Journal Articles

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    Dynamics of Porcine Circovirus Type 3 Detection in Pre-Weaning Piglets: Insight From Multiple Sampling Methods
    (John Wiley and Sons Ltd, 2025-01-24) Yang DA; Li M; Wang Y; Zhao K; Zhang Q; Laven RA; Yang Z; Chen N-H
    Porcine circovirus type 3 (PCV3) has been identified worldwide and is associated with reproductive and systemic diseases, yet the dynamics of PCV3 within pig farms remain unclear. Building upon our previous study, which initialised comparisons of different sample types for the detection of PCV3 in a sow farm, this study expanded both the range of sample types and the timeline of sampling in piglets and sows to better understand the PCV3 dynamics. This study collected two additional sample types—oropharyngeal swab (OS) and oral fluid (OF) along with placental umbilical cord (PUC) blood and processing fluid (PF) that were used in the previous study. Data were collected from July to August and October 2022; the aforementioned four sample types from 51 litters were collected, and additional OS samples were collected from two to three identified piglets per litter on days 1, 7, 14, and 21 post-farrowing. Besides, blood swabs were taken from 135 sows subject to both PCR test and oestrogen measurement. PF showed the highest detection rates (50/51), while OS and OF revealed 33/51 (95% confidence interval [CI]: 51.2%–76.8%) and 37/51 (95% CI: 59.5%–83.5%) detection rates; both were higher than that of PUC blood (22/51, 95% CI: 30.2%–56.8%). Despite the similarity between OS and OF samples, they did not identify the same population as infected, as the agreement between the samples was only fair at 90% level. The Bayesian generalised linear mixed model suggested PCV3 was more likely to be detected in both OS and OF compared to PUC blood, and PCV3 was present in the farrowing room throughout the pre-weaning period using an OS. Finally, we observed higher PCV3 detection rates in sows after farrowing; however, no evidence was found that such a pattern was associated with the decreased concentration of oestrogen.
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    Digestion of food proteins: the role of pepsin.
    (Taylor and Francis Group, 2025-01-21) Yang M; Yang Z; Everett DW; Gilbert EP; Singh H; Ye A
    The nutritive value of a protein is determined not only by its amino acid composition, but also by its digestibility in the gastrointestinal tract. The interaction between proteins and pepsin in the gastric stage is the first step and plays an important role in protein hydrolysis. Moreover, it affects the amino acid release rates and the allergenicity of the proteins. The interaction between pepsin and proteins from different food sources is highly dependent on the protein species, composition, processing treatment, and the presence of other food components. Coagulation of milk proteins under gastric conditions to form a coagulum is a unique behavior that affects gastric emptying and further hydrolysis of proteins. The processing treatment of proteins, either from milk or other sources, may change their structure, interactions with pepsin, and allergenicity. For example, the heat treatment of milk proteins results in the formation of a looser curd in the gastric phase and facilitates protein digestion by pepsin. Heated meat proteins undergo denaturation and conformational changes that enhance the rate of pepsin digestion. This review provides new ideas for the design of food products containing high protein concentrations that optimize nutrition while facilitating low allergenicity for consumers.
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    Pangenome graphs in infectious disease: a comprehensive genetic variation analysis of Neisseria meningitidis leveraging Oxford Nanopore long reads.
    (Frontiers Media S.A., 2023-08-10) Yang Z; Guarracino A; Biggs PJ; Black MA; Ismail N; Wold JR; Merriman TR; Prins P; Garrison E; de Ligt J; Hane J
    Whole genome sequencing has revolutionized infectious disease surveillance for tracking and monitoring the spread and evolution of pathogens. However, using a linear reference genome for genomic analyses may introduce biases, especially when studies are conducted on highly variable bacterial genomes of the same species. Pangenome graphs provide an efficient model for representing and analyzing multiple genomes and their variants as a graph structure that includes all types of variations. In this study, we present a practical bioinformatics pipeline that employs the PanGenome Graph Builder and the Variation Graph toolkit to build pangenomes from assembled genomes, align whole genome sequencing data and call variants against a graph reference. The pangenome graph enables the identification of structural variants, rearrangements, and small variants (e.g., single nucleotide polymorphisms and insertions/deletions) simultaneously. We demonstrate that using a pangenome graph, instead of a single linear reference genome, improves mapping rates and variant calling for both simulated and real datasets of the pathogen Neisseria meningitidis. Overall, pangenome graphs offer a promising approach for comparative genomics and comprehensive genetic variation analysis in infectious disease. Moreover, this innovative pipeline, leveraging pangenome graphs, can bridge variant analysis, genome assembly, population genetics, and evolutionary biology, expanding the reach of genomic understanding and applications.
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    Reprocessable Epoxy-Anhydride Resin Enabled by a Thermally Stable Liquid Transesterification Catalyst.
    (MDPI (Basel, Switzerland), 2024-11-20) Liang H; Tian W; Xu H; Ge Y; Yang Y; He E; Yang Z; Wang Y; Zhang S; Wang G; Chen Q; Wei Y; Ji Y; Jang K-S
    Introducing dynamic ester bonds into epoxy-anhydride resins enhances the reprocessability of the crosslinked network, facilitated by various types of transesterification catalysts. However, existing catalysts, such as metal salts and organic molecules, often struggle with dispersion, volatility, or structural instability issues. Here, we propose to solve such problems by incorporating a liquid-state, thermally stable transesterification catalyst into epoxy resins. This catalyst, an imidazole derivative, can be uniformly dispersed in the epoxy resin at room temperature. In addition, it shows high-temperature structural stability above at least 200 °C as the synergistic effects of the electron-withdrawing group and steric bulk can be leveraged. It can also effectively promote transesterification at elevated temperatures, allowing for the effective release of shear stress. This property enables the thermal recycling and reshaping of the fully crosslinked epoxy-anhydride resin. This strategy not only enhances the functionality of epoxy resins but also broadens their applicability across various thermal and mechanical environments.
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    Probing structural modification of milk proteins in the presence of pepsin and/or acid using small- and ultra-small-angle neutron scattering
    (Elsevier Ltd, 2025-02) Yang M; Ye A; Yang Z; Everett DW; de Campo L; Singh H; Gilbert EP
    Acid- and pepsin-induced milk protein coagulation plays a crucial role in the gastric digestion of milk. Real-time structural evolution at a nano- (e.g. colloidal calcium phosphate (CCP) and micelle) and micro- (gel network) level of unheated and heated (85 °C for 30 min) bovine milk was examined under acidic conditions and at low and high concentrations of pepsin using ultra-small- and small-angle neutron scattering (USANS and SANS), small-amplitude oscillatory rheometry and confocal scanning laser microscopy. Milk was treated with glucono-δ-lactone (GDL), pepsin or a combination of GDL and pepsin to induce coagulation. Heat-treated milk showed a faster increase in elastic storage modulus (G′) and scattering intensity (USANS and SANS) compared with unheated milk when coagulated with GDL or the combination of GDL and pepsin. At pH 6.3, heat treatment retarded pepsin (1.10 U/mL)-induced milk coagulation, with slower increases in G′ and scattering intensity. At a high concentration of pepsin (2000 U/mL) that mimics the concentration found in the stomach, general proteolysis followed coagulation. Heat treatment retarded coagulation but accelerated curd proteolysis. This study demonstrates how time-resolved USANS and SANS can be used to investigate the structural evolution of protein coagulation and degradation under gastric environment conditions at nano- and micro-metre length scales.
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    Understanding changes of laser backscattering imaging parameters through the kiwifruit softening process using time series analysis
    (Taylor and Francis Group on behalf of the Royal Society of New Zealand, 2024-05-12) Yang Z; Li M; East A; Zude-Sasse M; Gould N
    During kiwifruit storage, quality monitoring is required for inventory planning and consistent quality maintenance. Commercial near-infrared (NIR) spectrophotometers showed reduced performance in the estimation of kiwifruit flesh firmness (FF) as the FF estimation is indirect and can be affected when both, textural structures and absorbing compounds, change during postharvest ripening. Laser backscattering imaging (LBI) records the backscattered signal after a single laser beam interacts with kiwifruit tissue, including merged information on light absorption and scattering. Measurements were carried out at 830 nm, where scattering is most dominant. In this work, time series of kiwifruit ‘Zesy002’ (n = 30) and ‘Hayward’ (n = 30) LBI were collected through the postharvest ripening during a 15-day shelf life at 20°C. Four LBI parameters capturing DIP, FWHM, SLP and HWQM were selected in this study. ‘‘Zesy002’ DIP, FWHM, SLP, and HWQM increased approx. 0.6 cm, 0.2 cm, 0.3 and 0.14 cm, respectively. ‘Hayward’ LBI increased approx. 0.2 cm, 0.1 cm, 0.2 and 0.04 cm, respectively. Different initial LBI values between cultivars and LBI changes may reflect the actual stage of softening, affected by kiwifruit ripeness. In conclusion, time series analysis could be useful in describing kiwifruit LBI change during ripening and making forecasts.
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    High-coverage genomes to elucidate the evolution of penguins
    (Oxford University Press and BGI, 2019-09-18) Pan H; Cole TL; Bi X; Fang M; Zhou C; Yang Z; Ksepka DT; Hart T; Bouzat JL; Argilla LS; Bertelsen MF; Boersma PD; Bost C-A; Cherel Y; Dann P; Fiddaman SR; Howard P; Labuschagne K; Mattern T; Miller G; Parker P; Phillips RA; Quillfeldt P; Ryan PG; Taylor H; Thompson DR; Young MJ; Ellegaard MR; Gilbert MTP; Sinding M-HS; Pacheco G; Shepherd LD; Tennyson AJD; Grosser S; Kay E; Nupen LJ; Ellenberg U; Houston DM; Reeve AH; Johnson K; Masello JF; Stracke T; McKinlay B; Borboroglu PG; Zhang D-X; Zhang G
    BACKGROUND: Penguins (Sphenisciformes) are a remarkable order of flightless wing-propelled diving seabirds distributed widely across the southern hemisphere. They share a volant common ancestor with Procellariiformes close to the Cretaceous-Paleogene boundary (66 million years ago) and subsequently lost the ability to fly but enhanced their diving capabilities. With ∼20 species among 6 genera, penguins range from the tropical Galápagos Islands to the oceanic temperate forests of New Zealand, the rocky coastlines of the sub-Antarctic islands, and the sea ice around Antarctica. To inhabit such diverse and extreme environments, penguins evolved many physiological and morphological adaptations. However, they are also highly sensitive to climate change. Therefore, penguins provide an exciting target system for understanding the evolutionary processes of speciation, adaptation, and demography. Genomic data are an emerging resource for addressing questions about such processes. RESULTS: Here we present a novel dataset of 19 high-coverage genomes that, together with 2 previously published genomes, encompass all extant penguin species. We also present a well-supported phylogeny to clarify the relationships among penguins. In contrast to recent studies, our results demonstrate that the genus Aptenodytes is basal and sister to all other extant penguin genera, providing intriguing new insights into the adaptation of penguins to Antarctica. As such, our dataset provides a novel resource for understanding the evolutionary history of penguins as a clade, as well as the fine-scale relationships of individual penguin lineages. Against this background, we introduce a major consortium of international scientists dedicated to studying these genomes. Moreover, we highlight emerging issues regarding ensuring legal and respectful indigenous consultation, particularly for genomic data originating from New Zealand Taonga species. CONCLUSIONS: We believe that our dataset and project will be important for understanding evolution, increasing cultural heritage and guiding the conservation of this iconic southern hemisphere species assemblage.
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    Impact of thermosonication at neutral pH on the structural characteristics of faba bean protein isolate dispersions and their physicochemical and techno-functional properties
    (Elsevier Ltd, 2024-09) Hu Y; Cheng L; Gilbert EP; Lee SJ; Yang Z
    The effect of thermosonication (TS) (90 °C, 10–30 min) on faba bean protein isolate (FPI) at pH 7 was investigated. The microstructural and techno-functional properties of TS-treated FPI were compared with native FPI or FPI treated with conventional prolonged heating (CH, up to 8 h) at 90 °C. TS treatment effectively converted FPI to amorphous aggregates containing predominant β-sheet secondary structures, as determined by Thioflavin T (ThT) fluorescence and circular dichroism (CD). According to sodium dodecyl sulphate-polyacrylamide gel electrophoresis (SDS-PAGE), these amorphous aggregates could be formed by disulfide bonds. Additionally, TS treatment is efficient in disrupting large protein aggregates of FPI, thus improving their solubility. Both TS and CH treatments induced formation of viscoelastic FPI hydrogels, whose gel strength depends on the type and time of treatment. Hydrogels formation is likely to arise from the entanglement and interaction of protein aggregates as revealed by small angle neutron scattering (SANS) and scanning electron microscopy (SEM). TS-treated FPI was also used to prepare O/W emulsions and whose structural and physical properties were compared with those stabilised by untreated FPI. At all oil volume fractions (φ = 0.2, 0.5, and 0.7) and FPI concentrations (1, 3, and 5 wt %), emulsions stabilised by TS-treated FPI exhibited smaller oil droplet size, greater mechanical strength and superior stability compared to those stabilised by untreated FPI. The study suggests that TS treatment is promising in improving techno-functional properties of FPI; further studies are needed to exploit TS-treated plant proteins as a novel food ingredient in food product development.
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    Application of Absorption and Scattering Properties Obtained through Image Pre-Classification Method Using a Laser Backscattering Imaging System to Detect Kiwifruit Chilling Injury
    (MDPI (Basel, Switzerland), 2021-06-22) Yang Z; Li M; East AR; Zude-Sasse M; Ruiz-Altisent M; Diezma B
    Kiwifruit chilling injury (CI) damage occurs after long-term exposure to low temperature. A non-destructive approach to detect CI injury was tested in the present study, using a laser backscattering image (LBI) technique calibrated with 56 liquid phantoms for providing absorption coefficient (µa) and reduced scattering coefficient (µs'). Calibration of LBI resulted in a true-positive (TP) classification of 91.5% and 65.6% of predicted µs' and µa, respectively. The optical properties of 'SunGold™'and 'Hayward' kiwifruit were analysed at 520 nm with a two-step protocol capturing pre-classification according to the LBI parameters used in the calibration and estimation with the Farrell equation. Severely injured kiwifruit showed white corky tissue and water soaking, reduced soluble solids content and firmness measured destructively. Non-destructive classification results for 'SunGold™' showed a high percentage of TP for severe CI of 92% and 75% using LBI parameters directly and predicted µa and µs' after pre-classification, respectively. The classification accuracy for severe CI 'Hayward' kiwifruit with LBI parameter was low (58%) and with µa and µs' decreased further (35%), which was assumed to be due to interference caused by the long trichomes on the fruit surface.
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    Fibrillisation of faba bean protein isolate by thermosonication for process efficacy: Microstructural characteristics, assembly behaviour, and physicochemical properties
    (Elsevier Ltd, 2024-09) Hu Y; Cheng L; Gilbert EP; Loo TS; Lee SJ; Harrison J; Yang Z
    The effect of thermosonication (TS) (90 °C, 10–30 min) on the fibrillisation of faba bean protein isolate (FPI) was studied. The self-assembly behaviour, microstructural characteristics and techno-functional (gelation and emulsification) properties of FPI fibrils obtained from TS treatment were compared with those obtained from conventional prolonged heating (CH) at 90 °C up to 8 h. Compared to CH treatment, TS treatment was shown to significantly accelerate the formation of FPI fibrils with prominent β-sheet structures as revealed by Thioflavin T (ThT) fluorescence, Fourier-transform infrared spectroscopy (FTIR) and circular dichroism (CD). The characteristics of fibril building blocks were analysed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) and liquid chromatography linked to tandem mass spectrometry (LC-MS/MS) to obtain the differences between TS and CH induced fibrillisation of FPI. Transmission electron microscopy (TEM) and small-angle neutron scattering (SANS) showed that 4 h CH and 10 min TS treatments resulted in the fibrils with similar radius (from 5 to 10 nm). Furthermore, SANS indicated that TS treatment induced the formation of an entangled FPI fibrillar network, which could lead to the observed viscoelastic properties of FPI at a high concentration (10 wt%). Finally, high internal phase O/W emulsions (HIPE, φ = 0.75) stabilised by 30 min TS induced FPI fibrils (3 wt%) demonstrated a stronger gel strength and smaller oil droplet size compared to those prepared with untreated FPI, suggesting a superior emulsification capability of FPI fibrils. This finding demonstrates that TS treatment is a promising and efficient method for fibrillisation of plant proteins with the resultant fibrils generating excellent gelation and emulsification properties.