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Industrial Chemistry & Materials 2023年第3期1卷 431-442页

作者： Sapanbir S.Thind Mathias Paul John B.Hayden Anuj Joshi David Goodlett J.Scott McIndoe Department of Chemistry University of Victoria3800 Finnerty RoadVictoriaBCV8P 5C2 Canada Waterdrape LLC Paradise ValleyArizonaUSA genome bc proteomics centre University of VictoriaVictoriaBritish ColumbiaCanada

Sustainable and efficient water treatment techniques to improve the quality of water for various applications include advanced oxidation processes(AOP),mainly focusing on heterogeneous *** science and nanotechnology have contributed to tailoring the properties of photocatalytic materials to significantly enhance their photoactivity and *** we report the development of a well-organized nanoporous TiO_(2)-based photocatalytic reactor for water *** TiO_(2) materials were directly grown using a two-step electrochemical anodization process in ethylene glycol+0.3 wt%NH_(4)F+2 wt%H_(2)*** prepared nanomaterials were characterized by X-ray diffraction(XRD),scanning electron microscope(SEM),and energy-dispersive X-ray spectroscopy(EDX).To enhance the photocatalytic activity of the system,water scrubbing was incorporated to boost the presence of oxygen in the water,enhancing the electron uptake at the conduction band thus significantly reducing the electron–hole recombination and increasing the photocatalytic *** further enhance the efficiency and reduce the negative environmental impact of the technology,a UVA-LED assembly was used instead of the typical mercury-based UV lamps for *** nanoporous TiO_(2) was tested as a catalyst for the photochemical oxidation of various categories of pollutants;dye(methylene blue),and the removal of microbes such as *** photoreactor developed in this research work was also successfully applied and tested in real-world applications such as keeping heavily used hot-tub water clean without using harmful chemicals(chlorine,bromine,ozone,etc.)or expensive *** simplicity and efficacy of the new approach described in this study make possible the integration of nanoporous TiO_(2) in the design of high-performance air and water purification technologies.

关键词： TiO_(2)photocatalyst UVA-LEDs Nanostructured materials Photochemical oxidation Wastewater treatment Water scrubbing

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Poly-hydroxylated bile acids and their prognostic roles in Alagille syndrome

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World Journal of Pediatrics 2023年第7期19卷 652-662页

作者： Meng-Xuan Wang Jun Han Teng Liu Ren-Xue Wang Li-Ting Li Zhong-Die Li Jun-Cong Yang Lang-Li Liu Yi Lu Xin-Bao XieJing-Yu Gong Shi-Yu Lei Zhang Victor Ling J Jian-She Wang Department of Pediatrics Jinshan Hospital of Fudan UniversityShanghai 201508China The Center for Pediatric Liver Diseases Children's Hospital of Fudan UniversityShanghai 201102China University of Victoria-genome bc proteomics centre and Division of Medical Sciences VictoriaBritish ColumbiaCanada bc Cancer Research centre VancouverBritish ColumbiaCanadaDepartment of PediatricsJinshan Hospital of Fudan UniversityShanghai 201508China Institutes of Biomedical Sciences Fudan UniversityShanghai 201199China Shanghai Key Laboratory of Birth Defect Shanghai 201102China

Background The liver manifestations of Alagille syndrome(ALGS)are highly variable,and factors affecting its prognosis are poorly *** asked whether the composition of bile acids in ALGS patients with good clinical outcomes differs from that in patients with poor outcomes and whether bile acids could be used as prognostic *** Blood for bile acid profiling was collected from genetically confirmed JAG1-associated ALGS patients before one year of age.A good prognosis was defined as survival with native liver and total bilirubin(TB)607.69 nmol/L was associated with native liver survival[hazard ratio:13.03,95%confidence interval(CI):(2.662-63.753),P=0.002].Conclusions We identified two poly-hydroxylated bile acids as liver prognostic biomarkers of ALGS *** hydroxylation of bile acids may result in better clinical outcomes.

关键词： Alagille syndrome Bile acid profile Poly-hydroxylated bile acids Prognostic biomarkers

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Comparative Genomic Study Reveals a Transition from TA Richness in Invertebrates to GC Richness in Vertebrates at CpG Flank-ing Sites:An Indication for Context-Dependent Mutagenicity of Methylated CpG Sites

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Genomics, proteomics & Bioinformatics 2008年第3期6卷 144-154页

作者： Frederick C.C. Leung School of Biological Sciences and genome Research centre The University of Hong Kong

Vertebrate genomes are characterized with CpG deficiency, particularly for GCpoor regions. The GC content-related CpG deficiency is probably caused by context-dependent deamination of methylated CpG sites. This hypothesis was examined in this study by comparing nucleotide frequencies at CpG flanking positions among invertebrate and vertebrate genomes. The finding is a transition of nucleotide preference of 5＇ T to 5＇ A at the invertebrate-vertebrate boundary, indicating that a large number of CpG sites with 5＇ Ts were depleted because of global DNA methylation developed in vertebrates. At genome level, we investigated CpG observed/expected （obs/exp） values in 500 bp fragments, and found that higher CpG obs/exp value is shown in GC-poor regions of invertebrate genomes （except sea urchin） but in GC-rich sequences of vertebrate genomes. We next compared GC content at CpG flanking positions with genomic average, showing that the GC content is lower than the average in invertebrate genomes, but higher than that in vertebrate genomes. These results indicate that although 5＇ T and 5＇ A are different in inducing deamination of methylated CpG sites, GC content is even more important in affecting the deamination rate. In all the tests, the results of sea urchin are similar to vertebrates perhaps due to its fractional DNA methylation. CpG deficiency is therefore suggested to be mainly a result of high mutation rates of methylated CpG sites in GC-poor regions.

关键词： CpG deficiency DNA methylation invertebrate genomes GC content

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Oxford Nanopore MinION Sequencing and genome Assembly

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Genomics, proteomics & Bioinformatics 2016年第5期14卷 265-279页

作者： Hengyun Lu Francesca Giordano Zemin Ning National centre of Gene Research Chinese Academy of Sciences The Wellcome Trust Sanger Institute Wellcome Genome Campus

The revolution of genome sequencing is continuing after the successful secondgeneration sequencing （SGS） technology. The third-generation sequencing （TGS） technology, led by Pacific Biosciences （PacBio）, is progressing rapidly, moving from a technology once only capable of providing data for small genome analysis, or for performing targeted screening, to one that promises high quality de novo assembly and structural variation detection for human-sized genomes. In 2014, the MinION, the first commercial sequencer using nanopore technology, was released by Oxford Nanopore Technologies （ONT）. MiniON identifies DNA bases by measuring the changes in electrical conductivity generated as DNA strands pass through a biological pore. Its portability, affordability, and speed in data production makes it suitable for real-time applications, the release of the long read sequencer MiniON has thus generated much excitement and interest in the genomics community. While de novo genome assemblies can be cheaply produced from SGS data, assem- bly continuity is often relatively poor, due to the limited ability of short reads to handle long repeats. Assembly quality can be greatly improved by using TGS long reads, since repetitive regions can be easily expanded into using longer sequencing lengths, despite having higher error rates at the base level. The potential of nanopore sequencing has been demonstrated by various studies in genome surveillance at locations where rapid and reliable sequencing is needed, but where resources are limited.

关键词： Third-generation sequencing Oxford nanopore MiniON-device De novo assembly Structural variations Molecular clinical diagnostics

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Thirty Years of Multiple Sequence Codes

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Genomics, proteomics & Bioinformatics 2011年第1期9卷 1-6页

作者： Edward N. Trifonov genome Diversity Center Institute of Evolution University of Haifa Haifa 31905 Israel Division of Functional Genomics and proteomics Faculty of Science Masaryk University Brno 61137 Czech Republic

An overview is presented on the status of studies on multiple codes in genetic sequences. Indirectly, the existence of multiple codes is recognized in the form of several rediscoveries of Second Genetic Code that is different each time. A due credit is given to earlier seminal work related to the codes often neglected in literature. The latest developments in the field of chromatin code are discussed, as well as perspectives of single-base resolution studies of nucleosome positioning, including rotational setting of DNA on the surface of the histone octamers.

关键词： genomic code chromatin code second genetic code code interaction code degeneracy

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Comparative analysis of mitochondrial fragments transferred to the nucleus in vertebrate

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Journal of Genetics and Genomics 2008年第8期35卷 485-490页

作者： Hongying Qu Fei Ma Qingwei Li Institute of Marine Genomics ＆ proteomics Liaoning Normal University Dalian 116029 China

Mitochondrial DNA sequences transferred to the nucleus give rise to the so-called nuclear mitochondrial DNA （numt）. In the GenBank database, 244 numts have been found in six orders of birds （Anseriformes, Columbiformes, Falconiformes, Charadriiformes, Galliformes and Passeriformes）. Sequences alignment （NCBI-BLASTN） was carded out with mitochondrial and corresponding nuclear genome sequences in nine vertebrate species. The sequences with high homology were considered as numts. The number of numts ranged from 15 in chicken to 159 in chimpanzee. The sequences of numts in macaque, chimpanzee, and human spanned 100% of the entire mammalian mitochondrial genome. The reconstructed frequency of the mitochondrial gene transferred to the nucleus demonstrated that the rRNA genes had high frequencies than other mitochondrial genes. Using the RepeatMasker program, the transposable elements were detected in the flanking regions of each numt. The results showed that less than 5% of the flanking sequences were made up of repetitive elements in chicken. The GC content of 5＇- and 3＇-flanking regions of numts in nine species was less than 44%. The analysis of the flanking sequences provided a valuable understanding for future study on mechanism of mitochondrial gene transfer to the nucleus and the site of numt integration.

关键词： mitochondrial DNA numts nuclear insertion flanking sequence vertebrate

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RegVar:Tissue-specific Prioritization of Non-coding Regulatory Variants

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Genomics, proteomics & Bioinformatics 2023年第2期21卷 385-395页

作者： Hao Lu Luyu Ma Cheng Quan Lei Li Yiming Lu Gangqiao Zhou Chenggang Zhang Beijing Institute of Radiation Medicine State Key Laboratory of ProteomicsBeijing 100850China

Non-coding genomic variants constitute the majority of trait-associated genome variations;however,the identification of functional non-coding variants is still a challenge in human genetics,and a method for systematically assessing the impact of regulatory variants on gene expression and linking these regulatory variants to potential target genes is still ***,we introduce a deep neural network(DNN)-based computational framework,RegVar,which can accurately predict the tissue-specific impact of non-coding regulatory variants on target *** show that by robustly learning the genomic characteristics of massive variant-gene expression associations in a variety of human tissues,RegVar vastly surpasses all current non-coding variant prioritization methods in predicting regulatory variants under different *** unique features of RegVar make it an excellent framework for assessing the regulatory impact of any variant on its putative target genes in a variety of tissues.

关键词： Non-coding variant Variantprioritization Expressionregulation Expressionquantitative trait locus Deep neural network

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Comprehensive Bile Acid Profiling of AbcB4-mutated Patients and the Prognostic Role of Taurine-conjugated􀀖􀄮􀀏􀀙􀄮􀀏􀀚􀄮􀀏􀀔􀀕􀄮􀀐􀀷􀁈􀁗􀁕􀁄􀁋􀁜􀁇􀁕􀁒􀁛􀁜􀁏􀁄􀁗􀁈􀁇􀀃􀀥􀁌􀁏􀁈􀀃􀀤􀁆􀁌􀁇􀀃􀁌􀁑􀀃􀀦􀁋􀁒􀁏􀁈􀁖􀁗􀁄􀁖􀁌􀁖

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Journal of Clinical and Translational Hepatology 2024年第2期12卷 151-161页

作者： Teng Liu Ren-Xue Wang Jun Han Zhong-Die Li Jonathan ASheps Li-Juan Zheng Xiao-Xiao Xu Victor Ling Jian-She Wang Department of Pediatrics Shanghai Medical CollegeFudan UniversityThe Center for Pediatric Liver DiseasesChildren’s Hospital of Fudan UniversityShanghaiChina bc Cancer Agency VancouverBritish Columbia V5Z 1L3Canada University of Victoria-genome bc proteomics Center University of VictoriaVictoriaBritish Columbia V8Z 7X8Canada Shanghai Key Laboratory of Birth Defect ShanghaiChina

Background and Aims:We asked if comprehensive bile acid profiling could provide insights into the physiopathology of AbcB4-mutated patients and evaluated the prognostic value of taurine-conjugated tetrahydroxylated bile acid(tauro-THBA)in ***:Serum bile acid profiles were evaluated in 13 AbcB4-mutated patients with 65 healthy controls by ultra-high-performance liquid chromatography/multiple-reaction monitoring-mass spectrometry(UPLC/MRM-MS).The concentration of tauro-THBA was compared between AbcB4-mutated patients with different *** areas under the curve(AUCs)of tauro-THBA were compared between AbcB11-mutated patients with native liver survival and those who died or underwent liver transplantation before 3 years of age by receiver operating characteristic curve(ROC),with another patient cohort for further ***:The overall hydrophobicity indices of bile acids in AbcB4-mutated patients(12.99±3.25 m)were significantly lower than those of healthy controls(14.02±1.74 m,pbcB4-mutated patients with different prognoses were not *** analysis indicated that levels of tauro-THBA ofbcB11-mutated patients with different prognoses(p=0.0192).Of the 15 patients with good prognosis,14 were classified correctly and four of the five patients with a poor prognosis were classified correctly(14:15 vs.1:5,p=0.005)with tauro-THBA as a ***:Tauro-THBA concentration may be a biomarker for predicting the clinical outcome in low gammaglutamyl transferase intrahepatic cholestasis patients.

关键词： Bile acids MDR3 BSEP PFIC Liquid chromatography-mass spectrometry

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Neonatal Dubin-Johnson Syndrome and its Differentiation from Biliary Atresia

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Journal of Clinical and Translational Hepatology 2023年第1期11卷 163-173页

作者： Teng Liu Jing Zhao Jia-Yan Feng Yi Lu Jonathan A.Sheps Ren-Xue Wang Jun Han Victor Ling Jian-She Wang The Center for Pediatric Liver Diseases Children’s Hospital of Fudan UniversityShanghaiChina The Department of Pathology Children’s Hospital of Fudan UniversityShanghaiChina bc Cancer Agency VancouverBritish ColumbiaV5Z 1L3Canada University of Victoria-genome bc proteomics Center University of VictoriaVictoriaBritish ColumbiaV8Z 7X8Canada Shanghai Key Laboratory of Birth Defects ShanghaiChina

Background and Aims:The aim was to determine if liver biochemistry indices can be used as biomarkers to help differentiate patients with neonatal Dubin–Johnson syndrome(nDJS)from those with biliary atresia(BA).Methods:Patients with genetically-confirmed nDJS or cholangiographically confirmed BA were retrospectively enrolled and randomly assigned to discovery or verification *** liver chemistries,measured during the neonatal period,were *** values were calculated by receiver operating characteristic curve ***:A cohort of 53 nDJS patients was recruited,of whom 13 presented with acholic stools,and 14 underwent diagnostic cholangiography or needle liver biopsy to differentiate from ***-five patients in the cohort,with complete biochemical information measured during the neonatal period,were compared with 133 infants with cholangiographically confirmed *** and direct bilirubin,alanine aminotransferase(ALT),aspartate aminotransferase(AST),total bile acids,alkaline phosphatase,and gamma-glutamyl transferase were significantly lower in nDJS than in *** the discovery cohort,the areas under the curve for ALT and AST were 0.908 and 0.943,*** the validation cohort,13/15 patients in the nDJS group were classified as nDJS,and 10/53 in the BA control group were positive(p<0.00001)with an ALT biomarker cutoff value of 75 IU/*** of 15 patients were classified as nDJS and none were classified positive in the BA group(13/15 vs.0/53,p<0.00001)with an AST cutoff of 87 IU/***:Having assembled and investigated the largest cohort of nDJS patients reported to date,we found that nDJS patients could be distinguished from BA patients using the serum AST level as a *** finding may be clinically useful to spare cholestatic nDJS patients unnecessary invasive procedures.

关键词： Jaundice AbcC2 Cholestasis MRP2 Acholic stools

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An integrated view of the correlations between genomic and phenomic variables

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Journal of Genetics and Genomics 2009年第11期36卷 645-651页

作者： Dong Yang,Ying Jiang,Fuchu He State Key Laboratory of proteomics,Beijing Proteome Research Center,Beijing Institute of Radiation Medicine,Beijing 102206,China State Key Laboratory of proteomics Beijing Proteome Research Center Beijing Institute of Radiation Medicine Beijing 102206 China

genome sequencing opened the flood gate of ＂-omics＂ studies, among which the research about correlations between genomic and phenomic variables is an important part. With the development of functional genomics and systems biology, genome-wide investigation of the correlations between many genomic and phenomic variables became possible. In this review, five genomic variables, such as evolution rate （or ＂age＂ of the gene）, the length of intron and ORF （protein length） in one gene, the biases of amino acid composition and codon usage, along with the phenomic variables related to expression patterns （level and breadth） are focused on. In most cases, genes with higher mRNA/protein expression level tend to evolve slowly, have less intronic DNA, code for smaller proteins, and have higher biases of amino acid composition and codon usage. In addition, broadly expressed proteins evolve more slowly and are shorter than tissue-specific proteins. Studies in this field are helpful for deeper understanding the signatures of selection mediated by the features of gene expression and are of great significance to enrich the evolution theory.

关键词： genomic variable phenomic variable expression pattern evolution selection

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