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  1. 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.
  2. 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
  3. Chai CY, Maran S, Thew HY, Tan YC, Rahman NMANA, Cheng WH, et al.
    Biology (Basel), 2022 Nov 02;11(11).
    PMID: 36358305 DOI: 10.3390/biology11111604
    The Harvey rat sarcoma (HRAS) proto-oncogene belongs to the RAS family and is one of the pathogenic genes that cause cancer. Deleterious nsSNPs might have adverse consequences at the protein level. This study aimed to investigate deleterious nsSNPs in the HRAS gene in predicting structural alterations associated with mutants that disrupt normal protein-protein interactions. Functional and structural analysis was employed in analyzing the HRAS nsSNPs. Putative post-translational modification sites and the changes in protein-protein interactions, which included a variety of signal cascades, were also investigated. Five different bioinformatics tools predicted 33 nsSNPs as "pathogenic" or "harmful". Stability analysis predicted rs1554885139, rs770492627, rs1589792804, rs730880460, rs104894227, rs104894227, and rs121917759 as unstable. Protein-protein interaction analysis revealed that HRAS has a hub connecting three clusters consisting of 11 proteins, and changes in HRAS might cause signal cascades to dissociate. Furthermore, Kaplan-Meier bioinformatics analyses indicated that the HRAS gene deregulation affected the overall survival rate of patients with breast cancer, leading to prognostic significance. Thus, based on these analyses, our study suggests that the reported nsSNPs of HRAS may serve as potential targets for different proteomic studies, diagnoses, and therapeutic interventions focusing on cancer.
  4. Chai CY, Tan IS, Foo HCY, Lam MK, Tong KTX, Lee KT
    Bioresour Technol, 2021 Jun;330:124930.
    PMID: 33735730 DOI: 10.1016/j.biortech.2021.124930
    Managing plastic waste remains an urgent environmental concern and switching to biodegradable plastics can reduce the dependence on depleting fossil fuels. This study emphasises the efficacy of macroalgae wastes, Eucheuma denticulatum residues (EDRs), as potential alternate feedstock to produce l-lactic acid (l-LA), the monomer of polylactic acid, through fermentation. An innovative environmental friendly strategy was explored in this study to develop a glucose platform from EDRs: pretreatment with microwave-assisted autohydrolysis (MAA) applied to enhance enzymatic hydrolysis of EDRs. The results indicate that MAA pretreatment significantly increased the digestibility of EDRs during the enzymatic hydrolysis process. The optimum pretreatment conditions were 120 °C and 50 min, resulting in 96.5% of enzymatic digestibility after 48 h. The high l-LA yield of 98.6% was obtained using pretreated EDRs and supplemented with yeast extract. The energy analysis implies that MAA pretreatment could further improve the overall energy efficiency of the process.
  5. Surif S, Chai CY
    Environ Pollut, 1995;88(2):177-81.
    PMID: 15091558
    The study of lead exposure among workers in Selangor and the Federal Territory was carried out based on the delta-aminolevulinic acid (ALA) level in urine. Occupations which are expected to have higher lead exposure were chosen in this research. The ALA level in the workers' urine was linked to a few variables which may contribute to the lead level in the body. The result of this study showed that the ALA level of the urine of university students (0.352 +/- 0.038 mg/100 ml) < clerical staff (0.560 +/- 0.043 mg/100 ml) < traffic police (0.612 +/- 0.064 mg/100 ml) < vehicle workshop workers (0.673 +/- 0.099 mg/100 ml) < petrol kiosk workers (0.717 +/- 0.069 mg/100 ml) < bus drivers/conductors (0.850 +/- 0.055 mg/100 ml) which was similar to workers in the printing industry (0.852 +/- 0.110 mg/100 ml). The ALA levels in the urine of the exposed workers were significantly different from the control group (university students). However, results obtained from clerical staff revealed that they were also in the exposed group category. Analysis of variance showed that the exposed groups are in a population which is different from the control population. Correlation tests suggest that there is no significant connection between the ALA level in the urine and the variables tested. Furthermore, Duncan's Multiple Range Test showed no significant differences between the smoking/non smoking group, alcoholic/non-alcoholic group, race and sex (p > 0.05).
  6. Lim SS, Chai CY, Loh HS
    Mater Sci Eng C Mater Biol Appl, 2017 Jul 01;76:144-152.
    PMID: 28482510 DOI: 10.1016/j.msec.2017.03.075
    Hydrothermally synthesized TiO2nanotubes (TNTs) were first used as a filler for chitosan scaffold for reinforcement purpose. Chitosan-TNTs (CTNTs) scaffolds prepared via direct blending and freeze drying retained cylindrical structure and showed enhanced compressive modulus and reduced degradation rate compared to chitosan membrane which experienced severe shrinkage after rehydration with ethanol. Macroporous interconnectivity with pore size of 70-230μm and porosity of 88% were found in CTNTs scaffolds. Subsequently, the functionalization of CTNTs scaffolds with CaCl2solutions (0.5mM-40.5mM) was conducted at physiological pH. The adsorption isotherm of Ca2+ions onto CTNTs scaffolds fitted well with Freundlich isotherm. CTNTs scaffolds with Ca2+ions showed high biocompatibility by promoting adhesion, proliferation and early differentiation of MG63 in a non-dose dependent manner. CTNTs scaffolds with Ca2+ions can be an alternative for bone regeneration.
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