Flanking V and J sequences of complementary determining region 3 of T cell receptor (TCR) δ1 (CDR3δ1) determine the structure and function of TCRγ4δ1

The γδ T cell receptor (TCR) differs from immunoglobulin and αβ TCR in its overall binding mode. In human, genes δ1, δ2, and δ3 are used for TCRδ chains. Previously, we have studied antigen binding determinants of TCRδ2 derived from dominant γδ T cells residing in peripheral blood. In this study we have investigated the critical determinants for antigen recognition and TCR function in TCRδ1 originated from gastric tumor-infiltrating γδ T lymphocytes using three independent experimental strategies including complementary determining region 3 (CDR3) of TCRδ1 (CDR3δ1)-peptide mediated binding, CDR3δ1-grafted TCR fusion protein-mediated binding, and TCRγ4δ1- and mutant-expressing cell-mediated binding. All three approaches consistently showed that the conserved flanking V and J sequences but not the diverse D segment in CDR3δ1 determine the antigen binding. Most importantly, we found that mutations in the V and J regions of CDR3δ1 also abolish the assembly of TCR and TCR-CD3 complexes in TCRγ4δ1-transduced J.RT3-T3.5 cells. Together with our previous studies on CDR3δ2 binding, our finding suggests that both human TCRδ1 and TCRδ2 recognize antigen predominately via flanking V and J regions. These results indicate that TCRγδ recognizes antigens using conserved parts in their CDR3, which provides an explanation for a diverse repertoire of γδTCRs only recognizing a limited number of antigens.     

A survey of the availability of primary bioinformatics web resources

The explosive growth of the bioinformatics field has led to a large amount of data and software applications publicly available as web resources. However, the lack of persistence of web references is a barrier to a comprehensive shared access. We conducted a study of the current availability and other features of primary bioinforo matics web resources （such as software tools and databases）. The majority （95%） of the examined bioinformatics web resources were found running on UNIX/Linux operating systems, and the most widely used web server was found to be Apache （or Apache-related products）. Of the overall 1,130 Uniform Resource Locators （URLs） examined, 91% were highly available （more than 90% of the time）, while only 4% showed low accessibility （less than 50% of the time） during the survey. Furthermore, the most common URL failure modes are presented and analyzed.     

Association Models for Clustered Data with Binary and Continuous Responses

Summary .  We consider analysis of clustered data with mixed bivariate responses, i.e., where each member of the cluster has a binary and a continuous outcome. We propose a new bivariate random effects model that induces associations among the binary outcomes within a cluster, among the continuous outcomes within a cluster, between a binary outcome and a continuous outcome from different subjects within a cluster, as well as the direct association between the binary and continuous outcomes within the same subject. For the ease of interpretations of the regression effects, the marginal model of the binary response probability integrated over the random effects preserves the logistic form and the marginal expectation of the continuous response preserves the linear form. We implement maximum likelihood estimation of our model parameters using standard software such as PROC NLMIXED of SAS . Our simulation study demonstrates the robustness of our method with respect to the misspecification of the regression model as well as the random effects model. We illustrate our methodology by analyzing a developmental toxicity study of ethylene glycol in mice.     

A FANCD2 domain activates Tip60‐dependent apoptosis

The FA (Fanconi anaemia) FANCD2 protein is pivotal in the cellular response to DNA interstrand cross‐links. Establishing cells expressing exogenous FANCD2 has proven to be difficult compared with other DNA repair genes. We find that in transformed normal human fibroblasts, exogenous nuclear expression of FANCD2 induces apoptosis, dependent specifically on exons 10–13. This is the same region required for interaction with the histone acetyltransferase, Tip60. Deletion of exons 10–13 from FANCD2 N‐terminal constructs (nucleotides 1–1100) eliminates the binary interaction with Tip60 and the cellular apoptotic response; moreover, cells can stably express FANCD2 at high levels if Tip60 is depleted. The results indicate that FANCD2‐sponsored apoptosis requires an interaction with Tip60 and depends on Tip60.     

The log multinomial regression model for nominal outcomes with more than two attributes

An estimate of the risk or prevalence ratio, adjusted for confounders, can be obtained from a log binomial model (binomial errors, log link) fitted to binary outcome data. We propose a modification of the log binomial model to obtain relative risk estimates for nominal outcomes with more than two attributes (the "log multinomial model"). Extensive data simulations were undertaken to compare the performance of the log multinomial model with that of an expanded data multinomial logistic regression method based on the approach proposed by Schouten et al. (1993) for binary data, and with that of separate fits of a Poisson regression model based on the approach proposed by Zou (2004) and Carter, Lipsitz and Tilley (2005) for binary data. Log multinomial regression resulted in "inadmissable" solutions (out-of-bounds probabilities) exceeding 50% in some data settings. Coefficient estimates by the alternative methods produced out-of-bounds probabilities for the log multinomial model in up to 27% of samples to which a log multinomial model had been successfully fitted. The log multinomial coefficient estimates generally had lesser relative bias and mean squared error than the alternative methods. The practical utility of the log multinomial regression model was demonstrated with a real data example. The log multinomial model offers a practical solution to the problem of obtaining adjusted estimates of the risk ratio in the multinomial setting, but must be used with some care and attention to detail.     

Two into One Won’t Go: Conceptual, Clinical, Ethical and Legal Impedimenta to the Convergence of CAM and Orthodox Medicine

The convergence of complementary and alternative medicine (CAM) and evidence-based medicine (EBM) is a prominent feature of healthcare in western countries, but it is currently undertheorised, and its implications have been insufficiently considered. Two models of convergence are described – the totally integrated evidence-based model (TI) and the multicultural-pluralistic model (MP). Both models are being incorporated into general medical practice. Against the background of the reasons for the increasing utilisation of CAM by the public and by general practitioners, TI-convergence is supported and MP-convergence is rejected. MP-convergence is epistemologically and clinically incoherent, and it cannot be regulated. It is also inconsistent with developments in the legal determination of the standard of care for both diagnosis/treatment and disclosure. These claims concerning MP-convergence are justified by the fact that science is not a member of the group of perspectives or world-views which postmodernism treats as equally valid, and this is especially important for healthcare.     

黄河三角洲滨海滩涂不同密度柽柳林的根系形态及生长特征

为探讨黄河三角洲滨海滩涂不同密度柽柳根系形态及生长特征,以山东省滨州港附近滨海滩涂的低密度（1100株/hm²）、中密度（4100株/hm²）和高密度（7100株/hm²）柽柳林为研究对象,采用全挖法对不同密度柽柳根系进行挖掘,测定分析柽柳地上生物量、根系生物量、空间分布特征、拓扑结构和连接长度等指标。结果表明：（1）中、高密度下,柽柳对根系生长的投入量更大,以保证对地下资源的吸收利用,根冠比分别为0.59、0.53;而低密度柽柳根冠比为0.44。（2）低、中密度下柽柳根冠生长关系均表现为异速生长,高密度下为等速生长。（3）不同密度柽柳根系生长都以水平分布为主,表现出水平根型特征。中、高密度柽柳根幅及侧根长均小于低密度,低密度柽柳根系水平分布范围最大,可利于增强觅养和固定能力。（4）林分密度与拓扑指数显著相关,低密度柽柳根系拓扑结构趋向于叉状结构（拓扑指数TI=0.62）;中、高密度柽柳拓扑结构趋向于鱼尾形分支（TI=0.86;TI=0.81）。（5）不同密度柽柳根系外部连接长度显著大于内部连接长度,呈现滨海滩涂柽柳根系向外扩张的生长策略。滨海滩涂不同密度柽柳根冠异速生长关系、根系形态及生长特征既有差异性又有相似性,表现出不同的密度适应特征。不同密度柽柳根系均以地表分布、向外扩张为主。低密度柽柳主要通过增加分支,扩大根系生长空间;中、高密度柽柳减少分支,加强对内部资源的利用,以降低与邻株间的竞争。柽柳密度与土壤含水量、电导率、扎根深度、侧根长、拓扑指数显著相关。     

菌丝桥在日本落叶松幼苗间磷传递和植株生长中的作用

 应用四室隔网系统研究了菌丝桥在日本落叶松(Larix kaempferi)幼苗间传递磷的作用。结果表明,供体接种卷缘桩菇(Paxillus involutus)和彩色豆马勃（Pisolithus tinctorius）后,其外延菌丝可以穿过隔离层侵染受体落叶松,在供体和受体落叶松间形成了菌丝桥。供体植株接种菌根真菌后生物量明显增加,但是对受体植株没有显著的影响。菌根真菌侵染的供体和受体植株的根、地上部吸磷量均分别显著高于对照,而且供体植株根、地上部吸磷量增加的程度明显高于受体。被卷缘桩菇和彩色豆马勃侵染的受体植株体内32P的放射性强度分别是对照的10倍和6倍,两者形成菌丝桥后传递到受体植株的32P分别为供体植株体内32P的1.10%和0.22%。供体植株吸收的32P可以通过菌丝桥传递给受体,但是绝对数量十分有限,对受体植株磷营养没有产生显著的影响,但P. involutus和P. tinctorius侵染受体植株后,促进了受体落叶松对磷的吸收,这是菌丝桥形成后,真菌帮助受体植株吸收磷引起的。     

Thermal stability and energetics of 15-mer DNA duplex interstrand crosslinked by trans-diamminedichloroplatinum(II)

The effect of the location of the interstrand cross-link formed by trans-diamminedichloroplatinum(II) (transplatin) on the thermal stability and energetics of 15-mer DNA duplex has been investigated. The duplex containing single, site-specific cross-link, thermodynamically equivalent model structures (hairpins) and nonmodified duplexes were characterized by differential scanning calorimetry, temperature-dependent uv absorption, and circular dichroism. The results demonstrate that the formation of the interstrand cross-link of transplatin does not affect pronouncedly thermodynamic stability of DNA: the cross-link induces no marked changes not only in enthalpy, but also in "reduced" (concentration independent) monomolecular transition entropy. These results are consistent with the previous observations that interstrand cross-links of transplatin structurally perturb DNA only to a relatively small extent. On the other hand, constraining the duplex with the interstrand cross-link of transplatin results in a significant increase in thermal stability that is primarily due to entropic effects: the cross-link reduces the molecularity of the oligomer system from bimolecular to monomolecular. Importantly, the position of the interstrand cross-link within the duplex modulates cooperativity of the melting transition of the duplex and consequently its thermal stability.