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Biomedical subjects

J Barber

Publications and source records attributed to J Barber.

At least 37 records · Page 2Linked to original sources
PubMed2001

Oxyphotobacteria. Antenna ring around photosystem I.

The oceanic picoplankton Prochlorococcus - probably the most abundant photosynthetic organism on our planet - can grow at great depths where light intensity is very low. We have found that the chlorophyll-binding proteins in a deep-living strain of this oxyphotobacterium form a ring around a trimer of the photosystem I (PS I) photosynthetic reaction centre, a clever arrangement that maximizes the capture of light energy in such dim conditions.

Bacterial Proteins↗
PubMed2001

Localisation of the PsbH subunit in photosystem II: a new approach using labelling of His-tags with a Ni(2+)-NTA gold cluster and single particle analysis.

Photosystem II core dimers were isolated from the green alga Chlamydomonas reinhardtii by Ni(2+)-affinity chromatography exploiting a 6 x His tag located at the N terminus of the PsbH protein. This protein is predicted to have a single transmembrane helix. In order to identify the location of PsbH within the photosystem II complex, the His-tagged core dimers were labelled using a Ni(2+)-NTA gold cluster and subjected to electron microscopy and image analysis. This new method enabled us to identify the location of the labelled His tag by statistical analysis of electron micrographs of the gold-labelled photosystem II complex. Comparison of these data with electron and X-ray crystallographic analysis of photosystem II indicates that the N terminus of PsbH is close to the two transmembrane helices of cytochrome b(559). Our analysis suggests that this approach is a powerful method to locate specific proteins within multisubunit complexes like photosystem II when crystallographic analysis is of insufficient resolution to directly identify amino acid side-chains. Moreover, it can be combined with cross-linking studies, and here we demonstrate that PsbH is a near neighbour of PsbX, which is consistent with the latter subunit being located close to the alpha and beta-subunits of cytochrome b(559). However, cross-linking between PsbH and PsbW was not detected despite the fact that the latter cross-linked with the alpha-subunit of cytochrome b(559).

Animals↗
PubMed2001

Subunit positioning and transmembrane helix organisation in the core dimer of photosystem II.

Recently 3D structural models of the photosystem II (PSII) core dimer complexes of higher plants (spinach) and cyanobacteria (Synechococcus elongatus) have been derived by electron [Rhee et al. (1998) Nature 396, 283-286; Hankamer et al. (2001) J. Struct. Biol., in press] and X-ray [Zouni et al. (2001) Nature 409, 739-743] crystallography respectively. The intermediate resolutions of these structures do not allow direct identification of side chains and therefore many of the individual subunits within the structure are unassigned. Here we review the structure of the higher plant PSII core dimer and provide evidence for the tentative assignment of the low molecular weight subunits. In so doing we highlight the similarities and differences between the higher plant and cyanobacterial structures.

Cell Membrane↗
PubMed2001

Three-dimensional model and characterization of the iron stress-induced CP43'-photosystem I supercomplex isolated from the cyanobacterium Synechocystis PCC 6803.

The cyanobacterium Synechocystis PCC 6803 has been subjected to growth under iron-deficient conditions. As a consequence, the isiA gene is expressed, and its product, the chlorophyll a-binding protein CP43', accumulates in the cell. Recently, we have shown for the first time that 18 copies of this photosystem II (PSII)-like chlorophyll a-binding protein forms a ring around the trimeric photosystem I (PSI) reaction center (Bibby, T. S., Nield, J., and Barber, J. (2001) Nature, 412, 743-745). Here we further characterize the biochemical and structural properties of this novel CP43'-PSI supercomplex confirming that it is a functional unit of approximately 1900 kDa where the antenna size of PSI is increased by 70% or more. Using electron microscopy and single particle analysis, we have constructed a preliminary three-dimensional model of the CP43'-PSI supercomplex and used it as a framework to incorporate higher resolution structures of PSI and CP43 recently derived from x-ray crystallography. Not only does this work emphasize the flexibility of cyanobacterial light-harvesting systems in response to the lowering of phycobilisome and PSI levels under iron-deficient conditions, but it also has implications for understanding the organization of the related chlorophyll a/b-binding Pcb proteins of oxychlorobacteria, formerly known as prochlorophytes.

Bacterial Proteins↗
PubMed2001

Iron deficiency induces the formation of an antenna ring around trimeric photosystem I in cyanobacteria.

Although iron is the fourth most abundant element in the Earth's crust, its concentration in the aquatic ecosystems-particularly the open oceans-is sufficiently low to limit photosynthetic activity and phytoplankton growth. Cyanobacteria, a major class of phytoplankton, respond to iron deficiency by expressing the 'iron-stress-induced' gene, isiA(ref. 3). The protein encoded by this gene has an amino-acid sequence that shows significant homology with one of the chlorophyll a-binding proteins (CP43) of photosystem II (PSII). The precise function of the CP43-like protein, here called CP43', has not been elucidated, although there have been many suggestions. Here we show that CP43' associates with photosystem I (PSI) to form a complex that consists of a ring of 18 CP43' molecules around a PSI trimer. This significantly increases the size of the light-harvesting system of PSI. The utilization of a PSII-like protein as an extra antenna for PSI emphasises the flexibility of cyanobacterial light-harvesting systems, and seems to be a strategy which compensates for the lowering of phycobilisome and PSI levels in response to iron deficiency.

Bacterial Proteins↗
PubMed2001

Photosynthetic water oxidation in cytochrome b(559) mutants containing a disrupted heme-binding pocket.

The role of cytochrome b(559) in photosynthetic oxygen evolution has been investigated in three chloroplast mutants of Chlamydomonas reinhardtii, in which one of the two histidine axial ligands to the heme, provided by the alpha subunit, has been replaced by the residues methionine, tyrosine, and glutamine. Photosystem two complexes functional for oxygen evolution could be assembled in the methionine and tyrosine mutants up to approximately 15% of wild type levels, whereas no complexes with oxygen evolution activity could be detected in the glutamine mutant. PSII supercomplexes isolated from the tyrosine and methionine mutants were as active as wild type in terms of light-saturated rates of oxygen evolution but in contrast to wild type contained no bound heme despite the presence of the alpha subunit. Oxygen evolution in the tyrosine and methionine mutants was, however, more sensitive to photoinactivation than the WT. Overall, these data establish unambiguously that a redox role for the heme of cytochrome b(559) is not required for photosynthetic oxygen evolution. Instead, our data provide new evidence of a role for cytochrome b(559) in the protection of the photosystem two complex in vivo.

Animals↗
PubMed2001

Relationship between excitation energy transfer, trapping, and antenna size in photosystem II.

We present a systematic study of the effect of antenna size on energy transfer and trapping in photosystem II. Time-resolved fluorescence experiments have been used to probe a range of particles isolated from both higher plants and the cyanobacterium Synechocystis 6803. The isolated reaction center dynamics are represented by a quasi-phenomenological model that fits the extensive time-resolved data from photosystem II reaction centers and reaction center mutants. This representation of the photosystem II "trapping engine" is found to correctly predict the extent of, and time scale for, charge separation in a range of photosystem II particles of varying antenna size (8-250 chlorins). This work shows that the presence of the shallow trap and slow charge separation kinetics, observed in isolated D1/D2/cyt b559 reaction centers, are indeed retained in larger particles and that these properties are reflected in the trapping dynamics of all larger photosystem II preparations. A shallow equilibrium between the antennae and reaction center in photosystem II will certainly facilitate regulation via nonphotochemical quenching, and one possible interpretation of these findings is therefore that photosystem II is optimized for regulation rather than for efficiency.

Chlorophyll↗
PubMed2001

Surgery versus radiotherapy for muscle invasive bladder cancer.

BACKGROUND: Muscle invasive bladder cancer is a serious clinical problem and is fatal for the majority of patients. Alternative treatments for this condition are radical cystectomy or radical radiotherapy. The choice of treatment varies according to the resident country. The ideal treatment would be a bladder preserving therapy with total eradication of the tumour without compromising survival. OBJECTIVES: The objective of this review was to compare the survival after radical surgery (cystectomy) versus radical radiotherapy in patients with muscle invasive cancer. SEARCH STRATEGY: We searched the Cochrane Controlled Trials Register (July 2000), Medline (July 2000), EMBASE (July 2000), Cancerlit (July 2000), Healthstar (July 2000) and the Database of Abstracts of Reviews of Effectiveness (July 2000). Attempts to contact authors of unpublished data were undertaken. SELECTION CRITERIA: Randomised trials comparing surgery versus radiotherapy were eligible for assessment. DATA COLLECTION AND ANALYSIS: Three reviewers assessed trial quality based on the Cochrane Guidelines. Data was extracted from the text of the article or extrapolated from the Kaplan-Meier plot. The Peto odds ratio was determined to compare the overall-survival and disease-specific survival. Analysis was performed on an intention-to-treat basis and treatment actually received. MAIN RESULTS: Three randomised trials comparing pre-operative radiotherapy followed by radical cystectomy (surgery) versus radical radiotherapy with salvage cystectomy (radical radiotherapy) were eligible for assessment. These trials represented a total of 439 patients, 221 randomised to surgery and 218 to radical radiotherapy. Peto odds ratio analysis consistently favoured surgery in terms of survival. It was significant at 3 (OR = 2.11, 95% CI 1.10,4.07) and 5 years (OR = 2.40, 95% CI 1.35, 4.29) for overall survival and at 3 years (OR = 1.96, 95% CI 1.06,3.65) for disease-specific survival for patients that actually received the protocol treatment. On an intention-to-treat analysis for disease-specific survival, the results were significantly in favour of surgery at 3 years (OR = 1.96, 95% CI 1.06,3.65) but not at 5 years. REVIEWER'S CONCLUSIONS: The evidence from this review suggests that there is no overall statistically significant benefit to radiotherapy or surgery ( with pre-operative radiotherapy) in muscle invasive bladder cancer in terms of survival, but the trends consistently favour surgery.

Confidence Intervals↗
PubMed2001

Three-dimensional structure of the photosystem II core dimer of higher plants determined by electron microscopy.

Here we report the first three-dimensional structure of a higher plant photosystem II core dimer determined by electron crystallography at a resolution sufficient to assign the organization of its transmembrane helices. The locations of 34 transmembrane helices in each half of the dimer have been deduced, 22 of which are assigned to the major subunits D1 (5), D2 (5), CP47 (6), and CP43 (6). CP47 and CP43, located on opposite sides of the D1/D2 heterodimer, are structurally similar to each other, consisting of 3 pairs of transmembrane helices arranged in a ring. Both CP47 and CP43 have densities protruding from the lumenal surface, which are assigned to the loops joining helices 5 and 6 of each protein. The remaining 12 helices within each half of the dimer are attributed to low-molecular-weight proteins having single transmembrane helices. Comparison of the subunit organization of the higher plant photosystem II core dimer reported here with that of its thermophilic cyanobacterial counterpart recently determined by X-ray crystallography shows significant similarities, indicative of a common evolutionary origin. Some differences are, however, observed, and these may relate to variations between the two classes of organisms in antenna linkage or thermostability.

Dimerization↗
PubMed2001

Freedom from smoking: integrating hypnotic methods and rapid smoking to facilitate smoking cessation.

Hypnotic intervention can be integrated with a Rapid Smoking treatment protocol for smoking cessation. Reported here is a demonstration of such an integrated approach, including a detailed description of treatment rationale and procedures for such a short-term intervention. Of 43 consecutive patients undergoing this treatment protocol, 39 reported remaining abstinent at follow-up (6 months to 3 years posttreatment).

Adult↗
PubMed2001

Physicochemical consequences of the perdeuteriation of glutathione S-transferase from S. japonicum.

Glutathione S:-transferase (GST) from Schistosoma japonicum has been prepared in both normal protiated (pGST) and fully deuteriated (dGST) form by recombinant DNA technology. Electrospray mass spectrometry showed that the level of deuteriation in dGST was 96% and was homogeneous across the sample. This result is attributed to the use of a deuterium-tolerant host Escherichia coli strain in the preparation of the protein. 10 heteroatom-bound deuteriums (in addition to the carbon-bound deuteriums) were resistant to exchange when dGST was incubated in protiated buffer. The physicochemical and biological properties of the two proteins were compared. dGST was relatively less stable to heat denaturation and to proteolytic cleavage than was pGST. The midpoint transition temperature for pGST was 54.9 degrees C, whereas that for dGST was 51.0 degrees C. Static light-scattering measurements revealed that the association behavior of dGST is also different from that of pGST. The perdeuteriated enzyme shows a tendency to associate into dimers of the fundamental dimer. This is in contrast with results that have been obtained for other perdeuteriated proteins in which perdeuteriation has been shown to promote dissociation of aggregates. dGST showed a similar K(m) to pGST; similar results had been obtained previously with bacterial alkaline phosphatase. However, whereas the alkaline phosphatase showed a reduced rate of catalysis on deuteriation, dGST exhibited a slightly higher rate of catalysis than pGST. It is clear that the bulk substitution of deuterium for protium has significant effects on the properties of proteins. Until many more examples have been studied, it will be difficult to predict these effects for any given protein. Nevertheless, deuteriation represents an intriguing method of preparing functional analogs of recombinant proteins.

Animals↗
PubMed2000

Supermolecular structure of photosystem II and location of the PsbS protein.

This paper addresses the question of whether the PsbS protein of photosystem two (PS II) is located within the LHC II PS II supercomplex for which a three-dimensional structure has been obtained by cryoelectron microscopy and single particle analysis. The PsbS protein has recently been implicated as the site for non-photochemical quenching. Based both on immunoblotting analyses and structural considerations of an improved model of the spinach LHC II PS II supercomplex, we conclude that the PsbS protein is not located within the supercomplex. Analyses of other fractions resulting from the solubilization of PS Il-enriched membranes derived from spinach suggest that the PsbS protein is located in the LHC II-rich regions that interconnect the supercomplex within the membrane.

Photosynthetic Reaction Center Complex Proteins↗
PubMed2000

Three-dimensional structure of Chlamydomonas reinhardtii and Synechococcus elongatus photosystem II complexes allows for comparison of their oxygen-evolving complex organization.

Electron microscopy and single-particle analyses have been carried out on negatively stained photosystem II (PSII) complexes isolated from the green alga Chlamydomonas reinhardtii and the thermophilic cyanobacterium Synechococcus elongatus. The analyses have yielded three-dimensional structures at 30-A resolution. Biochemical analysis of the C. reinhardtii particle suggested it to be very similar to the light-harvesting complex II (LHCII).PSII supercomplex of spinach, a conclusion borne out by its three-dimensional structure. Not only was the C. reinhardtii LHCII.PSII supercomplex dimeric and of comparable size and shape to that of spinach, but the structural features for the extrinsic OEC subunits bound to the lumenal surface were also similar thus allowing identification of the PsbO, PsbP, and PsbQ OEC proteins. The particle isolated from S. elongatus was also dimeric and retained its OEC proteins, PsbO, PsbU, and PsbV (cytochrome c(550)), which were again visualized as protrusions on the lumenal surface of the complex. The overall size and shape of the cyanobacterial particle was similar to that of a PSII dimeric core complex isolated from spinach for which higher resolution structural data are known from electron crystallography. By building the higher resolution structural model into the projection maps it has been possible to relate the positioning of the OEC proteins of C. reinhardtii and S. elongatus with the underlying transmembrane helices of other major intrinsic subunits of the core complex, D1, D2, CP47, and CP43 proteins. It is concluded that the PsbO protein is located over the CP47 and D2 side of the reaction center core complex, whereas the PsbP/PsbQ and PsbV/PsbU are positioned over the lumenal surface of the N-terminal region of the D1 protein. However, the mass attributed to PsbV/PsbU seems to bridge across to the PsbO, whereas the PsbP/PsbQ proteins protrude out more from the lumenal surface. Nevertheless, within the resolution and quality of the data, the relative positions of the center of masses for OEC proteins of C. reinhardtii and S. elongatus are similar and consistent with those determined previously for the OEC proteins of spinach.

Animals↗
PubMed2000

Revealing the structure of the photosystem II chlorophyll binding proteins, CP43 and CP47.

A review of the structural properties of the photosystem II chlorophyll binding proteins, CP47 and CP43, is given and a model of the transmembrane helical domains of CP47 has been constructed. The model is based on (i) the amino acid sequence of the spinach protein, (ii) an 8 A three-dimensional electron density map derived from electron crystallography and (iii) the structural homology which the membrane spanning region of CP47 shares with the six N-terminal transmembrane helices of the PsaA/PsaB proteins of photosystem I. Particular emphasis has been placed on the position of chlorophyll molecules assigned in the 8 A three-dimensional map of CP47 (K.-H. Rhee, E.P. Morris, J. Barber, W. Kühlbrandt, Nature 396 (1998) 283-286) relative to histidine residues located in the transmembrane regions of this protein which are likely to form axial ligands for chlorophyll binding. Of the 14 densities assigned to chlorophyll, the model predicted that five have their magnesium ions within 4 A of the imidazole nitrogens of histidine residues. For the remaining seven histidine residues the densities attributed to chlorophylls were within 4-8 A of the imidazole nitrogens and thus too far apart for direct ligation with the magnesium ion within the tetrapyrrole head group. Improved structural resolution and reconsiderations of the orientation of the porphyrin rings will allow further refinement of the model.

Amino Acid Sequence↗
PubMed2000

Six year survey of screening for Down's syndrome by maternal age and mid-trimester ultrasound scans.

OBJECTIVE: To assess the effectiveness of antenatal screening for Down's syndrome by maternal age and routine mid-pregnancy ultrasound scanning. DESIGN: Retrospective six year survey. SETTING: Maternity units of a district general hospital. SUBJECTS: Pregnant women booked for delivery in hospital between 1 January 1993 and 31 December 1998. MAIN OUTCOME MEASURES: All cases of Down's syndrome occurring in district identified from regional congenital anomaly register and cytogenetic laboratory records. Women's case notes were examined to identify indication for karyotyping, gestation at diagnosis, and outcome of pregnancy. RESULTS: 31 259 deliveries occurred during study period, and 57 cases of Down's syndrome were identified, four in failed pregnancies and 53 in ongoing pregnancies or in neonates. The analysis was confined to ongoing pregnancies or liveborn children. Invasive antenatal tests were performed in 6.6% (2053/31 259), and 68% (95% confidence interval 56% to 80%) of cases of Down's syndrome were detected antenatally, giving a positive predictive value of 1.8%. There were 17 undetected cases, and in seven of these the women had declined an offer of invasive testing. In women aged less than 35 years the detection rate was 53% (30% to 76%). Most of the cases detected in younger women followed identification of ultrasound anomalies. CONCLUSIONS: The overall detection rate was considerably higher than assumed in demonstration projects for serum screening. As a result, the benefits of serum screening are much less than supposed. Before any new methods to identify Down's syndrome are introduced, such as nuchal translucency or first trimester serum screening, the techniques should be tested in properly controlled trials.

Adult↗