Next-Generation Sequencing of MicroRNAs for Breast Cancer Detection

It is reported that different microRNA (miRNA) profiles can be detected in the blood of cancer patients. We investigated that whether the key serum miRNAs could discriminate patients with and without breast cancer. This study was divided into three parts: (1) miRNA marker discovery using SOLiD sequencing-based miRNA profiling on cancerous and adjacent noncancerous breast tissue of one breast cancer patient; (2) marker selection and validation by real-time PCR on a small set of serum; (3) gene ontology analysis of the key miRNA target genes. Of genome-wide tissue miRNA expression analysis, five miRNAs were found to be altered more than fivefold by SOLiD sequencing (i.e., miR-29a, miR-23a, miR-23b, miR-192, and miR-21). All the five miRNAs were validated on the 20 breast cancer patients and 20 controls. miR-29a and miR-21 were significantly increased in the serum of breast cancer patients (P < .05). Gene ontology analysis of the target genes revealed enrichment for special biological process categories, that is, signal transduction, development, apoptosis, cell proliferation, and cell adhesion. SOLiD sequencing provides a promising method for cancer-related miRNA profiling. Serum miRNAs may be useful biomarkers for breast cancer detection

A novel method to quantify local CpG methylation density by regional methylation elongation assay on microarray

<p>Abstract</p> <p>Background</p> <p>DNA methylation based techniques are important tools in both clinical diagnostics and therapeutics. But most of these methods only analyze a few CpG sites in a target region. Indeed, difference of site-specific methylation may also lead to a change of methylation density in many cases, and it has been found that the density of methylation is more important than methylation of single CpG site for gene silencing.</p> <p>Results</p> <p>We have developed a novel approach for quantitative analysis of CpG methylation density on the basis of microarray-based hybridization and incorporation of Cy5-dCTP into the Cy3 labeled target DNA by using Taq DNA Polymerase on microarray. The quantification is achieved by measuring Cy5/Cy3 signal ratio which is proportional to methylation density. This methylation-sensitive technique, termed RMEAM (regional methylation elongation assay on microarray), provides several advantages over existing methods used for methylation analysis. It can determine an exact methylation density of the given region, and has potential of high throughput. We demonstrate a use of this method in determining the methylation density of the promoter region of the tumor-related gene <it>MLH1, TERT </it>and <it>MGMT </it>in colorectal carcinoma patients.</p> <p>Conclusion</p> <p>This technique allows for quantitative analysis of regional methylation density, which is the representative of all allelic methylation patterns in the sample. The results show that this technique has the characteristics of simplicity, rapidness, specificity and high-throughput.</p

Pair-barcode high-throughput sequencing for large-scale multiplexed sample analysis

<p>Abstract</p> <p>Background</p> <p>The multiplexing becomes the major limitation of the next-generation sequencing (NGS) in application to low complexity samples. Physical space segregation allows limited multiplexing, while the existing barcode approach only permits simultaneously analysis of up to several dozen samples.</p> <p>Results</p> <p>Here we introduce pair-barcode sequencing (PBS), an economic and flexible barcoding technique that permits parallel analysis of large-scale multiplexed samples. In two pilot runs using SOLiD sequencer (Applied Biosystems Inc.), 32 independent pair-barcoded miRNA libraries were simultaneously discovered by the combination of 4 unique forward barcodes and 8 unique reverse barcodes. Over 174,000,000 reads were generated and about 64% of them are assigned to both of the barcodes. After mapping all reads to pre-miRNAs in miRBase, different miRNA expression patterns are captured from the two clinical groups. The strong correlation using different barcode pairs and the high consistency of miRNA expression in two independent runs demonstrates that PBS approach is valid.</p> <p>Conclusions</p> <p>By employing PBS approach in NGS, large-scale multiplexed pooled samples could be practically analyzed in parallel so that high-throughput sequencing economically meets the requirements of samples which are low sequencing throughput demand.</p

The Chinese Open Science Network (COSN): Building an Open Science Community From Scratch

Open Science is becoming a mainstream scientific ideology in psychology and related fields. However, researchers, especially early-career researchers (ECRs) in developing countries, are facing significant hurdles in engaging in Open Science and moving it forward. In China, various societal and cultural factors discourage ECRs from participating in Open Science, such as the lack of dedicated communication channels and the norm of modesty. To make the voice of Open Science heard by Chinese-speaking ECRs and scholars at large, the Chinese Open Science Network (COSN) was initiated in 2016. With its core values being grassroots-oriented, diversity, and inclusivity, COSN has grown from a small Open Science interest group to a recognized network both in the Chinese-speaking research community and the international Open Science community. So far, COSN has organized three in-person workshops, 12 tutorials, 48 talks, and 55 journal club sessions and translated 15 Open Science-related articles and blogs from English to Chinese. Currently, the main social media account of COSN (i.e., the WeChat Official Account) has more than 23,000 subscribers, and more than 1,000 researchers/students actively participate in the discussions on Open Science. In this article, we share our experience in building such a network to encourage ECRs in developing countries to start their own Open Science initiatives and engage in the global Open Science movement. We foresee great collaborative efforts of COSN together with all other local and international networks to further accelerate the Open Science movement

Association Study between BDNF Gene Polymorphisms and Autism by Three-Dimensional Gel-Based Microarray

Single nucleotide polymorphisms (SNPs) are important markers which can be used in association studies searching for susceptible genes of complex diseases. High-throughput methods are needed for SNP genotyping in a large number of samples. In this study, we applied polyacrylamide gel-based microarray combined with dual-color hybridization for association study of four BDNF polymorphisms with autism. All the SNPs in both patients and controls could be analyzed quickly and correctly. Among four SNPs, only C270T polymorphism showed significant differences in the frequency of the allele (χ2 = 7.809, p = 0.005) and genotype (χ2 = 7.800, p = 0.020). In the haplotype association analysis, there was significant difference in global haplotype distribution between the groups (χ2 = 28.19, p = 3.44e-005). We suggest that BDNF has a possible role in the pathogenesis of autism. The study also show that the polyacrylamide gel-based microarray combined with dual-color hybridization is a rapid, simple and high-throughput method for SNPs genotyping, and can be used for association study of susceptible gene with disorders in large samples

6G Network AI Architecture for Everyone-Centric Customized Services

Mobile communication standards were developed for enhancing transmission and network performance by using more radio resources and improving spectrum and energy efficiency. How to effectively address diverse user requirements and guarantee everyone's Quality of Experience (QoE) remains an open problem. The Sixth Generation (6G) mobile systems will solve this problem by utilizing heterogenous network resources and pervasive intelligence to support everyone-centric customized services anywhere and anytime. In this article, we first coin the concept of Service Requirement Zone (SRZ) on the user side to characterize and visualize the integrated service requirements and preferences of specific tasks of individual users. On the system side, we further introduce the concept of User Satisfaction Ratio (USR) to evaluate the system's overall service ability of satisfying a variety of tasks with different SRZs. Then, we propose a network Artificial Intelligence (AI) architecture with integrated network resources and pervasive AI capabilities for supporting customized services with guaranteed QoEs. Finally, extensive simulations show that the proposed network AI architecture can consistently offer a higher USR performance than the cloud AI and edge AI architectures with respect to different task scheduling algorithms, random service requirements, and dynamic network conditions

Maternal plasmamiRNAs expression in preeclamptic pregnancies. BioMed research international

Objective. Preeclampsia (PE) is a pregnancy-specific syndrome and one of the leading causes of maternal and fetal morbidity and mortality. The pathophysiological mechanisms of PE remain poorly known. Recently, circulating miRNAs are considered as potential useful noninvasive biomarkers. The aim of this study was to identify differentially expressed plasma miRNAs in preeclamptic pregnancies compared with normal pregnancies. Methods. Maternal plasma miRNA expression profiles were detected by SOLiD sequencing. Differential expressions between mPE/sPE and control group were found. Next, four differentially expressed plasma miRNAs were chosen to validate their expression in other large scale samples by real-time PCR. Results. In terms of sequencing results, we identified that 51 miRNAs were differentially expressed. Four differentially expressed plasma miRNAs (miR-141, miR-144, miR-221, and miR-29a) were selected to validate the sequencing results. RT-PCR data confirmed the reliability of sequencing results. The further statistical analysis showed that maternal plasma miR-141 and miR-29a are significantly overexpressed in mPE ( &lt; 0.05). Maternal plasma miR-144 is significantly underexpressed in mPE and sPE ( &lt; 0.05). Conclusions. Results showed that there were differentially expressed maternal plasma miRNAs in patients with preeclampsia. These plasma miRNAs might be used as notable biomarkers for diagnosis of preeclampsia

Maternal Plasma miRNAs Expression in Preeclamptic Pregnancies

Objective. Preeclampsia (PE) is a pregnancy-specific syndrome and one of the leading causes of maternal and fetal morbidity and mortality. The pathophysiological mechanisms of PE remain poorly known. Recently, circulating miRNAs are considered as potential useful noninvasive biomarkers. The aim of this study was to identify differentially expressed plasma miRNAs in preeclamptic pregnancies compared with normal pregnancies. Methods. Maternal plasma miRNA expression profiles were detected by SOLiD sequencing. Differential expressions between mPE/sPE and control group were found. Next, four differentially expressed plasma miRNAs were chosen to validate their expression in other large scale samples by real-time PCR. Results. In terms of sequencing results, we identified that 51 miRNAs were differentially expressed. Four differentially expressed plasma miRNAs (miR-141, miR-144, miR-221, and miR-29a) were selected to validate the sequencing results. RT-PCR data confirmed the reliability of sequencing results. The further statistical analysis showed that maternal plasma miR-141 and miR-29a are significantly overexpressed in mPE (P<0.05). Maternal plasma miR-144 is significantly underexpressed in mPE and sPE (P<0.05). Conclusions. Results showed that there were differentially expressed maternal plasma miRNAs in patients with preeclampsia. These plasma miRNAs might be used as notable biomarkers for diagnosis of preeclampsia

An Emulsion System Based on a Chip Polymerase Chain Reaction

In this paper we describe a novel method for detecting many DNA fragments through efficient amplification by using an emulsion system based on “on-chip” PCR instead of conventional multiplex polymerase chain reaction (PCR). During the preparation of on-chip PCR, a set of primers were immobilized on a slide and other sets were in an emulsion system. Different emulsion phase primers and other related PCR components were dispersed in different droplets of the emulsion system, and then, due to the thermal instability of emulsion droplets, they would be released onto the surface of the slide after preheating in the first PCR step. To test the above method, we used plasma DNAs from pregnant women who was carrying a male fetus for gender identification. Four different Y chromosome DNA fragments were selected. Results showed that different DNA fragments could be simultaneously amplified with satisfactory results. It is suggested that a simple, convenient and inexpensive on-chip PCR method has been developed