The transcriptomic responses of the eastern oyster, Crassostrea virginica, to environmental conditions.

Understanding the mechanisms by which organisms adapt to environmental conditions is a fundamental question for ecology and evolution. In this study, we evaluate changes in gene expression of a marine mollusc, the eastern oyster Crassostrea virginica, associated with the physico-chemical conditions and the levels of metals and other contaminants in their environment. The results indicate that transcript signatures can effectively disentangle the complex interactive gene expression responses to the environment and are also capable of disentangling the complex dynamic effects of environmental factors on gene expression. In this context, the mapping of environment to gene and gene to environment is reciprocal and mutually reinforcing. In general, the response of transcripts to the environment is driven by major factors known to affect oyster physiology such as temperature, pH, salinity, and dissolved oxygen, with pollutant levels playing a relatively small role, at least within the range of concentrations found in the studied oyster habitats. Further, the two environmental factors that dominate these effects (temperature and pH) interact in a dynamic and nonlinear fashion to impact gene expression. Transcriptomic data obtained in our study provide insights into the mechanisms of physiological responses to temperature and pH in oysters that are consistent with the known effects of these factors on physiological functions of ectotherms and indicate important linkages between transcriptomics and physiological outcomes. Should these linkages hold in further studies and in other organisms, they may provide a novel integrated approach for assessing the impacts of climate change, ocean acidification and anthropogenic contaminants on aquatic organisms via relatively inexpensive microarray platforms.

Visualization of a guinea pig T lymphocyte surface component cross-reactive with immunoglobulin.

Thymus-derived lymphocytes (T cells) show exquisite specificity in recognition of antigens, but the nature of the cell surface receptor is controversial. Although antigen recognition mediated by immunoglobulin variable (V) regions remains the minimal hypothesis, it has been extremely difficult to definitely establish the presence of immunoglobulins on these cells. Chicken antibodies, produced against the (Fab')2fragment of mouse immunoglobulin G (IgG) and purified by binding to and elution from IgG-Sepharose 4B, bind to an endogenously synthesized surface component of guinea pig T cells. The binding occurred via a cross-reaction with murine k chain and a heavy chain determinant localized in the Fd region, and was visualized by immunofluorescence and immunoelectronmicroscopy using both transmission and scanning techniques. These data provide direct evidence for the presence of a surface component related to immunoglobulin on T lymphocytes.

A transcriptomic analysis of the stress induced by capture-release health assessment studies in wild dolphins (Tursiops truncatus).

The health of wild bottlenose dolphins (Tursiops truncatus) is typically evaluated by the study of animals that are captured and released back into the wild after examination. The impact of such studies on gene expression in peripheral blood cells was investigated using microarray and quantitative polymerase chain reaction methods. Significantly increased expression was observed in two major classes of genes: (i) energy metabolism, and (ii) responsiveness to stress and trauma, the latter effect suggesting the initiation of an acute-phase response. The value of data obtained in capture/release studies may need to be weighed against the potential physiological impacts of such studies.

Behavior of unreduced polymeric and monomdric immunoglobulins in sodium dodecyl sulfate-polyacrylamide gel electrophoresis.

Investigation of the electrophoretic behavior, in SDS-polyacrylamide and SDS-polyacrylamide-agarose gels, of IgMs and low mol. wt. Igs from four classes of vertebrates, as well as fragments derived from them, was carried out. A clear but unexpected straight-line relationship was observed for all Igs (and fragments) tested when relative mobility was plotted against log mol. wt for the unreduced molecules. Aberrant behavior of the low mol. wt Ig of Bufo marinus was shown to be due to the complete dissociation of the molecule into free light chains and heavy-chain dimers, in the presence of SDS.

Immunoglobulin VH genes of the goldfish, Carassius auratus: a re-examination.

Five VH-related genomic sequences from the goldfish, Carassius auratus, have been characterized. One of these sequences appeared to be a functional gene, and four to be pseudogenes. The main conclusions drawn from this study were that: (1) With minor exceptions, goldfish VH genes conform to the typical pattern of vertebrate VH genes in terms of their structure (they encode an intron-split hydrophobic leader, 3 framework and 2 complementarity-determining regions, and possess a typical 3' recombination signal sequence for VH to D joining) and regulatory sequences (possession of a typical upstream octameric promoter). (2) The sequences indicate that goldfish possess multiple families of VH sequences (at least three). Two of these families contain approximately 6 and 10 members, as judged from Southern blot hybridization experiments. (3) Goldfish VH gene families are distributed throughout the members of the species in the manner typical of that of VH families in other vertebrate species. Thus, this observation corrects the previous conclusion (Wilson et al., Proc. natn. Acad. Sci. U.S.A. 85, 1566-1570, 1988) that VH genes are discontinuously distributed in the goldfish population.

Beta 2 microglobulin-like polypeptide of the goldfish, Carassius auratus.

Antisera to human beta 2 microglobulin (beta 2M) detected a plasma membrane molecule on goldfish (Carassius auratus) cells in immunofluorescence. A goldfish molecule detected by radioimmunoassay (RIA) co-eluted with human beta 2M on gel filtration. By affinity chromatography on immobilized antibody to human beta 2M, a molecule was purified (from extracts of goldfish) that showed, on SDS-polyacrylamide gel electrophoresis, a mobility similar to that of human beta 2M (apparent Mr 12,800 +/- 500).

Expression of a mouse-channel catfish chimeric IgM molecule in a mouse myeloma cell.

Fusion genes encoding a murine VH domain and the constant region domains of the mu chain from the channel catfish, Ictalurus punctatus, were stably expressed in the lambda light chain producing mouse myeloma cell line J558L. Although the pathways of pre-mRNA processing for expression of membrane (micron and secreted (microsecond) forms of the mu chain differ between mammals and teleosts, mRNAs encoding both catfish micron and microsecond were correctly expressed in the mouse myeloma cells. The mouse-channel catfish chimeric mu chain polypeptide was able to associate covalently with the mouse lambda light chain and assemble, intracellularly, into polymers of covalent structure (microL)2-8 which resembled those seen with native catfish IgM. In contrast to native catfish IgM, the mouse-catfish chimeric IgM showed the property of binding strongly to protein A of Staphylococcus aureus. The mouse-channel catfish chimeric IgM was core-glycosylated, but did not contain terminal sialic acid. Secretion rates for the chimeric IgM were low, and the possibility could not be excluded that extracellular chimeric IgM was released from dead or dying cells. The reason(s) for the intracellular retention of the chimeric IgM (probably in the endoplasmic reticulum) are not known, but those mechanisms involving retention via cysteine residues were excluded.

T-cell receptors in channel catfish: structure and expression of TCR alpha and beta genes.

Herein are reported full length cDNA sequences for TCR alpha- and beta-chains of the channel catfish. Included are sequences belonging to four Valpha and six Vbeta families which share hallmarks in common with the Valpha and Vbeta genes of other species. Similar to the situation in other vertebrates, the catfish Calpha and Cbeta sequences exhibit distinct immunoglobulin, connecting peptide, transmembrane and cytoplasmic domains. However, the catfish TCR Calpha and Cbeta regions are shorter than those of mammals and the catfish Cbeta chain lacks a cysteine in its connecting peptide region. Two different catfish Cbeta cDNA sequences were identified, suggesting the existence of either two Cbeta loci or allotypes. Based on Southern blot analyses, each of the catfish TCR gene loci appear to be arranged in a translocon (as opposed to multicluster) organization with multiple V elements and a single or few copies of C region DNA. At the deduced amino acid level, the catfish Cbeta sequence exhibits 42% identity with the Cbeta of Atlantic salmon, 41% identity with the Cbeta of rainbow trout and 26% identity with Cbeta of the horned shark. The catfish Calpha amino acid sequence exhibits 44 and 29% identity with Calpha of the rainbow trout and southern pufferfish, respectively. TCRalpha and beta messages are selectively expressed and rearranged in a catfish clonal cell line that appears to be of the T lineage. This TCR alpha/beta expressing clonal lymphocyte line, designated 28S.1, has T-cell like function in that it constitutively produces a supernatant factor(s) with growth promoting activity. These findings should facilitate functional studies of fish TCRs and T cells in ways not previously possible with other 'lower' vertebrate models.

Mitogen and growth factor-induced activation of a STAT-like molecule in channel catfish lymphoid cells.

This article describes the identification of a putative STAT molecule in the channel catfish (Ictalurus punctatus), the first report of such a molecule in a 'lower' vertebrate. A monoclonal antibody against human STAT6 recognizes an approximately 100 kDa molecule that becomes activated and translocates to the nucleus upon both growth factor and mitogen stimulation of catfish leukocytes. This presumed catfish STAT binds the mammalian interferon-gamma activation site, a known motif of mammalian STAT binding, as shown by electromobility shift assays. Purification of the proteins present in these DNA complexes confirms that the catfish reactive molecule binds to the interferon-gamma activation site sequence. These results suggest that STAT molecules have been highly conserved in vertebrate evolution.

Use and abuse of sepharose-conjugated antibodies for the isolation of lymphocyte-surface immunoglobulins.

Immunoadsorbents of Sepharose-4B-conjugated antibodies were shown to be suitable for the characterization, by subsequent SDS-polyacrylamide gel electrophoresis, of splenocyte-membrane Immunoglobulin (Ig) solubilized by detergent lysis of surface 125I-labelled cells. However, high non-specific binding of 125I-labelled lymphocyte-membrane components to Sepharose-4B prevented accurate quantition of Ig in such lysates. 125I-labelled lymphocyte-membrane components solubilized by metabolic release also showed high non-specific binding to Sepharose-4B, and this interfered with both quantitative and qualitative analysis of Ig solubilized in this manner. Initial attempts to overcome the nonspecific binding of 125I-labelled lymphocyte-membrane components to Sepharose-4B were unsuccessful, and attention is drawn to the technical problems of using Sepharose-4B as a matrix for solid-phase immunoadsorbent studies of lymphocyte-membrane Ig.

Evidence for low-molecular weight antibodies in the serum of a urodele amphibian, Ambystoma mexicanum.

Adult axolotls (A. mexicanum) were hyperimmunized with the haptenic determinant, azobenzene-arsonate (ARS). Specific antibodies were isolated from their serum by immune-affinity chromatography on immobilized ARS columns. Analysis of the specific ARS-binding molecules by sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) indicated that these animals were capable of producing both high molecular-weight (presumably IgM) and low molecular-weight antibodies to the ARS hapten. The low molecular-weight anti-ARS antibody produced by one inbred colony of axolotls did not show any restricted heterogeneity, as assessed by isoelectric focusing. Our results suggest that regulatory events, not the absence of genetic information, may be responsible for the apparent lack of Ig isotype diversity in this species.

A 12 kDa protein in chicken serum antigenically cross-reactive with, but unrelated to, beta 2-microglobulin.

A protein, isolated from chicken serum, showed the following beta 2-microglobulin-like properties; an apparent molecular size of 12000 Mr, predominantly beta-sheet secondary structure, and antigenic cross-reaction with human beta 2-microglobulin. However, amino acid composition analysis and partial amino acid sequence analysis showed that this molecule was not only not a beta 2-microglobulin, but was unrelated to any other known class of protein.

Phylogenetic origins of immune recognition: naturally occurring DNP-binding molecules in chordate sera and hemolymph.

A method is described which allows the isolation of small quantities of DNP-binding antibodies of both high- and low-molecular-weight classes. The only detectable DNP-binding protein in the serum of placoderm-derived vertebrates was immunoglobulin in nature, and of the order of less than or equal to 1% total serum immunoglobulin. Proteins in the serum of the urochordate Pyura stolonifera, which bind to both DNP and erythrocyte antigens, showed charge heterogeneity and an apparent subunit molecular weight of approximately 65,000 to 70,000 daltons.

Serological characterization of humoral lectins from the freshwater prawn Macrobrachium rosenbergii.

We have detected and partially characterized multiple lectins present in the serum of the freshwater prawn Macrobrachium rosenbergii. Since agglutination of erythrocytes (RBC) is not abolished by treatment with Vibrio cholerae neuraminidase (VCN), Macrobrachium shows an agglutination pattern different from that of other sialic acid-specific lectins such as Limulus polyphemus lectin. However, after absorption with primate and bird VCN-treated RBC, Macrobrachium serum exhibits high titers with untreated and pronase-treated RBC and no agglutination of VCN-treated RBC, suggesting a typical sialic acid specific lectin agglutination profile. Hemagglutination-inhibition tests indicate that sialic acid containing compounds are the best inhibitors for Macrobrachium lectins. Subterminal sugars and type of linkage are probably important for the lectin binding since bovine submaxillary mucin (containing mainly terminal NANA-alpha-2 6-GalNAc-) is a better inhibitor than fetuin (containing mainly terminal NANA-alpha-2 leads to 3-Gal-) and colominic acid (-NANA-alpha-2 leads to 8-NANA-) is a weak inhibitor.

cDNA sequence and organization of the immunoglobulin light chain gene of the duck, Anas platyrhynchos.

A cDNA was cloned which encoded an immunoglobulin (Ig) light (L) chain of the White Pekin duck. The organization of the variable (V) and constant (C) domains was analyzed by genomic Southern blotting. The duck L chain gene has a similar chromosomal organization to that of the chicken, with a single lambda-like C region and multiple VL, hybridizing elements. The amino acid sequence of the VL region of the White Pekin duck L chain showed 88% identity with the Muscovy duck and 87% identity with the chicken, the JL region showed 92% identity with these species, and the CL region showed 88% identity with Muscovy duck and 66% with chicken. The constraints imposed by the gene-conversion mechanism of generating antibody diversity might account for the similarities of the avian V region sequences.

Immune gene discovery by expressed sequence tag analysis of hemocytes and hepatopancreas in the Pacific White Shrimp, Litopenaeus vannamei, and the Atlantic White Shrimp, L. setiferus.

A pilot program was undertaken in immune gene discovery in two sister species of litopenaeid shrimp, the Pacific white shrimp, Litopenaeus vannamei and the Atlantic white shrimp, L. setiferus. RNA from the hemocytes and hepatopancreas of single individuals from each species was recovered, 4 cDNA libraries (one from each tissue/species) were made by a PCR-based method and a total of approximately 2045 randomly selected clones were sequenced. A total of 268 expressed sequence tags (ESTs) were found that corresponded to 44 immune function genes. The most common immune-function ESTs (172) were antimicrobial peptides, which were restricted to the hemocyte libraries. Lectins were the largest group of immune-function ESTs found in the hepatopancreas. Analysis of these libraries indicates that EST approaches are effective for immune gene discovery in shrimp and that the diversity of these PCR-generated libraries would support full-scale EST collection.

Diversity of the immunoglobulin heavy chain in the Atlantic salmon (Salmo salar L.) is contributed by genes from two parallel IgH isoloci.

Immunoglobulin heavy chain (IgH) variable (V) region cDNAs from the Atlantic salmon, Salmo salar L., have been isolated and analysed with respect to diversity and transcription of the two parallel IgH isoloci in this species. A total of nine V(H) families were defined according to the 80% identity criterion, of which seven were highly related (>80% identity) to the V(H) families defined in rainbow trout and arctic charr. The variability of the CDR1 and 2 was low, although mutational hot-spot consensus sequences were accumulated in these regions. The CDR3 showed largest variability, expressing at least eight different groups of D motifs diversified by fusion of the D motifs, possible N and P nucleotide insertions and exonuclease activity. Presumably functional transcripts expressing D motifs in all three reading frames were identified for two of the motifs. The cDNAs were mapped to either of the two parallel loci, and sequence analysis revealed that the repertoire of V(H) segments was contributed by transcription of genes from both of the IgH isoloci. Transcription of genes from both isoloci generated no obvious effects on variability in the CDR3 of the Atlantic salmon IgH chains, although one additional J(H)-segment with altered N-terminal was generated by the process of duplication and divergence. Thus, the issue of biological significance of the two IgH isoloci remains unclear.

Membrane immunoglobulin-associated molecules on channel catfish B lymphocytes.

Membrane immunoglobulin (mIgM) on the surface of channel catfish B lymphocytes is non-covalently associated with 64 and 70 kDa molecules which are composed of covalent 32 kDa dimers and covalent 45/25 kDa subunits, respectively. Cross-linking of mIgM on catfish B cells leads to rapid phosphorylation of tyrosine residues in these presumed accessory as well as numerous other cytoplasmic molecules. These data indicate that fish likely use a signal transduction system containing elements similar to those of mammalian B cells.

Light chain variable region diversity in Atlantic cod (Gadus morhua L.).

This study was undertaken to determine if a lack of V(L) domain variability could explain, in part, the failure of Atlantic cod to respond to immunization with the production of specific antibodies. The variability of cod V(L) regions was studied in 33 cDNA and two genomic clones. The variability of the CDRs was estimated by the Shannon entropy method and compared with that in other species. It was found to be lowest in the little skate (Raja erinacea), higher in cod, and highest in Xenopus and mouse. While the variability of the CDRs is slightly lower in cod than in Xenopus and mouse, it is spread over broader areas of the amino acid sequence. The length of CDR1 and CDR3 in cod is equal to or exceeds that found in skate, Xenopus, chicken and mammals. Isoelectric points and hydrophobicity vary substantially among the studied Ig light chain domains. Thus, neither the length, nor the variability, nor the physicochemical properties (pI and hydrophobicity) of the L chain CDRs can explain the absence of antibody response to immunization in cod.

Phylogeny of immune recognition: fine specificity of fish immune repertoires to cytochrome C.

Using the structurally defined protein antigen cytochrome C, studies were conducted in an attempt to delineate the fine specificities of channel catfish immune repertoires. We have previously reported that species variants of cytochrome C were cross-stimulatory to peripheral blood leukocytes (PBL) from catfish immunized with the pigeon variant. Molecular database analyses revealed the existence of overlapping epitopes that appear to define the specificity of the immune response to a "family" of closely related antigens. To further explore these observations, studies were conducted to determine the contribution of peptide 81-104 to the immunogenicity of cytochrome C. Current data showed that peptide 81-104 and intact cytochrome C were stimulatory to PBL from fish previously immunized with the native molecule. In contrast, PBL from fish previously primed with the peptide 81-104 responded only to the immunizing peptide as well as to some, but not all, variants of the peptide 81-104. The differences in the stimulatory capacities of the peptide variants appeared to correlate with amino acid substitutions at various positions of the peptide and changes in their predicted secondary structures.