| 11. |
|
|
| 12. |
- Grapotte, M, et al.
(author)
-
Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network
- 2021
-
In: Nature communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 12:1, s. 3297-
-
Journal article (peer-reviewed)abstract
- Using the Cap Analysis of Gene Expression (CAGE) technology, the FANTOM5 consortium provided one of the most comprehensive maps of transcription start sites (TSSs) in several species. Strikingly, ~72% of them could not be assigned to a specific gene and initiate at unconventional regions, outside promoters or enhancers. Here, we probe these unassigned TSSs and show that, in all species studied, a significant fraction of CAGE peaks initiate at microsatellites, also called short tandem repeats (STRs). To confirm this transcription, we develop Cap Trap RNA-seq, a technology which combines cap trapping and long read MinION sequencing. We train sequence-based deep learning models able to predict CAGE signal at STRs with high accuracy. These models unveil the importance of STR surrounding sequences not only to distinguish STR classes, but also to predict the level of transcription initiation. Importantly, genetic variants linked to human diseases are preferentially found at STRs with high transcription initiation level, supporting the biological and clinical relevance of transcription initiation at STRs. Together, our results extend the repertoire of non-coding transcription associated with DNA tandem repeats and complexify STR polymorphism.
|
|
| 13. |
- Hülsmann, Lisa, et al.
(author)
-
Latitudinal patterns in stabilizing density dependence of forest communities
- 2024
-
In: Nature. - 0028-0836 .- 1476-4687. ; 627, s. 564-571
-
Journal article (peer-reviewed)abstract
- Numerous studies have shown reduced performance in plants that are surrounded by neighbours of the same species1,2, a phenomenon known as conspecific negative density dependence (CNDD)3. A long-held ecological hypothesis posits that CNDD is more pronounced in tropical than in temperate forests4,5, which increases community stabilization, species coexistence and the diversity of local tree species6,7. Previous analyses supporting such a latitudinal gradient in CNDD8,9 have suffered from methodological limitations related to the use of static data10–12. Here we present a comprehensive assessment of latitudinal CNDD patterns using dynamic mortality data to estimate species-site-specific CNDD across 23 sites. Averaged across species, we found that stabilizing CNDD was present at all except one site, but that average stabilizingCNDD was not stronger toward the tropics. However, in tropical tree communities, rare and intermediate abundant species experienced stronger stabilizing CNDD than did common species. This pattern was absent in temperate forests, which suggests that CNDD influences species abundances more strongly in tropical forests than it does in temperate ones13. We also found that interspecific variation in CNDD, which might attenuate its stabilizing effect on species diversity14,15, was high but not significantly different across latitudes. Although the consequences of these patterns for latitudinal diversity gradients are difficult to evaluate, we speculate that a more effective regulation of population abundances could translate into greater stabilization of tropical tree communities and thus contribute to the high local diversity of tropical forests.
|
|
| 14. |
- Nocerino, E., et al.
(author)
-
Q-dependent electron-phonon coupling induced phonon softening and non-conventional critical behavior in the CDW superconductor LaPt 2 Si 2
- 2023
-
In: Journal of Science: Advanced Materials and Devices. - 2468-2284 .- 2468-2179. ; 8:4
-
Journal article (peer-reviewed)abstract
- This paper reports the first experimental observation of phonons and their softening on single crystalline LaPt2Si2 via inelastic neutron scattering. From the temperature dependence of the phonon frequency in close proximity to the charge density wave (CDW) q-vector, we obtain a CDW transition temperature of TCDW = 230 K and a critical exponent β = 0.28 ± 0.03. This value is suggestive of a non-conventional critical behavior for the CDW phase transition in LaPt2Si2, compatible with a scenario of CDW discommensuration (DC). The DC would be caused by the existence of two CDWs in this material, propagating separately in the non equivalent (Si1–Pt2–Si1) and (Pt1–Si2–Pt1) layers, respectively, with transition temperatures TCDW−1 = 230 K and TCDW−2 = 110 K. A strong q-dependence of the electron-phonon coupling has been identified as the driving mechanism for the CDW transition at TCDW−1 = 230 K while a CDW with 3-dimensional character, and Fermi surface quasi-nesting as a driving mechanism, is suggested for the transition at TCDW−2 = 110 K. Our results clarify some aspects of the CDW transition in LaPt2Si2 which have been so far misinterpreted by both theoretical predictions and experimental observations and give direct insight into its actual temperature dependence.
|
|
| 15. |
- Nocerino, Elisabetta, et al.
(author)
-
Q-dependent electron-phonon coupling induced phonon softening and non-conventional critical behavior in the CDW superconductor LaPt2Si2
- 2023
-
In: Journal of Science: Advanced Materials and Devices. - : Elsevier BV. - 2468-2284 .- 2468-2179. ; 8:4
-
Journal article (peer-reviewed)abstract
- This paper reports the first experimental observation of phonons and their softening on single crystalline LaPt2Si2 via inelastic neutron scattering. From the temperature dependence of the phonon frequency in close proximity to the charge density wave (CDW) q-vector, we obtain a CDW transition temperature of TCDW = 230 K and a critical exponent β = 0.28 ± 0.03. This value is suggestive of a non-conventional critical behavior for the CDW phase transition in LaPt2Si2, compatible with a scenario of CDW discommensuration (DC). The DC would be caused by the existence of two CDWs in this material, propagating separately in the non equivalent (Si1–Pt2–Si1) and (Pt1–Si2–Pt1) layers, respectively, with transition temperatures TCDW−1 = 230 K and TCDW−2 = 110 K. A strong q-dependence of the electron-phonon coupling has been identified as the driving mechanism for the CDW transition at TCDW−1 = 230 K while a CDW with 3-dimensional character, and Fermi surface quasi-nesting as a driving mechanism, is suggested for the transition at TCDW−2 = 110 K. Our results clarify some aspects of the CDW transition in LaPt2Si2 which have been so far misinterpreted by both theoretical predictions and experimental observations and give direct insight into its actual temperature dependence.
|
|
| 16. |
- Onodera, J., et al.
(author)
-
Interannual Variation of Settling Particles Reflects Upper-Ocean Circulation in the Southern Chukchi Borderland, 2010-2014
- 2021
-
In: Journal of Geophysical Research: Oceans. - 2169-9275. ; 126:12
-
Journal article (peer-reviewed)abstract
- Time series monitoring of hydrography and marine settling particles supplies a large amount of information regarding the marine lower-trophic ecosystem with respect to the changing Arctic Ocean. To investigate the interannual relationship between the settling particles and hydrographic conditions of the western Arctic Ocean, bottom-tethered sediment trap moorings were deployed at the Northwind Abyssal Plain (NAP) from October 2010 to September 2014 and at the Chukchi Abyssal Plain (CAP) from October 2012 to September 2013 to the east and west of the Chukchi Borderland. The settling particles at both stations contained a significant amount of lithogenic matter, with biogenic particles being a lateral advection of shelf materials from shelf to basin. The many peaks of settling particle fluxes at NAP in 2013–2014 corresponded to the hydrographic events of passing oceanic eddies over the station, in addition to seasonal biological production. The settling particle flux at CAP remarkably increased when Pacific-origin water advected over the northern shelf of the Chukchi Sea in March–April 2013. Additionally, abundant gelatinous matter was found at NAP and CAP in July–September 2011 and 2014 and in July–August 2013, respectively. The settling flux data of particulate organic matter and the mole ratio and stable isotope ratios of particulate organic carbon and nitrogen reflected the changes in the composition of trapped plankton assemblages under various hydrographic conditions over the course of the four years of the study. © 2021. The Authors.
|
|
| 17. |
- Walsh, Roddy, et al.
(author)
-
Enhancing rare variant interpretation in inherited arrhythmias through quantitative analysis of consortium disease cohorts and population controls
- 2021
-
In: Genetics in Medicine. - : Nature Publishing Group. - 1098-3600 .- 1530-0366. ; 23:1, s. 47-58
-
Journal article (peer-reviewed)abstract
- Purpose: Stringent variant interpretation guidelines can lead to high rates of variants of uncertain significance (VUS) for genetically heterogeneous disease like long QT syndrome (LQTS) and Brugada syndrome (BrS). Quantitative and disease-specific customization of American College of Medical Genetics and Genomics/Association for Molecular Pathology (ACMG/AMP) guidelines can address this false negative rate.Methods: We compared rare variant frequencies from 1847 LQTS (KCNQ1/KCNH2/SCN5A) and 3335 BrS (SCN5A) cases from the International LQTS/BrS Genetics Consortia to population-specific gnomAD data and developed disease-specific criteria for ACMG/AMP evidence classes-rarity (PM2/BS1 rules) and case enrichment of individual (PS4) and domain-specific (PM1) variants.Results: Rare SCN5A variant prevalence differed between European (20.8%) and Japanese (8.9%) BrS patients (p = 5.7 x 10(-18)) and diagnosis with spontaneous (28.7%) versus induced (15.8%) Brugada type 1 electrocardiogram (ECG) (p = 1.3 x 10(-13)). Ion channel transmembrane regions and specific N-terminus (KCNH2) and C-terminus (KCNQ1/KCNH2) domains were characterized by high enrichment of case variants and >95% probability of pathogenicity. Applying the customized rules, 17.4% of European BrS and 74.8% of European LQTS cases had (likely) pathogenic variants, compared with estimated diagnostic yields (case excess over gnomAD) of 19.2%/82.1%, reducing VUS prevalence to close to background rare variant frequency.Conclusion: Large case-control data sets enable quantitative implementation of ACMG/AMP guidelines and increased sensitivity for inherited arrhythmia genetic testing.
|
|
