The biosynthesis of the lincosamide antibiotics lincomycin A and celesticetin involves the pyridoxal-5'-phosphate (PLP)-dependent enzymes LmbF and CcbF, which are responsible for bifurcation of the biosynthetic pathways. Despite recognizing the same S-glycosyl-L-cysteine structure of the substrates, LmbF catalyses thiol formation through β-elimination, whereas CcbF produces S-acetaldehyde through decarboxylation-coupled oxidative deamination. The structural basis for the diversification mechanism remains largely unexplored. Here we conduct structure-function analyses of LmbF and CcbF. X-ray crystal structures, docking and molecular dynamics simulations reveal that active-site aromatic residues play important roles in controlling the substrate binding mode and the reaction outcome. Furthermore, the reaction selectivity and oxygen-utilization of LmbF and CcbF were rationally engineered through structure- and calculation-based mutagenesis. Thus, the catalytic function of CcbF was switched to that of LmbF, and, remarkably, both LmbF and CcbF variants gained the oxidative-amidation activity to produce an unnatural S-acetamide derivative of lincosamide.

• MeSH
• katalytická doména MeSH
• krystalografie rentgenová MeSH
• linkosamidy * chemie   biosyntéza   metabolismus   MeSH
• pyridoxalfosfát * metabolismus   chemie   MeSH
• simulace molekulární dynamiky MeSH
• simulace molekulového dockingu MeSH
• Publikační typ
• časopisecké články MeSH

Phlebotomine sand flies (Diptera: Psychodidae: Phlebotominae) are the principal vectors of Leishmania spp. (Kinetoplastida: Trypanosomatidae) worldwide. The subgenus Adlerius is taxonomically challenging and currently comprises about 20 species with a wide geographic distribution from eastern Asia to southeastern Europe. Some species are confirmed or suspected vectors of Leishmania donovani/infantum, L. major, and L. tropica, and are thus of high medical and veterinary relevance. A single record of Phlebotomus (Adlerius) simici in Austria from 2018 marks its sporadic northernmost and westernmost occurrence, with the origin of its appearance remaining unclear. To better understand Adlerius diversification and particularly post-glacial spread of Ph. simici to northern parts of Europe, we combined phylogenetic analyses with climatic suitability modelling. Divergence time estimates well supported the currently observed geographic distribution of the studied species and revealed several taxonomic challenges in the subgenus. We clearly delineated three distinct genetic and geographic Ph. simici lineages and phylogeographically assessed diversification that were well supported by climatic models. This study provides a comprehensive phylogenetic analysis of the subgenus Adlerius, enhancing our understanding of the diversification in relation to changing climate of this understudied group, and we present new insights into the post-glacial spread of Ph. simici, a suspected vector of L. infantum.

• MeSH
• fylogeneze * MeSH
• fylogeografie * MeSH
• hmyz - vektory genetika   klasifikace   MeSH
• Phlebotomus * klasifikace   genetika   MeSH
• podnebí MeSH
• zvířata MeSH
• Check Tag
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• Geografické názvy
• Evropa MeSH

UNLABELLED: Lyme disease, caused by spirochetes in the Borrelia burgdorferi sensu lato clade within the Borrelia genus, is transmitted by Ixodes ticks and is currently the most prevalent and rapidly expanding tick-borne disease in Europe and North America. We report complete genome sequences of 47 isolates that encompass all established species in this clade while highlighting the diversity of the widespread human pathogenic species B. burgdorferi. A similar set of plasmids has been maintained throughout Borrelia divergence, indicating that they are a key adaptive feature of this genus. Phylogenetic reconstruction of all sequenced Borrelia genomes revealed the original divergence of Eurasian and North American lineages and subsequent dispersals that introduced B. garinii, B. bavariensis, B. lusitaniae, B. valaisiana, and B. afzelii from East Asia to Europe and B. burgdorferi and B. finlandensis from North America to Europe. Molecular phylogenies of the universally present core replicons (chromosome and cp26 and lp54 plasmids) are highly consistent, revealing a strong clonal structure. Nonetheless, numerous inconsistencies between the genome and gene phylogenies indicate species dispersal, genetic exchanges, and rapid sequence evolution at plasmid-borne loci, including key host-interacting lipoprotein genes. While localized recombination occurs uniformly on the main chromosome at a rate comparable to mutation, lipoprotein-encoding loci are recombination hotspots on the plasmids, suggesting adaptive maintenance of recombinant alleles at loci directly interacting with the host. We conclude that within- and between-species recombination facilitates adaptive sequence evolution of host-interacting lipoprotein loci and contributes to human virulence despite a genome-wide clonal structure of its natural populations. IMPORTANCE: Lyme disease (also called Lyme borreliosis in Europe), a condition caused by spirochete bacteria of the genus Borrelia, transmitted by hard-bodied Ixodes ticks, is currently the most prevalent and rapidly expanding tick-borne disease in the United States and Europe. Borrelia interspecies and intraspecies genome comparisons of Lyme disease-related bacteria are essential to reconstruct their evolutionary origins, track epidemiological spread, identify molecular mechanisms of human pathogenicity, and design molecular and ecological approaches to disease prevention, diagnosis, and treatment. These Lyme disease-associated bacteria harbor complex genomes that encode many genes that do not have homologs in other organisms and are distributed across multiple linear and circular plasmids. The functional significance of most of the plasmid-borne genes and the multipartite genome organization itself remains unknown. Here we sequenced, assembled, and analyzed whole genomes of 47 Borrelia isolates from around the world, including multiple isolates of the human pathogenic species. Our analysis elucidates the evolutionary origins, historical migration, and sources of genomic variability of these clinically important pathogens. We have developed web-based software tools (BorreliaBase.org) to facilitate dissemination and continued comparative analysis of Borrelia genomes to identify determinants of human pathogenicity.

• MeSH
• Borrelia burgdorferi komplex genetika   klasifikace   MeSH
• Borrelia burgdorferi genetika   klasifikace   MeSH
• Borrelia genetika   klasifikace   MeSH
• fylogeneze * MeSH
• genetická variace MeSH
• genom bakteriální * MeSH
• interakce mikroorganismu a hostitele genetika   MeSH
• klíště mikrobiologie   MeSH
• lidé MeSH
• lipoproteiny * genetika   MeSH
• lymeská nemoc * mikrobiologie   přenos   MeSH
• molekulární evoluce MeSH
• plazmidy genetika   MeSH
• rekombinace genetická * MeSH
• sekvenování celého genomu MeSH
• selekce (genetika) * MeSH
• zvířata MeSH
• Check Tag
• lidé MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• Geografické názvy
• Evropa MeSH
• Severní Amerika MeSH

• Publikační typ
• úvodníky MeSH

Different types of spiral ganglion neurons (SGNs) are essential for auditory perception by transmitting complex auditory information from hair cells (HCs) to the brain. Here, we use deep, single cell transcriptomics to study the molecular mechanisms that govern their identity and organization in mice. We identify a core set of temporally patterned genes and gene regulatory networks that may contribute to the diversification of SGNs through sequential binary decisions and demonstrate a role for NEUROD1 in driving specification of a Ic-SGN phenotype. We also find that each trajectory of the decision tree is defined by initial co-expression of alternative subtype molecular controls followed by gradual shifts toward cell fate resolution. Finally, analysis of both developing SGN and HC types reveals cell-cell signaling potentially playing a role in the differentiation of SGNs. Our results indicate that SGN identities are drafted prior to birth and reveal molecular principles that shape their differentiation and will facilitate studies of their development, physiology, and dysfunction.

• MeSH
• buněčná diferenciace genetika   MeSH
• ganglion spirale * MeSH
• myši MeSH
• neurony * metabolismus   MeSH
• RNA metabolismus   MeSH
• vláskové buňky metabolismus   MeSH
• zvířata MeSH
• Check Tag
• myši MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

This paper explores to what extent product and marketing channel diversification contributed to the economic success of small-scale agricultural producers involved in short food supply chains after the outbreak of the COVID-19 pandemic. A survey was conducted between April and July 2020 in four countries of the European Union-Estonia, Hungary, Portugal and Romania,-resulting in a relatively large sample of farmers (N = 421). The analysis was built on a semi-nonparametric approach. Approximately 19 percent of small-scale producers were able to increase sales during the first wave of the pandemic, although country-level variation was significant. Fruits and vegetables were by far the most popular products. The importance of specific channels varied across countries, but farm gate sales were among the most important marketing channels both before and during the first wave. The importance of channels that were based on digital resources and home delivery increased. Our evidence indicates that diversification was a strategy that paid off, both in terms of marketing channels and different product categories. However, the impact appears to be nonlinear; the initial advantage generated by diversification rapidly tapered off, either temporarily (in the case of products), or permanently (in the case of marketing channels). Later research may clarify whether these findings are generalizable in other socio-economic contexts, as well as in a non-COVID situation.

• MeSH
• COVID-19 ekonomika   epidemiologie   MeSH
• ekonomické modely * MeSH
• karanténa ekonomika   statistika a číselné údaje   MeSH
• lidé MeSH
• průzkumy a dotazníky MeSH
• zemědělci psychologie   MeSH
• zemědělství metody   statistika a číselné údaje   MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Geografické názvy
• Evropa MeSH

In pathogenic fungi and oomycetes, interspecific hybridization may lead to the formation of new species having a greater impact on natural ecosystems than the parental species. From the early 1990s, a severe alder (Alnus spp.) decline due to an unknown Phytophthora species was observed in several European countries. Genetic analyses revealed that the disease was caused by the triploid hybrid P. × alni, which originated in Europe from the hybridization of P. uniformis and P. × multiformis. Here, we investigated the population structure of P. × alni (158 isolates) and P. uniformis (85 isolates) in several European countries using microsatellite markers. Our analyses confirmed the genetic structure previously observed in other European populations, with P. uniformis populations consisting of at most two multilocus genotypes (MLGs) and P. × alni populations dominated by MLG Pxa-1. The genetic structure of P. × alni populations in the Czech Republic, Hungary and Sweden seemed to reflect the physical isolation of river systems. Most rare P. × alni MLGs showed a loss of heterozygosity (LOH) at one or a few microsatellite loci compared with other MLGs. This LOH may allow a stabilization within the P. × alni genome or a rapid adaptation to stress situations. Alternatively, alleles may be lost because of random genetic drift in small, isolated populations, with no effect on fitness of P. × alni. Additional studies would be necessary to confirm these patterns of population diversification and to better understand the factors driving it.

• MeSH
• ekosystém MeSH
• genetická variace MeSH
• genotyp MeSH
• mikrosatelitní repetice genetika   MeSH
• nemoci rostlin MeSH
• Phytophthora * genetika   MeSH
• Publikační typ
• časopisecké články MeSH
• Geografické názvy
• Evropa MeSH
• Švédsko MeSH

Amyloidóza lehkých řetězců imunoglobulinů (ALA) je hematologické onemocnění, které se může vyskytovat současně s jinými dyskraziemi plazmatických buněk (PC). Udává se, že zhruba 10% pacientů s ALA má současně i mnohočetný myelom (MM). Přesto je stále nejasné, zda je tato klinická manifestace způsobena evolucí pouze jednoho aberantního klonu plazmatických buněk či koexistencí více aberantních klonů plazmatických buněk současně. Díky rozvoji techniky sekvenování nové generace (NGS) je dnes možné modelovat diferenciaci buněčných klonů v průběhu progrese onemocnění. Domníváme se, že přítomnost různých klonů ALA a MM lze chápat jako výsledek diverzifikace jednoho klonu během progrese nemoci (rozvětvená evoluce). Popřípadě mohou kritické genomické změny v aberantních plazmatických buňkách dát vzniknout novému unikátnímu klonu (lineární evoluce), který je odpovědný za klinickou manifestaci onemocnění. Získané poznatky tohoto projektu budou znamenat zásadní posun ve stanovení diagnózy onemocnění a volbě následné léčby.; Immunoglobulin light chain amyloidosis (ALA) is a haematological disorder and may coexist with other plasma cell (PC) dyscrasias. It has been reported that 10% of ALA patients may have multiple myeloma (MM) at the same time. Nevertheless, it is still unclear if such clinical manifestation is defined by aberrant PC clones architecture or subsequent clone evolution. Due to the development in next generation sequencing (NGS) technology, it is possible now to model clonal differentiation during tumour progression. We suspect that, presence of different ALA and MM clones can be explained as a result of clone diversification during disease progression (branched evolution). Alternatively, severe genomic changes in aberrant PC can cause forming of new unique clone responsible for mentioned clinical manifestation (linear evolution). Learning outcomes of the offered project would mean certainly progress in the terms of diagnosis and subsequent treatment of ALA patients.

• MeSH
• buněčné klony patologie   MeSH
• lidé MeSH
• mutace MeSH
• plazmatické buňky patologie   MeSH
• primární amyloidóza diagnóza   MeSH
• vysoce účinné nukleotidové sekvenování metody   MeSH
• Check Tag
• lidé MeSH

• Konspekt
• Patologie. Klinická medicína
• NLK Obory
• alergologie a imunologie
• genetika, lékařská genetika
• onkologie
• NLK Publikační typ
• závěrečné zprávy o řešení grantu AZV MZ ČR

Reflektujíc nedávný objev potenciálního využití beauverolidů (cyklotetradepsipeptidů produkovaných entomopatogenními houbami) v lékařství, předkládaný projekt navrhuje výzkum beauverolidů z pohledu jejich využitelnosti pro ovlivnění patologických stavů spojených s metabolickým syndromem a s deregulací buněk imunitního systému. Dopady stávající masivní aplikace beauverolidů v zemědělství a lesnictví na člověka dosud nebyly studovány. Zároveň bychom tedy v rámci předkládaného projektu rádi zjistili, zda stávající způsoby využití beauverolidů nejsou spojeny s nežádoucími účinky na člověka. Prostřednictvím modifikací v kultivačních podmínkách zdrojových organismů předpokládáme produkci širokého spektra beauverolidů navzájem odlišného chemického složení, které budou přečištěny, podrobně biochemicky charakterizovány, a následně testovány pomocí baterie biologických testů na lidských buněčných liniích a primárních buněčných izolátech. Zkoumán bude i způsob metabolizace beauverolidů.; Beauverolides represent a group of fungal cyclotetradepsipeptides, with only recently recognized potential for human medicine. Reflecting recent preclinical data, this project focuses at the use of beauverolides in modulation of pathologies associated with human metabolic syndrome and with immune system dysregulation. Current massive application of beauverolides in agriculture and forestry raises also the question on potential adverse effects of these applications on the humans, which were never addressed in detail. Thus, we would like to also focus on the association of current use of beauverolides with adverse effects on humans. Beauverolides will be produced under a spectrum of diverse cultivation conditions, which will result in a diversification of their chemical composition. Obtained fungal products will be purified and biochemically characterized in detail, and tested using the battery of biological tests, including those involving human cell lines primary cell isolates. Besides that, the exact mechanisms of metabolisation of beauverolides will be addressed as well.

• MeSH
• Beauveria izolace a purifikace   MeSH
• depsipeptidy MeSH
• imunitní systém mikrobiologie   patologie   MeSH
• kultivované buňky mikrobiologie   MeSH
• lidé MeSH
• metabolický syndrom mikrobiologie   patologie   MeSH
• Check Tag
• lidé MeSH

• Konspekt
• Patologie. Klinická medicína
• NLK Obory
• mikrobiologie, lékařská mikrobiologie
• botanika
• NLK Publikační typ
• závěrečné zprávy o řešení grantu AZV MZ ČR

Pneumococcus je hlavním původcem pneumonie, meningitidy a bakterémie. Existence multirezistence k antibiotikům je významným problémem komplikujícím léčbu. Navzdory tomu, že pneumokokové konjugované vakcíny svým složením pokrývají většinu sérotypů sdružených s multirezistencí, celková prevalence antibiotické rezistence se po zavedení plošné vakcinace proti pneumokokům výrazně nesnížila. Mezi sérotypy, které mají v současnosti největší podíl na výskytu rezistence, patří sérotyp 19A. Analýza post-vakcinačních 19A izolátů prokázala jejich příbuznost s klonem Taiwan19F-14, který byl před začátkem plošné vakcinace sdružen se sérotypem 19F. Důvody nárůstu právě tohoto sérotypu nejsou přesně objasněny. V ČR se po zavedení očkování pomocí PCV10 a PCV13 v roce 2010 stal sérotyp 19A dominantním multirezistentním sérotypem, ačkoliv výskyt tohoto sérotypu byl v předchozím období pouze sporadický. Aplikace celogenomové sekvenace umožní detailní popis evoluce tohoto sérotypu a pomůže popsat faktory, které v konkurenci s dalšími nevakcinačními sérotypy umožnily propagaci tohoto sérotypu.; Pneumococcus is the major cause of pneumonia, meningitis and bacteremia. A major concern is the occurence of multidrug-resistant (MDR) pneumococci. As the pneumococcal conjugate vaccines target most of MDR serotypes, it was postulated that introduction of vaccination would reverse the success MDR pneumococci. However, the effect of vaccine use on relative prevalence of antibiotic resistance in pneumococci was not that impressive. The serotype 19A was found to be the most problematic. Analysis of post-vaccine MDR 19A isolates have identified their relatedness with Taiwan19F-14 clone which was initially associated with vaccine serotype 19F. The causal factors enhancing spread of 19A serotype remain unclear. In the Czech Republic, serotype 19A become one of the most MDR prevalent serotypes in post-vaccine era, however before beginning of routinne immunisation using PCV10 or PCV13 in 2010, the occurence of this serotype was rare. The use of whole genome sequencing allows a precise reconstruction of the emergence and diversification of the 19A serotype.

• MeSH
• lidé MeSH
• mnohočetná bakteriální léková rezistence MeSH
• pneumokokové infekce MeSH
• pneumokokové vakcíny MeSH
• sekvenování celého genomu MeSH
• séroskupina MeSH
• Streptococcus pneumoniae MeSH
• vakcíny konjugované MeSH
• Check Tag
• lidé MeSH

• Konspekt
• Patologie. Klinická medicína
• NLK Obory
• infekční lékařství
• preventivní medicína
• NLK Publikační typ
• závěrečné zprávy o řešení grantu AZV MZ ČR