Sequence analysis of adenovirus DNA. IV. The genomic sequences encoding the common tripartite leader of late adenovirus messenger RNA.
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Adenoviruses, Human↗
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Results for “Sequence analysis”
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Amino acid sequence of the basic trypsin inhibitor from bovine splenic capsule. A new fluorescent reagent for protein sequence analysis.
The amino acid sequences of tryptic peptides from the performic acid-oxidized trypsin inhibitor were determined. The degradation was performed with a new reagent, 3-isothiocyanato-4-methoxy-4'-nitrostilbene, and compared with the dansyl-Edman technique. The amino acid sequence of the trypsin inhibitor from bovine splenic capsule was found to be the same as that of the basic trypsin inhibitor from bovine pancreas, established by Kress & Laskowski (J. Biol. Chem. 1967, 242, 4925-4928).
Amino Acid Sequence↗
A double-labeling procedure for sequence analysis of picomole amounts of nonradioactive RNA fragments.
A double-labeling procedure for sequence analysis of nonradioactive polyribonucleotides is detailed, which is based on controlled endonucleolytic degradation of 3'-terminally (3H)-labeled oligonucleotide-(3') dialcohols and 5"-terminal analysis of the partial (3H)-labeled fragments following their separation according to chain length by polyethyleneimine- (PEI-)cellulose TLC and detection by fluorography. Undesired nonradioactive partial digestion products are eliminated by periodate oxidation. The 5'-termini are assayed by enzymic incorporation of (32p)-label into the isolated fragments, enzymic release of (32p)-labeled nucleoside-(5') monophosphates, two-dimensional PEI-cellulose chromatography, and autoradiography. Using this procedure, as little as 0.1 - 0.3 A260 unit of tRNA is needed to sequence all fragments in complete ribonuclease T1 and A digests, whereas radioactive derivative methods previously described by us1-4 required 4 - 6 A260 units.
Base Sequence↗
Structural studies on the murine Ia alloantigens. IV. NH2-terminal sequence analysis of allelic products of the I-A and I-E/C subregions.
Murine Ia alloantigens encoded by the I-A and I-E/C subregions were isolated from radiolabeled splenic lysates and examined by NH2-terminal sequence analysis. Haplotype-associated sequence variation was detected in the beta, but not alpha, subunits of both the A and E/C alloantigens. The A beta-polypeptides from k and b haplotypes show four differences in the 12 positions compared, whereas the E/C beta-polypeptides from k and r haplotypes show two differences in the 13 positions compared. No sequence variation was detected between the Ak and Ab alpha-chains (six positions compared) or between the E/Ck and E/Cr alpha-chains (11 positions compared). Homology relationships between these murine Ia alloantigens and the human Ia (DR) alloantigens are also presented.
Alleles↗
DNA sequence analysis of Tn10 insertions: origin and role of 9 bp flanking repetitions during Tn10 translocation.
The sequences of insertions of the translocatable tetracycline-resistance element Tn10 into the repressor (cl) gene of bacteriophage lambda have been analyzed. Each insertion contains the same discrete set of Tn10 sequences flanked by a direct repetition of a 9 bp cl-gene sequence. The flanking repititions are generated by duplication of information present only in the target DNA molecule rather than by a Campbell-type recombination event between one 9 bp sequence on the target DNA and a second one provided on the incoming element. The repetitions do not contain genetic or structural information important for translocation. A genetically constructed Tn10 insertion which lacks flanking repetitions is fully functional in translocation to a new position. Tn10 insertions cluster at preferred positions along a target DNA (Kleckner et al., 1979). Sequence analysis shows that four independently isolated cl::Tn10 insertions occur at identical positions in the cl gene. We speculate that homology between Tn10 and its target, at some distance from the site of the actual recombination event, could be relevant to the preference of Tn10 for particular insertion sites.
Base Sequence↗
Manual solid phase sequence analysis of polypeptides using 4-N-N,-dimethylaminoazobenzene 4'-isothiocyanate.
A manual solid-phase method for sequence analysis of polypeptides is described. The immobilized polypeptide was subjected to stepwise degradation by Edman-type reagent, using the 4-N,N-dimethylaminoazobenzene 4'-isothiocyanate phenyllisothiocyanate double coupling method. The N-terminal amino acids were released (after conversion reaction) as 4-N,N-dimethylaminoazobenzene 4'-thiohydantoin (identified by thin layer chromatography) and phenylthiohydantoin derivatives. The method required 2--10 nmol polypeptide.
Amino Acid Sequence↗
4-NN-dimethylaminoazobenzene 4'-isothiocyanate, a new chromophoric reagent for protein sequence analysis.
4-NN-Dimethylaminoazobenzene 4'-isothiocyanate was synthesized for the purpose of improving the ease and sensitivity of peptide sequence analysis. The method of 4-NN-dimethylaminoazobenzene 4'-isothiocyanate synthesis, the preparation of 24 4-NN-dimethylaminoazobenzene-4'-thiohydantoins of amino acids and their t.l.c. separation are described. All the thiohydantoins, except those of leucine and isoleucine, could be satisfactorily separated by chromatography on a two-dimensional polyamide sheet. The sensitive azo group permits the detection of 4-NN-dimethylaminoazobenzene-4'-thiohydantoins of amino acids as red spots down to pmol amounts directly on the sheet. A simple sensitive method for sequencing dipeptides and the first two or three N-terminal amino acids of proteins is also reported. The colour change of the spots from purple to blue to red after being exposed to HCl vapour, corresponding to the chemical change from 4-NN-dimethylaminoazobenzene-4' isothiocyanate to the 4-NN-dimethylaminoazobenzene-4'-thiocarbamoyl amino acid derivative to the 4-NN-dimethylaminoazobenzene-4'-thiohydantoin amino acid derivative, reveals a very interesting and valuable feature of this reagent.
Amino Acid Sequence↗
Nucleotide sequence analysis of two simian virus 40 mutants with deletions in the region coding for the carboxyl terminus of the T antigen.
Nucleotide sequence analysis of two simian virus 40 early mutants dl1263 and dl1265, which lack a DNA segment around map positions 0.21 and 0.18, respectively (C. Cole, T. Landers, S. Goff, S. MAnteuil-Brutlag, and P. Berg, J. Virol. 24:277--294, 1977), revealed in-phase deletions of 33 nucleotide pairs for dl1263 and 39 nucleotide paris for dl1265. The 33-base-pair deletion in dl1263 does not correspond to an apparent shortening by 6,000 daltons observed for the mutant T antigen. In dl1265 the normal termination signal as well as most of the proline-rich terminal tryptic peptide has been removed, and the carboxyl terminus of the mutant T antigen is a series of three cysteine residues.
Antigens, Viral↗
Detection and partial sequence analysis of gastrin mRNA by using an oligodeoxynucleotide probe.
We have used a specific deoxyoligonucleotide probe to detect gastrin mRNA in poly(A)-enriched RNA preparations from hog antrum. The nucleotide sequence of the oligonucleotide, d(C-T-C-C-T-C-C-A-T-C-C-A), was deduced from the unique amino acid sequence Trp-Met-Glu-Glu of gastrin. When used with hog antral RNA, the dodecanucleotide is an effective primer for the synthesis of gastrin-specific cDNA as judged by nucleotide sequence analysis of cDNA isolated by polyacrylamide gel electrophoresis. We have determined an 81-nucleotide sequence corresponding to the region of the gastrin mRNA that codes for the known amino acid sequence of the G34 progastrin intermediate species, and we have demonstrated the presence of two consecutive basic residues preceding the G34 sequence in the prohormone. Hybridization of gastrin cDNA or synthetic dodecanucleotide to hog antral RNA separated by gel electrophoresis on agarose gels in the presence of methylmercuric hydroxide indicates that the mRNA coding for gastrin is about 620 nucleotides long. These results suggest that the gastrin precursor peptide contains 110-140 amino acids. This method should be of general application for detection and characterization of mRNAs corresponding to proteins of known amino acid sequence.
Animals↗
Sequence analysis of two yeast mitochondrial DNA fragments containing the genes for tRNA Ser UCR and tRNA Phe UUY.
Two restriction enzyme fragments containing yeast mitochondrial tRNA genes have been characterized by DNA sequence analysis. One of these fragments is 320 base pairs long and contains a tRNA Ser gene. The corresponding tRNA SER was isolated from yeast mitochondria and its nucleotide sequence also was determined. This mitochondrial tRNA is 90 nucleotides in length, has a G + C content of 38%, and has UGA as the anticodon. A portion of a 680-base-pair DNA fragment containing a tRNA Phe gene was also sequenced. The portion of this gene which codes for the mature tRNA is 75 base pairs in length, has a G + C content of 33%, and contains the anticodon GAA. Neither gene contains an intervening sequence or codes for the 3' CCA terminus. Both are surrounded by regions of more than 90% A + T. The significance of these sequences is discussed.
Base Sequence↗
Nucleotide sequence analysis of viable deletion mutants lacking segments of the simian virus 40 genome coding for small t antigen.
The deletions in nine viable simian virus 40 mutants have been mapped by direct DNA sequence analysis. The mutant DNAs lack small segments of the early region of the viral chromosome (between 0.535 and 0.600 map unit). The deletions are all located in the region which is removed from the large T antigen transcript by splicing. No one deletion removes this entire region, but no part of this segment is conserved in all of the mutants except for several nucleotides near the splice points of the transcript. Although the deletions do not alter the region coding for the large T polypeptide, they do delete portions of the segment coding for the C-terminal half of the small t polypeptide.
Antigens, Viral↗
Conversion of rat pre-proalbumin to proalbumin in vitro by ascites membranes. Demonstration by NH2-TERMINAL SEQUENCE ANALYSIS.
Rat liver poly(A)-containing RNA was translated in an ascites cell-free system. Labeled protein precipitable by antibody directed against rat serum albumin was identified as pre-proalbumin based on its size and partial NH2-terminal sequence. However, when an ascites membrane fraction was added to the translation reaction, the albumin antibody-precipitable material was smaller than pre-proalbumin. Partial NH2-terminal sequence analysis of this protein revealed that it was proalbumin. Conversion of pre-proalbumin to proalbumin by the ascites membrane fraction was complete and precise--i.e. no serum albumin was observed. Reconstitution in vitro of the processing of pre-proalbumin to its stable intracellular form, proalbumin, provides a method for studying the initial proteloytic event involved in secretion of rat serum albumin.
Amino Acid Sequence↗
Methylation analysis of complex carbohydrates: general procedure and application for sequence analysis.
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Acetylation↗
Disulfide-linked cyanogen bromide peptides of bovine fibrinogen. III. Isolation and identification by sequence analysis of the chain constituents in peptides F-CB2, F-CB4 and F-CB5.
Three disulfide-linked peptides with molecular weights of about 6000, 7000 and 45000, respectively, were isolated from bovine fibrinogen cleaved with cyanogen bromide. The chain constituents of these peptides were separated after reduction and alkylation and identified by partial amino acid sequence analysis. Of the five polypeptide chains of the largest fragment F-CB2, three are derived from the central region of Bbeta chain, one from the Aalpha chain and one from the gamma chain. The smaller peptides F-CB4 and F-CB5 consist of one and two polypeptide chains and originate from central regions of the Bbeta and gamma chains, respectively, indicating that they represent intrachain disulfide loops. These and previous data show that the disulfide-bonded regions of bovine fibrinogen are similar to those in human fibrinogen.
Amino Acid Sequence↗
Nucleotide sequence analysis of two simian virus 40 mutants with deletions in the late region of the genome.
Two mutants of simian virus 40, dl-1261 and dl-1262, have deletions that map between coordinated 0.90 and 0.95 (Cole et al., J. Virol 24:277--294, 1977). Both affect the structure of the two minor proteins VP2 and VP3. The precise location and size of the deletions have now been determined by nucleotide sequence analysis. Mutant dl-1261 is deleted of 54 base pairs, is temperature sensitive for the protein defined by the D complementation group, and promotes the synthesis of shorter VP2 and VP3 polypeptides. Mutant dl-1262 is viable irrespective of temperature and has a deletion of 36 base pairs, 23 of which overlap the deletion in dl-1261. Since these mutants produce normal VP1, the deleted regions probably have no function in the splicing of precursor RNA to the VP1 mRNA.
Base Sequence↗
Nucleotide clusters in deoxyribonucleic acids: sequence analysis of DNA using pyrimidine oligonucleotides as primers in the DNA polymerase I repair reaction.
Pyrimidine oligonucleotides have been shown to prime the E. coli DNA polymerase I repair reaction, specifically and reproducibly. DNA molecules up to 30 nucleotides long have been obtained from the extension of oligopyrimidine primers, 9 to 11 nucleotides long isolated from the complementary (minus) strand of bacteriophage S13 RFDNA using S13 viral DNA as the template molecule. The sequences of the extended primers were determined from mobility shift following separation of partially extended primers by ionophoresis and homochromatography, and by a modification of the "plus" system of Sanger and Coulson (1975). The 3' leads to 5' exonuclease activity of E. coli DNA polymerase was utilized for the "plus" system in the presence of single dNTPs and also with two dNTPs in the reaction, to give a nearest neighbor type of analysis for sequence confirmation. The ready availability of oligopyrimidine primers from any DNA and the simplification of the "plus" method broaden the range of applicability of the primed DNA polymerase I repair reaction for DNA sequence analysis.
Bacteriophages↗
The impact of the COVID-19 pandemic on the incidence of invasive pneumococcal disease in the Czech Republic and whole genome sequencing analysis of Streptococcus pneumoniae serotypes 3 and 19A from 2018-2024.
AIM: To describe in detail changes in the incidence of invasive pneumococcal disease in the Czech Republic during and after the COVID-19 pandemic. Another objective is molecular analysis of S. pneumoniae isolates of serotypes 3 and 19A recovered in the Czech Republic between 2018 and 2024. MATERIAL AND METHODS: Data on the incidence of invasive pneumococcal disease and S. pneumoniae serotypes were obtained from the invasive pneumococcal disease surveillance program in the Czech Republic. S. pneumoniae isolates of serotypes 3 (63) and 19A (66) from 2018-2024 were subjected to whole genome sequencing (WGS) to characterize the GPSCs (Global Pneumococcal Sequence Clusters) and STs (sequence types) and place them in a global context. RESULTS: Results: During the COVID-19 pandemic, a significant decline was observed in the incidence of invasive pneumococcal disease in the Czech Republic. Following the pandemic, the incidence of invasive pneumococcal disease rose again to significantly higher levels than before the pandemic. Compared to the 2018–2019 period, the incidence of certain serotypes increased in 2023–2024, including vaccine serotypes 3, 4, 14, and 15B, while the incidence of serotypes 8, 12F, and 15A, among others, decreased. Whole genome sequencing analysis demonstrated the dominance of GPSC12 ST-180 among serotype 3 isolates throughout the study period. Among serotype 19A isolates, GPSC4 prevailed, particularly ST-416. CONCLUSIONS: The COVID-19 pandemic has demonstrated how rapidly the epidemiological situation of invasive pneumococcal disease can change and that continuous, systematic surveillance of invasive pneumococcal disease is necessary. The best prevention against invasive pneumococcal disease is vaccination, primarily with higher valency pneumococcal conjugate vaccines.
Czech Republic↗
SIMS: A deep-learning label transfer tool for single-cell RNA sequencing analysis.
Cell atlases serve as vital references for automating cell labeling in new samples, yet existing classification algorithms struggle with accuracy. Here we introduce SIMS (scalable, interpretable machine learning for single cell), a low-code data-efficient pipeline for single-cell RNA classification. We benchmark SIMS against datasets from different tissues and species. We demonstrate SIMS's efficacy in classifying cells in the brain, achieving high accuracy even with small training sets (<3,500 cells) and across different samples. SIMS accurately predicts neuronal subtypes in the developing brain, shedding light on genetic changes during neuronal differentiation and postmitotic fate refinement. Finally, we apply SIMS to single-cell RNA datasets of cortical organoids to predict cell identities and uncover genetic variations between cell lines. SIMS identifies cell-line differences and misannotated cell lineages in human cortical organoids derived from different pluripotent stem cell lines. Altogether, we show that SIMS is a versatile and robust tool for cell-type classification from single-cell datasets.
Single-Cell Analysis↗