TRAPR: R Package for Statistical Analysis and Visualization of RNA-Seq Data

High-throughput transcriptome sequencing, also known as RNA sequencing (RNA-Seq), is a standard technology for measuring gene expression with unprecedented accuracy. Numerous bioconductor packages have been developed for the statistical analysis of RNA-Seq data. However, these tools focus on specific aspects of the data analysis pipeline, and are difficult to appropriately integrate with one another due to their disparate data structures and processing methods. They also lack visualization methods to confirm the integrity of the data and the process. In this paper, we propose an R-based RNA-Seq analysis pipeline called TRAPR, an integrated tool that facilitates the statistical analysis and visualization of RNA-Seq expression data. TRAPR provides various functions for data management, the filtering of low-quality data, normalization, transformation, statistical analysis, data visualization, and result visualization that allow researchers to build customized analysis pipelines.

A rare case of tick infestation of the eyelid: case report and literature review / Um caso raro de infestação de carrapatos da pálpebra: relato de caso e revisão da literatura

ABSTRACT This article presents a case of tick infestation of the lower eyelid by a previously unreported species. A 71-year-old male presented with a tick attached to the lower eyelid. The tick was identified morphologically, and then molecularly via polymerase chain reaction (PCR) and sequencing of its DNA. In addition, a review of the literature relevant to the genera of ticks associated with infestation of the human eye is provided. The tick, which was in the nymphal developmental stage, was first identified according to taxonomic keys as Dermacentor sp. For complete species identification, 16s rDNA gene PCR and sequencing were performed, which showed that the tick was D. marginatus. Systematizing tick species could assist physicians in determining the potential for transmission of tick-borne human diseases.

RESUMO Este artigo apresenta um caso de infestação por carrapatos da pálpebra inferior por uma espécie previamente não declarada. Um homem de 71 anos de idade apresentou-se com um carrapato grudado na pálpebra inferior. O carrapato foi identificado morfologicamente, e, em seguida, uma estrutura molecular através de reacção em cadeia da polimerase (PCR) e a sequenciação do seu DNA. Além disso, uma análise da literatura pertinente aos gêneros de carrapatos associados à infestação do olho humano é fornecido. O carrapato, que estava em fase de desenvolvimento das ninfas, foi identificado pela primeira vez de acordo com chaves taxonômicas com o Dermacentor sp. Para identificação de espécies completa, gene 16S rDNA PCR e sequenciamento foram realizadas, que mostrou que o carrapato foi D. marginatus. Sistematizando espécie de carrapato poderia ajudar os médicos a determinar o potencial de transmissão de doenças humanas transmitidas por carrapatos.

Screening of TYR gene mutations and clinical classification in oculocutaneous albinism patients / 中华实验眼科杂志

Background Oculocutaneous albinism (OCA) is a hereditary disease of pigment absence in eyes,skin and hair due to the lack of congenital melanocyte.OCA is classified into 7 types based on different genetic mutations,and the mutation of tyrosinase (TYR) gene causes OCA type 1 (OCA1).OCA has obvious genetic heterogeneity and phenotypic heterogeneity.The molecular diagnosis of the mutant gene is helpful for the classification and molecular pathogenesis study of OCA.Objective This study was to screen the TYR mutation in OCA patients,and to analyze the association between the gene mutation type and clinical phenotype.Methods Ten patients with OCA were enrolled in Tianjin Ophthalmological Hospital from January 2011 to December 2014.The clinical and ocular manifestations of the patients were examined.Peripheral venous blood 3 ml was collected in the patients and their lineal relatives for the extraction of genomic DNA.Extracted DNA was amplified by PCR and the TYR gene sequence was analyzed,including all 5 exon coding sequence and exon 5 ' and 3' end and the non-coding region sequence of intron splicing in TYR gene.This study complied with Helsinki Declaration and the protocol was approved by Ethic Committee of Tianjin Eye Hospital.Informed consent was obtained from each subject.Results All the patients showed white or reddish hair and snow-white skin,and different degrees of pigment lack was seen in iris.The best corrected visual acuity of the patients was 0.05-0.2,and 3 patients complicated with nystagmus.Fundus findings showed a sunset-like change and dysplasia of macula.The TYR gene sequencing revealed that patient 1 was OCA1A subtype,with the compound heterozygous mutant of c.832C＞T (p.R278X) and c.1217C＞T (p.P406L),and his/her parents occurred the heterozygous mutation of exons P406L and R278X.The phenotype of the patient 1 was white hair and white iris.The patient 3 was OCA1B subtype,with the compound heterozygous mutations of c.1265G＞A (p.R422Q) and c.1217C＞T (p.P406L),showing an appearance of reddish brown hair and sallow iris.TYR gene mutant was not detected in other 8 patients.Conclusions The mutation of TYR gene is the main cause of OCA1 type.The phenotype of OCA1A subtype is no pigment in eyes and hair,and one of OCA1B subtype was obviously lessening of pigment.The difference of mutant genes of OCA is the cause of genetic and phenotypic heterogeneity.

A novel PAX6 mutation in a Chinese family with congenital aniridia / 中华实验眼科杂志

Background Aniridia is a rare congenital hereditary eye disease.Studies determined that PAX6 gene mutation is closely associated with congenital aniridia,but the mutation locus are varied.Objective This study was to identify virulence mutation locus of PAX6 gene of a Chinese family pedigree with autosomal dominant aniridia.Methods A Chinese family affected with autosomal dominant aniridia was collected and examined in Affiliated First Hospital of Zhengzhou University in August 2014.Periphery blood of 10 ml was collected from all the families and 100 unrelated health controls.The genomic DNA was extracted by standardized phenol-chloroform method,and all exons and splicing junctions of PAX6 were amplified by PCR.Real-time fluorescence quantitative PCR was performed to examine the relative expression of PAX6 mRNA in patients and normal phenotype families and heahh controls.This study protocol was approved by Ethic Committee of Affiliated First Hospital of Zhengzhou University and complied with Helsinki Declaration.Written informed consent was obtained from subjects or custodian before any medical examination.Results This Chinese family inclued 3 generations and 9 members,with a classic autosomal dominant inheritance mode.Five patients were found,showing the absence of iris and cataract in 3 adult patients and only absence of the iris in 2 children,and other 4 members showed the normal phenotype.A novel heterozygous PAX6 deletion mutation c.796 del G (p.A266 fs) (GenBank ID:KP255960) in exon 10 was exclusively found in all affected individuals but not in any of the unaffected families or unrelated health controls.PAX6 mRNA level in lymphocytes was about 50％ lower in aniridia patients than in unaffected family members,indicating that this mutation caused nonsense-mediated mRNA decay.Conclusions A novel deletion mutation in PAX6 gene results in an abnormal PAX6 COOH-terminal extension in the Chinese aniridia family.This finding expands the mutation spectrum of PAX6 gene.

Panfacial Bone Fracture and Medial to Lateral Approach

Panfacial bone fracture is challenging. Even experienced surgeons find restoration of original facial architecture difficult because of the severe degree of fragmentation and loss of reference segments that could guide the start of facial reconstruction. To restore the facial contour, surgeons usually follow a general sequence for panfacial bone reduction. Among the sequences, the bottom-to-top and outside-in sequence is reported to be the most widely used in recent publications. However, a single sequence cannot be applied to all cases of panfacial fractures because of the variations in panfacial bone fracture patterns. In this article, we intend to find the reference and discuss the efficacy of inside-out sequence in facial bone fracture reconstruction.

Application of hexon gene sequencing of adenovirus in pathogen detection of epidemic keratoconjunctivitis / 中华实验眼科杂志

Background Epidemic keratoconjunctivitis is a common eye disease,and adenovirus is one of the common pathogens.The hexon protein,one main capsid protein of the virus,is an important target of antibody binding.Thus,sequencing the coding region of the hexon protein is an important way for adenovirus fast typing.Objective This study was to complete a molecular epidemiology survey of epidemic keratoconjunctivitis and investigate its association with adenovirus in Shanghai area by sequencing the coding region of hexon protein.Methods Two hundred and fourteen sacconjunctival swab specimens were collected from 214 patients with suspicious epidemic keratoconjunctivitis who visited Shanghai Eye Disease Prevention and Treatment Center and the clinical sites supervised by the Shanghai Prevention and Monitoring Office of Acute Hemerragic Conjunctivitis under the informed consent from January 2010 to December 2012.DNA was extracted from the specimens and then the 140 bp conserved sequence in hexon protein coding region was amplified by PCR initially to determine an adenovirus pathogen.Furtherly,956 bp conserved sequence of the hexon codind district was sequencied to clarify the serotype of adenovirus in the adenovirus-positive specimens.Results 50.93％ patients (109/214) were detected to be adenovirus-positive by generic PCR,in which AdV1 + was in 4 patiens,AdV2+ was in 33 patients,AdV3+ was in 15 patients,AdV4+ was in 12 patients,AdV8+ was in 19 patiens,AdV19+ was in 15 patients,AdV37+ was in 8 patients.The subgenus D adenoviruses,including AdV8+,AdV19+ and AdV37+ often resulted in corneal inflammation,pseudomembranous conjunctivitis and preauricular lymph nodes;while subgenus B adenovirus induced much frequent tract infection and less corneal response.Conclusions PCR-sequence of conserved region of hexon protein coding district is applicable for the detection and serotyping of adenovirus in epidemic keratoconjunctivitis.

Analysis of MYOC gene mutation in a primary open angle glaucoma family from China / 中华实验眼科杂志

Background Primary open angle glaucoma (POAG) is one of the frequent glaucomatous types,and genetic factor participates in pathogenesis and development of the disease.Recently,MYOC mutation was found to be associated with POAG.Objective This study was to describe the clinical and genetic findings in a POAG family from Luoyang,China.Methods This study protocol was approved by Ethic Committee of Affiliated First Hospital of Henan University of Science and Technology.The study adhered to Declaration of Helsinki.A POAG family with 29 members of 5 generations was surveyed and followed-up for 5-year duration.The mode of inheritance was determined by the pedigree analysis.The periphery blood sample was collected form 12 families and 100 health controls for the extraction of genomic DNA under the informed consent.The third exon and its flanking introns of MYOC were amplified,and quantitative real time PCR products were sequenced,and the structure and function of mutated gene were examined by restriction fragment length polymorphism analysis.The predicted effects of the detected variants on the secondary structure of MYOC protein were evaluated using Garnier-Osguthorpe-Robson (GOR) method,and homology analysis of protein was carried out by Blast software provided by National Center for Biotechnology Information (NCBI).Results This POAG family included 29 members of 5 generations,and the clinical data were not clear in 11 family members.Three individuals from 3 generations were determined POAG,another one was ocular hypertension,and 2 were carriers.Pedigree analysis appeared an autosomal dominant inheritance.In 12 subjects included 6 members genetically affected and 6 members with normal phenotype,the heterozygous mutation was found in the third exon of MYOC gene in 6 genetically affected members,which revealed a T→C transition at position 1021 (p.S341P),resulting in a switch of serine (Ser) to proline (Pro).It was a missense mutation abolished a CviKI-1 restriction site that segregated with the affected members.Secondary structure prediction of p.S341P suggested that myocilin protein was misfolded.Analysis of protein homology and switched Ser was conservative amine acid at position 1021 (p.S341P).No similar change was found in the 6 normal families and the normal controls.Conclusions Ser341Pro MYOC mutation is disease-causing factor in the POAG family of Luoyang.The clinical and genetic features of this mutation warrant further investigation.The mutation spectrum of MYOC is expanded to offer a better diagnosis and treatment for POAG patients.

The relation of cationic trypsinogen gene G191R mutation and pathogenesis of pancreatitis / 中华胰腺病杂志

Objective To observe the prevalence of anionic trypsinogen (PRSS2) gene G191R mutation in patients with acute pancreatitis (AP) and chronic pancreatitis (CP),and to investigate the effect of PRSS2 gene G191R mutation on susceptibility to pancreatitis.Methods The blood samples of 82 patients with acute pancreatitis,73 patients with chronic pancreatitis and 138 healthy subjects were collected,and genomic DNA was extracted.Nest PCR were performed to amplify PRSS2 gene and restriction fragment length polymorphism (RFLP) was followed by using Hpy188Ⅲ to distinguish the G191R mutation.DNA sequencing analysis was performed to confirm the mutation status.Results The size of nest PCR products was 436 bp.RFLP2 produced 309 bp and 127 bp fragments,which were resulted from PRSS2 gene G191R mutation (GGA →AGA).DNA sequencing analysis of the PCR products further confirmed the PRSS2 gene G191R mutation.Five of eighty-two(6.1％) patients with acute pancreatitis had PRSS2 gene G191R mutation (OR=0.682,95％ CI 0.231 ～ 2.010); one of seventy-three (1.4％) patients with chronic pancreatitis had the mutation (OR =0.145,95％ CI 0.019 ～ 1.145),and the corresponding value in healthy group was 8.7％ (12/138).The G191R mutation rate in patients with chronic pancreatitis was significantly lower than that in healthy group (x2 =0.432,P =0.035),but the G191R mutation rates were not significantly different between AP group and healthy group (x2 =0.487,P =0.485).Conclusions PRSS2 gene G191R mutation facilitates the degradation of anionic trypsin,and may reduce the incidence of chronic pancreatitis.

Application of heteroduplex mobility assay in quick identification of adenovirus subtypes in epidemic keratoconjunctivitis / 中华实验眼科杂志

Background The commonly used method of typing the adenovirus (AdV) for epidemic keratoconjunctivitis is direct DNA sequence.However,heteroduplex mobility assay (HMA) is found to be a faster method to identify the subtypes of adenovirus and is more conforming to the principle of cost and economic benefit.There are few studies to illustrate the application of HMA in epidemic keratoconjunctivitis.Objective This study analyzed the conserved region of hexon coding sequence and compared the outcomes between direct DNA sequence and HMA for classification of adenovirus in epidemic keratoconjunctivitis patients.The validity of HMA is evaluated by comparing the result of both studies Methods Two hundreds and fourteen patients with suspicious epidemic keratoconjunctivitis were included in Shanghai Eye Disease Prevention and Treatment Center or the clinical sites supervised by the Shanghai Prevention and Monitoring Office of Acute Hemerragic Conjunctivitis from January 2010 to December 2012.Sacconjunctival swab samples were collected from each patient under the informed consent.DNA of pathogens was extracted from the samples using QIA-amp minikit,and the conserved sequence with 366 bp at hexon protein coding region was amplified by PCR and sequenced subsequently to determine the infected adenovirus and their subtypes.These samples were simultaneously assayed by HMA,and the outcomes between DNA sequence and HMA were compared.Results Extracted DNA presented a yellow fluorescence band with the fragment size 35 kb and absorbance ratio at the wavelength 260 nm and 280 nm (A260/A280) was I.7.In the 214 samples,AdV type 1 (AdV1) was found in 4 samples,AdV2 in 33 samples,AdV3 in 15 samples,AdV4 in 12 samples,AdV8 in 19 samples,AdV19 in 15 samples and AdV37 in 8 samples.HMA showed the same outcome for the identification of AdV1,AdV2,AdV3,AdV8,AdV19 and AdV37 with direct DNA sequence.AdV4 was not feasible to HMA owing to 59.6％ (over 10％) mutation sites.Conclusions Direct DNA sequencing for conserved regions in coding sequence of hexon is an important way to identify causing-disease adenovirus subtypes in the patients with epidemic keratoconjunctivitis.HMA can offer a consistent result with the DNA sequencing,and it might be used as a suitable tool for large-scale molecular epidemiology researches.

CFTR gene mutation in patients with congenital bilateral absence of vas deferens / 中华泌尿外科杂志

Objective To study the frequency of cystic fibrosis transmembrane conductance regulator(CFTR)mutations in patients with congenital bilateral absence of vas deferens(CBAVD).Methods Eighty-five CBAVD patients were collected from May 2007 to May 2009.The diagnosis of CBAVD included azoospermia,normal of 4 sex hormone items,absence of seminal vesicle,normal volume of testicular and epididymis dilated siltation.And 85 normal fertile men served as controls.Genomic DNA was isolated from peripheral blood.The mutations of CFTR exons 10,11 were detected by PCR-single strand conformation polymorphism,and direct sequencing was performed on 85 cases of CBAVD and the control males.Results Of the 85 CBAVD,10 cases(11.8％)exhibited an abnormal CFTR gene mutation,with 4 cases I556V,2 cases M469V,and 1 case of E527N,A F508,L558S,S485C.No mutations were detected in 85 controls.There was a significant difference between the 2 groups(x2 =8.606,P =0.003).Conclusions CBAVD might be caused by the CFTR mutations.The frequencies and the spectrum of CFTR mutations might be different from those Caucasian population in the west country.

Epidemiological study on viral diarrhea during 2009-2011 in Liaoning Province / 中华传染病杂志

Objective To understand the epidemiologic characteristics and pathogenic virus of cases of viral diarrhea in sentinel hospitals in Liaoning Province.Methods From Jan 2009 to Dec 2011,639 stool samples from sentinel hospitals of Liaoning Province were collected.Rotavirus,human calicivirus,astrovirus and adenovirus were detected by polymerase chain reaction and reverse transcriptase-polymerase chain reaction.The data analysis used chi-squanetest and Fisher's exact test.Results Rotavirus,human calicivirus,astrovirus and adenovirus were detected in 15.96 ％,11.25 ％,1.25％ and 0.31％ of the 639 specimens,respectively.G3 was the most prevailing serotype and P[8] was the most common genotype among 101 group A rotavirus isolates.One strain of group C rotavirus was also detected,which was reported for the first time from Liaoning Province.Phylogenetic analysis showed that this group C rotavirus JX407109 in the present study had the closest genetic relationship with the outbreak strain AB648916 from Japan,with nucleotide sequence consistency of 99 ％.Among the 72 samples of human calicivirus,70 samples were norovirus with G Ⅱ/4 being the predominant genotype,and 2 samples were sapovirus.Astrovirus was detected in 8 samples,most of which were genotype 1.Adenovirus was detected in 2 samples,and both were genotype 41.High incidences of viral diarrhea were noted during the months from December to next year February,and children under 5 years of age had high incidence of rotavirus and astrovirus,while the incidence of calicivirus were similar among different age groups.Conclusions The predominant pathogens of viral diarrhea in Liaoning Province are group A rotavirus and calicivirus.Notably,the group C rotavirus in Liaoning Province shares high genetic consistency with the outbreak strain from Japan.

Laboratory diagnosis and genetic characterization analysis of the subtype A3 influenza viruses in Quanzhou / 中华检验医学杂志

Objective To obtain the information of the 2009 influenza outbreak and the variations of influenza virus strains in quanzhou, and explore the relationship between the genetic variation of influenza virus and influenza epidemic. Methods During the influenza outbreak in quanzhou,one hundred and ninetyeight throat swabs specimens from the patients with influenza were collected. Viruses were isolated with MDCK cells and identified with serological test, followed by real-time RT-PCR. RNA of four influenza virus strains were extracted, then HA1 gene was amplified by RT-PCR. The purified PCR products were sequenced. The data were analyzed with the software DNAstar megalign. Results Total 98 pieces of H3N2 subtype influenza virus nucleic acid were detected in 198 throat swabs specimens,among which 62 influenza virus strains were identified as subtype influenza A( H3N2 ). The sequencing results of HA1 gene in these positive strains showed that their genetic characterization were more closed to strains A/Ningbo/333/2008 with a nucleotide homology of 98.7%, which was 96.8% as compared with A/Xiamen/70/2004. The amino acids sequences deduced from the nucleotide sequences in HA1 region of the isolated strain had 7 mutant sites compared with A/Brisbane/10/2007 vaccine strain. One variant amino acids were found located in the antigenic determinant sites A( 144 ), two were in the sites B( 158,189 ). Phylogenetic analysis also confirmed the difference in HAl domain. Conclusion The influenza virus strains causing the flu outbreak among some communities of quanzhou in 2009 are subtype influenza A ( H3N2 ), whose genetic characterization and antigenicity were different from the vaccine strain.

The role of molecular genetic factors in age-related macular degeneration / A importância dos fatores genéticos na degeneração macular relacionada à idade

Age-related macular degeneration (AMD) is the most frequent cause of irreversible blindness in the elderly in developed countries. Although the etiology of AMD remains largely unknown, numerous studies have suggested that both genes and environmental risk factors significantly influence the risk of developing AMD. Recently, single nucleotide polymorphisms, DNA sequence variations found within the complement factor H (CFH) gene, have been found to be strongly associated with the development of AMD. Several other genes have had at least one positive association finding and deserve further exploration. The purpose of this review is to provide an extensive report of the current data of AMD genetics and the contribution of this knowledge helps to the better understanding of its pathophysiology.

A degeneração macular relacionada à idade (DMRI) é a causa mais frequente de cegueira irreversível em idosos em países desenvolvidos. Apesar da etiologia da DMRI ainda permanecer desconhecida, numerosos estudos tem sugerido que tanto fatores genéticos quanto ambientais influenciam significativamente no risco do desenvolvimento da doença. Recentemente, polimorfismos de base única, variações na sequência de DNA encontradas no gene fator H do complemento (CFH), tem sido fortemente associado com o desenvolvimento da DMRI. Muitos outros genes tiveram ao menos um resultado positivo para esta associação e merecem estudos posteriores. O objetivo dessa revisão é proporcionar descrição atual dos dados publicados.

Application of heterozygous ambiguity resolution primers resolving ambiguous genotyping results of human leukocyte antigen genes / 中华检验医学杂志

Objective To evaluate the heterozygous ambiguity resolution primers (HARPs) method in resolving ambiguous genotyping results of human leukocyte antigen (HLA) genes in Chinese Hart population, and choose some appropriate HARPs primers. Methods HLA-A, HLA-B and HLA-DRB1 genes of 416 southern Chinese Han individuals were genotyped by sequence-based-typing(SBT) method and then the ambiguous genotyping samples were sequenced again by HARPs primers provided by American Atria company. Results The percentage of ambiguous genotyping samples resolved by HARPs for HLA-A, HLA-B and HLA-DRBI locus was 86.3% (132/153), 73.9% (130/176) and 38.1% (85/223) respectively. Among them, 48.5% (64/132)HLA-A, 80.0% (104/130)HLA-B and all HLA-DRB1(85/85)samples only need one primer, 47.7 % (63/132)HLA-A and 20.0% (26/130)HLA-B samples need two primers. Three to six different HARPs primers can resolve more than 90% ambiguities. Conclusion HARPs is a convenient method and could be a routine method to resolve ambiguities for HLA-A, HLA-B and HLA-DRB1 genes genotyped by SBT in Chinese Han population.

Detection and analysis of nucleotide sequence of enteroviros 71 from four adults with hand, foot and mouth disease / 中华传染病杂志

Objective To identify the pathogens that cause hand, foot and mouth disease (HFMD) in adults and analyze the nucleotide sequences characteristics of enterovirus 71 (EV71). Methods The reverse transcription-polymerase chain reaction (RT-PCR) method was used to detect the enterovirus from the samples of four adult HFMD patients. The 227 bp amplified segments of EVT1 were then sequenced and compared with the sequences of previously isolated EVT1 strains available from GenBank by homogeneity and phylogenetic tree analyses. Results All the results of RT-PCR with enterovirus universal primers and EVT1 specific primers were positive. The EV71 sequences analysis showed that the four new sequences (named as GZ19610, GZ99310, GZ99355 and GZ46477) shared 96.0% to 99.1% nucleotide identify themselves and shared 96.9% to 100.0% homology with the strain Fuyang/17.08/3 isolated in 2008 from Fuyang, Anhui Province. Phylogenetic tree analysis showed that the genotype of the four new sequences was all subtype C4, they were the same sub-genotype as those strains isolated from Chinese mainland and Chinese Taiwan in 2004, and the genetic distance between them was most closely. Conclusions EV71 can cause adult HFMD. Compared with the nucleotide sequences of EV71 strains that isolated now and formerly in China, there is no large variation of the EV71 sequences isolated from four adult HFMD patients in Guangzhou this time. The adult HFMD patients should be isolated for treatment to avoid them transmitting the virus and causing disease spreading.

Study on aminoglycoside resistance and drug resistance gene of ESBLs-producing Escherichia coil / 国际检验医学杂志

Objective To investigate the characteristics of aminoglycoside resistance of extend-ed-spectrum β-lactamases(ESBLs)-producing Escherichia coli(E, cold and expression of aminoglyco-side-modifying enzyme genes. Methods The minimal inhibitory concentrations(MICs) of gentamicin,amikacin, kanamycin, tobramycin, netilmicin and neomycin for 37 strains of ESBLs-producing E. Coli were detected by agar dilution. In addition, six aminoglycoside-modifying enzyme genes were amplified by polymersae chain reaction(PCR) and verified by DNA sequencing. Results MICand MIC90 of gentamicin, amikacin, kanamycin, tobramycin and netilmicin for 37 strains of ESBLs-producing E. Co-Il all excelled 256 μg/mL, the resistance rates of the above antibiotics were 78.4%, 45.9%, 72.9%,83.8%and 64.90%, respectively. However, neomycin still had powerful antibacterial activity. In ad-dition, five modifying enzyme genes, including aac(3)-Ⅱ , aac(6′)-Ⅰ b, aac(6′)-Ⅱ , ant(2″)-Ⅰ and ant(3″)- Ⅰ genes, were found in 37 isoaltes except aac(3)- Ⅰ , and their positive rates were 56.8%,27.0 %, 2.7 %, 5.4 % and 13. 5 %, respectively. Conclusion The aminoglycoside resistance of ES-BLs-producing E. Coil may be associated with the expression of aminoglycoside-modifying enzyme genes.

Pathological and molecular genetic studies on oculopharyngeal muscular dystrophy / 中华神经科杂志

Objective To study the pathologic and molecular genetic characteristics of Chinese patients with oculopharyngeal muscular dystrophy(OPMD).Methods The ultrastructural muscle biopsies in 6 patients were carried out by using transmission electron microscopy.The DNA was obtained through blood samples from patients(n=11) and the at-risk individuals(n=16).Amplification of the PABPN1 gene mutation region was performed by polymerase chain reaction(PCR).The sequences were obtained and compared with the genomic sequence of the human PABPN1 gene.Results Intranuclear inclusions(INIs) were found by electron microscopy in 4 patients,and the rate of appearance was 18%,20%,34% and 40%.Sequence analysis of exon 1 of PABPN1 gene showed abnormal expansions of the GCG-repeat—(GCG)_8 and(GCG)_(10) in 9 patients.Conclusions INIs might be found by electron microscopy in muscle biopsies of OPMD patients.The rate of appearance of INIs should have positive relationship with the amount of the GCG-repeat.PABPN1 gene mutations might be present among Chinese patients with OPMD,and should have a negative relationship with the age of onset.

Study of a 27-bp variable number of tandem repeat polymorphism of the endothelial nitric oxide synthase gene in patients with transient ischemic attack of brain / 中华老年医学杂志

Objective To investigate the association between a 27-bp variable number of tandem repeat(VNTR) polymorphism of the endothetial nitric-oxide synthase(eNOS)gene and transient ischemic attack(TIA) of brain.Methods Polymerase chain reaction was performed for the genotypes of all patients and control subjects.Data were compared between patients and control subjects using ?~(2)test. Results The genotype ab distribution and allele a frequencies of eNOS gene were significantly higher in TIA group(25.0%,14.3%) than in control group(16.3%,9.2%)(P

Molecular analysis of two strains of hantavirus isolated from Zhejiang province / 中华检验医学杂志

Objective To compare the molecular characteristics of hantanvirus strains isolated from 1980 to 2002 in Zhejiang Province by PCR and nucleotide sequencing.Methods Total RNA was extracted from hantanvirus infected Vero-E6 cells. The M segment cDNA of hantaan ZJ4 and ZJ7 strains were obtained by reverse transcription and polymerase chain reaction, subsequently cloned into pUCm-T vector and sequencing.Results Two strains ZJ4 and ZJ7 of hantanvirus isolated from Rottus in Zhejiang province were HTN viruses. HTN virus strain Z10 was isolated in 1980. Comparison ZJ4 and ZJ7 with Z10 strains indicated that there were 88.3% and 92.3% homology at the nucleotide level.Conclusion The HTN virus were very conserved. The homology of HTN virus isolated from Zhejiang Province was high nucleotide level, though they were isolated at more than 20-year intervals.

Caracterización Molecular de la Secuencia parcialdel Gen de la Glicoproteína NS1 del Virus Dengue 1 proveniente de Máncora, Perú

Se caracterizó una región genética que codifica la glicoproteína NS1 del virus dengue 1 proveniente de Máncora, Piura. Comparaciones de secuencias de nucleótidos revelaron un 93,32% de identidad entre el aislamiento peruano y una cepa de Hawai. A nivel de aminoácidos, se observaron cambios de tipo no conservativos en dominios epitópicos de reconocimiento humoral. De otro lado, el perfil hidropático de la región estudiada fue similar al de otros aislamientos referenciales. Los resultados sugieren realizar mayores análisis de identidad genética y mutaciones en dominios epitópicos en el virus dengue 1 peruano.

A 419bp-NS1 genetic region corresponding to Dengue virus 1 was characterised from an outbreak in Máncora Piura. The comparison of nucleotide sequences revealed that Peruvian isolates showed high correlation (93.32%) with a Hawaii strain. Amino acids comparisons revealed non-conservative changes into humoral response epitope domains. On the other hand, the hydropathy profile of NS1 was similar to other referential strains. The results suggest that more comparisons are needed regarding genetic identity and mutations into the epitope domain of Peruvian dengue 1 virus.