CpG_MPs: identification of CpG methylation patterns of genomic regions from high-throughput bisulfite sequencing data

High-throughput bisulfite sequencing is widely used to measure cytosine methylation at single-base resolution in eukaryotes. It permits systems-level analysis of genomic methylation patterns associated with gene expression and chromatin structure. However, methods for large-scale identification of methylation patterns from bisulfite sequencing are lacking. We developed a comprehensive tool, CpG_MPs, for identification and analysis of the methylation patterns of genomic regions from bisulfite sequencing data. CpG_MPs first normalizes bisulfite sequencing reads into methylation level of CpGs. Then it identifies unmethylated and methylated regions using the methylation status of neighboring CpGs by hotspot extension algorithm without knowledge of pre-defined regions. Furthermore, the conservatively and differentially methylated regions across paired or multiple samples (cells or tissues) are identified by combining a combinatorial algorithm with Shannon entropy. CpG_MPs identified large amounts of genomic regions with different methylation patterns across five human bisulfite sequencing data during cellular differentiation. Different sequence features and significantly cell-specific methylation patterns were observed. These potentially functional regions form candidate regions for functional analysis of DNA methylation during cellular differentiation. CpG_MPs is the first user-friendly tool for identifying methylation patterns of genomic regions from bisulfite sequencing data, permitting further investigation of the biological functions of genome-scale methylation patterns.     

围产期克罗米酚处理改变雄性小鼠性取向

由于体内激素水平的变化,围产期和青春期是决定动物大脑发育的关键和敏感时期,而大脑发育是成年动物性取向行为的生物基础。该研究根据这一假说,对实验动物分别于围产期给予药物处理或于青春期予以阉割,并观察其个体成年后的性取向行为。结果显示,围产期克罗米酚(clomiphene citrate)处理9 d(分娩前3天到生育后6天)和14 d(分娩前7天到生育后7天)组,雄性后代的同性取向和雌性化行为明显增多,而正常生长状态下的21日龄雄性后代经阉割后,其性取向无明显改变。即围产期抑制雌激素,可导致雄性小鼠大脑雌性化,产生同性取向,且围产期雌激素对动物雄性化的影响较青春期更为明显。     

树鼩解剖数据的测定与分析

解剖数据是实验动物主要的生物学特性指标。该文对实验室驯养树鼩(7～9月龄)的体尺、骨骼、乳头、肠道及脏器重量与系数等解剖学数据进行了测定与分析。31项解剖数据测量结果显示雌、雄个体间体高、右耳宽、回肠及结肠差异显著(P<0.05),体斜长、胸深、躯干长、左右两前肢长、右后肢长、左右两侧耳长、左耳宽、龙骨长、左右两侧胫长、十二指肠及空肠长等差异极显著(P<0.01)。以体长为因变量,尾长、躯干长、左前肢长、右前肢长、左后肢长及右后肢长等为自变量作逐步回归分析,回归方程为:体长=13.90+尾长×0.16。37项脏器及系数测定结果:雌雄间比较,体重、心、肺、脾、左肾、右肾、膀胱、左海马、右海马、左颌下腺、左甲状腺、右甲状腺重量差异极显著(P<0.01)。小肠、右颌下腺、左肾上腺之间差异显著(P<0.05);心、肺、胃、膀胱、小肠、大肠、脑、右海马、左肾上腺系数雌雄间差异极显著(P<0.01)。右肾、左海马、左颌下腺、右肾上腺、左右两侧甲状腺系数之间达到了显著性水平(P<0.05)。以动物体重为因变量,以主要脏器指标:心脏、肺、肝、脾、左肾、右肾、脑为自变量,作逐步回归分析,回归方程为:体重=62.73+左肾×79.213+心脏×24.09。实验室驯养树鼩不同性别对体尺、脏器及系数、肠道等解剖数据有一定影响,为树鼩实验动物化及人类疾病动物模型研究提供基础数据。     

Role of autophagy in early brain injury after subarachnoid hemorrhage in rats

Early brain injury (EBI) occurred after aneurismal subarachnoid hemorrhage (SAH) strongly determined the patients’ prognosis. Autophagy was activated in neurons in the acute phase after SAH, while its role in EBI has not been examined. This study was designed to explore the effects of autophagy on EBI post-SAH in rats. A modified endovascular perforating SAH model was established under monitoring of intracranial pressure. Extent of autophagy was regulated by injecting autophagy-regulating drugs (3-methyladenine, wortmannin and rapamycin) 30 min pre-SAH intraventricularly. Simvastatin (20 mg/kg) was prophylactically orally given 14 days before SAH induction. Mortality, neurological scores, brain water content and blood–brain barrier (BBB) permeability were evaluated at 24 h post-SAH. Microtubule-associated protein light chain-3 (LC3 II/I) and beclin-1 were detected for monitoring of autophagy flux. Terminal deoxynucleotidyl transferase-mediated biotinylated UTP nick end labeling, expression of cleaved caspase-3 and cytoplasmic histone-associated DNA fragments were used to detect apoptosis. The results showed that mortality was reduced in rapamycin and simvastatin treated animals. When autophagy was inhibited by 3-methyladenine and wortmannin, the neurological scores were decreased, brain water content and BBB permeability were further aggravated and neuronal apoptosis was increased when compared with the SAH animals. Autophagy was further activated by rapamycin and simvastatin, and apoptosis was inhibited and EBI was ameliorated. The present results indicated that activation of autophagy decreased neuronal apoptosis and ameliorated EBI after SAH. Aiming at autophagy may be a potential effective target for preventing EBI after SAH.     

岷江百合类萌发素蛋白基因LrGLP2的克隆及表达特性分析

类萌发素蛋白是植物中普遍存在的一类可溶性糖蛋白,在植物抗逆胁迫中起着重要作用。依据岷江百合编码GLP的EST序列设计引物,采用快速扩增cDNA末端技术,从岷江百合犯ilium regale Wilson）克隆得到一个新的GLＰt基因的全长eDNA序列,命名为LrGLP2。LrGLP2全长cDNA为921bp,含有654bp的开放阅读框,49bp5’非编码区以及218bp3’UTR,编码217个氨基酸的蛋白质。LrGLP2编码蛋白质与已知植物GLPs家族成员间的同源性和聚类分析表明LrGLP2与来源于水稻（Oryza sativa）、节节麦似egilopstauschii）、葡萄（Vitis vinifera）中的GLPs具有较高的相似性。qRT-PCR分析显示,LrGLP2在岷江百合正常生长发育的根中有一定量的表达,而在茎和叶中几乎检测不到表达量。水杨酸、茉莉酸以及H202处理均不同程度抑制LrGLP2的转录水平,但乙烯处理能明显诱导LrGLP2的表达。此外,岷江百合接种尖孢镰刀菌（Fusari—umoxysporumfsp．tiliO后,LrGLP2在接种后2h表达迅速上调,12h表达量急剧上升,至24h表达量达到最大值,之后表达量下降,可见￡rGLP2参与岷江百合对尖孢镰刀菌的防卫反应。     

Impact of cranberry juice on initial adhesion of the EPS producing bacterium Burkholderia cepacia

The impact of cranberry juice was investigated with respect to the initial adhesion of three isogenic strains of the bacterium Burkholderia cepacia with different extracellular polymeric substance (EPS) producing capacities, viz. a wild-type cepacian EPS producer PC184 and its mutant strains PC184rml with reduced EPS production and PC184bceK with a deficiency in EPS production. Adhesion experiments conducted in a parallel-plate flow chamber demonstrated that, in the absence of cranberry juice, strain PC184 had a significantly higher adhesive capacity compared to the mutant strains. In the presence of cranberry juice, the adhesive capacity of the EPS-producing strain PC184 was largely reduced, while cranberry juice had little impact on the adhesion behavior of either mutant strain. Thermodynamic modeling supported the results from adhesion experiments. Surface force apparatus (SFA) and scanning electron microscope (SEM) studies demonstrated a strong association between cranberry juice components and bacterial EPS. It was concluded that cranberry juice components could impact bacterial initial adhesion by adhering to the EPS and impairing the adhesive capacity of the cells, which provides an insight into the development of novel treatment strategies to block the biofilm formation associated with bacterial infection.     

S100 protein-immunoreactive trigeminal neurons innervating the rat molar tooth pulp

S100-immunoreactivity (ir) was examined in tooth pulp primary neurons of the rat. An immunofluorescence method demonstrated that the molar tooth pulp contained S100-immunoreactive (ir) nerve fibers. In the root pulp, pulp horn and roof of the pulp chamber, S100-ir smooth and varicose fibers ramified and formed subodontoblastic nerve plexuses. All the fibers became varicose at the base of the odontoblastic layer and extended to the odontoblastic layer. Some varicose endings could be traced into the dentin. The trigeminal neurons retrogradely labeled with fluorogold (FG) from the first and second maxillary molar tooth pulps exhibited S100- and parvalbumin-ir. Approximately 60% and 24% of the labeled cells were ir for S100 and parvalbumin, respectively. Virtually all parvalbumin-ir FG-labeled cells showed S100-ir, while 40% of S100-ir ones coexpressed parvalbumin-ir. An immunoelectron microscopic method revealed that all myelinated axons and half of the unmyelinated axons in the root pulp contained S100-ir. In the odontoblastic layer, predentin and dentin, S100-ir neurites lost the Schwann cell ensheathment and made close contact with cell bodies and processes of odontoblasts. The odontoblastic layer also contained parvalbumin-ir neurites. These neurites were devoid of the Schwann cell ensheathment and in close apposition to cell bodies and processes of odontoblasts. S100-ir pulpal axons seemed to be insensitive to repeated neonatal capsaicin treatment. This study suggests that S100-ir tooth pulp primary neurons are mostly myelinated and that S100-ir unmyelinated axons in the root pulp are preterminal segments of myelinated stem axons.