Deep learning extends de novo protein modelling coverage of genomes using iteratively predicted structural constraints

The inapplicability of amino acid covariation methods to small protein families has limited their use for structural annotation of whole genomes. Recently, deep learning has shown promise in allowing accurate residue-residue contact prediction even for shallow sequence alignments. Here we introduce DMPfold, which uses deep learning to predict inter-atomic distance bounds, the main chain hydrogen bond network, and torsion angles, which it uses to build models in an iterative fashion. DMPfold produces more accurate models than two popular methods for a test set of CASP12 domains, and works just as well for transmembrane proteins. Applied to all Pfam domains without known structures, confident models for 25% of these so-called dark families were produced in under a week on a small 200 core cluster. DMPfold provides models for 16% of human proteome UniProt entries without structures, generates accurate models with fewer than 100 sequences in some cases, and is freely available.Comment: JGG and SMK contributed equally to the wor

An Analysis of the Quasicontinuum Method

The aim of this paper is to present a streamlined and fully three-dimensional version of the quasicontinuum (QC) theory of Tadmor et al. and to analyze its accuracy and convergence characteristics. Specifically, we assess the effect of the summation rules on accuracy; we determine the rate of convergence of the method in the presence of strong singularities, such as point loads; and we assess the effect of the refinement tolerance, which controls the rate at which new nodes are inserted in the model, on the development of dislocation microstructures.Comment: 30 pages, 16 figures. To appear in Jornal of the Mechanics and Physics of Solid

Effects of Various Treatments on the Distribution in Rats of Immune Complexes Containing Antigens of MuLV Leukemia Virus

Immune complexes (IC) containing antigens of MuLV (¹²⁵lp30-anti-p30 or ¹²⁵lp70-anti-gp70) and formed in vitro or in vivo were sequestered primarily in the spleen. Treatments of rats with trypan blue, known to inhibit the reticuloendothelial system (RES) and diethylstilbestrol (DES), known to stimulate the RES, resulted in slight but not significant reduction of uptake of IC by the spleen. Splenectomy did not increase sequestration of IC by the liver nor did it change the distribution of IC in other tissues. Protein A, a cell wall protein of Staphylococcus aureus, when injected with IC resulted in a 10-fold reduction of uptake of IC by the spleen. This effect was seen at 4 hours, 1 day, and 8 days after injection. Protein A did not change the binding of antigen to its respective antibody. The mechanism whereby Protein A exerts its effect is discussed

The genome sequence and effector complement of the flax rust pathogen Melampsora lini

Rust fungi cause serious yield reductions on crops, including wheat, barley, soybean, coffee, and represent real threats to global food security. Of these fungi, the flax rust pathogen Melampsora lini has been developed most extensively over the past 80 years as a model to understand the molecular mechanisms that underpin pathogenesis. During infection, M. lini secretes virulence effectors to promote disease. The number of these effectors, their function and their degree of conservation across rust fungal species is unknown. To assess this, we sequenced and assembled de novo the genome of M. lini isolate CH5 into 21,130 scaffolds spanning 189 Mbp (scaffold N50 of 31 kbp). Global analysis of the DNA sequence revealed that repetitive elements, primarily retrotransposons, make up at least 45% of the genome. Using ab initio predictions, transcriptome data and homology searches, we identified 16,271 putative protein-coding genes. An analysis pipeline was then implemented to predict the effector complement of M. lini and compare it to that of the poplar rust, wheat stem rust and wheat stripe rust pathogens to identify conserved and species-specific effector candidates. Previous knowledge of four cloned M. lini avirulence effector proteins and two basidiomycete effectors was used to optimize parameters of the effector prediction pipeline. Markov clustering based on sequence similarity was performed to group effector candidates from all four rust pathogens. Clusters containing at least one member from M. lini were further analyzed and prioritized based on features including expression in isolated haustoria and infected leaf tissue and conservation across rust species. Herein, we describe 200 of 940 clusters that ranked highest on our priority list, representing 725 flax rust candidate effectors. Our findings on this important model rust species provide insight into how effectors of rust fungi are conserved across species and how they may act to promote infection on their hosts.This work was funded by a grant from the CSIRO Transformational Biology Capability Platform to Adnane Nemri. Claire Anderson was supported by an ARC Discovery Grant (DP120104044) awarded to David A. Jones and Peter N. Dodds

Initial experience of dedicated breast PET imaging of ER+ breast cancers using [F-18]fluoroestradiol.

Dedicated breast positron emission tomography (dbPET) is an emerging technology with high sensitivity and spatial resolution that enables detection of sub-centimeter lesions and depiction of intratumoral heterogeneity. In this study, we report our initial experience with dbPET using [F-18]fluoroestradiol (FES) in assessing ER+ primary breast cancers. Six patients with >90% ER+ and HER2- breast cancers were imaged with dbPET and breast MRI. Two patients had ILC, three had IDC, and one had an unknown primary tumor. One ILC patient was treated with letrozole, and another patient with IDC was treated with neoadjuvant chemotherapy without endocrine treatment. In this small cohort, we observed FES uptake in ER+ primary breast tumors with specificity to ER demonstrated in a case with tamoxifen blockade. FES uptake in ILC had a diffused pattern compared to the distinct circumscribed pattern in IDC. In evaluating treatment response, the reduction of SUVmax was observed with residual disease in an ILC patient treated with letrozole, and an IDC patient treated with chemotherapy. Future study is critical to understand the change in FES SUVmax after endocrine therapy and to consider other tracer uptake metrics with SUVmax to describe ER-rich breast cancer. Limitations include variations of FES uptake in different ER+ breast cancer diseases and exclusion of posterior tissues and axillary regions. However, FES-dbPET has a high potential for clinical utility, especially in measuring response to neoadjuvant endocrine treatment. Further development to improve the field of view and studies with a larger cohort of ER+ breast cancer patients are warranted

Anti-tubulin drugs conjugated to anti-ErbB antibodies selectively radiosensitize.

Tumour resistance to radiotherapy remains a barrier to improving cancer patient outcomes. To overcome radioresistance, certain drugs have been found to sensitize cells to ionizing radiation (IR). In theory, more potent radiosensitizing drugs should increase tumour kill and improve patient outcomes. In practice, clinical utility of potent radiosensitizing drugs is curtailed by off-target side effects. Here we report potent anti-tubulin drugs conjugated to anti-ErbB antibodies selectively radiosensitize to tumours based on surface receptor expression. While two classes of potent anti-tubulins, auristatins and maytansinoids, indiscriminately radiosensitize tumour cells, conjugating these potent anti-tubulins to anti-ErbB antibodies restrict their radiosensitizing capacity. Of translational significance, we report that a clinically used maytansinoid ADC, ado-trastuzumab emtansine (T-DM1), with IR prolongs tumour control in target expressing HER2+ tumours but not target negative tumours. In contrast to ErbB signal inhibition, our findings establish an alternative therapeutic paradigm for ErbB-based radiosensitization using antibodies to restrict radiosensitizer delivery

Childhood adversity subtypes and depressive symptoms in early and late adolescence.

This is the final version of the article. It first appeared from Cambridge University Press via http://dx.doi.org/10.1017/S0954579414000625Within a longitudinal study of 1,005 adolescents, we investigated how exposure to childhood psychosocial adversities was associated with the emergence of depressive symptoms between 14 and 17 years of age. The cohort was classified into four empirically determined adversity subtypes for two age periods in childhood (0-5 and 6-11 years). One subtype reflects normative/optimal family environments (n = 692, 69%), while the other three subtypes reflect differential suboptimal family environments (aberrant parenting: n = 71, 7%; discordant: n = 185, 18%; and hazardous: n = 57, 6%). Parent-rated child temperament at 14 years and adolescent self-reported recent negative life events in early and late adolescence were included in models implementing path analysis. There were gender-differentiated associations between childhood adversity subtypes and adolescent depressive symptoms. The discordant and hazardous subtypes were associated with elevated depressive symptoms in both genders but the aberrant parenting subtype only so in girls. Across adolescence the associations between early childhood adversity and depressive symptoms diminished for boys but remained for girls. Emotional temperament was also associated with depressive symptoms in both genders, while proximal negative life events related to depressive symptoms in girls only. There may be neurodevelopmental factors that emerge in adolescence that reduce depressogenic symptoms in boys but increase such formation in girls.This work was supported by a Wellcome Trust programme grant (Grant 74296) for the ROOTS data collection, and the NIHR Collaboration for Leadership in Applied Health Research and Care (CLAHRC; Grant RNAG/186) for Cambridgeshire and Peterborough for data analysis and manuscript preparation. The second author's (T.C.) contribution was partially supported by a Department of Health Career Scientist Award (Public Mental Health). We thank Matthew Owens, Rosie Abbott, Paul Wilkinson, and Jenny Gibson for informative discussions and suggestions throughout manuscript preparation