Long- and short-range signals control the dynamic expression of an animal hemisphere-specific gene in Xenopus

Little is known of the control of gene expression in the animal hemisphere of the Xenopus embryo. Here we show that expression of FoxI1e, a gene essential for normal ectoderm formation, is expressed regionally within the animal hemisphere, in a highly dynamic fashion. In situ hybridization shows that FoxI1e is expressed in a wave-like fashion that is initiated on the dorsal side of the animal hemisphere, extends across to the ventral side by the mid-gastrula stage, and is then turned off in the dorsal ectoderm, the neural plate, at the neurula stage. It is confined to the inner layers of cells in the animal cap, and is expressed in a mosaic fashion throughout. We show that this dynamic pattern of expression is controlled by both short- and long-range signals. Notch signaling controls both the mosaic, and dorsal/ventral changes in expression, and is controlled, in turn, by Vg1 signaling from the vegetal mass. FoxI1e expression is also regulated by nodal signaling downstream of VegT. Canonical Wnt signaling contributes only to late changes in the FoxI1e expression pattern.These results provide new insights into the roles of vegetally localized mRNAs in controlling zygotic genes expressed in the animal hemisphere by long-range signaling. They also provide novel insights into the role of Notch signaling at the earliest stages of vertebrate development.     

Long- and short-range interactions in native protein structures are consistent/minimally frustrated in sequence space

We show that long- and short-range interactions in almost all protein native structures are actually consistent with each other for coarse-grained energy scales; specifically we mean the long-range inter-residue contact energies and the short-range secondary structure energies based on peptide dihedral angles, which are potentials of mean force evaluated from residue distributions observed in protein native structures. This consistency is observed at equilibrium in sequence space rather than in conformational space. Statistical ensembles of sequences are generated by exchanging residues for each of 797 protein native structures with the Metropolis method. It is shown that adding the other category of interaction to either the short- or long-range interactions decreases the means and variances of those energies for essentially all protein native structures, indicating that both interactions consistently work by more-or-less restricting sequence spaces available to one of the interactions. In addition to this consistency, independence by these interaction classes is also indicated by the fact that there are almost no correlations between them when equilibrated using both interactions and significant but small, positive correlations at equilibrium using only one of the interactions. Evidence is provided that protein native sequences can be regarded approximately as samples from the statistical ensembles of sequences with these energy scales and that all proteins have the same effective conformational temperature. Designing protein structures and sequences to be consistent and minimally frustrated among the various interactions is a most effective way to increase protein stability and foldability.     

Neutron diffraction from cannabinoids in phospholipid membranes

Neutron diffraction measurements have been utilized to study the effects of delta 9-tetrahydrocannabinol (delta 9-THC) and delta 8-tetrahydrocannabinol (delta 8-THC) incorporated in phospholipid membranes of dipalmitoylphosphatidylcholine (DPPC). Low-angle diffraction indicated that these cannabinoids induce increases in interlamellar spacing similar to those produced by cholesterol. Wide-angle diffraction indicated significant differences in how the intralamellar structure is affected by the inclusion of either cannabinoids or cholesterol. Similar weight percentages of cholesterol and cannabinoids in membranes yielded different thermal analysis profiles but the profiles for membranes with either delta 8 or delta 9-THC were similar. Since the neutron diffraction results for inclusions of delta 8 and delta 9-THC were also similar, this suggests that the difference in psychoactivity of delta 8 and delta 9-THC is probably due to interactions with membrane proteins rather than with phospholipids.     

Role of chemical short-range order in atomic dynamics decoupling

Abstract

Using molecular dynamics simulation, α-relaxation times τ_α and self-diffusion coefficients D for Al₉₀Fe₁₀, Al₈₀Fe₂₀, Al₇₀Fe₃₀, Al₆₀Fe₄₀ and Al₈₀Ni₂₀ (as a contrast system) melts have been systematically computed over a wide temperature range (1000–2000 K). The computed results reveal that τ_Fe/τ_Al (or D_Al/D_Fe) for the Al₉₀Fe₁₀ and Al₈₀Fe₂₀ melts exhibit an accelerating increase with cooling at temperatures lower than 1400 K, implying a clear decoupling of dynamics of Al and Fe (here referred to as component decoupling). This component decoupling diminishes in Al₇₀Fe₃₀ melt and disappears in Al₆₀Fe₄₀ melt. We simultaneously checked the relaxation decoupling (i.e. the decoupling between α-relaxation and diffusion). The relaxation decoupling is clear in Al₆₀Fe₄₀ melt, less clear in Al₇₀Fe₃₀ melt and not shown in Al₈₀Fe₂₀ and Al₉₀Fe₁₀ melt. It exhibits a tendency counter to that of component decoupling with changing composition, arguing that relaxation decoupling does not necessarily lead to component decoupling. This finding is contradicted against the conventional view that component decoupling is believed as a result of relaxation decoupling. We further attributed such a contradiction to the difference in the degree of chemical short-range order (CSRO) in melts. The existence of CSRO can increase the cooperativity in dynamics of different components. So it is better to consider component decoupling as a combined effect of relaxation decoupling and CSRO. This work would be helpful in improving our understanding of the relationship between the two kinds of decoupling.     

Optically active molecule-based magnets: enantioselective self-assembling, optical, and magnetic properties.

In this short communication we describe the synthesis and the optical and magnetic properties of optically active three dimensional (3D) bimetallic [Cr-Mn] networks [[Delta Cr(III) Delta Mn(II)(ox)(3)][Delta Ru(II)(bpy)(3)]ClO(4)](n)1 - Delta, [[Lambda Cr(III)Lambda Mn(II)(ox)(3)][Lambda Ru(II) (bpy)(3)]ClO(4)](n) 1 - Lambda and [[Delta Cr(III)Delta Mn(II)(ox)(3)][Delta Ru(II)(bpy)(2)p p y]](n) 2 - Delta,[[Lambda Cr(III)Lambda Mn(II)(ox)(3)][Lambda Ru(II)(bpy)(2)ppy]](n) 2 - Lambda (ox = oxalate, bpy = bipyridine, ppy = phenyl-pyridine).     

Neutron diffraction of chromatin in interphase nuclei and metaphase chromosomes

We have used neutron diffraction to study chromatin structure in interphase nuclei and metaphase chromosomes as a function of decreasing ion concentration. Aliquots of a suspension of rat liver nuclei prepared in a polyamine-free buffer were washed in buffers of 1/3, 1/6 and 1/12 if the original concentration of monovalent and divalent cations (40 mM KCl; 20 mM NaCl; 1.2 mM MgCl2). After the first dilution step (1/1 to 1/3), only small changes occurred in the diffraction pattern. They can be interpreted by a loosening of the original structure, i.e. by the formation of isolated buffer-filled spaces with an overall size of the order of 35-45 nm. Drastic changes in the diffraction pattern were observed, however, when the nuclei were washed in the more diluted buffers (1/6 and 1/12). The profiles of the distances distribution functions indicate the formation of supranucleosomal particles with an overall diameter of 40-50 nm. The compact chromatin structure disassembled directly into these fundamental structural units. Structural transformations in the Chinese hamster ovary metaphase chromosomes were induced by diminishing the Ca2+ ion concentration of the buffer from originally 3.0 mM to 0.3 mM and/or by increasing the pH value of the buffer from originally 7.0 up to 8.0. The neutron diffraction patterns remained essentially unchanged during these treatments, i.e. the decondensation of the chromosomes as observed in the light microscope is not accompanied by disassembly at the ultrastructural level between 2 nm and 150 nm.     

Neutron diffraction studies of collagen in fully mineralized bone

Neutron diffraction measurements have been made of the equatorial and meridional spacings of collagen in fully mineralized mature bovine bone and demineralized bone collagen, in both wet and dry conditions. The collagen equatorial spacing in wet mineralized bovine bone is 1.24 nm, substantially lower than the 1.53 nm value observed in wet demineralized bovine bone collagen. Corresponding spacings for dry bone and demineralized bone collagen are 1.16 nm and 1.12 nm, respectively. The collagen meridional long spacing in mineralized bovine bone is 63.6 nm wet and 63.4 nm dry. These data indicate that collagen in fully mineralized bovine bone is considerably more closely packed than had been assumed previously, with a packing density similar to that of the relatively crystalline collagens such as wet rat tail tendon. The data also suggest that less space is available for mineral within the collagen fibrils in bovine bone than had previously been assumed, and that the major portion of the mineral in this bone must be located outside the fibrils.     

Neutron and X-ray diffraction structural analysis of phosphatidylinositol bilayers

Phosphatidylinositol (PI) bilayers, squeezed together by applied osmotic pressures, were studied by both neutron diffraction and X-ray diffraction. The lamellar repeat period for PI bilayers decreased from 9.5 nm at an applied pressure of 1.1.10(6) dyn/cm2 (1.1 atm) to 5.4 nm at an applied pressure of 1.6.10(7) dyn/cm2 (16 atm). Further increases in applied pressure, up to 2.7.10(9) dyn/cm2 (2700 atm) reduced the repeat period by only about 0.3 nm, to 5.1 nm. Thus, a plot of applied pressure versus repeat period shows a sharp upward break for repeat periods less than about 5.4 nm. For repeat periods of less than 5.4 nm, analysis of neutron-scattering density profiles and electron-density profiles indicates that the structure of the PI bilayers changes as the bilayers are dehydrated, even though there are only small changes in the repeat period. These structural changes are most likely due to removal of water from the headgroup regions of the bilayer. D2O/H2O exchange experiments show that, at an applied pressure of 2.8.10(7) dyn/cm2, water is located between adjacent PI headgroups in the plane of the bilayer. We conclude that, although electrostatics provide the dominant long-range repulsive interaction, hydration repulsion and steric hindrance between PI headgroups from apposing bilayers provide the major barriers for the close approach of adjacent PI bilayers for repeat periods less than 5.4 nm. This structural analysis also indicates that the phosphoinositol group extends from the plane of the bilayer into the fluid space between adjacent bilayers. This extended orientation for the headgroup is consistent with electrophoretic measurements on PI vesicles.     

Single base mismatches in DNA. Long- and short-range structure probed by analysis of axis trajectory and local chemical reactivity

We have devised a procedure to generate any single base mismatch in a constant sequence context, and have studied these from two points of view. (1) We have examined electrophoretic mobility of 458 base-pair fragments containing approximately centrally located single mismatches, in polyacrylamide gels, compared to fully matched DNA fragments. We found that no single mismatch caused a significant perturbation of gel mobility, and we conclude that all the mismatches may be accommodated within a helical geometry such that there is no alteration of the path of the helix axis in a straight DNA molecule. (2) We have studied all the single mismatches with respect to reactivity to a number of chemical probes. We found that: (a) No mispaired adenine bases are reactive to diethyl pyrocarbonate and are therefore not simply unpaired such that N-7 is exposed. (b) A number of mispaired thymine bases are reactive to osmium tetroxide, and cytosine bases to hydroxylamine. (c) Where crystal or nuclear magnetic resonance structures are available, the reactivity correlates with exposure of the pyrimidine 5,6 double bonds to attack in the major groove as a result of wobble base-pair formation. This is particularly clear for G.T and I.T base-pairs. (d) Reactivity of bases in mismatched pairs can be dependent on sequence context. (e) Reactivity of the C.C mismatch to hydroxylamine is suppressed at low pH, suggesting that a rearrangement of base-pairing occurs on protonation. The results overall are consistent with the formation of stacked intrahelical base-pairs wherever possible, resulting in no global distortion of the DNA structure, but specific enhancement of chemical reactivity in some cases.     

Neutron scatter and diffraction techniques applied to nucleosome and chromatin structure

Neutron scatter and diffraction techniques have made substantial contributions to our understanding of the structure of the nucleosome, the structure of the 10-nm filament, the "10-nm----30-nm" filament transition, and the structure of the "34-nm" supercoil or solenoid of nucleosomes. Neutron techniques are unique in their properties, which allows for the separation of the spatial arrangements of histones and DNA in nucleosomes and chromatin. They have equally powerful applications in structural studies of any complex two-component biological system. A major success for the application of neutron techniques was the first clear proof that DNA was located on the outside of the histone octamer in the core particle. A full analysis of the neutron-scatter data gave the parameters of Table 3 and the low-resolution structure of the core particle in solution shown in Fig. 6. Initial low-resolution X-ray diffraction studies of core particle crystals gave a model with a lower DNA pitch of 2.7 nm. Higher-resolution X-ray diffraction studies now give a structure with a DNA pitch of 3.0 nm and a hole of 0.8 nm along the axis of the DNA supercoil. The neutron-scatter solution structure and the X-ray crystal structure of the core particle are thus in full agreement within the resolution of the neutron-scatter techniques. The model for the chromatosome is largely based on the structural parameters of the DNA supercoil in the core particle, nuclease digestion results showing protection of a 168-bp DNA length by histone H1 and H1 peptide, and the conformational properties of H1. The path of the DNA outside the chromatosome is not known, and this information is crucial for our understanding of higher chromatin structure. The interactions of the flexible basic and N- and C-terminal regions of H1 within chromatin and how these interactions are modulated by H1 phosphorylation are not known. The N- and C-terminal regions of H1 represent a new type of protein behavior, i.e., extensive protein domains that are designed not to fold up into secondary and tertiary protein structures. This behavior is increasingly observed in DNA and chromatin binding proteins, and in the case of the high-mobility group proteins HMG 14 and 17, the entire polypeptide chain is a flexible random coil over a wide range of solution, ionic, and pH conditions. It follows that the native conformations are probably imposed on these flexible domains and molecules by their binding sites in chromatin.(ABSTRACT TRUNCATED AT 400 WORDS)     

Polysaccharide structures from powder diffraction data: molecular models of arabinan

X-ray intensity data from a polycrystalline sample of debranched arabinan, [-->5)-alpha-L-Ara(f)-(1-->](n), have been obtained using a powder diffractometer in order to determine its three-dimensional structure. The observed peaks index on a monoclinic cell with a=5.444(7), b=6.395(10), c=8.680(5) A, and gamma=99.6(3) degrees , V=298 A3. One 2-fold helix along the c-axis can be accommodated in the unit cell. Molecular and packing models have been analyzed using the seven C-2'-endo/C-3'-endo allomorphs originally proposed by Radha and Chandrasekaran [Carbohydr. Res. 1997, 298, 105]. The generated powder pattern matches closely with the observed diffraction only for one C-2'-endo model. In this structure, the three main chain conformation angles are in the trans domains, there are no intra-chain hydrogen bonds, and the packing arrangement is stabilized by inter-chain O-3-H...O-2 bonds.     

Golgi impregnation with mercuric chloride: studies on the precipitate by X-ray powder diffraction and selected area electron diffraction

Summary An investigation was carried out to determine the nature of the precipitate in a technique which was originally proposed by Golgi and, later, modified by Cox, to stain nerve cells by the treatment of tissue with potassium dichromate and mercuric chloride.The approach was a twofold one: the study of the patterns of X-ray diffraction of successfully impregnated tissue and the analysis of electron diffraction patterns of selected areas of tissue where impregnated structures were observed.Evidence has been obtained that the precipitate, prior to the final alkalinization process, is mercurous chloride (calomel, Hg₂Cl₂). There appears to be no formation, at any time, of mercurous or mercuric chromate. The mercurous chloride is topographically associated exclusively with the presence of stained structures and cannot be detected in the non-stained background.Following the alkalinizing process necessary for the final darkening of the stained structures, the X-ray diffraction pattern of mercurous chloride usually was no longer detectable. It appears reasonable to assume that, when no crystalline compounds can be detected, metallic liquid mercury is formed.This study was supported by U.S. P.H.S. Grant NS 07998 and by the Medical Research Council of Canada. We are indebted to Mrs. K. Sörensen and Mr. A. Meier for technical assistance.     

Neutron diffraction analysis of cytochrome b5 reconstituted in deuterated lipid multilayers

Cytochrome b5 was reconstituted with a highly deuterated phospholipid to form ordered multilayers consisting of repeated centrosymmetric pairs of asymmetric lipid-protein bilayers. Lamellar neutron diffraction data were collected to approximately 29 A resolution, and have been interpreted using models for the interaction of the membrane-binding domain of cytochrome b5 with the lipid bilayer. A range of different models was examined, and those in which the protein penetrates well into the bilayer, possibly spanning it, are favored.     

Pockets of short-range transient order and restricted topological heterogeneity in the guanidine-denatured state ensemble of GED of dynamin

The nature and variety in the denatured state of a protein, a non-native state under a given set of conditions, has been a subject of intense debate. Here, using multidimensional NMR, we have characterized the 6 M Gdn-HCl-denatured state of GED, the assembly domain of dynamin. Even under such strongly denaturing conditions, we detected the presence of conformations in slow exchange on the NMR chemical shift time scale. Although the GED oligomer as well as the SDS-denatured monomeric GED were seen to be predominantly helical [Chugh et al. (2006) FEBS J. 273, 388-397], the 6 M Gdn-HCl-denatured GED has largely beta-structural preferences. However, against such a background, we could detect the presence of a population with a short helical stretch (Arg42-Ile47) in the ensemble. The 1H-1H NOEs suggested presence of pockets of transient short-range order along the chain. Put together these segments may lead to a rather small number of interconverting topologically distinguishable ensembles. Spectral density analysis of 15N relaxation rates and {1H}-15N NOE, measured at 600 and 800 MHz, and comparison of J(0) with hydrophobic patches calculated using AABUF approach, indicated presence of four domains of slow motions. These coincided to a large extent with those showing significant Rex. Additionally, a proline residue in the connection between two of these domains seems to cause a fast hinge motion. These observations help enhance our understanding of protein denatured states, and of folding concepts, in general.     

Neutron diffraction studies of fluid bilayers with transmembrane proteins: structural consequences of the achondroplasia mutation

Achondroplasia, the most common form of human dwarfism, is due to a G380R mutation in the transmembrane domain of fibroblast growth factor receptor 3 (FGFR3) in >97% of the studied cases. While the molecular mechanism of pathology induction is under debate, the structural consequences of the mutation have not been studied. Here we use neutron diffraction to determine the disposition of FGFR3 transmembrane domain in fluid lipid bilayers, and investigate whether the G380R mutation affects the topology of the protein in the bilayer. Our results demonstrate that, in a model system, the G380R mutation induces a shift in the segment that is embedded in the membrane. The center of the hydrocarbon core-embedded segment in the mutant is close to the midpoint between R380 and R397, supporting previous measurements of arginine insertion energetics into the endoplasmic reticulum. The presented results further our knowledge about basic amino-acid insertion into bilayers, and may lead to new insights into the mechanism of pathogenesis in achondroplasia.     

Neutron activation analysis: A powerful tool for assay of rare-earth elements in terrestrial materials

Neutron activation analysis methods for determination of rare-earth elements in different matrices have been developed at the University of Pavia using the 250 Kw TRIGA Mark II reactor. A critical review of both instrumental and destructive methods is presented, as well as the indication of the best working conditions for irradiation, counting and radiochemical separations. The optimized procedures were utilized in the determination of rare-earth elements in standard reference materials of both mineral and biological origin. The adopted radiochemical procedure is based on the separation of the rare-earth element group by fluoride precipitation.Results, given as the average of six independent determinations and relative standard deviations, are reported and discussed. Precision of the methods can be deduced from the reproducibility of data, whereas accuracy is evaluated by comparison with existing values in the literature. Sensitivity limits under the described operational conditions are also reported, as are trends and correlations among data.     

Hydration properties of N-(alpha-hydroxyacyl)-sphingosine: X-ray powder diffraction and FT-Raman spectroscopic studies

The thermotropic properties of N-(alpha-hydroxyacyl)-sphingosine (CER[AS]) in dry and hydrated state were studied by means of X-ray powder diffraction and FT-Raman spectroscopy. The polymorphic states of the CER[AS]/water mixture (lamellar crystalline, lamellar hexagonal gel, liquid crystalline) depend on the thermal pre-treatment of the sample. Only by heating the CER[AS]/water mixture above the melting chain transition can the system be hydrated. At room temperature, both dry and hydrated states form lamellar structures, which differ in their repeat distance and packing of hydrocarbon chains. Above the melting chain transition, hydrated CER[AS] forms a liquid crystalline hexagonal phase, whereas anhydrous CER[AS] forms an isotropic liquid phase. The various phases of hydrated CER[AS] are distinguished on the basis of the corresponding Raman spectra.     

Variation in crystalline type with amylose content in maize starch granules: an X-ray powder diffraction study

Comparative studies of native maize starches with different amylose contents were carried out using X-ray powder diffraction. The results show a transition of crystalline type from A through C to B, accompanying a decrease in degree of crystallinity from 41.8% to 17.2% across a range of apparent amylose content from 0% to 84%. Hydration induces an increase in degree of granule crystallinity, but does not change the transition of crystal type. Progressively from A-type to C-type, crystallinity decreases rapidly with an increase in amylose content. From C-type to B-type, overall crystallinity decreases more slowly. The crystal type is strongly dependent on amylose content and on average chain length of the respective amylopectin. Waxy A-types have an average chain length of about 20, while in high amylose B-types this rises to ≈35. The proportion of short chains (10–13 glucose units) appears to affect crystal type significantly. Some V-type material was detected at high amylose levels. The proportion of this increased after prolonged exposure of the granules to iodine vapour. Implications for the arrangement of starch components in the granule are discussed.