BatAlign: an incremental method for accurate alignment of sequencing reads

Structural variations (SVs) play a crucial role in genetic diversity. However, the alignments of reads near/across SVs are made inaccurate by the presence of polymorphisms. BatAlign is an algorithm that integrated two strategies called ‘Reverse-Alignment’ and ‘Deep-Scan’ to improve the accuracy of read-alignment. In our experiments, BatAlign was able to obtain the highest F-measures in read-alignments on mismatch-aberrant, indel-aberrant, concordantly/discordantly paired and SV-spanning data sets. On real data, the alignments of BatAlign were able to recover 4.3% more PCR-validated SVs with 73.3% less callings. These suggest BatAlign to be effective in detecting SVs and other polymorphic-variants accurately using high-throughput data. BatAlign is publicly available at https://goo.gl/a6phxB.     

High Resolution Size Analysis of Fetal DNA in the Urine of Pregnant Women by Paired-End Massively Parallel Sequencing

Background

Fetal DNA in maternal urine, if present, would be a valuable source of fetal genetic material for noninvasive prenatal diagnosis. However, the existence of fetal DNA in maternal urine has remained controversial. The issue is due to the lack of appropriate technology to robustly detect the potentially highly degraded fetal DNA in maternal urine.

Methodology

We have used massively parallel paired-end sequencing to investigate cell-free DNA molecules in maternal urine. Catheterized urine samples were collected from seven pregnant women during the third trimester of pregnancies. We detected fetal DNA by identifying sequenced reads that contained fetal-specific alleles of the single nucleotide polymorphisms. The sizes of individual urinary DNA fragments were deduced from the alignment positions of the paired reads. We measured the fractional fetal DNA concentration as well as the size distributions of fetal and maternal DNA in maternal urine.

Principal Findings

Cell-free fetal DNA was detected in five of the seven maternal urine samples, with the fractional fetal DNA concentrations ranged from 1.92% to 4.73%. Fetal DNA became undetectable in maternal urine after delivery. The total urinary cell-free DNA molecules were less intact when compared with plasma DNA. Urinary fetal DNA fragments were very short, and the most dominant fetal sequences were between 29 bp and 45 bp in length.

Conclusions

With the use of massively parallel sequencing, we have confirmed the existence of transrenal fetal DNA in maternal urine, and have shown that urinary fetal DNA was heavily degraded.     

肺动脉内皮细胞与肺动脉平滑肌细胞增殖的相互调节

血管内皮细胞和血管平滑肌细胞在结构和功能上关系密切,二者的相互关系在血管舒缩和血管壁结构的调节中起重要作用。本文观察了培养的小牛肺动脉内皮细胞（ＰＡＥＣ）和肺动脉平滑肌细胞（ＰＡＳＭ）在细胞增殖方面的相互调节作用。混合培养的ＰＡＥＣ和ＰＡＳＭ细胞的３Ｈ－ＴｄＲ参入明显降低（Ｐ＜０．００１,与对照组相比）。无论向培养的ＰＡＥＣ和ＰＡＳＭ中分别加入ＰＡＳＭ和ＰＡＥＣ的条件培养基还是二者共培养时,均发现ＰＡＥＣ的３Ｈ－ＴｄＲ参入明显降低,而ＰＡＳＭ的３Ｈ－ＴｄＲ明显升高（Ｐ＜０．０５,与对照组相比）。流式细胞测定也发现共培养时ＰＡＥＣ的Ｇ１期细胞增多,Ｇ２／Ｍ期细胞减少;而ＰＡＳＭ的Ｇ１期细胞减少,Ｇ２／Ｍ期细胞增多。共培养的ＰＡＳＭ细胞内ｃＡＭＰ增加,ｃＧＭＰ含量降低;而ＰＡＥＣ细胞的ｃＡＭＰ和ｃＧＭＰ含量均降低（Ｐ＜０．０１,与对照组相比）。上述结果提示,ＰＡＥＣ和ＰＡＳＭ相互作用可能通过第二信使而调节它们本身的增殖     

Flavonoids of <Emphasis Type="Italic">Rosa roxburghii</Emphasis> Tratt exhibit radioprotection and anti-apoptosis properties via the Bcl-2(Ca<Superscript>2+</Superscript>)/Caspase-3/PARP-1 pathway

The objective of our study was to assess the radioprotective effect of flavonoids extracted from Rosa roxburghii Tratt (FRT) and investigate the role of Bcl-2(Ca²⁺)/Caspase-3/PARP-1 pathway in radiation-induced apoptosis. Cells and mice were exposed to ⁶⁰Co γ-rays at a dose of 6 Gy. The radiation treatment induced significant effects on tissue pathological changes, apoptosis, Ca²⁺, ROS, DNA damage, and expression levels of Bcl-2, Caspase-3 (C-Caspase-3), and PARP-1. The results showed that FRT acted as an antioxidant, reduced DNA damage, corrected the pathological changes of the tissue induced by radiation, promoted the formation of spleen nodules, resisted sperm aberration, and protected the thymus. FRT significantly reduced cell apoptosis compared with the irradiation group. The expression of Ca²⁺ and C-Caspase-3 was decreased after FRT treatment compared with the radiation-treated group. At the same time, expression of prototype PARP-1 and Bcl-2 increased, leading to a decrease in the percentage of apoptosis cells in FRT treatment groups. We conclude that FRT acts as a radioprotector. Apoptosis signals were activated via the Bcl-2(Ca²⁺)/Caspase-3/PARP-1 pathway in irradiated cells and FRT inhibited this pathway of apoptosis by down-regulation of C-Caspase-3 and Ca²⁺ and up-regulation of prototype PARP-1 and Bcl-2.     

Temporal-spatial distribution,environmental significance and release risks of phosphorus in the sediments of a tropical mountain’s deep drinking water reservoir in southeastern China

In this study, the fractionation and distribution of phosphorus (P) in the core sediments of the Shanmei reservoir were investigated by using the chemical extraction method in directions for the first time in order to understand its bio-availability, adsorption characteristics, potential release and environmental significance. The results of the study showed that P in the sediments mainly consisted of inorganic phosphorus (IP) and that IP mainly consisted of non-apatite phosphorus (NAIP). The horizontal and temporal distributions of the P fractions were different from each other, but the vertical distribution was similar, which indicated a trend of stabilization after falling. The content of total phosphorus (TP), IP, organic phosphorus (OP), NAIP, apatite phosphorus (AP), and bio-available phosphorus (BAP) in the sediments during the three seasons ranged from 193.85 to 1664.05 mg·kg^?1, 126.90 to 1127.70 mg·kg^?1, 43.74 to 669.29 mg·kg^?1, 57.62 to 937.07 mg·kg^?1, 32.58 to 250.71 mg·kg^?1, and 41.06 to 871.82 mg·kg^?1, respectively. NAIP contents in the sediments accounted for more than 50% of TP. Using an analysis from three aspects, the eutrophication risk index (ERI) could be used to assess the potential release of P in the sediments, and there was a high release risk of P in the sediments in the Shanmei reservoir.     

河口浮游植物生态学研究进展

综述了河口浮游植物种类组成、时空分布、初级生态及其影响因素等方面的主要研究进展,同时,对河口浮游植物在水环境监测中的作用以及河口浮游植物多样性与边缘效应进行了初步探讨。研究表明,通常河口区重要的浮游植物有硅藻、甲藻等,微型、超微型浮游植物在河口生态系统中占有重要地位。河口浮游植物种类组成、初级生产的时空变化明显,并受到光、温度、营养盐、动物摄食以及径流等因素的影响。     

松嫩平原朝鲜碱茅无性系种群构件生物量结构及相关模型分析

从构件水平对松嫩平原碱化草甸朝鲜碱茅无性系种群各功能构件的生物量结构,各功能构件生物量与丛径之间的关系,以及各功能构件生物量之间的关系均建立相应的模型进行了定量分析。结果表明,在孕穗和果后营养两个生育期,朝鲜碱茅无性系种群各功能构件生物量及所占总生物量的比率具有相同的规律;各功能构件生物量与丛径之间的定量关系在孕穗期以直线函数模型相关性最大,在果后营养期以幂函数模型相关性最大;各功能构件生物量之间的定量关系除光合构件与支持构件在孕穗期以直线函数模型相关性最大外,其他各构件生物量之间在两个生长期均以幂函数模型相关性最大。