Complete analysis of the B-cell response to a protein antigen, from in vivo germinal centre formation to 3-D modelling of affinity maturation

Somatic hypermutation of immunoglobulin variable region genes occurs within germinal centres (GCs) and is the process responsible for affinity maturation of antibodies during an immune response. Previous studies have focused almost exclusively on the immune response to haptens, which may be unrepresentative of epitopes on protein antigens. In this study, we have exploited a model system that uses transgenic B and CD4<sup>+</sup> T cells specific for hen egg lysozyme (HEL) and a chicken ovalbumin peptide, respectively, to investigate a tightly synchronized immune response to protein antigens of widely differing affinities, thus allowing us to track many facets of the development of an antibody response at the antigen-specific B cell level in an integrated system <i>in</i> <i>vivo</i>. Somatic hypermutation of immunoglobulin variable genes was analysed in clones of transgenic B cells proliferating in individual GCs in response to HEL or the cross-reactive low-affinity antigen, duck egg lysozyme (DEL). Molecular modelling of the antibody–antigen interface demonstrates that recurring mutations in the antigen-binding site, selected in GCs, enhance interactions of the antibody with DEL. The effects of these mutations on affinity maturation are demonstrated by a shift of transgenic serum antibodies towards higher affinity for DEL in DEL-cOVA immunized mice. The results show that B cells with high affinity antigen receptors can revise their specificity by somatic hypermutation and antigen selection in response to a low-affinity, cross-reactive antigen. These observations shed further light on the nature of the immune response to pathogens and autoimmunity and demonstrate the utility of this novel model for studies of the mechanisms of somatic hypermutation

Fourier Magnetic Imaging with Nanoscale Resolution and Compressed Sensing Speed-up using Electronic Spins in Diamond

Optically-detected magnetic resonance using Nitrogen Vacancy (NV) color centres in diamond is a leading modality for nanoscale magnetic field imaging, as it provides single electron spin sensitivity, three-dimensional resolution better than 1 nm, and applicability to a wide range of physical and biological samples under ambient conditions. To date, however, NV-diamond magnetic imaging has been performed using real space techniques, which are either limited by optical diffraction to 250 nm resolution or require slow, point-by-point scanning for nanoscale resolution, e.g., using an atomic force microscope, magnetic tip, or super-resolution optical imaging. Here we introduce an alternative technique of Fourier magnetic imaging using NV-diamond. In analogy with conventional magnetic resonance imaging (MRI), we employ pulsed magnetic field gradients to phase-encode spatial information on NV electronic spins in wavenumber or k-space followed by a fast Fourier transform to yield real-space images with nanoscale resolution, wide field-of-view (FOV), and compressed sensing speed-up.Comment: 31 pages, 10 figure

Neoliberalisation and 'lad cultures' in higher education

This paper links HE neoliberalisation and ‘lad cultures’, drawing on interviews and focus groups with women students. We argue that retro-sexist ‘laddish’ forms of masculine competitiveness and misogyny have been reshaped by neoliberal rationalities to become modes of consumerist sexualised audit. We also suggest that neoliberal frameworks scaffold an individualistic and adversarial culture among young people that interacts with perceived threats to men’s privilege and intensifies attempts to put women in their place through misogyny and sexual harassment. Furthermore, ‘lad cultures’, sexism and sexual harassment in higher education may be invisibilised by institutions to preserve marketability in a neoliberal context. In response, we ask if we might foster dialogue and partnership between feminist and anti-marketisation politics

Data-as-a-Service Platform for Delivering Healthy Lifestyle and Preventive Medicine: Concept and Structure of the DAPHNE Project

Background: Overweight and obesity is related to many health problems and diseases. The current obesity epidemic, which is a major health problem, is closely related to a lack of physical activity, high levels of sedentary behavior, and increased energy intake; with evidence to show increasing incidence of these issues in the younger population. Tackling obesity and its comorbid conditions requires a holistic approach encompassing attention on physical activity, healthy diet, and behavioral activation in order to enable and maintain meaningful and long-term weight loss and weight maintenance. Objective: The objective of the Data-as-a-Service Platform for Healthy Lifestyle and Preventive Medicine (DAPHNE) project is to develop a breakthrough information communications technology (ICT) platform for tracking health, weight, physical activity, diet, lifestyle, and psychological components within health care systems, whereby the platform and clinical support is linked. Methods: The DAPHNE platform aims to deliver personalized guidance services for lifestyle management to the citizen/patient by means of (1) advanced sensors and mobile phone apps to acquire and store continuous/real-time data on lifestyle aspects, behavior, and surrounding environment; (2) individual models to monitor their health and fitness status; (3) intelligent data processing for the recognition of behavioral trends; and (4) specific services for personalized guidance on healthy lifestyle and disease prevention. It is well known that weight loss and maintenance of weight loss are particularly difficult. This tool will address some of the issues found with conventional treatment/advice in that it will collect data in real time, thereby reducing reliability issues known with recalling events once they have passed and will also allow adjustment of behavior through timely support and recommendations sent through the platform without the necessity of formal one-to-one visits between patient and clinician. Patient motivation/compliance is a particular issue with conventional weight loss regimes; DAPHNE aims to increase the individuals’ awareness of their own behavior and fosters their accountability. Results: The project has been funded and the research work has started. Results for the validation of the different components is due imminently. Conclusions: In contrast with previous existing solutions, the DAPHNE project tackles the obesity problem from a clinical point of view, designing the different interfaces for its use by patients (adults and children), physicians, and caregivers. A specific design for children and adolescent patients treated for obesity has been followed, guided by pediatric physicians at hospitals in Europe. The final clinical validation of the DAPHNE platform will be carried out in different European hospitals, testing the platform in both adolescents and adults

Insights into the regulation of DMSP synthesis in the diatom Thalassiosira pseudonana through APR activity, proteomics and gene expression analyses on cells acclimating to changes in salinity, light and nitrogen

Despite the importance of dimethylsulphoniopropionate (DMSP) in the global sulphur cycle and climate regulation, the biological pathways underpinning its synthesis in marine phytoplankton remain poorly understood. The intracellular concentration of DMSP increases with increased salinity, increased light intensity and nitrogen starvation in the diatom Thalassiosira pseudonana. We used these conditions to investigate DMSP synthesis at the cellular level via analysis of enzyme activity, gene expression and proteome comparison. The activity of the key sulphur assimilatory enzyme, adenosine 5′- phosphosulphate reductase was not coordinated with increasing intracellular DMSP concentration. Under all three treatments coordination in the expression of sulphur assimilation genes was limited to increases in sulphite reductase transcripts. Similarly, proteomic 2D gel analysis only revealed an increase in phosphoenolpyruvate carboxylase following increases in DMSP concentration. Our findings suggest that increased sulphur assimilation might not be required for increased DMSP synthesis, instead the availability of carbon and nitrogen substrates may be important in the regulation of this pathway. This contrasts with the regulation of sulphur metabolism in higher plants, which generally involves upregulation of several sulphur assimilatory enzymes. In T. pseudonana changes relating to sulphur metabolism were specific to the individual treatments and, given that little coordination was seen in transcript and protein responses across the three growth conditions, different patterns of regulation might be responsible for the increase in DMSP concentration seen under each treatment

Genome-wide linkage analysis of 972 bipolar pedigrees using single-nucleotide polymorphisms.

Because of the high costs associated with ascertainment of families, most linkage studies of Bipolar I disorder (BPI) have used relatively small samples. Moreover, the genetic information content reported in most studies has been less than 0.6. Although microsatellite markers spaced every 10 cM typically extract most of the genetic information content for larger multiplex families, they can be less informative for smaller pedigrees especially for affected sib pair kindreds. For these reasons we collaborated to pool family resources and carried out higher density genotyping. Approximately 1100 pedigrees of European ancestry were initially selected for study and were genotyped by the Center for Inherited Disease Research using the Illumina Linkage Panel 12 set of 6090 single-nucleotide polymorphisms. Of the ~1100 families, 972 were informative for further analyses, and mean information content was 0.86 after pruning for linkage disequilibrium. The 972 kindreds include 2284 cases of BPI disorder, 498 individuals with bipolar II disorder (BPII) and 702 subjects with recurrent major depression. Three affection status models (ASMs) were considered: ASM1 (BPI and schizoaffective disorder, BP cases (SABP) only), ASM2 (ASM1 cases plus BPII) and ASM3 (ASM2 cases plus recurrent major depression). Both parametric and non-parametric linkage methods were carried out. The strongest findings occurred at 6q21 (non-parametric pairs LOD 3.4 for rs1046943 at 119 cM) and 9q21 (non-parametric pairs logarithm of odds (LOD) 3.4 for rs722642 at 78 cM) using only BPI and schizoaffective (SA), BP cases. Both results met genome-wide significant criteria, although neither was significant after correction for multiple analyses. We also inspected parametric scores for the larger multiplex families to identify possible rare susceptibility loci. In this analysis, we observed 59 parametric LODs of 2 or greater, many of which are likely to be close to maximum possible scores. Although some linkage findings may be false positives, the results could help prioritize the search for rare variants using whole exome or genome sequencing

Glazed tiles from Lodhi and Mughal northern India: a technological appraisal

Glazed tiles were used by the Lodhis and Mughals to embellish their buildings in northern India from the late fifteenth to seventeenth century. Tile-work from this region and period is understudied, particularly on matters related to its origin and technology. This thesis presents findings of a research undertaken on a series of tiled buildings located at Delhi, Agra, and Punjab in northern India, from the period of Lodhi and Mughal rule. Tile samples from the buildings have been scientifically analysed - mainly using scanning electron microscopy with energy dispersive spectrometry, and electron microprobe microanalysis with wavelength dispersive spectrometry - for their characterisation. Ethno-archaeological studies on related traditional craft industries have been used to build a more accurate rendition of the technologies employed in their manufacture. A field survey of in situ tile-work has been used to correlate stylistic and physical attributes with data determined through analyses. Results from the study show that different methods were utilized for the production of tiles at Delhi/Agra and Punjab. Those of the Delhi type have indigenous features in their technology, while the Punjab specimens are shown to be technologically closer to those from the core Islamic lands. The industry at Delhi is further shown to have evolved locally, developing gradually from the Lodhi to Mughal period, while the Punjab tile industry at the time of the Mughals is demonstrated to be an import, its establishment clearly influenced externally, with the sudden appearance of a new technological style. The tile-work at both places is however determined to be of the same basic character as Islamic tile-work of the stonepaste variety. This study, besides presenting a comprehensive picture on Lodhi and Mughal tiling traditions, provides important new information in the discipline of Islamic ceramic studies, particularly on the development of stonepaste technology and its transfer

Statistical Inference for Valued-Edge Networks: Generalized Exponential Random Graph Models

Across the sciences, the statistical analysis of networks is central to the production of knowledge on relational phenomena. Because of their ability to model the structural generation of networks, exponential random graph models are a ubiquitous means of analysis. However, they are limited by an inability to model networks with valued edges. We solve this problem by introducing a class of generalized exponential random graph models capable of modeling networks whose edges are valued, thus greatly expanding the scope of networks applied researchers can subject to statistical analysis

Polycation-π Interactions Are a Driving Force for Molecular Recognition by an Intrinsically Disordered Oncoprotein Family

Molecular recognition by intrinsically disordered proteins (IDPs) commonly involves specific localized contacts and target-induced disorder to order transitions. However, some IDPs remain disordered in the bound state, a phenomenon coined "fuzziness", often characterized by IDP polyvalency, sequence-insensitivity and a dynamic ensemble of disordered bound-state conformations. Besides the above general features, specific biophysical models for fuzzy interactions are mostly lacking. The transcriptional activation domain of the Ewing's Sarcoma oncoprotein family (EAD) is an IDP that exhibits many features of fuzziness, with multiple EAD aromatic side chains driving molecular recognition. Considering the prevalent role of cation-π interactions at various protein-protein interfaces, we hypothesized that EAD-target binding involves polycation- π contacts between a disordered EAD and basic residues on the target. Herein we evaluated the polycation-π hypothesis via functional and theoretical interrogation of EAD variants. The experimental effects of a range of EAD sequence variations, including aromatic number, aromatic density and charge perturbations, all support the cation-π model. Moreover, the activity trends observed are well captured by a coarse-grained EAD chain model and a corresponding analytical model based on interaction between EAD aromatics and surface cations of a generic globular target. EAD-target binding, in the context of pathological Ewing's Sarcoma oncoproteins, is thus seen to be driven by a balance between EAD conformational entropy and favorable EAD-target cation-π contacts. Such a highly versatile mode of molecular recognition offers a general conceptual framework for promiscuous target recognition by polyvalent IDPs. © 2013 Song et al