Regulatory interactions between IRG resistance GTPases in the cellular response to Toxoplasma gondii

Members of the immunity-related GTPase (IRG) family are interferon-inducible resistance factors against a broad spectrum of intracellular pathogens including Toxoplasma gondii. The molecular mechanisms governing the function and regulation of the IRG resistance system are largely unknown. We find that IRG proteins function in a system of direct, nucleotide-dependent regulatory interactions between family members. After interferon induction but before infection, the three members of the GMS subfamily of IRG proteins, Irgm1, Irgm2 and Irgm3, which possess an atypical nucleotide-binding site, regulate the intracellular positioning of the conventional GKS subfamily members, Irga6 and Irgb6. Following infection, the normal accumulation of Irga6 protein at the parasitophorous vacuole membrane (PVM) is nucleotide dependent and also depends on the presence of all three GMS proteins. We present evidence that an essential role of the GMS proteins in this response is control of the nucleotide-bound state of the GKS proteins, preventing their GTP-dependent activation before infection. Accumulation of IRG proteins at the PVM has previously been shown to be associated with a block in pathogen replication: our results relate for the first time the enzymatic properties of IRG proteins to their role in pathogen resistance

Self-Affirmation Improves Problem-Solving under Stress

High levels of acute and chronic stress are known to impair problem-solving and creativity on a broad range of tasks. Despite this evidence, we know little about protective factors for mitigating the deleterious effects of stress on problem-solving. Building on previous research showing that self-affirmation can buffer stress, we tested whether an experimental manipulation of self-affirmation improves problem-solving performance in chronically stressed participants. Eighty undergraduates indicated their perceived chronic stress over the previous month and were randomly assigned to either a self-affirmation or control condition. They then completed 30 difficult remote associate problem-solving items under time pressure in front of an evaluator. Results showed that self-affirmation improved problem-solving performance in underperforming chronically stressed individuals. This research suggests a novel means for boosting problem-solving under stress and may have important implications for understanding how self-affirmation boosts academic achievement in school settings. © 2013 Creswell et al

Improved THETA-1 for light olefins oligomerization to diesel: Influence of textural and acidic properties

The increase in diesel demand, especially in Europe, and the need for high fuel quality requirements are forcing refiners to move into additional processes for production of high cetane diesel in order to meet the present market trends. Oligomerization of light olefins into middle distillate range products is a viable option. The fuel produced through this technology is environmentally friendly, free of sulfur and aromatics, and the adequate choice of the heterogeneous catalyst will direct the selectivity towards low branched oligomers, which will result in a high quality product. In this work we show the benefits of combining basic desilication treatments for generation of additional mesoporosity in mono-directional Theta-1 zeolite, with selective acid dealumination steps that restore not only the microporosity to values close to those of the parent samples, but also the total and strong Bronsted acidity. These modified Theta-1 zeolites present an outstanding catalytic behavior for oligomerization of propene, with a largely increased initial activity, a much higher resistance to deactivation with time on stream, and an improved selectivity to products in the diesel fraction, as compared to the original microporous Theta-1.The authors thank BP Products of North America for their financial support and permission to publish this work, and Consolider Ingenio 2010-Multicat, the "Severo Ochoa Program", and MAT2012-31657 for financial support. R. Sanchis is acknowledged for technical support.Martínez, C.; Doskocil, EJ.; Corma Canós, A. (2014). Improved THETA-1 for light olefins oligomerization to diesel: Influence of textural and acidic properties. Topics in Catalysis. 57(6-9):668-682. https://doi.org/10.1007/s11244-013-0224-xS668682576-9Bellussi G, Mizia F, Calemma V, Pollesel P, Millini R (2012) Microporous Mesoporous Mater 164:127–134Bellussi G, Carati A, Millini R (2010) In: Cejka J, Corma A, Zones S (eds) Zeolites and Catalysis. Wiley-VCH Verlag GmbH & Co., Weinheim, pp 449–491Martinez C, Corma A (2011) Coord Chem Rev 255:1558–1580de Klerk A (2005) Ind Eng Chem Res 44:3887–3893de Klerk A (2006) Energy Fuels 20:439–445de Klerk A (2006) Energy Fuels 20:1799–1805Egloff G (1936) Ind Eng Chem Res 28:1461–1467Degnan TF Jr, Smith CM, Venkat CR (2001) Appl Catal A Gen 221:283–294Apelian MR, Boulton JR, Fung AS (1994) US5284989, to Mobil OilQuann RJ, Green LA, Tabak SA, Krambeck FJ (1988) Ind Eng Chem Res 27:565–570Tabak SA, Krambeck FJ, Garwood WE (1986) AIChE J 32:1526–1531Corma A, Martínez C, Doskocil EJ (2013) J Catal 300:183–196Martens JA, Ravishankar R, Mishin IE, Jacobs PE (2000) Angew Chem Int Ed Engl 39:4376–4379Martens JA, Verrelst WH, Mathys GM, Brown SH, Jacobs PA (2005) Angew Chem Int Ed Engl 117(5833–583):6Pater JPG, Jacobs PA, Martens JA (1998) J Catal 179:477–482Tabak SA (1981) US4254295, to Mobil OilOccelli ML, Hsu JT, Galya LG (1985) J Mol Catal A: Chem 32:377–390Tabak SA (1984) US4504693, to Mobil Oil CorpKholer E, Schmidt F, Wernicke HJ, Pontes MD, Roberts HL (1995, Summer) Hydrocarbon Technology InternationalMartens JA, Verduijn JP (1995) WO95/19945, to Exxon Chemical Patents Inc.Verrelst WH (1995) Martens LRM, WO95/22516, to Exxon Chemical Patents Inc.Verrelst WH, Martens LRM (2000) US6143942, to Exxon Chemical Patents Inc.Verrelst WH, Martens LRM, Verduijn JP (2006) US6013851, to Exxon Chemical Patents Inc.Dakka JM, Mathys GMK, Puttemans MPH (2003) WO03/035583 to Exxon-Mobil Chemical LimitedMatias P, Sa CC, Graca I, Lopes JM, Carvalho AP, Ramoa RF, Guisnet M (2011) Appl Catal A 399:100–109Chal R, Gérardin C, Bulut M, van Donk S (2011) ChemCatChem 3:67–81Perez-Ramirez J, Christensen CH, Egeblad K, Groen JC (2008) Chem Soc Rev 37:2530–2542Verboekend D, Perez-Ramirez J (2011) Catal Sci Technol 1:879–890Serrano DP, Escola JM, Pizarro P (2013) Chem Soc Rev 42:4004–4035Verboekend D, Chabaneix AM, Thomas K, Gilson JP, Perez-Ramirez J (2011) Cryst Eng Comm 13:3408–3416Emeis CA (1993) J Catal 141:347–354Perego C, Peratello S (1999) Catal Today 52:133–145Abello S, Bonilla A, Perez-Ramirez J (2009) Appl Catal A Gen 364:191–198Corma A, Martinez C, Doskocil EJ, Yaluris G (2011) WO2011002631A2, to BP Oil International Limited. BP Corporation North America Inc., UKCorma A, Martinez C, Doskocil EJ, Yaluris G (2011) WO2011002630A2, to BP Oil International Limited. BP Corporation North America Inc, UKHan S, Heck RH, DiGuiseppi FT (1993) US5234875, to Mobil Oil CorporationPeratello S, Molinari M, Bellussi G, Perego C (1999) Catal Today 52:271–27

Plant-RRBS, a bisulfite and next-generation sequencing-based methylome profiling method enriching for coverage of cytosine positions

Background: Cytosine methylation in plant genomes is important for the regulation of gene transcription and transposon activity. Genome-wide methylomes are studied upon mutation of the DNA methyltransferases, adaptation to environmental stresses or during development. However, from basic biology to breeding programs, there is a need to monitor multiple samples to determine transgenerational methylation inheritance or differential cytosine methylation. Methylome data obtained by sodium hydrogen sulfite (bisulfite)-conversion and next-generation sequencing (NGS) provide genome- wide information on cytosine methylation. However, a profiling method that detects cytosine methylation state dispersed over the genome would allow high-throughput analysis of multiple plant samples with distinct epigenetic signatures. We use specific restriction endonucleases to enrich for cytosine coverage in a bisulfite and NGS-based profiling method, which was compared to whole-genome bisulfite sequencing of the same plant material. Methods: We established an effective methylome profiling method in plants, termed plant-reduced representation bisulfite sequencing (plant-RRBS), using optimized double restriction endonuclease digestion, fragment end repair, adapter ligation, followed by bisulfite conversion, PCR amplification and NGS. We report a performant laboratory protocol and a straightforward bioinformatics data analysis pipeline for plant-RRBS, applicable for any reference-sequenced plant species. Results: As a proof of concept, methylome profiling was performed using an Oryza sativa ssp. indica pure breeding line and a derived epigenetically altered line (epiline). Plant-RRBS detects methylation levels at tens of millions of cytosine positions deduced from bisulfite conversion in multiple samples. To evaluate the method, the coverage of cytosine positions, the intra-line similarity and the differential cytosine methylation levels between the pure breeding line and the epiline were determined. Plant-RRBS reproducibly covers commonly up to one fourth of the cytosine positions in the rice genome when using MspI-DpnII within a group of five biological replicates of a line. The method predominantly detects cytosine methylation in putative promoter regions and not-annotated regions in rice. Conclusions: Plant-RRBS offers high-throughput and broad, genome- dispersed methylation detection by effective read number generation obtained from reproducibly covered genome fractions using optimized endonuclease combinations, facilitating comparative analyses of multi-sample studies for cytosine methylation and transgenerational stability in experimental material and plant breeding populations

Current challenges in software solutions for mass spectrometry-based quantitative proteomics

This work was in part supported by the PRIME-XS project, grant agreement number 262067, funded by the European Union seventh Framework Programme; The Netherlands Proteomics Centre, embedded in The Netherlands Genomics Initiative; The Netherlands Bioinformatics Centre; and the Centre for Biomedical Genetics (to S.C., B.B. and A.J.R.H); by NIH grants NCRR RR001614 and RR019934 (to the UCSF Mass Spectrometry Facility, director: A.L. Burlingame, P.B.); and by grants from the MRC, CR-UK, BBSRC and Barts and the London Charity (to P.C.

Estimating geological CO2 storage security to deliver on climate mitigation

Carbon capture and storage (CCS) can help nations meet their Paris CO2 reduction commitments cost-effectively. However, lack of confidence in geologic CO2 storage security remains a barrier to CCS implementation. Here we present a numerical program that calculates CO2 storage security and leakage to the atmosphere over 10,000 years. This combines quantitative estimates of geological subsurface CO2 retention, and of surface CO2 leakage. We calculate that realistically well-regulated storage in regions with moderate well densities has a 50% probability that leakage remains below 0.0008% per year, with over 98% of the injected CO2 retained in the subsurface over 10,000 years. An unrealistic scenario, where CO2 storage is inadequately regulated, estimates that more than 78% will be retained over 10,000 years. Our modelling results suggest that geological storage of CO2 can be a secure climate change mitigation option, but we note that long-term behaviour of CO2 in the subsurface remains a key uncertainty

Early Childhood Caries among a Bedouin community residing in the eastern outskirts of Jerusalem

<p>Abstract</p> <p>Background</p> <p>ECC is commonly prevalent among underprivileged populations. The Jahalin Bedouin are a severely deprived, previously nomadic tribe, dwelling on the eastern outskirts of Jerusalem. The aim of this study was to assess ECC prevalence and potentially associated variables.</p> <p>Methods</p> <p>102 children aged 12–36 months were visually examined for caries, mothers' anterior dentition was visually subjectively appraised, demographic and health behavior data were collected by interview.</p> <p>Results</p> <p>Among children, 17.6% demonstrated ECC, among mothers, 37.3% revealed "fairly bad" anterior teeth. Among children drinking bottles there was about twice the level of ECC (20.3%) than those breast-fed (13.2%). ECC was found only among children aged more than one year (p < 0.001); more prevalent ECC (55.6%) was found among large (10–13 children) families than among smaller families (1–5 children: 13.5%, 6–9 children: 15.6%) (p = 0.009); ECC was more prevalent among children of less educated mothers (p = 0.037); ECC was more prevalent among mothers with "fairly poor" anterior dentition (p = 0.04). Oral hygiene practices were poor.</p> <p>Conclusion</p> <p>ECC levels in this community were not very high but neither low. This changing population might be on the verge of a wider dental disease "epidemic". Public health efforts clearly need to be invested towards the oral health and general welfare of this community.</p

A proposed method to investigate reliability throughout a questionnaire

<p>Abstract</p> <p>Background</p> <p>Questionnaires are used extensively in medical and health care research and depend on validity and reliability. However, participants may differ in interest and awareness throughout long questionnaires, which can affect reliability of their answers. A method is proposed for "screening" of systematic change in random error, which could assess changed reliability of answers.</p> <p>Methods</p> <p>A simulation study was conducted to explore whether systematic change in reliability, expressed as changed random error, could be assessed using unsupervised classification of subjects by cluster analysis (CA) and estimation of intraclass correlation coefficient (ICC). The method was also applied on a clinical dataset from 753 cardiac patients using the Jalowiec Coping Scale.</p> <p>Results</p> <p>The simulation study showed a relationship between the systematic change in random error throughout a questionnaire and the slope between the estimated ICC for subjects classified by CA and successive items in a questionnaire. This slope was proposed as an awareness measure - to assessing if respondents provide only a random answer or one based on a substantial cognitive effort. Scales from different factor structures of Jalowiec Coping Scale had different effect on this awareness measure.</p> <p>Conclusions</p> <p>Even though assumptions in the simulation study might be limited compared to real datasets, the approach is promising for assessing systematic change in reliability throughout long questionnaires. Results from a clinical dataset indicated that the awareness measure differed between scales.</p