parallelization
Dotaz
Zobrazit nápovědu
BACKGROUND: Next generation sequencing (NGS) technology allows laboratories to investigate virome composition in clinical and environmental samples in a culture-independent way. There is a need for bioinformatic tools capable of parallel processing of virome sequencing data by exactly identical methods: this is especially important in studies of multifactorial diseases, or in parallel comparison of laboratory protocols. RESULTS: We have developed a web-based application allowing direct upload of sequences from multiple virome samples using custom parameters. The samples are then processed in parallel using an identical protocol, and can be easily reanalyzed. The pipeline performs de-novo assembly, taxonomic classification of viruses as well as sample analyses based on user-defined grouping categories. Tables of virus abundance are produced from cross-validation by remapping the sequencing reads to a union of all observed reference viruses. In addition, read sets and reports are created after processing unmapped reads against known human and bacterial ribosome references. Secured interactive results are dynamically plotted with population and diversity charts, clustered heatmaps and a sortable and searchable abundance table. CONCLUSIONS: The Vipie web application is a unique tool for multi-sample metagenomic analysis of viral data, producing searchable hits tables, interactive population maps, alpha diversity measures and clustered heatmaps that are grouped in applicable custom sample categories. Known references such as human genome and bacterial ribosomal genes are optionally removed from unmapped ('dark matter') reads. Secured results are accessible and shareable on modern browsers. Vipie is a freely available web-based tool whose code is open source.
- MeSH
- genetická variace MeSH
- genomika metody MeSH
- internet * MeSH
- lidé MeSH
- mikrobiota genetika MeSH
- software * MeSH
- viry genetika MeSH
- vysoce účinné nukleotidové sekvenování * MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
W. B. Shute zkonstruoval svůj forceps v 50. letech a vnesl jím do konstrukce porodnických kleští zcela nový princip, který se vyznačuje především vyšší bezpečností pro plod. Jeho hlavní výhodou je, že umožňuje velmi exaktně kontrolovat sílu, která působí na hlavičku. Je vysvětlena konstrukce a použití nástroje, jenž se indikacemi shoduje s Kjellandovým. Je připojen přehled literárních sdělení týkajících se nástroje a stručné představení jeho tvůrce. Autoři soudí, že pokud je Shuteho forceps k dispozici, mĕla by mu být dávána přednost před forcepsem Kjellandovým, neboť je bezpečnĕjší a snazší k ovládnutí a provedení.
By invention of his forceps in 1950´s W. B. Shute introduces a new principle of parallelism, which is characterised by higher safety for the foetus. The main advantage is that the force acting on the head can be exactly controlled. Authors explain design and use of the instrument which is, by it´s indications and versatility, similar to Kjelland´s forceps. Literary review is cited and brief biografy of inventor is added. Where Shute´s instrument is available, priority shoud be given to it, as parallel forceps exceeds the Kjelland´s one by it´s safety for the foetus and moreover is easier to use and to learn too. Keywords: parallel forceps, W. B Shute, obstetrical operations, obstetrical forceps
The aim of this study was to identify the molecular genetic cause of disease in posterior polymorphous corneal dystrophy (PPCD) probands of diverse origin and to assess the utility of massively parallel sequencing in the detection of ZEB1 mutations. We investigated a total of 12 families (five British, four Czech, one Slovak and two Swiss). Ten novel and two recurrent disease-causing mutations in ZEB1, were identified in probands by Sanger (n = 5), exome (n = 4) and genome (n = 3) sequencing. Sanger sequencing was used to confirm the mutations detected by massively parallel sequencing, and to perform segregation analysis. Genome sequencing revealed that one proband harboured a novel ∼0.34 Mb heterozygous de novo deletion spanning exons 1-7 and part of exon 8. Transcript analysis confirmed that the ZEB1 transcript is detectable in blood-derived RNA samples and that the disease-associated variant c.482-2A>G leads to aberrant pre-mRNA splicing. De novo mutations, which are a feature of PPCD3, were found in the current study with an incidence rate of at least 16.6%. In general, massively parallel sequencing is a time-efficient way to detect PPCD3-associated mutations and, importantly, genome sequencing enables the identification of full or partial heterozygous ZEB1 deletions that can evade detection by both Sanger and exome sequencing. These findings contribute to our understanding of PPCD3, for which currently, 49 pathogenic variants have been identified, all of which are predicted to be null alleles.
- MeSH
- dědičné dystrofie rohovky diagnóza genetika metabolismus MeSH
- dítě MeSH
- DNA genetika MeSH
- dospělí MeSH
- exony MeSH
- heterozygot MeSH
- lidé středního věku MeSH
- lidé MeSH
- mladiství MeSH
- mladý dospělý MeSH
- mutace * MeSH
- mutační analýza DNA MeSH
- předškolní dítě MeSH
- rodokmen MeSH
- sekvence nukleotidů MeSH
- sekvenční delece MeSH
- senioři MeSH
- transkripční faktor Zeb1 genetika metabolismus MeSH
- vysoce účinné nukleotidové sekvenování MeSH
- zinkové prsty MeSH
- Check Tag
- dítě MeSH
- dospělí MeSH
- lidé středního věku MeSH
- lidé MeSH
- mladiství MeSH
- mladý dospělý MeSH
- předškolní dítě MeSH
- senioři MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
Východiska: Karcinom ovaria, závažné nádorové onemocnění s vysokou mortalitou, je v České republice diagnostikováno každým rokem přibližně u 1 000 žen. Riziko vzniku onemocnění je zvýšeno u nosiček mutací v některých nádorových predispozičních genech. S vysokým relativním rizikem (RR > 5) jsou spojeny mutace v genech BRCA1, BRCA2, BRIP1, geny Lynchova syndromu, RAD51C, RAD51D, STK11; s možným zvýšením rizika mutace v genech ATM, CHEK2, NBN, PALB2, BARD1. Cílem práce bylo určit frekvenci mutací v nádorových predispozičních genech v naší populaci. Metody a výsledky: Celkem 1 057 pacientek s karcinomem ovaria a 617 nenádorových kontrol bylo vyšetřeno pomocí panelového sekvenování nové generace na platformě Illumina. Patogenní mutace ve vysoko rizikových genech, vč. velkých genomových přestaveb, byly v našem souboru zachyceny u 30,6 % pacientek; u neselektovaných pacientek byla frekvence mutací téměř 25 %, u pacientek s negativní rodinnou anamnézou 18 %. Nejčastěji mutovanými predispozičními geny byly BRCA1 a BRCA2, součet frekvence mutací v ostatních ovariálních predispozičních genech odpovídal frekvenci mutací v genu BRCA2. Záchyt mutací u pacientek starších 70 let byl více než třikrát vyšší v porovnání s pacientkami ve věku pod 30 let. Závěr: Karcinom ovaria je heterogenní onemocnění s vysokým podílem dědičné formy onemocnění. Vzhledem k nedostatku adekvátních screeningových modalit pro včasnou diagnostiku onemocnění je identifikace nosiček mutací v ovariálních predispozičních genech klíčová, s vysokým potenciálem k celkovému snížení mortality z důvodu karcinomu ovaria.
Background: Ovarian cancer is a disease with high mortality. Approximately 1,000 women are diagnosed with ovarian cancer in the Czech Republic annually. Women harboring a mutation in cancer-predisposing genes face an increased risk of tumor development. Mutations in BRCA1, BRCA2, BRIP1, and Lynch syndrome genes (RAD51C, RAD51D, and STK11) are associated with a high risk of ovarian cancer, and mutations in ATM, CHEK2, NBN, PALB2, and BARD1 appear to increase the risk. Our aim was to examine the frequency of mutations in cancer-predisposing genes in the Czech Republic. Materials and methods: We analyzed 1,057 individuals including ovarian cancer patients and 617 non-cancer controls using CZECANCA panel next-generation sequencing on the Illumina platform. Pathogenic mutations in high-risk genes, including CNVs, were detected in 30.6% of patients. The mutation frequency reached 25.0% and 18.2% in subgroups of unselected ovarian cancer patients and patients with a negative family cancer history, respectively. The most frequently mutated genes were BRCA1 and BRCA2. The overall frequency of mutations in non-BRCA genes was comparable to that in BRCA2. The mutation frequency in ovarian cancer patients aged > 70 years was three times higher than that in patients diagnosed before the age of 30. Conclusion: Ovarian cancer is a heterogeneous disease with a high proportion of hereditary cases. The lack of efficient screening for early diagnosis emphasizes the importance of identifying carriers of mutations in ovarian cancer-predisposing genes; this is because proper follow-up and prevention strategies can reduce overall ovarian cancer-related mortality.
- Klíčová slova
- panel genů,
- MeSH
- geny nádorové MeSH
- klinická studie jako téma MeSH
- lidé MeSH
- mutace MeSH
- nádory vaječníků * genetika MeSH
- vysoce účinné nukleotidové sekvenování metody MeSH
- Check Tag
- lidé MeSH
- ženské pohlaví MeSH
- Publikační typ
- práce podpořená grantem MeSH
- Geografické názvy
- Česká republika MeSH
Guanine quadruplexes (G4s) are non-canonical nucleic acids structures common in important genomic regions. Parallel-stranded G4 folds are the most abundant, but their folding mechanism is not fully understood. Recent research highlighted that G4 DNA molecules fold via kinetic partitioning mechanism dominated by competition amongst diverse long-living G4 folds. The role of other intermediate species such as parallel G-triplexes and G-hairpins in the folding process has been a matter of debate. Here, we use standard and enhanced-sampling molecular dynamics simulations (total length of ∼0.9 ms) to study these potential folding intermediates. We suggest that parallel G-triplex per se is rather an unstable species that is in local equilibrium with a broad ensemble of triplex-like structures. The equilibrium is shifted to well-structured G-triplex by stacked aromatic ligand and to a lesser extent by flanking duplexes or nucleotides. Next, we study propeller loop formation in GGGAGGGAGGG, GGGAGGG and GGGTTAGGG sequences. We identify multiple folding pathways from different unfolded and misfolded structures leading towards an ensemble of intermediates called cross-like structures (cross-hairpins), thus providing atomistic level of description of the single-molecule folding events. In summary, the parallel G-triplex is a possible, but not mandatory short-living (transitory) intermediate in the folding of parallel-stranded G4.
- MeSH
- DNA chemie genetika metabolismus MeSH
- G-kvadruplexy * MeSH
- guanin chemie metabolismus MeSH
- jednovláknová DNA chemie genetika metabolismus MeSH
- kinetika MeSH
- konformace nukleové kyseliny * MeSH
- lidé MeSH
- sekvence nukleotidů MeSH
- simulace molekulární dynamiky * MeSH
- zvířata MeSH
- Check Tag
- lidé MeSH
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
Germline DNA testing using the next-gene-ration sequencing (NGS) technology has become the analytical standard for the diagnostics of hereditary diseases, including cancer. Its increasing use places high demands on correct sample identification, independent confirmation of prioritized variants, and their functional and clinical interpretation. To streamline these processes, we introduced parallel DNA and RNA capture-based NGS using identical capture panel CZECANCA, which is routinely used for DNA analysis of hereditary cancer predisposition. Here, we present the analytical workflow for RNA sample processing and its analytical and diagnostic performance. Parallel DNA/RNA analysis allowed credible sample identification by calculating the kinship coefficient. The RNA capture-based approach enriched transcriptional targets for the majority of clinically relevant cancer predisposition genes to a degree that allowed analysis of the effect of identified DNA variants on mRNA processing. By comparing the panel and whole-exome RNA enrichment, we demonstrated that the tissue-specific gene expression pattern is independent of the capture panel. Moreover, technical replicates confirmed high reproducibility of the tested RNA analysis. We concluded that parallel DNA/RNA NGS using the identical gene panel is a robust and cost-effective diagnostic strategy. In our setting, it allows routine analysis of 48 DNA/RNA pairs using NextSeq 500/550 Mid Output Kit v2.5 (150 cycles) in a single run with sufficient coverage to analyse 226 cancer predisposition and candidate ge-nes. This approach can replace laborious Sanger confirmatory sequencing, increase testing turnaround, reduce analysis costs, and improve interpretation of the impact of variants by analysing their effect on mRNA processing.
- MeSH
- DNA genetika MeSH
- genetická predispozice k nemoci * MeSH
- lidé MeSH
- nádory genetika diagnóza MeSH
- reprodukovatelnost výsledků MeSH
- RNA genetika MeSH
- sekvenční analýza DNA metody MeSH
- sekvenční analýza RNA metody MeSH
- vysoce účinné nukleotidové sekvenování * metody MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
Three dimensions of chromatographic separation, using split-flow two-dimensional liquid chromatography (SF-2D-LC) with two parallel second dimensions, LC × 2LC, combined with quadruple parallel mass spectrometry (LC3MS4) is demonstrated for analysis of NIST SRM 1849a adult/infant formula. The first dimension, 1D, was a conventional non-aqueous reversed-phase (NARP) HPLC separation using two C18 columns in series, followed by detection using an ultraviolet (UV) detector, a fluorescence detector (FLD), with flow then split to a corona charged aerosol detector (CAD), and then dual parallel mass spectrometry (MS), conducted in atmospheric pressure photoionization (APPI) and electrospray ionization (ESI) modes. The first second dimension, 2D(1), UHPLC was conducted on a 50.0 mm C30 column using a NARP-UHPLC parallel gradient for separation of short-chain triacylglycerols (TAGs) from long-chain TAGs, with detection by UV and ESI-MS. The second dimension, 2D(2), UHPLC was conducted using a 100.0 mm C30 column with a NARP-UHPLC parallel gradient for improved separation of TAG isomers, with detection by UV, an evaporative light scattering detector, and high-resolution, accurate-mass (HRAM) ESI-MS. Transferred eluent dilution was used to refocus peaks and keep them sharp during elution in both 2Ds. The separation space in the 2D(2) was optimized using multi-cycle (aka, "constructive wraparound") elution, which employed flow rate programming. In the 1D, calibration lines for quantification of fat-soluble vitamins were constructed. A lipidomics approach to TAG identification and quantification by HRAM-ESI-MS was applied to the 2D(2). These experiments can be represented: LC1MS2 × (LC1MS1 + LC1MS1) = LC3MS4, or three-dimensional liquid chromatography with quadruple parallel mass spectrometry.
An important problem in current computational systems biology is to analyze models of biological systems dynamics under parameter uncertainty. This paper presents a novel algorithm for parameter synthesis based on parallel model checking. The algorithm is conceptually universal with respect to the modeling approach employed. We introduce the algorithm, show its scalability, and examine its applicability on several biological models.
Infarkt myokardu (IM) a cévní mozková příhoda (CMP) patří mezi tři nejčastější příčiny úmrtí. Vrchol mortality u IM byl v polovině šedesátých let, od té doby má křivka výrazně sestupnou tendenci. Trend mortality u CMP má spíše stacionární charakter. Obě onemocněním jsou stejného typu a následkem stejné příčiny- aterosklerózy. Významně se však liší cílová struktura, všechny výhody jsou na straně myokardu. Zatímco v léčbě IM jsme v poslední době svědky obrovských pokroků, u ischemické CMP stále převažuje rigidní přístup a pokroky jsou minimální. O léčení IM se stará úzce spolupracující tým kardiologů a kardiochirurgů, do problematiky CMP zasahuje velké množství nesourodých odborností. Kardiovaskulární problematika je nesrovnatelně více medializována než problematika cerebrovaskulární. V oblasti diagnostiky, terapie a timingu léčení IM existují na rozdíl od CMP jasná kritéria. Je třeba zdůraznit existující paralely mezi angínou pectoris a transitorní ischemickou atakou (T1A), která vyžaduje stejnou pozornost jako koronární syndromy. Volá se po změně původní definice T1A, která je zastaralá a matoucí. Terapeutické okno mezi TIA a CMP je mnohem kratší než se původně předpokládalo. Naléhavost tohoto zjištění podporují metaanalýzy studií prokazující významně časově vázaný přínos karotické endarterektomie. Smyslem sdělení je poukázat na mnohé paralely, ale zejména paradoxy mezi managementem CMP a IM.
Myocardial infarction and ischemic stroke are among the three most common causes of death. The peak of heart attack mortality was in the mid 60s. Since then the mortality curve has markedly declined. The death rate of cerebral ischemia is, for the most part, unchanging. Both disorders are of the samé type and the samé cause - atherosclerosis. The target organ is significantly different. All the advantages are on the myocardium side. Whereas in the treatment of cardiac infarction there has recently been great progress, in the čase of stroke, traditional techniques are still prevalent and there has been minimal progress. The management of cardiac infarct is run by a dosely linked team of cardiologists and cardiac surgeons. The management of stroke involves a large number of various specialities. Cardiovascular problems are overreported in comparison to cerebrovascular topics. Diagnosis, therapy and the timing of treatment of cardiac infarction háve obvious criteria in contrast to stroke. It is necessary to underline parallels between angina pectoris and transient ischemic attack, which demand the samé attention as stenocardia. It calls for a change of definition. The originál formula is outdated and misleading. The therapeutic window between transient ischemic attack and completed stroke is shorter than initially presumed. The urgency of these findings supports metaanalyses of studies, shoving carotid endarterectomy markedly depends on time. The reason for this páper is to point out frequent parallels and especially paradox in the management of ischemic stroke and cardiac infarction.
- MeSH
- arterioskleróza etiologie komplikace metabolismus MeSH
- cerebrovaskulární poruchy komplikace terapie MeSH
- cévní mozková příhoda terapie MeSH
- infarkt myokardu komplikace terapie MeSH
- kardiovaskulární nemoci epidemiologie klasifikace terapie MeSH
- lidé MeSH
- rehabilitace po cévní mozkové příhodě MeSH
- tranzitorní ischemická ataka komplikace terapie MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- srovnávací studie MeSH
Recently, we reported an inhibitory effect of guanine substitutions on the conformational switch from antiparallel to parallel quadruplexes (G4) induced by dehydrating agents. As a possible cause, we proposed a difference in the sensitivity of parallel and antiparallel quadruplexes to the guanine substitutions in the resulting thermodynamic stability. Reports on the influence of guanine substitutions on the biophysical properties of intramolecular parallel quadruplexes are rare. Moreover, such reports are often complicated by the multimerisation tendencies of parallel quadruplexes. To address this incomplete knowledge, we employed circular dichroism spectroscopy (CD), both as stopped-flow-assisted fast kinetics measurements and end-point measurements, accompanied by thermodynamic analyses, based on UV absorption melting profiles, and electrophoretic methods. We showed that parallel quadruplexes are significantly more sensitive towards guanine substitutions than antiparallel ones. Furthermore, guanine-substituted variants, which in principle might correspond to native genomic sequences, distinctly differ in their biophysical properties, indicating that the four guanines in each tetrad of parallel quadruplexes are not equal. In addition, we were able to distinguish by CD an intramolecular G4 from intermolecular ones resulting from multimerisation mediated by terminal tetrad association, but not from intermolecular G4s formed due to inter-strand Hoogsteen hydrogen bond formation. In conclusion, our study indicates significant variability in parallel quadruplex structures, otherwise disregarded without detailed experimental analysis.
