RNA-seq provides insights into potato deubiquitinase responses to drought stress in seedling stage

Ubiquitination is a specific protein degradation and reversible post-translational modification process that can be reversed by deubiquitinase (DUBs). DUBs can hydrolyze and release ubiquitin in the substrate protein so that the substrate can avoid degradation or change its activity, and it has an impact on plant growth and development, cell cycle, abiotic stress response, and other biological processes. Transcript sequences of potato varieties “DM1-3”, “Atlantic” and “Cooperation-88” downloaded from Potato Genome Resources were used for genome-wide identification of the DUB gene family using Hidden Markov Models and verified in the NCBI CD-Search tool. The characteristics of DUB genes from different potato varieties were analyzed including subcellular localization, gene structural motifs, phylogenetic tree, and sequence homology. Polyethylene glycol 6000 (PEG6000) induced drought stress transcriptome analysis was performed on the “Atlantic”, and differentially expressed genes were screened, with emphasis on the characterization of deubiquitinase. DUB genes have a complex gene structure, often with a large number of exons and alternative splicing. Their promoters contain abundant abiotic stress-responsive elements, such as 425 MYC, 325 ABRE, and 320 MYB. There are also a large number of orthologous genes in the DUBs of the three potato varieties, and these genes are often clustered in similar regions on the genome. We performed transcriptome sequencing of the potato under PEG-induced drought stress and analyzed it for the first time using the Atlantic as a reference genome. We identified a total of 6067 down-regulated differentially expressed genes (DEGs) and 4950 up-regulated DEGs under PEG-induced drought stress. We screened the expression of DUBs and observed that 120 DUBs were up-regulated where most of them functioned in the nucleus, and the interacting proteins of DUBs were also localized in the nucleus. We have comprehensively identified and analyzed potato DUBs, and the accurately aligned transcriptome data which will further deepen the understanding of DUBs involved in the regulation of osmotic stress

Discovering rare-earth-free magnetic materials through the development of a database

We develop an open-access database that provides a large array of datasets specialized for magnetic compounds as well as magnetic clusters. Our focus is on rare-earth-free magnets. Available datasets include (i) crystallography, (ii) thermodynamic properties, such as the formation energy, and (iii) magnetic properties that are essential for magnetic-material design. Our database features a large number of stable and metastable structures discovered through our adaptive genetic algorithm (AGA) searches. Many of these AGA structures have better magnetic properties when compared to those of the existing rare-earth-free magnets and the theoretical structures in other databases. Our database places particular emphasis on site-specific magnetic data, which are obtained by high-throughput first-principles calculations. Such site-resolved data are indispensable for machine-learning modeling. We illustrate how our data-intensive methods promote efficiency of the experimental discovery of new magnetic materials. Our database provides massive datasets that will facilitate an efficient computational screening, machine-learning-assisted design, and the experimental fabrication of new promising magnets

A genetic variation map for chicken with 2.8 million single-nucleotide polymorphisms

We describe a genetic variation map for the chicken genome containing 2.8 million single-nucleotide polymorphisms ( SNPs). This map is based on a comparison of the sequences of three domestic chicken breeds ( a broiler, a layer and a Chinese silkie) with that of their wild ancestor, red jungle fowl. Subsequent experiments indicate that at least 90% of the variant sites are true SNPs, and at least 70% are common SNPs that segregate in many domestic breeds. Mean nucleotide diversity is about five SNPs per kilobase for almost every possible comparison between red jungle fowl and domestic lines, between two different domestic lines, and within domestic lines - in contrast to the notion that domestic animals are highly inbred relative to their wild ancestors. In fact, most of the SNPs originated before domestication, and there is little evidence of selective sweeps for adaptive alleles on length scales greater than 100 kilobases

[Avian cytogenetics goes functional] Third report on chicken genes and chromosomes 2015

High-density gridded libraries of large-insert clones using bacterial artificial chromosome (BAC) and other vectors are essential tools for genetic and genomic research in chicken and other avian species... Taken together, these studies demonstrate that applications of large-insert clones and BAC libraries derived from birds are, and will continue to be, effective tools to aid high-throughput and state-of-the-art genomic efforts and the important biological insight that arises from them

Microplasmin and tissue plasminogen activator: comparison of therapeutic effects in rat stroke model at multiparametric MR imaging

Purpose: To prospectively compare therapeutic and hemorrhagic effects of microplasmin and tissue plasminogen activator (tPA) in stroke therapy by using multiparametric magnetic resonance (MR) imaging in a photothrombotic rat stroke model. Materials and Methods: The animal experiment complied with institutional regulations for laboratory animals. Stroke was induced in rats with photothrombotic occlusion of middle cerebral artery (MCA). T2-weighted, perfusion-weighted (PW), and diffusion-weighted (DW) MR imaging was performed 1 hour and 24 hours after occlusion. On the basis of PW and DW images at 1 hour, 49 rats with cortex and subcortex involvement and with perfusion-diffusion mismatch were randomly assigned into one of four groups: control group, group treated with 7.5 mg microplasmin, group treated with 10 mg/kg microplasmin, or group treated with 10 mg/kg tPA. Agents were intravenously injected 1.5 hours after occlusion. Infarct size and hemorrhagic transformation were assessed with MR imaging and histomorphologic findings. Neurologic deficit was scored. Measurements were statistically analyzed. Results: There were 13 rats in the control group, 13 in the 7.5 mg/kg microplasmin group, nine in the 10 mg/kg microplasmin group, and 14 in the 10 mg/kg tPA group. Despite similar baseline perfusion-diffusion mismatch, histochemically defined total infarct volume was reduced from 25% +/- 5 (standard deviation) in control group to 21% +/- 2, 20% +/- 4, and 20% +/- 5 in 7.5 mg/kg microplasmin, 10 mg/kg microplasmin, and tPA groups, respectively, as similarly shown on T2-weighted, DW, and PW images at 24 hours (P < .05). Cerebral hemorrhage rate at 24 hours was higher in tPA group than in the other three groups. Bederson score of neurologic deficits was significantly reduced in treated groups compared with that in control group. Conclusion: Perfusion-diffusion mismatch appeared useful in selecting candidates for thrombolytic therapy. Multiparametric MR imaging allowed noninvasive assessment of effects of microplasmin and tPA in rats; microplasmin had a significantly lower hemorrhagic rate. (c) RSNA, 2007.status: publishe

Glass-forming ability and magnetic properties of CoFeMoYB bulk glassy alloys with large supercooled liquid region

Co-based bulk glassy alloys with diameters up to 4 mm were formed in Co41+ xFe28Mo4Y5-xB22 (x = 0-1.5) system. The effect of Y content on the glass-forming ability and soft-magnetic properties of the Co-based bulk glassy alloys was investigated. With an increase of Y content from 3.5 to 5 at%, in addition to slight increases of glass transition temperature from 843 to 847K and supercooled liquid region increases from 73 to 94 K, the addition of Y was found to be effective in approaching alloy to a eutectic point. Except for high glass-forming ability, the Co-based bulk glassy alloys exhibit good soft-magnetic properties, i.e., high saturation magnetization of 0.80-0.87 T, low coercive force of 2.87-3.34 A/m, high effective permeability at 1 kHz of 1.26-1.74x10(4) under a field of 1 A/m. (C) 2010 Elsevier B.V. All rights reserved

Effect of Nb addition on the glass-forming ability, mechanical and soft-magnetic properties in (Co0.942Fe0.058)(72-x)NbxB22.4Si5.6 bulk glassy alloys

The effect of Nb addition on the glass-forming ability (GFA), mechanical and soft-magnetic properties in (Co0.942Fe0.058)(72-x)NbxB22.4Si5.6 alloys system was investigated. In addition to the increase of glass-forming ability, the increase of Nb content was found to be effective for the improvement of mechanical and soft-magnetic properties. By copper mold casting, Co-based bulk glassy alloys with diameters up to 4 mm were formed in (Co0.942Fe0.058)(67)Nb5B22.4Si5.6 glassy alloy. The bulk glassy alloys exhibit a superhigh fracture strength of 2980-3600 MPa and Young's modulus of 121-166 GPa. The bulk glassy alloys also exhibit excellent soft-magnetic properties, i.e., high saturation magnetization of 0.6 T, low coercive force within 0.2-0.5 A/m, high permeability of 47165 at 1 KHz and zero magnetostriction. (C) 2010 Elsevier B.V. All rights reserved

Alternative pathway of bile acid biosynthesis contributes to ameliorate NASH after induction of NAMPT/NAD+/SIRT1 axis

Non-alcoholic steatohepatitis (NASH) is emerging as a serious liver disorder characterized by hepatic steatosis and liver inflammation. Nicotinamide adenine dinucleotide (NAD+) and NAD+-dependent deacetylase, SIRT1, play important roles in lipid metabolism in non-alcoholic fatty liver disease (NAFLD). However, their effects on liver inflammation and homeostasis of bile acids (BAs), the extensively proved pathophysiological actors in NASH, have not been fully understood. NASH animal model was induced by a methionine-choline-deficient (MCD) diet in C57BL/6J mice and intraperitoneally injected with NAD+ precursor, an agonist of upstream rate-limiting enzyme NAMPT or downstream SIRT1, or their vehicle solvents. Free fatty acid (FFA) was applied to HepG2 cells to construct the cell model. Induction of NAMPT/NAD+/SIRT1 axis could remarkably alleviate the aggravated inflammation in the liver of NASH mice, accompanied by decreased levels of total BAs throughout the enterohepatic system and a switch of BA synthesis from the classic pathway to the alternative pathway, resulting in less production of pro-inflammatory 12-OH BAs. The expressions of key enzymes including cyp7a1, cyp8b1, cyp27a1 and cyp7b1 in BA synthesis were significantly modulated after NAMPT/NAD+/SIRT1 axis induction in both animal and cell models. The levels of pro-inflammatory cytokines in liver were significantly negatively correlated with the intermediates in NAD+ metabolism, which may also be related to their regulation on BA homeostasis. Our results indicated that induction of NAMPT/NAD+/SIRT1 axis may be a potential therapeutic strategy for NASH or its complications related with BAs

Pt/ZSM-22 with Partially Filled Micropore Channels as Excellent Shape-Selective Hydroisomerization Catalyst

Pt/ZSM-22 with partially filled micropore channels (Pt/Z22-PF) was prepared through a facile in-situ coke deposition approach. Compared with conventional Pt/ZSM-22 with evacuated micropore channels (Pt/Z22-E), Pt/Z22-PF exhibits much higher activity and isomer yield in n-dodecane hydroisomerization. Specifically, the turnover frequency of n-dodecane and the maximum multibranched isomer yield on Pt/Z22-PF are about twice that on Pt/Z22-E (314 vs. 144 h(-1), 49 % vs. 29 %). Theoretical simulations and adsorption experiments demonstrate that the diffusion limitation of hydrocarbon and the accessibility of acid sites inside the micropore channels are reduced dramatically because of the partial fill. This is beneficial for the diffusion of alkene intermediates and the suppression of cracking reactions, resulting in a superior activity and high yield of isomers, especially multibranched isomers