Shade from neighboring plants limits light for photosynthesis; as a consequence, plants have a variety of strategies to avoid canopy shade and compete with their neighbors for light. Collectively the ...response to foliar shade is called the shade avoidance syndrome (SAS). The SAS includes elongation of a variety of organs, acceleration of flowering time, and additional physiological responses, which are seen throughout the plant life cycle. However, current mechanistic knowledge is mainly limited to shade-induced elongation of seedlings. Here we use phenotypic profiling of seedling, leaf, and flowering time traits to untangle complex SAS networks. We used over-representation analysis (ORA) of shade-responsive genes, combined with previous annotation, to logically select 59 known and candidate novel mutants for phenotyping. Our analysis reveals shared and separate pathways for each shade avoidance response. In particular, auxin pathway components were required for shade avoidance responses in hypocotyl, petiole, and flowering time, whereas jasmonic acid pathway components were only required for petiole and flowering time responses. Our phenotypic profiling allowed discovery of seventeen novel shade avoidance mutants. Our results demonstrate that logical selection of mutants increased success of phenotypic profiling to dissect complex traits and discover novel components.
Although applied over extremely short timescales, artificial selection has dramatically altered the form, physiology, and life history of cultivated plants. We have used RNAseq to define both gene ...sequence and expression divergence between cultivated tomato and five related wild species. Based on sequence differences, we detect footprints of positive selection in over 50 genes. We also document thousands of shifts in gene-expression level, many of which resulted from changes in selection pressure. These rapidly evolving genes are commonly associated with environmental response and stress tolerance. The importance of environmental inputs during evolution of gene expression is further highlighted by large-scale alteration of the light response coexpression network between wild and cultivated accessions. Human manipulation of the genome has heavily impacted the tomato transcriptome through directed admixture and by indirectly favoring nonsynonymous over synonymous substitutions. Taken together, our results shed light on the pervasive effects artificial and natural selection have had on the transcriptomes of tomato and its wild relatives.
The mapping and functional analysis of quantitative traits in Brassica rapa can be greatly improved with the availability of physically positioned, gene-based genetic markers and accurate genome ...annotation. In this study, deep transcriptome RNA sequencing (RNA-Seq) of Brassica rapa was undertaken with two objectives: SNP detection and improved transcriptome annotation. We performed SNP detection on two varieties that are parents of a mapping population to aid in development of a marker system for this population and subsequent development of high-resolution genetic map. An improved Brassica rapa transcriptome was constructed to detect novel transcripts and to improve the current genome annotation. This is useful for accurate mRNA abundance and detection of expression QTL (eQTLs) in mapping populations. Deep RNA-Seq of two Brassica rapa genotypes-R500 (var. trilocularis, Yellow Sarson) and IMB211 (a rapid cycling variety)-using eight different tissues (root, internode, leaf, petiole, apical meristem, floral meristem, silique, and seedling) grown across three different environments (growth chamber, greenhouse and field) and under two different treatments (simulated sun and simulated shade) generated 2.3 billion high-quality Illumina reads. A total of 330,995 SNPs were identified in transcribed regions between the two genotypes with an average frequency of one SNP in every 200 bases. The deep RNA-Seq reassembled Brassica rapa transcriptome identified 44,239 protein-coding genes. Compared with current gene models of B. rapa, we detected 3537 novel transcripts, 23,754 gene models had structural modifications, and 3655 annotated proteins changed. Gaps in the current genome assembly of B. rapa are highlighted by our identification of 780 unmapped transcripts. All the SNPs, annotations, and predicted transcripts can be viewed at http://phytonetworks.ucdavis.edu/.
This article describes a formal proof of the Kepler conjecture on dense sphere packings in a combination of the HOL Light and Isabelle proof assistants. This paper constitutes the official published ...account of the now completed Flyspeck project.
With the growing demand for automotive LiDAR and the maturation of silicon photonics platforms, optical phased arrays (OPAs) have emerged as a key technology for solid-state optical beam-steering. In ...order to meet realistic automotive specifications with OPAs, >500 antenna elements should work reliably under tight power and cost budgets. Existing multi-chip solutions necessitate expensive packaging and assembly to achieve high interconnect density. Even with 2-D monolithic integration, high-voltage drivers to deliver sufficient power to resistive phase shifters typically result in significant overhead in die area and limited power efficiency. In this article, we introduce a single-chip OPA realized through wafer-scale 3-D integration of silicon photonics and CMOS. Flexible and ultra-dense connections with through-oxide vias (TOVs) in our platform resolve the I/O density issue. Moreover, low-voltage L-shaped phase shifters and compact, efficient switch-mode drivers, connected vertically using TOVs, remove wiring/placement overhead and achieve a large active array aperture within a compact die. Our OPA prototype achieves wide-range 2-D steering over 18.5°×16° by leveraging wavelength tuning and phase control, and array scaling up to 125 elements with a large aperture size of 0.5 mm×0.5 mm and 0.15°×0.25° beamwidth while consuming 20 mW/element average power. Since our system supports per-element independent phase control, increased sensitivity to process variations in L-shaped shifters is fully compensated by a simple calibration process.
Development of efficacious in vivo delivery platforms for CRISPR-Cas9-based epigenome engineering will be critical to enable the ability to target human diseases without permanent modification of the ...genome. Toward this, we utilized split-Cas9 systems to develop a modular adeno-associated viral (AAV) vector platform for CRISPR-Cas9 delivery to enable the full spectrum of targeted in situ gene regulation functionalities, demonstrating robust transcriptional repression (up to 80%) and activation (up to 6-fold) of target genes in cell culture and mice. We also applied our platform for targeted in vivo gene-repression-mediated gene therapy for retinitis pigmentosa. Specifically, we engineered targeted repression of Nrl, a master regulator of rod photoreceptor determination, and demonstrated Nrl knockdown mediates in situ reprogramming of rod cells into cone-like cells that are resistant to retinitis pigmentosa-specific mutations, with concomitant prevention of secondary cone loss. Furthermore, we benchmarked our results from Nrl knockdown with those from in vivo Nrl knockout via gene editing. Taken together, our AAV-CRISPR-Cas9 platform for in vivo epigenome engineering enables a robust approach to target disease in a genomically scarless and potentially reversible manner.
We developed a modular adeno-associated viral vector platform for CRISPR-Cas9 delivery to enable targeted in situ gene regulation, demonstrating robust transcriptional repression and activation of genes in cell culture and mice. This approach could potentially enable disease targeting in a genomically scarless and reversible manner.
In response to cell death signals, an active apoptosome is assembled from Apaf-1 and procaspase-9 (pc-9). Here we report a near atomic structure of the active human apoptosome determined by ...cryo-electron microscopy. The resulting model gives insights into cytochrome c binding, nucleotide exchange and conformational changes that drive assembly. During activation an acentric disk is formed on the central hub of the apoptosome. This disk contains four Apaf-1/pc-9 CARD pairs arranged in a shallow spiral with the fourth pc-9 CARD at lower occupancy. On average, Apaf-1 CARDs recruit 3 to 5 pc-9 molecules to the apoptosome and one catalytic domain may be parked on the hub, when an odd number of zymogens are bound. This suggests a stoichiometry of one or at most, two pc-9 dimers per active apoptosome. Thus, our structure provides a molecular framework to understand the role of the apoptosome in programmed cell death and disease.
Blastomycose Tat, Jennifer; Nadarajah, Jeya; Kus, Julianne V
Canadian Medical Association journal (CMAJ),
11/2023, Letnik:
195, Številka:
43
Journal Article
Blastomycosis Tat, Jennifer; Nadarajah, Jeya; Kus, Julianne V
Canadian Medical Association journal (CMAJ),
2023-Jul-31, 2023-07-31, 20230731, Letnik:
195, Številka:
29
Journal Article
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Although rates of blastomycosis in Canada remain low outside of historically endemic areas, the range for Blastomyces now includes Quebec, Manitoba, Saskatchewan, Ontario -- the Kenora area has the ...highest global rates -- and the eastern US. Changes in climate and land use are hypothesized to be causing the expansion. Although a travel and exposure history remains important to differential diagnosis, cases are increasingly described in patients who have not traveled to traditional endemic areas. Blastomyces grows in soil and decaying vegetative material. Blastomycosis is typically acquired through inhalation of spores from the disrupted environment and, occasionally, through cutaneous inoculation; it does not spread person-to-person. Indigenous people have a higher incidence of disease. Other mammals, including domestic dogs, are susceptible.
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