蛋白酶活化受体-2的研究进展

蛋白酶活化受体(protease-activated receptors,PARs)属于G蛋白偶联受体家族成员,其N-末端被蛋白酶裂解后,可形成新的N-末端。新N-末端能够结合、激活自身受体。PAR-2是PARs的成员之一,其激活、灭活、脱敏、复敏、及其与信号转导途径的关系,尤其是与疾病(如呼吸道慢性炎症)的关系正倍受关注。     

Predicting demographic group structures based on DNA sequence data

The ability to infer relationships between groups of sequences, either by searching for their evolutionary history or by comparing their sequence similarity, can be a crucial step in hypothesis testing. Interpreting relationships of human immunodeficiency virus type 1 (HIV-1) sequences can be challenging because of their rapidly evolving genomes, but it may also lead to a better understanding of the underlying biology. Several studies have focused on the evolution of HIV-1, but there is little information to link sequence similarities and evolutionary histories of HIV-1 to the epidemiological information of the infected individual. Our goal was to correlate patterns of HIV-1 genetic diversity with epidemiological information, including risk and demographic factors. These correlations were then used to predict epidemiological information through analyzing short stretches of HIV-1 sequence. Using standard phylogenetic and phenetic techniques on 100 HIV-1 subtype B sequences, we were able to show some correlation between the viral sequences and the geographic area of infection and the risk of men who engage in sex with men. To help identify more subtle relationships between the viral sequences, the method of multidimensional scaling (MDS) was performed. That method identified statistically significant correlations between the viral sequences and the risk factors of men who engage in sex with men and individuals who engage in sex with injection drug users or use injection drugs themselves. Using tree construction, MDS, and newly developed likelihood assignment methods on the original 100 samples we sequenced, and also on a set of blinded samples, we were able to predict demographic/risk group membership at a rate statistically better than by chance alone. Such methods may make it possible to identify viral variants belonging to specific demographic groups by examining only a small portion of the HIV-1 genome. Such predictions of demographic epidemiology based on sequence information may become valuable in assigning different treatment regimens to infected individuals.     

Hybrid methods for automated diagnosis of breast tumors

OBJECTIVE: To design and analyze a new family of hybrid methods for the diagnosis of breast tumors using fine needle aspirates. STUDY DESIGN: We present a radically new approach to the design of diagnosis systems. In the new approach, a nonlinear classifier with high sensitivity but low specificity is hybridized with a linear classifier having low sensitivity but high specificity. Data from the Wisconsin Breast Cancer Database are used to evaluate, computationally, the performance of the hybrid classifiers. RESULTS: The diagnosis scheme obtained by hybridizing the nonlinear classifier ellipsoidal multisurface method (EMSM) with the linear classifier proximal support vector machine (PSVM) was found to have a mean sensitivity of 97.36% and a mean specificity of 95.14% and was found to yield a 2.44% improvement in the reliability of positive diagnosis over that of EMSM at the expense of 0.4% degradation in the reliability of negative diagnosis, again compared to EMSM. At the 95% confidence level we can trust the hybrid method to be 96.19-98.53% correct in its malignant diagnosis of new tumors and 93.57-96.71% correct in its benign diagnosis. CONCLUSION: Hybrid diagnosis schemes represent a significant paradigm shift and provide a promising new technique to improve the specificity of nonlinear classifiers without seriously affecting the high sensitivity of nonlinear classifiers.     

A Wnt-Wnt situation

A recent Juan March Foundation workshop on "wnt genes and Wnt signaling" brought developmental and cancer biologists together to share some of the latest advances in Wnt research. Discussion topics included molecular, genetic, and genomic dissections of wnt genes in embryogenesis and cancer, Wnt signaling components and downstream targets, interactions with other signaling pathways, cell biological aspects of Wnt signaling, and a first glimpse of a purified Wnt protein.     

High throughput detection of small genomic insertions or deletions by Pyrosequencing

Small insertions or deletions of nucleotides are common polymorphic variations in the human genome and can result in a predisposition to disease. However, high throughput methods for detecting these variations are limited. This report describes a method to detect this variation based on sequencing the boundaries of nucleotide alterations using the Pyrosequencing technique. This method can optimally detect up to 100 base pair nucleotide insertions and deletions, and also complicated genomic rearrangements.     

Nuclease activities and DNA fragmentation during programmed cell death of megagametophyte cells of white spruce (Picea glauca) seeds

The haploid megagametophyte of white spruce (Picea glauca) seeds undergoes programmed cell death (PCD) during post-germinative seedling growth. Death of the megagametophyte storage parenchyma cells was preceded by reserve mobilization and vacuolation. TUNEL (terminal deoxynucleotidyltransferase-mediated dUTP nick-end labeling)-positive nuclei indicated that the first megagametophyte cells to die were those closest to the radicle at the micropylar end of the seed as well as those that comprised the most peripheral and innermost layers at the chalazal end of the seed. The death process was accompanied by nuclear fragmentation and internucleosomal DNA cleavage and the sequential activation of several nucleases. The latter comprised at least two groups: those induced relatively early during post-germinative seedling growth, that had pH optima in the neutral range (33, 31, 17 and 15 kDa), and those induced later that had pH optima in the acidic range (73, 62, 48, 43 and 29 kDa). Activities of all of the nucleases were stimulated by Ca²⁺, Mg²⁺ and Mn²⁺; only the nucleases active at neutral pH were inhibited by Zn²⁺. The temporal pattern of induction of the neutral and acidic nucleases may suggest that the latter function after tonoplast rupture.     

Allopolyploidy alters gene expression in the highly stable hexaploid wheat

Hexaploid wheat (Triticum aestivum) contains triplicated genomes derived from three distinct species. To better understand how different genomes are coordinated in the same nucleus of the hexaploid wheat, we globally compared gene expression of a synthetic hexaploid wheat with its diploid (Aegilops tauschii) and tetraploid (T. turgidum) parents by cDNA-AFLP display. The results suggested that the expression of a significant fraction of genes was altered in the synthetic hexaploid; most appeared to be diminished and some were activated. We characterized nine cDNA clones in details. Cytogenetic as well as genomic sequence analyses indicated that the gene silencing was not due to chromosome/DNA loss but was caused by gene regulation. Northern and RT-PCR divided these genes into three groups: (I) four genes were down-regulated nonspecifically, likely involving both parental orthologues; (II) four genes were down-regulated in an orthologue-dependent manner; (III) one gene was activated specifically in the synthetic hexaploid wheat. These genes were often altered non-randomly in different synthetic hexaploids as well as natural hexaploid wheat, suggesting that many of the gene expression changes were intrinsically associated with polyploidy.     

Increased expression of CD95-ligand and other apoptotic signaling factors by fumonisin B1, a hepatotoxic mycotoxin, in livers of mice lacking tumor necrosis factor alpha

Fumonisin B1 (FB1), a mycotoxin, is a potent inhibitor of ceramide synthase, and produces organ-, species-, and even gender-specific toxic responses in animals. The hepatotoxic response of FB1 in mice involves accumulation of free sphingoid bases and induction of inflammatory cytokines including tumor necrosis factor alpha (TNFalpha). The FB1-induced hepatotoxic responses were reduced in mice lacking TNFalpha receptor (TNFR) 1 or TNFR2. However, the hepatotoxicity was exacerbated in mice lacking TNFalpha. We therefore investigated the modulation of various other apoptotic signaling factors in TNFalpha-knockout (TKO) mice compared to wild-type (WT) strain after repeated daily subcutaneous injections of 2.25 mg/kg FB1 treatment for 5 days. Expression of various signaling genes in liver was evaluated by ribonuclease protection assay. Expression of CD95-ligand (FasL) was more than doubled in TKO animals after FB1 whereas it was unaltered in the WT group. FB1 did not alter CD95 expression in either strain; however, expressions of TRAIL, and downstream signaling factors FADD, TRADD, and caspase 8 were higher in FB1-treated TKO mice than in the corresponding WT animals. The TKO strain had a higher constitutive expression of apoptotic factors except CD95L. In addition to the CD95 and TNFalpha systems, the expression of apoptotic molecules bcl-2, b-myc, c-myc, bax, max, mad and IL1alpha was induced by FB1 in TKO mice to a greater extent than in WT animals; many of these factors also had a higher constitutive expression in TKO animals than WT mice. Results indicated that FB1 can induce CD95 modulated signaling when TNFalpha is absent. Differential constitutive expression of apoptotic genes in TKO mice may explain their increased sensitivity to FB1. These results are important in characterizing the modulating effect of TNFalpha on apoptotic signaling and in explaining the unexpected sensitivity of mice lacking this cytokine in response to hepatotoxic xenobiotics.     

Notch signalling in B cells

Notch signalling is likely to regulate multiple aspects of lymphoid development and function. During T cell development, Notch signalling is required for commitment of the earliest progenitor, and may also function during other developmental stages. T cell commitment from a common lymphoid progenitor occurs at the expense of B cell development, suggesting that Notch signalling inhibits the earliest stage of B lymphopoiesis. In contrast, recent evidence suggests that Notch promotes the development of marginal zone lymphocytes. Not only is Notch required for later stages of B cell development, but several viral proteins appear to utilize Notch signalling in B cells to mediate their functions. In this review, we will focus on potential roles of Notch signalling in B lymphopoiesis and also consider how viral proteins may utilize Notch signalling in B cells.