Exploration of the binding affinities between ecdysone agonists and EcR/USP by docking and MM-PB/GBSA approaches

Ecdysone receptor (EcR) is a significant target in the identification of new environmentally friendly pesticides. There are two types of ecdysone agonists: steroidal ecdysone agonists and dibenzoylhydrazines (DBHs). In this study, various modeling methods (homology modeling, molecular docking, MD simulation, binding free energy calculation, and per-residue binding free energy decomposition) were utilized to study the different binding mechanisms of two types of ecdysone agonists. Our theoretical results indicated that the relative binding potencies of DBHs can be ranked sufficiently accurately using the MOE docking method. However, MM/PBSA calculations more accurately predicted the binding affinities between steroidal ecdysone agonists and EcR-LBD. To identify the key residues involved in ecdysone agonist binding, the binding free energy (ΔG _Bind) was decomposed into the energy contributions of individual residues. The results revealed that nine residues—Ile339, Thr343, Met380, Met381, Tyr403, Tyr408, Asp419, Gln503, and Asn504—determined the binding affinities of the DBHs. Glu309, Met342, Arg383, Arg387, and Leu396 were important influences on the binding affinities of the steroidal ecdysone agonists.

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Graphical abstract The ecdysone receptor (EcR) is related to insect growth and has been shown to be a useful target for insecticides

     

Effect of Polymer–Fullerene Interaction on the Dielectric Properties of the Blend

It is commonly believed that large dielectric constants are required for efficient charge separation in polymer photovoltaic devices. However, many polymers used in high‐performance solar cells do not possess high dielectric constants. In this work, the effect of polymer–fullerene interactions on the dielectric environment of the active layer blend and the device performance for several donor–acceptor conjugated polymer systems is investigated. It is found that, while none of the high‐performing polymers studied has a dielectric constant value larger than 3, all polymer–fullerene blends have a significantly larger dielectric constant compared to their pristine constituents. Additionally, it is found that the blend dielectric constant reaches a maximum value in fully optimized devices. Using PTB7:PC₇₁BM blends as an example, it is showed that, in addition to a small increase in the dielectric constant, devices fabricated using the optimum processing additive concentration exhibit almost 3X larger excited state polarizability. This large increase in excited state polarizability results in a substantial difference in short‐circuit current and ultimately device performance. The results show that the excited state polarizability critically depends on polymer–fullerene interactions, and can be a leading indicator of device performance for a given material system.     

Scale-up cultivation enhanced arachidonic acid accumulation by red microalgae Porphyridium purpureum

Bioprocess and Biosystems Engineering - The present study attempts to cultivate Porphyridium purpureum under different scale-up conditions for further development and commercialization of...     

褪黑激素对休情期银黑狐腔前卵泡卵母细胞超微结构的影响

为了研究褪黑激素(Melatonin,MLT)对休情期银黑狐腔前卵泡卵母细胞超微结构的影响。本研究选取健康7月龄埋植和未埋植MLT的银黑狐各5只,取其左侧卵巢共计10枚,制备超薄切片后利用透射电镜分别观察每枚卵巢的各级腔前卵泡各1-5个,并进行拍照。结果埋植和未埋植MLT的银黑狐原始卵泡卵母细胞内均有少量线粒体和高尔基体,而未埋植MLT的银黑狐卵母细胞中还可见少量滑面内质网;初级卵泡卵母细胞内,均开始形成不完整透明带,线粒体及内质网数量均有所增加,沿透明带出现少量皮质颗粒;次级卵泡阶段,未埋植MLT银黑狐卵母细胞微绒毛数量较埋植MLT的多,其余细胞器未见差异。结果表明,MLT对休情期银黑狐卵巢腔前卵泡卵母细胞的线粒体、脂滴、高尔基体、皮质颗粒等细胞器的发育没有影响,仅对初级卵泡阶段内质网的发育有抑制作用。     

蕨类植物不同孢子裂缝类型在中国的分布格局

孢子在蕨类植物分类及有性生殖过程中具有重要地位, 一般都具有裂缝构造, 常见的是单裂缝和三裂缝, 极少数情况下有多裂缝的变异类型。我们统计了中国蕨类2,281种(含种下单位)的孢子裂缝类型, 来探讨两种不同裂缝类型的分布格局。结果表明: (1)具有单裂缝类型的物种数多于三裂缝类型, 单裂缝与三裂缝物种数目的比值(单/三比)与纬度和海拔呈正相关。随着温度下降以及降水量的降低, 具单裂缝孢子的物种比例增加。推测具单裂缝孢子的蕨类分布范围更广, 更适宜生活在干旱及高纬度或高海拔寒冷地区, 而具三裂缝孢子的蕨类更适宜存在于低纬度或低海拔的温暖地区; (2)蕨类植物孢子裂缝类型不是单次起源, 可能存在平行演化。本研究可以为蕨类植物的起源演化与生态适应等研究提供一定的证据。     

TiGER: A database for tissue-specific gene expression and regulation

Background  

Understanding how genes are expressed and regulated in different tissues is a fundamental and challenging question. However, most of currently available biological databases do not focus on tissue-specific gene regulation.     

Antigen retrieval for proteomic characterization of formalin-fixed and paraffin-embedded tissues

Formalin-fixed and paraffin-embedded tissues represent the vast majority of archived tissue. Access to such tissue specimens via shotgun-based proteomic analyses may open new avenues for both prospective and retrospective translational research. In this study, we evaluate the effects of fixation time on antigen retrieval for the purposes of shotgun proteomics. For the first time, we demonstrate the capability of a capillary isotachophoresis (CITP)-based proteomic platform for the shotgun proteomic analysis of proteins recovered from FFPE tissues. In comparison to our previous studies utilizing capillary isoelectric focusing, the CITP-based analysis is more robust and increases proteome coverage. In this case, results from three FFPE liver tissues yield a total of 4098 distinct Swiss-Prot identifications at a 1% false-discovery rate. To judge the accuracy of these assignments, immunohistochemistry is performed on a panel of 17 commonly assayed proteins. These proteins span a wide range of protein abundances as inferred from relative quantitation via spectral counting. Among the panel were 4 proteins identified by a single peptide hit, including three clusters of differentiation (CD) markers: CD74, CD117, and CD45. Because single peptide hits are often regarded with skepticism, it is notable that all proteins tested by IHC stained positive.     

沙利度胺对实验性矽肺血管生成的干预研究

目的观察实验性矽肺形成过程中肺组织局部血管生成的动态变化,以及沙利度胺对矽肺肺纤维化血管生成的干预作用。方法SD大鼠54只,随机分为3组,矽肺组和沙利度胺组气管内注入二氧化硅混旋液复制实验性大鼠矽肺模型,对照组在相同条件下给予生理盐水。第二天起沙利度胺组给予沙利度胺饲料喂养,其余各组在相同条件下给予普通饲料喂养。采用HE染色、羟脯氨酸含量测定、免疫组织化学染色等方法,观察实验性大鼠矽肺的发病过程,肺组织中p-Akt蛋白和局部血管生成的动态变化及其与肺胶原蛋白含量的关系。结果矽肺组第7天新生血管明显增多,第30天较第7天有所减少,到第60天肺组织正常结构基本消失,取代为广泛结节性纤维化,少见血管;沙利度胺组血管生成在第7天轻于矽肺组,但仍高于对照组。免疫组化显示p-Akt蛋白在矽肺组第7天明显达到高峰,第30天时较第7天有所减弱,第60天时明显减弱。沙利度胺组p-Akt蛋白和羟脯氨酸含量均低于矽肺组,但高于对照组。结论矽肺早期血管生成显著,血管生成在矽肺肺纤维化发生早期可能起重要作用;沙利度胺能在一定程度上抑制过度的血管生成,对实验性矽肺具有一定的阻抑作用。     

Genetic Determinants of Symptoms on Viral DNA Satellites

Begomovirus-DNA-β disease complexes induce different symptom phenotypes in their hosts. To investigate the genetic determinants of the phenotypic differences, Nicotiana spp. and tomato plants were inoculated with infectious clones of Tobacco curly shoot virus (TbCSV)/TbCSV DNA-β (TbCSB) and Tomato yellow leaf curl China virus (TYLCCNV)/TYLCCNV DNA-β (TYLCCNB) pseudorecombinants and showed that TYLCCNB induced characteristic vein-thickening and enation symptoms, while TbCSB only slightly exacerbated the leaf-curling symptoms, regardless of the helper virus being used. The roles of DNA-β-encoded βC1 and a 430-nucleotide fragment containing the A-rich region and the putative βC1 promoter region of the βC1 gene (referred to as AP) in symptom development were further investigated by constructing hybrid satellites in which the βC1 coding region or AP was exchanged between the two satellite molecules. A TYLCCNB hybrid with TbCSB βC1 lost the ability to elicit the vein-thickening and enation phenotypes. TbCSB hybrids containing the TYLCCNB βC1 or AP fragment failed to induce the characteristic vein thickening and enations. A TYLCCNB hybrid having the TbCSB AP fragment produced the enations, but the number of enations was less and their sizes were reduced. Differently from the phloem-specific pattern of the TYLCCNB promoter, a full-length fragment upstream of the TbCSB βC1 gene confers a constitutive β-glucuronidase expression pattern in transgenic tobacco plants. The above results indicate that the DNA-β-encoded βC1 protein is the symptom determinant, but the promoter of the βC1 gene has influence on symptom production.Geminiviruses are small plant viruses with circular single-stranded DNA (ssDNA) genomes that are encapsidated in unique twinned (geminate) particles. Members of the genus Begomovirus are transmitted by whiteflies (Bemisia tabaci) and infect dicotyledonous plants (42). Begomoviruses have either one or two circular ssDNA genomic components (DNA-A and DNA-B). The DNA-A component is capable of autonomous replication and encapsidation, whereas the DNA-B component encodes two proteins (BC1 and BV1) involved in movement (14). Recently, some monopartite begomoviruses have been found in association with a novel satellite DNA molecule, referred to as DNA-β and now known as a betasatellite (2, 5, 20, 22, 38, 45). DNA-β is approximately half the size of the viral genomic DNA, and apart from a nonanucleotide sequence (TAATATTAC), it has little sequence identity with viral genomic DNA. DNA-β depends on the helper virus for replication and encapsidation and, in turn, is required for the induction of bona fide disease symptoms. DNA-β bears a βC1 open reading frame (ORF) on the complementary-sense strand, which is conserved among distinct betasatellites in terms of position and size. Mutational analyses and constitutive expression have shown that βC1 is a strong pathogenicity/symptom determinant (7, 34, 39).Begomovirus-DNA-β disease complexes are associated with a wide range of plant species and induce different sets of symptom phenotypes in their natural hosts (25). However, the contributions of the helper virus and the satellite molecule to symptom development are not clear. Tomato yellow leaf curl China virus (TYLCCNV) and Tobacco curly shoot virus (TbCSV) are monopartite begomoviruses associated with DNA-β, but they differ in the symptom phenotypes induced in Nicotiana spp. and Solanum lycopersicum (7, 22). In the present work, we report that the symptom differences between TYLCCNV/TYLCCNV DNA-β (TYLCCNB) and TbCSV/TbCSV DNA-β (TbCSB) are determined by DNA-β and the DNA-β-encoded βC1 protein is the symptom determinant, but the promoter of the βC1 gene has influence on symptom production.