optical mapping Dotaz Zobrazit nápovědu
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
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
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
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
Acute lymphoblastic leukemia (ALL) is the most prevalent type of cancer occurring in children. ALL is characterized by structural and numeric genomic aberrations that strongly correlate with prognosis and clinical outcome. Usually, a combination of cyto- and molecular genetic methods (karyotyping, array-CGH, FISH, RT-PCR, RNA-Seq) is needed to identify all aberrations relevant for risk stratification. We investigated the feasibility of optical genome mapping (OGM), a DNA-based method, to detect these aberrations in an all-in-one approach. As proof of principle, twelve pediatric ALL samples were analyzed by OGM, and results were validated by comparing OGM data to results obtained from routine diagnostics. All genomic aberrations including translocations (e.g., dic(9;12)), aneuploidies (e.g., high hyperdiploidy) and copy number variations (e.g., IKZF1, PAX5) known from other techniques were also detected by OGM. Moreover, OGM was superior to well-established techniques for resolution of the more complex structure of a translocation t(12;21) and had a higher sensitivity for detection of copy number alterations. Importantly, a new and unknown gene fusion of JAK2 and NPAT due to a translocation t(9;11) was detected. We demonstrate the feasibility of OGM to detect well-established as well as new putative prognostic markers in an all-in-one approach in ALL. We hope that these limited results will be confirmed with testing of more samples in the future.
- Publikační typ
- časopisecké články 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
Po CRAO (akutní okluze centrální sítnicové arterie) vzniká ischemický edém sítnice a následná regresní fáze je obvykle bez možnosti objektivizace. Cíl studie: Stanovit dynamiku edematózních změn centra sítnice metodou optické koherentní tomografie (OCT). Soubor a metodika: Na očním oddělení Pardubické krajské nemocnice bylo v období 6/2004–1/2005 vyšetřeno na přístroji STRATUS Stratus OCT 3 celkem 10 nemocných s diagnózou CRAO v akutní fázi onemocnění (1. až 5. den po okluzi). K hodnocení byl použit protokol určený pro analýzu tloušťky a objemu makuly (Fast Macular Thickness Map). Naměřené hodnoty byly porovnány se zdravým okem. Následná OCT vyšetření byla provedena po 2., 5. a 10. týdnech. Výsledky: Průměrný objem makuly (Average Total Macula Volume) postiženého oka v den stanovení diagnózy byl (průměr ± SD/rozmezí hodnot/) mm3: 9,196 ± 1,376 /10,315–7,301/, druhý týden 7,313 ± 1,209 /9,441–5,854/, pátý týden 5,970 ± 0,688 /7,401–4,971/ a desátý týden 5,091 ± 0,558 /5,768–3,989/. Průměrný objem edémem nejvíce zasaženého makulárního segmentu v den stanovení diagnózy byl: 0,695 ± 0,319 /1,526–0,359/, druhý týden 0,607 ± 0,206 /1,118–0,416/, pátý týden 0,520 ± 0,220 /1,070–0,334/ a desátý týden 0,409 ± 0,195 /0,948–0,282/. Pátý týden byl již u některých nemocných zaznamenán nástup atrofické fáze makuly. Analýza provedená 10. týden po vzniku CRAO neprokázala u žádného nemocného otok v oblasti makuly. Závěr: Prokázali jsme v průměru 5týdenní regresní fázi sítnicového edému po CRAO. OCT vyšetření se jeví jako vhodná metoda pro stanovení dynamiky edematózních změn makulární oblasti při CRAO.
Purpose: Ischemic edema of the retina develops after CRAO and a regressive phase follows usually without any possibility of objectification.The aim of the study is to determine dynamics of edematous changes in the central retina using the OCT (Optical Coherence Tomography). Setting: Department of Ophthalmology, Regional Hospital in Pardubice, Czech Republic, E.U. Methods: During the period between June 2004 and January 2005, ten patients with the diagnosis of CRAO were examined by means of Stratus OCT3 (Zeiss). A protocol designed for analysis of the thickness and volume of the macula (Fast Macular Thickness Map) was used for the evaluation. Obtained readings were compared with the healthy eye. Examinations were performed on the 1st up to the 5th day after the CRAO onset and 2, 5, and 10 weeks thereafter. Results:The average volume of the macula (Average Total Macula Volume) of the affected eye was (mean ± SD; mm3): at the day of diagnosis (the initial examination) 9.196 ± 1.376 (range, 10.315–7.301), the 2nd week 7.313 ± 1.209 (range, 9.441–5.854), the 5th week 5.970 ± 0.688 (range, 7.401–4.971), and the 10th week 5.091 ± 0.558 (range, 5.768–3.989). The average volume of the most swollen macular quadrate was (mean±SD; mm3): at the day of diagnosis (the initial examination) 0.695 ± 0.319 (range, 1.526–0.359), the 2nd week 0.607 ± 0.206 (range, 1.118–0.416), the 5th week 0.520 ± 0.220 (range, 1.070–0.334), and the 10th week 0.409 ± 0.195 (range 0.948–0.282). In some patients, the onset of macular atrophy was found 5 weeks after the CRAO. No edema in the macular area was confirmed in any patient 10 weeks after the CRAO. Conclusion: On the average, we proved the regression phase of the retinal edema 5 weeks after the CRAO appearance.The OCT examination appears to be a suitable method for the determination of the dynamics of the edematous changes in the macular area after the CRAO.
