Measurement of lead concentration in biological tissues by atomic spectroscopy techniques

Dissertation for the degree of Doctor of Philosophy in Physics

The characteristic time of glucose diffusion measured for muscle tissue at optical clearing

The study of agent diffusion in biological tissues is very important to understand and characterize the optical clearing effects and mechanisms involved: tissue dehydration and refractive index matching. From measurements made to study the optical clearing, it is obvious that light scattering is reduced and that the optical properties of the tissue are controlled in the process. On the other hand, optical measurements do not allow direct determination of the diffusion properties of the agent in the tissue and some calculations are necessary to estimate those properties. This fact is imposed by the occurrence of two fluxes at optical clearing: water typically directed out of and agent directed into the tissue. When the water content in the immersion solution is approximately the same as the free water content of the tissue, a balance is established for water and the agent flux dominates. To prove this concept experimentally, we have measured the collimated transmittance of skeletal muscle samples under treatment with aqueous solutions containing different concentrations of glucose. After estimating the mean diffusion time values for each of the treatments we have represented those values as a function of glucose concentration in solution. Such a representation presents a maximum diffusion time for a water content in solution equal to the tissue free water content. Such a maximum represents the real diffusion time of glucose in the muscle and with this value we could calculate the corresponding diffusion coefficient.

QUANTITATIVE VS. CONVENTIONAL PCR FOR DETECTION OF HUMAN ADENOVIRUSES IN WATER AND SEDIMENT SAMPLES

SUMMARY Human Adenoviruses (HAdV) are notably resistant in the environment. These agents may serve as effective indicators of fecal contamination, and may act as causative agents of a number of different diseases in human beings. Conventional polymerase chain reaction (PCR) and, more recently, quantitative PCR (qPCR) are widely used for detection of viral agents in environmental matrices. In the present study PCR and SYBR(r)Green qPCR assays were compared for detection of HAdV in water (55) and sediments (20) samples of spring and artesian wells, ponds and streams, collected from dairy farms. By the quantitative methodology HAdV were detected in 87.3% of the water samples and 80% of the sediments, while by the conventional PCR 47.3% and 35% were detected in water samples and sediments, respectively.

Characterization of sol-gel matrices with entrapped cutinase

Dissertação para obtenção do Grau de Doutor em Engenharia Química e Bioquímica

Storage of water molecules into biomimetic heterostructures: the role of roughness

The development of devices based on heterostructured thin films of biomolecules conveys a huge contribution on biomedical field. However, to achieve high efficiency of these devices, the storage of water molecules into these heterostructures, in order to maintain the biological molecules hydrated, is mandatory. Such hydrated environment may be achieved with lipids molecules which have the ability to rearrange spontaneously into vesicles creating a stable barrier between two aqueous compartments. Yet it is necessary to find conditions that lead to the immobilization of whole vesicles on the heterostructures. In this work, the conditions that govern the deposition of open and closed liposomes of 1.2-dipalmitoyl-sn-Glycero-3-[Phospho-rac-(1-glycerol)] (sodium Salt) (DPPG) onto polyelectrolytes cushions prepared by the layer-by-layer (LbL) method were analyzed. Electronic transitions of DPPG molecules as well as absorption coefficients were obtained by vacuum ultraviolet spectroscopy, while the elemental composition of the heterostructures was characterized by x-ray photoelectron spectroscopy (XPS). The presence of water molecules in the films was inferred by XPS and infrared spectroscopy. Quartz crystal microbalance (QCM) data analysis allowed to conclude that, in certain cases, the DPPG adsorbed amount is dependent of the bilayers number already adsorbed. Moreover, the adsorption kinetics curves of both adsorbed amount and surface roughness allowed to determine the kinetics parameters that are related with adsorption processes namely, electrostatic forces, liposomes diffusion and lipids re-organization on surface. Scaling exponents attained from atomic force microscopy images statistical analysis demonstrate that DPPG vesicles adsorption mechanism is ruled by the diffusion Villain model confirming that adsorption is governed by electrostatic forces. The power spectral density treatment enabled a thorough description of the accessible surface of the samples as well as of its inner structural properties. These outcomes proved that surface roughness influences the adsorption of DPPG liposomes onto surfaces covered by a polyelectrolyte layer. Thus, low roughness was shown to induce liposome rupture creating a lipid bilayer while high roughness allows the adsorption of whole liposomes. In addition, the fraction of open liposomes calculated from the normalized maximum adsorbed amounts decreases with the cushion roughness increase, allowing us to conclude that the surface roughness is a crucial variable that governs the adsorption of open or whole liposomes. This conclusion is fundamental for the development of well-designed sensors based on functional biomolecules incorporated in liposomes. Indeed, LbL films composed of polyelectrolytes and liposomes with and without melanin encapsulated were successfully applied to sensors of olive oil.

Biochemical and physical surface functionalization of polycaprolactone as a key mediator of osteogenic differentiation and vascularized tissue morphogenesis

Tese de Doutoramento em Engenharia de Tecidos, Medicina Regenerativa e Células Estaminais.

Development of advanced cell/tissue culture systems, based on enhanced polymeric scaffolds and sophisticated bioreactors, for tissue engineering applications

Programa Doutoral em Engenharia Biomédica

Approved Drug Products with Theurapeutic Equivalence Evaluation - 34th edition

The publication, Approved Drug Products with Therapeutic Equivalence Evaluations (the List, commonly known as the Orange Book), identifies drug products approved on the basis of safety and effectiveness by the Food and Drug Administration (FDA) under the Federal Food, Drug, and Cosmetic Act (the Act). Drugs on the market approved only on the basis of safety (covered by the ongoing Drug Efficacy Study Implementation [DESI] review [e.g., Donnatal® Tablets and Librax® Capsules] or pre-1938 drugs [e.g., Phenobarbital Tablets]) are not included in this publication. The main criterion for the inclusion of any product is that the product is the subject of an application with an effective approval that has not been withdrawn for safety or efficacy reasons. Inclusion of products on the List is independent of any current regulatory action through administrative or judicial means against a drug product. In addition, the List contains therapeutic equivalence evaluations for approved multisource prescription drug products. These evaluations have been prepared to serve as public information and advice to state health agencies, prescribers, and pharmacists to promote public education in the area of drug product selection and to foster containment of health care costs. Therapeutic equivalence evaluations in this publication are not official FDA actions affecting the legal status of products under the Act.

Quantitative method of viral pollution determination for large volume of water using ferric hydroxide gel impregnated on the surface of glassfibre cartridge

Quantitative method of viral pollution determination for large volume of water using ferric hydroxide gel impregnated on the surface of glassfibre cartridge filter. The use of ferric hydroxide gel, impregnated on the surface of glassfibre cartridge filter enable us to recover 62.5% of virus (Poliomylitis type I, Lsc strain) exsogeneously added to 400 liters of tap-water. The virus concentrator system consists of four cartridge filters, in which the three first one are clarifiers, where the contaminants are removed physically, without significant virus loss at this stage. The last cartridge filter is impregnated with ferric hydroxide gel, where the virus is adsorbed. After the required volume of water has been processed, the last filter is removed from the system and the viruses are recovered from the gel, using 1 liter of glycine/NaOH buffer, at pH 11. Immediately the eluate is clarified through series of cellulose acetate membranes mounted in a 142mm Millipore filter. For the second step of virus concentration, HC1 1N is added slowly to the eluate to achieve pH 3.5-4. MgC1, is added to give a final concentration of 0.05M and the viruses are readsorbed on a 0.45 , porosity (HA) cellulose acetate membrane, mounted in a 90 mm Millipore filter. The viruses are recovered using the same eluent plus 10% of fetal calf serum, to a final volume of 3 ml. In this way, it was possible to concentrate virus from 400 liters of tap-water, into 1 liter in the first stage of virus concentration and just to 3 ml of final volume in a second step. The efficiency, simplicity and low operational cost, provded by the method, make it feasible to study viral pollution of recreational and tap-water sources.

Segmental copy number variation shapes tissue transcriptomes

Abstract : Copy number variation (CNV) of DNA segments has recently gained considerable interest as a source of genetic variation likely to play a role in phenotypic diversity and evolution. Much effort has been put into the identification and mapping of regions that vary in copy number among seemingly normal individuals, both in humans and in a number of model organisms, using both bioinformatic and hybridization-based methods. Synteny studies suggest the existence of CNV hotspots in mammalian genomes, often in connection with regions of segmental duplication. CNV alleles can be in equilibrium within a population, but can also arise de novo between generations, illustrating the highly dynamic nature of these regions. A small number of studies have assessed the effect of CNV on single loci, however, at the genome-wide scale, the functional impact of CNV remains poorly studied. We have explored the influence of CNV on gene expression, first using the Williams-Beuren syndrome (WBS) associated deletion as a model, and second at the genome-wide scale in inbred mouse strains. We found that the WBS deletion influences the expression levels not only of the hemizygous genes, but also affects the euploid genes mapping nearby. Consistently, on a genome wide scale we observe that CNV genes are expressed at more variable levels than genes that do not vary in copy number. Likewise, CNVs influence the relative expression levels of genes that map to the flank of the genome rearrangements, thus globally influencing tissue transcriptomes. Further studies are warranted to complete cataloguing and fine mapping of CNV regions, as well as to elucidate the different mechanisms by which CNVs influence gene expression. Résumé : La variation en nombre de copies (copy number variation ou CNV) de segments d'ADN suscite un intérêt en tant que variation génétique susceptible de jouer un r81e dans la diversité phénotypique et l'évolution. Les régions variables en nombre de copies parmi des individus apparemment normaux ont été cartographiées et cataloguées au moyen de puces à ADN et d'analyse bioinformatique. L'étude de la synténie entre plusieurs espèces de mammifères laisse supposer l'existence de régions à haut taux de variation, souvent liées à des duplications segmentaires. Les allèles CNV peuvent être en équilibre au sein d'une population ou peuvent apparaître de novo. Ces faits illustrent la nature hautement dynamique de ces régions. Quelques études se sont penchées sur l'effet de la variation en nombre de copies de loci isolés, cependant l'impact de ce phénomène n'a pas été étudié à l'échelle génomique. Nous avons examiné l'influence des CNV sur l'expression des gènes. Dans un premier temps nous avons utilisé la délétion associée au syndrome de Williams-Beuren (WBS), puis, dans un second temps, nous avons poursuivi notre étude à l'échelle du génome, dans des lignées consanguines de souris. Nous avons établi que la délétion WBS influence l'expression non seulement des gènes hémizygotes, mais également celle des gènes euploïdes voisins. A l'échelle génomique, nous observons des phénomènes concordants. En effet, l'expression des gènes variant en nombre de copies est plus variable que celles des gènes ne variant pas. De plus, à l'instar de la délétion WBS, les CNV influencent l'expression des gènes adjacents, exerçant ainsi un impact global sur les profils d'expression dans les tissus. Résumé pour un large public : De nombreuses maladies ont pour cause un défaut génétique. Parmi les types de mutations, on compte la disparition (délétion) d'une partie de notre génome ou sa duplication. Bien que l'on connaisse les anomalies associées à certaines maladies, les mécanismes moléculaires par lesquels ces réarrangements de notre matériel génétique induisent les maladies sont encore méconnus. C'est pourquoi nous nous sommes intéressés à la régulation des gènes dans les régions susceptibles à délétion ou duplication. Dans ce travail, nous avons démontré que les délétions et les duplications influencent la régulation des gènes situés à proximité, et que ces changements interviennent dans plusieurs organes.

Orthogonal organic and aqueous-based washes of tissue sections to enhance protein sensitivity by MALDI imaging mass spectrometry.

Imaging mass spectrometry (IMS) is an emergent and innovative approach for measuring the composition, abundance and regioselectivity of molecules within an investigated area of fixed dimension. Although providing unprecedented molecular information compared with conventional MS techniques, enhancement of protein signature by IMS is still necessary and challenging. This paper demonstrates the combination of conventional organic washes with an optimized aqueous-based buffer for tissue section preparation before matrix-assisted laser desorption/ionization (MALDI) IMS of proteins. Based on a 500 mM ammonium formate in water-acetonitrile (9:1; v/v, 0.1% trifluororacetic acid, 0.1% Triton) solution, this buffer wash has shown to significantly enhance protein signature by profiling and IMS (~fourfold) when used after organic washes (70% EtOH followed by 90% EtOH), improving the quality and number of ion images obtained from mouse kidney and a 14-day mouse fetus whole-body tissue sections, while maintaining a similar reproducibility with conventional tissue rinsing. Even if some protein losses were observed, the data mining has demonstrated that it was primarily low abundant signals and that the number of new peaks found is greater with the described procedure. The proposed buffer has thus demonstrated to be of high efficiency for tissue section preparation providing novel and complementary information for direct on-tissue MALDI analysis compared with solely conventional organic rinsing.

Development of a real time polymerase chain reaction for quantitation of Schistosoma mansoni DNA

This report describes the development of a SYBR Green I based real time polymerase chain reaction (PCR) protocol for detection on the ABI Prism 7000 instrument. Primers targeting the gene encoding the SSU rRNA were designed to amplify with high specificity DNA from Schistosoma mansoni, in a real time quantitative PCR system. The limit of detection of parasite DNA for the system was 10 fg of purified genomic DNA, that means less than the equivalent to one parasite cell (genome ~580 fg DNA). The efficiency was 0.99 and the correlation coefficient (R²) was 0.97. When different copy numbers of the target amplicon were used as standards, the assay could detect at least 10 copies of the specific target. The primers used were designed to amplify a 106 bp DNA fragment (Tm 83ºC). The assay was highly specific for S. mansoni, and did not recognize DNA from closely related non-schistosome trematodes. The real time PCR allowed for accurate quantification of S. mansoni DNA and no time-consuming post-PCR detection of amplification products by gel electrophoresis was required. The assay is potentially able to quantify S. mansoni DNA (and indirectly parasite burden) in a number of samples, such as snail tissue, serum and feces from patients, and cercaria infested water. Thus, these PCR protocols have potential to be used as tools for monitoring of schistosome transmission and quantitative diagnosis of human infection.

Segmental copy number variation shapes tissue transcriptomes.

Copy number variation (CNV) is a key source of genetic diversity, but a comprehensive understanding of its phenotypic effect is only beginning to emerge. We have generated a CNV map in wild mice and classical inbred strains. Genome-wide expression data from six major organs show not only that expression of genes within CNVs tend to correlate with copy number changes, but also that CNVs influence the expression of genes in their vicinity, an effect that extends up to half a megabase. Genes within CNVs show lower expression and more specific spatial expression patterns than genes mapping elsewhere. Our analyses reveal differential constraint on copy number changes of genes expressed in different tissues. Dosage alterations of brain-expressed genes are less frequent than those of other genes and are buffered by tighter transcriptional regulation. Our study provides initial evidence that CNVs shape tissue transcriptomes on a global scale.

Atomic parity nonconservation, neutron radii, and effective field theories of nuclei

Accurately calibrated effective field theories are used to compute atomic parity nonconserving (APNC) observables. Although accurately calibrated, these effective field theories predict a large spread in the neutron skin of heavy nuclei. Whereas the neutron skin is strongly correlated to numerous physical observables, in this contribution we focus on its impact on new physics through APNC observables. The addition of an isoscalar-isovector coupling constant to the effective Lagrangian generates a wide range of values for the neutron skin of heavy nuclei without compromising the success of the model in reproducing well-constrained nuclear observables. Earlier studies have suggested that the use of isotopic ratios of APNC observables may eliminate their sensitivity to atomic structure. This leaves nuclear structure uncertainties as the main impediment for identifying physics beyond the standard model. We establish that uncertainties in the neutron skin of heavy nuclei are at present too large to measure isotopic ratios to better than the 0.1% accuracy required to test the standard model. However, we argue that such uncertainties will be significantly reduced by the upcoming measurement of the neutron radius in 208^Pb at the Jefferson Laboratory.

Programme latin de don d'organes (PLDO): une initiative efficace pour augmenter les dons d'organes en Suisse [Latin organ donation programme (LODP): an effective initiative to increase organ donation in Switzerland].

The 1st federal transplant law was enforced in July 2007 with the obligation to promote quality and efficiency in the procedures for organ and tissue donation for transplantation. The Latin organ donation programme (LODP) created in 2008 aims to develop organ donation in 17 public hospitals in 7 Latin cantons, covering 2.2 million people; 29% of the Swiss population. The implementation of various effective measures by the LODP enabled the increase in the number of donors by 70% between 2008 and 2010, with four organs procured per donor; greatly exceeding the European average of three. The results show that LODP has successfully professionalised the system and we can only hope that similar organisations will be put into place throughout Switzerland.