Biomedical subjects

R Unger

Publications and source records attributed to R Unger.

At least 19 recordsLinked to original sources

PubMed2004

Age-dependence of lipid parameters in the general population and vegetarians.

Age-dependent changes of lipid metabolism may arise both as a result of mechanisms of biological ageing and factors influencing age-dependent changes. To study possible influences of nutrition and life-style of vegetarians on age-dependence of lipid parameters, subjects of general population were compared with vegetarians. In the frame of population-based lipid screening projects in the city of Leipzig/Germany (Lipid Study Leipzig, LSL) 10 550 subjects (3,816 men and 6,734 women, age 18-99 years) of general population were compared with 417 vegetarians (vegans, lacto-vegetarians, lacto-ovo-vegetarians, 148 men and 269 women, age 18-93 years). Most of the vegetarians included in the study were members of the German Society of Vegetarians. The study program included capillary blood cholesterol measurements and the determination of high-density lipoprotein (HDL)-cholesterol, the measurement of other cardiovascular risk factors and the evaluation of dietary and life-style factors. Evaluation of cardiovascular risk profile within LSL was connected with individual consultation. The mean total cholesterol and non-HDL-cholesterol level and the total: HDL-cholesterol ratio showed the expected age-dependence, with maximum values within the decade 60-70 years. Vegetarians showed lower total and non-HDL-cholesterol levels in comparison with the general population. Furthermore, the age-dependent increase of these parameters is less pronounced under the conditions of vegetarian nutrition and life-style. Especially in young adulthood a significant difference is observed. Thus, the results of the present study reveal the role of nutritional and life-style factors that determine the lipid profile on a population basis and suggest that the known age-dependent rise of the level of atherogenic plasma lipoproteins is partly preventable.

Adolescent↗

PubMed2002

Relation between glycaemic control, hyperinsulinaemia and plasma concentrations of soluble adhesion molecules in patients with impaired glucose tolerance or Type II diabetes.

AIMS/HYPOTHESIS: Increased plasma concentrations of circulating adhesion molecules in patients with Type II (non-insulin-dependent) diabetes mellitus could be associated with the increased cardiovascular risk in these patients. However, it is controversial whether increased adhesion molecule plasma concentrations are primarily related to hyperglycaemia or to hyperinsulinaemia. METHODS: We evaluated the plasma concentrations of soluble E-selectin, intracellular adhesion molecule-1 (ICAM-1), and vascular cell adhesion molecule-1 (VCAM-1) at baseline and during euglycaemic hyperinsulinaemic clamp in three different groups without additional cardiovascular risk factors: group A (control group), 28 healthy volunteers with normal glucose tolerance; group B, 24 subjects with fasting hyperinsulinaemia, normal fasting glucose but impaired glucose tolerance; group C, 32 patients with Type II diabetes, fasting hyperinsulinaemia and chronic hyperglycaemia. RESULTS: Plasma soluble E-selectin, ICAM-1, and VCAM-1 concentrations were higher ( p < 0.05) in patients with Type II diabetes (group C) compared with the other groups. The adhesion molecule concentrations correlate with the fasting plasma glucose ( r = 0.59, p < 0.001), the 2-h OGTT plasma glucose ( r = 0.70, p < 0.01), and the HbA(1 c) value ( r = 0.61, p < 0.05). The E-selectin but not the ICAM-1 and VCAM-1 plasma concentrations correlated with the fasting insulin concentrations ( r = 0.62, p < 0.05) or the whole body glucose uptake ( r = 0.59, p < 0.05) in the clamp. The hyperinsulinaemia during the euglycaemic hyperinsulinaemic clamp had no significant effect on the plasma concentrations of E-selectin, ICAM-1, and VCAM-1 in all three groups. CONCLUSION/INTERPRETATION: Our results suggest that increased E-selectin concentrations are related to hyperglycaemia, hyperinsulinaemia and insulin resistance, whereas increased ICAM-1 and VCAM-1 plasma concentrations in patients with Type II diabetes are rather related to hyperglycaemia than to hyperinsulinaemia or insulin resistance.

Adult↗

PubMed2002

[Active life expectancy in Germany and in the United States. A cohort analysis based on the "German Socio-Economic Panel" (GSOEP) and the "Panel Study of Income Dynamics" (PSID)].

Using the method of multistate life-tables, the article presents results on active life expectancy on the basis of the German Socio-Economic Panel (GSOEP) and the Panel Study of Income Dynamics (PSID). The transitions into and out of active life are based on event-history analysis and are calculated for different cohorts. Compared to cross-sectional analysis, the longitudinal analysis carried out here describes active life expectancy with reference to single birth cohorts. Results show that in Germany there has been substantial improvement in active life expectancy while in the USA there has been some deterioration.

Activities of Daily Living↗

PubMed2002

Child pedestrian injuries at tram and bus stops.

In order to analyse these injuries and to create guidelines for prevention, injuries at bus or tram stops were analysed retrospectively. Medical records were analysed and questionnaires were sent to the parents in order to obtain detailed information about the mode and physical sequelae or post-traumatic behavioural disturbances of the injury.Thirty children of a median age of 9.5 years (2.7-15.3 years) were treated within a 6-year period. Sixteen out of 30 children (53.3%) were injured on their way to school and 3 (10.0%) on their way to kindergarten. Nine out of 30 children (30%) were injured when crossing the street from behind the bus or the tram. Five children (16.7%) were injured by buses, 6 (20.0%) by trams and 19 (63.3%) by passing motorised vehicles. Twelve (40.0%) were injured in the presence of accompanying adults. In 17 of 30 cases (56.7%) the visibility of the vehicle and/or the child was obstructed. The median Injury Severity Score (ISS) was 4.5 (1-75) and the mortality rate 2 out of 30 (6.7%), both children had been killed at bus stops alongside country roads. Nine out of 28 surviving children (32.1%) suffer from minor physical sequelae and 6 (21.4%) from post-traumatic behavioural disturbances. Crossing the road from behind a bus in the area of a stop alongside a country road is extremely dangerous. It is mandatory to increase the safety at bus stops along country roads.

Accidents, Traffic↗

PubMed2001

Naturally occurring circular permutations in proteins.

A pair of proteins is defined to be related by a circular permutation if the N-terminal region of one protein has significant sequence similarity to the C-terminal of the other and vice versa. To detect pairs of proteins that might be related by circular permutation, we implemented a procedure based on a combination of a fast screening algorithm that we had designed and manual verification of candidate pairs. The screening algorithm is a variation of a dynamic programming string matching algorithm, in which one of the sequences is doubled. This algorithm, although not guaranteed to identify all cases of circular permutation, is a good first indicator of protein pairs related by permutation events. The candidate pairs were further validated first by application of an exhaustive string matching algorithm and then by manual inspection using the dotplot visual tool. Screening the whole Swissprot database, a total of 25 independent protein pairs were identified. These cases are presented here, divided into three categories depending on the level of functional similarity of the related proteins. To validate our approach and to confirm further the small number of circularly permuted protein pairs, a systematic search for cases of circular permutation was carried out in the Pfam database of protein domains. Even with this more inclusive definition of a circular permutation, only seven additional candidates were found. None of these fitted our original definition of circular permutations. The small number of cases of circular permutation suggests that there is no mechanism of local genetic manipulation that can induce circular permutations; most examples observed seem to result from fusion of functional units.

Algorithms↗

PubMed2000

Slow recovery of body fat lost during adenovirus-induced hyperleptinemia.

In normal rats, adenovirus-induced hyperleptinemia causes disappearance of visible body fat, downregulation of lipogenic enzymes, and upregulation of oxidative enzymes and thermogenic proteins. In addition, preadipocyte markers replace mature adipocyte markers, suggesting dedifferentiation. In weight loss induced by caloric restriction, by contrast, the lipogenic machinery is essentially intact. To determine if the radical changes induced by leptin would slow the reappearance of body fat, we compared normal lean rats made hyperleptinemic by infusing an adenovirus-leptin construct with diet-matched littermates. Initially, in plasma leptin the hyperleptinemic rats averaged approximately 50x the controls and, although it declined progressively, it was still slightly elevated at 150 days (P < 0.05). In the hyperleptinemics, body fat mass, quantified by magnetic resonance spectroscopy, remained below the pretreatment value for 60 days, while in diet-matched controls it exceeded the pretreatment value. Epididymal fat pad weight in hyperleptinemics was still 28% below paired controls at 150 days posttreatment. Histologic examination revealed adipocytes of hyperleptinemic animals to be smaller 60 days after treatment. At 60 days, adipose tissue UCP-2 gene expression in hyperleptinemics was still above controls, but expression of other lipogenic and oxidative enzymes had returned to baseline expression levels. We conclude that in normal rats recovery of body fat following adenovirus-induced hyperleptinemia is much slower than after caloric restriction, possibly because of persistent upregulation of adipocyte UCP-2.

Adenoviridae↗

PubMed2000

Evaluation of direct and cooperative contributions towards the strength of buried hydrogen bonds and salt bridges.

An experimental approach to evaluate the net binding free energy of buried hydrogen bonds and salt bridges is presented. The approach, which involves a modified multiple-mutant cycle protocol, was applied to selected interactions between TEM-1-beta-lactamase and its protein inhibitor, BLIP. The selected interactions (two salt bridges and two hydrogen bonds) all involving BLIP-D49, define a distinct binding unit. The penta mutant, where all side-chains constructing the binding unit were mutated to Ala, was used as a reference state to which combinations of side-chains were introduced. At first, pairs of interacting residues were added allowing the determination of interaction energies in the absence of neighbors, using double mutant cycles. Addition of neighboring residues allowed the evaluation of their cooperative effects on the interaction. The two isolated salt bridges were either neutral or repulsive whereas the two hydrogen bonds contribute 0.3 kcal mol(-1 )each. Conversely, a double mutant cycle analysis of these interactions in their native environment showed that they all stabilize the complex by 1-1.5 kcal mol(-1). Examination of the effects of neighboring residues on each of the interactions revealed that the formation of a salt bridge triad, which involves two connected salt bridges, had a strong cooperative effect on stabilizing the complex independent of the presence or absence of additional neighbors. These results demonstrate the importance of forming net-works of buried salt bridges. We present theoretical electrostatic calculations which predict the observed mode of cooperativity, and suggest that the cooperative networking effect results from the favorable contribution of the protein to the interaction. Furthermore, a good correlation between calculated and experimentally determined interaction energies for the two salt bridges, and to a lesser extent for the two hydrogen bonds, is shown. The data analysis was performed on values of DeltaDeltaG(double dagger)K(d) which reflect the strength of short range interactions, while DeltaDeltaG(o)K(D) values which include the effects of long range electrostatic forces that alter specifically DeltaDeltaG(double dagger)k(a) were treated separately.

Allosteric Site↗

PubMed2000

[Effect of choice of baseline correction interval on localization of electrical heart activity].

The electric heart activity can be localised from body surface mapping data with computer algorithms. At higher heart rates the T and P waves merge. Thus, the offset can not be subtracted in the TP segment. We investigated 28 healthy volunteers with signal averaged 31-lead magnetocardiography. The offset of the baseline was determined in the TP-segment and in the PR-segment, respectively. The electrical heart activity was localised in the initial 30 ms of the QRS complex (Q), at the QRS maximum (R), and at the T wave maximum (T). The volume currents were considered by using a boundary element model with the compartments lungs and torso. The 3D positions of the dipoles, the dipole orientations, and the dipole strengths were calculated using the data preprocessed with two different offset correction intervals. The offsets of the TP and PR segments significantly differed one from another. The average deviations of the dipole localisation were within a few centimetres (Q: 20 +/- 31 mm, R: 6 +/- 13 mm, T: 14 +/- 30 mm). However, in a small number of subjects (Q: n = 5, R: n = 2, T: n = 5) we observed a deviation of more than 30 mm. These deviations were not linearly correlated to the differences in the baseline offsets. High resolution recordings continuously detect heart activity in the PR segment. The correction of the baseline in the PR segment instead of the TP segment may introduce artefacts in the source localisation and therefore should be avoided.

Adolescent↗

PubMed1999

A simple algorithm for detecting circular permutations in proteins.

MOTIVATION: Circular permutation of a protein is a genetic operation in which part of the C-terminal of the protein is moved to its N-terminal. Recently, it has been shown that proteins that undergo engineered circular permutations generally maintain their three dimensional structure and biological function. This observation raises the possibility that circular permutation has occurred in Nature during evolution. In this scenario a protein underwent circular permutation into another protein, thereafter both proteins further diverged by standard genetic operations. To study this possibility one needs an efficient algorithm that for a given pair of proteins can detect the underlying event of circular permutations. A possible formal description of the question is: given two sequences, find a circular permutation of one of them under which the edit distance between the proteins is minimal. A naive algorithm might take time proportional to N3 or even N4, which is prohibitively slow for a large-scale survey. A sophisticated algorithm that runs in asymptotic time of N2 was recently suggested, but it is not practical for a large-scale survey. RESULTS: A simple and efficient algorithm that runs in time N2 is presented. The algorithm is based on duplicating one of the two sequences, and then performing a modified version of the standard dynamic programming algorithm. While the algorithm is not guaranteed to find the optimal results, we present data that indicate that in practice the algorithm performs very well. AVAILABILITY: A Fortran program that calculates the optimal edit distance under circular permutation is available upon request from the authors. CONTACT: ron@biocom1.ls.biu.ac.il.

Algorithms↗

PubMed1999

[Active life expectancy in Germany].

Using the method of multistate life-tables, the article presents results on active life expectancy on the basis of the German Socio-Economic Panel Survey (SOEP). Different determinants of mortality and morbidity are revealed by event-history analysis. Results show that men live a greater proportion of their lives without disability than do women. Results on the association between mortality/morbidity and socio-economic factors suggest that studies which usually focussed either on mortality or on morbidity cannot fully explain differences in active life expectancy.

Adult↗

PubMed1998

Fenfluramine challenge test as a marker of serotonin activity in patients with Alzheimer's dementia and agitation.

BACKGROUND: Changes in serotonin (5-HT) have been described in both Alzheimer's disease (AD) and aggressive/agitated behaviors. This paper explores a possible association between 5-HT deficits and agitation in AD, using prolactin response to d,1-fenfluramine administration as a probe for 5-HT activity. METHODS: Five AD patients with agitation and 5 without agitation received a 60-mg oral dose of d,1-fenfluramine. Prolactin levels were obtained at baseline, and 2 and 3 hours following administration. RESULTS: Change in prolactin levels from baseline to 3 hours was significantly larger among the agitated than the nonagitated Alzheimer's patients. Further, there was a positive and significant correlation between change in prolactin levels from baseline and level of agitation. CONCLUSIONS: These findings suggest an association between 5-HT responsiveness and agitation in AD.

Aged↗

PubMed1998

Pooled analysis of p53 mutations in hematological malignancies.

A computerized database is described that contains information about 507 mutations in the p53 gene of hematologic tumors and corresponding cell lines. Analysis of these mutations indicated the following findings: First, mutational spectrum analysis in these tumors was found to be similar to the pattern found for other solid tumors. However, when the patterns of base substitutions were examined separately according to the types of hematologic malignancies, followed by subgroup analysis, notable differences (in some cases of statistical significance) emerged. Second, mutational pattern analysis indicates that about 48% of base substitutions in hematologic tumors are suspected to be associated with carcinogen exposure. Third, deletions and insertions are localized mainly to exons 5-8 and repeated DNA sequences. However, the unusual profile of variations in frequency within each type of tumor suggests that, in addition to endogenous damage to template DNA, there is the factor of exposure to environmental physical and chemical carcinogens/mutagens. Fourth, p53 protein alterations analysis indicate that most of the changes in the amino acids are "semiconservative," presumably in order to avoid disrupting the structure of the p53 monomer. Consistent with this notion, structural mutations are more conservative than the binding mutations. Finally, molecular mechanisms that lead to p53 mutations, etiological factors that play a role in their formation, and the pathophysiological significance of consequent p53 protein alterations are discussed.

Amino Acid Substitution↗

PubMed1998

A simple model for evolution of proteins towards the global minimum of free energy.

BACKGROUND: Proteins seem to have their native structure in a global minimum of free energy. No mechanism is known, however, for ensuring this property. Furthermore, computational complexity studies suggest that such a mechanism is not feasible. These seemingly contradictory observations can be reconciled by the suggestion that evolutionary selection can yield proteins whose native conformation is in the global minimum of free energy. The aim of this study is to investigate such evolutionary processes in a simple model of protein folding. RESULTS: Three possible evolutionary processes are explored.First, if the free energy of the chain is kept below a fixed threshold there is no improvement towards the global minimum. Second, if free energy is minimized directly, sequences emerge whose native conformation is in the global minimum of free energy. Third, when evolutionary pressure is applied within a small set of close homologs, sequences emerge whose functional conformation is in the global minimum of free energy. CONCLUSIONS: Although minimizing free energy does select for sequences whose functional conformation is in the global free energy minimum, we argue that for most proteins, which typically have free energy values of only 5-15 kcal/mol, such evolutionary pressure cannot be considered biologically plausible. In contrast, by repeatedly forcing sequences to avoid drifting towards competing "non-native" conformations, sequences emerge whose native conformation becomes very close to the global minimum of free energy. We argue that such a mechanism is both efficient and biologically plausible.

Algorithms↗

PubMed1998

Genetic algorithms for protein threading.

Despite many years of efforts, a direct prediction of protein structure from sequence is still not possible. As a result, in the last few years researchers have started to address the "inverse folding problem": Identifying and aligning a sequence to the fold with which it is most compatible, a process known as "threading". In two meetings in which protein folding predictions were objectively evaluated, it became clear that threading as a concept promises a real breakthrough, but that much improvement is still needed in the technique itself. Threading is a NP-hard problem, and thus no general polynomial solution can be expected. Still a practical approach with demonstrated ability to find optimal solutions in many cases, and acceptable solutions in other cases, is needed. We applied the technique of Genetic Algorithms in order to significantly improve the ability of threading algorithms to find the optimal alignment of a sequence to a structure, i.e. the alignment with the minimum free energy. A major progress reported here is the design of a representation of the threading alignment as a string of fixed length. With this representation validation of alignments and genetic operators are effectively implemented. Appropriate data structure and parameters have been selected. It is shown that Genetic Algorithm threading is effective and is able to find the optimal alignment in a few test cases. Furthermore, the described algorithm is shown to perform well even without pre-definition of core elements. Existing threading methods are dependent on such constraints to make their calculations feasible. But the concept of core elements is inherently arbitrary and should be avoided if possible. While a rigorous proof is hard to submit yet an, we present indications that indeed Genetic Algorithm threading is capable of finding consistently good solutions of full alignments in search spaces of size up to 10(70).

Algorithms↗

PubMed1997

The impact of residual disease on local recurrence in patients treated by initial unplanned resection for soft tissue sarcoma of the extremity.

BACKGROUND AND OBJECTIVES: "Unplanned excision" in soft tissue sarcoma (STS) is defined as the gross removal of tumor without preoperative staging or consideration of the need for removal of normal tissue around the tumor. This study evaluated whether unplanned excision in patients with extremity STS would have an impact on local relapse (LR), even if reexcision of the tumor bed was undertaken. METHOD: Two hundred thirty-nine (239) patients with primary, extremity STS treated with limb salvage surgery were included in this study. Of the 239, 78% were treated with surgery and irradiation. Forty-seven tumors were low-grade and 192 high grade. Mean tumor diameter was 7.5 cm. Twenty had local recurrences and 64 relapsed systemically. RESULTS: Only margin and prior surgery were significant in univariate analysis (P < 0.05, log-rank test). The Cox multivariate analysis revealed that both margin of resection (P < 0.001) and the status of the local tumor site (P < 0.05) at definitive surgery were significant predictors of local relapse. CONCLUSIONS: These results suggest that the presence of microscopic disease in the reexcised specimen following unplanned resection is a risk factor for local disease recurrence.

Adolescent↗

PubMed1997

Chaos in protein dynamics.

MD simulations, currently the most detailed description of the dynamic evolution of proteins, are based on the repeated solution of a set of differential equations implementing Newton's second law. Many such systems are known to exhibit chaotic behavior, i.e., very small changes in initial conditions are amplified exponentially and lead to vastly different, inherently unpredictable behavior. We have investigated the response of a protein fragment in an explicit solvent environment to very small perturbations of the atomic positions (10(-3)-10(-9) A). Independent of the starting conformation (native-like, compact, extended), perturbed dynamics trajectories deviated rapidly, leading to conformations that differ by approximately 1 A RMSD within 1-2 ps. Furthermore, introducing the perturbation more than 1-2 ps before a significant conformational transition leads to a loss of the transition in the perturbed trajectories. We present evidence that the observed chaotic behavior reflects physical properties of the system rather than numerical instabilities of the calculation and discuss the implications for models of protein folding and the use of MD as a tool to analyze protein folding pathways.

Bacterial Proteins↗

PubMed1996

Local interactions dominate folding in a simple protein model.

Recent computational studies of simple models of protein folding have concluded that a pronounced energy minimum (i.e. large gap in energy between low-energy states of the model) is a necessary and sufficient condition to ensure folding of a sequence to its lowest-energy conformation. Here, we show that this conclusion strongly depends on the particular temperature scheme selected to govern the simulations. On the other hand, we show that there is a dominant factor determining if a sequence is foldable. That is, the strength of possible interactions between residues close in the sequence. We show that sequences with many possible strong local interactions (either favorable or, more surprisingly, a mixture of strong favorable and unfavorable ones) are easy to fold. Progressively increasing the strength of such local interactions makes sequences easier and easier to fold. These results support the idea that initial formation of local substructures is important to the foldability of real proteins.

Mathematical Computing↗

PubMed1996

Positive and negative cooperativities at subsequent steps of oxygenation regulate the allosteric behavior of multistate sebacylhemoglobin.

Cross-linked human hemoglobin (HbA) is obtained by reaction with bis(3,5-dibromosalicyl) sebacate. Peptide maps and crystallographic analyses confirm the presence of the 10 carbon atom long sebacyl residue cross-linking the two beta82 lysines of the beta-cleft (DecHb). The Adair's constants, obtained from the oxygen binding isotherms, show that at the first step of oxygenation normal hemoglobin and DecHb have a very similar oxygen affinity. In DecHb negative binding cooperativity is present at the second step of oxygenation, which has an affinity 27 times lower than at the first step. Positive cooperativity is present at the third binding step, whose affinity is 380 times that of the second step. The fourth binding step shows a weak negative cooperativity with an affinity one-half that of the third step. Crystals of deoxy-DecHb diffracted to 1.9 angstroms resolution. The resulting atomic coordinates are very similar to those of Fermi et al. [(1984) J. Mol.Biol. 175, 159-174] and Fronticelli et al. [(1994) J. Biol Chem. 269, 23965-23969] for deoxy-HbA. The electron density map of deoxy-DecHb indicates the presence of the 10 carbon bridge between the beta82 lysines. Molecular modeling confirms that insertion of the linker into the T structure requires only slight displacement of the two beta82 lysines. Instead, insertion of the linker into the R and R2 structures [Shaanan (1983) J. Mol. Biol. 171, 31-59; Silva et al. (1992) J. Biol. Chem. 267, 17248-17256] is hindered by serious sterical restrictions. The linker primarily affects the partially and fully liganded states of hemoglobin. The data suggest in DecHb concerted conformational changes at each step of oxygenation.

Allosteric Regulation↗