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Results for “Sanger sequencing”

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PubMed1990

Cloning and sequencing of a cDNA for the hemolymph juvenile hormone binding protein of larval Manduca sexta.

A cDNA for the hemolymph juvenile hormone binding protein (JHBP) of larval Manduca sexta has been cloned and sequenced. The JHBP was purified to homogeneity from fifth instar larval hemolymph using gel filtration chromatography, ion exchange chromatography, and preparative sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Polyclonal rabbit antibodies, generated in response to this protein, were used to identify and isolate JHBP cDNAs from a fat body expression library in bacteriophage lambda ZAPII. Eleven putative JHBP cDNA clones were isolated and subcloned into Bluescript plasmid; cDNA inserts were approximately 750 base pairs in length. A 36-kDa immunoreactive protein was expressed from these plasmids; this beta-galactosidase fusion protein, like the authentic 32-kDa JHBP, was specifically photoaffinity labeled with [3H] epoxyhomofarnesyl diazoacetate (EHDA). Single-stranded DNA from one clone was sequenced by the Sanger dideoxynucleotide method, using deletion and custom primer techniques. A mature translation product was identified which had 226 amino acid residues, a molecular mass of 25,111 daltons, and a predicted isoelectric point (pI) of 5.40. The cDNA correctly predicts the N-terminal amino acid sequence and the amino acid composition of an authentic M. sexta hemolymph JHBP. A computer search of protein and nucleic acid data bases failed to reveal any related sequences. Thus, M. sexta hemolymph JHBP appears to be the first member of a new superfamily of insect hormone binding proteins.

Affinity Labels↗

PubMed1991

DNA sequences for the specific detection of Cryptosporidium parvum by the polymerase chain reaction.

The objective of this project was to construct specific and sensitive molecular probes and amplification primers for Cryptosporidium parvum that could be used in diagnosis, retrospective tissue studies, and in epidemiologic surveys. Whole genomic DNA was extracted from oocysts of C. parvum purified from human and bovine feces. A genomic library was constructed in plasmid pUC18 and propagated in Escherichia coli DH5 alpha. Transformants were screened by colony hybridization and autoradiography. The 2.3-kilobase segment in plasmid pHC1, a clone specific for C. parvum, was sequenced by the Sanger method. Computer analysis gave a G+C content of 35%. A 400-base region (bases 470-870) was selected as an amplification target because it contained a unique restriction endonuclease site that could serve as a useful marker. Primers of 26 nucleotides each were synthesized. Sensitive and specific amplification of the target sequence was demonstrated both by ethidium bromide staining of agarose and acrylamide gels, and by hybridization with chemiluminescence-labeled synthetic oligonucleotide probes.

Animals↗

PubMed1979

Rapid sequence determination of late simian virus 40 16S mRNA leader by using inhibitors of reverse transcriptase.

A method for the determination of the primary structure of spliced mRNA junction and leader sequences is described. By analogy to the DNA sequencing procedure of Sanger et al. [Sanger, F., Nicklen, S. & Coulson, A. R. (1977) Proc. Natl. Acad. Sci USA 74, 5463--5467], we use 2",3'-dideoxynucleoside triphosphates as chain-terminating inhibitors of the reverse transcriptase (RNA-dependent DNA polymerase) reaction. By using specific DNA restriction fragments as primers in combination with this technique, we have determined the sequence of the spliced junction between the body and the leader sequence of the 16S late mRNA of simian virus 40. The method described should be of general utility in mapping spliced mRNA regions for which the corresponding protein sequence (if any) is unknown.

Base Sequence↗

PubMed2001

Primer-independent RNA sequencing with bacteriophage phi6 RNA polymerase and chain terminators.

Here we propose a new general method for directly determining RNA sequence based on the use of the RNA-dependent RNA polymerase from bacteriophage phi6 and the chain terminators (RdRP sequencing). The following properties of the polymerase render it appropriate for this application: (1) the phi6 polymerase can replicate a number of single-stranded RNA templates in vitro. (2) In contrast to the primer-dependent DNA polymerases utilized in the sequencing procedure by Sanger et al. (Proc Natl Acad Sci USA, 1977, 74:5463-5467), it initiates nascent strand synthesis without a primer, starting the polymerization on the very 3'-terminus of the template. (3) The polymerase can incorporate chain-terminating nucleotide analogs into the nascent RNA chain to produce a set of base-specific termination products. Consequently, 3' proximal or even complete sequence of many target RNA molecules can be rapidly deduced without prior sequence information. The new technique proved useful for sequencing several synthetic ssRNA templates. Furthermore, using genomic segments of the bluetongue virus we show that RdRP sequencing can also be applied to naturally occurring dsRNA templates. This suggests possible uses of the method in the RNA virus research and diagnostics.

Bacteriophage phi 6↗

PubMed1996

Familial dementia of frontal lobe type.

OBJECTIVE: To describe an unusual case of familial frontal lobe dementia (FLD) with probable spongiform encephalopathy (SE). METHOD: The patient's clinical presentation, neuropsychological test results, family history, and results on magnetic resonance imaging (MRI) and positron emission tomography (PET) scans, among other routine investigations, are described. His leucocyte deoxyriboneucleic acid (DNA) was isolated, and his Prp (prion protein) gene was amplified with the polymerase chain reaction and sequenced using the Sanger method. RESULTS: Clinically, the patient had a presenile frontal lobe dementia. Four of the 8 members of the generation preceding the patient had presenile dementia. Autopsies performed on 2 of these cases revealed SE, and a pathological diagnosis of Creutzfeldt-Jakob disease (CJD) was made. One other member of that generation died of a limbic encephalitis, although the neuropathological findings were atypical. Sequencing of the patient's Prp gene did not reveal the abnormalities expected in a familial case of CJD. The results of other investigations were compatible with FLD but were not specific to a particular diagnosis. CONCLUSIONS: This case is a novel type of SE. The patient presented clinically with FLD, but based on the family history and neuropathology, a diagnosis of prion dementia seems likely. There were no mutations found in the Prp gene, so it is possible that there are SEs caused by genes or other pathological processes unrelated to the Prp gene.

Adult↗

PubMed2001

[Expression of GM-CSF in patients with pulmonary alveolar proteinosis].

OBJECTIVE: To investigate the expression of granulocyte-macrophage colony-stimulating factor (GM-CSF) protein and mRNA in four patients with pulmonary alveolar proteinosis (PAP). METHODS: GM-CSF levels were measured with a commercial ELISA kit. RT-PCR was employed to detect the expression of the GM-CSF mRNA in peripheral blood mononuclear cells (PBMC) and alveolar macrophages. To discover the possible mutations, the entire coding region of the GM-CSF cDNA was sequenced by the Sanger dideoxy-mediated chain termination method. RESULTS: All patients, except for the one with secondary PAP showed no release of GM-CSF either from PBMC or from alveolar macrophages. The expression of the GM-CSF mRNA was normal in all patients, whereas a point mutation at position 382 of the GM-CSF cDNA from "T" to "C" was revealed by cDNA sequencing in one idiopathic PAP patient, which caused a change from isoleucine to threonine in amino acid 117 of the protein. CONCLUSIONS: Decreased GM-CSF production is associated with the pathogenesis of idiopathic PAP. A point mutation of the GM-CSF cDNA may partly contribute to the decreased GM-CSF production.

Adult↗

PubMed2002

Analysis of the GM-CSF and GM-CSF/IL-3/IL-5 receptor common beta chain in a patient with pulmonary alveolar proteinosis.

OBJECTIVE: To investigate the expression of the granulocyte-macrophage colony-stimulating factor (GM-CSF) and GM-CSF/IL-3/IL-5 receptor common beta chain (beta c receptor) in an adult patient with idiopathic pulmonary alveolar proteinosis (PAP), so as to demonstrate the possible association of the GM-CSF and beta c receptor with the pathogenesis of human PAP. METHODS: The GM-CSF levels were measured with a commercial ELISA kit (sensitivity 5 pg/ml) and the beta c receptor expression on the cell surface was detected by flow cytometry analysis. Reverse transcription polymerase chain reaction (RT-PCR) analysis was employed to detect the expression of the GM-CSF mRNA and the beta c receptor mRNA in peripheral blood mononuclear cells and alveolar macrophages. The entire coding regions of the GM-CSF cDNA and the beta c receptor cDNA were sequenced by the Sanger dideoxy-mediated chain termination method to detect possible mutations. RESULTS: The patient with PAP failed to release the GM-CSF protein either from circulating mononuclear cells or from alveolar macrophages. The expression of the GM-CSF mRNA was normal after the stimulation of lipopolysaccharide, whereas a point mutation at position 382 of the GM-CSF cDNA from "T" to "C" was revealed by cDNA sequencing, which caused a change in amino acid 117 of the protein from isoleucine to threonine. The beta c receptor expression on the cell surface was normal, and the beta c receptor mRNA expression and the sequence of the entire coding region of the beta c receptor were also normal. CONCLUSIONS: The decreased GM-CSF production is associated with the pathogenesis of human PAP. A point mutation of the GM-CSF cDNA may contribute to the decreased GM-CSF production in our adult PAP patient. The mutation of the beta c receptor in some of paediatric patients with PAP may not be a common problem in adult patients.

DNA, Complementary↗

PubMed1997

[Identification of 5 variants of the hemoglobin beta chain using DNA analysis (amplification, sequencing and restriction enzymes)].

PURPOSE: To confirm the conventional techniques for studying structural haemoglobinopathies and to show off the simplicity and efficacy of new methods based on the study of DNA. PATIENTS AND METHODS: Peripheral blood samples of 17 patients with 5 haemoglobin variants detected by conventional and shown off by means of sequencing according to Sanger's method, plus PCR-RFLP, were studied. RESULTS: Five structural haemoglobin variants were found, which distributed as follows: 7 cases of Hb Complutense (beta 127 Gln-->Glu), 1 Hb D-Punjab (beta 121 Glu-->Gln), 3 Hb Hofu (beta 126 Val-->Glu), 3 Hb J-Baltimore (beta 16 Gly-->Asp) and 3 Hb San Diego (beta 109 Val-->Met). CONCLUSIONS: These results allow us to stress the simplicity and usefulness of DNA analysis (sequencing , amplification and enzymatic digestion) to identify haemoglobin variants as opposed to laborious analysis of the primary structure by means of HPLC peptide separation.

DNA Mutational Analysis↗

PubMed2005

Differences in gene content between Salmonella enterica serovar Enteritidis isolates and comparison to closely related serovars Gallinarum and Dublin.

Salmonella enterica serovar Enteritidis is often transmitted into the human food supply through eggs of hens that appear healthy. This pathogen became far more prevalent in poultry following eradication of the fowl pathogen S. enterica serovar Gallinarum in the mid-20th century. To investigate whether changes in serovar Enteritidis gene content contributed to this increased prevalence, and to evaluate genetic heterogeneity within the serovar, comparative genomic hybridization was performed on eight 60-year-old and nineteen 10- to 20-year-old serovar Enteritidis strains from various hosts, using a Salmonella-specific microarray. Overall, almost all the serovar Enteritidis genomes were very similar to each other. Excluding two rare strains classified as serovar Enteritidis in the Salmonella reference collection B, only eleven regions of the serovar Enteritidis phage type 4 (PT4) chromosome (sequenced at the Sanger Center) were absent or divergent in any of the other serovar Enteritidis strains tested. The more recent isolates did not have consistent differences from 60-year-old field isolates, suggesting that no large genomic additions on a whole-gene scale were needed for serovar Enteritidis to become more prevalent in domestic fowl. Cross-hybridization of phage genes on the array with related genes in the examined genomes grouped the serovar Enteritidis isolates into two major lineages. Microarray comparisons of the sequenced serovar Enteritidis PT4 to isolates of the closely related serovars Dublin and Gallinarum (biovars Gallinarum and Pullorum) revealed several genomic areas that distinguished them from serovar Enteritidis and from each other. These differences in gene content could be useful in DNA-based typing and in understanding the different phenotypes of these related serovars.

Bacterial Typing Techniques↗

PubMed1985

Site-directed mutagenesis of aspartate aminotransferase from E. coli.

The gene for aspartate aminotransferase from E. coli (aspC) was subcloned into M13 phage and sequenced using the Sanger dideoxy method with synthetic oligonucleotide primers. A mutant gene was constructed using site-directed mutagenesis techniques in which the codon for the lysine that forms the Schiffs base with pyridoxal phosphate was replaced with one coding for alanine. The mutant gene was expressed under control of the Tac promoter to overproduce a mutant protein lacking enzymatic activity.

Aspartate Aminotransferases↗

PubMed2003

Computational and experimental analysis reveals a novel Src family kinase in the C. elegans genome.

MOTIVATION: The complete genomes of a number of organisms have already been sequenced. However, the vast majority of annotated genes are derived by gene prediction methods. It is important to not only validate the predicted coding regions but also to identify genes that may have been missed by these programs. METHODS: We searched the entire C.elegans genomic sequence database maintained by the Sanger Center using human c-Src sequence in a TBLASN search. We have confirmed one of the predicted regions by isolation of a cDNA and carried out a phylogenetic analysis of Src kinase family members in the worm, fly and several vertebrate species. RESULTS: Our analysis identified a novel tyrosine kinase in the C.elegans genome that contains functional features typical of the Src family kinases that we have designated as Src-1. The open reading frame contains a conserved N-terminal myristoylation site and a tyrosine residue within the C-terminus that is crucial for regulating the activity of Src kinases. Our phylogenetic analysis of Src family members from C. elegans, Drosophila and other higher organisms revealed a relationship among Src kinases from C. elegans and Drosophila.

Amino Acid Sequence↗

PubMed2003

The phusion assembler.

The Phusion assembler has assembled the mouse genome from the whole-genome shotgun (WGS) dataset collected by the Mouse Genome Sequencing Consortium, at ~7.5x sequence coverage, producing a high-quality draft assembly 2.6 gigabases in size, of which 90% of these bases are in 479 scaffolds. For the mouse genome, which is a large and repeat-rich genome, the input dataset was designed to include a high proportion of paired end sequences of various size selected inserts, from 2-200 kbp lengths, into various host vector templates. Phusion uses sequence data, called reads, and information about reads that share common templates, called read pairs, to drive the assembly of this large genome to highly accurate results. The preassembly stage, which clusters the reads into sensible groups, is a key element of the entire assembler, because it permits a simple approach to parallelization of the assembly stage, as each cluster can be treated independent of the others. In addition to the application of Phusion to the mouse genome, we will also present results from the WGS assembly of Caenorhabditis briggsae sequenced to about 11x coverage. The C. briggsae assembly was accessioned through EMBL, http://www.ebi.ac.uk/services/index.html, using the series CAAC01000001-CAAC01000578, however, the Phusion mouse assembly described here was not accessioned. The mouse data was generated by the Mouse Genome Sequencing Consortium. The C. briggsae sequence was generated at The Wellcome Trust Sanger Institute and the Genome Sequencing Center, Washington University School of Medicine.

Animals↗

PubMed1998

Nucleotide sequence and deduced amino acid sequence of the nonstructural proteins of dengue type 3 virus, Bangkok genotype.

The nucleotide sequence of the nonstructural protein gene (1,610 bases) of dengue 3 virus (Bangkok genotype; CH53489 isolated in 1973) has been determined in both forward and reverse directions. The PCR based cycle sequencing technic by the enzymatic method of Sanger et al using a sequencing primer 5'-end labeled with gamma-32P-ATP was the method of our choice for sequence analysis. Two cDNA templates were prepared by RT-PCR technique starting from the nucleotides 6,306-6,969 and 6,925-7,915 of the dengue 3 genome with the lengths of 663 and 990 base pairs respectively. In our cycle sequencing experiments, it has been observed that the substitution of 7-deaza-dG for dG in DNA eliminated most of the secondary structures that produce gel artifacts. The final sequence results of these two cDNA templates were established from their sequence data determined on both strands in opposite directions. Alignment between the newly established nucleotide sequences as well as their deduced amino acid sequences of the Bangkok dengue 3 (CH53489) virus and the published sequence data of the dengue 3 prototype (H87) was manipulated by the PC-DOS-GIBIO DNASIS TM 06-00 software. The homology of the nucleotide sequences between the two dengue 3 viruses was 96.65%. The deduced amino acid sequence from nucleotides 6,306-7,915 of the two viruses showed conserved amino acids of the nonstructural protein NS4a and 6 amino acid changes in NS4b and NS5.

Amino Acid Sequence↗

PubMed1994

[Cloning cDNA of human S26 ribosomal protein and determination of its primary structure].

The polymerase chain reaction technique was employed to isolate cDNA encoding S26 human ribosomal protein. Based on the known sequence of rat S26 ribosomal protein we have designed primers and amplified the corresponding sequence of human cDNA from total placenta cDNA. The fragment of S26 cDNA was cloned in a plasmid vector and sequenced by the Sanger method. Extremely high homology (87.7%) between coding regions of S26 mRNAs in rat liver and human placenta was revealed. The only amino acid substitution (Ser-->Val) at position 38 was observed. Results of blot hybridization with partially digested human genomic DNA suggest the presence of more than 6 copies of the S26 gene.

Amino Acid Sequence↗

PubMed1999

Molecular analysis of PRNP gene in Polish population and in Creutzfeldt-Jakob disease.

In our study we have examined allelic variation of codon 129 among the Polish population as well as Polish and Dutch CJD cases. The open reading frame of the PrP gene was amplified using the polymerase chain reaction (PCR). PCR product was digested with Nsp I and Mae II endonucleases and separated by 2% agarose gel electrophoresis and, finally, sequenced by the Sanger dideoxy-mediated chain-termination method. To obtain population data we have screened 109 unrelated Polish adults. There were 45% of methionine homozygotes, 16% of valine homozygotes and 3% of heterozygotes. Among Polish CJD cases, 75% were methionine homozygous, 12.5% were valine homozygous and 12.5% were heterozygous, whereas among Dutch CJD cases it was 29% of Met/Met and 71% of Met/Val genotypes.

Adult↗

PubMed1985

Rapid and reliable dideoxy sequencing of double-stranded DNA.

We report a simple and reliable protocol for nucleotide sequencing using the Sanger dideoxy technique on linearized double-stranded DNA molecules with specific oligonucleotide primers. The method is demonstrated for restriction fragments cloned into the plasmid vectors pSP64 and pSP65 using two vector-specific primers, the M13 reverse primer and a new SP6 primer, flanking the multiple cloning site. Template DNA may be prepared by a rapid alkaline lysis procedure. Mild linearization conditions with the appropriate restriction endonuclease avoid the appearance of artifact bands.

Base Sequence↗

PubMed1998

Automated sequence preprocessing in a large-scale sequencing environment.

A software system for transforming fragments from four-color fluorescence-based gel electrophoresis experiments into assembled sequence is described. It has been developed for large-scale processing of all trace data, including shotgun and finishing reads, regardless of clone origin. Design considerations are discussed in detail, as are programming implementation and graphic tools. The importance of input validation, record tracking, and use of base quality values is emphasized. Several quality analysis metrics are proposed and applied to sample results from recently sequenced clones. Such quantities prove to be a valuable aid in evaluating modifications of sequencing protocol. The system is in full production use at both the Genome Sequencing Center and the Sanger Centre, for which combined weekly production is approximately 100, 000 sequencing reads per week.

Automation↗

PubMed2006

Comprehensive mutation identification in an evolved bacterial cooperator and its cheating ancestor.

Precise characterization of the mutation histories of evolutionary lineages is crucial for understanding the evolutionary process, yet mutation identification has been constrained by traditional techniques. We sought to identify all accumulated mutations in an experimentally evolved lineage of the cooperative bacterium Myxococcus xanthus, which constructs fruiting bodies by a process of social multicellular development in response to starvation. This lineage had undergone two major transitions in social phenotype: from an ancestral cooperator to a socially defective cheater, and from the cheater to a competitively dominant cooperator that re-evolved social and developmental proficiency. The 9.14-Mb genome of the evolved, dominant cooperator (strain "PX") was sequenced to approximately 19-fold coverage by using recent "sequencing-by-synthesis" technology and partially sequenced (approximately 45%) by using capillary technology. The resulting data revealed 15 single-nucleotide mutations relative to the laboratory ancestor of PX after the two phases of experimental evolution but no evidence of duplications, transpositions, or multiple-base deletions. No mutations were identified by capillary sequencing beyond those found by pyrosequencing, resulting in a high probability that all mutations were discovered. Seven errors in the reference strain previously sequenced by the Sanger approach were revealed, as were five mutational differences between two distinct laboratory stocks of the reference strain. A single mutation responsible for the restoration of development in strain PX was identified, whereas 14 mutations occurred during the prior phase of experimental evolution. These results provide insight into the genetic basis of two large adaptive transitions in a social bacterium.

Adaptation, Biological↗