Chemiluminescence – based bioanalytical devices for astrobiological, food safety and clinical applications

At the intersection of biology, chemistry, and engineering, biosensors are a multidisciplinary innovation that provide a cost-effective alternative to traditional laboratory techniques. Due to their advantages, biosensors are used in medical diagnostics, environmental monitoring, food safety and many other fields. The first part of the thesis is concerned with learning the state of the art of paper-based immunosensors with bioluminescent (BL) and chemiluminescent (CL) detection. The use of biospecific assays combined with CL detection and paper-based technology offers an optimal approach to creating analytical tools for on-site applications and we have focused on the specific areas that need to be considered more in order to ensure a future practical implementation of these methods in routine analyses. The subsequent part of the thesis addresses the development of an autonomous lab-on-chip platform for performing chemiluminescent-based bioassays in space environment, exploiting a CubeSat platform for astrobiological investigations. An origami-inspired microfluidic paper-based analytical device has been developed with the purpose of assesses its performance in space and to evaluate its functionality and the resilience of the (bio)molecules when exposed to a radiation-rich environment. Subsequently, we designed a paper-based assay to detect traces of ovalbumin in food samples, creating a user-friendly immunosensing platform. To this purpose, we developed an origami device that exploits a competitive immunoassay coupled with chemiluminescence detection and magnetic microbeads used to immobilize ovalbumin on paper. Finally, with the aim of exploring the use of biomimetic materials, an hydrogel-based chemiluminescence biosensor for the detection of H2O2 and glucose was developed. A guanosine hydrogel was prepared and loaded with luminol and hemin, miming a DNAzyme activity. Subsequently, the hydrogel was modified by incorporating glucose oxidase enzyme to enable glucose biosensing. The emitted photons were detected using a portable device equipped with a smartphone's CMOS (complementary metal oxide semiconductor) camera for CL emission detection.

Ultracold Bose-Fermi mixtures with pairing: quantum phase transition, mechanical stability, and trap confinement

Ultracold dilute gases occupy an important role in modern physics and they are employed to verify fundamental quantum theories in most branches of theoretical physics. The scope of this thesis work is the study of Bose-Fermi (BF) mixtures at zero temperature with a tunable pairing between bosons and fermions. The mixtures are treated with diagrammatic quantum many-body methods based on the so-called T-matrix formalism. Starting from the Fermi-polaron limit, I will explore various values of relative concentrations up to mixtures with a majority of bosons, a case barely considered in previous works. An unexpected quantum phase transition is found to occur in a certain range of BF coupling for mixture with a slight majority of bosons. The mechanical stability of mixtures has been analysed, when the boson-fermion interaction is changed from weak to strong values, in the light of experimental results recently obtained for a double-degenerate Bose-Fermi mixture of 23 Na - 40 K. A possible improvement in the description of the boson-boson repulsion based on Popov's theory is proposed. Finally, the effects of a harmonic trapping potential are described, with a comparison with the experimental data for the condensate fraction recently obtained for a trapped 23 Na - 40 K mixture.

Deployment of a data analysis workflow of the ATLAS experiment on HPC systems

LHC experiments produce an enormous amount of data, estimated of the order of a few PetaBytes per year. Data management takes place using the Worldwide LHC Computing Grid (WLCG) grid infrastructure, both for storage and processing operations. However, in recent years, many more resources are available on High Performance Computing (HPC) farms, which generally have many computing nodes with a high number of processors. Large collaborations are working to use these resources in the most efficient way, compatibly with the constraints imposed by computing models (data distributed on the Grid, authentication, software dependencies, etc.). The aim of this thesis project is to develop a software framework that allows users to process a typical data analysis workflow of the ATLAS experiment on HPC systems. The developed analysis framework shall be deployed on the computing resources of the Open Physics Hub project and on the CINECA Marconi100 cluster, in view of the switch-on of the Leonardo supercomputer, foreseen in 2023.

Quantum phase estimation algorithms

Al contrario dei computer classici, i computer quantistici lavorano tramite le leggi della meccanica quantistica, e pertanto i qubit, ovvero l'unità base di informazione quantistica, possiedono proprietà estremamente interessanti di sovrapposizione ed entanglement. Queste proprietà squisitamente quantistiche sono alla base di innumerevoli algoritmi, i quali sono in molti casi più performanti delle loro controparti classiche. Obiettivo di questo lavoro di tesi è introdurre dal punto di vista teorico la logica computazionale quantistica e di riassumere brevemente una classe di tali algoritmi quantistici, ossia gli algoritmi di Quantum Phase Estimation, il cui scopo è stimare con precisione arbitraria gli autovalori di un dato operatore unitario. Questi algoritmi giocano un ruolo cruciale in vari ambiti della teoria dell'informazione quantistica e pertanto verranno presentati anche i risultati dell'implementazione degli algoritmi discussi sia su un simulatore che su un vero computer quantistico.

Quantum error correction with the IBM quantum experience

Mentre si svolgono operazioni su dei qubit, possono avvenire vari errori, modificando così l’informazione da essi contenuta. La Quantum Error Correction costruisce algoritmi che permettono di tollerare questi errori e proteggere l’informazione che si sta elaborando. Questa tesi si focalizza sui codici a 3 qubit, che possono correggere un errore di tipo bit-flip o un errore di tipo phase-flip. Più precisamente, all’interno di questi algoritmi, l’attenzione è posta sulla procedura di encoding, che punta a proteggere meglio dagli errori l’informazione contenuta da un qubit, e la syndrome measurement, che specifica su quale qubit è avvenuto un errore senza alterare lo stato del sistema. Inoltre, sfruttando la procedura della syndrome measurement, è stata stimata la probabilità di errore di tipo bit-flip e phase-flip su un qubit attraverso l’utilizzo della IBM quantum experience.

Brittle and ductile removal modes observed during diamond turning of carbon nanotube composites

Ultraprecision diamond turning was used to evaluate the surface integrity of a carbon nanotube (CNT) composite as a function of the cutting conditions and the percentage of CNT in the epoxy matrix. The effects of cutting conditions on the chip morphology and surface roughness were analysed. The results showed that an increase in the percentage of CNT may influence the mechanism of material removal and consequently improve the quality of the machined surface. When smaller quantities of CNT (0.02 and 0.07 wt %) are present in the matrix, microcracks form within the cutting grooves (perpendicular to the cutting direction). This indicates that the amount of CNT on the epoxy matrix may have a direct influence on the mechanical properties of these materials. Chips removed from the CNT composite samples were analysed by scanning electron microscopy in order to correlate the material removal mechanism and the surface generation process. The area average surface roughness Sa was influenced by the material removal mechanism (Sa ranging from 0.28 to 1.1 mu m).

Structure of an Odorant-Binding Protein from the Mosquito Aedes aegypti Suggests a Binding Pocket Covered by a pH-Sensitive ""Lid""

Background: The yellow fever mosquito, Aedes aegypti, is the primary vector for the viruses that cause yellow fever, mostly in tropical regions of Africa and in parts of South America, and human dengue, which infects 100 million people yearly in the tropics and subtropics. A better understanding of the structural biology of olfactory proteins may pave the way for the development of environmentally-friendly mosquito attractants and repellents, which may ultimately contribute to reduction of mosquito biting and disease transmission. Methodology: Previously, we isolated and cloned a major, female-enriched odorant-binding protein (OBP) from the yellow fever mosquito, AaegOBP1, which was later inadvertently renamed AaegOBP39. We prepared recombinant samples of AaegOBP1 by using an expression system that allows proper formation of disulfide bridges and generates functional OBPs, which are indistinguishable from native OBPs. We crystallized AaegOBP1 and determined its three-dimensional structure at 1.85 angstrom resolution by molecular replacement based on the structure of the malaria mosquito OBP, AgamOBP1, the only mosquito OBP structure known to date. Conclusion: The structure of AaegOBP1 (= AaegOBP39) shares the common fold of insect OBPs with six alpha-helices knitted by three disulfide bonds. A long molecule of polyethylene glycol (PEG) was built into the electron-density maps identified in a long tunnel formed by a crystallographic dimer of AaegOBP1. Circular dichroism analysis indicated that delipidated AaegOBP1 undergoes a pH-dependent conformational change, which may lead to release of odorant at low pH (as in the environment in the vicinity of odorant receptors). A C-terminal loop covers the binding cavity and this ""lid"" may be opened by disruption of an array of acid-labile hydrogen bonds thus explaining reduced or no binding affinity at low pH.

Characterization of feather-degrading bacteria from Brazilian soils

Studies on keratinolytic microorganisms have been mainly related to their biotechnological applications and association with animal pathologies. However, these organisms have an ecological relevance to recycling keratinous residues in nature. This work aimed to select and identify new culturable feather-degrading bacteria isolated from soils of Brazilian Amazon forest and Atlantic forest. Bacteria that were isolated from temperate soils and bacteria from Amazonian basin soil were tested for their capability to grow on feather meal agar (FMA). Proteolytic bacteria were tested for feather degradation and were further identified according to their morphological and biochemical characteristics. Also, molecular identification based on 165 rDNA gene sequencing was carried out. A total of 24 proteolytic and 20 feather-degrading isolates were selected; Most of the isolates were from the Bacillus genus (division Firmicutes), but one Aeromonas, two Serratia (gamma-Proteobacteria), and one Chryseobacterium (Cytophaga-Flavobacterium group). (C) 2010 Elsevier Ltd. All rights reserved.

Downscaling a multicommuted flow injection analysis system for the photometric determination of iodate in table salt

In this work a downscaled multicommuted flow injection analysis setup for photometric determination is described. The setup consists of a flow system module and a LED based photometer, with a total internal volume of about 170 mu L The system was tested by developing an analytical procedure for the photometric determination of iodate in table salt using N,N-diethyl-henylenediamine (DPD) as the chromogenic reagent. Accuracy was accessed by applying the paired r-test between results obtained using the proposed procedure and a reference method, and no significant difference at the 95% confidence level was observed. Other profitable features, such as a low reagent consumption of 7.3 mu g DPD per determination: a linear response ranging from 0.1 up to 3.0 m IO(3)(-), a relative standard deviation of 0.9% (n = 11) for samples containing 0.5 m IO(3)(-), a detection limit of 17 mu g L(-1) IO(3)(-), a sampling throughput of 117 determination per hour, and a waste generation 600 mu L per determination, were also achieved. (C) 2010 Elsevier B.V. All rights reserved.

New records of Rhagomys rufescens (Rodentia : Sigmodontinae) in the Atlantic forest of Brazil

Since it was trapped in the XIX(th) century, Rhagomys rufescens has been considered a rare endangered sigmodontine rodent and an endemic species of the Atlantic forest. Only a handful of vouchers of this taxon were known by Thomas, 1886. Recently, eight new individuals were collected, providing new geographical, morphological and phylogenetic (based on molecular evidence) information on this species. In the present work we report the southernmost occurrence record for R. rufescens at Indaial, Santa Catarina State, with the largest collected series of this species, the northernmost occurrence record at Santa Teresa, Espirito Santo State, and new records from Pocos de Caldas, Minas Gerais State, from Ibiuna and Ribeirao Grande, Sao Paulo State.

Teleportation with a uniformly accelerated partner

In this work, we give a description of the process of teleportation between Alice in an inertial frame, and Rob who is in uniform acceleration with respect to Alice. The fidelity of the teleportation is reduced due to Davies-Unruh radiation in Rob's frame. In so far as teleportation is a measure of entanglement, our results suggest that quantum entanglement is degraded in noninertial frames.

Atoms in squeezed light fields

Squeezed light is of interest as an example of a non-classical state of the electromagnetic field and because of its applications both in technology and in fundamental quantum physics. This review concentrates on one aspect of squeezed light, namely its application in atomic spectroscopy. The general properties, detection and application of squeezed light are first reviewed. The basic features of the main theoretical methods (master equations, quantum Langevin equations, coupled systems) used to treat squeezed light spectroscopy are then outlined. The physics of squeezed light interactions with atomic systems is dealt with first for the simpler case of two-level atoms and then for the more complex situation of multi-level atoms and multi-atom systems. Finally the specific applications of squeezed light spectroscopy are reviewed.

Is cell surface calreticulin involved in phagocytosis by insect hemocytes?

The innate immune system of insects consists of humoral and cellular components involved in the recognition of and responses to intruding foreign micro- or macroorganisms. Several molecules have been identified so far that recognize molecular patterns present on microorganisms, such as lipopolysaccharides, peptidoglycans and lipoteichonic acid. These molecules, acting as opsonins, trigger immune responses such as phagocytosis, nodule formation, melanization and encapsulation. Here, we investigated the role of calreticulin (CRT) present on the surface of Pieris rapae hemocytes in phagocytosis. Comparative phagocytosis assays using yeast cells showed that hemocytes from different insects exhibit significant variation in their phagocytosing potential and relative CRT involvement. (C) 2003 Elsevier Science Ltd. All rights reserved.

Interfacial interactions and structure of organic-inorganic nanohybrids

Understanding the interfacial interactions and structure is important to better design and application of organic-inorganic nanohybrids. This paper presents our recent molecular dynamic studies on organoclays and polymer nanocomposites, including the layering behavior of organoclays, structural and dynamic properties of dioctadecyldimethyl ammoniums in organoclays, and interfacial interactions and structure of polyurethane nanocomposites. The results demonstrate that the layering behaviors of organoclays are closely related to the chain length of quaternary alkyl ammoniums and cation exchangeable capacity of clays. In addition to typical layered structures such as monolayer, bilayer and pseudo-trilayer, a pseudo-quadrilayer structure was also observed in organoclays modified with dioctadecyldimethyl ammoniums (DODDMA). In such a structure, alkyl chains do not lie flat within a single layer but interlace, and also jump to the next layer or even the next nearest layer. Moreover, the diffusion constants of nitrogen and methylene atoms increase with the temperature and methelene towards the tail groups. For polyurethane nanocomposite, the van der Waals interaction between apolar alkyl chains and soft segments of polyurethane predominates the interactions between organoclay and polyurethane. Different from most bulk polyurethane systems, there is no distinct phase-separated structure for the polyurethane.

Real-time quantitative PCR in cerebral toxoplasmosis diagnosis of Brazilian human immunodeficiency virus-infected patients

Cerebral toxoplasmosis is the most common cerebral mass lesion in AIDS patients in Brazil, and results in high mortality and morbidity, despite free access to HAART (highly active antiretroviral treatment). Molecular diagnosis based on conventional PCR (cnPCR) or real-time quantitative PCR (qrtPCR) has been indispensable for definitive diagnosis. We report here the evaluation of qrtPCR with blood and cerebrospinal fluid (CSF) samples from AIDS patients in Brazil. This prospective study was conducted for 2 years, analysing DNA samples extracted from 149 AIDS patients (98 blood and 51 CSF samples) with confirmed clinical and radiological diagnosis The laboratory diagnosis included cnPCR (with the B22/B23 primer set) and indirect immunofluorescence (IF). For qrtPCR, two primer sets were simultaneously designed based on described genes and using a 6-carboxyfluorescein dye-labelled TaqMan MGB (minor groove binder) probe One was Bug, which amplified a sequence from the B1 gene The other was the RETg, which amplified a PCR product of the 529 bp sequence. The overall cnPCR and qrtPCR results were positive results were observed in 33.6% (50) patients The sensitivities were 98% for cnPCR (B22/B23), and 86 and 98% for qrtPCR (B1Tg and RETg, respectively). Negative reactions were observed in 66 4% patients. The specificities were 97% for cnPCR and qrtPCR (B1Tg). and 88.8% for RETg These data show that RETg PCR is highly sensitive as it amplifies a repeat region with many copies; however, its specificity is lower than the other markers However, B1Tg PCR had good specificity, but lower sensitivity Among the patients, 20 had blood and CSF collected simultaneously Thus, their results permitted us to analyse and compare molecular, serological and clinical diagnosis for a better understanding of the different scenarios of laboratorial and clinical diagnosis. For nine patients with confirmed cerebral toxoplasmosis diagnosis, four scenarios were observed: (i) and (ii) negative molecular diagnosis for CSF and positive for blood with variable IF titres for the sera and CSF (negative or positive), (iii) positive molecular diagnosis with CSF and negative with blood, and (iv) positive molecular diagnosis in both samples. In the latter two situations, normally the IF titres in sera and CSF are variable. Other opportunistic infections were shown in 11 patients Despite the IF titres in sera and CSF being variable, all of them had negative molecular diagnosis for both samples qrtPCR allows for a rapid identification of Toxoplasma gondii DNA in patient samples; in a minority of cases discrepancies occur with the cnPCR.