Author
Changxin Lu
Bio: Changxin Lu is an academic researcher. The author has contributed to research in topics: Pyrolysis & Porosity. The author has an hindex of 2, co-authored 2 publications receiving 1064 citations.
Topics: Pyrolysis, Porosity, Gene, Gene conversion, Pseudocapacitance
Papers
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Crops Research Institute1, Australian Centre for Plant Functional Genomics2, Agriculture and Agri-Food Canada3, Purdue University4, Plant Genome Mapping Laboratory5, Southwest University6, University of York7, Seoul National University8, Southern Cross University9, University of Missouri10, Centre national de la recherche scientifique11, Huazhong Agricultural University12, Hunan Agricultural University13, University of Queensland14, National Research Council15, Central University, India16, Sahmyook University17, King Abdulaziz University18
TL;DR: A draft genome sequence of Brassica oleracea is described, comparing it with that of its sister species B. rapa to reveal numerous chromosome rearrangements and asymmetrical gene loss in duplicated genomic blocks.
Abstract: Polyploidization has provided much genetic variation for plant adaptive evolution, but the mechanisms by which the molecular evolution of polyploid genomes establishes genetic architecture underlying species differentiation are unclear Brassica is an ideal model to increase knowledge of polyploid evolution Here we describe a draft genome sequence of Brassica oleracea, comparing it with that of its sister species B rapa to reveal numerous chromosome rearrangements and asymmetrical gene loss in duplicated genomic blocks, asymmetrical amplification of transposable elements, differential gene co-retention for specific pathways and variation in gene expression, including alternative splicing, among a large number of paralogous and orthologous genes Genes related to the production of anticancer phytochemicals and morphological variations illustrate consequences of genome duplication and gene divergence, imparting biochemical and morphological variation to B oleracea This study provides insights into Brassica genome evolution and will underpin research into the many important crops in this genus
884 citations
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Northwest A&F University1, Commonwealth Scientific and Industrial Research Organisation2, Kunming Institute of Zoology3, University of Edinburgh4, Utah State University5, Institut national de la recherche agronomique6, Baylor College of Medicine7, Inner Mongolia Agricultural University8, University of Otago9, AgResearch10, European Bioinformatics Institute11, Wellcome Trust Sanger Institute12, University of Copenhagen13, United States Department of Agriculture14, Washington State University15, Sichuan Agricultural University16, The Roslin Institute17, University of New England (Australia)18, University of Sydney19
TL;DR: A genome for ewe and ewe Sheep-specific genetic changes underlie differences in lipid metabolism between sheep and other mammals, and may have contributed to the production of wool.
Abstract: Sheep (Ovis aries) are a major source of meat, milk, and fiber in the form of wool and represent a distinct class of animals that have a specialized digestive organ, the rumen, that carries out the initial digestion of plant material. We have developed and analyzed a high-quality reference sheep genome and transcriptomes from 40 different tissues. We identified highly expressed genes encoding keratin cross-linking proteins associated with rumen evolution. We also identified genes involved in lipid metabolism that had been amplified and/or had altered tissue expression patterns. This may be in response to changes in the barrier lipids of the skin, an interaction between lipid metabolism and wool synthesis, and an increased role of volatile fatty acids in ruminants compared with nonruminant animals.
386 citations
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TL;DR: In this article , microwave technology is utilized to prepare porous carbon from the chili straw pyrolysis residue in order to obtain better electrical properties compared to conventional heating, and the biochar obtained at higher pyrotechnic temperature has a richer pore structure after activation.
Abstract: Microwave technology is utilized to prepare porous carbon from the chili straw pyrolysis residue in this study. As the pyrolysis temperature increases, the thermal stability of biochar is higher. The carbon speciation of the porous carbon PC500 is closest to that of graphite, and its inorganic-C reaches to 51.21%. Notably, the specific surface area of the activated porous carbon increases with increasing pyrolysis temperature, with a maximum value of 2768.52 m2/g for PC500. Further testing of the electrochemical properties of the porous carbon, PC500 possesses a high specific capacitance of 352 F/g at 1 A/g while that of conventional heating is only 226.1 F/g. The porous carbon prepared by microwave heating has better electrical properties compared to conventional heating, and the biochar obtained at higher pyrolysis temperature has a richer pore structure after activation.
7 citations
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TL;DR: In this paper , enzymatic asymmetric reduction offers an alternative biotransformation method for reducing 2-(5H)-furanone-4-propyl (3a) to (R)-4-propyldihydrofuran-2(3 H)-one (3b), which is a key intermediate in synthesizing brivaracetam.
Abstract: Brivaracetam is an effective third-generation antiepileptic drug, and its two chiral centers are a major challenge for designing an inexpensive large-scale synthesis process. Enzymatic asymmetric reduction offers an alternative biotransformation method for reducing 2-(5H)-furanone-4-propyl (3a) to (R)-4-propyldihydrofuran-2(3 H)-one (3b), which is a key intermediate in synthesizing brivaracetam. However, no enzymes have been reported to catalyze this reaction with both high activity and stereoselectivity. In this study, fourteen ene-reductases were compared, and the old yellow enzyme OYE2 was identified as having strict stereoselectivity but unsatisfactory activity. Through evaluations with structurally similar substrates and alanine-screening methods, two key residues were identified, T37 and Y82, playing critical roles in catalytic activity. The hydrogenation activity of mutants Y82W and T37C increased by 2.97 and 7.13 times, respectively. Molecular dynamics simulation indicates that mutant Y82W might shorten the distance between the electron acceptor and donor, while T37A might decrease the redox potential of FMN and then accelerate hydrogen transfer. These results indicate that tuning the redox potential properties of FMN is an important consideration for engineering FMN-dependent oxidoreductases. During the gram-scale synthesis of 3b, T37C exhibited excellent stereoselectivity (>99 % ee) and conversion (>99 %), laying a foundation for a simple one-step route in producing the chiral precursor brivaracetam.
1 citations
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TL;DR: In this paper , N-self-doped porous carbon enriched with hierarchical pore structures was prepared via microwave-assisted pyrolysis of water hyacinth, and the porous carbon obtained at a heating power of 500 W and a final temperature of 700 °C (WPC-T7P5) has the highest specific surface area (SSA) of 2649 m2/g.
Cited by
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University of Évry Val d'Essonne1, Crops Research Institute2, Agriculture and Agri-Food Canada3, Fujian Agriculture and Forestry University4, J. Craig Venter Institute5, Plant Genome Mapping Laboratory6, University of Giessen7, French Alternative Energies and Atomic Energy Commission8, Institut national de la recherche agronomique9, National Research Council10, Australian Centre for Plant Functional Genomics11, University of Cologne12, Purdue University13, University of California, Berkeley14, University of British Columbia15, Fondation Jean Dausset Centre d'Etude du Polymorphisme Humain16, Huazhong Agricultural University17, Hunan Agricultural University18, Chungnam National University19, University of Arizona20, University of York21, University of Missouri22, Southern Cross University23, University of Western Australia24, Centre national de la recherche scientifique25
TL;DR: The polyploid genome of Brassica napus, which originated from a recent combination of two distinct genomes approximately 7500 years ago and gave rise to the crops of rape oilseed, is sequenced.
Abstract: Oilseed rape (Brassica napus L.) was formed ~7500 years ago by hybridization between B. rapa and B. oleracea, followed by chromosome doubling, a process known as allopolyploidy. Together with more ancient polyploidizations, this conferred an aggregate 72× genome multiplication since the origin of angiosperms and high gene content. We examined the B. napus genome and the consequences of its recent duplication. The constituent An and Cn subgenomes are engaged in subtle structural, functional, and epigenetic cross-talk, with abundant homeologous exchanges. Incipient gene loss and expression divergence have begun. Selection in B. napus oilseed types has accelerated the loss of glucosinolate genes, while preserving expansion of oil biosynthesis genes. These processes provide insights into allopolyploid evolution and its relationship with crop domestication and improvement.
1,743 citations
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TL;DR: Genomic signatures of selection and domestication are associated with positively selected genes (PSGs) for fiber improvement in the A subgenome and for stress tolerance in the D subgenomes, suggesting asymmetric evolution.
Abstract: Upland cotton is a model for polyploid crop domestication and transgenic improvement. Here we sequenced the allotetraploid Gossypium hirsutum L. acc. TM-1 genome by integrating whole-genome shotgun reads, bacterial artificial chromosome (BAC)-end sequences and genotype-by-sequencing genetic maps. We assembled and annotated 32,032 A-subgenome genes and 34,402 D-subgenome genes. Structural rearrangements, gene loss, disrupted genes and sequence divergence were more common in the A subgenome than in the D subgenome, suggesting asymmetric evolution. However, no genome-wide expression dominance was found between the subgenomes. Genomic signatures of selection and domestication are associated with positively selected genes (PSGs) for fiber improvement in the A subgenome and for stress tolerance in the D subgenome. This draft genome sequence provides a resource for engineering superior cotton lines.
1,221 citations
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TL;DR: The Ensembl gene annotation system has been used to annotate over 70 different vertebrate species across a wide range of genome projects and generates the automatic alignment-based annotation for the human and mouse GENCODE gene sets.
Abstract: The Ensembl gene annotation system has been used to annotate over 70 different vertebrate species across a wide range of genome projects. Furthermore, it generates the automatic alignment-based ann ...
849 citations
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TL;DR: These questions are addressed, and insights are discussed from genomic studies of gene loss in populations and their relevance in evolutionary biology and biomedicine.
Abstract: The recent increase in genomic data is revealing an unexpected perspective of gene loss as a pervasive source of genetic variation that can cause adaptive phenotypic diversity. This novel perspective of gene loss is raising new fundamental questions. How relevant has gene loss been in the divergence of phyla? How do genes change from being essential to dispensable and finally to being lost? Is gene loss mostly neutral, or can it be an effective way of adaptation? These questions are addressed, and insights are discussed from genomic studies of gene loss in populations and their relevance in evolutionary biology and biomedicine.
540 citations
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TL;DR: This paper provides an update to the previous publications about the Ensembl Genomes, with a focus on recent developments, including the development of new analyses and views to represent polyploid genomes and the continued up-scaling of the resource.
Abstract: Ensembl Genomes (http://www.ensemblgenomes.org) is an integrating resource for genome-scale data from non-vertebrate species, complementing the resources for vertebrate genomics developed in the context of the Ensembl project (http://www.ensembl.org). Together, the two resources provide a consistent set of programmatic and interactive interfaces to a rich range of data including reference sequence, gene models, transcriptional data, genetic variation and comparative analysis. This paper provides an update to the previous publications about the resource, with a focus on recent developments. These include the development of new analyses and views to represent polyploid genomes (of which bread wheat is the primary exemplar); and the continued up-scaling of the resource, which now includes over 23 000 bacterial genomes, 400 fungal genomes and 100 protist genomes, in addition to 55 genomes from invertebrate metazoa and 39 genomes from plants. This dramatic increase in the number of included genomes is one part of a broader effort to automate the integration of archival data (genome sequence, but also associated RNA sequence data and variant calls) within the context of reference genomes and make it available through the Ensembl user interfaces.
512 citations