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Automatic annotation of organellar genomes with DOGMA

Description: Dual Organellar GenoMe Annotator (DOGMA) automates the annotation of extra-nuclear organellar (chloroplast and animal mitochondrial) genomes. It is a web-based package that allows the use of comparative BLAST searches to identify and annotate genes in a genome. DOGMA presents a list of putative genes to the user in a graphical format for viewing and editing. Annotations are stored on our password-protected server. Complete annotations can be extracted for direct submission to GenBank. Furthermore, intergenic regions of specified length can be extracted, as well the nucleotide sequences and amino acid sequences of the genes.
Date: June 1, 2004
Creator: Wyman, Stacia; Jansen, Robert K. & Boore, Jeffrey L.
Partner: UNT Libraries Government Documents Department

Comparative chloroplast genomics: Analyses including new sequencesfrom the angiosperms Nuphar advena and Ranunculus macranthus

Description: The number of completely sequenced plastid genomes available is growing rapidly. This new array of sequences presents new opportunities to perform comparative analyses. In comparative studies, it is most useful to compare across wide phylogenetic spans and, within angiosperms, to include representatives from basally diverging lineages such as the new genomes reported here: Nuphar advena (from a basal-most lineage) and Ranunculus macranthus (from the basal group of eudicots). We report these two new plastid genome sequences and make comparisons (within angiosperms, seed plants, or all photosynthetic lineages) to evaluate features such as the status of ycf15 and ycf68 as protein coding genes, the distribution of simple sequence repeats (SSRs) and longer dispersed repeats (SDR), and patterns of nucleotide composition.
Date: March 1, 2007
Creator: Raubeso, Linda A.; Peery, Rhiannon; Chumley, Timothy W.; Dziubek,Chris; Fourcade, H. Matthew; Boore, Jeffrey L. et al.
Partner: UNT Libraries Government Documents Department


Description: The basic information about the path of carbon in photosynthesis is reviewed together with the methods that were used to discover it. This has led to the knowledge of what is required of the photochemical reaction in the form of chemical species. Attention is then directed to the structure of the photochemical apparatus itself insofar as it is viewable by electron microscopy, and some principoles of ordered structure are devised for the types of molecules to be found in the chloroplasts. From the combination of these, a structure for the grana lamella is suggested and a mode of function proposed. Experimental test for this mode of function is underway; one method is to examine photoproduced unpaired electrons. This is discussed.
Date: September 23, 1958
Creator: Calvin, Melvin
Partner: UNT Libraries Government Documents Department

The Primary Quantum Conversion Process in Photosynthesis: ElectronSpin Resonance

Description: Photoinduced electron spin resonance signals have been observed in isolated chloroplasts and other green materials with a growth time not affected by reducing the temperature to -140 deg. This is interpreted in terms of conduction-band and trapped-electron theory.
Date: January 28, 1957
Creator: Calvin, Melvin & Sogo, Power B.
Partner: UNT Libraries Government Documents Department

Proteolysis in Plastids of Arabidopsis Thaliana: Functional Analysis of ClpS1,2,T and their Physical and Genetic Interactions with the ClpPR Protease Core Complex and Clp Chaperones

Description: Chloroplasts are essential organelles required for plant growth and biomass production. They synthesize many essential secondary metabolites (e.g. hormones, isoprenoids, amino acids, etc.) and house the photosynthetic apparatus needed for conversion of light energy and CO2 into chemical energy [in the form of reduced carbohydrates, ATP and NADPH]. Thus chloroplasts are essential for life on earth and essential for production of bioenergy. Formation and maintenance of a functional chloroplast requires an extensive investment in the biogenesis and homeostasis apparatus. Protease and proteolysis play a critical role in these processes, with the Clp gene family being particularly central. Proteolysis of proteins and protein complexes in plastids is poorly understood, and is not only critical for biogenesis, adaptation and maintenance but is also important for plant development. Several years ago, the vanWijk lab identified a large and relatively abundant ClpP/R/S complex, along with ClpC1,C2 and ClpD chaperones and a putative Clp affinity modulator in plastids. So far, no substrate recognition mechanism has been determined for any Clp complex in plants. The purpose of this grant was to initiate functional analysis of three members of the Clp family.
Date: January 12, 2009
Creator: van Wijk, Klaas
Partner: UNT Libraries Government Documents Department

Metabolism of Thioctic Acid in Algae

Description: Thioctic acid labeled with sulfur-35 has been prepared and i t s metabolism b y algae has been studied. It i s converted by the algae into a number of forms, all of which upon hydrolysis yield either the disulfide o r i t s sulfoxide. One of these constituted the major portion of the labeled material in the chloroplasts. Aerobic metabolism for some minutes i s required to produce this form. Preliminary studies of the chemical nature of this form suggest i t to be esterified on the carboxyl group with a moiety of very high lipid solubility.
Date: April 17, 1956
Creator: Grisebach, Hans; Fuller, R.C. & Calvin, M.
Partner: UNT Libraries Government Documents Department


Description: Di-tertiarybutylnitroxide (DTBN), which they have tried to use as a trapping agent to identify the species giving rise to the photo-induced EPR signals in photosynthetic materials, functions as a Hill reagent with spinach chloroplasts. Evidence is presented which indicates that the reduction of DTBN is affected by photosystem II of the electron transport system of spinach chloroplasts. The reduced form of DTBN, the hydroxylamine, undergoes a photo-oxidation with spinach chloroplasts. Possible explanations of this apparent inconsistency are presented. A product which could be ascribed to a chemical coupling reaction between the nitroxide and the radical species giving rise to the photo-induced EPR signals in spinach chloroplasts was not detected, even using radioactive tracer methods.
Date: January 1, 1970
Creator: Corker, Gerald A.; Klein, Melvin P.; La Font, Didier & Calvin,Melvin.
Partner: UNT Libraries Government Documents Department

From Microstructure to Macrostructure and Function in thePhotochemical Apparatus

Description: A discussion is presented of the macrostructure of the chloroplast insofar as it is known and knowable by means of microscopy (visible, ultraviolet and electron). This leads to a number of principles of structure to be found in the granum universally distributed throughout the plant kingdom. A chemical analysis of the constitution of these lamellar structures leads to a deduction of structural principles for such molecules as are found therein. The application of these structural principles to the visible structure of the lamella leads to a microstructure on a molecular level of these lamellae which, in turn, leads to a theory of their function.
Date: October 22, 1958
Creator: Calvin, Melvin
Partner: UNT Libraries Government Documents Department

A Comparison of the First Two Sequenced Chloroplast Genomes in Asteraceae: Lettuce and Sunflower

Description: Asteraceae is the second largest family of plants, with over 20,000 species. For the past few decades, numerous phylogenetic studies have contributed to our understanding of the evolutionary relationships within this family, including comparisons of the fast evolving chloroplast gene, ndhF, rbcL, as well as non-coding DNA from the trnL intron plus the trnLtrnF intergenic spacer, matK, and, with lesser resolution, psbA-trnH. This culminated in a study by Panero and Funk in 2002 that used over 13,000 bp per taxon for the largest taxonomic revision of Asteraceae in over a hundred years. Still, some uncertainties remain, and it would be very useful to have more information on the relative rates of sequence evolution among various genes and on genome structure as a potential set of phylogenetic characters to help guide future phylogenetic structures. By way of contributing to this, we report the first two complete chloroplast genome sequences from members of the Asteraceae, those of Helianthus annuus and Lactuca sativa. These plants belong to two distantly related subfamilies, Asteroideae and Cichorioideae, respectively. In addition to these, there is only one other published chloroplast genome sequence for any plant within the larger group called Eusterids II, that of Panax ginseng (Araliaceae, 156,318 bps, AY582139). Early chloroplast genome mapping studies demonstrated that H. annuus and L. sativa share a 22 kb inversion relative to members of the subfamily Barnadesioideae. By comparison to outgroups, this inversion was shown to be derived, indicating that the Asteroideae and Cichorioideae are more closely related than either is to the Barnadesioideae. Later sequencing study found that taxa that share this 22 kb inversion also contain within this region a second, smaller, 3.3 kb inversion. These sequences also enable an analysis of patterns of shared repeats in the genomes at fine level and of RNA editing by comparison ...
Date: January 20, 2006
Creator: Timme, Ruth E.; Kuehl, Jennifer V.; Boore, Jeffrey L. & Jansen, Robert K.
Partner: UNT Libraries Government Documents Department

Mechanism of the Mg-chelatase step in chlorophyll biosynthesis. Final technical report

Description: Mg-chelatase catalyzes the insertion of Mg2+ into protoporphyrin-IX (Proto) in the chlorophyll biosynthetic pathway. This is the first step unique to the chlorophyll pathway and is at the branchpoint between heme and chlorophyll biosynthesis. Previous work from our laboratory has shown that the enzyme from pea chloroplasts requires three distinct protein fractions (now known to contain the D, I and H subunits). The reaction requires ATP in two distinct steps: activation requiring two of the fractions (I and D) and metal ion insertion, requiring all three fractions. Work covered in this granting period includes the cloning and expression of the active form of one of the pea subunits and demonstration of the change in chromatographic behavior of the subunits upon activation with ATP.
Date: May 2, 2002
Creator: Weinstein, Jon
Partner: UNT Libraries Government Documents Department

The Magnesium Chelation Step in Chlorophyll Biosynthesis

Description: The progress described in this report encompasses work supported by DOE grant DE-FG09-89ER13989 for the period 2/15/92 to the present 6/14/94. The goals of the project were to continue investigating the enzymology of Mg-chelatase and to investigate the co-regulation of heme and chlorophyll formation in intact plastids. During this period the laboratory had additional support (two years) from USDA to investigate heme metabolism in chloroplasts. This report is arranged so that the progress is described by reference to manuscripts which are published, under review or in preparation.
Date: January 17, 2001
Creator: Dilworth, Gregory L.
Partner: UNT Libraries Government Documents Department

The iojap gene in maize

Description: The classical maize mutant iojap (Iodent japonica) has variegated green and white leaves. Green sectors have cells with normal chloroplasts whereas white sectors have cells where plastids fail to differentiate. These mutant plastids, when transmitted through the female gametophyte, do not recover in the presence of wild type Iojap. We cloned the Ij locus, and we have investigated the mechanism of epigenetic inheritance and phenotypic expression. More recently, a modifier of this type of variegation, ''Inhibitor of striate'', has also been cloned. Both the iojap and inhibitor of striate proteins have homologs in bacteria and are members of ancient conserved families found in multiple species. These tools can be used to address fundamental questions of inheritance and variegation associated with this classical conundrum of maize genetics. Since the work of Rhoades there has been considerable speculation concerning the nature of the Iojap gene product, the origin of leaf variegation and the mechanism behind the material inheritance of defective plastids. This has made Iojap a textbook paradigm for cytoplasmic inheritance and nuclear-organellar interaction for almost 50 years. Cloning of the Iojap gene in maize, and homologs in other plants and bacteria, provides a new means to address the origin of heteroplastidity, variegation and cytoplasmic inheritance in higher plants.
Date: December 1, 2001
Creator: Martienssen, Robert
Partner: UNT Libraries Government Documents Department

Regulation of chloroplast number and DNA synthesis in higher plants. Final report

Description: The long term objective of this research is to understand the process of chloroplast development and its coordination with leaf development in higher plants. This is important because the photosynthetic capacity of plants is directly related to leaf and chloroplast development. This research focuses on obtaining a detailed description of leaf development and the early steps in chloroplast development including activation of plastid DNA synthesis, changes in plastid DNA copy number, activation of chloroplast transcription and increases in plastid number per cell. The grant will also begin analysis of specific biochemical mechanisms by isolation of the plastid DNA polymerase, and identification of genetic mutants which are altered in their accumulation of plastid DNA and plastid number per cell.
Date: November 10, 1995
Creator: Mullet, J.E.
Partner: UNT Libraries Government Documents Department

[Calcium gating of proton fluxes in chloroplasts]. Progress report, April 1989--April 1991

Description: Work supported by this grant has been aimed at better understanding the still-mysterious phenomenon of sequestered proton gradients which strong evidence suggests can energize ATP formation in chloroplast organelle membranes. Results from several laboratories support the notion that chloroplasts can couple the energy of H{sup +} gradients. Research in may lab has, since 1983, been deeply involved in a two-pronged approach, (A) identifying and quantitating sequestered proton buffering groups and (B) trying to elucidate just how the sequestered H{sup +} gradient is maintained and what regulates the switching between the localized and delocalized coupling modes. One aspect we have worked on under DOE auspices is the question whether the localized H{sup +} coupling, routinely detected in my lab by a protocol which measures the number of single-turnover flashes (usually fired at 5 Hz) required to reach the energization threshold for ATP formation, can continue in steady illumination. It is possible to consider that a localized coupling response could be observed in the initial energization transient followed obligatorily by the sustained H{sup +} gradient equilibrating with the lumen bulk phase. If that occurred, it would have very important ramifications as to how one evaluates the possible physiological meaning of ``localized`` coupling. To test this, we developed a steady illumination protocol which is briefly discussed.
Date: December 31, 1991
Creator: Dilley, R. A.
Partner: UNT Libraries Government Documents Department

Genetic analysis of photoreceptor action pathways in Arabidopsis thaliana. Progress report

Description: The specific strategies and long-term goals of this proposal remain intact relative to the original proposal. We continue to isolate and characterize photomorphogenic mutants of Arabidopsis thaliana. The molecular and biochemical characterization of one of these mutants, det1, has led to one publication of original data and to one Society for Experimental Biology Symposium paper (see below). The phenotype of a second mutant, det2, has also been studied during this funding period. In addition, we have continued work on a general strategy to isolate mutations in trans-acting regulatory factors that mediate light-regulated gene expression, and have identified several potentially interesting regulatory mutants. In the third funding period, we will concentrate on the genetical, biochemical, and molecular characterization of these new mutants. Construction of double mutants between the new mutants and the previously characterized morphological mutants should allow us to construct a pathway for light-regulated seedling development in Arabidopsis.
Date: December 31, 1991
Partner: UNT Libraries Government Documents Department