[Retrospective investigation of anti-VEGF treatment reality and effectiveness in patients with neovascular age-related macular degeneration (AMD) in Germany: treatment reality of ranibizumab for neovascular AMD in Germany]. / Retrospektive Untersuchung der Anti-VEGF-Behandlungsrealität und Wirksamkeit bei Patienten mit neovaskulärer altersabhängiger Makuladegeneration (nAMD) in Deutschland : Behandlungsrealität von Ranibizumab bei nAMD in Deutschland.

BACKGROUND: Neovascular (wet) age-related macular degeneration (wAMD) is a progressive and degenerative retinal disease. This study reports the real-life use in Germany of the standard anti-vascular endothelial growth factor (VEGF) therapy for wAMD as an intravitreal operative drug application. PATIENTS AND METHODS: Within the framework of an international retrospective study the medical records of patients with wAMD who were first treated with ranibizumab between 1 January and 31 August 2009 were evaluated. Data were collected until the end of treatment and/or monitoring or until 31 August 2011. The primary objective was to evaluate changes in visual acuity after the start of anti-VEGF therapy. Secondary outcomes included determining real-life anti-VEGF treatment regimens and disease-monitoring practices. RESULTS: Out of 2227 patients who received ≥ 1 anti-VEGF injection with a baseline visual acuity assessment and ≥ 1 post-baseline visual acuity assessment for the treated eye, 420 were included in the German cohort. Visual acuity improved until about day 90 but these gains in visual acuity were not maintained. The mean changes in visual acuity scores from baseline to years 1 and 2 were 1.1 ± 15.7 and - 0.8 ± 17.2 letters, respectively. Patients received a mean of 4.3 ± 1.9 and 1.3 ± 2.2 injections in years 1 and 2, respectively. The majority of visits ( 98.6 %) were conducted irregularly and outside the time frame recommended at the time of the study, with an average of 47.7 ± 36.7 days between visits. More frequent visits and injections were associated with greater improvements in visual acuity. CONCLUSION: Treatment intensity was not sufficient to maintain the initial improvement in visual acuity by ranibizumab treatment. Real-life results for visual acuity and injection frequency in the German cohort were worse at that time than in other countries. Regular follow-up visits as well as timely retreatment in the presence of signs of disease activity are required to achieve optimal results in wAMD when applying a pro re nata-based strategy.

Comparing simple root phenotyping methods on a core set of rice genotypes.

Interest in belowground plant growth is increasing, especially in relation to arguments that shallow-rooted cultivars are efficient at exploiting soil phosphorus while deep-rooted ones will access water at depth. However, methods for assessing roots in large numbers of plants are diverse and direct comparisons of methods are rare. Three methods for measuring root growth traits were evaluated for utility in discriminating rice cultivars: soil-filled rhizotrons, hydroponics and soil-filled pots whose bottom was sealed with a non-woven fabric (a potential method for assessing root penetration ability). A set of 38 rice genotypes including the OryzaSNP set of 20 cultivars, additional parents of mapping populations and products of marker-assisted selection for root QTLs were assessed. A novel method of image analysis for assessing rooting angles from rhizotron photographs was employed. The non-woven fabric was the easiest yet least discriminatory method, while the rhizotron was highly discriminatory and allowed the most traits to be measured but required more than three times the labour of the other methods. The hydroponics was both easy and discriminatory, allowed temporal measurements, but is most likely to suffer from artefacts. Image analysis of rhizotrons compared favourably to manual methods for discriminating between cultivars. Previous observations that cultivars from the indica subpopulation have shallower rooting angles than aus or japonica cultivars were confirmed in the rhizotrons, and indica and temperate japonicas had lower maximum root lengths in rhizotrons and hydroponics. It is concluded that rhizotrons are the preferred method for root screening, particularly since root angles can be assessed.

The structure of eukaryotic and prokaryotic complex I.

The structures of the NADH dehydrogenases from Bos taurus and Aquifex aeolicus have been determined by 3D electron microscopy, and have been analyzed in comparison with the previously determined structure of Complex I from Yarrowia lipolytica. The results show a clearly preserved domain structure in the peripheral arm of complex I, which is similar in the bacterial and eukaryotic complex. The membrane arms of both eukaryotic complexes show a similar shape but also significant differences in distinctive domains. One of the major protuberances observed in Y. lipolytica complex I appears missing in the bovine complex, while a protuberance not found in Y. lipolytica connects in bovine complex I a domain of the peripheral arm to the membrane arm. The structural similarities of the peripheral arm agree with the common functional principle of all complex Is. The differences seen in the membrane arm may indicate differences in the regulatory mechanism of the enzyme in different species.

DoG Picker and TiltPicker: software tools to facilitate particle selection in single particle electron microscopy.

Solving the structure of macromolecular complexes using transmission electron microscopy can be an arduous task. Many of the steps in this process rely strongly on the aid of pre-existing structural knowledge, and are greatly complicated when this information is unavailable. Here, we present two software tools meant to facilitate particle picking, an early stage in the single-particle processing of unknown macromolecules. The first tool, DoG Picker, is an efficient and reasonably general, particle picker based on the Difference of Gaussians (DoG) image transform. It can function alone, as a reference-free particle picker with the unique ability to sort particles based on size, or it can also be used as a way to bootstrap the creation of templates or training datasets for other particle pickers. The second tool is TiltPicker, an interactive graphical interface application designed to streamline the selection of particle pairs from tilted-pair datasets. In many respects, TiltPicker is a re-implementation of the SPIDER WEB tilted-particle picker, but built on modern computer frameworks making it easier to deploy and maintain. The TiltPicker program also includes several useful new features beyond those of its predecessor.

The three-dimensional structure of complex I from Yarrowia lipolytica: a highly dynamic enzyme.

The structure of complex I from Yarrowia lipolytica was determined by three-dimensional electron microscopy. A random conical data set was collected from deep stain embedded particles. More than 14000 image pairs were analyzed. Through extensive classification combined with three-dimensional reconstruction, it was possible for the first time to show a much more detailed substructure of the complex. The peripheral arm is subdivided in at least six domains. The membrane arm shows two major protrusions on its matrix facing side and exhibits a channel like feature on the side facing the cytoplasm. Structures resembling a tether connecting the subunits near the catalytic center with the protrusions of the membrane arm provide a second connection between matrix and membrane domain.

Pigment epithelial detachment in the elderly. Clinical differentiation, natural course and pathogenetic implications.

BACKGROUND: A prospective analysis was performed to characterize the angiographic appearance, natural course and prognosis of serous pigment epithelial detachments (PEDs) in elderly patients. The aim was to differentiate PEDs according to their angiographic characteristics and to analyze the specific clinical, visual and morphologic course of the different PEDs. METHODS: Fluorescein and indocyanine green angiography were performed in 101 consecutive patients (53-87 years; 63 female, 38 male) with clinical signs of serous PED and drusen. RESULTS: Different types of serous PED were identified: polypoidal choroidal vasculopathy (PCV)-associated PED in 14 patients (13.9%), vascular PED in 72 (71.2%), and avascular PED in 15 (14.9%). All PEDs resulted initially in similar visual loss. Avascular PEDs were smaller than vascular PEDs, and the latter were smaller than PCV-PEDs. During follow-up these differences were always present, but all PEDs enlarged initially followed by regression. This course was associated in all PEDs with progressive visual loss, accompanied by the development of RPE atrophy in avascular PEDs or disciform scars or RPE tears in the two other types. CONCLUSION: Despite different associations, all PEDs have a similar clinical course with respect to visual loss and enlargement or regression. This is compatible with the proposed common pathogenetic background with a hydrophobic barrier in Bruch's membrane causing fluid resulting from RPE pumping activity to accumulate between the pigment epithelium and Bruch's membrane.

[Pigment epithelium detachments in AMD (age-associated macular degeneration) and "polypoid choroidal vasculopathy". A fluorescein and indocyanine green angiography study]. / Pigmentepithelabhebungen bei AMD und "polypoidal choroidal vasculopathy". Eine fluoreszein- und indozyaningrünangiographische Studie.

AIMS: A prospective analysis to differentiate the angiographic appearance of pigment epithelial detachments (PED) in age-related macular degeneration (AMD) was performed. The aim was to verify if characteristics of polypoidal choroidal vasculopathy (PCV) can be observed in elderly patients with Central European background. PATIENTS AND METHODS: Fluorescein and indocyanine green angiography was performed in 101 consecutive patients (53-87 years, 63 females, 38 males) with clinical signs of PED and drusen. RESULTS: Different types of PED could be differentiated: PCV-associated PED in 14 patients (13.9%), vascularized PED in 72 patients (71.2%), and nonvascularized PED in 15 patients (14.9%). CONCLUSIONS: The clinical diagnosis of PED in AMD can be differentiated by angiography into PCV-associated PED, vascularized PED, and nonvascularized PED. This differentiation is important because PCV-associated PED may have a pathogenetic and genetic background other than age-related changes in Bruch's membrane. These patients also may share a natural course and treatment options different from PED in AMD.

The structure of the V(1)-ATPase determined by three-dimensional electron microscopy of single particles.

We determined the structure of the V(1)-ATPase from Manduca sexta to a resolution of 1.8 nm, which for the first time reveals internal features of the enzyme. The V(1)-ATPase consists of a headpiece of 13.5 nm in diameter, with six elongated subunits, A(3) and B(3), of approximately equal size, and a stalk of 6 nm in length that connects V(1) with the membrane-bound domain, V(O). At the center of the molecule is a cavity that extends throughout the length of the A(3)B(3) hexamer. Inside the cavity the central stalk can be seen connected to only two of the catalytic A subunits. The structure was obtained by a combination of the Random Conical Reconstruction Technique and angular refinements. Additional recently developed techniques that were used include methods for simultaneous translational rotational alignment of the 0 degrees images, contrast transfer function correction for tilt images, and the Two-Step Radon Inversion Algorithm.

The DnaB.DnaC complex: a structure based on dimers assembled around an occluded channel.

Replicative helicases are motor proteins that unwind DNA at replication forks. Escherichia coli DnaB is the best characterized member of this family of enzymes. We present the 26 A resolution three-dimensional structure of the DnaB hexamer in complex with its loading partner, DnaC, obtained from cryo-electron microscopy. Analysis of the volume brings insight into the elaborate way the two proteins interact, and provides a structural basis for control of the symmetry state and inactivation of the helicase by DnaC. The complex is arranged on the basis of interactions among DnaC and DnaB dimers. DnaC monomers are observed for the first time to arrange as three dumb-bell-shaped dimers that interlock into one of the faces of the helicase. This could be responsible for the freezing of DnaB in a C(3) architecture by its loading partner. The central channel of the helicase is almost occluded near the end opposite to DnaC, such that even single-stranded DNA could not pass through. We propose that the DnaB N-terminal domain is located at this face.

The first three-dimensional structure of phosphofructokinase from Saccharomyces cerevisiae determined by electron microscopy of single particles.

Phosphofructokinaseis a key regulatory enzyme of the glycolytic pathway. We have determined the structure of this enzyme from Saccharomyces cerevisiae to a resolution of 2.0 nm. This is the first structure available for this family of enzymes in eukaryotic organisms. Phosphofructokinase is an octamer composed of 4alpha and 4beta subunits arranged in a dihedral point group symmetry D(2). The enzyme has a very open and elongated structure, with dimensions of 24 nm in length and 17 nm in width. The final structure, calculated from 0 degrees tilt projections of the molecule at random orientations using as reference the volume obtained by the random conical reconstruction technique in ice, has allowed us to discern the shapes of the subunits and their mutual arrangement in the octamer.

The structure of ribosome-channel complexes engaged in protein translocation.

Cotranslational translocation of proteins requires ribosome binding to the Sec61p channel at the endoplasmic reticulum (ER) membrane. We have used electron cryomicroscopy to determine the structures of ribosome-channel complexes in the absence or presence of translocating polypeptide chains. Surprisingly, the structures are similar and contain 3-4 connections between the ribosome and channel that leave a lateral opening into the cytosol. Therefore, the ribosome-channel junction may allow the direct transfer of polypeptides into the channel and provide a path for the egress of some nascent chains into the cytosol. Moreover, complexes solubilized from mammalian ER membranes contain an additional membrane protein that has a large, lumenal protrusion and is intercalated into the wall of the Sec61p channel. Thus, the native channel contains a component that is not essential for translocation.

A comparison of the yeast and rabbit 80 S ribosome reveals the topology of the nascent chain exit tunnel, inter-subunit bridges and mammalian rRNA expansion segments.

Protein synthesis in eukaryotes is mediated by both cytoplasmic and membrane-bound ribosomes. During the co-translational translocation of secretory and membrane proteins, eukaryotic ribosomes dock with the protein conducting channel of the endoplasmic reticulum. An understanding of these processes will require the detailed structure of a eukaryotic ribosome. To this end, we have compared the three-dimensional structures of yeast and rabbit ribosomes at 24 A resolution. In general, we find that the active sites for protein synthesis and translocation have been highly conserved. It is interesting that a channel was visualized in the neck of the small subunit whose entrance is formed by a deep groove. By analogy with the prokaryotic small subunit, this channel may provide a conserved portal through which mRNA is threaded into the decoding center. In addition, both the small and large subunits are built around a dense tubular network. Our analysis further suggests that the nascent chain exit tunnel and the docking surface for the endoplasmic reticulum channel are formed by this network. We surmise that many of these features correspond to rRNA, based on biochemical and structural data. Ribosomal function is critically dependent on the specific association of small and large subunits. Our analysis of eukaryotic ribosomes reveals four conserved inter-subunit bridges with a geometry similar to that found in prokaryotes. In particular, a double-bridge connects the small subunit platform with the interface canyon on the large subunit. Moreover, a novel bridge is formed between the platform and the base of the L1 domain. Finally, size differences between mammalian and yeast large subunit rRNAs have been correlated with five expansion segments that form two large spines and three extended fingers. Overall, we find that expansion segments within the large subunit rRNA have been incorporated at positions distinct from the active sites for protein synthesis and translocation.

Biophysical and structural characterization of proton-translocating NADH-dehydrogenase (complex I) from the strictly aerobic yeast Yarrowia lipolytica.

Mitochondrial proton-translocating NADH-dehydrogenase (complex I) is one of the largest and most complicated membrane bound protein complexes. Despite its central role in eukaryotic oxidative phosphorylation and its involvement in a broad range of human disorders, little is known about its structure and function. Therefore, we have started to use the powerful genetic tools available for the strictly aerobic yeast Yarrowia lipolytica to study this respiratory chain enzyme. To establish Y. lipolytica as a model system for complex I, we purified and characterized the multisubunit enzyme from Y lipolytica and sequenced the nuclear genes coding for the seven central subunits of its peripheral part. Complex I from Y lipolytica is quite stable and could be isolated in a highly pure and monodisperse state. One binuclear and four tetranuclear iron-sulfur clusters, including N5, which was previously known only from mammalian mitochondria, were detected by EPR spectroscopy. Initial structural analysis by single particle electron microscopy in negative stain and ice shows complex I from Y. lipolytica as an L-shaped particle that does not exhibit a thin stalk between the peripheral and the membrane parts that has been observed in other systems.

Three-dimensional structure and subunit topology of the V(1) ATPase from Manduca sexta midgut.

The three-dimensional structure of the Manduca sexta midgut V(1) ATPase has been determined at 3.2 nm resolution from electron micrographs of negatively stained specimens. The V(1) complex has a barrel-like structure 11 nm in height and 13.5 nm in diameter. It is hexagonal in the top view, whereas in the side view, the six large subunits A and B are interdigitated for most of their length (9 nm). The topology and importance of the individual subunits of the V(1) complex have been explored by protease digestion, resistance to chaotropic agents, MALDI-TOF mass spectrometry, and CuCl(2)-induced disulfide formation. Treatment of V(1) with trypsin or chaotropic iodide resulted in a rapid cleavage or release of subunit D from the enzyme, indicating that this subunit is exposed in the complex. Trypsin cleavage of V(1) decreased the ATPase activity with a time course that was in line with the cleavage of subunits B, C, G, and F. When CuCl(2) was added to V(1) in the presence of CaADP, the cross-linked products A-E-F and B-H were generated. In experiments where CuCl(2) was added after preincubation of CaATP, the cross-linked products E-F and E-G were formed. These changes in cross-linking of subunit E to near-neighbor subunits support the hypothesis that these are nucleotide-dependent conformational changes of the E subunit.

[Volume determination of pigment epithelium detachment in AMD by laser scanning tomography]. / Volumenbestimmung von Pigmentepithelabhebungen bei AMD mittels Laser-Scanning-Tomographie.

BACKGROUND: The possibility of using 3D mapping of AMD-related RPE detachments by means of laser scanning tomography was evaluated to correlate the fluorescein and tomographic findings. METHODS: Sixty eyes with AMD-related RPE detachments of 55 consecutive patients (19 men, 36 women) between 54 and 87 years of age (mean: 72.2 years) were examined using the Heidelberg Retina Tomograph (HRT). The parameters considered were area, volume, maximal height and 3D configuration of the RPE detachments. The tomographic data were analyzed and correlated with the fluorescein angiographic findings. Follow-up examinations were done at 3 and 6 months later. RESULTS: The mean +/- SD area of elevation was 10.59 +/- 5.51 mm2 (range, 0.93-19.73), which correlated well with the angiographic measurements. The mean maximal height was 0.42 +/- 0.19 mm (range, 0.11-0.83), mean volume was 2.55 +/- 1.9 mm3 (range, 0.073-6.63). We found a tendency to grow for untreated RPE detachments, depending on the volume at the first measurement. Three RPE detachments of high volume (mean 0.501 +/- 1.3 mm3) resulted in tearing of the RPE. The angiographic findings of localized neovascularizations in the RPE detachment area (39 of 60 eyes) showed a corresponding irregularity of the surface in most of the correlating 3D HRT figures. CONCLUSIONS: Confocal laser scanning tomography allows analysis of 3D configurations and a quantitative measurement of RPE detachments in AMD. Therefore, this diagnostic technique appears to be useful, especially for differentiated follow-up examinations (as in therapy-control studies). Furthermore, the analysis of 3D configurations seems to be useful to estimate the risk of tearing of the RPE and may help to indicate underlying neovascularizations.

Fast and accurate three-dimensional reconstruction from projections with random orientations via radon transforms

A new algorithm for three-dimensional reconstruction from randomly oriented projections has been developed. The algorithm recovers the 3D Radon transform from the 2D Radon transforms (sinograms) of the projections. The structure in direct space is obtained by an inversion of the 3D Radon transform. The mathematical properties of the Radon transform are exploited to design a special filter that can be used to correct inconsistencies in a data set and to fill the gaps in the Radon transform that originate from missing projections. Several versions of the algorithm have been implemented, with and without a filter and with different interpolation methods for merging the sinograms into the 3D Radon transform. The algorithms have been tested on analytical phantoms and experimental data and have been compared with a weighted back projection algorithm (WBP). A quantitative analysis of phantoms reconstructed from noise-free and noise-corrupted projections shows that the new algorithms are more accurate than WBP when the number of projections is small. Experimental structures obtained by the new methods are strictly comparable to those obtained by WBP. Moreover, the algorithm is more than 10 times faster than WPB when applied to a data set of 1000-5000 projections. Copyright 1999 Academic Press.

A fluorescein and indocyanine green angiographic study of choriocapillaris in age-related macular disease.

OBJECTIVE: To examine the phenomenon of a prolonged choroidal filling phase (PCFP) as seen on fluorescein and indocyanine green (ICG) angiography in patients with early age-related macular disease (AMD). METHODS: One hundred eyes of consecutive patients with early AMD were studied. Patchy and slow choroidal filling in early fluorescein and distinct areas of reduced choroidal fluorescence in ICG angiography were interpreted as PCFP. In addition, associated drusen characteristics and the AMD status of the fellow eye were recorded. RESULTS: A PCFP was observed in 26% of eyes using fluorescein and 32% of eyes using ICG angiography, with good concordance between findings using both techniques (K = 0.9). A PCFP was associated with confluent drusen (P = .01), the presence of focal retinal pigment epithelial-atrophic patches in the study eye (P=.005), and geographic atrophy in the fellow eye (P=.03). Other drusen characteristics and the distribution of visual acuity (P = .90) were not different between eyes with and without PCFP. CONCLUSIONS: A PCFP on fluorescein and ICG angiography is a common feature in early AMD. This sign has been interpreted as indicating reduced choroidal perfusion caused by change in diffusional characteristics of Bruch membrane. A PCFP is a clinical marker for diffuse deposits in Bruch membrane and a risk factor for the development of geographic atrophy.

Molecular architecture of Manduca sexta midgut V1 ATPase visualized by electron microscopy.

The structure of the V1 ATPase from the tobacco hornworm Manduca sexta has been determined from electron micrographs of isolated, negatively stained specimens. The resulting images clearly show a pseudohexagonal arrangement of six equal-sized protein densities, presumably representing the three copies each of subunits A and B, which comprise the headpiece of the enzyme. A seventh density could be observed either centrally or asymmetrically to the hexamer. The maximum diameter of the V1 complex in the hexagonal projection is 13 nm with each of the six peripheral densities being 3-4 nm in diameter.

3D reconstruction of the ATP-bound form of CCT reveals the asymmetric folding conformation of a type II chaperonin.

The type II chaperonin CCT (chaperonin containing Tcp-1) of eukaryotic cytosol is a heteromeric 16-mer particle composed of eight different subunits. Three-dimensional reconstructions of apo-CCT and ATP-CCT have been obtained at 28 A resolution by cryo-electron microscopy. Binding of ATP generates an asymmetric particle; one ring has a slightly different conformation from the apo-CCT ring, while the other has undergone substantial movements in the apical domains. Upon ATP binding the apical domains rotate and point towards the cylinder axis, so that the helical protrusions present at their tips could act as a lid closing the ring cavity.