Selective Capture of 5-hydroxymethylcytosine from Genomic DNA

5-methylcytosine (5-mC) constitutes ~2-8% of the total cytosines in human genomic DNA and impacts a broad range of biological functions, including gene expression, maintenance of genome integrity, parental imprinting, X-chromosome inactivation, regulation of development, aging, and cancer¹. Recently, the presence of an oxidized 5-mC, 5-hydroxymethylcytosine (5-hmC), was discovered in mammalian cells, in particular in embryonic stem (ES) cells and neuronal cells^2-4. 5-hmC is generated by oxidation of 5-mC catalyzed by TET family iron (II)/α-ketoglutarate-dependent dioxygenases^{2, 3}. 5-hmC is proposed to be involved in the maintenance of embryonic stem (mES) cell, normal hematopoiesis and malignancies, and zygote development^{2, 5-10}. To better understand the function of 5-hmC, a reliable and straightforward sequencing system is essential. Traditional bisulfite sequencing cannot distinguish 5-hmC from 5-mC¹¹. To unravel the biology of 5-hmC, we have developed a highly efficient and selective chemical approach to label and capture 5-hmC, taking advantage of a bacteriophage enzyme that adds a glucose moiety to 5-hmC specifically¹².Here we describe a straightforward two-step procedure for selective chemical labeling of 5-hmC. In the first labeling step, 5-hmC in genomic DNA is labeled with a 6-azide-glucose catalyzed by β-GT, a glucosyltransferase from T4 bacteriophage, in a way that transfers the 6-azide-glucose to 5-hmC from the modified cofactor, UDP-6-N3-Glc (6-N3UDPG). In the second step, biotinylation, a disulfide biotin linker is attached to the azide group by click chemistry. Both steps are highly specific and efficient, leading to complete labeling regardless of the abundance of 5-hmC in genomic regions and giving extremely low background. Following biotinylation of 5-hmC, the 5-hmC-containing DNA fragments are then selectively captured using streptavidin beads in a density-independent manner. The resulting 5-hmC-enriched DNA fragments could be used for downstream analyses, including next-generation sequencing.Our selective labeling and capture protocol confers high sensitivity, applicable to any source of genomic DNA with variable/diverse 5-hmC abundances. Although the main purpose of this protocol is its downstream application (i.e., next-generation sequencing to map out the 5-hmC distribution in genome), it is compatible with single-molecule, real-time SMRT (DNA) sequencing, which is capable of delivering single-base resolution sequencing of 5-hmC.     

Improving aquaporin Z expression in <Emphasis Type="Italic">Escherichia coli</Emphasis> by fusion partners and subsequent condition optimization

Aquaporin Z (AqpZ), a typical orthodox aquaporin with six transmembrane domains, was expressed as a fusion protein with TrxA in E. coli in our previous work. In the present study, three fusion partners (DsbA, GST and MBP) were employed to improve the expression level of this channel protein in E. coli. The result showed that, compared with the expression level of TrxA-AqpZ, five- to 40-fold increase in the productivity of AqpZ with fusion proteins was achieved by employing these different fusion partners, and MBP was the most efficient fusion partner to increase the expression level. By using E. coli C43 (DE3)/pMAL-AqpZ, the effects of different expression conditions were investigated systematically to improve the expression level of MBP-AqpZ in E. coli. The high productivity of MBP-AqpZ (200 mg/l) was achieved under optimized conditions. The present work provides a novel approach to improve the expression level of membrane proteins in E. coli.     

季节、环境温度与黄鼠冬眠的关系

观察了达乌尔黄鼠在实验室内冬眠的一般情况。常温黄鼠的体温有着规律性的年周期,与环境温度的年周期变动不完全呈依从关系。出眠初期(4月下旬),动物体温高而稳定。4月至6月常温黄鼠的平均体温(皮温)为35.6℃,波动菹围32—37.5℃。随着体重达到顶峰,体温逐渐降低。8月份部分黄鼠出现低于32℃的低常体温,表明部分黄鼠自8月盛夏开始冬眠。但就整个种群而言,北京地区实验室内黄鼠冬眠季自9月下半月开始。3月底止,共6.5个月。秋季室温下降,动物入眠趋势增长。浅低体温(31.9—15℃)的比数逐渐升高。9月至12月,低体温(低于31.9℃)的百分比从47％增至84.8％,反映了动物从浅冬眠向深冬眠过渡。1月至2月份,低体温占85％以上,深低体温(低于15℃)占绝对优势。标志着动物种群的深眠月份。秋季动物从常温期向冬眠期转化的界线是不清的,而春季从冬眠期向常温相转化的界限却比较明显。     

An Ultralong Lifespan and Low‐Temperature Workable Sodium‐Ion Full Battery for Stationary Energy Storage

Presently, commercialization of sodium‐ion batteries (SIBs) is still hindered by the relatively poor energy‐storage performance. In addition, low‐temperature (low‐T) Na storage is another principal concern for the wide application of SIBs. Unfortunately, the Na‐transfer kinetics is extremely sluggish at low‐T, as a result, there are few reports on low‐T SIBs. Here, an advanced low‐T sodium‐ion full battery (SIFB) assembled by an anode of 3D Se/graphene composite and a high‐voltage cathode (Na₃V₂(PO₄)₂O₂F) is developed, exhibiting ultralong lifespan (over even 15 000 cycles, the capacity retention is still up to 86.3% at 1 A g^?1), outstanding low‐T energy storage performance (e.g., all values of capacity retention are >75% after 1000 cycles at temperatures from 25 to ?25 °C at 0.4 A g^?1), and high‐energy/power properties. Such ultralong lifespan signifies that the developed sodium‐ion full battery can be used for longer than 60 years, if batteries charge/discharge once a day and 80% capacity retention is the standard of battery life. As a result, the present study not only promotes the practicability and commercialization of SIBs but also points out the new developing directions of next‐generation energy storage for wider range applications.     

Lack of association between AQP4 polymorphisms and risk of inflammatory demyelinating disease in a Korean population

Multiple sclerosis (MS) and neuromyelitis optica (NMO) are demyelinating autoimmune inflammatory diseases that affect the central nervous system (CNS). Previous genome-wide or candidate gene studies have suggested that genetic variants might be associated with the risk of MS or NMO. Aquaporin 4 (AQP4) is a commonly distributed water channel in astrocytes of the CNS, and its expression is decreased in NMO lesions due to astrocyte cytotoxicity. Previous studies have suggested the associations of AQP4 single nucleotide polymorphisms (SNPs) with MS and/or NMO. However, there have been few replication studies in various ethnic populations. This study, as the first of its kind performed in an Asian population, investigated associations of AQP4 SNPs with the risk of inflammatory demyelinating disease (IDD), including MS and NMO, in a Korean population. A total of seven common AQP4 SNPs were selected based on status of linkage disequilibrium (LD), and then genotyped in 178 IDD cases (79 MS and 99 NMO patients) and 237 normal controls. Statistical analyses showed no significant associations between AQP4 SNPs/haplotypes and development of IDD, including MS and NMO (P > 0.05). Further replications in larger cohorts and other ethnic groups are needed.     

An efficient algorithm for DNA fragment assembly in MapReduce

Fragment assembly is one of the most important problems of sequence assembly. Algorithms for DNA fragment assembly using de Bruijn graph have been widely used. These algorithms require a large amount of memory and running time to build the de Bruijn graph. Another drawback of the conventional de Bruijn approach is the loss of information. To overcome these shortcomings, this paper proposes a parallel strategy to construct de Bruijin graph. Its main characteristic is to avoid the division of de Bruijin graph. A novel fragment assembly algorithm based on our parallel strategy is implemented in the MapReduce framework. The experimental results show that the parallel strategy can effectively improve the computational efficiency and remove the memory limitations of the assembly algorithm based on Euler superpath. This paper provides a useful attempt to the assembly of large-scale genome sequence using Cloud Computing.