Differential Gene Expression following DHX36/G4R1 Knockout Is Associated with G-Quadruplex Content and Cancer.

G-quadruplexes (G4s) are secondary DNA and RNA structures stabilized by positive cations in a central channel formed by stacked tetrads of Hoogsteen base-paired guanines. G4s form from G-rich sequences across the genome, whose biased distribution in regulatory regions points towards a gene-regulatory role. G4s can themselves be regulated by helicases, such as DHX36 (aliases: G4R1 and RHAU), which possess the necessary activity to resolve these stable structures. G4s have been shown to both positively and negatively regulate gene expression when stabilized by ligands, or through the loss of helicase activity. Using DHX36 knockout Jurkat cell lines, we identified widespread, although often subtle, effects on gene expression that are associated with the presence or number of observed G-quadruplexes in promoters or gene regions. Genes that significantly change their expression, particularly those that show a significant increase in RNA abundance under DHX36 knockout, are associated with a range of cellular functions and processes, including numerous transcription factors and oncogenes, and are linked to several cancers. Our work highlights the direct and indirect role of DHX36 in the transcriptome of T-lymphocyte leukemia cells and the potential for DHX36 dysregulation in cancer.

Delirium-associated medication in people at risk: A systematic update review, meta-analyses, and GRADE-profiles.

BACKGROUND: Drug-associated delirium is a common but potentially preventable neuropsychiatric syndrome associated with detrimental outcomes. Empirical evidence for delirium-associated medication is uncertain due to a lack of high-quality studies. We aimed to further investigate the body of evidence for drugs suspected to trigger delirium. METHODS: A systematic update review and meta-analyses of prospective studies presenting drug associations with incident delirium in adult study populations was conducted. Two authors independently searched MEDLINE, PsycINFO, Embase, and Google Scholar dated from October 1, 2009 to June 23, 2020, after screening a previous review published in 2011. The most reliable results on drug-delirium associations were pooled in meta-analyses using the random-effects model. Quality of evidence was assessed using the GRADE-approach. This study is preregistered with OSF (DOI https://doi.org.10.17605/OSF.IO/4PUHY). RESULTS: The 31 eligible studies, presenting results for 24 medication classes were identified. Meta-analyses and GRADE level of evidence ratings show no increased delirium risk for Haloperidol (OR: 0.96, 95% CI 0.72-1.28; high-quality evidence), Olanzapine (OR: 0.25, 95% CI 0.15-0.40), Ketamine (OR: 0.72, 95% CI 0.35-1.46) or corticosteroids (OR: 0.69, 95% CI 0.32-1.50; moderate quality evidence, respectively). Low-level evidence suggests a three-fold increased risk for anticholinergics (OR: 3.11, 95% CI 1.04-9.26). Opioids, benzodiazepines, H1 -antihistamines, and antidepressants did not reach reliable evidence levels in our analyses. CONCLUSION: We investigated the retrievable body of evidence for delirium-associated medication. The results of this systematic review were then interpreted in conjunction with other evidence-based works and guidelines providing conclusions for clinical decision-making.

Probing the composition dependence of residual stress distribution in tungsten-titanium nanocrystalline thin films.

Nanocrystalline alloy thin films offer a variety of attractive properties, such as high hardness, strength and wear resistance. A disadvantage is the large residual stresses that result from their fabrication by deposition, and subsequent susceptibility to defects. Here, we use experimental and modelling methods to understand the impact of minority element concentration on residual stresses that emerge after deposition in a tungsten-titanium film with different titanium concentrations. We perform local residual stress measurements using micro-cantilever samples and employ machine learning for data extraction and stress prediction. The results are correlated with accompanying microstructure and elemental analysis as well as atomistic modelling. We discuss how titanium enrichment significantly affects the stress stored in the nanocrystalline thin film. These findings may be useful for designing stable nanocrystalline thin films.

The RNA helicase DHX36-G4R1 modulates C9orf72 GGGGCC hexanucleotide repeat-associated translation.

GGGGCC (G4C2) hexanucleotide repeat expansions in the endosomal trafficking gene C9orf72 are the most common genetic cause of ALS and frontotemporal dementia. Repeat-associated non-AUG (RAN) translation of this expansion through near-cognate initiation codon usage and internal ribosomal entry generates toxic proteins that accumulate in patients' brains and contribute to disease pathogenesis. The helicase protein DEAH-box helicase 36 (DHX36-G4R1) plays active roles in RNA and DNA G-quadruplex (G4) resolution in cells. As G4C2 repeats are known to form G4 structures in vitro, we sought to determine the impact of manipulating DHX36 expression on repeat transcription and RAN translation. Using a series of luciferase reporter assays both in cells and in vitro, we found that DHX36 depletion suppresses RAN translation in a repeat length-dependent manner, whereas overexpression of DHX36 enhances RAN translation from G4C2 reporter RNAs. Moreover, upregulation of RAN translation that is typically triggered by integrated stress response activation is prevented by loss of DHX36. These results suggest that DHX36 is active in regulating G4C2 repeat translation, providing potential implications for therapeutic development in nucleotide repeat expansion disorders.

G-Quadruplex Helicase DHX36/G4R1 Engages Nuclear Lamina Proteins in Quiescent Breast Cancer Cells.

G-quadruplexes (G4s) are nucleic acid structures found enriched within gene regulatory sequences. G4s control fundamental cellular processes, including replication, transcription, and translation. Proto-oncogenes are enriched with G4 sequences, while tumor-suppressor genes are depleted, suggesting roles for G4s in cell survival and proliferation. Specialized helicases participate in G4-mediated gene regulation via enzymatic unwinding activity. One such enzyme, DHX36/G4R1, is the major G4-helicase and is a master regulator of G4-DNAs and mRNAs. G4-resolution promotes the expression of proproliferative genes; as such, DHX36/G4R1 promotes cell proliferation. Little is known about how DHX36/G4R1 itself is regulated in nondividing cells. We hypothesized that DHX36/G4R1 protein binding partners are altered when a cell transitions from a dividing to a quiescent state. We found that DHX36/G4R1 co-purifies with a distinct set of proteins under quiescent conditions, which may represent a novel complex that regulates DHX36/G4R1 during cell cycle transitions and have implications for development and cancer.

Disintegration of the agricultural by-product wheat bran under subcritical conditions.

BACKGROUND: The disintegration of destarched wheat bran in water and sulfuric acid (pH 3) under subcritical conditions (275-300 °C) and at short reaction times (1-4 min) was investigated. A cascade process comprising a stepwise separation of the liquid was applied to reduce the formation of undesired degradation products. RESULTS: The highest degree of biomass disintegration (67% dry mass solubilization) was achieved by application of a cascade process at 275 °C (pH 3). Regarding the dissolution of carbohydrates (monomeric and oligomeric form), the total glucose yields remained below 60%, while the total xylose and arabinose yields were about 76% and 67%. Approximately 74% of the protein and 95% of the mineral fraction could be extracted. The application of the cascade process enabled a substantially reduced formation of degradation products. CONCLUSION: When operating hydrothermally and subcritically in order to avoid some problematic aspects of a biorefinery, an extensive disintegration and monomerization of wheat bran and its constituents remains difficult even under the tested conditions (300 °C, pH 3). However, the applied cascade process proved to be useful to increase the yields and to substantially reduce the formation of undesired degradation products. Despite this fact, increased water consumption has to be conceded. © 2018 Society of Chemical Industry.

Separation and characterization of oligomeric hindered amine light stabilizers using high-performance liquid chromatography with UV and quadrupole time-of-flight mass spectrometric detection.

Hindered amine light stabilizers are an important class of stabilizers that protect synthetic polymers from degradation and thus from changing mechanical and optical properties. The current study presents an HPLC method capable of separating oligomeric hindered amine light stabilizers on a commercially available stationary phase, employing an MS-compatible novel mobile phase. Based on the exact masses observed with Q-TOF-MS, a comprehensive characterization of five different types of oligomeric hindered amine light stabilizers was achieved, leading to structural information not included in the datasheets provided by the suppliers. For the different investigated hindered amine light stabilizers, a number of recurring units up to 17 and a molecular weight of 5200 g/mol were detected. Furthermore, the analysis of stabilizer extracts of processed polypropylene samples containing different types of hindered amine light stabilizers revealed significant differences in the oligomeric pattern between standards and polymer samples. Thus, changes in the analytes' oligomeric pattern resulting from processing or aging of polymer materials can be monitored with the presented method.

Wheat bran biorefinery--an insight into the process chain for the production of lactic acid.

The present study investigates a wheat bran biorefinery including major processing steps pre-extraction, pre-treatment and lactic acid fermentation. Concerning the dry mass distribution, during the pre-extraction 32% of the feedstock was recovered, offering some perspectives for applications in food area. The pre-treatment (hydrothermal/enzymatic hydrolysis) of the remaining cake solubilized 34% of dry mass and led to a fermentable sugar concentration of 21g/L. The fermentation resulted in a lactic acid yield of 0.73g/g substrate. Concentrating the fermentation feed via nanofiltration did not improve the lactic acid productivity. Taking into account that Lactobacillus pentosus, a heterofermentative microorganism was used, the dry mass balance revealed a product yield of 47% (32% extract, 15% lactic acid). Based on a theoretical consideration involving a cellulolytic enzyme production (10% feedstock allocation) and lignin utilization, under optimized conditions a maximum product yield of around 80% (35% extract, 39% lactic acid, 6% lignin) could be expected.

Investigations on a wheat bran biorefinery involving organosolv fractionation and enzymatic treatment.

The present study elucidates the organosolv treatment of wheat bran, the major by-product of the milling industry. The influence of temperature (160-200°C) and ethanol concentration (30-60% (w/w)) at a given process time of 30min was investigated. Enzymatic treatments of the organosolv extracts including solid residues led to an overall glucose yield of 75%. The conversion of hemicelluloses into xylose and arabinose was approximately 60% and 45%, respectively. Proteins could be almost completely dissolved, however, practically no free amino acids were obtained. Surprisingly, only around 30% of lignin and 65% of minerals were dissolved. Severe treatment conditions induced the disintegration of fat into glycerol and fatty acids as well as the formation of sugar degradation products. During the lignin precipitation step, proteins partially coprecipitated.

Wheat bran biorefinery: an investigation on the starch derived glucose extraction accompanied by pre- and post-treatment steps.

Wheat bran, a side product of the milling industry, can be considered as a feedstock for biorefineries. Unlike other lignocellulosic feedstock, wheat bran contains a reasonable amount of starch, which is not of recalcitrant nature. Therefore, it can be extracted without a costly pretreatment process. The present work evaluates the extraction of starch derived glucose in relation to a wheat bran biorefinery. The purity of free glucose extracted quantitatively was 44%. The extract was concentrated by threefold via nanofiltration, thereby reaching a glucose concentration of 49 g/L. Hydrothermal treatment (180°C - 20 min) of the starch-free bran did not induce the formation of hydroxymethylfurfural and levulinic acid. Interestingly, the furfural level increased compared to the process, in which bran was treated hydrothermally without a preceding starch extraction. By separation of water-extractables prior to enzymatic hydrolysis, the free glucose purity was increased to 58%, however the yield of glucose decreased to 61%.

High-throughput quantification of stabilizers in polymeric materials by flow injection tandem mass spectrometry.

RATIONALE: High-throughput methods for identification and quantification of stabilizers in plastic materials are of significant importance in order to evaluate the suitability of materials of unknown origin for specific application areas, to clarify reasons for failure of materials, or for comparison of materials from different sources. METHODS: In the present study, a highly sensitive and rapid flow injection method coupled to selected reaction monitoring mass spectrometry (MS) for comprehensive analysis of 21 polymer stabilizers in polyolefins is demonstrated. A critical factor for this approach is the choice of ionization mode, as no separation was performed prior to MS detection. Differences between several ionization techniques regarding matrix effects are reported. RESULTS: Atmospheric pressure chemical ionization was found to be the most suitable ionization technique, with no significant matrix effects observed. The developed method has a linear dynamic range over two to three orders of magnitude with correlation coefficients better than 0.99 for all studied analytes. Following a multistep sample preparation protocol, the method allowed quantification down to minimum values of between 0.0001 and 0.04 wt% depending on the type of stabilizer. Results were compared to an established chromatographic approach and showed very good correlation (bias below 7.5%). CONCLUSIONS: The applicability of the optimized method could be demonstrated for both the qualitative and quantitative determination of polymer stabilizers in polyolefins. Furthermore, the described approach yields a complete analysis in a much shorter time than can be achieved with commonly applied chromatographic methods.

Wheat bran biorefinery--a detailed investigation on hydrothermal and enzymatic treatment.

Due to the enormous quantities arising in the milling industry and its specific properties, wheat bran can be considered as a feedstock for future biorefineries. In the present work, a detailed investigation was carried out on the hydrothermal (140-200°C) and enzymatic treatment of wheat bran. After hydrothermal pretreatment and a subsequent enzymatic hydrolysis a glucose yield of 65% and 90% was achieved, respectively. Interestingly, the hemicelluloses could be disintegrated to monomers only to approx. 50%. About 70% of the proteins were dissolved, however, practically no free amino acids were obtained under given conditions. Severe treatment conditions induce elevated losses of some amino acids. Minerals could be extracted almost completely. To disintegrate fat into glycerol and fatty acids severe process conditions were necessary. The formation of undesired by-products such as furfural or hydroxymethylfurfural starts at approx. 180°C.

Fast screening of stabilizers in polymeric materials by flow injection-tandem mass spectrometry.

In the present study, the applicability of rapid flow injection-triple quadrupole mass spectrometry for simultaneous qualitative screening of different classes of stabilizers in polymeric materials is demonstrated. Electrospray ionization and atmospherical pressure chemical ionization were compared, whereby the latter yielded generally poorer detection limits and only single charged ions that were for some analytes beyond the mass range of the quadrupole mass spectrometry. Positive electrospray ionization allowed the interference-free monitoring of multiple reaction monitoring transitions selective for 36 commonly used stabilizers without chromatographic separation. Real polymer samples were extracted by toluene and the method allowed the detection of analytes down to 0.00001-0.025 wt% depending on the stabilizer.