Electrochemical Study of DPPH Radical Scavenging for Evaluating the Antioxidant Capacity of Carbon Nanodots

Carbon nanodots (CNDs) have become one of the potential candidates for antioxidants due to their excellent luminescence, biocompatibility, and lower cytotoxicity. While CNDs have experienced some research on radical scavenging activity via UV–vis spectroscopy, the relationship between reserved 2,2-diphenyl-1-picrylhydrazyl radical (DPPH^•) concentration and CNDs’ incubation concentration remains unclear. This work describes an electrochemical study on the changes of redox peaks of the oxidation of DPPH^• at gold electrodes with addition of different concentrations of a type of microwave-synthesized CND (U-dots). The result is consistent with a UV–vis absorption dose-dependent study used to quantify the antioxidation activities. Combined with standard heterogeneous electron-transfer rate constant analysis, electrochemical study gives a coupled hydrogen atom transfer (HAT) mechanism for DPPH^• scavenging by the U-dots. This work provides a new perspective on the antioxidative study of the U-dots, which may aid their development for practical use in biomedicine

Magnetoreception of Photoactivated Cryptochrome 1 in Electrochemistry and Electron Transfer

Cryptochromes are flavoproteins whose photochemistry is important for crucial functions associated with phototropism and circadian clocks. In this report, we, for the first time, observed a magnetic response of the cryptochrome 1 (CRY1) immobilized at a gold electrode with illumination of blue light. These results present the magnetic field-enhanced photoinduced electron transfer of CRY1 to the electrode by voltammetry, exhibiting magnetic responsive rate constant and electrical current changes. A mechanism of the electron transfer, which involves photoinduced radicals in the CRY, is sensitive to the weak magnetic field; and the long-lived free radical FAD^•– is responsible for the detected electrochemical Faradaic current. As a photoreceptor, the finding of a 5.7% rate constant change in electron transfer corresponding to a 50 μT magnetic field may be meaningful in regulation of magnetic field signaling and circadian clock function under an electromagnetic field

Data_Sheet_2_Genetic insights into the crude protein and fiber content of ramie leaves.xlsx

Ramie (Boehmeria nivea L.) is a perennial plant with vigorously vegetative growth and high nutritive value that is an excellent source of green feed in China. Crude protein and fiber content are the most important traits associated with ramie forage quality; however, their genetic basis remains largely unknown. In this study, we investigated the genetic architecture of these two traits using an F2 population derived from cultivated Zhongsizhu 1 (ZSZ1) and wild Boehmeria nivea var. tenacissima (tenacissima). Linkage mapping identified eight quantitative trait loci (QTLs) in crude fiber and one QTL in crude protein. Of these, five were further validated by association analysis. Then, two major QTLs for crude fiber content, CF7 and CF13, were further identified using bulked segregant analysis (BSA) sequencing, and their exact physical intervals were determined via genotype analysis of F2 progenies with extremely low crude fiber content. In total, 10 genes in the CF7 and CF13 regions showed differential expression in ZSZ1 and tenacissima leaves, including an MYB gene whole_GLEAN_10016511 from the CF13 region. Wide variation was observed in the promoter regions of whole_GLEAN_10016511, likely responsible for its downregulated expression in tenacissima. Interestingly, more fiber cells were observed in Arabidopsis with overexpression of whole_GLEAN_10016511, indicating that the downregulated expression of this gene could have an association with the relatively low fiber content in wild tenacissima. These results provided evidence that whole_GLEAN_10016511 is a logical candidate for CF13. This study provides important insights into the genetic basis underlying ramie crude protein and fiber content, and it presents genetic loci for improving the forage quality of ramie using marker-assisted selection.</p

Selected primer sequences for expression and structure validation.

<p>Selected primer sequences for expression and structure validation.</p

Analysis of Unannotated Equine Transcripts Identified by mRNA Sequencing

<div><p>Sequencing of equine mRNA (RNA-seq) identified 428 putative transcripts which do not map to any previously annotated or predicted horse genes. Most of these encode the equine homologs of known protein-coding genes described in other species, yet the potential exists to identify novel and perhaps equine-specific gene structures. A set of 36 transcripts were prioritized for further study by filtering for levels of expression (depth of RNA-seq read coverage), distance from annotated features in the equine genome, the number of putative exons, and patterns of gene expression between tissues. From these, four were selected for further investigation based on predicted open reading frames of greater than or equal to 50 amino acids and lack of detectable homology to known genes across species. Sanger sequencing of RT-PCR amplicons from additional equine samples confirmed expression and structural annotation of each transcript. Functional predictions were made by conserved domain searches. A single transcript, expressed in the cerebellum, contains a putative kruppel-associated box (KRAB) domain, suggesting a potential function associated with zinc finger proteins and transcriptional regulation. Overall levels of conserved synteny and sequence conservation across a 1MB region surrounding each transcript were approximately 73% compared to the human, canine, and bovine genomes; however, the four loci display some areas of low conservation and sequence inversion in regions that immediately flank these previously unannotated equine transcripts. Taken together, the evidence suggests that these four transcripts are likely to be equine-specific.</p></div

Dot plots depicting sequence comparisons between the genomic regions of the four unannotated equine transcripts and the corresponding regions in the human, canine, and bovine genomes (A).

<p>The genomic intervals of the unannotated transcripts are highlighted in yellow and the nearest conserved Ensembl protein-coding gene prediction in the flanking regions are highlighted in blue. Dot plots depicting sequence comparisons between the specific interval of the unannotated equine transcripts (yellow segment in panel A) and the corresponding regions in the human, canine, and bovine genomes (B).</p

The number of splice junctions and genes specific to each tissue.

<p>Maximum values of the y-axis are set to the number of junctions/genes found in testes (9,234 splice junctions and 1,028 genes).</p

Text mining validation.

<p>Text mining results indicating the relationship between genes containing the tissue-specific RNA-seq splice junctions in each tissue (x-axis) and top tissue concepts (y-axis).</p

Plots for filtering splice junctions.

<p>(A) An example, from heart, plotting entropy versus average mismatches for annotated and novel splice junctions. Selected thresholds (0.75 entropy and 1.5 or 1 average mismatches, paired and single-end, respectively) are indicated by the dark lines and the lower right quadrants retained for further splice junction analyses. (B) Plots are for annotated only and novel splice junctions across all tissues for both paired-end and single end data. A vertical dark line indicates the applied threshold of 50 nucleotides. The main graphs are zoomed in to <1000bp intron sizes, while the sub-graphs show all natural log scaled intron sizes.</p

Example of an unannotated equine transcript.

<p>The upper panel shows approximately 3KB of ECA14 containing a single unannotated transcript (A). The black peaks represent depth of coverage by the RNA-seq reads and the red lines represent putative splice junctions identified by MapSplice <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0070125#pone.0070125-Wang1" target="_blank">[20]</a>. The gene model immediately below is the annotation for this transcript derived from the RNA-seq data. The lower panel shows a 700 KB region of ECA14 surrounding the transcript (dotted box outline) illustrating that there is no annotated gene or <i>in silico</i> gene prediction overlapping this genomic interval (B). The nearest RNA-seq data not included in the transcript model is approximately 60 KB away and the nearest gene prediction is nearly 120 KB away.</p