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- 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. |
- Liu, Shiping, et al.
(författare)
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Population Genomics Reveal Recent Speciation and Rapid Evolutionary Adaptation in Polar Bears
- 2014
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Ingår i: Cell. - : Elsevier BV. - 0092-8674 .- 1097-4172. ; 157:4, s. 785-794
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Tidskriftsartikel (refereegranskat)abstract
- Polar bears are uniquely adapted to life in the High Arctic and have undergone drastic physiological changes in response to Arctic climates and a hyper-lipid diet of primarily marine mammal prey. We analyzed 89 complete genomes of polar bear and brown bear using population genomic modeling and show that the species diverged only 479-343 thousand years BP. We find that genes on the polar bear lineage have been under stronger positive selection than in brown bears; nine of the top 16 genes under strong positive selection are associated with cardiomyopathy and vascular disease, implying important reorganization of the cardiovascular system. One of the genes showing the strongest evidence of selection, APOB, encodes the primary lipoprotein component of low-density lipoprotein (LDL); functional mutations in APOB may explain how polar bears are able to cope with life-long elevated LDL levels that are associated with high risk of heart disease in humans.
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- Mahajan, Mayank
(författare)
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Evolution of cellular complexity and other remarkable features in Gemmataceae : Complex bacterial lineages defy prokaryotic trends
- 2019
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Bacteria of the family Gemmataceae belong the phylum Planctomycetes and are remarkable because of their complex cellular architectures, previously considered to be traits exclusive to eukaryotes. This thesis provides clues to the atypical cell envelope, the enhanced radiotolerance and the amazing cellular complexity of these bacteria.A comparative genomics study of these bacteria revealed massive duplications and new combinations of structural domains that are highly abundant in eukaryotes but rare in bacteria. These domains are known to facilitate signalling and protein interactions. The proteins of these bacteria also contain long regions with no predicted domains. On average, eukaryotic proteins are longer and more disordered than prokaryotic proteins. Intriguingly, the length and fraction of disordered regions in proteins of some bacteria are higher than in many other prokaryotes, and these bacteria also have complex lifestyles. Many bacteria in the Planctomycetes, including the Gemmataceae, are among these few bacteria. This suggests that there is no sharp boundary between prokaryotes and eukaryotes with respect to protein length and domain composition patterns, as previously thought.A bioinformatics analysis revealed the loss of genes for the peptidoglycan cell wall in some lineages of the Planctomycetes. Loss of the gene for the FtsZ protein, the major cell division protein in bacteria, may have facilitated the evolution of budding in the Planctomycetales and led to the gradual loss of the cell wall and cell division gene cluster. These changes may have enabled the expansion of the inner membrane and triggered adaptive changes in conserved membrane proteins and transport systems. The loss of the peptidoglycan cell wall may also explain the altered cell morphology. A subcellular proteomics study showed that the DNA replication and repair proteins are associated with the cell envelope, which supports the cell factory model of DNA replication.T. immobilis, which has the simplest genome of all members of the Gemmataceae, was found to be naturally competent and most suitable for transformation experiments. T. immobilis was transformed to produce mutants in which the gene for DdrA, a double stranded break DNA repair protein, has been inactivated. The DdrA-null mutant showed a major loss in radiotolerance.
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