BS-RNA: An efficient mapping and annotation tool for RNA bisulfite sequencing data

Cytosine methylation is one of the most important RNA epigenetic modifications. With the development of experimental technology, scientists attach more importance to RNA cytosine methylation and find bisulfite sequencing is an effective experimental method for RNA cytosine methylation study. However, there are only a few tools can directly deal with RNA bisulfite sequencing data efficiently. Herein, we developed a specialized tool BS-RNA, which can analyze cytosine methylation of RNA based on bisulfite sequencing data and support both paired-end and single-end sequencing reads from directional bisulfite libraries. For paired-end reads, simply removing the biased positions from the 5′ end may result in “dovetailing” reads, where one or both reads seem to extend past the start of the mate read. BS-RNA could map “dovetailing” reads successfully. The annotation result of BS-RNA is exported in BED (.bed) format, including locations, sequence context types (CG/CHG/CHH, H = A, T, or C), reference sequencing depths, cytosine sequencing depths, and methylation levels of covered cytosine sites on both Watson and Crick strands. BS-RNA is an efficient, specialized and highly automated mapping and annotation tool for RNA bisulfite sequencing data. It performs better than the existing program in terms of accuracy and efficiency. BS-RNA is developed by Perl language and the source code of this tool is freely available from the website: http://bs-rna.big.ac.cn.     

Novel quasi-interpenetrating network/gold nanoparticles composite matrices for DNA sequencing by CE

In order to further improve ssDNA sequencing performances using quasi-interpenetrating network (quasi-IPN) as a matrix composed of linear polyacrylamide (LPA) with lower viscosity-average molecular mass (3.3 MDa) and poly(N,N-dimethylacrylamide) (PDMA), gold nanoparticles (GNPs) were prepared and added into this quasi-IPN to form polymer/metal composite sieving matrices. The studies of intrinsic viscosity and differential scanning calorimetry (DSC) on quasi-IPN and quasi-IPN/GNPs indicate that there were interactions between GNPs and polymer chains. The sequencing performances on ssDNA using quasi-IPN and quasi-IPN/GNPs (with different GNPs concentrations) as sieving matrices were studied and compared by CE at different temperatures. The results show that resolutions of quasi-IPN/GNPs were higher than those of quasi-IPN without GNPs and approximated those of quasi-IPN composed of LPA with higher MW (6.5 MDa) and PDMA without GNPs in the bare fused-silica capillaries. Furthermore, the sequencing time of quasi-IPN/GNPs was shorter than that of quasi-IPN under the same sequencing conditions. The influences of GNPs and sequencing temperature on the sequencing performances of ssDNA were also discussed. The separation reproducibility of quasi-IPN/GNPs solution was excellent and its shelf life was more than 8 months.     

Influence of temperature on performance of an anaerobic sequencing biofilm batch reactor with circulation applied to treatment of low-strength wastewater

The effect of temperature on the performance of an anaerobic sequencing biofilm batch reactor (ASBBR) with liquid-phase recirculation was assessed. Assays were performed using a recirculation velocity of 0.20 cm/s, 8-h cycles, and an average treated synthetic wastewater volume of 2 L/cycle with a concentration of 500 mg of Chemical Oxygen Demand (COD)/L. Operation temperatures were 15, 20, 25, 30, and 35°C. At 25, 30, and 35°C, organic matter removal efficiencies for filtered samples ranged from 81 to 83%. At lower temperatures, namely 15 and 20°C, removal efficiency decreased significantly to 61 and 65%, respectively. A first-order model could be fitted to the experimental concentration profile values. The first-order kinetic parameter value of this model varied from 0.46 to 0.81 h¹ considering the lowest and highest temperature studied. Moreover, analysis of the removal profile values allowed fitting of an Arrhenius-type equation with an activation energy of 5715 cal/mol.     

Polymer translocation through nanopore under external electric field: dissipative particle dynamics study

The DNA sequencing technology has achieved a leapfrog development in recent years. As a new generation of the DNA sequencing technology, nanopore sequencing has shown a broad application prospect and attracted vast research interests since it was proposed. In the present study, the dynamics of the electric-driven translocation of a homopolymer through a nanopore is investigated by the dissipative particle dynamics(DPD), in which the homopolymer is modeled as a worm-like chain(WLC). The DPD simulations show that the polymer chain undergoes conformation changes during the translocation process. The different structures of the polymer in the translocation process, i.e., single-file, double folded, and partially folded, and the induced current blockades are analyzed. It is found that the current blockades have different magnitudes due to the polymer molecules traversing the pore with different folding conformations. The nanoscale vortices caused by the concentration polarization layers(CPLs) in the vicinity of the sheet are also studied. The results indicate that the translocation of the polymer has the effect of eliminating the vortices in the polyelectrolyte solution. These findings are expected to provide the theoretical guide for improving the nanopore sequencing technique.     

Large-scale pyrosequencing of synthetic DNA: a comparison with results from Sanger dideoxy sequencing

Pyrosequencing is a relatively recent method for sequencing short stretches of DNA. Because both Pyrosequencing and Sanger dideoxy sequencing were recently used to characterize and validate DNA molecular barcodes in a large yeast gene-deletion project, a meta-analysis of those data allow an excellent and timely opportunity for evaluating Pyrosequencing against the current gold standard, Sanger dideoxy sequencing. Starting with yeast genomic DNA, parallel PCR amplification methods were used to prepared 4747 short barcode-containing constructs from 6000 Saccharomyces cerevisiae gene-deletion strains. Pyrosequencing was optimized for average read lengths of 25-30 bases, which included in each case a 20-mer barcode sequence. Results were compared with sequence data obtained by the standard Sanger dideoxy chain termination method. In most cases, sequences obtained by Pyrosequencing and Sanger dideoxy sequencing were of comparable accuracy, and the overall rate of failure was similar. The DNA in the barcodes is derived from synthetic oligonucleotide sequences that were inserted into yeast-deletion-strain genomic DNA by homologous recombination and represents the most significant amount of DNA from a synthetic source that has been sequenced to date. Although more automation and quality control measures are needed, Pyrosequencing was shown to be a fast and convenient method for determining short stretches of DNA sequence.     

A biosensor based on graphene nanoribbon with nanopores: a first-principles devices-design

A biosensor device,built from graphene nanoribbons(GNRs) with nanopores,was designed and studied by firstprinciples quantum transport simulation.We have demonstrated the intrinsic transport properties of the device and the effect of different nucleobases on device properties when they are located in the nanopores of GNRs.It was found that the device’s current changes remarkably with the species of nucleobases,which originates from their different chemical compositions and coupling strengths with GNRs.In addition,our first-principles results clearly reveal that the distinguished ability of a device’s current depends on the position of the pore to some extent.These results may present a new way to read off the nucleobases sequence of a single-stranded DNA(ssDNA) molecule by such GNRs-based device with designed nanopores     

第二代测序序列比对方法综述

使用聚合酶合成技术的Illumina和454平台以及使用连接酶合成测序技术的SOLiD平台是目前三种主流的第二代测序平台.对第二代测序平台产生的高通量序列片段进行比对的方法一般分为两步：①预处理,②序列比对.预处理方法有两类,即基于哈希表的方法和基于后缀trie的Burrows-Wheeler转换思想.序列比对方法也可分为两类,一是空位种子片段索引,二是Smith-Waterman动态规划算法.本文使用Illumina和SOLiD两种平台产生的数据对常用的比对软件SHRiMP,MAQ,BFAST,BWA,BOWTIE等进行了单机测试,结果显示：BOW-TIE在对Illumina平台数据进行比对时,在内存使用、比对速度以及准确性等方面表现比其他几种好,BWA比较适合用于比对SOLiD平台产生的数据.在处理第二代以及以纳米孔技术为标志的第三代测序平台高通量数据时,第二代比对技术仍不能完全满足要求,本文认为以云计算为基础的新序列比对方法是未来研究和发展的一个重要方向.     

Effects of ultrasound-assisted chitosan grafted caffeic acid coating on the quality and microbial composition of pompano during ice storage

The effects of ultrasound-assisted chitosan grafted caffeic acid coating on the quality and microbial composition of fresh pompano (Trachinotus ovatus) fillets during ice storage for 24 days were evaluated. Samples were treated by distilled water (CK), ultrasound (US), chitosan grafted caffeic acid coating (G), and chitosan grafted caffeic acid coating with ultrasound-assisted (USG). Results showed that samples treated with USG could inhibit the formation of corrupt substances such as TVB-N, TBA, biogenic amines (BAs), hypoxanthine (Hx), and hypoxanthine riboside (HxR) when compared to the CK group. The results of high-throughput sequencing technology observed that the major bacteria genus of fresh samples was Acinetobacter. The diversity of bacterial communities at the initial stage was more diverse than that at the end of stage. With the extension of storage time, the USG treatment could maintain the microbial diversity. The dominant microbiota was Shewanella and Brochothrix in the CK group after 24 days of storage. In addition, Brochothrix in treated groups was effectively decreased. The microbial communities of samples in all treatments were changed during storage. At the end of storage, there was a significant difference in bacterial composition between the CK and treated samples, indicating that the treatment can effectively inhibit the growth of microorganisms, especially spoilage microorganisms, and reduce the quality deterioration caused by bacteria.     

Batch picking in narrow-aisle order picking systems with consideration for picker blocking

This paper develops strategies to control picker blocking that challenge the traditional assumptions regarding the tradeoffs between wide- and narrow-aisle order picking systems. We propose an integrated batching and sequencing procedure called the indexed batching model (IBM), with the objective of minimizing the total retrieval time (the sum of travel time, pick time and congestion delays). The IBM differs from traditional batching formulations by assigning orders to indexed batches, whereby each batch corresponds to a position in the batch release sequence. We develop a mixed integer programming solution for exact control, and demonstrate a simulated annealing procedure to solve large practical problems. Our results indicate that the proposed approach achieves a 5–15% reduction in the total retrieval time primarily by reducing picker blocking. We conclude that the IBM is particularly effective in narrow-aisle picking systems.     

Comparison of CID,ETD and metastable atom‐activated dissociation (MAD) of doubly and triply charged phosphorylated tau peptides

The fragmentation behavior of the 2+ and 3+ charge states of eleven different phosphorylated tau peptides was studied using collision‐induced dissociation (CID), electron transfer dissociation (ETD) and metastable atom‐activated dissociation (MAD). The synthetic peptides studied contain up to two known phosphorylation sites on serine or threonine residues, at least two basic residues, and between four and eight potential sites of phosphorylation. CID produced mainly b‐/y‐type ions with abundant neutral losses of the phosphorylation modification. ETD produced c‐/z‐type ions in highest abundance but also showed numerous y‐type ions at a frequency about 50% that of the z‐type ions. The major peaks observed in the ETD spectra correspond to the charge‐reduced product ions and small neutral losses from the charge‐reduced peaks. ETD of the 2+ charge state of each peptide generally produced fewer backbone cleavages than the 3+ charge state, consistent with previous reports. Regardless of charge state, MAD achieved more extensive backbone cleavage than CID or ETD, while retaining the modification(s) in most cases. In all but one case, unambiguous modification site determination was achieved with MAD. MAD produced 15–20% better sequence coverage than CID and ETD for both the 2+ and 3+ charge states and very different fragmentation products indicating that the mechanism of fragmentation in MAD is unique and complementary to CID and ETD. Copyright © 2012 John Wiley & Sons, Ltd.