• MeSH
• mapování mozku MeSH
• nemoci mozku MeSH

• Konspekt
• Patologie. Klinická medicína
• NLK Obory
• neurologie

BACKGROUND: Fuchs endothelial corneal dystrophy (FECD) is the most common repeat-mediated disease in humans. It exclusively affects corneal endothelial cells (CECs), with ≤81% of cases associated with an intronic TCF4 triplet repeat (CTG18.1). Here, we utilise optical genome mapping (OGM) to investigate CTG18.1 tissue-specific instability to gain mechanistic insights. METHODS: We applied OGM to a diverse range of genomic DNAs (gDNAs) from patients with FECD and controls (n = 43); CECs, leukocytes and fibroblasts. A bioinformatics pipeline was developed to robustly interrogate CTG18.1-spanning DNA molecules. All results were compared with conventional polymerase chain reaction-based fragment analysis. FINDINGS: Analysis of bio-samples revealed that expanded CTG18.1 alleles behave dynamically, regardless of cell-type origin. However, clusters of CTG18.1 molecules, encompassing ∼1800-11,900 repeats, were exclusively detected in diseased CECs from expansion-positive cases. Additionally, both progenitor allele size and age were found to influence the level of leukocyte-specific CTG18.1 instability. INTERPRETATION: OGM is a powerful tool for analysing somatic instability of repeat loci and reveals here the extreme levels of CTG18.1 instability occurring within diseased CECs underpinning FECD pathophysiology, opening up new therapeutic avenues for FECD. Furthermore, these findings highlight the broader translational utility of FECD as a model for developing therapeutic strategies for rarer diseases similarly attributed to somatically unstable repeats. FUNDING: UK Research and Innovation, Moorfields Eye Charity, Fight for Sight, Medical Research Council, NIHR BRC at Moorfields Eye Hospital and UCL Institute of Ophthalmology, Grantová Agentura České Republiky, Univerzita Karlova v Praze, the National Brain Appeal's Innovation Fund and Rosetrees Trust.

• MeSH
• alely MeSH
• expanze trinukleotidových repetic MeSH
• Fuchsova endoteliální dystrofie * genetika   patologie   MeSH
• lidé středního věku MeSH
• lidé MeSH
• mapování chromozomů MeSH
• nestabilita genomu MeSH
• orgánová specificita genetika   MeSH
• senioři MeSH
• transkripční faktor 4 * genetika   metabolismus   MeSH
• trinukleotidové repetice genetika   MeSH
• Check Tag
• lidé středního věku MeSH
• lidé MeSH
• mužské pohlaví MeSH
• senioři MeSH
• ženské pohlaví MeSH
• Publikační typ
• časopisecké články MeSH

BACKGROUND: Numerous scaffold-level sequences for wheat are now being released and, in this context, we report on a strategy for improving the overall assembly to a level comparable to that of the human genome. RESULTS: Using chromosome 7A of wheat as a model, sequence-finished megabase-scale sections of this chromosome were established by combining a new independent assembly using a bacterial artificial chromosome (BAC)-based physical map, BAC pool paired-end sequencing, chromosome-arm-specific mate-pair sequencing and Bionano optical mapping with the International Wheat Genome Sequencing Consortium RefSeq v1.0 sequence and its underlying raw data. The combined assembly results in 18 super-scaffolds across the chromosome. The value of finished genome regions is demonstrated for two approximately 2.5 Mb regions associated with yield and the grain quality phenotype of fructan carbohydrate grain levels. In addition, the 50 Mb centromere region analysis incorporates cytological data highlighting the importance of non-sequence data in the assembly of this complex genome region. CONCLUSIONS: Sufficient genome sequence information is shown to now be available for the wheat community to produce sequence-finished releases of each chromosome of the reference genome. The high-level completion identified that an array of seven fructosyl transferase genes underpins grain quality and that yield attributes are affected by five F-box-only-protein-ubiquitin ligase domain and four root-specific lipid transfer domain genes. The completed sequence also includes the centromere.

• MeSH
• centromera metabolismus   MeSH
• chromozomy rostlin genetika   MeSH
• fruktany analýza   MeSH
• fyzikální mapování chromozomů metody   MeSH
• genom rostlinný * MeSH
• optické jevy * MeSH
• pšenice genetika   MeSH
• semena rostlinná genetika   MeSH
• umělé bakteriální chromozomy genetika   MeSH
• zemědělství * MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Research Support, U.S. Gov't, Non-P.H.S. MeSH

Motion artifacts are one of the issues in cardiac optical mapping studies. This paper is focused on the description of the motion artifacts caused by planar movement. The theory of its origin and possibilities of its suppression is described. The suppression of the motion artifacts is based on image registration techniques. There are introduced the characteristics about influence of the weighted area averages on presence of these artifacts. In this study conventional pharmacological or mechanical ways of motion artifacts suppression were not involved.

• MeSH
• algoritmy MeSH
• artefakty MeSH
• diagnostické zobrazování metody   MeSH
• fluorescenční mikroskopie metody   MeSH
• komprese dat MeSH
• krysa rodu rattus MeSH
• optika a fotonika MeSH
• počítačové zpracování obrazu metody   MeSH
• pohyb těles MeSH
• software MeSH
• srdce fyziologie   MeSH
• srdeční elektrofyziologie metody   MeSH
• statistické modely MeSH
• zvířata MeSH
• Check Tag
• krysa rodu rattus MeSH
• zvířata MeSH
• Publikační typ
• práce podpořená grantem MeSH

Optical mapping is a fluorescence-based physiological method to image spreading of action potential in excitable tissues, such as the heart and central nervous system. Because of the requirements for high speed imaging in low light conditions, highly sensitive high-speed cameras together with an optical system with maximum photon efficiency are required. While the optimization of these two components is relatively straightforward, the choice of the perfect light source is less simple; depending on the other (usually fixed) components, various parameters may acquire different weight in decision-making process. Here we describe the rationale for building an optical mapping setup and consider the relative advantages and disadvantages of three different commonly available light sources: mercury vapor lamp (HBO), xenon lamp (XBO), and light emitting diode (LED). Using the same optical system (fluorescence macroscope) and high-speed camera (Ultima L), we have tested each of the sources for its ability to provide bright and even illumination of the field of view and measured its temporal fluctuations in intensity. Then we used each in the actual optical mapping experiment using isolated, perfused adult mouse heart or chick embryonic heart to determine the actual signal to noise ratio at various acquisition rates. While the LED sources have undergone significant improvements in the recent past, the other alternatives may still surpass them in some parameters, so they may not be the automatic number one choice for every application.

• MeSH
• akční potenciály MeSH
• fluorescenční barviva chemie   MeSH
• kuřecí embryo MeSH
• myši MeSH
• srdce fyziologie   MeSH
• světlo MeSH
• vápník analýza   metabolismus   MeSH
• zobrazování pomocí barviva citlivého na potenciál metody   normy   MeSH
• zvířata MeSH
• Check Tag
• kuřecí embryo MeSH
• myši MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH

Quantitative genomic mapping of DNA damage may provide insights into the underlying mechanisms of damage and repair. Sequencing based approaches are bound to the limitations of PCR amplification bias and read length which hamper both the accurate quantitation of damage events and the ability to map them to structurally complex genomic regions. Optical Genome mapping in arrays of parallel nanochannels allows physical extension and genetic profiling of millions of long genomic DNA fragments, and has matured to clinical utility for characterization of complex structural aberrations in cancer genomes. Here we present a new mapping modality, Repair-Assisted Damage Detection - Optical Genome Mapping (RADD-OGM), a method for single-molecule level mapping of DNA damage on a genome-wide scale. Leveraging ultra-long reads to assemble the complex structure of a sarcoma cell-line genome, we mapped the genomic distribution of oxidative DNA damage, identifying regions more susceptible to DNA oxidation. We also investigated DNA repair by allowing cells to repair chemically induced DNA damage, pinpointing locations of concentrated repair activity, and highlighting variations in repair efficiency. Our results showcase the potential of the method for toxicogenomic studies, mapping the effect of DNA damaging agents such as drugs and radiation, as well as following specific DNA repair pathways by selective induction of DNA damage. The facile integration with optical genome mapping enables performing such analyses even in highly rearranged genomes such as those common in many cancers, a challenging task for sequencing-based approaches.

• MeSH
• bromičnany toxicita   MeSH
• lidé MeSH
• mapování chromozomů * přístrojové vybavení   metody   MeSH
• mikrofluidní analytické techniky * přístrojové vybavení   metody   MeSH
• nádorové buněčné linie MeSH
• nanotechnologie * přístrojové vybavení   metody   MeSH
• oprava DNA genetika   MeSH
• oxidační stres účinky léků   genetika   MeSH
• poškození DNA * genetika   MeSH
• regulace genové exprese MeSH
• stanovení celkové genové exprese MeSH
• toxikogenetika * přístrojové vybavení   metody   MeSH
• variabilita počtu kopií segmentů DNA MeSH
• zobrazení jednotlivé molekuly * přístrojové vybavení   metody   MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH

Cancer cells display complex genomic aberrations that include large-scale genetic rearrangements and epigenetic modulation that are not easily captured by short-read sequencing. This study presents a novel approach for simultaneous profiling of long-range genetic and epigenetic changes in matched cancer samples, focusing on clear cell renal cell carcinoma (ccRCC). ccRCC is a common kidney cancer subtype frequently characterized by a 3p deletion and the inactivation of the von Hippel-Lindau (VHL) gene. We performed integrated genetic, cytogenetic, and epigenetic analyses on paired tumor and adjacent nontumorous tissue samples. Optical genome mapping identified genomic aberrations as structural and copy number variations, complementing exome-sequencing findings. Single-molecule methylome and hydroxymethylome mapping revealed a significant global reduction in 5hmC level in both sample pairs, and a correlation between both epigenetic signals and gene expression was observed. The single-molecule epigenetic analysis identified numerous differentially modified regions, some implicated in ccRCC pathogenesis, including the genes VHL, PRCC, and PBRM1. Notably, pathways related to metabolism and cancer development were significantly enriched among these differential regions. This study demonstrates the feasibility of integrating optical genome and epigenome mapping for comprehensive characterization of matched tumor and adjacent tissue, uncovering both established and novel somatic aberrations.

• MeSH
• DNA vazebné proteiny MeSH
• epigeneze genetická * genetika   MeSH
• epigenom * genetika   MeSH
• karcinom z renálních buněk * genetika   patologie   MeSH
• lidé středního věku MeSH
• lidé MeSH
• mapování chromozomů metody   MeSH
• metylace DNA * genetika   MeSH
• nádorový supresorový protein VHL genetika   MeSH
• nádory ledvin * genetika   patologie   MeSH
• regulace genové exprese u nádorů MeSH
• transkripční faktory MeSH
• variabilita počtu kopií segmentů DNA * genetika   MeSH
• Check Tag
• lidé středního věku MeSH
• lidé MeSH
• mužské pohlaví MeSH
• ženské pohlaví MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Research Support, N.I.H., Extramural MeSH

Cieľ práce: Zhodnotiť prínos optickej koherentnej tomografie (OCT) v diagnostike foveálnej hypoplázie u detí. Materiál a metodika: Deti s foveálnou hypopláziou (FH) boli vyšetrované prístrojom RTVue Fourier – domain (FD) – OCT, softvérom – verzia 6.80 (Optovue Inc, Fremont, USA). Makulárna oblasť bola kvalitatívne vyšetrená jednotlivým horizontálnym skenom (1024 A-skenov/obraz). Hrúbka makuly bola zmeraná a kvantitatívne vyhodnotená automatickým rýchlym protokolom pre oblasť makuly MM5 (makulárna mapa 5x5 mm). Pre porovnanie sme vyšetrili kontrolnú skupinu detí. Výsledky: Kvalitatívne bol zhodnotený OCT obraz makuly a kvantitatívne vyhodnotená hrúbka a konfigurácia makuly u detí s foveálnou hypopláziou. Následne bolo zrealizované porovnanie OCT nálezov makuly so zdravými deťmi. OCT ukázalo redukciu foveálnej depresie, kontinuálne rozšírenie vnútorných vrstiev sietnice cez oblasť, v ktorej by mala byť zvyčajne umiestnená fovea. Pacienti s foveálnou hypopláziou mali hrubšiu centrálnu makulu a foveolu než deti v kontrolnej skupine. Záver: OCT v našom súbore pacientov potvrdilo konečnú diagnózu foveálnej hypoplázie. FD-OCT je neinvazívna a rýchla metóda nápomocná pri identifikácii retinálnej abnormality v diagnostike foveálnej hypoplázie u detí a môže byť užitočná pri diagnostike pacientov s nevysvetliteľným poklesom videnia.

Purpose: To evaluate the contribution of optical coherence tomography (OCT) in the diagnosis of foveal hypoplasia in children. Material and methods: Children with foveal hypoplasia (FH) were examinated with device RTVue Fourier – domain (FD) – OCT, software – version 6.8 (Optovue Inc., Fremont, USA). A qualitative examination of the macular area was performed with single horizontal scan (1024 A-scans/frame). Macular thickness was measured and evaluated quantitatively with an automatic fast macular area protocol MM5 (Macular Map 5x5 mm). A control group of children was used for comparison. Results: The quality was assessed with OCT image of the macula and quantitatively evaluated macular thickness and configuration in children with foveal hypoplasia. It was subsequently realized the comparison of macular OCT findings in healthy children. The OCT showed a reduction of foveal depression, continuous extension of the inner retinal layers through the area in which should be normally found fovea. Patients with foveal hypoplasia had thicker central macula and fovea than children in the control group. Conclusion: OCT in our group of patients confirmed the final diagnosis of foveal hypoplasia. FD-OCT is a noninvasive and quick method helpful in identifying retinal abnormalities in the diagnosis of foveal hypoplasia in children and may be useful in diagnosing patients with unexplained decrease in vision.

• Klíčová slova
• foveální hypoplazie, fovea plana, foveální aplazie,
• MeSH
• albinismus MeSH
• aniridie MeSH
• dítě MeSH
• fovea centralis * abnormality   MeSH
• lidé MeSH
• mladiství MeSH
• nemoci retiny * diagnóza   patologie   vrozené   MeSH
• optická koherentní tomografie * metody   statistika a číselné údaje   MeSH
• poruchy barevného vidění MeSH
• poruchy zraku patofyziologie   MeSH
• předškolní dítě MeSH
• zraková ostrost fyziologie   MeSH
• Check Tag
• dítě MeSH
• lidé MeSH
• mladiství MeSH
• mužské pohlaví MeSH
• předškolní dítě MeSH
• ženské pohlaví MeSH
• Publikační typ
• hodnotící studie MeSH

Extramedullary disease (EMM) represents a rare, aggressive and mostly resistant phenotype of multiple myeloma (MM). EMM is frequently associated with high-risk cytogenetics, but their complex genomic architecture is largely unexplored. We used whole-genome optical mapping (Saphyr, Bionano Genomics) to analyse the genomic architecture of CD138+ cells isolated from bone-marrow aspirates from an unselected cohort of newly diagnosed patients with EMM (n = 4) and intramedullary MM (n = 7). Large intrachromosomal rearrangements (> 5 Mbp) within chromosome 1 were detected in all EMM samples. These rearrangements, predominantly deletions with/without inversions, encompassed hundreds of genes and led to changes in the gene copy number on large regions of chromosome 1. Compared with intramedullary MM, EMM was characterised by more deletions (size range of 500 bp-50 kbp) and fewer interchromosomal translocations, and two EMM samples had copy number loss in the 17p13 region. Widespread genomic heterogeneity and novel aberrations in the high-risk IGH/IGK/IGL, 8q24 and 13q14 regions were detected in individual patients but were not specific to EMM/MM. Our pilot study revealed an association of chromosome 1 abnormalities in bone marrow myeloma cells with extramedullary progression. Optical mapping showed the potential for refining the complex genomic architecture in MM and its phenotypes.

• MeSH
• buňky kostní dřeně patologie   MeSH
• celogenomová asociační studie metody   MeSH
• chromozomální aberace * MeSH
• cytogenetické vyšetření metody   MeSH
• kohortové studie MeSH
• kostní dřeň diagnostické zobrazování   metabolismus   patologie   MeSH
• lidé středního věku MeSH
• lidé MeSH
• lidské chromozomy, pár 1 * genetika   MeSH
• mnohočetný myelom genetika   patologie   MeSH
• pilotní projekty MeSH
• senioři nad 80 let MeSH
• senioři MeSH
• Check Tag
• lidé středního věku MeSH
• lidé MeSH
• mužské pohlaví MeSH
• senioři nad 80 let MeSH
• senioři MeSH
• ženské pohlaví MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Geografické názvy
• Česká republika MeSH

Mammalian bodies are hierarchical systems whose internal cooperation and coherent activity require high capacity information transfer between the central control unit--the brain--and the periphery--the organs. A communication system capable of meeting information capacity requirements should be based on transmission of electromagnetic signals. Structures that fulfill requirements for such information transfer have not yet been analyzed. Acupuncture meridians have been demonstrated experimentally in some animals. They might represent systems of information transfer between the brain and the peripheral organs. The ducts of the meridians may correspond to optical fibers operating from the far infrared to the visible wavelength region. The main features of a model of the duct as an optical fiber are delineated and its properties outlined. However, to analyze essentials of the transmission capabilities, the whole meridian structure should be mapped and a more comprehensive set of physical parameters measured. In particular, experimental data concerning morphological arrangements of ordered water in the ducts and corpuscles, and a complete content of the biological particles in the flowing water and its permittivity are missing.

• MeSH
• akupunktura MeSH
• akupunkturní dráhy MeSH
• akupunkturní terapie MeSH
• biologické modely MeSH
• informační teorie MeSH
• lidé MeSH
• mozek MeSH
• optická vlákna MeSH
• savci MeSH
• systémová biologie MeSH
• zvířata MeSH
• Check Tag
• lidé MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH