Molecular verification of the integration of Tripsacum dactyloides DNA into wheat genome through wide hybridization

RAPD and RFLP analyses of double haploid lines which derived from hybridization between hexaploid wheat (Triticum aestivum L.2n=42) and eastern gamagrass (Tripsacum dactyloides L.2n=4x=72) are reported.Two of the 340 Operon primers have been screened,which stably amplified Tripsacum dactyloides (male parent) specific bands in the double haploid lines.These results confirm the fact that Tripsacum dactyloides DNA has been integrated into wheat genome by sexual hybridization at molecular level.This idea has been further testified by RFLP analysis.Application and potentials of transferring Tripsacum dactyloides DNA into wheat genome by sexual hybridization in wheat breeding are discussed.     

Merlin--rapid analysis of dense genetic maps using sparse gene flow trees.

Efforts to find disease genes using high-density single-nucleotide polymorphism (SNP) maps will produce data sets that exceed the limitations of current computational tools. Here we describe a new, efficient method for the analysis of dense genetic maps in pedigree data that provides extremely fast solutions to common problems such as allele-sharing analyses and haplotyping. We show that sparse binary trees represent patterns of gene flow in general pedigrees in a parsimonious manner, and derive a family of related algorithms for pedigree traversal. With these trees, exact likelihood calculations can be carried out efficiently for single markers or for multiple linked markers. Using an approximate multipoint calculation that ignores the unlikely possibility of a large number of recombinants further improves speed and provides accurate solutions in dense maps with thousands of markers. Our multipoint engine for rapid likelihood inference (Merlin) is a computer program that uses sparse inheritance trees for pedigree analysis; it performs rapid haplotyping, genotype error detection and affected pair linkage analyses and can handle more markers than other pedigree analysis packages.     

American pikas inhabit low-elevation sites outside the species’ previously described bioclimatic envelope

It has been suggested that Nearctic pikas ( Ochotona spp.) are good biogeographic indicators of regions containing rocky, mesic, and cool habitat characterized by long winters and short summers. I examined whether populations of pikas inhabiting distinct low-elevation locales (121–255 m) are faithfully restricted to long-winter and shortsummer conditions by monitoring the climate associated with American pikas ( Ochotona princeps ) in the southern part of the Columbia River Gorge, Oregon. Ambient air temperatures and weather conditions in the vicinity of 4 pika-occupied rockslides were monitored with remote temperature loggers and weather stations from June 2000 to June 2001. Temperatures were compared to long-term averages recorded within the area. I detected pikas inhabiting locales where some temperatures lie outside of the limiting climatic values previously calculated for regions containing pikas. Mild winter temperatures at these pika locations show that long-winter temperatures and snow accumulation associated with typical habitat may not be requirements for pikas in some low-elevation habitat. When using climatic conditions experienced by extant pikas to estimate local paleoenvironments surrounding fossil sites and to anticipate effects of climate change on future pika distributions, I determined that pika sites in the Columbia River Gorge indicate that the association of pikas with long-winter habitat should be considered uncertain. These results highlight the need for further investigation into how local temperatures affect the distribution, behavior, and persistence of low-elevation pikas.     

New records for Monotropa hypopithys (Ericaceae) from Colorado

Monotropa hypopithys L., rarely collected in Colorado, was taken five times during 1984. Coupled with previous collections, it is now known from 10 Colorado counties. The cool, moist August of 1984 may have contributed to its apparent ubiquity.     

Exome sequencing identifies GRIN2A as frequently mutated in melanoma

The incidence of melanoma is increasing more than any other cancer, and knowledge of its genetic alterations is limited. To systematically analyze such alterations, we performed whole-exome sequencing of 14 matched normal and metastatic tumor DNAs. Using stringent criteria, we identified 68 genes that appeared to be somatically mutated at elevated frequency, many of which are not known to be genetically altered in tumors. Most importantly, we discovered that TRRAP harbored a recurrent mutation that clustered in one position (p. Ser722Phe) in 6 out of 167 affected individuals (～4%), as well as a previously unidentified gene, GRIN2A, which was mutated in 33% of melanoma samples. The nature, pattern and functional evaluation of the TRRAP recurrent mutation suggest that TRRAP functions as an oncogene. Our study provides, to our knowledge, the most comprehensive map of genetic alterations in melanoma to date and suggests that the glutamate signaling pathway is involved in this disease.     

How broadly tuned olfactory receptors equally recognize their agonists. Human OR1G1 as a test case

The molecular features that dominate the binding mode of agonists by a broadly tuned olfactory receptor are analyzed through a joint approach combining cell biology, calcium imaging, and molecular modeling. The odorant/receptor affinities, estimated through statistics accrued during molecular dynamics simulations, are in accordance with the experimental ranking. Although in many systems receptors recognize their target through a network of oriented interactions, such as H-bonding, the binding by broadly tuned olfactory receptors is dominated by non-polar terms. We show how such a feature allows chemicals belonging to different chemical families to similarly activate the receptors through compensations of interactions within the binding site.     

The genome of Cryptosporidium hominis

Cryptosporidium species cause acute gastroenteritis and diarrhoea worldwide. They are members of the Apicomplexa--protozoan pathogens that invade host cells by using a specialized apical complex and are usually transmitted by an invertebrate vector or intermediate host. In contrast to other Apicomplexans, Cryptosporidium is transmitted by ingestion of oocysts and completes its life cycle in a single host. No therapy is available, and control focuses on eliminating oocysts in water supplies. Two species, C. hominis and C. parvum, which differ in host range, genotype and pathogenicity, are most relevant to humans. C. hominis is restricted to humans, whereas C. parvum also infects other mammals. Here we describe the eight-chromosome approximately 9.2-million-base genome of C. hominis. The complement of C. hominis protein-coding genes shows a striking concordance with the requirements imposed by the environmental niches the parasite inhabits. Energy metabolism is largely from glycolysis. Both aerobic and anaerobic metabolisms are available, the former requiring an alternative electron transport system in a simplified mitochondrion. Biosynthesis capabilities are limited, explaining an extensive array of transporters. Evidence of an apicoplast is absent, but genes associated with apical complex organelles are present. C. hominis and C. parvum exhibit very similar gene complements, and phenotypic differences between these parasites must be due to subtle sequence divergence.     

The worldwide leaf economics spectrum

Bringing together leaf trait data spanning 2,548 species and 175 sites we describe, for the first time at global scale, a universal spectrum of leaf economics consisting of key chemical, structural and physiological properties. The spectrum runs from quick to slow return on investments of nutrients and dry mass in leaves, and operates largely independently of growth form, plant functional type or biome. Categories along the spectrum would, in general, describe leaf economic variation at the global scale better than plant functional types, because functional types overlap substantially in their leaf traits. Overall, modulation of leaf traits and trait relationships by climate is surprisingly modest, although some striking and significant patterns can be seen. Reliable quantification of the leaf economics spectrum and its interaction with climate will prove valuable for modelling nutrient fluxes and vegetation boundaries under changing land-use and climate.     

Identification of diploid endosperm in an early angiosperm lineage

In flowering plants, the developmental and genetic basis for the establishment of an embryo-nourishing tissue differs from all other lineages of seed plants. Among extant nonflowering seed plants (conifers, cycads, Ginkgo, Gnetales), a maternally derived haploid tissue (female gametophyte) is responsible for the acquisition of nutrients from the maternal diploid plant, and the ultimate provisioning of the embryo. In flowering plants, a second fertilization event, contemporaneous with the fusion of sperm and egg to yield a zygote, initiates a genetically biparental and typically triploid embryo-nourishing tissue called endosperm. For over a century, triploid biparental endosperm has been viewed as the ancestral condition in extant flowering plants. Here we report diploid biparental endosperm in Nuphar polysepalum, a basal angiosperm. We show that diploid endosperms are common among early angiosperm lineages and may represent the ancestral condition among flowering plants. If diploid endosperm is plesiomorphic, the triploid endosperms of the vast majority of flowering plants must have evolved from a diploid condition through the developmental modification of the unique fertilization process that initiates endosperm.     

Zircon U-Pb and Hf isotopes of volcanic rocks from the Batamayineishan Formation in the eastern Junggar Basin

An internal structural study was conducted to investigate U-Pb age, trace elements and Hf isotopes of basaltic zircons from the Batamayineishan Formation. The basalt was obtained from drill well San-Can 1 on the eastern Luliang uplift within the Junggar Basin. Trace element data of zircons show that all samples are magmatic, with similar REE patterns, including positive Ce (δCe=5.06–134), but negative Eu (δEu=0.06⦒0.55) anomalies and enrichment in heavy rare earth elements. Among 25 grains, the concordant ages were subdivided into three groups; ages of 300.4±1.3 Ma (n=11), 339.2±2.7 Ma (n=3) and 392.0±1.7 Ma (n=8). Three remaining grains were nearly concordant, with ²⁰⁶Pb/²³⁸U ages of 510±7, 488±6 and 453±6 Ma, respectively. The youngest concordant age (i.e., 300.4±1.3 Ma) could be interpreted as the formation age of the studied basaltic rock; this is consistent with the sampling position at the upper part of the Batamayineishan Formation. On the other hand, ages such as Ordovician and early Devonian are consistent with the ages of island-arc volcanic rocks (enrichment in Pb) or ophiolites around the basin. Moreover, the positive ɛ _Hf(t) values of the early and middle Paleozoic zircons (+3.6–+10.5) may suggest that the basement traversed by the studied volcanic rocks may be Paleozoic in age, formed from the residual oceanic crust and island-arc complex. The ɛ _Hf(t) values (+4.2–+17.1) of the late Paleozoic (∼300.4 Ma) zircons suggest that the basaltic magmas were derived from partial melting of the asthenospheric mantle or depleted lithospheric mantle. These magmas were slightly contaminated by the existence of early-middle Paleozoic materials. The late Carboniferous basalts represent direct eruption of mantle-derived magmas at the upper crustal level during a post-collisional tectonic setting. We therefore consider that extensive vertical growth of the continental crust to have occurred before the late Carboniferous.