A trabecular plate-like phenotype is overrepresented in Chinese-American versus Caucasian women.

UNLABELLED: This study used extreme phenotype selection to define two trabecular bone phenotypes in a cohort of Chinese-American and Caucasian women. A trabecular plate-predominant phenotype is more common in Chinese-Americans while the rod-predominant phenotype is more typical of Caucasians. The robustness of these phenotypic associations with respect to lifestyle factors suggests that this trait may have a genetic basis and that these phenotypes can be utilized in future genetic studies. INTRODUCTION: Compared to Caucasians, Chinese-Americans have more plate-like trabecular bone when measured by individual trabecula segmentation (ITS). These findings suggest a phenotypic difference between the races, which may be amenable to genetic analysis. We sought to identify a single ITS plate trait to pursue in genetic studies by conducting an extreme phenotype selection strategy to numerically define two distinct phenotypes-plate-like and rod-like-and determine whether the selected phenotypic associations were independent of lifestyle factors in order to conduct future genetic studies. METHODS: A previously described cohort of 146 Chinese-American and Caucasian women with high-resolution peripheral quantitative computed tomography imaging and ITS analyses were studied with logistic regression and receiver operator characteristic analyses. RESULTS: The tibial plate-to-rod (TPR) ratio was the best ITS discriminator of race. Using extreme phenotypic selection, two TPR ratio phenotypes were defined numerically: plate-like as a TPR ratio value in the highest quartile (≥1.336) and rod-like as a TPR ratio value in the lowest quartile (≤0.621). Women with a plate-like phenotype were 25.7 times more likely (95 % CI 7.3-90.1) to be Chinese-American than women with rod-like morphology. After controlling for constitutional and lifestyle covariates, women in the highest vs. lowest TPR ratio quartile were 85.0 times more likely (95 % CI 12.7-568.0) to be Chinese-American. CONCLUSION: Using extreme phenotype selection, we defined a plate- and rod-like trabecular bone phenotype for the TPR ratio trait. The former phenotype is more common in Chinese-American women, while the latter is more typical of Caucasian women. The robustness of these phenotypic associations after controlling for differences in constitution and lifestyle suggest that the TPR ratio may have a genetic basis and that the extreme phenotypes defined in this analysis can be utilized for future studies.

Mapping, cloning and genetic characterization of the region containing the Wilson disease gene.

Wilson disease (WD) is an autosomal recessive disorder of copper transport which map to chromosome 13q14.3. In pursuit of the WD gene, we developed yeast artificial chromosome and cosmid contigs, and microsatellite markers which span the WD gene region. Linkage disequilibrium and haplotype analysis of 115 WD families confined the disease locus to a single marker interval. A candidate cDNA clone was mapped to this interval which, as shown in the accompanying paper, is very likely the WD gene. Our haplotype and mutation analyses predict that approximately half of all WD mutations will be rare in the American and Russian populations.

Kaposi's sarcoma-associated herpesvirus encodes a functional bcl-2 homologue.

Kaposi's sarcoma-associated herpesvirus (KSHV) is a newly discovered herpesvirus etiologically associated with Kaposi's sarcoma (KS) and two lymphoproliferative disorders. We describe a KSHV vbcl-2 gene with homology to the proto-oncogene bcl-2. It is expressed in KS lesions and in cell lines derived from primary effusion lymphomas. Using yeast and human cells we demonstrate the ability of KSHV vBcl-2 protein to suppress Bax toxicity. We show that KSHV vBcl-2 heterodimerizes with human Bcl-2 in a yeast two-hybrid system. These results suggest that KSHV vBcl-2 plays an anti-apoptotic role in virus infected cells.

Genetic architecture of the human tryptophan hydroxylase 2 Gene: existence of neural isoforms and relevance for major depression.

Impaired brain serotonin neurotransmission is a potential component of the diathesis of major depression. Tryptophan hydroxylase-2 (TPH2), is the rate limiting biosynthetic isoenzyme for serotonin that is preferentially expressed in the brain and a cause of impaired serotonin transmission. Here, we identify a novel TPH2 short isoform with truncated catalytic domain expressed in human brainstem, prefrontal cortex, hippocampus and amygdala. An exploratory study of 166 Caucasian subjects revealed association with major depression or suicide of a novel single nucleotide polymorphism (SNP) g.22879A>G located in exon 6 of this short isoform. This SNP and additional SNPs were discovered through a systematic characterization of the genetic architecture of the TPH2 gene for further genetic and functional investigations of its relationship to major depression and other psychopathology.

Combinatorial fluorescence energy transfer tags for multiplex biological assays.

We report an approach for developing combinatorial fluorescence energy transfer (CFET) tags by tuning the tags' fluorescence emission signatures. The tags can all be excited at a single wavelength and analyzed by a simple optical system. We constructed eight CFET tags with unique fluorescence signatures, detected by a three-color capillary array electrophoresis (CAE) system with 488 nm excitation, using only three fluorescent dyes. A 1',2'-dideoxyribose phosphate spacer was used to separate the donor and acceptor to tune the energy transfer efficiency, generating unique fluorescence signatures. The spacer also served as an electrophoretic mobility tag to tune the mobility of CFET-labeled DNA for multiplex detection of single-nucleotide polymorphisms (SNPs). Six nucleotide variations were identified simultaneously using six CFET tags on synthetic DNA templates and on a PCR product from the retinoblastoma tumor suppressor gene.

A cytochrome P450 immunochemically related to P450c,d (P450I) localized to the smooth microsomes and inner zone of the guinea pig adrenal.

In addition to their capacity for steroid synthesis, guinea pig adrenal microsomes have a well documented ability to metabolize foreign compounds. The capacity for metabolism of foreign compounds is localized to the smooth endoplasmic reticulum-filled cells of the inner zone. However, it has not been clear whether they possess cytochrome P450(s) specific for this function, distinct from the two known steroid hydroxylases, P450(21) and P450(17)alpha. Multiple prominent protein bands in the mol wt range of known cytochrome P450s are seen on sodium dodecyl sulfate gels of guinea pig adrenal microsomes. Most are more intense in smooth microsomes, where the concentration of cytochrome P450 is highest. However, one band (52K) appears unique to the smooth microsomes. This band is also characteristic of microsomes obtained from the inner zone. This protein and two others (54K and 50K) are concentrated in the membrane pellet after carbonate treatment of the microsomes, indicating that they are integral membrane proteins. All three decrease in intensity after treatment of the animals with spironolactone, a compound known to cause depletion of adrenal cytochrome P450s. On Western blots of microsomal proteins the 54K and 50K proteins react with antibodies specific for P450(17) alpha and P450(21), respectively. The 52K protein, characteristic of the smooth microsomes and inner zone, does not react with anti-P450(21) or anti-P450(17) alpha, but does react with polyclonal antibody raised against microsomal cytochrome P450s induced by methylcholanthrene in rat liver (P450c,d). These results suggest that there is at least one additional cytochrome P450 in adrenal microsomes which is immunochemically distinct from P450(21) and P450(17) alpha. Its localization to the smooth microsomes and inner zone microsomes correlates with the high activity for ethylmorphine metabolism detected in these fractions. This suggests that this cytochrome P450, which is immunochemically related to members of the P450I subfamily, may be associated with the ability of guinea pig adrenal microsomes to metabolize foreign compounds.

Tools for visualization and integration of intermediate sequencing results in large disease gene discovery projects.

We describe two Java applets which are useful for insightful presentation of intermediate experimental data in gene discovery projects involving large scale sequencing. One of these applets provides a physical map of a genomic region and provides easy access to the second applet, which furnishes a detailed map of sequence contigs associated with clones on the physical map. In particular, the second applet displays all the known information about each contig, including the presence of exons, database homology 'hits', repetitive elements and other features; the graphics are linked to other World Wide Web pages, providing detailed information on each feature. These applets should be useful to other research groups working on large sequencing projects.

Analysis of a 69-kb contiguous genomic sequence at a putative tumor suppressor gene locus on human chromosome 6q27.

Multiple neoplasias including B-cell non-Hodgkin's lymphoma, breast carcinoma, and ovarian carcinoma, have been associated with frequent deletions of the distal region on the long arm of human chromosome 6, suggesting the presence of one or more tumor suppressor gene(s) at this locus. Loss of heterozygosity analysis of breast and ovarian tumors has further restricted the minimal region of loss within 6q27. To further characterize this genomic region for gene content including putative tumor suppressor genes as well as other elements that may contribute to tumorigenesis, a 68940-bp contiguous sequence, encompassing markers D6S193 and D6S297, was generated by random shotgun sequencing of a cosmid, P1, and PAC contig. In addition, exon trapping was performed utilizing a subset of these clones. Sixteen trapped exons, ranging in size from 44 to 399 bp, span this approximately 69-kb region. Many other putative exons have been identified computationally. Further analysis has identified 13 potential promoters and 13 putative polyadenylation sites in the region. Northern analysis identified a transcript mapping within this interval that is expressed in ovarian, breast, and lymphoid-derived tumor cell lines. Consideration of these data, together with the demonstration of several regions of high CpG content, suggests the possibility of several genes at this locus.

Healthcare compliance plans: good business practice for the new millennium.

Recent developments indicate that government scrutiny of healthcare providers will continue well into the next century. This article sheds light on the Federal False Claims Act and its recent interpretation by the Department of Health and Human Services' Office of the Inspector General and the United States Attorney's Office, the OIG's 1998 workplan, and current fraud and abuse initiatives. It also presents the fundamental elements of a compliance plan.

Is contingency-fee consulting an endangered species?

Consulting firms that assist hospitals in optimizing Medicare and Medicaid reimbursement sometimes charge contingency fees for their services. These fees are based on a percentage of the increased revenue they can help a hospital capture. Although contingency-fee arrangements are not considered unethical, they can result in illegal billing practices because consulting firms may be tempted to up-code to increase their fees. The 1994 investigation of Metzinger Associates, Voorhees, New Jersey, a consulting firm providing services to 200 hospitals in 17 states, found evidence of illegal billing practices and resulted in a complaint filed by the United States Attorney's Office. Several hospitals were named as defendants. A Fraud Alert issued by the HHS's Office of the Inspector General earlier this year indicates the government intends to target consulting firms that charge contingency fees. Before engaging consulting firms that charge contingency fees, hospitals should carefully evaluate each firms to determine whether its recommended billing submissions will be accurate, credible, and defensible.

Stereological analysis of the guinea pig adrenal: effects of dexamethasone and ACTH treatment with emphasis on the inner cortex.

This paper describes the morphological responses of adult male guinea pig adrenals to dexamethasone (DEX) and adrenocorticotrophic hormone (ACTH), in both qualitative and quantitative terms. Most organelles and inclusions are affected, but their responses often vary in the different cell types examined: zona fasciculata externa and interna, and zona reticularis. Following DEX the volume of lipid droplets increases in cells of zona fasciculata externa but decreases in zona reticularis; smooth endoplasmic reticulum decreases in fasciculata externa but increases in reticularis. Following ACTH, exactly the opposite occurs. This strongly suggests differing functions for these subcellular entities in each cell type, particularly for the smooth reticulum, as well as for the cells themselves. The volume of the Golgi complex markedly decreases following DEX in all cells but increases only in zona fasciculata interna and zona reticularis following ACTH. These deeper cortical cells are known to secrete at least one sulfated steroid, dehydroepiandrosterone sulfate, and these changes in the Golgi complex strengthen the suggestion that the Golgi plays a role in sulfation of steroids. Mitochondrial volume and number decrease in all cells following DEX, supporting their role in steroidogenesis. Further decreases in their volume, accompanied by increases in their number following ACTH, may be related to a proliferation of mitochondria in response to ACTH. Changes in peroxisome volume and number, following DEX and ACTH, suggest a possible role for these organelles in steroid cell metabolism. Lysosomes decrease in volume in all cells following ACTH. This does not support the recently suggested concept that they play a role in steroid secretion.

Na(+)-K(+)-ATPase subunit isoform pattern modification by mitogenic insulin concentration in 3T3-L1 preadipocytes.

When 3T3 preadipocyte cell lines are induced to differentiate to the adipocyte phenotype, the expression of Na(+)-K(+)-ATPase isoforms changes. Some disparities have been noted by investigators who used different hormonal conditions to stimulate adipocyte conversion, however. In the present report we investigated the effect of high concentrations of insulin on the 3T3-L1 cell line, to determine whether it affected Na(+)-K(+)-ATPase expression separately from its ability to promote phenotypic conversion. The effect of insulin was compared with that of dexamethasone and 3-isobutyl-1-methylxanthine. Changes in Na(+)-K(+)-ATPase subunit expression were seen regardless of the hormonal stimulus. Induction of alpha 2-mRNA and reduction of beta 1-mRNA were always observed. At the protein level, too, induction of alpha 2-protein was noted; alpha 1-protein levels were not markedly affected. The change in alpha-isoform protein and mRNA levels did not correspond quantitatively with the fraction of cells that were morphologically converted, suggesting that it is an early event in differentiation.

Relationships between a new type IV secretion system and the icm/dot virulence system of Legionella pneumophila.

We describe here a Legionella pneumophila type IV secretion system that is distinct from the previously described icm/dot system. This type IV secretion system contains 11 genes (lvh ) homologous to genes of other type IV secretion systems, arranged in a similar manner. The lvh genes were found to be located on a DNA island with a GC content higher than the L. pneumophila chromosome. In contrast to the icm/dot system that was shown to be required for intracellular growth in HL-60-derived human macrophages and Acanthamoeba castellanii, the lvh system was found to be dispensable for intracellular growth in these two hosts. The lvh system was found to be partially required for RSF1010 conjugation, a process that was previously shown to be completely dependent on several icm/dot genes. However, results obtained from analysis of double mutants in the icm/dot genes and the lvh genes revealed that lvh genes can substitute for some components of the icm/dot system for RSF1010 conjugation, but not for intracellular growth. These results indicate that components of the icm/dot system and components of the lvh type IV secretion system are able to interact with one another.

Characterization and use of polyclonal antibody to Na+,K+-ATPase: immunocytochemical localization in salt glands of the duck.

The amount of Na+,K+-ATPase of the avian salt gland increased concomitantly with plasma membrane surface area during salt feeding of ducklings (adaptation), and both enzyme content and membrane surface area decreased upon return to fresh water (deadaptation). In a further study of the enzyme, a marker for plasma membrane biogenesis, polyvalent antibodies were raised to the denatured alpha-subunit of the purified ATPase. Antisera did not inhibit enzymatic activity but immunoprecipitated the phosphorylated intermediate of the alpha-subunit. Furthermore, the alpha-subunit, which was not glycosylated, was immunoprecipitated from homogenates of tissue slices metabolically labelled with [35S]-methionine, using antisera raised against either duck salt gland or dog kidney alpha-subunit. The former antisera also recognized the alpha-subunit in the brain, heart, kidney, liver, intestine and skeletal muscle of the duck. Immunocytochemistry with the antisera raised to the duck salt gland alpha-subunit revealed reaction at basolateral as well as apical plasma membrane in the duck salt gland principal cells, with essentially no deposits on peripheral cells, fibroblasts, erythrocytes, endothelial cells and neural elements. Within the principal cells, immunolabelling was also detected on small vesicles, multivesicular bodies and lysosomes; deposits on extracellular debris and vesicles in the lateral and lumenal spaces were also apparent. The labelling patterns were qualitatively but not quantitatively similar in salt glands of control, adapted and deadapted ducklings, and are discussed in the context of a model for plasma membrane biogenesis and turnover in which degradative events may play a major role.

Serum independence of low K+ induction of Na,K-ATPase: possible role of c-fos.

Cultured ARL15 cells respond to abnormally low extracellular K+ concentrations by increasing the abundance of Na,K-ATPase (the Na/K pump). This response is preceded by significant increases in the mRNAs of the alpha 1 and beta 1 subunits of this enzyme, implying transcriptional or post-transcriptional regulation in the response. The present study concerned the possible participation of serum factors in low K+ induction of Na,K-ATPase. In normal K+ (4.5 mM) or low K+ (0.68 mM) the presence of 10% calf serum had no effect on Na,K-ATPase activity. The serum independence of the response to low K+ raised the possibility that low K+ may itself elicit a "growth" response. Accordingly, the effect of low K+ on mRNA abundances of four proto-oncogenes (c-fos, c-myc, c-jun and c-ski) was evaluated in the early phase of the response by quantitative Northern blot analysis. The mRNA for c-fos was transiently elevated by low K+, with a peak at 30 min. In contrast, low K+ had no measurable effect on the abundances of c-myc, c-jun and c-ski, for up to 2 hr of exposure. The early elevation of c-fos mRNA makes it a candidate mediator in this signal-transduction pathway. Induction of c-fos mRNA by the phorbol ester, PMA, or by dioctanoyl glycerol, however, had no effect on Na,K-ATPase activity. These results indicate that an increase in c-fos mRNA alone is not sufficient to induce Na,K-ATPase. Whether induction of c-fos is necessary for the response to low K+ remains to be determined in future studies.

Integrated mapping package--a physical mapping software tool kit.

We have developed an integrated physical mapping computer software package (IMP), originally designed to support the physical mapping of human chromosome 13 and expanded to support several gene-identification projects based on the positional candidate approach. IMP displays map data in a form that provides useful guidelines to the end users. An integrated map with high resolution and confidence is constructed from different types of mapping data, including hybridization experiments, STS-based PCR assays, genetic linkage mapping, cDNA localization, and FISH data. The map is also designed to provide suggestions for specific experiments that are required to obtain maps with even higher resolution and confidence. To this end, the optimization employs multiple constraints that take into account already established STS "scaffold" maps. This software thus serves as an important general tool kit for physical mapping, sequencing, and gene-hunting projects.

Na(+)-K(+)-ATPase in adipocyte differentiation in culture.

Differentiation of 3T3-L1 cells from a fibroblast to an adipocyte phenotype results in an approximately 50% decline in Na(+)-K(+)-ATPase activity and ouabain-sensitive 86Rb uptake. Kinetic analysis revealed a K 1/2 for Na+ of approximately 14 mM, a Km for ATP of approximately 0.4 mM, and maximal activation by sodium dodecyl sulfate at a 0.05 (wt/wt) detergent/protein ratio in both mature fibroblasts and adipocytes. Both fibroblasts and adipocytes exhibited Na(+)-K(+)-ATPase activity with an inhibition constant (Ki) for ouabain of approximately 10(-4) M. In addition, adipocytes exhibited a second component representing 30% of total activity with a Ki of approximately 5 x 10(-7) M. The emergence of biphasic ouabain inhibition kinetics in adipocytes raised the possibility of a change in alpha-subunit isoform composition with cytodifferentiation. This inference was evaluated by isoform-specific mRNA analysis (Northern blots) and by alpha-isoform-specific immunoassays (Western blots). Northern blots revealed a modest decrease in mRNA alpha 1, a striking increase in mRNA alpha 2, and a significant loss of mRNA beta content with differentiation of fibroblasts to adipocytes. By immunoassay, fibroblasts exhibited the alpha 1-isoform. Adipocytes exhibited an admixture of alpha 1- and alpha 2-isoforms, with alpha 2 being the more abundant isoform. There was no one-to-one correspondence either between the mRNA isoform and alpha-subunit abundances or between alpha-subunit abundances and enzymatic activity, suggesting that regulation occurs at multiple levels in this system. Findings indicate, however, that a shift in alpha-isoform composition accompanied by a change in ouabain inhibition kinetics occurs with cytodifferentiation.

Assembly of ordered contigs of cosmids selected with YACs of human chromosome 13.

We have developed an efficient method for assembling ordered cosmid contigs aligned to mega-YACs and midi-YACs (average insert sizes of 1.0 and 0.35 Mb, respectively) and used this general method to initiate high-resolution physical mapping of human chromosome 13 (Chr 13). Chr 13-enriched midi-YAC (mYAC) and mega-YAC (MYAC) sublibraries were obtained from corresponding CEPH total human YAC libraries by selecting colonies with inter-Alu PCR probes derived from Chr 13 monochromosomal cell hybrid DNA. These sublibraries were arrayed on filters at high density. In our approach, the MYAC 13 sublibrary is screened by hybridization with cytogenetically assigned Chr 13 DNA probes to select one or a small subset of MYACs. Inter-Alu PCR products from each MYAC are then hybridized to the MYAC and mYAC sublibraries to identify overlapping YACs and to an arrayed Chr 13-specific cosmid library to select corresponding cosmids. The set of selected cosmids, gridded on filters at high density, is hybridized with inter-Alu PCR products from each of the overlapping YACs to identify subsets of cosmids and also with riboprobes from each cosmid of the arrayed set ("cosmid matrix cross-hybridization"). From these data, cosmid contigs are assembled by a specifically designed computer program. Application of this method generates cosmid contigs spanning the length of a MYAC with few gaps. To provide a high-resolution map, ends of cosmids are sequenced at preselected sites to position densely spaced sequence-tagged sites.

A knowledge model for analysis and simulation of regulatory networks.

MOTIVATION: In order to aid in hypothesis-driven experimental gene discovery, we are designing a computer application for the automatic retrieval of signal transduction data from electronic versions of scientific publications using natural language processing (NLP) techniques, as well as for visualizing and editing representations of regulatory systems. These systems describe both signal transduction and biochemical pathways within complex multicellular organisms, yeast, and bacteria. This computer application in turn requires the development of a domain-specific ontology, or knowledge model. RESULTS: We introduce an ontological model for the representation of biological knowledge related to regulatory networks in vertebrates. We outline a taxonomy of the concepts, define their 'whole-to-part' relationships, describe the properties of major concepts, and outline a set of the most important axioms. The ontology is partially realized in a computer system designed to aid researchers in biology and medicine in visualizing and editing a representation of a signal transduction system.

Kaposi's sarcoma-associated herpesvirus contains G protein-coupled receptor and cyclin D homologs which are expressed in Kaposi's sarcoma and malignant lymphoma.

A new human herpesvirus was recently identified in all forms of Kaposi's sarcoma (Kaposi's sarcoma-associated herpesvirus [KSHV] or human herpesvirus 8), as well as in primary effusion (body cavity-based) lymphomas (PELs). A 12.3-kb-long KSHV clone was obtained from a PEL genomic library. Sequencing of this clone revealed extensive homology and colinearity with the right end of the herpesvirus saimiri (HVS) genome and more limited homology to the left end of the Epstein-Barr virus genome. Four open reading frames (ORFs) were sequenced and characterized; these are homologous to the following viral and/or cellular genes: (i) Epstein-Barr virus membrane antigen p140 and HVS p160, (ii) HVS and cellular type D cyclins, (iii) HVS and cellular G protein-coupled receptors, and (iv) HVS. Since there is considerable evidence that cyclin D1 and some G protein-coupled receptors contribute to the development of specific cancers, the presence of KSHV homologs of these genes provides support for a role for KSHV in malignant transformation. All ORFs identified are transcribed in PELs and Kaposi's sarcoma tissues, further suggesting an active role for KSHV in these diseases.