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Fluorogenic RNA aptamers, which specifically bind to fluorogens and dramatically enhance their fluorescence, are valuable for imaging and detecting RNAs and metabolites in living cells. Most fluorogenic RNA aptamers have been identified and engineered through iterative rounds of in vitro selection based on their binding to target fluorogens. While such selection is an efficient approach for generating RNA aptamers, it is less efficient for isolating fluorogenic aptamers because it does not directly screen for fluorogenic properties. In this study, we combined a fluorescence-based in vitro selection technique using water-in-oil microdroplets with an affinity-based selection technique to obtain fluorogenic RNA aptamers. This approach allowed us to identify novel fluorogenic aptamers for a biotin-modified thiazole orange derivative. Our results demonstrate that our approach can expand the diversity of fluorogenic RNA aptamers, thus leading to new applications for the imaging and detection of biomolecules., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 The Authors. Published by Elsevier B.V. All rights reserved.)

Green fluorescent protein (GFP) has a chromophore that forms autocatalytically within the folded protein. Although many studies have focused on the precise mechanism of chromophore maturation, little is known about the kinetics of de novo chromophore maturation. Here we present a simple and efficient method for examining the de novo kinetics. GFP with an immature chromophore was synthesized in a reconstituted cell-free protein synthesis system under anaerobic conditions. Chromophore maturation was initiated by rapid dilution in an air-saturated maturation buffer, and the time course of fluorescence development was monitored. Comparison of the de novo maturation rates in various GFP variants revealed that some folding mutations near the chromophore promoted rapid chromophore maturation and that the accumulation of mutations could reduce the maturation rate. Our method will contribute to the design of rapidly maturing fluorescent proteins with improved characteristics for real-time monitoring of cellular events., (Copyright © 2011 Elsevier Inc. All rights reserved.)

Prefoldin (PFD) is a heterohexameric molecular chaperone that is found in eukaryotic cytosol and archaea. PFD is composed of alpha and beta subunits and forms a "jellyfish-like" structure. PFD binds and stabilizes nascent polypeptide chains and transfers them to group II chaperonins for completion of their folding. Recently, the whole genome of Thermococcus kodakaraensis KOD1 was reported and shown to contain the genes of two alpha and two beta subunits of PFD. The genome of Thermococcus strain KS-1 also possesses two sets of alpha (alpha1 and alpha2) and beta subunits (beta1 and beta2) of PFD (TsPFD). However, the functions and roles of each of these PFD subunits have not been investigated in detail. Here, we report the crystal structure of the TsPFD beta1 subunit at 1.9 A resolution and its functional analysis. TsPFD beta1 subunits form a tetramer with four coiled-coil tentacles resembling the jellyfish-like structure of heterohexameric PFD. The beta hairpin linkers of beta1 subunits assemble to form a beta barrel "body" around a central fourfold axis. Size-exclusion chromatography and multi-angle light-scattering analyses show that the beta1 subunits form a tetramer at pH 8.0 and a dimer of tetramers at pH 6.8. The tetrameric beta1 subunits can protect against aggregation of relatively small proteins, insulin or lysozyme. The structural and biochemical analyses imply that PFD beta1 subunits act as molecular chaperones in living cells of some archaea.

Prefoldin is a heterohexameric molecular chaperone complex that is found in the eukaryotic cytosol and also in archaea. It captures a nonnative protein and subsequently delivers it to a group II chaperonin for proper folding. Archaeal prefoldin is a heterocomplex containing two alpha subunits and four beta subunits with the structure of a double beta-barrel assembly, with six long coiled coils protruding from it like a jellyfish with six tentacles. We have studied the protein folding mechanism of group II chaperonin using those of Thermococcus sp. strain KS-1 (T. KS-1) because they exhibit high protein folding activity in vitro. We have also demonstrated functional cooperation between T. KS-1 chaperonins and prefoldin from Pyrococcus horikoshii OT3. Recent genome analysis has shown that Thermococcus kodakaraensis KOD1 contains two pairs of prefoldin subunit genes, correlating with the existence of two different chaperonin subunits. In this study, we characterized four different recombinant prefoldin complexes composed of two pairs of prefoldin subunits (alpha1, alpha2, beta1, and beta2) from T. KS-1. All of them (alpha1-beta1, alpha2-beta1, alpha1-beta2, and alpha2-beta2) exist as alpha(2)beta(4) heterohexamers and can protect several proteins from forming aggregates with different activities. We have also compared the collaborative activity between the prefoldin complexes and the cognate chaperonins. Prefoldin complexes containing the beta1 subunit interacted with the chaperonins more strongly than those with the beta2 subunit. The results suggest that Thermococcus spp. express different prefoldins for different substrates or conditions as chaperonins.

Prefoldin (PFD) is a heterohexameric molecular chaperone complex in the eukaryotic cytosol and archaea with a jellyfish-like structure containing six long coiled-coil tentacles. PFDs capture protein folding intermediates or unfolded polypeptides and transfer them to group II chaperonins for facilitated folding. Although detailed studies on the mechanisms for interaction with unfolded proteins or cooperation with chaperonins of archaeal PFD have been performed, it is still unclear how PFD captures the unfolded protein. In this study, we determined the X-ray structure of Pyrococcus horikoshii OT3 PFD (PhPFD) at 3.0 A resolution and examined the molecular mechanism for binding and recognition of nonnative substrate proteins by molecular dynamics (MD) simulation and mutation analyses. PhPFD has a jellyfish-like structure with six long coiled-coil tentacles and a large central cavity. Each subunit has a hydrophobic groove at the distal region where an unfolded substrate protein is bound. During MD simulation at 330 K, each coiled coil was highly flexible, enabling it to widen its central cavity and capture various nonnative proteins. Docking MD simulation of PhPFD with unfolded insulin showed that the beta subunit is essentially involved in substrate binding and that the alpha subunit modulates the shape and width of the central cavity. Analyses of mutant PhPFDs with amino acid replacement of the hydrophobic residues of the beta subunit in the hydrophobic groove have shown that beta Ile107 has a critical role in forming the hydrophobic groove.

Prefoldin is a molecular chaperone that captures a protein-folding intermediate and transfers it to a group II chaperonin for correct folding. The manner by which prefoldin interacts with a group II chaperonin is poorly understood. Here, we have examined the prefoldin interaction site in the archaeal group II chaperonin, comparing the interaction of two Thermococcus chaperonins and their mutants with Pyrococcus prefoldin by surface plasmon resonance. We show that the mutations of Lys250 and Lys256 of Thermococcus alpha chaperonin residues to Glu residues increase the affinity to Pyrococcus prefoldin to the level of Thermococcus beta chaperonin and Pyrococcus chaperonin, indicating that their Glu250 and Glu256 residues of the helical protrusion region are responsible for relatively stronger binding to Pyrococcus prefoldin than Thermococcus alpha chaperonin. Since the putative chaperonin binding sites in the distal ends of Pyrococcus prefoldin are rich in basic residues, electrostatic interaction seems to be important for their interaction. The substrate protein transfer rate from prefoldin correlates well with its affinity for chaperonin.

The crystal structures of the group II chaperonins consisting of the alpha subunit with amino acid substitutions of G65C and/or I125T from the hyperthermophilic archaeum Thermococcus strain KS-1 were determined. These mutants have been shown to be active in ATP hydrolysis but inactive in protein folding. The structures were shown to be double-ring hexadecamers in an extremely closed form, which was consistent with the crystal structure of native alpha8beta8-chaperonin from Thermoplasma acidophilum. Comparisons of the present structures with the atomic structures of the GroEL14-GroES7-(ADP)7 complex revealed that the deficiency in protein-folding activity with the G65C amino acid substitution is caused by the steric hindrance of the local conformational change in an equatorial domain. We concluded that this mutant chaperonin with G65C substitution is deprived of the smooth conformational change in the refolding-reaction cycle. We obtained a new form of crystal with a distinct space group at a lower concentration of sulfate ion in the presence of nucleotide. The crystal structure obtained at the lower concentration of sulfate ion tilts outward, and has much looser inter-subunit contacts compared with those in the presence of a higher concentration of sulfate ion. Such subunit rotation has never been characterized in group II chaperonins. The crystal structure obtained at the lower concentration of sulfate ion tilts outward, and has much looser inter-subunit contacts compared with those in the presence of a higher concentration of sulfate ion.

It has been suggested that transglutaminase 1 is proteolytically activated upon the terminal differentiation of the keratinocyte, but the mechanisms are not well understood. We have established two mouse hybridoma cell lines producing monoclonal antibodies that specifically detect proteolytically cleaved transglutaminase 1. One detects the amino-terminus of the fragment produced by cleavage between Arginine 93 and Glycine 94, and the other detects the amino-terminus of the fragment produced by cleavage between Arginine 573 and Glycine 574. Using these two antibodies, immunohistochemical analyses of the epidermis revealed that the cleavages of the transglutaminase 1 protein occur early in the terminal differentiation of keratinocytes in the basal layer of the epidermis, that the cleavage between Arginine 573 and Glycine 574 (producing the 574G fragment) precedes the cleavage between Arginine 93 and Glycine 94 (producing the 94G fragment), that the 94G fragment is localized to the plasma membrane of keratinocytes and has cross-linking activity, whereas the 574G fragment is dispersed in the cytosol and does not have detectable levels of activity on in situ transglutaminase assay, and that 1-alpha-25-dihydroxycholecalciferol or all-trans retinoic acid treatment and ultraviolet B exposure disturb the localization of the transglutaminase 1 fragments with changes in the morphology of differentiating keratinocytes. All these results demonstrate that the antibodies generated in this work are useful to dissect the mechanism by which transglutaminase 1 is activated, and would provide us with novel insights into the biogenesis of the epidermis.

In the previous study, we have found that G65C and I125T double mutant of alpha chaperonin homo-oligomer from a hyperthermophilic archaeum, Thermococcus sp. strain KS-1, lacks ATP-dependent protein refolding activity despite showing ATPase activity and the ability to bind the denatured proteins. In this study, we have characterized several mutant Thermococcus chaperonin homo-oligomers with the amino acid substitutions of Gly-65 or Ile-125. The results showed that amino acid residue at 65th position should be a small amino acid such as glycine or alanine for the ATP-dependent refolding activity. The alpha chaperonin homo-oligomers with amino acid substitution of Gly-65 by amino acids whose side chains are larger than the methyl group did not have ATP-dependent protein refolding activity, but exhibited an increase of the binding affinity for unfolded proteins in the presence of ATP or AMP-PNP. (c)2001 Elsevier Science.

A selective and sensitive high-performance liquid chromatographic method with chemiluminescence detection for the determination of 5-hydroxyindoles is described, based on the reaction of 5-hydroxyindoles with 4-dimethylaminobenzylamine. Serotonin, 5-hydroxyindole-3-acetic acid, 5-hydroxytryptophol, 5-hydroxyindole-3-acetamide and N-acetyl-5-hydroxytryptamine were used as model compounds to optimize the derivatization and chemiluminescent reaction. The reagent reacts with 5-hydroxyindoles in slightly alkaline media in the presence of potassium hexacyanoferrate(III) to give the corresponding derivatives, which can be separated on a reversed-phase column, Wakosil-II 5C18RS, with aqueous acetonitrile as an eluent. The derivatives were detected by peroxyoxalate chemiluminescence detection. The detection limits are in the range of 0.5-1.2 fmol per 100-microl injection. The method was applied to the simultaneous determination of serotonin and 5-hydroxyindole-3-acetic acid in human platelet-poor plasma.

We found an amber mutation in the open reading frame of the prion protein (PrP) gene. The codon 145 mutation (tyrosine to stop) was recognized on a PrP allele of a patient with Alzheimer-type clinical course. Pathologic examination revealed many amyloid plaques and neurofibrillary changes. However, the amyloid plaques in this patient were not composed of beta/A4 protein, but of PrP. Both wild and mutant PrP alleles were detected in the cerebral mRNA; however, only C-terminal truncated PrP was detected in the kuru plaques. We herein present evidence that only mutant PrP aggregates to make kuru plaques in the central nervous system.

The main purpose of this paper is to present our hypothesis concerning the antigen-antibody complex formation and the resolution system inside the syncytiotrophoblast to explain immunologic fetomaternal relationships. This hypothesis, derived from the results of our experiments, might be an answer to why the fetus is not rejected by the mother, in contradistinction to other allografts. We also believe that this hypothesis makes important contributions to the explanation of the immunologic processes of cells, i.e., those processes which work against antigens inside a living body.

Concentrations of free amino acids were measured in the temporal cortex of postmortem brains from four histologically verified cases with Alzheimer-type dementia (ATD) and eight histologically normal controls. The concentrations of taurine, glutamate, and gamma-aminobutyric acid, which are all neurotransmitter candidates, were significantly lower in the ATD brains than in the controls. These findings suggest that the involvement of amino acid neurons in ATD cannot be ruled out.

Steroidogenesis in the unfertilized hamster ova was investigated by indirect immunofluorescence study. delta 5-3 beta-Hydroxysteroid dehydrogenase (delta 5-3 beta-HSD) activity was found in hamster follicular and ovulatory ova with pregnenolone used as the substrate. A significant quantity of 17 beta-estradiol was detected in the ooplasm of follicular and ovulatory ova. No progesterone was found. The activity of delta 5-3 beta-HSD in follicular and ovulatory ova was inhibited by preincubation with 10 IU of human chorionic gonadotropin (hCG) in 1 ml of phosphate buffer solution. Trilostane, a potent new inhibitor of the delta 5-3 beta-HSD system, was found to inhibit the activity of delta 5-3 beta-HSD in ovulatory ova in 1 ml of phosphate buffer solution at a concentration of 10(-7)M. After these results were obtained, steroidogenesis of hamster ova was suggested in an indirect immunofluorescence study, and the implications of steroidogenesis for oocyte maturation and subsequent fertilization are discussed.

To determine a phenotypic difference between normal endometrium and endometrial adenocarcinoma, a new monoclonal antibody (MSN-1) was produced by immunizing a new endometrial cancer cell line (SNG-II), which was established in 1981 from a 43-year-old Japanese woman with stage II uterine endometrial cancer. MSN-1 recognized the Lewis-b carbohydrate moiety on the cell surface glycolipid and seldom reacted immunohistochemically with normal endometrium but with about 90% of endometrial cancer cases. By application of MSN-1 to flow cytometry, the possibility of differentiating endometrial normal cells from cancer cells was demonstrated.

One-cell embryos from certain mouse strains were found incapable of developing beyond the 2-cell stage in vitro (2-cell block), but a microinjection of EDTA effectively overcame this block. When 2-cell arrested embryos were fused with embryos that had developed to the late 2-cell stage in vivo, the fusants developed beyond the 2-cell stage. Microinjection of cytoplasm of in vivo 2-cell embryos into 1-cell embryos also obviated the 2-cell block. Analyses of 35S-labeled embryos by 2-dimensional polyacrylamide gel electrophoresis indicated changes in synthetic protein patterns possibly related to this block.

Analysis of cell surface charge of human sperm by means of free-flow electrophoresis revealed that the electrophoretic mobility of X-bearing sperm was faster than that of Y-bearing sperm, indicating that X-bearing sperm have a higher net negative charge on the cell surface than do Y-bearing sperm. Sialidase treatment of X- and Y-bearing sperm caused an obvious and progressive reduction in the electrophoretic mobilities of the two types of cells, until they finally merged into a single peak. This observation suggests that the difference in net negative charge between X- and Y-bearing sperm is due mainly to sialic acid content on the cell surface.

Several new histological findings in six cases of the trisomy D1 syndrome are described: hyperplasia of fetal structures (indusium griseum, median raphe of the medulla oblongata) and completely developed cerebellar cortical heterotopia in the dentate nucleus. In one case, a heterotopic pontine nucleus was found within the cerebellar white matter. The coexistence of overdeveloped and remaining fetal structures is emphasized. Several hypotheses regarding cerebellar dysgenesis are discussed.

Concentrations of free amino acids were measured in the cerebral cortices of post-mortem brains from 5 histologically verified cases of Alzheimer-type dementia (ATD) and 8 histologically normal controls. The concentration of glutamate in the ATD brains was significantly lower in the superior frontal, orbital, cingulate and inferior temporal cortices when compared with the control brains. The concentrations of taurine and gamma-aminobutyric acid in the ATD brains were significantly lower in the inferior temporal cortex. These findings suggest that amino acid neurons could be involved in ATD.

The sulfated form of cholecystokinin octapeptide (CCK-8) and ceruletide (CER), but not their non-sulfated forms of CCK-4, significantly decreased the rates of locomotor activity and rearing during the first 10 min test session 10 min after intracerebroventricular (ICV) administration at doses more than 25 and 3.125 mg, respectively. CER-S antagonized methylphenidate-induced hypermotility after ICV administration at a dose of 800 ng. Plasma levels of CER-like immunoreactivity (CER-LI) measured at 120 min after subcutaneous injection, when the locomotor suppressive activity induced by 100 and 200 micrograms was no longer observed, were similar to or much higher than that 30 min after ICV administration at a dose of 800ng, suggesting that the effects of ICV CER-S are not mediated by a peripheral redistribution. These findings indicate that (1) the structural requirement for the locomotor suppressive activity is sulfated tyrosine residue; (2) the behavioural effects of ICV-administered CCK-8-S and CER-S are due to their central actions and mediated by the/inhibition of the central dopamine (DA) function; and (3) CCK-8-S in the brain is functionally associated with the central DA system.

Diplococcal beta-galactosidase, which is known to be useful for the structural studies of glycoprotein-linked oligosaccharides, was found to show the same substrate specificity in cleaving Gal beta 1-4 linkages of glycolipids as that of the oligosaccharides. The optimum conditions of beta-galactosidase in the 80% ammonium sulfate precipitates of the culture medium of Streptococcus (Diplococcus) pneumoniae were determined with nLcOse4Cer radiolabeled by the galactose oxidase-NaB3H4 procedure. Detergent was required for the highest activity, and different combinations of several buffers and detergents showed different properties in stimulating beta-galactosidase, and in enhancing or suppressing N-acetyl-beta-hexosaminidase which was contaminated in the enzyme preparation. The optimum pH was found to be at 6.5, and specific activity and Km were 8.1 nmol/mg protein/h and 1 nmol, respectively. While more than 70% of beta-galactose was liberated from LacCer and nLcOse4Cer within 1 h under the optimum conditions to form GlcCer and nLcOse3Cer, respectively, none was liberated from LcOse4Cer, GalCer, GgOse4Cer, GbOse3Cer, IV3 alpha GalnLcOse4Cer, and Il3NeuAcGgOse4Cer, showing the substrate specificity solely to Gal beta 1-4 linkage.

The human uterine endometrium is a tissue in which cell proliferation and differentiation are strictly controlled by sex steroid hormones, and these hormone-controlled cellular events occurring in association with the menstrual cycle of the uterine endometrium should be accompanied by characteristic molecular and metabolic changes. To characterize the menstrual cycle at the molecular level, we analyzed the glycolipids of human uterine endometrium in the proliferative and secretory phases of the menstrual cycle. Neutral glycosphingolipids from uterine endometrium comprised globo-series glycosphingolipids, such as GlcCer, LacCer, Gb3Cer, and Gb4Cer, and the relative concentrations remained constant in the two phases. However, in the case of acidic glycosphingolipids, although the concentrations of sialoglycosphingolipids remained at constant levels in the two phases, sulfatide, I3-SulfoGalCer, dramatically increased from the proliferative to the secretory phase, amounting to 7-17 nmol/g dry weight in the proliferative phase and 115-245 nmol/g dry weight in the secretory phase. Since sulfatide was the only glycolipid that changed in association with the menstrual cycle, it is likely that the sulfotransferase responsible for the synthesis of sulfatide might be induced by sex steroid hormones, estrogen and progesterone, and that sulfatide might play an essential biological role in the secretory phase of the menstrual cycle in the uterine endometrium.

Total biopterin concentrations in the post-mortem human brain (caudate nucleus) and in the urine of controls and parkinsonian patients were measured by a newly developed radioimmunoassay. There was good correlation between the total biopterin level and tyrosine hydroxylase activity in the human brain. Biopterin concentrations in the caudate nucleus were greatly reduced in parkinsonian patients. In contrast, the reduction of urinary biopterin in parkinsonian patients was slight and not statistically significant, as compared with normal controls.