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PubMed2002

Physiological and genetic characterization of fluorescent Pseudomonas associated with Cantharellus cibarius.

Fluorescent Pseudomonas spp. isolated from fruiting bodies (FB) of Cantharellus cibarius were characterized physiologically and genetically and were compared with fluorescent Pseudomonas from forest soil and with sequences from the GenBank database. Pseudomonas spp. from FB differed physiologically from isolates from soil lacking FB and had some similarities with the strains obtained from soil underneath the FB. Analyses of the polymerase chain reaction (PCR) and restriction fragment length polymorphism (RFLP) patterns and partial sequencing analysis of the 16S-rDNA region indicated that the bacteria isolated from these environments were different. However, there was no specific Pseudomonas genotype restricted to the FB environment. Utilization of the reported fungal exudates trehalose and mannitol may explain how millions of bacteria survive in the C. cibarius FB without deteriorating the fungal mycelium. The importance of the metabolic characterization of bacteria and the possible mechanisms involved in the association with C cibarius are discussed. Our study showed that standard processes for bacterial identification, e.g., Biolog and 16S-rDNA are insufficient until databases for different ecosystems are created.

Base Sequence↗

PubMed2003

Molecular genetic characterization of the Fennoscandian cervid strain, a new genotypic group (G10) of Echinococcus granulosus.

The northern biotype of Echinococcus granulosus occurs in North America and northern Eurasia in life-cycles involving cervids. Previously, cervid isolates of E. granulosus from North America have been characterized using molecular genetic techniques as the G8 genotype. In this study, 5 isolates of E. granulosus were collected from 4 reindeer and 1 moose in north-eastern Finland. DNA sequences within regions of mitochondrial cytochrome c oxidase I (COI) and NADH dehydrogenase I (NI)I) genes and the internal transcribed spacer 1 (ITS-1) fragment of the ribosomal DNA were analysed. The mitochondrial nucleotide sequences were identical in all isolates, but high sequence variation was found in the ITS-1 region. Mitochondrial and nuclear sequences of the Finnish cervid E. granulosus and the camel strain (G6) of E. granulosus resembled closely each other. According to phylogenetic analyses, the Finnish isolates have close relationships also with the pig (G7) and cattle (G5) strains. Although some similarities were found with the previously published North American cervid strain (G8), particularly in the NDI sequence and some of the ITS-1 clones, the Finnish E. granulosus form represents a distinct, previously undescribed genotype of E. granulosus. The novel genotype is hereby named as the Fennoscandian cervid strain (G10).

Animals↗

PubMed2005

Genetic characterization of parthenogenic Fasciola sp. in Japan on the basis of the sequences of ribosomal and mitochondrial DNA.

Accurate identification of aspermic Fasciola forms in Japan remains difficult because of their morphological variations. In order to characterize the forms genetically, nucleotide sequences of ribosomal internal transcribed spacer (ITS1 and ITS2) and mitochondrial cytochrome c oxidase I (COI) and NADH dehydrogenase I (NDI) genes in 34 liver flukes from 16 prefectures in Japan were analysed. Two major forms represented by Fsp 1 and Fsp 2 had sequences identical to or closely resembling those of F. hepatica and F. gigantica, respectively, in all the 4 DNA markers and were mainly distributed in northern and eastern-western parts of Japan, respectively. Fsp 1 and Fsp 2 would have been introduced into Japan with infected cattle of 2 distinct lineages via the Korean Peninsula and spread through limited parts of Japan (northern and eastern-western parts) together with the movement of each cattle lineage. The Japanese form (Fsp 1/2), which showed heterozygosity in ribosomal DNA and Fsp 2 haplotype in mitochondrial DNA, may have originated in interspecific cross hybridization between paternal F. hepatica and maternal F. gigantica.

Animals↗

PubMed2004

[Influenza surveillance and antigenic and genetic characterization of predominant strains in Wuhan area in 2003].

OBJECTIVE: To study influenza epidemic and analyze antigenic and genetic characterization of the predominant strains in Wuhan area in 2003. METHODS: Epidemiological data and specimens from influenza patients were collected from surveillance sites weekly. Viruses were isolated from the specimens. Three H3 isolates were chosen to do antigenic analysis by hemagglutination inhibition (HI) test and their HA1 region was sequenced. RESULTS: Totally 58 influenza viruses were isolated from 418 specimens, 57 of them were identified as H3 subtype and 1 of them was B subtype; both monthly positive rate and numbers of influenza like illness had two peaks of winter and summer, the highest peak appeared in July. The 3 new H3 isolates were antigenically different from vaccine strain A/Panama/2007/99, 14 amino acid changes have been found in HA1 domain of these 3 strains compared with A/Panama/2007/99, phylogenetic analysis also confirmed the difference in HA1 domain. CONCLUSIONS: Influenza epidemic had two peaks in Wuhan area in 2003. The activity of H3 virus was strengthened remarkably. And they are antigenically and genetically different from the vaccine strain.

Amino Acid Sequence↗

PubMed2025

Comprehensive clinical and genetic characterization of hyperprogressive biliary tract cancer during PD-1 blockade monotherapy: case report and literature review.

BACKGROUND: Some genetically characterized patients show the rapid disease progression during immune checkpoint inhibitors (ICIs) monotherapy, a phenomenon known as hyperprogressive disease (HPD). CASE PRESENTATION: Herein we report a relevant case of biliary tract cancer (BTC) that initially responded to gemcitabine plus oxaliplatin (GEMOX) and PD-1 blockade but subsequently developed HPD in the process of PD-1 blockade maintenance therapy, leading to death within two weeks. Genomic analysis revealed mutations in CDKN2A, PIK3CA, KRAS and EPHA2 in both baseline and hyperprogressive plasma and tumor samples. Notably, higher KRAS mutation abundance was observed in plasma and ascites after disease progression. CONCLUSIONS: These findings suggest a potential association between these negative genes especially KRAS mutation and HPD. Therefore, administration of PD-1 blockade monotherapy in this subgroup of patients harboring KRAS mutation should be performed with caution. Further studies are warranted to confirm these results and explore the correlation between genomic mutations and HPD.

Humans↗

PubMed1999

Isolation and genetic characterization of a hantavirus (Bunyaviridae: Hantavirus) from a rodent, Oligoryzomys microtis (Muridae), collected in northeastern Peru.

This paper describes the isolation and partial genetic characterization of a hantavirus from a pygmy rice rat, Oligoryzomys microtis, collected within the urban area of Iquitos, Loreto Department, Peru. The virus, designated HTN-007, exhibited the highest degree of genetic similarity to Rio Mamore virus, which was originally described from the same rodent species in eastern Bolivia. Comparison of small and medium segment nucleotide sequence data from HTN-007 and Rio Mamore virus revealed 87% and 85% sequence identity, respectively. Based on these analyses, HTN-007 appears to be a variant of Rio Mamore virus. As such, it represents the first successful isolation of Rio Mamore virus and the first evidence for the existence of a hantavirus in Peru. Serologic studies done by immunofluorescence on blood samples of 56 O. microtis trapped at the collection site indicated that 21.4% had antibodies to hantavirus. In view of the proximity of this rodent species to humans and the close phylogenetic relationship of Rio Mamore virus to hantaviruses that have been associated with human disease, Rio Mamore virus may be a hantavirus of some public health importance in tropical South America.

Animals↗

PubMedDate not supplied

Molecular and genetic characterization and physical mapping of 11 new markers detecting multiallele restriction fragment length polymorphisms on the short arm of human chromosome 3.

Genetic markers with high degrees of polymorphisms are of vital importance in the construction of high resolution (2-4 cM) linkage maps of human chromosomes as specified in the short-term goals of the Human Genome Initiative. In this paper, we report on molecular and genetic characterization and physical localization of 11 new multiallele restriction fragment length polymorphism markers on human chromosome 3p. Ten of these represent three- and four-allele polymorphisms of the base substitution type probably at two adjacent restriction sites. One has been identified as a novel mini-satellite sequence comprising a variable copy number tandem repeat array of a G/T-rich 79-bp sequence. This collection of multiallele polymorphic (PIC values: 0.40-0.60) markers should prove valuable and increase the resolution power of the available chromosome 3p genetic markers.

Alleles↗

PubMed1993

Multiple drug resistance and genetic characterization of Salmonella typhimurium isolated at Chandigarh.

A total of 1072 strains of S. typhimurium were isolated in Chandigarh during 1985-1988. Genetic characterization of 'R' plasmids was attempted in 21 multiple drug resistant strains (ACKSSu TT p-19, ACKSSu, TP-I, AKSSu Tp-1). All the 21 strains were sensitive to gentamicin, furoxone and nalidixic acid. Level of resistance to different antimicrobial drugs varied from 200 to 1000 mg/L. Majority of the strains were untypable by the present set of 31 typing phages (Ut-17, Phage type 21-2, Phase type 99-2). All the plasmids belonged to class I transfer system. All the plasmids restricted some or all the typing phages of S. typhimurium and 39 also restricted phage phi 2. These plasmids belonged to F1me or I1 incompatibility groups and did not inhibit the function of fertility factor (fi-).

Adult↗

PubMed2004

Genetic characterization of four strains of Nile tilapia (Oreochromis niloticus L.) using microsatellite markers.

Four domesticated strains of Nile tilapia (Oreochromis niloticus L.) were genetically characterized using 14 microsatellite markers and 64 animals per strain. Two strains, Chitralada (AIT) and International Development Research Centers (IDRC) were obtained from the AIT institute, Bangkok, Thailand. The GIFT strain (5th generation) came from NAGRI, Thailand, and the GOTT strain was supplied by the University of Göttingen, Germany. The average numbers of alleles per marker were 5.0 (GOTT), 5.4 (AIT), 5.6 (IDRC) and 7.5 (GIFT). Private alleles were found at all markers with the exception of two. No fixation of alleles was found at any marker. Population differentiation, FST, was 0.178 (great genetic differentiation) and confirmed grouping of the animals in strains. The expected level of heterozygosity ranged from 0.624 to 0.711, but the observed level of heterozygosity significantly deviated from the expected level in three strains. This was probably because of small population size. Moderate to great genetic differentiation was found between strains. A phylogenetic tree reflected the strains known histories. Application of the Weitzman approach showed that all strains have added value for the total genetic diversity and thus should be retained.

Animals↗

PubMed2001

Genetic characterization of contemporary wild-type measles viruses from Vietnam and the People's Republic of China: identification of two genotypes within clade H.

Genetic characterization was conducted on 17 wild-type measles viruses isolated near Hanoi, Vietnam, during 1998 as well as on eight viruses isolated in the Hunan, Hainan, Shandong, and Anhui provinces of the People's Republic of China during 1995, 1998, and 1999. Previous studies had shown that, compared to wild-type measles viruses found in other parts of the world, wild-type viruses from China were genetically distinct and comprised a new clade of viruses, clade H. In this study, sequence analyses of the nucleotides coding for the COOH terminal 150 amino acids of the nucleoprotein (N) and the entire hemagglutinin (H) protein indicated that although all of the viruses from Vietnam were members of clade H, they were clearly distinct from the Chinese viruses. With the exception of MVi/Beijing.China/94/1, the Vietnamese viruses differed from all of the Chinese viruses by at least 3.5 and 2.5% at the nucleotide level for the N and H genes, respectively. These data suggest that clade H should be divided into two genotypes with the Chinese viruses placed in genotype H1 and the Vietnamese viruses in genotype H2. Sequence analysis of measles viruses imported into the United States from either China or Vietnam demonstrated that this designation of genotypes will be helpful in future measles surveillance activities.

China↗

PubMed2006

Genetic characterization of the dihydrofolate reductase gene of Pneumocystis jirovecii isolates from Portugal.

OBJECTIVES: The aim of the present study was to evaluate the genetic variation of Pneumocystis jirovecii dihydrofolate reductase (DHFR) gene in an immunocompromised Portuguese population and to investigate the possible association between DHFR genotypes and P. jirovecii pneumonia (PcP) prophylaxis with co-trimoxazole. METHODS: One hundred and thirty-eight P. jirovecii isolates were submitted to DHFR genetic characterization by PCR and sequencing. RESULTS: In the studied population, 72.7% of the patients presented sequences identical to the wild-type sequence of the P. jirovecii DHFR gene and 27.3% presented point substitutions. A total of nine substitution sites were identified; four synonymous substitutions at nucleotide positions 201, 272, 312 and 381 were detected in 31 patients. Five non-synonymous substitutions were observed, leading to the DHFR mutations Leu-13-->Ser, Asn-23-->Ser, Ser-31-->Phe, Met-52-->Leu and Ala-67-->Val. With the exception of the polymorphism at position 312 and the mutation at codon 52, all polymorphisms were reported in this study for the first time. CONCLUSIONS: Our results suggest that DHFR gene polymorphisms are frequent in the Portuguese immunocompromised population but do not seem to be associated with PcP prophylaxis failure (P = 0.748 and P = 0.730).

Amino Acid Substitution↗

PubMed1999

Genetic characterization of the nef gene from human immunodeficiency virus type 1 group M strains representing genetic subtypes A, B, C, E, F, G, and H.

Most efforts to characterize sequence variation of HIV isolates has been directed toward the structural envelope gene. Few studies have evaluated the sequence variability of auxiliary genes such as nef. In this study 41 new HIV-1 strains, representing the majority of the described envelope subtypes of HIV-1 (A to H), were genetically characterized in the nef region. Phylogenetic analysis showed that 34 strains could be classified in the same subtype in nef and env, and 7 (19%) of the 41 new viruses were recombinants. For two of the seven strains, recombination occurred upstream of the nef gene, whereas for five of the seven strains recombination occurred within the nef gene with a crossover close to the 5' end of the LTR (long terminal repeat). The low intersubtype distance between subtype B and D in the nef gene confirms previous observations in the pol, env, and gag genes, which suggest a common ancestor for these subtypes. The majority of all the previously described functional domains in the nef gene were relatively conserved among the different subtypes, with only minor differences being observed. The myristoylation signal among the different subtypes, with only minor differences being observed. The myristoylation signal was less conserved for subtype C, with one or more amino acid changes being observed at positions 3, 4, and 5. The highly conserved acidic region (positions 62 to 65), critical for the enhancement of viral synthesis with an increased virus growth rate, was less conserved among the subtype G strains from our study. At least three epitopic regions of the nef gene have been defined and each can be recognized by CTLs under a variety of HLA restrictions; all were also relatively well conserved between the different genetic subtypes. Despite the relatively important genetic variation in nef sequences obtained among the different genetic subtypes, functional domains and CTL epitopes were relatively well conserved. In vitro and/or in vivo studies are necessary to study the relevance of the observed differences.

Amino Acid Sequence↗

PubMed2005

Genetic characterization of Nipah virus, Bangladesh, 2004.

Until 2004, identification of Nipah virus (NV)-like outbreaks in Bangladesh was based on serology. We describe the genetic characterization of a new strain of NV isolated during outbreaks in Bangladesh (NV-B) in 2004, which confirms that NV was the etiologic agent responsible for these outbreaks.

Animals↗

PubMed1999

[The feature of influenza virus activity and genetic characterization of HA1 gene of influenza A H3N2 viruses isolated from 1994-1997 in Shenzhen].

OBJECTIVE: To understand the feature of influenza virus activity and genetic characterization of HA1 gene of influenza A H3N2 viruses isolated in recently years in Shenzhen. METHODS: The specimens were inoculated into amniotic and allantoic cavities of the embryonated chicken eggs for viral isolation. The isolates were typed with HI test. Virion RNA extracted from allantoic fluid by Rneasy RNA extraction kit was used for RT-PCR amplification. Afterward, the product of PCR was purified with purification kit. RNA sequence analysis was performed by Sanger dideoxy-mediated nucleotide chain termination method. RESULTS: Influenza A H3N2, H1N1 and B viruses were cocirculating in men in Shenzhen in recent years. However, the extent of their activities was not the same in a single year. The influenza B virus was the predominant strain in 1994 and 1997, but the predominant strain was H3N2 virus in 1996. The genetic analysis showed that the substitution of amino acids occured year by year and was mainly located at antigenic determinants or receptor binding site on HA1 domain of H3N2 viruses. CONCLUSION: Influenza A H3N2, H1N1 and B viruses were still co-circulating in men in Shenzhen in recent years, the predominant strain of influenza virus was different in different years. An increase of influenza A H3N2 virus activity in 1996 was due to the substitution of amino acids sequences on viral HA1 domain.

Amino Acid Sequence↗

PubMed2005

Genetic characterization of wild type measles virus isolated in Croatia during the 2003-2004 outbreak.

Viral epidemiology is determined by the movement of infected people within and between geographical areas. The genetic characterization of wild-type isolates combined with standard epidemiological methods may enable the identification of the source and transmission pathways and permit differentiation between indigenous and imported viruses. We investigated the genetic characteristics of the wild-type measles virus isolated in Croatia during a 2003-2004 outbreak. The results of this study indicate the presence of the D4 measles virus genotype in Europe. The isolated virus is closely related to virus isolates from the India-like subgroup of the D4 measles virus genotype. The virus responsible for this outbreak differs in the hemagglutinin gene sequence from other virus strains belonging to the D4 genotype. The hemagglutinin gene sequence also differs when compared to viruses from other genotypes that are known to circulate in Europe and from vaccine strains.

Croatia↗

PubMed2004

Genetic characterization of non-spoilage variant isolated from beer-spoilage Lactobacillus brevis ABBC45.

AIMS: To characterize the non-spoilage variant obtained from beer-spoilage Lactobacillus brevis ABBC45C and to identify a potential genetic marker capable of discriminating beer-spoilage L. brevis strains from non-spoilers. METHODS AND RESULTS: A non-spoilage variant was obtained from beer-spoilage L. brevis ABBC45C by repeatedly subculturing the strain at 37 degrees C. Genetic characterization of the variant revealed that 12,605 bp portion of one plasmid, designated pRH45II, was lost in the variant. The sequence analysis indicates the presence of 12 ORFs in the deleted region of pRH45II. The PCR and Southern hybridization study revealed that the homologues of ORF5 found in the deleted region were present in all of the beer-spoilage L. brevis strains examined in this study. In contrast, the homlogues appeared to be absent in non-spoilage L. brevis strains. CONCLUSIONS: The presence or absence of ORF5 homologues was found to be highly correlated with the beer-spoilage ability of L. brevis strains, indicating this ORF is potentially a useful genetic marker capable of differentiating beer-spoilage strains among L. brevis. SIGNIFICANCE AND IMPACT OF THE STUDY: A non-spoilage variant was successfully isolated from beer-spoilage L. brevis ABBC45C. This study could facilitate the understanding of mechanisms underlying beer-spoilage ability of L. brevis.

Bacterial Proteins↗

PubMed1996

Genetic characterization of a mammalian protein-protein interaction domain by using a yeast reverse two-hybrid system.

Many biological processes rely upon protein-protein interactions. Hence, detailed analysis of these interactions is critical for their understanding. Due to the complexities involved, genetic approaches are often needed. In yeast and phage, genetic characterizations of protein complexes are possible. However, in multicellular organisms, such characterizations are limited by the lack of powerful selection systems. Herein we describe genetic selections that allow single amino acid changes that disrupt protein-protein interactions to be selected from large libraries of randomly generated mutant alleles. The strategy, based on a yeast reverse two-hybrid system, involves a first-step negative selection for mutations that affect interaction, followed by a second-step positive selection for a subset of these mutations that maintain expression of full-length protein (two-step selection). We have selected such mutations in the transcription factor E2F1 that affect its ability to heterodimerize with DP1. The mutations obtained identified a putative helix in the marked box, a region conserved among E2F family members, as an important determinant for interaction. This two-step selection procedure can be used to characterize any interaction domain that can be tested in the two-hybrid system.

Alleles↗

PubMed2006

Genetic characterization of novel reassortant H1N2 influenza A viruses isolated from pigs in southeastern China.

In December 2004, three influenza H1N2 viruses were isolated from lung samples of pigs that had died from respiratory disease on a farm in southeastern China. To determine the genetic characterization and probable origin, one of the three isolates, A/Swine/Zhejiang/1/2004 (Sw/ZJ/1/2004), was genetically analyzed. Sw/ZJ/1/2004 was a reassortant with an NA gene most closely related to the corresponding gene from a human-like H3N2 virus circulating in 1995. The remaining seven genes were most closely related to those from the classical swine H1N1 virus. Sw/ZJ/1/2004 appeared to be a novel reassortant H1N2 virus that was genetically distinguishable from other H1N2 viruses found in pigs worldwide. The isolation of Sw/ZJ/1/2004 provided further evidence for pigs serving as a "mixing vessel" for the generation of new reassortant genotypes of influenza viruses and emphasizes the importance of reinforcing influenza virus surveillance in pigs in China.

Amino Acid Sequence↗