Zamilon,a Novel Virophage with Mimiviridae Host Specificity

Virophages, which are potentially important ecological regulators, have been discovered in association with members of the order Megavirales. Sputnik virophages target the Mimiviridae, Mavirus was identified with the Cafeteria roenbergensis virus, and virophage genomes reconstructed by metagenomic analyses may be associated with the Phycodnaviridae. Despite the fact that the Sputnik virophages were isolated with viruses belonging to group A of the Mimiviridae, they can grow in amoebae infected by Mimiviridae from groups A, B or C. In this study we describe Zamilon, the first virophage isolated with a member of group C of the Mimiviridae family. By co-culturing amoebae with purified Zamilon, we found that the virophage is able to multiply with members of groups B and C of the Mimiviridae family but not with viruses from group A. Zamilon has a 17,276 bp DNA genome that potentially encodes 20 genes. Most of these genes are closely related to genes from the Sputnik virophage, yet two are more related to Megavirus chiliensis genes, a group B Mimiviridae, and one to Moumouvirus monve transpoviron.     

Structural Studies of the Giant Mimivirus

Mimivirus is the largest known virus whose genome and physical size are comparable to some small bacteria, blurring the boundary between a virus and a cell. Structural studies of Mimivirus have been difficult because of its size and long surface fibers. Here we report the use of enzymatic digestions to remove the surface fibers of Mimivirus in order to expose the surface of the viral capsid. Cryo-electron microscopy (cryoEM) and atomic force microscopy were able to show that the 20 icosahedral faces of Mimivirus capsids have hexagonal arrays of depressions. Each depression is surrounded by six trimeric capsomers that are similar in structure to those in many other large, icosahedral double-stranded DNA viruses. Whereas in most viruses these capsomers are hexagonally close-packed with the same orientation in each face, in Mimivirus there are vacancies at the systematic depressions with neighboring capsomers differing in orientation by 60°. The previously observed starfish-shaped feature is well-resolved and found to be on each virus particle and is associated with a special pentameric vertex. The arms of the starfish fit into the gaps between the five faces surrounding the unique vertex, acting as a seal. Furthermore, the enveloped nucleocapsid is accurately positioned and oriented within the capsid with a concave surface facing the unique vertex. Thus, the starfish-shaped feature and the organization of the nucleocapsid might regulate the delivery of the genome to the host. The structure of Mimivirus, as well as the various fiber components observed in the virus, suggests that the Mimivirus genome includes genes derived from both eukaryotic and prokaryotic organisms. The three-dimensional cryoEM reconstruction reported here is of a virus with a volume that is one order of magnitude larger than any previously reported molecular assembly studied at a resolution of equal to or better than 65 Å.     

Broad Spectrum of Mimiviridae Virophage Allows Its Isolation Using a Mimivirus Reporter

The giant virus Mimiviridae family includes 3 groups of viruses: group A (includes Acanthamoeba polyphaga Mimivirus), group B (includes Moumouvirus) and group C (includes Megavirus chilensis). Virophages have been isolated with both group A Mimiviridae (the Mamavirus strain) and the related Cafeteria roenbergensis virus, and they have also been described by bioinformatic analysis of the Phycodnavirus. Here, we found that the first two strains of virophages isolated with group A Mimiviridae can multiply easily in groups B and C and play a role in gene transfer among these virus subgroups. To isolate new virophages and their Mimiviridae host in the environment, we used PCR to identify a sample with a virophage and a group C Mimiviridae that failed to grow on amoeba. Moreover, we showed that virophages reduce the pathogenic effect of Mimivirus (plaque formation), establishing its parasitic role on Mimivirus. We therefore developed a co-culture procedure using Acanthamoeba polyphaga and Mimivirus to recover the detected virophage and then sequenced the virophage''s genome. We present this technique as a novel approach to isolating virophages. We demonstrated that the newly identified virophages replicate in the viral factories of all three groups of Mimiviridae, suggesting that the spectrum of virophages is not limited to their initial host.     

Structural Studies of G Protein-Coupled Receptors

G protein-coupled receptors (GPCRs) constitute the largest and the most physiologically important membrane protein family that recognizes a variety of environmental stimuli, and are drug targets in the treatment of numerous diseases. Recent progress on GPCR structural studies shed light on molecular mechanisms of GPCR ligand recognition, activation and allosteric modulation, as well as structural basis of GPCR dimerization. In this review, we will discuss the structural features of GPCRs and structural insights of different aspects of GPCR biological functions.     

Structural Studies of Truncated Forms of the Prion Protein PrP

Prions are proteins that adopt self-propagating aberrant folds. The self-propagating properties of prions are a direct consequence of their distinct structures, making the understanding of these structures and their biophysical interactions fundamental to understanding prions and their related diseases. The insolubility and inherent disorder of prions have made their structures difficult to study, particularly in the case of the infectious form of the mammalian prion protein PrP. Many investigators have therefore preferred to work with peptide fragments of PrP, suggesting that these peptides might serve as structural and functional models for biologically active prions. We have used x-ray fiber diffraction to compare a series of different-sized fragments of PrP, to determine the structural commonalities among the fragments and the biologically active, self-propagating prions. Although all of the peptides studied adopted amyloid conformations, only the larger fragments demonstrated a degree of structural complexity approaching that of PrP. Even these larger fragments did not adopt the prion structure itself with detailed fidelity, and in some cases their structures were radically different from that of pathogenic PrP^Sc.     

Structural Equation Modeling for Observational Studies

Abstract Structural equation modeling (SEM) represents a framework for developing and evaluating complex hypotheses about systems. This method of data analysis differs from conventional univariate and multivariate approaches familiar to most biologists in several ways. First, SEMs are multiequational and capable of representing a wide array of complex hypotheses about how system components interrelate. Second, models are typically developed based on theoretical knowledge and designed to represent competing hypotheses about the processes responsible for data structure. Third, SEM is conceptually based on the analysis of covariance relations. Most commonly, solutions are obtained using maximum-likelihood solution procedures, although a variety of solution procedures are used, including Bayesian estimation. Numerous extensions give SEM a very high degree of flexibility in dealing with nonnormal data, categorical responses, latent variables, hierarchical structure, multigroup comparisons, nonlinearities, and other complicating factors. Structural equation modeling allows researchers to address a variety of questions about systems, such as how different processes work in concert, how the influences of perturbations cascade through systems, and about the relative importance of different influences. I present 2 example applications of SEM, one involving interactions among lynx (Lynx pardinus), mongooses (Herpestes ichneumon), and rabbits (Oryctolagus cuniculus), and the second involving anuran species richness. Many wildlife ecologists may find SEM useful for understanding how populations function within their environments. Along with the capability of the methodology comes a need for care in the proper application of SEM.     

Structural Studies of 2-Thiouridine in RNA

Abstract

A pentamer RNA sequence, Gs²UUUC, and a s²U containing 14-mer RNA tetraloop hairpin were synthesized and characterized by NMR and by UV melting studies. These oligonucleotides were used as models to understand the effect of 2-thiouridine substitution on RNA structure and the potential for stabilization of tRNA codon-anticodon interactions through sU-34 modification. The magnitude of the effect of sU in our model system is comparable to the 20° C stabilization reported for 2-thiolation in a codonanticodon model system composed of two tRNAs with complementary anticodon sequences.     

Studies on Structural Proteins of Chikungunya Virus

Chikungunya virus (CHIKV) was purified and subjected to sodium dodecyl sulfate-polyacrylamide gel electrophoresis in discontinuous buffer systems. Three bands were revealed by staining with Coomassie blue; two of them (E₁ and E₂) were associated with the membrane, and one (C) with the core. Their molecular weights were estimated to be 56,000 (E₁), 52,000 (E₂), and 36,000 (C), irrespective of the concentration of acrylamide in the gels. The molar ratios of Ei, E2, and C were almost equal when the sample buffer was Tris-HCl, whereas they were different when phosphate buffer was used.     

Structural Studies of Overlapping Dinucleosomes in Solution

An overlapping dinucleosome (OLDN) is a structure composed of one hexasome and one octasome and appears to be formed through nucleosome collision promoted by nucleosome remodeling factor(s). In this study, the solution structure of the OLDN was investigated through the integration of small-angle x-ray and neutron scattering (SAXS and SANS, respectively), computer modeling, and molecular dynamics simulations. Starting from the crystal structure, we generated a conformational ensemble based on normal mode analysis and searched for the conformations that reproduced the SAXS and SANS scattering curves well. We found that inclusion of histone tails, which are not observed in the crystal structure, greatly improved model quality. The obtained structural models suggest that OLDNs adopt a variety of conformations stabilized by histone tails situated at the interface between the hexasome and octasome, simultaneously binding to both the hexasomal and octasomal DNA. In addition, our models define a possible direction for the conformational changes or dynamics, which may provide important information that furthers our understanding of the role of chromatin dynamics in gene regulation.     

T细胞抗原受体的结构与功能研究进展

T细胞抗原受体(T ceIl receptor,TCR)是T细胞表面关键的受体分子。TCR特异性地识别各种多肽抗原并通过胞内区ITAM磷酸化传递抗原刺激信号,进而引发T细胞的免疫效应。TCR的活性异常将会导致自身免疫病和免疫缺陷病的发生。对于TCR结构和功能的深入研究有助于我们更好地理解免疫反应的分子机理,从而为相关免疫疾病的预防和治疗提供重要的理论依据。该文对TCR的分类、基因重排机制、受体组装方式及其结构基础、TCR对抗原的识别以及活化机制等方面的研究成果进行了总结,综述了近几年来的最新研究进展。     

Fine Structural Studies on the Pycnidiospores of Botryodiplodia theobromae Pat.

The structure of the pycnidiospores of B. theobromae was investigatedby a combination of light microscope, a scanning electron microscopeand a transmission electron microscope observations. As observedwith the light microscope the hyaline non-septate pycnidiosporeis highly vesiculated while the pigmented septate one exhibitslongitudinal hyaline striations. Investigations with the scanningelectron microscope showed the hyaline non-septate pycnidiosporeto be smooth-walled without any form of ornamentation. The pigmentedseptate pycnidiospore on the other hand had a rough outer surfacewith a transverse groove, which probably indicated the positionof the septum. The longitudinal striations seen on such pycnidiosporeswith the light microscope were not observed under these conditions.Observations with the transmission electron microscope showedthat the outermost layer of the hyaline pycnidiospore was smootherthan that of the pigmented one. The pigment was on the outerlayer of the double-layered wall of the pigmented pycnidiospore.The inner non-pigmented wall layer was continuous with the septum.The septum tapered gradually to a thin layer in the centre whereit was perforated by a simple pore. The observations indicatedthat the pigmented spore was multinucleate while the hyalineone was uninucleate.     

Structural Studies of T200 Glycoprotein and the Il-2 Receptor

Abstract

Immunological analysis of the cell surface of hematopoietic cells has led to the identification of many different cell membrane molecules, some of which have well-defined functions as receptors. In general, however, the role of most lymphocyte cell surface molecules remains ill-defined even in cases in which antibody inhibition studies have given some insight into the biological processes in which they participate. Here we describe molecular and biochemical studies of T200 glycoprotein (leukocyte-common antigen) and the IL-2 receptor which illustrate the kinds of approaches that can be currently used to characterize individual molecules. T200 glycoprotein is a large M_r glycoprotein found exclusively on leukocytes. However, the exact M_r varies in a cell-type-specific fashion and this property is conserved between different species. Comparison of the rat, mouse and human cDNA sequences show that the large cytoplasmic portion of the molecule is well-conserved, approximately 90%, whereas the exterior portion is only about 50% homologous. Cell-type-specific differences in the primary sequence of the molecule have been identified in the N-terminal portion of the molecules. In contrast to T200, the function of the IL-2 receptor is well-known. The interaction of IL-2 with its receptor provides a growth signal that determines the magnitude and duration of T-cell responses. Limited proteolysis studies provide the first direct biochemical evidence that the external region of the IL-2 receptor consists of two independent domains. ¹²⁵I-labeled IL-2 has been chemically crosslinked to the receptor and proteolytic cleavage of the crosslinked product indicates that IL-2 is selectively bound to the N-terminal domain of the receptor.