Modeling repetitive,non‐globular proteins

While ab initio modeling of protein structures is not routine, certain types of proteins are more straightforward to model than others. Proteins with short repetitive sequences typically exhibit repetitive structures. These repetitive sequences can be more amenable to modeling if some information is known about the predominant secondary structure or other key features of the protein sequence. We have successfully built models of a number of repetitive structures with novel folds using knowledge of the consensus sequence within the sequence repeat and an understanding of the likely secondary structures that these may adopt. Our methods for achieving this success are reviewed here.     

下一代益生菌Akk菌的研究进展

Akk菌(Akkermansia muciniphila)是具有巨大发展潜力的下一代益生菌,被广泛认为是改善炎症性肠病、肠易激综合征、糖尿病、肥胖症和渐冻症等疾病的一种新的潜在候选菌。近年来,随着人们对肠道共生菌重视程度的加深和各种组学技术的发展,Akk菌迅速成为益生菌研究领域的热点。然而,目前国内外有关Akk菌最新研究进展的归纳总结仍较少。因此,本文对近十年国内外有关Akk菌取得的最新研究进展进行综述,从Akk菌对宿主健康的调控作用,Akk菌的分离、鉴定和培养,以及Akk菌研究面临的挑战、机遇和前景等几方面进行阐述,以期为国内外同行对Akk菌的进一步深入研究和开发提供参考。     

绿色杜氏藻转录组分析

为了深入了解绿色杜氏藻(Dunaliella viridis)基因信息及功能、耐盐相关通路(甘油脂代谢)及关键酶,本文首次通过Illumina HiSeq^TM 2000高通量测序技术对绿色杜氏藻转录组进行测序,利用Trinity软件将数据组装形成转录本,对所有转录本进行COG(Clusters of Orthologous Groups)、GO(Gene Ontology)和KEGG(Kyoto Encyclopedia of Genes and Genomes)分类和功能注释、Pathway注释以及蛋白编码区(Opening reading fragment,ORF)的预测,并对甘油脂代谢通路关键酶基因进行了分析。转录组测序共获得81 593个转录本,其中ORF共有77 117条,约占所有转录本的94.50%。COG分类结果表明,16 569条转录本被分为24个类别。GO分类结果表明,76 436条转录本被注释。在所有注释分类中,生物学过程转录本数量最多,为30 678条,占总转录本数的40.14%。KEGG分析结果表明,317个标准途径中包含26 428条转录本,含转录本最多的类别是代谢,为9949条(37.65%)。与代谢有关的途径为131条,占所有注释途径的41.32%。在甘油脂代谢通路中仅发现1条关键酶转录本(二羟丙酮激酶),该酶可能与绿色杜氏藻耐盐胁迫中甘油的合成有较大关系。本研究进一步完善了绿色杜氏藻的基因信息,为绿色杜氏藻代谢途径研究奠定了坚实的基础。     

Re-Evaluation of a Bacterial Antifreeze Protein as an Adhesin with Ice-Binding Activity

A novel role for antifreeze proteins (AFPs) may reside in an exceptionally large 1.5-MDa adhesin isolated from an Antarctic Gram-negative bacterium, Marinomonas primoryensis. MpAFP was purified from bacterial lysates by ice adsorption and gel electrophoresis. We have previously reported that two highly repetitive sequences, region II (RII) and region IV (RIV), divide MpAFP into five distinct regions, all of which require mM Ca²⁺ levels for correct folding. Also, the antifreeze activity is confined to the 322-residue RIV, which forms a Ca²⁺-bound beta-helix containing thirteen Repeats-In-Toxin (RTX)-like repeats. RII accounts for approximately 90% of the mass of MpAFP and is made up of ∼120 tandem 104-residue repeats. Because these repeats are identical in DNA sequence, their number was estimated here by pulsed-field gel electrophoresis. Structural homology analysis by the Protein Homology/analogY Recognition Engine (Phyre2) server indicates that the 104-residue RII repeat adopts an immunoglobulin beta-sandwich fold that is typical of many secreted adhesion proteins. Additional RTX-like repeats in RV may serve as a non-cleavable signal sequence for the type I secretion pathway. Immunodetection shows both repeated regions are uniformly distributed over the cell surface. We suggest that the development of an AFP-like domain within this adhesin attached to the bacterial outer surface serves to transiently bind the host bacteria to ice. This association would keep the bacteria within the upper reaches of the water column where oxygen and nutrients are potentially more abundant. This novel envirotactic role would give AFPs a third function, after freeze avoidance and freeze tolerance: that of transiently binding an organism to ice.     

三江源区沼泽湿地退化过程中植被变化特征及评价指标体系

湿地退化评价指标体系研究是湿地退化研究的重要科学问题,该研究以隆宝高寒沼泽湿地为例,分析了不同退化程度湿地植被的变化特征,并利用主成分分析法以多个植被指标构建了湿地退化的植被评价指数。结果表明：(1)随着湿地退化程度加剧,沼生植物重要值减小,湿中生植物重要值增大,植物群落由小苔草(Carex parva)群落向藏嵩草(Kobresia tibetica)群落演替。(2)随着湿地退化程度加剧,物种多样性指数、均匀度指数和丰富度均逐渐增大,其中,重度退化阶段与未退化阶段间差异显著(P<0.05)。(3)地上生物量随着湿地退化显著降低(P<0.05),而地下生物量则呈先增加后降低的变化趋势,其中,在10~20 cm和20~30 cm土层,重度退化阶段与轻度退化阶段间均差异显著(P<0.05)。(4)主成分分析显示,9个植物群落指标简化为第1和第2主成分,累计解释量达91.7%。第一主成分上盖度、地上生物量、沼生植物重要值和中生植物重要值具有较高载荷,达0.9以上,对于湿地退化的指示性较好。(5)不同退化阶段的湿地植被评价指数(SVEI)分别为,未退化阶段-3.23～-1.98,轻度退化阶段-0.54～0.51,重度退化阶段2.15～3.26。研究认为,利用多个植被指标构建的湿地退化植被评价指数可以很好地指示隆宝湿地的退化程度,且湿地植被评价指数值越大,湿地退化越严重;不同退化程度湿地的植被评价指数阈值为：未退化阶段SVEI<-1,轻度退化阶段-1≤SVEI≤1,重度退化阶段SVEI>1。     

Enhanced intracellular delivery and chemotherapy for glioma rats by transferrin-conjugated biodegradable polymersomes loaded with doxorubicin

A brain drug delivery system for glioma chemotherapy based on transferrin-conjugated biodegradable polymersomes, Tf-PO-DOX, was made and evaluated with doxorubicin (DOX) as a model drug. Biodegradable polymersomes (PO) loaded with doxorubicin (DOX) were prepared by the nanoprecipitation method (PO-DOX) and then conjugated with transferrin (Tf) to yield Tf-PO-DOX with an average diameter of 107 nm and surface Tf molecule number per polymersome of approximately 35. Compared with PO-DOX and free DOX, Tf-PO-DOX demonstrated the strongest cytotoxicity against C6 glioma cells and the greatest intracellular delivery. It was shown in pharmacokinetic and brain distribution experiments that Tf-PO significantly enhanced brain delivery of DOX, especially the delivery of DOX into brain tumor cells. Pharmacodynamics results revealed a significant reduction of tumor volume and a significant increase of median survival time in the group of Tf-PO-DOX compared with those in saline control animals, animals treated with PO-DOX, and free DOX solution. By terminal deoxynucleotidyl transferase-mediated dUTP nick-end-labeling, Tf-PO-DOX could extensively make tumor cell apoptosis. These results indicated that Tf-PO-DOX could significantly enhance the intracellular delivery of DOX in glioma and the chemotherapeutic effect of DOX for glioma rats.     

Responses of wheat and rice to factorial combinations of ambient and elevated CO2 and temperature in FACE experiments

Elevated CO₂ and temperature strongly affect crop production, but understanding of the crop response to combined CO₂ and temperature increases under field conditions is still limited while data are scarce. We grew wheat (Triticum aestivum L.) and rice (Oryza sativa L.) under two levels of CO₂ (ambient and enriched up to 500 μmol mol^?1) and two levels of canopy temperature (ambient and increased by 1.5–2.0 °C) in free‐air CO₂ enrichment (FACE) systems and carried out a detailed growth and yield component analysis during two growing seasons for both crops. An increase in CO₂ resulted in higher grain yield, whereas an increase in temperature reduced grain yield, in both crops. An increase in CO₂ was unable to compensate for the negative impact of an increase in temperature on biomass and yield of wheat and rice. Yields of wheat and rice were decreased by 10–12% and 17–35%, respectively, under the combination of elevated CO₂ and temperature. The number of filled grains per unit area was the most important yield component accounting for the effects of elevated CO₂ and temperature in wheat and rice. Our data showed complex treatment effects on the interplay between preheading duration, nitrogen uptake, tillering, leaf area index, and radiation‐use efficiency, and thus on yield components and yield. Nitrogen uptake before heading was crucial in minimizing yield loss due to climate change in both crops. For rice, however, a breeding strategy to increase grain number per m² and % filled grains (or to reduce spikelet sterility) at high temperature is also required to prevent yield reduction under conditions of global change.     

Small molecule targeting CELF1 RNA-binding activity to control HSC activation and liver fibrosis

CUGBP Elav-like family member 1 (CELF1), an RNA-binding protein (RBP), plays important roles in the pathogenesis of diseases such as myotonic dystrophy, liver fibrosis and cancers. However, targeting CELF1 is still a challenge, as RBPs are considered largely undruggable. Here, we discovered that compound 27 disrupted CELF1-RNA binding via structure-based virtual screening and biochemical assays. Compound 27 binds directly to CELF1 and competes with RNA for binding to CELF1. Compound 27 promotes IFN-γ secretion and suppresses TGF-β1-induced hepatic stellate cell (HSC) activation by inhibiting CELF1-mediated IFN-γ mRNA decay. In vivo, compound 27 attenuates CCl₄-induced murine liver fibrosis. Furthermore, the structure-activity relationship analysis was performed and compound 841, a derivative of compound 27, was identified as a selective CELF1 inhibitor. In conclusion, targeting CELF1 RNA-binding activity with small molecules was achieved, which provides a novel strategy for treating liver fibrosis and other CELF1-mediated diseases.     

All‐Printed MnHCF‐MnOx‐Based High‐Performance Flexible Supercapacitors

Here, a simple active materials synthesis method is presented that boosts electrode performance and utilizes a facile screen‐printing technique to prepare scalable patterned flexible supercapacitors based on manganese hexacyanoferrate‐manganese oxide and electrochemically reduced graphene oxide electrode materials (MnHCF‐MnO_x/ErGO). A very simple in situ self‐reaction method is developed to introduce MnO_x pseudocapacitor material into the MnHCF system by using NH₄F. This MnHCF‐MnO_x electrode materials can deliver excellent capacitance of 467 F g^?1 at a current density of 1 A g^?1, which is a 2.4 times capacitance increase compared to MnHCF. In addition a printed, patterned, flexible MnHCF‐MnO_x/ErGO supercapacitor is fabricated, showing a remarkable areal capacitance of 16.8 mF cm^?2 and considerable energy and power density of 0.5 mWh cm^?2 and 0.0023 mW cm^?2, respectively. Furthermore, the printed patterned flexible supercapacitors also exhibit exceptional flexibility, and the capacitance remains stable, even while bending to various angles (60°, 90°, and 180°) and for 100 cycles. The flexible supercapacitor arrays integrated by multiple prepared single supercapacitors can power various LEDs even in the bent states. This approach offers promising opportunities for the development of printable energy storage materials and devices with high energy density, large scalability, and excellent flexibility.