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Badger territoriality maintained despite disturbance of major road construction
Get PDFPublication history: Accepted - 19 August 2021; Published - 3 September 2021.Road ecology has traditionally focused on the impact of in-situ and functional roads on wildlife.
However, road construction also poses a major, yet understudied, threat and the implications
for key aspects of animal behaviour are unknown. Badgers (Meles meles) have
been implicated in the transmission of tuberculosis to cattle. There are concerns that environmental
disturbances, including major road construction, can disrupt badger territoriality,
promoting the spread of the disease to cattle. To address these knowledge gaps the ranging
behaviour of a medium-density Irish badger population was monitored using GPS-tracking
collars before, during, and after a major road realignment project that bisected the study
area. We estimated badgers’ home range sizes, nightly distances travelled, and the distance
and frequency of extra-territorial excursions during each phase of the study and quantified
any changes to these parameters. We show that road construction had a very limited
effect on ranging behaviour. A small increase in nightly distance during road construction
did not translate into an increase in home range size, nor an increase in the distance or frequency
of extra-territorial excursions during road construction. In addition, suitable mitigation
measures to prevent badger deaths appeared to ensure that normal patterns of ranging
behaviour continued once the new road was in place. We recommend that continuous badger-
proof fencing be placed along the entire length of new major roads, in combination with
appropriately sited underpasses. Our analysis supports the view that road construction did
not cause badgers to change their ranging behaviour in ways likely to increase the spread of
tuberculosis.AG was supported by a PhD scholarship
provided by the Department of Agriculture, Food
and the Marine, Ireland. This project was
conceived, carried out and funded by the
Department of Agriculture, Food and the Marine,
Ireland, and the National Parks and Wildlife
Service, Ireland
Optimism and pasture access in dairy cows
Get PDFPublication history: Accepted - 16 February 2021; Published online - 1 March 2021Allowing dairy cattle to access pasture can promote natural behaviour and improve their health. However, the psychological benefits are poorly understood. We compared a cognitive indicator of emotion in cattle either with or without pasture access. In a crossover experiment, 29 Holstein–Friesian dairy cows had 18 days of overnight pasture access and 18 days of full-time indoor housing. To assess emotional wellbeing, we tested cows on a spatial judgement bias task. Subjects learnt to approach a rewarded bucket location, but not approach another, unrewarded bucket location. We then presented cows with three “probe” buckets intermediate between the trained locations. Approaching the probes reflected an expectation of reward under ambiguity—an “optimistic” judgement bias, suggesting positive emotional states. We analysed the data using linear mixed-effects models. There were no treatment differences in latency to approach the probe buckets, but cows approached the known rewarded bucket slower when they had pasture access than when they were indoors full-time. Our results indicate that, compared to cattle housed indoors, cattle with pasture access display less anticipatory behaviour towards a known reward. This reduced reward anticipation suggests that pasture is a more rewarding environment, which may induce more positive emotional states than full-time housing.A.C. was supported by a postgraduate studentship from Northern Ireland’s Department for the Economy. This research is part of a project that has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme, Grant Number 851145
An economic analysis of anaerobic digestate fuel pellet production: can digestate fuel pellets add value to existing operations?
Get PDFPublication history: Accepted - 9 April 2021; Published online - 16 April 2021.Anaerobic digestion provides renewable energy through waste valorisation, but the digestate by-product is
underutilised and presents a risk to water quality. Mechanical separation partitions phosphorous into the solid
fraction and further processing into a fuel pellet can provide an additional source of energy and revenue. Previous
economic analyses looked only at aspects of the system (e.g. operational costs solely) and the system requires
further investigation to determine viability. In this paper, an economic assessment of digestate fuel pellet production
at farm-scale anaerobic digestion plants was carried out. The significance of this work is to provide a
comprehensive assessment of the energy, phosphorous, and economic balances involved in digestate fuel pellet
production at existing anaerobic digestion plants. The aim of this paper is to determine the financial viability of
digestate fuel pellet production with objectives to compare two mechanical separation technologies: screw press,
and decanting centrifuge. Economies of scale hold true for digestate pellet production and the available digestate
in typical UK farm-based anaerobic digestion plants ( 500 kWe) is insufficient for profitability, with pellet
production costing from £176/t (decanting centrifuge) to £215/t (screw press), compared to a typical wood pellet
sale price of £185/t. Increasing digestate quantity by collaboration of plant operators can reduce the cost of pellet
production to between £95/t and £121/t, improving financial viability and increasing the profit per head of cattle
by 9–20% on a typical dairy farm utilising anaerobic digestion. The system has potential to aid rural development
while also protecting the environment and contributing to the diversification of energy supply.This project was supported by The Bryden Centre. The Bryden Centre
project is supported by the European Union’s INTERREG VA Programme,
managed by the Special EU Programmes Body (SEUPB). The views and
opinions expressed in this paper do not necessarily reflect those of the
European Commission or the Special EU Programmes Body (SEUPB). The
work was also supported by Queen’s University Belfast and the Agri-Food
and Biosciences Institute in Northern Ireland
Current Trends and Challenges for Rapid SMART Diagnostics at Point-of-Site Testing for Marine Toxins
Get PDFPublication history: Accepted - 24 March 2021; Published - 3 April 2021.In the past twenty years marine biotoxin analysis in routine regulatory monitoring has
advanced significantly in Europe (EU) and other regions from the use of the mouse bioassay (MBA)
towards the high-end analytical techniques such as high-performance liquid chromatography (HPLC)
with tandem mass spectrometry (MS). Previously, acceptance of these advanced methods, in progressing
away from the MBA, was hindered by a lack of commercial certified analytical standards for
method development and validation. This has now been addressed whereby the availability of a
wide range of analytical standards from several companies in the EU, North America and Asia has
enhanced the development and validation of methods to the required regulatory standards. However,
the cost of the high-end analytical equipment, lengthy procedures and the need for qualified personnel
to perform analysis can still be a challenge for routine monitoring laboratories. In developing
regions, aquaculture production is increasing and alternative inexpensive Sensitive, Measurable,
Accurate and Real-Time (SMART) rapid point-of-site testing (POST) methods suitable for novice end
users that can be validated and internationally accepted remain an objective for both regulators and
the industry. The range of commercial testing kits on the market for marine toxin analysis remains
limited and even more so those meeting the requirements for use in regulatory control. Individual
assays include enzyme-linked immunosorbent assays (ELISA) and lateral flow membrane-based
immunoassays (LFIA) for EU-regulated toxins, such as okadaic acid (OA) and dinophysistoxins
(DTXs), saxitoxin (STX) and its analogues and domoic acid (DA) in the form of three separate tests
offering varying costs and benefits for the industry. It can be observed from the literature that not
only are developments and improvements ongoing for these assays, but there are also novel assays
being developed using upcoming state-of-the-art biosensor technology. This review focuses on both
currently available methods and recent advances in innovative methods for marine biotoxin testing
and the end-user practicalities that need to be observed. Furthermore, it highlights trends that
are influencing assay developments such as multiplexing capabilities and rapid POST, indicating
potential detection methods that will shape the future market.This research was funded by the UK BBSRC project “Safe and Sustainable Shellfish:
Introducing local testing and management solutions” (reference BB/S004211/1)
Determination of maintenance energy requirement and responses of dry ewes to dietary inclusion of lucerne versus concentrate meal
Get PDFPublication history: Accepted - 2 February 2021; Published online - 23 May 2021An accurate value for metabolizable energy (ME) requirement for maintenance (MEm) is essential to enable sheep husbandry practice to reach its potential. The objectives of the study were to use calorimetry chamber data of dry ewes (Hu × thin-tail Han F1 crossbred) to develop updated MEm, examine effects of substituting concentrate feed with lucerne hay on energy partitioning, and explore the relationships between energy utilization and fasting heat production (FHP). Data were collected from three experiments. In Exps. 1, 2a and 2b, lucerne hay was used to replace concentrates in three levels (0:40%, 15:25% and 30:10%), with diets containing 60% maize stover (Exp. 1), fresh rye forage (Exp. 2a) or dry rye forage (Exp. 2b). Within each experiment, diets were isoenergetic (digestible energy, DE) and isonitrogenous. Exp. 3 aimed at evaluating effects of three BW levels on nutrient utilization of dry ewes offered diets containing 60% maize stover, 15% lucerne hay and 25% concentrates. Energy metabolism data were measured using the respiration calorimeter chamber technique in all three experiments, followed by the measurement of FHP in Exps. 1, 2b and 3. The MEm derived from the linear regression between energy balance (EB) and ME intake was 0.440 MJ/kg BW0.75. The average FHP was 0.326 MJ/kg BW0.75. The fasting metabolism, net energy requirement for maintenance (NEm) and MEm were estimated to be 0.336, 0.359 and 0.511 MJ/kg BW0.75, respectively, through adjustment of FHP using fasting urinary energy output, activity allowance and efficiency of ME use for maintenance. The FHP was negatively correlated to EB/metabolic BW, ME/gross energy (GE), ME/DE, EB/GE intake and EB/ME intake, while positively correlated to HP/GE intake, HP/ME intake and CH4-E/GE intake. Compared to zero lucerne hay diet, the 15% lucerne hay intake decreased HP (MJ/d), and had no negative effects on EB (MJ/d) or energy utilization efficiencies. The results indicate that nutrient requirement standards currently used across the world are likely to underestimate MEm for dry ewes, and the selection of low FHP ewes for breeding has the potential to improve sheep production efficiency.This study was funded by the Strategic Priority Research Program of the Chinese Academy of Sciences (XDA2010010203), Gansu Provincial Science and Technology Support for Returning Grazing to Grass (18-0284), Gansu Provincial Key Project of Scientific and Technical Supporting Programs (18ZD2FA009), and the Program for Innovative Research Team of Chinese Ministry of Education (IRT_17R250)
Effect of two vs. three year harvest intervals on yields of Short Rotation Coppice (SRC) willow
No full textPublished online: Accepted - 14 November 2021; Published online - 24 November 2021Five genotypes of Short Rotation Coppice (SRC) willow: ‘Beagle’ ((S. viminalis ‘L810203’ x viminalis ‘L81102’) x ‘Astrid’ x male parent unknown), ‘Olof’ (S. viminalis ‘Bowles Hybrid’) x ((S. schwerinii ‘L79069’) x ((S. viminalis ‘L78195’ x viminalis ‘L78101’) ‘Orm’) ‘Bjorn’). ‘Ashton Stott’ (S.viminalis ‘Bowles Hybrid’) x S.dasyclados ‘Korso’, ‘Tora’ (S. schwerinii ‘L79069’) x ((S. viminalis ‘L78195’ x viminalis ‘L78101’) ‘Orm’), and ‘Torhild’ ((S. schwerinii ‘79,069’) x ((S. viminalis) x S. viminalis ‘L78195’ x viminalis ‘L78101’)) ‘Orm’) ‘Tora’) x ((S.viminalis ‘L78195’ x viminalis ‘L78101’) ‘Orm’) were grown in large mono-plots or within plots of intimate mixtures. Over a seven year period half of the plots were harvested on a two-year harvest cycle (three harvests) and the rest on a three-year harvest cycle (two harvests). At the end of this 7 year trial period there were no significant differences between total dry weights or stool survival, irrespective of harvest interval. With the realisation of the importance of this finding for more regular crop management practices, the experiment was continued for a further six years allowing for a further round of two and three year harvests. Results suggest that there ultimately are yield penalties, although these may be minimised by careful and appropriate clonal selection.This work was funded by the Department of Agriculture, Environment and Rural Affairs for Northern Ireland (DAERA)
Novel Insights into the Role of Probiotics in Respiratory Infections, Allergies, Cancer, and Neurological Abnormalities
Get PDFPublication history: Accepted - 31 August 2021; Published online - 2 September 2021.In recent years, probiotics have attracted public attention and transformed the social perception of microorganisms, convening a beneficial role/state on human health. With aging, the immune system, body physiology, and intestinal microbiota tend to change unfavorably, resulting in many chronic conditions. The immune-mediated disorders can be linked to intestinal dysbiosis, consequently leading to immune dysfunctions and a cluster of conditions such as asthma, autoimmune diseases, eczema, and various allergies. Probiotic bacteria such as Lactobacillus and Bifidobacterium species are considered probiotic species that have a great immunomodulatory and anti-allergic effect. Moreover, recent scientific and clinical data illustrate that probiotics can regulate the immune system, exert anti-viral and anti-tumoral activity, and shields the host against oxidative stress. Additionally, microbiota programming by probiotic bacteria can reduce and prevent the symptoms of respiratory infections and ameliorate the neurological status in humans. This review describes the most recent clinical findings, including safe probiotic therapies aiming to medicate respiratory infections, allergies, cancer, and neurological disorders due to their physiological interconnection. Subsequently, we will describe the major biological mechanism by which probiotic bacteriotherapy expresses its anti-viral, anti-allergic, anticancer, and neuro-stimulatory effectsThis work was supported by Environtech grant awarded to NC
A rapid fungal DNA extraction method suitable for PCR screening fungal mutants, infected plant tissue and spore trap samples
Get PDFPublication history: Accepted - 19 November 2021; Published online - 26 November 2021.Current DNA extraction methods from filamentous fungi take from an hour to a full day. These methods require
buffers and tools for grinding fungal tissues. Although commercial extraction kits can reduce the amount of time
spent preparing and extracting genomic DNA from fungal samples, these can be expensive.
Here we describe a quick and inexpensive sonication technique to extract genomic DNA from filamentous
fungi without buffer which can be used to perform PCR in under an hour. DNA was extracted from Zymoseptoria
tritici, Fusarium graminearum and Botrytis cinerea in vitro cultures, Z. tritici asexual fruiting bodies and directly
from spore trap tapes.Science Foundation Ireland (SFI) 16/SPP/3296 and 15/CDA/3451
Combining Ecosystem and Single-Species Modeling to Provide Ecosystem-Based Fisheries Management Advice Within Current Management Systems
Get PDFPubication history: Accepted - 7 December 2020; Published online - 8 January 2021Although many countries have formally committed to Ecosystem-Based Fisheries Management (EBFM), actual progress toward these goals has been slow. This paper presents two independent case studies that have combined strategic advice from ecosystem modeling with the tactical advice of single-species assessment models to provide practical ecosystem-based management advice. With this approach, stock status, reference points, and initial target F are computed from a single-species model, then an ecosystem model rescales the target F according to ecosystem indicators without crossing pre-calculated single-species precautionary limits. Finally, the single-species model computes the quota advice from the rescaled target F, termed here Feco. Such a methodology incorporates both the detailed population reconstructions of the single-species model and the broader ecosystem perspective from ecosystem-based modeling, and fits into existing management schemes. The advocated method has arisen from independent work on EBFM in two international fisheries management systems: (1) Atlantic menhaden in the United States and (2) the multi species fisheries of the Irish Sea, in the Celtic Seas ecoregion. In the Atlantic menhaden example, the objective was to develop ecological reference points (ERPs) that account for the effect of menhaden harvest on predator populations and the tradeoffs associated with forage fish management. In the Irish Sea, the objective was to account for ecosystem variability when setting quotas for the individual target species. These two exercises were aimed at different management needs, but both arrived at a process of adjusting the target F used within the current single-species management. Although the approach has limitations, it represents a practical step toward EBFM, which can be adapted to a range of ecosystem objectives and applied within current management systems.The Atlantic menhaden work was supported by National Oceanic and Atmospheric Administration Award No. NA15NMF4740069 and Lenfest Ocean Program grants nos. 00025536 and 00032187, and thanks all of the members of the ASMFC Menhaden Technical Committee and the ERP WG for their critical contributions to model development and helpful discussions. We acknowledge the members of the ICES Benchmark Workshop WKIrish for their participation and collaboration, and the NWWAC and BIM for facilitating the meetings. The EwE modeling work was carried out with the support of the Marine Institute and funded under the Marine Research Sub-programme by the Irish Government (Grant-Aid Agreement No. CF/16/08). DP was supported by the Science Foundation Ireland (www.sfi.ie) Investigator Programme (grant no. 14/IA/2549), and DR by Project FishKOSM funded by the Department of Agriculture, Food and the Marine’s Competitive Research Funding programmes. DH acknowledges support from the Institute of Marine Research strategic project Reduced Uncertainty in Stock Assessment (REDUS). Open access funding was provided by the Institute of Marine Research, Norway
Elucidation of the Host Bronchial Lymph Node miRNA Transcriptome Response to Bovine Respiratory Syncytial Virus
Get PDFPublication history: Accepted - 19 March 2021; Published - 22 April 2021.Bovine respiratory disease (BRD) causes substantial morbidity and mortality, affecting
cattle of all ages. One of the main causes of BRD is an initial inflammatory response
to bovine respiratory syncytial virus (BRSV). MicroRNAs are novel and emerging noncoding
small RNAs that regulate many biological processes and are implicated in
various inflammatory diseases. The objective of the present study was to elucidate
the changes in the bovine bronchial lymph node miRNA transcriptome in response
to BRSV following an experimental viral challenge. Holstein-Friesian calves were either
administered a challenge dose of BRSV (103:5 TCID50/ml 15 ml) (n = 12) or were
mock inoculated with sterile phosphate buffered saline (n = 6). Daily scoring of clinical
signs was performed and calves were euthanized at day 7 post-challenge. Bronchial
lymph nodes were collected for subsequent RNA extraction and sequencing (75 bp).
Read counts for known miRNAs were generated using the miRDeep2 package using
the UMD3.1 reference genome and the bovine mature miRNA sequences from the
miRBase database (release 22). EdgeR was used for differential expression analysis
and Targetscan was used to identify target genes for the differentially expressed (DE)
miRNAs. Target genes were examined for enriched pathways and gene ontologies using
Ingenuity Pathway Analysis (Qiagen). Multi-dimensional scaling (MDS) based on miRNA
gene expression changes, revealed a clearly defined separation between the BRSV
challenged and control calves, although the clinical manifestation of disease was only
mild. One hundred and nineteen DE miRNAs (P 1.5)
were detected between the BRSV challenged and control calves. The DE miRNAs
were predicted to target 465 genes which were previously found to be DE in bronchial
lymph node tissue, between these BRSV challenged and control calves. Of the DE
predicted target genes, 455 had fold changes that were inverse to the corresponding
DE miRNAs. There were eight enriched pathways among the DE predicted target genes
with inverse fold changes to their corresponding DE miRNA including: granulocyte
and agranulocyte adhesion and diapedesis, interferon signalling and role of pathogen recognition receptors in recognition of bacteria and viruses. Functions predicted to be
increased included: T cell response, apoptosis of leukocytes, immune response of cells
and stimulation of cells. Pathogen recognition and proliferation of cytotoxic T cells are
vital for the recognition of the virus and its subsequent elimination.This project was funded by the Irish Department of Agriculture
and the Department of Agriculture, Environment and Rural
Affairs, Northern Ireland, as part of the United States-Ireland
R&D partnership call (RMIS_0033 Project 16/RD/US-ROI/11).
JT and JK were supported by grant number 2017-67015-26760
from the United States Department for Agriculture National
Institute for Food and Agriculture