Towards Drugs Targeting Multiple Proteins in a Systems Biology Approach

Protein-protein interactions are increasingly becoming drug targets. This is understandable, since they are crucial at all levels of cellular expression and growth. In practice, targeting specific disease-related interactions has proven difficult, with success varying with specific complexes. Here, we take a Systems Biology approach to targeting protein-protein interactions. Below, we first briefly review drug discovery targeted at protein-protein interactions; we classify protein-protein complexes with respect to their types of interactions and their roles in cellular function and as being targets in drug design; we describe the properties of the interfaces as related to drug design, focusing on hot spots and surface cavities; and finally, in particular, we cast the interactions into the cellular network system, highlighting the challenge of partially targeting multiple interactions in the networks as compared to hitting a specific protein-protein interaction target. The challenge we now face is how to pick the targets and how to improve the efficiency of designed partially-specific multi-target drugs that would block parallel pathways in the network.

Comparing pairwise and simultaneous joint registrations of decorrelating interval exams using entropic graphs

The interest in registering a set of images has quickly risen in the field of medical image analysis. Mutual information (MI) based methods are well-established for pairwise registration but their extension to higher dimensions (multiple images) has encountered practical implementation difficulties. We extend the use of alpha mutual information (alphaMI) as the similarity measure to simultaneously register multiple images. alphaMI of a set of images can be directly estimated using entropic graphs spanning feature vectors extracted from the images, which is demonstrated to be practically feasible for joint registration. In this paper we are specifically interested in monitoring malignant tumor changes using simultaneous registration of multiple interval MR or CT scans. Tumor scans are typically a decorrelating sequence due to the cycles of heterogeneous cell death and growth. The accuracy of joint and pairwise registration using entropic graph methods is evaluated by registering several sets of interval exams. We show that for the parameters we investigated simultaneous joint registration method yields lower average registration errors compared to pairwise. Different degrees of decorrelation in the serial scans are studied and registration performance suggests that an appropriate scanning interval can be determined for efficiently monitoring lesion changes. Different levels of observation noise are added to the image sequences and the experimental results show that entropic graph based methods are robust and can be used reliably for multiple image registration.

Gene therapy by membrane-expressed superantigen for α-fetoprotein-producing hepatocellular carcinoma

Staphylococcus enterotoxin A (SEA) is a powerful immunostimulant, which can stimulate T cells bearing certain T-cell receptor beta-chain variable regions, when bound to major histocompatibility complex II molecules. In vivo administration of intact superantigen in sufficient therapeutic amounts risks unwanted cytotoxicity against normal cells. In this study, we used SEA fused with CD80 transmembrane region (named as SEAtm) driven by alpha-fetoprotein (AFP) enhancer/promoter to reduce toxicity and to improve safety and efficiency in the application of SEA. We demonstrated that SEAtm by adenovirus from the AFP enhancer/promoter (AdAFPSEA) could be expressed on the surface of AFP-producing cell line Hepa1-6 instead of non-AFP-producing cell lines. Hepa1-6 infected by recombinant adenovirus stimulated proliferation of splenocytes and activated CD4(+) and CD8(+) T cells in vitro. After AdAFPSEA was injected into the subcutaneously established hepatoma in vivo, the expression of SEA was detected in tumor tissues, which subsequently induced tumor-specific cytotoxic T cells in spleen. Moreover, hepatocellular carcinoma (HCC) xenografts were suppressed by treatment with AdAFPSEA and the survival time of treated mice was prolonged. These findings suggest that membrane-expressed SEA by adenovirus from AdAFPSEA can generate stronger local and systemic antitumor responses against HCC.

A phase I/II study to assess the safety, tolerability and pharmacokinetics (PK) of intravenous (IV) infusion of MB07133 in subjects with unresectable hepatocellular carcinoma (HCC)

2054

Background: MB07133 is a novel cytarabine (araC) prodrug that uses the HepDirect technology to target production of the active form of araC, araC triphosphate (araCTP), to the liver. The study objectives were to determine the maximum tolerated dose, toxicity profile (NCI-CTC 2.0), PK & antitumor activity of MB07133 in patients (pts) with unresectable HCC. MB07133 was given as a continuous IV infusion at escalating doses during the first 7 days of a 28-day cycle until disease progression or unacceptable toxicity occurred. To date, 22 pts with Child-Pugh Class A liver function have been enrolled in 4 cohorts (300, 600, 1200, 1800 mg/m2/d, D1–7), with 3–6 pts/cohort. Enrolled pts had a median age of 57 yrs (range 20–67) & consisted of 21 males, 1 female, 19 Asians & 3 Caucasians. A total of 66 cycles have been administered (maximum 10 cycles in 1 pt) with no dose-limiting toxicities associated with therapy. Most drug-related toxicities (67%) were mild to moderate (gr 1–2 neutropenia, thrombocytopenia & increased ALT). There was 1 gr 3 ascites unrelated to study drug and no gr 4 toxicity. Six pts experienced 10 serious adverse events, all unrelated or unlikely related to study drug. The very low araC concentrations in the plasma (see table ) were consistent with previous animal studies, which demonstrated MB07133 to target araCTP production in the liver. 36% of pts who had ≥ 2 cycles of MB07133 had disease stabilization. Conclusions: MB07133 is well tolerated at doses up to 1800 mg/m2/d in pts with unresectable HCC. Enrollment of a 2400 mg/m2 cohort is ongoing. The disease stabilization observed in this study, although preliminary, warrants further investigation in Phase 2.

[Table: see text]

[Table: see text]

Phase II study of gefitinib in metastatic or locoregionally recurrent nasopharyngeal carcinoma (NPC)

15509

Background: Our preclinical work has shown that epidermal growth factor receptor (EGFR) is expressed in ∼ 80% of undifferentiated NPC & gefitinib is a small molecule inhibitor against EGFR with anti-proliferative activity in NPC in vitro. Methods: We report the preliminary result of a phase II study of gefitinib in patients (pts) who progressed after 1–2 lines of chemotherapy (at least 1 line had to contain platinum) for metastatic or locoregionally recurrent NPC. Fourteen Chinese pts were accrued, of whom the median age was 48 years (range 34–64 years), 12 were males, 9 had metastatic & 5 had locoregionally recurrent NPC. All received gefitinib at 500mg/day orally, every 28 days with radiological assessment performed every 2 cycles for a maximum of 8 cycles. Ten pts had 1 line & 5 pts had 2 lines of prior chemotherapy. Results: The median number of administered cycles was 2 (range 1–8). Of the 14 pts evaluable for toxicity, the most commonly reported were acneiform rash (86%, grade 1–2, n = 10; grade 3, n = 4), dry skin (86%, grade 1–2), diarrhea (71%, grade 1–2), fatigue (64%, grade 1–2), anorexia (64%, grade 1–2) & nausea (20%, grade 2). Other grade 3–4 toxicities included fever (n = 2, skin cellulitis, infective pneumonia), hyponatremia (n = 2), near-syncope (n = 2), anemia (n = 1). Dose reduction to 250mg/day was required in 4 pts who encountered grade 3 skin rash. Of the 11 pts evaluable for response, 2 had stable disease (SD) for ≥ 6 months (m) (mean 6.8 m) 9 progressed and no partial responders. Five pts have died mostly of progressive disease & there were no treatment-related deaths. Conclusions: Gefitinib is well tolerated in pts with advanced NPC with some pts experiencing disease stabilization for over 6 months & study accrual is ongoing.

No significant financial relationships to disclose.

Irofulven as first line therapy in recurrent or metastatic gastric cancer: a phase II multicenter study by the Cancer Therapeutics Research Group (CTRG)

BACKGROUND

The purpose of this study was to evaluate the tolerability and efficacy of irofulven, a DNA interacting acylfulvene analog, as first line therapy for patients with recurrent or metastatic gastric cancer.

PATIENTS AND METHODS

Twenty-three patients with recurrent or metastatic gastric cancer received irofulven at a dose of 0.45 mg/kg administered intravenously over 30-min infusion (up to a maximum of 50 mg), on days 1 and 8, every 3 weeks.

RESULTS

The median number of cycles delivered per patient was 2 (range 1-6). Two patients (9%) had >or= 1-week delay in administration of subsequent cycle of chemotherapy. For the day 8 chemotherapy, dose reductions were required in seven patients (30%); dose omitting occurred in five patients (22%). Grade 3/4 anemia and neutropenia occurred in 22 and 17% of patients, respectively. There was no grade 4 thrombocytopenia and no neutropenic fever was observed. Of the 20 evaluable patients, there were no responses observed, 3 patients had stable disease after 2 cycles of treatment which was not confirmed by a further assessment. Median overall survival was 6.05 months (95% CI 4.55-9.39).

CONCLUSIONS

Irofulven was tolerated at the dose of 0.45 mg/kg on days 1 and 8, every 3 weeks but showed no evidence of antitumor activity in patients with advanced gastric cancer.

Trabecular anisotropy and collagen fibre orientation in the mandibular condyle following experimental functional appliance treatment using sheep

In order to study the modifying effects of functional appliances on the mechanical environment of the temporomandibular joint (TMJ), we characterised the structure of the mandibular condyle subsequent to an experimental functional appliance intervention. Eight, four-month-old, castrated male Merino sheep, were randomly allocated to experimental and control groups (n = 4 in each group). Forward mandibular displacement was induced with an intraoral appliance. The study period was 15 weeks, during which time fluorochromes were administered to all of the animals. Midsagittal sections of the TMJ were selected for analysis and trabecular anisotropy was estimated using bone histomorphometry. Only the experimental group demonstrated that the trabecular bone in the central condylar region was less anisotropic when compared to the subchondral region. Also, the variation in trabecular anisotropy of the central condylar region was found to be smaller in the experimental group. The collagen fibre orientation was analysed under polarised light as the proportion of the dark or bright fibres observed in regions which existed before, and regions which formed during the experiment, as determined by the fluorochrome labels. In the experimental group, more bright collagen fibres were found in the most superior region of the mandibular condyle when compared with the controls. These results suggested that the experimental functional appliances changed the orientation and pattern of the mechanical forces acting on the mandibular condyle, and possibly increased the magnitude of the lateral functional forces applied to the most superior part of the condyle during such treatments.

Activation of antitumor cytotoxic T lymphocytes by fusion of patient-derived dendritic cells with autologous osteosarcoma

BACKGROUND AND AIM

Fusion of human dendritic cells (DCs) with tumor cells is an effective approach for delivering tumor antigens to DCs, and DC/tumor fusion cells are potent stimulators of autologous T cells. However, the integration and morphology of DC/osteosarcoma fusion cells has not been examined. This study was designed to investigate the antitumor effects of tumor vaccine produced by electrofusion between human osteosarcoma cells and DCs.

METHODS

In the present study, we eletrofused patient-derived DCs to autologous osteosarcoma cells. The fusion cells possessed the properties of both patient cells. After electrofusion, the cytoplasm of the two cells was integrated, whereas their nuclei remained separate entities. The intracellular structure was observed on fusion cells under the transmission electron microscope.

RESULTS

Coculture of patient-derived peripheral blood mononuclear cells (PBMC) with DC/tumor fusion cells resulted in activation of T cells as assessed by standard cytotoxic T lymphocytes (CTLs) assays.

CONCLUSIONS

The present study provides valid evidence on integration of human DCs and tumor cells and links their properties to T cell activation. The fusion cells may thus represent a promising strategy for DC-based immunotherapy of patients with osteosarcoma.

Visual acuity in northern China in an urban and rural population: the Beijing Eye Study

AIM

To evaluate prevalence and demographic associations of visual impairment in an urban and rural population in northern China.

METHODS

In the Beijing Eye Study, a population based cohort study in northern China, visual acuity was assessed for 8876 eyes (4438 subjects) according to a response rate of 83.4%. The study was divided into a rural part (1972 subjects) and an urban part (n=2466). Mean age was 56.20 (SD 10.59) years (median 56 years; range 40-101 years).

RESULTS

Mean uncorrected visual acuity measured 0.72 (0.32) (median, 0.80), and mean best corrected visual acuity measured 0.91 (0.21) (median, 1.0). In a multiple regression analysis, best corrected visual acuity was significantly correlated with age (p<0.001), degree of nuclear cataract (p<0.001), amount of cortical cataract (p=0.014), amount of subcapsular cataract (p<0.001), educational background (p<0.001), and refractive error (p<0.001). Rural region versus urban region (p=0.34) and sex (p=0.053) were not statistically significantly associated with best corrected visual acuity.

CONCLUSIONS

In northern China, determinants of a low degree of best corrected visual acuity are age, cataract, low educational background, and myopia. Despite marked differences in educational background and family income, sex, and rural area versus urban area are not markedly associated with best corrected visual acuity.

A point-selection algorithm based on spatial-stiffness analysis of rigid registration

OBJECTIVE

We propose a model of shape-based registration that leads to a task-specific algorithm for preoperatively selecting a set of model registration points.

MATERIALS AND METHODS

We performed five sets of computer simulations using registration points generated by our algorithm and two noise amplification index (NAI) algorithms on the basis of the research of Simon 20. We used several different bone surface models (distal radius, proximal femur and tibia) computed from CT images of patient volunteers. The number of registration points used varied between 6 and 30.

RESULTS

Our algorithm was faster than the NAI-based algorithms by factors of approximately 4 and 200. It had equal or better performance in terms of target registration error (TRE) when compared with the other algorithms. Our simulations also showed that point selection can have a large effect on TRE behavior; in particular, poor point selection does not necessarily decrease TRE as more registration points are added.

CONCLUSIONS

Our point-selection algorithm produces model registration points with similar or better TRE behavior than the NAI-based algorithms we tested, and it does so with significantly less computation time.

Computer-assisted deformity correction using the ilizarov method

The Taylor spatial frame is a fixation device used to implement the Ilizarov method of bone deformity correction to gradually distract an osteotomized bone at regular intervals, according to a prescribed schedule. We improve the accuracy of Ilizarov's method of osteogenesis by preoperatively planning the correction, intraoperatively measuring the location of the frame relative to the patient, and computing the final shape of the frame. In four of five tibial phantom experiments, we were able to achieve correction errors of less than 2 degrees of total rotation. We also demonstrate how registration uncertainty can be propagated through the planned transformation to visualize the range of possible correction outcomes. Our method is an improvement over an existing computer-assisted technique (Iyun et al.) in that the surgeon has the same flexibility as in the conventional technique when fixating the frame to the patient.

Liver Resection after Irinotecan, 5-Fluorouracil, and Folinic Acid for Patients with Unresectable Colorectal Liver Metastases: A Multicenter Phase II Study by the Cancer Therapeutic Research Group

The main objectives of this study were to assess the use of irinotecan, 5-fluorouracil (5-FU), and leucovorin (FA) as neoadjuvant chemotherapy for patients with unresectable colorectal liver metastases and to determine the response rate and proportion of patients that could be down-staged to resectable tumors. Forty patients were treated with irinotecan (180 mg/m2 over 30 min) on d 1, FA (200 mg/m2 over 30 min) followed by 5-FU (400 mg/m2 bolus and continuous infusion of 600 mg/m2 over 22 h) on d 1 and 2 every 2 wk. The overall response rate was 55% (95% CI: 39.5-70.4%). The progression-free survival was 12.1 mo (95% CI: 11.4-14.8 mo). The median overall survival was 20 mo (95% CI: 17.7-26.6 mo). Four patients (10%) have undergone liver resection after a median of eight cycles. Those patients remained alive with a median follow up period of 33 mo. The principal grade 3-4 toxicity was neutropenia in 20 patients (50%). We conclude that the regimen of irinotecan/5-FU/FA was highly active in patients with colorectal cancer and liver metastases with limited toxicity. In a subgroup of patients with initial inoperable liver metastases, this regimen was able to down-stage the disease to an operable stage.

Hepatitis B reactivation in patients with hepatocellular carcinoma undergoing systemic chemotherapy

BACKGROUND

Cancer patients who are hepatitis B virus (HBV) carriers and undergoing chemotherapy (CT) may be complicated by HBV reactivation. Over 80% of hepatocellular carcinoma (HCC) patients are HBV carriers; however, the incidence of HBV reactivation during CT has not been well-reported. A prospective study was conducted to determine the incidence of HBV reactivation, the associated morbidity and mortality, and possible risk factors.

PATIENTS AND METHODS

102 HBsAg-positive patients with inoperable HCC underwent systemic CT. Patients received either combination cisplatin, interferon, doxorubicin and fluorouracil (PIAF) or single-agent doxorubicin. They were followed up during and for 8 weeks after CT.

RESULTS

In 102 patients, 59 (58%) developed hepatitis amongst whom 37 (36%) were attributable to HBV reactivation. Twelve (30%) died of HBV reactivation. CT was interrupted in 32 patients (86%) with reactivation and 54 (83%) without reactivation (P>0.05). The median survivals were 6.00 and 5.62 months, respectively (P=0.694). Elevated baseline alanine aminotransferase (ALT) was found to be a risk factor.

CONCLUSION

HBV reactivation is a common cause of liver damage during CT in HBsAg-positive HCC patients. The only identifiable associated risk factor was elevated pre-treatment ALT. Further studies into the role of antiviral and novel anticancer therapies are required to improve the prognosis of these patients.

Stereoselective metabolism of silybin diastereoisomers in the glucuronidation process

A separation method for the hepatoprotective drug silybin and its metabolites by RP-HPLC was described. Based on this separation, the stereoselectivity of the metabolism of silybin was investigated by incubation of the drug and its two diastereoisomers with bovine liver microsomes. Information about the structures of these metabolites was obtained, using UV, HPLC/MS and NMR spectra. Four major metabolites (M(1), M(4) of silybin A and M(2), M(5) of silybin B), were prepared by preparative HPLC, and their configurations were accomplished by NMR spectra. A HPLC method was used to quantify the metabolites. The results showed that silybin was extensively metabolized and the major sites for glucuronidation were the C-20, C-7, at phenolic OH groups. Furthermore, the results obtained reveal that there was significant stereoselectivity in the glucuronidation process of silybin. Silybin B was glucuronidated at a more efficient rate than its diastereoisomer, and glucuronidation of silybin B was much preferred at the 20 position, while that of silybin A was similar at both 7 and 20 position.

Robust registration for computer-integrated orthopedic surgery: laboratory validation and clinical experience

In order to provide navigational guidance during computer-integrated orthopedic surgery, the anatomy of the patient must first be registered to a medical image or model. A common registration approach is to digitize points from the surface of a bone and then find the rigid transformation that best matches the points to the model by constrained optimization. Many optimization criteria, including a least-squares objective function, perform poorly if the data include spurious data points (outliers). This paper describes a statistically robust, surface-based registration algorithm that we have developed for orthopedic surgery. To find an initial estimate, the user digitizes points from predefined regions of bone that are large enough to reliably locate even in the absence of anatomic landmarks. Outliers are automatically detected and managed by integrating a statistically robust M-estimator with the iterative-closest-point algorithm. Our in vitro validation method simulated the registration process by drawing registration data points from several sets of densely digitized surface points. The method has been used clinically in computer-integrated surgery for high tibial osteotomy, distal radius osteotomy, and excision of osteoid osteoma.

Protein folding: binding of conformationally fluctuating building blocks via population selection

Here we review different aspects of the protein folding literature. We present a broad range of observations, showing them to be consistent with a general hierarchical protein folding model. In such a model, local relatively stable, conformationally fluctuating building blocks bind through population selection, to yield the native state. The model includes several components: (1) the fluctuating building blocks that constitute local minima along the polypeptide chain, which even if unstable still possess higher population times than all alternate conformations; (2) the landscape around the bottom of the funnels; (3) the consideration that protein folding involves intramolecular recognition; (4) similar landscapes are observed for folding and for binding, and that (5) the landscape is dynamic, changing with the conditions. The model considers protein folding to be guided by native interactions. The reviewed literature includes the effects of changing the conditions, intermediates and kinetic traps, mutations, similar topologies, fragment complementation experiments, fragments and pathways, focusing on one specific well-studied example, that of the dihydrofolate reductase, chaperones, and chaperonines, in vivo vs. in vitro folding, still using the dihydrofolate example, amyloid formation, and molecular "disorder". These are consistent with the view that binding and folding are similar events, with the differences stemming from different stabilities and hence population times.

Differences in the absorption, metabolism and biliary excretion of a diastereomeric pair of alphavbeta3-antagonists in rat: limited role of P-glycoprotein

1. The study investigated mechanisms underlying the pharmacokinetic differences of two zwitterionic diastereomers ((3S)-3-[(3R or 3S)-2-oxo-3-[3-(5,6,7,8-tetrahydro-1,8-naphthyridin-2-yl)propyl]pyrrolidin-1-yl]-3-quinolin-3-ylpropanoic acid) with different lipophilicities using a combination of in vivo and in vitro approaches. 2. In rat, both isomers possessed comparable plasma clearances (CL). However, the more lipophilic diastereomer I exhibited a higher metabolic clearance (>2-fold higher than II), whereas the hydrophilic zwitterion II exhibited a higher biliary clearance (approximately 5-fold higher than I). Following oral administration, the bioavailability (F) of I (17%) was much higher than that of II (1%). 3. Consistent with these in vivo observations and the expectation based on their lipophilicity differences, the metabolism in rat liver microsomes was faster and the permeability in Caco-2 and LLC-PK1 cells and in situ rat intestinal loop was better for I than for II. 4. Only the absorption of the more lipophilic diastereomer I was subjected to an efflux system in the Caco-2 and in situ rat intestinal loop models. I was a good substrate for P-glycoprotein (P-gp) in both the human MDR1 and mouse mdr1a transfected cell lines, and in the wild-type mdr1a (-/-) mouse when compared with the P-gp-deficient mdr1a (-/-) mouse. Concomitant administration of I with verapamil in rat caused significant increases in oral AUC, F and Cmax of I without affecting its CL, further supporting the effect of P-gp in limiting the intestinal absorption of I in vivo in this animal model. 5. Since the findings that the lipophilic diastereomer I, but not II, was a good P-gp substrate were not in line with the observations that I was excreted to bile much slower than II and that I was absorbed better than II, the results suggested that P-gp played a minor role to the observed differences in the biliary excretion and intestinal absorption of the diastereomers I and II in rat.

Molecular dynamics simulations of the denaturation and refolding of an RNA tetraloop

Tetraloops are very abundant structural elements of RNA that are formed by four nucleotides in a hairpin loop which is closed by a double stranded helical stem with some Watson-Crick base pairs. A tetraloop r(GCGAAGGC) was identified from the crystal structure of the central domain of 16S rRNA (727-730) in the Thermus thermophilus 30S ribosomal complex. The crystal structure of the 30S complex includes a total of 104 nucleotides from the central domain of the 16S rRNA and three ribosomal proteins S6, S15 and S18. Independent biochemical experiments have demonstrated that protein S15 plays the role in initiating the formation of the central domain of this complex. In the crystal, the tetraloop interacts with the protein S15 at two sites: one of them is associated with hydrogen bond interactions between residue His50 and nucleotide G730, and the other is associated with the occurrence of residue Arg53 beside A728. This paper uses molecular dynamics (MD) simulations to investigate the protein-dependent structural stability of the tetraloop and demonstrates the folding pathway of this tetraloop via melting denaturation and its subsequent refolding. Three important results are derived from these simulations: (i) The stability of nucleotide A728 appears to be protein dependent. Without the interaction with S15, A728 flips away from stacking with A729. (ii) The melting temperature demonstrated by the simulations is analogous to the results of thermodynamic experiments. In addition, the simulated folding of the tetraloop is stepwise: the native shape of the backbone is formed first; this is then followed by the formation of the Watson- Crick base pairs in the stem; and finally the hydrogen bonds and base stacking in the loop are formed. (iii) The tetraloop structure is similar to the crystal structure at salt concentrations of 0.1 M and 1.0 M used for the simulations, but the refolded structure at 0.1 M salt is more comparable to the crystal structure than at 1.0 M. The results from the simulations using both the Generalized Born continuum model and explicit solvent model (Particle Mesh Ewald) generate a similar pathway for unfolding/refolding of the tetraloop.

Cure of pulmonary Rhizomucor pusillus infection in a patient with hairy-cell leukemia: role of liposomal amphotericin B and GM-CSF

We describe a case of successfully treated multifocal pulmonary Rhizomucor pusillus, a condition which has previously been universally fatal. A 77 year-old man had a background of chronic neutropenia due to hairy-cell leukemia, splenectomy, corticosteroid therapy and an obstructing left ureteric transitional-cell carcinoma. He was successfully treated with 3 months of high-dose liposomal amphotericin B and 7 months of granulocyte-macrophage colony-stimulating factor. Treatment was complicated by mild reversible deterioration of renal function. There was a near complete radiological response to the therapy at 6 months and the patient remains well 20 months following diagnosis of R. pusillus and 13 months following cessation of treatment.

Induced mandibular condylar growth in a sheep model after functional appliance treatment

This paper reports on changes in mandibular condylar growth in sheep fitted with experimental functional appliances. The paper also addresses the similarities of mandibular condylar growth in sheep and humans. Experimental functional appliances were developed, constructed and applied to four, four-month old, male sheep. Another four sheep served as matched controls. All animals received fluorochrome bone labels during the study and their weight gain also was recorded. Fifteen weeks later, all animals were sacrificed and each temporo-mandibular joint and left metacarpus were removed. Undecalcified mid-sagittal sections of the joint and metacarpus were prepared for fluorescence microscopy. The mandibular condylar growth vector in sheep was found to be in a postero-superior direction. Condylar growth in the control sheep during the experimental period varied from 8.8 to 11.9 mm, with the mean being 10.6 mm, which is quantitatively similar to two years of condylar growth in human adolescents. In the experimental sheep, the condylar growth varied from 8.5 to 13.3 mm, with the mean being 11.4 mm. When metacarpal growth and weight gain were taken into consideration using multivariant analysis, the coefficients for growth in the postero-superior and posterior direction were found to be high, with adjusted r2 as 0.84 and 0.82 respectively. The induced condylar growth was estimated to be largest in the posterior direction (2.30 mm), which is also similar to previous reports in humans. These findings suggest the appropriateness of using sheep as a model for quantitative histological analysis when investigating the mechanisms of functional appliance treatment.

Transition metal-catalyzed [4 + 2 + 2] cycloadditions of bicyclo[2.2.1]hepta-2,5-dienes (norbornadienes) and bicyclo[2.2.2]octa-2,5-dienes

The transition-metal-catalyzed [4 + 2 + 2] cycloadditions of norbornadienes, bicyclo[2.2.2]octa-2,5-diene, and benzobarrelene with 1,3-butadienes proceed in excellent yields using cobalt-based catalytic systems. Two key distinctions between these [4 + 2 + 2] cycloadditions and the corresponding transition-metal-catalyzed [2 + 2 +2] reactions of norbornadiene are the requirement of a bimetal catalytic system with a bisphosphine ligand for the former and exclusive regioselectivity in the [4 + 2 + 2] reaction of 2-substituted norbornadienes to produce 1-substituted adducts. These distinctions may indicate two distinct mechanisms for the [4 + 2 + 2] and [2 + 2 + 2] reactions.

beta-Oxidation of simvastatin in mouse liver preparations

All current 3-hydroxy-3-methylglutaryl-CoA reductase inhibitors [simvastatin (SV), lovastatin (LV), atorvastatin, pravastatin, fluvastatin, and cerivastatin] are believed to undergo an atypical beta-oxidation of the dihydroxy heptanoic or heptanoic acid side chain. Metabolites, which are shortened by two- and/or four-carbon units consistent with beta-oxidation products, have been reported exclusively in rodents following LV and SV administration and across species (rodents, dogs, and humans) following the other statins. In this study, in vitro formation of a beta-oxidation product of simvastatin hydroxy acid (SVA) and its intermediates in mouse livers is described. Incubation of SVA with mouse liver preparations fortified with CoASH and ATP led to formation of SV and two major products (P1 and P2). Based on mass spectrometry (MS), tandem mass spectrometry, and/or NMR spectral characteristics, P1 was an alpha,beta-unsaturated metabolite, formed by dehydration of the D,D-dihydroxy heptanoic acid side chain, whereas P2 was probably the L,D-dihydroxy acid isomer of SVA, formed by stereospecific hydration of P1. When NAD(+) was also included in the incubation mixture, there were two additional metabolites with the MS and/or NMR characteristics consistent with a two-carbon shortened product (P3) and its dehydrated derivative (P4). In a complete incubation system with all cofactors (ATP, CoASH, NAD(+), and NADPH) present, there was an additional product with MS spectra and liquid chromatography retention time identical to the beta-oxidized, unsubstituted pentanoic acid metabolite (P5) detected in rats and mice following simvastatin administration. The involvement of CoASH and NAD(+) and the presence of the four metabolic intermediates suggest that SVA (and presumably the other statins) is a substrate for the beta-oxidation enzyme complex in mice. Additionally, the present finding of CoASH-dependent formation of SV substantiates a mechanism proposed previously for the in vivo lactonization of statin hydroxy acids.

Structured disorder and conformational selection

Traditionally, molecular disorder has been viewed as local or global instability. Molecules or regions displaying disorder have been considered inherently unstructured. The term has been routinely applied to cases for which no atomic coordinates can be derived from crystallized molecules. Yet, even when it appears that the molecules are disordered, prevailing conformations exist, with population times higher than those of all alternate conformations. Disordered molecules are the outcome of rugged energy landscapes away from the native state around the bottom of the funnel. Ruggedness has a biological function, creating a distribution of structured conformers that bind via conformational selection, driving association and multimolecular complex formation, whether chain-linked in folding or unlinked in binding. We classify disordered molecules into two types. The first type possesses a hydrophobic core. Here, even if the native conformation is unstable, it still has a large enough population time, enabling its experimental detection. In the second type, no such hydrophobic core exists. Hence, the native conformations of molecules belonging to this category have shorter population times, hindering their experimental detection. Although there is a continuum of distribution of hydrophobic cores in proteins, an empirical, statistically based hydrophobicity function may be used as a guideline for distinguishing the two disordered molecule types. Furthermore, the two types relate to steps in the protein folding reaction. With respect to protein design, this leads us to propose that engineering-optimized specific electrostatic interactions to avoid electrostatic repulsion would reduce the type I disordered state, driving the molten globule (MG) --> native (N) state. In contrast, for overcoming the type II disordered state, in addition to specific interactions, a stronger hydrophobic core is also indicated, leading to the denatured --> MG --> N state.

Characterization of a thrombin-like serine protease, Kangshuanmei, isolated from the venom of a Chinese snake, Agkistrodon halys brevicaudus stejneger

An enzyme, referred to as Kangshuanmei, was isolated from the venom of the Chinese snake Agkistrodon halys brevicaudus stejneger by gel filtration chromatography followed by affinity chromatography. Kangshuanmei is composed of a single polypeptide chain with a molecular weight of approximately 34,000, estimated by SDS-PAGE. The enzyme hydrolyzed both benzoyl-arginine ethyl ester and H-D-Phe-Pip-Arg-p-nitroanilide, specific substrates for thrombin. The protease activity of Kangshuanmei was inhibited by 4-(2-aminoethyl)-benzensulfonyl fluoride, but was not affected by EDTA. The enzyme acted on human fibrinogen to form a fibrin clot and released three fragments. These fragments were shown to be fibrinopeptide A, fibrinopeptide B, and the Bbeta1-42 peptide of fibrinogen, respectively. These results indicate that Kangshuanmei is a thrombin-like serine protease with coagulant activity. However, the enzyme did not induce activation of blood coagulation factor XIII, unlike thrombin. Moreover, antithrombin-III, the specific thrombin inhibitor in plasma, had no inhibitory effect on the thrombin-like amidolytic activity of Kangshuanmei. The N-terminal amino acid sequence of the enzyme up to 50 residues was determined by a peptide sequencer. The N-terminal sequence of Kangshuanmei was highly homologous to most thrombin-like serine proteases from the venom of the snakes of the crotalidae family.

[Analysis of immunophenotype of hematopoietic stem/progenitor cells in human umbilical cord blood with flow cytometry and its significance]

OBJECTIVE

To study the difference of immunophenotype of hematopoietic stem/progenitor cells (HSPCs) between human umbilical cord blood(UCB) and bone marrow(BM).

METHODS

The expression of CD antigens and cell adhesion molecules on HSPCs in 38 UCB and 10 cases BM were investigated with monoclonal antibodies and double immunofluorescence using flow cytometry.

RESULTS

1. The CD34+ cell population in nucleated cells of UCB was similar to that of BM, being about 0.5%; 2. The frequencies of CD34+CD38-, CD34+HLA-DR- and CD34+H-CAM+ (CD44+) cells in UCB CD34+ cells were higher, while the frequencies of CD34+CD13+ and CD34+CD19+ cells in UCB were lower than that in BM.

CONCLUSION

The total number of CD34+ cells in UCB and BM was very similar. However, there was a higher proportion of more primary HSPCs in UCB, which was able to reconstitute hematopoiesis as an potential source of HSPCs, the proportion of relatively mature HSPCs (CD34+ CD19+ and CD34+CD13+) were less in UCB than in BM, which probably accounted for the relatively slow haematopoietic reconstitution following UCB transplantation.

Use of the tetracycline-controlled transcriptional silencer (tTS) to eliminate transgene leak in inducible overexpression transgenic mice

The doxycycline-inducible reverse tetracycline transactivator (rtTA) is frequently used to overexpress transgenes in a temporally regulated fashion in vivo. These systems are, however, often limited by the levels of transgene expression in the absence of dox administration. The tetracycline-controlled transcriptional silencer (tTS), a fusion protein containing the tet repressor and the KRAB-AB domain of the kid-1 transcriptional repressor, is inhibited by doxycycline. We hypothesized that tTS would tighten control of transgene expression in rtTA-based systems. To test this hypothesis we generated mice in which the CC10 promoter targeted tTS to the lung, bred these mice with CC10-rtTA-interleukin 13 (IL-13) mice in which IL-13 was overexpressed in an inducible lung-specific fashion, and compared the IL-13 production and phenotypes of parental mice and the triple transgenic CC10-rtTA/tTS-IL-13 progeny of these crosses. In the CC10-rtTA-IL-13 mice, IL-13, mucus metaplasia, inflammation, alveolar enlargement, and enhanced lung volumes were noted at base line and increased greatly after doxycycline administration. In the triple transgenic tTS animals, IL-13 and the IL-13-induced phenotype could not be appreciated without doxycycline. In contrast, tTS did not alter the induction of IL-13 or the generation of the IL-13 phenotype by doxycycline. Thus, tTS effectively eliminated the baseline leak without altering the inducibility of rtTA-regulated transgenes in vivo. Optimal "off/on" regulation of transgene expression can be accomplished with the combined use of tTS and rtTA.

Combined modality treatment for locally advanced squamous-cell carcinoma of the oropharynx in a woman with Bloom's syndrome: a case report and review of the literature

We describe a case of locally advanced unresectable squamous-cell carcinoma of the oropharynx in a young woman with Bloom's syndrome. She was treated with radical radiation therapy and concurrent chemotherapy (cisplatin and 5-flurouracil). She was unable to complete treatment due to the development of severe side effects: confluent mucositis, moist desquamating skin reaction, severe diarrhea and severe myelosupression with neutropenic sepsis. The limited relevant literature is presented. We conclude that chemotherapy should be used with extreme caution in Bloom's syndrome patients.

[Sequencing and comparative analysis of the complete glycoprotein gene of three Crimean-Congo hemorrhagic fever virus Chinese isolates]

OBJECTIVE

To determine the complete sequences of glycoprotein (M) gene of Crimean-Congo hemorrhagic fever virus (CCHFV) Chinese isolates (Xinjiang hemorrhagic fever virus, XHFV) BA66019, BA8402 BA88166 and to compare and analyze the relationships among the viruses.

METHODS

Based on the conserved reverse complementarity of the CCHFV genomic termini, a primer PCM-Tag was designed and used together with random hexmers to initiate reverse transcription of viral RNA to synthesize cDNA. The latter was amplified with single primer PCM-Tag using the proof-reading DNA polymerase to produce the complete M gene. The PCR products were gel-purified and the whole M segment was sequenced and the comparison and analysis were performed aided by computer for the phylogenesis and coding strategy.

RESULTS

Comparison of the whole M gene sequences of XHFV reference strain BA66019 with international prototype CCHFV IbAr10200 showed an excess of 5 base pairs in length, resulting in 5,365 bp; while BA8402 and BA8816 are 5,365 bp long, 4 more base pairs than IbAr10200. The first start codons of long ORFs were located at the 78th base pair in M gene of BA66019, BA8402 and BA88166, which were 15 base pairs prior to that of IbAr10200. The precursors encoded by these M genes were totaled 1,689 amino acids (AA), 6 AAs more than that of IbAr10200. The similaries between CCHFV M genes in nucleotide level were: 80.9% (IbAr10200-BA66019), 80.2% (IbAr10200-BA8402), 80.2% (IbAr10200-BA88166), 83.7% (BA8402-BA66019), 83.6% (BA88166-BA66019), and 99.0% (BA8402-BA88166), respectively. The corresponding similarities in amino acid level were 85.1%, 86.3%, 86.6%, 87.8%, 88.0%, and 98.8%, respectively. The similarities of M genes of CCHFVs and Dugbe virus in both nucleotide and amino acid levels were around 55% and 37%, which were much lower than those among CCHFVs.

CONCLUSION

The M genes of XHFVs and IbAr10200 formed respective independent phylogenetic branches genetically and the human-origin isolate BA88166 might be a variant of tick-borne BA8402, suggesting that there was only one kind virus prevailing in Xinjiang epidemic areas in 1980s.

Protein functional epitopes: hot spots, dynamics and combinatorial libraries

Recent studies increasingly point to the importance of structural flexibility and plasticity in proteins, highlighting the evolutionary advantage. There are an increasing number of cases in which given, presumably specific, binding sites have been shown to bind a range of ligands with different compositions and shapes. These studies have also revealed that evolution tends to find convergent solutions for stable intermolecular associations, largely via conservation of polar residues as hot spots of binding energy. On the other hand, the ability to bind multiple ligands at a given site is largely derived from hinge-based motions. The consideration of these two factors in functional epitopes allows more realism and robustness in the description of protein binding surfaces and, as such, in applications to mutants, modeled structures and design. Efficient multiple structure comparison and hinge-bending structure comparison tools enable the construction of combinatorial binding epitope libraries.

[Transcatheter arterial embolization in intractable postpartum hemorrhage]

OBJECTIVE

To asses the value of transcatheter arterial embolization treatment in intractable postpartum hemorrhage.

METHODS

Fourteen patients of postpartum hemorrhage failed to the drugs treatment were performed transcatheter arterial embolization (TAE). Superselective catheterization to the bilateral uterial arteries or anterior branches of internal iliac arteries was carried out after intubation to single-side femoral artery by Seldinger's technique. When the catheter tip was proved in right place by digital substraction angiography (DSA) techniques, antibiotic solution was poured into arteries and then the arterial embolization with gelfoam particles was followed.

RESULTS

All the patients were performed TAE successfully. The duration of TAE was 30-50 minutes [mean (41.8 +/- 6.4) minutes]. Bleeding was found in DSA mostly as diffuse intrauterine flow outward sign from one side or both side of uterial artery branches. After one time of TAE, the vaginal bleeding of all patients was stopped in 3-10 minutes [mean (6.1 +/- 3.6) minutes]. The follow-up showed that all patients had normal menstrual periods in 2-60 months and no serious complications were found.

CONCLUSION

With the characteristic of fast homeostasis and less complications, TAE was proved to be an effective method for intractable postpartum hemorrhage.

A map of protein-protein contacts within the small nuclear RNA-activating protein complex SNAPc

The nucleation of RNA polymerases I-III transcription complexes is usually directed by distinct multisubunit factors. In the case of the human RNA polymerase II and III small nuclear RNA (snRNA) genes, whose core promoters consist of a proximal sequence element (PSE) and a PSE combined with a TATA box, respectively, the same multisubunit complex is involved in the establishment of RNA polymerase II and III initiation complexes. This factor, the snRNA-activating protein complex or SNAP(c), binds to the PSE of both types of promoters and contains five types of subunits, SNAP190, SNAP50, SNAP45, SNAP43, and SNAP19. SNAP(c) binds cooperatively with both Oct-1, an activator of snRNA promoters, and in the RNA polymerase III snRNA promoters, with TATA-binding protein, which binds to the TATA box located downstream of the PSE. Here we have defined subunit domains required for SNAP(c) subunit-subunit association, and we show that complexes containing little more than the domains mapped here as required for subunit-subunit contacts bind specifically to the PSE. These data provide a detailed map of the subunit-subunit interactions within a multifunctional basal transcription complex.

The green fluorescent protein gene functions as a reporter of gene expression in Phanerochaete chrysosporium

The enhanced green fluorescent protein (GFP) gene (egfp) was used as a reporter of gene expression driven by the glyceraldehyde-p-dehydrogenase (gpd) gene promoter and the manganese peroxidase isozyme 1 (mnp1) gene promoter in Phanerochaete chrysosporium. Four different constructs were prepared. pUGGM3' and pUGiGM3' contain the P. chrysosporium gpd promoter fused upstream of the egfp coding region, and pUMGM3' and pUMiGM3' contain the P. chrysosporium mnp1 promoter fused upstream of the egfp gene. In all constructs, the egfp gene was followed by the mnp1 gene 3' untranslated region. In pUGGM3' and pUMGM3', the promoters were fused directly with egfp, whereas in pUGiGM3' and pUMiGM3', following the promoters, the first exon (6 bp), the first intron (55 bp), and part of the second exon (9 bp) of the gpd gene were inserted at the 5' end of the egfp gene. All constructs were ligated into a plasmid containing the ura1 gene of Schizophyllum commune as a selectable marker and were used to transform a Ural1 auxotrophic strain of P. chrysosporium to prototrophy. Crude cell extracts were examined for GFP fluorescence, and where appropriate, the extracellular fluid was examined for MnP activity. The transformants containing a construct with an intron 5' of the egfp gene (pUGiGM3' and pUMiGM3') exhibited maximal fluorescence under the appropriate conditions. The transformants containing constructs with no introns exhibited minimal or no fluorescence. Northern (RNA) blots indicated that the insertion of a 5' intron resulted in more egfp RNA than was found in transformants carrying an intronless egfp. These results suggest that the presence of a 5' intron affects the expression of the egfp gene in P. chrysosporium. The expression of GFP in the transformants carrying pUMiGM3' paralled the expression of endogenous mnp with respect to nitrogen and Mn levels, suggesting that this construct will be useful in studying cis-acting elements in the mnp1 gene promoter.

Effect of long-range interactions on the scaling of the noisy Kuramoto-Sivashinsky equation

The effects of long-range interactions on the scaling properties of the noisy Kuramoto-Sivashinsky (KS) equation are studied by the dynamic renormalization-group technique. It is found that the presence of long-range nonlinearity in the KS equation can produce new stable fixed points with varying critical exponents that depend on both the long-range interaction parameter rho and the substrate dimension d.

Molecular dynamics simulation of Escherichia coli dihydrofolate reductase and its protein fragments: relative stabilities in experiment and simulations

We have carried out molecular dynamics simulations of the native dihydrofolate reductase from Escherichia coli and several of its folded protein fragments at standard temperature. The simulations have shown fragments 1--36, 37--88, and 89--159 to be unstable, with a C(alpha)RMSD (C(alpha) root mean squared deviation) >5 A after 3.0 nsec of simulation. The unfolding of fragment 1--36 was immediate, whereas fragments 37--88 and 89--159 gradually unfolded because of the presence of the beta-sheet core structure. In the absence of residues 1--36, the two distinct domains comprising fragment 39--159 associated with each other, resulting in a stable conformation. This conformation retained most of its native structural elements. We have further simulated fragments derived from computational protein cutting. These were also found to be unstable, with the exception of fragment 104--159. In the absence of alpha(4), the loose loop region of residues 120--127 exhibited a beta-strand-like behavior, associating itself with the beta-sheet core of the protein fragment. The current study suggests that the folding of dihydrofolate reductase involves cooperative folding of distinct domains which otherwise would have been unstable as independent folded units in solution. Finally, the critical role of residues 1--36 in allowing the two distinct domains of fragment 104--159 to fold into the final native conformation is discussed.

A systematic study of the vibrational free energies of polypeptides in folded and random states

Molecular vibrations, especially low frequency motions, may be used as an indication of the rigidity or the flatness of the protein folding energy landscape. We have studied the vibrational properties of native folded as well as random coil structures of more than 60 polypeptides. The picture we obtain allows us to perceive how and why the energy landscape progressively rigidifies while still allowing potential flexibility. Compared with random coil structures, both alpha-helices and beta-hairpins are vibrationally more flexible. The vibrational properties of loop structures are similar to those of the corresponding random coil structures. Inclusion of an alpha-helix tends to rigidify peptides and so-called building blocks of the structure, whereas the addition of a beta-structure has less effect. When small building blocks coalesce to form larger domains, the protein rigidifies. However, some folded native conformations are still found to be vibrationally more flexible than random coil structures, for example, beta(2)-microglobulin and the SH3 domain. Vibrational free energy contributes significantly to the thermodynamics of protein folding and affects the distribution of the conformational substates. We found a weak correlation between the vibrational folding energy and the protein size, consistent with both previous experimental estimates and theoretical partition of the heat capacity change in protein folding.