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Статті в журналах з теми "Nucleotide sequence"

Автор: Grafiati

Опубліковано: 4 червня 2021

Оновлено: 25 липня 2025

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1

Fatchiyah, Fatchiyah, Rista Nikmatu Rohmah, Lidwina Faraline Tripisila, et al. "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 (2022): 105–9. http://dx.doi.org/10.23869/bphjbr.27.2.20228.

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Анотація:

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

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2

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 interg

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3

Kuśmirek, Wiktor. "Estimated Nucleotide Reconstruction Quality Symbols of Basecalling Tools for Oxford Nanopore Sequencing." Sensors 23, no. 15 (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 estim

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4

Bradford, Patricia A. "Automated Thermal Cycling Is Superior to Traditional Methods for Nucleotide Sequencing ofblaSHV Genes." Antimicrobial Agents and Chemotherapy 43, no. 12 (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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5

Lee, Byoungsang, So Yeon Ahn, Charles Park, et al. "Revealing the Presence of a Symbolic Sequence Representing Multiple Nucleotides Based on K-Means Clustering of Oligonucleotides." Molecules 24, no. 2 (2019): 348. http://dx.doi.org/10.3390/molecules24020348.

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Анотація:

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 inheri

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6

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 (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 n

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7

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 (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 n

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8

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 (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

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9

Ojkic, Davor, and éva Nagy. "The complete nucleotide sequence of fowl adenovirus type 8." Microbiology 81, no. 7 (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-as

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10

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 (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 processin

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11

Geliebter, J., R. A. Zeff, D. H. Schulze, et al. "Interaction between Kb and Q4 gene sequences generates the Kbm6 mutation." Molecular and Cellular Biology 6, no. 2 (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, re

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12

Geliebter, J., R. A. Zeff, D. H. Schulze, et al. "Interaction between Kb and Q4 gene sequences generates the Kbm6 mutation." Molecular and Cellular Biology 6, no. 2 (1986): 645–52. http://dx.doi.org/10.1128/mcb.6.2.645.

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Анотація:

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, re

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13

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

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14

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 (1994): 87–95. http://dx.doi.org/10.18388/abp.1994_4778.

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Анотація:

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

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15

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 (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 sequenc

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16

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 (1986): 15–25. http://dx.doi.org/10.1128/mcb.6.1.15.

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Анотація:

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 sequenc

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17

Mathis, Diane, and Christophe Benoist. "Nucleotide Sequence: Correction." Science 279, no. 5348 (1998): 151.2–151. http://dx.doi.org/10.1126/science.279.5348.151-b.

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18

Mathis, D. "Nucleotide Sequence: Correction." Science 279, no. 5348 (1998): 151b—151. http://dx.doi.org/10.1126/science.279.5348.151b.

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19

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 (1986): 435–39. http://dx.doi.org/10.1042/bj2350435.

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Анотація:

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

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20

Klimentov, A. S., A. P. Gmyl, A. M. Butenko, et al. "Taxonomic status of Bhanja and Kismayo viruses (family Bunyaviridae)." Epidemiology and Infectious Diseases 17, no. 4 (2012): 4–8. http://dx.doi.org/10.17816/eid40625.

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Анотація:

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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21

Wiuf, Carsten, and Jotun Hein. "The Ancestry of a Sample of Sequences Subject to Recombination." Genetics 151, no. 3 (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

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22

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 (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. Nucl

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23

Netolitzky, Donald J., Fay L. Schmaltz, Michael D. Parker, et al. "Complete genomic RNA sequence of western equine encephalitis virus and expression of the structural genes." Microbiology 81, no. 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 nucl

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24

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 (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 wer

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25

Górski, Andrzej Z., and Monika Piwowar. "Nucleotide spacing distribution analysis for human genome." Mammalian Genome 32, no. 2 (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 correlat

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26

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.

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27

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 (2003): 678–81. http://dx.doi.org/10.1590/s0100-41582003000600015.

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Анотація:

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 ref

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28

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 (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 sequ

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29

Mauser, AE, J. Whitlark, KM Whitney, and CD Jr Lothrop. "A deletion mutation causes hemophilia B in Lhasa Apso dogs." Blood 88, no. 9 (1996): 3451–55. http://dx.doi.org/10.1182/blood.v88.9.3451.bloodjournal8893451.

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Анотація:

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 i

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30

Dvořák, J., D. Jue, and M. Lassner. "Homogenization of Tandemly Repeated Nucleotide Sequences by Distance-Dependent Nucleotide Sequence Conversion." Genetics 116, no. 3 (1987): 487–98. http://dx.doi.org/10.1093/genetics/116.3.487.

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Анотація:

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 li

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31

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 (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 substa

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32

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 (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 sequ

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33

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,

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34

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 (1985): 2405–13. http://dx.doi.org/10.1128/mcb.5.9.2405-2413.1985.

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Анотація:

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

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35

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 (1985): 2405–13. http://dx.doi.org/10.1128/mcb.5.9.2405.

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Анотація:

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

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36

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 (2023): 118–27. http://dx.doi.org/10.30598/biofaal.v4i2pp118-127.

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Анотація:

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, whe

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37

Volobuev, AN N., ES S. Petrov, and NP P. Romanchuk. "BIOPHYSICAL BASES OF GENOME ORGANIZATION." Science and Innovations in Medicine 2, no. 4 (2017): 13–17. http://dx.doi.org/10.35693/2500-1388-2017-0-4-13-17.

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Анотація:

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

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38

Takasaka, Tomokazu, Nobuyuki Goya, Hideki Ishida, et al. "Stability of the BK polyomavirus genome in renal-transplant patients without nephropathy." Journal of General Virology 87, no. 2 (2006): 303–6. http://dx.doi.org/10.1099/vir.0.81368-0.

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Анотація:

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 su

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39

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 (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

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40

Xu, Deshun, Lei Ji, Xiaofang Wu, and Liping Chen. "Whole-genome sequence analysis of SFTS bunyavirus in Huzhou, China." PLOS ONE 20, no. 2 (2025): e0318742. https://doi.org/10.1371/journal.pone.0318742.

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Severe fever with thrombocytopenia syndrome (SFTS), a tick-borne emerging infectious disease caused by SFTS virus (SFTSV), is a growing public health threat due to its high mortality rate. To understand the genomic characteristics of SFTSV samples isolated in Huzhou, China, the full-length genomes of Huzhou SFTSV isolates obtained between February 1, 2019 and December 30, 2023 were sequenced, and the gene loci, evolution, and sequence identity of the genome sequences were analyzed using MEGA. The complete genome sequences of seven SFTSV samples were obtained successfully. The full-length genom

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41

Chaves, L. D., J. A. Rowe, and K. M. Reed. "Survey of a cDNA library from the turkey (Meleagris gallopavo)." Genome 48, no. 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 singleton

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42

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 (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 com

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43

Herman, Herman, Mayang Sari, Nella Multivasari, and Dewi Indriyani Roslim. "DNA Barcoding Analysis Kitolod (Hippobroma longiflora) from Riau Based on matk Gene." Jurnal Biologi Tropis 25, no. 1 (2025): 653–59. https://doi.org/10.29303/jbt.v25i1.8479.

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Анотація:

The kitolod plant (Hippobroma longiflora) is a traditional medicinal plant originating from the Campanulaceae family. DNA barcoding is a technique for identifying an organism using short nucleotide sequences known as DNA barcoding. One of the DNA barcodes in plants is matK. This research aims to analyze DNA barcode sequence in the matK region of the kitolod plant using the DNA barcode. Samples were taken from the area of Tarai Bangun Village, Kampar Regency, Riau Province, Indonesia as many as two different individuals. The research stages carried out are sampling, followed by DNA isolation us

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44

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 (1985): 242–46. http://dx.doi.org/10.1515/znc-1985-3-418.

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Анотація:

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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45

Maina, Solomon, Brenda A. Coutts, Owain R. Edwards, et al. "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 (2017): 1236–45. http://dx.doi.org/10.1094/pdis-11-16-1672-re.

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Анотація:

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 sequen

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46

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 (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 e

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47

Brunak, S. "Nucleotide Sequence Database Policies." Science 298, no. 5597 (2002): 1333b—1333. http://dx.doi.org/10.1126/science.298.5597.1333b.

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48

Koehler, C. M., G. L. Lindberg, D. R. Brown, et al. "Replacement of bovine mitochondrial DNA by a sequence variant within one generation." Genetics 129, no. 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 homopla

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49

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 (2003): 1633–37. http://dx.doi.org/10.1128/jvi.77.2.1633-1637.2003.

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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 nucleotid

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50

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 (2012): 848–50. http://dx.doi.org/10.56093/ijans.v82i8.23006.

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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 differen

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