The Phaeodactylum genome reveals the evolutionary history of diatom genomes

Diatoms are photosynthetic secondary endosymbionts found throughout marine and freshwater environments, and are believed to be responsible for around one-fifth of the primary productivity on Earth. The genome sequence of the marine centric diatom Thalassiosira pseudonana was recently reported, revealing a wealth of information about diatom biology. Here we report the complete genome sequence of the pennate diatom Phaeodactylum tricornutum and compare it with that of T. pseudonana to clarify evolutionary origins, functional significance and ubiquity of these features throughout diatoms. In spite of the fact that the pennate and centric lineages have only been diverging for 90 million years, their genome structures are dramatically different and a substantial fraction of genes ( approximately 40%) are not shared by these representatives of the two lineages. Analysis of molecular divergence compared with yeasts and metazoans reveals rapid rates of gene diversification in diatoms. Contributing factors include selective gene family expansions, differential losses and gains of genes and introns, and differential mobilization of transposable elements. Most significantly, we document the presence of hundreds of genes from bacteria. More than 300 of these gene transfers are found in both diatoms, attesting to their ancient origins, and many are likely to provide novel possibilities for metabolite management and for perception of environmental signals. These findings go a long way towards explaining the incredible diversity and success of the diatoms in contemporary oceans.     

The genome of the choanoflagellate Monosiga brevicollis and the origin of metazoans

Choanoflagellates are the closest known relatives of metazoans. To discover potential molecular mechanisms underlying the evolution of metazoan multicellularity, we sequenced and analysed the genome of the unicellular choanoflagellate Monosiga brevicollis. The genome contains approximately 9,200 intron-rich genes, including a number that encode cell adhesion and signalling protein domains that are otherwise restricted to metazoans. Here we show that the physical linkages among protein domains often differ between M. brevicollis and metazoans, suggesting that abundant domain shuffling followed the separation of the choanoflagellate and metazoan lineages. The completion of the M. brevicollis genome allows us to reconstruct with increasing resolution the genomic changes that accompanied the origin of metazoans.     

Translating molecular discoveries into new therapies for atherosclerosis

Atherosclerosis is characterized by the thickening of the arterial wall and is the primary cause of coronary artery disease and cerebrovascular disease, two of the most common causes of illness and death worldwide. Clinical trials have confirmed that certain lipoproteins and the renin-angiotensin-aldosterone system are important in the pathogenesis of atherosclerotic cardiovascular disease, and that interventions targeted towards these are beneficial. Furthermore, efforts to understand how risk factors such as high blood pressure, dysregulated blood lipids and diabetes contribute to atherosclerotic disease, as well as to understand the molecular pathogenesis of atherosclerotic plaques, are leading to new targets for therapy.     

高技术指标：2007年度33国(地区)技术竞争力报告

文中的高技术指标（High Tech Indicators,HTI）为佐治亚理工大学发布的沿用多年的指标。数据对
比的时间段分别为1993年、1996年、1999年、2002/3年和2007年。论文给出了33个国家（地区）当前的竞争
力指标——技术排名(Technological Standing, TS), 同时提供了四个表征未来竞争力前景的主要指标——国家
发展取向指标(National Orientation, NO)、社会经济基础指标(Socio-Economic Infrastructure, SE)、技术基础指
标(Technological Infrastructure, TI)与生产能力指标(Productive Capacity, PC)。论文无意在高技术指标的结果上
多加笔墨,但是也的确注意到,中国已经取代美国占据了技术排名的首位。这一结果反映了高技术指标的特
点,更重要的是,它反映了中国过去15年的惊人发展速度。     

Isotopic evidence for Mesoarchaean anoxia and changing atmospheric sulphur chemistry

The evolution of the Earth's atmosphere is marked by a transition from an early atmosphere with very low oxygen content to one with an oxygen content within a few per cent of the present atmospheric level. Placing time constraints on this transition is of interest because it identifies the time when oxidative weathering became efficient, when ocean chemistry was transformed by delivery of oxygen and sulphate, and when a large part of Earth's ecology changed from anaerobic to aerobic. The observation of non-mass-dependent sulphur isotope ratios in sedimentary rocks more than approximately 2.45 billion years (2.45 Gyr) old and the disappearance of this signal in younger sediments is taken as one of the strongest lines of evidence for the transition from an anoxic to an oxic atmosphere around 2.45 Gyr ago. Detailed examination of the sulphur isotope record before 2.45 Gyr ago also reveals early and late periods of large amplitude non-mass-dependent signals bracketing an intervening period when the signal was attenuated. Until recently, this record has been too sparse to allow interpretation, but collection of new data has prompted some workers to argue that the Mesoarchaean interval (3.2-2.8 Gyr ago) lacks a non-mass-dependent signal, and records the effects of earlier and possibly permanent oxygenation of the Earth's atmosphere. Here we focus on the Mesoarchaean interval, and demonstrate preservation of a non-mass-dependent signal that differs from that of preceding and following periods in the Archaean. Our findings point to the persistence of an anoxic early atmosphere, and identify variability within the isotope record that suggests changes in pre-2.45-Gyr-ago atmospheric pathways for non-mass-dependent chemistry and in the ultraviolet transparency of an evolving early atmosphere.     

Minkowski Generalizations of Ward’s Method in Hierarchical Clustering

In this paper, we consider several generalizations of the popular Ward’s method for agglomerative hierarchical clustering. Our work was motivated by clustering software, such as the R function hclust, which accepts a distance matrix as input and applies Ward’s definition of inter-cluster distance to produce a clustering. The standard version of Ward’s method uses squared Euclidean distance to form the distance matrix. We explore the effect on the clustering of using other definitions of distance, such as the Minkowski distance.