A bulky DNA lesion derived from a highly potent polycyclic aromatic tumorigen stabilizes nucleosome core particle structure

The impact of a bulky DNA lesion on the structure and dynamics of a nucleosome core particle (NCP) containing a lesion derived from the unusually potent tumorigen dibenzo[a,l]pyrene that resists nucleotide excision repair (NER) in free DNA was investigated using 65 ns molecular dynamics simulations. Our results reveal that, relative to unmodified NCP, the lesion stabilizes the nucleosome via stacking interactions, improved Watson-Crick base pairing, hydrogen bonding between DNA and histones, and damped dynamics. These findings suggest that such lesions should be as resistant to NER in the nucleosome environment as they are in free DNA.     

Effect of abscisic acid on heat stress tolerance in the calli from two ecotypes of <Emphasis Type="Italic">Phragmites communis</Emphasis>

Dune reed (DR) and swamp reed (SR) are two ecotypes of reed (Phragmites communis Trin.) that displayed differences in stress tolerance. To uncover the molecular basis for such difference, the effects of heat stress were studied using the calli derived from the two ecotypes. Heat stress caused increased ion leakage, inhibited growth, decreased cell viability, and elevated hydrogen peroxide (H₂O₂) and malondialdehyde (MDA) contents in the calli of both ecotypes, but DR callus showed better heat tolerance than SR callus. In DR callus, heat stress caused significant increase in the endogenous ABA content but not in SR callus. Application of fluridone (an ABA synthesis inhibitor) aggravated the heat stress damages on the DR callus whereas it had only minimal impact on the SR callus. Exogenous application of ABA alleviated the heat stress symptoms in the calli of both ecotypes. ABA treatment increased the activities of superoxide dismutase, catalase, ascorbate peroxidase and peroxidase, and also decreased H₂O₂ and MDA contents. These results indicate that the ability of ABA synthesis under heat stress is a key factor attributing to the higher heat tolerance of DR than SR.     

百日咳杆菌粘附素对猪源支气管败血波氏杆菌的保护性抗原的筛选

摘要：【目的】本研究通过百日咳杆菌黏附素(PRN)基因的分段克隆表达及其在BALB/c小鼠的主动和被动免疫保护试验筛选PRN中的保护性抗原肽。【方法和结果】利用大肠杆菌进行PRN的完整蛋白、N端和C端多肽及其RI和RII区域多肽（双拷贝）的表达,命名为GST-PRN、GST-PN、GST-PC、GST-2PRI和GST-2PRII。Western blot检测证实5种表达产物均具有良好的反应原性。在主动免疫保护试验中,5种表达产物均能诱导小鼠产生较高的PRN抗体水平;当使用3 LD50的支气管败血波氏杆菌     

厌氧氨氧化菌富集培养物对羟胺的转化研究

【目的】羟胺是厌氧氨氧化的重要中间产物,本研究旨在探明厌氧氨氧化菌对羟胺的转化特性。【方法】采用厌氧氨氧化菌富集培养物,以羟胺和亚硝酸盐为基质进行分批培养试验,检测反应液中基质和产物的消涨情况。【结果】不接种厌氧氨氧化富集培养物时,羟胺和亚硝酸盐具有化学稳定性,彼此不发生化学反应;接种厌氧氨氧化富集培养物后,羟胺和亚硝酸盐发生化学反应;反应过程中有中间产物氨的产生和转化,最大氨氮积累浓度为0.338mmol/L;液相中总氮浓度从起始的4.694mmol/L降至结束时的0.812mmol/L,转化率为82.7%。羟胺和亚硝氮浓度均为2.5mmol/L时,羟胺最大比污泥转化速率为0.535mmol/(gVSS.h),是厌氧氨氧化反应体系中氨氮最大比污泥转化速率的1.81倍。将羟胺浓度提高至5.0mmol/L时,羟胺和亚硝氮转化速率分别提高26.7%和120.7%,最大氨氮积累浓度为0.795mmol/L;将亚硝氮浓度提高至5.0mmol/L时,羟胺和亚硝氮转化速率分别提高6.9%和9.0%,最大氨氮积累浓度为1.810mmol/L。【结论】厌氧氨氧化富集培养物能够转化羟胺,其对羟胺的转化速率高于对氨的转化速率。羟胺相对过量可显著加快羟胺和亚硝酸盐的转化速率,亚硝酸盐相对过量对羟胺和亚硝氮转化速率影响不大,提高羟胺或亚硝氮浓度均会增大中间产物氨氮的积累。实验现象可用van de Graaf模型解释,对于进一步开发厌氧氨氧化工艺具有重要的理论意义。     

马立克氏病病毒meq基因敲除株感染性克隆的免疫效果评价

【目的】比较和评价了敲除meq基因的MDV感染性克隆作为新型DNA疫苗的免疫保护效果。【方法】将1日龄SPF鸡饲养于正压过滤空气的SPF动物饲养隔离罩内。1日龄时,将SPF鸡以10μg/只的剂量通过大腿肌肉注射的方式接种溶解于PBS缓冲液中的敲除meq基因的MDV感染性克隆GX0101 Δmeq-BAC,分别在免疫后5天或12天以500PFU/只的剂量接种超强毒rMd5。饲养90天,观察死亡情况,对每一只鸡剖检并取心脏与肝脏做石蜡切片,进行病理观察。【结果】免疫5天后攻毒,CVI988/Rispens对超强毒rMd5的保护指数可达到87%,GX0101 Δmeq-BAC对rMd5的保护指数仅达33%;而免疫12天后对rMd5的保护指数为53%。【结论】相对于细胞结合疫苗CVI988/Rispens,DNA疫苗在机体内的病毒拯救是使其获得保护力的前提条件,因此有一定的免疫空当期。以GX0101 Δmeq-BAC作为疫苗免疫不仅能使雏鸡在受到超强毒感染时发病延迟,而且还能提供较好的免疫保护效果。     

The Notch signaling pathway in retinal dysplasia and retina vascular homeostasis

The retina is one of the most essential elements of vision pathway in vertebrate. The dysplasia of retina cause congenital blindness or vision disability in individuals, and the misbalance in adult retinal vascular homeostasis leads to neovaseularization-associated diseases in adults, such as diabetic retinopathy or age-related macular degeneration. Many developmental signaling pathways are involved in the process of retinal development and vascular homeostasis. Among them, Notch signaling pathway has long been studied, and Notch signaling-interfered mouse models show both neural retina dysplasia and vascular abnormality. In this review, we discuss the roles of Notch signaling in the maintenance of retinal progenitor cells, specification of retinal neurons and glial cells, and the sustaining of retina vascular homeostasis, especially from the aspects of conditional knockout mouse models. The potential of Notch signal mampulation may provide a powerful cell fate- and neovascularization-controlling tool that could have important applications in la'eatment of retinal diseases.     

Activation of gibberellin 2-oxidase 6 decreases active gibberellin levels and creates a dominant semi-dwarf phenotype in rice （Oryza sativa L.）

Gibberellin (GA) 2-oxidase plays a key role in the GA catabolic pathway through 2β-hydroxylation.In the present study,we isolated a CaMV 35S-enhancer activation tagged mutant,H032.This mutant exhibited a dominant dwarf and GA-deficient phenotype,with a final stature that was less than half of its wild-type counterpart.The endogenous bioactive GAs are markedly decreased in the H032 mutant,and application of bioactive GAs (GA3 or GA4) can reverse the dwarf phenotype.The integrated T-DNA was detected 12.8 kb upstream of the OsGA2ox6 in the H032 genome by TAIL-PCR.An increased level of OsGA2ox6 mRNA was detected at a high level in the H032 mutant,which might be due to the enhancer role of the CaMV 35S promoter.RNAi and ectopic expression analysis of OsGA2ox6 indicated that the dwarf trait and the decreased levels of bioactive GAs in the H032 mutant were a result of the up-regulation of the OsGA2ox6 gene.BLASTP analysis revealed that OsGA2ox6 belongs to the class III of GA 2-oxidases,which is a novel type of GA2ox that uses C20-GAs (GA12 and/or GA53) as the substrates.Interestingly,we found that a GA biosynthesis inhibitor,paclobutrazol,positively regulated the OsGA2ox6 gene.Unlike the over-expression of OsGA2ox1,which led to a high rate of seed abortion,the H032 mutant retained normal flowering and seed production.These results indicate that OsGA2ox6 mainly affects plant stature,and the dominant dwarf trait of the H032 mutant can be used as an efficient dwarf resource in rice breeding.     

The nucleocytoplasmic transport of viral proteins

Molecules can enter the nucleus by passive diffusion or active transport mechanisms, depending on their size. Small molecules up to size of 50-60 kDa or less than 10 nm in diameter can diffuse passively through the nuclear pore complex (NPC), while most proteins are transported by energy driven transport mechanisms. Active transport of viral proteins is mediated by nuclear localization signals (NLS), which were first identified in Simian Virus 40 large T antigen and had subsequently been identified in a large number of viral proteins. Usually they contain short stretches of lysine or arginine residues. These signals are recognized by the importin super-family (importin α and β) proteins that mediate the transport across the nuclear envelope through Ran-GTP. In contrast, only one class of the leucine-rich nuclear export signal (NES) on viral proteins is known at present. Chromosome region maintenance 1 (CRM1) protein mediates nuclear export of hundreds of viral proteins through the recognition of the leucine-rich NES.     

Determining modular organization of protein interaction networks by maximizing modularity density

Background

With ever increasing amount of available data on biological networks, modeling and understanding the structure of these large networks is an important problem with profound biological implications. Cellular functions and biochemical events are coordinately carried out by groups of proteins interacting each other in biological modules. Identifying of such modules in protein interaction networks is very important for understanding the structure and function of these fundamental cellular networks. Therefore, developing an effective computational method to uncover biological modules should be highly challenging and indispensable.

Results

The purpose of this study is to introduce a new quantitative measure modularity density into the field of biomolecular networks and develop new algorithms for detecting functional modules in protein-protein interaction (PPI) networks. Specifically, we adopt the simulated annealing (SA) to maximize the modularity density and evaluate its efficiency on simulated networks. In order to address the computational complexity of SA procedure, we devise a spectral method for optimizing the index and apply it to a yeast PPI network.

Conclusions

Our analysis of detected modules by the present method suggests that most of these modules have well biological significance in context of protein complexes. Comparison with the MCL and the modularity based methods shows the efficiency of our method.