Brucellosis is endemic in many livestock worldwide especially developing countries. The aims of this study were to estimate the seroprevalence of bovine brucellosis and risk factors associated with the seropositivity in rural and peri-urban buffaloes and cattle populations of Sindh. Firstly, a cross sectional study was conducted to estimate the seroprevalence of bovine brucellosis in cattle and buffaloes of Sindh province, Pakistan. Serum samples (2600) were tested using Rose Bengal Plate Test. The overall seroprevalence of brucellosis in Sindh province was 13.96% (95% C.I.; 11.55 - 16.37). Of the 917 herds tested, 232 or 25.30% herds (95%C.I.; 22.51-28.24) were positive for brucellosis. The adult animals were 2.05 (95% C.I.; 1.14-3.68, P= 0.02) times more likely to test positive for brucellosis. The animals in a peri-urban dairy production system were 2.07 times (95%C.I.; 1.09-3.90, P = 0.03) times more likely have brucellosis. The species or sex of animal did not appear to affect the risk of seropositivity in cattle or buffalo in this population. Secondly, a cross sectional survey was conducted to understand the structure and composition of farms, animal husbandry and management practices in peri-urban dairy colonies in Karachi and farmers’ awareness of zoonoses. The mean herd size was 93.58 animals and 88.01% of these animals were female buffaloes. Of 326 farms surveyed, only 37.42% were able to associate animals with transmission of diseases in human. The characteristics of peri-urban dairy farms in Karachi are discussed. Thirdly, the value of FTA® cards in detecting the Brucella DNA in milk samples was estimated by determining the detection limits of genus specific ERI PCR assay for FTA® cards and comparing the PCR results from whole sediments taken from culturing pooled milk samples with taking sediment on FTA® cards. The detection limits of this method ranged from 6.6 x 103 cfu/ml for B. abortus to 7.17 x 106 cfu/ml for B. suis. Assuming the results of ERI PCR for the whole sediment as gold standard (method 1), the method using sediment on FTA® cards as test samples (method 2) showed a diagnostic sensitivity of 81.44% (95% C.I.; 75.54-87.33) but a poor diagnostic specificity of 42.86% (95%C.I.; 16.95-68.78). The kappa value, κ, was 0.14 (p = 0.02) demonstrating a poor agreement between the two methods. Lastly, 181 bulk milk samples were used to estimate the herd level prevalence of bovine brucellosis in Landhi dairy colony, Karachi. The ERI PCR was used to test these samples. The herd prevalence was estimated as 92.26% (95% C.I.; 88.34-96.19). For each level (50 animals) increase in herd size, the risk of herd being brucellosis positive increases by 2.38 times. The herds that have a male animal for breeding are 0.09 times less likely to have brucellosis. The history of abortion, presence of small ruminants or the regions of animal purchase don’t appear to have any association with the risk of brucellosis at a herd level in this population at LDC, Karachi. A high seroprevalence of bovine brucellosis in livestock population in Sindh and a very high herd level prevalence in peri-urban dairy farms in particular poses a serious threat to the public health and livestock production in Sindh, Pakistan.

The subject of this study was to investigate the species composition and spatial distribution pastern of iving (Rose Bengal stained) benthic foraminifera in sediment surface samples (0-1 cm) off the Southwestern Taiwan and Dongsha Atoll. The main objectives of this study was to document the living benthic foraminiferal assemblages off the Southwestern Taiwan and Dongsha Atoll and to examine their distribution in relation to environmental parameters. Four benthic foraminiferal biofacies were recognized within the substrate type in Dongsha Atoll: A1 (Fine-grained) is represented by Pseudomassilina spp. - Quinqueloculina parkeri, A2 (Fine-grained) is represented by Hauerina spp. - Pseudomassilina spp., B1 (Coarse-grained) is characterised by Calcarina spp. - Quinqueloculina spp., B2 (Coarse-grained) is characterised by Amphistegina spp. - Quinqueloculina spp. Sediment surface samples off the Southwestern Taiwan during May 2009 led to the identification of four assemblages. Assemblage A is characterised by Ammonia spp. - Bolivina spp., Assemblage B between is characterized by Asterorotalia spp. - Globobulimina spp., Assemblage C is represented by Cibicides spp. - Nummulites spp., Assemblage D is represented by Ammonia spp. - Cibicides spp. Sediment surface samples off the Southwestern Taiwan during Nov. 2009 led to the identification of three assemblages. Assemblage A is dominated by Ammonia spp. - Cibicides spp., Assemblage B is characterised by Ammonia spp. - Bolivina spp., Assemblage C is characterised by Asterorotalia spp. - Bolivina spp. Stained benthic foraminifera form Dongsha Atoll correlated with current wave, collected site, coarse fraction and TOC contents. Living benthic foraminifera off the Southwestern Taiwan seems not to be related with TOC contents and coarse fraction, the assemblages were found to be more related to tidal energy and lateral transport.

Water contamination through substances called per- and polyfluoroalkyl substances (PFAS) is a worldwide problem. Being able to measure the concentrations of PFAS in water is a first step towards beating this contamination. One alternative is to use a field test kit instead of extensive lab equipment to monitor the contaminated areas. This thesis has investigated the possibility of using amine-functionalized mesoporous carbon as adsorbent to develop a detection method based on adsorbing first PFAS and then dye in aqueous solutions. The non-adsorbed dye concentrations are depending on the amount of PFAS, and hence the colour intensity in the remaining solution is proportional to PFAS concentration. Mesoporous carbon with amine functional groups were chosen as specific adsorbents for PFAS because of its large surface area and high adsorption capacity. It has been shown that some colorants would react in a similar way as PFAS on sorbents and thus can be used as an indicator for the user. In the study, the two most common PFAS, PFOA and PFOS, were studied and Rose Bengal was the dye. The adsorbent’s morphology, pore structure and pore size was verified with scanning electron microscopy (SEM), transmission electron microscopy (TEM) and nitrogen sorption before being tested. Adsorption tests were performed using different PFAS concentrations and a dye solution range in order to find three things: the detection range, the ratio powder/solution in order to see a difference, and the adsorption or saturation time for both PFAS and dye. This thesis concluded that even though the adsorbent was not as efficient as predicted, this method could be used for detecting PFAS concentrations down to at least 0.1 pg/ml and could be a possible approach for quick field tests in the future.

Water pollution is a profound ecological concern, exerting detrimental effects on human well-being, ecological systems, and animal life. Among the emerging contaminants that critically influence water quality and have garnered substantial scientific interest in recent times are per- and polyfluoroalkyl substances (PFAS). It is crucial to investigate the de- velopment of an easy technique for PFAS detection and measurement that can be used for quick analysis. This thesis explores the possibility to use amine-functionalized mesoporous carbon as an adsorbent to develop a detection method based on sequential adsorption of per- and polyfluoroalkyl substances (PFAS) and a dye, Rose Bengal, onto the adsorbent. The hypothesis is that the concentration of non-adsorbed dye is dependent on the amount of PFAS present, making the color intensity of the remaining solution proportional to the PFAS concentration. Mesoporous carbon was chosen as the adsorbent due to their high specific surface area, providing a high adsorption capacity, and the potential to functionalize the surface with amine groups which will attract the PFAS. Rose Bengal was selected as a concentration indicator as it has been shown that it can be used as a proxy for PFAS. In this study, the most prevalent PFAS compounds, namely PFOA and PFOS, were investigated. Prior to testing, the adsorbent underwent characterization using diverse techniques to show the porosity and particle morphology. The adsorption experiments encompassed varying PFAS concentrations and a range of dye solutions to determine the detection range, the powder-to-solution ratio necessary for discernible differentiation, and the adsorption or saturation time for both PFAS and dye. This thesis concludes that it was not possible to detect neither PFOA nor PFOS in the range of 0.1 pg/mL to 1 μg/mL with the setup, even though Rose Bengal adsorption could be detected down to 0.6 μg/mL. It was further observed that amine-functionalized hard templated mesoporous carbon has a higher adsorption capacity compared to the soft templated material.

Over the last two centuries, the discovery and application of catalysts has had a substantial impact on how and what chemicals are produced.Given their broad significance, our group has focused on developing new catalyst systems that are recoverable and reusable, in an attempt to reduce concomitant costs. Our efforts have centered on constructing a recyclable chiral heterogeneous catalyst capable of effecting asymmetric hydrogenations of olefins with high stereoselectivity. A class of phosphinoimidazoline ligands, developed by researchers at Boehringer-Ingelheim, known as BIPI ligands, have proven efficacious in the asymmetric reduction of alkenes. However, these chiral ligands are homogeneous and coordinated to precious metals, rendering them irrecoverable and expensive. To address these issues, our group has derivatized the BIPI ligand-metal complex and immobilized it to the surface of graphene oxide as well as polystyrene. Their efficacy and recyclability toward the asymmetric hydrogenation of a functionalized olefin have been evaluated. Another facet of our work has included developing a cost effective synthetic process to artemisinin, the gold standard drug in the treatment of malaria.As a natural product, artemisinin’s worldwide supply remains highly unpredictable, contributing to great price volatility.Combining the benefits of catalysis and the advantages of continuous flow chemistry, our research has sought to develop an economical approach to convert a biosynthetic precursor, artemisinic acid, to artemisinin in three chemical transformations. High-throughput experimentation allowed us to screen a prodigious number of catalysts and identify those effective in the asymmetric hydrogenation artemisinic acid to dihydroartemisinic acid, the first step in the transformation. This screening directed us to an inexpensive, heterogeneous ruthenium catalyst. The second step of the process includes the photooxygenation of dihydroartemisinic acid, which involves photochemically generated singlet oxygen. We have evaluated a commercially available heterogeneous photocatalyst packed in a transparent bed, surrounded by light emitting diodes in the continuous photooxygenation of dihydroartemisinic acid to dihydroartemisinic acid hydroperoxide. The third and final step, an acid induced hock cleavage, initiates an intricate cascading reaction that installs an endoperoxide bridge to deliver artemisinin. Our process afforded a 57% yield from dihydroartemisinic acid to artemisinin.

Les transporteurs vésiculaires du glutamate (VGLUTs) sont impliqués dans la recapture du glutamate du cytosol vers les vésicules présynaptiques. Depuis leurs caractérisations récentes en 2000, leurs implications dans plusieurs maladies neurodégénératives ont été démontrées. Ils jouent ainsi un rôle primordial dans la transmission nerveuse glutamatergique. Deux colorants naturels, le Rose Bengale et le Bleu Trypan, restent les meilleurs inhibiteurs connus à ce jour, avec respectivement des CI50 de 25 et 50 nM. Dans un premier temps, nous avons conçu et optimisé une série d’analogues basée sur le synthon Rose Bengale (inhibiteur non-compétitif). Ce travail a notamment permis de mettre en évidence l’effet des formes tautomères (quinone et lactone) sur l’inhibition des VGLUTs. Ainsi la forme quinonique, présente à pH physiologique, a été confirmée comme étant la seule capable de bloquer la recapture du glutamate. Dans un second temps, nous nous sommes intéressés à la famille du Bleu Trypan (inhibiteur compétitif) et nous avons déterminé la structure minimale active avec l’objectif de rendre ces molécules plus « drug-like ». En effet, l’intérêt de ce projet est de développer de petites structures aisément radiomarquables pour une utilisation dans un contexte physio-pathologique. / Vesicular glutamate transporters (VGLUTs) are involved in the recapture and storage of glutamate from cytol to secretory synaptic vesicules. Since their recent characterization in 2000, their implication in several neurodegenerative disorders have been demonstrated. They play a crucial role in glutamatergic neurotransmission. Natural dyes, such as Rose Bengal and Tryptan Blue are the best known inhibitors with IC50 values of 25 and 50 nM, respectively. Firstly, we designed and optimized a series of analogues based on the synthon Rose Bengal (non-competitive inhibitor). This work has especially enabled to highlight the effect of tautomeric forms (quinone and lactone) on the inhibition of VGLUTs. Thus, the quinone form, present at physiological pH, was confirmed as the only able to block the reuptake of glutamate. Secondly, we have been interested in the family of Trypan Blue (competitive inhibitor) and we determined the minimal active structure in order to render these molecules more "drug-like". Indeed, the interest of this project is to develop small structures easily radiomarquable to use in a physiopathological context.

<p>Biotherapeutics, such as monoclonal antibodies (mAbs), represent a primary mechanism for treatment of human disease, and there has been a steady increase in Food and Drug Administration approvals since the first one in 1982. Subcutaneous (SC) injection of protein-based therapeutics is a convenient and clinically established drug delivery method that increases the convenience and reduces cost compared to other delivery methods. However, progress is needed to optimize bioavailability via this route. This dissertation describes the methods for evaluation of mass transport of high molecular weight proteins, such as mAbs, following SC injection using <em>in vitro</em> and <em>ex vivo</em> modeling developed to describe the factors relevant for optimal distribution prior to uptake into systemic circulation. The first chapter describes a novel collagen and hyaluronic acid (HA) based hydrogel for investigation of macromolecule transport based on the physiochemical properties of the diffusing molecule and the tissue matrix. This initial study demonstrated that, in collagen alone, collagen combined with HA, and HA alone, the molecules demonstrated different transport paradigms dependent primarily on molecule size, matrix viscosity, and electrostatic charge, respectively. This showed that the local tissue heterogeneity and therapeutic properties could be determining factors for molecule transport and bioavailability. The second, third, and fourth chapters describe two novel platforms for the investigation of injection plume formation in SC tissue utilizing three-dimensional X-ray tomography. Injection plume analysis has been studied comprehensively in the context of insulin transport using co-injection of radiopaque dyes to track the protein distribution. However high molecular weight therapeutics have vastly different physiochemical properties than insulin and are injected under different rates, concentrations, volumes, and viscosities due to dosing considerations. To address the gap mAb distribution, we first developed a novel protein conjugated to an x-ray contrast agent to directly track injection plume formation and investigated the effects of injection rate and tissue location through injections into ex vivo porcine tissue, described in chapters three and four. Ex vivo tissue analysis showed that the rate did not influence the distribution, however, plume volume was lower in porcine belly compared to neck tissue. Whereas porcine tissue is an excellent model to represent the structural features of human injection, the large heterogeneity between animal subjects and collected samples is a disadvantage. Therefore, the fourth chapter describes the fabrication of a gelatin hydrogel-based injection platform representing the dermal and subcutaneous tissue layers for controlled injection plume analysis. In summary, all three models represent useful platforms for the assessment of macromolecular mass transport, pharmaceutical autoinjector performance, as well as the potential impact of tissue properties and intersubject heterogeneity on plume formation. Overall, the findings in these studies might better inform drug designers and clinicians on how to most optimally engineer an injection to deliver the most efficient patient outcomes through better dosing and increased cost savings. </p>

[ES] Los estudios sobre los daños en el ADN se han incrementado en las últimas décadas con el fin de profundizar en su implicación en la aparición del cáncer. Entre el gran número de lesiones del ADN, los aductos de tipo eteno han sido objeto de interés debido a su presencia en los tejidos humanos crónicamente inflamados. Asimismo, su cuantificación es útil para su uso como potencial biomarcador del cáncer de colon, próstata, pulmón, etc. Además, estas lesiones presentan propiedades altamente mutagénicas e inducen transiciones de bases o transversiones en las células de mamíferos. Los aductos de tipo eteno se generan principalmente de forma endógena como resultado de la peroxidación lipídica. Este proceso bioquímico produce aldehídos reactivos como el malondialdehído, que pueden combinarse con las bases del ADN creando un anillo exocíclico.Este anillo exocíclico proporciona a la nucleobase un sistema extendido p-conjugado que puede conferirles propiedades ópticas diferentes a las de las bases canónicas, lo que puede suponer una amenaza para la fotoestabilidad del ADN. Las bases canónicas tienen la capacidad de disipar la mayor parte de la energía recibida a través de canales no radiativos eficientes que conducen de nuevo al estado fundamental. Por lo tanto, los estudios sobre las propiedades ópticas de estos aductos etenos son clave para establecer si estas lesiones pueden poner en peligro la relajación eficiente de los estados excitados de las bases y desencadenar una fotorreactividad indeseada del ADN. La primera parte de la tesis trata de evaluar la fotoactividad potencial de estas lesiones del ADN mediante un estudio espectroscópico. En el Capítulo 3 se combinan experimentos de upconversión de fluorescencia en la escala de femtosegundos y cálculos teóricos (en los niveles PCM-TD-DFT y CASPT2/CASSCF) para proporcionar una imagen completa de la relajación de los estados excitados del aducto mutagénico 3,N4-eteno-2'-desoxicitidina (edC). El Capítulo 4 aborda las propiedades fotofísicas de los aductos junto con su fotorreactividad en presencia de fotosensibilizadores comunes como la Rosa de Bengala (RB) y la 4-carboxibenzofenona (CBP), prestando especial atención a la interacción con el 1O2. En condiciones aeróbicas, se observa una interacción con 1O2 para los tres aductos estudiados. Curiosamente, se observan los mismos fotoproductos, las nucleobases originales, para la irradiación en condiciones anaeróbicas, abriendo la posibilidad de un mecanismo mixto de Tipo I y Tipo II cuando se utiliza Rosa de Bengala como fotosensibilizador, y de Tipo I para la 4-carboxibenzofenona. Finalmente, el último capítulo trata de unir todos los conocimientos adquiridos sobre la fotorreactividad de los e-aductos para elegir el mejor cromóforo tratando de optimizar el proceso de reparación observado en el Capítulo 4. Para ello se utilizan sistemas híbridos de nanopartículas metálicas de Ag como matriz de soporte para la Rosa de Bengala. Las NPs metálicas, como las Ag NPs, poseen una resonancia plasmónica superficial localizada (LSPR), este efecto amplifica una gran variedad de fenómenos ópticos que pueden mejorar las propiedades ópticas de la Rosa de Bengala. / [CA] Els estudis sobre els danys en l'ADN s'han incrementat en les últimes dècades amb la finalitat d'aprofundir en la seua implicació en l'aparició del càncer. Entre el gran nombre de lesions de l'ADN, els adductes de tipus eteno han sigut objecte d'interés degut a la seua presència en els teixits humans crònicament inflamats, la qual cosa fa que la seua quantificació siga útil com a potencials biomarcadors del càncer de còlon, pròstata, pulmó, etc. A més, aquestes lesions presenten propietats altament mutagèniques i indueixen transicions de bases o transversions en les cèl·lules dels mamífers. Els adductes de tipus eteno es formen principalment de manera endògena com a resultat de la peroxidació dels lípids. Aquest procés bioquímic produeix aldehids reactius com el malondialdehid, que poden combinar-se amb les bases de l'ADN creant un anell exocíclic. Aquest anell exocíclic proporciona a les nucleobases un sistema estés p-conjugat que pot conferir-les propietats òptiques diferents a les de les bases canòniques, i que poden suposar una amenaça per a la fotoestabilitat de l'ADN. Les bases canòniques tenen la capacitat de dissipar la major part de l'energia d'excitació a través de canals no radiatius eficients que condueixen de nou a l'estat bàsic. No obstant això, els estudis sobre les propietats òptiques d'aquests adductes de tipus eteno són fonamentals per a deixar clar si aquestes lesions poden posar en perill aquesta relaxació eficient i desencadenar una fotoreactivitat indesitjada de l'ADN. La primera part de la tesi tracta d'estimar el potencial fotoactiu d'aquestes lesions de l'ADN mitjançant un estudi espectroscòpic. En el Capítol 3 es combinen experiments de "upconversió" de fluorescència en una escala de femtosegons i càlculs teòrics (en els nivells PCM-TD-DFT i CASPT2/CASSCF) per a proporcionar una imatge completa de la relaxació dels estats excitats del adducte mutagènic 3,N4-eteno-2'-desoxicitidina (edC). El Capítol 4 aborda les propietats fotofísiques dels adductes restants juntament amb el seua fotoreactivitat en presència d'alguns fotosensibilitzadors comuns com la Rosa de Bengala (RB) i la 4-carboxibenzofenona (CBP), prestant especial atenció a la interacció amb el 1O2. S'observa la interacció amb 1O2 per als tres adductes estudiats. Curiosament, s'observa la mateixa formació de nucleobases per a la irradiació en condicions anaeròbiques, obrint la possibilitat d'un mecanisme mixt de Tipus I i Tipus II quan s'utilitza Rosa de Bengala com fotosensibilitzador i de Tipus I per a la 4-carboxibenzofenona. Finalment, l'últim capítol tracta d'unir tots els coneixements adquirits sobre la fotoreactivitat dels adductes de tipus eteno per a triar el millor cromòfor tractant d'optimitzar el procés de reparació observat en el Capítol 4. Per a això s'utilitzen sistemes híbrids de nanopartícules metàl·liques de Ag com a matriu de suport per a la Rosa de Bengala. Les NPs metàl·liques, com les de Ag, posseeixen ressonància plasmónica superficial localitzada (LSPR), aquest efecte amplifica una gran varietat de fenòmens òptics que poden millorar les propietats òptiques de la Rosa de Bengala. / [EN] Studies dealing with DNA damages have increased during the last decades in order to get more insight into their involvement in the appearance of cancer. Among the large number of DNA lesions, etheno adducts have been the matter of interest because of their presence in chronically inflamed human tissues, making their quantification useful as potential biomarkers for cancer of colon, prostate, lung, etc. Moreover, these lesions exhibit highly mutagenic properties and induce base transitions or transversion in mammal cells. Etheno adducts are mainly formed endogenously as a result of lipid peroxidation. This biochemical process produces reactive aldehydes such as malondialdehyde, which can combine with DNA bases creating the exocyclic ring. This exocyclic ring provides to the nucleobases an extended p- conjugated system that might confer them optical properties different from those of the canonical bases, and can pose a threat to the DNA photostability. Canonical bases have the ability to dissipate most of the excitation energy through efficient nonradiative channels leading back to the ground state. However, the studies about the optical properties of this etheno adducts are basics to make it clear whether these lesions can jeopardize this efficient relaxation and trigger undesired DNA photoreactivity. The first part of the thesis establishes the potential photoactivity of these DNA lesions through a spectroscopic study. Chapter 3 joints femtosecond fluorescence upconversion experiments and theoretical calculations (at the PCM-TD-DFT and CASPT2/CASSCF levels) to provide a comprehensive picture of the mutagenic etheno adduct 3,N4-etheno-2'-deoxycytidine (edC) excited states relaxation. Chapter 4 addresses the photophysical properties of the adducts together with its photoreactivity in the presence of some common photosensitizers as Rose Bengal and 4-carboxybenzophenone, paying a special attention to interaction with 1O2. Interaction with 1O2 is observed for the three studied e-adducts. Interestingly, the same nucleobase formation is detected for irradiation under anaerobic conditions, opening the possibility of a mixed Type I and Type II mechanism when Rose Bengal is used as photosensitizer, and Type I for 4-carboxybenzophenone. Finally, the last chapter takes advantage of all the gained knowledge about the photoreactivity of e-adducts to choose the best chromophore and optimize the repair process observed in Chapter 4. To achieve this, hybrid systems of Ag metal nanoparticles are used as a support matrix for the Rose Bengal. Metal NPs, such as Ag NP, possess localized surface plasmon resonance (LSPR). This effect amplifies a wide variety of optical phenomena that can enhance the Rose Bengal optical properties. / Lizondo Aranda, P. (2022). Photoreactivity of DNA Etheno Adducts: Spectroscopic and Mechanistic Study [Tesis doctoral]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/189688