Incorporating the speciation process into species delimitation

The “multispecies” coalescent (MSC) model that underlies many genomic species-delimitation approaches is problematic because it does not distinguish between genetic structure associated with species versus that of populations within species. Consequently, as both the genomic and spatial resolution of data increases, a proliferation of artifactual species results as within-species population lineages, detected due to restrictions in gene flow, are identified as distinct species. The toll of this extends beyond systematic studies, getting magnified across the many disciplines that rely upon an accurate framework of identified species. Here we present the first of a new class of approaches that addresses this issue by incorporating an extended speciation process for species delimitation. We model the formation of population lineages and their subsequent development into independent species as separate processes and provide for a way to incorporate current understanding of the species boundaries in the system through specification of species identities of a subset of population lineages. As a result, species boundaries and within-species lineages boundaries can be discriminated across the entire system, and species identities can be assigned to the remaining lineages of unknown affinities with quantified probabilities. In addition to the identification of species units in nature, the primary goal of species delimitation, the incorporation of a speciation model also allows us insights into the links between population and species-level processes. By explicitly accounting for restrictions in gene flow not only between, but also within, species, we also address the limits of genetic data for delimiting species. Specifically, while genetic data alone is not sufficient for accurate delimitation, when considered in conjunction with other information we are able to not only learn about species boundaries, but also about the tempo of the speciation process itself.     

Zinc silicate phosphor: Insights of X-ray induced and temperature enabled luminescence

The present investigation deals with the effect of calcination temperature on the structural and thermoluminescent (TL) properties of Zn₂SiO₄ materials. For this study, Zn₂SiO₄ was prepared via a simple hydrothermal route and calcinated at temperatures from 700°C to 1100°C in an air atmosphere. TL data of all Zn₂SiO₄ samples showed two peaks at around 240°C and 330°C due to the formation of the luminescence centre during X-ray irradiation. More interestingly, the Zn₂SiO₄ sample calcinated at 900°C exhibited a shift in the TL peak (282°C and 354°C) with an optimal TL intensity attributed to its good crystallinity with a well-defined hexagonal plate-like morphology. X-ray-irradiated Zn₂SiO₄ samples calcinated at 900°C exhibited a high-temperature TL glow curve peak, suggesting that the present material could be used for high-temperature dosimetry applications.     

Trivalent rare‐earth activated hexagonal lanthanum fluoride (LaF3:RE3+, where RE = Tb,Sm, Dy and Tm) nanocrystals: Synthesis and optical properties

The LaF₃ nanocrystals through a facile hydrothermal route with hexagonal structures have been synthesized via doping of trivalent rare earth (RE³⁺) ions – RE = Tb, Sm, Dy and Tm – with rod‐like and perforated morphologies using NH₄F as fluorine precursor. Hexagonal phase formation was confirmed by powder X‐ray diffraction. The crystalline sizes were calculated by the Scherrer equation where found to have an average crystalline size of 12 to 35 nm. The morphological studies of the nanocrystals were carried out by means of transmission electron microscopy (TEM). The LaF₃:Tm³⁺,Sm³⁺ ions show the characteristic emission of Tb³⁺ and Tm³⁺ respectively. In Sm³⁺‐doped LaF₃, three prominent emission peaks at 561, 597 and 641 nm were found, which belong to ⁴G_5/2 → ⁶H_5/2, ⁴G_5/2 → ⁶H_7/2 (magnetic dipole) and ⁴G_5/2 → ⁶H_9/2 (electric dipole) transitions, respectively. The Dy³⁺ activated LaF₃ shows blue and yellow emission and the corresponding CIE color coordinate show white light emission (CCT value 10650 K).     

Hydroxyapatite from Cuttlefish Bone: Isolation,Characterizations, and Applications

Hydroxyapatite (HA), a bioceramic, is a widely utilized material for bone tissue repair and regeneration because of its excellent properties such as biocompatibility, exceptional mechanical strength, and osteoconductivity. HA can be obtained by both synthetic and natural means. Animal bones are often considered a promising natural resource for the preparation of pure HA for biological and biomedical applications. Cuttlefish bone, also called as cuttlebone, mainly consists of calcium carbonate, and pure HA can be produced by adding phosphoric acid or ammonium hydrogen phosphate to it. Recently, cuttlefish bone-derived HA has shown promising results in terms of bone tissue repair and regeneration. The synthesized cuttlefish bone-derived has shown excellent biocompatibility, cell proliferation, increased alkaline phosphate activity, and efficient biomineralization ability with mesenchymal stem cells and osteoblastic cells. To further improve the biological properties of cuttlefish bone-derived HA, bioglass, polycaprolactone, and polyvinyl alcohol were added to it, which gave better results in terms of cell proliferation and osteogenic differentiation. Cuttlefish bone-derived HA with polymeric substances provides excellent bone formation under in vivo conditions. The studies indicate that cuttlefish bone-derived HA, along with polymeric and, protein materials, will be promising biomaterials in the field of bone tissue regeneration.     

Characterization of a Sulfoglucuronyl Carbohydrate Binding Protein in the Developing Nervous System

Abstract: The developmentally regulated and stage-specifically expressed HNK-1 carbohydrate found on sulfoglucuronylglycolipids (SGGLs) and certain glycoproteins has been proposed to be involved in neural cell adhesion and recognition processes through its interaction with protein "receptors." We have isolated and purified a ∼30-kDa SGGL-binding protein (SBP-1) from neonatal rat brain. SBP-1 specifically bound to SGGLs and sulfatide both in solid-phase immunobinding and high-performance thin-layer chromatography-immunooverlay assays. N-terminal sequence analysis showed that SBP-1 is similar to an adhesive neurite outgrowth promoting protein amphoterin. Desulfation of SGGLs resulted in abolition of SBP-1 binding. However, chemical modification of glucuronic acid moiety by either esterification or reduction of the carboxyl group had no effect, suggesting requirement of the carbohydrate-linked sulfate group for SBP-1 binding. The binding of SBP-1 to SGGLs was specifically inhibited by HNK-1 antibody but not by other IgM antibodies. The binding of SBP-1 to sulfatide, however, was not inhibited by HNK-1 antibody. Heparin, fucoidan, and dextran sulfate (50K) also inhibited the binding of SBP-1 to SGGLs. During development of the rat cerebral cortex, the level of SBP-1 decreased after embryonic day 18 to an almost undetectable level by postnatal day 10; whereas in the cerebellum, the expression of SBP-1 was maximal at postnatal day 7. SBP-1 also bound specifically to the HNK-1 glycoproteins isolated from rat brain by HNK-1 immunoaffinity chromatography. Proteins without HNK-1 carbohydrate did not bind SBP-1. The binding to HNK-1 glycoproteins was inhibited by HNK-1 antibody, but not by other IgM antibodies, indicating that the binding was mediated through the HNK-1 carbohydrate moiety of the proteins. The interaction and coexpression of SBP-1 with SGGLs and HNK-1 glycoproteins, during the perinatal brain development, suggest a functional role for this protein.     

Nuclear magnetic resonance study of the solution structure of alpha 1-purothionin. Sequential resonance assignment, secondary structure and low resolution tertiary structure

The solution structure of the 45-residue plant protein, alpha 1-purothionin, is investigated by nuclear magnetic resonance (n.m.r.) spectroscopy. Using a combination of two-dimensional n.m.r. techniques to demonstrate through-bond and through-space (less than 5 A) connectivities, the 1H n.m.r. spectrum of alpha 1-purothionin is assigned in a sequential manner. The secondary structure elements are then delineated on the basis of a qualitative interpretation of short-range nuclear Overhauser effects (NOE) involving the NH, C alpha H and C beta H protons. There are two helices extending from residues 10 to 19 and 23 to 28, two short beta-strands from residues 3 to 5 and 31 to 34 which form a mini anti-parallel beta-sheet, and five turns. In addition, a number of long-range NOE connectivities are assigned and a low resolution tertiary structure is proposed.     

The three-dimensional structure of alpha1-purothionin in solution: combined use of nuclear magnetic resonance, distance geometry and restrained molecular dynamics

The determination of the three-dimensional solution structure of α1-purothionin using a combination of metric matrix distance geometry and restrained molecular dynamics calculations based on n.m.r. data is presented. The experimental data comprise complete sequence-specific proton resonance assignments, a set of 310 approximate interproton distance restraints derived from nuclear Overhauser effects, 27 Ø backbone torsion angle restraints derived from vicinal coupling constants, 4 distance restraints from hydrogen bonds and 12 distance restraints from disulphide bridges. The average atomic rms difference between the final nine converged structures and the mean structure obtained by averaging their coordinates is 1.5 ± 0.1 å for the backbone atoms and 2.0 ± 0.1 å for all atoms. The overall shape of α1-purothionin is that of the capital letter L, similar to that of crambin, with the longer arm comprising two approximately parallel α-helices and the shorter arm a strand and a mini anti-parallel β sheet.     

The conformations of hirudin in solution: a study using nuclear magnetic resonance, distance geometry and restrained molecular dynamics

The solution conformations of the protein hirudin have been investigated by the combined use of distance geometry and restained molecular dynamics calculations. The basis for the structure determination comprised 359 approximate inter-proton distance restrains and 10 phi backbone torsion angle restrains derived from n.m.r. measurements. It is shown that hirudin is composed of three domains: a central core made up of residues 3-30, 37-46 and 56-57; a protruding 'finger' (residues 31-36) consisting of the tip of an antiparallel beta sheet, and an exposed loop (residues 47-55). The structure of each individual domain is relatively well defined with average backbone atomic r.m.s. differences of <2 A between the final seven converged restrained dynamic structures and the mean structure obtained by averaging their coordinates. The orientation of the two minor domains relative to the central core, however, could not be determined as no long-range (i-h >5) interdomain proton-proton contacts could be observed in the two-dimensional nuclear Overhauser enhancement spectra. From the restrained molecular dynamics calculations it appears that the two minor domains exhibit large rigid-body motions relative to the central core.     

The cyclic AMP-dependent protein kinase from bovine cardiac muscle is a homoserine kinase

The catalytic subunit of the cAMP-dependent protein kinase from bovine cardiac muscle phosphorylates homoserine in the synthetic peptide Leu-Arg-Arg-Ala-Hse-Leu-Gly. Phosphorylation of the primary alcohol of the homoserine residue was established via NMR spectroscopy. Two-dimensional correlated and nuclear Overhauser effect spectroscopies provided the sequence-specific chemical shift assignments of the substrate peptide and its phosphorylated counterpart. Coupled and decoupled 31P NMR experiments established the presence of phosphate on the homoserine residue. The maximal velocity (6.4 mumol/min.mg) obtained for homoserine-peptide phosphorylation at 12.5 mM Mg2+ compares favorably to the velocities observed for the corresponding serine- (21 mumol/min.mg), threonine- (3.2 mumol/min.mg), and hydroxyproline-peptides (1 mumol/min.mg). However, the Km for homoserine kinase activity is modest (1.3 mM) relative to the Km associated with the phosphorylation of the serine-containing substrate (22 microM). The effect of Mg2+ concentration on the kinetic parameters kcat, Km, and kcat/Km was investigated for both serine- and homoserine-peptides. Both substrates display similar kcat/Km versus [Mg2+] profiles, with the most notable difference that the optimal Mg2+ concentration is higher for the homoserine-containing peptide. In addition, the Km for the serine-peptide was found to be independent of [Mg2+], whereas the Km for the homoserine-peptide was observed to be dependent upon [Mg2+]. These results suggest that the long homoserine side chain may induce an unusually large off rate for the peptide and/or may misalign the hydroxyl moiety in the active site.