Original Building Blocks Research Articles

Homogeneous Photometry VI: Variable Stars in the Leo I Dwarf Spheroidal Galaxy

From archival ground-based images of the Leo I dwarf spheroidal galaxy, we have identified and characterized the pulsation properties of 164 candidate RR Lyrae variables and 55 candidate anomalous and/or short-period Cepheids. We have also identified 19 candidate long-period variable stars and 13 other candidate variables whose physical nature is unclear, but due to the limitations of our observational material we are unable to estimate reliable periods for them. On the basis of its RR Lyrae star population, Leo I is confirmed to be an Oosterhoff-intermediate type galaxy, like several other dwarf spheroidals. From the RR Lyrae stars we have derived a range of possible distance moduli for Leo I : 22.06 ± 0.08 ≲ μ0 ≲ 22.25 ± 0.07 mag depending on the metallicity assumed for the old population ([Fe/H] from -1.43 to -2.15). This is in agreement with previous independent estimates. We show that in their pulsation properties, the RR Lyrae stars—representing the oldest stellar population in the galaxy—are not significantly different from those of five other nearby, isolated dwarf spheroidal galaxies. A similar result is obtained when comparing them to RR Lyrae stars in recently discovered ultra-faint dwarf galaxies. We are able to compare the period distributions and period-amplitude relations for a statistically significant sample of ab-type RR Lyrae stars in dwarf galaxies (∼1300 stars) with those in the Galactic halo field (∼14,000 stars) and globular clusters (∼1000 stars). Field RRLs show a significant change in their period distribution when moving from the inner (dG ≲ 14 kpc) to the outer (dG ≳ 14 kpc) halo regions. This suggests that the halo formed from (at least) two dissimilar progenitors or types of progenitor. Considered together, the RR Lyrae stars in classical dwarf spheroidal and ultra-faint dwarf galaxies—as observed today—do not appear to follow the well defined pulsation properties shown by those in either the inner or the outer Galactic halo, nor do they have the same properties as RR Lyraes in globular clusters. In particular, the samples of fundamental-mode RR Lyrae stars in dwarf galaxies seem to lack High Amplitudes and Short Periods (“HASP”: AV≥1.0 mag and P ≲ 0.48 d) when compared with those observed in the Galactic halo field and globular clusters. The observed properties of RR Lyrae stars do not support the idea that currently existing classical dwarf spheroidal and ultra-faint dwarf galaxies are surviving representative examples of the original building blocks of the Galactic halo.

Exceptionally stable, redox-active supramolecular protein assemblies with emergent properties

The designed assembly of proteins into well-defined supramolecular architectures not only tests our understanding of protein-protein interactions, but it also provides an opportunity to tailor materials with new physical and chemical properties. Previously, we described that RIDC3, a designed variant of the monomeric electron transfer protein cytochrome cb562, could self-assemble through Zn(2+) coordination into uniform 1D nanotubes or 2D arrays with crystalline order. Here we show that these 1D and 2D RIDC3 assemblies display very high chemical stabilities owing to their metal-mediated frameworks, maintaining their structural order in ≥90% (vol/vol) of several polar organic solvents including tetrahydrofuran (THF) and isopropanol (iPrOH). In contrast, the unassembled RIDC3 monomers denature in ∼30% THF and 50% iPrOH, indicating that metal-mediated self-assembly also leads to considerable stabilization of the individual building blocks. The 1D and 2D RIDC3 assemblies are highly thermostable as well, remaining intact at up to ∼70 °C and ∼90 °C, respectively. The 1D nanotubes cleanly convert into the 2D arrays on heating above 70 °C, a rare example of a thermal crystalline-to-crystalline conversion in a biomolecular assembly. Finally, we demonstrate that the Zn-directed RIDC3 assemblies can be used to spatiotemporally control the templated growth of small Pt(0) nanocrystals. This emergent function is enabled by and absolutely dependent on both the supramolecular assembly of RIDC3 molecules (to form a periodically organized structural template) and their innate redox activities (to direct Pt(2+) reduction).

Models and the mosaic of scientific knowledge. The case of immunology

A survey of models in immunology is conducted and distinct kinds of models are characterized based on whether models are material or conceptual, the distinctiveness of their epistemic purpose, and the criteria for evaluating the goodness of a model relative to its intended purpose. I argue that the diversity of models in interdisciplinary fields such as immunology reflects the fact that information about the phenomena of interest is gathered from different sources using multiple methods of investigation. To each model is attached a description specifying how information about a phenomenon of interest has been acquired, highlighting points of commonality and difference between the methodological and epistemic histories of the information encapsulated in different models. These points of commonality and difference allow investigators to integrate findings from different models into more comprehensive explanatory accounts, as well as to troubleshoot anomalies and faulty accounts by going back to the original building blocks.

On the antiquity of metalloenzymes and their substrates in bioenergetics

Many metalloenzymes that inject and extract reducing equivalents at the beginning and the end of electron transport chains involved in chemiosmosis are suggested, through phylogenetic analysis, to have been present in the Last Universal Common Ancestor (LUCA). Their active centres are affine with the structures of minerals presumed to contribute to precipitate membranes produced on the mixing of hydrothermal solutions with the Hadean Ocean ~4billion years ago. These mineral precipitates consist of transition element sulphides and oxides such as nickelian mackinawite ([Fe>Ni]2S2), a nickel-bearing greigite (~FeSS[Fe3NiS4]SSFe), violarite (~NiSS[Fe2Ni2S4]SSNi), a molybdenum bearing complex (~MoIV/VI2Fe3S0/2−9) and green rust or fougerite (~[FeIIFeIII(OH)4]+[OH]−). They may be respectively compared with the active centres of Ni–Fe hydrogenase, carbon monoxide dehydrogenase (CODH), acetyl coenzyme-A synthase (ACS), the complex iron–sulphur molybdoenzyme (CISM) superfamily and methane monooxygenase (MMO). With the look of good catalysts – a suggestion that gathers some support from prebiotic hydrothermal experimentation – and sequestered by short peptides, they could be thought of as the original building blocks of proto-enzyme active centres. This convergence of the makeup of the LUCA-metalloenzymes with mineral structure and composition of hydrothermal precipitates adds credence to the alkaline hydrothermal (chemiosmotic) theory for the emergence of life, specifically to the possibility that the first metabolic pathway – the acetyl CoA pathway – was initially driven from either end, reductively from CO2 to CO and oxidatively and reductively from CH4 through to a methane thiol group, the two entities assembled with the help of a further thiol on a violarite cluster sequestered by peptides. By contrast, the organic coenzymes were entirely a product of the first metabolic pathways. This article is part of a Special Issue entitled: Metals in Bioenergetics and Biomimetics Systems.

Bimetallic coordination networks based on Al(acacCN)3: a building block between inertness and lability

The Al(III) complex of 3-cyanopentane-2,4-dionate (acacCN) features peripheric nitrile groups which may coordinate to silver cations. As the Al(acacCN)(3) building block ranges between inertness and lability, its reactivity towards Ag(I) salts depends on the solvent and the weakly or non-coordinating counter anions; an impressive range of different extended structures has been encountered. With AgPF(6), the original building block is retained and hexafluorophosphate remains uncoordinated. A highly symmetric 3D crystalline solid forms in the presence of trichloromethane, and with benzene a tetrasolvate with large solvent-filled voids is obtained. Two different classes of reaction products with silver triflate have been observed. In addition to networks incorporating Al(acacCN)(3), partial solvolysis may lead to a dinuclear methoxide-bridged derivative. The resulting Al(2)(μ-OMe)(2) core may be perceived as a four-connected node in a self-interpenetrating 3D network. Earlier studies reported transmetalation for the reaction of Al(acacCN)(3) with AgNO(3) and we find the same reactivity for silver tetrafluoroborate. Full degradation of the Al(III) building block with formation of [Ag(acacCN)] is observed.

Tunable ferroelectricity in artificial tri-layer superlattices comprised of non-ferroic components

Heterostructured material systems devoid of ferroic components are presumed not to display ordering associated with ferroelectricity. In heterostructures composed of transition metal oxides, however, the disruption introduced by an interface can affect the balance of the competing interactions among electronic spins, charges and orbitals. This has led to the emergence of properties absent in the original building blocks of a heterostructure, including metallicity, magnetism and superconductivity. Here we report the discovery of ferroelectricity in artificial tri-layer superlattices consisting solely of non-ferroelectric NdMnO(3)/SrMnO(3)/LaMnO(3) layers. Ferroelectricity was observed below 40 K exhibiting strong tunability by superlattice periodicity. Furthermore, magnetoelectric coupling resulted in 150% magnetic modulation of the polarization. Density functional calculations indicate that broken space inversion symmetry and mixed valency, because of cationic asymmetry and interfacial polar discontinuity, respectively, give rise to the observed behaviour. Our results demonstrate the engineering of asymmetric layered structures with emergent ferroelectric and magnetic field tunable functions distinct from that of normal devices, for which the components are typically ferroelectrics.

Oriented-aggregation of organic organization: Morphology-controllable synthesis, surface photovoltage spectroscopy and morphology-dependent optical property

Assembled ZnQ 2·2H 2O microstructures, such as microsheet, sandwich-like structure and hexangular microflake, have been successfully prepared in CTAB microemulsion system through the stacking of ZnQ 2·2H 2O molecules and oriented aggregation of ZnQ 2·2H 2O original building blocks. Controlled experiments demonstrated that the morphologies of building block and final product could be readily tuned by reaction parameters, and a formation mechanism, involving re-precipitation, growth and oriented aggregation process, has been proposed on the basis of time-dependent experimental results. The obtained products were carefully characterized by X-ray powder diffraction (XRD), thermal gravimetric analysis (TGA), transmission electron microscope (TEM), field-emission scanning electron microscope (FESEM), FT-IR spectrum, UV–vis spectrum and photoluminescence (PL) spectrum. The surface photovoltage (SPV) of the obtained ZnQ 2·2H 2O microstructures was investigated by means of surface photovoltage spectroscopy (SPS) and field-induced surface photovoltage spectroscopy (FISPS). The SPS and FISPS revealed that the photogenerated charges of ZnQ 2·2H 2O could be separated distinctly and ZnQ 2·2H 2O possessed p-type semiconductor characteristics, respectively. Furthermore, UV–vis and PL spectra evidenced the optical properties of ZnQ 2·2H 2O were sensitive to its microstructure or morphology.

Ultrafast and Reversible Multiblock Formation by the SET-Nitroxide Radical Coupling Reaction

The single electron transfer-nitroxide radical coupling (SET-NRC) reaction has been used to produce multiblock polymers with high molecular weights in under 3 min at 50°C by coupling a difunctional telechelic polystyrene (Br-PSTY-Br) with a dinitroxide. The well known combination of dimethyl sulfoxide as solvent and Me6TREN as ligand facilitated the in situ disproportionation of CuIBr to the highly active nascent Cu0 species. This SET reaction allowed polymeric radicals to be rapidly formed from their corresponding halide end-groups. Trapping of these carbon-centred radicals at close to diffusion controlled rates by dinitroxides resulted in high-molecular-weight multiblock polymers. Our results showed that the disproportionation of CuI was critical in obtaining these ultrafast reactions, and confirmed that activation was primarily through Cu0. We took advantage of the reversibility of the NRC reaction at elevated temperatures to decouple the multiblock back to the original PSTY building block through capping the chain-ends with mono-functional nitroxides. These alkoxyamine end-groups were further exchanged with an alkyne mono-functional nitroxide (TEMPO–≡) and ‘clicked’ by a CuI-catalyzed azide/alkyne cycloaddition (CuAAC) reaction with N3–PSTY–N3 to reform the multiblocks. This final ‘click’ reaction, even after the consecutive decoupling and nitroxide-exchange reactions, still produced high-molecular-weight multiblocks efficiently. These SET-NRC reactions would have ideal applications in re-usable plastics and possibly as self-healing materials.

MALDI-ToF investigation of furanic polymer foams before and after carbonization: Aromatic rearrangement and surviving furanic structures

A MALDI-ToF investigation of furanic foams before and after carbonization at 900 °C has been carried out. Comparison between MALDI-ToF spectra, before and after carbonization, shows how original building blocks of the network are modified, rearranged or survived during the process. Even if most of the constituents are transformed to more stable aromatic structures, some of the starting compounds resist intact the process of carbonization. The results appeared to indicate that some furanic oligomers are particularly stable and unaffected by carbonisation. The hypothesis that these may be cyclic furanic oligomers has been checked by molecular mechanics calculation of their relative energies.

Interstellar Chemistry Recorded in Organic Matter from Primitive Meteorites

Organic matter in extraterrestrial materials has isotopic anomalies in hydrogen and nitrogen that suggest an origin in the presolar molecular cloud or perhaps in the protoplanetary disk. Interplanetary dust particles are generally regarded as the most primitive solar system matter available, in part because until recently they exhibited the most extreme isotope anomalies. However, we show that hydrogen and nitrogen isotopic compositions in carbonaceous chondrite organic matter reach and even exceed those found in interplanetary dust particles. Hence, both meteorites (originating from the asteroid belt) and interplanetary dust particles (possibly from comets) preserve primitive organics that were a component of the original building blocks of the solar system.

Synthesis of a Convenient Thymidine Glycol Phosphoramidite Monomer and Its Site-specific Incorporation into DNA Fragments

An original phosphoramidite building block of the thymidine glycol lesion has been prepared taking into account the additional diol function and the high lability of this oxidatively induced nucleobase damage. Then the modified nucleoside was site-specifically inserted into DNA fragments by solid support assembling followed by a “one-step” mild final deprotection treatment.

Soft antimicrobial agents: synthesis and activity of labile environmentally friendly long chain quaternary ammonium compounds.

A series of soft quaternary ammonium antimicrobial agents, which are analogues to currently used quaternary ammonium preservatives such as cetyl pyridinium chloride and benzalkonium chloride, were synthesized. These soft analogues consist of long alkyl chain connected to a polar headgroup via chemically labile spacer group. They are characterized by facile nonenzymatic and enzymatic degradation to form their original nontoxic building blocks. However, their chemical stability has to be adequate in order for them to have antimicrobial effects. Stability studies and antibacterial and antiviral activity measurements revealed relationship between activity, lipophilicity, and stability. Their minimum inhibitory concentration (MIC) was as low as 1 microg/mL, and their viral reduction was in some cases greater than 6.7 log. The structure-activity studies demonstrate that the bioactive compounds (i.e., MIC for Gram-positive bacteria of <10 microg/mL) have an alkyl chain length between 12 and 18 carbon atoms, with a polar headgroup preferably of a small quaternary ammonium group, and their acquired inactivation half-life must be greater than 3 h at 60 degrees C.

ChemInform Abstract: Claisen Rearrangements of Allylic and Propargylic Alcohols Prepared by an N‐Boc‐2‐acyloxazolidine Methodology — Application to the Synthesis of Original Chiral Building Blocks.

AbstractChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.

Claisen Rearrangements of Allylic and Propargylic Alcohols Prepared by an N-Boc-2-acyloxazolidine Methodology − Application to the Synthesis of Original Chiral Building Blocks

Stereodefined alkenols prepared in two steps from a Weinreb amide derived from (R)-phenylglycinol undergo highly stereoselective Claisen rearrangements. The masked aldehyde moiety of the produced N-Boc-alkenyloxazolidines can then be recovered and reduced without epimerization, to yield new enantiopure chiral building blocks. Alternatively, epoxidation of these N-Boc-2-alkenyloxazolidines by a well-established intramolecular bromocarbamation involving the Boc protecting group occurs stereoselectively. The resulting α,β-epoxyoxazolidines are then transformed into trisubstituted stereodefined cyclopropanes. Claisen rearrangements of propargylic alcohols, on the other hand, stereoselectively give α-allenyloxazolidines. These compounds follow a different pathway to α-alkenyloxazolidines as regards bromocarbamation. An original route to enantiopure 3-hydroxy-4-phenylpiperidine was found in the course of this study.

Mechanical stability of compact modules of barnase

Globular proteins are composed of structural elements such as secondary structures and modules. Modules are compact segments consisting of 10–40 contiguous amino acid residues and are often encoded by exons. Therefore, the view that the modular organization of proteins is a result of exon-shuffling or -fusion is given support. Secondary structures such as α-helix and β-sheet are stabilized by hydrogen bonds and are thus considered to be stable, structural elements of a globular domain. Since module boundaries are often located on α-helices or β-sheets, it is not obvious whether the modules are mechanically stable. We carried out molecular dynamics simulations on modules of barnase, a bacterial RNase from Bacillus amyloliquefaciens, for 1 ns in vacuo and 150 ps in water. Five of six modules (M1, 1–24; M2, 25–52; M3, 53–73; M4, 74–88; M5, 89–98) retained native-like conformations during these simulations. Only the C-terminal module (M6, 99–110) was deformed; it is less compact than the other modules. As the modules are mechanically stable they are suitable as parts combined into proteins. Together with RNase activity of the three isolated modules of barnase, M2, M3 and M6, our study supports the view that modules were indeed original building blocks of proteins. © 1997 Federation of European Biochemical Societies.

Exons – original building blocks of proteins?

In a recent paper, Walter Gilbert's group has estimated the number of original exons from which all extant proteins might have been constructed. The approach used is subjected to a critical analysis here. It is shown that there are flawed assumptions about both the mechanism and generality of exon-shuffling and in the sequence comparison procedures employed, the latter failing to distinguish chance similarity from similarity due to common ancestry. These methodological errors lead to the omission of many known cases of exon-shuffling and the inclusion of others which may not be genuine. In consequence, the analysis from the Gilbert group cannot give a reliable estimate of those modules that actually participated in exon-shuffling and provides no information on the number of protein archetypes that did not participate in these processes.

The all pervasive principle of repetitious recurrence governs not only coding sequence construction but also human endeavor in musical composition.

Organisms which have evolved on this earth are governed by multitudes of periodicities; tomorrow is another today, and the next year is going to be much like this year. Accordingly, the principle of repetitious recurrence pervades every aspect of life on this earth. Thus, individual genes in the genome have been duplicated and triplicated often to the point of redundancy, and each coding sequence consists of numerous variously truncated as well as variously base-substituted copies of the original primordial building block base oligomers and their allies. This principle even appears to govern the manifestations of human intellect; musical compositions also rely on this principle of repetitious recurrence. Accordingly, coding base sequences can be transformed into musical scores using one set rule. Conversely, musical scores can be transcribed to coding base sequences of long open reading frames.