Prospective estimation of recombination signal efficiency and identification of functional cryptic signals in the genome by statistical modeling

The recombination signals (RS) that guide V(D)J recombination are phylogenetically conserved but retain a surprising degree of sequence variability, especially in the nonamer and spacer. To characterize RS variability, we computed the position-wise information, a measure correlated with sequence conservation, for each nucleotide position in an RS alignment and demonstrate that most position-wise information is present in the RS heptamers and nonamers. We have previously demonstrated significant correlations between RS positions and here show that statistical models of the correlation structure that underlies RS variability efficiently identify physiologic and cryptic RS and accurately predict the recombination efficiencies of natural and synthetic RS. In scans of mouse and human genomes, these models identify a highly conserved family of repetitive DNA as an unexpected source of frequent, cryptic RS that rearrange both in extrachromosomal substrates and in their genomic context.     

Regulation of inherently autoreactive VH4-34 B cells in the maintenance of human B cell tolerance

The study of human B cell tolerance has been hampered by difficulties in identifying a sizable population of autoreactive B lymphocytes whose fate could be readily determined. Hypothesizing that B cells expressing intrinsically autoreactive antibodies encoded by the VH4-34 heavy chain gene (VH4-34 cells) represent such a population, we tracked VH4-34 cells in healthy individuals. Here, we show that naive VH4-34 cells are positively selected and mostly restricted to the follicular mantle zone. Subsequently, these cells are largely excluded from the germinal centers and underrepresented in the memory compartment. In healthy donors but not in patients with systemic lupus erythematosus (SLE), these cells are prevented from differentiating into antibody-producing plasma cells. This blockade can be overcome ex vivo using cultures of naive and memory VH4-34 cells in the presence of CD70, IL-2, and IL-10. VH4-34 cells may therefore represent an experimentally useful surrogate for autoantibody transgenes and should prove valuable in studying human B cell tolerance in a physiological, polyclonal environment. Our initial results suggest that both positive and negative selection processes participate in the maintenance of tolerance in autoreactive human B cells at multiple checkpoints throughout B cell differentiation and that at least some censoring mechanisms are faulty in SLE.     

Extensive and selective mutation of a rearranged VH5 gene in human B cell chronic lymphocytic leukemia

B cell chronic lymphocytic leukemia (CLL) is the malignant, monoclonal equivalent of a human CD5+ B cell. Previous studies have shown that the VH and VL genes rearranged and/or expressed in CLL have few and apparently random mutations. However, in this study, we have found that the rearranged VH251 gene, one of the three-membered VH5 family, has extensive and selective mutations in B-CLL cells. Somatic mutation at the nucleotide level is 6.03% in B-CLLs whereas the somatic mutation levels are much lower in CD5+ and CD5- cord B cells, adult peripheral blood B cells, and Epstein-Barr virus-transformed CD5+ B cell lines (0.45, 0.93, and 1.92%, respectively). Complementary determining region 1 (CDR1) mutation in CLLs is particularly prevalent, and interchanges in CDRs often lead to acquisition of charge. Analysis of somatic mutations and mutations to charged residues demonstrated that the mutations in CLLs are highly selected.     

Antigen-independent appearance of recombination activating gene (RAG)-positive bone marrow B cells in the spleens of immunized mice

Splenic B lineage cells expressing recombination activation genes (RAG(+)) in mice immunized with 4-hydroxy-3-nitrophenyl-acetyl coupled to chicken gamma-globulin (NP-CGG) and the adjuvant aluminum-hydroxide (alum) have been proposed to be mature B cells that reexpress RAG after an antigen encounter in the germinal center (GC), a notion supported by findings of RAG expression in peripheral B lymphocyte populations activated in vitro. However, recent studies indicate that these cells might be immature B cells that have not yet extinguished RAG expression. Here, we employ RAG2-green fluorescent protein (GFP) fusion gene knock-in mice to show that RAG(+) B lineage cells do appear in the spleen after the administration of alum alone, and that their appearance is independent of T cell interactions via the CD40 pathway. Moreover, splenic RAG(+) B lineage cells were detectable in immunized RAG2-deficient mice adoptively transferred with bone marrow (BM) cells, but not with spleen cells from RAG(+) mice. Although splenic RAG(+) B cells express surface markers associated with GC B cells, we also find the same basic markers on progenitor/precursor BM B cells. Finally, we did not detect RAG gene expression after the in vitro stimulation of splenic RAG(-) mature B cells with mitogens (lipopolysaccharide and anti-CD40) and cytokines (interleukin [IL]-4 and IL-7). Together, our studies indicate that RAG(+) B lineage cells from BM accumulate in the spleen after immunization, and that this accumulation is not the result of an antigen-specific response.     

Diversification, not use, of the immunoglobulin VH gene repertoire is restricted in DiGeorge syndrome

Immunoglobulin (Ig) genes were isolated from unamplified conventional as well as polymerase chain reaction-generated cDNA libraries constructed from the peripheral blood cells of a patient with complete DiGeorge syndrome. Comparison of the sequences of 36 heavy chain clones to the recently expanded database of human VH genes permitted identification of the germline VH genes that are expressed in this patient as well as placement of 19 of these genes in a partially resolved 0.8-mb region of the human VH locus. The pattern of VH gene use does not resemble the fetal (early) repertoire. However, as in the fetal repertoire, there are a number of cDNAs derived from germline genes that previously have been identified as autoantibodies. Two D mu sequences also were identified, as was another sequence resulting from a unique recombination event linking JH to an unidentified sequence containing a recombination signal sequence-like heptamer. All of the DiGeorge cDNAs are closely related to germline VH genes, showing little or no evidence of somatic mutation. In contrast, comparably selected IgM VH sequences derived from normal adult and age-matched human libraries, and from a second DiGeorge syndrome patient in whom the degree of thymic dysfunction is much less severe, exhibit considerable evidence of somatic mutation. The absence of somatic mutation is consistent with the atypical development of functional antibody responses associated with complete DiGeorge syndrome and implicates a role for T cells in the generation of diversity within the B cell repertoire.     

Restricted use of fetal VH3 immunoglobulin genes by unselected B cells in the adult. Predominance of 56p1-like VH genes in common variable immunodeficiency.

The large VH3 family of human immunoglobulin genes is commonly used throughout B cell ontogeny. However, B cells of the fetus and certain autoantibody-producing clones are restricted to a recurrent subset of VH3 genes, and VH3 B cells are deficient in certain immunodeficiency diseases. In this study, we have sequenced a set of rearranged VH3 genes generated by genomic polymerase chain reaction (PCR) from normal adults and those with common variable immunodeficiency (CVI). In both groups, all cones were readily identifiable with the fetal VH3 subset, and were further distinguished by limited DH motifs and exclusive use of JH4. In CVI, the residual population of VH3 B cells were notable for predominant use of 56p1-like VH genes. All clones displayed sequence divergence (including somatic mutation) with evidence of strong selection against complementarity-determining region (CDR) coding change. A survey of other V gene families indicates that human V gene diversity may be restricted in general by germline mechanisms. These findings suggest that the expressed antibody repertoire in the human adult may be much smaller than anticipated, and selected by processes in part distinct from the paradigm of maximal antigen-binding diversity.     

V(D)J recombination in peritoneal B cells of leaky scid mice

Developing lymphocytes in immune-deficient severe combined immunodeficient (scid) mice express a defective recombinase activity and rarely succeed in making an antigen receptor; those cells that do succeed account for the known B and T cell leakiness in this mutant mouse strain. To gain more insight into the nature of the scid defect, we assessed the status of heavy (H) and light (L)k, chain genes in immunoglobulin (Ig)Mk-secreting B cells from the peritoneal cavity of old leaky scid mice, the only lymphoid site where scid B cells have been routinely detected. We found these cells to be unusual in that their nonexpressed H chain alleles were either abnormally rearranged or in germline configuration (wild-type B cells generally show normal rearrangements at both H chain alleles). The VDJH junctions of the expressed alleles showed little or no nontemplated (N) addition, similar to neonatal B cells from wild-type mice. About half of the V(D)J junctions lacking N additions contained nucleotides that could have been encoded by either of the participating coding elements (VDH, DJH, or VJk), indicating that the recombination occurred between short stretches of homology. Unusually long templated (P) additions were seen in both VDJH and VJK junctions, and many recombinations appeared to involve P-based homologies. These findings suggest that: (a) B cell leakiness results from a low frequency of coding joint formation in cells expressing the defective scid recombinase activity; (b) joining of scid coding ends is facilitated when the ends contain short stretches of sequence homology, where in many cases, one of the homologous sequences results from a P addition; and (c) scid peritoneal B cells may arise early in ontogeny.     

Differential expression of VH gene families in peripheral B cell repertoires of newborn or adult immunoglobulin H chain congenic mice

The pattern of VH gene family expression in the primary B cell repertoire of the mouse is strain dependent. In C57Bl/6 mice, the VH J558 family is expressed by more than 45% of the cells, while the expression of VH 7183, VH Q52, and VH 36-60 families together does not exceed 20%. In BALB/c mice, relative expression of VH J558 is lower than 35%, while the sum of the other three families reaches 25%. To assess which genetic loci control strain-specific VH gene family expression, we studied VH gene family usage in splenic B cell repertoires of different congenic strains of mice. Changes in major histocompatibility complex or immunoglobulin (Ig) K light chain genes did not modify VH gene family expression in adult mice. Differences at the IgH locus, however, modified VH gene family usage. In 1-d-old mice, the strain-specific VH gene family expression pattern is determined by the IgH haplotype. In adult mice, the VH gene family expression pattern of resting B cells is independent of the IgH locus and follows the genetic background of the congenic strain, while it is determined by the IgH haplotype among Ig-secreting spleen cells. In F1(B6 x BALB/c) mice, each of the two spleen B cell populations, sorted on the basis of mu heavy chain allotype expression, shows an independent VH gene family expression pattern, determined by the IgH locus. The implications of these results in the control of VH gene family expression, and in the selection of peripheral B cell repertoires are discussed.     

Multiple novel nonsynonymous CYP2B6 gene polymorphisms in Caucasians: demonstration of phenotypic null alleles

The human microsomal cytochrome P450, CYP2B6, is involved in the biotransformation of several clinically important drugs. By complete sequence analysis of the human CYP2B6 gene coding regions in selected Caucasian DNA samples, we identified the five novel missense mutations 62A>T (Q21L in exon 1), 136A>G (M46V in exon 1), 12820G>A (G99E in exon 2), 13076G>A (R140Q in exon 3), and 21388T>A (I391N in exon 8). The recently described but functionally uncharacterized variant 13072A>G (K139E) was also observed. Haplotype analysis indicated the presence of at least six novel alleles that code for the protein variants CYP2B6.10 (Q21L, R22C), CYP2B6.11 (M46V), CYP2B6.12 (G99E), CYP2B6.13 (K139E, Q172H, K262R), CYP2B6.14 (R140Q), and CYP2B6.15 (I391N). Heterologous expression in COS-1 cells revealed comparable levels of CYP2B6 apoprotein and bupropion hydroxylase activity for CYP2B6.1 (wild type) and CYP2B6.10, whereas all other variants exhibited reduced expression and/or function. The three amino acid changes M46V, G99E, and I391N resulted in almost unmeasurable (M46V) or undetectable (G99E and I391N) enzyme activity, despite the presence of residual protein. The K139E change led to completely abolished protein expression; as a consequence, no function was detected. Expression in insect cells by recombinant baculoviruses confirmed these results and demonstrated the virtual absence of incorporated heme in these protein variants. The collective allele frequency of the four very low or null activity variants M46V, G99E, K139E, and I391N was 2.6% in a Caucasian study population. These data provide further insight into the genetic variability of CYP2B6 and demonstrate the existence of phenotypic null alleles in this gene.     

Immunization and infection change the number of recombination activating gene (RAG)-expressing B cells in the periphery by altering immature lymphocyte production

Recombination activating gene (RAG) expression in peripheral B cells increases after immunization with (4-hydroxy-3-nitrophenyl) acetyl coupled to chicken gamma globulin (NP-CGG) in alum. This increase could result from reinduction of RAG expression or, alternatively, from accumulation of RAG-expressing immature B cells in the periphery. We have used mice that carry a green fluorescent protein (GFP) RAG indicator transgene (RAG2-GFP) to characterize the RAG-expressing B cells in immunized spleens. Most of the RAG2-GFP-expressing B cells in unimmunized spleen are immature B cells. Injection with NP-CGG in alum initially suppresses lymphopoiesis in the bone marrow and decreases the number of immature RAG2-GFP-expressing B cells in the spleen. Recovery of lymphopoiesis in the bone marrow coincides with accumulation of RAG-expressing immature B cells in the spleen. Most of the RAG-expressing cells that accumulate in the spleen after immunization do not proliferate and they are not germinal center cells. Neither the initial suppression of lymphopoiesis nor the subsequent accumulation of RAG-expressing cells in the spleen is antigen dependent, since similar changes are seen with alum alone. Furthermore, such changes in the numbers of developing and circulating immature lymphoid cells are seen after injection with complete Freund's adjuvant or malaria infection. Our experiments suggest that adjuvants and infectious agents cause previously unappreciated alterations in lymphopoiesis resulting in the accumulation of RAG-expressing immature B cells in the spleen.     

Immunomagnetic bead-based biotin-streptavidin system for highly efficient detection of aflatoxin B1 in agricultural products

The potential homogeneous assay employing immunomagnetic beads (IMB) has been receiving attention as a screening tool in food-safety control; the method is simple, efficient, and does not require long incubation times or complex separation steps. In this study, a homogeneous immunoassay has been successfully developed and applied in the determination of aflatoxin B₁ (AFB₁) contamination in agricultural products by coupling IMB and the biotin-streptavidin (BSA) (BSA-IMB) system. Under optimal conditions, the limit of detection (LOD, IC₁₀), half-maximal inhibition concentration (IC₅₀) and detection range (IC₂₀–IC₈₀) of BSA-IMB are 0.00579, 0.573 and 0.0183–17.9 ng mL⁻¹, respectively, for AFB₁. The detection of AFB₁ by BSA-IMB can be achieved in 40 min (ELISA needs at least 180 min). The cross-reactivities of BSA-IMB with its analogues are negligible (<3.82%); these results indicate high selectivity. The spiked recoveries are in the range from 89.6 to 118.2% with relative standard deviations (RSDs) of 3.4 to 13.2% for AFB₁ in agricultural product samples. Furthermore, the results of BSA-IMB for authentic samples show reliability and high correlation of 0.9928 with an HPLC-fluorescence detector. The proposed BSA-IMB system is demonstrated to be a satisfactory tool for homogeneous, efficient, sensitive, and alternative detection of AFB₁ in a wide detection range for agricultural product samples.

A strategy of immunomagnetic beads coupled with biotin-streptavidin system (BAS-IMB) for detecting AFB₁ was suggested and applied in agricultural products.     

Effect of specimen storage,antibiotics, and feminine hygiene products on the detection of Group B Streptococcus by culture and the STREP B OIA test

Agar culture from vaginal swabs is the routine method for diagnosis of maternal Group B Streptococcus (GBS) colonization. Swab specimens are often transported to a clinical laboratory for processing. In these studies, specimen transport was simulated by inoculating swabs with GBS and storing them at selected temperatures and with or without transport medium. The recovery of viable GBS was assessed by agar culture. GBS antigen was detected immunologically with an Optical ImmunoAssay (OIA®) method. Swabs that were stored with transport medium harbored viable but rapidly declining numbers of GBS. In contrast, a strong OIA signal was maintained. Recovery of viable GBS organisms declined more quickly when swabs were stored in the absence of transport medium, whereas detection of GBS antigen remained consistent. Both methods were tested for interference from either antibiotics or feminine hygiene products. These compounds inhibited the detection of GBS by culture but had no detrimental effect on the OIA result.     

川芎嗪可影响肿瘤坏死因子a刺激肝星状细胞结缔组织生长因子、核因子κB及相关基因产物的表达

背景:川芎嗪延缓肝纤维化形成的机制尚不清楚.目的:观察川芎嗪对肿瘤坏死因子a 刺激的肝星状细胞增殖及结缔组织生长因子、核因子κB 及其相关基因产物白细胞介素6 表达的影响.方法:体外培养HSC-T6 细胞株,取对数生长期的细胞用于实验.实验分为4 组:对照组仅加入细胞;TNF-a 组加入10 μg/LTNF-a;川芎嗪干预组先加入终浓度为10 μg/L 的TNF-a 作用30 min 后,分别加入川芎嗪50,100,200,400,600,1 000 mg/L;PDTC组先加入终浓度为10 μg/L的TNF-a 作用30 min 后,再加入终浓度18 μmol/L 的核因子κB 阻断剂PDTC.结果与结论:MTT 结果显示100,200,400,600,1 000 mg/L 的川芎嗪均能抑制HSC-T6 增殖,且呈剂量依赖性.免疫细胞化学染色及Western blot 检测发现10 μg/L 的肿瘤坏死因子a 刺激后,HSC-T6 细胞结缔组织生长因子、核因子κB 及白细胞介素6 的表达明显增多(P < 0.01 或P < 0.05),200,400,600 mg/L 的川芎嗪及18 μmol/L 的PDTC均可明显降低肿瘤坏死因子a 刺激后HSC-T6 细胞结缔组织生长因子、核因子κB 及白细胞介素6 的表达(P < 0.01),且随着川芎嗪质量浓度的增加,抑制作用增强,PDTC的抑制作用最明显.相关性分析结果显示HSC-T6 细胞结缔组织生长因子和核因子κB 的表达呈正相关(r=0.980,P < 0.01).说明川芎嗪可以抑制肝星状细胞结缔组织生长因子、核因子κB 及白细胞介素6 的表达,抑制肝星状细胞的增殖.     

川芎嗪可影响肿瘤坏死因子α刺激肝星状细胞结缔组织生长因子、核因子κB及相关基因产物的表达

背景：川芎嗪延缓肝纤维化形成的机制尚不清楚。目的：观察川芎嗪对肿瘤坏死因子α刺激的肝星状细胞增殖及结缔组织生长因子、核因子κB及其相关基因产物白细胞介素6表达的影响。方法：体外培养HSC-T6细胞株,取对数生长期的细胞用于实验。实验分为4组：对照组仅加入细胞;TNF-α组加入10μg/L TNF-α;川芎嗪干预组先加入终浓度为10μg/L的TNF-α作用30min后,分别加入川芎嗪50,100,200,400,600,1000mg/L;PDTC组先加入终浓度为10μg/L的TNF-α作用30min后,再加入终浓度18μmol/L的核因子κB阻断剂PDTC。结果与结论：MTT结果显示100,200,400,600,1000mg/L的川芎嗪均能抑制HSC-T6增殖,且呈剂量依赖性。免疫细胞化学染色及Western blot检测发现10μg/L的肿瘤坏死因子α刺激后,HSC-T6细胞结缔组织生长因子、核因子κB及白细胞介素6的表达明显增多（P〈0.01或P〈0.05）,200,400,600mg/L的川芎嗪及18μmol/L的PDTC均可明显降低肿瘤坏死因子α刺激后HSC-T6细胞结缔组织生长因子、核因子κB及白细胞介素6的表达（P〈0.01）,且随着川芎嗪质量浓度的增加,抑制作用增强,PDTC的抑制作用最明显。相关性分析结果显示HSC-T6细胞结缔组织生长因子和核因子κB的表达呈正相关（r=0.980,P〈0.01）。说明川芎嗪可以抑制肝星状细胞结缔组织生长因子、核因子κB及白细胞介素6的表达,抑制肝星状细胞的增殖。