Assessment of the nucleotide modifications in the high-resolution cryo-electron microscopy structure of the Escherichia coli 50S subunit.

Post-transcriptional ribosomal RNA (rRNA) modifications are present in all organisms, but their exact functional roles and positions are yet to be fully characterized. Modified nucleotides have been implicated in the stabilization of RNA structure and regulation of ribosome biogenesis and protein synthesis. In some instances, rRNA modifications can confer antibiotic resistance. High-resolution ribosome structures are thus necessary for precise determination of modified nucleotides' positions, a task that has previously been accomplished by X-ray crystallography. Here, we present a cryo-electron microscopy (cryo-EM) structure of the Escherichia coli 50S subunit at an average resolution of 2.2 Å as an additional approach for mapping modification sites. Our structure confirms known modifications present in 23S rRNA and additionally allows for localization of Mg2+ ions and their coordinated water molecules. Using our cryo-EM structure as a testbed, we developed a program for assessment of cryo-EM map quality. This program can be easily used on any RNA-containing cryo-EM structure, and an associated Coot plugin allows for visualization of validated modifications, making it highly accessible

Recent Advances in Geotechnical Post-earthquake Reconnaissance

Field observations are particularly important in geotechnical engineering, because it is difficult to replicate in the laboratory the response of soil deposits built by nature over thousands of years. Detailed mapping of damaged and undamaged areas provides the data for the well-documented case histories that drive the development of many current design procedures. Thus, documenting key insights from earthquakes advance research and practice. This has been a primary goal of the National Science Foundation-sponsored Geotechnical Extreme Events Reconnaissance (GEER) Association since its inception almost 20 years ago. New technologies are continually employed by GEER teams to capture ground deformation and its effects. These technologies include Light Imaging Detection and Ranging (LIDAR) and Structure-from-Motion (SfM) image processing techniques for generating and visualizing three-dimensional point cloud data sets. New sensor deployment platforms such as Unmanned Aerial Vehicles (UAVs) are playing an integral role in the data collection process. Unanticipated observations from major events often catalyze new research directions. An overview of some of these recent integrated technology deployments and their role at the core of earthquake disaster analysis is presented. Important advancements are possible through post-event research if their effects are captured and shared effectively

Suicide and unintentional poisoning mortality trends in the United States, 1987-2006: two unrelated phenomena?

Background Two counter trends in injury mortality have been separately reported in the US in recent times - a declining suicide rate and a rapidly rising unintentional poisoning mortality rate. Poisoning suicides are especially difficult to detect, and injury of undetermined intent is the underlying cause-of-death category most likely to reflect this difficulty. We compare suicide and poisoning mortality trends over two decades in a preliminary assessment of their independence and implications for suicide misclassification. Methods Description of overall and gender- and age-specific trends using national mortality data from WISQARS, the Web-based Injury Statistics Query and Reporting System, maintained by the Centers for Disease Control and Prevention (CDC). Subjects were the 936,633 residents dying in the 50 states and the District of Columbia between 1987 and 2006 whose underlying cause of death was classified as suicide, unintentional poisoning, or injury mortality of undetermined intent. Results The official US suicide rate declined 18% between 1987 and 2000, from 12.71 to 10.43 deaths per 100,000 population. It then increased to 11.15 deaths per 100,000 by 2006, a 7% rise. By contrast to these much smaller rate changes for suicide, the unintentional poisoning mortality rate rose more than fourfold between 1987 and 2006, from 2.19 to 9.22 deaths per 100,000. Only the population aged 65 years and older showed a sustained decline in the suicide rate over the entire observation period. Consistently highest in gender-age comparisons, the elderly male rate declined by 35%. The elderly female rate declined by 43%. Unlike rate trends for the non-elderly, both declines appeared independent of corresponding mortality trends for unintentional poisoning and poisoning of undetermined intent. The elderly also deviated from younger counterparts by having a smaller proportion of their injury deaths of undetermined intent classified as poisoning. Poisoning manifested as a less common method of suicide for this group than other decedents, except for those aged 15-24 years. Although remaining low, the undetermined poisoning mortality rate increased over the observation period. Conclusions The official decline in the suicide rate between 1987 and 2000 may have been a partial artifact of misclassification of non-elderly suicides within unintentional poisoning mortality. We recommend in-depth national, regional, and local population-based research investigations of the poisoning-suicide nexus, and endorse calls for widening the scope of the definition of suicide and evaluation of its risk factors

Inconsistent emotion recognition deficits across stimulus modalities in Huntington's disease

This study has been supported by the European Union - PADDINGTON project, Contract no. HEALTH-F2-2010-261358. SJT acknowledges support of the National Institute for Health Research through the Dementias and Neurodegenerative Research Network, DeNDRoN.Background: Recognition of negative emotions is impaired in Huntington's Disease (HD). It is unclear whether these emotion-specific problems are driven by dissociable cognitive deficits, emotion complexity, test cue difficulty, or visuoperceptual impairments. This study set out to further characterise emotion recognition in HD by comparing patterns of deficits across stimulus modalities; notably including for the first time in HD, the more ecologically and clinically relevant modality of film clips portraying dynamic facial expressions. Methods: Fifteen early HD and 17 control participants were tested on emotion recognition from static facial photographs, non-verbal vocal expressions and one second dynamic film clips, all depicting different emotions. Results: Statistically significant evidence of impairment of anger, disgust and fear recognition was seen in HD participants compared with healthy controls across multiple stimulus modalities. The extent of the impairment, as measured by the difference in the number of errors made between HD participants and controls, differed according to the combination of emotion and modality (p=0.013, interaction test). The largest between-group difference was seen in the recognition of anger from film clips. Conclusions: Consistent with previous reports, anger, disgust and fear were the most poorly recognised emotions by the HD group. This impairment did not appear to be due to task demands or expression complexity as the pattern of between-group differences did not correspond to the pattern of errors made by either group; implicating emotion-specific cognitive processing pathology. There was however evidence that the extent of emotion recognition deficits significantly differed between stimulus modalities. The implications in terms of designing future tests of emotion recognition and care giving are discussed.PostprintPeer reviewe

Effects of seed lots and seed production time on growth, flowering and cut flower quality in Bupleurum rotundifolium L.

Effects of three planting patterns; two-row-planting high density (25 plants·m(-2)), two-row-planting low density (12.5 plants·m(-2)), and four-row-planting (25 plants·m(-2)) on the cut flower number and quality of spray carnation (Dianthus caryophyllus L.) cv. ‘Barbara’ and ‘Cherry Tessino’ grown by fertigation cultivation were investigated. In ‘Barbara’, there was no difference in total cut flower number between two-row-planting high density and four-row-planting. Total cut flower number of two-row-planting low density decreased to 60% of two-row-planting high density or four-row-planting. In ‘Cherry Tessino’, the total cut flower number of two-row-planting high density was 15% more than that of four-row-planting. The total cut flower number of two-row-planting low density decreased to 60~70% of two-row-planting high density or four-row-planting. There was no difference in cut flower quality between two-row-planting high density and four-row-planting in both cultivars. Cut flower weight and stem diameter of two-row-planting low density increased compared to those of two-row-planting high density or four-row-planting. Thus, the result indicates that two-row-planting high density may be suitable for fertigation cultivation in carnation

Experimental Constraints on the Ferric Fe Content and Oxygen Fugacity in Subducted Serpentinites

Serpentinites play an important role in the delivery of water into subduction zones. In addition, serpentinites also contain ferric Fe and can transport significant redox potential. We present high-pressure and high-temperature experiments and Mössbauer spectroscopy measurements on natural lizardite and antigorite samples equilibrated at various oxygen fugacities in order to quantify the relationship between the oxygen fugacity f(O2) and the Fe3+/Fetot ratio in these two phases. In antigorite, Fe3+ partitions into the octahedral site and is charge balanced by tetrahedral Al. In lizardite, tetrahedral Fe3+ is observed only at low temperature as well as under high f(O2), whereas Fe3+ prefers the octahedral site at temperatures exceeding 500 °C and at 3 to 5 GPa. Although metastable, lizardite remains in redox equilibrium in our experiments at conditions above the lizardite to antigorite phase transformation at 300 °C and demonstrates a similar stability to antigorite. The Al concentration of lizardite is found to be temperature dependent, and it was possible to reequilibrate the Fe3+/Fetot ratio of lizardite from 0.1 to 0.9 by using redox buffers such as Fe metal, graphite, graphite–calcite, Re–ReO2 and Ru–RuO2. Our experiments on antigorite demonstrate that antigorite does not adjust its Al concentration on experimental time scales. Since Fe3+ is charge balanced by Al, it was also not possible to manipulate the Fe3+/Fetot ratio of antigorite. The coexisting phases, however, show chemical equilibration with this antigorite composition. We have retrieved the standard Gibbs energy for Fe3+- and Al-endmembers of antigorite and lizardite and calculated the metamorphic evolution of subducting serpentinites. The lizardite to antigorite transformation does not cause a decrease in the bulk Fe3+/Fetot ratio under f(O2) buffered conditions, in contrast to observations from some natural settings, but does result in the formation of additional magnetite due to antigorite having a lower Fe3+/Fetot ratio than lizardite at equilibrium. If the f(O2) of antigorite serpentinite is buffered during subduction, such as due to the presence of graphite and carbonate, the bulk Fe3+/Fetot ratio decreases progressively. On the other hand, in a closed system where the bulk serpentinite Fe3+/Fetot ratio remains constant, the f(O2) increases during subduction. In this scenario, the f(O2) of an antigorite serpentinite with a typical Fe3+/Fetot ratio of 0.4 increases from the fayalite–magnetite–quartz to the hematite–magnetite f(O2) buffer during dehydration. These f(O2) results confirm earlier inferences that fluids produced by antigorite dehydration may not contain sufficient oxidised sulphur species to oxidise the mantle wedge. Sufficiently high levels of f(O2) to mobilise oxidised sulphur species may be reached upon antigorite dehydration, however, if closed system behaviour maintains a high bulk redox potential across the lizardite to antigorite phase transformation. Alternatively, oxidation of the mantle wedge might be achieved by oxidising agents from sources in subducted oceanic crust and sediments

Transmitted Drug Resistance in the CFAR Network of Integrated Clinical Systems Cohort: Prevalence and Effects on Pre-Therapy CD4 and Viral Load

Human immunodeficiency virus type 1 (HIV-1) genomes often carry one or more mutations associated with drug resistance upon transmission into a therapy-naïve individual. We assessed the prevalence and clinical significance of transmitted drug resistance (TDR) in chronically-infected therapy-naïve patients enrolled in a multi-center cohort in North America. Pre-therapy clinical significance was quantified by plasma viral load (pVL) and CD4+ cell count (CD4) at baseline. Naïve bulk sequences of HIV-1 protease and reverse transcriptase (RT) were screened for resistance mutations as defined by the World Health Organization surveillance list. The overall prevalence of TDR was 14.2%. We used a Bayesian network to identify co-transmission of TDR mutations in clusters associated with specific drugs or drug classes. Aggregate effects of mutations by drug class were estimated by fitting linear models of pVL and CD4 on weighted sums over TDR mutations according to the Stanford HIV Database algorithm. Transmitted resistance to both classes of reverse transcriptase inhibitors was significantly associated with lower CD4, but had opposing effects on pVL. In contrast, position-specific analyses of TDR mutations revealed substantial effects on CD4 and pVL at several residue positions that were being masked in the aggregate analyses, and significant interaction effects as well. Residue positions in RT with predominant effects on CD4 or pVL (D67 and M184) were re-evaluated in causal models using an inverse probability-weighting scheme to address the problem of confounding by other mutations and demographic or risk factors. We found that causal effect estimates of mutations M184V/I ( pVL) and D67N/G ( and pVL) were compensated by K103N/S and K219Q/E/N/R. As TDR becomes an increasing dilemma in this modern era of highly-active antiretroviral therapy, these results have immediate significance for the clinical management of HIV-1 infections and our understanding of the ongoing adaptation of HIV-1 to human populations

Integrated Analytical and Statistical Two-Dimensional Spectroscopy Strategy for Metabolite Identification: Application to Dietary Biomarkers

A major purpose of exploratory metabolic profiling is for the identification of molecular species that are statistically associated with specific biological or medical outcomes; unfortunately the structure elucidation process of unknowns is often a major bottleneck in this process. We present here new holistic strategies that combine different statistical spectroscopic and analytical techniques to improve and simplify the process of metabolite identification. We exemplify these strategies using study data collected as part of a dietary intervention to improve health and which elicits a relatively subtle suite of changes from complex molecular profiles. We identify three new dietary biomarkers related to the consumption of peas (N-methyl nicotinic acid), apples (rhamnitol) and onions (N-acetyl-S-(1Z)-propenyl-cysteine-sulfoxide) that can be used to enhance dietary assessment and assess adherence to diet. As part of the strategy, we introduce a new probabilistic statistical spectroscopy tool, RED-STORM (Resolution EnhanceD SubseT Optimization by Reference Matching), that uses 2D J-resolved ¹H-NMR spectra for enhanced information recovery using the Bayesian paradigm to extract a subset of spectra with similar spectral signatures to a reference. RED-STORM provided new information for subsequent experiments (e.g. 2D-NMR spectroscopy, Solid-Phase Extraction, Liquid Chromatography prefaced Mass Spectrometry) used to ultimately identify an unknown compound. In summary, we illustrate the benefit of acquiring J-resolved experiments alongside conventional 1D ¹H-NMR as part of routine metabolic profiling in large datasets and show that application of complementary statistical and analytical techniques for the identification of unknown metabolites can be used to save valuable time and resource

Slower Decline in C-Reactive Protein after an Inflammatory Insult Is Associated with Longer Survival in Older Hospitalised Patients

Background Enhancing biological resilience may offer a novel way to prevent and ameliorate disease in older patients. We investigated whether changes in C-reactive protein (CRP), as a dynamic marker of the acute inflammatory response to diverse stressors, may provide a way to operationalize the concept of resilience in older adults. We tested this hypothesis by examining whether such changes could predict prognosis by identifying which individuals are at greater risk of 6-month mortality. Methods Analysis of prospective, routinely collected datasets containing data on hospitalization, clinical chemistry and rehabilitation outcomes for rehabilitation inpatients between 1999 and 2011. Maximum CRP response during acute illness and CRP recovery indices (time and slope of CRP decay to half maximum, and t