A study of patient-specific prognosis of ovarian cancer

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Tissue-specific selection of reference genes is required for expression studies in the mouse model of maternal protein undernutrition

Suboptimal maternal nutrition during gestation results in the establishment of long-term phenotypic changes and an increased disease risk in the offspring. To elucidate how such environmental sensitivity results in physiological outcomes, the molecular characterisation of these offspring has become the focus of many studies. However, the likely modification of key cellular processes such as metabolism in response to maternal undernutrition raises the question of whether the genes typically used as reference constants in gene expression studies are suitable controls. Using a mouse model of maternal protein undernutrition, we have investigated the stability of seven commonly used reference genes (18s, Hprt1, Pgk1, Ppib, Sdha, Tbp and Tuba1) in a variety of offspring tissues including liver, kidney, heart, retro-peritoneal and inter-scapular fat, extra-embryonic placenta and yolk sac, as well as in the preimplantation blastocyst and blastocyst-derived embryonic stem cells. We find that although the selected reference genes are all highly stable within this system, they show tissue, treatment and sex-specific variation. Furthermore, software-based selection approaches rank reference genes differently and do not always identify genes which differ between conditions. Therefore, we recommend that reference gene selection for gene expression studies should be thoroughly validated for each tissue of interest. © 2011 Elsevier Inc.

Application of Classification Methods to a Problem Related to Specific Groups of E-Government Users

This paper was partly supported by ELOST – a SSA EU project – No 27287.

Fast pyrolysis of biomass for the production of liquids

This chapter examines the fast pyrolysis of biomass to produce liquids for use as fuels and chemicals. The technology for fast pyrolysis is described and the characteristics of the main product bio-oil. This primary liquid is characterised by the many properties that affect its use. These properties have caused increasingly extensive research to be undertaken to address properties that need modification and this area is reviewed in terms of physical, catalytic and chemical upgrading. Of particular note is the increasing diversity of upgrading methods. © 2013 Woodhead Publishing Limited All rights reserved.

Residue-specific investigation of the relationship between oxidation and activity of a dual specificity phosphatase by mass spectrometry

Redox regulation of signalling pathways is critical in proliferation and apoptosis; redox imbalance can lead to pathologies such as inflammation and cancer. Vaccinia H1-related protein (VHR; DUSP3) is a dual-specificity phosphatase important in controlling MAP kinase activity during cell cycle. the active-site motif contains a cysteine that acts as a nucleophile during catalysis. We used VHR to investigate the effect of oxidation in vitro on phosphatase activity, with the aim of determining how the profile of site-specific modification related to catalytic activity. Recombinant human VHR was expressed in E. coli and purified using a GST-tag. Protein was subjected to oxidation with various concentrations of SIN-1 or tetranitromethane (TNM) as nitrating agents, or HOCl. the activity was assayed using either 3-O-methylfluorescein phosphate with fluorescence detection or PIP3 by phosphate release with malachite green. the sites of oxidation were mapped using HPLC coupled to tandem mass spectrometry on an ABSciex 5600TripleTOF following in-gel digestion. More than 25 different concentration-dependent oxidative modifications to the protein were detected, including oxidations of methionine, cysteine, histidine, lysine, proline and tyrosine, and the % oxidized peptide (versus unmodified peptide) was determined from the extracted ion chromatograms. Unsurprisingly, methionine residues were very susceptible to oxidation, but there was a significant different in the extent of their oxidation. Similarly, tyrosine residues varied greatly in their modifications: Y85 and Y138 were readily nitrated, whereas Y38, Y78 and Y101 showed little modification. Y138 must be phosphorylated for MAPK phosphatase activity, so this susceptibility impacts on signalling pathways. Di- and tri- oxidations of cysteine residues were observed, but did not correlate directly with loss of activity. Overall, the catalytic activity did not correlate with redox state of any individual residue, but the total oxidative load correlated with treatment concentration and activity. This study provides the first comprehensive analysis of oxidation modifications of VHR, and demonstrates both heterogenous oxidant effects and differential residue susceptibility in a signalling phosphatase.

Localized surface plasmon fiber device coated with carbon nanotubes for the specific detection of CO2

We explored the potential of a carbon nanotube (CNT) coating working in conjunction with a recently developed localized surface plasmon (LSP) device (based upon a nanostructured thin film consisting of of nano-wires of platinum) with ultra-high sensitivity to changes in the surrounding index. The uncoated LSP sensor’s transmission resonances exhibited a refractive index sensitivity of Δλ/Δn ~ -6200nm/RIU and ΔΙ/Δn ~5900dB/RIU, which is the highest reported spectral sensitivity of a fiber optic sensor to bulk index changes within the gas regime. The complete device provides the first demonstration of the chemically specific gas sensing capabilities of CNTs utilizing their optical characteristics. This is proven by investigating the spectral response of the sensor before and after the adhesion of CNTs to alkane gases along with carbon dioxide. The device shows a distinctive spectral response in the presence of gaseous CO2 over and above what is expected from general changes in the bulk refractive index. This fiber device yielded a limit of detection of 150ppm for CO2 at a pressure of one atmosphere. Additionally the adhered CNTs actually reduce sensitivity of the device to changes in bulk refractive index of the surrounding medium. The polarization properties of the LSP sensor resonances are also investigated and it is shown that there is a reduction in the overall azimuthal polarization after the CNTs are applied. These optical devices offer a way of exploiting optically the chemical selectivity of carbon nanotubes, thus providing the potential for real-world applications in gas sensing in many inflammable and explosive environments. © (2015) COPYRIGHT Society of Photo-Optical Instrumentation Engineers (SPIE). Downloading of the abstract is permitted for personal use only.

Cell-specific effects of Nox2 on the acute and chronic response to myocardial infarction

BACKGROUND: Increased reactive oxygen species (ROS) production is involved in the process of adverse cardiac remodeling and development of heart failure after myocardial infarction (MI). NADPH oxidase-2 (Nox2) is a major ROS source within the heart and its activity increases after MI. Furthermore, genetic deletion of Nox2 is protective against post-MI cardiac remodeling. Nox2 levels may increase both in cardiomyocytes and endothelial cells and recent studies indicate cell-specific effects of Nox2, but it is not known which of these cell types is important in post-MI remodeling. METHODS AND RESULTS: We have generated transgenic mouse models in which Nox2 expression is targeted either to cardiomyocytes (cardio-Nox2TG) or endothelial cells (endo-Nox2TG). We here studied the response of cardio-Nox2TG mice, endo-Nox2TG mice and matched wild-type littermates (WT) to MI induced by permanent left coronary artery ligation up to 4weeks. Initial infarct size assessed by magnetic resonance imaging (MRI) and cardiac dysfunction were similar among groups. Cardiomyocyte hypertrophy and interstitial fibrosis were augmented in cardio-Nox2TG compared to WT after MI and post-MI survival tended to be worse whereas endo-Nox2TG mice showed no significant difference compared to WT. CONCLUSIONS: These results indicate that cardiomyocyte rather than endothelial cell Nox2 may have the more important role in post-MI remodeling.

A kapitalizmus néhány rendszerspecifikus vonása (Some system-specific features of capitalism)

A szerző korábban a szocialista rendszer és a posztszocialista átmenet elemzésére használta azt a szemléletet és módszertant, amelyet rendszerparadigmának nevezett el. A jelen tanulmány a kapitalizmus néhány általános vonásának vizsgálatára alkalmazza ezt a megközelítést. A cikk - fogalmi tisztázás után - példákat sorol fel a kapitalizmus néhány rendszerspecifikus vonására, majd kettővel részletesebben foglalkozik. Az egyik: a rendszer dinamizmusa. Az elmúlt évszázad nagy újításai, amelyek mélyrehatóan átalakították nemcsak a termelés technológiáját, hanem az emberek mindennapi életét is, a kapitalista rendszer és annak főszereplője, a vállalkozó vezette be és terjesztette el. Csak a kapitalizmusban tud kialakulni a vállalkozás és újítás mechanizmusa, az ehhez szükséges erőteljes ösztönzés és rugalmas tőkepiac. A másik példa: a kapitalista rendszer immanens tulajdonsága a munkaerőpiacon jelentkező tartós többlet, szemben a szocialista rendszerrel, amelynek kifejlett formájában tartós munkaerőhiány mutatkozik. Elméletileg és tapasztalatilag is igazolható, hogy minél dinamikusabb a kapitalista gazdaság állandó átalakulása, annál inkább keletkezik strukturális munkanélküliség. A hatékony bér elmélete megmagyarázza, miért érdeke a munkaadónak, hogy a piactisztító bérnél magasabb bért fizessen, és ezzel munkanélküliséget idézzen elő. A kapitalizmus reformálható rendszer. Ám ügyelni kell arra, hogy a részreformok között milyen a kapcsolat. Szerencsés esetben kiegészítik egymást. Ám ennél sokkal gyakoribb, hogy miközben szembeszállunk a rendszer egyik kedvezőtlen hajlamával, utat engedünk egy másik kedvezőtlen hajlam megerősödésének. ___________________ The author previously applied the outlook and methodology he named the system paradigm to analysing the socialist system and post-socialist transition. This study takes the same approach to some general attributes of capitalism. After clarifying some concepts, the author presents examples of some system-specific features of capitalism, before ad-dressing two of them in detail. One is the dynamism of the system. The great innovations of the last century that radically altered both the technology of production and people s daily lives were all introduced and disseminated by the capitalist system and its protago-nist, the entrepreneur. Only under capitalism can the mechanism of entrepreneurship and innovation emerge, with the strong incentives and flexible capital market they require. The other immanent feature is a chronic surplus on the labour market that contrasts sharply with the chronic labour shortage prevalent under the mature socialist system. Theory and experience confirm that the faster the ongoing transformation of a capitalist economy proceeds, the greater the propensity for structural unemployment to appear. It is explained by the efficiency pay hypothesis how an employer has an incentive to pay more than a market-clearing wage, thereby introducing unemployment. Capitalism is a system that can be reformed, but attention needs paying to relations between reforms of different parts of the system. In fortunate cases they complement each other, but it is commoner to find that tackling one unfavourable tendency only allows another such tendency to increase.

Country-specific determinants of horizontal and vertical intra-industry agri-food trade: the case of Bulgaria and Romania

The article analyses patterns and country-specific determinants of agri-food trade of Bulgaria and Romania with the European Union. As literature focusing on agricultural aspects of the topic is limited, the paper seeks to contribute to the literature by providing up to date results and suggestions as well as by identifying the determinants of horizontal and vertical intra-industry trade of the Bulgaria and Romania after EU accession. Results suggest that intra-industry agri-food trade is mainly of vertical nature, referring to trade of different quality products. Results verify that determinants of horizontal and vertical IIT are similar and suggest that economic size and FDI are positively, while factor endowments and distance are negatively related to both sides of IIT. Results are mainly in line with the majority of empirical literature in the field.

Variables motivating parents to choose a specific type of private school

The purpose of this study was to investigate the reasons associated with parents' choices of specific types of private schools. The researcher hoped to determine if there were any significant differences in the reasons parents reported for enrolling their child in a specific private school. Studies in the past have explored why parents choose private schools. This study focused on why parents chose a specific type of private school, what were the variables involved, and were there any significant differences in the motivation of parents with children enrolled in different types of private schools.^ The study gathered data using a survey instrument which centered on 14 variables generally associated with the choice of private schools. The survey asked parents to rate the variables using a Likert type scale. The Likert rating was used because it does not require respondents to choose between variables. The general areas of emphasis were (a) academics, (b) religion and values/morals, (c) nurturing educational environment, and (d) proximity and convenience of the school. The survey also gather qualitative data in the form of comments volunteered by over a third of the respondents.^ The survey was mailed to 560 randomly selected families from 30 private high schools in a 50 mile radius of Miami, Florida. The 10 high schools, represented five types of private schools, Roman Catholic, Episcopal, Independent, Jewish, and Fundamentalist Christian. After four mailings a total of 401 surveys were returned for a rate 72%.^ Significant differences appeared as the data was analyzed using ANOVA and Tukey's HSD pairwise analysis. The variables showing significant differences between types of schools were (a) quality of instruction, (b) commitment of teachers, (c) emphasis on religion, (d) small class size, (e) well-defined academic goals, (f) proximity of the school's location, (g) preparation for desired secondary schools/colleges, and (h) convenience of school's operating schedule.^ Parents appeared to have specific reasons for choosing a particular private school. They appeared to look for a school that would satisfy the special needs of their child and would be compatible with their own values, morals, and personal philosophy. ^

The discrimination and association of float glass and the quantitative analysis of liquids from aerosols and microdrops using laser induced breakdown spectroscopy

Glass is a common form of trace evidence found at many scenes of crimes in the form of small fragments. These glass fragments can transfer to surrounding objects and/or persons and may provide forensic investigators valuable information to link a suspect to the scene of a crime. Since the elemental composition of different glass sources can be very similar, a highly discriminating technique is required to distinguish between fragments that have originated from different sources. ^ The research presented here demonstrates that Laser Induced Breakdown Spectroscopy (LIBS) is a viable analytical technique for the association and discrimination of glass fragments. The first part of this research describes the optimization of the LIBS experiments including the use of different laser wavelengths to investigate laser-material interaction. The use of a 266 nm excitation laser provided the best analytical figures of merit with minimal damage to the sample. The resulting analytical figures of merit are presented. The second part of this research evaluated the sensitivity of LIBS to associate or discriminate float glass samples originating from the same manufacturing plants and produced at approximately the same time period. Two different sample sets were analyzed ranging in manufacturing dates from days to years apart. Eighteen (18) atomic emission lines corresponding to the elements Sr, K, Fe, Ca, Al, Ba, Na, Mg and Ti, were chosen because of their detection above the method detection limits and for presenting differences between the samples. Ten elemental ratios producing the most discrimination were selected for each set. When all the ratios are combined in a comparison, 99% of the possible pairs were discriminated using the optimized LIBS method generating typical analytical precisions of ∼5% RSD. ^ The final study consisted of the development of a new approach for the use of LIBS as a quantitative analysis of ultra-low volume solution analysis using aerosols and microdrops. Laser induced breakdown spectroscopy demonstrated to be an effective technique for the analysis of as low as 90 pL for microdrop LIBS with 1 pg absolute LOD and 20 µL for aerosol LIBS with an absolute LOD of ∼100 fg.^

Selective and specific activation of Rab5 during endocytosis of receptor tyrosine kinases

The Rab family of proteins are low molecular weight GTPases that have the ability to switch between GTP- (active) and GDP- (inactive) bound form, and in that sense act as molecular switches. Through distinct localization on various vesicles and organelles and by cycling through GTP/GDP bound forms, Rabs are able to recruit and activate numerous effector proteins, both spatially and temporally, and hence behave as key regulators of trafficking in both endocytic and biosynhtetic pathways. The Rab5 protein has been shown to regulate transport from plasma membrane to the early endosome as well as activate signaling pathways from the early endosome. This dissertation focused on understanding Rab5 activation via endocytosis of receptor tyrosine kinases (RTKs). First, tyrosine kinase activity of RTKs was linked to endosome fusion by demonstrating that tyrosine kinase inhibitors block endosome fusion and activation of Rab5, and a constitutively active form of Rab5 is able to rescue endosome fusion. However, depending on how much ligand is available at the cell surface, the receptor-ligand complexes can be internalized via a number of distinct pathways. Similarly, Rab5 was activated in a ligand-dependent concentration dependent manner via clathrin- and caveolin-mediated pathways, as well as a pathway independent of both. However, overexpression Rabex-5, a nucleotide exchange factor for Rab5, is able to rescue activation even when all of the pathways of EGF-receptor internalization were blocked. Next, the three naturally occurring splice variants of Rabex-5 selectively activated Rab5. Lastly, Rabex-5 inhibits differentiation of 3T3-L1 and PC12 cells through 1) degradation of signaling endosome via Rab5-dependent fusion with the early endosome, 2) and inhibition of signaling cascade via ubiquitination of Ras through the ZnF domain at the N-terminus of Rabex-5. In conclusion, these data shed light on complexity of the endosomal trafficking system where tyrosine kinase activity of the receptor is able to affect endosome fusion; how different endocytic pathways affect activation of one of the key regulators of early endocytic events; and how selective activation of Rab5 via Rabex-5 can control adipogenesis and neurogenesis.

Specific binding of the mammalian high mobility group protein AT-hook 2 to the minor groove of AT -rich DNAs: Thermodynamic and specificity studies

The mammalian high mobility group protein AT-hook 2 (HMGA2) is a small transcriptional factor involved in cell development and oncogenesis. It contains three "AT-hook" DNA binding domains, which specifically recognize the minor groove of AT-rich DNA sequences. It also has an acidic C-terminal motif. Previous studies showed that HMGA2 mediates all its biological effects through interactions with AT-rich DNA sequences in the promoter regions. In this dissertation, I used a variety of biochemical and biophysical methods to examine the physical properties of HMGA2 and to further investigate HMGA2's interactions with AT-rich DNA sequences. The following are three avenues perused in this study: (1) due to the asymmetrical charge distribution of HMGA2, I have developed a rapid procedure to purify HMGA2 in the milligram range. Preparation of large amounts of HMGA2 makes biophysical studies possible; (2) Since HMGA2 binds to different AT-rich sequences in the promoter regions, I used a combination of isothermal titration calorimetry (ITC) and DNA UV melting experiment to characterize interactions of HMGA2 with poly(dA-dT) 2 and poly(dA)poly(dT). My results demonstrated that (i) each HMGA2 molecule binds to 15 AT bp; (ii) HMGA2 binds to both AT DNAs with very high affinity. However, the binding reaction of HMGA2 to poly(dA-dT) 2 is enthalpy-driven and the binding reaction of HMGA2 with poly(dA)poly(dT) is entropy-driven; (iii) the binding reactions are strongly depended on salt concentrations; (3) Previous studies showed that HMGA2 may have sequence specificity. In this study, I used a PCR-based SELEX procedure to examine the DNA binding specificity of HMGA2. Two consensus sequences for HMGA2 have been identified: 5'-ATATTCGCGAWWATT-3' and 5'-ATATTGCGCAWWATT-3', where W represents A or T. These consensus sequences have a unique feature: the first five base pairs are AT-rich, the middle four to five base pairs are GC-rich, and the last five to six base pairs are AT-rich. All three segments are critical for high affinity binding. Replacing either one of the AT-rich sequences to a non-AT-rich sequence causes at least 100-fold decrease in the binding affinity. Intriguingly, if the GC-segment is substituted by an AT-rich segment, the binding affinity of HMGA2 is reduced approximately 5-fold. Identification of the consensus sequences for HMGA2 represents an important step towards finding its binding sites within the genome.

Site specific growth of metal catalyzed silica nanowires for biological and chemical sensing

In this research the integration of nanostructures and micro-scale devices was investigated using silica nanowires to develop a simple yet robust nanomanufacturing technique for improving the detection parameters of chemical and biological sensors. This has been achieved with the use of a dielectric barrier layer, to restrict nanowire growth to site-specific locations which has removed the need for post growth processing, by making it possible to place nanostructures on pre-pattern substrates. Nanowires were synthesized using the Vapor-Liquid-Solid growth method. Process parameters (temperature and time) and manufacturing aspects (structural integrity and biocompatibility) were investigated. Silica nanowires were observed experimentally to determine how their physical and chemical properties could be tuned for integration into existing sensing structures. Growth kinetic experiments performed using gold and palladium catalysts at 1050°C for 60 minutes in an open-tube furnace yielded dense and consistent silica nanowire growth. This consistent growth led to the development of growth model fitting, through use of the Maximum Likelihood Estimation (MLE) and Bayesian hierarchical modeling. Transmission electron microscopy studies revealed the nanowires to be amorphous and X-ray diffraction confirmed the composition to be SiO2 . Silica nanowires were monitored in epithelial breast cancer media using Impedance spectroscopy, to test biocompatibility, due to potential in vivo use as a diagnostic aid. It was found that palladium catalyzed silica nanowires were toxic to breast cancer cells, however, nanowires were inert at 1μg/mL concentrations. Additionally a method for direct nanowire integration was developed that allowed for silica nanowires to be grown directly into interdigitated sensing structures. This technique eliminates the need for physical nanowire transfer thus preserving nanowire structure and performance integrity and further reduces fabrication cost. Successful nanowire integration was physically verified using Scanning electron microscopy and confirmed electrically using Electrochemical Impedance Spectroscopy of immobilized Prostate Specific Antigens (PSA). The experiments performed above serve as a guideline to addressing the metallurgic challenges in nanoscale integration of materials with varying composition and to understanding the effects of nanomaterials on biological structures that come in contact with the human body.