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PubMed2002

Tumor cell dissemination in follicular lymphoma.

The derivation of follicular lymphomas (FLs) from germinal centers is not only supported by their morphologic appearance with a nodular growth pattern and a germinal center-like cellular composition, but also by the presence of ongoing somatic hypermutation (a germinal center B cell-specific process) during their clonal expansion. The intraclonal sequence diversity of the tumor cells and their follicular growth pattern allows one to analyze lymphoma cell dissemination and the way the tumor "metastasizes" to distinct follicles. In the present study, we analyzed individual follicles of 3 FLs by micromanipulation of single cells from individual lymphoma follicles and amplification of immunoglobulin V region genes. Genealogical trees for the V(H) and the V(L) gene rearrangements were constructed to analyze the clonal relationship among individual cells of 3 distinct follicles of each case. In all 3 cases there is evidence that distinct tumor follicles are founded by many tumor cells, suggesting that there is extensive migration of the tumor cells among follicles. The observation that the tumor cells of FLs retain their follicular growth patterns despite this cellular migration supports the idea that they depend on the follicular microenvironment for their clonal expansion.

Cell Movement↗
PubMed2005

Recent progress in relaxin-3-related research.

Relaxin-3 (R3) is the latest member of the insulin (INSL) superfamily, which is composed of peptides with diverse sequences held together by characteristic disulfide links connecting A and B peptide chains. R3 has nearly exclusive expression in the brainstem and was demonstrated to be an additional ligand for LGR7. We recently identified R3 as a ligand for two orphan G-protein coupled receptors, GPCR135 and GPCR142. The predominant brain expression for both R3 and GPCR135, coupled with their high affinity interaction, strongly suggests that R3 is the endogenous ligand for GPCR135. Both R3 and GPCR135 from different species are highly conserved from genetic sequences to in vitro pharmacology. By contrast, GPCR142 is a pseudogene in the rat, and the mouse gene is less conserved with human GPCR142, suggesting that GPCR142 may have a diminished role as a receptor for R3 in the rodent. In addition, the tissue expression pattern of GPCR142, which is primarily in peripheral tissue, is drastically different from that of R3, suggesting that GPCR142 may have an endogenous ligand other than R3. Sequence analysis among INSL/relaxin family members shows that INSL5 is the closest member of R3. We were able to demonstrate that INSL-5 is an agonist for GPCR142 but not for GPCR135. We also showed that the mRNA expression pattern of INSL-5 overlaps with that of GPCR142. By substituting the A chain of R3 with the A chain of INSL-5, we devised a chimeric peptide (R3/I5) that is about 1000-fold selective for GPCR135 and GPCR142 over LGR7. Autoradiographic distribution of GPCR135 binding sites using [125I]R3/I5 in rat brain shows that GPCR135 receptor is most prominent in areas known for the processing of sensory signals.

Animals↗
PubMed2002

Analysis of antibody gene rearrangement, usage, and specificity in chronic focal encephalitis.

BACKGROUND: Autoantibodies have been implicated in the development of chronic focal encephalitis (CFE) or Rasmussen's disease, a progressive and intractable form of epilepsy characterized by uncontrollable unilateral focal seizures, brain atrophy, and inflammation. OBJECTIVE: To investigate the origin and characteristics of the B cell population that trigger or sustain brain inflammation in patients with CFE. METHODS: The authors used immunoglobulin (Ig) complementary determining region 3 (CDR3)-size spectratyping and DNA sequencing to examine the rearranged IgG heavy chain (IgGH) transcript repertoire in resected brain samples from four patients with CFE. They also performed Western blotting on human and rat brain homogenates and immunostaining on a human neuronal cell line to test the reactivity of sera from patients with CFE. RESULTS: The authors observed substantial perturbations from the normal, unstimulated repertoire of immunoglobulin genes. Sequencing of randomly selected clones confirmed the restricted profile and provided evidence for somatic mutation patterns characteristic of antigen-specific stimulation. They also observed IgGVH-CDR3 sequence diversity among patients. When sera were assayed from patients with CFE for specificity against rat and human brain homogenates, heterogeneous reactivity patterns were detected among patients. Immunostaining of postmitotic human neuronal cells demonstrated reactivity of some patients' sera against neural antigens. CONCLUSIONS: These findings support an important role for clonally expanded B lymphocytes in some forms of epilepsy, but also indicate a wide spectrum of reactivity characteristic of antigenic heterogeneity.

Animals↗
PubMed2005

Evidence for domesticated and wild populations of Saccharomyces cerevisiae.

Saccharomyces cerevisiae is predominantly found in association with human activities, particularly the production of alcoholic beverages. S. paradoxus, the closest known relative of S. cerevisiae, is commonly found on exudates and bark of deciduous trees and in associated soils. This has lead to the idea that S. cerevisiae is a domesticated species, specialized for the fermentation of alcoholic beverages, and isolates of S. cerevisiae from other sources simply represent migrants from these fermentations. We have surveyed DNA sequence diversity at five loci in 81 strains of S. cerevisiae that were isolated from a variety of human and natural fermentations as well as sources unrelated to alcoholic beverage production, such as tree exudates and immunocompromised patients. Diversity within vineyard strains and within saké strains is low, consistent with their status as domesticated stocks. The oldest lineages and the majority of variation are found in strains from sources unrelated to wine production. We propose a model whereby two specialized breeds of S. cerevisiae have been created, one for the production of grape wine and one for the production of saké wine. We estimate that these two breeds have remained isolated from one another for thousands of years, consistent with the earliest archeological evidence for wine-making. We conclude that although there are clearly strains of S. cerevisiae specialized for the production of alcoholic beverages, these have been derived from natural populations unassociated with alcoholic beverage production, rather than the opposite.

Journal Article↗
PubMed2006

Background selection in single genes may explain patterns of codon bias.

Background selection involves the reduction in effective population size caused by the removal of recurrent deleterious mutations from a population. Previous work has examined this process for large genomic regions. Here we focus on the level of a single gene or small group of genes and investigate how the effects of background selection caused by nonsynonymous mutations are influenced by the lengths of coding sequences, the number and length of introns, intergenic distances, neighboring genes, mutation rate, and recombination rate. We generate our predictions from estimates of the distribution of the fitness effects of nonsynonymous mutations, obtained from DNA sequence diversity data in Drosophila. Results for genes in regions with typical frequencies of crossing over in Drosophila melanogaster suggest that background selection may influence the effective population sizes of different regions of the same gene, consistent with observed differences in codon usage bias along genes. It may also help to cause the observed effects of gene length and introns on codon usage. Gene conversion plays a crucial role in determining the sizes of these effects. The model overpredicts the effects of background selection with large groups of nonrecombining genes, because it ignores Hill-Robertson interference among the mutations involved.

Animals↗
PubMed2004

A call for replicating vector prime-protein boost strategies in HIV vaccine design.

A key challenge to HIV vaccine development is the integration of HIV proviral DNA into the host genome upon infection. Therefore, an optimal vaccine should block infection within hours of viral exposure, providing 'sterilizing immunity' at mucosal sites and in blood via potent, broadly reactive antibody to the HIV envelope glycoprotein. This is difficult due to the envelope's conformational complexity and sequence diversity. Antibodies that do not completely prevent infection nevertheless could reduce the viral infectious burden, allowing strong cellular immunity to control viremia, delay disease progression and prevent viral transmission, while also providing help for T- and B-cell responses. Rapidly responsive, potent, persistent immunity might best be achieved using prime-boost strategies incorporating a replicating vector and an optimally designed envelope subunit.

AIDS Vaccines↗
PubMed1999

IL-4-producing gamma delta T cells that express a very restricted TCR repertoire are preferentially localized in liver and spleen.

IL-4-producing gamma delta thymocytes in normal mice belong to a distinct subset of gamma delta T cells characterized by low expression of Thy-1. This gamma delta thymocyte subset shares a number of phenotypic and functional properties with the NK T cell population. Thy-1dull gamma delta thymocytes in DBA/2 mice express a restricted repertoire of TCRs that are composed of the V gamma 1 gene product mainly associated with the V delta 6.4 chain and exhibit limited junctional sequence diversity. Using mice transgenic for a rearranged V gamma 1J gamma 4C gamma 4 chain and a novel mAb (9D3) specific for the V delta 6.3 and V delta 6.4 murine TCR delta chains, we have analyzed the peripheral localization and functional properties of gamma delta T cells displaying a similarly restricted TCR repertoire. In transgenic mice, IL-4 production by peripheral gamma delta T cells was confined to the gamma delta+9D3+ subset, which contains cells with a TCR repertoire similar to that found in Thy-1dull gamma delta thymocytes. In normal DBA/2 mice such cells represent close to half of the gamma delta T cells present in the liver and around 20% of the splenic gamma delta T cells.

Animals↗
PubMed1999

Principles and applications of the polymerase chain reaction.

The polymerase chain reaction (PCR), a primer-directed in vitro enzymatic reaction for the production of a specific DNA fragment, has dramatically facilitated molecular biology approaches to fundamental research questions, as well introduced DNA testing into a variety of clinical diagnostic areas. Some of the principles of PCR, several recent advances in PCR technology and selected applications are reviewed. A variety of methods for analyzing allelic sequence diversity in amplified DNA have been developed. Genetic testing of the HLA loci, and other genes encoding cytokines and cytokine receptors, has had a significant impact on disease susceptibility studies and in clinical transplantation.

DNA↗
PubMed2001

Eosinophils, eosinophil ribonucleases, and their role in host defense against respiratory virus pathogens.

Eosinophils remain among the most enigmatic of cells, as our appreciation of their detrimental activities--e.g., asthma and allergic disease--far outweighs our understanding of their beneficial effects. Among the major secretory effector proteins of eosinophils are the ribonucleases eosinophil-derived neurotoxin (EDN) and eosinophil cationic protein (ECP) in primates and their orthologs, the eosinophil-associated ribonucleases (EARs) in rodents. The rapid diversification observed among these ribonucleases suggested that the ultimate target(s) might be similarly efficient at generating sequence diversity while maintaining an unalterable susceptibility to ribonucleolytic cleavage. This has prompted us to consider a role for these proteins and by extension, for eosinophils, in host defense against single-stranded RNA virus pathogens. We detail our studies of the antiviral activity of eosinophils and eosinophil ribonucleases against respiratory syncytial virus (RSV) in vitro and the related, natural rodent pathogen, pneumonia virus of mice (PVM), in vivo, and consider the possibility that antiviral host defense and the dysregulated responses leading to asthma represent opposing sides of an eosinophil-mediated double-edged sword.

Animals↗
PubMed2005

Interactive selective pressures of HLA-restricted immune responses and antiretroviral drugs on HIV-1.

HIV-specific cytotoxic T lymphocyte (CTL) responses mediated by human leukocyte antigen (HLA) recognition and antiretroviral drugs exert selection pressure on HIV-1 in vivo. The selection of CTL escape mutations strongly underpins the failure of CTL control in most untreated infections whilst drug-resistance mutations predict failure of drug control. These two evolutionary forces share common target residues in HIV-1 at which their selection effects could be synergistic or antagonistic, such that the propensity to develop drug resistance and virological treatment failure may be influenced by HLA type. We examined HIV-1 reverse transcriptase (RT) and protease sequences in a large clinical observational cohort of 487 HIV-infected individuals and found evidence of site-specific interactions between specific antiretroviral drug exposures, HLA alleles and HIV sequence diversity at population level. Such interactions may have general and specific implications for explaining in vivo/in vitro discordance of drug resistance, host-specific susceptibility to drug resistance, individualization of therapy and therapeutic vaccine design.

Anti-HIV Agents↗
PubMed1991

Simplified PCR-based detection and typing strategy for human papillomaviruses utilizing a single oligonucleotide primer set.

Utilizing the PCR, we have devised a detection and typing system for the human papillomaviruses (HPVs) that are commonly associated with preneoplastic and cancerous lesions of the genital and aero-digestive tracts: HPV 6, 11, 16 and 18. Utilizing computer sequence analysis, we designed a single, "consensus" set of oligomeric nucleotide primers capable of amplifying a 571-594-bp region of the E1 open reading frame of all of these HPVs. Detection via PCR amplification is followed by restriction endonuclease digestion of the resultant products that yield distinctive and reproducible banding patterns by polyacrylamide gel electrophoresis because of their internal sequence diversity. The system is sensitive, does not require sophisticated molecular biology expertise or radioisotopes and can be modified as new information on HPV types and their relationship to diseases becomes available.

Electrophoresis, Agar Gel↗
PubMed2006

Anion exchangers in flux: functional differences between human and mouse SLC26A6 polypeptides.

The SLC26 anion transporter polypeptides exhibit considerably greater sequence diversity among near-species orthologues than is found among the SLC4 bicarbonate transporters, and among SLC26 transporters is most marked among SLC26A6 orthologues. This observation prompted systematic functional comparison in Xenopus oocytes of mouse Slc26a6 with several human SLC26A6 polypeptide variants. Mouse and human polypeptides exhibited similar rates of bidirectional [14C]oxalate flux, Cl-/HCO3- exchange, and Cl-/OH- exchange, and similar cAMP-stimulation and enhancement of that stimulation by wild-type but not delta F508 CFTR. However, high rates of 36Cl- and 35S-sulfate transport by mouse Slc26a6 contrasted with low transport rates of the human proteins. The high 36Cl- transport phenotype cosegregated with the transmembrane domain of mouse Slc26a6 in chimera studies. Mouse Slc26a6 and human SLC26A6 each mediated electroneutral Cl-/HCO3- and Cl-/OH- exchange. But, whereas Cl-/oxalate exchange by mouse Slc26a6 was electrogenic, that mediated by human SLC26A6 appeared electroneutral. Oocyte expression of either mouse or human orthologue elicited currents that were pharmacologically distinct from the monovalent anion exchange activities measured in the same lots of oocytes. The human SLC26A6 polypeptide variants SLC26A6c and SLC26A6d were inactive in isotopic flux assays. Understanding of SLC26 transport mechanisms and pathophysiology will benefit from recognition of substantial differences in transport properties among orthologues.

Animals↗
PubMed1977

Effect of bleomycin on the synthesis and function of RNA.

Bleomycin inhibits cellular RNA synthesis and the inhibition is nonspecific. The ratio of polyadenylate- [poly(A)] containing RNA to non-poly(A)-containing RNA in the drug-treated human lymphocytic cells, line Wil2, was the same as that in untreated cells. Poly(A) RNA isolated from untreated cells was used as a template for reverse transcriptase to synthesize complementary DNA, which was then used as a probe to assay the sequence diversity of poly(A)RNA's from treated and untreated cells. It was found that essentially all of the poly(A) RNA's in the untreated cells were also present in the treated cells. The effect of bleomycin on the biological activity of messenger RNA (mRNA) was tested with globin mRNA in a wheat germ embryo translation system. Although bleomycin inhibited protein synthesis at high concentrations, the inhibition was not due to a modification of mRNA. This was evidenced by the fact that no decrease in the ability of mRNA to function in the test system was found when globin mRNA was pretreated with high concentrations of bleomycin followed by removal of the drug.

Bleomycin↗
PubMed1995

Redox-shift of the pheromone-binding protein in the silkmoth Antheraea polyphemus.

In pheromone-sensitive hairs of the male silkmoth Antheraea polyphemus, two electrophoretically distinct pheromone-binding proteins (PBPs) are present. They indicate no amino acid sequence diversity according to peptide mapping, but differ in their redox state, as shown by free-sulfhydryl-group-specific cleavage at cysteine residues with 2-nitro-5-thiocyanobenzoic acid. In kinetic studies, the pheromone was initially bound mainly by the reduced PBP but later by the oxidized PBP, where all six cysteine residues form disulfide bonds. This redox shift was observed only in the homogenate of isolated olfactory hairs, where proteins of the sensillum lymph and receptive dendrites are present. In control experiments with purified binding proteins, the proportion of pheromone bound to the oxidized PBP did not increase with increasing incubation time, suggesting that disulfide formation does not occur spontaneously but is mediated by the sensory hairs, possibly by interaction with the receptor cell membrane. These data suggest that arriving hydrophobic pheromone molecules are first bound by the reduced PBP and transported through the aqueous sensillum lymph towards the receptor molecules of the dendritic membrane. The oxidized complex might not be able to activate further receptors and, thus, effectively deactivate the pheromone molecules within the sensillum lymph.

Animals↗
PubMed1998

Identification of diverse BoLA DQA3 genes consistent with non-allelic sequences.

Genetic diversity within the DQA genes of the major histocompatibility complex (Mhc) of cattle is characterised by multiple polymorphic loci that can vary in number between haplotypes. Previous analysis of the second exon sequences derived from genomic BoLA DQA3 genes identified two distinct families, DQA3*01 and DQA3*02. In this report, we describe the nucleotide and predicted amino acid sequences of the entire coding region of three transcribed BoLA DQA3 genes representing each of these families. These data provide additional evidence that the BoLA DQA3 locus is distinct from BoLA DQA1 and BoLA DQA2. In addition, the amino acid sequence of DQA3 genes from the two families is shown to differ by 35 out of the 254 amino acids. Putative locus-specific amino acid sequence motifs within the transmembrane and intracytoplasmic domains of DQA genes are shown to differ between the DQA3*01 and DQA3*02 genes. Phylogenetic analysis reveals a genetic distance that is considerably larger than that seen between orthologous Mhc allelic families. These data are consistent with either an extremely divergent family of DQA3 genes or an allele at an additional BoLA DQA4 locus.

Alleles↗
PubMed1993

Sequence and antigenic diversity in two immunodominant regions of the L2 protein of human papillomavirus types 6 and 16.

To assess the extent of sequence and antigenic diversity in the minor capsid proteins (L2) of human papillomavirus (HPV) types 6 and 16, 24 clinical samples were obtained, and the regions encoding the immunodominant epitopes 6U3 and 16REx were amplified by polymerase chain reaction, sequenced, cloned into pATH plasmids, and tested for reactivity with human sera. Two of 11 HPV-6 DNAs were identical to the prototype strain in the 6U3 region, while 9 variants had a G to A transition at nt5020, changing a valine residue to isoleucine. Of 16 sera that did not react with the prototype HPV-6L2 fusion protein, 2 reacted with the 6U3-isoleucine variant, and all 8 sera that reacted with the prototype also reacted with the variant. Twelve of 13 HPV-16 DNAs were identical to the prototype strain in the 16REx region, while 1 variant had a C to G transversion at nt4825, changing a proline to an arginine, but not affecting antigenicity.

Amino Acid Sequence↗
PubMed2003

Prion gene sequence variation within diverse groups of U.S. sheep, beef cattle, and deer.

Prions are proteins that play a central role in transmissible spongiform encephalopathies in a variety of mammals. Among the most notable prion disorders in ungulates are scrapie in sheep, bovine spongiform encephalopathy in cattle, and chronic wasting disease in deer. Single nucleotide polymorphisms in the sheep prion gene ( PRNP) have been correlated with susceptibility to natural scrapie in some populations. Similar correlations have not been reported in cattle or deer; however, characterization of PRNP nucleotide diversity in those species is incomplete. This report describes nucleotide sequence variation and frequency estimates for the PRNP locus within diverse groups of U.S. sheep, U.S. beef cattle, and free-ranging deer ( Odocoileus virginianus and O. hemionus from Wyoming). DNA segments corresponding to the complete prion coding sequence and a 596-bp portion of the PRNP promoter region were amplified and sequenced from DNA panels with 90 sheep, 96 cattle, and 94 deer. Each panel was designed to contain the most diverse germplasm available from their respective populations to facilitate polymorphism detection. Sequence comparisons identified a total of 86 polymorphisms. Previously unreported polymorphisms were identified in sheep (9), cattle (13), and deer (32). The number of individuals sampled within each population was sufficient to detect more than 95% of all alleles present at a frequency greater than 0.02. The estimation of PRNP allele and genotype frequencies within these diverse groups of sheep, cattle, and deer provides a framework for designing accurate genotype assays for use in genetic epidemiology, allele management, and disease control.

Amyloid↗
PubMed1990

Diversity in junctional sequences associated with the common human V gamma 9 and V delta 2 gene segments in normal blood and lung compared with the limited diversity in a granulomatous disease.

The T cell receptor (TCR) junctional regions (N regions) of the common human V gamma 9 and V delta 2 gene segments were sequenced from the blood and lung of normal individuals (195 transcripts) and a group of individuals with sarcoidosis (220 transcripts), a granulomatous disease in which increased numbers of V gamma 9+ gamma/delta + T cells are often observed. In normal individuals, the vast majority (86%) of blood V gamma 9 transcripts used the J gamma P gene segment. In contrast to this restriction of J region usage, there was a large diversity of the junctional region, with less than 20% of blood V gamma 9 junctional regions showing identical sequences for any one normal individual. For the blood V delta 2 transcripts in normal individuals, there was restriction of J region usage, with 93% using J delta 1. The junctional regions were even more diverse than for V gamma 9, with a unique sequence observed in each transcript examined. Compared with blood, sequences from the normal lung showed a small increase in identical junctional regions, particularly in one individual where 46% of V gamma 9 transcripts examined were identical, suggesting a response of some gamma/delta T cells to antigens found in the lung in the normal state. In marked contrast to normals, some individuals with sarcoidosis had large numbers of V gamma 9 transcripts, as well as V delta 2 transcripts, sharing identical sequences. For V gamma 9 blood transcripts, two individuals showed 84 and 56% of junctional region sequences to be identical, respectively. Similarly, blood V delta 2 transcripts showed 43, 33, and 25% identical junctional region sequences in three individuals. In the sarcoid patient with the most striking over-representation of blood V gamma 9 junctional sequences, lung V gamma 9 transcripts showed increased (67%) use of the same junctional region sequence as in blood. This limited diversity of TCR junctional regions among some individuals with sarcoidosis suggests a response from specific stimuli, possibly antigenic, and that gamma/delta T cells may play a specific role in granuloma formation in sarcoidosis, as has been suggested in other granulomatous diseases.

Adult↗