Comparison between computational alanine scanning and per-residue binding free energy decomposition for protein-protein association using MM-GBSA: application to the TCR-p-MHC complex.

Recognition by the T-cell receptor (TCR) of immunogenic peptides (p) presented by Class I major histocompatibility complexes (MHC) is the key event in the immune response against virus-infected cells or tumor cells. A study of the 2C TCR/SIYR/H-2K(b) system using a computational alanine scanning and a much faster binding free energy decomposition based on the Molecular Mechanics-Generalized Born Surface Area (MM-GBSA) method is presented. The results show that the TCR-p-MHC binding free energy decomposition using this approach and including entropic terms provides a detailed and reliable description of the interactions between the molecules at an atomistic level. Comparison of the decomposition results with experimentally determined activity differences for alanine mutants yields a correlation of 0.67 when the entropy is neglected and 0.72 when the entropy is taken into account. Similarly, comparison of experimental activities with variations in binding free energies determined by computational alanine scanning yields correlations of 0.72 and 0.74 when the entropy is neglected or taken into account, respectively. Some key interactions for the TCR-p-MHC binding are analyzed and some possible side chains replacements are proposed in the context of TCR protein engineering. In addition, a comparison of the two theoretical approaches for estimating the role of each side chain in the complexation is given, and a new ad hoc approach to decompose the vibrational entropy term into atomic contributions, the linear decomposition of the vibrational entropy (LDVE), is introduced. The latter allows the rapid calculation of the entropic contribution of interesting side chains to the binding. This new method is based on the idea that the most important contributions to the vibrational entropy of a molecule originate from residues that contribute most to the vibrational amplitude of the normal modes. The LDVE approach is shown to provide results very similar to those of the exact but highly computationally demanding method.

Pharmacokinetics of synthetic atrial natriuretic peptides in normal men.

The kinetics of atrial natriuretic peptides (ANP) and the kinetic profile of their effect on blood pressure and renal hemodynamic and electrolyte excretion were investigated in 20 salt-loaded healthy volunteers during and after constant rate infusion. At steady state, mean plasma concentrations of ANP were measured at 210, 430, and 2990 pg/ml and mean systemic clearance was 2.6, 2.5, and 1.7 L/min for ANP infusion rates of 0.5, 1, and 5 micrograms/min, respectively, which corresponds to the clearance rate of other vasoactive peptide hormones. The apparent volume of distribution averaged 17 L and the mean half-life was 4.5 minutes. ANP induced dose-related effects on systemic and renal hemodynamic, as well as urinary electrolyte excretion, albeit with a time lag between onset and full effect.

Adjuvant or radical fractionated stereotactic radiotherapy for patients with pituitary functional and nonfunctional macroadenoma.

Purpose: To evaluate the efficacy and toxicity of stereotactic fractionated radiotherapy (SFRT) for patients with pituitary macroadenoma (PMA).Methods and Materials: Between March 2000 and March 2009, 27 patients (male to female ratio, 1.25) with PMA underwent SFRT (median dose, 50.4 Gy). Mean age of the patients was 56.5 years (range, 20.3 - 77.4). In all but one patient, SFRT was administered for salvage treatment after surgical resection (transphenoidal resection in 23, transphenoidal resection followed by craniotomy in 2 and multiple transphenoidal resections in another patient). In 10 (37%) patients, the PMAs were functional (3 ACTH-secreting, 3 prolactinomas, 2 growth hormone-secreting and 2 multiple hormone-secretion). Three (11.1%) and 9 (33.3%) patients had PMA abutting and compressing the optic chiasm, respectively. Mean tumor volume was 2.9 +/- 4.6 cm(3). Eighteen (66.7%) patients had hypopituitarism prior to SFRT. The mean follow-up period after SFRT was 72.4 +/- 37.2 months.Results: Tumor size decreased for 6 (22.2%) patients and remained unchanged for 19 (70.4%) other patients. Two (7.4%) patients had tumor growth inside the prescribed treatment volume. The estimated 5-year tumor growth control was 95.5% after SFRT. Biochemical remission occurred in 3 (30%) patients with functional PMA. Two patients with normal anterior pituitary function before SFRT developed new deficits 25 and 65 months after treatment. The 5-year survival without new anterior pituitary deficit was thus 95.8%. Five patients with visual field defect had improved visual function and 1 patient with no visual defect prior to SFRT, but an optic chiasm abutting tumor, had a decline in visual function. The estimated 5-year vision and pituitary function preservation rates were 93.2% and 95.8%, respectively.Conclusions: SFRT is a safe and effective treatment for patients with PMA, although longer follow-up is needed to evaluate long-term outcomes. In this study, approximately 1 patient with visual field defect out of two had an improved visual.

[R74W;R1070W;D1270N]: a new complex allele responsible for cystic fibrosis.

Since the beginning of population screening for CF carriers, it has become apparent that complex CFTR alleles are not uncommon. Deciphering their impact in disease pathogenesis remains a challenge for both clinicians and researchers. We report the observation of a new complex allele p.[R74W+R1070W+D1270N] found in trans with a type 1 mutation and associated with clinical diagnosis of cystic fibrosis in a one year-old Moroccan patient. This case underlines the difficulties in counseling patients with uncommon mutations and the necessity of functional studies to evaluate the structure-function relationships, since the association of several variations in cis can dramatically alter CFTR function.

Secretory IgA's complex roles in immunity and mucosal homeostasis in the gut.

Secretory IgA (SIgA) serves as the first line of defense in protecting the intestinal epithelium from enteric toxins and pathogenic microorganisms. Through a process known as immune exclusion, SIgA promotes the clearance of antigens and pathogenic microorganisms from the intestinal lumen by blocking their access to epithelial receptors, entrapping them in mucus, and facilitating their removal by peristaltic and mucociliary activities. In addition, SIgA functions in mucosal immunity and intestinal homeostasis through mechanisms that have only recently been revealed. In just the past several years, SIgA has been identified as having the capacity to directly quench bacterial virulence factors, influence composition of the intestinal microbiota by Fab-dependent and Fab-independent mechanisms, promote retro-transport of antigens across the intestinal epithelium to dendritic cell subsets in gut-associated lymphoid tissue, and, finally, to downregulate proinflammatory responses normally associated with the uptake of highly pathogenic bacteria and potentially allergenic antigens. This review summarizes the intrinsic biological activities now associated with SIgA and their relationships with immunity and intestinal homeostasis.

High bi-atrial organization in patients with long-standing persistent atrial fibrillation terminated within the left atrium

Sustained atrial fibrillation (AF) is maintained by sites displaying high dominant frequency (DF). In patients (pts) with long-standing persistent AF (LS-pAF), their spatial distribution and the presence of a left-to-right atrial DF gradient remain poorly known. We hypothesized that the pre-ablation bi-atrial frequency characteristics of LS-pAF pts terminated within the left atrium (LT) are different from that of non terminated (NT) ones. Methods: 23 consecutive pts (59±7y, LS-pAF duration 19±12m) underwent stepwise catheter ablation (step-CA) consisting in pulmonary veins isolation, left atrial (LA) defragmentation, and right atrial (RA) ablations for non terminated AF. A quadripolar catheter (CAT) was placed into the RA appendage (RAA), a decapolar CAT into the coronary sinus (CS) and a duodecapolar CAT into the LA divided into 8 segments. For each segment, 20-sec of bipolar recording was acquired. The DF was defined as the largest peak in the power spectrum (3-15 Hz). The inter-atrial DF gradient was defined as the DF difference between LA and RA appendages. Results: LS-pAF was terminated in 83% (19/23) of the pts: 17 LT, 2 during RA ablation and 4 NT. The figure shows that before ablation bi-atrial DF values of LT pts are significantly lower than that of NT pts for each LA segment as well as for the RAA (p < 0.05). No significant LA-to-RA DF gradient was observed both for LT (0.3±0.5 Hz, p=ns) and NT (0.5±0.03 Hz, p=ns) pts. No significant difference in DF values was observed between LA segments. Conclusions: The lower DF of LT pts is suggestive of a higher organization within both atria compared to NT pts. Our findings suggest that low bi-atrial DF values, but not inter-atrial DF gradient, might be of interest for selecting LS-pAF candidates for sinus rhythm restoration by step-CA.

Analyzing complex rock slope deformation at Stampa, western Norway, by integrating geomorphology, kinematics and numerical modeling

The unstable rock slope, Stampa, above the village of Flåm, Norway, shows signs of both active and postglacial gravitational deformation over an area of 11 km2. Detailed structural field mapping, annual differential Global Navigation Satellite System (GNSS) surveys, as well as geomorphic analysis of high-resolution digital elevation models based on airborne and terrestrial laser scanning indicate that slope deformation is complex and spatially variable. Numerical modeling was used to investigate the influence of former rockslide activity and to better understand the failure mechanism. Field observations, kinematic analysis and numerical modeling indicate a strong structural control of the unstable area. Based on the integration of the above analyses, we propose that the failure mechanism is dominated by (1) a toppling component, (2) subsiding bilinear wedge failure and (3) planar sliding along the foliation at the toe of the unstable slope. Using differential GNSS, 18 points were measured annually over a period of up to 6 years. Two of these points have an average yearly movement of around 10 mm/year. They are located at the frontal cliff on almost completely detached blocks with volumes smaller than 300,000 m3. Large fractures indicate deep-seated gravitational deformation of volumes reaching several 100 million m3, but the movement rates in these areas are below 2 mm/year. Two different lobes of prehistoric rock slope failures were dated with terrestrial cosmogenic nuclides. While the northern lobe gave an average age of 4,300 years BP, the southern one resulted in two different ages (2,400 and 12,000 years BP), which represent most likely multiple rockfall events. This reflects the currently observable deformation style with unstable blocks in the northern part in between Joasete and Furekamben and no distinct blocks but a high rockfall activity around Ramnanosi in the south. With a relative susceptibility analysis it is concluded that small collapses of blocks along the frontal cliff will be more frequent. Larger collapses of free-standing blocks along the cliff with volumes > 100,000 m3, thus large enough to reach the fjord, cannot be ruled out. A larger collapse involving several million m3 is presently considered of very low likelihood.

Atrial fibrillation and minimally invasive coronary artery bypass grafting: risk factor analysis.

Atrial fibrillation (AF) is a frequent arrhythmia after conventional coronary artery bypass grafting. With the advent of minimally invasive technique for left internal mammary artery-left anterior descending coronary artery (LIMA-LAD) grafting, we analyzed the incidence and the risk factors of postoperative AF in this patient population. This prospective study involves all patients undergoing isolated LIMA-LAD grafting with minimally invasive technique between January 1994 and June 2000. Twenty-four possible risk factors for postoperative AF were entered into univariate and multivariate logistic regression analyses. Postoperative AF occurred in 21 of the 90 patients (23.3%) analyzed. Double- or triple-vessel disease was present in 12/90 patients (13.3%). On univariate analysis, right coronary artery disease (p <0.01), age (p = 0.01), and diabetes (p = 0.04) were found to be risk factors for AF. On multivariate analysis, right coronary artery disease was identified as the sole significant risk factor (p = 0.02). In this patient population, the incidence of AF after minimally invasive coronary artery bypass is in the range of that reported for conventional coronary artery bypass grafting. Right coronary artery disease was found to be an independent predictor, and this may be related to the fact that in this patient population the diseased right coronary artery was not revascularized at the time of the surgical procedure. For the same reason, this risk factor may find a broader application to noncardiac thoracic surgery.

Diagnostic accuracy of free and total metanephrines in plasma and fractionated metanephrines in urine of patients with pheochromocytoma.

BACKGROUND: Plasma free and urinary metanephrines are recognized biomarkers for the assessment of pheochromocytoma. Plasma total metanephrines with a long half-life may represent another useful biomarker. OBJECTIVE: The aim of this study is to evaluate the diagnostic performances of plasma total metanephrines alone or combined with free metanephrines and fractionated 24-h urinary metanephrines. METHODS: A retrospective, case-control diagnostic test study was conducted between 1999 and 2007 in two university hospitals in Switzerland and two institutions in France. The patients included 46 cases with histologically proven pheochromocytoma, and 181 controls suspected of tumor with negative investigations and 3-year follow-up. None had renal dysfunction. Sensitivity and specificity were compared after expressing each measurement result as a ratio over its upper reference limit, adding the ratios of normetanephrine and metanephrine, and defining cut-off values of 1 or 2 for this sum. RESULTS: Applying a cut-off value of 1, plasma free and total metanephrines and urinary fractionated metanephrines had similar sensitivities of 96% (95% confidence interval, 86-99%), 95% (85-99%), and 95% (84-99%) along with similar specificities of 89% (83-94%), 91% (84-95%), and 86% (80-91%). A cut-off of 2 for the sum of ratios over reference limit improves the specificity, and it can be used for a confirmation test based on another biomarker taken among the three biomarkers. CONCLUSION: All three metanephrine-based tests perform equivalently for diagnosing pheochromocytoma in the absence of renal insufficiency, and can be conveniently associated two by two for confirming/excluding tumor.

An experimental study on the shallow-level migmatization of ferrogabbros from the Fuerteventura Basal Complex, Canary Islands

Spectacular shallow-level migmatization of ferrogabbroic rocks occurs in a metamorphic contact aureole of a gabbroic pluton of the Tierra Mala massif (TM) on Fuerteventura (Canary Islands). In order to improve our knowledge of the low pressure melting behavior of gabbroic rocks and to constrain the conditions of migmatization of the TM gabbros, we performed partial melting experiments on a natural ferrogabbro, which is assumed as protolith of the migmatites. The experiments were performed in an internally heated pressure vessel (IHPV) at 200 MPa, 930-1150 degreesC at relatively oxidizing conditions. Distinct amounts of water were added to the charge. From 930 to 1000 degreesC, the observed experimental phases are plagioclase (An(60-70)), clinopyroxene, amphibole (titanian magnesiohastingsites), two Fe-Ti oxides, and a basaltic, K-poor melt. Above 1000 degreesC, amphibole is no longer stable. The first melts are very rich in non-native plagioclase (>70 wt.%). This indicates that at the beginning of partial melting plagioclase is the major phase which is consumed to produce melt. In the experiments, plagioclase is stable up to high temperatures (1060 degreesC) showing increasing An content with temperature. This is not compatible with the natural migmatites, in which An-rich plagioclase is absent in the melanosomes, while amphibole is stable. Our results show that the partial melting of the natural rocks cannot be regarded as an ``in-situ'' process that occurred in a closed system. Considerable amounts of alkalis probably transported by water-rich fluids, derived from the mafic pluton underplating the TM gabbro, were necessary to drive the melting reaction out of the stability range of plagioclase. A partial melting experiment with a migmatite gabbro showing typical ``in-situ'' textures as starting material supports this assumption. Crystallization experiments performed at 1000 degreesC on a glass of the fitised ferrogabbro with different water contents added to the charge show that generally high water activities could be achieved (crystallization of amphibole), independently of the bulk water content, even in a system with very low initial bulk water content (0.3 wt.%). Increasing water contents produce plagioclase richer in An, reduces the modal proportion of plagioclase in the crystallizing assemblage and extends the melt fraction. High melt fractions of >30 wt.% could only be observed in systems with high bulk water contents (> - 2 wt.%). This indicates that the migmatites were generated under water-rich conditions (probably water-saturated), since those migmatites, which are characterized as ``in-situ'' formations, show generally high amounts of leucosomes (>30 wt.%). (C) 2003 Elsevier B.V. All rights reserved.

Late Jurassic oceanic crust and Upper Cretaceous Caribbean plateau picritic basalts exposed in the Duarte igneous complex, Hispaniola

Four distinct rock units have been recognized near El Aguacate, in the Janico-Juncalito-La Vega area of the Duarte complex (Dominican Republic): (1) serpentinites crosscut by numerous diabasic dikes, (2) basalts interbedded with Late Jurassic ribbon cherts, (3) picrites and ankaramites relatively enriched in incompatible trace elements, and (4) amphibolites and gneissic amphibolites chemically similar to Oceanic Plateau Basalts. Similar Ar-Ar ages of late magmatic amphibole from a picrite, and hornblende from an amphibolite (86.1 +/- 1.3 Ma and 86.7 +/- 1.6 Ma, respectively), suggest that the Duarte picrites are contemporaneous with the Deep Sea Drilling Program Leg 15 and Ocean Drilling Program Leg 126 basalts drilled from the Caribbean oceanic plateau. These basalts are associated with sediments containing Late Cretaceous faunas. Sr, Nd, and Pb data show that enriched picrites and amphibolites are isotopically similar to mafic lavas from previously described Caribbean plateau and Galapagos hotspot basalts. Major element, trace element, and lead isotopic features of Late Jurassic basalts and diabases are consistent with those of normal oceanic crust basalt. However, these basalts differ from typical N-MORB because they have lower epsilon Nd ratios that plot within the range of Ocean Island Basalts. These rocks appear to represent remnants of the Caribbean Jurassic oceanic crust formed from an oceanic ridge possibly close to a hotspot. Later, they were tectonically juxtaposed with Late Cretaceous slices of the Caribbean-Colombian plateau.

Arrested kinetic Li isotope fractionation at the margin of the llimaussaq complex, South Greenland: Evidence for open-system processes during final cooling of peralkaline igneous rocks

Li contents [Li] and isotopic composition (delta Li-7) of mafic minerals (mainly amphibole and clinopyroxene) from the alkaline to peralkaline Ilimaussaq plutonic complex, South Greenland, track the behavior of Li and its isotopes during magmatic differentiation and final cooling of an alkaline igneous system. [Li] in amphibole increase from < 10 ppm in Caamphiboles of the least differentiated unit to >3000 ppm in Na-amphiboles of the highly evolved units. In contrast, [Li] in clinopyroxene are comparatively low (<85 ppm) and do not vary systematically with differentiation. The distribution of Li between amphibole and pyroxene is controlled by the major element composition of the minerals (Ca-rich and Na-rich, respectively) and changes in oxygen fugacity (due to Li incorporation via coupled substitution with ferric iron) during magmatic differentiation. delta(7) Li values of all minerals span a wide range from + 17 to - 8 parts per thousand, with the different intrusive units of the complex having distinct Li isotopic systematics. Amphiboles, which dominate the Li budget of whole-rocks from the inner part of the complex, have constant delta Li-7 of + 1.8 +/- 2.2 parts per thousand (2 sigma, n = 15). This value reflects a homogeneous melt reservoir and is consistent with their mantle derivation, in agreement with published O and Nd isotopic data. Clinopyroxenes of these samples are consistently lighter, with Delta Li-7(amph-cpx). as large as 8 parts per thousand and are thus not in Li isotope equilibrium. These low values probably reflect late-stage diffusion of Li into clinopyroxene during final cooling of the rocks, thus enriching the clinopyroxene in 6 Li. At the margin of the complex delta(7) Li in the syenites increases systematically, from +2 to high values of + 14 parts per thousand. This, coupled with the observed Li isotope systematics of the granitic country rocks, reflects post-magmatic open-system processes occurring during final cooling of the intrusion. Although the shape and magnitude of the Li isotope and elemental profiles through syenite and country rock are suggestive of diffusion-driven isotope fractionation, they cannot be modeled by one-dimensional diffusive transport and point to circulation of a fluid having a high 67 Li value (possibly seawater) along the chilled contact. In all, this study demonstrates that Li isotopes can be used to identify complex fluid- and diffusion-governed processes taking place during the final cooling of such rocks. (c) 2007 Elsevier B.V All rights reserved.