Divalent metal ion complexes of S100B in the absence and presence of pentamidine

As part of an effort to inhibit S100B, structures of pentamidine (Pnt) bound to Ca²⁺-loaded and Zn²⁺,Ca²⁺-loaded S100B were determined by X-ray crystallography at 2.15 Å (R_free = 0.266) and 1.85 Å (R_free = 0.243) resolution, respectively. These data were compared to X-ray structures solved in the absence of Pnt, including Ca²⁺-loaded S100B and Zn²⁺,Ca²⁺-loaded S100B determined here (1.88 Å; R_free = 0.267). In the presence and absence of Zn²⁺, electron density corresponding to two Pnt molecules per S100B subunit was mapped for both drug-bound structures. One Pnt binding site (site 1) was adjacent to a p53 peptide binding site on S100B (± Zn²⁺), and the second Pnt molecule was mapped to the dimer interface (site 2; ± Zn²⁺) and in a pocket near residues that define the Zn²⁺ binding site on S100B. In addition, a conformational change in S100B was observed upon the addition of Zn²⁺ to Ca²⁺-S100B, which changed the conformation and orientation of Pnt bound to sites 1 and 2 of Pnt-Zn²⁺,Ca²⁺-S100B when compared to Pnt-Ca²⁺-S100B. That Pnt can adapt to this Zn²⁺-dependent conformational change was unexpected and provides a new mode for S100B inhibition by this drug. These data will be useful for developing novel inhibitors of both Ca²⁺- and Ca²⁺,Zn²⁺-bound S100B.     

Glycodelin protein and mRNA is downregulated in human first trimester abortion and partially upregulated in mole pregnancy.

Glycodelin (Gd) is a major reproductive glycoprotein and a mediator for immunomodulatory effects directed to cellular, humoral, and innate immunity. Human pregnancy depends on a diversity of physiological processes including modulation of the maternal immunosystem. We evaluated the expression of Gd protein and mRNA in first trimester decidual tissue of normal pregnancies and spontaneous abortion and hydatidiform moles. Furthermore, in vitro experiments on endometrial cancer cells to analyze the effect of human chorionic gonadotropin (hCG) on Gd regulation were performed. In decidual tissue of abortion patients, Gd expression was significantly decreased compared with normal gestation, which was confirmed by in situ hybridization. In mole pregnancy, an upregulation of Gd in the first 8 weeks of pregnancy was present. Gd is a main product of decidual tissue in the first trimester of human pregnancy. Reduced Gd expression in abortive pregnancy could lead to an increased activation of the maternal immunosystem, thus causing rejection of the developing fetus. Moreover, Gd expression in endometrial cancer cells in vitro could be stimulated by addition of hCG. Therefore, we speculate that hCG could be one of the factors regulating Gd expression because hCG is downregulated in women with abortion and upregulated in mole pregnancy. In addition, we found a positive feedback loop in Gd and hCG expression in human pregnancy.     

Comparison of Methods for Estimating Bird Abundance and Trends From Historical Count Data

Abstract: The use of bird counts as indices has come under increasing scrutiny because assumptions concerning detection probabilities may not be met, but there also seems to be some resistance to use of model-based approaches to estimating abundance. We used data from the United States Forest Service, Southern Region bird monitoring program to compare several common approaches for estimating annual abundance or indices and population trends from point-count data. We compared indices of abundance estimated as annual means of counts and from a mixed-Poisson model to abundance estimates from a count-removal model with 3 time intervals and a distance model with 3 distance bands. We compared trend estimates calculated from an autoregressive, exponential model fit to annual abundance estimates from the above methods and also by estimating trend directly by treating year as a continuous covariate in the mixed-Poisson model. We produced estimates for 6 forest songbirds based on an average of 621 and 459 points in 2 physiographic areas from 1997 to 2004. There was strong evidence that detection probabilities varied among species and years. Nevertheless, there was good overall agreement across trend estimates from the 5 methods for 9 of 12 comparisons. In 3 of 12 comparisons, however, patterns in detection probabilities potentially confounded interpretation of uncorrected counts. Estimates of detection probabilities differed greatly between removal and distance models, likely because the methods estimated different components of detection probability and the data collection was not optimally designed for either method. Given that detection probabilities often vary among species, years, and observers investigators should address detection probability in their surveys, whether it be by estimation of probability of detection and abundance, estimation of effects of key covariates when modeling count as an index of abundance, or through design-based methods to standardize these effects.     

Identification and characterization of FUS/TLS as a new target of ATM

ATM (ataxia-telangiectasia mutated), ATR (ATM- and Rad3-related) and DNA-PK (DNA-dependent protein kinase), important regulators of genome stability, belong to the PIKK (phosphoinositide 3-kinase-like kinase) family of protein kinases. In the present study, DNA-affinity chromatography was used to identify DNA-binding proteins phosphorylated by these kinases. This resulted in the identification of FUS (fused in sarcoma)/TLS (translocated in liposarcoma) as an in vitro target of the PIKKs. FUS is a member of the Ewing's sarcoma family of proteins that appears to play a role in regulating genome stability, since mice lacking FUS show chromosomal instability and defects in meiosis. The residues in FUS that are phosphorylated in vitro and in vivo were identified, and phospho-specific antibodies were generated to demonstrate that FUS becomes phosphorylated at Ser(42) in vivo, primarily in response to agents that cause DSBs (double-strand breaks). DSB-induced FUS phosphorylation in vivo at Ser(42) requires ATM and not DNA-PK. Although Ser(42) is retained in the oncogenic FUS-CHOP [C/EBP (CCAAT/enhancer-binding protein)-homologous protein 10] fusion generated by a t(12;16)(q13;p11) chromosomal translocation, Ser(42) in FUS-CHOP is not phosphorylated after DNA damage. These results identify FUS as a new target of the ATM-signalling pathway and strengthen the notion that FUS regulates genome stability.     

Recent Advances in Design and Synthesis of Self-Adjuvanting Lipopeptide Vaccines

Synthetic lipopeptide vaccines are being increasingly investigated mainly because of the advantages they offer over traditional vaccines, including safety of use in humans, high specificity in eliciting immune responses, greater purity and large scale/cost-effective production capacity. Moreover, a number of lipopeptide vaccines designed to possess self-adjuvanting properties have been developed and tested in vitro and in vivo. Producing high levels of serum-specific antibodies against incorporated peptide epitopes, they are showing their potential as effective vaccine candidates without the need for a co-administered adjuvant and/or carrier protein, often associated with undesirable effects in humans. This review presents recent insights on lipopeptide vaccine research and development, particularly on (1) the influence of the orientation of peptide epitopes and lipids on immune responses, (2) the use of carbohydrates for vaccine targeting, adjuvanting or as peptide epitope carriers, and (3) synthetic approaches to highly pure, multi-epitopic vaccine molecules using native chemical ligation techniques. Incorporation of different types of antigens within the same lipopeptide construct could provide a lipopeptide vaccine candidate suitable for safe and effective mucosal administration, which is a comfortable way of drug delivery.     

Bifurcation structure of a chemostat model for an age-structured predator and its prey

We model a chemostat containing an age-structured predator and its prey using a linear function for the uptake of substrate by the prey and two different functional responses (linear and Monod) for the consumption of prey by the predator. Limit cycles (LCs) caused by the predator's age structure arise at Hopf bifurcations at low values of the chemostat dilution rate for both model cases. In addition, LCs caused by the predator-prey interaction arise for the case with the Monod functional response. At low dilution rates in the Monod case, the age structure causes cycling at lower values of the inflowing resource concentration and conversely prevents cycling at higher values of the inflowing resource concentration. The results shed light on a similar model by Fussmann et al. [G. Fussmann, S. Ellner, K. Shertzer, and N. Hairston, Crossing the Hopf bifurcation in a live predator-prey system, Science 290 (2000), pp. 1358-1360.], which correctly predicted conditions for the onset of cycling in a chemostat containing an age-structured rotifer population feeding on algal prey.     

Ndel1 promotes axon regeneration via intermediate filaments

Failure of axons to regenerate following acute or chronic neuronal injury is attributed to both the inhibitory glial environment and deficient intrinsic ability to re-grow. However, the underlying mechanisms of the latter remain unclear. In this study, we have investigated the role of the mammalian homologue of aspergillus nidulans NudE, Ndel1, emergently viewed as an integrator of the cytoskeleton, in axon regeneration. Ndel1 was synthesized de novo and upregulated in crushed and transected sciatic nerve axons, and, upon injury, was strongly associated with neuronal form of the intermediate filament (IF) Vimentin while dissociating from the mature neuronal IF (Neurofilament) light chain NF-L. Consistent with a role for Ndel1 in the conditioning lesion-induced neurite outgrowth of Dorsal Root Ganglion (DRG) neurons, the long lasting in vivo formation of the neuronal Ndel1/Vimentin complex was associated with robust axon regeneration. Furthermore, local silencing of Ndel1 in transected axons by siRNA severely reduced the extent of regeneration in vivo. Thus, Ndel1 promotes axonal regeneration; activating this endogenous repair mechanism may enhance neuroregeneration during acute and chronic axonal degeneration.     

拉萨河谷上段江孜沙棘Hippophea gyantsensis(Rousi) Lian种群的海拔梯度性变异

江孜沙棘[Hippophea gyantsensis(Rousi)Lian]是青藏高原特有的一种广生态幅的小乔木,在拉萨河谷地区的海拔3500~4200m范围内均有分布。前人工作多集中在江孜沙棘果实的开发利用方面,对其基础生态学研究较少。本研究旨在探讨江孜沙棘沿海拔梯度的群落组成和表型变异的规律。为此,在拉萨河谷上段沿海拔梯度由东向西设置了4个样带:3850m、3950m、4050m和4200m,每个样带设置2至3个10m×10m的样方进行研究。首先,详细记录了每个样方内林下维管植物的物种组成、样方内的沙棘盖度、海拔、样方与河岸的实际距离,并用DCA[detrended correspondence analysis(去势对应分析)]排序方法对群落及其组成物种进行排序分析。随机抽取了每个样方内的20个江孜沙棘植株个体,测定其胸径、基径、株高和叶片长度,用回归分析法分析这些变量和海拔之间的关系。研究结果表明,江孜沙棘在拉萨河谷内的主要生境分为4种类型,即:河边砾石滩地、河阶草滩、河边草甸和河边林缘,样方排序结果主要受海拔的影响;同时,江孜沙棘植株的基径、胸径和高度都随着海拔的升高而显著减小,而叶片长度与海拔之间无显著相关。本文研究结果表明,对江孜沙棘而言,海拔所代表的综合环境因子对其分布和表型有显著的影响,而局部光照可能也是影响其表型特征的重要生态因子。     

Investigation toward multi-epitope vaccine candidates using native chemical ligation

We applied native chemical ligation (NCL) method to the synthesis of highly pure lipid-core peptide (LCP) vaccines to attach various peptide epitopes. In the case of the synthesis of LCP vaccine with two different peptide epitopes, LCP moieties having two free Cys and two protected Cys derivatives (S-acetamidemethyl-Cys, (Cys(Acm)), N-methylsulfonylethyloxycarbonyl-Cys (Msc-Cys), or 1,3-thiazolidine-4-carboxylic acid (Thz)) on oligolysine branches were prepared in order to couple two different epitopes by stepwise NCL. It was found that the difficulty in NCL of first two peptide antigen was associated with the steric hindrance. Using Thz instead of Cys(Acm) and Msc-Cys was important to reduce the steric hindrance and improve NCL yield.