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W Kasprzak

Publications and source records attributed to W Kasprzak.

At least 19 recordsLinked to original sources
PubMed1999

Stem Trace: an interactive visual tool for comparative RNA structure analysis.

MOTIVATION: Stem Trace is one of the latest tools available in STRUCTURELAB, an RNA structure analysis computer workbench. The paradigm used in STRUCTURELAB views RNA structure determination as a problem of dealing with a database of a large number of computationally generated structures. Stem Trace provides the capability to analyze this data set in a novel, visually driven, interactive and exploratory way. In addition to providing graphs at a high level of ion, it is also connected with complementary visualization tools which provide orthogonal views of the same data, as well as drawing of structures represented by a stem trace. Thus, on top of being an analysis tool, Stem Trace is a graphical user interface to an RNA structural information database. RESULTS: We illustrate Stem Trace's capabilities with several examples of the analysis of RNA folding data performed on 24 strains of HIV-1, HIV-2 and SIV sequences around the HIV dimerization region. This dimer linkage site has been found to play a role in encapsidation, reverse transcription, recombination, and inhibition of translation. Our examples show how Stem Trace elucidates preservation of structures in this region across the various strains of HIV. AVAILABILITY: The program can be made available upon request. It runs on SUN, SGI and DEC (Compaq) Unix workstations.

Algorithms↗
PubMed1997

On neural blind separation with noise suppression and redundancy reduction.

Noise is an unavoidable factor in real sensor signals. We study how additive and convolutive noise can be reduced or even eliminated in the blind source separation (BSS) problem. Particular attention is paid to cases in which the number of sensors is larger than the number of sources. We propose various methods and associated adaptive learning algorithms for such an extended BSS problem. Performance and validity of the proposed approaches are demonstrated by extensive computer simulations.

Algorithms↗
PubMed1996

STRUCTURELAB: a heterogeneous bioinformatics system for RNA structure analysis.

STRUCTURELAB is a computational system that has been developed to permit the use of a broad array of approaches for the analysis of the structure of RNA. The goal of the development is to provide a large set of tools that can be well integrated with experimental biology to aid in the process of the determination of the underlying structure of RNA sequences. The approach taken views the structure determination problem as one of dealing with a database of many computationally generated structures and provides the capability to analyze this data set from different perspectives. Many algorithms are integrated into one system that also utilizes a heterogeneous computing approach permitting the use of several computer architectures to help solve the posed problems. These different computational platforms make it relatively easy to incorporate currently existing programs as well as newly developed algorithms and to best match these algorithms to the appropriate hardware. The system has been written in Common Lisp running on SUN or SGI Unix workstations, and it utilizes a network of participating machines defined in reconfigurable tables. A window-based interface makes this heterogeneous environment as transparent to the user as possible.

Algorithms↗
PubMed1995

[Viruses of parasitic protozoa].

The authors present the actual review on several publications concerning the molecular characterizations of the viruses found in parasitic protozoa such as Giardia, Trichomonas, Leishmania and Entamoeba histolytica. All of the RNA viruses observed in parasitic protozoa showed several similarities and did not considerably differ from the viruses found in simple eukaryotic cells; they closely correspond to dsRNA viruses of yeast. The supposition that the protozoan symbionts detected in laboratories transfer to their hosts in natural conditions seemed to be rational, though, there are no evidences that these symbionts are potential pathogens. However, the opinion reiterates that intestinal protozoa (e.g. Entamoeba histolytica) may serve as vectors for HIV or cofactors of HIV infection. The authors point out that irrespective of the potential role of viruses as vectors in the transfection system for parasitic protozoa, the observed viral system constitutes an unusual experimental system to solve the problems of gene expression.

Animals↗
PubMed1995

[Cryptosporidiosis--a typical environmental parasitosis].

The article reviews the problems on epidemiology of cryptosporidiosis and gives a detailed description of the massive waterborne outbreak in Milwaukee (Wisconsin, USA) associated with a break in filtration capacity of a public water supply. The authors emphasize the need for high-quality diagnostic procedures as current coprodiagnostic microscopical techniques seemed to fail to detect Cryptosporidium oocysts.

Animals↗
PubMed1995

[Detection of coproantigens in parasitic diseases].

The author presented general issues in detecting of parasite's coproantigens and carried out a critical review of abstracts submitted to the scientific session (17th Congress of the Polish Parasitological Society, September 1994, Gdynia, Poland). The abstracts are being published in a special edition of the "Methodical and Organisational Bulletin" (Institute of Marine and Tropical Medicine, Gdynia, Poland).

Animals↗
PubMed1995

[Waterborne outbreaks of Giardia].

The authors present the actual informations on waterborne outbreaks of giardiasis as well as the evidences of Giardia cyst transmission by municipal water supply. In the article a recommendations is given to molecular biology techniques which contributed to the armentarium applied in the modern diagnostics of giardiasis.

Disease Outbreaks↗
PubMed1995

[Usefulness of genome analysis methods for diagnosis of giardiasis and cryptosporidiosis].

The article comprises a critical review on practical applications of molecular technology in parasitological diagnostics in a broad sense, also as a diagnosis of species and a method of epidemiological analysis. Techniques of genome analysis at different levels, as specific nucleic acid probes, DNA restriction profiles (RFLP), hybridization techniques, pulse-field gel electrophoresis, in vitro nucleic acid amplification, and DNA fingerprint technique used in studies on Giardia and Cryptosporidium were discussed. The essential reservation as far as this technology is concerned refers to its usefulness in parasitological diagnostics; there is no sense in working out methods for recognizing parasites which could otherwise be identified by well trained parasitologists and simple microscopic methods. The improved diagnosis of parasites resulting from the application of molecular technology significantly contributed to the armarium of parasitologists. Application of recent molecular technology in diagnosis of giardiasis and cryptosporidiosis may basically support clinical diagnosis which provides possibilities of early and selective treatment and makes possible epidemiological studies. These assays will permit not only a rapid diagnosis and exact differentiation but will also enable a better recognition of Giardia and Cryptosporidium genome organization. However, in spite of the wide availability of this new techniques they have not been fully applied--as yet--in diagnosis and in epidemiological studies on these parasites. The authors share the opinion of Busch (1991) on the need of proper recognition of high-quality and rigorous work in employing new molecular assays, because their wide availability and high sensitivity could cause "false-positive" results by contamination with amplified DNA sequences.(ABSTRACT TRUNCATED AT 250 WORDS)

Animals↗
PubMed1992

Comparison of Giardia isolates from different laboratories by isoenzyme analysis and recombinant DNA probes.

A total of 13 new Giardia isolates were established in axenic culture. All of the new isolates were obtained by excystation of Giardia cysts from the feces of patients in Dutch hospitals. These isolates were subjected to isoenzyme and DNA analysis together with isolates from Poland, Belgium, and various other parts of the world. Isoenzyme analysis revealed that nearly all of the newly established isolates exhibited unique zymodemes. Isolates obtained from individuals from Belgium and Poland, on the other hand, displayed single zymodemes. Genomic DNA libraries were constructed from isolates belonging to the latter two zymodemes; specific and common recombinant DNA clones were selected from these libraries. Differential screening revealed that the two isolates had only 80% of the clones in common. Restriction-fragment-length polymorphism analysis using three different probes together with two synthetic probes that are complementary to Giardia structural protein genes led to the separation of all isolates into two major groups; within these groups, a further division could be made by application of other techniques or probes. The results of DNA analysis and zymodeme classification were in general agreement; in the present report they are compared with the data in the literature and discussed.

Animals↗
PubMed1990

Giardia isolates from primates and rodents display the same molecular polymorphism as human isolates.

Five Giardia isolates from primates and rodents were grown axenically and compared by different electrophoretic techniques. One isolate from a lemur (slow loris) contained a dsRNA virus also found in some of the Giardia of human origin. Using ethidium bromide stained gels and also Southern blots hybridized with a rDNA probe, two profiles of restriction fragment length polymorphism were found in the animal Giardia, which are identical to two profiles found previously in strains of human origin. Isoenzyme and total protein patterns obtained with agarose isoelectric focusing divided the strains in the same two groups. With pulsed field gradient gel electrophoresis, the isolates showed 6-8 chromosomal bands but none of the band patterns were identical. The size of the chromosomes varied from 0.8 to over 3.0 Mb. A ribosomal DNA probe hybridized with different bands.

Acid Phosphatase↗
PubMed1990

Axenic isolation of Giardia strains from primates and rodents.

During the examination of animals at the Poznan Zoological Gardens, attempts were made to isolate Giardia strains. Using an in vitro excystation procedure, eight samples of cysts from animals with asymptomatic giardiasis were inoculated on BI-S-33 medium. The ease of isolation and axenization of Giardia was surprising; five axenic isolates of Giardia, belonging to the G. duodenalis morphological group, were established from primates (slow loris, lesser slow loris and siamang) and from rodents (Gambian giant pouched rat and cuis). The growth of all isolates was abundant and similar; the peak number of trophozoites on the seventh day (depending on the Giardia isolate) was 2.3 X 10(6)-3.2 X 10(6) and generation times were 8.2-19.3 h. The easy establishment of these isolates confirmed that they belong to the G. duodenalis morphological group. The recent hypothesis that Giardia may be introduced to a human population from an animal source implies the necessity to isolate and differentiate parasite strains from various hosts. In this respect, the first isolation of Giardia strains from non-human primates and from rodents is of particular importance.

Animals↗
PubMed1989

Zoonotic aspects of giardiasis: a review.

Several studies suggested that some water-borne epidemics of giardiasis in the U.S.A. were of zoonotic origin. Also, cats and dogs were suspected of being sources of giardiasis for man. These observations have been partly supported by experimental cross-transmissions. However, there are also some indications that zoonotic giardiasis may not be common. The host-specificity of Giardia spp. is still controversial. To date, morphological characteristics can only differentiate three very basic types of Giardia: G. intestinalis, G. muris and G. agilis. Host-specific and morphometric criteria resulted in the description of more than 40 species of Giardia; many of them probably invalid. Only a few subtle antigenic differences among G. intestinalis (lamblia) strains have been observed. The comparison of isoenzymes and DNA banding patterns revealed 3 basic groups, not necessarily related to host origin. Further biochemical, immunological, genetic and cross-transmission studies in host and parasite populations are needed to better understand host-specificity of various Giardia isolates. At the present time one may only conclude that although mammals and man do not seem to possess their own unique species of Giardia, in reality the major methods of transmission of giardiasis probably remain basically host-specific.

Animals↗
PubMed1989

[Prevalence of Entamoeba histolytica and other intestinal protozoa among the inhabitants of Poznan province over a period of 30 years].

The aim of the study was to present the past and actual prevalence of Entamoeba histolytica and other intestinal protozoa in Poznań Province. Although in Poland there are only few accurate data concerning the prevalence of intestinal protozoa, the results of some studies were found reliable. In a survey conducted in 1958 in an orphanage in Poznań (Kasprzak and Karlewiczowa) the intestinal protozoa were found with high prevalence (Table 1). After six years this prevalence decreased considerably (Karlewiczowa and Kasprzak, 1964). Because at the same time such a decrease in intestinal protozoa prevalence, especially that in Entamoeba coli, was observed in the whole population of the Poznań Province, long-term surveys were undertaken. The diagnosing of intestinal protozoa in faeces of 4165 persons, performed at more points in time in the period of 1963 to 1986 in the Poznań Province, were conducted by the same highly skilled staff. Decreasing rates of infection were seen for each amoeba species at nearly each point in time, particularly in the first eight years of observation (Table 2). By using the "amoebic index" and "amoebic prevalence rate" in assessing epidemiological factors (acc. WHO, 1969), the considerable reduction in both indices should be accounted for the improvement of the sanitation and socio-economic status in our country. After the Second World War some Polish authors expressed the fear that after returning to the country, the Polish soldiers who had fought in the endemic regions of invasive amoebiasis, infected with E. histolytica, would constitute sources for spreading amoebiasis and that the disease would be a nucleus of a new, hitherto unknown, social calamity in Poland. Fortunately, the fear did not come true. Although in this country the infection with amoebae, also with E. histolytica, decreased considerably after several years, unfortunately, some opinions still prevail, being the source of an amoebo-mania in the medical staff and corresponding amoebophobia in the patients.

Amebiasis↗