Journal Articles
Permanent URI for this collectionhttps://mro.massey.ac.nz/handle/10179/7915
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Item Bioinformatics role of the WGCNA analysis and co-expression network identifies of prognostic marker in lung cancer(Elsevier B.V. on behalf of King Saud University, 2022-05-01) Chengcheng L; Raza SHA; Shengchen Y; Mohammedsaleh ZM; Shater AF; Saleh FM; Alamoudi MO; Aloufi BH; Mohajja Alshammari A; Schreurs NM; Zan LLung cancer is the most talked about cancer in the world. It is also one of the cancers that currently has a high mortality rate. The aim of our research is to find more effective therapeutic targets and prognostic markers for human lung cancer. First, we download gene expression data from the GEO database. We performed weighted co-expression network analysis on the selected genes, we then constructed scale-free networks and topological overlap matrices, and performed correlation modular analysis with the cancer group. We screened the 200 genes with the highest correlation in the cyan module for functional enrichment analysis and protein interaction network construction, found that most of them focused on cell division, tumor necrosis factor-mediated signaling pathways, cellular redox homeostasis, reactive oxygen species biosynthesis, and other processes, and were related to the cell cycle, apoptosis, HIF-1 signaling pathway, p53 signaling pathway, NF-κB signaling pathway, and several cancer disease pathways are involved. Finally, we used the GEPIA website data to perform survival analysis on some of the genes with GS > 0.6 in the cyan module. CBX3, AHCY, MRPL12, TPGB, TUBG1, KIF11, LRRC59, MRPL17, TMEM106B, ZWINT, TRIP13, and HMMR was identified as an important prognostic factor for lung cancer patients. In summary, we identified 12 mRNAs associated with lung cancer prognosis. Our study contributes to a deeper understanding of the molecular mechanisms of lung cancer and provides new insights into drug use and prognosis.Item Comparison of meat quality characteristics of lambs weaned at eight or 14 weeks of age grazing perennial ryegrass-white clover or a plantain-clover mix(New Zealand Society of Animal Production, 2019-07) Kok JC; Schreurs NM; Cranston LM; Corner-Thomas RA; Ekanayake WEMLJ; Morris ST; Kenyon PRThis study compared the meat quality of lambs grazing either perennial ryegrass-white clover pasture or a plantain-clover mix (plantain, red clover, and white clover) from eight to 14 weeks of age followed by a six-week finishing period on perennial ryegrass-white clover pasture. Ewes and their lambs were allocated to four treatments: 1) lambs weaned early (eight weeks of age) on a plantain-clover mix (EARLY), 2) lambs with dam grazing a plantain-clover mix (HERB), 3) lambs with dam grazing pasture >1200 kgDM/ha (HIGH), and 4) lambs with dam grazing pasture <1200 kgDM/ha (LOW). Following the treatment period, all lambs weighing a minimum of 35 kg were sent for slaughter and all remaining lambs were managed and finished as one mob on perennial ryegrass-white clover pasture for a further six weeks. Lambs that reached a minimum 35 kg live weight were slaughtered and meat samples from each lamb were analysed for ultimate pH, meat colour (L*, a*, b*), drip loss and shear force but, no difference was found in objective meat quality characteristics of lambs from different treatments.Item Using poultry by-product meal to replace soybean meal in grower -finisher pig diets(Elsevier B V, 2024-07-01) Nguyen TT; Chidgey KL; Wester TJ; Schreurs NM; Morel PCHThis study investigated the effect of replacing soybean meal (SBM) with poultry by-product meal (PBM) in grower-finisher diets on pig feeding, growth performance, carcass yield and meat quality. The replacement levels were increased from no PBM (PBM0) to 37 g/kg PBM (PBM37), 85 g/kg PBM (PM85) and 111 g/kg PBM (PBM111). All diets met or exceeded nutrient requirements for pigs between 20 – 100 kg live weight (NRC, 2012). Sixty-four entire males (PIC 337 x PIC Camborough 42), at an average live weight (LW) of 27.60 ± 2.48 kg (mean ±SD) were blocked by LW and randomly assigned to 8 pens, with each diet replicated across 2 pens. Pigs had ad libitum access to diets via electronic feeders until they reached approximately 100 kg LW, at which time they were slaughtered. Results showed no significant effect of replacing SBM with PBM on pig feeding behavior parameters and the majority of pig growth performance, carcass yield, and meat quality traits, with the exception of higher feed conversion ratio (FCR) in pigs fed the PBM37 diet. Loin muscles from the group fed the PBM111 diet had significantly lower ultimate pH and a greater cooking loss than the other treatments (P < 0.05). Loin muscles from pigs fed high levels of PBM (PBM85 and PBM111) had greater ash content than those fed the PBM37 and control diets (P = 0.001). Overall, the present research indicated that PBM could be a viable primary protein source in diets for growing-finishing pigs, as it did not appear to have any adverse effects on pig feeding behavior, growth performance and meat quality. In addition, PBM is potentially a good source of calcium and phosphorus for growing–finishing pigs. However, due to the variation in quality and composition of available PBM, it is essential to measure nutritional composition before including PBM in diets for growing-finishing pigs.Item Growth, carcass and meat quality characteristics of Charolais-sired steers and heifers born to Angus-cross-dairy and Angus breeding cows(Elsevier Ltd, 2023-07) Coleman LW; Schreurs NM; Kenyon PR; Morris ST; Hickson RECharolais-sired heifers and steers from Angus, Angus × Holstein-Friesian, Angus × Holstein-Friesian-Jersey and Angus × Jersey cows were measured for growth, carcass, and meat quality characteristics. Despite differences in weaning weight and growth rate, the progeny of different breed-crosses did not differ in final live weight or carcass weight (P > 0.05). Carcass and meat quality characteristics did not differ among breed-crosses (P > 0.05), except for fat that was more yellow in progeny from Angus and Angus-cross-Jersey dams. Steers were slaughtered older and had heavier carcasses with greater fat depth and intramuscular fat than heifers. Meat quality differed between the sex classes, with steers having greater pH and shear force, redder meat, and yellower fat than heifers. Angus-cross-dairy cows when crossed with a beef breed sire such as the Charolais will provide progeny for meat production which are competitive to beef breeds for beef finishing and meat production and therefore, a useful mechanism to utilize surplus animals from the dairy industry.Item Proteomic Profile of M. longissimus thoracis from Commercial Lambs Reared in Different Forage Systems(MDPI (Basel, Switzerland), 2022-05-13) Ye Y; Maes E; Deb-Choudhury S; Hefer CA; Schreurs NM; Realini CE; Colgrave M; Mora LThis study compared the protein composition of M. longissimus thoracis of lambs from six commercial forage production systems in New Zealand. A total of 286 proteins were identified based on liquid chromatography-tandem mass spectrometry. First, a binomial model showed that different production groups could be distinguished based on abundances of 16 proteins. Second, pair-wise comparisons were performed to search for protein abundance differences in meat due to animal sex (ewe vs. wether), diet (perennial ryegrass vs. chicory), and age (4 vs. 6-8 months old). Greater abundance of some myofibrillar and sarcoplasmic proteins were observed in lamb loins from ewes compared to wethers. Chicory diet and older age at slaughter were associated with meat with lower abundance of some myofibrillar proteins, possibly due to a greater proportion of muscle glycolytic fibres. The proteins that showed significant differences in their abundances due to production factors could be further investigated to understand their influence on meat quality.Item Drivers of Palatability for Cats and Dogs-What It Means for Pet Food Development(MDPI (Basel, Switzerland), 2023-03-23) Watson PE; Thomas DG; Bermingham EN; Schreurs NM; Parker ME; Biagi GThe pet food industry is an important sector of the pet care market that is growing rapidly. Whilst the number of new and innovative products continues to rise, research and development to assess product performance follows traditional palatability methodology. Pet food palatability research focuses on the amount of food consumed through use of one-bowl and two-bowl testing, but little understanding is given to why differences are observed, particularly at a fundamental ingredient level. This review will highlight the key differences in feeding behaviour and nutritional requirements between dogs and cats. The dominant pet food formats currently available and the ingredients commonly included in pet foods are also described. The current methods used for assessing pet food palatability and their limitations are outlined. The opportunities to utilise modern analytical methods to identify complete foods that are more palatable and understand the nutritional factors responsible for driving intake are discussed.Item Genetic Association of PPARGC1A Gene Single Nucleotide Polymorphism with Milk Production Traits in Italian Mediterranean Buffalo.(Hindawi Limited, 2021-03-20) Hosseini SM; Tingzhu Y; Pasandideh M; Liang A; Hua G; Farmanullah; Schreurs NM; Raza SHA; Salzano A; Campanile G; Gasparrini B; Yang L; Kontos CKPPARGC1A gene plays an important role in the activation of various important hormone receptors and transcriptional factors involved in the regulation of adaptive thermogenesis, gluconeogenesis, fiber-type switching in skeletal muscle, mitochondrial biogenesis, and adipogenesis, regulating the reproduction and proposed as a candidate gene for milk-related traits in cattle. This study identified polymorphisms in the PPARGC1A gene in Italian Mediterranean buffaloes and their associations to milk production and quality traits (lactation length, peak milk yield, fat and protein yield, and percentage). As a result, a total of seven SNPs (g.-78A>G, g.224651G>C, g.286986G>A, g.304050G>A, g.325647G>A, g.325817T>C, and g.325997G>A) were identified by DNA pooled sequencing. Analysis of productivity traits within the genotyped animals revealed that the g.286986G>A located at intron 4 was associated with milk production traits, but the g.325817T>C had no association with milk production. Polymorphisms in g.-78A>G was associated with peak milk yield and milk yield, while g.304050G>A and g.325997 G>A were associated with both milk yield and protein percentage. Our findings suggest that polymorphisms in the buffalo PPARGC1A gene are associated with milk production traits and can be used as a candidate gene for milk traits and marker-assisted selection in the buffalo breeding program.Item Agent-Based Modelling to Improve Beef Production from Dairy Cattle: Young Beef Production(MDPI (Basel, Switzerland), 2023-04-19) Addis AH; Blair HT; Kenyon PR; Morris ST; Schreurs NM; Garrick DJ; Zaborowicz M; Frankowski JApproximately 42% of the total calves born in New Zealand’s dairy industry are either euthanized on farms or commercially slaughtered as so-called bobby calves within 2 weeks of age. These practices have perceived ethical issues and are considered a waste of resources because these calves could be grown on and processed for beef. Young beef cattle harvested between 8 and 12 months of age would represent a new class of beef production for New Zealand and would allow for a greater number of calves to be utilized for beef production, reducing bobby calf numbers in New Zealand. However, the acceptance of such a system in competition with existing sheep and beef cattle production systems is unknown. Therefore, the current study employed an agent-based model (ABM) developed for dairy-origin beef cattle production systems to understand price levers that might influence the acceptance of young beef production systems on sheep and beef cattle farms in New Zealand. The agents of the model were the rearer, finisher, and processor. Rearers bought in 4-days old dairy-origin calves and weaned them at approximately 100 kg live weight before selling them to finishers. Finishers managed the young beef cattle until they were between 8 and 12 months of age in contrast to 20 to 30 months for traditional beef cattle. Processing young beef cattle in existing beef production systems without any price premium only led to an additional 5% of cattle being utilized compared to the traditional beef cattle production system in New Zealand. This increased another 2% when both weaner cattle and young beef were sold at a price premium of 10%. In this scenario, Holstein Friesian young bull contributed more than 65% of total young beef cattle. Further premium prices for young beef cattle production systems increased the proportion of young beef cattle (mainly as young bull beef), however, there was a decrease in the total number of dairy-origin cattle processed, for the given feed supply, compared to the 10% premium price. Further studies are required to identify price levers and other alternative young beef production systems to increase the number of young beef cattle as well the total number of dairy-origin beef cattle for beef on sheep and beef cattle farms. Some potential options for investigation are meat quality, retailer and consumer perspectives, and whether dairy farmers may have to pay calf rearers to utilize calves with lower growth potentialItem Growth and Carcass Characteristics of Beef-Cross-Dairy-Breed Heifers and Steers Born to Different Dam Breeds.(MDPI (Basel, Switzerland), 2022-03-29) Williamson HR; Schreurs NM; Morris ST; Hickson RE; Ebrahimie EApproximately two thirds of the annual beef kill in New Zealand originates from the dairy industry. The recent increase in Jersey genetics in the dairy herd will inevitably result in an increase in Jersey genetics entering the beef herd from retention of dairy-origin calves for finishing. Limited literature is available on the effect of dam breed on the performance of beef-cross-dairy-breed progeny. The aim of this study was to investigate the effect of dam breed from dams with varying proportions of Friesian and Jersey genetics on growth traits and carcass characteristics of their 24-month-old beef-cross-dairy-breed heifer and steer progeny. Liveweights of 142 heifers and 203 steers from Friesian (F), Friesian-cross (FX), Friesian-Jersey (FJ) and Jersey-cross (JX) dams were recorded at birth, weaning, as yearlings and at slaughter. Carcass characteristics were also recorded. At each point measured, liveweight was greatest for calves born to F dams. Calves born to F dams took 93 days to reach a weaning weight of 100 kg, whereas those from FX, FJ and JX dams took 99, 101 and 102 days, respectively. Carcass weight was greatest for progeny of F dams (286 kg, compared with 279, 275 and 276 for progeny of FX, FJ and JX dams, respectively). The progeny of JX dams had yellower fat than all other dam breed groups and a greater incidence of excessively yellow fat (fat score ≥ 5).Item Transcriptomic in silico analysis of bovine Escherichia coli mastitis highlights its immune-related expressed genes as an effective biomarker.(Elsevier B.V., 2021-12) Farmanullah F; Liang X; Khan FA; Salim M; Rehman ZU; Khan M; Talpur HS; Schreurs NM; Gouda M; Khan SU; Shujun ZBACKGROUND: Mastitis is one of the major diseases causing economic loss to the dairy industry by reducing the quantity and quality of milk. Thus, the objective of this scientific study was to find new biomarkers based on genes for the early prediction before its severity. METHODS: In the present study, advanced bioinformatics including hierarchical clustering, enrichment analysis, active site prediction, epigenetic analysis, functional domain identification, and protein docking were used to analyze the important genes that could be utilized as biomarkers and therapeutic targets for mastitis. RESULTS: Four differentially expressed genes (DEGs) were identified in different regions of the mammary gland (teat cistern, gland cistern, lobuloalveolar, and Furstenberg's rosette) that resulted in 453, 597, 577, and 636 DEG, respectively. Also, 101 overlapped genes were found by comparing 27 different expressed genes. These genes were associated with eight immune response pathways including NOD-like receptor signaling pathway (IL8, IL18, IL1B, PYDC1) and chemokine signaling pathway (PTK2, IL8, NCF1, CCR1, HCK). Meanwhile, 241 protein-protein interaction networks were developed among overlapped genes. Fifty-seven regulatory events were found between miRNAs, expressed genes, and the transcription factors (TFs) through micro-RNA and transcription factors (miRNA-DEG-TF) regulatory network. The 3D structure docking model of the expressed genes proteins identified their active sites and the binding ligands that could help in choosing the appropriate feed or treatment for affected animals. CONCLUSIONS: The novelty of the distinguished DEG and their pathways in this study is that they can precisely improve the detection biomarkers and treatments techniques of cows' Escherichia coli mastitis disease due to their high affinity with the target site of the mammary gland before appearing the symptoms.