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| 2. |
- Beal, Jacob, et al.
(författare)
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Robust estimation of bacterial cell count from optical density
- 2020
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Ingår i: Communications Biology. - : Springer Science and Business Media LLC. - 2399-3642. ; 3:1
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Tidskriftsartikel (refereegranskat)abstract
- Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals <1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data.
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| 3. |
- 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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| 4. |
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- 2019
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Tidskriftsartikel (refereegranskat)
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| 5. |
- Barnes, Brian R, et al.
(författare)
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5'-AMP-activated protein kinase regulates skeletal muscle glycogen content and ergogenics
- 2005
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Ingår i: The FASEB Journal. - : Wiley. - 0892-6638 .- 1530-6860. ; 19:7, s. 773-779
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Tidskriftsartikel (refereegranskat)abstract
- 5'-AMP-activated protein kinase (AMPK) activity is increased during exercise in an intensity- and glycogen-dependent manner. We previously reported that a mutation in the AMPK3 subunit (Prkag3225Q) increases AMPK activity and skeletal muscle glycogen content. Transfection experiments revealed the R225Q mutation is associated with high basal AMPK activity and diminished AMP dependence. Thus, the R225Q mutation can be considered a loss-of-function mutation that abolished allosteric regulation by AMP/ATP, causing increased basal AMPK activity. We used AMPK3 transgenic (Tg-Prkag3225Q) and knockout (Prkag3-/-) mice to determine the relationship between AMPK activity, glycogen content, and ergogenics (ability to perform work) in isolated extensor digitorum longus skeletal muscle after contractions induced by electrical stimulation. Contraction-induced AMPK activity was inversely coupled to glycogen content in wild-type and Tg-Prkag3225Q mice, but not in Prkag3-/- mice, highlighting a partial feedback control of glycogen on contraction-induced AMPK activity in the presence of a functional AMPK3 isoform. Skeletal muscle glycogen content was positively correlated to work performance, regardless of genotype. Thus, chronic activation of AMPK by the Prkag3225Q mutation directly influences skeletal muscle ergogenics by enhancing glycogen content. In conclusion, functional studies of the AMPK3 isoform further support the close connection between glycogen content and exercise performance in skeletal muscle.
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| 6. |
- Long, Yun Chau, et al.
(författare)
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Differential expression of metabolic genes essential for glucose and lipid metabolism in skeletal muscle from spinal cord injured subjects
- 2011
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Ingår i: Journal of applied physiology. - Bethesda, MD : American Physiological Society. - 8750-7587 .- 1522-1601. ; 110:5, s. 1204-1210
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Tidskriftsartikel (refereegranskat)abstract
- Skeletal muscle plays an important role in the regulation of energy homeostasis; therefore, the ability of skeletal muscle to adapt and alter metabolic gene expression in response to changes in physiological demands is critical for energy balance. Individuals with cervical spinal cord lesions are characterized by tetraplegia, impaired thermoregulation, and altered skeletal muscle morphology. We characterized skeletal muscle metabolic gene expression patterns, as well as protein content, in these individuals to assess the impact of spinal cord injury on critical determinants of skeletal muscle metabolism. Our results demonstrate that mRNA levels and protein expression of skeletal muscle genes essential for glucose storage are reduced, whereas expression of glycolytic genes is reciprocally increased in individuals with spinal cord injury. Furthermore, expression of genes essential for lipid oxidation is coordinately reduced in spinal cord injured subjects, consistent with a marked reduction of mitochondrial proteins. Thus spinal cord injury resulted in a profound and tightly coordinated change in skeletal muscle metabolic gene expression program that is associated with the aberrant metabolic features of the tissue. © 2011 the American Physiological Society.
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| 7. |
- Long, Yun Chau
(författare)
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Skeletal muscle metabolic flexibility : the roles of AMP-activated protein kinase and calcineurin
- 2007
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Skeletal muscle fibers differ considerably in their metabolic and physiological properties. The metabolic properties of skeletal muscle display a high degree of flexibility which adapts to various physiological demands by shifting energy substrate metabolism. Studies were conducted to evaluate the roles of AMP-activated protein kinase (AMPK) and calcineurin in the regulation of skeletal muscle metabolism. Fasting elicited a coordinated expression of genes involved in lipid utilization and glucose metabolism in white gastrocnemius muscle from wild-type mice. The fasting-induced transcriptional responses were impaired in the AMPKgamma3 knockout (Prkag3-/-) mice. Conversely, in mice transgenic for an activating mutant form of AMPKã3(R225Q) (Tg-Prkag3225Q), an enhanced expression of several fasting-responsive metabolic genes, and a reciprocal down-regulation of glycolytic genes was observed. The results support the role of AMPKã3 subunit in the coordinated expression of fasting-responsive metabolic genes in skeletal muscle. Exercise stimulated glucose uptake in EDL muscles from wild-type, Tg-Prkag3225Q and Prkag3-/ mice to the same degree. In Tg-Prkag3225Q mice, elevated acetyl-CoA carboxylase phosphorylation, enhanced intramuscular triglyceride utilization and metabolic gene expression was observed after exercise. Conversely, an impaired gene expression was seen in the Prkag3-/- mice. Thus, the AMPKã3 subunit is dispensable for exercise-stimulated glucose transport and the mutant AMPKã3(R225Q) subunit promotes metabolic and gene expression adaptations in response to exercise. Enhanced insulin-, but suppressed AICAR-induced glucose uptake was observed in EDL muscles from transgenic mice expressing an activated form of the calcium/calmodulin dependent protein phosphatase calcineurin (MCK-CnA*). Impaired AMPK-activated glucose uptake was associated with a decrease in the expression of the AMPKã3 subunit. Contractioninduced glucose uptake however was unaltered in MCK-CnA* mice, despite a decrease in contraction-induced AMPK phosphorylation. Therefore, calcineurin-induced skeletal muscle remodeling altered AMPK-activated glucose uptake. An enhanced glucose incorporation into glycogen and a reciprocal suppression of glucose oxidation was seen in the EDL muscle from MCK-CnA* mice. These changes were accompanied by an increase in lipid oxidation and lactate release. The alterations in glucose partitioning were supported by a coordinated decrease in glycolytic genes and an elevation in Pdk4 expression. Consistent with the increase in lipid oxidation, expression lipid metabolic and mitochondrial genes were activated in EDL muscle from MCK-CnA* mice, concomitant with an induction of several transcription regulators including PPARá, PPARä and PGC1á. Therefore, calcineurin altered skeletal muscle metabolism via coordinated changes in gene expression. In conclusion, AMPK regulates skeletal muscle lipid and glucose metabolism, as well as gene regulatory responses to fasting and exercise. Calcineurin-mediated skeletal muscle remodeling alters the expression of AMPK subunits and AMPK-mediated glucose uptake. Furthermore, calcineurin alters lipid and glucose metabolism in skeletal muscle via coordinated changes in gene expression program. Therefore, the flexibility of lipid and glucose utilization in skeletal muscle is not only regulated at the level of covalent and allosteric modifications, but the reciprocity is also conserved at transcriptional level.
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| 8. |
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| 9. |
- Sögård, Peter, et al.
(författare)
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Validation of the in vitro incubation of extensor digitorum longus muscle from mice with a mathematical model
- 2010
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Ingår i: Journal of biological systems. - : World Scientific. - 0218-3390. ; 18:3, s. 687-707
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Tidskriftsartikel (refereegranskat)abstract
- In vitro incubation of tissues; in particular, skeletal muscles from rodents, is a widely-used experimental method in diabetes research. This experimental method has previously been validated, both experimentally and theoretically. However, much of the method's experimental data remains unclear, including the high-rate of lactate production and the lack of an observable increase in glycogen content, within a given time. The predominant hypothesis explaining the high-rate of lactate production is that this phenomenon is dependent on a mechanism in glycolysis that works as a safety valve, producing lactate when glucose uptake is super-physiological. Another hypothesis is that existing anoxia forces more ATP to be produced from glycolysis, leading to an increased lactate concentration. The lack of an observable increase in glycogen content is assumed to be dependent on limitations in sensitivity of the measuring method used. We derived a mathematical model to investigate which of these hypotheses is most likely to be correct. Using our model, data analysis indicates that the in vitro incubated muscle specimens, most likely are sensing the presence of existing anoxia, rather than an overflow in glycolysis. The anoxic milieu causes the high lactate production. The model also predicts an increased glycogenolysis. After mathematical analyses, an estimation of the glycogen concentration could be made with a reduced model. In conclusion, central anoxia is likely to cause spatial differences in glycogen concentrations throughout the entire muscle. Thus, data regarding total glycogen levels in the incubated muscle do not accurately represent the entire organ. The presented model allows for an estimation of total glycogen, despite spatial differences present in the muscle specimen.
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| 10. |
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The Seventeenth Data Release of the Sloan Digital Sky Surveys : Complete Release of MaNGA, MaStar, and APOGEE-2 Data
- 2022
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Ingår i: Astrophysical Journal Supplement Series. - : Institute of Physics (IOP). - 0067-0049 .- 1538-4365. ; 259:2
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Tidskriftsartikel (refereegranskat)abstract
- This paper documents the seventeenth data release (DR17) from the Sloan Digital Sky Surveys; the fifth and final release from the fourth phase (SDSS-IV). DR17 contains the complete release of the Mapping Nearby Galaxies at Apache Point Observatory (MaNGA) survey, which reached its goal of surveying over 10,000 nearby galaxies. The complete release of the MaNGA Stellar Library accompanies this data, providing observations of almost 30,000 stars through the MaNGA instrument during bright time. DR17 also contains the complete release of the Apache Point Observatory Galactic Evolution Experiment 2 survey that publicly releases infrared spectra of over 650,000 stars. The main sample from the Extended Baryon Oscillation Spectroscopic Survey (eBOSS), as well as the subsurvey Time Domain Spectroscopic Survey data were fully released in DR16. New single-fiber optical spectroscopy released in DR17 is from the SPectroscipic IDentification of ERosita Survey subsurvey and the eBOSS-RM program. Along with the primary data sets, DR17 includes 25 new or updated value-added catalogs. This paper concludes the release of SDSS-IV survey data. SDSS continues into its fifth phase with observations already underway for the Milky Way Mapper, Local Volume Mapper, and Black Hole Mapper surveys.
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