Protein networks as logic functions in development and cancer

Many biological and clinical outcomes are based not on single proteins, but on modules of proteins embedded in protein networks. A fundamental question is how the proteins within each module contribute to the overall module activity. Here, we study the modules underlying three representative biological programs related to tissue development, breast cancer metastasis, or progression of brain cancer, respectively. For each case we apply a new method, called Network-Guided Forests, to identify predictive modules together with logic functions which tie the activity of each module to the activity of its component genes. The resulting modules implement a diverse repertoire of decision logic which cannot be captured using the simple approximations suggested in previous work such as gene summation or subtraction. We show that in cancer, certain combinations of oncogenes and tumor suppressors exert competing forces on the system, suggesting that medical genetics should move beyond cataloguing individual cancer genes to cataloguing their combinatorial logic.     

Prevalence of the most frequent BRCA1 mutations in Polish population

The purpose of our study was to establish the frequency and distribution of the four most common BRCA1 mutations in Polish general population and in a series of breast cancer patients. Analysis of the population frequency of 5382insC (c.5266dupC), 300T >G (p.181T >G), 185delAG (c.68_69delAG) and 3819del5 (c.3700_3704del5) mutations of the BRCA1 gene were performed on a group of respectively 16,849, 13,462, 12,485 and 3923 anonymous samples collected at birth in seven Polish provinces. The patient group consisted of 1845 consecutive female breast cancer cases. The most frequent BRCA1 mutation in the general population was 5382insC found in 29 out of 16,849 samples (0.17%). 300T >G and 3819del5 mutations were found in respectively 11 of 13,462 (0.08%) and four of 3923 (0.1%) samples. The population prevalence for combined Polish founder 5382insC and 300T >G mutations was 0.25% (1/400). The frequencies of 5382insC and 300T >G carriers among consecutive breast cancer cases were, respectively, 1.9% (35/1845) and 1.2% (18/1486). Comparing these data with the population frequency, we calculated the relative risk of breast cancer for 5382insC mutation at OR = 17 and for 300T >G mutation at OR = 26. Our results, based on large population studies, show high frequencies of founder 5382insC and 300T >G BRCA1 mutations in Polish general population. Carriage of one of these mutations is connected with a very high relative risk of breast cancer.     

Anatomy-corresponding method of IMRT verification

Background

During a proper execution of dMLC plans, there occurs an undesired but frequent effect of the dose locally accumulated by tissue being significantly different than expected. The conventional dosimetric QA procedures give only a partial picture of the quality of IMRT treatment, because their solely quantitative outcomes usually correspond more to the total area of the detector than the actually irradiated volume.

Aim

The aim of this investigation was to develop a procedure of dynamic plans verification which would be able to visualize the potential anomalies of dose distribution and specify which tissue they exactly refer to.

Materials & methods

The paper presents a method discovered and clinically examined in our department. It is based on a Gamma Evaluation concept and allows accurate localization of deviations between predicted and acquired dose distributions, which were registered by portal as well as film dosimetry. All the calculations were performed on the self-made software GammaEval, the γ-images (2-dimensional distribution of γ-values) and γ-histograms were created as quantitative outcomes of verification.

Results

Over 150 maps of dose distribution have been analyzed and the cross-examination of the gamma images with DRRs was performed.

Conclusions

It seems, that the complex monitoring of treatment would be possible owing to the images obtained as a cross-examination of γ-images and corresponding DRRs.     

Five years of experience teaching pathology to dental students using the WebMicroscope

Background

We describe development and evaluation of the user-friendly web based virtual microscopy - WebMicroscope for teaching and learning dental students basic and oral pathology. Traditional students microscopes were replaced by computer workstations.

Methods

The transition of the basic and oral pathology courses from light to virtual microscopy has been completed gradually over a five-year period. A pilot study was conducted in academic year 2005/2006 to estimate the feasibility of integrating virtual microscopy into a traditional light microscopy-based pathology course. The entire training set of glass slides was subsequently converted to virtual slides and placed on the WebMicroscope server. Giving access to fully digitized slides on the web with a browser and a viewer plug-in, the computer has become a perfect companion of the student.

Results

The study material consists now of over 400 fully digitized slides which covering 15 entities in basic and systemic pathology and 15 entities in oral pathology. Digitized slides are linked with still macro- and microscopic images, organized with clinical information into virtual cases and supplemented with text files, syllabus, PowerPoint presentations and animations on the web, serving additionally as material for individual studies. After their examinations, the students rated the use of the software, quality of the images, the ease of handling the images, and the effective use of virtual slides during the laboratory practicals. Responses were evaluated on a standardized scale. Because of the positive opinions and support from the students, the satisfaction surveys had shown a progressive improvement over the past 5 years. The WebMicroscope as a didactic tool for laboratory practicals was rated over 8 on a 1-10 scale for basic and systemic pathology and 9/10 for oral pathology especially as various students’ suggestions were implemented. Overall, the quality of the images was rated as very good.

Conclusions

An overwhelming majority of our students regarded a possibility of using virtual slides at their convenience as highly desirable. Our students and faculty consider the use of the virtual microscope for the study of basic as well as oral pathology as a significant improvement over the light microscope.

     

I – V characteristics and electrical conductivity of synthetic melanin

I – V characteristics for synthetic melanin were investigated at – 10 and 25°C. It was found that the Ohm law is valid for low voltages whereas the Child law holds for higher ones. Furthermore, the steady state electrical conductivity was estimated. The change of activation energy from 0.76 eV for low temperatures to 1.58 eV was noticeable near 0°C.