Motilin and ghrelin gene experienced episodic evolution during primitive placental mammal evolution

Motilin and ghrelin, members of a structure-function-related hormone family, play important roles in gastrointestinal function, regulation of energy homeostasis and growth hormone secretion. We observed episodic evolution in both of their prehormone gene sequences during primitive placental mammal evolution, during which most of the nonsynonymous changes result in radical substitution. Of note, a functional obestatin hormone might have only originated after this episodic evolution event. Early in placental mammal evolution, a series of biology complexities evolved. At the same time the motilin and ghrelin prehormone genes, which play important roles in several of these processes, experienced episodic evolution with dramatic changes in their coding sequences. These observations suggest that some of the lineage-specific physiological adaptations are due to episodic evolution of the motilin and ghrelin genes.

Prion protein gene (PRNP) polymorphisms in native Chinese cattle

Le polymorphisme au sein de quatre regions du gene codant pour la proteine prion bovine (PRNP) confere la susceptibilite a l'encephalopathie bovine spongiforme (BSE). Ceux-ci comprennent un polymorphisme d'insertion/deletion (indel) de 23 pb dans le promoteur, un indel de 12 pb dans l'intron 1, un octapeptide repete ou un indel de 24 pb au sein du cadre de lecture, et un polymorphisme mononucleotidique (SNP) dans la region codante. Dans ce travail, les auteurs ont examine la frequence des genotypes, des alleles et des haplotypes pour ces indel au sein de 349 bovins d'origine chinoise, de meme que la sequence nucleotidique de ce gene chez 50 de ces animaux. Leurs resultats montrent que l'allele ayant la deletion de 12 pb et l'haplotype combinant la deletion de 23 pb et la deletion de 12 pb, lesquels ont ete suggeres comme etant importants pour la susceptibilite a la BSE, sont rares au sein des bovins du sud de la Chine. Une difference significative a ete observee entre les bovins affectes par la BSE et les bovins chinois sains pour ce qui est de l'indel de 12 pb. Au total, 14 SNP ont ete observes dans la region codante du gene PRNP chez les bovins chinois. Trois de ces SNP etaient associes a des changements d'acides amines (K3T, P54S et S154N). La substitution E211K qui a ete rapportee recemment chez un cas atypique de la BSE chez un bovin americain n'a pas ete detectee dans ce travail.

Origin and evolution of new exons in rodents

Gene number difference among organisms demonstrates that new gene origination is a fundamental biological process in evolution. Exon shuffling has been universally observed in the formation of new genes. Yet to be learned are the ways new exons originate and evolve, and how often new exons appear. To address these questions, we identified 2695 newly evolved exons in the mouse and rat by comparing the expressed sequences of 12,419 orthologous genes between human and mouse, using 743,856 pig ESTs as the outgroup. The new exon origination rate is about 2.71 x 10(-3) per gene per million years. These new exons have markedly accelerated rates both of nonsynonymous substitutions and of insertions/ deletions (indels). A much higher proportion of new exons have Kappa(a)/Kappa(s) ratios > 1 (where K-a is the nonsynonymous substitution rate and K-s is the synonymous substitution rate) than K do the old exons shared by human and mouse, implying a role of positive selection in the rapid evolution. The majority of these new exons have sequences unique in the genome, suggesting that most new exons might originate through "exonization" of intronic sequences. Most of the new exons appear to be alternative exons that are expressed at low levels.

Species identification and authentication of some of the most important seafood products in Iranian markets using biotechnological methods based on DNA

This study describes the molecular identification of sixteen fish species present in processed products imported into Iran for human consumption. DNA barcoding using direct sequencing of about 650 bp of the mitochondrial Cytochrome Oxidase subunit I gene revealed incorrect labeling (31.25%). Substitution of fish species constitutes serious economic fraud, and our results increase concern regarding the trading of processed fish products in Iran from both health and conservation points of view.

Identification of triosephosphate isomerase (TIM) genes from Microcystis (Cyanobacteria : Chroococcales) and theoretical analyses of the potential of cyanobacterial TIM as a target for designing specific inhibitors

The genes encoding triosephosphate isomerase (TIM) in three species of Microcystis (M. aeruginosa, M. viridis and M. wesenbergii) were investigated. Reverse transcriptase-polymerase chain reaction indicated that they were transcribed in the cells. Analyses showed that their DNA and deduced amino acid sequences were highly conserved between all the three species, only a single nonsynonymous substitution was seen at position 31, from an Asp in M. aeruginosa and M. viridis to Glu in M. wesenbergii. Sequence alignment of these with 12 other known cyanobacterial TIM sequences showed that all the cyanobacterial TIMs had a very high level of amino acid identity (over 50% between each two). Comparison of the cyanobacterial TIMs with other reported TIMs (from diverse lineages of the three Domains) showed that they possessed common active-site residues and sequence motifs. All cyanobacterial TIMs have two common cysteine residues (Cys127 and Cys176), and the Cys176 is almost cyanobacteria-specific with only one exception in Streptomyces coelicolor. Both secondary structure alignment and comparative modelling of Synechocystis sp. TIM showed that Cys176 was located at the hinge region of the flexible loop-6 and might therefore be critical to the movement of TIM's loop-6, which is important to the function of the enzyme. Thus, the cyanobacterial TIM-specific Cys176 may be a potential site for the discovery of suitable drugs against cyanobacteria, and such drugs may have utility in controlling water blooms due to cyanobacteria.

溴代胞嘧啶对三螺旋DNA 稳定性的影响

研究了三螺旋DNA 中胞嘧啶被5 - 溴胞嘧啶取代后的稳定性问题。通过建立CGC , CGBrC , BrCGC 和BrCGBrC 4 种模型, 并采用Insight Ⅱ软件包中的Discover 程序进行计算模拟, 发现用5 - 溴胞嘧啶取代三 螺旋DNA 分子中的胞嘧啶后, 整个分子的稳定性有所降低。同时, 当用5 - 溴胞嘧啶取代三螺旋DNA 不 同链上的胞嘧啶时, 被取代链的碱基堆积能显著增高, 导致分子链内稳定性降低, 但被取代链和相邻链间 相互作用能有所降低, 使得链间作用趋向稳定。

Material efficiency: providing material services with less material production.

Material efficiency, as discussed in this Meeting Issue, entails the pursuit of the technical strategies, business models, consumer preferences and policy instruments that would lead to a substantial reduction in the production of high-volume energy-intensive materials required to deliver human well-being. This paper, which introduces a Discussion Meeting Issue on the topic of material efficiency, aims to give an overview of current thinking on the topic, spanning environmental, engineering, economics, sociology and policy issues. The motivations for material efficiency include reducing energy demand, reducing the emissions and other environmental impacts of industry, and increasing national resource security. There are many technical strategies that might bring it about, and these could mainly be implemented today if preferred by customers or producers. However, current economic structures favour the substitution of material for labour, and consumer preferences for material consumption appear to continue even beyond the point at which increased consumption provides any increase in well-being. Therefore, policy will be required to stimulate material efficiency. A theoretically ideal policy measure, such as a carbon price, would internalize the externality of emissions associated with material production, and thus motivate change directly. However, implementation of such a measure has proved elusive, and instead the adjustment of existing government purchasing policies or existing regulations-- for instance to do with building design, planning or vehicle standards--is likely to have a more immediate effect.

Local structure of Mn in (La1-xHox) 2/3Ca1/3MnO3 studied by X-ray absorption fine structure

Results of X-ray absorption fine structure measurements in manganites (La1-xHox)2/3Ca1/3MnO3 with 0.15 < x < 0.50 are presented. When LaMnO3 is doped with a, divalent element such as Ca2+, substituting for La3+, holes are induced in the filled Mn d orbitais. This leads to a, strong ferromagnetic coupling between Mn sites. Ca ions in La1-xCa xMnO3 introduce a distortion of the crystal lattice and mixed valence Mn ions (Mn3+ and Mn4+). On the other hand, in manganites (La1-xHox)2/3Ca 1/3MnO3 the substitution of La for Ho causes a lattice distortion and induces a disorder, which reduces a magnetic interaction. The ferromagnetic transition temperature and conductivity decrease very quickly with increasing x. The magnetic and transport properties of compounds depend on the local atomic structure around Mn ions. The information on the bond lengths and Debye-Waller factor are obtained from the extended X-ray absorption fine structure (EXAFS) data analysis. The charge state of Mn is determined from the position of the absorption edge in X-ray absorption near edge structure (XANES) data. XAFS results are in good agreement with magnetic characteristics of the studied materials.

LiMn2-xTixO4 spinel-type compounds (x ≤ 1): Structural, electrical and magnetic properties

LiMn2-xTixO4 compounds with 0 ≤ x ≤ 1 were prepared by solid state reaction and Pechini technique. Powder X-ray diffraction showed that all samples crystallize with the spinel crystal structure (S.G. Fd3-m). The cubic unit-cell parameter increases with the Ti content. The influence of the Ti content and cationic distribution on the magnetic properties of the compounds was studied by measuring the temperature and magnetic field dependences of the magnetization: substitution by non-magnetic d0 Ti4+ ions appeared to weaken the magnetic interactions between the manganese ions. The electrical properties of LiMnTiO4 were studied by AC impedance spectroscopy and DC polarisation measurements, which revealed the electronic character of the conduction process. © 2006 Elsevier B.V. All rights reserved.

Spin-cluster effect and lattice-deformation-induced Kondo effect, spin-glass freezing, and strong phonon scattering in La 0.7 Ca 0.3Mn 1-xCr xO 3

Besides the Kondo effect observed in dilute magnetic alloys, the Cr-doped perovskite manganate compounds La0.7 Ca0.3 Mn1-x Crx O3 also exhibit Kondo effect and spin-glass freezing in a certain composition range. An extensive investigation for the La0.7 Ca0.3 Mn1-x Crx O3 (x=0.01, 0.05, 0.10, 0.3, 0.6, and 1.0) system on the magnetization and ac susceptibility, the resistivity and magnetoresistance, as well as the thermal conductivity is done at low temperature. The spin-glass behavior has been confirmed for these compounds with x=0.05, 0.1, and 0.3. For temperatures above Tf (the spin-glass freezing temperature) a Curie-Weiss law is obeyed. The paramagnetic Curie temperature θ is dependent on Cr doping. Below Tf there exists a Kondo minimum in the resistivity. Colossal magnetoresistance has been observed in this system with Cr concentration up to x=0.6. We suppose that the substitution of Mn with Cr dilutes Mn ions and changes the long-range ferromagnetic order of La0.7 Ca0.3 MnO3. These behaviors demonstrate that short-range ferromagnetic correlation and fluctuation exist among Mn spins far above Tf. Furthermore, these interactions are a precursor of the cooperative freezing at Tf. The "double bumps" feature in the resistivity-temperature curve is observed in compounds with x=0.05 and 0.1. The phonon scattering is enhanced at low temperatures, where the second peak of double bumps comes out. The results indicate that the spin-cluster effect and lattice deformation induce Kondo effect, spin-glass freezing, and strong phonon scattering in mixed perovskite La0.7 Ca0.3 Mn1-x Crx O3. © 2005 American Institute of Physics.

Deep mixing for excavation support: Design issues

Deep mixing is effectively used in excavations both in conjunction with and in substitution of traditional techniques, where it results in more economical and convenient solutions for the stability of the system and the prevention of seepage. Deep mixed walls constructed as part of a soldier pile and tie-backs system act also as temporary support, prevent seepage like a sheet pile wall, but require a lower amount of steel. The deep mixed treatment can also contribute to the stability of the wall system against deep-seated failures. Although deep mixing is currently used for excavation control in numerous projects, no standard procedure has been developed and the different applications have not been evaluated. As this technique emerges as a more economical and effective alternative to traditional excavation shoring, there is a need for guidelines describing proven procedures for evaluation of design, analysis and construction. This paper presents comparisons in the design of excavation support using deep mixing and other traditional techniques. Issues important for design, analysis, and construction of deep mixed excavation walls are also discussed.

Fishtail effects and improved critical current density in polycrystalline bulk MgB2 containing carbon nanotubes

Bulk, polycrystalline MgB2 samples containing 2.5 wt.% multi-walled carbon nanotubes (CNTs) have been prepared by conventional solid state reaction at 800 °C. The effect of Mg precursor powders composed of two different particle sizes on the critical current density (Jc) of the as-sintered samples has been investigated. An enhancement of Jc at high field has been observed in MgB2 samples containing CNTs prepared with fine Mg powders, whereas the values of Jc in the sample prepared using the coarser Mg powders was slightly decreased. These results contrast significantly with measurements on pure, undoped, MgB2 samples prepared from the same Mg precursor powders. They suggest that carbon substitution into the MgB2 lattice, which accounts for increased flux pinning, and therefore Jc, is more effective in precursor Mg powders with a larger surface area. Rather surprisingly, the so-called fishtail effect, observed typically in MgB2 single crystals and in the (RE)BCO family of high temperature superconductors (HTSs), was observed in both sets of CNT-containing polycrystalline samples as a result of lattice defects associated with C substitution. Significantly, analytical fits to the data for each sample suggest that the same flux pinning mechanism accounts for the fishtail effect in polycrystalline MgB2 and (RE)BCO. © 2013 Elsevier B.V. All rights reserved.

Tests of an adaptive QM/MM calculation on free energy profiles of chemical reactions in solution.

We present reaction free energy calculations using the adaptive buffered force mixing quantum mechanics/molecular mechanics (bf-QM/MM) method. The bf-QM/MM method combines nonadaptive electrostatic embedding QM/MM calculations with extended and reduced QM regions to calculate accurate forces on all atoms, which can be used in free energy calculation methods that require only the forces and not the energy. We calculate the free energy profiles of two reactions in aqueous solution: the nucleophilic substitution reaction of methyl chloride with a chloride anion and the deprotonation reaction of the tyrosine side chain. We validate the bf-QM/MM method against a full QM simulation, and show that it correctly reproduces both geometrical properties and free energy profiles of the QM model, while the electrostatic embedding QM/MM method using a static QM region comprising only the solute is unable to do so. The bf-QM/MM method is not explicitly dependent on the details of the QM and MM methods, so long as it is possible to compute QM forces in a small region and MM forces in the rest of the system, as in a conventional QM/MM calculation. It is simple, with only a few parameters needed to control the QM calculation sizes, and allows (but does not require) a varying and adapting QM region which is necessary for simulating solutions.

Controlled amine functionality in self-assembled monolayers via the hidden amine route: chemical and electronic tunability.

A synthetic strategy for fabricating a dense amine functionalized self-assembled monolayer (SAM) on hydroxylated surfaces is presented. The assembly steps are monitored by X-ray photoelectron spectroscopy, Fourier transform infrared- attenuated total reflection, atomic force microscopy, variable angle spectroscopic ellipsometry, UV-vis surface spectroscopy, contact angle wettability, and contact potential difference measurements. The method applies alkylbromide-trichlorosilane for the fabrication of the SAM followed by surface transformation of the bromine moiety to amine by a two-step procedure: S(N)2 reaction that introduces the hidden amine, phthalimide, followed by the removal of the protecting group and exposing the free amine. The use of phthalimide moiety in the process enabled monitoring the substitution reaction rate on the surface (by absorption spectroscopy) and showed first-order kinetics. The simplicity of the process, nonharsh reagents, and short reaction time allow the use of such SAMs in molecular nanoelectronics applications, where complete control of the used SAM is needed. The different molecular dipole of each step of the process, which is verified by DFT calculations, supports the use of these SAMs as means to tune the electronic properties of semiconductors and for better synergism between SAMs and standard microelectronics processes and devices.

Distinct Evolutionary Patterns Between Two Duplicated Color Vision Genes Within Cyprinid Fishes

We investigated the molecular evolution of duplicated color vision genes (LWS-1 and SWS2) within cyprinid fish, focusing on the most cavefish-rich genus-Sinocyclocheilus. Maximum likelihood-based codon substitution approaches were used to analyze the evolution of vision genes. We found that the duplicated color vision genes had unequal evolutionary rates, which may lead to a related function divergence. Divergence of LWS-1 was strongly influenced by positive selection causing an accelerated rate of substitution in the proportion of pocket-forming residues. The SWS2 pigment experienced divergent selection between lineages, and no positively selected site was found. A duplicate copy of LWS-1 of some cyprinine species had become a pseudogene, but all SWS2 sequences remained intact in the regions examined in the cyprinid fishes examined in this study. The pseudogenization events did not occur randomly in the two copies of LWS-1 within Sinocyclocheilus species. Some cave species of Sinocyclocheilus with numerous morphological specializations that seem to be highly adapted for caves, retain both intact copies of color vision genes in their genome. We found some novel amino acid substitutions at key sites, which might represent interesting target sites for future mutagenesis experiments. Our data add to the increasing evidence that duplicate genes experience lower selective constraints and in some cases positive selection following gene duplication. Some of these observations are unexpected and may provide insights into the effect of caves on the evolution of color vision genes in fishes.