GFAP and antibodies against NMDA receptor subunit NR2 as biomarkers for acute cerebrovascular diseases

We studied whether the serum levels of glial fibrillary acidic protein (GFAP) and of antibodies against the N‐methyl‐d ‐aspartate receptor subunit NR2 (NR2 R_NMDA) can discriminate between intracerebral haemorrhage (ICH) and ischaemic stroke (IS) in stroke patients. We prospectively recruited patients with suspected stroke (72 confirmed) and 52 healthy controls. The type of brain lesion (ICH or IS) was established using brain imaging. The levels of GFAP and of antibodies against NR2 R_NMDA were measured in blood samples obtained within 12 hrs after stroke onset and 24, 48 and 72 hrs and 1 and 2 weeks later using ELISA immunoassay. Improvement in diagnostic performance was assessed in logistic regression models designed to predict the diagnosis and the type of stroke. GFAP peaks early during haemorrhagic brain lesions (at significantly higher levels), and late in ischaemic events, whereas antibodies against NR2 R_NMDA have significantly higher levels during IS at all time‐points. Neither of the two biomarkers used on its own could sufficiently discriminate patients, but when they are used in combination they can differentiate at 12 hrs after stroke, between ischaemic and haemorrhagic stroke with a sensitivity and specificity of 94% and 91%, respectively.     

Seroprevalence of Neospora caninum infection on dairy cattle in farms from southern Romania

Neospora caninum, a coccidian parasite closely related to Toxoplasma gondii, is one of the major causes of abortion in cattle worldwide. Conventional serological techniques, such as the indirect fluorescent antibody test and enzyme-linked immunosorbent assay (ELISA), are routinely used in adult animals and aborted fetuses for the detection of anti- N. caninum antibodies. In Romania, infection with N. caninum in cattle has been reported recently, but only in limited areas from the north and central parts of the country. Therefore, the aim of this study was to obtain additional seroepidemiological data on infection with N. caninum on dairy farms from the south of Romania. A total of 258 blood samples was analyzed from 230 dairy cows and 28 calves from 9 dairy farms in southern Romania; the presence of specific IgG antibodies against N. caninum was determined using an indirect ELISA test. The average seroprevalence was 40.3%, but the within-herd prevalence ranged between 11.5 and 80.0%; the seroprevalence in dairy cows was 41.7%, while in calves it was 28.6%. Of the positive samples, 74.0% (77/104) had a high positive reaction (S/P ratio more than 1.0), while 26.0% (27/104) had a low positive reaction (S/P ratio between 0.5 and 1.0). This study indicates that N. caninum infection is widespread in the south of Romania, which could explain the causes of abortions registered in some herds in the studied area. However, a serological screening across the country is planned in order to assess the actual national prevalence of N. caninum infection, followed by implementation of a prevention and control program.     

A rivet model for channel formation by aerolysin-like pore-forming toxins

The bacterial toxin aerolysin kills cells by forming heptameric channels, of unknown structure, in the plasma membrane. Using disulfide trapping and cysteine scanning mutagenesis coupled to thiol-specific labeling on lipid bilayers, we identify a loop that lines the channel. This loop has an alternating pattern of charged and uncharged residues, suggesting that the transmembrane region has a beta-barrel configuration, as observed for Staphylococcal alpha-toxin. Surprisingly, we found that the turn of the beta-hairpin is composed of a stretch of five hydrophobic residues. We show that this hydrophobic turn drives membrane insertion of the developing channel and propose that, once the lipid bilayer has been crossed, it folds back parallel to the plane of the membrane in a rivet-like fashion. This rivet-like conformation was modeled and sequence alignments suggest that such channel riveting may operate for many other pore-forming toxins.     

Altering FVE/MSI4 results in a substantial increase of biomass in Arabidopsis—the functional analysis of an ontogenesis accelerator

FVE/MSI4, a highly conserved gene through evolution, is considered a classical flowering time gene from the autonomous pathway in Arabidopsis thaliana. Our work provides complementary, yet distinct, evidence that mutations in FVE/MSI4 have highly pleiotropic effects on plant architecture and organ production and growth, indicating an overall role in reprogramming the genome. First, this is illustrated by the fact that fve mutants and transgenic versions of the gene show no morphological aberrations while living, on average, twice as long and producing more biomass and seeds than the wild type. For example, depending on the photoperiod, the vegetative biomass in the mutants is increased three- to eightfold. FVE/MSI4 can therefore be considered a multifactor component of biomass and yield. Second, the gene functions primarily at the shoot apical meristem, acting to calibrate its overall cell proliferation activity and organ initiation. At the same time, FVE/MSI4 regulates cell growth during organ formation mainly by modulating the timing of proliferation—differentiation transition and that of endoreduplication. FVE/MSI4 is an accelerator of ontogenesis. The function of the gene is to scale-down meristem activities, while accelerating developmental transitions and cellular differentiation. Genes of the kind are ideal tools in biotech for engineering biomass and yield according to geographical or climate constraints. The results enhance our understanding on the role epigenetic components of the genome, such as FVE/MSI4, play in adaptation and biomass calibration. They also illustrate the kind of functional characterization biotech applications might require during the first steps of product development. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Microscopic Basis for the Mesoscopic Extensibility of Dendrimer-Compacted DNA

The mechanism of DNA compaction by dendrimers is key to the design of nanotechnologies that can deliver genetic material into cells. We present atomistic simulations, mesoscopic modeling and single-molecule pulling experiments describing DNA dendrimer interactions. All-atom molecular dynamics were used to characterize pulling-force-dependent interactions between DNA and generation-3 PAMAM amine-terminated dendrimers, and a free energy profile and mean forces along the interaction coordinate are calculated. The energy, force, and geometry parameters computed at the atomic level are input for a Monte Carlo model yielding mesoscopic force-extension curves. Actual experimental single-molecule curves obtained with optical tweezers are also presented, and they show remarkable agreement with the virtual curves from our model. The calculations reveal the microscopic origin of the hysteresis observed in the phase transition underlying compaction. A broad range of ionic and pulling parameters is sampled, and suggestions for windows of conditions to probe new single-molecule behavior are made.     

Pathway alterations during glioma progression revealed by reverse phase protein lysate arrays

The progression of gliomas has been extensively studied at the genomic level using cDNA microarrays. However, systematic examinations at the protein translational and post-translational levels are far more limited. We constructed a glioma protein lysate array from 82 different primary glioma tissues, and surveyed the expression and phosphorylation of 46 different proteins involved in signaling pathways of cell proliferation, cell survival, apoptosis, angiogenesis, and cell invasion. An analysis algorithm was employed to robustly estimate the protein expressions in these samples. When ranked by their discriminating power to separate 37 glioblastomas (high-grade gliomas) from 45 lower-grade gliomas, the following 12 proteins were identified as the most powerful discriminators: IBalpha, EGFRpTyr845, AKTpThr308, phosphatidylinositol 3-kinase (PI3K), BadpSer136, insulin-like growth factor binding protein (IGFBP) 2, IGFBP5, matrix metalloproteinase 9 (MMP9), vascular endothelial growth factor (VEGF), phosphorylated retinoblastoma protein (pRB), Bcl-2, and c-Abl. Clustering analysis showed a close link between PI3K and AKTpThr308, IGFBP5 and IGFBP2, and IBalpha and EGFRpTyr845. Another cluster includes MMP9, Bcl-2, VEGF, and pRB. These clustering patterns may suggest functional relationships, which warrant further investigation. The marked association of phosphorylation of AKT at Thr308, but not Ser473, with glioblastoma suggests a specific event of PI3K pathway activation in glioma progression.     

Dependence of DNA polymerase replication rate on external forces: a model based on molecular dynamics simulations

Molecular dynamics simulations are presented for a Thermus aquaticus (Taq) DNA polymerase I complex (consisting of the protein, the primer-template DNA strands, and the incoming nucleotide) subjected to external forces. The results obtained with a force applied to the DNA template strand provide insights into the effect of the tension on the activity of the enzyme. At forces below 30 pN a local model based on the parameters determined from the simulations, including the restricted motion of the DNA bases at the active site, yields a replication rate dependence on force in agreement with experiment. Simulations above 40 pN reveal large conformational changes in the enzyme-bound DNA that may have a role in the force-induced exonucleolysis observed experimentally.     

Domain organization and structure-function relationship of the HET-s prion protein of Podospora anserina

The [Het-s] infectious element of the fungus Podospora anserina is a prion protein involved in a genetically controlled cell death reaction termed heterokaryon incompatibility. Previous analyses indicate that [Het-s] propagates as a self-perpetuating amyloid aggregate. The HET-s protein is 289 amino acids in length. Herein, we identify the region of the HET-s protein that is responsible for amyloid formation and prion propagation. The region of HET-s spanning residues 218-289 forms amyloid fibers in vitro and allows prion propagation in vivo. Conversely, a C-terminal deletion in HET-s prevents amyloid aggregation in vitro and prion propagation in vivo, and abolishes the incompatibility function. In the soluble form of HET-s, the region from residue 1 to 227 forms a well-folded domain while the C-terminal region is highly flexible. Together, our data establish a domain structure-function relationship for HET-s amyloid formation, prion propagation and incompatibility activity.     

In situ non-invasive spectral discrimination between bone cell phenotypes used in tissue engineering

Raman micro-spectroscopy was used to discriminate between different types of bone cells commonly used in tissue engineering of bone, with the aim of developing a method of phenotypic identification and classification. Three types of bone cells were analysed: human primary osteoblasts (HOB), retroviral transfected human alveolar bone cells with SV40 large T antigen (SV40 AB), and osteoblast-like human osteosarcoma derived MG63 cell line. Unsupervised principal component analysis (PCA) and linear discriminant analysis (LDA) of the Raman spectra succeeded in discriminating the osteosarcoma derived MG63 cells from the non-tumour cells (HOB and SV40 AB). No significant differences were observed between the Raman spectra of the HOB and SV40 AB cells, confirming the biochemical similarities between the two cell types. Difference spectra between tumour and non-tumour cells suggested that the spectral discrimination is based on the fact that MG63 osteosarcoma derived cells are characterised by lower concentrations of nucleic acids and higher relative concentrations of proteins compared to the non-tumour bone cells. A supervised classification model (LDA) was built and showed high cross-validation sensitivity (100%) and specificity (95%) for discriminating the MG63 cells and the non-tumour cells, with 96% of the cells being correctly classified either as tumour or non-tumour derived cells. This study proves the feasibility of using Raman spectroscopy to identify in situ phenotypic differences in living cells.