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A functional gene-array analysis of microbial communities settling on microplastics in a peat-draining environment

Rahman I, Mujahid A, Palombo EA, Müller M

Mar Pollut Bull, 2021 May;166:112226.
PMID: 33711605 DOI: 10.1016/j.marpolbul.2021.112226

Concerns about microplastic (MP) pollution arise from the rafting potential of these durable particles which potentially propagate harmful chemicals and bacteria across wide spatial gradients. While many studies have been conducted in the marine environment, knowledge of MPs in coastal and freshwater systems is limited. For this study, we exposed two MPs (polyethylene terephthalate and polylactic acid) to the undisturbed peat-draining Maludam River in Malaysia, for 6 months. The microbial communities on these MPs and the surrounding water were sequenced by MiSeq, while the genetic responses of these communities were assessed by GeoChip 5.0S. Microbial communities were dominated by the phyla Proteobacteria, Acidobacteria and Actinobacteria. Metabolic processes involved with carbon, nitrogen, sulfur, metal homeostasis, organic remediation and virulence had significantly different gene expression among the communities on MPs and in the surrounding water. Our study is the first to look at changes in gene expression of whole plastisphere communities.
Fulltext Construction of an infectious cDNA clone of Enterovirus 71: insights into the factors ensuring experimental success

Lazouskaya NV, Palombo EA, Poh CL, Barton PA

J Virol Methods, 2014 Mar;197:67-76.
PMID: 24361875 DOI: 10.1016/j.jviromet.2013.12.005

Enterovirus 71 (EV 71) is a causative agent of mild Hand Foot and Mouth Disease but is capable of causing severe complications in the CNS in young children. Reverse genetics technology is currently widely used to study the pathogenesis of the virus. The aim of this work was to determine and evaluate the factors which can contribute to infectivity of EV 71 RNA transcripts in vitro. Two strategies, overlapping RT-PCR and long distance RT-PCR, were employed to obtain the full-length genome cDNA clones of the virus. The length of the poly(A) tail and the presence of non-viral 3'-terminal sequences were studied in regard to their effects on infectivity of the in vitro RNA transcripts of EV 71 in cell culture. The data revealed that only cDNA clones obtained after long distance RT-PCR were infectious. No differences were observed in virus titres after transfection with in vitro RNA harbouring a poly(A) tail of 18 or 30 adenines in length, irrespective of the non-viral sequences at the 3'-terminus.
Fulltext The Ethics of the Reuse of Disposable Medical Supplies

Das AK, Okita T, Enzo A, Asai A

Asian Bioeth Rev, 2020 Jun;12(2):103-116.
PMID: 33717332 DOI: 10.1007/s41649-020-00114-6

The use of single-use items (SUDs) is now ubiquitous in medical practice. Because of the high costs of these items, the practice of reusing them after sterilisation is also widespread especially in resource-poor economies. However, the ethics of reusing disposable items remain unclear. There are several analogous conditions, which could shed light on the ethics of reuse of disposables. These include the use of restored kidney transplantation and the use of generic drugs etc. The ethical issues include the question of patient safety and the possibility of infection. It is also important to understand the role (or otherwise) of informed consent before reuse of disposables. The widespread practice of reuse may bring down high healthcare costs and also reduce the huge amount of hospital waste that is generated. The reuse of disposables can be justified on various grounds including the safety and the cost effectiveness of this practice.
Fulltext Anthelmintic activity of selected ethno-medicinal plant extracts on parasitic stages of Haemonchus contortus

Kumarasingha R, Preston S, Yeo TC, Lim DS, Tu CL, Palombo EA, et al.

Parasit Vectors, 2016;9(1):187.
PMID: 27036205 DOI: 10.1186/s13071-016-1458-9

Parasitic roundworms (nematodes) cause substantial morbidity and mortality in livestock animals globally, and considerable productivity losses to farmers. The control of these nematodes has relied largely on the use of a limited number of anthelmintics. However, resistance to many of these these anthelmintics is now widespread, and, therefore, there is a need to find new drugs to ensure sustained and effective treatment and control into the future.
Fulltext Transcriptional alterations in Caenorhabditis elegans following exposure to an anthelmintic fraction of the plant Picria fel-terrae Lour

Kumarasingha R, Young ND, Yeo TC, Lim DSL, Tu CL, Palombo EA, et al.

Parasit Vectors, 2019 Apr 25;12(1):181.
PMID: 31023350 DOI: 10.1186/s13071-019-3429-4

BACKGROUND: Natural compounds from plants are known to provide a source of anthelmintic molecules. In previous studies, we have shown that plant extracts from the plant Picria fel-terrae Lour. and particular fractions thereof have activity against the free-living nematode Caenorhabditis elegans, causing quite pronounced stress responses in this nematode. We have also shown that a fraction, designated Pf-fraction 5, derived from this plant has a substantial adverse effect on this worm; however, nothing is known about the molecular processes affected in the worm. In the present study, we explored this aspect.
RESULTS: Key biological processes linked to upregulated genes (n = 214) included 'response to endoplasmic reticulum stress' and 'lipid metabolism', and processes representing downregulated genes (n = 357) included 'DNA-conformation change' and 'cellular lipid metabolism'.
CONCLUSIONS: Exposure of C. elegans to Pf-fraction 5 induces significant changes in the transcriptome. Gene ontology analysis suggests that Pf-fraction 5 induces endoplasmic reticulum and mitochondrial stress, and the changes in gene expression are either a direct or indirect consequence of this. Further work is required to assess specific responses to sub-fractions of Pf-fraction 5 in time-course experiments in C. elegans, to define the chemical(s) with potent anthelmintic properties, to attempt to unravel their mode(s) of action and to assess their selectivity against nematodes.
Fulltext A data-driven machine learning approach for discovering potent LasR inhibitors

Koh CMM, Ping LSY, Xuan CHH, Theng LB, San HS, Palombo EA, et al.

Bioengineered, 2023 Dec;14(1):2243416.
PMID: 37552115 DOI: 10.1080/21655979.2023.2243416

The rampant spread of multidrug-resistant Pseudomonas aeruginosa strains severely threatens global health. This severity is compounded against the backdrop of a stagnating antibiotics development pipeline. Moreover, with many promising therapeutics falling short of expectations in clinical trials, targeting the las quorum sensing (QS) system remains an attractive therapeutic strategy to combat P. aeruginosa infection. Thus, our primary goal was to develop a drug prediction algorithm using machine learning to identify potent LasR inhibitors. In this work, we demonstrated using a Multilayer Perceptron (MLP) algorithm boosted with AdaBoostM1 to discriminate between active and inactive LasR inhibitors. The optimal model performance was evaluated using 5-fold cross-validation and test sets. Our best model achieved a 90.7% accuracy in distinguishing active from inactive LasR inhibitors, an area under the Receiver Operating Characteristic Curve value of 0.95, and a Matthews correlation coefficient value of 0.81 when evaluated using test sets. Subsequently, we deployed the model against the Enamine database. The top-ranked compounds were further evaluated for their target engagement activity using molecular docking studies, Molecular Dynamics simulations, MM-GBSA analysis, and Free Energy Landscape analysis. Our data indicate that several of our chosen top hits showed better ligand-binding affinities than naringenin, a competitive LasR inhibitor. Among the six top hits, five of these compounds were predicted to be LasR inhibitors that could be used to treat P. aeruginosa-associated infections. To our knowledge, this study provides the first assessment of using an MLP-based QSAR model for discovering potent LasR inhibitors to attenuate P. aeruginosa infections.
Fulltext Metabolic profiling and in vitro assessment of anthelmintic fractions of Picria fel-terrae Lour

Kumarasingha R, Karpe AV, Preston S, Yeo TC, Lim DSL, Tu CL, et al.

Int J Parasitol Drugs Drug Resist, 2016 12;6(3):171-178.
PMID: 27639945 DOI: 10.1016/j.ijpddr.2016.08.002

Anthelmintic resistance is widespread in gastrointestinal nematode populations, such that there is a consistent need to search for new anthelmintics. However, the cost of screening for new compounds is high and has a very low success rate. Using the knowledge of traditional healers from Borneo Rainforests (Sarawak, Malaysia), we have previously shown that some traditional medicinal plants are a rich source of potential new anthelmintic drug candidates. In this study, Picria fel-terrae Lour. plant extract, which has previously shown promising anthelmintic activities, was fractionated via the use of a solid phase extraction cartridge and each isolated fraction was then tested on free-living nematode Caenorhabditis elegans and the parasitic nematode Haemonchus contortus. We found that a single fraction was enriched for nematocidal activity, killing ≥90% of C. elegans adults and inhibiting the motility of exsheathed L3 of H. contortus, while having minimal cytotoxic activity in mammalian cell culture. Metabolic profiling and chemometric analysis of the effective fraction indicated medium chained fatty acids and phenolic acids were highly represented.