A versatile toolkit for high throughput functional genomics with Trichoderma reesei

<p>Abstract</p> <p>Background</p> <p>The ascomycete fungus, <it>Trichoderma reesei </it>(anamorph of <it>Hypocrea jecorina</it>), represents a biotechnological workhorse and is currently one of the most proficient cellulase producers. While strain improvement was traditionally accomplished by random mutagenesis, a detailed understanding of cellulase regulation can only be gained using recombinant technologies.</p> <p>Results</p> <p>Aiming at high efficiency and high throughput methods, we present here a construction kit for gene knock out in <it>T. reesei</it>. We provide a primer database for gene deletion using the <it>pyr4, amdS </it>and <it>hph </it>selection markers. For high throughput generation of gene knock outs, we constructed vectors using yeast mediated recombination and then transformed a <it>T. reesei </it>strain deficient in non-homologous end joining (NHEJ) by spore electroporation. This NHEJ-defect was subsequently removed by crossing of mutants with a sexually competent strain derived from the parental strain, QM9414.</p> <p>Conclusions</p> <p>Using this strategy and the materials provided, high throughput gene deletion in <it>T. reesei </it>becomes feasible. Moreover, with the application of sexual development, the NHEJ-defect can be removed efficiently and without the need for additional selection markers. The same advantages apply for the construction of multiple mutants by crossing of strains with different gene deletions, which is now possible with considerably less hands-on time and minimal screening effort compared to a transformation approach. Consequently this toolkit can considerably boost research towards efficient exploitation of the resources of <it>T. reesei </it>for cellulase expression and hence second generation biofuel production.</p

Effects of erythropoietin therapy on the lipid profile in end-stage renal failure

Effects of erythropoietin therapy on the lipid profile in end-stage renal failure. To evaluate the effects of erythropoietin (EPO) therapy on the lipid profile in end-stage renal failure, we undertook a prospective study in patients on both hemodialysis (HD) and continuous ambulatory peritoneal dialysis (CAPD). One hundred and twelve patients (81 HD, 31 CAPD) were enrolled into the study. Lipid parameters [that is, total cholesterol and the LDL and HDL subfractions, triglycerides, lipoprotein (a), apoproteins A and B], full blood count, iron studies, B12, folate, blood urea, aluminium and serum parathyroid hormone were measured prior to commencement of EPO therapy. Ninety-five patients were reassessed 5.2 ± 0.3 (mean ± SEM) months later and 53 patients underwent a further assessment 13.1 ± 0.6 months after the commencement of EPO, giving an overall follow-up of 10.0 ± 0.6 months in 95 patients. As expected, EPO treatment was associated with an increase in hemoglobin (7.7 ± 0.1 vs. 9.9 ± 0.2 g/dl; P < 0.001) and a decrease in ferritin (687 ± 99 vs. 399 ± 69 µg/liter; P < 0.01). A significant fall in total cholesterol occurred (5.8 ± 0.1 vs. 5.4 ± 0.2 mmol/liter; P < 0.05) in association with a fall in apoprotein B (1.15 ± 0.04 vs. 1.04 ± 0.06; P < 0.05) and serum triglycerides (2.26 ± 0.14 vs. 1.99 ± 0.21; P < 0.05) during the course of the study. Other lipid parameters did not change, although there was a trend towards improvement. These changes correlated with the increase in Hb (P < 0.001 in each case), and the reduction in ferritin for total cholesterol (P < 0.02), LDL cholesterol (P < 0.03), and to a lesser extent apoprotein B (P < 0.07). No difference was observed in patients using maintenance HD or CAPD, and similar trends were observed in male and female patients. Improvements in the lipid profile occurred independently of the time on dialysis prior to the commencement of EPO. We conclude that EPO treatment is associated with alterations in the lipid profile which may suggest a long-term improvement in the vascular morbidity of chronic renal failure. The causes of the improved lipids are not addressed by this study and may be equally due to a direct or secondary benefit of EPO therapy

Effects of SlowMo, a Blended Digital Therapy Targeting Reasoning, on Paranoia Among People With Psychosis: A Randomized Clinical Trial.

IMPORTANCE: Persistent paranoia is common among patients with psychosis. Cognitive-behavioral therapy for psychosis can be effective. However, challenges in engagement and effectiveness remain. OBJECTIVE: To investigate the effects on paranoia and mechanisms of action of SlowMo, a digitally supported reasoning intervention, plus usual care compared with usual care only. DESIGN, SETTING, AND PARTICIPANTS: This parallel-arm, assessor-blinded, randomized clinical trial recruited participants at UK community health services from May 1, 2017, to May 14, 2019. Eligible participants consisted of a referral sample with schizophrenia-spectrum psychosis and distressing, persistent (≥3 months) paranoia. INTERVENTIONS: Individuals were randomized 1:1 to SlowMo, consisting of 8 digitally supported face-to-face sessions and a mobile app, plus usual care (n = 181) and usual care only (n = 181). MAIN OUTCOMES AND MEASURES: The primary outcome was paranoia, measured by the Green et al Paranoid Thoughts Scale (GPTS) total score at 24 weeks. Secondary outcomes included GPTS total score at 12 weeks and GPTS Part A (reference) and Part B (persecutory) scores, the Psychotic Symptom Rating Scales (PSYRATS Delusion subscale), reasoning (belief flexibility, possibility of being mistaken [Maudsley Assessment of Delusions, rated 0%-100%]), and jumping to conclusions (Beads Task). RESULTS: A total of 361 participants were included in intention-to-treat analysis, of whom 252 (69.8%) were male and 249 (69.0%) were White; the mean (SD) age was 42.6 (11.6) years. At 24 weeks, 332 participants (92.0%) provided primary outcome data. Of 181 participants in the SlowMo group, 145 (80.1%) completed therapy. SlowMo plus usual care was not associated with greater reductions than usual care in GPTS total score at 24 weeks (Cohen d, 0.20; 95% CI, −0.02 to 0.40; P = .06). There were significant effects on secondary paranoia outcomes at 12 weeks, including GPTS total score (Cohen d, 0.30; 95% CI, 0.09-0.51; P = .005), Part A score (Cohen d, 0.22; 95% CI, 0.06-0.39; P = .009), and Part B score (Cohen d, 0.32; 95% CI, 0.08-0.56; P = .009), and at 24 weeks, including Part B score (Cohen d, 0.25; 95% CI, 0.01-0.49; P = .04) but not Part A score (Cohen d, 0.12; 95% CI, −0.05 to 0.28; P = .18). Improvements were observed in an observer-rated measure of persecutory delusions (PSYRATS delusion) at 12 weeks (Cohen d, 0.47; 95% CI, 0.17-0.78; P = .002) and 24 weeks (Cohen d, 0.50; 95% CI, 0.20-0.80; P = .001) and belief flexibility at 12 weeks (Cohen d, 0.29; 95% CI, 0.09-0.49; P = .004) and 24 weeks (Cohen d, 0.28; 95% CI, 0.08-0.49; P = .005). There were no significant effects on jumping to conclusions. Improved belief flexibility and worry mediated paranoia change (range mediated, 36%-56%). CONCLUSIONS AND RELEVANCE: SlowMo did not demonstrate significant improvements in the primary measure of paranoia at 24 weeks; however, a beneficial effect of SlowMo on paranoia was indicated by the results on the primary measure at an earlier point and on observer-rated paranoia and self-reported persecution at 12 and 24 weeks. Further work to optimize SlowMo’s effects is warranted. TRIAL REGISTRATION: isrctn.org Identifier: ISRCTN 3244867

The Comparative RNA Web (CRW) Site: an online database of comparative sequence and structure information for ribosomal, intron, and other RNAs

BACKGROUND: Comparative analysis of RNA sequences is the basis for the detailed and accurate predictions of RNA structure and the determination of phylogenetic relationships for organisms that span the entire phylogenetic tree. Underlying these accomplishments are very large, well-organized, and processed collections of RNA sequences. This data, starting with the sequences organized into a database management system and aligned to reveal their higher-order structure, and patterns of conservation and variation for organisms that span the phylogenetic tree, has been collected and analyzed. This type of information can be fundamental for and have an influence on the study of phylogenetic relationships, RNA structure, and the melding of these two fields. RESULTS: We have prepared a large web site that disseminates our comparative sequence and structure models and data. The four major types of comparative information and systems available for the three ribosomal RNAs (5S, 16S, and 23S rRNA), transfer RNA (tRNA), and two of the catalytic intron RNAs (group I and group II) are: (1) Current Comparative Structure Models; (2) Nucleotide Frequency and Conservation Information; (3) Sequence and Structure Data; and (4) Data Access Systems. CONCLUSIONS: This online RNA sequence and structure information, the result of extensive analysis, interpretation, data collection, and computer program and web development, is accessible at our Comparative RNA Web (CRW) Site http://www.rna.icmb.utexas.edu. In the future, more data and information will be added to these existing categories, new categories will be developed, and additional RNAs will be studied and presented at the CRW Site

H0LiCOW X: Spectroscopic/imaging survey and galaxy-group identification around the strong gravitational lens system WFI2033-4723

Galaxies and galaxy groups located along the line of sight towards gravitationally lensed quasars produce high-order perturbations of the gravitational potential at the lens position. When these perturbation are too large, they can induce a systematic error on $H_0$ of a few-percent if the lens system is used for cosmological inference and the perturbers are not explicitly accounted for in the lens model. In this work, we present a detailed characterization of the environment of the lens system WFI2033-4723 ($z_{\rm src} = 1.662$, $z_{\rm lens}$ = 0.6575), one of the core targets of the H0LICOW project for which we present cosmological inferences in a companion paper (Rusu et al. 2019). We use the Gemini and ESO-Very Large telescopes to measure the spectroscopic redshifts of the brightest galaxies towards the lens, and use the ESO-MUSE integral field spectrograph to measure the velocity-dispersion of the lens ($\sigma_{\rm {los}}= 250^{+15}_{-21}$ km/s) and of several nearby galaxies. In addition, we measure photometric redshifts and stellar masses of all galaxies down to $i < 23$ mag, mainly based on Dark Energy Survey imaging (DR1). Our new catalog, complemented with literature data, more than doubles the number of known galaxy spectroscopic redshifts in the direct vicinity of the lens, expanding to 116 (64) the number of spectroscopic redshifts for galaxies separated by less than 3 arcmin (2 arcmin) from the lens. Using the flexion-shift as a measure of the amplitude of the gravitational perturbation, we identify 2 galaxy groups and 3 galaxies that require specific attention in the lens models. The ESO MUSE data enable us to measure the velocity-dispersions of three of these galaxies. These results are essential for the cosmological inference analysis presented in Rusu et al. (2019).Comment: Matches the version accepted for publication by MNRAS. Note that this paper previously appeared as H0LICOW X

Application of Inelastic Neutron Scattering to the Methanol-to-Gasoline Reaction Over a ZSM-5 Catalyst

Inelastic neutron scattering (INS) is used to investigate a ZSM-5 catalyst that has been exposed to methanol vapour at elevated temperature. In-line mass spectrometric analysis of the catalyst exit stream confirms methanol-to-gasoline chemistry, whilst ex situ INS measurements detect hydrocarbon species formed in/on the catalyst during methanol conversion. These preliminary studies demonstrate the capability of INS to complement infrared spectroscopic characterisation of the hydrocarbon pool present in/on ZSM-5 during the MTG reaction

Assessing methods for dealing with treatment switching in randomised controlled trials: a simulation study

<p>Abstract</p> <p>Background</p> <p>We investigate methods used to analyse the results of clinical trials with survival outcomes in which some patients switch from their allocated treatment to another trial treatment. These included simple methods which are commonly used in medical literature and may be subject to selection bias if patients switching are not typical of the population as a whole. Methods which attempt to adjust the estimated treatment effect, either through adjustment to the hazard ratio or via accelerated failure time models, were also considered. A simulation study was conducted to assess the performance of each method in a number of different scenarios.</p> <p>Results</p> <p>16 different scenarios were identified which differed by the proportion of patients switching, underlying prognosis of switchers and the size of true treatment effect. 1000 datasets were simulated for each of these and all methods applied. Selection bias was observed in simple methods when the difference in survival between switchers and non-switchers were large. A number of methods, particularly the AFT method of Branson and Whitehead were found to give less biased estimates of the true treatment effect in these situations.</p> <p>Conclusions</p> <p>Simple methods are often not appropriate to deal with treatment switching. Alternative approaches such as the Branson & Whitehead method to adjust for switching should be considered.</p

The DES bright arcs survey: hundreds of candidate strongly lensed galaxy systems from the Dark Energy Survey Science Verification and year 1 observations

We report the results of searches for strong gravitational lens systems in the Dark Energy Survey (DES) Science Verification and Year 1 observations. The Science Verification data span approximately 250 sq. deg. with a median i-band limiting magnitude for extended objects (10σ) of 23.0. The Year 1 data span approximately 2000 sq. deg. and have an i-band limiting magnitude for extended objects (10σ) of 22.9. As these data sets are both wide and deep, they are particularly useful for identifying strong gravitational lens candidates. Potential strong gravitational lens candidate systems were initially identified based on a color and magnitude selection in the DES object catalogs or because the system is at the location of a previously identified galaxy cluster. Cutout images of potential candidates were then visually scanned using an object viewer and numerically ranked according to whether or not we judged them to be likely strong gravitational lens systems. Having scanned nearly 400,000 cutouts, we present 374 candidate strong lens systems, of which 348 are identified for the first time. We provide the R.A. and decl., the magnitudes and photometric properties of the lens and source objects, and the distance (radius) of the source(s) from the lens center for each system