Covering with Ellipses

We address the problem of how to cover a set of required points by a small number of axis-parallel ellipses that avoid a second set of forbidden points. We study geometric properties of such covers and present an efficient randomized approximation algorithm for the cover construction. This question is motivated by a special pattern recognition task where one has to identify ellipse-shaped protein spots in two-dimensional electrophoresis images.     

Peptide biomarkers as a way to determine meat authenticity

Meat fraud implies many illegal procedures affecting the composition of meat and meat products, something that is commonly done with the aim to increase profit. These practices need to be controlled by legal authorities by means of robust, accurate and sensitive methodologies capable to assure that fraudulent or accidental mislabelling does not arise. Common strategies traditionally used to assess meat authenticity have been based on methods such as chemometric analysis of a large set of data analysis, immunoassays or DNA analysis. The identification of peptide biomarkers specific of a particular meat species, tissue or ingredient by proteomic technologies constitutes an interesting and promising alternative to existing methodologies due to its high discriminating power, robustness and sensitivity. The possibility to develop standardized protein extraction protocols, together with the considerably higher resistance of peptide sequences to food processing as compared to DNA sequences, would overcome some of the limitations currently existing for quantitative determinations of highly processed food samples. The use of routine mass spectrometry equipment would make the technology suitable for control laboratories.     

Proteome changes in the insoluble protein fraction of bovine Longissimus dorsi muscle as a result of low-voltage electrical stimulation

Changes induced by low-voltage electrical stimulation (ES; 0-95 V for 8 s; 95 V for 32 s) in the insoluble protein fraction of bovine longissimus dorsi (LD) muscle at 1 and 24h post-ES were investigated by proteomics. Protein abundance patterns from ten Norwegian Red (NRF) young bulls were compared, and significant changes due to ES were found by rotation test and partial least square (PLS) regression analyses. Five protein spots showed lower abundance in ES samples at both sampling times, and in addition, 10 proteins at 1 h post-ES and 13 proteins at 24 h post-ES changed significantly in abundance due to ES. Reduced abundance of full-length structural proteins in ES samples indicates an accelerated proteolysis due to ES. Moreover, increased abundance of small heat shock proteins indicates earlier initiation of stress responses due to ES. These findings provide a better understanding of the biochemical processes taking place as a result of ES during post mortem storage of meat.     

Early post-mortem sarcoplasmic proteome of porcine muscle related to lipid oxidation in aged and cooked meat

In order to identify specific markers of lipid oxidation generated in meat during refrigerated storage and cooking an analysis was conducted to investigate the relationships between the early post-mortem sarcoplasmic proteome, which contains the majority of enzymes involved in the oxidative process, and the level of lipid oxidation. This study was performed in Longissimus lumborum pig muscle. Proteome was analysed by 2-D electrophoresis in combination with liquid chromatography–tandem mass spectrometry (LC–MS/MS) and lipid oxidation was estimated by the TBA reactive substances (TBA-RS) measurement. Many markers of lipid oxidation were identified, but no single marker covered the oxidative process in its entirety. The role of five protein groups (albumin, redoxins, annexins, lipid transporters and enzymes of aerobic respiration), from which a link with lipid oxidation can be established, is discussed. This study, which completes a precedent work focused on protein oxidation, clearly demonstrates that a combination of several markers is needed to assess the sensitivity of meat to oxidation during both ageing and cooking.     

Early post-mortem sarcoplasmic proteome of porcine muscle related to protein oxidation

Oxidative deterioration or modifications of proteins which appear during meat storage and processes can result in the impairment of technological, sensorial and nutritional qualities. Improving the quality involves a better understanding of the biochemical mechanisms responsible for protein oxidation in meat. For that purpose, an analysis was conducted to investigate the relationships between the early post-mortem sarcoplasmic proteome, which contains the majority of enzymes involved in the oxidative process, and protein oxidation generated during meat storage and cooking. This study was performed in Longissimus lumborum pig muscle. In order to have sufficient variability in the proteome and in the meat oxidation level, five groups of 10 animals issued from two different breeds and raised in three different rearing systems were analysed. Protein oxidation was estimated by the measurement of carbonyl groups after 1 and 4 days of refrigerated storage, and after 100 °C experimental cooking of the 4 days aged meat. Significant correlations (p < 0.05) were observed between the level of carbonyl groups and the intensities of 104 spots of the 2D electrophoresis, out of which 52 were clearly identified. The possible involvement of some proteins in the muscle oxidative stress leading to protein oxidation is discussed.     

Proteomic analysis of the gene DR1709 mutant in Deinococcus radiodurans

DR1709 is a predicted Mn~(2+) transporter in Deinococcus radiodurans(D.radiodurans). The mensuration method to evaluate protein viability with two-dimensional electrophoresis in D.radiodurans and the mutants was established in this study. The results showed that after DR1709 was disrupted, the expressions of DR1120(acetokinase), DR1691 (heat shock protein), DR1485 (putative lipase), DR2095 (putative c-type cytochrome) and other three hypothetical proteins (DR0124, DR0047 and DR2474) were repressed. However the expression of DR1794 (putative nosX) was induced. Phenomena above suggested that the increased radiation-sensitivity of the mutant cells may be attributed to not only the protection of gene DR1709, but also the proteins' different expressions between the wild type and the mutant might also play important roles in protecting D.radiodurans from irradiation.Although DR2095 was a homologue of c-type cytochrome, it has no realitic functions.     

Proteomic analysis of processing by-products from canned and fresh tuna: Identification of potentially functional food proteins

Proteomic approaches have been used to identify the main proteins present in processing by-products generated by the canning tuna-industry, as well as in by-products derived from filleting of skeletal red muscle of fresh tuna. Following fractionation by using an ammonium sulphate precipitation method, three proteins (tropomyosin, haemoglobin and the stress-shock protein ubiquitin) were identified in the highly heterogeneous and heat-treated material discarded by the canning-industry. Additionally, this fractionation method was successful to obtain tropomyosin of high purity from the heterogeneous starting material. By-products from skeletal red muscle of fresh tuna were efficiently fractionated to sarcoplasmic and myofibrillar fractions, prior to the identification based mainly on the combined searching of the peptide mass fingerprint (MALDI–TOF) and peptide fragment fingerprinting (MALDI LIFT-TOF/TOF) spectra of fifteen bands separated by 1D SDS–PAGE. Thus, the sarcoplasmic fraction contained myoglobin and several enzymes that are essential for efficient energy production, whereas the myofibrillar fraction had important contractile proteins, such as actin, tropomyosin, myosin or an isoform of the enzyme creatine kinase. Application of proteomic technologies has revealed new knowledge on the composition of important by-products from tuna species, enabling a better evaluation of their potential applications.     

Analysis of mass spectrometry data of cerebral stroke samples: an evolutionary computation approach to resolve and quantify peptide peaks

A preliminary investigation of cerebral stroke samples injected into a mass spectrometer is performed from an evolutionary computation perspective. The detection and resolution of peptide peaks is pursued for the purpose of automatically and accurately determining unlabeled peptide quantities. A theoretical peptide peak model is proposed and a series of experiments are then pursued (most within a distributed computing environment) along with a data preprocessing strategy that includes (i) a deisotoping step followed by (ii) a peak picking procedure, followed by (iii) a series of evolutionary computation experiments oriented towards the investigation of their capability for achieving the aforementioned goal. Results from four different genetic algorithms (GA) and one differential evolution (DE) algorithm are reported with respect to their ability to find solutions that fit within the framework of the presented theoretical peptide peak model. Both unconstrained and constrained (as determined by a course grained preprocessing stage) solution space experiments are performed for both types of evolutionary algorithms. Good preliminary results are obtained.