Accounting for calibration uncertainty in phylogenetic estimation of evolutionary divergence times

The estimation of phylogenetic divergence times from sequence data is an important component of many molecular evolutionary studies. There is now a general appreciation that the procedure of divergence dating is considerably more complex than that initially described in the 1960s by Zuckerkandl and Pauling (1962, 1965). In particular, there has been much critical attention toward the assumption of a global molecular clock, resulting in the development of increasingly sophisticated techniques for inferring divergence times from sequence data. In response to the documentation of widespread departures from clocklike behavior, a variety of local- and relaxed-clock methods have been proposed and implemented. Local-clock methods permit different molecular clocks in different parts of the phylogenetic tree, thereby retaining the advantages of the classical molecular clock while casting off the restrictive assumption of a single, global rate of substitution (Rambaut and Bromham 1998; Yoder and Yang 2000).

Branch-length estimation bias misleads molecular dating for a vertebrate mitochondrial phylogeny

Despite recent methodological advances in inferring the time-scale of biological evolution from molecular data, the fundamental question of whether our substitution models are sufficiently well specified to accurately estimate branch-lengths has received little attention. I examine this implicit assumption of all molecular dating methods, on a vertebrate mitochondrial protein-coding dataset. Comparison with analyses in which the data are RY-coded (AG → R; CT → Y) suggests that even rates-across-sites maximum likelihood greatly under-compensates for multiple substitutions among the standard (ACGT) NT-coded data, which has been subject to greater phylogenetic signal erosion. Accordingly, the fossil record indicates that branch-lengths inferred from the NT-coded data translate into divergence time overestimates when calibrated from deeper in the tree. Intriguingly, RY-coding led to the opposite result. The underlying NT and RY substitution model misspecifications likely relate respectively to “hidden” rate heterogeneity and changes in substitution processes across the tree, for which I provide simulated examples. Given the magnitude of the inferred molecular dating errors, branch-length estimation biases may partly explain current conflicts with some palaeontological dating estimates.

Diesel knock combustion and its detection using acoustic emission

This paper presents an experimental investigation into the detection of excessive Diesel knock using acoustic emission signals. Three different dual-fuel Diesel engine operating regimes were induced into a compression ignition (Diesel) engine operating on both straight Diesel fuel and two different mixtures of fumigated ethanol and Diesel. The experimentally induced engine operating regimes were; normal, or Diesel only operation, acceptable dual-fuel operation and dual-fuel operation with excessive Diesel knock. During the excessive Diesel knock operating regime, high rates of ethanol substitution induced potentially damaging levels of Diesel knock. Acoustic emission data was captured along with cylinder pressure, crank-angle encoder, and top-dead centre signals for the different engine operating regimes. Using these signals, it was found that acoustic emission signals clearly distinguished between the two acceptable operating regimes and the operating regime experiencing excessive Diesel knock. It was also found that acoustic emission sensor position is critical. The acoustic emission sensor positioned on the block of the engine clearly related information concerning the level of Diesel knock occurring in the engine whist the sensor positioned on the head of the engine gave no indication concerning Diesel knock severity levels.

Nitrate reduction over nanoscale zero-valent iron prepared by hydrogen reduction of goethite

Nitrate reduction with nanoscale zero-valent iron (NZVI) was reported as a potential technology to remove nitrate from nitrate-contaminated water. In this paper, nitrate reduction with NZVI prepared by hydrogen reduction of natural goethite (NZVI-N, -N represents natural goethite) and hydrothermal goethite (NZVI-H, -H represents hydrothermal goethite) was conducted. Besides, the effects of reaction time, nitrate concentration, iron-to-nitrate ratio on nitrate removal rate over NZVI-H and NZVI-N were investigated. To prove their excellent nitrate reduction capacities, NZVI-N and NZVI-H were compared with ordinary zero-valent iron (OZVI-N) through the static experiments. Based on all above investigations, the mechanism of nitrate reduction with NZVI-N was proposed. The result showed that reaction time, nitrate concentration, iron-to-nitrate ratio played an important role in nitrate reduction by NZVI-N and NZVI-H. Compared with OZVI, NZVI-N and NZVI-H showed little relationship with pH. And NZVI-N for nitrate composition offers a higher stability than NZVI-H because of the existence of Al-substitution. Furthermore, NZVI-N, prepared by hydrogen reduction of goethite, has higher activity for nitrate reduction and the products contain hydrogen, nitrogen, NH 4 +, a little nitrite, but no NOx, meanwhile NZVI-N was oxidized to Fe 2+. It is a relatively easy and cost-effective method for nitrate removal, so NZVI-N reducing nitrate has a great potential application in nitrate removal of groundwater. © 2012 Elsevier B.V.

Preparation, characterization and in vitro angiogenic capacity of cobalt substituted β-tricalcium phosphate ceramics

Divalent cobalt ions (Co2+) have been shown to possess the capacity to induce angiogenesis by activating hypoxia inducible factor-1α (HIF-1α) and subsequently inducing the production of vascular endothelial growth factor (VEGF). However, there are few reports about Co-containing biomaterials for inducing in vitro angiogenesis. The aim of the present work was to prepare Co-containing β-tricalcium phosphate (Co-TCP) ceramics with different contents of calcium substituted by cobalt (0, 2, 5 mol%) and to investigate the effect of Co substitution on their physicochemical and biological properties. Co-TCP powders were synthesized by a chemistry precipitation method and Co-TCP ceramics were prepared by sintering the powder compacts. The effect of Co substitution on phase transition and the sintering property of the β-TCP ceramics was investigated. The proliferation and VEGF expression of human bone marrow mesenchymal stem cells (HBMSCs) cultured with both powder extracts and ceramic discs of Co-TCP was further evaluated. The in vitro angiogenesis was evaluated by the tube-like structure formation of human umbilical vein endothelial cells (HUVECs) cultured on ECMatrix™ in the presence of powder extracts. The results showed that Co substitution suppressed the phase transition from β- to α-TCP. Both the powder extracts and ceramic discs of Co-TCP had generally good cytocompatibility to support HBMSC growth. Importantly, the incorporation of Co into β-TCP greatly stimulated VEGF expression of HBMSCs and Co-TCP showed a significant enhancement of network structure formation of HUVECs compared with pure TCP. Our results suggested that the incorporation of Co into bioceramics is a potential viable way to enhance angiogenic properties of biomaterials. Co-TCP bioceramics may be used for bone tissue regeneration with improved angiogenic capacity.

An analysis of construction productivity in Malaysia

The construction industry is an industry of major strategic importance. Its level of productivity has a significant effect on national economic growth. Productivity indicators are examined. The indicators consist of labour productivity, capital productivity, labour competitiveness, capital intensity and added value content of data, which are obtained from the published census/biannual surveys of the construction industry between the years 1999 and 2011 from the Department of Statistics of Malaysia. The results indicated that there is an improvement in the labour productivity, but the value-added content is declining. The civil engineering and special trades subsectors are more productive than the residential and non-residential subsectors in terms of labour productivity because machine-for-labour substitution is a more important process in those subsectors. The capital-intensive characteristics of civil engineering and special trade works enable these subsectors to achieve higher added value per labour cost but not the capital productivity. The added value per labour cost is lower in larger organizations despite higher capital productivity. However, the capital intensity is lower and unit labour cost is higher in the larger organizations.

Gene duplication is an evolutionary mechanism for expanding spectral diversity in the long-wavelength photopigments of butterflies

Butterfly long-wavelength (L) photopigments are interesting for comparative studies of adaptive evolution because of the tremendous phenotypic variation that exists in their wavelength of peak absorbance (lambda(max) value). Here we present a comprehensive survey of L photopigment variation by measuring lambda(max) in 12 nymphalid and 1 riodinid species using epi-microspectrophotometry. Together with previous data, we find that L photopigment lambda(max) varies from 510-565 nm in 22 nymphalids, with an even broader 505- to 600-nm range in riodinids. We then surveyed the L opsin genes for which lambda(max) values are available as well as from related taxa and found 2 instances of L opsin gene duplication within nymphalids, in Hermeuptychia hermes and Amathusia phidippus, and 1 instance within riodinids, in the metalmark butterfly Apodemia mormo. Using maximum parsimony and maximum likelihood ancestral state reconstructions to map the evolution of spectral shifts within the L photopigments of nymphalids, we estimate the ancestral pigment had a lambda(max) = 540 nm +/- 10 nm standard error and that blueshifts in wavelength have occurred at least 4 times within the family. We used ancestral state reconstructions to investigate the importance of several amino acid substitutions (Ile17Met, Ala64Ser, Asn70Ser, and Ser137Ala) previously shown to have evolved under positive selection that are correlated with blue spectral shifts. These reconstructions suggest that the Ala64Ser substitution has indeed occurred along the newly identified blueshifted L photopigment lineages. Substitutions at the other 3 sites may also be involved in the functional diversification of L photopigments. Our data strongly suggest that there are limits to the evolution of L photopigment spectral shifts among species with only one L opsin gene and that opsin gene duplication broadens the potential range of lambda(max) values.

Adaptive evolution of color vision as seen through the eyes of butterflies

Butterflies and primates are interesting for comparative color vision studies, because both have evolved middle- (M) and long-wavelength- (L) sensitive photopigments with overlapping absorbance spectrum maxima (lambda(max) values). Although positive selection is important for the maintenance of spectral variation within the primate pigments, it remains an open question whether it contributes similarly to the diversification of butterfly pigments. To examine this issue, we performed epimicrospectrophotometry on the eyes of five Limenitis butterfly species and found a 31-nm range of variation in the lambda(max) values of the L-sensitive photopigments (514-545 nm). We cloned partial Limenitis L opsin gene sequences and found a significant excess of replacement substitutions relative to polymorphisms among species. Mapping of these L photopigment lambda(max) values onto a phylogeny revealed two instances within Lepidoptera of convergently evolved L photopigment lineages whose lambda(max) values were blue-shifted. A codon-based maximum-likelihood analysis indicated that, associated with the two blue spectral shifts, four amino acid sites (Ile17Met, Ala64Ser, Asn70Ser, and Ser137Ala) have evolved substitutions in parallel and exhibit significant d(N)/d(S) >1. Homology modeling of the full-length Limenitis arthemis astyanax L opsin placed all four substitutions within the chromophore-binding pocket. Strikingly, the Ser137Ala substitution is in the same position as a site that in primates is responsible for a 5- to 7-nm blue spectral shift. Our data show that some of the same amino acid sites are under positive selection in the photopigments of both butterflies and primates, spanning an evolutionary distance >500 million years.

Kallikrein 14 is down-regulated by androgen receptor signalling and harbours genetic variation that is associated with prostate tumour aggressiveness

Kallikrein 14 (KLK14) has been proposed as a useful prognostic marker in prostate cancer, with expression reported to be associated with tumour characteristics such as higher stage and Gleason score. KLK14 tumour expression has also shown the potential to predict prostate cancer patients at risk of disease recurrence after radical prostatectomy. The KLKs are a remarkably hormone-responsive family of genes, although detailed studies of androgen regulation of KLK14 in prostate cancer have not been undertaken to date. Using in vitro studies, we have demonstrated that unlike many other prostatic KLK genes that are strictly androgen responsive, KLK14 is more broadly expressed and inversely androgen regulated in prostate cancer cells. Given these results and evidence that KLK14 may play a role in prostate cancer prognosis, we also investigated whether common genetic variants in the KLK14 locus are associated with risk and/or aggressiveness of prostate cancer in approximately 1200 prostate cancer cases and 1300 male controls. Of 41 single nucleotide polymorphisms assessed, three were associated with higher Gleason score (≥7): rs17728459 and rs4802765, both located upstream of KLK14, and rs35287116, which encodes a p.Gln33Arg substitution in the KLK14 signal peptide region. Our findings provide further support for KLK14 as a marker of prognosis in prostate cancer.

A three-nucleotide mutation altering the Maize streak virus Rep pRBR-interaction motif reduces symptom severity in maize and partially reverts at high frequency without restoring pRBR-Rep binding

Geminivirus infectivity is thought to depend on interactions between the virus replication-associated proteins Rep or RepA and host retinoblastoma-related proteins (pRBR), which control cell-cycle progression. It was determined that the substitution of two amino acids in the Maize streak virus (MSV) RepA pRBR-interaction motif (LLCNE to LLCLK) abolished detectable RepA-pRBR interaction in yeast without abolishing infectivity in maize. Although the mutant virus was infectious in maize, it induced less severe symptoms than the wild-type virus. Sequence analysis of progeny viral DNA isolated from infected maize enabled detection of a high-frequency single-nucleotide reversion of C(601)A in the 3 nt mutated sequence of the Rep gene. Although it did not restore RepA-pRBR interaction in yeast, sequence-specific PCR showed that, in five out of eight plants, the C(601)A reversion appeared by day 10 post-inoculation. In all plants, the C(601)A revertant eventually completely replaced the original mutant population, indicating a high selection pressure for the single-nucleotide reversion. Apart from potentially revealing an alternative or possibly additional function for the stretch of DNA that encodes the apparently non-essential pRBR-interaction motif of MSV Rep, the consistent emergence and eventual dominance of the C(601)A revertant population might provide a useful tool for investigating aspects of MSV biology, such as replication, mutation and evolution rates, and complex population phenomena, such as competition between quasispecies and population turnover. © 2005 SGM.

Experimental evidence indicating that mastreviruses probably did not co-diverge with their hosts

Background. Despite the demonstration that geminiviruses, like many other single stranded DNA viruses, are evolving at rates similar to those of RNA viruses, a recent study has suggested that grass-infecting species in the genus Mastrevirus may have co-diverged with their hosts over millions of years. This "co-divergence hypothesis" requires that long-term mastrevirus substitution rates be at least 100,000-fold lower than their basal mutation rates and 10,000-fold lower than their observable short-term substitution rates. The credibility of this hypothesis, therefore, hinges on the testable claim that negative selection during mastrevirus evolution is so potent that it effectively purges 99.999% of all mutations that occur. Results. We have conducted long-term evolution experiments lasting between 6 and 32 years, where we have determined substitution rates of between 2 and 3 × 10 -4substitutions/site/year for the mastreviruses Maize streak virus (MSV) and Sugarcane streak Réunion virus (SSRV). We further show that mutation biases are similar for different geminivirus genera, suggesting that mutational processes that drive high basal mutation rates are conserved across the family. Rather than displaying signs of extremely severe negative selection as implied by the co-divergence hypothesis, our evolution experiments indicate that MSV and SSRV are predominantly evolving under neutral genetic drift. Conclusion. The absence of strong negative selection signals within our evolution experiments and the uniformly high geminivirus substitution rates that we and others have reported suggest that mastreviruses cannot have co-diverged with their hosts. © 2009 Harkins et al; licensee BioMed Central Ltd.

Dating the origins of the maize-adapted strain of maize streak virus, MSV-A

Maize streak virus (MSV), which causes maize streak disease (MSD), is one of the most serious biotic threats to African food security. Here, we use whole MSV genomes sampled over 30 years to estimate the dates of key evolutionary events in the 500 year association of MSV and maize. The substitution rates implied by our analyses agree closely with those estimated previously in controlled MSV evolution experiments, and we use them to infer the date when the maize-adapted strain, MSV-A, was generated by recombination between two grass-adapted MSV strains. Our results indicate that this recombination event occurred in the mid-1800s, ∼20 years before the first credible reports of MSD in South Africa and centuries after the introduction of maize to the continent in the early 1500s. This suggests a causal link between MSV recombination and the emergence of MSV-A as a serious pathogen of maize. © 2009 SGM.

Inhibition of maize streak virus (MSV) replication by transient and transgenic expression of MSV replication-associated protein mutants

Maize streak disease is a severe agricultural problem in Africa and the development of maize genotypes resistant to the causal agent, Maize streak virus (MSV), is a priority. A transgenic approach to engineering MSV-resistant maize was developed and tested in this study. A pathogen-derived resistance strategy was adopted by using targeted deletions and nucleotide-substitution mutants of the multifunctional MSV replication-associated protein gene (rep). Various rep gene constructs were tested for their efficacy in limiting replication of wild-type MSV by co-bombardment of maize suspension cells together with an infectious genomic clone of MSV and assaying replicative forms of DNA by quantitative PCR. Digitaria sanguinalis, an MSV-sensitive grass species used as a model monocot, was then transformed with constructs that had inhibited virus replication in the transient-expression system. Challenge experiments using leafhopper-transmitted MSV indicated significant MSV resistance - from highly resistant to immune - in regenerated transgenic D. sanguinalis lines. Whereas regenerated lines containing a mutated full-length rep gene displayed developmental and growth defects, those containing a truncated rep gene both were fertile and displayed no growth defects, making the truncated gene a suitable candidate for the development of transgenic MSV-resistant maize. © 2007 SGM.

Toward a theory of the architectural subject

The extraordinary event, for Deleuze, is the object becoming subject – not in the manner of an abstract formulation, such as the substitution of one ideational representation for another but, rather, in the introduction of a vast, new, impersonal plane of subjectivity, populated by object processes and physical phenomena that in Deleuze’s discovery will be shown to constitute their own subjectivities. Deleuze’s polemic of subjectivity (the refusal of the Cartesian subject and the transcendental ego of Husserl) – long attempted by other thinkers – is unique precisely because it heralds the dawning of a new species of objecthood that will qualify as its own peculiar subjectivity. A survey of Deleuze’s early work on subjectivity, Empirisme et subjectivité (Deleuze 1953), Le Bergsonisme (Deleuze 1968), and Logique du sens (Deleuze 1969), brings the architectural reader into a peculiar confrontation with what Deleuze calls the ‘new transcendental field’, the field of subjectproducing effects, which for the philosopher takes the place of both the classical and modern subject. Deleuze’s theory of consciousness and perception is premised on the critique of Husserlian phenomenology; and ipso facto his question is an architectural problematic, even if the name ‘architecture’ is not invoked...

Catalytic cracking of tars derived from rice hull gasification over goethite and palygorskite

Palygorskite (P), goethite (G), and hydrothermally synthesized goethite (HG) were used as supports for Fe and Ni. The catalytic activity of these materials was investigated involving in P, G and HG (supported Fe and Ni) for catalytic decomposition of biomass tar derived from rice hull gasification. The materials were characterized by X-ray diffraction (XRD), X-ray fluorescence (XRF), and transmission electron microscopy (TEM) with an energy dispersive X-ray (EDS). The catalytic activity of P for removal of tar was significantly better than that of G and HG. However, the activity of G with 6 mass% Ni labeled as Ni6/G (tar conversion 94.6%), which was equal to Fe6Ni6/P (94.4%), was better than Ni6/P (64.4%) and Ni6/HG (46.7%). When the loading of Ni (mass%) was 6 mass% on G, tar conversion had the best value (94.6%) and yield of gaseous products reached 486.9, 167.8 and 22.2 mL/(g·tar) for H2, CO, CH4, respectively. The catalytic activity of goethite supported Ni was better in improving tar conversion and improving increased yield of H2, CO, CH4, which was attributed to the existence of Al/Fe substitution of goethite