jmzIdentML API: A Java interface to the mzIdentML standard for peptide and protein identification data

We present a Java application programming interface (API), jmzIdentML, for the Human Proteome Organisation (HUPO) Proteomics Standards Initiative (PSI) mzIdentML standard for peptide and protein identification data. The API combines the power of Java Architecture of XML Binding (JAXB) and an XPath-based random-access indexer to allow a fast and efficient mapping of extensible markup language (XML) elements to Java objects. The internal references in the mzIdentML files are resolved in an on-demand manner, where the whole file is accessed as a random-access swap file, and only the relevant piece of XMLis selected for mapping to its corresponding Java object. The APIis highly efficient in its memory usage and can handle files of arbitrary sizes. The APIfollows the official release of the mzIdentML (version 1.1) specifications and is available in the public domain under a permissive licence at http://www.code.google.com/p/jmzidentml/.     

Agricultural practices for enhanced human health

Phytochemicals in vegetables are known to be responsible for protective effects against many human diseases, including cardiovascular diseases and different types of cancer. Environmental conditions and physiological factors may modify the amounts of these compounds present in vegetables and fruits, but also crop management strategies could increase the production of phytochemicals. Therefore, the effects of mineral nutrition, soil composition and water content on the production of phytochemicals have been considered in the development of different fertilisation strategies, efficient water management and techniques such as grafting. Finally, the contents of health-promoting compounds in vegetables and fruits depend both quantitatively and qualitatively on their genetic bases. Thus, conventional breeding and genetic modification have been developed as new methodologies to enhance the nutritional properties of plants. M. C. Martínez-Ballesta, L. López-Pérez, M. Hernández, C. López-Berenguer, N. Fernández-García contributed equally.     

Non-redox-active small-molecules can accelerate oxidative protein folding by novel mechanisms

Multi-disulfide-bond-containing proteins acquire their native structures through an oxidative folding reaction which involves formation of native disulfide bonds through thiol-disulfide exchange reactions between cysteines and disulfides coupled to a conformational folding event. Oxidative folding rates of the four-disulfide-bond-containing protein bovine pancreatic ribonuclease A (RNase A) in the presence of the synthetic redox-active molecule, (+/-)-trans-1,2-bis(2-mercaptoacetamido)cyclohexane (BMC), and in combination with non-redox-active trimethylamine-N-oxide (TMAO), and trifluorethanol were determined by HPLC analysis. The data indicate that regeneration of RNase A is enhanced 2-fold by BMC (50 microM) and 3-fold upon addition of TMAO (0.2 M) and TFE (3% v/v) relative to control experiments performed in the absence of small-molecules. Examination of the native tendency of the fully-reduced polypeptide and the stability of key folding intermediates suggests that the increased oxidative folding rate can be attributed to native-like elements induced within the fully-reduced polypeptide and the stabilization of native-like species by added non-redox-active molecules.     

Partial demethylation of oligogalacturonides by pectin methyl esterase 1 is required for eliciting defence responses in wild strawberry (Fragaria vesca)

In addition to the role of the cell wall as a physical barrier against pathogens, some of its constituents, such as pectin-derived oligogalacturonides (OGA), are essential components for elicitation of defence responses. To investigate how modifications of pectin alter defence responses, we expressed the fruit-specific Fragaria  ×  ananassa pectin methyl esterase FaPE1 in the wild strawberry Fragaria vesca . Pectin from transgenic ripe fruits differed from the wild-type with regard to the degree and pattern of methyl esterification, as well as the average size of pectin polymers. Purified oligogalacturonides from the transgenic fruits showed a reduced degree of esterification compared to oligogalacturonides from wild-type fruits. This reduced esterification is necessary to elicit defence responses in strawberry. The transgenic F. vesca lines had constitutively activated pathogen defence responses, resulting in higher resistance to the necrotropic fungus Botrytis cinerea . Further studies in F. vesca and Nicotiana benthamiana leaves showed that the elicitation capacity of the oligogalacturonides is more specific than previously envisaged.     

Removal of detergents from protein digests for mass spectrometry analysis

Detergents are commonly used for the extraction of hydrophobic proteins and must be removed for sensitive detection of peptides by mass spectrometry. We demonstrate that ethyl acetate is able to extract octylglycoside from a protease digest without loss of peptides or interference with the peptide mass spectral profile. Ethyl acetate extraction was also found to reduce interference by sodium dodecyl sulfate, Nonidet P-40, or Triton X-100 in the mass spectrometry analysis.     

Detection of a Salmonella enterica Serovar California Strain Spreading in Spanish Feed Mills and Genetic Characterization with DNA Microarrays

We performed an epidemiological study on Salmonella isolated from raw plant-based feed in Spanish mills. Overall, 32 different Salmonella serovars were detected. Despite its rare occurrence in humans and animals, Salmonella enterica serovar California was found to be the predominant serovar in Spanish feed mills. Different typing techniques showed that isolates of this serovar were genetically closely related, and comparative genomic hybridization using microarray technology revealed 23 S. enterica serovar Typhimurium LT2 gene clusters that are absent from serovar California.     

Field performance of artificial seed-derived sugarcane plants

This study shows the behaviour of sugarcane plants cv. CP-5243 derived from artificial seed compared with traditional and isolated bud methods. Artificial seed-acclimatised plants were planted in field conditions simultaneously with two-control treatments previously germinated: macropropagated plants derived from stems of three buds and axillary buds isolated from field-grown plants. Plants from artificial seed were taller and had a smaller diameter at 8 months, but these differences disappeared at 12 months. With respect to sugar analysis and yield, no differences in all parameters evaluated were found between artificial seed-derived plants and plants derived from the two other methods.