Countdown to 2010: Can we assess Ireland’s insect species diversity and loss?

peer-reviewedThe insects are the most diverse organisms on this planet and play an essential role in ecosystem functioning, yet we know very little about them. In light of the Convention on Biological Diversity, this paper summarises the known insect species numbers for Ireland and questions whether this is a true refl ection of our insect diversity. The total number of known species for Ireland is 11,422. Using species accumulation curves and a comparison with the British fauna, this study shows that the Irish list is incomplete and that the actual species number is much higher. However, even with a reasonable knowledge of the species in Ireland, insects are such speciose, small, and inconspicuous animals that it is diffi cult to assess species loss. It is impossible to know at one point in time the number of insect species in Ireland and, although it is useful to summarise the known number of species, it is essential that biodiversity indicators, such as the Red List Index, are developed

GWIPS-viz: 2018 update

The GWIPS-viz browser (http://gwips.ucc.ie/) is an on-line genome browser which is tailored for exploring ribosome profiling (Ribo-seq) data. Since its publication in 2014, GWIPS-viz provides Ribo-seq data for an additional 14 genomes bringing the current total to 23. The integration of new Ribo-seq data has been automated thereby increasing the number of available tracks to 1792, a 10-fold increase in the last three years. The increase is particularly substantial for data derived from human sources. Following user requests, we added the functionality to download these tracks in bigWig format. We also incorporated new types of data (e.g. TCP-seq) as well as auxiliary tracks from other sources that help with the interpretation of Ribo-seq data. Improvements in the visualization of the data have been carried out particularly for bacterial genomes where the Ribo-seq data are now shown in a strand specific manner. For higher eukaryotic datasets, we provide characteristics of individual datasets using the RUST program which includes the triplet periodicity, sequencing biases and relative inferred A-site dwell times. This information can be used for assessing the quality of Ribo-seq datasets. To improve the power of the signal, we aggregate Ribo-seq data from several studies into Global aggregate tracks for each genome

Metal ion binding to the amyloid beta monomer studied by native top-down FTICR mass spectrometry

Native top-down mass spectrometry is a fast, robust biophysical technique that can provide molecular-scale information on the interaction between proteins or peptides and ligands, including metal cations. Here we have analyzed complexes of the full-length amyloid β (1-42) monomer with a range of (patho)physiologically relevant metal cations using native Fourier transform ion cyclotron resonance mass spectrometry and three different fragmentation methods—collision-induced dissociation, electron capture dissociation, and infrared multiphoton dissociation—all yielding consistent results. Amyloid β is of particular interest as its oligomerization and aggregation are major events in the etiology of Alzheimer’s disease, and it is known that interactions between the peptide and bioavailable metal cations have the potential to significantly damage neurons. Those metals which exhibited the strongest binding to the peptide (Cu2+, Co2+, Ni2+) all shared a very similar binding region containing two of the histidine residues near the N-terminus (His6, His13). Notably, Fe3+ bound to the peptide only when stabilized toward hydrolysis, aggregation, and precipitation by a chelating ligand, binding in the region between Ser8 and Gly25. We also identified two additional binding regions near the flexible, hydrophobic C-terminus, where other metals (Mg2+, Ca2+, Mn2+, Na+, and K+) bound more weakly—one centered on Leu34, and one on Gly38. Unexpectedly, collisional activation of the complex formed between the peptide and [CoIII(NH3)6]3+ induced gas-phase reduction of the metal to CoII, allowing the peptide to fragment via radical-based dissociation pathways. This work demonstrates how native mass spectrometry can provide new insights into the interactions between amyloid β and metal cations

Atmospheric composition and climate impacts of a future hydrogen economy

Hydrogen is expected to play a key role in the global energy transition to net zero emissions in many scenarios. However, fugitive emissions of hydrogen into the atmosphere during its production, storage, distribution and use could reduce the climate benefit and also have implications for air quality. Here we explore the atmospheric composition and climate impacts of increases in atmospheric hydrogen abundance using the UKESM1 chemistry-climate model. We find that increases in hydrogen result in increases in methane, tropospheric ozone and stratospheric water vapour, resulting in a positive radiative forcing. However, some of the impacts of hydrogen leakage are partially offset by potential reductions in emissions of methane, carbon monoxide, nitrogen oxides and volatile organic compounds from the consumption of fossil fuels. We derive a new methodology for determining indirect Global Warming Potentials from steady-state simulations which is applicable to both shorter-lived species and those with intermediate and longer lifetimes, such as hydrogen. Using this methodology, we determine a 100-year Global Warming Potential for hydrogen of 12 &plusmn; 6. To maximise the benefit of hydrogen as an energy source, emissions associated with hydrogen leakage and emissions of the ozone precursor gases need to be minimised.</p

The Paranormal is (Still) Normal: The Sociological Implications of a Survey of Paranormal Experiences in Great Britain

Historically, there has been limited sociological interest in the paranormal and no systematic study of reported paranormal experiences. There are also few medium-to-large-scale survey results with nationally representative populations focusing on paranormal experiences. This paper provides details of an exploratory survey conducted in 2009 with a nationally representative sample of 4,096 adults aged 16 years and over across Great Britain. Our findings show that 37% of British adults report at least one paranormal experience and that women, those who are middle-aged or individuals resident in the South West are more likely to report such experiences. These results establish incidence levels of reported paranormal experiences in contemporary Britain. We argue also that they merit a more sustained sociological consideration of the paranormal. In this respect we renew and update the robust justification and call for serious research positioning the paranormal as a social phenomenon, originally proposed well over thirty years ago by Greeley (1975)

A feasibility study of pre-sleep audio and visual alpha brain entrainment for people with chronic pain and sleep disturbance

Introduction: Chronic pain and sleep disturbance are bi-directionally related. Cortical electrical activity in the alpha frequency band can be enhanced with sensory stimulation via the phenomenon of entrainment, and may reduce pain perception. A smartphone based programme which delivers 10Hz stimulation through flickering light or binaural beats was developed for use at night, pre-sleep, with the aim of improving night time pain and sleep and thereby subsequent pain and related daytime symptoms. The aim of this study was to assess the feasibility and give an indication of effect of this programme for individuals with chronic pain and sleep disturbance. Materials and methods: In a non-controlled feasibility study participants used audio or visual alpha entrainment for 30 minutes pre-sleep each night for 4 weeks, following a 1 week baseline period. The study was pre-registered at ClinicalTrials.gov with the ID NCT04176861. Results: 28 participants (79% female, mean age 45 years) completed the study with high levels of data completeness (86%) and intervention adherence (92%). Daily sleep diaries showed an increase compared to baseline in total sleep time of 29 minutes (p=0.0033), reduction in sleep onset latency of 13 minutes (p=0.0043), and increase in sleep efficiency of 4.7% (p=0.0009). Daily 0-10 numerical rating scale of average pain at night improved by 0.5 points compared to baseline (p=0.027). Standardised questionnaires showed significant within-participant improvements in sleep quality (change in median Global PSQI from 16 to 12.5), pain interference (change in median BPI Pain Interference from 7.5 to 6.8), fatigue (change in median MFI total score from 82.5 to 77), and depression and anxiety (change in median HADS depression score from 12 to 10.5 and anxiety from 13.5 to 11). Discussion: Pre-sleep use of a smartphone programme for alpha entrainment by audio or visual stimulation was feasible for individuals with chronic pain and sleep disturbance. The effect on symptoms requires further exploration in controlled studies

A One Health overview, facilitating advances in comparative medicine and translational research.

Table of contentsA1 One health advances and successes in comparative medicine and translational researchCheryl StroudA2 Dendritic cell-targeted gorilla adenoviral vector for cancer vaccination for canine melanomaIgor Dmitriev, Elena Kashentseva, Jeffrey N. Bryan, David T. CurielA3 Viroimmunotherapy for malignant melanoma in the companion dog modelJeffrey N. Bryan, David Curiel, Igor Dmitriev, Elena Kashentseva, Hans Rindt, Carol Reinero, Carolyn J. HenryA4 Of mice and men (and dogs!): development of a commercially licensed xenogeneic DNA vaccine for companion animals with malignant melanomaPhilip J. BergmanA5 Successful immunotherapy with a recombinant HER2-expressing Listeria monocytogenes in dogs with spontaneous osteosarcoma paves the way for advances in pediatric osteosarcomaNicola J. Mason, Josephine S. Gnanandarajah, Julie B. Engiles, Falon Gray, Danielle Laughlin, Anita Gaurnier-Hausser, Anu Wallecha, Margie Huebner, Yvonne PatersonA6 Human clinical development of ADXS-HER2Daniel O'ConnorA7 Leveraging use of data for both human and veterinary benefitLaura S. TremlA8 Biologic replacement of the knee: innovations and early clinical resultsJames P. StannardA9 Mizzou BioJoint Center: a translational success storyJames L. CookA10 University and industry translational partnership: from the lab to commercializationMarc JacobsA11 Beyond docking: an evolutionarily guided OneHealth approach to drug discoveryGerald J. Wyckoff, Lee Likins, Ubadah Sabbagh, Andrew SkaffA12 Challenges and opportunities for data applications in animal health: from precision medicine to precision husbandryAmado S. GuloyA13 A cloud-based programmable platform for healthHarlen D. HaysA14 Comparative oncology: One Health in actionAmy K. LeBlancA15 Companion animal diseases bridge the translational gap for human neurodegenerative diseaseJoan R. Coates, Martin L. Katz, Leslie A. Lyons, Gayle C. Johnson, Gary S. Johnson, Dennis P. O'BrienA16 Duchenne muscular dystrophy gene therapyDongsheng DuanA17 Polycystic kidney disease: cellular mechanisms to emerging therapiesJames P. CalvetA18 The domestic cat as a large animal model for polycystic kidney diseaseLeslie A. Lyons, Barbara GandolfiA19 The support of basic and clinical research by the Polycystic Kidney Disease FoundationDavid A. BaronA20 Using naturally occurring large animal models of human disease to enable clinical translation: treatment of arthritis using autologous stromal vascular fraction in dogsMark L. WeissA21 Regulatory requirements regarding clinical use of human cells, tissues, and tissue-based productsDebra A. WebsterA22 Regenerative medicine approaches to Type 1 diabetes treatmentFrancis N. KaranuA23 The zoobiquity of canine diabetes mellitus, man's best friend is a friend indeed-islet transplantationEdward J. RobbA24 One Medicine: a development model for cellular therapy of diabetesRobert J. Harman

The REFLECT Statement: Methods and Processes of Creating Reporting Guidelines for Randomized Controlled Trials for Livestock and Food Safety by Modifying the CONSORT Statement

The conduct of randomized controlled trials in livestock with production, health and food-safety outcomes presents unique challenges that may not be adequately reported in trial reports. The objective of this project was to modify the CONSORT (Consolidated Standards of Reporting Trials) statement to reflect the unique aspects of reporting these livestock trials. A 2-day consensus meeting was held on 18–19 November 2008 in Chicago, IL, USA, to achieve the objective. Prior to the meeting, a Web-based survey was conducted to identify issues for discussion. The 24 attendees were biostatisticians, epidemiologists, food-safety researchers, livestock-production specialists, journal editors, assistant editors and associate editors. Prior to the meeting, the attendees completed a Web-based survey indicating which CONSORT statement items may need to be modified to address unique issues for livestock trials. The consensus meeting resulted in the production of the REFLECT (Reporting Guidelines for Randomized Control Trials) statement for livestock and food safety and 22-item checklist. Fourteen items were modified from the CONSORT checklist and an additional sub-item was proposed to address challenge trials. The REFLECT statement proposes new terminology, more consistent with common usage in livestock production, to describe study subjects. Evidence was not always available to support modification to or inclusion of an item. The use of the REFLECT statement, which addresses issues unique to livestock trials, should improve the quality of reporting and design for trials reporting production, health and food-safety outcomes

BCMA Is Essential for the Survival of Long-lived Bone Marrow Plasma Cells

Long-lived humoral immunity is manifested by the ability of bone marrow plasma cells (PCs) to survive for extended periods of time. Recent studies have underscored the importance of BLyS and APRIL as factors that can support the survival of B lineage lymphocytes. We show that BLyS can sustain PC survival in vitro, and this survival can be further enhanced by interleukin 6. Selective up-regulation of Mcl-1 in PCs by BLyS suggests that this α-apoptotic gene product may play an important role in PC survival. Blockade of BLyS, via transmembrane activator and cyclophilin ligand interactor–immunoglobulin treatment, inhibited PC survival in vitro and in vivo. Heightened expression of B cell maturation antigen (BCMA), and lowered expression of transmembrane activator and cyclophilin ligand interactor and BAFF receptor in PCs relative to resting B cells suggests a vital role of BCMA in PC survival. Affirmation of the importance of BCMA in PC survival was provided by studies in BCMA−/− mice in which the survival of long-lived bone marrow PCs was impaired compared with wild-type controls. These findings offer new insights into the molecular basis for the long-term survival of PCs