Proteomic Analysis of Ubiquitinated Proteins in Rice (\u3ci\u3eOryza sativa\u3c/i\u3e) After Treatment With Pathogen-Associated Molecular Pattern (PAMP) Elicitors

Reversible protein ubiquitination plays essential roles in regulating cellular processes. Although many reports have described the functions of ubiquitination in plant defense responses, few have focused on global changes in the ubiquitome. To better understand the regulatory roles of ubiquitination in rice pattern-triggered immunity (PTI), we investigated the ubiquitome of rice seedlings after treatment with two pathogen-associated molecular patterns, the fungal-derived chitin or the bacterialderived flg22, using label-free quantitative proteomics. In chitin-treated samples, 144 and 167 lysine-ubiquitination sites in 121 and 162 proteins showed increased and decreased ubiquitination, respectively. In flg22-treated samples, 151 and 179 lysine-ubiquitination sites in 118 and 166 proteins showed increased and decreased ubiquitination, respectively. Bioinformatic analyses indicated diverse regulatory roles of these proteins. The ubiquitination levels of many proteins involved in the ubiquitination system, protein transportation, ligand recognition, membrane trafficking, and redox reactions were significantly changed in response to the elicitor treatments. Notably, the ubiquitination levels of many enzymes in the phenylpropanoid metabolic pathway were up-regulated, indicating that this pathway is tightly regulated by ubiquitination during rice PTI. Additionally, the ubiquitination levels of some key components in plant hormone signaling pathways were up- or down-regulated, suggesting that ubiquitination may fine-tune hormone pathways for defense responses. Our results demonstrated that ubiquitination, by targeting a wide range of proteins for degradation or stabilization, has a widespread role in modulating PTI in rice. The large pool of ubiquitination targets will serve as a valuable resource for understanding how the ubiquitination system regulates defense responses to pathogen attack

Identification of optimal endogenous reference RNAs for RT-qPCR normalization in hindgut of rat models with anorectal malformations

Background Quantitative real-time polymerase chain reaction (RT-qPCR) is a sensitive method for quantifying mRNA abundance. With relative expression analysis, however, reliable data output is dependent on stably expressed reference genes across the samples being studied. In anorectal malformations (ARMs), there is limited data on the selection of appropriate reference genes. Purpose This study was aimed to investigate the optimal reference genes for PCR in ARM rat models. Methods We selected 15 commonly used reference genes (Rps18, Actb, B2m, Gapdh, Ppia, Hprt1, Pgk1, Ywhaz, Tbp, Ubc, Rps16, Rpl13a, Rplp1, Sdha, and Hmbs) as candidate reference genes and detected their mRNA expression in ARM samples by RT-qPCR. The expression stability and variability of these transcripts were subsequently evaluated using four methods (geNorm, NormFinder, comparative ΔCt, and BestKeeper). Results The abundance of the candidate reference genes was qualified by RT-qPCR and the cycle threshold (Ct) values ranged between 14.07 (Rplp1) and 21.89 (Sdha). In the overall candidate genes, different variations existed across the different algorithms. A comprehensive analysis revealed that Rpl13a ranked first among the relatively stable genes, followed by Ywhaz, Rps18, Sdha, and Hmbs. Conclusions The most stable reference genes for RT-qPCR were Rpl13a, Ywhaz, and Rps18 in ETU-induced ARMs in rat fetus. This study provided a foundation for reference gene selection for future gene expression analyses

Preparation and characterization of \u3ba-carrageenase immobilized onto magnetic iron oxide nanoparticles

Background: Carboxyl-functionalized magnetic nanoparticles were synthesized via chemical co-precipitation method and modified with oleic acid which was oxidized by potassium permanganate, and \u3ba-carrageenase from Pseudoalteromonas sp. ASY5 was subsequently immobilized onto them. The immobilization conditions were further optimized, and the characterizations of the immobilized \u3ba-carrageenase were investigated. Results: The \u3ba-carrageenase was immobilized onto magnetic iron oxide nanoparticles, and the bonding was verified by Fourier transform infrared spectroscopy. The optimal conditions for \u3ba-carrageenase immobilization were 2.5% (w/v) glutaraldehyde, 13.9 U \u3ba-carrageenase for 20 mg of magnetic nanoparticles, a 2-h cross-linking time, and a 2-h immobilization time at 25\ub0C. Under these conditions, the activity of the immobilized enzyme and the enzyme recovery rate were 326.0 U \ub7 g-1 carriers and 46.9%, respectively. The properties of the immobilized \u3ba-carrageenase were compared with those of the free enzyme. The optimum temperatures of the free and immobilized \u3ba-carrageenase were 60 and 55\ub0C, respectively, and the optimum pH of \u3ba-carrageenase did not change before and after immobilization (pH 7.5). After immobilization, \u3ba-carrageenase exhibited lower thermal stability and improved pH stability, as well as better storage stability. The immobilized \u3ba-carrageenase maintained 43.5% of the original activity after being used 4 times. The kinetic constant value (Km) of \u3ba-carrageenase indicates that the immobilized enzyme had a lower binding affinity for the substrate. Conclusions: Under optimal conditions, the activity of the immobilized enzyme and enzyme recovery rate were 326.0 U \ub7 g-1\ub7\u3ba-carrageenase-CMNPs and 46.9%, respectively. The thermal, pH, and storage stabilities of \u3ba-carrageenase-CMNPs were relatively higher than those of free \u3ba-carrageenase

Preparation and Characterization of Glycosylated Rice Bran Protein-Chitosan Composite Film

In order to improve the mechanical properties, water resistance and barrier properties of rice bran protein (RBP) film, glycosylated RBP (RBP-G) film and RBP-G-chitosan composite (RBP-G-CS) film were prepared. The effects of the mass ratio of glucose to RBP and the mass ratio of RBP-G to chitosan on the mechanical properties of the films were investigated. The color, transparency, water resistance, water vapor permeability and thermal characteristics of RBP, RBP-G and RBP-G-CS films prepared under the optimal conditions were compared and analyzed. The structure of the films was characterized by scanning electron microscopy (SEM) and Fourier transform infrared (FTIR) spectroscopy. The results showed that the mechanical properties of RBP-G film with a glucose to RBP ratio of 1:1 were obviously improved, and the tensile strength increased by 28.00% and the elongation at break by 33.13% compared with RBP film. RBP-G-CS film with a RBP-G to chitosan ratio of 1:1 had better mechanical properties, and its tensile strength and elongation at break increased by 197.33% and 84.42% compared with RBP film, respectively. The transparency, water resistance, barrier properties and thermal properties of RBP-G-CS film were significantly improved (P < 0.05). The structure of RBP-G-CS film was uniform and compact, owing to the strong hydrogen bonding forces. These results show that glycosylation modification can improve the performance of RBP film, and a good combination of modified RBP and chitosan can greatly improve the mechanical properties and water resistance of the film

H5N1 Influenza a Virus Replicates Productively in Pancreatic Cells and Induces Apoptosis and Pro-Inflammatory Cytokine Response

The inflammatory response and apoptosis have been proved to have a crucial role in the pathogenesis of the influenza A virus (IAV). Previous studies indicated that while IAV commonly causes pancreatitis and pancreatic damage in naturally and experimentally infected animals, the molecular mechanisms of the pathogenesis of IAV infection are less reported. In the present study, we showed for the first time that both avian-like (α-2,3-linked) and human-like (α-2,6-linked) sialic acid (SA) receptors were expressed by the mouse pancreatic cancer cell line PAN02 and the human pancreatic cancer cell line PANC-1. Using growth kinetics experiments, we also showed that PAN02 and PANC-1 cells supported the productive replication of the H5N1 highly pathogenic avian influenza while exhibited the limited replication of IAV subtypes H1N1 and H7N2 in vitro. The in vivo infection of H5N1 in pancreatic cells was confirmed by the histopathological and immunohistochemical staining of pancreas tissue from mice. Other than H1N1 and H7N2, severe damage and extensive positive signals were observed in pancreas of H5N1 infected mice. All three virus subtypes induced apoptosis but also triggered the infected PAN02 and PANC-1 cells to release pro-inflammatory cytokines and chemokines including interferon (IFN)-α, IFN-β, IFN-γ, chemokine (C-C motif) ligand 2 (CCL2), tumor necrosis factor (TNF)-α, and interleukin (IL)-6. Notably, the subtypes of H5N1 could significantly upregulate these cytokines and chemokines in both two cells when compared with H1N1 and H7N2. The present data provide further understanding of the pathogenesis of H5N1 IAV in pancreatic cells derived from humans and mammals and may also benefit the development of new treatment against H5N1 influenza virus infection

Observation of nonrelativistic plaid-like spin splitting in a noncoplanar antiferromagnet

Spatial, momentum and energy separation of electronic spins in condensed matter systems guides the development of novel devices where spin-polarized current is generated and manipulated. Recent attention on a set of previously overlooked symmetry operations in magnetic materials leads to the emergence of a new type of spin splitting besides the well-studied Zeeman, Rashba and Dresselhaus effects, enabling giant and momentum dependent spin polarization of energy bands on selected antiferromagnets independent of relativistic spin-orbit interaction. Despite the ever-growing theoretical predictions, the direct spectroscopic proof of such spin splitting is still lacking. Here, we provide solid spectroscopic and computational evidence for the existence of such materials. In the noncoplanar antiferromagnet MnTe$_2$, the in-plane components of spin are found to be antisymmetric about the high-symmetry planes of the Brillouin zone, comprising a plaid-like spin texture in the antiferromagnetic ground state. Such an unconventional spin pattern, further found to diminish at the high-temperature paramagnetic state, stems from the intrinsic antiferromagnetic order instead of the relativistic spin-orbit coupling. Our finding demonstrates a new type of spin-momentum locking with a nonrelativistic origin, placing antiferromagnetic spintronics on a firm basis and paving the way for studying exotic quantum phenomena in related materials.Comment: Version 2, 30 pages, 4 main figures and 8 supporting figure

Genome sequence of the cultivated cotton <i>Gossypium arboreum</i>

The complex allotetraploid nature of the cotton genome (AADD; 2n = 52) makes genetic, genomic and functional analyses extremely challenging. Here we sequenced and assembled the Gossypium arboreum (AA; 2n = 26) genome, a putative contributor of the A subgenome. A total of 193.6 Gb of clean sequence covering the genome by 112.6-fold was obtained by paired-end sequencing. We further anchored and oriented 90.4% of the assembly on 13 pseudochromosomes and found that 68.5% of the genome is occupied by repetitive DNA sequences. We predicted 41,330 protein-coding genes in G. arboreum. Two whole-genome duplications were shared by G. arboreum and Gossypium raimondii before speciation. Insertions of long terminal repeats in the past 5 million years are responsible for the twofold difference in the sizes of these genomes. Comparative transcriptome studies showed the key role of the nucleotide binding site (NBS)-encoding gene family in resistance to Verticillium dahliae and the involvement of ethylene in the development of cotton fiber cells.Genetics &amp; HereditySCI(E)[email protected]; [email protected]; [email protected]

Atomically resolved electrically active intragrain interfaces in perovskite semiconductors

Deciphering the atomic and electronic structures of interfaces is key to developing state-of-the-art perovskite semiconductors. However, conventional characterization techniques have limited previous studies mainly to grain-boundary interfaces, whereas the intragrain-interface microstructures and their electronic properties have been much less revealed. Herein using scanning transmission electron microscopy, we resolved the atomic-scale structural information on three prototypical intragrain interfaces, unraveling intriguing features clearly different from those from previous observations based on standalone films or nanomaterial samples. These intragrain interfaces include composition boundaries formed by heterogeneous ion distribution, stacking faults resulted from wrongly stacked crystal planes, and symmetrical twinning boundaries. The atomic-scale imaging of these intragrain interfaces enables us to build unequivocal models for the ab initio calculation of electronic properties. Our results suggest that these structure interfaces are generally electronically benign, whereas their dynamic interaction with point defects can still evoke detrimental effects. This work paves the way toward a more complete fundamental understanding of the microscopic structure–property–performance relationship in metal halide perovskites

Roles of Peroxisomes in the Rice Blast Fungus

The rice blast fungus, Magnaporthe oryzae, is a model plant pathogenic fungus and is a severe threat to global rice production. Over the past two decades, it has been found that the peroxisomes play indispensable roles during M. oryzae infection. Given the importance of the peroxisomes for virulence, we review recent advances of the peroxisomes roles during M. oryzae infection processes. We firstly introduce the molecular mechanisms and life cycles of the peroxisomes. And then, metabolic functions related to the peroxisomes are also discussed. Finally, we provide an overview of the relationship between peroxisomes and pathogenicity