Computational insights into binding of bisphosphates to farnesyl pyrophosphate synthase

Bisphosphonates (BPs) are the most widely used and effective treatment for osteoporosis and Paget's disease. Non-nitrogen containing BPs (non-N-BPs), namely etidronate, clodronate, tiludronate, as well as nitrogen-containing BPs (N-BPs), namely pamidronate, alendronate, ibandronate, risedronate, zoledronate and minodronate have been launched on the market to date. N-BPs act by inhibiting the enzyme farnesyl pyrophosphate synthase (FPPS), and several crystal structures of complexes between FPPS and N-BPs have been revealed. Understanding the physical basis of the binding between protein and small molecules is an important goal in both medicinal chemistry and structural biology. In this review, we analyze in detail the energetic basis of molecular recognition between FPPS and N-BPs. First, we summarize the interactions between ligands and proteins observed in N-BPs-FPPS complexes in the Protein Data Bank (PDB). Second, we present an interaction energy analysis on the basis of full quantum mechanical calculation of FPPS and N-BP complexes using the fragment molecular orbital (FMO) method. The FMO result revealed that not only hydrogen bond and electrostatic interaction but also CH-O and π-π interaction with FPPS are important for N-BP’s potency. Third, we describe a binding site analysis of FPPS on the basis of the inhomogeneous solvation theory which, by clustering the results from an explicit solvent molecular dynamics simulation (MD), is capable of describing the entropic and enthalpic contributions to the free energies of individual hydration sites. Finally, we also discuss the structure-activity relationship (SAR) of the series of minodronate derivatives.

Abstract 281: Prevalence of Human papilloma virus in oral squamous cell carcinoma using Liner Array HPV genotyping kit

Background. The major risk factors for oral squamous cell carcinoma (OSCC) are cigarette smoking, alcohol consumption, and betel quid chewing. In addition, human papillomavirus (HPV) infection has been associated with some OSCC. However, the relationships of HPVs to OSCCs remain unclear because of the difficulties in interpreting studies that demonstrate various prevalence rates of HPVs. We examined the prevalence of HPV in OSCCs. For HPV detection and genotyping, a sensitive and specific PCR-based method, the Roche Linear Array HPV genotyping kit test was used for these studies.

Materials and Methods. Forty-five Japanese patients with OSCC were included in the present study. Surgical resection of primary tumors and normal tissues from all patients was performed at the Hospital of Tokyo Dental College, between December 2007 and December 2010. We assessed HPV infection in OSCC patients using the Roche Liner Array HPV genotyping Test, which can detect 37 different HPV types.

Results. HPV was detected in 9 OSCC patients (20%). HPV subtype 39, 42 was the most prevalent type, but other types detected included 31, 33, 45 . . . high-risk types and 3, 6, 8 . . . low-risk types.

Conclusion. The Roche Liner Array HPV genotyping Test is currently used as a standardized diagnostic test for HPV detection in cervical carcinoma in Europe. Some studies have shown that the most prevalent HPV subtype was the high-risk type HPV-16, However we showed that HPV is detected multiple type involved low- and high-risk type in oral carcinoma. We suggested that multiple subtypes of HPV implicated OSCC.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 281. doi:10.1158/1538-7445.AM2011-281

Myasthenic syndrome caused by plectinopathy

BACKGROUND

Plectin crosslinks intermediate filaments to their targets in different tissues. Defects in plectin cause epidermolysis bullosa simplex (EBS), muscular dystrophy (MD), and sometimes pyloric atresia. Association of EBS with a myasthenic syndrome (MyS) was documented in a single patient in 1999.

OBJECTIVES

To analyze the clinical, structural, and genetic aspects of a second and fatal case of EBS associated with a MyS and search for the genetic basis of the disease in a previously reported patient with EBS-MD-MyS.

METHODS

Clinical observations; histochemical, immunocytochemical, and electron microscopy studies of skeletal muscle and neuromuscular junction; and mutation analysis.

RESULTS

An African American man had EBS since early infancy, and progressive muscle weakness, hyperCKemia, and myasthenic symptoms refractory to therapy since age 3 years. Eventually he became motionless and died at age 42 years. At age 15 years, he had a marked EMG decrement, and a reduced miniature endplate potential amplitude. The myopathy was associated with dislocated muscle fiber organelles, structurally abnormal nuclei, focal plasmalemmal defects, and focal calcium ingress into muscle fibers. The neuromuscular junctions showed destruction of the junctional folds, and remodeling. Mutation analysis demonstrated a known p.Arg2319X and a novel c.12043dupG mutation in PLEC1. The EBS-MD-MyS patient reported in 1999 also carried c.12043dupG and a novel p.Gln2057X mutation. The novel mutations were absent in 200 Caucasian and 100 African American subjects.

CONCLUSIONS

The MyS in plectinopathy is attributed to destruction of the junctional folds and the myopathy to defective anchoring of muscle fiber organelles and defects in sarcolemmal integrity.

Expression of fibrosis-related genes in canine chronic hepatitis

Molecular regulation of fibrosis in chronic canine hepatitis is poorly understood. The authors employed quantitative polymerase chain reaction (PCR) to determine the expression levels of genes reported to be related to fibrosis in other species (human, mouse, and rat) and to elucidate the relationship of these genes with the degree of fibrosis and the presence or absence of ascites and/or jaundice in dogs with hepatitis. Nine fibrosis-related genes were assayed: PDGFB, PDGFD, MMP2, TIMP1, THBS1, COL1A1, COL3A1, TGFB1, and TGFB2. Liver samples of 15 dogs with chronic hepatitis and 4 healthy control dogs were obtained via laparoscopic biopsy and subjected to histologic and quantitative PCR analyses. The expression of all 9 genes showed significant positive correlation (P<.01, r>.70) with the degree of fibrosis. Furthermore, the expression levels of all genes except TGFB1 were significantly higher (P<.05) in dogs with hepatic failure-related symptoms (ascites/jaundice). Results suggest that these 9 genes are integral to the development of fibrosis in canine chronic hepatitis.

First-principles study of blue silicate phosphors

First-principles calculations were performed to investigate the optical property of blue silicate phosphor, CMS:Eu. The optical absorption property is discussed based on electronic band structure and density of states. Our calculation results indicate that hybridization of the wavefunction plays an important role for nonradiative migration of electrons and holes. The calculated optical absorption spectrum could reproduce the optical features of the experimental excitation spectrum. It is also demonstrated that a practical approach using computational materials screening is effective in phosphor materials development.

Clinical system engineering of long-term automatic thermal control during brain hypothermia under changing conditions

Automatic control systems of brain temperature for water surface-cooling were first-ever applied to the brain hypothermic treatment of patients. A patient in ICU was regarded as a unity controlled system with an input (temperature of water into blanket) and an output (tympanic membrane temperature). The proposed algorithm of optimal-adaptive and fuzzy control laws inclusive of our developed cooling and warming machine were well confirmed during the hypothermic course to keep brain temperature of patients within its allowable range. It was well controlled without much influence due to room temperature, metabolic and circulatory change caused by various medical treatments including the effect of nonlinear and time-varying characteristics of individual patients. The clinical control of brain temperature was almost continuously performed in around 10 days, under the brain temperature between 35 degrees C and 37 degrees C scheduled by physicians according to the state of patients. Their state had been monitored during the therapeutic course of pharmacological treatment with almost everyday examinations by CT imaging, referring various vital signs inclusive of the temperature of urinary bladder with continuous measurement of intracranial pressure by a catheter placement in cerebral sinus. The patients had good recovery to their rehabilitation after mild hypothermia by the proposed automatic control systems.

Paediatric CT examinations in 19 developing countries: frequency and radiation dose

The aims of this study were to investigate the frequency of computed tomography (CT) examinations for paediatric patients below 15 y of age in 128 CT facilities in 28 developing countries of Africa, Asia and Eastern Europe and to assess the magnitude of CT doses. Radiation dose data were available from 101 CT facilities in 19 countries. The dose assessment was performed in terms of weighted CT dose index (CTDI(w)), volume CT index and dose length product (DLP) for chest, chest (high resolution), lumbar spine, abdomen and pelvis CT examinations using standard methods. The results show that on average the frequency of paediatric CT examinations was 20, 16 and 5 % of all CT examinations in participating centres in Africa, Asia and Eastern Europe, respectively. Eleven CT facilities in six countries were found to use adult CT exposure parameters for paediatric patients, thus indicating limited awareness and the need for optimisation. CT images were of adequate quality for diagnosis. The CTDI(w) variations ranged up to a factor of 55 (Africa), 16.3 (Asia) and 6.6 (Eastern Europe). The corresponding DLP variations ranged by a factor of 10, 20 and 8, respectively. Generally, the CTDI(w) and DLP values in Japan are lower than the corresponding values in the three regions in this study. The study has indicated a stronger need in many developing countries to justify CT examinations in children and their optimisation. Awareness, training and monitoring of radiation doses is needed as a way forwards.

Inhibition of osteopontin reduces liver metastasis of human pancreatic cancer xenografts injected into the spleen in a mouse model

PURPOSE

Pancreatic cancer is associated with the poorest prognosis of any digestive cancer due to the high incidence of liver metastasis. This study evaluated the possibility that osteopontin (OPN) RNA interference (RNAi) and anti-OPN antibody (Ab) could have antimetastatic effects.

METHODS

The differential gene expression was measured in a parental cell line, HPC-3, and an established highly liver metastatic cell line, HPC-3H4. This study investigated the effect of OPN RNAi and anti-OPN Ab on the metastatic ability of HPC-3H4 to the liver. An OPN RNAi-expressing vector was introduced into HPC-3H4 cells (HPC-3H4/miOPN), in which OPN production was reduced to the level of the parental HPC-3 cells. Finally, the ability of anti-OPN Ab to suppress liver metastasis was investigated.

RESULTS

Osteopontin was upregulated 11.1-fold in HPC-3H4 in comparison to HPC-3. The metastatic rate of HPC-3H4/miOPN was significantly reduced to 25% in comparison to the 100% metastatic rate of HPC-3H4 and control HPC-3H4/miNeg cells (P < 0.01). The metastatic rate of the group given anti-OPN Ab was 50%.

CONCLUSION

OPN RNAi and anti-OPN Ab had remarkable inhibitory effects against liver metastasis by the pancreatic cancer cell line.

Histamine-1 receptor is not required as a downstream effector of orexin-2 receptor in maintenance of basal sleep/wake states

AIM

The effect of orexin on wakefulness has been suggested to be largely mediated by activation of histaminergic neurones in the tuberomammillary nucleus (TMN) via orexin receptor-2 (OX(2)R). However, orexin receptors in other regions of the brain might also play important roles in maintenance of wakefulness. To dissect the role of the histaminergic system as a downstream mediator of the orexin system in the regulation of sleep/wake states without compensation by the orexin receptor-1 (OX(1)R) mediated pathways, we analysed the phenotype of Histamine-1 receptor (H(1)R) and OX(1)R double-deficient (H(1)R(-/-);OX(1)R(-/-)) mice. These mice lack OX(1)R-mediated pathways in addition to deficiency of H(1)R, which is thought to be the most important system in downstream of OX(2)R.

METHODS

We used H(1)R deficient (H(1)R(-/-)) mice, H(1)R(-/-);OX(1)R(-/-) mice, OX(1)R and OX(2)R double-deficient (OX(1)R(-/-);OX(2)R(-/-)) mice, and wild type controls. Rapid eye movement (REM) sleep, non-REM (NREM) sleep and awake states were determined by polygraphic electroencephalographic/electromyographic recording.

RESULTS

No abnormality in sleep/wake states was observed in H(1)R(-/-) mice, consistent with previous studies. H(1)R(-/-);OX(1)R(-/-) mice also showed a sleep/wake phenotype comparable to that of wild type mice, while OX(1)R(-/-); OX(2)R(-/-) mice showed severe fragmentation of sleep/wake states.

CONCLUSION

Our observations showed that regulation of the sleep/wake states is completely achieved by OX(2)R-expressing neurones without involving H(1)R-mediated pathways. The maintenance of basal physiological sleep/wake states is fully achieved without both H(1) and OX(1) receptors. Downstream pathways of OX(2)R other than the histaminergic system might play an important role in the maintenance of sleep/wake states.

Estimation of norovirus removal performance in a coagulation-rapid sand filtration process by using recombinant norovirus VLPs

Norovirus (NV) is an important human pathogen that causes epidemic acute nonbacterial gastroenteritis worldwide. Because of the lack of a cell culture system or an animal model for this virus, studies of drinking water treatment such as separation and disinfection processes are still hampered. We successfully estimated NV removal performance during a coagulation-rapid sand filtration process by using recombinant NV virus-like particles (rNV-VLPs) morphologically and antigenically similar to native NV. The behaviors of two widely accepted surrogates for pathogenic waterborne viruses, bacteriophages Qbeta and MS2, were also investigated for comparison with that of rNV-VLPs. Approximately 3-log(10) removals were observed for rNV-VLPs with a dose of 40 muM-Al or -Fe, as polyaluminum chloride at pH 6.8 or ferric chloride at pH 5.8, respectively. Smaller removal ratios were obtained with alum and ferric chloride at pH 6.8. The removal performance for MS2 was somewhat larger than that for rNV-VLPs, meaning that MS2 is not recommended as an appropriate surrogate for native NV. By comparison, the removal performance for Qbeta was similar to, or smaller than, that for rNV-VLPs. However, the removal performances for rNV-VLPs and Qbeta differed between the coagulation process and the following rapid sand filtration process. Therefore, Qbeta also is not recommended as an appropriate surrogate for native NV.

Geosmin and 2-methylisoborneol adsorption on super-powdered activated carbon in the presence of natural organic matter

Geosmin and 2-methylisoborneol (2-MIB) are naturally occurring compounds responsible for musty-earthy-odors in surface water supplies. They are a severe problem confronting utilities worldwide. Adsorption by powdered activated carbon (PAC) is a widely used process to control this problem, but it has low efficiency, which engenders large budget spending for utilities services. Super-powdered activated carbon (S-PAC) is activated carbon with much finer particles than those of PAC. Experiments on geosmin and 2-MIB adsorptions on S-PAC and PAC were conducted. Geosmin and 2-MIB adsorption capacities on S-PAC were not smaller than those on PAC although natural organic matter, which adversely impacted the adsorption capacity of geosmin and 2-MIB, was more adsorbed on S-PAC than on PAC, meaning that the adsorption competition is less severe for S-PAC than for PAC.

Evaluation of norovirus removal performance in a coagulation-ceramic microfiltration process by using recombinant norovirus virus-like particles

Norovirus (NV) is a prototype strain of a group of human caliciviruses responsible for epidemic outbreaks of acute gastroenteritis worldwide. Because of the lack of a cell culture system or an animal model for this virus, studies on drinking water treatment such as separation and disinfection processes are still hampered. In the present study, we investigated NV removal performance as particles during a coagulation-ceramic microfiltration (MF) process by using recombinant NV virus-like particles (rNV-VLPs), which are morphologically and antigenically similar to native NV. We also experimentally investigated the behaviors of two widely accepted surrogates for pathogenic waterborne viruses, bacteriophages Qbeta and MS2, for comparison with the behavior of rNV-VLPs. More than 4-log removal was observed for rNV-VLPs with a 1.08 mg-Al/L dose of polyaluminium chloride in the coagulation-ceramic MF process. This high removal ratio of rNV-VLPs satisfies the U.S. Environmental Protection Agency requirement of 4-log removal or inactivation. In addition, the removal ratios of Qbeta and MS2 were approximately 2-log and 1-log, smaller than the ratio of rNV-VLPs. Accordingly, both bacteriophages have the potential to become appropriate surrogates for native NV in the coagulation-ceramic MF process, and, of the two, Qbeta is the more conservative surrogate.

Validation of an in vitro screening test for predicting the tumor promoting potential of chemicals based on gene expression

Chemical carcinogenesis is a multifactorial process comprising two main stages: initiation and promotion. Tumor promoters cause the development of tumors in initiated cells and the majority of them are non-genotoxic carcinogens. The identification of tumor promoters is important for preventing cancer. We previously identified 22 specific gene markers using a global gene expression analysis of chemically induced tumor promotion and established an in vitro real-time PCR screening assay for the assessment of the tumor promoting potential of chemicals in BALB/c 3T3 cells. Our in vitro tumor promoter screening test, based on these marker genes, enables earlier assessment, and is easier to conduct than classical methods. The general applicability of these markers, however, was unknown. In this study, to evaluate the performance of a set of markers, we independently validated a separate sample set, which had various structures and properties. Independent validation of the signature of 63 test chemicals showed an accuracy, sensitivity, and specificity of the assay of 96.8%, 97.0% and 96.7%, respectively. These results indicate that the tumor promoting activity assay, based on the expression of 22 marker genes, will become a valuable tool for rapid screening of potential tumor promoters.

Patient doses in CT examinations in 18 countries: initial results from International Atomic Energy Agency projects

The purpose of this prospective study at 73 facilities in 18 countries in Africa, Asia and Eastern Europe was to investigate if the CT doses to adult patients in developing countries are higher than international standards. The dose assessment was performed in terms of weighted computed tomography dose index (CTDIw) and dose length product (DLP) for chest, chest (high resolution), lumbar spine, abdomen and pelvis CT examinations using standard methods. Except in one case, the mean CTDIw values were below diagnostic reference level (DRL) while for DLP, 17 % of situations were above DRLs. The resulting CT images were of adequate quality for diagnosis. The CTDIw and DLP data presented herein are largely similar to those from two recent national surveys. The study has shown a stronger need to create awareness and training of radiology personnel as well as monitoring of radiation doses in many developing countries so as to conform to the ALARA principle.