Genome constitutions of Hystrix patula, H-duthiei ssp duthiei and H-duthiei ssp longearistata (Poaceae : Triticeae) revealed by meiotic pairing behavior and genomic in-situ hybridization

Genomic constitutions of three taxa of Hystrix Moench, H. patula, H. duthiei ssp. duthiei and H. duthiei ssp. longearistata, were examined by meiotic pairing behavior and genomic in-situ hybridization. Meiotic pairing in hybrids of H. patula x Pseudoroegneria spicata (St), H. patula x Elymus wawawaiensis (StH), H. patula x H. duthiei ssp. longearistata, H. patula x Psathyrostachys huashanica (Ns(h)), H. duthiei ssp. duthiei x Psa. huashanica, H. duthiei ssp. longearistata x Psa. huashanica, Leymus multicaulis (NsXm) x H. duthiei ssp. longearistata averaged 6.53, 12.83, 1.32, 0.29, 5.18, 5.11 and 10.47 bivalents per cell, respectively. The results indicate that H. patula has the StH genome and H. duthiei ssp. duthiei and H. duthiei ssp. longearistata have the NsXm genome. Results of genomic in-situ hybridization analysis strongly supported the chromosome pairing data; therefore it is concluded that the type species of Hystrix, H. patula, should be included in Elymus, and that H. duthiei ssp. duthiei and H. duthiei ssp. longearistata should be transferred to Leymus.

贵州碳酸盐岩风化壳形成地球化学过程、对比及年代学研究Geochemical Processes, Comparison and Dating for the Weathering Crusts in Karst Regions of Guizhou Province

由于缺乏相应的沉积地层，贵州新生代地质、环境演化恢复一直是学术界的难点问题。夷平面研究的兴起，为陆地地壳抬升、地貌演变等反演提供了理论基础，而风化壳正是夷平面研究的重要替代对象，尤其是对各类沉积地层不发育的地区。因而，贵州高原各级台地上发育有较为广泛的红色风化壳自然地、就成了主要研究载体。然而一与其它岩类不同，碳酸盐岩风化成土作用过程研究并没有得到同等重视，其研究范围和程度均很不充分。显然，要想利用碳酸盐岩风化壳进行夷平面等地质、地貌意义研究，就必需详细了解贵州或中国南方碳酸盐岩风化成土的基本过程。也只有如此，才能明确各种对比指标的使用条件和范围，才能明确各种测年结果的具体意义，才能真正地通过贵州碳酸盐岩风化壳获取全省地质、环境演化信息。本论文通过对贵州省岩溶台地碳酸盐岩石灰土、红色风化壳剖面形成地球化学过程的剖析，开展石灰土与红色风化壳之间的关联和差异性综合对比、红色风化壳之间发育程度的比较，以及风化壳剖面尝试性的侧年等方面研究，取得了以下儿点认识：1、石灰土形成地球化学过程及对比通过矿物组成、粒度分布特征、地球化学方法判别，确定了本文所选石灰土剖面物质来源于下伏碳酸盐岩中的酸不溶物，是碳酸盐岩风化后酸不溶物原地残余堆积的结果。石灰土形成的地球化学过程都遵循碳酸盐岩风化成土之两阶段模式：母岩－酸不溶物，大量可溶性物质Ca、Mg、Mn、P、Na淋失，而Si、K·Fe、Al、Ti则相对富集。该过程的矿物组成变化表现为，伴随碳酸盐矿物（方解石、白云石等）的溶解、迁移，硅酸盐相矿物（长石、2:1型粘土矿物等）残余、累积。酸不溶物，土层或土层的演化，K、Si（长石、伊利石）不断淋失，而Al（伊利石、高岭石、三水铝石）、Fe（针铁矿、赤铁矿等）逐渐富集，体现出脱硅、富铝（铁）过程。我们强调碳酸盐岩风化成土分为两个阶段，但也认识到风化作用是综合的、复杂的：在碳酸盐矿物大量淋失过程中，同时也进行着酸不溶物的风化。石灰土分为原生和次生两种成因类型。原生石灰土的风化程度总体较低，剖面中还残留一定量的CaCO3，剖面从下到上矿物组成、地球化学各种指标具有逐渐演化的过渡特征。原生石灰上土层演化过程显示出正风化序列，从下到上风化程度逐渐增大、可溶性物质逐渐减少、稳定和相对稳定组分（Al、Fe．、REE）含量不断增大。另外，主量元素的质量迁移系数在剖面中的变化与风化程度呈明显的相关性。而次生石灰土不但具有很高的风化程度，而且剖面无过渡特征，显示可能是由遭受强烈风化作用的物质直接转变形成的。剖面中也含有一定量后期加入的碳酸盐，但与高CIA值特征不相匹配；SiO2、Al2O3、Fe2O3组分具有不同的变化特征，与）成化程度无明显关联；REE在剖面岩一上界面出现富集层。2、碳酸盐岩红色风化壳形成地球化学过程及其与石灰土的对比红色风化壳形成的地球化学过程也遵循碳酸盐岩风化成土之两阶段模式：母岩一酸不溶物，大量可溶性物质Ca、Mg、Mn、P、Na淋失，而Si、K、Fe、Al、Ti则相对富集。该过程的矿物组成变化表现为，伴随碳酸盐矿物（方解石、白云石等）的溶解、迁移，硅酸盆相矿物（长石、2:1型粘土矿物等）残余、累积。酸不济物一土层或上层的演化，K、Si（长石、伊利石）不断淋失，而Al（伊利石、高岭石、三水铝石）、Fe（针铁矿、赤铁矿等）逐渐富集，体现出脱硅、富铝（铁）过程。石灰土与红色风化壳之间既存在共性，又有一定的差异性。红色风化壳与原生石灰土一样都具有过渡特征，但后者仅在剖面下部出现一定的过渡层位；原生石灰士的城化程度远低于红色风化壳，仅与后者底部土层相当；原生石灰土不具有红色风化壳之岩-土REE（超常）富集层。总体上，原生石灰土可以作为红色风化壳的前身。次生石灰土与红色风化壳在矿物组成、风化程度等各种地球化学指标等都十分接近（略低），显示与红色风化壳之间存在某种关联：由红色风化壳物质直接转变，或由酸不溶物已强烈风化的（白云岩）岩粉、碎裂岩风化形成。3、碳酸盐岩风化成土母岩差异性碳酸盐岩风化成土存在母岩差异性，石灰土母岩差异性较为明显，而红色风化壳的母岩差异性较弱，体现出红色风化壳的均一化特征。石灰土母岩差异性体现为：母岩为灰岩的石灰土剖面主量元素含量变化特征较为一致，而白云岩则具有不同的变化；灰岩石灰土Fe3＋、Al具有不同的富集、亏损特征，且具有富集层的补偿亏损层，而白云岩石灰上两组分都呈现无补偿层位的相同富集态势；灰岩石灰土剖面出现负Eu异常和具以Gd为中心的倒“V”型MREE稀土富集特征（母岩标准化），而白云岩石灰土无明显Eu异常和具L既E或HREE稀士．富集特征；灰岩和白云岩石灰土的微量元素富集、亏损特征也有所不同，前者从上到下逐渐富集，而后者无明显变化趋势。红色风化壳形成的基本过程、主量元素地球化学行为无明显的母岩相关性，没有如石灰土剖面灰岩和白云岩之间存在的差异性，显示出红土化作用的均一化过程；微量元素中受重矿物影响的元素与母岩类型有一定的关联，但大多数元素的亏损、富集等与具体剖面的微环境关系密切。4、碳酸盐岩红色风化壳发育程度的对比及意义多利指标对比显示所选红色风化壳的风化程度有一定的强弱差别：平坝剖面＞湖潮剖面＞天龙剖面、大兴剖面＞花溪剖面、新蒲剖面，但这种差异性不足以否定各剖面隶属于贵州山盆期广泛夷平面的基本推测。各剖面之间的微弱差异是红色风化壳形成时纬度分带和垂向分带的体现。低纬度的平坝、湖潮、天龙剖面经历的风化作用强于高纬度的新蒲、大兴剖面；高海拔的新蒲剖面风化程度低于海拔低的大兴剖面。5、红色风化壳次生石英裂变径迹测年红色风化壳次生石英裂变径迹方法测年尝试，得到一定的结果和认识：晶形相对较好的石英，是次生的，与母岩中碎屑及成岩阶段没有关联；各剖面上部与中、下部次生石英的诱发裂变径迹的密度有着明显的区别，可能暗示它们的形成环境不同；名一剖面石英的形成或退火年龄分布较为分散，1.2-25.2Ma，同一剖面的石英年龄也不均一，变化较大；从下到上，年龄值呈现出逐渐减小的规律性，与风化作用的正常序列相反。如果能确切其成因，次生石英裂变径迹年代学研究将是确定风化壳形成时代及揭示主要风化作用信，却钩有利武器。

A Note of Zipf's Law, Natural Languages, and Noncoding DNA Regions

In Phys. Rev. Letters (73:2), Mantegna et al. conclude on the basis of Zipf rank frequency data that noncoding DNA sequence regions are more like natural languages than coding regions. We argue on the contrary that an empirical fit to Zipf"s "law" cannot be used as a criterion for similarity to natural languages. Although DNA is a presumably "organized system of signs" in Mandelbrot"s (1961) sense, and observation of statistical featurs of the sort presented in the Mantegna et al. paper does not shed light on the similarity between DNA's "gramar" and natural language grammars, just as the observation of exact Zipf-like behavior cannot distinguish between the underlying processes of tossing an M-sided die or a finite-state branching process.

Competitiveness in a globalised world: Michael Porter on the microeconomic foundations of the competitiveness of nations, regions, and firms.

In this paper, we provide the text of an interview with Professor Michael Porter discussing his research and ideas relating to the microeconomic foundations of global competitiveness. The discussion provides a microeconomic perspective on some of the key issues relating to recent research on competitiveness, productivity, clusters, US economic leadership, economic growth and development.

Integration of genomic and phenotypic data

Clare, A. (2005) Integration of genomic and phenotypic data. In Data Analysis and Visualization in Genomics and Proteomics, Eds. Francisco Azuaje and Joaquin Dopazo, Wiley, London. ISBN: 0-470-09439-7

Functional genomic hypothesis generation and experimentation by a robot scientist

King R. D., Whelan, K. E., Jones, F. M., Reiser, P. G. K., Bryant, C. H., Muggleton, S., Kell, D. B. and Oliver, S. G. (2004) Functional genomic hypothesis generation and experimentation by a robot scientist. Nature 427 (6971) p247-252

Public service employment and the public-private wage differential in British regions

Thomas, Dennis, Henley, Andrew, 'Public service employment and the public-private wage differential in British regions', Regional Studies (2001) 35(3) pp.229-240 RAE2008

Construction of a Festuca pratensis BAC library for map-based cloning in IFestulolium substitution lines

Iain S. Donnison, Donal M. O Sullivan, Ann Thomas, Peter Canter, Beverley Moore, Ian Armstead, Howard Thomas, Keith J. Edwards and Ian P. King (2005). Construction of a Festuca pratensis BAC library for map-based cloning in Festulolium substitution lines. Theoretical and Applied Genetics, 110 (5) pp.846-851 Sponsorship: BBSRC;BBSRC RAE2008

Molecular analysis of the anaerobic rumen fungus Orpinomyces - insights into an AT-rich genome

Matthew J. Nicholson, Michael K. Theodorou and Jayne L. Brookman. (2005). Molecular analysis of the anaerobic rumen fungus Orpinomyces - insights into an AT-rich genome. Microbiology, 151 (1), 121-133. Sponsorship: BBSRC RAE2008

Genes involved in complex adaptive processes tend to have highly conserved upstream regions in mammalian genomes

BACKGROUND:Recent advances in genome sequencing suggest a remarkable conservation in gene content of mammalian organisms. The similarity in gene repertoire present in different organisms has increased interest in studying regulatory mechanisms of gene expression aimed at elucidating the differences in phenotypes. In particular, a proximal promoter region contains a large number of regulatory elements that control the expression of its downstream gene. Although many studies have focused on identification of these elements, a broader picture on the complexity of transcriptional regulation of different biological processes has not been addressed in mammals. The regulatory complexity may strongly correlate with gene function, as different evolutionary forces must act on the regulatory systems under different biological conditions. We investigate this hypothesis by comparing the conservation of promoters upstream of genes classified in different functional categories.RESULTS:By conducting a rank correlation analysis between functional annotation and upstream sequence alignment scores obtained by human-mouse and human-dog comparison, we found a significantly greater conservation of the upstream sequence of genes involved in development, cell communication, neural functions and signaling processes than those involved in more basic processes shared with unicellular organisms such as metabolism and ribosomal function. This observation persists after controlling for G+C content. Considering conservation as a functional signature, we hypothesize a higher density of cis-regulatory elements upstream of genes participating in complex and adaptive processes.CONCLUSION:We identified a class of functions that are associated with either high or low promoter conservation in mammals. We detected a significant tendency that points to complex and adaptive processes were associated with higher promoter conservation, despite the fact that they have emerged relatively recently during evolution. We described and contrasted several hypotheses that provide a deeper insight into how transcriptional complexity might have been emerged during evolution.

3'-UTR SIRF: A database for identifying clusters of short interspersed repeats in 3' untranslated regions

BACKGROUND:Short (~5 nucleotides) interspersed repeats regulate several aspects of post-transcriptional gene expression. Previously we developed an algorithm (REPFIND) that assigns P-values to all repeated motifs in a given nucleic acid sequence and reliably identifies clusters of short CAC-containing motifs required for mRNA localization in Xenopus oocytes.DESCRIPTION:In order to facilitate the identification of genes possessing clusters of repeats that regulate post-transcriptional aspects of gene expression in mammalian genes, we used REPFIND to create a database of all repeated motifs in the 3' untranslated regions (UTR) of genes from the Mammalian Gene Collection (MGC). The MGC database includes seven vertebrate species: human, cow, rat, mouse and three non-mammalian vertebrate species. A web-based application was developed to search this database of repeated motifs to generate species-specific lists of genes containing specific classes of repeats in their 3'-UTRs. This computational tool is called 3'-UTR SIRF (Short Interspersed Repeat Finder), and it reveals that hundreds of human genes contain an abundance of short CAC-rich and CAG-rich repeats in their 3'-UTRs that are similar to those found in mRNAs localized to the neurites of neurons. We tested four candidate mRNAs for localization in rat hippocampal neurons by in situ hybridization. Our results show that two candidate CAC-rich (Syntaxin 1B and Tubulin beta4) and two candidate CAG-rich (Sec61alpha and Syntaxin 1A) mRNAs are localized to distal neurites, whereas two control mRNAs lacking repeated motifs in their 3'-UTR remain primarily in the cell body.CONCLUSION:Computational data generated with 3'-UTR SIRF indicate that hundreds of mammalian genes have an abundance of short CA-containing motifs that may direct mRNA localization in neurons. In situ hybridization shows that four candidate mRNAs are localized to distal neurites of cultured hippocampal neurons. These data suggest that short CA-containing motifs may be part of a widely utilized genetic code that regulates mRNA localization in vertebrate cells. The use of 3'-UTR SIRF to search for new classes of motifs that regulate other aspects of gene expression should yield important information in future studies addressing cis-regulatory information located in 3'-UTRs.

Generalized Methods for Discovering Frequent Poly-Regions in DNA

The problem of discovering frequent poly-regions (i.e. regions of high occurrence of a set of items or patterns of a given alphabet) in a sequence is studied, and three efficient approaches are proposed to solve it. The first one is entropy-based and applies a recursive segmentation technique that produces a set of candidate segments which may potentially lead to a poly-region. The key idea of the second approach is the use of a set of sliding windows over the sequence. Each sliding window covers a sequence segment and keeps a set of statistics that mainly include the number of occurrences of each item or pattern in that segment. Combining these statistics efficiently yields the complete set of poly-regions in the given sequence. The third approach applies a technique based on the majority vote, achieving linear running time with a minimal number of false negatives. After identifying the poly-regions, the sequence is converted to a sequence of labeled intervals (each one corresponding to a poly-region). An efficient algorithm for mining frequent arrangements of intervals is applied to the converted sequence to discover frequently occurring arrangements of poly-regions in different parts of DNA, including coding regions. The proposed algorithms are tested on various DNA sequences producing results of significant biological meaning.