The genomic sequence and analysis of the swine major histocompatibility complex

We describe the generation and analysis of an integrated sequence map of a 2.4-Mb region of pig chromosome 7, comprising the classical class I region, the extended and classical class II regions, and the class III region of the major histocompatibility complex (MHC), also known as swine leukocyte antigen (SLA) complex. We have identified and manually annotated 151 loci, of which 121 are known genes (predicted to be functional), 18 are pseudogenes, 8 are novel CDS loci, 3 are novel transcripts, and 1 is a putative gene. Nearly all of these loci have homologues in other mammalian genomes but orthologues could be identified with confidence for only 123 genes. The 28 genes (including all the SLA class I genes) for which unambiguous orthology to genes within the human reference MHC could not be established are of particular interest with respect to porcine-specific MHC function and evolution. We have compared the porcine MHC to other mammalian MHC regions and identified the differences between them. In comparison to the human MHC, the main differences include the absence of HLA-A and other class I-like loci, the absence of HLA-DP-like loci, and the separation of the extended and classical class II regions from the rest of the MHC by insertion of the centromere. We show that the centromere insertion has occurred within a cluster of BTNL genes located at the boundary of the class II and III regions, which might have resulted in the loss of an orthologue to human C6orf10 from this region.

The semantics of procedures and diseases in SNOMED CT

OBJECTIVES

SNOMED CT is emerging as a reference terminology for the entire health care process. It claims to be founded on logic-based modelling principles. In this article, we analyze a special encoding scheme for diseases and procedures in SNOMED CT, the so-called relationship groups (RGs), which had been devised to avoid ambiguities in definitions.

METHODS

We reformulate SNOMED CT's relationship groups in the format of description logics in order to check whether RGs serve the needs they were designed for.

RESULTS

We show that a considerable proportion of relationship groups represent hidden mereological relations. We also report discrepancies encountered between the defined semantics of many SNOMED CT terms and their intuitive meaning, as well as inconsistencies detected between the definition of various complex composed terms and the definition of their top-level parents.

CONCLUSIONS

We formulate recommendations for improving SNOMED CT by replacing most occurrences of relation groups by formally more adequate "part-of" relations.

What should we say?

Abstract ethics mostly focuses on what we do. One form of action is a speech act. What we say can have profound effects. We can and should choose our words and how we speak wisely. When someone close to us suffers an injury or serious illness, a duty of beneficence requires that we support that person through beneficial words or actions. Though our intentions are most often benign, by what we say we often make the unfortunate person feel worse. Beginning with two personal accounts, this article explains what can go wrong in the compassionate speech of wellwishers, and uncovers some of the reasons why people say things that are hurtful or harmful. Despite a large body of clinical evidence, there is no perfect strategy for comforting a friend or relative who is ill, and sometimes even the best thing to say can still be perceived as insensitive and hurtful. In some cases, we may have good reason to knowingly say a hurtful or insensitive thing. Saying these 'wrong' things can sometimes be the best way to help a person in the long term. To complicate matters, there can be moral reasons for overriding what is good for the patient. What kind of admonishments should we make to a badly behaved patient? What is the value of authenticity in our communication with the people we love? These questions demand an ethical defence of those speech acts which are painful to hear but which need to be said, and of those which go wrong despite the best efforts of the wellwisher. We offer an ethical account, identifying permissible and impermissible justifications for the things we say to a person with a serious injury or illness.

Impact of the Metabolic Syndrome on Long-Term Outcomes in Simultaneous Kidney-Pancreas Transplantation

The metabolic syndrome (MS) has been implicated as an important nonimmunologic risk factor for chronic renal transplant dysfunction. The aim of this study was to determine the impact of the MS on outcomes in simultaneous kidney-pancreas transplantation (SKPT). Data were available on 241 patients enrolled in a prospective, multicenter randomized study of daclizumab compared with no antibody induction in SKPT. Presence of MS before and after SKPT was defined using NCEP-ATP III (National Cholesterol Education Program Adult Treatment Panel III) criteria. Body mass index (BMI) was used as a surrogate for waist circumference. MS was present in 59% of patients pretransplantation but only in 19% of patients 1 year after SKPT (P < .0001). Demographic and transplant characteristics were well matched for those with MS (MS+) and without MS (MS-) at 1 year. Presence of MS at 1 year was associated with the following changes at 3 years: increased serum creatinine level (1.65 mg/dL MS- vs 2.05 mg/dL MS+; P = .13); decreased modification of diet in renal disease calculated glomerular filtration rate (GFR; 58 mL/min MS- vs 48 mL/min MS+; P = .02); increased HgbA1C level (5.6% MS- vs 6.6% MS+; P < .001); and lower pancreas graft (PG) survival rate (88% MS- vs 71% MS+; P = .01). Linear regression analysis identified MS+ and the subgroup of MS+ without functioning PG at 1 year as independent risk factors for renal dysfunction, whereas MS+ with functioning PG at 1 year was not a risk factor for renal dysfunction. Presence of MS at 1 year is associated with long-term renal dysfunction after SKPT. Efforts to decrease early PG failure may help mitigate against MS-associated renal dysfunction.

Cross-species replication of a serum osteocalcin quantitative trait locus on human chromosome 16q in pedigreed baboons

Osteocalcin (OC), a serum marker of bone formation, in its intact form reflects osteoblast activity. It is of interest to clinicians and bone biologists due to easy measurability and potential utility as an identifier of those at risk for fracture and other complications associated with bone metabolism disorders. The only published linkage study in humans shows significant evidence for a quantitative trait locus (QTL) affecting OC levels on 16q. We used the baboon, a primate model for skeletal maintenance and turnover, to detect and quantify the effects of genes on serum OC levels and to localize chromosomal regions harboring the responsible loci. We assayed OC levels in 591 pedigreed animals, assessed OC heritability, and conducted a genomewide linkage scan for evidence of QTLs affecting this phenotype. Heritability in these baboons is 0.24. Suggestive linkage is evident with markers in a region homologous to human chromosome 16q. This first genomewide linkage scan in a nonhuman primate for QTLs affecting bone formation as reflected by OC levels provides cross-species replication of the QTL on chromosome 16q previously localized in humans. Given the concordance of results of the only two genome scans for this trait in two primate species, further studies of this region are warranted.

Inferior Late Functional and Metabolic Outcomes in African American Simultaneous Kidney-Pancreas Recipients

The aim of this study was to determine the impact of ethnicity on the major endpoints of a prospective, multi-center, randomized trial of 2 dosing regimens of daclizumab compared with no antibody induction in simultaneous kidney-pancreas transplantation (SKPT). A total of 298 patients were randomized into 3 groups: daclizumab 1 mg/kg/dose every 14 days for 5 doses (Group I, n = 107), daclizumab 2 mg/kg/dose every 14 days for 2 doses (Group II, n = 113), and no antibody induction (Group III, n = 78). All patients received tacrolimus (TAC), mycophenolate mofetil (MMF), and steroids. Thirty-seven patients (12.4%) were African American (AA) and 261 were non-African American (NAA). Demographic and transplant characteristics were comparable between AA and NAA patients. At 3 years, there were no differences in patient, kidney, or pancreas graft survival rates. Rejection rate was similar between AA and NAA. Although mean serum creatinine (SCr) levels at 1 year were comparable between AA and NAA patients (AA 1.5 mg/dL vs NAA 1.3 mg/dL; P = .23), by 3 years AA patients had higher mean SCr levels (AA 2.1 mg/dL vs NAA 1.5 mg/dL; P < .0001) and lower calculated glomerular filtration rate (GFR) (AA 45 mL/min vs NAA 56 mL/min; P = .01). Mean HgbA1C, total cholesterol, and diastolic blood pressure (BP) were higher in AA patients at 3 years, compared with NAA patients. In conclusion, in this study, AA patients had worse late functional and metabolic outcomes after SKPT compared with NAA patients. Further longitudinal follow-up is needed to determine the ultimate impact of these findings on long-term patient and graft survival.

Surface complexation studied via combined grazing-incidence EXAFS and surface diffraction: arsenate on hematite (0001) and (10–12)

X-ray diffraction [crystal-truncation-rod (CTR)] studies of the surface structure of moisture-equilibrated hematite reveal sites for complexation not present on the bulk oxygen-terminated surface, and impose constraints on the types of inner-sphere sorption topologies. We have used this improved model of the hematite surface to analyze grazing-incidence EXAFS results for arsenate sorption on the c (0001) and r (10-12) surfaces measured in two electric vector polarizations. This work shows that the reconfiguration of the surface under moist conditions is responsible for an increased adsorption density of arsenate complexes on the (0001) surface relative to predicted ideal termination, and an abundance of "edge-sharing" bidentate complexes on both studied surfaces. We consider possible limitations on combining the methods due to differing surface sensitivities, and discuss further analysis possibilities using both methods.

Genome-wide scan of resistin mRNA expression in omental adipose tissue of baboons

INTRODUCTION

The hormone resistin was recently discovered in adipose tissue of mice. Functional tests suggest a role for resistin in the regulation of insulin sensitivity. However, human studies have reported controversial results on the metabolic function of this hormone.

METHODS

A 1 g omental adipose tissue biopsy was obtained from 404 adult baboons. Resistin mRNA expression was assayed by real-time, quantitative RT-PCR, and univariate and bivariate quantitative genetic analyses were performed, via the variance decomposition approach. A genome scan analysis was conducted using resistin mRNA abundance in omental adipose tissue as a quantitative phenotype.

RESULTS

A significant heritability of h2 = 0.23 (P = 0.003) was found for resistin mRNA abundance in omental adipose tissue. A genome scan detected a quantitative trait locus for resistin expression with an LOD score of 3.8, in the region between markers D19S431 and D19S714, corresponding to human chromosome 19 p13. This chromosomal region contains genes related to insulin resistance phenotypes, such as resistin, insulin receptor, angiopoietin-like 4 protein and LDL receptor.

CONCLUSIONS

Individual variation in resistin mRNA expression has a significant genetic component, and a gene or genes on chromosome 19 p13 may regulate resistin mRNA levels in baboon omental adipose tissue.

A quantitative trait locus for normal variation in forearm bone mineral density in pedigreed baboons maps to the ortholog of human chromosome 11q

Baboons share many anatomical, physiological, and developmental characteristics with humans that make them excellent models for human bone maintenance and turnover. We conducted statistical genetic analyses, including a whole-genome linkage screen, of dual-energy x-ray absorptiometry-acquired measures of areal bone mineral density (aBMD), currently the most reliable single predictor of susceptibility to osteoporotic fracture in humans, from three forearm sites on the radius and ulna of 667 pedigreed baboons. We used a maximum likelihood-based variance decomposition approach to detect and quantify the effects of genes on normal variation in aBMD in the forearm of these baboons and to localize these effects to chromosomal regions. We estimated significant heritability for aBMD at all three sites and found evidence for a quantitative trait locus (QTL) contributing significantly to the genetic effects on this trait in a region of the baboon genome homologous to human chromosome 11q12-13. This first reported genome-wide linkage screen in a nonhuman primate for QTLs affecting forearm aBMD provides important cross-species replication of a QTL found in humans. The concordance of our results in a nonhuman primate with those reported for humans provides strong evidence that a gene (or genes) in this region affects normal variation in BMD.

Valganciclovir prophylaxis in patients at high risk for the development of cytomegalovirus disease

BACKGROUND

Despite advances in antiviral therapies, cytomegalovirus (CMV) remains the leading opportunistic infection in the transplant population. Valganciclovir (VGC), the L-valyl ester prodrug of ganciclovir (GCV), provides an excellent oral alternative to GCV for the prevention of CMV in transplant recipients. We investigated the use of VGC for CMV prevention in high-risk renal and pancreas transplant recipients.

METHODS

Patients at high risk for development of CMV disease were defined as either those who had donor positive, recipient-negative serostatus (D+/R-), or those who received antilymphocyte antibody (ALA) therapy for either rejection treatment or induction. A retrospective review was conducted of all kidney and pancreas transplants performed between August 2001 and December 2003. A total of 341 transplants were performed, of which 109 received VGC, and 88 were included in this analysis.

RESULTS

The overall incidence of CMV disease was 5.7% (5/88). All of the CMV episodes were in patients who were D+/R- (17.2% [5/29] versus 0% [0/59], P<0.001). Of these patients, all the episodes of CMV were in patients who received VGC prophylaxis for<100 days post transplant (29% [5/17] versus 0% [0/12], P=0.06). The overall incidence of leukopenia was 11% and thrombocytopenia was 7%, with the incidence between the D+/R- group and the ALA group being similar.

CONCLUSION

VGC is an effective agent in preventing CMV disease in kidney and pancreas transplant recipients who are at high risk for developing the disease. The optimal length of prophylaxis in D+/R- patients is still undefined, while 3 months of prophylaxis appears to be sufficient in patients who received ALA therapy.

Genotype-by-sex and environment-by-sex interactions influence variation in serum levels of bone-specific alkaline phosphatase in adult baboons (Papio hamadryas)

While more than 77% of the people in the US with osteoporosis are women, the contributions of genotype-by-sex (G x S) and environment-by-sex interactions to sex differences in osteoporosis risk factors have not been studied. To address this issue, we conducted a statistical genetic analysis of serum concentrations of bone-specific alkaline phosphatase (Bone ALP), a highly specific marker of osteoblast function that is elevated in persons with conditions like osteoporosis characterized by excessive bone turnover or rapid bone loss. We assayed Bone ALP from 657 pedigreed baboons using a commercially available ELISA kit. Using a maximum likelihood variance decomposition approach, we treated sex as an environmental milieu in which genes influencing Bone ALP levels are expressed. We modeled the genetic covariance in Bone ALP between all relative pairs conditional on their sex so that the covariance is the product of the kinship, the genetic correlation between trait levels in the two sexes, and the genetic variances in the two sexes. Sex-specific maximum likelihood estimates (MLE) of residual heritability for Bone ALP were greater for females than for males (h2 = 0.44 vs. h2 = 0.26, respectively), but likelihood ratio tests revealed only a marginally significant difference in sex-specific genetic variances (P = 0.057). In contrast, the between-sex genetic correlation (rhoG = 0.43) was significantly less than 1.0 (P = 0.037), and the difference in sex-specific environmental variances was highly significant (P = 0.00006). We report the first evidence for G x S interactions influencing variation in an osteoporosis risk factor. The diminished between-sex genetic correlation implies that different genes influence Bone ALP levels in the two sexes. The significant differences between environmental variances suggest that unmeasured factors, including those from the internal, biological environments of the two sexes, account for a greater proportion of the Bone ALP variation in males.

DNA sequence and analysis of human chromosome 9

Chromosome 9 is highly structurally polymorphic. It contains the largest autosomal block of heterochromatin, which is heteromorphic in 6-8% of humans, whereas pericentric inversions occur in more than 1% of the population. The finished euchromatic sequence of chromosome 9 comprises 109,044,351 base pairs and represents >99.6% of the region. Analysis of the sequence reveals many intra- and interchromosomal duplications, including segmental duplications adjacent to both the centromere and the large heterochromatic block. We have annotated 1,149 genes, including genes implicated in male-to-female sex reversal, cancer and neurodegenerative disease, and 426 pseudogenes. The chromosome contains the largest interferon gene cluster in the human genome. There is also a region of exceptionally high gene and G + C content including genes paralogous to those in the major histocompatibility complex. We have also detected recently duplicated genes that exhibit different rates of sequence divergence, presumably reflecting natural selection.

Long-Term outcome of sirolimus rescue in Kidney–Pancreas transplantation

The aim of this study was to evaluate long-term outcome of sirolimus (SRL) rescue in kidney-pancreas transplantation (KPTx). We reviewed 112 KPTx performed at our institution from 12/3/95 to 6/27/02. All patients received antibody (Ab) induction, tacrolimus (TAC), mycophenolate mofetil (MMF), and steroids. Thirty-five patients (31%) had SRL substituted for MMF for the following indications: (1) acute rejection (AR) of kidney or pancreas despite adequate TAC levels; (2) intolerance of full-dose MMF; (3) rising creatinine; and (4) TAC-induced hyperglycemia. Target SRL and TAC levels were 10 ng/mL and 5 ng/mL, respectively. Mean follow-up was 3 +/- 2 years overall and 1.2 +/- 0.5 years after SRL rescue. No patients died. One- and 3-year actuarial kidney and pancreas graft survival was 97%, 97%, and 95%, 90%, respectively. Of 10 patients switched to SRL for AR, 1 kidney failed from Ab-resistant AR, 1 kidney developed borderline AR, and the other 8 remain AR-free. Seven other patients developed AR despite therapeutic SRL levels; of these, 6 (86%) had mean TAC levels of <4.5 in the month preceding AR. Mean creatinine overall and for the rising creatinine group remained stable. All patients switched to SRL for TAC-induced hyperglycemia or MMF intolerance demonstrated biochemical or clinical improvement. Sirolimus-related infection or other serious adverse events (SAE) were uncommon. In conclusion, KPTx recipients can be safely switched to SRL with long-term stabilization of renal function, excellent graft and patient survival, and no increase in SAE. A minimum TAC level of 4.5 ng/mL may be necessary to prevent late AR.

Does treatment of cadaveric organ donors with desmopressin increase the likelihood of pancreas graft thrombosis? results of a preliminary study

Desmopressin (DDAVP) is commonly used in cadaveric organ donors to treat diabetes insipidus. The thrombogenic potential of DDAVP is well known. Recent animal data have demonstrated that DDAVP impairs pancreas graft (PG) microcirculation and perfusion. The aim of this study was too evaluate the effect of DDAVP on the incidence of PG thrombosis in clinical pancreas transplantation. A retrospective review of simultaneous kidney-pancreas transplant (SKPT) entered in the Scientific Registry of Transplant Recipients (SRTR) between 10/5/87 and 9/27/02 was performed. Patients were included for analysis if there was definitive documentation as to whether DDAVP was (DDAVP-Y) or was not (DDAVP-N) administered to the donor. Both dose and duration of DDAVP treatment were not recorded by SRTR. A total of 2804 SKPTs were available for analysis. Mean follow-up was 1.75 years (range, 1 month to 8.4 years). A total of 1287 SKPT patients (46%) received a PG from a DDAVP-Y donor. Graft ischemia times, donor and recipient ages, recipient gender distribution, surgical techniques, and immunosuppressive regimens were similar in both groups. The overall incidence of PG thrombosis was 4.3%. The incidence of PG thrombosis in recipients of grafts from DDAVP-Y donors was 5.1% compared to 3.5% in recipients of grafts from DDAVP-N donors (P =.04). Fifty-eight percent of thrombosed PG came from DDAVP-Y donors compared to 42% from DDAVP-N donors (P =.04). We conclude that there appears to be a relationship between donor treatment with DDAVP and PG thrombosis. A prospective study is needed to verify these findings and to determine their clinical significance.

African-American ethnicity is no longer a risk factor for early adverse outcomes in simultaneous kidney–pancreas transplantation with contemporary immunosuppression

The influence of ethnicity on the outcome of simultaneous kidney-pancreas transplantation (SKPT) is controversial. The aim of this study was to determine the impact of ethnicity on the major endpoints of a prospective, multicenter, randomized trial of two dosing regimens of daclizumab compared to no-antibody induction in SKPT. A total of 297 patients were randomized into three groups: daclizumab 1 mg/kg/dose every 14 days for five doses (group I, n = 107); daclizumab 2 mg/kg/dose every 14 days for two doses (group II, n = 112), and no-antibody induction (group III, n = 78). All patients received tacrolimus, mycophenolate mofetil, and steroids for maintenance immunosuppression. Thirty-seven patients (12.5%) were African-American (AA) and 260 were non-African-American (NAA). Demographics and transplant characteristics were comparable between AA and NAA patients. At 1 year, no differences were seen in patient survival (97% AA, 96% NAA), kidney graft survival (94% AA, 93% NAA), and pancreas graft survival (84% AA, 85% NAA). Rejection rate and incidence of adverse events were similar between AA and NAA subjects. Kidney graft function was comparable between AA and NAA patients at 1 year; however, mean HgbA1C was higher, C-peptide was lower, and oral hypoglycemic use was more common in AA subjects. Thus, in this prospective multicenter study, AA ethnicity was not associated with an increased risk of early adverse outcomes in SKPT. Follow-up will be required to determine whether long-term outcomes remain equivalent, particularly with regard to pancreas graft function.

The DNA sequence and comparative analysis of human chromosome 10

The finished sequence of human chromosome 10 comprises a total of 131,666,441 base pairs. It represents 99.4% of the euchromatic DNA and includes one megabase of heterochromatic sequence within the pericentromeric region of the short and long arm of the chromosome. Sequence annotation revealed 1,357 genes, of which 816 are protein coding, and 430 are pseudogenes. We observed widespread occurrence of overlapping coding genes (either strand) and identified 67 antisense transcripts. Our analysis suggests that both inter- and intrachromosomal segmental duplications have impacted on the gene count on chromosome 10. Multispecies comparative analysis indicated that we can readily annotate the protein-coding genes with current resources. We estimate that over 95% of all coding exons were identified in this study. Assessment of single base changes between the human chromosome 10 and chimpanzee sequence revealed nonsense mutations in only 21 coding genes with respect to the human sequence.

The DNA sequence and analysis of human chromosome 13

Chromosome 13 is the largest acrocentric human chromosome. It carries genes involved in cancer including the breast cancer type 2 (BRCA2) and retinoblastoma (RB1) genes, is frequently rearranged in B-cell chronic lymphocytic leukaemia, and contains the DAOA locus associated with bipolar disorder and schizophrenia. We describe completion and analysis of 95.5 megabases (Mb) of sequence from chromosome 13, which contains 633 genes and 296 pseudogenes. We estimate that more than 95.4% of the protein-coding genes of this chromosome have been identified, on the basis of comparison with other vertebrate genome sequences. Additionally, 105 putative non-coding RNA genes were found. Chromosome 13 has one of the lowest gene densities (6.5 genes per Mb) among human chromosomes, and contains a central region of 38 Mb where the gene density drops to only 3.1 genes per Mb.

Asthma deaths during sports: report of a 7-year experience

BACKGROUND

Asthma mortality and the mortality of athletes during sports have been described separately in detail in the medical literature. However, asthma has not been reported as a cause of death in competitive athletes.

OBJECTIVE

The object of this study was to raise the awareness of physicians, coaches, trainers, and parents that children and adults can have fatal asthma exacerbations during and immediately after participating in sports.

METHODS

The Temple Sports Asthma Research Center identified athletes from 1993 until 2000 who died during or after sporting activity by using the nationwide Burrell's Information Service. Once a possible asthma-related sports death was identified, the autopsy report was requested from the coroner or medical examiner, and an attempt was made to contact the family. Contact with the family was limited to information about the death, medical history, sports involvement, and any medication usage by the person who had died. Secondary sources, including news reports, were used to confirm whether the subject died of asthma during or immediately after a sporting activity.

RESULTS

Two hundred sixty-three possible cases were identified. Sixty-one deaths met the criteria for study inclusion. White deaths outnumbered black deaths by 2 to 1. Deaths among male subjects predominated. Most subjects were younger than the age of 20 years, with the most prevalent age group being between 10 to 14 years old. Fifty-one percent (18 of 35) of the competitive athletes had their fatal event while participating in organized sport, 14 in a practice situation and 4 deaths during a game or meet setting. Basketball and track were the 2 most frequent activities performed at the time of the fatal event.

CONCLUSION

The subjects who had fatal asthma exacerbations were usually white male subjects between the ages of 10 and 20 years. Mild intermittent or persistent asthma by history was commonly identified. Sudden fatal asthma exacerbations occur in both competitive and recreational athletes and can be precipitated by sporting activity.

Bone mineral density reference standards in adult baboons (Papio hamadryas) by sex and age

Osteoporosis is a progressive condition involving structural deterioration of bone tissue, leading to skeletal fragility and an increased susceptibility to fractures due to low bone mass and high rates of bone turnover. Areal bone mineral density (aBMD) serves as the most reliable predictor of susceptibility to osteoporotic fracture. The development of animal models, including Old World Monkeys, has been essential to studies of bone mineral density. These animals, including the baboon, exhibit many biological similarities with our own species relevant to the variation in age-related changes and pathology in bone that may make them an excellent model for studies of skeletal structure and maintenance in humans. The baboon has been shown to exhibit extensive biological similarities to humans regarding skeletal biology, but little is known about the range of normal variation in skeletal traits, such as bone mineral density, in this species. Our data, collected on baboons (Papio hamadryas) that are part of a large breeding colony at the Southwest Foundation for Biomedical Research and the Southwest National Primate Research Center (San Antonio, TX), involve 466 females and 210 males, ranging in age from 5.5 to 30 years. Student's t tests, bivariate correlations, and likelihood ratio tests show sex and age effects at all spinal sites. Age effects are minimal or absent in the forearm sites. This study is the first to characterize normal variation in aBMD in baboons, to assess the effect of age and sex on this variation, and to compare this variation to those data currently available from experimental control animals. As such, it provides much-needed reference standards that will allow researchers to evaluate the status of their animals in cross-sectional studies and more fully assess the meaning of aBMD changes in longitudinal studies.

The DNA sequence and analysis of human chromosome 6

Chromosome 6 is a metacentric chromosome that constitutes about 6% of the human genome. The finished sequence comprises 166,880,988 base pairs, representing the largest chromosome sequenced so far. The entire sequence has been subjected to high-quality manual annotation, resulting in the evidence-supported identification of 1,557 genes and 633 pseudogenes. Here we report that at least 96% of the protein-coding genes have been identified, as assessed by multi-species comparative sequence analysis, and provide evidence for the presence of further, otherwise unsupported exons/genes. Among these are genes directly implicated in cancer, schizophrenia, autoimmunity and many other diseases. Chromosome 6 harbours the largest transfer RNA gene cluster in the genome; we show that this cluster co-localizes with a region of high transcriptional activity. Within the essential immune loci of the major histocompatibility complex, we find HLA-B to be the most polymorphic gene on chromosome 6 and in the human genome.

Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs

Only a small proportion of the mouse genome is transcribed into mature messenger RNA transcripts. There is an international collaborative effort to identify all full-length mRNA transcripts from the mouse, and to ensure that each is represented in a physical collection of clones. Here we report the manual annotation of 60,770 full-length mouse complementary DNA sequences. These are clustered into 33,409 'transcriptional units', contributing 90.1% of a newly established mouse transcriptome database. Of these transcriptional units, 4,258 are new protein-coding and 11,665 are new non-coding messages, indicating that non-coding RNA is a major component of the transcriptome. 41% of all transcriptional units showed evidence of alternative splicing. In protein-coding transcripts, 79% of splice variations altered the protein product. Whole-transcriptome analyses resulted in the identification of 2,431 sense-antisense pairs. The present work, completely supported by physical clones, provides the most comprehensive survey of a mammalian transcriptome so far, and is a valuable resource for functional genomics.

Cadaveric renal transplantation in African-Americans in South Carolina

The renal transplant program at the MUSC was established in 1968 and is the only transplant center in South Carolina. It serves a large population of African American patients who constitute nearly two-thirds of the waiting list and more than half of all renal transplants. Between 1968-2000, 969 transplants were performed in 906 AA patients. Most received organs from cadaveric donors, while only 99 (10%) of AA patients received living donor transplants. The acceptance of living unrelated donors and the use of laparoscopic nephrectomy have had a negligible impact on living donations in this racial group. Primary disease had little effect on outcome except in diabetics whose mortality was higher. The one-year graft survival rates improved dramatically with the aggressive use of CsA without the use of antibody induction. The overall one- and 5-year graft survival rates improved from 53% and 32%, respectively, in the 1978-1983 era to 87% and 59%, respectively, in the 1993-2001 era. At MUSC, the emphasis has been on reducing mortality due to sepsis by limiting the number of rejections treated particularly in recipients of cadaveric organs. While this has resulted in reduced overall early mortality, it has not adversely affected graft survival. Our experience suggests that while short-term graft survival has improved significantly over the years for AA patients, the long-term outcome still remains relatively unchanged.

A convenient preparation of 2-fluoro-3-alkoxy-1,3-butadienes

[reaction: see text] 1-Chloro-1-fluoro-2-methoxy-2-methylcyclopropane eliminates HCl on heating in quinoline solution above 50 degrees C to give 2-fluoro-3-methoxy-1,3-butadiene in high yield. If an alcohol is added to the reaction then a 2-fluoro-3-alkoxy-1,3-butadiene is obtained in high yield. The dienes give smooth 4 + 2 cycloaddition reactions.

Paget's disease in an archeological population

The aim of this investigation was to study the prevalence and distribution of Paget's disease in an archeological population. Paget's disease, first described over 100 years ago, is a well-recognized chronic disorder involving abnormal bone turnover with established radiological features. Prevalence within modern populations varies both within individual countries and between them. Paleopathological examples are uncommon and sporadically reported both from Europe and the Americas and from many periods of history. A large skeletal assemblage (2,770 individuals) from Barton on Humber, UK, provided an opportunity to examine the prevalence of Paget's disease in one area of the northern England over the period 900-1,850 AD. All bones were examined visually for evidence of Paget's disease of the bone (PDB) and all abnormal bones were examined further by plain radiography. Fifteen cases of probable Paget's disease were found. The overall prevalence was 2.1% in those aged >40 years. The prevalence before 1500 AD was 1.7% and post-1500 AD was 3.1%. The distribution of disease mirrored modern disease, with the lumbar spine, pelvis, and proximal femur being the commonest sites. The prevalence of Paget's disease in the United Kingdom over the last 1,000 years has been assessed. Although there is a trend of increasing prevalence, this did not reach statistical significance. This is likely caused by the small sample size, but this is by far the greatest number of cases of PDB described in a single skeletal assemblage to date. The distribution of lesions within the skeleton is unchanged.

Further improvements in laparoscopic donor nephrectomy: decreased pain and accelerated recovery

Fear of postoperative pain is a disincentive to living donor kidney transplantation. Laparoscopic donor nephrectomy (LDN) was developed in part to dispel this disincentive. The dramatic increase in the number of laparoscopic donor nephrectomies performed at our institution has been in part due to the reduction in postoperative pain as compared to traditional, open donor nephrectomy. We sought to further diminish the pain associated with this surgical technique. The purpose of this study was to compare the efficacy of three different postoperative pain management regimens after LDN. All living kidney donors performed laparoscopically (n=43) between September 1998 and April 2000 were included for analysis. Primary endpoints included postoperative narcotic requirements and length of stay. Narcotic usage was converted to morphine equivalents (ME) for comparison purposes. Patients received one of three pain control regimens (group 1: oral and intravenous narcotics; group II: oral and intravenous narcotics and the On-Q pump delivering a continuous infusion of subfascial bupivicaine 0.5%; and group III: oral and intravenous narcotics and subfascial bupivicaine 0.5% injection). Postoperative intravenous and oral narcotic use as measured in morphine equivalents was significantly less in group III versus groups I and II (group III: 28.7 ME versus group I: 40.2 ME, group II: 44.8 ME; P<0.05). Postoperative length of stay was also shorter for group III (1.8 days) versus group I (2.5 days) and group II (2.9 days). LDN has been shown to be a viable alternative to traditional open donor nephrectomy for living kidney donation. We observed that the use of combined oral and intravenous narcotics alone is associated with greater postoperative narcotic use and increased length of stay compared to either a combined oral and intravenous narcotics plus continuous or single injection subfascial administration of bupivicaine. The progressive modification of our analgesic regimen has resulted in decreased postoperative oral and intravenous narcotic use and a reduction in the length of stay. We recommend subfascial infiltration with bupivicaine to the three laparoscopic sites and the pfannenstiel incision at the conclusion of the procedure to reduce postoperative pain. We believe this improvement in postoperative pain management will continue to make LDN even more appealing to the potential living kidney donor.

Asthma screening of high school athletes: identifying the undiagnosed and poorly controlled

BACKGROUND

It is believed that there are many high school-age athletes who have undiagnosed asthma or exercise-induced asthma (EIA). The screening of these athletes for EIA will allow them to be identified and treated.

OBJECTIVES

1) To obtain reliable peak expiratory flow rate (PEFR) measurements and administer questionnaires to high school-age athletes to evaluate their asthma risk. 2) To identify high-risk athletes for having EIA or asthma by a free run challenge test. 3) To evaluate whether an athlete's present asthma control is adequate. 4) To evaluate these tools for their value as screening tools for asthma or EIA.

METHODS

Eight hundred one student athletes from 10 suburban Pittsburgh schools were screened for more than 18 months for asthma as part of their preparticipation sports physicals. The screening included all athletes from all high school sports. The athletes were given a brief questionnaire, had PEFR measured, and then participated in a free running exercise challenge.

RESULTS

Forty-six of 801 athletes had asthma or EIA, Of the remaining 755 athletes, 49 athletes were identified as having undiagnosed asthma. In the previously unrecognized athletes with EIA, the positive and negative predictive value of the questionnaire was 42% and 97%, respectively. Eighty-five percent (39 of 46) of the known asthmatic athletes, using their recommended medication, failed their free running test by a >15% drop of their PEFR.

CONCLUSIONS

The free running test is a good test for identifying and assessing the athlete with EIA. The PEFR meter is not a good screening tool for EIA in the high school athlete. A questionnaire may be a good negative screening tool, but further development is needed before it can be used for widespread screening.

Assessment of the GALEN methodology on holistic classifications for professions allied to medicine

In the field of health care terminology it has proven to be difficult, but not impossible, to build a formal Reference Model (knowledge-model) for medical terminology. The intuition is that it is even more difficult to build such a reference model for the so called â holistic' classification schemes as used by Nursing and Allied Health Care Professionals. There is a growing perceived need for formal reference models for specific professional groups. These reference models are used in many different ways, such as for building, maintaining and manipulating classification schemes. This paper focuses on the usability of the GALEN methodology for the formalisation of the Dutch Classification of Pain (NCP) as an example of such a â holistic classification'. The first results of this exploration show that the GALEN methodology is very useful for analysing and understanding a' holistic classification'. A high number of necessary concepts from the NCP already exist within the OpenGalen Common Reference Model-2 (OCRM2). A substantial number of concepts from the NCP do not yet exist in the OCRM2 or are underspecified. Additional modelling of the OCRM2 has to be performed, to enrich the expressivity of the model.

GALEN ten years on: tasks and supporting tools

The GALEN technology has matured over more than a decade of use. We describe a set of software tools and associated methodologies that together are supporting ontological engineering in a production, rather than a research setting.

The DNA sequence and comparative analysis of human chromosome 20

The finished sequence of human chromosome 20 comprises 59,187,298 base pairs (bp) and represents 99.4% of the euchromatic DNA. A single contig of 26 megabases (Mb) spans the entire short arm, and five contigs separated by gaps totalling 320 kb span the long arm of this metacentric chromosome. An additional 234,339 bp of sequence has been determined within the pericentromeric region of the long arm. We annotated 727 genes and 168 pseudogenes in the sequence. About 64% of these genes have a 5' and a 3' untranslated region and a complete open reading frame. Comparative analysis of the sequence of chromosome 20 to whole-genome shotgun-sequence data of two other vertebrates, the mouse Mus musculus and the puffer fish Tetraodon nigroviridis, provides an independent measure of the efficiency of gene annotation, and indicates that this analysis may account for more than 95% of all coding exons and almost all genes.

A quantitative trait locus influencing activin-to-estrogen ratio in pedigreed baboons maps to a region homologous to human chromosome 19

Activin is a multifunctional hormone playing a major role in the regulation of reproduction and growth and development. We performed a genomewide scan using multipoint linkage analysis implemented in a general pedigree-based variance component approach to identify genes with measurable effects on variation in the activin-to-estrogen ratio in baboons. A microsatellite polymorphism, D19S714, which maps to human chromosome 19p13.2, showed marginal evidence of linkage with a lod (log10 of the odds in favor of genetic linkage) score of 1.95 (0.014). This region contains several potential candidate genes including PKA (protein kinase, cAMP-dependent, catalytic alpha) and the gene pair JUN-B and JUN-D. This is the first evidence of a quantitative trait locus with a significant effect on the activin-to-estrogen ratio.

Superparamagnetic iron oxide MION as a contrast agent for sodium MRI in myocardial infarction

An intravascular iron-based contrast agent was used as a sodium (23Na) MRI T2 relaxant in an effort to suppress the blood signal from the ventricular cavities in normal and infarcted canine myocardium in vivo. 23Na MRI signal decreases in blood were attributed to decreases in the fast (T2f) and slow (T2s) transverse relaxation components, which were quantified as a function of dose and MRI echo time (TE). In vivo 23Na MRI signal decreases up to 65% were noted in ventricular blood when imaging under dose and TE conditions of 10 mg/kg body weight and 5 ms, respectively. Contrast injection followed by subsequent 23Na MRI in canine myocardial infarction led to a clear delineation of the location of the injured tissue, as identified by postmortem triphenyltetrazolium chloride staining, and to an improvement in the contrast-to-noise ratio between the blood in the ventricular chamber and the infarcted tissue that was as high as 3.3-fold in the postcontrast images in comparison to the precontrast images.

Results of simultaneous and sequential pediatric liver and kidney transplantation

BACKGROUND

The indications for simultaneous and sequential pediatric liver (LTx) and kidney (KTx) transplantation have not been well defined. We herein report the results of our experience with these procedures in children with end-stage liver disease and/or subsequent end-stage renal disease.

PATIENTS AND METHODS

Between 1984 and 1995, 12 LTx recipients received 15 kidney allografts. Eight simultaneous and seven sequential LTx/KTx were performed. There were six males and six females, with a mean age of 10.9 years (1.5-23.7). One of the eight simultaneous LTx/KTx was part of a multivisceral allograft. Five KTx were performed at varied intervals after successful LTx, one KTx was performed after a previous simultaneous LTx/KTx, and one KTx was performed after previous sequential LTx/KTx. Immunosuppression was with tacrolimus or cyclosporine and steroids. Indications for LTx were oxalosis (four), congenital hepatic fibrosis (two), cystinosis (one), polycystic liver disease (one), A-1-A deficiency (one), Total Parenteral Nutrition (TPN)-related (one), cryptogenic cirrhosis (one), and hepatoblastoma (one). Indications for KTx were oxalosis (four), drug-induced (four), polycystic kidney disease (three), cystinosis (one), and glomerulonephritis (1).

RESULTS

With a mean follow-up of 58 months (0.9-130), the overall patient survival rate was 58% (7/12). One-year and 5-year actuarial patient survival rates were 66% and 58%, respectively. Patient survival rates at 1 year after KTx according to United Network of Organ Sharing (liver) status were 100% for status 3, 50% for status 2, and 0% for status 1. The overall renal allograft survival rate was 47%. Actuarial renal allograft survival rates were 53% at 1 and 5 years. The overall hepatic allograft survival rate was equivalent to the overall patient survival rate (58%). Six of seven surviving patients have normal renal allograft function, and one patient has moderate chronic allograft nephropathy. All surviving patients have normal hepatic allograft function. Six (86%) of seven sequentially transplanted kidneys developed acute cellular rejection compared with only two (25%) of eight simultaneously transplanted kidneys (P<0.04).

CONCLUSIONS

Simultaneously transplanted kidneys were less likely to develop rejection than sequentially transplanted kidneys in this series. This did not have any bearing on patient or graft survival rates. Mortality correlated directly with the severity of United Network of Organ Sharing status at the time of kidney transplantation. Candidates for simultaneous or sequential LTx/KTx should be prioritized based on medical stability to optimize distribution of scarce renal allografts.

Topography and volume measurements of the optic nerve usingen-face optical coherence tomography

A special imaging instrument was developed which can acquire optical coherence tomography (OCT) en-face images from the eye fundus, and simultaneously a confocal image. Using this instrument we illustrate for the first time the application of en-face OCT imaging to produce topography and perform area and volume measurements of the optic nerve. The procedure is compared with the topography, area and volume measurements using a confocal scanning laser ophthalmoscope.

Microglial chemotaxis, activation, and phagocytosis of amyloid beta-peptide as linked phenomena in Alzheimer's disease

Microglia are widely held to play important pathophysiologic roles in Alzheimer's disease (AD). On exposure to amyloid beta peptide (A beta) they exhibit chemotactic, phagocytic, phenotypic and secretory responses consistent with scavenger cell activity in a localized inflammatory setting. Because AD microglial chemotaxis, phagocytosis, and secretory activity have common, tightly linked soluble intermediaries (e.g., cytokines, chemokines), cell surface intermediaries (e.g., receptors, opsonins), and stimuli (e.g., highly inert A beta deposits and exposed neurofibrilly tangles), the mechanisms for microglial clearance of A beta are necessarily coupled to localized inflammatory mechanisms that can be cytotoxic to nearby tissue. This presents a critical dilemma for strategies to remove A beta by enhancing micoglial activation--a dilemma that warrants substantial further investigation.

Modeling microglial activation in Alzheimer's disease with human postmortem microglial cultures

Alzheimer's disease (AD) is a uniquely human disorder. Despite intense research, the lack of availability of model systems has hindered AD studies though in recent years transgenic mouse models have been produced, which develop AD-like amyloid beta peptide (Abeta) plaques. For the study of inflammatory changes in AD brains, these transgenic mice may have limitations due to differences in the innate immune system of humans and rodents. Many studies of inflammatory processes in AD have focused on the role of activated microglia. Over the last 8 years, our research has focused on the properties of human microglia cultured from brain tissues of AD and non-demented (ND) individuals. As these are the cells observed to be activated in AD tissues, they represent a useful system for modeling the inflammatory components of AD. In this review, we summarize data by our group and others on the use of microglia for AD-related inflammatory research, with emphasis on results using human postmortem brain microglia. A range of products have been shown to be produced by human postmortem microglia, both constitutively and in response to treatment with Abeta, including proinflammatory cytokines such as interleukin (IL)-1beta, IL-6, tumor necrosis factor (TNF) alpha, and macrophage colony stimulating factor (M-CSF), along with complement proteins, especially C1q, superoxide radicals and neurotoxic factors. In our studies, we have demonstrated that there was a significant difference between AD and ND microglia in terms of their secretion of M-CSF and C1q. We also discuss the role of putative Abeta microglial receptors, particular recent data showing a role for the receptor for advanced glycation endproducts (RAGE) in mediating the responses of human microglia to Abeta. Finally, our studies on the use of an Abeta spot paradigm to model microglia interactions with plaques demonstrated that many of the features of AD inflammation can be modeled with postmortem brain derived microglia.