CORRIE: enzyme sequence annotation with confidence estimates

Using a previously developed automated method for enzyme annotation, we report the re-annotation of the ENZYME database and the analysis of local error rates per class. In control experiments, we demonstrate that the method is able to correctly re-annotate 91% of all Enzyme Classification (EC) classes with high coverage (755 out of 827). Only 44 enzyme classes are found to contain false positives, while the remaining 28 enzyme classes are not represented. We also show cases where the re-annotation procedure results in partial overlaps for those few enzyme classes where a certain inconsistency might appear between homologous proteins, mostly due to function specificity. Our results allow the interactive exploration of the EC hierarchy for known enzyme families as well as putative enzyme sequences that may need to be classified within the EC hierarchy. These aspects of our framework have been incorporated into a web-server, called CORRIE, which stands for Correspondence Indicator Estimation and allows the interactive prediction of a functional class for putative enzymes from sequence alone, supported by probabilistic measures in the context of the pre-calculated Correspondence Indicators of known enzymes with the functional classes of the EC hierarchy. The CORRIE server is available at:

Predicting DNA-Binding Specificities of Eukaryotic Transcription Factors

Today, annotated amino acid sequences of more and more transcription factors (TFs) are readily available. Quantitative information about their DNA-binding specificities, however, are hard to obtain. Position frequency matrices (PFMs), the most widely used models to represent binding specificities, are experimentally characterized only for a small fraction of all TFs. Even for some of the most intensively studied eukaryotic organisms (i.e., human, rat and mouse), roughly one-sixth of all proteins with annotated DNA-binding domain have been characterized experimentally. Here, we present a new method based on support vector regression for predicting quantitative DNA-binding specificities of TFs in different eukaryotic species. This approach estimates a quantitative measure for the PFM similarity of two proteins, based on various features derived from their protein sequences. The method is trained and tested on a dataset containing 1 239 TFs with known DNA-binding specificity, and used to predict specific DNA target motifs for 645 TFs with high accuracy

MMPs Regulate both Development and Immunity in the Tribolium Model Insect

BACKGROUND: Matrix metalloproteinases (MMPs) are evolutionarily conserved and multifunctional effector molecules in development and homeostasis. In spite of previous, intensive investigation in vitro and in cell culture, their pleiotrophic functions in vivo are still not well understood. METHODOLOGY/PRINCIPAL FINDINGS: We show that the genetically amenable beetle Tribolium castaneum represents a feasible model organism to explore MMP functions in vivo. We silenced expression of three insect-type Tribolium MMP paralogs and their physiological inhibitors, TIMP and RECK, by dsRNA-mediated genetic interference (RNAi). Knock-down of MMP-1 arrested development during pupal morphogenesis giving phenotypes with altered antennae, compound eyes, wings, legs, and head. Parental RNAi-mediated knock-down of MMP-1 or MMP-2 resulted in larvae with non-lethal tracheal defects and with abnormal intestines, respectively, implicating additional roles of MMPs during beetle embryogenesis. This is different to findings from the fruit fly Drosophila melanogaster, in which MMPs have a negligible role in embryogenesis. Confirming pleiotrophic roles of MMPs our results also revealed that MMPs are required for proper insect innate immunity because systemic knock-down of Tribolium MMP-1 resulted in significantly higher susceptibility to the entomopathogenic fungus Beauveria bassiana. Moreover, mRNA levels of MMP-1, TIMP, and RECK, and also MMP enzymatic activity were significantly elevated in immune-competent hemocytes upon stimulation. To confirm collagenolytic activity of Tribolium MMP-1 we produced and purified recombinant enzyme and determined a similar collagen IV degrading activity as observed for the most related human MMP, MMP-19. CONCLUSIONS/SIGNIFICANCE: This is the first study, to our knowledge, investigating the in vivo role of virtually all insect MMP paralogs along with their inhibitors TIMP and RECK in both insect development and immunity. Our results from the Tribolium model insect indicate that MMPs regulate tracheal and gut development during beetle embryogenesis, pupal morphogenesis, and innate immune defense reactions thereby revealing the evolutionarily conserved roles of MMPs

The reticular formation and the neuromodulatory systems

Almost a century ago, Constantin von Economo observed that in patients with encephalitis lethargica lesions in the upper brain stem and posterior hypothalamus impaired consciousness. From lesion studies in cats and anatomical data, the idea arose that the brain stem reticular formation is the origin of the ascending reticular activating system (ARAS) that would operate through the intralaminar nuclei and activate widespread regions of the cerebral cortex. This view of the reticular formation has been extensively modified, and nowadays the reticular formation is viewed as a series of highly specific cell groups, which closely surround the individual motor and sensory nuclei of the brain stem (Sects. 5.2 and 5.4). The diffuse system, driving arousal and consciousness, is now attributed to the neuromodulatory system, including the serotonergic raphe nuclei, the locus coeruleus and other noradrenergic or adrenergic cell groups and cholinergic cell groups, all close to the reticular formation (Sects. 5.3 and 5.5). The English terms of the Terminologia Neuroanatomica are used throughout. Although the basic notion of the ARAS concept that structures in the brain stem regulate states of consciousness still holds true, a much more complex picture has emerged. Experimental work in laboratory animals suggests that the following structures play key roles in the maintenance and modulation of wakefulness: cholinergic nuclei in the upper brain stem and basal forebrain; noradrenergic nuclei, in particular the locus coeruleus; a histaminergic projection from the tuberomamillary nucleus in the posterior hypothalamus; and dopaminergic and serotonergic pathways from the ventral tegmental area and raphe nuclei, respectively. These nuclei all participate in an ascending activating system to the cerebral cortex (Sect. 5.5). The hypothalamus also contains orexinergic neurons that are crucial for maintaining normal wakefulness and a sleep-promoting region in the ventrolateral preoptic area. These groups have mutually inhibiting connections, known as the sleep switch (Sect. 5.6). Some sleep disorders in which these structures are involved are discussed in Clinical Cases (Sect. 5.7). Damage to the upper brain stem reticular formation is known to cause the most radical disturbance of consciousness, i.e. coma, as illustrated in several Clinical Cases (Sect. 5.8)