Mutational analysis of immunoglobulin germline derived Vlambda4B light chains in rheumatoid arthritis.

OBJECTIVE: We investigated the somatic mutational pattern of a specific Vlambda light chain variable region (V) gene in rheumatoid arthritis (RA) patients. The Vlambda4B light chain was chosen because of its location on the lambda locus and because of its previously observed use in IgM rheumatoid factors. METHODS: We sequenced 13 different mRNA transcripts of Vlambda4B from the synovium of three different RA patients. These were compared to 31 identifiable Vlambda4B sequences from GenBank, which were obtained from the PBL of patients without RA. RESULTS: A subset of Vlambda4B had a high rate of mutation, especially in the framework regions within the RA synovium. Furthermore, a set of codons within the first complementary determining region of Vlambda4B displayed frequent replacement mutations but did not possess any silent mutations. CONCLUSION: The hypermutation of RA synovial-derived Vlambda4B sequences, especially in the framework areas, may contribute to or may be the result of altered mutational mechanisms and/or prolonged B cell life.

Mutational analysis of immunoglobulin germline derived Vlambda4A light chains in rheumatoid arthritis.

In order to better characterize the expression of a family of light chains previously expressed in IgM rheumatoid factors, we studied the usage and somatic mutational pattern of the Vlambda4A light chain gene in rheumatoid arthritis (RA) patients. We sequenced 11 different transcripts of Vlambda4A from the synovial tissue of three different RA patients. For comparison, we found 8 rearranged transcripts of Vlambda4A from 4 normal peripheral blood lymphocyte libraries and 1 rearranged transcript from a non-RA con-A-resistant hybridoma in GenBank. A previously undescribed polymorphism of Vlambda4A was noted. Furthermore, conserved replacement mutations in the complementary determining regions, common silent mutations around these replacement mutations, and two subsets of mutated sequences were detected in multiple RA patients. These mutation patterns also correlated with observed consistencies in the rearrangements of the Vlambda4A/Jlambda junction. These data suggest that there is clonal expansion of Vlambda4A light chains in the RA synovium in response to a RA-specific antigen or as the result of an idiotypic response in RA.

Analysis of the molecular basis of synovial rheumatoid factors in rheumatoid arthritis.

The objective of this study was to better understand the molecular basis of IgM rheumatoid factor in rheumatoid arthritis (RA). We recently generated 10 different monoclonal IgM RF (mRF) molecules isolated from the synovium of a single patient with RA. The heavy (H) and light chain (L) variable region (V) genes of these 10 mRFs were cloned and sequenced. Six mRFs used kappa light chains and 4 mRFs used lambda light chains. Of particular interest, 8 of 10 heavy chains used the JH4 joining region gene, and all five VH4 heavy chains used the DK4 diversity region gene with the JH4. Four of the VH4 clones used the same germline gene, likely representing a novel but closely related germline gene to VH4.18, and may be clonally related because of the extensive homology in their heavy chain sequence. Two VH4 clones shared the same light chain gene, VkappaIIIb kv325 (99% homology) and the same JK4 joining region gene, while three VH4 clones used two different light chain genes, an uncommon Vkappa4 and a Vlambda4 gene, respectively. In this RA patient, there was recurrent utilization of VH4-DK4-21/10-JH4 genes and a recurring association with gene elements Vkappa3 and Vlambda4. Recurring usage of Vkappa3 (kv325) and Vlambda4 (lv418) gene elements may result from a light chain editing process whereby immature autoreactive B cells encountering self-antigen attempt, and often succeed, in altering their specificities through secondary Ig light chain gene rearrangement. Moreover, the oligoclonality of these RFs suggest clonal relatedness secondary to an antigen-driven response.

New directions in scientific computing: impact of advances in microprocessor architecture and system design.

The new generation of microcomputers has brought computing power previously restricted to mainframe and supermini computers within the reach of individual scientific laboratories. Microcomputers can now provide computing speeds rivaling mainframes and computational accuracies exceeding those available in most computer centers. Inexpensive memory makes possible the transfer to microcomputers of software packages developed for mainframes and tested by years of experience. Combinations of high level languages and assembler subroutines permit the efficient design of specialized applications programs. Microprocessor architecture is approaching that of superminis, with coprocessors providing major contributions to computing power. The combined result of these developments is a major and perhaps revolutionary increase in the computing power now available to scientists.

Computer simulation of rapidly responding forced exponential systems.

Two common problems in computer simulations are the decisions to ignore or include a particular element of a system under study in a model and the choice of an appropriate integration algorithm. To examine aspects of these problems, a simple exponential system is considered in which a large simulation error is induced by a rather small truncation error. The effect of computational precision, step size and hardware selection on this error is examined at standard and extended precisions over a range of step sizes and on a variety of computers. For this model, simulation accuracy is an exponential function of the number of bits in the mantissa of the computer word. Optimal step size is a function of accuracy required and precision used; a trade-off between truncation and round-off errors becomes important as accuracy requirements increase. Machine selection is important primarily in economic terms if the required precision is available. We conclude that the effect on a simulation of small terms such as truncation errors can be unexpectedly large, that solutions should always be checked, and that high precision and wide dynamic range are important to the successful computer simulation of models such as that examined.