Thermodynamic and Kinetic Analyses of DNA Triplex Formation: Application of Filter-Binding Assay

Abstract

We have developed a simple and efficient method for studying equilibrium thermodynamics and kinetics of DNA triplex formation, which utilizes a filter-binding procedure. The application of this method to the triplex formation between a double-stranded homopurine-homopyrimidine and a single-stranded homopyrimidine oligonucleotides has demonstrated its ability in the quantitative estimation of equilibrium binding constants and rate constants under various conditions. Thus, this simple method can serve as a powerful tool for the systematic analysis of sequence and environmental effects on the equilibrium and kinetic quantities in the triplex formation.     

Optogenetic Probing and Manipulation of the Calyx-Type Presynaptic Terminal in the Embryonic Chick Ciliary Ganglion

The calyx-type synapse of chick ciliary ganglion (CG) has been intensively studied for decades as a model system for the synaptic development, morphology and physiology. Despite recent advances in optogenetics probing and/or manipulation of the elementary steps of the transmitter release such as membrane depolarization and Ca²⁺ elevation, the current gene-manipulating methods are not suitable for targeting specifically the calyx-type presynaptic terminals. Here, we evaluated a method for manipulating the molecular and functional organization of the presynaptic terminals of this model synapse. We transfected progenitors of the Edinger-Westphal (EW) nucleus neurons with an EGFP expression vector by in ovo electroporation at embryonic day 2 (E2) and examined the CG at E8–14. We found that dozens of the calyx-type presynaptic terminals and axons were selectively labeled with EGFP fluorescence. When a Brainbow construct containing the membrane-tethered fluorescent proteins m-CFP, m-YFP and m-RFP, was introduced together with a Cre expression construct, the color coding of each presynaptic axon facilitated discrimination among inter-tangled projections, particularly during the developmental re-organization period of synaptic connections. With the simultaneous expression of one of the chimeric variants of channelrhodopsins, channelrhodopsin-fast receiver (ChRFR), and R-GECO1, a red-shifted fluorescent Ca²⁺-sensor, the Ca²⁺ elevation was optically measured under direct photostimulation of the presynaptic terminal. Although this optically evoked Ca²⁺ elevation was mostly dependent on the action potential, a significant component remained even in the absence of extracellular Ca²⁺. It is suggested that the photo-activation of ChRFR facilitated the release of Ca²⁺ from intracellular Ca²⁺ stores directly or indirectly. The above system, by facilitating the molecular study of the calyx-type presynaptic terminal, would provide an experimental platform for unveiling the molecular mechanisms underlying the morphology, physiology and development of synapses.     

Crucial Role for CD69 in the Pathogenesis of Dextran Sulphate Sodium-Induced Colitis

CD69 is a membrane molecule transiently expressed on activated lymphocytes, and its selective expression in inflammatory infiltrates suggests that it plays a role in the pathogenesis of inflammatory diseases. In this study, we used CD69-deficient (CD69 KO) mice to assess the role of CD69 in the pathogenesis of dextran sulphate sodium (DSS)-induced acute and chronic colitis. The severity of colitis was assessed by the survival rate, clinical signs, colon length, histological examination and the expression of cytokines and chemokines in the large intestines. Both acute and chronic colitis were attenuated in the CD69 KO mice, as reflected by the lower lethality, weight loss, clinical signs, and improved histological findings. CD69⁺ cells infiltrated extensively into the inflamed mucosa of the colon in WT mice after DSS treatment. Experiments with the transfer of WT CD4 T cells into CD69 KO mice restored the induction of colitis. The administration of an anti-CD69 antibody also inhibited the induction of the DSS-induced colitis. These results indicate that CD69 expressed on CD4 T cells plays an important role in the pathogenesis of DSS-induced acute and chronic colitis, and that CD69 could be a possible therapeutic target for colitis.     

Effects of sampling seasons and locations on fish environmental DNA metabarcoding in dam reservoirs

Environmental DNA (eDNA) analysis has seen rapid development in the last decade, as a novel biodiversity monitoring method. Previous studies have evaluated optimal strategies, at several experimental steps of eDNA metabarcoding, for the simultaneous detection of fish species. However, optimal sampling strategies, especially the season and the location of water sampling, have not been evaluated thoroughly. To identify optimal sampling seasons and locations, we performed sampling monthly or at two‐monthly intervals throughout the year in three dam reservoirs. Water samples were collected from 15 and nine locations in the Miharu and Okawa dam reservoirs in Fukushima Prefecture, respectively, and five locations in the Sugo dam reservoir in Hyogo Prefecture, Japan. One liter of water was filtered with glass‐fiber filters, and eDNA was extracted. By performing MiFish metabarcoding, we successfully detected a total of 21, 24, and 22 fish species in Miharu, Okawa, and Sugo reservoirs, respectively. From these results, the eDNA metabarcoding method had a similar level of performance compared to conventional long‐term data. Furthermore, it was found to be effective in evaluating entire fish communities. The number of species detected by eDNA survey peaked in May in Miharu and Okawa reservoirs, and in March and June in Sugo reservoir, which corresponds with the breeding seasons of many of fish species inhabiting the reservoirs. In addition, the number of detected species was significantly higher in shore, compared to offshore samples in the Miharu reservoir, and a similar tendency was found in the other two reservoirs. Based on these results, we can conclude that the efficiency of species detection by eDNA metabarcoding could be maximized by collecting water from shore locations during the breeding seasons of the inhabiting fish. These results will contribute in the determination of sampling seasons and locations for fish fauna survey via eDNA metabarcoding, in the future.     

Quantitative analysis of condensation/decondensation status of pDNA in the nuclear sub-domains by QD-FRET

Recent studies indicate that controlling the nuclear decondensation and intra-nuclear localization of plasmid DNA (pDNA) would result in an increased transfection efficiency. In the present study, we established a technology for imaging the nuclear condensation/decondensation status of pDNA in nuclear subdomains using fluorescence resonance energy transfer (FRET) between quantum dot (QD)-labeled pDNA as donor, and rhodamine-labeled polycations as acceptor. The FRET-occurring pDNA/polycation particle was encapsulated in a nuclear delivery system; a tetra-lamellar multifunctional envelope-type nano device (T-MEND), designed to overcome the endosomal membrane and nuclear membrane via step-wise fusion. Nuclear subdomains (i.e. heterochromatin and euchromatin) were distinguished by Hoechst33342 staining. Thereafter, Z-series of confocal images were captured by confocal laser scanning microscopy. pDNA in condensation/decondensation status in heterochromatin or euchromatin were quantified based on the pixel area of the signals derived from the QD and rhodamine. The results obtained indicate that modulation of the supra-molecular structure of polyrotaxane (DMAE-ss-PRX), a condenser that is cleaved in a reductive environment, conferred euchromatin-preferred decondensation. This represents the first demonstration of the successful control of condensation/decondensation in specific nuclear sub-domain via the use of an artificial DNA condenser.     

Fluctuation and variation in stream-fish assemblages after a catastrophic flood in the Miyagawa River,Japan

In the autumn of 2004, a typhoon caused a catastrophic flood of the Miyagawa River in Japan. Based upon snorkeling surveys conducted every autumn from 2005 to 2009, we monitored the post flood fluctuation of the local fish assemblages at nine sites of both the main stream and subsidiary streams of the river. Results revealed that species richness significantly increased from 2005 to 2009. In addition, the fish densities of eight species significantly increased over the same period, whereas the density of one species decreased, and that of eight others remained unchanged. Categorization based on Euclidean distance revealed five main clusters from the nine sites. Among these sites, fish assemblages within subsidiary streams were stable as they remained within the same clusters while those in the main stream were dynamically variable through time as they changed cluster membership. In addition, the Euclidean distance between two arbitrary fish assemblages was positively correlated with environmental distance (the Euclidean distance calculated based on river width, depth, velocity and pebble size), time distance, and spatial distance along the river. In conclusion, the fish assemblages were dynamically and regularly altered and varied in the five years after the flood, except for those in the subsidiary streams, and such variation was related to environmental, temporal and spatial variation.     

Dioxin-like polychlorinated biphenyl adsorbent obtained from enzymatic saccharification residue of lignocellulose

In this study, the effective utilization of lignocellulose residue as an adsorbent was investigated. Japanese cypress wood flour subjected to hydrothermal pretreatment and ball-mill grinding was saccharified with an enzyme. The residual wood flour was carbonized and activated by physical and chemical activation to produce adsorbents for persistent organic pollutant removal. The adsorption properties were investigated by pore analysis using the N₂ adsorption/desorption isotherm and adsorption tests for dioxin-like polychlorinated biphenyls in a hexane solution. The obtained adsorbents showed high production yields and adsorption properties for dioxin-like polychlorinated biphenyls.