Development of Genomic Resources in \u3cem\u3eVitis Riparia\u3c/em\u3e for Discoveries on Pre- And Post-Transcriptional Molecular Regulators of Early Induction into Endodormancy

Grapevine is one of the most important fruit crops in the world, responsible for billions in global sales annually. The largest threat to grapevine and other crop production is global climate change resulting human activities. This brings unpredictable and drastic changes in ambient air temperatures to many climates in which grapes are grown. Lower temperatures and inclement weather are already responsible for millions in lost revenue due to tissue damage of established plants. Thus, protecting grapevine crops from weather-related damage is the biggest concern to growers aside from pathogen- and diseaserelated crop damage. The primary mechanism for winter survival in woody perennial plants is bud endodormancy, a state of hibernation that is activated in response to decreasing temperatures and photoperiod. The current understanding of this process is limited, but it is believed that induction into endodormancy is controlled by a combination of hormones and transcriptional regulators internal to the cell. Grapevines have variable resistance to cold depending on species. Of the approximately 80 identified grapevine species, North American and Asian grapevines have more enhanced winter survival. Vitis riparia, the riverbank grapevine, is one of the most resistant of the genus and has been identified to enter endodormancy at longer day lengths. Investigating why V. riparia responds differently may reveal key genes and molecular mechanisms needed for photoperiod induced endodormancy induction. To investigate this speciesspecific response, we first sought to establish a genome assembly for this nonmodel species. Sequencing and assembly of DNA from V. riparia resulted in 69,616 scaffolds at an N50 of 518,740. Reference, mapping, and nonhomologous estimates of misassembly suggest that this draft assembly is of a high quality. cDNA sequence prediction from multiple RNA-seq studies resulted in 40,019 genes. Variations in gene families demonstrated that there were genetic differences between V. riparia and V. vinifera which could explain the difference in response to photoperiod and winter survival. One of the best indicators in plants of the physiological response to external regulators is changes in gene expression. We measured changes in expression during endodormancy transition in two F2 genotypes at multiple time periods of exposure to short day (SD, 13h) and long day (LD, 15h) photoperiods. Expression of genes associated with cell cycle control and phenylpropanoid biosynthesis were downregulated in response to SD treatment. The F2-110 genotype which more closely resembled V. riparia had greater natural expression of auxin signaling genes than the F2-040. This was further confirmed by coexpression networks that were highly correlated with short day induced endodormancy transition and F2-110 genotypes. Regulation of endodormancy induction is a primary concern for this study. We performed small-RNA seq to find miRNA that were differentially regulated during dormancy transition. A machine learning based prediction of miRNA identified 216 regulatory sequences in the non-model V. riparia genome. We found that miRNA families 166 and 167 were predominantly upregulated during dormancy transition. This coincided with downregulation of cell cycle control genes and suppression of cyclins and expansins by the MYB3R1 transcription factor. Motif enrichment of gene co-expression clusters identified PLETHORA 1 as a major regulator of the stem cell state during dormant conditions. These results suggest that auxin is a major regulator of endodormancy through control of cell differentiation in the bud apical meristem. Auxin signaling may therefore also be a contributor to the enhanced dormancy response in V. riparia due to an increased sensitivity to auxin in the buds. Further research is needed to determine auxin’s role in regulation of the process of endodormancy and what effect it has in crop winter survival

The State of Applying Artificial Intelligence to Tissue Imaging for Cancer Research and Early Detection

Artificial intelligence represents a new frontier in human medicine that could save more lives and reduce the costs, thereby increasing accessibility. As a consequence, the rate of advancement of AI in cancer medical imaging and more particularly tissue pathology has exploded, opening it to ethical and technical questions that could impede its adoption into existing systems. In order to chart the path of AI in its application to cancer tissue imaging, we review current work and identify how it can improve cancer pathology diagnostics and research. In this review, we identify 5 core tasks that models are developed for, including regression, classification, segmentation, generation, and compression tasks. We address the benefits and challenges that such methods face, and how they can be adapted for use in cancer prevention and treatment. The studies looked at in this paper represent the beginning of this field and future experiments will build on the foundations that we highlight

Corporealities of violence in Southern and Eastern Africa

no abstract availabl

ISLES 2015 - A public evaluation benchmark for ischemic stroke lesion segmentation from multispectral MRI

Ischemic stroke is the most common cerebrovascular disease, and its diagnosis, treatment, and study relies on non-invasive imaging. Algorithms for stroke lesion segmentation from magnetic resonance imaging (MRI) volumes are intensely researched, but the reported results are largely incomparable due to different datasets and evaluation schemes. We approached this urgent problem of comparability with the Ischemic Stroke Lesion Segmentation (ISLES) challenge organized in conjunction with the MICCAI 2015 conference. In this paper we propose a common evaluation framework, describe the publicly available datasets, and present the results of the two sub-challenges: Sub-Acute Stroke Lesion Segmentation (SISS) and Stroke Perfusion Estimation (SPES). A total of 16 research groups participated with a wide range of state-of-the-art automatic segmentation algorithms. A thorough analysis of the obtained data enables a critical evaluation of the current state-of-the-art, recommendations for further developments, and the identification of remaining challenges. The segmentation of acute perfusion lesions addressed in SPES was found to be feasible. However, algorithms applied to sub-acute lesion segmentation in SISS still lack accuracy. Overall, no algorithmic characteristic of any method was found to perform superior to the others. Instead, the characteristics of stroke lesion appearances, their evolution, and the observed challenges should be studied in detail. The annotated ISLES image datasets continue to be publicly available through an online evaluation system to serve as an ongoing benchmarking resource (www.isles-challenge.org).Peer reviewe

Parasite fate and involvement of infected cells in the induction of CD4+ and CD8+ T cell responses to Toxoplasma gondii

During infection with the intracellular parasite Toxoplasma gondii, the presentation of parasite-derived antigens to CD4+ and CD8+ T cells is essential for long-term resistance to this pathogen. Fundamental questions remain regarding the roles of phagocytosis and active invasion in the events that lead to the processing and presentation of parasite antigens. To understand the most proximal events in this process, an attenuated non-replicating strain of T. gondii (the cpsII strain) was combined with a cytometry-based approach to distinguish active invasion from phagocytic uptake. In vivo studies revealed that T. gondii disproportionately infected dendritic cells and macrophages, and that infected dendritic cells and macrophages displayed an activated phenotype characterized by enhanced levels of CD86 compared to cells that had phagocytosed the parasite, thus suggesting a role for these cells in priming naïve T cells. Indeed, dendritic cells were required for optimal CD4+ and CD8+ T cell responses, and the phagocytosis of heat-killed or invasion-blocked parasites was not sufficient to induce T cell responses. Rather, the selective transfer of cpsII-infected dendritic cells or macrophages (but not those that had phagocytosed the parasite) to naïve mice potently induced CD4+ and CD8+ T cell responses, and conferred protection against challenge with virulent T. gondii. Collectively, these results point toward a critical role for actively infected host cells in initiating T. gondii-specific CD4+ and CD8+ T cell responses

Pratos e mais pratos: louças domésticas, divisões culturais e limites sociais no Rio de Janeiro, século XIX

Reply to ten comments on a paper published in the last issue of this journal. The discussion follows along six main lines: History museums, identity, ideology and the category of nation; the need of material collections and their modalities: patrimonial, operational, virtual; theater versus laboratory; visitors and their ambiguities; Public History: the museum and the academy.Resposta aos comentários de dez especialistas que contribuíram no debate de texto publicado no último número desta revista. A discussão orientou-se segundo seis tópicos principais: museus históricos, identidade, ideologia e a categoria de nação; a necessidade de acervos materiais e suas modalidades: acervo patrimonial, operacional, virtual; teatro versus laboratório; o público e suas ambigüidades; História Pública: o museu e a Academia

Transcriptome Analysis of the Heritable Salt Tolerance of Prairie Cordgrass (Spartina pectinata Link)

The salt-tolerant capability of the candidate bioenergy crop prairie cordgrass greatly surpasses that of previously characterized prairie grass species and most other plants. To understand the mechanism of inherited salt tolerance, we compared phenotypic and genetic qualities in half-sib families of prairie cordgrass after salt treatment. Each family was treated with a 400 mM NaCl solution or a water control and then measured for various health phenotypes. Phenotypes associated with salt tolerance were shown to be moderately heritable between parent and offspring. RNA-seq analysis revealed differential regulation in unique pathways including metabolism, signaling, photosynthesis, and the circadian rhythm. The studies herein suggest that alternative regulation of the photosynthetic pathway could confer increased salt resistance in halophytes and can be monitored phenotypically or genetically in breeding programs. The improvement of salt-tolerant traits in prairie cordgrass would increase its potential to be grown as a bioenergy crop on lands that are not suitable for the growth of food crops