Electrophoretic analysis of sequence variability in three mitochondrial DNA regions for ascaridoid parasites of human and animal health significance

Sequence variability in three mitochondrial DNA (mtDNA) regions, namely cytochrome c oxidase subunit 1 (cox1), NADH dehydrogenase subunits 1 and 4 (nad1 and nad4), among and within Toxocara canis, T. cati, T. malaysiensis, T. vitulorum and Toxascaris leonina from different geographical origins was examined by a mutation-scanning approach. A portion of the cox1 gene (pcox1), a portion of the nad1 and nad4 genes (pnad1 and pnad4) were amplified separately from individual ascaridoid nematodes by polymerase chain reaction and the amplicons analyzed by single-strand conformation polymorphism (SSCP). Representative samples displaying sequence variation in SSCP profiles were subjected to sequencing in order to define genetic markers for their specific identification and differentiation. While the intra-specific sequence variations within each of the five ascaridoid species were 0.2-3.7% for pcox1, 0-2.8% for pnad1 and 0-2.3% for pnad4, the inter-specific sequence differences were significantly higher, being 7.9-12.9% for pcox1, 10.7-21.1% for pnad1 and 12.9-21.7% for pnad4, respectively. Phylogenetic analyses based on the combined sequences of pcox1, pnad1 and pnad4 revealed that the recently described species T. malaysiensis was more closely related to T. cati than to T. canis. These findings provided mtDNA evidence for the validity of T. malaysiensis and also demonstrated clearly the usefulness and attributes of the mutation-scanning sequencing approach for studying the population genetic structures of these and other nematodes of socio-economic importance.     

Glycyrrhizin (Glycyrrhizic Acid) HMGB1 (high mobility group box 1) inhibitor upregulate mitochondrial function in adipocyte,cell viability and in-silico study

BackgroundMitochondrial plays a vital role in regulating obesity and related comorbidity. Targeting mitochondrial function could be a potent therapeutic approach to inhibit metabolic-related diseases like obesity, liver disease. Prolonged use of existing drug moieties demonstrated severe adverse effects.MethodsWe apply Ucp1-A-GFP immortalized reporter cell lines and HEK293T cell lines to evaluate cell viability, mitochondrial ATP production, and the in-silico model.ResultsWe found Glycyrrhizin, an HMGB1 (high mobility group box 1) inhibitor, plays a significant role in modulating mitochondrial function against obesity. At the cellular level, the adipocytes treated with Glycyrrhizin have increased mitochondrial function. Further analysis shows that compared with the control group, the cells in the treatment group contain more mitochondria. Glycyrrhizin demonstrated a nontoxic effect on the HEK293T cell line, upregulating mitochondrial DNA and reducing mitochondrial ATP production levels. In-silico study exhibited drug-protein interaction and binding side with UCP1.ConclusionGlycyrrhizin improves mitochondrial function that would be an effective drug candidate to treat metabolic diseases and obesity-related diseases. Further investigation will require both the human and animal models to reveal new insight into the mechanism against obesity, metabolic diseases or mitochondrial dysfunction-related diseases.     

Capillary electrophoresis-laser induced fluorescence analysis of endogenous damage in mitochondrial and genomic DNA

Reactive oxygen molecules are formed in vivo as by-products of normal aerobic metabolism. All organisms dependent on oxygen are inevitably exposed to these species so that DNA damage can occur in both genomic and mitochondrial DNA (mtDNA). In order to determine endogenous DNA damage we have developed an analytical method that involves the isolation and hydrolysis of genomic DNA or mtDNA, the labeling of modified and unmodified nucleotides and micellar electrokinetic chromatography with laser-induced fluorescence detection. With this method we have found etheno-adenine, thymine glycol, uracil, hypoxanthine, and 5-methylcytosine. These were identified by the addition of internal standards to the genomic or mtDNA. There are a large number of other signals in the electropherograms of mtDNA that we have never found in genomic DNA analysis because they are at lower concentration in the genome. In the DNA of untreated patients with chronic lymphocytic leukemia (CLL), uracil and high levels of etheno-adenine were found, which can be explained by antioxidant enzyme alterations and oxidative stress in the CLL lymphocytes.     

New invariant of DNA sequence based on 3DD-curves and its application on phylogeny

The Z_inv, a new invariant based on 3DD-curves of DNA sequence, which is simple for calculation and it approximates to the leading eigenvalues of the matrix associated with DNA sequence. The utility of our invariant is illustrated on the DNA sequence of 11 species. In this study, we use the Z_inv to analyze the phylogenetic relationships for the seven HA (H5N1) sequences of avian influenza virus.     

Nonisotopic single-strand conformation polymorphism analysis of sequence variability in ribosomal DNA expansion segments within the genus Trichinella (Nematoda: Adenophorea)

A nonisotopic single-strand conformation polymorphism (SSCP) approach was employed to 'fingerprint' sequence variability in the expansion segment 5 (ES5) of domain IV and the D3 domain of nuclear ribosomal DNA within and/or among isolates and individual muscle (first-stage) larvae representing all currently recognized species/genotypes of Trichinella. In addition, phylogenetic analyses of the D3 sequence data set, employing three different tree-building algorithms, examined the relationships among all of them. These analyses showed strong support that the encapsulated species T. spiralis and T. nelsoni formed a group to the exclusion of the other encapsulated species T. britovi and its related genotypes Trichinella T8 and T9 and T. murrelli, and T. nativa and Trichinella T6, and strong support that T. nativa and Trichinella T6 grouped together. Also, these eight encapsulated members grouped to the exclusion of the nonencapsulated species T. papuae and T. zimbabwensis and the three representatives of T. pseudospiralis investigated. The findings showed that nonencapsulated species constitute a complex group which is distinct from the encapsulated species and supported the current hypothesis that encapsulated Trichinella group external to the nonencapsulated forms, in accordance with independent biological and biochemical data sets.     

Cyano‐bridged Molecular Square: [Ni(iprtacn)Fe(phen)2(CN)2]2(PF6)4·6CH3CN – Preparation,Structure, Magnetic Properties and Binding with DNA

The cyano‐bridged molecular square Ni(iprtacn)]₂[Fe(phen)₂(CN)₂]₂(PF₆)₄ · 6CH₃CN ( 1 ) (iprtacn = 1,4,7‐triisopropyl‐1,4,7‐triazacyclononane, phen = 1, 10‐phenanthroline) was prepared and its crystal structure, magnetic properties, and binding with DNA were characterized. The four metal ions Ni^IIFe^IINi^IIFe^II of the complex 1 are almost coplanar. Magnetic susceptibilities measured over the range of 2–300 K show weak antiferromagnetic interactions between the two nickel(II) ions; best fitting for the experimental data leads to J = –1.27 cm^–1. UV/Vis and fluorescence spectra show that the complex is able to displace DNA‐bound EB and bind to DNA with strong interactions.     

Normal Mode Analysis on Three Different Structures of a Duplex DNA d(CGCGAATTCGCG)

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Application of a Highly Robust and Efficient Fluorescence‐Resonance‐Energy‐Transfer (FRET) System in DNA

We report a feasibility study for the application of our newly developed highly efficient and robust fluorescence‐resonance‐energy‐transfer (FRET) system to DNA. A 2′‐oligodeoxynucleotide, 12 , equipped with a quinolinone derivative as donor and a (bathophenanthroline)ruthenium(II) complex as acceptor and having a single uridine as potential cleavage site under basic conditions revealed an intensive FRET, which almost vanished after cleavage of the oligonucleotide under basic conditions (Fig. 7). Furthermore, in the arrangement of a molecular beacon (MB) DNA (see 13 ), a significant decrease of the FRET was observed after hybridization to a target sequence (Fig. 9). Due to the long decay times of the fluorescence of the Ru‐complex, the system allows for highly sensitive time‐gated measurements.     

Mutation scanning-coupled analysis of haplotypic variability in mitochondrial DNA regions reveals low gene flow between human and porcine Ascaris in endemic regions of China

Haplotypic variation within and among the Ascaris populations representing six provinces in China was investigated. Mitochondrial DNA regions in the cytochrome c oxidase subunit 1 (cox1) and NADH dehydrogenase subunit 1 (nad1) genes were amplified by PCR from total genomic DNA samples (n > 720) from Ascaris individuals from humans and pigs, and subjected to mutation scanning and subsequent selective sequencing. For the cox1, ten different electrophoretic profiles were recorded for human Ascaris, and the same number for pig Ascaris, one of them being common to both host species. For the nad1, 11 different profiles were detected for human Ascaris, and 15 for pig Ascaris. Having defined all haplotypes (20 for pcox1 and 26 for pnad1) by sequencing, their frequencies were estimated in each of the two host species and each of the six provinces. For each mitochondrial region, the frequency of the different haplotypes varied considerably, depending on host species and geographical origin. Analysis of the sequence data (representing all haplotypes for each mitochondrial locus) by F-statistics indicated restricted gene flow between human Ascaris and pig Ascaris, and supported the conclusions from previous molecular epidemiological investigations that pigs are not a significant source of Ascaris infection in humans in endemic regions.     

Theoretical study of the interaction between a high-valent manganese porphyrin oxyl-(hydroxo)-Mn(IV)-TMPyP and double-stranded DNA

Cationic porphyrin derivatives such as meso-tetrakis(4-N-methylpyridinium)porphyrin, TMPyP, have been shown to interact with double-stranded DNA. The manganese derivative, Mn(III)-TMPyP, activated by an oxygen donor like potassium monopersulfate, provides an efficient DNA-cleaving system. Previous experimental work1 has shown that DNA cleavage by the Mn(III)-TMPyP/KHSO(5) system was due to an oxidative attack, within the minor groove of B-DNA, at the C5' or C1' carbons of deoxyribose units. The aim of this study was to use molecular modeling to elucidate the specificity of the interactions between the transient active species oxyl-Mn(IV)-TMPyP and the DNA target. Geometric parameters, charges, and force field constants consistent with the AMBER 98 force field were calculated by DFT methods. Molecular modeling (mechanics and dynamic simulations) were performed for oxyl-(hydroxo)-Mn(IV)-TMPyP bound in the minor groove of the dodecamer d(5'-TCGTCAAACCGC)-d(5'-GCGGTTTGACGA). Geometry, interactions, and binding energy of the metalloporphyrin located at the A.T triplet region of the dodecamer were analyzed. These studies show no significant structural change of the DNA structure upon ligand binding. Mobility of the metalloporphyrin in the minor groove was restrained by the formation of a hydrogen bond between the hydroxo ligand trans to the metal-oxyl and a DNA phosphate, restricting the access of the oxyl group to the (pro-S) H atom at C5'.     

Ag(I) ion mediated formation of a C-A mispair by DNA polymerases

Silver turns up the A-C: In the presence of Ag(I) ions, a DNA polymerase incorporated deoxyadenosine (from dATP) at the site opposite cytosine in the template strand to afford the full-length product (see scheme), meaning that DNA polymerases prefer a C-Ag(I)-A base pair to the more thermodynamically stable C-Ag(I)-C base pair.     

Sequence‐specific nucleic acid mobility using a reversible block copolymer gel matrix and DNA amphiphiles (lipid‐DNA) in capillary and microfluidic electrophoretic separations

Reversible noncovalent but sequence‐dependent attachment of DNA to gels is shown to allow programmable mobility processing of DNA populations. The covalent attachment of DNA oligomers to polyacrylamide gels using acrydite‐modified oligonucleotides has enabled sequence‐specific mobility assays for DNA in gel electrophoresis: sequences binding to the immobilized DNA are delayed in their migration. Such a system has been used for example to construct complex DNA filters facilitating DNA computations. However, these gels are formed irreversibly and the choice of immobilized sequences is made once off during fabrication. In this work, we demonstrate the reversible self‐assembly of gels combined with amphiphilic DNA molecules, which exhibit hydrophobic hydrocarbon chains attached to the nucleobase. This amphiphilic DNA, which we term lipid‐DNA, is synthesized in advance and is blended into a block copolymer gel to induce sequence‐dependent DNA retention during electrophoresis. Furthermore, we demonstrate and characterize the programmable mobility shift of matching DNA in such reversible gels both in thin films and microchannels using microelectrode arrays. Such sequence selective separation may be employed to select nucleic acid sequences of similar length from a mixture via local electronics, a basic functionality that can be employed in novel electronic chemical cell designs and other DNA information‐processing systems.     

DNA binding and nuclease activity of cationic iron(IV) and manganese(III) corrole complexes

Cationic meso(4‐N‐methylpyridyl)‐based metallocorroles, μ‐oxo iron corrole dimer ( 1b ) and manganese corrole monomer ( 2b ), were synthesized and characterized. The interactions of these two metal corrole complexes with CT‐DNA were studied by UV–visible, fluorescence and circular dichroism spectroscopic methods, as well as by viscosity measurements. The results revealed that 1b interacts with CT‐DNA in a difunctional binding mode, i.e. non‐classical intercalation and outside groove binding with H‐aggregation, while 2b can interact with CT‐DNA via an outside groove binding mode only. The binding constants K_b of 1b and 2b were 4.71 × 10⁵ m ^?1 and 2.17 × 10⁵ m ^?1, respectively, indicating that 1b can bind more tightly to CT‐DNA than 2b . Furthermore, both complexes may cleave the supercoiled plasmid DNA efficiently in the presence of hydrogen peroxide or tert‐butyl hydroperoxide (TBHP), albeit 1b exhibited a little higher efficiency. The inhibitor tests suggested that singlet oxygen and high‐valent (oxo)iron(VI) corrole or (oxo)manganese(V) corrole might be the active intermediates responsible for the oxidative DNA scission. Copyright © 2014 John Wiley & Sons, Ltd.     

Solution Structure of a Parallel-Stranded Oligoisoguanine DNA Pentaplex Formed by d(T(iG)(4) T) in the Presence of Cs(+) Ions

What a pentaplexing situation: Isoguanine (iG) is an isomer of guanine, where the positions of the C2 amino group and the C6 carboxy group are swapped. iG can self-assemble into pentads in the presence of alkali metal cations. Cs(+) ions were found to stabilize a pentaplex of d(T(iG)(4) T). Solution NMR studies of this pentaplex in the presence of Cs(+) ions (or Na(+) , K(+) , Rb(+) , or NH(4) (+) cations) demonstrate its stability and structure.     

Thread Insertion of a Bis(dipyridophenazine) Diruthenium Complex into the DNA Double Helix by the Extrusion of AT Base Pairs and Cross‐Linking of DNA Duplexes

The crystal structure of the Δ,Δ enantiomer of the binuclear “light‐switch” ruthenium complex [μ‐(11,11′‐bidppz)(1,10‐phenanthroline)₄ Ru₂]⁴⁺ bound to the oligonucleotide d(CGTACG) shows that one dppz moiety of the dumbbell‐like compound inserts into the DNA stack through the extrusion of an AT base pair. The second dppz moiety recruits a neighboring DNA molecule, and the complex thus cross‐links two adjacent duplexes by bridging their major grooves.     

Biomethylation and biotransformation of arsenic in a freshwater food chain: Green alga (chlorella vulgaris)→shrimp (neocaridina denticulata)→killifish (oryzias iatipes)

Tolerance, bioaccumulation, biotransformation and excretion of arsenic compounds by the fresh–water shrimp (Neocaridina denticulata) and the killifish (Oryzias latipes) (collected from the natural environment) were investigated. Tolerances (LC₅₀) of the shrimp against disodium arsenate [abbreviated as As(V)], methylarsonic acid (MAA), dimethylarsinic acid (DMAA), and arsenobetaine (AB) were 1.5, 10, 40, and 150μg As ml^?1, respectively. N. denticulata accumulated arsenic from an aqueous phase containing 1 μg As ml^?1 of As(V), 10 μg As ml^?1 of MAA, 30 μg As ml^?1 of DMAA or 150 μg As ml^?1 of AB, and biotransformed and excreted part of these species. Both methylation and demethylation of the arsenicals were observed in vivo. When living N. denticulata accumulating arsenic was transferred into an arsenic–free medium, a part of the accumulated arsenic was excreted. The concentration of methylated arsenicals relative to total arsenic was higher in the excrement than in the organism. Total arsenic accumulation in each species via food in the food chain Green algae (Chlorella vulgaris) → shrimp (N. denticulata) → killifish (O. latipes) decreased by one order of magnitude or more, and the concentration of methylated arsenic relative to total arsenic accumulated increased successively with elevation in the trophic level. Only trace amounts of monomethylarsenic species were detected in the shrimp and fish tested. Dimethylarsenic species in alga and shrimp, and trimethylarsenic species in killifish, were the predominant methylated arsenic species, respectively.