Which polypeptides are characteristic for photosystem II? Analysis of active photosystem II particles from the blue-green alga Anacystis nidulans

A thylakoid membrane preparation isolated from the blue-green alga Anacystis nidulans was freed from carboxysomes, soluble enzymes and the pigment P750 by floating in a discontinuous sucrose density gradient. In a buffer containing sucrose and the zwitterionic detergent Miranol S2M-SF the thylakoids were loaded on a linear 10-18% sucrose density gradient which also contained Miranol. The sedimentation yielded three bands, the lower two of which were green and the upper one was orange. The light green band in the middle of the gradient was the only one to show any photosystem II activity. This was measured as light-induced electron transport from diphenylcarbazide (DPC) to dichlorophenol-indophenol (DCPIP). The activity was sensitive to dichlorophenyl-dimethylurea (DCMU). The red absorption maximum of the particles in this middle band - henceforth called photosystem II particles - was found at 672 nm and the maximum of their low temperature fluorescence emission spectrum at 685 nm upon excitation with blue light. Cytochrome b559 was the only cytochrome found in these particles; it was present at an average ratio of one molecule cytochrome per 40 -50 molecules chlorophyll a. C550 photoreduction with accompanying photooxidation of cytochrome b559 was also observed in the photosystem II particles. Good photosystem II preparations did not contain any detectable amounts of P 700. By means of sodium dodecylsulfate polyacrylamide gel electrophoresis the polypeptide composition of the photosystem II particles was studied. Dissolution of the chlorophyll protein complexes was done under strongly denaturing conditions; consequently, no green bands were observed on the gels. The polypeptide pattern of the photosystem II particles showed two strong predominant bands of protein components with apparent molecular weights (app. mol. wts.) of about 50 000 and 48 000. These two bands are unique for photosystem II. Two other weaker bands were also found characteristic for photosystem II, the band of a polypeptide with an app. mol. wt. of 38 000 and that of a polypeptide with an app. mol. wt. of 31 000. Sometimes in addition the weak band of a polypeptide with the app. mol. wt. 27 000 was observed on the gel. The polypeptide 38 000 aggregated upon boiling of the sample in the presence of the denaturing agents prior to the electrophoresis, yielding an aggregate with an app. mol. wt. of 50 000. Additional polypeptides which were often found in the photosystem II particle preparation could be identified as subunits of the coupling factor of photophosphorylation CF1. None of the polypeptides described as characteristic for photosystem II are due to proteolytic activity. As the observed photosystem II activity was found to be DCMU-sensitive it appears that the DCMU-binding protein is among the here described photosystem II polypeptides. Moreover, the authors have reason to believe that one of the major protein components found characteristic for photosystem II is cytochrome b559

How to Search for Biological Data? A Comparison of User Interfaces in a Semantic Search

Data discovery is a frequent task in a scholar's daily work. In biodiversity, data search is a particular challenge. Here, scholars have complex information needs such as the rich interplay of organisms and their environments that cannot be unambiguously expressed with a traditional keyword search, e.g., Does tree diversity reduce competition in a subtropical forest? Therefore, data repositories usually offer interfaces that enable users to browse datasets by a pre-determined set of categories or facets. Faceted search is a good compromise between cumbersome user interfaces for structured queries (e.g., using SPARQL) and natural language queries that are hard to interpret for machines. Thus, developers can specify relevant relationships between entities explicitly and users can filter search results by selecting proper categories. For the given query, appropriate categories could be Organism and Habitat. However, there are two crucial design issues that have an impact on the effectiveness of category-based query interfaces: The choice of proper categories and the visual presentation of these categories in the query interface. In our work, we focus on the second aspect. We aim to develop two query interfaces: (a) a common one-box keyword search interface that analyzes the entered terms with respect to their categories automatically (b) a form-based query interface where users can enter their search keywords into a form with a query field per category. In both interfaces, the query keywords are matched against concepts in a knowledge base to make their semantics explicit. In case of a successful match the URI is used to obtain the labels of all sub-concepts to expand the query before sending it to the search engine. Retrieved results are displayed in a list. The aim of our system is not to answer the question completely but to support users in retrieving relevant datasets that give hints to answer a research question. In our talk, we will introduce the two interfaces and invite the conference participants to give feedback. We are particularly interested in a discussion on the appropriateness of the suggested user interfaces. Do scholars prefer a form-based user interface or only a one-field search? What other functions might be helpful, e.g., providing more information about other relations and properties from the concept in the ontology? What kind of explanations might be helpful to understand why a certain result was returned

ADOnIS: An ontology-based information system providing seamless integration of structured and unstructured data

Scientific information is contained in structured data like spreadsheets as well as in unstructured data like text. For example, scientific results can manifest themselves in one or more data sets containing main characteristics of the scientific process and one or more publications related to the dataset(s). From a scientist's perspective, it is desirable to obtain seamless access to this information regardless of whether it is based on structured or unstructured data. To this end, we developed and continuously extend the AquaDiva Ontology-based Information System, ADOnIS, which endeavors to provide such functionality

ADOnIS - An ontology-based information system providing seamless integration of structured and unstructured data

The CRC AquaDiva is a large collaborative project spanning a variety of domains, such as biology, geology, chemistry, and computer science with the common goal to better understand the Earth's critical zone in particular how environmental conditions and surface properties shape the structure, properties, and functions of the subsurface. This necessitates the collection and integration of large volumes of heterogeneous data. Besides this structured data, knowledge is also encoded in an unstructured form in publications. Ideally, scientists should be able to seamlessly access both types of information. To this end, we are developing the AquaDiva Ontology-based Information System, ADOnIS. This system gives scientists various ways to upload their datasets into a common repository based on the BExIS framework. To enhance the integration process and to resolve conflicts among heterogeneous datasets, we build a conceptual, ontology-based layer on top of the common repository. Finally, the system grants different mechanisms to search and look for a specific piece of information and/or knowledge, including keyword search, semantic search, and interactive search. In all cases, search results will contain structured data as well as publications obtained from PubMed by using SeMedico. The normal search provides the possibility for a scientist to enter a keyword (or a set of keywords) looking for the existence of this keyword either in the set of available metadata or primary data applying an exact match technique. This kind of search completely ignores the semantics of keywords as well as their relationships. Therefore, ADOnIS also provides semantic search exploiting features introduced by the conceptual layer. Finally, interactive search offers a view covering all the geo-related datasets displayed on a map

Impact of allergy and atopy on the risk of pseudophakic cystoid macular edema

To assess the risk of pseudophakic cystoid macular edema (PCME) following cataract surgery in patients with allergies and/or atopic disorders. Medical records of 3,850 consecutive eyes that underwent cataract surgery were retrospectively reviewed for prevalence of allergies and atopic status and development of PCME. Patients with any known risk factors for PCME were excluded. Macular examination was performed using spectral-domain optical coherence tomography (SD-OCT) before and at 4, 8, 12, 16, 24, and 36 weeks after surgery. If both eyes in one patient underwent cataract surgery, one eye was randomly selected. Odds ratios and confidence intervals were estimated. Out of 240 patients enrolled in this series, 65 patients (27.1 %) showed positive allergic status, 19 patients (7.9 %) suffered from atopic syndromes, and 11 (4.6 %) showed both (allergies and atopic diseases). PCME occurred in eight patients (12.3 %) of the allergy cohort, whereas no patient (0 %) of the atopy cohort developed PCME. The risk of PCME was comparable in patients with allergies or atopic diseases to patients without allergies or atopy (allergy: p = 0.635; odds ratio (OR) 1.303, 95 % confidence interval (CI) 0.461-3.398; atopy: p = 0.234; OR 0.000, 95 % CI 0-1.815). Positive status of allergy or atopy does not seem to increase the risk of PCME. Therefore, postoperative treatment after cataract surgery does not have to be modified in allergic or atopic patients

Preexisting epiretinal membrane is associated with pseudophakic cystoid macular edema

The purpose of the present study was to evaluate whether preexisting epiretinal membrane (ERM) is a significant risk factor for developing pseudophakic cystoid macular edema (PCME). Two hundred four consecutive eyes and 153 consecutive eyes without preexisting epiretinal membranes were retrospectively compared regarding PCME development following phacoemulsification with posterior chamber lens implantation. Patients with vascular retinal diseases, uveitis, trauma, neovascular macular degeneration, chronic inflammatory conditions, diabetic retinopathy, endophthalmitis, eventful cataract surgery, and combination of cataract surgery and vitrectomy during the observation period were excluded. Macular examination was performed using spectral-domain optical coherence tomography (SD-OCT) before as well as at 4, 8, 12, 16, 24, and 36 weeks after cataract surgery. Univariate and multivariate logistic regression analyses were calculated. PCME occurred in 32 of 204 eyes with preexisting ERM (15.7%), whereas 9 of 153 eyes without preexisting ERM (5.9%) developed PCME. The risk of PCME was significantly increased in eyes with ERM (p = 0.007). By multivariate logistic regression analysis, factors predictive of PCME included the history of previous pars plana vitrectomy for retinal detachment (odds ratio (OR) 3.619 [95% confidence interval (CI) 1.242 to 10.258]; p = 0.016) as well as the preexistence of ERM (OR 3.885 [95% CI 1.162 to 17.762]; p = 0.04). Preexisting ERM seems to be associated with an increased risk of PCME following cataract surgery. Therefore, this risk should be considered in surgery planning, preoperative medication, and follow-up care after surgery