Publications by authors named "Michael Barker"

Invasive species offer outstanding opportunities to identify the genomic sources of variation that contribute to rapid adaptation, as well as the genetic mechanisms facilitating invasions. The Eurasian plant yellow starthistle (Centaurea solstitialis) is highly invasive in North and South American grasslands and known to have evolved increased growth and reproduction during invasion. Here, we develop new genomic resources for C.

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All flowering plants are now recognized as diploidized paleopolyploids (Jiao et al., 2011; One Thousand Plant Transcriptomes Initiative, 2019), and polyploid species comprise approximately 30% of contemporary plant species (Wood et al., 2009; Barker et al.

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Premise: The history of angiosperms is marked by repeated rounds of ancient whole-genome duplications (WGDs). Here we used state-of-the-art methods to provide an up-to-date view of the distribution of WGDs in the history of angiosperms that considers both uncertainty introduced by different WGD inference methods and different underlying species-tree hypotheses.

Methods: We used the distribution synonymous divergences (K) of paralogs and orthologs from transcriptomic and genomic data to infer and place WGDs across two hypothesized angiosperm phylogenies.

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Introduction: Peritoneal dialysis (PD)-related peritonitis (PDRP) is a common cause of transfer to hemodialysis, patient morbidity, and is a risk factor for mortality. Associated patient anxiety can deter selection of PD for renal replacement therapy. Diagnosis relies on hospital laboratory tests; however, this might be achieved earlier if such information was available at the point-of-care (POC), thereby significantly improving outcomes.

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The sacred datura plant (Solanales: Solanaceae: Datura wrightii) has been used to study plant-herbivore interactions for decades. The wealth of information that has resulted leads it to have potential as a model system for studying the ecological and evolutionary genomics of these interactions. We present a de novo Datura wrightii genome assembled using PacBio HiFi long-reads.

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The synthesis and characterisation of fluorosulfate covalent inhibitors of the lipid kinase PI4KIIIβ is described. The conserved lysine residue located within the ATP binding site was targeted, and optimised compounds based upon reversible inhibitors with good activity and physicochemical profile showed strong reversible interactions and slow onset times for the covalent inhibition, resulting in an excellent selectivity profile for the lipid kinase target. X-Ray crystallography demonstrated a distal tyrosine residue could also be targeted using a fluorosulfate strategy.

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Introduction: Health workers faced overwhelming demands and experienced crisis levels of burnout before the COVID-19 pandemic; the pandemic presented unique challenges that further impaired their mental health.

Methods: Data from the General Social Survey Quality of Worklife Module were analyzed to compare self-reported mental health symptoms among U.S.

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Model species continue to underpin groundbreaking plant science research. At the same time, the phylogenetic resolution of the land plant tree of life continues to improve. The intersection of these 2 research paths creates a unique opportunity to further extend the usefulness of model species across larger taxonomic groups.

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Unlabelled: Delay in diagnosing multidrug-resistant tuberculosis (MDR-pTB) in children prolongs time to effective treatment. Data on risk factors for pediatric MDR from low-incidence countries are scarce. Retrospective nationwide case-control study to analyze MDR-pTB cases in Germany between 2010 and 2020 in comparison to a drug-susceptible (DS)-pTB group.

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Premise: The functional annotation of genes is a crucial component of genomic analyses. A common way to summarize functional annotations is with hierarchical gene ontologies, such as the Gene Ontology (GO) Resource. GO includes information about the cellular location, molecular function(s), and products/processes that genes produce or are involved in.

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A database that links patents to NIH awards enables evaluation of key milestones along the research translation pathway.

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Polyploidy is an important generator of evolutionary novelty across diverse groups in the Tree of Life, including many crops. However, the impact of whole-genome duplication depends on the mode of formation: doubling within a single lineage (autopolyploidy) versus doubling after hybridization between two different lineages (allopolyploidy). Researchers have historically treated these two scenarios as completely separate cases based on patterns of chromosome pairing, but these cases represent ideals on a continuum of chromosomal interactions among duplicated genomes.

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Nearly all lineages of land plants have experienced at least one whole-genome duplication (WGD) in their history. The legacy of these ancient WGDs is still observable in the diploidized genomes of extant plants. Genes originating from WGD-paleologs-can be maintained in diploidized genomes for millions of years.

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Article Synopsis
  • Cortical visual impairment (CVI) is a leading cause of visual impairment in children, especially affecting those who use augmentative and alternative communication (AAC); this study examines 13 children with CVI using AAC in an integrated program.
  • The researchers reviewed de-identified student records to gather data on demographics, functional vision, communication skills, and educational profiles, establishing reliability in their findings.
  • The results highlighted both similarities and differences among the participants, emphasizing the necessity for educators to regularly assess vision functioning alongside AAC to create effective communication and educational strategies for children with CVI.
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  • Researchers have studied the genome of the model fern Ceratopteris richardii, revealing its complex evolution and adaptations due to a significant genome duplication event 60 million years ago.
  • This evolution includes gene loss, duplications, and horizontal gene transfers from bacteria, highlighting changes in defense-related gene families.
  • The study enhances our understanding of plant biology and the evolution of seed plants by demonstrating how fern genes influenced seed development.
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Objectives: Post-measles increased susceptibility to subsequent infections seems particularly relevant in low-resource settings. We tested the hypothesis that measles causes a specifically increased rate of infections in children, also in a high-resource setting.

Methods: We conducted a retrospective cohort study on a large measles outbreak in Berlin, Germany.

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  • Genome size affects a species' form, function, and ecological success, and this study investigates how polyploidy and repetitive element activity drive genome evolution in caddisflies.
  • Researchers assembled genomes from 17 caddisfly species and found a significant variation in genome size, linking larger genomes to the expansion of transposable elements (TEs).
  • The study concludes that caddisfly clades with more ecological diversity tend to have larger genomes, indicating a relationship between TE activity and evolutionary adaptations in diverse environments.
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Substantial morphological variation in land plants remains inaccessible to genetic analysis because current models lack variation in important ecological and agronomic traits. The genus Gilia was historically a model for biosystematics studies and includes variation in morphological traits that are poorly understood at the genetic level. We assembled a chromosome-scale reference genome of G.

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  • Many plants in dry environments have developed a process called Crassulacean Acid Metabolism (CAM) to conserve water, but the aquatic plant Isoetes taiwanensis has also adapted this mechanism for low CO availability underwater.
  • This study generates a high-quality genome and RNA sequence data to explore CAM in Isoetes and finds significant similarities and key differences compared to terrestrial plants.
  • Notably, Isoetes uses a different type of PEPC for carbon fixation and shows divergent control of CAM genes, suggesting there are multiple evolutionary pathways to CAM that we are just beginning to understand.
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Plant genomes demonstrate significant presence/absence variation (PAV) within a species; however, the factors that lead to this variation have not been studied systematically in Brassica across diploids and polyploids. Here, we developed pangenomes of polyploid Brassica napus and its two diploid progenitor genomes B. rapa and B.

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Understanding the mechanisms that underlie chromosome evolution could provide insights into the processes underpinning the origin, persistence and evolutionary tempo of lineages. Here, we present the first database of chromosome counts for animals (the Animal Chromosome Count database, ACC) summarizing chromosome numbers for ~15,000 species. We found remarkable a similarity in the distribution of chromosome counts between animals and flowering plants.

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  • Chinese goldthread (Coptis chinensis) is an important medicinal plant with a newly assembled high-quality genome that gives insights into its biology.
  • The study identifies a historical whole-genome duplication event in the Ranunculaceae family and characterizes key genes related to the production of protoberberine-type alkaloids.
  • A specific gene, CYP719, plays a crucial role in synthesizing berberine, which may have implications for the development of other related medicinal compounds.
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  • * A new genome sequence related to Brassiceae helped confirm the hybridization model, revealing a significant time gap between the initial hybridizations and notable gene losses, particularly before the addition of the third subgenome.
  • * The analysis showed that each of the three subgenomes displays unique rates of gene loss but functions together seamlessly, suggesting a "mix and match" model where subgenome origin influences gene retention without affecting overall functionality.
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