Mikrofluidika je inovativní obor, který se zabývá zpracováním malého množství kapaliny v mikrokanálech. V kombinaci s pokročilými analytickými technikami, jako je např. mikrofluidní PCR, nabízí významné výhody nejen pro analýzu genové exprese. Tato metoda využívá mikrokanály a mikroventily k přesnému dávkování a míchání činidel, čímž se minimalizuje spotřeba vzorku a činidla a také čas stráve‐ ný pipetováním. Tyto vlastnosti činí mikrofluidní PCR ideální pro analýzu genové exprese, kde je vyžadováno podrobné monitorování a kvantifikace mRNA. Jedním z přístrojů umožňujícím mikrofluidní PCR je Biomark X. Díky své schopnosti multiplexování a také díky své‐ mu mikrofluidnímu designu umožňuje analýzu mnoha vzorků současně. Tato pokročilá technologie má široké uplatnění v biologickém výzkumu, diagnostice a personalizované medicíně a nabízí nové příležitosti k objevování a pochopení genetických procesů.
Microfluidics is an innovative science that deals with the manipulation of small volumes of fluid in microchannels. In combination with advanced analytical techniques such as microfluidic PCR, it offers significant advantages not only for gene expression analysis. Microflui‐ dic PCR enables PCR reactions to be performed using very small sample volumes, as it utilizes microchannels and microvalves for precise reagent dispensing and mixing. This fact increases both sensitivity and accuracy of the analysis. The Biomark X instrument utilizes micro‐ fluidic PCR for gene expression analysis, as it is ideal for mRNA quantification. With its multiplexing capability and microfluidic design, it enables the analysis of multiple samples simultaneously. This advanced technology finds broad applications in biological research, diagnostics, and provides new opportunities for the discovery and understanding of genetic processes.
Multicolor flow cytometry allows for analysis of tens of cellular parameters in millions of cells at a single-cell resolution within minutes. The lack of technologies that would facilitate feasible and relatively cheap profiling of such a number of cells with an antibody-based approach led us to the development of a high-throughput cytometry-based platform for surface profiling. We coupled the fluorescent cell barcoding with preexisting, commercially available screening tools to analyze cell surface fingerprint at a large scale. This powerful approach will help to identify novel biomarkers and druggable targets and facilitate the discovery of new concepts in immunology, oncology, and developmental biology.
Závěrečná zpráva o řešení grantu Agentury pro zdravotnický výzkum MZ ČR
nestr.
V letech 2017 – 2020 bude vyšetřeno 200 pacientů s odstraněnými adenomy >10 mm. Za asistence endoskopisty bude v rizikových oblastech adenomu provedeno histopatologické hodnocení a molekulární vyšetření intratumorové heterogenity a klonálních profilů s využitím panelu genů obsahující frekventně mutované geny (KRAS, TP53, PIK3CA, APC). Bude stanovena míra heterogenity na základě výskytu a kvantifikace sledovaných mutací (skóre 1 – 5). Následně budou pacienti kolonoskopicky sledováni v jednoletém intervalu. U rizikových pacientů (vysoký stupeň dysplázie, vysoké skóre heterogenity, rekurence adenomů) a vybraných kontrolních subjektů bude provedeno rozsáhlé profilování somatických mutací cíleným „multitarget“ sekvenováním technologií NGS (sekvenování nové generace). Cílem projektu je provedení statistické analýzy za účelem vytipování kandidátních genů pro predikci rekurence kolorektální neoplázie po endoskopické terapii a detailní charakterizace topografické heterogenity adenomů se stanovením doporučení pro odběr bioptických vzorků.; In years 2017–2020, there will be 200 patients with removed colorectal adenomas >10 mm included. In adenomas high risk areas identified by endoscopist, the histopathology evaluation and molecular examination of intratumoral heterogenity and clonal profiles of highly frequent mutated genes (KRAS, TP53, PIK3CA and APC) will be done. The level of heterogenity will be determined based on the presence and quantification of mutations (score of heterogenity 1-5). All patients will have follow-up colonoscopy in one-year intervals. In a high-risk patients group (high grade dysplasia; high heterogenity score; adenoma recurrence) and selected control subjects, the extensive somatic mutations profiling will be carried out according to multitarget sequencing by NGS technologies (next generation sequencing). The aims are to identify the candidate genes for the prediction of colorectal neoplasia recurrence after endoscopic therapy and detailed adenomas topographic heterogenity characterization to set the biopsy sampling recommendations.
- MeSH
- Genes, Neoplasm MeSH
- Colonoscopy MeSH
- Colorectal Neoplasms genetics MeSH
- Mutation MeSH
- Recurrence MeSH
- Tertiary Prevention MeSH
- High-Throughput Nucleotide Sequencing methods MeSH
- Check Tag
- Male MeSH
- Conspectus
- Patologie. Klinická medicína
- NML Fields
- onkologie
- koloproktologie
- genetika, lékařská genetika
- NML Publication type
- závěrečné zprávy o řešení grantu AZV MZ ČR
Therapeutic enzymes are valuable biopharmaceuticals in various biomedical applications. They have been successfully applied for fibrinolysis, cancer treatment, enzyme replacement therapies, and the treatment of rare diseases. Still, there is a permanent demand to find new or better therapeutic enzymes, which would be sufficiently soluble, stable, and active to meet specific medical needs. Here, we highlight the benefits of coupling computational approaches with high-throughput experimental technologies, which significantly accelerate the identification and engineering of catalytic therapeutic agents. New enzymes can be identified in genomic and metagenomic databases, which grow thanks to next-generation sequencing technologies exponentially. Computational design and machine learning methods are being developed to improve catalytically potent enzymes and predict their properties to guide the selection of target enzymes. High-throughput experimental pipelines, increasingly relying on microfluidics, ensure functional screening and biochemical characterization of target enzymes to reach efficient therapeutic enzymes.
With the expansion of molecular techniques, the historical collections have become widely used. The last boom started with using next- and second-generation sequencing in which massive parallel sequencing replaced targeted sequencing and third-generation technology involves single molecule technology. Studying plant DNA using these modern molecular techniques plays an important role in understanding evolutionary relationships, identification through DNA barcoding, conservation status, and many other aspects of plant biology. Enormous herbarium collections are an important source of material especially for taxonomic long-standing issues, specimens from areas difficult to access or from taxa that are now extinct. The ability to utilize these specimens greatly enhances the research. However, the process of extracting DNA from herbarium specimens is often fraught with difficulty related to such variables as plant chemistry, drying method of the specimen, and chemical treatment of the specimen. The result of these applications is often fragmented DNA. The reason new sequencing approaches have been so successful is that the template DNA needs to be fragmented for proper library building, and herbarium DNA is exactly that. Although many methods have been developed for extraction of DNA from herbarium specimens, the most frequently used are modified CTAB and DNeasy Plant Mini Kit protocols. Nine selected protocols in this chapter have been successfully used for high-quality DNA extraction from different kinds of plant herbarium tissues. These methods differ primarily with respect to their requirements for input material (from algae to vascular plants), type of the plant tissue (leaves with incrustations, sclerenchyma strands, mucilaginous tissues, needles, seeds), and further possible applications (PCR-based methods, microsatellites, AFLP or next-generation sequencing).
- MeSH
- Amplified Fragment Length Polymorphism Analysis MeSH
- Chemical Fractionation methods MeSH
- DNA, Plant genetics isolation & purification MeSH
- Plant Leaves genetics MeSH
- Microsatellite Repeats MeSH
- Organ Specificity MeSH
- Polymerase Chain Reaction MeSH
- Reagent Kits, Diagnostic MeSH
- Plants classification genetics MeSH
- Sequence Analysis, DNA MeSH
- DNA Barcoding, Taxonomic methods MeSH
- High-Throughput Nucleotide Sequencing MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
The demand for food and beverage markets has increased as a result of population increase and in view of health awareness. The quality of products from food processing industry has to be improved economically by incorporating greener methodologies that enhances the safety and shelf life via the enzymes application while maintaining the essential nutritional qualities. The utilization of enzymes is rendered more favorable in industrial practices via the modification of their characteristics as attested by studies on enzyme immobilization pertaining to different stages of food and beverage processing; these studies have enhanced the catalytic activity, stability of enzymes and lowered the overall cost. However, the harsh conditions of industrial processes continue to increase the propensity of enzyme destabilization thus shortening their industrial lifespan namely enzyme leaching, recoverability, uncontrollable orientation and the lack of a general procedure. Innovative studies have strived to provide new tools and materials for the development of systems offering new possibilities for industrial applications of enzymes. Herein, an effort has been made to present up-to-date developments on enzyme immobilization and current challenges in the food and beverage industries in terms of enhancing the enzyme stability.
- MeSH
- Enzymes, Immobilized * metabolism MeSH
- Food Industry * MeSH
- Enzyme Stability MeSH
- Technology MeSH
- Publication type
- Journal Article MeSH
INTRODUCTION: Driver mutations in Philadelphia chromosome-negative myeloproliferative neoplasms are well known. In the past, whole-genome sequencing identified nondriver mutations in other genes, potentially contributing to evolution of malignant clones. METHODS: Next-generation sequencing was used to assess the presence of any mutations in 14 candidate genes at the point of diagnosis and the resultant impact on the clinical course of the disease. RESULTS: The study analysed 63 patients with myelofibrosis (MF). Nondriver mutations were detected in 44% of them. The most frequently affected genes were ASXL1 (27%), TET2 (11%) and SF3B1 (6%). The frequency of such mutations was highest in primary MF (59%) and lowest in the prefibrotic phase of primary MF (21%). Patients with prognostically unfavourable sequence variants in genes had significantly worse overall survival (53 vs 71 months; HR = 2.77; 95% CI 1.17-6.56; P = .017). CONCLUSION: In our study, multivariate analysis proved DIPSS to be the only significant factor to predict patient survival. DIPSS contains all of the important clinical and laboratory factors except genetic changes. Stratification of patients according to DIPSS is still beneficial although there are newer and improved scoring systems like GIPSS or MIPSS70. Assessing subclonal mutations in candidate genes during diagnosis may aid in the identification of high-risk MF patients and is therefore relevant for making a prediction for overall survival more accurate.
- MeSH
- Dioxygenases genetics MeSH
- DNA-Binding Proteins genetics MeSH
- Adult MeSH
- Phosphoproteins genetics MeSH
- Middle Aged MeSH
- Humans MeSH
- Mutation MeSH
- Primary Myelofibrosis genetics MeSH
- Repressor Proteins genetics MeSH
- Aged MeSH
- RNA Splicing Factors genetics MeSH
- High-Throughput Nucleotide Sequencing methods MeSH
- Check Tag
- Adult MeSH
- Middle Aged MeSH
- Humans MeSH
- Male MeSH
- Aged MeSH
- Female MeSH
- Publication type
- Journal Article MeSH
Although our knowledge regarding oocyte quality and development has improved significantly, the molecular mechanisms that regulate and determine oocyte developmental competence are still unclear. Therefore, the objective of this study was to identify and analyze the transcriptome profiles of porcine oocytes derived from large or small follicles using RNA high-throughput sequencing technology. RNA libraries were constructed from oocytes of large (LO; 3-6 mm) or small (SO; 1.5-1.9 mm) ovarian follicles and then sequenced in an Illumina HiSeq4000. Transcriptome analysis showed a total of 14,557 genes were commonly detected in both oocyte groups. Genes related to the cell cycle, oocyte meiosis, and quality were among the top highly expressed genes in both groups. Differential expression analysis revealed 60 up- and 262 downregulated genes in the LO compared with the SO group. BRCA2, GPLD1, ZP3, ND3, and ND4L were among the highly abundant and highly significant differentially expressed genes (DEGs). The ontological classification of DEGs indicated that protein processing in endoplasmic reticulum was the top enriched pathway. In addition, biological processes related to cell growth and signaling, gene expression regulations, cytoskeleton, and extracellular matrix organization were among the highly enriched processes. In conclusion, this study provides new insights into the global transcriptome changes and the abundance of specific transcripts in porcine oocytes in correlation with follicle size.
- MeSH
- Gene Regulatory Networks physiology MeSH
- Oocytes metabolism MeSH
- Oogenesis genetics MeSH
- Ovarian Follicle cytology MeSH
- Reverse Transcriptase Polymerase Chain Reaction MeSH
- Swine genetics growth & development MeSH
- Signal Transduction genetics MeSH
- Gene Expression Profiling MeSH
- Transcriptome * MeSH
- High-Throughput Nucleotide Sequencing MeSH
- Gene Expression Regulation, Developmental physiology MeSH
- Animals MeSH
- Check Tag
- Female MeSH
- Animals MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
Design and development of scale-down approaches, such as microbioreactor (μBR) technologies with integrated sensors, are an adequate solution for rapid, high-throughput and cost-effective screening of valuable reactions and/or production strains, with considerably reduced use of reagents and generation of waste. A significant challenge in the successful and widespread application of μBRs in biotechnology remains the lack of appropriate software and automated data interpretation of μBR experiments. Here, it is demonstrated how mathematical models can be usedas helpful tools, not only to exploit the capabilities of microfluidic platforms, but also to reveal the critical experimental conditions when monitoring cascade enzymatic reactions. A simplified mechanistic model was developed to describe the enzymatic reaction of glucose oxidase and glucose in the presence of catalase inside a commercial microfluidic platform with integrated oxygen sensor spots. The proposed model allowed an easy and rapid identification of the reaction mechanism, kinetics and limiting factors. The effect of fluid flow and enzyme adsorption inside the microfluidic chip on the optical sensor response and overall monitoring capabilities of the presented platform was evaluated via computational fluid dynamics (CFD) simulations. Remarkably, the model predictions were independently confirmed for μL- and mL- scale experiments. It is expected that the mechanistic models will significantly contribute to the further promotion of μBRs in biocatalysis research and that the overall study will create a framework for screening and evaluation of critical system parameters, including sensor response, operating conditions, experimental and microbioreactor designs.
Závěrečná zpráva o řešení grantu Agentury pro zdravotnický výzkum MZ ČR
Nestr.
Šetření epidemií listerióz je obtížnější než šetření ostatních alimentárních onemocnění, a to zejména kvůli delší inkubační době onemocnění, nízkému počtu případů, velkému geografickému rozptýlení nemocných a komplikované komunikaci s postiženými a jejich příbuznými při hledání vehikula infekce. Technologie založené na analýze genetických charakteristik kmenů jsou zásadním epidemiologickým nástrojem v oblasti prevence a kontroly listerióz. V rámci projektu budou k typizaci kmenů používány jak standardní, tak i nové laboratorní techniky. Tento nový metodologický přístup umožní zefektivnění práce epidemiologů v ČR a posílí spolupráci s ostatními evropskými zeměmi v oblasti molekulární epidemiologie a inter-laboratorní výměny dat.; Listeriosis outbreak investigation is more difficult than other foodborne diseases investigation, mainly because longer incubation period of the disease, the small number of cases, a large geographical dispersion of patients and complicated communication with affected persons and their families in the search for a vehicle of infection. Technologies based on genetic analysis used for strain characteristics are essential epidemiological tool in the prevention and control of listeriosis. Both standard and new laboratory techniques for enhanced surveillance and outbreak detection will be implemented. New methodological approach will strengthen cooperation with other European countries in the field of molecular epidemiology and inter-laboratory data exchange.
- MeSH
- Epidemics MeSH
- Humans MeSH
- Listeria monocytogenes genetics isolation & purification MeSH
- Listeriosis epidemiology genetics microbiology MeSH
- Molecular Epidemiology methods MeSH
- Molecular Typing methods MeSH
- High-Throughput Nucleotide Sequencing methods MeSH
- Check Tag
- Humans MeSH
- Conspectus
- Patologie. Klinická medicína
- NML Fields
- infekční lékařství
- epidemiologie
- molekulární biologie, molekulární medicína
- NML Publication type
- závěrečné zprávy o řešení grantu AZV MZ ČR
