Genome-wide gene phylogeny of CIPK family in cassava and expression analysis of partial drought-induced genes

Cassava is an important food and potential biofuel crop that is tolerant to multiple abiotic stressors. The mechanisms underlying these tolerances are currently less known. CBL-interacting protein kinases (CIPKs) have been shown to play crucial roles in plant developmental processes, hormone signaling transduction, and in the response to abiotic stress. However, no data is currently available about the CPK family in cassava. In this study, a total of 25 CIPK genes were identified from cassava genome based on our previous genome sequencing data. Phylogenetic analysis suggested that 25 MeCIPKs could be classified into four subfamilies, which was supported by exon-intron organizations and the architectures of conserved protein motifs. Transcriptomic analysis of a wild subspecies and two cultivated varieties showed that most MeCIPKs had different expression patterns between wild subspecies and cultivatars in different tissues or in response to drought stress. Some orthologous genes involved in CIPK interaction networks were identified between Arabidopsis and cassava. The interaction networks and co-expression patterns of these orthologous genes revealed that the crucial pathways controlled by CIPK networks may be involved in the differential response to drought stress in different accessions of cassava. Nine MeCIPK genes were selected to investigate their transcriptional response to various stimuli and the results showed the comprehensive response of the tested MeCIPK genes to osmotic, salt, cold, oxidative stressors, and ABA signaling. The identification and expression analysis of CIPK family suggested that CIPK genes are important components of development and multiple signal transduction pathways in cassava. The findings of this study will help lay a foundation for the functional characterization of the CIPK gene family and provide an improved understanding of abiotic stress responses and signaling transduction in cassava

Switchable Catalytic DNA Catenanes

Two-ring interlocked DNA catenanes are synthesized and characterized. The supramolecular catenanes show switchable cyclic catalytic properties. In one system, the catenane structure is switched between a hemin/G-quadruplex catalytic structure and a catalytically inactive state. In the second catenane structure the catenane is switched between a catalytically active Mg²⁺-dependent DNAzyme-containing catenane and an inactive catenane state. In the third system, the interlocked catenane structure is switched between two distinct catalytic structures that include the Mg²⁺- and the Zn²⁺-dependent DNAzymes

Electrogenerated ChemiluminescenceProtocols and Applications /

XIII, 152 p. 54 illus., 22 illus. in color.onlin

Hairpin-structured probe conjugated nano-graphene oxide for the cellular detection of connective tissue growth factor mRNA

Identification of abnormal scars at their early stage has attracted increasing attentions as the scars can only be assessed qualitatively and subjectively upon maturity, when no invasive procedure is involved. This report introduces a fluorescent probe that targets a potential abnormal scar biomarker (connective tissue growth factor (CTGF) mRNA) in skin fibroblasts. This probe is constructed of hairpin-structured probes (HPs) targeting CTGF mRNA and the nano-graphene oxide (nano-GO) base. The HPs are non-covalently absorbed on the surface of nano-GO, which pre-quenches the fluorescence of HPs. Close proximity of complementary CTGF mRNA would lead to preferential HP hybridization and dissociation from nano-GO, which restores the fluorescence signal from HPs. Utilizing this probe, we can distinguish abnormal fibroblasts derived from abnormal scars and assess the effectiveness of anti-scarring drugs like Repsox and transforming growth factor-beta type I receptor (TGF-βRI) siRNA.ASTAR (Agency for Sci., Tech. and Research, S’pore)MOE (Min. of Education, S’pore)Accepted versio

Dual Switchable CRET-Induced Luminescence of CdSe/ZnS Quantum Dots (QDs) by the Hemin/G-Quadruplex-Bridged Aggregation and Deaggregation of Two-Sized QDs

The hemin/G-quadruplex-catalyzed generation of chemiluminescence through the oxidation of luminol by H₂O₂ stimulates the chemiluminescence resonance energy transfer (CRET) to CdSe/ZnS quantum dots (QDs), resulting in the luminescence of the QDs. By the cyclic K⁺-ion-induced formation of the hemin/G-quadruplex linked to the QDs, and the separation of the G-quadruplex in the presence of 18-crown-6-ether, the ON-OFF switchable CRET-induced luminescence of the QDs is demonstrated. QDs were modified with nucleic acids consisting of the G-quadruplex subunits sequences and of programmed domains that can be cross-linked through hybridization, using an auxiliary scaffold. In the presence of K⁺-ions, the QDs aggregate through the cooperative stabilization of K⁺-ion-stabilized G-quadruplex bridges and duplex domains between the auxiliary scaffold and the nucleic acids associated with the QDs. In the presence of 18-crown-6-ether, the K⁺-ions are eliminated from the G-quadruplex units, leading to the separation of the aggregated QDs. By the cyclic treatment of the QDs with K⁺-ions/18-crown-6-ether, the reversible aggregation/deaggregation of the QDs is demonstrated. The incorporation of hemin into the K⁺-ion-stabilized G-quadruplex leads to the ON-OFF switchable CRET-stimulated luminescence of the QDs. By the mixing of appropriately modified two-sized QDs, emitting at 540 and 610 nm, the dual ON-OFF activation of the luminescence of the QDs is demonstrated

Topoisomerase-Based Preparation and AFM Imaging of Multi-Interlocked Circular DNA

Multi-interlocked circular DNA structures have been in high demand for fabricating complicated functional DNA architectures and nanodevices such as molecular switches, shuttles, and motors. Even though various innovative methods have been developed in the past, creation of multi-interlocked circular DNA structures with defined numbers of DNA molecules and linking patterns is still a challenging task nowadays. Here, we propose a top-down decatenation of kinetoplast DNA as a new approach for creating multi-interlocked circular DNA structures. Through optimizing the amount and reaction time of topoisomerase II, we synthesized completely mutually interlocked tricircular, tetra-circular, and oligo-circular DNA structures, which have not yet been acquirable through any other existing synthetic means. The catenation structures of multiple circular DNA were further verified through atomic force microscopic analysis of the backbone overlapping patterns and the circumference. It accordingly is our expectation that the top-down enzymatic approaches could offer a highly interlocked network with defined numbers of circular DNA with simple protocols, and could consequently be beneficial to the design and fabrication of sophisticated functional molecules and nanodevices in the areas of supramolecular chemistry, DNA nanotechnology, and material science

Accelerating the Phosphatase-like Activity of Uio-66-NH₂ by Catalytically Inactive Metal Ions and Its Application for Improved Fluorescence Detection of Cardiac Troponin I

Compared with natural enzymes, nanozymes usually exhibit much lower catalytic activities, which limit the sensitivities of nanozyme-based immunoassays. Herein, several metal ions without enzyme-like activities were engineered onto Uio-66-NH2 nanozyme through postsynthetic modification. The obtained Mn+@Uio-66-NH2 (Mn+ = Zn2+, Cd2+, Co2+, Ca2+and Ni2+) exhibited improved phosphatase-like catalytic activities. In particular, a 12-fold increase in the catalytic efficiency (kcat/Km) of Uio-66-NH2 was observed after the modification with Zn2+. Mechanism investigations indicate that both the amino groups and oxygen-containing functional groups in Uio-66-NH2 are the binding sites of Zn2+, and the modified Zn2+ ions on Uio-66-NH2 serve as the additional catalytic sites for improving the catalytic performance. Furthermore, the highly active Zn2+@Uio-66-NH2 was used as a nanozyme label to develop a fluorescence immunoassay method for the detection of cardiac troponin I (cTnI). Compared with pristine Uio-66-NH2, Zn2+@Uio-66-NH2 can widen the linear range by 1 order of magnitude (from 10 pg/mL–1 μg/mL to 1 pg/mL–1 μg/mL) and also lower the detection limit by 5 times (from 4.7 pg/mL to 0.9 pg/mL)