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

Genetic and functional characterization of disease associations explains comorbidity

Understanding relationships between diseases, such as comorbidities, has important socio-economic implications, ranging from clinical study design to health care planning. Most studies characterize disease comorbidity using shared genetic origins, ignoring pathway-based commonalities between diseases. In this study, we define the disease pathways using an interactome-based extension of known disease-genes and introduce several measures of functional overlap. The analysis reveals 206 significant links among 94 diseases, giving rise to a highly clustered disease association network. We observe that around 95% of the links in the disease network, though not identified by genetic overlap, are discovered by functional overlap. This disease network portraits rheumatoid arthritis, asthma, atherosclerosis, pulmonary diseases and Crohn's disease as hubs and thus pointing to common inflammatory processes underlying disease pathophysiology. We identify several described associations such as the inverse comorbidity relationship between Alzheimer's disease and neoplasms. Furthermore, we investigate the disruptions in protein interactions by mapping mutations onto the domains involved in the interaction, suggesting hypotheses on the causal link between diseases. Finally, we provide several proof-of-principle examples in which we model the effect of the mutation and the change of the association strength, which could explain the observed comorbidity between diseases caused by the same genetic alterations

Dynamic electro-optic response of graphene/graphitic flakes in nematic liquid crystals

Electric field induced dynamic reorientation phenomenon of graphene/graphitic flakes in homogeneously aligned nematic liquid crystal (NLC) medium has been demonstrated by optical microscopy. The flakes reorient from parallel to perpendicular configuration with respect to boundary plates of confining cells for an applied field strength of as low as tens of millivolt per micrometer. After field removal the reoriented flakes recover to their initial state with the help of relaxation of NLC. Considering flake reorientation phenomenon both in positive and negative dielectric anisotropy NLCs, the reorientation process depends on interfacial Maxwell-Wagner polarization and NLC director reorientation. We propose a phenomenological model based on electric field induced potential energy of graphitic flakes and coupling contribution of positive NLC to generate the rotational kinetic energy for flake reorientation. The model successfully explains the dependence of flake reorientation time over flake shape anisotropy, electric-field strength, and flake area. Using present operating scheme it is possible to generate dark field-off state and bright field-on state, having application potential for electro-optic light modulation devices. (C) 2013 Optical Society of Americ

Dynamic Response of Graphitic Flakes in Nematic Liquid Crystals: Confinement and Host Effect

Electric field-induced reorientation of suspended graphitic (GP) flakes and its relaxation back to the original state in a nematic liquid crystal (NLC) host are of interest not only in academia, but also in industrial applications, such as polarizer-free and optical film-free displays, and electro-optic light modulators. As the phenomenon has been demonstrated by thorough observation, the detailed study of the physical properties of the host NLC (the magnitude of dielectric anisotropy, elastic constants, and rotational viscosity), the size of the GP flakes, and cell thickness, are urgently required to be explored and investigated. Here, we demonstrate that the response time of GP flakes reorientation associated with an NLC host can be effectively enhanced by controlling the physical properties. In a vertical field-on state, higher dielectric anisotropy and higher elasticity of NLC give rise to quicker reorientation of the GP flakes (switching from planar to vertical alignment) due to the field-induced coupling effect of interfacial Maxwell-Wagner polarization and NLC reorientation. In a field off-state, lower rotational viscosity of NLC and lower cell thickness can help to reduce the decay time of GP flakes reoriented from vertical to planar alignment. This is mainly attributed to strong coupling between GP flakes and NLC originating from the strong π-π interaction between benzene rings in the honeycomb-like graphene structure and in NLC molecules. The high-uniformity of reoriented GP flakes exhibits a possibility of new light modulation with a relatively faster response time in the switching process and, thus, it can show potential application in field-induced memory and modulation devices

Distribution and Mobility of Coseismic Landslides Triggered by the 2018 Hokkaido Earthquake in Japan

At 3:08 on 6 September 2018 (UTC +9), massive landslides were triggered by an earthquake of Mw 6.6 that occurred in Hokkaido, Japan. In this paper, a coseismic landslide inventory that covers 388 km2 of the earthquake-impacted area and includes 5828 coseismic landslides with a total landslide area of 23.66 km2 was compiled by using visual interpretations of various high-resolution satellite images. To analyze the spatial distribution and characteristics of coseismic landslides, five factors were considered: the peak ground acceleration (PGA), elevation, slope gradient, slope aspect, and lithology. Results show more than 87% of the landslides occurred at 100 to 200 m elevations. Slopes in the range of 10~20°are the most susceptible to failure. The landslide density of the places with peak ground acceleration (PGA) greater than 0.16 g is obviously larger than those with PGA less than 0.02 g. Compared with the number and scale of coseismic landslides caused by other strong earthquakes and the mobility of the coseismic landslides caused by the Haiyan and Wenchuan earthquakes, it was found that the distribution of coseismic landslides was extremely dense and that the mobility of the Hokkaido earthquake was greater than that of the Wenchuan earthquake and weaker than that of the Haiyuan earthquake, and is described by the following relationship: L = 18.454 ∗ H0.612. Comparative analysis of coseismic landslides with similar magnitude has important guiding significance for disaster prevention and reduction and reconstruction planning of landslides in affected areas

Comparative Transcriptional Analysis of Two Contrasting Rice Genotypes in Response to Salt Stress

Improving rice salt-tolerance is an effective way to deal with the increasing food demand caused by soil salinization and population growth. Nevertheless, the molecular mechanisms of rice salt-tolerance remain elusive. In this study, comparative transcriptomic analyses were performed to identify salt-tolerance genes that were either specifically regulated or more changed in salt-tolerant cultivar FL478 relative to salt-sensitive cultivar 93-11. In total, 1423, 175, and 224 salt-tolerance genes were identified under 200 mM NaCl treatment for 6 h, 24 h, and 72 h, respectively. These genes were commonly enriched in transport and peroxidase/oxidoreductase activity across all timepoints, but specially enriched in transcription regulator activity at 6 h under salt stress. Further analysis revealed that 53 transporters, 38 transcription factors (TFs), and 23 reactive oxygen species (ROS) scavenging enzymes were involved in salt adaptation of FL478, and that overall, these salt-tolerance genes showed a faster transcriptional expression response in FL478 than in 93-11. Finally, a gene co-expression network was constructed to highlight the regulatory relationships of transporters, TFs, and ROS scavenging genes under salt-stress conditions. This work provides an overview of genome-wide transcriptional analysis of two contrasting rice genotypes in response to salt stress. These findings imply a crucial contribution of quickly transcriptional changes to salt tolerance and provide useful genes for genetic improvement of salt tolerance in rice

The Late Embryogenesis Abundant Protein Family in Cassava (Manihot esculenta Crantz): Genome-Wide Characterization and Expression during Abiotic Stress

Late embryogenesis abundant (LEA) proteins, as a highly diverse group of polypeptides, play an important role in plant adaptation to abiotic stress; however, LEAs from cassava have not been studied in cassava. In this study, 26 LEA members were genome-wide identified from cassava, which were clustered into seven subfamily according to evolutionary relationship, protein motif, and gene structure analyses. Chromosomal location and duplication event analyses suggested that 26 MeLEAs distributed in 10 chromosomes and 11 MeLEA paralogues were subjected to purifying selection. Transcriptomic analysis showed the expression profiles of MeLEAs in different tissues of stem, leaves, and storage roots of three accessions. Comparative transcriptomic analysis revealed that the function of MeLEAs in response to drought may be differentiated in different accessions. Compared with the wild subspecies W14, more MeLEA genes were activated in cultivated varieties Arg7 and SC124 after drought treatment. Several MeLEA genes showed induction under various stresses and related signaling treatments. Taken together, this study demonstrates the transcriptional control of MeLEAs in tissue development and the responses to abiotic stress in cassava and identifies candidate genes for improving crop resistance to abiotic stress

The Class III Peroxidase (POD) Gene Family in Cassava: Identification, Phylogeny, Duplication, and Expression

The class III peroxidase (POD) enzymes participate in plant development, hormone signaling, and stress responses. However, little is known about the POD family in cassava. Here, we identified 91 cassava POD genes (MePODs) and classified them into six subgroups using phylogenetic analysis. Conserved motif analysis demonstrated that all MePOD proteins have typical peroxidase domains, and gene structure analysis showed that MePOD genes have between one and nine exons. Duplication pattern analysis suggests that tandem duplication has played a role in MePOD gene expansion. Comprehensive transcriptomic analysis revealed that MePOD genes in cassava are involved in the drought response and postharvest physiological deterioration. Several MePODs underwent transcriptional changes after various stresses and related signaling treatments were applied. In sum, we characterized the POD family in cassava and uncovered the transcriptional control of POD genes in response to various stresses and postharvest physiological deterioration conditions. These results can be used to identify potential target genes for improving the stress tolerance of cassava crops

Effects of carbon nanotubes on electro-optic characteristics in vertically aligned liquid crystal display

Size- and aggregation-controlled dispersion of thin multiwalled carbon nanotube (t-MWCNT) in negative dielectric anisotropic liquid crystal (LC) material exhibits remarkable improvement in electro-optic response time in vertically aligned LC cells. The physical properties such as birefringence, dielectric anisotropy and clearing temperature of nanotube dispersed LC material appear to be almost invariant to that of pristine LC. Nevertheless, the response time shows noticeable improvement, especially in decaying time associated with transition from maximum to minimum transmission, hence important for faster switching LC devices. The effect is attributed to that vertically aligned t-MWCNTs along the field direction play role of vertical alignment layer between LCs, consequently resulting in increased bend elastic constant of LCs.116181sciescopu