Fluorescence Redox Blinking Adaptable to Structural Analysis of Nucleic Acids.

The phenomenon of blinking is unique to single-molecule fluorescence measurements. By designing a fluorophore with an appropriate dark-state lifetime τoff , a kinetic analysis based on the control of fluorescence blinking (KACB) was devised to investigate the dynamics of biomolecules. By controlling the redox-reaction-based blinking (rKACB), conformational dynamics of RNA at the single-molecule level was previously investigated. However, there is little knowledge about suitable fluorescent molecules for rKACB, and the application of rKACB has been limited to the analysis of hairpins and duplex structures of nucleic acids. In this work, various fluorescent molecules, including Alexa 488, R6G, TAMRA, ATTO 647N and ATTO 655, were evaluated for rKACB. Moreover, rKACB was adapted to the discrimination of DNA/DNA and DNA/RNA nucleic acid duplexes and investigation of antigen-antibody interactions. By changing the size of the oxidant, it was possible to determine the solvent accessibility of the target domain of the analyzed biomolecules.

Single-Molecule Monitoring of the Structural Switching Dynamics of Nucleic Acids through Controlling Fluorescence Blinking.

Single-molecule fluorescence resonance energy transfer (smFRET) is a powerful tool to investigate the dynamics of biomolecular events in real time. However, it requires two fluorophores and can be applied only to dynamics that accompany large changes in distance between the molecules. Herein, we introduce a method for kinetic analysis based on control of fluorescence blinking (KACB), a general approach to investigate the dynamics of biomolecules by using a single fluorophore. By controlling the kinetics of the redox reaction the blinking kinetics or pattern can be controlled to be affected by microenvironmental changes around a fluorophore (rKACB), thereby enabling real-time single-molecule measurement of the structure-changing dynamics of nucleic acids.

Self-consistent field model simulations for statistics of amorphous polymer chains in crystalline lamellar structures.

We calculate statistical properties of amorphous polymer chains between crystalline lamellae by self-consistent field model simulations. In our model, an amorphous subchain is modelled as a polymer chain of which ends are grafted onto the crystal-amorphous interfaces. The crystal-amorphous interfaces are expressed as impenetrable surfaces. We incorporate the interaction between segments to satisfy the incompressible condition for the segment density field. The simulation results show that amorphous polymer chains feel thin potential layers, which are mainly repulsive, near the crystal-amorphous interfaces. The impenetrable and incompressible conditions affect the statistics of polymer chains and the chain statistics becomes qualitatively different from the ideal Gaussian chain statistics without any constraints. We show the effects of the system size and the graft density to statistical quantities. We also show that the tie subchain statistics obey rather simple statistics.

Elevation of serum interleukins 8, 4, and 1ß levels in patients with gastrointestinal low-grade B-cell lymphoma.

Proinflammatory cytokines that are produced by helper T cells (Th) regulate immune reactions, facilitate class switching of B cells, and prolong the lifespan of B and T cells. Eradication therapy using antibiotics is sometimes effective against gastrointestinal (GI) malignant lymphoma, suggesting that the tumor development or progression is affected by the inflammatory microenvironment. In the present study, serum samples from 148 patients with various subtypes of malignant lymphoma were tested for 11 proinflammatory Th1/Th2 cytokines. In the comparison by subtype or GI lesions, serum interleukin (IL)-8 (P = 6.7E-05), IL-4 (P = 7.5E-05), and IL-1ß (P = 0.0043) levels showed significant differences among subtypes, being particularly elevated in follicular lymphomas (FL) and mucosa-associated lymphoid tissue (MALT) lymphomas. Serum IL-8 levels were elevated in GI-FL and MALT lymphomas, and serum IL-4 and IL-1 ß levels were elevated in MALT lymphomas. These findings show that GI low-grade B-cell lymphoma could develop against the background of an inflammatory microenvironment. Thus, these cytokines may be useful as diagnostic markers and could provide new insights into tumor development.

Clinicopathologic analysis of 6 lymphomatoid gastropathy cases: expanding the disease spectrum to CD4-CD8+ cases.

Lymphomatoid gastropathy, which was first reported in 2010, is a rare NK-cell proliferation of cyCD3, CD4, CD5, CD8, CD56 phenotypes with unknown etiology. The diagnosis is challenging, as there is histopathologic similarity to malignant lymphoma. In the 2010 report on 10 cases, all lesions were located in the stomach, and all regressed without any therapy. In the present study, we analyzed 6 cases of lymphomatoid gastropathy by investigating the clinicopathologic, immunohistochemical, and molecular findings. Endoscopic and morphologic appearances of all cases were consistent with previous reports, but 2 cases showed previously unreported unique immunophenotypes of CD4CD8. Three of 6 patients underwent lower gastrointestinal examination (1 case underwent double-balloon endoscopic examination), but no patient had lesions in the lower gastrointestinal tract. No obvious difference of histology was found between the cases of CD4-CD8-typical phenotype and ones of CD4CD8 phenotype. Both cases had similar clinical behavior as the other 4 cases, implying that the spectrum of the disease is broader than initially thought. Careful clinical and endoscopic follow-up is required for the diagnosis of lymphomatoid gastropathy, and additional case studies and molecular studies are warranted to further investigate the pathophysiology of this peculiar benign mimic of lymphoma.