Antibody modeling assessment

A blinded study to assess the state of the art in three‐dimensional structure modeling of the variable region (Fv) of antibodies was conducted. Nine unpublished high‐resolution x‐ray Fab crystal structures covering a wide range of antigen‐binding site conformations were used as benchmark to compare Fv models generated by four structure prediction methodologies. The methodologies included two homology modeling strategies independently developed by CCG (Chemical Computer Group) and Accerlys Inc, and two fully automated antibody modeling servers: PIGS (Prediction of ImmunoGlobulin Structure), based on the canonical structure model, and Rosetta Antibody Modeling, based on homology modeling and Rosetta structure prediction methodology. The benchmark structure sequences were submitted to Accelrys and CCG and a set of models for each of the nine antibody structures were generated. PIGS and Rosetta models were obtained using the default parameters of the servers. In most cases, we found good agreement between the models and x‐ray structures. The average rmsd (root mean square deviation) values calculated over the backbone atoms between the models and structures were fairly consistent, around 1.2 Å. Average rmsd values of the framework and hypervariable loops with canonical structures (L1, L2, L3, H1, and H2) were close to 1.0 Å. H3 prediction yielded rmsd values around 3.0 Å for most of the models. Quality assessment of the models and the relative strengths and weaknesses of the methods are discussed. We hope this initiative will serve as a model of scientific partnership and look forward to future antibody modeling assessments. Proteins 2011; © 2011 Wiley‐Liss, Inc.     

N-Arylalkyl-2-azaadamantanes as cage-expanded polycarbocyclic sigma (σ) receptor ligands

A series of racemic N-arylalkyl-2-azaadamantan-1-ols (9-15) and the corresponding deoxygenated, achiral N-arylalkyl-2-azaadamantanes (23-29) were synthesized and screened in competition binding assays against a panel of CNS targets. Adamantyl hemiaminals 9-15 displayed generally low affinity for both σ(1) (K(i) values= 294-1950 nM) and σ(2) receptors (K(i) values=201-1020 nM), and negligible affinity for 42 other CNS proteins. Deoxygenation of 9-15 to give the corresponding achiral azaadamantanes 23-29 greatly improved affinity for σ(1) (K(i) values=8.3-239 nM) and σ(2) receptors (K(i) values=34-312 nM).     

俄罗斯堪察加地区热泉及其周边生境的泉古菌多样性

【目的】泉古菌为陆地热泉系统的主要古菌类群,可能在自然界生源元素的地球化学循环中发挥着重要作用。本研究旨在揭示俄罗斯堪察加地区热泉以及热泉周边区域的泉古菌多样性,同时基于之前已获得的我国云南地区热泉数据,比较两地区泉古菌群落差异。【方法】通过构建16S rRNA基因片段克隆文库获得序列信息和丰度,随后进行物种多样性、系统发育和群落结构差异分析。【结果】高温热泉Burlyashi Liza(BSL,89℃)中的泉古菌全部属于热变形菌纲(Thermoprotei)内的物种。中温热泉TF Vent 2(TFV,49℃)的群落结构主要由不确定的热变形菌纲类群、不确定的泉古菌类群、高温水环境泉古菌类群Ⅱ(HWCG-Ⅱ)和奇古菌下的Group1.1b类群组成。热泉周边常温环境的主要物种与热泉环境的代表性克隆pJP41一起聚成一个较大的遗传分枝。Jackknife聚类树和主坐标分析(Principal coordinates analysis,PCoA)的结果显示:温度相似的样点,其泉古菌群落结构相对来说更为相似。【结论】俄罗斯堪察加地区与我国云南地区热泉中的泉古菌存在着一定程度上的不同。陆地热泉系统影响着其周边环境的泉古菌类群。热泉中泉古菌群落结构受温度的明显影响。     

激光辐射奶牛冷冻精液对精子诱变效应的研究

为了探索激光辐射精子的诱变效应,本试验采用ＴＳＴ（Ｔｒｉｐｌｅ Ｓｔａｉｎ Ｔｅｃｈｎｉｑｕｅ,即精子三重染色法）、ＳＰＡ（Ｓｐｅｒｍ Ｐｅｎｅｔｒａｉｔｉｏｎ Ａｓｓａｙ,即精子穿透分析法和ＣＡＳ（Ｃｈｒｏｍｏｓｏｍａｌ Ａｎｅｕｐｌｏｉｄｙ ｉｎ Ｓｐｅｒｍａｔｏｚｏａ,即精子单倍染色体制备技术）,三项有关精子的现代分析技术,对激光辐射精子的受精学、遗传学效应进行了研究。结果表明：Ｈｅ－Ｎｅ激     

A subset of skin-expressed microRNAs with possible roles in goat and sheep hair growth based on expression profiling of mammalian microRNAs

The microRNAs (miRNAs) are an extensive class of small noncoding RNAs (18-25 nucleotides) with probable roles in the regulation of gene expression. Due to the fact that miRNAs are conserved in closely related eukaryotes and some are also conserved across a larger evolutionary distance, their potential functions in mammalian development are under active study. In order to identify mammalian miRNAs that might function in hair growth, we characterized the expression of 159 miRNAs in adult body side skin and ear skin from goat and sheep using microarray analysis. Of these, 19 miRNAs were specifically expressed or greatly enriched in body side skin in goats and sheep. This suggests hair growth-specific functions for miRNAs. Of the coexpressed 105 miRNAs, the degree of correlation within species is higher than interspecies. Nine of the expressed miRNAs were detected exclusively in the goat body side skin area where more cashmere was grown than coat hair; mmu-miR-720 and mmu-miR-199b were expressed primarily in goat skin. The identification of 105 of skin-expressed miRNAs whose expression behavior is conserved in goats and sheep differentiating hair follicles implicates these miRNAs have functions in mammalian hair follicles growth and development. We demonstrate that miRNAs previously associated with hair follicles in the mouse are also expressed in the adult skin of goats and sheep. In addition, 69 more conserved miRNAs cross-species were discerned in the study. Of them, the let-7, mir-17, mir-30, mir-15, and mir-8 gene families were expressed in high frequency. These results reveal critical roles of them in skin and hair follicle development and function.     

A Peptide Derived from the HIV-1 gp120 Coreceptor-Binding Region Promotes Formation of PAP248-286 Amyloid Fibrils to Enhance HIV-1 Infection

BackgroundSemen is a major vehicle for HIV transmission. Prostatic acid phosphatase (PAP) fragments, such as PAP248-286, in human semen can form amyloid fibrils to enhance HIV infection. Other endogenous or exogenous factors present during sexual intercourse have also been reported to promote the formation of seminal amyloid fibrils.

Methodology and Principal Findings

Here, we demonstrated that a synthetic 15-residue peptide derived from the HIV-1 gp120 coreceptor-binding region, designated enhancing peptide 2 (EP2), can rapidly self-assemble into nanofibers. These EP2-derivated nanofibers promptly accelerated the formation of semen amyloid fibrils by PAP248-286, as shown by Thioflavin T (ThT) and Congo red assays. The amyloid fibrils presented similar morphology, assessed via transmission electron microscopy (TEM), in the presence or absence of EP2. Circular dichroism (CD) spectroscopy revealed that EP2 accelerates PAP248-286 amyloid fibril formation by promoting the structural transition of PAP248-286 from a random coil into a cross-β-sheet. Newly formed semen amyloid fibrils effectively enhanced HIV-1 infection in TZM-bl cells and U87 cells by promoting the binding of HIV-1 virions to target cells.

Conclusions and Significance

Nanofibers composed of EP2 promote the formation of PAP248-286 amyloid fibrils and enhance HIV-1 infection.     

福建省耕地土壤全氮密度和储量动态变化

准确估算土壤全氮密度和储量的动态变化能为氮肥优化管理和水体富营养化防控提供重要依据。以位于福建省不同地区的闽侯县、同安区、武平县和永定县1982年11087个样点及2008年1616个样点建立的1∶5万土壤数据库为基础,利用尺度上推的方法分析了1982—2008年福建省耕地全氮密度和储量的动态变化。结果表明,近30年来福建省耕地土壤氮素富集明显,全氮密度和储量分别上升了0.08 kg/m2和1.22 Tg,但不同土壤类型差异较大,紫色土土类、酸性紫色土亚类和猪肝土土属氮素富集最明显,全氮密度均上升了0.18 kg/m2;赤红壤土类、淹育水稻土亚类和赤土土属氮素损失最多,全氮密度均下降了0.10 kg/m2。水稻土土类、渗育水稻土亚类和黄泥田土属全氮储量增加最多,分别达1.24、0.80 Tg和0.71 Tg;赤红壤土类、赤红壤亚类和灰砂泥田土属下降最多,分别达0.13、0.13 Tg和0.08 Tg。因此,在今后的福建省耕地管理中根据不同土壤类型氮素富集程度合理指导施肥,以节约资源和减少氮素流失是十分必要的。     

冠层水平互花米草叶片光合色素含量的高光谱遥感估算模型

以闽江河口鳝鱼滩湿地互花米草(Spartina alterniflora)的实测冠层高光谱反射率和叶片光合色素含量(LPPC)为数据源,在分析LPPC与原始光谱反射率、一阶导数光谱反射率、22种已报道光谱指数和14种新构建的植被指数相关性的基础上,利用直线回归、指数回归、对数回归以及乘幂回归方法,系统地比较了36种植被指数在估算互花米草LPPC中的表现。研究表明:(1)一阶导数光谱反射率组合的植被指数用于估算互花米草的LPPC优于原始光谱反射率;(2)红边区域一阶导数光谱是估测互花米草LPPC的最佳波段;(3)对于单一色素含量的估算,叶绿素a(Chla)的最佳估算指数为FDNDVI[723,703];叶绿素b(Chlb)的最佳估算指数为FDRVI[723,525];类胡萝卜素(Cars)的最佳估算指数为FDNDVI[723,703];(4)对于使用统一参量同时估算Chla、Chlb、Cars,由FDRVI[723,703]建立的对数估算模型效果最佳。研究成果可为湿地植物生化参量反演提供参考,也可为闽江河口湿地入侵种互花米草的动态监测和生态评估管理提供有力的科学依据。     

Induced conformational change in human IL‐4 upon binding of a signal‐neutralizing DARPin

The crystal structure of DARPin 44C12V5 that neutralizes IL‐4 signaling has been determined alone and bound to human IL‐4. A significant conformational change occurs in the IL‐4 upon DARPin binding. The DARPin binds to the face of IL‐4 formed by the A and C α‐helices. The structure of the DARPin remains virtually unchanged. The conformational changes in IL‐4 include a reorientation of the C‐helix Trp91 side chain and repositioning of CD‐loop residue Leu96. Both side chains move by >9 Å, becoming buried in the central hydrophobic region of the IL‐4:DARPin interface. This hydrophobic region is surrounded by a ring of hydrophilic interactions comprised of hydrogen bonds and salt bridges and represents a classical “hotspot.” The structures also reveal how the DARPin neutralizes IL‐4 signaling. Comparing the IL‐4:DARPin complex structure with the structures of IL‐4 bound to its receptors (Hage et al., Cell 1999; 97 , 271‐281; La Porte et al., Cell 2008, 132, 259‐272), it is found that the DARPin binds to the same IL‐4 face that interacts with the junction of the D1 and D2 domains of the IL‐4Rα receptors. Signaling is blocked since IL‐4 cannot bind to this receptor, which it must do first before initiating a productive receptor complex with either the IL‐13α1 or the γ_c receptor. Proteins 2015; 83:1191–1197. © 2015 The Authors. Proteins: Structure, Function, and Bioinformatics Published by Wiley Periodicals, Inc.     

香蕉种植密度对蕉园光能利用与产量的影响

本试验研究了福建沿海地区蕉园种植密度与光能利用效率和产量之间的关系。结果表明,适当提高种植密度,可增加香蕉单位空间的光能利用,充分利用地力,改善蕉园生态条件,显著地提高香蕉亩产量。亩植160～180株是沿海地区达到高产稳产的有效措施。