| 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. |
- Palmer, Nicholette D, et al.
(författare)
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A genome-wide association search for type 2 diabetes genes in African Americans.
- 2012
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Ingår i: PloS one. - San Francisco : Public Library of Science (PLoS). - 1932-6203. ; 7:1, s. e29202-
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Tidskriftsartikel (refereegranskat)abstract
- African Americans are disproportionately affected by type 2 diabetes (T2DM) yet few studies have examined T2DM using genome-wide association approaches in this ethnicity. The aim of this study was to identify genes associated with T2DM in the African American population. We performed a Genome Wide Association Study (GWAS) using the Affymetrix 6.0 array in 965 African-American cases with T2DM and end-stage renal disease (T2DM-ESRD) and 1029 population-based controls. The most significant SNPs (n = 550 independent loci) were genotyped in a replication cohort and 122 SNPs (n = 98 independent loci) were further tested through genotyping three additional validation cohorts followed by meta-analysis in all five cohorts totaling 3,132 cases and 3,317 controls. Twelve SNPs had evidence of association in the GWAS (P<0.0071), were directionally consistent in the Replication cohort and were associated with T2DM in subjects without nephropathy (P<0.05). Meta-analysis in all cases and controls revealed a single SNP reaching genome-wide significance (P<2.5×10(-8)). SNP rs7560163 (P = 7.0×10(-9), OR (95% CI) = 0.75 (0.67-0.84)) is located intergenically between RND3 and RBM43. Four additional loci (rs7542900, rs4659485, rs2722769 and rs7107217) were associated with T2DM (P<0.05) and reached more nominal levels of significance (P<2.5×10(-5)) in the overall analysis and may represent novel loci that contribute to T2DM. We have identified novel T2DM-susceptibility variants in the African-American population. Notably, T2DM risk was associated with the major allele and implies an interesting genetic architecture in this population. These results suggest that multiple loci underlie T2DM susceptibility in the African-American population and that these loci are distinct from those identified in other ethnic populations.
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| 3. |
- Ballantyne, Kaye N., et al.
(författare)
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Toward Male Individualization with Rapidly Mutating Y-Chromosomal Short Tandem Repeats
- 2014
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Ingår i: Human Mutation. - : John Wiley & Sons. - 1059-7794 .- 1098-1004. ; 35:8, s. 1021-1032
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Tidskriftsartikel (refereegranskat)abstract
- Relevant for various areas of human genetics, Y-chromosomal short tandem repeats (Y-STRs) are commonly used for testing close paternal relationships among individuals and populations, and for male lineage identification. However, even the widely used 17-loci Yfiler set cannot resolve individuals and populations completely. Here, 52 centers generated quality-controlled data of 13 rapidly mutating (RM) Y-STRs in 14,644 related and unrelated males from 111 worldwide populations. Strikingly, greater than99% of the 12,272 unrelated males were completely individualized. Haplotype diversity was extremely high (global: 0.9999985, regional: 0.99836-0.9999988). Haplotype sharing between populations was almost absent except for six (0.05%) of the 12,156 haplotypes. Haplotype sharing within populations was generally rare (0.8% nonunique haplotypes), significantly lower in urban (0.9%) than rural (2.1%) and highest in endogamous groups (14.3%). Analysis of molecular variance revealed 99.98% of variation within populations, 0.018% among populations within groups, and 0.002% among groups. Of the 2,372 newly and 156 previously typed male relative pairs, 29% were differentiated including 27% of the 2,378 father-son pairs. Relative to Yfiler, haplotype diversity was increased in 86% of the populations tested and overall male relative differentiation was raised by 23.5%. Our study demonstrates the value of RMY-STRs in identifying and separating unrelated and related males and provides a reference database.
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| 4. |
- Bard-Chapeau, Emilie A, et al.
(författare)
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Transposon mutagenesis identifies genes driving hepatocellular carcinoma in a chronic hepatitis B mouse model.
- 2014
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Ingår i: Nature Genetics. - : Springer Science and Business Media LLC. - 1061-4036 .- 1546-1718. ; 46:1
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Tidskriftsartikel (refereegranskat)abstract
- The most common risk factor for developing hepatocellular carcinoma (HCC) is chronic infection with hepatitis B virus (HBV). To better understand the evolutionary forces driving HCC, we performed a near-saturating transposon mutagenesis screen in a mouse HBV model of HCC. This screen identified 21 candidate early stage drivers and a very large number (2,860) of candidate later stage drivers that were enriched for genes that are mutated, deregulated or functioning in signaling pathways important for human HCC, with a striking 1,199 genes being linked to cellular metabolic processes. Our study provides a comprehensive overview of the genetic landscape of HCC.
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| 5. |
- Hadjikhani, Nouchine, 1966, et al.
(författare)
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Emotional contagion for pain is intact in autism spectrum disorders.
- 2014
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Ingår i: Translational psychiatry. - : Springer Science and Business Media LLC. - 2158-3188. ; 4
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Tidskriftsartikel (refereegranskat)abstract
- Perceiving others in pain generally leads to empathic concern, consisting of both emotional and cognitive processes. Empathy deficits have been considered as an element contributing to social difficulties in individuals with autism spectrum disorders (ASD). Here, we used functional magnetic resonance imaging and short video clips of facial expressions of people experiencing pain to examine the neural substrates underlying the spontaneous empathic response to pain in autism. Thirty-eight adolescents and adults of normal intelligence diagnosed with ASD and 35 matched controls participated in the study. In contrast to general assumptions, we found no significant differences in brain activation between ASD individuals and controls during the perception of pain experienced by others. Both groups showed similar levels of activation in areas associated with pain sharing, evidencing the presence of emotional empathy and emotional contagion in participants with autism as well as in controls. Differences between groups could be observed at a more liberal statistical threshold, and revealed increased activations in areas involved in cognitive reappraisal in ASD participants compared with controls. Scores of emotional empathy were positively correlated with brain activation in areas involved in embodiment of pain in ASD group only. Our findings show that simulation mechanisms involved in emotional empathy are preserved in high-functioning individuals with autism, and suggest that increased reappraisal may have a role in their apparent lack of caring behavior.
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| 6. |
- Ward, Anthony B., et al.
(författare)
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Evaluation of the Post Stroke Checklist: a pilot study in the United Kingdom and Singapore
- 2014
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Ingår i: International Journal of Stroke. - : SAGE Publications. - 1747-4949 .- 1747-4930. ; 9, s. 76-84
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Tidskriftsartikel (refereegranskat)abstract
- Background There is currently no standardized process for long-term follow-up care. As a result, management of post-stroke care varies greatly, and the needs of stroke survivors are not fully addressed. The Post Stroke Checklist was developed by the Global Stroke Community Advisory Panel as a means of standardizing long-term stroke care. Since its development, the Post Stroke Checklist has gained international recognition from various stroke networks and is endorsed by the World Stroke Organization to support improved stroke survivor follow-up and care. Aims The aim of this study was to evaluate the feasibility and usefulness of the Post Stroke Checklist in clinical practice and assess its relevance to stroke survivors in pilot studies in the United Kingdom and Singapore. Methods The Post Stroke Checklist was administered to stroke survivors in the United Kingdom (n = 42) and Singapore (n = 100) by clinicians. To assess the feasibility of the Post Stroke Checklist in clinical practice, an independent researcher observed the assessment and made notes relating to the patient-clinician interaction and their interpretations of the Post Stroke Checklist items. Patient and clinician satisfaction with the Post Stroke Checklist was assessed by three questions, responded to on a 0-10 numerical rating scale. Clinicians also completed a Pragmatic Face and Content Validity test to evaluate their overall impressions of the Post Stroke Checklist. In the United Kingdom, a subset of patients (n = 14) took part in a concept elicitation interview prior to being administered the Post Stroke Checklist, followed by a cognitive debriefing interview to assess relevance and comprehension of the Post Stroke Checklist. Results The Post Stroke Checklist identified frequently reported problems for stroke survivors including cognition (reported by 47.2% of patients), mood (43.7%), and life after stroke (38%). An average of 3.2 problems per patient was identified across both countries (range 0-10). An average of 5 and 2.6 problems per patient were identified in the United Kingdom and Singapore, respectively. The average time taken to administer the Post Stroke Checklist was 17 mins (standard deviation 7.5) in Singapore and 13 mins (standard deviation 7.6) in the United Kingdom. Satisfaction ratings were high for patients (8.6/10) and clinicians (7.7/10), and clinician feedback via the Pragmatic Face and Content Validity test indicated that the Post Stroke Checklist is 'useful', 'informative', and 'exhaustive'. All concepts measured by the Post Stroke Checklist were spontaneously discussed by patients during the concept elicitation interviews, suggesting that the Post Stroke Checklist is relevant to stroke survivors. Cognitive debriefing data indicated that the items were generally well understood and relevant to stroke. Minor revisions were made to the Post Stroke Checklist based on patient feedback. Conclusions The findings suggest that the Post Stroke Checklist is a feasible and useful measure for identifying long term stroke care needs in a clinical practice setting. Pilot testing indicated that the Post Stroke Checklist is able to identify a wide range of unmet needs, and patient and clinician feedback indicated a high level of satisfaction with the Post Stroke Checklist assessment. The items were generally well understood and considered relevant to stroke survivors, indicating the Post Stroke Checklist is a feasible, useful, and relevant measure of poststroke care.
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