| 1. |
- 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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| 2. |
- Grundberg, Elin, et al.
(författare)
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Global Analysis of the Impact of Environmental Perturbation on cis-Regulation of Gene Expression
- 2011
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Ingår i: PLoS Genetics. - : Public Library of Science (PLoS). - 1553-7390 .- 1553-7404. ; 7:1, s. e1001279-
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Tidskriftsartikel (refereegranskat)abstract
- Genetic variants altering cis-regulation of normal gene expression (cis-eQTLs) have been extensively mapped in human cells and tissues, but the extent by which controlled, environmental perturbation influences cis-eQTLs is unclear. We carried out large-scale induction experiments using primary human bone cells derived from unrelated donors of Swedish origin treated with 18 different stimuli (7 treatments and 2 controls, each assessed at 2 time points). The treatments with the largest impact on the transcriptome, verified on two independent expression arrays, included BMP-2 (t = 2h), dexamethasone (DEX) (t = 24h), and PGE(2) (t = 24h). Using these treatments and control, we performed expression profiling for 18,144 RefSeq transcripts on biological replicates of the complete study cohort of 113 individuals (n(total) = 782) and combined it with genome-wide SNP-genotyping data in order to map treatment-specific cis-eQTLs (defined as SNPs located within the gene +/- 250 kb). We found that 93% of cis-eQTLs at 1% FDR were observed in at least one additional treatment, and in fact, on average, only 1.4% of the cis-eQTLs were considered as treatment-specific at high confidence. The relative invariability of cis-regulation following perturbation was reiterated independently by genome-wide allelic expression tests where only a small proportion of variance could be attributed to treatment. Treatment-specific cis-regulatory effects were, however, 2- to 6-fold more abundant among differently expressed genes upon treatment. We further followed-up and validated the DEX-specific cis-regulation of the MYO6 and TNC loci and found top cis-regulatory variants located 180 kb and 250 kb upstream of the transcription start sites, respectively. Our results suggest that, as opposed to tissue-specificity of cis-eQTLs, the interactions between cellular environment and cis-variants are relatively rare (similar to 1.5%), but that detection of such specific interactions can be achieved by a combination of functional genomic approaches as described here.
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| 3. |
- Lange, Leslie A, et al.
(författare)
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Whole-Exome Sequencing Identifies Rare and Low-Frequency Coding Variants Associated with LDL Cholesterol.
- 2014
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Ingår i: American Journal of Human Genetics. - : Elsevier BV. - 0002-9297. ; 94:2, s. 233-245
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Tidskriftsartikel (refereegranskat)abstract
- Elevated low-density lipoprotein cholesterol (LDL-C) is a treatable, heritable risk factor for cardiovascular disease. Genome-wide association studies (GWASs) have identified 157 variants associated with lipid levels but are not well suited to assess the impact of rare and low-frequency variants. To determine whether rare or low-frequency coding variants are associated with LDL-C, we exome sequenced 2,005 individuals, including 554 individuals selected for extreme LDL-C (>98(th) or <2(nd) percentile). Follow-up analyses included sequencing of 1,302 additional individuals and genotype-based analysis of 52,221 individuals. We observed significant evidence of association between LDL-C and the burden of rare or low-frequency variants in PNPLA5, encoding a phospholipase-domain-containing protein, and both known and previously unidentified variants in PCSK9, LDLR and APOB, three known lipid-related genes. The effect sizes for the burden of rare variants for each associated gene were substantially higher than those observed for individual SNPs identified from GWASs. We replicated the PNPLA5 signal in an independent large-scale sequencing study of 2,084 individuals. In conclusion, this large whole-exome-sequencing study for LDL-C identified a gene not known to be implicated in LDL-C and provides unique insight into the design and analysis of similar experiments.
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| 4. |
- Loth, Daan W, et al.
(författare)
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Genome-wide association analysis identifies six new loci associated with forced vital capacity
- 2014
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Ingår i: Nature Genetics. - : Springer Science and Business Media LLC. - 1061-4036 .- 1546-1718. ; 46, s. 669-677
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Tidskriftsartikel (refereegranskat)abstract
- Forced vital capacity (FVC), a spirometric measure of pulmonary function, reflects lung volume and is used to diagnose and monitor lung diseases. We performed genome-wide association study meta-analysis of FVC in 52,253 individuals from 26 studies and followed up the top associations in 32,917 additional individuals of European ancestry. We found six new regions associated at genome-wide significance (P < 5 × 10(-8)) with FVC in or near EFEMP1, BMP6, MIR129-2-HSD17B12, PRDM11, WWOX and KCNJ2. Two loci previously associated with spirometric measures (GSTCD and PTCH1) were related to FVC. Newly implicated regions were followed up in samples from African-American, Korean, Chinese and Hispanic individuals. We detected transcripts for all six newly implicated genes in human lung tissue. The new loci may inform mechanisms involved in lung development and the pathogenesis of restrictive lung disease.
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| 5. |
- Zhang, Qing, et al.
(författare)
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A case of Meniere's disease in the left ear and Lermoyez syndrome in the right ear - a 32-month longitudinal observation and literature review
- 2010
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Ingår i: Acta Oto-Laryngologica. - : Informa UK Limited. - 0001-6489 .- 1651-2251. ; 130:9, s. 1084-1088
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Tidskriftsartikel (refereegranskat)abstract
- We here present a 32-month follow-up of a case of Lermoyez syndrome combined with Meniere's disease. The patient was a 49-year-old male, with a stabilized severe hearing loss in the left ear for about 15 years after Meniere's disease. He started to show typical symptoms of Lermoyez syndrome in the right ear about 32 months ago. Audiologic data were obtained and imaging examinations were performed 0, 9, 15, 28, and 32 months after the onset of the Lermoyez syndrome. Pure tone threshold data obtained 5 months before the onset are also reported. The results show that the hearing thresholds, mainly at low frequencies, elevated rapidly during the first months shortly after the onset of the disease and slowly in later months. The glycerol test resulted in a remarkable hearing improvement at the beginning of the disease, but showed no detectable improvements as the disease advanced. Electrocochleogram revealed a -SP/AP value with click stimulus 0.65 at the 9th month and > 1.0 at the 28th month after the onset. Clinical manifestations of this patient fit well with a pathological endolymphatic hydrops.
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| 6. |
- Zhang, Qing, et al.
(författare)
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Prevalence of Otitis Media With Effusion Among Children in Xi'an, China : A Randomized Survey in China's Mainland
- 2011
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Ingår i: Annals of Otology, Rhinology and Laryngology. - : SAGE Publications. - 0003-4894 .- 1943-572X. ; 120:9, s. 617-621
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Tidskriftsartikel (refereegranskat)abstract
- Objectives: We sought to identify the prevalence of otitis media with effusion (OME) in urban Chinese children in Xi'an, China. Methods: Five kindergartens and 3 primary schools were randomly selected in the urban area of Xi'an. Screening otoscopic and tympanometric examinations were performed on 2,902 children (1,491 boys and 1,411 girls) 2 to 8 years of age. Children with an abnormal tympanogram and simultaneous otomicroscopic signs of effusion were given a diagnosis of OME. Results: The overall prevalence of OME was 4.3%. By age group, the prevalence was 14.0% in 2-year-olds, 8.3% in 3-year-olds, 5.0% in 4-year-olds, 4.9% in 5-year-olds, 2.8% in 6-year-olds, 1.7% in 7-year-olds, and 3.2% in 8-year-olds. The prevalence rate for OME was 4.7% for boys versus 3.9% for girls, and 3.0% in the right ear versus 2.7% in the left, showing no statistically significant difference between genders or between ear sides (p > 0.05). Conclusions: The prevalence of OME in urban areas of Xi'an is not high in comparison with that of the same age group in surrounding areas.
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| 7. |
- Zhang, Xiao-Tong, et al.
(författare)
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Congenital unilateral pulmonary malformation misdiagnosed as bronchial foreign body : A review of 14 cases
- 2010
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Ingår i: Acta Oto-Laryngologica. - : Informa UK Limited. - 0001-6489 .- 1651-2251. ; 130:8, s. 971-976
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Tidskriftsartikel (refereegranskat)abstract
- Conclusion: Congenital unilateral pulmonary malformation can easily be misdiagnosed as a bronchial foreign body. Although rigid bronchoscopy helps the proper diagnosis, high risks associated with anesthesia and operative complications may limit its application. However, high-resolution computed tomography (CT) and three-dimensional lung reconstruction provide a non-invasive tool to improve the diagnosis of congenital unilateral pulmonary malformation. Objectives: To compare clinical manifestations, physical signs, and radiological examinations of congenital unilateral pulmonary malformation and bronchial foreign body, and summarize the characteristics and methods for diagnosis of congenital unilateral pulmonary malformation. Methods: Fourteen patients (five males and nine females, aged from 3 months to 14 years) with congenital unilateral pulmonary malformation, who were misdiagnosed or suspected as having bronchial foreign body or bronchial foreign body with pulmonary atelectasis, were analyzed retrospectively. Three typical cases are presented in detail. Results: All patients were previously misdiagnosed and treated as having pneumonia. From onset to final diagnosis, the longest misdiagnosis time was 10 years, and the shortest was 2 days. Only three patients presented with a history of foreign body inhalation. Six cases were finally diagnosed as having unilateral pulmonary malformation by rigid bronchoscope, five cases by X-ray and high-resolution CT scan, two cases by CT and three-dimensional lung reconstruction, and one case by autopsy. The malformation of left and right lungs was present in five and nine cases, respectively. Among these patients, four patients also had congenital cardiovascular diseases and other malformations, two patients underwent tracheotomy, and one patient died during salvage surgery.
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