Isolation and analysis of high quality nuclear DNA with reduced organellar DNA for plant genome sequencing and resequencing

<p>Abstract</p> <p>Background</p> <p>High throughput sequencing (HTS) technologies have revolutionized the field of genomics by drastically reducing the cost of sequencing, making it feasible for individual labs to sequence or resequence plant genomes. Obtaining high quality, high molecular weight DNA from plants poses significant challenges due to the high copy number of chloroplast and mitochondrial DNA, as well as high levels of phenolic compounds and polysaccharides. Multiple methods have been used to isolate DNA from plants; the CTAB method is commonly used to isolate total cellular DNA from plants that contain nuclear DNA, as well as chloroplast and mitochondrial DNA. Alternatively, DNA can be isolated from nuclei to minimize chloroplast and mitochondrial DNA contamination.</p> <p>Results</p> <p>We describe optimized protocols for isolation of nuclear DNA from eight different plant species encompassing both monocot and eudicot species. These protocols use nuclei isolation to minimize chloroplast and mitochondrial DNA contamination. We also developed a protocol to determine the number of chloroplast and mitochondrial DNA copies relative to the nuclear DNA using quantitative real time PCR (qPCR). We compared DNA isolated from nuclei to total cellular DNA isolated with the CTAB method. As expected, DNA isolated from nuclei consistently yielded nuclear DNA with fewer chloroplast and mitochondrial DNA copies, as compared to the total cellular DNA prepared with the CTAB method. This protocol will allow for analysis of the quality and quantity of nuclear DNA before starting a plant whole genome sequencing or resequencing experiment.</p> <p>Conclusions</p> <p>Extracting high quality, high molecular weight nuclear DNA in plants has the potential to be a bottleneck in the era of whole genome sequencing and resequencing. The methods that are described here provide a framework for researchers to extract and quantify nuclear DNA in multiple types of plants.</p

Sensory substitution information informs locomotor adjustments when walking through apertures

The study assessed the ability of the central nervous system (CNS) to use echoic information from sensory substitution devices (SSDs) to rotate the shoulders and safely pass through apertures of different width. Ten visually normal participants performed this task with full vision, or blindfolded using an SSD to obtain information regarding the width of an aperture created by two parallel panels. Two SSDs were tested. Participants passed through apertures of +0%, +18%, +35%, and +70% of measured body width. Kinematic indices recorded movement time, shoulder rotation, average walking velocity across the trial, peak walking velocities before crossing, after crossing and throughout a whole trial. Analyses showed participants used SSD information to regulate shoulder rotation, with greater rotation associated with narrower apertures. Rotations made using an SSD were greater compared to vision, movement times were longer, average walking velocity lower and peak velocities before crossing, after crossing and throughout the whole trial were smaller, suggesting greater caution. Collisions sometimes occurred using an SSD but not using vision, indicating that substituted information did not always result in accurate shoulder rotation judgements. No differences were found between the two SSDs. The data suggest that spatial information, provided by sensory substitution, allows the relative position of aperture panels to be internally represented, enabling the CNS to modify shoulder rotation according to aperture width. Increased buffer space indicated by greater rotations (up to approximately 35% for apertures of +18% of body width), suggests that spatial representations are not as accurate as offered by full vision

Differential modulation of corticospinal excitability during haptic sensing of 2-D patterns vs. textures

<p>Abstract</p> <p>Background</p> <p>Recently, we showed a selective enhancement in corticospinal excitability when participants actively discriminated raised 2-D symbols with the index finger. This extra-facilitation likely reflected activation in the premotor and dorsal prefrontal cortices modulating motor cortical activity during attention to haptic sensing. However, this parieto-frontal network appears to be finely modulated depending upon whether haptic sensing is directed towards material or geometric properties. To examine this issue, we contrasted changes in corticospinal excitability when young adults (n = 18) were engaged in either a roughness discrimination on two gratings with different spatial periods, or a 2-D pattern discrimination of the relative offset in the alignment of a row of small circles in the upward or downward direction.</p> <p>Results</p> <p>A significant effect of task conditions was detected on motor evoked potential amplitudes, reflecting the observation that corticospinal facilitation was, on average, ~18% greater in the pattern discrimination than in the roughness discrimination.</p> <p>Conclusions</p> <p>This differential modulation of corticospinal excitability during haptic sensing of 2-D patterns vs. roughness is consistent with the existence of preferred activation of a visuo-haptic cortical dorsal stream network including frontal motor areas during spatial vs. intensive processing of surface properties in the haptic system.</p

The Toronto prehospital hypertonic resuscitation-head injury and multi organ dysfunction trial (TOPHR HIT) - Methods and data collection tools

<p>Abstract</p> <p>Background</p> <p>Clinical trials evaluating the use of hypertonic saline in the treatment of hypovolemia and head trauma suggest no survival superiority over normal saline; however subgroup analyses suggest there may be a reduction in the inflammatory response and multiorgan failure which may lead to better survival and enhanced neurocognitive function. We describe a feasibility study of randomizing head injured patients to hypertonic saline and dextran vs. normal saline administration in the out of hospital setting.</p> <p>Methods/Design</p> <p>This feasibility study employs a randomized, placebo-controlled design evaluating normal saline compared with a single dose of 250 ml of 7.5% hypertonic saline in 6% dextran 70 in the management of traumatic brain injuries. The primary feasibility endpoints of the trial were: 1) baseline survival rates for the treatment and control group to aid in the design of a definitive multicentre trial, 2) randomization compliance rate, 3) ease of protocol implementation in the out-of-hospital setting, and 4) adverse event rate of HSD infusion.</p> <p>The secondary objectives include measuring the effect of HSD in modulating the immuno-inflammatory response to severe head injury and its effect on modulating the release of neuro-biomarkers into serum; evaluating the role of serum neuro-biomarkers in predicting patient outcome and clinical response to HSD intervention; evaluating effects of HSD on brain atrophy post-injury and neurocognitive and neuropsychological outcomes.</p> <p>Discussion</p> <p>We anticipate three aspects of the trial will present challenges to trial success; ethical demands associated with a waiver of consent trial, challenging follow up and comprehensive accurate timely data collection of patient identifiers and clinical or laboratory values. In addition all the data collection tools had to be derived de novo as none existed in the literature.</p> <p>Trial registration number</p> <p>NCT00878631</p

Multi-level analysis of electronic health record adoption by health care professionals: A study protocol

<p>Abstract</p> <p>Background</p> <p>The electronic health record (EHR) is an important application of information and communication technologies to the healthcare sector. EHR implementation is expected to produce benefits for patients, professionals, organisations, and the population as a whole. These benefits cannot be achieved without the adoption of EHR by healthcare professionals. Nevertheless, the influence of individual and organisational factors in determining EHR adoption is still unclear. This study aims to assess the unique contribution of individual and organisational factors on EHR adoption in healthcare settings, as well as possible interrelations between these factors.</p> <p>Methods</p> <p>A prospective study will be conducted. A stratified random sampling method will be used to select 50 healthcare organisations in the Quebec City Health Region (Canada). At the individual level, a sample of 15 to 30 health professionals will be chosen within each organisation depending on its size. A semi-structured questionnaire will be administered to two key informants in each organisation to collect organisational data. A composite adoption score of EHR adoption will be developed based on a Delphi process and will be used as the outcome variable. Twelve to eighteen months after the first contact, depending on the pace of EHR implementation, key informants and clinicians will be contacted once again to monitor the evolution of EHR adoption. A multilevel regression model will be applied to identify the organisational and individual determinants of EHR adoption in clinical settings. Alternative analytical models would be applied if necessary.</p> <p>Results</p> <p>The study will assess the contribution of organisational and individual factors, as well as their interactions, to the implementation of EHR in clinical settings.</p> <p>Conclusions</p> <p>These results will be very relevant for decision makers and managers who are facing the challenge of implementing EHR in the healthcare system. In addition, this research constitutes a major contribution to the field of knowledge transfer and implementation science.</p

Tactual perception: a review of experimental variables and procedures

This paper reviews literature on tactual perception. Throughout this review we will highlight some of the most relevant variables in touch literature: interaction between touch and other senses; type of stimuli, from abstract stimuli such as vibrations, to two- and three-dimensional stimuli, also considering concrete stimuli such as the relation between familiar and unfamiliar stimuli or the haptic perception of faces; type of participants, separating studies with blind participants, studies with children and adults, and an analysis of sex differences in performance; and finally, type of tactile exploration, considering conditions of active and passive touch, the relevance of movement in touch and the relation between exploration and time. This review intends to present an organised overview of the main variables in touch experiments, attending to the main findings described in literature, to guide the design of future works on tactual perception and memory.This work was funded by the Portuguese “Foundation for Science and Technology” through PhD scholarship SFRH/BD/35918/2007

Ancillary human health benefits of improved air quality resulting from climate change mitigation

<p>Abstract</p> <p>Background</p> <p>Greenhouse gas (GHG) mitigation policies can provide ancillary benefits in terms of short-term improvements in air quality and associated health benefits. Several studies have analyzed the ancillary impacts of GHG policies for a variety of locations, pollutants, and policies. In this paper we review the existing evidence on ancillary health benefits relating to air pollution from various GHG strategies and provide a framework for such analysis.</p> <p>Methods</p> <p>We evaluate techniques used in different stages of such research for estimation of: (1) changes in air pollutant concentrations; (2) avoided adverse health endpoints; and (3) economic valuation of health consequences. The limitations and merits of various methods are examined. Finally, we conclude with recommendations for ancillary benefits analysis and related research gaps in the relevant disciplines.</p> <p>Results</p> <p>We found that to date most assessments have focused their analysis more heavily on one aspect of the framework (e.g., economic analysis). While a wide range of methods was applied to various policies and regions, results from multiple studies provide strong evidence that the short-term public health and economic benefits of ancillary benefits related to GHG mitigation strategies are substantial. Further, results of these analyses are likely to be underestimates because there are a number of important unquantified health and economic endpoints.</p> <p>Conclusion</p> <p>Remaining challenges include integrating the understanding of the relative toxicity of particulate matter by components or sources, developing better estimates of public health and environmental impacts on selected sub-populations, and devising new methods for evaluating heretofore unquantified and non-monetized benefits.</p