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molecular diagnosis and direct quantification of cereal cyst nematode(Heterodera filipjevi) from field soil using TaqMan real-time PCR

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Journal of Integrative Agriculture 2023年第8期22卷 2591-2601页

作者： JIAN Jin-zhuo HUANG Wen-kun KONG Ling-an JIAN Heng Sulaiman ABDULSALAM PENG De-liang PENG Huan State Key Laboratory for Biology of Plant Diseases and Insect Pests Institute of Plant ProtectionChinese Academy of Agricultural SciencesBeijing 100193P.R.China Key Laboratory of Plant Pathology of Ministry of Agriculture and Rural Affairs College of Plant ProtectionChina Agricultural UniversityBeijing100193P.R.China Division of Agricultural Colleges/Department of Crop Protection Ahmadu Bello UniversityZaria 810107Nigeria

Heterodera filipjevi continues to be a major threat to wheat production *** detection and quantification of cyst nematodes are essential for more effective control against this nematode *** the present study,a TaqManminor groove binder(TaqMan-MGB)probe-based fluorescence quantitative real-time PCR(qPCR)was successfully developed and used for quantifying *** from DNA extracts of *** primers and probe designed from the obtained RAPD-SCAR marker fragments of *** showed high specificity to *** using DNA from isolatesconfirmed species of 23 Heterodera spp.,1 Globodera *** 3 Pratylenchus *** qPCR assay is highly sensitive and provides improved *** detection sensitivity of as low as 4^(-3) single second-stage juvenile(J2)DNAs,10^(-3) female DNAs,and 0.01μgμL^(-1) genomic DNAs.A standard curve relating to the threshold cycle and log values of nematode numbers was generated and validated from artificially infested soils and was used to quantify *** in naturally infested field *** was a high correlation between the *** numbers estimated from 32 naturally infested field soils by both conventional methods and the numbers quantified using the qPCR *** potentially provides a useful platform for the efficient detection and quantification of *** directly from field soils and to quantify this species directly from DNA extracts of field soils.

关键词： cereal cyst nematode Heterodera filipjevi molecular diagnosis quantification TaqMan real-time PCR

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molecular diagnosis and treatment of drug-resistant hepatitis B virus

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World Journal of Gastroenterology 2014年第19期20卷 5708-5720页

作者： Jeong Han Kim Yong Kwang Park Eun-Sook Park Kyun-Hwan Kim Digestive Disease Center Department of Internal MedicineSchool of MedicineKonkuk UniversitySeoul 143-729South Korea Department of Pharmacology and Center for Cancer Research and Diagnostic Medicine IBSTSchool of MedicineKonkuk UniversitySeoul 143-729South Korea Institute of Functional Genomics Konkuk UniversitySeoul 143-729South Korea

Oral antiviral agents have been developed in the last two decades for the treatment of chronic hepatitis B(CHB).However,antiviral resistance remains an important challenge for long-term CHB *** of the clinically available oral antiviral agents are nucleoside or nucleotide analogues that target the activity of viral reverse transcriptase(RT),and all are reported to have resistant *** the hepatitis B virus(HBV)RT,like other viral polymerases,lacks proofreading activity,the emergence of drug-resistance occurs readily under selective pressure from the administration of antiviral *** molecular diagnosis of drug-resistant HBV is based on sequence variations,and current diagnostic methods include sequencing,restriction fragment polymorphism analysis,and ***,we will discuss the currently available molecular diagnosis tools,in vitro phenotypic assays for validation of drug-resistant HBV,and treatment options for drug-resistant HBV.

关键词： Hepatitis B virus Drug-resistance molecular diagnosis Antiviral treatment Chronic hepatitis B

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molecular diagnosis and therapy of hepatocellular carcinoma: achievements and challenges

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Hepatoma Research 2019年第5期5卷 1-9页

作者： Xiao-Dong Zhang Man Zhao Department of Cancer Research College of Life SciencesNankai UniversityTianjin 300071China

Hepatocellular carcinoma(HCC)is often associated with pre-existing chronic liver pathologies of different origin infections of hepatitis B virus(HBV)and hepatitis C ***,the diagnosis and therapy for HCC are very important for the prognosis of ***,current methods for HCC diagnosis and therapy have no an optimal accuracy due to the tumor heterogeneity and the frequent late *** review summarizes the new advances in molecular diagnosis and therapy of HCC,based on the recent novel biomarkers and new therapeutic strategies for HCC,including alpha-fetoprotein-L3,glypican-3,heat shock protein 90,dickkopf WNT signaling pathway inhibitor 1,paraoxonase 1,highly up-regulated in liver ***,epigenetic regulation,signal pathway,cellular and molecular targets for the immunotherapy,tumor microenviroment and genome sequencing analysis may serve as the molecular expression signatures in clinical *** promising new treatment strategy of HCC,targeting molecular therapy based on the restoration of tumor suppressor genes lost and inhibition of oncogenic genes is *** new clinical trials for other molecular-targeted agents,including pembrolizumab,nivolumab,tivantinib,lenvatinib,cabozantinib,and ramucirumab,are ongoing in ***,anti-HBV drugs display an amazing therapy for HBV-related *** future,the global determination of more biomarkers may provide new insights into the diagnosis of *** importantly,the diagnostic markers should be used to trace patient's follow-up disease progression,guiding doctors to judge and prescribe drugs for status of an illness,prognosis and other processes.

关键词： molecular diagnosis therapy hepatocellular carcinoma hepatitis B virus hepatitis C virus

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Accuracy of endoscopic ultrasound-guided needle aspiration specimens for molecular diagnosis of non-small-cell lung carcinoma

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World Journal of Clinical Cases 2020年第21期8卷 5139-5148页

作者： Wei Su Xiang-Dong Tian Peng Liu De-Jun Zhou Fu-Liang Cao Department of Endoscopy Tianjin Medical University Cancer Institute and HospitalNational Clinical Research Center for CancerKey Laboratory of Cancer Prevention and TherapyTianjin’s Clinical Research Center for CancerTianjin 300060China

BACKGROUND Endoscopic ultrasonography-guided fine-needle aspiration(EUS-FNA)and endobronchial ultrasound-guided transbronchial needle aspiration(EBUS-TBNA)are highly sensitive for diagnosing and staging lung *** recent years,targeted therapy has shown great significance in the treatment of non-small cell lung carcinoma(NSCLC).Using these minimally invasive techniques to obtain specimens for molecular testing will provide patients with a more convenient diagnostic *** To evaluate the feasibility and accuracy of tissue samples obtained using EUSFNA and EBUS-TBNA for molecular diagnosis of *** A total of 83 patients with NSCLC underwent molecular testing using tissues obtained from EUS-FNA or EBUS-TBNA at the Tianjin Medical University Cancer Hospital from January 2017 to June *** enrolled patients underwent chest computed tomography or positron emission tomography/computed tomography prior to *** detected abnormal expression of EGFR,KRAS,MET,HER2,ROS1 and anaplastic lymphoma kinase *** patients failed to complete molecular testing due to insufficient tumor *** clinical features,puncture records,molecular testing results and targeted treatment in the remaining 81 patients were *** In a total of 99 tissue samples obtained from 83 patients,molecular testing was successfully completed in 93 samples with a sample adequacy ratio of 93.9%(93/99).Biopsy samples from two patients failed to provide test results due to insufficient tumor *** the remaining 81 patients,62 cases(76.5%)were found to have adenocarcinoma,11 cases(13.6%)had squamous cell carcinoma,3 cases(3.7%)had adenosquamous carcinoma and 5 cases(6.2%)had NSCLC-not otherwise *** results of molecular testing showed EGFR mutations in 21 cases(25.9%),KRAS mutations in 9 cases(11.1%),ROS-1 rearrangement in 1 case(1.2%)and anaplastic lymphoma kinase-positive in 5 cases(6.2%).Twentyfour patients with positive results received targeted ther

关键词： Endobronchial ultrasound-guided transbronchial needle aspiration Endoscopic ultrasonography-guided fine-needle aspiration Non-small cell lung carcinoma molecular diagnosis Targeted therapy

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Dawn of ocular gene therapy:implications for molecular diagnosis in retinal disease

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Science China(Life Sciences) 2013年第2期56卷 125-133页

作者： ZANEVELD Jacques WANG Feng WANG Xia CHEN Rui Human Genome Sequencing Center Department of Molecular and Human GeneticsBaylor College of Medicine

Personalized medicine aims to utilize genomic information about patients to tailor treatment. Gene replacement therapy for ra- re genetic disorders is perhaps the most extreme form of personalized medicine, in that the patients＇ genome wholly determines their treatment regimen. Gene therapy for retinal disorders is poised to become a clinical reality. The eye is an optimal site for gene therapy due to the relative ease of precise vector delivery, immune system isolation, and availability for monitoring of any potential damage or side effects. Due to these advantages, clinical trials for gene therapy of retinal diseases are currently underway. A necessary precursor to such gene therapies is accurate molecular diagnosis of the mutation（s） underlying disease. In this review, we discuss the application of Next Generation Sequencing （NGS） to obtain such a diagnosis and identify disease causing genes, using retinal disorders as a case study. After reviewing ocular gene therapy, we discuss the application of NGS to the identification of novel Mendelian disease genes. We then compare current, array based mutation detection methods against next NGS-based methods in three retinal diseases： Leber＇s Congenital Amaurosis, Retinitis Pigmentosa, and Stargardt＇s disease. We conclude that next-generation sequencing based diagnosis offers several advantages over array based methods, including a higher rate of successful diagnosis and the ability to more deeply and efficiently assay a broad spectrum of mutations. However, the relative difficulty of interpreting sequence results and the development of standardized, reliable bioinforrnatic tools remain outstanding concerns. In this review, recent advances NGS based molecular diagnoses are discussed, as well as their implications for the development of personalized medicine.

关键词： next-generation sequencing (NGS) retinal disease molecular diagnosis Leber's Congenital Amarosis (LCA) Retinitus Pigmentosa (RP) Stargardt disease APEX personal medicine

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molecular diagnosis of Chagas disease:a systematic review and meta-analysis

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Infectious Diseases of Poverty 2023年第5期12卷 93-93页

作者： Guillermo Pascual-Vázquez Montserrat Alonso-Sardón Beatriz Rodríguez-Alonso Javier Pardo-Lledías Angela Romero Alegría Pedro Fernández-Soto Juan Luis Muñoz Bellido Antonio Muro Moncef Belhassen-García Infectious and Tropical Diseases Group (E-INTRO) Biomedical Research Institute of Salamanca (IBSAL) Tropical Diseases Research Center of the University of Salamanca (CIETUS) Faculty of Pharmacy University of Salamanca Salamanca Spain Area of Preventive Medicine Epidemiology and Public Health Department of Biomedical and Diagnostic Sciences Faculty of Medicine E-INTRO IBSAL CIETUS University of Salamanca Salamanca Spain Internal Medicine Service University Health Care Complex of Salamanca (CAUSA) E-INTRO IBSAL CIETUS Salamanca Spain Internal Medicine Department Hospital Marqués de Valdecilla University of Cantabria IDIVAL (Valdecilla Research Institute) Santander Spain Internal Medicine Service CAUSA. E-INTRO IBSAL CIETUS Salamanca Spain Infectious and Tropical Diseases Group (E-INTRO) IBSAL. CIETUS. Faculty of Pharmacy University of Salamanca Salamanca Spain Microbiology and Parasitology Service CAUSA IBSAL CIETUS CSIC Department of Biomedical and Diagnostic Sciences University of Salamanca Salamanca Spain Internal Medicine Service. Infectious Diseases Section CAUSA IBSAL CIETUS University of Salamanca Salamanca Spain

Background The complexity of the Chagas disease and its phases is impossible to have a unique test for both phases and a lot of different epidemiological ***,serology is the reference standard technique;occasionally,results are inconclusive,and a different diagnostic technique is *** guidelines recommend molecular testing.A systematic review and meta-analysis of available molecular tools/techniques for the diagnosis of Chagas disease was performed to measure their heterogeneity and efficacy in detecting Trypanosoma cruzi infection in blood *** A systematic review was conducted up to July 27,2022,including studies published in international *** and exclusion criteria were defined to select eligible *** were extracted and presented according to PRISMA 2020 *** quality was assessed using Quality Assessment of Diagnostic Accuracy Studies-2(QUADAS-2).A random-effects model was used to calculate pooled sensitivity,specificity,and diagnostic odds ratio(DOR).Forest plots and a summary of the receiving operating characteristics(SROC)curves displayed the *** was determined by I^(2)and Tau^(2)statistics and P *** plots and Deek's test were used to assess publication bias.A quantitative meta-analysis of the different outcomes in the two different clinical phases was *** We identified 858 records and selected 32 *** pertained to endemic countries and nonendemic areas with adult and paediatric *** sample sizes ranged from 17 to 708 *** were no concerns regarding the risk of bias and applicability of all included studies.A positive and nonsignificant correlation coefficient(S=0.020;P=0.992)was obtained in the set of studies that evaluated diagnostic tests in the acute phase population(ACD).A positive and significant correlation coefficient(S=0.597;P<0.000)was obtained in the case of studies performed in the chronic phase population(

关键词： Chagas disease Trypanosoma cruzi molecular diagnosis Polymerase chain reaction Loop-mediated isothermal amplification

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Impact of next-generation sequencing on molecular diagnosis of inherited non-syndromic hearing loss

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Journal of Otology 2014年第3期9卷 122-125页

作者： Xue Gao Pu Dai Department of Otolaryngology Head and Neck SurgeryPLA General Hospital Department of Otolaryngology Hainan Branch of PLA General Hospital Department of Otolaryngology the Second Artillery General Hospital

Hearing loss is one of the most common birth defects,with inherited genetic defects play an important role,contributing to about 60%of deafness occurring in ***,hearing impairment is genetically heterogeneous,with both common and rare forms occurring due to mutations in estimated 500 *** to the large number and presumably low mutation frequencies of those genes,it would be highly expensive and time-consuming to address this issue by conventional gene-by-gene Sanger ***-generation sequencing is a revolutionary technology that allows the simultaneous screening of mutations in a large number of *** is cost effective compared to classical strategies of linkage analysis and direct sequencing when the number or size of genes is large,and thus has become a highly efficient strategy for identifying novel causative genes and mutations involved in heritable *** this review, we describe major NGS methodologies currently used for genetic disorders and highlight applications of these technologies in studies of molecular diagnosis and the discovery of genes implicated in non-syndromic hearing loss.

关键词： Next-generation sequencing molecular diagnosis Inherited non-syndromic hearing loss Whole genome sequencing Whole exome sequencing

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Diagnostic utility of microRNA profiles in cavitatory and noncavitatory pulmonary tuberculosis:Research protocol

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World Journal of Experimental Medicine 2025年第1期15卷 88-95页

作者： Swathy Moorthy Emmanuel Bhaskar Shivakumar Singh Santhi Silambanan Department of General Medicine Sri Ramachandra Institute of Higher Education and ResearchChennai 600116Tamil NāduIndia Department of Medicine Railway HospitalPerumburChennaiChennai 600023Tamil NāduIndia Department of Biochemistry Sri Ramachandra Institute of Higher Education and ResearchChennai 600116Tamil NāduIndia

BACKGROUND Tuberculosis(TB)is a common infection causing huge morbidity and mortality to *** analytical methods used in diagnosing TB are not sensitive in paucibacillary infections and also require trained technical *** are stable in serum and other body fluids,and hold great potential in the diagnosis of *** To analyze the dysregulated microRNA profiles among patients with cavitatory and non-cavitatory pulmonary *** The prospective study will be conducted in a tertiary care center in *** patients with newly diagnosed pulmonary TB will be *** will be two groups:Patients with sputum positive pulmonary TB with cavity and without cavity(group1),and apparently healthy individuals(group 2).The participants will undergo sputum examination,Xpert Mycobacterium TB complex/resistance to rifampin(Mtb/RIF)assay,chest X-ray,and blood investigations and serum microRNA *** approval has been *** informed consent will be *** statistical analyses will be *** MicroRNAs will be correlated with sputum positivity,Xpert Mtb/RIF assay,radiological involvement,inflammatory markers,and course of the disease among cases and *** MicroRNAs could serve as potential diagnostic biomarkers in diagnostically challenging TB patients.

关键词： Imaging Inflammatory marker MicroRNA molecular diagnosis Pulmonary tuberculosis CBNAAT

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SARS-CoV-2 induced myocarditis:Current knowledge about its molecular and pathophysiological mechanisms

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BIOCELL 2022年第8期46卷 1779-1788页

作者： DOMENICO MARIA CARRETTA MARINA DI DOMENICO ROBERTO LOVERO ROBERTO ARRIGONI ANGELIKA ELZBIETA WEGIERSKA MARIAROSARIA BOCCELLINO ANDREA BALLINI IOANNIS ALEXANDROS CHARITOS LUIGI SANTACROCE AOU Policlinico Consorziale di Bari-Ospedale Giovanni XXIII Cardiology UnitPoliclinico University Hospital of BariBari70124Italy Department of Precision Medicine University of Campania Luigi VanvitelliNaples80138Italy AOU Policlinico Consorziale di Bari-Ospedale Giovanni XXIII Clinical Pathology UnitPoliclinico University Hospital of BariBari70124Italy CNR Institute of Biomembranes Bioenergetics and Molecular Biotechnologies(IBIOM)Bari70125Italy Department Interdisciplinary of Medicine University of Bari Aldo MoroBari70124Italy School of Medicine University of Bari Aldo MoroBari70124Italy Department of Emergency and Urgency National Poisoning CentreRiuniti University Hospital of FoggiaFoggia71122Italy

The existence of an inflammatory process in the heart muscle,related to a progressive worsening of myocardial function,different etiopathogenetic mechanisms concur and often overlap,thus making the diagnosis and the therapeutic approach *** the COVID-19 pandemic progresses,the effects of the disease on the organ systems and in particular on the cardiovascular system are becoming more and more *** involvement is a well-known event with a high percentage of findings in the heart’s magnetic field,even in asymptomatic *** are numerous uncertainties regarding their evolution,in the long and short term,due not only to a difficult to determine the varied clinical expression and the rarely performed intramyocardial biopsy which additionally presents diagnostic problems but also in part to different clinical ***,the new SARS-CoV-2 virus that uses the angiotensin converting enzyme 2(ACE2)which is present at high levels in myocardial cells as its entrance it can create even severe heart *** pathophysiology in all of these cases can involve multiple immune and non-immune mechanisms within organs and vessels and can be occur in the clinical *** mechanisms of direct and indirect myocardial infarction in patients with COVID-19 include additional lesion and oxygen-rich and generalized inflammation response with myocardial immune hyperactivity(myocarditis).Therefore,these can occur through the excessive release of cytokines,the presence of thrombocytopenia,endocrine damage,heart failure,arrhythmias and *** can show average signs of myocardial damage,and some develop spontaneous cardiac complications,such as heart failure,arrhythmias and,rarely,rare cardiogenic *** in all of these may involve multiple mechanisms within the cytokine cephalic membrane,endocrine damage and *** diagnosis of this myocardial injuri is mainly based on the myocardial enzyme *** viewpoint paper

关键词： Viruses Infections SARS-CoV-2 Pandemics Myocarditis molecular diagnosis

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A PCR and RFLP-based molecular diagnostic algorithm for visceral leishmaniasis

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Asian Pacific Journal of Tropical Medicine 2020年第2期13卷 62-70页

作者： Natalia Souza de Godoy Manoel Sebastiao da Costa Lima-Junior Jose Angelo Lauletta Lindoso Vera Lucia Pereira-Chioccola Thelma Suely Okay Lucia Maria Almeida Braz Laboratorio de Parasitologia Médica Departamento de Moléstias Infecciosas e Parasitárias do Hospital das Clinicas HCFMUSPFaculdade de MedicinaUniversidade de Sao PauloSao PauloBrazil Laboratorio de Imunopatologia e Biologia molecular-Instituto Aggeu Magalhaes/IAM-FIOCRUZ RecifeBrazil Laboratorio de Soroepidemiologia e Imunobiologia-FMUSP Sao PauloBrazil Laboratorio de Biologia molecular de Parasitas e Fungos-Instituto Adolfo Lutz Sao PauloBrazil Laboratorio de Parasitologia-Instituto de Medicina Tropical de Sao Paulo-USP Sao PauloBrazil

Objective:To determine an algorithm for molecular diagnosis of visceral leishmaniasis(VL)by kinetoplast DNA(kDNA)(RV1/RV2)and internal transcriber spacer(ITS1)(LITSR/L5.8 S)polymerase chain reaction(PCR),complemented by ITS 1 PCR restriction fragment length polymorphism(RFLP),using peripheral blood or bone marrow aspirate from patients with suspected ***:Biological samples were submitted to the gold standard for the diagnosis of VL and molecular diagnosis represented by ITS 1 PCR,kDNA PCR,and ITS 1 PCR *** samples were obtained from seven groups:groupⅠ,82 samples from patients with confirmed VL;groupⅡ,16 samples from patients under treatment for VL;groupⅢ,14 samples from dogs with canine visceral leishmaniasis(CVL);groupⅣ,a pool of six experimentally infected sandflies(Lutzomya longipalpis);group V,18 samples from patients with confirmed tegumentary leishmaniasis(TL)and groupsⅥandⅦwere from control groups without ***:The following gold standard and molecular examination results were obtained for each of the seven groups:groupⅠ:parasitologic and immunochromatographic tests showed a sensitivity of 76.3%(61 of 80)and 68.8%(55 of 80),respectively,and a sensitivity of 97.6%(80 of 82)and 92.7%(76 of 82)by ITS1 and kDNA PCR,*** ITS1 PCR RFLP(HaeⅢ)analysis of the 80 positive samples,52.5%(42 of 80)generated three fragments of 180,70,and 50 bp,corresponding to the pattern of Leishmania infantum infantum;groupⅡ:negative for the parasitologic methods and positive for IrK39(100%,16 of 16),presented 12.5%(2 of 16)of positivity by ITS 1 PCR and 25.0%(4 of 16)by kDNA PCR;groupⅢ:positive in the parasitologic and serologic tests(100%,14 of 14),presented 85.7%(12 of 14)of positivity by ITS1 PCR and kDNA ***1 PCR RFLP showed that 83.3%(10 of 12)of the canine samples contained parasites with profiles similar to ***;groupⅣpresented amplifications by ITS1 PCR and kDNA ***1 PCR products were analyzed by RFLP,generating a profile similar to

关键词： Leishmania infantum molecular diagnosis Visceral leishmaniasis PCR RFLP

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