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Genetic characterization of myeloperoxidase deficiency in Italy.

Hereditary myeloperoxidase (MPO) deficiency (MPOD) is the most common neutrophil biochemical defect, and is characterized by a lack of peroxidase activity. In order to extend the epidemiological studies on hereditary MPOD in Italy, a population screening was carried out to detect mutations in the MPO gene. Of approximately 40,000 individuals analyzed, seven partial and eight total MPO-deficient subjects were identified. The genetic characterization of the subjects showed the presence of three already-known mutations (c.752T>C, c.1705C>T, and c.1566_1579del14) and six novel mutations: four missense mutations (c.995C>T, c.1112A>G, c.1715T>G, and c.1927T>C), then a deletion of an adenine within exon 3 (c.325delA) and a mutation within the 3' splice site of intron 11 (c.2031-2A>C). The novel missense mutations cause the substitution of the residues p.A332V, p.D371G, p.L572W, and p.W643R, respectively, and the potential structural changes are discussed. The c.325delA deletion causes a shift of the reading frame with the occurrence of a premature stop codon within the propeptide. Then, considering the difficulty in obtaining bone marrow samples from MPO-deficient subjects to study MPO mRNA splicing in vivo, we set up an eukaryotic expression system to investigate how the c.2031-2A>C mutation alters the MPO pre-mRNA splicing. The activation of a cryptic 3' splice site located 109nt upstream of the authentic 3' splice site was observed. The 109nt-insertion causes a shift in the reading frame that should lead to the generation of an abnormal MPO precursor lacking the enzymatic activity.

Amino Acid Sequence↗

Genetic characterization of the inducible SOS-like system of Bacillus subtilis.

The SOS-like system of Bacillus subtilis consists of several coordinately induced phenomena (e.g., cellular filamentation, prophage induction, and Weigle reactivation of UV-damaged bacteriophage) which are expressed after cellular insult such as DNA damage or inhibition of DNA replication. Mutagenesis of the bacterial chromosome and the development or maintenance of competence also appear to be involved in the SOS-like response in this bacterium. The genetic characterization of the SOS-like system has involved an analysis of (i) the effects of various DNA repair mutations on the expression of inducible phenomena and (ii) the tsi-23 mutation, which renders host strains thermally inducible for each of the SOS-like functions. Bacterial filamentation was unaffected by any of the DNA repair mutations studied. In contrast, the induction of prophage after thermal or UV pretreatment was abolished in strains carrying the recE4, recA1, recB2, or recG13 mutation. The Weigle reactivation of UV-damaged bacteriophage was also inhibited by the recE4, recA1, recB2, or recG13 mutation, whereas levels of Weigle reactivation were lower in strains which carried the uvrA42, polA5, or rec-961 mutation than in the DNA repair-proficient strain. Strains which carried the recE4 mutation were incapable of chromosomal DNA-mediated transformation, and the frequency of this event was decreased in strains carrying the recA1, recB2, or tsi-23 mutation. Plasmid DNA transformation efficiency was decreased only in strains carrying the tsi-23 mutation in addition to the recE4, recA1, or recB2 mutation. The results indicate that the SOS-like system of B. subtilis is regulated at different levels by two or more gene products. In this report, the current data regarding the genetic regulation of inducible phenomena are summarized, and a model is proposed to explain the mechanism of SOS-like induction in B. subtilis.

Bacillus subtilis↗

Erysipelothrix rhusiopathiae: genetic characterization of midwest US isolates and live commercial vaccines using pulsed-field gel electrophoresis.

This is the first report of molecular characterization of US erysipelas field isolates and vaccine strains of Erysipelothrix rhusiopathiae by pulsed-field gel electrophoresis (PFGE). Erysipelas in pigs is mainly caused by E. rhusiopathiae serotypes 1a, 1b, and 2. In 2001, erysipelas reemerged as a clinical problem in pigs in the midwestern United States. In this work 90 erysipelas isolates (58 recent and 28 archived field isolates as well as 4 live-vaccine strains) were genetically characterized. Because of the limited availability of antiserum, 74/90 isolates (44/58 recent isolates) were serotyped. The serotype of the majority (79.6%) of the 44 recent isolates tested was determined to be 1a, 13.6% were serotype 1b, and 6.8% of recent isolates were serologically untypeable. Among all 90 isolates, 23 different PFGE patterns were identified. There were 43 isolates identified as serotype 1a with 4 genetic patterns: 38/43, 1A(I); 3/43, 1A(III); 1/43, 1B(V); and 1/43, 3B. Sixteen serotype 1b isolates had 11 unique genetic patterns: 4/16 were genotype 1B(III), 2/16 were genotype 3A(I), and 1/16 was in genotype groups 1A(V), 1A(VI), 1A(VII), 1B(I), 1B(IV), 1B(VII), 2, 4, and 5. Six genetic patterns were distinguished among the 10 serotype 2 isolates: 1A(IV) (1/10), 1A(V) (1/10), 1B(VI) (1/10), 2 (4/10), 7 (1/10), and 8 (2/8). Erysipelas vaccine strains (modified live) were similar to each other but different from current field strains, sharing 78.6% identity with the most prevalent genotype 1A(I) based on the PFGE-SmaI pattern. Compared with serotyping, PFGE genotyping is a more distinguishing technique, easy to perform and not dependent on the limited availability of antiserum.

Animals↗

Biological, serological, and genetic characterization of HIV-1 subtype E isolates from northern Thailand.

Twenty-three HIV-1 isolates were recovered from PBMCs from 26 HIV-1-seropositive individuals in northern Thailand. The viruses grew readily in human PBMCs but only 7 of 17 (41.2%) and 5 of 17 (29.4%) replicated and only at a low level in primary macrophages and in established T cell lines, respectively. By immunoblot assays, sera from Thai subjects were strongly reactive with gp120 from a Thailand isolate, moderately reactive with a Rwandan isolate, and weakly reactive with a North American strain. These three viruses represent, respectively, examples of subtypes E, A, and B as classified by the sequences of the envelope region. Serological assays indicated that broadly reactive rather than type-specific neutralizing activity was detected among these northern Thai sera. The majority of the sera (approximately 75%) neutralized a representative Thailand isolate and the Rwanda isolate but only 55% neutralized the North American strain. However, the difference was not statistically significant. The genetic analyses indicated that nearly all the Thai isolates were highly homogeneous and distinct from the North American/European consensus sequence (subtype B); they belong to subtype E. This is the first report providing biological, serological, and genetic characterization of HIV-1 strains from Thailand. The findings suggest these viruses were recently introduced into the country and that serological evaluation of viral strains needs to be considered along with genetic subtyping when developing an HIV-1 vaccine.

Adult↗

First genetic characterization of a bacterial beta-phenylethylamine biosynthetic enzyme in Enterococcus faecium RM58.

Enterococcus faecium RM58 produces beta-phenylethylamine and tyramine. A gene from Ent. faecium RM58 coding for a 625 amino-acid residues protein that shows 85% identity to Enterococcus faecalis tyrosine decarboxylase has been expressed in Escherichia coli, resulting in L-phenylalanine and L-tyrosine decarboxylase activities. Both activities were lost when a truncated protein lacking 84 amino acids at its C-terminus was expressed in E. coli. This study constitutes the first genetic characterization of a bacterial protein having L-phenylalanine decarboxylase activity and solves a long-standing question regarding the specificity of tyrosine decarboxylases in enterococci.

Carboxy-Lyases↗

Genetic characterization of diverse HIV-1 strains in an immigrant population living in New York City.

New York City (NYC) is one of the original foci of the HIV-1 epidemic and has a greater number of AIDS cases than any other city in the United States. NYC also hosts the highest number of immigrants among the nation's cities: more than 2 million among a total population of 8 million. Such a high rate of immigration could act as a potential source for introducing and disseminating novel HIV-1 strains into the United States. Our current study focuses on the genetic characterization of HIV-1 strains circulating in an immigrant population in NYC. Of the 505 HIV-1-positive specimens obtained, 196 were available for viral sequencing from the C2 to V3 region of env. Phylogenetic analysis using maximum-likelihood and neighbor-joining methods demonstrated that non-B subtypes and circulating recombinant forms (CRFs) accounted for 43.4% (85 of 196 cases), whereas the remaining 56.6% (111 of 196) cases had viral variants similar to the typical North American subtype B virus. Of those non-B subtypes and CRFs, subtype A and CRF02 dominated (63.5% combined); other subtypes, including C, D, F1, G, CRF01_AE, and CRF06_cpx, were also detected. Two HIV-1 sequences do not cluster with any known subtypes or CRFs. Furthermore, the distribution of non-B subtypes and CRFs was consistent with the countries of origin, suggesting that many of the study subjects were likely infected in their home country before they entered the United States. Subtype B viruses identified in the immigrant population showed no significant differences from the typical North American B subtype, however, indicating that a significant proportion of the immigrants must have been infected after they came to the United States. Public health officials and physicians should be aware of the growing genetic diversity of HIV-1 in this country, particularly in areas with sizable immigrant populations.

Adolescent↗

Genetic characterization of Swedish patients with familial hypercholesterolemia: a heterogeneous pattern of mutations in the LDL receptor gene.

Familial hypercholesterolemia (FH) is an autosomal codominant disease, caused by mutations in the LDL receptor gene. To characterize the distribution of genetic aberrations in Swedish FH-patients fulfilling the clinical criteria of FH, we have investigated 150 unrelated Swedish patients for mutations in the LDL receptor gene and for the most common mutation causing familial ligand defective apo B-100 (FDB). Of the patients, 77 were recruited from Huddinge University Hospital in Stockholm and 73 from Sahlgren's University Hospital in Göteborg. Screening was carried out using SSCP and Southern blotting techniques, combined with DNA sequence analysis. In total, mutations regarded as cause for disease were identified in 55 patients (37%), representing 32 different types of mutations. In the LDL receptor gene we detected four nonsense mutations, 13 missense mutations, seven splice junction mutations, and four major rearrangements. In addition, two small deletions were identified and one base exchange in the promoter region. The most common mutation (apo B3500) causing FDB was found in three patients. The most frequent mutation was FH-Helsinki, reflecting the admixture of Finnish immigrants. We further identified 15 point mutations which were not considered to affect the function of the gene, and thus were regarded as polymorphic changes. This multitude of mutations reflects a heterogeneous genetic background in our series of Swedish FH-patients and differs from the situation in the other Scandinavian countries. Future studies should aim at characterizing the importance of other genes for the development of the FH phenotype.

Adult↗

Viral gastroenteritis and genetic characterization of recombinant norovirus circulating in Eastern Russia.

From November 2003 to March 2004 a total of 100 fecal specimens from infants and children with acute gastroenteritis in the city of Birobidzhan, Eastern Russia were tested for the presence of diarrheal viruses by RT-multiplex PCR. Of these, 74 fecal specimens were positive for diarrheal viruses and this represented 74%. Among the diarrheal viruses detected, group A rotavirus was the most prevalent (67%; 67 of 100), followed by norovirus (4%; 4 of 100), group C rotavirus (1%, 1 of 100), sapovirus (1%; 1 of 100), and hepatitis A virus (1%; 1 of 100). It was found that 86.6% (58 of 67) of group A rotavirus were serotyped as G3. Sapovirus and hepatitis A virus were genetically determined to belong to GI/1 and subgenotype 1A, respectively. Interestingly, all norovirus isolates in the study turned out to make a novel cluster when polymerase-based grouping was performed. It is noteworthy to point out that these norovirus isolates were further genetically characterized as naturally occurring recombinants, which were firstly found circulating in the Russian population studied. Breakpoint analysis of recombinant norovirus showed that the recombination site was at the open reading frame (ORF)1/ORF2 overlap. This is the first report of the existence of acute gastroenteritis caused by recombinant norovirus in Eastern Russia.

Acute Disease↗

Genetic characterization of the M RNA segment of a Balkan Crimean-Congo hemorrhagic fever virus strain.

Crimean-Congo hemorrhagic fever (CCHF) virus causes one of the most severe diseases in humans, with a mortality rate of up to 30%. It is transmitted to humans by the bite of hard ticks or by contact with blood or tissues from human patients or infected livestock. Balkan Peninsula is an endemic region of the disease, and sporadic cases or even outbreaks are observed every year. The M RNA segment encodes for the glycoprotein precursor of two surface glycoproteins Gn and Gc. Up to now complete M RNA CCHF virus sequences have been published from strains isolated in Nigeria, China, Pakistan, Tajikistan, and Russia. In the present study, the genetic characterization of the complete nucleotide sequence of the M RNA segment of a Balkan CCHF virus strain, Kosovo/9553/2001, isolated in summer of 2001 from a human fatal case in Kosovo is reported. This is the first published complete M nucleotide sequence of a CCHF virus strain isolated in Balkans. It was found that the Balkan strain is similar to the Russian strain, both strains differing from all other completely sequenced CCHF virus strains by approximately 22% at the nucleotide level forming an independent clade in the phylogenetic tree.

DNA, Complementary↗

Ecological, morphological and genetic characterization of sympatric Haemonchus spp. parasites of domestic ruminants in Mauritania.

The 4 species of ruminants (dromedary, zebu cattle, sheep and goat) in arid areas of Mauritania harboured Haemonchus spp. as the most frequent internal parasite. This was a rare situation where the 3 putative species, H. longistipes (dromedary), H. placei (zebu cattle) and H. contortus (sheep and goat) occurred sympatrically. The study was undertaken on hosts slaughtered at the Nouakchott abattoir, on the basis of monthly collection of worms. The environment was very unfavourable to H. placei and unfavourable to H. contortus, as intensity of infection remained low throughout the year, whereas infection in the dromedary was 10 to 20-fold higher. The survival strategies during the long, dry season were different: the surviving stages were either 4th-stage larvae in digesta (dromedaries), 4th-stage larvae either in digesta or mucosae (cattle), or 4th-stage larvae in mucosae and few adults (sheep and goats). The prolificacy of female worms, indicative of the potential to contaminate pastures, was similar for all Haemonchus spp. in the rainy season. H. longistipes behave differently during the pre-rainy season as no increase of prolificacy could be demonstrated as observed in the other species. Traits of vulvar morphology are considered as markers of ecological adaptation and were studied. The knobbed and smooth female morphs (in equal proportions) were the most frequent in H. longistipes, the knobbed morph out-numbered the other morphs in H. placei, and all 3 morphs were present in sheep and goats with the linguiform form being predominant. Genetic characterization of the 3 species was performed by means of Random Amplified Polymorphic DNA (RAPD). Three groups were obtained from analysis of these data: 1 group with individuals of H. contortus, 1 group with individuals of H. placei, and 1 group with individuals of H. longistipes. This indicated that, although the 3 species were valid, H. contortus and H. placei were more similar. Intraspecific variability was 2-fold higher in H. contortus than in the 2 other species. The ecological, morphological and genetical studies showed that H. longistipes, H. placei and H. contortus could be arranged in increasing order of variability.

Adaptation, Physiological↗

Cloning and genetic characterization of Helicobacter pylori catalase and construction of a catalase-deficient mutant strain.

The N-terminal sequence of a protein, originally described as an adhesin of Helicobacter pylori, was used in an oligonucleotide-based screening procedure of an H. pylori plasmid library in Escherichia coli. Five independent plasmid clones were isolated, all mapping to the same chromosomal region and encoding the H. pylori catalase. The gene, designated katA, comprises 1,518 nucleotides and encodes a putative protein of 505 amino acids with a predicted Mr of 58,599. A second open reading frame, orf2, encoding a putative 32,715-Da protein of unknown function, follows katA. The transcriptional start site of katA mRNA was determined, but no typical consensus promoter sequence was present. A potential binding site for the Fur protein is located upstream of katA. When introduced into the catalase-deficient E. coli double-mutant UM255, the cloned gene readily complemented E. coli for catalase activity. H. pylori KatA is highly homologous to catalases in both prokaryotes and eukaryotes, with the highest homology being shown to Bordetella pertussis (64.9%), Bacteroides fragilis (59.8%), and Haemophilus influenzae (57.9%) catalases. Transposon insertion mutants were generated in three independent H. pylori strains by TnMax5-mediated transposon shuttle mutagenesis. In contrast to the wild-type strains, no significant catalase-specific enzymatic activity could be detected in the mutant strains, consistent with the fact that no additional katA-homologous gene copies were found in the H. pylori chromosome. No significant difference between wild-type and mutant strains for binding to epithelial cells was apparent, suggesting that KatA is not involved in H. pylori adhesion. The cloning and genetic characterization of katA are essential steps for further investigation of the role of catalase in the defense of H. pylori against oxygen-dependent killing mechanisms by polymorphonuclear granulocytes, a process not well understood for this chronically persisting pathogen.

Amino Acid Sequence↗

A dominant negative allele of the Escherichia coli uvrD gene encoding DNA helicase II. A biochemical and genetic characterization.

A site-specific lysine to methionine mutation has been engineered at the invariant Lys35 residue in the ATPase A binding site of the Escherichia coli uvrD gene encoding DNA helicase II. The mutant protein (UvrDK35M) has been purified to apparent homogeneity and characterized. The kcat for DNA-dependent ATP hydrolysis was less than 0.5% that of the wild-type enzyme with no change in the apparent Km for ATP. No unwinding of partial duplex DNA substrates could be detected using the mutant protein. Moreover, the mutant protein inhibited the unwinding reaction catalyzed by the wild-type protein at ratios of mutant enzyme to wild-type enzyme < 1. We conclude that the K35M mutation renders helicase II catalytically inactive as a DNA helicase with little or no effect on the ability of the enzyme to bind ATP, DNA, or other proteins. In vivo complementation assays indicate that the mutant protein cannot substitute for the wild-type protein in methyl-directed mismatch repair, suggesting that the ATPase and/or helicase activity of helicase II is required in this repair pathway. Additional genetic characterization of the uvrDK35M allele, supplied on a plasmid, suggests that expression of the mutant protein, at levels equivalent to that of the wild-type protein, results in a dominant negative phenotype. Expression of lower levels of the mutant protein, both in the presence and absence of wild-type helicase II, results in a constitutive induction of the cellular SOS response and extensive filamentation of cells. This induction of the SOS response is not due to a defect in methyl-directed mismatch repair. Taken together, these data are consistent with the notion that E. coli helicase II may have a role in DNA replication.

Adenosine Triphosphatases↗

The next challenge for psychiatric genetics: characterizing the risk associated with identified genes.

BACKGROUND: As advances in genetics further our ability to identify genes influencing psychiatric disorders, the next challenge facing psychiatric genetics is to characterize the risk associated with specific genetic variants in order to better understand how these susceptibility genes are involved in the pathways leading to illness. METHODS: To further this goal, findings from behavior genetic analyses about how genetic influences act can be used to guide hypothesis testing about the effects associated with specific genes. RESULTS: Using the phenotype of alcohol dependence as an example, this paper provides an overview of how the integration of behavioral and statistical genetics can advance our knowledge about the genetics of psychiatric disorders. Areas currently being investigated in behavior genetics include careful delineation of phenotypes, to examine the heritability of various aspects of normal and abnormal behavior; developmental changes in the nature and magnitude of genetic and environmental effects; the extent to which different behaviors are influenced by common genes; and different forms of gene-environment correlation and interaction. CONCLUSIONS: Understanding how specific genes are involved in these processes has the potential to significantly enhance our understanding of the development of psychiatric disorders.

Alcoholism↗

Simple and rapid strategy for genetic characterization of influenza B virus reassortants.

Genetic reassortment of influenza viruses is widely used for creating viruses with specific phenotypes. Reassortment of two influenza viruses, each with eight RNA segments potentially yields as many as 256 gene segment combinations. Therefore, confirmation that progeny viruses possess genomes corresponding to the specified phenotypes can be laborious and time-consuming. To establish a convenient method for genotyping influenza virus reassortants, we adapted single-strand conformation polymorphism analysis (SSCP) using standard laboratory equipment. By varying the concentration of polyacrylamide between 4-6% and the concentration of glycerol between 5-8% in the gel, together with adding PCR primers to the DNA sample during the denaturing step, optimal conditions can be found for SSCP with little effort. The described method has high accuracy and reliability, and provides a tool for rapid, cost-effective genetic screening and assessment of the purity and genetic stability of the reassortant viruses. This method should be useful in basic research applications and in preparing reassortant viruses for vaccine use.

Base Composition↗

Molecular genetic characterization of the senescence-accelerated mouse (SAM) strains.

Senescence-Accelerated Mouse (SAM) is a murine model of accelerated senescence, which consists of the senescence-prone P series and the senescence-resistant R series of strains. In order to characterize these SAM strains molecular genetically, we have performed a series of Southern hybridization experiments using oligonucleotide probes designed to recognize the endogenous mouse retrovirus sequences. The repertoires of endogenous retroviruses in different SAM strains indicated that each SAM strain is distinct. Comparisons of the SAM strains with the parental AKR/J strain revealed significant differences between them, suggesting the involvement of other strains in the course of the development of SAM. While some of the endogenous retroviruses were found in all of the SAM strains, others were found to be distributed uniquely, indicating their potential usefulness as genetic markers in the analysis of strain-specific phenotypes, and possibly of the phenomenon of accelerated senescence itself.

Aging↗

Molecular genetic characterization of the Escherichia coli gntT gene of GntI, the main system for gluconate metabolism.

The Escherichia coli gntT gene was subcloned from the Kohara library, and its expression was characterized. The cloned gntT gene genetically complemented mutant E. coli strains with defects in gluconate transport and directed the formation of a high-affinity gluconate transporter with a measured apparent Km of 6 microM for gluconate. Primer extension analysis indicated two transcriptional start sites for gntT, which are separated by 66 bp and which give rise to what appears on a Northern blot to be a single, gluconate-inducible, 1.42-kb gntT transcript. Thus, it was concluded that gntT is monocistronic and is regulated by two promoters. Both of the promoters have - 10 and -35 sequence elements typical of sigma70 promoters and catabolite gene activator protein binding sites in appropriate locations to exert glucose catabolite repression. In addition, two putative gnt operator sites were identified in the gntT regulatory region. A search revealed the presence of nearly identical palindromic sequences in the regulatory regions of all known gluconate-inducible genes, and these seven putative gnt operators were used to derive a consensus gnt operator sequence. A gntT::lacZ operon fusion was constructed and used to examine gntT expression. The results indicated that gntT is maximally induced by 500 microM gluconate, modestly induced by very low levels of gluconate (4 microM), and partially catabolite repressed by glucose. The results also showed a pronounced peak of gntT expression very early in the logarithmic phase, a pattern of expression similar to that of the Fis protein. Thus, it is concluded that GntT is important for growth on low concentrations of gluconate, for entry into the logarithmic phase, and for cometabolism of gluconate and glucose.

Bacterial Proteins↗

Genetic characterization of rabies field isolates from Venezuela.

Twenty samples from cases of rabies in humans and domestic animals diagnosed in Venezuela between 1990 and 1994 and one sample from a vampire bat collected in 1976 were characterized by reactivity to monoclonal antibodies against the viral nucleoprotein and by patterns of nucleotide substitution in the nucleoprotein gene. Three antigenic variants were found: 1, 3, and 5. Antigenic variant 1 included all samples from dogs and humans infected by contact with rabid dogs. Unique substitutions permitted identification of two separate outbreaks of dog rabies in the Maracaibo Depression and Los Llanos region and in the Andean region of Venezuela. Samples from the vampire bat and two head of cattle were characterized as antigenic variant 3 and showed a nucleotide sequence homology of 96 to 98% to each other and to samples of vampire bat-associated rabies throughout Latin America. Ten of the remaining 12 samples were characterized as antigenic variant 5. Genetic studies indicated that 11 of these samples formed a highly homologous and distinctive group but were closely related to samples of vampire bat-associated rabies. The 12th sample of variant 5 (from a cat) showed only 78 to 80% genetic homology to samples of rabies associated with vampire bats. The application of antigenic and genetic typing to rabies surveillance in Latin America is essential to improve control programs. Recognition of the source of outbreaks of dog rabies and identification of wildlife species maintaining sylvatic cycles of rabies transmission permit better utilization of public health resources.

Animals↗