Optical mapping discerns genome wide DNA methylation profiles

BACKGROUND: Methylation of CpG dinucleotides is a fundamental mechanism of epigenetic regulation in eukaryotic genomes. Development of methods for rapid genome wide methylation profiling will greatly facilitate both hypothesis and discovery driven research in the field of epigenetics. In this regard, a single molecule approach to methylation profiling offers several unique advantages that include elimination of chemical DNA modification steps and PCR amplification. RESULTS: A single molecule approach is presented for the discernment of methylation profiles, based on optical mapping. We report results from a series of pilot studies demonstrating the capabilities of optical mapping as a platform for methylation profiling of whole genomes. Optical mapping was used to discern the methylation profile from both an engineered and wild type Escherichia coli. Furthermore, the methylation status of selected loci within the genome of human embryonic stem cells was profiled using optical mapping. CONCLUSION: The optical mapping platform effectively detects DNA methylation patterns. Due to single molecule detection, optical mapping offers significant advantages over other technologies. This advantage stems from obviation of DNA modification steps, such as bisulfite treatment, and the ability of the platform to assay repeat dense regions within mammalian genomes inaccessible to techniques using array-hybridization technologies

Preserving the palaeoenvironmental record in Drylands: Bioturbation and its significance for luminescence-derived chronologies

Luminescence (OSL) dating has revolutionised the understanding of Late Pleistocene dryland activity. However, one of the key assumptions for this sort of palaeoenvironmental work is that sedimentary sequences have been preserved intact, enabling their use as proxy indicators of past changes. This relies on stabilisation or burial soon after deposition and a mechanism to prevent any subsequent re-mobilisation. As well as a dating technique OSL, especially at the single grain level, can be used to gain an insight into post-depositional processes that may distort or invalidate the palaeoenvironmental record of geological sediment sequences. This paper explores the possible impact of bioturbation (the movement of sediment by flora and fauna) on luminescence derived chronologies from Quaternary sedimentary deposits in Texas and Florida (USA) which have both independent radiocarbon chronologies and archaeological evidence. These sites clearly illustrate the ability of bioturbation to rejuvenate ancient weathered sandy bedrock and/or to alter depositional stratigraphies through the processes of exhumation and sub-surface mixing of sediment. The use of multiple OSL replicate measurements is advocated as a strategy for checking for bioturbated sediment. Where significant OSL heterogeneity is found, caution should be taken with the derived OSL ages and further measurements at the single grain level are recommended. Observations from the linear dunes of the Kalahari show them to have no bedding structure and to have OSL heterogeneity similar to that shown from the bioturbated Texan and Florida sites. The Kalahari linear dunes could have therefore undergone hitherto undetected post-depositional sediment disturbance which would have implications for the established OSL chronology for the region

“Hummingbird” floral traits interact synergistically to discourage visitation by bumble bee foragers

Pollination syndromes are suites of floral traits presumed to reflect adaptations to attract and utilize a “primary” type of animal pollinator. However, syndrome traits may also function to deter “secondary” flower visitors that reduce plant fitness through their foraging activities. Here we use the hummingbird-pollinated plant species Mimulus cardinalis as a model to investigate the potential deterrent effects of classic bird syndrome traits on bumble bee foragers. To establish that M. cardinalis flowers elicit an avoidance response in bees, we assessed the choice behavior of individual foragers on a mixed experimental array of M. cardinalis and its bee-pollinated sister species M. lewisii. As expected, bees showed a strong preference against M. cardinalis flowers (only 22% of total bee visits were to M. cardinalis), but surprisingly also showed a high degree of individual specialization (95.2% of total plant transitions were between conspecifics). To determine M. cardinalis floral traits that discourage bee visitation, we then assessed foraging responses of individuals to M. cardinalis-like and M. lewisii-like floral models differing in color, orientation, reward, and combinations thereof. Across experiments, M. cardinalis-like trait combinations consistently produced a higher degree of flower avoidance behavior and individual specialization than expected based on bee responses to each trait in isolation. We then conducted a series of flower discrimination experiments to assess the ability of bees to utilize traits and trait combinations associated with each species. Relative to M. lewisii-like alternatives, M. cardinalis-like traits alone had a minimal effect on bee foraging proficiency but together increased the time bees spent searching for rewarding flowers from 1.49 to 2.65 s per visit. Collectively, our results show that M. cardinalis flowers impose foraging costs on bumble bees sufficient to discourage visitation and remarkably, generate such costs through synergistic color-orientation and color-reward trait interactions. Floral syndromes therefore represent complex adaptations to multiple pollinator groups, rather than simply the primary pollinator

Active involvement of learning disabilities service users in the development and delivery of a teaching session to pre-registration nurses : students' perspectives

A teaching session about service users' experiences of accessing and receiving health and social care was designed and delivered by service users to first year BSc Nursing students. The aim was to enhance students' knowledge, skills and confidence in caring for people with a learning disability. An evaluation research study was undertaking at one university in London into the perceived effectiveness of the teaching session, including students' perceptions of the extent to which the service users' teaching session was useful, the impact of the session, its benefits and challenges and the sustainability of teaching sessions delivered by service users. Data were collected through an online questionnaire. Quantitative analysis was undertaken of Likert-style questions and qualitative analysis was undertaken using the Framework Method. The session impacted on students' knowledge and understanding of people with a learning disability. Students reported that they felt more comfortable and confident interacting with people with a learning disability. In addition, they reflected on their feelings about caring for people with a learning disability

Effects of global change on insect pollinators: multiple drivers lead to novel communities

Global change drivers, in particular climate change, exotic species introduction, and habitat alteration, affect insect pollinators in numerous ways. In response, insect pollinators show shifts in range and phenology, interactions with plants and other taxa are altered, and in some cases pollination services have diminished. Recent studies show some pollinators are tracking climate change by moving latitudinally and elevationally, while others are not. Shifts in insect pollinator phenology generally keep pace with advances in flowering, although there are exceptions. Recent data demonstrate competition between exotic and native bees, along with rapid positive effects of exotic plant removal on pollinator richness. Genetic analyses tie bee fitness to habitat quality. Across drivers, novel communities are a common outcome that deserves more study

Observation of Exclusive Gamma Gamma Production in p pbar Collisions at sqrt{s}=1.96 TeV

We have observed exclusive \gamma\gamma production in proton-antiproton collisions at \sqrt{s}=1.96 TeV, using data from 1.11 \pm 0.07 fb^{-1} integrated luminosity taken by the Run II Collider Detector at Fermilab. We selected events with two electromagnetic showers, each with transverse energy E_T > 2.5 GeV and pseudorapidity |\eta| < 1.0, with no other particles detected in -7.4 < \eta < +7.4. The two showers have similar E_T and azimuthal angle separation \Delta\phi \sim \pi; 34 events have two charged particle tracks, consistent with the QED process p \bar{p} to p + e^+e^- + \bar{p} by two-photon exchange, while 43 events have no charged tracks. The number of these events that are exclusive \pi^0\pi^0 is consistent with zero and is < 15 at 95% C.L. The cross section for p\bar{p} to p+\gamma\gamma+\bar{p} with |\eta(\gamma)| < 1.0 and E_T(\gamma) > 2.5$ GeV is 2.48^{+0.40}_{-0.35}(stat)^{+0.40}_{-0.51}(syst) pb.Comment: 7 pages, 4 figure

Combined search for the standard model Higgs boson decaying to a bb pair using the full CDF data set

We combine the results of searches for the standard model Higgs boson based on the full CDF Run II data set obtained from sqrt(s) = 1.96 TeV p-pbar collisions at the Fermilab Tevatron corresponding to an integrated luminosity of 9.45/fb. The searches are conducted for Higgs bosons that are produced in association with a W or Z boson, have masses in the range 90-150 GeV/c^2, and decay into bb pairs. An excess of data is present that is inconsistent with the background prediction at the level of 2.5 standard deviations (the most significant local excess is 2.7 standard deviations).Comment: To be published in Phys. Rev. Lett (v2 contains minor updates based on comments from PRL

Measurement of the WZWZ Cross Section and Triple Gauge Couplings in ppˉp \bar p Collisions at s=1.96\sqrt{s} = 1.96 TeV

This Letter describes the current most precise measurement of the $WZ$ production cross section as well as limits on anomalous $WWZ$ couplings at a center-of-mass energy of 1.96 TeV in proton-antiproton collisions for the Collider Detector at Fermilab (CDF). $WZ$ candidates are reconstructed from decays containing three charged leptons and missing energy from a neutrino, where the charged leptons are either electrons or muons. Using data collected by the CDF II detector (7.1 fb$^{-1}$ of integrated luminosity), 63 candidate events are observed with the expected background contributing $8 \pm 1$ events. The measured total cross section $\sigma (p \bar p \to WZ) = 3.93_{-0.53}^{+0.60}(\text{stat})_{-0.46}^{+0.59}(\text{syst})$ pb is in good agreement with the standard model prediction of $3.50\pm 0.21$. The same sample is used to set limits on anomalous $WWZ$ couplings.Comment: Resubmission to PRD-RC after acceptance (27 July 2012