Genome-wide patterns of genetic variation among elite maize inbred lines

We have resequenced a group of six elite maize inbred lines, including the parents of the most productive commercial hybrid in China. This effort uncovered more than 1,000,000 SNPs, 30,000 indel polymorphisms and 101 low-sequence-diversity chromosomal intervals in the maize genome. We also identified several hundred complete genes that show presence/absence variation among these resequenced lines. We discuss the potential roles of complementation of presence/absence variations and other deleterious mutations in contributing to heterosis. High-density SNP and indel polymorphism markers reported here are expected to be a valuable resource for future genetic studies and the molecular breeding of this important crop.     

Geobotany of the Niobrara chalk barrens in Colorado: a study of edaphic endemism

The chalk barrens of the Niobrara Formation in the Arkansas River valley of Colorado exhibit a high degree of plant endemism and rarity. We examined their geochemistry and structure as well as the reproductive ecology of their signature species Mirabilis rotundifolius to assess factors influencing endemism. While no single component consistently identified the barren soils, the natural locations that support Mirablilis can be identified using elemental profiles from a cluster analysis of soil extracts. Because seeds germinate and plants proliferate in transplant gardens with non-calcic soils, bedrock and soil chemistry do not appear to be determinant components of endemism. Mirabilis rotundifoilus utilizes diverse pollinators but is capable of autogamy when insects are excluded; seed predation by harvester ants may be a limiting factor for population spread outside the barrens habitat. Mirabilis rotundifolius is a disturbance-tolerant species, part of a barrens cohort that shares traits of suffrutescence, woody caudices, or multibranched rhizomes penetrating the chalk strata. Its presence may be enhanced when disturbance inhibits the presence of other species that compete for limited water resources. We conclude that endemism is dictated not by unusual soil chemistry requirements but rather by structural components of the barrens. In a water-limited environment, shallow soils and thin chalk strata coupled with a functionally adaptive growth habit allow M. rotundifolius to survive when other species are excluded by disturbance or the physiochemical aspects of the barrens.     

Virginia opossum ( Didelphis virginiana virginiana ) from Yavapai County, Arizona

The Virginia opossum ( Didelphis virginiana ) is the only marsupial native to the United States. In recent times, D. virginiana has expanded its range through natural movements and anthropogenic introductions. Didelphis virginiana has been present in southern Arizona owing to range expansion by the Mexican subspecies ( D. v. californica ) and anthropogenic introductions of the eastern subspecies ( D. v. virginiana ). Here, we document the recent collection of an opossum in central Arizona. We also discuss how it possibly moved there and report on its stomach contents at the time of collection. El tlacuache norteño ( Didelphis virginiana ) es el único marsupial nativo de Estados Unidos. En tiempos recientes, D. virginiana ha expandido su área de distribución tanto por movimientos naturales como por introducciones antropogénicas. Didelphis virginiana se ha encontrado en el sur de Arizona debido a la expansión de la subespecie mexicana ( D. v. californica ) y a introducciones antropogénicas de la subespecie oriental ( D. v. virginiana ). Aquí documentamos la colecta reciente de un tlacuache en el centro de Arizona. También discutimos cómo podría haber llegado hasta allí e informamos sobre los contenidos de su estómago al tiempo de la colecta.     

沈括

介绍沈括其人及其时代政治环境;论述沈括的科学思想与本体的关系,沈括的科学思想与儒学思想的关系,民事事务对沈括科学和技术的影响,沈括的自然观及其他知识.     

Compartmentalization of S-RNase and HT-B degradation in self-incompatible Nicotiana

Pollen-pistil interactions are crucial for controlling plant mating. For example, S-RNase-based self-incompatibility prevents inbreeding in diverse angiosperm species. S-RNases are thought to function as specific cytotoxins that inhibit pollen that has an S-haplotype that matches one of those in the pistil. Thus, pollen and pistil factors interact to prevent mating between closely related individuals. Other pistil factors, such as HT-B, 4936-factor and the 120 kDa glycoprotein, are also required for pollen rejection but do not contribute to S-haplotype-specificity per se. Here we show that S-RNase is taken up and sorted to a vacuolar compartment in the pollen tubes. Antibodies to the 120 kDa glycoprotein label the compartment membrane. When the pistil does not express HT-B or 4936-factor, S-RNase remains sequestered, unable to cause rejection. Similarly, in wild-type pistils, compatible pollen tubes degrade HT-B and sequester S-RNase. We suggest that S-RNase trafficking and the stability of HT-B are central to S-specific pollen rejection.     

Modest stabilization by most hydrogen-bonded side-chain interactions in membrane proteins

Understanding the energetics of molecular interactions is fundamental to all of the central quests of structural biology including structure prediction and design, mapping evolutionary pathways, learning how mutations cause disease, drug design, and relating structure to function. Hydrogen-bonding is widely regarded as an important force in a membrane environment because of the low dielectric constant of membranes and a lack of competition from water. Indeed, polar residue substitutions are the most common disease-causing mutations in membrane proteins. Because of limited structural information and technical challenges, however, there have been few quantitative tests of hydrogen-bond strength in the context of large membrane proteins. Here we show, by using a double-mutant cycle analysis, that the average contribution of eight interhelical side-chain hydrogen-bonding interactions throughout bacteriorhodopsin is only 0.6 kcal mol(-1). In agreement with these experiments, we find that 4% of polar atoms in the non-polar core regions of membrane proteins have no hydrogen-bond partner and the lengths of buried hydrogen bonds in soluble proteins and membrane protein transmembrane regions are statistically identical. Our results indicate that most hydrogen-bond interactions in membrane proteins are only modestly stabilizing. Weak hydrogen-bonding should be reflected in considerations of membrane protein folding, dynamics, design, evolution and function.     

DNA sequencing of a cytogenetically normal acute myeloid leukaemia genome

Acute myeloid leukaemia is a highly malignant haematopoietic tumour that affects about 13,000 adults in the United States each year. The treatment of this disease has changed little in the past two decades, because most of the genetic events that initiate the disease remain undiscovered. Whole-genome sequencing is now possible at a reasonable cost and timeframe to use this approach for the unbiased discovery of tumour-specific somatic mutations that alter the protein-coding genes. Here we present the results obtained from sequencing a typical acute myeloid leukaemia genome, and its matched normal counterpart obtained from the same patient's skin. We discovered ten genes with acquired mutations; two were previously described mutations that are thought to contribute to tumour progression, and eight were new mutations present in virtually all tumour cells at presentation and relapse, the function of which is not yet known. Our study establishes whole-genome sequencing as an unbiased method for discovering cancer-initiating mutations in previously unidentified genes that may respond to targeted therapies.