BACKGROUND: Haynaldia villosa (H. villosa) has been recognized as a species potentially useful for wheat improvement. The availability of its genomic sequences will boost its research and application. RESULTS: In this work, the short arm of H. villosa chromosome 4V (4VS) was sorted by flow cytometry and sequenced using Illumina platform. About 170.6 Mb assembled sequences were obtained. Further analysis showed that repetitive elements accounted for about 64.6% of 4VS, while the coding fraction, which is corresponding to 1977 annotated genes, represented 1.5% of the arm. The syntenic regions of the 4VS were searched and identified on wheat group 4 chromosomes 4AL, 4BS, 4DS, Brachypodium chromosomes 1 and 4, rice chromosomes 3 and 11, and sorghum chromosomes 1, 5 and 8. Based on genome-zipper analysis, a virtual gene order comprising 735 gene loci on 4VS genome was built by referring to the Brachypodium genome, which was relatively consistent with the scaffold order determined for Ae. tauschii chromosome 4D. The homologous alleles of several cloned genes on wheat group 4 chromosomes including Rht-1 gene were identified. CONCLUSIONS: The sequences provided valuable information for mapping and positional-cloning genes located on 4VS, such as the wheat yellow mosaic virus resistance gene Wss1. The work on 4VS provided detailed insights into the genome of H. villosa, and may also serve as a model for sequencing the remaining parts of H. villosa genome.

• MeSH
• chromozomy rostlin genetika   MeSH
• druhová specificita MeSH
• genomika MeSH
• lipnicovité genetika   MeSH
• mapování chromozomů MeSH
• pořadí genů genetika   MeSH
• repetitivní sekvence nukleových kyselin genetika   MeSH
• sekvenční analýza DNA * MeSH
• Publikační typ
• časopisecké články MeSH

BACKGROUND: A complete genome sequence is an essential tool for the genetic improvement of wheat. Because the wheat genome is large, highly repetitive and complex due to its allohexaploid nature, the International Wheat Genome Sequencing Consortium (IWGSC) chose a strategy that involves constructing bacterial artificial chromosome (BAC)-based physical maps of individual chromosomes and performing BAC-by-BAC sequencing. Here, we report the construction of a physical map of chromosome 6B with the goal of revealing the structural features of the third largest chromosome in wheat. RESULTS: We assembled 689 informative BAC contigs (hereafter reffered to as contigs) representing 91% of the entire physical length of wheat chromosome 6B. The contigs were integrated into a radiation hybrid (RH) map of chromosome 6B, with one linkage group consisting of 448 loci with 653 markers. The order and direction of 480 contigs, corresponding to 87% of the total length of 6B, were determined. We also characterized the contigs that contained a part of the nucleolus organizer region or centromere based on their positions on the RH map and the assembled BAC clone sequences. Analysis of the virtual gene order along 6B using the information collected for the integrated map revealed the presence of several chromosomal rearrangements, indicating evolutionary events that occurred on chromosome 6B. CONCLUSIONS: We constructed a reliable physical map of chromosome 6B, enabling us to analyze its genomic structure and evolutionary progression. More importantly, the physical map should provide a high-quality and map-based reference sequence that will serve as a resource for wheat chromosome 6B.

• MeSH
• chromozomy rostlin MeSH
• fyzikální mapování chromozomů metody   MeSH
• genetické markery MeSH
• genová přestavba MeSH
• molekulární evoluce MeSH
• organizátor jadérka MeSH
• pořadí genů MeSH
• pšenice genetika   MeSH
• umělé bakteriální chromozomy genetika   MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

BACKGROUND: Within the last decade, macrophages have been shown to be capable of differentiating toward a classically activated phenotype (M1) with a high antimicrobial potential or an alternatively activated phenotype (M2). Some pathogens are capable of interfering with differentiation in order to down-regulate the anti-microbial activity and enhance their survival in the host. RESULTS: To test this ability in Salmonella enterica serovar Typhimurium, we infected porcine alveolar macrophages with wild-type Salmonella Typhimurium and its isogenic mutants devoid of two major pathogenicity islands, SPI-1 and SPI-2. The induction of genes linked with M1 or M2 polarization was determined by quantification of gene expression by RT-qPCR. The ΔSPI-1 mutant induced a high, dose-dependent M1 response but a low M2 response in infected macrophages. On the other hand, wild-type Salmonella Typhimurium induced a low M1 response but a high, dose-dependent M2 response in infected macrophages. The response to ΔSPI-2 mutant infection was virtually the same as the wild-type strain. CONCLUSIONS: We therefore propose that Salmonella Typhimurium DT104 studied here can polarize macrophages towards the less bactericidal M2 phenotype and that this polarization is dependent on the type III secretion system encoded by SPI-1.

• MeSH
• alveolární makrofágy cytologie   fyziologie   MeSH
• bakteriální proteiny genetika   metabolismus   MeSH
• cytokiny metabolismus   MeSH
• polymerázová řetězová reakce s reverzní transkripcí MeSH
• prasata MeSH
• regulace genové exprese u bakterií fyziologie   MeSH
• Salmonella typhimurium genetika   metabolismus   MeSH
• signální transdukce MeSH
• transkriptom MeSH
• zvířata MeSH
• Check Tag
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Research Support, U.S. Gov't, Non-P.H.S. MeSH

The analysis of large genomes is hampered by a high proportion of repetitive DNA, which makes the assembly of short sequence reads difficult. This is also the case in meadow fescue (Festuca pratensis), which is known for good abiotic stress resistance and has been used in intergeneric hybridization with ryegrasses (Lolium spp.) to produce Festulolium cultivars. In this work, we describe a new approach to analyze the large genome of meadow fescue, which involves the reduction of sample complexity without compromising information content. This is achieved by dissecting the genome to smaller parts: individual chromosomes and groups of chromosomes. As the first step, we flow sorted chromosome 4F and sequenced it by Illumina with approximately 50× coverage. This provided, to our knowledge, the first insight into the composition of the fescue genome, enabled the construction of the virtual gene order of the chromosome, and facilitated detailed comparative analysis with the sequenced genomes of rice (Oryza sativa), Brachypodium distachyon, sorghum (Sorghum bicolor), and barley (Hordeum vulgare). Using GenomeZipper, we were able to confirm the collinearity of chromosome 4F with barley chromosome 4H and the long arm of chromosome 5H. Several new tandem repeats were identified and physically mapped using fluorescence in situ hybridization. They were found as robust cytogenetic markers for karyotyping of meadow fescue and ryegrass species and their hybrids. The ability to purify chromosome 4F opens the way for more efficient analysis of genomic loci on this chromosome underlying important traits, including freezing tolerance. Our results confirm that next-generation sequencing of flow-sorted chromosomes enables an overview of chromosome structure and evolution at a resolution never achieved before.

• MeSH
• chromozomy rostlin genetika   MeSH
• Festuca genetika   MeSH
• genom rostlinný genetika   MeSH
• genomika metody   MeSH
• hybridizace in situ fluorescenční MeSH
• ječmen (rod) genetika   MeSH
• karyotypizace metody   MeSH
• mapování chromozomů MeSH
• molekulární sekvence - údaje MeSH
• pořadí genů MeSH
• reprodukovatelnost výsledků MeSH
• rýže (rod) MeSH
• sekvenční analýza DNA metody   MeSH
• Sorghum genetika   MeSH
• Southernův blotting MeSH
• syntenie MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

• MeSH
• biochemie MeSH
• enzymy MeSH
• hemoglobiny MeSH
• molekulární biologie MeSH
• proteiny MeSH

• Konspekt
• Biochemie. Molekulární biologie. Biofyzika
• NLK Obory
• biochemie

The capacity of the bread wheat (Triticum aestivum) genome to tolerate introgression from related genomes can be exploited for wheat improvement. A resistance to powdery mildew expressed by a derivative of the cross-bread wheat cv. Tähti × T. militinae (Tm) is known to be due to the incorporation of a Tm segment into the long arm of chromosome 4A. Here, a newly developed in silico method termed rearrangement identification and characterization (RICh) has been applied to characterize the introgression. A virtual gene order, assembled using the GenomeZipper approach, was obtained for the native copy of chromosome 4A; it incorporated 570 4A DArTseq markers to produce a zipper comprising 2132 loci. A comparison between the native and introgressed forms of the 4AL chromosome arm showed that the introgressed region is located at the distal part of the arm. The Tm segment, derived from chromosome 7G, harbours 131 homoeologs of the 357 genes present on the corresponding region of Chinese Spring 4AL. The estimated number of Tm genes transferred along with the disease resistance gene was 169. Characterizing the introgression's position, gene content and internal gene order should not only facilitate gene isolation, but may also be informative with respect to chromatin structure and behaviour studies.

• MeSH
• Ascomycota patogenita   MeSH
• chléb MeSH
• chromozomy rostlin genetika   metabolismus   MeSH
• DNA rostlinná genetika   MeSH
• genetické markery MeSH
• mapování chromozomů MeSH
• mikrosatelitní repetice MeSH
• nemoci rostlin genetika   mikrobiologie   MeSH
• odolnost vůči nemocem MeSH
• počítačová simulace MeSH
• pšenice genetika   mikrobiologie   MeSH
• rostlinné geny MeSH
• sekvence nukleotidů MeSH
• translokace genetická MeSH
• Publikační typ
• časopisecké články MeSH

With the advent of OMICs technologies, both individual research groups and consortia have spear-headed the characterization of human samples of multiple pathophysiologic origins, resulting in thousands of archived genomes and transcriptomes. Although a variety of web tools are now available to extract information from OMICs data, their utility has been limited by the capacity of nonbioinformatician researchers to exploit the information. To address this problem, we have developed CANCERTOOL, a web-based interface that aims to overcome the major limitations of public transcriptomics dataset analysis for highly prevalent types of cancer (breast, prostate, lung, and colorectal). CANCERTOOL provides rapid and comprehensive visualization of gene expression data for the gene(s) of interest in well-annotated cancer datasets. This visualization is accompanied by generation of reports customized to the interest of the researcher (e.g., editable figures, detailed statistical analyses, and access to raw data for reanalysis). It also carries out gene-to-gene correlations in multiple datasets at the same time or using preset patient groups. Finally, this new tool solves the time-consuming task of performing functional enrichment analysis with gene sets of interest using up to 11 different databases at the same time. Collectively, CANCERTOOL represents a simple and freely accessible interface to interrogate well-annotated datasets and obtain publishable representations that can contribute to refinement and guidance of cancer-related investigations at all levels of hypotheses and design.Significance: In order to facilitate access of research groups without bioinformatics support to public transcriptomics data, we have developed a free online tool with an easy-to-use interface that allows researchers to obtain quality information in a readily publishable format. Cancer Res; 78(21); 6320-8. ©2018 AACR.

• MeSH
• algoritmy MeSH
• databáze faktografické MeSH
• databáze genetické MeSH
• genomika MeSH
• internet MeSH
• lékařská onkologie MeSH
• lidé MeSH
• nádory genetika   MeSH
• počítačová grafika MeSH
• proteomika MeSH
• průběh práce MeSH
• software MeSH
• transkriptom MeSH
• uživatelské rozhraní počítače MeSH
• výpočetní biologie metody   MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

Prediktivní diagnostika karcinomu prsu přináší řadu novinek, největší změny se - přinejmenším v podmínkách České republiky - týkají detekce HER2 - tedy diagnostiky overexprese onkoproteinu HER-2/neu, resp. amplifikace genu c-erbB-2. V ČR je rutinně prováděno primární testování pomocí imunohistochemie, která je doplněna v indikovaných případech in situ hybridizací. V roce 2013 došlo k aktualizaci pravidel - snížení relativního podílu nádorových buněk pro stanovení imunohistochemické HER2 pozitivity z původních 30 % na 10 %, hranice pro stanovení amplifikace genu se posunula z HER2/CEP17 hodnoty 2,2 na 2,0. Došlo také ke změně kritérií pro vyhodnocení exprese jako 2+. Tyto změny vedly k poměrně významnému nárůstu počtu případů hodnocených jako „hraniční“ či „neurčité“, a tím k navýšení případů vyžadujících doplnění in situ hybridizace. Aby bylo sníženo riziko falešně negativních i falešně pozitivních výsledků, je pro finální potvrzení HER2 pozitivity před zahájením cílené terapie prováděno v ČR ověření v síti tzv. referenčních laboratoří. U core-cut biopsie je vyšetření HER2 vhodné provádět prakticky vždy, zcela nezbytné je u nemocných podstupujících neoadjuvantní systémovou léčbu. U nemocných primárně léčených chirurgicky lze vyšetření molekulárních prediktivních markerů provést až z definitivního resekátu. Je však třeba vzít v úvahu, že přesnost stanovení některých parametrů v core-cut biopsii může být limitovaná, i bez ovlivnění neoadjuvantní chemoterapií (NACHT) dosahuje shoda grade v core-cut vzorku a v definitivním resekátu jen 67 %, shoda v přesné histologické typizaci pak 84 %; shoda v hodnocení exprese HER2 dosahuje mezi punkčními vzorky a resekáty nad 90%. Při pozitivním výsledku HER2 v core-cut biopsii již není nezbytné opakování vyšetření z resekátu, naproti tomu při negativním výsledku HER2 v core-cut biopsii je doporučeno opakování vyšetření z resekátu, aby bylo eliminováno, resp. minimalizováno riziko falešně negativního výsledku. Pravděpodobnost patologické kompletní odpovědi (pCR) je různá u jednotlivých molekulárních subtypů karcinomu prsu - u triple-negativních a HER2+ karcinomů prsu dosahuje 27-51 %, u hormonálně dependentních nádorů, zejména těch s nízkou proliferační aktivitou, je významně nižší. I v rámci skupiny HER2+ karcinomu se pravděpodobnost pCR liší. HER2+ karcinomy se současnou expresí ER a PR mají procento pCR nižší než nádory HER2+ bez koexprese hormonálních receptorů. Karcinomy s expresí vysokomolekulárních keratinů (CK14, CK 5/6) s bazálním fenotypem nebo nádory s mutací genů HER2/AKT signální dráhy (PI3K, PTEN) mají rovněž nižší odpověď na léčbu a horší prognózu.

Detection of predictive markers in breast carcinoma has undergone significant changes, the most important ones - at least in the context of Czech Republic - are related to the detection of HER2 - detection of both over-expression of oncoprotein HER-2/neu and amplification of the c-erbB-2 gene, respectively. In the Czech Republic, immunohistochemical testing is performed as a method of first choice, followed, if needed, by in situ hybridization. The update of the guidelines published in 2013 decreased the threshold for positive tumor cells from 30% to 10%, shifted the threshold for gene amplification (HER2/CEP17 ratio) from 2.2 to 2.0 and slightly changed criteria for classification of expression as 2+. These changes resulted in relatively significant increase of cases classified as „borderline“ or „equivocal“, requiring confirmation by in situ hybridization. In order to reduce the risk of false results, the cases diagnosed as positive in small (primary) laboratories, have to be confirmed in one of the large central laboratories. This confirmation of HER2 positivity is required before targeted therapy can be started. HER2 testing is recommended in core-cut biopsies virtually always; it is absolutely essential in patients undergoing neoadjuvant systemic therapy. In patients treated primarily by surgery can be the testing performed either in the core cut biopsy or in the final resection specimen. However, it should be kept in mind that the accuracy of some parameters in the core-cut biopsies may be limited, even in cases not influenced by the neoadjuvant chemotherapy (NACHT). The degree of concordance between results of molecular tests in the core-cut biopsy and resection specimen can achieve only 67 % and the precise concordance of histological typing reaches only 84 %, respectively; the concordance of HER2 expression, on the other hand, reaches more than 90%. In patients with positive HER2 result in core-cut biopsy, it is no longer required to repeat the testing in the resection specimen, whereas in case of HER2 negative core-cut biopsy, it is required to repeat the test from resection specimen to minimize the risk of false negative result. The probability of pathological complete response (pCR) varies in individual breast carcinoma subtypes - it reaches 27-51% in triple-negative and HER2+ cases, while in hormone-dependent tumors, namely in those with low proliferative activity, it is significantly lower. Even within the HER2+ carcinoma subgroup, the probability of pCR varies. HER2+ tumors co-expressing ER and PR have a lower rate of pCR than HER2+ carcinomas without co-expression of hormonal receptors. Carcinomas expressing high-molecular weight keratins (CK14, CK 5/6) with basal phenotype or tumors with mutations of HER2/AKT signal pathway (PI3K, PTEN) have also lower response to treatment and worse prognosis.

• MeSH
• amplifikace genu MeSH
• exprese genu MeSH
• geny erbB-2 genetika   MeSH
• hybridizace in situ fluorescenční MeSH
• imunohistochemie MeSH
• jehlová biopsie MeSH
• lidé MeSH
• molekulární patologie MeSH
• nádory prsu * diagnóza   MeSH
• neoadjuvantní terapie MeSH
• prediktivní hodnota testů * MeSH
• Check Tag
• lidé MeSH
• ženské pohlaví MeSH
• Publikační typ
• přehledy MeSH

Wild emmer wheat (Triticum turgidum ssp. dicoccoides) is the progenitor of wheat. We performed chromosome-based survey sequencing of the 14 chromosomes, examining repetitive sequences, protein-coding genes, miRNA/target pairs and tRNA genes, as well as syntenic relationships with related grasses. We found considerable differences in the content and distribution of repetitive sequences between the A and B subgenomes. The gene contents of individual chromosomes varied widely, not necessarily correlating with chromosome size. We catalogued candidate agronomically important loci, along with new alleles and flanking sequences that can be used to design exome sequencing. Syntenic relationships and virtual gene orders revealed several small-scale evolutionary rearrangements, in addition to providing evidence for the 4AL-5AL-7BS translocation in wild emmer wheat. Chromosome-based sequence assemblies contained five novel miRNA families, among 59 families putatively encoded in the entire genome which provide insight into the domestication of wheat and an overview of the genome content and organization.

• MeSH
• chromozomy rostlin genetika   MeSH
• genetické lokusy genetika   MeSH
• genom rostlinný genetika   MeSH
• konzervovaná sekvence genetika   MeSH
• lipnicovité genetika   MeSH
• mikro RNA genetika   MeSH
• nekódující RNA genetika   MeSH
• polyploidie MeSH
• průtoková cytometrie MeSH
• pšenice genetika   MeSH
• repetitivní sekvence nukleových kyselin genetika   MeSH
• rostlinné geny genetika   MeSH
• tetraploidie MeSH
• vysoce účinné nukleotidové sekvenování MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

After induced mutagenesis and transgenesis, genome editing is the next step in the development of breeding techniques. Genome editing using site-directed nucleases - including meganucleases, zinc-finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), and the CRISPR/Cas9 system - is based on the mechanism of double strand breaks. The nuclease is directed to cleave the DNA at a specific place of the genome which is then repaired by natural repair mechanisms. Changes are introduced during the repair that are either accidental or can be targeted if a DNA template with the desirable sequence is provided. These techniques allow making virtually any change to the genome including specific DNA sequence changes, gene insertion, replacements or deletions with unprecedented precision and specificity while being less laborious and more straightforward compared to traditional breeding techniques or transgenesis. Therefore, the research in this field is developing quickly and, apart from model species, multiple studies have focused on economically important species and agronomically important traits that were the key subjects of this review. In plants, studies have been undertaken on disease resistance, herbicide tolerance, nutrient metabolism and nutritional value. In animals, the studies have mainly focused on disease resistance, meat production and allergenicity of milk. However, none of the promising studies has led to commercialization despite several patent applications. The uncertain legal status of genome-editing methods is one of the reasons for poor commercial development, as it is not clear whether the products would fall under the GMO regulation. We believe this issue should be clarified soon in order to allow promising methods to reach their full potential.

• MeSH
• editace genu metody   MeSH
• endonukleasy genetika   metabolismus   MeSH
• genetické inženýrství metody   MeSH
• geneticky modifikovaná zvířata * MeSH
• geneticky modifikované rostliny * MeSH
• genom rostlinný * MeSH
• odolnost vůči nemocem genetika   MeSH
• zemědělské plodiny genetika   MeSH
• zinkové prsty MeSH
• zvířata MeSH
• Check Tag
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• přehledy MeSH