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1
Diagnostyka talasemii i hemoglobinopatii w Zakładzie Immunologii Hematologicznej i Transfuzjologicznej IHiT
Brojer Ewa, Klimczak-Jajor Edyta, Majewska-Wierzbicka Monika, Skulimowska Joanna
Laboratorium Medyczne
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2019
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nr 2
20--24
PL
Hemoglobinopatie to różnorodna grupa chorób należąca do niedokrwistości hemolitycznych uwarunkowanych genetycznie. Występują one przede wszystkim w rejonach tropikalnych i subtropikalnych. Podłożem choroby mogą być zaburzenia syntezy (hemoglobinopatie ilościowe: talasemie) i/lub struktury hemoglobiny (hemoglobinopatie jakościowe: warianty hemoglobin) spowodowane mutacjami w genach kodujących to białko. W Zakładzie Immunologii Hematologicznej i Transfuzjologicznej diagnostyka hemoglobinopatii opiera się na badaniach biochemicznych (oznaczanie HbA2, HbF, Hb patologicznych metodą HPLC) oraz molekularnych (gap-PCR, MLPA, sekwencjonowanie HBB, HBA2 i HBA1). W wyniku postępującej migracji ludności choroby te są coraz częściej wykrywane w Polsce. Dzięki udoskonalonej diagnostyce wykrywane są przypadki o bardzo zróżnicowanym podłożu.
EN
Haemoglobinopathies are a diverse group of hereditary hemolytic anemias caused by mutations that affect the synthesis (quantitative haemoglobinopathies: thalassemias) and/or the structure (qualitative haemoglobinopathies: structural hemoglobin variants) of haemoglobin. In the Department of Immunohaematology and Immunology of Transfusion Medicine, the diagnostics of haemoglobinopathy is based on biochemical tests (determination on HbA2, HbF and abnormal haemoglobin by the HPLC method) and molecular tests (gap-PCR, MLPA, the sequencing of HBB, HBA2 and HBA1). As a result of the progressive migration of the population, various haemoglobinopathies are also detected in Poland.
2
Content available remote Computational Aspects of DNA Sequencing by Hybridization : a Survey
Kwarciak K., Radom M., Formanowicz P.
Computational Methods in Science and Technology
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2018
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Vol. 24, No. 4
259--271
EN
Sequencing by hybridization (SBH) is a method of reading DNA sequence from its smaller fragments. Such a method has been proposed in late 1980s and until the emergence of the new generation sequencing it has been widely used and improved. Since the initial, classical approach to SBH, many modifications and enhancements was proposed, aimed at improving the preciseness and the length of sequences which can be unambiguously read. Even now, for some DNA sequences sequencing by hybridization can still be used effectively and at a low cost. In this paper many different approaches to the SBH will be described, mainly from the points of view of algorithms and computational complexity.
3
Content available Skład biocenozy bakteryjnej osadu czynnego na przykładzie miejskiej oczyszczalni ścieków w Zgierzu
Liwarska-Bizukojć E.
Ochrona Środowiska
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2017
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Vol. 39, nr 4
3--7
EN
Molecular biology techniques allow for increasingly more thorough identification and understanding of functionality of microorganisms consortia involved in wastewater treatment or waste degradation processes. In this work, the bacterial community of activated sludge from the wastewater treatment plant in Zgierz (Poland) was identified. As a result, a somewhat limited database of microorganisms living in Polish wastewater treatment plants was supplemented with new data. The composition of bacterial community was identified with molecular biology techniques in two main stages: (1) isolation of genomic DNA, (2) DNA sequencing and bioinformatics analysis of the isolated sequences. The analyses revealed that the most abundant phylum was Proteobacteria with Betaproteobacteria present in highest numbers. Composition of the activated sludge was relatively low in Chloroflexi class bacteria. It is in alignment with macroscopic observations indicating good settlement properties of the activated sludge from the wastewater treatment plant in Zgierz. It was determined that aerobic (redox) conditions in the activated sludge chamber did not influence the composition of bacterial community. They might only cause increase in the contribution of aerobic bacteria in the aerated (oxygenated) part of the chamber or the anaerobic organisms in its anaerobic (deoxygenated) section.
PL
Techniki biologii molekularnej pozwalają w coraz większym stopniu poznać skład i zrozumieć funkcjonowanie konsorcjów mikroorganizmów biorących udział w procesach oczyszczania ścieków czy biodegradacji odpadów. W pracy zidentyfikowano skład biocenozy osadu czynnego w oczyszczalni ścieków komunalnych w Zgierzu, dzięki czemu została poszerzona, jak na razie dość skromna, baza danych o mikroorganizmach w polskich oczyszczalniach ścieków. Skład biocenozy bakteryjnej zidentyfikowano za pomocą technik biologii molekularnej. Analiza składała się z dwóch zasadniczych etapów – izolacji genomowego DNA oraz sekwencjonowania wraz z analizą bioinformatyczną sekwencji. Badania wykazały, że na poziomie typu największy udział w biocenozie osadu czynnego miały Proteobacteria, a wśród nich najwięcej było bakterii należących do klasy Betaproteobacteria. Osad z oczyszczalni ścieków w Zgierzu wyróżniał się stosunkowo małą liczebnością bakterii z klasy Chloroflexi, co pokrywa się z obserwacjami makroskopowymi, wskazującymi na dobre właściwości sedymentacyjne tego osadu. Stwierdzono, że warunki tlenowe panujące w komorze osadu czynnego nie miały znaczącego wpływu na skład bakteryjny osadu czynnego. Mogły one powodować jedynie większy udział bakterii aerofilnych w części napowietrzanej komory (tlenowej) i/lub większy udział beztlenowców w jej części nienapowietrzanej (beztlenowej).
4
Content available remote Preprocessing and Storing High - Throughput Sequencing Data
Świercz A., Bosak B., Chłopkowski M., Hoffa A., Kasprzak M., Kurowski M., Piontek T., Błażewicz J.
Computational Methods in Science and Technology
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2014
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Vol. 20, No. 1
9--20
EN
DNA sequencing is a process of recognizing DNA sequences of genomes. The process consists in reading short sequences, that are subsequences of a genome, and merging them into longer sequences, preferably the whole genome. In the first phase even billions of short sequences are read at once. To simplify and speed up the second phase, we develop a pipeline of preprocessing the initial set of short sequences that is removing low quality reads and duplicated reads.We also propose a method for preliminary joining overlapping sequences, which resulted in decreasing the cardinality of initial sets to 13.9% and 27.8%. We also examine possible ways to store the huge amount of experimental data. We compare different compression methods, from which the best appeared to be DSRC, developed for special type of text files containing short sequences and their quality. We test the parameters for TCP data transferring to find the best transfer rate.
5
Content available A greedy algorithm for the DNA sequencing by hybridization with positive and negative errors and information about repetitions
Kwarciak K., Formanowicz P.
Bulletin of the Polish Academy of Sciences. Technical Sciences
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2011
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Vol. 59, nr 1
111-115
EN
In this paper a greedy algorithm for some variants of the sequencing by hybridization method is presented. In the standard version of the method information about repetitions is not available. In the paper it is assumed that a partial information of this type is a part of the problem instance. Here two simple but realistic models of this information are taken into consideration. The first one assumes it is known if a given element of a spectrum appears in the target sequence once or more than once. The second model uses the knowledge is a given element of a spectrum occurs in the analyzed sequence once, twice or at least three times. The proposed greedy algorithm solves the variant of the problem with positive and negative errors. Results of a computational experiment are reported which, among others, confirm that the additional information leads to the improvement of the obtained solutions. They also show that the more precise model of information increases the quality of reconstructed sequences.
6
Content available remote Algorytmy dla problemów sekwencjonowania przez hybrydyzację opartych o nieklasyczne chipy DNA
Radom M., Formanowicz P.
Przegląd Elektrotechniczny
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2010
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R. 86, nr 9
97-100
PL
W niniejszym artykule przedstawione zostaną algorytmy dla problemów sekwencjonowania przez hybrydyzację opartych o dwa nieklasyczne chipy DNA. Opisane zostaną zasady kontrukcji rozpatrywanych chipów oraz sposób działania algorytmów rozwiązujących problem SBH z ich pomocą. Przedstawione zostaną także wyniki eksperymentów obliczeniowych, w których testowane będą omawiane algorytmy oraz algorytm klasyczny.
EN
In this paper algorithms for sequencing by hybridization problems based on two non-classical DNA chips are presented. The idea of these chips is briefly described and the algorithms are presented and analyzed in detail. Also the results of an extensive experiment are showed and commented.
7
Content available remote Metody i techniki biologii molekularnej w biotechnologii środowiskowej
Raszka A., Ziembińska A., Wiechetek A.
Czasopismo Techniczne. Środowisko
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2009
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R. 106, z. 2-Ś
101-114
PL
W ostatnich latach pojawiło się dużo różnorodnych metod pozwalających na analizę składu biocenozy oraz rozmieszczenia przestrzennego mikroorganizmów. Metody molekularne górują nad tradycyjnymi technikami, gdyż nie są uzależnione od hodowli mikroorganizmów na podłożach mikrobiologicznych. Jest to ważna cecha metod analitycznych, ponieważ przyspiesza to całą procedurę badawczą. Dodatkowo metody oparte na analizie materiału genetycznego charakteryzują się dużą czułością i powtarzalnością. W artykule opisano metody najczęściej wykorzystywane w biotechnologii środowiskowej.
EN
During last several years a wide variety of methods useful in the analyzing of biocenosis' composition and spatial microorganisms distribution appeared. A significant aspect of molecular techniques usage is its independence from traditional microbiological methods. It is an important analytical feature, because it enables a speedier research. Additionally, methods based on genetic material are more sensitive and repeatable. This article contains the description of the techniques of the most commonly used in environmental biotechnology.
8
Sekwencjonowanie DNA z błędami negatywnymi oraz informacją o powtórzeniach
Kwarciak K., Radom M., Formanowicz P.
Zeszyty Naukowe. Automatyka / Politechnika Śląska
|
2008
|
z. 151
215-222
PL
W pracy przedstawiony jest algorytm typu podziału i ograniczeń dla problemu sekwencjonowania przez hybrydyzację z błędami negatywnymi oraz częściową informacją o powtórzeniach. Uwzględnienie tego rodzaju informacji możliwe jest ze względu na rozwój technologii stosowanej w eksperymencie hybrydyzacyjnym. Prowadzi ono do rozszerzenia standardowej wersji metody sekwencjonowania przez hybrydyzację oraz do polepszenia jakości uzyskiwanych rozwiązań.
EN
In this paper a branch and bound algorithm for sequencing by hybridization problem with negative errors and partial information about repetitions is presented. Taking into account information of this type is possible because of the development of the technology used in the hybridization experiment. It leads to an extension of the standard sequencing by hybridization method and to an improvement of the quality of the obtained results.
9
Content available remote A Low-complexity Distance for DNA Strings
Dinu L.P., Sgarro A.
Fundamenta Informaticae
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2006
|
Vol. 73, nr 3
361-372
EN
We exhibit a low-complexity but non-trivial distance between strings to be used in biology. The experimental results we provide were obtained on a standard laptop and, even if preliminary, are quite encouraging.
10
Content available remote DNA sequencing by hybridization with additional information available
Formanowicz P.
Computational Methods in Science and Technology
|
2005
|
Vol. 11, nr 1
21-29
EN
In classical DNA sequencing by hybridization it is assumed that the information obtained in the biochemical stage of the method is a set of the l-tuples composing the target sequence. It means that the information concerning the number of the repeated l-tuples is not available. Such an assumption was justified by the DNA chip technology constraints. However, nowadays some approximate information about l-tuple multiplicities can be obtained in the experiments, where DNA chips are used. It was a motivation for formulating combinatorial problems which arise when such additional information is taken into account. The goal of this paper is to formulate and classify these problems, what should establish a good starting point for further research concerning algorithmic methods solving DNA sequencing problems with multiplicity information. Moreover, the computational complexity of the new problems is determined, which in most cases is analogous to the complexity of their classical counterparts.
11
Genomic Maps and Novel Approaches to Sequencing of Repetitive versus Non-repetitive DNA
Szybalski W.
Polish Journal of Chemistry
|
2004
|
Vol. 78 / nr 8
1007-1017
EN
As first demonstrated by Avery et al., DNA is a macromolecule which governs most aspects of life [1]. Thus our role as chemists was to determine the structure of this macromolecule, synthesize it, and possibly relate its structure to the genetic function. The first task was to determine the subunit structure of DNA, namely the structure of bases and their organization in relation to the deoxyribose and phosphate backbone. This was done in decades around the 1950-s. Independently, and around the same time, the concept of genes and the gene maps emerged as to relate the linear structure of DNAto its function. Next came the visualization ofDNAby electron microscopy (EM) and its physical mapping using the heteroduplexes between DNA strands of various mutants. This permitted a precise way of measuring the length of DNA, positioning various deletions or other rearrangements and relating these to the genetic and transcriptional maps. The final step was the precise sequencing of DNA, either by the now abandoned chemical based method or by the presently used enzymatic procedure, which led to progressively more genomes being sequenced. Taken together, all this important scientific milestones led to our present day understanding of the chemical structure and function of DNAin relation to the 'puzzle of life'! However, it was soon realized that the precise entire sequence ofDNAcould not be determined for many genomes, especially the eukaryotic ones, because they contain numerous long stretches of highly repetitive sequences, which defy the present computerized overlap procedure required for aligning of fragments and determining the final sequence. Therefore, we had to develop novel strategies to accurately sequence repetitive elements of DNA, as outlined here. These comprise construction and use of special transposons and pBAC/oriV vectors, both equipped with very rare cutting sites. Transposons (Tn) allow determination of 500-1000 nucleotide (nt) sequences on both sides of their insertion, whereas the very rare cutting sites (like I-SceI, PI-SceI or our Achilles heel cleavage sites) allow precise mapping of the positions of the insertions, using pulsed field gel electrophoresis (PFGE) or other physical means, including electron microscopic (EM) mapping. Thus we had to return to some of our earlier methods of physical mapping, which together with transposon-associated priming would allow sequencing of large eukaryotic genomes to be completed. This would be the final triumph of the structural chemistry of the DNA macromolecules which are the essence of genomes and genomics.
12
Content available remote Resolving power of isothermic DNA sequencing chips
Formanowicz P.
Bulletin of the Polish Academy of Sciences. Technical Sciences
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2004
|
Vol. 52, nr 3
231-237
EN
DNA sequencing remains one of the most important problems in molecular and computational biology. One of the methods used for this purpose is sequencing by hybridization. In this approach usually DNA chips composed of a flul library of oligonucleotides of a given length are used, but in principle it is possible to use another types of chips. Isothermic DNA chips, being one of them, when used for sequencing may reduce hybridization error rate. However, it was not clear if a number of errors following from subsequence repetitions is also reduced in this case. In this paper a method for estimating resolving power of isothermic DNA chips is described which allows for a comparison of such chips and the classical ones. The analysis of the resolving power shows that the probability of sequencing errors caused by subsequence repetitions is greater in the case of isothermic chips in comparison to their classical counterparts of a similar cardinality. This result suggests that isothermic chips should be chosen carefully since in some cases they may not give better results than the classical ones.
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