Construction of a whole-genome radiation hybrid panel for high-resolution gene mapping in pigs

We have developed a panel of 152 whole-genome radiation hybrids by fusing irradiated diploid pig lymphocytes or fibroblasts with recipient hamster permanent cells. The number and size of the porcine chromosome fragments retained in each hybrid clone were checked by fluorescence in situ hybridization with a SINE probe or by primed in situ labeling (PRINS) with SINE-specific primers. A strategy based on the interspersed repetitive sequence polymerase chain reaction (IRS-PCR) was developed for selected clones to determine if the large fragments painted by the SINE probe corresponded to one pig chromosome or to different fragments of several chromosomes. This strategy was buttressed by a double PRINS approach using primers specific for alpha-satellite sequences of two different groups of swine chromosomes. Genome retention frequency was estimated for each clone by PCR with 32 markers localized on different porcine chromosomes. Of the 152 hybrids produced, 126 were selected on the basis of cytogenetic content and chromosome retention frequency to construct a radiation hybrid map of swine chromosome 8. Our initial results for this chromosome indicate that the resolution of the radiation hybrid map is 18 times higher than that obtained by linkage analysis.

IMpRH server: an RH mapping server available on the Web

SUMMARY

The INRA-Minnesota Porcine Radiation Hybrid (IMpRH) Server provides both a mapping tool (IMpRH mapping tool) and a database (IMpRH database) of officially submitted results. The mapping tool permits the mapping of a new marker relatively to markers previously mapped on the IMpRH panel. The IMpRH database is the official database for submission of new results and queries. The database not only permits the sharing of public data but also semi-private and private data.

African-American attitudes regarding cancer clinical trials and research studies: results from focus group methodology

Despite federal recommendations highlighting the need to include special population groups (mainly minorities and women) in clinical research, recruitment and retention of these groups present a great challenge to researchers. This paper describes a focus group study that was conducted to examine factors related to minority participation and retention in cancer clinical research studies. In 1996, the National Cancer Institute submitted a request for applicants to receive support for regional conferences. The purpose of the proposed conferences was to share current information and strategies to aid cancer clinical investigators in recruiting and retaining minority participants in clinical cancer research and to stimulate local/regional adaptations of these strategies. The University of Alabama at Birmingham (UAB), The University of Alabama, and Tuskegee University collaborated to respond to the request. Funding was granted by NCI for the regional conference in Alabama. The conference was held in Tuskegee, Alabama, the site of the infamous US Public Health Syphilis Study at Tuskegee. In planning for the conference, focus group sessions were conducted with African-American men and women who represented all regions of Alabama. The focus group information was used to identify important issues to be addressed at the conference.

Unusual polymorphisms in human immunodeficiency virus type 1 associated with nonprogressive infection

Factors accounting for long-term nonprogression may include infection with an attenuated strain of human immunodeficiency virus type 1 (HIV-1), genetic polymorphisms in the host, and virus-specific immune responses. In this study, we examined eight individuals with nonprogressing or slowly progressing HIV-1 infection, none of whom were homozygous for host-specific polymorphisms (CCR5-Delta32, CCR2-64I, and SDF-1-3'A) which have been associated with slower disease progression. HIV-1 was recovered from seven of the eight, and recovered virus was used for sequencing the full-length HIV-1 genome; full-length HIV-1 genome sequences from the eighth were determined following amplification of viral sequences directly from peripheral blood mononuclear cells (PBMC). Longitudinal studies of one individual with HIV-1 that consistently exhibited a slow/low growth phenotype revealed a single amino acid deletion in a conserved region of the gp41 transmembrane protein that was not seen in any of 131 envelope sequences in the Los Alamos HIV-1 sequence database. Genetic analysis also revealed that five of the eight individuals harbored HIV-1 with unusual 1- or 2-amino-acid deletions in the Gag sequence compared to subgroup B Gag consensus sequences. These deletions in Gag have either never been observed previously or are extremely rare in the database. Three individuals had deletions in Nef, and one had a 4-amino-acid insertion in Vpu. The unusual polymorphisms in Gag, Env, and Nef described here were also found in stored PBMC samples taken 3 to 11 years prior to, or in one case 4 years subsequent to, the time of sampling for the original sequencing. In all, seven of the eight individuals exhibited one or more unusual polymorphisms; a total of 13 unusual polymorphisms were documented in these seven individuals. These polymorphisms may have been present from the time of initial infection or may have appeared in response to immune surveillance or other selective pressures. Our results indicate that unusual, difficult-to-revert polymorphisms in HIV-1 can be found associated with slow progression or nonprogression in a majority of such cases.

The primary sequence of rhesus monkey rhadinovirus isolate 26-95: sequence similarities to Kaposi's sarcoma-associated herpesvirus and rhesus monkey rhadinovirus isolate 17577

The primary sequence of the long unique region L-DNA (L for low GC) of rhesus monkey rhadinovirus (RRV) isolate 26-95 was determined. The L-DNA consists of 130,733 bp that contain 84 open reading frames (ORFs). The overall organization of the RRV26-95 genome was found to be very similar to that of human Kaposi sarcoma-associated herpesvirus (KSHV). BLAST search analysis revealed that in almost all cases RRV26-95 coding sequences have a greater degree of similarity to corresponding KSHV sequences than to other herpesviruses. All of the ORFs present in KSHV have at least one homologue in RRV26-95 except K3 and K5 (bovine herpesvirus-4 immediate-early protein homologues), K7 (nut-1), and K12 (Kaposin). RRV26-95 contains one MIP-1 and eight interferon regulatory factor (vIRF) homologues compared to three MIP-1 and four vIRF homologues in KSHV. All homologues are correspondingly located in KSHV and RRV with the exception of dihydrofolate reductase (DHFR). DHFR is correspondingly located near the left end of the genome in RRV26-95 and herpesvirus saimiri (HVS), but in KSHV the DHFR gene is displaced 16,069 nucleotides in a rightward direction in the genome. DHFR is also unusual in that the RRV26-95 DHFR more closely resembles HVS DHFR (74% similarity) than KSHV DHFR (55% similarity). Of the 84 ORFs in RRV26-95, 83 contain sequences similar to the recently determined sequences of the independent RRV isolate 17577. RRV26-95 and RRV17577 sequences differ in that ORF 67.5 sequences contained in RRV26-95 were not found in RRV17577. In addition, ORF 4 is significantly shorter in RRV26-95 than was reported for RRV17577 (395 versus 645 amino acids). Only four of the corresponding ORFs between RRV26-95 and RRV17577 exhibited less than 95% sequence identity: glycoproteins H and L, uracil DNA glucosidase, and a tegument protein (ORF 67). Both RRV26-95 and RRV17577 have unique ORFs between positions 21444 to 21752 and 110910 to 114899 in a rightward direction and from positions 116524 to 111082 in a leftward direction that are not found in KSHV. Our analysis indicates that RRV26-95 and RRV17577 are clearly independent isolates of the same virus species and that both are closely related in structural organization and overall sequence to KSHV. The availability of detailed sequence information, the ability to grow RRV lytically in cell culture, and the ability to infect monkeys experimentally with RRV will facilitate the construction of mutant strains of virus for evaluating the contribution of individual genes to biological properties.

Generational differences in male sexuality that may affect Zimbabwean women's risk for sexually transmitted diseases and HIV/AIDS

OBJECTIVE

To determine generational differences in male sexuality, which could predispose men's female sexual partners to STDs/HIV.

DESIGN

Cross-sectional study.

SETTING

Harare, Zimbabwe.

SUBJECTS

Three hundred and ninety seven male adults aged eighteen years and above.

MAIN OUTCOME MEASURES

Number of sexual partners, condom use, likelihood of sharing information on HIV status with wife or with other sexual partners, preference for women with dry vaginas prior to sex and discussion about sexual satisfaction with wife or with girl friend.

RESULTS

Fewer men in the 27-39 year age group when compared to men aged 18-26 years (22.2% versus 28.9%) had two or more sexual partners. The greatest proportion of ever condom users were men aged 27-39 years, but this proportion was not significantly different from the proportion of ever condom users aged 18-26 years (76.5% versus 69.5%; Odds Ratio[OR] = 1.42, 95% Confidence interval [CI] 0.81-2.51). Men aged > or = 40 years (43.8%, OR = 0.34, 95% CI 0.20-0.84) were significantly fewer than men aged 18-26 years in ever use of condoms. In the event that they contracted HIV, 79.5%, 82.4% and 85.9% of men aged 18-26, 27-39 and 40 years and above respectively indicated that they would disclose their HIV status to their wives. On the other hand, men aged 18-26 years (56.8%), 27-39 years (54.0%) and > or = 40 years (53.1%) indicated that they would disclose their HIV status to girl friends or other sexual partners. Significantly, more men aged 40 years (OR = 2.23; 95% CI 1.19-4.18) and 27-39 years (OR = 1.82; 95% CI 1.00-3.32) in comparison to 18-26 year old men indicated their preference for women with dry vaginas prior to sex. The greatest proportion of men who discussed sexual satisfaction with their wives (85.7%) and girl friends or other sexual partners (23.5%) were aged 27-39 years.

CONCLUSION

It is recommended that public health and behavioural scientists in Zimbabwe devote more time to understanding the intricacies of male sexual behaviour at different stages of life. This would provide the important insight needed to develop effective targeted interventions to reduce the spread of STDs/HIV in Zimbabwe.

Species specificity of macaque rhadinovirus glycoprotein B sequences

All members of the Herpesviridae family contain sequences for a highly conserved glycoprotein B (gB) gene. We investigated the phylogenetic relationships of gB sequences from eight independent rhadinovirus isolates obtained from three species: rhesus (Macaca mulatta), cynomologus (Macaca fasicularis), and pig-tailed (Macaca nemestrina) macaques. Samples were derived from monkeys housed at four separate facilities. Analysis of these eight independent gB sequences revealed five regions of heterogeneity within the 823- to 829-amino-acid polypeptides: residues 1 to 65, 120 to 185, 255 to 300, 352 to 393, and 412 to 457. The remaining regions of gB were highly conserved among the different macaque isolates. Overall divergence among these gene sequences ranged from 0.1 to 7.2% at the amino acid level. Phylogenetic trees constructed with our macaque rhadinovirus gB sequences and those derived from additional subfamilies or genera (alpha, beta, gamma-1, and gamma-2) revealed that the macaque gB sequences branched with other gamma-2 herpesvirus gB sequences and that within the gamma-2 genera, the macaque gB sequences clustered as a distinct branch. The eight macaque rhadinovirus gB sequences were all approximately equidistant from Kaposi sarcoma-associated herpesvirus (KSHV) gB sequences and had a shorter evolutionary distance to KSHV gB sequences than to any other herpesvirus, including the gamma-2 herpesvirus saimiri (HVS) of New World squirrel monkeys. The macaque gB sequences did not cluster according to the facility of origin, but did cluster according to the species of origin, displaying less intraspecies divergence (0.1 to 2.9%) than interspecies divergence (3.3 to 7.2%). These results demonstrate a close relatedness of rhadinovirus isolates from different macaque species.

Long-term nonprogressive infection with human immunodeficiency virus type 1 in a hemophilia cohort

Seven long-term nonprogressors (LTNPs) have been identified in a cohort of 128 human immunodeficiency virus (HIV)-1 infected individuals with hemophilia. Studies included quantitation of virus by polymerase chain reaction, characterization of primary virus isolates in vitro, analysis of lymphocyte surface markers, and measurement of virus-specific cytotoxic T lymphocytes (CTLs). Viruses of LTNPs exhibited slow growth in vivo and in vitro. LTNPs had expansion of CD8 T cells with increased expression of HLA-DR. Intermittent HIV-1-specific CTL effector activity was detected in freshly isolated peripheral blood mononuclear cells of most LTNPs. CTL precursor frequencies were higher in LTNPs than in patients with progressive disease. Virus antigen-specific lymphoproliferation was vigorous in some LTNPs. Thus, LTNPs in this cohort have maintained remarkably low virus burdens and vigorous HIV-1-specific cell-mediated immunity over a 15-year period. The presence of expanded, activated CD8 T cells with cytotoxic effector function in the peripheral blood suggests ongoing viral replication.

Induction of AIDS in rhesus monkeys by a recombinant simian immunodeficiency virus expressing nef of human immunodeficiency virus type 1

A nef gene is present in all primate lentiviruses, including human immunodeficiency virus type 1 (HIV-1) and simian immunodeficiency virus of macaque monkeys (SIVmac). However, the nef genes of HIV-1 and SIVmac exhibit minimal sequence identity, and not all properties are shared by the two. Nef sequences of SIVmac239 were replaced by four independent nef alleles of HIV-1 in a context that was optimal for expression. The sources of the HIV-1 nef sequences included NL 4-3, a variant NL 4-3 gene derived from a recombinant-infected rhesus monkey, a patient nef allele, and a nef consensus sequence. Of 16 rhesus monkeys infected with these SHIVnef chimeras, 9 maintained high viral loads for prolonged periods, as observed with the parental SIVmac239, and 6 have died with AIDS 52 to 110 weeks postinfection. Persistent high loads were observed at similar frequencies with the four different SIV recombinants that expressed these independent HIV-1 nef alleles. Infection with other recombinant SHIVnef constructions resulted in sequence changes in infected monkeys that either created an open nef reading frame or optimized the HIV-1 nef translational context. The HIV-1 nef gene was uniformly retained in all SHIVnef-infected monkeys. These results demonstrate that HIV-1 nef can substitute for SIVmac nef in vivo to produce a pathogenic infection. However, the model suffers from an inability to consistently obtain persisting high viral loads in 100% of the infected animals, as is observed with the parental SIVmac239.

Identification of the R1 oncogene and its protein product from the rhadinovirus of rhesus monkeys

Rhesus monkey rhadinovirus (RRV) is a gamma-2 herpesvirus that is most closely related to the human Kaposi's sarcoma-associated herpesvirus (KSHV). We have identified a distinct open reading frame at the left end of RRV and designated it R1. The position of the R1 gene is equivalent to that of the saimiri transforming protein (STP) of herpesvirus saimiri (HVS) and of K1 of KSHV, other members of the gamma-2 or rhadinovirus subgroup of herpesviruses. The R1 sequence revealed an open reading frame encoding a product of 423 amino acids that was predicted to contain an extracellular domain, a transmembrane domain, and a C-terminal cytoplasmic tail reflective of a type I membrane-bound protein. The predicted structural motifs of R1, including the presence of immunoreceptor tyrosine-based activation motifs, resembled those in K1 of KSHV but were distinct from those of STP. R1 sequences from four independent isolates from three different macaque species revealed 0.95 to 7.3% divergence over the 423 amino acids. Variation was located predominantly within the predicted extracellular domain. The R1 protein migrated at 70 kDa by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and was extensively glycosylated. Tagged R1 protein was localized to the cytoplasmic and plasma membranes of transfected cells. Expression of the R1 gene in Rat-1 fibroblasts induced morphologic changes and focus formation, and injection of R1-expressing cells into nude mice induced the formation of multifocal tumors. A recombinant herpesvirus in which the STP oncogene of HVS was replaced by R1 immortalized T lymphocytes to interleukin-2-independent growth. These results indicate that R1 is an oncogene of RRV.

Recombinant simian immunodeficiency virus expressing green fluorescent protein identifies infected cells in rhesus monkeys

We engineered recombinant derivatives of simian immunodeficiency virus (SIV) to express enhanced green fluorescent protein (EGFP). Replacement of vpr sequences with EGFP resulted in a genome that did not produce detectable levels of replication-competent virus. Replication-competent virus and bright fluorescence of infected cells were obtained with two other constructs, one in which SIV nef sequences were replaced by EGFP and another in which EGFP was inserted into the SIV nef locus and HIV-1 nef sequences were expressed by downstream placement of an internal ribosomal entry site. These strains were infectious in rhesus monkeys and green fluorescing cells were detected in the tissues of infected monkeys by FACS analysis and by direct microscopic visualization. EGFP sequences were absent from recovered virus by 8 weeks following infection. We conclude that recombinant SIV that is engineered to express EGFP can be used to directly detect productively infected cells and aid in the immunophenotypic characterization of these cells within the first 2 weeks of infection of rhesus monkeys.

Livestock variation of linked microsatellite markers in diverse swine breeds

A panel of nine framework microsatellites (MS) linked to the Calcium Release Channel (CRC) locus on swine chromosome 6 (SSC6) was developed from the consensus genetic map. MS were screened across groups of unrelated animals from Yorkshire, Hampshire, Duroc, Landrace and Meishan swine breeds. Unique MS alleles for Yorkshire, Duroc, Landrace and Meishan breeds, and statistically significant (P < .05) associations between breeds and allele frequencies were found for each MS. Although breed marker heterozygosities ranged from 0.0 (S0035 in Duroc) to 0.92 (S0087 in Meishan), Correspondence Analysis identified MS alleles uniquely associated with either the Meishan breed, western breeds or alleles common to all breeds. Furthermore, an overall marker heterozygosity of < 0.70 demonstrates the need for multiple MS panels to accommodate reduced within-breed differences for identification of quantitative trait loci (QTL), marker assisted selection (MAS) programs or parental identification in commercial breeds.

Substitution of ras for the herpesvirus saimiri STP oncogene in lymphocyte transformation

STP-C488 (STP of herpesvirus saimiri [HVS] group C strain 488 [C488]) is the only virus-encoded protein found to associate with cellular ras and activate ras signal transduction pathways. To investigate an important role for ras signal transduction in STP-dependent growth transformation, we constructed recombinant strains of HVS C488 in which the STP-C488 oncogene was replaced with cellular normal ras (c-ras) or viral oncogenic ras (v-ras). Recombinant HVS deltaSTP/v-ras immortalized primary common marmoset T lymphocytes to interleukin-2-independent growth as efficiently as wild-type HVS C488 (wt HVS), while recombinant HVS deltaSTP/c-ras did so with low efficiency. Whereas wt HVS immortalized CD4- CD8+ single-positive T lymphocytes, HVS deltaSTP/c-ras- and HVS deltaSTP/v-ras-immortalized cells were principally CD4+ CD8+ double-positive T lymphocytes. In addition, HVS deltaSTP/v-ras-immortalized T cells showed a high level of ras expression and exhibited an adherent macrophage-like morphology. These phenotypes were likely caused by the drastic activation of AP-1 transcriptional factor activity. Finally, HVS deltaSTP/v-ras and HVS deltaSTP/c-ras each induced lymphoma in one of two common marmosets, although onset of disease was more rapid with the v-ras virus. These results demonstrate that ras can substitute for the STP oncogene of HVS C488 to allow immortalized growth of primary lymphoid cells and that an activated form of ras does so more efficiently than the normal cellular form of ras.

An audit of the management of thyroid cancer in a district general hospital

OBJECTIVE

Thyroid cancer is the commonest endocrine malignancy yet it appeared to present infrequently to the endocrinologists at this large District General Hospital. The management of well-differentiated thyroid cancer remains controversial with a wide variation in clinical practice. The aim of this survey was to determine the characteristics of the patients diagnosed with thyroid cancer and whether any deficiencies existed in the management of subjects diagnosed with thyroid cancer over a five-year period using standards of care based upon long-term outcome data and recently published USA guidelines.

DESIGN AND PATIENTS

Retrospective case-note survey of all patients newly registered with thyroid cancer from 1990 to 1994 in North Staffordshire (estimated total population 450,000).

RESULTS

The annual incidence of all thyroid cancer was two per 100,000 of which well-differentiated tumours comprised 70%. Medical records were obtained in 48 new cases (91% of total) identified. Fifteen subjects who presented as surgical emergencies received only palliative treatment and had a poor outcome. Two patients presented with metastatic medullary thyroid carcinoma (3% of total). Thirty-one patients (97% of whom presented with a thyroid nodule) were referred electively to either surgical (n = 22), ENT (n = 2) or endocrinology (n = 7) outpatients with well-differentiated papillary (n = 17) and follicular (n = 14) tumours. Thirteen patients (42%) had fine-needle aspiration cytology performed preoperatively. Of the 22 tumours (71%) greater than 1.5 cm, five (27%) had a total thyroidectomy and two (9%) also had radioiodine ablation. There was inadequate serum thyrotrophin suppression postoperatively in 12 patients (39%) and only five (16%) were being monitored for recurrence with serum thyroglobulin measurements.

CONCLUSIONS

Deficiencies in the optimum management of small, well-differentiated thyroid cancers were identified. Improved communication between specialties has led to the development of an agreed management protocol to increase the quality of care offered to patients with thyroid cancer and for auditing the coordinated service in the future.

A profile of sexual health behaviors among college women

This study examined the risk taking and preventive behaviors related to sexually transmitted diseases among sexually active college women. Self-report questionnaires were distributed at two mid-Atlantic universities yielding a final sample of 556 students. Data were collected regarding frequencies of pelvic examinations, numbers of vaginal, oral, and anal sex partners, and number of partners who had forced sex against their will. Also, frequencies of tests for sexually transmitted disease and HIV before having sex with new partners, methods of protection and birth control, and types of relationships were assessed. Finally, subjects reported the types of questions asked before having sex with a new partner and diagnoses of sexually transmitted diseases. Because most college-aged women are sexually active and vulnerable to a host of short- and long-term complications from sexually transmitted infections, educational interventions, in addition to promoting condom use, must focus on the need for regular pelvic examinations, screenings for sexually transmitted disease/HIV (self and partner), and lower risk sexual activity.

Evaluating evolutionary divergence with microsatellites

We report the use of microsatellites (MS) to track the recent evolution of swine. Allelic frequencies for nine MS loci linked on swine chromosome 6 (SSC6) representing four western and one Chinese swine breeds were used to estimate genetic distances and times of breed divergence. A phylogenetic tree was constructed which partitioned into western and Meishan breed branches. Yorkshire and Hampshire breeds exhibited the most recent divergence with a calculated distance of 391 years. The oldest divergence, of 2,227 years, was between Meishan and Hampshire swine. Estimates of breed divergence are consistent with historical records. Additional analysis suggests that polymorphic MS linked on a single chromosome are sufficient to determine evolutionary relationships within a single species.

Prevalence of obesity with increased blood pressure in elementary school-aged children

The objectives of this study were to estimate the prevalence of obesity in school-aged children in Jefferson County, Alabama; to learn when school-aged children become obese; to determine the susceptible groups; and to study the association between obesity and blood pressure. During the school year, 5,953 children, ranging in age from 5 years to 11 years, were screened for weight, height, and blood pressure, using standardized techniques. We found that obesity, defined as > or = 120% of ideal body weight for height, is prevalent in 5-year-old to 11-year-old children. The prevalence of obesity in girls at age 5 was 23% in blacks and 10% in whites, rising to 47% in blacks and 27% in whites by age 11. In boys, the prevalence of obesity at age 5 was 13% in blacks and 6% in whites, rising to 29% in blacks and 22% in whites by age 11. The prevalence of obesity is significantly greater in black than in white children and is also significantly greater in girls than boys. The systolic and diastolic blood pressures were significantly higher in obese than in non-obese children. We conclude that the significant prevalence of childhood obesity and an associated complication, increased blood pressure, emerge in school-aged children. Thus, we recommend investigations of prevention and intervention programs to be used in the school setting.

A role for natural simian immunodeficiency virus and human immunodeficiency virus type 1 nef alleles in lymphocyte activation

A T-lymphoid cell line termed 221 was derived from a rhesus monkey infected with herpesvirus saimiri. Growth of 221 cells was dependent on the addition of interleukin-2 (IL-2) to the culture medium. In the absence of IL-2, 221 cells arrested in G0-G1 but did not die. Simian immunodeficiency virus (SIV) replicated efficiently in IL-2-stimulated 221 cells whether or not the nef gene was present. In the absence of IL-2, nef-containing SIV replicated 8 to 100 times more efficiently in 221 cells than did the same virus lacking nef. nef-containing virus preferentially stimulated the production of IL-2 from 221 cells. HIV-1 nef and v-ras genes, but not the c-ras gene, were shown to substitute functionally for SIV nef when tested as recombinant viruses in this assay system. These results demonstrate a role for natural nef in causing lymphoid cell activation, and they provide a system for delineating the biochemical mechanisms responsible for this activation.

Tibial fracture in a basketball player: treatment dilemmas and complications

A 19-year-old male basketball player suffered a spiral fracture of the tibia with an intact fibula, an uncommon injury in basketball. Treatment options for these injuries include cast immobilization, external fixation, and internal fixation using an intramedullary rod or plates and screws. Numerous complications can occur in these injuries, possibly including interference with healing by the intact fibula. The player was treated with an intramedullary rod, but delayed union ensued. Treatment of the patient's delayed union with closed exchange intramedullary nailing and fibular osteotomy enabled him to return to basketball participation.