Double-stranded Fragments Research Articles

Differential effects of purified low molecular weight Poly(I:C) in the maternal immune activation model depend on the laboratory environment

The Poly (I:C) (polyriboinosinic-polyribocytidilic acid) paradigm of maternal immune activation (MIA) is most widely used as experimental model for the evaluation of the effects of gestational infection on the brain and behavior of the progeny. We have previously reported significant batch-to-batch variability in the effects of Poly (I:C), purchased from the same supplier (Sigma–Aldrich), on maternal and fetal immune responses and found these differences to be dependent on the relative amount of synthetic double-stranded RNA fragments in the high versus low molecular weight (LMW) range contained in the compound. We here resorted to Poly (I:C) purified for LMW dsRNA fragments to establish a MIA paradigm with increased reproducibility and enhanced standardization in an effort to refine the MIA paradigm and characterize its effect on offspring behavior. We found that the parallel application of LMW Poly (I:C) in two different MIA-experienced laboratories (Vienna and Zurich) yielded differential outcomes in terms of maternal immune responses and behavioral phenotypes in the offspring generation. In both experimental sites, administration of LMW Poly (I:C) induced a significant sickness response and cytokine induction in the pregnant dam and fetal brains, while the expected deficit in sociability as one main behavioral outcome parameter in the MIA progeny, was only present in the Zurich, but not the Vienna cohort. We conclude that although using Poly (I:C) purified for a defined molecular weight range reduces batch-to-batch variability, it does not make the MIA model more reliable and robust. The differential response in behavioral phenotypes of the MIA offspring between the two laboratories illustrates the highly complex interaction between prenatal and postnatal milieus - including the laboratory environment - that determine offspring phenotypic outcomes after MIA. Consequently, establishing a new MIA protocol or implementing the MIA model firstly under new or changed environmental conditions must include the assessment of offspring behavior to ensure solid and reproducible experimental outcomes.

P-082 Use of TetraSOD® in male infertility: double-blind randomized placebo-controlled study

Abstract Study question Can the use of TetraSOD® (microalgae with high content of the antioxidant enzyme superoxide dismutase) improve semen quality and reduce oxidative stress in sperm? Summary answer The use of TetraSOD® reduces the oxidative stress of sperm, increasing the total sperm count in oligozoospermia and reducing the double-stranded DNA sperm fragmentation. What is known already Male factor is present in approximately 50% of the infertile couples, a large number of them of unknown or idiopathic origin. It has been demonstrated that semen quality is deteriorating over time, perhaps as a result of exposure to several environmental factors related with lifestyle that could impact both directly and indirectly on the complex process of spermatogenesis. Some of these bad habits of lifestyle increase the levels of oxidative stress in semen, which is associated with lower sperm concentration and motility. In this scenario, the use of antioxidants can be useful to increase sperm quality. Study design, size, duration Double-blind randomized placebo-controlled clinical study to assess the effect of 250 mg of TetraSOD® (microalgae with high content of the primary antioxidant enzyme superoxide dismutase). Eighty patients with idiopathic infertility showing asthenozoospermia, oligozoospermia or oligoasthenozoospermia were recruited and randomized to receive 250 mg of TetraSOD® (TSOD group) or placebo (Placebo group) for 3 months. Participants/materials, setting, methods Men with asthenozoospermia, oligozoospemia or aligoastenozoospermia and idiopatic infertility were recruited after informed consent signature. Patients were randomized into two groups. TetraSOD® group received 250 mg of TetraSOD®during 3 months, and Placebo group received capsules without TetraSOD® during the same period of time. Seminogram, double-strand sperm DNA fragmentation (COMET assay) and sORP (static oxidation- reduction potential) were studied at baseline (V0) and after 3 months (V3). Main results and the role of chance TetraSOD® consumption for three months elicited a statistically significant increase (Wilcoxon matched-pairs signed rank test; p=0.02) in the average number of sperms per ejaculate (from 17.06 x 106 to 41.94 x 106) in participants displaying oligozoospermia (<39 x 106 sperms) at V0. In contrast, the lower variation in the measured values in the Placebo group was not statistically significant. Regarding sORP, a statistically significant decrease (Wilcoxon matched-pairs signed rank test; p=0.0233) was observed in participants who displayed a value at V0 between 1.34-10. After TetraSOD® consumption, the average changed from 2.96 to 1.91 mv/106 sperm/ml from V0 to V3. However, not statistically significant changes were detected in the Placebo group between sORP values at V0 and V3. Moreover, in relation to double-stranded DNA breaks, a statistically significant decrease (Wilcoxon matched-pairs signed rank test; p=0.01) in the average percentages (from 31.81% to 25.93%) was measured after consumption of TetraSOD® at V3 in participants displaying a compromised redox status (sORP>1.34-10) at V0. No significant changes were found in the Placebo group. Limitations, reasons for caution The study was performed only in one ethnic group, so in future studies other ethnicities should be included. Wider implications of the findings TetraSOD® may improve male fertility because increases the number of sperms per ejaculate in oligozoospermia and reduces double-stranded DNA fragmentation in sperm when individuals display an altered redox status in semen. Such results might be related to the indirect antioxidant effect of TetraSOD®, reducing oxidative stress in seminal fluid. Trial registration number Not applicable

Diversity of RNA viruses in the cosmopolitan monoxenous trypanosomatid Leptomonas pyrrhocoris

BackgroundTrypanosomatids are parasitic flagellates well known because of some representatives infecting humans, domestic animals, and cultural plants. Many trypanosomatid species bear RNA viruses, which, in the case of human pathogens Leishmania spp., influence the course of the disease. One of the close relatives of leishmaniae, Leptomonas pyrrhocoris, has been previously shown to harbor viruses of the groups not documented in other trypanosomatids. At the same time, this species has a worldwide distribution and high prevalence in the natural populations of its cosmopolitan firebug host. It therefore represents an attractive model to study the diversity of RNA viruses.ResultsWe surveyed 106 axenic cultures of L. pyrrhocoris and found that 64 (60%) of these displayed 2–12 double-stranded RNA fragments. The analysis of next-generation sequencing data revealed four viral groups with seven species, of which up to five were simultaneously detected in a single trypanosomatid isolate. Only two of these species, a tombus-like virus and an Ostravirus, were earlier documented in L. pyrrhocoris. In addition, there were four new species of Leishbuviridae, the family encompassing trypanosomatid-specific viruses, and a new species of Qinviridae, the family previously known only from metatranscriptomes of invertebrates. Currently, this is the only qinvirus with an unambiguously determined host. Our phylogenetic inferences suggest reassortment in the tombus-like virus owing to the interaction of different trypanosomatid strains. Two of the new Leishbuviridae members branch early on the phylogenetic tree of this family and display intermediate stages of genomic segment reduction between insect Phenuiviridae and crown Leishbuviridae.ConclusionsThe unprecedented wide range of viruses in one protist species and the simultaneous presence of up to five viral species in a single Leptomonas pyrrhocoris isolate indicate the uniqueness of this flagellate. This is likely determined by the peculiarity of its firebug host, a highly abundant cosmopolitan species with several habits ensuring wide distribution and profuseness of L. pyrrhocoris, as well as its exposure to a wider spectrum of viruses compared to other trypanosomatids combined with a limited ability to transmit these viruses to its relatives. Thus, L. pyrrhocoris represents a suitable model to study the adoption of new viruses and their relationships with a protist host.

Steroid receptor coactivator TAIMAN is a new modulator of insect circadian clock.

TAIMAN (TAI), the only insect ortholog of mammalian Steroid Receptor Coactivators (SRCs), is a critical modulator of ecdysone and juvenile hormone (JH) signaling pathways, which govern insect development and reproduction. The modulatory effect is mediated by JH-dependent TAI's heterodimerization with JH receptor Methoprene-tolerant and association with the Ecdysone Receptor complex. Insect hormones regulate insect physiology and development in concert with abiotic cues, such as photo- and thermoperiod. Here we tested the effects of JH and ecdysone signaling on the circadian clock by a combination of microsurgical operations, application of hormones and hormone mimics, and gene knockdowns in the linden bug Pyrrhocoris apterus males. Silencing taiman by each of three non-overlapping double-strand RNA fragments dramatically slowed the free-running period (FRP) to 27-29 hours, contrasting to 24 hours in controls. To further corroborate TAIMAN's clock modulatory function in the insect circadian clock, we performed taiman knockdown in the cockroach Blattella germanica. Although Blattella and Pyrrhocoris lineages separated ~380 mya, B. germanica taiman silencing slowed the FRP by more than 2 hours, suggesting a conserved TAI clock function in (at least) some insect groups. Interestingly, the pace of the linden bug circadian clock was neither changed by blocking JH and ecdysone synthesis, by application of the hormones or their mimics nor by the knockdown of corresponding hormone receptors. Our results promote TAI as a new circadian clock modulator, a role described for the first time in insects. We speculate that TAI participation in the clock is congruent with the mammalian SRC-2 role in orchestrating metabolism and circadian rhythms, and that TAI/SRCs might be conserved components of the circadian clock in animals.

P-053 Sperm aneuploidy and DNA integrity pre- and post-chemotherapy in men with testicular cancer

Abstract Study question Are fragmentation levels (single-double stranded DNA breaks) or aneuploidy frequencies in sperm increased in patients with testicular cancer who recovered spermatogenesis after chemotherapy (CT)? Summary answer Similar levels of sperm DNA fragmentation and sperm aneuploidy frequency are found in men with testicular cancer pre- and post-chemotherapy. What is known already Testicular cancer is the most frequent solid tumor among young men. Therefore, the restoration of fertility and achievement of fatherhood in survivors have become important concerns. The integrity of genetic material in sperm is crucial since some paternal genes are essential for early embryo development. Although previous studies analyzed the effect of CT on sperm DNA integrity, they did not differentiate single vs. double-stranded DNA breaks. Few data are available on aneuploidy in sperm from testicular cancer survivors, so it remains to be elucidated whether cancer treatments may lead to an increased risk of aneuploidy syndromes in offspring. Study design, size, duration Prospective multicenter study including 31 males with a history of testicular cancer who requested semen cryopreservation between 2007-2021. All patients included underwent CT and recovered spermatogenesis once treatment ended. Post-CT samples were collected and seminal parameters, single-double stranded DNA breaks and the proportion of sperm aneuploidies were compared with one aliquot of the initial ejaculate. The project was approved by an Institutional Review Board and written informed consent for participation was obtained from each subject. Participants/materials, setting, methods Patient´s age prior CT was 31.23yrs (IC 95%: 29.29-33.17). Mean interval time between 1st and 2nd samples was 4.53yrs (IC 95%: 3.42-5.64). TUNEL quantified overall sperm DNA fragmentation by flow cytometry analyzing at least 20,000 cells, while γH2AX staining was applied for double DNA fragmentation assessment. Sperm aneuploidies were calculated by using fluorescence in situ hybridization (FISH) probes for chromosomes 13, 18, 21, X, Y. A paired t-test was used to compare variables pre- and post-CT. Main results and the role of chance Similar results were found when sperm quality parameters were compared. Mean sperm concentration pre-CT was 33.03M/mL (IC 95%: 23.98-42.07) and 36.41 M/mL (IC 95%: 27.85-44.96) in post-CT ejaculates (N.S.). A comparable rate of motile spermatozoa was observed in pre-CT vs. post-CT samples [(43.81% (IC 95%: 38.42-49.19) vs. 44.73% (IC 95%: 38.95-50.51), N.S.]. Regarding TUNEL assay results, the sperm DNA fragmentation rate was 21.65% (IC 95%: 17.66-25.63) in pre-CT samples and 23.00% (IC 95%: 19.90-26.61) in post-CT samples (N.S.). Furthermore, similar results were obtained when double-stranded fragmentation levels (H2AX) were compared between pre and post-CT [10.2% (IC 95%: 6.45-13.96) vs. 12.44% (IC 95%: 8.75-16.13) N.S.]. Comparable sperm disomic proportions were found in PRE and POST-CT samples: [(Cr.13 =0.02%, Cr.18 =0.01%, Cr.21=0.30%, Cr.XY=0.84%) vs. (Cr.13 =0%, Cr.18 =0%, Cr.21=0%, Cr.XY=0.33%), N.S]. Results were also evaluated according to the time elapsed between the PRE and POST -CT samples. No significant differences were found for seminal values (sperm concentration, p = 0.26; motility, p = 0.68), overall sperm DNA fragmentation (p = 0.68), double-strand DNA fragmentation (p = 0.90) and the frequency of sperm disomies (Cr. 13 p = 0.79, Cr.18 p = 0.46, Cr. 21 p = 0.85, Cr.XY p = 0.05). Limitations, reasons for caution The main limitations of the present study are that we only recruited patients who recovered spermatogenesis and that our data evaluated a long-term effect of CT. Wider implications of the findings All men wishing to have their own children after gonadotoxic treatment should receive adequate counseling about the side effects of the therapy. Based on our results on sperm DNA integrity and euploidy, patients who recovered spermatogenesis should not be advised to use samples that were preserved before undergoing CT. Trial registration number na

Oxidative probing of the G4 DNA structure induced in double-stranded DNA by molecular crowding or pyridostatin

Major advances have been made recently in the application of the highly selective G4 DNA ligand pyridostatin (PDS) for targeting and visualization of this noncanonical DNA structure in eukaryotic genomes. However, the interaction of PDS with the G4 structure constrained by double-stranded DNA has not yet been analyzed. Here, we induced folding of G4 structures in double-stranded DNA promoter fragments of several oncogenes by annealing the DNA under molecular crowding conditions created by polyethylene glycol (PEG) or in the presence of PDS. Both PEG and PDS induced similar DNA folding, as demonstrated by gel mobility assays and S1 nuclease cleavage. The cationic porphyrin derivative ZnP1 was used to probe the G4 structure in both conditions and thus provided with “footprint” of PDS. The PEG-stabilized G4 structure was susceptible to photo-induced oxidation by ZnP1 and tended to revert to a duplex after oxidation. Guanines in the 5′-tetrad were the most accessible to ZnP1 and became protected from oxidation upon binding of PDS which prevented the G4 structure from rearranging into a double helix. The study demonstrates the applicability of porphyrin ZnP1 for the probing of G4 structures in the genomic context and footprinting of G4 specific ligands.

History and main directions of research on plant protection in the Nikitsky Botanical Gardens

The article provides information on the history of the creation and development of the Department of plant protection in the Nikitsky Botanical Gardens and the results of modern theoretical and applied research on the protection of native and introduced plants for 2000-2020. The main concepts, directions and methods in the development of integrated plant protection systems for fruit and park plantations are considered. There are five stages in solving the main task of plant protection-the rational management of the phytosanitary state of agrobiocenoses: 1. use of agrotechnical methods of control, including mechanical destruction of phytophages; 2. chemical method of plant protection using polytoxic broad-spectrum pesticides; 3. integrated control in the form of the concept of a reduced treatment scheme, taking into account the economic thresholds of abundance and harmfulness and combining all existing methods of control; 4. managing the growth of populations of harmful organisms using biologically active substances of the information type according to integrated indicators; 5. development of a post-genomic approach to limiting the number of phytophages, based on the use of fragments of natural polymers of nucleic acids, development of contact DNA insecticides based on short antisense fragments of genes, as well as preparations based on double-stranded RNA fragments. Modern research has a high theoretical and applied significance for the development of integrated protection systems for fruit, ornamental, and forest crops in the Russian Federation and Crimea. It allows us to objectively assess the phytosanitary state of the garden and park agrobiocenosis, identify the dominant types of pathogens and pests, predict their development trends, and select environmentally safe, cost-effective methods for controlling their numbers.

Effect of 3-subsitution of quinolinehydroxamic acids on selectivity of histone deacetylase isoforms

A series of 3-subsituted quinolinehydroxamic acids has been synthesised and evaluated for their effect on human lung cancer cell line (A549), human colorectal cancer cell line (HCT116) and HDAC isoforms 1, 2, 6, and 8. The results indicated that substitution at C3 of quinoline is favoured for HDAC6 selectivity. Two compounds (25 and 26) were also found to be potent anti-proliferative compounds with IC50 values ranging from 1.29 to 2.13 µM against A549 and HCT116 cells. These compounds displayed remarkable selectivity for HDAC6 over other HDAC isoforms with nanomolar IC50 values. Western blot analysis revealed that compounds of this series activate apoptotic caspase pathway as indicated by cleavage of caspase 3, 8, and 9 and also increase phosphorylated H2AX thus inducing DNA double strand fragmentation in a concentration dependent manner. Flow cytometric analysis also displayed a dose dependent increase of cell population in sub G1 phase.

Influence of Sieving Polymer Concentration and Applied Voltage on Separation Accuracy of the Capillary Gel Electrophoresis for Small DNA Fragments

In this study, measurement conditions of Capillary gel electrophoresis (CGE) were optimized in order to increase the separation accuracy for small DNA fragments. We adopted a 20-bp DNA Ladder including 13 small double-stranded fragments (20, 40, 60, 80, 100, 120, 140, 160, 180, 200, 300, 400, and 500-bp). The applied voltage and sieving polymer concentration were assessed because these two factors significantly affect the separation accuracy of DNA fragments. As a result, we succeeded in optimizing CGE separation conditions for small DNA fragments with a sufficient degree of accuracy.

Silencing Dicer-Like Genes Reduces Virulence and sRNA Generation in Penicillium italicum, the Cause of Citrus Blue Mold.

The Dicer protein is one of the most important components of RNAi machinery because it regulates the production of small RNAs (sRNAs) in eukaryotes. Here, Dicer1-like gene (Pit-DCL1) and Dicer2-like gene (Pit-DCL2) RNAi transformants were generated via pSilent-1 in Penicillium italicum (Pit), which is the causal agent of citrus blue mold. Neither transformant showed a change in mycelial growth or sporulation ability, but the pathogenicity of the Pit-DCL2 RNAi transformant to citrus fruits was severely impaired, compared to that of the Pit-DCL1 RNAi transformant and the wild type. We further developed a citrus wound-mediated RNAi approach with a double-stranded fragment of Pit-DCL2 generated in vitro, which achieved an efficiency in reducing Pi-Dcl2 expression and virulence that was similar to that of protoplast-mediated RNAi in P. italicum, suggesting that this approach is promising in the exogenous application of dsRNA to control pathogens on the surface of citrus fruits. In addition, sRNA sequencing revealed a total of 69.88 million potential sRNAs and 12 novel microRNA-like small RNAs (milRNAs), four of which have been predicated on target innate immunity or biotic stress-related genes in Valencia orange. These data suggest that both the Pit-DCL1 and Pit-DCL2 RNAi transformants severely disrupted the biogenesis of the potential milRNAs, which was further confirmed for some milRNAs by qRT-PCR or Northern blot analysis. These data suggest the sRNAs in P. italicum that may be involved in a molecular virulence mechanism termed cross-kingdom RNAi (ck-RNAi) by trafficking sRNA from P. italicum to citrus fruits.

A new DNA-based model for finite field arithmetic

A Galois field GF(pn) with p≥2 a prime number and n≥1 is a mathematical structure widely used in Cryptography and Error Correcting Codes Theory. In this paper, we propose a novel DNA-based model for arithmetic over GF(pn). Our model has three main advantages over other previously described models. First, it has a flexible implementation in the laboratory that allows the realization arithmetic calculations in parallel for p≥2, while the tile assembly and the sticker models are limited to p=2. Second, the proposed model is less prone to error, because it is grounded on conventional Polymerase Chain Reaction (PCR) amplification and gel electrophoresis techniques. Hence, the problems associated to models such as tile-assembly and stickers, that arise when using more complex molecular techniques, such as hybridization and denaturation, are avoided. Third, it is simple to implement and requires 50 ng/μL per DNA double fragment used to develop the calculations, since the only feature of interest is the size of the DNA double strand fragments. The efficiency of our model has execution times of order O(1) and O(n), for the addition and multiplication over GF(pn), respectively. Furthermore, this paper provides one of the few experimental evidences of arithmetic calculations for molecular computing and validates the technical applicability of the proposed model to perform arithmetic operations over GF(pn).

Use of synthesized double-stranded gene fragments as qPCR standards for the quantification of antibiotic resistance genes

Pollution of various environmental matrices by antibiotic resistance genes (ARGs) has become a growing threat to human health. For the quantitative analysis of the presence of ARGs, there is a need for sensitive and robust qPCR assays which can detect various genes from different types of DNA extracts. Fourteen ARGs were selected as target genes in this study including: blaTEM, blaOXA-1 and blaCTX-M coded for resistance to β-lactams; ermB for macrolides; tetA, tetG, tetM, tetQ, tetW and tetX for tetracyclines; sul I and sul II for sulfonamides; drfA1 and drfA12 d for trimethoprim; and integron gene intI 1 and intI 2. Chemically synthesized double-stranded gene fragments were modified using molecular biology methods and used as real-time PCR standards as well as to establish in-house qPCR assays. The ermB gene from a naturally occurring plasmid was used to compare the performance of qPCR assay with the chemically synthesized ermB. Additionally, environmental water, soil and faeces samples were used to validate the established qPCR assays. Importantly, the study proves the usefulness of rapidly synthesized oligonucleotides serving as qPCR standards for ARG analysis and provides comparable sensitivity and reliability to a traditional amplicon standard.

Theory of tailor automata

In the paper, a fragment of the new theory of tailor automata is presented, within which a deterministic finite automaton was defined. The proposed automaton provides a theoretical model of an informally characterized biomolecular automaton. The idea of working of which is founded on the concept of alternating cut of some double-stranded fragments of DNA, with the use of a restriction enzyme and ligations of some double-stranded fragments of DNA, with the use of the ligase enzyme.

Expression of Human VH Single Domains as Fc Fusions in Mammalian Cells.

Single-domain antibodies represent an emerging class of antibody fragments with promising therapeutic and diagnostic potential. As a result, multiple strategies have been developed in order to improve their biophysical and/or biological properties. In particular, the fusion of single-domain antibodies to the Fc part of an IgG molecule has become a common protein engineering approach toward this aim. Here, we describe a detailed protocol for a streamlined laboratory-scale production of VH single-domain antibodies as Fc fusions in mammalian cells. Firstly, DNA sequence encoding VH domain of interest fused to an IgG Fc is synthesized as a double-stranded gene fragment. Secondly, the DNA fragment is directly assembled into a restriction enzyme-digested vector in an assembly reaction. Finally, vector carrying the VH-Fc-fusion construct is introduced into suspension-adapted mammalian cells for transient expression of the Fc chimeric fusion. One-week post-transfection, the expressed Fc-fusion protein is purified using protein A/G affinity chromatography. Using this protocol, we were able to clone, express, and purify milligrams of isolated anti-HER2 VH domain as a mouse IgG2c Fc fusion in less than 2weeks. This protocol can be readily modified to express proteins of interest other than VH domains as Fc fusions.

In vitro acellular method to reveal O-fucosylation on EGF-like domains.

A hundred of human proteins have one or more EGF-like domains (EGF-LD) bearing the O-fucosylation consensus motif C2X4(S/T)C3 but to date, only a few of them have been shown to be O-fucosylated. The protein O-fucosyltransferase (POFUT1) specifically recognizes correctly folded EGF-LD of the human EGF (hEGF) type and transfers fucose on serine or threonine residue within the O-fucosylation motif. Here, we propose a strategy for a rapid screening for ability of any EGF-LD to be O-fucosylated, using copper-catalyzed azide-alkyne cycloaddition (CuAAC). By an oligonucleotide hybridization approach, double-stranded fragments encoding any EGF-LD can be first rapidly cloned into the prokaryotic vector pET-25b to promote its targeting to periplasm and formation of the three conserved disulfide bonds. After protein production and purification, an in vitro POFUT1-mediated O-fucosylation can be performed with azido GDP-fucose. Successful transfer of O-fucose is finally revealed by blotting technique after CuAAC. In this study, we specially focused on mouse NOTCH1 EGF12 and EGF26, which are both known to be O-fucosylated although having different binding affinities towards POFUT1. Indeed, we clearly showed here that addition of O-fucose by POFUT1 was much more efficient for EGF26 than for EGF12. This experimental approach is rapid and sufficiently sensitive to reveal propensity of any EGF-LD to be O-fucosylated; it is thus useful prior to perform structure-function studies on target proteins containing one or several EGF-LD.

Genomic characterization, phylogenetic position and in situ localization of a novel putative mononegavirus in Lepeophtheirus salmonis

The complete genome sequence of a novel mononegavirus, Lepeophtheirus salmonis negative-stranded RNA virus 1 (LsNSRV-1), obtained from a salmonid ectoparasite, Lepeophtheirus salmonis was determined. The viral genome contains five open reading frames encoding three unknown proteins (ORF I, II and III), a putative glycoprotein (G), and a large (L) protein. Phylogenetic analysis placed LsNSRV-1 in the recently established mononegaviral family Artoviridae. LsNSRV-1 showed a prevalence of around 97% and was detected in all L. salmonis developmental stages. Viral genomic and antigenomic RNA was localized to nerve tissue, connective tissue, epithelial cells of the gut, subepidermal tissue, exocrine and cement glands, as well as the testis, vas deferens and spermatophore sac of male L. salmonis and the ovaries and oocytes of females. Viral RNA was detected in both the cytoplasm and the nucleoli of infected cells, and putative nuclear export and localization signals were found within the ORF I, III and L proteins, suggesting nuclear replication of LsNSRV-1. RNA interference (RNAi) was induced twice during development by the introduction of a double-stranded RNA fragment of ORF I, resulting in a transient knockdown of viral RNA. A large variation in the knockdown level was seen in adult males and off springs of knockdown animals, whereas the RNA level was more stable in adult females. Together with the localization of viral RNA within the male spermatophore and female oocytes and the amplification of viral RNA in developing embryos, this suggests that LsNSRV-1 is transmitted both maternally and paternally. Small amounts of viral RNA were detected at the site where chalimi were attached to the skin of Atlantic salmon (Salmo salar). However, as the RNAi-mediated treatment did not result in LsNSRV-1-negative offspring and the virus failed to replicate in the tested fish cell cultures, it is difficult to investigate the influence of secreted LsNSRV-1 on the salmon immune response.

DNA nanostructures from palindromic rolling circle amplification for the fluorescent detection of cancer-related microRNAs

Herein, DNA nanostructures were prepared via a palindromic padlock probe-based rolling circle amplification (called P-RCA) and then employed to implement the sensitive and specific detection of let-7a miRNA extracted from cancer cells without chemical modification. The presence of target let-7a miRNA as a polymerization primer can trigger the P-RCA process, generating a long tandemly repetitive DNA strand. The resulting products can fold into nanostructures via self-hybridization of palindromic regions and possess numerous double-stranded fragments. In this case, the strong fluorescent signal is detected upon exposure to SYBR Green I. As a result, in homogeneous solution, target miRNA can be detected down to 6.4 pM with a wide dynamic range. A high specificity was demonstrated by the excellent discrimination between let-7 miRNA family members, while the applicability of this sensing system in complex biological environments was confirmed by the analysis of target miRNAs extracted from HeLa cells. It should be noted that increasing numbers of palindromic fragments in padlock probe further increases signal amplification efficiency. The experimental results indicate that the newly proposed P-RCA DNA nanostructures have potential to become a promising analytical platform in biomedical research and clinical diagnosis for the miRNA detection with high sensitivity and good specificity.

Ultrasonic Footprinting

Ligand binding influences the dynamics of the DNA helix in both the binding site and adjacent regions. This, in particular, is reflected in the changing pattern of cleavage of complexes under the action of ultrasound. The specificity of ultrasound-induced cleavage of the DNA sugar-phosphate backbone was studied in actinomycin D (AMD) complexes with double-stranded DNA restriction fragments. After antibiotic binding, the cleavage intensity of phosphodiester bonds between bases was shown to decrease at the chromophore intercalation site and to increase in adjacent positions. The character of cleavage depended on the sequences flanking the binding site and the presence of other AMD molecules bound in the close vicinity. A comparison of ultrasonic and DNase I cleavage patterns of AMD-DNA complexes provided more detail on the local conformation and dynamics of the DNA double helix in both binding site and adjacent regions. The results pave the way for developing a novel approach to studies of the nucleotide sequence dependence of DNA conformational dynamics and new techniques to identify functional genome regions.

A Biofunctional Molecular Beacon for Detecting Single Base Mutations in Cancer Cells.

The development of a convenient and sensitive biosensing system to detect specific DNA sequences is an important issue in the field of genetic disease therapy. As a classic DNA detection technique, molecular beacon (MB) is often used in the biosensing system. However, it has intrinsic drawbacks, including high assay cost, complicated chemical modification, and operational complexity. In this study, we developed a simple and cost-effective label-free multifunctional MB (LMMB) by integrating elements of polymerization primer, template, target recognition, and G-quadruplex into one entity to detect target DNA. The core technique was accomplished by introducing a G-hairpin that features fragments of both G-quadruplex and target DNA recognition in the G-hairpin stem. Hybridization between LMMB and target DNA triggered conformational change between the G-hairpin and the common C-hairpin, resulting in significant SYBR-green signal amplification. The hybridization continues to the isothermal circular strand-displacement polymerization and accumulation of the double-stranded fragments, causing the uninterrupted extension of the LMMB without a need of chemical modification and other assistant DNA sequences. The novel and programmable LMMB could detect target DNA with sensitivity at 250 pmol/l with a linear range from 2 to 100 nmol/l and the relative standard deviation of 7.98%. The LMMB could sense a single base mutation from the normal DNA, and polymerase chain reaction (PCR) amplicons of the mutant-type cell line from the wild-type one. The total time required for preparation and assaying was only 25 minutes. Apparently, the LMMB shows great potential for detecting DNA and its mutations in biosamples, and therefore it opens up a new prospect for genetic disease therapy.

The exonuclease activity of DNA polymerase γ is required for ligation during mitochondrial DNA replication.

Mitochondrial DNA (mtDNA) polymerase γ (POLγ) harbours a 3′–5′ exonuclease proofreading activity. Here we demonstrate that this activity is required for the creation of ligatable ends during mtDNA replication. Exonuclease-deficient POLγ fails to pause on reaching a downstream 5′-end. Instead, the enzyme continues to polymerize into double-stranded DNA, creating an unligatable 5′-flap. Disease-associated mutations can both increase and decrease exonuclease activity and consequently impair DNA ligation. In mice, inactivation of the exonuclease activity causes an increase in mtDNA mutations and premature ageing phenotypes. These mutator mice also contain high levels of truncated, linear fragments of mtDNA. We demonstrate that the formation of these fragments is due to impaired ligation, causing nicks near the origin of heavy-strand DNA replication. In the subsequent round of replication, the nicks lead to double-strand breaks and linear fragment formation.