Dirk Labudde

Selection of a DNA aptamer against norovirus capsid protein VP1

The genetically and antigenically diverse group of noroviruses is the major cause of human viral epidemic gastroenteritis worldwide. Virus detection and control are thus crucial topics when aiming at containing and preventing the resulting large and often persisting outbreaks. Aptamers provide a promising alternative to antibodies concerning their ability to bind and thus detect and influence bio-active molecules. These small, single-stranded oligonucleotides are able to bind to a multitude of possible target molecules with high affinity. For a specific target the highest affinity aptamers are found by screening a randomized library. In this work a DNA aptamer capable of binding to the norovirus genotype II.4 capsid protein VP1 was found. The general approach is thereby not limited to norovirus capsid, but could be extended to almost any kind of biologically relevant molecule. The development of the library enrichment was further computationally analyzed in order to describe the enrichment during screening. This is the basis for a later extensive characterization of both target and aptamers that could lead to insights regarding the functional coherence of both partners. An abstract model describing this coherence could be utilized to generate a target-specific library, from which future aptamer screening runs could benefit.

New Strategies for Evaluation and Analysis of SELEX Experiments

Aptamers are an interesting alternative to antibodies in pharmaceutics and biosensorics, because they are able to bind to a multitude of possible target molecules with high affinity. Therefore the process of finding such aptamers, which is commonly a SELEX screening process, becomes crucial. The standard SELEX procedure schedules the validation of certain found aptamers via binding experiments, which is not leading to any detailed specification of the aptamer enrichment during the screening. For the purpose of advanced analysis of the accrued enrichment within the SELEX library we used sequence information gathered by next generation sequencing techniques in addition to the standard SELEX procedure. As sequence motifs are one possibility of enrichment description, the need of finding those recurring sequence motifs corresponding to substructures within the aptamers, which are characteristically fitted to specific binding sites of the target, arises. In this paper a motif search algorithm is presented, which helps to describe the aptamers enrichment in more detail. The extensive characterization of target and binding aptamers may later reveal a functional connection between these molecules, which can be modeled and used to optimize future SELEX runs in case of the generation of target-specific starting libraries.

eProS—a database and toolbox for investigating protein sequence–structure–function relationships through energy profiles

Gaining information about structural and functional features of newly identified proteins is often a difficult task. This information is crucial for understanding sequence–structure–function relationships of target proteins and, thus, essential in comprehending the mechanisms and dynamics of the molecular systems of interest. Using protein energy profiles is a novel approach that can contribute in addressing such problems. An energy profile corresponds to the sequence of energy values that are derived from a coarse-grained energy model. Energy profiles can be computed from protein structures or predicted from sequences. As shown, correspondences and dissimilarities in energy profiles can be applied for investigations of protein mechanics and dynamics. We developed eProS (energy profile suite, freely available at http://bioservices.hs-mittweida.de/Epros/), a database that provides ∼76 000 pre-calculated energy profiles as well as a toolbox for addressing numerous problems of structure biology. Energy profiles can be browsed, visualized, calculated from an uploaded structure or predicted from sequence. Furthermore, it is possible to align energy profiles of interest or compare them with all entries in the eProS database to identify significantly similar energy profiles and, thus, possibly relevant structural and functional relationships. Additionally, annotations and cross-links from numerous sources provide a broad view of potential biological correspondences.

Structure Topology Prediction of Discriminative Sequence Motifs in Membrane Proteins with Domains of Unknown Functions

Motivation. Membrane proteins play essential roles in cellular processes of organisms. Photosynthesis, transport of ions and small molecules, signal transduction, and light harvesting are examples of processes which are realised by membrane proteins and contribute to a cells specificity and functionality. The analysis of membrane proteins has shown to be an important part in the understanding of complex biological processes. Genome-wide investigations of membrane proteins have revealed a large number of short, distinct sequence motifs. Results. The in silico analysis of 32 membrane protein families with domains of unknown functions discussed in this study led to a novel approach which describes the separation of motifs by residue-specific distributions. Based on these distributions, the topology structure of the majority of motifs in hypothesised membrane proteins with unknown topology can be predicted. Conclusion. We hypothesise that short sequence motifs can be separated into structure-forming motifs on the one hand, as such motifs show high prediction accuracy in all investigated protein families. This points to their general importance in α-helical membrane protein structure formation and interaction mediation. On the other hand, motifs which show high prediction accuracies only in certain families can be classified as functionally important and relevant for family-specific functional characteristics.

Gesichtsweichteilrekonstruktion mithilfe einer Open-Source-Software

ZusammenfassungHintergrundEine wichtige Aufgabe der forensischen Anthropologie liegt in der Identifizierung von unbekannten Verstorbenen. Hierfür kommen etablierte Identifizierungsverfahren, wie Daktyloskopie, Odontostomatologie und genetischer Fingerabdruck zum Einsatz, die das Vorhandensein von Vergleichsmaterial der vermissten Person voraussetzen. Gibt es jedoch keine Hinweise auf die Person, verbleibt oftmals nur die Möglichkeit einer forensischen Gesichtsweichteilrekonstruktion. Die Methode basiert auf dem hohen Widererkennungsgrad des Gesichts auf Grundlage der knöchernen Strukturen des Schädels und deren anatomischer Merkmale.Ziel der ArbeitEs sollte der Anwendungsversuch eines neuartigen, kostengünstigen und flexiblen Prozesses zur computergestützten 3D-Gesichtsweichteilrekonstruktion mithilfe digitaler Fotoaufnahmen eines Schädels erfolgen.Material und MethodenDie Rekonstruktion wurde an einem ausgewählten forensischen Fall und unter Einsatz einer Open-Source-Software durchgeführt.ErgebnisseFür die vollständige Gesichtsweichteilrekonstruktion einer verstorbenen Person wurden 76 digitale Fotoaufnahmen des Schädels aus unterschiedlichen Perspektiven angefertigt (Nikon D7100 SLR-Digitalkamera und Drehteller). Hierbei konnten antemortalen Vergleichsfotos ähnliche Rekonstruktionsergebnisse erzielt werden. Zudem wurde eine Modellbibliothek für Gesichtsmerkmale entwickelt.SchlussfolgerungDer vorgestellte Prozess der computergestützten 3D-Gesichtsweichteilrekonstruktion, basierend auf Open-Source-Software, stellt eine kostengünstige und flexible Alternative zu bisherigen Rekonstruktionsverfahren dar. Ob das Rekonstruktionsergebnis tatsächlich zum Wiedererkennen der Person führt, hängt von zahlreichen weiteren Faktoren ab.AbstractBackgroundThe identification of an unknown deceased person is an important task in forensic anthropology. There are various methods for identification, such as fingerprinting, odontostomatology and genetic fingerprinting, which presuppose the existence of reference material of the missing person; however, if there is no evidence of a person’s identity the only possibility is often the use of forensic facial soft tissue reconstruction. This method is based on the high recognition level of a human face on the basis of bony structures of the skull and its anatomical features.AimThe aim of this study was the design and application of a novel process for a computer-aided 3D facial soft tissue reconstruction on the basis of digital photographs of a skull.Material and methodsThe facial soft tissue reconstruction was carried out on a selected forensic case and based on open source software.ResultsA complete facial soft tissue reconstruction of the deceased person was created based on 76 photographs of the skull taken with a Nikon D7100 SLR digital camera. The results show that for actual comparison images similar reconstruction results can be achieved. In addition, a model library for facial features was created.ConclusionThe presented workflow of a computer-aided 3D facial soft tissue reconstruction based on open source software is a cost-effective and flexible alternative to conventional reconstruction methods. It could be demonstrated that comparable reconstruction results can be achieved. Whether the reconstruction result actually leads to the recognition of the person depends on many other factors.

The observation of evolutionary interaction pattern pairs in membrane proteins

BackgroundOver the last two decades, many approaches have been developed in bioinformatics that aim at one of the most promising, yet unsolved problems in modern life sciences - prediction of structural features of a protein. Such tasks addressed to transmembrane protein structures provide valuable knowledge about their three-dimensional structure. For this reason, the analysis of membrane proteins is essential in genomic and proteomic-wide investigations. Thus, many in-silico approaches have been utilized extensively to gain crucial advances in understanding membrane protein structures and functions.ResultsIt turned out that amino acid covariation within interacting sequence parts, extracted from a evolutionary sequence record of α-helical membrane proteins, can be used for structure prediction. In a recent study we discussed the significance of short membrane sequence motifs widely present in nature that act as stabilizing ’building blocks’ during protein folding and in retaining the three-dimensional fold. In this work, we used motif data to define evolutionary interaction pattern pairs. These were obtained from different pattern alignments and were used to evaluate which coupling mechanisms the evolution provides. It can be shown that short interaction patterns of homologous sequence records are membrane protein family-specific signatures. These signatures can provide valuable information for structure prediction and protein classification. The results indicate a good agreement with recent studies.ConclusionsGenerally, it can be shown how the evolution contributes to realize covariation within discriminative interaction patterns to maintain structure and function. This points to their general importance for α-helical membrane protein structure formation and interaction mediation. In the process, no fundamentally energetic approaches of previous published works are considered. The low-cost rapid computational methods postulated in this work provides valuable information to classify unknown α-helical transmembrane proteins and to determine their structural similarity.

Graph representation of high-dimensional alpha-helical membrane protein data

BackgroundIn genomics and proteomics, membrane protein analysis have shown that such analyses are very important to support the understanding of complex biological processes. In Genome-wide investigations of membrane proteins a large number of short, distinct sequence motifs has been revealed. Such motifs found so far support the understanding of the folded membrane protein in the membrane environment. They provide important information about functional or stabilizing properties. Recently several integrative approaches have been proposed to extract meaningful information out of the membrane environment. However, many information based approaches deliver results having deficits of visualisation outputs. Outgoing from high-throughput protein data analysis, these outputs play an important role in the evaluation of high-dimensional protein data, to establish a biological relationship and ultimately to provide useful information for research.ResultsWe have evaluated different resulting graphs generated from statistical analysis of consecutive motifs in helical structures of the membrane environment. Our results show that representative motifs with high occurrence in all investigated protein families are responsible for the general importance in alpha-helical membrane structure formation. Further, motifs which often occur with others in their function as so called “hubs” lead to the assumption, that these motifs constitute as important components in helical structures within the membrane. Otherwise, consecutive motifs and hubs which show a high occurrence in certain families only can be classified as important for family-specific functional characteristics. Summarized, we are able to bridge our graphical results from high-throughput analysis of membrane proteins over networking with databases to a biological context.ConclusionsOur results and the corresponding graphical visualisation support the understanding and interpretation of structure forming and functional motifs of membrane proteins. Our results are useful to interpret and refine results of common developed approaches. At last we show a simple way to visualise high-dimensional protein data in context to biological relevant information.

Analysis of Membrane Protein Stability in Diabetes Insipidus

Diabetes insipidus (DI) is a rare endocrine disorder, with an incidence in the general population assessed on one case per 25,000-30,000 people (Robertson, 1995; Ananthakrishnan, 2009; Krysiak, et al., 2010). It is a disease characterized by polyuria and compensatory polydipsia. The underlying causes of DI are diverse and can be central defects, in which no functional arginine-vasopressin is released from the pituitary, or may becaused by defects in the kidney (nephrogenic DI, NDI). Four different types of NDI are known. First, acquired NDI can originate as a side-effect of drugs, with the most prominent being the antibipolar drug lithium. Second and third, autosomal recessive and dominant inheritable NDI, are caused by gene mutations in the AQP2 gene encoding aquaporin-2. Finally, mutations in the AVPR2 gene (Deen et al., 1994; Mulders, 1998), which encodes the V2 vasopressin receptor (V2R), are the cause of the X-linked inheritable form of NDI (Fig. 1 right) (Van den Ouweland et al., 1992; Rosenthal, 1992).

Computergestützte Gesichtsweichteil- und Tatortrekonstruktion

Eine wichtige Aufgabe der forensischen Anthropologie liegt in der Identifizierung von unbekannten Verstorbenen. Fur die Identifizierung kommen etablierte Identifizierungsverfahren, wie Daktyloskopie, Odontostomatologie und genetischer Fingerabdruck zum Einsatz, welche das Vorhandensein von Vergleichsmaterial einer vermissten Person voraussetzen. Gibt es jedoch keine Hinweise auf eine Person, verbleibt oftmals nur noch die Moglichkeit einer forensischen Gesichtsweichteilrekonstruktion. Die Methode basiert auf dem hohen Wiedererkennungsgrad des Gesichtes auf Grundlage der knochernen Strukturen des Schadels und deren anatomischer Merkmale. Nicht selten ist die Umgebung des Auffindeortes eines unbekannten Leichnams hinsichtlich moglicher Tatablaufe ebenfalls von Interesse. In diesen Fallen erfolgt eine Tatortrekonstruktion mit dem Ziel eben jene Tatablaufe nachvollziehen und analysieren zu konnen und um zusatzliche und wertvolle Informationen zu erhalten. Bislang existieren verschiedene Verfahren zur Rekonstruktion von Tatorten, welche jedoch sehr kosten- und zeitintensiv sind. Aus diesem Grund war das Ziel dieser Arbeit der Anwendungsversuch eines neuartigen Prozesses zur computergestutzten 3D-Gesichtsweichteil- und Tatortrekonstruktion, basierend auf Fotografien des Schadels und Tatortes und unter der ausschlieslichen Anwendung von Open-Source-Software.

Analysis of X-Ray Images of Femora for Age at Death Estimation of Skeletal Individuals

This work focuses on an in silico analysis of age specific changes of human femora based on X-ray images. Thereby an alternative technique should be found to support classic anthropological methods for individual age estimation. Overall it is achievable to correlate age-related changes in the bone structure with the individual age. With this new approach it is possible to generate grey levels of digital images of specific bone features and correlate categories of grey level variation with the individual age. This method was applied to selected femora of an excavation site, that originates from the age of the Roman Empire/early migration period (365-416 AD). The obtained ages (grouping in defined classes) were then evaluated with the results of classical anthropological methods by a confusion matrix.