Deoxyribonucleic Acid Species Research Articles

Use of Fourier-Transform Infrared Spectroscopy for DNA Identification on Recycled PET Composite Substrate

Fourier-transform infrared (FTIR) spectroscopy has been extensively used in plastic pollution research, since it has the advantages of great simplicity, rapidity, and low cost, being widely employed in the fingerprint identification of molecular composition and structure. The present study evaluates attenuated total reflection (ATR)–FTIR spectroscopy as a sensitive and effective assay for the identification of deoxyribonucleic acid (DNA) isolated from experimental animals. Various composite materials based on recycled polyethylene terephthalate (PET) as the main component, along with high-density polyethylene (HDPE), polypropylene (PP), and aluminum nanopowder obtained using an injection-molding machine, were used as substrate contaminants. The contamination was performed using quantified nucleic acid solution added in droplets to the clean, decontaminated samples, which were then dried and kept in a protective environment until the analysis. ATR–FTIR (with an FTIR spectrometer equipped with an ATR accessory) spectroscopy was used to analyze the bare composite materials’ substrates and the DNA-contaminated samples. To the best of our knowledge, the evaluation of PET packaging contamination with DNA species by FTIR has not been reported previously. This study demonstrated that FTIR spectroscopy could provide a rapid, sensitive, and reliable approach for screening of biochemical contaminants on composite materials based on recycled PET.

Elongation method for electronic structure calculations of random DNA sequences.

We applied ab initio order-N elongation (ELG) method to calculate electronic structures of various deoxyribonucleic acid (DNA) models. We aim to test potential application of the method for building a database of DNA electronic structures. The ELG method mimics polymerization reactions on a computer and meets the requirements for linear scaling computational efficiency and high accuracy, even for huge systems. As a benchmark test, we applied the method for calculations of various types of random sequenced A- and B-type DNA models with and without counterions. In each case, the ELG method maintained high accuracy with small errors in energy on the order of 10(-8) hartree/atom compared with conventional calculations. We demonstrate that the ELG method can provide valuable information such as stabilization energies and local densities of states for each DNA sequence. In addition, we discuss the "restarting" feature of the ELG method for constructing a database that exhaustively covers DNA species.

Molecular population dynamics of DNA structures in a bcl-2 promoter sequence is regulated by small molecules and the transcription factor hnRNP LL.

Minute difference in free energy change of unfolding among structures in an oligonucleotide sequence can lead to a complex population equilibrium, which is rather challenging for ensemble techniques to decipher. Herein, we introduce a new method, molecular population dynamics (MPD), to describe the intricate equilibrium among non-B deoxyribonucleic acid (DNA) structures. Using mechanical unfolding in laser tweezers, we identified six DNA species in a cytosine (C)-rich bcl-2 promoter sequence. Population patterns of these species with and without a small molecule (IMC-76 or IMC-48) or the transcription factor hnRNP LL are compared to reveal the MPD of different species. With a pattern recognition algorithm, we found that IMC-48 and hnRNP LL share 80% similarity in stabilizing i-motifs with 60 s incubation. In contrast, IMC-76 demonstrates an opposite behavior, preferring flexible DNA hairpins. With 120–180 s incubation, IMC-48 and hnRNP LL destabilize i-motifs, which has been previously proposed to activate bcl-2 transcriptions. These results provide strong support, from the population equilibrium perspective, that small molecules and hnRNP LL can modulate bcl-2 transcription through interaction with i-motifs. The excellent agreement with biochemical results firmly validates the MPD analyses, which, we expect, can be widely applicable to investigate complex equilibrium of biomacromolecules.

An efficient protocol for total DNA extraction from the members of order Zingiberales- suitable for diverse PCR based downstream applications

Different protocols are usually used for extracting total deoxyribonucleic acid (DNA) from different plant species of same order and DNA of the associated viruses. Here, we describe a rapid, efficient and universal protocol for isolating total DNA from the members of Zingiberales which harbor a high amount of polysaccharides and secondary metabolites. DNA isolated with this protocol was successfully used for PCR based downstream applications viz. random amplified polymorphic DNA (RAPD), Inter-simple sequence repeats (ISSR), DNA barcoding gene (Internal transcribed spacer and trnl-f) amplification and detection of the viruses.

Comparison of narrow-band imaging cystoscopy and white-light imaging cystoscopy to detect bladder lesions – Northern Ireland initial experience

Comparison of narrow-band imaging cystoscopy and white-light imaging cystoscopy to detect bladder lesions – Northern Ireland initial experience

Prevalence of Rickettsia species antibodies and Rickettsia species DNA in the blood of cats with and without fever

Rickettsia species antibodies have been detected in some cats but it is unknown whether infected cats develop clinical signs. The prevalence of Rickettsia species deoxyribonucleic acid (DNA) in blood from clinically ill cats has not been determined. The objective of this study was to determine if cats with fever (body temperature >or=102.5 degrees F [39.2 degrees C]) were more likely to have evidence of rickettsial infection than healthy, age-matched, control cats with a body temperature<102.5 degrees F. Rickettsia species polymerase chain reaction (PCR) assays were performed to detect rickettsial DNA extracted from blood (71 paired samples), indirect immunofluorescence assays (IFA) were performed to detect serum antibodies against Rickettsia felis (90 paired samples) and Rickettsia rickettsii (91 paired samples), and the results between pairs were compared. All samples were negative for Rickettsia species DNA. More cats with fever were seropositive for R felis or R rickettsii than control cats, but results were not statistically significant. Results of this pilot study failed to show an association between Rickettsia species DNA or Rickettsia species antibodies and fever.

Species identification of animal cells by nested PCR targeted to mitochondrial DNA

We developed a highly sensitive and convenient method of nested polymerase chain reaction (PCR) targeted to mitochondrial deoxyribonucleic acid (DNA) to identify animal species quickly in cultured cells. Fourteen vertebrate species, including human, cynomolgus monkey, African green monkey, mouse, rat, Syrian hamster, Chinese hamster, guinea pig, rabbit, dog, cat, cow, pig, and chicken, could be distinguished from each other by nested PCR. The first PCR amplifies mitochondrial DNA fragments with a universal primer pair complementary to the conserved regions of 14 species, and the second PCR amplifies the DNA fragments with species-specific primer pairs from the first products. The species-specific primer pairs were designed to easily distinguish 14 species from each other under standard agarose gel electrophoresis. We further developed the multiplex PCR using a mixture of seven species-specific primer pairs for two groups of animals. One was comprised of human, mouse, rat, cat, pig, cow, and rabbit, and the other was comprised of African green monkey, cynomolgus monkey, Syrian hamster, Chinese hamster, guinea pig, dog, and chicken. The sensitivity of the PCR assay was at least 100 pg DNA/reaction, which was sufficient for the detection of each species of DNA. Furthermore, the nested PCR method was able to identify the species in the interspecies mixture of DNA. Thus, the method developed in this study will provide a useful tool for the authentication of animal species.

An Alignment of Toxigenic Gibberella Strains Having Anamorphs in Section Liseola of Fusarium

Click to increase image sizeClick to decrease image sizeKey Words: Deoxyribonucleic acidspecies conceptsDNA relatednessFusarium

Use of plasmid profiles in epidemiologic surveillance of disease outbreaks and in tracing the transmission of antibiotic resistance.

Plasmids are circular deoxyribonucleic acid molecules that exist in bacteria, usually independent of the chromosome. The study of plasmids is important to medical microbiology because plasmids can encode genes for antibiotic resistance or virulence factors. Plasmids can also serve as markers of various bacterial strains when a typing system referred to as plasmid profiling, or plasmid fingerprinting is used. In these methods partially purified plasma deoxyribonucleic acid species are separated according to molecular size by agarose gel electrophoresis. In a second procedure, plasmid deoxyribonucleic acid which has been cleaved by restriction endonucleases can be separated by agarose gel electrophoresis and the resulting pattern of fragments can be used to verify the identity of bacterial isolates. Because many species of bacteria contain plasmids, plasmid profile typing has been used to investigate outbreaks of many bacterial diseases and to trace inter- and intra-species spread of antibiotic resistance.

Section Liseola of Fusarium

Click to increase image sizeClick to decrease image sizeKey Words: deoxyribonucleic acidspecies conceptsDNA renaturation

Section Liseola of Fusarium

Click to increase image sizeClick to decrease image sizeKey Words: deoxyribonucleic acidspecies conceptsDNA renaturation

Deoxyribonucleic Acid Base Compositions and Nucleotide Distributions of 65 Strains of Budding Bacteria

A total of 65 strains of appendaged or prosthecate, budding bacteria from our culture collection were selected for a study of deoxyribonucleic acid (DNA) base composition and nucleotide distribution. These strains represented 11 genera, including 4 genera of hyphal, budding bacteria which have not been formally described yet. The DNA species were thermally denatured, and absorbance-temperature profiles were recorded. The midpoints, widths, and asymmetries of the melting transitions were determined. When the DNA base compositions and nucleotide distributions were plotted on a dissimilarity map, it became evident that the strains of each genus occupied a distinct area. The distribution of strains within such an area indicated the degree of heterogeneity of a genus. When 16 Hyphomicrobium strains were analyzed, they formed five clusters within their generic area. These clusters correlated well with groups which had been previously established by DNA base composition analyses, by DNA-DNA homology studies, and by numerical taxonomy. Nine of the strains investigated were distinguished by melting profiles which were skewed uniquely to the left.

Transfer of Plasmid-Borne Beta-Lactamase in Neisseria gonorrhoeae

Neisseria gonorrhoeae strain GC82 contains a plasmid specifying a beta-lactamase (beta-Lam(+)). Mixed incubation of strain GC82 with a penicillin-susceptible (beta-Lam(-)), streptomycin-resistant mutant of strain GC9 results in the expression of beta-lactamase activity and streptomycin resistance in the transcipients. The frequency of transfer of the plasmid-specified resistance to penicillin seems to be proportional to the initial input ratio of the mating mixture of donor to recipient and to correlate positively with bacterial density. Cell-to-cell transmission of the deoxyribonucleic acid (DNA) appears to be by a conjugal mechanism or, alternatively, by an as yet undescribed transducing phage. Additionally, whole-cell DNA from a beta-lactamase-producing strain could be used to transform streptomycin-resistant recipients, resulting in the expression of both beta-lactamase activity and streptomycin resistance in the transformants, and purified gonococcal plasmid DNA transformed Escherichia coli but not the gonococcus. Circular DNA extracted from donor GC82 comprised three molecular species (approximately 2.7, 4.8, and 25 megadaltons [Mdal]), whereas the recipients GC9-S (Str(r)) contained only the 2.7-Mdal cryptic DNA species. DNA from the GC9-S82 (Str(r), beta-Lam(+)) transcipient contained a 4.8-Mdal species in addition to the cryptic molecular species (2.7 Mdal). The finding that the transcipient will not retransfer beta-lactamase is consistent with the hypothesis that the 25-Mdal plasmid promotes mobilization of the smaller 4.8-Mdal R plasmid.

Characterization of SmSu plasmids by restriction endonuclease cleavage and compatibility testing.

Twelve plasmids carrying genes for streptomycin and sulfonamide resistance were studied for the number and distribution of sites on the plasmid moleucles susceptible to cleavage by the restriction endonuclease EcoRI. Ten of the twelve were found to have a single cut site, one plasmid (R678) had three such sites, and plasmid PB165, which was isolated as three supercoiled deoxyribonucleic acid species with molecular weights 7.4 x 10(6), 14.7 x 10(6), and 21.4 x 10(6) was reduced to a single (linear) species of molecular weight 7.6 x 10(6) after cutting with EcoRI. We conclude that PB165 forms oligomers in Escherichia coli and that the number of copies of these per chromosome is more consistant and that the number of copies of these per chromosome is more consistent with a negative than a positive control mechanism for plasmid replication. Compatibility testing of a positive control mechanism for plasmid replication. Compatibility testing of these plasmids showed they all belong to the same incompatibility group, which we designate IncQ, suggesting that they may have come from a common ancestor.

Antiviral Activity of Arabinosyladenine and Arabinosylhypoxanthine in Herpes Simplex Virus-Infected KB Cells: Selective Inhibition of Viral Deoxyribonucleic Acid Synthesis in the Presence of an Adenosine Deaminase Inhibitor

The antiviral activity of the fraudulent nucleoside arabinosyladenine (ara-A) against herpes simplex virus (HSV) type 1 was increased nearly 20-fold by the adenosine deaminase inhibitor, coformycin. The combination of ara-A plus coformycin was 90 times more potent in blocking HSV replication than was arabinosylhypoxanthine (ara-H). In suspension culture both drugs were more active than they were in monolayer culture. Deoxyribonucleic acid (DNA) synthesis also was inhibited by the nucleosides. Depending upon the species of DNA examined, ara-A was 8 to 15 times more active in the presence of coformycin, and the combination was 35 to 70 times more potent than ara-H. Both drugs inhibited total DNA synthesis to the same extent in uninfected and HSV-infected KB cells. In contrast, viral DNA synthesis was three to six times more susceptible to inhibition than was cellular DNA synthesis. Inhibition of viral DNA synthesis was more pronounced in suspension culture than in monolayer culture. However, the method of cell propagation did not alter the degree to which the drugs inhibited DNA synthesis in uninfected KB cells. An index has been derived to quantitate the extent of the selective inhibition of viral or cellular DNA synthesis. Fifty percent inhibitory concentrations of a drug were calculated for uninfected KB DNA synthesis and viral DNA synthesis and expressed as a ratio. The logarithm of this ratio was termed the selective index and was positive if viral DNA synthesis was inhibited preferentially or negative if uninfected KB DNA synthesis was more strongly inhibited. Data from experiments performed in monolayer culture gave positive selective index values of 0.3, 0.5, and 0.4 for ara-A plus coformycin, ara-A, and ara-H, respectively. Values of 0.7 and 0.6 were obtained from suspension culture data for ara-A plus coformycin and ara-H, respectively. Considered collectively, the data presented in this communication establish that coformycin increased the potency of ara-A but did not increase its selectivity.

Isolation of plasmid deoxyribonucleic acid from two strains of Bacteroides.

Two clinical isolates of Bacteroides contained covalently closed circular deoxyribonucleic acid (DNA) as shown by sedimentation in an alkaline sucrose gradient, CsCl ethidium bromide equilibrium centrifugation, and electron microscopy. Bacteriodes fragilis N1175 contained a homogeneous species of plasmid DNA with a molecular weight of 25 x 10(6). Bacteroides ochraceus 2228 contained two distinct, covalently closed circular DNA elements. The larger cosedimented with the covalently closed circular DNA form of the R plasmid, R100, corresponding to a molecular weight of 70 x 10(6); the smaller sedimented as a 58S molecule with a calculated molecular weight of 25 x 10(6). The roles of these plasmids are unknown. Neither strain transferred antibiotic resistance to plasmid-negative Bacteroides or Escherichia coli, and neither produced bacteriocins active against other Bacteroides or sensitive indicator strains of E. coli.

Binding of Bacteriocin Clo DF13 to Clo DF13 Plasmid Deoxyribonucleic Acid In Vivo and In Vitro

The bacteriocinogenic plasmid Clo DF13 is present in Escherichia coli to the extent of 10 copies per cell. A complex of Clo DF13 plasmid deoxyribonucleic acid (DNA) and protein can be isolated from cells. Treatment of the complex with ionic detergents or proteases dissociates the complex but does not convert any supercoiled Clo DF13 DNA to the open circular form, indicating that this complex is not a relaxation complex. The complex is stable in 0.5 M NaCl and contains one polypeptide species. The protein, present in the complex, appeared to be bacteriocin Clo DF13 for the following reasons: (i) the protein is de novo synthesized in Clo DF13-harboring minicells, indicating that this protein is Clo DF13 specific; (ii) this protein shows bacteriocinogenic activity on a bacteriocin Clo DF13-susceptible indicator strain; (iii) this protein has the same molecular weight (60,000) as bacteriocin Clo DF13. DNA-protein binding experiments, involving QAE-Sephadex column chromatography and nitrocellulose membrane filters, demonstrate that bacteriocin Clo DF13 has also affinity in vitro for Clo DF13 DNA. Membrane filter binding experiments revealed that bacteriocin Clo DF13 does not interact with other DNA species, such as ColE1 DNA, yeast DNA, calf thymus DNA, phiX174 DNA, and also not with denatured Clo DF13 DNA. In addition no binding to Clo DF13 DNA of a related bacteriocin, colicin E3, could be detected. These results indicate that the binding of bacteriocin Clo DF 13 to double-stranded Clo DF13 DNA is very specific.

Nuclear and mitochondrial deoxyribonucleic acid replication during mitosis in Saccharomyces cerevisiae.

To study nuclear and mitochondrial deoxyribonucleic acid (DNA) synthesis during the cell cycle, a 15N-labeled log-phase population of Saccharomyces cervisiae was shifted to 14N medium. After one-half generation, the cells were centrifuged on a sorbitol gradient in a zonal rotor to fractionate the population according to cell size and age into fractions representing the yeast cell cycle. DNA samples isolated from the zonal rotor cell samples were centrifuged to equilibrium in CsC1 in an analytical ultracentrifuge to separate the nuclear and mitochondrial DNA components. The amount of 14N incorporated into each 15N-labeled DNA species was measured. The extent of nuclear DNA replication per sample was obtained by measuring the amount of hybrid DNA. The percentage of hybrid nuclear DNA increased from 6 to 68% and then decreased to 44% during the cell cycle. Upon ultracentrifugation, mitochondrial DNA banded as a unimodal peak in all zonal rotor samples. Mitochondrial DNA replication could be ascertained only by the 14N level in each mitochondrial peak and not, as with nuclear DNA, by hybrid DNA level. In contrast to the nuclear incorporation pattern, the 14N percentage in mitochondrial DNA remained effectively constant during the cell cycle. Comparison of the data to theoretical distributions showed that nuclear DNA was replicated discontinuously during the cell cycle, whereas mitochondrial DNA was replicated continuously throughout the entire mitotic cycle.

Self-transferable plasmids determining the hemolysin and bacteriocin of Streptococcus faecalis var. zymogenes.

Strains of Streptococcus faecalis var. zymogenes, designated JH1 and JH3, produced a hemolysin and a bacteriocin. Hemolytic activity was lost from a low percentage of cells grown in broth at either 37 or 45 C. All nonhemolytic (Hly-) variants had lost bacteriocin activity (Ben-), and those from strain JH3 had also lost resistance to the bacteriocin (Bnr-). The majority of Hly-, Ben- variants from JH1 retained bacteriocin resistance (Bnrplus). Strains JH1 and JH3 contained a plasmid deoxyribonucleic acid species of molecular weight 38 times 10-6 (plasmids pJH2 and pJH3, respectively), and strain JH1 also contained a 50 times 10-6 molecular weight plasmid (pJH1) which has previously been shown to carry the genes determining resistance to the antibiotics kanamycin, neomycin, streptomycin, erythromycin, and tetracycline. Hly-, Bcn-, Bnr- variants of strain JH3 had completely lost plasmid pJH3. Hly-, Bcn-, Bnr- variants of strain JH1 had completely lost plasmid pJH2 and retained plasmid pJH1, but Hly-, Bcn-, Bnrplus variants had retained both plasmids pJH2 and pJH1. The Hlyplus, Bcnplus, Bnrplus traits from both parental strains were transferable to nonhemolytic S. faecalis strains during mixed incubation in broth at 37 C, and hemolytic recipient strains were found to have received plasmid pJH2 from strain JH1 and pJH3 from JH3. We conclude that the Hlyplus, Bnrplus traits are borne on plasmid pJH2 in strain JH1 and pJH3 in strain JH3 and that, in Hly-, Bcn-, Bnrplus variants of strain JH1, plasmic pJH2 has suffered a mutation affecting hemolysin and bacteriocin expression. We infer that the plasmids transfer by conjugation. Beta-hemolytic activity is the only property distinguishing the zymogenes variety from S. faecalis. Since we have shown that this activity is plasmid borne in strains JH1 and JH3, we endorse the view that the varietal status of zymogenes should be dropped.

Transformation of Salmonella typhimurium by plasmid deoxyribonucleic acid.

A modified transformation procedure that is effective for the introduction of plasmid deoxyribonucleic acid at high frequency into Salmonella typhimurium, as well as into Escherichia coli, is described. Transformed bacteria acquire a circular deoxyribonucleic acid species having the genetic and molecular characteristics of the transforming plasmid.