Exploring the loblolly pine (Pinus taeda L.) genome by BAC sequencing and Cot analysis.

Loblolly pine (LP; Pinus taeda L.) is an economically and ecologically important tree in the southeastern U.S. To advance understanding of the loblolly pine (LP; Pinus taeda L.) genome, we sequenced and analyzed 100 BAC clones and performed a Cot analysis. The Cot analysis indicates that the genome is composed of 57, 24, and 10% highly-repetitive, moderately-repetitive, and single/low-copy sequences, respectively (the remaining 9% of the genome is a combination of fold back and damaged DNA). Although single/low-copy DNA only accounts for 10% of the LP genome, the amount of single/low-copy DNA in LP is still 14 times the size of the Arabidopsis genome. Since gene numbers in LP are similar to those in Arabidopsis, much of the single/low-copy DNA of LP would appear to be composed of DNA that is both gene- and repeat-poor. Macroarrays prepared from a LP bacterial artificial chromosome (BAC) library were hybridized with probes designed from cell wall synthesis/wood development cDNAs, and 50 of the "targeted" clones were selected for further analysis. An additional 25 clones were selected because they contained few repeats, while 25 more clones were selected at random. The 100 BAC clones were Sanger sequenced and assembled. Of the targeted BACs, 80% contained all or part of the cDNA used to target them. One targeted BAC was found to contain fungal DNA and was eliminated from further analysis. Combinations of similarity-based and ab initio gene prediction approaches were utilized to identify and characterize potential coding regions in the 99 BACs containing LP DNA. From this analysis, we identified 154 gene models (GMs) representing both putative protein-coding genes and likely pseudogenes. Ten of the GMs (all of which were specifically targeted) had enough support to be classified as intact genes. Interestingly, the 154 GMs had statistically indistinguishable (α = 0.05) distributions in the targeted and random BAC clones (15.18 and 12.61 GM/Mb, respectively), whereas the low-repeat BACs contained significantly fewer GMs (7.08 GM/Mb). However, when GM length was considered, the targeted BACs had a significantly greater percentage of their length in GMs (3.26%) when compared to random (1.63%) and low-repeat (0.62%) BACs. The results of our study provide insight into LP evolution and inform ongoing efforts to produce a reference genome sequence for LP, while characterization of genes involved in cell wall production highlights carbon metabolism pathways that can be leveraged for increasing wood production

The internal thoracic artery skeletonization study: A paired, within-patient comparison [NCT00265499]

BACKGROUND: Traditional harvesting of the internal thoracic artery (ITA) for use as a conduit in coronary bypass surgery involves the dissection of a rim of tissue surrounding the artery on either side. Recent studies, primarily observational, have suggested that skeletonization of the ITA can improve conduit flow, increase length, and reduce the risk of deep sternal infection in high risk patients. Furthermore, skeletonization of the ITA can potentially preserve intercostal nerves and reduce post-operative pain and dysesthesias associated with ITA harvesting. In order to assess the effects of ITA skeletonization, we report a prospective, randomized, within-patient study design that shares many features of a cross-over study. METHODS: Patients undergoing bilateral internal thoracic artery harvest will be randomized to having one side skeletonized and the other harvested in a non-skeletonized manner. Outcome measures include ITA flow and length measured intra-operatively, post-operative pain and dysesthesia, evaluated at discharge, four weeks, and three months post-operatively, and sternal perfusion assessed using single photon emission computed tomography. Harvest times as well as safety endpoints of ITA injury will be recorded. DISCUSSION: This study design, using within-patient comparisons and paired analyses, minimizes the variability of the outcome measures, which is seldom possible in the evaluation of surgical techniques, with minimal chance of carryover effects that can hamper the interpretation of traditional cross-over studies. This study will provide a valid evaluation of clinically relevant effects of internal thoracic artery skeletonization in improving outcomes following coronary artery bypass surgery

A Tale of Four “Carp”: Invasion Potential and Ecological Niche Modeling

. We assessed the geographic potential of four Eurasian cyprinid fishes (common carp, tench, grass carp, black carp) as invaders in North America via ecological niche modeling (ENM). These “carp” represent four stages of invasion of the continent (a long-established invader with a wide distribution, a long-established invader with a limited distribution, a spreading invader whose distribution is expanding, and a newly introduced potential invader that is not yet established), and as such illustrate the progressive reduction of distributional disequilibrium over the history of species' invasions.We used ENM to estimate the potential distributional area for each species in North America using models based on native range distribution data. Environmental data layers for native and introduced ranges were imported from state, national, and international climate and environmental databases. Models were evaluated using independent validation data on native and invaded areas. We calculated omission error for the independent validation data for each species: all native range tests were highly successful (all omission values <7%); invaded-range predictions were predictive for common and grass carp (omission values 8.8 and 19.8%, respectively). Model omission was high for introduced tench populations (54.7%), but the model correctly identified some areas where the species has been successful; distributional predictions for black carp show that large portions of eastern North America are at risk.ENMs predicted potential ranges of carp species accurately even in regions where the species have not been present until recently. ENM can forecast species' potential geographic ranges with reasonable precision and within the short screening time required by proposed U.S. invasive species legislation

Tonic Shock Induces Detachment of Giardia lamblia

The single-celled organism Giardia lamblia colonizes the small intestine of a wide variety of hosts, including humans. Giardiasis infections can cause severe gastrointestinal symptoms and pose a major health concern in the developing world. Giardia are known to attach robustly to a variety of surfaces, but the conditions that influence this attachment are not known. In this study, we examined the behavior of attached Giardia parasites exposed to rapid changes in solution properties, like those Giardia might encounter in the intestine. After systematically varying media concentration and composition, we found that only one solution property caused rapid detachment of Giardia cells: tonicity, which is a measure of the total concentration of solutes in the solution that are unable to pass through a semi-permeable membrane (here, the cell membrane of Giardia). We found similar results for Giardia initially attached to monolayers of intestinal cells. Giardia cells remaining attached after a change in tonicity are able to adapt to the change, highlighting the general ability of this organism to weather normal changes in the intestinal environment. We propose that Giardia's susceptibility to large changes in tonicity could be explored as a possible new route for treatment of giardiasis

Effect of probe characteristics on the subtractive hybridization efficiency of human genomic DNA

<p>Abstract</p> <p>Background</p> <p>The detection sensitivity of low abundance pathogenic species by polymerase chain reaction (PCR) can be significantly enhanced by removing host nucleic acids. This selective removal can be performed using a magnetic bead-based solid phase with covalently immobilized capture probes. One of the requirements to attain efficient host background nucleic acids subtraction is the capture probe characteristics.</p> <p>Findings</p> <p>In this study we investigate how various capture probe characteristics influence the subtraction efficiency. While the primary focus of this report is the impact of probe length, we also studied the impact of probe conformation as well as the amount of capture probe attached to the solid phase. The probes were immobilized on magnetic microbeads functionalized with a phosphorous dendrimer. The subtraction efficiency was assessed by quantitative real time PCR using a single-step capture protocol and genomic DNA as target. Our results indicate that short probes (100 to 200 bp) exhibit the best subtraction efficiency. Additionally, higher subtraction efficiencies with these probes were obtained as the amount of probe immobilized on the solid phase decreased. Under optimal probes condition, our protocol showed a 90 - 95% subtraction efficiency of human genomic DNA.</p> <p>Conclusions</p> <p>The characteristics of the capture probe are important for the design of efficient solid phases. The length, conformation and abundance of the probes determine the capture efficiency of the solid phase.</p

The acceptance of the clinical photographic posture assessment tool (CPPAT)

Abstract Background There is a lack of evidence-based quantitative clinical methods to adequately assess posture. Our team developed a clinical photographic posture assessment tool (CPPAT) and implemented this tool in clinical practice to standardize posture assessment. The objectives were to determine the level of acceptance of the CPPAT and to document predictors as well as facilitators of and barriers to the acceptance of this tool by clinicians doing posture re-education. Methods This is a prospective study focussing on technology acceptance. Thirty-two clinician participants (physical therapists and sport therapists) received a 3–5 h training workshop explaining how to use the CPPAT. Over a three-month trial, they recorded time-on-task for a complete posture evaluation (photo - and photo-processing). Subsequently, participants rated their acceptance of the tool and commented on facilitators and barriers of the clinical method. Results Twenty-three clinician participants completed the trial. They took 22 (mean) ± 10 min (SD) for photo acquisition and 36 min ± 19 min for photo-processing. Acceptance of the CPPAT was high. Perceived ease of use was an indirect predictor of intention to use, mediated by perceived usefulness. Analysis time was an indirect predictor, mediated by perceived usefulness, and a marginally significant direct predictor. Principal facilitators were objective measurements, visualization, utility, and ease of use. Barriers were time to do a complete analysis of posture, quality of human-computer interaction, non-automation of posture index calculation and photo transfer, and lack of versatility. Conclusion The CPPAT is perceived as useful and easy to use by clinicians and may facilitate the quantitative analysis of posture. Adapting the user-interface and functionality to quantify posture may facilitate a wider adoption of the tool

Internet-based medical education: a realist review of what works, for whom and in what circumstances

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Assessing Historical Fish Community Composition Using Surveys, Historical Collection Data, and Species Distribution Models

Accurate establishment of baseline conditions is critical to successful management and habitat restoration. We demonstrate the ability to robustly estimate historical fish community composition and assess the current status of the urbanized Barton Creek watershed in central Texas, U.S.A. Fish species were surveyed in 2008 and the resulting data compared to three sources of fish occurrence information: (i) historical records from a museum specimen database and literature searches; (ii) a nearly identical survey conducted 15 years earlier; and (iii) a modeled historical community constructed with species distribution models (SDMs). This holistic approach, and especially the application of SDMs, allowed us to discover that the fish community in Barton Creek was more diverse than the historical data and survey methods alone indicated. Sixteen native species with high modeled probability of occurrence within the watershed were not found in the 2008 survey, seven of these were not found in either survey or in any of the historical collection records. Our approach allowed us to more rigorously establish the true baseline for the pre-development fish fauna and then to more accurately assess trends and develop hypotheses regarding factors driving current fish community composition to better inform management decisions and future restoration efforts. Smaller, urbanized freshwater systems, like Barton Creek, typically have a relatively poor historical biodiversity inventory coupled with long histories of alteration, and thus there is a propensity for land managers and researchers to apply inaccurate baseline standards. Our methods provide a way around that limitation by using SDMs derived from larger and richer biodiversity databases of a broader geographic scope. Broadly applied, we propose that this technique has potential to overcome limitations of popular bioassessment metrics (e.g., IBI) to become a versatile and robust management tool for determining status of freshwater biotic communities

Clinically diagnosed childhood asthma and follow-up of symptoms in a Swedish case control study

BACKGROUND: Childhood asthma has risen dramatically not only in the western societies and now forms a major and still increasing public health problem. The aims of this study were to follow up at the age of ten the patterns of asthma symptoms and associations among children with a clinically diagnosed asthma in a sizeable urban-rural community and to in compare them with demographic controls using a standardised questionnaire. METHODS: In a defined region in Sweden with a population of about 150 000 inhabitants, all children (n = 2 104) born in 1990 were recorded. At the age of seven all primary care and hospital records of the 1 752 children still living in the community were examined, and a group of children (n = 191) was defined with a well-documented and medically confirmed asthma diagnosis. At the age of ten, 86 % of these cases (n = 158) and controls (n = 171) completed an ISAAC questionnaire concerning asthma history, symptoms and related conditions. RESULTS: Different types of asthma symptoms were highly and significantly over-represented in the cases. Reported asthma heredity was significantly higher among the cases. No significant difference in reported allergic rhinitis or eczema as a child was found between cases and controls. No significant difference concerning social factors or environmental exposure was found between case and controls. Among the control group 4.7 % of the parents reported that their child actually had asthma. These are likely to be new asthma cases between the age of seven and ten and give an estimated asthma prevalence rate at the age of ten of 15.1 % in the studied cohort. CONCLUSION: A combination of medical verified asthma diagnosis through medical records and the use of self-reported symptom through the ISAAC questionnaire seem to be valid and reliable measures to follow-up childhood asthma in the local community. The asthma prevalence at the age of ten in the studied birth cohort is considerably higher than previous reports for Sweden. Both the high prevalence figure and allowing the three-year lag phase for further settling of events in the community point at the complementary roles of both hospital and primary care in the comprehensive coverage and control of childhood asthma in the community