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genotype-phenotype correlations in Chinese patients with TGFBI gene-linked corneal dystrophy

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Journal of Zhejiang University-Science B(Biomedicine & Biotechnology) 2011年第4期12卷 287-292页

作者： Yan LONG Yang-shun GU Wei HAN Xiu-yi LI Ping YU Ming QI Department of Ophthalmology the First Affiliated Hospital School of Medicine Zhejiang University Hangzhou 310003 China Department of Medical Genetics School of Medicine Zhejiang University Hangzhou 310029 China

In this paper,we report the clinical and molecular features of the distinct TGFBI (human transforming growth factor β-induced,OMIM No.601692) gene-linked corneal ***,five pedigrees and ten unrelated individuals diagnosed as corneal dystrophy were *** venous DNA was extracted,and then amplified by polymerase chain reaction (PCR) and scanned for mutation by single-stranded conformation polymorphism (SSCP).Direct DNA sequencing was used to analyze the mutations of the TGFBI *** our study,thirty patients from five pedigrees and ten sporadic patients were diagnosed as four TGFBI gene-linked corneal dystrophies of granular corneal dystrophy type I (GGCD I),Avellino corneal dystrophy (ACD),lattice corneal dystrophy type I (LCD I),and lattice corneal dystrophy type ⅢA (LCD IIIA),and in total,seven disease-causing mutations,namely R555W,A546D,A546T,and T538P mutations in exon 12,R124H and R124C mutations in exon 4,and P501T mutation in exon 11,were identified,while four polymorphisms of V327V,L472L,F540F,and 1665-1666insC were screened in exons 8,11,and *** study ascertained the tight genotype-phenotype relationship and confirmed the clinical and genetic features of four TGFBI gene-linked corneal dystrophies.

关键词： TGFBI gene Corneal dystrophy genotype Phenotype Mutation

genotype-phenotype relationship in hereditary amyotrophic lateral sclerosis

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Translational Neurodegeneration 2015年第1期4卷 92-104页

作者： Satoshi Yamashita Yukio Ando Department of Neurology Graduate School of Medical SciencesKumamoto University1-1-1 HonjoKumamoto 860-8556Japan

Amyotrophic lateral sclerosis(ALS)is the most common adult-onset motor neuron *** is characterized by neuronal loss and degeneration of the upper motor neurons(UMNs)and lower motor neurons(LMNs),and is usually fatal due to respiratory failure within 3–5 years of *** approximately 5–10%of patients with ALS have an inherited form of the disease,the distinction between hereditary and apparently sporadic ALS(SALS)seems to be ***,genetic factors play a role in all types of ALS,to a greater or lesser *** the decade of upheaval,the evolution of molecular genetics technology has rapidly advanced our genetic knowledge about the causes of ALS,and the relationship between the genetic subtypes and clinical *** this review,we will focus on the possible genotype-phenotype correlation in hereditary *** the identity of the genetic factors in ALS will not only improve the accuracy of ALS diagnosis,but may also provide new approaches for preventing and treating the disease.

关键词： Amyotrophic lateral sclerosis(ALS) genotype Phenotype Sporadic ALS(SALS) Familial ALS(FALS)

Preliminary Analysis of Gene Expression Profiles in HepG2 Cell Line Induced by Different genotype Core Proteins of HCV

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Cellular & Molecular Immunology 2006年第3期3卷 227-233页

作者： Jun Dou Pengbo Liu Jing Wang Xinjian Zhang Department of Pathogenic Biology and Immunology Southeast University School of Basic Medical Science Nanjing 210009 China Department of Pathology and Laboratory Medicine Emory University School of Medicine Atlanta Georgia 30222 USA Department of Obstetrics and Gynecology affiliated Zhongda Hospital Southeastern University Nanjing 210009 China Department of Microbiology and Molecular Genetics Harvard Medical School Boston MA02115 USA

In present investigation, we constructed recombinants expressing the HCV genotypes 1b, 2a, and 4d core proteins, and established human hepatocellular carcinoma （HepG2） cell line that expressed various genotype core proteins. The gene expression profiles in the cells expressing different HCV genotype core proteins were compared with those in the control by microarray analysis. In data analysis, a threshold was set to eliminate all genes that were not increased or decreased by 2.5-fold change in a comparison between the transfected cells and control cells. The preliminary microarray analysis suggests that the gene expression profiles regulated by three kinds of genotype core proteins are mainly involved in transport, signal transduction, regulation of transcription, protease activity, etc., and that some pathogenesis/oncogenesis gene expressions are up/down- regulated simultaneously in the HepG2 cell line. The data suggest that each core protein has its gene expressions profile and that the profiles are implicated in HCV replication and pathogenesis, which may open up a novel way to understand the function of the HCV variant core proteins biological and their pathogenic mechanism. Cellular ＆ Molecular Immunology. 2006;3（3）：227-233.

关键词： hepatitis C virus core protein genotype microarray

Comparing the genotype and Drug Susceptibilities between Mycobacterium avium and Mycobacterium intracellulare in China

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Biomedical and Environmental Sciences 2017年第7期30卷 517-525页

作者： ZHENG Hui Wen PANG Yu HE Guang Xue SONG Yuan Yuan ZHAO Yan Lin National institute for communicable disease control and prevention Chinese center for disease control and prevention Beijing 102206 China National Tuberculosis Reference Laboratory Chinese Center for Disease Control and Prevention Beijing 102206 China Science and Technology Department Chinese Center for Disease Control and Prevention Beijing 102206 China

Objective Mycobacterium avium （M. avium） and Mycobacterium intracellulare （M. intracellulare） are the major causative agents of nontuberculous mycobacteria （NTM）-related pulmonary infections. However, little is known about the differences in drug susceptibility profiles between these two species. Methods A total of 393 NTM isolates were collected from Shanghai Pulmonary Disease Hospital. Sequencing of partial genes was performed to identify the strains at species level. The minimum inhibitory concentration （MIC） was used to evaluate the drug susceptibility against 20 antimicrobial agents. Variable number of tandem repeat （VNTR） typing was conducted to genotype these two species. Results A total of 173 （44.0%） M. avium complex （MAC） isolates were identified, including 41 （10.4%） M. avium isolates and 132 （33.6%） M. intracellulare isolates. Clarithromycin and amikacin were the two most effective agents against MAC isolates. The Hunter-Gaston Discriminatory Index （HGDI） values for VNTR typing of M. avium and M. intracellulare isolates were 0.993 and 0.995, respectively. Levofloxacin resistance was more common among the unclustered strains than among the clustered strains of M. intracellulare. Conclusion M. intrecellulare was the most common NTM species in China. Clarithromycin and amikacin had high antimicrobial activities against MAC. VNTR typing of MAC isolates revealed a high discriminatory power. Levofloxacin resistance was associated with unclustered strains of M. intracellulare.

关键词： Nontuberculous mycobacterium, Phenotype genotype Susceptibility Resistance

Host niche, genotype, and field location shape the diversity and composition of the soybean microbiome

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Journal of Integrative Agriculture 2023年第8期22卷 2412-2425页

作者： YANG Hong-jun YE Wen-wu YU Ze SHEN Wei-liang LI Su-zhen WANG Xing CHEN Jia-jia WANG Yuan-chao ZHENG Xiao-bo Department of Plant Pathology Nanjing Agricultural UniversityNanjing 210095P.R.China Key Laboratory of Soybean Disease and Pest Control of Ministry of Agriculture and Rural Affairs Nanjing Agricultural UniversityNanjing210095P.R.China College of Agronomy and Horticulture Jiangsu Vocational College of Agriculture and ForestryZhenjiang 212400P.R.China Suzhou Academy of Agricultural Sciences Suzhou 234000P.R.China Jining Academy of Agricultural Sciences Jining 272131P.R.China Xuzhou Academy of Agricultural Sciences Xuzhou 221131P.R.China College of Landscape Architecture Jiangsu Vocational College of Agriculture and ForestryZhenjiang 212400P.R.China

Plant-associated microbes represent a key determinant of plant fitness through acquiring nutrients,promoting growth,and resisting to abiotic and biotic ***,an extensive characterization of the bacterial and fungal microbiomes present in different plant compartments of soybean in field conditions has remained *** this study,we investigated the effects of four niches(roots,stems,leaves,and pods),four genotypes(Andou 203,Hedou 12,Sanning 16,and Zhonghuang 13),and three field locations(Jining,Suzhou,and Xuzhou)on the diversity and composition of bacterial and fungal communities in soybean using 16S and internal transcribed spacer rRNA amplicon sequencing,*** soybean microbiome significantly differed across *** genotypes explained more variation in stem bacterial community composition and leaf fungal community *** location significantly affected the composition of bacterial communities in all compartments and the effects were stronger in the root and stem than in the leaf and pod,whereas field location explained more variation in stem and leaf fungal community composition than in the root and *** relative abundances of potential soybean fungal pathogens also differed among host organs and genotypes,reflecting the niches of these microbes in the host and probably their compatibility to the host *** profiling of the microbiome composition and diversity will aid the development of plant protection technologies to benefit soybean health.

关键词： microbiome soybean plant pathogen endophytes host niche genotype field location

The Leu477 and Leu613 of ORF2-Encoded Protein Are Critical in Forming Neutralization Antigenic Epitope of Hepatitis E Virus genotype 4

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Cellular & Molecular Immunology 2008年第6期5卷 447-456页

作者： Hongmei Zhang Xing Dai Xiangnian Shan Jsihong Meng Department of Microbiology and Immunology Southeast University Schoolof Medicine Nanjing 210009 China Genetic Research Center of Southeast University Nanjing 210009 China Department of Dermatology of Zhongda Hospital Nanjing 210009 China

Hepatitis E virus （HEV） genotype 4 was originally identified in China. Its neutralization antigenic epitopes have not been characterized. Recently, we identified a neutralizing monoclonal antibody （mAb） IG10, which was generated following immunization of mice with p166Chn, a recombinant protein comprising 464-629 amino acids （aa） of the HEV genotype 4 capsid protein. In this study, a panel of 22 N- and/or C-terminal truncated and 6 site-directed mutated p166Chn proteins were prepared. Only those N- or C-terminal truncated proteins containing the region 477-613 aa could react with the mAb 1G10, suggesting the neutralization epitope of HEV genotype 4 is located between aa477 and aa613. However, a both N- and C-terminal truncated protein, pN477-C613, neither reacted to 1G10 nor elicited neutralizing antibodies in mice, while another both terminal truncated protein, pN472-C617, did, suggesting the flanking regions of the pN477-C613 could help to stabilize and allow presentation of the neutralization epitope to the immune system. Substituting Leu477 and/or Leu613 with the polar, uncharged threonine （Thr） caused 〉 50% reduction of the mutants＇ immunoreactivity to IG10, whereas replacement by hydrophobic phenylalanine （Phe） made little impact on the immunoreactivity, revealing functional associations between hydrophobicity of aa at positions 477 and 613 and the antigenicity of p166Chn. These data suggested Leu477 and Leu613 are critical in forming the neutralization epitope of HEV genotype 4. Cellular ＆ Molecular Immunology. 2008;5（6）：447-456.

关键词： hepatitis E virus neutralizing epitope monoclonal antibody genotype

genotype-based precision nutrition strategies for the prediction and clinical management of type 2 diabetes mellitus

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World Journal of Diabetes 2024年第2期15卷 142-153页

作者： Omar Ramos-Lopez Medicine and Psychology School Autonomous University of Baja CaliforniaTijuana 22390Baja CaliforniaMexico

Globally,type 2 diabetes mellitus(T2DM)is one of the most common metabolic disorders.T2DM physiopathology is influenced by complex interrelationships between genetic,metabolic and lifestyle factors(including diet),which differ between populations and geographic *** fact,excessive consumptions of high fat/high sugar foods generally increase the risk of developing T2DM,whereas habitual intakes of plant-based healthy diets usually exert a protective ***,genomic studies have allowed the characterization of sequence DNA variants across the human genome,some of which may affect gene expression and protein functions relevant for glucose *** comprehensive literature review covers the impact of gene-diet interactions on T2DM susceptibility and disease progression,some of which have demonstrated a value as biomarkers of personal responses to certain nutritional ***,novel genotype-based dietary strategies have been developed for improving T2DM control in comparison to general lifestyle ***,progresses in other omics areas(epigenomics,metagenomics,proteomics,and metabolomics)are improving current understanding of genetic insights in T2DM clinical *** more investigation is still needed,the analysis of the genetic make-up may help to decipher new paradigms in the pathophysiology of T2DM as well as offer further opportunities to personalize the screening,prevention,diagnosis,management,and prognosis of T2DM through precision nutrition.

关键词： Type 2 diabetes mellitus Nutrigenetics Single nucleotide polymorphism genotype Diet Precision nutrition

Associations between NOD2/CARD15 genotype andphenotype in Crohn’s disease-Are we there yet?

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World Journal of Gastroenterology 2006年第44期12卷 7097-7103页

作者： Graham Radford-Smith Nirmala Pandeya IBD Unit Department of Gastroenter-ology Royal Brisbane and Womens Hospital Brisbane Queensland 4029 Australia Cancer and Population studies group Queensland Institute of Medical Research Brisbane Australia

There have been multiple NOD2/CARD15 genotype- phenotype analyses undertaken in patients with Crohn’s disease since the gene’s discovery in 2001. This review focuses on the major published series based upon their size and on the presence of specific clinical and genetic information provided in the published material from 2001 to 2005. Twelve studies provided raw data to carry out comparisons of disease location while ten studies included analysis of NOD2/CARD15 genotypes. NOD2/CARD15 variant frequency in ileal disease did not differ significantly among studies, whereas a comparison of disease location demonstrated highly significant differences among studies. Meta-analysis confirmed significant associations between NOD2/CARD15 variants and both ileal and ileocolonic disease locations, and with both stricturing and penetrating forms of disease behavior. This review underlines the significant phenotypic differences that exist among populations, including similar ethnic groups, and has demonstrated the need for further studies of patients with long-term “inflammatory” Crohn’s disease.

关键词： Crohn's disease Phenotypic heterogeneity genotype Inter-observer agreement Disease location Disease behavior

Microalbuminuria in hepatitis C-genotype 4:Effect of pegylated interferon and ribavirin

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World Journal of Gastroenterology 2010年第10期16卷 1226-1231页

作者： Moutaz Derbala Fatma M Shebl Awad Rashid Aliaa Amer Abdulbari Bener Department of Gastroenterology and Hepa-tology Hamad Medical Corporation Department of Medicine Weill Cornell Medical College in Qatar Infections & Immunoepidemiology Branch Division of Cancer Epidemiology and GeneticsNational Cancer Institute Epidemiology Branch National Liver Institute Department of Nephrology Hamad Medical Corporation Department of Laboratory Medicine and Histo-pathology Hematology SectionHamad Medical Corporation Department of Medical Statistics and Epidemiology Hamad Medical Corporation

AIM:To study the relation between hepatitis C virus (HCV) genotype 4 and microalbuminuria and renal impairment in relation to hepatic histology, and viremia in the absence of cryoglobulinemia, and to examine the effect of treatment on ***: Three hundred subjects, including 233 HCV genotype-4 infected patients, were tested for cryoglobulinemia, microalbuminuria, albumin creatinine ratio (ACR), urea, creatinine, and estimated glomerular filtration rate (eGFR). The parameters were measured again in the HCV patients after 48 wk of treatment with pegylated interferon and ***: Significantly higher levels of microalbumin- uria were detected in HCV-positive patients compared to HCV-negative controls (median 9.5 vs 5.9, respectively, Kruskal-Wallis P=0.017). Log microalbuminuria was significantly correlated with hepatic inflammation (r=0.13, P=0.036) and f ibrosis (r=0.12, P=0.061), but not with viral load (r=-0.03, P=0.610), or alanine transaminase (r=-0.03, P=0.617). Diabetes mellitus neither significantly moderated (χ2=0.13, P=0.720), nor mediated (Sobel test P=0.49) the HCV effect. HCV status was signifi cantly associated with log microalbu-minuria (χ2=4.97, P=0.026), adjusting for age, gender, diabetes, cryoglobulinemia, urea and creatinine. A positive HCV status was not significantly associated with low eGFR (<60 mL/min every 1.73 m2) [odds ratio (OR): 0.5, 95% confidence interval (CI):0.2-1.4], nor with high ACR (OR: 1.7, 95% CI:0.7-4.1). End-of-treatment response (ETR) was achieved in 51.9% of patients. Individuals with ETR had significantly lower microalbuminuria post-treatment (χ2=8.19, P=0.004).CONCLUSION: HCV affected the development of microalbuminuria independent of diabetes or cryoglobulinemia. Combination therapy of pegylated interferon-ribavirin had a positive effect in reducing microalbuminuria.

关键词： Hepatitis C virus genotype Kidney diseases Albuminuria Proteinuria Peginterferon α-2a Ribavirin