Possible Role of Metal(II) Octacyanomolybdate(IV) in Chemical Evolution: Interaction with Ribose Nucleotides

We have proposed that double metal cyanide compounds (DMCs) might have played vital roles as catalysts in chemical evolution and the origin of life. We have synthesized a series of metal octacyanomolybdates (MOCMos) and studied their interactions with ribose nucleotides. MOCMos have been shown to be effective adsorbents for 5′-ribonucleotides. The maximum adsorption level was found to be about 50 % at neutral pH under the conditions studied. The zinc(II) octacyanomolybdate(IV) showed larger adsorption compared to other MOCMos. The surface area seems to important parameter for the adsorption of nucleotides. The adsorption followed a Langmuir adsorption isotherms with an overall adsorption trends of the order of 5′-GMP > 5′-AMP > 5′-CMP > 5′-UMP. Purine nucleotides were adsorbed more strongly than pyrimidine nucleotides on all MOCMos possibly because of the additional binding afforded by the imidazole ring in purines. Infrared spectral studies of adsorption adducts indicate that adsorption takes place through interaction between adsorbate molecules and outer divalent ions of MOCMos.     

Interaction of Aromatic Amines with Iron Oxides: Implications for Prebiotic Chemistry

The interaction of aromatic amines (aniline, p-chloroaniline, p-toludine and p-anisidine) with iron oxides (goethite, akaganeite and hematite) has been studied. Maximum uptake of amines was observed around pH 7. The adsorption data obtained at neutral pH were found to follow Langmuir adsorption. Anisidine was found to be a better adsorbate probably due to its higher basicity. In alkaline medium (pH?>?8), amines reacted on goethite and akaganeite to give colored products. Analysis of the products by GC–MS showed benzoquinone and azobenzene as the reaction products of aniline while p-anisidine afforded a dimer. IR analysis of the amine–iron oxide hydroxide adduct suggests that the surface acidity of iron oxide hydroxides is responsible for the interaction. The present study suggests that iron oxide hydroxides might have played a role in the stabilization of organic molecules through their surface activity and in prebiotic condensation reactions.     

Lithium/Oxygen Incorporation and Microstructural Evolution during Synthesis of Li‐Rich Layered Li[Li0.2Ni0.2Mn0.6]O2 Oxides

As promising cathode materials, the lithium‐excess 3d‐transition‐metal layered oxides can deliver much higher capacities (>250 mAh g^?1 at 0.1 C) than the current commercial layered oxide materials (≈180 mAh g^?1 at 0.1 C) used in lithium ion batteries. Unfortunately, the original formation mechanism of these layered oxides during synthesis is not completely elucidated, that is, how is lithium and oxygen inserted into the matrix structure of the precursor during lithiation reaction? Here, a promising and practical method, a coprecipitation route followed by a microwave heating process, for controllable synthesis of cobalt‐free lithium‐excess layered compounds is reported. A series of the consistent results unambiguously confirms that oxygen atoms are successively incorporated into the precursor obtained by a coprecipitation process to maintain electroneutrality and to provide the coordination sites for inserted Li ions and transition metal cations via a high‐temperature lithiation. It is found that the electrochemical performances of the cathode materials are strongly related to the phase composition and preparation procedure. The monoclinic layered Li[Li_0.2Ni_0.2Mn_0.6]O₂ cathode materials with state‐of‐the‐art electrochemical performance and comparably high discharge capacities of 171 mAh g^?1 at 10 C are obtained by microwave annealing at 750 °C for 2 h.     

Adsorption of Cu and Zn onto Mn/Fe Oxides and Organic Materials in the Extractable Fractions of River Surficial Sediments

The roles of the extractable components (Mn oxides, Fe oxides, and organic materials) of surficial sediments in controlling metals adsorption were investigated. Cu and Zn adsorptions were conducted before and after the surficial sediments extracted with hydroxylamine hydrochloride, an oxalate solution, and H ₂ O ₂ , respectively. The extraction removed target components with extraction efficiencies from 63 to 98%. Nonlinear regression analyses of Cu and Zn adsorptions based on the assumption of additive Langmuir adsorption isotherm were employed to estimate the relative contributions of sediment components to Cu and Zn adsorptions. The results indicate that the greatest contribution to total Cu and Zn adsorption to the surficial sediments on a molar basis was from Mn oxides in the extractable fractions. Both Cu and Zn adsorption capacities of Mn oxides exceeded those of Fe oxides by approximately one order of magnitude, fewer roles were attributed to the adsorption of organic material (OM), and the estimated contribution of the residual fraction to total Cu and Zn adsorption was insignificant. These information implied that the roles of metal oxides (Fe and Mn oxides) in the extractable form of the surficial sediments, especially Mn oxides, was the most important component in controlling heavy metal transportation in aquatic environments.     

Evolution of the Relaxin/Insulin-like Gene Family in Placental Mammals: Implications for Its Early Evolution

The relaxin (RLN) and insulin-like (INSL) gene family is a group of genes involved in a variety of physiological roles that includes bone formation, testicular descent, trophoblast development, and cell differentiation. This family appears to have expanded in vertebrates relative to non-vertebrate chordates, but the relative contribution of whole genome duplications (WGDs) and tandem duplications to the observed diversity of genes is still an open question. Results from our comparative analyses favor a model of divergence post vertebrate WGDs in which a single-copy progenitor found in the last common ancestor of vertebrates experienced two rounds of WGDs before the functional differentiation that gave rise to the RLN and INSL genes. One of the resulting paralogs was subsequently lost, resulting in three proto-RLN/INSL genes on three separate chromosomes. Subsequent rounds of tandem gene duplication and divergence originated the set of paralogs found on a given cluster in extant vertebrates. Our study supports the hypothesis that differentiation of the RLN and INSL genes took place independently in each RLN/INSL cluster after the two WGDs during the evolutionary history of vertebrates. In addition, we show that INSL4 represents a relatively old gene that has been apparently lost independently in all Euarchontoglires other than apes and Old World monkeys, and that RLN2 derives from an ape-specific duplication.     

Oligomerization of Glycine and Alanine Catalyzed by Iron Oxides: Implications for Prebiotic Chemistry

Iron oxide minerals are probable constituents of the sediments present in geothermal regions of the primitive earth. They might have adsorbed different organic monomers (amino acids, nucleotides etc.) and catalyzed polymerization processes leading to the formation of the first living cell. In the present work we tested the catalytic activity of three forms of iron oxides (Goethite, Akaganeite and Hematite) in the intermolecular condensation of each of the amino acids glycine and L-alanine. The effect of zinc oxide and titanium dioxide on the oligomerization has also been studied. Oligomerization studies were performed for 35 days at three different temperatures 50, 90 and 120°C without applying drying/wetting cycling. The products formed were characterized by HPLC and ESI-MS techniques. All three forms of iron oxides catalyzed peptide bond formation (23.2% of gly2 and 10.65% of ala2). The reaction was monitored every 7 days. Formation of peptides was observed to start after 7 days at 50°C. Maximum yield of peptides was found after 35 days at 90°C. Reaction at 120°C favors formation of diketopiperazine derivatives. It is also important to note that after 35 days of reaction, goethite produced dimer and trimer with the highest yield among the oxides tested. We suggest that the activity of goethite could probably be due to its high surface area and surface acidity.     

Evolution of heliobacteria: Implications for photosynthetic reaction center complexes

The evolutionary position of the heliobacteria, a group of green photosynthetic bacteria with a photosynthetic apparatus functionally resembling Photosystem I of plants and cyanobacteria, has been investigated with respect to the evolutionary relationship to Gram-positive bacteria and cyanobacteria. On the basis of 16S rRNA sequence analysis, the heliobacteria appear to be most closely related to Gram-positive bacteria, but also an evolutionary link to cyanobacteria is evident. Interestingly, a 46-residue domain including the putative sixth membrane-spanning region of the heliobacterial reaction center protein shows rather strong similarity (33% identity and 72% similarity) to a region including the sixth membrane-spanning region of the CP47 protein, a chlorophyll-binding core antenna polypeptide of Photosystem II. The N-terminal half of the heliobacterial reaction center polypeptide shows a moderate sequence similarity (22% identity over 232 residues) with the CP47 protein, which is significantly more than the similarity with the Photosystem I core polypeptides in this region. An evolutionary model for photosynthetic reaction center complexes is discussed, in which an ancestral homodimeric reaction center protein (possibly resembling the heliobacterial reaction center protein) with 11 membrane-spanning regions per polypeptide has diverged to give rise to core of Photosystem I, Photosystem II, and of the photosynthetic apparatus in green, purple, and heliobacteria.     

New O2/P2‐type Li‐Excess Layered Manganese Oxides as Promising Multi‐Functional Electrode Materials for Rechargeable Li/Na Batteries

A new and promising P2‐type layered oxide, Na_5/6[Li_1/4Mn_3/4]O₂ is prepared using a solid‐state method. Detailed crystal structures of the sample are analyzed by synchrotron X‐ray diffraction combined with high‐resolution neutron diffraction. P2‐type Na_5/6[Li_1/4Mn_3/4]O₂ consists of two MeO₂ layers with partial in‐plane √3a × √3a‐type Li/Mn ordering. Na/Li ion‐exchange in a molten salt results in a phase transition accompanied with glide of [Li_1/4Mn_3/4]O₂ layers without the destruction of in‐plane cation ordering. P2‐type Na_5/6[Li_1/4Mn_3/4]O₂ translates into an O2‐type layered structure with staking faults as the result of ion‐exchange. Electrode performance of P2‐type Na_5/6[Li_1/4Mn_3/4]O₂ and O2‐type Li_x[Li_1/4Mn_3/4]O₂ is examined and compared in Na and Li cells, respectively. Both samples show large reversible capacity, ca. 200 mA h g^?1, after charge to high voltage regardless of the difference in charge carriers. Structural analysis suggests that in‐plane structural rearrangements, presumably associated with partial oxygen loss, occur in both samples after charge to a high‐voltage region. Such structural activation process significantly influences electrode performance of the P2/O2‐type phases, similar to O3‐type Li₂MnO₃‐based materials. Crystal structures, phase‐transition mechanisms, and the possibility of the P2/O2‐type phases as high‐capacity and long‐cycle‐life electrode materials with the multi‐functionality for both rechargeable Li/Na batteries are discussed in detail.     

Evolution of Xylan Substitution Patterns in Gymnosperms and Angiosperms: Implications for Xylan Interaction with Cellulose

The interaction between cellulose and xylan is important for the load-bearing secondary cell wall of flowering plants. Based on the precise, evenly spaced pattern of acetyl and glucuronosyl (MeGlcA) xylan substitutions in eudicots, we recently proposed that an unsubstituted face of xylan in a 2-fold helical screw can hydrogen bond to the hydrophilic surfaces of cellulose microfibrils. In gymnosperm cell walls, any role for xylan is unclear, and glucomannan is thought to be the important cellulose-binding polysaccharide. Here, we analyzed xylan from the secondary cell walls of the four gymnosperm lineages (Conifer, Gingko, Cycad, and Gnetophyta). Conifer, Gingko, and Cycad xylan lacks acetylation but is modified by arabinose and MeGlcA. Interestingly, the arabinosyl substitutions are located two xylosyl residues from MeGlcA, which is itself placed precisely on every sixth xylosyl residue. Notably, the Gnetophyta xylan is more akin to early-branching angiosperms and eudicot xylan, lacking arabinose but possessing acetylation on alternate xylosyl residues. All these precise substitution patterns are compatible with gymnosperm xylan binding to hydrophilic surfaces of cellulose. Molecular dynamics simulations support the stable binding of 2-fold screw conifer xylan to the hydrophilic face of cellulose microfibrils. Moreover, the binding of multiple xylan chains to adjacent planes of the cellulose fibril stabilizes the interaction further. Our results show that the type of xylan substitution varies, but an even pattern of xylan substitution is maintained among vascular plants. This suggests that 2-fold screw xylan binds hydrophilic faces of cellulose in eudicots, early-branching angiosperm, and gymnosperm cell walls.The plant secondary cell wall is a complex network of various polysaccharides and phenolic compounds that act in concert to provide strength to the cell wall (Kumar et al., 2016). Cellulose, formed of strong crystalline fibrils of linear β1,4 glucan, comprises about 40% of dry plant biomass. The other secondary cell wall polysaccharides, largely xylan and glucomannan, comprise about 30% of dry plant biomass. The abundance and structure of these hemicelluloses vary with plant species and tissues, but they have in common that they are tightly associated with cellulose. It is believed that the most important biological role of hemicelluloses is their contribution to strengthening the cell wall by interaction with cellulose and, in some walls, with lignin (Scheller and Ulvskov, 2010). However, it is unclear how hemicelluloses interact with cellulose in the cell wall (Cosgrove and Jarvis, 2012). In this work, we were interested in the interaction of cellulose with xylan, one of the most abundant polysaccharides in nature.To understand polysaccharide interactions in the cell wall, we need to know not only the hemicellulose primary structure, but also the conformation of the polysaccharide chains. The glucan chains in cellulose are similar to a flat ribbon known as a 2-fold helical screw and associate through lateral hydrogen bonding into sheets. The sheets of glucan chains stack on top of each other, resulting in highly ordered crystalline cellulose. It is still unclear how many glucan chains form a microfibril and whether the microfibril has a hexagonal or rectangular cross section. However, recent studies shed some light onto these questions (Fernandes et al., 2011; Newman et al., 2013; Thomas et al., 2013; Cosgrove, 2014; Oehme et al., 2015; Thomas et al., 2015; Wang and Hong, 2016; Vandavasi et al., 2016). Whichever model is favored, hydrophobic (e.g. 100 or 200) and hydrophilic (e.g. 110 or 010) crystal faces are exposed for interaction with other molecules such as hemicelluloses (Zhao et al., 2014; Cosgrove, 2014; Li et al., 2015).The β1,4 xylan backbone is always further modified, often by acetyl (Ac), arabinosyl (Ara), and glucuronosyl (MeGlcA) side-chain substitutions. These substitutions are supposed to be necessary to maintain xylan solubility (Mikkelsen et al., 2015). Unsubstituted xylan forms crystalline fibers of chains adopting a 3-fold screw helix (Nieduszynski and Marchessault, 1971). Consequently, xylan substitutions are essential for xylan function and vascular plant viability (Mortimer et al., 2010; Xiong et al., 2013, 2015). In vitro experiments and in silico modeling suggest xylan interacts with cellulose, and it is widely accepted that this is partly through interactions on the hydrophobic faces of the cellulose fibrils (Bosmans et al., 2014; Köhnke et al., 2011; Kabel et al., 2007; Busse-Wicher et al., 2014). In contrast to the binding to the hydrophobic faces, the backbones of highly substituted hemicelluloses are thought to be unable to hydrogen bond effectively with the hydrophilic surfaces of cellulose fibrils because of steric hindrance. For example, hydrogen bonding of the xyloglucan backbone to cellulose would be blocked by steric restrictions of the side chains (Finkenstadt et al., 1995; Zhang et al., 2011). How then does the naturally occurring, highly substituted, xylan interact with cellulose? Our recent findings in the eudicot Arabidopsis (Arabidopsis thaliana) revealed that the majority of xylan bears substitutions solely on alternate xylosyl residues. Every second Xyl is acetylated (Busse-Wicher et al., 2014; Chong et al., 2014), and MeGlcA side chains reside on evenly spaced xylosyl residues, largely at 6-, 8-, 10-, or 12-residue intervals (Bromley et al., 2013). In this scenario, on a xylan backbone in the ribbon-like 2-fold helical screw conformation, all the decorations will face one side, creating an unsubstituted xylan surface. Therefore, in addition to forming stacking interactions on the hydrophobic surface, this xylan structure is compatible with hydrogen bonding to the hydrophilic surface of cellulose (Busse-Wicher et al., 2014; Busse-Wicher et al., 2016).Both xylan and glucomannan are substantial components of vascular plant secondary cell walls (Timell, 1967; Willfor et al., 2005; McKee et al., 2016). In conifers (gymnosperms, Pinales), the main hemicellulose is glucomannan, but eudicots possess relatively little glucomannan (Scheller and Ulvskov, 2010; Huang et al., 2015), and the secondary cell walls are dominated by xylan, suggesting xylan might have adopted additional functions in these flowering plants that produce hardwoods (Dammström et al., 2009). Conifers, providing softwood for the paper, pulp, and construction industries, are of major ecological and economical value. Consequently, understanding the function and architecture of the cell wall components of softwoods and hardwoods is of great importance.To investigate whether the precise arrangement of xylan decorations on evenly spaced xylosyl residues, as seen in eudicots, is a novel feature of hardwood xylan, we analyzed the pattern of xylan substitution in various gymnosperms and angiosperms. In addition to conifers, there are three further gymnosperm lineages: Cycad, Gingko and Gnetophyta (Fig. 1). There has been a debate whether Gnetophyta are the gymnosperm lineage most closely related to the angiosperms (Davis and Schaefer, 2011; Uddenberg et al., 2015). There are few studies across gymnosperm lineages to determine any divergence in the structure of xylans.Open in a separate windowFigure 1.Schematic representation of the phylogenetic relationship between gymnosperm and angiosperm species studied in this work. The distances do not correspond to phylogenetic distances.Our work shows that some gymnosperm xylans have decorations and decoration patterns that are different to those of eudicot xylans. Nevertheless, these modifications largely reside on even xylosyl residues on the backbone. Molecular dynamics simulations support the hypothesis that this highly conserved organization of substitutions allows an unsubstituted surface of xylan to bind stably to hydrophilic faces of cellulose fibrils.     

The Evolution of Tumour Composition During Fractionated Radiotherapy: Implications for Outcome

Current protocols for delivering radiotherapy are based primarily on tumour stage and nodal and metastases status, even though it is well known that tumours and their microenvironments are highly heterogeneous. It is well established that the local oxygen tension plays an important role in radiation-induced cell death, with hypoxic tumour regions responding poorly to irradiation. Therefore, to improve radiation response, it is important to understand more fully the spatiotemporal distribution of oxygen within a growing tumour before and during fractionated radiation. To this end, we have extended a spatially resolved mathematical model of tumour growth, first proposed by Greenspan (Stud Appl Math 51:317–340, 1972), to investigate the effects of oxygen heterogeneity on radiation-induced cell death. In more detail, cell death due to radiation at each location in the tumour, as determined by the well-known linear-quadratic model, is assumed also to depend on the local oxygen concentration. The oxygen concentration is governed by a reaction-diffusion equation that is coupled to an integro-differential equation that determines the size of the assumed spherically symmetric tumour. We combine numerical and analytical techniques to investigate radiation response of tumours with different intratumoral oxygen distribution profiles. Model simulations reveal a rapid transient increase in hypoxia upon regrowth of the tumour spheroid post-irradiation. We investigate the response to different radiation fractionation schedules and identify a tumour-specific relationship between inter-fraction time and dose per fraction to achieve cure. The rich dynamics exhibited by the model suggest that spatial heterogeneity may be important for predicting tumour response to radiotherapy for clinical applications.     

Evolution of Human Polyomavirus JC: Implications for the Population History of Humans

The polyomavirus JC virus (JCV), the etiological agent of progressive multifocal leukoencephalopathy, is ubiquitous in the human population, infecting children asymptomatically, then persisting in the kidney. The main mode of transmission of JCV is from parents to children through long-term cohabitation. Twelve JCV subtypes that occupy unique domains in Europe, Africa, and Asia have been identified. Here, we attempted to elucidate the evolutionary relationships among JCV strains worldwide using the whole-genome approach with which a highly reliable phylogeny of JCV strains can be reconstructed. Sixty-five complete JCV DNA sequences, derived from various geographical regions and belonging to 11 of the 12 known subtypes, were subjected to phylogenetic analysis using three independent methods: the neighbor-joining, maximum parsimony, and maximum likelihood methods. The trees obtained with these methods consistently indicated that ancestral JCVs were divided into three superclusters, designated as Types A, B, and C. A split in Type A generated two subtypes, EU-a and -b, mainly containing European and Mediterranean strains. The first split in Type B generated Af2 (the major African subtype). Subsequent splits in Type B generated B1-c (a minor European subtype) and all seven Asian subtypes (B1-a, -b, -d, B2, MY, CY, and SC). Type C generated a single subtype (Af1), consisting of strains derived from western Africa. While the present findings provided a basis on which to classify JCV into types or subtypes, they have several implications for the divergence and migration of human populations. Received: 4 April 2001 / Accepted: 31 July 2001     

Adsorption of Mn atom on pristine and defected graphene: a density functional theory study

The functionalization of graphene with transition metals is of great interest due to its wide range of applications, such as hydrogen storage, spintronics, information storage, etc. Due to its magnetic property adsorption of Mn atom on graphene has a high consequence on the electronic properties of graphene. The increase in size of the graphene sheet with hydrogen termination has a high impact on the transformation of electronic properties of the graphene sheet. Hence in this work, we investigate the size as well as change in structural and electronic properties of pristine/defective graphene sheets on adsorption of Mn atom using density functional theory methods. From the results obtained a higher adsorption energy value of 3.04 eV is found for Mn adatom on the defected graphene sheet than the pristine, 1.85 eV. It is subject to the coverage effect which decreases on increasing number of carbon atoms. Moreover, a decrease in energy gap is observed in pristine and defected graphene sheets with a high number of carbon atoms. The density of states illustrates the significant effect for hydrogen termination in the conduction band of the Mn adsorbed graphene sheet with low carbon atoms.

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Graphical Abstract Mn adatom on graphene at different sites

     

Aminoacylation of RNA Minihelices: Implications for tRNA Synthetase Structural Design and Evolution

Abstract

The genetic code is based on the aminoacylation of tRNA with amino acids catalyzed by the aminoacyl-tRNA synthetases. The synthetases are constructed from discrete domains and all synthetases possess a core catalytic domain that catalyzes amino acid activation, binds the acceptor stem of tRNA, and transfers the amino acid to tRNA. Fused to the core domain are additional domains that mediate RNA interactions distal to the acceptor stem. Several synthetases catalyze the aminoacylation of RNA oligonucleotide substrates that recreate only the tRNA acceptor stems. In one case, a relatively small catalytic domain catalyzes the aminoacylation of these substrates independent of the rest of the protein. Thus, the active site domain may represent a primordial synthetase in which polypeptide insertions that mediate RNA acceptor stem interactions are tightly integrated with determinants for aminoacyl adenylate synthesis. The relationship between nucleotide sequences in small RNA oligonucleotides and the specific amino acids that are attached to these oligonucleotides could constitute a second genetic code.     

The Evolution of Avian Senescence Patterns: Implications for Understanding Primary Aging Processes

SYNOPSIS. The long life spans of birds relative to those ofmammals are intriguing to biogerontologists, particularly inlight of birds' high body temperatures, high blood glucose levels,and high metabolic rates—all of which should theoreticallyincrease their biochemical liability for rapid aging. The comparativelongevity of birds and other flying homeotherms is consistentwith evolutionary senescence theory, which posits that specieswith low mortality rates from predation or accident will bereleased from selection for rapid maturity and early reproduction,and will exhibit retarded aging. Comparative analyses of avianlife history parameters to date, although not as extensive asthose for mammals, broadly support an association between lowmortality rates, slow reproduction, and long lifespan. The diversityof bird life histories suggests the importance of developinga diversity of avian models for studies of aging mechanisms,both proximate and ultimate, and for using wild as well as domesticrepresentatives. Birds studied in the laboratory thus far showmany of the same manifestations of aging as mammals, includinghumans, and many ornithologists are beginning to document actuarialevidence consistent with aging in their study populations. Weencourage greater communication and collaboration among comparativegerontologists and ornithologists, in the hope that the studyof aging in birds will lead to an integrated understanding ofphysiological aging processes well grounded in an evolutionaryparadigm.     

Molecular Evolution of Three Avian Neurotrophin Genes: Implications for Proregion Functional Constraints

Neurotrophin proteins are essential for the survival, differentiation, and maintenance of neurons in the peripheral and central nervous systems. Recent studies have shown that the unprocessed proforms of the neurotrophins are preferential high-affinity ligands for p75^NTR and potent inducers of p75^NTR-mediated cell death. Here, we explore differences in the selective constraints acting on the proregions of the three avian neurotrophin genes—NT-3, BDNF, and NGF—in an explicit phylogenetic context. We found a 50-fold difference in levels of constraint as estimated by d _N/d _S ratios, with the NGF proregion showing the lowest degree of constraint and BDNF the highest. These patterns suggest that the high conservation exhibited by the BDNF proregion results from intense functional constraints that are relaxed in NGF and somewhat relaxed in NT-3. The proregion of BDNF is likely to have a function that differentiates it from the corresponding regions of the NGF and NT-3 genes, suggesting that BDNF is the avian neurotrophin most likely to be used both in its precursor and mature forms in vivo.