RNA-SEQ Assisted Gene Modeling and Annotation, Transcriptome Study and Functional Analysis of Stress Responsive Peptides of Manduca Sexta

Manduca sexta is a widely used model insect. The genome sequence was determined using 454 sequencing technology, and Official Gene Set (OGS) 2.0 was generated with help from RNA-seq data and manually annotation by researchers all over the world. To improve gene models, we developed methods to compare and select gene models by MAKER2, Cufflinks, Oases and Trinity, and generate a new gene set, called MCOT 1.0. Compared with OGS 2.0, MCOT 1.0 has higher quality score as evaluated by BUSCO, and with nearly 50% more unique proteins being predicted.The immune signaling pathways are critical for proper defense against pathogens for insects. To facilitate systematic studies of M. sexta immune system, we have identified and verified participant genes in the genome of M. sexta. We annotated 186 genes which encode 199 proteins in Toll, Imd, MAPK-JNK-p38, JAK-STAT, autophagy, apoptosis and RNA interference pathways, analyzed their evolution and mRNA levels in different tissues and different developmental stages. To date, 67 cDNA libraries have been sequenced from different tissues and different developing stages of M. sexta. However, there is no systematic analyzation of these RNA-seq data. We examined each library, found possible contaminant reads in each of these libraries, compared library similarity based on associated genes, and analyzed gene expression in different libraries. We found that most genes were expressed in library-specific manner, and their expression patterns would help functional study in the future.Stress Responsive Peptides (SRPs) are cytokines activated under biotic and abiotic stresses, which may act as key signaling molecules for humoral and neural regulation of immune or other responses. Eight SRPs were identified in the genome of M. sexta. With similar amino acid sequence, their functions are very different. SRP6 can inhibit the growth of larvae, while SRP1 and SRP2 can induce the expression of different anti-microbial peptides. We verified activation site of SRP1 and SRP2 with MALDI-MS, and identified PAP3 as the upstream enzyme which can activate them. This study will help understand the roles of insect cytokines.Biochemistry & Molecular Biolog

Inflating hollow nanocrystals through a repeated Kirkendall cavitation process.

The Kirkendall effect has been recently used to produce hollow nanostructures by taking advantage of the different diffusion rates of species involved in the chemical transformations of nanoscale objects. Here we demonstrate a nanoscale Kirkendall cavitation process that can transform solid palladium nanocrystals into hollow palladium nanocrystals through insertion and extraction of phosphorus. The key to success in producing monometallic hollow nanocrystals is the effective extraction of phosphorus through an oxidation reaction, which promotes the outward diffusion of phosphorus from the compound nanocrystals of palladium phosphide and consequently the inward diffusion of vacancies and their coalescence into larger voids. We further demonstrate that this Kirkendall cavitation process can be repeated a number of times to gradually inflate the hollow metal nanocrystals, producing nanoshells of increased diameters and decreased thicknesses. The resulting thin palladium nanoshells exhibit enhanced catalytic activity and high durability toward formic acid oxidation

Spin-dependent Andreev reflection tunneling through a quantum dot with intradot spin-flip scattering

We study Andreev reflection (AR) tunneling through a quantum dot (QD) connected to a ferromagnet and a superconductor, in which the intradot spin-flip interaction is included. By using the nonequibrium-Green-function method, the formula of the linear AR conductance is derived at zero temperature. It is found that competition between the intradot spin-flip scattering and the tunneling coupling to the leads dominantes resonant behaviours of the AR conductance versus the gate voltage.A weak spin-flip scattering leads to a single peak resonance.However, with the spin-flip scattering strength increasing, the AR conductance will develop into a double peak resonannce implying a novel structure in the tunneling spectrum of the AR conductance. Besides, the effect of the spin-dependent tunneling couplings, the matching of Fermi velocity, and the spin polarization of the ferromagnet on the AR conductance is eximined in detail.Comment: 14 pages, 4 figure

Experimental and Computational Validation and Verification of the Stokes-Darcy and Continuum Pipe Flow Models for Karst Aquifers with Dual Porosity Structure

In our previous study, we developed the Stokes-Darcy (SD) model was developed for flow in a karst aquifer with a conduit bedded in matrix, and the Beavers-Joseph (BJ) condition was used to describe the matrix-conduit interface. We also studied the mathematical well-posedness of a coupled continuum pipe flow (CCPF) model as well as convergence rates of its finite element approximation. in this study, to compare the SD model with the CCPF model, we used numerical analyses to validate finite element discretisation methods for the two models. using computational experiments, simulation codes implementing the finite element discretisations are then verified. Further model validation studies are based on the results of laboratory experiments. Comparing the results of computer simulations and experiments, we concluded that the SD model with the Beavers-Joseph interface condition is a valid model for conduit-matrix systems. on the other hand, the CCPF model with the value of the exchange parameter chosen within the range suggested in the literature perhaps does not result in good agreement with experimental observations. We then examined the sensitivity of the CCPF model with respect to the exchange parameter, concluding that, as has previously been noted, the model is highly sensitive for small values of the exchange parameter. However, for larger values, the model becomes less sensitive and, more important, also produces results that are in better agreement with experimental observations. This suggests that the CCPF model may also produce accurate simulation results, if one chooses larger values of the exchange parameter than those suggested in the literature. © 2011 John Wiley & Sons, Ltd

Plasmons in a two-dimensional nonsymmorphic nodal-line semimetal

Recent experiments have established a type of nonsymmorphic symmetry protected nodal lines in the family of two-dimensional (2D) composition tunable materials NbSi$_x$Te$_2$. Here, we theoretically study the plasmonic properties of such nonsymmorphic nodal-line semimetals. We show that the nonsymmorphic character endows the plasmons with extremely strong anisotropy. There exist both intraband and interband plasmon branches. The intraband branch is gapless and has a $q^{1/2}$ dispersion. It is most dispersive and is independent of carrier density in direction normal to the nodal line, whereas along the nodal line, its dispersion is largely suppressed and its frequency scales linearly with carrier density. The interband branches are gapped and their long wavelength limits are connected with van Hove singularities of the band structure. We find that the single particle excitations are strongly suppressed in such systems, which decreases the Landau damping of plasmons. These characters are further verified by first-principles calculations on 2D NbSi$_x$Te$_2$. Interesting features in static screening of charged impurity are also discussed. Our result reveals characteristic plasmons in a class of nonsymmorphic topological semimetals and offers guidance for its experimental detection and possible applications.Comment: 10 pages, 8 figure

Finite Element Approximations for Stokes-Darcy Flow with Beavers-Joseph Interface Conditions

Numerical solutions using finite element methods are considered for transient flow in a porous medium coupled to free flow in embedded conduits. Such situations arise, for example, for groundwater flows in karst aquifers. the coupled flow is modeled by the Darcy equation in a porous medium and the Stokes equations in the conduit domain. on the interface between the matrix and conduit, Beavers-Joseph interface conditions, instead of the simplified Beavers-Joseph-Saffman conditions, are imposed. Convergence and error estimates for finite element approximations are obtained. Numerical experiments illustrate the validity of the theoretical results. © 2010 Society for Industrial and Applied Mathematics

Transcriptomics-based analysis of genes related to lead stress and their expression in the roots of Pogonatherum crinitum

Revealing plants’ tolerance and transport genes to heavy metal stress play an important role in exploring the potential of phytoremediation. Taking the heavy metal lead (Pb) hyperaccumulator plant Pogonatherum crinitum (Thunb.) Kunth as the research object, a hydroponic simulation stress experiment was set up to determine the physiological indicators such as antioxidant enzymes and non-enzymatic antioxidants in the roots of P. crinitum under different Pb concentrations (0, 300, 500, 1000, 2000 mg·L-1). RNA-Seq was performed, the Unigenes obtained by transcriptome sequencing were enriched and annotated by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases, and the differential expression genes (DEGs) of root were screened and verified by quantitative real-time polymerase chain reaction (qRT-PCR). The results are as follows: with the increase of Pb concentration, superoxide dismutase (SOD), catalase (CAT), and ascorbic acid (AsA) content increased. Peroxidase (POD), malondialdehyde (MDA), and ascorbic acid–glutathione (AsA-GSH) cycles showed low promotion with high inhibition. A total of 38.21 Gb of bases were obtained by transcriptome sequencing, and the base quality of each sample reached Q20 and Q30, accounting for 90%, making the sequencing results reliable. Combined with transcriptome sequencing, functional annotation, and qRT-PCR validation results, 17 root Pb-tolerant genes of P. crinitum were screened out, which were related to antioxidation, transportation, and transcription functions. Moreover, qRT-PCR verification results under different Pb stress concentrations were consistent with the transcriptome sequencing results and changes in physiological indicators. In brief, the root of P. crinitum can adapt to the Pb stress environment by up-regulating the expression of related genes to regulate the physiological characteristics