Detection of cofilin mRNA by hybridization-sensitive double-stranded fluorescent probes

We have developed hybridization-sensitive fluorescent oligonucleotide probes that, in the presence of quencher strands, undergo efficient fluorescence quenching through the formation of partial DNA/DNA duplexes. In the presence of target RNA, rapid displacement of the quencher strands results in highly enhanced fluorescence.

We have developed hybridization-sensitive fluorescent oligonucleotide probes that, in the presence of quencher strands, undergo efficient fluorescence quenching through the formation of partial DNA/DNA duplexes.

The detection of biomolecules is an important part of any investigation into their biological mechanisms and phenomena. Fluorescence-based methods are particularly useful for providing interpretable signals for various targets (e.g., genes, proteins, small molecules). When nucleic acids are used as probes, they can provide sequence-specific information regarding the binding (through hydrogen bonding) of target nucleic acids. Because of their high sequence-specificity, many fluorescent hybridization probes, including molecular beacons (MBs), have been developed and applied for nucleic acid detection and visualization.^1,2In previous studies, we found that a quencher-free molecular beacon (QF-MB) containing the pyrene-modified nucleoside ^PyU exhibited a high fluorescence enhancement in the presence of trinucleotide repeats, especially for RNA.^3,4 Among various fluorescent nucleobase derivatives, uracil derivatives have been particularly useful for selective detection of specific sequences, taking advantage of changes in photoinduced electron transfer between the fluorophore and the neighboring base.^3–5 To apply such systems to various other target sequences, here we designed fully complementary sequences and incorporated the internal fluorescent nucleoside ^PyU in place of a thymine residue, resulting in a significantly increased fluorescence signal based on strand displacement (Fig. 1). Incorporation of a ^PyU unit in a single strand of the probe sequence and hybridization with a strand partially complementary to the probe strand containing a pyrene unit as a fluorescence quencher can lead to improved discrimination factors.^4,6 Such partially double-stranded probes have several attractive features.Open in a separate windowFig. 1(A) Schematic representation of the strand displacement process developed in this present system. (B) Structures of the internal fluorophore ^PyU.First, the probe sequence does not require an additional sequence in its strand that is not complementary to the target sequence to ensure formation of a secondary structure (e.g., a hairpin). Such additional sequences might interfere with the specific hybridization between the probe and the target sequence. Accordingly, double-stranded fluorescence probes should allow the specific detection of many kinds of targets. Second, the highly quenched initial fluorescence signal, due to the formation of a partial duplex, results in significantly increased fluorescence in the presence of the target; the incorporation of a hybridization-sensitive internal fluorophore provides a stable and sensitive fluorescence signal upon perfect hybridization with the target.Cofilin is a protein that regulates the activity of actin, which is related to the formation of the cytoskeleton in cells. Actin plays a crucial role in the growth and elongation of cells,⁷ especially in neurons and, therefore, in the control of neurotransmission. We designed probe strands complementary to the 3′-untranslated region (3′-UTR) of target cofilin mRNA and synthesized three kinds of 19-mer probe strands (P1–P3) containing one or two ^PyU units in each strand (Fig. 2A and S1, ESI^†). The fluorescence intensities of P1 and P3 increased dramatically after binding with the target RNA T19—by 17.6- and 16.0-fold, respectively. For the probe P2 (in which the ^PyU residue was located close to the 3′-end), however, the fluorescence enhancement was very low: only 1.8-fold (Table S2, ESI^†). We assume that terminal modification of the ^PyU unit in the probe resulted in weak base pairs around the ^PyU residue than did central modification, resulting in a decrease in fluorescence enhancement (Table S3, ESI^†).⁸ Because flanking base pairs around the ^PyU unit are relatively less rigid compared to central base pairs, the microenvironment of ^PyU in the duplex formed from P2 and T19 is different from the central modification. Therefore, the fluorescence intensity did not increase significantly compared to the single-stranded P2. The absorption spectrum of P2 in the presence of T19 exhibited a relatively less intense absorption band than that of the duplex formed from P1 and T19—the latter featured an intense signal corresponding to the high fluorescence intensity (Fig. S1, ESI^†).^9,10 Even though two ^PyU units were incorporated into the single strand P3, its fluorescence enhancement was similar to that of probe P1 containing only one ^PyU unit. Among other examined probe sequences complementary to other parts of 3′-UTR in cofilin mRNA, P6 (containing two ^PyU units) also exhibited fluorescence intensity similar to those of P4 and P5, single-^PyU – containing probes each modified in the central position (Fig. S2, ESI^†). These results suggest that single modification of a ^PyU unit in the probe sequence is more efficient than dual modification, in terms of inducing high fluorescence enhancement with target RNA.Oligonucleotide sequences of probe and target strands

Input–output analysis on the economic impact of medical care in Japan

Objectives

Since the Cabinet’s decision concerning the Basic Policies 2005, the Japanese government has implemented specific measures to suppress increases in national medical care expenditure. However, we believe that the economic significance of medical care should be quantified in terms of its economic impact on national medical care expenditure. No one has examined the economic impact of all medical institutions in Japan using data from a statement of profits and losses. We used an input–output analysis to quantitatively estimate economic impact of medical care and examined its estimation range with a probabilistic sensitivity analysis.

Methods

To estimate the economic impact and economic impact multipliers of all medical institutions in Japan, an input–output analysis model was developed using an input–output table, statement of profits and losses, margin rates, employee income rates, consumption propensity and an equilibrium output model. Probabilistic sensitivity analysis was conducted using a Monte Carlo simulation.

Results

Economic impact of medical care in all medical institutions was ¥72,107.4 billion ($661.5 billion). This impact yielded a 2.78-fold return of medical care expenditure with a 95 % confidence interval ranging from 2.74 to 2.90.

Conclusion

Economic impact of medical care in Japan was two to three times the medical care expenditure (per unit). Production inducement of medical care is comparable to other industrial sectors that are highly influential toward the economy. The contribution to medical care should be evaluated more explicitly in national medical care expenditure policies.     

Left trisegmentectomy and combined resection of the inferior vena cava, without reconstruction, for giant cystadenocarcinoma of the liver

A 54-year-old woman with giant liver cystadenocarcinoma underwent left trisegmentectomy with combined resection of the inferior vena cava (IVC) and the right hepatic vein. As a result, only the right inferior hepatic vein was preserved as a drainage vein. Because the perivertebral plexus and the azygos vein were both well developed, neither veno-venous bypass nor IVC reconstruction was performed. The developed collateral veins acted as the venous drainage pathway to maintain a stable systemic circulation. On the seventh postoperative day, portal vein flow dramatically decreased and the patient tended to liver failure. Prostaglandin E₁ (PGE₁) was administrated via the superior mesenteric artery. The portal flow then gradually increased and liver failure was avoided. Six months after the operation, she was re-admitted due to obstructive jaundice and presented with complete stenosis of the common bile duct (CBD). The jaundice persisted and liver dysfunction progressed. The patient died seven months after the operation. The confluence of the right inferior vein and the IVC could have been deformed, causing outflow blockade. The intrinsic shunt was not good enough to act as the drainage pathway, and IVC reconstruction may have been needed.     

Conductance of P2X4 purinergic receptor is determined by conformational equilibrium in the transmembrane region

Ligand-gated ion channels are partially activated by their ligands, resulting in currents lower than the currents evoked by the physiological full agonists. In the case of P2X purinergic receptors, a cation-selective pore in the transmembrane region expands upon ATP binding to the extracellular ATP-binding site, and the currents evoked by α,β-methylene ATP are lower than the currents evoked by ATP. However, the mechanism underlying the partial activation of the P2X receptors is unknown although the crystal structures of zebrafish P2X₄ receptor in the apo and ATP-bound states are available. Here, we observed the NMR signals from M339 and M351, which were introduced in the transmembrane region, and the endogenous alanine and methionine residues of the zebrafish P2X₄ purinergic receptor in the apo, ATP-bound, and α,β-methylene ATP-bound states. Our NMR analyses revealed that, in the α,β-methylene ATP-bound state, M339, M351, and the residues that connect the ATP-binding site and the transmembrane region, M325 and A330, exist in conformational equilibrium between closed and open conformations, with slower exchange rates than the chemical shift difference (<100 s⁻¹), suggesting that the small population of the open conformation causes the partial activation in this state. Our NMR analyses also revealed that the transmembrane region adopts the open conformation in the state bound to the inhibitor trinitrophenyl-ATP, and thus the antagonism is due to the closure of ion pathways, except for the pore in the transmembrane region: i.e., the lateral cation access in the extracellular region.In chemical neurotransmission, various neurotransmitters bind to ligand-gated ion channels expressed in the plasma membrane of postsynaptic cells, such as the NMDA, AMPA, and P2X receptors, leading to changes in membrane potential and the concentration of intracellular ions. Each ligand for a ligand-gated ion channel has a distinct ability to evoke currents (1), and the ligands are classified according to the evoked current level: such as, full agonists, partial agonists, and antagonists. Partial agonists of ligand-gated ion channels reportedly offer clinical advantages over antagonists and full agonists in antidepressant and smoking-cessation treatment (2, 3).Two mechanisms have been proposed for the partial activation of the ligand-gated ion channels: the equilibrium between the open and closed conformations and the distinct conformation of the partial agonist-bound states from the closed and open conformations (4, 5). In the crystal structures of the extracellular region of the AMPA receptor, in which the distances between the two extracellular domains are changed upon agonist binding, the interdomain distances in the partial agonist-bound states correlated with the conductance level, suggesting that the AMPA receptor adopts specific intermediately permeable conformations (4, 6).The P2X receptors are a family of cation channels gated by extracellular ATP (1, 7–9) and are involved in many physiological and pathophysiological processes (10–12). Seven subtypes of the P2X receptors have been identified in mammals (13), and they share ∼40% sequence identity. The P2X₄ receptor is involved in the pathogenesis of chronic neuropathic, inflammatory pain and the endothelial cell-mediated control of vascular tone (11, 14, 15). Compared with ATP, α,β-methylene ATP (α,β-meATP), in which the oxygen atom linking the α- and β-phosphorous atoms of ATP is replaced by a methylene group (Fig. S1A), reportedly induces a lower maximum current in cells expressing the mouse, rat, and human P2X₄ receptors and other P2X receptors (16, 17).Open in a separate windowFig. S1.Characterization of the P2X₄ receptor. (A) Chemical structures of ATP and α,β-meATP. (B and C) TEVC recordings of ATP- and α,β-meATP-evoked currents from rat P2X₄ receptor expressed in Xenopus oocytes, respectively. In B, the currents were evoked twice by ATP (30 μM, 1 min, black bar). In C, the currents were firstly evoked by ATP (30 μM, 1 min, black bar) and subsequently by α,β-meATP (300 μM, 1 min, black bar). (D) TEVC recording of the ATP-evoked current (30 μM, 30 s, black bar) from the N-terminally EGFP-tagged ΔzfP2X₄–A′ construct expressed in Xenopus oocytes. (E) Size exclusion chromatogram of purified EGFP-tagged ΔzfP2X₄–A′ in rHDLs. Elution volumes corresponding to 17.0, 12.2, 10.4, and 7.1 nm Stokes diameters were determined by thyroglobulin, ferritin, catalase, and BSA, respectively. V₀ and 1CV are void volume and single column volume, respectively. (F) SDS/PAGE analyses of purified ΔzfP2X₄–A′ embedded in rHDLs. The samples were analyzed by 12% SDS/PAGE with Coomassie Brilliant Blue staining. (G) Measurement of [³H]ATP saturation binding to the purified ΔzfP2X₄–A′ in rHDLs. (H and I) Estimation of the effects of deuteration based on the crystal structures of zfP2X₄ (PDB ID code 4DW1) and the deuteration incorporation rates. The plots on the Left (without deuteration) and the Right (with deuteration) are the sums of the inverse sixth power of the distances between pseudoatoms centered on the methyl hydrogens of M108, M249, M268, or M325 and each hydrogen atom in the crystal structure of zfP2X₄ (sums of the r⁻⁶) and the sums of the r⁻⁶ multiplied by [1 − (deuterium incorporation rates)] of each hydrogen atom, respectively. The graphs in H and I were calculated from the crystal structure in the apo state (PDB ID code 4DW0) and that in the ATP-bound state (PDB ID code 4DW1), respectively. Sums of the r⁻⁶ of each methionine methyl group and Hαβγ of the intraresidue methionine (green), Hαβγ of the interresidue methionine (light green), Hαβ of tyrosine (light violet), Hδεζη of tryptophan (orange), Hαβδεζ of phenylalanine (pink), Hαβγ of valine (blue), Hαβγδ of leucine (light blue), Hαβγδ of isoleucine (cyan), Hαβγ of threonine (light cyan), Hαβ of alanine (red), Hαβγδ of arginine (dark blue), Hα of glycine (dark green), and Hαβ of serine (magenta) residues, and the other hydrogens connected to carbon atoms (other unexchangeable hydrogens, light gray) are shown with colors. Hydrogen atoms connected to nitrogen, oxygen, or sulfur atoms were not considered in these calculations because these hydrogens should be exchanged with deuterium in D₂O. The deuterium incorporation rates of the hydrogen atoms within each methionine residue (intraresidue) and the deuterium incorporation rates of other methionine residues (interresidue) were set to 98% and 85%, respectively, because the methionine residues would be derived from 85% of [α-, β-, γ-98% ²H-, methyl-¹³C]-methionine and 15% of nonlabeled methionine in the medium.The crystal structures of zebrafish P2X₄ receptor (zfP2X₄) (18, 19), together with mutational analyses (20–26), provided the structural basis for the channel opening of P2X receptors upon ATP binding. In the crystal structures, zfP2X₄ forms a homotrimer (27, 28), in which the transmembrane region of each subunit is composed of two helices (19). In the crystal structure of zfP2X₄ in the ATP-bound state, three ATP molecules are bound to the intersubunit nucleotide binding pockets. In addition, the region that connects the ATP-binding site and the transmembrane region, which is referred to as the “lower body” (Fig. 1 A and B), is expanded by ∼10 Å in the ATP-bound state, and a pore is formed in the transmembrane region, which is proposed to expand by the iris-like movement of the transmembrane helices (18). However, the mechanism underlying the partial activation of P2X receptors is unknown because the structures of the P2X receptors have not been examined in the partial agonist-bound states.Open in a separate windowFig. 1.NMR resonances from the endogenous methionine residues of zfP2X₄ in rHDL. (A and B) Distribution of the methionine residues in the ΔzfP2X₄–A′. One subunit from the crystal structure of zfP2X₄ in the apo form (A) (PDB ID code 4DW0) and one from the ATP-bound form (B) (PDB ID code 4DW1) are shown in ribbons. The lower body and the right flipper are yellow. The A330 residues, the methionine residues, and the residues in which methionine mutations were introduced, L339 and L351, are depicted by green sticks. ATP is depicted by red sticks. Dummy atoms generated by Orientations of Proteins in Membranes (OPM), which represent membrane boundary planes, are gray. (C) Overlaid ¹H-¹³C HMQC spectra of [²H-11AA, α, β-²H, methyl-¹³C-Met]ΔzfP2X₄-A′, embedded in rHDLs, in the apo state (black) and the ATP-bound state (red). The regions with resonances from methionine residues are shown, and the assigned resonances are indicated. The centers of the resonances are indicated with dots. Cross-sections at lines through the centers of each resonance in the ATP-bound state and the cross-sections of the spectra using [α, β-²H, methyl-¹³C-Met]ΔzfP2X₄-A′ are shown on the top of the overlaid spectra. The intensities of the cross-sections were normalized by the concentration of ΔzfP2X₄-A′ and the conditions of the NMR measurements.The P2X₄ receptor used in the previous crystallographic studies was solubilized by detergents, which are widely used for structural investigations of membrane proteins, but the P2X₄ receptor is embedded in lipid bilayers under physiological conditions. It was recently reported that reconstituted high-density lipoproteins (rHDLs), which are also known as nanodiscs (29), can accommodate membrane proteins within a 10-nm-diameter disk-shaped lipid bilayer (30). The rHDLs reportedly provide a lipid environment with more native-like properties, compared with liposomes, in terms of the lateral pressure and curvature profiles because detergent micelles have strong curvature and different lateral pressure profiles from lipid membranes (31). Our NMR analyses of a G protein-coupled receptor (GPCR) and an ion channel in rHDL lipid bilayers revealed that the population and the exchange rates of the conformational equilibrium determine their signal transduction and ion transport activities (32–34) and that the population of the active conformation of the GPCR in rHDLs correlated better with the signaling levels than that in detergent micelles (32). Therefore, NMR investigations of membrane proteins in the lipid bilayer environments of rHDLs are necessary for accurate measurements of the exchange rates and the populations in conformational equilibrium.Here, we used NMR to observe the conformational equilibrium of the alanine and methionine residues of zfP2X₄ bound to α,β-meATP in rHDLs. Based on the conformational equilibrium, we discuss the mechanism underlying the partial activation of P2X receptors.     

Stimulation of adenylate cyclase in homogenates of isolated intestinal epithelial cells from hamsters. Effects of gastrointestinal hormones, prostaglandins, and deoxycholic and ricinoleic acids

The mechanism by which intestinal secretagogues evoke fluid secretion in the small bowel and colon has been suggested to involve mucosal adenylate cyclase. Adenylate cyclase activity was assayed by conversion of [32P]ATP to [32P]cyclic AMP in a system of pure epithelial cells isolated from the small intestine of the hamster by vibration in buffer. Several gastrointestinal hormones were tested for their capacity to stimulate adenylate cyclase; vasoactive intestinal peptide and impure cholecystokinin-pancreozymin (but not the 99% pure preparation or pure cholecystokinin octapeptide) were potent stimuli, but pentagastrin, glucagon, secretin, and gastric inhibitory peptide were impotent. Two prostaglandins, PGE1 and PGE2, were potent stimuli of adenylate cyclase. Two other compounds that provoke intestinal secretion of fluid, deoxycholic acid and ricinoleic acid (castor oil), were ineffective stimuli of adenylate cyclase. These experiments do not support a clear-cut relationship between a compound's ability to stimulate adenylate cylase and its activity as an intestinal secretagogue.     

Some aspects of fungi multifocal invasions connected with the genital organs in women

The aim of presented study was analysis of fungal invasions of the genital organs, oral cavity and digestive tract in 799 women. Fungal strains were identified using API 20C and API 20C AUX (bioMérieux); they were as follows: Candida albicans, C. krusei, C. tropicalis, C. guilliermondii, C. kefyr, C. glabrata, C. famata, C. parapsilosis, Rhodotorula rubra, Geotrichum candidum. The number of fungal strains isolated from the oral cavity ontocenosis was the highest (41.8 +/- 2.4%). Fungal strains isolated from the vagina were less numerous (34.6 +/- 2.3%), and from the rectum the least numerous (23.6 +/- 2.1%). Multifocal invasions (limited to one ontocenosis) were present in about 50% of women; bifocal were less frequent, and this difference was statistically significant (p < 0.01): fungi in the vagina and oral cavity were detected in 28.6 +/- 3.0%, in the oral cavity and rectum in 19.0 +/- 2.6%, and in the vagina and rectum in 13.0 +/- 2.2%. Trifocal invasions were more frequent (39.4 +/- 3.2%). There was a visible trend of increasing prevalence of fungi in genital organs over 10 year period from 17.9 +/- 1.4% to 34.5 +/- 1.7%.     

Endosonographic features in patients with non-alcoholic early chronic pancreatitis improved with treatment at one year follow up

Since the prevention of early chronic pancreatitis (ECP) into chronic pancreatitis might be critical for the reduction of pancreatic cancer, we tried to clarify the pathophysiology of ECP patients, focusing on ECP patients without alcoholic chronic pancreatitis. 27 ECP patients without alcoholic chronic pancreatitis and 33 patients with functional dyspepsia with pancreatic enzyme abnormalities (FD-P) were enrolled in this study. Diagnosis of ECP was made when imaging findings showed the presence of more than 2 out of 7 endoscopic ultrasound features. Duodenal degranulated eosinophils and glucagon-like peptide 1 producing cells were estimated by immunostaining. There were no significant differences in characteristics and psychogenic factors between ECP and FD-P patients. Interestingly, endoscopic ultrasound score in ECP patients significantly improved, albeit clinical symptoms in ECP patients showed no improvement at one year follow up. The extent of migration of duodenal degranulated eosinophils in FD-P patients was significantly higher compared to that in ECP patients. The levels of elastase-1 and trypsin in ECP patients with improved endoscopic ultrasound features were significantly reduced by the treatment. Further studies will be needed to clarify whether clinical symptoms and endoscopic ultrasound features in ECP patients without alcoholic chronic pancreatitis were improved in longer follow up study.     

Characteristics of gram-negative bacteremia during febrile neutropenia among allogeneic hematopoietic stem cell transplant recipients on levofloxacin prophylaxis

European Journal of Clinical Microbiology & Infectious Diseases - The aim of this study is to clarify the characteristics of gram-negative bacteremia (GNB), including extended-spectrum...