On elongation factor eEFSec,its role and mechanism during selenium incorporation into nascent selenoproteins

Background

Selenium, an essential dietary micronutrient, is incorporated into proteins as the amino acid selenocysteine (Sec) in response to in-frame UGA codons. Complex machinery ensures accurate recoding of Sec codons in higher organisms. A specialized elongation factor eEFSec is central to the process.

Identification and Characterization of Highly Divergent Simian Foamy Viruses in a Wide Range of New World Primates from Brazil

Foamy viruses naturally infect a wide range of mammals, including Old World (OWP) and New World primates (NWP), which are collectively called simian foamy viruses (SFV). While NWP species in Central and South America are highly diverse, only SFV from captive marmoset, spider monkey, and squirrel monkey have been genetically characterized and the molecular epidemiology of SFV infection in NWPs remains unknown. We tested a large collection of genomic DNA (n  = 332) comprising 14 genera of NWP species for the presence of SFV polymerase (pol) sequences using generic PCR primers. Further molecular characterization of positive samples was carried out by LTR-gag and larger pol sequence analysis. We identified novel SFVs infecting nine NWP genera. Prevalence rates varied between 14–30% in different species for which at least 10 specimens were tested. High SFV genetic diversity among NWP up to 50% in LTR-gag and 40% in pol was revealed by intragenus and intrafamilial comparisons. Two different SFV strains infecting two captive yellow-breasted capuchins did not group in species-specific lineages but rather clustered with SFVs from marmoset and spider monkeys, indicating independent cross-species transmission events. We describe the first SFV epidemiology study of NWP, and the first evidence of SFV infection in wild NWPs. We also document a wide distribution of distinct SFVs in 14 NWP genera, including two novel co-speciating SFVs in capuchins and howler monkeys, suggestive of an ancient evolutionary history in NWPs for at least 28 million years. A high SFV genetic diversity was seen among NWP, yet these viruses seem able to jump between NWP species and even genera. Our results raise concerns for the risk of zoonotic transmission of NWP SFV to humans as these primates are regularly hunted for food or kept as pets in forest regions of South America.     

Accurate assembly of minority viral haplotypes from next-generation sequencing through efficient noise reduction

Rapidly evolving RNA viruses continuously produce minority haplotypes that can become dominant if they are drug-resistant or can better evade the immune system. Therefore, early detection and identification of minority viral haplotypes may help to promptly adjust the patient’s treatment plan preventing potential disease complications. Minority haplotypes can be identified using next-generation sequencing, but sequencing noise hinders accurate identification. The elimination of sequencing noise is a non-trivial task that still remains open. Here we propose CliqueSNV based on extracting pairs of statistically linked mutations from noisy reads. This effectively reduces sequencing noise and enables identifying minority haplotypes with the frequency below the sequencing error rate. We comparatively assess the performance of CliqueSNV using an in vitro mixture of nine haplotypes that were derived from the mutation profile of an existing HIV patient. We show that CliqueSNV can accurately assemble viral haplotypes with frequencies as low as 0.1% and maintains consistent performance across short and long bases sequencing platforms.     

A map of taste neuron projections in the Drosophila CNS

We provide a map of the projections of taste neurons in the CNS of Drosophila. Using a collection of 67 GAL4 drivers representing the entire repertoire of Gr taste receptors, we systematically map the projections of neurons expressing these drivers in the thoracico-abdominal ganglion and the suboesophageal ganglion (SOG). We define 9 categories of projections in the thoracico-abdominal ganglia and 10 categories in the SOG. The projection patterns are modular, and can be interpreted as combinations of discrete pattern elements. The elements can be interpreted in terms of the taste organ from which the projections originate, the structures from which they originate, and the quality of taste information that they represent. The extensive diversity in projection patterns provides an anatomical basis for functional diversity in responses elicited by different taste stimuli.     

Hydrogen peroxide-induced apoptosis-like cell death in Entamoeba histolytica

The microaerophilic intestinal parasitic protozoan Entamoeba histolytica has been previously shown to be highly susceptible to oxidative stress induced by hydrogen peroxide. However the mechanism of cell death was not investigated. Studies presented in this paper demonstrate several morphological features in the parasite when exposed to H₂O₂ which are identical to metazoan apoptotic phenotype indicating a possible apoptosis-like cell death exhibited by E. histolytica in response to H₂O₂ treatment. Trophozoite cell shrinkage, DNA fragmentation, phosphatidyl serine externalization and increased endogenous reactive oxygen species level have been observed in the protozoan parasite when exposed to 2.0 mM H₂O₂ for different time periods. Although the parasite genome is completely devoid of any of the homologues of mammalian caspases it still codes for a huge number of cysteine proteases which may take over the apoptotic function of the caspases. But the present study indicates the existence of a cysteine protease independent programmed cell death in the parasite since E-64 the specific cysteine protease inhibitor could not rescue the cells from H₂O₂ induced apoptosis-like cell death.     

Nanodisc-Incorporated Hemagglutinin Provides Protective Immunity against Influenza Virus Infection

Every year, influenza virus infection causes significant mortality and morbidity in human populations. Although egg-based inactivated viral vaccines are available, their effectiveness depends on the correct prediction of the circulating viral strains and is limited by the time constraint of the manufacturing process. Recombinant subunit vaccines are easier to manufacture with a relatively short lead time but are limited in their efficacy partly because the purified recombinant membrane proteins in the soluble form most likely do not retain their native membrane-bound structure. Nanodisc (ND) particles are soluble, stable, and reproducibly prepared discoid shaped nanoscale structures that contain a discrete lipid bilayer bound by two amphipathic scaffold proteins. Because ND particles permit the functional reconstitution of membrane/envelope proteins, we incorporated recombinant hemagglutinin (HA) from influenza virus strain A/New Caledonia/20/99 (H1N1) into NDs and investigated their potential to elicit an immune response to HA and confer immunity to influenza virus challenge relative to the commercial vaccines Fluzone and FluMist. HA-ND vaccination induced a robust anti-HA antibody response consisting of predominantly the immunoglobulin G1 (IgG1) subclass and a high hemagglutination inhibition titer. Intranasal immunization with HA-ND induced an anti-HA IgA response in nasal passages. HA-ND vaccination conferred protection that was comparable to that of Fluzone and FluMist against challenge with influenza virus strain A/Puerto Rico/8/1934 (H1N1).The influenza A virus-type viral genome encodes 11 proteins including hemagglutinin (HA) and neuraminidase (NA). HA is important in virus transmission and is also a major determinant of host range (16). NA prevents viral aggregation and helps in the release of new viruses from the infected cell (25). These glycoproteins are the principal antigens against which humoral immune responses of the host are directed. Vaccination has been accepted as the most effective method of preventing influenza virus. Current licensed vaccines against influenza virus include conventional inactivated virus vaccine, live-attenuated vaccine, or inactivated “split-virus” vaccines, all grown in embryonated chicken eggs. Influenza virus vaccines may contain residual egg-derived antigens, which is a risk factor for persons with hypersensitivity to eggs. In the case of live-attenuated vaccines that are delivered by the mucosal route, there are several potential safety concerns including the possibility that the vaccine strain could undergo spontaneous genetic change and in a rare case of simultaneous infection with another influenza virus could undergo antigenic shift. These factors are of special concern for children and the elderly, who are the primary populations at risk for influenza virus infection (9). Therefore, there is a continuing need for developing more efficacious and safer vaccines.Apart from licensed vaccines, a number of different vaccine formulations including soluble glycoproteins, virus-like particles, and subunit vaccines (6, 9, 14) with various efficacies have been developed. Recombinant glycoprotein vaccines offer many distinct advantages, including cost, the possibility of adapting them to rapidly changing strains within a short time, and independence from egg-based formulations. In experimental setups, recombinant HA (rHA) and recombinant NA have provided protection against lethal challenge to mice (18, 27). The safety, immunogenicity, and efficacy of trivalent rHA vaccines have been established (26), and a potential trivalent HA vaccine (FluBlok; Protein Sciences Corporation) is currently in phase III clinical trials.Some rHA-based vaccines elicit high titers of anti-HA antibodies. However, these antibodies do not necessarily possess a high capacity for virus neutralization. This apparent discrepancy likely results from the use of soluble HA protein that may not accurately mimic the native structure of the membrane-embedded glycoprotein on the viral envelope for immunization. This could result in a robust antibody response with a limited ability to react with “native epitopes.” This notion is supported by data from previously reported studies that indicated that antigens expressed in their native three-dimensional conformation can elicit a more effective antibody response than proteins in their nonnative forms (19). Therefore, we investigated whether rHA presented in a lipid-bilayer-embedded formulation would elicit a potent neutralizing antibody response.The Nanodisc (ND) system was developed as a novel method for functionally reconstituting membrane proteins into soluble nanoscale lipid bilayers (3, 4, 12, 22). NDs are robust, reproducible, and monodisperse discoidal particles 5.5 nm high and nominally 10 nm in diameter that are formed via a self-assembly process. ND particles contain two copies of an alpha-helical, amphipathic protein, termed membrane scaffold protein (MSP), which encircles a lipid bilayer in a “belt-like” fashion (Fig. ​(Fig.1a).1a). A mixture of phospholipids and MSP are placed in a nonequilibrium solubilized state, for instance, using detergent or high hydrostatic pressure, and the system is then allowed to approach equilibrium by the gentle removal of the perturbant. This initiates a process of self-assembly, wherein the phospholipids and MSP find each other and generate a discoidal phospholipid bilayer encircled by the MSP. The resulting nanostructures represent a highly stable and homogeneous population with an aqueous solubility in the millimolar range (11).Open in a separate windowFIG. 1.Construction of HA-NDs. (a) Schematic showing an ND particle that contains a phospholipid bilayer encircled by membrane scaffold proteins (left) (5) and the same ND particle with an embedded transmembrane protein (right) (17). (b) HA-ND assemblies were first purified by Ni²⁺ affinity chromatography. (Top left) Silver-stained SDS-PAGE showing flowthrough, wash, and elution of HA-ND assembly mix over a Ni-nitrilotriacetic acid column (FT1 and FT2 are flowthrough, and the eluate contains the eluted protein). Arrows show the positions of the 72-kDa HA band and the 25-kDa MSPs. (Top right) Anti-HA Western blotting of the same SDS-PAGE gel. Depending on the quality of purification, a certain fraction of full-length 72-kDa rHA (HA0) can exist as proteolytically cleaved HA1 (∼50-kDa) and HA2 (∼28-kDa) subunits. (Bottom left) Ni²⁺ column eluates were further purified by SEC. Silver-stained SDS-PAGE gel shows size-based fractionation of Ni²⁺ column eluate. The numbers at the bottom correspond to the fractions collected. The MSP amounts are largest at fractions 27 to 30, showing that empty NDs eluted at those fractions. (Bottom right) Anti-HA Western blotting of the same SDS-PAGE gel showing that HA-ND assemblies eluted mainly between fractions 18 and 26. (c) Elution profile of HA-ND following SEC separation. The elution times for protein standards used for calibration are indicated at the top. The control profile for empty NDs is superimposed. HA-ND assemblies have a shorter retention time than empty NDs. inj, injection. (d) HA-ND assemblies from different SEC fractions separate as discrete-sized molecules upon native PAGE separation. Silver staining (left) and anti-HA Western blotting (right) of native PAGE gels from size exclusion fractions show different HA polymers contained in NDs. Earlier fractions are rich in higher-polymeric forms of HA, while later fractions are richer in monomeric HA. Control HA was loaded in the last well to the right in both cases.The value of the ND self-assembly process is that one can simply and reproducibly incorporate membrane proteins into these structures. This is accomplished by including the membrane protein in the initial mixture of MSP, lipid, and detergent prior to the initiation of the self-assembly process. An incorporated membrane protein then finds itself in a native-like environment with stability and activity normally found in vivo. By using phospholipids with different chemical characteristics (charge, degree of unsaturation, and length of acyl chains), the bilayer environment can be optimized to accommodate functional requirements. Furthermore, larger scaffold proteins, which in turn create a larger-diameter particle, can be employed to incorporate multimers or membrane protein complexes. Numerous membrane proteins from the three major classes-integral, tethered, and embedded (including monomers and multimers)-in the lipid bilayer environment created by NDs have been studied (2-5, 8, 10, 13, 20, 23). Since the ND system creates a stable bilayer environment that mimics that encountered by a membrane protein in the cell membrane, membrane proteins display normal folding, native ligand binding kinetics, and intact signaling activity (1, 3, 5, 8, 10, 13, 17, 23).In this study, we successfully incorporated recombinant baculovirus-derived HA into NDs (HA-ND) and compared its efficacy to induce a relevant immune response and confer protection against influenza virus challenge with those of existing licensed vaccines by using a mouse model.     

Multivalent glycomimetics: synthesis of nonavalent mannoside clusters with variation of spacer properties

Oligosaccharide mimetics are important tools in the glycosciences. In this work, we have employed spaced glycodendrons for the synthesis of oligomannoside mimetics. Starting from a number of trivalent, branched molecular wedges, the preparation of nonavalent cluster mannosides was accomplished, which were varied with regard to the chemical characteristics of their spacer moieties and spacer lengths. For ligation of the various trivalent dendrons to the nonavalent target molecules peptide coupling was employed.     

First among equals: competition between genetically identical cells

Competition between genetically identical organisms is considered insignificant in evolutionary theory because it is presumed to have little selective consequence. We argue that competition between genetically identical cells could improve the fitness of a multicellular organism by directing fitter cells to the germ line or by eliminating unfit cells, and that cell-competition mechanisms have been conserved in multicellular organisms. We propose that competition between genetically identical or highly similar units could have similar selective advantages at higher organizational levels, such as societies.