Comprehensive survey of developmental genes in the pea aphid, Acyrthosiphon pisum: frequent lineage-specific duplications and losses of developmental genes.

Aphids exhibit unique attributes, such as polyphenisms and specialized cells to house endosymbionts, that make them an interesting system for studies at the interface of ecology, evolution and development. Here we present a comprehensive characterization of the developmental genes in the pea aphid, Acyrthosiphon pisum, and compare our results to other sequenced insects. We investigated genes involved in fundamental developmental processes such as establishment of the body plan and organogenesis, focusing on transcription factors and components of signalling pathways. We found that most developmental genes were well conserved in the pea aphid, although many lineage-specific gene duplications and gene losses have occurred in several gene families. In particular, genetic components of transforming growth factor beta (TGFbeta) Wnt, JAK/STAT (Janus kinase/signal transducer and activator of transcription) and EGF (Epidermal Growth Factor) pathways appear to have been significantly modified in the pea aphid.

Annelids in evolutionary developmental biology and comparative genomics.

Annelids have had a long history in comparative embryology and morphology, which has helped to establish them in zoology textbooks as an ideal system to understand the evolution of the typical triploblastic, coelomate, protostome condition. In recent years there has been a relative upsurge in embryological data, particularly with regard to the expression and function of developmental control genes. Polychaetes, as well as other annelids such as the parasitic leech, are now also entering the age of comparative genomics. All of this comparative data has had an important impact on our views of the ancestral conditions at various levels of the animal phylogeny, including the bilaterian ancestor and the nature of the annelid ancestor. Here we review some of the recent advances made in annelid comparative development and genomics, revealing a hitherto unsuspected level of complexity in these ancestors. It is also apparent that the transition to a parasitic lifestyle leads to, or requires, extensive modifications and derivations at both the genomic and embryological levels.

Identification and characterisation of five novel miniature inverted-repeat transposable elements (MITEs) in amphioxus (Branchiostoma floridae).

As the sister group to vertebrates, amphioxus is consistently used as a model of genome evolution for understanding the invertebrate/vertebrate transition. The amphioxus genome has not undergone massive duplications like those in the vertebrates or disruptive rearrangements like in the genome of Ciona, a urochordate, making it an ideal evolutionary model. Transposable elements have been linked to many genomic evolutionary changes including increased genome size, modified gene expression, massive gene rearrangements, and possibly intron evolution. Despite their importance in genome evolution, few previous examples of transposable elements have been identified in amphioxus. We report five novel Miniature Inverted-repeat Transposable Elements (MITEs) identified by an analysis of amphioxus DNA sequence, which we have named LanceleTn-1, LanceleTn-2, LanceleTn-3a, LanceleTn-3b and LanceleTn-4. Several of the LanceleTn elements were identified in the amphioxus ParaHox cluster, and we suggest these have had important implications for the evolution of this highly conserved gene cluster. The estimated high copy numbers of these elements implies that MITEs are probably the most abundant type of mobile element in amphioxus, and are thus likely to have been of fundamental importance in shaping the evolution of the amphioxus genome.

Analysis of intact heparin by capillary electrophoresis using short end injection configuration.

A capillary electrophoresis method for the analysis of intact heparin was developed using a phosphate buffer and a fused silica capillary. Operational parameters such as pH and concentration of the running buffer were investigated. The short end injection configuration permitted a gain on peak efficiency, on the analysis time and on the repeatability of both migration times and peak areas, through a reduction of the migration distance. Moreover, the beneficial effect of the presence of sodium chloride in the heparin sample on the peak efficiency was demonstrated and the influence of the salts on the conformation of the heparin was discussed. The optimized method (short end injection configuration, 50mM phosphate buffer pH 3, heparin sample prepared in 10 g/L NaCl solution) was validated in terms of linearity, reproducibility and specificity according to ICH requirements.

Safety and quality of food contact materials. Part 1: evaluation of analytical strategies to introduce migration testing into good manufacturing practice.

The results of a research project (EU AIR Research Programme CT94-1025) aimed to introduce control of migration into good manufacturing practice and into enforcement work are reported. Representative polymer classes were defined on the basis of chemical structure, technological function, migration behaviour and market share. These classes were characterized by analytical methods. Analytical techniques were investigated for identification of potential migrants. High-temperature gas chromatography was shown to be a powerful method and 1H-magnetic resonance provided a convenient fingerprint of plastic materials. Volatile compounds were characterized by headspace techniques, where it was shown to be essential to differentiate volatile compounds desorbed from those generated during the thermal desorption itself. For metal trace analysis, microwave mineralization followed by atomic absorption was employed. These different techniques were introduced into a systematic testing scheme that is envisaged as being suitable both for industrial control and for enforcement laboratories. Guidelines will be proposed in the second part of this paper.

Assessment of the retention properties of poly(vinyl alcohol) stationary phase for lipid class profiling in liquid chromatography.

Potentialities of polymerized vinyl alcohol on silica gel were assessed for class separation of simple lipids, sphingolipids, glyceroglycolipids and phospholipids by high-performance liquid chromatography. A screening of pure solvents in binary gradient elution and a chemometric approach was used to define a rugged two segment linear gradient formed from four solvents for total lipid class separation. Triethylamine and formic acid were added in all mobile phase components for acidic phospholipid separation and evaporative light scattering response enhancement. Simple analytical procedures are described for the analysis of complex lipid materials.

Amphioxus Evx genes: implications for the evolution of the Midbrain-Hindbrain Boundary and the chordate tailbud.

Evx genes are widely used in animal development. In vertebrates they are crucial in gastrulation, neurogenesis, appendage development and tailbud formation, whilst in protostomes they are involved in gastrulation and neurogenesis, as well as segmentation at least in Drosophila. We have cloned the Evx genes of amphioxus (Branchiostoma floridae), and analysed their expression to understand how the functions of Evx have evolved between invertebrates and vertebrates, and in particular at the origin of chordates and during their subsequent evolution. Amphioxus has two Evx genes (AmphiEvxA and AmphiEvxB) which are genomically linked. AmphiEvxA is prototypical to the vertebrate Evx1 and Evx2 genes with respect to its sequence and expression, whilst AmphiEvxB is very divergent. Mapping the expression of AmphiEvxA onto a phylogeny shows that a role in gastrulation, dorsal-ventral patterning and neurogenesis is probably retained throughout bilaterian animals. AmphiEvxA expression during tailbud development implies a role for Evx throughout the chordates in this process, whilst lack of expression at the homologous region to the vertebrate Midbrain-Hindbrain Boundary (MHB) is consistent with the elaboration of the full organiser properties of this region being a vertebrate innovation.

Sipunculan ParaHox genes.

Our perspective on the origin and evolution of the Hox gene cluster changed with the discovery of the ParaHox gene cluster in amphioxus (Cephalochordata; Branchiostoma floridae) (Brooke et al. 1998). The ParaHox gene cluster contains three homeobox genes (Gsx, Xlox, Cdx) and is deduced to be a paralogue (evolutionary sister) of the Hox gene cluster. If this deduction is correct, animals with Hox genes should also possess ParaHox genes. Paradoxically, however, only deuterostome animals have thus far been shown to contain all three ParaHox genes. Here we report the cloning of all three ParaHox genes from each of two species within the phylum Sipuncula. This is the first demonstration of all three ParaHox genes in the genome of a protostome animal and confirms that the common ancestor of protostomes and deuterostomes possessed all three ParaHox genes. Furthermore, it implies that the ParaHox genes are of sufficient functional importance in both protostomes and deuterostomes that they have all been conserved in both of these bilaterian clades.

The Mnx homeobox gene class defined by HB9, MNR2 and amphioxus AmphiMnx.

The HB9 homeobox gene has been cloned from several vertebrates and is implicated in motor neuron differentiation. In the chick, a related gene, MNR2, acts upstream of HB9 in this process. Here we report an amphioxus homologue of these genes and show that it diverged before the gene duplication yielding HB9 and MNR2. AmphiMnx RNA is detected in two irregular punctate stripes along the developing neural tube, comparable to the distribution of 'dorsal compartment' motor neurons, and also in dorsal endoderm and posterior mesoderm. We propose a new homeobox class, Mnx, to include AmphiMnx, HB9, MNR2 and their Drosophila and echinoderm orthologues; we suggest that vertebrate HB9 is renamed Mnx1 and MNR2 be renamed Mnx2.

Ancient origin of the Hox gene cluster.

The Hox gene cluster has a crucial function in body patterning during animal development. How and when this gene cluster originated is being clarified by recent data from Cnidaria, a basal animal phylum. The characterization of Hox-like genes from Hydra, sea anemones and jellyfish has revealed that a Hox gene cluster is extremely ancient, having originated even before the divergence of these basal animals.

Plasma-based sterilization: effect on surface and bulk properties and hydrolytic stability of reprocessed polyurethane electrophysiology catheters.

Plasma-based sterilization is a promising alternative to ethylene oxide (EO) for reprocessing of electrophysiology catheters. To assess its safety in terms of material damage, modifications of surface and bulk properties as well as hydrolytic stability of sterilized catheters were evaluated. Polyurethane (PU) single-use electrophysiology catheters were subjected to one, five, and ten sterilization cycles by Sterrad-100S and Plazlyte, as well as by pure EO for comparison. Surface analysis techniques (ATR-FTIR, XPS, DCA) showed oxidation limited to the near-surface layer induced by both plasma-based sterilizers, whereas EO induced slight but deeper alkylation. Using bulk analysis techniques (RP-HPLC, SEC), oligomer alteration was observed after all three sterilization techniques, without modification of molecular weights. Hydrolytic stability of catheters was slightly changed by plasma-based sterilization, with a small increase in released oligomers. Finally, although Plazlyte and Sterrad are both plasma-based techniques, they induced different impacts on catheters, such as the degradation of an additive with Sterrad, and a clear difference in coloration with Plazlyte.

Retention behaviour of ceramides in sub-critical fluid chromatography in comparison with non-aqueous reversed-phase liquid chromatography.

This study was devoted to the development of an analytical method for ceramide analysis in packed subcritical fluid chromatography (pSubFC). Monofunctional grafted silica support was found to be more suitable for ceramide analysis. Five Kromasil columns were coupled and the parameters, temperature, pressure and percentage of organic modifier in CO2 were optimised, considering selectivity and analysis time. The final conditions were 31 degrees C, 6% of methanol (MeOH) and 13 MPa. In these conditions the selectivity for structural differences (methylene group, unsaturation or two different bases) were studied. As classically observed, the methylene selectivity decreased with the increase of the eluotropic strength. Moreover, unlike in non-aqueous reversed-phase liquid chromatography (NARP-LC), adding a further unsaturation and two further methylene groups on ceramide results to an increase of retention in pSubFC. Moreover, this last technique allowed to separate ceramides with the same total number of carbons containing unsaturated fatty acids, when the distribution of carbon number of the two chain is very different. These results had enabled to plot retention chart in order to predict ceramide structure in view to identify additional ceramide. This retention chart was finally compared with the one already obtained in NARP-LC.

Interactions between chitosan and glycosaminoglycans (chondroitin sulfate and hyaluronic acid): physicochemical and biological studies.

Chitosan is a polysaccharide well known for its numerous and interesting biological properties, indeed, it is a biocompatible, bioresorbable and bioactive biopolymer. It is therefore often introduced in the human body, where it happens to be in contact with glycosaminoglycans (GAG's), especially chondroitin sulfates and hyaluronic acid which play important part in living media. Thus it seems interesting to consider systems associating chitosan and GAG's. The aim of our work is to study the mechanism of formation of biomaterials constituted of chitosan and GAG's which could have interesting biological properties such as improving the wound-healing acceleration and the cellular assistance for skin and cartilage recovery. In the same time, it was interesting to try to understand what can happen when chitosan is introduced in a natural surrounding containing GAG's. In a first part, the complexes between chitosan and GAG's were characterised by various physicochemical techniques: pH-metry, conductometry and Infra-red spectrometry. They appeared to be polyelectrolyte complexes obtained by the formation of polyanion-polycation interactions held between ammonium functions of chitosan and carboxylate and/or sulfate groups of GAG's. The complexes formed are very strong and can, in some cases, even conduct to the deprotonation of carboxylic functions. In a second part we considered the biological properties of the complexes previously obtained. The hydrolysis activity in presence of specific enzymes was investigated. We also studied the cytocompatibility of chitosan alone and its complexes with the two considered GAG's toward two kinds of cells (chondrocytes and keratinocytes). At the end of the work, a short animal experimentation on rats was performed allowing the comparison between in vitro and in vivo results.

One-step capillary isoelectric focusing for the separation of the recombinant human immunodeficiency virus envelope glycoprotein glycoforms.

One-step capillary isoelectric focusing was investigated as a rapid method to resolve the glycoforms of the heterogeneous recombinant human immunodeficiency virus (HIV) envelope glycoprotein (rgp 160sMN/LAI). The separation was performed in a poly(vinyl alcohol) (PVA) coated capillary using a mixture of ampholyte of narrow and wide pH range. A combination of saccaharose and 3-(cyclohexylamino)-1-propanesulfonic acid was shown to be the most efficient additive to avoid protein precipitation which occurs at a pH close to its pI. Although the calibration curve [isoelectric point (pI) vs. migration times] showed a non-linear relationship, an adequate linearity could be yielded for short pI ranges permitting to exhibit the acidic character of the different glycoforms of the rgp 160s MN/LAI (pI from 4.00 to 4.95). Reproducibility evaluated by comparing the performance of a polyacrylamide and a PVA coated capillary showed that low RSD values were obtained for intra-day (0.5 to 1.9%) and inter-day (1.6 to 7.6%) measurements using the PVA capillary. Moreover, the long term stability of the PVA capillary was demonstrated by measuring the variation of migration times of the protein markers for a long period of use. Finally, this method was able to differentiate the glycoform pattern of two close glycoproteins such as the rgp 160 of two sub-populations of the virus HIV-1.

The amphioxus Hox cluster: deuterostome posterior flexibility and Hox14.

The amphioxus (Branchiostoma floridae) Hox cluster is a model for the ancestral vertebrate cluster, prior to the hypothesized genome-wide duplications that may have facilitated the evolution of the vertebrate body plan. Here we describe the posterior (5') genes of the amphioxus cluster, and report the isolation of four new homeobox genes. Vertebrates possess 13 types of Hox gene (paralogy groups), but we show that amphioxus possesses more than 13 Hox genes. Amphioxus is now the first animal in which a Hox14 gene has been found. Our mapping and phylogenetic analysis of amphioxus "Posterior Class" Hox genes reveals that these genes are evolving at a faster rate in deuterostomes than in protostomes, a phenomenon we term Posterior Flexibility.

A sensitive mapping strategy for monitoring the reproducibility of glycan processing in an HIV vaccine, RGP-160, expressed in a mammalian cell line.

The external envelope glycoprotein (gp160) of HIV-1 is a candidate for vaccines against AIDS. Most of the surface of the molecule is shielded by carbohydrate and the structures and locations of these glycans may be important in defining the immunogenicity of the viral coat. Here we report a sensitive mapping strategy for profiling and analysing the N-glycosylation of gp160, based on chemical release of glycans, fluorescent labelling and HPLC analysis. This approach has been validated in terms of establishing the reproducibility of all steps in the analytical procedure and on overall reproducibility on a run-to-run and day-to-day basis. The validated analysis technique was used to monitor the consistency of N-glycosylation of one rgp 160 vaccine candidate produced in baby hamster kidney (BHK) cell culture. It was demonstrated that the variation in the glycan profiles of 6 different lots was not statistically significant.

Postcolumn fluorescence as an alternative to evaporative light scattering detection for ceramide analysis with gradient elution in non-aqueous reversed-phase liquid chromatography.

Ceramide analysis was developed with gradient elution in non-aqueous reversed-phase liquid chromatography with evaporative light scattering detection (ELSD) or postcolumn fluorescence detection. Fluorescence detection (excitation, 360 nm; emission, 425 nm) after postcolumn formation of mixed assemblies between eluted ceramides and 1,6-diphenyl-1,3,5-hexatriene was developed. In comparison with ELSD, fluorescence detection allows a better detection of the minor species ceramide from ceramide type III (commercial mixture of non-hydroxy fatty acid-sphingosine) and appears to be more sensitive for quantitation of ceramides at low concentrations. The fluorescence response is linear over a wide range of injected amount of ceramide III (expressed as stearoyl-phytosphingosine): 10 ng to 1000 ng. The response of ELSD is non linear but can be linearized in double logarithmic coordinates for calculations over a narrow range, e.g. between 10 to 350 ng ceramide III injected. The lower quantitation limits of these two detectors are similar: 5 ng ceramide III was injected.

A multi-mode chromatographic method for the comparison of the N-glycosylation of a recombinant HIV envelope glycoprotein (gp160s-MN/LAI) purified by two different processes.

The glycosylation pattern of a recombinant gp160s-MN/LAI variant of human immunodeficiency virus type 1 (HIV-1) was studied in relation to two alternative purification techniques one of which involves an immunoprecipitation step. For analysis a multi-mode high performance liquid chromatography (HPLC) method which combines gel permeation chromatography on the RAAM 2000 GlycoSequencer, weak anion exchange chromatography and normal phase chromatography was developed and profiles were obtained for the fluorescently-labelled glycans released from the two gp160s-MN/LAI preparations. Charged glycans accounted for 77 and 80% of the total glycans for the IAP- and SP-purified samples, respectively. The acidic character of these glycans was mainly due to the presence of sialic acids. However, following sialidase treatment, residual charged glycans were still found. No differences were found in the glycan distributions of the two gp160s-MN/LAI preparations either in their degree of sialylation or in their relative proportion of each separated structure. Although this did not reach statistical significance, a lower proportion of large glycan structures regardless of their charge status was found on the gp160s-MN/LAI prepared by the procedure which involved an immunoaffinity chromatography step.

Electrophoretic methods for process monitoring and the quality assessment of recombinant glycoproteins.

In many ways electrophoretic techniques appear ideal for quality monitoring of proteins and are thus well suited for the analysis of recombinant glycoproteins. The requirements of high throughput, comparative analysis and resolution of many variants are met by several electrophoretic techniques. A wide variety of such techniques are available to biotechnologists in the rapidly developing area of recombinant glycoproteins. It is the aim of this review to specifically cover recent work which has been applied to the analysis of DNA-derived glycoproteins, both from a process control standpoint and final product validation. All major areas of electrophoresis including sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE), isoelectric focusing and techniques utilizing capillary electrophoresis are covered, with emphasis on analysis of glycoforms and oligosaccharide profiles of recombinant glycoproteins. As illustration, actual examples rather than standard glycoproteins are given to indicate the potential and limitations which may be encountered. It is anticipated that this review will prove a useful and practical guide to the latest developments by indicating the relevant merits of different methods.

Investigation of micelles and anionic cyclodextrins as pseudostationary phases for the capillary electrophoresis separation of oligosaccharides derivatized with 2-amino-benzamide.

Oligomers of glucose and oligosaccharides released from glycoproteins were derivatized with 2-aminobenzamide. As this fluorophore imparts no charge to the oligosaccharides, several strategies were investigated to achieve capillary electrophoresis (CE) separation of both neutral and charged derivatized glycans. Micellar electrokinetic capillary chromatography (MEKC) with the addition of anionic surfactants was evaluated as a first approach: sodium dodecyl sulfate (SDS) produced the best separation of the oligoglucose fragments, where the migration was inversely related to their degree of polymerization. To demonstrate the applicability of this method for complex carbohydrate analysis, oligosaccharide mixtures derived from ribonuclease B (RNase B) and alpha-acid glycoprotein (alpha-AGP) were analyzed. A satisfactory separation for the high-mannose structures found in RNase B could be obtained, whereas charged oligosaccharides from alpha-AGP were poorly resolved. Cyclodextrin-modified CE was chosen as the second approach: the effect of the addition of sulfobutylether-beta-cyclodextrin (SBE-beta-CD) or sulfobutylether-gamma-cyclodextrin (SBE-gamma-CD) on the electrophoretic mobilities and resolution of neutral and charged oligosaccharides was then studied. Selectivity of sialylated structures could be further improved by using anionic cyclodextrins (CDs) instead of micelles. However, this latter approach failed to baseline-resolve the different high-mannose structures of RNase B. A successful separation of the complex mixture of oligosaccharides from alphaalpha-AGP was obtained with the addition of 4% of SBE-gamma-CD and triethylamine (TEA) in a phosphate buffer, pH 6.7.