Quantitative PCR (qPCR) has become a frequently employed direct method for the detection and quantification of Mycobacterium avium subsp. paratuberculosis (MAP). The quantity of MAP determined by qPCR, however, may be affected by the type of qPCR quantification standard used (PCR product, plasmid, genomic DNA) and the way in which standard DNA quantity is determined (absorbance, fluorescence). In practice, this can be reflected in the inability to properly compare quantitative data from the same qPCR assays in different laboratories. Thus, the aim of this study was to prepare a prototype of an international MAP reference standard, which could be used to calibrate routinely used qPCR quantification standards in various laboratories to promote clinical data comparability. Considering stability, storage and shipment issues, a lyophilised fecal suspension artificially contaminated with a MAP reference strain was chosen as the most suitable form of the standard. The effect of five types of lyophilisation matrices on standard stability was monitored on 2-weeks interval basis for 4 months by F57 qPCR. The lyophilisation matrix with 10% skimmed milk provided the best recovery and stability in time and was thus selected for subsequent comparative testing of the standard involving six diagnostic and research laboratories, where DNA isolation and qPCR assay procedures were performed with the parallel use of the identical supplied genomic DNA solution. Furthermore, the effect of storage conditions on the standard stability was tested for at least 6 months. The storage at room temperature in the dark and under light, at + 4 °C, - 20 °C and - 80 °C showed no significant changes in the stability, and also no substantial changes in MAP viability were found using phage amplification assay. The prepared MAP quantification standard provided homogeneous and reproducible results demonstrating its suitability for utilisation as an international reference qPCR standard.

• MeSH
• DNA bakterií klasifikace   genetika   MeSH
• feces chemie   mikrobiologie   MeSH
• kvantitativní polymerázová řetězová reakce normy   MeSH
• lyofilizace MeSH
• Mycobacterium avium subsp. paratuberculosis klasifikace   genetika   izolace a purifikace   MeSH
• nemoci skotu diagnóza   MeSH
• paratuberkulóza diagnóza   mikrobiologie   MeSH
• referenční standardy MeSH
• senzitivita a specificita MeSH
• skot MeSH
• zvířata MeSH
• Check Tag
• skot MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

Rye is a valuable food and forage crop, an important genetic resource for wheat and triticale improvement and an indispensable material for efficient comparative genomic studies in grasses. Here, we sequenced the genome of Weining rye, an elite Chinese rye variety. The assembled contigs (7.74 Gb) accounted for 98.47% of the estimated genome size (7.86 Gb), with 93.67% of the contigs (7.25 Gb) assigned to seven chromosomes. Repetitive elements constituted 90.31% of the assembled genome. Compared to previously sequenced Triticeae genomes, Daniela, Sumaya and Sumana retrotransposons showed strong expansion in rye. Further analyses of the Weining assembly shed new light on genome-wide gene duplications and their impact on starch biosynthesis genes, physical organization of complex prolamin loci, gene expression features underlying early heading trait and putative domestication-associated chromosomal regions and loci in rye. This genome sequence promises to accelerate genomic and breeding studies in rye and related cereal crops.

• MeSH
• délka genomu MeSH
• duplikace genu MeSH
• genetické lokusy MeSH
• genom rostlinný * MeSH
• kontigové mapování metody   MeSH
• kvantitativní znak dědičný * MeSH
• pšenice genetika   MeSH
• regulace genové exprese u rostlin MeSH
• retroelementy MeSH
• rostlinné proteiny genetika   metabolismus   MeSH
• škrob biosyntéza   MeSH
• šlechtění rostlin MeSH
• vysoce účinné nukleotidové sekvenování MeSH
• zemědělské plodiny genetika   MeSH
• žito genetika   MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

Background: In order to estimate the prevalence of plasmid borne colistin resistance and to characterize in detail the mcr-positive isolates, we carried out a sentinel testing survey on the intestinal carriage of plasmid-mediated colistin-resistant Enterobacteriaceae in hospitalized patients. Methods: Between June 2018 and September 2019, 1922 faecal samples from hospitalised patients were analysed by selective culture in presence of colistin (3.5 mg/L), and in parallel by direct detection of the mcr-1 to mcr-8 genes by qPCR. The mcr-positive isolates were characterised by whole-genome sequencing. Results: The prevalence of the mcr-1 gene was 0.21% (n = 4/1922); the mcr-2 to 8 genes were not detected. The mcr-1 gene was found to be localised in the IncX4 (n = 3) and IncHI2 (n = 1) plasmid type. One Escherichia coli isolate was susceptible to colistin due to the inactivation of the mcr-1 gene through the insertion of the IS2 element; however, the colistin resistance was inducible by culture in low concentrations of colistin. One human mcr-1 positive E. coli isolate was related genetically to the mcr-1 E. coli isolate derived from turkey meat of Czech origin. Conclusions:mcr-mediated colistin resistance currently poses little threat to patients hospitalised in Czech healthcare settings. The presence of the mcr-1 gene in the human population has a possible link to domestically produced, retail meat.

• Publikační typ
• časopisecké články MeSH

BACKGROUND: Whole-genome sequencing (WGS) of Treponema pallidum subspecies pallidum (TPA) has been constrained by the lack of in vitro cultivation methods for isolating spirochetes from patient samples. METHODS: We built upon recently developed enrichment methods to sequence TPA directly from primary syphilis chancre swabs collected in Guangzhou, China. RESULTS: By combining parallel, pooled whole-genome amplification with hybrid selection, we generated high-quality genomes from 4 of 8 chancre-swab samples and 2 of 2 rabbit-passaged isolates, all subjected to challenging storage conditions. CONCLUSIONS: This approach enabled the first WGS of Chinese samples without rabbit passage and provided insights into TPA genetic diversity in China.

• MeSH
• králíci MeSH
• lidé MeSH
• sekvenování celého genomu MeSH
• syfilis * diagnóza   mikrobiologie   MeSH
• Treponema pallidum klasifikace   genetika   MeSH
• tvrdý vřed * diagnóza   mikrobiologie   MeSH
• zvířata MeSH
• Check Tag
• králíci MeSH
• lidé MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Research Support, N.I.H., Extramural MeSH
• Geografické názvy
• Čína MeSH

Impulsem k zahájení procesu, jenž postupně vedl až ke vzniku zdravotnické profese adiktologa v České repub- lice, byla reakce na nedostatek dostatečně vzdělaných profesionálů v nově vznikajících službách v 90. letech. Postupem času však došlo k natolik výrazné a úspěšné profilaci této nové profese, že byl uvedený rámec překročen a vznikl zcela svébytný a originální koncept studijního programu na pozadí emancipujícího se transdisciplinárního oboru. Jeho zaměření dostalo plný rozsah tematického záběru od prevence, přes léčbu a rehabilitaci, až procesu přirozené úzdravy. Své pevné místo zde má také celá oblast strategií a metod minimalizace rizik a škod. Cílem studie je popsat okolnosti vzniku, vývoje a současného ukotvení studijního oboru adiktologie na pozadí vývoje v oblasti závislostního chování v České republice. Dílčím cíle je upozornit na měnící se profil podobně zaměřených studijních programů a startující vlnu zájmu o ně ve světě, včetně vzniku prvních modelových mezinárodních kurikulí pro tento typ studia na univerzitách. Výzkumný soubor tvoří identifikované dokumenty a evaluační studie vztahující se k oboru adiktologie v ČR a související studie zaměřené na tento obor v zahraničí, mající vztah k formování mezinárodních kurikulí. Přestože byl vznik samotného původního konceptu studijního oboru ovlivněn dobovými požadavky poskytovatelů péče, ukázalo se rychle, že dynamika vývoje tohoto oboru překročila uvedený rámec a dala vzniknout zcela originálnímu konceptu studijního oboru pod názvem „pražský model adiktologického studia“. Následnými srovnáními se ukázalo, že podobnou cestou prošly také další země a že mnohé z těchto programů se podobají. Unikátnost tuzemského modelu tkví v jeho konzistentní stavbě a systematickém budování a následném pevném legislativním ukotvení. Současně se ukázala být velmi dobře nastavená vazba mezi tímto oborem a praxí, tj. především poskytovateli péči a dobře zvládnutému institucionálnímu rámci rodícího se nového oboru. Paralelním procesem se pak stalo formování mezinárodní spolupráce univerzit s těmito studijními programy a vznik prvních mezinárodních kurikulí. Česká republika se stala průkopníkem nového modelu studia oboru adiktologie a její model studijního programu na úrovni bakalářského, magisterského a doktorského se stal vzorovým pro rozvoj podobných programů v dalších zemích a pro ukotvení této nové profese v systému péče o osoby se závislostí.

A shortage of appropriately qualified and trained practitioners to staff the emerging addiction services in the 1990s initiated a process which eventually led to the establishment of the health profession of an addictologist in the Czech Republic. In the course of time, this new profession developed into a distinctive and well-acclaimed field of expertise which went beyond its original scope and gave rise to a unique concept of a study programme against the background of an emancipating transdisciplinary field of study. It is intended to address the full scope of relevant topics, ranging from prevention, treatment, and rehabilitation to the process of natural recovery. All aspects of harm reduction strategies and methods are also given significant attention. The Aim was to describe the details of the origin, development, and current status of the study programme in addictology in the context of the addictive behaviour-related developments in the Czech Republic. Another objective is to point out the changing profile of similarly-oriented study programmes and the emerging wave of interest in them internationally, including the development of the first international model curricula for this type of study at universities. The sample comprises retrieved documents and evaluation studies pertaining to the field of addictology in the Czech Republic and related studies on this discipline abroad which address the constitution of international curricula. While the development of the original concept of the discipline was influenced by the requirements of the service providers of the time, it became apparent before long that the dynamics of the development of the field had gone beyond its original scope and given rise to a brand-new concept of a study programme referred to as the “Prague Model of Addiction Studies”. Subsequent comparisons showed that other countries, too, followed a similar path and that many of these programmes were similar. The Czech model is unique in its consistent structure, systematic building, and subsequent legislative grounding. In addition, a firm link between the field of study and practice, especially service providers, and a solid institutional framework for the new field have been established. Finally, in parallel with the domestic efforts, activities aimed at establishing and maintaining networks of international universities offering relevant academic programmes and developing the first international curricula have been pursued. The Czech Republic has pioneered a new model of addiction studies, and its concept of bachelor’s, master’s, and doctoral study programmes has become a blueprint for the development of similar programmes and the integration of the new profession within the system of addiction services in other countries.

• MeSH
• adiktologie dějiny   organizace a řízení   trendy   výchova   zákonodárství a právo   MeSH
• Geografické názvy
• Česká republika MeSH

Impulsem k zahájení procesu, jenž postupně vedl až ke vzniku zdravotnické profese adiktologa v České repub- lice, byla reakce na nedostatek dostatečně vzdělaných profesionálů v nově vznikajících službách v 90. letech. Postupem času však došlo k natolik výrazné a úspěšné profilaci této nové profese, že byl uvedený rámec překročen a vznikl zcela svébytný a originální koncept studijního programu na pozadí emancipujícího se transdisciplinárního oboru. Jeho zaměření dostalo plný rozsah tematického záběru od prevence, přes léčbu a rehabilitaci, až procesu přirozené úzdravy. Své pevné místo zde má také celá oblast strategií a metod minimalizace rizik a škod. Cílem studie je popsat okolnosti vzniku, vývoje a současného ukotvení studijního oboru adiktologie na pozadí vývoje v oblasti závislostního chování v České republice. Dílčím cíle je upozornit na měnící se profil podobně zaměřených studijních programů a startující vlnu zájmu o ně ve světě, včetně vzniku prvních modelových mezinárodních kurikulí pro tento typ studia na univerzitách. Výzkumný soubor tvoří identifikované dokumenty a evaluační studie vztahující se k oboru adiktologie v ČR a související studie zaměřené na tento obor v zahraničí, mající vztah k formování mezinárodních kurikulí. Přestože byl vznik samotného původního konceptu studijního oboru ovlivněn dobovými požadavky poskytovatelů péče, ukázalo se rychle, že dynamika vývoje tohoto oboru překročila uvedený rámec a dala vzniknout zcela originálnímu konceptu studijního oboru pod názvem „pražský model adiktologického studia“. Následnými srovnáními se ukázalo, že podobnou cestou prošly také další země a že mnohé z těchto programů se podobají. Unikátnost tuzemského modelu tkví v jeho konzistentní stavbě a systematickém budování a následném pevném legislativním ukotvení. Současně se ukázala být velmi dobře nastavená vazba mezi tímto oborem a praxí, tj. především poskytovateli péči a dobře zvládnutému institucionálnímu rámci rodícího se nového oboru. Paralelním procesem se pak stalo formování mezinárodní spolupráce univerzit s těmito studijními programy a vznik prvních mezinárodních kurikulí. Česká republika se stala průkopníkem nového modelu studia oboru adiktologie a její model studijního programu na úrovni bakalářského, magisterského a doktorského se stal vzorovým pro rozvoj podobných programů v dalších zemích a pro ukotvení této nové profese v systému péče o osoby se závislostí.

A shortage of appropriately qualified and trained practitioners to staff the emerging addiction services in the 1990s initiated a process which eventually led to the establishment of the health profession of an addictologist in the Czech Republic. In the course of time, this new profession developed into a distinctive and well-acclaimed field of expertise which went beyond its original scope and gave rise to a unique concept of a study programme against the background of an emancipating transdisciplinary field of study. It is intended to address the full scope of relevant topics, ranging from prevention, treatment, and rehabilitation to the process of natural recovery. All aspects of harm reduction strategies and methods are also given significant attention. The Aim was to describe the details of the origin, development, and current status of the study programme in addictology in the context of the addictive behaviour-related developments in the Czech Republic. Another objective is to point out the changing profile of similarly-oriented study programmes and the emerging wave of interest in them internationally, including the development of the first international model curricula for this type of study at universities. The sample comprises retrieved documents and evaluation studies pertaining to the field of addictology in the Czech Republic and related studies on this discipline abroad which address the constitution of international curricula. While the development of the original concept of the discipline was influenced by the requirements of the service providers of the time, it became apparent before long that the dynamics of the development of the field had gone beyond its original scope and given rise to a brand-new concept of a study programme referred to as the “Prague Model of Addiction Studies”. Subsequent comparisons showed that other countries, too, followed a similar path and that many of these programmes were similar. The Czech model is unique in its consistent structure, systematic building, and subsequent legislative grounding. In addition, a firm link between the field of study and practice, especially service providers, and a solid institutional framework for the new field have been established. Finally, in parallel with the domestic efforts, activities aimed at establishing and maintaining networks of international universities offering relevant academic programmes and developing the first international curricula have been pursued. The Czech Republic has pioneered a new model of addiction studies, and its concept of bachelor’s, master’s, and doctoral study programmes has become a blueprint for the development of similar programmes and the integration of the new profession within the system of addiction services in other countries.

Understanding the genetic changes underlying phenotypic variation in sheep (Ovis aries) may facilitate our efforts towards further improvement. Here, we report the deep resequencing of 248 sheep including the wild ancestor (O. orientalis), landraces, and improved breeds. We explored the sheep variome and selection signatures. We detected genomic regions harboring genes associated with distinct morphological and agronomic traits, which may be past and potential future targets of domestication, breeding, and selection. Furthermore, we found non-synonymous mutations in a set of plausible candidate genes and significant differences in their allele frequency distributions across breeds. We identified PDGFD as a likely causal gene for fat deposition in the tails of sheep through transcriptome, RT-PCR, qPCR, and Western blot analyses. Our results provide insights into the demographic history of sheep and a valuable genomic resource for future genetic studies and improved genome-assisted breeding of sheep and other domestic animals.

• MeSH
• alely MeSH
• chov zvířat metody   MeSH
• chov MeSH
• destičkový růstový faktor metabolismus   MeSH
• divoká zvířata genetika   MeSH
• druhová specificita MeSH
• fenotyp MeSH
• frekvence genu MeSH
• genetická variace MeSH
• genetika MeSH
• genomika MeSH
• genotyp MeSH
• jednonukleotidový polymorfismus MeSH
• mutace MeSH
• ovce domácí genetika   MeSH
• ovce MeSH
• sekvenční analýza DNA MeSH
• sekvenování celého genomu MeSH
• selekce (genetika) MeSH
• vazebná nerovnováha MeSH
• vysoce účinné nukleotidové sekvenování MeSH
• zvířata MeSH
• Check Tag
• ženské pohlaví MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

The present pilot study aimed at evaluating air sampling as a novel method for monitoring Campylobacter in poultry farms. We compared the bacteriological isolation of Campylobacter from boot swabs and air filter samples using ISO 10272-1:2017. A secondary aim was to evaluate the use of molecular methods, i.e. real time PCR, on the same sample set. Samples from 44 flocks from five European countries were collected, and included air samples, in parallel with boot swabs. Campylobacter spp. was isolated from seven of 44 boot swabs from three of five partners using the enrichment method. Two of these positive boot swab samples had corresponding positive air samples. Using enrichment, one positive air sample was negative in the corresponding boot swabs, but Campylobacter spp. was isolated from direct plating of the boot swab sample. One partner isolated Campylobacter spp. from six of 10 boot swabs using direct plating. Overall, 33 air filter samples were screened directly with PCR, returning 14 positive results. In conclusion, there was a lack of correspondence between results from analysis of boot swabs and air filters using ISO 10272-1:2017. In contrast, the combination of air filters and direct real-time PCR might be a way forward. Despite the use of the detailed ISO protocols, there were still sections that could be interpreted differently among laboratories. Air sampling may turn into a multi-purpose and low-cost sampling method that may be integrated into self-monitoring programs.

• MeSH
• Campylobacter genetika   izolace a purifikace   MeSH
• drůbež mikrobiologie   MeSH
• farmy statistika a číselné údaje   MeSH
• feces mikrobiologie   MeSH
• internacionalita MeSH
• kampylobakterové infekce veterinární   MeSH
• kur domácí mikrobiologie   MeSH
• mikrobiologie vzduchu normy   MeSH
• nemoci drůbeže mikrobiologie   prevence a kontrola   přenos   MeSH
• pilotní projekty MeSH
• zvířata MeSH
• Check Tag
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• hodnotící studie MeSH
• multicentrická studie MeSH
• Geografické názvy
• Evropa MeSH

BACKGROUND: The domestic cat (Felis catus) is an important companion animal and is used as a large animal model for human disease. However, the comprehensive study of adaptive immunity in this species is hampered by the lack of data on lymphocyte antigen receptor genes and usage. The objectives of this study were to annotate the feline T cell receptor (TR) loci and to characterize the expressed repertoire in lymphoid organs of normal cats using high-throughput sequencing. RESULTS: The Felis catus TRG locus contains 30 genes: 12 TRGV, 12 TRGJ and 6 TRGC, the TRB locus contains 48 genes: 33 TRBV, 2 TRBD, 11 TRBJ, 2 TRBC, the TRD locus contains 19 genes: 11 TRDV, 2 TRDD, 5 TRDJ, 1 TRDC, and the TRA locus contains 127 genes: 62 TRAV, 64 TRAJ, 1 TRAC. Functional feline V genes form monophyletic clades with their orthologs, and clustering of multimember subgroups frequently occurs in V genes located at the 5' end of TR loci. Recombination signal (RS) sequences of the heptamer and nonamer of functional V and J genes are highly conserved. Analysis of the TRG expressed repertoire showed preferential intra-cassette over inter-cassette rearrangements and dominant usage of the TRGV2-1 and TRGJ1-2 genes. The usage of TRBV genes showed minor bias but TRBJ genes of the second J-C-cluster were more commonly rearranged than TRBJ genes of the first cluster. The TRA/TRD V genes almost exclusively rearranged to J genes within their locus. The TRAV/TRAJ gene usage was relatively balanced while the TRD repertoire was dominated by TRDJ3. CONCLUSIONS: This is the first description of all TR loci in the cat. The genomic organization of feline TR loci was similar to that of previously described jawed vertebrates (gnathostomata) and is compatible with the birth-and-death model of evolution. The large-scale characterization of feline TR genes provides comprehensive baseline data on immune repertoires in healthy cats and will facilitate the development of improved reagents for the diagnosis of lymphoproliferative diseases in cats. In addition, these data might benefit studies using cats as a large animal model for human disease.

• MeSH
• adaptivní imunita genetika   MeSH
• fylogeneze MeSH
• genetické lokusy genetika   MeSH
• genomika metody   MeSH
• kočky genetika   imunologie   MeSH
• lidé MeSH
• lymfoidní tkáň metabolismus   MeSH
• receptory antigenů T-buněk klasifikace   genetika   MeSH
• sekvence aminokyselin MeSH
• sekvenční homologie aminokyselin MeSH
• vysoce účinné nukleotidové sekvenování metody   MeSH
• zvířata MeSH
• Check Tag
• kočky genetika   imunologie   MeSH
• lidé MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články 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