Pressure dependence of the sound velocity in a 2D lattice of Hertz-Mindlin balls: a mean field description

We study the dependence on the external pressure $P$ of the velocities $v_{L,T}$ of long wavelength sound waves in a confined 2D h.c.p. lattice of 3D elastic frictional balls interacting via one-sided Hertz-Mindlin contact forces, whose diameters exhibit mild dispersion. The presence of an underlying long range order enables us to build an effective medium description which incorporates the radial fluctuations of the contact forces acting on a single site. Due to the non linearity of Hertz elasticity, self-consistency results in a highly non-linear differential equation for the "equation of state" linking the effective stiffness of the array with the applied pressure, from which sound velocities are then obtained. The results are in excellent agreement with existing experimental results and simulations in the high and intermediate pressure regimes. It emerges from the analysis that the departure of $v_{L}(P)$ from the ideal $P^{1/6}$ Hertz behavior must be attributed primarily to the fluctuations of the stress field, rather than to the pressure dependence of the number of contacts

CEMENTITIOUS BARRIERS PARTNERSHIP FY13 MID-YEAR REPORT

In FY2013, the Cementitious Barriers Partnership (CBP) is continuing in its effort to develop and enhance software tools demonstrating tangible progress toward fulfilling the objective of developing a set of tools to improve understanding and prediction of the long‐term structural, hydraulic and chemical performance of cementitious barriers used in nuclear applications. In FY2012, the CBP released the initial inhouse “Beta‐version” of the CBP Software Toolbox, a suite of software for simulating reactive transport in cementitious materials and important degradation phenomena. The current primary software components are LeachXS/ORCHESTRA, STADIUM, and a GoldSim interface for probabilistic analysis of selected degradation scenarios. THAMES is a planned future CBP Toolbox component (FY13/14) focused on simulation of the microstructure of cementitious materials and calculation of resultant hydraulic and constituent mass transfer parameters needed in modeling. This past November, the CBP Software Toolbox Version 1.0 was released that supports analysis of external sulfate attack (including damage mechanics), carbonation, and primary constituent leaching. The LeachXS component embodies an extensive material property measurements database along with chemical speciation and reactive mass transport simulation cases with emphasis on leaching of major, trace and radionuclide constituents from cementitious materials used in DOE facilities, such as Saltstone (Savannah River) and Cast Stone (Hanford), tank closure grouts, and barrier concretes. STADIUM focuses on the physical and structural service life of materials and components based on chemical speciation and reactive mass transport of major cement constituents and aggressive species (e.g., chloride, sulfate, etc.). The CBP issued numerous reports and other documentation that accompanied the “Version 1.0” release including a CBP Software Toolbox User Guide and Installation Guide. These documents, as well as, the presentations from the CBP Software Toolbox Demonstration and User Workshop, which are briefly described below, can be accessed from the CBP webpage at http://cementbarriers.org/. The website was recently modified to describe the CBP Software Toolbox and includes an interest form for application to use the software. The CBP FY13 program is continuing research to improve and enhance the simulation tools as well as develop new tools that model other key degradation phenomena not addressed in Version 1.0. Also efforts to continue to verify the various simulation tools thru laboratory experiments and analysis of field specimens are ongoing to quantify and reduce the uncertainty associated with performance assessments are ongoing. This mid‐year report also includes both a summary on the FY13 software accomplishments in addition to the release of Version 1.0 of the CBP Software Toolbox and the various experimental programs that are providing data for calibration and validation of the CBP developed software. The focus this year for experimental studies was to measure transport in cementitious material by utilization of a leaching method and reduction capacity of saltstone field samples. Results are being used to calibrate and validate the updated carbonation model

Class I major histocompatibility complexes loaded by a periodate trigger

Class I major histocompatibility complexes (MHCs) present peptide ligands on the cell surface for recognition by appropriate cytotoxic T cells. The unstable nature of unliganded MHC necessitates the production of recombinant class I complexes through in vitro refolding reactions in the presence of an added excess of peptides. This strategy is not amenable to high-throughput production of vast collections of class I complexes. To address this issue, we recently designed photocaged MHC ligands that can be cleaved by a UV light trigger in the MHC bound state under conditions that do not affect the integrity of the MHC structure. The results obtained with photocaged MHC ligands demonstrate that conditional MHC ligands can form a generally applicable concept for the creation of defined peptide−MHCs. However, the use of UV exposure to mediate ligand exchange is unsuited for a number of applications, due to the lack of UV penetration through cell culture systems and due to the transfer of heat upon UV irradiation, which can induce evaporation. To overcome these limitations, here, we provide proof-of-concept for the generation of defined peptide−MHCs by chemical trigger-induced ligand exchange. The crystal structure of the MHC with the novel chemosensitive ligand showcases that the ligand occupies the expected binding site, in a conformation where the hydroxyl groups should be reactive to periodate. We proceed to validate this technology by producing peptide−MHCs that can be used for T cell detection. The methodology that we describe here should allow loading of MHCs with defined peptides in cell culture devices, thereby permitting antigen-specific T cell expansion and purification for cell therapy. In addition, this technology will be useful to develop miniaturized assay systems for performing high-throughput screens for natural and unnatural MHC ligands

Ligand-Receptor Interactions

The formation and dissociation of specific noncovalent interactions between a variety of macromolecules play a crucial role in the function of biological systems. During the last few years, three main lines of research led to a dramatic improvement of our understanding of these important phenomena. First, combination of genetic engineering and X ray cristallography made available a simultaneous knowledg of the precise structure and affinity of series or related ligand-receptor systems differing by a few well-defined atoms. Second, improvement of computer power and simulation techniques allowed extended exploration of the interaction of realistic macromolecules. Third, simultaneous development of a variety of techniques based on atomic force microscopy, hydrodynamic flow, biomembrane probes, optical tweezers, magnetic fields or flexible transducers yielded direct experimental information of the behavior of single ligand receptor bonds. At the same time, investigation of well defined cellular models raised the interest of biologists to the kinetic and mechanical properties of cell membrane receptors. The aim of this review is to give a description of these advances that benefitted from a largely multidisciplinar approach

Cementitious Barriers Partnership FY2013 End-Year Report

In FY2013, the Cementitious Barriers Partnership (CBP) demonstrated continued tangible progress toward fulfilling the objective of developing a set of software tools to improve understanding and prediction of the long‐term structural, hydraulic and chemical performance of cementitious barriers used in nuclear applications. In November 2012, the CBP released “Version 1.0” of the CBP Software Toolbox, a suite of software for simulating reactive transport in cementitious materials and important degradation phenomena. In addition, the CBP completed development of new software for the “Version 2.0” Toolbox to be released in early FY2014 and demonstrated use of the Version 1.0 Toolbox on DOE applications. The current primary software components in both Versions 1.0 and 2.0 are LeachXS/ORCHESTRA, STADIUM, and a GoldSim interface for probabilistic analysis of selected degradation scenarios. The CBP Software Toolbox Version 1.0 supports analysis of external sulfate attack (including damage mechanics), carbonation, and primary constituent leaching. Version 2.0 includes the additional analysis of chloride attack and dual regime flow and contaminant migration in fractured and non‐fractured cementitious material. The LeachXS component embodies an extensive material property measurements database along with chemical speciation and reactive mass transport simulation cases with emphasis on leaching of major, trace and radionuclide constituents from cementitious materials used in DOE facilities, such as Saltstone (Savannah River) and Cast Stone (Hanford), tank closure grouts, and barrier concretes. STADIUM focuses on the physical and structural service life of materials and components based on chemical speciation and reactive mass transport of major cement constituents and aggressive species (e.g., chloride, sulfate, etc.). THAMES is a planned future CBP Toolbox component focused on simulation of the microstructure of cementitious materials and calculation of resultant hydraulic and constituent mass transfer parameters needed in modeling. Two CBP software demonstrations were conducted in FY2013, one to support the Saltstone Disposal Facility (SDF) at SRS and the other on a representative Hanford high‐level waste tank. The CBP Toolbox demonstration on the SDF provided analysis on the most probable degradation mechanisms to the cementitious vault enclosure caused by sulfate and carbonation ingress. This analysis was documented and resulted in the issuance of a SDF Performance Assessment Special Analysis by Liquid Waste Operations this fiscal year. The two new software tools supporting chloride attack and dual‐regime flow will provide additional degradation tools to better evaluate performance of DOE and commercial cementitious barriers. The CBP SRNL experimental program produced two patent applications and field data that will be used in the development and calibration of CBP software tools being developed in FY2014. The CBP software and simulation tools varies from other efforts in that all the tools are based upon specific and relevant experimental research of cementitious materials utilized in DOE applications. The CBP FY2013 program involved continuing research to improve and enhance the simulation tools as well as developing new tools that model other key degradation phenomena not addressed in Version 1.0. Also efforts to continue to verify the various simulation tools through laboratory experiments and analysis of field specimens are ongoing and will continue into FY2014 to quantify and reduce the uncertainty associated with performance assessments. This end‐year report summarizes FY2013 software development efforts and the various experimental programs that are providing data for calibration and validation of the CBP developed software

Recognition of vitamin B metabolites by mucosal-associated invariant T cells

The mucosal-associated invariant T-cell antigen receptor (MAIT TCR) recognizes MR1 presenting vitamin B metabolites. Here we describe the structures of a human MAIT TCR in complex with human MR1 presenting a non-stimulatory ligand derived from folic acid and an agonist ligand derived from a riboflavin metabolite. For both vitamin B antigens, the MAIT TCR docks in a conserved manner above MR1, thus acting as an innate-like pattern recognition receptor. The invariant MAIT TCR a-chain usage is attributable to MR1-mediated interactions that prise open the MR1 cleft to allow contact with the vitamin B metabolite. Although the non-stimulatory antigen does not contact the MAIT TCR, the stimulatory antigen does. This results in a higher affinity of the MAIT TCR for a stimulatory antigen in comparison with a non-stimulatory antigen. We formally demonstrate a structural basis for MAIT TCR recognition of vitamin B metabolites, while illuminating how TCRs recognize microbial metabolic signatures

Degenerate T-cell Recognition of Peptides on MHC Molecules Creates Large Holes in the T-cell Repertoire

The cellular immune system screens peptides presented by host cells on MHC molecules to assess if the cells are infected. In this study we examined whether the presented peptides contain enough information for a proper self/nonself assessment by comparing the presented human (self) and bacterial or viral (nonself) peptides on a large number of MHC molecules. For all MHC molecules tested, only a small fraction of the presented nonself peptides from 174 species of bacteria and 1000 viral proteomes (0.2%) is shown to be identical to a presented self peptide. Next, we use available data on T-cell receptor-peptide-MHC interactions to estimate how well T-cells distinguish between similar peptides. The recognition of a peptide-MHC by the T-cell receptor is flexible, and as a result, about one-third of the presented nonself peptides is expected to be indistinguishable (by T-cells) from presented self peptides. This suggests that T-cells are expected to remain tolerant for a large fraction of the presented nonself peptides, which provides an explanation for the “holes in the T-cell repertoire” that are found for a large fraction of foreign epitopes. Additionally, this overlap with self increases the need for efficient self tolerance, as many self-similar nonself peptides could initiate an autoimmune response. Degenerate recognition of peptide-MHC-I complexes by T-cells thus creates large and potentially dangerous overlaps between self and nonself

Induction of viral and tumour specific CTL responses using antibody targeted HLA class I peptide complexes

The production of cytotoxic T cells with specificity for cancer cells is a rapidly evolving branch of cancer therapeutics. A variety of approaches aim to amplify anti-tumour cytotoxic T cell responses using purified peptides, tumour cell lysates or recombinant HLA/peptide complexes in differing antigen presenting systems. Using a two-step biotin-streptavidin antibody targeting system, recombinant HLA-class I/peptide complexes were attached to the surface of B cells via the anti-CD20 B9E9-scFvSA antibody-streptavidin fusion protein. Flow cytometry with a conformation dependant monoclonal antibody to HLA class I indicated that targeted HLA-class I/peptide complexes remain on the surface of B cells in culture for periods in excess of 72 h. PBMCs were stimulated in vitro for 8–14 days using the autologous B cells as antigen presenting cells. Following a single cycle of stimulation specific cytotoxic T cell responses to targeted HLA-A2 complexes containing the M1, BMLF1 and Melan A peptides could be demonstrated by tetramer staining and Cr release assays. With the HLA-A2/BMLF1 complex up to 2.99% of CD8+ve cells were tetramer positive producing 20% lysis (E : T 10 : 1) of CIR-A2 target cells in an in vitro cytotoxicity assay compared to baseline levels of 0.09% tetramer +ve and 2% lysis in the unstimulated population. PBMCs from a healthy donor treated with two cycles of stimulations with targeted HLA-A2/Melan A complexes, demonstrated expansion of the melanA tetramer +ve population from 0.03% to 1.4% producing 15% lysis of Melan A pulsed target cells. With further consideration to the key variables of HLA/peptide complex density, the ratio of stimulator to effector cells and optimum cytokine support, this system should offer an easy and effective method for the in vitro amplification of specific cytotoxic T cell responses and warrants development for the in vivo induction of cytotoxic T cell responses in cancer therapy

Crystal Structure of EHEC Intimin: Insights into the Complementarity between EPEC and EHEC

Enterohaemorrhagic E. coli (EHEC) O157:H7 is a primary food-borne bacterial pathogen capable of causing life-threatening human infections which poses a serious challenge to public health worldwide. Intimin, the bacterial outer-membrane protein, plays a key role in the initiating process of EHEC infection. This activity is dependent upon translocation of the intimin receptor (Tir), the intimin binding partner of the bacteria-encoded host cell surface protein. Intimin has attracted considerable attention due to its potential function as an antibacterial drug target. Here, we report the crystal structure of the Tir-binding domain of intimin (Int188) from E. coli O157:H7 at 2.8 Å resolution, together with a mutant (IntN916Y) at 2.6 Å. We also built the structural model of EHEC intimin-Tir complex and analyzed the key binding residues. It suggested that the binding pattern of intimin and Tir between EHEC and Enteropathogenic E. coli (EPEC) adopt a similar mode and they can complement with each other. Detailed structural comparison indicates that there are four major points of structural variations between EHEC and EPEC intimins: one in Domain I (Ig-like domain), the other three located in Domain II (C-type lectin-like domain). These variations result in different binding affinities. These findings provide structural insight into the binding pattern of intimin to Tir and the molecular mechanism of EHEC O157: H7