Mitochondrial genome-based synthesis and timeline of Eurasian otter (Lutra lutra) phylogeography

Sarah J. du Plessis,홍성원,이보영,Klaus-Peter Koepfli,Elizabeth A. Chadwick,Frank Hailer 한국통합생물학회 2023 Animal cells and systems Vol.27 No.1

Eurasian otters (Lutra lutra) have a broad distribution across Eurasia, but biogeographic dataoutside of western Europe is limited to disconnected pockets. Based on current subspeciesdesignations, Asia appears to harbour a large proportion of the species’ diversity, with 10 of 12Eurasian otter subspecies found in Asia. Here we provide a range-wide synthesis ofmitochondrial data, inferring a timeline and pattern of phylogeographic signals. Wholemitochondrial genomes of 27 Eurasian otters across 4 subspecies are presented from newlygenerated data (n = 6; 4 from Korea, 1 from Hong Kong and 2 from UK), assembled from theSequence Read Archive (n = 4), and sourced from GenBank (n = 17). We then combined wholemitochondrial genome results with cytochrome b data to increase the sample size andcontextualise our results with prior studies. We identified five distinct lineages that werediscordant with current subspecies classification. Phylogenetic dating revealed that the earliestdiverging lineage was the Japanese lineage, with remaining lineages diverging ≥0.08 millionyears ago. Mitochondrial diversity calculated by sample locations seemed mainly driven by thepresence of multiple lineages. When grouping samples by lineage, genetic diversity was highestin Lineage 1 (primarily found in China and Laos), followed by Lineage 2 (primarily found inKorea), and lowest diversity identified in Lineage 3 (primarily found in Europe). Our findingshighlight previously undetected lineage diversity within Eurasian otters, but also the need forfurther taxonomic and genomic evaluation of the species in Asia. The identified unique, distinctlineages of Eurasian otters also warrant urgent conservation attention.

Congenital malformations in the vertebral column: associations and possible embryologic origins

Anneli M. Du Plessis,Quenton Wessels,Albert Van Schoor,Natalie Keough 대한해부학회 2022 Anatomy & Cell Biology Vol.55 No.4

Cases of associations between random spinal congenital defects have previously been reported, yet several questions remain unanswered. Firstly, why are associations between what seems to be random combinations of vertebral malformations observed? Secondly, is there a common event or pattern that connects the associated defects? Therefore, this study aimed to identify congenital defects in the vertebral column and also to determine whether any associations, if present, between vertebral malformations exist. This article consequently discusses the possible embryological disruptions that may lead to the formation of various defects in the vertebral column. A random skeletal sample (n=187) was selected from the Pretoria Bone Collection housed in the Department of Anatomy, University of Pretoria (Ethics 678/2018). The sample was evaluated to determine the frequencies of spinal congenital defects in each set of remains. Identifiable congenital malformations were observed in 48.1% (n=90/187) of the sample. The results demonstrated a high probability of association between the different defects observed in the vertebral column. Findings are of value as they provide a reasonable explanation to why seemingly random cases of associations have been reported by several authors. This study is clinically relevant as severe spinal defects have been shown to have high morbidity in patients and mortality in infants.

THE EFFECT OF PROTEIN LEVEL AND DEGRADABILITY ON PARTIAL DIGESTION IN FEEDLOT STEERS

Meissner, H.H.,du Plessis, P.C. Asian Australasian Association of Animal Productio 1989 Animal Bioscience Vol.2 No.3

The effect of streptozotocin induced diabetes on sperm function: a closer look at AGEs, RAGEs, MAPKs and activation of the apoptotic pathway

Omolaoye Temidayo S.,Du Plessis Stefan S. 한국독성학회 2021 Toxicological Research Vol.37 No.1

This study was designed to (1) investigate the possible mechanisms through which diabetes-induced advanced glycation end products (AGEs) and receptor for AGEs (RAGE) activation can affect male reproductive function; and (2) corroborate the interaction of previously established independent pathways. Male albino Wistar rats (14-weeks old) weighing 250–300 g received either a single intraperitoneal injection of streptozotocin (30 mg/kg or 60 mg/kg), represented as STZ30 or STZ60 respectively, or citrate buffer (control). Diabetes mellitus (DM) was confirmed if plasma glucose levels were ≥ 14 mmol/L after 1 week. Animals were sacrificed after 8 weeks of treatment by an overdose of sodium pentobarbital (160 mg/kg body weight). The testes and epididymides were harvested. The testes were used for biochemical and Western blot analysis, while sperm was retrieved from the epididymis and analysed with computer-aided sperm analysis. The blood glucose levels of STZ60 animals were above the cut-off point and hence these animals were regarded as diabetic. Diabetic animals presented with a non-significant increase in AGE and RAGE expression. Diabetic animals showed a significant increase in the expression of cleaved caspase 3 compared to control (p < 0.001), and these animals also presented with an increase in the expression of JNK (p < 0.05), PARP (p = 0.059) and p38 MAPK (p = 0.1). Diabetic animals also displayed decreased catalase activity accompanied by a non-significant increase in malondialdehyde levels. Additionally, there was a significant decrease in the percentage of progressively motile spermatozoa (p < 0.05) in diabetic animals. This study has shed some light on the interplay between DM, AGE, RAGE and mitogen-activated protein kinase signalling in the testes of diabetic rats, which can result in altered sperm function and contribute to male infertility. However, more studies are needed to better understand this complicated process.

Direct Divergence Approximation between Probability Distributions and Its Applications in Machine Learning

Sugiyama, Masashi,Liu, Song,du Plessis, Marthinus Christoffel,Yamanaka, Masao,Yamada, Makoto,Suzuki, Taiji,Kanamori, Takafumi Korean Institute of Information Scientists and Eng 2013 Journal of Computing Science and Engineering Vol.7 No.2

Approximating a divergence between two probability distributions from their samples is a fundamental challenge in statistics, information theory, and machine learning. A divergence approximator can be used for various purposes, such as two-sample homogeneity testing, change-point detection, and class-balance estimation. Furthermore, an approximator of a divergence between the joint distribution and the product of marginals can be used for independence testing, which has a wide range of applications, including feature selection and extraction, clustering, object matching, independent component analysis, and causal direction estimation. In this paper, we review recent advances in divergence approximation. Our emphasis is that directly approximating the divergence without estimating probability distributions is more sensible than a naive two-step approach of first estimating probability distributions and then approximating the divergence. Furthermore, despite the overwhelming popularity of the Kullback-Leibler divergence as a divergence measure, we argue that alternatives such as the Pearson divergence, the relative Pearson divergence, and the $L^2$-distance are more useful in practice because of their computationally efficient approximability, high numerical stability, and superior robustness against outliers.

Environmental Exposure of Sperm Sex-Chromosomes: A Gender Selection Technique

Oyeyipo, Ibukun P.,van der Linde, Michelle,du Plessis, Stefan S. Korean Society of ToxicologyKorea Environmental Mu 2017 Toxicological Research Vol.33 No.4

Preconceptual sex selection is still a highly debatable process whereby X- and Y-chromosome-bearing spermatozoa are isolated prior to fertilization of the oocyte. Although various separation techniques are available, none can guarantee 100% accuracy. The aim of this study was to separate X- and Y-chromosome-bearing spermatozoa using methods based on the viability difference between the X- and Y-chromosome-bearing spermatozoa. A total of 18 experimental semen samples were used, written consent was obtained from all donors and results were analysed in a blinded fashion. Spermatozoa were exposed to different pH values (5.5, 6.5, 7.5, 8.5, and 9.5), increased temperatures ($37^{\circ}C$, $41^{\circ}C$, and $45^{\circ}C$) and ROS level ($50{\mu}M$, $750{\mu}M$, and $1,000{\mu}M$). The live and dead cell separation was done through a modified swim-up technique. Changes in the sex-chromosome ratio of samples were established by double-label fluorescent in situ hybridization (FISH) before and after processing. The results indicated successful enrichment of X-chromosome-bearing spermatozoa upon incubation in acidic media, increased temperatures, and elevated $H_2O_2$. This study demonstrated the potential role for exploring the physiological differences between X-and Y-chromosome-bearing spermatozoa in the development of preconceptual gender selection.

Insights Into Emissions and Exposures From Use of Industrial-Scale Additive Manufacturing Machines

Stefaniak, A.B.,Johnson, A.R.,du Preez, S.,Hammond, D.R.,Wells, J.R.,Ham, J.E.,LeBouf, R.F.,Martin, S.B. Jr.,Duling, M.G.,Bowers, L.N.,Knepp, A.K.,de Beer, D.J.,du Plessis, J.L. Occupational Safety and Health Research Institute 2019 Safety and health at work Vol.10 No.2

Background: Emerging reports suggest the potential for adverse health effects from exposure to emissions from some additive manufacturing (AM) processes. There is a paucity of real-world data on emissions from AM machines in industrial workplaces and personal exposures among AM operators. Methods: Airborne particle and organic chemical emissions and personal exposures were characterized using real-time and time-integrated sampling techniques in four manufacturing facilities using industrial-scale material extrusion and material jetting AM processes. Results: Using a condensation nuclei counter, number-based particle emission rates (ERs) (number/min) from material extrusion AM machines ranged from $4.1{\times}10^{10}$ (Ultem filament) to $2.2{\times}10^{11}$ [acrylonitrile butadiene styrene and polycarbonate filaments). For these same machines, total volatile organic compound ERs (${\mu}g/min$) ranged from $1.9{\times}10^4$ (acrylonitrile butadiene styrene and polycarbonate) to $9.4{\times}10^4$ (Ultem). For the material jetting machines, the number-based particle ER was higher when the lid was open ($2.3{\times}10^{10}number/min$) than when the lid was closed ($1.5-5.5{\times}10^9number/min$); total volatile organic compound ERs were similar regardless of the lid position. Low levels of acetone, benzene, toluene, and m,p-xylene were common to both AM processes. Carbonyl compounds were detected; however, none were specifically attributed to the AM processes. Personal exposures to metals (aluminum and iron) and eight volatile organic compounds were all below National Institute for Occupational Safety and Health (NIOSH)-recommended exposure levels. Conclusion: Industrial-scale AM machines using thermoplastics and resins released particles and organic vapors into workplace air. More research is needed to understand factors influencing real-world industrial-scale AM process emissions and exposures.

Insights Into Emissions and Exposures From Use of Industrial-Scale Additive Manufacturing Machines

A.B. Stefaniak,A.R. Johnson,S. du Preez,D.R. Hammond,J.R. Wells,J.E. Ham,R.F. LeBouf,S.B. Martin Jr.,M.G. Duling,L.N. Bowers,A.K. Knepp,D.J. de Beer,J.L. du Plessis 한국산업안전보건공단 산업안전보건연구원 2019 Safety and health at work Vol.10 No.2

Background: Emerging reports suggest the potential for adverse health effects from exposure to emissions from some additive manufacturing (AM) processes. There is a paucity of real-world data on emissions from AM machines in industrial workplaces and personal exposures among AM operators. Methods: Airborne particle and organic chemical emissions and personal exposures were characterized using real-time and time-integrated sampling techniques in four manufacturing facilities using industrial-scale material extrusion and material jetting AM processes. Results: Using a condensation nuclei counter, number-based particle emission rates (ERs) (number/min) from material extrusion AM machines ranged from 4.1 1010 (Ultem filament) to 2.2 1011 [acrylonitrile butadiene styrene and polycarbonate filaments). For these same machines, total volatile organic compound ERs (mg/min) ranged from 1.9 104 (acrylonitrile butadiene styrene and polycarbonate) to 9.4 104 (Ultem). For the material jetting machines, the number-based particle ER was higher when the lid was open (2.3 1010 number/min) than when the lid was closed (1.5e5.5 109 number/min); total volatile organic compound ERs were similar regardless of the lid position. Low levels of acetone, benzene, toluene, and m,p-xylene were common to both AM processes. Carbonyl compounds were detected; however, none were specifically attributed to the AM processes. Personal exposures to metals (aluminum and iron) and eight volatile organic compounds were all below National Institute for Occupational Safety and Health (NIOSH)-recommended exposure levels. Conclusion: Industrial-scale AM machines using thermoplastics and resins released particles and organic vapors into workplace air. More research is needed to understand factors influencing real-world industrial- scale AM process emissions and exposures.

Effect of Oxidative Stress on Male Reproduction

Ashok Agarwal,Gurpriya Virk,Chloe Ong,Stefan S du Plessis 대한남성과학회 2014 The World Journal of Men's Health Vol.32 No.1

Infertility affects approximately 15% of couples trying to conceive, and a male factor contributes to roughly half of these cases. Oxidative stress (OS) has been identified as one of the many mediators of male infertility by causing sperm dysfunction. OS is a state related to increased cellular damage triggered by oxygen and oxygen-derived free radicals known as reactive oxygen species (ROS). During this process, augmented production of ROS overwhelms the body’s antioxidant defenses. While small amounts of ROS are required for normal sperm functioning, disproportionate levels can negatively impact the quality of spermatozoa and impair their overall fertilizing capacity. OS has been identified as an area of great attention because ROS and their metabolites can attack DNA, lipids, and proteins; alter enzymatic systems; produce irreparable alterations; cause cell death; and ultimately, lead to a decline in the semen parameters associated with male infertility. This review highlights the mechanisms of ROS production, the physiological and pathophysiological roles of ROS in relation to the male reproductive system, and recent advances in diagnostic methods; it also explores the benefits of using antioxidants in a clinical setting.

Teaching out-of-field in Home Economics: A Systematic Quantitative Literature Review

Donna Pendergast,Sarah McManus,Jay R. Deagon,Anna Du Plessis 한국가정과교육학회 2022 한국가정과교육학회지 Vol.34 No.5

Out-of-field teaching (OOFT) is a global phenomenon impacting student learning outcomes and teacher attrition. Anecdotal evidence suggests that home economics teacher shortages drive OOFT, yet there is an absence of research regarding its impacts. A systematic quantitative literature review (SQLR) was conducted to address this research gap and establish a baseline. The inclusion criteria were secondary school home economics education and OOFT, peer reviewed, full-text, and published in English. The date of publication was not a limiting factor. Nine databases were searched in March 2022 and, following exclusion protocols, 25 papers were retained. The qualifying papers were published between 1979 and 2021 with authors from 13 countries. Five papers focussed exclusively on OOFT and home economics. The most used terminology to describe OOFT was 'qualified/unqualified' (n=19; 76%). A global shortage of in-field home economics teachers was the most reported cause for OOFT (n=17; 68%). Impacts on students included lower-quality teaching experiences. OOF teacher self-efficacy was negatively impacted. The impacts on students, teachers, and schools were found to be interlinked. This study provides a baseline to understand the causes and impacts of OOFT in home economics classrooms. Overall, t here was a p aucity o f data available regarding this t opic, e specially concerning i ts p revalence and reported experiences. This gap indicates the need for further research regarding OOFT in home economics, especially as OOFT is increasingly under scrutiny in all fields of education due to the negative effects on teachers, student learning outcomes, and school operations. The study also affirmed the need for advocacy to ensure policymakers are aware of the negative impacts of OOFT in home economics and act to seek remedies.