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Implementation of omics research to enhance phytoremediation efficiency - a review

Jaskulak M.

Inżynieria i Ochrona Środowiska

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2018

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T. 21, nr 4

361--373

EN

Phytoremediation is recognized as a cost-effective and widely acceptable alternative to chemical and physical technologies of soil remediation but requires an overall longer time to achieve success. In the last decade, the vast progress in omics research had led to improvements in our understanding of plants metabolism under exposure to toxic substances and the interactions between microbial communities and plants. Omics research includes a numer of disciplines aimed at explaining the biological and chemical principles of functioning a particular organism exposed to selected factors using modern methods of molecular biology (example: rt-qPCR - Quantitative polymerase chain reaction in real time). The names of individual branches of omics studies arise from a group of studied substances, example: transcriptomic refers to research related to changes occurring in the organism at the level of its transcriptome, and proteomics deals with the determination of complete information on the proteomic composition of a given sample. By merging available omics tools with new bioinformatic approaches, it is possible to understand and determinate the specific patterns of plants response to various stress factors. In this review, we provide an overview of how omics research including transcriptomic, proteomic, genomic and metagenomic approaches might be used to reduce the negative impact of toxic elements to plants growth and development in order to ultimately enhance the phytoremediation efficiency.

PL

Fitoremediacja jest uznawana za opłacalną i powszechnie akceptowaną alternatywę dla chemicznych i fizycznych technologii remediacji gleby, ale wymaga dłuższego czasu, aby osiągnąć sukces. W ostatnim dziesięcioleciu ogromny postęp w badaniach omicznych doprowadził do poprawy zrozumienia metabolizmu roślin poddanych ekspozycji na substancje toksyczne oraz interakcji pomiędzy mikroorganizmami symbiotycznymi a roślinami. Badania omiczne obejmują szereg dyscyplin zmierzających do wyjaśniania biologiczno-chemicznych zasad funkcjonowania wybranego organizmu poddanego danym czynnikom za pomocą nowoczesnych metod biologii molekularnej (np. rt-qPCR - ilościowa reakcja łańcuchowa polimerazy w czasie rzeczywistym). Nazwy poszczególnych gałęzi badań omicznych powstają od grupy badanych substancji, np. transkryptomika dotyczy badań związanych ze zmianami zachodzącymi w organizmie na poziomie jego transkryptomu, a proteomika zajmuje się określeniem pełnej informacji o składzie proteomicznym danej próbki. Łącząc dostępne narzędzia omiczne z nowymi technikami bioinformatycznymi, możliwe jest zrozumienie i określenie specyficznych wzorców reakcji komórek roślin na różne czynniki stresowe. W pracy przedstawiono przegląd najnowszych badań omicznych, w tym transkryptomicznych, proteomicznych, genomicznych i metagenomicznych, stosowanych w badaniach nad zmniejszeniem negatywnego wpływu toksycznych substancji na wzrost i rozwój roślin w celu zwiększenia skuteczności procesu fitoremediacji.

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Missing data in open-data era - a barrier to multiomics integration

Piwowar M., Jurkowski W.

Bio-Algorithms and Med-Systems

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2018

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Vol. 14, no. 1

art. no. 20170026

EN

The exploration of complex interactions in biological systems is one of the main aims in nature science nowadays. Progress in this area is possible because of high-throughput omics technologies and the computational surge. The development of analytical methods “is trying to keep pace” with the development of molecular biology methods that provide increasingly large amounts of data - omics data. Specialized databases consist of ever-larger collections of experiments that are usually conducted by one next-generation sequencing technique (e.g. RNA-seq). Other databases integrate data by defining qualitative relationships between individual objects in the form of ontologies, interactions, and pathways (e.g. GO, KEGG, and String). However, there are no open-source complementary quantitative data sets for the biological processes studied, including information from many levels of the organism organization, which would allow the development of multidimensional data analysis methods (multiscale and insightful overviews of biological processes). In the paper, the lack of omics complementary quantitative data set, which would help integrate the defined qualitative biological relationships of individual biomolecules with statistical, computational methods, is discussed.

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Sekwencjonowanie nowej generacji przyszłością genomiki - Ośrodek Genomiki Medycznej OMICRON

Garniewska A.

Laboratorium - Przegląd Ogólnopolski

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2015

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nr 9-10

11--15

PL

Ośrodek Genomiki Medycznej OMICRON jest samodzielną jednostką Wydziału Lekarskiego Collegium Medicum Uniwersytetu Jagiellońskiego. Ośrodek powstał na bazie projektu Unii Europejskiej, realizowanego do niedawna w Collegium Medicum. Prowadzone są w nim projekty naukowe bazujące na technologiach wysokoprzepustowych w obszarach genomiki, transkryptomiki i proteomiki. Ośrodek współpracuje z wieloma jednostkami badawczymi, zarówno krajowymi, jak i zagranicznymi.

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Genomic Virtual Laboratory

Cegielska B., Kaliszan D., Handschuh L., Figlerowicz M., Meyer N.

Computational Methods in Science and Technology

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2010

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Vol. 16, No. 1

39-49

EN

In contemporary science, virtual laboratories give a chance to improve research by facilitating access to high-throughput technologies and bioinformatics methods. The Genomic Virtual Laboratory (GVL) presented here was developed for automate analysis of data retrieved from a microarray experiment. The system was implemented for R Bioconductor-based analysis of results obtained in the study on human acute myeloid leukaemia (AML). The article extends the theoretical aspects of GVL presented earlier [8] and describes how the particular elements were integrated to establish the advanced system of two-colour microarray data analysis.

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New approach to Genomics Experiments Taking Advantage of Virtual Laboratory System

Handschuh L., Lawenda M., Stępniak P., Figlerowicz M., Stroiński M., Węglarz J.

Computational Methods in Science and Technology

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2009

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Vol. 15, nr 1

31-40

EN

Specialized software, on-line tools and computational resources are very common in contemporary science. One of the exemplary domain is genomics – a new branch of science that developed rapidly in the last decade. As the genome research is very complex, it must be supported by professional informatics. In a microarray field the following steps cannot be performed without computational work: design of probes, quantitative analysis of hybridization results, post-processing, and finally data storage and management. Here, the general aspects of virtual laboratory systems are presented together with perspectives of their implementation in genomics in order to automate and facilitate this area of research.

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Strategia badania mechanizmu dezaktywacji metali przez rośliny. Cz. II: Genomika i specjacja bionieorganiczna "za pan brat"

Pawlak K., Ruzik R., Lipiec E., Ciurzyńska M., Gawrońska H.

Analityka : nauka i praktyka

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2007

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nr 1

20-23

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Genomic Maps and Novel Approaches to Sequencing of Repetitive versus Non-repetitive DNA

Szybalski W.

Polish Journal of Chemistry

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2004

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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.