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Fulltext Guidelines for the use and interpretation of assays for monitoring autophagy (3rd edition)

Klionsky DJ, Abdelmohsen K, Abe A, Abedin MJ, Abeliovich H, Acevedo Arozena A, et al.

Autophagy, 2016;12(1):1-222.
PMID: 26799652 DOI: 10.1080/15548627.2015.1100356
Chania multitudinisentens gen. nov., sp. nov., an N-acyl-homoserine-lactone-producing bacterium in the family Enterobacteriaceae isolated from landfill site soil

Ee R, Madhaiyan M, Ji L, Lim YL, Nor NM, Tee KK, et al.

Int J Syst Evol Microbiol, 2016 Jun;66(6):2297-2304.
PMID: 26978486 DOI: 10.1099/ijsem.0.001025

Phylogenetic and taxonomic characterization was performed for bacterium RB-25T, which was isolated from a soil sample collected in a former municipal landfill site in Puchong, Malaysia. Growth occurred at 20-37 °C at pH 5-8 but not in the presence of 9 % (w/v) NaCl or higher. The principal fatty acids were C16:0, C18:1ω7c and summed feature 3 (C16:1ω7c and/or iso-C15:0 2-OH). Ubiquinone-8 was the only isoprenoid quinone detected. Polar lipid analysis revealed the presence of phospholipid, phosphoaminolipid, phosphatidylethanolamine, phosphatidylglycerol and one unidentified aminolipid. DNA G+C content was 50.9 mol% phylogenetic analysis based on 16S rRNA gene sequence showed that strain RB-25T formed a distinct lineage within the family Enterobacteriaceae of the class Gammaproteobacteria. It exhibited a low level of 16S rRNA gene sequence similarity with its phylogenetic neighbours Pantoea rwandensis LMG 26275T (96.6 %), Rahnella aquatilis CIP 78.65T (96.5 %), Pectobacterium betavasculorum ATCC 43762T (96.4 %), Pantoea rodasii LMG 26273T (96.3 %), Gibbsiella dentisursi NUM 1720T (96.3 %) and Serratia glossinae C1T (96.2 %). Multilocus sequence analyses based on fusA, pyrG, rplB, rpoB and sucA sequences showed a clear distinction of strain RB-25T from the most closely related genera. Isolate RB-25T could also be distinguished from members of these genera by a combination of the DNA G+C content, respiratory quinone system, fatty acid profile, polar lipid composition and other phenotypic features. Strain RB-25T represents a novel species of a new genus, for which the name Chaniamultitudinisentens gen. nov., sp. nov. is proposed. The type strain is RB-25T (=DSM 28811T=LMG 28304T).
Insights into the diversity of blood donation practice across Asia: How blood collection agencies adapt donor criteria and processes to their population

Fung YL, Alcantara RM, Cavalli LB, Chen JW, Chen YY, Donkin R, et al.

Vox Sang, 2023 Sep 27.
PMID: 37753662 DOI: 10.1111/vox.13530

BACKGROUND AND OBJECTIVES: Securing an adequate blood supply relies on accurate knowledge of blood donors and donation practices. As published evidence on Asian populations is sparse, this study aims to gather up-to-date information on blood donors and donation practices in Asia to assist planning and strategy development.
MATERIALS AND METHODS: Ten blood collection agencies (BCAs) provided 12 months' data on donors who met eligibility criteria or were deferred, as well as details of their donation practices. Body mass index and blood volumes were calculated and analysed.
RESULTS: Data on 9,599,613 donations and 154,834 deferrals from six national and four regional BCAs revealed varied donation eligibility and collection practices. Seven used haemoglobin (Hb) criteria below the World Health Organization anaemia threshold. Seven accepted donors weighing <50 kg. Data collection on the weight and height of donors and on deferrals was inconsistent, often not routine. Deferred donors appear to weigh less, with corresponding lower estimated blood volume.
CONCLUSION: The diversity in eligibility criteria and donation practices reflects each BCA's strategy for balancing donor health with securing an adequate blood supply. Use of lower Hb criteria substantiate their appropriateness in Asia and indicate the need to define Hb reference intervals relevant to each population. We encourage routine gathering of donor weight and height data to enable blood volume estimation and local optimization of donation volumes. Blood volume estimation formulae specific for the Asian phenotype is needed. Information from this study would be useful for tailoring donation criteria of Asian donors around the world.
Pandoraea fibrosis sp. nov., a novel Pandoraea species isolated from clinical respiratory samples

See-Too WS, Ambrose M, Malley R, Ee R, Mulcahy E, Manche E, et al.

Int J Syst Evol Microbiol, 2019 Mar;69(3):645-651.
PMID: 30676309 DOI: 10.1099/ijsem.0.003147

Pandoraea species have been isolated from diverse environmental samples and are emerging important respiratory pathogens, particularly in people with cystic fibrosis (CF). In the present study, two bacterial isolates initially recovered from consecutive sputum samples collected from a CF patient and identified as Pandoraea pnomenusa underwent a polyphasic taxonomic analysis. The isolates were found to be Gram-negative, facultative anaerobic motile bacilli and subsequently designated as strains 6399T (=LMG29626T=DSM103228T) and 7641 (=LMG29627=DSM103229), respectively. Phylogenetic analysis based on 16S rRNA and gyrB gene sequences revealed that 6399T and 7641 formed a distinct phylogenetic lineage within the genus Pandoraea. Genome sequence comparison analysis indicated that strains 6399T and 7641 are clonal and share 100 % similarity, however, similarity to other type strains (ANIb 73.2-88.8 %, ANIm 83.5-89.9 % and OrthoANI 83.2-89.3 %) indicates that 6399T and 7641 do not belong to any of the reported type species. The major cellular fatty acids of 6399T were C16 : 0 (32.1 %) C17 : 0cyclo (18.7 %) and C18 : 1ω7c (14.5 %), while Q-8 was the only respiratory quinone detected. The major polar lipids identified were phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. The genomic DNA G+C content of 6399T was 62.9 (mol%). Strain 6399T can be differentiated from other members of Pandoraea by the absence of C19 : 0ω8c cyclo and by the presence of C17 : 0ω8c cyclo. Together our data show that the bacterial strains 6399T and 7641 represent a novel species of the genus Pandoraea, for which the name Pandoraea fibrosis sp. nov. is proposed (type strain 6399T).
Combined chemotherapy and EUS-guided intra-tumoral 32-P implantation for locally advanced pancreatic ductal adenocarcinoma: a pilot study

Naidu J, Bartholomeusz D, Zobel J, Safaeian R, Hsieh W, Crouch B, et al.

Endoscopy, 2021 Jan 13.
PMID: 33440437 DOI: 10.1055/a-1353-0941

AIM: This study evaluated clinical outcomes of combined chemotherapy and Endoscopic Ultrasound (EUS) guided intra-tumoral radioactive phosphorus-32 (32P OncoSil) implantation in locally advanced pancreatic adenocarcinoma (LAPC).
METHODS: Consecutive patients with a new histological diagnosis of LAPC were recruited over 20 months. Baseline CT and 18FDG PET-CT were performed and repeated after 12 weeks to assess response to treatment. Following 2 cycles of conventional chemotherapy, patients underwent EUS-guided 32P OncoSil implantation followed by a further six cycles of chemotherapy.
RESULTS: Twelve patients with LAPC (8M:4F; median age 69 years, IQR 61.5-73.3) completed the treatment. Technical success was 100% and no procedural complications were reported. At 12 weeks, there was a median reduction of 8.2cm3 (95% CI 4.95-10.85; p=0.003) in tumour volume, with minimal or no 18FDG uptake in 9 (75%) patients. Tumour downstaging was achieved in 6 (50%) patients, leading to successful resection in 5 (42%) patients, of which 4 patients (80%) had clear (R0) resection margins.
CONCLUSIONS: EUS guided 32P OncoSil implantation is feasible and well tolerated and was associated with a 42% rate of surgical resection in our cohort. However, further evaluation in a larger randomized multicenter trial is warranted. (32P funded by OncoSil Medical Ltd, equipment and staff funded by the Royal Adelaide Hospital, ClinicalTrials.gov number, NCT03003078).
Fulltext Tandem mass spectrometry detection of quorum sensing activity in multidrug resistant clinical isolate Acinetobacter baumannii

Chan KG, Cheng HJ, Chen JW, Yin WF, Ngeow YF

ScientificWorldJournal, 2014;2014:891041.
PMID: 25101326 DOI: 10.1155/2014/891041

Many Proteobacteria communicate via production followed by response of quorum sensing molecules, namely, N-acyl homoserine lactones (AHLs). These molecules consist of a lactone moiety with N-acyl side chain with various chain lengths and degrees of saturation at C-3 position. AHL-dependent QS is often associated with regulation of diverse bacterial phenotypes including the expression of virulence factors. With the use of biosensor and high resolution liquid chromatography tandem mass spectrometry, the AHL production of clinical isolate A. baumannii 4KT was studied. Production of short chain AHL, namely, N-hexanoyl-homoserine lactone (C6-HSL) and N-octanoyl-homoserine lactone (C8-HSL), was detected.
Differential regulation of fatty acid biosynthesis in two Chlorella species in response to nitrate treatments and the potential of binary blending microalgae oils for biodiesel application

Cha TS, Chen JW, Goh EG, Aziz A, Loh SH

Bioresour Technol, 2011 Nov;102(22):10633-40.
PMID: 21967717 DOI: 10.1016/j.biortech.2011.09.042

This study was undertaken to investigate the effects of different nitrate concentrations in culture medium on oil content and fatty acid composition of Chlorella vulgaris (UMT-M1) and Chlorella sorokiniana (KS-MB2). Results showed that both species produced significant higher (p<0.05) oil content at nitrate ranging from 0.18 to 0.66 mM with C. vulgaris produced 10.20-11.34% dw, while C. sorokiniana produced 15.44-17.32% dw. The major fatty acids detected include C16:0, C18:0, C18:1, C18:2 and C18:3. It is interesting to note that both species displayed differentially regulated fatty acid accumulation patterns in response to nitrate treatments at early stationary growth phase. Their potential use for biodiesel application could be enhanced by exploring the concept of binary blending of the two microalgae oils using developed mathematical equations to calculate the oil mass blending ratio and simultaneously estimated the weight percentage (wt.%) of desirable fatty acid compositions.
Fulltext Complete Genome Sequence of Dyella japonica Strain A8 Isolated from Malaysian Tropical Soil

Hui RK, Chen JW, Chan KG, Leung FC

Genome Announc, 2014;2(6).
PMID: 25395638 DOI: 10.1128/genomeA.01164-14

We previously identified and presented the draft genome of a Xanthomonadaceae bacterial strain Dyella japonica A8 which shows quorum-quenching activity. Here, we report the complete, closed genome sequence of this bacterium. This complete genome may help to further investigate the comparative quorum-quenching activity among D. japonica strains.
Machine learning methods for the modelling and optimisation of biogas production from anaerobic digestion: a review

Ling JYX, Chan YJ, Chen JW, Chong DJS, Tan ALL, Arumugasamy SK, et al.

Environ Sci Pollut Res Int, 2024 Feb 20.
PMID: 38376778 DOI: 10.1007/s11356-024-32435-6

Biogas plant operators often face huge challenges in the monitoring, controlling and optimisation of the anaerobic digestion (AD) process, as it is very sensitive to surrounding changes, which often leads to process failure and adversely affects biogas production. Conventional implemented methods and mechanistic models are impractical and find it difficult to model the nonlinear and intricate interactions of the AD process. Thus, the development of machine learning (ML) algorithms has attracted considerable interest in the areas of process optimization, real-time monitoring, perturbation detection and parameter prediction. This paper provides a comprehensive and up-to-date overview of different machine learning algorithms, including artificial neural network (ANN), fuzzy logic (FL), adaptive network-based fuzzy inference system (ANFIS), support vector machine (SVM), genetic algorithm (GA) and particle swarm optimization (PSO) in terms of working mechanism, structure, advantages and disadvantages, as well as their prediction performances in modelling the biogas production. A few recent case studies of their applications and limitations are also critically reviewed and compared, providing useful information and recommendation in the selection and application of different ML algorithms. This review shows that the prediction efficiency of different ML algorithms is greatly impacted by variations in the reactor configurations, operating conditions, influent characteristics, selection of input parameters and network architectures. It is recommended to incorporate mixed liquor volatile suspended solids (MLVSS) concentration of the anaerobic digester (ranging from 16,500 to 46,700 mg/L) as one of the input parameters to improve the prediction efficiency of ML modelling. This review also shows that the combination of different ML algorithms (i.e. hybrid GA-ANN model) could yield better accuracy with higher R2 (0.9986) than conventional algorithms and could improve the optimization model of AD. Besides, future works could be focused on the incorporation of an integrated digital twin system coupled with ML techniques into the existing Supervisory Control and Data Acquisition (SCADA) system of any biogas plant to detect any operational abnormalities and prevent digester upsets.
Cholesterol-linoleic acid liposomes induced extracellular vesicles secretion from immortalized adipose-derived mesenchymal stem cells for in vitro cell migration

Chen JW, Liew FF, Tan HW, Misran M, Chung I

Artif Cells Nanomed Biotechnol, 2023 Dec;51(1):346-360.
PMID: 37524112 DOI: 10.1080/21691401.2023.2237534

Extracellular vesicles (EVs) are small vesicles that are naturally released by cells and play a crucial role in cell-to-cell communication, tissue repair and regeneration. As naturally secreted EVs are limited, liposomes with different physicochemical properties, such as 1,2-dioleoyl-3-trimethylammonium propane (DOTAP) and linoleic acid (LA) with modifications have been formulated to improve EVs secretion for in vitro wound healing. Various analyses, including dynamic light scattering (DLS) and transmission electron microscopy (TEM) were performed to monitor the successful preparation of different types of liposomes. The results showed that cholesterol-LA liposomes significantly improved the secretion of EVs from immortalized adipose-derived mesenchymal stem cells (AD-MSCs) by 1.5-fold. Based on the cell migration effects obtained from scratch assay, both LA liposomal-induced EVs and cholesterol-LA liposomal-induced EVs significantly enhanced the migration of human keratinocytes (HaCaT) cell line. These findings suggested that LA and cholesterol-LA liposomes that enhance EVs secretion are potentially useful and can be extended for various tissue regeneration applications.
Tunable photoelectrochemical performance of Au/BiFeO3 heterostructure

Huang YL, Chang WS, Van CN, Liu HJ, Tsai KA, Chen JW, et al.

Nanoscale, 2016 Aug 25;8(34):15795-801.
PMID: 27533610 DOI: 10.1039/c6nr04997d

Ferroelectric photoelectrodes, other than conventional semiconductors, are alternative photo-absorbers in the process of water splitting. However, the capture of photons and efficient transfer of photo-excited carriers remain as two critical issues in ferroelectric photoelectrodes. In this work, we overcome the aforementioned issues by decorating the ferroelectric BiFeO3 (BFO) surface with Au nanocrystals, and thus improving the photoelectrochemical (PEC) performance of BFO film. We demonstrate that the internal field induced by the spontaneous polarization of BFO can (1) tune the efficiency of the photo-excited carriers' separation and charge transfer characteristics in bare BFO photoelectrodes, and (2) modulate an extra optical absorption within the visible light region, created by the surface plasmon resonance excitation of Au nanocrystals to capture more photons in the Au/BFO heterostructure. This study provides key insights for understanding the tunable features of PEC performance, composed of the heterostructure of noble metals and ferroelectric materials.
Energy Band Gap Modulation in Nd-Doped BiFeO3/SrRuO3 Heteroepitaxy for Visible Light Photoelectrochemical Activity

Tan KH, Chen YW, Van CN, Wang H, Chen JW, Lim FS, et al.

ACS Appl Mater Interfaces, 2019 Jan 09;11(1):1655-1664.
PMID: 30561192 DOI: 10.1021/acsami.8b17758

The ability of band offsets at multiferroic/metal and multiferroic/electrolyte interfaces in controlling charge transfer and thus altering the photoactivity performance has sparked significant attention in solar energy conversion applications. Here, we demonstrate that the band offsets of the two interfaces play the key role in determining charge transport direction in a downward self-polarized BFO film. Electrons tend to move to BFO/electrolyte interface for water reduction. Our experimental and first-principle calculations reveal that the presence of neodymium (Nd) dopants in BFO enhances the photoelectrochemical performance by reduction of the local electron-hole pair recombination sites and modulation of the band gap to improve the visible light absorption. This opens a promising route to the heterostructure design by modulating the band gap to promote efficient charge transfer.
Fulltext Recent Advances in Molecular Diagnosis of Pseudomonasaeruginosa Infection by State-of-the-Art Genotyping Techniques

Chen JW, Lau YY, Krishnan T, Chan KG, Chang CY

Front Microbiol, 2018;9:1104.
PMID: 29892277 DOI: 10.3389/fmicb.2018.01104

Pseudomonas aeruginosa is a rod-shaped Gram-negative bacterium which is notably known as a pathogen in humans, animals, and plants. Infections caused by P. aeruginosa especially in hospitalized patients are often life-threatening and rapidly increasing worldwide throughout the years. Recently, multidrug-resistant P. aeruginosa has taken a toll on humans' health due to the inefficiency of antimicrobial agents. Therefore, the rapid and advanced diagnostic techniques to accurately detect this bacterium particularly in clinical samples are indeed necessary to ensure timely and effective treatments and to prevent outbreaks. This review aims to discuss most recent of state-of-the-art molecular diagnostic techniques enabling fast and accurate detection and identification of P. aeruginosa based on well-developed genotyping techniques, e.g., polymerase chain reaction, pulse-field gel electrophoresis, and next generation sequencing. The advantages and limitations of each of the methods are also reviewed.
Fulltext Whole-Genome Analysis of Quorum-Sensing Burkholderia sp. Strain A9

Chan KG, Chen JW, Tee KK, Chang CY, Yin WF, Chan XY

Genome Announc, 2015;3(2).
PMID: 25745000 DOI: 10.1128/genomeA.00063-15

Burkholderia spp. rely on N-acyl homoserine lactone as quorum-sensing signal molecules which coordinate their phenotype at the population level. In this work, we present the whole genome of Burkholderia sp. strain A9, which enables the discovery of its N-acyl homoserine lactone synthase gene.
Fulltext Draft Genome Sequence of Lysinibacillus sp. Strain A1, Isolated from Malaysian Tropical Soil

Chan KG, Chen JW, Chang CY, Yin WF, Chan XY

Genome Announc, 2015;3(2).
PMID: 25814592 DOI: 10.1128/genomeA.00095-15

In this work, we describe the genome of Lysinibacillus sp. strain A1, which was isolated from tropical soil. Analysis of its genome sequence shows the presence of a gene encoding for a putative peptidase responsible for nitrogen compounds.
Fulltext Draft Genome Sequence of Kocuria rhizophila strain TPW45, an Actinobacterium Isolated from Freshwater

Adrian TG, Tan PW, Chen JW, Yin WF, Chan KG

J Genomics, 2016;4:16-8.
PMID: 27326264 DOI: 10.7150/jgen.15063

Kocuria rhizophila is a ubiquitous bacterium which is well known for its industrial value. Here, we present the draft genome of Kocuria rhizophila strain TPW45 which was isolated from Sungai Gabai, Selangor, Malaysia. The assembled genome comprised of 46 contigs and the estimated genome size is 2.7 Mb. Based on the RAST annotation, a gene cluster responsible for aromatic compound degradation was identified in this strain.
Fulltext Short chain N-acylhomoserine lactone production by clinical multidrug resistant Klebsiella pneumoniae strain CSG20

Ngeow YF, Cheng HJ, Chen JW, Yin WF, Chan KG

Sensors (Basel), 2013;13(11):15242-51.
PMID: 24284772 DOI: 10.3390/s131115242

Klebsiella pneumoniae is one of the most common Gram-negative bacterial pathogens in clinical practice. It is associated with a wide range of disorders, ranging from superficial skin and soft tissue infections to potentially fatal sepsis in the lungs and blood stream. Quorum sensing, or bacterial cell-cell communication, refers to population density-dependent gene expression modulation. Quorum sensing in Proteobacteria relies on the production and sensing of signaling molecules which are mostly N-acylhomoserine lactones. Here, we report the identification of a multidrug resistant clinical isolate, K. pneumoniae strain CSG20, using matrix-assisted laser desorption ionization-time-of-flight (MALDI-TOF) mass spectrometry. We further confirmed quorum sensing activity in this strain with the use of high resolution tandem liquid chromatography quadrupole mass spectrometry and provided evidence K. pneumoniae strain CSG20 produced N-hexanoyl-homoserine lactone (C6-HSL). To the best of our knowledge, this is the first report on the production of N-hexanoylhomoserine lactone (C6-HSL) in clinical isolate K. pneumoniae.
Fulltext N-acyl homoserine lactone-producing Pseudomonas putida strain T2-2 from human tongue surface

Chen JW, Chin S, Tee KK, Yin WF, Choo YM, Chan KG

Sensors (Basel), 2013;13(10):13192-203.
PMID: 24084113 DOI: 10.3390/s131013192

Bacterial cell-to-cell communication (quorum sensing) refers to the regulation of bacterial gene expression in response to changes in microbial population density. Quorum sensing bacteria produce, release and respond to chemical signal molecules called autoinducers. Bacteria use two types of autoinducers, namely autoinducer-1 (AI-1) and autoinducer-2 (AI-2) where the former are N-acylhomoserine lactones and the latter is a product of the luxS gene. Most of the reported literatures show that the majority of oral bacteria use AI-2 for quorum sensing but rarely the AI-1 system. Here we report the isolation of Pseudomonas putida strain T2-2 from the oral cavity. Using high resolution mass spectrometry, it is shown that this isolate produced N-octanoylhomoserine lactone (C8-HSL) and N-dodecanoylhomoserine lactone (C12-HSL) molecules. This is the first report of the finding of quorum sensing of P. putida strain T2-2 isolated from the human tongue surface and their quorum sensing molecules were identified.
Fulltext Short chain N-acyl homoserine lactone production by soil isolate Burkholderia sp. strain A9

Chen JW, Koh CL, Sam CK, Yin WF, Chan KG

Sensors (Basel), 2013;13(10):13217-27.
PMID: 24084115 DOI: 10.3390/s131013217

In the bacteria kingdom, quorum sensing (QS) is a cell-to-cell communication that relies on the production of and response to specific signaling molecules. In proteobacteria, N-acylhomoserine lactones (AHLs) are the well-studied signaling molecules. The present study aimed to characterize the production of AHL of a bacterial strain A9 isolated from a Malaysian tropical soil. Strain A9 was identified as Burkholderia sp. using matrix-assisted laser desorption ionization-time-of-flight mass spectrometry and 16S rDNA nucleotide sequence analysis. AHL production by A9 was detected with two biosensors, namely Chromobacterium violaceum CV026 and Escherichia coli [pSB401]. Thin layer chromatography results showed N-hexanoylhomoserine lactone (C6-HSL) and N-octanoylhomoserine lactone (C8-HSL) production. Unequivocal identification of C6-HSL and C8-HSL was achieved by high resolution triple quadrupole liquid chromatography-mass spectrometry analysis. We have demonstrated that Burkholderia sp. strain A9 produces AHLs that are known to be produced by other Burkholderia spp. with CepI/CepR homologs.
Fulltext Degradation of bacterial quorum sensing signaling molecules by the microscopic yeast Trichosporon loubieri isolated from tropical wetland waters

Wong CS, Koh CL, Sam CK, Chen JW, Chong YM, Yin WF, et al.

Sensors (Basel), 2013;13(10):12943-57.
PMID: 24072030 DOI: 10.3390/s131012943

Proteobacteria produce N-acylhomoserine lactones as signaling molecules, which will bind to their cognate receptor and activate quorum sensing-mediated phenotypes in a population-dependent manner. Although quorum sensing signaling molecules can be degraded by bacteria or fungi, there is no reported work on the degradation of such molecules by basidiomycetous yeast. By using a minimal growth medium containing N-3-oxohexanoylhomoserine lactone as the sole source of carbon, a wetland water sample from Malaysia was enriched for microbial strains that can degrade N-acylhomoserine lactones, and consequently, a basidiomycetous yeast strain WW1C was isolated. Morphological phenotype and molecular analyses confirmed that WW1C was a strain of Trichosporon loubieri. We showed that WW1C degraded AHLs with N-acyl side chains ranging from 4 to 10 carbons in length, with or without oxo group substitutions at the C3 position. Re-lactonisation bioassays revealed that WW1C degraded AHLs via a lactonase activity. To the best of our knowledge, this is the first report of degradation of N-acyl-homoserine lactones and utilization of N-3-oxohexanoylhomoserine as carbon and nitrogen source for growth by basidiomycetous yeast from tropical wetland water; and the degradation of bacterial quorum sensing molecules by an eukaryotic yeast.

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