Uncovering Cryptic Parasitoid Diversity in Horismenus (Chalcidoidea, Eulophidae)

The file attached is the Published/publisher’s pdf version of the article.© 2015 Kenyon et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited

A Complex Legacy: Louis Bouyer and the Metaphysics of the Reformation

Based on a discussion of Louis Bouyer’s thesis about the metaphysics of the Reformation in The Spirit and Forms of Protestantism, this essay considers the methodological and hermeneutical issues involved in enquiring into the metaphysical commitments of Reformation theology. A case study of the theology of the Reformer Peter Maryr Vermigli is employed for the argument that Reformation metaphysics was a hybrid of elements pertaining both to a nominalist and a participatory ontology. This argument is then taken further by a reflection on the history of reception of the metaphysical complexity which is at the heart of the Reformation legacy

Analysis of Cytokinin Response Factors in Artemisia tridentata

For my contribution to the research on Artemisia tridentata, I identified and analyzed Cytokinin Response Factors (CRFs) from the recent reference genome3. CRFs have been found to potentially be regulators of the developmental processes within vascular tissues and they also play an important role in environmental stress response. This makes CRFs essential in the regulation of plant development and have impacts on a plant’s drought stress tolerance. The understanding of these pathways can lead in many directions including more sustainable, drought resistant species. I hypothesized that due to an evolutionary history with whole genome duplications, CRFs in the Artemisia tridentata genome may be duplicated. To test this hypothesis, I Identified A. tridentata cytokinin response factor proteins and reconstructed the phylogeny of CRFs. The finding of only twelve CRFs indicates there is no retention of duplicated CRFs in the A. tridentata genome

Functional relevance of novel p300-mediated lysine 314 and 315 acetylation of RelA/p65

Nuclear factor kappaB (NF-kappaB) plays an important role in the transcriptional regulation of genes involved in immunity and cell survival. We show here in vitro and in vivo acetylation of RelA/p65 by p300 on lysine 314 and 315, two novel acetylation sites. Additionally, we confirmed the acetylation on lysine 310 shown previously. Genetic complementation of RelA/p65-/- cells with wild type and non-acetylatable mutants of RelA/p65 (K314R and K315R) revealed that neither shuttling, DNA binding nor the induction of anti-apoptotic genes by tumor necrosis factor alpha was affected by acetylation on these residues. Microarray analysis of these cells treated with TNFalpha identified specific sets of genes differently regulated by wild type or acetylation-deficient mutants of RelA/p65. Specific genes were either stimulated or repressed by the acetylation-deficient mutants when compared to RelA/p65 wild type. These results support the hypothesis that site-specific p300-mediated acetylation of RelA/p65 regulates the specificity of NF-kappaB dependent gene expressio

Functional relevance of novel p300-mediated lysine 314 and 315 acetylation of RelA/p65

Nuclear factor kappaB (NF-κB) plays an important role in the transcriptional regulation of genes involved in immunity and cell survival. We show here in vitro and in vivo acetylation of RelA/p65 by p300 on lysine 314 and 315, two novel acetylation sites. Additionally, we confirmed the acetylation on lysine 310 shown previously. Genetic complementation of RelA/p65−/− cells with wild type and non-acetylatable mutants of RelA/p65 (K314R and K315R) revealed that neither shuttling, DNA binding nor the induction of anti-apoptotic genes by tumor necrosis factor α was affected by acetylation on these residues. Microarray analysis of these cells treated with TNFα identified specific sets of genes differently regulated by wild type or acetylation-deficient mutants of RelA/p65. Specific genes were either stimulated or repressed by the acetylation-deficient mutants when compared to RelA/p65 wild type. These results support the hypothesis that site-specific p300-mediated acetylation of RelA/p65 regulates the specificity of NF-κB dependent gene expression

A Haploid Pseudo-Chromosome Genome Assembly for a Keystone Sagebrush Species of Western North American Rangelands

Increased ecological disturbances, species invasions, and climate change are creating severe conservation problems for several plant species that are widespread and foundational. Understanding the genetic diversity of these species and how it relates to adaptation to these stressors are necessary for guiding conservation and restoration efforts. This need is particularly acute for big sagebrush (Artemisia tridentata; Asteraceae), which was once the dominant shrub over 1,000,000 km2 in western North America but has since retracted by half and thus has become the target of one of the largest restoration seeding efforts globally. Here, we present the first reference-quality genome assembly for an ecologically important subspecies of big sagebrush (A. tridentata subsp. tridentata) based on short and long reads, as well as chromatin proximity ligation data analyzed using the HiRise pipeline. The final 4.2-Gb assembly consists of 5,492 scaffolds, with nine pseudo-chromosomal scaffolds (nine scaffolds comprising at least 90% of the assembled genome; n = 9). The assembly contains an estimated 43,377 genes based on ab initio gene discovery and transcriptional data analyzed using the MAKER pipeline, with 91.37% of BUSCOs being completely assembled. The final assembly was highly repetitive, with repeat elements comprising 77.99% of the genome, making the Artemisia tridentata subsp. tridentata genome one of the most highly repetitive plant genomes to be sequenced and assembled. This genome assembly advances studies on plant adaptation to drought and heat stress and provides a valuable tool for future genomic research

Role of synovial fibroblast subsets across synovial pathotypes in rheumatoid arthritis: a deconvolution analysis

OBJECTIVES: To integrate published single-cell RNA sequencing (scRNA-seq) data and assess the contribution of synovial fibroblast (SF) subsets to synovial pathotypes and respective clinical characteristics in treatment-naïve early arthritis. METHODS: In this in silico study, we integrated scRNA-seq data from published studies with additional unpublished in-house data. Standard Seurat, Harmony and Liger workflow was performed for integration and differential gene expression analysis. We estimated single cell type proportions in bulk RNA-seq data (deconvolution) from synovial tissue from 87 treatment-naïve early arthritis patients in the Pathobiology of Early Arthritis Cohort using MuSiC. SF proportions across synovial pathotypes (fibroid, lymphoid and myeloid) and relationship of disease activity measurements across different synovial pathotypes were assessed. RESULTS: We identified four SF clusters with respective marker genes: PRG4(+) SF (CD55, MMP3, PRG4, THY1(neg)); CXCL12(+) SF (CXCL12, CCL2, ADAMTS1, THY1(low)); POSTN(+) SF (POSTN, collagen genes, THY1); CXCL14(+) SF (CXCL14, C3, CD34, ASPN, THY1) that correspond to lining (PRG4(+) SF) and sublining (CXCL12(+) SF, POSTN(+) + and CXCL14(+) SF) SF subsets. CXCL12(+) SF and POSTN(+) + were most prominent in the fibroid while PRG4(+) SF appeared highest in the myeloid pathotype. Corresponding, lining assessed by histology (assessed by Krenn-Score) was thicker in the myeloid, but also in the lymphoid pathotype + the fibroid pathotype. PRG4(+) SF correlated positively with disease severity parameters in the fibroid, POSTN(+) SF in the lymphoid pathotype whereas CXCL14(+) SF showed negative association with disease severity in all pathotypes. CONCLUSION: This study shows a so far unexplored association between distinct synovial pathologies and SF subtypes defined by scRNA-seq. The knowledge of the diverse interplay of SF with immune cells will advance opportunities for tailored targeted treatments

A haploid pseudo-chromosome genome assembly for a keystone sagebrush species of western North American rangelands

Increased ecological disturbances, species invasions, and climate change are creating severe conservation problems for several plant species that are widespread and foundational. Understanding the genetic diversity of these species and how it relates to adaptation to these stressors are necessary for guiding conservation and restoration efforts. This need is particularly acute for big sagebrush (Artemisia tridentata; Asteraceae), which was once the dominant shrub over 1,000,000 km2 in western North America but has since retracted by half and thus has become the target of one of the largest restoration seeding efforts globally. Here, we present the first reference-quality genome assembly for an ecologically important subspecies of big sagebrush (A. tridentata subsp. tridentata) based on short and long reads, as well as chromatin proximity ligation data analyzed using the HiRise pipeline. The final 4.2-Gb assembly consists of 5,492 scaffolds, with nine pseudo-chromosomal scaffolds (nine scaffolds comprising at least 90% of the assembled genome; n = 9). The assembly contains an estimated 43,377 genes based on ab initio gene discovery and transcriptional data analyzed using the MAKER pipeline, with 91.37% of BUSCOs being completely assembled. The final assembly was highly repetitive, with repeat elements comprising 77.99% of the genome, making the Artemisia tridentata subsp. tridentata genome one of the most highly repetitive plant genomes to be sequenced and assembled. This genome assembly advances studies on plant adaptation to drought and heat stress and provides a valuable tool for future genomic research.This research was made possible by 2 NSF Idaho EPSCoR grants (award numbers OIA-1757324 and OIA-1826801), as well as a Dovetail Genomics Tree of Life Award.Introduction Materials and methods Sample collection, in vitro tissue propagation, and biomass production Flow cytometry and genome complexity analysis PacBio and Omni-C sequence data generation PacBio long-read de novo assembly and validation Pseudomolecule construction with HiRise Genome annotation RNA sequencing Repeat identification Functional annotation Results and discussion Validation of genome assembly and annotation Genome complexity and evidence of past polyploidization Comparing the A. tridentata and A. annua genome assemblies Applications of the sagebrush reference genome Data availability Acknowledgments Literature cite

Spectroscopic study of impurities and associated defects in nanodiamonds from Efremovka (CV3) and Orgueil (CI) meteorites

The results of spectroscopic and structural studies of phase composition and of defects in nanodiamonds from Efremovka (CV3) and Orgueil (CI) chondrites indicate that nitrogen atomic environment in meteoritic nanodiamonds (MND) is similar to that observed in synthetic counterparts produced by detonation and by the Chemical Vapour Deposition (CVD)-process. Most of the nitrogen in MND appears to be confined to lattice imperfections, such as crystallite/twin boundaries and other extended defects, while the concentration of nitrogen in the MND lattice is low. It is suggested that the N-rich sub-population of MND grains may have been formed with high growth rates in environments rich in accessible N (i.e., N in atomic form or as weakly bonded compounds). For the first time the silicon-vacancy complex (the "silicon" defect) is observed in MND by photoluminescence spectroscopy.Comment: 33 pages, 5 figures, submitted to Geochimica et Cosmochimica Act