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Journal articles on the topic 'Nucleotide sequence'
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1
Fatchiyah, Fatchiyah, Rista Nikmatu Rohmah, Lidwina Faraline Tripisila, Dewi Ratih Tirto Sari, Adelia Adrianne Tapiory, Jihan Safira Ainnayah, Viona Faiqoh, Fajar Mustika Alam, and Ahmad Faizal Abdul Razis. "Three-dimension Glyceraldehyde-3-Phosphate Dehydrogenase protein structure of substitution and insertion sequences of GAPDH gene of chicken drumstick meat (Gallus gallus)." Berkala Penelitian Hayati 27, no. 2 (April 5, 2022): 105–9. http://dx.doi.org/10.23869/bphjbr.27.2.20228.
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The study aimed to observed the 3-D structure of GAPDH protein and identify the GAPDH gene sequences mutation of chicken drumstick meat (Gallus gallus). The sample of chicken meat was randomly taken in four districts in Malang city. In this study, the DNA was isolated from drumstick meat chicken samples, amplified using proper primers, and then sequenced using ABI 3730xl DNA Sequencer. The DNA sequences alignments analyzed by BioEdit software and the control sequence of GAPDH gene was obtained from NCBI GenBank (sequence Gene ID: 374193). Then, the amino acid sequence and 3D structure of GAPDH protein were determined based on the change of nucleotide sequences using Swiss model and PyMol software. The nucleotide sequence of a partially GAPDH gene of drumstick meat chicken from districts two is completely different with a 97 percent similarity level, which found twelve nucleotides’ substitutions mutation between nucleotide base number 354 until 777 and three nucleotides inserted between T753 and G754 nucleotide base. These mutations changed the amino acid sequence and 3D structure of GAPDH protein. This result suggests that the differential drumstick chicken meat GAPDH sequences and 3D structure may induce the change of protein-protein interaction and induction.
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Harasawa, Ryô, and Yasuo Kanamoto. "Differentiation of Two Biovars of Ureaplasma urealyticum Based on the 16S-23S rRNA Intergenic Spacer Region." Journal of Clinical Microbiology 37, no. 12 (1999): 4135–38. http://dx.doi.org/10.1128/jcm.37.12.4135-4138.1999.
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The 16S-23S rRNA intergenic spacer regions of 14 strains representing the 14 serovars of Ureaplasma urealyticum were amplified by PCR and sequenced for genetic differentiation between the two biovars Parvo and T960. Although the spacer region of the Parvo and T960 biovars comprised 302 nucleotides and lacked spacer tRNA genes, 15 nucleotides were different between the two biovars. The four nucleotide sequences of the 16S-23S rRNA intergenic spacer region of serovars 1, 3, 6, and 14 in the Parvo biovar were found to be identical. Similarly, the 10 nucleotide sequences of the 16S-23S rRNA intergenic spacer region of serovars 2, 4, 5, and 7 to 13 in the T960 biovar were found to be identical. The nucleotide sequence of the T960 biovar contains multiple restriction sites for restriction endonucleaseSspI, which allows differentiation of the T960 biovar from the Parvo biovar.
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Kuśmirek, Wiktor. "Estimated Nucleotide Reconstruction Quality Symbols of Basecalling Tools for Oxford Nanopore Sequencing." Sensors 23, no. 15 (July 29, 2023): 6787. http://dx.doi.org/10.3390/s23156787.
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Currently, one of the fastest-growing DNA sequencing technologies is nanopore sequencing. One of the key stages involved in processing sequencer data is the basecalling process, where the input sequence of currents measured on the nanopores of the sequencer reproduces the DNA sequences, called DNA reads. Many of the applications dedicated to basecalling, together with the DNA sequence, provide the estimated quality of the reconstruction of a given nucleotide (quality symbols are contained on every fourth line of the FASTQ file; each nucleotide in the FASTQ file corresponds to exactly one estimated nucleotide reconstruction quality symbol). Herein, we compare the estimated nucleotide reconstruction quality symbols (signs from every fourth line of the FASTQ file) reported by other basecallers. The conducted experiments consisted of basecalling the same raw datasets from the nanopore device by other basecallers and comparing the provided quality symbols, denoting the estimated quality of the nucleotide reconstruction. The results show that the estimated quality reported by different basecallers may vary, depending on the tool used, particularly in terms of range and distribution. Moreover, we mapped basecalled DNA reads to reference genomes and calculated matched and mismatched rates for groups of nucleotides with the same quality symbol. Finally, the presented paper shows that the estimated nucleotide reconstruction quality reported in the basecalling process is not used in any investigated tool for processing nanopore DNA reads.
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Bradford, Patricia A. "Automated Thermal Cycling Is Superior to Traditional Methods for Nucleotide Sequencing ofblaSHV Genes." Antimicrobial Agents and Chemotherapy 43, no. 12 (December 1, 1999): 2960–63. http://dx.doi.org/10.1128/aac.43.12.2960.
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ABSTRACT Genes encoding SHV-1 and SHV-2 were sequenced by different methods. Nucleotide sequencing of the coding strand by standard dideoxy-chain termination methods resulted in errors in the interpretation of the nucleotide sequence and the derived amino acid sequence in two main regions which corresponded to nucleotide and amino acid changes that had been reported previously. The automated thermal cycling method was clearly superior and consistently resulted in the correct sequences for these genes.
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Lee, Byoungsang, So Yeon Ahn, Charles Park, James J. Moon, Jung Heon Lee, Dan Luo, Soong Ho Um, and Seung Won Shin. "Revealing the Presence of a Symbolic Sequence Representing Multiple Nucleotides Based on K-Means Clustering of Oligonucleotides." Molecules 24, no. 2 (January 18, 2019): 348. http://dx.doi.org/10.3390/molecules24020348.
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In biological systems, a few sequence differences diversify the hybridization profile of nucleotides and enable the quantitative control of cellular metabolism in a cooperative manner. In this respect, the information required for a better understanding may not be in each nucleotide sequence, but representative information contained among them. Existing methodologies for nucleotide sequence design have been optimized to track the function of the genetic molecule and predict interaction with others. However, there has been no attempt to extract new sequence information to represent their inheritance function. Here, we tried to conceptually reveal the presence of a representative sequence from groups of nucleotides. The combined application of the K-means clustering algorithm and the social network analysis theorem enabled the effective calculation of the representative sequence. First, a “common sequence” is made that has the highest hybridization property to analog sequences. Next, the sequence complementary to the common sequence is designated as a ‘representative sequence’. Based on this, we obtained a representative sequence from multiple analog sequences that are 8–10-bases long. Their hybridization was empirically tested, which confirmed that the common sequence had the highest hybridization tendency, and the representative sequence better alignment with the analogs compared to a mere complementary.
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Fukasawa, Kayoko M., Masako Tanimura, Ikuya Sakai, Farida S. Sharief, Fu-Zon Chung, and Steven S.-L. Li. "Molecular Nature of Spontaneous Mutations in Mouse Lactate Dehydrogenase-A Processed Pseudogenes." Genetics 115, no. 1 (January 1, 1987): 177–84. http://dx.doi.org/10.1093/genetics/115.1.177.
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ABSTRACT The presence of at least ten mouse LDH-A pseudogenes was demonstrated in the genomic blot analysis, and four different processed pseudogenes have thus far been isolated and characterized. In this report, the nucleotide sequences of two different mouse lactate dehydrogenase-A processed pseudogenes, M11 and M14, were determined and compared with the protein-coding sequences of the mouse and rat LDH-A functional genes. In the pseudogene M11, the sequence of 64 nucleotides from codon no. 257 to 278 was tandemly duplicated. In the pseudogene M14, the sequence of 22 nucleotides from codon no. 68 to 75 was replaced by an inserted repetitive sequence of 242 nucleotides homologous to a mouse truncated R element. The pattern of nucleotide substitutions accumulated in mouse LDH-A pseudogenes M11 and M14, as well as that of pseudogene M10 identified previously, was analyzed, and the substitution frequencies of the C or G at the CG dinucleotide were found to be high.
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Furlong, N. Burr, and Koenraad Marien. "Further Observations on Periodicities of Nucleotide Occurrences in Natural DNA's." Zeitschrift für Naturforschung C 40, no. 11-12 (October 1, 1985): 854–57. http://dx.doi.org/10.1515/znc-1985-11-1218.
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Abstract There are non-random features in the occurrences of nucleotides in the DNA’s of certain organisms which are detectable by statistical analyses of the entire sequence. Earlier, using the bacteriophage Phi-X 174 DNA sequence, we had reported that the self-information values for one type of dinucleotide association showed a marked periodicity when their autocorrelation coefficients were graphed. A similar, but computationally simpler, analysis has been developed which gives a comparable indication of periodicity. The difference, in average autocorrelation coefficients obtained with this analysis, between the peak values and all others has been used as an index to compare the extent of periodic non-randomness for a series of natural DNA sequences and for various artificial sequences. Calculations show that triplet periodicity, the relationship between dinucleotides separated by a single nucleotide, is characteristic only of the natural sequences of certain filamentous phages and is not found prominently in any other DNA analyzed (including sequences of similar length from plasmids, yeast, bacteria and higher animals). By shuffling nucleotides in a given sequence or by substituting selected nucleotides to alter various positions in both periodic and aperiodic sequences, we have found that an excess or deficiency of a given nucleotide at one of the three positions in a triplet reading frame can simulate the periodic characteristic. Thus, it appears that this global statistical analysis detects the tendency for single strand phages to utilize a specific nucleotide, rather than one randomly selected, to constitute codons.
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Ojkic, Davor, and éva Nagy. "The complete nucleotide sequence of fowl adenovirus type 8." Microbiology 81, no. 7 (July 1, 2000): 1833–37. http://dx.doi.org/10.1099/0022-1317-81-7-1833.
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The fowl adenovirus type 8 (FAdV-8) genome was sequenced and found to be 45063 nucleotides in length, the longest adenovirus (AdV) genome for which the complete nucleotide sequence has been determined so far. No regions homologous to early regions 1, 3 and 4 (E1, E3 and E4) of mastadenoviruses were recognized. Gene homologues for early region 2 (E2) proteins, intermediate protein IVa2 and late proteins were found by their similarities to protein sequences from other AdVs. However, sequences homologous to intermediate protein IX and late protein V could not be identified. Sequences for virus-associated RNA could also not be recognized. Two regions of repeated sequences were found on the FAdV-8 genome. The shorter repeat region contained five identical and contiguous direct repeats that were each 33 bp long, while the longer repeat region was made of 13 identical and contiguous, 135 bp long repeated subunits.
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Ansell, D. M., A. R. Samuel, W. C. Carpenter, and N. J. Knowles. "Genetic relationships between foot–and–mouth disease type Asia 1 viruses." Epidemiology and Infection 112, no. 1 (February 1994): 213–24. http://dx.doi.org/10.1017/s0950268800057587.
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SummaryThe sequence of 165 nucleotides at the 3´ end of the 1D (VP1) gene of foot-and-mouth disease (FMD) virus was determined for 44 type Asia 1 strains isolated from throughout Asia between 1954–92. Analysis of the relationships between the virus genomes showed epidemiological links not previously evident. The possible origin of the only outbreak of FMD Asia 1 to have occurred in Europe, in Greece in 1984, was identified because the nucleotide sequence of this virus was closely-related to the sequences of those present in the Middle East between 1983–5.Variation in the region sequenced was not as great as that seen in the other FMDV serotypes and all viruses shared greater than 85% nucleotide identity. Thus all the virus isolates examined were considered to belong to a single genotype.A database of Asia 1 virus sequences has been established which will facilitate the rapid analysis of new outbreaks strains.
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Mathis, Diane, and Christophe Benoist. "Nucleotide Sequence: Correction." Science 279, no. 5348 (January 9, 1998): 151.2–151. http://dx.doi.org/10.1126/science.279.5348.151-b.
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Mathis, D. "Nucleotide Sequence: Correction." Science 279, no. 5348 (January 9, 1998): 151b—151. http://dx.doi.org/10.1126/science.279.5348.151b.
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Nadel, B., and A. J. Feeney. "Nucleotide deletion and P addition in V(D)J recombination: a determinant role of the coding-end sequence." Molecular and Cellular Biology 17, no. 7 (July 1997): 3768–78. http://dx.doi.org/10.1128/mcb.17.7.3768.
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During V(D)J recombination, the coding ends to be joined are extensively modified. Those modifications, termed coding-end processing, consist of removal and addition of various numbers of nucleotides. We previously showed in vivo that coding-end processing is specific for each coding end, suggesting that specific motifs in a coding-end sequence influence nucleotide deletion and P-region formation. In this study, we created a panel of recombination substrates containing actual immunoglobulin and T-cell receptor coding-end sequences and dissected the role of each motif by comparing its processing pattern with those of variants containing minimal nucleotide changes from the original sequence. Our results demonstrate the determinant role of specific sequence motifs on coding-end processing and also the importance of the context in which they are found. We show that minimal nucleotide changes in key positions of a coding-end sequence can result in dramatic changes in the processing pattern. We propose that each coding-end sequence dictates a unique hairpin structure, the result of a particular energy conformation between nucleotides organizing the loop and the stem, and that the interplay between this structure and specific sequence motifs influences the frequency and location of nicks which open the coding-end hairpin. These findings indicate that the sequences of the coding ends determine their own processing and have a profound impact on the development of the primary B- and T-cell repertoires.
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Garcia Machado, Erik, Mario Oliva Suarez, Nicole Dennebouy, Monique Monnerot, and Jean-Claude Mounolou. "Mitochondrial 16S-rRna Gene of Two Species of Shrimps: Sequence Variability and Secondary Structure." Crustaceana 65, no. 3 (1993): 279–86. http://dx.doi.org/10.1163/156854093x00711.
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AbstractPart of the mitochondrial 16S-ribosomal RNA gene (around 400 nucleotides) of Penaeus notialis and Penaeus schmitti has been amplified and sequenced. The comparison of sequences reveals an 11% nucleotide divergence between the two species. When compared with that of the homologous fragment in Artemia salina and Drosophila yakuba, the secondary structure appears well conserved in spite of high nucleotide divergence due to numerous substitutions and additions/deletions. Sequences have been obtained for six individuals of P. notialis belonging to the same population, their comparison shows a 0.7% nucleotide diversity.
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Geliebter, J., R. A. Zeff, D. H. Schulze, L. R. Pease, E. H. Weiss, A. L. Mellor, R. A. Flavell, and S. G. Nathenson. "Interaction between Kb and Q4 gene sequences generates the Kbm6 mutation." Molecular and Cellular Biology 6, no. 2 (February 1986): 645–52. http://dx.doi.org/10.1128/mcb.6.2.645-652.1986.
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Genetic interaction as a mechanism for the generation of mutations is suggested by recurrent, multiple nucleotide substitutions that are identical to nucleotide sequences elsewhere in the genome. We have sequenced the mutant K gene from the bm6 mouse, which is one of a series of eight closely related, yet independently occurring mutants known collectively as the "bg series." Two changes from the Kb gene are found, positioned 15 nucleotides apart: an A-to-T change and a T-to-C change in the codons corresponding to amino acids 116 and 121, resulting in Tyr-to-Phe and Cys-to-Arg substitutions, respectively. Hybridization analysis with an oligonucleotide specific for the altered Kbm6 sequence identifies one donor gene, Q4, located in the Qa region of the H-2 complex. The two altered nucleotides that differentiate Kbm6 and Kb are present in Q4 in a region where Kb and Q4 are otherwise identical for 95 nucleotides, delineating the maximum genetic transfer between the two genes. Because the Kbm6 mutation arose in an homozygous mouse these data indicate that the Q4 gene contains the only donor sequence and demonstrates that Q-region gene sequences can interact with the Kb gene to generate variant K molecules.
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Geliebter, J., R. A. Zeff, D. H. Schulze, L. R. Pease, E. H. Weiss, A. L. Mellor, R. A. Flavell, and S. G. Nathenson. "Interaction between Kb and Q4 gene sequences generates the Kbm6 mutation." Molecular and Cellular Biology 6, no. 2 (February 1986): 645–52. http://dx.doi.org/10.1128/mcb.6.2.645.
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Genetic interaction as a mechanism for the generation of mutations is suggested by recurrent, multiple nucleotide substitutions that are identical to nucleotide sequences elsewhere in the genome. We have sequenced the mutant K gene from the bm6 mouse, which is one of a series of eight closely related, yet independently occurring mutants known collectively as the "bg series." Two changes from the Kb gene are found, positioned 15 nucleotides apart: an A-to-T change and a T-to-C change in the codons corresponding to amino acids 116 and 121, resulting in Tyr-to-Phe and Cys-to-Arg substitutions, respectively. Hybridization analysis with an oligonucleotide specific for the altered Kbm6 sequence identifies one donor gene, Q4, located in the Qa region of the H-2 complex. The two altered nucleotides that differentiate Kbm6 and Kb are present in Q4 in a region where Kb and Q4 are otherwise identical for 95 nucleotides, delineating the maximum genetic transfer between the two genes. Because the Kbm6 mutation arose in an homozygous mouse these data indicate that the Q4 gene contains the only donor sequence and demonstrates that Q-region gene sequences can interact with the Kb gene to generate variant K molecules.
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Fukasawa, K. M., and S. S. L. Li. "Nucleotide sequence of the putative regulatory region of mouse lactate dehydrogenase-A gene." Biochemical Journal 235, no. 2 (April 15, 1986): 435–39. http://dx.doi.org/10.1042/bj2350435.
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The nucleotide sequence of approx. 3 kilobases including the regulatory region, a non-coding exon and the first protein-coding exon from mouse lactate dehydrogenase-A (LDH-A) gene has been determined. The putative initiation sites of transcription and translation were deduced by comparing the nucleotide sequence of mouse LDH-A gene with those of a mouse LDH-A processed pseudogene and the LDH-A full-length cDNAs from rat and human. The tentative TATA and CAAT boxes, and the hexanucleotides CCGCCC have been identified. The sequence of AAATCTTGCTCAA of mouse LDH-A gene has also been found to show striking homology to the cyclic AMP-responsive sequences of eukaryotic genes regulated by cyclic AMP. It has been reported previously that the protein-coding sequence of mouse LDH-A gene is interrupted by six introns and the 3′ untranslated sequence of 485 nucleotides is not interrupted [Li, Tiano, Fukasawa, Yagi, Shimiza, Sharief, Nakashima & Pan (1985) Eur. J. Biochem. 149, 215-225]. An additional intron of 1653 base-pairs was found in the 5′ untranslated sequence of 101 nucleotides at 24 nucleotides upstream to the translation start site. Thus, mouse LDH-A gene containing seven introns spans approx. 11 kilobases and its length of mature mRNA is 1582 nucleotides, excluding the poly(A) tail.
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Wypijewski, K., T. Malinowski, W. Musiał, and J. Augustyniak. "Nucleotide sequence of the coat protein gene of the Skierniewice isolate of plum pox virus (PPV)." Acta Biochimica Polonica 41, no. 1 (March 31, 1994): 87–95. http://dx.doi.org/10.18388/abp.1994_4778.
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The coat protein (CP) gene of the Skierniewice isolate of plum pox virus (PPV-S) has been amplified using the reverse transcription--polymerase chain reaction (RT-PCR), cloned and sequenced. The nucleotide sequence of the gene and the deduced amino-acid sequence of PPV-S CP were compared with those of other PPV strains. The nucleotide sequence showed very high homology to most of the published sequences. The motif: Asp-Ala-Gly (DAG), important for the aphid transmissibility, was present in the amino-acid sequence. Our isolate did not react in ELISA with monoclonal antibodies MAb06 supposed to be specific for PPV-D.
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Hu, M. C., S. B. Sharp, and N. Davidson. "The complete sequence of the mouse skeletal alpha-actin gene reveals several conserved and inverted repeat sequences outside of the protein-coding region." Molecular and Cellular Biology 6, no. 1 (January 1986): 15–25. http://dx.doi.org/10.1128/mcb.6.1.15-25.1986.
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The complete nucleotide sequence of a genomic clone encoding the mouse skeletal alpha-actin gene has been determined. This single-copy gene codes for a protein identical in primary sequence to the rabbit skeletal alpha-actin. It has a large intron in the 5'-untranslated region 12 nucleotides upstream from the initiator ATG and five small introns in the coding region at codons specifying amino acids 41/42, 150, 204, 267, and 327/328. These intron positions are identical to those for the corresponding genes of chickens and rats. Similar to other skeletal alpha-actin genes, the nucleotide sequence codes for two amino acids, Met-Cys, preceding the known N-terminal Asp of the mature protein. Comparison of the nucleotide sequences of rat, mouse, chicken, and human skeletal muscle alpha-actin genes reveals conserved sequences (some not previously noted) outside of the protein-coding region. Furthermore, several inverted repeat sequences, partially within these conserved regions, have been identified. These sequences are not present in the vertebrate cytoskeletal beta-actin genes. The strong conservation of the inverted repeat sequences suggests that they may have a role in the tissue-specific expression of skeletal alpha-actin genes.
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Hu, M. C., S. B. Sharp, and N. Davidson. "The complete sequence of the mouse skeletal alpha-actin gene reveals several conserved and inverted repeat sequences outside of the protein-coding region." Molecular and Cellular Biology 6, no. 1 (January 1986): 15–25. http://dx.doi.org/10.1128/mcb.6.1.15.
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The complete nucleotide sequence of a genomic clone encoding the mouse skeletal alpha-actin gene has been determined. This single-copy gene codes for a protein identical in primary sequence to the rabbit skeletal alpha-actin. It has a large intron in the 5'-untranslated region 12 nucleotides upstream from the initiator ATG and five small introns in the coding region at codons specifying amino acids 41/42, 150, 204, 267, and 327/328. These intron positions are identical to those for the corresponding genes of chickens and rats. Similar to other skeletal alpha-actin genes, the nucleotide sequence codes for two amino acids, Met-Cys, preceding the known N-terminal Asp of the mature protein. Comparison of the nucleotide sequences of rat, mouse, chicken, and human skeletal muscle alpha-actin genes reveals conserved sequences (some not previously noted) outside of the protein-coding region. Furthermore, several inverted repeat sequences, partially within these conserved regions, have been identified. These sequences are not present in the vertebrate cytoskeletal beta-actin genes. The strong conservation of the inverted repeat sequences suggests that they may have a role in the tissue-specific expression of skeletal alpha-actin genes.
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Netolitzky, Donald J., Fay L. Schmaltz, Michael D. Parker, George A. Rayner, Glen R. Fisher, Dennis W. Trent, Douglas E. Bader, and Les P. Nagata. "Complete genomic RNA sequence of western equine encephalitis virus and expression of the structural genes." Microbiology 81, no. 1 (January 1, 2000): 151–59. http://dx.doi.org/10.1099/0022-1317-81-1-151.
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The complete nucleotide sequence of the 71V-1658 strain of western equine encephalitis virus (WEE) was determined (minus 25 nucleotides from the 5′ end). A 5′ RACE reaction was used to sequence the 5′ terminus from WEE strain CBA87. The deduced WEE genome was 11508 nucleotides in length, excluding the 5′ cap nucleotide and 3′ poly(A) tail. The nucleotide composition was 28% A, 25% C, 25% G and 22% U. Comparison with partial WEE sequences of strain 5614 (nsP2–nsP3 of the nonstructural region) and strain BFS1703 (26S structural region) revealed comparatively little variation; a total of 149 nucleotide differences in 8624 bases (1·7% divergence), of which only 28% (42 nucleotides) altered the encoded amino acids. Comparison of deduced nsP1 and nsP4 amino acid sequences from WEE with the corresponding proteins from eastern equine encephalitis virus (EEE) yielded identities of 84·9 and 83·8%, respectively. Previously uncharacterized stem–loop structures were identified in the nontranslated terminal regions. A cDNA clone of the 26S region encoding the structural polyprotein of WEE strain 71V-1658 was placed under the control of a cytomegalovirus promoter and transfected into tissue culture cells. The viral envelope proteins were functionally expressed in tissue culture, as determined by histochemical staining with monoclonal antibodies that recognize WEE antigens, thus, forming the initial step in the investigation of subunit vaccines to WEE.
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Wiuf, Carsten, and Jotun Hein. "The Ancestry of a Sample of Sequences Subject to Recombination." Genetics 151, no. 3 (March 1, 1999): 1217–28. http://dx.doi.org/10.1093/genetics/151.3.1217.
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Abstract In this article we discuss the ancestry of sequences sampled from the coalescent with recombination with constant population size 2N. We have studied a number of variables based on simulations of sample histories, and some analytical results are derived. Consider the leftmost nucleotide in the sequences. We show that the number of nucleotides sharing a most recent common ancestor (MRCA) with the leftmost nucleotide is ≈log(1 + 4N Lr)/4Nr when two sequences are compared, where L denotes sequence length in nucleotides, and r the recombination rate between any two neighboring nucleotides per generation. For larger samples, the number of nucleotides sharing MRCA with the leftmost nucleotide decreases and becomes almost independent of 4N Lr. Further, we show that a segment of the sequences sharing a MRCA consists in mean of 3/8Nr nucleotides, when two sequences are compared, and that this decreases toward 1/4Nr nucleotides when the whole population is sampled. A measure of the correlation between the genealogies of two nucleotides on two sequences is introduced. We show analytically that even when the nucleotides are separated by a large genetic distance, but share MRCA, the genealogies will show only little correlation. This is surprising, because the time until the two nucleotides shared MRCA is reciprocal to the genetic distance. Using simulations, the mean time until all positions in the sample have found a MRCA increases logarithmically with increasing sequence length and is considerably lower than a theoretically predicted upper bound. On the basis of simulations, it turns out that important properties of the coalescent with recombinations of the whole population are reflected in the properties of a sample of low size.
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Klimentov, A. S., A. P. Gmyl, A. M. Butenko, L. V. Gmyl, O. V. Isaeva, V. F. Larichev, N. V. Khutoretskaya, and G. G. Karganova. "Taxonomic status of Bhanja and Kismayo viruses (family Bunyaviridae)." Epidemiology and Infectious Diseases 17, no. 4 (August 15, 2012): 4–8. http://dx.doi.org/10.17816/eid40625.
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The nucleotide sequence of M= (1398 nucleotides and L= (6186 nucleotides) segments of the genome of Bhanja virus and L-segment (1297 nucleotides) of Kismayo virus has been partially determined. Phylogenetic analysis of deduced amino acid sequences showed that these viruses are novel members of the Flebovirus (Phlebovirus) genus in the family Bunyaviridae
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Górski, Andrzej Z., and Monika Piwowar. "Nucleotide spacing distribution analysis for human genome." Mammalian Genome 32, no. 2 (March 15, 2021): 123–28. http://dx.doi.org/10.1007/s00335-021-09865-5.
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AbstractThe distribution of nucleotides spacing in human genome was investigated. An analysis of the frequency of occurrence in the human genome of different sequence lengths flanked by one type of nucleotide was carried out showing that the distribution has no self-similar (fractal) structure. The results nevertheless revealed several characteristic features: (i) the distribution for short-range spacing is quite similar to the purely stochastic sequences; (ii) the distribution for long-range spacing essentially deviates from the random sequence distribution, showing strong long-range correlations; (iii) the differences between (A, T) and (C, G) nucleotides are quite significant; (iv) the spacing distribution displays tiny oscillations.
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Bravo, Enrique, Lee A. Calvert, and Francisco J. Morales. "THE COMPLETE NUCLEOTIDE SEQUENCE OF THE GENOMIC RNA OF BEAN COMMON MOSAIC VIRUS STRAIN NL4." Revista de la Academia Colombiana de Ciencias Exactas, Físicas y Naturales 32, no. 122 (November 28, 2023): 37–46. http://dx.doi.org/10.18257/raccefyn.32(122).2008.2228.
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The complete nucleotide sequence of the genomic RNA of the NL4 strain of Bean common mosaic virus (BCMV-NL4) was determined. The viral genome is 10037 nucleotides in length, excluding the 3’ terminal poly (A) tail, and contains a single open reading frame (ORF) of 9666 nucleotides encoding a polyprotein of 3222 amino acids. The ORF is flanked by 5’ and 3’ untranslated regions (UTRs) of 133 and 235 nucleotides, respectively. Comparative analyses of the predicted BCMV-NL4 polyprotein with other species of the genus Potyvirus revealed nine cleavage sites resulting in ten functional proteins. Nucleotide and amino acid sequence identities indicated a close relationship between BCMV-NL4 and BCMV-NL1. Blast comparisons using coat protein (CP) and 3’UTR sequences showed 100% identity between BCMV-NL4 and the Mexican variant (US6) of this strain.
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Dvořák, J., D. Jue, and M. Lassner. "Homogenization of Tandemly Repeated Nucleotide Sequences by Distance-Dependent Nucleotide Sequence Conversion." Genetics 116, no. 3 (July 1, 1987): 487–98. http://dx.doi.org/10.1093/genetics/116.3.487.
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ABSTRACT Previous work revealed that recurrent mutations (=mutation occurring more than once) in the tandemly repeated arrays present in nontranscribed spacers (NTS) of ribosomal RNA genes (rDNA) are clustered, i.e., they most frequently occur in repeats with adjacent or alternate distribution. A possible explanation is that the likelihood of heteroduplex formation, a prerequisite of gene conversion, decreases with the distance between repeats. To test this possibility, evolution of an array of 11 initially homogeneous repeats was computer simulated using three models, two assuming that the likelihood of heteroduplex formation decreases with increasing distance between the repeats and one assuming that it is constant. Patterns of mutations distribution obtained in computer simulations were compared with the distribution of mutations found in the repeated arrays in the NTS of seven rDNA clones. The patterns of mutations generated by the models assuming that the likelihood of heteroduplex formation decreases as distance between the repeats increases agreed with the patterns observed in rDNA; the patterns generated by the model assuming that the likelihood is independent of distance between repeats disagreed with the patterns observed in the rDNA clones. The topology of the heteroduplex formed between DNA in adjacent repeats predicts that the most frequently occurring conversions in the NTS repeated arrays will be shorter than the length of the repeat. The topology of the heteroduplex also predicts that if the heteroduplex leads to crossing over a circular repeat is excised. It is speculated that the circle can transpose or can be amplified via rolling circle replication and subsequently transpose. It is also shown that homogenization of the NTS repeated arrays proceeds at different rates in different species.
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Gaina, Cynthia Dewi, Filphin Adolfin Amalo, and Yustinus O. P. Wuhan. "Analisis Genetik Gen Leptin Berdasarkan Sekuen DNA GenBank dan Asosiasinya dengan Reproduksi Ternak Babi." JURNAL KAJIAN VETERINER 11, no. 1 (June 20, 2023): 93–102. http://dx.doi.org/10.35508/jkv.v11i1.10162.
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A candidate gene suspected of affecting pigs' reproductive traits is known as the leptin (LEP) gene. Based on the information found in Leptin GenBank's DNA sequence database, this research aimed to determine single nucleotide polymorphisms (SNPs) and changes in nucleotides and phylogenetic trees in pigs. The data from NCBI GenBank was used to obtain three different DNA sequences of the Leptin gene in pigs. The DNA sequence data for leptin were aligned using BioEdit to establish the sites of SNPs and alterations in nucleotides. A phylogenetic tree was constructed using Mega X. DNA sequences were, and the pig LEP gene was sequenced resulted in 11 SNPs. These findings are based on the sequence regions. The phylogenetic analysis revealed that the sequence of the Leptin gene in pigs (Sus scrofa) clustered more closely with that of goats (Capra hircus) than it did with the sequence of the LEP gene among the cattle (Bos taurus and Bos indicus). The outcomes of this study can serve as a basis for more investigation into the connection between the LEP gene SNP and reproductive traits in pigs as one of potential genes for molecular selection.
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Jalbert, Louise, Elliot Rosen, Ann Lissens, Peter Carmeliet, Désiré Collen, and Francis Castellino. "Nucleotide Structure and Characterization of the Murine Gene Encoding Anticoagulant Protein C." Thrombosis and Haemostasis 79, no. 02 (1998): 310–16. http://dx.doi.org/10.1055/s-0037-1615006.
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SummaryThe 15,160 bp murine gene encoding anticoagulation protein C (PC) was cloned and sequenced, including 414 bp upstream of exon 1 and 80 bp downstream of the translation stop codon. Nine exons and eight introns were identified. The first exon was untranslated and contained the major transcriptional start site, the surrounding nucleotide sequence of which matched reasonably well with the consensus eukaryotic Cap element sequence. The translational initiator methio-nine residue was located in exon 2. The other introns were positioned as splices between the major domain units of the protein. The 5’ untranslated region contained two possible CCAAT sequences and GC boxes, but no TATA box was obvious within the optimal range of distances from the transcription start site. The 3’-flanking nucleotides included a probable polyadenylation site (ATTAAA), beginning 80 nucleotides downstream of the translation stop codon, and a downstream consensus sequence (AGTGTTTC) required for the efficient formation of a 3’ terminus of mRNA. Several high probability transcription factor recognition sequences, including proteins that are enriched in, or specific to, the liver, such as C/EBP, C/EBP, HNF1, and HNF3, have been located in the 5’ region of the gene. These results indicate that all elements are present for liver-based transcription of the gene for murine PC.
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Della Vecchia, Marilia G. S., Luis E. A. Camargo, and Jorge A. M. Rezende. "Comparação da seqüência de nucleotídeos do gene da proteína capsidial de estirpes severas e premunizantes do Papaya ringspot virus." Fitopatologia Brasileira 28, no. 6 (December 2003): 678–81. http://dx.doi.org/10.1590/s0100-41582003000600015.
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This study compared three mild and three severe strains of Papaya ringspot virus - type W (PRSV-W), based on nucleotide and amino acid sequences of the capsid protein (CP) gene. The CP nucleotide sequences of the mild strains shared 98% to 100% identity. When compared to the severe strains the identity ranged from 93% to 95%, except in the case of PRSV-W-2R, which resulted from reversion of the mild strains PRSV-W-2. The CP sequence of the reverting strain showed 100% identity with the sequence of its parental strain. An insertion of six nucleotides in the core region of the CP gene, which reflected the addition of two amino acids (Asn and Asp) in the deduced sequence of the protein, was found in all mild strains. These sequence comparisons were used to design strain-specific primers that were used to specifically amplify regions for either the mild or severe strains.
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Tarès, S., J. M. Cornuet, and P. Abad. "Characterization of an unusually conserved AluI highly reiterated DNA sequence family from the honeybee, Apis mellifera." Genetics 134, no. 4 (August 1, 1993): 1195–204. http://dx.doi.org/10.1093/genetics/134.4.1195.
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Abstract An AluI family of highly reiterated nontranscribed sequences has been found in the genome of the honeybee Apis mellifera. This repeated sequence is shown to be present at approximately 23,000 copies per haploid genome constituting about 2% of the total genomic DNA. The nucleotide sequence of 10 monomers was determined. The consensus sequences is 176 nucleotides long and has an A + T content of 58%. There are clusters of both direct and inverted repeats. Internal subrepeating units ranging from 11 to 17 nucleotides are observed, suggesting that it could have evolved from a shorter sequence. DNA sequence data reveal that this repeat class is unusually homogeneous compared to the other class of invertebrate highly reiterated DNA sequences. The average pairwise sequence divergence between the repeats is 2.5%. In spite of this unusual homogeneity, divergence has been found in the repeated sequence hybridization ladder between four different honeybee subspecies. Therefore, the AluI highly reiterated sequences provide a new probe for fingerprinting in A. m. mellifera.
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Mauser, AE, J. Whitlark, KM Whitney, and CD Jr Lothrop. "A deletion mutation causes hemophilia B in Lhasa Apso dogs." Blood 88, no. 9 (November 1, 1996): 3451–55. http://dx.doi.org/10.1182/blood.v88.9.3451.bloodjournal8893451.
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Hemophilia B is a bleeding disorder caused by a deficiency of clotting factor IX (FIX). A colony of FIX deficient Lhasa Apso dogs has been established and the molecular basis of hemophilia B has been determined. The plasma factor IX levels were < 1% of normal canine levels in affected dogs. A complex deletion mutation at nucleotides 772–777 was found when hepatocyte cDNA from a hemophilia B dog was sequenced. The sequence was identical to the normal canine sequence except for a deletion including nucleotides 772–776 and a C-->T transition at nucleotide 777. The mutation results in mRNA instability and a premature termination codon in the nucleotide sequence encoding the activation peptide. The mutation was verified by sequencing genomic DNA from an FIX-deficient dog. A genetic test for the detection of heterozygous animals was established using heteroduplex analysis. Although hemophilia B has been described in many dog breeds, this is only the second mutation to be sequenced. The Lhasa Apso dog model should be valuable for evaluating novel strategies for treating hemophilia B such as gene therapy.
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Tilgner, Mark, and Pei-Yong Shi. "Structure and Function of the 3′ Terminal Six Nucleotides of the West Nile Virus Genome in Viral Replication." Journal of Virology 78, no. 15 (August 1, 2004): 8159–71. http://dx.doi.org/10.1128/jvi.78.15.8159-8171.2004.
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ABSTRACT Using a self-replicating reporting replicon of West Nile (WN) virus, we performed a mutagenesis analysis to define the structure and function of the 3′-terminal 6 nucleotides (nt) (5′-GGAUCUOH-3′) of the WN virus genome in viral replication. We show that mutations of nucleotide sequence or base pair structure of any of the 3′-terminal 6 nt do not significantly affect viral translation, but exert discrete effects on RNA replication. (i) The flavivirus-conserved terminal 3′ U is optimal for WN virus replication. Replacement of the wild-type 3′ U with a purine A or G resulted in a substantial reduction in RNA replication, with a complete reversion to the wild-type sequence. In contrast, replacement with a pyrimidine C resulted in a replication level similar to that of the 3′ A or G mutants, with only partial reversion. (ii) The flavivirus-conserved 3′ penultimate C and two upstream nucleotides (positions 78 and 79), which potentially base pair with the 3′-terminal CUOH, are absolutely essential for viral replication. (iii) The base pair structures, but not the nucleotide sequences at the 3rd (U) and the 4th (A) positions, are critical for RNA replication. (iv) The nucleotide sequences of the 5th (G) position and its base pair nucleotide (C) are essential for viral replication. (v) Neither the sequence nor the base pair structure of the 6th nucleotide (G) is critical for WN virus replication. These results provide strong functional evidence for the existence of the 3′ flavivirus-conserved RNA structure, which may function as contact sites for specific assembly of the replication complex or for efficient initiation of minus-sense RNA synthesis.
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Lúquez, Carolina, Brian H. Raphael, and Susan E. Maslanka. "Neurotoxin Gene Clusters in Clostridium botulinum Type Ab Strains." Applied and Environmental Microbiology 75, no. 19 (August 14, 2009): 6094–101. http://dx.doi.org/10.1128/aem.01009-09.
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ABSTRACT There is limited knowledge of the neurotoxin gene diversity among Clostridium botulinum type Ab strains. Only the sequences of the bont/A and bont/B genes in C. botulinum type Ab strain CDC1436 and the sequence of the bont/B gene in C. botulinum type Ab strain CDC588 have been reported. In this study, we sequenced the entire bont/A- and bont/B-associated neurotoxin gene clusters of C. botulinum type Ab strain CDC41370 and the bont/A gene of strain CDC588. In addition, we analyzed the organization of the neurotoxin gene clusters in strains CDC588 and CDC1436. The bont/A nucleotide sequence of strain CDC41370 differed from those of the known bont/A subtypes A1 to A4 by 2 to 7%, and the predicted amino acid sequence differed by 4% to 14%. The bont/B nucleotide sequence in strain CDC41370 showed 99.7% identity to the sequence of subtype B1. The bont/A nucleotide sequence of strain CDC588 was 99.9% identical to that of subtype A1. Although all of the C. botulinum type Ab strains analyzed contained the two sets of neurotoxin clusters, similar to what has been found in other bivalent strains, the intergenic spacing of p21-orfX1 and orfX2-orfX3 varied among these strains. The type Ab strains examined in this study had differences in their toxin gene cluster compositions and bont/A and bont /B nucleotide sequences, suggesting that they may have arisen from separate recombination events.
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Dresch, Jacqueline M., Regan D. Conrad, Daniel Klonaros, and Robert A. Drewell. "Investigating the sequence landscape in the Drosophila initiator core promoter element using an enhanced MARZ algorithm." PeerJ 11 (June 22, 2023): e15597. http://dx.doi.org/10.7717/peerj.15597.
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The core promoter elements are important DNA sequences for the regulation of RNA polymerase II transcription in eukaryotic cells. Despite the broad evolutionary conservation of these elements, there is extensive variation in the nucleotide composition of the actual sequences. In this study, we aim to improve our understanding of the complexity of this sequence variation in the TATA box and initiator core promoter elements in Drosophila melanogaster. Using computational approaches, including an enhanced version of our previously developed MARZ algorithm that utilizes gapped nucleotide matrices, several sequence landscape features are uncovered, including an interdependency between the nucleotides in position 2 and 5 in the initiator. Incorporating this information in an expanded MARZ algorithm improves predictive performance for the identification of the initiator element. Overall our results demonstrate the need to carefully consider detailed sequence composition features in core promoter elements in order to make more robust and accurate bioinformatic predictions.
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Brunak, S. "Nucleotide Sequence Database Policies." Science 298, no. 5597 (November 15, 2002): 1333b—1333. http://dx.doi.org/10.1126/science.298.5597.1333b.
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Bhat, B. M., H. A. Brady, and W. S. Wold. "Virus deletion mutants that affect a 3' splice site in the E3 transcription unit of adenovirus 2." Molecular and Cellular Biology 5, no. 9 (September 1985): 2405–13. http://dx.doi.org/10.1128/mcb.5.9.2405-2413.1985.
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Five viable virus mutants were constructed with deletions near a 3' splice site located at nucleotide 2157 in the E3 transcription unit of adenovirus 2. The mutants were examined for splicing activity at the 2157 3' splice site in vivo by nuclease-gel analysis of steady-state cytoplasmic mRNA. Splicing was not prevented by an exon deletion (dl719) that leaves 16 5'-proximal exon nucleotides intact or by intron deletions that leave 34 (dl717, dl712) or 18 (dl716) 3'-proximal intron nucleotides intact. The sequences deleted in one of these intron mutants (dl716) include the putative branchpoint site used in lariat formation during splicing. Thus, a surrogate branchpoint site apparently can be used for splicing. Another intron mutant (dl714) has a deletion that leaves 15 3'-proximal intron nucleotides intact; remarkably, this deletion virtually abolished splicing, even though the deletion is only 3 nucleotides closer to the splice site than is the deletion in dl716 which splices normally. The three nucleotides deleted in dl714 that are retained by dl716 are the sequence TGT. The TGT sequence is located on the 5' boundary of the pyrimidine-rich region upstream of the nucleotide 2157 3' splice site. Such pyrimidine-rich regions are ubiquitous at 3' splice sites. Most likely, the TGT is required for splicing at the nucleotide 2157 3' splice site. The TGT may be important because of its specific sequence or because it forms the 5' boundary of the pyrimidine-rich region.
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Bhat, B. M., H. A. Brady, and W. S. Wold. "Virus deletion mutants that affect a 3' splice site in the E3 transcription unit of adenovirus 2." Molecular and Cellular Biology 5, no. 9 (September 1985): 2405–13. http://dx.doi.org/10.1128/mcb.5.9.2405.
Full textAbstract:
Five viable virus mutants were constructed with deletions near a 3' splice site located at nucleotide 2157 in the E3 transcription unit of adenovirus 2. The mutants were examined for splicing activity at the 2157 3' splice site in vivo by nuclease-gel analysis of steady-state cytoplasmic mRNA. Splicing was not prevented by an exon deletion (dl719) that leaves 16 5'-proximal exon nucleotides intact or by intron deletions that leave 34 (dl717, dl712) or 18 (dl716) 3'-proximal intron nucleotides intact. The sequences deleted in one of these intron mutants (dl716) include the putative branchpoint site used in lariat formation during splicing. Thus, a surrogate branchpoint site apparently can be used for splicing. Another intron mutant (dl714) has a deletion that leaves 15 3'-proximal intron nucleotides intact; remarkably, this deletion virtually abolished splicing, even though the deletion is only 3 nucleotides closer to the splice site than is the deletion in dl716 which splices normally. The three nucleotides deleted in dl714 that are retained by dl716 are the sequence TGT. The TGT sequence is located on the 5' boundary of the pyrimidine-rich region upstream of the nucleotide 2157 3' splice site. Such pyrimidine-rich regions are ubiquitous at 3' splice sites. Most likely, the TGT is required for splicing at the nucleotide 2157 3' splice site. The TGT may be important because of its specific sequence or because it forms the 5' boundary of the pyrimidine-rich region.
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Plucienniczak, G., J. Skowronski, A. Plucienniczak, and J. Jaworski. "Nucleotide Sequence of Bovine 1.723 Satellite DNA." Zeitschrift für Naturforschung C 40, no. 3-4 (April 1, 1985): 242–46. http://dx.doi.org/10.1515/znc-1985-3-418.
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The nucleotide sequence of the bovine 1.723 satellite DNA repeated unit was determined. The 680 bp long period of this satellite DNA does not show any significant sequence similarities with the known bovine satellite DNAs. Short repetitive sequences which are parts of 680 bp long repeated units do not form any orderly periodical structure. It seems, however, that the basic repeated unit of the 1.723 bovine satellite DNA has been formed by successive duplications of two, about 100 bp long sequences. The sequence divergence between different copies of the 680 bp repeated unit was also analyzed.
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Apituley, Edwin Thomas, Efraim Samson, and Amos Killay. "Analisis Filogenetik Gen gyrA dan gyrB dari Genus Mesorhizobium, Rhizobium dan Ensifer." Biofaal Journal 4, no. 2 (December 1, 2023): 118–27. http://dx.doi.org/10.30598/biofaal.v4i2pp118-127.
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Nucleotide sequence of gyrA and gyrB genes encoding subunit A and B of gyrase enzyme from genus of Rhizobium, Ensifer and Mesorhizobium were analyzed to determine evolutionary relationship among them. Maximum Likelihood and Kimura 2 parameter methods were used to construct phylogenetic tree and measure genetic distance. Phylogenetic tree based on nucleotide sequence of gyrA gene was compared to phylogenetic tree based on nucleotide sequence of gyrB gene. Comparison of identity percentage among nucleotide sequence of gyrA gene from genus Rhizobium, Ensifer and Mesorhizobium show similarity, where each of them have narrow range of identity percentage, however nucleotide sequence of gyrB gene from genus Rhizobium and Ensifer show wider identity percentage range than genus Mesorhizobium. Several member of genus Rhizobium and Ensifer have double copy of gyrB gene with identity percentage less than 50 percent between them. Topology of phylogenetic tree based on nucleotide sequence of gyrA gene have similar topology to topology of phylogenetic tree based on nucleotide sequence of gyrB gene, except for additional branch formed by one of additional copy of gyrB sequences. .
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Volobuev, AN N., ES S. Petrov, and NP P. Romanchuk. "BIOPHYSICAL BASES OF GENOME ORGANIZATION." Science and Innovations in Medicine 2, no. 4 (December 15, 2017): 13–17. http://dx.doi.org/10.35693/2500-1388-2017-0-4-13-17.
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Aim - the analysis of nucleotide sequences of DNA molecules and the bases of the information storage with the help of DNA. Material and methods - the study is based on Markov chain theory and Bayesian Information Criterion. Results. Principles of genetic code construction were investigated. Specific nucleotide sequences were analyzed using Markov chain theory; the method of sequencing nucleotide sequences was described. Conclusion. A nucleotide sequence has certain restrictions associated with complementarity of the bases along DNA chain. These restrictions at the level of triplet sequence can be eliminated by degeneracy of the genetic code.
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Takasaka, Tomokazu, Nobuyuki Goya, Hideki Ishida, Kazunari Tanabe, Hiroshi Toma, Tomoaki Fujioka, So Omori, et al. "Stability of the BK polyomavirus genome in renal-transplant patients without nephropathy." Journal of General Virology 87, no. 2 (February 1, 2006): 303–6. http://dx.doi.org/10.1099/vir.0.81368-0.
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To clarify the stability of the BK polyomavirus (BKPyV) genome in renal transplant (RT) recipients, three to five complete BKPyV genomes from each of six RT recipients with surviving renal allografts were molecularly cloned. The complete sequences of these clones were determined and compared in each patient. No nucleotide difference was detected among clones in two patients, and a few nucleotide variations were found among those in four patients. In each of these patients a parental sequence (usually the major sequence), from which variant sequences (usually minor sequences) with nucleotide substitutions would have been generated, were identified. A comparison between the parental and variant sequences in each patient identified a single nucleotide substitution in each variant sequence. From these findings, it was concluded that the genome of BKPyV is stable in RT recipients without nephropathy, with only minor nucleotide substitutions in the coding region.
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Chang, P. C., M. L. Hsieh, J. H. Shien, D. A. Graham, M. S. Lee, and H. K. Shieh. "Complete nucleotide sequence of avian paramyxovirus type 6 isolated from ducks." Journal of General Virology 82, no. 9 (September 1, 2001): 2157–68. http://dx.doi.org/10.1099/0022-1317-82-9-2157.
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There are nine serotypes of avian paramyxovirus (APMV). Only the genome of APMV type 1 (APMV-1), also called Newcastle disease virus (NDV), has been completely sequenced. In this study, the complete nucleotide sequence of an APMV-6 serotype isolated from ducks is reported. The 16236 nt genome encodes eight proteins, nucleocapsid protein (NP), phosphoprotein (P), V protein, matrix protein (M), fusion protein (F), small hydrophobic (SH) protein, haemagglutinin–neuraminidase (HN) protein and large (L) protein, which are flanked by a 55 nt leader sequence and a 54 nt trailer sequence. Sequence comparison reveals that the protein sequences of APMV-6 are most closely related to those of APMV-1 (NDV) and -2, with sequence identities ranging from 22 to 44%. However, APMV-6 contains a gene that might encode the SH protein, which is absent in APMV-1, but present in the rubulaviruses simian virus type 5 and mumps virus. The presence of an SH gene in APMV-6 might provide a link between the evolution of APMV and rubulaviruses. Phylogenetic analysis demonstrates that APMV-6, -1, -2 (only the F and HN sequences were available for analysis) and -4 (only the HN sequences were available for analysis) all cluster into a single lineage that is distinct from other paramyxoviruses. This result suggests that APMV should constitute a new genus within the subfamily Paramyxovirinae.
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Hisada, Sunao, Tomoya Akihama, Tomoko Endo, Takaya Moriguchi, and Mitsuo Omura. "Expressed Sequence Tags of Citrus Fruit during Rapid Cell Development Phase." Journal of the American Society for Horticultural Science 122, no. 6 (November 1997): 808–12. http://dx.doi.org/10.21273/jashs.122.6.808.
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A cDNA library was constructed from satsuma mandarin (Citrus unshiu Marc.) fruit tissues during the rapid cell enlargement phase. A total of 950 individual cDNA clones was partially sequenced and compared with GenBank databases for characterizing the gene repertoire expressed during this developmental phase. Among these, 426 cDNA clones (44.8%) showed sequence identity with previously characterized genes with optimized (OPT) scores of ≥200, while 524 clones (55.2%) resulted in low OPT scores (<200) and did not show any significant sequence identity with previously published genes. Based on nucleotide sequence, most clones with OPT scores of ≥200 were assumed to be transcription-, translation-, cell-wall-metabolism-, and stress-response-related genes. Other clones showed homology with published sequences related to housekeeping and stress-response-related genes, including metallothionein-like proteins, late-embryogenesis-abundant (LEA) proteins, and heat-shock proteins. These results suggested that Citrus fruit during rapid cell enlargement were metabolically active and expanding in response to biotic and abiotic stress. For clones with low nucleotide sequence homology, the recurrence was evaluated by aligning nucleotide sequences of each clone and generating contig maps. Expressed sequence tags (ESTs) of 162 clones with OPT scores <200 have not been reported for any other organism. Collectively, randomly sequenced cDNA clones described in this study provided information on types of genes expressed during the rapid cell enlargement phase in Citrus fruit. These genes should be used as candidates for Citrus genome mapping projects.
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Caputo, A., D. E. Sauer, and P. B. Rowe. "Nucleotide sequence and genomic organization of a human T lymphocyte serine protease gene." Journal of Immunology 145, no. 2 (July 15, 1990): 737–44. http://dx.doi.org/10.4049/jimmunol.145.2.737.
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Abstract We have determined the nucleotide sequence of 4508 base pairs of human genomic DNA which contain the human serine esterase gene from cytotoxic T lymphocytes (SECT) (equivalent to the 1-3E cDNA clone) and include 879 bp of 5' flanking DNA and 393 bp of 3' flanking DNA. The gene consists of five exons of 88, 148, 136, 261, and 257 nucleotides separated by four introns of 1043, 455, 205, and 643 nucleotides. The location of introns with respect to protein coding sequences in the SECT gene is identical to that of the human cathepsin G and murine granzyme B genes. Comparison of SECT gene exonic sequences to murine granzyme B-F cDNA sequences indicates similarities of 75 and 72% for granzymes B and C and 61, 59, and 61% for granzymes D, E, and F, respectively. The 5' flanking sequence of the SECT gene showed similarity only to the 5' flanking sequence of the murine granzyme B gene, indicating that these genes are homologous. Comparison of the SECT gene sequence to the human cathepsin G sequence indicated no similarity in the 5' flanking DNA although the exonic sequences show 64% sequence similarity overall and 45% sequence similarity in the respective 3' untranslated regions. These similarities suggest that the SECT and cathepsin G genes are members of the same family of serine protease genes. Evidence from high and low stringency Southern transfer analysis of human genomic DNA indicates the presence of another gene of at least 85% sequence similarity to the SECT gene.
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Chaves, L. D., J. A. Rowe, and K. M. Reed. "Survey of a cDNA library from the turkey (Meleagris gallopavo)." Genome 48, no. 1 (February 1, 2005): 12–17. http://dx.doi.org/10.1139/g04-088.
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Genome characterization and analysis is an imperative step in identifying and selectively breeding for improved traits of agriculturally important species. Expressed sequence tags (ESTs) represent a transcribed portion of the genome and are an effective way to identify genes within a species. Downstream applications of EST projects include DNA microarray construction and interspecies comparisons. In this study, 694 ESTs were sequenced and analyzed from a library derived from a 24-day-old turkey embryo. The 437 unique sequences identified were divided into 76 assembled contigs and 361 singletons. The majority of significant comparative matches occurred between the turkey sequences and sequences reported from the chicken. Whole genome sequence from the chicken was used to identify potential exon–intron boundaries for selected turkey clones and intron-amplifying primers were developed for sequence analysis and single nucleotide polymorphism (SNP) discovery. Identified SNPs were genotyped for linkage analysis on two turkey reference populations. This study significantly increases the number of EST sequences available for the turkey.Key words: turkey, cDNA, expressed sequence tag, single nucleotide polymorphism.
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Maina, Solomon, Brenda A. Coutts, Owain R. Edwards, Luis de Almeida, Monica A. Kehoe, Abel Ximenes, and Roger A. C. Jones. "Zucchini yellow mosaic virus Populations from East Timorese and Northern Australian Cucurbit Crops: Molecular Properties, Genetic Connectivity, and Biosecurity Implications." Plant Disease 101, no. 7 (July 2017): 1236–45. http://dx.doi.org/10.1094/pdis-11-16-1672-re.
Full textAbstract:
Zucchini yellow mosaic virus (ZYMV) isolates from cucurbit crops growing in northern Australia and East Timor were investigated to establish possible genetic connectivity between crop viruses in Australia and Southeast Asia. Leaves from symptomatic plants of pumpkin (Cucurbita moschata and C. maxima), melon (Cucumis melo), and zucchini (C. pepo) were sampled near Broome, Darwin, and Kununurra in northern Australia. Leaves from symptomatic plants of cucumber (C. sativus) and pumpkin sampled in East Timor were sent to Australia on FTA cards. These samples were subjected to high-throughput sequencing and 15 complete new ZYMV genomic sequences obtained. When their nucleotide sequences were compared with those of 48 others from GenBank, the East Timorese and Kununurra sequences (three per location) and single earlier sequences from Singapore and Reunion Island were all in major phylogroup B. The seven Broome and two Darwin sequences were in minor phylogroups I and II, respectively, within larger major phylogroup A. When coat protein (CP) nucleotide sequences from the 15 new genomes and 47 Australian isolates sequenced previously were compared with 331 other CP sequences, the closest genetic match for a sequence from Kununurra was with an East Timorese sequence (95.5% nucleotide identity). Analysis of the 63 complete genomes found firm recombination events in 12 (75%) and 2 (4%) sequences from northern Australia or Southeast Asia versus the rest of the world, respectively; therefore, the formers’ high recombination frequency might reflect adaptation to tropical conditions. Both parents of the recombinant Kununurra sequence were East Timorese. Phylogenetic analysis, nucleotide sequence identities, and recombination analysis provided clear evidence of genetic connectivity between sequences from Kununurra and East Timor. Inoculation of a Broome isolate to zucchini and watermelon plants reproduced field symptoms observed in northern Australia. This research has important biosecurity implications over entry of damaging viral crop pathogens not only into northern Australia but also moving between Australia’s different agricultural regions.
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Koehler, C. M., G. L. Lindberg, D. R. Brown, D. C. Beitz, A. E. Freeman, J. E. Mayfield, and A. M. Myers. "Replacement of bovine mitochondrial DNA by a sequence variant within one generation." Genetics 129, no. 1 (September 1, 1991): 247–55. http://dx.doi.org/10.1093/genetics/129.1.247.
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Abstract Inheritance of mitochondrial DNA (mtDNA) in Holstein cattle was characterized by pedigree analysis of nucleotide sequence variation. mtDNA was purified from leukocytes of 174 individuals representing 35 independent maternal lineages, and analyzed for nucleotide sequence variation by characterization of restriction fragment length polymorphism and direct sequence determination. These data revealed 11 maternal lineages in which leukocytes from some individuals seemingly were homoplasmic for the reference mtDNA sequence at nucleotide 364, whereas those from other individuals were homoplasmic for a sequence variant at this position. Both alternative alleles were detected in all branches of these 11 lineages, suggesting that mutation at nucleotide 364 and fixation of the variant sequence occurred frequently in independent events. Thirteen instances were detected of mother-daughter pairs in which leukocytes of each of the two animals seemingly were homoplasmic for a different allele at nucleotide 364, demonstrating the bovine mitochondrial genome can be replaced completely by a nucleotide sequence variant within a single generation. The two alternative sequences seemingly arose de novo at similar frequency, ruling out replicative advantage or other selective bias as the explanation for rapid fixation of mutations at nucleotide 364. Another instance of intralineage sequence variation was detected at nucleotide 5602. This variation was detected in only one of the lineages examined, and evidently arose within three generations.
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Zhu, Y. L., Q. J. Song, D. L. Hyten, C. P. Van Tassell, L. K. Matukumalli, D. R. Grimm, S. M. Hyatt, E. W. Fickus, N. D. Young, and P. B. Cregan. "Single-Nucleotide Polymorphisms in Soybean." Genetics 163, no. 3 (March 1, 2003): 1123–34. http://dx.doi.org/10.1093/genetics/163.3.1123.
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Abstract Single-nucleotide polymorphisms (SNPs) provide an abundant source of DNA polymorphisms in a number of eukaryotic species. Information on the frequency, nature, and distribution of SNPs in plant genomes is limited. Thus, our objectives were (1) to determine SNP frequency in coding and noncoding soybean (Glycine max L. Merr.) DNA sequence amplified from genomic DNA using PCR primers designed to complete genes, cDNAs, and random genomic sequence; (2) to characterize haplotype variation in these sequences; and (3) to provide initial estimates of linkage disequilibrium (LD) in soybean. Approximately 28.7 kbp of coding sequence, 37.9 kbp of noncoding perigenic DNA, and 9.7 kbp of random noncoding genomic DNA were sequenced in each of 25 diverse soybean genotypes. Over the >76 kbp, mean nucleotide diversity expressed as Watterson’s θ was 0.00097. Nucleotide diversity was 0.00053 and 0.00111 in coding and in noncoding perigenic DNA, respectively, lower than estimates in the autogamous model species Arabidopsis thaliana. Haplotype analysis of SNP-containing fragments revealed a deficiency of haplotypes vs. the number that would be anticipated at linkage equilibrium. In 49 fragments with three or more SNPs, five haplotypes were present in one fragment while four or less were present in the remaining 48, thereby supporting the suggestion of relatively limited genetic variation in cultivated soybean. Squared allele-frequency correlations (r2) among haplotypes at 54 loci with two or more SNPs indicated low genome-wide LD. The low level of LD and the limited haplotype diversity suggested that the genome of any given soybean accession is a mosaic of three or four haplotypes. To facilitate SNP discovery and the development of a transcript map, subsets of four to six diverse genotypes, whose sequence analysis would permit the discovery of at least 75% of all SNPs present in the 25 genotypes as well as 90% of the common (frequency >0.10) SNPs, were identified.
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Nagy, Miklós, Éva Nagy, and Tamás Tuboly. "The complete nucleotide sequence of porcine adenovirus serotype 5." Journal of General Virology 82, no. 3 (March 1, 2001): 525–29. http://dx.doi.org/10.1099/0022-1317-82-3-525.
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The complete nucleotide sequence of porcine adenovirus serotype 5 (PAdV-5) has been determined and the putative genomic map was constructed. The size of the genome was found to be 32621 nucleotides. Twenty-eight putative ORFs were identified by their homology to other adenovirus or other virus and eukaryotic genes. Several special protein sequence motifs were identified by their homology to similar protein motifs. The putative promoter regions, polyadenylation and splice sites were predicted and the early and late transcription units were determined. Based on sequence analysis and RNA secondary structure prediction, sequences for virus-associated RNA could not be recognized. Phylogenetic analysis showed that PAdV-5 was more closely related to certain bovine adenoviruses than to other porcine adenoviruses.
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Patil, S. S., D. Hemadri, K. Sreekala, H. Veeresh, B. M. Chandranaik, and K. Prabhudas. "Genetic characterization of bovine herpesvirus 1 (BoHV-1) isolates from India." Indian Journal of Animal Sciences 82, no. 8 (August 14, 2012): 848–50. http://dx.doi.org/10.56093/ijans.v82i8.23006.
Full textAbstract:
Two bovine herpesvirus-1 (BoHV-1) isolates previously recovered from 2 animals showing different clinical symptoms, i.e. respiratory disease and balanoposthitis, were partially nucleotide sequenced at the gB gene. Aligned nucleotide sequences revealed high degree of identity among all the alphaherpesviruses compared in the study. The nucleotide sequence identity among the Indian isolates varied from 99–99.5% and so was their identity with reference Cooper strain. The phylogenetic analysis indicated that both the isolates belonged to subtype 1.1 despite being isolated from animals with different clinical manifestations.
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Yamamoto, Masato, Julia Davydova, Koichi Takayama, Ramon Alemany, and David T. Curiel. "Transcription Initiation Activity of Adenovirus Left-End Sequence in Adenovirus Vectors with E1 Deleted." Journal of Virology 77, no. 2 (January 15, 2003): 1633–37. http://dx.doi.org/10.1128/jvi.77.2.1633-1637.2003.
Full textAbstract:
ABSTRACT We analyzed the transcription initiation activity of the left-end sequence (first 342 bp) of the adenovirus genome in the context of an adenovirus vector with E1 deleted in in vitro and in vivo gene transfer models. While nucleotide sequences 1 to 190 and 1 to 342 showed strong activity in three out of three lung cancer cell lines, nucleotide sequence 1 to 103 showed limited activity in H358, cells which show characteristics of type 2 alveolar cells. In vivo, the transcription initiation activities of nucleotide sequence 1 to 103 in the liver and the lung were minimal, while nucleotide sequences 1 to 190 and 1 to 342 showed strong activity comparable to that of the cytomegalovirus promoter. Further understanding of the transcription initiation activity of the left-end sequence of the adenovirus genome should lead to optimization of adenovirus vectors.