Evolution: functional evolution of nuclear structure.

The evolution of the nucleus, the defining feature of eukaryotic cells, was long shrouded in speculation and mystery. There is now strong evidence that nuclear pore complexes (NPCs) and nuclear membranes coevolved with the endomembrane system, and that the last eukaryotic common ancestor (LECA) had fully functional NPCs. Recent studies have identified many components of the nuclear envelope in living Opisthokonts, the eukaryotic supergroup that includes fungi and metazoan animals. These components include diverse chromatin-binding membrane proteins, and membrane proteins with adhesive lumenal domains that may have contributed to the evolution of nuclear membrane architecture. Further discoveries about the nucleoskeleton suggest that the evolution of nuclear structure was tightly coupled to genome partitioning during mitosis

Impacts of Urbanization on Base Flow and Recharge Rates, Northeastern Illinois: Summary of Year 1 Activities

During year one of a two-year project to investigate the impacts of urbanization on base flow and ground-water recharge rates in northeastern Illinois, three gaged watersheds in urbanized areas of northeastern Illinois, and one watershed located in rural northwestern Illinois, have been selected for study. The gages have a common period of record extending from October 1952 through the present, a period during which the northeastern Illinois watersheds underwent substantial urbanization. Mean daily discharge data from the gages have been analyzed using an automated hydrograph separation technique, and monthly estimates of mean total discharge, base flow, and direct runoff have been calculated. Spearman rank correlation coefficients indicate a stronger correlation between precipitation and total discharge, base flow, and direct runoff in the northeastern Illinois watersheds than in the rural watershed. Smoothed time-series plots of total discharge, base flow, and direct runoff in the urban watersheds are less consistent with precipitation than similar plots constructed from the rural watershed data. The trends indicate that rates of direct runoff have overtaken rates of base flow in two of the three northeastern Illinois watersheds, but in one of these watersheds, this relationship probably reflects the cessation of effluent discharges to the stream. In general, double-mass curve analysis suggests that, relative to the rural watershed, base flow in the urban watersheds has proportionally decreased, and direct runoff has proportionally increased. The trends suggested by the smoothed time-series plots and the double-mass curves are consistent with a conceptual model of the northeastern Illinois watersheds in which sewering and impervious surfaces have reduced infiltration, and thence ground-water recharge and base flow, in the watersheds.Ope

Bayesian model search and multilevel inference for SNP association studies

Technological advances in genotyping have given rise to hypothesis-based association studies of increasing scope. As a result, the scientific hypotheses addressed by these studies have become more complex and more difficult to address using existing analytic methodologies. Obstacles to analysis include inference in the face of multiple comparisons, complications arising from correlations among the SNPs (single nucleotide polymorphisms), choice of their genetic parametrization and missing data. In this paper we present an efficient Bayesian model search strategy that searches over the space of genetic markers and their genetic parametrization. The resulting method for Multilevel Inference of SNP Associations, MISA, allows computation of multilevel posterior probabilities and Bayes factors at the global, gene and SNP level, with the prior distribution on SNP inclusion in the model providing an intrinsic multiplicity correction. We use simulated data sets to characterize MISA's statistical power, and show that MISA has higher power to detect association than standard procedures. Using data from the North Carolina Ovarian Cancer Study (NCOCS), MISA identifies variants that were not identified by standard methods and have been externally ``validated'' in independent studies. We examine sensitivity of the NCOCS results to prior choice and method for imputing missing data. MISA is available in an R package on CRAN.Comment: Published in at http://dx.doi.org/10.1214/09-AOAS322 the Annals of Applied Statistics (http://www.imstat.org/aoas/) by the Institute of Mathematical Statistics (http://www.imstat.org

Heart enhancers with deeply conserved regulatory activity are established early in zebrafish development.

During the phylotypic period, embryos from different genera show similar gene expression patterns, implying common regulatory mechanisms. Here we set out to identify enhancers involved in the initial events of cardiogenesis, which occurs during the phylotypic period. We isolate early cardiac progenitor cells from zebrafish embryos and characterize 3838 open chromatin regions specific to this cell population. Of these regions, 162 overlap with conserved non-coding elements (CNEs) that also map to open chromatin regions in human. Most of the zebrafish conserved open chromatin elements tested drive gene expression in the developing heart. Despite modest sequence identity, human orthologous open chromatin regions recapitulate the spatial temporal expression patterns of the zebrafish sequence, potentially providing a basis for phylotypic gene expression patterns. Genome-wide, we discover 5598 zebrafish-human conserved open chromatin regions, suggesting that a diverse repertoire of ancient enhancers is established prior to organogenesis and the phylotypic period

Identification of the Plasticity-Relevant Fucose-α(1−2)-Galactose Proteome from the Mouse Olfactory Bulb

Fucose-α(1−2)-galactose [Fucα(1−2)Gal] sugars have been implicated in the molecular mechanisms that underlie neuronal development, learning, and memory. However, an understanding of their precise roles has been hampered by a lack of information regarding Fucα(1−2)Gal glycoproteins. Here, we report the first proteomic studies of this plasticity-relevant epitope. We identify five classes of putative Fucα(1−2)Gal glycoproteins: cell adhesion molecules, ion channels and solute carriers/transporters, ATP-binding proteins, synaptic vesicle-associated proteins, and mitochondrial proteins. In addition, we show that Fucα(1−2)Gal glycoproteins are enriched in the developing mouse olfactory bulb (OB) and exhibit a distinct spatiotemporal expression that is consistent with the presence of a “glycocode” to help direct olfactory sensory neuron (OSN) axonal pathfinding. We find that expression of Fucα(1−2)Gal sugars in the OB is regulated by the α(1−2)fucosyltransferase FUT1. FUT1-deficient mice exhibit developmental defects, including fewer and smaller glomeruli and a thinner olfactory nerve layer, suggesting that fucosylation contributes to OB development. Our findings significantly expand the number of Fucα(1−2)Gal glycoproteins and provide new insights into the molecular mechanisms by which fucosyl sugars contribute to neuronal processes

A colourful new Australian reaches Talaroo: the Tawny Coster butterfly, Acraea terpsicore.

Since being first found in Australia near Darwin in 2012, the Tawny Coster butterfly (Acraea terpsicore; Lepidoptera, Nymphalidae) has spread rapidly. We report its presence at Talaroo Station between Mt Surprise and Georgetown in far north Queensland, the species being detected at six of 13 sites that were surveyed for butterflies in February 2017. More than ten individuals were present at three sites, and breeding was confirmed at one of these. Talaroo falls a little outside the predicted preference envelope for the species in being in uplands well away from the coast, and in that the vegetation is little-disturbed, prompting the notion that the Tawny Coster may be even more versatile in its occurrence than previously suggested

The central density of a neutron star is unaffected by a binary companion at linear order in μ/R\mu/R

Recent numerical work by Wilson, Mathews, and Marronetti [J. R. Wilson, G. J. Mathews and P. Marronetti, Phys. Rev. D 54, 1317 (1996)] on the coalescence of massive binary neutron stars shows a striking instability as the stars come close together: Each star's central density increases by an amount proportional to 1/(orbital radius). This overwhelms any stabilizing effects of tidal coupling [which are proportional to 1/(orbital radius)^6] and causes the stars to collapse before they merge. Since the claimed increase of density scales with the stars' mass, it should also show up in a perturbation limit where a point particle of mass $\mu$ orbits a neutron star. We prove analytically that this does not happen; the neutron star's central density is unaffected by the companion's presence to linear order in $\mu/R$. We show, further, that the density increase observed by Wilson et. al. could arise as a consequence of not faithfully maintaining boundary conditions.Comment: 3 pages, REVTeX, no figures, submitted to Phys Rev D as a Rapid Communicatio

Effect of physio-chemical seed treatments on opium poppy downy mildews caused by Peronospora meconopsidis and P. somniferi

Downy mildew of opium poppy is the single biggest disease constraint afflicting the Australian poppy industry. Within the pathosystem, the transmission of infections via infested seed is of major concern. Both downy mildew pathogens of poppy; Peronospora meconopsidis and P. somniferi, are known contaminants of commercial seed stocks. Using seed naturally infested with these pathogens, the effect of physio-chemical seed treatments on seedling health and disease transmission were evaluated. Individual seed treatments were tested to determine optimal treatment parameters for each; including incubation time, temperature and treatment concentration. Optimised physiochemical treatments were then compared. The most effective treatment methods were seed washes in acidified electrolytic water (400 ppm hypochlorous acid for 5 min) and hypochlorite solution (2% NaOCI for 5 min). In seed to seedling transmission assays, these two treatments reduced transmission of P. somniferi by 88.8% and 74.61%, and P. meconopsidis by 93.3% and 100%, respectively. These methods are recommended for seed treatment of commercial opium poppy seed to assist in the control of the downy mildew diseases

Excimer laser processing of inkjet-printed and sputter-deposited transparent conducting SnO2:Sb for flexible electronics

The feasibility of low-temperature fabrication of transparent electrode elements from thin films of antimony-doped tin oxide (SnO2:Sb, ATO) has been investigated via inkjet printing, rf magnetron sputtering and post-deposition excimer laser processing. Laser processing of thin films on both glass and plastic substrates was performed using a Lambda Physik 305i excimer laser, with fluences in the range 20–100 mJ cm− 2 reducing sheet resistance from as-deposited values by up to 3 orders of magnitude. This is consistent with TEM analysis of the films that shows a densification of the upper 200 nm of laser-processed regions