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BMC Genomics Feb 2024Pecan scab is a devastating disease that causes damage to pecan (Carya illinoinensis (Wangenh.) K. Koch) fruit and leaves. The disease is caused by the fungus Venturia...
Pecan scab is a devastating disease that causes damage to pecan (Carya illinoinensis (Wangenh.) K. Koch) fruit and leaves. The disease is caused by the fungus Venturia effusa (G. Winter) and the main management practice for controlling the disease is by application of fungicides at 2-to-3-week intervals throughout the growing season. Besides disease-related yield loss, application of fungicides can result in considerable cost and increases the likelihood of fungicide resistance developing in the pathogen. Resistant cultivars are available for pecan growers; although, in several cases resistance has been overcome as the pathogen adapts to infect resistant hosts. Despite the importance of host resistance in scab management, there is little information regarding the molecular basis of genetic resistance to pecan scab.The purpose of this study was to elucidate mechanisms of natural pecan scab resistance by analyzing transcripts that are differentially expressed in pecan leaf samples from scab resistant and susceptible trees. The leaf samples were collected from trees in a provenance collection orchard that represents the natural range of pecan in the US and Mexico. Trees in the orchard have been exposed to natural scab infections since planting in 1989, and scab ratings were collected over three seasons. Based on this data, ten susceptible trees and ten resistant trees were selected for analysis. RNA-seq data was collected and analyzed for diseased and non-diseased parts of susceptible trees as well as for resistant trees. A total of 313 genes were found to be differentially expressed when comparing resistant and susceptible trees without disease. For susceptible samples showing scab symptoms, 1,454 genes were identified as differentially expressed compared to non-diseased susceptible samples. Many genes involved in pathogen recognition, defense responses, and signal transduction were up-regulated in diseased samples of susceptible trees, whereas differentially expressed genes in pecan scab resistant samples were generally down-regulated compared to non-diseased susceptible samples.Our results provide the first account of candidate genes involved in resistance/susceptibility to pecan scab under natural conditions in a pecan orchard. This information can be used to aid pecan breeding programs and development of biotechnology-based approaches for generating pecan cultivars with more durable scab resistance.
Topics: Fungicides, Industrial; Carya; Transcriptome; Trees; Ascomycota; Plant Diseases; Plant Breeding
PubMed: 38355402
DOI: 10.1186/s12864-024-10010-0 -
Scientific Reports Feb 2024In forensic investigations involving the identification of unknown deceased individuals, isotope analysis can provide valuable provenance information. This is especially...
In forensic investigations involving the identification of unknown deceased individuals, isotope analysis can provide valuable provenance information. This is especially pertinent when primary identifiers (i.e., DNA, dactyloscopy, etc.) fail to yield matches. The isotopic composition of human tissues is linked to that of the food consumed, potentially allowing the identification of regions of origin. However, the isotopic composition of deceased newborns and infants fed with milk formula may be influenced by that of the prepared milk. The findings contribute towards the possibility to isotopically identify bottle-fed infants. More importantly, the data convincingly show that the Sr isotope composition of the prepared milk is determined by that of the formula and not the (local) tap water, thereby limiting the potential of Sr isotope analysis for determining the geological or geographical origin in formula-fed babies in medico-legal cases.
Topics: Animals; Humans; Infant; Infant, Newborn; Isotopes; Milk
PubMed: 38351055
DOI: 10.1038/s41598-024-54173-y -
Frontiers in Digital Health 2024Population health data integration remains a critical challenge in low- and middle-income countries (LMIC), hindering the generation of actionable insights to inform... (Review)
Review
INTRODUCTION
Population health data integration remains a critical challenge in low- and middle-income countries (LMIC), hindering the generation of actionable insights to inform policy and decision-making. This paper proposes a pan-African, Findable, Accessible, Interoperable, and Reusable (FAIR) research architecture and infrastructure named the INSPIRE datahub. This cloud-based Platform-as-a-Service (PaaS) and on-premises setup aims to enhance the discovery, integration, and analysis of clinical, population-based surveys, and other health data sources.
METHODS
The INSPIRE datahub, part of the Implementation Network for Sharing Population Information from Research Entities (INSPIRE), employs the Observational Health Data Sciences and Informatics (OHDSI) open-source stack of tools and the Observational Medical Outcomes Partnership (OMOP) Common Data Model (CDM) to harmonise data from African longitudinal population studies. Operating on Microsoft Azure and Amazon Web Services cloud platforms, and on on-premises servers, the architecture offers adaptability and scalability for other cloud providers and technology infrastructure. The OHDSI-based tools enable a comprehensive suite of services for data pipeline development, profiling, mapping, extraction, transformation, loading, documentation, anonymization, and analysis.
RESULTS
The INSPIRE datahub's "On-ramp" services facilitate the integration of data and metadata from diverse sources into the OMOP CDM. The datahub supports the implementation of OMOP CDM across data producers, harmonizing source data semantically with standard vocabularies and structurally conforming to OMOP table structures. Leveraging OHDSI tools, the datahub performs quality assessment and analysis of the transformed data. It ensures FAIR data by establishing metadata flows, capturing provenance throughout the ETL processes, and providing accessible metadata for potential users. The ETL provenance is documented in a machine- and human-readable Implementation Guide (IG), enhancing transparency and usability.
CONCLUSION
The pan-African INSPIRE datahub presents a scalable and systematic solution for integrating health data in LMICs. By adhering to FAIR principles and leveraging established standards like OMOP CDM, this architecture addresses the current gap in generating evidence to support policy and decision-making for improving the well-being of LMIC populations. The federated research network provisions allow data producers to maintain control over their data, fostering collaboration while respecting data privacy and security concerns. A use-case demonstrated the pipeline using OHDSI and other open-source tools.
PubMed: 38347885
DOI: 10.3389/fdgth.2024.1329630 -
Dendrochronologia Feb 2024Dendrochronology is not a new method for attaining high-precision dates for archaeological and historic remains of timber. But the extent to which dendrochronology is...
Dendrochronology is not a new method for attaining high-precision dates for archaeological and historic remains of timber. But the extent to which dendrochronology is utilized to attain detailed precision of the dating of complex wooden structures can suffer from the fact that the method is often applied in commercial archaeology, where the extent of analysis is severely limited by cost constraints. Instead of lamenting the potentially lost levels of detail that might have slipped through over the years, it is hoped that by presenting the potential of high chronological precision, that necessitates extensive sampling of timber and wood remains on archaeological sites, a new future will be promoted, in which new wide-ranging sampling strategies will become a more normal practice in archaeology, in both the research and commercial spheres. In this paper, I present some case studies where extensive tree-ring analysis of well-preserved wood remains have resulted in annual chronological detail, allowing an insight into the processes of building, and into the duration of structures that comprised the built environment of past peoples' lives. In addition, we should not discuss precision dating for urban archaeological study without also touching on the subject of timber trade and timber provenance. Tree-ring studies are increasingly providing us with high precision provenance identification, not just for shipwrecks, barrels and other 'portable' objects. It is also allowing us to map trade in bulk structural timber. These analyses are providing us with insights into links between territories.
PubMed: 38343661
DOI: 10.1016/j.dendro.2024.126164 -
Plants (Basel, Switzerland) Feb 2024Forest genetic conservation is typically species-specific and does not integrate interspecific interaction and community structure. It mainly focuses on the theories of... (Review)
Review
Forest genetic conservation is typically species-specific and does not integrate interspecific interaction and community structure. It mainly focuses on the theories of population and quantitative genetics. This approach depicts the intraspecific patterns of population genetic structure derived from genetic markers and the genetic differentiation of adaptive quantitative traits in provenance trials. However, it neglects possible interspecific interaction in natural forests and overlooks natural hybridization or subspeciation. We propose that the genetic diversity of a given species in a forest community is shaped by both intraspecific population and interspecific community evolutionary processes, and expand the traditional forest genetic conservation concept under the community ecology framework. We show that a community-specific phylogeny derived from molecular markers would allow us to explore the genetic mechanisms of a tree species interacting with other resident species. It would also facilitate the exploration of a species' ecological role in forest community assembly and the taxonomic relationship of the species with other species specific to its resident forest community. Phylogenetic β-diversity would assess the similarities and differences of a tree species across communities regarding ecological function, the strength of selection pressure, and the nature and extent of its interaction with other species. Our forest genetic conservation proposal that integrates intraspecific population and interspecific community genetic variations is suitable for conserving a taxonomic species complex and maintaining its evolutionary potential in natural forests. This provides complementary information to conventional population and quantitative genetics-based conservation strategies.
PubMed: 38337968
DOI: 10.3390/plants13030435 -
BMC Ecology and Evolution Feb 2024Living birds comprise the most speciose and anatomically diverse clade of flying vertebrates, but their poor early fossil record and the lack of resolution around the...
BACKGROUND
Living birds comprise the most speciose and anatomically diverse clade of flying vertebrates, but their poor early fossil record and the lack of resolution around the relationships of the major clades have greatly obscured extant avian origins.
RESULTS
Here, I describe a Late Cretaceous bird from North America based on a fragmentary skeleton that includes cranial material and portions of the forelimb, hindlimb, and foot and is identified as a juvenile based on bone surface texture. Several features unite this specimen with crown Aves, but its juvenile status precludes the recognition of a distinct taxon. The North American provenance of the specimen supports a cosmopolitan distribution of early crown birds, clashes with the hypothesized southern hemisphere origins of living birds, and demonstrates that crown birds and their closest relatives coexisted with non-avian dinosaurs that independently converged on avian skeletal anatomy, such as the alvarezsaurids and dromaeosaurids.
CONCLUSIONS
By revealing the ecological and biogeographic context of Cretaceous birds within or near the crown clade, the Lance Formation specimen provides new insights into the contingent nature of crown avian survival through the Cretaceous-Paleogene mass extinction and the subsequent origins of living bird diversity.
Topics: Animals; Dinosaurs; Phylogeny; Ecosystem; Birds; North America; Skull
PubMed: 38336630
DOI: 10.1186/s12862-024-02210-9 -
Journal of Imaging Informatics in... Apr 2024The rapid growth of artificial intelligence (AI) and deep learning techniques require access to large inter-institutional cohorts of data to enable the development of...
The rapid growth of artificial intelligence (AI) and deep learning techniques require access to large inter-institutional cohorts of data to enable the development of robust models, e.g., targeting the identification of disease biomarkers and quantifying disease progression and treatment efficacy. The Observational Medical Outcomes Partnership Common Data Model (OMOP CDM) has been designed to accommodate a harmonized representation of observational healthcare data. This study proposes the Medical Imaging CDM (MI-CDM) extension, adding two new tables and two vocabularies to the OMOP CDM to address the structural and semantic requirements to support imaging research. The tables provide the capabilities of linking DICOM data sources as well as tracking the provenance of imaging features derived from those images. The implementation of the extension enables phenotype definitions using imaging features and expanding standardized computable imaging biomarkers. This proposal offers a comprehensive and unified approach for conducting imaging research and outcome studies utilizing imaging features.
PubMed: 38315345
DOI: 10.1007/s10278-024-00982-6 -
Heliyon Jan 2024Petrographical characterization and field observations were caried out to evaluate Kamlial Formation in Bagh district, Azad Jammu and Kashmir. Based on detailed...
Provenance, diagenesis, and depositional environment of Miocene Kamlial Formation, Azad Jammu and Kashmir, Sub Himalayas, Pakistan: Evidences from field observations and petrography.
Petrographical characterization and field observations were caried out to evaluate Kamlial Formation in Bagh district, Azad Jammu and Kashmir. Based on detailed petrography, the lithic arenite consisted of quartz (20-25%), feldspar (7-11%), rock fragments (20-37%), cementing materials (11-21%), and accessory minerals. Grains are mostly angular to subrounded and poorly to moderately sorted. The analysis revealed that the lithic arenite is mineralogically immature; also, the current activity during the time of deposition was low. Polycrystalline quartz indicates that the sandstone was derived from metamorphic source, while monocrystalline quartz indicates a granitic origin. Quartz having an angular shape suggests the source rock was near the depositional site, while quartz having a rounded shape represents long transportation. The presence of feldspar in the lithic arenite suggests the rocks were deposited at high relief or cold temperatures. Primary porosity in sandstone was reduced by calcite cements around the grain, while secondary porosity was developed by fracturing of quartz and feldspar. Tectonic uplift in the study area was demonstrated by fractured quartz and mica in thin sections. Field observations of various sedimentary structures were observed such as load casts, ripple marks, and mud cracks, etc. The presence of conglomerates and load casts in the study area indicates that the Kamlial sandstone was deposited by fluvial and shallow marine environment. Furthermore, the ripple marks indicate that the tidal flat environment controlled the deposition of the sediments.
PubMed: 38293448
DOI: 10.1016/j.heliyon.2024.e24309 -
ACS Omega Jan 2024The Ordos Basin is an important sandstone-type uranium enrichment region in China, and the Lower Cretaceous Huanhe Formation has attracted significant attention as a...
The Ordos Basin is an important sandstone-type uranium enrichment region in China, and the Lower Cretaceous Huanhe Formation has attracted significant attention as a newly discovered ore-bearing stratum. To elucidate the provenance, tectonic background, and sedimentary environment constraints on uranium enrichment in the Huanhe Formation sandstone-type uranium deposits, 10 representative sandstone samples from the study area were analyzed by using electron microscopy, X-ray fluorescence (XRF), inductively coupled plasma mass spectrometry (ICP-MS), and electron probe microanalysis. Independent uranium minerals in the Yihewusu area of Hangjin Banner were shown for the first time to be composed mainly of coffinite and titanium-uranium oxide, with trace amounts of pitchblende. The major element diagrams of the sandstone and ratios of Sr/Ba, V/Cr, and U/Th and enrichment factors of Mo and U revealed that the source rocks of the Huanhe Formation sandstone in the study area were intermediate-felsic igneous rocks. The tectonic setting is characterized as an active continental margin, with later deposition in brackish-to-marine water environments. The ore-bearing strata indicate a reducing environment, whereas the nonore-bearing strata indicate a weakly oxidizing environment. With reference to previous studies, the sedimentary material primarily originated from the medium-acidic intrusive rocks exposed in the northern portion of the basin, including the Daqing-Wula Mountains, the Yin Mountains, and middle-acidic intrusions along the eastern margin of the Alxa region in the western part of the basin. The uranium-rich granitic pluton of the source area contributed to the preenrichment of uranium in the target sandstone layer. Under oxidizing aqueous conditions, U migration was activated, whereas under reducing aqueous conditions, U was reduced to U, resulting in eventual sedimentation of coffinite as ore.
PubMed: 38284064
DOI: 10.1021/acsomega.3c06163 -
Evolutionary Applications Jan 2024The successes of introduced populations in novel habitats often provide powerful examples of evolution and adaptation. In the 1950s, opossum shrimp () individuals from...
The successes of introduced populations in novel habitats often provide powerful examples of evolution and adaptation. In the 1950s, opossum shrimp () individuals from Clearwater Lake in Minnesota, USA were transported and introduced to Twin Lakes in Colorado, USA by fisheries managers to supplement food sources for trout. were subsequently introduced from Twin Lakes into numerous lakes throughout Colorado. Because managers kept detailed records of the timing of the introductions, we had the opportunity to test for evolutionary divergence within a known time interval. Here, we used reduced representation genomic data to investigate patterns of genetic diversity, test for genetic divergence between populations, and for evidence of adaptive evolution within the introduced populations in Colorado. We found very low levels of genetic diversity across all populations, with evidence for some genetic divergence between the Minnesota source population and the introduced populations in Colorado. There was little differentiation among the Colorado populations, consistent with the known provenance of a single founding population, with the exception of the population from Gross Reservoir, Colorado. Demographic modeling suggests that at least one undocumented introduction from an unknown source population hybridized with the population in Gross Reservoir. Despite the overall low genetic diversity we observed, outlier and environmental association analyses identified multiple loci exhibiting signatures of selection and adaptive variation related to elevation and lake depth. The success of introduced species is thought to be limited by genetic variation, but our results imply that populations with limited genetic variation can become established in a wide range of novel environments. From an applied perspective, the observed patterns of divergence between populations suggest that genetic analysis can be a useful forensic tool to determine likely sources of invasive species.
PubMed: 38283609
DOI: 10.1111/eva.13637