Reliable gene signatures for microarray classification: assessment of stability and performance

MOTIVATION: Two important questions for the analysis of gene expression measurements from different sample classes are (1) how to classify samples and (2) how to identify meaningful gene signatures (ranked gene lists) exhibiting the differences between classes and sample subsets. Solutions to both questions have immediate biological and biomedical applications. To achieve optimal classification performance, a suitable combination of classifier and gene selection method needs to be specifically selected for a given dataset. The selected gene signatures can be unstable and the resulting classification accuracy unreliable, particularly when considering different subsets of samples. Both unstable gene signatures and overestimated classification accuracy can impair biological conclusions. METHODS: We address these two issues by repeatedly evaluating the classification performance of all models, i.e. pairwise combinations of various gene selection and classification methods, for random subsets of arrays (sampling). A model score is used to select the most appropriate model for the given dataset. Consensus gene signatures are constructed by extracting those genes frequently selected over many samplings. Sampling additionally permits measurement of the stability of the classification performance for each model, which serves as a measure of model reliability. RESULTS: We analyzed a large gene expression dataset with 78 measurements of four different cartilage sample classes. Classifiers trained on subsets of measurements frequently produce models with highly variable performance. Our approach provides reliable classification performance estimates via sampling. In addition to reliable classification performance, we determined stable consensus signatures (i.e. gene lists) for sample classes. Manual literature screening showed that these genes are highly relevant to our gene expression experiment with osteoarthritic cartilage. We compared our approach to others based on a publicly available dataset on breast cancer. AVAILABILITY: R package at http://www.bio.ifi.lmu.de/~davis/edaprakt     

On the mechanism of lactate dehydrogenase release from skeletal muscle in relation to the control of cell volume

The mechanism of enzyme release from isolated skeletal muscle was illustrated by the study of the release of lactate dehydrogenase (LDH). In hypotonic media of different composition but of same tonicity the increase of LDH permeability was triggered at the same range of relative osmolality R (0.45 less than R less than 0.55), although the swelling in the respective media showed appreciable differences. The kinetics of muscle swelling showed that a deviation from the theoretically computed swelling curve to lower values of swelling was connected with an increased LDH permeability. The reduction of swelling was ATP- and Ca2+ and/or Mg2-dependent. It is concluded that swelling of cells generally precedes the leakage of soluble enzymes, and the cross-linking of filaments at the sarcoplasmic side of the sarcolemma under appropriate conditions can counteract swelling, thereby blebbing off the cell membrane from the filament meshwork. In the course of this process, sufficiently large membrane lesions are produced through which macromolecules may escape into the extracellular space.     

Separation and quantitation ofcis- andtrans-thiothixene in human plasma by high-performance liquid chromatography

A high-performance liquid chromatographic procedure is described for the separation ofcis andtrans isomers of thiothixene, a thioxanthene derivative used as an antipsychotic agent. A radial compression module (RCM-100) was used with both silica and cyanopropyl cartridges. A fixed-wavelength UV detector (254 nm) was used in these studies for quantitation. Mesoridazine is used as an internal standard because of its separation characteristics and reproducible quantitation. C₁₈ Sep-Pak cartridges are used for biological sample cleanup. Plasma samples from patients treated with thiothixene (Navane) were assayed forcis andtrans-thiothixene. Notrans-thiothixene was detectable andcis-thiothixene concentrations ranged from 0 to 22.5 ng/ml.     

Insect yolk protein precursor, a juvenile hormone induced phosphoprotein

The juvenile hormone induced vitellogenic female-specific protein of $\text{Leucophaea}$$\text{maderae}$ was isolated from hemolymph of egg maturing females on DEAE or QAE anion-exchange columns. Minor contaminants could be removed by centrifugation to equilibrium on CsCl gradients. The buoyant density of this purified protein is 1.344 g/ml. It is a lipophosphoprotein of low phosphorus (0.14%) content. Essentially all ³²P label from in vivo labelled protein was recovered in phosphoserine. The amino acid residues of the vitellogenic protein compare well with the purified yolk protein.     

ProCope--protein complex prediction and evaluation

SUMMARY: Recent advances in high-throughput technology have increased the quantity of available data on protein complexes and stimulated the development of many new prediction methods. In this article, we present ProCope, a Java software suite for the prediction and evaluation of protein complexes from affinity purification experiments which integrates the major methods for calculating interaction scores and predicting protein complexes published over the last years. Methods can be accessed via a graphical user interface, command line tools and a Java API. Using ProCope, existing algorithms can be applied quickly and reproducibly on new experimental results, individual steps of the different algorithms can be combined in new and innovative ways and new methods can be implemented and integrated in the existing prediction framework. AVAILABILITY: Source code and executables are available at http://www.bio.ifi.lmu.de/Complexes/ProCope/.     

Monoclonal antibody to dengue capsid protein: Its application in dengue studies

Dengue fever (DF) and dengue hemorrhagic fever/dengue shock syndrome (DHF/DSS) are considered the most important arthropod-borne viral diseases in terms of morbidity and mortality. The emergency and severity of dengue (Den) infections increase the necessity of an early, quick and effective dengue laboratory diagnostic. Viral isolation is considered a gold standard for diagnosis of dengue infection using monoclonal antibodies (mAbs) as a tool for determining serotype specificity. Alternatives have been used to improve sensitivity and time to dengue diagnosis. Based on the early expression of dengue C protein in the life cycle, we focused our study on the application of an anti-dengue 2 virus capsid protein mAb in dengue diagnosis. The kinetic expression of dengue-2 capsid in mosquito cells and its immuno-localization in experimentally infected suckling albin Swiss (OF-1) mice brain tissues was established. The results demonstrate the possible utility of this mAb in early dengue diagnosis versus traditional isolation. In addition, a preliminary study of an enzyme immunoassay method using 8H8 mAb for specific detection of dengue C protein antigen was performed, making possible recombinant C protein quantification. The results suggest that detection of dengue capsid protein could be useful in the diagnosis of early dengue infection.Key words: monoclonal antibodies, capsid protein, dengue virus, diagnosis, immunoassays     

Evaluation of a vermicompost and leachates on <i>Solidago x hybrida</i> and organic carbon mineralization under aerobic incubations

In the floriculture region of Tenancingo in the State of Mexico, the application of stabilized organic matter, such as vermicompost and leachates, contributes to improve the quality of the soil and plant nutrition. However, it is important to know the chemical composition of a vermicompost and the mineralization process. This is because the amount and speed of nutrient release which will be available to the crop will depend on that knowledge. The objective of the study was to evaluate the effect of the application of a vermicompost and leachates on various quantitative variables of Solidago x hybrid, and the mineralization of organic carbon under aerobic incubations. Vermicompost (74 and 36 g/kg soil), leachates (5 and 10 L/kg soil), 0.33 g/kg soil of chemical fertilizer Ca (NO₃)₂, and not treated soil (control) were applied under greenhouse conditions to evaluate their effects on plant growth variables. Mixtures of 100 g of soil with vermicompost and leachates were made in the laboratory which were incubated during 9 weeks to obtain the potentially mineralizable organic carbon (Corg PM) and the rate of mineralization (k) after adjusting an exponential model. In the greenhouse experiment there were no statistical differences after applying vermicompost and leachates on the quantitative variables (number of stems per plant, diameter of the panicle, fresh weight, plant length and stem diameter) with respect to the control (p>0.05). The effect among the applied doses was evident only for variables such as fresh weight, panicle length and stem diameter with respect to the control. In incubated soils, k values ranged between 0.209-0.325 C mg/kg soil/week. Only with the application of leachates in high doses two pools of organic matter were shown: one soluble labile (102.9 mg/kg soil) and the other hydrolysable (819 mg/kg soil). The soluble, labile fraction favored nutrient availability immediately after its application to the soil. However, a single pool of hydrolysable organic C (987-1074 mg/kg soil) was found when vermicompost was applied. It was associated with a release of organic matter during crop development, and to a possible stimulation of microbial activity. High values of electrical conductivity in vermicompost and leachates (8.2-11.7 mS/m) suggest a moderate application of both products.