Bioinformatics tools for cancer metabolomics

It is well known that significant metabolic change take place as cells are transformed from normal to malignant. This review focuses on the use of different bioinformatics tools in cancer metabolomics studies. The article begins by describing different metabolomics technologies and data generation techniques. Overview of the data pre-processing techniques is provided and multivariate data analysis techniques are discussed and illustrated with case studies, including principal component analysis, clustering techniques, self-organizing maps, partial least squares, and discriminant function analysis. Also included is a discussion of available software packages

Bioinformatics and molecular modeling in glycobiology

The field of glycobiology is concerned with the study of the structure, properties, and biological functions of the family of biomolecules called carbohydrates. Bioinformatics for glycobiology is a particularly challenging field, because carbohydrates exhibit a high structural diversity and their chains are often branched. Significant improvements in experimental analytical methods over recent years have led to a tremendous increase in the amount of carbohydrate structure data generated. Consequently, the availability of databases and tools to store, retrieve and analyze these data in an efficient way is of fundamental importance to progress in glycobiology. In this review, the various graphical representations and sequence formats of carbohydrates are introduced, and an overview of newly developed databases, the latest developments in sequence alignment and data mining, and tools to support experimental glycan analysis are presented. Finally, the field of structural glycoinformatics and molecular modeling of carbohydrates, glycoproteins, and protein–carbohydrate interaction are reviewed

Monoterpene emissions from rubber trees (Hevea brasiliensis) in a changing landscape and climate: chemical speciation and environmental control

Emissions of biogenic volatile organic compounds (VOCs) have important roles in ecophysiology and atmospheric chemistry at a wide range of spatial and temporal scales. Tropical regions are a major global source of VOC emissions and magnitude and chemical speciation of VOC emissions are highly plant-species specific. Therefore it is important to study emissions from dominant species in tropical regions undergoing large-scale land-use change, for example, rubber plantations in South East Asia. Rubber trees (Hevea brasiliensis) are strong emitters of light-dependent monoterpenes. Measurements of emissions from leaves were made in the dry season in February 2003 and at the beginning of the wet season in May 2005. Major emitted compounds were sabinene, alpha-pinene and beta-pinene, but beta-ocimene and linalool also contributed significantly at low temperature and light. Cis-ocimene was emitted with a circadian course independent of photosynthetic active radiation (PAR) and temperature changes with a maximum in the middle of the day. Total isoprenoid VOC emission potential at the beginning of the wet season (94 mu g gdw(-1) h(-1)) was almost two orders of magnitude higher than measured in the dry season (2 mu g g dw(-1) h(-1)). Composition of total emissions changed with increasing temperature or PAR ramps imposed throughout a day. As well as light and temperature, there was evidence that assimilation rate was also a factor contributing to seasonal regulating emission potential of monoterpenes from rubber trees. Results presented here contribute to a better understanding of an important source of biogenic VOC associated with land-use change in tropical South East Asia

Dew Formation, Eddy-Correlation Latent Heat Fluxes, and the Surface Energy Imbalance at Cabauw During Stable Conditions

Observations collected between 2000 and 2008 at the Cabauw meteorological measurement platform in the Netherlands were conditionally sampled to select nights with stably stratified atmospheric conditions, clear skies and weak horizontal wind speeds (<3ms?1). For these conditions the eddy-correlation latent heat fluxes are found to be negligibly small, while the conditionally sampled surface energy balance exhibits a maximum residual. However, inspection of the specific humidities for these conditions reveals systematic drying trends that are a maximum at the lowest measurement level above the surface. These drying trends occur for any prevailing wind direction. Latent heat fluxes are calculated from the humidity budget equation and from a Penman-Monteith dewfall model, with the results suggesting that during clear, stable nights the observed latent heat fluxes as obtained from the eddy-correlation technique are erroneously small.Multi-Scale PhysicsApplied Science