Structure to function studies in UDP-glucose dehydrogenases and nitroreductases

The thesis is divided into two parts corresponding to structural studies on two different proteins. The first part concerns the study of two UDP-glucose dehydrogenases (UGDs) from Sphingomonas elodea ATCC 31461 and Burkholderia cepacia IST 408, both involved in exopolysaccharide production. Their relevance arises because some of these bacterial exopolysaccharides are valuable as established biotechnological products, the former case, whilst others are highly problematic, when used by pathogens in biofilm formation over biological surfaces, as the latter case, namely in the human lungs. The goal of these studies is to increase our knowledge regarding UGDs structural properties, which can potentiate either the design of activity enhancers to respond to the increased demand of useful biofilms, or the design of inhibitors of biofilm production, in order to fight invading pathogens present in several infections. The thesis reports the production and crystallisation of both proteins, the determination of initial phases by single-wavelength anomalous dispersion (SAD) in S. elodea crystals using a seleno-methionine isoform, and phasing of B. cepacia crystals by molecular replacement (MR) using the S. elodea model, as well as the refinement, structural analysis and comparison between the several UGDs structures available during this work.(...)

Three transducers for one photodetector: essays for optical communications

Dissertation presented to obtain the PhD degree in Electrical and Computer Engineering - Electronics

Periplasmic nitrate reductase revisited: a sulfur atom completes the sixth coordination of the catalytic molybdenum

J Biol Inorg Chem. 2008 Jun;13(5):737-53. doi: 10.1007/s00775-008-0359-6

Transimpedance amplifier for early detection of breast cancer

Breast cancer is the most common type of cancer worldwide. The effectiveness of its treatment depends on early stage detection, as well as on the accuracy of its diagnosis. Recently, diagnosis techniques have been submitted to relevant breakthroughs with the upcoming of Magnetic Resonance Imaging, Ultrasound Sonograms and Positron Emission Tomography (PET) scans, among others. The work presented here is focused on studying the application of a PET system to a Positron Emission Mammography (PEM) system. A PET/PEM system works under the principle that a scintillating crystal will detect a gamma-ray pulse, originated at the cancerous cells, converting it into a correspondent visible light pulse. The latter must then be converted into an electrical current pulse by means of a Photo- -Sensitive Device (PSD). After the PSD there must be a Transimpedance Amplifier (TIA) in order to convert the current pulse into a suitable output voltage, in a time period lower than 40 ns. In this Thesis, the PSD considered is a Silicon Photo-Multiplier (SiPM). The usage of this recently developed type of PSD is impracticable with the conventional TIA topologies, as it will be proven. Therefore, the usage of the Regulated Common-Gate (RCG) topology will be studied in the design of the amplifier. There will be also presented two RCG variations, comprising a noise response improvement and differential operation of the circuit. The mentioned topology will also be tested in a Radio-Frequency front-end, showing the versatility of the RCG. A study comprising a low-voltage self-biasing feedback TIA will also be shown. The proposed circuits will be simulated with standard CMOS technology (UMC 130 nm), using a 1.2 V power supply. A power consumption of 0.34 mW with a signal-to-noise ratio of 43 dB was achieved.

Writing/erasing 3D micro and nano wrinkles in flexible elastomers for volatile organic compounds sensor

Micro/nano wrinkled patterns on cross-linked urethane/urea polymeric flexible free standing films with two soft segments, polypropylene oxide and polybutadiene, can be induced by UV-irradiation. The ability to write/erase these 3D structures, in a controlled manner, is the main focus of this work. The imprinting of the wrinkled structures was accomplished by swelling in an appropriate solvent followed by drying the membranes after the cross-linking process and UV irradiation. The surface tailoring of the elastomeric membranes was imaged by optical microscopy, scanning electronic microscopy and by atomic force microscopy. To erase the wrinkled structures the elastomers were swollen. The swelling as well as the sol/gel fraction and the UV radiation were tuned in order to control the wrinkles characteristics. It was found that the wrinkles wavelength, in the order of microns (1±0,25μm), was stamped by the UV radiation intensity and exposure time while the wrinkles' amplitude, in the order of nanometers (150-450 nm), was highly dependent on the swelling and sol/gel fraction. A prototype for volatile organic compounds detection was developed taking advantage of the unique 3D micro/nano wrinkles features.

Design of a CMOS amplifier for breast cancer detection

A transimpedance amplifier (TIA) is used, in radiation detectors like the positron emission tomography(PET), to transform the current pulse produced by a photo-sensitive device into an output voltage pulse with a desired amplitude and shape. The TIA must have the lowest noise possible to maximize the output. To achieve a low noise, a circuit topology is proposed where an auxiliary path is added to the feedback TIA input, In this auxiliary path a differential transconductance block is used to transform the node voltage in to a current, this current is then converted to a voltage pulse by a second feedback TIA complementary to the first one, with the same amplitude but 180º out of phase with the first feedback TIA. With this circuit the input signal of the TIA appears differential at the output, this is used to try an reduced the circuit noise. The circuit is tested with two different devices, the Avalanche photodiodes (APD) and the Silicon photomultiplier (SIPMs). From the simulations we find that when using s SIPM with Rx=20kΩ and Cx=50fF the signal to noise ratio is increased from 59 when using only one feedback TIA to 68.3 when we use an auxiliary path in conjunction with the feedback TIA. This values where achieved with a total power consumption of 4.82mv. While the signal to noise ratio in the case of the SIPM is increased with some penalty in power consumption.

Reconfigurable photonic logic architecture

The amorphous silicon photo-sensor studied in this thesis, is a double pin structure (p(a-SiC:H)-i’(a-SiC:H)-n(a-SiC:H)-p(a-SiC:H)-i(a-Si:H)-n(a-Si:H)) sandwiched between two transparent contacts deposited over transparent glass thus with the possibility of illumination on both sides, responding to wave-lengths from the ultra-violet, visible to the near infrared range. The frontal il-lumination surface, glass side, is used for light signal inputs. Both surfaces are used for optical bias, which changes the dynamic characteristics of the photo-sensor resulting in different outputs for the same input. Experimental studies were made with the photo-sensor to evaluate its applicability in multiplexing and demultiplexing several data communication channels. The digital light sig-nal was defined to implement simple logical operations like the NOT, AND, OR, and complex like the XOR, MAJ, full-adder and memory effect. A pro-grammable pattern emission system was built and also those for the validation and recovery of the obtained signals. This photo-sensor has applications in op-tical communications with several wavelengths, as a wavelength detector and to execute directly logical operations over digital light input signals.