DNA Base Sequence Research Articles

Degradation of Polyaromatic Hydrocarbons by Fungi Isolated from Soil in Japan

There are fewer studies on the degradation of polyaromatic hydrocarbons (PAHs) by fungi than those by bacteria. Three fungi (strains A, B, and C), which could grow on pyrene as the sole source of carbon, were isolated from soils at the side of a freeway, a gas station, and a lake in Japan. Strain A was tentatively classified as members of the Trichoderma/Hypocrea genus, and both strains B and C were classified as belonging to the Fusarium genus on the basis of their base sequence of 18S ribosomal DNA and morphological characteristics. After an incubation period of 7 and 14 days at 28°C in an inorganic Czapek-Dox medium with PAHs as the substrate, both strains A and B assimilated anthracene and fluoranthene, whereas strain C assimilated neither of them. The pyrene-degrading activity and the growth of strain A improved by adding 0.02% yeast extract, 0.1% sucrose, or 0.1% lactose. The pyrene-degrading activity was also found to be more effective at pH 4 rather than at pH 6.5.

Hypoxia and environmental epigenetics.

Epigenetics refers to long-term modifications of gene activity that can be inherited, either somatically or transgenerationally, but that are independent of alterations in the primary base sequence of the organism's DNA. These changes can include chemical modifications of both the DNA bases and the proteins that associate with the DNA helices to form chromatin, the nucleic acid:protein complex of which the chromosomes are comprised. Epigenetic modifications can affect the accessibility of the DNA for transcription factors (the DNA-binding proteins that specify which genes are to be active or silent by modulating the recruitment of the transcriptional machinery that reads the information encoded in the sequence) and thereby regulate the expression of genes and alter the phenotype of the organism. Epigenetic marks can also be re-established following mitosis, allowing patterns of differential gene expression to be transmitted from one cell generation to the next, and can even be maintained through meiosis, allowing transgenerational transfer of regulatory cues. Unlike the information encoded in the DNA sequence, which is invariant between most cell types and over time, epigenetic information is tissue specific and can change in response to exogenous and endogenous perturbations. This responsive capacity enables a sensitive and reactive system that can optimize gene expression in relevant tissue in response to environmental change. The realization that organisms are capable of genetically 'reprograming' themselves as well as 'preprograming' future cells, and even future offspring to optimize gene expression for a given environment may have tremendous ramifications on our understanding of both acclimatization and adaptation to hypoxia.

Redefining Ceratocystis and allied genera

The genus Ceratocystis was established in 1890 and accommodates many important fungi. These include serious plant pathogens, significant insect symbionts and agents of timber degradation that result in substantial economic losses. Virtually since its type was described from sweet potatoes, the taxonomy of Ceratocystis has been confused and vigorously debated. In recent years, particulary during the last two decades, it has become very obvious that this genus includes a wide diversity of very different fungi. These have been roughly lumped together due to their similar morphological structures that have clearly evolved through convergent evolution linked to an insect-associated ecology. As has been true for many other groups of fungi, the emergence of DNA-based sequence data and associated phylogenetic inferences, have made it possible to robustly support very distinct boundaries defined by morphological characters and ecological differences. In this study, DNA-sequence data for three carefully selected gene regions (60S, LSU, MCM7) were generated for 79 species residing in the aggregate genus Ceratocystis sensu lato and these data were subjected to rigorous phylogenetic analyses. The results made it possible to distinguish seven major groups for which generic names have been chosen and descriptions either provided or emended. The emended genera included Ceratocystis sensu stricto, Chalaropsis, Endoconidiophora, Thielaviopsis, and Ambrosiella, while two new genera, Davidsoniella and Huntiella, were described. In total, 30 new combinations have been made. This major revision of the generic boundaries in the Ceratocystidaceae will simplify future treatments and work with an important group of fungi including distantly related species illogically aggregated under a single name.

Expectations of Epigenetic Research Studies Focusing on Mesenchymal Stem Cells

Epigenetic alternations are not associated with any changing the base sequence of DNA, but are closely related to phenome together with genome [1]. Most of them are determined differently under various external and internal influences and, even if abnormal, memorized over individual life

What controls DNA looping?

The looping of DNA provides a means of communication between sequentially distant genomic sites that operate in tandem to express, copy, and repair the information encoded in the DNA base sequence. The short loops implicated in the expression of bacterial genes suggest that molecular factors other than the naturally stiff double helix are involved in bringing the interacting sites into close spatial proximity. New computational techniques that take direct account of the three-dimensional structures and fluctuations of protein and DNA allow us to examine the likely means of enhancing such communication. Here, we describe the application of these approaches to the looping of a 92 base-pair DNA segment between the headpieces of the tetrameric Escherichia coli Lac repressor protein. The distortions of the double helix induced by a second protein—the nonspecific nucleoid protein HU—increase the computed likelihood of looping by several orders of magnitude over that of DNA alone. Large-scale deformations of the repressor, sequence-dependent features in the DNA loop, and deformability of the DNA operators also enhance looping, although to lesser degrees. The correspondence between the predicted looping propensities and the ease of looping derived from gene-expression and single-molecule measurements lends credence to the derived structural picture.

Bos indicusintrogression into (peri-)alpine cattle breeds - evidence from the analysis of bovine whey protein variants

The major bovine whey proteins, α-lactalbumin (α-LA) and β-lactoglobulin (β-LG), exhibit breed-specific genetic variation. The aim of this study was to identify possible new protein variants and determine the distribution of variants across a variety of 18 taurine and indicine cattle breeds applying a DNA-based sequencing approach. To this end, the open reading frames of the respective genes (LALBA and LGB) were sequenced in 476 animals. Within the LALBA gene, a previously unknown synonymous and a previously undesignated non-synonymous nucleotide exchange were identified. Furthermore, two known α-LA variants (A and B) and four known β-LG variants (A, B, C and W) were determined. The occurrence of typical indicine variants in some taurine cattle breeds, such as Suisse Eringer, German Hinterwälder and Hungarian Grey Steppe, further supports the hypothesis of ancient Bos indicus introgression into (peri-)alpine cattle breeds.

Switchable Reconfiguration of Nucleic Acid Nanostructures by Stimuli-Responsive DNA Machines

CONSPECTUS: The base sequence in DNA dictates structural and reactivity features of the biopolymer. These properties are implemented to use DNA as a unique material for developing the area of DNA nanotechnology. The design of DNA machines represents a rapidly developing research field in the area of DNA nanotechnology. The present Account discusses the switchable reconfiguration of nucleic acid nanostructures by stimuli-responsive DNA machines, and it highlights potential applications and future perspectives of the area. Programmed switchable DNA machines driven by various fuels and antifuels, such as pH, Hg(2+) ions/cysteine, or nucleic acid strands/antistrands, are described. These include the assembly of DNA tweezers, walkers, a rotor, a pendulum, and more. Using a pH-oscillatory system, the oscillatory mechanical operation of a DNA pendulum is presented. Specifically, the synthesis and "mechanical" properties of interlocked DNA rings are described. This is exemplified with the preparation of interlocked DNA catenanes and a DNA rotaxane. The dynamic fuel-driven reconfiguration of the catenane/rotaxane structures is followed by fluorescence spectroscopy. The use of DNA machines as functional scaffolds to reconfigurate Au nanoparticle assemblies and to switch the fluorescence features within fluorophore/Au nanoparticle conjugates between quenching and surface-enhanced fluorescence states are addressed. Specifically, the fluorescence features of the different DNA machines are characterized as a function of the spatial separation between the fluorophore and Au nanoparticles. The experimental results are supported by theoretical calculations. The future development of reconfigurable stimuli-responsive DNA machines involves fundamental challenges, such as the synthesis of molecular devices exhibiting enhanced complexities, the introduction of new fuels and antifuels, and the integration of new payloads being reconfigured by the molecular devices, such as enzymes or catalytic nanoparticles. Exciting applications of these systems are ahead of us, and switchable catalytic nanoparticle systems, switchable enzyme cascades, and spatially programmed nanoparticles for innovative nanomedicine may be envisaged. Also, the intracellular reconfiguration of nucleic acids by stimuli-responsive DNA machines holds great promise as a means to silence genes or inhibit metabolic pathways.

Towards understanding of poly-guanine activated fluorescent silver nanoclusters

It has been recently reported that the fluorescence of some DNA-templated silver nanoclusters (AgNCs) can be significantly enhanced upon by hybridizing with a partially complementary DNA containing a G-rich overhang near the AgNCs. This discovery has found a number of analytical applications but many fundamental questions remain to be answered. In this work, the photostability of these activated AgNCs is reported. After adding the G-rich DNA activator, the fluorescence intensity peaks in ∼1 h and then starts to decay, where the decaying rate is much faster with light exposure. The lost fluorescence is recovered by adding NaBH4, suggesting that the bleaching is an oxidative process. Once activated, the G-rich activator can be removed while the AgNCs still maintain most of their fluorescence intensity. UV–vis spectroscopy suggests that new AgNC species are generated upon hybridization with the activator. The base sequence and length of the template DNA have also been varied, leading to different emission colors and color change after hybridization. G-rich aptamers can also serve as activators. Our results indicate that activation of the fluorescence by G-rich DNA could be a convenient method for biosensor development since the unstable NaBH4 is not required for the activation step.

Genomic Privacy in the Information Age

One premise of the notion of “personalized medicine” is that an individual's unique genetic makeup provides key information to guide prevention, diagnosis, and treatment of disease. Indeed, it is highly probable that no one besides you has ever been born, or ever will be again, with your precise DNA base sequence (except, perhaps, if you are an identical twin, and even then maybe not). Hence, in principle, your complete DNA sequence precisely identifies you, and anyone with access to even partial information about your genotype could, in theory, identify you as the source of your DNA sequence. This risk of breach of privacy is frequently included in consent forms for DNA sequencing or genotyping, whether for medical reasons, research, or recreation (such as searching for ancestors). To date, the risk has been theoretical, but a recent report by Gymrek et al. (1) shows that real breach of privacy is feasible with access to limited genomic data, bare-bones demographic information, and publicly available Internet tools. Now that we know it can be done, how should this potential for breach of privacy change our approach to collection of genomic data? Gymrek et al. focused on identification of male surnames from Y chromosome short tandem repeat (Y-STR)2 genotypes (2) (Fig. 1). These repeats are stretches of 3–5 DNA bases (usually 4), repeated multiple times (in the range of 10–20), that are located at multiple sites along the Y chromosome. The exact number of repeats of any particular sequence differs from one Y chromosome to another, but it is a stable heritable trait. Genotyping or sequencing can easily identify specific alleles at dozens of these loci, providing a kind of “fingerprint” of a specific Y chromosome. Indeed, a major use of Y-STR genotyping is forensic, for example in identifying the source of DNA …

Study of DNA conducting properties: Reversible and irreversible evolution

A hole transport through DNA base sequences was modeled. The fact that DNA consists of two polynucleotide strands was taken into consideration. Specific DNA base locations are determined in the model. The model predicts the behavior of a hole acting on the DNA chain, taking into account reversible and irreversible dynamics. It was shown that the transfer mechanisms depend on the sequence type and can be either of hopping nature or of superexchange one. Distance dependence of the hole transport relative rate on the number of hopping steps was investigated. The results obtained were compared with the experimental data. The investigation demonstrates the utilization of the formalism in practical problems for description of the charge migration through the different molecular sequences.

Highly fluorescent peptide nanoribbon impregnated with Sn-porphyrin as a potent DNA sensor

Highly fluorescent and thermo-stable peptide nanoribbons (PNRs) were fabricated by solvothermal self-assembly of a single peptide (D,D-diphenyl alanine peptides) with Sn-porphyrin (trans-dihydroxo[5,10,15,20-tetrakis(p-tolyl)porphyrinato] Sn(IV) (SnTTP(OH)2)). The structural characterization of the as-prepared nanoribbons was performed by transmitting electron microscopy (TEM), scanning electron microscopy (SEM) and atomic force microscopy (AFM), FT-IR and Raman spectroscopy, indicating that the lipophilic Sn-porphyrins are impregnated into the porous surface formed in the process of nanoribbon formation through intermolecular hydrogen bonding of the peptide main chains. Consequently the Sn-porphyrin-impregnated peptide nanoribbons (Sn-porphyrin-PNRs) exhibited typical UV-visible absorption spectrum of the monomer porphyrin with a red shifted Q-band, and their fluorescence quantum yield was observed to be enhanced compared to that of free Sn-porphyrin. Interestingly the fluorescence intensity and lifetimes of Sn-porphyrin-PNRs were selectively affected upon interaction with nucleotide base sequences of DNA while those of free Sn-porphyrins were not affected by binding with any of the DNA studied, indicating that DNA-induced changes in the fluorescence properties of Sn-porphyrin-PNRs are due to interaction between DNA and the PNR scaffold. These results imply that Sn-porphyrin-PNR will be useful as a potent fluorescent protein analogue and as a biocompatible DNA sensor.

Layer‐by‐layer assembly of photonic crystal using DNA

AbstractPhotonic crystals are a key component for optical next‐generation communication and computing in that they have a periodic 3D structure on the same scale as optical wavelengths. The major difficulty in the practical use of photonic crystals exists in its fabrication process. As an optical component, it must be a defect‐free large crystal with waveguide patterns affecting the propagation of photons. Many attempts have been made to realize such a crystal, but low‐cost and rapid fabrication of a defect‐free large crystal is still a difficult problem. Here, we propose a novel fabrication method combining colloidal crystallization and DNA nanotechnology. In this method, a face‐centered lattice made of 1‐µm polystyrene particles is assembled on a patterned template in a layer‐by‐layer fashion. In order to control the binding among particles, DNA‐gold nano‐particle conjugates (10‐nm GNP modified with 52mer DNA) are used. Specific bonding rules between particles and GNPs defined by the base sequence of DNA results in the layer‐by‐layer growth of the crystal. We have built two‐layer crystals using the proposed method, and the results show its feasibility. We also found some important factors necessary to improve the quality of the crystal. © 2013 Wiley Periodicals, Inc. Electron Comm Jpn, 96(5): 42–49, 2013; Published online in Wiley Online Library (wileyonlinelibrary.com). DOI 10.1002/ecj.11377

The Genetic Polymorphisms and Colonization Process of Olive Fly Populations in Turkey

The olive fruit fly, Bactrocera oleae, is the most important pest of olives in olive growing regions worldwide, especially in the Mediterranean basin and North America. Despite the economic importance of the olive fly, the colonization route of this species is unclear. We used nuclear microsatellite markers and mitochondrial DNA to provide information about the population structure and invasion route of olive fly populations in Turkey, as representative of the Eastern Mediterranean region. Adult fly samples were collected from 38 sublocations covering all olive growing regions in Turkey. The simple sequence variability data revealed a significant genetic variability in olive fly populations and a certain degree of differentiation between Mediterranean and Aegean populations. Mediterranean populations harbor higher levels of microsatellite variation than Aegean populations, which points to the eastern part of the Mediterranean as the putative source of invasion. mtDNA results suggest olive flies from the western part of Turkey are closely related to Italo-Aegean flies of the Mediterranean basin and the olive fly populations have invaded the northern part of the Mediterranean basin through western Turkey. In addition, finding specific American haplotypes in high frequencies might indicate that Turkey is the possible source of American olive fly populations. In order to more precisely characterize the population structure and invasion routes of this organism, more DNA-based sequence analysis should be carried out worldwide.

The role of transgenerational epigenetic inheritance in diversification and speciation

Inheritance is crucial to the evolutionary process. Although most evolutionary biologists assume that inheritance occurs exclusively through changes in DNA base sequence, it has long been known that inheritance can also occur through epigenetic mechanisms, such as chromatin marking, maternal effects, parasite transmission, or learning. In recent years, the possibility that such transgenerational epigenetic inheritance mechanisms can mediate long-term evolutionary change has received increased attention. Here, we consider the potential contribution of transgenerational epigenetic inheritance in driving diversification and speciation. As we describe, a growing body of theoretical and empirical studies suggests that epigenetic inheritance can accelerate the likelihood that genetic change will occur and thereby facilitate speciation. Additionally, evolution and diversification can potentially unfold based solely upon inherited environmental or learned effects, completely independent of any changes in DNA base sequence. Generally, clarifying whether (and how) epigenetic inheritance promotes––or impedes––diversification and speciation remains a key frontier of evolutionary biology.

Synchronization Analysis of Four Symbolic Complex Dynamical Systems for Future Biology Research

The synchronization analysis of four symbolic complex dynamical systems will be discussed carefully in this paper. Grey system theory is mainly being used to study data sequences that are generated by 4-letter chaotic dynamical system, and the usual prediction accuracy has exceeded 90%. In this place we have found a generating rule that may at least realize chaotic synchronization in short and medium terms. Considering the current study of DNA base sequences A-G-C-T and the symbolic characteristic of four symbolic dynamical systems, which are formally in good corresponding relation. In this paper we have offered an effective research means to approach problems of this kind.

SRAP analysis of DNA base sequence changes in lotus mutants induced by Fe+ implantation

Ion implantation, a new biophysically mutagenic technique, has shown great potential for crop breeding. To reveal the mutation effect of low-energy ion implantation on Baiyangdian red lotus, sequence-related amplified polymorphism markers were used to amplify and detect the DNA sequence differences in mutants induced by Fe(+) ion implantation. A total of 121 primer combinations were tested in 6 mutants and a control. Seven primer combinations (me1 + em3, me1 + em14, me9 + em3, me8 + em2, me6 + em1, me11 + em5, and me6 + em5) generated clear bands with high polymorphism and good repeatability. The results showed that among 15,317 bases cloned, 146 bases in 6 mutants were different from those of the wild type, showing a variation frequency of 0.95%. The types of base changes included deletion, insertion, transversion, and transition. Adenine was more sensitive to the irradiation than were the other bases. The results suggested that mutational "hotspots" probably exists in lotus and are induced by low-energy ion implantation.

Application of two-layer ONIOM for studying the interaction of N-substituted piperazinylfluoroquinolones with ds-DNA

The pharmacological in vitro tests of four N-substituted piperazinylfluoroquinolones (N4-P-CIPRO, N4-P-ENOX, N4-P-Nor and N4-P-Nor-Ph) pointed out that these compounds have a significant cytotoxicity activity on human ovarian carcinoma comparable to that of ciprofloxacin, norfloxacin, enoxacin and etoposide as control tests, hypothesizing that this in vitro cytotoxic activity might be due to the interaction with DNA. To evaluate this hypothesis, we used two-layered ONIOM method (DFT MPWB1K 6-31+G(d):UFF) for studying the interaction of these N-substituted piperazinyl-fluoroquinolones compounds with modeled DNA(AT-AT)2 and DNA(CG-CG)2 in gas and aqueous phases. The calculated values of the interaction energy of these compounds with DNA(AT-AT)2 and DNA(CG-CG)2 as well as with AT and CG base pairs, supported a static higher affinity toward AT compared to CG DNA base sequences. Furthermore, the results revealed that the affinity of these compounds to DNA(AT-AT)2 base pairs is as follows: N4-P-NOR-Ph>N4-P-CIPRO>N4-P-NOR>N4-P-ENOX; and for DNA(CG-CG)2 base pair: N4-P-NOR-Ph>N4-P-CIPRO>N4-P-NOR>N4-P-ENOX. We concluded that, these compounds may have one possible mode of non-covalent binding of ligands to DNA, namely minor groove binding. However, our results are in agreement with the experimentally in vitro cytotoxicity test.

Resonant Tunneling In Graphene-DNA Base-Graphene Junctions

The current-voltage characteristics in electrode-DNA-electrode system are calculated for three types of graphene electrodes: a monolayer, AA and AB bilayers. We found that AA bilayer electrodes provide higher currents in comparison with both graphene monolayer and AB bilayer thus making this material more favourable for fabrication of DNA base sequencing devices.

Mesoscopic models for DNA stretching under force: New results and comparison with experiments

Single-molecule experiments on double-stranded B-DNA stretching have revealed one or two structural transitions, when increasing the external force. They are characterized by a sudden increase of DNA contour length and a decrease of the bending rigidity. The nature and the critical forces of these transitions depend on DNA base sequence, loading rate, salt conditions and temperature. It has been proposed that the first transition, at forces of 60-80 pN, is a transition from B to S-DNA, viewed as a stretched duplex DNA, while the second one, at stronger forces, is a strand peeling resulting in single-stranded DNAs (ssDNA), similar to thermal denaturation. But due to experimental conditions these two transitions can overlap, for instance for poly(dA-dT). In an attempt to propose a coherent picture compatible with this variety of experimental observations, we derive an analytical formula using a coupled discrete worm-like chain-Ising model. Our model takes into account bending rigidity, discreteness of the chain, linear and non-linear (for ssDNA) bond stretching. In the limit of zero force, this model simplifies into a coupled model already developed by us for studying thermal DNA melting, establishing a connection with previous fitting parameter values for denaturation profiles. Our results are summarized as follows: i) ssDNA is fitted, using an analytical formula, over a nano-Newton range with only three free parameters, the contour length, the bending modulus and the monomer size; ii) a surprisingly good fit on this force range is possible only by choosing a monomer size of 0.2 nm, almost 4 times smaller than the ssDNA nucleobase length; iii) mesoscopic models are not able to fit B to ssDNA (or S to ss) transitions; iv) an analytical formula for fitting B to S transitions is derived in the strong force approximation and for long DNAs, which is in excellent agreement with exact transfer matrix calculations; v) this formula fits perfectly well poly(dG-dC) and λ-DNA force-extension curves with consistent parameter values; vi) a coherent picture, where S to ssDNA transitions are much more sensitive to base-pair sequence than the B to S one, emerges. This relatively simple model might allow one to further study quantitatively the influence of salt concentration and base-pairing interactions on DNA force-induced transitions.

Testing potential effects of maize expressing the Bacillus thuringiensis Cry1Ab endotoxin (Bt maize) on mycorrhizal fungal communities via DNA- and RNA-based pyrosequencing and molecular fingerprinting.

The cultivation of genetically modified (GM) crops has increased significantly over the last decades. However, concerns have been raised that some GM traits may negatively affect beneficial soil biota, such as arbuscular mycorrhizal fungi (AMF), potentially leading to alterations in soil functioning. Here, we test two maize varieties expressing the Bacillus thuringiensis Cry1Ab endotoxin (Bt maize) for their effects on soil AM fungal communities. We target both fungal DNA and RNA, which is new for AM fungi, and we use two strategies as an inclusive and robust way of detecting community differences: (i) 454 pyrosequencing using general fungal rRNA gene-directed primers and (ii) terminal restriction fragment length polymorphism (T-RFLP) profiling using AM fungus-specific markers. Potential GM-induced effects were compared to the normal natural variation of AM fungal communities across 15 different agricultural fields. AM fungi were found to be abundant in the experiment, accounting for 8% and 21% of total recovered DNA- and RNA-derived fungal sequences, respectively, after 104 days of plant growth. RNA- and DNA-based sequence analyses yielded most of the same AM fungal lineages. Our research yielded three major conclusions. First, no consistent differences were detected between AM fungal communities associated with GM plants and non-GM plants. Second, temporal variation in AMF community composition (between two measured time points) was bigger than GM trait-induced variation. Third, natural variation of AMF communities across 15 agricultural fields in The Netherlands, as well as within-field temporal variation, was much higher than GM-induced variation. In conclusion, we found no indication that Bt maize cultivation poses a risk for AMF.