Beta2-microglobulin isoforms display an heterogeneous affinity for type I collagen

It has been claimed that beta2-microglobulin (beta2-m) interacts with type I and type II collagen, and this property has been linked to the tissue specificity of the beta2-m amyloid deposits that target the osteo-articular system. The binding parameters of the interaction between collagen and beta2-m were determined by band shift electrophoresis and surface plasma resonance by using bovine collagen of type I and type II and various isoforms of beta2-m. Wild-type beta2-m binds collagen type I with a Kd of 4.1 x 10(-4) M and type II with 2.3 x 10(-3) M. By the BIAcore system we monitored the binding properties of the conformers of the slow phase of folding of beta2-m. The folding intermediates during the slow phase of folding do not display any significant difference with respect to the binding properties of the fully folded molecule. The affinity of beta2-m truncated at the third N-terminal residue does not differ from that reported for the wild-type protein. Increased affinity for collagen type I is found in the case of N-terminal truncated species lacking of six residues. The Kd of this species is 3.4 x 10 (-5) M at pH 7.4 and its affinity increases to 4.9 x 10(-6) M at pH 6.4. Fluctuations of the affinity caused by beta2-m truncation and pH change can cause modifications of protein concentration in the solvent that surrounds the collagen, and could contribute to generate locally a critical protein concentration able to prime the protein aggregation.     

Stabilization of enzymes in nanoporous materials for biosensor applications

In this study we present the results obtained from efforts to stabilize the inherently unstable m-AChE in nanoporous materials, for the development of biosensors with increased operational stability. Based on existing theoretical models, the entrapment of proteins into relatively small rigid cages drastically increases the stability of these proteins, as this is manifested by their decreased tendency to unfold. The use of two different meso/nanomaterials for the immobilization of the m-AChE shows that there is both a decrease in the leaching of the protein from the biosensor membrane to the test solution, as well as a drastic increase in the operational stability of the resulting biosensor.     

Down-regulation of p53 by double-stranded RNA modulates the antiviral response

p53 has been well characterized as a tumor suppressor gene, but its role in antiviral defense remains unclear. A recent report has demonstrated that p53 can be induced by interferons and is activated after vesicular stomatitis virus (VSV) infection. We observed that different nononcogenic viruses, including encephalomyocarditis virus (EMCV) and human parainfluenza virus type 3 (HPIV3), induced down-regulation of p53 in infected cells. Double-stranded RNA (dsRNA) and a mutant vaccinia virus lacking the dsRNA binding protein E3L can also induce this effect, indicating that dsRNA formed during viral infection is likely the trigger for down-regulation of p53. The mechanism of down-regulation of p53 by dsRNA relies on translation inhibition mediated by the PKR and RNase L pathways. In the absence of p53, the replication of both EMCV and HPIV3 was retarded, whereas, conversely, VSV replication was enhanced. Cell cycle analysis indicated that wild-type (WT) but not p53 knockout (KO) fibroblasts undergo an early-G(1) arrest following dsRNA treatment. Moreover, in WT cells the onset of dsRNA-induced apoptosis begins after p53 levels are down-regulated, whereas p53 KO cells, which lack the early-G(1) arrest, rapidly undergo apoptosis. Hence, our data suggest that the down-regulation of p53 facilitates apoptosis, thereby limiting viral replication.     

Testing for adaptive evolution of the female reproductive protein ZPC in mammals,birds and fishes reveals problems with the M7-M8 likelihood ratio test

Background  

Adaptive evolution appears to be a common feature of reproductive proteins across a very wide range of organisms. A promising way of addressing the evolutionary forces responsible for this general phenomenon is to test for adaptive evolution in the same gene but among groups of species, which differ in their reproductive biology. One can then test evolutionary hypotheses by asking whether the variation in adaptive evolution is consistent with the variation in reproductive biology. We have attempted to apply this approach to the study of a female reproductive protein, zona pellucida C (ZPC), which has been previously shown by the use of likelihood ratio tests (LRTs) to be under positive selection in mammals.     

Automated prescan function for scanning fluorescently stained 2D-PAGE gels

To automate the acquisition of images from fluorescently stained gels, the power of the excitation laser(s) must be optimized for each sample to prevent spot saturation (or to allow unimportant spots to saturate) yet still retaining sensitivity. In this work, we describe the implementation and effectiveness of a pre-scan function in a robotic solution for the automation of 2D gel scanning.     

Adaptive energetics in house mice, Mus musculus domesticus, from the island of Porto Santo (Madeira archipelago, North Atlantic)

The bioenergetic strategies of house mice (Mus musculus domesticus) from the island of Porto Santo were investigated and compared with those of mice from mainland Portugal. Energy obtained from food ingestion was 18.2% lower in Porto Santo mice than in mainland mice (1.53 vs. 1.87 kJ/g/day). The same pattern was observed for metabolisable energy intake, which was 19.2% lower in island specimens (0.87 vs. 1.08 kJ/g/day for mainland specimens). Apparent digestibility was similar in both groups of mice. Basal metabolic rate (BMR) of Porto Santo individuals was low (1.16 ml O(2)/g/h), representing only 56% of the predicted value, based on body mass, while mainland individuals exhibited a BMR closer to the expected value, corresponding to 87% of the predicted value (1.80 ml O(2)/g/h). Thermoregulatory abilities within the range of 10-28 degrees C ambient temperature did not differ between island and mainland mice. Results suggest an adaptation of Porto Santo mice to the environmental aridity of the island of Porto Santo, leading to a conservative energetic strategy.     

The role of polyadenylation signal secondary structures on the resistance of plasmid vectors to nucleases

BACKGROUND: Nuclease degradation of plasmid DNA (pDNA) vectors after delivery and during trafficking to the nucleus is a barrier to gene expression. This barrier may be circumvented by shielding the pDNA from the nuclease-rich cell environment with adjuvants or by using nuclease inhibitors. A different alternative that is explored in this work is to make pDNA vectors more nuclease-resistant a priori. METHODS AND RESULTS: The hypothesis that a significant part of nuclease attack is directed towards certain labile sequences in a pDNA model (pVAX1/lacZ) was first tested. Homopurine-rich tracts in the bovine growth hormone polyadenylation signal (BGH poly A) were identified as labile sequences using S1 nuclease as a probe. Two pDNA variants were then created by replacing the BGH poly A region with the SV40 or a synthetic poly A signal. A study of plasmid degradation in eukaryotic cell lysates and mice plasma showed that the half-life of the supercoiled isoforms of the new vectors was always higher when compared with the control plasmid. An in vitro assay of the reporter beta-galactosidase in transfected CHO cells further showed that gene expression with the new pDNA variants was not affected negatively by the plasmid modifications. CONCLUSIONS: The replacement of labile sequences in plasmid DNA vectors improves resistance towards nuclease attack as shown by the increased half-lives of supercoiled plasmid isoforms incubated with endo/lysosomal, cytoplasmatic and blood plasma enzymes.     

Ascorbate potentiates the cytotoxicity of menadione leading to an oxidative stress that kills cancer cells by a non-apoptotic caspase-3 independent form of cell death

Hepatocarcinoma cells (TLT) were incubated in the presence of ascorbate and menadione, either alone or in combination. Cell death was only observed when such compounds were added simultaneously, most probably due to hydrogen peroxide (H2O2) generated by ascorbate-driven menadione redox cycling. TLT cells were particularly sensitive to such an oxidative stress due to its poor antioxidant status. DNA strand breaks were induced by this association but this process did not correspond to oligosomal DNA fragmentation (a hallmark of cell death by apoptosis). Neither caspase-3-like DEVDase activity, nor processing of procaspase-3 and cleavage of poly(ADP-ribose) polymerase (PARP) were observed in the presence of ascorbate and menadione. Cell death induced by such an association was actively dependent on protein phosphorylation since it was totally prevented by preincubating cells with sodium orthovanadate, a tyrosine phosphatase inhibitor. Finally, while H2O2, when administered as a bolus, strongly enhances a constitutive basal NF-kappaB activity in TLT cells, their incubation in the presence of ascorbate and menadione results in a total abolition of such a constitutive activity.     

Determination of alpha-bisabolol in human blood by micro-HPLC-ion trap MS and head space-GC-MS methods

Alpha-bisabolol is a compound present in some essential oils, widely distributed in several plants, including camomile. Two different methods for analysing an essential oil, such as alpha-bisabolol in human blood are reported: the first uses micro-liquid chromatography-electrospray ionisation-mass spectrometry (muHPLC-ESI-MS), whereas the second is based on "head space" injection coupled to gas chromatography-mass spectrometry (HS-GC-MS). For LC-ESI-MS, human blood samples, spiked with alpha-bisabolol, were extracted with hexane and evaporated to dryness under air stream. The residue was then reconstituted with methanol and injected into a C18 column, connected to an ion trap mass spectrometer equipped with an ESI source. Spectra were recorded in the positive ion, selected ion monitoring mode. The detection limit of alpha-bisabolol in blood was 0.125 micromol/l. The preparation of samples for the analysis in HS-GC-MS was limited to blood dilution with water (0.5 ml blood + 1 ml water). Head space vials were heated at 125 degrees C for 1 h before automatic injection. The HS-GC-MS detection limit (0.13 micromol/l) was similar to that achieved with the muHPLC-ESI-MS method. Successful tests were performed to verify if alpha-bisabolol could be directly measured by the HS-GC-MS method in different biological samples (blood, urine, faeces, homogenate tissues) from rats treated with the camomile essential oil.     

Microcolinearity between a 2-cM region encompassing the grain protein content locus<Emphasis Type="Italic"> Gpc-6B1</Emphasis> on wheat chromosome 6B and a 350-kb region on rice chromosome 2

The conservation of the linear order (colinearity) of genetic markers along large chromosome segments in wheat and rice is well established, but less is known about the microcolinearity between both genomes at subcentimorgan distances. In this study we focused on the microcolinearity between a 2.6-cM interval flanked by markers Xcdo365 and Xucw65 on wheat chromosome 6B and rice chromosome 2. A previous study has shown that this wheat segment includes the Gpc-6B1 locus, which is responsible for large differences in grain protein content (GPC) and is the target of a positional cloning effort in our laboratories. Twenty-one recombination events between Xcdo365 and Xucw65 were found in a large segregating population (935 gametes) and used to map 17 genes selected from rice chromosome 2 in the wheat genetic map. We found a high level of colinearity between a 2.1-cM region flanked by loci Xucw75 and Xucw67 on wheat chromosome 6B and a 350-kb uninterrupted sequenced region in rice chromosome arm 2S. Colinearity between these two genomes was extended to the region proximal to Xucw67 (eight colinear RFLP markers), but was interrupted distal to Xucw75 (six non-colinear RFLP markers). Analysis of different comparative studies between rice and wheat suggests that microcolinearity is more frequently disrupted in the distal region of the wheat chromosomes. Fortunately, the region encompassing the Gpc-6B1 locus showed an excellent conservation between the two genomes, facilitating the saturation of the target region of the wheat genetic map with molecular markers. These markers were used to map the Gpc-6B1 locus into a 0.3-cM interval flanked by PCR markers Xucw79 and Xucw71, and to identify five candidate genes within the colinear 64-kb region in rice.