基于修正的转移概率方法进行城市景观动态研究——以南昌市区为例

利用南昌市1988～2000年期间5个时段的TM卫星影像数据编制了景观组分类型图,并通过叠图分析统计了全部组分类型在4个比较时段的转移概率矩阵。在此基础上构建了组分转入、转出贡献率和特定转移过程贡献率等3个动态分析参数,对南昌市的景观动态变化特征和驱动机制进行了研究。结果显示,城市化引发的建设用地规模急剧膨胀是工作区内景观结构在研究时段内急剧调整的主要原因;农业经营的稳定性需要作为一种重要驱动因素,在农业用地大量流失的同时,使其它景观组分向农田转移成为优势性转移过程类型;地形和水文变化对于林地和水体等组分变化具有次要约束性影响,但对于一些特定优势转移过程的出现则具有决定性作用。研究结果还证实了所提出的3种基于组分转移概率矩阵的量化参数在景观动态变化特征和驱动机制研究中的合理性和有效性。     

Preservation of a pseudogene by gene conversion and diversifying selection

Interlocus gene conversion is considered a crucial mechanism for generating novel combinations of polymorphisms in duplicated genes. The importance of gene conversion between duplicated genes has been recognized in the major histocompatibility complex and self-incompatibility genes, which are likely subject to diversifying selection. To theoretically understand the potential role of gene conversion in such situations, forward simulations are performed in various two-locus models. The results show that gene conversion could significantly increase the number of haplotypes when diversifying selection works on both loci. We find that the tract length of gene conversion is an important factor to determine the efficacy of gene conversion: shorter tract lengths can more effectively generate novel haplotypes given the gene conversion rate per site is the same. Similar results are also obtained when one of the duplicated genes is assumed to be a pseudogene. It is suggested that a duplicated gene, even after being silenced, will contribute to increasing the variability in the other locus through gene conversion. Consequently, the fixation probability and longevity of duplicated genes increase under the presence of gene conversion. On the basis of these findings, we propose a new scenario for the preservation of a duplicated gene: when the original donor gene is under diversifying selection, a duplicated copy can be preserved by gene conversion even after it is pseudogenized.     

Nonallelic gene conversion is not GC-biased in Drosophila or primates

Gene conversion is the unidirectional transfer of genetic information between allelic (orthologous) or nonallelic (paralogous) DNA segments. Recently, there has been much interest in understanding how gene conversion shapes the nucleotide composition of the genomic landscape. A widely held hypothesis is that gene conversion is universally GC-biased. However, direct experimental evidence of this hypothesis is limited to a single study of meiotic crossovers in yeast. Although there have been a number of indirect studies of gene conversion, evidence of GC-biased replacements gathered from such studies can also be attributed to positive selection, which has the same evolutionary dynamics as biased gene conversion. Here, we apply a direct phylogenetic approach to examine nucleotide replacements produced by nonallelic gene conversion in Drosophila and primate genomes. We find no evidence for GC-biased gene conversion in either lineage, suggesting that previously observed GC biases may be due to positive selection rather than to biased gene conversion.     

Gene Conversion: A Hitherto Overlooked Parameter in Population Genetics

Gene conversion causes deviations from the 2:2 segregation of allele pairs in meiosis. Thus, gene conversion is a potential cause for changes of allele frequencies in populations. Equations are derived for the effects of conversion in a large random-mating population. The influence of gene conversion on allele frequencies is compared with that of spontaneous mutation and meiotic drive.     

Biocatalytic conversion of lignocellulose to platform chemicals

Naturally occurring lignocellulose can be used as a renewable resource for the sustainable production of platform chemicals that can in turn be converted to valuable fine chemicals, polymers, and fuels. The biocatalytic conversion of lignocellulose is a very promising approach due to its high selectivity, mild conditions, and low exergy loss. However, such biocatalytic processes are still seldom applied at the industrial scale since the single conversion steps (pretreatment, hydrolysis, and fermentation) may exhibit low conversion rates, low efficiencies, or high costs. The biocatalytic conversion of lignocellulose to platform chemicals is reviewed in this work. Structures and production rates of lignocellulose are described, and platform chemicals that may be produced from lignocellulose are summarized. Biocatalytic conversion of lignocellulose is distinguished from conventional non-selective approaches. All essential conversion steps used in biocatalytic approaches (pretreatment, hydrolysis, and fermentation) are reviewed in detail. Finally, potential interactions between these conversion steps are highlighted and the advantages as well as disadvantages of integrated process configurations are elucidated. In conclusion, a comprehensive understanding of the biocatalytic conversion of lignocellulose is provided in this review.     

Resource conversion: a generalizable mechanism for resource-mediated positive species interactions

Positive species interactions are ubiquitous in natural communities, but the mechanisms through which they operate are poorly understood. One proposed mechanism is resource conversion – the conversion by a benefactor species of a resource from a resource state that is inaccessible to a potential beneficiary species into a resource state that is accessible. Such conversion often occurs as a byproduct of resource consumption, and sometimes in exchange for non-resource benefits to the benefactor species. At least five known classes of interactions, including both facilitative and mutualistic ones, may be classified as resource conversion interactions. We formulated a generalizable mathematical model for resource conversion interactions and examined two model variants that represent processing chain and nurse plant interactions. We examined the conditions under which these conformed to the stress-gradient hypothesis (SGH), which predicts increased interaction benefits in more stressful environments. These yielded four key insights: 1) resource conversion interactions can be positive (towards the resource recipient) only when facilitator-mediated resource conversion is more efficient than the baseline, spontaneous, facilitator-independent resource conversion; 2) the sign of resource conversion interaction outcomes never switches (e.g. from net positive to net negative) with changing levels of resource availability, when all other parameters are kept constant; 3) processing chain interactions at equilibrium can never be positive in a manner that conforms to the SGH; 4) nurse plant interactions can be positive and conform to the SGH, although the manner in which they do depends largely on how resource stress is defined, and the environmental supply rate of surface soil moisture. The first two insights are likely to be generalizable across all resource conversion interactions. The general agreement of the model with empirical studies suggest that resource conversion is the mechanism underlying the aforementioned interactions, and an ecologically meaningful way of classifying these previously unassociated positive species interactions.     

Evidence for the participation of two soluble noncatalytic proteins in hepatic microsomal cholesterol synthesis

The capacity of liver soluble fraction to stimulate hepatic microsomal conversion of squalene to cholesterol is lost on treatment with trypsin. Heat treatment of the soluble fraction results in a selective loss of its capacity to stimulate conversion of squalene to cholesterol; the ability to stimulate conversion of lanosterol and desmosterol to cholesterol is however retained. It is proposed that the liver soluble fraction contains at least two noncatalytic proteins, one heat-labile and the other heat-stable, which participate in microsomal cholesterol synthesis. The heat-labile protein mediates the conversion of squalene to lanosterol while the heat-stable protein is needed for the conversion of lanosterol and other sterol precursors to cholesterol.     

IdBean: a Java GUI application for conversion of biological identifiers

We have developed a biologist-friendly, stand-alone Java GUI application, IdBean, for ID conversion. Our tool integrated most of the widely used ID conversion services that provide programmatic access. It is the first GUI ID conversion application that supports the direct merging as well as comparison of conversion results from multiple ID conversion services without manual effort. This tool will greatly help biologists who handle multiple ID types for the analyses of gene or gene product lists. By referring to multiple conversion services, the number of failed IDs can be reduced. By accessing ID conversion service online, it will potentially provide the most up-to-date conversion results. The application was developed in modular form; however, it can be re-packaged into plug-in form. For the development of a bioinformatics analysis tool, the module can be used as a built-in ID conversion component. It is available at http://neon.gachon.ac.kr/IdBean/.     

The processive kinetics of gene conversion in bacteria

Gene conversion, non‐reciprocal transfer from one homologous sequence to another, is a major force in evolutionary dynamics, promoting co‐evolution in gene families and maintaining similarities between repeated genes. However, the properties of the transfer – where it initiates, how far it proceeds and how the resulting conversion tracts are affected by mismatch repair – are not well understood. Here, we use the duplicate tuf genes in Salmonella as a quantitatively tractable model system for gene conversion. We selected for conversion in multiple different positions of tuf, and examined the resulting distributions of conversion tracts in mismatch repair‐deficient and mismatch repair‐proficient strains. A simple stochastic model accounting for the essential steps of conversion showed excellent agreement with the data for all selection points using the same value of the conversion processivity, which is the only kinetic parameter of the model. The analysis suggests that gene conversion effectively initiates uniformly at any position within a tuf gene, and proceeds with an effectively uniform conversion processivity in either direction limited by the bounds of the gene.     

A strong deletion bias in nonallelic gene conversion

Gene conversion is the unidirectional transfer of genetic information between orthologous (allelic) or paralogous (nonallelic) genomic segments. Though a number of studies have examined nucleotide replacements, little is known about length difference mutations produced by gene conversion. Here, we investigate insertions and deletions produced by nonallelic gene conversion in 338 Drosophila and 10,149 primate paralogs. Using a direct phylogenetic approach, we identify 179 insertions and 614 deletions in Drosophila paralogs, and 132 insertions and 455 deletions in primate paralogs. Thus, nonallelic gene conversion is strongly deletion-biased in both lineages, with almost 3.5 times as many conversion-induced deletions as insertions. In primates, the deletion bias is considerably stronger for long indels and, in both lineages, the per-site rate of gene conversion is orders of magnitudes higher than that of ordinary mutation. Due to this high rate, deletion-biased nonallelic gene conversion plays a key role in genome size evolution, leading to the cooperative shrinkage and eventual disappearance of selectively neutral paralogs.     

High-frequency germ line gene conversion in transgenic mice.

Gene conversion is the nonreciprocal transfer of genetic information between two related genes or DNA sequences. It can influence the evolution of gene families, having the capacity to generate both diversity and homogeneity. The potential evolutionary significance of this process is directly related to its frequency in the germ line. While measurement of meiotic inter- and intrachromosomal gene conversion frequency is routine in fungal systems, it has hitherto been impractical in mammals. We have designed a system for identifying and quantitating germ line gene conversion in mice by analyzing transgenic male gametes for a contrived recombination event. Spermatids which undergo the designed intrachromosomal gene conversion produce functional beta-galactosidase (encoded by the lacZ gene), which is visualized by histochemical staining. We observed a high incidence of lacZ-positive spermatids (approximately 2%), which were produced by a combination of meiotic and mitotic conversion events. These results demonstrate that gene conversion in mice is an active recombinational process leading to nonparental gametic haplotypes. This high frequency of intrachromosomal gene conversion seems incompatible with the evolutionary divergence of newly duplicated genes. Hence, a process may exist to uncouple gene pairs from frequent conversion-mediated homogenization.     

Estimating meiotic gene conversion rates from population genetic data

Gene conversion plays an important part in shaping genetic diversity in populations, yet estimating the rate at which it occurs is difficult because of the short lengths of DNA involved. We have developed a new statistical approach to estimating gene conversion rates from genetic variation, by extending an existing model for haplotype data in the presence of crossover events. We show, by simulation, that when the rate of gene conversion events is at least comparable to the rate of crossover events, the method provides a powerful approach to the detection of gene conversion and estimation of its rate. Application of the method to data from the telomeric X chromosome of Drosophila melanogaster, in which crossover activity is suppressed, indicates that gene conversion occurs approximately 400 times more often than crossover events. We also extend the method to estimating variable crossover and gene conversion rates and estimate the rate of gene conversion to be approximately 1.5 times higher than the crossover rate in a region of human chromosome 1 with known recombination hotspots.     

Structural requirements for efficient prion protein conversion: Cofactors may promote a conversion-competent structure for PrPC

To understand why cross-species infection of prion disease often results in inefficient transmission and reduced protein conversion, most research has focused on defining the effect of variations in PrP primary structures, including sequence compatibility of substrate and seed. By contrast, little research has been aimed at investigating structural differences between different variants of PrP^C and secondary structural requirements for efficient conversion. This is despite a clear role for molecular chaperones in formation of prions in non-mammalian systems, indicating the importance of secondary/tertiary structure during the conversion process. Recent data from our laboratory on the cellular location of disease-specific prion cofactors supports the critical role of specific secondary structural motifs and the stability of these motifs in determining the efficiency of disease-specific prion protein conversion. In this paper we summarize our recent results and build on the hypothesis previously suggested by Wuthrich and colleagues, that stability of certain regions of the prion protein is crucial for protein conversion to abnormal isoforms in vivo. It is suggested that one role for molecular cofactors in the conversion process is to stabilize PrP^C structure in a form that is amenable for conversion to PrP^Sc.Key words: cofactor, structure, cell-free conversion assay, fibrillization, stability, loop region     

The ATPase activity of phosphorylase kinase is regulated in parallel with its protein kinase activity.

Phosphorylase kinase from rabbit skeletal muscle has been found to have an intrinsic ATPase activity that occurs at a rate approximately 0.2% of that of its phosphorylase conversion activity and about three times that of its autophosphorylation activity. The characteristics of this ATPase activity were in all aspects tested essentially the same as the kinase's phosphorylase conversion activity. The ATPase requires Mg2+ and is dramatically stimulated by Ca2+ ions. At neutral pH there is a pronounced lag in the rate of product formation that is not present at alkaline pH, a condition that greatly stimulates both the phosphorylase conversion and ATPase activities. ATP is preferentially hydrolyzed over GTP and the Km for MgATP determined in the ATPase assay is 0.14 mM. ADP, an allosteric activator of phosphorylase conversion, also stimulates the ATPase activity, whereas beta-glycerophosphate, an inhibitor of phosphorylase conversion, is an inhibitor of the ATPase activity. Phosphorylation or partial proteolysis of the kinase, which are known to activate phosphorylase conversion, also activate the ATPase activity. Because the phosphorylase conversion and ATPase activities are regulated in parallel, we conclude that activation of the two catalytic activities must share a common underlying basis, namely an enhanced phosphotransferase activity that is independent of the phosphoryl acceptor.     

Structural requirements for efficient prion protein conversion

To understand why cross species infection of prion disease often results in inefficient transmission and reduced protein conversion, most research has focussed on defining the effect of variations in PrP primary structures, including sequence compatibility of substrate and seed. By contrast, little research has been aimed at investigating structural differences between different variants of PrP^C and secondary structural requirements for efficient conversion. This is despite a clear role for molecular chaperones in formation of prions in non-mammalian systems, indicating the importance of secondary/tertiary structure during the conversion process. Recent data from our laboratory on the cellular location of disease-specific prion cofactors supports the critical role of specific secondary structural motifs and the stability of these motifs in determining the efficiency of disease-specific prion protein conversion. In this paper we summarise our recent results and build on the hypothesis previously suggested by Wuthrich and colleagues, that stability of certain regions of the prion protein is crucial for protein conversion to abnormal isoforms in vivo. It is suggested that one role for molecular co-factors in the conversion process is to stabilise PrP^C structure in a form that is amenable for conversion to PrP^Sc.     

同一染色体上基因转换在HLA多态性形成中的作用

摘要: 人类白细胞抗原(Human leukocyte antigens, HLA)是人类基因组中已知多态性最高的基因家族, 为人类面对异源多变的外界生物分子所必须。以往对HLA多态性形成的研究多集中在互换式重组机制上, 文章研究了基因转换这一重要的多态性形成机制在HLA-DRB基因多态性形成中的作用。应用已知的各基因座的等位基因序列对其进行多态性分析表明, HLA-DRB是一高度多态的基因家族。用Ester Betran模型检测到32个基因转换的区域, 最小的基因转换区域长2 bp, 最远差异位点间隔为204 bp。在71~75、18~221等几个区域上出现基因转换的频数高, 成为基因转换的热点。进一步的分析显示, 71~75、205~217等热点区域分别与东方人、高加索人这两个人群密切相关, 提示基因转换的热点可能具有一定的人群特异性     

Variation of the cytoplasm type in sugar beet (Beta vulgaris L.) upon inbreeding. The influence of hybridization

Hybrid combinations of inbred sugar beet lines that undergo conversion of N-cytoplasm into S-state were screened for the marker mitochondrial genes atpA and atp6. The involvement of nuclear factors into cytoplasm conversion and possible identity of these factors in different lines have been studied. The cytoplasm conversion factor was localized to nucleus. In different lines with cytoplasm conversion, the nuclear conversion factors are not identical. The state of the mitochondrial genome is normalized after outcrosses with plants having the stable cytoplasm.     

The Timing of Growth Promotion and Conversion to Indole-3-acetic Acid for Auxin Precursors

Using a high resolution continuous recording technique, the length of the latent period preceding the growth response to two suspected precursors of indole-3-acetic acid (IAA) indole-3-acetonitrile (IAN), and indole-3-ethanol was studied in corn (Zea mays L.), wheat (Triticum aestivum L.), and peas (Pisum sativum L.). The timing of the conversion in vivo of these presumed precursors to IAA was also examined. In wheat the rate of conversion of IAN to IAA is rapid, and the latent period in the growth response to IAN is correspondingly short. In corn the rate of conversion in vivo of IAN to IAA is slow, and there is a long latent period in the growth response. In peas there is no conversion of IAN to IAA, and there is no measurable growth response to IAN. These data indicate that IAN is active in promoting growth only after conversion to IAA. This conclusion is strengthened by transport studies. Using a similar approach, we have also obtained data indicating that indole-3-ethanol is active only after conversion to IAA.     

Interchromosomal Biased Gene Conversion, Mutation and Selection in a Multigene Family

A mathematical model of the effects of interchromosomal biased gene conversion, mutation and natural selection on a multigene family is developed and analyzed. The model assumes two allelic states at each of n loci. The effects of genetic drift are ignored. The model is developed under the assumption of no recombination, but the analysis shows that, at equilibrium, there is no linkage disequilibrium, which implies that the conclusions are valid for arbitrary recombination among loci. At equilibrium, the balance between mutation, gene conversion and selection depends on the ratio of the mutation rates to the quantity [s + g(2α - 1)/ n], where s is the increment or decrement in relative fitness with each additional copy of one of the alleles, g is the conversion rate, and α is a measure of the bias in favor of one of the alleles. When this quantity is large relative to the mutation rates, the allele that has the net advantage, combining the effects of selection and conversion, will be nearly fixed in the multigene family. A comparison of these results with those from a comparable model of intrachromosomal biased conversion shows that biased interchromosomal conversion leads to approximately the same equilibrium copy number as does intrachromosomal conversion of the same strength. Interchromosomal conversion is much more effective in causing the substitution of one allele by another. The relative frequencies of interchromosomal and intrachromosomal conversion is indicated by the extent of the linkage disequilibrium among the loci in a multigene family.