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1

Stability analysis of fractional order SEIR model for malaria disease in Khyber Pakhtunkhwa

Badshah Noor, Akbar Haji

Demonstratio Mathematica

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2021

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Vol. 54, nr 1

326--334

EN

We discussed stability analysis of susceptible-exposed-infectious-removed (SEIR) model for malaria disease through fractional order and check that malaria is epidemic or endemic in Khyber Pakhtunkhwa (Pakistan). We show that the model has two types of equilibrium points and check their stability through Routh-Hurwitz criterion. We find basic reproductive number using next-generation method. Finally, numerical simulations are also presented.

2

Zastosowanie analiz kopalnego DNA w badaniach osadów czwartorzędowych

Demianiuk E. J., Majewski W.

Przegląd Geologiczny

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2018

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Vol. 66, nr 11

680--691

EN

During the past few decades genetic research has been developed in parallel with paleogenetics. A dynamic progress in this field of studies is possible due to the advance in laboratory and computer technologies. Today, scientists have the Next Generation Sequencing methods at their disposal, which enable them to read millions ofsequences at the same time, thus furthermore significantly reducing time needed for laboratory procedures. Concurrently, costs of analysis and equipment have been decreasing, which makes paleogenetical analyses widely available. They are commonly used in medicine, biotechnology, genetic engineering, food industry and forensics, as well as in life sciences like biology, paleobiology, archeology, geology and environmental protection sciences. This paper presents seda DNA (sedimentary ancient DNA) analyses and their use in Quaternary research, as well as describes sources of DNA in sediments and main processes contributing to its degradation or preservation.

3

Life in Extreme Habitats : Diversity of Endolithic Microorganisms from Cold Desert Ecosystems of Eastern Pamir

Khomutovska N., Jerzak M., Kostrzewska-Szlakowska I., Kwiatowski J., Suska-Malawska M., Syczewski M., Jasser I.

Polish Journal of Ecology

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2017

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Vol. 65, nr 4

303--319

EN

The aim of this study was to identify cyanobacteria diversity in rock communities from the cold desert ecosystem in Eastern Pamir Mountains (Tajikistan) and assess if the rock type and rock`s porosity can be indicators of microbial diversity in this extreme environment. Seven samples were collected in July 2015 from hillsides (ca 4000-4500 m a.s.l.) of the Eastern Pamir Mountains. Petrographic and scanning microscopy (SEM) allowed for the characterization of the rocks inhabited by endolithic communities as granite, gneiss and limestone with variable porosity. Based on next-generation sequencing (NGS) of amplicon of V3-V4 hypervariable region of 16S rRNA gene, we established that Actinobacteria, Proteobacteria and Cyanobacteria dominated the endolithic communities of microorganisms in the rocks studied, which distinguishes these communities from those described for other cold arid regions. Chroococcidiopsis and Leptolyngbya were dominant genera in the cyanobacterial communities according to culture-dependent analysis, as well as microscopic analyses of endoliths scraps from the rocks. Culture-independent metagenomic analyses revealed that Microcoleus, Acaryochloris, Chroococcidiopsis and Thermosynechococcus reads were the most abundant from all reads and dominated interchangeably in the samples. Endolithic communities of microorganisms in the rocks from the cold desert shrubland of Eastern Pamir Mts. appear to be diverse and different from communities described for other cold deserts.

4

Zastosowanie NGS i GWAS w diagnostyce i prognozowaniu chorób hematologicznych

Pierzyna-Świtała M., Sędek Ł.

Laboratorium - Przegląd Ogólnopolski

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2017

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nr 9-10

22--27

PL

W ostatnich latach obserwujemy gwałtowny rozwój diagnostyki laboratoryjnej w kierunku diagnostyki spersonalizowanej. W pracy przedstawiono nowoczesne metody molekularne, ich praktyczne zastosowanie we współczesnej diagnostyce chorób hematologicznych oraz perspektywy wykorzystania tych metod w przyszłości.

EN

In recent years we have observed a rapid development of laboratory diagnostics into personalized diagnostics. The article presents modern molecular methods and their practical application in the contemporary diagnostics of haematological diseases, as well as the prospects of their future clinical use.

5

Metody sekwencjonowania nowej generacji oraz ich wykorzystanie w genetyce, hodowli i biotechnologii roślin

Orłowska M., Sobczyk M.

Aparatura Badawcza i Dydaktyczna

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2017

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T. 22, nr 1

54--61

PL

W niniejszej pracy przedstawiono i scharakteryzowano metody sekwencjonowania nowej generacji – NGS (ang. Next-Generation Sequencing). W tym krótkim przeglądzie zaprezentowano najważniejsze techniki sekwencjonowania drugiej generacji. Metody te umożliwiają odczytanie kolejności nukleotydów w łańcuchu DNA. Szybki rozwój technik sekwencjonowania zaczął się na początku lat 70. XX wieku, kiedy to opublikowano dwie techniki pierwszej generacji – metodę Sangera, na której bazują techniki NGS, oraz metodę Maxama i Gilberta. Późniejsze ich modyfikacje (m.in. wprowadzenie elektroforezy kapilarnej, fluorescencyjne znakowanie nukleotydów, zastosowanie mikroprocesora) doprowadziły do pełnej automatyzacji procesu i przyczyniły się do jego udoskonalenia. Obecnie metody NGS są narzędziem wykorzystywanym w wielu dziedzinach nauki, m.in. w genetyce, biotechnologii, biologii molekularnej i w nowoczesnej hodowli roślin. Technologie prezentowane w artykule cechują się wieloma zaletami, ale nie są też pozbawione wad. Dokładność odczytu sekwencji oraz ogólne koszty eksploatacyjne wskazują na to, że najbardziej obiecująca metoda sekwencjonowania nowej generacji opiera się na systemie SOLiD. Z kolei zaś sekwencjonowanie poprzez ligację (platforma SOLIiD) oprócz dużej dokładności charakteryzuje się dłuższym czasem analiz w porównaniu do innych omawianych metod.

EN

In this article next generation sequencing (NGS) methods were characterized. This short review focus on the most important methods of second and third generation sequencing techniques. NGS techniques give unique opportunity to read nucleotides order in DNA strand. Fast, rapid development and progress of genetic sequencing methods began in the seventies. Then two new sequencing techniques were established – enzymatic method (Sanger’s sequencing), chemical method (Maxam’s and Gilbert’s sequencing). Later modifications such as use of capillary electrophoresis, fluorescent nucleotides and application of microprocessor led to total automation of the process and contributed to the methods improvements. Nowadays NGS methods are tools used in many scientific fields e.g. genetic, biotech- nology, molecular biology and modern plant breeding programs. Technologies presented in this article have many advantages, but are also not without flaws. Reading accuracy and the overall costs indicate that method based on SOLiD system is the most promising next generation sequencing. Sequencing by ligation (SOLiD) characterized by high precision but also run time is longer compared to the other method described in this article.

6

Zastosowanie technik sekwencjonowania nowej generacji w wirusologii

Janiak P.

Laboratorium - Przegląd Ogólnopolski

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2015

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nr 5-6

24--30

PL

Technologie sekwencjonowania nowej generacji dowiodły swojej przydatności w wielu dziedzinach nauk medycznych. Dzięki wysokiej wydajności i czułości znalazły szczególne zastosowanie w diagnostyce wirusologicznej. Z powodzeniem wykorzystywane są m.in. w badaniach nad zmiennością genetyczną i mechanizmami oporności na leczenie wirusa zapalenia wątroby typu C (HCV).

EN

The next generation sequencing technologies have proved their usefulness in many fields of medical science. Due to high throughput and sensitivity thay have been particularly applied in diagnostic virology. They have been successfully used in research of genetic variability and drug resistance mechanisms of hepatitis C virus.

7

Assembly of repetitive regions using next-generation sequencing data

Nowak R. M.

Biocybernetics and Biomedical Engineering

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2015

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Vol. 35, no. 4

276--283

EN

High read depth can be used to assemble short sequence repeats. The existing genome assemblers fail in repetitive regions of longer than average read. I propose a new algorithm for a DNA assembly which uses the relative frequency of reads to properly reconstruct repetitive sequences. The mathematical model for error-free input data shows the upper limits of accuracy of the results as a function of read coverage. For high coverage, the estimation error depends linearly on repetitive sequence length and inversely proportional to the sequencing coverage. The model depicts, the smaller de Bruijn graph dimensions, the more accurate assembly of long repetitive regions. The algorithm requires high read depth, provided by the next-generation sequencers and could use the existing data. The tests on errorless reads, generated in silico from several model genomes, pointed the properly reconstructed repetitive sequences, where existing assemblers fail. The C++ sources, the Python scripts and the additional data are available at http://dnaasm.sourceforge.net.