Publications by authors named "Brad Barbazuk"

Stroke is a major cause of disability for adults over 40 years of age. While research into animal models has prioritized treatments aimed at diminishing post-stroke damage, no studies have investigated the response to a severe stroke injury in a highly regenerative adult mammal. Here we investigate the effects of transient ischemia on adult spiny mice, Acomys cahirinus, due to their ability to regenerate multiple tissues without scarring.

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Premise: The extraction of high-quality RNA is the critical first step for the analysis of gene expression and gene space. This remains particularly challenging in plants, and especially in ferns, where the disruption of the cell wall and separation of organic compounds from nucleic acids is not trivial.

Methods: We developed a cetyltrimethylammonium bromide (CTAB)-based RNA extraction protocol that consistently performs well across a large phylogenetic breadth of ferns-a lineage of plants high in secondary compounds-and in an array of tissue types.

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Physiologically relevant in vitro models are a priority in predictive toxicology to replace and/or reduce animal experiments. The compromised toxicant metabolism of many immortalized human liver cell lines grown as monolayers as compared to in vivo metabolism limits their physiological relevance. However, recent efforts to culture liver cells in a 3D environment, such as spheroids, to better mimic the in vivo conditions, may enhance the toxicant metabolism of human liver cell lines.

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Polyploidy is an important evolutionary process throughout eukaryotes, particularly in flowering plants. Duplicated gene pairs (homoeologs) in allopolyploids provide additional genetic resources for changes in molecular, biochemical, and physiological mechanisms that result in evolutionary novelty. Therefore, understanding how divergent genomes and their regulatory networks reconcile is vital for unraveling the role of polyploidy in plant evolution.

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Osteoderms are bony plates found in the skin of vertebrates, mostly commonly in reptiles where they have evolved independently multiple times, suggesting the presence of a gene regulatory network that is readily activated and inactivated. They are absent in birds and mammals except for the armadillo. However, we have discovered that in one subfamily of rodents, the Deomyinae, there are osteoderms in the skin of their tails.

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Historically, xenia effects were hypothesized to be unique genetic contributions of pollen to seed phenotype, but most examples represent standard complementation of Mendelian traits. We identified the imprinted dosage-effect defective1 (ded1) locus in maize (Zea mays) as a paternal regulator of seed size and development. Hypomorphic alleles show a 5-10% seed weight reduction when ded1 is transmitted through the male, while homozygous mutants are defective with a 70-90% seed weight reduction.

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U12-type or minor introns are found in most multicellular eukaryotes and constitute ∼0.5% of all introns in species with a minor spliceosome. Although the biological significance for the evolutionary conservation of U12-type introns is debated, mutations disrupting U12 splicing cause developmental defects in both plants and animals.

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Ferns are the second largest clade of vascular plants with over 10,000 species, yet the generation of genomic resources for the group has lagged behind other major clades of plants. Transcriptomic data have proven to be a powerful tool to assess phylogenetic relationships, using thousands of markers that are largely conserved across the genome, and without the need to sequence entire genomes. We assembled the largest nuclear phylogenetic dataset for ferns to date, including 2884 single-copy nuclear loci from 247 transcriptomes (242 ferns, five outgroups), and investigated phylogenetic relationships across the fern tree, the placement of whole genome duplications (WGDs), and gene retention patterns following WGDs.

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MicroRNAs (miRNAs) are ~ 22 nucleotide ubiquitous gene regulators. They modulate a broad range of essential cellular processes linked to human health and diseases. Consequently, identifying miRNA targets and understanding how they function are critical for treating miRNA associated diseases.

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The spiny mouse (Acomys species) has emerged as an exciting research organism due to its remarkable ability to undergo scarless regeneration of skin wounds and ear punches. Excitingly, Acomys species demonstrate scar-free healing in a wide-range of tissues beyond the skin. In this perspective article, we discuss published findings from a variety of tissues to highlight how this emerging research organism could shed light on numerous clinically relevant human diseases.

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Unlabelled: Jasmonate is an essential phytohormone regulating plant growth, development, and defense. Alternative splicing (AS) in jasmonate ZIM-domain (JAZ) repressors is well-characterized and plays an important role in jasmonate signaling regulation. However, it is unknown whether other genes in the jasmonate signaling pathway are regulated by AS.

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Ferns are notorious for possessing large genomes and numerous chromosomes. Despite decades of speculation, the processes underlying the expansive genomes of ferns are unclear, largely due to the absence of a sequenced homosporous fern genome. The lack of this crucial resource has not only hindered investigations of evolutionary processes responsible for the unusual genome characteristics of homosporous ferns, but also impeded synthesis of genome evolution across land plants.

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The avocado, , is a fruit crop of immense importance to Mexican agriculture with an increasing demand worldwide. Avocado lies in the anciently diverged magnoliid clade of angiosperms, which has a controversial phylogenetic position relative to eudicots and monocots. We sequenced the nuclear genomes of the Mexican avocado race, var.

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Background: Natural rubber, an indispensable commodity used in approximately 40,000 products, is fundamental to the tire industry. The rubber tree species Hevea brasiliensis (Willd. ex Adr.

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The African spiny mouse, Acomys spp., is capable of scar-free dermal wound healing. Here, we have performed a comprehensive analysis of gene expression throughout wound healing following full-thickness excisional dermal wounds in both Acomys cahirinus and Mus musculus.

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Plants grown in spaceflight experience novel environmental signals, including those associated with microgravity and ionizing radiation. Spaceflight triggers a response involving transcriptional re-programming and altered cell morphology, though many aspects of this response remain uncharacterized. We analyzed the spaceflight-induced transcriptome with a focus on genes that undergo alternative splicing to examine differential splicing associated with spaceflight-an unstudied characteristic of the molecular response to spaceflight exposure.

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The last eukaryotic common ancestor had two classes of introns that are still found in most eukaryotic lineages. Common U2-type and rare U12-type introns are spliced by the major and minor spliceosomes, respectively. Relatively few splicing factors have been shown to be specific to the minor spliceosome.

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Computational analyses play crucial roles in characterizing splicing isoforms in plant genomes. In this review, we provide a survey of computational tools used in recently published, genome-scale splicing analyses in plants. We summarize the commonly used software and pipelines for read mapping, isoform reconstruction, isoform quantification, and differential expression analysis.

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Article Synopsis
  • Polyploidy is crucial in angiosperm evolution, particularly through the formation of allotetraploids from hybridization and the presence of duplicated gene copies.
  • A new analytical approach has been developed to effectively assess homeolog-specific expression, involving the assembly of parental transcriptomes and a robust statistical model to analyze data while reducing redundancy.
  • The study found that in recent allopolyploids, there is largely balanced expression between homeologs without strong parental bias, and the methods can be broadly applied to other tetrapolyploid systems.
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The maize W22 inbred has served as a platform for maize genetics since the mid twentieth century. To streamline maize genome analyses, we have sequenced and de novo assembled a W22 reference genome using short-read sequencing technologies. We show that significant structural heterogeneity exists in comparison to the B73 reference genome at multiple scales, from transposon composition and copy number variation to single-nucleotide polymorphisms.

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  • This study investigates the genetic diversity and adaptation of eastern cottonwood, a crucial bioenergy crop and ecological species, by analyzing 425 individuals from 13 southeastern U.S. states.
  • Researchers used targeted resequencing methods to evaluate a large number of genes, identifying single nucleotide polymorphisms (SNPs) and revealing low subpopulation differentiation but high genetic diversity among the trees.
  • The findings highlight potential local adaptation genes linked to environmental factors, with implications for improving management and breeding strategies amidst climate change, and suggest a pattern of convergent evolution with another poplar species.
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Article Synopsis
  • Three newly isolated phages, Findley, Hurricane, and TBond007, were found to infect a specific strain called mc155.
  • These phages were discovered in different geographic locations and are categorized under cluster K mycobacteriophages.
  • Findley is closely related to subcluster K2, while Hurricane and TBond007 belong to subcluster K3.
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One difficulty when identifying alternative splicing (AS) events in plants is distinguishing functional AS from splicing noise. One way to add confidence to the validity of a splice isoform is to observe that it is conserved across evolutionarily related species. We use a high throughput method to identify junction-based conserved AS events from RNA-Seq data across nine plant species, including five grass monocots (maize, sorghum, rice, , and foxtail millet), plus two nongrass monocots (banana and African oil palm), the eudicot , and the basal angiosperm In total, 9804 AS events were found to be conserved between two or more species studied.

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Article Synopsis
  • Alternative splicing (AS) is important for transcript and protein diversity, but studying it in species without clear genomes is challenging.
  • Researchers used Iso-Seq™ data to analyze AS in Amborella trichopoda, which is crucial for understanding angiosperm evolution.
  • The Iso-Seq™ method outperformed RNA-Seq in identifying large transcripts and gene structures, revealing a higher percentage of multi-exonic genes undergoing AS and offering a new de novo detection pipeline that could benefit various biological studies without needing a reference genome.
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Article Synopsis
  • RNA splicing of U12-type introns is crucial for cell differentiation in humans, but its role in plants, specifically maize, is still unclear.
  • The maize protein ROUGH ENDOSPERM3 (RGH3) is similar to the human splicing factor ZRSR2, and mutations in RGH3 lead to cell differentiation issues in maize endosperm.
  • Retained U12-type introns in maize mutants indicate splicing defects, affecting key biological pathways and suggesting that U12 splicing is vital for proper cell development across different species.
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