DNA methylation at the 5 position of cytosine (5mC) in the mammalian genome is a key epigenetic event critical for various cellular processes. The ten-eleven translocation (Tet) family of ...5mC-hydroxylases, which convert 5mC to 5-hydroxymethylcytosine (5hmC), offers a way for dynamic regulation of DNA methylation. Here we report that Tet1 binds to unmodified C or 5mC- or 5hmC-modified CpG-rich DNA through its CXXC domain. Genome-wide mapping of Tet1 and 5hmC reveals mechanisms by which Tet1 controls 5hmC and 5mC levels in mouse embryonic stem cells (mESCs). We also uncover a comprehensive gene network influenced by Tet1. Collectively, our data suggest that Tet1 controls DNA methylation both by binding to CpG-rich regions to prevent unwanted DNA methyltransferase activity, and by converting 5mC to 5hmC through hydroxylase activity. This Tet1-mediated antagonism of CpG methylation imparts differential maintenance of DNA methylation status at Tet1 targets, ultimately contributing to mESC differentiation and the onset of embryonic development.
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► Defined Tet1 as a CpG-rich DNA-binding protein that binds to C, 5mC, and 5hmC ► Established genome-wide maps of 5hmC, Tet1, and Tet1-associated gene profiling ► Revealed complex modes of Tet1 action in 5mC, 5hmC, and gene expression regulations ► Provided a basis for understanding how Tet1 and 5hmC contribute to ESC epigenome
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
Single-atom catalysts, especially with single Pt atoms, have attracted more and more attention due to their high catalytic activity for CO oxidation. The outstanding stability and catalytic activity ...of a single Pt atom supported on nitrogen doped graphene (Pt/NG) are revealed using first-principles calculations. We find that the stability of a Pt atom on the NG can be promoted by picking an appropriate doping configuration. The exceptionally stable Pt/NG catalyst exhibits excellent catalytic activity for CO oxidation via a new tri-molecular Eley-Rideal mechanism (2CO + O2 → OCO-OCO → 2CO2) with an energy barrier of 0.16 eV for the rate-limiting step of OCO-OCO dissociation, which is more preferable than the other two normal Langmuir-Hinshelwood and Eley-Rideal mechanisms.
For the first time, gasoline and jet fuel range C
7
-C
8
cycloalkanes and aromatics were selectively synthesized by the alcoholysis of poly(ethylene terephthalate) (PET) waste, followed by ...solvent-free hydrogenation and hydrodeoxygenation (HDO). It was found that methanol is highly reactive for the alcoholysis of PET waste. In the absence of any catalyst, a high yield of dimethyl terephthalate (97.3%) was achieved under mild conditions (473 K, 3.5 h). Dimethyl terephthalate exists as a solid and can be automatically separated from methanol with a decrease in temperature. Subsequently, dimethyl terephthalate was liquefied to dimethyl cyclohexane-1,4-dicarboxylate by hydrogenation over noble metal catalysts. Among the investigated catalysts, Pt/C exhibited the highest activity. Finally, the dimethyl cyclohexane-1,4-dicarboxylate as obtained was further hydrodeoxygenated to C
7
-C
8
cycloalkanes and aromatics that can be used as gasoline or additives to improve the densities (or volumetric heat value) and sealabilities of current bio-jet fuels. Bimetallic Ru-Cu/SiO
2
was found to be a promising HDO catalyst. According to the characterization results, the excellent HDO performance of Ru-Cu/SiO
2
can be explained by the formation of smaller Ru-Cu alloy particles during the catalyst preparation. In real applications, dimethyl cyclohexane-1,4-dicarboxylate can also be simultaneously hydrodeoxygenated with biomass derived oxygenates to produce jet fuel with a suitable content of cycloalkanes and aromatics.
Gasoline and jet fuel range C
7
-C
8
cycloalkanes and aromatics were synthesized for the first time in high overall yield (∼95%) from poly(ethylene terephthalate) waste.
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•Revealed the characteristics of MCL values in China between 2010 and 2020.•Identified the trade-off/synergy relationship characteristics of MCL values in China.•Utilized Geographical ...detector to identify dominant and interaction factors for trade-off/synergy in MCL values.
In China, the fast growth of the economy and society is causing a change in the multifunction of cultivated land (MCL), but there is still a lack of proper understanding of the structural connections between these internal functions. Based on exploring the theoretical concept of MCL and quantitative measurement, this paper applied the trade-off/synergy model and the bivariate spatial autocorrelation model to investigate the relationships between the various dimensions of MCL, and the influential factors was revealed by Geographical Detectors. Our research demonstrated that the function of China's cultivated land has obviously changed from a single grain production to a complex including social security, ecological and cultural functions during 2010–2020. Through quantitative measurement of MCL, the results show that, on the one hand, the total amount of MCL increases significantly over time; on the other hand, MCL shows a typical spatial differentiation characteristic of “high in the southern and low in the northern”. According to the analysis of trade-off/synergy, overall, the MCL presents a positive synergy situation, and this situation has been enhanced over time. As to the influencing factors, the socio-economic development, especially the rural development, significantly affected the trade-off/synergy. Moreover, multi-factor interaction considerably improves the explanatory power of the trade-off/synergy relationship for MCL. These results provide evidence for establishing a more efficient use of cultivated land and can also provide food security management strategies.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
Bivalve molluscs are descendants of an early-Cambrian lineage superbly adapted to benthic filter feeding. Adaptations in form and behavior are well recognized, but the underlying molecular mechanisms ...are largely unknown. Here, we investigate the genome, various transcriptomes, and proteomes of the scallop Chlamys farreri, a semi-sessile bivalve with well-developed adductor muscle, sophisticated eyes, and remarkable neurotoxin resistance. The scallop's large striated muscle is energy-dynamic but not fully differentiated from smooth muscle. Its eyes are supported by highly diverse, intronless opsins expanded by retroposition for broadened spectral sensitivity. Rapid byssal secretion is enabled by a specialized foot and multiple proteins including expanded tyrosinases. The scallop uses hepatopancreas to accumulate neurotoxins and kidney to transform to high-toxicity forms through expanded sulfotransferases, probably as deterrence against predation, while it achieves neurotoxin resistance through point mutations in sodium channels. These findings suggest that expansion and mutation of those genes may have profound effects on scallop's phenotype and adaptation.
The enzymatic control of the setting and maintenance of symmetric and non-symmetric DNA methylation patterns in a particular genome context is not well understood. Here, we describe a comprehensive ...analysis of DNA methylation patterns generated by high resolution sequencing of hairpin-bisulfite amplicons of selected single copy genes and repetitive elements (LINE1, B1, IAP-LTR-retrotransposons, and major satellites). The analysis unambiguously identifies a substantial amount of regional incomplete methylation maintenance, i.e. hemimethylated CpG positions, with variant degrees among cell types. Moreover, non-CpG cytosine methylation is confined to ESCs and exclusively catalysed by Dnmt3a and Dnmt3b. This sequence position-, cell type-, and region-dependent non-CpG methylation is strongly linked to neighboring CpG methylation and requires the presence of Dnmt3L. The generation of a comprehensive data set of 146,000 CpG dyads was used to apply and develop parameter estimated hidden Markov models (HMM) to calculate the relative contribution of DNA methyltransferases (Dnmts) for de novo and maintenance DNA methylation. The comparative modelling included wild-type ESCs and mutant ESCs deficient for Dnmt1, Dnmt3a, Dnmt3b, or Dnmt3a/3b, respectively. The HMM analysis identifies a considerable de novo methylation activity for Dnmt1 at certain repetitive elements and single copy sequences. Dnmt3a and Dnmt3b contribute de novo function. However, both enzymes are also essential to maintain symmetrical CpG methylation at distinct repetitive and single copy sequences in ESCs.
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DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
We provide two sufficient and necessary conditions to characterize any
-bit partial Boolean function with exact quantum query complexity 1. Using the first characterization, we present all
-bit ...partial Boolean functions that depend on
bits and can be computed exactly by a 1-query quantum algorithm. Due to the second characterization, we construct a function
that maps any
-bit partial Boolean function to some integer, and if an
-bit partial Boolean function
depends on
bits and can be computed exactly by a 1-query quantum algorithm, then F(f) is non-positive. In addition, we show that the number of all
-bit partial Boolean functions that depend on
bits and can be computed exactly by a 1-query quantum algorithm is not bigger than an upper bound depending on
and
. Most importantly, the upper bound is far less than the number of all
-bit partial Boolean functions for all efficiently big
.
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IZUM, KILJ, NUK, PILJ, PNG, SAZU, UL, UM, UPUK
is a herb in traditional Chinese medicine where
polysaccharides (DOP) are the main active ingredient. This study aimed at evaluating DOP efficiency at inhibiting 1-Methyl-2-nitro-1-nitrosoguanidine ...(MNNG) induced precancerous lesions of gastric cancer (PLGC) in rats through the Wnt/b-catenin pathway and analyzing the variations of serum endogenous metabolites. PLGC was established in male Sprague-Dawley (SD) rats by administering 150 μg/mL MNNG in drinking water for 7 months and giving 0.1 mL of 10% NaCl once weekly during the initial 20 weeks. Treatment with DOP inhibited the progress of PLGC through decreasing the expression of β-catenin by immunohistochemical analysis. The futher study indicated DOP downregulated gene expression of Wnt2β, Gsk3β, PCNA, CyclinD1, and β-catenin, as well as protein expression of Wnt2β, PCNA, and β-catenin. On the other hand, there were nine endogenous metabolites identified after the DOP treatment. Among these, the most significant one is betaine because of its strong antioxidant activity, leading to an anti-tumor effect. DOP can inhibit MNNG-induced PLGC models via regulating Wnt/β-catenin pathway and by changing endogenous metabolites.
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IZUM, KILJ, NUK, PILJ, PNG, SAZU, UL, UM, UPUK
Histone methylation and DNA methylation cooperatively regulate chromatin structure and gene activity. How these two systems coordinate with each other remains unclear. Here we study the biological ...function of lysine-specific demethylase 1 (LSD1, also known as KDM1 and AOF2), which has been shown to demethylate histone H3 on lysine 4 (H3K4) and lysine 9 (H3K9). We show that LSD1 is required for gastrulation during mouse embryogenesis. Notably, targeted deletion of the gene encoding LSD1 (namely, Aof2) in embryonic stem (ES) cells induces progressive loss of DNA methylation. This loss correlates with a decrease in DNA methyltransferase 1 (Dnmt1) protein, as a result of reduced Dnmt1 stability. Dnmt1 protein is methylated in vivo, and its methylation is enhanced in the absence of LSD1. Furthermore, Dnmt1 can be methylated by Set7/9 (also known as KMT7) and demethylated by LSD1 in vitro. Our findings suggest that LSD1 demethylates and stabilizes Dnmt1, thus providing a previously unknown mechanistic link between the histone and DNA methylation systems.
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DOBA, IJS, IZUM, KILJ, NUK, PILJ, PNG, SAZU, UILJ, UKNU, UL, UM, UPUK
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