Role of Nucleotide Identity in Effective CRISPR Target Escape Mutations

Prokaryotes use primed CRISPR adaptation to update their memory bank of spacers against invading genetic elements that have escaped CRISPR interference through mutations in their protospacer target site. We previously observed a trend that nucleotide-dependent mismatches between crRNA and the protospacer strongly influence the efficiency of primed CRISPR adaptation. Here we show that guanine-substitutions in the target strand of the protospacer are highly detrimental to CRISPR interference and interference-dependent priming, while cytosine-substitutions are more readily tolerated. Furthermore, we show that this effect is based on strongly decreased binding affinity of the effector complex Cascade for guanine-mismatched targets, while cytosine-mismatched targets only minimally affect target DNA binding. Structural modeling of Cascade-bound targets with mismatches shows that steric clashes of mismatched guanines lead to unfavorable conformations of the RNA-DNA duplex. This effect has strong implications for the natural selection of target site mutations that lead to effective escape from type I CRISPR–Cas systems

Posterior cricoid region fluoroscopic findings: the posterior cricoid plication.

The region posterior to the cricoid cartilage is challenging to assess fluoroscopically. The purpose of this investigation is to critically evaluate the posterior cricoid (PC) region on fluoroscopy and describe patterns of common findings. This was a case control study. All fluoroscopic swallowing studies performed between June 16, 2009, and February 9, 2010, were reviewed for features seen in the PC region. These findings were categorized into distinct patterns and compared to fluoroscopic studies performed in a cohort of normal volunteers. Two hundred patient studies and 149 healthy volunteer studies were reviewed. The mean age of the referred patient cohort and the volunteer cohort was 57 years (±19) and 61 years (±16), respectively (p > 0.05). The patient cohort was 53% male and the control cohort was 56% female (p > 0.05). Four groups were identified. Pharyngoesophageal webs were seen in 7% (10/149) of controls and 14% (28/200) of patients (p = 0.03). A PC arch impression was seen in 16% of patients (32/200) and controls (24/149) (p = 1). A PC plication was demonstrated in 23% (34/149) of controls and 30% (60/200) of patients (p = 0.13). No distinctive PC region findings were seen in 54% (81/149) of controls and 42% (84/200) of referred patients (p = 0.02). Four patients (2%) had both a web and a PC plication. Four categories of PC region findings were identified (unremarkable PC region, web, PC arch impression, and PC plication). Both patients referred for swallowing studies and healthy volunteers demonstrated esophageal webs, PC arch impressions, and PC plications. Only webs were more common in patients than in control subjects (p = 0.03). The PC impression and PC plication are likely to represent normal variants that may be identified on fluoroscopic swallow studies

Synthesis without meta-analysis (SWiM) in systematic reviews : reporting guideline

In systematic reviews that lack data amenable to meta-analysis, alternative synthesis methods are commonly used, but these methods are rarely reported. This lack of transparency in the methods can cast doubt on the validity of the review findings. The Synthesis Without Meta-analysis (SWiM) guideline has been developed to guide clear reporting in reviews of interventions in which alternative synthesis methods to meta-analysis of effect estimates are used. This article describes the development of the SWiM guideline for the synthesis of quantitative data of intervention effects and presents the nine SWiM reporting items with accompanying explanations and examples

How Americans Feel About Terrorism And Security: Two Years After 9/11

Understanding attitudes, concerns and reactions of individuals and families is critical to emergency planning efforts on all levels. In order to have effective implementation of a disaster plan, people need to be confident in (a) the reliability of information from official sources, (b) the capacity of government to perform effectively in a crisis and (c) the capability of response systems, particularly the health systems and first responders. Absence of confidence in response systems or leadership may undermine the best of crisis plans, leading to unnecessary panic and potential excess loss of life. In August 2003, The National Center for Disaster Preparedness at Columbia University's Mailman School of Public Health, in collaboration with The Children's Health Fund, commissioned the Marist Institute for Public Opinion to conduct a survey of adults nearly two years after the multiple terrorist attacks on New York, Washington, D.C. and Pennsylvania. The survey included both a national and a New York City representative sample of households contacted by telephone. Questions covered a wide range of issues including people's concern about potential new additional acts of terrorism in the U.S., the government's ability to protect citizens, and the health system's capacity to respond. Throughout, specific questions were asked of a subset of parents of children from four to eighteen years of age. To the extent possible, specific questions were replicated from four previous surveys commissioned by The Children's Health Fund since September 11, 2001 to identify trends in public attitudes and perceptions

Loading of Silica Nanoparticles in Block Copolymer Vesicles during Polymerization-Induced Self-Assembly: Encapsulation Efficiency and Thermally Triggered Release

Poly(glycerol monomethacrylate)-poly(2-hydroxypropyl methacrylate) diblock copolymer vesicles can be prepared in the form of concentrated aqueous dispersions via polymerization-induced self-assembly (PISA). In the present study, these syntheses are conducted in the presence of varying amounts of silica nanoparticles of approximately 18 nm diameter. This approach leads to encapsulation of up to hundreds of silica nanoparticles per vesicle. Silica has high electron contrast compared to the copolymer which facilitates TEM analysis, and its thermal stability enables quantification of the loading efficiency via thermogravimetric analysis. Encapsulation efficiencies can be calculated using disk centrifuge photosedimentometry, since the vesicle density increases at higher silica loadings while the mean vesicle diameter remains essentially unchanged. Small angle X-ray scattering (SAXS) is used to confirm silica encapsulation, since a structure factor is observed at q ≈ 0.25 nm–1. A new two-population model provides satisfactory data fits to the SAXS patterns and allows the mean silica volume fraction within the vesicles to be determined. Finally, the thermoresponsive nature of the diblock copolymer vesicles enables thermally triggered release of the encapsulated silica nanoparticles simply by cooling to 0–10 °C, which induces a morphological transition. These silica-loaded vesicles constitute a useful model system for understanding the encapsulation of globular proteins, enzymes, or antibodies for potential biomedical applications. They may also serve as an active payload for self-healing hydrogels or repair of biological tissue. Finally, we also encapsulate a model globular protein, bovine serum albumin, and calculate its loading efficiency using fluorescence spectroscopy

The largest deep-ocean silicic volcanic eruption of the past century

© The Author(s), 2018. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Science Advances 4 (2018): e1701121, doi:10.1126/sciadv.1701121.The 2012 submarine eruption of Havre volcano in the Kermadec arc, New Zealand, is the largest deep-ocean eruption in history and one of very few recorded submarine eruptions involving rhyolite magma. It was recognized from a gigantic 400-km2 pumice raft seen in satellite imagery, but the complexity of this event was concealed beneath the sea surface. Mapping, observations, and sampling by submersibles have provided an exceptionally high fidelity record of the seafloor products, which included lava sourced from 14 vents at water depths of 900 to 1220 m, and fragmental deposits including giant pumice clasts up to 9 m in diameter. Most (>75%) of the total erupted volume was partitioned into the pumice raft and transported far from the volcano. The geological record on submarine volcanic edifices in volcanic arcs does not faithfully archive eruption size or magma production.This research was funded by Australian Research Council Postdoctoral fellowships (DP110102196 and DE150101190 to R. Carey), a short-term postdoctoral fellowship grant from the Japan Society for the Promotion of Science (to R. Carey), National Science Foundation grants (OCE1357443 to B.H., OCE1357216 to S.A.S., and EAR1447559 to J.D.L.W.), and a New Zealand Marsden grant (U001616 to J.D.L.W.). J.D.L.W. and A.M. were supported by a research grant and PhD scholarship from the University of Otago. R.W. was supported by NIWA grant COPR1802. J.D.L.W. and F.C.-T. were supported by GNS Science grants CSA-GHZ and CSA-EEZ. M.J. was supported by the U.S. Department of Defense (DoD) through the National Defense Science and Engineering Graduate Fellowship (NDSEG) Program

Balancing a sustained pursuit of nutrition, health, affordability and climate goals: exploring the case of Indonesia

Background: To guide the transformation of food systems to provide for healthy and sustainable diets, countries need to assess their current diet and food supply in comparison to nutrition, health, affordability, and environmental goals. Objectives: We sought to compare Indonesia’s food utilization to diets optimized for nutritional value and cost and to diets that are increasingly plant-based in order to meet further health and environmental goals, including the EAT-Lancet planetary health diet, to explore whether multiple goals could be achieved simultaneously. Methods: We compared 13 dietary scenarios (2 current, 7 optimized, 3 increasingly plant-based, 1 EAT-Lancet) for nutrient content, cost, greenhouse gas emissions (GHGe), and water footprints, using the FAO food balance sheet, Indonesia Household Income and Expenditure Survey household food expenditure, food composition, life cycle assessment, food losses, and trade data. Results: The diversity of modeled scenarios was higher than that of current consumption, reflecting nutritional deficiencies underlying Indonesia’s burden of different forms of malnutrition. Nutrient intake targets were met best by nutrient- and cost-optimized diets, followed by the EAT-Lancet diet. Those diets also had high GHGe, although less than 40% of a scenario in which Indonesia would adopt a typical high-income country’s diet. Only the low food chain diet had a GHGe below the 2050 target set by the EAT-Lancet commission. Its nutrient content was comparable to that of a no-dairy diet, slightly above those of fish-and-poultry and current diets, and somewhat below those of the EAT-Lancet diets. To meet nutrient needs, some animal-source foods had to be included. Costs of all except the optimized diets were above the current national average food expenditure. No scenario met all goals simultaneously. Conclusions: Indonesia’s consumption of rice and unhealthy foods should decrease; food production, trade, and processing should prioritize diversification, (bio)fortification, and limiting environmental impacts; and consumer and institutional demands for healthy, nutritious, and sustainable foods should be stimulated. More granula

Lineage Abundance Estimation for SARS-CoV-2 in Wastewater Using Transcriptome Quantification Techniques

Effectively monitoring the spread of SARS-CoV-2 mutants is essential to efforts to counter the ongoing pandemic. Predicting lineage abundance from wastewater, however, is technically challenging. We show that by sequencing SARS-CoV-2 RNA in wastewater and applying algorithms initially used for transcriptome quantification, we can estimate lineage abundance in wastewater samples. We find high variability in signal among individual samples, but the overall trends match those observed from sequencing clinical samples. Thus, while clinical sequencing remains a more sensitive technique for population surveillance, wastewater sequencing can be used to monitor trends in mutant prevalence in situations where clinical sequencing is unavailable

A Systematic Mapping Approach of 16q12.2/FTO and BMI in More Than 20,000 African Americans Narrows in on the Underlying Functional Variation: Results from the Population Architecture using Genomics and Epidemiology (PAGE) Study

Genetic variants in intron 1 of the fat mass- and obesity-associated (FTO) gene have been consistently associated with body mass index (BMI) in Europeans. However, follow-up studies in African Americans (AA) have shown no support for some of the most consistently BMI-associated FTO index single nucleotide polymorphisms (SNPs). This is most likely explained by different race-specific linkage disequilibrium (LD) patterns and lower correlation overall in AA, which provides the opportunity to fine-map this region and narrow in on the functional variant. To comprehensively explore the 16q12.2/FTO locus and to search for second independent signals in the broader region, we fine-mapped a 646-kb region, encompassing the large FTO gene and the flanking gene RPGRIP1L by investigating a total of 3,756 variants (1,529 genotyped and 2,227 imputed variants) in 20,488 AAs across five studies. We observed associations between BMI and variants in the known FTO intron 1 locus: the SNP with the most significant p-value, rs56137030 (8.3×10-6) had not been highlighted in previous studies. While rs56137030was correlated at r2>0.5 with 103 SNPs in Europeans (including the GWAS index SNPs), this number was reduced to 28 SNPs in AA. Among rs56137030 and the 28 correlated SNPs, six were located within candidate intronic regulatory elements, including rs1421085, for which we predicted allele-specific binding affinity for the transcription factor CUX1, which has recently been implicated in the regulation of FTO. We did not find strong evidence for a second independent signal in the broader region. In summary, this large fine-mapping study in AA has substantially reduced the number of common alleles that are likely to be functional candidates of the known FTO locus. Importantly our study demonstrated that comprehensive fine-mapping in AA provides a powerful approach to narrow in on the functional candidate(s) underlying the initial GWAS findings in European populations