A critical role for the histidine residues in the catalytic function of acyl-CoA:cholesterol acyltransferase catalysis: evidence for catalytic difference between ACAT1 and ACAT2

To investigate a role for histidine residues in the expression of normal acyl-CoA:cholesterol acyltransferase (ACAT) activity, the histidine residues located at five different positions in two isoenzymes were substituted by alanine, based on the sequence homology between ACAT1 and ACAT2. Among the 10 mutants generated by baculovirus expression technology, H386A-ACAT1, H460A-ACAT1, H360A-ACAT2, and H399A-ACAT2 lost their enzymatic activity completely. A reduction in catalytic activity is unlikely to result from structural changes in the substrate-binding pocket, because their substrate-binding affinities were normal. However, the enzymatic activity of H386A-ACAT1 was restored to <37% of the level of the wild-type activity when cholesterol was replaced by 25-hydroxycholesterol as substrate. H527A-ACAT1 and H501A-ACAT2, termed carboxyl end mutants, exhibit activities of ∼96% and ∼75% of that of the wild-type. Interestingly, H425A-ACAT1 showed 59% of the wild-type activity, in contrast to its equivalent mutant, H399A-ACAT2. These results demonstrate that the histidine residues located at the active site are very crucial both for the catalytic activity of the enzyme and for distinguishing ACAT1 from ACAT2 with respect to enzyme catalysis and substrate specificity.     

Mutations at Asp112 adjacent to the trinuclear Cu center in CueO as the proton donor in the four-electron reduction of dioxygen

Asp112 adjacent to the trinuclear Cu center of a multicopper oxidase, CueO was mutated for Glu, Ala and Asn. Mutations on Asp112 affected not only spectroscopic and magnetic properties derived from the trinuclear Cu center but also enzyme activities. The uncoordinated Asp112 was found to play multiple roles to promote the binding of dioxygen at the trinuclear Cu center and to accelerate the conversion of dioxygen to water molecules by facilitating the supply of H+ to the reaction intermediates.     

Zasp/Cypher internal ZM-motif containing fragments are sufficient to co-localize with alpha-actinin--analysis of patient mutations

Z-band alternatively spliced PDZ-containing protein (ZASP/Cypher) has an important role in maintaining Z-disc stability in striated and cardiac muscle. ZASP/Cypher interacts through its PDZ domain with the major Z-disc actin cross-linker, alpha-actinin. ZASP/Cypher also has a conserved sequence called the ZM-motif, and it is found in two alternatively spliced exons 4 and 6. We have shown earlier that the ZM-motif containing internal regions of two related proteins ALP and CLP36 interact with alpha-actinin rod region, and that the ZM-motif is important in targeting ALP to the alpha-actinin containing structures in cell. Here, we show that the ZASP/Cypher internal fragments containing either ZM exon 4 or 6 co-localized with alpha-actinin in cultured myoblasts and nonmuscle cells. Fragments of 130 residues around the ZM-consensus were sufficient for localization, which is similar to our previous results of ALP. Moreover, ZASP/Cypher protein interacted directly with the alpha-actinin rod and competed with ALP in binding to the rod. During the inhibition of stress fiber assembly ZASP/Cypher and alpha-actinin co-localization could be partially disturbed, suggesting that ZASP/Cypher is bound to alpha-actinin mainly when alpha-actinin is localizing in stress fibers. Many point mutations found in cardiomyopathy patients are located in the internal region of ZASP/Cypher. However, we found no evidence that human patient mutations in the internal domain would affect the ZASP/Cypher co-localization with alpha-actinin, or that the mutations would destabilize the ZASP/Cypher protein.     

The importance of nutrient source in determining the influence of retention time on phytoplankton: an explorative modelling study of a naturally well-flushed lake

Two models were used to examine the relationship between hydraulic retention time, nutrient source and total chlorophyll in a shallow lake (Bassenthwaite Lake, UK). The first model was a derivation of the Vollenweider model and the second was the phytoplankton community model, PROTECH. The adapted Vollenweider model produced two different responses to changing the retention time that were phosphorus source dependent. If the phosphorus was totally from a point source, then annual mean chlorophyll steadily declined with increasing flushing rate. However, when a diffuse source was used, the chlorophyll changed little and even increased with short retention times (retention time <40 days). The PROTECH model produced some similar responses but they were more season dependent. Winter mean chlorophyll always declined with decreasing retention time, regardless of nutrient source, but the summer mean curves were source dependent and similar to those produced by the adapted Vollenweider model. Further simulations with PROTECH using a standardized flow regime provided strong evidence as to the mechanisms behind these responses. Analysis showed that the decline in chlorophyll with decreasing retention time was the prevalent response of the PROTECH simulations due to flushing loss of both nutrients and algae. Furthermore, the curve formed an asymptote at long retention times because other factors (e.g. light) limited growth; retention times >100 days had little effect on chlorophyll. However, with a diffuse phosphorus source and short retention times, an increase in biomass was observed when the nutrient was limiting for growth. Handling editor: Luigi Naselli-Flores     

转基因植物在环境污染监测中的应用

在通常情况下,污染物的存在很难被发现。它们对环境和人类的潜在危害就更加难以估计。在众多生物监测体系中,转基因植物监测系统脱颖而出。综述了几种成功应用于污染物质遗传毒性监测的转基因植物系统,并对今后生产高效率转基因植物监测体系的关键问题进行了探讨。     

生物序列比对算法的研究现状

序列比对是生物信息学研究的一个重要工具,它在序列拼接、蛋白质结构预测、蛋白质结构功能分析、系统进化分析、数据库检索以及引物设计等问题的研究中被广泛使用。本文详细介绍了在生物信息学中常用的一些序列比对算法,比较了这些算法所需的计算复杂度,优缺点,讨论了各自的使用范围,并指出今后序列比对研究的发展方向。     

Comparing the performances of Diggle's tests of spatial randomness for small samples with and without edge-effect correction: application to ecological data

Diggle's tests of spatial randomness based on empirical distributions of interpoint distances can be performed with and without edge-effect correction. We present here numerical results illustrating that tests without the edge-effect correction proposed by Diggle (1979, Biometrics 35, 87-101) have a higher power for small sample sizes than those with correction. Ignoring the correction enables detection of departure from spatial randomness with smaller samples (down to 10 points vs. 30 points for the tests with correction). These results are confirmed by an example with ecological data consisting of maps of two species of trees in a West African savanna. Tree numbers per species per map were often less than 20. For one of the species, for which maps strongly suggest an aggregated pattern, tests without edge-effect correction enabled rejection of the null hypothesis on three plots out of five vs. on only one for the tests with correction.     

Bayesian point estimation of quantitative trait loci

In this article, we consider the problem of the estimation of quantitative trait loci (QTL), those chromosomal regions at which genetic information affecting some quantitative trait is encoded. Generally the number of such encoding sites is unknown, and associations between neutral molecular marker genotypes and observed trait phenotypes are sought to locate them. We consider a Bayesian model for simple experimental designs, and discuss the existing approaches to inference for this problem. In particular, we focus on locating positions of the best candidate markers segregating for the trait, a situation which is of primary interest in comparative mapping. We introduce a loss function for estimating both the number of QTL and their location, and we illustrate its application via simulated and real data.     

HISTORICAL ALLOPATRY AND THE BIOGEOGRAPHY OF SPECIATION IN THE PROSOBRANCH SNAIL GENUS NUCELLA

Two recently diverged northeastern Pacific sibling snail species, Nucella ostrina and N. emarginata, currently inhabit adjacent zoogeographic provinces. Their distributions overlap in central California to the north of a major faunal boundary at Point Conception, California (PC). To test the hypothesis that modern sympatry is due to a recent northward range expansion by N. emarginata, I analyzed the population structures of both species with nuclear (allozyme) and mitochondrial DNA (mtDNA) markers. Populations of N. emarginata in the region of overlap exhibit significantly lower heterozygosity and allelic diversity than either populations to the south of PC or populations of N. ostrina. A single mtDNA haplotype characterizes all but one population of N. emarginata sampled in this region, but no haplotype to the south of PC is found at more than one locality. MtDNA haplotypes and allozyme allele frequencies also indicate monophyly of central California populations of N. emarginata. Sharp differences in allelic diversity over small geographic distances may reflect the action of natural selection, but because both nuclear and mtDNA markers display concordant patterns, a range expansion across PC best explains patterns of genetic variation in N. emarginata. Allozymes and mtDNA also reveal that the geologically older N. ostrina is paraphyletic with respect to N. emarginata. This pattern is consistent with, but not indicative of, a peripheral isolation model of speciation. Low genetic diversity is also expected if a significant bottleneck occurred at speciation. However, low allelic diversity is not universal throughout the geographic range of N. emarginata; high allelic diversity at the southern end of the distribution of N. emarginata suggests that in the past N. emarginata has been geographically restricted much further south than PC. A northward range expansion across PC by N. emarginata may thus represent only the most recent postglacial movement by the species. The thermal and oceanographic discontinuities found at PC may not have been directly involved in geographic isolation if N. emarginata originated much further south of this modern boundary. Despite uncertainty regarding the exact spatial distribution of populations at speciation, genetic data indicate that even though N. ostrina and N. emarginata currently exhibit a broad range of geographic overlap, speciation was likely allopatric and was initiated by physical isolation of populations in different zoogeographic provinces.