Digitized Cathodoluminescence Imaging of Minerals

Digital imaging with cathodoluminescence (CL) capability, provides an additional, quantitative imaging perspective. While CL images can be useful by themselves, most microbeam instruments allow simultaneous acquisition of other signals including backscattered electron (BSE), secondary electron (SE), and X-ray images providing a powerful set of data for interpretation. Digital panchromatic images allow the use of standard and advanced image processing now available on laboratory computers to enhance single images or provide a means of combining information from two or more images. Other advantages of digital CL images include: 1) selective scan rates to avoid image distortion; 2) adjustable dwell times at any point to collect sufficient light due to weak CL; 3) calibrated image scales allowing relocation of features for additional study. Many minerals and synthetic phases show CL and these images often reveal textures either difficult or impossible to observe with other signals. Examples of digital CL images are presented for: 1) diamond, where complex internal textures are revealed including the presence of features possibly corresponding to giant platelets; 2) forsterite from the Allende meteorite where CL reveals complex zoning within single grains the intensity of which correlates with the Al and Ti; 3) terrestrial carbonate showing intricate banding, the intensity of which can be compared with X-ray images; 4) meteoritic melilite where the CL reveals complex zoning and intensity variation within minor included spinel phases

Assessing the Potential Effects of Fungicides on Nontarget Gut Fungi (Trichomycetes) and Their Associated Larval Black Fly Hosts

Fungicides are moderately hydrophobic and have been detected in water and sediment, particularly in agricultural watersheds, but typically are not included in routine water quality monitoring efforts. This is despite their widespread use and frequent application to combat fungal pathogens. Although the efficacy of these compounds on fungal pathogens is well documented, little is known about their effects on nontarget fungi. This pilot study, a field survey in southwestern Idaho from April to December 2010 on four streams with varying pesticide inputs (two agricultural and two reference sites), was conducted to assess nontarget impact of fungicides on gut fungi, or trichomycetes. Tissues of larval black flies (Diptera: Simuliidae), hosts of gut fungi, were analyzed for pesticide accumulation. Fungicides were detected in hosts from streams within agricultural watersheds but were not detected in hosts from reference streams. Gut fungi from agricultural sites exhibited decreased percent infestation, density and sporulation within the gut, and black fly tissues had elevated pesticide concentrations. Differences observed between the sites demonstrate a potential effect on this symbiotic system. Future research is needed to parse out the details of the complex biotic and abiotic relationships; however, these preliminary results indicate that impacts to nontarget organisms could have far-reaching consequences within aquatic ecosystems

Local CpG density affects the trajectory and variance of age-associated DNA methylation changes

Acknowledgements We thank Riccardo Marioni, Chris Haley, Ailith Ewing, David Porteous, Chris Ponting, Rob Illingworth, Tamir Chandra, Sara Hagg, Yunzhang Wang, Chantriolnt-Andreas Kapourani, Nick Gilbert, Hannes Becher and members of the Sproul lab for helpful discussions about the study and the manuscript. This work has made use of the resources provided by the University of Edinburgh digital research services and the MRC IGC compute cluster. We are grateful to all the families who took part in the Generation Scotland study along with the general practitioners and the Scottish School of Primary Care for their help in recruiting them, and the entire Generation Scotland team, which includes interviewers, computer and laboratory technicians, clerical workers, research scientists, volunteers, managers, receptionists, healthcare assistants, and nurses. Peer review information Anahita Bishop and Kevin Pang were the primary editors of this article and managed its editorial process and peer review in collaboration with the rest of the editorial team. Review history The review history is available as Additional file 3. Funding DS is a Cancer Research UK Career Development fellow (reference C47648/A20837), and work in his laboratory is also supported by an MRC university grant to the MRC Human Genetics Unit. LK is a cross-disciplinary postdoctoral fellow supported by funding from the University of Edinburgh and Medical Research Council (MC_UU_00009/2). S.R.C. and I.J.D. were supported by a National Institutes of Health (NIH) research grant R01AG054628, and S.R.C is supported by a Sir Henry Dale Fellowship jointly funded by the Wellcome Trust and the Royal Society (221890/Z/20/Z). AMM is supported by the Wellcome Trust (104036/Z/14/Z, 216767/Z/19/Z, 220857/Z/20/Z) and UKRI MRC (MC_PC_17209, MR/S035818/1). PMV acknowledges support from the Australian National Health and Medical Research Council (1113400) and the Australian Research Council (FL180100072). DMH is supported by a Sir Henry Wellcome Postdoctoral Fellowship (Reference 213674/Z/18/Z). We thank the LBC1936 participants and team members who contributed to the study. Further study information can be found at https://www.ed.ac.uk/lothian-birth-cohorts. The LBC1936 is supported by a jointly funded grant from the BBSRC and ESRC (BB/W008793/1), and also by Age UK (Disconnected Mind project), the Medical Research Council (G0701120, G1001245, MR/M013111/1, MR/R024065/1), and the University of Edinburgh. Genotyping of LBC1936 was funded by the BBSRC (BB/F019394/1), and methylation typing of LBC1936 was supported by Centre for Cognitive Ageing and Cognitive Epidemiology (Pilot Fund award), Age UK, The Wellcome Trust Institutional Strategic Support Fund, The University of Edinburgh, and The University of Queensland. Work on Generation Scotland was supported by a Wellcome Strategic Award “STratifying Resilience and Depression Longitudinally” (STRADL; 104036/Z/14/Z) to AMM, KLE, and others, and an MRC Mental Health Data Pathfinder Grant (MC_PC_17209) to AMM. Generation Scotland received core support from the Chief Scientist Office of the Scottish Government Health Directorates (CZD/16/6) and the Scottish Funding Council (HR03006). DNA methylation profiling and analysis of the GS:SFHS samples was supported by Wellcome Investigator Award 220857/Z/20/Z and Grant 104036/Z/14/Z (PI: AM McIntosh) and through funding from NARSAD (Ref: 27404; awardee: Dr DM Howard) and the Royal College of Physicians of Edinburgh (Sim Fellowship; Awardee: Dr HC Whalley).Peer reviewedPublisher PD

Marine bacterial, archaeal and protistan association networks reveal ecological linkages

Microbes have central roles in ocean food webs and global biogeochemical processes, yet specific ecological relationships among these taxa are largely unknown. This is in part due to the dilute, microscopic nature of the planktonic microbial community, which prevents direct observation of their interactions. Here, we use a holistic (that is, microbial system-wide) approach to investigate time-dependent variations among taxa from all three domains of life in a marine microbial community. We investigated the community composition of bacteria, archaea and protists through cultivation-independent methods, along with total bacterial and viral abundance, and physico-chemical observations. Samples and observations were collected monthly over 3 years at a well-described ocean time-series site of southern California. To find associations among these organisms, we calculated time-dependent rank correlations (that is, local similarity correlations) among relative abundances of bacteria, archaea, protists, total abundance of bacteria and viruses and physico-chemical parameters. We used a network generated from these statistical correlations to visualize and identify time-dependent associations among ecologically important taxa, for example, the SAR11 cluster, stramenopiles, alveolates, cyanobacteria and ammonia-oxidizing archaea. Negative correlations, perhaps suggesting competition or predation, were also common. The analysis revealed a progression of microbial communities through time, and also a group of unknown eukaryotes that were highly correlated with dinoflagellates, indicating possible symbioses or parasitism. Possible ‘keystone’ species were evident. The network has statistical features similar to previously described ecological networks, and in network parlance has non-random, small world properties (that is, highly interconnected nodes). This approach provides new insights into the natural history of microbes

Discoveries from a Near-infrared Proper Motion Survey using Multi-epoch 2MASS Data

We have conducted a 4030-square-deg near-infrared proper motion survey using multi-epoch data from the Two Micron All-Sky Survey (2MASS). We find 2778 proper motion candidates, 647 of which are not listed in SIMBAD. After comparison to DSS images, we find that 107 of our proper motion candidates lack counterparts at B-, R-, and I-bands and are thus 2MASS-only detections. We present results of spectroscopic follow-up of 188 targets that include the infrared-only sources along with selected optical-counterpart sources with faint reduced proper motions or interesting colors. We also establish a set of near-infrared spectroscopic standards with which to anchor near-infrared classifications for our objects. Among the discoveries are six young field brown dwarfs, five "red L" dwarfs, three L-type subdwarfs, twelve M-type subdwarfs, eight "blue L" dwarfs, and several T dwarfs. We further refine the definitions of these exotic classes to aid future identification of similar objects. We examine their kinematics and find that both the "blue L" and "red L" dwarfs appear to be drawn from a relatively old population. This survey provides a glimpse of the kinds of research that will be possible through time-domain infrared projects such as the UKIDSS Large Area Survey, various VISTA surveys, and WISE, and also through z- or y-band enabled, multi-epoch surveys such as Pan-STARRS and LSST.Comment: To appear in the September 2010 issue of The Astrophysical Journal, Supplement Serie

Associations of negative affective biases and depressive symptoms in a community-based sample

Acknowledgements. We thank professor Jonathan Roiser (University College London, UK) and professor emeritus Ian Deary (University of Edinburgh, UK) for their input on task selection and statistical analysis. We also acknowledge all researchers who have contributed to the collection of data for the current study. Most importantly, we would like to thank all participants of Generation Scotland, and particularly those of the STRADL subcohort, for their participation in the research. Financial support. Stratifying Resilience and Depression Longitudinally is supported by the Wellcome Trust through a Strategic Award (Grant No. 104036/Z/14/Z) and through an Investigator Award (Grant No. 220857/Z/ 20/Z). The Chief Scientist Office of the Scottish Government Health Department (Grant No. CZD/16/6), Scottish Funding Council (Grant No. HR03006) and Wellcome Trust (Grant No. 216767/Z/19/Z) provided core support for Generation Scotland.Peer reviewedPublisher PD