LoopIng: A template-based tool for predicting the structure of protein loops

MOTIVATION: Predicting the structure of protein loops is very challenging, mainly because they are not necessarily subject to strong evolutionary pressure. This implies that, unlike the rest of the protein, standard homology modeling techniques are not very effective in modeling their structure. However, loops are often involved in protein function, hence inferring their structure is important for predicting protein structure as well as function. RESULTS: We describe a method, LoopIng, based on the Random Forest automated learning technique, which, given a target loop, selects a structural template for it from a database of loop candidates. Compared to the most recently available methods, LoopIng is able to achieve similar accuracy for short loops (4-10 residues) and significant enhancements for long loops (11-20 residues). The quality of the predictions is robust to errors that unavoidably affect the stem regions when these are modeled. The method returns a confidence score for the predicted template loops and has the advantage of being very fast (on average: 1 min/loop)

Double Bind: (Trans)materiality and Tactics of Abstraction

By analysing trans embodiment and the dissociative narratives attached to ‘the trans body’, this research project demonstrates how abstraction offers a counter-reading of trans representation and therefore provides a way to discuss trans embodiment both with and without an image or trace of a body. This thesis asks how abstract art practices, when considered in the context of trans visibility and representation, can be a way of newly understanding the social, political and ethical forces that animate trans embodiment. The project situates itself at the intersection of abstract art practice and trans theory, employing an interdisciplinary and practice-led methodology to explore a phenomenology of transness, specifically, trans masculinity. Engaging with both materiality and embodiment, the project seeks to refute the demand for trans legibility as well as offer a way of thinking about trans representation that is grounded in relationality, recognition, autonomy and solidarity. Through sculpture, installation, leadlight, text and photography, my studio practice draws on material tactics of repetition, cuts/breaks, transformation, coded forms and language. I draw on the material qualities of these mediums to facilitate encounters and forge relations between bodily pressures and architectures of safety and exclusion. These issues have informed the development of several bodies of work made between 2017 and 2021 that will be analysed throughout the thesis alongside the practice of Edie Fake, Jos Charles and Jes Fan. The principal objective of this research is to position living within the space of social and political abstraction as a generative stance that is not only concerned with resisting or responding to terms that are imposed from elsewhere. For trans people these terms often require one to defend the right to access to care, legal protections, stable housing and employment; they also determine if one can occupy public space and if one has the right to live in the first place. Living within abstraction departs from merely responding on someone else's terms and is articulated as the ways that trans people can be embodied, autonomous, in solidarity with community and able to experience deep connections to the world, others and ourselves. This project contributes new knowledge to the fields of trans studies and art practice by revealing how material abstraction can be used as a tactic for claiming presence within absence, self-recognition within misrecognition and opacity within obscurity

PIGSPro: prediction of immunoGlobulin structures v2

PIGSpro is a significant upgrade of the popular PIGS server for the prediction of the structure of immunoglobulins. The software has been completely rewritten in python following a similar pipeline as in the original method, but including, at various steps, relevant modifications found to improve its prediction accuracy, as demonstrated here. The steps of the pipeline include the selection of the appropriate framework for predicting the conserved regions of the molecule by homology; the target template alignment for this portion of the molecule; the selection of the main chain conformation of the hypervariable loops according to the canonical structure model, the prediction of the third loop of the heavy chain (H3) for which complete canonical structures are not available and the packing of the light and heavy chain if derived from different templates. Each of these steps has been improved including updated methods developed along the years. Last but not least, the user interface has been completely redesigned and an automatic monthly update of the underlying database has been implemented. The method is available as a web server at http://biocomputing.it/pigspro

Assessment of circulating MCP-1 level and 2518A>G gene polymorphism in systemic lupus erythematosus

Lupus nephritis (LN) is a major contributor to morbidity and mortality in patients with Systemic Lupus Erythematosus (SLE). This study aims to investigate the possible role of a functional polymorphism in the regulatory region of the monocyte chemo-attractant protein-1 (MCP-1) gene and MCP-1 blood level in the diagnosis of LN and in correlating the MCP-1 blood levels with disease activity. The study included 56 SLE patients and 56 controls. All the SLE patients suffered from LN. An analysis of MCP-1 gene polymorphism by polymerase chain reaction was performed followed by restriction fragment length polymorphism (PCR-RFLP) analysis and MCP-1 blood level was determined using the ELISA technique. Calculation of Systemic Lupus Erythematosus Disease Activity Index (SLEDAI) was performed. Serologic tests included the determination of antinuclear antibody (ANA) and anti-double-stranded (ds) DNA antibodies, Complement C3 and C4 levels. A significant increase in the frequency of genotype A/G and a decrease in the frequency of genotype A/A were found among patients with active LN compared to inactive LN. There was a statistically significant difference in the blood level of MCP-1 between LN patients and controls. Also, MCP-1 blood levels were significantly higher in active LN patients than inactive LN. A significant positive linear correlation was detected between MCP-1 blood level and SLEDAI, creatinine, and 24 hours protein in LN patients. These results suggest that an A/G genotype together with the measurement of the blood level of MCP-1 can be a useful tool for detection and follow up of active LN

Preparing for and executing a randomised controlled trial of podoconiosis treatment in Northern Ethiopia: the utility of rapid ethical assessment

Background Community-based randomized controlled trials are often complex pieces of research with significant challenges around the approach to the community, information provision, and decision-making, all of which are fundamental to the informed consent process. We conducted a rapid ethical assessment to guide the preparation for and conduct of a randomized controlled trial of podoconiosis treatment in northern Ethiopia. Methods A qualitative study was carried out in Aneded woreda, East Gojjam Zone, Amhara Regional State from August to September, 2013. A total of 14 In-depth Interviews (IDIs) with researchers, experts, and leaders, and 8 Focus Group Discussions (FGDs) involving 80 participants (people of both gender, with and without podoconiosis), were conducted. Interviews were carried out in Amharic. Data analysis was started alongside collection. Final data analysis used a thematic approach based on themes identified a priori and those that emerged during the analysis. Results Respondents made a range of specific suggestions, including that sensitisation meetings were called by woreda or kebele leaders or the police; that Health Extension Workers were asked to accompany the research team to patients’ houses; that detailed trial information was explained by someone with deep local knowledge; that analogies from agriculture and local social organisations be used to explain randomisation; that participants in the ‘delayed’ intervention arm be given small incentives to continue in the trial; and that key community members be asked to quell rumours arising in the course of the trial. Conclusion Many of these recommendations were incorporated into the preparatory phases of the trial, or were used during the course of the trial itself. This demonstrates the utility of rapid ethical assessment preceding a complex piece of research in a relatively research-naive setting

Improving the accuracy of the structure prediction of the third hypervariable loop of the heavy chains of antibodies

Motivation: Antibodies are able to recognize a wide range of antigens through their complementary determining regions formed by six hypervariable loops. Predicting the 3D structure of these loops is essential for the analysis and reengineering of novel antibodies with enhanced affinity and specificity. The canonical structure model allows high accuracy prediction for five of the loops. The third loop of the heavy chain, H3, is the hardest to predict because of its diversity in structure, length and sequence composition.Results: We describe a method, based on the Random Forest automatic learning technique, to select structural templates for H3 loops among a dataset of candidates. These can be used to predict the structure of the loop with a higher accuracy than that achieved by any of the presently available methods. The method also has the advantage of being extremely fast and returning a reliable estimate of the model quality.Availability and implementation: The source code is freely available at http://www.biocomputing.it/H3Loopred/Contact: [email protected] Information: Supplementary data are available at Bioinformatics online

Campylobacter Infection as a Trigger for Guillain-Barré Syndrome in Egypt

BACKGROUND: Most studies of Campylobacter infection triggering Guillain-Barré Syndrome (GBS) are conducted in western nations were Campylobacter infection and immunity is relatively rare. In this study, we explored Campylobacter infections, Campylobacter serotypes, autoantibodies to gangliosides, and GBS in Egypt, a country where Campylobacter exposure is common. METHODS: GBS cases (n = 133) were compared to age- and hospital-matched patient controls (n = 374). A nerve conduction study was performed on cases and a clinical history, serum sample, and stool specimen obtained for all subjects. RESULTS: Most (63.3%) cases were demyelinating type; median age four years. Cases were more likely than controls to have diarrhea (29.5% vs. 22.5%, Adjusted Odds Ratio (ORa) = 1.69, P = 0.03), to have higher geometric mean IgM anti-Campylobacter antibody titers (8.18 vs. 7.25 P<0.001), and to produce antiganglioside antibodies (e.g., anti-Gd1a, 35.3 vs. 11.5, ORa = 4.39, P<0.0001). Of 26 Penner:Lior Campylobacter serotypes isolated, only one (41:27, C. jejuni, P = 0.02) was associated with GBS. CONCLUSIONS: Unlike results from western nations, data suggested that GBS cases were primarily in the young and cases and many controls had a history of infection to a variety of Campylobacter serotypes. Still, the higher rates of diarrhea and greater antibody production against Campylobacter and gangliosides in GBS patients were consistent with findings from western countries