Molecular data analysis Dotaz Zobrazit nápovědu
Feature-based molecular networking (FBMN) is a popular analysis approach for liquid chromatography-tandem mass spectrometry-based non-targeted metabolomics data. While processing liquid chromatography-tandem mass spectrometry data through FBMN is fairly streamlined, downstream data handling and statistical interrogation are often a key bottleneck. Especially users new to statistical analysis struggle to effectively handle and analyze complex data matrices. Here we provide a comprehensive guide for the statistical analysis of FBMN results, focusing on the downstream analysis of the FBMN output table. We explain the data structure and principles of data cleanup and normalization, as well as uni- and multivariate statistical analysis of FBMN results. We provide explanations and code in two scripting languages (R and Python) as well as the QIIME2 framework for all protocol steps, from data clean-up to statistical analysis. All code is shared in the form of Jupyter Notebooks ( https://github.com/Functional-Metabolomics-Lab/FBMN-STATS ). Additionally, the protocol is accompanied by a web application with a graphical user interface ( https://fbmn-statsguide.gnps2.org/ ) to lower the barrier of entry for new users and for educational purposes. Finally, we also show users how to integrate their statistical results into the molecular network using the Cytoscape visualization tool. Throughout the protocol, we use a previously published environmental metabolomics dataset for demonstration purposes. Together, the protocol, code and web application provide a complete guide and toolbox for FBMN data integration, cleanup and advanced statistical analysis, enabling new users to uncover molecular insights from their non-targeted metabolomics data. Our protocol is tailored for the seamless analysis of FBMN results from Global Natural Products Social Molecular Networking and can be easily adapted to other mass spectrometry feature detection, annotation and networking tools.
In this study, the relationships of the cestode order Bothriocephalidea, parasites of marine and freshwater bony fish, were assessed using multi-gene molecular phylogenetic analyses. The dataset included 59 species, covering approximately 70% of currently recognised genera, a sample of bothriocephalidean biodiversity gathered through an intense 15year effort. The order as currently circumscribed, while monophyletic, includes three non-monophyletic and one monophyletic families. Bothriocephalidae is monophyletic and forms the most derived lineage of the order, comprised of a single freshwater and several marine clades. Biogeographic patterns within the freshwater clade are indicative of past radiations having occurred in Africa and North America. The earliest diverging lineages of the order comprise a paraphyletic Triaenophoridae. The Echinophallidae, consisting nearly exclusively of parasites of pelagic fish, was also resolved as paraphyletic with respect to the Bothriocephalidae. Philobythoides sp., the only representative included from the Philobythiidae, a unique family of parasites of bathypelagic fish, was sister to the genus Eubothrium, the latter constituting one of the lineages of the paraphyletic Triaenophoridae. Due to the weak statistical support for most of the basal nodes of the Triaenophoridae and Echinophallidae, as well as the lack of obvious morphological synapomorphies shared by taxa belonging to the statistically well-supported lineages, the current family-level classification, although mostly non-monophyletic, is provisionally retained, with the exception of the family Philobythiidae, which is recognised as a synonym of the Triaenophoridae. In addition, Schyzocotyle is resurrected to accommodate the invasive Asian fish tapeworm, Schyzocotyle acheilognathi (Yamaguti, 1934) n. comb. (syn. Bothriocephalus acheilognathi Yamaguti, 1934), which is of veterinary importance, and Schyzocotyle nayarensis (Malhotra, 1983) n. comb. (syn. Ptychobothrium nayarensis Malhotra, 1983). The genus is morphologically characterised by a wide, heart-shaped scolex with narrow, deep bothria.
- Klíčová slova
- Asian fish tapeworm, Biogeography, Bothriate, Bothriocephalidea, Schyzocotyle, Tapeworms, cox1, rDNA,
- MeSH
- Cestoda anatomie a histologie klasifikace genetika izolace a purifikace MeSH
- cestodózy parazitologie veterinární MeSH
- fylogeografie * MeSH
- molekulární sekvence - údaje MeSH
- nemoci ryb parazitologie MeSH
- ryby MeSH
- sekvenční analýza DNA MeSH
- zvířata MeSH
- Check Tag
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
The phylogeny of European species of the tapeworm genus Proteocephalus was studied, based on partial 18S rDNA and morphological data. The group was found to be monophyletic. The analysis showed a low informative value of available morphological characters in comparison with molecular data. The morphological matrix resulted in a poorly resolved tree which is, however, compatible with the topology (Proteocephalus osculatus (Proteocephalus torulosus (Proteocephalus macrocephalus, Proteocephalus filicollis) (Proteocephalus tetrastomus, Proteocephalus percae, Proteocephalus longicollis))) based on the 18S rDNA data. A comparison performed by the program TreeMap showed a lack of significant congruency between parasite and host phylogenies. Therefore, the distribution of species in their hosts appears to be independent of the phylogeny and it is likely to be a result of host-switching, rather than co-speciation events.
- MeSH
- Cestoda anatomie a histologie klasifikace genetika MeSH
- DNA helmintů chemie genetika izolace a purifikace MeSH
- fylogeneze * MeSH
- interakce hostitele a parazita MeSH
- molekulární evoluce * MeSH
- molekulární sekvence - údaje MeSH
- polymerázová řetězová reakce MeSH
- RNA ribozomální 18S chemie genetika izolace a purifikace MeSH
- sekvence nukleotidů MeSH
- sekvenční analýza DNA MeSH
- sekvenční homologie nukleových kyselin MeSH
- sekvenční seřazení MeSH
- zvířata MeSH
- Check Tag
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Geografické názvy
- Evropa MeSH
- Názvy látek
- DNA helmintů MeSH
- RNA ribozomální 18S MeSH
BACKGROUND: The digenean species of Echinostoma (Echinostomatidae) with 37 collar spines that comprise the so-called 'revolutum' species complex, qualify as cryptic due to the interspecific homogeneity of characters used to differentiate species. Only five species were considered valid in the most recent revision of the group but recent molecular studies have demonstrated a higher diversity within the group. In a study of the digeneans parasitising molluscs in central and northern Europe we found that Radix auricularia, R. peregra and Stagnicola palustris were infected with larval stages of two cryptic species of the 'revolutum' complex, one resembling E. revolutum and one undescribed species, Echinostoma sp. IG. This paper provides morphological and molecular evidence for their delimitation. METHODS: Totals of 2,030 R. auricularia, 357 R. peregra and 577 S. palustris were collected in seven reservoirs of the River Ruhr catchment area in Germany and a total of 573 R. peregra was collected in five lakes in Iceland. Cercariae were examined and identified live and fixed in molecular grade ethanol for DNA isolation and in hot/cold 4% formaldehyde solution for obtaining measurements from fixed materials. Partial fragments of the mitochondrial gene nicotinamide adenine dinucleotide dehydrogenase subunit 1 (nad1) were amplified for 14 isolates. RESULTS: Detailed examination of cercarial morphology allowed us to differentiate the cercariae of the two Echinostoma spp. of the 'revolutum' species complex. A total of 14 partial nad1 sequences was generated and aligned with selected published sequences for eight species of the 'revolutum' species complex. Both NJ and BI analyses resulted in consensus trees with similar topologies in which the isolates from Europe formed strongly supported reciprocally monophyletic lineages. The analyses also provided evidence that North American isolates identified as E. revolutum represent another cryptic species of the 'revolutum' species complex. CONCLUSION: Our findings highlight the need for further analyses of patterns of interspecific variation based on molecular and morphological evidence to enhance the re-evaluation of the species and advance our understanding of the relationships within the 'revolutum' group of Echinostoma.
- MeSH
- Echinostoma anatomie a histologie klasifikace genetika izolace a purifikace MeSH
- fylogeneze MeSH
- hlemýždi parazitologie MeSH
- jezera parazitologie MeSH
- molekulární sekvence - údaje MeSH
- řeky parazitologie MeSH
- zvířata MeSH
- Check Tag
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Geografické názvy
- Island MeSH
- Německo MeSH
The complete genomes of three Czech isolates VIRUBRA 1/045, VIRUBRA 1/046, and VIRUBRA 1/047 of Potato leafroll virus (PLRV) were sequenced and compared with 13 complete sequences of PLRV isolates available in GenBank. Among the Czech isolates, VIRUBRA 1/046 and 1/047 showed the highest nucleotide (nt) identity (98.7%). PLRV was the most conserved virus in both open reading frames (ORFs) 3 and 4. The most variable regions were ORFs 0 and Rap1. Interestingly, isolate VIRUBRA 1/045 significantly differed from the other two Czech isolates in ORFs 0 and 1. Moreover, we identified mutations in the amino acid (aa) sequences, which were specific for the Czech isolates. Phylogenetic analysis based on ORF0 showed that the Czech isolates could be classified in two of the three groupings of the phylogenetic tree obtained. This is the first report on sequence analysis of the genome sequences of PLRV isolates from the Czech Republic.
- MeSH
- fylogeneze MeSH
- genom virový * MeSH
- Luteoviridae klasifikace genetika izolace a purifikace MeSH
- molekulární sekvence - údaje MeSH
- sekvenční analýza DNA * MeSH
- sekvenční homologie MeSH
- shluková analýza MeSH
- Solanum tuberosum virologie MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Geografické názvy
- Česká republika MeSH
The diversity of ZYMV isolates was analysed by the biological and molecular characterisation of 11 isolates sampled from cucumber, squash and zucchini between 2001 and 2006 in various localities of Slovakia and Czech Republic. Analysis of the molecular variability targeting three separate genomic regions of the ZYMV genome [P1, P3 and (Cter)NIb-(Nter)CP] revealed a remarkable low level of nucleotide variability between isolates, despite their temporal and spatial distinction. Phylogenetic analysis based on the 5'-terminal part of the CP gene highlighted the close relatedness of Slovak, Czech and other central European isolates. Low level of genetic diversity within central European ZYMV isolates is in contrast to the diversity observed for isolates from other geographical regions, in particular Asia. No evidence of recombination in the ZYMV genome was detected. Sequence comparison between aggressive and moderate ZYMV isolates revealed one amino acid difference in the N-terminal part of the P3 protein, potentially involved in the tolerance breaking.
- MeSH
- Cucurbita virologie MeSH
- genetická variace * MeSH
- molekulární sekvence - údaje MeSH
- Potyvirus klasifikace genetika izolace a purifikace MeSH
- sekvence aminokyselin MeSH
- sekvenční analýza RNA MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- srovnávací studie MeSH
- Geografické názvy
- Česká republika MeSH
- Slovenská republika MeSH
16S-23S rDNA internal transcribed spacer regions (ITS) similarities were determined in 8 Acetobacter and 1 Gluconacetobacter strains. ITS-PCR amplification of the 16S-23S spacers showed 2 products of similar size in 7 strains; only 1 product of similar size was found in the 2 remaining strains. Analysis of the PCR products using restriction endonucleases HaeIII, HpaII and AluI revealed 3 different restriction groups of A. pasteurianus for AluI and HaeIII, and 4 restriction groups for HpaII. ITS nucleotide sequences of all studied strains exhibited a 52-98% similarity.
- MeSH
- Acetobacter klasifikace genetika MeSH
- DNA bakterií analýza MeSH
- Gluconacetobacter klasifikace genetika MeSH
- mezerníky ribozomální DNA analýza MeSH
- molekulární sekvence - údaje MeSH
- polymerázová řetězová reakce metody MeSH
- restrikční mapování MeSH
- RNA ribozomální 16S genetika MeSH
- RNA ribozomální 23S genetika MeSH
- sekvence nukleotidů MeSH
- sekvenční analýza DNA MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- srovnávací studie MeSH
- Názvy látek
- DNA bakterií MeSH
- mezerníky ribozomální DNA MeSH
- RNA ribozomální 16S MeSH
- RNA ribozomální 23S MeSH
Molecular networking has become a key method to visualize and annotate the chemical space in non-targeted mass spectrometry data. We present feature-based molecular networking (FBMN) as an analysis method in the Global Natural Products Social Molecular Networking (GNPS) infrastructure that builds on chromatographic feature detection and alignment tools. FBMN enables quantitative analysis and resolution of isomers, including from ion mobility spectrometry.
- MeSH
- biologické přípravky chemie MeSH
- databáze faktografické MeSH
- hmotnostní spektrometrie * MeSH
- metabolomika metody MeSH
- software MeSH
- výpočetní biologie metody MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Research Support, N.I.H., Extramural MeSH
- Research Support, U.S. Gov't, Non-P.H.S. MeSH
- Názvy látek
- biologické přípravky MeSH
The small planorbid snail Gyraulus cf. laevis (Alder) from Lake Mývatn in Iceland was found to emit large-tailed cercariae with 19 collar spines, and three-spined sticklebacks Gasterosteus aculeatus L. were infected with metacercariae of a species of Petasiger Dietz, 1909. Comparative sequence analysis using ND1 mitochondrial DNA sequences revealed that the rediae and cercariae are conspecific with P. islandicus Kostadinova & Skirnisson, 2007, recently described from an isolated population of the horned grebe Podiceps auritus (L.) at the lake. The redia, cercaria and metacercaria are described and compared with related forms.
- MeSH
- Acanthaceae parazitologie MeSH
- DNA helmintů chemie genetika MeSH
- Echinostomatidae anatomie a histologie genetika růst a vývoj izolace a purifikace MeSH
- fylogeneze MeSH
- mikroskopie MeSH
- mitochondriální DNA chemie genetika MeSH
- molekulární sekvence - údaje MeSH
- sekvenční analýza DNA MeSH
- shluková analýza MeSH
- Smegmamorpha parazitologie MeSH
- stadia vývoje * MeSH
- zvířata MeSH
- Check Tag
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Geografické názvy
- Island MeSH
- Názvy látek
- DNA helmintů MeSH
- mitochondriální DNA MeSH
The main aim of data analysis in biochemical metrology is the extraction of relevant information from biochemical data measurements. A system of extended exploratory data analysis (EDA) based on the concept of graphical tools for sample data summarization and exploration is proposed and the original EDA algorithm in S-Plus is available on the Internet at http://www.trilobyte.cz/EDA. To check basic assumptions about biochemical and medical data is to examine the independence of sample elements, sample normality and homogeneity. The exact assessment of the mean-value and the variance of steroid levels in controls is necessary for the correct assessment of the samples from patients. Data examination procedures are illustrated by a determination of the mean-value of 17-hydroxypregnenolone in the umbilical blood of newborns. For an asymmetric, strongly skewed sample distribution corrupted with outliers the best estimate of location seems to be the median. The Box-Cox transformation improves a sample symmetry. The proposed procedure gives reliable estimates of a mean-value for an asymmetric distribution of 17-hydroxypregnenolone when the arithmetic mean can not be used.
- MeSH
- 17-alfa-hydroxypregnenolon krev MeSH
- algoritmy MeSH
- fetální krev chemie MeSH
- interpretace statistických dat MeSH
- lidé MeSH
- matematické výpočty počítačové MeSH
- novorozenec MeSH
- software MeSH
- velikost vzorku MeSH
- výpočetní biologie MeSH
- Check Tag
- lidé MeSH
- novorozenec MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Názvy látek
- 17-alfa-hydroxypregnenolon MeSH
