| 1. |
- Klionsky, Daniel J., et al.
(author)
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Guidelines for the use and interpretation of assays for monitoring autophagy
- 2012
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In: Autophagy. - : Informa UK Limited. - 1554-8635 .- 1554-8627. ; 8:4, s. 445-544
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Research review (peer-reviewed)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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| 2. |
- Axelsson, Josefine, et al.
(author)
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A Precipitation Isotopic Response in 2014-2015 to Moisture Transport Changes in the Central Himalayas
- 2023
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In: Journal of Geophysical Research - Atmospheres. - 2169-897X .- 2169-8996. ; 128:13
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Journal article (peer-reviewed)abstract
- The impact of moisture transport and sources on precipitation stable isotopes (d(18)O and d-excess) in the central Himalayas are crucial to understanding the climatic archives. However, this is still unclear due to the lack of in-situ observations. Here we present measurements of stable isotopes in precipitation at two stations (Yadong and Pali) in the central Himalayas during 2014-2015. Combined with simulations from the dispersion model FLEXPART, we investigate effects on precipitation stable isotopes related to changes in moisture sources and convections in the region, and possible influence by El Nino. Our results suggest that the moisture supplies related to evaporation over northeastern India and moisture losses related to convective activities over the Bay of Bengal (BoB) and Bangladesh region play important roles in changes in d(18)O and d-excess in precipitation in the Yadong Valley. Outgoing longwave radiation and moisture flux divergence analysis further confirm that the contribution from continental evaporation dominates the moisture supply in the central Himalayas with a lesser contribution from convection over the BoB during the 2015 monsoon season compared with 2014. A change in the altitude effect is observed in 2015, which is more significant than the temperature and precipitation amount effect during the observation period. These findings provide valuable insights into climatic interpretations of paleo-isotopic archives with an isotopic response to changes in moisture transport to the central Himalayas.
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| 3. |
- Buus, Richard, et al.
(author)
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Novel 18-gene signature for predicting relapse in ER-positive, HER2-negative breast cancer
- 2018
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In: Breast Cancer Research. - : Springer Science and Business Media LLC. - 1465-5411 .- 1465-542X. ; 20:1
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Journal article (peer-reviewed)abstract
- Background: Several prognostic signatures for early oestrogen receptor-positive (ER+) breast cancer have been established with a 10-year follow-up. We tested the hypothesis that signatures optimised for 0-5-year and 5-10-year follow-up separately are more prognostic than a single signature optimised for 10 years. Methods: Genes previously identified as prognostic or associated with endocrine resistance were tested in publicly available microarray data set using Cox regression of 747 ER+/HER2- samples from post-menopausal patients treated with 5 years of endocrine therapy. RNA expression of the selected genes was assayed in primary ER+/HER2- tumours from 948 post-menopausal patients treated with 5 years of anastrozole or tamoxifen in the TransATAC cohort. Prognostic signatures for 0-10, 0-5 and 5-10 years were derived using a penalised Cox regression (elastic net). Signature comparison was performed with likelihood ratio statistics. Validation was done by a case-control (POLAR) study in 422 samples derived from a cohort of 1449. Results: Ninety-three genes were selected by the modelling of microarray data; 63 of these were significantly prognostic in TransATAC, most similarly across each time period. Contrary to our hypothesis, the derived early and late signatures were not significantly more prognostic than the 18-gene 10-year signature. The 18-gene 10-year signature was internally validated in the TransATAC validation set, showing prognostic information similar to that of Oncotype DX Recurrence Score, PAM50 risk of recurrence score, Breast Cancer Index and IHC4 (score based on four IHC markers), as well as in the external POLAR case-control set. Conclusions: The derived 10-year signature predicts risk of metastasis in patients with ER+/HER2- breast cancer similar to commercial signatures. The hypothesis that early and late prognostic signatures are significantly more informative than a single signature was rejected.
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| 4. |
- Chasman, Daniel I., et al.
(author)
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Integration of genome-wide association studies with biological knowledge identifies six novel genes related to kidney function
- 2012
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In: Human Molecular Genetics. - : Oxford University Press (OUP). - 0964-6906 .- 1460-2083. ; 21:24, s. 5329-5343
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Journal article (peer-reviewed)abstract
- In conducting genome-wide association studies (GWAS), analytical approaches leveraging biological information may further understanding of the pathophysiology of clinical traits. To discover novel associations with estimated glomerular filtration rate (eGFR), a measure of kidney function, we developed a strategy for integrating prior biological knowledge into the existing GWAS data for eGFR from the CKDGen Consortium. Our strategy focuses on single nucleotide polymorphism (SNPs) in genes that are connected by functional evidence, determined by literature mining and gene ontology (GO) hierarchies, to genes near previously validated eGFR associations. It then requires association thresholds consistent with multiple testing, and finally evaluates novel candidates by independent replication. Among the samples of European ancestry, we identified a genome-wide significant SNP in FBXL20 (P 5.6 10(9)) in meta-analysis of all available data, and additional SNPs at the INHBC, LRP2, PLEKHA1, SLC3A2 and SLC7A6 genes meeting multiple-testing corrected significance for replication and overall P-values of 4.5 10(4)2.2 10(7). Neither the novel PLEKHA1 nor FBXL20 associations, both further supported by association with eGFR among African Americans and with transcript abundance, would have been implicated by eGFR candidate gene approaches. LRP2, encoding the megalin receptor, was identified through connection with the previously known eGFR gene DAB2 and extends understanding of the megalin system in kidney function. These findings highlight integration of existing genome-wide association data with independent biological knowledge to uncover novel candidate eGFR associations, including candidates lacking known connections to kidney-specific pathways. The strategy may also be applicable to other clinical phenotypes, although more testing will be needed to assess its potential for discovery in general.
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| 5. |
- Hou, Yandong, et al.
(author)
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Sahara's surface transformation forced an abrupt hydroclimate decline and Neolithic culture transition in northern China
- 2024
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In: The Innovation. - 2666-6758. ; 5:1
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Journal article (peer-reviewed)abstract
- The remote forcing from land surface changes in the Sahara is hypothesized to play a pivotal role in modulating the intensity of the East Asian summer monsoon (EASM) through ocean-atmospheric teleconnections. This modu-lation has far-reaching consequences, particularly in facilitating societal shifts documented in northern China. Here, we present a well-dated lake-level record from the Daihai Lake Basin in northern China, providing quantitative assessments of Holocene monsoonal precipitation and the consequent mi-grations of the northern boundary of the EASM. Our reconstruction, informed by a water-and-energy balance model, indicates that annual precipitation reached -700 mm during 8-5 ka, followed by a rapid decline to -550 mm be-tween 5 and 4 ka. This shift coherently aligns with a significant -300 km northwestward movement of the EASM northern boundary during the Middle Holocene (MH), in contrast to its current position. Our findings underscore that these changes cannot be entirely attributed to orbital forcing, as corrob-orated by simulation tests. Climate model simulations deployed in our study suggest that the presence of the Green Sahara during the MH significantly strengthened the EASM and led to a northward shift of the monsoon rainfall belt. Conversely, the Sahara's reversion to a desert landscape in the late Ho-locene was accompanied by a corresponding southward retraction of monsoon influence. These dramatic hydroclimate changes during -5-4 ka likely triggered or at least contributed to a shift in Neolithic cultures and societal transformation in northern China. With decreasing agricultural pro-ductivity, communities transitioned from millet farming to a mixed rainfed agriculture and animal husbandry system. Thus, our findings elucidate not only the variability of the EASM but also the profound implications of a remote forcing, such as surface transformations of the Sahara, on climatic changes and cultural evolution in northern China.
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| 6. |
- Hu, Jiwen, et al.
(author)
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A new ratiometric fluorescent chemodosimeter based on an ICT modulation for the detection of Hg2
- 2016
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In: Sensors and actuators. B, Chemical. - : ELSEVIER SCIENCE SA. - 0925-4005 .- 1873-3077. ; 230, s. 639-644
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Journal article (peer-reviewed)abstract
- We design and synthesize a new ratiometric fluorescent chemodosimeter (S1) for the selective and sensitive detection of Hg2+. Upon addition of Hg2+, the emission of the S1 exhibits a large bathochromic shift from 393 to 515 nm (up to 122 nm) which is ascribed to an intramolecular charge transfer process in the resultant. The Hg2+-induced dethioacetalization for sensing mechanism has been demonstrated by using high-performance liquid chromatography analysis of the sensing process. The interference experiments further demonstrate that S1 exhibits very high selectivity towards Hg2+ over other coexisting cations/anions. Subsequently, a good linearity of the concentrations of Hg2+ (0-15 mu M) vs the ratiometric signals (I-515/I-393) allows a fluorogenic method for the quantitative detection of Hg2+, with the limitation of detection determined to be 5.22 x 10(-7) M. (C) 2016 Elsevier B.V. All rights reserved.
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| 7. |
- Hu, Zhang-Jun, et al.
(author)
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A TPA-caged precursor of (imino)coumarin for "turn-on" fluorogenic detection of Cu
- 2016
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In: Analytica Chimica Acta. - : ELSEVIER SCIENCE BV. - 0003-2670 .- 1873-4324. ; 933, s. 189-195
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Journal article (peer-reviewed)abstract
- We strategize to utilize the precursors of (imino) coumarin fluorophores to deliver novel reactive Cu+ probes, where tris[(2-pyridyl)-methyl] amine (TPA) works as a reactive receptor towards Cu+. To verify this strategy, CP1, a representative probe and relevant sensing behaviors towards Cu+ are presented here. CP1 features good solubility and fast response for monitoring labile copper in aqueous solution and live cells. The sensing mechanism of CP1 is determined by HPLC titration and mass spectrometric analysis. The probe CP1 exhibits a 60-fold fluorescence enhancement and a detection limitation of 10.8 nM upon the detection of Cu+. CP1 is further applied for imaging labile copper in live cells. This work provides a starting point for future development of Cu+ probes, based on in situ formation of (imino) coumarin scaffolds, as well as their further investigations of copper signaling and biological events. (C) 2016 Elsevier B.V. All rights reserved.
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| 8. |
- Köttgen, Anna, et al.
(author)
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New loci associated with kidney function and chronic kidney disease
- 2010
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In: Nature Genetics. - : Springer Science and Business Media LLC. - 1061-4036 .- 1546-1718. ; 42:5, s. 376-384
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Journal article (peer-reviewed)abstract
- Chronic kidney disease (CKD) is a significant public health problem, and recent genetic studies have identified common CKD susceptibility variants. The CKDGen consortium performed a meta-analysis of genome-wide association data in 67,093 individuals of European ancestry from 20 predominantly population-based studies in order to identify new susceptibility loci for reduced renal function as estimated by serum creatinine (eGFRcrea), serum cystatin c (eGFRcys) and CKD (eGFRcrea < 60 ml/min/1.73 m2; n = 5,807 individuals with CKD (cases)). Follow-up of the 23 new genome-wide–significant loci (P < 5 × 10−8) in 22,982 replication samples identified 13 new loci affecting renal function and CKD (in or near LASS2, GCKR, ALMS1, TFDP2, DAB2, SLC34A1, VEGFA, PRKAG2, PIP5K1B, ATXN2, DACH1, UBE2Q2 and SLC7A9) and 7 loci suspected to affect creatinine production and secretion (CPS1, SLC22A2, TMEM60, WDR37, SLC6A13, WDR72 and BCAS3). These results further our understanding of the biologic mechanisms of kidney function by identifying loci that potentially influence nephrogenesis, podocyte function, angiogenesis, solute transport and metabolic functions of the kidney.
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| 9. |
- Li, Man, et al.
(author)
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SOS2 and ACP1 Loci Identified through Large-Scale Exome Chip Analysis Regulate Kidney Development and Function
- 2017
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In: Journal of the American Society of Nephrology: JASN. - 1533-3450. ; 28:3, s. 981-994
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Journal article (peer-reviewed)abstract
- Genome-wide association studies have identified >50 common variants associated with kidney function, but these variants do not fully explain the variation in eGFR. We performed a two-stage meta-analysis of associations between genotypes from the Illumina exome array and eGFR on the basis of serum creatinine (eGFRcrea) among participants of European ancestry from the CKDGen Consortium (nStage1: 111,666; nStage2: 48,343). In single-variant analyses, we identified single nucleotide polymorphisms at seven new loci associated with eGFRcrea (PPM1J, EDEM3, ACP1, SPEG, EYA4, CYP1A1, and ATXN2L; PStage1<3.7×10-7), of which most were common and annotated as nonsynonymous variants. Gene-based analysis identified associations of functional rare variants in three genes with eGFRcrea, including a novel association with the SOS Ras/Rho guanine nucleotide exchange factor 2 gene, SOS2 (P=5.4×10-8 by sequence kernel association test). Experimental follow-up in zebrafish embryos revealed changes in glomerular gene expression and renal tubule morphology in the embryonic kidney of acp1- and sos2-knockdowns. These developmental abnormalities associated with altered blood clearance rate and heightened prevalence of edema. This study expands the number of loci associated with kidney function and identifies novel genes with potential roles in kidney formation.
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| 10. |
- Ngo, Debby, et al.
(author)
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Circulating testican-2 is a podocyte-derived marker of kidney health
- 2020
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In: Proceedings of the National Academy of Sciences of the United States of America. - : Proceedings of the National Academy of Sciences. - 1091-6490 .- 0027-8424. ; 117:40, s. 25026-25035
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Journal article (peer-reviewed)abstract
- In addition to their fundamental role in clearance, the kidneys release select molecules into the circulation, but whether any of these anabolic functions provides insight on kidney health is unknown. Using aptamer-based proteomics, we characterized arterial (A)-to-renal venous (V) gradients for >1,300 proteins in 22 individuals who underwent invasive sampling. Although most of the proteins that changed significantly decreased from A to V, consistent with renal clearance, several were found to increase, the most significant of which was testican-2. To assess the clinical implications of these physiologic findings, we examined proteomic data in the Jackson Heart Study (JHS), an African-American cohort (n = 1,928), with replication in the Framingham Heart Study (FHS), a White cohort (n = 1,621). In both populations, testican-2 had a strong, positive correlation with estimated glomerular filtration rate (eGFR). In addition, higher baseline testican-2 levels were associated with a lower rate of eGFR decline in models adjusted for age, gender, hypertension, type 2 diabetes, body mass index, baseline eGFR, and albuminuria. Glomerular expression of testican-2 in human kidneys was demonstrated by immunohistochemistry, immunofluorescence, and electron microscopy, while single-cell RNA sequencing of human kidneys showed expression of the cognate gene, SPOCK2, exclusively in podocytes. In vitro, testican-2 increased glomerular endothelial tube formation and motility, raising the possibility that its secretion has a functional role within the glomerulus. Taken together, our findings identify testican-2 as a podocyte-derived biomarker of kidney health and prognosis.
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