Alpha Sequences Research Articles

Molecular phylogenetic and scanning electron microscopical analyses places the Choanephoraceae and the Gilbertellaceae in a monophyletic group within the Mucorales (Zygomycetes, Fungi)

A multi-gene genealogy based on maximum parsimony and distance analyses of the exonic genes for actin (act) and translation elongation factor 1 alpha (tef), the nuclear genes for the small (18S) and large (28S) subunit ribosomal RNA (comprising 807, 1092, 1863, 389 characters, respectively) of all 50 genera of the Mucorales (Zygomycetes) suggests that the Choanephoraceae is a monophyletic group. The monotypic Gilbertellaceae appears in close phylogenetic relatedness to the Choanephoraceae. The monophyly of the Choanephoraceae has moderate to strong support (bootstrap proportions 67% and 96% in distance and maximum parsimony analyses, respectively), whereas the monophyly of the Choanephoraceae-Gilbertellaceae clade is supported by high bootstrap values (100% and 98%). This suggests that the two families can be joined into one family, which leads to the elimination of the Gilbertellaceae as a separate family. In order to test this hypothesis single-locus neighbor-joining analyses were performed on nuclear genes of the 18S, 5.8S, 28S and internal transcribed spacer (ITS) 1 ribosomal RNA and the translation elongation factor 1 alpha (tef) and beta tubulin (betatub) nucleotide sequences. The common monophyletic origin of the Choanephoraceae-Gilbertellaceae clade could be confirmed in all gene trees and by investigation of their ultrastructure. Sporangia with persistent, sutured walls splitting in half at maturity and ellipsoidal sporangiospores with striated ornamentations and polar ciliate appendages arising from spores in persistent sporangia and dehiscent sporangiola represent synapomorphic characters of this group. We discuss our data in the context of the historical development of their taxonomy and physiology and propose a reduction of the two families to one family, the Choanephoraceae sensu lato comprising species which are facultative plant pathogens and parasites, especially in subtropical to tropical regions.

Mapping of the IgE and IgG4 sequential epitopes of milk allergens with a peptide microarray–based immunoassay

Peptide microarray analysis is a novel method that can provide useful information on the nature of specific allergies. We sought to determine the specificity and diversity of IgE and IgG4 antibodies binding to sequential epitopes of alpha(s1)-, alpha(s2)-, beta-, and kappa-caseins and beta-lactoglobulin by using a peptide microarray-based immunoassay. A microarray immunoassay was performed with sera from 31 children with IgE-mediated milk allergy (16 with positive oral milk challenge results [ie, the reactive group] and 15 with negative oral milk challenge results [ie, the tolerant group]). A library of peptides, consisting of 20 amino acids (AAs) overlapping by 17 (3-offset), corresponding to the primary sequences of alpha(s1)-, alpha(s2)-, beta-, and kappa-caseins and beta-lactoglobulin was printed on epoxy-coated slides. A region was defined as an epitope if it was statistically associated with reactive groups and recognized by at least 75% of reactive patients. By using this method, a total of 10 epitopes were identified: alpha(s1), AAs 28 to 50, 75% reactive and 26.7% tolerant; alpha(s2), AAs 1 to 20, 75% reactive and 13.3% tolerant; AAs 13 to 32, 75% reactive and 26.7% tolerant; AAs 67 to 86, 75% reactive and 33.3% tolerant; and AAs 181 to 207, 75% reactive and 20% tolerant; beta-casein, AAs 25 to 50, 75% reactive and 33.3% tolerant, AAs 52 to 74, 81.3% reactive and 26.7% tolerant; and AAs 154 to 173, 75% reactive and 33.3% tolerant; beta-lactoglobulin, AAs 58 to 77, 81.3% reactive and 40% tolerant; and kappa-casein, AAs 34 to 53, 87.5% reactive and 40% tolerant. Several regions have been defined as epitopes, which showed differential recognition patterns between reactive and tolerant patients. Further studies are needed to validate the utility of this assay in clinical practice.

Globins and hypoxia adaptation in the goldfish, Carassius auratus

Goldfish (Carassius auratus) may survive in aquatic environments with low oxygen partial pressures. We investigated the contribution of respiratory proteins to hypoxia tolerance in C. auratus. We determined the complete coding sequence of hemoglobin alpha and beta and myoglobin, as well as partial cDNAs from neuroglobin and cytoglobin. Like the common carp (Cyprinus carpio), C. auratus possesses two paralogous myoglobin genes that duplicated within the cyprinid lineage. Myoglobin is also expressed in nonmuscle tissues. By means of quantitative real-time RT-PCR, we determined the changes in mRNA levels of hemoglobin, myoglobin, neuroglobin and cytoglobin in goldfish exposed to prolonged hypoxia (48 h at Po(2) ~ 6.7 kPa, 8 h at Po(2) ~ 1.7 kPa, 16 h at Po(2) ~ 6.7 kPa) at 20 degrees C. We observed small variations in the mRNA levels of hemoglobin, neuroglobin and cytoglobin, as well as putative hypoxia-responsive genes like lactate dehydrogenase or superoxide dismutase. Hypoxia significantly enhanced only the expression of myoglobin. However, we observed about fivefold higher neuroglobin protein levels in goldfish brain compared with zebrafish, although there was no significant difference in intrinsic myoglobin levels. These observations suggest that both myoglobin and neuroglobin may contribute to the tolerance of goldfish to low oxygen levels, but may reflect divergent adaptive strategies of hypoxia preadaptation (neuroglobin) and hypoxia response (myoglobin).

Cloning, expression and immunolocalization of 1-adrenoceptor in different tissues from rhesus monkey and human male reproductive tract

This study reports the genomic organization of the rhesus alpha(1A)-adrenoceptor gene (ADRA1A). Full-length cloning of rhesus ADRA1A splice variants was achieved by combining PCR screening of a seminal vesicle cDNA library and 5'-RACE assays with total RNA from seminal vesicle. The classical ADRA1A mRNA (ADRA1A_v1) and six full-length ADRA1A splice variants were identified representing transcripts that code for functional (ADRA1A_v1, ADRA1A_v2a, ADRA1A_v3a, ADRA1A_v3d, ADRA1A_v3e) and truncated (ADRA1A_v2c and ADRA1A_v3c) receptor isoforms. Comparative analysis of the deduced amino acid sequence indicated that rhesus ADRA1A_i1 isoform (corresponding to the ADRA1A_v1 transcript) shares high identity to the amino acid sequence present in the classical alpha(1A)-adrenoceptor from human and other mammalian species. Partial nucleotide sequences for rhesus alpha(1B)-(ADRA1B) and alpha(1D)-adrenoceptor (ADRA1D) transcripts were also characterized. RT-PCR studies indicated differential distribution of all ADRA1A-related splice variants as well as ADRA1B and ADRA1D mRNAs, in tissues from rhesus and human male reproductive tract. Immunohistochemistry revealed alpha(1A)-adrenoceptor (ADRA1A_i1) immunostaining in smooth muscle cells and epithelial cells of rhesus efferent ductules, epididymis and seminal vesicle. Taken together the present results demonstrate that the complexity of the splicing mechanisms involved in the regulation of the ADRA1A gene is not restricted to human and is a common characteristic among Old World monkeys.

Selecting highly affine and well-expressed TCRs for gene therapy of melanoma

AbstractA recent phase 1 trial has demonstrated that the generation of tumor-reactive T lymphocytes by transfer of specific T-cell receptor (TCR) genes into autologous lymphocytes is feasible. However, compared with results obtained by infusion of tumor-infiltrating lymphocytes, the response rate observed in this first TCR gene therapy trial is low. One strategy that is likely to enhance the success rate of TCR gene therapy is the use of tumor-reactive TCRs with a higher capacity for tumor cell recognition. We therefore sought to develop standardized procedures for the selection of well-expressed, high-affinity, and safe human TCRs. Here we show that TCR surface expression can be improved by modification of TCR alpha and beta sequences and that such improvement has a marked effect on the in vivo function of TCR gene-modified T cells. From a panel of human, melanoma-reactive TCRs we subsequently selected the TCR with the highest affinity. Furthermore, a generally applicable assay was used to assess the lack of alloreactivity of this TCR against a large series of common human leukocyte antigen alleles. The procedures described in this study should be of general value for the selection of well- and stably expressed, high-affinity, and safe human TCRs for subsequent clinical testing.

Redirection of peroxisomal alcohol oxidase ofHansenula polymorphato the secretory pathway

We report on the rerouting of peroxisomal alcohol oxidase (AO) to the secretory pathway of Hansenula polymorpha. Using the leader sequence of the Saccharomyces cerevisiae mating factor alpha (MFalpha) as sorting signal, AO was correctly sorted to the endoplasmic reticulum (ER), which strongly proliferated in these cells. The MFalpha presequence, but not the prosequence, was cleaved from the protein. AO protein was present in the ER as monomers that lacked FAD, and hence was enzymatically inactive. Furthermore, the recombinant AO protein was subject to gradual degradation, possibly because the protein did not fold properly. However, when the S. cerevisiae invertase signal sequence (ISS) was used, secretion of AO protein was observed in conjunction with bulk of the protein being localized to the ER. The amount of secreted AO protein increased with increasing copy numbers of the AO expression cassette integrated into the genome. The secreted AO protein was correctly processed and displayed enzyme activity.

Translocation of a phycoerythrin alpha subunit across five biological membranes.

Cryptophytes, unicellular algae, evolved by secondary endosymbiosis and contain plastids surrounded by four membranes. In contrast to cyanobacteria and red algae, their phycobiliproteins do not assemble into phycobilisomes and are located within the thylakoid lumen instead of the stroma. We identified two gene families encoding phycoerythrin alpha and light-harvesting complex proteins from an expressed sequence tag library of the cryptophyte Guillardia theta. The proteins bear a bipartite topogenic signal responsible for the transport of nuclear encoded proteins via the ER into the plastid. Analysis of the phycoerythrin alpha sequences revealed that more than half of them carry an additional, third topogenic signal comprising a twin arginine motif, which is indicative of Tat (twin arginine transport)-specific targeting signals. We performed import studies with several derivatives of one member using a diatom transformation system, as well as intact chloroplasts and thylakoid vesicles isolated from pea. We demonstrated the different targeting properties of each individual part of the tripartite leader and show that phycoerythrin alpha is transported across the thylakoid membrane into the thylakoid lumen and protease-protected. Furthermore, we showed that thylakoid transport of phycoerythrin alpha takes place by the Tat pathway even if the 36 amino acid long bipartite topogenic signal precedes the actual twin arginine signal. This is the first experimental evidence of a protein being targeted across five biological membranes.

Sequence analysis of OmNramp α and quantitative expression of Nramp homologues in different trout strains after infection with Myxobolus cerebralis

Salmonid whirling disease caused by the metazoan parasite Myxobolus cerebralis is an ongoing problem in wild and farmed rainbow trout Oncorhynchus mykiss populations. Rainbow trout from different strains vary in susceptibility to the parasite. Identification of underlying mechanisms could be a starting point for improved control of the disease. We conducted infection trials using 2 rainbow trout strains and brown trout Salmo trutta fario, a species not susceptible to the parasite, to investigate host immune response and resistance mechanisms. We compared expression levels of 2 natural resistance-associated macrophage proteins (Nramp alpha and beta) after infection with M. cerebralis. Total RNA was extracted from skin, muscle, kidney, head and spinal column, and gene expression was quantified by real-time PCR. Significant decreases in expression of both genes were observed at different time points in the infected susceptible rainbow trout compared to the non-infected group. Furthermore, the OmNramp alpha (O. mykiss natural resistance-associated macrophage protein alpha) sequences in 2 resistant and 1 non-resistant rainbow trout strain were analysed and compared for sequence aberrations.

Specificity Analysis of Anti-gliadin Mouse Monoclonal Antibodies Used for Detection of Gliadin in Food for Gluten-free Diet

A gluten-free diet (GFD) is the sole effective long-lasting treatment of celiac disease. Four monoclonal antibodies (Abs) were prepared by immunization of animals kept on GFD with gliadin. The specificity of these Abs to decapeptides of alpha- and gamma-gliadin and omega-secalin was analyzed by the PEPSCAN technique. Repetitive sequences of alpha- and gamma-gliadin and omega-secalin containing the motifs QPFPXQ (X = Q, L, P) were recognized by all Abs tested. These Abs also frequently reacted with peptides containing the sequences QQSFPQQ, QQTFPQP, and QPFRPQ. On the basis of PEPSCAN results two Abs--8D4 and 7C6--were selected for the construction of a new ELISA kit for the detection of gliadin in food. The comparison of data obtained using the newly developed ELISA kit and commercially available ones indicated that Abs selection on the basis of their fine specificity to gliadin is useful for sensitive detection of gliadin in foods.

Blood donor derived dendritic cells and cytotoxic T cells for specific fusion‐gene adoptive immunotherapy

Therapeutic immunological reagents tailored to individual patients have been shown to be a viable treatment strategy for some forms of leukaemia. This work investigates the possibility of using blood donations as a source of leukaemia-specific immune therapeutics. The acute promyelocytic cell line NB4 carrying the PML-RAR alpha fusion was used as a target for cytotoxic T lymphocytes (CTL) stimulated to recognize the fusion. Stimulation of CTL was by production of dendritic cells pulsed with plasmid vectors containing polymerase chain reaction (PCR)-generated sequences of PML-RAR alpha derived from NB4 cells. PCR primer design included a Kozak consensus sequence to allow correct translation of the nucleic acid into protein. Identification of specific cytotoxicity was by both Granzyme B ELISPOT and by (51)Cr-release assays. Specific CTL activity targeting NB4 cells can be generated from donor-derived peripheral blood mononuclear cells. However, individual donors appear to respond differently to the length of stimulatory sequence encoded in the vector. Use of an internal methionine in the PML gene, which also satisfies the Kozak rules, allows translation in vitro and, thus, might provide a suitable start site for stimulation using acute promyelocytic leukaemia-specific sequence. The work presented here suggests that blood donor derived dendritic cells can be used to stimulate leukaemia-specific CTL from the same donation ex vivo. This would enable the generation of patient-specific therapeutics from major histocompatibility (MHC)-matched allogeneic donors. However, different MHC-matched donors might vary in their response depending on the length of the antigenic sequence.

Sooty mangabey (Cercocebus torquatus atys) IGHG and IGHA genes

Antibodies are adaptor molecules of the immune system that link antigen recognition with the effector mechanisms responsible for antigen clearance. Several nonhuman primate species are widely used in biomedical research, especially for vaccine development and for AIDS-related studies. However, nonhuman primate antibody molecules have been characterized only partially and only in a few species. Here, we describe sooty mangabey (Cercocebus torquatus atys) IGHG and IGHA genes, which encode the heavy-chain constant region of IgG and IgA molecules, respectively. The four mangabey IGHG genes are highly homologous to the rhesus macaque and baboon IGHG genes (percent identity varies between 94.0 and 98.8, depending on the subclass), with most amino acid differences located in the hinge regions. Results obtained by real-time reverse transcription polymerase chain reaction show that the four IGHG genes are expressed at least at the mRNA level. The mangabey IGHA gene is highly homologous to the corresponding gene from rhesus macaques (percent identity ranges from 88.6 to 96.7, depending on the allele considered), the only other nonhominoid primate species for which the complete sequence of the IGHA gene is currently available. In the mangabey analyzed, two IGHA alleles are present, confirming that high levels of IGHA gene heterozygosity are present in monkey species. These results show that nonhuman primate gamma and alpha heavy chains differ from each other mostly at the level of the hinge region and that alpha sequence heterogeneity in nonhuman primate species is also present in other gamma regions. In addition, these results provide sequence information that can be used for residue frequency analysis of antibody heavy-chain constant region sequences.

Specific integrin subunits in bovine oocytes, including novel sequences for alpha 6 and beta 3 subunits

Integrins facilitate attachment of cells to the extra-cellular matrix, often binding the arginine-glycine-aspartic acid tri-peptide motif, thus facilitating cell migration, mediating cell-cell adhesion, linking the extracellular matrix (ECM) with cytoskeletal elements, and acting as signaling molecules. Adhesion activates signaling mechanisms that regulate integrin function, cytoskeletal assembly, cell behavior, and protein synthesis. Immunofluorescence was used to determine the presence of integrin alpha and beta subunits on the surface of bovine oocytes using a panel of monoclonal antibodies (mAbs) specific for alphaL, alphaM, alphaX, alphaV, alpha2, alpha4, alpha6, beta1, beta2, and beta3 antigens, with multiple antibodies for each subunit. Confocal microscopy indicated the presence of alphaV, alpha6, alpha4, alpha2, ss1, and ss3 integrin subunits on the plasma membrane of bovine oocytes. The presence of these subunits was verified by RT-PCR analysis using primers designed based on known gene sequences of bovine integrin subunits, or by using sequence information using bovine expressed sequence tags (EST) compared with known human and murine integrin subunit gene sequence information. Previously unpublished sequence information for bovine alpha6 and beta3 integrins was determined. The presence of these integrin subunits on the bovine oocyte vitelline membrane supports the hypothesis that sperm-oocyte interactions in the bovine are mediated by integrins.

DNA microarray to detect and identify trichothecene- and moniliformin-producing Fusarium species

To develop a DNA microarray for easy and fast detection of trichothecene- and moniliformin-producing Fusarium species. A DNA microarray was developed for detection and identification of 14 trichothecene- and moniliformin-producing species of the fungal genus Fusarium. The array could also differentiate between four species groups. Capture probes were designed based on recent phylogenetic analyses of translation elongation factor-1 alpha (TEF-1alpha) sequences. Particular emphasis was put on designing capture probes corresponding to groups or species with particular mycotoxigenic synthetic abilities. A consensus PCR amplification of a part of the TEF-1alpha is followed by hybridization to the Fusarium chip and the results are visualized by a colorimetric Silverquant detection method. We validated the Fusarium chip against five naturally infected cereal samples for which we also have morphological and chemical data. The limit of detection was estimated to be less than 16 copies of genomic DNA in spiked commercial wheat flour. The current Fusarium chip proved to be a highly sensitive and fast microarray for detection and identification of Fusarium species. We postulate that the method also has potential for (semi-)quantification. The Fusarium chip may prove to be a very valuable tool for screening of cereal samples in the food and feed production chain, and may facilitate detection of new or introduced Fusarium spp.

Molecular cloning and functional expression of rabbit α2-antiplasmin

The rabbit is frequently employed in small animal models of in-vivo coagulation and fibrinolysis, but the degree to which its plasma proteins resemble their human counterparts is incompletely known. Our aims were: to determine the nucleotide sequence of a full-length rabbit liver alpha(2)-antiplasmin (alpha(2)AP) cDNA; compare it with its human, murine, and bovine counterparts; and express it in functional form. Partial cDNAs encoding 5' and 3' portions of the alpha(2)AP mRNA were obtained by reverse transcriptase (RT)-polymerase chain reaction (PCR), using rabbit liver RNA and 'guessmer' oligonucleotides based on known sequences. This information was employed to design additional oligonucleotides for RT-PCR and rapid amplification of cDNA ends (RACE) procedures yielding overlapping clones corresponding to the entire rabbit alpha(2)AP mRNA sequence. Mature alpha(2)AP was expressed as a hexahistidine-tagged recombinant protein in Escherichia coli, purified by nickel-chelate affinity and ion exchange chromatography, and its reaction with plasmin and soluble fibrin assessed electrophoretically and compared with an analogous recombinant human alpha(2)AP. The consensus rabbit alpha(2)AP cDNA is 2,157 bp long, and encodes a 464-residue mature sequence and a 27-amino-acid presequence. The mature protein is 82% identical to its human counterpart, and its recombinant form produced denaturation-resistant complexes with both plasmin and fibrin. The region of greatest sequence divergence lies within the C-terminal extension of alpha(2)AP, unique in the serpin family of proteins to which alpha(2)AP belongs. The highly conserved nature of rabbit alpha(2)AP reinforces its role as a vital antifibrinolytic protein and supports fibrinolytic investigations in models employing this small animal.

Biodiversity and Biogeography of Fusarium Species from Northeastern North American Asparagus Fields Based on Microbiological and Molecular Approaches

Sixteen Fusarium species were recovered from 52 asparagus commercial fields, representing all major ecological (edaphic and climatic) area of asparagus production in the province of Québec, eastern Canada. This study extends our understanding of the geographic range of these species. It also provides climatological and edaphic properties linked to community changes and adaptations. Fusarium oxysporum and F. proliferatum were omnipresent and abundant in all five ecological area under study, whereas F. redolens was less frequently found. Species of Fusarium that produce carmine red pigmentation on potato dextrose agar, i.e., F. acuminatum, F. avenaceum, etc., were common at the northern limit of asparagus production. Abundance of red Fusarium species corresponded with a low isolation frequency of F. proliferatum. Nevertheless, F. proliferatum had a high recovery rate throughout Québec asparagus growing areas, under climatic conditions as cold as those of northern Europe where this species is uncommon in asparagus fields. In the light of these results, redefinition of the geographical distribution of F. proliferatum in asparagus fields is proposed. Intraspecific molecular differences in F. proliferatum and F. oxysporum were detected in the EF-1 alpha sequences and compared with well-characterized strains of North America.

Where is the weak linkage in the globin chain?

Hemoglobinopathies are important inherited disorders with high prevalence in many tropical countries. Prediction of protein nanostructure and function is a great challenge in proteomics and structural genomics. Identifying the point vulnerable to mutation is a new trend in research on disorders at the genomic and proteomic level. A bioinformatics analysis was performed to determine the positions that tend to correspond with peptide motifs in the amino acid sequence of alpha and beta globin chains. To identify the weak linkage in alpha globin and beta globin chains, a new bioinformatics tool, GlobPlot, was used. For the alpha globin chain, 22 positions were identified: the disorders were found at positions 3-8, 38-42, 46-51, and 75-79. For the beta globin chain, 46 positions were identified: the disorders were found at positions 61-146. The study showed that weak linkages in alpha globin and beta globin chains can be identified and provide good information for predicting possible new mutations that could lead to new hemoglobinopathies.

The cytoplasmic tail of the α3 integrin subunit promotes neurite outgrowth in PC12 cells

Binding of integrins to proteins of the extracellular matrix (ECM) provides structural and signaling information for biological processes such as cell proliferation, migration, neurite outgrowth, and differentiation. Integrins represent a family of heterodimeric transmembrane cell surface receptors. Besides connecting the ECM with the cytoskeleton, integrins also induce various signaling pathways in response to ligand binding. Integrin ligation leads to cytoplasmic protein-protein interactions requiring both integrin cytoplasmic tails. These sequences are initiation points for focal adhesion formation and subsequent signal transduction cascades. In this study, we addressed the question of whether the short cytoplasmic tail of the alpha(3) integrin subunit of alpha(3)beta(1) integrin is required for alpha(3)beta(1) integrin-dependent processes. For this purpose, cDNA representing the extracellular and transmembrane domain of the interleukin 2 receptor (IL2R) alpha subunit and the cytoplasmic sequence of the alpha(3) integrin subunit was transfected into PC12 cells. Autonomous expression of the cytoplasmic alpha(3) tail does not affect attachment but leads to inhibition of neuronal differentiation on laminin 5. This indicates that the cytoplasmic alpha(3) sequence is not required for cell attachment but is necessary for long-term adhesion and for the reorganization of the cytoskeleton that precedes neuronal differentiation. Inhibition of neurite outgrowth by chimeric IL2R-alpha(3) can be rescued by treatment of transfected cells with the pharmacological inhibitor Y27632, which inhibits the RhoA downstream effector Rho kinase alpha.

Proteolytic Processing of the Laminin α3 G Domain Mediates Assembly of Hemidesmosomes but Has No Role on Keratinocyte Migration

Laminin-5 (Lm5), the major adhesion ligand of basal epithelial cells, undergoes complex extracellular proteolytic processing that influences cell adhesion and migration. In tumor cell lines, the proteolytic truncation of the C-terminal G domain of the Lm alpha3 chain induces assembly of hemidesmosomes and downregulates cell migration. To define the biological functions of the alpha3 G domain processing in physiological conditions, we have expressed a series of mutant alpha3 complementary DNA in human primary alpha3-null keratinocytes immortalized by human papillomavirus E6E7 (HKalpha3 cells). Using monolayer and organotypic cell cultures we show that: (1) the hinge region between subdomains G3 and G4 carries the proteolytic cleavage sites; (2) nucleation of the hemidesmosomal proteins is independent of the proteolytic maturation of the alpha3 G domain, whereas formation of mature hemidesmosomes relies on proteolytic cleavage of alpha3; and (3) the proteolytic processing plays no role in cell migration, which suggests that nucleation of hemidesmosomal structures in culture does not reflect the migratory potential of the epithelial cells. Our results also demonstrate that HKalpha3 cells are a unique model system, which will be useful to dissect the functions and molecular interactions of Lm5.

Bacterial Endosymbioses of Gutless Tube-Dwelling Worms in Nonhydrothermal Vent Habitats

Gutless tube-dwelling worms of pogonophorans (also known as frenulates) and vestimentiferans depend on primary production of endosymbiotic bacteria. The endosymbionts include thiotrophs that oxidize sulfur for autotrophic production and methanotrophs that oxidize and assimilate methane. Although most of the pogonophoran and vestimentiferan tube worms possess single thiotrophic 16S rRNA genes (16S rDNA) related to gamma-proteobacteria, some pogonohorans are known to bear single methanotroph species or even dual symbionts of thiotrophs and methanotrophs. The vestimentiferan Lamellibrachia sp. L1 shows symbiotic 16S rDNA sequences of alpha-, beta-, gamma-, and epsilon-proteobacteria, varying among specimens, with RuBisCO form II gene (cbbM) sequences related to beta-proteobacteria. An unidentified pogonophoran from the world's deepest cold seep, 7326-m deep in the Japan Trench, hosts a symbiotic thiotroph based on 16S rDNA with the RuBisCO form I gene (cbbL). In contrast, a shallow-water pogonophoran (Oligobrachia mashikoi) in coastal Japan Sea has a methanotrophic 16S rDNA and thiotrophic cbbL, which may suggest the feature of type X methanotrophs. These observations demonstrate that pogonophoran and vestimentiferan worms have higher plasticity in bacterial symbioses than previously suspected.

Differentiation of bovine from porcine gelatines using polyclonal anti-peptide antibodies in indirect and competitive indirect ELISA

Gelatine is a collagen derivative obtained from bones and hides/skin mainly from bovine and pigs. As a consequence of the outbreak of bovine spongiform encephalopathy (BSE), the use of bovine gelatine in feed, food and pharmaceutical products has been restricted by regulatory authorities. However, no method was presently available for its specific detection. The large similarity in amino-acid sequences of collagens from different species make their immunochemical differentiation difficult when using polyclonal antibodies raised against the whole molecule [A. Venien, D. Levieux, J. Immunoassay Immunochem., in press]. To obtain bovine-specific antibodies, we immunized rabbits against putative species-specific sequences of the bovine collagen alpha 1(I) chain. Using these antibodies, an indirect ELISA was developed to allow a quick and easy differentiation between bovine and porcine gelatines. Moreover, a competitive indirect ELISA was found suitable to detect bovine gelatine in porcine gelatine purchased from laboratory chemicals suppliers down to a dilution of 2–4 parts per 1000 with CVs ranging from 5.7 to 7.7%. When testing mixtures of the largest possible range of industrial batches of bovine and porcine gelatines (skin/hides or bones origin, acid or alkaline processes, high or low Bloom) the detection limit was down to a dilution of 8 parts per 100 bovine gelatine in porcine gelatine. These ELISAs could be routinely used by pharmaceutical and food manufacturers to secure their supply chain.