Three-dimensional morphology and gene expression in the Drosophila blastoderm at cellular resolution II: dynamics.

BackgroundTo accurately describe gene expression and computationally model animal transcriptional networks, it is essential to determine the changing locations of cells in developing embryos.ResultsUsing automated image analysis methods, we provide the first quantitative description of temporal changes in morphology and gene expression at cellular resolution in whole embryos, using the Drosophila blastoderm as a model. Analyses based on both fixed and live embryos reveal complex, previously undetected three-dimensional changes in nuclear density patterns caused by nuclear movements prior to gastrulation. Gene expression patterns move, in part, with these changes in morphology, but additional spatial shifts in expression patterns are also seen, supporting a previously proposed model of pattern dynamics based on the induction and inhibition of gene expression. We show that mutations that disrupt either the anterior/posterior (a/p) or the dorsal/ventral (d/v) transcriptional cascades alter morphology and gene expression along both the a/p and d/v axes in a way suggesting that these two patterning systems interact via both transcriptional and morphological mechanisms.ConclusionOur work establishes a new strategy for measuring temporal changes in the locations of cells and gene expression patterns that uses fixed cell material and computational modeling. It also provides a coordinate framework for the blastoderm embryo that will allow increasingly accurate spatio-temporal modeling of both the transcriptional control network and morphogenesis

Faecal microbiota of individuals with autism spectrum disorder

Many children with autistic spectrum disorders (ASDs) suffer from gastrointestinal problems such as diarrhoea, constipation and abdominal pain. Such symptoms may be due to a disruption of the indigenous gut microbiota promoting the overgrowth of potentially pathogenic micro-organisms. These observations have stimulated investigations into possible abnormalities of intestinal microbiota in autistic patients. The purpose of the present study was to determine if a relationship exists between ASD severity (mild – severe) and GI microbial populations. The faecal microbiota of 22 male and 6 female participants with ASDs (aged 7 ± 6 years) were analyzed by standard microbial culture methods and compared within-group (based on ASD severity) and with a standard laboratory reference range. Comparisons between children with mild ASD and those with moderate to severe ASD, as well as comparisons to a neurotypical control group previously reported, revealed that no significant differences appear to exist in the composition of the gut microbiota. Nevertheless, examination of each individual’s gut microbial composition showed 10 cases of unusual findings witch means 1out of 3 cases have unusual microbiota. Our data do not support consistent GI microbial abnormalities in ASD children, but the findings do suggest that aberrations may be found in a minority subset of ASD children. Further studies are required to determine the possible association between the microbiota and gastrointestinal dysfunctions in a subset of children with both ASD and gastro-intestinal problems

Bayesian optimization for materials design

We introduce Bayesian optimization, a technique developed for optimizing time-consuming engineering simulations and for fitting machine learning models on large datasets. Bayesian optimization guides the choice of experiments during materials design and discovery to find good material designs in as few experiments as possible. We focus on the case when materials designs are parameterized by a low-dimensional vector. Bayesian optimization is built on a statistical technique called Gaussian process regression, which allows predicting the performance of a new design based on previously tested designs. After providing a detailed introduction to Gaussian process regression, we introduce two Bayesian optimization methods: expected improvement, for design problems with noise-free evaluations; and the knowledge-gradient method, which generalizes expected improvement and may be used in design problems with noisy evaluations. Both methods are derived using a value-of-information analysis, and enjoy one-step Bayes-optimality

Negotiating identities: ethnicity and social relations in a young offenders' institution

This article explores the situated nature of male prisoner identities in the late modern British context, using the contrasting theoretical frames of Sykes's (1958) indigenous model and Jacobs' (1979) importation model of prisoner subcultures and social relations. Drawing on eight months of ethnographic fieldwork in an ethnically, religiously and nationally diverse young offenders institution, consideration is given to how prisoners manage and negotiate difference, exploring the contours of racialization and racism which can operate in ambiguous and contradictory ways. Sociological understandings of identity, ethnicity, racialization and racism are used to inform a more empirically grounded theoretical criminology

Applied utility and the auto-ethnographic short story: persuasions for, and illustrations of, writing critical social science

In some quarters it is argued that, narrative researchers might be classified as being either storyanalysts or storytellers. They go on to suggest that one feature of storytellers is that they undertake a form of analysis as the process of writing unfolds. With these sentiments in mind, in the present paper, we consider how auto-ethnographical accounts of traumatic and challenging life events might, through the analysis contained within, demonstrate value within the realm of applied pedagogy. In making our case we embrace and adapt the literary genre of storytelling, more specifically, the short story. The story presented here, ‘Travel Writer’, offers an opaque, multicontextualised and lifelong view of career transition. The present paper, in more general terms, considers the capacity of auto-ethnography and, more specifically, the short storied version of it, to engender critical reader engagement, to encourage personal reflection in others, and to act as a point of stimulus for the enactment of applied debate through the lens of critical social science. With regards to the assumptions of critical social science, the final discussion also considers how the auto-ethnographic text, as a pedagogic tool, might help others to contest and challenge the meta-narratives that, we argue, risk stagnating established thinking

Prevalence of mental health disorders in inflammatory bowel disease: an Australian outpatient cohort

BACKGROUND: This study aimed to characterize prevalence of anxiety and depressive conditions and uptake of mental health services in an Australian inflammatory bowel disease (IBD) outpatient setting. METHODS: Eighty-one IBD patients (39 males, mean age 35 years) attending a tertiary hospital IBD outpatient clinic participated in this study. Disease severity was evaluated according to the Manitoba Index. Diagnosis of an anxiety or depressive condition was based upon the Mini-International Neuropsychiatric Interview and the Hospital Anxiety and Depression Scale. RESULTS: Based on Hospital Anxiety and Depression Scale subscale scores >8 and meeting Mini-International Neuropsychiatric Interview criteria, 16 (19.8%) participants had at least one anxiety condition, while nine (11.1%) had a depressive disorder present. Active IBD status was associated with higher prevalence rates across all anxiety and depressive conditions. Generalized anxiety was the most common (12 participants, 14.8%) anxiety condition, and major depressive disorder (recurrent) was the most common depressive condition reported (five participants, 6.2%). Seventeen participants (21%) reported currently seeking help for mental health issues while 12.4% were identified has having at least one psychological condition but not seeking treatment. CONCLUSION: We conclude that rates of anxiety and depression are high in this cohort, and that IBD-focused psychological services should be a key component of any holistic IBD service, especially for those identified as having active IBD

Kinetic model of the aggregation of alpha-synuclein provides insights into prion-like spreading.

The protein alpha-synuclein (αS) self-assembles into small oligomeric species and subsequently into amyloid fibrils that accumulate and proliferate during the development of Parkinson's disease. However, the quantitative characterization of the aggregation and spreading of αS remains challenging to achieve. Previously, we identified a conformational conversion step leading from the initially formed oligomers to more compact oligomers preceding fibril formation. Here, by a combination of single-molecule fluorescence measurements and kinetic analysis, we find that the reaction in solution involves two unimolecular structural conversion steps, from the disordered to more compact oligomers and then to fibrils, which can elongate by further monomer addition. We have obtained individual rate constants for these key microscopic steps by applying a global kinetic analysis to both the decrease in the concentration of monomeric protein molecules and the increase in oligomer concentrations over a 0.5-140-µM range of αS. The resulting explicit kinetic model of αS aggregation has been used to quantitatively explore seeding the reaction by either the compact oligomers or fibrils. Our predictions reveal that, although fibrils are more effective at seeding than oligomers, very high numbers of seeds of either type, of the order of 10(4), are required to achieve efficient seeding and bypass the slow generation of aggregates through primary nucleation. Complementary cellular experiments demonstrated that two orders of magnitude lower numbers of oligomers were sufficient to generate high levels of reactive oxygen species, suggesting that effective templated seeding is likely to require both the presence of template aggregates and conditions of cellular stress.We thank Dr. Nadia Shivji and Beata Blaszczyk for ɑS protein expression, Dr. Peter Jönsson for help with preliminary TIRFM imaging experiments, Chris Taylor for help with preliminary autodilution experiments and Prof. Michel Goedert for critical reading of the manuscript. M.I. is funded by Dr. Tayyeb-Hussain Scholarship. G.A.G. is funded by the Schiff Foundation . S.G. is funded through a Wellcome Trust Intermediate Clinical Fellowship. Funding from the Frances and Augustus Newman Foundation, the European Research Council and the Biothechnology and Biophysical Sciences Research Council is gratefully acknowledged.This is the author accepted manuscript. The final version is available from the National Academy of Sciences via http://dx.doi.org/10.1073/pnas.152412811

Structural characterization of toxic oligomers that are kinetically trapped during alpha-synuclein fibril formation

This is the author accepted manuscript. The final version is avialble via PNAS at http://www.pnas.org/content/112/16/E1994.long#ack-1.We describe the isolation and detailed structural characterization of stable toxic oligomers of α-synuclein that have accumulated during the process of amyloid formation. Our approach has allowed us to identify distinct subgroups of oligomers and to probe their molecular architectures by using cryo-electron microscopy (cryoEM) image reconstruction techniques. Although the oligomers exist in a range of sizes, with different extents and nature of β-sheet content and exposed hydrophobicity, they all possess a hollow cylindrical architecture with similarities to certain types of amyloid fibril, suggesting that the accumulation of at least some forms of amyloid oligomers is likely to be a consequence of very slow rates of rearrangement of their β-sheet structures. Our findings reveal the inherent multiplicity of the process of protein misfolding and the key role the β-sheet geometry acquired in the early stages of the self-assembly process plays in dictating the kinetic stability and the pathological nature of individual oligomeric species.We thank Dr. Katherine Stott, from the Biophysics Facility, Department of Biochemistry, University of Cambridge, for her assistance in using these facilities. This work was supported by the Agency for Science, Technology and Research, Singapore (S.W.C.), the “La Caixa” foundation (S.D.), Wellcome/MRC (Medical Research Council) Parkinson’s Disease Consortium Grant WT089698 (to E.D. and N.W.W.), National Institute for Health Research Biomedical Research Centres funding at University College London (to N.W.W.), the BBSRC through Grants BB/H003843/1 (to M.O.) and BB/E019927/1 (to C.M.D.), the Spanish Ministry of Economy and Competitiveness through Grants SAF 2012-39720 (to C.R.), BFU2013-44202 (to J.M.V.), and BIO2011-28941-C03-03 (to C.A. and G.R.), the Spanish Ministry of Health with cofunding by The European Regional Development Fund through Grant CP10/00527 (to C.R.), the Madrid Regional Government through Grant S2013/MIT-2807 (to J.M.V.), Parkinson’s UK through Grant H-0903 (to T.G.), the Wellcome Trust, the Leverhulme Trust, the European Commission through project LSHM-CT-2006-037525 (to C.M.D.), the Medical Research Council through Grant MRC G1002272 (to E.J.D.-G. and C.M.D.), and the Engineering and Physical Sciences Research Council (C.M.D.). A.Y.A. was a Parkinson’s UK Senior Research Fellow. N.C. is a Royal Society Research Fellow and also acknowledges financial support by the Human Frontier Science Program from Long-Term Fellowship LT000795/2009

Atomic structures of TDP-43 LCD segments and insights into reversible or pathogenic aggregation.

The normally soluble TAR DNA-binding protein 43 (TDP-43) is found aggregated both in reversible stress granules and in irreversible pathogenic amyloid. In TDP-43, the low-complexity domain (LCD) is believed to be involved in both types of aggregation. To uncover the structural origins of these two modes of β-sheet-rich aggregation, we have determined ten structures of segments of the LCD of human TDP-43. Six of these segments form steric zippers characteristic of the spines of pathogenic amyloid fibrils; four others form LARKS, the labile amyloid-like interactions characteristic of protein hydrogels and proteins found in membraneless organelles, including stress granules. Supporting a hypothetical pathway from reversible to irreversible amyloid aggregation, we found that familial ALS variants of TDP-43 convert LARKS to irreversible aggregates. Our structures suggest how TDP-43 adopts both reversible and irreversible β-sheet aggregates and the role of mutation in the possible transition of reversible to irreversible pathogenic aggregation