Emerging patterns and gene expression data

One important purpose of conducting gene expression experiments is to understand the correlation of gene expression profiles to disease states. Based on the notion of emerging patterns and an entropy-oriented discretization method, we discover groups of genes that are correlated to disease states in a significant way. In each group, every member gene constrained by a specific expression interval, unanimously occurs only in one type of cells with a maximally large frequency, but never unanimously happens in the other types of cells. According to our studies on the colon tumor dataset, such gene groups (also called patterns) can reach a frequency of 90%, providing good insight into the correlation of gene expression profiles to disease states. The patterns can be used to correctly predict whether a new cell is normal or cancerous.

The effect of sucrose application frequency and basal nutrient conditions on the calcium and phosphate content of experimental dental plaque

A reduced pool of calcium in dental plaque would be expected to increase the ability of plaque fluid to dissolve the underlying enamel when the pH falls during sugar exposure. We have examined the relationship between frequency of sugar application and Ca and P(i) concentrations in artificial mouth plaque microcosm biofilms. Ten plaques were grown simultaneously from a human saliva inoculum using a continuous flow of simulated saliva, DMM, supplemented with either urea or glucose to modulate the resting pH. In addition the plaques received sucrose applications of varying frequency: 12-, 8-, 6-, or 4-hourly, or not at all. After 15 days the plaques were sampled by taking 4 full-thickness specimens of each, and acid-extractable Ca and P(i), and alkali-soluble protein and carbohydrate were determined. Ca and P(i) concentrations were in a range comparable with those in human plaque, except in the DMM + urea plaque receiving no sucrose, when concentrations were higher. Plaque Ca concentration decreased significantly as sucrose application frequency increased. Increasing sucrose application frequency also reduced the protein, i.e. the cell biomass, content of the plaques and, in the case of DMM + urea plaques, increased the water-insoluble hexose content, presumably extracellular polysaccharide. Reduced biomass was partly due to the bulking of plaque with extracellular polysaccharide, but the marked effect of urea on polysaccharide formation is not understood. This study shows that increasing frequency of sugar application alters dental plaque by reducing its mineral protection capacity.

Visualization and manipulation of pedigree diagrams

The Pedigree Visualizer is a system for visualization of pedigree diagrams. It accepts a simple text-based specification of a pedigree diagram. The pedigree diagram is then layout automatically. Both GIF- and PS-formatted output files are produced. In addition, the Pedigree Visualizer also provides a rich set of functions for the manipulation and management of large pedigree files.

Outcome of hypospadias fistula repair

Objectives To examine the long-term results of hypospadias fistula repair, the factors involved in recurrence and the outcome in cases where this has occurred. Patients and methods The study comprised 113 children undergoing urethrocutaneous fistula repair between 1984 and 1996. Most of the fistulae were closed in two to three layers, with or without a transpositional skin flap. Tunica vaginalis or a scrotal dartos flap was used in patients with inadequate vascularized tissue adjacent to the fistula. Success rates were calculated for each attempt at fistula repair until the patient was cured. Results The median (range) age at primary fistula repair was 40 (18-169) months and the median follow-up after the most recent repair 7.5 (2.3-17) years. The overall success rate of primary fistula repair was 71%. Fistulae which were >2 mm (11 of 21, 52%) were more likely to recur than were those < or = 2 mm (22 of 92, 24%). Recurrence did not relate to the initial form of hypospadias repair, to the means of skin closure nor, with the exception of multiple lesions, to the location of the fistula. The success rates of subsequent repairs were 70% at the second and 50% at the third, fourth and fifth repairs. One child was cured at the sixth attempt. The use of tunica vaginalis or scrotal dartos as a 'waterproofing' layer was limited to the third or subsequent repairs and was successful in five of six cases. Conclusion A simple layered closure with or with no transpositional skin flap is effective in 71% of repairs. For recurrent fistulae, tissues from an unscarred area (tunica vaginalis or scrotal dartos layer) should be used to cover the fistula.

Incidence of Helicobacter pylori in patients with interstitial cystitis

OBJECTIVE

Chronic gastritis has compelling similarities to interstitial cystitis (IC). It is characterised by chronic pain in a tubular organ. Histologically, epithelial damage, inflammatory response in the lamina propria and epithelial ulcerations are seen. An infective cause was rarely considered until the emergence of Helicobacter pylori over the past 15 years. We have had experience of patients with bladder pain and irritability reporting improvement with antihistamines. It has also been reported that IC symptoms improved dramatically after treatment for H. pylori infection. Previous studies have determined the incidence of H. pylori antibodies in women with IC but we examined bladder material histologically and performed the Campylobacter-like organism (CLO) test on the biopsy specimens.

MATERIALS AND METHODS

A prospective controlled study was performed. Patients with urinary symptoms fulfilling the National Institute of Diabetes and Digestive and Kidney Diseases criteria for IC underwent GA cystoscopy at which the macroscopic appearance of the bladder was noted and biopsies were taken. The biopsy material underwent histological examination and CLO test. Control patients who were undergoing cystoscopy for reasons other than investigation of IC also had biopsy taken and the CLO test was performed on these specimens.

RESULTS

Five of 15 patients with symptoms and signs of IC had a positive CLO test. Three of 15 patients of the control group had a positive CLO test. With the 2-sided chi(2) test there was no statistical difference between the 2 groups.

CONCLUSION

Our small prospective control study does not support the hypothesis that H. pylori is an important component in the pathogenesis of interstitial cystitis.

The glucose challenge test for screening gestational diabetes in pregnant women with no risk factors

AIM OF STUDY

To evaluate the 50 g glucose challenge test as a screening tool for gestational diabetes in pregnant women with no risk factors, to determine the prevalence of gestational diabetes in this population and to determine the perinatal outcomes of pregnancy according to the glucose challenge test.

METHODOLOGY

A descriptive prospective study. A total of 146 patients with no risk factors who booked a particular obstetrician and delivered between May 1996 and April 1997 were recruited. Pregnancy outcomes were assessed by the gestation and mode of delivery, neonatal outcomes included birth weights, apgar scores and other neonatal complications.

RESULTS

The detected incidence of gestational diabetes was 8.2%. With the threshold plasma glucose level at 7.1 mmol/l, 53 women or 36% needed to undergo the 75 g oral glucose tolerance test and 12 women were found to have gestational diabetes. The diagnostic yield was 22.6%. With 7.8 mmol/l as the threshold value, 28 women or 20% needed the oral glucose tolerance test and eight women with gestational diabetes were detected. The diagnostic yield was 28.6%. Perinatal outcome for these diabetic women who were well-controlled during pregnancy was similar to the rest of the women with normal glucose challenge test.

CONCLUSIONS

The 50 g glucose challenge test is a useful screening test for diabetes in Singaporean women with no risk factors. A threshold value at 7.8 mmol/l with a smaller number of women requiring the 75 g oral glucose challenge test may be more acceptable.

Effects of a hemoglobin-based oxygen carrier (HBOC-201) on coagulation testing

Polymerized bovine hemoglobin (HBOC-201) is currently under investigation as an alternative to blood banked human red cells. Due to the dark red, hemolyzed appearance of HBOC-201, we sought to describe the effects of HBOC-201 on coagulation analyzers that perform prothrombin times (PT), activated partial thromboplastin times, fibrinogen, and antithrombin. Pooled normal plasma was combined with HBOC-201 to achieve plasma hemoglobin levels of 1.4, 2.6 3.8, 4.8, and 6.2 g/dL. Results for each test from HBOC-201 prepared plasmas were compared to saline matched controls. Two consecutive absolute result differences of > 10% between saline controls and HBOC-201 samples were used for determining interference on test accuracy by the concentration of HBOC-201. Mechanical detection methods (fibrometer, STA, CS-190) and the MDA-180 were less affected by increasing levels of HBOC-201 than optical detection devices for all test parameters.

A crucial role of macrophages in the immune responses to oral DNA vaccination against hepatitis B virus in a murine model

In the previous study, we had shown that live oral vaccination with Salmonella typhimurium delivering plasmid DNA-HBsAg (oral DNA vaccine) evoked a vigorous T cell response and a weak antibody response with predominant subclass IgG2a in mice, suggesting a significant involvement by professional antigen presenting cells (APC). In the present study, this possibility was further studied by infecting peritoneal macrophages (MPhi) with the oral DNA vaccine. Although, the infected cells could only express low level of the viral antigen, they nevertheless stimulated a vigorous lymphocyte proliferation of splenocytes from immune mice, induced these cells to elaborate interferon-gamma and stimulated development of HBV-specific cytotoxicity against target cells expressing the viral antigen. Infusion of the infected MPhi evoked a vigorous Th 1 and cytotoxic T lymphocyte (CTL) response and a weak IgG2a antibody response in mice, which was essentially the same as response to the oral DNA vaccine. In contrast, recombinant protein vaccine evoked a vigorous IgG1 antibody response and a weak T cell response. While, given intramuscularly, the same plasmid DNA vaccine as that contained in the oral DNA vaccine evoked a vigorous IgG1 antibody response and a moderate T cell response in these animals. It was concluded that professional APC may orchestrate the immune response to live oral DNA vaccine and it was of interest to note that different vaccine formulation and routes of administration evoke distinct immune response to HBV.

Parathyroidectomy promotes wound healing and prolongs survival in patients with calciphylaxis from secondary hyperparathyroidism

BACKGROUND

Calciphylaxis is a rare but life-threatening condition occasionally affecting patients with secondary hyperparathyroidism. Parathyroidectomy has been advocated as the only potentially curative intervention.

METHODS

Between January 1989 and May 2000, 13 patients with pathologic/clinical criteria of calciphylaxis were treated at our institution. Of these 13 patients, 7 were managed with medical therapy alone, and 6 were referred for parathyroidectomy. The medical records were reviewed, and patients/relatives were interviewed.

RESULTS

All patients had cutaneous wounds requiring local debridement predominantly located on the lower extremities or abdominal wall. Six patients underwent subtotal (3.5 gland) parathyroidectomy without morbidity. All 6 had significant reductions in parathyroid hormone levels after surgery (mean decrease, 94% +/- 0%), and all reported resolution of pain and healing of cutaneous wounds. Of the remaining 7 patients who had medical management alone, 5 eventually died of complications related to calciphylaxis. In comparing the 2 groups, patients who underwent parathyroidectomy had a significantly longer median survival than those who did not have surgery (36 vs 3 months, P =.021).

CONCLUSIONS

Calciphylaxis frequently causes gangrene, sepsis, and eventual death. Parathyroidectomy can be performed with minimal morbidity and is associated with resolution of pain, wound healing, and a significantly longer median survival. Therefore, patients with secondary hyperparathyroidism and signs/symptoms of calciphylaxis should be referred promptly for consideration of parathyroidectomy.

Folic acid supplements during pregnancy and risk of miscarriage

BACKGROUND

Although taking supplements that contain 400 microg of folic acid before and during early pregnancy reduces a woman's risk for having a baby with a neural-tube defect (NTD), the effects of such supplements on other pregnancy outcomes remain unclear. We examined whether the use of such supplements affects the occurrence of miscarriage.

METHODS

Participants were women in China who had taken part in a recent folic acid campaign to prevent NTDs and who had registered in this campaign before they became pregnant for the first time. We examined the risk for miscarriage among women who had confirmed pregnancies and who had or had not taken pills containing only 400 microg of folic acid before and during early pregnancy.

RESULTS

The overall rate of miscarriage was 9.1% (2155/23806). The rates of miscarriage among women who had and had not taken folic acid pills before and during the first trimester were 9.0% and 9.3%, respectively (risk ratio 0.97 [95% CI 0.84-1.12]). The distributions of gestational age at pregnancy diagnosis and at miscarriage were similar for both groups of women.

INTERPRETATION

In this population-based study of a cohort of women whose use of folic acid supplements while pregnant had been previously documented and who had been pregnant for the first time, we found no evidence that daily consumption of 400 microg of folic acid before and during early pregnancy influenced their risk for miscarriage.

Intraoperative positioning for circumferential extremity burns

A technique for intra-operative patient positioning is described which allows circumferential access to burned extremities for prepping and surgery. This technique avoids the need for turning the patient during the operative procedure. In our 13 yr experience, there have been no complications attributed to this technique.

Retinoic acid receptor-independent mechanism of apoptosis of melanoma cells by the retinoid CD437 (AHPN)

Retinoic acid (RA) induces differentiation of S91 melanoma cells through activation of RA receptor (RAR)gamma without affecting cell viability. The novel RARgamma-agonist CD437 (AHPN), however, also induces concomitant apoptosis through an unknown mechanism which was investigated here. By utilizing DNA microarray analysis, five apoptosis-associated, CD437-induced transcripts (CITs) were identified. Interestingly, all CITs are also regulated by p53 in a DNA damage response, and consistent with this interpretation, CD437 was found to cause DNA adduct-formation. However, p53 is not required for CD437-dependent regulation of CITs. Among this set of genes, induction of p21(WAF1/CIP1) is likely to be responsible for early S-phase growth-arrest of CD437-treated cells, whereas ei24 is a critical mediator of CD437-induced apoptosis in S91 cells. These data suggest an RAR-independent mechanism in which CD437 causes DNA adduct-formation, resulting in induction of a p53-independent DNA damage response, and subsequent growth-arrest and apoptosis. CD437-mediated DNA adduct-formation may also explain its apoptotic effects in other cell types.

Pharmacodynamics induced by direct electric current for the treatment of 5-fluorouracil resistant tumor: an animal experiment

The repeated use of chemotherapy to treat patients with colorectal carcinoma may be limited by the fact it creates resistance cells. However, we have observed a remarkable decrease in certain types of drug resistance in patients treated with direct electric current. Experimental studies were therefore performed in animals to determine the differences in pharmacodynamics between chemotherapy with and that without electric treatment. Tumors were created in BALB/c mice by intradermal injection of 0.25 ml 4 x 10(6) Colon 26 cells/ml in the abdomen. Seven days later the mice were divided into two groups: controls and those that underwent electric treatment. Direct electric current (1,000 V, 0.2-0.8 microA) was passed between a platinum electrode inserted intradermally and the earth during and for 1 h after a single intravenous injection of 5-fluorouracil (5-FU; 12.5 mg ml(-1) kg(-1)). Peripheral blood samples were collected before and 5, 10, 20, 30, 45, and 60 min after the injection of 5-FU. Concentrations of 5-FU in the sera and tissues were measured by HPLC. The intratumoral concentrations of 5-FU in the electric treatment group were higher than those in the controls (P<0.05, two-factor analysis of variance), but the serum concentrations were not statistically different between the two groups. Pharmacodynamic changes were thus observed as a result of electrostatic treatment during chemotherapy. This elevated 5-FU concentration in the tumor tissue is considered one of the reasons for the effective inhibition of 5-FU resistance in clinical cases.

The combined effect of isolation and Fasciola hepatica infection on the life history traits of Fossaria cubensis

Life history traits of Fossaria cubensis were compared between isolated and paired snails after infection with three miracidia of Fasciola hepatica. Four experimental groups were tested: isolated-unexposed, paired-unexposed, isolated-infected, and paired-infected. A repeated-measures ANOVA showed statistically significant interactions among isolation, infection, and age effects for shell size, number of egg masses per snail, number of eggs per snail, and number of viable eggs per snail. Isolated-unexposed snails exhibited the higher values of these variables and those of survival and finite and intrinsic rates of natural increase. Infection stimulated shell growth during the prepatent period, but differences were present only in paired snails since isolation causes a similar effect. Reproduction, in terms of the number of egg masses per snail and the number of eggs per mass per snail, decreases in the presence of parasitic infection, whereas isolation stimulates it. These effects were observed from early stages of infection.

Newly developed drug delivery system in cancer chemotherapy using direct electric current

To improve the antitumor effect of chemotherapy on a target organ, we experimentally investigated pharmacokinetic alteration of methotrexate (MTX) induced by an electric current in rats to ascertain whether the local concentration of MTX could be enhanced while reducing the concentration in blood. Six male Wistar rats had platinum electrodes introduced into both kidneys. Three rats were subjected to direct current (3.5 V, 50 microA) for 3 hours, while another three control rats received no current. While providing the current to the treated group, all of the rats were intravenously injected with MTX at a dose of 1 mg/kg. The MTX concentration in urine (excreted from each ureter) and serum was measured by fluorescence polarization immunoassay. Cumulative MTX renal excretion rate was significantly higher in the cathode than anode side in the treated group (p < 0.01). Serum MTX concentration at 0 to 5 min was significantly reduced in the treated group (p < 0.03). The first part of the area under the curve (i.e., alpha curve) was markedly increased in the treated group versus controls (p = 0.05). Electric therapy using a slight direct current could gather anionized MTX to the cathode, while reducing MTX concentration in the serum of experimental rats.

PIES, a protein interaction extraction system

We consider the problem of extracting, manipulating, and managing biological pathways, especially protein-protein interaction pathways. We discuss here the Protein Interaction Extraction System (PIES). PIES is contructed on top of three main technologies: Kleisli, BioNLP, and Graphviz. Kleisli is a broad-scale data integration system that we use for downloading Medline abstracts and for general manipulation and management of pathway/interaction databases. BioNLP is a natural language-based information extraction module that we use for analysing Medline abstracts and to extract precise protein-protein and other interaction information. Graphviz is a graphical layout package developed for directed graphs that we use for visualization of the extracted pathways. PIES can be augmented with various means for extracting protein interaction information from sequence databases, for example, by using Kleisli's power to integrate sequence comparison tools to detect gene fusion events in sequence databases.

Redox control of retinoic acid receptor activity: a novel mechanism for retinoic acid resistance in melanoma cells

Retinoic acid (RA) slows growth and induces differentiation of tumor cells through activation of RA receptors (RARs). However, melanoma cell lines display highly variable responsiveness to RA, which is a poorly understood phenomenon. By using Northern and Western blot analyses, we show that RA-resistant A375 and RA-responsive S91 melanoma cells express comparable levels of major components of RAR-signaling pathways. However, A375 cells have substantially higher intracellular reactive oxygen species (ROS) levels than S91 cells. Lowering ROS levels in A375 cells through hypoxic culture conditions restores RAR-dependent trans-activity, which could be further enhanced by addition of the antioxidant N-acetyl-cysteine. Hypoxia also enhances RAR activity in the moderately RA-responsive C32 cells, which have intermediate ROS levels. Conversely, increasing oxidative stress in highly RA-responsive S91 and B16 cells, which have low ROS levels, by treatment with H(2)O(2) impairs RAR activity. Consistent with these observations, RA more potently inhibited the proliferation of hypoxic A375 cells than that of normoxic cells. Oxidative states diminish, whereas reducing conditions enhance, DNA binding of retinoid X receptor/RAR heterodimers in vitro, providing a molecular basis for the observed inverse correlation between RAR activity and ROS levels. The redox state of melanoma cells provides a novel, epigenetic control mechanism of RAR activity and RA resistance.

A comparison of human dental plaque microcosm biofilms grown in an undefined medium and a chemically defined artificial saliva

The growth and pathogenic properties of dental plaque result from interactions between the microbiota and the oral environment and have been studied in laboratory experimental systems ranging from single or a few species (such as in chemostats) to dental plaque microcosms. Microcosm plaque is an in vitro version of natural plaque and has been explored as a microflora model because it is sited a more manipulable and controllable environment. It is obtained as microcosm biofilms in an 'artificial mouth' plaque culture system by culturing the bacteria in natural plaque-enriched saliva (i.e. salivary bacteria where a whole-saliva donor has abstained from oral hygiene for 24 h to increase the plaque bacteria in the saliva). The aim here was to examine whether a new, chemically defined analogue of saliva (defined medium mucin, DMM) could substitute for a previously used, chemically undefined medium (basal medium mucin, BMM) as an analogue of saliva for large-scale biofilm culturing. DMM contains various ions, mucin, amino acids, vitamins and growth factors at concentrations generally similar to those in saliva, whereas BMM contains yeast extract, peptones and mucin. To model the nutrient functions of salivary proteins, amino acids equivalent to 5 g/l casein were also included in DMM. In earlier studies, BMM-grown plaques were similar to natural plaques in structure, composition, growth rate and pH response to substrates. Their doubling-time patterns over a 20-day period were similar, except that the DMM-grown plaques showed biphasic growth patterns that were more pronounced than with BMM. Variation in enzyme profiles between BMM- and DMM-grown plaque, measured using the API-ZYM technique, provided evidence of nutritional effects on plaque composition. It was concluded that realistic growth rates and patterns are generated in microcosm plaque biofilms by supplying both DMM and BMM. However, the use of DMM enables specific modifications to be made to nutrient conditions during large-scale culture in our 'artificial mouth' biofilm system.

Epidermal growth factor (EGF) receptor kinase-independent signaling by EGF

The ErbB family of receptors, which includes the epidermal growth factor receptor (EGFR), ErbB2, ErbB3, and ErbB4, mediate signaling by EGF-like polypeptides. To better understand the role of the EGFR tyrosine kinase, we analyzed signaling by a kinase-inactive EGFR (K721M) in ErbB-devoid 32D cells. K721M alone exhibited no detectable signaling capacity, whereas coexpression of K721M with ErbB2, but not ErbB3 or ErbB4, resulted in EGF-dependent mitogen-activated protein kinase (MAPK) activation. The kinase activity, but not tyrosine phosphorylation, of ErbB2 was required for EGF-induced MAPK activation. The presence of tyrosine phosphorylation sites in K721M was not a requisite for signaling, indicating that transphosphorylation of K721M by ErbB2 was not an essential mechanism of receptor activation. Conversely, the mutated kinase domain of K721M (residues 648-973) and tyrosine phosphorylation of at least one of the receptors were necessary. EGF was found to activate the pro-survival protein kinase Akt in stable cell lines expressing K721M and ErbB2 but, unlike cells expressing wild-type EGFR, was incapable of activating signal transducers and activators of transcription (STAT) or driving cell proliferation. These results demonstrate that EGFR-ErbB2 oligomers are potent activators of MAPK and Akt, and this signaling does not require EGFR kinase activity.

Intercostal Neuromas: A Treatable Cause of Postoperative Breast Surgery Pain

Patients presenting with pain after breast surgery were selected to undergo resection of intercostal neuromas. The patients had localized Tinel's signs at one or more intercostal nerves at the lateral chest wall with radiation in the distribution of the pain. Patients also responded to diagnostic injections of local anesthetic. The patients were felt to have pain not related to breast implants and capsular contracture or intercostobrachial nerve injury. Neuromas were found in all patients meeting these requirements. Surgical resection resulted in complete pain relief. Diagnosis of this entity and consideration of surgical treatment may be underrecognized.

Prolonged, symptomatic hypocalcemia with pamidronate administration and subclinical hypoparathyroidism

A 62-yr-old woman with thyroid carcinoma metastatic to bone, and a history of subclinical hypoparathyroidism was admitted to the hospital in hypocalcemic crisis 5 wk after receiving iv pamidronate. The patient had tetany and laryngospasm. An electrocardiogram showed junctional rhythm with QT segment prolongation. The patient had previously maintained a low-normal serum calcium on 500-750 mg of calcium carbonate and 600 IU of vitamin D daily. One week after pamidronate administration the patient's calcium and vitamin D supplementation were inadvertently discontinued. She continued to take daily intranasal calcitonin. At the time of her hospitalization for hypocalcemia, the patient's serum calcium was 4.3 mg/dL. The patient received aggressive calcium and vitamin D supplementation. However, her serum calcium remained below 6 mg/dL for a 2-wk period, and took another week to return to the normal range. In this article, we discuss the counterregulatory responses necessary to maintain calcium homeostasis following osteoclast inhibition by bisphosphonates. We also review the risk factors for hypocalcemia following bisphosphonate administration. Pamidronate and other bisphosphonates are becoming an integral part of the management of normocalcemic patients with malignant bone disease. Therefore, awareness of risk factors for hypocalcemia and familiarity with avenues available for protection from potentially catastrophic hypocalcemia are both crucial.

Children with persistent conduct problems who dropout of treatment

Dropout of treatment is one of the key issues in outcome in a child and adolescent mental health service. We report two studies focusing on the treatment process and the dropout rate of children with persistent conduct problems presenting to a community mental health service, using a prospective design. The first study included 32 children and used a randomised controlled treatment design comparing a CBT approach with conjoint family therapy and an eclectic approach. The overall dropout rate was 36%. Dropout occurred significantly less frequently in the CBT group. The dropout group was associated with mothers who were younger and less educated, a poorer rating by the clinicians at the last meeting, parental dissatisfaction with the treatment service and perception that the treatment was less organised and having less behavioural tasks. In the second study we used a naturalistic follow-up design. Forty-six children were included. The overall dropout rate was 48%. Again, the children who defaulted were rated by clinicians as less likely to have improved and dropout was also significantly associated with parental perception of a less organised treatment. In both studies dropout usually occurred after assessment and at the early phase of treatment.

Effects of retinoic acid and sodium butyrate on gene expression, histone acetylation and inhibition of proliferation of melanoma cells

Retinoic acid (RA) induces growth-arrest of many tumor cell lines but it is an ineffective therapeutic against melanoma. We investigated whether the histone deacetylase (HDAC)-inhibitor sodium butyrate (BUT) can restore or potentiate the RA-response of RA-resistant human A375, and RA-responsive S91 murine melanoma cells. BUT induced expression of RARbeta and p21(waf1/cip1) mRNA in A375 cells but in S91 cells only p21(waf1/cip1) was induced. RA and BUT synergistically activated transcription of an RA-dependent reporter gene in S91, but not A375 cells. BUT increased histone H4-acetylation in both cell types. RA potentiated BUT-mediated inhibition of S91 cell proliferation, whereas A375 cells remained largely resistant to both compounds. HDAC-inhibitors may enhance the activity of RA on RA-responsive melanoma cells.

Efficacy and cognitive effects of right unilateral electroconvulsive therapy

The efficacy, memory, and cognitive effects of right unilateral (RUL) electroconvulsive therapy (ECT) at 2.5 times threshold in 32 inpatients with moderate to severe major depressive disorder were evaluated at baseline, during the course of treatment, and 1 month after treatment. Neuropsychological assessment included the Randt Memory Test, Personal Memory Test, short-version Wechsler Adult Intelligence Scale-Revised, and Self-Rating Scale of Memory Functions. At the treatment end point, although the Hamilton Depression Rating Scale mean score was decreased by 54.2%. the response rate of 2.5 times threshold RUL ECT using stringent criteria was only 31.2%. Treatment was associated with significant anterograde memory impairment in the short term. Mean total scores of the Randt Memory Test and Personal Memory Test were decreased from baseline by 14.8% and 32.5%, respectively, after six sessions of ECT. These memory deficits were significantly improved by the 1 month follow-up examination. Subjective memory scores increased consistently during treatment, correlating with improvements in mood. No adverse effects on nonmemory cognition were found. Although RUL ECT at 2.5 times threshold is not associated with marked or persistent cognitive disturbances, its efficacy may be insufficient in clinical practice.

Survivin and the inner centromere protein INCENP show similar cell-cycle localization and gene knockout phenotype

BACKGROUND

Survivin is a mammalian protein that carries a motif typical of the inhibitor of apoptosis (IAP)proteins, first identified in baculoviruses. Although baculoviral IAP proteins regulate cell death, the yeast Survivin homolog Bir1 is involved in cell division. To determine the function of Survivin in mammals, we analyzed the pattern of localization of Survivin protein during the cell cycle, and deleted its gene by homologous recombination in mice.

RESULTS

In human cells, Survivin appeared first on centromeres bound to a novel para-polar axis during prophase/metaphase, relocated to the spindle midzone during anaphase/telophase, and disappeared at the end of telophase. In the mouse, Survivin was required for mitosis during development. Null embryos showed disrupted microtubule formation, became polyploid, and failed to survive beyond 4.5days post coitum. This phenotype, and the cell-cycle localization of Survivin, resembled closely those of INCENP. Because the yeast homolog of INCENP, Sli15, regulates the Aurora kinase homolog Ipl1p, and the yeast Survivin homolog Bir1 binds to Ndc10p, a substrate of Ipl1p, yeast Survivin, INCENP and Aurora homologs function in concert during cell division.

CONCLUSIONS

In vertebrates, Survivin and INCENP have related roles in mitosis, coordinating events such as microtubule organization, cleavage-furrow formation and cytokinesis. Like their yeast homologs Bir1 and Sli15, they may also act together with the Aurora kinase.

Attitudes on organ donation among Hawaii physicians

A survey of physicians attending the recent Hawaii Medical Association meeting was conducted in order to assess physician attitudes on organ donation. Physicians were asked 6 questions and demographics were collected. Results indicate that Hawaii physicians generally support organ donation and are aware of some of the current federal legislation regarding donation.

Well-defined sulfobetaine-based statistical copolymers as potential antibioadherent coatings

The potential use of novel poly(sulfobetaine) copolymers as antibioadherent coatings was investigated using Pseudomonas aeruginosa as a model microorganism and human macrophages and 3T3 mouse embryonic fibroblasts. Two well-defined statistical copolymers with narrow molecular weight distributions were prepared by group transfer copolymerization of n-butyl methacrylate (nBuMA) with either 10 or 30 mol % 2-(dimethylamino)ethyl methacrylate (DMAEMA). Sulfobetainized nBuMA-DMAEMA copolymers (poly[sulfobetaine-stat-nBuMA]) were obtained by treating these precursor polymers with 1,3-propanesultone under mild conditions. Both proton NMR spectroscopy and elemental microanalyses indicated that essentially all the DMAEMA residues were derivatized in both copolymers. Poly(methyl methacrylate) (PMMA) discs were coated with the sulfobetainized nBuMA-DMAEMA copolymers and the bioadherent properties of these coated materials were compared with those of PMMA. Statistically significantly fewer (p<.05) bacteria, macrophages, and fibroblasts adhered to the poly(sulfobetaine-stat-nBuMA)-coated PMMA than to the uncoated PMMA. The poly(sulfobetaine-stat-nBuMA) copolymer containing the higher proportion (30 mol %) sulfobetainized DMAEMA residues proved to be the more effective antibioadherent coating. The antibioadherent properties of these coating materials may allow the cost-effective production of dirt-resistant, easy to clean work surfaces, bioinert coatings for medical devices, and antifouling coatings for marine, agricultural, and industrial applications.

Carboxy terminus of human herpesvirus 8 latency-associated nuclear antigen mediates dimerization, transcriptional repression, and targeting to nuclear bodies

Human herpesvirus 8 (HHV-8; also known as Kaposi's sarcoma-associated herpesvirus) is the causative agent of Kaposi's sarcoma and certain B-cell lymphomas. In most infected cells, HHV-8 establishes a latent infection characterized by the expression of latency-associated nuclear antigen (LANA) encoded by open reading frame 73. Although unrelated by sequence, there are functional similarities between LANA and the EBNA-1 protein of Epstein-Barr virus. Both accumulate as subnuclear speckles and are required for maintenance of the viral episome. EBNA-1 also regulates viral gene expression and is required for cell immortalization, suggesting that LANA performs similar functions in the context of HHV-8 infection. Here we show that LANA forms stable dimers, or possibly higher-order multimers, and that this is mediated by a conserved region in the C terminus. By expressing a series of truncations, we show that both the N- and C-terminal regions localize to the nucleus, although only the C terminus accumulates as nuclear speckles characteristic of the intact protein. Lastly, we show that LANA can function as a potent transcriptional repressor when tethered to constitutively active promoters via a heterologous DNA-binding domain. Domains in both the N and C termini mediate repression. This suggests that one function of LANA is to suppress the expression of the viral lytic genes or cellular genes involved in the antiviral response.

Probing the active center gorge of acetylcholinesterase by fluorophores linked to substituted cysteines

To examine the influence of individual side chains in governing rates of ligand entry into the active center gorge of acetylcholinesterase and to characterize the dynamics and immediate environment of these residues, we have conjugated reactive groups with selected charge and fluorescence characteristics to cysteines substituted by mutagenesis at specific positions on the enzyme. Insertion of side chains larger than in the native tyrosine at position 124 near the constriction point of the active site gorge confers steric hindrance to affect maximum catalytic throughput (k(cat)/K(m)) and rates of diffusional entry of trifluoroketones to the active center. Smaller groups appear not to present steric constraints to entry; however, cationic side chains selectively and markedly reduce cation ligand entry through electrostatic repulsion in the gorge. The influence of side chain modification on ligand kinetics has been correlated with spectroscopic characteristics of fluorescent side chains and their capacity to influence the binding of a peptide, fasciculin, which inhibits catalysis peripherally by sealing the mouth of the gorge. Acrylodan conjugated to cysteine was substituted for tyrosine at position 124 within the gorge, for histidine 287 on the surface adjacent to the gorge and for alanine 262 on a mobile loop distal to the gorge. The 124 position reveals the most hydrophobic environment and the largest hypsochromic shift of the emission maximum with fasciculin binding. This finding likely reflects a sandwiching of the acrylodan in the complex with the tip of fasciculin loop II. An intermediate spectral shift is found for the 287 position, consistent with partial occlusion by loops II and III of fasciculin in the complex. Spectroscopic properties of the acrylodan at the 262 position are unaltered by fasciculin addition. Hence, combined spectroscopic and kinetic analyses reveal distinguishing characteristics in various regions of acetylcholinesterase that influence ligand association.

Inhibition of myosin/moesin phosphatase by expression of the phosphoinhibitor protein CPI-17 alters microfilament organization and retards cell spreading

Cell migration and cytokinesis require reorganization of the cytoskeleton, involving phosphorylation and dephosphorylation of proteins such as myosin II and moesin. Myosin and moesin bind directly to a regulatory subunit of myosin/moesin phosphatase (MMP) that contains a protein type-1 phosphatase (PP1) catalytic subunit. Here we examined the role of MMP in cytoskeletal dynamics using a phosphorylation-dependent inhibitor protein specific for MMP, called CPI-17. Fibroblasts do not express CPI-17, making them a null background to study effects of expression. Wild type CPI-17 in rat embryo fibroblasts caused (1) abnormal accumulation of cortical F-actin fibers, distinct from the stress fibers induced by expression of active RhoA; (2) progressive contraction of cell area, leaving behind filamentous extensions that stained for F-actin and moesin, but not myosin; and (3) significantly retarded spreading of fibroblasts on fibronectin with elevated myosin II light chain phosphorylation. A phosphorylation site mutant CPI-17(T38A) and inhibitor-2 (Inh2), another PP1-specific inhibitor protein, served as controls and did not elicit these same responses when expressed at the same level as CPI-17. Inhibition of myosin light chain kinase by ML-9 prevented the abnormal accumulation of cortical microfilaments by CPI-17, but did not reverse shrinkage in area, whereas kinase inhibitors HA1077 and H7 prevented CPI-17-induced changes in microfilament distribution and cell contraction. These results highlight the physiological importance of myosin/moesin phosphatase regulation to dynamic remodeling of the cytoskeleton.

Autonomously replicating macronuclear DNA pieces are the physical basis of genetic coassortment groups in Tetrahymena thermophila

The macronucleus of the ciliate Tetrahymena thermophila contains a fragmented somatic genome consisting of several hundred identifiable chromosome pieces. These pieces are generated by site-specific fragmentation of the germline chromosomes and most of them are represented at an average of 45 copies per macronucleus. In the course of successive divisions of an initially heterozygous macronucleus, the random distribution of alleles of loci carried on these copies eventually generates macronuclei that are pure for one allele or the other. This phenomenon is called phenotypic assortment. We have previously reported the existence of loci that assort together (coassort) and hypothesized that these loci reside on the same macronuclear piece. The work reported here provides new, rigorous genetic support for the hypothesis that macronuclear autonomously replicating chromosome pieces are the physical basis of coassortment groups. Thus, coassortment allows the mapping of the somatic genome by purely genetic means. The data also strongly suggest that the random distribution of alleles in the Tetrahymena macronucleus is due to the random distribution of the MAC chromosome pieces that carry them.

Mechanism of oxime reactivation of acetylcholinesterase analyzed by chirality and mutagenesis

Organophosphates inactivate acetylcholinesterase by reacting covalently with the active center serine. We have examined the reactivation of a series of resolved enantiomeric methylphosphonate conjugates of acetylcholinesterase by two oximes, 2-pralidoxime (2-PAM) and 1-(2'-hydroxyiminomethyl-1'-pyridinium)-3-(4'-carbamoyl-1-pyridinium) (HI-6). The S(p) enantiomers of the methylphosphonate esters are far more reactive in forming the conjugate with the enzyme, and we find that rates of oxime reactivation also show an S(p) versus R(p) preference, suggesting that a similar orientation of the phosphonyl oxygen toward the oxyanion hole is required for both efficient inactivation and reactivation. A comparison of reactivation rates of (S(p))- and (R(p))-cycloheptyl, 3,3-dimethylbutyl, and isopropyl methylphosphonyl conjugates shows that steric hindrance by the alkoxy group precludes facile access of the oxime to the tetrahedral phosphorus. To facilitate access, we substituted smaller side chains in the acyl pocket of the active center and find that the Phe295Leu substitution enhances the HI-6-elicited reactivation rates of the S(p) conjugates up to 14-fold, whereas the Phe297Ile substitution preferentially enhances 2-PAM reactivation by as much as 125-fold. The fractional enhancement of reactivation achieved by these mutations of the acyl pocket is greatest for the conjugated phosphonates of the largest steric bulk. By contrast, little enhancement of the reactivation rate is seen with these mutants for the R(p) conjugates, where limitations on oxime access to the phosphonate and suboptimal positioning of the phosphonyl oxygen in the oxyanion hole may both slow reactivation. These findings suggest that impaction of the conjugated organophosphate within the constraints of the active center gorge is a major factor in influencing oxime access and reactivation rates. Moreover, the individual oximes differ in attacking orientation, leading to the presumed pentavalent transition state. Hence, their efficacies as reactivating agents depend on the steric bulk of the intervening groups surrounding the tetrahedral phosphorus.

Drug-induced linear immunoglobulin A bullous disease that clinically mimics toxic epidermal necrolysis

Drug-induced linear immunoglobulin A bullous disease is a subepidermal blistering disorder that most commonly occurs after exposure to vancomycin. It can clinically mimic toxic epidermolytic necrolysis. We describe an 87-year-old white woman in whom linear immunoglobulin A bullous disease developed while she was taking vancomycin and phenytoin. A few days after the linear immunoglobulin A bullous disease developed, both medications were discontinued. No new bullae developed, and the eruption completely resolved within 2 weeks. The patient was treated with only topical therapy.

Reconstruction of complex cranial wounds with demineralized bone matrix and bilayer artificial skin

Complex wounds involving loss of both cranium and scalp are difficult to reconstruct. Current solutions include both autogenous and alloplastic materials. Tissue engineering provides interesting alternatives for reconstruction of missing bone and soft tissue. Demineralized bone matrix and Integra, artificial bilayer skin substitute, have been used successfully to reconstruct bone and skin as isolated defects, but never in combination. This study investigates the possibility of using demineralized bone matrix in a gel carrier and Integra for combined cranial and scalp defects. The study was divided into two parts. In the first, demineralized bone matrix in the forms of Grafton Flex (n = 12) and Grafton putty (n = 12) was used to reconstruct 15-mm critical size cranial defects in female adult New Zealand White rabbits. In the control group (n = 6), the defect was left empty. The second part of the study investigated the use of Integra and Grafton Flex to reconstruct a 15-mm cranial defect with an overlying full-thickness scalp defect (n = 6). The first study revealed bony healing of the critical-size cranial defect with demineralized bone matrix. The second study demonstrated successful reconstitution of scalp and cranium with both demineralized bone matrix and Integra. We conclude that complex cranial defects involving bone and soft tissue may be successfully reconstructed with their tissue-engineered substrates, demineralized bone matrix (Grafton) and Integra artificial skin.

Escharotomy and fasciotomy of the burned upper extremity

Escharotomy and fasciotomy are performed in the burned upper extremity to prevent and treat the sequelae of circumferential full-thickness burns and high-voltage electrical burns. Indications to perform these procedures are determined primarily by clinical examination but can be supplemented by measurements of subfascial pressures. The techniques are designed to avoid further complications. Options for wound closure are discussed. The use of allograft as temporary coverage of fasciotomy incisions may allow delayed primary closure.

Structural basis for selectivity of a small molecule, S1-binding, submicromolar inhibitor of urokinase-type plasminogen activator

BACKGROUND

Urokinase-type plasminogen activator (uPA) is a protease associated with tumor metastasis and invasion. Inhibitors of uPA may have potential as drugs for prostate, breast and other cancers. Therapeutically useful inhibitors must be selective for uPA and not appreciably inhibit the related, and structurally and functionally similar enzyme, tissue-type plasminogen activator (tPA), involved in the vital blood-clotting cascade.

RESULTS

We produced mutagenically deglycosylated low molecular weight uPA and determined the crystal structure of its complex with 4-iodobenzo[b]thiophene 2-carboxamidine (K(i) = 0.21 +/- 0.02 microM). To probe the structural determinants of the affinity and selectivity of this inhibitor for uPA we also determined the structures of its trypsin and thrombin complexes, of apo-trypsin, apo-thrombin and apo-factor Xa, and of uPA, trypsin and thrombin bound by compounds that are less effective uPA inhibitors, benzo[b]thiophene-2-carboxamidine, thieno[2,3-b]-pyridine-2-carboxamidine and benzamidine. The K(i) values of each inhibitor toward uPA, tPA, trypsin, tryptase, thrombin and factor Xa were determined and compared. One selectivity determinant of the benzo[b]thiophene-2-carboxamidines for uPA involves a hydrogen bond at the S1 site to Ogamma(Ser190) that is absent in the Ala190 proteases, tPA, thrombin and factor Xa. Other subtle differences in the architecture of the S1 site also influence inhibitor affinity and enzyme-bound structure.

CONCLUSIONS

Subtle structural differences in the S1 site of uPA compared with that of related proteases, which result in part from the presence of a serine residue at position 190, account for the selectivity of small thiophene-2-carboxamidines for uPA, and afford a framework for structure-based design of small, potent, selective uPA inhibitors.

Microdochectomy for single-duct nipple discharge

INTRODUCTION

Isolated single-duct nipple discharge is worrying and poses a surgical dilemma. Factors predicting malignancy are controversial.

MATERIALS AND METHODS

Retrospective review of 92 consecutive microdochectomies for single-duct nipple discharge in a tertiary referral centre over 8 years.

RESULTS

The commonest causes were ductal papilloma (52%) and fibrocystic diseases of the breast (21%). Five (5%) patients had breast carcinoma, of whom only 1 had an invasive component. The median age of these patients was 43 years (range 26 to 72 years) which was similar to median age of the whole cohort. Sixty-seven (73%) patients presented with blood-stained nipple discharge. The 5 patients with breast carcinoma had blood-stained discharge. Mammography was abnormal in 1 out of 4 patients in the carcinoma group.

CONCLUSIONS

The incidence of breast carcinoma in patients presenting with isolated single-duct nipple discharge was low (5%) among Singaporean women. There was no reliable predictors of malignancy, though all patients with carcinoma presented with blood-stained discharge. Microdochectomy still remains an effective treatment for nipple discharge both for cure and diagnosis.

Differential response to low-fat diet between low and normal HDL-cholesterol subjects

Heart attacks frequently occur in normolipidemic subjects with low concentration of high density lipoproteins (</=35 mg/dL). A low-fat diet is generally recommended to patients with coronary heart disease. A low-fat diet decreases both low density (LDL) and high density lipoproteins (HDL). We have shown that on an Average American Diet, subjects with different HDL-cholesterol (HDL-C) levels have different HDL subpopulation profiles. In low HDL-C subjects (</=35 mg/dL), the apoA-I-only subpopulation alpha(1) is significantly decreased compared to individuals with normal HDL-C levels (>35 mg/dL). We hypothesized that as subjects with low HDL-C already have low HDL concentrations, the major decrease of HDL-C will occur in subjects with normal HDL-C when a low-fat diet is consumed. Normolipidemic male subjects consumed three diets differing in total fat and saturated fat composition (AAD: 37%, Step-1: 28%, Step-2: 24% total fat) for 6 weeks in a three-period double-blind randomized crossover design. Plasma lipids and apolipoproteins were determined and changes in distribution of HDL subpopulations were evaluated. As a result of a low-fat diet, low HDL-C individuals slightly decreased their HDL-C, but substantially decreased their LDL-C resulting in a significant improvement in the LDL-C/HDL-C ratio. However, subjects with normal HDL-C levels decreased both their LDL-C and HDL-C resulting in an unchanged LDL-C/HDL-C ratio. We also observed significant differences in response to low-fat diets in HDL-C and alpha(1) concentrations between low and normal HDL-C subjects. In the normal HDL-C group, consumption of a low-fat diet also resulted in redistribution of apoA-I-containing HDL subpopulations, indicated by a decrease in the large apoA-I-only alpha(1) subpopulation. These data demonstrate that male subjects with low HDL-C respond to a low-fat diet differently than individuals with normal HDL-C.

FIMM, a database of functional molecular immunology

FIMM database (http://sdmc.krdl.org.sg:8080/fimm ) contains data relevant to functional molecular immunology, focusing on cellular immunology. It contains fully referenced data on protein antigens, major histocompatibility complex (MHC) molecules, MHC-associated peptides and relevant disease associations. FIMM has a set of search tools for extraction of information and results are presented as lists or as reports.

Assessing the in vitro cell based ocular compatibility of contact lens materials

A series of in vitro assays for determining the biocompatibility of ocular biomaterials have been developed and used to assess the differences in performance of omafilcon A, etafilcon A and nelfilcon A contact lens materials. The assays assessed bacterial attachment, macrophage adhesion, granulocyte adhesion and activation, epithelial cell adhesion and corneal cell contact damage. Overall, omafilcon A was found to be more biocompatible than the other materials although there was no significant difference between the epithelial cell adhesion and granulocyte adhesion and activation on any of the hydrogels. Etailcon A performed less well compared to nelfilcon A and omafilcon A with respect macrophage adhesion and bacterial adhesion. The results indicate that these biological assays can be successfully applied for the testing of contact lens materials and may be particularly useful in the in vitro screening of new extended wear contact lens materials where cell adhesion and activation may have a greater influence on clinical performance.

Development of multi-species consortia biofilms of oral bacteria as an enamel and root caries model system

The aim was to establish defined-species consortium plaque biofilms to investigate enamel and root caries in an artificial mouth. Strains of the putative enamel and root caries pathogens, Streptococcus mutans, Strep. sobrinus, Actinomyces naeslundii and Lactobacillus rhamnosus, were screened in batch culture for potential cariogenic properties: a low terminal pH, ability to aggregate, and catabolic diversity. The strains selected were grown as monoculture biofilms and as consortium plaque biofilms in a multiplaque artificial mouth. The biofilms were supplied with a constant flow of a simulated oral fluid and were given periodic sucrose (and in some instances glucose) to simulate meals. All the bacteria except L. rhamnosus formed large, monospecies biofilms with resting pH in the range 5.3-5.8. The consortia biofilms were larger and had a resting pH of 4.9-5.3. The consortia biofilms supplied with 8-hourly carbohydrate comprised mainly 'mutans' streptococci (58, SD 5.5%) and L. rhamnosus (42, SD 5.7%). A. naeslundii characteristically was absent or present in a low percentage (up to 4% colony-forming units). All biofilms demineralized polished bovine enamel and dentine blocks, as assessed by microradiography and enamel-surface microhardness measurement. The consortia also demineralized intact enamel and tooth roots; they were more cariogenic to enamel than any of the monoculture biofilms, as measured by enamel-surface softening, but variation in lesion depth was proportional to biofilm wet weight irrespective of acidogen composition (r = 0.93, p < 0.05). Enamel lesions had a well-mineralized intact surface and a zone of subsurface demineralization, typical of early natural lesions. Dentine and root lesions showed extensive demineralization but lacked a pronounced surface mineralized zone. Substitution of glucose for sucrose had no effect on the cariogenicity of the consortium to bovine enamel or human roots and had no major effect on the plaque composition. Continuously supplied fluoride (19 parts/10(6)) resulted in a substantially reduced enamel surface softening and subsurface demineralization of intact roots. It was concluded that consortia biofilms of selected caries pathogens generate realistic caries lesions in all tooth hard tissues under controlled growth conditions in the artificial mouth. This in vitro caries experimental model may prove useful for the study of interrelations between the plaque biofilm, tooth tissues and the oral environment, and for the development of procedures to modify the course of caries development.

Needle-tract implantation from hepatocellular cancer: is needle biopsy of the liver always necessary?

Percutaneous needle biopsies are frequently used to evaluate focal lesions of the liver. Needle-tract implantation of hepatocellular cancer has been described in case reports, but the true risk for this problem has not been clearly defined. We retrospectively reviewed 91 cases of hepatocellular cancer during a 4-year period from 1994 to 1997. Data on diagnostic studies, therapy, and outcome were noted. Of 91 patients with hepatocellular cancer, 59 patients underwent percutaneous needle biopsy as part of their diagnostic workup for a liver mass. Three patients (5.1%) were identified with needle-tract implantation of tumor. Two patients required en bloc chest wall resections for implantation of hepatocellular cancer in the soft tissues and rib area. The third patient, who also received percutaneous ethanol injection of his tumor, required a thoracotomy and lung resection for implanted hepatocellular cancer. Percutaneous needle biopsy of suspicious hepatic lesions should not be performed indiscriminately because there is a significant risk for needle-tract implantation. These biopsies should be reserved for those lesions in which no definitive surgical intervention is planned and pathological confirmation is necessary for a nonsurgical therapy.

Cyclic 3-deaza-adenosine diphosphoribose: a potent and stable analog of cyclic ADP-ribose

Cyclic 3-deaza-adenosine diphosphoribose (3-deaza-cADPR), an analog of cyclic adenosine diphosphoribose (cADPR) was synthesized. 3-deaza-cADPR differs from cADPR by only the substitution of carbon for nitrogen at the 3-position of the purine ring. Similar to cADPR, the analog has potent calcium releasing activity in sea urchin egg homogenates and was able to induce calcium release at concentrations as low as 0.3 nM. The EC(50) value for 3-deaza-cADPR-induced calcium release was 1 nM, which is about 70 times more potent than cADPR. The properties of calcium release induced by 3-deaza-cADPR in all other respects were similar to those of cADPR. Thus, 3-deaza-cADPR and cADPR were capable of cross-desensitizing each other and their calcium releasing activities were potentiated by Sr(2+) as well as caffeine. 8-amino-cADPR, a selective antagonist of cADPR, was also able to inhibit 3-deaza-cADPR induced calcium release. Taken together, these data suggest that 3-deaza-cADPR releases calcium through the same mechanism as cADPR. 3-deaza-cADPR was found to be resistant to both heat and enzymatic hydrolysis. Only 15% of 3-deaza-cADPR was destroyed after boiling this compound for 2 h. No loss of 3-deaza-cADPR was observed when treated with CD38 under conditions where cADPR was completely hydrolyzed. Thus, 3-deaza-cADPR is a potent and stable analog of cADPR. These properties should make 3-deaza-cADPR a useful probe in studies focused on the mechanism of cADPR action.

Kleisli: a new tool for data integration in biology

One of the central problems in bioinformatics is data retrieval and integration. The existing biological databases are geographically distributed across the Internet, complex and heterogeneous in data types and data structures, and constantly changing. With the current rapid growth of biomedical data, the challenge is how large volumes of data retrieved from multiple databases can be transformed and integrated automatically and flexibly. This article describes a powerful new tool, the Kleisli system, for complex queries across multiple databases and data integration.