| 1. |
|
|
| 2. |
|
|
| 3. |
|
|
| 4. |
- Bowers, Robert M., et al.
(författare)
-
Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea
- 2017
-
Ingår i: Nature Biotechnology. - : NATURE PUBLISHING GROUP. - 1087-0156 .- 1546-1696. ; 35:8, s. 725-731
-
Tidskriftsartikel (refereegranskat)abstract
- We present two standards developed by the Genomic Standards Consortium (GSC) for reporting bacterial and archaeal genome sequences. Both are extensions of the Minimum Information about Any (x) Sequence (MIxS). The standards are the Minimum Information about a Single Amplified Genome (MISAG) and the Minimum Information about a Metagenome-Assembled Genome (MIMAG), including, but not limited to, assembly quality, and estimates of genome completeness and contamination. These standards can be used in combination with other GSC checklists, including the Minimum Information about a Genome Sequence (MIGS), Minimum Information about a Metagenomic Sequence (MIMS), and Minimum Information about a Marker Gene Sequence (MIMARKS). Community-wide adoption of MISAG and MIMAG will facilitate more robust comparative genomic analyses of bacterial and archaeal diversity.
|
|
| 5. |
- Faber, Zachary J, et al.
(författare)
-
The genomic landscape of core-binding factor acute myeloid leukemias
- 2016
-
Ingår i: Nature Genetics. - : Springer Science and Business Media LLC. - 1546-1718 .- 1061-4036. ; 48, s. 1551-1556
-
Tidskriftsartikel (refereegranskat)abstract
- Acute myeloid leukemia (AML) comprises a heterogeneous group of leukemias frequently defined by recurrent cytogenetic abnormalities, including rearrangements involving the core-binding factor (CBF) transcriptional complex. To better understand the genomic landscape of CBF-AMLs, we analyzed both pediatric (n = 87) and adult (n = 78) samples, including cases with RUNX1-RUNX1T1 (n = 85) or CBFB-MYH11 (n = 80) rearrangements, by whole-genome or whole-exome sequencing. In addition to known mutations in the Ras pathway, we identified recurrent stabilizing mutations in CCND2, suggesting a previously unappreciated cooperating pathway in CBF-AML. Outside of signaling alterations, RUNX1-RUNX1T1 and CBFB-MYH11 AMLs demonstrated remarkably different spectra of cooperating mutations, as RUNX1-RUNX1T1 cases harbored recurrent mutations in DHX15 and ZBTB7A, as well as an enrichment of mutations in epigenetic regulators, including ASXL2 and the cohesin complex. This detailed analysis provides insights into the pathogenesis and development of CBF-AML, while highlighting dramatic differences in the landscapes of cooperating mutations for these related AML subtypes.
|
|
| 6. |
|
|
| 7. |
- Chen, G, et al.
(författare)
-
Single-cell analyses of X Chromosome inactivation dynamics and pluripotency during differentiation
- 2016
-
Ingår i: Genome research. - : Cold Spring Harbor Laboratory. - 1549-5469 .- 1088-9051. ; 26:10, s. 1342-1354
-
Tidskriftsartikel (refereegranskat)abstract
- Pluripotency, differentiation, and X Chromosome inactivation (XCI) are key aspects of embryonic development. However, the underlying relationship and mechanisms among these processes remain unclear. Here, we systematically dissected these features along developmental progression using mouse embryonic stem cells (mESCs) and single-cell RNA sequencing with allelic resolution. We found that mESCs grown in a ground state 2i condition displayed transcriptomic profiles diffused from preimplantation mouse embryonic cells, whereas EpiStem cells closely resembled the post-implantation epiblast. Sex-related gene expression varied greatly across distinct developmental states. We also identified novel markers that were highly enriched in each developmental state. Moreover, we revealed that several novel pathways, including PluriNetWork and Focal Adhesion, were responsible for the delayed progression of female EpiStem cells. Importantly, we “digitalized” XCI progression using allelic expression of active and inactive X Chromosomes and surprisingly found that XCI states exhibited profound variability in each developmental state, including the 2i condition. XCI progression was not tightly synchronized with loss of pluripotency and increase of differentiation at the single-cell level, although these processes were globally correlated. In addition, highly expressed genes, including core pluripotency factors, were in general biallelically expressed. Taken together, our study sheds light on the dynamics of XCI progression and the asynchronicity between pluripotency, differentiation, and XCI.
|
|
| 8. |
|
|
| 9. |
- Haddaway, Neal R., et al.
(författare)
-
How does tillage intensity affect soil organic carbon? A systematic review
- 2017
-
Ingår i: Environmental Evidence. - : Springer Science and Business Media LLC. - 2047-2382. ; 6:1
-
Forskningsöversikt (refereegranskat)abstract
- Background: The loss of carbon (C) from agricultural soils has been, in part, attributed to tillage, a common practice providing a number of benefits to farmers. The promotion of less intensive tillage practices and no tillage (NT) (the absence of mechanical soil disturbance) aims to mitigate negative impacts on soil quality and to preserve soil organic carbon (SOC). Several reviews and meta-analyses have shown both beneficial and null effects on SOC due to no tillage relative to conventional tillage, hence there is a need for a comprehensive systematic review to answer the question: what is the impact of reduced tillage intensity on SOC? Methods: We systematically reviewed relevant research in boreoerate regions using, as a basis, evidence identified within a recently completed systematic map on the impacts of farming on SOC. We performed an update of the original searches to include studies published since the map search. We screened all evidence for relevance according to predetermined inclusion criteria. Studies were appraised and subject to data extraction. Meta-analyses were performed to investigate the impact of reducing tillage [from high (HT) to intermediate intensity (IT), HT to NT, and from IT to NT] for SOC concentration and SOC stock in the upper soil and at lower depths. Results: A total of 351 studies were included in the systematic review: 18% from an update of research published in the 2 years since the systematic map. SOC concentration was significantly higher in NT relative to both IT [1.18 g/kg ± 0.34 (SE)] and HT [2.09 g/kg ± 0.34 (SE)] in the upper soil layer (0-15 cm). IT was also found to be significant higher [1.30 g/kg ± 0.22 (SE)] in SOC concentration than HT for the upper soil layer (0-15 cm). At lower depths, only IT SOC compared with HT at 15-30 cm showed a significant difference; being 0.89 g/kg [± 0.20 (SE)] lower in intermediate intensity tillage. For stock data NT had significantly higher SOC stocks down to 30 cm than either HT [4.61 Mg/ha ± 1.95 (SE)] or IT [3.85 Mg/ha ± 1.64 (SE)]. No other comparisons were significant. Conclusions: The transition of tilled croplands to NT and conservation tillage has been credited with substantial potential to mitigate climate change via C storage. Based on our results, C stock increase under NT compared to HT was in the upper soil (0-30 cm) around 4.6 Mg/ha (0.78-8.43 Mg/ha, 95% CI) over ≥ 10 years, while no effect was detected in the full soil profile. The results support those from several previous studies and reviews that NT and IT increase SOC in the topsoil. Higher SOC stocks or concentrations in the upper soil not only promote a more productive soil with higher biological activity but also provide resilience to extreme weather conditions. The effect of tillage practices on total SOC stocks will be further evaluated in a forthcoming project accounting for soil bulk densities and crop yields. Our findings can hopefully be used to guide policies for sustainable management of agricultural soils.
|
|
| 10. |
- Haddaway, Neal R., et al.
(författare)
-
The benefits of systematic mapping to evidence-based environmental management
- 2016
-
Ingår i: Ambio. - : Springer Science and Business Media LLC. - 0044-7447 .- 1654-7209. ; 45:5, s. 613-620
-
Tidskriftsartikel (refereegranskat)abstract
- Reviews of evidence are a vital means of summarising growing bodies of research. Systematic reviews (SRs) aim to reduce bias and increase reliability when summarising high priority and controversial topics. Similar to SRs, systematic maps (SMs) were developed in social sciences to reliably catalogue evidence on a specific subject. Rather than providing answers to specific questions of impacts, SMs aim to produce searchable databases of studies, along with detailed descriptive information. These maps (consisting of a report, a database, and sometimes a geographical information system) can prove highly useful for research, policy and practice communities, by providing assessments of knowledge gaps (subjects requiring additional research), knowledge gluts (subjects where full SR is possible), and patterns across the research literature that promote best practice and direct research resources towards the highest quality research. Here, we introduce SMs in detail using three recent case studies that demonstrate their utility for research and decision-making.
|
|
