Biomedical subjects

M Zacharias

Publications and source records attributed to M Zacharias.

At least 19 recordsLinked to original sources

PubMed2006

RNA aptamers as potential pharmaceuticals against infections with African trypanosomes.

Protozoal pathogens cause symptomatic as well as asymptomatic infections. They have a worldwide impact, which in part is reflected in the long-standing search for antiprotozoal chemotherapy. Unfortunately, effective treatments for the different diseases are by and large not available. This is especially true for African trypanosomiasis, also known as sleeping sickness. The disease is an increasing problem in many parts of sub-Saharan Africa, which is due to the lack of new therapeutics and the increasing resistance against traditional drugs such as melarsoprol, berenil and isometamidium. Considerable progress has been made over the past 10 years in the development of nucleic acid-based drug molecules using a variety of different technologies. One approach is a combinatorial technology that involves an iterative Darwinian-type in vitro evolution process, which has been termed SELEX for "systematic evolution of ligands by exponential enrichment". The procedure is a highly efficient method of identifying rare ligands from combinatorial nucleic acid libraries of very high complexity. It allows the selection of nucleic acid molecules with desired functions, and it has been instrumental in the identification of a number of synthetic DNA and RNA molecules, so-called aptamers that recognize ligands of different chemical origin. Aptamers typically bind their target with high affinity and high specificity and have successfully been converted into pharmaceutically active compounds. Here we summarize the recent examples of the SELEX technique within the context of identifying high-affinity RNA ligands against the surface of the protozoan parasite Trypanosoma brucei, which is the causative agent of sleeping sickness.

Animals↗

PubMed2006

Diagnostics and therapy of lymphoceles after kidney transplantation.

Lymphocele incidence after kidney transplantation is as high as 18%. We retrospectively studied the therapy of 42 lymphoceles that occurred in our clinic between 1990 and 2005, focusing on possible predisposing factors for their formation and the results of several therapy variants: conservative, operative, percutaneous puncture, and laparoscopic or open marsupialization. There was no connection between lymphocele formation and the following parameters: the extent to which the iliac vessels had been prepared, the materials used for the preparation, or whether clips or ligatures were applied. Lymphoceles may originate either from the lymphatic system of the recipient or the transplanted kidney. The most sensible measures to prevent their occurrence therefore seems to be to restrict the transplant bed to the smallest permissible level with careful ligature of the lymphatic vessels in the area of the kidney hilus. Treatment for lymphoceles should start with minimally invasive measures. We use the following algorithm in our clinic: puncture to differentiate between urinoma/lymphocele and to test for bacterial infection, sclerotization (200 mg doxycyclin), and finally marsupialization if persistent. The choice of operative technique depends on the location. This algorithm resulted in a relapse rate of 9.5% during the postoperative observation period of up to 15 years.

Diagnosis, Differential↗

PubMed2005

Interventions for protecting renal function in the perioperative period.

BACKGROUND: A number of methods have been used to try to protect kidney function in patients undergoing surgery. These include the administration of dopamine, diuretics, calcium channel blockers, angiotensin converting enzyme inhibitors and hydration fluids. OBJECTIVES: For this review, we selected randomized controlled trials, which employed different methods to protect renal function during the perioperative period. In examining these trials, we looked at outcomes such as renal failure and mortality, as well as changes in the renal function tests, including urine output, creatinine clearance, free water clearance, fractional excretion of sodium and renal plasma flow. SEARCH STRATEGY: We searched the Cochrane Central register of Controlled Trials (CENTRAL) (The Cochrane Library, Issue 4, 2004), MEDLINE (1966 to 2004) and EMBASE (1988 to 2004) and hand searched six journals (British Journal of Anaesthesia; Anesthesia and Analgesia; Anesthesiology; Annals of Surgery; Journal of Thoracic and Cardiovascular Surgery and Journal of Vascular Surgery). SELECTION CRITERIA: We selected all randomized controlled trials in adult population undergoing surgery where a treatment measure was used for the purpose of renal protection in the perioperative period. DATA COLLECTION AND ANALYSIS: We selected 37 studies for inclusion in this review. As well as analysis of the data from all the studies, we also performed subgroup analysis for type of interventions, types of surgical procedures and those with pre-existing renal dysfunction. We undertook sensitivity analysis on studies with high methodological quality. MAIN RESULTS: The review included data from 37 studies, comprising a total of 1227 patients. Of these, 658 received some form of treatment and 569 acted as controls. The interventions were mostly employing different pharmaceutical agents such as dopamine, diuretics, calcium channel blockers. ACE inhibitors or selected hydration fluids. The results indicated that certain interventions showed some benefits, but all the results suffered from significant heterogeneity. Hence we can draw no conclusions about the effectiveness of these interventions in protecting the kidneys during surgery. AUTHORS' CONCLUSIONS: There is no reliable evidence from available literature to suggest that interventions during surgery can protect the kidneys from damage. However, there is a need for more studies of high methodological quality. One particular area for further studies may be on patients with pre-existing renal dysfunction undergoing surgery.

Creatinine↗

PubMed2005

Sensitive assay for laboratory evolution of hydroxylases toward aromatic and heterocyclic compounds.

Powerful directed evolution methods have been developed for tailoring proteins to our needs in industrial applications. Here, the authors report a medium-throughput assay system designed for screening mutant libraries of oxygenases capable of inserting a hydroxyl group into a C-H bond of aromatic or O-heterocyclic compounds and for exploring the substrate profile of oxygenases. The assay system is based on 4-aminoantipyrine (4-AAP), a colorimetric phenol detection reagent. By using 2 detection wavelengths (509 nm and 600 nm), the authors achieved a linear response from 50 to 800 microM phenol and standard deviations below 11% in 96-well plate assays. The monooxygenase P450 BM-3 and its F87A mutant were used as a model system for medium-throughput assay development, identification of novel substrates (e.g., phenoxytoluene, phenylallyether, and coumarone), and discovery of P450 BM-3 F87A mutants with 8-fold improvement in 3-phenoxytoluene hydroxylation activity. This activity increase was achieved by screening a saturation mutagenesis library of amino acid position Y51 using the 4-AAP protocol in the 96-well format.

Bacterial Proteins↗

PubMed2004

[New techniques in uro-sonography].

New sonographic techniques in urology, together with their principles of operation, will be presented. Together with the utilization of broadband ultrasound scanners and digital beam formers, leading to better spatial resolution and increased line density in ultrasound imaging, panorama sonography enables the outline of wide lateral regions independent of the width of the scanner. Spatial compound sonography achieves a comparatively better visualization of details in the b-mode image than has yet been available. The continuously improved 3-D, now leading to 4-D, techniques, which means real time capabilities, make the visualization of unrestricted imaging planes, which are not seen in conventional 2-D techniques, possible. The second harmonic imaging technique, including the special applications tissue harmonic imaging (THI) and contrast harmonic imaging (CHI), uses special ultrasound signal processing procedures for capturing and evaluating tissue hemoperfusion-here in combination with ultrasound contrast agents (UCA). Furthermore, microvascular imaging (MVI) enables the visualization of perfusion in tissues reaching the microcirculation regions. This leads to new possibilities for the assessment of pathological perfusion patterns, e.g. in andrology (perfusion of testicles) and uro-oncology (hyperperfusion of malignant regions).

Animals↗

PubMed2004

[Experimental investigations of the optimal therapy of systemic BCG infection in vivo].

PURPOSE: Hematogenous spread of BCG after intravesical instillation against bladder cancer is rare, but may result in systemic infection and hypersensitivity reaction. We investigated fluoroquinolones and steroids in an animal model to improve the therapeutic options in local and systemic BCG infection. Furthermore, we tested the antitumor effectiveness of intravesical BCG with simultaneous application of fluoroquinolones and/or steroids. METHODS: After systemic BCG infection, experiments were performed with quinolones as antimicrobial agent. Trimethoprim/sulfamethoxazole (TMS) was also tested in comparison to quinolones as a non-specific antimicrobial agent. To evaluate the hyperergic reaction after repeated BCG infection (hypersensitivity model), re-infection was performed seven days after primary infection with accompanying oral antimicrobial therapy with and without steroids. Intravesical tumor therapy was carried out with BCG in orthotopic murine bladder tumor model MB 49 together with simultaneous antimicrobial therapy. RESULTS: After primary infection, quinolones led to a significant prolonged survival independent of steroid administration. Steroids alone after primary BCG infection reduced the survival. In contrast to these experiments, only steroid-treated mice had a significant improvement in survival after a second challenge with BCG. Therapeutic efficacy of BCG was not affected by antibacterial therapy with quinolones. Steroids alone induced a significantly increased death rate during intravesical BCG therapy. CONCLUSION: Quinolones have a positive effect on survival in acute systemic BCG infection in mice. Re-infection with BCG led to severe hyperergic reaction that can only be influenced by steroids. Thus, quinolones can be used in primary systemic BCG infection after topical application as a sufficient alternative to common tuberculostatics. Repeated BCG instillation may lead to hyperergic reaction, making additional administration of steroids essential. In this animal model, therapeutic efficacy of BCG obviously was not affected by additional administration of antimicrobials.

Adrenal Cortex Hormones↗

PubMed2004

[Minimal invasiveness of laparoscopic radical prostatectomy: reality or dream?].

Currently, radical retropubic prostatectomy is the standard procedure for clinically localized prostate cancer. The surgical technique has been continuously refined for decades, resulting in reduced morbidity and improved functional and oncologic results. Since the late 90s, radical prostatectomy has been increasingly performed laparoscopically. A search of the available data has found that the articles published so far have proven the feasibility of the laparoscopic procedure but never confirmed its less invasiveness. In accordance with previous studies that have evaluated the invasiveness of various open and laparoscopic procedures, our clinic, which has routinely performed both techniques for several years, addressed the question whether laparoscopic prostatovesiculectomy indeed induces less severe surgical trauma. This prospective nonrandomized comparison study of the University Clinic of Urology at the Martin-Luther University at Halle-Wittenberg recruited a total of 64 patients, who underwent laparoscopic radical prostatectomy (n = 32) or open retropubic prostatectomy (n = 32) from January 2003 to April 2004. Both patient groups were comparable as to preoperative staging, PSA value and Gleason score. Besides perioperative parameters, such as surgical time, intra- and postoperative complications, blood loss and transfusion rate, need for analgetics and length of hospital stay, the comparison included oncologic data, such as Gleason score, pathologic stage and numbers of positive specimen margins. To get objectively reproducible data, the range of the systemic answers concerning the surgically induced tissue trauma was recorded as laboratory data. In all patients, pre-, intra-, and postsurgical markers of the acute-phase C-reactive protein, serum amyloid A (SAA), interleukin-6 (IL-6) and interleukin-10 (IL-10) were measured. The transfusion rate was 6 % for laparoscopic prostatectomies and 12 % for open prostatectomies. A rectal tear had to be intraoperatively repaired in one laparoscopically operated patient. The postoperative use of analgetics was comparable in both groups. The median hospital stay was 12.4 days for the laparoscopic and 11.2 days for the open surgical group. For T2 tumors, positive specimen margins were found in 6 cases (17 %) of the laparoscopic and in 4 cases (12 %) of the open surgical group. As to the indicators of any systemic reaction, no significant difference could be found during the entire clinical course between both surgical methods. In comparison with patients who underwent conventional open prostatectomy, patients with laparoscopically radical prostatectomy had identical to slightly higher serum levels of the acute-phase parameters, as evidence of an equal or a discretely manifested systemic response to the surgical trauma. The so far assumed less invasiveness of laparoscopic radical prostatectomy is not objectively supported by the data from this study. Thus, surgical trauma and its linked invasiveness must be considered equal for both methods, at least for the time being.

Adult↗

PubMed2004

Efficient search on energy minima for structure prediction of nucleic acid motifs.

Structure prediction of non-canonical motifs such as mismatches, extra unmatched nucleotides or internal and hairpin loop structures in nucleic acids is of great importance for understanding the function and design of nucleic acid structures. Systematic conformational analysis of such motifs typically involves the generation of many possible combinations of backbone dihedral torsion angles for a given motif and subsequent energy minimization (EM) and evaluation. Such approach is limited due to the number of dihedral angle combinations that grows very rapidly with the size of the motif. Two conformational search approaches have been developed that allow both an effective crossing of barriers during conformational searches and the computational demand grows much less with system size then search methods that explore all combinations of backbone dihedral torsion angles. In the first search protocol single torsion angles are flipped into favorable states using constraint EM and subsequent relaxation without constraints. The approach is repeated in an iterative manner along the backbone of the structural motif until no further energy improvement is obtained. In case of two test systems, a DNA-trinucleotide loop (sequence: GCA) and a RNA tetraloop (sequence: UUCG), the approach successfully identified low energy states close to experiment for two out of five start structures. In the second method randomly selected combinations of up to six backbone torsion angles are simultaneously flipped into preset ranges by a short constraint EM followed by unconstraint EM and acceptance according to a Metropolis acceptance criterion. This combined stochastic/EM search was even more effective than the single torsion flip approach and selected low energy states for the two test cases in between two and four cases out of five start structures.

Biophysical Phenomena↗

PubMed2004

Reversible scaling of dihedral angle barriers during molecular dynamics to improve structure prediction of cyclic peptides.

Peptide cyclization or chemical cross-linking has frequently been used to restrict the conformational freedom of a peptide, for example, to enhance its capacity for selective binding to a target receptor molecule. Structure prediction of cyclic peptides is important to evaluate possible conformations prior to synthesis. Because of the conformational constraints imposed by cyclization low energy conformations of cyclic peptides can be separated by large energy barriers. In order to improve the conformational search properties of molecular dynamics (MD) simulations a potential scaling method has been designed. The approach consists of several consecutive MD simulations with a specific lowering of dihedral energy barriers and reduced nonbonded interactions between atoms separated by three atoms followed by gradually scaling the potential until the original barriers are reached. Application to four cyclic penta- and hexa-peptide test cases and a protein loop of known structure indicates that the potential scaling method is more efficient and faster in locating low energy conformations than standard MD simulations. Combined with a generalized Born implicit solvation model the low energy cyclic peptide conformations and the loop structure are in good agreement with experiment. Applications in the presence of explicit water molecules during the simulations showed also improved convergence to structures close to experiment compared with regular MD.

Amino Acid Sequence↗

PubMed2004

A randomized crossover trial of tenoxicam compared with rofecoxib for postoperative dental pain control.

Two non-steroidal anti-inflammatory drugs, tenoxicam and rofecoxib, were compared for the control of postoperative pain following surgical extraction of bilaterally and symmetrically impacted wisdom teeth performed under intravenous sedation and local anaesthesia. Thirty-five young fit adult patients received each analgesic treatment for four days in a randomized, crossover design. The results suggest statistically better pain relief for the selective COX-2 inhibitor rofecoxib compared to tenoxicam, a traditional NSAID. There were side-effects with both treatments. Abdominal discomfort was significantly more common following rofecoxib compared to tenoxicam. Both analgesics were acceptable to most participants in the trial.

Adolescent↗

PubMed2003

[Standardized positioning and trocar placement for laparoscopic interventions in urology].

Over the last few years, laparoscopy has become more common in urology. Nevertheless only a few centres carry out more than 40 laparoscopies a year. A reduction to two standard techniques has led to the simplification and time optimisation in preparation for surgery and thus to an increase in quality. Two standard positionings and trocar placements are described for all important urological laparoscopies. At the same time, operations involving the small pelvis and the retroperitoneum are differentiated.

Female↗

PubMed2003

[Laparoscopic vs. open nephrectomy. 10 years' results of a nonrandomized comparative study of 549 patients with benign kidney diseases].

We report the results from a nonrandomized comparison of open flank vs laparoscopic nephrectomy in patients with benign renal disease. Between 1993 and 2002, 549 nephrectomies for benign renal disease were performed at the Department of Urology of the Medical University of Lübeck and the Urological Department of the Martin Luther University in Halle/Wittenberg. There were 236 patients in the open flank nephrectomy group and 313 patients in the laparoscopic nephrectomy group. Clinical parameters were compared among both groups. Median operative time in the open flank nephrectomy group was 90 min (range: 30-240 min) and also 90 min in the laparoscopic nephrectomy group (range: 41-210 min). There were 54 complications (17.2%) in the laparoscopic nephrectomy group compared to 60 complications (25.4%) in the open flank nephrectomy group. Patients in the laparoscopy group demonstrated clear advantages in terms of analgesic use for pain control, hospital stay, and convalescence. Laparoscopic nephrectomy results in a significantly briefer postoperative course when compared to open flank nephrectomy. However, due to a limited number of patients, a laparoscopic nephrectomy is mainly reserved for laparoscopic centers. Nevertheless, the laparoscopic approach should be offered to the majority of patients with benign renal disease requiring nephrectomy.

Adolescent↗

PubMed2002

[Transrectal ultrasound of the prostate. Current status and prospects].

In recent years the role of ultrasound in the diagnosis of prostate carcinoma has increased in importance. In view of the increasing incidence of prostate cancer, which is the most frequent malignant neoplasm in men, TRUS (transrectal ultrasound) is an important imaging method in the diagnosis of various prostate diseases. This paper provides a basic overview of physical and technical bases of TRUS investigation of the prostate. It concerns technical developments and modern techniques designed to improve its value in diagnosis. Impressive innovations in ultrasound equipment, particularly in the area of colour-coded Doppler sonography in association with microbubble-enhanced colour Doppler ultrasound, have given rise to justifiable hope of improvements in the early diagnosis of prostate cancer.

Diagnosis, Differential↗

PubMed2002

[Determination of acoustic parameters from ultrasound raw and HF data--a comparison].

Different methods for determination of acoustical tissue parameters based on rf data acquisition as well as the analysis of B-mode image data are well established. Because of limitations of the dynamic range and the restricted control of the tgc and focus settings the analysis of image data is not achievable in clinical practice. On the other side rf data are not available in most of the clinical scanners. So the analysis of raw data can be used as an compromise. Raw- and rf-data of complete B-mode scans obtained form a set of test phantoms by a clinical ultrasound device (HDI 5000, Philips) in connection with the applied gain settings were analyzed. For different system settings the estimated parameters showed a good agreement with the acoustical properties of the phantoms.

Acoustics↗

PubMed2001

Modelling ion binding to AA platform motifs in RNA: a continuum solvent study including conformational adaptation.

Binding of monovalent and divalent cations to two adenine-adenine platform structures from the Tetrahymena group I intron ribozyme has been studied using continuum solvent models based on the generalised Born and the finite-difference Poisson-Boltzmann approaches. The adenine-adenine platform RNA motif forms an experimentally characterised monovalent ion binding site important for ribozyme folding and function. Qualitative agreement between calculated and experimental ion placements and binding selectivity was obtained. The inclusion of solvation effects turned out to be important to obtain low energy structures and ion binding placements in agreement with the experiment. The calculations indicate that differences in solvation of the isolated ions contribute to the calculated ion binding preference. However, Coulomb attraction and van der Waals interactions due to ion size differences and RNA conformational adaptation also influence the calculated ion binding affinity. The calculated alkali ion binding selectivity for both platforms followed the order K(+) > Na(+) > Rb(+) > Cs(+) > Li(+) (Eisenman series VI) in the case of allowing RNA conformational relaxation during docking. With rigid RNA an Eisenman series V was obtained (K(+) > Rb(+) > Na(+) > Cs(+) > Li(+)). Systematic energy minimisation docking simulations starting from several hundred initial placements of potassium ions on the surface of platform containing RNA fragments identified a coordination geometry in agreement with the experiment as the lowest energy binding site. The approach could be helpful to identify putative ion binding sites in nucleic acid structures determined at low resolution or with experimental methods that do not allow identification of ion binding sites.

Adenine Nucleotides↗

PubMed2001

Conformations of an adenine bulge in a DNA octamer and its influence on DNA structure from molecular dynamics simulations.

Molecular dynamics simulations have been applied to the DNA octamer d(GCGCA-GAAC). d(GTTCGCGC), which has an adenine bulge at the center to determine the pathway for interconversion between the stacked and extended forms. These forms are known to be important in the molecular recognition of bulges. From a total of ~35 ns of simulation time with the most recent CHARMM27 force field a variety of distinct conformations and subconformations are found. Stacked and fully looped-out forms are in excellent agreement with experimental data from NMR and x-ray crystallography. Furthermore, in a number of conformations the bulge base associates with the minor groove to varying degrees. Transitions between many of the conformations are observed in the simulations and used to propose a complete transition pathway between the stacked and fully extended conformations. The effect on the surrounding DNA sequence is investigated and biological implications of the accessible conformational space and the suggested transition pathway are discussed, in particular for the interaction of the MS2 replicase operator RNA with its coat protein.

Adenine↗

PubMed2001

Conformational analysis of DNA-trinucleotide-hairpin-loop structures using a continuum solvent model.

A number of trinucleotide sequences in DNA can form compact and stable hairpin loops that may have significance for DNA replication and transcription. The conformational analysis of these motifs is important for an understanding of the function and design of nucleic acid structures. Extensive conformational searches have been performed on three experimentally known trinucleotide hairpin loops (AGC, AAA, and GCA) closed by a four-base-pair stem. An implicit solvation model based on the generalized Born method has been employed during energy minimization and conformational search. In addition, energy-minimized conformers were evaluated using a finite-difference Poisson-Boltzmann approach. For all three loop sequences, conformations close to experiment were found as lowest-energy structures among several thousand alternative energy minima. The inclusion of reaction-field contributions was found to be important for a realistic conformer ranking. Most generated hairpin loop structures within approximately 5 kcal x mol(-1) of the lowest-energy structure have a similar topology. Structures within approximately 10 kcal x mol(-1) could be classified into about five structural families representing distinct arrangements of loop nucleotides. Although a large number of backbone torsion angle combinations were compatible with each structural class, some specific patterns could be identified. Harmonic mode analysis was used to account for differences in conformational flexibility of low-energy sub-states. Class-specific differences in the pattern of atomic fluctuations along the sequence were observed; however, inclusion of conformational entropy contributions did not change ranking of structural classes. For an additional loop sequence (AAG) with no available experimental structure, the approach suggests a lowest-energy loop topology overall similar to the other three loop sequences but closed by a different non-canonical base-pairing scheme.

Biophysical Phenomena↗

PubMed2000

Comparison of molecular dynamics and harmonic mode calculations on RNA.

Conformational fluctuations of a double-stranded RNA oligonucleotide have been calculated from a two nanosecond molecular dynamics simulation including explicit waters and ions and from a harmonic mode analysis. The harmonic mode analysis was performed in the absence of solvent using various effective dielectric screening functions. RNA flexibility was analyzed and compared at the level of atomic position fluctuations, helical base-pair descriptor fluctuations and global helix bending, stretching, and twisting flexibilities. Although quantitative differences were found, the qualitative pattern of atomic position and helical descriptor fluctuations along the sequence was similar for both methods. For the helical descriptor flexibility, the largest differences were observed for base-pair roll and rise that showed two times larger fluctuations in the molecular dynamics simulation. A significant overlap between the sub-space spanned by soft principal components calculated from the molecular dynamics simulation and harmonic modes was found. Both approaches predict a negative covariation for most helical base-pair step descriptors of neighboring base pair steps (with the exception of rise), which tend to stiffen the RNA at the global level. The RNA persistence length extracted from the molecular dynamics simulation (350-600 A) is smaller than the experimental value ( approximately 720 A) and estimates based on the harmonic mode approach (1100-1700 A).

Base Pairing↗