Science Collected Works - Research Publications
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ItemEffects of chitin and chitosan on root growth, biochemical defense response and exudate proteome of Cannabis sativa(Wiley, 2023-01-01)Fungal pathogens pose a major threat to Cannabis sativa production, requiring safe and effective management procedures to control disease. Chitin and chitosan are natural molecules that elicit plant defense responses. Investigation of their effects on C. sativa will advance understanding of plant responses towards elicitors and provide a potential pathway to enhance plant resistance against diseases. Plants were grown in the in vitro Root-TRAPR system and treated with colloidal chitin and chitosan. Plant morphology was monitored, then plant tissues and exudates were collected for enzymatic activity assays, phytohormone quantification, qPCR analysis and proteomics profiling. Chitosan treatments showed increased total chitinase activity and expression of pathogenesis-related (PR) genes by 3–5 times in the root tissues. In the exudates, total peroxidase and chitinase activities and levels of defense proteins such as PR protein 1 and endochitinase 2 were increased. Shoot development was unaffected, but root development was inhibited after chitosan exposure. In contrast, chitin treatments had no significant impact on any defense parameters, including enzymatic activities, hormone quantities, gene expression levels and root secreted proteins. These results indicate that colloidal chitosan, significantly enhancing defense responses in C. sativa root system, could be used as a potential elicitor, particularly in hydroponic scenarios to manage crop diseases.
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ItemImpact of Chronic Multi-Generational Exposure to an Environmentally Relevant Atrazine Concentration on Testicular Development and Function in Mice(MDPI, 2023-02-01)A common herbicide, atrazine, is associated with poor health. Atrazine acts as an endocrine disruptor at supra-environmental levels. Little research, however, has been conducted regarding chronic exposure to environmental atrazine concentrations across generations. This study utilized comprehensive endpoint measures to investigate the effects of chronic exposure to a conservative atrazine concentration (0.02 ng/mL), measured in Australian waterways, on male mice fertility across two generations. Mice were exposed through the maternal line, from the pre-conception period and through the F1 and F2 generations until three or six months of age. Atrazine did not impact sperm function, testicular morphology nor germ cell parameters but did alter the expression of steroidogenic genes in the F1, down-regulating the expression of Cyp17a1 (Cytochrome P450 family 17, subfamily A member 1; p = 0.0008) and Ddx4 (DEAD-box helicase 4; p = 0.007), and up-regulating the expression of Star (Steroidogenic acute regulatory protein; p = 0.017). In the F2, atrazine induced up-regulation in the expression of Star (p = 0.016). The current study demonstrates that chronic exposure to an environmentally relevant atrazine concentration perturbs testicular steroid-associated gene expression that varies across generations. Future studies through the paternal and combined parental lineages should be undertaken to further elucidate the multigenerational effects of atrazine on male fertility.
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ItemInfertile human endometrial organoid apical protein secretions are dysregulated and impair trophoblast progenitor cell adhesion(FRONTIERS MEDIA SA, 2022-12-14)INTRODUCTION: Embryo implantation failure leads to infertility. As an important approach to regulate implantation, endometrial epithelial cells produce and secrete factors apically into the uterine cavity in the receptive phase to prepare the initial blastocyst adhesion and implantation. Organoids were recently developed from human endometrial epithelium with similar apical-basal polarity compared to endometrial gland making it an ideal model to study endometrial epithelial secretions. METHODS: Endometrial organoids were established using endometrial biopsies from women with primary infertility and normal fertility. Fertile and infertile organoids were treated with hormones to model receptive phase of the endometrial epithelium and intra-organoid fluid (IOF) was collected to compare the apical protein secretion profile and function on trophoblast cell adhesion. RESULTS: Our data show that infertile organoids were dysregulated in their response to estrogen and progesterone treatment. Proteomic analysis of organoid apical secretions identified 150 dysregulated proteins between fertile and infertile groups (>1.5-fold change). Trophoblast progenitor spheroids (blastocyst surrogates) treated with infertile organoid apical secretions significantly compromised their adhesion to organoid epithelial cell monolayers compared to fertile group (P < 0.0001). DISCUSSION: This study revealed that endometrial organoid apical secretions alter trophoblast cell adhesiveness relative to fertility status of women. It paves the way to determine the molecular mechanisms by which endometrial epithelial apical released factors regulate blastocyst initial attachment and implantation.
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ItemDiverse monogenic subforms of human spermatogenic failure(NATURE PORTFOLIO, 2022-12-26)Non-obstructive azoospermia (NOA) is the most severe form of male infertility and typically incurable. Defining the genetic basis of NOA has proven challenging, and the most advanced classification of NOA subforms is not based on genetics, but simple description of testis histology. In this study, we exome-sequenced over 1000 clinically diagnosed NOA cases and identified a plausible recessive Mendelian cause in 20%. We find further support for 21 genes in a 2-stage burden test with 2072 cases and 11,587 fertile controls. The disrupted genes are primarily on the autosomes, enriched for undescribed human "knockouts", and, for the most part, have yet to be linked to a Mendelian trait. Integration with single-cell RNA sequencing data shows that azoospermia genes can be grouped into molecular subforms with synchronized expression patterns, and analogs of these subforms exist in mice. This analysis framework identifies groups of genes with known roles in spermatogenesis but also reveals unrecognized subforms, such as a set of genes expressed across mitotic divisions of differentiating spermatogonia. Our findings highlight NOA as an understudied Mendelian disorder and provide a conceptual structure for organizing the complex genetics of male infertility, which may provide a rational basis for disease classification.
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ItemTrade-off between conservation of biological variation and batch effect removal in deep generative modeling for single-cell transcriptomics(BMC, 2022-11-03)BACKGROUND: Single-cell RNA sequencing (scRNA-seq) technology has contributed significantly to diverse research areas in biology, from cancer to development. Since scRNA-seq data is high-dimensional, a common strategy is to learn low-dimensional latent representations better to understand overall structure in the data. In this work, we build upon scVI, a powerful deep generative model which can learn biologically meaningful latent representations, but which has limited explicit control of batch effects. Rather than prioritizing batch effect removal over conservation of biological variation, or vice versa, our goal is to provide a bird's eye view of the trade-offs between these two conflicting objectives. Specifically, using the well established concept of Pareto front from economics and engineering, we seek to learn the entire trade-off curve between conservation of biological variation and removal of batch effects. RESULTS: A multi-objective optimisation technique known as Pareto multi-task learning (Pareto MTL) is used to obtain the Pareto front between conservation of biological variation and batch effect removal. Our results indicate Pareto MTL can obtain a better Pareto front than the naive scalarization approach typically encountered in the literature. In addition, we propose to measure batch effect by applying a neural-network based estimator called Mutual Information Neural Estimation (MINE) and show benefits over the more standard maximum mean discrepancy measure. CONCLUSION: The Pareto front between conservation of biological variation and batch effect removal is a valuable tool for researchers in computational biology. Our results demonstrate the efficacy of applying Pareto MTL to estimate the Pareto front in conjunction with applying MINE to measure the batch effect.
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ItemInsect Antennal Morphology: The Evolution of Diverse Solutions to Odorant Perception(Yale University, 2018-12-01)Chemical communication involves the production, transmission, and perception of odors. Most adult insects rely on chemical signals and cues to locate food resources, oviposition sites or reproductive partners and, consequently, numerous odors provide a vital source of information. Insects detect these odors with receptors mostly located on the antennae, and the diverse shapes and sizes of these antennae (and sensilla) are both astonishing and puzzling: what selective pressures are responsible for these different solutions to the same problem - to perceive signals and cues? This review describes the selection pressures derived from chemical communication that are responsible for shaping the diversity of insect antennal morphology. In particular, we highlight new technologies and techniques that offer exciting opportunities for addressing this surprisingly neglected and yet crucial component of chemical communication.
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ItemObjectively Diagnosing Characteristics of Mesoscale Organization from Radar Reflectivity and Ambient Winds(American Meteorological Society, 2022-11-30)In the classical model of mesoscale convective systems (MCSs), a system generates new convective cells on the down-shear side of its cold pool, with the cells fed at low levels from the front, and the stratiform cloud trailing behind the system in the up-shear direction, where “front” and “behind” typically refer to the system’s ground-relative velocity. In this study we present an algorithm for identifying and tracking MCSs in radar reflectivity data, and objectively diagnosing organisational characteristics related to the classical model, namely the offset of stratiform cloud from convective cloud relative to system velocity, the low-level inflow direction, and the shear-relative tilt and propagation directions. When applied to the 15 year radar record covering the Darwin region of northern Australia, the algorithm indicates 65–80% of MCS observations are consistent with the classical model, at least when the four classifications can be made unambiguously. However, these observed characteristics occur almost entirely in the drier phases of the Australian monsoon. During the humid, active monsoon phase, observed characteristics consistent with the classical model are rare, and most systems exhibit non-classical up-shear propagation.
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ItemValuing and evaluating musical practice as research in ethnomusicology and its implications for research assessment(ROUTLEDGE JOURNALS, TAYLOR & FRANCIS LTD, 2022-01-02)
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ItemHepatotoxicity and Mutagenicity assessment during chronic in vivo exposure to aqueous extracts from Peperomia pellucida(ACAD BRASILEIRA DE CIENCIAS, 2022-01-01)Studies on herbal medicine have exposed some toxic effects on humans. Peperomia pellucida (L.) HBK (P. pellucida) is one of the herbal medicines recommended as an alternative to synthetic medicine for diseases. Studies exist on the pharmacological activities of P. pellucida extracts, but studies on the potential hepatotoxic and mutagenic effects of subchronic administration of P. pellucida aqueous extracts, which is very important knowledge when we venture into alternative medicine, are lacking. In this study, two concentrations (60 mg/kg and 30 mg/kg) of P. pellucida aqueous extracts - decoction and freeze-dried extracts -were administered in vivo to BALB/c mice for nine (9) weeks. Significant differences were observed between the 60 mg/kg freeze-dried extract and the control in terms of mice weight and micronucleus frequency at 7-8 weeks of treatment. Also, no significant differences were found between groups in serum transaminases levels. Generally, there is no sufficient evidence to show that subchronic exposure to P. pellucida aqueous extracts is hepatotoxic though 60 mg/kg concentration may be mutagenic. This study suggests that although the herbal medicine is safe for prolonged consumption, users are advised to take precautions and moderations of its use due to the possibility of potential mutagenic effects.
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ItemOrangutan Ecotourism on Sumatra Island: Current Conditions and a Call for Further Development(MDPI, 2022-09-01)This paper aimed to provide a narrative review of the current conditions of orangutan ecotourism on Sumatra Island, problems in the current management systems, and some recommendations for further development. Orangutan conservation centers have been developed on Sumatra Island since 1973. The Bukit Lawang Conservation Station is one of the orangutan conservation centers that have practiced ecotourism to overcome ecological and socio-economic issues. Even though the Bukit Lawang Conservation Station has operated for decades, this station has faced several issues, in particular a monetary crisis in 1997, a flash flood in 2003, and the COVID-19 pandemic. We identified that orangutan conservation centers on Sumatra Island have the potential to support orangutan ecotourism. These conservation centers have ecological support, available facilities, and rich local wisdom that can provide added value for orangutan ecotourism. Therefore, we propose that the development of orangutan ecotourism on Sumatra Island should accommodate surrounding communities through community-based wildlife ecotourism. We also recommend the following strategies to develop orangutan ecotourism on Sumatra Island: (1) mapping the location and distribution of wild orangutans in their natural habitats; (2) managing captive and semi-captive orangutans in conservation centers; (3) provision of tour packages; (4) community empowerment; (5) institutional strengthening of community-based ecotourism management (CBEM); (6) developing ecotourism through a benefit-sharing model; (7) anticipating and minimizing the negative impacts of ecotourism on orangutans; and (8) integrating orangutan tourism with local wisdom.