Elevated nocturnal desaturation index predicts mortality in interstitial lung disease.

BACKGROUND: Nocturnal desaturation may contribute to long-term pulmonary vascular stress in interstitial lung disease (ILD). We study the prevalence, severity and prognostic utility of nocturnal desaturation across ILD. METHODS: ILD patients with overnight oximetry (June 2006-August 2008) were reviewed (n = 134). Significant nocturnal desaturation was considered as > 10% of sleep with SpO2 < 90%. Desaturation index (DI) was defined as the number of desaturation events > 4%/hr. Covariates, including indices of nocturnal desaturation, were evaluated against mortality. RESULTS: Nocturnal desaturation was present in 49 (37%) patients. 31% of patients had pulmonary hypertension (PH) on echocardiography. Increased DI was associated with higher mortality independent of age, gender and BMI (HR 1.04; 95% CI 1.00, 1.06; p = 0.009). In separate models, DI and a) elevated brain natriuretic peptide (BNP; HR 1.04; 95% CI 1.00, 1.08; p = 0.04); b) moderate-severe PH on echocardiography (HR 3.15; 95% CI 1.24, 8.00; p = 0.02); and c) daytime resting SpO2 (HR 0.92; 95% CI 0.85, 0.99; p = 0.04) independently predicted mortality following adjustment for age, gender and BMI. CONCLUSION: Nocturnal desaturation is common and may be severe in ILD. Elevated nocturnal DI predicts higher mortality across ILD, independent of other vascular parameters. This finding may have important implications for the pathogenesis of PH in IPF.

Elevated brain natriuretic peptide predicts mortality in interstitial lung disease.

Elevated pulmonary vascular resistance portends a poor prognosis across interstitial lung disease (ILD), irrespective of the histospecific diagnosis. Currently, no noninvasive surrogate prognostic marker exists. We explore the prognostic value of brain natriuretic peptide (BNP) and echocardiography across ILD. ILD patients with BNP concentrations performed during 2005-2007 were reviewed (n = 90). Echocardiography tapes were reviewed by a cardiologist blinded to other results. Outcome was evaluated for survival against BNP and echocardiograph parameters. A priori threshold values and composite markers were evaluated against survival. During follow-up (20±9 months) there were 28 deaths (31%). BNP correlated with right heart echocardiographic indices, including right ventricular systolic pressure (RVSP) (R(2) = 0.18, p = 0.0002) but not with parameters of left heart function. Nonsurvivors had higher BNP and RVSP levels than survivors. BNP ≥20 pmol·L(-1) (hazard ratio (HR) 2.93, 95% CI 1.28-6.73; p = 0.01) and moderate-severe pulmonary hypertension (HR 2.53, 95% CI 1.15-5.57; p = 0.02) were associated with increased mortality, independent of age, sex and pulmonary function. Patients with BNP ≥20 pmol·L(-1) had a 14-fold increased mortality over those with BNP <4 pmol·L(-1). Increased BNP levels and/or echocardiographic markers of right ventricular dysfunction were associated with increased mortality across ILD. The link between vascular parameters and mortality supports the concept that pulmonary vascular disease contributes to the final common pathway seen across ILD.

RNA localization goes direct.

Direct injection of RNA provides a new view of localization during Drosophila oogenesis.

Translational regulation of maternal mRNAs.

Translational regulation of maternal mRNAs serves to constrain their activities in both time and space. Both types of constraint might be expected to be critical for normal development and the rather short list of maternal mRNAs for which this has been shown to be true has expanded considerably over the past year. Substantial progress has also been reported in the identification and characterization of the cis-acting elements and trans-acting factors that mediate translational regulation and their interactions with one another.

Formation of germ cells in Drosophila.

In Drosophila, germ-cell formation is directed by the posterior pole plasm of the embryo. Genes acting to provide the germ-cell determinant have been identified and characterized, and some are now being manipulated to test their roles. Although recent results largely support the notion of a simple pathway for assembly of pole plasm, complexities are becoming apparent.

Mutational analysis of an RNA recognition element that mediates localization of bicoid mRNA.

Localization signals are RNA regulatory elements that direct the localization of mRNAs to subcellular sites. Localization signals presumably function by mediating RNA recognition events through which the mRNA becomes associated with the localization machinery. At present little is known about individual RNA recognition events, which in turn has limited progress in identifying the trans-acting binding factors involved in these events. Here we describe a detailed characterization of the RNA elements required for the RNA recognition event, event A, that initiates localization of bicoid mRNA in the Drosophila ovary. One element is a helix in which nucleotide identities are not important, suggesting that it plays a primarily structural role. Immediately adjacent to the helix is a recognition domain in which the identities of some, but not all, nucleotides are important for function. Comparison of two related but different RNAs that both support recognition event A further defines the important features of the recognition domain.

BSF binds specifically to the bicoid mRNA 3' untranslated region and contributes to stabilization of bicoid mRNA.

The early stages of Drosophila melanogaster development rely extensively on posttranscriptional forms of gene regulation. Deployment of the anterior body patterning morphogen, the Bicoid protein, requires both localization and translational regulation of the maternal bicoid mRNA. Here we provide evidence that the bicoid mRNA is also selectively stabilized during oogenesis. We identify and isolate a protein, BSF, that binds specifically to IV/V RNA, a minimal form of the bicoid mRNA 3' untranslated region that supports a normal program of mRNA localization during oogenesis. Mutations that disrupt the BSF binding site in IV/V RNA or substantially reduce the level of BSF protein lead to reduction in IV/V RNA levels, indicating a role for BSF in RNA stabilization. The BSF protein is novel and lacks all of the characterized RNA binding motifs. However, BSF does include multiple copies of the PPR motif, whose function is unknown but appears in other proteins with roles in RNA metabolism.

Nucleotide chain length and the morphology of complexes with cationic amphiphiles: (31)P-NMR observations.

31P-NMR and UV spectroscopies were used to study the interactions between cationic amphiphile-containing lipid bilayers and either a phosphorothioate oligonucleotide (OligoS) (n=21) or polyadenylic acid (PolyA) (n approximately 18,000). Multilamellar vesicles (MLVs) were composed of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) or 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine (DOPE) in binary mixture with either of the cationic lipids, N-[1-(2, 3-dioleoyloxy)propyl]-N',N',N'-trimethylammonium chloride (DOTAP) or cetyltrimethylammonium bromide (CTAB). A UV-difference assay showed that OligoS binding ceased above a 1:1 anion/cation ratio, while PolyA binding continued until a 2:1 ratio was reached, indicating a 'flat' conformation for bound OligoS, but not necessarily for PolyA. Cross-polarization (31)P-NMR of the nucleotide chains bound to 100% DOTAP MLVs produced spectra virtually identical to those of dry powders of OligoS or PolyA, indicating effective immobilization of the surface-bound nucleotide chains. Hahn echo (31)P-NMR showed that MLVs composed of binary mixtures of POPC with DOTAP or CTAB retained a lamellar bilayer architecture upon adding nucleotide chains. At less than stoichiometric anion/cation ratios little or no signal attributable to free nucleotide chains was visible. A narrow signal at the chemical shift expected for phosphorothiodiesters or phosphodiesters became visible at greater levels of added OligoS or PolyA, respectively, indicating the presence of mobile nucleotide chains. Salt addition caused complete desorption of the nucleotide chains. When POPC was replaced with DOPE, binding of OligoS or PolyA produced non-bilayer lipid phases in the presence of DOTAP, but not in the presence of CTAB.

Influence of staphylococcal delta-toxin on the phosphatidylcholine headgroup as observed using 2H-NMR.

The interaction of the 8-toxin peptide isolated from Staphylococcus aureus with the headgroup region of lipid bilayer membranes composed of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) was investigated using deuterium (2H) and phosphorus (31P) nuclear magnetic resonance (NMR) spectroscopy. At relatively low peptide/lipid ratios (P/L < 0.10), all 2H- and 31P-NMR spectral lineshapes at 25 degrees C were indicative of a single population of liquid-crystalline lipids in a bilayer arrangement. At these P/L ratios, delta-toxin had only marginal effects on the size of the quadrupole splitting measured from POPC labelled at either the alpha-methylene (POPC-alpha-d2) or the beta-methylene segment (POPC-beta-d2) of the choline headgroup and, similarly small effects on the magnitude of the chemical shift anisotropy (CSA) of the 31P-NMR spectrum. With increasing amounts of delta-toxin (0.10 < P/L < 0.15) the size of the 2H quadrupole splitting from POPC-alpha-d2, as well as the magnitude of the 31P-CSA, decreased progressively and rapidly. The quadrupole splitting from POPC-beta-d2, however, remained relatively unaffected. At yet higher levels of delta-toxin (P/L > 0.15), all 2H- and 31P-NMR spectra indicated the presence of multiple lipid populations experiencing varying degrees of increased conformational disordering. The spectral lineshapes of these apparently nonbilayer spectral components reverted to bilayer-type lineshapes upon lowering the measuring temperature to 5 degrees C. At the utmost highest level of delta-toxin measured here (P/L = 0.20), all 2H- and 31P-NMR spectra consisted of a single, broad, apparently nonbilayer-type component, indicative of hindered but virtual isotropic motional averaging of the POPC headgroups. In this case no reversion to bilayer-type spectra could be obtained by decreasing the temperature. We could obtain no evidence that the conformation of the choline headgroup of POPC was responding to any specific influence of delta-toxin on bilayer surface electrostatics.

Determination of the pKa of membrane-bound N,N-dimethylsphingosine using deuterium NMR spectroscopy.

Deuterium nuclear magnetic resonance (2H-NMR) spectroscopy was applied to determine the pKa of the protein kinase C (PKC) inhibitor, N,N-dimethylsphingosine (DMS), when bound to lipid bilayers composed of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC). The quadrupolar splittings from the deuterium labels at the alpha- and the beta-choline positions of the headgroup of POPC responded to the presence of DMS in a manner indicative of an accumulation of cationic charges near the surface plane occupied by the phospholipid phosphate group. Both quadrupolar splittings varied linearly with the amount of added DMS at pH 7.0. Conversely, at pH 10.0 DMS had virtually no influence on either quadrupole splitting, an effect attributed to titration of the dimethyl amino group of DMS to its neutral form. A DMS titration curve was obtained by quantifying the change in the quadrupolar splittings as a function of pH. The pKa of membrane-bound DMS was extracted from this 2H-NMR data by simulating the quadrupole splitting-titration curve for different values of the pKa, yielding a pKa of 8.8 after non-linear least squares fitting.

Cationic amphiphile interactions with polyadenylic acid as probed via 2H-NMR.

2H-NMR spectroscopy was used to investigate the effects of polyadenylic acid (PolyA) on three aminomethyl-deuterated cationic amphiphiles: specifically, N-[1-(2,3-dioleoyloxy)propyl]-N',N',N'-trimethylammonium chloride (DOTAP-gamma-d3), 3beta-[N-(N',N',N'-trimethylaminoethane)carbamoyl] cholesterol (TC-CHOL-gamma-d3), and cetyltrimethylammonium bromide (CTAB-gamma-d9). When mixed with 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) and incorporated into lipid bilayer membranes, each of the cationic amphiphiles yielded 2H-NMR spectra consisting of a motionally averaged Pake powder pattern. The 2H-NMR quadrupolar splitting generally increased with increasing mole fraction of cationic amphiphile in the lipid bilayer with the exception of CTAB-gamma-d9. Adding PolyA caused the quadrupolar splitting to increase progressively in every case, until a 1:1 cation:anion charge ratio was achieved, after which the quadrupolar splitting changed no further. Deuterium NMR relaxation time measurements showed a parallel increase in T(qe)2 with increasing PolyA. The size of these changes produced by PolyA increased in the order: TC-CHOL < DOTAP < CTAB. NaCl addition reversed much, but not all, of the PolyA-related changes in 2H-NMR quadrupolar splittings and T(qe)2 relaxation times. A UV-based PolyA-membrane binding assay showed that salt addition caused PolyA desorption, and that the salt concentration required to do so increased in the order: TC-CHOL < DOTAP < CTAB. The results are consistent with an electrostatic binding of PolyA to the cationic lipid bilayer surface, accompanied by formation of a stoichiometric charge complex between PolyA and the cationic amphiphile, in which the cationic amphiphile retains considerable motional freedom. The strength of the complex increases in the order: TC-CHOL < DOTAP < CTAB.

Partial purification and properties of mammalian phosphatidylglycerophosphatase.

The phosphatidylglycerophosphatase (EC 3.1.3.27) activity of rat liver mitochondria was investigated by assaying the conversion of 14C-labelled phosphatidylglycerophosphate to phosphatidylglycerol. The activity was associated with a mitochondrial membrane fraction and could not be released into solution employing techniques applicable to a peripheral membrane protein. The enzyme was partially purified by sonication, pH 5.0 precipitation, and gel filtration. Various ionic and nonionic detergents as well as numerous divalent cations inhibited the phosphatase. The enzyme displayed a high affinity for phosphatidylglycerophosphate.

Surface charge response of the phosphatidylcholine head group in bilayered micelles from phosphorus and deuterium nuclear magnetic resonance.

Solid-state phosphorus (31P) and deuterium (2H) nuclear magnetic resonance (NMR) spectroscopy over the temperature range of 25-50 degreesC were used to investigate bilayered micelles (bicelles) composed of 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) and 1, 2-dihexanoyl-sn-glycero-3-phosphocholine (DHPC) in the presence of either the anionic lipid 1,2-dimyristoyl-sn-3-phosphoglycerol (DMPG) or the cationic lipid 1,2-dimyristoyl-3-trimethylammonium-propane (DMTAP). The 31P-NMR spectra demonstrate that bicellar structures form with DMPG/DMPC ratios ranging from 0 to 50/50 and with DMTAP/DMPC ratios from 0 to 40/60, while the overall concentration of DHPC remains constant. The formation of bicelles containing charged amphiphiles is contingent upon the presence of NaCl, with 50 mM NaCl being sufficient for bicelle formation at all concentrations of charged amphiphile investigated, while 150 mM NaCl affords better resolution of the various 31P-NMR resonance signals. The 2H-NMR spectra demonstrate that the quadrupolar splittings (Deltanu) of head group-deuterated DMPC change inversely as a function of the amount of negative versus positive charge present, and that the changes for deuterons on the alpha-carbon are opposite in sense to those for deuterons on the beta-carbon. This indicates that head group-deuterated phosphatidylcholine functions as a molecular voltmeter in bicelles in much the same fashion as it does in spherical vesicles.

Deuterium NMR studies of the interactions of polyhydroxyl compounds and of glycolipids with lipid model membranes.

The physical properties of bilayers composed of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) in the presence of four water-soluble polyhydroxyl compounds, trehalose, sorbitol, glycerol, and ethyleneglycol, and three neutral glycolipids - monogalactosyldiacylglycerol (MGDG), digalactosyldiacylglycerol (DGDG) and nonhydroxy fattyacyl-cerebrosides (NHFA-Cer) - were investigated using 2H-NMR. All four polyhydroxyl compounds induced small, but comparable concentration-dependent changes in the choline headgroup conformation which were consistent with the presence of a small negative charge being conferred upon the bilayer surface. The latter may be explained by dipolar interactions brought about by changes in the long-range order of the water layer at the membrane surface. Trehalose had a small ordering effect on the hydrophobic interior of the membrane while ethyleneglycol induced a disordering, at both the head group level and in the hydrophobic interior. The presence of high amounts of carbohydrate at the membrane surface was ensured when POPC was mixed with various proportions of one of three glycolipids, MGDG, DGDG and NHFA-Cer. In these cases the conformation of the choline headgroup was only marginally altered when not masked by macroscopic phase changes. The headgroup conformational changes observed in the presence of any of the above-mentioned compounds were modest in comparison to the effects induced by charged substances.

Influence of lipid lateral distribution on the surface charge response of the phosphatidylcholine headgroup as detected using 2H nuclear magnetic resonance.

The effect of lipid lateral distribution on the surface charge response of the phosphatidylcholine headgroup, in bilayers composed of binary mixtures of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) and 1,2-dimyristoyl-sn-glycero-3-phosphate (DMPA), was investigated by monitoring the deuterium nuclear magnetic resonance (2H-NMR) spectrum of choline-deuterated phosphatidylcholine as a function of temperature and DMPA concentration. Addition of DMPA at temperatures corresponding to fully liquid-crystalline membranes caused a progressive increase (decrease) in the 2H-NMR quadrupole splitting from POPC-alpha-d2 (POPC-beta-d2), in agreement with the known response of phosphatidylcholine to negative membrane surface charge (Seelig, J., Macdonald, P.M. and Scherer, P.G. (1987) Biochemistry 26, 7535-7541). Lateral phase separation of DMPA-rich domains was induced in these mixtures by lowering the temperature in the range from 60 degrees C to -15 degrees C, and was accompanied by a reversal of the original effects of DMPA on the quadrupole splitting. Analysis of the 2H-NMR spectral response allows one to generate a temperature/composition phase diagram for the POPC/DMPA system. We conclude that 2H-NMR of headgroup-deuterated phosphatidylcholine can be employed to sense and to quantify inhomogeneities in the lateral distribution of charged membrane components.

Destabilization of cationic lipid vesicles by an anionic hydrophobically modified poly(N-isopropylacrylamide) copolymer: a solid-state 31P NMR and 2H NMR study.

The effect of binding PNIPAM-Py-Gly, a copolymer of N-isopropylacrylamide, N-[4-(1-pyrenyl)butyl]-N-n-octadecylacrylamide and N-glycydyl-acrylamide, on membrane stability in cationic multilamellar vesicles (MLVs) was examined using solid-state phosphorus (31P) and deuterium (2H) nuclear magnetic resonance (NMR) spectroscopy. For MLVs of composition n-octadecyldiethylene oxide (ODEO)+cholesterol (CHOL)+1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC)+dimethyldioctadecylammonium bromide (DODAB) (molar ratios 75:10.5:10.5:4), PNIPAM-Py-Gly induced a complete conversion from a bilayer-type 31P NMR spectrum to one characteristic of lipids undergoing isotropic motional averaging, indicating the existence of regions of high local membrane curvature. This response was sustained even at elevated temperatures. For MLVs of composition POPC+1,2-dioleoyloxy-3-(trimethylammonio)-propane (DOTAP), only at high levels of DOTAP and ionic strength did PNIPAM-Py-Gly induce even a partial conversion to an isotropic-type 31P NMR spectrum. At lower pH this effect was diminished. Raising the temperature eliminated the isotropic 31P NMR spectral component, and this effect was not reversible upon returning to room temperature. 2H NMR spectroscopy of headgroup-deuterated DOTAP and POPC confirmed the 31P NMR results, but did not provide specific surface electrostatic information. We conclude that the binding of PNIPAM-Py-Gly to phospholipid-based vesicles is dominated by electrostatic attraction between cationic lipids and the polymer's glycine residues. At high binding levels, the polymer assumes a collapsed conformation at the surface, resulting in regions of high local curvature of the lipid assembly. For ODEO-based liposomes, these effects are magnified by the additional contribution of hydrogen bonding to the strength of polymer binding.

Genetic evidence for physical interactions between enzymes of nucleotide synthesis and proteins involved in DNA replication in bacteriophage T4.

We have found that mutations in phage T4 genes 41 (five of five) and 61 (three of three) cause resistance to the folate analogue pyrimethamine that inhibits T4 dihydrofolate (FH2) reductase. These genes code for subunits of a T4 primase and are part of a putative T4 replication complex. In contrast to many previously isolated folate analogue-resistant (Far) T4 mutants, these T4 primase mutants do not overproduce FH2 reductase nor do they alter its primary structure. A new mutant with a single lesion in gene 41 was isolated which proved resistant to the folate analogue at 30 degrees and was lethal at 42 degrees. This mutant induced normal levels of FH2 reductase (encoded by the frd gene) and appeared to have normal expression of other T4 genes at 30 degrees. Like other mutations in gene 41, tsP129 reduced phage-induced DNA synthesis to about 15% that of wild-type T4 as measured by thymidine incorporation under restrictive conditions. Double mutants carrying mutations in genes 41 and 61, 41 and frd or 61 and frd showed allele-specific suppression suggesting that the products of these genes interact. We suggest that abnormal interactions between components of the replication complex and a DNA precursor synthesizing complex cause folate analog resistance by allosterically altering the T4 FH2 reductase.

Cloning and physical mapping of an early region of the bacteriophage T4 genome.

We have cloned DNA restriction fragments from the largely nonessential region of bacteriophage T4 located between genes 39 and 56. The cloned DNA fragments were used to construct a precise map of the sites in this region recognized by eight restriction endonucleases. This restriction map allowed us to compare the cytosine-containing T4 DNA used for cloning with the hydroxymethylcytosine-containing DNA of wild-type T4; there were no detectable rearrangements in the region tested. We were also able to determine the physical locations of several deletion end points and of several genes.

Regulation of a bacteriophage T4 late gene, soc, which maps in an early region.

We have sequenced and analyzed the expression of an early region of the bacteriophage T4 genome that surprisingly contains a late gene, soc. soc is oriented in the same direction as early genes, like the T4 lysozyme gene. Northern hybridization of early and late T4 RNA, using cloned T4 restriction fragments as probes, identified two long early transcripts and a short late transcript, all containing the soc-coding sequence. Thus, soc is transcribed both early and late. It is, however, translated only late. The inhibition of soc translation from the long early transcripts can be explained by formation of a hairpin in the RNA that sequesters the soc ribosome-binding site. The transcript initiated at the late promoter cannot form this hairpin and is, therefore, translated.

Components acting in localization of bicoid mRNA are conserved among Drosophila species.

Substantial insights into basic strategies for embryonic body patterning have been obtained from genetic analyses of Drosophila melanogaster. This knowledge has been used in evolutionary comparisons to ask if genes and functions are conserved. To begin to ask how highly conserved are the mechanisms of mRNA localization, a process crucial to Drosophila body patterning, we have focused on the localization of bcd mRNA to the anterior pole of the embryo. Here we consider two components involved in that process: the exuperantia (exu) gene, required for an early step in localization; and the cis-acting signal that directs bcd mRNA localization. First, we use the cloned D. melanogaster exu gene to identify the exu genes from Drosophila virilis and Drosophila pseudoobscura and to isolate them for comparisons at the structural and functional levels. Surprisingly, D. pseudoobscura has two closely related exu genes, while D. melanogaster and D. virilis have only one each. When expressed in D. melanogaster ovaries, the D. virilis exu gene and one of the D. pseudoobscura exu genes can substitute for the endogenous exu gene in supporting localization of bcd mRNA, demonstrating that function is conserved. Second, we reevaluate the ability of the D. pseudoobscura bcd mRNA localization signal to function in D. melanogaster. In contrast to a previous report, we find that function is retained. Thus, among these Drosophila species there is substantial conservation of components acting in mRNA localization, and presumably the mechanisms underlying this process.