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1.
The effects of mispair and nonpair correction in hybrid DNA on base ratios (G + C content) and total amounts of DNA 总被引:1,自引:0,他引:1
Base ratios and total DNA amounts can vary substantially between and within
higher taxa and genera, and even within species. Gene conversion is one of
several mechanisms that could cause such changes. For base substitutions,
disparity in conversion direction is accompanied by an equivalent disparity
in base ratio at the heterozygous site. Disparity in the direction of gene
conversion at meiosis is common and can be extreme. For transitions (which
give purine [R]/pyrimidine [Y] mispairs) and for transversions giving
unlike R/R and Y/Y mispairs in hybrid DNA, this disparity could give slow
but systematic changes in G + C percentage. For transversions giving like
R/R and Y/Y mispairs, it could change AT/TA and CG/GC ratios. From the
extent of correction direction disparity, one can deduce properties of
repair enzymes, such as the ability (1) to excise preferentially the purine
from one mispair and the pyrimidine from the other for two different R/Y
mispairs from a single heterozygous site and (2) to excise one base
preferentially from unlike R/R or Y/Y mispairs. Frame-shifts usually show
strong disparity in conversion direction, with preferential cutting of the
nonlooped or the looped-out strand of the nonpair in heterozygous h-DNA.
The opposite directions of disparity for frame-shifts and their intragenic
suppressors as Ascobolus suggest that repair enzymes have a strong,
systematic bias as to which strand is cut. The conversion spectra of
mutations induced with different mutagens suggest that the nonlooped strand
is preferentially cut, so that base additions generally convert to mutant
and deletions generally convert to wild-type forms. Especially in
nonfunctional or noncoding DNA, this could cause a general increase in DNA
amounts. Conversion disparity, selection, mutation, and other processes
interact, affecting rates of change in base ratios and total DNA.
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Tapan Kumar Mohanta Nibedita Mohanta Pratap Parida Sujogya Kumar Panda Lakshmi Narayanan Ponpandian Hanhong Bae 《PloS one》2016,11(2)
The mitogen-activated protein kinase (MAPK) is characterized by the presence of the T-E-Y, T-D-Y, and T-G-Y motifs in its activation loop region and plays a significant role in regulating diverse cellular responses in eukaryotic organisms. Availability of large-scale genome data in the fungal kingdom encouraged us to identify and analyse the fungal MAPK gene family consisting of 173 fungal species. The analysis of the MAPK gene family resulted in the discovery of several novel activation loop motifs (T-T-Y, T-I-Y, T-N-Y, T-H-Y, T-S-Y, K-G-Y, T-Q-Y, S-E-Y and S-D-Y) in fungal MAPKs. The phylogenetic analysis suggests that fungal MAPKs are non-polymorphic, had evolved from their common ancestors around 1500 million years ago, and are distantly related to plant MAPKs. We are the first to report the presence of nine novel activation loop motifs in fungal MAPKs. The specificity of the activation loop motif plays a significant role in controlling different growth and stress related pathways in fungi. Hence, the presences of these nine novel activation loop motifs in fungi are of special interest. 相似文献
4.
Neha Bhardwaj Sanjeev K. Bhardwaj Jyotsana Mehta Girish C. Mohanta Akash Deep 《Analytical biochemistry》2016
Bacteriophages are a class of viruses that specifically infect and replicate within a bacterium. They possess inherent affinity and specificity to the particular bacterial cells. This property of bacteriophages makes them an attractive biorecognition element in the field of biosensor development. In this work, we report the use of an immobilized bacteriophage for the development of a highly sensitive electrochemical sensor for Staphylococcus arlettae, bacteria from the pathogenic family of coagulase-negative staphylococci (CNS). The specific bacteriophages were covalently immobilized on the screen-printed graphene electrodes. Thus, the fabricated bacteriophage biosensor displayed quantitative response for the target bacteria (S. arlettae) for a broad detection range (2.0–2.0 × 106 cfu). A fast response time (2 min), low limit of detection (2 cfu), specificity, and stability over a prolonged period (3 months) are some of the important highlights of the proposed sensor. The practical utility of the developed sensor has been demonstrated by the analysis of S. arlettae in spiked water and apple juice samples. 相似文献
5.
M Matsuda A Tazumi S Kagawa T Sekizuka O Murayama JE Moore BC Millar 《BMC veterinary research》2006,2(1):1-4
Background
At present, six accessible sequences of 16S rDNA from Taylorella equigenitalis (T. equigenitalis) are available, whose sequence differences occur at a few nucleotide positions. Thus it is important to determine these sequences from additional strains in other countries, if possible, in order to clarify any anomalies regarding 16S rDNA sequence heterogeneity. Here, we clone and sequence the approximate full-length 16S rDNA from additional strains of T. equigenitalis isolated in Japan, Australia and France and compare these sequences to the existing published sequences.Results
Clarification of any anomalies regarding 16S rDNA sequence heterogeneity of T. equigenitalis was carried out. When cloning, sequencing and comparison of the approximate full-length 16S rDNA from 17 strains of T. equigenitalis isolated in Japan, Australia and France, nucleotide sequence differences were demonstrated at the six loci in the 1,469 nucleotide sequence. Moreover, 12 polymorphic sites occurred among 23 sequences of the 16S rDNA, including the six reference sequences.Conclusion
High sequence similarity (99.5% or more) was observed throughout, except from nucleotide positions 138 to 501 where substitutions and deletions were noted. 相似文献6.
Das BB Sen N Roy A Dasgupta SB Ganguly A Mohanta BC Dinda B Majumder HK 《Nucleic acids research》2006,34(4):1121-1132
Emergence of the bi-subunit topoisomerase I in the kinetoplastid family (Trypanosoma and Leishmania) has brought a new twist in topoisomerase research related to evolution, functional conservation and preferential sensitivities to the specific inhibitors of type IB topoisomerase family. In the present study, we describe that naturally occurring flavones baicalein, luteolin and quercetin are potent inhibitors of the recombinant Leishmania donovani topoisomerase I. These compounds bind to the free enzyme and also intercalate into the DNA at a very high concentration (300 µM) without binding to the minor grove. Here, we show that inhibition of topoisomerase I by these flavones is due to stabilization of topoisomerase I–DNA cleavage complexes, which subsequently inhibit the religation step. Their ability to stabilize the covalent topoisomerase I–DNA complex in vitro and in living cells is similar to that of the known topoisomerase I inhibitor camptothecin (CPT). However, in contrast to CPT, baicalein and luteolin failed to inhibit the religation step when the drugs were added to pre-formed enzyme substrate binary complex. This differential mechanism to induce the stabilization of cleavable complex with topoisomerase I and DNA by these selected flavones and CPT led us to investigate the effect of baicalein and luteolin on CPT-resistant mutant enzyme LdTOP1Δ39LS lacking 1–39 amino acids of the large subunit [B. B. Das, N. Sen, S. B. Dasgupta, A. Ganguly and H. K. Majumder (2005) J. Biol. Chem. 280, 16335–16344]. Baicalein and luteolin stabilize duplex oligonucleotide cleavage with LdTOP1Δ39LS. This observation was further supported by the stabilization of in vivo cleavable complex by baicalein and luteolin with highly CPT-resistant L.donovani strain. Taken together, our data suggest that the interacting amino acid residues of topoisomerase I may be partially overlapping or different for flavones and CPT. This study illuminates new properties of the flavones and provide additional insights into the ligand binding properties of L.donovani topoisomerase I. 相似文献
7.
Insect seed predation may vary depending on seed production. The present study considers the hypothesis that the rates of seed predation tend to be smaller in years of higher fruit production. Thus, we monitored the production of fruits and predation of seeds of the palm Syagrus romanzoffiana over 2?years in the Atlantic Forest (Parque Municipal da Lagoa do Peri, Florianópolis, SC, Brazil), between July 2006 and June 2008. Plots of 0.25?m2 were fitted under 20 mother plants and fruits were monthly collected for assessment of abundance and seed predation. There was variation in fruit production between the 2?years and among reproductive plants. Predation rates were high and occurred in the predispersal phase by the Curculionidae Revena rubiginosa Boheman, Anchylorhynchus aegrotus Fahraeus, and Anchylorhynchus variabilis Gyllenhal. Seed predation by these species of Anchylorhynchus is first registered in the present study. In average, about 60% of the seeds monthly produced in the population tend to escape insect predation in year of high or low production, becoming available for recruitment. The predation rate was not related to the amount of fruits produced per reproductive plant. Also, different than expected, there was a positive relation between the rates of seed predation and the total of fruits produced monthly on the plots. Thus, no evidence for the satiation of insect seed predators was found in this study with S. romanzoffiana. 相似文献
8.
Ginkgo biloba responds to herbivory by activating early signaling and direct defenses 总被引:1,自引:0,他引:1
Mohanta TK Occhipinti A Atsbaha Zebelo S Foti M Fliegmann J Bossi S Maffei ME Bertea CM 《PloS one》2012,7(3):e32822
Background
Ginkgo biloba (Ginkgoaceae) is one of the most ancient living seed plants and is regarded as a living fossil. G. biloba has a broad spectrum of resistance or tolerance to many pathogens and herbivores because of the presence of toxic leaf compounds. Little is known about early and late events occurring in G. biloba upon herbivory. The aim of this study was to assess whether herbivory by the generalist Spodoptera littoralis was able to induce early signaling and direct defense in G. biloba by evaluating early and late responses.Methodology/Principal Findings
Early and late responses in mechanically wounded leaves and in leaves damaged by S. littoralis included plasma transmembrane potential (Vm) variations, time-course changes in both cytosolic calcium concentration ([Ca2+]cyt) and H2O2 production, the regulation of genes correlated to terpenoid and flavonoid biosynthesis, the induction of direct defense compounds, and the release of volatile organic compounds (VOCs). The results show that G. biloba responded to hebivory with a significant Vm depolarization which was associated to significant increases in both [Ca2+]cyt and H2O2. Several defense genes were regulated by herbivory, including those coding for ROS scavenging enzymes and the synthesis of terpenoids and flavonoids. Metabolomic analyses revealed the herbivore-induced production of several flavonoids and VOCs. Surprisingly, no significant induction by herbivory was found for two of the most characteristic G. biloba classes of bioactive compounds; ginkgolides and bilobalides.Conclusions/Significance
By studying early and late responses of G. biloba to herbivory, we provided the first evidence that this “living fossil” plant responds to herbivory with the same defense mechanisms adopted by the most recent angiosperms. 相似文献9.
10.
Sofie De Cooman Nathalie De Mey Bram BC Dewulf Rik Carette Thierry Deloof Maurice Sosnowski Andre M De Wolf Jan FA Hendrickx 《BMC anesthesiology》2008,8(1):1-6