Angiotensin-converting Enzyme Gene Insertion/Deletion Polymorphism in Children with Henoch-Schonlein Purpua Nephritis

This study investigated the relationship between angiotensin-converting enzyme (ACE) gene insertion/deletion polymorphism and the occurrence, severity, prognosis of HSPN. The polymorphism of ACE gene in 103 HSPN cases and 100 healthy children was studied by using the polymerase chain reactions (PCR). Its relation to the clinical manifestation, pathological classification and prognosis of HSPN was analyzed accordingly. The results showed that: (1) there was a significantly higher frequency for DD genotype in HSPN children (P<0.01); (2) DD genotype was more frequently seen in HSPN children with gross hematuria and massive proteinuria (P<0.05), while DI genotype was more common in HSPN children group with renal insufficiency (P<0.05); (3) although mesangial proliferative lesion was most frequently observed in 21 biopsied HSPN children, and DD genotype frequency was still higher in children with severe pathology (Class Ⅲ Ⅳ); (4)II genotype was significantly frequent in HSPN children with complete remission in the follow-up of 32 HSPN children. It was concluded that the deletion allele of ACE gene might play a role, at least to some extent, in the occurrence, deterioration and progression in juvenile HSPN.

A new insertion sequence for incremental Delaunay triangulation

Incremental algorithm is one of the most popular procedures for constructing Delaunay triangulations （DTs）. However, the point insertion sequence has a great impact on the amount of work needed for the construction of DTs. It affects the time for both point location and structure update, and hence the overall computational time of the triangulation algorithm. In this paper, a simple deterministic insertion sequence is proposed based on the breadth-first-search on a Kd-tree with some minor modifications for better performance. Using parent nodes as search-hints, the proposed insertion sequence proves to be faster and more stable than the Hilbert curve order and biased randomized insertion order （BRIO）, especially for non-uniform point distributions over a wide range of benchmark examples.

Insertion Sequence-Dependent <i>OmpK</i>36 Mutation Associated Ertapenem Resistance in Clinical <i>Klebsiella pneumoniae</i>

Extended-spectrum β-lactamases (ESBLs) and/or AmpC enzymes combined with deficiency of porins OmpK35 and OmpK36 are important for the development of carbapenem-resistant Klebsiella pneumoniae. We characterized the clinical K. pneumoniae human isolates and investigated the effect of meropenem induction on the ompK35 and ompK36 mutation to develop carbapenem resistance from six carbapenem-susceptible ESBL-producing K. pneumoniae strains. 163 clinical K. pneumoniae isolates were grouped mostly into the ESBL + AmpC (44.2%) and ESBL (42.9%) phenotypes. The resistance rate differed between cephalosporins (52.1% for cefepime - 97.5% for cefotaxime) and carbapenems (16% for meropenem - 28.2% for imipenem) (P blaTEM, blaSHV, blaCTX-M-3-like, and blaCTX-M-14-like of AmpA β-lactamase genes and blaDHA and blaCMY of AmpC β-lactamase genes. Compared to all 163 clinical isolates, the 56 carbapenem-resistant isolates carried less frequently of blaTEM, blaCTXM-14-like, and blaCTXM-3-like and more frequently of blaDHA-1 and blaCMY-2. The carbapenem-resistant isolates differed in prevalence against imipenem, ertapenem, and meropenem and lacked OmpK35 more frequently than OmpK36, but abnormal PCR amplicons were detected fewer in the Omp K35-deficient group than in the OmpK36-deficient group (32.5% vs. 68.4%, respectively). The carbapenem-resistant isolate mostly carried blaDHA (91.1%) and three isolates carried blaKPC-2. Following induction with meropenem insertion sequences in ompK36, not ompK36, were identified as IS5 for KP08, IS1 for KP15, and IS903 for KP16 isolates. OmpK36 deficiency increased resistance to ertapenem, but not imipenem and meropenem. Clinical isolates belonged mainly to ESBL + AmpC group and ESBL group with difference in resistance to cephalosporins and carbapenems, the bla genes. Carbapenem resistant isolates lacked OmpK35 expression, than the OmpK36 expression, Meropenem induction developed the carbapenem resistant isolates with insertion of different insertion sequences in ompK36, not ompK35.

Association study between the angiotensin converting enzyme gene insertion/deletion polymorphism and Qinghai Han Chinese with congenital heart disease

Objective: The aim of this work is to determine whether the angiotensin converting enzyme(ACE) I/D(insertion/deletion) polymorphism is associated with the susceptibility to congenital heart disease(CHD) in the Qinghai Han Chinese. Methods: This study enrolled 59 CHD patients and 193 CHD controls from Qinghai Cardiovascular Diseases Vocational Hospital. Blood samples were collected from each of the patient and control groups. The ACE-I/D polymorphism was detected by polymerase chain reaction(PCR). Results: The genotype frequencies of ACE-I/D for II, ID, DD in patients and controls were 0.475, 0.441, 0.085 and 0.430, 0.446, 0.124, respectively. The allelic frequencies of I and D were 0.650, 0.350 and 0.695, 0.305, respectively. The OR of ID, DD and D alleles relative to II for CHD was 1.116(0.604-2.060), 1.619(0.564-4.648) and 1.211(0.777-1.889). There was no significant difference of the genotypic and the allelic frequencies in ACE-I/D polymorphism between the patient and control groups. Conclusion: There is no relation between ACE-I/D polymorphism and CHD in current Qinghai Han Chinese.

Correlation between the Insertion/Deletion Mutations of Prion Protein Gene and BSE Susceptibility and Milk Performance in Dairy Cows

Objective To investigate the 23 bp and 12 bp insertion/deletion(indel)mutations within the bovine prion protein(PRNP)gene in Chinese dairy cows,and to detect the associations of two indel mutations with BSE susceptibility and milk performance.Methods Based on bovine PRNP gene sequence,two pairs of primers for testing the 23 bp and 12 bp indel mutations were designed.The PCR amplification and agarose electrophoresis were carried out to distinguish the different genotypes within the mutations.Moreover,based on previous data from other cattle breeds and present genotypic and allelic frequencies of two indels mutations in this study,the corrections between the two indel mutations and BSE susceptibility were tested,as well as the relationships between the mutations and milk performance traits were analyzed in this study based on the statistical analyses.Results In the analyzed Chinese Holstein population,the frequencies of two"del"alleles in 23 bp and 12 bp indel muations were more frequent.The frequency of haplotype of 23del-12del was higher than those of 23del-12ins and 23ins-12del.From the estimated r2and D’values,two indel polymorphisms were linked strongly in the Holstein population(D’=57.5%,r2=0.257).Compared with the BSE-affected cattle populations from the reported data,the significant differences of genotypic and allelic frequencies were found among present Holstein and some BSE-affected populations(P<0.05 or P<0.01).Similarly,there were significant frequency distribution differences of genotypes and alleles among Chinese Holstein and several previous reported healthy dairy cattle(P<0.05 or P<0.01).Moreover,association of genotype and combined genotypes of two indel polymorphisms with milk performance and resistant mastitis traits were analyzed in Holstein population,but no significant differences were found(P>0.05).Conclusions These observations revealed that the influence of two indel mutations within the bovine PRNP gene on BSE depended on the breed and they did not affect the milk production traits,which layed the foundation for future selection of resistant animals,and for improving health conditions for dairy breeding against BSE in China.

Extended role for insertion sequence elements in the antibiotic resistance of Bacteroides

The Bacteroides species are important micro-organisms, both in the normal physiology of the intestines and as frequent opportunistic anaerobic pathogens, with a deeply-rooted phylogenetic origin endowing them with some interesting biological features. Their prevalence in anaerobic clinical specimens is around 60%-80%, and they display the most numerous and highest rates of antibiotic resistance among all pathogenic anaerobes. In these antibiotic resistance mechanisms there is a noteworthy role for the insertion sequence(IS) elements, which are usually regarded as representatives of ‘selfish' genes; the IS elements of Bacteroides are usually capable of up-regulating the antibiotic resistance genes. These include the cep A(penicillin and cephalosporin), cfx A(cephamycin), cfi A(carbapenem), nim(metronidazole) and erm F(clindamycin) resistance genes. This is achieved by outwardoriented promoter sequences on the ISs. Although some representatives are well characterized, e.g., the resistance gene-IS element pairs in certain resistant strains, open questions remain in this field concerning a better understanding of the molecular biology of theantibiotic resistance mechanisms of Bacteroides, which will have clinical implications.

Complicated expansion trajectories of insertion sequences and potential association with horizontal transfer of Wolbachia DNA

DEAR EDITOR,Insertion sequences(ISs) are the simplest structural transposable elements(TEs) in prokaryotes, consisting only of a transposase coding sequence and its bilateral short terminal inverted repeats. Due to their gradually streamlined genomic construction, TEs rarely exist in the genomes of obligate endosymbionts. However, TE content, especially ISs.

Machine-learning-aided precise prediction of deletions with next-generation sequencing

When detecting deletions in complex human genomes,split-read approaches using short reads generated with next-generation sequencing still face the challenge that either false discovery rate is high,or sensitivity is low.To address the problem,an integrated strategy is proposed.It organically combines the fundamental theories of the three mainstream methods(read-pair approaches,split-read technologies and read-depth analysis) with modern machine learning algorithms,using the recipe of feature extraction as a bridge.Compared with the state-of-art split-read methods for deletion detection in both low and high sequence coverage,the machine-learning-aided strategy shows great ability in intelligently balancing sensitivity and false discovery rate and getting a both more sensitive and more precise call set at single-base-pair resolution.Thus,users do not need to rely on former experience to make an unnecessary trade-off beforehand and adjust parameters over and over again any more.It should be noted that modern machine learning models can play an important role in the field of structural variation prediction.

Identification of transgene insertions in two genetically modified soybeans using high throughput next generation sequencing

Genetically modified(GM) organisms are widely adopted. However, their safety assessments and control are still of special concern to the public. Identifying and localizing transgene insertion is an essentially prerequisite step. In this study, 2 independent transgene soybean lines were selected(LB4-AtDCGS-1-20-5-2 and CGS-ZG11) as typical cases. Both lines contained expression cassette of At-DCGS that encoding a feedback-insensitive cystathionine gamma-synthase to produce higher level methionine(Met). LB4-AtDCGS-1-20-5-2 was whole genome sequenced with one paired-end 500 bp library and two mate-paired 1 kb and 2 kb libraries using Illumina HiSeq sequencing platform. CGS-ZG11 was sequenced with only one paired-end 500 bp library. Both genomes were assembled,and 2 scaffold sequences(1 for each line) were screened out by aligning with transgene.Then the transgene insertion and its flanking regions in soybean genome were further identified and confirmed by PCR cloning and Sanger sequencing. Results showed that these 2 transgene lines had single copy of inserted transgene. Their transgene insertion contents were identified, which facilitates further safety assessment. These results indicated that genome assembly using high throughput sequencing is a powerful tool for identifying transgene insertions, even with limited knowledge.

PCR analysis of Yq microdeletions in infertile males, a study from South India

AIM: To estimate the frequency of microdeletions in the long arm of Y-chromosome of 20 infertile males from South India. METHODS: Polymerase chain reaction (PCR) amplification using Y-specific STS of azoospermia factor (AZF) regions i.e., SY 84 for AZFa, SY 127 for AZFb and SY 254 for AZFc. RESULTS: Of the 20 infertile subjects 3 (15 %), one azoospermic and two oligozoospermic, showed microdeletions in the AZF region of Y-chromosome. CONCLUSION: The frequency of deletions involving AZF region of the Y-chromosome is 15 % in azoospermic and severely oligozoospermic infertile men. PCR amplification of AZF locus is useful for the diagnosis of microdeletions in the Y-chromosome.

Novel approach to identifying the hepatitis B virus pre-S deletions associated with hepatocellular carcinoma

AIM: To develop a novel non-sequencing method for the detection of hepatitis B virus (HBV) pre-S deletion mutants in HBV carriers.

微课-INSERT AND DELETE的使用的设计与制作

随着现代信息科学技术的不断发展,一种新型的教学模式——"微课"开始走进学生的生活,"微课"以其潜在的优势在学生的学习生活中发挥了积极作用。与此同时在数据库中对数据库的录入和删除尤为重要,因此我们结合微课的使用和SQL中的INSERT INTO...VALUES、delete的作用,制作和设计了该微课,本微课主要针对INSERT INTO...VALUES和delete的定义和特点以及微课设计及制作进行了介绍,生动形象的展现了数据的录入和删除的作用。

高血压患者ACE基因Insertion/Deletion多态性中的罕见突变1例

高血压是最强的心血管危险因素之一,目前我国高血压的患病人数已达约2.45亿[1]。《中国心血管健康与疾病报告2021》数据显示,我国≥18岁成人高血压知晓率41.0%,治疗率34.9%,控制率仅11.0%。在高血压的用药治疗方面,由于用药种类繁多,且存在药物反应的个体差异,通常会导致抗高血压药物的疗效不佳或不良反应[2]。2015年,国家卫生和计划生育委员会发布的《药物代谢酶和药物作用靶点基因检测技术指南(试行)》[3]。

Construction of Mutant Populations by T-DNA Insertion for Functional Genomic Study in Cotton

The use of transfer DNA(T-DNA)as amutagen has been developed for tagging genes inmany crops,and results showed that T-DNAinsertion is a random event,and that theinserted genes are stable through multiplegenerations.Through sequencing PCR-amplifiedfragments adjacent to the inserted elements,wecan construct the T-DNA flanking database,which would be useful for cloning the genestagged by T-DNA.

De novel heterozygous copy number deletion on 7q31.31-7q31.32 involving TSPAN12 gene with familial exudative vitreoretinopathy in a Chinese family

AIM:To investigate the genetic and clinical characteristics of patients with a large heterozygous copy number deletion on 7q31.31-7q31.32.METHODS:A family with familial exudative vitreoretinopathy(FEVR)phenotype was included in the study.Whole-exome sequencing(WES)was initially used to locate copy number variations(CNVs)on 7q31.31-31.32,but failed to detect the precise breakpoint.The long-read sequencing,Oxford Nanopore sequencing Technology(ONT)was used to get the accurate breakpoint which is verified by quantitative real-time polymerase chain reaction(QPCR)and Sanger Sequencing.RESULTS:The proband,along with her father and younger brother,were found to have a heterozygous 4.5 Mb CNV deletion located on 7q31.31-31.32,which included the FEVRrelated gene TSPAN12.The specific deletion was confirmed as del(7)(q31.31q31.32)chr7:g.119451239_123956818del.The proband exhibited a phase 2A FEVR phenotype,characterized by a falciform retinal fold,macular dragging,and peripheral neovascularization with leaking of fluorescence.These symptoms led to a significant decrease in visual acuity in both eyes.On the other hand,the affected father and younger brother showed a milder phenotype.CONCLUSION:The heterozygous CNV deletion located on 7q31.31-7q31.32 is associated with the FEVR phenotype.The use of long-read sequencing techniques is essential for accurate molecular diagnosis of genetic disorders.

Hemizygous deletion in the OTC gene results in ornithine transcarbamylase deficiency:A case report

BACKGROUND Ornithine transcarbamylase deficiency(OTCD)is a common ornithine cycle disorder,and OTC gene variation is the main pathogenic factor of this disease.This study explored and validated a variant in the OTC gene.CASE SUMMARY The neonate exhibited high blood ammonia,lactic acid,and homocysteine levels on the fifth day after birth.A novel deletion variant in the OTC gene[NM_000531.5,c.970_979delTTCCCAGAGG,p.Phe324GlnfsTer16]was uncovered by exome sequencing.The variant caused a protein-coding frameshift and resulted in early translation termination at the 16th amino acid after the variant site.CONCLUSION Our results provide a novel pathogenic variant in OTC and related clinical features for further OTCD screening and clinical consultation.

Efficacy of EGFR-TKI sequential therapy in patients with EGFR exon 19 insertion-positive non-small-cell lung cancer:A case report

BACKGROUND Insertions in exon 19 in the epidermal growth factor receptor gene(EGFR)is a rarely seen mutation in non-small cell lung cancer.These patients have been effectively treated with sequential EGFR tyrosine kinase inhibitors(TKIs).CASE SUMMARY Here,we presented a case of non-small cell lung cancer,stage IIIB,with EGFR exon 19 insertion mutation as detected in the right lower lobe by next-generation sequencing.The patient was sequentially treated with first,second,and thirdgeneration EGFR TKIs after the surgical operation.The overall survival of the patient was 21.3 mo.There was no dynamic analysis of drug resistance mechanisms in targeted therapy.CONCLUSION This case emphasized the importance of following the guidelines.In patients with EGFR mutations,repeated and dynamic next-generation sequencing monitoring is necessary to prescribe a personalized treatment plan.

Insertion sequence transposition activates antimycobacteriophage immunity through an Isr2-silenced lipid metabolism gene island

Insertion sequences(ISs)exist widely in bacterial genomes,but their roles in the evolution of bacterial antiphage defense remain to be clarified.Here,we report that,under the pressure of phage infection,the IS1o96 transposition of Mycobacterium smegmatis into the Isr2 gene can occur at high frequencies,which endows the mutant mycobacterium with a broad-spectrum antiphage ability.Lsr2 functions as a negative regulator and directly silences expression of a gene island composed of 11 lipid metabolism-related genes.The complete or partial loss of the gene island leads to a significant decrease of bacteriophage adsorption to the mycobacterium,thus defending against phage infection.Strikingly,a phage that has evolved mutations in two tail-filament genes can re-escape from the Isr2 inactivation-triggered host defense.This study uncovered a new signaling pathway for activating antimycobacteriophage immunity by Is transposition and provided insight into the natural evolution of bacterial antiphage defense.

Lack of association between ADRA2B-4825 gene insertion/deletion poly- morphism and migraine in Chinese Han population

Objective The present study aimed to estimate the association between susceptibility to migraine and the 12nucleotide insertion/deletion （indel） polymorphism in promoter region ofα 2B -adrenergic receptor gene （ADRA2B）.Methods A case-control study was carried out in Chinese Han population,including 368 cases of migraine and 517 controls.Genomic DNA was extracted from blood samples,and DNA fragments containing the site of polymorphism were amplified by PCR.Data were adjusted for sex,age,migraine history and family history,and analyzed using a logistic regression model.Results There was no association between indel polymorphism and migraine,at either the allele or the genotype level.Conclusion These findings do not support a functional significance of ADRA2B indel polymorphism at position-4825 relative to the start codon in the far upstream region of the promoter in the present migraine subjects.

Identification of selenocyst-eine insertion sequence(SECIS) element in eukaryotic selenoproteins by RNA Draw program

The computer program RNA Draw was used to identify the secondary structures in the 3’untranslated regions (3’UTRs) of the mRNAs from 46 eukaryotic seleno-proteins among 7 species. The program found one or two possible SECIS elements in these selenoproteins. The SECIS element consists of a stem-loop or hairpin structure with three conserved sequences of AUGA-(A)AA-GA. SECIS element was not found by the RNA Draw program in randomly selected non-selenoproteins. The results showed that SECIS element is the unique character of the genes ofeukaryotic selenoproteins. Thus it is possible to use RNA Draw to search the SECIS elements in gene bank for potential new selenoproteins.