CARMEN - Comparative Analysis and in silico Reconstruction of organism-specific MEtabolic Networks.

New sequencing technologies provide ultra-fast access to novel microbial genome data. For their interpretation, an efficient bioinformatics pipeline that facilitates in silico reconstruction of metabolic networks is highly desirable. The software tool CARMEN performs in silico reconstruction of metabolic networks to interpret genome data in a functional context. CARMEN supports the visualization of automatically derived metabolic networks based on pathway information from the KEGG database or from user-defined SBML templates; this software also enables comparative genomics. The reconstructed networks are stored in standardized SBML format. We demonstrated the functionality of CARMEN with a major application example focusing on the reconstruction of glycolysis and related metabolic reactions of Xanthomonas campestris pv. campestris B100. The curation of such pathways facilitates enhanced visualization of experimental results, simulations and comparative genomics. A second application of this software was performed on a set of corynebacteria to compare and to visualize their carbohydrate metabolism. In conclusion, using CARMEN, we developed highly automated data analysis software that rapidly converts sequence data into new knowledge, replacing the time-consuming manual reconstruction of metabolic networks. This tool is particularly useful for obtaining an overview of newly sequenced genomes and their metabolic blueprints and for comparative genome analysis. The generated pathways provide automated access to modeling and simulation tools that are compliant with the SBML standard. A user-friendly web interface of CARMEN is available at http://carmen.cebitec.uni-bielefeld.de.

Performance of D-amino acid oxidase in presence of ionic liquids.

The activity and stability of free and immobilized D-amino acid oxidase (DAAO, EC 1.4.3.3) from Trigonopsis variabilis CBS 4095 in different water-soluble and water-insoluble ionic liquids (ILs) as well as in organic solvents were studied for comparison. The most promising ILs ([BMIM][BF(4)] and [MMIM][MMPO(4)]) were investigated in detail. The kinetic parameters (v(max) = 187 nkat/g dry weight, K(M) = 1.38 mM) with D-phenylalanine as substrate were calculated in 40% [BMIM][BF(4)]. Bioconversions of D/L-phenylalanine in 40% [BMIM][BF(4)] and 20% [MMIM][MMPO(4)] on a 3 ml scale using immobilized DAAO were performed by addition of free catalase from Micrococcus lysodeikticus. After total conversion of substrate in presence of 20% [MMIM][MMPO(4)] the residual activity of the immobilized DAAO was 79% and 100% of the free catalase.

Comparison of topical travoprost eye drops given once daily and timolol 0.5% given twice daily in patients with open-angle glaucoma or ocular hypertension.

PURPOSE: This 9-month study compared the intraocular pressure (IOP)-lowering efficacy and safety of once-daily travoprost ophthalmic solutions (0.0015% and 0.004%) with twice-daily timolol 0.5%. PATIENTS AND METHODS: This study was conducted using a double-masked, randomized, parallel-group design; adult patients with open-angle glaucoma or ocular hypertension (IOP between 24 and 36 mm Hg, inclusive at 9 am and between 21 and 36 mm Hg, inclusive, at 11 am and 4 pm on two eligibility visits after an appropriate washout of previous treatments). In both eyes, the travoprost vehicle (placebo) was instilled at 9 am and travoprost (0.0015% or 0.004%) was instilled at 9 pm, or timolol 0.5% was instilled at both times. The primary efficacy variable was mean IOP measured at 9 am, 11 am, and 4 pm at baseline and follow-up visits. RESULTS: Five hundred seventy-three patients were randomized to the study treatments. Mean IOP, which was combined across study visits, was lower with travoprost 0.004% than with timolol 0.5% at 9 am (P = 0.0246), 11 am (P = 0.0039), and 4 pm (P = 0.0004). Intraocular pressure was lower with travoprost 0.004% than with travoprost 0.0015% at 11 am (P = 0.0314), the time of peak drug activity. Mean IOP was consistently lower with travoprost 0.0015% than with timolol 0.5%. Mean IOP reductions from baseline were significantly (P less than equal 0.0001) greater with travoprost 0.004% (8.0-8.9 mm Hg) than with timolol 0.5% (6.3-7.9 mm Hg). The most frequent related adverse events were hyperemia, pruritus, discomfort, pain, and iris pigmentation changes. The local tolerance was better in the timolol group compared with patients receiving travoprost. There were no serious unexpected treatment-related adverse events in any group. CONCLUSIONS: Travoprost 0.004% reduced diurnal mean intraocular pressure significantly more than timolol 0.5%. Both concentrations of travoprost were well tolerated and safe for use in patients with open-angle glaucoma or ocular hypertension.

[Early prognosis in severe cranio-cerebral trauma using the Glasgow Coma Score and evoked potentials]. / Frühzeitige Prognose beim schweren Schädel-Hirn-Trauma mittels Glasgow-Koma-Score und evozierter Potentiale.

During 72 h following severe head injury, 103 patients in acute posttraumatic coma were assessed by clinical examinations (documented by Glasgow Coma Score) and brain stem auditory evoked potentials (BAEP) as well as short-latency somatosensory evoked potentials (SEP) following median-nerve stimulation. Patient outcomes were classified at 6 months or more according to the following categories: good recovery, severely disabled or vegetative, and brain dead. Patients who had died of systemic complications (pneumonia, septicemia, renal failure, etc.) were excluded from the study. The Glasgow Coma Score was reliable in forecasting a favorable outcome; all patients with a Score over 9 points had a good recovery. The Glasgow Coma Score was not reliable in predicting an unfavorable outcome, however; some patients with the lowest possible Glasgow Coma Score (3 points) at the early clinical examination survived with good recovery. The BAEPs were reliable predictors of an unfavorable outcome; the outcome was unfavorable when a missing wave V or more missing waves pointed toward a secondary brainstem lesion. Normal BAEPs were not reliable, however, in predicting a favorable outcome. SEP data served as a prognostic indicator of unfavorable as well as favorable outcomes. In summary, evoked potentials add valuable information to the clinical examination in assessing a patient's outcome after severe head injury.

[Early prognostic assessment using evoked potentials in severe craniocerebral trauma]. / Frühzeitige prognostische Aussage mittels evozierter Potentiale beim schweren Schädel-Hirn-Trauma.

103 patients in acute posttraumatic coma were assessed during 72 hours following severe head injury by clinical examinations (documented with a modified Glasgow-Coma-Score and a brain-stem-score and brainstem auditory evoked potentials (BAEP) as well as short latency somatosensory evoked potentials (SEP). Patient outcomes were classified at 6 months or more, according to the following categories: good recovery, severely disabled or vegetative, and brain dead. Patients who had died by systemic complications were excluded from the study. The Glasgow-Coma-Score was reliable in forecasting a favorable outcome, but tended to produce false-pessimistic predictions. The brainstemscore and the BAEPs were reliable predictors of an unfavorable but not a favorable outcome. SEP data however, performed well as a prognostic indicant in predicting an unfavorable as well as a favorable outcome. Using the BAEP, the amplitude ratio Wave V/Wave I is more sensitive to detect a lesion than the interpeak-latency Wave I-Wave V, and--using the SEP--the amplitude ratio N20/N13b (over C2) is more sensitive than the central conduction time (N13a (over C7)--N20).

Short-latency somatosensory evoked potentials in brain death.

Simultaneous recording of somatosensory evoked potentials to median nerve stimulation above the upper and lower neck in brain-dead patients revealed that all cervical responses were preserved in 10%, whereas a marked reduction in amplitude or even loss of N 13b at the level of the C2 spinous process was observed in 90%. Of the patients, 55% revealed an additional loss of N 13a, recorded at the level of the C7 spinous process; in 15% all cortical and spinal evoked potentials were missing, but Erb's point waves were still normal. These results suggest two different origins of the main negative waves (N 13a and N 13b), recorded above the upper and lower cervical spinal cord. N 13a (C7) is supposed to arise in the dorsal horn at the C6/7 level, N 13b (C2) in the cervicomedullary junction.

[Significance of somatosensory evoked potentials in determining brain death]. / Bedeutung der somatosensibel evozierten Potentiale (SEP) bei der Feststellung des Hirntodes.

Electrophysiological examinations are useful to confirm the clinical diagnosis of brain death and to substantiate the loss of brain function and of brain stem function. In addition to the EEG, which has been an useful ancillary test for many years to diagnose brain death, auditory and somatosensory evoked potentials are other electrophysiological techniques that give useful information on the assessment of brain death. In this study, short-latency somatosensory evoked potentials following median nerve stimulation were recorded in 20 patients who fulfilled the clinical criteria of brain death. The primary cortical responses N 20/P 25 recorded above the somatosensory cortex disappeared in all patients. Furthermore, except in two patients, there was a loss of the N 13 b component recorded above the spinous process C2 (N 13 b is assumed to originate in the cervicomedullary junction). Nine patients in whom brain death had occurred exhibited additionally changes of N 13 a - recorded above the spinous process C7 - a potential generated in the lower cervical cord. These data point to the occasional involvement of the cervical cord in the loss of function in patients in whom brain death had become manifest.

[Significance of early acoustic evoked potentials in the diagnosis of brain death]. / Bedeutung der frühen akustisch evozierten Potentiale bei der Feststellung des Hirntodes.

Tests of early acoustic evoked potentials in 49 patients in whom clinical and EEG criteria indicated brain death demonstrated a bilateral loss of brainstem-generated components III to V in 12.6%, a loss of the components II-V in 16.8% and a loss of all early acoustic evoked potentials in 47.4%. This method, practicable in an intensive care unit, seems thus suitable for demonstrating loss of brainstem function as demanded for diagnosis of brain death.

[Acoustic evoked potentials of medium latency]. / Akustisch evozierte Potentiale mittlerer Latenz.

Medium latency auditory evoked potentials (8-50 ms latency interval) are not yet established as an important diagnostic procedure. This is mainly due to the fact that the origins of the single components are not yet known. Components of the MLAEP were investigated and normal values were calculated in order to distinguish neurogenic and myogenic components. Based on this investigation the role of the MLAEP in clinical practice can be judged. Mean values (31 subjects) for ipsi- and contralaterally recorded potentials were calculated independently for recordings with and without myogenic contamination. The following components were measured: V, VI, VII, No, Po, Na, Pa, Nb. In addition sixteen patients with idiopathic facial paresis - consequently lacking the postauricular reflex - were investigated. Normal values of the myogenic component Po (when present) are presented to determine the so called "crossed acoustic response".