PROSPECT II: protein structure prediction program for genome-scale applications

A new method for fold recognition is developed and added to the general protein structure prediction package PROSPECT (http://compbio.ornl.gov/PROSPECT/). The new method (PROSPECT II) has four key features. (i) We have developed an efficient way to utilize the evolutionary information for evaluating the threading potentials including singleton and pairwise energies. (ii) We have developed a two-stage threading strategy: (a) threading using dynamic programming without considering the pairwise energy and (b) fold recognition considering all the energy terms, including the pairwise energy calculated from the dynamic programming threading alignments. (iii) We have developed a combined z-score scheme for fold recognition, which takes into consideration the z-scores of each energy term. (iv) Based on the z-scores, we have developed a confidence index, which measures the reliability of a prediction and a possible structure-function relationship based on a statistical analysis of a large data set consisting of threadings of 600 query proteins against the entire FSSP templates. Tests on several benchmark sets indicate that the evolutionary information and other new features of PROSPECT II greatly improve the alignment accuracy. We also demonstrate that the performance of PROSPECT II on fold recognition is significantly better than any other method available at all levels of similarity. Improvement in the sensitivity of the fold recognition, especially at the superfamily and fold levels, makes PROSPECT II a reliable and fully automated protein structure and function prediction program for genome-scale applications.     

Molecular engineering of biotin-glutamic acid decarboxylase 65 fusion protein (Biotin-GAD65) for non-radioactive GAD65 antibody assay

We constructed biotinylated fusion proteins that linked to three detection tags to GAD65 at the N-terminus, and expressed them in an E. coli expression system. The Biotin14-GAD65 protein exhibited the strongest binding to both the GAD65 antibody and the streptavidin among the three constructs. We describe the optimal conditions using a Biotin14-GAD65-based immunoassay for the detection of GAD65 antibody.     

叶酸靶向载顺铂羧甲基-β-环糊精纳米复合物的制备及对鼻咽癌的体外抑制效应

为达到鼻咽癌（nasopharyngeal carcinoma,NeC）的靶向化疗,该研究通过酰胺化反应和配位偶联技术制备叶酸（folicacid,FA）分子靶向载川页铂（cisplatin,CDDP）羧甲基-β-环糊精（carboxymethyl-β-cyclodextrin,CM—β—CD）纳米复合物（FA-CM—β—CD—CDDP）,采用邻苯二胺（o-phenylenediamine,OPDA）比色法检测复合物中CDDP含量,紫外分光光谱检测FA含量,透射电镜观察复合物形态,激光粒度仪测定复合物粒径大小。荧光显微镜观察NPC叶酸受体（folatereceptor,FR）阳性HNE-1细胞及FR阴性CNE-2细胞对偶联FITC的复合物的吞噬及OPDA比色法检测细胞内CDDP的浓度。通过MTT法、集落形成实验和流式细胞术检测复合物对HNE-1细胞增殖能力和凋亡的影响。研究结果显示,复合物中偶联的FA和CDDP浓度分别为340gg／mL和2mg／mL,CDDP包封率达20．00％,复合物粒径均匀且大小为157．8nm。HNE-1细胞内见较多FITC,细胞内CDDP浓度为6．24ng／mL,而CNE-2细胞内FITC较少,细胞内CDDP浓度仅约2．01ng／mL。HNE-1生长抑制率在24h明显高于对照组（CM—β—CD—CDDP）,其IC50（4．80μg／mL）明显低于对照组（6．97μg／mL）,但当所载的CDDP终浓度达到16．00μg／mL时,两组抑制率均达到80％以上;作用48h两组抑制率无明显差异。在24h,当复合物的CDDP终浓度为1．00μg／mL时,HNE—1的集落形成率为33．21％,明显低于对照组（52．27％）。当复合物的CDDP终浓度为0．25μg／mL和1．00μg／mL时,HNE-1的凋亡率分别达12．65％和22．35％,明显高于对照组（6．91％和14.21％）。研究结果表明,成功构建的FA—CM—β—CD．cDDP纳米复合物能够靶向抑制FR阳性的NPC细胞增殖并促进其凋亡。     

Daphnane‐Type Diterpenoid Glucosides and Further Constituents of Euphorbia pilosa

Phytochemical investigation of whole plants of Euphorbia pilosa led to the isolation and identification of two new daphnane‐diterpenoid glucosides, euphopilosides A and B ( 1 and 2 , resp.), and a new ent‐abietane, euphopilolide ( 3 ), together with eight known compounds. Compounds 1 and 2 are the first daphnane‐type diterpenoid glycosides. Their structures were elucidated by a combination of 1D‐ and 2D‐NMR, and MS analyses, and acid hydrolysis. Compounds 1 – 9 were evaluated for their in vitro cytotoxicities against five human tumor cell lines, HL‐60, SMMC‐7721, A‐549, MCF‐7, and SW‐480. Compound 7 showed moderate inhibitory activity against all five cell lines.     

Polycomb-group histone methyltransferase CLF is required for proper somatic recombination in Arabidopsis

Homologous recombination(HR) is a key process during meiosis in reproductive cells and the DNA damage repair process in somatic cells. Although chromatin structure is Researchthought to be crucial for HR, only a small number of chromatin modifiers have been studied in HR regulation so far. Here, we investigated the function of CURLY LEAF(CLF), a Polycomb-group(PcG) gene responsible for histone3 lysine 27 trimethylation(H3K27me3), in somatic and meiotic HR in Arabidopsis thaliana. Although fluorescent protein reporter assays in pollen and seeds showed that the frequency of meiotic cross-over in the loss-of-function mutant clf-29 was not significantly different from that in wild type, there was a lower frequency of HR in clf-29 than in wild type under normal conditions and under bleomycin treatment. The DNA damage levels were comparable between clf-29 and wild type, even though several DNA damage repair genes(e.g. ATM, BRCA2 a, RAD50, RAD51, RAD54,and PARP2) were expressed at lower levels in clf-29. Under bleomycin treatment, the expression levels of DNA repair genes were similar in clf-29 and wild type, thus CLF may also regulate HR via other mechanisms. These findings expand the current knowledge of PcG function and contribute to general interests of epigenetic regulation in genome stability regulation.     

Adiponectin Alleviates Genioglossal Mitochondrial Dysfunction in Rats Exposed to Intermittent Hypoxia

Background

Genioglossal dysfunction is involved in the pathophysiology of obstructive sleep apnea hypoxia syndrome (OSAHS) characterized by nocturnal chronic intermittent hypoxia (CIH). The pathophysiology of genioglossal dysfunction and possible targeted pharmacotherapy for alleviation of genioglossal injury in CIH require further investigation.

Methodology/Principal Findings

Rats in the control group were exposed to normal air, while rats in the CIH group and CIH+adiponectin (AD) group were exposed to the same CIH condition (CIH 8 hr/day for 5 successive weeks). Furthermore, rats in CIH+AD group were administrated intravenous AD supplementation at the dosage of 10 µg, twice a week for 5 consecutive weeks. We found that CIH-induced genioglossus (GG) injury was correlated with mitochondrial dysfunction, reduction in the numbers of mitochondrias, impaired mitochondrial ultrastructure, and a reduction in type I fibers. Compared with the CIH group, impaired mitochondrial structure and function was significantly improved and a percentage of type I fiber was elevated in the CIH+AD group. Moreover, compared with the control group, the rats’ GG in the CIH group showed a significant decrease in phosphorylation of LKB1, AMPK, and PGC1-α, whereas there was significant rescue of such reduction in phosphorylation within the CIH+AD group.

Conclusions

CIH exposure reduces mitochondrial biogenesis and impairs mitochondrial function in GG, while AD supplementation increases mitochondrial contents and alleviates CIH-induced mitochondrial dysfunction possibly through the AMPK pathway.     

AtSARK互作蛋白的筛选与鉴定

植物LRR型类受体蛋白激酶在植物生命活动中发挥着重要作用。前期研究发现了一个通过生长素和乙烯的协同作用参与拟南芥叶片衰老过程正调控的类受体蛋白激酶, AtSARK。为深入研究 AtSARK 蛋白的作用机制, 文章采用酵母双杂交系统, 以AtSARK胞内域（AtSARK-CD）为诱饵蛋白, 对拟南芥均一化cDNA文库进行筛选, 得到83个AtSARK的候选互作组分, 经过复筛, 初步发现AtSARK的互作组分包括14-3-3蛋白、FKBP-型肽脯氨酰顺反异构酶、醛缩酶超家族成员、RING/U-box 超家族成员以及WRKY转录因子家族成员。我们对其中一个功能未知的醛缩酶家族基因AtFBA5 （AT4G26530）的表达模式进行了分析, 并用GST pulldown实验证实了AtSARK-CD与 AtFBA5间存在直接的相互作用。At-SARK互作组分的文库筛选及AtFBA5的分离有利于进一步研究 AtSARK 基因在衰老信号通路中的作用机制。     

Methyl-CpG-Binding Domain Protein MBD7 Is Required for Active DNA Demethylation in Arabidopsis

Although researchers have established that DNA methylation and active demethylation are dynamically regulated in plant cells, the molecular mechanism for the regulation of active DNA demethylation is not well understood. By using an Arabidopsis (Arabidopsis thaliana) line expressing the Promoter RESPONSIVE TO DEHYDRATION 29A:LUCIFERASE (ProRD29A:LUC) and Promoter cauliflower mosaic virus 35S:NEOMYCIN PHOSPHOTRANSFERASE II (Pro35S:NPTII) transgenes, we isolated an mbd7 (for methyl-CpG-binding domain protein7) mutant. The mbd7 mutation causes an inactivation of the Pro35S:NPTII transgene but does not affect the expression of the ProRD29A:LUC transgene. The silencing of the Pro35S:NPTII reporter gene is associated with DNA hypermethylation of the reporter gene. MBD7 interacts physically with REPRESSOR OF SILENCING5/INCREASED DNA METHYLATION2, a protein in the small heat shock protein family. MBD7 prefers to target the genomic loci with high densities of DNA methylation around chromocenters. The Gypsy-type long terminal repeat retrotransposons mainly distributed around chromocenters are most affected by mbd7 in all transposons. Our results suggest that MBD7 is required for active DNA demethylation and antisilencing of the genomic loci with high densities of DNA methylation in Arabidopsis.DNA methylation is an important epigenetic marker for genome stability and the regulation of gene expression in both plants and animals (Law and Jacobsen, 2010; He et al., 2011). In plants, the molecular mechanisms for DNA methylation have been well characterized by the use of powerful genetic screening systems (Bartee et al., 2001; Lindroth et al., 2001; Matzke et al., 2004; He et al., 2009). A transgene or an endogenous gene may be silenced because of DNA hypermethylation in the promoter region. Screenings for mutants with release of the silenced marker genes have identified many components that are involved in RNA-directed DNA methylation (RdDM) and in maintaining DNA methylation (Matzke and Birchler, 2005; Law and Jacobsen, 2009; He et al., 2011; Bender, 2012). DNA methylation is catalyzed by DNA methyltransferases including DNA METHYLTRANSFERASE1 (MET1) and CHROMOMETHYLASE3 (CMT3), which maintain symmetric CG and CHG methylation, respectively, during DNA replication, and DOMAINS REARRANGED METHYLASE2 (DRM2) and CMT2, which are required for establishing CHG and asymmetric CHH methylation during each cell cycle. DRM2 also catalyzes CG methylation (Law and Jacobsen, 2010; Haag and Pikaard, 2011; He et al., 2011; Zemach et al., 2013; Stroud et al., 2014). Twenty-four-nucleotide small RNAs produced through the RdDM pathway target genomic regions to guide the establishment of DNA methylation by DRM2 (Cao et al., 2003).DNA methylation can be actively removed by a subfamily of bifunctional DNA glycosylases/lyases including REPRESSOR OF SILENCING1 (ROS1; Gong et al., 2002) and its paralogs DEMETER and DEMETER-LIKE2/3 (Gehring et al., 2006; Ortega-Galisteo et al., 2008). DNA methylation can also be passively lost during DNA replication when DNA methylation cannot be maintained (Zhu, 2009). Promoter RESPONSIVE TO DEHYDRATION 29A:LUCIFERASE (ProRD29A:LUC) in the ProRD29A:LUC/Promoter cauliflower mosaic virus 35S:NEOMYCIN PHOSPHOTRANSFERASE II (Pro35S:NPTII) transgenic Arabidopsis (Arabidopsis thaliana) line has been used as a marker to identify ros1 and ros3 mutants in which both ProRD29A:LUC and Pro35S:NPTII are silenced (Gong et al., 2002; Zheng et al., 2008). ROS3 is an RNA-binding protein that facilitates the function of ROS1 in active DNA demethylation at certain genomic loci. Using Pro35S:NPTII as a selection marker for kanamycin-sensitive mutants and the 35S-SUC2 transgene or a chop PCR marker for assaying DNA methylation at the 3′ region of At1g26400 from transfer DNA (T-DNA) insertion mutants, researchers recently identified two genes involved in active DNA demethylation: ROS4/INCREASED DNA METHYLATION1 (IDM1) and ROS5/IDM2 (Li et al., 2012; Qian et al., 2012, 2014; Zhao et al., 2014). ROS4/IDM1 is a plant homeodomain-finger domain-containing histone acetyltransferase that catalyzes histone H3 lysine18 (H3K18) and lysine23 (H3K23) acetylation (Li et al., 2012; Qian et al., 2012). ROS5/IDM2 is a member of the small heat shock protein family that interacts physically with ROS4/IDM1 for the regulation of active DNA demethylation. Genetic analysis indicates that ROS1, ROS4/IDM1, and ROS5/IDM2 are in the same genetic pathway and that ROS4/IDM1 and ROS5/IDM2 may form a protein complex for the regulation of active DNA demethylation (Qian et al., 2014; Zhao et al., 2014).During the genetic screening for kanamycin-sensitive mutants using the ProRD29A:LUC/Pro35S:NPTII transgenic line in this study, we identified another mutant, mbd7, where the Pro35S:NPTII transgene is specifically silenced. MBD7 is a methyl-CpG-binding domain (MBD) protein containing three MBD motifs that bind in vitro to methylated symmetric CG sites. MBD7 localizes to all highly CpG-methylated chromocenters in vivo (Zemach and Grafi, 2003; Zemach et al., 2008). Recruitment of MBD7 to chromocenters is disrupted in decrease in DNA methylation1 (ddm1) and met1, two mutants with great reductions in DNA methylation, suggesting that DNA methylation is required for proper MBD7 localization (Zemach et al., 2005). In this study, we found that MBD7 interacts physically with ROS5/IDM2 and is required for the active DNA demethylation of certain genomic loci, especially for the Gypsy-type long terminal repeat (LTR) retrotransposons with high densities of DNA methylation around chromocenters in Arabidopsis.     

Familial Clarification of Saucrosmylidae stat. nov. and New Saucrosmylids from Daohugou,China (Insecta,Neuroptera)

BackgoundSaucrosmylids are characterized by the typically large body size, complicated venation and diverse wing markings, which were only discovered in Middle Jurassic of Daohugou, Ningcheng county, Inner Mongolia, China.Conclusions/SignificanceThe intriguing group represents a particular lineage of Neuroptera in the Mesozoic Era. The familial status of Saucrosmylidae was firstly advanced that clarified the former incorrect citation and use of the family name. As an extinct clade, many species of the saucrosmylids were erected just based on a single fore- or hindwing, and it should be realized that providing more stable characters is necessary when describing new lacewing taxa just based on an isolated hindwing. It is vital for the systematics of Saucrosmylidae.     

New Labdane Diterpenes and Their Glycoside Derivatives from the Roots of Isodon adenantha

Two new labdane‐type diterpenes (adenanthic acids A and B; 1 and 2 , resp.) and three new labdane diterpene glycosides (adenanthosides A–C; 3 – 5 , resp.) were isolated from the roots of Isodon adenantha, together with 23 known constituents including seven diterpenoids ( 6 – 12 ), eight triterpenoids ( 13 – 20 ), one lignan glycoside ( 21 ), six steroids ( 22 – 27 ), and one ceramide ( 28 ). Their structures were elucidated by spectroscopic methods including extensive 2D‐NMR techniques. Cytotoxicity and antibacterial activities of the samples were measured by the MTT method and the filter paper disc agar diffusion method. But none of them showed significant activities.