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Gene co-expression networks contributing to variation in residual feed intake in bovine hepatic tissue.
No full textGene co-expression network analyses were performed on hepatic transcriptome data of two breed types
(Charolais (CH) and Holstein-Friesian (HF)), divergent for feed efficiency status through measurement
of residual feed intake (RFI). The relationship between co-expressed genes and RFI was further assessed
through correlation of co-expression networks with trait data including RFI, average daily gain (ADG) and
dry matter intake (DMI). Across both breeds examined, one network of co-expressed genes was positively
correlated with DMI (r=0.48, P=0.03), with a tendency also identified between the same network and RFI
(r=0.42, P=0.07). Functional annotation of genes within this network revealed enrichment (P<0.05) of
pathways related to both amino acid and fatty acid metabolism. Our results suggest a role for these processes
in the hepatic tissue of cattle divergent for RFI. Moreover, genes within this network may represent potential
biomarkers for the selection of improved feed efficiency in cattle across varying breed types
Clubroot and soil biology – from ecology to biocontrol?
No full textInteractions between plants, soil, and microbiota makes the rhizosphere of central importance for ecosystem functioning. Although non-pathogenic organism dominate this rhizobiome, plant pathogens have an important functional role for plant performance. In fact, plant pathogens trigger plant defence and alter the metabolism, nutrient flow and survival of the host, leading to changes in overall plant performance which feeds-back to the rhizobiome. However, the links between soil-borne pathogens and the rhizobiome are only starting to be explored. Here we focus on the clubroot pathogen Plasmodiophora brassicae, a pathogen that forces farmers to abandon cultivation of Brassica species for more than a decade, to decipher pathogen impact on the rhizobiome. Furthermore, we aim to identify potentially disease suppressive and disease conducive microbiome members, including bacteria, fungi, protists and animals. We are performing complex plant and soil physicochemical analyses to decipher underlying drivers of taxonomic and functional changes in the rhizobiome to clubroot infection including the impact of the detritusphere. The results of this studies will give an important insight of the ecological role of plasmodiophorid species on the plants and its rhizobiome. Additionally, by identifying pathogen suppressive and conducive soil biota new biocontrol applications can be developed that will also be useful to control other soil-borne pathogens. In this presentation we will provide the framework of the research and initial findings that provide first ideas on the importance of the plant-clubroot-rhizobiome connections
Irish research response to dairy quality in an era of change
Get PDFpeer-reviewedThe Irish dairy sector is recognised for its very significant contribution to the national economic status; it is now worth ∼€5 billion annually and represents the largest food and drink export category, which, in turn, represents one of the four largest manufacturing industries in the country. Given anticipated further growth in global demand for dairy products and the positive attributes and capabilities that Ireland has to meet that demand, in terms of pasture-based production and cost competitiveness, it is incumbent for the sector to attain the highest quality milk and dairy products. The combined collaborative approach between research and industry has ensured significant progress and enabled Ireland to remain at the forefront globally in terms of production of quality milk and dairy products. This paper highlights some specific scientific platforms and technologies currently shaping the industry in this regard and discusses current research activity as well as anticipating key requirements for future progress. While research, and farm and processing plant management have accomplished very significant advances in milk and dairy product quality, some overarching emerging challenges include product substitution and sustainability. Some key pillars for the future have been identified on which a strong, efficient dairy sector can be maintained and progressed. Specifically, the use of evidence-based information and real-time measures in prediction and decision-making will be a crucial pillar for the dairy sector of the future. This can promote an approach of proactive maintenance and optimisation of production through improved predictability and control of manufacturing processes
Current research and emerging tools to improve fresh red meat quality
Get PDFpeer-reviewedA consumer’s decision to purchase red meat is guided by a combination of many interacting factors including safety, nutrition, sustainability and perception of healthiness along with a variety of sensory characteristics such as colour, marbling, tenderness, juiciness and flavour. Red meat quality is complex and influenced by many intrinsic and extrinsic factors, spanning the chain from breed/genetics through to the final end product with key influences coming from on-farm management and post-mortem processing. As a result of various factors, including consumer demands, the importance of both red meat quality and safety has in recent times come to the fore for the meat industry, with steps to meet these requirements having a large bearing on profitability. Therefore, a critical review of steps which can help control these traits is very important. Accordingly, several processing strategies were proposed at the research and industry level aiming to improve fresh red meat quality traits. This review summarises the current methods applied to improve fresh red meat quality and safety, including the advances in management and prediction tools for carcass and technological and sensory quality traits. These methods are also relevant to the safety and microbiological status of carcasses and meat produced, along with the recent developments in sensory analysis, which aim to understand the sensory properties of red meat and consumers responses. The potential of foodomics approaches is discussed under the topics of genomics, proteomics and metabolomics, which help our understanding of the underlying biological mechanisms behind the variation of sensory and technological quality traits and their use for the discovery of putative biomarkers. We further considered the current and emerging sequencing-based methods used to understand microbial community composition of fresh red meat
Shared and non-shared sIgA-coated and uncoated bacteria in intestine of mother-infant pairs
Get PDFpreprintBackground
The infant gut microbiota is critical for promoting and maintaining early life health. Bacteria coated by
secretory immunoglobulin A (sIgA) may help commensal bacteria colonize the gastrointestinal tract. The
study aimed to analyze the composition of sIgA-coated and sIgA-uncoated bacterial communities at
genus level, and lactobacilli and bifidobacterial communities at species level in human breast milk
(HBM), infant, and maternal feces.
Results
Eleven pregnant women were recruited successfully. HBM, infant feces during colostrum, transition, and
mature stages, and maternal feces within the mature stage were collected. sIgA-coated and sIgAuncoated
bacteria were separated with magnetic-activated cell sorting. Then 16S rRNA sequencing,
bifidobacterial groEL gene sequencing, and lactobacilli groEL gene sequencing were performed to
analyze the bacterial community. The richness of sIgA-coated bacteria was significantly higher than that
of sIgA-uncoated bacteria in HBM. PCoA revealed that the compositions of sIgA-coated and sIgAuncoated
bacteria were different among HBM, infant and maternal feces. The dominant sIgA-coated
bacteria in those samples were Escherichia/shigella and the dominant sIgA-uncoated bacteria was
Pseudomonas. Higher relative abundance of sIgA-uncoated Bifidobacterium was found in the three
lactation stages in infant feces compared to the corresponding HBM, and a higher relative abundance of
sIgA-uncoated Faecalibacterium was found in maternal feces compared to HBM and infant feces. For the
bifidobacterial community, PCoA analysis revealed a significantly different Bifidobacterium composition
only in the sIgA-uncoated segments of infant feces and maternal feces. sIgA-coated and sIgA-uncoated
B. longum subsp. infantis and B. pseudocatenulatum was dominant in infant feces and maternal feces,
respectively. Additionally, the relative abundance of sIgA-uncoated B. longum subsp. infantis was
significantly higher in infant feces compared to that in maternal feces. For the Lactobacillus community,
the composition was significantly different in infant and maternal feces, while at species level, L.
paragasseri and L. mucosae were dominant in infant and maternal feces, respectively.
Conclusion
HBM, infant, and maternal feces showed distinct diversity and composition of both sIgA-coated and sIgAuncoated
bacteria at genus level. Infant and maternal feces showed similar diversity and similar
composition of Bifidobacterium at species level. The same Bifidobacterium species could be detected
both in sIgA-coated and sIgA-uncoated for
Biomass and nutrient dynamics of major green tides in Ireland: Implications for biomonitoring
Get PDFpeer-reviewedThe control of macroalgal bloom development is central for protecting estuarine ecosystems. The identification of the nutrients limiting the development of macroalgal blooms, and their most likely sources is crucial for management strategies. Three Irish estuaries (Argideen, Clonakilty and Tolka) affected by green tides were monitored from June 2016 to August 2017. During each sampling occasion, biomass abundances, tissue N and P contents, and δ15N were determined for tubular and laminar morphologies of Ulva. All estuaries showed maximum biomass during summer and minimum during winter. Tissue nutrient contents revealed P rather than N limitation. The δ15N during the peak bloom indicated agriculture as the most likely source of nitrogen in the Argideen and Clonakilty, and urban wastewaters in the Tolka. No differences in the δ15N, and the tissue nutrients content were observed between morphologies. The period between May and July is most suitable for bioassessment of green tides
HOW CAN ORGANIZATIONS SUPPORT PUBLIC ENGAGEMENT BY RESEARCH SCIENTISTS IN IRELAND? UNDERSTANDING THE PUBLIC ENGAGEMENT BEHAVIOURS AND PERCEPTIONS OF AGRI-FOOD RESEARCHERS
Get PDFA study submitted in part fulfilment of the requirement for the award of MSc in Science and Health Communication, Dublin City UniversityScience communication scholars and Research Performing Organizations advocate public
engagement (PE) by scientists. EU and Irish research funders see PE as essential to deliver
the full benefits of the outputs of funded research for society. PE should be a dialogue
between science and society, building trust in science. Scientists are required to participate
in public engagement actions.
To support and encourage this, it is necessary to characterize the PE behaviors, motivations,
and perceptions of scientists. Prior studies identified motivations for, and barriers to, public
engagement, and found the level and type of activity is varied. There is evidence of
influences from gender, career-status, age, and discipline, but it is not conclusive.
There has been little study of scientists’ perceptions of PE in Ireland. To address the
knowledge gap, this study surveyed Agri-food researchers in Ireland. The survey gathered
data about their participation in PE, their motivations, perceived barriers, their future PE
intentions, and identified training and supports needed. The data was analyzed to establish
any influences of gender, career-status, age, or discipline. The aim was to establish how
organizations can support, encourage, and build public engagement.
These scientists have a high level of participation in Public Engagement, with high levels of
largely altruistic motivations. However, they are time-poor, and unhappy with the current
situation regarding institutional support. They would like PE to be recognized in career
progression processes. They need relevant training. Gender, career-status, age, and
discipline all influence public engagement behaviors. There is a pronounced gender effect
relating to engagement with children. Senior scientists interact more with the media.
Agricultural scientists are more motivated to involve the public in their research. Research
organizations must recognize and value public engagement in their career assessment
processes, provide training and supply supports to encourage more participation and deeper
engagemen
The clubroot pathogen Plasmodiophora brassicae: A profile update
Get PDFpeer-reviewedBackground
Plasmodiophora brassicae is the causal agent of clubroot disease of cruciferous plants and one of the biggest threats to the rapeseed (Brassica napus) and brassica vegetable industry worldwide.
Disease symptoms
In the advanced stages of clubroot disease wilting, stunting, yellowing, and redness are visible in the shoots. However, the typical symptoms of the disease are the presence of club-shaped galls in the roots of susceptible hosts that block the absorption of water and nutrients.
Host range
Members of the family Brassicaceae are the primary host of the pathogen, although some members of the family, such as Bunias orientalis, Coronopus squamatus, and Raphanus sativus, have been identified as being consistently resistant to P. brassicae isolates with variable virulence profile.
Taxonomy
Class: Phytomyxea; Order: Plasmodiophorales; Family: Plasmodiophoraceae; Genus: Plasmodiophora; Species: Plasmodiophora brassicae (Woronin, 1877).
Distribution
Clubroot disease is spread worldwide, with reports from all continents except Antarctica. To date, clubroot disease has been reported in more than 80 countries.
Pathotyping
Based on its virulence on different hosts, P. brassicae is classified into pathotypes or races. Five main pathotyping systems have been developed to understand the relationship between P. brassicae and its hosts. Nowadays, the Canadian clubroot differential is extensively used in Canada and has so far identified 36 different pathotypes based on the response of a set of 13 hosts.
Effectors and resistance
After the identification and characterization of the clubroot pathogen SABATH-type methyltransferase PbBSMT, several other effectors have been characterized. However, no avirulence gene is known, hindering the functional characterization of the five intercellular nucleotide-binding (NB) site leucine-rich-repeat (LRR) receptors (NLRs) clubroot resistance genes validated to dateCanadian Network for Research and Innovation in Machining Technology, Natural Sciences and Engineering Research Council of Canad
Effects of concentrate supplementation and genotype on milk production and nitrogen utilisation efficiency in late-lactation, spring-calving grazing dairy cows
Get PDFpeer-reviewedThe study objectives were to evaluate the effects of (1) concentrate supplementation (CS), (2) cow genotype, and (3) a potential interaction between CS and cow genotype on milk production, dry matter (DM) intake (DMI) and cow nitrogen (N) utilisation efficiency (NUE) in late lactation (+208 ± 14.1 days in milk), spring-calving grazing dairy cows. The experiment was a complete randomised block design with a 2 × 2 factorial arrangement of treatments and was conducted over a 52-day period. There were two feeding strategies (pasture-only (PO) and pasture + 2.7 kg DM CS) and two genotype groups [lower milk genotype (LM; milk kg PTA = -48 ± 59.9, fat kg PTA = +7 ± 4.7 and protein kg PTA = +3 ± 3.2) and higher milk genotype (HM; milk kg PTA = +190 ± 109.7, fat kg PTA = +12 ± 5.7 and protein kg PTA = +9 ± 3.6)]. Cows in their respective genotype group were randomly assigned to one of two feeding strategies, resulting in four treatment groups (n = 12). Cows grazed full time and were allocated 17 kg DM pasture/cow per d. No interactions were observed for any parameters measured. Cows offered CS had increased daily yields of fat + protein (+0.18 kg), lactose (+0.13 kg) and ECM (+2.46 kg) compared to cows offered PO. The HM cows had increased yields of daily fat + protein (+0.13 kg) and lactose (+0.1 kg) compared to the LM cows. Cows offered CS had decreased daily protein (-0.14%) but increased lactose (+0.08%) concentration compared to cows offered PO. The HM cows had decreased daily fat (-0.2%), protein (-0.16%) and casein (-0.07%) concentration compared to the LM cows. Cows offered CS had a reduced daily pasture DMI (-1.41 kg) but an increased daily total DMI (+1.29 kg) and feed N intake (+0.085 kg) compared to cows offered PO. Cows offered CS had decreased NUE (-0.1%) compared to cows offered PO. In conclusion, offering cows 2.7 kg DM CS per day improved milk production in late lactation but resulted in a poorer NUE. The poorer NUE was due to no difference in milk N output and an increase in the partitioning of feed N to urine. The HM cows had an increased milk response to CS with respect to milk fat + protein kg compared to the MR obtained from LM cows
Optimisation of a bead-beating procedure for simultaneous extraction of bacterial and fungal DNA from pig faeces and liquid feed for 16S and ITS2 rDNA amplicon sequencing
Get PDFpeer-reviewedEfficient cell lysis is critical for the extraction of DNA from difficult-to-lyse microorganisms such as Gram-positive bacteria and filamentous fungi. A bead-beating (BB) step is usually included in DNA extraction protocols to improve cell lysis. However, there is no consensus on the duration of BB that is necessary for complete lysis of the microbial communities present in complex microbial ecosystems, but which will still maintain the integrity of DNA released from easy-to-lyse microbes. Another consideration is that most protocols are tailored to one particular target group of microbes, typically either bacteria or fungi, in a given sample matrix. In this study, we investigated the impact of five BB durations (0, 3, 10, 15 and 20 min) during DNA extraction with the QIAamp® Fast DNA Stool Mini Kit, on the bacterial and fungal communities of single pig faecal and liquid feed samples, extracted in triplicate, with the objective of determining a suitable ‘catch-all’ method. Both sample types were subjected to the BB durations in triplicate, followed by 16S (bacterial) and ITS2 (fungal) rDNA amplicon sequencing. The performance of the different BB durations was assessed based on the quantity of total DNA extracted, alpha- and beta-diversity analyses of the resultant microbial communities and differential abundance of bacterial and fungal taxa. Our results suggest that 20 min of BB is most appropriate for maximising the lysis of difficult-to-lyse bacteria and fungi in both pig faeces and liquid feed, while minimising the negative impact on easier-to-lyse microbes. Total DNA yield increased with BB duration for both sample types; however, the yield from faeces decreased after 20 min of BB. Despite this, DESeq2 analysis indicated that changes in the differential abundances of the dominant taxa at this point were limited, which was supported by the Shannon diversity results. Maximising the BB duration appeared to be necessary in order to obtain a representative profile of the Gram-positive bacteria, particularly in liquid feed, and of the filamentous fungi present in both sample types. However, considering the small sample size, along with the reliance on differential as opposed to absolute abundances to validate increases or decreases in taxa, a larger-scale study is necessary to verify the findings of the present study