Synthesis of Reagents for Fluorescence-Tagging of DNA

Abstract

A general route for the synthesis of alkynylamino nucleoside triphosphates is described. These nucleosides can be selectively coupled through the alkynylamino group to a variety of reporter groups and used to enzymatically label DNA.     

Multimodality registration without a dedicated multimodality scanner

Multimodality scanners that allow the acquisition of both functional and structural image sets on a single system have recently become available for animal research use. Although the resultant registered functional/structural image sets can greatly enhance the interpretability of the functional data, the cost of multimodality systems can be prohibitive, and they are often limited to two modalities, which generally do not include magnetic resonance imaging. Using a thin plastic wrap to immobilize and fix a mouse or other small animal atop a removable bed, we are able to calculate registrations between all combinations of four different small animal imaging scanners (positron emission tomography, single-photon emission computed tomography, magnetic resonance, and computed tomography [CT]) at our disposal, effectively equivalent to a quadruple-modality scanner. A comparison of serially acquired CT images, with intervening acquisitions on other scanners, demonstrates the ability of the proposed procedures to maintain the rigidity of an anesthetized mouse during transport between scanners. Movement of the bony structures of the mouse was estimated to be 0.62 mm. Soft tissue movement was predominantly the result of the filling (or emptying) of the urinary bladder and thus largely constrained to this region. Phantom studies estimate the registration errors for all registration types to be less than 0.5 mm. Functional images using tracers targeted to known structures verify the accuracy of the functional to structural registrations. The procedures are easy to perform and produce robust and accurate results that rival those of dedicated multimodality scanners, but with more flexible registration combinations and while avoiding the expense and redundancy of multimodality systems.     

Plasma and salivary 6beta-hydroxycortisol measurements for assessing adrenocortical activity in patients with adrenocortical adenomas.

The aim of this study was to examine and compare the potential usefulness of plasma and salivary 6beta-hydroxycortisol measurements for assessing adrenocortical activity in patients with adrenocortical adenomas. Plasma and salivary cortisol as well as 6beta-hydroxycortisol determinations were performed by radioimmunoassay after extraction with ethyl acetate followed by chromatographic separation using a modified paper chromatographic system. Samples were obtained from 36 control subjects and 37 patients with non-hyperfunctioning adrenocortical adenomas in the morning at 8 a.m. after a low-dose of dexamethasone and after stimulation with synthetic depot ACTH. Basal and post-dexamethasone hormone levels were also measured in plasma and salivary samples of 4 patients with Cushing's syndrome from adrenal adenomas. In the baseline state, patients with non-hyperfunctioning adrenocortical adenomas had significantly higher plasma and salivary 6beta-hydroxycortisol levels (mean+/-SE, 79.0+/-7 and 17.1+/-2.2 ng/dl, respectively) compared to those measured in controls (62.0+/-4 and 7.7+/-0.6 ng/dl, respectively), whereas baseline plasma and salivary cortisol levels (9.6+/-0.5 microg/dl and 342+/-39 ng/dl, respectively) were similar to those measured in the control group (9.9+/-0.4 microg/dl and 366+/-24 ng/dl, respectively). In all groups, the changes in plasma and salivary 6beta-hydroxycortisol concentrations after dexamethasone suppression and ACTH stimulation were similar to the changes in plasma and salivary cortisol levels, although the differing ratios of 6betaOHF to cortisol indicated potentially important variations in the induction of 6beta-hydroxylase activity between the three groups. In patients with Cushing's syndrome, baseline plasma and salivary 6beta-hydroxycortisol concentrations (754+/-444 and 104+/-88 ng/dl, respectively) were more markedly increased than plasma and salivary cortisol levels (24.8+/-6.7 microg/dl and 1100+/-184 ng/dl, respectively), and all remained non-suppressible after dexamethasone administration. These results suggests that plasma and salivary 6beta-hydroxycortisol determinations may precisely detect not only overt increases of cortisol secretion in patients with Cushing's syndrome but also mild glucocorticoid overproduction presumably present in patients with non-hyperfunctioning adrenocortical tumors.     

Failure modelling of trabecular bone using a non-linear combined damage and fracture voxel finite element approach

Trabecular bone tissue failure can be considered as consisting of two stages: damage and fracture; however, most failure analyses of 3D high-resolution trabecular bone samples are confined to damage mechanisms only, that is, without fracture. This study aims to develop a computational model of trabecular bone consisting of an explicit representation of complete failure, incorporating damage criteria, fracture criteria, cohesive forces, asymmetry and large deformation capabilities. Following parameter studies on a test specimen, and experimental testing of bone sample to complete failure, the asymmetric critical tissue damage and fracture strains of ovine vertebral trabecular bone were calibrated and validated to be compression damage ?1.16 %, tension damage 0.69 %, compression fracture ?2.91 % and tension fracture 1.98 %. Ultimate strength and post–ultimate strength softening were captured by the computational model, and the failure of individual struts in bending and shear was also predicted. This modelling approach incorporated a cohesive parameter that provided a facility to calibrate ductile–brittle behaviour of bone tissue in this non-linear geometric and non-linear constitutive property analyses tool. Finally, the full accumulation of tissue damage and tissue fracture has been monitored from range of small magnitude (normal daily loading) through to specimen yielding, ultimate strength and post–ultimate strength softening.     

A multigene framework for polychaete phylogenetic studies

Producing a robust phylogenetic reconstruction for Polychaeta using either morphological or molecular data sets has proven very difficult. There remain many conflicts between morphological analyses and hypotheses based on DNA data, the latter principally derived from 18S rRNA sequences. For the present study a data set covering a broad range of polychaete diversity was assembled, including 38 new sequences from 21 species. Besides available 18S rRNA data, five additional gene segments were examined: the D1 and D9-10 expansion regions of 28S rRNA, histone H3, snU2 RNA and cytochrome c oxidase subunit I. Maximum parsimony, maximum likelihood and Bayesian analyses were conducted.Annelida and Mollusca were reciprocally monophyletic in maximum likelihood analyses, but Polychaeta included a cephalopod in maximum parsimony analyses, and a patellogastropod in Bayesian analyses. When rooted on the Mollusca, optimal topologies from maximum likelihood analyses showed a recognisable basal group of taxa, including Oweniidae, Chaetopteridae and Amphinomidae. The six studied phyllodocidan families plus Orbiniidae (as the sister group of the scale-worms) formed the next most basal group. All analyses support the inclusion of Echiura, Clitellata and Siboglinidae within polychaetes. Bayesian analyses show Echiura as the sister group of Capitellidae, in agreement with previous 18S rRNA results, In contrast, Echiura formed the sister group to Trichobranchidae in maximum likelihood and maximum parsimony analyses.Supra-familial groupings consistently recovered within Polychaeta in the analyses are: (i) Terebellida without Ampharetidae; (ii) Scolecida (excepting Orbiniidae); (iii) Eunicidae, Lumbrineridae and Clitellata; and (iv) “Cirratuliformia” (including Sternaspidae) plus Sabellidae, Serpulidae and Spionidae.     

A comparison of dynamic-state-dependent models of the trade-off between growth, damage, and reproduction

Fast growth can be costly, so trade-offs between growth and fitness are to be predicted when organisms adjust their growth to compensate for earlier environmental conditions. We developed four generic models of increasing complexity with different processes to predict the indeterminate growth of vertebrate ectotherms, which is sensitive to ambient temperature even when food is not limiting. We contrast the predictions of the models with observed experimental data on growth trajectories, feeding activity, and reproductive investment of three-spined sticklebacks and inferred patterns of accumulation of biomolecular damage arising from activity and growth. All models predicted observed patterns of compensatory growth (both accelerating and decelerating) in response to earlier temperature perturbations, but the more complex models provided the best fit to experimental data. Growth trajectories influenced future reproductive investment regardless of final body size at breeding. Our findings suggest that while models with fewer parameters can predict basic patterns of growth in stable conditions, they cannot capture the costly long-term effects of deviations from steady growth trajectories. In contrast, models in which foraging activity is assumed to carry costs are capable of predicting the complex patterns of feeding, growth, and reproductive investment seen in animals, with the cost of a heightened mortality risk (e.g., through predation) being more important than the cost of increased physiological damage.     

Epidemiology of Acute Pancreatitis in Hospitalized Children in the United States from 2000–2009

Background

Single-center studies suggest an increasing incidence of acute pancreatitis (AP) in children. Our specific aims were to (i) estimate the recent secular trends, (ii) assess the disease burden, and (iii) define the demographics and comorbid conditions of AP in hospitalized children within the United States.

Methods

We used the Healthcare Cost and Utilization Project Kids’ Inpatient Database, Agency for Healthcare Research and Quality for the years 2000 to 2009. Extracted data were weighted to generate national-level estimates. We used the Cochrane-Armitage test to analyze trends; cohort-matching to evaluate the association of AP and in-hospital mortality, length of stay, and charges; and multivariable logistic regression to test the association of AP and demographics and comorbid conditions.

Results

We identified 55,012 cases of AP in hospitalized children (1–20 years of age). The incidence of AP increased from 23.1 to 34.9 (cases per 10,000 hospitalizations per year; P<0.001) and for all-diagnoses 38.7 to 61.1 (P<0.001). There was an increasing trend in the incidence of both primary and all-diagnoses of AP (P<0.001). In-hospital mortality decreased (13.1 to 7.6 per 1,000 cases, P<0.001), median length of stay decreased (5 to 4 days, P<0.001), and median charges increased ($14,956 to $22,663, P<0.001). Children with AP compared to those without the disease had lower in-hospital mortality (adjusted odds ratio, aOR 0.86, 95% CI, 0.78–0.95), longer lengths of stay (aOR 2.42, 95% CI, 2.40–2.46), and higher charges (aOR 1.62, 95% CI, 1.59–1.65). AP was more likely to occur in children older than 5 years of age (aORs 2.81 to 5.25 for each 5-year age interval). Hepatobiliary disease was the comorbid condition with the greatest association with AP.

Conclusions

These results demonstrate a rising incidence of AP in hospitalized children. Despite improvements in mortality and length of stay, hospitalized children with AP have significant morbidity.     

Molecular genetic advances in tuberous sclerosis

Over the past decade, there has been considerable progress in understanding the molecular genetics of tuberous sclerosis, a disorder characterised by hamartomatous growths in numerous organs. We review this progress, from cloning and characterising TSC1 and TSC2, the genes responsible for the disorder, through to gaining insights into the functions of their protein products hamartin and tuberin, and the identification and engineering of animal models. We also present the first comprehensive compilation and analysis of all reported TSC1 and TSC2 mutations, consider their diagnostic implications and review genotype/phenotype relationships.