Crystal structure of the complex between thrombin and the central "E" region of fibrin

Nonsubstrate interactions of thrombin with fibrin play an important role in modulating its procoagulant activity. To establish the structural basis for these interactions, we crystallized d-Phe-Pro-Arg-chloromethyl ketone-inhibited human thrombin in complex with a fragment, E(ht), corresponding to the central region of human fibrin, and solved its structure at 3.65-A resolution. The structure revealed that the complex consists of two thrombin molecules bound to opposite sides of the central part of E(ht) in a way that seems to provide proper orientation of their catalytic triads for cleavage of fibrinogen fibrinopeptides. As expected, binding occurs through thrombin's anion-binding exosite I. However, only part of it is involved in forming an interface with the complementary negatively charged surface of E(ht). Among residues constituting the interface, Phe-34, Ser-36A, Leu-65, Tyr-76, Arg-77A, Ile-82, and Lys-110 of thrombin and the A alpha chain Trp-33, Phe-35, Asp-38, Glu-39, the B beta chain Ala-68 and Asp-69, and the gamma chain Asp-27 and Ser-30 of E(ht) form a net of polar contacts surrounding a well defined hydrophobic interior. Thus, despite the highly charged nature of the interacting surfaces, hydrophobic contacts make a substantial contribution to the interaction.     

Reconstitution of the hippocampal mossy fiber and associational-commissural pathways in a novel dissociated cell culture system.

Synapses of the hippocampal mossy fiber pathway exhibit several characteristic features, including a unique form of long-term potentiation that does not require activation of the N-methyl-D-aspartate receptor by glutamate, a complex postsynaptic architecture, and sprouting in response to seizures. However, these connections have proven difficult to study in hippocampal slices because of their relative paucity (<0.4%) compared to commissural-collateral synapses. To overcome this problem, we have developed a novel dissociated cell culture system in which we have enriched mossy fiber synapses by increasing the ratio of granule-to-pyramidal cells. As in vivo, mossy fiber connections are composed of large dynorphin A-positive varicosities contacting complex spines (but without a restricted localization). The elementary synaptic connections are glutamatergic, inhibited by dynorphin A, and exhibit N-methyl-D-aspartate-independent long-term potentiation. Thus, the simplicity and experimental accessibility of this enriched in vitro mossy fiber pathway provides a new perspective for studying nonassociative plasticity in the mammalian central nervous system.     

Inter-rater reliability of surgical reviews for AREN03B2: A COG renal tumor committee study

Purpose

The Children's Oncology Group (COG) renal tumor study (AREN03B2) requires real-time central review of radiology, pathology, and the surgical procedure to determine appropriate risk-based therapy. The purpose of this study was to determine the inter-rater reliability of the surgical reviews.

Methods

Of the first 3200 enrolled AREN03B2 patients, a sample of 100 enriched for blood vessel involvement, spill, rupture, and lymph node involvement was selected for analysis. The surgical assessment was then performed independently by two blinded surgical reviewers and compared to the original assessment, which had been completed by another of the committee surgeons. Variables assessed included surgeon-determined local tumor stage, overall disease stage, type of renal procedure performed, presence of tumor rupture, occurrence of intraoperative tumor spill, blood vessel involvement, presence of peritoneal implants, and interpretation of residual disease. Inter-rater reliability was measured using the Fleiss' Kappa statistic two-sided hypothesis tests (Kappa, p-value).

Results

Local tumor stage correlated in all 3 reviews except in one case (Kappa = 0.9775, p < 0.001). Similarly, overall disease stage had excellent correlation (0.9422, p < 0.001). There was strong correlation for type of renal procedure (0.8357, p < 0.001), presence of tumor rupture (0.6858, p < 0.001), intraoperative tumor spill (0.6493, p < 0.001), and blood vessel involvement (0.6470, p < 0.001). Variables that had lower correlation were determination of the presence of peritoneal implants (0.2753, p < 0.001) and interpretation of residual disease status (0.5310, p < 0.001).

Conclusion

The inter-rater reliability of the surgical review is high based on the great consistency in the 3 independent review results. This analysis provides validation and establishes precedent for real-time central surgical review to determine treatment assignment in a risk-based stratagem for multimodal cancer therapy.     

LPS and IL‐1 differentially activate mouse and human astrocytes: Role of CD14

Treatment of cultures with toll‐like receptor (TLR) ligands or cytokines has become a popular approach to investigate astrocyte neuroinflammatory responses and to simulate the neural environment in various CNS disorders. However, despite much effort, the mechanism of astrocyte activation such as their responses to the TLR ligands and IL‐1 remain highly debated. We compared highly pure primary mouse and human astrocyte cultures in their ability to produce proinflammatory mediators (termed “A1”) and immunoregulatory mediators (termed “A2”) in response to LPS, poly IC, and IL‐1 stimulation. In human astrocytes, IL‐1 induced both A1 and A2 responses, poly IC induced mostly A2, and LPS induced neither. In mouse astrocytes, LPS induced mostly an A1‐predominant response, poly IC induced both A1 and A2, and IL‐1 neither. In addition, mouse astrocytes produce abundant IL‐1 protein, whereas human astrocytes did not, despite robust IL‐1 mRNA expression. Of the TLR4 receptor complex proteins, human astrocytes expressed TLR4 and MD2 but not CD14, whereas mouse astrocytes expressed all three. Mouse astrocyte CD14 (cell‐associated and soluble) was potently upregulated by LPS. Silencing TLR4 or CD14 by siRNA suppressed LPS responses in mouse astrocytes. In vivo, astrocytes in LPS‐injected mouse brains also expressed CD14. Our results show striking differences between human and mouse astrocytes in the use of TLR/IL‐1R and subsequent downstream signaling and immune activation. IL‐1 translational block in human astrocytes may be a built‐in mechanism to prevent autocrine and paracrine cell activation and neuroinflammation. These results have important implications for translational research of human CNS diseases. GLIA 2014;62:999–1013     

Genome Sequencing of Mycobacterium abscessus Isolates from Patients in the United States and Comparisons to Globally Diverse Clinical Strains

Nontuberculous mycobacterial infections caused by Mycobacterium abscessus are responsible for a range of disease manifestations from pulmonary to skin infections and are notoriously difficult to treat, due to innate resistance to many antibiotics. Previous population studies of clinical M. abscessus isolates utilized multilocus sequence typing or pulsed-field gel electrophoresis, but high-resolution examinations of genetic diversity at the whole-genome level have not been well characterized, particularly among clinical isolates derived in the United States. We performed whole-genome sequencing of 11 clinical M. abscessus isolates derived from eight U.S. patients with pulmonary nontuberculous mycobacterial infections, compared them to 30 globally diverse clinical isolates, and investigated intrapatient genomic diversity and evolution. Phylogenomic analyses revealed a cluster of closely related U.S. and Western European M. abscessus subsp. abscessus isolates that are genetically distinct from other European isolates and all Asian isolates. Large-scale variation analyses suggested genome content differences of 0.3 to 8.3%, relative to the reference strain ATCC 19977^T. Longitudinally sampled isolates showed very few single-nucleotide polymorphisms and correlated genomic deletion patterns, suggesting homogeneous infection populations. Our study explores the genomic diversity of clinical M. abscessus strains from multiple continents and provides insight into the genome plasticity of an opportunistic pathogen.     

Theoretical and Experimental Research of Hydrogen Solid Solution in Mg and Mg-Al System

The study of hydrogen storage properties of Mg-based thin films is of interest due to their unique composition, interface, crystallinity, and high potential for use in hydrogen-storage systems. Alloying Mg with Al leads to the destabilization of the magnesium hydride reducing the heat of reaction, increases the nucleation rate, and decreases the dehydriding temperature. The purpose of our study is to reveal the role of the aluminum atom addition in hydrogen adsorption and accumulation in the Mg-H solid solution. Ab initio calculations of aluminum and hydrogen binding energies in magnesium were carried out in the framework of density functional theory. Hydrogen distribution and accumulation in Mg and Mg-10%Al thin films were experimentally studied by the method of glow-discharge optical emission spectroscopy and using a hydrogen analyzer, respectively. It was found that a hydrogen distribution gradient is observed in the Mg-10%Al coating, with more hydrogen on the surface and less in the bulk. Moreover, the hydrogen concentration in the Mg-10%Al is lower compared to Mg. This can be explained by the lower hydrogen binding energy in the magnesium-aluminum system compared with pure magnesium.     

Thermal,Mechanical, and Acoustic Properties of Polydimethylsiloxane Filled with Hollow Glass Microspheres

Polydimethylsiloxane (PDMS) is the most widely used silicon-based polymer due to its versatility and its various attractive properties. The fabrication of PDMS involves liquid phase cross-linking to obtain hydrophobic and mechanically flexible material in the final solid form. This allows to add various fillers to affect the properties of the resulting material. PDMS has a relatively low Thermal Conductivity (TC), in the order of 0.2 W/mK, which makes it attractive for thermal insulation applications such as sealing in construction. Although a further decrease in the TC of PDMS can be highly beneficial for such applications, most research on the thermal properties of PDMS composites have focused on fillers that increase the TC rather than decrease it. In the present work, we propose a simple and reliable method for making a PDMS-based composite material with significantly improved thermal insulation properties, by adding hollow glass microspheres (HGMs) to the mixture of the liquid base and the cross-linker (10:1 ratio), followed by degassing and heat-assisted crosslinking. We obtained a 31% reduction of thermal conductivity and a 60% increase in the elastic modulus of samples with HGM content of 17% by weight. At the same time, the sound insulation capacity of the PDMS-HGM composite is slightly decreased in comparison to pure PDMS, as a result of its lower density. Finally, the wettability of the samples had no dependence on HGM content.     

Changes in future time perception of day hospital psychiatric patients in response to small group treatment approaches

Attempted to assess the effects of small group approaches on future time perception of psychiatric patients in a da hospital. The research employed two patient groups within the day hospital A control group, (N = 12) which received routine day hospital treatment, and an experimental group,(N = 12) which received, in addition, the small group treatment. Measures of future time perception were administered to both groups before and after a 12-week treatment. Results indicated significant positive changes in response to group treatment on Future Events and the dimension of Importance. However, no positive significant differences were found on Time Extension, Directionality, and Quality of Affect. While it is not within the scope of this research to evaluate whether the, secured change can be maintained, it was clear that in immediate posttesting important changes had resulted from the treatment strategy.     

Structure Refinement and Fragmentation of Precipitates under Severe Plastic Deformation: A Review

During severe plastic deformation (SPD), the processes of lattice defect formation as well as their relaxation (annihilation) compete with each other. As a result, a dynamic equilibrium is established, and a steady state is reached after a certain strain value. Simultaneously, other kinetic processes act in opposite directions and also compete with each other during SPD, such as grain refinement/growth, mechanical strengthening/softening, formation/decomposition of solid solution, etc. These competing processes also lead to dynamic equilibrium and result in a steady state (saturation), albeit after different strains. Among these steady-state phenomena, particle fragmentation during the second phase of SPD has received little attention. Available data indicate that precipitate fragmentation slows down with increasing strain, though saturation is achieved at higher strains than in the case of hardness or grain size. Moreover, one can consider the SPD-driven nanocrystallization in the amorphous phase as a process that is opposite to the fragmentation of precipitates. The size of these crystalline nanoprecipitates also saturates after a certain strain. The fragmentation of precipitates during SPD is the topic of this review.