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| 2. |
- Noguchi, S, et al.
(author)
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FANTOM5 CAGE profiles of human and mouse samples
- 2017
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In: Scientific data. - : Springer Science and Business Media LLC. - 2052-4463. ; 4, s. 170112-
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Journal article (peer-reviewed)abstract
- In the FANTOM5 project, transcription initiation events across the human and mouse genomes were mapped at a single base-pair resolution and their frequencies were monitored by CAGE (Cap Analysis of Gene Expression) coupled with single-molecule sequencing. Approximately three thousands of samples, consisting of a variety of primary cells, tissues, cell lines, and time series samples during cell activation and development, were subjected to a uniform pipeline of CAGE data production. The analysis pipeline started by measuring RNA extracts to assess their quality, and continued to CAGE library production by using a robotic or a manual workflow, single molecule sequencing, and computational processing to generate frequencies of transcription initiation. Resulting data represents the consequence of transcriptional regulation in each analyzed state of mammalian cells. Non-overlapping peaks over the CAGE profiles, approximately 200,000 and 150,000 peaks for the human and mouse genomes, were identified and annotated to provide precise location of known promoters as well as novel ones, and to quantify their activities.
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| 3. |
- Fresard, Laure, et al.
(author)
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Identification of rare-disease genes using blood transcriptome sequencing and large control cohorts
- 2019
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In: Nature Medicine. - : NATURE PUBLISHING GROUP. - 1078-8956 .- 1546-170X. ; 25:6, s. 911-919
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Journal article (peer-reviewed)abstract
- It is estimated that 350 million individuals worldwide suffer from rare diseases, which are predominantly caused by mutation in a single gene(1). The current molecular diagnostic rate is estimated at 50%, with whole-exome sequencing (WES) among the most successful approaches(2-5). For patients in whom WES is uninformative, RNA sequencing (RNA-seq) has shown diagnostic utility in specific tissues and diseases(6-8). This includes muscle biopsies from patients with undiagnosed rare muscle disorders(6,9), and cultured fibroblasts from patients with mitochondrial disorders(7). However, for many individuals, biopsies are not performed for clinical care, and tissues are difficult to access. We sought to assess the utility of RNA-seq from blood as a diagnostic tool for rare diseases of different pathophysiologies. We generated whole-blood RNA-seq from 94 individuals with undiagnosed rare diseases spanning 16 diverse disease categories. We developed a robust approach to compare data from these individuals with large sets of RNA-seq data for controls (n = 1,594 unrelated controls and n = 49 family members) and demonstrated the impacts of expression, splicing, gene and variant filtering strategies on disease gene identification. Across our cohort, we observed that RNA-seq yields a 7.5% diagnostic rate, and an additional 16.7% with improved candidate gene resolution.
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| 4. |
- Lue, L. F., et al.
(author)
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Age-Dependent Relationship Between Plasma A beta 40 and A beta 42 and Total Tau Levels in cognitively Normal Subjects
- 2019
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In: Frontiers in Aging Neuroscience. - : Frontiers Media SA. - 1663-4365. ; 11
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Journal article (peer-reviewed)abstract
- Both amyloid plaques and neurofibrillary tangles are pathological hallmarks in the brains of patients with Alzheimer's disease (AD). However, the constituents of these hallmarks, amyloid beta (A beta) 40, A beta 42, and total Tau (t-Tau), have been detected in the blood of cognitively normal subjects by using an immunomagnetic reduction (IMR) assay. Whether these levels are age-dependent is not known, and their interrelation remains undefined. We determined the levels of these biomarkers in cognitively normal subjects of different age groups. A total of 391 cognitively normal subjects aged 23-91 were enrolled from hospitals in Asia, Europe, and North America. Healthy cognition was evaluated by NIA-AA guidelines to exclude subjects with mild cognitive impairment (MCI) and AD and by cognitive assessment using the Mini Mental State Examination and Clinical Dementia Rating (CDR). We examined the effect of age on plasma levels of A beta 40, A beta 42, and t-Tau and the relationship between these biomarkers during aging. Additionally, we explored age-related reference intervals for each biomarker. Plasma t-Tau and A beta 42 levels had modest but significant correlations with chronological age (r = 0.127, p = 0.0120 for t-Tau; r = -0.126, p = 0.0128 for A beta 42), ranging from ages 23 to 91. Significant positive correlations were detected between A beta 42 and t-Tau in the groups aged 50 years and older, with Rho values ranging from 0.249 to 0.474. Significant negative correlations were detected between A beta 40 and t-Tau from age 40 to 91 (r ranged from -0.293 to -0.582) and between A beta 40 and A beta 42 in the age groups of 30-39 (r = -0.562, p = 0.0235), 50-59 (r = -0.261, p = 0.0142), 60-69 (r = -0.303, p = 0.0004), and 80-91 (r = 0.459, p = 0.0083). We also provided age-related reference intervals for each biomarker. In this multicenter study, age had weak but significant effects on the levels of A beta 42 and t-Tau in plasma. However, the age group defined by decade revealed the emergence of a relationship between A beta 40, A beta 42, and t-Tau in the 6th and 7th decades. Validation of our findings in a large-scale and longitudinal study is warranted.
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| 6. |
- Bälter, Magnus, 1986, et al.
(author)
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Emission color tuning and white-light generation based on photochromic control of energy transfer reactions in polymer micelles
- 2016
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In: Chemical Science. - 2041-6539 .- 2041-6520. ; 7:9, s. 5867-5871
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Journal article (peer-reviewed)abstract
- We encapsulate a fluorescent donor molecule and a photochromic acceptor unit (photoswitch) in polymer micelles and show that the color of the emitted fluorescence is continuously changed from blue to yellow upon light-induced isomerization of the acceptor. Interestingly, white-light generation is achieved in between. With the photoswitch in the colorless form, intense blue emission from the donor is observed, while UV-induced isomerization to the colored form induces an energy transfer reaction that quenches the donor emission and sensitizes the yellow emission from the colored photoswitch. The process is reversed by exposure to visible light, triggering isomerization to the colorless form.
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| 7. |
- Kuriyama, T., et al.
(author)
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Cellular basis of anti-predator adaptation in a lizard with autotomizable blue tail against specific predators with different colour vision
- 2016
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In: Journal of Zoology. - : Wiley. - 0952-8369 .- 1469-7998. ; 300:2, s. 89-98
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Journal article (peer-reviewed)abstract
- Juveniles of numerous lizard species have a vividly blue-coloured tail that likely serves to deflect predator attacks toward the autotomizable tail rather than the lizard's body. The shades of blue colour in the tails of juvenile Plestiodon latiscutatus lizards vary across populations, most notably among those island populations with different predator assemblages. Here, we determine if this intraspecific variation is associated with the differences in colour vision capabilities of lizard predator species. If associated, it would be evidence for local adaptation of tail colour phenotype – natural selection is maximizing the conspicuousness of the tail to the dominant predator species to increase the chance of successfully deflecting attacks. We also use transmission electron microscopy (TEM) to determine the proximate cellular mechanisms that produce the shades of blue in different populations. We revealed that lizard tails with vivid blue reflectance evolved in communities with either weasel or snake predators, two groups of animals with the ability to detect blue wavelengths. However, lizard tail UV reflectance was much higher in populations with only snake predators; that snakes can detect UV, yet weasels cannot, suggests that high UV reflectance is an adaptation to increase tail conspicuousness specifically to snake predators. Finally, a cryptic brown tail evolved independently on the islands where birds are the primary lizard predator. We suggest that because birds have keen visual acuity; a brown, camouflaged phenotype is more advantageous. We also determined through TEM that the thickness of light reflecting platelets in iridophores, and densities of iridophores and xanthophores, predicted the wavelengths and intensity of light reflected by the lizard tail. For example, blue coloration was produced by selective reflection of short wavelengths of light by the thin light reflecting platelets of the iridophore. Greater iridophore density increased light reflectance, while greater xanthophore density decreased light reflectance.
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| 8. |
- Naren, Gaowa, 1990, et al.
(author)
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An all-photonic full color RGB system based on molecular photoswitches
- 2019
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In: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723 .- 2041-1723. ; 10:1
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Journal article (peer-reviewed)abstract
- On-command changes in the emission color of functional materials is a sought-after property in many contexts. Of particular interest are systems using light as the external trigger to induce the color changes. Here we report on a tri-component cocktail consisting of a fluorescent donor molecule and two photochromic acceptor molecules encapsulated in polymer micelles and we show that the color of the emitted fluorescence can be continuously changed from blue-to-green and from blue-to-red upon selective light-induced isomerization of the photochromic acceptors to the fluorescent forms. Interestingly, isomerization of both acceptors to different degrees allows for the generation of all emission colors within the red-green-blue (RGB) color system. The function relies on orthogonally controlled FRET reactions between the blue emitting donor and the green and red emitting acceptors, respectively.
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| 10. |
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