Associating Drugs, Targets and Clinical Outcomes into an Integrated Network Affords a New Platform for Computer-Aided Drug Repurposing

Finding new uses for old drugs is a strategy embraced by the pharmaceutical industry, with increasing participation from the academic sector. Drug repurposing efforts focus on identifying novel modes of action, but not in a systematic manner. With intensive data mining and curation, we aim to apply bio- and cheminformatics tools using the DRUGS database, containing 3,837 unique small molecules annotated on 1,750 proteins. These are likely to serve as drug targets and antitargets (i.e., associated with side effects, SE). The academic community, the pharmaceutical sector and clinicians alike could benefit from an integrated, semantic-web compliant computer-aided drug repurposing (CADR) effort, one that would enable deep data mining of associations between approved drugs (D), targets (T), clinical outcomes (CO) and SE. We report preliminary results from text mining and multivariate statistics, based on 7,684 approved drug labels, ADL (Dailymed) via text mining. From the ADL corresponding to 988 unique drugs, the "adverse reactions" section was mapped onto 174 SE, then clustered via principal component analysis into a 5x5 self-organizing map that was integrated into a Cytoscape network of SE-D-T-CO. This type of data can be used to streamline drug repurposing and may result in novel insights that can lead to the identification of novel drug actions.

Structural simplification of bioactive natural products with multicomponent synthesis. 3. Fused uracil-containing heterocycles as novel topoisomerase-targeting agents

After the initial discovery of antiproliferative and apoptosis-inducing properties of a camptothecin-inspired pentacycle based on a 1H-indeno[2',1':5,6]dihydropyrido[2,3-d]pyrimidine scaffold, a library of its analogues as well as their oxidized planar counterparts were prepared utilizing a practical multicomponent synthetic protocol. The synthesized compounds exhibited submicromolar to low micromolar antiproliferative potencies toward a panel of human cancer cell lines. Biochemical experiments are consistent with the dihydropyridine library members undergoing intracellular oxidation to the corresponding planar pyridines, which then inhibit topoisomerase II activity, leading to inhibition of proliferation and cell death. Because of facile synthetic preparation and promising antitopoisomerase activity, both the dihydropyridine and planar pyridine-based compounds represent a convenient starting point for anticancer drug discovery.

A genome-wide approach identifies that the aspartate metabolism pathway contributes to asparaginase sensitivity

Asparaginase is an important component for treatment of childhood acute lymphoblastic leukemia (ALL). The basis for interindividual differences in asparaginase sensitivity remains unclear. To comprehensively identify genetic variants important in the cytotoxicity of asparaginase, we used a genome-wide association approach using the HapMap lymphoblastoid cell lines (87 CEU trio members) and 54 primary ALL leukemic blast samples at diagnosis. Asparaginase sensitivity was assessed as the drug concentration necessary to inhibit 50% of growth (inhibitory concentration (IC)(50)). In CEU lines, we tested 2,390,203 single-nucleotide polymorphism (SNP) genotypes at the individual SNP (P<0.001) and gene level (P<0.05), and identified 329 SNPs representing 94 genes that were associated with asparaginase IC(50). The aspartate metabolism pathway was the most overrepresented among 199 pathways evaluated (P=8.1 × 10(-3)), with primary involvement of adenylosuccinate lyase and aspartyl-tRNA synthetase genes. We validated that SNPs in the aspartate metabolism pathway were also associated with asparaginase sensitivity in primary ALL leukemic blast samples (P=5.5 × 10(-5)). Our genome-wide interrogation of CEU cell lines and primary ALL blasts revealed that inherited genomic interindividual variation in a plausible candidate pathway can contribute to asparaginase sensitivity.

Effects of acute hypervolaemic haemodilution on the expression of plasma interferon-inducible protein-10 and bactericidal/permeability-increasing protein in patients undergoing total hip replacement

This prospective, randomized controlled study evaluated the effects of acute hypervolaemic haemodilution (AHH) on the expression of plasma interferon-inducible protein-10 (IP-10) and bactericidal/permeability-increasing protein (BPI) in patients undergoing elective total hip replacement. Twenty patients were randomized to receive an infusion of either hydroxyethyl starch (HES group) or lactated Ringer's solution (LR group) immediately after anaesthesia. Plasma concentrations of IP-10 and BPI were measured before anaesthesia (baseline), at the start of surgery, 30 min after the start of surgery and at the end of surgery. Blood loss and the volume of blood transfused were significantly lower in the HES group compared with the LR group. Compared with baseline, IP-10 and BPI concentrations increased significantly in both groups 30 min after the start of surgery. The IP-10 concentrations were significantly lower and BPI concentrations significantly higher in the HES group compared with the LR group 30 min after the start of surgery and at the end of surgery. It is concluded that AHH with HES may be helpful in ameliorating immune function during total hip replacement and in reducing blood loss and the extent of blood transfusion.

Mating-induced neuroendocrine responses during pseudopregnancy in the female mouse

Pseudopregnancy (PSP) is a neuroendocrine reflex triggered by vaginocervical stimulation similar to the neuroendocrine response of early pregnancy and is characterised by short-term neural activity, resulting in long-term neuroendocrine responses that cause repeated release of pituitary prolactin (PRL) over many days. PSP is a useful model to study how somatosensory input is transduced in the brain into neuroendocrine responses, and has been extensively characterised in rats. With increasing use of mice as an experimental model, however, and to allow use of transgenic mice to investigate mechanisms of this sensory response, it is important to characterise the principal neuroendocrine response of pseudopregnancy in this species. The present study aimed to examine the induction and neuroendocrine responses of PSP in mice using vasectomised stud males, to investigate mating-induced changes in vaginal cytology, uterine growth, and PRL secretion, and to map certain aspects of somatosensory transduction by assessing the neural activity marker FOS. Unlike the induction of pseudopregnancy in rats, which can be induced simply by multiple intromissions from a male or artificial mechanical stimulation of the cervix, PSP induction in mice required the receipt of an ejaculation from a male. In mice that received PSP-inducible mating stimuli, FOS expression was observed in a slightly different range of brain regions than has been observed in rats, with increases in the bed nucleus of the stria terminalis, medial preoptic area, and ventromedial hypothalamus, but not in limbic areas examined. Moreover, PSP mice expressed a single diurnal PRL surge on day 6 of PSP. Thus, the data demonstrate important species differences in the neuroendocrine mechanisms activated in response to a mating stimulus in mice compared with rats. A clear understanding of the species-specific response will be required in interpreting research into the reproductive biology of this species.

Consumption of sugars by Anastrepha suspensa (Diptera: Tephritidae)

We were interested in determining the feeding response of the Caribbean fruit fly, Anastrepha suspensa Loew (Diptera: Tephritidae), to various sugar concentrations to develop an improved bait for adults. We compared the consumption of 0.01-1.00 M concentrations of glucose, fructose, raffinose, and sucrose in no-choice tests for 24-h- and 6-d-old male and female flies. Sucrose was the most consumed sugar or within the most consumed group of sugars at 0.02-0.20 M concentrations. There were no differences in consumption among sugars at 0.01, 0.40, and 1.00 M. Consumption generally increased with increasing sugar concentration except that sucrose consumption peaked at 0.20 M. Twenty-four-hour females consumed less fructose than other sugars; 24-h males consumed more sucrose than fructose or raffinose, with an intermediate response to glucose. Females in the 6-d group consumed more sucrose than the other three sugars, whereas 6-d males exhibited no difference in consumption among sugars. In choice tests, flies consumed more sugar solution than water, but the difference between 0.20 M fructose and water was not significant for 24-h males or 24-h females. In choice tests between 0.20 M fructose and 0.20 M sucrose, both 24-h and 6-d females showed a preference for fructose. Males of both age classes showed no preference. These results indicate that the responses of flies to different sugars can vary by sugar, gender, and age.

Ketamine inhibits polymorphonuclear leucocyte CD11b expression and respiratory burst activity in endotoxemic rats

OBJECTIVE AND DESIGN

To observe the effect of ketamine on polymorphonuclear leucocytes (PMN) adhesion and respiratory burst activity in endotoxemia rats.

MATERIALS

30 rats were randomly allocated to five groups: rats challenged with intraperitoneal injection of saline (saline group); challenged with intraperitoneal injection of LPS 10 mg/kg (LPS group); challenged with intraperitoneal injection of LPS 10 mg/kg and treated by intraperitoneal injection of ketamine 5, 25, 50 mg/kg at 0, 1, 2, 3, 4, 5 h after the injection of LPS, respectively (three ketamine treatment groups).

METHODS

PMN respiratory burst and CD11b expression were measured with flow cytometry at the end of 1 h, 4 h, and 6 h.

RESULTS

LPS challenge significantly increased PMN respiratory burst activity and CD11b expression when compared with the saline group (p < 0.01). There was a significant decrease in LPS-induced PMN respiratory burst activity and CD11b expression in three ketamine treatment groups when compared with LPS group (p < 0.01).

CONCLUSIONS

Ketamine significantly inhibits PMN CD11b expression and respiratory burst activity in endotoxemic rats.

Which has the least immunity depression during postoperative analgesia—morphine, tramadol, or tramadol with lornoxicam?

BACKGROUND

Analgesics are commonly used to provide pain relief after surgery. These drugs produce some extended depression of immunity. A prospective randomized controlled trial was designed to observe expressions of T-lymphocyte subsets (CD3(+), CD3(+)CD4(+) and CD3(+)CD8(+)), natural-killer cells (CD3(-)CD16(+)CD56(+)), and activated T-lymphocytes (CD3(+)CD25(+)) of patients undergoing gastric cancer surgeries and receiving patient-controlled intravenous analgesia (PCIA).

METHODS

Forty-five patients undergoing elective gastric cancer surgeries under general anesthesia were randomly allocated into 3 groups. Group I received PCIA using morphine after surgery, group II using tramadol, and group III using tramadol with lornoxicam. The analgesic efficacy was evaluated by visual analog scale (VAS) and Bruggrmann comfort scale (BCS). Expressions of CD3(+), CD3(+)CD4(+), CD3(+)CD8(+), CD3(-)CD16(+)CD56(+), and CD3(+)CD25(+) were measured as percentages of total lymphocytes by flow cytometer at 5 time points.

RESULTS

There was no significant difference in analgesic efficacy and the baselines of CD3(+), CD3(+)CD4(+), CD3(+)CD8(+), CD3(-)CD16(+)CD56(+), and CD3(+)CD25(+) in all groups. Compared with the baseline, CD3(+)CD8(+) had no changes in all groups at any time point. Ninety minutes after incision, CD3(+), CD3(+)CD4(+), CD3(-)CD16(+)CD56(+), and CD3(+)CD25(+) were lower in all groups (P<0.05). 24 h after surgery, CD3(+), CD3(+)CD4(+), CD3(-)CD16(+)CD56(+), and CD3(+)CD25(+) were lower in group I and group II (P<0.05); meanwhile CD3(+), CD3(+)CD4(+), and CD3(+)CD25(+) returned to the baseline but CD3(-)CD16(+)CD56(+) was still low (P<0.05) in group III. 48 h after surgery, CD3(+), CD3(+)CD4(+), CD3(-)CD16(+)CD56(+), and CD3(+)CD25(+) returned to the baseline in group II and group III, but not in group I (P<0.05). 72 h after surgery, CD3(+), CD3(+)CD4(+), CD3(+)CD4(+)/CD3(+)CD8(+) returned to the baseline, but CD3(+)CD25(+) and CD3(-)CD16(+)CD56(+) were still low in group I (P<0.05).

CONCLUSION

PCIA using lornoxicam with tramadol has the same good analgesic efficacy and less immunity depression than PCIA using morphine or tramadol.

Local anesthesia for functional endoscopic sinus surgery employing small volumes of epinephrine-containing solutions of lidocaine produces profound hypotension

BACKGROUND

Local anesthetic containing epinephrine is commonly used in many operations for the main purpose of hemostasis. A randomized, controlled, prospective clinical trial was designed to find out hemodynamic changes after local infiltration of different concentrations and/or different dosages of epinephrine during functional endoscopic sinus surgery (FESS) under general anesthesia.

METHODS

One hundred and eight adult patients undergoing elective FESS under general anesthesia were randomly allocated into four groups. Group I received 2% lidocaine 2 ml with epinephrine (5 microg/ml); group II received 1% lidocaine 4 ml with epinephrine (2.5 microg/ml); group III received 1% lidocaine 4 ml with epinephrine (5 microg/ml); and group IV received 1% lidocaine 4 ml for local infiltration. Heart rate (HR), systolic blood pressure (SBP), diastolic blood pressure (DBP) and mean arterial pressure (MAP) were monitored continuously in the radial artery and recorded in 6 min: before infiltration (baseline), 0.5, 1, 1.5, 2, 2.5, 3, 3.5, 4, 5, and 6 min after local infiltration. The lowest blood pressure (BP) in this period was also recorded.

RESULTS

Significant hemodynamic changes, particularly a decrease in BP (P < 0.001) with a slight increase in HR (P < 0.001) at approximately 1.5 min and an increase in SBP at approximately 3 min (P < 0.01) after local infiltration, were observed in group I, group II and group III compared with the baseline, but not in group IV. No significant hemodynamic differences were observed between group I, group II and group III at the same time points (P > 0.05).

CONCLUSION

Local infiltration of low-dose epinephrine causes temporary significant hemodynamic changes particularly a marked decrease in BP during FESS under general anesthesia.

Methemoglobinemia misdiagnosed as ruptured ectopic pregnancy

A 22-year-old woman with an initial diagnosis of 'ruptured ectopic pregnancy' and 'hemorrhagic shock' was sent to the operation room for surgical treatment. The mucocutaneous color was deeply cyanosed and the pulse oximeter oxygen saturation (SpO2) was only 86% after tracheal intubation (100% O2). 'Chocolate-brown' blood was observed and methemoglobinemia was considered. Then the arterial blood gas (ABG) sample was obtained, an intravenous infusion of methylene blue and vitamin C followed. The patient recovered quickly, and later two other patients with similar symptoms were treated in the same way. The success was due to a correct diagnosis accompanied with prompt treatment and quick recognition of the etiology.

Diagnosis and management of uterine arteriovenous fistulas with massive vaginal bleeding

OBJECTIVE

To study the clinical manifestations, diagnosis, management, and prognosis of uterine arteriovenous fistulas with massive vaginal bleeding.

METHODS

The clinical records of 15 patients who satisfied the diagnostic criteria were retrospectively analyzed.

RESULTS

All patients had massive vaginal bleeding and a history of cesarean section, curettage, or gynecologic carcinoma. The disease was diagnosed by angiography or color Doppler ultrasonography. Vaginal bleeding can be aggravated by dilation and curettage. No complications occurred in the 14 patients who were treated with uterine artery embolization. Of the 11 patients who underwent successful embolizations, all returned to a normal menstrual cycle and 5 later became pregnant.

CONCLUSION

Uterine arteriovenous fistula is a rare and potentially life-threatening condition. Uterine artery embolization is a safe and effective choice of treatment for this condition, and it can preserve both uterus and ovary function.

Emergency craniotomy in patients with intracranial metastatic gestational trophoblastic tumor

OBJECTIVE

To study the diagnosis, management and prognosis of intracranial metastases of gestational trophoblastic tumor (GTT) patients who had emergency craniotomy.

METHODS

Sixty three intracranial metastases of GTT patients were hospitalized in Peking Union Medical College Hospital from 1985 to 2004. Thirteen of them had craniotomy that were retrospectively analyzed and all of them had a feature of raised intracranial pressure followed by intracranial hemorrhagic mass.

RESULTS

Of the thirteen patients who had undergone surgery combined with multiagent chemotherapy, seven got complete remission (CR), five got partial remission (PR), and one died of progress of the disease (PD). There were three patients who died (23.1%) during or after therapy.

CONCLUSIONS

Emergency craniotomy has a small but important role to play in selected patients with brain metastases who display rapidly deteriorating signs. An undetermined intracranial hemorrhage in young female patients of a reproductive age group should raise the suspicion of cerebral metastatic GTT.

Marked Hypotension Induced by Adrenaline Contained in Local Anesthetic

OBJECTIVES

Local anesthetics containing adrenaline, which often cause cardiovascular side effects, are routinely used in functional endoscopic sinus surgery (FESS) for the main purpose of hemostasis. The controversies concerning hemodynamic effects of adrenaline in local infiltration are widely discussed, but there is no definite conclusion. A prospective, randomized, double-blinded study was carried out to discover the hemodynamic effects after local infiltration of 1:200,000 adrenaline contained in 2% lidocaine under general anesthesia.

STUDY DESIGN

Seventy-six adult patients undergoing FESS during general anesthesia were allocated randomly into three groups. Group I patients (n = 26) received 2% lidocaine 2 mL with adrenaline (1:200,000), group II patients (n = 25) received saline 2 mL with adrenaline (1:200,000), and group III patients (control group, n = 25) received saline 2 mL without adrenaline for local infiltration. Electrocardiogram (ECG) and heart rate (HR) were monitored simultaneously; systolic blood pressure (SBP), diastolic blood pressure (DBP), and mean arterial blood pressure (MAP) were directly measured in radial artery continuously after local infiltration.

METHODS

SBP, DBP, MAP, and HR were recorded at 10 time points: before infiltration (baseline), 0.5 minutes, 1 minute, 1.5 minutes, 2 minutes, 2.5 minutes, 3 minutes, 3.5 minutes, 4 minute, and 5 minutes after infiltration.

RESULTS

Significant hemodynamic changes, particularly hypotension (P < .01), after local infiltration were observed in group I and group II compared with the baseline, but not in group III. However, there were no significant hemodynamic changes between group I and group II at the same time points (P > .05). The significant hemodynamic changes lasted no longer than 4 minutes.

CONCLUSIONS

Lidocaine (2%) or saline with adrenaline (1:200,000) does cause temporary hypotension and other hemodynamic changes during general anesthesia, which last no longer than 4 minutes. The causative mechanism is caused by the effect of adrenaline. This is a preliminary study.

Quantifying individual fruit fly consumption with Anastrepha suspensa (Diptera: Tephritidae)

We needed a technique to compare the consumption of baits by individual Carribbean fruit fly, Anastrepha suspensa (Loew). By improving consumption and determining individual dose, we could lower pesticide concentration while retaining bait/pesticide efficacy and potentially reduce the environmental impact of fruit fly bait/pesticide eradication methods. We report here a precise dye-based technique for the quantification of consumption by individual adult A. suspensa fruit flies. Fluorescein, measured at 491 nm, and cresol red, measured at 573 nm, were efficiently extracted with 0.1 M NaOH and quantified with a spectrophotometer. The lower limit for this method with 0.1% dye concentration is 300 nl consumed by an individual fly. Dye movement to the hindgut and possible defecation occurred in approximately 4 h; maximum ingestion occurred in approximately 1 h. Maximum experimental time is limited to 4 h. Flies preferred feeding upside down compared with right side up when given a choice; consumption was equal when flies were given no choice of feeding position. Thus, maximum bait/pesticide efficacy might be achieved with an upside-down presentation. Regurgitation led to a 100% overestimation of actual consumption with the J-tube presentation of food. Our individual fly consumption technique will be useful in comparing consumption in phagostimulant studies, estimating dose in oral toxicity tests, differentiating behavioral and physiological resistance in toxicant studies, ultimately leading to improved bait/pesticide methods and reduced environmental impact of area wide fruit fly eradication programs. This technique could be applied to studies of tephritid consumption, to the consumption of other insects, and to regurgitation studies.

Field studies on 32P movement and P leaching from flooded paddy soils in the region of Taihu Lake, China

Field experiments were done in two sites, Yixing and Changshu, Jiangsu province, China, to study P movement and leaching in flooded paddy soils. P movement in soil was investigated by using the KH2 32PO4 tracker method, and the amount of P leached from the soil layer in different depths was estimated by measuring P concentrations in the soil solution and saturated hydraulic conductivities in field. Determination was done about one month after P application. There was 46% and 42% of total 32P retained in the 0-5cm layer of soil in the Yixing site and in the Changshu site respectively. The 32P retained in the 25-30 cm layer was only about 1-2% of the total 32P added. Furthermore, 8.01% of 32P in the soil of Yixing site and 16.8% of 32P in the soil of Changshu site was lost from the layer 0-30 cm soil. The seasonal amounts of P leached from the top soil layer and from bottom layer are about 4.5-5.8% and 1.6-2.1% of the total P application, respectively. Changes of total P concentrations in soil solutions during rice growth showed that the fertilizer P applied before flooding of the paddy fields suffered a flash leaching loss and a slow leaching loss. We concluded that the fertilizer P could quickly move in the flooded paddy rice field and parts of it can enter into surface water and ground water. Unless the P application is well managed the risk of P loss and consequently environmental pollution exist.

Structural biology of the cell adhesion protein CD2: from molecular recognition to protein folding and design

CD2 (cluster of differentiation 2) is a cell adhesion molecule expressed on T cells and is recognized as a target for CD48 (rats) and CD58 (humans). Tremendous progress has been achieved in understanding the function of CD2, the mechanism of molecular recognition and protein folding, thus, leading towards the use of this protein as a scaffold for protein design. CD2 has been shown to set quantitative thresholds in T cell activation both in vivo and in vitro. Further, intracellular CD2 signaling pathways and networks are being discovered by the identification of several cytosolic tail binding proteins. In addition, a new method for directly measuring heterophilic adhesion has been developed. The functional "hot spot" for the adhesion surface of CD2 and CD58 has been dissected. Detailed NMR studies reveal that rat CD2 weakly self-associates to form a homodimeric structure in solution. Dynamic interaction of CD2 with the GYF and SH3 domains has been investigated. CD2 has been shown to form fibrils in the presence of 2,2,2-trifluoroethanol (TFE) and at low pH. Furthermore, kinetic studies have been completed to monitor the effect of surface hydrophobic residues and intramolecular bridges on the folding pathways of CD2. Our lab has de novo designed single calcium-binding sites into domain 1 of rat CD2 (CD2-D1) with strong metal selectivity. In addition, the EF-hand motifs have been grafted into CD2 to understand the site-specific calcium-binding affinity of calmodulin and calcium-dependent cell adhesion.

Microarray experimental design: power and sample size considerations

Gene expression analysis using high-throughput microarray technology has become a powerful approach to study systems biology. The exponential growth in microarray experiments has spawned a number of investigations into the reliability and reproducibility of this type of data. However, the sample size requirements necessary to obtain statistically significant results has not had as much attention. We report here statistical methods for the determination of the sufficient number of subjects necessary to minimize the false discovery rate while maintaining high power to detect differentially expressed genes. Two experimental designs were considered: 1) a comparison between two groups at a single time point, and 2) a comparison of two experimental groups with sequential time points. Computer programs are available for the methods discussed in this paper and are adaptable to more complicated situations.

Increased expression of the secretory leukocyte proteinase inhibitor in Wegener's granulomatosis

The secretory leucocyte proteinase inhibitor (SLPI) is a low molecular weight, tissue-specific inhibitor of proteases, such as elastase and cathepsin G. It is the major local protease inhibitor in the upper airways. Proteinase 3, the main autoantigen in Wegener's granulomatosis (WG), can degrade SLPI proteolytically. In addition, SLPI is sensitive to oxidative inactivation by myeloperoxidase-generated free oxygen radicals. SLPI also has an antimicrobial capacity that can be of interest, as infection is considered to play a role in the pathogenesis of WG. This study focuses on SLPI expression in patients suffering from WG, something that to our knowledge has not been explored hitherto. Serum samples and nasal biopsies were obtained from 12 Swedish WG patients, while buffy coats were obtained from 33 American WG patients. SLPI levels in serum were measured by means of ELISA and the protein was detected by means of immunohistochemistry in nasal biopsies. mRNA expression was studied by means of in situ hybridization on nasal biopsies and RT-PCR on leucocytes. IL-6 or ESR were measured as markers of inflammatory activity. Cystatin C or creatinine was measured as a marker of renal filtration. White blood cell counts were registered. In serum, we found close to normal SLPI levels, without any correlation to IL-6. Two patients had greatly elevated values, both of them suffering from severe renal engagement. Strong SLPI mRNA expression was found in nasal biopsies. RT-PCR on leucocyte mRNA showed normal or greatly elevated expression of SLPI mRNA, correlating with disease activity. Leukocyte SLPI expression seems to be up-regulated in active WG. Serum levels were measured in a small number of patients and were found to be close to normal. Lack of correlation to the acute phase response indicates a specific regulation. This might be linked to an altered protease/antiprotease balance. These findings could indicate that SLPI locally participates in the anti-inflammatory and perhaps antimicrobial response in WG.

Prostaglandin E2 is involved in the increase of cytochrome P-450 2B1 expression by alpha-tocopheryl succinate in primary rat hepatocytes in the presence of phenobarbital

The modulation of cytochrome P-450 2B1 expression by alpha-tocopheryl succinate and whether prostaglandin E2 is involved in this modulation in primary rat hepatocytes in the presence of phenobarbital were investigated. A primary rat hepatocyte culture model that faithfully reproduces the phenobarbital response observed in vivo was used. Intracellular alpha-tocopherol content was dose dependently increased by alpha-tocopheryl succinate incubation. Hepatocytes were demonstrated to have prostaglandin E2-synthesizing capability. alpha-Tocopheryl succinate inhibited prostaglandin E2 synthesis by hepatocytes and increased cytochrome P-450 2B1 expression in the presence of phenobarbital; however, it had little effect on intracellular cAMP level. To mimic the exogenous source of prostaglandin E2 from nonparenchymal cells, various concentrations of prostaglandin E2 were added to the cell culture. High doses of exogenous prostaglandin E2 (100 and 1,000 nM) inhibited the cytochrome P-450 2B1 expression in the presence of phenobarbital compared with low doses (1 and 10 nM); however, the presence of high doses of prostaglandin E2 had no effect on intracellular cAMP level. Forskolin significantly increased intracellular cAMP level and inhibited cytochrome P-450 2B1 expression in the presence of phenobarbital. The results of this study indicate that alpha-tocopheryl succinate increases cytochrome P-450 2B1 expression via its inhibition of prostaglandin E2 synthesis in the presence of phenobarbital; however, changes in intracellular cAMP level are not related to cytochrome P-450 2B1 expression.

Metal binding affinity and structural properties of an isolated EF-loop in a scaffold protein

To establish an approach to obtain the site-specific calcium binding affinity of EF-hand proteins, we have successfully designed a series of model proteins, each containing the EF-hand calcium-binding loop 3 of calmodulin, but with increasing numbers of Gly residues linking the loop to domain 1 of CD2. Structural analyses, using different spectroscopic methods, have shown that the host protein is able to retain its native structure after insertion of the 12-residue calcium-binding loop and retains a native thermal stability and thermal unfolding behavior. In addition, calcium binding to the engineered CD2 variants does not result in a significant change from native CD2 conformation. The CD2 variant with two Gly linkers has been shown to have the strongest metal binding affinity to Ca(II) and La(III). These experimental results are consistent with our molecular modeling studies, which suggest that this protein with the engineered EF-loop has a calmodulin-like calcium binding geometry and backbone conformation. The addition of two Gly linkers increases the flexibility of the inserted EF-loop 3 from calmodulin, which is essential for the proper binding of metal ions.

A statistical method for flagging weak spots improves normalization and ratio estimates in microarrays

Over the last few years, there has been a dramatic increase in the use of cDNA microarrays to monitor gene expression changes in biological systems. Data from these experiments are usually transformed into expression ratios between experimental samples and a common reference sample for subsequent data analysis. The accuracy of this critical transformation depends on two major parameters: the signal intensities and the normalization of the experiment vs. reference signal intensities. Here we describe and validate a new model for microarray signal intensity that has one multiplicative variation and one additive background variation. Using replicative experiments and simulated data, we found that the signal intensity is the most critical parameter that influences the performance of normalization, accuracy of ratio estimates, reproducibility, specificity, and sensitivity of microarray experiments. Therefore, we developed a statistical procedure to flag spots with weak signal intensity based on the standard deviation (delta(ij)) of background differences between a spot and the neighboring spots, i.e., a spot is considered as too weak if the signal is weaker than cdelta(ij). Our studies suggest that normalization and ratio estimates were unacceptable when this threshold (c) is small. We further showed that when a reasonable compromise of c (c = 6) is applied, normalization using trimmed mean of log ratios performed slightly better than global intensity and mean of ratios. These studies suggest that decreasing the background noise is critical to improve the quality of microarray experiments.

[Multi-slice CT scanners]

Some basic specifications of four commercial multi-slice CT scanners are compared with each other. The new technologies under the development of multi-slice CT are described and the image quality performance of multi-slice is discussed in this paper.

Nonnative intermediate state of acid-stable beta-sheet protein

Cell adhesion molecule, CD2, from the immunoglobulin superfamily, is comprised of antibodies and Ig-like domains and plays a fundamental role, not only in the immune system, but also in the interactions between cells, specifically in cell-cell adhesion. This study examines the N-terminal domain 1 of CD2 (CD2-1) at different pHs, and in 2,2,2-trifluoroethanol (TFE), using nears- and far-UV circular dichroism (CD), fluorescence, and 1H nuclear magnetic resonance to elucidate factors contributing to the Ig beta-structure. Contrary to the complete unfolding induced by guanidinehydrochloride, CD2-1 retains its native tertiary structure at pHs from 1.0 to 10.0. Like the effects of high temperatures that have previously been observed, TFE reduces the integrity of the tertiary structure, while reorganizing the secondary structure from a native all-beta-sheet to a significantly alpha-helical conformation. The induced helicity of CD2-1 correlates with the helicity inherent in its primary sequence. Our results suggest that electrostatic interactions are less important for the formation of the native secondary and tertiary structure of CD2-1, although they are crucial for CD2's adhesion function. Interference with the protein's hydrophobic interactions and hydrogen-bonding networks, however, causes significant changes in its conformation. Residues of CD2-1, with high conformational flexibility, may contribute for the formation of a metastable dimer by domain-swapping.