Differential microRNA expression between shoots and rhizomes in Oryza longistaminata using high-throughput RNA sequencing

AbstractPlant microRNAs (miRNAs) play important roles in biological processes such as development and stress responses. Although the diverse functions of miRNAs in model organisms have been well studied, their function in wild rice is poorly understood. In this study, high-throughput small RNA sequencing was performed to characterize tissue-specific transcriptomes in Oryza longistaminata. A total of 603 miRNAs, 380 known rice miRNAs, 72 conserved plant miRNAs, and 151 predicted novel miRNAs were identified as being expressed in aerial shoots and rhizomes. Additionally, 99 and 79 miRNAs were expressed exclusively or differentially, respectively, in the two tissues, and 144 potential targets were predicted for the differentially expressed miRNAs in the rhizomes. Functional annotation of these targets suggested that transcription factors, including squamosa promoter binding proteins and auxin response factors, function in rhizome growth and development. The expression levels of several miRNAs and target genes in the rhizomes were quantified by RT-PCR, and the results indicated the existence of complex regulatory mechanisms between the miRNAs and their targets. Eight target cleavage sites were verified by RNA ligase-mediated rapid 5′ end amplification. These results provide valuable information on the composition, expression and function of miRNAs in O. longistaminata, and will aid in understanding the molecular mechanisms of rhizome development

Genetic characterization and linkage disequilibrium mapping of resistance to gray leaf spot in maize (Zea mays L.)

AbstractGray leaf spot (GLS), caused by Cercospora zeae-maydis, is an important foliar disease of maize (Zea mays L.) worldwide, resistance to which is controlled by multiple quantitative trait loci (QTL). To gain insights into the genetic architecture underlying the resistance to this disease, an association mapping population consisting of 161 inbred lines was evaluated for resistance to GLS in a plant pathology nursery at Shenyang in 2010 and 2011. Subsequently, a genome-wide association study, using 41,101 single-nucleotide polymorphisms (SNPs), identified 51 SNPs significantly (P<0.001) associated with GLS resistance, which could be converted into 31 QTL. In addition, three candidate genes related to plant defense were identified, including nucleotide-binding-site/leucine-rich repeat, receptor-like kinase genes similar to those involved in basal defense. Two genic SNPs, PZE-103142893 and PZE-109119001, associated with GLS resistance in chromosome bins 3.07 and 9.07, can be used for marker-assisted selection (MAS) of GLS resistance. These results provide an important resource for developing molecular markers closely linked with the target trait, enhancing breeding efficiency

Transcriptome Profile Analysis Reveals an Estrogen Induced LncRNA Associated with Lipid Metabolism and Carcass Traits in Chickens (Gallus Gallus)

Background/Aims: Accumulating evidences have demonstrated that long noncoding RNAs (lncRNA) play important roles in hepatic lipid metabolism in mammals. However, no systematic screening of the potential lncRNAs in the livers of laying hens has been performed, and few studies have been reported concerning the effects of the lncRNAs on lipid metabolism in the livers of chickens during egg-laying period. The purpose of this study was to compare the difference in lncRNA expression in the livers of pre-laying and peak-laying hens at the age of 20 and 30 weeks old by transcriptome sequencing and to investigate the interaction networks among lncRNAs, mRNAs and miRNAs. Moreover, the regulatory mechanism and biological function of lncLTR, a significantly differentially expressed lncRNA in the liver between pre- and peak-laying hens, was explored in vitro and in vivo. Methods: Bioinformatics analyses were conducted to identify the differentially expressed (DE) lncRNAs between the two groups of hens. The target genes of the DE lncRNA were predicated for further functional enrichment. An integrated analysis was performed among the DE lncRNA datasets, DE mRNAs and DE miRNA datasets obtained from the same samples to predict the interaction relationship. In addition, in vivo and in vitro trials were carried out to determine the expression regulation of lncLTR, and polymorphism association analysis was conducted to detect the biological role of ncLTR. Results: A total of 124 DE lncRNAs with a P-value ≤ 0.05 were identified. Among them, 44 lncRNAs including 30 known and 14 novel lncRNAs were significant differentially expressed (SDE) with FDR ≤ 0.05. Thirty-two lncRNAs were upregulated and 12 were downregulated in peak-laying group compared with pre-laying group. The functional enrichment results revealed that target genes of some lncRNAs are involved in the lipid metabolism process. Integrated analysis suggested that some of the genes involved in lipid metabolism might be regulated by both the lncRNA and the miRNA. In addition, an upregulated lncRNA, designated lncLTR, was demonstrated to be induced by estrogen via ERβ signaling. The c242. G&#x3e;A SNP in lncLTR was significantly associated with chicken carcass weight, evisceration weight, semi-evisceration weight, head weight, double-wing weight, claw weight traits, and blood biochemical index, especially for the blood triglyceride content. Conclusion: A series of lncRNAs associated with lipid metabolism in the livers of chickens were identified by transcriptome sequencing and functional analysis, providing a valuable data resource for further studies on chicken hepatic metabolism activities. LncLTR was regulated by estrogen via ERβ signaling and associated with chicken carcass trait and blood triglyceride content

2D, 3D-QSAR study and docking of vascular endothelial growth factor receptor 3 (VEGFR3) inhibitors for potential treatment of retinoblastoma

Background: Retinoblastoma is currently the most common malignant tumor seen in newborns and children’s eyes worldwide, posing a life-threatening hazard. Chemotherapy is an integral part of retinoblastoma treatment. However, the chemotherapeutic agents used in clinics often lead to drug resistance. Thus there is a need to investigate new chemotherapy-targeted agents. VEGFR3 inhibitors are anti-tumour-growth and could be used to develop novel retinoblastoma-targeted agents.Objective: To predict drug activity, discover influencing factors and design new drugs by building 2D, 3D-QSAR models.Method: First, linear and non-linear QSAR models were built using heuristic methods and gene expression programming (GEP). The comparative molecular similarity indices analysis (COMISA) was then used to construct 3D-QSAR models through the SYBYL software. New drugs were designed by changing drug activity factors in both models, and molecular docking experiments were performed.Result: The best linear model created using HM had an R2, S2, and R2cv of 0.82, 0.02, and 0.77, respectively. For the training and test sets, the best non-linear model created using GEP had correlation coefficients of 0.83 and 0.72 with mean errors of 0.02 and 0.04. The 3D model designed using SYBYL passed external validation due to its high Q2 (0.503), R2 (0.805), and F-value (76.52), as well as its low standard error of SEE value (0.172). This demonstrates the model’s reliability and excellent predictive ability. Based on the molecular descriptors of the 2D model and the contour plots of the 3D model, we designed 100 new compounds using the best active compound 14 as a template. We performed activity prediction and molecular docking experiments on them, in which compound 14.d performed best regarding combined drug activity and docking ability.Conclusion: The non-linear model created using GEP was more stable and had a more substantial predictive power than the linear model built using the heuristic technique (HM). The compound 14.d designed in this experiment has the potential for anti-retinoblastoma treatment, which provides new design ideas and directions for retinoblastoma-targeted drugs

Strong nonlinear optical response and transient symmetry switching in Type-II Weyl semimetal β\beta-WP2

The topological Weyl semimetals with peculiar band structure exhibit novel nonlinear optical enhancement phenomena even for light at optical wavelengths. While many intriguing nonlinear optical effects were constantly uncovered in type-I semimetals, few experimental works focused on basic nonlinear optical properties in type-II Weyl semimetals. Here we perform a fundamental static and time-resolved second harmonic generation (SHG) on the three dimensional Type-II Weyl semimetal candidate $\beta$-WP$_2$. Although $\beta$-WP$_2$ exhibits extremely high conductivity and an extraordinarily large mean free path, the second harmonic generation is unscreened by conduction electrons, we observed rather strong SHG response compared to non-topological polar metals and archetypal ferroelectric insulators. Additionally, our time-resolved SHG experiment traces ultrafast symmetry switching and reveals that polar metal $\beta$-WP$_2$ tends to form inversion symmetric metastable state after photo-excitation. Intense femtosecond laser pulse could optically drive symmetry switching and tune nonlinear optical response on ultrafast timescales although the interlayer coupling of $\beta$-WP$_2$ is very strong. Our work is illuminating for the polar metal nonlinear optics and potential ultrafast topological optoelectronic applications.Comment: 8 pages, 5 figure

Arbuscular mycorrhizal fungi inoculation exerts weak effects on species- and community-level growth traits for invading or native plants under nitrogen deposition

Nitrogen deposition and biological invasion are two major components of global environmental change. Nitrogen deposition has been considered to enhance the resource availability of recipient habitats, which influences the invasiveness of plant invader and the invasibility of recipient native communities. Nitrogen deposition has been shown to reduce the relative abundances of arbuscular mycorrhizal fungi (AMF) globally. AMF have been found to mutualistically symbiose with approximately 75% of plant species and act as a nutrient supplier. AMF may modify the structure of native plant communities, collaborate with alien plant invaders and thus promote their invasion. The alien woody invader, Rhus typhina L. has been introduced into North China as a horticultural species, invaded the native plant community and outperformed the native competitors in growth and in photosynthetic efficiency. Nevertheless, little is known about if nitrogen deposition and AMF inoculation synergistically alter the invasibility of native plant community. In this study, R. typhina was subjected to the artificial plant community assembled by four co-existing native species – Chenopodium album L., Vitex negundo var. heterophylla (Franch.) Rehd., Rhus chinensis Mill. and Acer truncatum Bunge in a mesocosm experiment. Nitrogen deposition and AMF inoculation were simulated as environmental and biotic filters respectively. Aboveground biomass and biomass proportion, reflecting plant growth and performance, and specific leaf area and chlorophyll concentration correlated with carbon use and photosynthetic capacity of both the alien invader and the native plants were measured and calculated after harvest. We found that AMF inoculation did not alter the trait variation of alien and native species to increasing nitrogen deposition level in general, although AMF inoculation impeded the increase of aboveground biomass for C. album, V. negundo and native community with increasing nitrogen deposition level. In the scenario of nitrogen deposition and AMF inoculation, a stable status of invasion dynamic may be maintained and needs to be checked with integration of traits at extended temporal scale