Gene expression in histologically normal epithelium from breast cancer patients and from cancer-free prophylactic mastectomy patients shares a similar profile

INTRODUCTION

We hypothesised that gene expression in histologically normal (HN) epithelium (NlEpi) would differ between breast cancer patients and usual-risk controls undergoing reduction mammoplasty (RM), and that gene expression in NlEpi from cancer-free prophylactic mastectomy (PM) samples from high-risk women would resemble HN gene expression.

METHODS

We analysed gene expression in 73 NlEpi samples microdissected from frozen tissue. In 42 samples, we used microarrays to compare gene expression between 18 RM patients and 18 age-matched HN (9 oestrogen receptor (ER)+, 9 ER-) and 6 PM patients. Data were analysed using a Bayesian approach (BADGE), and validated with quantitative real-time PCR (qPCR) in 31 independent NlEpi samples from 8 RM, 17 HN, and 6 PM patients.

RESULTS

A total of 98 probe sets (86 genes) were differentially expressed between RM and HN samples. Performing hierarchical analysis with these 98 probe sets, PM and HN samples clustered together, away from RM samples. qPCR validation of independent samples was high (84%) and uniform in RM compared with HN patients, and lower (58%), but more heterogeneous, in RM compared with PM patients. The 86 genes were implicated in many processes including transcription and the MAPK pathway.

CONCLUSION

Gene expression differs between the NlEpi of breast cancer cases and controls. The profile of cancer cases can be discerned in high-risk NlEpi from cancer-free breasts. This suggests that the profile is not an effect of the tumour, but may mark increased risk and reveal the earliest genomic changes of breast cancer.

HIV risk behaviour knowledge, substance use and unprotected sex in men who have sex with men in Tallinn, Estonia

This study examines HIV risk behaviour knowledge, substance use and unprotected sex in a sample of 79 men who have sex with men (MSM) in Tallinn, Estonia. Median age of the study population was 30 years (range 18-62 years); 35 were bisexual; 56 answered correctly to at least 10 out of 13 questions about HIV risk behaviours; 23 consumed more than seven alcoholic drinks in the week before the survey; nearly half (n=34) of the participants reported some illicit drug use in the past 12 months; 40 did not use a condom regularly in the 12 months preceding the survey, and 41 did not use a condom during their last sexual intercourse. Alcohol consumption in the week before the survey was negatively associated with condom use during last intercourse (RR 0.48; 95% CI 0.41-0.56). Use of illicit drugs varied significantly by ethnicity (p-value = 0.02). Multivariable analysis showed that higher consumption of alcohol in the week before the survey could be predicted by education, age group and sexual orientation. In conclusion, socio-demographic factors such as education, age, ethnicity and sexual orientation may affect HIV risk behaviour knowledge, sexual behavior and substance use among MSM in Estonia, and need to be taken into consideration for targeted HIV prevention.

Raman chemical imaging of explosive-contaminated fingerprints

Raman chemical imaging (RCI) has been used to detect and identify explosives in contaminated fingerprints. Bright-field imaging is used to identify regions of interest within a fingerprint, which can then be examined to determine their chemical composition using RCI and fluorescence imaging. Results are presented where explosives in contaminated fingerprints are identified and their spatial distributions are obtained. Identification of explosives is obtained using Pearson's cosine cross-correlation technique using the characteristic region (500-1850 cm(-1)) of the spectrum. This study shows the ability to identify explosives nondestructively so that the fingerprint remains intact for further biometric analysis. Prospects for forensic examination of contaminated fingerprints are discussed.

Wavelength and intensity dependence of short pulse laser xenon double ionization between 500 and 2300 nm

The wavelength and intensity dependence of xenon ionization with 50 fs laser pulses has been studied using time-of-flight mass spectrometry. We compare the ion yield distribution of singly and doubly charged xenon with the Perelomov-Popov-Terent'ev (PPT) theory, Perelomov, Popov, and Terent'ev, Zh. Eksp. Teor. Fiz. 50, 1393 (1966) [Sov. Phys. JETP 23, 924 (1966)], in the regime between 500 and 2300 nm. The intensity dependence for each wavelength is measured in a range between 1 x 10(13) and 1 x 10(15) W/cm2. The Xe+-ion signal is in good agreement with the PPT theory at all used wavelengths. In addition we demonstrate that ionic 5s5p6 2S state is excited by an electron impact excitation process and contributes to the nonsequential double ionization process.

Characterization of the stuffed framework structures BaAlGaO4 and BaFeGaO4

The crystal structures of the compounds BaMGaO4 (M = Al, Fe) have been investigated using conventional single-crystal X-ray diffraction data for M = Fe and with synchrotron radiation data for M = Al. BaAlGaO4 (space group P6322, a = 5.2788(4) Å and c = 8.7835(7) Å, V = 211.97(4) Å3, Z = 2, D calc. = 4.67 g cm–3, wR2 = 0.089 for 242 independent reflections with I > 2σ(I)) is isostructural with BaAl2O4-I. Main building units are layers of six-membered rings of (Al,Ga)O4-tetrahedra perpendicular to [001]. The sequence of directedness of the tetrahedral apices in all single six membered rings (S6R) is UDUDUD (U: up, D: down). Stacking of layers parallel to c results in a three-dimensional framework containing tunnels, where the Ba atoms are located. They are coordinated by nine oxygen ligands in form of distorted tricapped trigonal antiprisms. BaFeGaO4 also belongs to the hexagonal crystal system (space group P63, a = 10.8377(6) Å and c = 8.6865(6) Å, V = 883.59(9) Å3, Z = 8, D calc. = 4.92 g cm–3, wR2 = 0.099 for 1042 independent observed reflections). The crystal showed twinning by merohedry which was accounted for in the refinement calculations. Within a single tetrahedral layer of the framework structure two different types of ditrigonal-shaped rings are distinguishable: one fourth of the rings have an UDUDUD topology, whereas the sequence of the remaining rings is UUUDDD. The Fe3+- and Ga3+-cations show an ordered distribution among the four symmetrically independent T-sites: two positions contain either Fe or Ga, whereas on the remaining two sites there is a definite preference for one of the two cation species. The Ba atoms in the cavities of the framework are coordinated by eight to nine oxygen neighbors. The observed twinning in BaFeGaO4 can be attributed to the existence of pseudo twofold axis within the tetrahedral layers, running parallel [100] and the corresponding symmetrically equivalent directions.

Antibacterial applications of silver nanoparticles synthesized by aqueous extract of Azadirachta indica (Neem) leaves

Silver nanoparticles are known to have bactericidal effects. A new generation of dressings incorporating antimicrobial agents like silver nanoparticles is being formulated to reduce or prevent infections. The particles can be incorporated in materials and cloth rendering them sterile. Recently, it was found that aqueous silver ions can be reduced by aqueous extract of plant parts to generate extremely stable silver nanoparticles in water. Apart from being environmentally friendly process, use of Neem leaves extract might add synergistic antibacterial effect of Neem leaves to the biosynthesized nanoparticles. With this hypothesis the biosynthetic production of silver nanoparticles by aqueous extract of Neem leaves and its bactericidal effect in cotton cloth against E. Coli were studied in this work. Silver nanoparticles were synthesized by short-term (1 day) and long-term (21 days) interaction of Neem extract (20% w/v) and 0.01 M AgNO3 solution in 1:4 mixing ratio. The synthesized particles were characterized by UV visible spectroscopy, transmission electron microscopy, and incorporated into cotton disks by (i) centrifuging the disks with liquid broth containing nanoparticles, (ii) in-situ coating process during synthesis, and (iii) coating with dried and purified nanoparticles. The antibacterial property of the nanoparticles coated cotton disks was studied by disk diffusion method. The effect of consecutive washing of the coated disks with distilled water on antibacterial property was also investigated. This work demonstrates the possible use of biologically synthesized silver nanoparticles by its incorporation in cloths leading them to sterilization.

Abstract B42: Polymorphism of CYP3A5 gene in Indian chronic myeloid leukemia patients

B42

Objective

Chronic myeloid leukemia (CML) is a clonal hematopoetic stem cell disorder characterized by the Philadelphia chromosome. Individuals vary in their ability to metabolize carcinogens and hence to detoxify chemicals, leading to different risk in getting cancer. The human CYP3A5 is a major P450 enzyme in the liver and represents 50% of the total hepatic CYP3A content in people expressing CYP3A5. Therefore, it is suggested that the CYP3A5 is an important genetic contributor to inter-individual differences in CYP3A-dependent drug metabolism. Owing to the importance of CYP3A5 genetic polymorphism as risk factor in various cancers, the study was aimed to detect the prevalence of genetic polymorphism of CYP3A5*3 gene in North Indian CML patients and racially matched controls. Further, it will help to determine the association of these allelic variants if any, as risk factor to develop CML.

Materials and Methods

Human blood was collected from 50 CML patients and 65 healthy individuals which were age and sex matched. DNA isolation was carried out by standard proteinase K and phenol chloroform method. The prevalence of CYP3A5*3 genotype was examined by PCR-RFLP method. PCR products were separated using 2% agarose gel.

In the analysis of the CYP3A5*3 polymorphism, a fragment of 155 base pairs (bp) was amplified by PCR, which was followed by restriction digestion by Dde I. The 155 bp product from the CYP3A5*1 allele was digested into 121 and 34 bp fragments, whereas the PCR product of the CYP3A5*3 was cleaved to 97, 34, and 24 bp fragments.

Results

The frequencies reported in controls were, 7/65 (10.76%) for homozygous CYP3A5*1/*1 , 28/65 (43.07%) for heterozygous CYP3A5*1/*3 and was 30/65 (46.15%) for homozygous CYP3A5*3/*3 respectively. The frequencies reported in cases were 5/50 (10%), 21/50 (42%) and 24/50 (48%) respectively. There was no significant difference between the frequencies of wild (*1/*1), heterozygous (*1/*3) & mutant allele (*3/*3), (control vs cases).

However, when these alleles where compared individually within a class, a higher frequency of

heterozygous & mutant allele, was reported as compared to the wild type, both in the cases and in controls. The combined frequency of heterozygous & mutant allele vs wild in controls was 89.22% and 10.76% respectively, and that in cases being 90% and 10% respectively.

Discussion

It is concluded that there is no association of this polymorphism with the risk of Chronic Myeloid Leukemia. However, due to the variable frequencies of xenobiotic metabolizing polymorphic alleles in different populations, further studies with different populations are required in order to investigate the association of polymorphic variability and its possible role in susceptibility to CML.

Citation Information: Cancer Prev Res 2008;1(7 Suppl):B42.

Observation of the suppression of the flux of cosmic rays above 4 x 10 (19) eV

The energy spectrum of cosmic rays above 2.5 x 10;{18} eV, derived from 20,000 events recorded at the Pierre Auger Observatory, is described. The spectral index gamma of the particle flux, J proportional, variantE;{-gamma}, at energies between 4 x 10;{18} eV and 4 x 10;{19} eV is 2.69+/-0.02(stat)+/-0.06(syst), steepening to 4.2+/-0.4(stat)+/-0.06(syst) at higher energies. The hypothesis of a single power law is rejected with a significance greater than 6 standard deviations. The data are consistent with the prediction by Greisen and by Zatsepin and Kuz'min.

KeV ion-induced effective surface modifications on InP

In the present study, we have analyzed the changes in surface morphology leading to formation of periodic structures known as ripples which arise due to an interplay between sputtering and surface diffusion. The 1.5 keV Ar atoms with a flux of 14.8 mA/cm2 are used in the present study. The InP(100) samples were bombarded at an incidence angle of 45 degrees to the normal at a base pressure of 1 x 10(-6) Torr at room temperature with fluences varying from 4 x 10(16) to 3.2 x 10(17) atoms/cm2. The rippled InP(100) surface was characterized with AFM. An increase in the ripple wavelengths, from 60 nm to 150 nm with the fluence has been observed. The width of the ripples varies from 38 nm to 128 nm and ripple amplitude varies from 0.8 nm to 16 nm with increasing fluence. One can control the dimension of the ripples in nano scale by controlling the fluence. Scaling studies have been performed to understand the mechanism responsible for such kind of surface evolution. The roughness parameter, alpha was found to be between 0.65 to 0.75 and the growth parameter, beta, as 1.14 +/- 0.12. The XPS characterization has also been employed to study the changes in the behavior of the InP with varying fluence.

Upper limit on the diffuse flux of ultrahigh energy tau neutrinos from the Pierre Auger Observatory

The surface detector array of the Pierre Auger Observatory is sensitive to Earth-skimming tau neutrinos that interact in Earth's crust. Tau leptons from nu(tau) charged-current interactions can emerge and decay in the atmosphere to produce a nearly horizontal shower with a significant electromagnetic component. The data collected between 1 January 2004 and 31 August 2007 are used to place an upper limit on the diffuse flux of nu(tau) at EeV energies. Assuming an E(nu)(-2) differential energy spectrum the limit set at 90% C.L. is E(nu)(2)dN(nu)(tau)/dE(nu)<1.3 x 10(-7) GeV cm(-2) s(-1) sr(-1) in the energy range 2 x 10(17) eV< E(nu)< 2 x 10(19) eV.

Synthesis of nanoscale copper nitride thin film and modification of the surface under high electronic excitation

Nanoscale (approximately 90 nm) Copper nitride (Cu3N) films are deposited on borosilicate glass and Si substrates by RF sputtering technique in the reactive environment of nitrogen gas. These films are irradiated with 200 MeV Au15+ ions from Pelletron accelerator in order to modify the surface by high electronic energy deposition of heavy ions. Due to irradiation (i) at incident ion fluence of 1 x 10(12) ions/cm2 enhancement of grains, (ii) at 5 x 10912) ions/cm2 mass transport on the films surface, (iii) at 2 x 10(13) ions/cm2 line-like features on Cu3N/glass and nanometallic structures on Cu3N/Si surface are observed. The surface morphology is examined by atomic force microscope (AFM). All results are explained on the basis of a thermal spike model of ion-solid interaction.

Setup for in situ x-ray diffraction study of swift heavy ion irradiated materials

An in situ x-ray diffraction (XRD) setup is designed and installed in the materials science beam line of the Pelletron accelerator at the Inter-University Accelerator Centre for in situ studies of phase change in swift heavy ion irradiated materials. A high vacuum chamber with suitable windows for incident and diffracted X-rays is integrated with the goniometer and the beamline. Indigenously made liquid nitrogen (LN2) temperature sample cooling unit is installed. The snapshots of growth of particles with fluence of 90 MeV Ni ions were recorded using in situ XRD experiment, illustrating the potential of this in situ facility. A thin film of C60 was used to test the sample cooling unit. It shows that the phase of the C60 film transforms from a cubic lattice (at room temperature) to a fcc lattice at around T=255 K.

Nanocrystalline SnO2 formation using energetic ion beam

Nanocrystalline tin oxide (SnO2) thin films grown by RF magnetron sputtering technique were characterized by UV-Visible absorption spectroscopy and Photoluminescence spectroscopy. From atomic force microscopic (AFM) and Glancing angle X-ray diffraction (GAXRD) measurements, the radius of grains was found to be approximately 6+/-2 nm. The thin films were bombarded with 250 keV Xe2+ ion beam to observe the stability of nanophases against radiation. For ion bombarded films, optical absorption band edge is shifted towards red region. Atomic force microscopy studies show that the radius of the grains was increased to approximately 8 +/- 1 nm and the grains were nearly uniform in size. The size of the grains has been reduced after ion bombardment in the case of films grown on Si. During this process, defects such as vacancies, voids were generated in the films as well as in the substrates. Ion bombardment induces local temperature increase of thin films causing melting of films. Ion beam induced defects enhances the diffusion of atoms leading to uniformity in size of grains. The role of matrix on ion beam induced grain growth is discussed.

Magnetic force microscopy of nano-size magnetic domain ordering in heavy ion irradiated fullerene films

In the present work, magnetic force microscopy is employed to investigate the magnetic ordering in ion irradiated fullerene films. It is observed that magnetic domain size is approximately 100-200 nm and magnetic signal is stronger at the domain boundaries. Magnetic signal arise in irradiated films is confirmed by magnetic measurements using a superconducting quantum interference device which increases with the ion fluence. The induced magnetism is possibly due to structural defects in the amorphous carbon phase formed by ion irradiation.