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Item Intra-molecular lysine-arginine derived advanced glycation end-product cross-linking in Type I collagen: A molecular dynamics simulation study.(2016-11) Collier TA; Nash A; Birch HL; de Leeuw NHCovalently cross-linked advanced glycation end products (AGE) are among the major post-translational modifications to proteins as a result of non-enzymatic glycation. The formation of AGEs has been shown to have adverse effects on the properties of the collagenous tissue; they are even linked to a number of age related disorders. Little is known about the sites at which these AGEs form or why certain sites within the collagen are energetically more favourable than others. In this study we have used a proven fully atomistic molecular dynamics approach to identify six sites where the formation of the intra-molecular 3-deoxyglucosone-derived imidazolium cross-link (DOGDIC) is energetically favourable. We have also conducted a comparison of these positions with those of the more abundant glucosepane cross-link, to determine any site preference. We show that when we consider both lysine and arginine AGEs, they exhibit a prevalence to form within the gap region of the collagen fibril.Item An experimental model of contusion injury in humans(Public Library of Science, 17/11/2022) Barnes M; Lomiwes D; Parry DAD; Stephen MIntroduction Contusion injuries are common in sport, but our knowledge of the responses to injury primarily come from animal studies and research using eccentric exercise. Therefore, the aim of this study was to develop a model of contusion injury in human participants and, additionally, investigate and compare physiological responses to four impact loads. Methods Thirty-two males were exposed to a single impact of either 4.2, 5.2, 6.2 or 7.2kg, dropped from 67 cm, on to the vastus lateralis of one leg. Maximum voluntary and electrically induced quadriceps force, and pressure pain threshold were measured, and blood sampling carried out, prior to and 30min, 24, 48 and 72h post-impact. Magnetic resonance imaging was carried out 24h post-impact to quantify oedema. Results Despite impact force with 7.2kg (1681.4 ± 235.6 N) not being different to 6.2kg (1690.7 ± 117.6 N), 7.2kg resulted in greater volume of oedema, voluntary force loss, pain and elevations in creatine kinase than the other loads. Although electrically induced force changed over time, post-hoc analysis failed to identify any changes. Interleukin-6 and prostaglandin-E2 did not change over time for any of the loads. Significant correlations were found between oedema volume, pressure pain threshold and maximum voluntary contraction force. Conclusions This is the first experimental study to investigate traumatic loading of skeletal muscle and the subsequent physiological responses associated with contusion injuries in humans. The absence of immediate elevations in creatine kinase and changes in electrically induced force suggest impact, with forces similar to those experienced in contact sport, does not cause significant, direct damage to skeletal muscle. However, the relationship between oedema volume, changes in pressure pain threshold and maximum voluntary contraction force suggests central inhibition plays a role in contusion-related muscle dysfunction.Item Nitrification rate in dairy cattle urine patches can be inhibited by changing soil bioavailable Cu concentration(Elsevier, 17/01/2023) Matse D; Jeyakumar P; Bishop P; Anderson CAmmonia oxidation to hydroxylamine is catalyzed by the ammonia monooxygenase enzyme and copper (Cu) is a key element for this process. We investigated the effect of soil bioavailable Cu changes induced through the application of Cu-complexing compounds on nitrification rate, ammonia-oxidizing bacteria (AOB) and archaea (AOA) amoA gene abundance, and mineral nitrogen (N) leaching in urine patches using the Manawatu Recent soil. Further, evaluated the combination of organic compound calcium lignosulphonate (LS) with a growth stimulant Gibberellic acid (GA). Treatments were applied in May 2021 as late-autumn treatments: control (no urine), urine-only at 600 kg N ha-1, urine + dicyandiamide (DCD), urine + co-poly-acrylic-maleic acid (PA-MA), urine + LS, urine + split-application of LS (2LS), and urine + combination of GA plus LS (GA + LS). In addition, another four treatments were applied in July 2021 as mid-winter treatments: control, urine-only at 600 kg N ha-1, urine + GA, and urine + GA + LS. Soil bioavailable Cu and mineral N leaching were examined during the experimental period. The AOB/AOA amoA genes were quantified using quantitative polymerase chain reaction. Changes in soil bioavailable Cu across treatments correlated with nitrification rate and AOB amoA abundance in late-autumn while the AOA amoA abundance did not change. The reduction in soil bioavailable Cu induced by the PA-MA and 2LS was linked to significant (P < 0.05) reduction in mineral N leaching of 16 and 30%, respectively, relative to the urine-only. The LS did not induce a significant effect on either bioavailable Cu or mineral N leaching relative to urine-only. The GA + LS reduced mineral N leaching by 10% relative to LS in late-autumn, however, there was no significant effect in mid-winter. This study demonstrated that reducing soil bioavailable Cu can be a potential strategy to reduce N leaching from urine patches.Item De novo transcriptome assembly, functional annotation and differential gene expression analysis of juvenile and adult E. fetida, a model oligochaete used in ecotoxicological studies(Sociedad de Biología de Chile, 17/02/2017) Thunders MC; Cavanagh J; Li YBACKGROUND: Earthworms are sensitive to toxic chemicals present in the soil and so are useful indicator organisms for soil health. Eisenia fetida are commonly used in ecotoxicological studies; therefore the assembly of a baseline transcriptome is important for subsequent analyses exploring the impact of toxin exposure on genome wide gene expression. RESULTS: This paper reports on the de novo transcriptome assembly of E. fetida using Trinity, a freely available software tool. Trinotate was used to carry out functional annotation of the Trinity generated transcriptome file and the transdecoder generated peptide sequence file along with BLASTX, BLASTP and HMMER searches and were loaded into a Sqlite3 database. To identify differentially expressed transcripts; each of the original sequence files were aligned to the de novo assembled transcriptome using Bowtie and then RSEM was used to estimate expression values based on the alignment. EdgeR was used to calculate differential expression between the two conditions, with an FDR corrected P value cut off of 0.001, this returned six significantly differentially expressed genes. Initial BLASTX hits of these putative genes included hits with annelid ferritin and lysozyme proteins, as well as fungal NADH cytochrome b5 reductase and senescence associated proteins. At a cut off of P = 0.01 there were a further 26 differentially expressed genes. CONCLUSION: These data have been made publicly available, and to our knowledge represent the most comprehensive available transcriptome for E. fetida assembled from RNA sequencing data. This provides important groundwork for subsequent ecotoxicogenomic studies exploring the impact of the environment on global gene expression in E. fetida and other earthworm species.Item An empirical analysis of the cost of rearing dairy heifers from birth to first calving and the time taken to repay these costs(Cambridge University Press, 8/02/2017) Boulton AC; Rushton J; Wathes DCRearing quality dairy heifers is essential to maintain herds by replacing culled cows. Information on the key factors influencing the cost of rearing under different management systems is, however, limited and many farmers are unaware of their true costs. This study determined the cost of rearing heifers from birth to first calving in Great Britain including the cost of mortality, investigated the main factors influencing these costs across differing farming systems and estimated how long it took heifers to repay the cost of rearing on individual farms. Primary data on heifer management from birth to calving was collected through a survey of 101 dairy farms during 2013. Univariate followed by multivariable linear regression was used to analyse the influence of farm factors and key rearing events on costs. An Excel spreadsheet model was developed to determine the time it took for heifers to repay the rearing cost. The mean±SD ages at weaning, conception and calving were 62±13, 509±60 and 784±60 days. The mean total cost of rearing was £1819±387/heifer with a mean daily cost of £2.31±0.41. This included the opportunity cost of the heifer and the mean cost of mortality, which ranged from £103.49 to £146.19/surviving heifer. The multivariable model predicted an increase in mean cost of rearing of £2.87 for each extra day of age at first calving and a decrease in mean cost of £6.06 for each percentile increase in time spent at grass. The model also predicted a decrease in the mean cost of rearing in autumn and spring calving herds of £273.20 and £288.56, respectively, compared with that in all-year-round calving herds. Farms with herd sizes⩾100 had lower mean costs of between £301.75 and £407.83 compared with farms with <100 milking cows. The mean gross margin per heifer was £441.66±304.56 (range £367.63 to £1120.08), with 11 farms experiencing negative gross margins. Most farms repaid the cost of heifer rearing in the first two lactations (range 1 to 6 lactations) with a mean time from first calving until breaking even of 530±293 days. The results of the economic analysis suggest that management decisions on key reproduction events and grazing policy significantly influence the cost of rearing and the time it takes for heifers to start making a profit for the farm.Item Crawfish shell- and Chinese banyan branch-derived biochars reduced phytoavailability of As and Pb and altered community composition of bacteria in a contaminated arable soil.(20/03/2023) Gu S; Yang X; Chen H; Jeyakumar P; Chen J; Wang HGlobally, soil contamination with arsenic (As) and lead (Pb) has become a severe environmental issue. Herein, a pot experiment was conducted using pak choi (Brassica chinensis L.) to investigate the effects of biochars derived from crawfish (Procambarus clarkia) shells (CSB) and Chinese banyan (Ficus microcarpa) branches (CBB) on the phytoavailability of As and Pb, and bacterial community composition in soils. Our results showed that the application of CSB and CBB decreased the concentrations of DTPA-extractable Pb in soils ranging from 26.8 % to 28.8 %, whereas CSB increased the concentration of NH4H2PO4-extractable As in soils, compared to the control. Application of both biochars reduced the uptake of As and Pb in the edible part of pak choi. In addition, application of CBB significantly (P < 0.05) increased the activities of α-glucosidase, β-glucosidase, cellobiohydrolase, and acid phosphomonoesterase by 55.0 %, 54.4 %, 195.1 %, and 76.7 %, respectively, compared to the control. High-throughput sequencing analysis revealed that the predominant bacteria at the phyla level in both biochar-treated soils were Firmicutes, Proteobacteria, and Actinobacteriota. Redundancy and correlation analyses showed that the changes in bacterial community composition could be related to soil organic carbon content, As availability, and nutrient availability in soils. Overall, the Chinese banyan branch biochar was more suitable than the crawfish shell biochar as a potential amendment for the remediation of soils co-contaminated with As and Pb.
