Single-cell RNA-seq methods can be used to delineate cell types and states at unprecedented resolution but do little to explain why certain genes are expressed. Single-cell ATAC-seq and multiome (ATAC + RNA) have emerged to give a complementary view of the cell state. It is however unclear what additional information can be extracted from ATAC-seq data besides transcription factor binding sites. Here, we show that ATAC-seq telomere-like reads counter-inituively cannot be used to infer telomere length, as they mostly originate from the subtelomere, but can be used as a biomarker for chromatin condensation. Using long-read sequencing, we further show that modern hyperactive Tn5 does not duplicate 9 bp of its target sequence, contrary to common belief. We provide a new tool, Telomemore, which can quantify nonaligning subtelomeric reads. By analyzing several public datasets and generating new multiome fibroblast and B-cell atlases, we show how this new readout can aid single-cell data interpretation. We show how drivers of condensation processes can be inferred, and how it complements common RNA-seq-based cell cycle inference, which fails for monocytes. Telomemore-based analysis of the condensation state is thus a valuable complement to the single-cell analysis toolbox.

• MeSH
• Single-Cell Analysis * methods   MeSH
• B-Lymphocytes metabolism   cytology   MeSH
• Cell Cycle * genetics   MeSH
• Chromatin Immunoprecipitation Sequencing methods   MeSH
• Chromatin * metabolism   chemistry   genetics   MeSH
• Fibroblasts metabolism   cytology   MeSH
• Humans MeSH
• RNA-Seq methods   MeSH
• Telomere * genetics   MeSH
• Binding Sites MeSH
• Check Tag
• Humans MeSH
• Publication type
• Journal Article MeSH

Proteomics provides an understanding of biological systems by enabling the detailed study of protein expression profiles, which is crucial for early disease diagnosis. Microfluidic-based proteomics enhances this field by integrating complex proteome analysis into compact and efficient systems. This review focuses on developing microfluidic chip structures for proteomics, covering on-chip sample pretreatment, protein extraction, purification, and identification in recent years. Furthermore, our work aims to inspire researchers to select proper methodologies in designing novel, efficient assays for proteomics applications by analyzing trends and innovations in this field.

• MeSH
• Biosensing Techniques instrumentation   methods   MeSH
• Equipment Design MeSH
• Lab-On-A-Chip Devices * MeSH
• Humans MeSH
• Microfluidics methods   MeSH
• Microfluidic Analytical Techniques instrumentation   MeSH
• Proteins analysis   isolation & purification   MeSH
• Proteome analysis   isolation & purification   chemistry   MeSH
• Proteomics * methods   MeSH
• Animals MeSH
• Check Tag
• Humans MeSH
• Animals MeSH
• Publication type
• Journal Article MeSH
• Review MeSH

This study investigates various microfluidic chip fabrication techniques, highlighting their applicability and limitations in the context of urgent diagnostic needs showcased by the COVID-19 pandemic. Through a detailed examination of methods such as computer numerical control milling of a polymethyl methacrylate, soft lithography for polydimethylsiloxane-based devices, xurography for glass-glass chips, and micromachining-based silicon-glass chips, we analyze each technique's strengths and trade-offs. Hence, we discuss the fabrication complexity and chip thermal properties, such as heating and cooling rates, which are essential features of chip utilization for a polymerase chain reaction. Our comparative analysis reveals critical insights into material challenges, design flexibility, and cost-efficiency, aiming to guide the development of robust and reliable microfluidic devices for healthcare and research. This work underscores the importance of selecting appropriate fabrication methods to optimize device functionality, durability, and production efficiency.

• MeSH
• COVID-19 * virology   MeSH
• Equipment Design MeSH
• Dimethylpolysiloxanes chemistry   MeSH
• Lab-On-A-Chip Devices * MeSH
• Humans MeSH
• Microfluidics methods   instrumentation   MeSH
• Microfluidic Analytical Techniques instrumentation   methods   MeSH
• Polymethyl Methacrylate chemistry   MeSH
• SARS-CoV-2 isolation & purification   MeSH
• Check Tag
• Humans MeSH
• Publication type
• Journal Article MeSH
• Comparative Study MeSH

Publikace se zaměřuje na různé možnosti hormonální antikoncepce pro ženy a na její bezpečnost. Určeno odborné veřejnosti.; Hormonální antikoncepce přestavuje nejefektivnější metodu plánovaného rodičovství. V České republice se jedná o metodu nejčastěji užívanou, kdy ji využívá vysoký počet žen různého věku - od pubertálního do perimenopauzálního období. Tato skutečnost otevírá klinický problém rizikových uživatelek. Jaká jsou skutečná rizika hormonální antikoncepce a v jakých případech se jedná o nepodložené mýty? Jaké jsou zásady bezpečné praxe? Odpověď tato publikace hledá v přehledu témat hormonální antikoncepce ve specifických klinických situacích (antikoncepce u adolescentních dívek, antikoncepce v klimakteriu, antikoncepce a kardiovaskulární morbidita, antikoncepce a nádorová onemocnění). Součástí přehledu je i reflexe pozitivních nekontracepčních účinků hormonální antikoncepce (hyperandrogenní stavy, ná

• MeSH
• Patient Safety MeSH
• Hormonal Contraception MeSH
• Women's Health MeSH
• Publication type
• Monograph MeSH

• Conspectus
• Hygiena. Lidské zdraví
• NML Fields
• farmacie a farmakologie
• reprodukční lékařství

As organoids and organ-on-chip (OoC) systems move toward preclinical and clinical applications, there is an increased need for method validation. Using a liquid chromatography-mass spectrometry (LC-MS)-based approach, we developed a method for measuring small-molecule drugs and metabolites in the cell medium directly sampled from liver organoids/OoC systems. The LC-MS setup was coupled to an automatic filtration and filter flush system with online solid-phase extraction (SPE), allowing for robust and automated sample cleanup/analysis. For the matrix, rich in, e.g., protein, salts, and amino acids, no preinjection sample preparation steps (protein precipitation, SPE, etc.) were necessary. The approach was demonstrated with tolbutamide and its liver metabolite, 4-hydroxytolbutamide (4HT). The method was validated for analysis of cell media of human stem cell-derived liver organoids cultured in static conditions and on a microfluidic platform according to Food and Drug Administration (FDA) guidelines with regards to selectivity, matrix effects, accuracy, precision, etc. The system allows for hundreds of injections without replacing chromatography hardware. In summary, drug/metabolite analysis of organoids/OoCs can be performed robustly with minimal sample preparation.

• MeSH
• Chromatography, Liquid methods   MeSH
• Solid Phase Extraction MeSH
• Mass Spectrometry methods   MeSH
• Liver * metabolism   MeSH
• Liquid Chromatography-Mass Spectrometry MeSH
• Small Molecule Libraries analysis   metabolism   chemistry   MeSH
• Lab-On-A-Chip Devices MeSH
• Pharmaceutical Preparations metabolism   analysis   MeSH
• Humans MeSH
• Organoids * metabolism   cytology   MeSH
• Tolbutamide metabolism   analysis   MeSH
• Check Tag
• Humans MeSH
• Publication type
• Journal Article MeSH
• Research Support, Non-U.S. Gov't MeSH
• Validation Study MeSH

The application of microfluidic devices as next-generation cell and tissue culture systems has increased impressively in the last decades. With that, a plethora of materials as well as fabrication methods for these devices have emerged. Here, we describe the rapid prototyping of microfluidic devices, using micromilling and vapour-assisted thermal bonding of polymethyl methacrylate (PMMA), to create a spheroid-on-a-chip culture system. Surface roughness of the micromilled structures was assessed using scanning electron microscopy (SEM) and atomic force microscopy (AFM), showing that the fabrication procedure can impact the surface quality of micromilled substrates with milling tracks that can be readily observed in micromilled channels. A roughness of approximately 153 nm was created. Chloroform vapour-assisted bonding was used for simultaneous surface smoothing and bonding. A 30-s treatment with chloroform-vapour was able to reduce the surface roughness and smooth it to approximately 39 nm roughness. Subsequent bonding of multilayer PMMA-based microfluidic chips created a durable assembly, as shown by tensile testing. MDA-MB-231 breast cancer cells were cultured as multicellular tumour spheroids in the device and their characteristics evaluated using immunofluorescence staining. Spheroids could be successfully maintained for at least three weeks. They consisted of a characteristic hypoxic core, along with expression of the quiescence marker, p27kip1. This core was surrounded by a ring of Ki67-positive, proliferative cells. Overall, the method described represents a versatile approach to generate microfluidic devices compatible with biological applications.

• MeSH
• Chloroform MeSH
• Lab-On-A-Chip Devices MeSH
• Microfluidics * methods   MeSH
• Microfluidic Analytical Techniques * MeSH
• Polymethyl Methacrylate chemistry   MeSH
• Publication type
• Journal Article MeSH

Zvyšující se výskyt antibiotických rezistencí patří k závažným problémům 21.století. Výskyt bakteriálních kmenů rezistentních k antibiotikům následně zužuje spektrum vhodných antibiotik použitelných pro léčbu i běžných bakteriálních infekcí nebo pro prevenci jejich výskytu, např. v chirurgii. Čistírny odpadních vod, nemocnice, ale i potravinový řetězec patří k ohniskům, kde nejčastěji dochází ke vzniku či šíření nových i stávajících kmenů bakterií rezistentních k antibiotikům a genů rezistence k antibiotikům. Ke stanovení antibiotických rezistencí se v laboratořích standardně používají fenotypové kultivační metody, které jsou však náročné na čas i práci a částečně i přesnou interpretaci výsledků. Z tohoto důvodu jsou hledány rychlejší alternativní metody detekce bakterií rezistentních k antibiotikům nebo přímo genů rezistence k antibiotikům. Příkladem alternativní metody detekce bakterií rezistentních k antibiotikům je například použití fenotypové metody využívající hmotnostní spektrometrie s laserovou desorpcí a ionizací za účasti matrice s průletovým analyzátorem pro stanovení producentů beta-laktamas. Zrychlení a zároveň větší přesnost detekce poskytují genotypové metody. Pomocí polymerasové řetězové reakce lze přímo detekovat a kvantifikovat geny rezistence k antibiotikům. Pro další zrychlení a vyšší specifitu detekce amplikonů z PCR lze použít mikročipy. Metody masivního paralelního sekvenování poskytují ucelenou informaci o rezistomu daného prostředí. Umožňují sekvenovat DNA amplikony či jednotlivé molekuly DNA pro detekci determinant antibiotické rezistence. Metody masivního paralelního sekvenování mají potenciál nahradit konvenční charakterizaci patogenů a umožňují detekci všech mikroorganismů ve vzorku (včetně obtížně kultivovatelných či nekultivovatelných mikroorganismů).

The increasing occurrence of antibiotic resistance is one of the major problems of the 21st century. The occurrence of bacterial strains resistant to antibiotics subsequently narrows the spectrum of suitable antibiotics usable for the treatment of common bacterial infections or for the prevention of their occurrence, e.g., in surgery. Wastewater treatment plants, hospitals, and also the food chain belong to the hotspots, where the emergence and spread of new or existing strains of antibiotic resistant bacteria and antibiotic resistance genes occur most frequently. Phenotypic culture methods are routinely used in laboratories to determine antibiotic resistance, but they are laborious and time-consuming and the interpretation of exact results is also difficult. For this reason, faster alternatives for the detection of antibiotic resistant bacteria or even antibiotic resistance genes are sought. Such an example of an alternative method for the detection of antibiotic resistant bacteria is the use of the matrix-assisted laser desorption/ionization time-of-flight mass spectrometry phenotypic method to identify the beta-lactamase producers. Genotype methods provide faster analysis and, at the same time, more accurate detection. Antibiotic resistance genes can be directly detected and quantified by polymerase chain reaction. Microarrays can be used to further speed up and increase the specificity of PCR amplicons detection. Massive parallel methods provide comprehensive information on the resistoma of the specific environment. They facilitate sequencing of individual DNA molecules or amplicons to detect determinants of antibiotic resistance. Massive parallel methods have the potential to replace conventional pathogen characterization and allow the detection of all microorganisms in a sample (including difficult-to-cultivate or noncultivable microorganisms).

• MeSH
• Drug Resistance, Microbial * genetics   MeSH
• Microbial Sensitivity Tests methods   MeSH
• Microbiological Techniques * classification   methods   MeSH
• Polymerase Chain Reaction methods   MeSH
• Oligonucleotide Array Sequence Analysis methods   MeSH
• Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization methods   MeSH
• High-Throughput Nucleotide Sequencing methods   MeSH
• Publication type
• Review MeSH

Ciele: Analýza prenatálnych vzoriek za obdobie 2015–2020. Porovnanie miery detekcie klinicky relevantných variant cytogenetickou analýzou karyotypu a cytogenomickými metódami MLPA (Multiplex Ligation-Depent Probe Amplification) a mikročipmi (CMA – chromosomal microarray). Súbor a metodika: Analyzovaných bolo 1 029 prenatálnych vzoriek cytogenetickým hodnotením karyotypu (n = 1 029), cytogenomickými metódami MLPA (n = 144) a CMA (n = 111). Všetky nebalansované zmeny boli potvrdené metódou MLPA alebo CMA. Výsledky: Z analyzovaného súboru plodov, po odčítaní aneuploidií – 107 (10,40 %, n = 1 029), bolo analýzou karyotypu zachytených 22 štruktúrnych aberácií (2,39 %, n = 922) – deväť nebalansovaných zmien (0,98 %), 10 balansovaných zmien (1,08 %), jeden prípad nejasnej mozaiky (0,09 %), jeden prípad prítomnosti marker chromozómu (0,09 %) a jeden prípad diskordancie pohlavia (0,09 %). U 255 vzoriek s fyziologickým karyotypom indikovaných k cytogenomickému vyšetreniu bolo zachytených celkom osem (7,21 %, n = 111) patologických variant metódou CMA. Metódou MLPA bolo z týchto ôsmich patogénnych variant zachytených päť (3,47 %, n = 144). Celkový záchyt patogénnych variant metódami MLPA a CMA vrátane konfirmačných vyšetrení patologického karyotypu je 14 (5,14 %) a 17 (6,25 %) (n = 272). Záchyt patologických variant v skupine s izolovanými poruchami bol nižší než v skupine s mnohopočetnými poruchami (5,08 vs. 21,42 %). Záver: Potvrdila sa vyššia úspešnosť záchytu patologických variant so zmenou v počte kópií, metódou CMA než MLPA.

Objective: Analysis of prenatal samples from 2015 to 2020. Comparison detection rates of clinically relevant variants by cytogenetic karyotype analysis and cytogenomic MLPA (Multiplex Ligation-Depent Probe Amplification) and microarray methods (CMA – chromosomal microarray). Material and method: 1,029 prenatal samples were analyzed by cytogenetic karyotyping (N = 1,029), cytogenomic methods – MLPA (N = 144) and CMA (N = 111). All unbalanced changes were confirmed by MLPA or CMA. Results: From the analyzed set of fetuses, after subtraction of aneuploidies – 107 (10.40%, N = 1,029), 22 structural aberrations (2.39%, N = 922) – nine unbalanced changes (0.98%), 10 balanced changes (1.08%), one case of unclear mosaicism (0.09%), one case of presence of a marker chromosome (0.09%) and one case of sex discordance (0.09%) – were detected by karyotype analysis. A total of eight (7.21%, N = 111) pathological variants were detected by CMA in 255 samples with physiological karyotype indicated for cytogenomic examination. Five (3.47%, N = 144) of eight pathogenic variants were detected by MLPA method. The total capture of pathogenic variants by MLPA and CMA methods was 14 (5.14%) and 17 (6.25%) (N = 272), including confirmatory pathological karyotype testing. Detection of pathological variants in the isolated disorders group was lower than in the multiple disorders group (5.08 vs. 21.42%). Conclusion: A higher success rate for the detection of pathological copy number variation variants by the microarray method than by the MLPA method was confirmed.

• MeSH
• Clinical Studies as Topic MeSH
• Humans MeSH
• Microarray Analysis methods   MeSH
• Mosaicism MeSH
• Multiplex Polymerase Chain Reaction methods   MeSH
• Fetus MeSH
• Prenatal Diagnosis * MeSH
• Pregnancy MeSH
• DNA Copy Number Variations MeSH
• Congenital Abnormalities * diagnosis   genetics   MeSH
• Check Tag
• Humans MeSH
• Pregnancy MeSH
• Female MeSH

Transfer RNAs acquire a large plethora of chemical modifications. Among those, modifications of the anticodon loop play important roles in translational fidelity and tRNA stability. Four human wobble U-containing tRNAs obtain 5-methoxycarbonylmethyluridine (mcm5U34) or 5-methoxycarbonylmethyl-2-thiouridine (mcm5s2U34), which play a role in decoding. This mark involves a cascade of enzymatic activities. The last step is mediated by alkylation repair homolog 8 (ALKBH8). In this study, we performed a transcriptome-wide analysis of the repertoire of ALKBH8 RNA targets. Using a combination of HITS-CLIP and RIP-seq analyses, we uncover ALKBH8-bound RNAs. We show that ALKBH8 targets fully processed and CCA modified tRNAs. Our analyses uncovered the previously known set of wobble U-containing tRNAs. In addition, both our approaches revealed ALKBH8 binding to several other types of noncoding RNAs, in particular C/D box snoRNAs.

• MeSH
• AlkB Homolog 8, tRNA Methyltransferase genetics   MeSH
• Anticodon MeSH
• Chromatin Immunoprecipitation Sequencing * MeSH
• Humans MeSH
• RNA, Untranslated genetics   MeSH
• RNA, Transfer * genetics   metabolism   MeSH
• Check Tag
• Humans MeSH
• Publication type
• Journal Article MeSH
• Research Support, Non-U.S. Gov't MeSH

Přestože se spektrum biomarkerů užívaných v onkologii neustále rozšiřuje, zůstává stanovení morfologie nádorů rozhodujícím kritériem diagnostiky. U karcinomů prsu bylo nedávno zjištěno, že stupeň diferenciace je provázen změnami exprese miRNA. Není však nic známo o tom, zda popsané změny souvisí se změnou morfologie a zda mají individuální nebo obecný charakter. Cílem navrhovaného projektu je použít zatím unikátní přístup a srovnat expresní profil miRNA z různých částí téhož nádoru s rozdílnou morfologickou charakteristikou i nádorů se stejnou morfologií od různých pacientek a zároveň zjistit, zda je možné tyto specifické miRNA detekovat v krvi. Pro řešení navrhujeme použít mikrodisekční metody izolace buněk z parafínových bloků TNBC a mikročipovou analýzu miRNA. Tkáňové a sérové hladiny vybraných miRNA budou sledovány pomocí qPCR v rozšířeném validačním souboru a jejich funkce bude studována pomocí experimentů na buněčných liniích. Projekt by mohl přispět k odhalení nových principů řídících morfogenezi v nádorech a rovněž k identifikaci nových diagnostických a prognostických znaků.; Although the spectrum of cancer biomarkers is constantly expanding, determining the morphology is a decisive criterion for diagnosis. Recent research in breast cancer has shown that the degree of differentiation is accompanied by changes in miRNA expression. However, nothing is known about relationship between the described changes and tumor morphology or whether these changes have an individual or general character. We suggest to compare the miRNA expression profiles from different parts of the same tumor which have different morphology as well as tumors with the same morphology from different patients and analyse whether specific miRNAs are released into blood. Microdissection of cells from paraffin blocks of TNBC and miRNA microarray analysis will be used. Tissue and serum levels of selected miRNAs will be monitored by qPCR in an extended validation set and their functions will be studied by experiments on cell lines. The project could contribute to the discovery of new principles governing morphogenesis in tumors as well as identify novel diagnostic and prognostic markers.

• MeSH
• Early Detection of Cancer MeSH
• Gene Expression MeSH
• Humans MeSH
• MicroRNAs MeSH
• Microarray Analysis MeSH
• Microdissection MeSH
• Morphogenesis MeSH
• Biomarkers, Tumor analysis   MeSH
• Prognosis MeSH
• Triple Negative Breast Neoplasms diagnosis   MeSH
• Check Tag
• Humans MeSH
• Female MeSH

• Conspectus
• Patologie. Klinická medicína
• NML Fields
• onkologie
• genetika, lékařská genetika
• NML Publication type
• závěrečné zprávy o řešení grantu AZV MZ ČR