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The regulatory roles for non-coding RNAs, the long non-coding RNAs and microRNAs, are emerging as crucial determinants of central nervous system development and function. Neuronal growth regulator 1 (NEGR1) is a cell adhesion molecule that has been shown to play an important role in neurite outgrowth during neuronal development. Precise expression of the Negr1 gene is crucial for proper brain development and is dysregulated during brain injury. Hence, we attempted to elucidate the non-coding RNAs that control Negr1 gene expression. A long non-coding RNA, BC048612, transcribed from the bidirectional GC-rich Negr1 gene promoter was found to influence Negr1 mRNA expression. In vitro knockdown of the long non-coding RNA resulted in significant down-regulation of Negr1 mRNA expression, NEGR1 protein levels and neurite length whereas over-expression enhanced Negr1 mRNA expression, NEGR1 protein levels and increased neurite length. Meanwhile, another non-coding RNA, microRNA-203, was found to target the 3' untranslated region of the Negr1 mRNA. Inhibition of microRNA-203 led to increased expression of Negr1 mRNA, elevated NEGR1 protein levels and increased neurite length. Conversely, microRNA-203 over-expression decreased the level of Negr1 mRNA, NEGR1 protein and neurite length. Neither microRNA-203 nor the long non-coding RNA, BC048612 could influence each other's expression. Hence, the long non-coding RNA, BC048612, and microRNA-203 were determined to be positive and negative regulators of Negr1 gene expression respectively. These processes have a direct effect on NEGR1 protein levels and neurite length, thus highlighting the importance of the regulatory non-coding RNAs in modulating Negr1 gene expression for precise neuronal development., (Copyright © 2015 Elsevier B.V. All rights reserved.)

Fourier transform infrared spectroscopy was applied to study the structural and thermal properties of bovine brain galactocerebroside (GalCer) containing amide linked non-hydroxylated or alpha-hydroxy fatty acids (NFA- and HFA-GalCer, respectively). Over the temperature range 0-90 degrees C, both GalCer displayed complex thermal transitions, characteristic of polymorphic phase behavior. Upon heating, aqueous dispersions of NFA- and HFA-GalCer exhibited high order-disorder transition temperatures near 80 and 72 degrees C, respectively. En route to the chain melting transition, the patterns of the amide I band of NFA-GalCer were indicative of two different lamellar crystalline phases, whereas those of HFA-GalCer were suggestive of lamellar gel and crystalline bilayers. Cooling from the liquid-crystalline phase resulted in the formation of another crystalline phase of NFA-GalCer and a gel phase of HFA-GalCer, with a phase transition near 62 and 66 degrees C, respectively. Prolonged incubation of GalCer bilayers at 38 degrees C revealed conversions among lamellar crystalline phases (NFA-GalCer) or between lamellar gel and crystalline bilayer structures (HFA-GalCer). Spectral changes indicated that the temperature and/or time induced formation of the lamellar crystalline structures of NFA- and HFA-GalCer was accompanied by partial dehydration and by rearrangements of the hydrogen bonding network and bilayer packing mode of GalCer.

The interactions of 6-lauroyl-2-dimethylaminonaphthalene (Laurdan) with L-alpha-dimyristoylphosphatidylcholine (DMPC) have been studied isothermally at 28 degrees C by Fourier-transform infrared spectroscopy (FTIR) at two pH values (6.8 and 3.0) and over the pressure range of 0.001-25 kbar. The results obtained with Laurdan are compared with those previously obtained with 6-propionyl-2-dimethylaminonaphthalene (Prodan) (Chong et al. (1989) Biochemistry 28, 8358-8363). The objective of this study is to delineate the differential interactions of Prodan and Laurdan with lipid membranes. The Laurdan carbonyl and naphthalene vibrational bands as well as the correlation field splitting of the methylene scissoring mode all indicate that in phospholipid model membrane systems, Laurdan behaves differently from Prodan. The data suggest that the chromophore of Laurdan is embedded somewhat deeper in the membrane than that of Prodan. The correlation field splitting pressure suggests that Laurdan causes more perturbation to DMPC vesicles than Prodan. Instead of being relocated to the exterior of the membrane as is the case of Prodan, Laurdan is found to remain in the membrane even when it is partially positively charged at pH 3. Apparently the stabilizing forces come from the strong van der Waals and hydrophobic interactions between the lauroyl chain and its neighboring lipid molecules. Laurdan seems to remain in the membrane at high pressures (up to 25 kbar). Using deuterated DMPC (d-DMPC) and deuterated L-alpha-dipalmitoylphosphatidylcholine (d-DPPC), we have demonstrated that, at 1 atm, there is a void space between the lauroyl chain of Laurdan and the acyl chain of the matrix lipid, regardless of the physical state of the matrix lipid. This void space, probably caused by the bulky naphthalene ring, is eventually diminished by elevated pressures.

Pressure-induced conformational changes in two proteins, bovine serum albumin (BSA) and immunoglobulin G (IgG), were studied to assess the application of hyperbaric manipulation to the dissociation of antigen-antibody complexes. Antigen-antibody dissociation is important in the product-recovery phase of immunoadsorption, an affinity purification process. Three techniques were used in parallel for this study, including fluorescence, Fourier transform infrared (FTIR) spectroscopy, and the enzyme-linked immunosorbent assay (ELISA). Employing a fluorescent probe, fluorescent intensity measurements were used to detect protein conformational changes. FTIR spectroscopy was used to determine changes in protein secondary structure induced by high pressure, while the ELISA test was used to examine antibody recognition after the proteins had been pressure-treated. The results from this work demonstrate that IgG is resistant to conformational changes induced by pressures below 2 kbar. In contrast, BSA undergoes reversible conformational changes in this pressure range. However, these conformational changes are not reflected in tests measuring antibody recognition. These findings indicate that IgGs have the potential to be used as recycled ligands in immunoadsorption separation processes. Different antigens that are being considered for purification by immunoadsorption and separated by means of high pressure could be screened by the methods disclosed to determine their stability under high pressure conditions.

For the first time, high-pressure infrared spectroscopy has been used in an enzyme kinetics study. This technique allows not only the investigation of kinetics under very high pressure, but it also allows simultaneous determinion of changes in the secondary structure of enzymes at the corresponding pressures. In the present study, a classical enzyme reaction, the conversion of p-nitrophenol phosphate into p-nitrophenol by alkaline phosphatase was selected to demonstrate the potential of infrared spectroscopy as an alternative physical method in the high-pressure study of enzyme kinetics. The rate constants of this enzyme reaction have been determined as a function of pressure in the pressure range 0.001-14 kbar. The first-order rate constants thus obtained increases with increasing pressure up to 8.3 kbar. At this pressure, the reaction rate decreases abruptly due to the denaturation of the enzyme arising from the conformational changes of some alpha-helical segments in the enzyme molecules into beta-sheet structure. The present results suggest that the pressure-enhanced overall hydrogen-bond strength in the amide groups of the enzyme is one of the factors which stimulate the enzyme activity. Moreover, the dissociation of the dimeric enzyme into its subunits does not inhibit the enzyme activity but only attributes to a slight change in activation volume.

Changes in the secondary structure and aggregation of chymotrypsinogen were investigated by infrared difference spectroscopy in conjunction with temperature and pressure tuning IR spectroscopy; both the amide I' band and side chain bands were studied. A prominent component of the amide I' band in the difference spectrum obtained upon cooling a chymotrypsinogen solution, or increasing the hydrostatic pressure, was observed in the region between 1627 and 1622 cm-1. Under denaturing conditions a white gel was formed, which is attributed to irreversible self-association or aggregation. This process was accompanied by the appearance of two new amide I' bands in the infrared spectrum of the protein: a very strong band at 1618 cm-1 and a weak band at 1685 cm-1. These bands are assigned to peptide segments with anti-parallel aligned beta-strands.

The barotropic behavior of aqueous dispersions of two representative omega-cyclohexyl phosphatidylcholines was investigated by pressure-tuning Fourier transform infrared spectroscopy. In the even-numbered homologue, 1,2-di-14-cyclohexyltetradecanoyl-sn-glycero-3-phosphocholine (14cyPC), the lipid molecules are orientationally disordered until the applied pressure reaches 2.1 kbar. This pressure marks the onset of correlation field splitting of the scissoring and rocking modes of the linear chain methylenes, as well as that of the cyclohexyl ring methylenes. It indicates immobilization of the entire acyl chains, whereby the zig-zag planes of the neighboring straight chain all-trans methylenes are oriented mainly perpendicular to each other. As judged from the magnitude of the correlation field splittings, the interchain interaction is weaker in 14cyPC than that in linear lipids (e.g., DMPC or DPPC). Upon an increase in pressure, up to 20 kbar, the zig-zag methylene planes in 14cyPC undergo a gradual transformation to a parallel orientation. In the odd-numbered homologue, 1,2-di-13-cyclohexyltridecanoyl-sn-glycero-3-phosphocholine (13cyPC), there is no correlation field splitting originating from the straight chain methylenes (up to 21 kbar). The linear, nonbranched segments of the omega-cyclohexyl chains in 13cyPC are closely packed with the all-trans methylene zig-zag planes oriented parallel to each other. There is, however, correlation field splitting of the ring methylenes, indicating interring interactions between the bulky cyclohexyl rings in opposing bilayer leaflets. There are major structural differences between the even- and odd-numbered homologues in the interfacial region, which remain even at high pressures. The ester carbonyl C = O stretching band in 14cyPC is a composite of two discrete bands which do not change considerably in intensity or frequency in the pressure range 2-20 kbar. In contrast, 13cyPC possesses an additional, low-frequency C = O stretching component at low pressures. As the pressure increases, the three component bands coalesce into a single C = O stretching band. Our results suggest equally oriented, fully hydrogen-bonded carbonyl groups in 13cyPC at pressures above approx. 10 kbar.

The Ca2(+)-ATPase of sarcoplasmic reticulum is irreversibly inactivated by exposure to 1.5-2.0 kbar pressure for 30-60 min in a Ca2(+)-free medium; mono- or decavanadate (5 mM) or to a lesser extent Ca2+ (2-20 mM) protect against inactivation (Varga et al. (1986) J. Biol. Chem. 261, 13943-13956). The structural basis of these effects was analyzed by FTIR spectroscopy of sarcoplasmic reticulum in 2H2O medium. The inactivation of the Ca2(+)-ATPase at 1.5-2.0 kbar pressure in a Ca2(+)-free medium was accompanied by changes in the Amide II region of the spectrum (1550 cm-1), that are consistent with increased hydrogen-deuterium (H-2H) exchange, and by the enhancement of a band at 1630 cm-1 in the Amide I region, that is attributed to an increase in beta sheet. The frequency of the peak of the Amide I band shifted from about 1648 cm-1 at atmospheric pressure to 1642 cm-1 at approximately equal to 12.5 kbar pressure, suggesting a decrease in alpha helix, and an increase in beta and/or random coil structures. Upon releasing the pressure, the shift of the Amide I band was partially reversed. Vanadate (5 mM), and to a lesser extent Ca2+ (2-20 mM), protected the Ca2(+)-ATPase against pressure-induced changes both in the Amide I and Amide II regions of the spectrum, together with protection of ATPase activity. These observations establish a correlation between the conformation of the Ca2(+)-ATPase and its sensitivity to pressure. The involvement of the ATP binding domain of the Ca2(+)-ATPase in the pressure-induced structural changes is suggested by the decreased polarization of fluorescence of fluorescein 5'-isothiocyanate covalently attached to the enzyme.

A new thermotropic phase transition, at -30 degrees C and atmospheric pressure, was found to occur in the gel phase of aqueous DPPC dispersions. The Raman spectral changes at this phase transition are similar to those observed in the gel phase of DMPC dispersions at -60 degrees C. The thermotropic phase transition at -30 degrees C is equivalent to the barotropic GII to GIII phase transition observed in DPPC at 1.7 kbar and 30 degrees C. It is shown that the rate of the large angle interchain reorientational fluctuations decreases gradually with decreasing temperature, and that the orientationally disordered acyl chain structure of the GII phase is extended into the GIII phase of DPPC. The interchain interaction, arising from the damping of the reorientational fluctuations, increases with decreasing temperature in the GII gel phase as well as in the GIII gel phase.

High-pressure infrared spectroscopy is used to compare the barotropic behaviour of various interdigitated lipid bilayer systems (1,2-di-O-hexadecyl-sn-glycero-3-phosphocholine, 1,3-dipalmitoyl-sn-glycero-2-phosphocholine and 1-palmitoyl-sn-glycero-3-phosphocholine) with non-interdigitated bilayers of 1,2-dipalmitoyl-sn-glycero-3-phosphocholine. In the pressure range between 0 and 20 kbar, we have monitored the pressure dependence of the relative peak height intensity ratio of the chain methylene scissoring band, delta CH2, and its correlation field component band, delta'CH2. We demonstrate that this parameter, in conjunction with a visual inspection of the pressure-induced correlation field splittings of the methylene scissoring and rocking mode bands, can provide reliable indications of chain interdigitation.

Small-angle neutron scattering of the trans-unsaturated DEPC has been investigated as a function of pressure at 12, 18.6 and 35 degrees C. A pressure-induced structural phase transition from a liquid-crystalline state to a gel state is observed at the temperatures studied. The critical pressure of this transition increases with increasing temperature with a delta P/delta T value of 51 bar/C degrees. The small-angle neutron scattering results indicate that the effect of the trans double bonds in DEPC is to enhance the conformational disorder in the hydrocarbon chains. In DEPC bilayers, a pressure-induced conformational ordering process is observed not only in the liquid-crystalline phase but also in the gel phase, which indicates that conformational disorder exists in the liquid-crystalline phase as well as in the gel phase.

Infrared spectra of chymotrypsinogen in 2H2O have been measured as a function of pressure up to 30 kbar. An irreversible denaturation is induced at 7.6 kbar where the contributions of the random coil and turn conformational substructures to the protein structure increase dramatically at the expense of the contributions of the alpha-helix and beta-sheet substructures. The pressure at which denaturation starts is higher when pressure is applied more slowly. The rate of H-2H exchange of the interior labile protons on the amide groups is dramatically increased by external pressure and is closely associated with the global conformational structure of the protein. This suggest that pressure denaturation involves the bulk of the molecule. The results are compared with those obtained from other experimental approaches and with temperature-induced denaturation.

Fourier transform infrared spectroscopy performed with a high pressure diamond anvil cell was used to study hydrogen bonding between anhydrous phosphatidylcholines and cholesterol at the molar ratio 4:1. The hydroxyl group of cholesterol which acts as a proton donor, engages in strong hydrogen bonding to the sn-2 chain carbonyl group of DMPC, DPPC and HPPC and in weak hydrogen bonding to the phosphate group of all these phospholipids. No evidence of hydrogen bonding between cholesterol and the sn-1 chain carbonyl group of DMPC and DPPC was found. From a comparison of the relative hydrogen-bond strengths between cholesterol or water and the sn-2 chain carbonyl and phosphate groups of all these phospholipids, it is predicted that in aqueous dispersions of cholesterol containing phospholipids, the hydrogen bond of cholesterol to the phosphate group would be replaced by that of water, while the hydrogen bond of cholesterol to the sn-2 chain carbonyl group would remain intact.

The effect of hydrostatic pressure on the conformational properties of the E. coli methionine repressor protein in aqueous solution was investigated by infrared spectroscopy. Changes in hydrostatic pressure produce dramatic changes in the spectral region of the conformation-sensitive amide I band. As the pressure is raised up to 18 kbar, the protein undergoes a rearrangement of alpha-helical segments into beta-type structures; after the pressure is released the beta-strands reconvert into less ordered alpha-helical or random segments.