Search PubMed⌕ Search

Biomedical subjects

D Fischer

Publications and source records attributed to D Fischer.

At least 19 recordsLinked to original sources
PubMed2001

Cationized human serum albumin as a non-viral vector system for gene delivery? Characterization of complex formation with plasmid DNA and transfection efficiency.

Cationized human serum albumin (cHSA) could serve as a potential non-viral vector system for gene delivery. Native human serum albumin was cationized by covalent coupling of hexamethylenediamine to the carboxyl groups resulting in a shift of the isoelectric point from pH 4-5 to 7-9. The cationized albumin underwent spontaneous self-assembly with DNA as demonstrated by retardation of CMV-nlacZ plasmid in agarose gel electrophoresis. Photon correlation spectroscopy showed a decrease of complex size with increasing cHSA/plasmid ratios. Under optimized conditions complexes were formed with 230-260 nm mean diameter and a homogenous, narrow size distribution. At room temperature complexes were stable in 0.9% sodium chloride solution pH 7.4 for 1 h without aggregation. Process parameters such as albumin concentration, incubation time, temperature, pH, order of reagent addition, the presence of bivalent ions and the ionic strength of the complexation medium all influenced the complex size. Confocal laser scanning microscopy showed interactions of a Texas Red labeled cationized albumin with cell membranes of ECV 304 cells and an enhanced endocytic uptake compared to native albumin. The potential for introducing exogeneous DNA into cells was shown using NIH 3T3 fibroblasts. Successful, albeit low reporter gene expression could be achieved in the presence of chloroquine. Under in vitro conditions no toxic effect could be observed. In conclusion, cationized albumin may have promise as a non-toxic vector for gene delivery, especially for DNA vaccination.

DNA↗
PubMed2001

High-throughput generation and engineering of recombinant human antibodies.

The first version of the Human Combinatorial Antibody Library (HuCAL) is a single-chain Fv-based phage display library (HuCAL-scFv) with 2x10(9) members optimised for high-throughput generation and targeted engineering of human antibodies. 61% of the library genes code for functional scFv as judged by sequencing. We show here that since HuCAL-scFv antibodies are expressed in high levels in Escherichia coli, automated panning and screening in miniaturised settings (96- and 384-well format) have now become feasible. Additionally, the unique modular design of HuCAL-genes and -vectors allows the distinctly facilitated conversion of scFv into Fab, miniantibody and immunoglobulin formats, and the fusion with a variety of effector functions and tags not only convenient for therapeutic applications but also for high-throughput purification and detection. Thus, the HuCAL principle enables the rapid and high-throughput development of human antibodies by optimisation strategies proven useful in classical low molecular weight drug development. We demonstrate in this report that HuCAL is a very convenient source of human antibodies for various applications.

Animals↗
PubMed2001

A study of quality measures for protein threading models.

BACKGROUND: Prediction of protein structures is one of the fundamental challenges in biology today. To fully understand how well different prediction methods perform, it is necessary to use measures that evaluate their performance. Every two years, starting in 1994, the CASP (Critical Assessment of protein Structure Prediction) process has been organized to evaluate the ability of different predictors to blindly predict the structure of proteins. To capture different features of the models, several measures have been developed during the CASP processes. However, these measures have not been examined in detail before. In an attempt to develop fully automatic measures that can be used in CASP, as well as in other type of benchmarking experiments, we have compared twenty-one measures. These measures include the measures used in CASP3 and CASP2 as well as have measures introduced later. We have studied their ability to distinguish between the better and worse models submitted to CASP3 and the correlation between them. RESULTS: Using a small set of 1340 models for 23 different targets we show that most methods correlate with each other. Most pairs of measures show a correlation coefficient of about 0.5. The correlation is slightly higher for measures of similar types. We found that a significant problem when developing automatic measures is how to deal with proteins of different length. Also the comparisons between different measures is complicated as many measures are dependent on the size of the target. We show that the manual assessment can be reproduced to about 70% using automatic measures. Alignment independent measures, detects slightly more of the models with the correct fold, while alignment dependent measures agree better when selecting the best models for each target. Finally we show that using automatic measures would, to a large extent, reproduce the assessors ranking of the predictors at CASP3. CONCLUSIONS: We show that given a sufficient number of targets the manual and automatic measures would have given almost identical results at CASP3. If the intent is to reproduce the type of scoring done by the manual assessor in in CASP3, the best approach might be to use a combination of alignment independent and alignment dependent measures, as used in several recent studies.

Computational Biology↗
PubMed2001

Separation of recollision mechanisms in nonsequential strong field double ionization of Ar: the role of excitation tunneling.

Vector momentum distributions of two electrons created in double ionization of Ar by 25 fs, 0.25 PW/cm(2) laser pulses at 795 nm have been measured using a "reaction microscope." At this intensity, where nonsequential ionization dominates, distinct correlation patterns are observed in the two-electron momentum distributions. A kinematical analysis of these spectra within the classical "recollision model" revealed an (e,2e)-like process and excitation with subsequent tunneling of the second electron as two different ionization mechanisms. This allows a qualitative separation of the two mechanisms demonstrating that excitation-tunneling is the dominant contribution to the total double ionization yield.

Journal Article↗
PubMed2001

Mammalian histone deacetylase 1 protein is posttranslationally modified by phosphorylation.

HDAC1, a member of the histone deacetylase family, is involved in transcription regulation through the modification of chromatin structure. Several studies also implicated HDAC1 in tumorigenesis. Much attention has been concentrated on protein-protein interactions involving HDAC1 and the possibility that posttranslational modifications may occur in mammalian HDAC1 proteins has not been carefully and systematically investigated. In this study, we utilized in vivo labeling assays to demonstrate that both human and murine HDAC1 proteins are phosphorylated in cells. Assays using HDAC1 deletion mutants indicated that phosphorylation occurs in its C-terminal domain. cAMP-dependent kinase and casein kinase II, but not protein kinase C, cdc2, or MAP kinase, could phosphorylate HDAC1 in vitro, although HDAC1 contains several protein kinase C consensus sites. We also found that phosphorylation did not influence HDAC1 enzymatic activity using a human histone H4 N-terminal peptide as the substrate. Interestingly, HDAC1-FLAG fusion protein immunoprecipitated from transfected cells was found to be in association with a kinase activity, providing an in vitro assay for further studies of this posttranslational modification.

Amino Acid Sequence↗
PubMed2001

CAFASP2: the second critical assessment of fully automated structure prediction methods.

The results of the second Critical Assessment of Fully Automated Structure Prediction (CAFASP2) are presented. The goals of CAFASP are to (i) assess the performance of fully automatic web servers for structure prediction, by using the same blind prediction targets as those used at CASP4, (ii) inform the community of users about the capabilities of the servers, (iii) allow human groups participating in CASP to use and analyze the results of the servers while preparing their nonautomated predictions for CASP, and (iv) compare the performance of the automated servers to that of the human-expert groups of CASP. More than 30 servers from around the world participated in CAFASP2, covering all categories of structure prediction. The category with the largest participation was fold recognition, where 24 CAFASP servers filed predictions along with 103 other CASP human groups. The CAFASP evaluation indicated that it is difficult to establish an exact ranking of the servers because the number of prediction targets was relatively small and the differences among many servers were also small. However, roughly a group of five "best" fold recognition servers could be identified. The CASP evaluation identified the same group of top servers albeit with a slightly different relative order. Both evaluations ranked a semiautomated method named CAFASP-CONSENSUS, that filed predictions using the CAFASP results of the servers, above any of the individual servers. Although the predictions of the CAFASP servers were available to human CASP predictors before the CASP submission deadline, the CASP assessment identified only 11 human groups that performed better than the best server. Furthermore, about one fourth of the top 30 performing groups corresponded to automated servers. At least half of the top 11 groups corresponded to human groups that also had a server in CAFASP or to human groups that used the CAFASP results to prepare their predictions. In particular, the CAFASP-CONSENSUS group was ranked 7. This shows that the automated predictions of the servers can be very helpful to human predictors. We conclude that as servers continue to improve, they will become increasingly important in any prediction process, especially when dealing with genome-scale prediction tasks. We expect that in the near future, the performance difference between humans and machines will continue to narrow and that fully automated structure prediction will become an effective companion and complement to experimental structural genomics.

Automation↗
PubMed2001

LiveBench-2: large-scale automated evaluation of protein structure prediction servers.

The aim of LiveBench is to provide a continuous evaluation of structure prediction servers to inform developers and users about the current state-of-the-art structure prediction tools. LiveBench differs from other evaluation experiments because it is a large-scale and a fully automated procedure. Since LiveBench-1, which finished in April 2000, and related but independent CASP3 and CAFASP1 experiments, significant progress in the field has occurred. Some of the new developments have already been assessed at the recent CASP4 and CAFASP2 experiments (both independently of LiveBench), but others have not been observed yet because they entail developments carried out only recently. These include the availability of new servers (Pcons, FUGUE, and Coblath) and the enhancement of previously existing tools (mGenThreader, Sam-T, and 3D-PSSM), which illustrate the fast rate at which the field is advancing. Consequently, to keep in pace with the development, we present the results of the second large-scale evaluation of protein structure prediction servers. Of the 11 fold recognition servers evaluated, two servers appear to be most sensitive. One of these is 3D-PSSM, a server significantly improved after LiveBench-1. The other top performer is the new consensus server Pcons, which significantly outperformed other servers in the specificity of predictions. LiveBench-2 shows that the top performing servers are able to accurately recognize a fold for about one third of the "difficult" targets, a clear improvement over LiveBench-1 results. Given that automated structure prediction is increasingly becoming a biologists companion, the guidelines drawn from the LiveBench experiments are likely to provide users with valuable and timely information for their prediction needs.

Automation↗
PubMed2001

Lens-injury-stimulated axonal regeneration throughout the optic pathway of adult rats.

Axonal regrowth and restoration of visual function were studied in adult rats. The optic nerve was completely cut behind the eye. The proximal and distal nerve stumps were realigned and the meninges sutured back together. During the same surgical procedure, the lens was lesioned in order to induce secondary cellular cascades, which are known to strongly support the survival of retinal ganglion cells (RGCs) and to promote axonal regeneration. The anatomical and topographic restoration of the visual pathway was assessed neuroanatomically with the aid of anterograde and retrograde tracing using fluorescent dyes. It appeared that the axons formed growth cones at the junction of the suture soon after injury, before glial cells and extracellular matrix proteins were able to cause local scar formation. Growth cones first entered the distal optic nerve stump 3 days after injury, grew through it to reach the optic chiasm approximately 3 weeks after the lesion was made, and terminated within the retinoreceptive layers of the superior colliculus 5 weeks after lesioning. Quantification of the retrogradely labeled cell bodies within the regenerating retina revealed that up to 30% of the RGCs, which includes all major cell types, were capable of regenerating their axons along the entire visual pathway. To assess whether topography was restored, double-labeling experiments were performed, revealing only crude topographic restoration during the initial stages of regeneration. However, visual-evoked potentials could be recorded, indicating that synaptic transmission in higher visual areas was relatively intact. The data show, in principle, that cut axons can regenerate over long distances within the white matter of a central nerve like the adult optic nerve, spanning over 11 mm to the chiasm and between 12 and 15 mm to the thalamus and midbrain. The findings suggest, for the first time, that lentogenic stimulation of RGCs is sufficient to induce the formation of growth cones that can override inhibitors at the site of injury, grow through the white matter of the optic nerve, pass through the optic chiasm, and make synaptic connections within the brain.

Animals↗
PubMed2001

Solving a linear model of nonfatal risk behavior and injuries in school children.

A calculating method and computer program have been developed for solving an overdetermined system of linear equations. It was applied for calculation of group risk exposure of school children (10-15 years) to nonfatal injuries in sport recreation and playing (SRP). Interviewed non-injured school children were separated into non-overlapping groups of risky behavior. Data on interviewed non-injured and non-interviewed injured children were put into a linear system of equations consisting of a 4 x 3 matrix scheme. Each equation represents children of the same age and sex and consists of the percentage of interviewed children grouped into high medium or low risk behavior and of the percentage of injured children. Four methods of calculating the matrix system were evaluated and the best implemented as a new developed computer program. The resulting linear group risk factors enable the prediction of behavior outcome. Data on interviewed injured children were compared with the results obtained. The validation procedure is proposed by testing the sensitivity and robustness of the method.

Adolescent↗
PubMed2001

Histochemical characterization of primary capillary endothelial cells from porcine brains using monoclonal antibodies and fluorescein isothiocyanate-labelled lectins: implications for drug delivery.

Primary endothelial cells isolated from cerebral microvessels by combined mechanical and enzymatic treatment from porcine brains were characterized with regard to identity, purity and membrane surface characteristics. Cells were grown in culture to adherent monolayers and characterized morphologically and histochemically by their binding for fluorescently-labelled lectins and monoclonal antibodies detected by indirect immunofluorescence. The binding patterns of the cells were compared with the affinity of frozen tissue sections of porcine brain cortex for the markers. Endothelial cells in culture were characterized by the binding of von Willebrand factor, vimentin and fibronectin antibodies. They failed to react with anti-glial fibrillary acid protein, anti-galactocerebroside C and anti-neurofilament 160 antibodies characteristic for astrocytes, oligodendrocytes and neurons, respectively. Cell cultures were stained by the lectins, wheat germ agglutinin, horse gram agglutinin and soybean agglutinin, demonstrating the presence of N-acetylglucosamine and N-acetylgalactosamine residues on membrane surface. Binding sites for concanavalin A and peanut agglutinin characteristic for mannose and galactose could not be detected. Cell age and differentiation had no effect on lectin and antibody staining. Cell cultures gave staining results similar to those of microvessels in frozen tissue sections. The results of morphology, antibody and lectin staining pattern indicate that our in vitro endothelial cell culture model retained many histological characteristics observed for capillary microvessels in vivo and appears to be suitable for studying uptake and targeting properties of drug carrier systems with regard to the blood-brain barrier.

Animals↗
PubMed2001

Internet relationships: people who meet people.

Current research suggests that the Internet has become a popular medium for forming interpersonal relationships. Not only are many people developing cyberfriendships, but some move beyond virtual communication and interact more directly through telephone contact and face-to-face encounters. This pilot study examined the personality characteristics of 30 participants (17 men and 13 women) who were regular Internet users and who had used the Internet to meet people mainly through chat rooms. The findings of this study suggest that people who use the Internet meet others tend to be truthful in general in their interactions although both men and women often did not reveal their true names. Eighty percent of the subjects formed casual or friendly relationships, whereas 6% formed intimate or romantic relationships. Approximately one-third of the subjects made some form of offline contact, with 40% talking on the telephone and 33.3% meeting face-to-face. Furthermore, examination of personality styles indicated that cyberfriends tend to be socially skilled, have strong verbal skills, and demonstrate empathy for others. Most subjects were careful about protecting their anonymity, and none of the subjects who met face-to-face did so without first talking on the phone. This suggests that individuals who make friends via the Internet tend to take appropriate precautions and find this medium an effective and safe way to interact with others and to expand one's social system.

Adult↗
PubMed2001

Structure prediction meta server.

UNLABELLED: The Structure Prediction Meta Server offers a convenient way for biologists to utilize various high quality structure prediction servers available worldwide. The meta server translates the results obtained from remote services into uniform format, which are consequently used to request a jury prediction from a remote consensus server Pcons. AVAILABILITY: The structure prediction meta server is freely available at http://BioInfo.PL/meta/, some remote servers have however restrictions for non-academic users, which are respected by the meta server. SUPPLEMENTARY INFORMATION: Results of several sessions of the CAFASP and LiveBench programs for assessment of performance of fold-recognition servers carried out via the meta server are available at http://BioInfo.PL/services.html.

Amino Acid Sequence↗
PubMed2001

LiveBench-1: continuous benchmarking of protein structure prediction servers.

We present a novel, continuous approach aimed at the large-scale assessment of the performance of available fold-recognition servers. Six popular servers were investigated: PDB-Blast, FFAS, T98-lib, GenTHREADER, 3D-PSSM, and INBGU. The assessment was conducted using as prediction targets a large number of selected protein structures released from October 1999 to April 2000. A target was selected if its sequence showed no significant similarity to any of the proteins previously available in the structural database. Overall, the servers were able to produce structurally similar models for one-half of the targets, but significantly accurate sequence-structure alignments were produced for only one-third of the targets. We further classified the targets into two sets: easy and hard. We found that all servers were able to find the correct answer for the vast majority of the easy targets if a structurally similar fold was present in the server's fold libraries. However, among the hard targets--where standard methods such as PSI-BLAST fail--the most sensitive fold-recognition servers were able to produce similar models for only 40% of the cases, half of which had a significantly accurate sequence-structure alignment. Among the hard targets, the presence of updated libraries appeared to be less critical for the ranking. An "ideally combined consensus" prediction, where the results of all servers are considered, would increase the percentage of correct assignments by 50%. Each server had a number of cases with a correct assignment, where the assignments of all the other servers were wrong. This emphasizes the benefits of considering more than one server in difficult prediction tasks. The LiveBench program (http://BioInfo.PL/LiveBench) is being continued, and all interested developers are cordially invited to join.

Computer Simulation↗
PubMed2001

Intravitreal invading cells contribute to vitreal cytokine milieu in proliferative vitreoretinopathy.

AIM: To examine the contribution of infiltrating cells in the local production of cytokines within the vitreous of patients with proliferative vitreoretinopathy (PVR). METHODS: The presence of mRNA coding for IL-6, IL-8, IL-1beta, IL-1alpha, TNFalpha, IFNgamma, IL-12, and HPRT was investigated in 25 vitreous samples from patients with PVR, 11 vitreous samples from patients with retinal detachment (RD) not complicated by PVR, and 10 vitreous samples from patients with macular hole (MH). A quantitative reverse transcriptase polymerase chain reaction (RT-PCR) using an internal competitor was used to investigate these samples. From these samples, 15 PVR, 8 RD, and 8 MH were analysed for the protein levels of the same cytokines using enzyme linked immunosorbent assay (ELISA). Spearman correlation was used to test any association between mRNA and cytokine protein levels, as an indicator of the contribution these cells make to the intravitreal cytokine milieu. RESULTS: A strong correlation was found between mRNA and their respective cytokine levels (protein products) for IL-6, IL-8, IL-1beta, IL-1alpha, TNFalpha, IFNgamma (Spearman r = 0.83, 0.73, 0.67, 0.91, 0.73, and 0.73 respectively), but not for IL-12. The median levels of IL-6, IL-8, IL-1beta, and IFNgamma mRNA and their respective cytokines were significantly higher (p <0.05) in patients with PVR than in those with macular hole. There was no statistically significant difference in the median levels of IL-1alpha mRNA between PVR and MH but the cytokine IL-1alpha was detected at a significantly higher level in PVR compared with MH patients. Between PVR and RD patients, there was no statistically significant difference in mRNA levels for all the investigated cytokines (p >0.05) except for IL-6 where there was a statistical significance (p= 0.038). In contrast, the median levels of IL-6, IL-8, and IL-1beta cytokines were significantly higher (p <0.05) in patients with PVR than in those with RD, whereas for IL-1alpha and IFNgamma no significant statistical difference was detected between PVR and RD patients (p >0.05). When results of RD and MH patients were compared, a statistical difference was only detected in mRNA levels of INFgamma (p = 0.008). However, no difference was detected for INFgamma (protein product) or for any of the other cytokines between RD and MH patients. CONCLUSION: Levels of both protein and mRNA encoding IL-6, IL-8, IL-1beta, and IFNgamma is significantly increased in vitreous samples from patients with PVR. The strong correlation between ELISA detectable cytokines (protein products) and their respective mRNA levels suggest that intravitreal, invasive cells are the major source of these cytokines, with the exception of IL-12. Cells invading the vitreous do not appear to locally produce IL-12 mRNA. This would appear to implicate cells peripheral to the vitreal mass as the major source of this cytokine.

Adult↗
PubMed2000

Glioanatomy assessed by cell-cell interactions and phagocytotic labelling.

In the last three decades of research in neuroscience, fluorescent probes have gone from technical tools in the studies of physicochemical reactions, to being versatile tools in developmental neurobiology, neuroanatomy, angiography, neuromorphology, connectivity, cell death and even photodynamic therapy. Fluorescent dyes belong to heterogeneous groups of substances, but the feature to emit light of a certain wavelength depends on the energy status of the corresponding chemical bond. Therefore, light emission can range from the blue to the infrared spectrum, thus allowing multiple stains of the same cell, or event. The heterogeneity in their structure allows application of some fluorescent dyes for anterograde long-tract labelling, whereas others can be used for retrograde tracing. Lipophilic dyes are suitable for intramembraneous diffusion along cell membranes post-mortem, whereas hydrophilic stains seem more suitable for genealogic cell studies over several cell divisions. In the same time, less attention has been paid by most researchers to the use of fluorescent dyes to monitor neuroglial interactions and glioanatomy in the healthy and diseased brain. Studies of cell-cell-interactions during apoptosis can now be carried out with sequestration and subsequent phagocytosis of intracellular dyes. The present review focuses on recent developments that include the use of fluorescent probes. These probes make it possible to transneuronally assess functions of glial cells during programmed cell death, or induced degeneration. The high variety of available dyes, and their particular accumulation within subcellular compartments, is promising to shed light on some glial cell geometry and functions. The lessons obtained from the vast number of studies in neurons are of increasing importance for cells too, as their functions are not directly accessible. In short, some glial-glial and neuroglial negotiations will be analysed in near future by developing new, or by modifying existing fluorescent probes.

Animals↗