Human repetitive sequence densities are mostly negatively correlated with R/Y-based nucleosome-positioning motifs and positively correlated with W/S-based motifs

AbstractWe examined statistical correlations between the frequencies of seven proposed nucleosome positioning motifs and the densities of repetitive sequences in the human genome. For both parametric and non-parametric measures of statistical correlations there is a tendency for repetitive sequence density to be negatively correlated with the density of R/Y-based nucleosome positioning motifs, while being positively correlated with that of W/S-based motifs. These results largely hold even when motifs are examined only within repeat-filtered sequences. The RRRRRYYYYY motif and its 5-base shift YYYYYRRRRR, in particular, is over-represented in the human genome; and its negative correlation is consistently present at different regions and at different length scales. For some other nucleosome positioning motifs, the relationship with repeats can be regional or length scale dependent. Considering the importance of nucleosome formation in epigenetic regulations, these results may provide new insight to the evolution of repetitive sequences

Unsteady shock front waviness in shock-buffet of transonic aircraft

The unsteady transonic aerodynamics of a wing-body configuration is investigated by solving the Unsteady Reynolds-averaged Navier-Stokes equations closed with the full Reynolds Stress Model. This work presents the prediction of flow field characteristics during deep shock-buffet penetration of a transport aircraft-representative geometry. Mach number of 0.85, and Reynolds number of 5 million based on the mean chord, are selected to reproduce experimental test conditions that serve as validating datasets. The results obtained give information about both surface and flow field shock-buffet dynamics. An unsteady shock front is observed on the suction side of the wing which gives birth to the so-called buffet cells. Flow field characteristics are dominated by the presence of lambda-shaped shocks and fully separated boundary layer over a significant part of the wing

OPORTUNIDADES DE CONSERVACIÓN DEL BOSQUE DE NIEBLA A TRAVÉS DEL MANEJO ALTERNATIVO: LOS AGROECOSISTEMAS CAFETALEROS

In México, the distribution of cloud forest or mountain mesophyll forest (MMF) coincides with that of shade-grown coffee (Coffea arabica L.) production. In this study, we discuss the way in which agroforestry coffee systems (ACS) can help MMF conservation, considering them as reservoirs of biodiversity, environmental services for the forest that the ACS displaced, fostering the regeneration potential; they are also a source of productive diversification that increases regional social welfare and therefore decreases the pressure on the MMF remnants. The productive diversification is exemplified with the research-action lines: use of timber-yielding native trees and exploitation of epiphytes in rustic nurseriesEn México, la distribución del bosque de niebla o bosque mesófilo de montaña (BMM) coincide con la del cultivo de café (Coffea arabica L.) bajo sombra. En este trabajo, se discute cómo los sistemas agroforestales en café (SAF) pueden ayudar a la conservación del BMM considerándolos como reservorios de biodiversidad, servicios ambientales hacia el bosque que los SAF desplazaron fomentando el potencial de regeneración; así como fuente de diversificación productiva que incrementan el bienestar social regional y por tanto disminuyen la presión sobre los remanentes del BMM. La diversificación productiva se ejemplifica con las líneas de investigación-acción: uso de árboles nativos maderables y aprovechamiento de epifitas en viveros rústicos

Activity of nitrifying bacteria and productivity of crops under the use of green manure

During the recycling of soil nitrogen, it is necessary to register the activity of nitrifying bacteria in nitrification. This process, in tropical conditions, is negatively affected by extreme variations in temperature, humidity, pH and organic matter during agronomic practices. Population changes of nitrifying bacteria in corn and soybean crops were evaluated under the use and management of green manure (GM). It was established as GM Mucuna pruriens var. utilis (CIAT No. 9349) - corn var. ICA 305. Ninety days later it was harvested and the residues were incorporated as LF or disposed on the soil surface as organic mulch (OM), the native weed Rottboellia cochinchinensis L. was managed as fallow (F). Then, corn-soybean crops were sown in an intercalated and monoculture system, each system was subject to organic fertilization (OF), chemical fertilization (CF) or no fertilization (NF). 11 treatments were structured under the design of Random Complete Blocks with 32 + 2 factorial arrangements with three repetitions. In the stage of blossoming and grain filling of the crops, the variables analyzed were; oxidizing bacteria of ammonium nitrate, volumetric humidity, temperature and yield. The populations of AOB and the production of NO3- did not vary significantly between treatments, but it did occur with soil temperature and humidity. The use of GM / OM promoted yields similar to those obtained with CF in corn, while in soybeans, when OM was added, yields exceeded CF

Effects of Crab Cavity Multipoles on JLEIC Ion Ring Dynamic Aperature

We study the effects of crab cavity multipole fields on the beam dynamic aperture of the Jefferson Lab Electron-Ion Collider (JLEIC) ion ring. Crab cavities are needed to compensate for luminosity loss due to a 50 mrad crossing angle at the interaction point. New compact crab cavity designs are interesting as they do not require considerable space in the ring but their non-linear field needs to be well understood. In this contribution, we study the impact of field multipoles on the beam dynamic aperture and report tolerance values for crab cavity multipoles

First Report of Diplodia seriata, Diplodia mutila, and Dothiorella omnivora Associated with Apple Cankers and Dieback in Rio Negro, Argentina

Apple (Malus domestica Borkh.) is an important fruit crop in Río Negro, Argentina. In recent years, the frequency of canker and dieback symptoms have increased affecting different apple cultivars. In September 2014, a higher occurrence of cankers (29%) and dieback (9%) was observed in a commercial orchard of 10-year-old apple trees (n=210) cv ʻItal Redʼ in General Roca, Río Negro, Argentina (39°2´36.73"S ? 67°32´44.55"W). Symptoms initially appeared as necrotic bark lesions on tree trunks and branches often associated with pruning wounds. Superficially, papyrus detachment of the bark and cracked bark were observed on the affected area. When the bark was removed, the diseased wood showed dark brown color. Cross sections of diseased branches revealed necrotic lesions that progress to branch death. Samples were collected from different symptomatic trees (n=30) and were superficially disinfected with 70% ethanol. Internal tissues (0.5 cm2) were excised from the advance margin of the necrotic lesions, plated on potato dextrose agar (PDA), and incubated at 22°C. Pycnidia were induced on sterilised pine needles overlaid on 2% water agar under near-UV light. Optimum temperature of culture growth on PDA was studied. According to their morpho-cultural characteristics, three different morphotypes were identified. The first, showed optimum growth at 30°C, had moderately dense white aerial mycelia and turned dark gray after 7 d. Conidia were ovoid, mostly aseptate, 20.8-25.6 × 8-11.4 µm (n=50) and hyaline to brown. The second, exhibited optimum growth from 25 to 30°C, was white to gray, with sparse to moderate aerial mycelium that turned dark olive green. Conidia were ovoid, 1-septate, 17.6-22.4 × 8.1-11.2 µm (n=50) and brown. Finally, the third showed optimum growth at 25°C, mycelium was grey to dark olive green. Conidia were oblong to ovoid with both ends rounded, aseptate and 1-septate at maturity, 20.8-24 × 11.2-14.4 µm (n=50), hyaline turned brown. Genomic DNA was extracted from one representative isolate of each morphotype and the ITS and EF1-α loci were amplified with the primer sets ITS1/ITS4 (White et al., 1990) and EF1-728F/EF1-986R (Carbone and Kohn, 1999), respectively. The nucleotide sequences indicated ≥99% identity to D. seriata (CBS 114796 and CBS 112555), D. mutila (CBS 302.36 and CBS 112553), and D. juglandis (CBS 188.87), reclassified as Dothiorella omnivora (Linaldeddu et al., 2016), for both DNA regions. The sequences were deposited in the GenBank database (MW596418, MW598375; MH665432, MK955889; MH665413, MK937229). To confirm pathogenicity, healthy 1-year-old twigs of adult apple trees were pruned and wounds of attached twigs immediately inoculated with 20 μL of conidial suspension (103 conidia.mL-1, n=9 per isolate) or sterile distilled water (control, n=9), and wrapped with Parafilm. The experimental design was randomized, and the experiment was repeated once. After 90 d, the area of lesion on all twigs inoculated was determined. D. mutila and Do. omnivora produced mean canker areas (65 and 73 mm2, respectively) significantly larger (p < 0.005) than D. seriata (48 mm2). No lesion occurred in the negative controls. Fulfilling Koch?s postulates, fungi were reisolated from all inoculated twigs and no fungus was recovered from controls. To our knowledge, this is the first report of D. seriata, D. mutila, and Do. omnivora associated with apple canker and dieback in Argentina, which shows the need of study the role of these fungi in orchard health.Fil: Lódolo, X. V.. Universidad Nacional del Comahue. Facultad de Ciencias Agrarias. Instituto de Biotecnología Agropecuaria del Comahue; ArgentinaFil: Lutz, M. C.. Universidad Nacional del Comahue. Facultad de Ciencias Agrarias. Instituto de Biotecnología Agropecuaria del Comahue; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Patagonia Norte. Centro de Investigaciones en Toxicología Ambiental y Agrobiotecnología del Comahue. Instituto de Biotecnología Agropecuaria del Comahue | Universidad Nacional del Comahue. Facultad de Ciencias Agrarias. Centro de Investigaciones en Toxicología Ambiental y Agrobiotecnología del Comahue. Instituto de Biotecnología Agropecuaria del Comahue; ArgentinaFil: Mondino, P.. Universidad de la República; UruguayFil: Oussett, J.. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Patagonia Norte. Centro de Investigaciones en Toxicología Ambiental y Agrobiotecnología del Comahue. Instituto de Biotecnología Agropecuaria del Comahue | Universidad Nacional del Comahue. Facultad de Ciencias Agrarias. Centro de Investigaciones en Toxicología Ambiental y Agrobiotecnología del Comahue. Instituto de Biotecnología Agropecuaria del Comahue; ArgentinaFil: Sosa, María Cristina. Universidad Nacional del Comahue. Facultad de Cs.agrarias. Departamento de Biología Aplicada. Cátedra de Fitopatologia; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Patagonia Norte. Centro de Investigaciones en Toxicología Ambiental y Agrobiotecnología del Comahue. Instituto de Biotecnología Agropecuaria del Comahue | Universidad Nacional del Comahue. Facultad de Ciencias Agrarias. Centro de Investigaciones en Toxicología Ambiental y Agrobiotecnología del Comahue. Instituto de Biotecnología Agropecuaria del Comahue; Argentin

Thermodynamic limits of sperm swimming precision

Sperm swimming is crucial to fertilise the egg, in nature and in assisted reproductive technologies. Modelling the sperm dynamics involves elasticity, hydrodynamics, internal active forces, and out-of-equilibrium noise. Here we demonstrate experimentally the relevance of energy dissipation for sperm beating fluctuations. For each motile cell, we reconstruct the time-evolution of the two main tail's spatial modes, which together trace a noisy limit cycle characterised by a maximum level of precision $p_{max}$. Our results indicate $p_{max} \sim 10^2 s^{-1}$, remarkably close to the estimated precision of a dynein molecular motor actuating the flagellum, which is bounded by its energy dissipation rate according to the Thermodynamic Uncertainty Relation. Further experiments under oxygen deprivation show that $p_{max}$ decays with energy consumption, as it occurs for a single molecular motor. Both observations can be explained by conjecturing a high level of coordination among the conformational changes of dynein motors. This conjecture is supported by a theoretical model for the beating of an ideal flagellum actuated by a collection of motors, including a motor-motor nearest neighbour coupling of strength $K$: when $K$ is small the precision of a large flagellum is much higher than the single motor one. On the contrary, when $K$ is large the two become comparable.Comment: Main Text with Appendices (14 pages, 9 figures) plus Supplementary Information, Accepted for Publication in PRX-Lif

Slim Epistemology with a Thick Skin

The distinction between ‘thick’ and ‘thin’ value concepts, and its importance to ethical theory, has been an active topic in recent meta-ethics. This paper defends three claims regarding the parallel issue about thick and thin epistemic concepts. (1) Analogy with ethics offers no straightforward way to establish a good, clear distinction between thick and thin epistemic concepts. (2) Assuming there is such a distinction, there are no semantic grounds for assigning thick epistemic concepts priority over the thin. (3) Nor does the structure of substantive epistemological theory establish that thick epistemic concepts enjoy systematic theoretical priority over the thin. In sum, a good case has yet to be made for any radical theoretical turn to thicker epistemology

Matter effects in neutrino visible decay at future long-baseline experiments

Neutrino visible decay in the presence of matter is re-evaluated. We study these effects in two future long-baseline experiments where matter effects are relevant: DUNE (1300 km) and a hypothetical beam aimed towards ANDES (7650 km). We find that matter effects are negligible for the visible component of neutrino decay at DUNE, being much more relevant at ANDES. We perform a detailed simulation of DUNE, considering $\nu_\mu$ disappearance and $\nu_e$ appearance channels, for both FHC and RHC modes. The sensitivity to the decay constant $\alpha_3$ can be as low as $2\times10^{-6}$ eV$^2$ at 90% C.L., depending on the neutrino masses and type of coupling. We also show the impact of neutrino decay in the determination of $\theta_{23}$ and $\delta_{\rm CP}$, and find that the best-fit value of $\theta_{23}$ can move from a true value at the lower octant towards the higher octant.Comment: 18 pages; v2: Minor changes, version accepted for publication in EPJ