Vision survival after open globe injury predicted by classification and regression tree analysis.

OBJECTIVE: To assist ophthalmologists in treating ocular trauma patients, this study developed and validated a prognostic model to predict vision survival after open globe injury. DESIGN: Retrospective cohort review. PARTICIPANTS: Two hundred fourteen patients who sought treatment at the Wilmer Ophthalmological Institute with open globe injuries from January 1, 2001, through December 31, 2004, were part of the data set used to build the classification tree model. Then, to validate the classification tree, 51 patients were followed up with the goal to compare their actual visual outcome with the outcome predicted by the tree grown from the classification and regression tree analysis. METHODS: Binary recursive partitioning was used to construct a classification tree to predict visual outcome after open globe injury. The retrospective cohort treated for open globe injury from January 1, 2001, through December 31, 2004, was used to develop the prognostic tree and constitutes the training sample. A second independent sample of patient eyes seen from January 1, 2005, through October 15, 2005, was used to validate the prognostic tree. MAIN OUTCOME MEASURES: Two main visual outcomes were assessed: vision survival (range, 20/20-light perception) and no vision (included no light perception, enucleation, and evisceration outcomes). RESULTS: A prognostic model for open globe injury outcome was constructed using 214 open globe injuries. Of 14 predictors determined to be associated with a no vision outcome in univariate analysis, presence of a relative afferent pupillary defect and poor initial visual acuity were the most predictive of complete loss of vision; presence of lid laceration and posterior wound location also predicted poor visual outcomes. In an independent cohort of 51 eyes, the prognostic model had 85.7% sensitivity to predict no vision correctly and 91.9% specificity to predict vision survival correctly. CONCLUSIONS: The open globe injury prognostic model constructed in this study demonstrated excellent predictive accuracy and should be useful in counseling patients and making clinical decisions regarding open globe injury management.

Isolated progressive visual loss after coiling of paraclinoid aneurysms.

BACKGROUND AND PURPOSE: The proximity of the paraclinoid segment of the internal carotid artery to the visual pathways may result in visual deficits when patients present with aneurysms in this segment. Although surgical clip ligation of these aneurysms has been the standard of care for decades, the advent of coil embolization has permitted endovascular therapy in those aneurysms with favorable dome-to-neck ratios. Although immediate nonprogressive visual loss after coil embolization of paraclinoid aneurysms has been well described, isolated progressive visual loss immediately or shortly following coil embolization, to our knowledge, has not. We have identified 8 patients who experienced progressive loss of vision, unassociated with any other neurologic deficits, developing immediately or shortly after apparently uncomplicated coil embolization of a paraclinoid aneurysm. MATERIALS AND METHODS: This study is a retrospective case series of 8 patients seen at 4 separate academic institutions. Inpatient and outpatient records were examined to determine patient demographics, previous ocular and medical history, and ophthalmic status before endovascular embolization. In addition, details of the primary endovascular therapy and subsequent surgical and nonsurgical interventions were recorded. Follow-up data, including most recent best-corrected visual acuity, postoperative course, and duration of follow-up were documented. RESULTS: Eight patients developed progressive visual loss in 1 or both eyes immediately or shortly after apparently uncomplicated coiling of a paraclinoid aneurysm. MR imaging findings suggested that the visual loss was most likely caused by perianeurysmal inflammation related to the coils used to embolize the aneurysm, enlargement or persistence of the aneurysm despite coiling, or a combination of these mechanisms. Most patients experienced improvement in vision, 2 apparently related to treatment with systemic corticosteroids. CONCLUSION: Patients in whom endovascular treatment of a paraclinoid aneurysm is contemplated should be warned about the potential for both isolated nonprogressive and progressive visual loss in 1 or both eyes. Patients in whom progressive visual loss occurs may benefit from treatment with systemic corticosteroids.

Ultrafast excitation dynamics of low energy pigments in reconstituted peripheral light-harvesting complexes of photosystem I.

Ultrafast dynamics of a reconstituted Lhca4 subunit from the peripheral LHCI-730 antenna of photosystem I of higher plants were probed by femtosecond absorption spectroscopy at 77 K. Intramonomeric energy transfer from chlorophyll (Chl) b to Chl a and energy equilibration between Chl a molecules observed on the subpicosecond time scale are largely similar to subpicosecond energy equilibration processes within LHCII monomers. However, a 5 ps equilibration process in Lhca4 involves unique low energy Chls in LHCI absorbing at 705 nm. These pigments localize the excitation both in the Lhca4 subunit and in LHCI-730 heterodimers. An additional 30-50 ps equilibration process involving red pigments of Lhca4 in the heterodimer, observed by transient absorption and picosecond fluorescence spectroscopy, was ascribed to intersubunit energy transfer.

Damage to photosystem II in symbiotic dinoflagellates: a determinant of coral bleaching.

Coral bleaching has been defined as a general phenomenon, whereby reef corals turn visibly pale because of the loss of their symbiotic dinoflagellates and/or algal pigments during periods of exposure to elevated seawater temperatures. During the summer of 1997, seawater temperatures in the Florida Keys remained at or above 30 degrees C for more than 6 weeks, and extensive coral bleaching was observed. Bleached colonies of the dominant Caribbean reef-building species, Montastrea faveolata and Montastrea franksi, were sampled over a depth gradient from 1 to 17 m during this period of elevated temperature and contained lower densities of symbiotic dinoflagellates in deeper corals than seen in previous "nonbleaching" years. Fluorescence analysis by pulse-amplitude modulation fluorometry revealed severe damage to photosystem II (PSII) in remaining symbionts within the corals, with greater damage indicated at deeper depths. Dinoflagellates with the greatest loss in PSII activity also showed a significant decline in the D1 reaction center protein of PSII, as measured by immunoblot analysis. Laboratory experiments on the temperature-sensitive species Montastrea annularis, as well as temperature-sensitive and temperature-tolerant cultured symbiotic dinoflagellates, confirmed the temperature-dependent loss of PSII activity and concomitant decrease in D1 reaction center protein seen in symbionts collected from corals naturally bleached on the reef. In addition, variation in PSII repair was detected, indicating that perturbation of PSII protein turnover rates during photoinhibition at elevated temperatures underlies the physiological collapse of symbionts in corals susceptible to heat-induced bleaching.

In vitro reconstitution of the photosystem I light-harvesting complex LHCI-730: heterodimerization is required for antenna pigment organization.

Here we describe the in vitro reconstitution of photosystem I light-harvesting complexes with pigments and proteins (Lhca1 and Lhca4) obtained by overexpression of tomato Lhca genes in Escherichia coli. Using Lhca1 and Lhca4 individually for reconstitution results in monomeric pigment-proteins, whereas a combination thereof yields a dimeric complex. Interactions of the apoproteins is highly specific, as reconstitution of either of the two constituent proteins in combination with a light-harvesting protein of photosystem II does not result in dimerization. The reconstituted Lhca1/4, but not complexes obtained with either Lhca1 or Lhca4 alone, closely resembles the native LHCI-730 dimer from tomato leaves with regard to spectroscopic properties, pigment composition, and stoichiometry. Monomeric complexes of Lhca1 or Lhca4 possess lower pigment/protein ratios, indicating that interactions of the two subunits not only facilitates pigment reorganization but also recruitment of additional pigments. In addition to higher averages of chlorophyll a/b ratios in monomeric complexes than in LHCI-730, comparative fluorescence and CD spectra demonstrate that heterodimerization involves preferential ligation of more chlorophyll b.

Requirement for the H phosphoprotein in photosystem II of Chlamydomonas reinhardtii.

To dissect the expression of the psbB gene cluster of the Chlamydomonas reinhardtii chloroplast genome and to assess the role of the photosystem II H-phosphoprotein (PSII-H) in the biogenesis and/or stabilization of PSII, an aadA gene cassette conferring spectinomycin resistance was employed for mutagenesis. Disruption of the gene cluster has no effect on the abundance of transcripts of the upstream psbB/T locus. Likewise, interruption of psbB/T and psbH with a strong transcriptional terminator from the rbcL gene does not influence transcript accumulation. Thus, psbB/T and psbH may be independently transcribed, and the latter gene seems to have its own promoter in C. reinhardtii. In the absence of PSII-H, translation and thylakoid insertion of chloroplast PSII core proteins is unaffected, but PSII proteins do not accumulate. Because the deletion mutant also exhibits PSII deficiency when dark-grown, the effect is unrelated to photoinhibition. Turnover of proteins B and C of PSII and the polypeptides PSII protein A and PSII protein D is faster than in wild-type cells but is much slower than that observed in other PSII-deficient mutants of C. reinhardtii, suggesting a peripheral location of PSII-H in PSII. The role of PSII-H on PSII assembly was examined by sucrose gradient fractionation of pulse-labeled thylakoids; the accumulation of high-molecular-weight forms of PSII is severely impaired in the psbH deletion mutant. Thus, a primary role of PSII-H may be to facilitate PSII assembly/stability through dimerization. PSII-H phosphorylation, which possibly occurs at two sites, may also be germane to its role in regulating PSII structure, stabilization, or activity.

Mitochondrial DNA migration events in yeast and humans: integration by a common end-joining mechanism and alternative perspectives on nucleotide substitution patterns.

In contrast to extensive infiltration of plant nuclear genomes by mitochondrial and chloroplast DNA fragments, a computer assessment method could only detect seven mitochondrial DNA integration events in Saccharomyces cerevisiae chromosomes and five examples of DNA migration into mammalian nuclear genes. No evidence could be detected for mitochondrial DNA insertion into chromosome III of Caenorhabditis elegans or in nuclear DNA sequences of Drosophila sp. or Plasmodium falciparum. Thus, the quantity of organellar DNA in the nucleus appears to vary amongst organisms and is lower in Saccharomyces cerevisiae than suggested by experimental plasmid systems. As in plants, migratory mitochondrial DNA fragments in yeast and mammals are found in intergenic regions and introns. Although many of these insertions are located near retroelements, mitochondrial DNA incorporation appears to be independent of retroelement insertion. Comparison of the mitochondrial DNA fragments with mitochondrial transcription maps suggest that two fragments may have transposed through DNA-based and one through RNA-based mechanisms. Analyses of the integration sites indicate that organellar DNA sequences are incorporated by an end-joining mechanism common to yeast, mammals, and plants. The transferred sequences also provide a novel perspective on rates and patterns of nucleotide substitution. Analysis of the D-loop region including a nuclear copy of mitochondrial DNA supports a progressive reduction in D-loop length within both monkey and great apes mitochondrial lineages. Relative distance tests polarized with nuclear copies of the mitochondrial 12S/16S rRNA region suggest that a constant number of transversions has accumulated within the great ape clade, but the number of transitions in orangutan is elevated with respect to members of the human/chimp/gorilla clade. In addition to DNA migration events, 29 nuclear/mitochondrial genes were identified in GenBank that appear to result from inadvertent ligation of nuclear and mitochondrial mRNA transcripts during the cloning process.

Pervasive migration of organellar DNA to the nucleus in plants.

A surprisingly large number of plant nuclear DNA sequences inferred to be remnants of chloroplast and mitochondrial DNA migration events were detected through computer-assisted database searches. Nineteen independent organellar DNA insertions, with a median size of 117 bp (range of 38 to > 785 bp), occur in the proximity of 15 nuclear genes. One fragment appears to have been passed through a RNA intermediate, based on the presence of an edited version of the mitochondrial gene in the nucleus. Tandemly arranged fragments from disparate regions of organellar genomes and from different organellar genomes indicate that the fragments joined together from an intracellular pool of RNA and/or DNA before they integrated into the nuclear genome. Comparisons of integrated sequences to genes lacking the insertions, as well as the occurrence of coligated fragments, support a model of random integration by end joining. All transferred sequences were found in noncoding regions, but the positioning of organellar-derived DNA in introns, as well as regions 5' and 3' to nuclear genes, suggests that the random integration of organellar DNA has the potential to influence gene expression patterns. A semiquantitative estimate was performed on the amount of organellar DNA being transferred and assimilated into the nucleus. Based on this database survey, we estimate that 3-7% of the plant nuclear genomic sequence files contain organellar-derived DNA. The timing and the magnitude of genetic flux to the nuclear genome suggest that random integration is a substantial and ongoing process for creating sequence variation.

Light-Harvesting Chlorophyll a/b Complexes: Interdependent Pigment Synthesis and Protein Assembly.

The biogenetic interdependence of light-harvesting chlorophyll (Chl) a/b proteins (LHCPs) and antenna pigments has been analyzed for two nuclear mutants of Chlamydomonas that have low levels of Chl b, neoxanthin, and loroxanthin. In mutant PA2.1, the apoprotein precursors (pLHCP II) of the major light-harvesting complex LHC II were synthesized at approximately wild-type rates, processed to their mature size, and rapidly degraded. Because the bulk of labile LHCP II in PA2.1 was soluble, a thylakoid integration factor apparently is defective in this strain. Chl a, Chl b, neoxanthin, and loroxanthin synthesis and accumulation were coordinately reduced in PA2.1, indicating that LHCP II play important regulatory or substrate roles in de novo synthesis of these pigments. Mutant GE2.27 is impaired principally in Chl b synthesis but nonetheless accumulated wild-type levels of all LHCPs. Topology studies of the GE2.27 LHCP II demonstrated that their insertion into thylakoids was incomplete even though they were not structurally altered. Thus, Chl b formation mediates conformational changes of LHCP II after thylakoid integration is initiated. GE2.27 also exhibited very low rates of neoxanthin synthesis and was unable to accumulate loroxanthin. Revertant GE2.27 strains with varying capacities for Chl b formation provided additional evidence that neoxanthin synthesis and accumulation are coupled with the final steps of LHCP II integration into thylakoids. We propose that biogenesis of LHC includes interdependent pigment synthesis/assembly events that occur during LHCP integration into the thylakoid membrane and that defects in these events account for the pleiotropic characteristics of many Chl b-deficient mutants.

The psbB gene cluster of the Chlamydomonas reinhardtii chloroplast: sequence and transcriptional analyses of psbN and psbH.

We have sequenced and characterized the complete psbB gene cluster of Chlamydomonas reinhardtii chloroplast DNA. Although the petB and petD genes are located elsewhere, the sequential order of psbB, ORF31, psbN and psbH is identical to that of the psbB operon in higher plants. Also, intergenic non-coding regions are much larger in the Chlamydomonas gene cluster. Northern blot analyses indicate the formation of dicistronic transcripts of psbB and ORF31 and monocistronic transcripts of psbN and psbH. It is unclear whether a psbB operon is transcribed to yield a large polycistronic precursor but northern blot analysis with total RNA from cells grown at 15 degrees C does not detect an increased complexity of the transcripts, as has been found in studies of the psbB operon of higher plants. From primer extension and nuclease protection assays, it is apparent that 5' and 3' processing of the primary psbH transcript results in the accumulation of a heterogenous population of mRNAs. Northern blot analyses reveal transcription of Chlamydomonas psbN and show that its mRNA is much larger than that identified in liverwort and pea. The sequence identities of the PSII-H and PSII-N polypeptides as compared to their vascular plant counterparts is 50 to 62%. While the amino acid sequences of PSII-H and PSII-N proteins are significantly conserved, the mass of PSII-H from Chlamydomonas is significantly larger.

Regulation of chlorophyll apoprotein expression and accumulation. Requirements for carotenoids and chlorophyll.

Chlorophyll apoprotein accumulation and expression were examined in mutants of Chlamydomonas reinhardtii blocked at specific steps of carotenoid or chlorophyll synthesis. In the absence of carotenoids: 1) apoproteins of the core and light-harvesting complexes of photosystem I (CCI and LHCI, respectively) and photosystem II (CCII and LHCII, respectively) do not accumulate; 2) mRNAs for the CCI, CCII, and LHCII apoproteins accumulate to normal levels; and 3) synthesis of the chlorophyll apoproteins is differentially affected, or in some cases, not affected. In the absence of chlorophylls: 1) the apoproteins fail to accumulate; 2) mRNA levels for CCI and CCII apoproteins are relatively unchanged; 3) levels of LHCII apoprotein mRNA, but not rates of LHCII mRNA synthesis, are reduced in a light-dependent chlorophyll-synthesis mutant (ya12); and 4) synthesis of chlorophyll apoproteins is differentially affected or not affected in the case of several chloroplast-encoded apoproteins. These results demonstrate a direct role for carotenoids as well as chlorophylls in the stabilization of certain chlorophyll apoproteins and, for others, possibly in their translation. The data also indicate a role for chlorophyll synthesis in the stability of LHCII mRNA.

In vitro reconstitution of a light-harvesting gene product: deletion mutagenesis and analyses of pigment binding.

AB96, a gene encoding a Pisum sativum chlorophyll a/b binding protein [Coruzzi et al. (1983) J. Biol. Chem. 258, 1399-1402], can be expressed in Escherichia coli and reconstituted with pigments by the procedure described by Plumley and Schmidt [(1987) Proc. Natl. Acad. Sci. U.S.A. 84, 146-150]. Following purification by polyacrylamide gel electrophoresis, the reconstituted pigment-protein complex (CP2) is shown to have similar pigment-binding characteristics to native CP2 complexes isolated from thylakoid membranes. Therefore, the AB96 gene product contains binding sites for chlorophylls a and b and xanthophylls, all of which are necessary for optimal reconstitution in vitro. Absorption, fluorescence, and circular dichroism spectroscopy indicate that the pigments are oriented accurately and that chlorophylls a and b are adjoined for energy transfer. Studies with proteins produced after deletion mutagenesis of AB96 indicate that NH2-terminal amino acids 1-21 and COOH-terminal amino acids 219-228 do not play a role in pigment binding. In contrast, amino acids 50-57 and 204-212 (encompassing one of three conserved histidine residues) are essential for reconstitution. Residues near the presumed NH2- and COOH-terminal alpha-helix boundaries (22-49 and 213-218, respectively) affect the stability of reconstituted CP2 during electrophoresis at 4 degrees C. Correlation of diminished chlorophyll a binding with disappearance of a negative circular dichroism near 684 nm suggests that amino acids 213-218 near the COOH-terminal boundary of the third membrane-spanning helix affect the binding of some chlorophyll a molecules.

Pigment and protein composition of reconstituted light-harvesting complexes and effects of some protein modifications.

The structure and heterogeneity of LHC II were studied by in vitro reconstitution of apoproteins with pigments (Plumley and Schmidt 1987, Proc Natl Acad Sci 84: 146-150). Reconstituted CP 2 complexes purified by LDS-PAGE were subsequently characterized and shown to have spectroscopic properties and pigment-protein compositions and stoichiometries similar to those of authentic complexes. Heterologous reconstitutions utilizing pigments and light-harvesting proteins from spinach, pea and Chlamydomonas reinhardtii reveal no evidence of specialized binding sites for the unique C. reinhardtii xanthophyll loroxanthin: lutein and loroxanthin are interchangeable for in vitro reconstitution. Proteins modified by the presence of a transit peptide, phosphorylation, or proteolytic removal of the NH2-terminus could be reconstituted. Evidence suggests that post-translational modification are not responsible for the presence of six electrophoretic variants of C. reinhardtii CP 2. Reconstitution is blocked by iodoacetamide pre-treatment of the apoproteins suggesting a role for cysteine in pigment ligation and/or proper folding of the pigment-protein complex. Finally, no effect of divalent cations on pigment reassembly could be detected.

Chlororespiration: an adaptation to nitrogen deficiency in Chlamydomonas reinhardtii.

When grown under nitrogen limitation, pronounced chlororespiratory activity develops together with an altered composition of thylakoid membranes in Chlamydomonas reinhardtii. Relative to control cultures, the flash-inhibited, chlororespiration-dependent O2 consumption signal increases 10-fold. Also augmented is the light-sensitive respiratory activity responsible for the "Kok effect," reflecting competitive inhibition of chlororespiratory electron transport by photosystem I. Fluorescence measurements show that the thylakoid plastoquinone pool is extensively reduced in dark-adapted, N-limited cells. Thylakoids of N-limited cells have reduced amounts of cytochrome b6, cytochrome f, and light-harvesting complexes. However, thylakoid-bound NADH-PQ oxidoreductase, with major subunits of 51 kDa and 17 kDa, is increased 7-fold and two novel cytochromes of 34 and 12.5 kDa are highly abundant. Thus, components of photosynthetic and chlororespiratory electron transport pathways are differentially regulated by N availability.

Chloroplast RNA Stability in Chlamydomonas: Rapid Degradation of psbB and psbC Transcripts in Two Nuclear Mutants.

Toward understanding regulation of chloroplast transcript abundance, we have isolated and analyzed nuclear mutant strains of Chlamydomonas reinhardtii that lack chloroplast-encoded mRNAs for photosystem II proteins. Mutant 6.2z5 accumulates no transcripts of the psbC locus for the 43-kilodalton chlorophyll-binding protein. In mutant GE2.10, transcripts of psbB, encoding the 47-kilodalton chlorophyll-binding protein, cannot be detected [Jensen, K.H., Herrin, D.L., Plumley, F.G., and Schmidt, G.W. (1986). J. Cell Biol. 103, 1315-1325]. Also, GE2.10 does not accumulate several low molecular weight transcripts from a region of the chloroplast genome proximal to psbB. The levels of mRNAs from other chloroplast genes are not affected in either mutant. Chloroplast transcription was analyzed in permeabilized cells and by in vivo pulse labeling. Although 5[prime] ribonuclease was found as an artifactual activity of permeabilized cells, the results from both assays demonstrated that wild-type levels of psbC transcription occur in mutant 6.2z5 and that chloroplasts of GE2.10 transcribe psbB and adjacent genes. Thus, it appears that the nuclear genes that are mutated in 6.2z5 and GE2.10 encode products that, respectively, confer stability to transcripts from the psbC and the psbB regions of the chloroplast genome.

RNA splicing in Chlamydomonas chloroplasts. Self-splicing of 23 S preRNA.

The 23 S rRNA gene of the Chlamydomonas reinhardtii chloroplast contains an 888-base pair intron with structural features characteristic of Group I introns. The nuclear, chloroplast ribosome-deficient mutant of C. reinhardtii, ac20, overaccumulates a approximately 3.6-kilobase unspliced 23 S preRNA compared to wild-type cells. We have used [alpha-32P]GTP labeling of total RNA preparations from ac20 to rapidly determine that 23 S preRNA is capable of self-splicing. The ability of the 23 S intron (with flanking exon sequences) to correctly catalyze its own splicing was confirmed using RNA produced by in vitro transcription of cloned DNA. These results identify the first example of a self-splicing RNA of chloroplast origin.

Nitrogen-dependent regulation of photosynthetic gene expression.

Nitrogen-limited Chlamydomonas reinhardtii is chlorotic and very deficient in chlorophyll a/b light-harvesting complexes (LHC). Rates of synthesis of photosynthetic proteins, but especially the LHC apoproteins, are reduced 10- to 40-fold. Moderately high levels of chloroplast transcripts accumulate in nitrogen-limited cells, and there is a correlation between chloroplast DNA levels and chloroplast mRNA abundance. In contrast, nuclear transcripts encoding LHCII and ribulose 1,5-bisphosphate carboxylase small subunits are markedly reduced. Thus, nitrogen availability affects chloroplast protein synthesis by inhibition of translation and, to a lesser extent, chloroplast DNA amplification. Regulation of nuclear-encoded photosynthetic proteins by nitrogen is achieved through mechanisms affecting transcription and/or mRNA stability.