This study characterized the coagulation properties and defined the cutting window (CW; time between storage modulus values of 35 and 70 Pa) using rheometry for milk standardized to 4, 5, or 6% protein and set at 28, 32, or 36°C. Milks were standardized to a protein-to-fat ratio of approximately 1 by blending ultrafiltration retentate, skim milk, and whole milk. The internal curd microstructure for selected curd samples was analyzed with transmission electron microscopy and scanning electron microscopy. Lowering the coagulation temperature caused longer rennet coagulation time and time to reach storage modulus of 35 Pa, translating into a wider CW. It also led to a lower maximum curd-firming rate (MCFR) with lower firmness at 40 min at a given protein level. Increasing protein levels resulted in the opposite effect, although without an effect on rennet coagulation time at a given temperature. On coagulation at 28°C, milk with 5% protein resulted in a similar MCFR (∼4 Pa/min) and CW (∼8.25 min) compared with milk with 4% protein at 32°C, which reflects more standard conditions, whereas increasing milk to 6% protein resulted in more than doubling of the curd-firming rate (MCFR = 9.20 Pa/min) and a shorter CW (4.60 min). Gels set at 28°C had lower levels of rearrangement of protein network after 40 min compared with those set at 36°C. Protein levels, on the other hand, had no influence on the levels of protein network rearrangement, as indicated by loss tangent values. The internal structure of curd particles, as investigated by both scanning electron microscopy and transmission electron microscopy, appeared to have less cross-linking and smaller casein aggregates when coagulated at 28°C compared with 36°C, whereas varying protein levels did not show a marked effect on aggregate formation. Overall, this study showed a marked interactive effect between coagulation temperature and protein standardization of milk on coagulation properties, which subsequently requires adjustment of the CW during cheesemaking. Lowering of the coagulation temperature greatly altered the curd microstructure, with a tendency for less syneresis during cutting. Further research is required to quantify the changes in syneresis and in fat and protein losses to whey due to changes in the microstructure of curd particles arising from the different coagulation conditions applied to the protein-fortified milk.

The bacteriocins bactofencin A (class IId) and pediocin PA-1 (class IIa) are encoded by operons with a similarly clustered gene organization including a structural peptide, an immunity protein, an ABC transporter and accessory bacteriocin transporter protein. Cloning of these operons in E. coli TunerTM (DE3) on a pETcoco-2 derived vector resulted in successful secretion of both bacteriocins. A corresponding approach, involving the construction of vectors containing different combinations of these genes, revealed that the structural and the transporter genes alone are sufficient to permit heterologous production and secretion in this host. Even though the accessory protein, usually associated with optimal disulfide bond formation, was not required for bacteriocin synthesis, its presence did result in greater pediocin PA-1 production. The simplicity of the system and the fact that the associated bacteriocins could be recovered from the extracellular medium provides an opportunity to facilitate protein engineering and the overproduction of biologically-active bacteriocins at industrial scale. Additionally, this system could enable the characterization of new bacteriocin operons where genetic tools are not available for the native producers.

The genetic mechanisms controlling residual feed intake (RFI) in beef cattle are still largely unknown. Here we performed whole transcriptome analyses to identify differentially expressed (DE) genes and their functional roles in liver tissues between six extreme high and six extreme low RFI steers from three beef breed populations including Angus, Charolais, and Kinsella Composite (KC). On average, the next generation sequencing yielded 34 million single-end reads per sample, of which 87% were uniquely mapped to the bovine reference genome. At false discovery rate (FDR) < 0.05 and fold change (FC) > 2, 72, 41, and 175 DE genes were identified in Angus, Charolais, and KC, respectively. Most of the DE genes were breed-specific, while five genes including TP53INP1, LURAP1L, SCD, LPIN1, and ENSBTAG00000047029 were common across the three breeds, with TP53INP1, LURAP1L, SCD, and LPIN1 being downregulated in low RFI steers of all three breeds. The DE genes are mainly involved in lipid, amino acid and carbohydrate metabolism, energy production, molecular transport, small molecule biochemistry, cellular development, and cell death and survival. Furthermore, our differential gene expression results suggest reduced hepatic lipid synthesis and accumulation processes in more feed efficient beef cattle of all three studied breeds.

We hypothesised that epigenetic regulation of CD4+ T lymphocytes contributes to a shift toward a dysfunctional T cell phenotype which may impact on their ability to clear mycobacterial infection. Combined RNA-seq transcriptomic profiling and Reduced Representation Bisulfite Sequencing identified 193 significantly differentially expressed genes and 760 differentially methylated regions (DMRs), between CD4+ T cells from M. bovis infected and healthy cattle. 196 DMRs were located within 10 kb of annotated genes, including GATA3 and RORC, both of which encode transcription factors that promote TH2 and TH17 T helper cell subsets respectively. Gene-specific DNA methylation and gene expression levels for the TNFRSF4 and Interferon-γ genes were significantly negatively correlated suggesting a regulatory relationship. Pathway analysis of DMRs identified enrichment of genes involved in the anti-proliferative TGF-β signaling pathway and TGFB1 expression was significantly increased in peripheral blood leukocytes from TB-infected cattle. This first analysis of the bovine CD4+ T cell methylome suggests that DNA methylation directly contributes to a distinct gene expression signature in CD4+ T cells from cattle infected with M. bovis. Specific methylation changes proximal to key inflammatory gene loci may be critical to the emergence of a non-protective CD4+ T cell response during mycobacterial infection in cattle.

The genus Barbarea has emerged as a model for evolution and ecology of plant defense compounds, due to its unusual glucosinolate profile and production of saponins, unique to the Brassicaceae. One species, B. vulgaris, includes two ‘types’, G-type and P-type that differ in trichome density, and their glucosinolate and saponin profiles. A key difference is the stereochemistry of hydroxylation of their common phenethylglucosinolate backbone, leading to epimeric glucobarbarins. Here we report a draft genome sequence of the G-type, and re-sequencing of the P-type for comparison. This enables us to identify candidate genes underlying glucosinolate diversity, trichome density, and study the genetics of biochemical variation for glucosinolate and saponins. B. vulgaris is resistant to the diamondback moth, and may be exploited for “dead-end” trap cropping where glucosinolates stimulate oviposition and saponins deter larvae to the extent that they die. The B. vulgaris genome will promote the study of mechanisms in ecological biochemistry to benefit crop resistance breeding.

The Towards Land Cover Accounting and Monitoring (TaLAM) project is part of Ireland’s response to creating a national land cover mapping programme. Its aims are to demonstrate how the new digital map of Ireland, Prime2, from Ordnance Survey Ireland (OSI), can be combined with satellite imagery to produce land cover maps.

The objective of this study was to determine if differences in grazing behaviour exist between lactating suckler cows diverse in genetic merit for the national Irish Replacement index and of two contrasting genotypes. Data from 103 cows: 41 high and 62 low genetic merit, 43 beef and 60 beef x dairy (BDX) cows were available over a single grazing season in 2015. Milk yield, grass dry matter intake (GDMI), cow live weight (BW) and body condition score (BCS) were recorded during the experimental period, with subsequent measures of production efficiency extrapolated. Grazing behaviour data were recorded twice in conjunction with aforementioned measures, using Institute of Grassland and Environmental Research headset behaviour recorders. The effect of genotype and cow genetic merit during mid- and late-lactation on grazing behaviour phenotypes, milk yield, BW, BCS and GDMI were estimated using linear mixed models. Genetic merit had no significant effect on any production parameters investigated, with the exception that low genetic merit had a greater BCS than high genetic merit cows. Beef cows were heavier, had a greater BCS but produced less milk per day than BDX. The BDX cows produced more milk per 100 kg BW and per unit intake and had greater GDMI, intake per bite and rate of GDMI per 100 kg BW than beef cows. High genetic merit cows spent longer grazing and took more bites per day but had a lower rate of GDMI than low genetic merit cows, with the same trend found when expressed per unit of BW. High genetic merit cows spent longer grazing than low genetic merit cows when expressed on a per unit intake basis. Absolute rumination measures were similar across cow genotype and genetic merit. When expressed per unit BW, BDX cows spent longer ruminating per day compared to beef. However, on a per unit intake basis, beef cows ruminated longer and had more mastications than BDX. Intake per bite and rate of intake was positively correlated with GDMI per 100 kg BW. The current study implies that despite large differences in grazing behaviour between cows diverse in genetic merit, few differences were apparent in terms of production efficiency variables extrapolated. Conversely, differences in absolute grazing and ruminating behaviour measurements did not exist between beef cows of contrasting genotype. However, efficiency parameters investigated illustrate that BDX will subsequently convert herbage intake more efficiently to milk production.

The hierarchical structure, pasting and digestibility of adlay seed starch (ASS) were investigated compared with maize starch (MS) and potato starch (PS). ASS exhibited round or polyglonal morphology with apparent pores/channels on the surface. It had a lower amylose content, a looser and more heterogeneous C-type crystalline structure, a higher crystallinity, and a thinner crystalline lamellae. Accordingly, ASS showed a higher slowly digestible starch content combined with less resistant starch fractions, and a decreased pasting temperature, a weakened tendency to retrogradation and an increased pasting stability compared with those of MS and PS. The ASS structure-functionality relationship indicated that the amylose content, double helical orders, crystalline lamellar structure, and surface pinholes should be responsible for ASS specific functionalities including pasting behaviors and in vitro digestibility. ASS showed potential applications in health-promoting foods which required low rearrangement during storage and sustainable energy-providing starch fractions.

Lotus seeds were identified by the Ministry of Public Health of China as both food and medicine. One general function of lotus seeds is to improve intestinal health. However, to date, studies evaluating the relationship between bioactive compounds in lotus seeds and the physiological activity of the intestine are limited. In the present study, by using medium pressure liquid chromatography coupled with evaporative light-scattering detector and diode-array detector, five oligosaccharides were isolated and their structures were further characterized by electrospray ionization-mass spectrometry and gas chromatography-mass spectrometry. In vitro testing determined that LOS3-1 and LOS4 elicited relatively good proliferative effects on Lactobacillus delbrueckii subsp. bulgaricus. These results indicated a structure-function relationship between the physiological activity of oligosaccharides in lotus seeds and the number of probiotics applied, thus providing room for improvement of this particular feature. Intestinal probiotics may potentially become a new effective drug target for the regulation of immunity.

Mole (M) and gravel-mole (GM) drainage systems improve the permeability of soils with high clay contents. They collect and carry away infiltrating water during episodic rainfall events. Characterisation of nutrient fluxes (concentration and flows) in overland flow (OF) and in mole drain flow (MF) across sequential rainfall events is important for environmental assessment of such drainage systems. The objective of this study is to assess the impact of drainage systems on soil nutrient losses. Three treatments were imposed on grazed permanent grassland on a clay loam soil in Ireland (52°30′N, 08°12′W) slope 1.48%: undrained control (C), mole drainage (M) and gravel mole drainage (GM). Plots (100 m × 15 m) were arranged in a randomized complete block design with four replicated blocks. Nitrogen (N) and phosphorus (P) concentrations in OF, MF and groundwater (GW) were measured from each plot over 15 consecutive rainfall events. The results showed that M and GM (P < 0.05) deepened the watertable depth and decreased OF. M and GM increased losses of nitrate-N (22%) and ammonium-N (14%) in GW. Nitrate-N concentrations from all the flow pathways (mean and standard error (s.e.): 0.99 s.e. 0.10 mg L−1) were well below the 11.3 mg L−1 threshold for drinking water. Ammonium-N concentrations from all the flow pathways (mean: 0.64 s.e. 0.14 mg L−1) exceeded drinking water quality standards. On the other hand M and GM lowered total P losses (mean annual losses from C, M and GM: 918, 755 and 853 s.e. 14.1 g ha−1 year−1) by enhancing soil P sorption. Hence M and GM can be implemented on farms under similar management to that described in the present study with a minor impact on N (increased concentration on averaged 18% to GW) and P (reduced by on avenged 114 g ha−1 year−1).