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  1. Xie Y, Zhou L
    J Environ Public Health, 2022;2022:7279233.
    PMID: 35996412 DOI: 10.1155/2022/7279233
    The sudden global pandemic of COVID-19 occurred in Malaysia at the beginning of new 2020, which increased the uncertainty of the economy. As a highly demanded industry during diseases, COVID-19-related news had a mixed influence on investors' confidence in the healthcare industry, so the short-term market reaction of the Malaysian healthcare industry is investigated during this unfolding event. This paper examines whether the "lockdown" suppressed the influence of COVID-19 pandemic on stock performance in 12 listed healthcare companies in Malaysia. We consider the "lockdown" order has different impacts on samples. The hardest hit among the four events is the first announcement of lockdown, whose cumulative average abnormal return (CAAR) is negative (CAAR<0), for its strict movement control. However, the impacts of the following three lockdown events are positive and less severe as the market gradually digest these kinds of news and the deregulation of movement control. Previous studies have justified the influence of disease outbreaks on the stock market; however, this study compensates for other studies by employing the event study methodology (ESM) approach to provide the first empirical evidence of the unprecedented influence of "lockdown" on Malaysian healthcare stock market. This study has practical implications for Malaysian financial markets that the lockdown orders matter for the Malaysian healthcare industry. The empirical results show that the stock market has positively affected the lockdown announcement after the first event. In turn, the policymakers could draw on these results related to stock performance to modify the regulations in the healthcare industry.
  2. Wang X, Xie Y, Zhou X
    Virus Genes, 2004 Dec;29(3):303-9.
    PMID: 15550769
    Six papaya samples showing downward leaf curling were collected in Guangdong and Guangxi provinces, China. The result of TAS-ELISA showed they were all infected by geminiviruses. Comparison of partial DNA-A sequences reveals that these virus isolates can be classified into two groups. Group I includes isolates G2, G4, G5, G28 and G29 from Guangxi province, while isolate GD2 from Guangdong province belongs to Group II. The complete DNA-A sequence of G2 and GD2 were characterized. Sequence comparisons showed that the DNA-A of G2 and GD2 were most closely related to that of Ageratum yellow vein China virus- [Hn2] and Ageratum yellow vein virus , respectively, with 83.4 and 75.2% nucleotide sequence identity, while DNA-A sequence between G2 and GD2 had only 73.4% sequence identity. The molecular data suggests that G2 and GD2 are two distinct begomoviruses, for which the name Papaya leaf curl China virus (PaLCuCNV) for G2 and Papaya leaf curl Guangdong virus (PaLCuGDV) for GD2 are proposed. Comparison of individual encoded proteins showed the coat protein of G2 and GD2 shared highest amino acid sequence identity (97.7 and 94.2%, respectively) with that of Pepper leaf curl virus -[Malaysia] (PepLCV-[MY]), suggesting the CP of these viruses may have identical ancestor.
  3. Liu N, Chen T, Peng Y, Xie Y
    Front Psychol, 2023;14:1217340.
    PMID: 37691799 DOI: 10.3389/fpsyg.2023.1217340
    INTRODUCTION: Language media from one's hometown is an important means of maintaining cultural identification, especially for minorities. Cantonese media plays an active role in shaping the Chinese cultural identification of ethnic Chinese all over the world. To date, few researchers have undertaken quantitative empirical analyses of the mechanism through which Cantonese media influences cultural identification.

    METHODS: Using data from 642 Malaysian Chinese, this study established a structural equation model with the partial least squares method.

    RESULTS: We found that the emotional affinity of ethnic Chinese to Cantonese media can influence identification with Chinese culture through the perceived value of Cantonese media and cognition of Chinese culture. The perceived value of Cantonese media (IE = 0.208) and cognition of Chinese culture (IE = 0.068) play partial mediation roles. Meanwhile, emotional affinity to Cantonese media influences cognition of Chinese culture (IE = 0.069) through the chain mediation of perceived value of Cantonese media and cognition of Chinese culture. Age has a partial moderating effect in the structural equation model. Compared with minors, adults' emotional affinity to Cantonese media can eventually influence identification with Chinese culture (TEdiff = 0.126) more strongly through several mediation paths.

    DISCUSSION: The study suggests a need to cultivate the emotional affinity of ethnic Chinese to Cantonese media, improve the multidimensional values of Cantonese media, and endow Cantonese media with functions of cultural dialog and knowledge transmission. The international transmission of Cantonese media could play a vital role in building a cultural community for ethnic Chinese globally.

  4. Ng S, Xie Y, Schaefer HF
    J Mol Model, 2024 Sep 14;30(10):333.
    PMID: 39276285 DOI: 10.1007/s00894-024-06135-4
    CONTEXT: 2,2,2-Trifluoroethanol (TFE) is known as a membrane mimetic solvent. The IR spectrum, 1H NMR spectrum, 13C NMR spin‒lattice relaxation times (T1), and nuclear Overhauser effect (NOE) data are consistent with extensive hydrogen bonding in TFE, but do not lead to structural features of the hydrogen bonding. Hence, DFT computations were carried out. The results predict the existence of a set of H-bonded dimers and trimers. The bond lengths and dihedral angles in these complexes are obtained, together with their dissociation energies. Computations were also performed for the geometry of the two conformers of the isolated monomer. The structure of one of the dimers consists of a 7-member cyclic fragment with a free CF3CH2 side chain. One set of the trimer structures involves the OH of a third monomer H-bonding to one of the F atoms in the CF3 group of the side chain of this dimer, thereby creating three trimer isomers. A fourth trimer cluster is formed from three monomers in which three OH∙∙∙O bonds create a cyclic fragment with three CF3CH2 side chains. The high dissociation energy (with respect to three monomers) indicates the high stability of the trimer complexes. The structural features of the trimer complexes resemble the structure of a conventional liquid crystal molecule and are postulated to resemble the latter in properties and function in solution, but at a much shorter timescale because of the noncovalent bonding. This hydrogen bonding phenomenon of TFE may be related to its function as a membrane memetic solvent.

    METHODS: Initially, IR and NMR spectroscopic methods were used. Standard procedures were followed. For the computations, a hybrid DFT method with empirical dispersion, ωB97X-D, was used. The basis set, 6-311++G**, is of triple-ζ quality, in which polarization functions and diffuse functions were added for all atoms.

  5. Xie Y, Jin Z, Ma D, Yin TH, Zhao K
    Bioeng Transl Med, 2023 May;8(3):e10510.
    PMID: 37206211 DOI: 10.1002/btm2.10510
    Nanoparticles (NPs) used for oral administration have greatly improved drug bioavailability and therapeutic efficacy. Nevertheless, NPs are limited by biological barriers, such as gastrointestinal degradation, mucus barrier, and epithelial barrier. To solve these problems, we developed the PA-N-2-HACC-Cys NPs loaded with anti-inflammatory hydrophobic drug curcumin (CUR) (CUR@PA-N-2-HACC-Cys NPs) by self-assembled amphiphilic polymer, composed of the N-2-Hydroxypropyl trimethyl ammonium chloride chitosan (N-2-HACC), hydrophobic palmitic acid (PA), and cysteine (Cys). After oral administration, the CUR@PA-N-2-HACC-Cys NPs had good stability and sustained release under gastrointestinal conditions, followed by adhering to the intestine to achieve drug mucosal delivery. Additionally, the NPs could penetrate mucus and epithelial barriers to promote cellular uptake. The CUR@PA-N-2-HACC-Cys NPs could open tight junctions between cells for transepithelial transport while striking a balance between mucus interaction and diffusion through mucus. Notably, the CUR@PA-N-2-HACC-Cys NPs improved the oral bioavailability of CUR, which remarkably relieved colitis symptoms and promoted mucosal epithelial repair. Our findings proved that the CUR@PA-N-2-HACC-Cys NPs had excellent biocompatibility, could overcome mucus and epithelial barriers, and had significant application prospects for oral delivery of the hydrophobic drugs.
  6. Zhong W, Tang M, Xie Y, Huang X, Liu Y
    Foodborne Pathog Dis, 2023 Jul;20(7):294-302.
    PMID: 37347934 DOI: 10.1089/fpd.2022.0085
    Staphylococcus aureus can cause bacterial food intoxication and seriously affect human health. Tea polyphenols (TP) are a kind of natural, safe, and broad-spectrum bacteriostatic substances, with a wide range of bacteriostatic effects. In the study, we explored the possible bacteriostatic mode of TP. The minimum inhibitory concentration of TP against S. aureus was 64 μg/mL. Protein, DNA, and K+ leak experiments, fluorescence microscopy, and transmission electron microscopy suggested that TP disrupt cell membranes, leading to intracellular component loss. By studying the effect of TP on the toxicity of S. aureus, it was found that the expression levels of two toxin genes, coa and spa, were downregulated by 2.37 and 32.6, respectively. Furthermore, after treatment with TP, a large number of reactive oxygen species (ROS) were propagated and released, leading to oxidative stress in cells. We speculated that the bacteriostatic mechanism of TP may be through the destruction of the cell membrane and ROS-mediated oxidative stress. Meanwhile, the hemolysis activity proved the safety of TP. Our results suggested that TP may be a potential antimicrobial agent for food.
  7. Hu Y, Xie Y, Su Q, Fu J, Chen J, Liu Y
    Foodborne Pathog Dis, 2023 Nov;20(11):521-530.
    PMID: 37722019 DOI: 10.1089/fpd.2023.0039
    The human gut flora is highly diverse. Most lactic acid bacteria (LAB) are widely used as probiotics in human and animal husbandry and have a variety of physiological benefits. This article mainly studied the bacteriostatic ability of LAB against four pathogenic bacteria, gastrointestinal environment tolerance, and adhesion ability to Caco-2 cells. The genome of Lactiplantibacillus plantarum L461 was sequenced and analyzed. The results showed that strains F512, L461, and D469 had the most significant inhibitory effects on Escherichia coli, Salmonella enterica B, Staphylococcus aureus, and Listeria monocytogenes. In addition, strains L461, C502, and P231 showed good tolerance after exposure to simulated gastric fluid for 0-4 h. Strains C502, H781, and L461 showed good tolerance in simulated intestinal fluid. Strains L461 and H781 showed good adhesion to Caco-2 cells. The number of viable bacteria was more than 60. Therefore, we screened L. plantarum L461 from 12 LAB strains through three aspects of evaluation, and conducted whole genome sequencing and analysis. Sequencing results showed that L. plantarum L461 had more defense mechanisms and phage annotation genes than L. plantarum WCFS1. Virulence factor studies showed that L. plantarum L461 has iron absorption system and adhesion-related gene annotation, indicating that L. plantarum L461 has survival advantage in intestinal tract. The predicted results showed that there were eight phages with phage resistance in L. plantarum L461. L. plantarum L461 is sensitive to several antibiotics, notably penicillin and oxacillin. In summary, the results of this study prove that L. plantarum L461 has good prebiotic function and is safe. Therefore, L. plantarum L461 can be safely used as a potential functional probiotic.
  8. Ng S, Sathasivam RV, Lo KM, Xie Y, Schaefer HF
    J Phys Chem A, 2005 Dec 29;109(51):12059-63.
    PMID: 16366662
    The Woessner approach is applied to the 13C relaxation data for tetraphenyltin (1) and tetra(p-tolyl)tin (2) in CDCl3 solution over the temperature range 5-42 degrees C to obtain correlation times for rotational motions and hence the activation barriers. Quantum mechanical computations were carried out to obtain the rotational energy barriers for comparison. For 2 the relaxation data indicate (1) slower ring rotation than in 1, (2) highly hindered internal rotation of the methyl group. IR and chemical shift data support the hypothesis of hyperconjugation of the methyl correlated with interaction between the pi-electrons and the 5d orbitals of tin in the (p-tolyl)Sn moiety to account for the hindrances to the rotations of the ring and the methyl. The activation barrier for the tolyl group rotation is found to be much higher than that for the phenyl rotation. However, the Woessner approach yields an anomalously high barrier for the methyl rotation. An explanation based on correlated rotations of the tolyl ring and the methyl is offered.
  9. Hu X, Xie Y, Zhao H, Sheng G, Lai KW, Zhang Y
    PeerJ Comput Sci, 2024;10:e1874.
    PMID: 38481705 DOI: 10.7717/peerj-cs.1874
    Epilepsy is a chronic, non-communicable disease caused by paroxysmal abnormal synchronized electrical activity of brain neurons, and is one of the most common neurological diseases worldwide. Electroencephalography (EEG) is currently a crucial tool for epilepsy diagnosis. With the development of artificial intelligence, multi-view learning-based EEG analysis has become an important method for automatic epilepsy recognition because EEG contains difficult types of features such as time-frequency features, frequency-domain features and time-domain features. However, current multi-view learning still faces some challenges, such as the difference between samples of the same class from different views is greater than the difference between samples of different classes from the same view. In view of this, in this study, we propose a shared hidden space-driven multi-view learning algorithm. The algorithm uses kernel density estimation to construct a shared hidden space and combines the shared hidden space with the original space to obtain an expanded space for multi-view learning. By constructing the expanded space and utilizing the information of both the shared hidden space and the original space for learning, the relevant information of samples within and across views can thereby be fully utilized. Experimental results on a dataset of epilepsy provided by the University of Bonn show that the proposed algorithm has promising performance, with an average classification accuracy value of 0.9787, which achieves at least 4% improvement compared to single-view methods.
  10. Xie Y, Gong L, Liu S, Yan J, Zhao S, Xia C, et al.
    Environ Res, 2023 Nov 01;236(Pt 1):116680.
    PMID: 37500036 DOI: 10.1016/j.envres.2023.116680
    Microbial degradation of pesticide residues has the potential to reduce their hazards to human and environmental health. However, in some cases, degradation can activate pesticides, making them more toxic to microbes. Here we report on the β-cypermethrin (β-CY) toxicity to Bacillus cereus GW-01, a recently described β-CY degrader, and effects of antioxidants on β-CY degradation. GW-01 exposed to β-CY negatively affected the growth rate. The highest maximum specific growth rate (μm) appeared at 25 mg/L β-CY. β-CY induced the oxidative stress in GW-01. The activities of superoxide dismutase (SOD), catalyse (CAT), and glutathione-S-transferase (GST) were significantly higher than that in control (p 
  11. Shi Y, Jiang J, Ye H, Sheng Y, Zhou Y, Foong SY, et al.
    Environ Res, 2023 Feb 01;218:114967.
    PMID: 36455630 DOI: 10.1016/j.envres.2022.114967
    We analyzed the problematic textile fiber waste as potential precursor material to produce multilayer cotton fiber biocomposite. The properties of the products were better than the current dry bearing type particleboards and ordinary dry medium-density fiberboard in terms of the static bending strength (67.86 MPa), internal bonding strength (1.52 MPa) and water expansion rate (9.57%). The three-layer, four-layer and five-layer waste cotton fiber composite (WCFC) were tried in the experiment, the mechanical properties of the three-layer WCFC are insufficient, the five-layer WCFC is too thick and the four-layer WCFC had the best comprehensive performance. The cross-section morphology of the four-layer WCFC shows a dense structure with a high number of adhesives attached to the fiber. The hardness and stiffness of the four-layer cotton fiber composite enhanced by the high crystallinity of cellulose content, and several chemical bondings were presence in the composites. Minimum mass loss (30%) and thermal weight loss rate (0.70%/°C) was found for the four-layer WCFC. Overall, our findings suggested that the use of waste cotton fiber (WCF) to prepare biocomposite with desirable physical and chemical properties is feasible, and which can potentially be used as building material, furniture and automotive applications.
  12. Xu T, Tang X, Qiu M, Lv X, Shi Y, Zhou Y, et al.
    J Environ Manage, 2023 Oct 15;344:118718.
    PMID: 37541001 DOI: 10.1016/j.jenvman.2023.118718
    Antibiotic-containing wastewater is a typical biochemical refractory organic wastewater and general treatment methods cannot effectively and quickly degrade the antibiotic molecules. In this study, a novel boron-doped diamond (BDD) pulse electrochemical oxidation (PEO) technology was proposed for the efficient removal of levofloxacin (LFXN) from wastewater. The effects of current density (j), initial pH (pH0), frequency (f), electrolyte types and initial concentration (c0(LFXN)) on the degradation of LFXN were systematically investigated. The degradation kinetics under four different processes have also been studied. The possible degradation mechanism of LFXN was proposed by Density functional theory calculation and analysis of degradation intermediates. The results showed that under the optimal parameters, the COD removal efficiency (η(COD)) was 94.4% and the energy consumption (EEC) was 81.43 kWh·m-3 at t = 120 min. The degradation of LFXN at pH = 2.8/c(H2O2) followed pseudo-first-order kinetics. The apparent rate constant was 1.33 × 10-2 min-1, which was much higher than other processes. The degradation rate of LFXN was as follows: pH = 2.8/c(H2O2) > pH = 2.8 > pH = 7/c(H2O2) > pH = 7. Ten aromatic intermediates were formed during the degradation of LFXN, which were further degraded to F-, NH4+, NO3-, CO2 and H2O. This study provides a promising approach for efficiently treating LFXN antibiotic wastewater by pulsed electrochemical oxidation with a BDD electrode without adding H2O2.
  13. Zhang Y, Li J, Xie Y, Wu D, Ong J, Marley G, et al.
    Nat Med, 2023 Sep;29(9):2241-2247.
    PMID: 37640859 DOI: 10.1038/s41591-023-02519-w
    Pay-it-forward incentives involve having a person receive a free test with community-generated messages and then asking if those who received a free test would like to donate money to support others to receive free testing. Here we undertook a two-arm cluster-randomized trial to evaluate pay-it-forward incentives with active community participation to promote hepatitis B virus (HBV) and hepatitis C virus (HCV) testing among men who have sex with men in China. Men randomized to the pay-it-forward arm received free HBV and HCV testing and were offered a chance to pay-it-forward by donating money to support the testing of another anonymous person. Each participant paid for their HCV and HBV test at 7.7 USD per test in the standard-of-care arm. The primary outcome was the proportion of men who tested for HBV and HCV. Between 28 March and 6 November 2021, 32 groups (10 men per group) of men were randomized to the pay-it-forward (n = 160, 16 clusters) and standard-of-care (n = 162, 16 clusters) arms, respectively. HBV and HCV rapid testing were higher in the pay-it-forward arm (59.4%) than in the standard-of-care arm (25.3%) (proportion difference 35.2%, 95% confidence interval 24.1-46.3%). No adverse events were reported. The community-led pay-it-forward incentives improved HBV and HCV testing among men who have sex with men. Clinical Trial registration: ChiCTR 2100046140.
  14. Yang XR, Devi BCR, Sung H, Guida J, Mucaki EJ, Xiao Y, et al.
    Breast Cancer Res Treat, 2017 Oct;165(3):687-697.
    PMID: 28664506 DOI: 10.1007/s10549-017-4356-8
    PURPOSE: To characterize the spectrum of germline mutations in BRCA1, BRCA2, and PALB2 in population-based unselected breast cancer cases in an Asian population.

    METHODS: Germline DNA from 467 breast cancer patients in Sarawak General Hospital, Malaysia, where 93% of the breast cancer patients in Sarawak are treated, was sequenced for the entire coding region of BRCA1; BRCA2; PALB2; Exons 6, 7, and 8 of TP53; and Exons 7 and 8 of PTEN. Pathogenic variants included known pathogenic variants in ClinVar, loss of function variants, and variants that disrupt splice site.

    RESULTS: We found 27 pathogenic variants (11 BRCA1, 10 BRCA2, 4 PALB2, and 2 TP53) in 34 patients, which gave a prevalence of germline mutations of 2.8, 3.23, and 0.86% for BRCA1, BRCA2, and PALB2, respectively. Compared to mutation non-carriers, BRCA1 mutation carriers were more likely to have an earlier age at onset, triple-negative subtype, and lower body mass index, whereas BRCA2 mutation carriers were more likely to have a positive family history. Mutation carrier cases had worse survival compared to non-carriers; however, the association was mostly driven by stage and tumor subtype. We also identified 19 variants of unknown significance, and some of them were predicted to alter splicing or transcription factor binding sites.

    CONCLUSION: Our data provide insight into the genetics of breast cancer in this understudied group and suggest the need for modifying genetic testing guidelines for this population with a much younger age at diagnosis and more limited resources compared with Caucasian populations.

  15. Chen A, Sun J, Viljoen A, Mostert D, Xie Y, Mangila L, et al.
    Pathogens, 2023 Jun 09;12(6).
    PMID: 37375510 DOI: 10.3390/pathogens12060820
    Fusarium wilt of banana is a devastating disease that has decimated banana production worldwide. Host resistance to Fusarium oxysporum f. sp. Cubense (Foc), the causal agent of this disease, is genetically dissected in this study using two Musa acuminata ssp. Malaccensis segregating populations, segregating for Foc Tropical (TR4) and Subtropical (STR4) race 4 resistance. Marker loci and trait association using 11 SNP-based PCR markers allowed the candidate region to be delimited to a 12.9 cM genetic interval corresponding to a 959 kb region on chromosome 3 of 'DH-Pahang' reference assembly v4. Within this region, there was a cluster of pattern recognition receptors, namely leucine-rich repeat ectodomain containing receptor-like protein kinases, cysteine-rich cell-wall-associated protein kinases, and leaf rust 10 disease-resistance locus receptor-like proteins, positioned in an interspersed arrangement. Their transcript levels were rapidly upregulated in the resistant progenies but not in the susceptible F2 progenies at the onset of infection. This suggests that one or several of these genes may control resistance at this locus. To confirm the segregation of single-gene resistance, we generated an inter-cross between the resistant parent 'Ma850' and a susceptible line 'Ma848', to show that the STR4 resistance co-segregated with marker '28820' at this locus. Finally, an informative SNP marker 29730 allowed the locus-specific resistance to be assessed in a collection of diploid and polyploid banana plants. Of the 60 lines screened, 22 lines were predicted to carry resistance at this locus, including lines known to be TR4-resistant, such as 'Pahang', 'SH-3362', 'SH-3217', 'Ma-ITC0250', and 'DH-Pahang/CIRAD 930'. Additional screening in the International Institute for Tropical Agriculture's collection suggests that the dominant allele is common among the elite 'Matooke' NARITA hybrids, as well as in other triploid or tetraploid hybrids derived from East African highland bananas. Fine mapping and candidate gene identification will allow characterization of molecular mechanisms underlying the TR4 resistance. The markers developed in this study can now aid the marker-assisted selection of TR4 resistance in breeding programs around the world.
  16. Stiller J, Feng S, Chowdhury AA, Rivas-González I, Duchêne DA, Fang Q, et al.
    Nature, 2024 Apr 01.
    PMID: 38560995 DOI: 10.1038/s41586-024-07323-1
    Despite tremendous efforts in the past decades, relationships among main avian lineages remain heavily debated without a clear resolution. Discrepancies have been attributed to diversity of species sampled, phylogenetic method and the choice of genomic regions1-3. Here we address these issues by analysing the genomes of 363 bird species4 (218 taxonomic families, 92% of total). Using intergenic regions and coalescent methods, we present a well-supported tree but also a marked degree of discordance. The tree confirms that Neoaves experienced rapid radiation at or near the Cretaceous-Palaeogene boundary. Sufficient loci rather than extensive taxon sampling were more effective in resolving difficult nodes. Remaining recalcitrant nodes involve species that are a challenge to model due to either extreme DNA composition, variable substitution rates, incomplete lineage sorting or complex evolutionary events such as ancient hybridization. Assessment of the effects of different genomic partitions showed high heterogeneity across the genome. We discovered sharp increases in effective population size, substitution rates and relative brain size following the Cretaceous-Palaeogene extinction event, supporting the hypothesis that emerging ecological opportunities catalysed the diversification of modern birds. The resulting phylogenetic estimate offers fresh insights into the rapid radiation of modern birds and provides a taxon-rich backbone tree for future comparative studies.
  17. Klionsky DJ, Abdel-Aziz AK, Abdelfatah S, Abdellatif M, Abdoli A, Abel S, et al.
    Autophagy, 2021 Jan;17(1):1-382.
    PMID: 33634751 DOI: 10.1080/15548627.2020.1797280
    In 2008, we published the first set of guidelines for standardizing research in autophagy. Since then, this topic has received increasing attention, and many scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Thus, it is important to formulate on a regular basis updated guidelines for monitoring autophagy in different organisms. Despite numerous reviews, there continues to be confusion regarding acceptable methods to evaluate autophagy, especially in multicellular eukaryotes. Here, we present a set of guidelines for investigators to select and interpret methods to examine autophagy and related processes, and for reviewers to provide realistic and reasonable critiques of reports that are focused on these processes. These guidelines are not meant to be a dogmatic set of rules, because the appropriateness of any assay largely depends on the question being asked and the system being used. Moreover, no individual assay is perfect for every situation, calling for the use of multiple techniques to properly monitor autophagy in each experimental setting. Finally, several core components of the autophagy machinery have been implicated in distinct autophagic processes (canonical and noncanonical autophagy), implying that genetic approaches to block autophagy should rely on targeting two or more autophagy-related genes that ideally participate in distinct steps of the pathway. Along similar lines, because multiple proteins involved in autophagy also regulate other cellular pathways including apoptosis, not all of them can be used as a specific marker for bona fide autophagic responses. Here, we critically discuss current methods of assessing autophagy and the information they can, or cannot, provide. Our ultimate goal is to encourage intellectual and technical innovation in the field.
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