-
PloS One 2022To select elite Robinia pseudoacacia L. germplasm resources for production, 13 phenotypes and three physiological indicators of 214 seedlings from 20 provenances were...
To select elite Robinia pseudoacacia L. germplasm resources for production, 13 phenotypes and three physiological indicators of 214 seedlings from 20 provenances were systematically evaluated and analyzed. The leaf phenotypic and physiological coefficients of variation among the genotypes ranged from 3.741% to 19.599% and from 8.260% to 42.363%, respectively. The Kentucky provenance had the largest coefficient of variation (18.541%). The average differentiation coefficients between and within provenances were 34.161% and 38.756%, respectively. These close percentages showed that R. pseudoacacia presented high genetic variation among and within provenances, which can be useful for assisted migration and breeding programs. Furthermore, based on the results of correlations, principal component analysis and cluster analysis, breeding improvements targeting R. pseudoacacia's ornamental value, food value, and stress resistance of were performed. Forty and 30 excellent individuals, accounting for 18.692% and 14.019%, respectively, of the total resources. They were ultimately screened, after comprehensively taking into considering leaf phenotypic traits including compound leaf length, leaflet number and leaflet area and physiological characteristics including proline and soluble protein contents. These selected individuals could provide a base material for improved variety conservation and selection.
Topics: Kentucky; Phenotype; Plant Breeding; Plant Leaves; Robinia; Seedlings
PubMed: 34986177
DOI: 10.1371/journal.pone.0262278 -
Scientific Data Aug 2022Provenance is information describing the lineage of an object, such as a dataset or biological material. Since these objects can be passed between organizations, each...
Provenance is information describing the lineage of an object, such as a dataset or biological material. Since these objects can be passed between organizations, each organization can document only parts of the objects life cycle. As a result, interconnection of distributed provenance parts forms distributed provenance chains. Dependant on the actual provenance content, complete provenance chains can provide traceability and contribute to reproducibility and FAIRness of research objects. In this paper, we define a lightweight provenance model based on W3C PROV that enables generation of distributed provenance chains in complex, multi-organizational environments. The application of the model is demonstrated with a use case spanning several steps of a real-world research pipeline - starting with the acquisition of a specimen, its processing and storage, histological examination, and the generation/collection of associated data (images, annotations, clinical data), ending with training an AI model for the detection of tumor in the images. The proposed model has become an open conceptual foundation of the currently developed ISO 23494 standard on provenance for biotechnology domain.
PubMed: 35977957
DOI: 10.1038/s41597-022-01537-6 -
Frontiers in Plant Science 2022In this review we summarize the current knowledge about the changes in secondary metabolism induced by biotic/abiotic stressors. It is known that the extreme... (Review)
Review
In this review we summarize the current knowledge about the changes in secondary metabolism induced by biotic/abiotic stressors. It is known that the extreme environmental conditions activate signaling pathways leading to triggering of enzymatic and non-enzymatic defense systems, which stimulate production of secondary metabolites with antioxidant and protective effects. Due to several groups of bioactive compounds including naphthodianthrones, acylphloroglucinols, flavonoids, and phenylpropanes, the world-wide represents a high-value medicinal crop of genus, which belongs to the most diverse genera within flowering plants. The summary of the up-to-date knowledge reveals a relationship between the level of defense-related phenolic compounds and interspecific differences in the stress tolerance. The chlorogenic acid, and flavonoids, namely the amentoflavone, quercetin or kaempferol glycosides have been reported as the most defense-related metabolites associated with plant tolerance against stressful environment including temperature, light, and drought, in association with the biotic stimuli resulting from plant-microbe interactions. As an example, the species-specific cold-induced phenolics profiles of 10 representatives of different provenances cultured are illustrated in the case-study. Principal component analysis revealed a relationship between the level of defense-related phenolic compounds and interspecific differences in the stress tolerance indicating a link between the provenance of species and inherent mechanisms of cold tolerance. The underlying metabolome alterations along with the changes in the activities of ROS-scavenging enzymes, and non-enzymatic physiological markers are discussed. Given these data it can be anticipated that some species native to divergent habitats, with interesting high-value secondary metabolite composition and predicted high tolerance to biotic/abiotic stresses would attract the attention as valuable sources of bioactive compounds for many medicinal purposes.
PubMed: 36531362
DOI: 10.3389/fpls.2022.1042375 -
The New Phytologist Dec 2017Contents 1034 I. 1034 II. 1035 III. 1037 IV. 1038 V. 1042 VI. 1043 VII. 1045 References 1045 SUMMARY: As temperatures warm and precipitation patterns shift as a result... (Review)
Review
Contents 1034 I. 1034 II. 1035 III. 1037 IV. 1038 V. 1042 VI. 1043 VII. 1045 References 1045 SUMMARY: As temperatures warm and precipitation patterns shift as a result of climate change, interest in the identification of tree genotypes that will thrive under more arid conditions has grown. In this review, we discuss the multiple definitions of 'drought tolerance' and the biological processes involved in drought responses. We describe the three major approaches taken in the study of genetic variation in drought responses, the advantages and shortcomings of each, and what each of these approaches has revealed about the genetic basis of adaptation to drought in conifers. Finally, we discuss how a greater knowledge of the genetics of drought tolerance may aid forest management, and provide recommendations for how future studies may overcome the limitations of past approaches. In particular, we urge a more direct focus on survival, growth and the traits that directly predict them (rather than on proxies, such as water use efficiency), combining research approaches with complementary strengths and weaknesses, and the inclusion of a wider range of taxa and life stages.
Topics: Adaptation, Physiological; Droughts; Forestry; Tracheophyta; Water
PubMed: 28895167
DOI: 10.1111/nph.14774 -
Cold Spring Harbor Perspectives in... Jul 2014Epigenetic information, which plays a major role in eukaryotic biology, is transmitted by covalent modifications of nuclear proteins (e.g., histones) and DNA, along with... (Review)
Review
Epigenetic information, which plays a major role in eukaryotic biology, is transmitted by covalent modifications of nuclear proteins (e.g., histones) and DNA, along with poorly understood processes involving cytoplasmic/secreted proteins and RNAs. The origin of eukaryotes was accompanied by emergence of a highly developed biochemical apparatus for encoding, resetting, and reading covalent epigenetic marks in proteins such as histones and tubulins. The provenance of this apparatus remained unclear until recently. Developments in comparative genomics show that key components of eukaryotic epigenetics emerged as part of the extensive biochemical innovation of secondary metabolism and intergenomic/interorganismal conflict systems in prokaryotes, particularly bacteria. These supplied not only enzymatic components for encoding and removing epigenetic modifications, but also readers of some of these marks. Diversification of these prokaryotic systems and subsequently eukaryotic epigenetics appear to have been considerably influenced by the great oxygenation event in the Earth's history.
Topics: Biodiversity; DNA Methylation; DNA, Bacterial; Epigenomics; Eukaryota; Evolution, Molecular; Histones; Models, Molecular; Phosphorylation; Phylogeny; Protein Processing, Post-Translational; Protein Structure, Tertiary; Proteins; Ubiquitination
PubMed: 24984775
DOI: 10.1101/cshperspect.a016063 -
Metabolites Mar 2021The red meat supply chain is a complex network transferring product from producers to consumers in a safe and secure way. There can be times when fragmentation can arise... (Review)
Review
The red meat supply chain is a complex network transferring product from producers to consumers in a safe and secure way. There can be times when fragmentation can arise within the supply chain, which could be exploited. This risk needs reduction so that meat products enter the market with the desired attributes. Rapid Evaporative Ionisation Mass Spectrometry (REIMS) is a novel ambient mass spectrometry technique originally developed for rapid and accurate classification of biological tissue which is now being considered for use in a range of additional applications. It has subsequently shown promise for a range of food provenance, quality and safety applications with its ability to conduct ex vivo and in situ analysis. These are regarded as critical characteristics for technologies which can enable real-time decision making in meat processing plants and more broadly throughout the sector. This review presents an overview of the REIMS technology, and its application to the areas of provenance, quality and safety to the red meat industry, particularly in an Australian context.
PubMed: 33804276
DOI: 10.3390/metabo11030171 -
Neuroinformatics Jan 2023We present here an online platform for sharing resources underlying publications in neuroscience. It enables authors to easily upload and distribute digital resources,...
We present here an online platform for sharing resources underlying publications in neuroscience. It enables authors to easily upload and distribute digital resources, such as data, code, and notebooks, in a structured and systematic way. Interactivity is a prominent feature of the Live Papers, with features to download, visualise or simulate data, models and results presented in the corresponding publications. The resources are hosted on reliable data storage servers to ensure long term availability and easy accessibility. All data are managed via the EBRAINS Knowledge Graph, thereby helping maintain data provenance, and enabling tight integration with tools and services offered under the EBRAINS ecosystem.
Topics: Ecosystem; Computational Biology; Neurosciences; Information Storage and Retrieval
PubMed: 35986836
DOI: 10.1007/s12021-022-09598-z -
Journal of Biomedical Semantics Sep 2018Biomedical knowledge graphs have become important tools to computationally analyse the comprehensive body of biomedical knowledge. They represent knowledge as...
BACKGROUND
Biomedical knowledge graphs have become important tools to computationally analyse the comprehensive body of biomedical knowledge. They represent knowledge as subject-predicate-object triples, in which the predicate indicates the relationship between subject and object. A triple can also contain provenance information, which consists of references to the sources of the triple (e.g. scientific publications or database entries). Knowledge graphs have been used to classify drug-disease pairs for drug efficacy screening, but existing computational methods have often ignored predicate and provenance information. Using this information, we aimed to develop a supervised machine learning classifier and determine the added value of predicate and provenance information for drug efficacy screening. To ensure the biological plausibility of our method we performed our research on the protein level, where drugs are represented by their drug target proteins, and diseases by their disease proteins.
RESULTS
Using random forests with repeated 10-fold cross-validation, our method achieved an area under the ROC curve (AUC) of 78.1% and 74.3% for two reference sets. We benchmarked against a state-of-the-art knowledge-graph technique that does not use predicate and provenance information, obtaining AUCs of 65.6% and 64.6%, respectively. Classifiers that only used predicate information performed superior to classifiers that only used provenance information, but using both performed best.
CONCLUSION
We conclude that both predicate and provenance information provide added value for drug efficacy screening.
Topics: Biological Ontologies; Computer Graphics; Drug Evaluation, Preclinical; False Negative Reactions; ROC Curve
PubMed: 30189889
DOI: 10.1186/s13326-018-0189-6 -
Ecology and Evolution Jul 2021Accurate identification of the botanical components of honey can be used to establish its geographical provenance, while also providing insights into honeybee ( L.) diet...
Accurate identification of the botanical components of honey can be used to establish its geographical provenance, while also providing insights into honeybee ( L.) diet and foraging preferences. DNA metabarcoding has been demonstrated as a robust method to identify plant species from pollen and pollen-based products, including honey. We investigated the use of pollen metabarcoding to identify the floral sources and local foraging preferences of honeybees using 15 honey samples from six bioregions from eastern and western Australia. We used two plant metabarcoding markers, ITS2 and the trnL P6 loop. Both markers combined identified a total of 55 plant families, 67 genera, and 43 species. The trnL P6 loop marker provided significantly higher detection of taxa, detecting an average of 15.6 taxa per sample, compared to 4.6 with ITS2. Most honeys were dominated by and other Myrtaceae species, with a few honeys dominated by (Proteaceae) and Fabaceae. Metabarcoding detected the nominal primary source provided by beekeepers among the top five most abundant taxa for 85% of samples. We found that eastern and western honeys could be clearly differentiated by their floral composition, and clustered into bioregions with the trnL marker. Comparison with previous results obtained from melissopalynology shows that metabarcoding can detect similar numbers of plant families and genera, but provides significantly higher resolution at species level. Our results show that pollen DNA metabarcoding is a powerful and robust method for detecting honey provenance and examining the diet of honeybees. This is particularly relevant for hives foraging on the unique and diverse flora of the Australian continent, with the potential to be used as a novel monitoring tool for honeybee floral resources.
PubMed: 34257922
DOI: 10.1002/ece3.7679 -
The VLDB Journal : Very Large Data... Oct 2018Debugging data processing logic in data-intensive scalable computing (DISC) systems is a difficult and time-consuming effort. Today's DISC systems offer very little...
Debugging data processing logic in data-intensive scalable computing (DISC) systems is a difficult and time-consuming effort. Today's DISC systems offer very little tooling for debugging programs, and as a result, programmers spend countless hours collecting evidence (e.g., from log files) and performing trial-and-error debugging. To aid this effort, we built , a library that enables -tracking data through transformations-in Apache Spark. Data scientists using the Titian Spark extension will be able to quickly identify the input data at the root cause of a potential bug or outlier result. Titian is built directly into the Spark platform and offers data provenance support at interactive speeds-orders of magnitude faster than alternative solutions-while minimally impacting Spark job performance; observed overheads for capturing data lineage rarely exceed 30% above the baseline job execution time.
PubMed: 31007500
DOI: 10.1007/s00778-017-0474-5