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High-throughput phenotyping is emerging as an important technology to dissect phenotypic components in plants. Efficient image processing and feature extraction are prerequisites to quantify plant growth and performance based on phenotypic traits. Issues include data management, image analysis, and result visualization of large-scale phenotypic data sets. Here, we present Integrated Analysis Platform (IAP), an open-source framework for high-throughput plant phenotyping. IAP provides user-friendly interfaces, and its core functions are highly adaptable. Our system supports image data transfer from different acquisition environments and large-scale image analysis for different plant species based on real-time imaging data obtained from different spectra. Due to the huge amount of data to manage, we utilized a common data structure for efficient storage and organization of data for both input data and result data. We implemented a block-based method for automated image processing to extract a representative list of plant phenotypic traits. We also provide tools for build-in data plotting and result export. For validation of IAP, we performed an example experiment that contains 33 maize (Zea mays ‘Fernandez’) plants, which were grown for 9 weeks in an automated greenhouse with nondestructive imaging. Subsequently, the image data were subjected to automated analysis with the maize pipeline implemented in our system. We found that the computed digital volume and number of leaves correlate with our manually measured data in high accuracy up to 0.98 and 0.95, respectively. In summary, IAP provides a multiple set of functionalities for import/export, management, and automated analysis of high-throughput plant phenotyping data, and its analysis results are highly reliable.Plant bioinformatics faces the challenge of integrating information from the related “omics” fields to elucidate the functional relationship between genotype and observed phenotype (Edwards and Batley, 2004), known as the genotype-phenotype map (Houle et al., 2010). One of the main obstacles is our currently limited ability of systemic depiction and quantification of plant phenotypes, representing the so-called phenotyping bottleneck phenomenon (Furbank and Tester, 2011). To get a comprehensive genotype-phenotype map, more accurate and precise phenotyping strategies are required to empower high-resolution linkage mapping and genome-wide association studies in order to uncover underlying genetic variants associated with complex phenotypic traits, which aim to improve the efficiency, effectiveness, and economy of cultivars in plant breeding (Cobb et al., 2013). In the era of phenomics, automatic high-throughput phenotyping in a noninvasive manner is applied to identify and quantify plant phenotypic traits. Plants are bred in fully automated greenhouses under predefined environmental conditions with controlled temperature, watering, and humidity. To meet the demand of data access, exchange, and sharing, several phenomics-related projects in the context of several consortia have been launched, such as the International Plant Phenotyping Network (http://www.plantphenomics.com/), the European Plant Phenotyping Network (http://www.plant-phenotyping-network.eu/), and the German Plant Phenotyping Network (http://www.dppn.de/).Thanks to the development of new imaging and transport systems, various automated or semiautomated high-throughput plant phenotyping systems are being developed and used to examine plant function and performance under controlled conditions. PHENOPSIS (Granier et al., 2006) is one of the pioneering platforms that was developed to dissect genotype-environment effects on plant growth in Arabidopsis (Arabidopsis thaliana). GROWSCREEN (Walter et al., 2007; Biskup et al., 2009; Jansen et al., 2009; Nagel et al., 2012) was designed for rapid optical phenotyping of different plant species with respect to different biological aspects. Other systems in the context of high-throughput phenotyping include Phenodyn/Phenoarch (Sadok et al., 2007), TraitMill (Reuzeau et al., 2005; Reuzeau, 2007), Phenoscope (Tisné et al., 2013), RootReader3D (Clark et al., 2011), GROW Map (http://www.fz-juelich.de/ibg/ibg-2/EN/methods_jppc/methods_node.html), and LemnaTec Scanalyzer 3D. These developments enable the phenotyping of specific organs (e.g. leaf, root, and shoot) or of whole plants. Some of them are even used for three-dimensional plant analysis (Clark et al., 2011). Consequently, several specific software applications (a comprehensive list can be found at http://www.phenomics.cn/links.php), such as HYPOTrace (Wang et al., 2009), HTPheno (Hartmann et al., 2011), LAMINA (Bylesjö et al., 2008), PhenoPhyte (Green et al., 2012), Rosette Tracker (De Vylder et al., 2012), LeafAnalyser (Weight et al., 2008), RootNav (Pound et al., 2013), SmartGrain (Tanabata et al., 2012), and LemnaGrid, were designed to extract a wide range of measurements, such as height/length, width, shape, projected area, digital volume, compactness, relative growth rate, and colorimetric analysis.The huge amount of generated image data from various phenotyping systems requires appropriate data management as well as an appropriate analytical framework for data interpretation (Fiorani and Schurr, 2013). However, most of the developed image-analysis tools are designed for a specific task, for specific plant species, or are not freely available to the research community. They lack flexibility in terms of needed adaptations to meet new analysis requirements. For example, it would be desirable that a system could handle imaging data from different sources (either from fully automated high-throughput phenotyping systems or from setups where images are acquired manually), different imaging modalities (fluorescence, near-infrared, and thermal imaging), and/or different species (wheat [Triticum aestivum], barley [Hordeum vulgare], maize [Zea mays], and Arabidopsis).In this work, we present Integrated Analysis Platform (IAP), a scalable open-source framework, for high-throughput plant phenotyping data processing. IAP handles different image sources and helps to organize phenotypic data by retaining the metadata from the input in the result data set. In order to measure phenotypic traits in new or modified setups, users can easily create new analysis pipelines or modify the predefined ones. IAP provides various user-friendly interfaces at different system levels to meet the demands of users (e.g. software developers, bioinformaticians, and biologists) with different experiences in software programming. 相似文献
3.
Clustered regularly interspaced short palindromic repeat (CRISPR) and CRISPR-associated (cas) genes constitute the adaptive immune system in bacteria and archaea. Although the CRISPR-Cas systems have been hypothesized to encode potential toxins, no experimental data supporting the hypothesis are available in the literature. In this work, we provide the first experimental evidence for the presence of a toxin gene in the type I-A CRISPR system of hyperthermophilic archaeon Sulfolobus. csa5, under the control of its native promoter in a shuttle vector, could not be transformed into CRISPR-deficient mutant Sulfolobus solfataricus Sens1, demonstrating a strong toxicity in the cells. A single-amino-acid mutation destroying the intersubunit bridge of Csa5 attenuated the toxicity, indicative of the importance of Csa5 oligomerization for its toxicity. In line with the absence of Csa5 toxicity in S. solfataricus InF1 containing functional CRISPR systems, the expression of csa5 is repressed in InF1 cells. Induced from the arabinose promoter in Sens1 cells, Csa5 oligomers resistant to 1% SDS co-occur with chromosome degradation and cell death, reinforcing the connection between Csa5 oligomerization and its toxicity. Importantly, a rudivirus was shown to induce Csa5 expression and the formation of SDS-resistant Csa5 oligomers in Sulfolobus cells. This demonstrates that the derepression of csa5 and the subsequent Csa5 oligomerization take place in native virus-host systems. Thus, csa5 is likely to act as a suicide gene under certain circumstances to inhibit virus spreading. 相似文献
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Liuji Chen William Sealy Hambright Ren Na Qitao Ran 《The Journal of biological chemistry》2015,290(47):28097-28106
Glutathione peroxidase 4 (GPX4), an antioxidant defense enzyme active in repairing oxidative damage to lipids, is a key inhibitor of ferroptosis, a non-apoptotic form of cell death involving lipid reactive oxygen species. Here we show that GPX4 is essential for motor neuron health and survival in vivo. Conditional ablation of Gpx4 in neurons of adult mice resulted in rapid onset and progression of paralysis and death. Pathological inspection revealed that the paralyzed mice had a dramatic degeneration of motor neurons in the spinal cord but had no overt neuron degeneration in the cerebral cortex. Consistent with the role of GPX4 as a ferroptosis inhibitor, spinal motor neuron degeneration induced by Gpx4 ablation exhibited features of ferroptosis, including no caspase-3 activation, no TUNEL staining, activation of ERKs, and elevated spinal inflammation. Supplementation with vitamin E, another inhibitor of ferroptosis, delayed the onset of paralysis and death induced by Gpx4 ablation. Also, lipid peroxidation and mitochondrial dysfunction appeared to be involved in ferroptosis of motor neurons induced by Gpx4 ablation. Taken together, the dramatic motor neuron degeneration and paralysis induced by Gpx4 ablation suggest that ferroptosis inhibition by GPX4 is essential for motor neuron health and survival in vivo. 相似文献
6.
Chu-Fang Chou Xiaolin Zhu Yi-Yu Lin Karen L. Gamble W. Timothy Garvey Ching-Yi Chen 《Journal of lipid research》2015,56(2):227-240
Hepatic lipid metabolism is controlled by integrated metabolic pathways. Excess accumulation of hepatic TG is a hallmark of nonalcoholic fatty liver disease, which is associated with obesity and insulin resistance. Here, we show that KH-type splicing regulatory protein (KSRP) ablation reduces hepatic TG levels and diet-induced hepatosteatosis. Expression of period 2 (Per2) is increased during the dark period, and circadian oscillations of several core clock genes are altered with a delayed phase in Ksrp−/− livers. Diurnal expression of some lipid metabolism genes is also disturbed with reduced expression of genes involved in de novo lipogenesis. Using primary hepatocytes, we demonstrate that KSRP promotes decay of Per2 mRNA through an RNA-protein interaction and show that increased Per2 expression is responsible for the phase delay in cycling of several clock genes in the absence of KSRP. Similar to Ksrp−/− livers, both expression of lipogenic genes and intracellular TG levels are also reduced in Ksrp−/− hepatocytes due to increased Per2 expression. Using heterologous mRNA reporters, we show that the AU-rich element-containing 3′ untranslated region of Per2 is responsible for KSRP-dependent mRNA decay. These findings implicate that KSRP is an important regulator of circadian expression of lipid metabolism genes in the liver likely through controlling Per2 mRNA stability. 相似文献
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The septins FaCdc3 and FaCdc12 are required for cytokinesis and affect asexual and sexual development,lipid metabolism and virulence in Fusarium asiaticum 下载免费PDF全文
Yu Zhang Tao Gao Wenyong Shao Zhitian Zheng Mingguo Zhou Changjun Chen 《Molecular Plant Pathology》2017,18(9):1282-1294
Septins are a highly conserved family of GTP‐binding proteins that contribute to many cellular and metabolic functions, including cell polarity, cytokinesis, cell morphogenesis and pathogenesis. In this study, we characterized the septins FaCdc3 and FaCdc12 in the filamentous fungus Fusarium asiaticum. The functions of FaCdc3 and FaCdc12 were evaluated by constructing deletion mutants of FaCdc3 and FaCdc12, designated ΔFaCdc3‐5 and ΔFaCdc12‐71, respectively. The deletion mutants exhibited a reduced rate of mycelial growth, increased aerial hyphae formation, irregularly shaped hyphae, reduced conidiation and a lack of sexual reproduction in wheat kernels. Histochemical analysis revealed that the conidia and hyphae of ΔFaCdc3‐5 and ΔFaCdc12‐71 formed large lipid droplets (LDs). ΔFaCdc3‐5 and ΔFaCdc12‐71 also exhibited increased resistance to agents that induce osmotic stress and damage the cell membrane and cell wall. In addition, the hyphae and conidia of the two mutants formed fewer septa than those of the wild‐type and exhibited aberrant nuclear distribution. Pathogenicity assays showed that ΔFaCdc3‐5 and ΔFaCdc12‐71 exhibited reduced virulence on wheat spikelets, which was indirectly correlated with a reduced level of deoxynivalenol accumulation. All of these defects were restored by genetic complementation of the two mutants with the parental FaCdc3 and FaCdc12. These results indicate that FaCdc3 and FaCdc12 play a critical role in various cellular processes in F. asiaticum. 相似文献
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LncRNA MALAT1 is dysregulated in diabetic nephropathy and involved in high glucose‐induced podocyte injury via its interplay with β‐catenin 下载免费PDF全文
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Da Huang Xiaohong Du Rongfa Yuan Leifeng Chen Tiande Liu Chongyu Wen Mingwen Huang Ming Li Liang Hao Jianghua Shao 《Biochemical and biophysical research communications》2014
Rho-associated coiled-coil-containing protein kinase 2 (Rock2) is a downstream effector of Rho that plays an important role in the tumorigenesis and progression of hepatocellular carcinoma (HCC). Matrix metalloproteinase 2 (MMP2) is a master regulator of tumor metastasis. In this study, we investigated the collections of Rock2 and MMP2 in HCCs and determined the potential role and molecular mechanism of Rock2 in MMP2-mediated invasiveness and metastasis. We found that Rock2 and MMP2 were markedly overexpressed in HCCs compared with the corresponding adjacent tissues, where a positive correlation in their expression was found. The knockdown of Rock2 significantly decreased MMP2 expression and inhibited the invasion and metastasis of HCC in vitro and in vivo. Additionally, the upregulation of MMP2 rescued the decreased migration and invasion induced by the knockdown of Rock2, whereas the knockdown of MMP2 decreased Rock2-enhanced HCC migration and invasion. Mechanistically, Rock2 stabilized MMP2 by preventing its ubiquitination and degradation. Together, our results link two drivers of invasion and metastasis in HCC and identify a novel pathway for MMP2 control. 相似文献