Research on sequence variations analysis of HPV-16 type in Southwestern China

OBJECTIVE

This study was designed to analyze sequence variations in E6, E7, and L1 of human papillomavirus type 16 (HPV-16) to identify novel HPV-6 variants and correlate them with the progression of cervical cancer.

MATERIALS AND METHODS

Cervical biopsies from 12 HPV-16 positive cervical neoplasia cases were analyzed by polymerase chain reaction (PCR) for E6,E7, and L1 gene. The products of PCR were ligated into pGEM-T vector and used to transform e. coli DH5a. Finally, the sequence of the insert was determined by an automated DNA sequencer.

RESULTS

Compared with the European-Germanyl31 (EG131), 20 mutations were detected, of which eight mutations were detected from all the four biopsies: 131(G-A)(Gly-Arg), 178 (T-G)(Asp-Glu),350 (G-T)(Val-Leu), 647 (A-G)(Asn-Asp),846 (T-C) (synonymous mutation), L1 966th (C-T)(synonymous mutation),L1 1302 (C-T)(synonymous mutation) and L1 1434th (A-G) (synonymous mutation).

CONCLUSIONS

Compared with other HPV-16 reference sequences, nucleotide sequencing analysis of the HPV-16, E6,E7, and L1 gene from cervical carcinoma biopses in Southwestern China consistently shows point mutations, including synonymous mutation and nonsynonymous mutation. Above all, the results may have implications for future researches of viral persistence, transmission, oncogenic potential, developing diagnostic probe, and designing vaccine or biological preparation for a particular population.

Effects of feeding corn naturally contaminated with aflatoxin B1 and B2 on hepatic functions of broilers

The purpose of this study was to evaluate the effects of feeding corn naturally contaminated with aflatoxin B(1) (AFB(1)) and aflatoxin B(2) (AFB(2)) on serum biochemical parameters, hepatic antioxidant enzyme activities, and pathological lesions of broilers. In total, 1,200 Cobb male broilers were randomly allocated into 5 treatments, with 8 replicates per treatment and 30 birds per replicate, in a 42-d experiment. The dietary treatments were as follows: control, 25, 50, 75, and 100% contaminated corn groups. Results showed that serum aspartate aminotransferase activity in the 75 and 100% contaminated groups were higher than that in the control group on d 21 (P < 0.05). Decreased content of hepatic total protein and increased activities of hepatic glutathione reductase and glutathione-S-transferase were observed as the percentage of contaminated corn increased (P < 0.05). The activity of superoxide dismutase and the content of hepatic malondialdehyde increased when the broilers were fed with more than 50% contaminated corn (P < 0.05). A reduction in glutathione peroxidase level was observed in the AFB(1)- and AFB(2)-contaminated groups on d 21 (P < 0.05). The average pathological lesion scores and apoptosis rate of liver cells increased as the concentration of dietary AFB(1) and AFB(2) increased. Ultrastructural changes were found in the livers of broilers fed 100% contaminated corn. In conclusion, diets containing AFB(1) and AFB(2) could induce pathological lesions in the livers, slightly change the serum biochemical parameters, and damage the hepatic antioxidant functions when the inclusion of AFB(1)- and AFB(2)-contaminated corn reached or exceeded 50%.

Docetaxel-cisplatin might be superior to docetaxel-capecitabine in the first-line treatment of metastatic triple-negative breast cancer

BACKGROUND

Triple-negative breast cancer (TNBC) may be more sensitive to platinum. This study was to compare platinum-based regimen with nonplatinum regimen in the first-line treatment of advanced TNBC.

PATIENTS AND METHODS

Eligible metastatic TNBC (mTNBC) women without prior treatment for advanced disease were randomized (1 : 1) to receive either docetaxel-cisplatin (TP) or docetaxel -capecitabine (TX) q3w for up to 6 cycles, until disease progression or unacceptable toxicity. The primary end point was objective response rate (ORR) and the secondary end points included progression-free survival (PFS) and overall survival (OS). In total 53 patients were enrolled.

RESULTS

The median follow-up was 24 months. ORR was higher in the TP group than in the TX group (63.0% versus 15.4%, P = 0.001). PFS was more than doubled (10.9 months versus 4.8 months, P < 0.001) and median OS was also greatly improved (32.8 months versus 21.5 months, P = 0.027). Toxic effects were not different except G3/4 vomiting and G2/3 hand-foot syndrome.

CONCLUSIONS

This study suggested that cisplatin-based chemotherapy was superior to capecitabine-based regimen in the first-line treatment of mTNBC, as measured by ORR, PFS and OS. Further large-scale study should be warranted. These results are not sufficient to change clinical practice.

High junction and twin boundary densities in driven dynamical systems

A novel mechanism for the generation of device materials with very high domain boundary densities is described: we shear the sample in a computer experiment and achieve higher twin densities than in rapid quench. These domain patterns are very stable. Elastically soft materials (image with 6.4$ \times $10(5) atoms) has greater twin densities than hard materials, even for nano-crystals.

Isolation and characterization of microsatellite markers in Chinese herb of Dendrobium loddigesii

As an invaluable herb, Dendrobium loddigesii is widely used in Chinese medicinal field. In order to develop a convenient and efficient identification method and investigate the genetic diversity and structure of this species, twelve microsatellite loci were isolated from two microsatellite-enriched libraries. Twenty-six individuals from Baise population were analysed. The observed and expected heterozygosities ranged from 0.174 to 0.617 and from 0.182 to 0.608, respectively. These microsatellite loci characterized from D. loddigesii will contribute to research on the individual authentication, population structure, genetic diversity and conservation of this species and its similar species.

Human papillomavirus infections in women with clinical gynaecological diseases in southwest China

The aim of this study was to determine the prevalence of human papillomavirus (HPV) infections in women with different gynaecological diseases (GDs) and ages in southwest China. With the assay of reverse dot blot, a total of 5544 cervical samples, including 1008 normal and 4536 abnormal specimens from women with GDs, were assayed for HPV detection. For the normal group, 20.2% (204/1008) tested positive for HPV, of which 40.2% (82/204) were high-risk (HR-HPV) genotypes. In the 4536 abnormal samples, 1569 women (34.6%) tested positive for HPV: 73.5% (1153/1569) had a single infection, 17.7% (277/1569) dual infection and 8.8% (138/1569) multiple HPV infection. Of 1569 HPV-positive specimens, 58.7% (921/1569) were infected with only HR-HPV genotypes. Significant differences in HPV infections were found among women of different ages (P < 0.01), number of pregnancies (P < 0.01), GDs (P < 0.01) and age at first sex (P < 0.01). In the present study, we found a high prevalence of HPV infection in women with GDs in southwest China. In addition to HPV types 16 and 18, a significant proportion of other HR-HPV genotypes were detected in this population.

cDNA, genomic sequence cloning and overexpression of giant panda (Ailuropoda melanoleuca) mitochondrial ATP synthase ATP5G1

The ATP5G1 gene is one of the three genes that encode mitochondrial ATP synthase subunit c of the proton channel. We cloned the cDNA and determined the genomic sequence of the ATP5G1 gene from the giant panda (Ailuropoda melanoleuca) using RT-PCR technology and touchdown-PCR, respectively. The cloned cDNA fragment contains an open reading frame of 411 bp encoding 136 amino acids; the length of the genomic sequence is of 1838 bp, containing three exons and two introns. Alignment analysis revealed that the nucleotide sequence and the deduced protein sequence are highly conserved compared to Homo sapiens, Mus musculus, Rattus norvegicus, Bos taurus, and Sus scrofa. The homologies for nucleotide sequences of the giant panda ATP5G1 to those of these species are 93.92, 92.21, 92.46, 93.67, and 92.46%, respectively, and the homologies for amino acid sequences are 90.44, 95.59, 93.38, 94.12, and 91.91%, respectively. Topology prediction showed that there is one protein kinase C phosphorylation site, one casein kinase II phosphorylation site, five N-myristoylation sites, and one ATP synthase c subunit signature in the ATP5G1 protein of the giant panda. The cDNA of ATP5G1 was transfected into Escherichia coli, and the ATP5G1 fused with the N-terminally GST-tagged protein gave rise to accumulation of an expected 40-kDa polypeptide, which had the characteristics of the predicted protein.

Mechanisms and prevention of thermal injury from gamma radiosurgery headframes during 3T MR imaging

Magnetic resonance imaging (MRI) is regularly used for stereotactic imaging of Gamma Knife (GK) radiosurgery patients for GK treatment planning. MRI-induced thermal injuries have occurred and been reported for GK patients with attached metallic headframes. Depending on the specific MR imaging and headframe conditions, a skin injury from MRI-induced heating can potentially occur where the four headframe screws contact the skin surface of the patient's head. Higher MR field strength has a greater heating potential. Two primary heating mechanisms, electromagnetic induction and the antenna effect, are possible. In this study, MRI-induced heating from a 3T clinical MRI scanner was investigated for stereotactic headframes used in gamma radiosurgery and neurosurgery. Using melons as head phantoms, optical thermometers were used to characterize the temperature profile at various points of the melon headframe composite as a function of two 3T MR pulse sequence protocols. Different combinations of GK radiosurgery headframe post and screw designs were tested to determine best and worst combinations for MRI-induced heating. Temperature increases were measured for all pulse sequences tested, indicating that the potential exists for MRI-induced skin heating and burns at the headframe attachment site. This heating originates with electromagnetic induction caused by the RF fields inducing current in a loop formed by the headframe, mounting screws, and the region of the patient's head located between any of the two screws. This induced current is then resistively dissipated, with the regions of highest resistance, located at the headframe screw-patient head interface, experiencing the most heating. Significant heating can be prevented by replacing the metallic threads holding the screw with electrically insulated nuts, which is the heating prevention and patient safety recommendation of the GK manufacturer. Our results confirm that the manufacturer's recommendation to use insulating nuts reduces the induced currents in the headframe nearly to zero, effectively preventing heating and minimizing the likelihood of thermal injury.

A meta-analysis of lymph node metastasis rate for patients with thoracic oesophageal cancer and its implication in delineation of clinical target volume for radiation therapy

OBJECTIVES

The objective of this study was to pool the lymph node metastasis rate (LNMR) in patients with thoracic oesophageal cancer (TOC) and to determine which node level should be included when undergoing radiation therapy.

METHODS

Qualified studies were identified on Medline, Embase, CBM and the Cochrane Library through to the end of April 2011. Pooled estimates of LNMR were obtained through a random-effect model. Possible effect modifiers which might lead to the statistical heterogeneity were identified through meta-regression, and further subgroup analyses of factors influencing LNMR were performed.

RESULTS

45 observational studies with a total of 18 415 patients were included in the meta-analysis. The pooled estimates of LNMR in upper, middle and lower TOC were 30.7%, 16.8% and 11.0% cervical, 42.0%, 21.1% and 10.5% upper mediastinal, 12.9%, 28.1% and 19.6% middle mediastinal, 2.6%, 7.8% and 23.0% lower mediastinal, and 9%, 21.4% and 39.9% abdominal, respectively. Lymph node metastasis most frequently happened to paratracheal, paraoesophageal, perigastric 106recR and station 7. The most obvious difference (≥15%) of LNMR between two-field and three-field lymphatic dissection occurred in cervical, paratracheal, 106recR and 108.

CONCLUSIONS

Through the meta-analysis, more useful information was obtained about clinical target volume (CTV) delineation of TOC patients treated with radiotherapy. However, our study is predominantly a description of squamous carcinoma and the results may not be valid for adenocarcinoma.

SU-E-T-202: Comprehensive Quality Assurance Procedures for Uniform Scanning Proton Therapy Machines

PURPOSE

Quality assurance (QA) is essential in safe and accurate delivery of radiation therapy. However, QA in proton therapy is challenging due to complicated and often facility-specific beam delivery systems and limited beam time for QA. The purpose of this study is to develop an efficient and comprehensive QA procedure for a multi-room proton therapy center using uniform scanning beams.

METHODS

Our proton therapy center is comprised of a 230 MeV cyclotron, one fixed beam room, two inclined beam rooms, and one gantry room. Uniform scanning is employed exclusively in all treatment rooms. A rfDaily QA3 (Sun Nuclear Inc., Melbourne, Florida) together with home-made devices is used for daily QA. Parallel plane chambers, a multi-layer ionization chamber array (Zebra, IBA dosimetry, Schwarzenbruck, German), and an IC profiler (Sun Nuclear Inc., Melbourne, Florida) are used to QA the characteristics of the uniform scanning beams, including output, range, modulation width, flatness, symmetry, and penumbra, for both monthly and annual QA. QA procedures and acceptance criteria were developed, taking into account the likelihood and potential risk of failure, as well as the available equipment, personnel and other resources.

RESULTS

QA procedures and tolerances were developed for daily, monthly and annual QA at our proton therapy center. Daily QA is performed by radiation therapists, and can be completed within 30 minutes for all rooms. Monthly QA and annual QA are performed by physicists, taking about 4 hours and a weekend respectively. Trend analysis was performed for various machine characteristics, such as machine output, range, flatness, and symmetry.

CONCLUSION

QA standards are desired in Radiation Oncology, but not many standards are developed and available for proton therapy. In the mean time, facility-specific QA procedures should be developed based on the equipment failure modes and available resources.

SU-E-T-127: Feasibility Study for Using a 2D Array Detector for All Beam Measurements in Monthly Quality Assurance Procedure for a Uniform Scanning Proton Therapy System

PURPOSE

To develop a more efficient monthly quality assurance (QA) process by utilizing one detector with multiple setups instead of multiple detectors with multiple setups.

METHOD

The Sun Nuclear IC Profiler was used to measure machine output, transverse profiles, and depth-dose profiles. The IC Profiler contains 251 ionization chambers aligned in the X, Y, and diagonal axes, and was designed to measure machine output and transverse profiles. In order to measure depth-doses, a Lucite compensator with an angled surface was fabricated. To test the capability of the detector, a proton beam of 10.5 cm range in water was used. The distal edge coincided with the overall water equivalent depth upstream of the detector on central axis. The measurement was repeated with an additional 1.0 mm of solid water placed in front of the detector. The measured profiles from both measurements were compared to quantify the IC Profiler response for a small range change.

RESULTS

The IC Profiler performs within vendor specification for measuring machine output and transverse profiles. When measuring depth-doses with an angled compensator, the IC profiler measures a change in profile along central axis of 17.0% for a 1.0mm range change. Based on overall reproducibility of the beam delivery system, the IC profiler is capable of detecting 0.3 mm range shift. Therefore, the sensivity of the IC profiler response is suffficient to detect sub millimeter changes in delivered range.

CONCLUSION

The Sun Nuclear IC Profiler is capable of measuring machine output, transverse profiles, and depth-dose profile constancy with a high degree of accuracy and precision. Using a single detector for all beam measurements increases the overall QA efficiency by reducing multiple detector overhead while not sacrificing the accuracy and precision of the measurements.

Neurobehavioral abnormalities in a brain-specific NADPH-cytochrome P450 reductase knockout mouse model

The aim of the present study was to test a new hypothesis that brain cytochrome P450 reductase (CPR) and CPR-dependent enzymes play important roles in behavioral performance. A mouse model with brain neuron-specific deletion of the Cpr gene (brain-Cpr-null) was recently generated. Brain-Cpr-null mice and wild-type (WT) littermates were compared in a variety of behavioral assays. Notable differences were found in the exploratory behavior assay: for both males and females, activity in the center of the chamber was significantly higher for brain-Cpr-null than for WT mice on days 2 and 3 of the assay, although no significant difference was found between the two groups in anxiety-like behavior in the elevated zero maze. Furthermore, in the fear-conditioning assay, brain-Cpr-null mice exhibited significantly less activity suppression than did WT controls. This deficit in activity suppression was not accompanied by any difference between WT and brain-Cpr-null mice in nociceptive responses to foot shocks. Abnormal activity suppression was also observed in both male and female brain-Cpr-null mice during the contextual memory test. However, in the Morris water maze assay, the brain-Cpr-null and WT mice were indistinguishable, indicating normal spatial memory in the mutant mice. These data collectively indicate a novel role of the Cpr gene in fear conditioning and memory.

Primary malignant lymphoma of the brain: analysis of MMAC1 (PTEN) tumor suppressor gene

With the use of RT-PCR (reverse transcriptase-polymerase chain reaction), Northern blot analysis, and Western blot analysis, seven primary brain lymphomas were examined for the state of the MMACI tumor suppressor gene. Nucleotide analysis of RT-PCR clones revealed no abnormality in the MMAC1 coding sequence in each case. Although Northern blot revealed variation among cases in the signal intensities for MMAC1 mRNA, Western blot revealed a distinct MMAC1 protein band in all cases, suggesting that the actual MMAC1 expressions were similar. In Western blot analysis of phosphorylated Akt (p-Akt), which is regulated positively by PI3K (phosphoinositide-3 kinase) and negatively by MMAC1, all the lymphomas revealed an Akt band but not a p-Akt band, suggesting that the MMAC1 phosphatase activity was maintained in each case. These findings suggest that the MMAC1 gene is normal in its coding sequence, gene expression, and phosphatase activity in the lymphomas. Thus, unlike the p16 and p15 tumor suppressor genes, which are frequently deleted and inactivated in brain lymphoma and represent a striking contrast to systemic lymphoma, MMAC1 may not play an important role in carcinogenesis in this tumor, as in the systemic counterpart.

A solid phase extraction-liquid chromatographic-tandem mass spectrometry method for determination of concentrations of GDC-0941, a small molecule class I phosphatidylinositide 3-kinase inhibitor, to support clinical development

A solid phase extraction (SPE) liquid chromatographic-tandem mass spectrometry (LC-MS/MS) method for the determination of GDC-0941 concentrations in human plasma has been developed and validated to support clinical development. An Oasis MCX 10mg 96-well SPE plate was used to extract plasma samples (50 μL) and the resulting extracts were analyzed using reverse-phase chromatography and mass spectrometer coupled with a turbo-ionspray interface. The method was validated over the calibration curve range 0.500-500 ng/mL with linear regression and 1/x(2) weighting. Within-run relative standard deviation (%RSD) ranged from 1.5 to 11.5%, while the between-run %RSD varied from 0.0 to 4.4%. The accuracy ranged from 96.0% to 110.0% of nominal for within-run and 98.0% to 108.0% of nominal for between-run at all concentrations including the LLOQ quality control at 0.500 ng/mL. Extraction recovery of GDC-0941 was between 79.0% and 86.2%. Stability of GDC-0941 was established in human plasma for 602 days at -70 °C and 598 days at -20°C, respectively, and established in reconstituted sample extracts for 167 h when stored at room temperature. Internal standard normalized matrix factor was 1.1, demonstrating that the use of the stable-labeled internal standard GDC-0941-d(8) effectively compensated observed matrix effect and resulting in no adverse impact on the quality of the data produced. This assay was used for the determination of GDC-0941 human plasma concentrations over a sufficient time period to determine pharmacokinetic parameters at relevant clinical doses.

Accuracy of genomic prediction using low-density marker panels

Genomic selection has been widely implemented in national and international genetic evaluation in the dairy cattle industry, because of its potential advantages over traditional selection methods and the availability of commercial high-density (HD) single nucleotide polymorphism (SNP) panels. However, this method may not be cost-effective for cow selection and for other livestock species, because the cost of HD SNP panels is still relatively high. One possible solution that can enable other species to benefit from this promising method is genomic selection with low-density (LD) SNP panels. In this simulation study, LD SNP panels designed with different strategies and different SNP densities were compared. The effects of number of quantitative trait loci, heritability, and effective population size were evaluated in the framework of genomic selection with LD SNP panels. Methodologies of Bayesian variable selection; BLUP with a trait-specific, marker-derived relationship matrix; and BLUP with a realized relationship matrix were employed to predict genomic estimated breeding values with both HD and LD SNP panels. Up to 95% of accuracy obtained by using an HD panel can be obtained by using only a small proportion of markers. The LD panel with markers selected on the basis of their effects always performs better than the LD panel with evenly spaced markers. Both the genetic architecture of the trait and the effective population size have a significant effect on the performance of the LD panels. We concluded that, to implement genomic selection with LD panels, a training population of sufficient size and genotyped with an HD panel is necessary. The trade-off between the LD panels with evenly spaced markers and selected markers must be considered, which depends on the number of target traits in a breeding program and the genetic architecture of these traits. Genomic selection with LD panels could be feasible and cost-effective, though before implementation, a further detailed genetic and economic analysis is recommended.