Hemichordates and deuterostome evolution: robust molecular phylogenetic support for a hemichordate plus echinoderm clade

Hemichordates were traditionally allied to the chordates, but recent molecular analyses have suggested that hemichordates are a sister group to the echinoderms, a relationship that has important consequences for the interpretation of the evolution of deuterostome body plans. However, the molecular phylogenetic analyses to date have not provided robust support for the hemichordate + echinoderm clade. We use a maximum likelihood framework, including the parametric bootstrap, to reanalyze DNA data from complete mitochondrial genomes and nuclear 18S rRNA. This approach provides the first statistically significant support for the hemichordate + echinoderm clade from molecular data. This grouping implies that the ancestral deuterostome had features that included an adult with a pharynx and a dorsal nerve cord and an indirectly developing dipleurula-like larva.

The draft genome of Ciona intestinalis: Insights into chordate and vertebrate origins

The first chordates appear in the fossil record at the time of the Cambrian explosion, nearly 550 million years ago. The modern ascidian tadpole represents a plausible approximation to these ancestral chordates. To illuminate the origins of chordate and vertebrates, we generated a draft of the protein-coding portion of the genome of the most studied ascidian, Ciona intestinalis. The Ciona genome contains similar to16,000 protein-coding genes, similar to the number in other invertebrates, but only half that found in vertebrates. Vertebrate gene families are typically found in simplified form in Ciona, suggesting that ascidians contain the basic ancestral complement of genes involved in cell signaling and development. The ascidian genome has also acquired a number of lineage-specific innovations, including a group of genes engaged in cellulose metabolism that are related to those in bacteria and fungi.

Testing the relationship between morphological and molecular rates of change along phylogenies

Molecular evolution has been considered to be essentially a stochastic process, little influenced by the pace of phenotypic change. This assumption was challenged by a study that demonstrated an association between rates of morphological and molecular change estimated for total-evidence phylogenies, a finding that led some researchers to challenge molecular date estimates of major evolutionary radiations. Here we show that Omland's (1997) result is probably due to methodological bias, particularly phylogenetic nonindependence, rather than being indicative of an underlying evolutionary phenomenon. We apply three new methods specifically designed to overcome phylogenetic bias to 13 published phylogenetic datasets for vertebrate taxa, each of which includes both morphological characters and DNA sequence data. We find no evidence of an association between rates of molecular and morphological rates of change.

The collision branching process

We consider a branching model, which we call the collision branching process (CBP), that accounts for the effect of collisions, or interactions, between particles or individuals. We establish that there is a unique CBP, and derive necessary and sufficient conditions for it to be nonexplosive. We review results on extinction probabilities, and obtain explicit expressions for the probability of explosion and the expected hitting times. The upwardly skip-free case is studied in some detail.

Theory manual to OctVCE – a cartesian cell CFD code with special application to blast wave problems, Department of Mechanical Engineering Report 2007/12

OctVCE is a cartesian cell CFD code produced especially for numerical simulations of shock and blast wave interactions with complex geometries, in particular, from explosions. Virtual Cell Embedding (VCE) was chosen as its cartesian cell kernel for its simplicity and sufficiency for practical engineering design problems. The code uses a finite-volume formulation of the unsteady Euler equations with a second order explicit Runge-Kutta Godonov (MUSCL) scheme. Gradients are calculated using a least-squares method with a minmod limiter. Flux solvers used are AUSM, AUSMDV and EFM. No fluid-structure coupling or chemical reactions are allowed, but gas models can be perfect gas and JWL or JWLB for the explosive products. This report also describes the code’s ‘octree’ mesh adaptive capability and point-inclusion query procedures for the VCE geometry engine. Finally, some space will also be devoted to describing code parallelization using the shared-memory OpenMP paradigm. The user manual to the code is to be found in the companion report 2007/13.

User guide for shock and blast simulation with the OctVCE code (version 3.5+), Department of Mechanical Engineering Report 2007/13

OctVCE is a cartesian cell CFD code produced especially for numerical simulations of shock and blast wave interactions with complex geometries. Virtual Cell Embedding (VCE) was chosen as its cartesian cell kernel as it is simple to code and sufficient for practical engineering design problems. This also makes the code much more ‘user-friendly’ than structured grid approaches as the gridding process is done automatically. The CFD methodology relies on a finite-volume formulation of the unsteady Euler equations and is solved using a standard explicit Godonov (MUSCL) scheme. Both octree-based adaptive mesh refinement and shared-memory parallel processing capability have also been incorporated. For further details on the theory behind the code, see the companion report 2007/12.

A dual catalyst bed system for the elimination of hydrogen from CO2 feed gas in urea synthesis

A dual catalyst bed system (Au/Fe2O3 + Pt-Pd/Al2O3) for eliminating hydrogen from the CO2 feed gas in urea synthesis is found to be far superior to commercially available and patented catalysts in catalytic activity. At relatively low temperatures, hydrogen is eliminated and coexistent CO is also oxidized completely to useful CO2. This can avoid effectively the accidental explosion of hydrogen-oxygen-ammonia mixed gases, thus ensuring the safety of urea synthesis.

Ultrasound imaging in rehabilitation: Just a fad?

Real-time ultrasound imaging provides an unrivalled opportunity to observe muscle morphology and contraction. This has obvious potential for clinical practice and the tool is beginning to be adopted into physical therapy. The implementation of ultrasound imaging has become particularly widespread for assessment of size and activation of deep trunk muscles, such as the transversus abdominis and lumbar multifidus, and for assessment of the pelvic floor muscles. The obvious benefit for these areas is that ultrasound permits observation of muscles that are difficult to assess through noninvasive means. This realization of the clinical potential of ultrasound imaging has been paralleled by an explosion of clinical and physiological research. However, despite the enthusiasm for utilization of ultrasound imaging, a question that is critical to address is whether ultrasound can actually improve rehabilitation.

The leucine-rich repeat as a protein recognition motif

Leucine-rich repeats (LRRs) are 20-29-residue sequence motifs present in a number of proteins with diverse functions. The primary function of these motifs appears to be to provide a versatile structural framework for the formation of protein-protein interactions. The past two years have seen an explosion of new structural information on proteins with LRRs. The new structures represent different LRR subfamilies and proteins with diverse functions, including GTPase-activating protein rna 1 p from the ribonuclease-inhibitor-like subfamily; spliceosomal protein U2A', Rab geranylgeranyltransferase, internalin B, dynein light chain 1 and nuclear export protein TAP from the SDS22-like subfamily; Skp2 from the cysteine-containing subfamily; and YopM from the bacterial subfamily. The new structural information has increased our understanding of the structural determinants of LRR proteins and our ability to model such proteins with unknown structures, and has shed new light on how these proteins participate in protein-protein interactions.

The evolution of controlled multitasked gene networks: The role of introns and other noncoding RNAs in the development of complex organisms

Eukaryotic phenotypic diversity arises from multitasking of a core proteome of limited size. Multitasking is routine in computers, as well as in other sophisticated information systems, and requires multiple inputs and outputs to control and integrate network activity. Higher eukaryotes have a mosaic gene structure with a dual output, mRNA (protein-coding) sequences and introns, which are released from the pre-mRNA by posttranscriptional processing. Introns have been enormously successful as a class of sequences and comprise up to 95% of the primary transcripts of protein-coding genes in mammals. In addition, many other transcripts (perhaps more than half) do not encode proteins at all, but appear both to be developmentally regulated and to have genetic function. We suggest that these RNAs (eRNAs) have evolved to function as endogenous network control molecules which enable direct gene-gene communication and multitasking of eukaryotic genomes. Analysis of a range of complex genetic phenomena in which RNA is involved or implicated, including co-suppression, transgene silencing, RNA interference, imprinting, methylation, and transvection, suggests that a higher-order regulatory system based on RNA signals operates in the higher eukaryotes and involves chromatin remodeling as well as other RNA-DNA, RNA-RNA, and RNA-protein interactions. The evolution of densely connected gene networks would be expected to result in a relatively stable core proteome due to the multiple reuse of components, implying,that cellular differentiation and phenotypic variation in the higher eukaryotes results primarily from variation in the control architecture. Thus, network integration and multitasking using trans-acting RNA molecules produced in parallel with protein-coding sequences may underpin both the evolution of developmentally sophisticated multicellular organisms and the rapid expansion of phenotypic complexity into uncontested environments such as those initiated in the Cambrian radiation and those seen after major extinction events.

Guilty? An explanation of the Lockerbie trial. (Case notes)

The Lockerbie Trial, concerning the explosion of Pan Am flight 103 over Lockerbie, Scotland, in 1988, took place in the Netherlands because of the fear that pre-trial publicity would make a fair trial impossible and also fears for the physical safety of the accused - case for the prosecution - application of Scottish law - report of an observer at the trial, Professor Kochler - the International Criminal Court - leave to appeal granted.

Recent work on gaseous detonations

The paper reviews recent progress in the field of gaseous detonations, with sections on shock diffraction and reflection, the transition to detonation, hybrid, spherically-imploding, and galloping and stuttering fronts, their structure, their transmission and quenching by additives, the critical energy for initiation and detonation of more unusual fuels. The final section points out areas where our understanding is still far from being complete and contains some suggestions of ways in which progress might be made.

Ancient colour vision: Multiple opsin genes in the ancestral vertebrates

Molecular investigation of the origin of colour vision has discovered five visual pigment (opsin) genes, all of which are expressed in an agnathan (jawless) fish, the lamprey Geotria australis. Lampreys are extant representatives of an ancient group of vertebrates whose origins are thought to date back to at least the early Cambrian, approximately 540 million years ago [1.]. Phylogenetic analysis has identified the visual pigment opsin genes of G. australis as orthologues of the major classes of vertebrate opsin genes. Therefore, multiple opsin genes must have originated very early in vertebrate evolution, prior to the separation of the jawed and jawless vertebrate lineages, and thereby provided the genetic basis for colour vision in all vertebrate species. The southern hemisphere lamprey Geotria australis (Figure 1A,B) possesses a predominantly cone-based visual system designed for photopic (bright light) vision [2. S.P. Collin, I.C. Potter and C.R. Braekevelt, The ocular morphology of the southern hemisphere lamprey Geotria australis Gray, with special reference to optical specializations and the characterisation and phylogeny of photoreceptor types. Brain Behav. Evol. 54 (1999), pp. 96–111.2. and 3.]. Previous work identified multiple cone types suggesting that the potential for colour vision may have been present in the earliest members of this group. In order to trace the molecular evolution and origins of vertebrate colour vision, we have examined the genetic complement of visual pigment opsins in G. australis.

The biocompatibility of carbon nanotubes

Carbon nanotubes (CNT) are well-ordered, high aspect ratio allotropes of carbon. The two main variants, single-walled carbon nanotubes (SWCNT) and multi-walled carbon nanotubes (MWCNT) both possess a high tensile strength, are ultra-light weight, and have excellent chemical and thermal stability. They also possess semi- and metallic-conductive properties. This startling array of features has led to many proposed applications in the biomedical field, including biosensors, drug and vaccine delivery and the preparation of unique biomaterials such as reinforced and/or conductive polymer nanocomposites. Despite an explosion of research into potential devices and applications, it is only recently that information on toxicity and biocompatibility has become available. This review presents a summary of the performance of existing carbon biomaterials and gives an outline of the emerging field of nanotoxicology, before reviewing the available and often conflicting investigations into the cytotoxicity and biocompatibility of CNT. Finally, future areas of investigation and possible solutions to current problems are proposed. (c) 2005 Elsevier Ltd. All rights reserved.