Статті в журналах: "Palindrome analyser"

1

Cunningham, Lesley A., Atina G. Coté, Cennet Cam-Ozdemir, and Susanna M. Lewis. "Rapid, Stabilizing Palindrome Rearrangements in Somatic Cells by the Center-Break Mechanism." Molecular and Cellular Biology 23, no. 23 (December 1, 2003): 8740–50. http://dx.doi.org/10.1128/mcb.23.23.8740-8750.2003.

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ABSTRACT DNA palindromes are associated with rearrangement in a variety of organisms. A unique opportunity to examine the impact of a long palindrome in mammals is afforded by the Line 78 strain of mice. Previously it was found that the transgene in Line 78 is likely to be palindromic and that the symmetry of the transgene was responsible for a high level of germ line instability. Here we prove that Line 78 mice harbor a true 15.4-kb palindrome, and through the establishment of cell lines from Line 78 mice we have shown that the palindrome rearranges at the impressive rate of about 0.5% per population doubling. The rearrangements observed to arise from rapid palindrome modification are consistent with a center-break mechanism where double-strand breaks, created through hairpin nicking of an extruded cruciform, are imprecisely rejoined, thus introducing deletions at the palindrome center. Significantly, palindrome rearrangements in somatic tissue culture cells almost completely mirrored the structures generated in vivo in the mouse germ line. The close correspondence between germ line and somatic events indicates the possibility that center-break modification of palindromes is an important mechanism for preventing mutation in both contexts. Permanent cell lines carrying a verified palindrome provide an essential tool for future mechanistic analyses into the consequences of palindromy in the mammalian genome.

2

Brázda, Václav, Jan Kolomazník, Jiří Lýsek, Lucia Hároníková, Jan Coufal, and Jiří Št'astný. "Palindrome analyser – A new web-based server for predicting and evaluating inverted repeats in nucleotide sequences." Biochemical and Biophysical Research Communications 478, no. 4 (September 2016): 1739–45. http://dx.doi.org/10.1016/j.bbrc.2016.09.015.

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3

Brázda, Václav, Jiří Lýsek, Martin Bartas, and Miroslav Fojta. "Complex Analyses of Short Inverted Repeats in All Sequenced Chloroplast DNAs." BioMed Research International 2018 (July 24, 2018): 1–10. http://dx.doi.org/10.1155/2018/1097018.

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Chloroplasts are key organelles in the management of oxygen in algae and plants and are therefore crucial for all living beings that consume oxygen. Chloroplasts typically contain a circular DNA molecule with nucleus-independent replication and heredity. Using “palindrome analyser” we performed complete analyses of short inverted repeats (S-IRs) in all chloroplast DNAs (cpDNAs) available from the NCBI genome database. Our results provide basic parameters of cpDNAs including comparative information on localization, frequency, and differences in S-IR presence. In a total of 2,565 cpDNA sequences available, the average frequency of S-IRs in cpDNA genomes is 45 S-IRs/per kbp, significantly higher than that found in mitochondrial DNA sequences. The frequency of S-IRs in cpDNAs generally decreased with S-IR length, but not for S-IRs 15, 22, 24, or 27 bp long, which are significantly more abundant than S-IRs with other lengths. These results point to the importance of specific S-IRs in cpDNA genomes. Moreover, comparison by Levenshtein distance of S-IR similarities showed that a limited number of S-IR sequences are shared in the majority of cpDNAs. S-IRs are not located randomly in cpDNAs, but are length-dependently enriched in specific locations, including the repeat region, stem, introns, and tRNA regions. The highest enrichment was found for 12 bp and longer S-IRs in the stem-loop region followed by 12 bp and longer S-IRs located before the repeat region. On the other hand, S-IRs are relatively rare in rRNA sequences and around introns. These data show nonrandom and conserved arrangements of S-IRs in chloroplast genomes.

4

Nobile, C., J. Nickol, and R. G. Martin. "Nucleosome phasing on a DNA fragment from the replication origin of simian virus 40 and rephasing upon cruciform formation of the DNA." Molecular and Cellular Biology 6, no. 8 (August 1986): 2916–22. http://dx.doi.org/10.1128/mcb.6.8.2916.

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Nucleosomes were reconstituted in vitro from a fragment of DNA spanning the simian virus 40 minimal replication origin. The fragment contains a 27-base-pair palindrome (perfect inverted repeat). DNA molecules with stable cruciform structures were generated by heteroduplexing this DNA fragment with mutants altered within the palindromic sequence (C. Nobile and R. G. Martin, Int. Virol., in press). Analyses of the structural features of the reconstituted nucleosomes by the DNase I footprint technique revealed two alternative DNA-histone arrangements, each one accurately phased with respect to the uniquely labeled DNA ends. As linear double-stranded DNA, a unique core particle was formed in which the histones strongly protected the regions to both sides of the palindrome. The cruciform structure seemed to be unable to associate with core histones and, therefore, an alternative phasing of the histone octamer along the DNA resulted. Thus, nucleosome positioning along a specific DNA sequence appears to be influenced in vitro by the secondary structure (linear or cruciform) of the 27-base-pair palindrome. The formation of cruciform structures in vivo, if they occur, might therefore represent a molecular mechanism by which nucleosomes are phased.

5

Nobile, C., J. Nickol, and R. G. Martin. "Nucleosome phasing on a DNA fragment from the replication origin of simian virus 40 and rephasing upon cruciform formation of the DNA." Molecular and Cellular Biology 6, no. 8 (August 1986): 2916–22. http://dx.doi.org/10.1128/mcb.6.8.2916-2922.1986.

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Nucleosomes were reconstituted in vitro from a fragment of DNA spanning the simian virus 40 minimal replication origin. The fragment contains a 27-base-pair palindrome (perfect inverted repeat). DNA molecules with stable cruciform structures were generated by heteroduplexing this DNA fragment with mutants altered within the palindromic sequence (C. Nobile and R. G. Martin, Int. Virol., in press). Analyses of the structural features of the reconstituted nucleosomes by the DNase I footprint technique revealed two alternative DNA-histone arrangements, each one accurately phased with respect to the uniquely labeled DNA ends. As linear double-stranded DNA, a unique core particle was formed in which the histones strongly protected the regions to both sides of the palindrome. The cruciform structure seemed to be unable to associate with core histones and, therefore, an alternative phasing of the histone octamer along the DNA resulted. Thus, nucleosome positioning along a specific DNA sequence appears to be influenced in vitro by the secondary structure (linear or cruciform) of the 27-base-pair palindrome. The formation of cruciform structures in vivo, if they occur, might therefore represent a molecular mechanism by which nucleosomes are phased.

6

Higa, M., T. Kitahashi, Y. Sasaki, H. Okada, and H. Ando. "Distinct promoter sequences of two precursor genes for salmon gonadotropin-releasing hormone in masu salmon." Journal of Molecular Endocrinology 19, no. 2 (October 1, 1997): 149–61. http://dx.doi.org/10.1677/jme.0.0190149.

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Two types of genes encode salmon gonadotropin-releasing hormone (sGnRH), which is thought to act on both sexual maturation and reproductive behavior, in salmonids. We characterized the two sGnRH genes (sGnRH-I and -II) and their upstream regions in masu salmon, Oncorhynchus masou, since such information is a prerequisite for molecular approaches to salmon reproduction. The two genes have similar exon-intron structures composed of four exons and three introns. Sequence analyses of the two genes showed that coding regions are highly conserved, but upstream regions are distinctively divergent. In the upstream regions, only the sGnRH-II gene has a large palindromic sequence, which has been proposed to be involved in control of transcription via estrogen receptors. In contrast, the sGnRH-I gene is missing the large palindromic sequence, but has three distinct palindromes in the upstream region. These results may suggest divergent transcription regulatory mechanisms between the two sGnRH genes in masu salmon. The differences in the upstream regions of sGnRH genes in Atlantic salmon (Salmo salar), sockeye salmon (Oncorhynchus nerka) and masu salmon are discussed with respect to the evolution of sGnRH genes in salmonid fish.

7

Ahmad, Sk Safique. "Perturbation analysis for palindromic and anti-palindromic nonlinear eigenvalue problems." ETNA - Electronic Transactions on Numerical Analysis 51 (2019): 151–68. http://dx.doi.org/10.1553/etna_vol51s151.

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8

Anderson, S. J., S. Miyake, and D. Y. Loh. "Transcription from a murine T-cell receptor V beta promoter depends on a conserved decamer motif similar to the cyclic AMP response element." Molecular and Cellular Biology 9, no. 11 (November 1989): 4835–45. http://dx.doi.org/10.1128/mcb.9.11.4835.

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We identified a regulatory region of the murine V beta promoter by both in vivo and in vitro analyses. The results of transient transfection assays indicated that the dominant transcription-activating element within the V beta 8.3 promoter is the palindromic motif identified previously as the conserved V beta decamer. Elimination of this element, by linear deletion or specific mutation, reduced transcriptional activity from this promoter by 10-fold. DNase I footprinting, gel mobility shift, and methylation interference assays confirmed that the palindrome acts as the binding site of a specific nuclear factor. In particular, the V beta promoter motif functioned in vitro as a high-affinity site for a previously characterized transcription activator, ATF. A consensus cyclic AMP response element (CRE) but not a consensus AP-1 site, can substitute for the decamer in vivo. These data suggest that cyclic AMP response element-binding protein (ATF/CREB) or related proteins activate V beta transcription.

9

Anderson, S. J., S. Miyake, and D. Y. Loh. "Transcription from a murine T-cell receptor V beta promoter depends on a conserved decamer motif similar to the cyclic AMP response element." Molecular and Cellular Biology 9, no. 11 (November 1989): 4835–45. http://dx.doi.org/10.1128/mcb.9.11.4835-4845.1989.

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We identified a regulatory region of the murine V beta promoter by both in vivo and in vitro analyses. The results of transient transfection assays indicated that the dominant transcription-activating element within the V beta 8.3 promoter is the palindromic motif identified previously as the conserved V beta decamer. Elimination of this element, by linear deletion or specific mutation, reduced transcriptional activity from this promoter by 10-fold. DNase I footprinting, gel mobility shift, and methylation interference assays confirmed that the palindrome acts as the binding site of a specific nuclear factor. In particular, the V beta promoter motif functioned in vitro as a high-affinity site for a previously characterized transcription activator, ATF. A consensus cyclic AMP response element (CRE) but not a consensus AP-1 site, can substitute for the decamer in vivo. These data suggest that cyclic AMP response element-binding protein (ATF/CREB) or related proteins activate V beta transcription.

10

He, Tian-Xiao, and Louis Shapiro. "Palindromes and pseudo-involution multiplication." Linear Algebra and its Applications 593 (May 2020): 1–17. http://dx.doi.org/10.1016/j.laa.2020.01.031.

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11

Boucher, P. D., M. P. Piechocki, and R. N. Hines. "Partial characterization of the human CYP1A1 negatively acting transcription factor and mutational analysis of its cognate DNA recognition sequence." Molecular and Cellular Biology 15, no. 9 (September 1995): 5144–51. http://dx.doi.org/10.1128/mcb.15.9.5144.

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Previous studies in our laboratory identified a negative regulatory domain in the 5'-flanking region of the human CYP1A1 gene containing two negative regulatory elements (NRE). Characterization of one of these elements revealed three nuclear protein binding regions: a 21-bp palindrome with a point of symmetry at -784 and two guanine- and cytosine-rich elements that flank the palindrome. Functional studies suggested the palindrome is critical for transcriptional repression, whereas the guanine- and cytosine-rich sequences play a secondary role. In this study, the interaction between nuclear proteins and the CYP1A1 NRE was further defined. Electrophoretic mobility shift assays (EMSA) indicated that the NRE -784 palindrome alone, but not the guanine- and cytosine-rich sequences minus the palindrome, was capable of specific nuclear protein binding. Competitive cotransfection experiments confirmed this observation in intact cells. Specific residues important for DNA-protein interactions were identified by site-directed mutagenesis and competitive EMSA. The loss of specific protein binding was also correlated with the loss of negative regulatory activity in a transient-expression assay. Finally, competitive EMSA was performed with consensus oligonucleotides for known transcription factors. An NF-Y consensus sequence efficiently competed with the NRE probe for specific nuclear protein binding. EMSA supershift analyses indicate that a protein immunologically related to NF-YB is part of the specific nuclear protein complex binding the human CYP1A1 NRE. These studies have refined our understanding of the sequences critical for the transcriptional repression of human CYP1A1. To our knowledge, this is also the first report implicating a member of the NF-Y transcription factor family in negative gene regulation.

12

Lancaster, Peter, Uwe Prells, and Leiba Rodman. "Canonical structures for palindromic matrix polynomials." Operators and Matrices, no. 4 (2007): 469–89. http://dx.doi.org/10.7153/oam-01-28.

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13

Sridhar, Settu, Mallapragada Nagamruta, and Kunchur Guruprasad. "Analyses of the Sequence and Structural Properties Corresponding to Pentapeptide and Large Palindromes in Proteins." PLOS ONE 10, no. 10 (October 14, 2015): e0139568. http://dx.doi.org/10.1371/journal.pone.0139568.

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14

O'Rourke, Kevin P., Jeremy D. Shaw, Mitchell W. Pesesky, Brian T. Cook, Susanne M. Roberts, Jeffrey P. Bond, and Grace A. Spatafora. "Genome-Wide Characterization of the SloR Metalloregulome in Streptococcus mutans." Journal of Bacteriology 192, no. 5 (November 13, 2009): 1433–43. http://dx.doi.org/10.1128/jb.01161-09.

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ABSTRACT Streptococcus mutans is the primary causative agent of human dental caries, a ubiquitous infectious disease for which effective treatment strategies remain elusive. We investigated a 25-kDa SloR metalloregulatory protein in this oral pathogen, along with its target genes that contribute to cariogenesis. Previous studies have demonstrated manganese- and SloR-dependent repression of the sloABCR metal ion transport operon in S. mutans. In the present study, we demonstrate that S. mutans coordinates this repression with that of certain virulence attributes. Specifically, we noted virulence gene repression in a manganese-containing medium when SloR binds to promoter-proximal sequence palindromes on the S. mutans chromosome. We applied a genome-wide approach to elucidate the sequences to which SloR binds and to reveal additional “class I” genes that are subject to SloR- and manganese-dependent repression. These analyses identified 204 S. mutans genes that are preceded by one or more conserved palindromic SloR recognition elements (SREs). We cross-referenced these genes with those that we had identified previously as SloR and/or manganese modulated in microarray and real-time quantitative reverse transcription-PCR (qRT-PCR) experiments. From this analysis, we identified a number of S. mutans virulence genes that are subject to transcriptional upregulation by SloR and noted that such “class II”-type regulation is dependent on direct SloR binding to promoter-distal SREs. These observations are consistent with a bifunctional role for the SloR metalloregulator and implicate it as a target for the development of therapies aimed at alleviating S. mutans-induced caries formation.

15

Khalil, Mohamed I., John Hay, and William T. Ruyechan. "Cellular Transcription Factors Sp1 and Sp3 Suppress Varicella-Zoster Virus Origin-Dependent DNA Replication." Journal of Virology 82, no. 23 (September 24, 2008): 11723–33. http://dx.doi.org/10.1128/jvi.01322-08.

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ABSTRACT The varicella-zoster virus (VZV) origin of DNA replication (oriS) contains a 46-bp AT-rich palindrome and three consensus binding sites for the VZV origin binding protein (OBP) encoded by VZV ORF51. All three OBP binding sites are upstream of the palindrome in contrast to the sequence of the herpes simplex virus oriS, which has required OBP binding sites upstream and downstream of the AT-rich region. We are investigating the roles that sequences downstream of the palindrome play in VZV oriS-dependent DNA replication. Computer analysis identified two GC boxes, GC box 1 and GC box 2, in the downstream region which were predicted to be binding sites for the cellular transcription factor Sp1. Electrophoretic mobility shift assay and supershift assays showed that two members of the Sp family (Sp1 and Sp3) stably bind to GC box 1, but not to GC box 2. A predicted binding site for the cellular factor Yin Yang 1 (YY1) that overlaps with GC box 2 was also identified. Supershift and mutational analyses confirmed the binding of YY1 to this site. Mutation of GC box 1 resulted in loss of Sp1 and Sp3 binding and an increase in origin-dependent replication efficiency in DpnI replication assays. In contrast, mutation of the YY1 site had a statistically insignificant effect. These results suggest a model where origin-dependent DNA replication and viral transcription are coupled by the binding of Sp1 and Sp3 to the downstream region of the VZV replication origin during lytic infection. They may also have implications regarding establishment or reactivation of viral latency.

16

De Terán, Fernando, Froilán M. Dopico, D. Steven Mackey, and Vasilije Perović. "Quadratic realizability of palindromic matrix polynomials." Linear Algebra and its Applications 567 (April 2019): 202–62. http://dx.doi.org/10.1016/j.laa.2019.01.003.

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17

Huang, Tsung-Ming, Wen-Wei Lin, and Jiang Qian. "Structure-Preserving Algorithms for Palindromic Quadratic Eigenvalue Problems Arising from Vibration of Fast Trains." SIAM Journal on Matrix Analysis and Applications 30, no. 4 (January 2009): 1566–92. http://dx.doi.org/10.1137/080713550.

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18

Zoephel, Judith, and Lennart Randau. "RNA-Seq analyses reveal CRISPR RNA processing and regulation patterns." Biochemical Society Transactions 41, no. 6 (November 20, 2013): 1459–63. http://dx.doi.org/10.1042/bst20130129.

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In bacteria and archaea, RNA-Seq deep sequencing methodology allows for the detection of abundance and processing sites of the small RNAs that comprise a CRISPR (clustered regularly interspaced short palindromic repeats) RNome. Comparative analyses of these CRISPR RNome sets highlight conserved patterns that include the gradual decline of CRISPR RNA abundance from the leader-proximal to the leader-distal end. In the present review, we discuss exceptions to these patterns that indicate the extensive impact of individual spacer sequences on CRISPR array transcription and RNA maturation. Spacer sequences can contain promoter and terminator elements and can promote the formation of CRISPR RNA–anti-CRISPR RNA duplexes. In addition, potential RNA duplex formation with host tRNA was observed. These factors can influence the functionality of CRISPR–Cas (CRISPR-associated) systems and need to be considered in the design of synthetic CRISPR arrays.

19

Kaur, Kanwal J., Pampi Sarkar, Sushma Nagpal, Tarique Khan, and Dinakar M. Salunke. "Structure-function analyses involving palindromic analogs of tritrypticin suggest autonomy of anti-endotoxin and antibacterial activities." Protein Science 17, no. 3 (March 2008): 545–54. http://dx.doi.org/10.1110/ps.073145008.

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20

Gupta, Madhu, Radovan Zak, Towia A. Libermann та Mahesh P. Gupta. "Tissue-Restricted Expression of the Cardiac α-Myosin Heavy Chain Gene Is Controlled by a Downstream Repressor Element Containing a Palindrome of Two Ets-Binding Sites". Molecular and Cellular Biology 18, № 12 (1 грудня 1998): 7243–58. http://dx.doi.org/10.1128/mcb.18.12.7243.

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ABSTRACT The expression of the α-myosin heavy chain (MHC) gene is restricted primarily to cardiac myocytes. To date, several positive regulatory elements and their binding factors involved in α-MHC gene regulation have been identified; however, the mechanism restricting the expression of this gene to cardiac myocytes has yet to be elucidated. In this study, we have identified by using sequential deletion mutants of the rat cardiac α-MHC gene a 30-bp purine-rich negative regulatory (PNR) element located in the first intronic region that appeared to be essential for the tissue-specific expression of the α-MHC gene. Removal of this element alone elevated (20- to 30-fold) the expression of the α-MHC gene in cardiac myocyte cultures and in heart muscle directly injected with plasmid DNA. Surprisingly, this deletion also allowed a significant expression of the α-MHC gene in HeLa and other nonmuscle cells, where it is normally inactive. The PNR element required upstream sequences of the α-MHC gene for negative gene regulation. By DNase I footprint analysis of the PNR element, a palindrome of two high-affinity Ets-binding sites (CTTCCCTGGAAG) was identified. Furthermore, by analyses of site-specific base-pair mutation, mobility gel shift competition, and UV cross-linking, two different Ets-like proteins from cardiac and HeLa cell nuclear extracts were found to bind to the PNR motif. Moreover, the activity of the PNR-binding factor was found to be increased two- to threefold in adult rat hearts subjected to pressure overload hypertrophy, where the α-MHC gene is usually suppressed. These data demonstrate that the PNR element plays a dual role, both downregulating the expression of the α-MHC gene in cardiac myocytes and silencing the muscle gene activity in nonmuscle cells. Similar palindromic Ets-binding motifs are found conserved in the α-MHC genes from different species and in other cardiac myocyte-restricted genes. These results are the first to reveal a role of the Ets class of proteins in controlling the tissue-specific expression of a cardiac muscle gene.

21

Iannazzo, Bruno, and Beatrice Meini. "Palindromic matrix polynomials, matrix functions and integral representations." Linear Algebra and its Applications 434, no. 1 (January 2011): 174–84. http://dx.doi.org/10.1016/j.laa.2010.09.013.

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22

Donahoo, R. S., J. B. Jones, G. H. Lacy, V. K. Stromberg, and D. J. Norman. "Genetic Analyses of Xanthomonas axonopodis pv. dieffenbachiae Strains Reveal Distinct Phylogenetic Groups." Phytopathology® 103, no. 3 (March 2013): 237–44. http://dx.doi.org/10.1094/phyto-08-12-0191-r.

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A comprehensive analysis of 175 Xanthomonas axonopodis pv. dieffenbachiae strains isolated from 10 Araceae hosts was done to identify pathogen variation. The strains were subjected to repetitive extragenic palindromic sequence polymerase chain reaction and four major phylogenetic clusters were generated. A subset of 40 strains isolated from Anthurium, Dieffenbachia, and Syngonium was further defined by amplified fragment length polymorphism and fatty acid methyl ester analysis and the same four phylogenetic clusters were observed. Comparison of representative strains in the first three clusters using DNA-DNA hybridization and multilocus sequence analysis supports the previous reclassification of strains in cluster I, including the X. axonopodis pv. dieffenbachiae pathovar reference strain (LMG695), to X. citri. Our research findings indicate that strains in cluster I, isolated primarily from anthurium, probably represent an undescribed pathovar. Other phylogenetic subclusters consisting primarily of strains isolated from xanthosoma and philodendron in clusters III and IV, respectively, may yet represent other undescribed species or pathovars of Xanthomonas.

23

Kon, T., S. C. Weir, J. T. Trevors, H. Lee, J. Champagne, L. Meunier, R. Brousseau, and L. Masson. "Microarray Analysis of Escherichia coli Strains from Interstitial Beach Waters of Lake Huron (Canada)." Applied and Environmental Microbiology 73, no. 23 (September 21, 2007): 7757–58. http://dx.doi.org/10.1128/aem.01333-07.

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ABSTRACT DNA microarray analyses revealed that clusters of repetitive extragenic palindromic PCR-related Escherichia coli isolates were isogenic only within interstitial Lake Huron beach water samples and not in surrounding waters. This suggested that adaptation and growth occurred within the interstitial water sites tested. All isolates were nonpathogenic, and three lake isolates possessed tetracycline resistance genes.

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Mukha, D. V., A. G. Chumachenko, M. J. Dykstra, T. J. Kurtti, and C. Schal. "Characterization of a new densovirus infecting the German cockroach, Blattella germanica." Journal of General Virology 87, no. 6 (June 1, 2006): 1567–75. http://dx.doi.org/10.1099/vir.0.81638-0.

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A new DNA virus (Parvoviridae: Densovirinae, Densovirus) was isolated and purified from descendants of field-collected German cockroaches, Blattella germanica. Viral DNA and cockroach tissues infected with B. germanica densovirus (BgDNV) were examined by electron microscopy. Virus particles, about 20 nm in diameter, were observed both in the nucleus and in the cytoplasm of infected cells. Virus DNA proved to be a linear molecule of about 1.2 μm in length. BgDNV isolated from infected cockroaches infected successfully and could be maintained in BGE-2, a B. germanica cell line. The complete BgDNV genome was sequenced and analysed. Five open reading frames (ORFs) were detected in the 5335 nt sequence: two ORFS that were on one DNA strand encoded structural capsid proteins (69.7 and 24.8 kDa) and three ORFs that were on the other strand encoded non-structural proteins (60.2, 30.3 and 25.9 kDa). Three putative promoters and polyadenylation signals were identified. Structural analysis of the inverted terminal repeats revealed the presence of extended palindromes. The genome structure of BgDNV was compared with that of other members of the family Parvoviridae; the predicted amino acid sequences were aligned and subjected to phylogenetic analyses.

25

Petrullo, P. "Palindromic Riordan arrays, classical orthogonal polynomials and Catalan triangles." Linear Algebra and its Applications 618 (June 2021): 158–82. http://dx.doi.org/10.1016/j.laa.2021.02.007.

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26

Li, Jun, Shuyan Dai, Xiaojuan Chen, Xujun Liang, Lingzhi Qu, Longying Jiang, Ming Guo, et al. "Mechanism of forkhead transcription factors binding to a novel palindromic DNA site." Nucleic Acids Research 49, no. 6 (February 12, 2021): 3573–83. http://dx.doi.org/10.1093/nar/gkab086.

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Abstract Forkhead transcription factors bind a canonical consensus DNA motif, RYAAAYA (R = A/G, Y = C/T), as a monomer. However, the molecular mechanisms by which forkhead transcription factors bind DNA as a dimer are not well understood. In this study, we show that FOXO1 recognizes a palindromic DNA element DIV2, and mediates transcriptional regulation. The crystal structure of FOXO1/DIV2 reveals that the FOXO1 DNA binding domain (DBD) binds the DIV2 site as a homodimer. The wing1 region of FOXO1 mediates the dimerization, which enhances FOXO1 DNA binding affinity and complex stability. Further biochemical assays show that FOXO3, FOXM1 and FOXI1 also bind the DIV2 site as homodimer, while FOXC2 can only bind this site as a monomer. Our structural, biochemical and bioinformatics analyses not only provide a novel mechanism by which FOXO1 binds DNA as a homodimer, but also shed light on the target selection of forkhead transcription factors.

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Jara, Mónica, Cinthia Núñuz, Susana Campoy, Antonio R. Fernández de Henestrosa, Derek R. Lovley, and Jordi Barbé. "Geobacter sulfurreducens Has Two Autoregulated lexA Genes Whose Products Do Not Bind the recA Promoter: Differing Responses of lexA and recA to DNA Damage." Journal of Bacteriology 185, no. 8 (April 15, 2003): 2493–502. http://dx.doi.org/10.1128/jb.185.8.2493-2502.2003.

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ABSTRACT The Escherichia coli LexA protein was used as a query sequence in TBLASTN searches to identify the lexA gene of the δ-proteobacterium Geobacter sulfurreducens from its genome sequence. The results of the search indicated that G. sulfurreducens has two independent lexA genes designated lexA1 and lexA2. A copy of a dinB gene homologue, which in E. coli encodes DNA polymerase IV, is present downstream of each lexA gene. Reverse transcription-PCR analyses demonstrated that, in both cases, lexA and dinB constitute a single transcriptional unit. Electrophoretic mobility shift assays with purified LexA1 and LexA2 proteins have shown that both proteins bind the imperfect palindrome GGTTN2CN4GN3ACC found in the promoter region of both lexA1 and lexA2. This sequence is also present upstream of the Geobacter metallireducens lexA gene, indicating that it is the LexA box of this bacterial genus. This palindrome is not found upstream of either the G. sulfurreducens or the G. metallireducens recA genes. Furthermore, DNA damage induces expression of the lexA-dinB transcriptional unit but not that of the recA gene. However, the basal level of recA gene expression is dramatically higher than that of the lexA gene. Likewise, the promoters of the G. sulfurreducens recN, ruvAB, ssb, umuDC, uvrA, and uvrB genes do not contain the LexA box and are not likely to bind to the LexA1 or LexA2 proteins. G. sulfurreducens is the first bacterial species harboring a lexA gene for which a constitutive expression of its recA gene has been described.

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Alzahrani, Dhafer A. "Complete Chloroplast Genome of Abutilon fruticosum: Genome Structure, Comparative and Phylogenetic Analysis." Plants 10, no. 2 (January 30, 2021): 270. http://dx.doi.org/10.3390/plants10020270.

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Abutilon fruticosum is one of the endemic plants with high medicinal and economic value in Saudi Arabia and belongs to the family Malvaceae. However, the plastome sequence and phylogenetic position have not been reported until this study. In this research, the complete chloroplast genome of A. fruticosum was sequenced and assembled, and comparative and phylogenetic analyses within the Malvaceae family were conducted. The chloroplast genome (cp genome) has a circular and quadripartite structure with a total length of 160,357 bp and contains 114 unique genes (80 protein-coding genes, 30 tRNA genes and 4 rRNA genes). The repeat analyses indicate that all the types of repeats (palindromic, complement, forward and reverse) were present in the genome, with palindromic occurring more frequently. A total number of 212 microsatellites were identified in the plastome, of which the majority are mononucleotides. Comparative analyses with other species of Malvaceae indicate a high level of resemblance in gene content and structural organization and a significant level of variation in the position of genes in single copy and inverted repeat borders. The analyses also reveal variable hotspots in the genomes that can serve as barcodes and tools for inferring phylogenetic relationships in the family: the regions include trnH-psbA, trnK-rps16, psbI-trnS, atpH-atpI, trnT-trnL, matK, ycf1 and ndhH. Phylogenetic analysis indicates that A. fruticosum is closely related to Althaea officinalis, which disagrees with the previous systematic position of the species. This study provides insights into the systematic position of A. fruticosum and valuable resources for further phylogenetic and evolutionary studies of the species and the Malvaceae family to resolve ambiguous issues within the taxa.

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Chung, K. L., and H. N. Chen. "Parallel finding all initial palindromes and periods of a string on reconfigurable meshes." Computing 61, no. 1 (March 1998): 11–21. http://dx.doi.org/10.1007/bf02684447.

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30

Hasegawa, Atsushi, Ritsuko Shimizu, Hirofumi Kurokawa, and Masayuki Yamamoto. "DNA Binding Diversity Achieved Through the Interaction of GATA1 N-Finger and GATA Motif Is Important for Embryonic Erythropoiesis." Blood 120, no. 21 (November 16, 2012): 3441. http://dx.doi.org/10.1182/blood.v120.21.3441.3441.

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Abstract Abstract 3441 Transcription factor GATA1 regulates a set of genes essential for the erythroid and megakaryocytic cell differentiation through the interaction with GATA motifs (consensus sequence: A/TGATAA/T). Two zinc fingers within GATA1 have been identified to be important in the DNA binding of GATA1, which are referred to as C-finger (CF) and N-finger (NF) domains. It has been shown that transactivation activity of GATA1 is completely abolished upon deletion of the CF domain, indicating that the CF domain is a requisite for the DNA binding of GATA1. While conventional reporter transactivation analyses hardly clarified the importance of the NF domain for the DNA binding, substitution mutations on 216th arginine (R216) located in the DNA-interacting surface of the NF domain have been identified to cause familial diseases of thrombocytopenia, thalassemia, and porphyria. As a consequence of the substitution of R216 to glutamine (Q) or tryptophan (W), DNA binding activity of GATA1 to a palindromic configuration of two GATA motifs (palindromic GATA) was largely diminished, while that to a single GATA motif was maintained. In this study we have examined the DNA binding diversity of GATA1 caused by the difference in the configuration of GATA motifs. We performed surface plasmon resonance (SPR) analyses of GATA1 to a single GATA, a palindromic GATA, and a repeating configuration of two GATA motifs (tandem GATA). We found that GATA1 binds to the palindromic GATA motif in a bivalent way, while it binds to the single GATA motif in a monovalent mode. We also found that a double quantity of GATA1 is associated with the tandem GATA motif and GATA1 lacking the NF domain binds to any configurations of GATA motif in a monovalent way. To further investigate contribution of the NF domain to the binding mode of GATA1, we have constructed two types of GATA1 mutants; one type was the substitution mutations on R216 (R216Q and R216W) that were mouse homologues of the human mutations, while the other type was the alanine substitution mutation on three lysine residues (K245, K246 and K312; referred to as 3KA mutant), whereby dimerization potential of GATA1 was reduced to trace level similar to the case for GATA1 lacking the NF domain. Impotantly, R216Q and R216W mutants bind the palindromic GATA motif in a monovalent way, while these mutants bind normally to the other configuration of GATA motifs. In contrast, we found that one molecule of 3KA mutant bound to the tandem GATA motif and this observation seems to explain well the fact that dimerization potential of GATA1 is an important requisite for the full-function of GATA1 in embryos. The binding modes of this 3KA mutant to the other configurations were not influenced. These results thus demonstrate that the both NF and CF domains recognize the multiple configurations of GATA motifs and specify the binding modes of GATA1. Importantly, GATA1-deficient mice rescued with R216Q were lethal during late gestation period due to abnormality in erythroid differentiation, indicating that the contribution of the NF domain to the recognition of the palindromic GATA motif configuration indeed functions in vivo. These results thus support our contention that the NF domain acts to regulate a proper spatio-temporal gene expression of a subset of GATA1 target genes utilizing the variations in the GATA motif configuration. Disclosures: No relevant conflicts of interest to declare.

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Gacki, Michał, Karolina Kafarska, Anna Pietrzak, Izabela Korona-Głowniak, and Wojciech M. Wolf. "Double Palindrome Water Chain in Cu(II) Theophylline Complex. Synthesis, Characterization, Biological Activity of Cu(II), Zn(II) Complexes with Theophylline." Crystals 10, no. 2 (February 8, 2020): 97. http://dx.doi.org/10.3390/cryst10020097.

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Two metal complexes of theophylline were synthesized. Namely, 1 with the formula [Cu(theop)2(H2O)3]·2H2O and 2, [Zn(theop)2]∙H2O (where: theop = theophylline ion). Their properties were thoroughly investigated by the elemental analysis (EA), flame atomic absorption spectrometry (FAAS), Fourier-transform infrared spectroscopy (FTIR), and thermogravimetric analysis (TGA) that were augmented by antimicrobial and antioxidant analyses. Their radical scavenging ability (RSA) is notably higher than that of a pure theophylline itself. Similarly to theophylline complexes already studied by us 3, [Mn(theop)2(H2O)4] 4, [Co(theop)2(H2O)4] and 5, [Ni(theop)2(H2O)4] title compounds are inactive against Gram-negative bacteria, but they show moderate or mild activity against Gram-positive rods. The low temperature, single crystal X-ray diffraction technique determines the crystal structure of 1. Its supramolecular crystal topology is affected by the unique, double palindrome water chain that formed by two conserved and a sole coordinated water molecules. Crystal packing arrangements were characterized by fingerprint plots that were derived from the Hirshfeld surfaces (HS), as calculated for all structures in the series 1, 3, 4, 5.

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Li, Tiexiang, Chun-Yueh Chiang, Eric King-wah Chu та Wen-Wei Lin. "The palindromic generalized eigenvalue problem A∗x=λAx: Numerical solution and applications". Linear Algebra and its Applications 434, № 11 (червень 2011): 2269–84. http://dx.doi.org/10.1016/j.laa.2009.12.020.

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Ren, Wei, Dongquan Guo, Guojie Xing, Chunming Yang, Yuanyu Zhang, Jing Yang, Lu Niu, et al. "Complete Chloroplast Genome Sequence and Comparative and Phylogenetic Analyses of the Cultivated Cyperus esculentus." Diversity 13, no. 9 (August 26, 2021): 405. http://dx.doi.org/10.3390/d13090405.

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Cyperus esculentus produces large amounts of oil as one of the main oil storage reserves in underground tubers, making this crop species not only a promising resource for edible oil and biofuel in food and chemical industry, but also a model system for studying oil accumulation in non-seed tissues. In this study, we determined the chloroplast genome sequence of the cultivated C. esculentus (var. sativus Boeckeler). The results showed that the complete chloroplast genome of C. esculentus was 186,255 bp in size, and possessed a typical quadripartite structure containing one large single copy (100,940 bp) region, one small single copy (10,439 bp) region, and a pair of inverted repeat regions of 37,438 bp in size. Sequence analyses indicated that the chloroplast genome encodes 141 genes, including 93 protein-coding genes, 40 transfer RNA genes, and 8 ribosomal RNA genes. We also identified 396 simple-sequence repeats and 49 long repeats, including 15 forward repeats and 34 palindromes within the chloroplast genome of C. esculentus. Most of these repeats were distributed in the noncoding regions. Whole chloroplast genome comparison with those of the other four Cyperus species indicated that both the large single copy and inverted repeat regions were more divergent than the small single copy region, with the highest variation found in the inverted repeat regions. In the phylogenetic trees based on the complete chloroplast genomes of 13 species, all five Cyperus species within the Cyperaceae formed a clade, and C. esculentus was evolutionarily more related to C. rotundus than to the other three Cyperus species. In summary, the chloroplast genome sequence of the cultivated C. esculentus provides a valuable genomic resource for species identification, evolution, and comparative genomic research on this crop species and other Cyperus species in the Cyperaceae family.

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Melanson, R. A., R. S. Sanderlin, A. R. McTaggart, and J. H. Ham. "A Systematic Study Reveals that Xylella fastidiosa Strains from Pecan Are Part of X. fastidiosa subsp. multiplex." Plant Disease 96, no. 8 (August 2012): 1123–34. http://dx.doi.org/10.1094/pdis-09-11-0730-re.

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Xylella fastidiosa causes disease in a number of economically important crops, ornamental plants, and shade trees, including grapevine, citrus, oleander, and sycamore. In pecan, X. fastidiosa causes pecan bacterial leaf scorch (PBLS), which leads to defoliation and reduces nut yield. No economically effective treatments are available for PBLS. In order to improve PBLS management practices, it is necessary to determine the subspecies of X. fastidiosa strains that infect pecan so that potential sources of inoculum may be identified. Multiprimer polymerase chain reaction (PCR) and phylogenetic analyses using nucleotide sequence data from the 16S-23S rRNA intergenic transcribed spacer (ITS) region and pglA consistently identified strains of X. fastidiosa isolated from pecan as X. fastidiosa subsp. multiplex. Enterobacterial repetitive intergenic consensus PCR and repetitive extragenic palindromic (REP)-PCR analyses were congruent with phylogenetic analyses. REP-PCR analyses indicated genetic variation within strains of X. fastidiosa from pecan. From these same analyses, X. fastidiosa strains from sycamore, grapevine, and oleander from Louisiana were identified as subsp. multiplex, subsp. fastidiosa, and subsp. sandyi, respectively. This study provides additional information about the host ranges of X. fastidiosa subspecies.

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Cai, Chuner, Kai Gu, Hui Zhao, Sophie Steinhagen, Peimin He, and Thomas Wichard. "Screening and verification of extranuclear genetic markers in green tide algae from the Yellow Sea." PLOS ONE 16, no. 6 (June 1, 2021): e0250968. http://dx.doi.org/10.1371/journal.pone.0250968.

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Over the past decade, Ulva compressa, a cosmopolitan green algal species, has been identified as a component of green tides in the Yellow Sea, China. In the present study, we sequenced and annotated the complete chloroplast genome of U. compressa (alpha-numeric code: RD9023) and focused on the assessment of genome length, homology, gene order and direction, intron size, selection strength, and substitution rate. We compared the chloroplast genome with the mitogenome. The generated phylogenetic tree was analyzed based on single and aligned genes in the chloroplast genome of Ulva compared to mitogenome genes to detect evolutionary trends. U. compressa and U. mutabilis chloroplast genomes had similar gene queues, with individual genes exhibiting high homology levels. Chloroplast genomes were clustered together in the entire phylogenetic tree and shared several forward/palindromic/tandem repetitions, similar to those in U. prolifera and U. linza. However, U. fasciata and U. ohnoi were more divergent, especially in sharing complementary/palindromic repetitions. In addition, phylogenetic analyses of the aligned genes from their chloroplast genomes and mitogenomes confirmed the evolutionary trends of the extranuclear genomes. From phylogenetic analysis, we identified the petA chloroplast genes as potential genetic markers that are similar to the tufA marker. Complementary/forward/palindromic interval repetitions were more abundant in chloroplast genomes than in mitogenomes. Interestingly, a few tandem repetitions were significant for some Ulva subspecies and relatively more evident in mitochondria than in chloroplasts. Finally, the tandem repetition [GAAATATATAATAATA × 3, abbreviated as TRg)] was identified in the mitogenome of U. compressa and the conspecific strain U. mutabilis but not in other algal species of the Yellow Sea. Owing to the high morphological plasticity of U. compressa, the findings of this study have implications for the rapid non-sequencing detection of this species during the occurrence of green tides in the region.

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Batzke, Leonhard, and Christian Mehl. "On the inverse eigenvalue problem for T -alternating and T -palindromic matrix polynomials." Linear Algebra and its Applications 452 (July 2014): 172–91. http://dx.doi.org/10.1016/j.laa.2014.03.037.

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37

Guillaume-Gentil, Olivier, Patsy Scheldeman, Joey Marugg, Lieve Herman, Han Joosten, and Marc Heyndrickx. "Genetic Heterogeneity in Bacillus sporothermodurans as Demonstrated by Ribotyping and Repetitive Extragenic Palindromic-PCR Fingerprinting." Applied and Environmental Microbiology 68, no. 9 (September 2002): 4216–24. http://dx.doi.org/10.1128/aem.68.9.4216-4224.2002.

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ABSTRACT Thirty-eight strains of Bacillus sporothermodurans isolated from ultra-high-temperature (UHT)-treated milk or sterilized milk (UHT isolates) and from animal feed or raw milk (farm isolates) were characterized by automated ribotyping and by repetitive extragenic palindromic (REP)-PCR fingerprinting. By investigating the genetic relationships among isolates from these various sources, the relative importance of different contamination sources could be evaluated. The results of the separate clustering analyses of the PvuII and EcoRI ribopatterns and the REP-PCR patterns were largely consistent with each other and revealed the existence of two main clusters; there was one homogeneous group containing all (REP-PCR) or most (ribotyping) of the UHT isolates, and there was a second more diverse group comprising the farm isolates. A combined three-dimensional analysis of all data showed that three German UHT isolates did not belong to the compact group containing the majority of the UHT isolates. These results demonstrate that B. sporothermodurans is more heterogeneous than previously assumed and that most of the UHT isolates form a genetically distinct subgroup and are capable of producing highly heat-resistant spores. The close genetic relationship of these UHT isolates suggests a clonal origin of a few predominant strains of B. sporothermodurans that can be found in UHT-treated or sterilized milk products.

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Rutkowska, Joanna, Malgorzata Lagisz, and Shinichi Nakagawa. "The long and the short of avian W chromosomes: no evidence for gradual W shortening." Biology Letters 8, no. 4 (March 14, 2012): 636–38. http://dx.doi.org/10.1098/rsbl.2012.0083.

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The well-established view of the evolution of sex chromosome dimorphism is of a gradual genetic and morphological degeneration of the hemizygous chromosome. Yet, no large-scale comparative analysis exists to support this view. Here, we analysed karyotypes of 200 bird species to test whether the supposed directional changes occur in bird sex chromosomes. We found no support for the view that W chromosomes gradually become smaller over evolutionary time. On the contrary, the length of the W chromosome can fluctuate over short time scales, probably involving both shortening and elongation of non-coding regions. Recent discoveries of near-identical palindromes and neo-sex chromosomes in birds may also contribute to the observed variation. Further studies are now needed to investigate how chromosome morphology relates to its gene content, and whether the changes in size were driven by selection.

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KHERROUCHE, Zoulika, Yvan DE LAUNOIT та Didier MONTE. "The NRF-1/α-PAL transcription factor regulates human E2F6 promoter activity". Biochemical Journal 383, № 3 (26 жовтня 2004): 529–36. http://dx.doi.org/10.1042/bj20040935.

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E2F6 is widely expressed in human tissues and cell lines. Recent studies have demonstrated its involvement in developmental patterning and in the regulation of various genes implicated in chromatin remodelling. Despite a growing number of studies, nothing is really known concerning the E2F6 expression regulation. To understand how cells control E2F6 expression, we analysed the activity of the previously cloned promoter region of the human E2F6 gene. DNase I footprinting, gel electrophoreticmobility shift, transient transfection and site-directed mutagenesis experiments allowed the identification of two functional NRF-1/α-PAL (nuclear respiratory factor-1/α-palindrome-binding protein)-binding sites within the human E2F6 core promoter region, which are conserved in the mouse and rat E2F6 promoter region. Moreover, ChIP (chromatin immunoprecipitation) analysis demonstrated that overexpressed NRF-1/α-PAL is associated in vivo with the E2F6 promoter. Furthermore, overexpression of full-length NRF-1/α-PAL enhanced E2F6 promoter activity, whereas expression of its dominant-negative form reduced the promoter activity. Our results indicate that NRF-1/α-PAL is implicated in the regulation of basal E2F6 gene expression.

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Matta, Meropi K., Efthimia E. Lioliou, Cynthia H. Panagiotidis, Dimitrios A. Kyriakidis, and Christos A. Panagiotidis. "Interactions of the Antizyme AtoC with Regulatory Elements of the Escherichia coli atoDAEB Operon." Journal of Bacteriology 189, no. 17 (July 6, 2007): 6324–32. http://dx.doi.org/10.1128/jb.00214-07.

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ABSTRACT AtoC has a dual function as both an antizyme, the posttranslational inhibitor of polyamine biosynthetic enzymes, and the transcriptional regulator of genes involved in short-chain fatty acid catabolism (the atoDAEB operon). We have previously shown that AtoC is the response regulator of the AtoS-AtoC two-component signal transduction system that activates atoDAEB when Escherichia coli is exposed to acetoacetate. Here, we show that the same cis elements control both promoter inducibility and AtoC binding. Chromatin immunoprecipitation experiments confirmed the acetoacetate-inducible binding of AtoC to the predicted DNA region in vivo. DNase I protection footprinting analysis revealed that AtoC binds two 20-bp stretches, constituting an inverted palindrome, that are located at −146 to −107 relative to the transcription initiation site. Analyses of promoter mutants obtained by in vitro chemical mutagenesis of the atoDAEB promoter verified both the importance of AtoC binding for the inducibility of the promoter by acetoacetate and the σ54 dependence of atoDAEB expression. The integration host factor was also identified as a critical component of the AtoC-mediated induction of atoDAEB.

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Seurinck, Sylvie, Willy Verstraete, and Steven D. Siciliano. "Use of 16S-23S rRNA Intergenic Spacer Region PCR and Repetitive Extragenic Palindromic PCR Analyses of Escherichia coli Isolates To Identify Nonpoint Fecal Sources." Applied and Environmental Microbiology 69, no. 8 (August 2003): 4942–50. http://dx.doi.org/10.1128/aem.69.8.4942-4950.2003.

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ABSTRACT Despite efforts to minimize fecal input into waterways, this kind of pollution continues to be a problem due to an inability to reliably identify nonpoint sources. Our objective was to find candidate source-specific Escherichia coli fingerprints as potential genotypic markers for raw sewage, horses, dogs, gulls, and cows. We evaluated 16S-23S rRNA intergenic spacer region (ISR)-PCR and repetitive extragenic palindromic (rep)-PCR analyses of E. coli isolates as tools to identify nonpoint fecal sources. The BOXA1R primer was used for rep-PCR analysis. A total of 267 E. coli isolates from different fecal sources were typed with both techniques. E. coli was found to be highly diverse. Only two candidate source-specific E. coli fingerprints, one for cow and one for raw sewage, were identified out of 87 ISR fingerprints. Similarly, there was only one candidate source-specific E. coli fingerprint for horse out of 59 BOX fingerprints. Jackknife analysis resulted in an average rate of correct classification (ARCC) of 83% for BOX-PCR analysis and 67% for ISR-PCR analysis for the five source categories of this study. When nonhuman sources were pooled so that each isolate was classified as animal or human derived (raw sewage), ARCCs of 82% for BOX-PCR analysis and 72% for ISR-PCR analysis were obtained. Critical factors affecting the utility of these methods, namely sample size and fingerprint stability, were also assessed. Chao1 estimation showed that generally 32 isolates per fecal source individual were sufficient to characterize the richness of the E. coli population of that source. The results of a fingerprint stability experiment indicated that BOX and ISR fingerprints were stable in natural waters at 4, 12, and 28°C for 150 days. In conclusion, 16S-23S rRNA ISR-PCR and rep-PCR analyses of E. coli isolates have the potential to identify nonpoint fecal sources. A fairly small number of isolates was needed to find candidate source-specific E. coli fingerprints that were stable under the simulated environmental conditions.

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Abedin, Paniz, M. Oğuzhan Külekci, and Shama V. Thankachan. "A Survey on Shortest Unique Substring Queries." Algorithms 13, no. 9 (September 6, 2020): 224. http://dx.doi.org/10.3390/a13090224.

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The shortest unique substring (SUS) problem is an active line of research in the field of string algorithms and has several applications in bioinformatics and information retrieval. The initial version of the problem was proposed by Pei et al. [ICDE’13]. Over the years, many variants and extensions have been pursued, which include positional-SUS, interval-SUS, approximate-SUS, palindromic-SUS, range-SUS, etc. In this article, we highlight some of the key results and summarize the recent developments in this area.

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Orcutt, K. M., U. Rasmussen, E. A. Webb, J. B. Waterbury, K. Gundersen, and B. Bergman. "Characterization of Trichodesmium spp. by Genetic Techniques." Applied and Environmental Microbiology 68, no. 5 (May 2002): 2236–45. http://dx.doi.org/10.1128/aem.68.5.2236-2245.2002.

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ABSTRACT The genetic diversity of Trichodesmium spp. from natural populations (off Bermuda in the Sargasso Sea and off North Australia in the Arafura and Coral Seas) and of culture isolates from two regions (Sargasso Sea and Indian Ocean) was investigated. Three independent techniques were used, including a DNA fingerprinting method based on a highly iterated palindrome (HIP1), denaturing gradient gel electrophoresis of a hetR fragment, and sequencing of the internal transcribed spacer (ITS) of the 16S-23S rDNA region. Low genetic diversity was observed in natural populations of Trichodesmium spp. from the two hemispheres. Culture isolates of Trichodesmium thiebautii, Trichodesmium hildebrandtii, Trichodesmium tenue, and Katagnymene spiralis displayed remarkable similarity when these techniques were used, suggesting that K. spiralis is very closely related to the genus Trichodesmium. The largest genetic variation was found between Trichodesmium erythraeum and all other species of Trichodesmium, including a species of Katagnymene. Our data obtained with all three techniques suggest that there are two major clades of Trichodesmium spp. The HIP1 fingerprinting and ITS sequence analyses allowed the closely related species to be distinguished. This is the first report of the presence of HIP1 in marine cyanobacteria.

44

Xiao, Wei, and Gerald H. Rank. "Branched chain amino acid regulation of the ILV2 locus in Saccharomyces cerevisiae." Genome 33, no. 4 (August 1, 1990): 596–603. http://dx.doi.org/10.1139/g90-088.

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Mutant regulatory loci of the branched pathway for the biosynthesis of isoleucine–valine and leucine were identified with the unusual phenotype of an amino acid dependent auxotrophy. Two mutant loci, bcs1 and bcs2, conferred branched chain amino acid sensitivity and showed independent segregation. Linkage studies defined bcs1 as a cis-acting regulatory site of ILV2 (SMR1). ILV2 upstream deletion analyses and high-copy transformation of the positive regulatory locus LEU3 ruled out the possibility of LEU3 protein binding palindromes mediating the branched chain amino acid dependent auxotrophy. In the presence of leucine and valine, the general amino acid control system (GCN4) was epistatic to bcs1 and bcs2, and under nonstarvation conditions GCN4 strains showed an increased acetolactate synthase activity over gcn4 strains. Thus in addition to general regulation of ILV2, GCN4 functions in basal level expression when the locus is subject to specific repression by pathway end product.Key words: yeast, isoleucine, leucine, valine pathway, amino acid sensitivity, gene regulation, multiple control.

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CATALANO, SARAH R., IAN D. WHITTINGTON, STEPHEN C. DONNELLAN, TERRY BERTOZZI, and BRONWYN M. GILLANDERS. "First comparative insight into the architecture ofCOImitochondrial minicircle molecules of dicyemids reveals marked inter-species variation." Parasitology 142, no. 8 (April 16, 2015): 1066–79. http://dx.doi.org/10.1017/s0031182015000384.

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SUMMARYDicyemids, poorly known parasites of benthic cephalopods, are one of the few phyla in which mitochondrial (mt) genome architecture departs from the typical ~16 kb circular metazoan genome. In addition to a putative circular genome, a series of mt minicircles that each comprises the mt encoded units (I–III) of the cytochromecoxidase complex have been reported. Whether the structure of the mt minicircles is a consistent feature among dicyemid species is unknown. Here we analyse the complete cytochromecoxidase subunit I (COI) minicircle molecule, containing theCOIgene and an associated non-coding region (NCR), for ten dicyemid species, allowing for first time comparisons between species of minicircle architecture, NCR function and inferences of minicircle replication. Divergence inCOInucleotide sequences between dicyemid species was high (average net divergence = 31·6%) while within species diversity was lower (average net divergence = 0·2%). The NCR and putative 5′ section of theCOIgene were highly divergent between dicyemid species (average net nucleotide divergence of putative 5′COIsection = 61·1%). No tRNA genes were found in the NCR, although palindrome sequences with the potential to form stem-loop structures were identified in some species, which may play a role in transcription or other biological processes.

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Haddad, F., P. W. Bodell, S. A. McCue, and K. M. Baldwin. "Effects of diabetes on rodent cardiac thyroid hormone receptor and isomyosin expression." American Journal of Physiology-Endocrinology and Metabolism 272, no. 5 (May 1, 1997): E856—E863. http://dx.doi.org/10.1152/ajpendo.1997.272.5.e856.

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Previous studies show that diabetes induces marked transformations in cardiac myosin heavy chain (MHC) gene expression that are somehow linked to the cellular action of thyroid hormone 3,5,3'-triiodothyronine (T3). In this study, we tested the hypothesis that diabetes induces a reduced expression of thyroid hormone receptors (TRs), which are known to be important transcription factors interacting with thyroid response elements (TREs) in the promoter region of both alpha- and beta-MHC genes. Adult female rats were randomly assigned to either a normal control (NC) or diabetic (D) group. Three and/or six weeks after induction of diabetes via streptozotocin injection, the hearts of the animals were analyzed for MHC and TR mRNA isoforms expression, nuclear T3 binding, and nuclear extract interaction with a palindromic TRE. Results showed that diabetes induced significant alteration in alpha- and beta-MHC expression. Northern blot analyses indicated no diabetes-associated differences in TR isoform mRNA signals. Cardiac nuclear T3 binding studies suggested no differences in either the binding capacity or the equilibrium binding constant among the two groups, indicating no changes in either the number of nuclear TRs or their affinity for T3. Furthermore, gel mobility shift assays detected no difference between NC and D groups for cardiac nuclear extract binding to palindromic TRE. Collectively, these findings suggest that, whereas diabetes exerts a profound effect on cardiac isomyosin gene expression, the underlying mechanism, although dependent on factors linked to T3 function, does not involve alterations in TR expression.

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Handy, D. E., M. T. Zanella, A. Kanemaru, A. Tavares, C. Flordellis та H. Gavras. "A negative regulatory element in the promoter region of the rat α2A-adrenergic receptor gene overlaps an SP1 consensus binding site". Biochemical Journal 311, № 2 (15 жовтня 1995): 541–47. http://dx.doi.org/10.1042/bj3110541.

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Three subtypes of alpha 2-adrenergic receptors (alpha 2A, alpha 2B and alpha 2C) have been described that differ in their primary sequence and tissue-specific expression and are encoded by three distinct genes. Previous work has shown that the human alpha 2A-adrenergic receptor gene promoter consists of a TATA-box (TATAAA), palindromic sequence (CCCACGTGGG) and GC-box (GGGGCGG) motif. Sequence analysis of the putative promoter region of the rat alpha 2A-adrenergic receptor gene showed that these promoter regions are conserved in their sequence and relative location. We analysed the transcriptional activity of these regions using RINm5F, a rat insulinoma cell line that expresses the endogenous alpha 2A-adrenergic receptor gene. These results showed that the region from -484 to -92 has a negative effect on transcription, as deletion of this region in alpha 2A-adrenergic receptor gene-chloramphenicol acetyltransferase reporter constructs increased reporter gene activity. This region included the GC-box sequence which is a consensus binding site for the nuclear factor SP1, which is a positive activator of transcription. Gel-mobility-shift assays and supershift assays with an antibody that recognizes SP1 showed binding of the SP1 nuclear factor as well as other nuclear factors to this GC-box region. Additional nuclear factors bind to the downstream palindromic region. We suggest that positive- and negative-acting nuclear factors contribute to the activity of the alpha 2-adrenergic receptor promoter.

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Singh, Desh D., Ravi Verma, Piyush Parimoo, Ashish Sahu, Vikram Kumar, Era Upadhyay, and Dharmendra K. Yadav. "Potential Therapeutic Relevance of CRISPR/Cas9 Guided Epigenetic Regulations for Neuropsychiatric Disorders." Current Topics in Medicinal Chemistry 21, no. 10 (June 17, 2021): 878–94. http://dx.doi.org/10.2174/1568026621666210317154502.

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Brain function activity is regulated by several mechanisms of genetic and epigenetic factors such as histone modelling, DNA methylation, and non-coding RNA. Alterations in these regulatory mechanisms affect the normal development of neurons that causes Neuropsychiatric Disorders (ND). However, it is required to analyse the functional significance of neuropsychiatric disorders associated with a molecular mechanism to bring about therapeutic advances in early diagnosis and treatment of the patients. The CRISPR/Cas 9 (Clustered Regularly Interspaced Short Palindromic Repeats) genome editing tools have revolutionized multiple genome and epigenome manipulation targets the same time. This review discussed the possibilities of using CRISPR/Cas 9 tools during molecular mechanism in the ND as a therapeutic approach to overcome ND that is caused due to genetic and epigenetic abnormalities.

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COX, NELSON A., MARK E. BERRANG, SANDRA L. HOUSE, DAVID MEDINA, KIMBERLY L. COOK, and NIKKI W. SHARIAT. "Population Analyses Reveal Preenrichment Method and Selective Enrichment Media Affect Salmonella Serovars Detected on Broiler Carcasses." Journal of Food Protection 82, no. 10 (September 19, 2019): 1688–96. http://dx.doi.org/10.4315/0362-028x.jfp-19-166.

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ABSTRACT Poultry is a major Salmonella reservoir, but conventional culture-based methods typically identify the most abundant serovars while those less abundant remain undetected. Choice of enrichment procedure also introduces bias, and for broiler carcasses, a 1-min rinse before preenrichment is insufficient to release all Salmonella present. The inability to assess serovar diversity means that serovars more often associated with human illness may be masked by more abundant Salmonella. CRISPR-SeroSeq (serotyping by sequencing clustered regularly interspaced short palindromic repeats), an amplicon-based, next-generation sequencing tool, allows detection of multiple serovars and maps the relative serovar frequencies in a sample. To address the preceding limitations, CRISPR-SeroSeq was used on broiler carcasses collected prechilled at a commercial plant. Standard carcass rinse aliquot preenrichments and whole carcass preenrichments that were enriched in Rappaport-Vassiliadis (RV) and tetrathionate (TT) broths were compared. On average, five serovars were observed per carcass, including nine on one carcass. CRISPR-SeroSeq detected serovars comprising as little as 0.005% of the population. CRISPR-SeroSeq data matched (28 of 32) standard culture analysis for abundant serovars. Salmonella serovars Kentucky, Typhimurium, and Schwarzengrund were found on each carcass. Overall, serovar diversity was higher in whole carcass preenrichments that were enriched in RV (P < 0.05). Serovar Schwarzengrund was present at higher frequencies in whole carcass preenrichments compared with rinse aliquot preenrichments (t test, P < 0.05), suggesting it adheres more strongly to the carcass. Salmonella serovar Enteritidis was enriched eightfold more in TT than in RV, and serovars Schwarzengrund and Reading were preferentially enriched in RV. Comparison of preenriched and enriched samples suggests that selective enrichment in RV or TT was inhibitory to some serovars. This article addresses limitations of Salmonella surveillance protocols and provides information related to Salmonella population dynamics.

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Subbulakshmi, S. "Thirugnana Sambandhar - A Mathematician." Shanlax International Journal of Arts, Science and Humanities 9, no. 1 (July 1, 2021): 136–40. http://dx.doi.org/10.34293/sijash.v9i1.3991.

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India has been the Land of notable poets whose exemplary works are world renowned. One such great poet is Thirugnana Sambandhar. He is a saint, poet, philosopher, composer who belongs to 7th Century. He was born in Seerkaazhi of Tamilnadu. He had coined many Special Geometrical poetic structures like Thiru ezhukkootrirukkai (poem with mathematical Triangular Pattern), Maalai Maatru (a poem with palindromic Structure), Mozhi Maatru (a poem in which the meaning of the poem can be observed by a systematic Chane of words), Gomuthri (Flow of the poem in such a way it forms a wave line), Chakramaatru (a poem which is constructed in a circular form ). By the above mentioned amazing structure He has no parallels in the worlds poetry Thirugnana Sambandhar is the epitome of Tamil Literature has penned down many such extraordinary poems. A Mathematician is one who uses an extensive knowledge of Mathematics in their work. Mathematicians are concerned with numbers, data, quantity, structure, space,models and change. Here in this poetic form Thiruezhukkootrirukkai Thirugnana Sambandhar had used numbers in a brilliant way to form a Triangle. This is called “Chitrakavi” in Tamil. By analyzing the whole poem we will get a geometrical structure. In this Thiruezhukkootrirukkai Thirugnana Sambandhar has constructed the words in such a way to form a symmetrical triangle. These triangle is arranged in a perfect mathematical calculation. This can be analysed through the law of binomial co- efficient. This is analysed and proved in this paper. Thirugnana Sambandhar belongs to 7th Century whereas the Scientist and Mathematician Pascal who discovered the law of Bi-nomial co-efficient belongs to 17th century. Other than this Mathematical diagram of triangle this poem has Palindromic numbers which add more beauty to this structure which is also a mathematical calculation. By constructing this amazing poetic structure Thirugnana Sambandhar proves beyond doubt that he is a “Mathematician” of India of the 7th Century itself who had applied the law of triangle earlier.

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