Sequence and analysis of chromosome 2 of the plant Arabidopsis thaliana

Arabidopsis thaliana (Arabidopsis) is unique among plant model organisms in having a small genome (130-140 Mb), excellent physical and genetic maps, and little repetitive DNA. Here we report the sequence of chromosome 2 from the Columbia ecotype in two gap-free assemblies (contigs) of 3.6 and 16 megabases (Mb). The latter represents the longest published stretch of uninterrupted DNA sequence assembled from any organism to date. Chromosome 2 represents 15% of the genome and encodes 4,037 genes, 49% of which have no predicted function. Roughly 250 tandem gene duplications were found in addition to large-scale duplications of about 0.5 and 4.5 Mb between chromosomes 2 and 1 and between chromosomes 2 and 4, respectively. Sequencing of nearly 2 Mb within the genetically defined centromere revealed a low density of recognizable genes, and a high density and diverse range of vestigial and presumably inactive mobile elements. More unexpected is what appears to be a recent insertion of a continuous stretch of 75% of the mitochondrial genome into chromosome 2.     

The Effects of Environmental Variables on Gas Exchange of Several Tree Species Under Boreal Field Conditions

１９９４年和１９９５年夏季在加拿大Ｓａｓｋａｔｃｈｅｗａｎ省ＰｒｉｎｃｅＡｌｂｅｒｔ市北部森林测定环境条件对欧洲杨（ＰｏｐｕｌｕｓｔｒｅｍｕｌｏｉｄｅｓＭｉｃｈｘ．）,胶杨（ＰｏｐｕｌｕｓｂａｌｓａｍｉｆｅｒａＬ．）,榛子（ＣｏｒｙｌｕｓｃｏｒｎｕｔａＭａｒｓｈ．）,短叶松（ＰｉｎｕｓｂａｎｋｓｉａｎａＬａｍｂ．）和黑云杉（Ｐｉｃｅａｍａｒｉａｎａ（Ｍｉｌ）ＢＳＰ）气体交换的影响。气体交换率的测定使用便携式气体交换系统（ＬＩ－６２００）。结果表明光合作用光流动量（ＰＰＦＤ）、气温（Ｔａ）、蒸气压差（ＶＰＤ）和体内二氧化碳浓度（Ｃｉ）均对气体交换有显著影响,但对不同树种影响程度不同。在大气二氧化碳浓度（Ｃａ）和相对稳定的气温和蒸气压差下,欧洲杨比短叶松和黑云杉有较高光饱和点、同化量子产量（Φ）、在饱和ＰＰＦＤ下最高同化率（Ｐｍ）和较低的光补偿点（ＬＣＰ）。对欧洲杨树,幼龄树比老龄树有较高光合能力,且生长季早期光合能力比后期高。欧洲杨和短叶松的气孔导度（ｇｓ）随ＰＰＦＤ增加而增加。但黑云杉ｇｓ不受ＰＰＦＤ影响。在高光强下（ＰＰＦＤ＞１０００μｍｏｌ·ｍ－２ｓ－１）,欧洲杨幼树被光叶片比曝光叶片表现较低的净二氧化     

Requirement for Wnt3 in vertebrate axis formation.

Several studies have implicated Wnt signalling in primary axis formation during vertebrate embryogenesis, yet no Wnt protein has been shown to be essential for this process. In the mouse, primitive streak formation is the first overt morphological sign of the anterior-posterior axis. Here we show that Wnt3 is expressed before gastrulation in the proximal epiblast of the egg cylinder, then is restricted to the posterior proximal epiblast and its associated visceral endoderm and subsequently to the primitive streak and mesoderm. Wnt3-/- mice develop a normal egg cylinder but do not form a primitive streak, mesoderm or node. The epiblast continues to proliferate in an undifferentiated state that lacks anterior-posterior neural patterning, but anterior visceral endoderm markers are expressed and correctly positioned. Our results suggest that regional patterning of the visceral endoderm is independent of primitive streak formation, but the subsequent establishment of anterior-posterior neural pattern in the ectoderm is dependent on derivatives of the primitive streak. These studies provide genetic proof for the requirement of Wnt3 in primary axis formation in the mouse.     

Comparing strategies to fine-map the association of common SNPs at chromosome 9p21 with type 2 diabetes and myocardial infarction

Noncoding variants at human chromosome 9p21 near CDKN2A and CDKN2B are associated with type 2 diabetes, myocardial infarction, aneurysm, vertical cup disc ratio and at least five cancers. Here we compare approaches to more comprehensively assess genetic variation in the region. We carried out targeted sequencing at high coverage in 47 individuals and compared the results to pilot data from the 1000 Genomes Project. We imputed variants into type 2 diabetes and myocardial infarction cohorts directly from targeted sequencing, from a genotyped reference panel derived from sequencing and from 1000 Genomes Project low-coverage data. Polymorphisms with frequency >5% were captured well by all strategies. Imputation of intermediate-frequency polymorphisms required a higher density of tag SNPs in disease samples than is available on first-generation genome-wide association study (GWAS) arrays. Our association analyses identified more comprehensive sets of variants showing equivalent statistical association with type 2 diabetes or myocardial infarction, but did not identify stronger associations than the original GWAS signals.     

Controls on tropical Pacific Ocean productivity revealed through nutrient stress diagnostics

In situ enrichment experiments have shown that the growth of bloom-forming diatoms in the major high-nitrate low-chlorophyll (HNLC) regions of the world's oceans is limited by the availability of iron. Yet even the largest of these manipulative experiments represents only a small fraction of an ocean basin, and the responses observed are strongly influenced by the proliferation of rare species rather than the growth of naturally dominant populations. Here we link unique fluorescence attributes of phytoplankton to specific physiological responses to nutrient stress, and use these relationships to evaluate the factors that constrain phytoplankton growth in the tropical Pacific Ocean on an unprecedented spatial scale. On the basis of fluorescence measurements taken over 12 years, we delineate three major ecophysiological regimes in this region. We find that iron has a key function in regulating phytoplankton growth in both HNLC and oligotrophic waters near the Equator and further south, whereas nitrogen and zooplankton grazing are the primary factors that regulate biomass production in the north. Application of our findings to the interpretation of satellite chlorophyll fields shows that productivity in the tropical Pacific basin may be 1.2-2.5 Pg C yr(-1) lower than previous estimates have suggested, a difference that is comparable to the global change in ocean production that accompanied the largest El Ni?o to La Ni?a transition on record.     

2013十大太空故事

正美国《天文学》杂志评选出2013年十大太空故事(发刊时"嫦娥三号"尚未发射),我们不会忘记在这一年出现了两颗明亮的彗星以及百年一遇的流星爆炸——对于空间科学而言,2013年无疑是一个丰收年2013年大部分的天文头条都涉及到了宇宙中最极端的天体和事件,例如黑洞、高能宇宙线以及宇宙的开端。不过,行星科学也不甘示弱。近期,美国《天文学》杂志评选出2013年十大太空故事。     

Food spectrum analysis of the Asian toad,Duttaphrynus melanostictus (Schneider, 1799) (Anura: Bufonidae), from Timor Island,Wallacea

The Asian toad, Duttaphrynus melanostictus (Schneider, 1799), is widespread throughout tropical Asia and very abundant where it occurs. It was relatively recently introduced to Timor, the second largest island in the biogeographic region called Wallacea. Timor Island shows an exceptionally high level of endemism in a wide range of faunal groups and there are concerns that D. melanostictus may have a negative impact on this diversity, including vertebrates, through direct predation. To evaluate the impact the diet of D. melanostictus might have on the local fauna, gut contents of 83 preserved toad specimens from five habitat types in Timor-Leste, a country occupying the eastern half of Timor Island, were examined. We identified 5581 prey items, comprising the following animal groups: annelids; snails and slugs; spiders and harvestmen; woodlice; millipedes and centipedes; grasshoppers, crickets and earwigs; termites; thrips and true bugs; beetles; ants; hymenopterans other than ants; true flies; butterflies; unidentified insects; and insect larvae. Small eusocial insects (ants and termites) constituted the major part of the diet (61.6% and 23.4%, respectively). No vertebrate prey was recorded. Prey item composition did not differ between habitats. The wide prey spectrum well indicates that D. melanostictus is a generalist invertebrate feeder, as other studies, from regions where this species occurs naturally, have already shown. Although the Asian toad seems to not generally prey on vertebrates, vertebrate species that are morphologically similar to invertebrates in their overall appearance may be consumed. Hence, a negative effect on some taxa (e.g. blindsnakes) may be possible. We also present some limited data on intestinal parasites occurring in D. melanostictus.