Conceptual modelling of genomic information

MOTIVATION

Genome sequencing projects are making available complete records of the genetic make-up of organisms. These core data sets are themselves complex, and present challenges to those who seek to store, analyse and present the information. However, in addition to the sequence data, high throughput experiments are making available distinctive new data sets on protein interactions, the phenotypic consequences of gene deletions, and on the transcriptome, proteome, and metabolome. The effective description and management of such data is of considerable importance to bioinformatics in the post-genomic era. The provision of clear and intuitive models of complex information is surprisingly challenging, and this paper presents conceptual models for a range of important emerging information resources in bioinformatics. It is hoped that these can be of benefit to bioinformaticians as they attempt to integrate genetic and phenotypic data with that from genomic sequences, in order to both assign gene functions and elucidate the different pathways of gene action and interaction.

RESULTS

This paper presents a collection of conceptual (i.e. implementation-independent) data models for genomic data. These conceptual models are amenable to (more or less direct) implementation on different computing platforms.

Mutation of waaN reduces Salmonella enterica serovar Typhimurium-induced enteritis and net secretion of type III secretion system 1-dependent proteins

Mutation of waaN, a gene involved in lipid A biosynthesis, reduced enteropathogenic responses induced by Salmonella enterica serovar Typhimurium in bovine ligated ileal loops. However, the secretion of key virulence determinants was also reduced, and therefore the reduction in enteropathogenicity cannot be solely attributed to a reduction in biological activity of lipid A.

Prostasomes: current concepts

BACKGROUND

Prostasomes are membranous vesicles secreted by prostate gland, and they contain large amounts of cholesterol, sphingomyelin, calcium, and several enzymes. Prostasomes are involved in a number of biological functions. At ejaculation, these prostasomes are expelled with prostate secretions and are to be found in the seminal plasma as seminal prostasomes, which facilitate sperm function in various ways.

METHODS

In this review, we discuss the structural and functional role of prostasomes, the various enzyme systems associated with these vesicles, and the biological role prostasomes play in male reproduction. RESULTS AND CONCLUSIONS Prostasomes are pluripotent and well-organized organelles secreted by the prostate gland. Prostasomes are ascribed to have many physiologiocal functions, the primary function being enhancement of sperm capacity. The several enzyme systems, small signaling molecules, and neuroendocrine markers associated with prostasomes reveal the complex nature of these vesicles in regulating sperm viability and vitality. The functional significance of these molecules that regulate complex pathways in these small vesicles is still a matter of dogma. Critical evaluation of the biological processes associated with prostasomes might be helpful in modeling new contraceptive agents, improving the techniques of in vitro fertilization, and in furthering our understanding and treatment of male factor infertility.

Role of individual monomers of a dimeric initiator protein in the initiation and termination of plasmid rolling circle replication

Plasmids of the pT181 family encode initiator proteins that act as dimers during plasmid rolling circle (RC) replication. These initiator proteins bind to the origin of replication through a sequence-specific interaction and generate a nick at the origin that acts as the primer for RC replication. Previous studies have demonstrated that the initiator proteins contain separate DNA binding and nicking-closing domains, both of which are required for plasmid replication. The tyrosine residue at position 191 of the initiator RepC protein of pT181 is known to be involved in nicking at the origin. We have generated heterodimers of RepC that consist of different combinations of wild type, DNA binding, and nicking mutant monomers to identify the role of each of the two monomers in RC replication. One monomer with DNA binding activity was sufficient for the targeting of the initiator to the origin, and the presence of Tyr-191 in one monomer was sufficient for the initiation of replication. On the other hand, a dimer consisting of one monomer defective in DNA binding and the other defective in origin nicking failed to initiate replication. Our results demonstrate that the monomer that promotes sequence-specific binding to the origin must also nick the DNA to initiate replication. Interestingly, whereas Tyr-191 of the initiator was required for nicking at the origin to initiate replication, it was dispensable for termination, suggesting that alternate amino acids in the initiator may promote termination but not initiation.

Transfer of erythromycin resistance from poultry to human clinical strains of Staphylococcus aureus

The transfer of ermA and ermC genes, the two most common resistance determinants of erythromycin resistance, was studied with Luria-Bertani broth in the absence of additional Ca(2+) or Mg(2+) ions. Fifteen human and five poultry isolates of Staphylococcus aureus, which were resistant to erythromycin but carried different genetic markers for erythromycin resistance, were used for conjugation. Since both the donors (Amp(s)-Tet(r)) and recipients (Amp(r)-Tet(s)) were resistant to erythromycin, the transconjugants were initially picked up as ampicillin- and tetracycline-resistant colonies. The resistance transfer mechanisms of the chromosomally located erythromycin rRNA methylase gene ermA and the plasmid-borne ermC gene were monitored by a multiplex PCR and gene-specific internal probing assay. Four groups of transconjugants, based upon the transfer of the ermA and/or ermC gene, were distinguished from each other by the use of this method. Selective antibiotic screening revealed only one type of transconjugant that was resistant to ampicillin and tetracycline. A high frequency of transfer (4.5 x 10(-3)) was observed in all of the 23 transconjugants obtained, and the direction of tetracycline and erythromycin resistance marker transfer was determined to be from poultry to clinical isolates. The transfers of the ermA and ermC genes were via transposition and transformation, respectively.

Evaluation of castor bean toxicosis in dogs: 98 cases

Castor beans (Ricinus communis) contain ricin. Ricin is a glycoprotein reported to cause hypotension, gastroenteritis, depression, and death. However, few deaths are reported following castor bean ingestion in animals. From January 1987 to December 1998, the American Society for the Prevention of Cruelty to Animals-National Animal Poison Control Center received 98 incidents of castor bean ingestion in dogs. The most commonly reported clinical signs were vomiting, depression, and diarrhea. Death or euthanasia occurred in 9% of the cases. The severity of clinical signs following castor bean ingestion may depend on whether the beans were chewed or swallowed whole.

Activation of transcription factors activator protein-1 and nuclear factor-kappaB by 2,3,7,8-tetrachlorodibenzo-p-dioxin

2,3,7,8-Tetrachlorodibenzo-p-dioxin (TCDD; dioxin), the prototype agonist of the aromatic hydrocarbon (Ah) receptor, is a potent tumor promoter as well as a complete liver carcinogen that produces an oxidative stress response in rodents and in cultured cell lines. It has been proposed that TCDD promotes neoplastic transformation through oxidative signal transduction pathways, which results in activation of immediate-early response transcription factors. To set the stage for a test of this hypothesis, we evaluated the effect of TCDD treatment on the activation of several transcription factors, including those in the nuclear factor-kappaB (NF-kappaB) and activator protein-1 (AP-1) families, which are activated by changes in the redox state of cells. In an extension of prior results, we found that TCDD treatment produced a sustained overexpression of AP-1 for at least 72 hr in wild-type mouse hepatoma Hepa-1 cells, but not in the Ah receptor-deficient derivative c35 or in cytochrome P450-1A1 (CYP1A1)-negative c37 cells. In addition, TCDD treatment caused a significant increase in the DNA binding activity of NF-kappaB, but not in the activities of the other transcription factors tested. AP-1 and NF-kappaB activation were blocked by the thiol antioxidant N-acetylcysteine and by nordihydroguaiaretic acid, an antioxidant and lipooxygenase inhibitor and an inhibitor of the epoxygenase activity of CYP1A1, and did not take place in c35, c37, or in Ah nuclear translator-deficient c4 cells. Hence, sustained activation of these two transcription factors by TCDD is likely to result from a CYP1A1-dependent and Ah receptor complex-dependent oxidative signal. Electrophoretic mobility supershift analyses with specific antibodies showed that most of the increase in NF-kappaB binding activity could be accounted for by increases in p50/p50 complexes. Since these complexes are known to repress NF-kappaB-dependent gene transcription, our results delineate a second molecular mechanism, in addition to the recently found block of tumor necrosis factor-alpha-mediated p50/p65 activation, that may be responsible for the immunosuppresive effects of TCDD.

Metastatic adenocarcinoma rib presenting as chondrosarcoma

A case of chondrosarcoma rib which turned out to be a case of metastatic adenocarcinoma on histopathological examination is being presented.

A fatal pseudallescheria boydii brain abscess

We present the clinical and radiological features of pseudallescheria boydii infection in a middle aged woman who presented with right frontal pseudallescheria abscess after two years use of prednisolone for rheumatoid arthritis. Despite early surgical excision and intravenous antifungal treatment she died after 7 weeks despite aggressive therapy.

Expression of fos and jun proto-oncogenes in benign versus malignant human uterine tissue

OBJECTIVE

The objective of this study was to evaluate expression of fos and jun proto-oncogenes in benign human uterine tissue compared with malignant uterine tissue.

METHODS

Forty-two endometrial tissue specimens were obtained at the time of hysterectomy. Tissue samples from different phases of the menstrual cycle and from postmenopausal patients were stained using immunohistochemical methods to detect Fos and Jun proteins, estrogen and progesterone receptor status, and Ki67 (detects a nuclear antigen associated with proliferating cells). Tissue was examined microscopically for nuclear staining in endometrial epithelium and stroma. The endometrium was based on the patient's last menstrual period, pathologic dating, and proliferative versus nonproliferative status as determined by Ki67. Benign and malignant specimens were subjected to Northern blot analysis to evaluate levels of expression of c-fos, c-jun, and jun-B mRNA. The pattern of c-fos mRNA expression in malignant samples was further evaluated using in situ hybridization.

RESULTS

In proliferative, secretory, postmenopausal, and progesterone-influenced, uterine specimens immunohistochemically stained and examined, the endometrial and stromal nuclei stained for both Fos and Jun in varying intensities. However, no pattern was found in the variation of intensity according to the phase of the endometrium. Similarly, in malignant and benign endometrial tissue examined by Northern blot and in situ hybridization analyses, expression of proto-oncogene mRNAs was readily detectable, but no statistical correlation between type of tissue examined, grade of adenocarcinoma, and stage of endometrial cancer was found in this study.

CONCLUSIONS

In rodent models, control of uterine cell proliferation is related to change in expression of fos and jun proto-oncogenes. Our results indicate that hormonal control is likely to be different in human endometrium and probably involves genes other than the proto-oncogenes under study. Expression of Fos and Jun do not correlate with endometrial cancer stage and grade.

Prophylactic mastectomy: pathologic findings in high-risk patients

BACKGROUND

According to recently published data, prophylactic mastectomy (PM) appears to prevent about 90% of the expected malignant neoplasms in women with a family history of breast cancer.

OBJECTIVES

To identify the frequency of high-risk lesions in PM specimens and to determine occurrence of any new primary breast cancer following PM.

DESIGN

We performed a retrospective study of women undergoing unilateral or bilateral PM. Medical charts and pathologic findings of 35 patients who underwent bilateral mastectomies at University Hospital, Syracuse, NY, from 1989 to 1996 were reviewed. Patients with biopsy-proven bilateral breast cancer were excluded. Patients were divided into 3 groups: (A) positive family history and no known breast cancer (n = 9), (B) positive family history and contralateral neoplasia (n = 13), and (C) negative family history and contralateral neoplasia (n = 13). These findings were compared with those found in reduction mammoplasty specimens from 10 women at standard risk of breast cancer.

RESULTS

The mean age of the control group of women undergoing reduction mammoplasty was 38 years. The pathologic specimens demonstrated no significant pathologic findings in 9 and fibrocystic change in 1. In group A, the mean number of affected relatives was 3.1, and the mean age was 38 years. Two of these 9 women had atypical duct hyperplasia and 1 had atypical lobular hyperplasia in their breasts (ie, 33% with high-risk pathologic findings). Of the 13 group B women (mean age, 46.6 years; mean of 2.5 affected relatives and unilateral breast cancer), the contralateral PM specimen contained duct carcinoma in situ in one and invasive ductal cancer in a second (15% with occult malignant neoplasms). In 13 group C patients (mean age, 47.1 years), 3 (23.1%) of the contralateral PM specimens displayed atypical duct hyperplasia or atypical lobular hyperplasia. At a mean follow-up of 4.8 years, there have been no new breast malignant neoplasms in these 45 women.

CONCLUSIONS

The occurrence of unilateral cancer in patients with family history of breast cancer is associated with a 15.4% probability of simultaneous occult malignant neoplasms in the contralateral breast. Patients with a strong family history but no evidence of breast cancer have a substantially similar rate of proliferative disease in their PM specimens as those women who have unilateral cancer but no significant family history.

Effects of oral administration of tamoxifen, toremifene, dehydroepiandrosterone, and vorozole on uterine histomorphology in the rat

Tamoxifen, toremifene, DHEA, and vorozole inhibit tumor growth in rodent mammary carcinoma models and are promising chemotherapeutic agents for use against breast cancer development. In the present study, the effect of these agents on uterine histomorphology following oral administration to mature ovary-intact rats (n = 380) was examined. Animals received diet only (control), tamoxifen (0.4 and 1 mg/kg of diet; 10 mg/kg BW by daily gavage), toremifene (3-30 mg/kg of diet), DHEA (24-2000 mg/kg of diet), or vorozole (0.08-1.25 mg/kg BW by daily gavage) for 28 days and were either sacrificed or returned to a basal diet and then sacrificed 21 days later. Treatment with toremifene (all doses) or tamoxifen (1 and 10 mg/kg) for 28 days produced a decrease (P<0.05) in overall uterine size and myometrial thickness; however, uterine luminal and glandular epithelia cell height increased (P<0.05) compared with control. These compartmentalized uterotrophic and antiestrogenic effects of toremifene and tamoxifen were still apparent after 21 days post-treatment. Administration of DHEA (2000 mg/kg of diet) for 28 days had dramatic uterotrophic effects, increasing (P<0.05) overall uterine size and stimulating all three uterine compartments (epithelia, stroma, and myometrium). The other doses of DHEA, however, were not uterotrophic. Interestingly, after removal of DHEA from the diet, uterine weight and myometrial thickness decreased (P<0.05). Vorozole (1.25 mg/kg) administration for 28 days had differential, compartmentalized uterine effects, producing an increase (P<0.05) in epithelial cell height, a decrease (P<0.05) in stromal size, but no change in myometrial thickness. After 21 days postadministration of vorozole, luminal epithelial cell height was increased (P<0.05) compared with control. The data suggest that oral administration of tamoxifen, toremifene, DHEA, and vorozole results in differential, compartmentalized effects in the uterus that are highly dependent on treatment dose. The data may have implications for risk assessment of these agents prior to administration to healthy, cancer-free women.

Recent nonsteroidal anti-inflammatory drug use increases the risk of early recurrence of bleeding in patients presenting with bleeding ulcer

BACKGROUND

Nonsteroidal anti-inflammatory drug (NSAID) use is a well-known risk factor for ulcer formation and ulcer complications. The purpose of this study was to determine whether recent NSAID use increases the risk of early recurrence of bleeding in patients who present with bleeding ulcer.

METHODS

Clinical and endoscopic data were collected prospectively. Dose, frequency, and duration of recent NSAID use were quantified. Recent NSAID use was defined as consumption of over-the-counter or prescription NSAIDs or aspirin for at least 5 days of the 2-week period preceding the index episode of bleeding. Endoscopy was performed within 24 hours of admission to confirm the source of bleeding and endoscopic intervention was applied for stigmata of bleeding. Early recurrence of bleeding was defined as melena, hematochezia or blood per nasogastric tube with a 2 gm or greater decrease in hemoglobin during a period of 48 hours, occurring less than 2 weeks from index episode of bleeding.

RESULTS

One hundred twenty patients (52 NSAID users and 68 nonusers) were enrolled in the study; mean age was 56 years. NSAID users were older than nonusers (p = 0.003); nonusers were more likely to have a history of ulcer disease (p < 0.0005) and higher prevalence of Helicobacter pylori infection (p = 0.05). Recent NSAID use was associated with a significantly higher frequency of early recurrence of bleeding and in-hospital recurrent bleeding compared with nonusers: 19% vs. 6%, p = 0.02, and 17% vs. 6%, p = 0.04, respectively. In multivariate logistic regression analysis, the significant association between recent NSAID use and early recurrence of bleeding persisted (p = 0.0048) while controlling for age and other covariates.

CONCLUSIONS

Recent NSAID use predisposes bleeding ulcer patients to early and in-hospital recurrent bleeding, probably via its effects on platelet function, mucosal prostaglandins, and ulcer healing.

Environmental estrogens induce transcriptionally active estrogen receptor dimers in yeast: activity potentiated by the coactivator RIP140

We used three yeast genetic systems to investigate the estrogen-like activity of octylphenol (OP), bisphenol-A (BPA), o,p'-DDT, and o, p'-DDE to induce human estrogen receptor (hER) dimerization and transcriptional activation. We have demonstrated that OP, BPA, and o, p'-DDT can induce hER ligand-dependent dimerization using a yeast two-hybrid assay. All three xenoestrogens, plus estradiol, enhanced estrogen response element (ERE)-dependent transcriptional activation of hER. In the presence of receptor interacting protein 140 (RIP140), ERE-dependent activity was dramatically amplified by 100-fold for estradiol, OP, BPA, and o,p'-DDT. A yeast whole-cell [(3)H]estradiol binding assay was developed to determine the site of interaction on the hER. We determined nonspecific binding by parallel incubations run in the presence of 5 microM unlabelled estradiol in PCY2 yeast. At the concentrations tested, unlabeled estradiol, OP, and BPA displaced [(3)H]estradiol in this binding assay, whereas the concentrations of o,p'-DDT and o,p'-DDE tested were insufficient to inhibit binding. Incubating yeast in the presence of increasing concentrations of estradiol and OP (1 microM) or BPA (1 microM) neither blocked nor altered the effect of estradiol on hER activity. We observed no agonistic activity of o,p'-DDE in any of the yeast models used. These results suggest that OP, BPA, and o,p'-DDT exert their estrogen-like activity through the ER in a manner similar to that of estradiol, and the coactivator RIP140 markedly potentiates this activity.

Weakness, tremors, and depression associated with macadamia nuts in dogs

The ASPCA National Animal Poison Center managed 29 cases of ingestion of commercially available macadamia nuts in dogs during a 5-y period. Clinical signs included, from most to least, weakness, depression, vomiting, ataxia, tremor, hyperthermia, abdominal pain, lameness, stiffness, recumbency, and pale mucous membranes. The onset of clinical signs was reported as < 12 h in 79% of the cases. The duration of clinical signs for the majority of cases was < 24 h. The amount of macadamia nuts ingested was estimated in 72% of the calls with a mean of 11.7 g/kg bw. In an attempt to reproduce the syndrome, 4 dogs were gavaged with 20 g macadamia nuts/kg bw in a water slurry. The experimentally dosed dogs developed weakness, manifested by the inability to rise 12 h after dosing, mild central nervous system depression, vomiting, and hyperthermia, with rectal temperatures up to 40.5 C. Mild elevations in serum triglycerides and serum alkaline phosphatase were detected. Lipase values peaked sharply at 24 h and returned to normal by 48 h after dosing. Other serum biochemical and electrolyte determinations were unremarkable. Serum lipoprotein electrophoresis determinations were unchanged from baseline. The mechanism of the syndrome is unknown. All field and experimental dogs recovered uneventfully within 1 to 2 d whether treated by a veterinarian or not.

Detection of multidrug-resistant Salmonella typhimurium DT104 by multiplex polymerase chain reaction

Salmonella typhimurium definitive type 104 (DT104) is a virulent pathogen for humans and animals with many strains having multiple drug resistance characteristics. The organism typically carries resistance to ampicillin, chloramphenicol, florfenicol, streptomycin, sulfonamides, and tetracycline (ACSSuT-resistant). A multiplex PCR method was developed to simultaneously amplify four genes, florfenicol (flo(st)), virulence (spvC), invasion (invA), and integron (int) from S. typhimurium DT104 (ACSSuT-type). Twenty-two ACSSuT-resistant DT104 isolates in our collection gave 100% positive reactions to this PCR assay by amplifying 584-, 392-, 321- and 265-bp PCR products, using primers specific to the respective target genes. One Salmonella strain DT23, ACSSuT-resistant, phage type 711 failed to amplify the 584-bp fragment, indicating that this method is specific for DT104-type ACSSuT-resistant S. typhimurium strains. One clinical and one bovine ASSuT-resistant strains that were sensitive to chloramphenicol and florfenicol did not yield a 584-bp fragment, indicating the absence of the flo(st) gene. This method will be useful for rapid identification of ACSSuT-type DT104 strains from clinical, food and environmental samples.

The use of intra aortic baloon pump in patients undergoing coronary artery bypass grafting at the Aga Khan University Hospital, Karachi

OBJECTIVE

To review the experience in the use of Intra Aortic Balloon Pump (IABP) in patients undergoing Coronary Artery Bypass Grafting (CABG) at a tertiary care hospital with a new Open Heart surgery program.

DESIGN

Retrospective study.

SETTING

The Aga Khan University Hospital, Karachi.

PATIENTS

Medical records of all patients undergoing CABG between November 1994 and July 1997 were reviewed and those in whom IABP device was used, were included in this study.

RESULTS

A total of 15 patients had IABP support during the study period. Four surgeries were done urgently while two were emergencies. There were three mortalities. Ejection fractions in all but one patient were impaired. Among the surviving patients, the average pre-IABP Cardiac Index was 2.6 litres/min/meter2 which registered an average increase of 21.15% after the initiation of the IABP. The Pulmonary Artery Wedge Pressure also showed an average reduction of 29.11% from the pre IABP levels reflecting an increase in the cardiac output with the use of the IABP.

CONCLUSION

This series represents the early experience of a new cardiac surgery center in Pakistan in the use of IABP. Although the numbers in this study are too small to derive any conclusions, the overall morbidity and mortality in this short series are within acceptable limits in the high risk patients included.

Care of the elderly: Parallel Thinking

Full text is available as a scanned copy of the original print version.

Ethylene glycol exposures managed by the ASPCA National Animal Poison Control Center from July 1995 to December 1997

Five-hundred and ten cases of ethylene glycol (EG) exposures in animals were compiled by the ASPCA National Animal Poison Control Center from July 1995 through December 1997. Case distribution was analyzed by species, sex, age, weight, seasonality, treatment intervention and final outcome. Dogs and cats were most commonly involved (98.0%). The sex distribution was approximately equal. Adult animals accounted for the majority of cases. Exposures were commonly (57.0%) from container spill, engine flush, or engine leak and were in or around the home (66.0%). Cases were reported throughout the year with slight increase during March-May. Among cases with a known final outcome, 59.0% did not show clinical signs and death/euthanasia, major and minor illness was reported in 28.0%, 5.0% and 8.0%. In view of the widespread use and potential toxicity of EG, the low number of EG exposures reported (510) among the total number of hazardous exposures (97,383) to all substances for the same period was remarkable. The EG exposures resulting in animal death/euthanasia were lower than previously published.

Muir-Torre syndrome: case report of a patient with concurrent jejunal and ureteral cancer and a review of the literature

BACKGROUND

Muir-Torre syndrome is a rare autosomal dominant genodermatosis, first described in 1967, characterized by the presence of sebaceous tumors and an internal malignancy in the absence of other predisposing factors.

OBJECTIVE

Our purpose was to review and update published literature on Muir-Torre syndrome.

METHODS

We describe a 66-year-old white man with a history of sebaceous tumors and newly diagnosed transitional cell cancer of the right ureter and adenocarcinoma of the jejunum. The literature on Muir-Torre syndrome is reviewed by means of MEDLINE search and available published reports and updated.

RESULTS

Only 205 cases of Muir-Torre syndrome with 399 internal malignancies have been reported. The common presentation is the presence of sebaceous tumors along with a low-grade visceral malignancy. Sebaceous tumors appeared before the internal malignancy in 45 cases (22%), concurrently in 12 (6%), and after the internal malignancy in 114 (56%). In 33 (16%) of 205 patients, a temporal relationship was not reported. The total number of sebaceous gland carcinomas reported is 44; 17 of 44 were neoplasms of the meibomian gland. Keratoacanthomas have been noted in 48 (23%) of 205 patients. Gastrointestinal cancers are the most common internal malignancies (61%), followed by genitourinary (22%).

CONCLUSION

The presence of sebaceous tumors warrants a search for an internal malignancy. In patients with Muir-Torre syndrome, regular follow-up and search for new malignancy is mandatory. Evaluation and monitoring of the family members of patients are also necessary. Patients and their families should be counseled for genetic testing. Genetic analysis of the primary tumor and skin lesions should be arranged as an added research tool if possible to better understand the disease.