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| 2. |
- Glasbey, JC, et al.
(författare)
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- 2021
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swepub:Mat__t
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| 6. |
- 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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| 9. |
- Spina, L., et al.
(författare)
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The GALAH survey : tracing the Galactic disc with open clusters
- 2021
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Ingår i: Monthly notices of the Royal Astronomical Society. - : Oxford University Press (OUP). - 0035-8711 .- 1365-2966. ; 503:3, s. 3279-3296
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Tidskriftsartikel (refereegranskat)abstract
- Open clusters are unique tracers of the history of our own Galaxy's disc. According to our membership analysis based on Gala astrometry, out of the 226 potential clusters falling in the footprint of the GALactic Archaeology with HERMES (GALAH) survey or the Apache Point Observatory Galactic Evolution Experiment (APOGEE) survey, we find that 205 have secure members that were observed by at least one of the surveys. Furthermore, members of 134 clusters have high-quality spectroscopic data that we use to determine their chemical composition. We leverage this information to study the chemical distribution throughout the Galactic disc of 21 elements, from C to Eu. The radial metallicity gradient obtained from our analysis is -0.076 +/- 0.009 dex kpc(-1), which is in agreement with previous works based on smaller samples. Furthermore, the gradient in the (Fe/Hi-guiding radius (r(guid)) plane is -0.073 +/- 0.008 dex kpc(-1). We show consistently that open clusters trace the distribution of chemical elements throughout the Galactic disc differently than field stars. In particular, at the given radius, open clusters show an age-metallicity relation that has less scatter than field stars. As such scatter is often interpreted as an effect of radial migration, we suggest that these differences are due to the physical selection effect imposed by our Galaxy: clusters that would have migrated significantly also had higher chances to get destroyed. Finally, our results reveal trends in the [X/Fe]-r(guid)-age space, which are important to understand production rates of different elements as a function of space and time.
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| 10. |
- 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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| 12. |
- Francis, E., et al.
(författare)
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Effect of Nb and Fe on damage evolution in a Zr-alloy during proton and neutron irradiation
- 2019
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Ingår i: Acta Materialia. - : PERGAMON-ELSEVIER SCIENCE LTD. - 1359-6454 .- 1873-2453. ; 165, s. 603-614
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Tidskriftsartikel (refereegranskat)abstract
- Detailed analysis was carried out on proton and a neutron irradiated Nb-containing Zr-alloy to study the evolution of dislocation loop size and densities as well as the formation and evolution of irradiation induced precipitation/clustering. The results obtained here have been contrasted against previously published work on a Nb-free Zr-alloy [1, 21 to investigate the mechanistic reason for the improved resistance to irradiation-induced growth of Nb-containing Zr alloys. The combined use of bright field scanning transmission electron microscopy, ultra-high-resolution energy dispersive spectroscopy and atom probe tomography analysis provides evidence of evenly distributed radiation-induced Nb dusters that have formed during the early stage of proton irradiation and Fe-rich nano-rods near Fe-containing second phase particles. The former seems to have a profound effect on loop and subsequent loop formation, keeping loop size small but number density high while loops seem to initially form at similar dose levels compared to a Nb-free alloy but loop line density does not increase during further irradiation. It is hypothesized that the formation of the Nb nano-precipitates/clusters significantly hinders mobility and growth of loops, resulting in a small size, high number density and limited ability of loops to arrange along basal traces compared to Nb-free Zr-alloys. It is suggested that it is the limited loop arrangement that slows down loop formation and the root cause for the high resistance of Nb-containing Zr-alloys to irradiation-induced growth.
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| 13. |
- Pasche, Boris, et al.
(författare)
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Somatic acquisition and signaling of TGFBR1*6A in cancer
- 2005
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Ingår i: Journal of the American Medical Association (JAMA). - : American Medical Association (AMA). - 0098-7484 .- 1538-3598. ; 294:13, s. 1634-1646
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Tidskriftsartikel (refereegranskat)abstract
- Context: TGFBR1*6A is a common polymorphism of the type I transforming growth factor 0 receptor (TGFBR1). Epidemiological studies suggest that TGFBR1*6A may act as a tumor susceptibility allele. How TGFBR1*6A contributes to cancer development is largely unknown.. Objectives: To determine whether TGFBR1*6A is somatically acquired by primary tumors and metastases during cancer development and whether the 3-amino acid deletion that differentiates TGFBR1*6A from TGFBR1 is part of the mature receptor or part of the signal sequence and to investigate TGFBR1*6A signaling in cancer cells. Design, Setting, and Patients: Tumor And germline tissues from 531 patients with a diagnosis of head and neck, colorectal, or breast cancer recruited from 3 centers in the United States and from 1 center in Spain from June 1, 1994, through June 30, 2004, In vitro translation assays, MCF-7 breast cancer cells stably transfected with TGFBR1*6A, TGFBR1, or the vector alone, DLD-1 colorectal cancer cells that endogenously carry TGFBR1*6A, and SW48 colorectal cancer cells that do not carry TGFBR1*6A. Main Outcome Measures: TGFBR1*6A somatic acquisition in cancer. Determination of the amino terminus of the mature TGFBR1*6A and TGFBR1 receptors. Determination of TGF-beta-dependent cell proliferation. Results: TGFBR1*6A was somatically acquired in 13 of 44 (29.5%) colorectal cancer metastases, in 4 of 157 (2.5%) of colorectal tumors, in 4 of 226 (1.8%) head and neck primary tumors, and in none of the 104 patients with breast cancer. TGFBR1*6A somatic acquisition is not associated with loss of heterozygosity, microsatellite instability, or a mutator phenotype. The signal sequences of TGFBR1 and TGFBR1*6A are cleaved at the same site resulting in identical mature receptors. TGFBR1*6A may switch TGF-beta growth inhibitory signals into growth stimulatory signals in MCF-7 breast cancer cells and in DLD-1 colorectal cancer cells. Conclusions: TGFBR1*6A is somatically acquired in 29.5% of liver metastases from colorectal cancer and may bestow cancer cells with a growth advantage in the presence of TGF-beta. The functional consequences of this conversion appear to be mediated by the TGFBR1*6A signal sequence rather than by the mature receptor. The results highlight a new facet of TGF-beta signaling in cancer and suggest that TGFBR1*6A may represent a potential therapeutic target in cancer.
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| 16. |
- Chuah, L. L., et al.
(författare)
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Measurement of glomerular filtration rate in patients undergoing obesity surgery
- 2018
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Ingår i: Bmc Nephrology. - : Springer Science and Business Media LLC. - 1471-2369. ; 19
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Tidskriftsartikel (refereegranskat)abstract
- BackgroundMost studies on obesity surgery have measured renal function using the estimated GFR. However, due to the reduction of muscle mass, and therefore creatinine that accompanies weight loss, such measures can falsely suggest an improvement in renal function. To balance the risks of surgery versus any potential benefits on renal function, we need to be able to determine renal function using valid and reliable methodologies. In this pilot study we aimed to measure renal function in patients with CKD undergoing obesity surgery using the gold standard Cr-51-EDTA GFR clearance methodology which is independent of measures of muscle mass.MethodsNine consecutive obese patients with CKD underwent obesity surgery. Their renal function was assessed using Cr-51-EDTA GFR, cystatin C and serum creatinine as well as using eGFR equations including MDRD CKD Epi, Cockcroft Gault and CKD Epi cystatin before and 12months after surgery.ResultsRenal function using the Cr-51-EDTA measured GFR did not change significantly after surgery. Similar results were obtained when Cystatin C, CKD Epi cystatin, CKD Epi cystatin creatinine and adjusted Cockcroft Gault Creatinine clearance methods were used. In contrast there were either trends or significant improvements in renal function measured using the MDRD and CKD Epi equations.ConclusionsIn this pilot study using the gold standard Cr-51-EDTA method we found stabilisation in renal function after obesity surgery. Until further definitive data emerge it is critical to balance the risk and benefits of surgery, especially if renal function may not improve as often as previously suggested.
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| 17. |
- Feuillet, Diane K., et al.
(författare)
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Spatial variations in the Milky Way disc metallicity-age relation
- 2019
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Ingår i: Monthly notices of the Royal Astronomical Society. - : Oxford University Press (OUP). - 0035-8711 .- 1365-2966. ; 489:2, s. 1742-1752
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Tidskriftsartikel (refereegranskat)abstract
- Stellar ages are a crucial component to studying the evolution of the Milky Way. Using Gaia DR2 distance estimates, it is now possible to estimate stellar ages for a larger volume of evolved stars through isochrone matching. This work presents [M/H]-age and [alpha/M]-age relations derived for different spatial locations in the Milky Way disc. These relations are derived by hierarchically modelling the star formation history of stars within a given chemical abundance bin. For the first time, we directly observe that significant variation is apparent in the [M/H]-age relation as a function of both Galactocentric radius and distance from the disc midplane. The [M/H]-age relations support claims that radial migration has a significant effect in the plane of the disc. Using the [M/H] bin with the youngest mean age at each radial zone in the plane of the disc, the present-day metallicity gradient is measured to be -0.059 +/- 0.010 dex kpc(-1), in agreement with Cepheids and young field stars. We find a vertically flared distribution of young stars in the outer disc, confirming predictions of models and previous observations. The mean age of the [M/H]-[alpha/M] distribution of the solar neighbourhood suggests that the high-[M/H] stars are not an evolutionary extension of the low-alpha sequence. Our observational results are important constraints to Galactic simulations and models of chemical evolution.
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| 18. |
- Frankel, R., et al.
(författare)
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Autocatalytic amplification of Alzheimer-associated A beta 42 peptide aggregation in human cerebrospinal fluid
- 2019
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Ingår i: Communications Biology. - : Springer Science and Business Media LLC. - 2399-3642. ; 2
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Tidskriftsartikel (refereegranskat)abstract
- Alzheimer's disease is linked to amyloid beta (A beta) peptide aggregation in the brain, and a detailed understanding of the molecular mechanism of A beta aggregation may lead to improved diagnostics and therapeutics. While previous studies have been performed in pure buffer, we approach the mechanism in vivo using cerebrospinal fluid (CSF). We investigated the aggregation mechanism of A beta 42 in human CSF through kinetic experiments at several A beta 42 monomer concentrations (0.8-10 mu M). The data were subjected to global kinetic analysis and found consistent with an aggregation mechanism involving secondary nucleation of monomers on the fibril surface. A mechanism only including primary nucleation was ruled out. We find that the aggregation process is composed of the same microscopic steps in CSF as in pure buffer, but the rate constant of secondary nucleation is decreased. Most importantly, the autocatalytic amplification of aggregate number through catalysis on the fibril surface is prevalent also in CSF.
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| 19. |
- López, Aida Rodríguez, et al.
(författare)
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Autophagy-mediated control of ribosome homeostasis in oncogene-induced senescence
- 2023
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Ingår i: Cell Reports. - 2211-1247. ; 42:11, s. 1-23
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Tidskriftsartikel (refereegranskat)abstract
- Oncogene-induced senescence (OIS) is a persistent anti-proliferative response that acts as a barrier against malignant transformation. During OIS, cells undergo dynamic remodeling, which involves alterations in protein and organelle homeostasis through autophagy. Here, we show that ribosomes are selectively targeted for degradation by autophagy during OIS. By characterizing senescence-dependent alterations in the ribosomal interactome, we find that the deubiquitinase USP10 dissociates from the ribosome during the transition to OIS. This release of USP10 leads to an enhanced ribosome ubiquitination, particularly of small subunit proteins, including lysine 275 on RPS2. Both reinforcement of the USP10-ribosome interaction and mutation of RPS2 K275 abrogate ribosomal delivery to lysosomes without affecting bulk autophagy. We show that the selective recruitment of ubiquitinated ribosomes to autophagosomes is mediated by the p62 receptor. While ribophagy is not required for the establishment of senescence per se, it contributes to senescence-related metabolome alterations and facilitates the senescence-associated secretory phenotype.
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| 21. |
- Muser, Daniele, et al.
(författare)
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Risk Stratification of Patients With Apparently Idiopathic Premature Ventricular Contractions A Multicenter International CMR Registry
- 2020
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Ingår i: JACC. - : ELSEVIER. - 2405-500X .- 2405-5018. ; 6:6, s. 722-735
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Tidskriftsartikel (refereegranskat)abstract
- OBJECTIVES This study investigated the prevalence and prognostic significance of concealed myocardial abnormalities identified by cardiac magnetic resonance (CMR) imaging in patients with apparently idiopathic premature ventricular contractions (PVCs). BACKGROUND The rote of CMR imaging in patients with frequent PVCs and otherwise negative diagnostic workup is uncertain. METHODS This was a multicenter, international study that included 518 patients (age 44 +/- 15 years; 57% men) with frequent (>1,000/24 h) PVCs and negative routine diagnostic workup. Patients underwent a comprehensive CMR protocol including late gadolinium enhancement imaging for detection of necrosis and/or fibrosis. The study endpoint was a composite of sudden cardiac death, resuscitated cardiac arrest, and nonfatal episodes of ventricular fibrillation or sustained ventricular tachycardia that required appropriate implantable cardioverter-defibrillator therapy. RESULTS Myocardial abnormalities were found in 85 (16%) patients. Mate gender (odds ratio [OR]: 4.28; 95% confidence interval [CI]: 2.06 to 8.93; p = 0.01), family history of sudden cardiac death and/or cardiomyopathy (OR: 3.61; 95% CI: 1.33 to 9.82; p = 0.01), multifocat PVCs (OR: 11.12; 95% CI: 4.35 to 28.46; p < 0.01), and non-left bundle branch block inferior axis morphology (OR: 14.11; 95% CI: 7.35 to 27.07; p < 0.01) were alt significantly related to the presence of myocardial abnormalities. After a median follow-up of 67 months, the composite endpoint occurred in 26 (5%) patients. Subjects with myocardial abnormalities on CMR had a higher incidence of the composite outcome (n = 25; 29%) compared with those without abnormalities (n = 1; 0.2%; p < 0.01). CONCLUSIONS CMR can identify concealed myocardial abnormalities in 16% of patients with apparently idiopathic frequent PVCs. Presence of myocardial abnormalities on CMR predict worse clinical outcomes. (C) 2019 by the American College of Cardiology Foundation.
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