Identification of miRNAs and their targets by high-throughput sequencing and degradome analysis in cytoplasmic male-sterile line NJCMS1A and its maintainer NJCMS1B of soybean

Table S1. Summary of small RNA annotations from NJCMS1A and NJCMS1B. Table S2. Known miRNAs identified in NJCMS1A and NJCMS1B. Table S3. Family member distribution in conserved miRNA families. Table S4. Summary of miRNA families found in NJCMS1A and NJCMS1B. Table S5. Novel miRNAs on the other arm of known pre-miRNAs. Table S6. Novel miRNAs identified in NJCMS1A and NJCMS1B. Table S7-1. High-confidence known miRNAs identified in NJCMS1A and NJCMS1B. Table S7-2. High-confidence novel miRNAs identified in NJCMS1A and NJCMS1B. Table S8-1. The up-regulated miRNAs identified in NJCMS1A and NJCMS1B. Table S8-2. The down-regulated miRNAs identified in NJCMS1A and NJCMS1B. Table S9. The targets of miRNAs identified in NJCMS1A and NJCMS1B. Table S10. Targets of novel miRNAs in NJCMS1A and NJCMS1B. Table S11. Primers used in this study. (ZIP 637 kb

Kondo effect in the Kohn-Sham conductance of multiple levels quantum dots

At zero temperature, the Landauer formalism combined with static density functional theory is able to correctly reproduce the Kondo plateau in the conductance of the Anderson impurity model provided that an exchange-correlation potential is used which correctly exhibits steps at integer occupation. Here we extend this recent finding to multi-level quantum dots described by the constant-interaction model. We derive the exact exchange-correlation potential in this model for the isolated dot and deduce an accurate approximation for the case when the dot is weakly coupled to two leads. We show that at zero temperature and for non-degenerate levels in the dot we correctly obtain the conductance plateau for any odd number of electrons on the dot. We also analyze the case when some of the levels of the dot are degenerate and again obtain good qualitative agreement with results obtained with alternative methods. As in the case of a single level, for temperatures larger than the Kondo temperature, the Kohn-Sham conductance fails to reproduce the typical Coulomb blockade peaks. This is attributed to {\em dynamical} exchange-correlation corrections to the conductance originating from time-dependent density functional theory.Comment: 8 pages, 4 figures, submitted to special issue of pss(b

Evolution of Cerebral Ischemia Assessed by Amide Proton Transfer-Weighted MRI

In today’s stressful world, psychopathy (especially anxiety) is receiving increased importance. Most of the drugs used to treat this disease have several side effects. Medicinal plants derived from natural products have fewer side effects and can be used in the treatment of this disease. The aim of this study was to evaluate the effect of the hydroalcoholic extract of Rosmarinus officinalis L. on anxiety in mice. In this experimental study, 50 male mice were randomly divided into 5 groups. To evaluate anxiety, the Elevated Plus Maze test was performed. The control group received normal saline, the positive control group received diazepam (1 mg/kg) as intraperitoneal injection, and the experimental groups received doses of 100, 200, and 400 mg/kg body weight of rosemary extract. The data were analyzed using SPSS 15 and ANOVA statistical tests. The results show that rosemary extract dose-dependently increases the mice spending time and the entries number of mice in plus maze open arms (indicating less stress). This effect at a dose of 400 mg/kg was similar to diazepam, which, in comparison to the control group, was statistically significant ( P .05). On the other hand, the rosemary extract, similar to the standard drug diazepam, showed an anti-anxiety effect. This effect is probably due to the presence of flavonoids in this plant and their antioxidant property

Pinellia ternata agglutinin expression in chloroplasts confers broad spectrum resistance against aphid, whitefly, Lepidopteran insects, bacterial and viral pathogens

Broad spectrum protection against different insects and pathogens requires multigene engineering. However, such broad spectrum protection against biotic stress is provided by a single protein in some medicinal plants. Therefore, tobacco chloroplasts were transformed with the agglutinin gene from Pinellia ternata (pta), a widely cultivated Chinese medicinal herb. Pinellia ternata agglutinin (PTA) was expressed up to 9.2% of total soluble protein in mature leaves. Purified PTA showed similar hemagglutination activity as snowdrop lectin. Artificial diet with purified PTA from transplastomic plants showed marked and broad insecticidal activity. In planta bioassays conducted with T0 or T1 generation PTA lines showed that the growth of aphid Myzus persicae (Sulzer) was reduced by 89%92% when compared with untransformed (UT) plants. Similarly, the larval survival and total population of whitefly (Bemisia tabaci) on transplastomic lines were reduced by 91%93% when compared with UT plants. This is indeed the first report of lectin controlling whitefly infestation. When transplastomic PTA leaves were fed to corn earworm (Helicoverpa zea), tobacco budworm (Heliothis virescens) or the beet armyworm (spodoptera exigua), 100% mortality was observed against all these three insects. In planta bioassays revealed Erwinia population to be 10 000-fold higher in control than in PTA lines. Similar results were observed with tobacco mosaic virus (TMV) challenge. Therefore, broad spectrum resistance to homopteran (sap-sucking), Lepidopteran insects as well as anti-bacterial or anti-viral activity observed in PTA lines provides a new option to engineer protection against biotic stress by hyper-expression of an unique protein that is naturally present in a medicinal plant

In silico comparative analysis of EST-SSRs in three cotton genomes

In this study, expressed sequence tags- simple sequence repeat (EST-SSRs) were surveyed in three cotton genomes (Gossypium arboreum, Ga; Gossypium raimondii, Gr and Gossypium hirsutum, Gh). The frequency of EST-SSRs was highest in Gr, and motif type for hexanucleotide was obviously abundant in Gr. Trinucleotide repeats were the most abundant motif; AT and AG, AAG and ATC were the most frequent motifs for dinucleotide and trinucleotide, respectively. The repeat number was greatly diverse between the three genomes with the highest variation in Gh. AG and AAG had a high frequency both in homologue groups (HGs) with and without repeat number change between genomes. The range of repeat number change in each HG was wider in Gr-Gh. The annotation of the SSR-ESTs showed that more Gene Ontology (GO) items targeted by SSR-ESTs of Ga and Gr than those of Gh. This study gave us new insights into the difference between the three cotton genomes, which will be more helpful to understand the differentiation and evolution of the three genomes.Key words: Cotton, simple sequence repeat, expressed sequence tags, motif, gene ontology

Realized Stable BP-N at Ambient Pressure by Phosphorus Doping

Black phosphorus nitrogen (BP-N) is an attractive high-energy-density material. However, high-pressure synthesized BP-N will decompose at low-pressure and cannot be quenched to ambient conditions. Finding a method to stabilize it at 0 GPa is of great significance for its practical applications. However, unlike cg-N, LP-N, and HLP-N, it is always a metastable phase at high-pressure up to 260 GPa, and decomposes into chains at 23 GPa. Here, based on the first-principles simulations, we find that P atom doping can effectively reduce the synthesis pressure of BP-N and maintain its stability at 0 GPa. Uniform distribution of P atom dopants within the layer helps maintain the structural stability of BP-N layer at 0 GPa, while interlayer electrostatic interaction induced by N-P dipoles enhances its dynamic stability by eliminating interlayer slipping. Furthermore, pressure is conducive to enhancing the stability of BP-N and its doped forms by suppressing N-chain dissociation. For the configuration with 12.5% doping concentration, a gravimetric energy density of 8.07 kJ/g can be realized, which is nearly two times higher than TNT.Comment: 27 pages, 6 figure

Engineered Chloroplast dsRNA Silences Cytochrome p450 Monooxygenase, V‐ATPase and Chitin Synthase Genes in the Insect Gut and Disrupts Helicoverpa Armigera Larval Development and Pupation

In the past two decades, chloroplast genetic engineering has been advanced to achieve high‐level protein accumulation but not for down‐regulation of targeted genes. Therefore, in this report, lepidopteran chitin synthase (Chi), cytochrome P450 monooxygenase (P450) and V‐ATPase dsRNAs were expressed via the chloroplast genome to study RNA interference (RNAi) of target genes in intended hosts. PCR and Southern blot analysis confirmed homoplasmy and site‐specific integration of transgene cassettes into the chloroplast genomes. Northern blots and real‐time qRT‐PCR confirmed abundant processed and unprocessed dsRNA transcripts (up to 3.45 million copies of P450 dsRNAs/μg total RNA); the abundance of cleaved dsRNA was greater than the endogenous psbA transcript. Feeding of leaves expressing P450,Chi and V‐ATPase dsRNA decreased transcription of the targeted gene to almost undetectable levels in the insect midgut, likely after further processing of dsRNA in their gut. Consequently, the net weight of larvae, growth and pupation rates were significantly reduced by chloroplast‐derived dsRNAs. Taken together, successful expression of dsRNAs via the chloroplast genome for the first time opens the door to study RNA interference/processing within plastids. Most importantly, dsRNA expressed in chloroplasts can be utilized for gene inactivation to confer desired agronomic traits or for various biomedical applications, including down‐regulation of dysfunctional genes in cancer or autoimmune disorders, after oral delivery of dsRNA bioencapsulated within plant cells