Bioinformatic design of dendritic cell-specific synthetic promoters

Next-generation DNA vectors for cancer immunotherapies and vaccine development require promoters eliciting predefined transcriptional activities specific to target cell types, such as dendritic cells (DCs), which underpin immune response. In this study, we describe the de novo design of DC-specific synthetic promoters via in silico assembly of cis-transcription factor response elements (TFREs) that harness the DC transcriptional landscape. Using computational genome mining approaches, candidate TFREs were identified within promoter sequences of highly expressed DC-specific genes or those exhibiting an upregulated expression during DC maturation. Individual TFREs were then screened in vitro in a target DC line and off-target cell lines derived from skeletal muscle, fibroblast, epithelial, and endothelial cells using homotypic (TFRE repeats in series) reporter constructs. Based on these data, a library of heterotypic promoter assemblies varying in the TFRE composition, copy number, and sequential arrangement was constructed and tested in vitro to identify DC-specific promoters. Analysis of the transcriptional activity and specificity of these promoters unraveled underlying design rules, primarily TFRE composition, which govern the DC-specific synthetic promoter activity. Using these design rules, a second library of exclusively DC-specific promoters exhibiting varied transcriptional activities was generated. All DC-specific synthetic promoter assemblies exhibited >5-fold activity in the target DC line relative to off-target cell lines, with transcriptional activities ranging from 8 to 67% of the nonspecific human cytomegalovirus (hCMV-IE1) promoter. We show that bioinformatic analysis of a mammalian cell transcriptional landscape is an effective strategy for de novo design of cell-type-specific synthetic promoters with precisely controllable transcriptional activities

A synonymous codon variant in two patients with autosomal recessive bestrophinopathy alters in vitro splicing of BEST1

Purpose: Autosomal recessive bestrophinopathy (ARB) is a newly defined retinal dystrophy caused by biallelic mutations in bestrophin-1 (BEST1) and is hypothesized to represent the null bestrophin-1 phenotype in humans. The aim was to determine whether a synonymous BEST1 variant, c.102C>T, identified in two unrelated ARB patients, alters pre-mRNA splicing of the gene. Additionally a detailed phenotypic characterization of this distinctive condition is presented for both patients.Methods: BEST1 was analyzed by direct sequencing. Patients underwent standard ophthalmic assessment. In silico and in vitro analysis using a minigene system was performed to assess whether a synonymous variant identified, c.102C>T p.Gly34Gly, alters pre-mRNA splicing of BEST1.Results: Both ARB patients harbored either proven (patient 1; c.102C>T p.Gly34Gly and c.572T>C p.Leu191Pro) or presumed (patient 2; c.102C>T p.Gly34Gly and c.1470_1471delCA, p.His490GlnfsX24) biallelic mutations in BEST1 and were found to have phenotypes consistent with ARB. In vitro analysis of the synonymous variant, c.102C>T p.Gly34Gly, demonstrated it to introduce a cryptic splice donor site 52 nucleotides upstream of the actual splice donor site.Conclusions: The novel BEST1 variant identified, c.102C>T p.Gly34Gly, alters pre-mRNA splicing in vitro and is potentially pathogenic. In vivo this splicing variant is predicted to lead to the production of an mRNA transcript with a premature termination codon (p.Glu35TrpfsX11) that is predicted to be degraded by NMD

Evaluation of effectiveness and efficiency of wild bird surveillance for avian influenza

This study aimed to assess which method of wild waterbird surveillance had the greatest probability of detecting highly pathogenic avian influenza (HPAI) H5N1 during a period of surveillance activity, the cost of each method was also considered. Lake Constance is a major wintering centre for migratory waterbirds and in 2006 it was the site of an HPAI H5N1 epidemic in wild birds. Avian influenza surveillance was conducted using harmonised approaches in the three countries around the lake, Austria, Germany and Switzerland, from 2006–2009. The surveillance consisted of testing birds sampled by the following methods: live birds caught in traps, birds killed by hunters, birds caught in fishing nets, dead birds found by the public and catching live Mute Swans (Cygnus olor); sentinel flocks of Mallards (Anas platyrhynchos) were also used. Scenario tree analysis was performed including sensitivity analysis, followed by assessment of cost-effectiveness. Results indicated that if HPAI H5N1 was present at 1% prevalence and assuming HPAI resulted in bird mortality, sampling dead birds found by the public and sentinel surveillance were the most sensitive approaches despite residual uncertainty over some parameters. The uncertainty over the mortality of infected birds was an influential factor. Sampling birds found dead was most cost-effective, but strongly dependent on mortality and awareness of the public. Trapping live birds was least cost-effective. Based on our results, we recommend that future HPAI H5N1 surveillance around Lake Constance should prioritise sentinel surveillance and, if high mortality is expected, the testing of birds found dead

Evolution of HCl Concentrations in the Lower Stratosphere from 1991 to 1996 Following the Eruption of Mt. Pinatubo

Geophysical Research Letters, Vol. 25, No. 7, pp. 995-998, April 1, 1998.In situ measurements of hydrochloric acid in the lower stratosphere reveal that its mean abundance relative to that of total inorganic chlorine..

Randomised controlled trial to evaluate the effect of foot trimming before and after first calving on subsequent lameness episodes and productivity in dairy heifers

The objective of this study was to assess both independent and combined effects of routine foot trimming of heifers at 3 weeks pre-calving and 100 days post calving on the first lactation lameness and lactation productivity. A total of 419 pre-calving dairy heifers were recruited from one heifer rearing operation over a 10-month period. Heifers were randomly allocated into one of four foot trimming regimens; pre-calving foot trim and post-calving lameness score (Group TL), pre-calving lameness score and post-calving foot trim (Group LT), pre-calving foot trim and post-calving foot trim (Group TT), and pre-calving lameness score and post-calving lameness score (Group LL, control group). All heifers were scored for lameness at 24 biweekly time points for 1 year following calving, and first lactation milk production data were collected. Following calving, 172/419 (41.1%) of heifers became lame during the study (period prevalence), with lameness prevalence at each time-point following calving ranging from 48/392 (12.2%) at 29–42 days post-calving to 4/379 (1.1%) between 295 and 383 days after calving. The effects of the four treatment groups were not significantly different from each other for overall lameness period prevalence, biweekly lameness point prevalence, time to first lameness event, type of foot lesion identified at dry off claw trimming, or the 4% fat corrected 305-day milk yield. However, increased odds lameness was significantly associated with a pre-calving trim alone (P = 0.044) compared to the reference group LL. The odds of heifer lameness were highest between 0 and 6 weeks post-partum, and heifer farm destination was significantly associated with lameness (OR 2.24), suggesting that even at high standard facilities, environment and management systems have more effect on heifer foot health than trimming

University-industry relationships and open innovation: Towards a research agenda

Accepted versio

Integrating sequence and array data to create an improved 1000 Genomes Project haplotype reference panel

A major use of the 1000 Genomes Project (1000GP) data is genotype imputation in genome-wide association studies (GWAS). Here we develop a method to estimate haplotypes from low-coverage sequencing data that can take advantage of single-nucleotide polymorphism (SNP) microarray genotypes on the same samples. First the SNP array data are phased to build a backbone (or 'scaffold') of haplotypes across each chromosome. We then phase the sequence data 'onto' this haplotype scaffold. This approach can take advantage of relatedness between sequenced and non-sequenced samples to improve accuracy. We use this method to create a new 1000GP haplotype reference set for use by the human genetic community. Using a set of validation genotypes at SNP and bi-allelic indels we show that these haplotypes have lower genotype discordance and improved imputation performance into downstream GWAS samples, especially at low-frequency variants. © 2014 Macmillan Publishers Limited. All rights reserved

On the mechanisms governing gas penetration into a tokamak plasma during a massive gas injection

A new 1D radial fluid code, IMAGINE, is used to simulate the penetration of gas into a tokamak plasma during a massive gas injection (MGI). The main result is that the gas is in general strongly braked as it reaches the plasma, due to mechanisms related to charge exchange and (to a smaller extent) recombination. As a result, only a fraction of the gas penetrates into the plasma. Also, a shock wave is created in the gas which propagates away from the plasma, braking and compressing the incoming gas. Simulation results are quantitatively consistent, at least in terms of orders of magnitude, with experimental data for a D 2 MGI into a JET Ohmic plasma. Simulations of MGI into the background plasma surrounding a runaway electron beam show that if the background electron density is too high, the gas may not penetrate, suggesting a possible explanation for the recent results of Reux et al in JET (2015 Nucl. Fusion 55 093013)

Measurement of the View the tt production cross-section using eμ events with b-tagged jets in pp collisions at √s = 13 TeV with the ATLAS detector

This paper describes a measurement of the inclusive top quark pair production cross-section (σtt¯) with a data sample of 3.2 fb−1 of proton–proton collisions at a centre-of-mass energy of √s = 13 TeV, collected in 2015 by the ATLAS detector at the LHC. This measurement uses events with an opposite-charge electron–muon pair in the final state. Jets containing b-quarks are tagged using an algorithm based on track impact parameters and reconstructed secondary vertices. The numbers of events with exactly one and exactly two b-tagged jets are counted and used to determine simultaneously σtt¯ and the efficiency to reconstruct and b-tag a jet from a top quark decay, thereby minimising the associated systematic uncertainties. The cross-section is measured to be: σtt¯ = 818 ± 8 (stat) ± 27 (syst) ± 19 (lumi) ± 12 (beam) pb, where the four uncertainties arise from data statistics, experimental and theoretical systematic effects, the integrated luminosity and the LHC beam energy, giving a total relative uncertainty of 4.4%. The result is consistent with theoretical QCD calculations at next-to-next-to-leading order. A fiducial measurement corresponding to the experimental acceptance of the leptons is also presented