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David K Smith

Publications and source records attributed to David K Smith.

At least 19 recordsLinked to original sources
PubMed2006

Intron length and accelerated 3' gene evolution.

Genetic evolution depends in part upon a balance between negative selection and environmentally driven mutation. To explore whether this balance is affected by gene structure, we have used phylogenetic data mining to compare gene compositions across a range of species. Here we show that genomes of higher species exhibit a greater frequency of 5' CpG islands and of CpG-->TpG/CpA transitions. This latter mutational pattern exhibits a 5'-to-3' trend in higher species, consistent with a length-dependent effect on methylation-dependent CpG suppression. Associated strand asymmetry (TpG>CpA) declines with gene length, implying attenuation of transcription-coupled repair 3' to introns. A sharp 3' rise in coding region single-nucleotide polymorphism frequency further supports a mechanistic role for intron length in promoting genetic variation by reducing repair and/or weakening negative selection. Consistent with this, the Ka/Ks ratio of 3' exons exceeds that of centrally located exons in intron-containing, but not in intronless, genes (p<0.0003). We conclude that the efficiency of transcription-coupled repair decreases with gene length, suggesting in turn that 3' gene evolution is accelerated both by introns and by gene methylation.

3' Untranslated Regions↗
PubMed2006

Dendron-protected Au nanoparticles--effect of dendritic structure on chemical stability.

A series of gold nanoparticles stabilised by 'Newkome-type' dendritic branching has been synthesised and fully characterised. In particular, the properties and behaviour of these hybrid materials are compared with those of a previously reported set of nanoparticles stabilised by dendrons constructed using l-lysine building blocks. The rates of cyanide-induced nanoparticle decomposition were determined, and it was found that the rate of decomposition increased on the introduction of dendritic branching. Furthermore, 'Newkome-type' dendrons were significantly more effective at protecting the encapsulated gold nanoparticle than the l-lysine based dendrons. It is proposed that this observation can be explained on the basis of more effective packing and surface coverage by the 'Newkome-type' dendrons. Importantly, this study therefore demonstrates that the organic chemical structure of dendritic ligands plays a crucial role in controlling the reactivity of self-assembled hybrid nanostructures.

Anthracenes↗
PubMed2006

Accelerated evolutionary rate may be responsible for the emergence of lineage-specific genes in ascomycota.

The evolutionary origin of "orphan" genes, genes that lack sequence similarity to any known gene, remains a mystery. One suggestion has been that most orphan genes evolve rapidly so that similarity to other genes cannot be traced after a certain evolutionary distance. This can be tested by examining the divergence rates of genes with different degrees of lineage specificity. Here the lineage specificity (LS) of a gene describes the phylogenetic distribution of that gene's orthologues in related species. Highly lineage-specific genes will be distributed in fewer species in a phylogeny. In this study, we have used the complete genomes of seven ascomycotan fungi and two animals to define several levels of LS, such as Eukaryotes-core, Ascomycota-core, Euascomycetes-specific, Hemiascomycetes-specific, Aspergillus-specific, and Saccharomyces-specific. We compare the rates of gene evolution in groups of higher LS to those in groups with lower LS. Molecular evolutionary analyses indicate an increase in nonsynonymous nucleotide substitution rates in genes with higher LS. Several analyses suggest that LS is correlated with the evolutionary rate of the gene. This correlation is stronger than those of a number of other factors that have been proposed as predictors of a gene's evolutionary rate, including the expression level of genes, gene essentiality or dispensability, and the number of protein-protein interactions. The accelerated evolutionary rates of genes with higher LS may reflect the influence of selection and adaptive divergence during the emergence of orphan genes. These analyses suggest that accelerated rates of gene evolution may be responsible for the emergence of apparently orphan genes.

Ascomycota↗
PubMed2006

Anion binding by catechols--an NMR, optical and electrochemical study.

The X-ray structure of the ClC chloride channel made it clear that O-H...chloride interactions play a key role in important biological membrane-bound systems, however, surprisingly this type of interaction has only been rarely exploited for the development of synthetic anion receptors. This paper therefore reports the anion binding strengths and selectivities of some simple commercially available bis-phenols. In particular, we compare catechol (1,2-dihydroxybenzene) and resorcinol (1,3-dihydroxybenzene) which show interesting and different selectivities between the halide anions in acetonitrile solution. Catechol binds tetrabutylammononium (TBA) chloride almost 30 times more strongly than TBA bromide, whilst for resorcinol, this difference drops to a factor of ca. 3.5. It is suggested that this is a consequence of the bite angle of the chelating hydrogen bonding groups of catechol being particularly appropriate for effective binding of the smaller anion. The oxidation of catechol to ortho-quinone is perturbed by the addition of chloride anions, as probed via cyclic voltammetry, and this compound can therefore be considered to act as an electrochemical sensor for chloride. Nitrocatechol is able to bind chloride anions more strongly than catechol as a consequence of its enhanced acidity and hence greater hydrogen bond donor character. Furthermore, nitrocatechol senses the bound anion via changes in its UV-visible spectrum. Notably, binding still occurs even in the presence of small amounts of competitive solvents (e.g. water). This observation has biomimetic importance as wet acetonitrile has some similarity in terms of overall polarity and hydrogen bond competition to the solvent shielded interiors of biological macromolecules and membranes--such as the environment within the ClC chloride channel itself. Finally, we report that catechol undergoes a unique colorimetric response on the addition of basic anions, such as fluoride. We can assign this response as being due to oxidative degradation of catechol catalysed by the basic anions (which bind to, and deprotonate, the catechol). This process is somewhat analogous to the well-known metal catalysed oxidation of catechol which can take place in aqueous solution. The speed of response and easily monitored and distinctive colour change induced by fluoride anions indicates this may be a useful mechanism for exploitation in the development of selective fluoride sensors.

Journal Article↗
PubMed2005

Unique nanoscale morphologies underpinning organic gel-phase materials.

This study investigates the self-assembly of simple aliphatic diamines with a dendritic peptide. By controlling the molar ratio of this two-component system, new nanoscale morphologies were generated. In the presence of relatively long aliphatic chains (C10, C12) a transition from nanoscale fibres to platelets was observed on changing the molar ratio, whereas, for shorter spacer chains (e.g., C9 and C8), interesting and unique morphological changes were observed by low voltage field emission gun scanning electron microscopy (SEM), with "nanosquares" or nanoscale "rosette" structures being formed. Remarkably, these discrete nanoscale structures were able to form sample-spanning networks capable of supporting a gel-phase material; whereas, most gels are usually based on fibrillar assemblies. In addition to SEM, the gels were characterised by using thermal measurements and circular dichroism spectroscopy. The length of the diamine spacer and the molar ratio of components controlled the self-assembly process by modifying the spatial organisation of the dendritic head groups at the molecular level, which is transcribed into the aspect ratio of the self-assembled state at the microscopic level. Ultimately, this led to diamine-induced control of the macroscopic material's behaviour. When present in excess, the diamine controlled the observed nanoscale morphology as a consequence of undergoing a dendritically controlled nanocrystallisation process to form a network, an unusual and significant result.

Anthracenes↗
PubMed2005

Two-component gel-phase materials--highly tunable self-assembling systems.

In the past 10 years, the molecular self-assembly and network formation of small molecule gelators has become one of the most active frontiers of the emergent area of nanochemistry. Increasingly, research efforts have begun to focus on multicomponent gelators, which rely on the initial interaction of distinct individual components to form a complex that subsequently self-assembles into a fibrous supramolecular polymer. In true two-component systems, an individual component can be present in isotropic solution, and only on addition of the second component will a gel actually form. In some cases, however, two-component gels are reported in which the second component significantly modifies the behaviour of a known gelator. Both systems are discussed in this article. The additional level of supramolecular control in the hierarchical self-assembly of two-component gels confers exquisite tunability and controllability. Functionality can be readily built into the material by simple variation of one of the individual components. This article discusses the key approaches used to control self-assembly by manipulating single molecular-recognition events and illustrates how controlling the transcription of information from the molecular to the macroscopic level by the simple addition of a second component allows complex functional materials to be selectively assembled from simple building blocks.

Journal Article↗
PubMed2005

Dendritic supermolecules--towards controllable nanomaterials.

Dendritic molecules constitute one of the most exciting areas of modern nanochemistry, largely as a consequence of the unique properties associated with their branched architectures. This article describes how 'dendritic function' can also be achieved using small, synthetically accessible branched building blocks (individual dendrons) which simply self-assemble via non-covalent interactions to generate dendritic nanoscale architectures with novel behaviour. (a) Using non-covalent interactions at the focal point of a dendron allows the self-assembly of nanometre-sized supramolecular dendrimers around an appropriate template species. Such systems have potential applications in the controlled encapsulation and release of active ingredients. (b) Employing non-covalent intermolecular dendron-dendron interactions can give rise to the hierarchical assembly of nanostructured materials. Such assemblies of dendritic molecules ultimately express their molecular scale information on a macroscopic scale, and therefore have applications in materials science, for example as gels. (c) The multiple surface groups of dendrons are capable of forming multiple interactions with large surfaces, such as those found on biomolecules or in biological systems. Employing multivalent interactions between dendron surfaces and biological molecules opens up the potential application of dendritic systems as medicinal therapies. In summary, dendritic supermolecules offer a potentially cost-effective approach to the future application of dendritic systems to a range of real-world problems.

Aurintricarboxylic Acid↗
PubMed2005

The N-terminal cytokine binding domain of LIFR is required for CNTF binding and signaling.

Ciliary neurotrophic factor (CNTF) forms a functional receptor complex containing the CNTF receptor, gp130, and the leukemia inhibitory factor receptor (LIFR). However, the nature and stoichiometry of the receptor-mediated interactions in this complex have not yet been fully resolved. We show here that signaling by CNTF, but not by LIF or oncostatin M (OSM), was abolished in cells overexpressing a LIFR mutant with the N-terminal cytokine binding domain deleted. Our results illustrate molecular differences between the CNTF active receptor complex and those of LIF and OSM and provide further support for the hexameric model of the CNTF receptor complex.

Ciliary Neurotrophic Factor↗
PubMed2005

A direct comparison of one- and two-component dendritic self-assembled materials: elucidating molecular recognition pathways.

This paper compares and contrasts, for the first time, one- and two-component gelation systems that are direct structural analogues and draws conclusions about the molecular recognition pathways that underpin fibrillar self-assembly. The new one-component systems comprise l-lysine-based dendritic headgroups covalently connected to an aliphatic diamine spacer chain via an amide bond. One-component gelators with different generations of headgroup (from first to third generation) and different length spacer chains are reported. The self-assembly of these dendrimers in toluene was elucidated using thermal measurements, circular dichroism (CD) and NMR spectroscopies, scanning electron microscopy (SEM), and small-angle X-ray scattering (SAXS). The observations are compared with previous results for the analogous two-component gelation system in which the dendritic headgroups are bound to the aliphatic spacer chain noncovalently via acid-amine interactions. The one-component system is inherently a more effective gelator, partly as a consequence of the additional covalent amide groups that provide a new hydrogen bonding molecular recognition pathway, whereas the two-component analogue relies solely on intermolecular hydrogen bond interactions between the chiral dendritic headgroups. Furthermore, because these amide groups are important in the assembly process for the one-component system, the chiral information preset in the dendritic headgroups is not always transcribed into the nanoscale assembly, whereas for the two-component system, fiber formation is always accompanied by chiral ordering because the molecular recognition pathway is completely dependent on hydrogen bond interactions between well-organized chiral dendritic headgroups.

Journal Article↗
PubMed2005

MBEToolbox: a MATLAB toolbox for sequence data analysis in molecular biology and evolution.

BACKGROUND: MATLAB is a high-performance language for technical computing, integrating computation, visualization, and programming in an easy-to-use environment. It has been widely used in many areas, such as mathematics and computation, algorithm development, data acquisition, modeling, simulation, and scientific and engineering graphics. However, few functions are freely available in MATLAB to perform the sequence data analyses specifically required for molecular biology and evolution. RESULTS: We have developed a MATLAB toolbox, called MBEToolbox, aimed at filling this gap by offering efficient implementations of the most needed functions in molecular biology and evolution. It can be used to manipulate aligned sequences, calculate evolutionary distances, estimate synonymous and nonsynonymous substitution rates, and infer phylogenetic trees. Moreover, it provides an extensible, functional framework for users with more specialized requirements to explore and analyze aligned nucleotide or protein sequences from an evolutionary perspective. The full functions in the toolbox are accessible through the command-line for seasoned MATLAB users. A graphical user interface, that may be especially useful for non-specialist end users, is also provided. CONCLUSION: MBEToolbox is a useful tool that can aid in the exploration, interpretation and visualization of data in molecular biology and evolution. The software is publicly available at http://web.hku.hk/~jamescai/mbetoolbox/ and http://bioinformatics.org/project/?group_id=454

Algorithms↗
PubMed2005

Conserved transcription factor binding sites of cancer markers derived from primary lung adenocarcinoma microarrays.

Gene transcription in a set of 49 human primary lung adenocarcinomas and 9 normal lung tissue samples was examined using Affymetrix GeneChip technology. A total of 3442 genes, called the set M AD, were found to be either up- or down-regulated by at least 2-fold between the two phenotypes. Genes assigned to a particular gene ontology term were found, in many cases, to be significantly unevenly distributed between the genes in and outside M AD. Terms that were overrepresented in M AD included functions directly implicated in the cancer cell metabolism. Based on their functional roles and expression profiles, genes in M AD were grouped into likely co-regulated gene sets. Highly conserved sequences in the 5 kb region upstream of the genes in these sets were identified with the motif discovery tool, MoDEL. Potential oncogenic transcription factors and their corresponding binding sites were identified in these conserved regions using the TRANSFAC 8.3 database. Several of the transcription factors identified in this study have been shown elsewhere to be involved in oncogenic processes. This study searched beyond phenotypic gene expression profiles in cancer cells, in order to identify the more important regulatory transcription factors that caused these aberrations in gene expression.

5' Flanking Region↗
PubMed2004

Solvent effects on supramolecular gel-phase materials: two-component dendritic gel.

The self-assembly of diaminododecane with dendritic l-lysine-based peptides to form gel-phase materials was investigated in a range of different solvents. The degree of structuring was modulated by the solvent employed, an effect which induced subtle changes in the mesoscale aggregate morphology and macroscopic behavior of the self-assembled state. In this paper a range of different solvent parameters are investigated, and it is clearly shown that macroscopic gelation can be related to a solvent polar solubility parameter for this system. The results also show a dependence on Kamlet-Taft hydrogen bonding parameters, and this clearly demonstrates the role of the solvent environment in terms of dendron--dendron intermolecular hydrogen bonding and its impact on the supramolecular chiral organization of the assembled superstructure.

Circular Dichroism↗
PubMed2004

Two-component dendritic gel: effect of stereochemistry on the supramolecular chiral assembly.

The self-assembly of diaminododecane solubilised by four different stereoisomeric dendritic peptides to form gel-phase materials in toluene was investigated. The second generation dendritic peptides were based on D- and L-lysine building blocks, and each contained three chiral centres. By designing dendritic peptides in which the configurations of the chiral centres were modified, and applying them as gelator units, the assembly of stereoisomers could be investigated. In all cases, the self-assembly of gelator units resulted in macroscopic gelation. However, the degree of structuring was modulated by the stereoisomers employed, an effect which changed the morphology and macroscopic behavior of the self-assembled state. Enantiomeric (L,L,L or D,D,D) gelator units formed fibrous molecular assemblies, whilst the racemic gel (50 % L,L,L : 50 % D,D,D) formed a flat structure with a "woven" appearance. Gelator units based on L,D,D or D,L,L dendritic peptides also formed fibrous assemblies, but small-angle X-ray scattering indicated significant morphological differences were caused by the switch in chirality. Furthermore, the macroscopic stability of the gel was diminished when these peptides were compared with their L,L,L or D,D,D analogues. In this paper it is clearly shown that individual stereocentres, on the molecular level, are directly related to the helicity within the fibre. It is argued that the chirality controls the pattern of hydrogen bonding within the assembly, and hence determines the extent of fibre formation and the macroscopic gel strength.

Circular Dichroism↗