded and perhaps when that version is available, use of the system will be improved. The documentation accompanying each package was relatively clear as to how to run the programs, but all three packages assumed that the user was familiar with the computational techniques employed. MicroGenie and IBI-Pustell further complicated their documentation by mixing instructions for the version based on floppy disk operation with that for the hard disk version.(ABSTRACT TRUNCATED AT 400 WORDS)〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Cannon, G C -- New York, N.Y. -- Science. 1987 Oct 2;238(4823):97-103.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Roche Institute of Molecular Biology, Roche Research Center, Nutley, NJ 07110.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/3659902" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Base Sequence ; Sequence Homology, Nucleic Acid ; *Software
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 2
    Publication Date: 2008-02-23
    Description: The carboxysome is a bacterial microcompartment that functions as a simple organelle by sequestering enzymes involved in carbon fixation. The carboxysome shell is roughly 800 to 1400 angstroms in diameter and is assembled from several thousand protein subunits. Previous studies have revealed the three-dimensional structures of hexameric carboxysome shell proteins, which self-assemble into molecular layers that most likely constitute the facets of the polyhedral shell. Here, we report the three-dimensional structures of two proteins of previously unknown function, CcmL and OrfA (or CsoS4A), from the two known classes of carboxysomes, at resolutions of 2.4 and 2.15 angstroms. Both proteins assemble to form pentameric structures whose size and shape are compatible with formation of vertices in an icosahedral shell. Combining these pentamers with the hexamers previously elucidated gives two plausible, preliminary atomic models for the carboxysome shell.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Tanaka, Shiho -- Kerfeld, Cheryl A -- Sawaya, Michael R -- Cai, Fei -- Heinhorst, Sabine -- Cannon, Gordon C -- Yeates, Todd O -- New York, N.Y. -- Science. 2008 Feb 22;319(5866):1083-6. doi: 10.1126/science.1151458.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry and Biochemistry, University of California at Los Angeles (UCLA), Los Angeles, CA 90095, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18292340" target="_blank"〉PubMed〈/a〉
    Keywords: Bacterial Proteins/*chemistry/physiology ; Crystallography, X-Ray ; Cytoplasmic Structures/*chemistry/ultrastructure ; Models, Molecular ; Protein Conformation ; Protein Folding ; Protein Structure, Quaternary ; Synechocystis/*chemistry/ultrastructure
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 3
    ISSN: 1432-072X
    Keywords: Carboxysomes ; d-Ribulose-1,5-bisphosphate carboxylase ; CO2 fixing capacity ; Thiobacillus neapolitanus ; Chemolithotroph ; Autotroph
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract An adaptation of the d-ribulose-1,5-bisphosphate carboxylase (RuBPCase) activity to changing CO2 concentrations in the growth medium in the chemostat was observed in the obligate chemolithotroph Thiobacillus neapolitanus. RuBPCase activity has been separated in a soluble and particulate fraction. The activity of the particulate fraction appeared to be associated with the carboxysomes. The total activity of RuBPCase of CO2 limited cultures was about 5-fold higher than the activity of thiosulphate limited cultures grown in the presence of 5% CO2 whilst the particulate activity and the soluble activity were about 8- and 1.5-fold higher, respectively. The fluctuation of the total and particulate RuBPCase activity correlated with the changes in volume density of carboxysomes in the cell. An inverse correlation between maximal CO2 fixing capacity by whole cells and the volume density of carboxysomes was observed. The change in ratio of soluble RuBPCase activity to particulate RuBPCase activity paralleled the change in maximal CO2 fixation by whole cells during the different growth conditions.
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  • 4
    ISSN: 1432-072X
    Keywords: Carboxysomes ; Ribulose-1,5-bisphosphate carboxylase-oxygenase ; Thiobacillus neapolitanus
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract A homogenous preparation of carboxysomes was isolated from Thiobacillus neapolitanus by means of density gradient centrifugation and preparative electrophoresis through agarose. Analysis of the carboxysomes by denaturing sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) revealed the presence of 12–15 polypeptides. Approximately 62% of the total protein was found to consist of the large and small subunits of ribulose-1,5-bisphosphate carboxylase-oxygenase (RubisCO). Two polypeptides were found to be components of the carboxysome shell. Ribose-5-phosphate isomerase, ribulose-5-phosphate kinase, and fructose-1,6-bisphosphatase could not be detected in the carboxysome. Purified carboxysomal and cytoplasmic RubisCO were shown to be similar if not identical by several criteria including specific activity, carboxylase/oxygenase activity, and electrophoretic mobility.
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  • 5
    Publication Date: 2008-02-22
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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