Molecular characterization of Ph1 as a major chromosome pairing locus in polyploid wheat

The foundation of western civilization owes much to the high fertility of bread wheat, which results from the stability of its polyploid genome. Despite possessing multiple sets of related chromosomes, hexaploid (bread) and tetraploid (pasta) wheat both behave as diploids at meiosis. Correct pairing of homologous chromosomes is controlled by the Ph1 locus. In wheat hybrids, Ph1 prevents pairing between related chromosomes. Lack of Ph1 activity in diploid relatives of wheat suggests that Ph1 arose on polyploidization. Absence of phenotypic variation, apart from dosage effects, and the failure of ethylmethane sulphonate treatment to yield mutants, indicates that Ph1 has a complex structure. Here we have localized Ph1 to a 2.5-megabase interstitial region of wheat chromosome 5B containing a structure consisting of a segment of subtelomeric heterochromatin that inserted into a cluster of cdc2-related genes after polyploidization. The correlation of the presence of this structure with Ph1 activity in related species, and the involvement of heterochromatin with Ph1 (ref. 6) and cdc2 genes with meiosis, makes the structure a good candidate for the Ph1 locus.     

Biomarker evidence for green and purple sulphur bacteria in a stratified Palaeoproterozoic sea

The disappearance of iron formations from the geological record approximately 1.8 billion years (Gyr) ago was the consequence of rising oxygen levels in the atmosphere starting 2.45-2.32 Gyr ago. It marks the end of a 2.5-Gyr period dominated by anoxic and iron-rich deep oceans. However, despite rising oxygen levels and a concomitant increase in marine sulphate concentration, related to enhanced sulphide oxidation during continental weathering, the chemistry of the oceans in the following mid-Proterozoic interval (approximately 1.8-0.8 Gyr ago) probably did not yet resemble our oxygen-rich modern oceans. Recent data indicate that marine oxygen and sulphate concentrations may have remained well below current levels during this period, with one model indicating that anoxic and sulphidic marine basins were widespread, and perhaps even globally distributed. Here we present hydrocarbon biomarkers (molecular fossils) from a 1.64-Gyr-old basin in northern Australia, revealing the ecological structure of mid-Proterozoic marine communities. The biomarkers signify a marine basin with anoxic, sulphidic, sulphate-poor and permanently stratified deep waters, hostile to eukaryotic algae. Phototrophic purple sulphur bacteria (Chromatiaceae) were detected in the geological record based on the new carotenoid biomarker okenane, and they seem to have co-existed with communities of green sulphur bacteria (Chlorobiaceae). Collectively, the biomarkers support mounting evidence for a long-lasting Proterozoic world in which oxygen levels remained well below modern levels.     

Developing a genome-wide selection model for genetic improvement of residual feed intake and carcass merit in a beef cattle breeding program

Residual feed intake (RFI) and carcass merit (CM) are both complex traits emerging as critical targets for beef genetic improvement.RFI and CM traits are difficult and expensive to measure and genetic improvement for these traits through traditional selection methods is not very effective.Therefore,genome-wide selection using DNA markers may be a potential alternative for genetic improvement of these traits.In this study,the efficiency of a genome-wide selection model for genetic improvement of RFI and CM was assessed.The Illumina Bovine50K bead chip was used to genotype 922 beef cattle from the Kinsella Beef Research Ranch of the University of Alberta.A Bayes model and multiple marker regression using a stepwise method were used to conduct the association test.The number of significant SNP markers for carcass weight (CWT),carcass back fat (BF),carcass rib eye area (REA),carcass grade fat (GDF),lean meat yield (LMY),and residual feed intake (RFI) were 75,54,67,57,44 and 50,respectively.Bi-variate analysis of marker scores and phenotypes for all traits were made using DMU Software.The genetic parameter for each trait was estimated.The genetic correlations of marker score and phenotype for CWT,BF,REA,GDF,LMY and RFI were 0.75,0.69,0.87,0.77,0.78,and 0.85,respectively.The average prediction accuracies of phenotypic EBV for the six traits were increased by 0.05,0.16,0.24,0.23,0.17 and 0.19,respectively.The results of this study indicated that the two-trait marker-assisted evaluation model used was a suitable alternative of genetic evaluation for these traits in beef cattle.     

Variation in styles of rifting in the Gulf of California

Constraints on the structure of rifted continental margins and the magmatism resulting from such rifting can help refine our understanding of the strength of the lithosphere, the state of the underlying mantle and the transition from rifting to seafloor spreading. An important structural classification of rifts is by width, with narrow rifts thought to form as necking instabilities (where extension rates outpace thermal diffusion) and wide rifts thought to require a mechanism to inhibit localization, such as lower-crustal flow in high heat-flow settings. Observations of the magmatism that results from rifting range from volcanic margins with two to three times the magmatism predicted from melting models to non-volcanic margins with almost no rift or post-rift magmatism. Such variations in magmatic activity are commonly attributed to variations in mantle temperature. Here we describe results from the PESCADOR seismic experiment in the southern Gulf of California and present crustal-scale images across three rift segments. Over short lateral distances, we observe large differences in rifting style and magmatism--from wide rifting with minor synchronous magmatism to narrow rifting in magmatically robust segments. But many of the factors believed to control structural evolution and magmatism during rifting (extension rate, mantle potential temperature and heat flow) tend to vary over larger length scales. We conclude instead that mantle depletion, rather than low mantle temperature, accounts for the observed wide, magma-poor margins, and that mantle fertility and possibly sedimentary insulation, rather than high mantle temperature, account for the observed robust rift and post-rift magmatism.     

Chemical reduction of three-dimensional silica micro-assemblies into microporous silicon replicas

The carbothermal reduction of silica into silicon requires the use of temperatures well above the silicon melting point (> or =2,000 degrees C). Solid silicon has recently been generated directly from silica at much lower temperatures (< or =850 degrees C) via electrochemical reduction in molten salts. However, the silicon products of such electrochemical reduction did not retain the microscale morphology of the starting silica reactants. Here we demonstrate a low-temperature (650 degrees C) magnesiothermic reduction process for converting three-dimensional nanostructured silica micro-assemblies into microporous nanocrystalline silicon replicas. The intricate nanostructured silica microshells (frustules) of diatoms (unicellular algae) were converted into co-continuous, nanocrystalline mixtures of silicon and magnesia by reaction with magnesium gas. Selective magnesia dissolution then yielded an interconnected network of silicon nanocrystals that retained the starting three-dimensional frustule morphology. The silicon replicas possessed a high specific surface area (>500 m(2) g(-1)), and contained a significant population of micropores (< or =20 A). The silicon replicas were photoluminescent, and exhibited rapid changes in impedance upon exposure to gaseous nitric oxide (suggesting a possible application in microscale gas sensing). This process enables the syntheses of microporous nanocrystalline silicon micro-assemblies with multifarious three-dimensional shapes inherited from biological or synthetic silica templates for sensor, electronic, optical or biomedical applications.     

Phenotypic consequences of 1,000 generations of selection at elevated CO2 in a green alga

Estimates of the effect of increasing atmospheric CO2 concentrations on future global plant production rely on the physiological response of individual plants or plant communities when exposed to high CO2 (refs 1-6). Plant populations may adapt to the changing atmosphere, however, such that the evolved plant communities of the next century are likely to be genetically different from contemporary communities. The properties of these future communities are unknown, introducing a bias of unknown sign and magnitude into projections of global carbon pool dynamics. Here we report a long-term selection experiment to investigate the phenotypic consequences of selection for growth at elevated CO2 concentrations. After about 1,000 generations, selection lines of the unicellular green alga Chlamydomonas failed to evolve specific adaptation to a CO2 concentration of 1,050 parts per million. Some lines, however, evolved a syndrome involving high rates of photosynthesis and respiration, combined with higher chlorophyll content and reduced cell size. These lines also grew poorly at ambient concentrations of CO2. We tentatively attribute this outcome to the accumulation of conditionally neutral mutations in genes affecting the carbon concentration mechanism.     

Epidermal growth factor receptors increase during the differentiation of embryonal carcinoma cells.

Mouse teratocarcinoma stem cells (embryonal carcinoma, or EC cells) bind very small amounts of mouse epidermal growth factor (EGF) and the latter hormone seems to have no stimulatory effect on the growth of two cloned lines of EC cells. However, when EC cells are induced to differentiate into large flat endodern-like cells (END cells), EGF receptors increase in number reaching a plateau in 6 to 8 days. At 8 to 10 days after induction, END cells multiply very slowly, but when EGF is added (3 x 10(-10) M) to the medium, cell division is stimulated and a further change in morphology occurs. This letter describes the binding characteristics and numbers of the EGF receptors on EC and END cells and shows that exogenous retinoic acid increases the numbers of EGF receptors on END cells. We were unable to find endogenous competing factors produced by EC cells. Such factors could account for the lack of detectable binding of EGF on these cells. As EC cells differentiate to END cells, so the ability of the cells to form tumours is reduced. Since this change is accompanied by an increase in the number of EGF receptors there may be a relationship between these two events.     

The DNA sequence, annotation and analysis of human chromosome 3

After the completion of a draft human genome sequence, the International Human Genome Sequencing Consortium has proceeded to finish and annotate each of the 24 chromosomes comprising the human genome. Here we describe the sequencing and analysis of human chromosome 3, one of the largest human chromosomes. Chromosome 3 comprises just four contigs, one of which currently represents the longest unbroken stretch of finished DNA sequence known so far. The chromosome is remarkable in having the lowest rate of segmental duplication in the genome. It also includes a chemokine receptor gene cluster as well as numerous loci involved in multiple human cancers such as the gene encoding FHIT, which contains the most common constitutive fragile site in the genome, FRA3B. Using genomic sequence from chimpanzee and rhesus macaque, we were able to characterize the breakpoints defining a large pericentric inversion that occurred some time after the split of Homininae from Ponginae, and propose an evolutionary history of the inversion.