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Biomedical subjects

P K Jena

Publications and source records attributed to P K Jena.

9 recordsLinked to original sources

Sequence heterogeneity in Ig kappa transcripts from single B lymphocytes.

Individually amplified kappa cDNA molecules from single B lymphocytes revealed sequence heterogeneity and aberrantly spliced products. The nature and frequency of the base changes and their absence from similarly amplified beta2 microglobulin transcripts indicate that they were not derived by Taq polymerase misincorporations or by a general infidelity in RNA polymerase. The trinucleotide sequences in which the base changes occurred are disfavored targets of the somatic hypermutation mechanism that modifies antibody variable (V) region genes during immunity. Taken together with the observation that the transcript alterations were absent from the kappa Ig gene, this suggests that somatic mutations were acquired by the kappa gene and rapidly repaired following limited transcription. Preferential repair of mutations located in specific trinucleotide contexts could be the basis for some of the microsequence-specific bias in mutation frequencies observed in antibody V region genes.

Animals↗

Tracing the development of single memory-lineage B cells in a highly defined immune response.

To study the development of B lymphocyte memory, we identified and isolated splenic B cells expressing a highly defined antibody variable region that constitutes a reproducible and predominant component of the memory antibody response to p-azophenylarsonate (Ars). Isolation was achieved during the primary immune response by surface staining and flow cytometry using a specific anti-idiotypic antibody called E4, which recognizes this canonical V region, encoded by one set of V gene segments. The isolated E4+ cells displayed all of the phenotypic characteristics of germinal center centrocytes, including a low level of surface Ig, a lack of surface IgD, a high level of receptor for peanut agglutinin, and expression of mutated antibody V genes. E4+ B cells were first detected in the spleen 7-8 d after primary immunization, reached peak numbers from days 10-13, and waned by day 16. Surprisingly, at their peak, E4+ cells comprised only 40,000 of all splenocytes, and half of these failed to bind Ars. Using this number, we estimate the total number of Ars-specific memory-lineage cells in the spleen to be no more than 50,000 (0.1%) at any one time, and presumably far fewer that are committed to the memory pool. Chromosomal copies of rearranged V genes from single E4+ cells were amplified by nested PCR, and the amplified products were sequenced directly without cloning, using standardized conditions that disclose virtually no Taq polymerase errors. V gene sequence analyses of E4+ cells isolated from single mice confirmed their canonical nature and revealed that they were derived from few precursors. In the average mouse, the E4+ pool was derived from fewer than five canonical precursors. Somatic mutations were found within the V genes of almost all cell isolates. At day 13, a significant fraction of E4+ cells had mutations known to increase antibody affinity for Ars, suggesting they were products of at least one cycle of post-mutational antigen-driven selection. However, the lack of shared mutations by clonally related cells indicated that the selective expansion of mutant subclones typical of memory responses had not yet taken place. This was supported by the observation that half of the E4+ cells failed to bind Ars. Collectively, our results indicate that the memory compartment is a highly selected entity, even at relatively early stages of the primary immune response when somatic mutation and clonal selection are still in progress. If germinal centers are the source of memory B cells, our data suggest that B cell memory may be derived from only a small fraction of all germinal centers.

Amino Acid Sequence↗

Amplification of genes, single transcripts and cDNA libraries from one cell and direct sequence analysis of amplified products derived from one molecule.

We report a procedure to generate and amplify cDNA libraries and to amplify and sequence genes and single RNA transcript molecules from the same cell without cloning. An absence of cloning steps minimizes potential sources of contamination, which can be especially problematic when working at the single cell level. Potential contamination is further reduced by an absence of any purification step prior to PCR amplification. Amplifications are designed to minimize the production of aberrant molecules in favor of full-length products, which is especially advantageous when generating cDNA libraries. Genes are amplified from isolated single nuclei, which are segregated from cytoplasmic lysates by microcentrifugation. Specific cDNA, total cDNA or both are synthesized from aliquots of the cytoplasmic lysate, and single cDNA molecules are isolated from others of the same species by limiting dilution prior to PCR amplification. In this way, the frequency of amplified products provides for a direct calculation of cDNA copy number by a Poisson analysis. Incorporation errors by Taq DNA polymerase occur at a low frequency and can be eliminated by sequencing independently amplified cDNA molecules from the same cell. Single molecule amplifications provide sufficient material for numerous (approximately 150) direct DNA sequencing reactions. The limiting dilution approach also permits sequence information to be obtained from a single cDNA, when highly related transcripts derived from distinct genes are present in the same cell and simultaneously amplified with the same primers. In sum, this method provides for a maximum amount of nucleic acid information to be extracted from one cell. It has a wide range of applications to studies of the immune system where, to a first approximation, each lymphocyte has a unique receptor identity, where specific states of differentiation may be difficult to assess in a mixed cell population, and where cell immortalization procedures are not always possible nor practical.

Animals↗

Di- and trinucleotide target preferences of somatic mutagenesis in normal and autoreactive B cells.

During Ag-driven development of memory B cells, Ab V genes are modified by somatic mutagenesis. Although V gene somatic mutations have important biologic consequences in both physiologic and autoimmune Ab responses, little is known about the mechanism of mutation, or whether it operates normally in autoreactive B cells. To approach these issues, we analyzed somatic mutations in Ab genes for evidence of sequence-specific target preferences. Our analysis was confined to noncoding segments of V genes so that the intrinsic characteristics of the somatic mutation process could be reliably dissociated from the indirect but substantial influences of cellular selection. We consistently observed that some dinucleotides, GC and TA in particular, mutated at frequencies that were higher than expected based on their frequency of occurrence. Most of the dinucleotide mutation preferences could not be extrapolated directly from mononucleotide mutation preferences. Specific trinucleotides, including AGC, TAC, and their inverse repeats (GCT, GTA), also mutated more frequently than expected. These and other mutation characteristics were virtually indistinguishable in V genes of normal and autoreactive B cells. An analysis of mutations in published flanking sequences confirmed the target preferences, as did an examination of reported "hot spots" within coding V sequences. The shared preferences in coding and noncoding regions of V genes suggests that somatic mutations are generated de novo. Collectively, our findings indicate that the somatic mutation process exhibits sequence-specific preferences, consistent with an untemplated mechanism, and appears to operate similarly in normal and autoreactive B cells.

Animals↗

Molecular cloning of cDNAs for auxin-induced mRNAs and developmental expression of the auxin-inducible genes.

By differential hybridization, two auxin-inducible cDNA clones (lambda SAR1 and lambda SAR2) have been isolated from a cDNA library constructed to poly(A)+ mRNA from auxin-treated strawberry receptacles. Both the clones have been used as probes to study the expression of the auxin-induced genes in pollinated and unpollinated fruits of various stages of development and in different organs. A high level of auxin-induced mRNAs is found in pollinated fruits as compared to unpollinated fruits of the same age, suggesting that the expression of the auxin-induced genes is developmentally regulated and the level of auxin-induced mRNAs is regulated by endogenous auxin. Furthermore, our data on the expression of lambda SAR1 and lambda SAR2 genes in pollinated and unpollinated fruits revealed a positive correlation between growth of strawberry fruit and the induction of mRNA corresponding to the lambda SAR1 and lambda SAR2 clones. Ethylene has no effect on the expression of the auxin-induced mRNAs. lambda SAR1 mRNA is not detected in other parts of strawberry plants whereas lambda SAR2 mRNA is present in roots. Furthermore, mRNA corresponding to lambda SAR1 and lambda SAR2 is not detected in other auxin-responsive plant systems such as pea epicotyls and bean explants.

Cloning, Molecular↗

Molecular cloning and sequencing of a cDNA for plant calmodulin: signal-induced changes in the expression of calmodulin.

A cDNA clone (pPCM-1) for plant calmodulin was isolated by screening a potato stolon tip cDNA library with a chicken calmodulin cDNA. Nucleotide sequence analysis of pPCM-1 revealed that it contained 80 base pairs of 5' untranslated region, the entire coding region, and 376 base pairs of 3' untranslated region. Comparison of the nucleotide sequence of coding regions of potato and chicken calmodulin mRNA showed 78% homology. Comparison of the predicted amino acid sequence of potato calmodulin with other known calmodulin sequences indicated a high degree of homology with a few exceptions. Three changes in the amino acid sequence were found to be unique to the potato calmodulin sequence. In our earlier studies we showed the involvement of calcium and calmodulin in potato tuberization. The pPCM-1 clone was used as a probe to study the expression of calmodulin mRNA during tuberization and to monitor calmodulin mRNA level in various parts of the potato plant. Stolon tips showed the highest levels of calmodulin mRNA, suggesting a role for calmodulin in the tuberization process. In addition, pPCM-1 was used to investigate the effect of auxin and light on calmodulin gene expression in auxin-responsive strawberry fruit and light-responsive Merit corn roots, respectively. Both auxin and light signals were found to increase the level of mRNA for calmodulin. These results suggest that the altered calmodulin gene expression could be one of the molecular events involved in the signal transduction process in plants.

Amino Acid Sequence↗

Multiseptate hypoplastic gallbladder.

A case is presented of multiseptate hypoplastic gallbladder, which is an extremely rare combination of two congenital anomalies. The patient was diagnosed as having cholecystitis and was relieved of her symptoms following cholecystectomy, even though the specimen did not show evidence of inflammation or calculi. The significance of this is emphasized by reviewing the 5 authenticated cases of multiseptate gallbladder reported in the literature. Awareness of this condition should avoid misinterpretation of cholecystograms.

Adult↗