The Ge(001) (2 × 1) reconstruction: asymmetric dimers and multilayer relaxation observed by grazing incidence X-ray diffraction

Grazing incidence X-ray diffraction has been used to analyze in detail the atomic structure of the (2 × 1) reconstruction of the Ge(001) surface involving far reaching subsurface relaxations. Two kinds of disorder models, a statistical and a dynamical were taken into account for the data analysis, both indicating substantial disorder along the surface normal. This can only be correlated to asymmetric dimers. Considering a statistical disorder model assuming randomly oriented dimers the analysis of 13 symmetrically independent in-plane fractional order reflections and of four fractional order reciprocal lattice rods up to the maximum attainable momentum transfer qz = 3c* (c* = 1.77 × 10−1 Å−1) indicates the formation of asymmetric dimers characterized by R>D = 2.46(5) Å as compared to the bulk bonding length of R = 2.45 Å. The dimer height of Δ Z = 0.74(15) Å corresponds to a dimer buckling angle of 17(4)°. The data refinement using anisotropic thermal parameters leads to a bonding length of RD = 2.44(4) Å and to a large anisotropy of the root mean-square vibration amplitudes of the dimer atoms (u112) 1/2 = 0.25 Å, (u222)1/2 = 0.14 Å, (u332)1/2 = 0.50 Å). We have evidence for lateral and vertical disp tenth layer below the surface

The Structure of Bovine Viral Diarrhea Virus RNA-Dependent RNA Polymerase and Its Amino-Terminal Domain

SummaryViral RNA-dependent RNA polymerases (RdRp) differ from DNA-dependent RNA polymerases, DNA-dependent DNA polymerases, and reverse transcriptases in that RdRps contain “fingertips” consisting of several polypeptide strands in the fingers domain interacting with the thumb domain. The crystal structure of bovine viral diarrhea virus (BVDV) RdRp containing an Asn438 duplication shows that the “N-terminal domain,” which occurs only in pestiviruses such as BVDV, interacts with the polymerase component of the same polypeptide chain. This contrasts with the domain swapping observed in the previously determined structure of the BVDV NADL strain RdRp. By comparison with the NADL structure and through the use of biochemical data, it is possible that the N-terminal domain, in conjunction with the fingertips, is required to bind and assist the translocation of the RNA template. The partial disorder of the loop containing the additional Asn438 residue may explain the low replication rate of the recombinant compared with the wild-type virus

A unified evaluation of iterative projection algorithms for phase retrieval

Iterative projection algorithms are successfully being used as a substitute of lenses to recombine, numerically rather than optically, light scattered by illuminated objects. Images obtained computationally allow aberration-free diffraction-limited imaging and the possibility of using radiation for which no lenses exist. The challenge of this imaging technique is transfered from the lenses to the algorithms. We evaluate these new computational ``instruments'' developed for the phase retrieval problem, and discuss acceleration strategies.Comment: 12 pages, 9 figures, revte

Assessing and Improving Library Technology with Service Blueprinting

Objective: The objective of this article is to illustrate the application of service blueprinting—a design tool that comes from the service design tradition—for assessing and improving library technology services. Setting: A mid-sized library at a public university in the western United States. Methods: A service blueprint was co-created by library and IT staff in a design workshop in order to map the operational flow of a data visualization display wall. Results: Guided by the service blueprint, the project team identified points of improvement for the service of the data visualization display wall, and developed recommendations to aid further applications of service blueprinting. Conclusions: Ultimately, service blueprinting was found to be a useful tool that can be applied to assess and improve library technology services

Antigenic Stimuli do not Influence Thymic B Lymphocytes: A Morphological and Functional Study in Germ-Free and Conventionally Reared Piglets

We have recently reported that thymic B lymphocytes (TBL) are the first B-cell subpopulation undergoing isotype switching to IgG and IgA during embryonic life. The aim of this study is to analyze the influence of antigenic stimulation on TBL location and activity using a germ-free (GF) newborn pig model, in which maternal antibodies and antigens do not affect B-cell development. Immunohistological analysis showed that TBL were disseminated mainly in the thymic medulla. There were no differences in the distribution of TBL, both in GF newborn piglets before and after colonization with Escherichia coli and in older conventionally reared (CONV) piglets. The number of immunoglobulin (Ig)-secreting cells measured by the ELISPOT method was not influenced by microflora and food antigens. IgM-positive cells secreting IgM and CD45RC-positive cells spontaneously producing IgM, IgG, and IgA were detected in newborn thymus

Conformational Changes of the Flavivirus E Glycoprotein

Dengue virus, a member of the Flaviviridae family, has a surface composed of 180 copies each of the envelope (E) glycoprotein and the membrane (M) protein. The crystal structure of an N-terminal fragment of E has been determined and compared with a previously described structure. The primary difference between these structures is a 10° rotation about a hinge relating the fusion domain DII to domains DI and DIII. These two rigid body components were used for independent fitting of E into the cryo-electron microscopy maps of both immature and mature dengue viruses. The fitted E structures in these two particles showed a difference of 27° between the two components. Comparison of the E structure in its postfusion state with that in the immature and mature virions shows a rotation approximately around the same hinge. Flexibility of E is apparently a functional requirement for assembly and infection of flaviviruses

Mapping the Structure and Function of the E1 and E2 Glycoproteins in Alphaviruses

The 9 Å resolution cryo-electron microscopy map of Sindbis virus presented here provides structural information on the polypeptide topology of the E2 protein, on the interactions between the E1 and E2 glycoproteins in the formation of a heterodimer, on the difference in conformation of the two types of trimeric spikes, on the interaction between the transmembrane helices of the E1 and E2 proteins, and on the conformational changes that occur when fusing with a host cell. The positions of various markers on the E2 protein established the approximate topology of the E2 structure. The largest conformational differences between the icosahedral surface spikes at icosahedral 3-fold and quasi-3-fold positions are associated with the monomers closest to the 5-fold axes. The long E2 monomers, containing the cell receptor recognition motif at their extremities, are shown to rotate by about 180^o and to move away from the center of the spikes during fusion