School of Science - Te Kura Pūtaiao

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https://hdl.handle.net/10292/1333

Research at AUT's School of Science - Te Kura Pūtaiao is focused on key scientific issues with regional and global significance. The common theme connecting all research areas is sustainability – in the broadest sense as it relates to environmental and human health. Our research is closely allied to teaching and learning opportunities at undergraduate and postgraduate level within the school. Research is organised in five main areas:

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A Comparative Study of Gender Disparities in Geoscience and Mining in Mongolia
(MDPI AG, 2023-08-29) Ochir, G; Baatar, M; Sanjaa, M; Williams, H
Mongolian women enjoy equal rights and actively participate in various sectors of the national economy, including the mineral and mining industry. The Mongolian University of Science and Technology (MUST), the largest university in Mongolia, plays a crucial role in preparing engineers for the Mongolian industry. Within MUST, the School of Geology and Mining Engineering (SGME) stands out as one of the largest schools, boasting a dedicated team of 136 staff members. Impressively, 92 of these staff members are female, constituting a remarkable 67.65% of the total staff. The directorial board of SGME, consisting of 12 members, also demonstrates a noteworthy level of gender diversity, with 5 of its members being female. This represents a proportion of 41.67% and highlights the inclusion of women in decision-making positions. Additionally, it is worth noting that the Geology and Hydrogeology department, one of the five departments within the School, is led by a capable female leader. However, despite the encouraging representation of women among staff and in leadership roles, there is a noticeable disparity in the enrollment and graduation rates of students at SGME. Currently, these rates stand at only about 20–24 percent, indicating the need for further efforts to encourage and support female students in pursuing geology and mining engineering studies. Outside of academia, within the mining industry, the Oyu Tolgoi large-scale mine, which in 2022 employed 20,328 workers, faces a significant gender imbalance. Out of this workforce, only 3577 are women, comprising a mere 18% of the total employees, while the remaining 82% are men. Among the 2997 total employees in the open pit mine, 737 women are employed in various roles, including 66 engineers and technicians, with the remaining 671 in other positions. In the newly opened underground mine, the total number of women employees stands at 2840, including 248 engineers and technicians and 2592 in other roles. Furthermore, on the Board of Directors, there are only 2 women out of a total of 23 managers, and a mere 104 women hold positions as senior staff and superintendents. A comparative analysis between Asia and other global regions reveals that female employment in Mongolia’s mining sector in general, at 18%, closely aligns with Oceania’s rates (17%) and surpasses those of both the broader Asian region (13%) and South America (11%). Addressing these statistical imbalances is crucial to improving gender equality in geoscience and mining. Historically, the mining industry has been male-dominated, but women-led professional geoscience and mining organizations in Mongolia play a vital role in promoting the recruitment, retention, and advancement of women in these industries. Recognizing the significance of gender diversity, these organizations strive to increase the representation of women in leadership positions. Women in leadership bring unique perspectives that contribute to well-rounded decision-making processes within organizations. By acknowledging the importance of gender dynamics, promoting inclusivity, and supporting the professional growth of Mongolian women in geoscience and mining, the overall development and sustainability of these sectors in the country will be greatly enhanced.
A Comprehensive Chemical Analysis of New Zealand Yacon Concentrate
(MDPI, ) Chessum, Keegan; Kam, Rothman; Chen, Tony; Yan, Mary
Yacon (Smallanthus sonchifolius) is an ancient Andean crop, traditionally used for both food and medicinal purposes, which was first introduced to New Zealand in the 1980s. In recent years, there has been growing global interest in yacon due to its potential as a functional food, which could be related to its unique profile of bioactive compounds, including prebiotic compounds, such as fructooligosaccharides (FOS), and phenolic compounds, which may have a range of activities, including antioxidant ones. FOS are non-digestible prebiotic carbohydrates, providing low calorific value and a positive impact on gut microflora. Our objective was to conduct a comprehensive chemical analysis of New Zealand yacon concentrate (NZYC, a sweet syrup produced from juice extracted from New Zealand grown yacon roots). Analysis included proximate composition, mineral, sugar, phenolic, amino acid, and organic acid profiles as well as antioxidant activity. The major mineral identified in NZYC was potassium (658 ± 6 mg/100 g), with significant concentrations of phosphorus, calcium, magnesium, and iron also determined by microwave plasma atomic emission spectrometry. The FOS content of NZYC ranged from 17.6 ± 0.3 to 52.7 ± 0.8 g/100 g as determined by high-performance liquid chromatography (HPLC), coupled with an evaporating light scattering detector (ELSD). The total phenolic content of NZYC ranged from 565 ± 9 to 785 ± 43 mg gallic acid equivalents per 100 g by the Folin-Ciocalteu method. Chlorogenic acid and caffeic acid were quantified as the major phenolic compounds. The major amino acids quantified were L-arginine, L-glutamic acid, L-proline, L-aspartic acid, and asparagine. The major organic acids quantified were citric, malic, quinic, and fumaric acids. The antioxidant activity of NZYC was determined by the ferric-reducing antioxidant power (FRAP) assay, cupric ion-reducing antioxidant capacity (CUPRAC) assay, and 2,2-diphenyl-1-picrylhydrazyl (DPPH) radical scavenging activity, and it was several times higher than both Manuka honey and goji berries by the basis of weight. These results support the classification of New Zealand yacon concentrate as a nutraceutical food product and its use in further development of novel food products.
A Peptidomic Approach to Discover the Potential Biomolecular Signatures Discriminating In-Bag Dry- and Wet-Aged Lamb
(Elsevier BV, 2024-03-05) Zhang, R; Maes, E; Hefer, C; Noble, A; Thomas, A; Yoo, MJY; Farouk, MM; Realini, CE; Deb-Choudhury, S
The study assessed the peptidomic profile of in-bag dry-aged (2 °C, RH 75 %, 0.5 m.s−1, n = 30) and wet-aged (-1.5 °C, n = 30) lamb with high and low levels of lipid oxidation. A total of 1056 low molecular weight peptides (< 10 kDa) were identified in aged lamb samples, using LC-MS/MS and label free quantification (data are available via ProteomeXchange with identifier PXD047738). Partial Least Squares – Discriminant analysis highlighted that all discriminating peptides in dry-aged lamb were from titin, whereas discriminating peptides in the wet-aged samples were predominantly from nebulin, myotilin, collagen type IV, LIM domain binding 3, and heat shock protein family B. Comparison of peptides from aged lamb meat with high- and low-levels of lipid oxidation showed that most discriminatory peptides within an ageing method are derived from oxidatively modified peptides from creatine kinase. These peptides could thus potentially be used as signature biomolecules to discriminate ageing techniques and indicate lipid oxidation levels.
A Review on Green-Lipped Mussel, Perna canaliculus Immunology: The Drivers, Virulence Factors, Advances, and Applications
(Informa UK Limited, 2023-10-25) Azizan, Awanis; Venter, Leonie; Alfaro, Andrea C
The endemic, green-lipped mussel (Perna canaliculus), trademarked as Greenshell™ mussel, contributes most to the New Zealand aquaculture industry based on tonnage and export value. Research on mussel immunity is motivated greatly by economical and biosecurity necessities. Indeed, mussel aquaculture is threatened by pathogenic micro-organisms and environmental stressors. As such there is a need to understand the mechanisms that drive mussel immune responses and the associated interactions with the environment. Specifically, this review (1) analyses the existing immunological studies conducted on P. canaliculus, (2) evaluates the literature pertaining to mussel immunity at the cellular and humoral levels, (3) identifies and discusses pathogens that are relevant to P. canaliculus, (4) focuses on the virulent factors employed by mussel pathogens likely to induce diseases, (5) provides a comprehensive analysis of the response mechanisms employed by mussels to various stressors, and (6) explores omics applications and future perspectives in mussel immunology. Finally, this review highlights various strategies from immunological research, such as gene rearrangement, probiotics, immunostimulants, and selective breeding, promising to enhance mussel health and resilience in aquaculture. By exploring these immunological findings and their practical applications, this review contributes to sustainable mussel aquaculture, improving productivity and disease management in the industry.
A Single Fungal Strain Was the Unexpected Cause of a Mass Aspergillosis Outbreak in the World’s Largest and Only Flightless Parrot
(Elsevier BV, 2022-11-02) Winter, DJ; Weir, BS; Glare, T; Rhodes, J; Perrott, J; Fisher, MC; Stajich, JE; Digby, A; Dearden, PK; Cox, MP
Kākāpō are a critically endangered species of parrots restricted to a few islands off the coast of New Zealand. Kākāpō are very closely monitored, especially during nesting seasons. In 2019, during a highly successful nesting season, an outbreak of aspergillosis affected 21 individuals and led to the deaths of 9, leaving a population of only 211 kākāpō. In monitoring this outbreak, cultures of aspergillus were grown, and genome sequenced. These sequences demonstrate that, very unusually for an aspergillus outbreak, a single strain of aspergillus caused the outbreak. This strain was found on two islands, but only one had an outbreak of aspergillosis; indicating that the strain was necessary, but not sufficient, to cause disease. Our analysis provides an understanding of the 2019 outbreak and provides potential ways to manage such events in the future.
Addressing the Persistence of Per- and Poly-Fluoroalkyl Substances (PFAS): Current Challenges and Potential Solutions
(Royal Society of Chemistry (RSC), 2024-08-14) Itumoh, Emeka J; Data, Shailja; Chen, Jack L-Y; Kah, Melanie; Padhye, Lokesh P; Leitao, Erin M
The combined stability, mobility, and bioaccumulation of per- and poly-fluoroalkyl substances (PFAS) has prompted a global environmental crisis. PFAS have unique properties owing to their strong, hydrophobic C–F bonds, which result in their resistance to water, oil, chemicals, and heat. Applications of PFAS include their use as water-, grease-, and fire-proof coatings, emulsifiers, and surfactants, spanning most manufacturing sectors. The continued regulation of specific PFAS provides significant research opportunities for chemists and their collaborators across environmental, social, engineering, and materials sciences. Solutions in the areas of detection and analysis, immobilisation and destruction, and the creation of viable and safe alternatives are urgently needed. In this tutorial review, PFAS and their associated challenges are described, followed by a summary of existing solutions and future research opportunities.
Advanced Photogrammetry to Assess Lichen Colonization in the Hyper-arid Namib Desert
(Frontiers Media, 2017-10-27) Hinchliffe, G; Bollard-Breen, B; Cowan, DA; Doshi, A; Gillman, LN; Rios-Murillo, A; Maggs-Kolling, G; Pointing, SB
The hyper-arid central region of the Namib Desert is characterised by quartz desert pavement terrain that is devoid of vascular plant covers. In this extreme habitat the only discernible surface covers are epilithic lichens that colonise exposed surfaces of quartz rocks. These lichens are highly susceptible to disturbance and so field surveys have been limited due to concerns about disturbing this unusual desert feature. Here we present findings that illustrate how non-destructive surveys based upon advanced photogrammetry techniques can yield meaningful and novel scientific data on these lichens. We combined ‘structure from motion analysis’, computer vision and GIS to create 3-dimensional point clouds from two-dimensional imagery. The data were robust in its application to estimating absolute lichen cover. An orange Stellarangia spp. assemblage had coverage of 22.8% of available substrate, whilst for a black Xanthoparmelia spp. assemblage coverage was markedly lower at 0.6% of available substrate. Hyperspectral signatures for both lichens were distinct in the near-infra red range indicating that Xanthoparmelia spp. was likely under relatively more moisture stress than Stellarangia spp. at the time of sampling, and we postulate that albedo effects may have contributed to this in the black lichen. Further transformation of the data revealed a colonisation preference for west-facing quartz surfaces and this coincides with prevailing winds for marine fog that is the major source of moisture in this system. Furthermore, a three-dimensional ‘fly through’ of the lichen habitat was created to illustrate how the application of computer vision in microbiology has further potential as a research and education tool. We discuss how advanced photogrammetry could be applied in astrobiology using autonomous rovers to add quantitative ecological data for visible surface colonisation on the surface of Mars.
Age, Growth and Reproductive Characteristics of the Blue-barred Parrotfish Scarus Ghobban From Taiwan and Solomon Islands
(Fisheries Society of the British Isles (FSBI), 2017-07-03) Visconti, V; Li-shu, C; Sabetian, A
Age, size, growth and sex ratio of the Blue barred parrot fish Scarus ghobban were investigated from Taiwan and Solomon Islands. While both populations exhibited similar rapid early growth, the longevity, maximum size and asymptotic length of S. ghobban in Taiwan were significantly higher than in the Solomon Islands. Gender analysis showed the oldest and largest size classes from the Solomon Islands to be males, while S. ghobban from Taiwan exhibited persistence of females in the oldest age classes, indicating that not all females in this protogynous hermaphrodite changed sex to males. The drivers for sex change in t this protogynous hermaphrodite may be more a function of genetics and longevity, and less so due to fishing pressure.
Aidi Injection, a Traditional Chinese Medicine Extract, Reverses Gefitinib Resistance in Non-small Cell Lung Cancer Cells
(Elsevier BV, 2021) Biswas, R; Yang, C-M; Lu, W; He, J; Chen, T; Tian, F; Li, Y
Introduction Aidi injection is a traditional Chinese medicine containing multiple anti-tumour and immunomodulatory phytochemicals. While it synergistically enhances the efficacy of conventional chemotherapy in patients with non-small cell lung cancer (NSCLC), its effect on epidermal growth factor receptor (EGFR) tyrosine kinase inhibitor (TKI) sensitivity in NSCLC remains unclear. This study aimed to investigate the effect and mechanisms of Aidi injection on the sensitivity of human NSCLC cell lines to gefitinib. Methods Effect of Aidi injection on gefitinib sensitivity was assessed by MTT, colony formation and apoptosis assays in three NSCLC cell lines (A549, HCC827 and H1975). The association between the expression of genes and the overall survival was analysed by accessing TCGA lung adenocarcinoma datasets. The effect of Aidi injection on multidrug resistance-associated protein 2 (MRP2, encoded by ABCC2 gene) function and gefitinib sensitivity was compared between parental HEK293 cell and HEK293 overexpressing MRP2 cells (HEK/MRP2). The principle components of Aidi injection were determined by LC-MS/MS and the interaction of Aidi components with MRP2 protein explored using molecular docking. Results Aidi injection enhanced gefitinib sensitivity (P < 0.05) and increased gefitinib-induced apoptosis rate (P < 0.05) in three NSCLC cell lines. Analysis of TCGA lung adenocarcinoma dataset showed that patients with a high expression of ABCC2 had significantly poorer survival (P = 0.007546). Aidi injection inhibited MRP2 activity in a concentration-dependant manner in HEK/MRP2 cells (P < 0.05). The combination of gefitinib with Aidi injection gave additive or weakly synergistic growth inhibition in HEK/MRP2 cells but exhibited antagonistic cytotoxicity in HEK293 cells. There were 11 main chemical components contained in Aidi injection, including astragalosides II and IV, cantharidin, etheutheroside E, ginsenosides Rb1, Rc, Rd, Re and Rg1, isofraxidin, and syringin. Docking studies showed strong affinity of Ginsenoside_Re towards MRP2. Conclusions Aidi injection may have the potential to be an adjuvant regimen to prevent and/or reverse common gefitinib resistance in NSCLC. The in silico and principle component analyses gives insight on ginsenoside_Re being a potential MRP2 inhibitor in Aidi injection.
Alkyl Linker Effects on the Coordination Topology of Ditopic Di(2-pyridylmethyl)amine Carboxylate Ligands with Znˡˡ and Cuˡˡ: Polymers Vs. Macrocycles
(The Royal Society of Chemistry, 2015) Rodpun, K; Blackman, AG; Gardiner, MG; Tan, EW; Meledandri, CJ; Lucas, NT
A series of ditopic ω-di(2-pyridylmethyl)amine carboxylic acid ligands incorporating a range of n-alkyl linkers (CnCOOH, n = 3-5, 7, 10 and 11) have been synthesised. Solution phase studies showed a 1:1 coordination stoichiometry between the ligands and M(ClO4)2·6H2O (M = ZnII or CuII) in all cases. The ZnII and CuII complexes were subsequently crystallised by liquid-liquid diffusion and the solid-state structures investigated by X-ray crystallography. The crystal structures obtained are entirely consistent with the 1:1 metal-ligand ratio of the solution-phase adducts. However, the coordination geometries and complex topologies are dependent on the alkyl chain length of the ligand CnCOOH. The ZnII and CuII complexes of the short alkyl chain ligands (n ≤ 5) exhibit 1D coordination polymeric structures with somewhat different conformations for {[Zn(C3COO)(H2O)](ClO4)·3.5H2O}n (1), {[Zn(C4COO)(H2O)]4(ClO4)4·1.5H2O}n (2), {[Zn(C5COO)(H2O)](ClO4)}n (3), {[Cu(C3COO)](ClO4)·MeOH}n (4), {[Cu(C4COO)(H2O)]2(ClO4)2·2H2O}n (5) and {[Cu(C5COO)(H2O)](ClO4)·2H2O}n (6). In contrast, the ligands with longer alkyl chains (n ≥ 7) participate in Zn2L2 metallomacrocyclic structures {[Zn(C7COO)(H2O)](ClO4)}2 (7), [Zn2(C10COO)2(H2O)2](ClO4)2·2H2O·MeOH (8) and {[Zn2(C11COO)2(H2O)2][Zn2(C11COO)2](ClO4)4·H2O}n (9). The formation of metallomacrocycles instead of the 1D coordination polymers is a persistent trend and, with identical crystal growth conditions and a non-coordinating anion employed, appears to be an effect of the longer alkyl chain.
Analysing Civilian Video Footage for Enhanced Scientific Understanding of the 2011 Tohoku Earthquake and Tsunami, Japan, with Implications for PNG and Pacific Islands
(MDPI AG, 2023-07-03) Mcdonough-Margison, Caitlin; Hinchliffe, Graham; Petterson, Michael G
Approximately 70% of global tsunamis are generated within the pan Pacific Ocean region. This paper reports on detailed analysis of civilian video footage from the 2011 Tohoku earthquake, Japan. Comprehensive scientific analysis of tsunami video footage can yield valuable insights into geophysical processes and impacts. Civili22an video footage captured during the 2011 Tohoku, East Honshu, Japan tsunami was critically examined to identify key tsunami processes and estimate local inundation heights and flow velocity in Kesennuma City. Significant tsunami processes within the video were captured and orientated in ArcGIS Pro to create an OIC (Oriented Imagery Catalogue). The OIC was published to ArcGIS Online, and the oriented imagery was configured into an interactive website. Flow velocity was estimated by quantifying the distance and time taken for an object to travel between two known points in the video. Estimating inundation height was achieved by taking objects with known or calculable dimensions and measuring them against maximum local inundation height observations. The oriented imagery process produced an interactive Experience Builder app in ArcGIS Online, highlighting key tsunami processes captured within the video. The estimations of flow velocity and local inundation height quantified during video analysis indicate flow speeds ranging from 2.5–4.29 m/s and an estimated maximum local run-up height of 7.85 m in Kesennuma City. The analysis of civilian video footage provides a remarkable opportunity to investigate tsunami impact in localised areas of Japan and around the world. These data and analyses inform tsunami hazard maps, particularly in reasonably well-mapped terrains with remote access to landscape data. The results can aid in the understanding of tsunami behaviours and help inform effective mitigation strategies in tsunami-vulnerable areas. The affordable, widely accessible analysis and methodology presented here has numerous applications, and does not require highly sophisticated equipment. Tsunamis are a significant to major geohazard globally including many Pacific Island states, e.g., Papua New Guinea, Solomon Islands, and Tonga. Video footage geoscientific analysis, as here reported, can benefit tsunami and cyclone storm surge hazards in the Pacific Islands region and elsewhere.
Annual (2023) Taxonomic Update of RNA-Directed RNA Polymerase-Encoding Negative-Sense RNA Viruses (Realm Riboviria: Kingdom Orthornavirae: Phylum Negarnaviricota)
(2023-08) Kuhn, Jens H; Abe, Junya; Adkins, Scott; Alkhovsky, Sergey V; Avšič-Županc, Tatjana; Ayllón, María A; Bahl, Justin; Balkema-Buschmann, Anne; Ballinger, Matthew J; Kumar Baranwal, Virendra; Beer, Martin; Bejerman, Nicolas; Bergeron, Éric; Biedenkopf, Nadine; Blair, Carol D; Blasdell, Kim R; Blouin, Arnaud G; Bradfute, Steven B; Briese, Thomas; Brown, Paul A; Buchholz, Ursula J; Buchmeier, Michael J; Bukreyev, Alexander; Burt, Felicity; Büttner, Carmen; Calisher, Charles H; Cao, Mengji; Casas, Inmaculada; Chandran, Kartik; Charrel, Rémi N; Kumar Chaturvedi, Krishna; Chooi, Kar Mun; Crane, Anya; Dal Bó, Elena; Carlos de la Torre, Juan; de Souza, William M; de Swart, Rik L; Debat, Humberto; Dheilly, Nolwenn M; Di Paola, Nicholas; Di Serio, Francesco; Dietzgen, Ralf G; Digiaro, Michele; Drexler, J Felix; Duprex, W Paul; Dürrwald, Ralf; Easton, Andrew J; Elbeaino, Toufic; Ergünay, Koray; Feng, Guozhong; Firth, Andrew E; Fooks, Anthony R; Formenty, Pierre BH; Freitas-Astúa, Juliana; Gago-Zachert, Selma; Laura García, María; García-Sastre, Adolfo; Garrison, Aura R; Gaskin, Thomas R; Gong, Wenjie; Gonzalez, Jean-Paul J; de Bellocq, JoëlleGoüy; Griffiths, Anthony; Groschup, Martin H; Günther, Ines; Günther, Stephan; Hammond, John; Hasegawa, Yusuke; Hayashi, Kazusa; Hepojoki, Jussi; Higgins, Colleen M; Hongō, Seiji; Horie, Masayuki; Hughes, Holly R; Hume, Adam J; Hyndman, Timothy H; Ikeda, Kenichi; Jiāng, Dàohóng; Jonson, Gilda B; Junglen, Sandra; Klempa, Boris; Klingström, Jonas; Kondō, Hideki; Koonin, Eugene V; Krupovic, Mart; Kubota, Kenji; Kurath, Gael; Laenen, Lies; Lambert, Amy J; Lǐ, Jiànróng; Li, Jun-Min; Liu, Ran; Lukashevich, Igor S; MacDiarmid, Robin M; Maes, Piet; Marklewitz, Marco; Marshall, Sergio H; Marzano, Shin-Yi L; McCauley, John W; Mirazimi, Ali; Mühlberger, Elke; Nabeshima, Tomoyuki; Naidu, Rayapati; Natsuaki, Tomohide; Navarro, Beatriz; Navarro, José A; Neriya, Yutaro; Netesov, Sergey V; Neumann, Gabriele; Nowotny, Norbert; Nunes, Márcio RT; Ochoa-Corona, Francisco M; Okada, Tomoyuki; Palacios, Gustavo; Pallás, Vicente; Papa, Anna; Paraskevopoulou, Sofia; Parrish, Colin R; Pauvolid-Corrêa, Alex; Pawęska, Janusz T; Pérez, Daniel R; Pfaff, Florian; Plemper, Richard K; Postler, Thomas S; Rabbidge, Lee O; Radoshitzky, Sheli R; Ramos-González, Pedro L; Rehanek, Marius; Resende, Renato O; Reyes, Carina A; Rodrigues, Thaís CS; Romanowski, Víctor; Rubbenstroth, Dennis; Rubino, Luisa; Runstadler, Jonathan A; Sabanadzovic, Sead; Sadiq, Sabrina; Salvato, Maria S; Sasaya, Takahide; Schwemmle, Martin; Sharpe, Stephen R; Shi, Mang; Shimomoto, Yoshifumi; Kavi Sidharthan, Venkidusamy; Sironi, Manuela; Smither, Sophie; Song, Jin-Won; Spann, Kirsten M; Spengler, Jessica R; Stenglein, Mark D; Takada, Ayato; Takeyama, Sawana; Tatara, Akio; Tesh, Robert B; Thornburg, Natalie J; Tian, Xin; Tischler, Nicole D; Tomitaka, Yasuhiro; Tomonaga, Keizō; Tordo, Noël; Tu, Changchun; Turina, Massimo; Tzanetakis, Ioannis E; Maria Vaira, Anna; van den Hoogen, Bernadette; Vanmechelen, Bert; Vasilakis, Nikos; Verbeek, Martin; von Bargen, Susanne; Wada, Jiro; Wahl, Victoria; Walker, Peter J; Waltzek, Thomas B; Whitfield, Anna E; Wolf, Yuri I; Xia, Han; Xylogianni, Evanthia; Yanagisawa, Hironobu; Yano, Kazutaka; Ye, Gongyin; Yuan, Zhiming; Zerbini, F Murilo; Zhang, Guilin; Zhang, Song; Zhang, Yong-Zhen; Zhao, Lu; Økland, Arnfinn Lodden
In April 2023, following the annual International Committee on Taxonomy of Viruses (ICTV) ratification vote on newly proposed taxa, the phylum Negarnaviricota was amended and emended. The phylum was expanded by one new family, 14 new genera, and 140 new species. Two genera and 538 species were renamed. One species was moved, and four were abolished. This article presents the updated taxonomy of Negarnaviricota as now accepted by the ICTV.
Anti-proliferation Potential and Content of Fucoidan Extracted From Sporophyll of New Zealand Undaria Pinnatifida
(Frontiers Media S. A., 2014) Mak, W; Wang, SK; Liu, T; Hamid, N; Lu, J; Li, Y; White, WL
Undaria pinnatifida is a species of brown seaweed known to contain rich amounts of fucoidan, a sulfated polysaccharide known to possess various biological activities. We isolated crude fucoidan (F0) from the sporophylls of U. pinnatifida grown in the Marlborough Sounds, New Zealand. Sulfate content, uronic acid content, and molecular weight of F0 were 15.02, 1.24, and >150 kDa, respectively. F0 was fractionated to yield three further fractions: F1, F2, and F3. Cytotoxicity of two major fractions was determined by the 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay. The algal fucoidans specifically suppressed the proliferation of three cancer cell lines with less cytotoxicity against the normal cells. Selective cytotoxicity could relate to the distinctive structures of each fucoidan fraction. Results from this study provide evidence that fucoidan, especially from U. pinnatifida grown in New Zealand, possesses great potential to be used as a functional food to reduce cancer risk or supplement cancer treatment.
An Appeal for a Code of Conduct for Marine Conservation
(Elsevier, 2017-07-01) Bennett, NJ; Teh, L; Ota, Y; Christie, P; Ayers, A; Day, JC; Franks, P; Gill, D; Gruby, RL; Kittinger, JN; Koehn, JZ; Lewis, N; Parks, J; Vierros, M; Whitty, TS; Wilhelm, A; Wright, K; Aburto, JA; Finkbeiner, EM; Gaymer, CF; Govan, H; Gray, N; Jarvis, RM; Kaplan-Hallam, M; Satterfield, T
Marine conservation actions are promoted to conserve natural values and support human wellbeing. Yet the quality of governance processes and the social consequences of some marine conservation initiatives have been the subject of critique and even human rights complaints. These types of governance and social issues may jeopardize the legitimacy of, support for and long-term effectiveness of marine conservation. Thus, we argue that a clearly articulated and comprehensive set of social standards - a code of conduct - is needed to guide marine conservation. In this paper, we draw on the results of an expert meeting and scoping review to present key principles that might be taken into account in a code of conduct, to propose a draft set of foundational elements for inclusion in a code of conduct, to discuss the benefits and challenges of such a document, and to propose next steps to develop and facilitate the uptake of a broadly applicable code of conduct within the marine conservation community. The objectives of developing such a code of conduct are to promote fair conservation governance and decision-making, socially just conservation actions and outcomes, and accountable conservation practitioners and organizations. The uptake and implementation of a code of conduct would enable marine conservation to be both socially acceptable and ecologically effective, thereby contributing to a truly sustainable ocean.
Application of CRISPR-Cas9 System to Study Biological Barriers to Drug Delivery
(MDPI AG, ) He, J; Biswas, R; Bugde, P; Li, J; Liu, D-X; Li, Y
In recent years, sequence-specific clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated (Cas) systems have been widely used in genome editing of various cell types and organisms. The most developed and broadly used CRISPR-Cas system, CRISPR-Cas9, has benefited from the proof-of-principle studies for a better understanding of the function of genes associated with drug absorption and disposition. Genome-scale CRISPR-Cas9 knockout (KO) screen study also facilitates the identification of novel genes in which loss alters drug permeability across biological membranes and thus modulates the efficacy and safety of drugs. Compared with conventional heterogeneous expression models or other genome editing technologies, CRISPR-Cas9 gene manipulation techniques possess significant advantages, including ease of design, cost-effectiveness, greater on-target DNA cleavage activity and multiplexing capabilities, which makes it possible to study the interactions between membrane proteins and drugs more accurately and efficiently. However, many mechanistic questions and challenges regarding CRISPR-Cas9 gene editing are yet to be addressed, ranging from off-target effects to large-scale genetic alterations. In this review, an overview of the mechanisms of CRISPR-Cas9 in mammalian genome editing will be introduced, as well as the application of CRISPR-Cas9 in studying the barriers to drug delivery.
Application of Multiple Intake Temporal Check All That Apply: A Case Study of Strawberry Yoghurt Formulated with Alternative Sweeteners.
(Wiley, 2023-12-12) Chadha, Diksha; Hamid, Nazimah; Kantono, Kevin
BACKGROUND: It is crucial to reduce the high sugar content of fruit yoghurts in response to the excessive weight gain epidemic. The use of alternative sweeteners in yoghurts is often associated with the negative sensory attributes that can have an impact on yoghurt liking. The main objective of this research was to investigate the effect of alternative sweeteners and strawberry puree addition on the temporal sensory profile of yoghurt using multiple-intake temporal check all that apply (TCATA). A novel approach to the statical analysis of the temporal sensory data was employed by using Aligned Rank Transformation (ART)-ANOVA to investigate the differences between sensory attributes within different product and within different intakes. RESULTS: Results showed that attributes sweet and fruity decreased when the concentration of fruit puree was increased at low concentration of sucrose. Interestingly, when the concentration of fruit puree was increased fruitiness increased and mouthcoating decreased at low concentration of stevia. With successive intakes, attributes sweet, sour, creamy and fruity significantly decreased in yoghurts sweetened with sucrose, xylitol and stevia. Yoghurts containing low concentration of sucrose or xylitol and fruit puree were liked the most. However, stevia-sweetened yoghurts varying in sweetener and puree concentration were not significantly different in liking. In order to investigate the consumer acceptance of yoghurts, a novel approach was used i.e., utilising TCATA temporal data to investigate temporal drivers of liking for each yoghurt type. CONCLUSION: The use of multiple statistical analysis to analyse temporal data suggested that both sweetener and puree concentration need to be considered when developing products using alternative sweeteners. This article is protected by copyright. All rights reserved.
Are Rare Plant Species Less Resistant Than Common Ones to Herbivores? A Multi-plant Species Study Using Above- and Below-Ground Generalist Herbivores
(Wiley, 2023-09-05) Bürli, S; Ensslin, A; Kempel, A; Fischer, M
Rare plant species are suggested to be less resistant to herbivores than common species. Their lower apparency and the fact that they often live in isolated populations, resulting in fewer herbivore encounters, might have led to the evolution of reduced defences. Moreover, their frequent lower levels of genetic diversity compared with common species could negatively affect their resistance against enemies. However, the hypothesis that plant resistance depends on plant regional and local rarity, independently of habitat and competitive and growth strategy, lacks evidence. To test this hypothesis, we assessed the performance and preference of one belowground and three aboveground generalist invertebrate herbivores from different taxonomic groups as indicators of plant resistance. Herbivores were fed a total of 62 regionally and locally rare and common plant species from Switzerland. We accounted for differences in a plant's growth and competitive strategy and habitat resource availability. We found that regionally and locally rare and common plant species did not generally differ in their resistance to most generalist herbivores. However, one herbivore species even performed better and preferred locally and regionally common plant species over rarer ones, indicating that common species are not more resistant, but tend to be less resistant. We also found that all herbivore species consistently performed better on competitive and large plant species, although different herbivore species generally preferred and performed better on different plant species. The latter indicates that the use of generalist herbivores as indicators of plant-resistance levels can be misleading. Synthesis: Our results show that rare plant species are not inherently less resistant than common ones to herbivores. Instead, our results suggest that the ability of plants to allocate resources away from defence towards enhancing their competitive ability might have allowed plants to tolerate herbivory, and to become locally and regionally common.
Array Comparative Genomic Hybridization Identifies a Heterozygous Deletion of Exon 3 of the RYR2 Gene
(Taylor & Francis, 2015) Leong, IU; Sucich, J; Prosser, DO; Skinner, JR; Crawford, JR; Higgins, C; Love, DR
Catecholaminergic polymorphic ventricular tachycardia (CPVT) is a heritable cardiac disorder characterized by life-threatening ventricular tachycardia caused by exercise or acute emotional stress. The standard diagnostic screening involves Sanger-based sequencing of 45 of the 105 translated exons of the RYR2 gene, and copy number changes of a limited number of exons that are detected using multiplex ligation-dependent probe amplification (MLPA).
Aspect Has a Greater Impact on Alpine Soil Bacterial Community Structure Than Elevation
(Oxford University Press (OUP), 2017-01-01) Wu, J; Anderson, BJ; Buckley, HL; Lewis, G; Lear, G
Gradients in environmental conditions, including climate factors and resource availability, occur along mountain inclines, providing a ‘natural laboratory’ to explore their combined impacts on microbial distributions. Conflicting spatial patterns observed across elevation gradients in soil bacterial community structure suggest that they are driven by various interacting factors at different spatial scales. Here, we investigated the relative impacts of non-resource (e.g. soil temperature, pH) and resource conditions (e.g. soil carbon and nitrogen) on the biogeography of soil bacterial communities across broad (i.e. along a 1500 m mountain elevation gradient) and fine sampling scales (i.e. along sunny and shady aspects of a mountain ridge). Our analysis of 16S rRNA gene data confirmed that when sampling across distances of < 1000 m, bacterial community composition was more closely related to the aspect of a site than its elevation. However, despite large differences in climate and resource-availability factors across elevation- and aspect-related gradients, bacterial community composition and richness were most strongly correlated with soil pH. These findings highlight the need to incorporate knowledge of multiple factors, including site aspect and soil pH for the appropriate use of elevation gradients as a proxy to explore the impacts of climate change on microbial community composition. NOTE: The publisher regrets that an error was introduced in the values of the color key of figure 2a. These values have now been corrected [Erratum doi: 10.1093/femsec/fix032]
Assessing the Sulfide Footprint of Mussel Farms With Sediment Profile Imagery: A New Zealand Trial
(PLOS, 2015) Wilson, PS; Vopel, K
Growing numbers and increased stocking of marine mussel farms make reliable techniques for environmental effect assessment a priority. Previously, we showed how the color intensity of soft sediment could be used to estimate its acid volatile sulfide (AVS) content, a product of the anaerobic microbial degradation of organic matter deposits. We then proposed to include assessments of the AVS farm footprint in marine farm monitoring, in particular, to investigate temporal changes in the extent of the seafloor area of elevated sediment AVS content. Such assessment requires accurate detection of the AVS footprint boundary. Here, we demonstrate how to detect this boundary with analyses of sediment color intensity. We analyzed 182 sediment profile images taken along three transects leading from approximately 50 m inside to 200 m outside a long-line mussel farm in New Zealand and found that the mean sediment color intensity inside the farm boundary was almost one third lower than that of the sediment distant from the farm. Segmented regression analysis of the combined color intensity data revealed a breakpoint in the trend of increasing grey values with increasing distance from the farm at 56 ± 13 m (± 95% confidence interval of the breakpoint) outside the mussel farm. Mapping of grey value data with ArcMap (ESRI, ArcGIS) indicated that the extent of the color intensity footprint is a function of water column depth; organic particles disperse further in a deeper seawater column. We conclude that for soft coastal sediments, our sampling and data analysis techniques may provide a rapid and reliable supplement to existing benthic surveys that assess environmental effects of mussel farms.

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