硝普纳处理对白刺愈伤组织膜脂过氧化及抗氧化酶活性的影响

以唐古特白刺（Nitraria tangutorum Bobr.）愈伤组织为材料,研究一氧化氮(NO)供体硝普钠（SNP）处理对其膜脂过氧化及抗氧化酶活性的影响。激光共聚焦扫描显微镜技术检测结果显示,白刺愈伤组织在SNP处理下细胞中NO含量显著增加,而N-硝基-L-精氨酸（L-NNA）处理使细胞中NO水平降低。低浓度SNP（10和25 μmol·L^-1）处理后,白刺愈伤组织中丙二醛（MDA）含量显著减少,而高浓度SNP（100 μmol·L^-1）和L-NNA(0.5 mmol·L^-1)处理后MDA含量明显高于对照。与对照比,SNP处理诱导白刺愈伤组织可溶性蛋白含量升高,却使脯氨酸含量减少。白刺愈伤组织在不同浓度SNP处理下过氧化氢酶（CAT）和抗坏血酸过氧化物酶（APX）活性呈增加的变化趋势,低浓度SNP处理使过氧化物酶（POD）活性减弱,而50 μmol·L^-1 SNP处理后POD活性约增加为对照的119%。结果提示,外源NO可促进白刺愈伤组织可溶性蛋白的合成,诱导抗氧化酶活性升高,增强了白刺愈伤组织的抗氧化能力,从而表现出对细胞的保护作用。     

Characterization of the smallest dimeric bile salt hydrolase from a thermophile Brevibacillus sp.

A thermophilic microorganism producing bile salt hydrolase was isolated from hot water springs, Pali, Maharashtra, India. This microorganism was identified as Brevibacillus sp. by 16S rDNA sequencing. Bile salt hydrolase (BSH) was purified to homogeneity from this thermophilic source using Q-sepharose chromatography and its enzymatic properties were characterized. The subunit molecular mass of the purified enzyme was estimated to be 28 kDa by SDS-PAGE and, 28.2 kDa by MALDI-TOF analysis. The native molecular mass was estimated to be 56 kDa by gel filtration chromatography, indicating the protein to be a homodimer. The pH and temperature optimum for the enzyme catalysis were 9.0 and 60°C, respectively. Even though BSH from Brevibacillus sp. hydrolyzed all of the six major human bile salts, the enzyme preferred glycine conjugated substrates with apparent K _M and k _cat values of 3.08 μM and 6.32 × 10² s⁻¹, respectively, for glycodeoxycholic acid. The NH₂-terminal sequence of the purified enzyme was determined and it did not show any homology with other bacterial bile salt hydrolases. To our knowledge, this is the first report describing the purification of BSH to homogeneity from a thermophilic source. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

沙枣（Elaeagnus angustifolia）和孩儿拳头（Grewia.biloba G.Don var.parviflora）幼苗气体交换特征与保护酶对干旱胁迫的响应

以沙枣和孩儿拳头2年生盆栽苗为材料,采用称重控水的方法设置4个土壤含水量梯度(CK、T1、T2、T3),研究不同干旱胁迫对沙枣和孩儿拳头气体交换特征与保护酶的影响.结果显示:(1)干旱胁迫不仅引起两物种净光合速率、蒸腾速率、气孔导度、胞间 CO2 浓度的下降,而且使其日变化曲线在一定程度上发生改变;在轻度(T1)和中度胁迫(T2)下,两物种净光合速率下降主要是由气孔因素引起的,重度胁迫(T3)下,净光合速率下降主要是非气孔因素引起的.(2)随着干旱胁迫增加,沙枣瞬时水分利用效率呈现增加下降再增加趋势,孩儿拳头呈现下降趋势;两物种表观光能利用效率显著下降,重度胁迫下(T3),下降率达50%左右,孩儿拳头表观光能利用效率对干旱胁迫比较敏感;两物种表观CO2利用效率总体呈现下降趋势,沙枣表观CO2利用效率日进程经历了单峰(T1)、双峰(T2)、单峰(T3)的变化,孩儿拳头各处理的表观CO2利用效率日变化均呈现单峰曲线.(3)随着干旱胁迫加剧,两物种叶片的超氧化物歧化酶(SOD)、过氧化物酶(POD)、过氧化氢酶(CAT)活性先升高后降低,土壤含水量高于12.8%时,两物种SOD酶活性均高于CK,随着土壤含水量的降低,SOD酶活性低于CK;重度胁迫下(T3),沙枣POD酶活性虽然有所下降,但仍高于CK,而孩儿拳头则和CK无显著差异;两物种CAT酶活性在重度胁迫下(T3)显著低于CK;随着干旱胁迫程度的增加,两物种叶片中的丙二醛(MDA)含量均呈现升高趋势,孩儿拳头脂质过氧化程度受干旱胁迫的影响较大.     

Unbiased chromatin accessibility profiling by RED-seq uncovers unique features of nucleosome variants in vivo

Background

Differential accessibility of DNA to nuclear proteins underlies the regulation of numerous cellular processes. Although DNA accessibility is primarily determined by the presence or absence of nucleosomes, differences in nucleosome composition or dynamics may also regulate accessibility. Methods for mapping nucleosome positions and occupancies genome-wide (MNase-seq) have uncovered the nucleosome landscapes of many different cell types and organisms. Conversely, methods specialized for the detection of large nucleosome-free regions of chromatin (DNase-seq, FAIRE-seq) have uncovered numerous gene regulatory elements. However, these methods are less successful in measuring the accessibility of DNA sequences within nucelosome arrays.

Results

Here we probe the genome-wide accessibility of multiple cell types in an unbiased manner using restriction endonuclease digestion of chromatin coupled to deep sequencing (RED-seq). Using this method, we identified differences in chromatin accessibility between populations of cells, not only in nucleosome-depleted regions of the genome (e.g., enhancers and promoters), but also within the majority of the genome that is packaged into nucleosome arrays. Furthermore, we identified both large differences in chromatin accessibility in distinct cell lineages and subtle but significant changes during differentiation of mouse embryonic stem cells (ESCs). Most significantly, using RED-seq, we identified differences in accessibility among nucleosomes harboring well-studied histone variants, and show that these differences depend on factors required for their deposition.

Conclusions

Using an unbiased method to probe chromatin accessibility genome-wide, we uncover unique features of chromatin structure that are not observed using more widely-utilized methods. We demonstrate that different types of nucleosomes within mammalian cells exhibit different degrees of accessibility. These findings provide significant insight into the regulation of DNA accessibility.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-1104) contains supplementary material, which is available to authorized users.     

Determination of restriction enzyme activity when cutting DNA labeled with the TOTO dye family

Optical mapping, a single DNA molecule genome analysis platform that can determine methylation profiles, uses fluorescently labeled DNA molecules that are elongated on the surface and digested with a restriction enzyme to produce a barcode of that molecule. Understanding how the cyanine fluorochromes affect enzyme activity can lead to other fluorochromes used in the optical mapping system. The effects of restriction digestion on fluorochrome labeled DNA (Ethidium Bromide, DAPI, H33258, EthD-1, TOTO-1) have been analyzed previously. However, TOTO-1 is a part of a family of cyanine fluorochromes (YOYO-1, TOTO-1, BOBO-1, POPO-1, YOYO-3, TOTO-3, BOBO-3, and POPO-3) and the rest of the fluorochromes have not been examined in terms of their effects on restriction digestion. In order to determine if the other dyes in the TOTO-1 family inhibit restriction enzymes in the same way as TOTO-1, lambda DNA was stained with a dye from the TOTO family and digested. The restriction enzyme activity in regards to each dye, as well as each restriction enzyme, was compared to determine the extent of digestion. YOYO-1, TOTO-1, and POPO-1 fluorochromes inhibited ScaI-HF, PmlI, and EcoRI restriction enzymes. Additionally, the mobility of labeled DNA fragments in an agarose gel changed depending on which dye was intercalated.     

Bicyclic γ-amino acids as inhibitors of γ-aminobutyrate aminotransferase

The γ-aminobutyrate (GABA)-degradative enzyme GABA aminotransferase (GABA-AT) is regarded as an attractive target to control GABA levels in the central nervous system: this has important implications in the treatment of several neurological disorders and drug dependencies. We have investigated the ability of newly synthesized compounds to act as GABA-AT inhibitors. These compounds have a unique bicyclic structure: the carbocyclic ring bears the GABA skeleton, while the fused 3-Br-isoxazoline ring contains an electrophilic warhead susceptible of nucleophilic attack by an active site residue of the target enzyme. Out of the four compounds tested, only the one named (+)-3 was found to significantly inhibit mammalian GABA-AT in vitro. Docking studies, performed on the available structures of GABA-AT, support the experimental findings: out of the four tested compounds, only (+)-3 suitably orients the electrophilic 3-Br-isoxazoline warhead towards the active site nucleophilic residue Lys329, thereby explaining the irreversible inhibition of GABA-AT observed experimentally.     

Synthesis and evaluation of sulfonamide-bearing thiazole as carbonic anhydrase isoforms hCA I and hCA II

Sulfonamide-bearing thiazole compounds were synthesized and their inhibitory effects on the activity of purified human carbonic anhydrase I and II were evaluated. Human carbonic anhydrase isoenzymes (hCA-I and hCA-II) were purified from erythrocyte cells by affinity chromatography. The inhibitory effects of the 12 synthesized sulfonamide (5a–l) on the hydratase and esterase activities of these isoenzymes (hCA-I and hCA-II) were studied in vitro. In relation to these activities, the inhibition equilibrium constants (Ki) were determined. The results showed that all the synthesized compounds inhibited the CA isoenzyme activity. Among them 5b was found to be the most active (IC_50?=_?0.35?μM; Ki: 0.33?μM) for hCA I and hCA II.     

热水处理对金柑果实采后腐烂及生理特性的影响

金柑是果皮和果肉同食的柑果类型,对采后处理要求极为严格。该研究以金柑(Fortunella crassifolia)为材料,研究了其经30、40和50℃热水浸泡后果实的腐烂率、失重率、可溶性固形物、硬度、有机酸、细胞渗透率以及抗氧化酶活性变化。结果表明:经30℃热水处理5 min的果实失重率高于对照,而经40℃和50℃处理的果实失重率低于对照或差异不显著。经热水处理的果实总酸含量略低于对照,可溶性固形物含量在18%上下波动且差异不显著。热水处理可提高果实硬度,降低贮藏前期果实细胞渗透率以及贮藏过程中果实过氧化物酶和超氧化物歧化酶活性,激发过氧化氢含量升高,可有效降低贮藏过程中金柑果实腐烂率,但不同采收期的金柑所需的热水处理温度和时间不同。对于1月初采收的果实,处理时间为5 min或10 min可降低果实腐烂率;2月初采收的果实,40℃或50℃热水处理10 min可有效降低果实腐烂率;3月初采收的果实,当处理温度达到50℃,处理时间达到10 min,才可有效降低果实腐烂率,且对果实品质没有明显的不利影响。     

Mammalian ER stress sensor IRE1β specifically down-regulates the synthesis of secretory pathway proteins

Accumulation of unfolded proteins in the endoplasmic reticulum (ER) causes ER stress. The ER stress sensor inositol requiring enzyme-1beta (IRE1β), which is specifically expressed in intestinal epithelial cells, is thought to be involved in translational repression. However, its mechanism of action is not fully understood. Using a reporter that can evaluate and distinguish between translation efficiency in the cytosol and on the ER membrane, we show here that IRE1β represses translation on the ER membrane but not in the cytosol, and that this selective repression depends on the RNase activity of IRE1β.     

用DREAM技术纠正人工合成基因中的突变

目的：介绍一种简便、有效的定点突变技术。方法：根据突变位点附近的DNA序列推导出氨基酸序列,再以此氨基酸序列进行逆翻译,这样在不改变氨基酸序列的前提下可以得到数目巨大的隐性突变体（silent mutants）,这些突变体中包含大量的限制性内切酶位点,选择合适的酶切位点设计引物用PCR技术扩增两侧DNA片段,然后以相应酶切融合这两个片段即可完成定点突变。结果：用该方法成功地在人工合成的含有缺失的可溶性组织因子基因的472位插入C,T两个碱基,校正了阅读框架,获得了预期的目的基因。结论：该方法简便、有效, 避免了多轮PCR和合成长引物导致突变的可能性,这种改进的PCR 定点诱变技术我们称之为“设计限制酶辅助突变”（Designed Restriction Enzyme Assisted Mutagenesis, DREAM）。此技术简单方便, 诱变的成功率高, 适于实验室常规应用。