Integrative analysis Dotaz Zobrazit nápovědu
Two new genera (Streptosarcina and Streptofilum) and three new species (Streptosarcina arenaria, S. costaricana and Streptofilum capillatum) of streptophyte algae were detected in cultures isolated from terrestrial habitats of Europe and Central America and described using an integrative approach. Additionally, a strain isolated from soil in North America was identified as Hormidiella parvula and proposed as an epitype of this species. The molecular phylogeny based on 18S rRNA and rbcL genes, secondary structure of ITS-2, as well as the morphology of vegetative and reproductive stages, cell ultrastructure, ecology and distribution of the investigated strains were assessed. The new genus Streptosarcina forms a sister lineage to the genus Hormidiella (Klebsormidiophyceae). Streptosarcina is characterized by packet-like (sarcinoid) and filamentous thalli with true branching and a cell organization typical for Klebsormidiophyceae. Streptofilum forms a separate lineage within Streptophyta. This genus represents an easily disintegrating filamentous alga which exhibits a cell coverage of unique structure: layers of submicroscopic scales of piliform shape covering the plasmalemma and exfoliate inside the mucilage envelope surrounding cells. The implications of the discovery of the new taxa for understanding evolutionary tendencies in the Streptophyta, a group of great evolutionary interest, are discussed.
- Klíčová slova
- Hormidiella, Streptofilum, Streptophyta, Streptosarcina, integrative approach, ultrastructure.,
- MeSH
- DNA rostlinná chemie genetika MeSH
- ekosystém * MeSH
- fylogeneze * MeSH
- konformace nukleové kyseliny MeSH
- mezerníky ribozomální DNA chemie genetika MeSH
- mikroskopie MeSH
- půdní mikrobiologie MeSH
- ribozomální DNA chemie genetika MeSH
- ribulosa-1,5-bisfosfát-karboxylasa genetika MeSH
- RNA ribozomální 18S genetika MeSH
- sekvenční analýza DNA MeSH
- shluková analýza MeSH
- Streptophyta klasifikace genetika ultrastruktura MeSH
- transmisní elektronová mikroskopie MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Geografické názvy
- Evropa MeSH
- Severní Amerika MeSH
- Střední Amerika MeSH
- Názvy látek
- DNA rostlinná MeSH
- mezerníky ribozomální DNA MeSH
- RbcL protein, plastid MeSH Prohlížeč
- ribozomální DNA MeSH
- ribulosa-1,5-bisfosfát-karboxylasa MeSH
- RNA ribozomální 18S MeSH
Invasion science is a very active subdiscipline of ecology. However, some scientists contend that theoretical integration has been limited and that predictive power remains weak. This paper, focusing on plants, proposes a new multi-pronged research strategy that builds on recent advances in invasion science. More intensive studies on particular model organisms and ecosystems are needed to improve our understanding of the full suite of interacting factors that influence invasions ('model system research'). At the same time, comparative studies across many study systems are essential for unravelling the context-dependencies of insights that emerge from particular studies ('multi-site studies'); and quantitative synthesis based on large datasets should be constrained to well-defined theoretical domains ('focused meta-analysis'). We also suggest ways for better integration of information about species biology and ecosystem characteristics ('invasion syndromes'). We expect that a resulting theory of invasions will need to be conceived as a somewhat heterogeneous conglomerate of elements of varying generality and predictive power: laws that apply to well-specified domains, general concepts and theoretical frameworks that can guide thinking in research and management, and in-depth knowledge about the drivers of particular invasions.
- Klíčová slova
- alien plants, invasibility, invasion syndrome, invasiveness, long-term research, meta-analysis, model organism, non-native plants,
- MeSH
- biologické modely MeSH
- ekologie * MeSH
- ekosystém * MeSH
- rostliny * MeSH
- zavlečené druhy * MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- přehledy MeSH
- MeSH
- hmotnostní spektrometrie metody MeSH
- software * MeSH
- Publikační typ
- dopisy MeSH
Oxysterols, oxidized derivatives of cholesterol, act in breast cancer (BC) as selective estrogen receptor modulators and affect cholesterol homeostasis, drug transport, nuclear and cell receptors, and other signaling proteins. Using data from three highly overlapping sets of patients (N = 162 in total) with early-stage estrogen-receptor-positive luminal BC-high-coverage targeted DNA sequencing (113 genes), mRNA sequencing, and full micro-RNA (miRNA) transcriptome microarrays-we describe complex oxysterol-related interaction (correlation) networks, with validation in public datasets (n = 538) and 11 databases. The ESR1-CH25H-INSIG1-ABCA9 axis was the most prominent, interconnected through miR-125b-5p, miR-99a-5p, miR-100-5p, miR-143-3p, miR-199b-5p, miR-376a-3p, and miR-376c-3p. Mutations in SC5D, CYP46A1, and its functionally linked gene set were associated with multiple differentially expressed oxysterol-related genes. STARD5 was upregulated in patients with positive lymph node status. High expression of hsa-miR-19b-3p was weakly associated with poor survival. This is the first study of oxysterol-related genes in BC that combines DNA, mRNA, and miRNA multiomics with detailed clinical data. Future studies should provide links between intratumoral oxysterol signaling depicted here, circulating oxysterol levels, and therapy outcomes, enabling eventual clinical exploitation of present findings.
- Klíčová slova
- breast cancer, integrative analysis, interaction network, multiomics, oxysterols, survival,
- MeSH
- lidé MeSH
- messenger RNA genetika MeSH
- mikro RNA * genetika metabolismus MeSH
- nádory prsu * patologie MeSH
- oxysteroly * MeSH
- transkriptom genetika MeSH
- Check Tag
- lidé MeSH
- ženské pohlaví MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Názvy látek
- messenger RNA MeSH
- mikro RNA * MeSH
- oxysteroly * MeSH
Live-imaging analysis is performed in many laboratories all over the world. Various tools have been developed to enable protein labeling either in plasmid or genomic context in live yeast cells. Here, we introduce a set of nine integrative modules for the C-terminal gene tagging that combines three fluorescent proteins (FPs)-ymTagBFP, mCherry and yTagRFP-T with three dominant selection markers: geneticin, nourseothricin and hygromycin. In addition, the construction of two episomal modules for Saccharomyces cerevisiae with photostable yTagRFP-T is also referred to. Our cassettes with orange, red and blue FPs can be combined with other fluorescent probes like green fluorescent protein to prepare double- or triple-labeled strains for multicolor live-cell imaging. Primers for PCR amplification of the cassettes were designed in such a way as to be fully compatible with the existing PCR toolbox representing over 50 various integrative modules and also with deletion cassettes either for single or repeated usage to enable a cost-effective and an easy exchange of tags. New modules can also be used for biochemical analysis since antibodies are available for all three fluorescent probes.
- Klíčová slova
- Integrative cassettes, dominant selectable markers, episomal tagging, fluorescent proteins, live-cell imaging, yeast,
- MeSH
- barvení a značení metody MeSH
- luminescentní proteiny analýza genetika MeSH
- mikrobiální genetika metody MeSH
- molekulární biologie metody MeSH
- optické zobrazování metody MeSH
- plazmidy MeSH
- rekombinace genetická MeSH
- rekombinantní fúzní proteiny analýza genetika MeSH
- reportérové geny * MeSH
- Saccharomyces cerevisiae cytologie genetika MeSH
- selekce (genetika) MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Názvy látek
- luminescentní proteiny MeSH
- rekombinantní fúzní proteiny MeSH
UNLABELLED: Genomic characterization of pediatric patients with acute myeloid leukemia (AML) has led to the discovery of somatic mutations with prognostic implications. Although gene-expression profiling can differentiate subsets of pediatric AML, its clinical utility in risk stratification remains limited. Here, we evaluate gene expression, pathogenic somatic mutations, and outcome in a cohort of 435 pediatric patients with a spectrum of pediatric myeloid-related acute leukemias for biological subtype discovery. This analysis revealed 63 patients with varying immunophenotypes that span a T-lineage and myeloid continuum designated as acute myeloid/T-lymphoblastic leukemia (AMTL). Within AMTL, two patient subgroups distinguished by FLT3-ITD and PRC2 mutations have different outcomes, demonstrating the impact of mutational composition on survival. Across the cohort, variability in outcomes of patients within isomutational subsets is influenced by transcriptional identity and the presence of a stem cell-like gene-expression signature. Integration of gene expression and somatic mutations leads to improved risk stratification. SIGNIFICANCE: Immunophenotype and somatic mutations play a significant role in treatment approach and risk stratification of acute leukemia. We conducted an integrated genomic analysis of pediatric myeloid malignancies and found that a combination of genetic and transcriptional readouts was superior to immunophenotype and genomic mutations in identifying biological subtypes and predicting outcomes. This article is highlighted in the In This Issue feature, p. 549.
Calibrated adsorption-based passive samplers were used for time-integrative monitoring of microcystins (MCs) in three full-scale drinking water treatment plants (DWTPs) in the Czech Republic during two vegetation seasons (Jun-Nov), in parallel with traditional discrete sampling. MCs were detected in epilimnetic water samples at concentrations up to 14 μg/L, but their levels in raw water in DWTPs were below 1 μg/L WHO guideline value for drinking water. Conventional treatment technologies (coagulation/filtration) eliminated cyanobacteria and intracellular toxins but had a limited removal efficiency for extracellular toxins. MCs were regularly detected in final treated water, especially in DWTPs equipped only with the conventional treatment, but their concentrations were below the quantitation limit of discrete sampling (<25 ng/L). Passive samplers in combination with LC-MS/MS analysis provided excellent sensitivity allowing to detect time-weighted average (TWA) concentrations of MCs as low as 20-200 pg/L after 14-d deployment. Median MC TWA concentrations in the treated water from the individual DWTPs were 1-12 ng/L, and most likely did not present significant health risks. Passive samplers well reflected spatiotemporal variations of MCs, actual concentrations of extracellular toxins, MC removal efficiency in DWTPs, and toxin concentrations in the treated water. Passive sampling can be effectively used for assessment and management of MC health risks during DWTP operation.
- Klíčová slova
- Cyanobacteria, Drinking water treatment, Microcystins, POCIS, Passive sampling, Time-integrative monitoring,
- MeSH
- bakteriální toxiny MeSH
- chromatografie kapalinová MeSH
- čištění vody * MeSH
- mikrocystiny MeSH
- monitorování životního prostředí MeSH
- mořské toxiny MeSH
- pitná voda * MeSH
- tandemová hmotnostní spektrometrie MeSH
- toxiny kmene Cyanobacteria MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Geografické názvy
- Česká republika MeSH
- Názvy látek
- bakteriální toxiny MeSH
- mikrocystiny MeSH
- mořské toxiny MeSH
- pitná voda * MeSH
- toxiny kmene Cyanobacteria MeSH
Over a half million new cases of Head and Neck Squamous Cell Carcinoma (HNSCC) are diagnosed annually worldwide, however, 5 year overall survival is only 50% for HNSCC patients. Recently, high throughput technologies have accelerated the genome-wide characterization of HNSCC. However, comprehensive pipelines with statistical algorithms that account for HNSCC biology and perform independent confirmatory and functional validation of candidates are needed to identify the most biologically relevant genes. We applied outlier statistics to high throughput gene expression data, and identified 76 top-scoring candidates with significant differential expression in tumors compared to normal tissues. We identified 15 epigenetically regulated candidates by focusing on a subset of the genes with a negative correlation between gene expression and promoter methylation. Differential expression and methylation of 3 selected candidates (BANK1, BIN2, and DTX1) were confirmed in an independent HNSCC cohorts from Johns Hopkins and TCGA (The Cancer Genome Atlas). We further performed functional evaluation of NOTCH regulator, DTX1, which was downregulated by promoter hypermethylation in tumors, and demonstrated that decreased expression of DTX1 in HNSCC tumors maybe associated with NOTCH pathway activation and increased migration potential.
- Klíčová slova
- DTX1, HNSCC, expression, integration, methylation,
- MeSH
- dospělí MeSH
- epigenomika * MeSH
- kohortové studie MeSH
- lidé středního věku MeSH
- lidé MeSH
- metylace DNA MeSH
- nádorové buněčné linie MeSH
- nádory hlavy a krku genetika patologie MeSH
- pohyb buněk genetika MeSH
- polymerázová řetězová reakce s reverzní transkripcí MeSH
- receptory Notch genetika MeSH
- regulace genové exprese u nádorů * MeSH
- RNA interference MeSH
- senioři nad 80 let MeSH
- senioři MeSH
- shluková analýza MeSH
- signální transdukce genetika MeSH
- spinocelulární karcinom genetika patologie MeSH
- stanovení celkové genové exprese metody MeSH
- tumor supresorové geny * MeSH
- ubikvitinligasy genetika MeSH
- výpočetní biologie metody MeSH
- Check Tag
- dospělí MeSH
- lidé středního věku MeSH
- lidé MeSH
- mužské pohlaví MeSH
- senioři nad 80 let MeSH
- senioři MeSH
- ženské pohlaví MeSH
- Publikační typ
- časopisecké články MeSH
- Názvy látek
- DTX1 protein, human MeSH Prohlížeč
- receptory Notch MeSH
- ubikvitinligasy MeSH
Our understanding of fungal diversity is far from complete. Species descriptions generally focus on morphological features, but this approach may underestimate true diversity. Using the morphological species concept, Hesperomyces virescens (Ascomycota, Laboulbeniales) is a single species with global distribution and wide host range. Since its description 120 years ago, this fungal parasite has been reported from 30 species of ladybird hosts on all continents except Antarctica. These host usage patterns suggest that H. virescens could be made up of many different species, each adapted to individual host species. Using sequence data from three gene regions, we found evidence for distinct clades within Hesperomyces virescens, each clade corresponding to isolates from a single host species. We propose that these lineages represent separate species, driven by adaptation to different ladybird hosts. Our combined morphometric, molecular phylogenetic and ecological data provide support for a unified species concept and an integrative taxonomy approach.
- MeSH
- analýza hlavních komponent MeSH
- Ascomycota klasifikace genetika izolace a purifikace fyziologie MeSH
- brouci parazitologie MeSH
- DNA fungální chemie genetika metabolismus MeSH
- fylogeneze MeSH
- mezerníky ribozomální DNA chemie genetika metabolismus MeSH
- sekvenční analýza DNA MeSH
- zvířata MeSH
- Check Tag
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Názvy látek
- DNA fungální MeSH
- mezerníky ribozomální DNA MeSH
BACKGROUND: The speckled-pelage brush-furred rats (Lophuromys flavopunctatus group) have been difficult to define given conflicting genetic, morphological, and distributional records that combine to obscure meaningful accounts of its taxonomic diversity and evolution. In this study, we inferred the systematics, phylogeography, and evolutionary history of the L. flavopunctatus group using maximum likelihood and Bayesian phylogenetic inference, divergence times, historical biogeographic reconstruction, and morphometric discriminant tests. We compiled comprehensive datasets of three loci (two mitochondrial [mtDNA] and one nuclear) and two morphometric datasets (linear and geometric) from across the known range of the genus Lophuromys. RESULTS: The mtDNA phylogeny supported the division of the genus Lophuromys into three primary groups with nearly equidistant pairwise differentiation: one group corresponding to the subgenus Kivumys (Kivumys group) and two groups corresponding to the subgenus Lophuromys (L. sikapusi group and L. flavopunctatus group). The L. flavopunctatus group comprised the speckled-pelage brush-furred Lophuromys endemic to Ethiopia (Ethiopian L. flavopunctatus members [ETHFLAVO]) and the non-Ethiopian ones (non-Ethiopian L. flavopunctatus members [NONETHFLAVO]) in deeply nested relationships. There were distinctly geographically structured mtDNA clades among the NONETHFLAVO, which were incongruous with the nuclear tree where several clades were unresolved. The morphometric datasets did not systematically assign samples to meaningful taxonomic units or agree with the mtDNA clades. The divergence dating and ancestral range reconstructions showed the NONETHFLAVO colonized the current ranges over two independent dispersal events out of Ethiopia in the early Pleistocene. CONCLUSION: The phylogenetic associations and divergence times of the L. flavopunctatus group support the hypothesis that paleoclimatic impacts and ecosystem refugia during the Pleistocene impacted the evolutionary radiation of these rodents. The overlap in craniodental variation between distinct mtDNA clades among the NONETHFLAVO suggests unraveling underlying ecomorphological drivers is key to reconciling taxonomically informative morphological characters. The genus Lophuromys requires a taxonomic reassessment based on extensive genomic evidence to elucidate the patterns and impacts of genetic isolation at clade contact zones.
- Klíčová slova
- Biogeography, East Africa, Integrative systematics, Kivumys, Lophuromys, Lophuromys flavopunctatus group,
- MeSH
- Bayesova věta MeSH
- ekosystém * MeSH
- fylogeneze MeSH
- krysa rodu Rattus MeSH
- mitochondriální DNA * genetika MeSH
- zvířata MeSH
- Check Tag
- krysa rodu Rattus MeSH
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Geografické názvy
- Etiopie MeSH
- Názvy látek
- mitochondriální DNA * MeSH
