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Biology↗
Biomedical subjects
L E Hood
Publications and source records attributed to L E Hood.
Testing for differentially-expressed genes by maximum-likelihood analysis of microarray data.
Although two-color fluorescent DNA microarrays are now standard equipment in many molecular biology laboratories, methods for identifying differentially expressed genes in microarray data are still evolving. Here, we report a refined test for differentially expressed genes which does not rely on gene expression ratios but directly compares a series of repeated measurements of the two dye intensities for each gene. This test uses a statistical model to describe multiplicative and additive errors influencing an array experiment, where model parameters are estimated from observed intensities for all genes using the method of maximum likelihood. A generalized likelihood ratio test is performed for each gene to determine whether, under the model, these intensities are significantly different. We use this method to identify significant differences in gene expression among yeast cells growing in galactose-stimulating versus non-stimulating conditions and compare our results with current approaches for identifying differentially-expressed genes. The effect of sample size on parameter optimization is also explored, as is the use of the error model to compare the within- and between-slide intensity variation intrinsic to an array experiment.
Galactose↗
Ataxia in prion protein (PrP)-deficient mice is associated with upregulation of the novel PrP-like protein doppel.
The novel locus Prnd is 16 kb downstream of the mouse prion protein (PrP) gene Prnp and encodes a 179 residue PrP-like protein designated doppel (Dpl). Prnd generates major transcripts of 1.7 and 2.7 kb as well as some unusual chimeric transcripts generated by intergenic splicing with Prnp. Like PrP, Dpl mRNA is expressed during embryogenesis but, in contrast to PrP, it is expressed minimally in the CNS. Unexpectedly, Dpl is upregulated in the CNS of two PrP-deficient (Prnp(0/0)) lines of mice, both of which develop late-onset ataxia, suggesting that Dpl may provoke neurodegeneration. Dpl is the first PrP-like protein to be described in mammals, and since Dpl seems to cause neurodegeneration similar to PrP, the linked expression of the Prnp and Prnd genes may play a previously unrecognized role in the pathogenesis of prion diseases or other illnesses.
Amino Acid Motifs↗
T-cell receptor vbeta deletion and valpha polymorphism are responsible for the resistance of SWR mouse to arthritis induction.
Collagen type II-induced arthritis (CIA) develops in susceptible mouse strains after intradermal injections of type II collagen (CII) in complete Freund's adjuvant (CFA). Susceptibility to CIA in mice is linked to genes of the major histocompatibility complex (MHC). Although the SWR mouse has a susceptible MHC haplotype (H2q), it is resistant to CIA. SWR exhibits at least two known immunological defects: (1) it contains a germline deletion of about 50% of T-cell receptor (TCR) Vbeta-chain gene segments, and (2) SWR is deficient in complement component C5. It has been shown that T cells that express TCRValpha11.1 and TCRVbeta8.2 play a substantial role in the pathogenesis of arthritis in the DBA/1 mouse (H2q). We generated SWR transgenic (tg) mice to determine whether the expression of pathogenic Valpha11.1 and/or Vbeta8.2 transgenes would confer arthritis susceptibility. Arthritis was induced in the SWR TCRalphabeta tg mice, but not in SWR TCRbeta tg mice. To address the role of Valpha11.1 in arthritis susceptibility, we examined the allelic polymorphisms of the Tcra-V11-gene subfamily members between the arthritis susceptible DBA/1 mouse and the arthritis-resistant SWR mouse strain. The amino acid sequences of the Valpha11.1 alleles differ at two positions (codons 18 and 68). Accordingly, these two amino acid changes are sufficient to allow the production of pathogenic T cells in SWR mice. This is the first demonstration of the association of a particular Tcra-V allele and arthritis susceptibility in mice.
Animals↗
OPG/FDCR-1, a TNF receptor family member, is expressed in lymphoid cells and is up-regulated by ligating CD40.
We have cloned a TNFR family member from a follicular dendritic cell (FDC)-like cell line, FDC-1. This molecule, FDC-derived receptor-1 (FDCR-1), is identical to osteoprotegerin (OPG), a soluble cytokine that regulates osteoclast differentiation. Recently, OPG/FDCR-1 has been characterized as a second receptor for receptor activator of NF-kappaB ligand (RANKL)/TNF-related activation-induced cytokine (TRANCE), a primarily T-cell restricted TNF family member that augments dendritic cell (DC) function. In this report, we demonstrate that OPG/FDCR-1 is membrane bound on the surface of transfected baby hamster kidney (BHK) and untransfected FDC-1 cells. We also found a restricted OPG/FDCR-1 expression pattern in lymphoid cells, specifically in B cells, DCs and FDC-enriched fractions, which in B cells and DCs is up-regulated by CD40 stimulation. Because OPG/FDCR-1 shares some properties with RANK, the first RANKL/TRANCE receptor, we discuss how the balance between RANK and OPG/FDCR-1 expression could influence immune responses and, ultimately, germinal center formation.
Animals↗
Expression of a type II collagen-specific TCR transgene accelerates the onset of arthritis in mice.
Animal models of autoimmune diseases have been instrumental in advancing our understanding of autoimmunity in humans. Collagen-induced arthritis in mice is an autoimmune disease model of rheumatoid arthritis, which is MHC class II restricted and CD4 T cell dependent. To better understand the fundamental role of T cells in arthritis, we have generated a transgenic mouse carrying the rearranged Valpha11.1 and Vbeta8.2 TCR chain genes isolated from a type II collagen (CII)-specific T cell hybridoma. Cell surface analysis indicated that Vbeta8.2 chain was expressed on the surface of nearly all peripheral T cells. Analysis of T cell subsets in transgenic mice revealed a profound skewing in peripheral T cells towards the CD4 population. Although peripheral T cells were not tolerant to CII and responded to CII stimulation in vitro, transgenic mice did not develop spontaneous arthritis. However, a rapid onset of arthritis with severe clinical signs was detected in transgenic mice after immunization with CII in complete Freund's adjuvant. Histological analysis of inflamed joints showed a great resemblance to arthritic joints in man. This unique transgenic mouse model provides valuable insights into the mechanism of arthritis and into potential specific immune interventions.
Animals↗
Complete genomic sequence and analysis of the prion protein gene region from three mammalian species.
The prion protein (PrP), first identified in scrapie-infected rodents, is encoded by a single exon of a single-copy chromosomal gene. In addition to the protein-coding exon, PrP genes in mammals contain one or two 5'-noncoding exons. To learn more about the genomic organization of regions surrounding the PrP exons, we sequenced 10(5) bp of DNA from clones containing human, sheep, and mouse PrP genes isolated in cosmids or lambda phage. Our findings are as follows: (1) Although the human PrP transcript does not include the untranslated exon 2 found in its mouse and sheep counterparts, the large intron of the human PrP gene contains an exon 2-like sequence flanked by consensus splice acceptor and donor sites. (2) The mouse Prnpa but not the Prnpb allele found in 44 inbred lines contains a 6593 nucleotide retroviral genome inserted into the anticoding strand of intron 2. This intracisternal A-particle element is flanked by duplications of an AAGGCT nucleotide motif. (3) We found that the PrP gene regions contain from 40% to 57% genome-wide repetitive elements that independently increased the size of the locus in all three species by numerous mutations. The unusually long sheep PrP 3'-untranslated region contains a "fossil" 1.2-kb mariner transposable element. (4) We identified sequences in noncoding DNA that are conserved between the three species and may represent biologically functional sites.
Amino Acid Sequence↗
Rapid detection of bovine type II collagen-specific T-cell hybridomas.
T-cell hybridomas are powerful tools in studying the fine specificities of antigen recognition by the T-cell receptor (TCR), the structure and genetic basis of the CD3-TCR complex, and the size of the TCR alpha/beta repertoire used in response to various antigens. A technical challenge in establishing T-cell hybridomas is the early identification of antigen-specific ones. We have established a rapid and efficient ELISA method for detecting antigen-specific T-cell hybridomas. Our ELISA technique significantly reduces the time and resources required for the primary screening of antigen-specific T-cell hybrids, eliminates the need of maintaining hundreds of rapidly growing nonspecific clones, and does not require the maintenance of IL-2/IL-4 dependent cell lines such as CTLL-2 or HT-2. In addition, the ELISA technique is designed to detect both types of CD4 T-cells: Th1 and Th2, by using a mixture of anti-IL-2 and anti-IL-4 monoclonal antibodies. Therefore, we believe that our ELISA technique provides a faster, less expensive, and higher throughput screening method for the early identification of antigen-specific T-cell hybridomas than the current bioassays.
Animals↗
SWR: an inbred strain suitable for generating transgenic mice.
Production of fertilized oocytes and generation of transgenic mice is generally more efficient using F2 hybrid embryos than embryos from inbred mice. Most F2 hybrids are of the C57BL/6 background because of its genetic and embryologic features. However, our goal of developing a transgenic mouse model for rheumatoid arthritis necessitated using a susceptible mouse strain such as DBA/1. We prepared alpha and beta T-cell receptor (TCR) chain gene constructs and microinjected them into embryos from DBA/1, SWR, (DBA/1 x SWR)F1, and (SWR x DBA/1)F1 strains. We found SWR female mice to be prolific ovulators in response to exogenous hormones, with oocyte numbers comparable to those produced by (C57BL/6 x C3H)F1 female mice. Embryos from the (SWR x DBA/1)F1 or SWR strain were large and had prominent pronuclei, whereas (DBA/1 x SWR)F1 embryos were smaller and had less visible pronuclei, similar to those of DBA/1 embryos. Therefore, the pronuclear size and visibility are features of the SWR female mice and are independent of the genotype of the fertilizing spermatozoa. Resistance to lysis after co-injection of alpha beta TCR constructs and the efficiency of generating DNA-positive founders were comparable in SWR, (SWR x DBA/1)F1, and (C57BL6 x C3H)F2 embryos. Thus, the SWR mouse is another inbred strain, in addition to the FVB inbred strain, found to be highly suitable for propagation of transgenes. Furthermore, the SWR mouse is well defined genetically, and SWR females have a high ovulation rate, comparable to that of F1 hybrid mice.
Animals↗
Rapid cloning of any rearranged mouse immunoglobulin variable genes.
Immunoglobulins (Ig) have been the focus of extensive study for several decades and have become an important research area for immunologists and molecular biologists. The use of polymerase chain reaction (PCR) technology has accelerated the cloning, sequencing, and characterization of genes of the immune system. However, cloning and sequencing the Ig variable (V) genes using the PCR technology has been a challenging task, primarily due to the very diverse nature of Ig V region genes. We have developed a simple, rapid, and reproducible PCR-based technique to clone any rearranged mouse Ig heavy or light chain genes. A close examination of all Ig heavy and light chain V gene families has resulted in the design of 5' and 3' universal primers from regions that are highly conserved across all heavy or light chain V gene families, and the joining or constant regions, respectively. We present our strategy for designing universal primers for Ig V gene families. These primers were able to rapidly amplify the rearranged Ig V genes, belonging to diverse Ig V gene families from very different cell lines, i.e., J558, MOPC-21, 36-60, and a chicken ovalbumin specific B-cell hybridoma. In addition, the present study provides the complete alignment of nucleotide sequences of all heavy and light chain variable gene families. This powerful method of cloning Ig V genes, therefore, allows rapid and precise analysis of B-cell hybridomas, B-cell repertoire, and B-cell ontogeny.
Amino Acid Sequence↗
Characterization of the mouse Tcra-V22 gene subfamily.
T-cell receptors (Tcrs) of higher organisms play a key role in the specific recognition of self and non-self molecules in the immune system. The large number of Tcr variable (V) genes have been organized into V gene subfamilies according to their sequence similarity at the nucleotide and amino acid level. We cloned and characterized four new members of the Tcra-V22 gene subfamily at the genomic level using a simple and sensitive technique that can rapidly clone members of any multi-member gene family. Sequence analysis reveals that the four Tcra-V22 gene subfamily members have more than 98% sequence similarity in their coding regions, at the nucleotide and amino acid levels. However, the intron between the leader and the coding region varies up to 7% between members of the Tcra-V22 gene subfamily. Comparison of the multi-member Tcra-V22 gene subfamily with other multi-member Tcra-V gene subfamilies (V2, V8, and V11), shows that Tcra-V22 is unique in that it has multiple members with nearly identical amino acid sequence and which are not inherently pseudogenes. Sequence similarity analysis of the Tcra-V22 subfamily with the prototypes of all other Tcra-V subfamilies revealed that the Tcra-V22 subfamily has the closest sequence similarity to that of Tcra-V18 (77% at the nucleotide level and 71% at the amino acid level).
Amino Acid Sequence↗
Sponge-like electrophoresis media: mechanically strong materials compatible with organic solvents, polymer solutions and two-dimensional electrophoresis.
A new range of sponge-like media, called "electrophoresis sponges", is presented. They differ from electrophoresis gels primarily in that they are mechanically stronger, providing a permanent structure of directly measurable pore size dimensions. The new media are similar to capillary electrophoresis in terms of pore size range, they are mechanically strong with directly definable walls, and are compatible with polymer solutions. The sponges differ from capillary electrophoresis in that they provide large numbers of channels, with a corresponding high load capacity for simultaneous runs in multiple channels and they are compatible directly with multi-dimensional separations, such as high resolution two-dimensional electrophoresis. Furthermore, they can be molded (or cut) to any shape and retain that shape, they can be handled more easily than gels, they can be reused if necessary, they can be distributed in the same format between labs easily, and they can be stored indefinitely. Chemically, they can be hydrophilic or hydrophobic, with capability ranging from inert to reactive surfaces. Pore sizes can range from the sub-nanometer to 100 micron scale. Results with various hydrophobic sponges are reported for the carrier ampholyte-based isoelectric focusing of proteins. Broad and narrow pH gradients are established in the sponges that are more linear than those achieved with polyacrylamide gels. One- and two-dimensional electrophoresis of proteins has been achieved, for example with high resolution of the charge isomers of the haptoglobin beta chain, using sponge-based isoelectric focusing. Isoelectric focusing is about threefold faster in the tested sponges than in equivalent polyacrylamide gels. This improved speed is probably related to the larger sponge pores.(ABSTRACT TRUNCATED AT 250 WORDS)
Electrophoresis, Gel, Two-Dimensional↗
Characterization of the T cell receptor repertoire causing collagen arthritis in mice.
Collagen type II-induced arthritis (CIA) is generated in susceptible rodent strains by intradermal injections of homologous or heterologous native type II collagen in complete Freund's adjuvant. Symptoms of CIA are analogous to those of the human autoimmune disease, rheumatoid arthritis. CIA is a model system for T cell-mediated autoimmune disease. To study the T cell receptor (TCR) repertoire of bovine type II-specific T cells that may be involved in the pathogenesis of CIA in DBA/1Lac.J (H-2q) mice, 13 clonally distinct T cell hybridomas specific for bovine type II collagen have been established and the alpha and beta chains of their TCRs have been analyzed. These T cell hybridomas recognize epitopes that are shared by type II collagens from distinct species and not by type I collagens, and exhibit a highly restricted TCR-alpha/beta repertoire. The alpha chains of the TCRs employ three V alpha gene subfamilies (V alpha 11, V alpha 8, and V alpha 22) and four J alpha gene segments (J alpha 42, J alpha 24, J alpha 37, and J alpha 32). The V alpha 22 is a newly identified subfamily consisting of approximately four to six members, and exhibits a high degree of polymorphism among four mouse strains of distinct V alpha haplotypes. In addition, the beta chains of the TCRs employ three V beta gene subfamilies (V beta 8, V beta 1, and V beta 6), however the V beta 8.2 gene segment is preferentially utilized (58.3%). In contrast, the J beta gene segment usage is more heterogeneous. On the basis of the highly limited TCR-alpha/beta repertoire of the TCRs of the panel of bovine type II-specific T cell hybrid clones, a significant reduction (60%) of the incidence of arthritis in DBA/1Lac.J mice is accomplished by the use of anti-V beta 8.2 antibody therapy.
Amino Acid Sequence↗
Susceptibility for multiple sclerosis is determined, in part, by inheritance of a 175-kb region of the TcR V beta chain locus and HLA class II genes.
Genetic makeup thought to affect susceptibility to multiple sclerosis (MS) and current evidence suggests that multiple genes may be involved. We have mapped a potential susceptibility gene or genes in the germ-line T cell receptor (TcR) V beta region of multiple sclerosis (MS) patients. Six restriction fragment length polymorphisms (RFLPs) spanning approximately 600 kb of the TcR V beta region were used to define TcR haplotypes in 197 Caucasian controls and 83 Caucasian MS patients in the chronic progressive stage of the disease. The distribution of TcR subhaplotype frequencies was significantly different only in the approx. 175-kb region between RFLPs defined by V beta 8.1 and V beta 11. Stratification of the MS patients into HLA-DR2+ (n = 51) and HLA-DR2- (n = 32) populations demonstrated that the subhaplotype frequencies differed from the control population significantly only in the HLA-DR2+ (corrected P = 0.00007) and not in the HLA-Dr2- (corrected P = 0.46) population. Subhaplotypes which are rare in the normal population are overrepresented in the HLA-DR2+ MS patient population and confer a relative risk of 4.06. These results indicate the existence of an MS susceptibility gene within the TcR V beta region, and provide new evidence for gene complementation between a HLA class II gene and TcR V beta gene(s) in conferring susceptibility to MS.
Chromosome Mapping↗
Complexity of sea urchin embryo nuclear proteins that contain basic domains.
We describe a quantitative two-dimensional gel electrophoretic analysis of nuclear extract from 24-hr sea urchin embryos. The extract was fractionated by using a weak cation-exchange resin, and eight known DNA-binding proteins were shown to be entirely included in a salt eluate that releases proteins containing basic domains. This fraction and a lower-salt fraction containing the majority of the protein species were mapped two-dimensionally by using new algorithms that permit reproducible spot identification, storage of intensity and map-position data, and subtractive comparison of one pattern with respect to another. By reference to a previously characterized DNA-binding factor, spot intensity could be interpreted in terms of the number of molecules per embryo nucleus. A map was constructed displaying all nuclear proteins containing basic domains that are present within the concentration range per nucleus of a set of known DNA-binding factors of the sea urchin embryo. The map includes 265 spots that fulfill both of these criteria, probably representing about 100 different protein species.
Animals↗
Automated sequential affinity chromatography of sea urchin embryo DNA binding proteins.
An automated method of running a tandem sequence of oligonucleotide affinity columns was used to purify factors that interact specifically with cis-regulatory sites of the CyIIIa cytoskeletal actin gene of the sea urchin embryo (Strongylocentrotus purpuratus). The method allows quantitative enrichment in a single chromatographic run of up to 12 different sequence-specific DNA binding proteins, each of which may then be readily purified to homogeneity by methods such as preparative gel electrophoresis. The affinity chromatography and identification of six different CyIIIa-regulatory factors is described, and the general utility of the method is discussed.
Actins↗
Aspartylglycosaminuria in the Finnish population: identification of two point mutations in the heavy chain of glycoasparaginase.
Aspartylglycosaminuria is an inherited lysosomal storage disease caused by deficiency of glycoasparaginase (EC 3.5.1.26) and occurs with higher frequency among Finns than other populations. We have purified human glycoasparaginase and determined about 90% of the amino acid sequence of its light subunit and greater than 70% of that of its heavy subunit by Edman degradation and mass spectrometry. Additional sequence data were obtained from the cloning and subsequent nucleotide analysis of a cDNA corresponding to the normal human glycoasparaginase gene. The enzyme is encoded by a single mRNA as a single polypeptide that is posttranslationally processed to generate the subunits and is glycosylated. After preparing first-strand cDNA from leukocyte and fibroblast total RNA, we used the polymerase chain reaction to amplify the glycoasparaginase cDNA of eight Finnish aspartylglycosaminuria patients. We demonstrate that the Finnish patients' mRNA sequence differed from the normal sequence by two single-base changes six nucleotides apart from one another in the heavy chain of glycoasparaginase. The first change resulted in the replacement of arginine by glutamine (R161Q), whereas the second change resulted in a cysteine to serine substitution (C163S). Both mutations resulted in novel restriction endonuclease sites and were present in all eight Finnish aspartylglycosaminuria patients originating from different pedigrees, but they were absent from Finnish and non-Finnish controls and a non-Finnish case of aspartylglycosaminuria. These results indicate molecular homogeneity in aspartylglycosaminuria alleles in the Finnish population.
Amino Acid Sequence↗
Glycosaparaginase from human leukocytes. Inactivation and covalent modification with diazo-oxonorvaline.
The apparent active site of human leukocyte glycoasparaginase (N4-(beta-acetylglucosaminyl)-L-asparaginase EC 3.5.1.26) has been studied by labeling with an asparagine analogue, 5-diazo-4-oxo-L-norvaline. Glycoasparaginase was purified 4,600-fold from human leukocytes with an overall recovery of 12%. The purified enzyme has a Km of 110 microM, a Vmax of 34 mumol x l-1 x min-1, and a specific activity of 2.2 units/mg protein with N4-(beta-N-acetylglucosaminyl)-L-asparagine as substrate. The carbohydrate content of the enzyme is 15%, and it exhibits a broad pH maximum between 7 and 9. The 88-kDa native enzyme is composed of 19-kDa light (L) chains and 25-kDa heavy (H) chains and it has a heterotetrameric structure of L2H2-type. The glycoasparaginase activity decreases rapidly and irreversibly in the presence of 5-diazo-4-oxo-L-norvaline. At any one concentration of the compound, the inactivation of the enzyme is pseudo-first-order with time. The inhibitory constant, K1, is 80 microM and the second-order rate constant 1.25 x 10(3) M-1 min-1 at pH 7.5. The enzyme activity is competitively protected against this inactivation by its natural substrate, aspartylglucosamine, indicating that this inhibitor binds to the active site or very close to it. The covalent incorporation of [5-14C]diazo-4-oxo-L-norvaline paralleled the loss of the enzymatic activity and one inhibitor binding site was localized to each L-subunit of the heterotetrameric enzyme. Four peptides with the radioactive label were generated, purified by high performance liquid chromatography, and sequenced by Edman degradation. The sequences were overlapping and all contained the amino-terminal tripeptide of the L-chain. By mass spectrometry, the reacting group of 5-diazo-4-oxo-L-norvaline was characterized as 4-oxo-L-norvaline that was bound through an alpha-ketone ether linkage to the hydroxyl group of the amino-terminal amino acid threonine.
Amino Acid Sequence↗