| 1. |
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- 2019
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Tidskriftsartikel (refereegranskat)
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| 2. |
- Klionsky, Daniel J., et al.
(författare)
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Guidelines for the use and interpretation of assays for monitoring autophagy
- 2012
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Ingår i: Autophagy. - : Informa UK Limited. - 1554-8635 .- 1554-8627. ; 8:4, s. 445-544
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Forskningsöversikt (refereegranskat)abstract
- In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process vs. those that measure flux through the autophagy pathway (i.e., the complete process); thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from stimuli that result in increased autophagic activity, defined as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (in most higher eukaryotes and some protists such as Dictyostelium) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the field understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular autophagy assays, we hope to encourage technical innovation in the field.
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| 3. |
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| 4. |
- Li, Qian, et al.
(författare)
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Genome-wide identification of resistance genes and cellular analysis of key gene knockout strain under 5-hydroxymethylfurfural stress in Saccharomyces cerevisiae
- 2023
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Ingår i: BMC Microbiology. - 1471-2180. ; 23:1
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Tidskriftsartikel (refereegranskat)abstract
- In bioethanol production, the main by-product, 5-hydroxymethylfurfural (HMF), significantly hinders microbial fermentation. Therefore, it is crucial to explore genes related to HMF tolerance in Saccharomyces cerevisiae for enhancing the tolerance of ethanol fermentation strains. A comprehensive analysis was conducted using genome-wide deletion library scanning and SGAtools, resulting in the identification of 294 genes associated with HMF tolerance in S. cerevisiae. Further KEGG and GO enrichment analysis revealed the involvement of genes OCA1 and SIW14 in the protein phosphorylation pathway, underscoring their role in HMF tolerance. Spot test validation and subcellular structure observation demonstrated that, following a 3-h treatment with 60 mM HMF, the SIW14 gene knockout strain exhibited a 12.68% increase in cells with abnormal endoplasmic reticulum (ER) and a 22.41% increase in the accumulation of reactive oxygen species compared to the BY4741 strain. These findings indicate that the SIW14 gene contributes to the protection of the ER structure within the cell and facilitates the clearance of reactive oxygen species, thereby confirming its significance as a key gene for HMF tolerance in S. cerevisiae.
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| 5. |
- Liao, Hong, et al.
(författare)
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Genome-wide identification of resistance genes and response mechanism analysis of key gene knockout strain to catechol in Saccharomyces cerevisiae
- 2024
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Ingår i: FRONTIERS IN MICROBIOLOGY. - 1664-302X. ; 15
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Tidskriftsartikel (refereegranskat)abstract
- Engineering Saccharomyces cerevisiae for biodegradation and transformation of industrial toxic substances such as catechol (CA) has received widespread attention, but the low tolerance of S. cerevisiae to CA has limited its development. The exploration and modification of genes or pathways related to CA tolerance in S. cerevisiae is an effective way to further improve the utilization efficiency of CA. This study identified 36 genes associated with CA tolerance in S. cerevisiae through genome-wide identification and bioinformatics analysis and the ERG6 knockout strain (ERG6 Delta) is the most sensitive to CA. Based on the omics analysis of ERG6 Delta under CA stress, it was found that ERG6 knockout affects pathways such as intrinsic component of membrane and pentose phosphate pathway. In addition, the study revealed that 29 genes related to the cell wall-membrane system were up-regulated by more than twice, NADPH and NADP(+) were increased by 2.48 and 4.41 times respectively, and spermidine and spermine were increased by 2.85 and 2.14 times, respectively, in ERG6 Delta. Overall, the response of cell wall-membrane system, the accumulation of spermidine and NADPH, as well as the increased levels of metabolites in pentose phosphate pathway are important findings in improving the CA resistance. This study provides a theoretical basis for improving the tolerance of strains to CA and reducing the damage caused by CA to the ecological environment and human health.
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| 6. |
- Xie, Cuicui, et al.
(författare)
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Neuroprotection by selective neuronal deletion of Atg7 in neonatal brain injury
- 2016
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Ingår i: Autophagy. - : Informa UK Limited. - 1554-8627 .- 1554-8635. ; 12:2, s. 410-423
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Tidskriftsartikel (refereegranskat)abstract
- Perinatal asphyxia induces neuronal cell death and brain injury, and is often associated with irreversible neurological deficits in children. There is an urgent need to elucidate the neuronal death mechanisms occurring after neonatal hypoxia-ischemia (HI). We here investigated the selective neuronal deletion of the Atg7 (autophagy related 7) gene on neuronal cell death and brain injury in a mouse model of severe neonatal hypoxia-ischemia. Neuronal deletion of Atg7 prevented HI-induced autophagy, resulted in 42% decrease of tissue loss compared to wild-type mice after the insult, and reduced cell death in multiple brain regions, including apoptosis, as shown by decreased caspase-dependent and -independent cell death. Moreover, we investigated the lentiform nucleus of human newborns who died after severe perinatal asphyxia and found increased neuronal autophagy after severe hypoxic-ischemic encephalopathy compared to control uninjured brains, as indicated by the numbers of MAP1LC3B/LC3B (microtubule-associated protein 1 light chain 3)-, LAMP1 (lysosomal-associated membrane protein 1)-, and CTSD (cathepsin D)-positive cells. These findings reveal that selective neuronal deletion of Atg7 is strongly protective against neuronal death and overall brain injury occurring after HI and suggest that inhibition of HI-enhanced autophagy should be considered as a potential therapeutic target for the treatment of human newborns developing severe hypoxic-ischemic encephalopathy.
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| 7. |
- Li, Hongfu, et al.
(författare)
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Lithium-mediated long-term neuroprotection in neonatal rat hypoxia-ischemia is associated with antiinflammatory effects and enhanced proliferation and survival of neural stem/progenitor cells.
- 2011
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Ingår i: Journal of cerebral blood flow and metabolism : official journal of the International Society of Cerebral Blood Flow and Metabolism. - : SAGE Publications. - 1559-7016. ; 31:10
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Tidskriftsartikel (refereegranskat)abstract
- The aim of this study was to evaluate the long-term effects of lithium treatment on neonatal hypoxic-ischemic brain injury, inflammation, and neural stem/progenitor cell (NSPC) proliferation and survival. Nine-day-old male rats were subjected to unilateral hypoxia-ischemia (HI) and 2 mmol/kg lithium chloride was injected intraperitoneally immediately after the insult. Additional lithium injections, 1 mmol/kg, were administered at 24-hour intervals for 7 days. Animals were killed 6, 24, 72 hours, or 7 weeks after HI. Lithium reduced total tissue loss by 69%, from 89.4±14.6 mm(3) in controls (n=15) to 27.6±6.2 mm(3) in lithium-treated animals (n=14) 7 weeks after HI (P<0.001). Microglia activation was inhibited by lithium treatment, as judged by Iba-1 and galectin-3 immunostaining, and reduced interleukin-1β and CCL2 levels. Lithium increased progenitor, rather than stem cell, proliferation in both nonischemic and ischemic brains, as judged by 5-bromo-2-deoxyuridine labeling 24 and 72 hours as well as by phospho-histone H3 and brain lipid-binding protein labeling 7 weeks after HI. Lithium treatment also promoted survival of newborn NSPCs, without altering the relative levels of neuronal and astroglial differentiation. In summary, lithium conferred impressive, morphological long-term protection against neonatal HI, at least partly by inhibiting inflammation and promoting NSPC proliferation and survival.Journal of Cerebral Blood Flow & Metabolism advance online publication, 18 May 2011; doi:10.1038/jcbfm.2011.75.
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| 8. |
- Li, P. F., et al.
(författare)
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Dynamics of low energy electrons transmitting throughstraight glass capillary: Tilt angle dependence br
- 2022
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Ingår i: Acta Physica Sinica. - : Acta Physica Sinica, Chinese Physical Society and Institute of Physics, Chinese Academy of Sciences. - 1000-3290. ; 71:8
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Tidskriftsartikel (refereegranskat)abstract
- It is a hot topic that using glass capillary to focus and shape the charged particle beam, for it isinexpensive and simple. There are the cases that single glass capillaries are used to make the microbeam of thepositive ions. When it comes to electrons, their transmitting through insulating capillaries is complex and theattempt to use the glass capillary to produce electron beams in the size of micrometer needs further exploring.In this paper, the charging-up process of the 900-eV electrons transmitting through a glass capillary withthe grounded conductive-coated outer surface is reported. Two-dimensional angular distributions of thetransmitted electrons and their time evolutions are measured for the cases of various tilt angles of glass tube. Itis found that there are a considerable number of transmitted electrons at the tilt angle exceeding thegeometrical opening angle (1 degrees) of the glass tube. The intensity of transmitted electrons for large tilt angle (i.e. -1.15 degrees)can be considered as first falling to zero, then keeping zero for a long time, finally rising to a certain stablevalue. Correspondingly, the angular distribution center experiences moving towards negative-positive-negative-settled. The energy losses are measured for various tilt angles. The larger the tilt angles, the larger the energyloss of transmitted electrons is. To better understand the physics behind the observed phenomena, thesimulations of the energy loss for transmitted electrons at various tilt angles are performed by the Monte Carlomethod. The comparation between the simulated energy losses and the measured energy losses shows that theexperimental results are well explained by multiple deflections from the wall.
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| 9. |
- Li, P. F., et al.
(författare)
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Stable transmission of low energy electrons in glass tube with outer surface grounded conductively shielding
- 2022
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Ingår i: Acta Physica Sinica. - : Acta Physica Sinica, Chinese Physical Society and Institute of Physics, Chinese Academy of Sciences. - 1000-3290. ; 71:7
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Tidskriftsartikel (refereegranskat)abstract
- The electron microbeam is useful for modifying certain fragments of biomolecule. It is successful to applythe guiding effect to making the microbeam of positively charged particles by using single glass capillary.However, the mechanism for the electron transport through insulating capillaries is unclear. Meanwhile,previous researches show that there are oscillations of the transmission intensity of electrons with time in theglass capillaries with outer serface having no grounded conductive shielding, So, the application of glasscapillary to making the microbeam of electrons is limited. In this paper, the transmission of 1.5 and 0.9 keV electrons through the glass capillary without/with thegrounded conductive-coated outer surface are investigated, respectively. This study aims to understand themechanism for low energy electron transport in the glass capillaries, and find the conditions for the steadytransport of the electrons. Two-dimensional angular distribution of the transported electrons and its timeevolution are measured. It is found that the intensity of the transported electrons with the incident energythrough the glass capillaries for the glass capillaries without and with the grounded conductive-coated outersurface show the typical geometrical transmission characteristics. The time evolution of the 1.5- keV electrontransport presents an extremely complex variation for the glass capillary without the grounded conductive-coated outer surface. The intensity first falls, then rises and finally oscillates around a certain mean value.Correspondingly, the angular distribution center experiences moving towards positive-negative-settlement. Incomparison, the charge-up process of the 0.9 keV electron transport through the glass capillary with thegrounded conductive-coated outer surface shows a relatively simple behavior. At first, the intensity declines rapidly with time. Then, it slowly rises till a certain value and stays steady subsequently. The angulardistribution of transported electrons follows the intensity distribution in general, but with some delay. It quicklymoves to negative direction then comes back to positive direction. Finally, it regresses extremely slowly andends up around the tilt angle. To better understand the physics behind the observed phenomena, the simulationfor the interaction of the electrons with SiO2 material is performed to obtain the possible deposited chargedistribution by the CASINO code. Based on the analysis of the experimental results and the simulated chargedeposition, the conditions for stabilizing the electron transport through glass capillary arepresented.
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| 10. |
- Li, Qian, 1983, et al.
(författare)
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Lithium reduces apoptosis and autophagy after neonatal hypoxia–ischemia
- 2010
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Ingår i: Cell death and Disease. - : Springer Science and Business Media LLC. - 2041-4889. ; 1:July 15
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Tidskriftsartikel (refereegranskat)abstract
- Lithium is used in the treatment of bipolar mood disorder. Reportedly, lithium can be neuroprotective in models of adult brain ischemia. The purpose of this study was to evaluate the effects of lithium in a model of neonatal hypoxic–ischemic brain injury. Nine-day-old male rats were subjected to unilateral hypoxia–ischemia (HI) and 2 mmol/kg lithium chloride was injected i.p. immediately after the insult. Additional lithium injections, 1 mmol/kg, were administered at 24-h intervals. Pups were killed 6, 24 or 72 h after HI. Lithium reduced the infarct volume from 24.7±2.9 to 13.8±3.3 mm3 (44.1%) and total tissue loss (degeneration + lack of growth) from 67.4±4.4 to 38.4±5.9 mm3 (43.1%) compared with vehicle at 72 h after HI. Injury was reduced in the cortex, hippocampus, thalamus and striatum. Lithium reduced the ischemia-induced dephosphorylation of glycogen synthase kinase-3β and extracellular signal-regulated kinase, the activation of calpain and caspase-3, the mitochondrial release of cytochrome c and apoptosis-inducing factor, as well as autophagy. We conclude that lithium could mitigate the brain injury after HI by inhibiting neuronal apoptosis. The lithium doses used were in the same range as those used in bipolar patients, suggesting that lithium might be safely used for the avoidance of neonatal brain injury.
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