Use of expression constructs to dissect the functional domains of the CHS/beige protein: identification of multiple phenotypes

The Chediak-Higashi Syndrome (CHS) and the orthologous murine disorder beige are characterized at the cellular level by the presence of giant lysosomes. The CHS1/Beige protein is a 3787 amino acid protein of unknown function. To determine functional domains of the CHS1/Beige protein, we generated truncated constructs of the gene/protein. These truncated proteins were transiently expressed in Cos-7 or HeLa cells and their effect on membrane trafficking was examined. Beige is apparently a cytosolic protein, as are most transiently expressed truncated Beige constructs. Expression of the Beige construct FM (amino acids 1-2037) in wild-type cells led to enlarged lysosomes. Similarly, expression of a 5.5-kb region (amino acids 2035-3787) of the carboxyl terminal of Beige (22B) also resulted in enlarged lysosomes. Expression of FM solely affected lysosome size, whereas expression of 22B led to alterations in lysosome size, changes in the Golgi and eventually cell death. The two constructs could be used to further dissect phenotypes resulting from loss of the Beige protein. CHS or beigej fibroblasts show an absence of nuclear staining using a monoclonal antibody directed against phosphatidylinositol 4,5 bisphosphate [PtdIns(4,5) P2]. Transformation of beige j fibroblasts with a YAC containing the full-length Beige gene resulted in the normalization of lysosome size and nuclear PtdIns(4,5)P2 staining. Expression of the carboxyl dominant negative construct 22B led to loss of nuclear PtdIns(4,5)P2 staining. Expression of the FM dominant negative clone did not alter nuclear PtdIns(4,5) P2 localization. These results suggest that the Beige protein interacts with at least two different partners and that the Beige protein affects cellular events, such as nuclear PtdIns(4,5)P2 localization, in addition to lysosome size.     

Immucillin-H binding to purine nucleoside phosphorylase reduces dynamic solvent exchange

The rate and extent of hydrogen/deuterium (H/D) exchange into purine nucleoside phosphorylase (PNP) was monitored by electrospray ionization mass spectrometry (ESI-MS) to probe protein conformational and dynamic changes induced by a substrate analogue, products, and a transition state analogue. The genetic deficiency of PNP in humans is associated with severe T-cell immunodeficiency, while B-cell immunity remains functional. Inhibitors of PNP have been proposed for treatment of T-cell leukemia, to suppress the graft-vs.-host response, or to counter type IV autoimmune diseases without destroying humoral immunity. Calf spleen PNP is a homotrimer of polypeptide chains with 284 amino residues, molecular weight 31,541. Immucillin-H inhibits PNP with a Kd of 23 pM when only one of the three catalytic sites is occupied. Deuterium exchange occurs at 167 slow-exchange sites in 2 h when no catalytic site ligands are present. The substrate analogue and product prevented H/D exchange at 10 of the sites. Immucillin-H protected 32 protons from exchange at full saturation. When one of the three subunits of the homotrimer is filled with immucillin-H, and 27 protons are protected from exchange in all three subunits. Deuterium incorporation in peptides from residues 132-152 decreased in all complexes of PNP. The rate and/or extent of deuterium incorporation in peptides from residues 29-49, 50-70, 81-98, and 112-124 decreased only in the complex with the transition state analogue. The peptide-specific H/D exchange demonstrates that (1) the enzyme is most compact in the complex with immucillin-H, and (2) filling a single catalytic site of the trimer reduces H/D exchange in the same peptides in adjacent subunits. The peptides most highly influenced by the inhibitor surround the catalytic site, providing evidence for reduced protein dynamic motion caused by the transition state analogue.     

Genetic evidence for posterior specification by convergent extension in the Xenopus embryo

Genetic studies substantiate that mesodermal convergent extension expressed behind the anteroposterior borderline, in the form of a gradient with the posterior apex after gastrulation, regulates morphogenesis of the posterior zone at the dorsal and dorso-lateral levels which is in full agreement with the model of dorsalization–caudalization. In contrast, how anteroposterior specification of mesodermal tissues occurs at the ventral and latero-ventral levels is not yet understood.     

Protein fold recognition without Boltzmann statistics or explicit physical basis.

We present a fast method for finding optimal parameters for a low-resolution (threading) force field intended to distinguish correct from incorrect folds for a given protein sequence. In contrast to other methods, the parameterization uses information from >10(7) misfolded structures as well as a set of native sequence-structure pairs. In addition to testing the resulting force field's performance on the protein sequence threading problem, results are shown that characterize the number of parameters necessary for effective structure recognition.     

参数仪器变量估计近似分布方差的一种算法

本文对更一般的结构模型给出了参数的一种常用的仪器变量估计近似分布方差的一种算法．并且给出了未知真值x服从指数分布的例子．此算法对生物科学中统计规律的探讨有一定的应用价值．     

火炬松胚性细胞悬浮培养物的生长参数变化

以火炬松（PinustaedaL.）成熟合子胚来源的胚性愈伤组织为材料建立了胚性细胞悬浮系,测定了其培养物的鲜重、干重、细胞体积和胚数及培养液中的pH值、电导率和蔗糖浓度等生长参数在培养过程中的变化动态。结果表明,在培养周期内,培养液中的pH值、电导率和蔗糖浓度的逐步降低与培养物的鲜重、干重、细胞体积和胚胎数的逐步增加保持一致性。在培养至18—21d,pH值、电导率和蔗糖浓度均接近或降到最低点,而胚数及细胞体积的增长都达到最高点。     

BINOMIAL COUNT ANALYSIS BASED ON THE SPATIAL DISTRIBUTION AND POPULATION DENSITY ESTIMATION OF COTTON APHIDS1)

Abstract  Based on field population sampling of Aphis gossypii on cotton seedlings in Quzhou Experiment Station of China Agricultural University in Hebei Province in 1991, we obtained a data set consisting of 24 estimates of mean aphid density ( m , number of aphids per plant), variance (s²) and the proportion of plants (P_T) with no more than T aphids (T=0, 1, 2,…, 8, 10, 15, 20, respectively and defined as tally threshold). Taylor's power law fitted the data well (r²= 0. 958). The resulting slope (1. 515) was significantly greater than 1, indicating that the spatial distribution of this aphid was in aggregated pattern. An empirical relationship between m and Pr was developed for each T value using the parameters from the linear regression In( m )= a +bln[- ln( P_T )}]. The importance of the T values in reduction of sampling errors and their application to binomial sampling plans are discussed. Small T values, particularly aphid-free plant (T = 0, conventional binomial sample), could lead to spurious estimates of m from P_T . A value of T from 10 to 15 was recommended to develop binomial sampling plans for the aphids on cotton seedlings because of the relatively small sampling errors.     

A Bayesian Long‐term Survival Model Parametrized in the Cured Fraction

The main goal of this paper is to investigate a cure rate model that comprehends some well‐known proposals found in the literature. In our work the number of competing causes of the event of interest follows the negative binomial distribution. The model is conveniently reparametrized through the cured fraction, which is then linked to covariates by means of the logistic link. We explore the use of Markov chain Monte Carlo methods to develop a Bayesian analysis in the proposed model. The procedure is illustrated with a numerical example.