Abstract 992: Credentialing UHRF1 as a target for prostate cancer therapy

Alterations in DNA methylation are a hallmark of prostate carcinogenesis. UHRF1 is an essential component in the machinery required for the maintenance of DNA methylation in actively dividing cells. In S-phase, UHRF1 binds nascent hemimethylated DNA and recruits DNA methyltransferases to copy the methylation pattern to the daughter DNA strand in a manner analogous to semi-conservative replication. Additionally, it has been shown that UHRF1 interacts with methylated histones and histone methyltransferases, making it an important epigenetic regulator in proliferating cells. Because of its ties to epigenetic gene silencing and cell proliferation, we hypothesized that UHRF1 could serve as a target for prostate cancer treatment. In this study, we have taken steps to credential UHRF1 as a therapeutic target in prostate cancer and have developed a high-throughput UHRF1-DNA binding assay to screen for UHRF1 inhibitors. We show that UHRF1 is overexpressed in a panel of prostate cancer cell lines and it appears to track with proliferation in prostate cancer tissue. Through loss-of-function studies in prostate cancer cell lines PC3 and DU145, we show that long-term UHRF1 depletion leads to a decrease in clonogenic survival and an overall reduction in global levels of DNA methylation. Further, we find that UHRF1 is required to maintain DNA methylation and epigenetic silencing of hypermethylated genes in prostate cancer cells. Additionally, ChIP experiments revealed that UHRF1 can be bound at the promoter CpG islands of epigenetically silenced genes in prostate cancer cells. With the goal of ultimately developing UHRF1 inhibitors, we have developed a time-resolved fluorescence resonance energy transfer (TR-FRET)-based assay, compatible with high-throughput screening, that can detect the binding of the SRA domain of UHRF1 to hemimethylated DNA. In summary, we have shown that UHRF1 plays a critical role in maintaining the DNA methylation of epigenetically silenced genes in prostate cancer and have developed an assay for high-throughput screening of UHRF1 inhibitors.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 992. doi:1538-7445.AM2012-992

Next-generation sequencing-based transcriptomic and proteomic analysis of the common reed, Phragmites australis (Poaceae), reveals genes involved in invasiveness and rhizome specificity

PREMISE OF THE STUDY

The common reed (Phragmites australis), one of the most widely distributed of all angiosperms, uses its rhizomes (underground stems) to invade new territory, making it one of the most successful weedy species worldwide. Characterization of the rhizome transcriptome and proteome is needed to identify candidate genes and proteins involved in rhizome growth, development, metabolism, and invasiveness.

METHODS

We employed next-generation sequencing technologies including 454 and Illumina platforms to characterize the reed rhizome transcriptome and used quantitative proteomics techniques to identify the rhizome proteome.

KEY RESULTS

Combining 336514 Roche 454 Titanium reads and 103350802 Illumina paired-end reads in a de novo hybrid assembly yielded 124450 unique transcripts with an average length of 549 bp, of which 54317 were annotated. Rhizome-specific and differentially expressed transcripts were identified between rhizome apical tips (apical meristematic region) and rhizome elongation zones. A total of 1280 nonredundant proteins were identified and quantified using GeLC-MS/MS based label-free proteomics, where 174 and 77 proteins were preferentially expressed in the rhizome elongation zone and apical tip tissues, respectively. Genes involved in allelopathy and in controlling development and potentially invasiveness were identified.

CONCLUSIONS

In addition to being a valuable sequence and protein data resource for studying plant rhizome species, our results provide useful insights into identifying specific genes and proteins with potential roles in rhizome differentiation, development, and function.

Next-generation sequencing-based transcriptomic and proteomic analysis of the common reed, Phragmites australis (Poaceae), reveals genes involved in invasiveness and rhizome specificity

PREMISE OF THE STUDY

The common reed (Phragmites australis), one of the most widely distributed of all angiosperms, uses its rhizomes (underground stems) to invade new territory, making it one of the most successful weedy species worldwide. Characterization of the rhizome transcriptome and proteome is needed to identify candidate genes and proteins involved in rhizome growth, development, metabolism, and invasiveness.

METHODS

We employed next-generation sequencing technologies including 454 and Illumina platforms to characterize the reed rhizome transcriptome and used quantitative proteomics techniques to identify the rhizome proteome.

KEY RESULTS

Combining 336514 Roche 454 Titanium reads and 103350802 Illumina paired-end reads in a de novo hybrid assembly yielded 124450 unique transcripts with an average length of 549 bp, of which 54317 were annotated. Rhizome-specific and differentially expressed transcripts were identified between rhizome apical tips (apical meristematic region) and rhizome elongation zones. A total of 1280 nonredundant proteins were identified and quantified using GeLC-MS/MS based label-free proteomics, where 174 and 77 proteins were preferentially expressed in the rhizome elongation zone and apical tip tissues, respectively. Genes involved in allelopathy and in controlling development and potentially invasiveness were identified.

CONCLUSIONS

In addition to being a valuable sequence and protein data resource for studying plant rhizome species, our results provide useful insights into identifying specific genes and proteins with potential roles in rhizome differentiation, development, and function.

The controversial relationship between benign prostatic hyperplasia and prostate cancer: the role of inflammation

CONTEXT

Prostate cancer (PCa) is the most common cancer in the adult male, and benign prostatic hyperplasia (BPH) represents the most frequent urologic diagnosis in elderly males. Recent data suggest that prostatic inflammation is involved in the pathogenesis and progression of both conditions.

OBJECTIVE

This review aims to evaluate the available evidence on the role of prostatic inflammation as a possible common denominator of BPH and PCa and to discuss its possible clinical implication for the management, prevention, and treatment of both diseases.

EVIDENCE ACQUISITION

The National Library of Medicine Database was searched for the following Patient population, Intervention, Comparison, Outcome (PICO) terms: male, inflammation, benign prostatic hyperplasia, prostate cancer, diagnosis, progression, prognosis, treatment, and prevention. Basic and clinical studies published in the past 10 yr were reviewed. Additional references were obtained from the reference list of full-text manuscripts.

EVIDENCE SYNTHESIS

The histologic signature of chronic inflammation is a common finding in benign and malignant prostate tissue. The inflammatory infiltrates are mainly represented by CD3(+) T lymphocytes (70-80%, mostly CD4), CD19 or CD20 B lymphocytes (10-15%), and macrophages (15%). Bacterial infections, urine reflux, dietary factors, hormones, and autoimmune response have been considered to cause inflammation in the prostate. From a pathophysiologic standpoint, tissue damage associated with inflammatory response and subsequent chronic tissue healing may result in the development of BPH nodules and proliferative inflammatory atrophy (PIA). The loss of glutathione S-transferase P1 (GSTP1) may be responsible in patients with genetic predisposition for the transition of PIA into high-grade intraepithelial neoplasia (HGPIN) and PCa. Although there is growing evidence of the association among inflammatory response, BPH, and PCa, we can only surmise on the immunologic mechanisms involved, and further research is required to better understand the role of prostatic inflammation in the initiation of BPH and PCa. There is not yet proof that targeting prostate inflammation with a pharmacologic agent results in a lower incidence and progression or regression of either BPH or PCa.

CONCLUSIONS

Evidence in the peer-reviewed literature suggested that chronic prostatic inflammation may be involved in the development and progression of chronic prostatic disease, such as BPH and PCa, although there is still no evidence of a causal relation. Inflammation should be considered a new domain in basic and clinical research in patients with BPH and PCa.

Differential classification of acute myocardial infarction into ST- and non-ST segment elevation is not valid or rational

BACKGROUND

The distinction between ST elevation and nonST elevation infarcts is widely accepted and is employed as a guide to management.

AIM

This is review of the world literature to assess the basis for this distinction, since the two studies on which it is based are seriously flawed in method and conclusions.

METHOD

Pathologic and clinical studies were reviewed from the world literature.

FINDING

The pathology of the two subsets is identical as are the morbidity, mortality and clinical course. Non-ST elevation infarcts are likely to be subsequent, to occur in older patients and to involve the circumflex artery: this subset therefore includes a high-risk group. ST deviation in any part of the electric field of the heart will predictably be accompanied by reciprocal deviation if the entire field of the heart is mapped. Further, ST deviation of infarction is often transient, resolving in minutes so that infarcts will be predictably misclassified. ST deviation per se is therefore not a rational basis for classification of infarcts. In fact, invasive therapy is indicated in both subsets with identical results.

CONCLUSION

The distinction between ST elevation and non-ST elevation infarcts is baseless. The high risk subgroup included in the non-ST elevation infarct set should not be denied the benefit of early invasive therapy.

Constraining the noncommutative spectral action via astrophysical observations

The noncommutative spectral action extends our familiar notion of commutative spaces, using the data encoded in a spectral triple on an almost commutative space. Varying a rather simple action, one can derive all of the standard model of particle physics in this setting, in addition to a modified version of Einstein-Hilbert gravity. In this Letter we use observations of pulsar timings, assuming that no deviation from general relativity has been observed, to constrain the gravitational sector of this theory. While the bounds on the coupling constants remain rather weak, they are comparable to existing bounds on deviations from general relativity in other settings and are likely to be further constrained by future observations.

Genome sequence of the palaeopolyploid soybean

Soybean (Glycine max) is one of the most important crop plants for seed protein and oil content, and for its capacity to fix atmospheric nitrogen through symbioses with soil-borne microorganisms. We sequenced the 1.1-gigabase genome by a whole-genome shotgun approach and integrated it with physical and high-density genetic maps to create a chromosome-scale draft sequence assembly. We predict 46,430 protein-coding genes, 70% more than Arabidopsis and similar to the poplar genome which, like soybean, is an ancient polyploid (palaeopolyploid). About 78% of the predicted genes occur in chromosome ends, which comprise less than one-half of the genome but account for nearly all of the genetic recombination. Genome duplications occurred at approximately 59 and 13 million years ago, resulting in a highly duplicated genome with nearly 75% of the genes present in multiple copies. The two duplication events were followed by gene diversification and loss, and numerous chromosome rearrangements. An accurate soybean genome sequence will facilitate the identification of the genetic basis of many soybean traits, and accelerate the creation of improved soybean varieties.

New Hampshire critical access hospitals: CEOs' report on ethical challenges

Research into the importance of organizational healthcare ethics has increasingly appeared in healthcare publications. However, to date, few published studies have examined ethical issues from the perspective of healthcare executives, and no empirical study has addressed organizational ethics with an explicit focus on rural hospitals. For our study, we sought to identify the frequency of ethical conflicts occurring within 12 general categories (domains) of administrative activities. Also, we wanted to determine what ethics resources are currently available and whether additional resources would be helpful. We conducted a structured telephone interview of all 13 chief executive officers (CEOs) of critical access hospitals in New Hampshire. All the CEOs in the study indicated that they encountered ethical conflicts. On average, the three most frequently noted domains were organizational-professional staff relations, reimbursement, and clinical care. All CEOs indicated they would like to have additional ethics resources to address these conflicts. This study verified that CEOs encounter a broad spectrum of ethical conflicts and need additional ethics resources to address them. Because this study used a small sample of CEOs and represented only one New England state, further ethics-related research in rural healthcare facilities is warranted. Follow-up study would allow for (1) a higher level of generalization of the findings, (2) clarity regarding specific ethical dilemmas that rural healthcare executives encounter, and (3) an assessment of ethics resources and training that healthcare executives need to address the ethical conflicts.

Integrating sequence with FPC fingerprint maps

Recent advances in both clone fingerprinting and draft sequencing technology have made it increasingly common for species to have a bacterial artificial clone (BAC) fingerprint map, BAC end sequences (BESs) and draft genomic sequence. The FPC (fingerprinted contigs) software package contains three modules that maximize the value of these resources. The BSS (blast some sequence) module provides a way to easily view the results of aligning draft sequence to the BESs, and integrates the results with the following two modules. The MTP (minimal tiling path) module uses sequence and fingerprints to determine a minimal tiling path of clones. The DSI (draft sequence integration) module aligns draft sequences to FPC contigs, displays them alongside the contigs and identifies potential discrepancies; the alignment can be based on either individual BES alignments to the draft, or on the locations of BESs that have been assembled into the draft. FPC also supports high-throughput fingerprint map generation as its time-intensive functions have been parallelized for Unix-based desktops or servers with multiple CPUs. Simulation results are provided for the MTP, DSI and parallelization. These features are in the FPC V9.3 software package, which is freely available.

Relationship of sex steroid hormones with bone mineral density (BMD) in a nationally representative sample of men

OBJECTIVE

Sex steroid hormones influence bone mineral density (BMD) in women, but are less well-studied in men. We evaluated the association of serum total and free sex steroid hormones and SHBG with osteopaenia in a nationally representative sample of men aged 20-90 years.

DESIGN

BMD and sex steroid hormones were measured among participants in NHANES III, a cross-sectional study of the US population.

POPULATION

A total of 1185 adult men in morning examination session of Phase I of NHANES III (1988-91).

MEASUREMENTS

Relation of oestradiol (E(2)), testosterone, and SHBG concentrations with BMD. Osteopaenia was defined as 1-2.5 SD below the mean for white men aged 20-29 years.

RESULTS

Men in the lowest quartile of free E(2) had 70% increased odds (OR = 1.69, 95% CI 0.95-2.98) of osteopaenia compared with men in the highest quartile. Men in the lowest quartile of free testosterone had nearly four times the odds of osteopaenia than those in the highest quartile (OR = 3.82, 95% CI 1.87-7.78). Lower concentrations of SHBG appeared protective against osteopaenia (P-trend = 0.01). Neither total testosterone nor total E(2) was associated with BMD, although men with clinically low E(2) (< 20 ng/l) had lower BMD (0.930 g/cm(2), 95% CI 0.88-0.98) than men with normal-range E(2) (1.024 g/cm(2), 95% CI 1.01-1.04; P = 0.004). Findings for free E(2) were most pronounced among elderly men, while the findings for free testosterone were most pronounced among younger men.

CONCLUSIONS

In this nationally representative study, men with lower free E(2), lower free testosterone, and higher SHBG concentrations in circulation were more likely to have low BMD.

Methylation-sensitive linking libraries enhance gene-enriched sequencing of complex genomes and map DNA methylation domains

Background

Many plant genomes are resistant to whole-genome assembly due to an abundance of repetitive sequence, leading to the development of gene-rich sequencing techniques. Two such techniques are hypomethylated partial restriction (HMPR) and methylation spanning linker libraries (MSLL). These libraries differ from other gene-rich datasets in having larger insert sizes, and the MSLL clones are designed to provide reads localized to "epigenetic boundaries" where methylation begins or ends.

Results

A large-scale study in maize generated 40,299 HMPR sequences and 80,723 MSLL sequences, including MSLL clones exceeding 100 kb. The paired end reads of MSLL and HMPR clones were shown to be effective in linking existing gene-rich sequences into scaffolds. In addition, it was shown that the MSLL clones can be used for anchoring these scaffolds to a BAC-based physical map. The MSLL end reads effectively identified epigenetic boundaries, as indicated by their preferential alignment to regions upstream and downstream from annotated genes. The ability to precisely map long stretches of fully methylated DNA sequence is a unique outcome of MSLL analysis, and was also shown to provide evidence for errors in gene identification. MSLL clones were observed to be significantly more repeat-rich in their interiors than in their end reads, confirming the correlation between methylation and retroelement content. Both MSLL and HMPR reads were found to be substantially gene-enriched, with the SalI MSLL libraries being the most highly enriched (31% align to an EST contig), while the HMPR clones exhibited exceptional depletion of repetitive DNA (to ~11%). These two techniques were compared with other gene-enrichment methods, and shown to be complementary.

Conclusion

MSLL technology provides an unparalleled approach for mapping the epigenetic status of repetitive blocks and for identifying sequences mis-identified as genes. Although the types and natures of epigenetic boundaries are barely understood at this time, MSLL technology flags both approximate boundaries and methylated genes that deserve additional investigation. MSLL and HMPR sequences provide a valuable resource for maize genome annotation, and are a uniquely valuable complement to any plant genome sequencing project. In order to make these results fully accessible to the community, a web display was developed that shows the alignment of MSLL, HMPR, and other gene-rich sequences to the BACs; this display is continually updated with the latest ESTs and BAC sequences.

The SQUIRE (Standards for QUality Improvement Reporting Excellence) guidelines for quality improvement reporting: explanation and elaboration

As the science of quality improvement in health care advances, the importance of sharing its accomplishments through the published literature increases. Current reporting of improvement work in health care varies widely in both content and quality. It is against this backdrop that a group of stakeholders from a variety of disciplines has created the Standards for QUality Improvement Reporting Excellence, which we refer to as the SQUIRE publication guidelines or SQUIRE statement. The SQUIRE statement consists of a checklist of 19 items that authors need to consider when writing articles that describe formal studies of quality improvement. Most of the items in the checklist are common to all scientific reporting, but virtually all of them have been modified to reflect the unique nature of medical improvement work. This "Explanation and Elaboration" document (E & E) is a companion to the SQUIRE statement. For each item in the SQUIRE guidelines the E & E document provides one or two examples from the published improvement literature, followed by an analysis of the ways in which the example expresses the intent of the guideline item. As with the E & E documents created to accompany other biomedical publication guidelines, the purpose of the SQUIRE E & E document is to assist authors along the path from completion of a quality improvement project to its publication. The SQUIRE statement itself, this E & E document, and additional information about reporting improvement work can be found at http://www.squire-statement.org.

Abstract CN01-01: Genetic and epigenetic changes in prostate cancer as targets for prevention

CN01-01

Prostate cancer cells are known to carry a variety of genetic defects, including gene translocations (eg. TMPRSS-ERG1), amplifications (eg. AR), mutations, and deletions. These changes are thought to endow the prostate cancer cells with new capabilities for dysregulated proliferation, inappropriate survival, tissue invasion and destruction, immune system evasion, and metastasis. In addition, cancer cells also carry epigenetic defects, manifest as changes in CpG dinucleotide methylation patterns and in chromatin structure and organization (eg. at GSTP1 and many others), which are equivalent to genetic changes in promoting malignant phenotypes. During the pathogenesis of prostate cancer, the somatic epigenetic alterations tend appear earlier during cancer development than genetic changes, as well as more commonly and consistently. For this presentation, new data concerning the mechanism(s) by which androgen action might promote translocations at AR target genes, and by which inflammatory processes might trigger CpG island hypermethylation, in prostate cells will be presented. These new insights into the formation of somatic genetic and epigenetic changes will provide new molecular biomarkers to aid in prostate cancer detection and diagnosis, and may lead to new opportunities for prostate cancer prevention and treatment.

Citation Information: Cancer Prev Res 2008;1(7 Suppl):CN01-01.

A dry-format field-deployable quantitative reverse transcriptase-polymerase chain reaction assay for diagnosis of dengue infections

We have systematically evaluated a dry-format, quantitative reverse transcriptase-polymerase chain reaction (qRT-PCR) assay developed by Tetracore Inc. for the Cepheid SmartCycler platform to facilitate rapid diagnosis of dengue virus infections. A panel of related flaviviruses was used to evaluate the clinical specificity of the assay, and it was found to be specific to dengue. Eighty-one clinical samples previously confirmed dengue positive by virus isolation, along with 25 dengue negative control specimens were used to validate this new diagnostic assay. Using these clinical samples, the assay exhibited 98.77% sensitivity and 100% specificity. Over 85% of the clinical specimen exhibited viral loads ranging from 10(3) to 10(7) plaque-forming units per milliliter (PFU/mL). In addition, this dry-format assay is stable at ambient temperatures and requires minimal technical expertise to perform in a small thermocycler platform. These characteristics make it a promising candidate for diagnosis of dengue in mobile laboratories in the field.

Physical and genetic structure of the maize genome reflects its complex evolutionary history

Maize (Zea mays L.) is one of the most important cereal crops and a model for the study of genetics, evolution, and domestication. To better understand maize genome organization and to build a framework for genome sequencing, we constructed a sequence-ready fingerprinted contig-based physical map that covers 93.5% of the genome, of which 86.1% is aligned to the genetic map. The fingerprinted contig map contains 25,908 genic markers that enabled us to align nearly 73% of the anchored maize genome to the rice genome. The distribution pattern of expressed sequence tags correlates to that of recombination. In collinear regions, 1 kb in rice corresponds to an average of 3.2 kb in maize, yet maize has a 6-fold genome size expansion. This can be explained by the fact that most rice regions correspond to two regions in maize as a result of its recent polyploid origin. Inversions account for the majority of chromosome structural variations during subsequent maize diploidization. We also find clear evidence of ancient genome duplication predating the divergence of the progenitors of maize and rice. Reconstructing the paleoethnobotany of the maize genome indicates that the progenitors of modern maize contained ten chromosomes.

As a cash crop and a model biological system, maize is of great public interest. To facilitate maize molecular breeding and its basic biology research, we built a high-resolution physical map with two different fingerprinting methods on the same set of bacterial artificial chromosome clones. The physical map was integrated to a high-density genetic map and further serves as a framework for the maize genome-sequencing project. Comparative genomics showed that the euchromatic regions between rice and maize are very conserved. Physically we delimited these conserved regions and thus detected many genome rearrangements. We defined extensively the duplication blocks within the maize genome. These blocks allowed us to reconstruct the chromosomes of the maize progenitor. We detected that maize genome has experienced two rounds of genome duplications, an ancient one before maize–rice divergence and a recent one after tetraploidization.

Construction, alignment and analysis of twelve framework physical maps that represent the ten genome types of the genus Oryza

Bacterial artificial chromosome (BAC) fingerprint and end-sequenced physical maps representing the ten genome types of Oryza are presented

We describe the establishment and analysis of a genus-wide comparative framework composed of 12 bacterial artificial chromosome fingerprint and end-sequenced physical maps representing the 10 genome types of Oryza aligned to the O. sativa ssp. japonica reference genome sequence. Over 932 Mb of end sequence was analyzed for repeats, simple sequence repeats, miRNA and single nucleotide variations, providing the most extensive analysis of Oryza sequence to date.

Comparative physical mapping between Oryza sativa (AA genome type) and O. punctata (BB genome type)

A comparative physical map of the AA genome (Oryza sativa) and the BB genome (O. punctata) was constructed by aligning a physical map of O. punctata, deduced from 63,942 BAC end sequences (BESs) and 34,224 fingerprints, onto the O. sativa genome sequence. The level of conservation of each chromosome between the two species was determined by calculating a ratio of BES alignments. The alignment result suggests more divergence of intergenic and repeat regions in comparison to gene-rich regions. Further, this characteristic enabled localization of heterochromatic and euchromatic regions for each chromosome of both species. The alignment identified 16 locations containing expansions, contractions, inversions, and transpositions. By aligning 40% of the punctata BES on the map, 87% of the punctata FPC map covered 98% of the O. sativa genome sequence. The genome size of O. punctata was estimated to be 8% larger than that of O. sativa with individual chromosome differences of 1.5-16.5%. The sum of expansions and contractions observed in regions >500 kb were similar, suggesting that most of the contractions/expansions contributing to the genome size difference between the two species are small, thus preserving the macro-collinearity between these species, which diverged approximately 2 million years ago.

Hyperoxaluric nephrolithiasis is a complication of Roux-en-Y gastric bypass surgery

Roux-en-Y bypass surgery is the most common bariatric procedure currently performed in the United States for medically complicated obesity. Although this leads to a marked and sustained weight loss, we have identified an increasing number of patients with episodes of nephrolithiasis afterwards. We describe a case series of 60 patients seen at Mayo Clinic-Rochester that developed nephrolithiasis after Roux-en-Y gastric bypass (RYGB), including a subset of 31 patients who had undergone metabolic evaluation in the Mayo Stone Clinic. The mean body mass index of the patients before procedure was 57 kg/m(2) with a mean decrease of 20 kg/m(2) at the time of the stone event, which averaged 2.2 years post-procedure. When analyzed, calcium oxalate stones were found in 19 and mixed calcium oxalate/uric acid stones in two patients. Hyperoxaluria was a prevalent factor even in patients without a prior history of nephrolithiasis, and usually presented more than 6 months after the procedure. Calcium oxalate supersaturation, however, was equally high in patients less than 6 months post-procedure due to lower urine volumes. In a small random sampling of patients undergoing this bypass procedure, hyperoxaluria was rare preoperatively but common 12 months after surgery. We conclude that hyperoxaluria is a potential complicating factor of RYGB surgery manifested as a risk for calcium oxalate stones.

A proposed rural healthcare ethics agenda

The unique context of the rural setting provides special challenges to furnishing ethical healthcare to its approximately 62 million inhabitants. Although rural communities are widely diverse, most have the following common features: limited economic resources, shared values, reduced health status, limited availability of and accessibility to healthcare services, overlapping professional-patient relationships and care giver stress. These rural features shape common healthcare ethical issues, including threats to confidentiality, boundary issues, professional-patient relationship and allocation of resources. To date, there exists a limited focus on rural healthcare ethics shown by the scarcity of rural healthcare ethics literature, rural ethics committees, rural focused ethics training and research on rural ethics issues. An interdisciplinary group of rural healthcare ethicists with backgrounds in medicine, nursing and philosophy was convened to explore the need for a rural healthcare ethics agenda. At the meeting, the Coalition for Rural Health Care Ethics agreed to a definition of rural healthcare ethics and a broad-ranging rural ethics agenda with the ultimate goal of enhancing the quality of patient care in rural America. The proposed agenda calls for increasing awareness and understanding of rural healthcare ethics through the development of evidence--informed, rural-attuned research, scholarship and education in collaboration with rural healthcare professionals, healthcare institutions and the diverse rural population.

SyMAP: A system for discovering and viewing syntenic regions of FPC maps

Previous approaches to comparing gene and chromosome organization between two genomes have been based on genetic maps or genomic sequences. We have developed a system to align an FPC-based physical map to a genomic sequence based on BAC end sequences and sequence-tagged hybridization markers and to align two FPC maps to one another based on shared markers and fingerprints. The system, called SyMAP (Synteny Mapping and Analysis Program), consists of an algorithm to compute synteny blocks and Web-based graphics to visualize the results. The approach to calculating the anchors (corresponding elements on the respective maps) maximizes the inclusion of anchors with different rates of divergence. Chains (putative syntenic sets of anchors) are computed using a dynamic programming algorithm, which includes off-diagonal anchors that result from map coordinate errors and small inversions. As the gap parameters (the distances allowed between anchors in a chain) can vary over different data sets and be difficult to set manually, they are automatically computed per data set. The criterion for a chain to be acceptable is based on the number of anchors and the Pearson correlation coefficient. Neighboring chains are merged into synteny blocks for display. This algorithm has been tested with three data sets that vary in the number of BACs, BAC end sequences, hybridization markers, distance between anchors, and number and antiquity of genome duplication events. The Web-based graphics uses Java for a highly interactive display that allows the user to interrogate the evidence of synteny.