Additional file 1: Table S1. of Downregulation of long noncoding RNA MEG3 is associated with poor prognosis and promoter hypermethylation in cervical cancer

Patients’ clinico-pathological characteristics. (DOC 40 kb

Automating Quantum Dot Barcode Assays Using Microfluidics and Magnetism for the Development of a Point-of-Care Device

The impact of detecting multiple infectious diseases simultaneously at point-of-care with good sensitivity, specificity, and reproducibility would be enormous for containing the spread of diseases in both resource-limited and rich countries. Many barcoding technologies have been introduced for addressing this need as barcodes can be applied to detecting thousands of genetic and protein biomarkers simultaneously. However, the assay process is not automated and is tedious and requires skilled technicians. Barcoding technology is currently limited to use in resource-rich settings. Here we used magnetism and microfluidics technology to automate the multiple steps in a quantum dot barcode assay. The quantum dot-barcoded microbeads are sequentially (a) introduced into the chip, (b) magnetically moved to a stream containing target molecules, (c) moved back to the original stream containing secondary probes, (d) washed, and (e) finally aligned for detection. The assay requires 20 min, has a limit of detection of 1.2 nM, and can detect genetic targets for HIV, hepatitis B, and syphilis. This study provides a simple strategy to automate the entire barcode assay process and moves barcoding technologies one step closer to point-of-care applications

Expression profiles of 35 expressed <i>Gmcupin</i> genes in different tissues.

<p>a. Heatmap showing hierarchical clustering of 35 expressed <i>Gmcupin</i> genes among various tissues analyzed. b. Heatmap showing hierarchical clustering of 35 expressed <i>Gmcupin</i> genes during the development of soybean seeds.</p

Selected sites of <i>Gmcupin</i> genes during soybean domestication.

<p>Selected sites of <i>Gmcupin</i> genes during soybean domestication.</p

Chromosomal locations and predicted clusters for <i>Gmcupin</i> genes.

<p>The schematic diagram of genome-wide chromosome organization and segmental duplication arising from the genome duplication event in soybean was derived from the CViT genome search and synteny viewer at the Legume Information System (<a href="http://comparative-legumes.org" target="_blank">http://comparative-legumes.org</a>). The chromosomal positions of all <i>Gmcupin</i> genes were mapped on each chromosome. Colored blocks to the left of each chromosome show duplications with chromosomes of the same color. The chromosome numbers are indicated at the top of each bar and sizes of chromosomes are represented by the vertical scale. The locations of centromeric repeats are shown as black rectangles over the chromosomes.</p

Conserved domains across cupin proteins in soybean.

<p>The sequence logos are based on alignments of 69 Gmcupin domains. Multiple alignment analysis of all typical Gmcupin domains (A: Gmcuppin 1; B: Gmcupin 2) were performed with Clustal W. The bit score indicates the information content for each position in the sequence.</p

A Comprehensive Analysis of the Cupin Gene Family in Soybean (<i>Glycine max</i>)

<div><p>Cupin superfamily of proteins, including germin and germin-like proteins (GLPs) from higher plants, is known to play crucial roles in plant development and defense. To date, no systematic analysis has been conducted in soybean (<i>Glycine max</i>) incorporating genome organization, gene structure, expression compendium. In this study, 69 putative <i>Cupin</i> genes were identified from the whole-genome of soybean, which were non-randomly distributed on 17 of the 20 chromosomes. These Gmcupin proteins were phylogenetically clustered into ten distinct subgroups among which the gene structures were highly conserved. Eighteen pairs (52.2%) of duplicate paralogous genes were preferentially retained in duplicated regions of the soybean genome. The distributions of <i>GmCupin</i> genes implied that long segmental duplications contributed significantly to the expansion of the <i>GmCupin</i> gene family. According to the RNA-seq data analysis, most of the <i>Gmcupins</i> were differentially expressed in tissue-specific expression pattern and the expression of some duplicate genes were partially redundant while others showed functional diversity, suggesting the <i>Gmcupins</i> have been retained by substantial subfunctionalization during soybean evolutionary processes. Selective analysis based on single nucleotide polymorphisms (SNPs) in cultivated and wild soybeans revealed sixteen <i>Gmcupins</i> had selected site(s), with all SNPs in <i>Gmcupin10.3</i> and <i>Gmcupin07.2</i> genes were selected sites, which implied these genes may have undergone strong selection effects during soybean domestication. Taken together, our results contribute to the functional characterization of <i>Gmcupin</i> genes in soybean.</p></div

Expression profile of <i>Gmcupin</i> genes in different tissues.

<p>The numbers in the expression profile are normalized data, which were calculated as reads/kilobase/million normalization of the raw data. All data were downloaded from the SoyBase.</p

Summary of Cupin family members in soybean.

<p>Summary of Cupin family members in soybean.</p

Phylogenetic relationships and gene structure of Gmcupin genes.

<p>The phylogenetic tree of Gmcupin proteins constructed from a complete alignment of 69 Gmcupin proteins using MEGA 5.0 by the neighbor-joining method. The bootstrap consensus tree inferred from 1000 replicates is taken to represent the evolutionary history of the taxa analyzed. Percentage bootstrap scores of>50% are indicated on the nodes. Ten major phylogenetic subgroups (designated as I to X) are indicated. Exons of <i>Gmcupin</i> genes are represented by green boxes and introns and untranslated region (UTR) by black and blue lines. The sizes of exons and introns can be estimated using the scale below.</p