Correlation Analysis Reveals an Important Role of GC Content in Accumulation of Deletion Mutations in the Coding Region of Angiosperm Plastomes

2021 ◽  
Vol 89 (1-2) ◽  
pp. 73-80
Author(s):  
Ying Yu ◽  
Hong-Tao Li ◽  
Yu-Huan Wu ◽  
De-Zhu Li
Keyword(s):  
Correlation Analysis ◽  
Gc Content ◽  
Coding Region ◽  
Deletion Mutations

scholarly journals Genetic and Phenotypic Analyses of therdx Locus of Rhodobacter sphaeroides2.4.1

2000 ◽  
Vol 182 (12) ◽  
pp. 3475-3481 ◽  
Author(s):  
Jung Hyeob Roh ◽  
Samuel Kaplan
Keyword(s):  
Gene Expression ◽  
Rhodobacter Sphaeroides ◽  
Redox Protein ◽  
Deletion Mutations ◽  
Metal Transporter ◽  
New Class ◽  
Mutant Strains ◽  
Membrane Bound ◽  
Photosynthesis Gene

ABSTRACT Previously, we reported that rdxB, encoding a likely membrane-bound two [4Fe-4S]-containing center, is involved in the aerobic regulation of photosystem gene expression in Rhodobacter sphaeroides 2.4.1. To further investigate the role ofrdxB as well as other genes of the rdxBHISoperon on photosystem gene expression, we constructed a series of nonpolar, in-frame deletion mutations in each of the rdxgenes. Using both puc and puf operonlacZ fusions to monitor photosystem gene expression, under aerobic conditions, in each of the mutant strains revealed significant increased photosynthesis gene expression. In the case of mutations in either rdxH, rdxI, or rdxS, the aerobic induction of photosystem gene expression is believed to be indirect by virtue of a posttranscriptional effect oncbb 3 cytochrome oxidase structure and integrity. For RdxB, we suggest that this redox protein has a more direct effect on photosystem gene expression by virtue of its interaction with the cbb 3 oxidase. An associated phenotype, involving the enhanced conversion of the carotenoid spheroidene to spheroidenone, is also observed in the RdxB, -H, -I, and -S mutant strains. This phenotype is also suggested to be the result of the role of the rdxBHIS locus incbb 3 oxidase activity and/or structure. RdxI is suggested to be a new class of metal transporter of the CPx-type ATPases.

The logical component of thinking as a predictor of decision-making about the presence of corruption risk in a situation

2021 ◽  
Vol 42 (6) ◽  
pp. 25-34
Author(s):  
I. N. Pogozhina ◽  
◽  
M. V. Sergeeva ◽  
Keyword(s):  
Decision Making ◽  
Emotional Intelligence ◽  
Correlation Analysis ◽  
University Students ◽  
Moral Values ◽  
Moral Judgments ◽  
Diagnostic Tools ◽  
Leading Role ◽  
Decision Making System

The links between elements of the decision-making system on the presence of corruption risk (CR) in a situation with the logical component of thinking as a predictor are considered. The hypothesis of the role of logical reasoning component as a predictor of (1) perceptions of corruption, (2) indicators of emotional intelligence and (3) moral judgement was tested on a sample of Moscow university students (N=134; M=35±11 years old). The following diagnostic tools were used: (1) the author's test for recognising CR situations, (2) the method for assessing the content of ideas about corruption (Pogozhina, Pshenichnyuk, Sergeyeva), (3) D. Lucin’s EmIn questionnaire, (4) Molchanov's Justice-Care technique. Correlation analysis and structural modeling were used to process the data. The logical component of thinking was a significant positive predictor of the level of development of perceptions of corruption and understanding one’s own emotions and those of others. Also, the logical component significantly negatively predicted moral judgments based on instrumental individualism, reflexive empathic orientation and unconscious but internalized moral values. The findings suggest that the logical component will play a leading role in the CR decision-making system and should be specifically shaped.

Role of specific simian virus 40 sequences in the nuclease-sensitive structure in viral chromatin

1985 ◽  
Vol 5 (1) ◽  
pp. 52-58
Author(s):  
R D Gerard ◽  
B A Montelone ◽  
C F Walter ◽  
J W Innis ◽  
W A Scott
Keyword(s):  
Simian Virus 40 ◽  
Simian Virus ◽  
Origin Of Replication ◽  
Viral Origin ◽  
Deletion Mutations ◽  
Sensitive Region ◽  
Complete Independence ◽  
Sensitive Structure ◽  
Nuclease Sensitivity

A nuclease-sensitive region forms in chromatin containing a 273-base-pair (bp) segment of simian virus 40 DNA encompassing the viral origin of replication and early and late promoters. We have saturated this region with short deletion mutations and compared the nuclease sensitivity of each mutated segment to that of an unaltered segment elsewhere in the partially duplicated mutant. Although no single DNA segment is required for the formation of a nuclease-sensitive region, a deletion mutation (dl45) which disrupted both exact copies of the 21-bp repeats substantially reduced nuclease sensitivity. Deletion mutations limited to only one copy of the 21-bp repeats had little, if any, effect. A mutant (dl135) lacking all copies of the 21- and 72-bp repeats, while retaining the origin of replication and the TATA box, did not exhibit a nuclease-sensitive region. Mutants which showed reduced nuclease sensitivity had this effect throughout the nuclease-sensitive region, not just at the site of the deletion, indicating that although multiple determinants must be responsible for the nuclease-sensitive chromatin structure they do not function with complete independence. Mutant dl9, which lacks the late portion of the 72-bp segment, showed reduced accessibility to BglI, even though the BglI site is 146 bp away from the site of the deletion.

scholarly journals Biochemical and genetic analysis of the role of the viral polymerase in enterovirus recombination

2016 ◽  
Vol 44 (14) ◽  
pp. 6883-6895 ◽  
Author(s):  
Andrew Woodman ◽  
Jamie J. Arnold ◽  
Craig E. Cameron ◽  
David J. Evans
Keyword(s):  
Genetic Recombination ◽  
Evolutionary Process ◽  
Virus Genome ◽  
Biochemical Assay ◽  
Strand Transfer ◽  
Turnover Rates ◽  
Coding Region ◽  
Cis Acting ◽  
Polymerase Fidelity

Abstract Genetic recombination in single-strand, positive-sense RNA viruses is a poorly understand mechanism responsible for generating extensive genetic change and novel phenotypes. By moving a critical cis-acting replication element (CRE) from the polyprotein coding region to the 3′ non-coding region we have further developed a cell-based assay (the 3′CRE-REP assay) to yield recombinants throughout the non-structural coding region of poliovirus from dually transfected cells. We have additionally developed a defined biochemical assay in which the only protein present is the poliovirus RNA dependent RNA polymerase (RdRp), which recapitulates the strand transfer events of the recombination process. We have used both assays to investigate the role of the polymerase fidelity and nucleotide turnover rates in recombination. Our results, of both poliovirus intertypic and intratypic recombination in the CRE-REP assay and using a range of polymerase variants in the biochemical assay, demonstrate that RdRp fidelity is a fundamental determinant of recombination frequency. High fidelity polymerases exhibit reduced recombination and low fidelity polymerases exhibit increased recombination in both assays. These studies provide the basis for the analysis of poliovirus recombination throughout the non-structural region of the virus genome and provide a defined biochemical assay to further dissect this important evolutionary process.

scholarly journals Genomic Basis of Aromatase Excess Syndrome: Recombination- and Replication-Mediated Rearrangements Leading to CYP19A1 Overexpression

2013 ◽  
Vol 98 (12) ◽  
pp. E2013-E2021 ◽  
Author(s):  
Maki Fukami ◽  
Takayoshi Tsuchiya ◽  
Heike Vollbach ◽  
Kristy A. Brown ◽  
Shuji Abe ◽  
...  
Keyword(s):  
Gc Content ◽  
Replication Timing ◽  
Nonhomologous End Joining ◽  
Coding Region ◽  
End Joining ◽  
Clinical Consequences ◽  
Underlying Mechanisms ◽  
Nonallelic Homologous Recombination ◽  
Genomic Disorders ◽  
Flanking Regions

Context: Genomic rearrangements at 15q21 have been shown to cause overexpression of CYP19A1 and resultant aromatase excess syndrome (AEXS). However, mutation spectrum, clinical consequences, and underlying mechanisms of these rearrangements remain to be elucidated. Objective: The aim of the study was to clarify such unsolved matters. Design, Setting, and Methods: We characterized six new rearrangements and investigated clinical outcome and local genomic environments of these rearrangements and of three previously reported duplications/deletions. Results: Novel rearrangements included simple duplication involving exons 1–10 of CYP19A1 and simple and complex rearrangements that presumably generated chimeric genes consisting of the coding region of CYP19A1 and promoter-associated exons of neighboring genes. Clinical severities were primarily determined by the copy number of CYP19A1 and the property of the fused promoters. Sequences at the fusion junctions suggested nonallelic homologous recombination, nonhomologous end-joining, and replication-based errors as the underlying mechanisms. The breakpoint-flanking regions were not enriched with GC content, palindromes, noncanonical DNA structures, or known rearrangement-associated motifs. The rearrangements resided in early-replicating segments. Conclusions: These results indicate that AEXS is caused by duplications involving CYP19A1 and simple and complex rearrangements that presumably lead to the usage of cryptic promoters of several neighboring genes. Our data support the notion that phenotypes depend on the dosage of CYP19A1 and the characteristics of the fused promoters. Furthermore, we show that the rearrangements in AEXS are generated by both recombination- and replication-mediated mechanisms, independent of the known rearrangement-inducing DNA features or late-replication timing. Thus, AEXS represents a unique model for human genomic disorders.

scholarly journals The S Segment of Rift Valley Fever Phlebovirus (Bunyaviridae) Carries Determinants for Attenuation and Virulence in Mice

2000 ◽  
Vol 74 (3) ◽  
pp. 1538-1543 ◽  
Author(s):  
P. Vialat ◽  
A. Billecocq ◽  
A. Kohl ◽  
M. Bouloy
Keyword(s):  
Rift Valley ◽  
Rift Valley Fever ◽  
Nonstructural Protein ◽  
Rift Valley Fever Virus ◽  
Virulent Strain ◽  
Coding Region ◽  
Valley Fever ◽  
Attenuated Virus ◽  
Infected Cells

ABSTRACT Unlike all the other Rift Valley fever virus strains (Bunyaviridae, Phlebovirus) studied so far, clone 13, a naturally attenuated virus, does not form the filaments composed of the NSs nonstructural protein in the nuclei of infected cells (R. Muller, J. F. Saluzzo, N. Lopez, T. Drier, M. Turell, J. Smith, and M. Bouloy, Am. J. Trop. Med. Hyg. 53:405–411, 1995). This defect is correlated with a large in-frame deletion in the NSs coding region of the S segment of the tripartite genome. Here, we show that the truncated NSs protein of clone 13 is expressed and remains in the cytoplasm, where it is degraded rapidly by the proteasome. Through the analysis of reassortants between clone 13 and a virulent strain, we localized the marker(s) of attenuation in the S segment of this attenuated virus. This result raises questions regarding the role of NSs in pathogenesis and highlights, for the first time in theBunyaviridae family, a major role of the S segment in virulence and attenuation, possibly associated with a defect in the nonstructural protein.

Abundance of Boeckella gracilis (Daday, 1902) (Copepoda, Calanoida) in seasonal coastal pools in the Araucania region (38°S, Chile)

Crustaceana ◽  
2018 ◽  
Vol 91 (10) ◽  
pp. 1211-1217
Author(s):  
Patricio De los Ríos
Keyword(s):  
Correlation Analysis ◽  
Environmental Stress ◽  
Relative Abundance ◽  
Calanoid Copepod ◽  
Inverse Correlation ◽  
Inland Waters ◽  
Absolute Abundance ◽  
Significant Inverse Correlation

Abstract The presence of the calanoid copepod Boeckella gracilis (Daday, 1902) in Chilean seasonal pools has been only poorly studied as yet. The aim of the present study thus is to investigate the role of conductivity and temperature on the relative and absolute abundance of B. gracilis in seasonal coastal pools in the Araucania region (38°S, Chile). The results of correlation analysis revealed the presence of a significant inverse correlation between conductivity and relative abundance, whereas no significant correlations were found between conductivity and absolute abundance, between temperature and absolute abundance, and between temperature and relative abundance. These results agree partially with similar observations for mountain pools in the same region, but they would not agree with observations for calanoids of saline and subsaline inland waters in the northern and southern extremes of Chile. Considering this scenario, the species would show different populational responses to environmental stress in different situations, which phenomenon deserves to be studied more extensively and in more detail.

scholarly journals Comparative reactions of recombinant papaya ringspot viruses with chimeric coat protein (CP) genes and wild-type viruses on CP-transgenic papaya

2001 ◽  
Vol 82 (11) ◽  
pp. 2827-2836 ◽  
Author(s):  
Chu-Hui Chiang ◽  
Ju-Jung Wang ◽  
Fuh-Jyh Jan ◽  
Shyi-Dong Yeh ◽  
Dennis Gonsalves
Keyword(s):  
Coat Protein ◽  
Sequence Similarity ◽  
Transcriptional Gene Silencing ◽  
Papaya Ringspot Virus ◽  
Wild Type ◽  
Coding Region ◽  
Transgenic Papaya ◽  
Cp Gene ◽  
Post Transcriptional Gene Silencing

Transgenic papaya cultivars SunUp and Rainbow express the coat protein (CP) gene of the mild mutant of papaya ringspot virus (PRSV) HA. Both cultivars are resistant to PRSV HA and other Hawaii isolates through homology-dependent resistance via post-transcriptional gene silencing. However, Rainbow, which is hemizygous for the CP gene, is susceptible to PRSV isolates from outside Hawaii, while the CP-homozygous SunUp is resistant to most isolates but susceptible to the YK isolate from Taiwan. To investigate the role of CP sequence similarity in overcoming the resistance of Rainbow, PRSV HA recombinants with various CP segments of the YK isolate were constructed and evaluated on Rainbow, SunUp and non-transgenic papaya. Non-transgenic papaya were severely infected by all recombinants, but Rainbow plants developed a variety of symptoms. On Rainbow, a recombinant with the entire CP gene of YK caused severe symptoms, while recombinants with only partial YK CP sequences produced a range of milder symptoms. Interestingly, a recombinant with a YK segment from the 5′ region of the CP gene caused very mild, transient symptoms, whereas recombinants with YK segments from the middle and 3′ parts of the CP gene caused prominent and lasting symptoms. SunUp was resistant to all but two recombinants, which contained the entire CP gene or the central and 3′-end regions of the CP gene and the 3′ non-coding region of YK, and the resulting symptoms were mild. It is concluded that the position of the heterologous sequences in the recombinants influences their pathogenicity on Rainbow.

scholarly journals Star-PAP RNA Binding Landscape Reveals Novel Role of Star-PAP in mRNA Metabolism That Requires RBM10-RNA Association

2021 ◽  
Vol 22 (18) ◽  
pp. 9980
Author(s):  
Ganesh R. Koshre ◽  
Feba Shaji ◽  
Neeraja K. Mohanan ◽  
Nimmy Mohan ◽  
Jamshaid Ali ◽  
...  
Keyword(s):  
Rna Binding ◽  
Coding Region ◽  
High Association ◽  
Target Mrnas ◽  
Mrna Metabolism ◽  
Mrna Targets ◽  
Genome Wide ◽  
Global Profile ◽  
Specific Mrna

Star-PAP is a non-canonical poly(A) polymerase that selects mRNA targets for polyadenylation. Yet, genome-wide direct Star-PAP targets or the mechanism of specific mRNA recognition is still vague. Here, we employ HITS-CLIP to map the cellular Star-PAP binding landscape and the mechanism of global Star-PAP mRNA association. We show a transcriptome-wide association of Star-PAP that is diminished on Star-PAP depletion. Consistent with its role in the 3′-UTR processing, we observed a high association of Star-PAP at the 3′-UTR region. Strikingly, there is an enrichment of Star-PAP at the coding region exons (CDS) in 42% of target mRNAs. We demonstrate that Star-PAP binding de-stabilises these mRNAs indicating a new role of Star-PAP in mRNA metabolism. Comparison with earlier microarray data reveals that while UTR-associated transcripts are down-regulated, CDS-associated mRNAs are largely up-regulated on Star-PAP depletion. Strikingly, the knockdown of a Star-PAP coregulator RBM10 resulted in a global loss of Star-PAP association on target mRNAs. Consistently, RBM10 depletion compromises 3′-end processing of a set of Star-PAP target mRNAs, while regulating stability/turnover of a different set of mRNAs. Our results establish a global profile of Star-PAP mRNA association and a novel role of Star-PAP in the mRNA metabolism that requires RBM10-mRNA association in the cell.

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