Exploration of multivariate analysis in microbial coding sequence modeling

ABSTRACT: BACKGROUND: Gene finding is a complicated procedure that encapsulates algorithms for coding sequence modeling, identification of promoter regions, issues concerning overlapping genes and more. In the present study we focus on coding sequence modeling algorithms; that is, algorithms for identification and prediction of the actual coding sequences from genomic DNA. In this respect, we promote a novel multivariate method known as Canonical Powered Partial Least Squares (CPPLS) as an alternative to the commonly used Interpolated Markov model (IMM). Comparisons between the methods were performed on DNA, codon and protein sequences with highly conserved genes taken from several species with different genomic properties. RESULTS: The multivariate CPPLS approach classified coding sequence substantially better than the commonly used IMM on the same set of sequences. We also found that the use of CPPLS with codon representation gave significantly better classification results than both IMM with protein (p < 0.001) and with DNA (p < 0.001). Further, although the mean performance was similar, the variation of CPPLS performance on codon representation was significantly smaller than for IMM (p < 0.001). CONCLUSIONS: The performance of coding sequence modeling can be substantially improved by using an algorithm based on the multivariate CPPLS method applied to codon or DNA frequencies.     

Targeting brain serotonin synthesis: insights into neurodevelopmental disorders with long-term outcomes related to negative emotionality, aggression and antisocial behaviour

Aggression, which comprises multi-faceted traits ranging from negative emotionality to antisocial behaviour, is influenced by an interaction of biological, psychological and social variables. Failure in social adjustment, aggressiveness and violence represent the most detrimental long-term outcome of neurodevelopmental disorders. With the exception of brain-specific tryptophan hydroxylase-2 (Tph2), which generates serotonin (5-HT) in raphe neurons, the contribution of gene variation to aggression-related behaviour in genetically modified mouse models has been previously appraised (Lesch 2005 Novartis Found Symp. 268, 111-140; Lesch & Merschdorf 2000 Behav. Sci. Law 18, 581-604). Genetic inactivation of Tph2 function in mice led to the identification of phenotypic changes, ranging from growth retardation and late-onset obesity, to enhanced conditioned fear response, increased aggression and depression-like behaviour. This spectrum of consequences, which are amplified by stress-related epigenetic interactions, are attributable to deficient brain 5-HT synthesis during development and adulthood. Human data relating altered TPH2 function to personality traits of negative emotionality and neurodevelopmental disorders characterized by deficits in cognitive control and emotion regulation are based on genetic association and are therefore not as robust as the experimental mouse results. Mouse models in conjunction with approaches focusing on TPH2 variants in humans provide unexpected views of 5-HT's role in brain development and in disorders related to negative emotionality, aggression and antisocial behaviour.     

Using mass spectrometry to explore the neglected glycan moieties of the antiophidic proteins DM43 and DM64

The resistance of the opossum Didelphis aurita to Bothrops snake venoms is attributed to the opossum's antihemorrhagic (DM43) and antimyotoxic (DM64) acidic serum glycoproteins. The aim of this study was to characterize the N-glycosylation sites of these antiophidic proteins and to determine whether their glycans influence the biological activity measured by in vitro assays. Our experimental pipeline included the sequential enzymatic digestion of the inhibitors with two different proteinases (trypsin and endoproteinase Asp-N) and eventually with trypsin, peptide-N-glycosidase F (PNGase F) and endoproteinase Asp-N, used in that order. All of the peptide and protein samples were analyzed by MALDI-TOF/TOF MS. The results experimentally confirmed the putative N-glycosylation sites of DM43 (Asn23, Asn156, Asn160, and Asn175) and DM64 (Asn46, Asn179, Asn183, and Asn379). Following treatments with specific glycosidases, complex-type oligosaccharides containing galactose and sialic acid could be assigned to both proteins. The removal of these monosaccharide units by exoglycosidase digestion did not measurably affect the inhibitory activity. In contrast, partially deglycosylated DM43 treated with PNGase F under nondenaturing conditions was half as effective as native DM43. In conclusion, we have demonstrated that the contribution of the carbohydrate portion of these potentially therapeutic molecules, for their mechanism of action, should not be overlooked.     

Proteomic profiling of skeletal muscle in an animal model of overtraining

Excessive training (i.e. overtraining, OT) may result in underperformance, which can be characterized by the time needed to re-establish performance (i.e. functional overreaching (FOR), nonfunctional overreaching, OT syndrome). The present study is an initial screening for proteins presenting altered abundance in the red (RG) and white (WG) portions of the gastrocnemius muscle from rats submitted to an OT protocol that induced FOR. In the RG, compared to the nontrained control, FOR demonstrated an increased abundance of proteins normally related to adaptation to endurance training (e.g. proteins of oxidative phosphorylation complexes, proteins related to lipid metabolism, antioxidants, and chaperones). In the WG, spots identified as mitochondrial aconitase and a component of the succinate dehydrogenase complex were downregulated in FOR, as were proteins related to myofibril stabilization; these latter were upregulated in the RG. This initial study shows that skeletal muscles with different fiber-type compositions respond differently to an OT period. Also, it is likely that actin-interacting proteins have an important role in muscle adaptation to endurance exercise.     

Search engine processor: Filtering and organizing peptide spectrum matches

The search engine processor (SEPro) is a tool for filtering, organizing, sharing, and displaying peptide spectrum matches. It employs a novel three-tier Bayesian approach that uses layers of spectrum, peptide, and protein logic to lead the data to converge to a single list of reliable protein identifications. SEPro is integrated into the PatternLab for proteomics environment, where an arsenal of tools for analyzing shotgun proteomic data is provided. By using the semi-labeled decoy approach for benchmarking, we show that SEPro significantly outperforms a commercially available competitor.     

Assessment of grassland use intensity by remote sensing to support conservation schemes

Grassland is a land cover in the area of conflict between agriculture and conservation, where intensification of land use is a major threat to grassland biodiversity. Grassland use intensity is a key factor for the conservation value of grassland, and detailed spatial data on grassland use intensity is needed to improve strategies for biodiversity conservation. A new remote sensing-based approach using multi-temporal high resolution RapidEye satellite data was developed in the present study that makes a large-scale assessment of grassland use intensity possible. RapidEye is a constellation of five satellites with 6.5 m spatial resolution, which allows frequent and timely image acquisition targeted at specific growing seasons. Semi-natural grassland, extensively used grassland, intensively used grassland and tilled grassland could be reliably differentiated at the management plot level in a study area in southern Germany. Various combinations of images from different observation dates have been tested as classification input and their overall classification accuracies were validated by field data. Best results were achieved using a combination of five multi-temporal scenes with an overall accuracy of 85.7%. A three-scene combination resulted in an overall accuracy of 82.2%. The analysis showed that seasonal aspects are very important when selecting adequate observation dates. Grassland use intensity was also assessed on peatlands using a peat soil map, since land use intensity significantly affects greenhouse gas emissions from peatlands. The results demonstrate the potential of targeted multi-spectral, high spatial resolution remote sensing for the large-scale monitoring of dynamic habitats, which is of vital importance to support various environmental conservation schemes through improved monitoring and reporting capabilities.     

Low charge density cationic polymers for gene delivery: exploring the influence of structural elements on in vitro transfection

A series of end-functionalized poly(trimethylene carbonate) DNA carriers, characterized by low cationic charge density and pronounced hydrophobicity, is used to study structural effects on in vitro gene delivery. As the DNA-binding moieties are identical in all polymer structures, the differences observed between the different polymers are directly related to the functionality and length of the polymer backbone. The transfection efficiency and cytotoxicity of the polymer/DNA complexes are thus found to be dependent on a combination of polymer charge density and functionality, highlighting the importance of such structural considerations in the development of materials for efficient gene delivery.