| 1. |
- Chen, Zhishan, et al.
(author)
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Fine-mapping analysis including over 254 000 East Asian and European descendants identifies 136 putative colorectal cancer susceptibility genes
- 2024
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In: Nature Communications. - : Springer Nature. - 2041-1723. ; 15:1
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Journal article (peer-reviewed)abstract
- Genome-wide association studies (GWAS) have identified more than 200 common genetic variants independently associated with colorectal cancer (CRC) risk, but the causal variants and target genes are mostly unknown. We sought to fine-map all known CRC risk loci using GWAS data from 100,204 cases and 154,587 controls of East Asian and European ancestry. Our stepwise conditional analyses revealed 238 independent association signals of CRC risk, each with a set of credible causal variants (CCVs), of which 28 signals had a single CCV. Our cis-eQTL/mQTL and colocalization analyses using colorectal tissue-specific transcriptome and methylome data separately from 1299 and 321 individuals, along with functional genomic investigation, uncovered 136 putative CRC susceptibility genes, including 56 genes not previously reported. Analyses of single-cell RNA-seq data from colorectal tissues revealed 17 putative CRC susceptibility genes with distinct expression patterns in specific cell types. Analyses of whole exome sequencing data provided additional support for several target genes identified in this study as CRC susceptibility genes. Enrichment analyses of the 136 genes uncover pathways not previously linked to CRC risk. Our study substantially expanded association signals for CRC and provided additional insight into the biological mechanisms underlying CRC development.
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| 2. |
- Bonner, Mark T. L., et al.
(author)
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Why does nitrogen addition to forest soils inhibit decomposition?
- 2019
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In: Soil Biology and Biochemistry. - : Elsevier BV. - 0038-0717 .- 1879-3428. ; 137
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Journal article (peer-reviewed)abstract
- Enrichment of forest soils with inorganic nitrogen (N) tends to inhibit oxidative enzyme expression by microbes and reduces plant litter and soil organic matter decomposition rates. Without further explanation than is currently presented in the scientific literature, we argue that upregulation of oxidative enzymes seems a more competitive response to prolonged N enrichment at high rates than the observed downregulation. Thus, as it stands, observed responses are inconsistent with predicted responses. In this article, we present a hypothesis that resolves this conflict. We suggest that high rates of N addition alter the competitive balance between enzymatic lignin mineralisation and non-enzymatic lignin oxidation. Using metatransciptomics and chemical assays to examine boreal forest soils, we found that N addition suppressed peroxidase activity, but not iron reduction activity (involved in non-enzymatic lignin oxidation). Our hypothesis seems positioned as a parsimonious and empirically consistent working model that warrants further testing.
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| 3. |
- Pocock, T H, et al.
(author)
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Susceptibility to low-temperature photoinhibition and the acquisition of freezing tolerance in winter and spring wheat : The role of growth temperature and irradiance
- 2001
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In: Physiologia Plantarum. - 0031-9317 .- 1399-3054. ; 113:4, s. 499-506
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Journal article (peer-reviewed)abstract
- Five winter and five spring wheat (Triticum aestivum L.) cultivars were grown under either control conditions (20 degreesC/250 photosynthetic photon flux density (PPFD) [mu mol m(-2) s(-1)]), high irradiance (20 degreesC/800 PPFD) or at low temperature (either 5 degreesC/250 PPFD or 5 degreesC/50 PPFD). To eliminate any potential bias, the wheat cultivars were arbitrarily chosen without any previous knowledge of their freezing tolerance or photosynthetic competence. We show that the differential susceptibilities to photoinhibition exhibited between spring and winter wheat cultivars, as assessed by chlorophyll fluorescence cannot be explained on the basis of either growth irradiance or low growth temperature per se. The role of excitation pressure is discussed. We assessed the correlation between susceptibility to low-temperature photoinhibition, maximum ribulose 1,5-bisphosphate carboxylase-oxygenase (EC 4.1.1.39) and NADP-dependent malate dehydrogenase (EC 1.1.1.82) activities, chlorophyll and protein concentrations and freezing tolerance determined by electrolyte leakage. Susceptibility to photoinhibition is the only parameter examined that is strongly and negatively correlated with freezing tolerance. We suggest that the assessment of susceptibility to photoinhibition may be a useful predictor of freezing tolerance and field survival of cereals.
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