Histone Modifications within the Human X Centromere Region

Human centromeres are multi-megabase regions of highly ordered arrays of alpha satellite DNA that are separated from chromosome arms by unordered alpha satellite monomers and other repetitive elements. Complexities in assembling such large repetitive regions have limited detailed studies of centromeric chromatin organization. However, a genomic map of the human X centromere has provided new opportunities to explore genomic architecture of a complex locus. We used ChIP to examine the distribution of modified histones within centromere regions of multiple X chromosomes. Methylation of H3 at lysine 4 coincided with DXZ1 higher order alpha satellite, the site of CENP-A localization. Heterochromatic histone modifications were distributed across the 400–500 kb pericentromeric regions. The large arrays of alpha satellite and gamma satellite DNA were enriched for both euchromatic and heterochromatic modifications, implying that some pericentromeric repeats have multiple chromatin characteristics. Partial truncation of the X centromere resulted in reduction in the size of the CENP-A/Cenp-A domain and increased heterochromatic modifications in the flanking pericentromere. Although the deletion removed ∼1/3 of centromeric DNA, the ratio of CENP-A to alpha satellite array size was maintained in the same proportion, suggesting that a limited, but defined linear region of the centromeric DNA is necessary for kinetochore assembly. Our results indicate that the human X centromere contains multiple types of chromatin, is organized similarly to smaller eukaryotic centromeres, and responds to structural changes by expanding or contracting domains

Evaluating a Proposed 20% National Renewable Portfolio Standard

This paper provides a preliminary analysis of the impacts of a proposed 20% national renewable portfolio standard (RPS) by 2021, which has been advanced in the U.S. Congress by Senator Jeff Bingaman of New Mexico. The paper was prepared before the America Recovery and Reinvestment Act was signed into law by President Barack Obama on February 17, 2009, and thus does not consider important changes in renewable energy (RE) policy that need to be addressed in follow-on analysis. We use NREL's Regional Energy Deployment System (ReEDS) model to evaluate the impacts of the RPS requirements on the energy sector and consider design issues associated with renewable energy certificate (REC) trading markets

The Grizzly, October 13, 1989

Berman Opening Draws Near • Sculptor Chadwick Visits UC • Frats Angered • Letters: Grizzly, Get on the Ball!; Shape up!; Dump Starkist! • Michener Opens Museum • Swarthmore, Hopkins Defeated • V-Ball Wins • Hockey Squad Beats Nationally Ranked Teams • 1989 Candidates for Homecoming Queen • Soccer Looks to Future • Wagner Runs Wild • Athletes of the Week • Control Pledging Power Abuses • The Wismer Beastieshttps://digitalcommons.ursinus.edu/grizzlynews/1243/thumbnail.jp

The Grizzly, September 8, 1989

Hudson Gets $ Flowing • Earth Day Seed Planted • French Studies Papa\u27s Notes • Lopez Lures Listeners • Kruse Spot to Dawleys House • Presidential Candidates • Victory at GB Classic • Captains Lead Attack • Gros Sets Goals • Quest Continues • V-ball: Ichiban! • Coaches Added • Optimistic Lady Bears Start Season • Beaches No Bumshttps://digitalcommons.ursinus.edu/grizzlynews/1239/thumbnail.jp

Dust Devil Tracks

Dust devils that leave dark- or light-toned tracks are common on Mars and they can also be found on the Earth’s surface. Dust devil tracks (hereinafter DDTs) are ephemeral surface features with mostly sub-annual lifetimes. Regarding their size, DDT widths can range between ∼1 m and ∼1 km, depending on the diameter of dust devil that created the track, and DDT lengths range from a few tens of meters to several kilometers, limited by the duration and horizontal ground speed of dust devils. DDTs can be classified into three main types based on their morphology and albedo in contrast to their surroundings; all are found on both planets: (a) dark continuous DDTs, (b) dark cycloidal DDTs, and (c) bright DDTs. Dark continuous DDTs are the most common type on Mars. They are characterized by their relatively homogenous and continuous low albedo surface tracks. Based on terrestrial and martian in situ studies, these DDTs most likely form when surficial dust layers are removed to expose larger-grained substrate material (coarse sands of ≥500 μm in diameter). The exposure of larger-grained materials changes the photometric properties of the surface; hence leading to lower albedo tracks because grain size is photometrically inversely proportional to the surface reflectance. However, although not observed so far, compositional differences (i.e., color differences) might also lead to albedo contrasts when dust is removed to expose substrate materials with mineralogical differences. For dark continuous DDTs, albedo drop measurements are around 2.5 % in the wavelength range of 550–850 nm on Mars and around 0.5 % in the wavelength range from 300–1100 nm on Earth. The removal of an equivalent layer thickness around 1 μm is sufficient for the formation of visible dark continuous DDTs on Mars and Earth. The next type of DDTs, dark cycloidal DDTs, are characterized by their low albedo pattern of overlapping scallops. Terrestrial in situ studies imply that they are formed when sand-sized material that is eroded from the outer vortex area of a dust devil is redeposited in annular patterns in the central vortex region. This type of DDT can also be found in on Mars in orbital image data, and although in situ studies are lacking, terrestrial analog studies, laboratory work, and numerical modeling suggest they have the same formation mechanism as those on Earth. Finally, bright DDTs are characterized by their continuous track pattern and high albedo compared to their undisturbed surroundings. They are found on both planets, but to date they have only been analyzed in situ on Earth. Here, the destruction of aggregates of dust, silt and sand by dust devils leads to smooth surfaces in contrast to the undisturbed rough surfaces surrounding the track. The resulting change in photometric properties occurs because the smoother surfaces have a higher reflectance compared to the surrounding rough surface, leading to bright DDTs. On Mars, the destruction of surficial dust-aggregates may also lead to bright DDTs. However, higher reflective surfaces may be produced by other formation mechanisms, such as dust compaction by passing dust devils, as this may also cause changes in photometric properties. On Mars, DDTs in general are found at all elevations and on a global scale, except on the permanent polar caps. DDT maximum areal densities occur during spring and summer in both hemispheres produced by an increase in dust devil activity caused by maximum insolation. Regionally, dust devil densities vary spatially likely controlled by changes in dust cover thicknesses and substrate materials. This variability makes it difficult to infer dust devil activity from DDT frequencies. Furthermore, only a fraction of dust devils leave tracks. However, DDTs can be used as proxies for dust devil lifetimes and wind directions and speeds, and they can also be used to predict lander or rover solar panel clearing events. Overall, the high DDT frequency in many areas on Mars leads to drastic albedo changes that affect large-scale weather patterns

Nothing lasts forever: Dominant species decline under rapid environmental change in global grasslands

Dominance often indicates one or a few species being best suited for resource capture and retention in a given environment. Press perturbations that change availability of limiting resources can restructure competitive hierarchies, allowing new species to capture or retain resources and leaving once dominant species fated to decline. However, dominant species may maintain high abundances even when their new environments no longer favour them due to stochastic processes associated with their high abundance, impeding deterministic processes that would otherwise diminish them. Here, we quantify the persistence of dominance by tracking the rate of decline in dominant species at 90 globally distributed grassland sites under experimentally elevated soil nutrient supply and reduced vertebrate consumer pressure. We found that chronic experimental nutrient addition and vertebrate exclusion caused certain subsets of species to lose dominance more quickly than in control plots. In control plots, perennial species and species with high initial cover maintained dominance for longer than annual species and those with low initial cover respectively. In fertilized plots, species with high initial cover maintained dominance at similar rates to control plots, while those with lower initial cover lost dominance even faster than similar species in controls. High initial cover increased the estimated time to dominance loss more strongly in plots with vertebrate exclosures than in controls. Vertebrate exclosures caused a slight decrease in the persistence of dominance for perennials, while fertilization brought perennials' rate of dominance loss in line with those of annuals. Annual species lost dominance at similar rates regardless of treatments. Synthesis. Collectively, these results point to a strong role of a species' historical abundance in maintaining dominance following environmental perturbations. Because dominant species play an outsized role in driving ecosystem processes, their ability to remain dominant—regardless of environmental conditions—is critical to anticipating expected rates of change in the structure and function of grasslands. Species that maintain dominance while no longer competitively favoured following press perturbations due to their historical abundances may result in community compositions that do not maximize resource capture, a key process of system responses to global change.Fil: Wilfahrt, Peter A.. University of Minnesota; Estados UnidosFil: Seabloom, Eric. University of Minnesota; Estados UnidosFil: Bakker, Jonathan. University of Washington; Estados UnidosFil: Biederman, Lori. Iowa State University; Estados UnidosFil: Bugalho, Miguel N.. Universidade Nova de Lisboa; PortugalFil: Cadotte, Marc W.. University of Toronto–Scarborough; Estados UnidosFil: Caldeira, Maria C.. Universidade Nova de Lisboa; PortugalFil: Catford, Jane A.. University of Melbourne; AustraliaFil: Chen, Qingqing. Peking University; China. German Centre for Integrative Biodiversity Research; AlemaniaFil: Donohue, Ian. Trinity College Dublin; IrlandaFil: Ebeling, Anne. University of Jena; AlemaniaFil: Eisenhauer, Nico. German Centre for Integrative Biodiversity Research; Alemania. Leipzig University; AlemaniaFil: Haider, Sylvia. Martin Luther University Halle-Wittenberg; Alemania. Leuphana University of Lüneburg; AlemaniaFil: Heckman, Robert W.. University of Texas; Estados Unidos. United States Forest Service; Estados UnidosFil: Jentsch, Anke. University of Bayreuth; AlemaniaFil: Koerner, Sally E.. University of North Carolina Greensboro; Estados UnidosFil: Komatsu, Kimberly J.. University of North Carolina Greensboro; Estados UnidosFil: Laungani, Ramesh. Poly Prep Country Day School; Estados UnidosFil: MacDougall, Andrew. University of Guelph; CanadáFil: Smith, Nicholas G.. Texas Tech University; Estados UnidosFil: Stevens, Carly J.. Lancaster University; Reino UnidoFil: Sullivan, Lauren L.. Michigan State University; Estados Unidos. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Tedder, Michelle. University of KwaZulu-Natal; SudáfricaFil: Peri, Pablo Luis. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro de Investigaciones y Transferencia de Santa Cruz. Universidad Tecnológica Nacional. Facultad Regional Santa Cruz. Centro de Investigaciones y Transferencia de Santa Cruz. Universidad Nacional de la Patagonia Austral. Centro de Investigaciones y Transferencia de Santa Cruz; ArgentinaFil: Tognetti, Pedro Maximiliano. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Veen, Ciska. Netherlands Institute of Ecology; Países BajosFil: Wheeler, George. University of Nebraska-Lincoln; Estados UnidosFil: Young, Alyssa L.. University of North Carolina Greensboro; Estados UnidosFil: Young, Hillary. University of California; Estados UnidosFil: Borer, Elizabeth. University of Minnesota; Estados Unido

Plant Species\u27 Origin Predicts Dominance and Response to Nutrient Enrichment and Herbivores in Global Grasslands

Exotic species dominate many communities; however the functional significance of species\u27 biogeographic origin remains highly contentious. This debate is fuelled in part by the lack of globally replicated, systematic data assessing the relationship between species provenance, function and response to perturbations. We examined the abundance of native and exotic plant species at 64 grasslands in 13 countries, and at a subset of the sites we experimentally tested native and exotic species responses to two fundamental drivers of invasion, mineral nutrient supplies and vertebrate herbivory. Exotic species are six times more likely to dominate communities than native species. Furthermore, while experimental nutrient addition increases the cover and richness of exotic species, nutrients decrease native diversity and cover. Native and exotic species also differ in their response to vertebrate consumer exclusion. These results suggest that species origin has functional significance, and that eutrophication will lead to increased exotic dominance in grasslands

We're in this Together: Sensation of the Host Cell Environment by Endosymbiotic Bacteria

Bacteria inhabit diverse environments, including the inside of eukaryotic cells. While a bacterial invader may initially act as a parasite or pathogen, a subsequent mutualistic relationship can emerge in which the endosymbiotic bacteria and their host share metabolites. While the environment of the host cell provides improved stability when compared to an extracellular environment, the endosymbiont population must still cope with changing conditions, including variable nutrient concentrations, the host cell cycle, host developmental programs, and host genetic variation. Furthermore, the eukaryotic host can deploy mechanisms actively preventing a bacterial return to a pathogenic state. Many endosymbionts are likely to use two-component systems (TCSs) to sense their surroundings, and expanded genomic studies of endosymbionts should reveal how TCSs may promote bacterial integration with a host cell. We suggest that studying TCS maintenance or loss may be informative about the evolutionary pathway taken toward endosymbiosis, or even toward endosymbiont-to-organelle conversion.Peer reviewe

Rare and low-frequency coding variants alter human adult height

Height is a highly heritable, classic polygenic trait with ~700 common associated variants identified so far through genome - wide association studies . Here , we report 83 height - associated coding variants with lower minor allele frequenc ies ( range of 0.1 - 4.8% ) and effects of up to 2 16 cm /allele ( e.g. in IHH , STC2 , AR and CRISPLD2 ) , >10 times the average effect of common variants . In functional follow - up studies, rare height - increasing alleles of STC2 (+1 - 2 cm/allele) compromise d proteolytic inhibition of PAPP - A and increased cleavage of IGFBP - 4 in vitro , resulting in higher bioavailability of insulin - like growth factors . The se 83 height - associated variants overlap genes mutated in monogenic growth disorders and highlight new biological candidates ( e.g. ADAMTS3, IL11RA, NOX4 ) and pathways ( e.g . proteoglycan/ glycosaminoglycan synthesis ) involved in growth . Our results demonstrate that sufficiently large sample sizes can uncover rare and low - frequency variants of moderate to large effect associated with polygenic human phenotypes , and that these variants implicate relevant genes and pathways