Multiple exon skipping strategies to by-pass dystrophin mutations.

Manipulation of dystrophin pre-mRNA processing offers the potential to overcome mutations in the dystrophin gene that would otherwise lead to Duchenne muscular dystrophy. Dystrophin mutations will require the removal of one or more exons to restore the reading frame and in some cases, multiple exon skipping strategies exist to restore dystrophin expression. However, for some small intra-exonic mutations, a third strategy, not applicable to whole exon deletions, may be possible. The removal of only one frame-shifting exon flanking the mutation-carrying exon may restore the reading frame and allow synthesis of a functional dystrophin isoform, providing that no premature termination codons are encountered. For these mutations, the removal of only one exon offers a simpler, cheaper and more feasible alternative approach to the dual exon skipping that would otherwise be considered. We present strategies to by-pass intra-exonic dystrophin mutations that clearly demonstrate the importance of tailoring exon skipping strategies to specific patient mutations

Editorial: crime patterns in time and space: the dynamics of crime opportunities in urban areas

The routine activity approach and associated crime pattern theory emphasise how crime emerges from spatio-temporal routines. In order to understand this crime should be studied in both space and time. However, the bulk of research into crime patterns and related activities has investigated the spatial distributions of crime, neglecting the temporal dimension. Specifically, disaggregation of crime by place and by time, for example hour of day, day of week, month of year, season, or school day versus none school day, is extremely relevant to theory. Modern data make such spatio-temporal disaggregation increasingly feasible, as exemplified in this special issue. First, much larger data files allow disaggregation of crime data into temporal and spatial slices. Second, new forms of data are generated by modern technologies, allowing innovative and new forms of analyses. Crime pattern analyses and routine activity inquiries are now able to explore avenues not previously available. The unique collection of nine papers in this thematic issue specifically examine spatio-temporal patterns of crime to; demonstrate the value of this approach for advancing knowledge in the field; consider how this informs our theoretical understanding of the manifestations of crime in time and space; to consider the prevention implications of this; and to raise awareness of the need for further spatio-temporal research into crime event

Mesoscale and Submesoscale Effects on Mixed Layer Depth in the Southern Ocean

Submesoscale dynamics play a key role in setting the stratification of the ocean surface mixed layer and mediating air–sea exchange, making them especially relevant to anthropogenic carbon uptake and primary productivity in the Southern Ocean. In this paper, a series of offline-nested numerical simulations is used to study submesoscale flow in the Drake Passage and Scotia Sea regions of the Southern Ocean. These simulations are initialized from an ocean state estimate for late April 2015, with the intent to simulate features observed during the Surface Mixed Layer at Submesoscales (SMILES) research cruise, which occurred at that time and location. The nested models are downscaled from the original state estimate resolution of 1/12° and grid spacing of about 8 km, culminating in a submesoscale-resolving model with a resolution of 1/192° and grid spacing of about 500 m. The submesoscale eddy field is found to be highly spatially variable, with pronounced hot spots of submesoscale activity. These areas of high submesoscale activity correspond to a significant difference in the 30-day average mixed layer depth ΔH_ML between the 1/12° and 1/192° simulations. Regions of large vertical velocities in the mixed layer correspond with high mesoscale strain rather than large ΔH_ML. It is found that ΔH_ML is well correlated with the mesoscale density gradient but weakly correlated with both the mesoscale kinetic energy and strain. This has implications for the development of submesoscale eddy parameterizations that are sensitive to the character of the large-scale flow.The authors gratefully acknowledge support from the Natural Environment Research Council Awards NE/J010472/1 and NE/J009857/1

Model Lipid Membranes Assembled from Natural Plant Thylakoids into 2D Microarray Patterns as a Platform to Assess the Organization and Photophysics of Light‐Harvesting Proteins

Natural photosynthetic “thylakoid” membranes found in green plants contain a large network of light‐harvesting (LH) protein complexes. Rearrangement of this photosynthetic machinery, laterally within stacked membranes called “grana”, alters protein–protein interactions leading to changes in the energy balance within the system. Preparation of an experimentally accessible model system that allows the detailed investigation of these complex interactions can be achieved by interfacing thylakoid membranes and synthetic lipids into a template comprised of polymerized lipids in a 2D microarray pattern on glass surfaces. This paper uses this system to interrogate the behavior of LH proteins at the micro‐ and nanoscale and assesses the efficacy of this model. A combination of fluorescence lifetime imaging and atomic force microscopy reveals the differences in photophysical state and lateral organization between native thylakoid and hybrid membranes, the mechanism of LH protein incorporation into the developing hybrid membranes, and the nanoscale structure of the system. The resulting model system within each corral is a high‐quality supported lipid bilayer that incorporates laterally mobile LH proteins. Photosynthetic activity is assessed in the hybrid membranes versus proteoliposomes, revealing that commonly used photochemical assays to test the electron transfer activity of photosystem II may actually produce false‐positive results

Derived neutrophil lymphocyte ratio is predictive of survival from intermittent therapy in advanced colorectal cancer: a post hoc analysis of the MRC COIN study

BACKGROUND: The phase III COntinuous or INtermittent (COIN) trial failed to show non-inferiority of intermittent compared with continuous chemotherapy for advanced colorectal cancer in overall survival (OS). The present analysis evaluated whether the derived neutrophil to lymphocyte ratio (dNLR) could predict the effect of intermittent vs continuous chemotherapy on OS in patients with advanced colorectal cancer. METHODS: A post hoc exploratory analysis of COIN arms A and C was performed. Landmark analysis was conducted on all patients with available WBC and neutrophils data. The dNLR was calculated using a formula which has previously demonstrated predictive power in cancer patients: dNLR=ANC/(WBC−ANC). A high dNLR was defined using a cut-off value of ⩾2.22. Derived neutrophil to lymphocyte ratio was then correlated with clinical outcomes. Survival curves were generated based on dNLR using the Kaplan–Meier method. Comparison between groups was performed using Cox regression. RESULTS: A total of 1630 patients were assigned to the continuous (N=815) or intermittent (N=815) arms. There was a strong association between dNLR level and OS. The median survival times in the ITT population were 18.6 months and 12.5 months for patients with low and high dNLR, respectively (HR=1.70; 95% CI=1.52–1.90; P<0.001). The estimate of the hazard ratio did not alter substantially (HR=1.54) after adjusting for treatment, tumour status, number of metastatic sites, alkaline phosphate and platelet count. CONCLUSIONS: Derived neutrophil to lymphocyte ratio is strongly prognostic for survival in the COIN intermittent vs continuous treatment arms. Derived neutrophil to lymphocyte ratio does not predict for detrimental survival in patients treated with intermittent therapy

Proteoliposomes as energy transferring nanomaterials: enhancing the spectral range of light-harvesting proteins using lipid-linked chromophores

Bio-hybrid nanomaterials have great potential for combining the most desirable aspects of biomolecules and the contemporary concepts of nanotechnology to create highly efficient light-harvesting materials. Light-harvesting proteins are optimized to absorb and transfer solar energy with remarkable efficiency but have a spectral range that is limited by their natural pigment complement. Herein, we present the development of model membranes (“proteoliposomes”) in which the absorption range of the membrane protein Light-Harvesting Complex II (LHCII) is effectively enhanced by the addition of lipid-tethered Texas Red (TR) chromophores. Energy transfer from TR to LHCII is observed with up to 94% efficiency and increased LHCII fluorescence of up to three-fold when excited in the region of lowest natural absorption. The new self-assembly procedure offers the modularity to control the concentrations incorporated of TR and LHCII, allowing energy transfer and fluorescence to be tuned. Fluorescence Lifetime Imaging Microscopy provides single-proteoliposome-level quantification of energy transfer efficiency and confirms that functionality is retained on surfaces. Designer proteoliposomes could act as a controllable light-harvesting nanomaterial and are a promising step in the development of bio-hybrid light-harvesting systems

Patients' perceptions of the potential of breathing training for asthma: a qualitative study.

Poor symptom control is common in asthma. Breathing training exercises may be an effective adjunct to medication; it is therefore important to understand facilitators and barriers to uptake of breathing training exercises

Investigating the poor outcomes of BRAF - mutant advanced colorectal cancer: Analysis from 2530 patients in randomised clinical trials

Background: To improve strategies for the treatment of BRAF-mutant advanced colorectal cancer (aCRC) patients we examined individual data from patients treated with chemotherapy alone in three randomised trials to identify points on the treatment pathway where outcomes differ from BRAF wild-types. Patients and Methods: 2530 aCRC patients were assessed from three randomised trials. End-points were progression free survival (PFS), response rate (RR), disease control rate (DCR), post-progression survival (P-PS) and overall survival (OS). Treatments included first-line oxaliplatin/fluorouracil (OxFU), and second-line irinotecan. Clinicians were unaware of BRAF-status Results 231 patients (9.1%) had BRAF-mutant tumours. BRAF-mutation conferred significantly worse survival independent of associated clinicopathological factors known to be prognostic. Compared with wild-type, BRAF-mutant patients treated with first-line OxFU had similar DCR (59.2% vs 72%; adjusted OR=0.76,p=0.24) and PFS (5.7 vs 6.3 months; adjusted HR=1.14, p=0.26). Following progression on first-line chemotherapy, BRAF-mutant patients had a markedly shorter P-PS (4.2 vs 9.2 months, adjusted HR=1.69,p6 months; OS=24.0 months), however 36.5% progressed rapidly through first-line chemotherapy and thereafter, with OS=4.7 months. Conclusions BRAF-mutant aCRC confers a markedly worse prognosis independent of associated clinicopathological features. Chemotherapy provides meaningful improvements in outcome throughout treatment lines. Post-progression survival is markedly worse and vigilance is required to ensure appropriate delivery of treatment after first-line progression

Evaluation of a manualised speech and language therapy programme for children with social communication disorder: the SCIP feasibility study

Background: Children with Social (Pragmatic) Communication Disorder (SPCD) have long-3 term needs in using and processing social language and have a high risk of later mental health difficulties. A manualised speech and language therapy programme, the Social Communication Intervention Programme (SCIP) provides therapy content for SPCD. A feasibility study is required to derive more precise estimates of key parameters for a future trial of SCIP. Aims: To assess the feasibility of conducting a substantive randomized controlled trial of SCIP for children with SPCD. Methods: A questionnaire was distributed to paediatric speech and language therapists in England. Survey questions addressed number of eligible children, routine intervention provision and trial recruitment factors. In the second phase, a single-arm intervention feasibility study was completed. 15 speech and language practitioners identified 24 children aged 5-11 years with SPCD. Practitioners received training/supervision to deliver 20 SCIP therapy sessions to each child. At Time 1 parents of participating children provided three communication goals; expected steps in each goal were defined. After intervention, parents and practitioners independently rated each goal compared to baseline ability. Two research practitioners compared parent post-intervention commentaries with outcome scores to derive guidance about clinical significance. All practitioners recorded audio commentaries on therapy experiences. Post-intervention interviews were conducted with 6 practitioners and 6 parents. An expert panel completed a Delphi consultation on trial design. Results: Routine practice for SPCD varies widely. Children tend to be embedded in autism provision. Participation in a future trial was well-supported, provided resources are available to services. Outcomes analysis indicated all children except one made some progress on parent ratings; all children made progress on practitioner ratings. A power analysis for a future trial was carried out using current outcome measure as putative primary endpoint. Practitioners’ audio-diaries provided suggestions for training and adaption in a future trial. Outcomes and therapy methods were acceptable to practitioners and parents. Conclusions: The feasibility study evaluated a novel outcome measure of social communication skills in SPCD. A power calculation indicated a feasible framework for a trial within a realistic period of time. Recommendations for recruitment methods, adaptation of manual and training were 6 supported by practitioners and an expert panel

Mismatched single stranded antisense oligonucleotides can induce efficient dystrophin splice switching

<p>Abstract</p> <p>Background</p> <p>Antisense oligomer induced exon skipping aims to reduce the severity of Duchenne muscular dystrophy by redirecting splicing during pre-RNA processing such that the causative mutation is by-passed and a shorter but partially functional Becker muscular dystrophy-like dystrophin isoform is produced. Normal exons are generally targeted to restore the dystrophin reading frame however, an appreciable subset of dystrophin mutations are intra-exonic and therefore have the potential to compromise oligomer efficiency, necessitating personalised oligomer design for some patients. Although antisense oligomers are easily personalised, it remains unclear whether all patient polymorphisms within antisense oligomer target sequences will require the costly process of producing and validating patient specific compounds.</p> <p>Methods</p> <p>Here we report preclinical testing of a panel of splice switching antisense oligomers, designed to excise exon 25 from the dystrophin transcript, in normal and dystrophic patient cells. These patient cells harbour a single base insertion in exon 25 that lies within the target sequence of an oligomer shown to be effective at removing exon 25.</p> <p>Results</p> <p>It was anticipated that such a mutation would compromise oligomer binding and efficiency. However, we show that, despite the mismatch an oligomer, designed and optimised to excise exon 25 from the normal dystrophin mRNA, removes the mutated exon 25 more efficiently than the mutation-specific oligomer.</p> <p>Conclusion</p> <p>This raises the possibility that mismatched AOs could still be therapeutically applicable in some cases, negating the necessity to produce patient-specific compounds.</p