Virtualization technology is becoming more and more popular, and when applicable, telecom equipment is being migrated to virtualized platforms. While virtualization technology provides many benefits, it also presents significant challenges. For example, the special hardware used for audio payload conversion can no longer be used. In legacy telecom equipment, the user plane, which processes voice over Internet Protocol (IP), was designed to use special hardware such as field programmable gate array/complex programmable logic devices (FPGA/CPLD) for optimum performance. However, in virtualized platforms the only choice is a general-purpose processor and therefore software-based payload conversion algorithms have to be used accordingly. This introduces a major performance issue in that a software-only solution is needed to reach the performance levels already possible with legacy equipment, and the prospect of reaching this goal using a software-based algorithm is a very challenging task. This letter describes our work to use a virtualized machine to replace the CPLD board used to convert the VoIP payload packets from the Real Time Transport Protocol (RTP) to the Transcoder and Rate Adaptation Unit over IP (TRAUP) protocol and vice versa. We also describe a conversion method that we developed to improve performance.

Each V, D, and J gene segment is flanked by a recombination signal sequence (RSS), composed of a conserved heptamer and nonamer separated by a 12- or 23-bp spacer. Variations from consensus in the heptamer or nonamer at specific positions can dramatically affect recombination frequency, but until recently, it had been generally held that only the length of the spacer, but not its sequence, affects the efficacy of V(D)J recombination. In this study, we show several examples in which the spacer sequence can significantly affect recombination frequencies. We show that the difference in spacer sequence alone of two VHS107 genes affects recombination frequency in recombination substrates to a similar extent as the bias observed in vivo. We show that individual positions in the spacer can affect recombination frequency, and those positions can often be predicted by their frequency in a database of RSS. Importantly, we further show that a spacer sequence that has an infrequently observed nucleotide at each position is essentially unable to support recombination in an extrachromosmal substrate assay, despite being flanked by a consensus heptamer and nonamer. This infrequent spacer sequence RSS shows only a 2-fold reduction of binding of RAG proteins, but the in vitro cleavage of this RSS is ∼9-fold reduced compared with a good RSS. These data demonstrate that the spacer sequence should be considered to play an important role in the recombination efficacy of an RSS, and that the effect of the spacer occurs primarily subsequent to RAG binding.

Much of the nonrandom usage of V, D, and J genes in the Ab repertoire is due to different frequencies with which gene segments undergo V(D)J rearrangement. The recombination signal sequences flanking each segment are seldom identical with consensus sequences, and this natural variation in recombination signal sequence (RSS) accounts for some differences in rearrangement frequencies in vivo. Here, we have sequenced the RSS of 19 individual V(H)7183 genes, revealing that the majority have one of two closely related RSS. One group has a consensus heptamer, and the other has a nonconsensus heptamer. In vitro recombination substrate studies show that the RSS with the nonconsensus heptamer, which include the frequently rearranging 81X, rearrange less well than the RSS with the consensus heptamer. Although 81X differs from the other 7183-1 genes at three positions in the spacer, this does not significantly increase its recombination potency in vitro. The rearrangement frequency of all members of the family was determined in mu MT mice, and there was no correlation between the in vitro recombination potential and VH gene rearrangement frequency in vivo. Furthermore, genes with identical RSS rearrange at different frequencies in vivo. This demonstrates that other factors can override differences in RSS potency in vivo. We have also determined the gene order of all V(H)7183 genes in a bacterial artificial chromosome contig and show that most of the frequently rearranging genes are in the 3 ' half of the region. This suggests that chromosomal location plays an important role in nonrandom rearrangement of the V(H)7183 genes.

Summary: V, D, and J gene segments rearrange at different frequencies in vivo. Each rearranging gene segment is flanked by a recombination signal sequence (RSS), which is composed of a conserved heptamer and nona­mer, separated by a spacer of conserved length but not conserved sequence. We summarize data from our lab and other labs showing that in many cases, but not all, the RSS can account for differences in recombination frequencies observed in vivo . Our approach is to determine the initial frequency of rearrangement of the V genes in vivo , and then place the RSSs of two V genes into a competition recombination substrate to determine the relative frequency with which the two RSSs support recombination. In one example, we have shown that a polymorphism in the heptamer of a Vk gene can result in a significant reduction in recombination frequency. This particular allele is prevalent in Navajos and absent in other populations. We suggest that this single change may play a major role in the high susceptibility of Navajos to Haemophilus influenzae infection, since this Vk gene is important in the antibody response to this bacteria. We also describe experiments showing that the sequence of the spacer of the RSS can play an important role in relative recombination frequencies.

Receptor editing is a process consisting of replacement of pre-existing H or L chain rearrangements by secondary rearrangements. This process could serve to remove autoreactive specificities, or to rescue loci with non-functional rearrangements. At the H chain locus, functional replacement of a V(H)DJ(H) rearrangement by an upstream V(H) requires the presence of an embedded RSS located in reverse orientation near the 3' end of the V(H) segment. Although most V(H) genes contain a fairly consensus embedded heptamer, the nonamer sequence bears little resemblance to the consensus RSS nonamer. Therefore, the physiologic rate of H chain editing by V(H) replacement is yet unknown. In this study, we used both conventional and sensitive competition recombination substrate assays to determine the recombination frequency of the V(H)1X embedded RSS relative to consensus and non-consensus RSS's. Results show no detectable recombination of the 81X embedded RSS in a recombination substrate, and the competition substrate allows us to estimate that the 81X embedded RSS recombines at least 1300 fold less often than a consensus RSS. This suggests that V(H) gene replacement is not responsible for the decrease in representation of the 81X gene during differentiation. Furthermore, since the sequence of the embedded RSS is very similar for many V(H) genes, our results suggest that receptor editing of the H chain will be an infrequent event, leaving L chain editing as the main mode of avoiding autoreactive specificities in vivo.

Navajos and genetically related populations have a 10-fold increased incidence of Haemophilus influenzae type b (Hib) disease compared with control populations. The Vkappa gene A2 is used to encode the majority of anti-Hib Abs, and these are the highest affinity anti-Hib Abs. Navajos carry a different allele of the A2 gene segment (A2b) that is defective in its ability to undergo V-J recombination. The A2b allele has only three nucleotide changes from the commonly occurring A2a allele, two of which could potentially affect its ability to recombine. In this study we used two independent in vitro assays to test whether the nucleotide change found in the A2b promoter and/or in the A2b recombination signal sequence (RSS) might be responsible for the decrease in recombination frequency observed in vivo. Using a luciferase reporter gene assay, we found no significant difference between A2a and A2b promoter activities. However, the competition recombination substrate assay showed a 4.5-fold reduction in the relative frequency of recombination of the A2b RSS compared with A2a. We show that this decreased frequency is due to a synergistic effect of the unique nucleotide change present in the heptamer of the A2b RSS and the shared nucleotide change present in the nonamer of both A2b and A2a. This in vitro relative frequency of rearrangement is not significantly different from that observed in vivo; therefore, the A2b RSS is probably the factor associated with the increased susceptibility to Hib disease among individuals carrying the A2b allele.

Functional variable (V), diversity (D), and joining (J) gene segments contribute unequally to the primary repertoire. One factor contributing to this nonrandom usage is the relative frequency with which the different gene segments rearrange. Variation from the consensus sequence in the heptamer and nonamer of the recombination signal sequence (RSS) is therefore considered a major factor affecting the relative representation of gene segments in the primary repertoire. In this study, we show that the sequence of the spacer is also a determinant factor contributing to the frequency of rearrangement. Moreover, the effect of the spacer on recombination rates of various human Vkappa gene segments in vitro correlates with their frequency of rearrangement in vivo in pre-B cells and with their representation in the peripheral repertoire.