The human T cell receptor (TCR) \u03b1/\u03b4 locus has been mapped and sequenced. This region occupies roughly one megabase (Mb) of DNA or equivalent to one three thousandth of the entire human genome, the longest continuous piece of human DNA yet sequenced. The sequence has provided new insights into the complex organization, structure and evolution of two intermingled multigene families (\u03b1 and \u03b4), and will hopefully in the future help answer interesting questions concerning the complex expression patterns of TCR \u03b1 and \u03b4 chains and about possible associations between specific polymorphisms in the TCR \u03b1/\u03b4 locus and susceptibility to autoimmune diseases. Comparison to cDNA data has provided information about expression of each of the TCR elements and about the striking diversification in the third hypervariable or junctional region. The sequence has contributed a glimpse of closely associated genomic DNA, in that the sequences surrounding the TCR locus, include the defender against death gene as well as five olfactory receptor genes. The sequence also harbors many other stretches of DNA, highly similar to previously identified genes, although in most cases, these have been found to be nonfunctional due to one or a few mutations. Comparison of 130 kilobases (kb) in the 3' region of the human sequence with its murine counterpart, suggests this region is highly conserved. The same 3' region has also been found to be limited in the concentration of genome wide repeats compared to the remainder of the locus. Furthermore, it contains a substantially reduced frequency of DNA variations compared to the rest of the locus. Apart from DNA variations in noncoding sequence, polymorphisms have also been identified in the coding regions of the TCR variable (V) gene segments, where, if they lead to amino acid changes, may alter the function of the TCR.
\r\n\r\nDuring the physical clone mapping and sequencing, new strategies were tested using primarily bacterial artificial chromosome (BAC) clones. These clones proved to be much more reliable and stable than clones currently employed in the human genome project (e.g., cosmids and yeast artificial chromosomes, YACs). BAC inserts can be sequenced completely by the high redundancy shotgun approach. Their insert size, stability, and capacity to be easily sequenced suggests that BAC clones are excellent mapping and sequencing reagents. The ends of BAC clone inserts can be sequenced directly. This has led to the proposal of a new strategy for obtaining the entire DNA sequence of the human genome without physical mapping.
", "doi": "10.7907/7x0h-qy95", "publication_date": "1996", "thesis_type": "phd", "thesis_year": "1996" }, { "id": "thesis:7352", "collection": "thesis", "collection_id": "7352", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:12262012-130125197", "primary_object_url": { "basename": "Meier_jt_1993.pdf", "content": "final", "filesize": 18944859, "license": "other", "mime_type": "application/pdf", "url": "/7352/1/Meier_jt_1993.pdf", "version": "v4.0.0" }, "type": "thesis", "title": "A Biological Arms Race: Site Specific DNA Recombination in Competing Immunofunctional Proteins", "author": [ { "family_name": "Meier", "given_name": "Joseph Thomas", "orcid": "0009-0005-2996-9768", "clpid": "Meier-Joseph-Thomas" } ], "thesis_advisor": [ { "family_name": "Hood", "given_name": "Leroy E.", "orcid": "0000-0001-7158-3678", "clpid": "Hood-L-E" } ], "thesis_committee": [ { "family_name": "Hood", "given_name": "Leroy E.", "orcid": "0000-0001-7158-3678", "clpid": "Hood-L-E" }, { "family_name": "Meyerowitz", "given_name": "Elliot M.", "orcid": "0000-0003-4798-5153", "clpid": "Meyerowitz-E-M" }, { "family_name": "Wold", "given_name": "Barbara J.", "orcid": "0000-0003-3235-8130", "clpid": "Wold-B-J" }, { "family_name": "Bjorkman", "given_name": "Pamela J.", "orcid": "0000-0002-2277-3990", "clpid": "Bjorkman-P-J" }, { "family_name": "Barbour", "given_name": "Alan G.", "orcid": "0000-0002-0719-5248", "clpid": "Barbour-A-G" } ], "local_group": [ { "literal": "div_biol" } ], "abstract": "This thesis is a compilation of inquiries into the molecular biology of two disparate\r\norganisms, each using site-specific recombination to generate diversity in and regulate the\r\nproduction of a protein. Coincidentally, each of these proteins functions in the context of the\r\nvertebrate immune system: one is the major defensive weapon of a eubacterial pathogen, and\r\nthe other the sine qua non of the system designed to recognize and destroy infectious agents, the\r\nantibody. The first section describes a series of experiments designed to explore the molecular\r\nbasis for antigenic variation in Borrelia hermsii, the eubacterial agent responsible for relapsing\r\nfever. A serotype 7 vmp gene fragment was cloned using mixed sequence oligonucleotide\r\nprobes derived from the sequencing of CNBr peptides from VMP 7. Use of this fragment in\r\nnorthern and southern blot experiments demonstrated that B. hermsii DNA sequences duplicate\r\nand rearrange, and that these duplications correlate with differential expression of VMPs (in a\r\npattern remarkably reminiscent of the trypanosomes). These striking results formed the basis\r\nfor several subsequent studies, which are also discussed. The final section details two separate\r\nprojects involving V(D)J recombination. Inital effort was directed at producing a non-lymphoid\r\ncell line capable of performing V(D)J recombination. Our strategy was based upon the ability of\r\nretroviruses to transcriptionally activate genes distant from the site of integration. Due to\r\nreports of the cloning of RAG-1 and -2, the project was discontinued, but not before producing\r\none line with an interesting phenotype. Following largely anecdotal reports of a previously\r\nunnoticed pattern of base addition during V(D)J recombination, we decided to perform a\r\nrigorous examination of the hypothesis, using both experiment and a detailed examination of\r\npublished data. While we were able to confirm the existence of palindromic, non-templated\r\nbases, our results contradicted other reports with regard to the origins and characteristics of\r\nthese inserts. Some surprises arose, most notably in the influence primary DNA sequence has\r\non the spectrum of product molecules; this adds a new dimension to a process previously\r\nthought to be well understood. 1his work represents the most thorough study of P nucleotide\r\naddition to date.", "doi": "10.7907/fd8q-cb34", "publication_date": "1993", "thesis_type": "phd", "thesis_year": "1993" }, { "id": "thesis:7340", "collection": "thesis", "collection_id": "7340", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:12182012-093217041", "primary_object_url": { "basename": "Hunkapiller_t_1993.pdf", "content": "final", "filesize": 95076367, "license": "other", "mime_type": "application/pdf", "url": "/7340/1/Hunkapiller_t_1993.pdf", "version": "v5.0.0" }, "type": "thesis", "title": "Diversity and Evolution of the Immunoglobulin Gene Superfamily", "author": [ { "family_name": "Hunkapiller", "given_name": "Tim", "clpid": "Hunkapiller-Tim" } ], "thesis_advisor": [ { "family_name": "Hood", "given_name": "Leroy E.", "orcid": "0000-0001-7158-3678", "clpid": "Hood-L-E" } ], "thesis_committee": [ { "family_name": "Hood", "given_name": "Leroy E.", "orcid": "0000-0001-7158-3678", "clpid": "Hood-L-E" }, { "family_name": "Strauss", "given_name": "James H.", "clpid": "Strauss-J-H" }, { "family_name": "Brokaw", "given_name": "Charles J.", "clpid": "Brokaw-C-J" }, { "family_name": "Davidson", "given_name": "Norman R.", "clpid": "Davidson-N-R" }, { "family_name": "Meyerowitz", "given_name": "Elliot M.", "orcid": "0000-0003-4798-5153", "clpid": "Meyerowitz-E-M" } ], "local_group": [ { "literal": "div_biol" } ], "abstract": "The Immunoglobulin Gene Superfamily is characterized by a common protein\r\nhomology unit that is present in arguably the largest and most diverse set of genes and\r\ngene families of any protein motif. This distribution indicates that the homology unit is\r\na remarkably versatile functional unit. Its central role in defining the complex\r\nphenotypes of the immune and nervous systems, likewise, is testament to the ability of\r\nthe motif to support an amazing and unique degree of diversification. Understanding\r\nmore about the function, structure and evolution of the Immunoglobulin Gene\r\nSuperfamily can provide insights into both the general issues of complex system\r\nevolution as well as the specific nature of the various systems the superfamily plays a\r\ncentral role in. This thesis is a collection of work aimed at a more thorough\r\nunderstanding of these elements. Particularly, these works summarize much of our\r\ncurrent understanding of the members of the Immunoglobulin Gene Superfamily along\r\nwith speculations on their evolutionary history as well as both the evolutionary and\r\nsomatic mechanisms responsible for their diversity. This work includes initial\r\ndescriptions of several features relevant to somatic diversification of rearranging\r\nimmune receptors, including: l) the role of joining imprecision in the generation of\r\njunctional diversity in immunoglobulin kappa chain; 2) the initial description of the T-cell\r\nbeta chain J/C locus; 3) the translation of T-cell beta chain D gene segments in all\r\nthree reading frames; 4) the occurrence of a cryptic rearrangement signal in most\r\nrearranging V families; 5) the first description of the mechanisms of class switching\r\nbetween heavy chain mu and delta genes; 6) the limited diversity of germline T-cell\r\nbeta chains; 7) the shared complementary determining region structure of T-cell beta\r\nchains and immunoglobulin heavy chains. Also, from these efforts, new members of\r\nthe superfamily have been identified including MHC class I molecules, L3T4 and\r\nMyelin Associated Glycoprotein. Various observations concerning the evolutionary\r\nrelationships of these molecules and motifs have been made. Particularly, a variation\r\non the basic homology unit motif has been proposed that probably more nearly\r\nrepresents the primordial sequence and function.
\r\n\r\nAs a result of these discoveries, a new, comprehensive picture of the\r\nimmunoglobulin superfamily is emerging that has implications for interpreting current\r\nfunctional relationships in the context of the evolutionary history of the members.\r\nParticularly, it is suggested from this work that the ability of the homology unit to\r\naccommodate diversity has made possible the evolution of the superfamily. Given the\r\ntremendous diversity within the superfamily, it might be assumed that selective\r\npressures favoring diversity have driven its evolution. However, much of the analysis\r\nwithin this collection suggests that, on the contrary, diversity is an inherent feature of\r\nthe conserved protein and gene structure of the homology unit and that it was the a\r\npriori diversity itself that drove and shaped the evolution of the complex systems that\r\nemploy the homology unit today. This basic diversity is the consequence of three\r\ncharacteristics of the homology unit. First, the tertiary structure of the protein motif is\r\nsuch that homology units tend to interact preferentially to form homo- or heterodimers,\r\nforming the basis of many of the receptors and the receptor/ligand interactions common\r\nwithin the superfamily. These combinatorial associations increase both the somatic and\r\nevolutionary potential for diversification. This can lead to the rather sudden\r\nappearance of new functional associations between existing members of the superfamily\r\npreadapted for otherwise unrelated functions. Second, except for a minimal number of\r\namino acid residues involved in critical intra- and interchain interactions, the primary\r\nstructure of these units can vary dramatically and still provide for essentially the same\r\ntertiary structure. This has been borne out by various crystallographic studies. The\r\nvariability is particularly true of the loop structures normally identified with antigen\r\nspecificity, but seen in other extended families as well. Reduced constraints on\r\nstructural sequences inherently promote the establishment of variation within\r\npopulations. Third, with very few exceptions the genes of the superfamily, the\r\nhomology units are not only encoded by discrete exons, but these exons have a shared\r\n1/2 splicing rule. That is, each is begun with the second 2 bases of a codon and ended\r\nwith the first base. This allows the in-frame splicing of any number of tandem\r\nhomology units, while maintaining functional protein domains. This rule generally\r\napplies to the non-homology unit exons of member genes as well. This allows, through\r\nrelatively simple genetic events, the development of new contexts for homology unit\r\nexpression, both by simple expansion and contraction of homology unit number and\r\nexon shuffling. This is probably at work, as well, in the frequent occurrence and\r\nutilization of alternative transcripts seen throughout the superfamily. Many of the\r\nrecognized occurrences of alternative splicing, such as that between membrane-bound\r\nand secreted forms, indicate that this gene structure provides for a further level of\r\nfunctional diversity and the expansion of the virtual genetic information.
\r\n\r\nBeyond the explicit discussion of the superfamily members, this work also\r\nspeaks to various issues of evolution in general. In particular, the history of the\r\nsuperfamily suggests the importance of canalization and non-gradual episodes of\r\nevolutionary change. It can contribute, as well, to the discussion of adaptive versus\r\nneutral change.
", "doi": "10.7907/mcbv-n026", "publication_date": "1993", "thesis_type": "phd", "thesis_year": "1993" }, { "id": "thesis:7391", "collection": "thesis", "collection_id": "7391", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:01102013-132313493", "type": "thesis", "title": "Transcriptional Regulation of T Cell Receptor Genes by a Novel CACCC Box Binding Protein", "author": [ { "family_name": "Wang", "given_name": "Yukang", "clpid": "Wang-Yukang" } ], "thesis_advisor": [ { "family_name": "Hood", "given_name": "Leroy E.", "orcid": "0000-0001-7158-3678", "clpid": "Hood-L-E" } ], "thesis_committee": [ { "family_name": "Hood", "given_name": "Leroy E.", "orcid": "0000-0001-7158-3678", "clpid": "Hood-L-E" }, { "family_name": "Wold", "given_name": "Barbara J.", "orcid": "0000-0003-3235-8130", "clpid": "Wold-B-J" }, { "family_name": "Zinn", "given_name": "Kai George", "orcid": "0000-0002-6706-5605", "clpid": "Zinn-K-G" }, { "family_name": "Parker", "given_name": "Carl Stevens", "orcid": "0000-0001-9795-4211", "clpid": "Parker-C-S" }, { "family_name": "Strauss", "given_name": "James H.", "clpid": "Strauss-J-H" } ], "local_group": [ { "literal": "div_biol" } ], "abstract": "The vertebrate immune response consists of humoral and cellular immune\r\nreactions, which are mediated mainly by immunoglobulins (Ig) and Tcell receptors (TCR)\r\nrespectively. The organization of Ig and TCR genes has been well established. Each of\r\nthe lg and TCR genes consists of multiple germ line gene segments that rearrange during\r\nlymphocyte development to generate diverse receptor structures expressed on mature B\r\nand T cells. The transcriptional regulation of Ig genes has been well studied. The\r\noctamer motif in the lg gene promoter or enhancer, the E-box and the KB site have been\r\nfunctionally characterized. The regulation of transcription factors that bind to these\r\nsites is well understood. The transcriptional regulation of TCR genes is not as well\r\nstudied as that of lg genes. TCR-\u03b1, -\u03b2, -\u03b3, -\u03b4 gene enhancers and a TCR \u03b1 gene\r\nsilencer have been reported. Some of the transcription factors that bind to these ciselements\r\nhave been cloned. A T cell-specific transcription factor, GATA-3, may play\r\nan important regulatory role on the expression of TCR genes in T cells. The promoters\r\nof TCR genes also have been investigated, however, the transcription factors that\r\ninteract with them have not been characterized. The aim of this thesis was to isolate\r\nand characterize transcription factors that function in TCR gene transcription.
\r\n\r\nA eDNA clone ht\u03b2, encoding a zinc finger protein that binds to the promoter\r\nregion of the human TCR gene V\u03b28.1, was cloned from a human peripheral blood T cell\r\nlibrary. The region of this protein containing four zinc fingers of the class Cys_2-X_(12)-\r\nHis_2 may be responsible for DNA binding to the TCR V\u03b28.1 promoter sequence\r\nGAAGTTGGGGGTGGTG. A putative transcriptional activation domain that is highly\r\nnegatively charged has also been found in ht\u03b2. Analysis of expression of ht\u03b2 mRNA\r\nreveales similar expression levels in Hela cells, Jurkat T cells, Ramos B cells and U -937\r\nmonocyte line. In addition to binding to the human TCR V\u03b28.1 promoter, ht\u03b2 also can\r\nbind to the mouse TCR gene \u03b1 silencer. The comparison of ht\u03b2 binding sites between\r\nthe human TCR V\u03b28.1 promoter and the mouse TCR gene \u03b1 silencer reveals a core\r\nsequence of the CACCC box. Gel-shift assay analysis of five repeats of the CACCC\r\nbox with bacterially expressed ht\u03b2 protein indicates that ht\u03b2 can bind to the CACCC\r\nbox. Gel-shift assays of the CACCC box with nuclear extracts from various cell lines\r\nreveal four common bands in T cell, B cell, monocyte and Hela cell lines, and one extra\r\nband in Hela cell extracts. CAT assay analysis indicates the CACCC box is essential for\r\nefficient transcription of the V\u03b28.l promoter. Cotransfection with a ht\u03b2 expression\r\nplasmid and a reporter plasmid show that ht\u03b2 can activate human TCR V\u03b28.1 gene\r\ntranscription. Ht\u03b2 also is able to counteract the silencing effect of the TCR \u03b1 silencer.\r\nHtl3 may have an interaction with the cAMP response element binding protein (CREB)\r\nto negatively regulate human V\u03b28.1 gene transcription in Hela cells, and that negative\r\neffect is not significant in Jurkat T cells. The CACCC box has been found in almost all\r\nV\u03b28 subfamily members (4 of 5 V\u03b28 members in human, and 2 of 3 V\u03b28 members in\r\nmouse), and both TCR \u03b1 and \u03b2 enhancers in human and mouse. These results suggest\r\nthat the CACCC box binding protein may have an important function in the immune\r\nsystem.
\r\n\r\nA murine zinc finger protein (M-zif) has been isolated and characterized. It has\r\nfour fingers in the zinc finger domain, the putative DNA binding domain. Also, a\r\nglutamine-rich region was found, which may be involved in transcriptional activation.\r\nA previously reported eDNA molecule was shown to contain in opposite orientatioins the\r\ncoding regions of both the interleukin-2 receptor \u03b1 (IL-2R\u03b1.) and M-zif genes. The\r\nresults presented here indicate that the cDNA is a chimeric molecule resulting from\r\ncloning artifact. The zinc finger domain of M-zif is highly homologous to that of ht\u03b2, a\r\nhuman T cell receptor V\u03b28.1 promoter binding protein. They may have a similar DNA\r\nbinding site. M-zif is not the mouse equivalent of ht\u03b2.
", "doi": "10.7907/x9cm-6a16", "publication_date": "1993", "thesis_type": "phd", "thesis_year": "1993" }, { "id": "thesis:6632", "collection": "thesis", "collection_id": "6632", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:08302011-103945566", "primary_object_url": { "basename": "Funkhouser_wk_1992.pdf", "content": "final", "filesize": 47915613, "license": "other", "mime_type": "application/pdf", "url": "/6632/1/Funkhouser_wk_1992.pdf", "version": "v5.0.0" }, "type": "thesis", "title": "Demyelinating autoimmunity: murine T cell epitopes of MBP and primate T cell receptor V\u03b2 variation", "author": [ { "family_name": "Funkhouser", "given_name": "William Keith Jr.", "clpid": "Funkhouser-William-Keith-Jr" } ], "thesis_advisor": [ { "family_name": "Wise", "given_name": "Mark B.", "orcid": "0000-0002-9125-801X", "clpid": "Wise-M-B" }, { "family_name": "Hood", "given_name": "Leroy E.", "orcid": "0000-0001-7158-3678", "clpid": "Hood-L-E" } ], "thesis_committee": [ { "family_name": "Hood", "given_name": "Leroy E.", "orcid": "0000-0001-7158-3678", "clpid": "Hood-L-E" }, { "family_name": "Bjorkman", "given_name": "Pamela J.", "orcid": "0000-0002-2277-3990", "clpid": "Bjorkman-P-J" }, { "family_name": "Davidson", "given_name": "Eric H.", "clpid": "Davidson-E-H" }, { "family_name": "Emr", "given_name": "Scott D.", "orcid": "0000-0002-5408-6781", "clpid": "Emr-S-D" }, { "family_name": "Rothenberg", "given_name": "Ellen V.", "orcid": "0000-0002-3901-347X", "clpid": "Rothenberg-E-V" }, { "family_name": "Wise", "given_name": "Mark B.", "orcid": "0000-0002-9125-801X", "clpid": "Wise-M-B" } ], "local_group": [ { "literal": "div_biol" } ], "abstract": "Autoimmune diseases result from inappropriate self-reactivity by lymphocytes. The long-term goal is to generate specific therapies for autoimmune diseases of humans, the success of which hinges on the definition of specific therapeutic targets. Experimental allergic encephalomyelitis (EAE) is a good animal model for the human demyelinating autoimmune disease, multiple sclerosis (MS). Risk for these diseases stratifies by major\r\nhistocompatibility complex (MHC) allele, as well as by T\r\ncell receptor (TCR) locus RFLP, in the case of MS. These\r\ndata suggest that (TCR-self peptide-MHC) complexes are\r\nassociated, possibly causally, with pathogenesis. This work\r\nfocused on the self peptide and TCR components of this\r\ncomplex. One specific aim was to document and characterize\r\nthe T cell epitopes of the autoantigen, myelin basic protein\r\n(MBP), in the EAE-susceptible mouse strain, B10.PL. Inbred\r\nB10.PL mice which were immunized with self MBP in complete\r\nFreund's adjuvant activated lymphocytes specific for\r\nepitopes estimated by peptides MBP(NAc1-20), MBP(31-50), and\r\nMBP(121-140). These mice generated the bulk of their immune\r\nresponse to the MBP(NAc1-20) epitope. The responses to self\r\nMBP immunization of B10.PL wildtype and MBP null \"shiverer\"\r\nmice were compared, and it was found that MBP(12I-140) is\r\ntolerogenic in animals which express MBP. A similar result\r\nwas observed in BALB/c wildtype and shiverer mice. These\r\ndata demonstrate that MBP is not a sequestered antigen, that\r\nmultiple epitopes tolerize T cells independently, and that\r\nincomplete, rather than absent, tolerance is present in mice\r\nsusceptible to EAE. A second specific aim was to document\r\nthe degree of variation in the primate TCR V\u03b2 8 subfamily,\r\nthree members of which are adjacent to a BamHI RFLP\r\nrestriction site linked to multiple sclerosis (MS) disease\r\nrisk. V\u03b2 8.1 and 8.2 were compared in a number of primates.\r\nIt was found that the overall coding sequences, but not the\r\nCDR coding sequences, were conserved compared with adjacent\r\nnon-coding flanking sequences. CDR coding sequences were\r\nnot demonstrably positively selected compared with noncoding\r\nflanking sequences or with synonymous coding sequences. A comparison of unrelated normal humans failed to demonstrate any non-synonymous Substitutions within V\u03b2 8.1 and 8.2, and demonstrated a single non-synonymous Substitution in V\u03b2 8.3. These data demonstrate that germline V\u03b2 8 gene segments are conserved and minimally polymorphic, implying that final TCR protein diversity derives from other mechanisms. Occasional allelism has been demonstrated in other V\u03b2 subfamilies, and our data does not rule out that certain TCR V\u03b2 alleles may ultimately be found to contribute to autoimmunity disease risk.\r\n", "doi": "10.7907/kmkw-9619", "publication_date": "1992", "thesis_type": "phd", "thesis_year": "1992" }, { "id": "thesis:6682", "collection": "thesis", "collection_id": "6682", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:09212011-131628448", "primary_object_url": { "basename": "Vernooij_btm_1992.pdf", "content": "final", "filesize": 5391320, "license": "other", "mime_type": "application/pdf", "url": "/6682/1/Vernooij_btm_1992.pdf", "version": "v4.0.0" }, "type": "thesis", "title": "The Mouse T Cell Receptor Gamma Genes", "author": [ { "family_name": "Vernooij", "given_name": "Bernardus Theodorus Maria", "clpid": "Vernooij-Bernardus-Theodorus-Maria" } ], "thesis_advisor": [ { "family_name": "Hood", "given_name": "Leroy E.", "orcid": "0000-0001-7158-3678", "clpid": "Hood-L-E" } ], "thesis_committee": [ { "family_name": "Hood", "given_name": "Leroy E.", "orcid": "0000-0001-7158-3678", "clpid": "Hood-L-E" }, { "family_name": "Rothenberg", "given_name": "Ellen V.", "orcid": "0000-0002-3901-347X", "clpid": "Rothenberg-E-V" }, { "family_name": "Simon", "given_name": "Melvin I.", "clpid": "Simon-M-I" }, { "family_name": "Meyerowitz", "given_name": "Elliot M.", "orcid": "0000-0003-4798-5153", "clpid": "Meyerowitz-E-M" }, { "family_name": "Bjorkman", "given_name": "Pamela J.", "orcid": "0000-0002-2277-3990", "clpid": "Bjorkman-P-J" } ], "local_group": [ { "literal": "div_biol" } ], "abstract": "Murine T cells express either of 2 antigen receptors on\r\ntheir surface: \u03b1\u03b2 or \u03b3\u03b4 T cell receptors. The \u03b3\u03b4 T cell\r\npopulation contains subsets which show tissue specific\r\nlocalization, invariant T cell receptors and/or specificity\r\nfor stress antigens. This makes these T cells unlike \u03b1\u03b2 T\r\ncells.
\r\n\r\nThis thesis describes the genomic organization of the entire mouse T cell receptor gamma locus. It contains 4 clusters of gene segments, each with a C, a J and 1 to 4 V gene segments. Compared to other T cell receptor and\r\nimmunoglobulin loci, this is an unusual organization. The\r\nC\u03b32 cluster is in an orientation that is opposite to that of\r\nall other clusters.
\r\n\r\nTwo new \u03b3 enhancer-like elements were identified in the\r\nlocus. Also shown is that the hinge region of C\u03b34 is encoded\r\nby at least 2 exons. This is similar to the gene\r\norganization of the human C\u03b32 gene segment, and different\r\nfrom the other mouse and human C\u03b3 gene segments.\r\nSequence comparison of the T cell receptor \u03b3 gene segments\r\nof various mammals reveals structural conservation during\r\nevolution. The C region is most conserved, except in the\r\nhinge region. This subdomain is variable in length and in\r\nsequence. The extracellular domain is well conserved and\r\ncontains amino acid residues which are also conserved in the\r\nother T cell receptor and immunoglobulin proteins.
\r\n\r\nThe V\u03b3 gene segments are less well conserved, but several\r\namino acid residues are found which are (nearly) invariant.\r\nDuring evolution, the 2 studied mammals each appear to have\r\nlost certain V gene segments relative to a hypothetical\r\nancestor.
\r\n", "doi": "10.7907/wnmy-rm49", "publication_date": "1992", "thesis_type": "phd", "thesis_year": "1992" }, { "id": "thesis:2573", "collection": "thesis", "collection_id": "2573", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-06132007-074646", "type": "thesis", "title": "Analysis of Expression, Structure and Evolution of Non-Classical Class I Major Histocompatibility Complex Genes", "author": [ { "family_name": "Brorson", "given_name": "Kurt Andrew", "clpid": "Brorson-Kurt-Andrew" } ], "thesis_advisor": [ { "family_name": "Hood", "given_name": "Leroy E.", "orcid": "0000-0001-7158-3678", "clpid": "Hood-L-E" } ], "thesis_committee": [ { "family_name": "Hood", "given_name": "Leroy E.", "orcid": "0000-0001-7158-3678", "clpid": "Hood-L-E" }, { "family_name": "Anderson", "given_name": "David J.", "orcid": "0000-0001-6175-3872", "clpid": "Anderson-D-J" }, { "family_name": "Rothenberg", "given_name": "Ellen V.", "orcid": "0000-0002-3901-347X", "clpid": "Rothenberg-E-V" }, { "family_name": "Attardi", "given_name": "Giuseppe", "clpid": "Attardi-G" }, { "family_name": "Owen", "given_name": "Ray David", "clpid": "Owen-R-D" } ], "local_group": [ { "literal": "div_biol" } ], "abstract": "Class I major histocompatibility molecules (MHC) are 45 kilodalton (kD) glycoproteins that associate with a smaller 12 kD polypeptide, \u03b2\u2082-microglobulin. In the BALB/c mouse, there are three classical class I molecules, H-2K\u1d48, D\u1d48, and L\u1d48, which are expressed throughout the body and present viral antigens to cytotoxic T lymphocytes (CTLs). In addition to the genes that encode the three classical class I antigens, the BALB/c genome contains 32 genes that structurally resemble the classical class I genes, and therefore possibly encode class I molecules. A few of the non-classical class I genes have been shown to encode molecules, TL, Qa-1, Qa-2, Q10, Qb-1, and Hmt, which are expressed in a generally tissue-specific manner, and probably do not act as restriction elements. However, it is unclear what function these molecules play, or why such a large gene family is maintained if only three viral antigen-presenting restriction elements are required by the murine immune system.
\r\n\r\nDNA sequences were obtained from each of the 35 class I genes of the BALB/c mouse of the transmembrane domain-encoding fifth exon. Based on nucleotide sequence similarity, the fifth exons could be divided into seven groups that share little similarity with each other. In addition, the majority of the fifth exons are able to encode a transmembrane domain that can be separated into a proline-rich connecting peptide, a hydrophobic transmembrane segment, and a ctyoplasmic portion that includes basic anchoring residues. Since this conservation occurs in spite of extensive variation of nucleotide sequence in these exons, it is likely that selective pressure exists to maintain a functional structure in the majority of class I genes.
\r\n\r\nA cDNA library was constructed from a thymus from a five-week-old BALB/c mouse. From this library, 69 class I cDNA transcripts from 15 different class I genes were isolated and analyzed. Included were three novel transcripts from Tla subregion genes, the T9\u1d9c, T17\u1d9c, and T18\u1d9c genes. Sequence analysis of these clones reveals that the T9\u1d9c gene is probably a pseudogene, while the T18\u1d9c gene has an open reading frame in at least exons 2, 3, 4, and 5. A fourth cDNA clone was a transcript from the Thy19.4 gene, a gene that had not been previously isolated on a recombinant DNA clone. The isolation of transcripts from such a relatively large number of genes suggests that the number of expressed and perhaps functionally important class I genes may be larger than previously believed, and that expression of class I recognition structures may be important for cell-cell interactions within the thymus.
\r\n\r\nTo further pursue the characterization of the Thy19.4 gene, a genomic clone containing this gene was isolated from a size-selected insert library, and the DNA sequence of the Thy19.4 gene was obtained. The Thy19.4 gene contains an open reading frame, and in several aspects resembles the genes that encode the transplantation antigens. These similarities include a shared exon/intron structure and shared amino acid sequence motifs. In addition, PCR amplification experiments using tissue cDNA demonstrates that the Thy19.4 gene is expressed in a variety of tissues. However, unlike the classical transplantation antigens, the Thy19.4 gene maps distal to the H-2 region, in the Hmt region.
\r\n\r\nThese studies have demonstrated that class I gene transcription is more extensive than previously believed. Some of the expressed genes, like the T18\u1d9c and Thy19.4 genes, appear to be able to encode class I molecules which may share structural characteristics with the classical transplantation antigens and may possibly serve as recognition structures in cell-cell interaction events. In addition, examination of the transmembrane domain exon of each of the 35 class I genes suggests that some selective constraint is acting on the majority of members of this family of genes, thus raising the possibility that many of the nonclassical class I genes encode functionally important products.
", "doi": "10.7907/5NHE-7929", "publication_date": "1990", "thesis_type": "phd", "thesis_year": "1990" }, { "id": "thesis:2500", "collection": "thesis", "collection_id": "2500", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-06072007-082551", "type": "thesis", "title": "Analysis of the Structure, Expression and Evolution of the Shark Myelin Proteins and Genes", "author": [ { "family_name": "Fors", "given_name": "Lance", "clpid": "Fors-Lance" } ], "thesis_advisor": [ { "family_name": "Hood", "given_name": "Leroy E.", "orcid": "0000-0001-7158-3678", "clpid": "Hood-L-E" } ], "thesis_committee": [ { "family_name": "Hood", "given_name": "Leroy E.", "orcid": "0000-0001-7158-3678", "clpid": "Hood-L-E" }, { "family_name": "Wold", "given_name": "Barbara J.", "orcid": "0000-0003-3235-8130", "clpid": "Wold-B-J" }, { "family_name": "Rothenberg", "given_name": "Ellen V.", "orcid": "0000-0002-3901-347X", "clpid": "Rothenberg-E-V" }, { "family_name": "Tanouye", "given_name": "Mark", "clpid": "Tanouye-M" }, { "family_name": "Emr", "given_name": "Scott D.", "orcid": "0000-0002-5408-6781", "clpid": "Emr-S-D" } ], "local_group": [ { "literal": "div_biol" } ], "abstract": "Myelin is a compacted multilamellar membrane which encases axons to provide electrical insulation and facilitates the rapid transmission of nerve impulses. The major myelin structural proteins produced by oligodendrocyctes in the central nervous system (CNS) of mammals are proteolipid protein (PLP) and myelin basic protein (MBP). In contrast, the major myelin structural proteins produced by the Schwann cells in the peripheral nervous system (PNS) of mammals are protein zero (Po) and MBP. Sharks (class Chondrichthyes) are the oldest living vertebrates that have a concentric multilamellar \"mammalian-like\" myelin structure around axons. In addition to this structural similarity, the shark and mammalian myelin proteins appeared to be distantly related biochemically and immunologically even though they diverged from each other about 400 million years ago. Logically those regions in the shared proteins, genes and promoters which are most similar between sharks and mammals are likely to be functionally important to both. Therefore by analyzing these elements in shark myelin and comparing them to what is already known about mammalian myelin we could learn about shark myelin, its evolution and what regions are essential for the proper function and expression of mammalian myelin. This thesis contains an analysis of the structure, expression and evolution of the shark myelin proteins and genes.
\r\n\r\nThe first chapter (Saavedra, R., Fors, L., Aebersold, R., Arden, B., Horvath, S., Sanders, J., and Hood, L. J. Mol. Evol. 29:149) describes the isolation and sequencing of the two major shark CNS proteins Po and MBP and their corresponding cDNAs. This study shows that the myelin proteins of the shark brain are similar to the myelin proteins of the mammalian peripheral nervous system in both primary and secondary structures.
\r\n\r\nThe second chapter (Fors, L., Saavedra, R., and Hood, L. Nuc. Acids Res., Submitted) contains a novel genomic walking technique that was developed to clone the shark Po and MBP promoters. Using this technique it was possible to clone approximately 400 nucleotides immediately upstream of the shark Po and MBP transcription initiation sites. This genomic walking technique will be generally useful for cloning promoters or other sequences of interest without the need for constructing or screening genomic libraries.
\r\n\r\nThe third chapter presents and discusses the similarity between these shark Po and MBP promoters, the JC virus enhancer (which directs tissue-specific expression in oligodendrocytes), and the mouse Po and MBP promoters. The implications of these findings on nervous system specific and CNS vs. PNS specific gene expression are discussed.
\r\n\r\nLastly, the appendix describes the current status of Shiverer transgenic mouse experiments in which constructs bearing the shark MBP gene are injected into mouse eggs. These transgenic experiments are testing if the structural similarity between shark and mammalian MBPs translates into any measurable functional similarity in vivo.
", "doi": "10.7907/840h-0p67", "publication_date": "1990", "thesis_type": "phd", "thesis_year": "1990" }, { "id": "thesis:332", "collection": "thesis", "collection_id": "332", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-01252005-085241", "type": "thesis", "title": "Regulation of Class I Genes by Interferons", "author": [ { "family_name": "Korber", "given_name": "Bette Tina Marie", "orcid": "0000-0002-2026-5757", "clpid": "Korber-Bette-Tina-Marie" } ], "thesis_advisor": [ { "family_name": "Hood", "given_name": "Leroy E.", "orcid": "0000-0001-7158-3678", "clpid": "Hood-L-E" } ], "thesis_committee": [ { "family_name": "Davidson", "given_name": "Norman R.", "clpid": "Davidson-N-R" }, { "family_name": "Campbell", "given_name": "Judith L.", "orcid": "0000-0001-8291-5551", "clpid": "Campbell-J-L" }, { "family_name": "Chan", "given_name": "Sunney I.", "orcid": "0000-0002-5348-2723", "clpid": "Chan-S-I" }, { "family_name": "Hood", "given_name": "Leroy E.", "orcid": "0000-0001-7158-3678", "clpid": "Hood-L-E" } ], "local_group": [ { "literal": "Caltech Distinguished Alumni Award" }, { "literal": "div_chem" } ], "abstract": "Major histocompatibility (MHC) class I gene expression is increased in response to interferons. In order to identify critical regulatory regions in mouse MHC (H-2) class I genes, the 5' flanking region and the DNA downstream of the transcription initiation site were analyzed separately. The promoters of H-2Dd and H-2Ld were linked to the reporter gene chloramphenicol acetyl transferase (CAT). Conversely, the H-2Ld structural gene was linked to non-interferon regulated promoters. These constructs were transfected into several different cell lines, and their ability to respond to interferons was assessed. Both regions, 5' and 3' of the transcriptional initiation site, were able to independently contribute to the regulation of class I genes by interferons. The basal levels of expression, interferon inducibility. and the relative contributions of the 3' and 5' responses to overall interferon regulation, were cell-type dependent.
\r\n\r\nSequence analysis of the 5' flanking region of class I genes led to the identification of multiple DNA motifs that are highly homologous to regulatory elements found in other genes. The H-2Dd promoter contains a TATA bog, CAAT elements, enhancer regions, and an interferon consensus sequence that is found in the promoters of many genes that are regulated by interferons. Deletion analysis and expression studies of the H-2Dd promoter revealed several interesting regulatory features of the interferon consensus sequence. It was required for both type I (alpha and beta) and type II interferon (gamma) responses. In some cell types an additional sequence was required for a type I interferon response; this sequence is located 5' and adjacent to the interferon consensus sequence. Type II interferon action was independent of this upstream sequence in all cell-types tested. Therefore the promoter controlled response to interferons is complex and the nature of the response depends both on the type of interferon and the cell-type being tested.
\r\n\r\nWe have noted that an interferon consensus sequence homology exists in the promoters of interferon genes. As interferons have a capacity to be auto-regulatory, we propose a model of gene regulation by interferons that incorporates what our studies and others have shown about the regulation of class I genes by interferon, and what is known about the regulation of interferon genes themselves.
\r\n", "doi": "10.7907/FWT2-VC76", "publication_date": "1988", "thesis_type": "phd", "thesis_year": "1988" }, { "id": "thesis:11862", "collection": "thesis", "collection_id": "11862", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:10252019-115550207", "type": "thesis", "title": "Organization and Evolution of the Class I Genes in the Murine Major Histocompatibility Complex", "author": [ { "family_name": "Sun", "given_name": "Yi Henry", "orcid": "0000-0001-8279-5270", "clpid": "Sun-Yi-Henry" } ], "thesis_advisor": [ { "family_name": "Hood", "given_name": "Leroy E.", "orcid": "0000-0001-7158-3678", "clpid": "Hood-L-E" } ], "thesis_committee": [ { "family_name": "Hood", "given_name": "Leroy E.", "orcid": "0000-0001-7158-3678", "clpid": "Hood-L-E" }, { "family_name": "Simon", "given_name": "Melvin I.", "clpid": "Simon-M-I" }, { "family_name": "Meyerowitz", "given_name": "Elliot M.", "orcid": "0000-0003-4798-5153", "clpid": "Meyerowitz-E-M" }, { "family_name": "Davidson", "given_name": "Norman R.", "clpid": "Davidson-N-R" }, { "family_name": "Rothenberg", "given_name": "Ellen V.", "orcid": "0000-0002-3901-347X", "clpid": "Rothenberg-E-V" } ], "local_group": [ { "literal": "div_biol" } ], "abstract": "This thesis contains studies of the organization and evolution of the class I gene family in the murine major histocompatibility complex (the H-2 complex).
\r\n\r\nThe first chapter presents the molecular characterization of the H-2dm1 mutation. The mutant gene is shown to be formed by the fusion of the 5' part of the Dd gene and the 3' part of the Ld gene, with the region in between deleted.
\r\n\r\nChapter Two describes the results of chromosome walking experiments and presents a molecular map of 500 kb of cloned DNA, which links the H-2D and Q\u03b1 regions and contains five D region and eight Q\u03b1 region class I genes.
\r\n\r\nChapter Three presents the DNA sequences of the transmembrane exon from 20 class I genes, and the use of 23 low copy-number flanking-region probes to detect homology between the regions containing each gene. The sequence comparison and the hybridization patterns indicate that multiple recombinational events, notably gene duplication and gene conversion, have occurred during the evolution of this large gene family.
\r\n\r\nChapter Four presents a rapid method of restriction site mapping of cosmids and plasmids. The method was developed due to the need of mapping a large number of clones during the course of this study.
", "doi": "10.7907/qfw5-kk48", "publication_date": "1986", "thesis_type": "phd", "thesis_year": "1986" }, { "id": "thesis:11810", "collection": "thesis", "collection_id": "11810", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:10102019-163948204", "type": "thesis", "title": "Class I Genes of the Major Histocompatibility Complex: Structural Studies on Genes of the Tla Locus", "author": [ { "family_name": "Fisher", "given_name": "Douglas Arthur", "clpid": "Fisher-Douglas-Arthur" } ], "thesis_advisor": [ { "family_name": "Hood", "given_name": "Leroy E.", "orcid": "0000-0001-7158-3678", "clpid": "Hood-L-E" } ], "thesis_committee": [ { "family_name": "Hood", "given_name": "Leroy E.", "orcid": "0000-0001-7158-3678", "clpid": "Hood-L-E" }, { "family_name": "Rothenberg", "given_name": "Ellen V.", "orcid": "0000-0002-3901-347X", "clpid": "Rothenberg-E-V" }, { "family_name": "Davidson", "given_name": "Norman R.", "clpid": "Davidson-N-R" }, { "family_name": "Wold", "given_name": "Barbara J.", "orcid": "0000-0003-3235-8130", "clpid": "Wold-B-J" } ], "local_group": [ { "literal": "div_biol" } ], "abstract": "This thesis contains investigations into the structure of molecules encoded within the mouse major histocompatibility complex. The first chapter [Steinmetz, M., J. G. Frelinger, D. Fisher, T. Hunkapiller, D. Pereira, S. M. Weissman, S. G. Nathenson, and L. Hood, Cell 24: 125] describes the isolation and characterization of the first cDNA clones encoding murine transplantation (H-2) antigens. This study showed that H-2 antigens contain DNA and protein sequences related to immunoglobulin (Ig) molecules, but that the similarity does not include the great somatic diversity characteristic of Ig molecules.
\r\n\r\nThe second chapter contains methods for cloning and sequencing in M13 bacteriophage vectors. Included is a novel method of generating overlapping subclones for DNA sequencing by making a family of deletions in a DNA insert cloned in M13.
\r\n\r\nIn the third chapter [Fisher, D. A., S. W. Hunt, and L. Hood J. Exp. Med. 162: 528], the complete structure of a gene encoding a serologically defined thymus leukemia (TL) antigen is elucidated. TL antigen is encoded in a gene, gene Tl3c, closely related to H-2 antigens, and appears to have undergone a gene conversion event with an H-2 gene. Tla-specific probes subcloned from T13C enabled us to examine the organization of the eighteen cross hybridizing class I genes of the Tla region.
\r\n\r\nThe last chapter contains the sequence of another gene, gene T1C, previously identified as encoding TL antigen. However, the T1C gene is a non-functional pseudogene, and was probably mis-identified. There is an apparent site of recombination in the T1C gene that occurs precisely at a B2 Alu repeat sequence.
", "doi": "10.7907/ymba-8s86", "publication_date": "1986", "thesis_type": "phd", "thesis_year": "1986" }, { "id": "thesis:11858", "collection": "thesis", "collection_id": "11858", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:10242019-102816056", "type": "thesis", "title": "Antigen Receptors on Lymphocytes", "author": [ { "family_name": "Siu", "given_name": "Gerald", "clpid": "Siu-Gerald" } ], "thesis_advisor": [ { "family_name": "Hood", "given_name": "Leroy E.", "orcid": "0000-0001-7158-3678", "clpid": "Hood-L-E" } ], "thesis_committee": [ { "family_name": "Davidson", "given_name": "Norman R.", "clpid": "Davidson-N-R" }, { "family_name": "Hood", "given_name": "Leroy E.", "orcid": "0000-0001-7158-3678", "clpid": "Hood-L-E" }, { "family_name": "Dervan", "given_name": "Peter B.", "orcid": "0000-0001-8852-7306", "clpid": "Dervan-P-B" }, { "family_name": "Meyerowitz", "given_name": "Elliot M.", "orcid": "0000-0003-4798-5153", "clpid": "Meyerowitz-E-M" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "The structure and evolution of a small VH gene family called the T15 family was analyzed. It was determined that although selection pressure appeared to be operating to maintain the coding region sequence of these VH gene segments, these gene segments were diverging from one another very rapidly. Sequences were identified in the 5' flanking region that were conserved between all VH gene segments and were hypothesized to be important for immunoglobulin heavy-chain gene transcription. Related sequences were identified in immunoglobulin VL gene segment and histone H2B 5' flanking regions, implying coordinate expression between these genes and the immunoglobulin heavy chain genes.
\r\n\r\nThe structure, organization, evolution, and the generation of diversity in the genes encoding the T-cell antigen receptor were analyzed. The T-cell antigen receptor consists of two chains, referred to as the \u03b1 and \u03b2 chains. Each chain consists of two regions, a variable region and a constant region, that are encoded by two different genes. The gene that encodes the variable region of the \u03b2 chain was found to consist of three gene segments, denoted V\u03b2, D\u03b2, and J\u03b2. The V\u03b2 gene segment encodes the first 280-300 bp, the D\u03b2 gene segment encodes the next 10-15 bp, and the J\u03b2 gene segment encodes the final 50 bp of the variable region gene. The rearrangement event that juxtaposes these gene segments during lymphocyte differentiation appears to be mediated by the same recognition signals that mediate immunoglobulin V gene rearrangement.
\r\n\r\nDiversity was found to be generated in at least three different manners in the V\u03b2 gene. Combinatorial joining permits the rearrangement of different V, D and J gene segments to each other to provide different V gene sequences. Deletion of nucleotides from the ends of the germline gene segments and the random addition of nucleotides at the junction of the rearrangement event are two other mechanisms for generating diversity. A comparison of a rearranged V gene with the corresponding germline gene segments showed that with the exception of the junctions, the sequences were identical. Therefore, there is no evidence that somatic hypermutation, the random addition of point mutations to the V gene during late stages of B lymphocyte differentiation, is utilized by the T-cell antigen receptor as it is by immunoglobulins.
\r\n\r\nThe initial stage of V\u03b2 gene formation was found to be the rearrangement of the D\u03b2 gene segment to the J\u03b2 gene segment. Both germ line D\u03b2 gene segments appear to have promoters in the 5' flanking regions that can often result in the transcription of a 1.0 kb mRNA containing D\u03b2-J\u03b2-C\u03b2 sequences after D\u03b2-J\u03b2 rearrangement. This 1.0 kb mRNA message is present at a high level in the thymus but at lower levels in the spleen, lymph nodes, and in mature T cells, implying that this message or a protein product encoded by this message may be important in T cell ontogeny.
\r\n\r\nAnalysis of the protein sequences of the variable regions of the \u03b1 and \u03b2 chains revealed conserved amino acids that are found in all variable region genes. Many of these amino acids were found to be important for V domain structure in immunoglobulins and may be important for the structure of the V\u03b1-V\u03b2 domain as well. In addition, analyses of the \u03b2-strand forming potential and the relative hydrophobicity of the side chains of the amino acids that make up the T-cell antigen receptor variable regions have indicated that these properties are very similar to those of the immunoglobulin variable regions. These analyses indicate that the immunoglobulin and T-cell receptor antigen-binding regions may be very similar in structure to each other.
", "doi": "10.7907/p1zd-zh51", "publication_date": "1986", "thesis_type": "phd", "thesis_year": "1986" }, { "id": "thesis:11415", "collection": "thesis", "collection_id": "11415", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:03012019-111236038", "primary_object_url": { "basename": "Winoto_A_1986.pdf", "content": "final", "filesize": 52440411, "license": "other", "mime_type": "application/pdf", "url": "/11415/1/Winoto_A_1986.pdf", "version": "v4.0.0" }, "type": "thesis", "title": "Structure and Function of the Murine T-Cell Receptor Genes and the Murine Class I Genes of the Major Histocompatability Complex", "author": [ { "family_name": "Winoto", "given_name": "Astar", "orcid": "0000-0003-4363-4591", "clpid": "Winoto-Astar" } ], "thesis_advisor": [ { "family_name": "Hood", "given_name": "Leroy E.", "orcid": "0000-0001-7158-3678", "clpid": "Hood-L-E" } ], "thesis_committee": [ { "family_name": "Hood", "given_name": "Leroy E.", "orcid": "0000-0001-7158-3678", "clpid": "Hood-L-E" } ], "local_group": [ { "literal": "div_biol" } ], "abstract": "This thesis can be divided into three parts: Chapter Two and Chapter Three contain study on the class I genes of the major histocompatibility complex (MHC), Chapter Four and Chapter Five contain study on the T-cell receptor genes, and the appendices deal with my initial attempt to clone the eDNA encoding the T-cell receptor \u03b1 chain and various other research projects that I have been involved in to some extent (mouse MHC class II genes, PDGF genes and rat class I and class II genes).
\r\n\r\nThe first part of my thesis describes the study of the organization of the genes encoding the mouse class I MHC molecule. 54 cosmid clones containing 36 class I genes were isolated and, by restriction enzyme mapping, the 54 clones could be divided into 13 clusters. Using low-copy probes isolated from each cosmid cluster and the restriction enzyme site polymorphism of those probes, I was able to map each of the class I gene clusters into the precise location of the mouse MHC. Surprisingly, most of the class I genes map into the Tla region, only five class I genes (three cosmid clusters) map into the classical H-2 region. The functions of these class I genes in the Tla region are still largely unknown.
\r\n\r\nThe remainder of my thesis contains the study on the T-cell receptor genes. In an effort to isolate the cDNA clone encoding the T-cell receptor \u03b1 chain, I have isolated 64 T\u2013cell specific cDNA clones, using a T-cell minus B-cell subtractive cDNA probe. The T-cell receptor \u03b1 and \u03b2 chain cDNA clones were among these 64 clones. Using the T-cell receptor \u03b1 chain cDNA as a probe, I subsequently isolated clones encoding a germline variable(V) gene segment and cosmid clones spanning 120 kb of DNA encoding the joining(J) and constant(C) gene segments of the T-cell receptor \u03b1 chain. Analysis of these clones, including sequencing of one germline V\u03b1 and six germline J\u03b1 gene segments, showed that the DNA recognition sequence for the \u03b1 chain DNA rearrangment is similar to that of the \u03b2 chain counterpart. In contrast to the general J gene segment organization in the \u03b2 chain, \u03b3 chain and the immunoglobulin gene families, I showed that the 18 J\u03b1 gene segments I analyzed were spread over 60 kb of DNA and lay as far as 63 kb 5' to the C\u03b1 gene.
\r\n\r\nIn a step to dissect the structure function relationship of the T-cell receptor molecules, I have cloned and determined the nucleotide sequences of seven functional \u03b1 chains and six \u03b2 chains of the T-cell receptor genes from nine T-helper hybridomas specific for the C-terminal peptide of pigeon cytochrome c and the E class II molecule. Northern blot analyses using the isolated V\u03b1 and V\u03b2 gene segments were performed on the RNAs isolated from a total of 15 T\u2013helper hybridomas specific for the C-terminal peptide of cytochrome c. A single V\u03b1 gene segment is predominantly used in these 15 T-helper hybridomas, whereas at least five different V\u03b2 gene segments are utilized. I conclude that the V\u03b1 gene segment mis important for the cytochrome c response and might provide most of the contact residues with the C-terminal region of cytochrome c. I also found that the junctional sequences of the \u03b2 chain may alter the antigen fine specificity of the T-cell clones. Finally, somatic hypermutation does not appear to play a crucial role in generating diversity for the T-cell receptor \u03b1 or \u03b2 chains.
", "doi": "10.7907/gmnb-h561", "publication_date": "1986", "thesis_type": "phd", "thesis_year": "1986" }, { "id": "thesis:11374", "collection": "thesis", "collection_id": "11374", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:01312019-165301208", "type": "thesis", "title": "Studies of Class I Genes in the Major Histocompatibility Complex of the BALB/c Mouse", "author": [ { "family_name": "Sher", "given_name": "Beverly Taylor", "clpid": "Sher-Beverly-Taylor" } ], "thesis_advisor": [ { "family_name": "Hood", "given_name": "Leroy E.", "orcid": "0000-0001-7158-3678", "clpid": "Hood-L-E" } ], "thesis_committee": [ { "family_name": "Davidson", "given_name": "Norman R.", "clpid": "Davidson-N-R" }, { "family_name": "Lewis", "given_name": "Edward B.", "clpid": "Lewis-E-B" }, { "family_name": "Owen", "given_name": "Ray David", "clpid": "Owen-R-D" }, { "family_name": "Meyerowitz", "given_name": "Elliot M.", "orcid": "0000-0003-4798-5153", "clpid": "Meyerowitz-E-M" }, { "family_name": "Hood", "given_name": "Leroy E.", "orcid": "0000-0001-7158-3678", "clpid": "Hood-L-E" } ], "local_group": [ { "literal": "div_biol" } ], "abstract": "This thesis contains the results of investigations into the structure and organization of Class I genes in the major histocompatibility complex of the BALB/c mouse.
\r\n\r\nIn the body of the thesis, the sequence of the BALB/c H-2Dd transplantation antigen gene is presented. This is the first complete sequence of an H-2Dd gene and is the only genomic sequence to be in full agreement with the available protein sequence. The H-2Dd gene sequence has been used to predict the protein sequence of the H-2Dd molecule, which has been compared to the protein sequences of other Class I molecules. The H-2Dd protein sequence is no more related to that of its closely linked partner, H-2Ld, than it is to the sequence of its presumptive allele, H-2Db, or to the sequence of the H-2Kb molecule, which is from not only another H-2 haplotype but another genetic subregion. The sequence differences between these transplantation antigens are spread throughout the molecules in a mosaic pattern that may have arisen,in part, from small gene conversion events. No obvious evidence of any recent gene conversion event affecting the H-2Dd gene was observed, however.
\r\n\r\nThree Class I genes have been cloned and mapped to the H-2D subregion in BALB/c. These include gene 16.1, whose product has not been identified; the H-2Dd gene; and the H-2Ld gene. There is serological evidence for the existence of additional H-2D-encoded transplantation antigen molecules in BALB/c, but no genes encoding these products have been identified. The sequence of the H-2Dd gene contains potential alternative splice sites in and around the exon encoding the first external domain. use of these splice sites could generate a transplantation antigen molecule with different serological determinants, and might help to resolve the discrepancy between the number of H-2D-subregion Class I genes and the number of serologically defined H-2D-subregion transplantation antigens.
\r\n\r\nThe appendices contain the results of a number of studies related to Class I gene organization and function. Appendix A contains the sequence of gene 27.1. This gene, also known as the Q8 gene, was identified as a Qa pseudogene based on the presence of termination codons in inappropriate locations in its sequence. Appendix B contains the sequence of the H-2Ld gene, which was the first transplantation antigen gene to be sequenced. Appendix C contains the results of DNA-mediated gene transfer experiments that Identified genomic clones containing the H-2Kd, H-2Ld, and H-2Dd transplantation antigen genes as well as Class I genes encoding the Qa2,3 molecule and two different TL differentiation antigen genes. Appendix D contains the results of calculations of protein sequence homology between different Class I molecules.
", "doi": "10.7907/4pj0-z147", "publication_date": "1985", "thesis_type": "phd", "thesis_year": "1985" }, { "id": "thesis:11361", "collection": "thesis", "collection_id": "11361", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:01242019-174640334", "primary_object_url": { "basename": "Livant_DL_1985.pdf", "content": "final", "filesize": 36438786, "license": "other", "mime_type": "application/pdf", "url": "/11361/1/Livant_DL_1985.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "The Size of a Murine Heavy Chain Variable Region Gene Family: Implications for the Magnitude and Evolution of the V\u2095 Locus in Mouse", "author": [ { "family_name": "Livant", "given_name": "Donna Lucy", "orcid": "0000-0002-6164-6580", "clpid": "Livant-Donna-Lucy" } ], "thesis_advisor": [ { "family_name": "Hood", "given_name": "Leroy E.", "orcid": "0000-0001-7158-3678", "clpid": "Hood-L-E" } ], "thesis_committee": [ { "family_name": "Hood", "given_name": "Leroy E.", "orcid": "0000-0001-7158-3678", "clpid": "Hood-L-E" }, { "family_name": "Davidson", "given_name": "Eric H.", "clpid": "Davidson-E-H" }, { "family_name": "Davidson", "given_name": "Norman R.", "clpid": "Davidson-N-R" }, { "family_name": "Lewis", "given_name": "Edward B.", "clpid": "Lewis-E-B" }, { "family_name": "Owen", "given_name": "Ray David", "clpid": "Owen-R-D" } ], "local_group": [ { "literal": "div_biol" } ], "abstract": "The problem of how much antibody diversity is encoded in the germline as variable region genes has long been of interest to immunologists. We have measured the size of the J558 VH family in the BALB/c mouse by a probe excess titration method, and found that the family contains approximately 1000 members. As a control for systematic error, we used the same method to measure the number of class I MHC genes in BALB/c. We found that the third domain of the class I Dd gene detects 36-40 class I genes. Dot blots and genome blots with copy number controls give results consistent with a J558 family size of 500-1000 VH genes. We note that each band evident on genomic blots of DNA from several mouse strains contains multiple VH genes, and that a significant fraction of these bands are polymorphic among the mouse strains tested. We discuss the implications of this result for both the size and evolution of the VH locus in mouse.
", "doi": "10.7907/22vp-vt51", "publication_date": "1985", "thesis_type": "phd", "thesis_year": "1985" }, { "id": "thesis:11375", "collection": "thesis", "collection_id": "11375", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:01312019-172314851", "type": "thesis", "title": "The Genes for Myelin Basic Protein in Normal and Shiverer Mutant Mice", "author": [ { "family_name": "Roach", "given_name": "Arthur Henry", "clpid": "Roach-Arthur-Henry" } ], "thesis_advisor": [ { "family_name": "Hood", "given_name": "Leroy E.", "orcid": "0000-0001-7158-3678", "clpid": "Hood-L-E" }, { "family_name": "Strumwasser", "given_name": "Felix", "clpid": "Strumwasser-F" } ], "thesis_committee": [ { "family_name": "Davidson", "given_name": "Eric H.", "clpid": "Davidson-E-H" }, { "family_name": "Kennedy", "given_name": "Mary B.", "orcid": "0000-0003-1369-0525", "clpid": "Kennedy-M-B" }, { "family_name": "Patterson", "given_name": "Paul H.", "clpid": "Patterson-P-H" }, { "family_name": "Wold", "given_name": "Barbara J.", "orcid": "0000-0003-3235-8130", "clpid": "Wold-B-J" }, { "family_name": "Hood", "given_name": "Leroy E.", "orcid": "0000-0001-7158-3678", "clpid": "Hood-L-E" }, { "family_name": "Strumwasser", "given_name": "Felix", "clpid": "Strumwasser-F" } ], "local_group": [ { "literal": "div_biol" } ], "abstract": "A cDNA library was constructed from the brains of 18 day old rats, and was screened with a synthetic DNA probe to yield clones representing myelin basic protein (MBP). One 1.9 kb clone was sequenced and found to encode the 14 kd MBP. Using this clone as a hybridization probe, cosmid clones from a library of wild type mouse DNA were selected and characterized. One clone was shown to carry five exons which encode 14 kd MBP, distributed over a 32 kb region. A sixth exon was detected with a synthetic DNA probe, and was found to encode the 41 amino acids which distinguish 18.5 kd from 14 kd MBP. The 5' end ot the gene was mapped with S1 nuclease protection and primer extension experiments to a position 47 bp 5' of the initator codon for MBP synthesis. It was shown that the gene cloned is probably the only MBP gene in the mouse genome.
\r\n\r\nCloned DNAs were used to analyze the MBP gene and its expression in the myelin deficient mutant mouse shiverer. It was shown that a deletion has removed five out of six MBP exons, leaving only the 5'-most exon and 13 kb of the first intervening sequence. The deletion completely prevents expression of normal 2.1 kb MBP mRNAs, but a 16-fold lower number of transcripts are observed which initiate correctly at the 5' end of the first exon, are not correctly spliced, and are rarely polyadenylated. If translated, they would direct synthesis of a 61 amino acid peptide containing the first 56 amino acids of MBP. The MBP gene was mapped to mouse chromosome 18 by hybridization of MBP probes with DNA from Chinese hamster-mouse hybrid cell lines, showing it to be linked to the shiverer mutation. It is proposed that the partial deletion of the MBP gene is the primary lesion of the shiverer mutation.
", "doi": "10.7907/4d7s-zs52", "publication_date": "1985", "thesis_type": "phd", "thesis_year": "1985" }, { "id": "thesis:11826", "collection": "thesis", "collection_id": "11826", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:10182019-143201215", "type": "thesis", "title": "Gene Expression in B and T Lymphocytes: (1) Evolution of Rat C\u03ba Alleles (2) The T-cell Receptor Problem", "author": [ { "family_name": "Kronenberg", "given_name": "Mitchell", "orcid": "0000-0001-6318-6445", "clpid": "Kronenberg-Mitchell" } ], "thesis_advisor": [ { "family_name": "Hood", "given_name": "Leroy E.", "orcid": "0000-0001-7158-3678", "clpid": "Hood-L-E" } ], "thesis_committee": [ { "family_name": "Hood", "given_name": "Leroy E.", "orcid": "0000-0001-7158-3678", "clpid": "Hood-L-E" }, { "family_name": "Attardi", "given_name": "Giuseppe", "clpid": "Attardi-G" }, { "family_name": "Davidson", "given_name": "Norman R.", "clpid": "Davidson-N-R" }, { "family_name": "Owen", "given_name": "Ray David", "clpid": "Owen-R-D" }, { "family_name": "Rothenberg", "given_name": "Ellen V.", "orcid": "0000-0002-3901-347X", "clpid": "Rothenberg-E-V" } ], "local_group": [ { "literal": "div_biol" } ], "abstract": "The amino acid sequence of the two kappa chain constant region allotypes found in inbred rat strains indicated that these alleles are very different and therefore may have had an unusual evolutionary history. To understand the evolution of these genes, serologic tests were performed to determine if inbred rats express latent or unexpected C\u03ba alleles. They apparently do not do so. Wild Norway rats were tested, and it was found that the laboratory strains do not represent a subset of the rat C\u03ba polymorphism. Further tests indicated that only one of the two serologic specificities could be found in related rodent species.
\r\n\r\nThe structure of the T cell antigen-binding receptor is a major controversial issue in immunology. It has been asserted that the T cell antigen-receptor is homologous to immunoglobulins, and one popular theory contends that VH genes are responsible for the specificity of the receptor. We tested these theories by hybridizing immunoglobulin DNA probes to RNA and DNA from cloned T cells. First, we determined that the C\u03bb, J\u03ba, C\u03ba, JH, C\u00b5 and C\u03b1 genes and the sequences involved in heavy chain class switching are not rearranged in a T helper, a cytotoxic T cell and a T lymphoma. These cells also do not transcribe C\u03ba, C\u03bb, JH, C\u00b5 and C\u03b1 RNA. Second, a cDNA clone encoding heavy chain variable region characteristic of most B cells which respond to the antigen GAT was isolated and sequenced. Poly(A)+ RNA was prepared from 12 cloned T lymphocytes specific for GAT. While six of these T cells display antigenic determinants present on immunoglobulins that bind GAT, none of them contained a transcript homologous to the cDNA probe. Finally, using a random primer, large cDNA libraries (105-106 colonies) were constructed from three T-cell hybridomas. These libraries were screened by two separate, well-characterized methods which should permit the detection of all or most VH gene segments. No VH cDNA colonies were found by these methods. Therefore immunoglobulin gene segments are not likely to be part of the T cell antigen receptor.
\r\n\r\nThe I-J serologic specificity has been reported to be present on T cell-derived antigen-binding molecules. Cosmid clones have been previously obtained containing all the sequences between the I-A and I-E subregions of the murine major histocompatibility complex, where I-J has been genetically mapped. The putative I-J DNA does not, however, hybridize to RNA from I-J positive suppressor T cells. Also, suppressor T lymphocytes do not rearrange this DNA. Therefore the I-J coding sequences must map elsewhere.
", "doi": "10.7907/p24z-a733", "publication_date": "1983", "thesis_type": "phd", "thesis_year": "1983" }, { "id": "thesis:11783", "collection": "thesis", "collection_id": "11783", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:08302019-152439482", "primary_object_url": { "basename": "Crews_ST_1983.pdf", "content": "final", "filesize": 42807254, "license": "other", "mime_type": "application/pdf", "url": "/11783/1/Crews_ST_1983.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "The Structure of Mammalian Genes: (1) Antibody Heavy Chain Variable Region Genes: Organization, Diversity, and Somatic Mutation. (2) Structure and Transcription of the DNA Encompassing the Origin of Replication of Human Mitochondrial DNA", "author": [ { "family_name": "Crews", "given_name": "Stephen Thomas", "orcid": "0000-0002-1432-401X", "clpid": "Crews-Stephen-Thomas" } ], "thesis_advisor": [ { "family_name": "Hood", "given_name": "Leroy E.", "orcid": "0000-0001-7158-3678", "clpid": "Hood-L-E" } ], "thesis_committee": [ { "family_name": "Attardi", "given_name": "Giuseppe", "clpid": "Attardi-G" }, { "family_name": "Davidson", "given_name": "Norman R.", "clpid": "Davidson-N-R" }, { "family_name": "Owen", "given_name": "Ray David", "clpid": "Owen-R-D" }, { "family_name": "Strauss", "given_name": "James H.", "clpid": "Strauss-J-H" }, { "family_name": "Hood", "given_name": "Leroy E.", "orcid": "0000-0001-7158-3678", "clpid": "Hood-L-E" } ], "local_group": [ { "literal": "div_biol" } ], "abstract": "This thesis describes two experimental systems utilized to study mammalian gene structure and expression: (1) antibody heavy chain variable region genes and (2) mitochondrial DNA.
\r\n\r\nIn order to study the organization and structure of antibody genes and the relative germline and somatic contributions towards antibody diversity, we have analyzed the germline genes encoding the murine immune response to phosphorylcholine. Molecular cloning studies were undertaken and conclusively show that there is only one germline VH gene segment encoding the immune response to phosphorylcholine. Protein sequencing work on monoclonal antibodies that bind phosphorylcholine reveals many different protein sequences related to one predominant sequence. We are able to conclude that these variant sequences are the result of somatic diversification operating on one germline gene segment. We are further able to show that this diversification is mutational and not recombinational. Finally, somatic mutation is correlated with the class of the antibody; IgG and IgA antibodies undergo somatic mutation, IgM antibodies do not.
\r\n\r\nWe have isolated and sequenced a family of four closely related VH gene segments designated V1, V3, V11 and V13. Their function varies: V1 encodes the immune response to phosphorylcholine, V3 is a pseudogene, V11 encodes the immune response to influenza hemagglutinin, and V13 has an unknown function but is not obviously a pseudogene. Structural analysis of recombinant clones containing this family of related VH gene segments and other VH gene segments reveals several important points about the organization of VH gene segments. First, closely related VH gene segments can be clustered together within the VH gene locus. Second, the spacing distance between adjacent VH gene segments is variable; it may be as short as 5 kb and greater than 30 kb. Finally, the average spacing distance between VH gene segments is large, at least 23 kb. Assuming a minimum of 200 germline VH gene segments, the size of the VH gene locus may be greater than 5 million base pairs.
\r\n\r\nThe human mitochondrial genome is the second system that has been chosen to study gene structure and expression, and to accomplish this, we have applied both DNA and RNA sequencing technologies. We sequenced the DNA encompassing the origin of DNA replication and then localized the origin at the nucleotide level. The human mitochondrial origin of DNA replication shares structural characteristics with other known origins of DNA replication; in particular, the presence of extensive secondary structure in the form of a stem-loop structure. In order to precisely localize mitochondrial transcripts to the DNA, we developed techniques that allowed the isolation and sequencing of the 5'-ends of mitochondrial transcripts. This technology was utilized to precisely localize the 5'-end of the mitocohndrial 12S rRNA species 457 nucleotide pairs 5'-to the origin of DNA replication. Analysis of the DNA sequence in this region revealed a phenylalanine tRNA gene whose 3'-end was joined end-to-end with the 5'-end of the 12S rRNA. This analysis first demonstrated the extreme enconomy of genetic material in mammalian mitochondrial DNA.
", "doi": "10.7907/4dgr-za66", "publication_date": "1983", "thesis_type": "phd", "thesis_year": "1983" }, { "id": "thesis:11787", "collection": "thesis", "collection_id": "11787", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:09032019-120820356", "primary_object_url": { "basename": "Ellison_JW_1983.pdf", "content": "final", "filesize": 37939184, "license": "other", "mime_type": "application/pdf", "url": "/11787/1/Ellison_JW_1983.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "Structure and Evolution of Human Immunoglobulin C\u03b3 Genes", "author": [ { "family_name": "Ellison", "given_name": "Jay William", "clpid": "Ellison-Jay-William" } ], "thesis_advisor": [ { "family_name": "Hood", "given_name": "Leroy E.", "orcid": "0000-0001-7158-3678", "clpid": "Hood-L-E" } ], "thesis_committee": [ { "family_name": "Hood", "given_name": "Leroy E.", "orcid": "0000-0001-7158-3678", "clpid": "Hood-L-E" }, { "family_name": "Davidson", "given_name": "Eric H.", "clpid": "Davidson-E-H" }, { "family_name": "Davidson", "given_name": "Norman R.", "clpid": "Davidson-N-R" }, { "family_name": "Lazarides", "given_name": "Elias", "clpid": "Lazarides-E" }, { "family_name": "Meyerowitz", "given_name": "Elliot M.", "orcid": "0000-0003-4798-5153", "clpid": "Meyerowitz-E-M" } ], "local_group": [ { "literal": "div_biol" } ], "abstract": "In order to learn about the evolution of the human immunoglobulin C\u03b3 gene family, the structural features of individual C\u03b3 genes were examined. The complete nucleotide sequences were determined for three members of the gene family-the C\u03b31, C\u03b32, and C\u03b34 genes. A comparison of these sequences with those of the three reported mouse C\u03b3 genes (C\u03b31, C\u03b32a, C\u03b32b) fails to reveal any pairs of corresponding genes in the two species. Moreover, the sequence homology shared by human C\u03b3 genes in both coding and noncoding regions (about 95%) is significantly greater than that seen within the mouse C\u03b3 family (about 70-80%). The presumably neutral mutations accumulated in the noncoding regions of the human genes have been used to estimate that approximately 6-8 million years have elapsed since the divergence of these genes from a common ancestral sequence. This divergence is considerably more recent than inferred for the mouse C\u03b3 genes, and suggests that gene duplication or gene correction events have occurred more recently in humans than in mice.
\r\n\r\nIn contrast to the CH domain exons and adjacent noncoding regions, the hinge exons of human C\u03b3 genes are quite divergent both in length and sequence. This coding sequence variability is seen to extend into the regions of CH domains which border the hinge in the polypeptide chain. This divergence is interpreted as being the result of natural selection for particular hinge structures in the IgG subclasses. The implication is that these polypeptide regions are important for immunologic effector functions carried out by IgG molecules.
\r\n\r\nThe arrangement of the C\u03b32 and C\u03b34 genes in human chromosomal DNA has been determined to be 5'-C\u03b32-17 kilobase pairs-C\u03b34-3'. The genetic processes generating hybrid IgG molecules from these two genes are discussed, along with the relationship of these processes to gene duplication and gene correction.
", "doi": "10.7907/9crt-qq78", "publication_date": "1983", "thesis_type": "phd", "thesis_year": "1983" }, { "id": "thesis:1544", "collection": "thesis", "collection_id": "1544", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-04292005-082735", "type": "thesis", "title": "Programmed DNA Rearrangements During Differentiation: Immunoglobulin Class Switching", "author": [ { "family_name": "Davis", "given_name": "Mark Morris", "orcid": "0000-0001-6868-657X", "clpid": "Davis-Mark-Morris" } ], "thesis_advisor": [ { "family_name": "Hood", "given_name": "Leroy E.", "orcid": "0000-0001-7158-3678", "clpid": "Hood-L-E" }, { "family_name": "Lewis", "given_name": "Edward B.", "clpid": "Lewis-E-B" } ], "thesis_committee": [ { "family_name": "Hood", "given_name": "Leroy E.", "orcid": "0000-0001-7158-3678", "clpid": "Hood-L-E" }, { "family_name": "Lewis", "given_name": "Edward B.", "clpid": "Lewis-E-B" }, { "family_name": "Davidson", "given_name": "Eric H.", "clpid": "Davidson-E-H" }, { "family_name": "Delbruck", "given_name": "Max", "clpid": "Delbr\u00fcck-M" }, { "family_name": "Davidson", "given_name": "Norman R.", "clpid": "Davidson-N-R" }, { "family_name": "Maniatis", "given_name": "Thomas P.", "clpid": "Maniatis-T-P" } ], "local_group": [ { "literal": "Caltech Distinguished Alumni Award" }, { "literal": "div_biol" } ], "abstract": "The events of B-lymphocyte differentiation can be reconstructed in part\r\nthrough an analysis of the organization of heavy-chain genes isolated from B-cell\r\ntumors (myelomas). A mouse immunoglobulin alpha heavy-chain gene is shown to be\r\ncomposed of at least three non-contiguous segments of germline DNA -- a VH gene\r\nsegment, a JH gene segment adjacent to the C\u03bc coding region, and a C\u03b1 gene\r\nsegment. These gene segments are joined together by two distinct types of DNA\r\nrearrangements: variable region formation and immunoglobulin class switching.\r\nThree examples of IgM \u2192 IgA elass switching were examined and in each case a\r\ndifferent site adjacent to C\u03bc and a different site adjacent to C\u03b1 were joined together\r\nin the process of switching. Two of the three C\u03bc sites shared significant homology to\r\neach other (15/25 nucleotides) and all three of C\u03b1 sites were highly homologous (22/30\r\nnucleotides). We believe these sequences serve as recognition sites for class\r\nswitching. Furthermore, the lack of homology between the C\u03b1 consensus sequence\r\nand sequences reported for C\u03b31 and c\u03b32b recombination sites suggests that this\r\nprocess is mediated by class-specific recognition sequences and, presumably, class-specific\r\nregulatory mechanisms. A number of predictions and possible explanations of\r\nimmune phenomena result from this observation. Apparently nonproductive DNA\r\nrearrangements, occurring in the same tumor lines, seem also to utilize some of the\r\n_same regulatory apparati. In addition, it appears that in one example, MClOl, class\r\nswitching has progressed from C\u03bc \u2192 C\u03b1 \u2192 C\u03b31. This switching pathway presents\r\ndifficulties for the simple deletional model of CH switching.", "doi": "10.7907/KFJS-G857", "publication_date": "1981", "thesis_type": "phd", "thesis_year": "1981" }, { "id": "thesis:10117", "collection": "thesis", "collection_id": "10117", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:03292017-102353875", "primary_object_url": { "basename": "Schilling_JW_1981.pdf", "content": "final", "filesize": 37440046, "license": "other", "mime_type": "application/pdf", "url": "/10117/1/Schilling_JW_1981.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "Antibody Diversity", "author": [ { "family_name": "Schilling", "given_name": "James Walter, Jr.", "clpid": "Schilling-James-Walter" } ], "thesis_advisor": [ { "family_name": "Hood", "given_name": "Leroy E.", "orcid": "0000-0001-7158-3678", "clpid": "Hood-L-E" } ], "thesis_committee": [ { "family_name": "Unknown", "given_name": "Unknown" } ], "local_group": [ { "literal": "div_biol" } ], "abstract": "Vertebrate organisms possess a large and diverse repertoire of\r\nantibody variable regions. A number of different genetic mechanisms\r\nhave been proposed to account for immunoglobulin variable (V) region\r\ndiversity, including multiple germline genes, somatic mutation,\r\nsomatic recombination, and multiple small gene segments which are\r\njoined to form a complete variable region gene segment. Analyses of\r\nvariable region amino acid sequences demonstrate the relative contribution\r\nof each of these mechanisms to antibody diversity.
\r\n\r\n\r\nTwenty-four VK21 chains have been examined. They suggest that the\r\nkappa chain variable region is encoded in two separate gene segments:\r\nVK and JK which are rearranged and joined during B cell differentiation.\r\nDiversification of the N terminus of the JK segment occurs as a consequence of VK-JK joining and has been explained by a site-specific\r\nrecombination model. The amino acid sequence data are consistent with\r\nthe existence of a minimum of six VK and five JK germline gene segments.\r\nPossible cases of somatic mutation are also observed. These conclusions\r\nare supported by nucleic acid sequence analyses performed by\r\nothers.
\r\n\r\n\r\nComplete variable region amino acid sequences have been determined\r\nfor twenty-one heavy chains from dextran binding antibodies. These\r\nsequences suggest that the heavy chain variable region is encoded by\r\nthree gene segments: VH, D, and JH. Nucleic acid sequence analyses\r\nare consistent with this conclusion. The existence of a minimum of\r\ntwo VH and four JH germline gene segments is suggested by these\r\nsequences. Possible examples of somatic mutation of VH and JH gene\r\nsegments have also been found. Diversification of the N-terminal residue\r\nof the JH segment may occur as a consequence of D-JH joining by a\r\nmechanism analogous to that observed in kappa chains. Although comprised\r\nof only two residues, the D segment is the most diverse portion\r\nof dextran binding heavy chains.
\r\n\r\n\r\nCombinatorial joining of VK and JK gene segments and VH, D, and\r\nJH gene segments contributes significantly to antibody diversity.
\r\n\r\n\r\nPrecise molecular locations of idiotypic determinants can be\r\nestablished in the dextran heavy chains. A cross-reactive idiotypic\r\ndeterminant (IdX) is located in the second hypervariable region of the\r\nVH segment. Individual idiotypic determinants (IdIs) correspond to\r\nparticular D segments.
\r\n\r\n\r\n\r\n\r\n", "doi": "10.7907/npny-et15", "publication_date": "1981", "thesis_type": "phd", "thesis_year": "1981" }, { "id": "thesis:10862", "collection": "thesis", "collection_id": "10862", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:05082018-140634895", "primary_object_url": { "basename": "Johnson_ND_1981.pdf", "content": "final", "filesize": 70033992, "license": "other", "mime_type": "application/pdf", "url": "/10862/1/Johnson_ND_1981.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "An Analysis of Patterns of Diversity in Antibodies with Defined Specificity", "author": [ { "family_name": "Johnson", "given_name": "Nelson Daniell", "clpid": "Johnson-Nelson-Daniell" } ], "thesis_advisor": [ { "family_name": "Hood", "given_name": "Leroy E.", "orcid": "0000-0001-7158-3678", "clpid": "Hood-L-E" } ], "thesis_committee": [ { "family_name": "Hood", "given_name": "Leroy E.", "orcid": "0000-0001-7158-3678", "clpid": "Hood-L-E" }, { "family_name": "Owen", "given_name": "Ray David", "clpid": "Owen-R-D" }, { "family_name": "Richards", "given_name": "John H.", "clpid": "Richards-J-H" }, { "family_name": "Attardi", "given_name": "Giuseppe", "clpid": "Attardi-G" }, { "family_name": "Maniatis", "given_name": "Thomas P.", "clpid": "Maniatis-T-P" } ], "local_group": [ { "literal": "div_biol" } ], "abstract": "Antibodies can recognize a large number of molecular determinants (antigens) because of the diversity present in antibody combining sites. This diversity resides in regions of extensive amino acid variability termed variable (V) regions. Variable region diversity is encoded in multiple germline variable region genes and can also arise from somatic modification of these genes. An important class of somatic modifications is the rearrangement of gene segments to form complete variable region genes. In this way complete VL genes arise from the joining of VL and JL gene segments while VH genes arise from VH, D, and JH gene segment joining.
\r\n\r\nStudies of the V region protein sequences of hybridoma and myeloma immunoglobulins which bind phosphorylcholine show that IgM antibody V regions are considerably less diverse than IgG and IgA V regions. A comparison of protein sequence data with experiments on germline DNA suggests that at least some V segment diversity in IgG and IgA antibodies is the result of somatic mutations. D segments from phosphorylcholine-binding IgM antibodies as well as from IgG and IgA antibodies show extensive amino acid interchanges and size differences. In addition, diversity in the antibody response to phosphorylcholine is generated by associating a single VH region with at least two different VL regions.
\r\n\r\nThe complete sequences of the V L and V H regions from two antibodies binding \u03b2 (2 \u2192 1) levan have also been determined. A comparison of these sequences to protein sequence data from other \u03b2 (2 \u2192 1)) levan-binding proteins and to a germline DNA sequence suggests that the levan-binding proteins may arise from multiple germline genes differing at the protein level by only a few amino acids. Unlike the D segments of the phosphorylcholine binding proteins, the levan-binding immunoglobulin D segments show very little diversity. In addition, the protein sequences of levan-binding immunoglobulins can be compared to published V region idiotype and antigen binding studies. These comparisons show that idiotypes may focus on certain sections of antibody V regions, and hence be of limited value as a probe of antibody V region fine structure.
", "doi": "10.7907/1wj1-r628", "publication_date": "1981", "thesis_type": "phd", "thesis_year": "1981" }, { "id": "thesis:17545", "collection": "thesis", "collection_id": "17545", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:07232025-144534720", "type": "thesis", "title": "Structure and Function of Murine Immunoglobulin M from Serum and Cell Membrane", "author": [ { "family_name": "Kehry", "given_name": "Marilyn Rose", "clpid": "Kehry-Marilyn-Rose" } ], "thesis_advisor": [ { "family_name": "Hood", "given_name": "Leroy E.", "orcid": "0000-0001-7158-3678", "clpid": "Hood-L-E" } ], "thesis_committee": [ { "family_name": "Unknown", "given_name": "Unknown" } ], "local_group": [ { "literal": "div_biol" } ], "abstract": "Immunoglobulin M (IgM) molecules are secreted into the bloodstream by\r\nplasma cells as soluble pentamers and also exist as monomeric integral membrane\r\nreceptor proteins on the surface of B lymphocytes. Investigation of the structure\r\nof membrane and secreted \u03bc chains has provided an understanding of the basis\r\nfor the existence of IgM molecules in two very different physical environments.
\r\n\r\nThe complete amino acid sequence of a \u03bc chain secreted by the murine\r\nmyeloma MOPC 104E has been determined. When the \u03bc chains of mouse, human\r\nand dog are compared, there is a striking gradient of increasing amino acid sequence\r\nhomology from the NH2-terminus to the COOR-terminus of the \u03bc chain, reflecting\r\na functional conservation of structure. There are five sites of carbohydrate attachment\r\nin the mouse \u03bc chain constant region, one of which is present 14 residues from\r\nthe carboxyterminus. The secreted \u03bc chain (\u03bcs) contains no stretches of unchanged\r\namino acids long enough to allow it to exist as an integral membrane protein.
\r\n\r\nIgM molecules synthesized by the murine B lymphoma, WEHI 279, have\r\nbeen characterized. The cells synthesize internal precursors to secreted \u03bc chains\r\nwhich contain incompletely glycosylated complex carbohydrate moieties but in\r\nall other respects are identical to secreted \u03bc chains. WEHI 279 membrane IgM\r\nis monomeric and contains mature complex carbohydrate structures. The \u03bcm\r\nand \u03bcs chains differ in the structure of their COOR-terminal regions. The carbos\r\nhydrate moiety and methionine residue present in the COOR-terminal 19 amino\r\nacids of \u03bcs chains are absent in \u03bcm chains. In addition, four COOR-terminal amino\r\nacids which are different from the carboxyterminus of \u03bcs chains are released by\r\ncarboxypeptidase treatment of \u03bcm chains. Based on these protein and other\r\nnucleic acid data, we believe \u03bcm chains possess an uncharged and hydrophobic\r\nC-membrane terminal domain which allows monomeric IgM molecules to be\r\nintegral receptor proteins in the B cell plasma membrane.
", "doi": "10.7907/nyc2-gv40", "publication_date": "1980", "thesis_type": "phd", "thesis_year": "1980" }, { "id": "thesis:18475", "collection": "thesis", "collection_id": "18475", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:04062026-221212098", "primary_object_url": { "basename": "Early_PW_1980.pdf", "content": "final", "filesize": 31573311, "license": "other", "mime_type": "application/pdf", "url": "/18475/1/Early_PW_1980.pdf", "version": "v2.0.0" }, "type": "thesis", "title": "Mouse Immunoglobulin Heavy Chain Gene Organization and Rearrangement: Genetic Bases for Antibody Diversity and Regulated Expression", "author": [ { "family_name": "Early", "given_name": "Philip Warren", "clpid": "Early-Philip-Warren" } ], "thesis_advisor": [ { "family_name": "Davidson", "given_name": "Norman R.", "clpid": "Davidson-N-R" }, { "family_name": "Hood", "given_name": "Leroy E.", "orcid": "0000-0001-7158-3678", "clpid": "Hood-L-E" } ], "thesis_committee": [ { "family_name": "Unknown", "given_name": "Unknown" } ], "local_group": [ { "literal": "div_biol" } ], "abstract": "Immunoglobulin heavy chains each display one of a wide range of diverse antigenbinding\r\nvariable regions. At least one class of immunoglobulin, IgM, contains heavy chains\r\nwhich exist as two forms, either bound to the outside of a cell membrane or linked by\r\ndisulfide bonds in secreted antibodies. I have used recombinant DNA techniques to isolate\r\nand determine the nucleotide sequences of genes encoding mouse immunoglobulin heavy\r\nchains. This has enabled me to examine genetic bases for the diversity of heavy chain\r\nvariable regions and for the synthesis of membrane-bound and secreted forms of IgM\r\nheavy chains.
\r\n\r\nI found that genes encoding heavy chain variable regions are created somatically\r\nby joining three segments of DNA: VH, D, and JH The JH gene segments are closely\r\nlinked to the IgM heavy chain constant region gene in germline DNA, where they are\r\nwidely separated from VH gene segments. In an immunoglobulin-producing cell, one VH\r\nand one JH gene segment are joined, together with a D sequence which is probably also\r\na germline gene segment, to form the expressed heavy chain variable region gene. Both\r\ncombinatorial association of gene segments and variations in the exact sites of DNA\r\njoining between gene segments can contribute to heavy chain variable region diversity.\r\nBased on observations of certain conserved nucleotides and spacer sequences adjacent\r\nto unrearranged immunoglobulin gene segments, I propose a mechanism for variable\r\nregion gene rearrangement during differentiation.
\r\n\r\nSecreted and membrane-bound forms of IgM heavy chains were found to be\r\nencoded by separate mRNAs transcribed from the same gene. These mRNAs differ only\r\nat their 3' ends, where one encodes a 20 amino acid secretory C-terminal segment, and\r\nthe other encodes a 41 amino acid transmembrane C-terminal segment. Synthesis of\r\nthe two forms of lgM heavy chain mRNA appears to be developmentally regulated by\r\ncontrolling the site of 3' terminal polyadenylation. The site of polyadenylation defines\r\nthe lengths of RNA transcripts and thereby determines which of two alternative RNA\r\nsplicing patterns will be followed, leading to mRNAs encoding either the secreted or\r\nmembrane-bound forms of IgM heavy chains.
", "doi": "10.7907/c5ya-yy20", "publication_date": "1980", "thesis_type": "phd", "thesis_year": "1980" }, { "id": "thesis:18416", "collection": "thesis", "collection_id": "18416", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:03122026-170817040", "primary_object_url": { "basename": "Frelinger_JG_1980.pdf", "content": "final", "filesize": 38406435, "license": "other", "mime_type": "application/pdf", "url": "/18416/1/Frelinger_JG_1980.pdf", "version": "v2.0.0" }, "type": "thesis", "title": "Studies on the Major Histocompatibility Complex of the Mouse and Rat", "author": [ { "family_name": "Frelinger", "given_name": "John Gregory", "clpid": "Frelinger-John-Gregory" } ], "thesis_advisor": [ { "family_name": "Hood", "given_name": "Leroy E.", "orcid": "0000-0001-7158-3678", "clpid": "Hood-L-E" } ], "thesis_committee": [ { "family_name": "Hood", "given_name": "Leroy E.", "orcid": "0000-0001-7158-3678", "clpid": "Hood-L-E" }, { "family_name": "Brockes", "given_name": "Jeremy P.", "orcid": "0000-0002-3395-5159", "clpid": "Brockes-Jeremy-P" }, { "family_name": "Lewis", "given_name": "Edward B.", "clpid": "Lewis-E-B" }, { "family_name": "Mitchell", "given_name": "Herschel K.", "clpid": "Mitchell-H-K" }, { "family_name": "Owen", "given_name": "Ray David", "clpid": "Owen-R-D" } ], "local_group": [ { "literal": "div_biol" } ], "abstract": "This thesis contains investigations into the Major Histocompatibility\r\nComplex (MHC) of two closely related species, rats and mice. In particular, I\r\nhave concentrated on molecules encoded in one part of the MHC, the I region\r\nin mice, and its equivalent in rats. The first part of the thesis consists of experiments\r\ndealing with the expression of molecules encoded by genes in the I region,\r\nthe Ia molecules. Ia molecules are expressed on immune related cells and surprisingly\r\non epidermal cells.
\r\n\r\nSeveral conclusions can be drawn from my studies on these epidermal\r\nIa molecules. The Ia molecules isolated from radiolabeled detergent solubilized\r\nepidermal cell extracts are not contributed by contaminating lymphocytes. The\r\nIa molecules from epidermal cell extracts are identical to their counterparts isolated\r\nfrom spleen cells by both sodium dodecyl sulfate (SDS) polyacrylamide gel electrophoresis\r\nand high pressure liquid chromatography tryptic peptide map analyses.\r\nThe Ia molecules are synthesized by a non-T and non-B cell bone-marrow-derived\r\ncell. This cell is probably the macrophage-like Langerhans cell. This work supports\r\nthe theory that Ia molecules are involved in the immune response and are present\r\nonly on immune related cells.
\r\n\r\nThe second part of this thesis deals with the Class II (Ia-like) molecules\r\nencoded by the rat equivalent of the I region. Two Class II molecules can be immunoprecipitated\r\nusing cross-reactive mouse anti-la sera. These reagents will be extremely\r\nuseful in the further elucidation of the rat MHC.
", "doi": "10.7907/d8rx-2d85", "publication_date": "1980", "thesis_type": "phd", "thesis_year": "1980" }, { "id": "thesis:18475", "collection": "thesis", "collection_id": "18475", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:04062026-221212098", "primary_object_url": { "basename": "Early_PW_1980.pdf", "content": "final", "filesize": 31573311, "license": "other", "mime_type": "application/pdf", "url": "/18475/1/Early_PW_1980.pdf", "version": "v2.0.0" }, "type": "thesis", "title": "Mouse Immunoglobulin Heavy Chain Gene Organization and Rearrangement: Genetic Bases for Antibody Diversity and Regulated Expression", "author": [ { "family_name": "Early", "given_name": "Philip Warren", "clpid": "Early-Philip-Warren" } ], "thesis_advisor": [ { "family_name": "Davidson", "given_name": "Norman R.", "clpid": "Davidson-N-R" }, { "family_name": "Hood", "given_name": "Leroy E.", "orcid": "0000-0001-7158-3678", "clpid": "Hood-L-E" } ], "thesis_committee": [ { "family_name": "Unknown", "given_name": "Unknown" } ], "local_group": [ { "literal": "div_biol" } ], "abstract": "Immunoglobulin heavy chains each display one of a wide range of diverse antigenbinding\r\nvariable regions. At least one class of immunoglobulin, IgM, contains heavy chains\r\nwhich exist as two forms, either bound to the outside of a cell membrane or linked by\r\ndisulfide bonds in secreted antibodies. I have used recombinant DNA techniques to isolate\r\nand determine the nucleotide sequences of genes encoding mouse immunoglobulin heavy\r\nchains. This has enabled me to examine genetic bases for the diversity of heavy chain\r\nvariable regions and for the synthesis of membrane-bound and secreted forms of IgM\r\nheavy chains.
\r\n\r\nI found that genes encoding heavy chain variable regions are created somatically\r\nby joining three segments of DNA: VH, D, and JH The JH gene segments are closely\r\nlinked to the IgM heavy chain constant region gene in germline DNA, where they are\r\nwidely separated from VH gene segments. In an immunoglobulin-producing cell, one VH\r\nand one JH gene segment are joined, together with a D sequence which is probably also\r\na germline gene segment, to form the expressed heavy chain variable region gene. Both\r\ncombinatorial association of gene segments and variations in the exact sites of DNA\r\njoining between gene segments can contribute to heavy chain variable region diversity.\r\nBased on observations of certain conserved nucleotides and spacer sequences adjacent\r\nto unrearranged immunoglobulin gene segments, I propose a mechanism for variable\r\nregion gene rearrangement during differentiation.
\r\n\r\nSecreted and membrane-bound forms of IgM heavy chains were found to be\r\nencoded by separate mRNAs transcribed from the same gene. These mRNAs differ only\r\nat their 3' ends, where one encodes a 20 amino acid secretory C-terminal segment, and\r\nthe other encodes a 41 amino acid transmembrane C-terminal segment. Synthesis of\r\nthe two forms of lgM heavy chain mRNA appears to be developmentally regulated by\r\ncontrolling the site of 3' terminal polyadenylation. The site of polyadenylation defines\r\nthe lengths of RNA transcripts and thereby determines which of two alternative RNA\r\nsplicing patterns will be followed, leading to mRNAs encoding either the secreted or\r\nmembrane-bound forms of IgM heavy chains.
", "doi": "10.7907/c5ya-yy20", "publication_date": "1980", "thesis_type": "phd", "thesis_year": "1980" }, { "id": "thesis:18402", "collection": "thesis", "collection_id": "18402", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:03022026-225028437", "primary_object_url": { "basename": "Loh_EY_1979.pdf", "content": "final", "filesize": 57371117, "license": "other", "mime_type": "application/pdf", "url": "/18402/1/Loh_EY_1979.pdf", "version": "v2.0.0" }, "type": "thesis", "title": "Amino Acid Sequence Studies of Immunoglobulins: Implications for the Storage, Processing, and Expression of Genetic Information", "author": [ { "family_name": "Loh", "given_name": "Elwyn Yuan", "clpid": "Loh-Elwyn-Yuan" } ], "thesis_advisor": [ { "family_name": "Hood", "given_name": "Leroy E.", "orcid": "0000-0001-7158-3678", "clpid": "Hood-L-E" } ], "thesis_committee": [ { "family_name": "Unknown", "given_name": "Unknown" } ], "local_group": [ { "literal": "div_biol" } ], "abstract": "Antibody molecules form a highly complex set of proteins. A central\r\nproblem in immunology has been how the information coding for these proteins\r\nis stored, processed, and expressed.
\r\n\r\nThe constant region sequences of two rat K light chain allotypes\r\nhave been partially sequenced. These allotypes segregate in the Mendelian\r\nfashion. In the eighty-one constant region residues compared, 10 amino acid\r\nsubstitutions and one size difference were found. This large number of substitutions\r\nraise the possibility that the structural genes for both forms may exist in all\r\nrats and the inherited marker is a regulatory gene controlling the expression\r\nof one or the other forms.
\r\n\r\nThe diversity of immunoglobulins is reflected in the diversity of myeloma\r\nproteins and much of our knowledge of antibodies comes from studies of myeloma\r\nproteins. However, the window, created by the myeloma tumors, may be a\r\nbiased one. By comparing the N-terminal amino acid sequences of myeloma\r\nlight chains from two inbred strains of mice, BALB/c and NZB, we have found\r\ndifferences which suggest that different populations of lymphocytes are being\r\ntransformed in the two strains. Thus the true diversity of immunoglobulins\r\nmay be greater than that seen in myeloma proteins.
\r\n\r\nBy sequencing a set of closely related variable regions, one can ask\r\nthe question -- what are the protein products co9ed by a single germ line gene?\r\nThe nearly complete variable regions of twenty-two K chains have been\r\nsequenced using newly developed automated sequencing technology. This data\r\nshows that at least six genes code for this set, assuming that the somatic diversity\r\ngenerating mechanisms cannot produce multiple parallel mutations. Within\r\neach subset of these sequences, coded for by at least one gene, additional\r\nvariations occur both inside and outside the hypervariable regions, although\r\npredominately inside. In addition, the sequence of the approximately twelve\r\nresidues preceeding the constant region do not correlate with the rest of the\r\nvariable region. We have termed this region the S or switch region and suggest\r\nthat it is coded for by a separate segment of DNA that is reorganized during\r\ndifferentiation much in the same way as V and C regions are rearranged.
", "doi": "10.7907/k7yv-gs86", "publication_date": "1979", "thesis_type": "phd", "thesis_year": "1979" }, { "id": "thesis:18846", "collection": "thesis", "collection_id": "18846", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:06172026-004821159", "primary_object_url": { "basename": "Huang_HV_1978.pdf", "content": "final", "filesize": 61042843, "license": "other", "mime_type": "application/pdf", "url": "/18846/1/Huang_HV_1978.pdf", "version": "v2.0.0" }, "type": "thesis", "title": "I. The Ontogenetic Expression of Antibody Variable-Region Genes in the Chicken. II. Methods for Fractionation of Plasma Membranes and Membrane Proteins", "author": [ { "family_name": "Huang", "given_name": "Henry Vincent", "clpid": "Huang-Henry-Vincent" } ], "thesis_advisor": [ { "family_name": "Hood", "given_name": "Leroy E.", "orcid": "0000-0001-7158-3678", "clpid": "Hood-L-E" } ], "thesis_committee": [ { "family_name": "Hood", "given_name": "Leroy E.", "orcid": "0000-0001-7158-3678", "clpid": "Hood-L-E" }, { "family_name": "Dreyer", "given_name": "William J.", "clpid": "Dreyer-W-J" }, { "family_name": "Owen", "given_name": "Ray David", "clpid": "Owen-R-D" }, { "family_name": "Revel", "given_name": "Jean-Paul", "clpid": "Revel-J-P" }, { "family_name": "Wood", "given_name": "William Barry", "clpid": "Wood-W-B" } ], "local_group": [ { "literal": "div_biol" } ], "abstract": "Immnunoglobulins and antibodies made by chickens\r\nbursectomized in ovo on day 11 of incubation were studied\r\nby two-dimensional gel electrophoresis. It was found that\r\nbursectomized chickens have limited immunoglobulin diversity. Antibodies made by bursectomized responders were also of limited diversity. The L chains showed the greatest range in diversity restriction, followed by \u03bc chains, while \u03b3 chains appeared normal. This limited diversity was stable\r\nover at least 20 weeks in that the same heavy and light\r\nchains were found over this time span. Thus bursectomy\r\nblocked the generation of immunoglobulin diversity in\r\nchickens.
\r\nIndividual bursectomized chickens showed a range of extent of diversity restriction, presumably because the development of their bursal cells had been blocked at slightly different stages. Analysis of the particular heavy and light chains of total serum immunoglobulins, serum IgM, and antigen-specific antibodies made by individual bursectomized chickens showed that they were extensively shared. Statistical calculations indicate that if chickens have a normal repertoire of 200-300 genes coding for variable-regions of L chains then it is very unlikely that random gene expression could result in such extensive similarities between bursectomized chickens. The implications of an orderly expression of variable-region genes are discussed.
", "doi": "10.7907/fvyd-c004", "publication_date": "1978", "thesis_type": "phd", "thesis_year": "1978" }, { "id": "thesis:13565", "collection": "thesis", "collection_id": "13565", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:11112019-161331927", "primary_object_url": { "basename": "Weiner_S_1977.pdf", "content": "final", "filesize": 32586065, "license": "other", "mime_type": "application/pdf", "url": "/13565/1/Weiner_S_1977.pdf", "version": "v2.0.0" }, "type": "thesis", "title": "Aspects of the Biochemistry of the Organic Matrix of Extant and Fossil Mollusks", "author": [ { "family_name": "Weiner", "given_name": "Stephen", "clpid": "Weiner-Stephen" } ], "thesis_advisor": [ { "family_name": "Lowenstam", "given_name": "Heinz A.", "clpid": "Lowenstam-H-A" }, { "family_name": "Hood", "given_name": "Leroy E.", "orcid": "0000-0001-7158-3678", "clpid": "Hood-L-E" } ], "thesis_committee": [ { "family_name": "Unknown", "given_name": "Unknown" } ], "local_group": [ { "literal": "div_gps" } ], "abstract": "The biochemistry of the organic matrix of mollusks is investigated to improve our understanding of the function of this material in shell formation and to explore the possibility of using fossil organic matrix components to study aspects of molecular evolution.
\r\n\r\nThe soluble fractions of the organic matrices of nine species of mollusks representing the three major classes of the phylum have been investigated. However, the organic matrix of the clam, Mercenaria mercenaria, has been studied in greatest detail. It is composed of protein with covalently bound carbohydrate. The protein-carbohydrate linkage is probably through serine and/or threonine residues. The organic matrix components vary greatly in their protein-carbohydrate proportions, amino acid compositions and hydrodynamic size.
\r\n\r\nThe discrete molecular weight components of the nine species of mollusks investigated exhibit great heterogeneity above the species level. A particular repeating amino acid sequence in which every second amino acid is an aspartic acid separated by either glycine or serine, is present in all mollusks examined to date. It is suggested that this amino acid sequence is a potential template for crystal nucleation.
\r\n\r\nThe organic matrix of an 80 million year old clam, Scabrotrigonia thoracica, still contains the repeating aspartic acid sequence and discrete molecular weight components, indicating that this material is unusually well preserved, and therefore could be of use in future studies of molecular evolution based on material derived from the fossil record. The glycine content of the organic matrices of eight of these fossil shells is a sensitive indicator of early diagenesis. The alloisoleucine/isoleucine ratios of the shell protein ranged from the equilibrium value to extremely low values. The potential uses of fossil organic matrices in evolution studies are discussed.
", "doi": "10.7907/Q5CV-RC94", "publication_date": "1977", "thesis_type": "phd", "thesis_year": "1977" }, { "id": "thesis:13565", "collection": "thesis", "collection_id": "13565", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:11112019-161331927", "primary_object_url": { "basename": "Weiner_S_1977.pdf", "content": "final", "filesize": 32586065, "license": "other", "mime_type": "application/pdf", "url": "/13565/1/Weiner_S_1977.pdf", "version": "v2.0.0" }, "type": "thesis", "title": "Aspects of the Biochemistry of the Organic Matrix of Extant and Fossil Mollusks", "author": [ { "family_name": "Weiner", "given_name": "Stephen", "clpid": "Weiner-Stephen" } ], "thesis_advisor": [ { "family_name": "Lowenstam", "given_name": "Heinz A.", "clpid": "Lowenstam-H-A" }, { "family_name": "Hood", "given_name": "Leroy E.", "orcid": "0000-0001-7158-3678", "clpid": "Hood-L-E" } ], "thesis_committee": [ { "family_name": "Unknown", "given_name": "Unknown" } ], "local_group": [ { "literal": "div_gps" } ], "abstract": "The biochemistry of the organic matrix of mollusks is investigated to improve our understanding of the function of this material in shell formation and to explore the possibility of using fossil organic matrix components to study aspects of molecular evolution.
\r\n\r\nThe soluble fractions of the organic matrices of nine species of mollusks representing the three major classes of the phylum have been investigated. However, the organic matrix of the clam, Mercenaria mercenaria, has been studied in greatest detail. It is composed of protein with covalently bound carbohydrate. The protein-carbohydrate linkage is probably through serine and/or threonine residues. The organic matrix components vary greatly in their protein-carbohydrate proportions, amino acid compositions and hydrodynamic size.
\r\n\r\nThe discrete molecular weight components of the nine species of mollusks investigated exhibit great heterogeneity above the species level. A particular repeating amino acid sequence in which every second amino acid is an aspartic acid separated by either glycine or serine, is present in all mollusks examined to date. It is suggested that this amino acid sequence is a potential template for crystal nucleation.
\r\n\r\nThe organic matrix of an 80 million year old clam, Scabrotrigonia thoracica, still contains the repeating aspartic acid sequence and discrete molecular weight components, indicating that this material is unusually well preserved, and therefore could be of use in future studies of molecular evolution based on material derived from the fossil record. The glycine content of the organic matrices of eight of these fossil shells is a sensitive indicator of early diagenesis. The alloisoleucine/isoleucine ratios of the shell protein ranged from the equilibrium value to extremely low values. The potential uses of fossil organic matrices in evolution studies are discussed.
", "doi": "10.7907/Q5CV-RC94", "publication_date": "1977", "thesis_type": "phd", "thesis_year": "1977" }, { "id": "thesis:10604", "collection": "thesis", "collection_id": "10604", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:12132017-081719269", "primary_object_url": { "basename": "Barstad_PA_1975.pdf", "content": "final", "filesize": 38029750, "license": "other", "mime_type": "application/pdf", "url": "/10604/1/Barstad_PA_1975.pdf", "version": "v2.0.0" }, "type": "thesis", "title": "A Current Look at the Biological Basis of Antibody Diversity and Specificity", "author": [ { "family_name": "Barstad", "given_name": "Paul Arlyn", "clpid": "Barstad-Paul-Arlyn" } ], "thesis_advisor": [ { "family_name": "Hood", "given_name": "Leroy E.", "orcid": "0000-0001-7158-3678", "clpid": "Hood-L-E" } ], "thesis_committee": [ { "family_name": "Unknown", "given_name": "Unknown" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Using automated protein sequence analysis of BALB/c\r\nmyeloma proteins, the genetic basis for antibody specificity\r\nand diversity is investigated. Studies on the N-terminal\r\nregions of the heavy chains from these immunoglobulins reveal\r\nthat a large amount of diversity must exist in the VH regions.\r\nExamination of the heavy and light chain sequences from myeloma\r\nproteins with hapten-binding activities indicates that\r\nthe heavy chain variable region sequence correlates closely\r\nwith all the specificities of intact molecules. The light\r\nchain appears to be less restricted in some specificities,\r\nhowever. The relevance of these data to the proposed \r\nmechanisms of antibody diversity is discussed.", "doi": "10.7907/0931-D337", "publication_date": "1975", "thesis_type": "phd", "thesis_year": "1975" } ]