Exploiting Homology Information in Nontemplate Based Prediction of Protein Structures

In this paper we describe a novel strategy for exploring the conformational space of proteins and show that this leads to better models for proteins the structure of which is not amenable to template based methods. Our strategy is based on the assumption that the energy global minimum of homologous proteins must correspond to similar conformations, while the precise profiles of their energy landscape, and consequently the positions of the local minima, are likely to be different. In line with this hypothesis, we apply a replica exchange Monte Carlo simulation protocol that, rather than using different parameters for each parallel simulation, uses the sequences of homologous proteins. We show that our results are competitive with respect to alternative methods, including those producing the best model for each of the analyzed targets in the CASP10 (10th Critical Assessment of techniques for protein Structure Prediction) experiment free modeling category

Objective measurement of the navicular bursa volume in horses from low field magnetic resonance imaging (MRI) images using 3D Slicer® software

Background: Navicular bursa (NB) effusion is considered a reaction of the structure to traumatic or degenerative processes. However, NB effusion can also be present in sound horses undergoing intense and regular exercise. To the best of the author’s knowledge an objective non invasive method for measuring the NB volume has not been described to date. Accurate measurement of the NB volume using magnetic resonance imaging MRI would allow a more precise diagnosis and monitoring of response to treatment in horses with navicular bursitis. Objectives: The overall objective was to validate an MRI based method for measuring NB volume in horses using 3D Slicer® software. This was achieved by two separate methodologies, ex vivo and clinical. During the ex vivo part of this study (Chapter 2 and 3) a method for measurement of the NB using MRI datasets was developed. During the clinical study (Chapter 4 and 5) the accuracy and precision of the method were calculated using MRI datasets. The second objective of this study was to evaluate the performance of the current gold standard (subjective assessment by a board certified radiologist) against the newly developed method for cases with normal, mild, moderate and severe NB effusion (Chapter 5). Hypothesis: The accuracy and precision of measurement of NB volume from MRI images in the horse using 3D Slicer® is sufficient for this method to be valuable in the investigation and management of lameness in clinical cases. Material and methods: During the ex-vivo part of the study (Chapter 2) two forelimbs harvested from two adult thoroughbreds euthanised for reasons other than lameness were evaluated. The study design was approved by the Ethics and Welfare Committee of the School of Veterinary Medicine, University of Glasgow. An MRI-compatible needle was positioned in the NB and connected to a syringe. 33 Waterwasinjectedin1000mm incrementsuptoatotalof3000mm.Lowfield ® (0.31T, O-Scan equine , Esaote Veterinary) sagittal T2 FSE and STIR MRI images were acquired before and after each injection. In order to visualise the landmarks for the NB boundaries 5000 mm3 of contrast medium (2 mmol/L, Gadovist®) 2 mmol/L were injected into the bursa of an additional forelimb prior to acquisition of T1 weighted sagittal MRI sequence. Volume was measured ® using 3D Slicer . In Chapter 3 the forelimbs of two adult thoroughbred euthanised for reasons unrelated to lameness were collected. The NB were each injected with water in 500 mm3 increments until a total of 6000 mm3 were injected. Sagittal T2 FSE MR sequences were acquired before the first injection and then after every injection. NB volume was measured by a single observer (intra-observer measurements) from the images using 3D Slicer® as described in Chapter 2. Three additional observers (two diplomates of the European College of Veterinary Surgeons and one diplomate of the American College of Veterinary Surgeons) performed volume measurements on NB injected with 1000, 1500, 2000 and 2500 mm3 in total (inter- observer measurements). The volume injected and volume measured were ®® recorded in a spreadsheet (Excel , Microsoft UK). Excel was used to perform arithmetical calculations and statistical analyses, including plotting graphs, with the exception the Ryan-Joiner statistic for which Minitab® 19 was used (Minitab Ltd). Data were tested for normality using Ryan- Joiner statistic. 3D Slicer® was used to plan the treatment of a clinical case diagnosed with a deep digital flexor tendon (DDFT) core lesion (Chapter 4). The DDFT lesion was treated using intralesional injection of platelet rich plasma (PRP). In chapter 5 twenty adult horses’ front feet MRI studies acquired using a low field ® MRI scanner (0.31T, O-Scan equine , Esaote Veterinary) were evaluated by a board certified radiologist who classified NB effusion as normal, mild, moderate or severe. NB volume was measured from sagittal T2 sequences using 3D Slicer® software. The ability of subjective measurements (current gold standard) to discriminate between groups was analysed using receiver operating characteristic (ROC) curves. Results: The ex-vivo part of the study (Chapter 2) highlighted reduced underestimation of the NB measurements performed on T2 weighted images. However the variability of T2 weighted images was increased compared to STIR images. T2 weighted images were therefore used in the clinical parts of the study (Chapter 4 and 5). Intra-observer accuracy (difference between injected and measured volume) was -40% (i.e. injected volume 1000 mm3 measured volume 600 mm3) over the range 500-6000 mm3 (Chapter 3). The accuracy was improved (-27%) for lower volumes (500-3000 mm3) (i.e. injected volume 1000 mm3 measured volume 730 mm3). Precision was similar for both volume ranges (28% and 30% respectively). The inter-observer accuracy was 54% and precision 73%. One of the observers’ measurements largely overestimated the NB volume. After these measurements were excluded the accuracy and precision were 32% and 69% respectively. Measurement of the volume of the DDFT core lesion after PRP injection resulted in underestimation of the lesion volume by 30% compared to the volume injected (Chapter 4). The results of the clinical study (Chapter 5) showed a statistically significant difference in the NB volume measured between NBs classified as having a normal or mild and severe degree of effusion. There was no statistically significant difference between moderate and all the other groups. A NB volume of 1768 mm3 was able to distinguish between normal/mild navicular bursa volume and moderate/severe navicular bursa effusion with sensitivity and specificity of 90%. Conclusion: The work presented supports the use of 3D Slicer® to objectively measure NB volume from sagittal T2w MR images in the horse. It also suggests that this method is superior to subjective assessment of NB volume. Objective measurement of NB volume may be helpful in indicating the presence of specific pathology (e.g. DDFT tear or fibrocartilage lesions), which may prompt further investigation and inform on best treatment and prognosis. Furthermore, the use of sequential measurement of synovial structures volume could be used to assess the response to the treatment

The MoVIN server for the analysis of protein interaction networks

<p>Abstract</p> <p>Background</p> <p>Protein-protein interactions are at the basis of most cellular processes and crucial for many bio-technological applications. During the last few years the development of high-throughput technologies has produced several large-scale protein-protein interaction data sets for various organisms. It is important to develop tools for dissecting their content and analyse the information they embed by data-integration and computational methods.</p> <p>Results</p> <p>Interactions can be mediated by the presence of specific features, such as motifs, surface patches and domains. The co-occurrence of these features on proteins interacting with the same protein can indicate mutually exclusive interactions and, therefore, can be used for inferring the involvement of the proteins in common biological processes.</p> <p>We present here a publicly available server that allows the user to investigate protein interaction data in light of other biological information, such as their sequences, presence of specific domains, process and component ontologies. The server can be effectively used to construct a high-confidence set of mutually exclusive interactions by identifying similar features in groups of proteins sharing a common interaction partner. As an example, we describe here the identification of common motifs, function, cellular localization and domains in different datasets of yeast interactions.</p> <p>Conclusions</p> <p>The server can be used to analyse user-supplied datasets, it contains pre-processed data for four yeast Protein Protein interaction datasets and the results of their statistical analysis. These show that the presence of common motifs in proteins interacting with the same partner is a valuable source of information, it can be used to investigate the properties of the interacting proteins and provides information that can be effectively integrated with other sources. As more experimental interaction data become available, this tool will become more and more useful to gain a more detailed picture of the interactome.</p

T-cell receptor cognate target prediction based on paired α and β chain sequence and structural CDR loop similarities

T-cell receptors (TCR) mediate immune responses recognizing peptides in complex with major histocompatibility complexes (pMHC) displayed on the surface of cells. Resolving the challenge of predicting the cognate pMHC target of a TCR would benefit many applications in the field of immunology, including vaccine design/discovery and the development of immunotherapies. Here, we developed a model for prediction of TCR targets based on similarity to a database of TCRs with known targets. Benchmarking the model on a large set of TCRs with known target, we demonstrated how the predictive performance is increased (i) by focusing on CDRs rather than the full length TCR protein sequences, (ii) by incorporating information from paired α and β chains, and (iii) integrating information for all 6 CDR loops rather than just CDR3. Finally, we show how integration of the structure of CDR loops, as obtained through homology modeling, boosts the predictive power of the model, in particular in situations where no high-similarity TCRs are available for the query. These findings demonstrate that TCRs that bind to the same target also share, to a very high degree, sequence, and structural features. This observation has profound impact for future development of prediction models for TCR-pMHC interactions and for the use of such models for the rational design of T cell based therapies.Fil: Lanzarotti, Esteban Omar. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Investigaciones Biotecnológicas. Universidad Nacional de San Martín. Instituto de Investigaciones Biotecnológicas; ArgentinaFil: Marcatili, Paolo. Technical University of Denmark; DinamarcaFil: Nielsen, Morten. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Investigaciones Biotecnológicas. Universidad Nacional de San Martín. Instituto de Investigaciones Biotecnológicas; Argentina. Technical University of Denmark; Dinamarc

Advancing Gender Equity by Improving Menstrual Health

Approximately one-quarter of the global population are women of reproductive age, most of whom menstruate every month.A core function of a woman's reproductive system, menstruation is a healthy and normal occurrence in the female body. However, it can—and often does—become a challenge when individuals lack access to the resources, infrastructure, and social support they need to appropriately manage it.This report captures key changes in the menstrual health and hygiene (MHH) space that have happened since the publication of An Opportunity to Address Menstrual Health and Gender Equity in 2016. We pay particular attention to the remaining gaps and highlight opportunities for further action and investment

Tabhu: tools for antibody humanization.

Antibodies are rapidly becoming essential tools in the clinical practice, given their ability to recognize their cognate antigens with high specificity and affinity, and a high yield at reasonable costs in model animals. Unfortunately, when administered to human patients, xenogeneic antibodies can elicit unwanted and dangerous immunogenic responses. Antibody humanization methods are designed to produce molecules with a better safety profile still maintaining their ability to bind the antigen. This can be accomplished by grafting the non-human regions determining the antigen specificity into a suitable human template. Unfortunately, this procedure may results in a partial or complete loss of affinity of the grafted molecule that can be restored by back-mutating some of the residues of human origin to the corresponding murine ones. This trial-and-error procedure is hard and involves expensive and time-consuming experiments. Here we present tools for antibody humanization (Tabhu) a web server for antibody humanization. Tabhu includes tools for human template selection, grafting, back-mutation evaluation, antibody modelling and structural analysis, helping the user in all the critical steps of the humanization experiment protocol

The 7-channel FIR HCN Interferometer on J-TEXT Tokamak

A seven-channel far-infrared hydrogen cyanide (HCN) laser interferometer has been established aiming to provide the line integrated plasma density for the J-TEXT experimental scenarios. A continuous wave glow discharge HCN laser designed with a cavity length 3.4 m is used as the laser source with a wavelength of 337 {\mu}m and an output power up to 100 mW. The system is configured as a Mach-Zehnder type interferometer. Phase modulation is achieved by a rotating grating, with a modulation frequency of 10 kHz which corresponds to the temporal resolution of 0.1 ms. The beat signal is detected by TGS detector. The phase shift induced by the plasma is derived by the comparator with a phase sensitivity of 0.06 fringe. The experimental results measured by the J-TEXT interferometer are presented in details. In addition, the inversed electron density profile done by a conventional approach is also given. The kinematic viscosity of dimethyl silicone and vibration control is key issues for the system performance. The laser power stability under different kinematic viscosity of silicone oil is presented. A visible improvement of measured result on vibration reduction is shown in the paper.Comment: conference (15th-International Symposium on Laser-Aided Plasma Diagnostics

A novel approach to probe host-pathogen interactions of bovine digital dermatitis, a model of a complex polymicrobial infection

Background: Polymicrobial infections represent a great challenge for the clarification of disease etiology and the development of comprehensive diagnostic or therapeutic tools, particularly for fastidious and difficult-to-cultivate bacteria. Using bovine digital dermatitis (DD) as a disease model, we introduce a novel strategy to study the pathogenesis of complex infections. Results: The strategy combines meta-transcriptomics with high-density peptide-microarray technology to screen for in vivo-expressed microbial genes and the host antibody response at the site of infection. Bacterial expression patterns supported the assumption that treponemes were the major DD pathogens but also indicated the active involvement of other phyla (primarily Bacteroidetes). Bacterial genes involved in chemotaxis, flagellar synthesis and protection against oxidative and acidic stress were among the major factors defining the disease. Conclusions: The extraordinary diversity observed in bacterial expression, antigens and host antibody responses between individual cows pointed toward microbial variability as a hallmark of DD. Persistence of infection and DD reinfection in the same individual is common; thus, high microbial diversity may undermine the host's capacity to mount an efficient immune response and maintain immunological memory towards DD. The common antigenic markers identified here using a high-density peptide microarray address this issue and may be useful for future preventive measures against DD.Fil: Marcatili, Paolo. Technical University of Denmark; DinamarcaFil: Nielsen, Martin W.. Technical University of Denmark; DinamarcaFil: Sicheritz Ponten, Thomas. Technical University of Denmark; DinamarcaFil: Jensen, Tim K.. Technical University of Denmark; DinamarcaFil: Schafer Nielsen, Claus. Schafer-N ApS; DinamarcaFil: Boye, Mette. Hospital of Southern Jutland; DinamarcaFil: Nielsen, Morten. Technical University of Denmark; Dinamarca. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Investigaciones Biotecnológicas. Instituto de Investigaciones Biotecnológicas ; ArgentinaFil: Klitgaard, Kirstine. Technical University of Denmark; Dinamarc

An atypical presentation of leiomyosarcoma causing extremity compartment syndrome of the crural region in a Dutch Warmblood mare: a case report

A 12-year-old Warmblood mare was presented with an acute onset left hindlimb lameness associated with generalised soft tissue swelling of the entire limb and medial saphenous vein (MSV) thrombophlebitis. A presumptive diagnosis of extremity compartment syndrome (ECS) was made. Due to the clinical deterioration, emergency fasciotomy of the crural fascia and biopsy was performed. Histological and immunohistochemical examination of the samples confirmed a diagnosis of leiomyosarcoma likely originating from the tunica media of the MSV. This report is the first to describe an unique combination of ECS and thrombophlebitis associated with a leiomyosarcoma in a horse