Molecular Characterization of the Calvin Cycle Enzyme Phosphoribulokinase in the Stramenopile Alga Vaucheria litorea and the Plastid Hosting Mollusc Elysia chlorotica

Phosphoribulokinase （PRK）, a nuclear-encoded plastid-localized enzyme unique to the photosynthetic carbon reduction （Calvin） cycle, was cloned and characterized from the stramenopile alga Vaucheria litorea. This alga is the source of plastids for the mollusc （sea slug） Elysia chlorotica which enable the animal to survive for months solely by photoautotrophic CO2 fixation. The 1633-bp V. litorea prk gene was cloned and the coding region, found to be interrupted by four introns, encodes a 405-amino acid protein. This protein contains the typical bipartite target sequence expected of nuclearencoded proteins that are directed to complex （i.e. four membrane-bound） algal plastids. De novo synthesis of PRK and enzyme activity were detected in E. chlorotica in spite of having been starved of V. litorea for several months. Unlike the algal enzyme, PRK in the sea slug did not exhibit redox regulation. Two copies of partial PRK-encoding genes were isolated from both sea slug and aposymbiotic sea slug egg DNA using PCR. Each copy contains the nucleotide region spanning exon 1 and part of exon 2 of V litorea prk, including the bipartite targeting peptide. However, the larger prk fragment also includes intron 1. The exon and intron sequences of prk in E. chlorotica and V/itorea are nearly identical. These data suggest that PRK is differentially regulated in V. litorea and E. chlorotica and at least a portion of the V. litorea nuclear PRK gene is present in sea slugs that have been starved for several months.     

Improved approach for transferring and cultivating Methanosarcina acetivorans C2A (DSM 2834)

Aim:  A method for cultivating Methanosarcina acetivorans was further developed to handle these anaerobic archaea without special equipment such as an anaerobic chamber.
Methods and Results:  Medium was filtered and oxygen removed under a nitrogen gas-phase. A dithiothreitol-filled syringe was used to transfer cells from high density grown cultures to new medium. Growth time and cell mass were determined, as well as cell viability was proven by light microscopy.
Conclusion:  Cell transfer and growth was successful using this approach.
Significance and Impact of the Study:  This updated technique allows almost every laboratory the opportunity to grow these methanogenic organisms for further studies. The described method could be used for proteomic analysis and is also interesting for further protein structure determination.     

Characterisation of Phenolics in Flor‐Essence®—a Compound Herbal product and its Contributing Herbs

Introduction – Commercially available herbal mixture FE, a proprietary natural health product manufactured by Flora Manufacturing and Distributing Ltd (Flora), is a unique North American traditional herbal product. FE is a chemically complex mixture of eight herbs and has not been subjected to phytochemical analysis. Objective – To develop analytical methods to undertake detailed phytochemical analyses of FE, and its eight contributing herbs, including burdock (Arctium lappa L.), sheep sorrel (Rumex acetosella L.), Turkish rhubarb (Rheum palmatum L.), slippery elm Muhl. (Ulmus rubra), watercress (Nasturtium officinale R. Br.), red clover (Trifolium pratense L.), blessed thistle (Cnicus benedictus L.) and kelp (Laminaria digitata Lmx.). Methodology – The identification was undertaken by a combination of reversed phase high performance liquid chromatography–diode array detection–atmospheric pressure chemical ionisation–mass selective detection (RP‐HPLC‐DAD‐APCI‐MSD) analysis and phenolics metabolomic library matching. Results – New separation methods facilitated the identification of 43 markers in the individual herbs which constitute FE. Sixteen markers could be identified in FE originating from four contributing herbs including four caffeoyl quinic acids, three dicaffeoyl quinic acids and two caffeic acid derivatives from A. lappa, luteolin‐7‐O‐glucoside, luteolin, five apigenin glycosides and apigenin from R. acetocella and N. officinale and sissostrin from T. pretense. A validated method for quantitative determination of three markers is reported with good intraday, interday and interoperator repeatability using a reliable alcohol based extraction technique. Conclusion – FE and its contributing herbs predominantly contain phenolics. This methodology can be applied to further develop full‐scale validation of this product. Copyright © 2009 John Wiley & Sons, Ltd.     

Red Bell Pepper Chromoplasts Exhibit in Vitro Import Competency and Membrane Targeting of Passenger Proteins from the Thylakoidal Sec and ΔpH Pathways but Not the Chloroplast Signal Recognition Particle Pathway

Chloroplast to chromoplast development involves new synthesis and plastid localization of nuclear-encoded proteins, as well as changes in the organization of internal plastid membrane compartments. We have demonstrated that isolated red bell pepper (Capsicum annuum) chromoplasts contain the 75-kD component of the chloroplast outer envelope translocon (Toc75) and are capable of importing chloroplast precursors in an ATP-dependent fashion, indicating a functional general import apparatus. The isolated chromoplasts were able to further localize the 33- and 17-kD subunits of the photosystem II O₂-evolution complex (OE33 and OE17, respectively), lumen-targeted precursors that utilize the thylakoidal Sec and ΔpH pathways, respectively, to the lumen of an internal membrane compartment. Chromoplasts contained the thylakoid Sec component protein, cpSecA, at levels comparable to chloroplasts. Routing of OE17 to the lumen was abolished by ionophores, suggesting that routing is dependent on a transmembrane ΔpH. The chloroplast signal recognition particle pathway precursor major photosystem II light-harvesting chlorophyll a/b protein failed to associate with chromoplast membranes and instead accumulated in the stroma following import. The Pftf (plastid fusion/translocation factor), a chromoplast protein, integrated into the internal membranes of chromoplasts during in vitro assays, and immunoblot analysis indicated that endogenous plastid fusion/translocation factor was also an integral membrane protein of chromoplasts. These data demonstrate that the internal membranes of chromoplasts are functional with respect to protein translocation on the thylakoid Sec and ΔpH pathways.Plastids are developmentally related organelles capable of interconversion among a variety of structurally and biochemically distinct forms in response to both environmental and tissue-specific cues (Whatley, 1978; Thomson and Whatley, 1980). Formation of chromoplasts in many fruits is one striking example of this plasticity. Heavily pigmented, photosynthetically inactive chromoplasts frequently develop from chloroplasts during ripening. This conversion involves dramatic changes in the organization and composition of the internal plastid compartment, which include the loss of proteins involved in carbon fixation in the stroma and replacement with chromoplast-specific proteins, the breakdown of the photosynthetic thylakoid membranes and loss of proteins involved in light capture and electron transfer, and, in some cases, the formation of new membranes (Spurr and Harris, 1968; Camara and Brangeon, 1981; Piechulla et al., 1987; Kuntz et al., 1989).Chromoplast formation is an active rather than simply a degradative process. New proteins, specific to or enhanced in chromoplasts, are synthesized and compartmentalized in the plastid (Camara et al., 1995; Price et al., 1995). Most chromoplast proteins are predicted to be nuclear encoded, translated on cytoplasmic ribosomes, and posttranslationally imported into the plastid, as are nuclear-encoded chloroplast proteins. Import of chloroplast proteins occurs via a general import machinery that appears to mediate translocation of most or all proteins that are delivered to the chloroplast stroma, either as a final destination or as an intermediate location (Cline and Henry, 1996; Robinson and Mant, 1997; Schnell, 1998). Proteins are targeted to the general import pathway by an N-terminal extension that is cleaved upon import, resulting in the appearance of a processed protein of reduced M_r. Presumably, the import of proteins into chromoplasts is accomplished by the same machinery that is responsible for import of proteins into chloroplasts, although this has never been directly examined.In some chromoplasts an extensive set of internal membranes accumulates, replacing the thylakoids. For example, in the fibrillar-type chromoplast of bell pepper (Capsicum annuum), the photosynthetic membranes are replaced by membranous sheets and vesicles in addition to the carotenoid-rich plastoglobules and fibrils (Spurr and Harris, 1968; Laborde and Spurr, 1973; Camara and Brangeon, 1981; Deruere et al., 1994). The often extensive internal membranes are the site of synthesis of keto-xanthophylls, which constitute the major carotenoids of red fruit (Bouvier et al., 1994).Our interests are in the biogenesis of the internal membranes of plastids, in particular the proteins that are integral to the bilayer, as well as those located in the luminal compartment formed by the bilayer. In chloroplasts, proteins destined for the thylakoid membrane or lumen are routed from the stroma into the thylakoid membrane and lumen by one of at least four distinct mechanisms: the ΔpH, chloroplast SRP, thylakoid Sec pathways, and an apparently spontaneous insertion mechanism (for review, see Cline and Henry, 1996; Robinson and Mant, 1997; Schnell, 1998). In view of the extensive internal membrane system of bell pepper chromoplasts, one would expect the presence of proteins and accompanying translocation machinery in these membranes. However, no chromoplast-specific proteins have been conclusively demonstrated to be either integral or luminal to these membranes.One protein, Pftf (plastid fusion/translocation factor), predicted to be membrane anchored by sequence analysis, has been purified from the stromal compartment of pepper chromoplasts (Hugueney et al., 1995). This raised the possibility that mature chromoplasts lack the ability to localize proteins into/across internal membranes. To address this question we developed a method for isolating protein import-competent chromoplasts from bell peppers. Immunoblotting confirmed that these chromoplasts contain known translocation machinery components. Chromoplasts were assayed in vitro for their ability to import and localize passenger proteins from the three known protein-machinery-dependent thylakoid-targeting pathways. We found mature chromoplasts to be capable of membrane targeting of proteins that utilize the thylakoidal Sec and ΔpH pathways but not capable of inserting a membrane protein, LHCP, which utilizes the chloroplast SRP pathway. Pftf was inserted into the membranes of these chromoplasts in a manner similar to that observed in chloroplasts, and resident Pftf was also found to be integrally associated with chromoplast membranes. The precise role of these pathways in the formation of bell pepper chromoplasts remains to be fully elucidated.     

Functional genomics reveals relationships between the retrovirus-like Ty1 element and its host Saccharomyces cerevisiae

Retroviruses and their relatives, the long terminal repeat (LTR) retrotransposons, carry out complex life cycles within the cells of their hosts. We have exploited a collection of gene deletion mutants developed by the Saccharomyces Genome Deletion Project to perform a functional genomics screen for host factors that influence the retrovirus-like Ty1 element in yeast. A total of 101 genes that presumably influence many different aspects of the Ty1 retrotransposition cycle were identified from our analysis of 4483 homozygous diploid deletion strains. Of the 101 identified mutants, 46 had significantly altered levels of Ty1 cDNA, whereas the remaining 55 mutants had normal levels of Ty1 cDNA. Thus, approximately half of the mutants apparently affected the early stages of retrotransposition leading up to the assembly of virus-like particles and cDNA replication, whereas the remaining half affected steps that occur after cDNA replication. Although most of the mutants retained the ability to target Ty1 integration to tRNA genes, 2 mutants had reduced levels of tRNA gene targeting. Over 25% of the gene products identified in this study were conserved in other organisms, suggesting that this collection of host factors can serve as a starting point for identifying host factors that influence LTR retroelements and retroviruses in other organisms. Overall, our data indicate that Ty1 requires a large number of cellular host factors to complete its retrotransposition cycle efficiently.     

Single nucleotide polymorphisms (SNPs) that map to gaps in the human SNP map

An international effort is underway to generate a comprehensive haplotype map (HapMap) of the human genome represented by an estimated 300000 to 1 million ‘tag’ single nucleotide polymorphisms (SNPs). Our analysis indicates that the current human SNP map is not sufficiently dense to support the HapMap project. For example, 24.6% of the genome currently lacks SNPs at the minimal density and spacing that would be required to construct even a conservative tag SNP map containing 300 000 SNPs. In an effort to improve the human SNP map, we identified 140 696 additional SNP candidates using a new bioinformatics pipeline. Over 51 000 of these SNPs mapped to the largest gaps in the human SNP map, leading to significant improvements in these regions. Our SNPs will be immediately useful for the HapMap project, and will allow for the inclusion of many additional genomic intervals in the final HapMap. Nevertheless, our results also indicate that additional SNP discovery projects will be required both to define the haplotype architecture of the human genome and to construct comprehensive tag SNP maps that will be useful for genetic linkage studies in humans.     

Akt signaling regulates side population cell phenotype via Bcrp1 translocation

Akt is an important regulator of cell survival, growth, and glucose metabolism in many cell types, but the role of this signaling molecule in hematopoietic stem cells is poorly defined. Side population (SP) cells are enriched for hematopoietic stem cell activity and are defined by their ability to efficiently efflux Hoechst 33342. Bone marrow from Akt1-null mice exhibited a reduced SP fraction. However, bone marrow cellularity, growth factor-responsive progenitor cultures, and engraftable stem cells were normal in these mice. Treatment of bone marrow with LY294002, an inhibitor of the Akt effector protein phosphatidylinositol 3-kinase, led to a reversible loss of the SP fraction. Bcrp1, which encodes the Hoechst dye transporter, was translocated from the membrane to the intracellular compartment under conditions that promote the SP-depleted state. Lentivirus-mediated overexpression of Akt1 in bone marrow markedly increased the SP fraction, whereas there was no effect on bone marrow from Bcrp(-/-) mice. These data suggest that Akt signaling modulates the SP cell phenotype by regulating the expression of Bcrp1.     

Fluorescein-labeled dextran concentration is increased in BAL fluid after ANTU-induced edema in rats

Several methodologies have been developed to assessalveolocapillary membrane permeability in acute lung injury. Thepurpose of this study was to determine the reliability of FITC-dextran compared with radioactive tracers to assess lung permeability alterations. After intraperitoneal administration of-naphthylthiourea (ANTU, 50 mg/kg) or DMSO-ANTU vehicle, the animalswere euthanized and their lungs were studied in an isolated-lungpreparation. FITC-dextran or radiolabeled tracers were added to theperfusate. At 2 h the bronchoalveolar lavage (BAL) fluid from the ANTUgroup showed a significantly greater amount of fluorescence in thesupernatant after centrifugation of BAL fluid compared with the DMSOgroup. Consistent results were observed with the radioactive tracers: there was an increase in extravascular albumin space and extravascular lung water compared with the control group. No cleavage of the FITCfrom the dextran molecule was evident by chromatography comparing samples recovered from the BAL fluid to the pure FITC-dextran molecule.In conclusion, measurement of FITC-dextran in the supernatant of BALfluid after intravascular administration is a reliable method ofassessing lung permeability changes in vivo and ex vivo.

     

Helminth communities of green frogs Rana clamitans Latreille, from southwestern Michigan.

A total of 239 green frogs Rana clamitans, collected between June 3 and August 27, 1998 from 6 locations in southwestern Michigan, was examined for helminths. Of the 26 helminth taxa found, the larval cestode Mesocestoides sp. had the highest mean intensity, followed by the larval trematode Fibricola sp. Of the helminths that mature in frogs, Haematoloechus varioplexus had the highest prevalence and Gorgodera amplicava had the highest mean intensity. Frogs from 118th Pond had the highest species richness (20), mean helminth species richness (5.2), and mean helminth abundance (153.7). Frogs from Constantine East had the highest mean helminth species diversity (0.8778) and evenness (0.6033), followed by frogs from 118th Pond. In all comparisons of mean helminth community species richness, abundance, diversity, and evenness, adult frogs had significantly higher or higher values than did juveniles at each location. Jaccard's coefficients of similarity for the helminth communities for location pairs ranged from 0.545 to 0.823. Nine and 2 core helminth taxa occurred at the local and regional levels, respectively. The differences in several helminth community measures in green frogs among locations stress the importance of local ecological conditions on helminth community structure.