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PubMed1999

The 82F late puff contains the L82 gene, an essential member of a novel gene family.

Metamorphosis in Drosophila results from a hierarchy of ecdysone-induced gene expression initiated at the end of the third larval instar. A now classical model of this hierarchy was proposed based on observations of the activity of polytene chromosome "puffs" which distinguished "early" puffs as those directly induced by ecdysone and "late" puffs as those which become active as a secondary response to the hormone. We report here the isolation and characterization of the L82 gene corresponding to the extensively characterized late puff at 82F. L82 is a complex gene that spans at least 50 kb of genomic DNA, produces at least seven different nested mRNAs, and has homology to a novel gene family. In contrast to most previously characterized puff genes, the broad developmental expression pattern of L82 suggests that it is controlled by both ecdysone-dependent and ecdysone-independent regulatory mechanisms. L82 mutations were identified by transgene rescue of developmental delay and eclosion lethal phenotypes.

Amino Acid Sequence↗

PubMed2000

Genetic manipulation of equine arteritis virus using full-length cDNA clones: separation of overlapping genes and expression of a foreign epitope.

Equine arteritis virus (EAV) is an enveloped, positive-stranded RNA virus belonging to the family Arteriviridae of the order Nidovirales. The unsegmented, infectious genome of EAV is 12,704 nt in length [exclusive of the poly(A) tail] and contains eight overlapping genes that are expressed from a 3'-coterminal nested set of seven leader-containing mRNAs. To investigate the importance of the overlapping gene arrangement in the viral life-cycle and to facilitate the genetic manipulation of the viral genome, a series of mutant full-length cDNA clones was constructed in which either EAV open reading frames (ORFs) 4 and 5 or ORFs 5 and 6 or ORFs 4, 5, and 6 were separated by newly introduced AflII restriction endonuclease cleavage sites. RNA transcribed from each of these plasmids was infectious, demonstrating that the overlapping gene organization is not essential for EAV viability. Moreover, the recombinant viruses replicated with almost the same efficiency, i.e., reached nearly the same infectious titers as the wildtype virus, and stably maintained the mutations that were introduced. The AflII site engineered between ORFs 5 and 6 was subsequently used to generate a virus in which the ectodomain of the ORF 6-encoded M protein was extended with nine amino acids derived from the extreme N-terminus of the homologous protein of mouse hepatitis virus (MHV; family Coronaviridae, order Nidovirales). This nonapeptide contains a functional O-glycosylation signal as well as an epitope recognized by an MHV-specific monoclonal antibody, both of which were expressed by the recombinant virus. Although the hybrid virus had a clear growth disadvantage in comparison to the parental virus, three serial passages did not result in the loss of the foreign genetic material.

5' Untranslated Regions↗

PubMed2001

Staphylococcus aureus in inflammatory bowel disease.

BACKGROUND: The potential role of superantigens in inflammatory bowel disease (IBD), particularly Crohn disease, has been broached in studies of the functions of T cell receptors. Staphylococcal cells have been found in intestinal lymph follicles of IBDs. To clarify a role of staphylococcal superantigens in IBD, we attempted to determine whether Staphylococcus aureus could be detected in intestinal mucosa, including surgical specimens and lymph follicles of initial cases. METHODS: One-hundred-and-six colonic and ileal specimens were obtained from 38 Crohn disease, 25 ulcerative colitis and 36 non-IBD patients through therapeutic surgery or endoscopic biopsy. In Crohn disease, 23 surgical specimens and 11 biopsy specimens from initial cases were included. DNA was extracted with phenol-chloroform after homogenization and proteinase K treatment in 73 mucosal specimens. Using an inverted microscope, lymph follicle tissue was microdissected from the remaining 33, mostly biopsy, specimens. DNA was then extracted by freeze-thawing. A coagulase gene characteristic of S. aureus was sought. A nested polymerase chain reaction was performed utilizing primers that amplify a region of the coagulase gene. Polymerase chain reaction products were analyzed with polyacrylamide gel electrophoresis. RESULTS: Only one surgically resected colonic specimen, from a 42-year-old male ulcerative colitis patient, registered positive staphylocoagulase amplification. CONCLUSIONS: Staphylococcal superantigens are not involved in either the early lesions or the established lesions of Crohn disease. However, S. aureus infection occasionally may occur during the course of IBD.

Adult↗

PubMed2005

Identification and functional analysis of 20 Box H/ACA small nucleolar RNAs (snoRNAs) from Schizosaccharomyces pombe.

Considering all small nucleolar RNAs (snoRNAs) enriched in the nucleolus, we generated a specialized cDNA library of small nuclear RNAs from Schizosaccharomyces pombe and isolated, for the first time, 20 novel box H/ACA snoRNAs. Thirteen of these were characterized as novel guides that were predicted to direct 19 pseudouridylations in 18 S and 25 S rRNAs. The remaining seven snoRNAs were considered as orphan guides that lack sequence complementarity to either rRNAs or snRNAs. We have experimentally demonstrated the function of the 10 novel snoRNAs by gene deletion in the fission yeast. The snoRNAs were shown to be dispensable for the viability of S. pombe, although an impact of snR94 depletion on yeast growth, especially at 23 degrees C, was revealed. A total of 30 pseudouridylation sites were precisely mapped in the S. pombe rRNAs, showing a distinctive pseudouridylation pattern in the budding yeast. Interestingly, the absence of pseudouridylation on U2347 in S. pombe 25 S rRNA pointed out a critical role for Psi2345 in conferring a growth advantage for yeast. In contrast to the intron-encoded box C/D sno-RNAs in yeast, all box H/ACA snoRNAs appeared to be transcribed independently from intergenic regions between two protein-coding genes, except for snR35, which was nested in an open reading frame encoding for a hypothetical protein, although expressed from the opposite strand. Remarkably, snR90 was cotranscribed with an intron-encoded box C/D snoRNA, and this is the first demonstration of a non-coding RNA gene that encodes two different types of snoRNAs by its exon and intron. A detailed comparison of the S. pombe snoRNAs, with their functional homologues in diverse organisms, suggests a mechanism by which the snoRNAs have evolved in coordination with rRNAs to preserve the post-transcriptional modification sites among distant eukaryotes.

Nucleic Acid Conformation↗

PubMed1991

Detection of enterotoxigenic Staphylococcus aureus in dried skimmed milk: use of the polymerase chain reaction for amplification and detection of staphylococcal enterotoxin genes entB and entC1 and the thermonuclease gene nuc.

The polymerase chain reaction was used to amplify the staphylococcal enterotoxin B and C genes (entB and entC1) and the staphylococcal nuclease gene (nuc). Two sets of primers ("nested primers") were found to be necessary for the detection of low copy numbers of purified DNA in diluent. These allowed detection of ca. 1 fg of purified target DNA, while 100 pg was required before detection of entB, entC1, and nuc with single primer pairs was possible. With nested primers, enterotoxigenic Staphylococcus aureus cells could be detected in artificially contaminated dried skimmed milk samples at levels of ca. 10(5) CFU ml-1 within 8 h. No cross-reaction was observed between the highly homologous entB and entC1 genes. The method showed total specificity for entC1 when tested against a wide variety of other bacteria.

Animals↗

PubMed1997

Detection of pseudorabies virus genomic sequences in apparently uninfected 'single reactor' pigs.

With a pseudorabies virus (PrV) gB ELISA, performed on 480,000 pigs on 8,900 Swedish farms, approximately 1,300 cases were observed with only one single animal reacting positively. These animals were termed 'single reactors' (SR). In order to find explanations for this peculiar phenomenon, the presence of PrV was investigated in organs of immunosuppressed and non-immunosuppressed SR animals. The virus was not detected by immunohistochemistry, virus isolation or co-cultivation. An in situ DNA hybridization test detected PrV gC gene sequences in the olfactory bulb of one sow. A nested polymerase chain reaction (PCR) assay revealed gB, gE and gD gene sequences of PrV in the tissues of trigeminal ganglia, olfactory bulb, tonsils and brain. The nucleotide sequences of the amplicons revealed 98 to 100% homology with the corresponding sequences of PrV. The large latency transcript (LLT) was not detected in the organs of the SR pigs. Transmission of the SR phenomenon to animals in contact or to the next generation was not observed. Considering the present observations and the facts that (i) PrV vaccination is not applied in Sweden; (ii) the SR animals occur not only in the South, but also in Northern Scandinavia, which has no history of PrV infection and (iii) viral reactivation was not observed under natural conditions or after experimental immunosuppression, it is concluded that the SR phenomenon should hardly be considered as a typical PrV latency. The present findings show that certain herpesviral genomic sequences exist in apparently uninfected individuals.

Animals↗

PubMed1996

Linkage of genes essential for synthesis of a polysaccharide capsule in Sphingomonas strain S88.

Several structurally related capsular polysaccharides that are secreted by members of the genus Sphingomonas are being developed as aqueous rheological control agents for diverse industrial and food applications. They include gellan (S-60), welan (S-130), rhamsan (S-194), S-657, S-88, S-198, S-7, and NW-11. We refer to these polysaccharides as sphingans, after the genus name. This paper characterizes the first gene cluster isolated from a Sphingomonas species (S88) that is required for capsule synthesis. Overlapping DNA segments which spanned about 50 kbp of S88 DNA restored the synthesis of sphingan S-88 in capsule-negative mutants. The mutations were mapped into functional complementation groups, and the contiguous nucleotide sequence for the 29-kbp cluster was determined. The genetic complementation map and the DNA sequences were interpreted as an extended multicistronic locus containing genes essential for the assembly and secretion of polysaccharide S-88. Many of the deduced amino acid sequences were similar to gene products from other polysaccharide-secreting bacteria such as Rhizobium meliloti (succinoglycan), Xanthomonas campestris (xanthan gum), and Salmonella enterica (O antigen). The S88 locus contained a four-gene operon for the biosynthesis of dTDP-L-rhamnose, an essential precursor for the sphingans. Unexpectedly, there were also two genes for secretion of a lytic or toxin-like protein nested within the polysaccharide cluster. The conservation and linkage of genes that code for a defensive capsule and genes for secretion of an offensive lysin or toxin suggest a heretofore unknown pathogenic life history for Sphingomonas strain S88.

ATP-Binding Cassette Transporters↗

PubMed2004

[Amplification and typing of Sta56 gene of Orientia tsutsugamushi from Shandong province].

OBJECTIVE: To clarify the gene type of Orientia tsutsugamushi (Ot) from Shandong province. METHODS: Nested-polymerase chain reaction (nPCR) was used to identify the gene type of 23 isolated Ot strains, 2 pools of homogenized leptotrombidium (L.) scutellare, 10 blood specimens of scrub typhus patients, and at the same time to compare with the international reference strains Gilliam, Karp, Kato. Sequencing analysis of the Sta56 gene was also used to further identify the precise gene types. RESULTS: Of the 35 samples, 33 had the same products in the amplification of template Ot-DNA. They all belonged to Kawasaki strains endemic in Japan while 2 (FXS4 and LHGM2 strain) belonged to Karp strains. The Sta56 gene sequence homologies to Japan Kawasaki strain of the 2 representative strains (B-16 and FXS2 strain) of the 33 samples were 94.22%, 95.21% respectively, but they were less than 75.87% to other prototype strains; The homologies to Karp strain of FXS4 and LHGM2 strain were 83.03%, 96.45% respectively. B-16 and FXS2 strain were designated as of types strain Japan Kawasaki, FXS4 and LHGM2 as Karp strain. CONCLUSION: The results indicated that the dominant Ot strains in Shandong Province were similar to Kawasaki strains, but Karp strains also existed.

Animals↗

PubMed1994

Dihydrofolate reductase of Drosophila. Cloning and expression of a gene with a rare transcript.

Traditionally, dihydrofolate reductase (DHFR) has been isolated and the corresponding gene cloned from drug-resistant cell lines which have amplified DHFR genes after selection. A Dhfr sequence has now been obtained by nested polymerase chain reaction (PCR) from Drosophila bearing a single gene copy. Using the PCR-amplified partial cDNA as a probe, Dhfr was cloned by screening a Drosophila genomic library. It consists of regulatory regions as well as a 599-nucleotide coding region with a single 50-base pair (bp) intron and encodes a protein of 182 amino acids. Previously we have shown that the enzyme has kinetic properties characteristic of both "prokaryotic" and "eukaryotic" DHFRs. Here we show that the organization of Drosophila Dhfr is strikingly different from its mammalian counterparts and most similar to that of mosquito. A 790-bp transcript was detected by Northern blot analysis, with a single transcription start site located 27 bp upstream of ATG codon. The Drosophila genome contains a single Dhfr copy at 89E and a selected cell line has not amplified the gene. Confirmation of the identity of this gene has been obtained by kinetic studies of recombinant DHFR over-expressed in Escherichia coli cells.

Amino Acid Sequence↗

PubMed1998

Preliminary study on the production of transgenic mice harboring hepatitis B virus X gene.

AIM:To establish transgenic mice lineage harboring hepatitis B virus X gene and to provide an efficient animal model for studying the exact role of the HBx gene in the process of hepatocarcinogenesis.METHODS:The HBx transgenic mice were produced by microinjecting the construct with X gene of HBV (subtype adr) DNA fragment into fertilzed eggs derived from inbred C57BL/6 strain; transgenic mice were identified by using Nested PCR; expression and phenotype of HBx gene were analyzed in liver from transgenic mic at the age of 8 weeks by RT-PCR, pathologic examination and periodic acid-schiff staining (PAS), respectively.RESULTS:Five hundred and fourteen fertilized eggs of C57 BL/6 mice were microinjected with recombinant retroviral DNA fragment, and 368 survival eggs injected were transferred to the oviducts of 18 pseudopregnant recipient mice, 8 of them became pregnant and gave birth to 20 F1 offspring. Of 20 offsprings, four males and two females carried the hybrid gene (HBx gene). Four male mice were determined as founder, named X 1, X 5, X 9 and X 15. These founders were back crossed to set up F1 generations with other ibred C57BL/6 mice or transgenic littermates, respectively.Transmission of HBx gene in F1 offspring of X 1, X 5 and X 9 except in X 15 followed Mendelian rules. The expression of HBx mRNA was detected in liver of F1 offspring from the founder mice (X 1 and X 9), which showed vacuolation lesion and glycogen positive foci.CONCLUSION:Transgenic mice harboring HBx gene were preliminarily established.

Journal Article↗

PubMed2004

Detection of Brazilian hantavirus by reverse transcription polymerase chain reaction amplification of N gene in patients with hantavirus cardiopulmonary syndrome.

We report a nested reverse transcription-polymerase chain reaction (RT-PCR) assay for hantavirus using primers selected to match high homology regions of hantavirus genomes detected from the whole blood of hantavirus cardiopulmonary syndrome (HCPS) patients from Brazil, also including the N gene nucleotide sequence of Araraquara virus. Hantavirus genomes were detected in eight out of nine blood samples from the HCPS patients by RT-PCR (88.9% positivity) and in all 9 blood samples (100% positivity) by nested-PCR. The eight amplicons obtained by RT-PCR (P1, P3-P9), including one obtained by nested-PCR (P-2) and not obtained by RT-PCR, were sequenced and showed high homology (94.8% to 99.1%) with the N gene of Araraquara hantavirus. Although the serologic method ELISA is the most appropriate test for HCPS diagnosis, the use of nested RT-PCR for hantavirus in Brazil would contribute to the diagnosis of acute hantavirus disease detecting viral genomes in patient specimens as well as initial genomic characterization of circulating hantaviruses.

Adolescent↗

PubMed2004

PCR-based detection of betanodaviruses from cultured and wild marine fish with no clinical signs.

Betanodaviruses are the causative agents of viral nervous necrosis (VNN) or viral encephalopathy and retinopathy (VER) in cultured marine fish. A total of 131 apparently healthy fish from 30 species were collected in two geographically remote aquaculture areas, Yashima Bay (Kagawa Prefecture) and Tamanoura Bay (Nagasaki Prefecture), in Japan. The brains of fish were examined by reverse transcriptase-polymerase chain reaction (RT-PCR) and nested PCR to detect the coat protein gene of betanodavirus. In Yashima Bay, two and 13 of 20 cultured fish were positive for nodavirus in RT-PCR and nested PCR, respectively, and four of five wild fish were positive only in nested PCR. In Tamanoura Bay, 28 and 99 of 106 wild fish were positive for the virus in RT-PCR and nested PCR, respectively. All the sequences of the nested PCR products (177 nt) from 27 fish species (10 cultured and 17 wild) were highly homologous to each other (99-100%) and were closely related to that of the known betanodavirus, redspotted grouper nervous necrosis virus (RGNNV). These results illustrate that large populations of cultured and wild marine fish in aquaculture areas are subclinically infected with genetically closely related betanodaviruses, suggesting an importance of such infected fish as a carrier or reservoir of betanodaviruses.

Animals↗

PubMed2006

[DNA sequence polymorphism of Chlamydia trachomatis omp1 gene].

A method for detection and genotyping of genital Chlamydia trachomatis infections based on omp1 gene amplification and sequencing was developed, and the character of omp1 gene of Chlamydia trachomatis was analysed. Urethral or endocervical specimens were collected from 323 patients attending STD clinics in Hengyang, Shanghai, Guangzhou and Jiangmen from November, 2003 to May, 2004. DNA was extracted by usual method, and an approximately 980bp fragment from the major outer membrane protein (omp1) gene of Chlamydia trachomatis was amplified by nested polymerase chain reaction (nPCR). The PCR products were purified by DNA agarose gel purification system and the sequence of the omp1 gene was determined by using an ABI PRISM 3700 Genetic Analyser, and genotyping was performed by BLAST similarity search. Multiple alignment was performed with CLUSTAL package (CLUSTAL X), and a phylogenetic tree was constructed by Mega3 software to illustrate the evolutionary relationships between clinical isolates and reference strains of C. trachomatis obtained from GenBank. All variable sequences were submitted to GenBank by Banklt programe. The overall prevalence of urogenital chlamydial infection was 29.7% (96 of 323). All the 96 C. trachomatis-positive cases were sequenced, and 10 genotypes and 28 genetic variants were detected. The most prevalent genotype was E(34.4%), followed by J(25.0%), D(12.5%), F(8.3%), G(7.3%), H(3.1%), Ba(3.1%), K(3.1%), Da (2.1% ), 1 (1.1%). The distribution of C. trachomatis genotypes in the four cities in sourth China was similar to other countries in the world. The omp1 gene was highly conserved for genotype E and F, but appeared slightly less conserved for other genotypes, where the sequences displayed one or several nucleotide substitutions relatived to the corresponding reference sequence. And a similar recombination was found between genotypes Ba and D in CD1. Phylogenetic tree showed that Chlamydia trachomatis genotypes were mainly divided into three clusters, according to previous grouping in the B, F-G, and C complexes. Clusters F-G and C were characterized by small genetic distances within each cluster, but clusters B displayed larger genetic distances. And the clinical isolates were highly related to the reference strains. It is concluded that the isolated Chlamydia trachomatis strains exhibit remarkable omp1 DNA sequence polymorphism, which can encourage for vaccine design and infection control.

Chlamydia Infections↗

PubMed2005

Molecular diagnosis. Classification, model selection and performance evaluation.

OBJECTIVES: We discuss supervised classification techniques applied to medical diagnosis based on gene expression profiles. Our focus lies on strategies of adaptive model selection to avoid overfitting in high-dimensional spaces. METHODS: We introduce likelihood-based methods, classification trees, support vector machines and regularized binary regression. For regularization by dimension reduction, we describe feature selection methods: feature filtering, feature shrinkage and wrapper approaches. In small sample-size situations efficient methods of data re-use are needed to assess the predictive power of a model. We discuss two issues in using cross-validation: the difference between in-loop and out-of-loop feature selection, and estimating model parameters in nested-loop cross-validation. RESULTS: Gene selection does not reduce the dimensionality of the model. Tuning parameters enable adaptive model selection. The feature selection bias is a common pitfall in performance evaluation. Model selection and performance evaluation can be combined by nested-loop cross-validation. CONCLUSIONS: Classification of microarrays is prone to overfitting. A rigorous and unbiased assessment of the predictive power of the model is a must.

Gene Expression Profiling↗

PubMed2005

Closely linked polymorphic marker: successful application in preimplantation genetic diagnosis for beta-thalassemia.

OBJECTIVE: To evaluate the applicability of the polymorphic marker closely linked with beta-globin gene for the preimplantation genetic diagnosis (PGD) in couples at risk of having child with beta-thalassemia. METHODS: Single cell multiplex nested PCR which coamplifies the beta-globin gene and the closely linked polymorphic marker, HumTHO1 gene, was applied in six clinical PGD cycles for four couples with beta-thalassemia. RESULTS: In six clinical PGD cycles, a total of 44 embryos were biopsied and 44 blastomeres were obtained. Forty-one blastomeres were amplified and thirty-five embryos were given definite diagnoses. Fourteen embryos were transferred back to the uterus of the patients and one pregnancy went on well and ended with one live healthy birth, which confirmed the results of PGD. The average amplification efficiency of single blastomere was 89.7% and the average allele drop-out(ADO) rate was 14.4%. The coamplification of HumTHO1 could help to detect the existence of ADO and contamination. CONCLUSION: This is the first report on unaffected pregnancy resulting from PGD using multiplex nested PCR in China. The simultaneous amplification of polymorphic marker closely linked to beta-globin gene(HumTHO1) could help to resist the risk of misdiagnosis in PGD caused by ADO and contamination.

Adult↗

PubMed2002

Gene family phylogenetics: tracing protein evolution on trees.

How have proteins taken on the remarkable diversity of biochemical and physiological functions necessary to create and maintain complex organisms? The majority of proteins are organized hierarchically into families and superfamilies, reflecting an ancient and continuing process of gene duplication and divergence. The techniques of molecular phylogenetics, developed to recover the nested hierarchy of taxa from character information in their gene sequences, can also reconstruct the evolutionary relationships among genes and provide a conceptual foundation for comparative evolutionary analysis of proteins and their functions. In this review, I outline the application of phylogenetic approaches to issues in gene family studies, beginning with the inference of phylogeny and the assessment of the two types of homology by which genes in a family can be related: orthology (common descent from a cladogenetic event) and paralogy (common descent from a gene duplication event). I show how the phylogenetic approach makes possible novel kinds of comparative analysis, including detection of exon shuffling, reconstruction of the evolutionary diversification of gene families, tracing of evolutionary change in protein function at the amino acid level, and prediction of structure-function relationships. A marriage of the principles of phylogenetic systematics with the copious sequence data being generated by molecular biology and genomics promises unprecedented insights into the nature of biological organization and the historical processes that created it.

Animals↗

PubMed1995

Detection of human parvovirus B19 DNA by nested polymerase chain reaction.

We describe the development of a nested polymerase chain reaction (PCR) technique used to detect human parvovirus B19 DNA. It was performed in a two-step reaction, first with a pair of outer primers, then with a pair of inner (ie, nested) primers. Primer sequences were selected in the VP1 gene, corresponding to the capsid protein, of human parvovirus B19. To establish the nested PCR assay, the plasmid pGEM-1 containing almost the entire coding sequence of a human parvovirus B19 isolate was used. The nested PCR could detect up to 1.8 x 10(-3) ag of B19 DNA, equivalent to 10(-4) genomes, by electrophoresis. No amplification product was detected by gel electrophoresis when the reaction mixture contained human placental DNA, cytomegalovirus DNA, and sterile distilled water as templates. We used this assay to evaluate four cases of maternal B19 infection that were diagnosed by determination of the presence of anti-B19 immunoglobulin-M in maternal serum. The advantages of our nested PCR for detecting B19 DNA are plating simplicity, safety, sensitivity, and specificity. Our results suggest that this method may have general applicability in the evaluation of nonimmune hydrops fetalis and in the documentation of the natural history of fetal infection with B19 when applied to specimens of amniotic fluid or fetal blood.

Adult↗

PubMed2001

[PCR amplification of anaerobic fungal 18S rDNA from landfill sites].

Nucleic acid based techniques are widely used to characterize microbial communities in environmental samples. In this study, seven landfill leachates were tested for the presence of 18S rRNA genes from anaerobic fungi from the family Chytridiomycetes. A nested Polymerase Chain Reaction (PCR) strategy was employed to amplify the 18S rRNA gene region of Chytridiomycetous fungi from landfill sites samples. All of the PCR products from landfill leachates amplified with the first primer pair NS1/NS8 and the second primer pair Chyt-719/Chyt-1553 were subjected to agarose gel electrophoresis to show seven samples containing fungi from the family Chytridiomycetes. One of the positive results was then selected for cloning and sequencing of the PCR product to confirm the identity of the amplified DNA. The molecular data presented here reveals for the first time that Chytridiomycetous fungi associated with the anaerobic rumen environment are also present in landfill sites.

Anaerobiosis↗