Browsing by Author "Cheng, Xi"

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    1000 human genomes carry widespread signatures of GC biased gene conversion
    (2018-04-16) Dutta, Rajib; Saha-Mandal, Arnab; Cheng, Xi; Qiu, Shuhao; Serpen, Jasmine; Fedorova, Larisa; Fedorov, Alexei
    Abstract Background GC-Biased Gene Conversion (gBGC) is one of the important theories put forward to explain profound long-range non-randomness in nucleotide compositions along mammalian chromosomes. Nucleotide changes due to gBGC are hard to distinguish from regular mutations. Here, we present an algorithm for analysis of millions of known SNPs that detects a subset of so-called “SNP flip-over” events representing recent gBGC nucleotide changes, which occurred in previous generations via non-crossover meiotic recombination. Results This algorithm has been applied in a large-scale analysis of 1092 sequenced human genomes. Altogether, 56,328 regions on all autosomes have been examined, which revealed 223,955 putative gBGC cases leading to SNP flip-overs. We detected a strong bias (11.7% ± 0.2% excess) in AT- > GC over GC- > AT base pair changes within the entire set of putative gBGC cases. Conclusions On average, a human gamete acquires 7 SNP flip-over events, in which one allele is replaced by its complementary allele during the process of meiotic non-crossover recombination. In each meiosis event, on average, gBGC results in replacement of 7 AT base pairs by GC base pairs, while only 6 GC pairs are replaced by AT pairs. Therefore, every human gamete is enriched by one GC pair. Happening over millions of years of evolution, this bias may be a noticeable force in changing the nucleotide composition landscape along chromosomes.
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    Cadmium Sulfide Based Catalysts for Photocatalytic Hydrogen Production and Lignin Photoconversion
    (2023-12-13) Cheng, Xi; Hu, Jinguang; Shimizu, Kisa Hayashi, Shimizu; Du, Ke; Mahinpey, Nader
    With the development of industrialization, the requirement for fossil fuels is becoming more and more huge, and as a consequence, the environment is degenerated by the combustion of fossil fuels such as coal and petroleum. There are two sources that are considered excellent candidates for solving this problem. One of them is hydrogen energy, green, pollution-free, renewable, and so on features that have attracted widespread attention. Another one, biomass, similar to fossil fuel in ingredients, is a widely distributed and renewable carbon-based substance. The usage of biomass has been proven to be an effective method to relieve the imbalance of the global carbon cycle and can even achieve a negative carbon economy scenario in the future. Among the composition of lignocellulosic biomass, the special structure makes lignin with bulk renewable aromatic groups possess the most potential for producing high-value chemicals. Achieving this promising conversion process with more moderate and green reaction conditions is a key point to propel the development of lignin conversion. Photocatalysis is a technology that realizes a series of catalytic reactions by directly using endless solar energy as a resource that has been recognized as a green and sustainable strategy. Therefore, applying photocatalysis to simultaneously achieve lignin conversion and hydrogen production will not only avoid harsh catalytic conditions but also achieve more efficient photoconversion of lignin. However, the high recombination rate between photogenerated electrons and holes, inefficient regulation of redox capacity, the photostability of photocatalysts, and the complex structure of lignin restrict the application of photocatalytic technology in lignin photo upgrading and hydrogen production by splitting water. Therefore, it is necessary to design photocatalytic materials with better performance to overcome the above problems to achieve more efficient hydrogen production and lignin photoconversion. In this work, cadmium sulfide (CdS) with good photo response ability and suitable bandgap position was selected as the base to study the photoconversion process of lignin and hydrogen evolution performance. The details are as follows: (1) A homojunction structured CdS with rich sulfur vacancies was successfully synthesized by the one-pot solvothermal method. Nanoparticle structured zinc blade phase CdS grew on nano prisms structured hexagonal wurtzite phase CdS. The perfect lattice matching between these two phases effectively guides the spatial separation of photogenerated electrons and holes. On the other hand, with the assistance of rich sulfur vacancies, the well-designed photocatalyst exhibited an unprecedented hydrogen production ability (835.8 μmol·g-1h-1) and value-added phenolic compounds were also generated by decomposing kraft lignin. (2) Using CdS as a base, nickel phosphide (Ni2P) was in-situ grown on the surface of CdS by high temperature phosphating strategy. The introduction of Ni2P created a synergistic effect between Ni2P and CdS, which not only improved the light response of CdS that enhanced photocarriers generation but also optimized the redistribution of photogenerated electrons, therefore, Ni2P/CdS exhibited a marvellous H2 evolution activity ca. 199.1 mmol·h-1·g-1 with lactic acid. Subsequently, replacing the substrates to lignin, cellulose, and hemicellulose, even the virgin biomass, significant amounts of hydrogen and value-added compounds are produced over Ni2P/CdS. In addition, density functional theory (DFT) calculation was also applied to reasonably reveal a possible catalytic pathway.