Biomedical subjects

Andreas Wagner

Publications and source records attributed to Andreas Wagner.

At least 19 recordsLinked to original sources

PubMed2006

Cooperation is fleeting in the world of transposable elements.

Composite transposons are key vehicles for the worldwide spreading of genes that allow bacteria to survive toxic compounds. Composite transposons consist of two smaller transposable elements called insertion sequences (ISs), which flank the genes that permit such survival. Each IS in a composite transposon can either transpose alone, selfishly, or it can transpose cooperatively, jointly with the other IS. Cooperative transposition can enhance an IS's chance of survival, but it also carries the risk of transposon destruction. I use game theory to show that the conditions under which cooperative transposition is an evolutionarily stable strategy (ESS) are not biologically realistic. I then analyze the distribution of thousands of ISs in more than 200 bacterial genomes to test the following prediction of the game-theoretical model: if cooperative transposition was an ESS, then the closely spaced ISs that characterize composite transposons should be more abundant in genomes than expected by chance. The data show that this is not the case. Cooperativity can only be maintained in a transitional, far-from-equilibrium state shortly after a selection pressure first arises. This is the case in the spreading of antibiotic resistance, where we are witnessing a fleeting moment in evolution, a moment in which cooperation among selfish DNA molecules has provided a means of survival. Because such cooperation does not pay in the long run, the vehicles of such survival will eventually disappear again. My analysis demonstrates that game theory can help explain behavioral strategies even for mobile DNA.

Animals↗

PubMed2006

Chemoradiotherapy with gemcitabine and continuous 5-FU in patients with primary inoperable pancreatic cancer.

CONTEXT: Gemcitabine and 5-fluorouracil (5-FU) sensitize tumor cells to radiation. Furthermore, 5-FU enhances the cytotoxic effect of gemcitabine. OBJECTIVE: We report the efficacy and the toxicity of concurrent chemoradiation with gemcitabine and 5-FU in the treatment of patients with locally advanced, unresectable pancreatic cancer. PATIENTS: Thirty-two patients (20 men, 12 women; median age 69.9 years) with histologically proven advanced pancreatic carcinoma were included in the study. INTERVENTIONS: The patients received chemotherapy with gemcitabine 300 mg/m2 on days 1, 15, 29 and 5-FU as continuous infusion 350 mg/m2/day of radiation while concurrent radiation (45-50 Gy) was given to the tumor and regional lymph nodes (1.8-2.0 Gy/fraction on 5 days/week). Subsequent to chemoradiotherapy, the treatment was continued with an additional two cycles of gemcitabine (1,000 mg/m2) and cisplatin (50 mg/m2) applied on days 1 and 15 of a four-week cycle. MAIN OUTCOME MEASURES: Patient survival, time to progression, and toxicity of chemoradiation. Tumor responses (complete resolution; partial response; stable disease, and progressive disease) were also evaluated. RESULTS: After the completion of chemoradiotherapy, 2 patients (6.3%) achieved complete resolution and 18 patients (56.3%) a partial response, for an overall response rate of 62.5%. Twelve patients (37.5%) were considered resectable and 9 underwent laparotomy, 7 of whom had definitive pancreatic resection. Four patients had negative surgical margins. With a median follow-up of 49.7 months (95% CI: 48.6-60.8 months) after the completion of chemoradiation, distant metastasis occurred in 25 patients (78.1%) while local recurrence was seen only in 4 of 32 patients (12.5%). Median time to progression was 9.2 months (95% CI: 8.2-10.2 months). Median survival amounted to 13.6 months (95% CI: 12.7-14.6 months) for all patients while it was prolonged to 16.4 months (95% CI: 13.4-19.4 months) for those undergoing secondary resection. In addition, performance status proved to be another prognostic factor for overall survival. The main toxicity of chemoradiation included grade 3-4 leukopenia in 18 patients (56.3%) and thrombocytopenia in 8 patients (25.0%). Episodes of cholangitis were observed in 7 patients (21.9%). CONCLUSION: Gemcitabine and 5-FU can safely be combined with external beam radiation. This preoperative treatment approach is highly effective and appears to improve survival in patients with good performance status and in those who are eligible for a secondary resection.

Aged↗

PubMed2006

Alternative routes and mutational robustness in complex regulatory networks.

Alternative pathways through a gene regulation network connect a regulatory molecule to its (indirect) regulatory target via different intermediate regulators. We here show for two large transcriptional regulation networks, and for 15 different signal transduction networks, that multiple alternative pathways between regulator and target pairs are the rule rather than the exception. We find that in the yeast transcriptional regulation network intermediate regulators that are part of many alternative pathways between a regulator and target pair evolve at faster rates. This variation is not solely explicable by higher expression levels of such regulators, nor is it solely explicable by their variable usage in different physiological or environmental conditions, as indicated by their variable expression. This suggests that such pathways can continue to function despite amino acid changes that may impair one intermediate regulator. Our results underscore the importance of systems biology approaches to understand functional and evolutionary constraints on genes and proteins.

Evolution, Molecular↗

PubMed2006

Identification of HLA-A*0201-presented T cell epitopes derived from the oncofetal antigen-immature laminin receptor protein in patients with hematological malignancies.

The oncofetal Ag immature laminin receptor (OFA-iLR) is a potential target molecule for immunotherapeutic studies in several tumor entities, including hematological malignancies. In the present study, we characterize two HLA-A*0201-presented epitopes eliciting strong OFA-iLR peptide-specific human cytotoxic T cell (CTLs) responses in vitro. Both allogeneic HLA-A*0201-matched and autologous CTLs recognized and killed endogenously OFA-iLR-expressing tumor cell lines and primary malignant cells from patients with hemopoietic malignancies in an MHC-restricted fashion but spared nonmalignant hemopoietic cells. Spontaneous OFA-iLR peptide-specific T cell reactivity was detectable in a significant proportion of leukemia patients. Interestingly, in patients with chronic lymphocytic leukemia and multiple myeloma but not in those with acute myeloid leukemia, significant frequencies of OFA peptide-specific CTLs could be detected in an early stage of disease but disappeared in patients with progressive disease. The identification of OFA-iLR-derived peptide epitopes provides a basis for tumor immunological studies and therapeutic vaccination strategies in patients with OFA-iLR-expressing malignancies.

Adult↗

PubMed2006

Influence of metabolic network structure and function on enzyme evolution.

BACKGROUND: Most studies of molecular evolution are focused on individual genes and proteins. However, understanding the design principles and evolutionary properties of molecular networks requires a system-wide perspective. In the present work we connect molecular evolution on the gene level with system properties of a cellular metabolic network. In contrast to protein interaction networks, where several previous studies investigated the molecular evolution of proteins, metabolic networks have a relatively well-defined global function. The ability to consider fluxes in a metabolic network allows us to relate the functional role of each enzyme in a network to its rate of evolution. RESULTS: Our results, based on the yeast metabolic network, demonstrate that important evolutionary processes, such as the fixation of single nucleotide mutations, gene duplications, and gene deletions, are influenced by the structure and function of the network. Specifically, central and highly connected enzymes evolve more slowly than less connected enzymes. Also, enzymes carrying high metabolic fluxes under natural biological conditions experience higher evolutionary constraints. Genes encoding enzymes with high connectivity and high metabolic flux have higher chances to retain duplicates in evolution. In contrast to protein interaction networks, highly connected enzymes are no more likely to be essential compared to less connected enzymes. CONCLUSION: The presented analysis of evolutionary constraints, gene duplication, and essentiality demonstrates that the structure and function of a metabolic network shapes the evolution of its enzymes. Our results underscore the need for systems-based approaches in studies of molecular evolution.

Amino Acid Substitution↗

PubMed2006

Histological and cell biological characterization of dissected cartilage fragments in human osteochondritis dissecans of the femoral condyle.

INTRODUCTION: Osteochondritis dissecans (OCD) within the weight-bearing femoral condyle carries a high risk of osteoarthritis. The definitive pathogenetic cause is unclear. Therefore biochemical and cellular features of OCD were analyzed and compared to macroscopically normal cartilage of the same joint surface. MATERIALS AND METHODS: Dissected fragments from 14 patients and biopsies of normal cartilage from the intercondylar notch as controls were harvested at arthroscopy. Staining with safranin O to monitor proteoglycan content, alkaline phosphatase activity, and immunohistochemistry with mouse monoclonal antibodies to collagen types I, II, and X. Chondrocytes were isolated for RT-PCR to detect GAPDH, collagen types I, II, X, aggrecan, TGF-beta, BMP-7, bFGF, VEGF and IL-1. RESULTS: The dissected cartilage displayed significant variability. Apart from normal cartilage matrix components also atypical molecules such as collagen type X and alkaline phosphatase were detected at the tidemark but also across the entire dissecate, suggesting chondrocyte hypertrophy. Extended fibrous degeneration associated with collagen type I deposition was observed at the surface and may indicate chondrocyte dedifferentiation. Viable cells could be extracted from OCD and notch. Both expressed similar mRNA levels for matrix molecules, growth factors, and interleukin-1 (IL-1), however significantly more Col X mRNA was detected in dissecates. CONCLUSION: Histology suggests focal alteration of cartilage matrix originating from the basis of the joint cartilage, potentially the mineralized layer or subchondral bone. The molecular analysis indicates a disorganization of cartilage homeostasis across the joint accompanied by embryogenetic processes. The surprisingly high viability and quality of the extracted cells suggests a still preserved intrinsic repair capacity of those vital dissecates.

Cartilage, Articular↗

PubMed2006

GMP production of liposomes--a new industrial approach.

A new scalable liposome production system is presented, which is based on the ethanol injection technique. The system permits liposome manufacture regardless of production scale, as scale is determined only by free disposable vessel volumes. Once the parameters are defined, an easy scale up can be performed by just changing the process vessels. These vessels are fully sterilizeable and all raw materials are transferred into the sanitized and sterilized system via 0.2 microm filters to guarantee an aseptic production. Liposome size can be controlled by the local lipid concentration at the injection point depending on process parameters like injection pressure, lipid concentration and injection rate. These defined process parameters are furthermore responsible for highly reproducible results with respect to vesicle diameters and encapsulation rates Compared to other technologies like the film method which is normally followed by size reduction through high pressure homogenization, ultrasonication or extrusion, no mechanical forces are needed to generate homogeneous and narrow distributed liposomes. Another important advantage of this method is the suitability for the entrapment of many different drug substances such as large hydrophilic proteins by passive encapsulation, small amphiphilic drugs by a one step remote loading technique or membrane association of antigens for vaccination approaches.

Liposomes↗

PubMed2006

Dietary supplementation with 11trans- and 12trans-18:1 and oxidative stress in humans.

BACKGROUND: High consumption of trans fat has been associated with high oxidative stress in humans, which could increase the risk of the development or acceleration of several diseases, such as atherosclerosis, cancer, and type 2 diabetes. OBJECTIVE: Several urinary and blood biomarkers of oxidative stress [8-iso-prostaglandin-F(2alpha) (PGF(2alpha)), 15-keto-dihydro-PGF(2alpha), and 7,8-dihydro-8-oxo-2'-deoxy-guanosine in urine and alpha-,beta-,gamma-,delta-tocopherol, and retinol in plasma] were monitored to evaluate the oxidative stress induced by dietary supplementation of 11trans- and 12trans-18:1 isomers in humans during a 6-wk intervention. DESIGN: After a 14-d adaptation period free of trans fatty acid supplementation (baseline), the test group (n = 12) received 3.0 g 11trans-18:1/d and 3.0 g 12trans-18:1/d (Sigma 6.0 g/d), and the control group (n = 12) consumed a control oil free of trans fatty acids and conjugated linoleic acids for 6 wk. RESULTS: The postintervention concentration of urinary 8-iso-PGF(2alpha) (free radical-induced lipid peroxidation) in the test group was significantly higher than baseline and significantly higher than that observed in the control group. The concentrations of 15-keto-dihydro-PGF(2alpha) (cyclooxygenase-mediated inflammatory response indicator) and 7,8-dihydro-8-oxo-2'-deoxy-guanosine (oxidative DNA damage) were not affected by the 11trans- and 12trans-18:1 supplementation. CONCLUSIONS: Although an increase in urinary 8-iso-PGF(2alpha) was observed and the effects of prolonged high (ie, >5.0 g/d) consumption of trans fat could be relevant to the development of disease, the mean intakes of 11trans- and 12trans-18:1 in Europeans are estimated to be significantly below the amounts administered in this study (ie, 6.0 g/d); such low intakes could minimize the possible risk of detrimental effects on human health.

8-Hydroxy-2'-Deoxyguanosine↗

PubMed2005

Periodic extinctions of transposable elements in bacterial lineages: evidence from intragenomic variation in multiple genomes.

Most previous work on the evolution of mobile DNA was limited by incomplete sequence information. Whole genome sequences allow us to overcome this limitation. I study the nucleotide diversity of prominent members of five insertion sequence families whose transposition activity is encoded by a single transposase gene. Eighteen among 376 completely sequenced bacterial genomes and plasmids carry between 3 and 20 copies of a given insertion sequence. I show that these copies generally show very low DNA divergence. Specifically, more than 68% of the transposase genes are identical within a genome. The average number of amino acid replacement substitutions at amino acid replacement sites is Ka = 0.013, that at silent sites is Ks = 0.1. This low intragenomic diversity stands in stark contrast to a much higher divergence of the same insertion sequences among distantly related genomes. Gene conversion among protein-coding genes is unlikely to account for this lack of diversity. The relation between transposition frequencies and silent substitution rates suggests that most insertion sequences in a typical genome are evolutionarily young and have been recently acquired. They may undergo periodic extinction in bacterial lineages. By implication, they are detrimental to their host in the long run. This is also suggested by the highly skewed and patchy distribution of insertion sequences among genomes. In sum, one can think of insertion sequences as slow-acting infectious diseases of cell lineages.

Bacteria↗

PubMed2005

Experimental design for in vitro skin penetration study of liposomal superoxide dismutase.

A computer-based technique using a 2((5-2)) fractional factorial design was applied for screening the factors affecting the penetration effectiveness of liposomal recombinant human-Cu/Zn-superoxide dismutase. Unilamellar liposomes, containing recombinant rh-Cu/Zn-SOD in the aqueous core, are aimed at enhancing the penetration of the drug applied topically. Factors that mainly influence the chemical and physical characteristics of liposomes such as charge, molar content of cholesterol, size, surfactant and lipid were evaluated at two levels. In vitro skin penetration studies with pigskin were carried out in Franz-type diffusion cells over a period of 4 and 8h. The response variables, namely the amounts of rh-Cu/Zn-SOD penetrated into the different skin layers, were analyzed by ELISA (enzyme linked immunosorbent assay). Analysis of variance showed that the size and the cholesterol content of liposomes as well as the duration of the penetration studies have a statistically significant influence on the amount of protein found in deeper skin layers.

1,2-Dipalmitoylphosphatidylcholine↗

PubMed2005

A model of protein translation including codon bias, nonsense errors, and ribosome recycling.

We present and analyse a model of protein translation at the scale of an individual messenger RNA (mRNA) transcript. The model we develop is unique in that it incorporates the phenomena of ribosome recycling and nonsense errors. The model conceptualizes translation as a probabilistic wave of ribosome occupancy traveling down a heterogeneous medium, the mRNA transcript. Our results show that the heterogeneity of the codon translation rates along the mRNA results in short-scale spikes and dips in the wave. Nonsense errors attenuate this wave on a longer scale while ribosome recycling reinforces it. We find that the combination of nonsense errors and codon usage bias can have a large effect on the probability that a ribosome will completely translate a transcript. We also elucidate how these forces interact with ribosome recycling to determine the overall translation rate of an mRNA transcript. We derive a simple cost function for nonsense errors using our model and apply this function to the yeast (Saccharomyces cervisiae) genome. Using this function we are able to detect position dependent selection on codon bias which correlates with gene expression levels as predicted a priori. These results indirectly validate our underlying model assumptions and confirm that nonsense errors can play an important role in shaping codon usage bias.

Animals↗

PubMed2005

Circuit topology and the evolution of robustness in two-gene circadian oscillators.

Many parameters driving the behavior of biochemical circuits vary extensively and are thus not fine-tuned. Therefore, the topology of such circuits (the who-interacts-with-whom) is key to understanding their central properties. I here explore several hundred different topologies of a simple biochemical model of circadian oscillations to ask two questions: Do different circuits differ dramatically in their robustness to parameter change? If so, can a process of gradual molecular evolution find highly robust topologies when starting from less robust topologies? I find that the distribution of robustness among different circuit topologies is highly skewed: Most show low robustness, whereas very few topologies are highly robust. To address the second evolutionary question, I define a topology graph, each of whose nodes corresponds to one circuit topology that shows circadian oscillations. Two nodes in this graph are connected if they differ by only one regulatory interaction within the circuit. For the circadian oscillator I study, most topologies are connected in this graph, making evolutionary transitions from low to high robustness easy. A similar approach has been used to study the evolution of robustness in biological macromolecules, with similar results. This suggests that the same principles govern the evolution of robustness on different levels of biological organization. The regulatory interlocking of several oscillating gene products in biological circadian oscillators may exist because it provides robustness.

Biological Clocks↗

PubMed2005

The rarity of gene shuffling in conserved genes.

BACKGROUND: Among three sources of evolutionary innovation in gene function - point mutations, gene duplications, and gene shuffling (recombination between dissimilar genes) - gene shuffling is the most potent one. However, surprisingly little is known about its incidence on a genome-wide scale. RESULTS: We have studied shuffling in genes that are conserved between distantly related species. Specifically, we estimated the incidence of gene shuffling in ten organisms from the three domains of life: eukaryotes, eubacteria, and archaea, considering only genes showing significant sequence similarity in pairwise genome comparisons. We found that successful gene shuffling is very rare among such conserved genes. For example, we could detect only 48 successful gene-shuffling events in the genome of the fruit fly Drosophila melanogaster which have occurred since its common ancestor with the worm Caenorhabditis elegans more than half a billion years ago. CONCLUSION: The incidence of gene shuffling is roughly an order of magnitude smaller than the incidence of single-gene duplication in eukaryotes, but it can approach or even exceed the gene-duplication rate in prokaryotes. If true in general, this pattern suggests that gene shuffling may not be a major force in reshaping the core genomes of eukaryotes. Our results also cast doubt on the notion that introns facilitate gene shuffling, both because prokaryotes show an appreciable incidence of gene shuffling despite their lack of introns and because we find no statistical association between exon-intron boundaries and recombined domains in the two multicellular genomes we studied.

Animals↗

PubMed2005

Intra-articular injections of high-molecular-weight hyaluronic acid have biphasic effects on joint inflammation and destruction in rat antigen-induced arthritis.

To assess the potential use of hyaluronic acid (HA) as adjuvant therapy in rheumatoid arthritis, the anti-inflammatory and chondroprotective effects of HA were analysed in experimental rat antigen-induced arthritis (AIA). Lewis rats with AIA were subjected to short-term (days 1 and 8, n = 10) or long-term (days 1, 8, 15 and 22, n = 10) intra-articular treatment with microbially manufactured, high-molecular-weight HA (molecular weight, 1.7 x 10(6) Da; 0.5 mg/dose). In both tests, 10 buffer-treated AIA rats served as arthritic controls and six healthy animals served as normal controls. Arthritis was monitored by weekly assessment of joint swelling and histological evaluation in the short-term test (day 8) and in the long-term test (day 29). Safranin O staining was employed to detect proteoglycan loss from the epiphyseal growth plate and the articular cartilage of the arthritic knee joint. Serum levels of IL-6, tumour necrosis factor alpha and glycosaminoglycans were measured by ELISA/kit systems (days 8 and 29). HA treatment did not significantly influence AIA in the short-term test (days 1 and 8) but did suppress early chronic AIA (day 15, P < 0.05); however, HA treatment tended to aggravate chronic AIA in the long-term test (day 29). HA completely prevented proteoglycan loss from the epiphyseal growth plate and articular cartilage on day 8, but induced proteoglycan loss from the epiphyseal growth plate on day 29. Similarly, HA inhibited the histological signs of acute inflammation and cartilage damage in the short-term test, but augmented acute and chronic inflammation as well as cartilage damage in the long-term test. Serum levels of IL-6, tumour necrosis factor alpha, and glycosaminoglycans were not influenced by HA. Local therapeutic effects of HA in AIA are clearly biphasic, with inhibition of inflammation and cartilage damage in the early chronic phase but with promotion of joint swelling, inflammation and cartilage damage in the late chronic phase.

Adjuvants, Immunologic↗

PubMed2005

Robustness, evolvability, and neutrality.

Biological systems, from macromolecules to whole organisms, are robust if they continue to function, survive, or reproduce when faced with mutations, environmental change, and internal noise. I focus here on biological systems that are robust to mutations and ask whether such systems are more or less evolvable, in the sense that they can acquire novel properties. The more robust a system is, the more mutations in it are neutral, that is, without phenotypic effect. I argue here that such neutral change--and thus robustness--can be a key to future evolutionary innovation, if one accepts that neutrality is not an essential feature of a mutation. That is, a once neutral mutation may cause phenotypic effects in a changed environment or genetic background. I argue that most, if not all, neutral mutations are of this sort, and that the essentialist notion of neutrality should be abandoned. This perspective reconciles two opposing views on the forces dominating organismal evolution, natural selection and random drift: neutral mutations occur and are especially abundant in robust systems, but they do not remain neutral indefinitely, and eventually become visible to natural selection, where some of them lead to evolutionary innovations.

Animals↗

PubMed2005

Energy constraints on the evolution of gene expression.

I here estimate the energy cost of changes in gene expression for several thousand genes in the yeast Saccharomyces cerevisiae. A doubling of gene expression, as it occurs in a gene duplication event, is significantly selected against for all genes for which expression data is available. It carries a median selective disadvantage of s > 10(-5), several times greater than the selection coefficient s = 1.47 x 10(-7) below which genetic drift dominates a mutant's fate. When considered separately, increases in messenger RNA expression or protein expression by more than a factor 2 also have significant energy costs for most genes. This means that the evolution of transcription and translation rates is not an evolutionarily neutral process. They are under active selection opposing them. My estimates are based on genome-scale information of gene expression in the yeast S. cerevisiae as well as information on the energy cost of biosynthesizing amino acids and nucleotides.

Amino Acids↗

PubMed2005

Distributed robustness versus redundancy as causes of mutational robustness.

A biological system is robust to mutations if it continues to function after genetic changes in its parts. Such robustness is pervasive on different levels of biological organization, from macromolecules to genetic networks and whole organisms. I here ask which of two possible causes of such robustness are more important on a genome-wide scale, for systems whose parts are genes, such as metabolic and genetic networks. The first of the two causes is redundancy of a system's parts: A gene may be dispensable if the genome contains redundant, back-up copies of the gene. The second cause, distributed robustness, is more poorly understood. It emerges from the distributed nature of many biological systems, where many (and different) parts contribute to system functions. I will here discuss evidence suggesting that distributed robustness is equally or more important for mutational robustness than gene redundancy. This evidence comes from the functional divergence of redundant genes, as well as from large-scale gene deletion studies. I also ask whether one can quantify the extent to which redundancy or distributed robustness contribute to mutational robustness.

Animals↗

PubMed2005

[Charcot foot treated by correction and arthrodesis of the hindfoot].

THE PROBLEM: First patient: neuropathic osteoarthropathy with severely deformed foot, plantar ulceration and recurrent purulent infections. Second patient: diabetic osteoarthropathy with pathologic fracture. CLINICAL FINDINGS: First patient: 50-year-old man with hereditary sensory and motor neuropathy, plantar ulceration, equinus of the hindfoot, and extensive destruction of all bones of the foot. Recurrent infections necessitated repeated surgical interventions during the last 7 years. At the time of admission purulent infection of the foot. Healing after debridement including a resection of metatarsal bones and part of sequestrated bones of the foot. Patient was left with a severe equinus of the hindfoot. TREATMENT OPTIONS: Orthopedic shoes with or without below-knee orthesis. Lengthening of the Achilles tendon and plantar alignment of the calcaneus. Arthrodesis of the hindfoot. Below-knee amputation, if necessary as a primary procedure to combat infection. THE SOLUTION: Arthrodesis of the hindfoot after realignment; an amputation of the foot was refused. SURGICAL TECHNIQUE: Two-stage procedure: treatment of infection followed by astragalectomy and tibiocalcaneal arthrodesis achieved with cancellous lag screws. Bridging of the area of resection with a segment of the fibula. RESULT: Bony fusion and full load bearing in an orthopedic shoe after 3 months. Recurrence of ulcerations after 20 and 27 months due to wear of ill-fitting shoes. The accompanying purulent process forced the authors to resort to a below-knee amputation and fitting of a prosthesis. Second patient: of this patient only radiographs with a retrograde introduced intramedullary nail are shown.

Ankle Joint↗