Unique Interplay between Sugar and Lipid in Determining the Antigenic Potency of Bacterial Antigens for NKT Cells

Structural and biophysical studies reveal the induced-fit mechanism underlying the stringent specificity of invariant natural killer T cells for unique glycolipid antigens from the pathogen Streptococcus pneumoniae

IEDB-3D: structural data within the immune epitope database

IEDB-3D is the 3D structural component of the Immune Epitope Database (IEDB) available via the ‘Browse by 3D Structure’ page at http://www.iedb.org. IEDB-3D catalogs B- and T-cell epitopes and Major Histocompatibility Complex (MHC) ligands for which 3D structures of complexes with antibodies, T-cell receptors or MHC molecules are available in the Protein Data Bank (PDB). Journal articles that are primary citations of PDB structures and that define immune epitopes are curated within IEDB as any other reference along with accompanying functional assays and immunologically relevant information. For each curated structure, IEDB-3D provides calculated data on intermolecular contacts and interface areas and includes an application, EpitopeViewer, to visualize the structures. IEDB-3D is fully embedded within IEDB, thus allowing structural data, both curated and calculated, and all accompanying information to be queried using multiple search interfaces. These include queries for epitopes recognized in different pathogens, eliciting different functional immune responses, and recognized by different components of the immune system. The query results can be downloaded in Microsoft Excel format, or the entire database, together with structural data both curated and calculated, can be downloaded in either XML or MySQL formats

Afshar's Experiment does not show a Violation of Complementarity

A recent experiment performed by S. Afshar [first reported by M. Chown, New Scientist {\bf 183}, 30 (2004)] is analyzed. It was claimed that this experiment could be interpreted as a demonstration of a violation of the principle of complementarity in quantum mechanics. Instead, it is shown here that it can be understood in terms of classical wave optics and the standard interpretation of quantum mechanics. Its performance is quantified and it is concluded that the experiment is suboptimal in the sense that it does not fully exhaust the limits imposed by quantum mechanics.Comment: 6 pages, 6 figure

Observation of off-diagonal geometric phase in polarized neutron interferometer experiments

Off-diagonal geometric phases acquired in the evolution of a spin-1/2 system have been investigated by means of a polarized neutron interferometer. Final counts with and without polarization analysis enable us to observe simultaneously the off-diagonal and diagonal geometric phases in two detectors. We have quantitatively measured the off-diagonal geometric phase for noncyclic evolutions, confirming the theoretical predictions. We discuss the significance of our experiment in terms of geometric phases (both diagonal and off-diagonal) and in terms of the quantum erasing phenomenon.Comment: pdf, 22 pages + 8 figures (included in the pdf). In print on Phys. Rev.

Quantitative wave-particle duality and non-erasing quantum erasure

The notion of wave-particle duality may be quantified by the inequality V^2+K^2 <=1, relating interference fringe visibility V and path knowledge K. With a single-photon interferometer in which polarization is used to label the paths, we have investigated the relation for various situations, including pure, mixed, and partially-mixed input states. A quantum eraser scheme has been realized that recovers interference fringes even when no which-way information is available to erase.Comment: 6 pages, 4 figures. To appear in Phys. Rev.

Double-slit interference pattern from single-slit screen and its gravitational analogues

The double slit experiment (DSE) is known as an important cornerstone in the foundations of physical theories such as Quantum Mechanics and Special Relativity. A large number of different variants of it were designed and performed over the years. We perform and discuss here a new verion with the somewhat unexpected results of obtaining interference pattern from single-slit screen. This outcome, which shows that the routes of the photons through the array were changed, leads one to discuss it, using the equivalence principle, in terms of geodesics mechanics. We show using either the Brill's version of the canonical formulation of general relativity or the linearized version of it that one may find corresponding and analogous situations in the framework of general relativity.Comment: 51 pages, 12 Figures five of them contain two subfigures and thus the number of figures is 17, 1 Table. Some minor changes introduced, especially, in the reference

A Delayed Choice Quantum Eraser

This paper reports a "delayed choice quantum eraser" experiment proposed by Scully and Dr\"{u}hl in 1982. The experimental results demonstrated the possibility of simultaneously observing both particle-like and wave-like behavior of a quantum via quantum entanglement. The which-path or both-path information of a quantum can be erased or marked by its entangled twin even after the registration of the quantum.Comment: twocolumn, 4pages, submitted to PR

Structure of a Classical MHC Class I Molecule That Binds “Non-Classical” Ligands

The chicken MHC YF1*7.1 X-ray structures reveal that this protein binds lipids and thus represents a "hybrid" class I complex with features of classical as well as non-classical MHC molecules

Determination of Cellular Lipids Bound to Human CD1d Molecules

CD1 molecules are glycoproteins that present lipid antigens at the cell surface for immunological recognition by specialized populations of T lymphocytes. Prior experimental data suggest a wide variety of lipid species can bind to CD1 molecules, but little is known about the characteristics of cellular ligands that are selected for presentation. Here we have molecularly characterized lipids bound to the human CD1d isoform. Ligands were eluted from secreted CD1d molecules and separated by normal phase HPLC, then characterized by mass spectroscopy. A total of 177 lipid species were molecularly identified, comprising glycerophospholipids and sphingolipids. The glycerophospholipids included common diacylglycerol species, reduced forms known as plasmalogens, lyso-phospholipids (monoacyl species), and cardiolipins (tetraacyl species). The sphingolipids included sphingomyelins and glycosylated forms, such as the ganglioside GM3. These results demonstrate that human CD1d molecules bind a surprising diversity of lipid structures within the secretory pathway, including compounds that have been reported to play roles in cancer, autoimmune diseases, lipid signaling, and cell death

Quantitative conditional quantum erasure in two-atom resonance fluorescence

We present a conditional quantum eraser which erases the a priori knowledge or the predictability of the path a photon takes in a Young-type double-slit experiment with two fluorescent four-level atoms. This erasure violates a recently derived erasure relation which must be satisfied for a conventional, unconditional quantum eraser that aims to find an optimal sorting of the system into subensembles with particularly large fringe visibilities. The conditional quantum eraser employs an interaction-free, partial which-way measurement which not only sorts the system into optimal subsystems with large visibility but also selects the appropriate subsystem with the maximum possible visibility. We explain how the erasure relation can be violated under these circumstances.Comment: Revtex4, 12pages, 4 eps figures, replaced with published version, changes in Sec. 3, to appear in Physical Review