One-step refolding and purification of disulfide-containing proteins with a C-terminal MESNA thioester

Background  

Expression systems based on self-cleavable intein domains allow the generation of recombinant proteins with a C-terminal thioester. This uniquely reactive C-terminus can be used in native chemical ligation reactions to introduce synthetic groups or to immobilize proteins on surfaces and nanoparticles. Unfortunately, common refolding procedures for recombinant proteins that contain disulfide bonds do not preserve the thioester functionality and therefore novel refolding procedures need to be developed.     

Integrating gene expression and GO classification for PCA by preclustering

Background  

Gene expression data can be analyzed by summarizing groups of individual gene expression profiles based on GO annotation information. The mean expression profile per group can then be used to identify interesting GO categories in relation to the experimental settings. However, the expression profiles present in GO classes are often heterogeneous, i.e., there are several different expression profiles within one class. As a result, important experimental findings can be obscured because the summarizing profile does not seem to be of interest. We propose to tackle this problem by finding homogeneous subclasses within GO categories: preclustering.     

Pneumocystis carinii enhances soluble mannose receptor production by macrophages

Phagocytosis of extracellular organisms in the alveolar spaces of the lungs represents the first-line of host defense against pulmonary pathogens. Disruption of this process is likely to interfere with the generation of appropriate specific immune responses, and lead to a delayed or inefficient clearance of the pathogen. Pneumocystis carinii, an opportunistic pathogen in immunodeficient individuals, is cleared from the lung by alveolar macrophages. In the absence of specific anti-Pneumocystis antibodies, phagocytosis is dependent on the non-opsonic macrophage mannose receptor (MR). Recent studies have demonstrated that alveolar macrophage MR activity is downregulated in individuals infected with HIV, and that functional MR is shed from the macrophage cell surface. Here we report that P. carinii enhances the formation of soluble MR by macrophages in vitro. Soluble MR was detected in cell-free alveolar fluid from humans infected with HIV and/or P. carinii, but not in alveolar fluid from healthy controls. Soluble MR was found in association with extracellular clumps of P. carinii in the lungs of mice with P. carinii pneumonia, and was associated with P. carinii organisms purified from these mice. When purified P. carinii organisms were incubated with soluble MR-containing supernatants, they were phagocytosed less readily by alveolar macrophages than were control organisms. Our results suggest that P. carinii organisms enhance the shedding of MR from the surface of alveolar macrophages, and that the resultant soluble MR binds to intra-alveolar organisms, thereby interfering with their non-opsonic uptake via the macrophage cell surface MR.     

Genetic dissection of Al tolerance QTLs in the maize genome by high density SNP scan

Background

Aluminum (Al) toxicity is an important limitation to food security in tropical and subtropical regions. High Al saturation on acid soils limits root development, reducing water and nutrient uptake. In addition to naturally occurring acid soils, agricultural practices may decrease soil pH, leading to yield losses due to Al toxicity. Elucidating the genetic and molecular mechanisms underlying maize Al tolerance is expected to accelerate the development of Al-tolerant cultivars.

Results

Five genomic regions were significantly associated with Al tolerance, using 54,455 SNP markers in a recombinant inbred line population derived from Cateto Al237. Candidate genes co-localized with Al tolerance QTLs were further investigated. Near-isogenic lines (NILs) developed for ZmMATE2 were as Al-sensitive as the recurrent line, indicating that this candidate gene was not responsible for the Al tolerance QTL on chromosome 5, qALT5. However, ZmNrat1, a maize homolog to OsNrat1, which encodes an Al³⁺ specific transporter previously implicated in rice Al tolerance, was mapped at ~40 Mbp from qALT5. We demonstrate for the first time that ZmNrat1 is preferentially expressed in maize root tips and is up-regulated by Al, similarly to OsNrat1 in rice, suggesting a role of this gene in maize Al tolerance. The strongest-effect QTL was mapped on chromosome 6 (qALT6), within a 0.5 Mbp region where three copies of the Al tolerance gene, ZmMATE1, were found in tandem configuration. qALT6 was shown to increase Al tolerance in maize; the qALT6-NILs carrying three copies of ZmMATE1 exhibited a two-fold increase in Al tolerance, and higher expression of ZmMATE1 compared to the Al sensitive recurrent parent. Interestingly, a new source of Al tolerance via ZmMATE1 was identified in a Brazilian elite line that showed high expression of ZmMATE1 but carries a single copy of ZmMATE1.

Conclusions

High ZmMATE1 expression, controlled either by three copies of the target gene or by an unknown molecular mechanism, is responsible for Al tolerance mediated by qALT6. As Al tolerant alleles at qALT6 are rare in maize, marker-assisted introgression of this QTL is an important strategy to improve maize adaptation to acid soils worldwide.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-153) contains supplementary material, which is available to authorized users.     

Mechanisms of monoclonal antibody-mediated protection against virulent Semliki Forest virus.

Both neutralizing and nonneutralizing immunoglobulin G2a monoclonal antibodies (MAs) directed against the E2 glycoprotein of Semliki Forest virus (SFV) protected mice prophylactically and therapeutically against virulent SFV infection. The neutralizing MAs, however, conferred protection to mice at lower doses than did nonneutralizing MAs. The antibody-dependent, complement-mediated cytolysis of SFV-infected L cells was effectuated by both kinds of antibodies, but again neutralizing MAs were more effective. Removal of the Fc part of the neutralizing MA UM 5.1 by pepsin digestion resulted in a 100-fold reduction of the neutralization titer (10(4) versus 10(6)) and a complete loss of its capacity to mediate antibody-dependent, complement-mediated cytolysis. Passive protection of infected mice occurred only after administration of relatively high doses of F(ab')2 of MA UM 5.1 (30.0 micrograms versus 0.1 microgram). F(ab')2 fragments prepared from the nonneutralizing MA UM 4.2 had lost their protective capacity completely. Surprisingly, the nonneutralizing MA UM 4.2 retarded virus growth in mouse fibroblasts (L cells), although inhibition was at much higher doses than with the neutralizing MA UM 5.1. Furthermore, both MAs promoted the uptake of virulent SFV in the Fc receptor-bearing WEHI-3 cells. The results suggest that nonneutralizing MAs protect mice not only by antibody-dependent, complement-mediated cytolysis but also by growth inhibition and enhanced uptake of SFV in the nonpermissive macrophages of BALB/c mice. This hypothesis is supported by the absence of viremia in recipients of nonneutralizing MA UM 4.2 at 24 h after infection.     

The effect of pyrethroid lambdacyhalothrin applications on the spatial distribution of phytophagous and predatory mites in apple orchards

The spatial distribution of three phytophagous mites,Panonychus ulmi (Koch),Tetranychus urticae Koch andAculus schlechtendali (Nalepa), and two predacious mites,Zetzellia mali (Ewing) andAmblyseius fallacis (Garman), and the effect of pyrethroid lambdacyhalothrin applications on mite spatial dispersion were investigated over a 3-year period in an apple orchard in Ontario. The index of dispersion and the slope of Taylor's power law were used to evaluate dispersion patterns of mites. Panonychus ulmi showed that between-tree spatial variation decreased with an increase of population densities, whereas between-leaf variation increased with population densities. With all other four species it appeared that between-tree variation is much greater than between-leaf variation at all field population density levels. The values ofb by Taylor's power law suggested that all five species of mites are aggregated, but that in generalP. ulmi andT. urticae (b=1.427–1.872) are more aggregated than their predators (b=1.254–1.393). Taylor's regression technique suggests that pyrethroid applications causedP. ulmi, T. urticae, Z. mali andA. fallacis to be less aggregated whileA. schlechtendali was more aggregated. The impact of changes in mite spatial distribution following pyrethroid applications on sampling plans is discussed.     

Desulforhabdus amnigenus gen. nov. sp. nov., a sulfate reducer isolated from anaerobic granular sludge

From granular sludge of an upflow anaerobic sludge bed (UASB) reactor treating paper-mill wastewater, a sulfate-reducing bacterium (strain ASRB1) was isolated with acetate as sole carbon and energy source. The bacterium was rod-shaped, (1.4–1.9×2.5–3.4 μm), nonmotile, and gram-negative. Optimum growth with acetate occurred around 37°C in freshwater medium (doubling time: 3.5–5.0 days). The bacterium grew on a range of organic acids, such as acetate, propionate, and butyrate, and on alcohols, and grew autotrophically with H₂, CO₂ and sulfate. Fastest growth occurred with formate, propionate, and ethanol (doubling time: approx. 1.5 days). Strain ASRB1 clusters with the delta subdivision of Proteobacteria and is closely related toSyntrophobacter wolinii a syntrophic propionate oxidizer. Strain ASRB1 was characterized as a new genus and species:Desulforhabdus amnigenus.     

Glycoprotein H of herpes simplex virus type 1 requires glycoprotein L for transport to the surfaces of insect cells.

In mammalian cells, formation of heterooligomers consisting of the glycoproteins H and L (gH and gL) of herpes simplex virus type 1 is essential for the cell-to-cell spread of virions and for the penetration of virions into cells. We examined whether formation of gH1/gL1 heterooligomers and cell surface expression of the complex occurs in insect cells. Three recombinant baculoviruses, expressing gL1, gH1, and truncated gH1 (gH1t), which lacks the transmembrane region, were constructed. It was shown that recombinant gH1/gL1 and gH1t/gL1 heterooligomers were produced in insect cells. As in mammalian cells, gH1 and gH1t were not detected on the surfaces of insect cells in the absence of gL1. When coexpressed with gL1, recombinant gH1 was displayed on the surfaces of insect cells. Coexpression of gH1t and gL1 resulted in secretion of the gH1t/gL1 complex into the cell culture medium, indicating that gH1t is also transported to the surfaces of insect cells. Our results indicate that the process of folding and intracellular transport of gH1 and gL1 is comparable in insect cells and mammalian cells and that the baculovirus expression system can be used to examine the complex formation and the intracellular transport of gH1 and gL1. The availability of secreted gH1t/gL1 complex offers the opportunity to further investigate the immunological properties of this complex.