Identification and functional characterisation of the promoter of the calcium sensor gene CBL1 from the xerophyte Ammopiptanthus mongolicus

<p>Abstract</p> <p>Background</p> <p><it>CBL1 </it>is a calcium sensor that regulates drought, cold and salt signals in <it>Arabidopsis</it>. Overexpression of <it>CBL1 </it>gene in <it>Arabidopsis </it>and in <it>Ammopiptanthus mongolicus </it>showed different tolerant activities. We are interested in understanding the molecular mechanism of the upstream region of the <it>CBL1 </it>gene of <it>A. mongolicus </it>(<it>AmCBL1</it>). We investigated and characterized the promoter of the <it>AmCBL1 </it>gene, for promoters play a very important role in regulating gene expression in eukaryotes.</p> <p>Results</p> <p>A 1683-bp 5' flanking region was isolated from <it>A. mongolicus</it>. The sequence was identified as <it>AmCBL1 </it>promoter. Analysis of the promoter sequence indicated a 690-bp intron and some basic cis-acting elements were related to various environmental stresses and plant hormones. To identify the functional region of the <it>AmCBL1 </it>promoter, five plant expression vectors fused with the GUS (β-glucuronidase) gene, driven by series deleted fragments of <it>AmCBL1 </it>promoter at different lengths from -1659, -1414, -1048, -296 to -167 bp relative to the transcriptional start site were constructed and transformed into <it>Nicotiana tabacum </it>L. cv. 89. Functional properties of each promoter segment were examined by GUS staining and fluorescence quantitative analyses using at least three single-copy PCR-positive plants of transgenic tobacco, treated with various environmental stresses and plant hormones for different times. We demonstrated that the <it>AmCBL1 </it>promoter was a vascular-specific and multiple-stress-inducible promoter. Our results further imply that the promoter fragment B1S3 possessed sufficient essential cis-acting elements, accounting for vascular-specific and stress-induced expression patterns. It may also indicate that for response to some stresses certain cis-elements are required in tissues outside the region of the B1S3 construct.</p> <p>Conclusions</p> <p>To help resolve uncertainties about the upstream regulatory mechanism of the <it>CBL1 </it>gene in desert plants, we suggest that the function of the <it>AmCBL1 </it>promoter, particularly under conditions of abiotic stress, to be examined for possible usefulness in molecular breeding. Regardless of the outcome, the allocation and relative quantification of the GUS-fusion <it>AmCBL1 </it>promoter segments at transcriptional levels in different tissues under various stresses across separate promoter segments suggests that the <it>AmCBL1 </it>promoter is a phloem-specific and multiple-stress-inducible promoter. These data coupled with the ongoing <it>AmCBL1 </it>5' UTR intron analyses provide a solid foundation for their future use in molecular breeding as new promoters of stress-resistance genes from desert plants.</p

High impact bug report identification with imbalanced learning strategies

Supplementary code and data available from GitHub: https://github.com/goddding/JCST</p

Populus trichocarpa PtNF-YA9, A Multifunctional Transcription Factor, Regulates Seed Germination, Abiotic Stress, Plant Growth and Development in Arabidopsis

NF-YAs play important roles in abiotic stress. However, their characteristics and functions in abiotic stress of poplar, a model woody plant, have not been fully investigated. Here, the biological functions of PtNF-YA9 (Potri.011G101000), an NF-YA gene from Populus trichocarpa, were first fully investigated. PtNF-YA9 is located in the nucleus. The expression of PtNF-YA9 was reduced by mannitol, NaCl, and abscisic acid (ABA). The GUS staining of ProNF-YA9::GUS transgenic lines was also reduced by mannitol treatments. In the PtNF-YA9-overexpressed Arabidopsis (OxPtNA9), OxPtNA9 lines exhibited sensitivity to simulated drought, ABA, and salinity stress during germination stage, and growth arrest emerged at post-germination stage. These phenomena might involve the ABA signaling pathway via the regulation of ABI3, ABI4, and ABI5. At vegetative stages, OxPtNA9 lines decreased in water loss via promoting stomatal closure and displayed high instantaneous water-use efficiency (WUE) of the leaf to exhibit enhanced drought tolerance. Furthermore, OxPtNA9 lines exhibited long primary root in the half-strength Murashige–Skoog agar medium supplemented with NaCl and conferred strong tolerance in the soil under salt stress. Additionally, PtNF-YA9 exhibited dwarf phenotype, short hypocotyl, small leaf area and biomass, delayed flowering, and increased chlorophyll content. Above all, our research proposes a model in which PtNF-YA9 not only plays a key role in reducing plant growth but also can play a primary role in the mechanism of an acclimatization strategy in response to adverse environmental conditions

Characterizing malicious Android apps by mining topic-specific data flow signatures

Context: State-of-the-art works on automated detection of Android malware have leveraged app descriptions to spot anomalies w.r.t the functionality implemented, or have used data flow information as a feature to discriminate malicious from benign apps. Although these works have yielded promising performance, we hypothesize that these performances can be improved by a better understanding of malicious behavior. Objective: To characterize malicious apps, we take into account both information on app descriptions, which are indicative of apps’ topics, and information on sensitive data flow, which can be relevant to discriminate malware from benign apps. Method: In this paper, we propose a topic-specific approach to malware comprehension based on app descriptions and data-flow information. First, we use an advanced topic model, adaptive LDA with GA, to cluster apps according to their descriptions. Then, we use information gain ratio of sensitive data flow information to build so-called “topic-specific data flow signatures”. Results: We conduct an empirical study on 3691 benign and 1612 malicious apps. We group them into 118 topics and generate topic-specific data flow signature. We verify the effectiveness of the topic-specific data flow signatures by comparing them with the overall data flow signature. In addition, we perform a deeper analysis on 25 representative topic-specific signatures and yield several implications. Conclusion: Topic-specific data flow signatures are efficient in highlighting the malicious behavior, and thus can help in characterizing malware