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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. |
- 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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| 4. |
- Ablikim, M., et al.
(författare)
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Measurements of cross section of e(+)e(-) -> p(p)over-bar pi(0) at center-of-mass energies between 4.008 and 4.600 GeV
- 2017
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Ingår i: Physics Letters B. - : ELSEVIER SCIENCE BV. - 0370-2693 .- 1873-2445. ; 771, s. 45-51
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Tidskriftsartikel (refereegranskat)abstract
- Based on e(+)e(-) annihilation data samples collected with the BESIII detector at the BEPCII collider at 13 center-of-mass energies from 4.008 to 4.600 GeV, measurements of the Born cross section of e(+)e(-) -> p (p) over bar pi(0) are performed. No significant resonant structure is observed in the measured energy dependence of the cross section. The upper limit on the Born cross section of e(+)e(-) -> Y (4260) -> p (p) over bar pi(0) at the 90% C. L. is determined to be 0.01 pb. The upper limit on the ratio of the branching fractions B(Y(4260) -> p (p) over bar pi(0))/B(Y(4260) -> pi(+)pi(-) j/Psi) at the 90% C. L. is determined to be 0.02%.
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| 5. |
- Albrechtsen, A., et al.
(författare)
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Exome sequencing-driven discovery of coding polymorphisms associated with common metabolic phenotypes
- 2013
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Ingår i: Diabetologia. - : Springer Science and Business Media LLC. - 0012-186X .- 1432-0428. ; 56:2, s. 298-310
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Tidskriftsartikel (refereegranskat)abstract
- Human complex metabolic traits are in part regulated by genetic determinants. Here we applied exome sequencing to identify novel associations of coding polymorphisms at minor allele frequencies (MAFs) > 1% with common metabolic phenotypes. The study comprised three stages. We performed medium-depth (8x) whole exome sequencing in 1,000 cases with type 2 diabetes, BMI > 27.5 kg/m(2) and hypertension and in 1,000 controls (stage 1). We selected 16,192 polymorphisms nominally associated (p < 0.05) with case-control status, from four selected annotation categories or from loci reported to associate with metabolic traits. These variants were genotyped in 15,989 Danes to search for association with 12 metabolic phenotypes (stage 2). In stage 3, polymorphisms showing potential associations were genotyped in a further 63,896 Europeans. Exome sequencing identified 70,182 polymorphisms with MAF > 1%. In stage 2 we identified 51 potential associations with one or more of eight metabolic phenotypes covered by 45 unique polymorphisms. In meta-analyses of stage 2 and stage 3 results, we demonstrated robust associations for coding polymorphisms in CD300LG (fasting HDL-cholesterol: MAF 3.5%, p = 8.5 x 10(-14)), COBLL1 (type 2 diabetes: MAF 12.5%, OR 0.88, p = 1.2 x 10(-11)) and MACF1 (type 2 diabetes: MAF 23.4%, OR 1.10, p = 8.2 x 10(-10)). We applied exome sequencing as a basis for finding genetic determinants of metabolic traits and show the existence of low-frequency and common coding polymorphisms with impact on common metabolic traits. Based on our study, coding polymorphisms with MAF above 1% do not seem to have particularly high effect sizes on the measured metabolic traits.
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| 6. |
- Hu, Hai-Xi, et al.
(författare)
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Structural insights into HetR-PatS interaction involved in cyanobacterial pattern formation
- 2015
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Ingår i: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 5
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Tidskriftsartikel (refereegranskat)abstract
- The one-dimensional pattern of heterocyst in the model cyanobacterium Anabaena sp. PCC 7120 is coordinated by the transcription factor HetR and PatS peptide. Here we report the complex structures of HetR binding to DNA, and its hood domain (HetR(Hood)) binding to a PatS-derived hexapeptide (PatS6) at 2.80 and 2.10 angstrom, respectively. The intertwined HetR dimer possesses a couple of novel HTH motifs, each of which consists of two canonical alpha-helices in the DNA-binding domain and an auxiliary alpha-helix from the flap domain of the neighboring subunit. Two PatS6 peptides bind to the lateral clefts of HetR(Hood), and trigger significant conformational changes of the flap domain, resulting in dissociation of the auxiliary alpha-helix and eventually release of HetR from the DNA major grove. These findings provide the structural insights into a prokaryotic example of Turing model.
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| 7. |
- Chen, Hua, et al.
(författare)
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Analytic smoothness effect of solutions for spatially homogeneous Landau equation
- 2010
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Ingår i: Journal of Differential Equations. - : Elsevier BV. - 0022-0396. ; 248:1, s. 77-94
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Tidskriftsartikel (refereegranskat)abstract
- In this paper, we study the smoothness effect of Cauchy problem for the spatially homogeneous Landau equation in the hard potential case and theMaxwellian molecules case. We obtain the analytic smoothing effect for the solutions under rather weak assumptions on the initial datum.
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| 8. |
- Chen, Hua, et al.
(författare)
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Gevrey hypoellipticity for a class of kinetic equations
- 2011
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Ingår i: Communications in Partial Differential Equations. - : Informa UK Limited. - 0360-5302 .- 1532-4133. ; 36:4, s. 693-728
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Tidskriftsartikel (refereegranskat)abstract
- In this paper, we study the Gevrey regularity of weak solutions for a class of linear and semi-linear kinetic equations, which are the linear model of spatially inhomogeneous Boltzmann equations without an angular cutoff
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| 9. |
- Chen, Hua, et al.
(författare)
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Gevrey regularity of subelliptic Monge-Ampère equations in the plane
- 2011
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Ingår i: Advances in Mathematics. - : Elsevier BV. - 0001-8708. ; 228:3, s. 1816-1841
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Tidskriftsartikel (refereegranskat)abstract
- In this paper, we establish the Gevrey regularity of solutions for a class of degenerate Monge–Ampère equations in the plane. Under the assumptions that one principal entry of the Hessian is strictly positive and the coefficient of the equation is degenerate with appropriately finite type degeneracy, we prove that the solution of the degenerate Monge–Ampère equation will be smooth in Gevrey classes.
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| 10. |
- Chen, XÍ, et al.
(författare)
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TDHQ Enabling Fine-granularity Adaptive Loading for SSB-DMT Systems
- 2018
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Ingår i: IEEE Photonics Technology Letters. - : Institute of Electrical and Electronics Engineers Inc.. - 1041-1135 .- 1941-0174. ; 30:19, s. 1687-1690
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Tidskriftsartikel (refereegranskat)abstract
- In this letter, we introduce time domain hybrid quadrature amplitude modulation (TDHQ) for the single sideband (SSB) discrete multi-tone (DMT) systems. Experimental results reveal that with a single precoding set and the proposed adaptive loading algorithm, the TDHQ scheme can achieve finer granularity and therefore smoother continuous growth of data rate than that with the conventional quadrature amplitude modulation (QAM). Besides, thanks to the frame construction and the tailored mapping rule, the scheme with TDHQ has an obviously better peak to average power ratio (PAPR).
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