We introduce ggbio, a new methodology to visualize and explore genomics annotations and high-throughput data. The plots provide detailed views of genomic regions, summary views of sequence alignments and splicing patterns, and genome-wide overviews with karyogram, circular and grand linear layouts. The methods leverage the statistical functionality available in R, the grammar of graphics and the data handling capabilities of the Bioconductor project. The plots are specified within a modular framework that enables users to construct plots in a systematic way, and are generated directly from Bioconductor data structures. The ggbio R package is available at http://www.bioconductor.org/packages/2.11/bioc/html/ggbio.html.

In soybean [Glycine max (L.) Merr.], iron deficiency results in interveinal chlorosis and decreased photosynthetic capacity, leading to stunting and yield loss. In this study, gene expression analyses investigated the role of soybean replication protein A (RPA) subunits during iron stress. Nine RPA homologs were significantly differentially expressed in response to iron stress in the near isogenic lines (NILs) Clark (iron efficient) and Isoclark (iron inefficient). RPA homologs exhibited opposing expression patterns in the two NILs, with RPA expression significantly repressed during iron deficiency in Clark but induced in Isoclark. We used virus induced gene silencing (VIGS) to repress GmRPA3 expression in the iron inefficient line Isoclark and mirror expression in Clark. GmRPA3-silenced plants had improved IDC symptoms and chlorophyll content under iron deficient conditions and also displayed stunted growth regardless of iron availability. RNA-Seq comparing gene expression between GmRPA3-silenced and empty vector plants revealed massive transcriptional reprogramming with differential expression of genes associated with defense, immunity, aging, death, protein modification, protein synthesis, photosynthesis and iron uptake and transport genes. Our findings suggest the iron efficient genotype Clark is able to induce energy controlling pathways, possibly regulated by SnRK1/TOR, to promote nutrient recycling and stress responses in iron deficient conditions.

BackgroundIron is an essential micronutrient for all living things, required in plants for photosynthesis, respiration and metabolism. A lack of bioavailable iron in soil leads to iron deficiency chlorosis (IDC), causing a reduction in photosynthesis and interveinal yellowing of leaves. Soybeans (Glycine max (L.) Merr.) grown in high pH soils often suffer from IDC, resulting in substantial yield losses. Iron efficient soybean cultivars maintain photosynthesis and have higher yields under IDC-promoting conditions than inefficient cultivars.ResultsTo capture signaling between roots and leaves and identify genes acting early in the iron efficient cultivar Clark, we conducted a RNA-Seq study at one and six hours after replacing iron sufficient hydroponic media (100 μM iron(III) nitrate nonahydrate) with iron deficient media (50 μM iron(III) nitrate nonahydrate). At one hour of iron stress, few genes were differentially expressed in leaves but many were already changing expression in roots. By six hours, more genes were differentially expressed in the leaves, and a massive shift was observed in the direction of gene expression in both roots and leaves. Further, there was little overlap in differentially expressed genes identified in each tissue and time point.ConclusionsGenes involved in hormone signaling, regulation of DNA replication and iron uptake utilization are key aspects of the early iron-efficiency response. We observed dynamic gene expression differences between roots and leaves, suggesting the involvement of many transcription factors in eliciting rapid changes in gene expression. In roots, genes involved iron uptake and development of Casparian strips were induced one hour after iron stress. In leaves, genes involved in DNA replication and sugar signaling responded to iron deficiency. The differentially expressed genes (DEGs) and signaling components identified here represent new targets for soybean improvement.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-702) contains supplementary material, which is available to authorized users.

Colorectal cancer (CRC) is a type of cancer with high morbidity and mortality rates worldwide and has become a global health problem. The conventional radiotherapy and chemotherapy regimen for CRC not only has a low cure rate but also causes side effects. Many studies have shown that adequate intake of fruits and vegetables in the diet may have a protective effect on CRC occurrence, possibly due to the special biological protective effect of the phytochemicals in these foods. Numerous in vitro and in vivo studies have demonstrated that phytochemicals play strong antioxidant, anti-inflammatory and anti-cancer roles by regulating specific signaling pathways and molecular markers to inhibit the occurrence and development of CRC. This review summarizes the progress on CRC prevention using the phytochemicals sulforaphane, curcumin and resveratrol, and elaborates on the specific underlying mechanisms. Thus, we believe that phytochemicals might provide a novel therapeutic approach for CRC prevention, but future clinical studies are needed to confirm the specific preventive effect of phytochemicals on cancer.

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Lead‐free double perovskites have emerged as a promising class of materials with potential to be integrated into a wide range of optical and optoelectronic applications. Herein, the first synthesis of 2D Cs2AgInxBi1‐xCl6 (0 ≤ x ≤ 1) alloyed double perovskite nanoplatelets (NPLs) with well controlled morphology and composition is demonstrated. The obtained NPLs show unique optical properties with the highest photoluminescence quantum yield of 40.1%. Both temperature dependent spectroscopic studies and density functional theory calculation results reveal that the morphological dimension reduction and In–Bi alloying effect together boost the radiative pathway of the self‐trapped excitons of the alloyed double perovskite NPLs. Moreover, the NPLs exhibit good stability under ambient conditions and against polar solvents, which is ideal for all solution‐processing of the materials in low‐cost device manufacturing. The first solution‐processed light‐emitting diodes is demonstrated using the Cs2AgIn0.9Bi0.1Cl6 alloyed double perovskite NPLs as the sole emitting component, showing luminance maximum of 58 cd m−2 and peak current efficiency of 0.013 cd A−1. This study sheds light on morphological control and composition‐property relationships of double perovskite nanocrystals, paving the way toward ultimate utilizations of lead‐free perovskite materials in diverse sets of real‐life applications.

Hybrid particulate composites consisting of noble metal nanoparticles (NPs) and polymeric particles have attracted intensive interest, due to the possibility of combining the precious optical and catalytic properties of the former with the stimuli responsiveness and biocompatibility of the latter. However, it is challenging to prepare hybrid particles that simultaneously have tunable optical and catalytic properties as well as excellent colloidal stability. In the current work, we report a strategy for such hybrid particles, through covalently decorating the outmost surface of mixed shell polymeric micelles (MSPMs) with gold NPs. For this, two block polymers, poly(3-caprolactone)-block-(ethylene glycol) (PCL-b-PEG) and poly(3caprolactone)-block-poly(N-isopropylacrylamide) (PCL-b-PNIPAM), were prepared by ring-opening polymerization and reversible addition fragmentation chain transfer (RAFT) polymerization, respectively. Co-self-assembly of the two block polymers result in MSPMs with a PCL core and a mixed shell consisting of PEG and PNIPAM. At the end of each PNIPAM chain in the shell, thiol groups are introduced to act as anchors for the in situ formation of gold NPs. The number density of the gold NPs is conveniently tuned through varying the relative amount of PEG/PNIPAM in the micellar shell. Reversible shrinking and extension of the PNIPAM chains regulated by temperature can be used to tune the interparticle distance of the gold NPs, while the whole hybrid particles are stabilized by the stretched PEG chains. The hybrid polymeric micelles exhibit thermoresponsive surface plasmon resonance and enhanced catalytic properties as well as excellent colloidal stability. † Electronic supplementary information (ESI) available: XPS, TEM images of gold NP decorated polymeric micelles of PNIPAM or MSPMs of a PEG/PNIPAM mass ratio 1 : 9 aer heating, UV-vis absorption spectra during the reduction of 4-NP catalyzed by pure gold NPs or MSPM@AuNPs aer heating, See

The objective of this study was to determine how prenatal and postnatal dietary omega-3 fatty acids alter white blood cell (leukocyte) DNA methylation of offspring. Fifteen gilts (n = 5 per treatment) were selected from one of three treatments: (i) control diet throughout gestation, lactation and nursery phase (CON); (ii) algal omega-3 fatty acid supplementation enriched in EPA and DHA (Gromega ) fed throughout gestation, lactation and nursery phase (Cn3); or (iii) Gromega supplementation maternally, during gestation and lactation only, and control diet during the nursery phase (Mn3). At 11 weeks of age and after 8 weeks of post-weaning nursery feeding, buffy coat genomic DNA was subjected to methyl CpG binding protein sequencing. The methylation enriched profile mapped to 26% of the porcine genome. On chromosome 4, a 27.7-kb differentially methylated region downstream of RUNX1T1 was hypomethylated in the Mn3 and Cn3 groups by 91.6% and 85.0% respectively compared to CON pigs. Conversely, hypermethylation was detected in intergenic regions of chromosomes 4 and 12. Regulatory impact factor and differential hubbing methods were used to identify pathways that were coordinately regulated by methylation due to feeding EPA and DHA during pregnancy. Despite limited ability to detect differential methylation, we describe methods that allow the identification of coordinated epigenetic regulation that could not otherwise be detected from subtle single locus changes in methylation. These data provide evidence of novel epigenetic regulation by maternal and early life supplementation of omega-3 fatty acids that may have implications to growth and inflammatory processes.