Advances in Plasmonic Technologies for Point of Care Applications

Demand for accessible and affordable healthcare for infectious and chronic diseases present significant challenges for providing high-value and effective healthcare. Traditional approaches are expanding to include point-of-care (POC) diagnostics, bedside testing, and community-based approaches to respond to these challenges. Innovative solutions utilizing recent advances in mobile technologies, nanotechnology, imaging systems, and microfluidic technologies are envisioned to assist this transformation.National Institutes of Health (U.S.) (RO1 AI093282)National Institutes of Health (U.S.) (RO1 AI081534)National Institutes of Health (U.S.) (U54EB15408)National Institutes of Health (U.S.) (R21 AI087107

Identification and Biosensing Application of Molecular Recognition Elements

Molecular recognition elements (MREs) are biomolecules such as single-stranded DNA (ssDNA), RNA, small peptides and antibody fragments that can bind to user defined targets with high affinities and specificities. This binding property allows MREs to have a wide range of applications, including therapeutic, diagnostic, and biosensor applications. The identification of MREs can be achieved by using the process called Systematic Evolution of Ligands by Exponential Enrichment (SELEX). This process begins with a large library of 109 to 1015 different random molecules, molecules that bind to the user defined target or positive target are enriched in the process. Subsequently, this process can be modified and tailored to direct the enriched library away from binding to related targets or negative targets, and thus increasing the specificity. Single-stranded DNA (ssDNA) MREs are particularly favorable for biosening applications due to their relative stability, reusability and low cost in production. This work investigated the identification and application of ssDNA MREs to detect different bacterial toxins and pesticide.;In Chapter 1, it begins by reviewing recent discovery and advancement in the SELEX technique for the identification and biosensing application of ssDNA MREs specific for bacteria, viruses, their related biomolecules, and selected environmental toxins. It is then followed by a brief discussion on major biosensing principles based upon ssDNA MREs. In Chapter 2, the pilot project of this work, ssDNA MRE specific for Pseudomonas aeruginosa exotoxin A was identified. In this chapter, a novel variation of SELEX called Decoy-SELEX, previously developed by our laboratory is described in greater detail. Additionally, the development of a ssDNA MRE modified enzyme-linked immunosorbent assay (ELISA) for the exotoxin A detection is also discussed. In Chapter 3, similar methodology was applied to identify a ssDNA MRE specific for the second target, Clostridium difficile toxin B. Subsequently, similar ssDNA MRE modified ELISA was developed for target detection in clinically relevant samples. In Chapter 4, ssDNA MRE specific for alpha toxin of Staphylococcus aureus was identified, and it was applied for sensitive detection of the target in clinically relevant samples. In Chapter 5, the overall conclusion and potential future studies as a result from this work is discussed. Lastly, in Appendix, the project of identifying and potential future application of ssDNA MREs specific for a pesticide, Fipronil is described.;Overall, this work has shown the proof-of-principle of using ssDNA MREs in biosensing application for target detections in clinically relevant samples. The work will be useful in the development of potential point-of-care diagnostic tools for rapid diagnosis of bacterial infections

Advances in plasmonic technologies for point of care applications

Infectious diseases have considerable economic and societal impact on developing settings. For instance, malaria is observed more commonly in sub-Saharan Africa and India. The societal impact of acquired immune deficiency syndrome (AIDS) and tuberculosis is high, through targeting adults in villages and leaving behind declining populations. Highly sensitive and specific lab assays such as cell culture methods, polymerase chain reaction (PCR), and enzyme-linked immunosorbent assay (ELISA) are available for diagnosis of infectious diseases in the developed world. They require sample transportation, manual preparation steps, and skilled and well-trained technicians. These clinical conventional methods provide results in several hours to days, precluding rapid detection and response at the primary care settings. Another diagnostic challenge is identifying multiple pathogens

Nanomaterials for Healthcare Biosensing Applications

In recent years, an increasing number of nanomaterials have been explored for their applications in biomedical diagnostics, making their applications in healthcare biosensing a rapidly evolving field. Nanomaterials introduce versatility to the sensing platforms and may even allow mobility between different detection mechanisms. The prospect of a combination of different nanomaterials allows an exploitation of their synergistic additive and novel properties for sensor development. This paper covers more than 290 research works since 2015, elaborating the diverse roles played by various nanomaterials in the biosensing field. Hence, we provide a comprehensive review of the healthcare sensing applications of nanomaterials, covering carbon allotrope-based, inorganic, and organic nanomaterials. These sensing systems are able to detect a wide variety of clinically relevant molecules, like nucleic acids, viruses, bacteria, cancer antigens, pharmaceuticals and narcotic drugs, toxins, contaminants, as well as entire cells in various sensing media, ranging from buffers to more complex environments such as urine, blood or sputum. Thus, the latest advancements reviewed in this paper hold tremendous potential for the application of nanomaterials in the early screening of diseases and point-of-care testing

Suspect screening of natural toxins in surface water reservoirs

[eng] Natural toxins include a multitude of toxic secondary metabolites produced by animals, bacteria, fungi algae, and plants that are generally not intended as environmental contaminants of concern for water quality. However, the presence of anthropogenic waste in the aquatic environment, both with the climate changes and the increase of temperatures, is creating favorable conditions for the development of undesired organisms able to produce natural toxins that sum with other well known anthropogenic pollutants such as pesticides. Among them, natural toxins produced by algae (cyanotoxins), fungi (mycotoxins), and plants (phytotoxins) are the most encountered in surface water environments. Some of them have various toxic effects on the human body. Carcinogenic, dermotoxic, and neurotoxic effects are generally associated with these compounds. Concern about the effects of cyanobacteria on human health has recently grown in many countries. Several human and livestock poisoning events, due to the contamination of water sources (especially lakes) attributed to toxic cyanobacterial bloom, resulted in a dramatic rise of interest in these toxins. Despite that, their presence in surface water was not evenly regulated, and only the highly toxic microcystin-LR was limited at 1 µg/L by the Drinking Water Directive (Consolidated text: Council Directive 98/83/EC of 3 November 1998 on the quality of water intended for human consumption) of the World Health Organization. Additionally, studies on their occurrence, chemical persistence, buoyancy, and the algal blooms onset prediction in the environment are still scarce. The environmental risk assessment is difficult and the degree of toxicity into surface water ecosystems is still poorly studied. Their fate in the environment can be described by distribution coefficients such as the octanol-water partitioning (Kow). Other data able to define other distribution and partition parameters are generally obtained using in-silico prediction tools. The identification and quantification are still difficult due to the availability of certified standards. Moreover, these compounds are found mixed with other groups of chemicals at low concentrations. Most of the published methods for their determination are specifically designed to identify a single compound or a group of toxins with similar characteristics, making stressful and time-consuming the process to identify other known-unknown compounds using non-targeted approaches. Since the dangerousness of natural toxins in surface water was recently reported by different authors, valuable data were produced and published to assess their presence and concentration in surface water environments. Several analytical techniques have been reported for their qualitative and quantitative analysis, among them MALDI- TOF/MS, LC-ESI/HRMS, LC-ESI-QqQ are the most used. However, due to the thousands of compounds and their extreme heterogeneity, suspect screening has taken a central role as screening purposes. Over the years, the suspect screening involved the use of in-silico approaches for the tentative identification of natural toxins, becoming one of the preferred methods for the suspect analysis of known-unknown compounds in surface water. It is of primary importance to develop and optimize new methods able to identify natural toxins in a various range of polarities, ranging from the most hydrophobic to the highest water affine. The screening approaches are generally focused on cyanotoxins with no implementations regarding plant toxins and mycotoxins which are very poorly studied in surface water. In this framework, this thesis has aimed to increase the knowledge about natural toxins in surface water. The first part of the study was focused on the recent advances in the detection of natural toxins retrieving a multitude of analytical approaches for their determination in surface and drinking water. Finally, two suspect screening approaches using suspect and target analysis with data- dependent (DDA) and data-independent acquisition (DIA) methods exploring the performances for the determination of multitargeted compounds have been proposed. The tentative compounds have been firstly filtered using a suspect list of 2784 compounds retrieved by different databases available in the literature. The validated methods were then applied to analyse surface water samples coming from different sites in Europe. The presence of natural toxins produced by both plants, fungi, and cyanobacteria is a reality in different water environments showing their presence at low levels also in unexpected zones with not favorable conditions for their production. Almost 80% of the natural toxins encountered were phytotoxins, while a small number of cyanotoxins and mycotoxins have been tentatively identified. The chemical diversity is generally driven by the botanical diversity and the anthropization of the area. Besides, the seasonality and the precipitations are crucial parameters to understand the presence of phytotoxins respect to the cyanotoxins which have been encountered also in unexpected seasons. However, the quantification was not possible for all natural toxins, since only 32 standards were available in our study. In conclusion, the work presented in this thesis, allowed to fill some of the gaps in the analysis of natural toxins presenting two approaches to increase the knowledge about the identification of natural toxins in surface waters. In the future, should be crucial to update the latest determination approaches with the newest quantification strategies to finally implement the suspect screening approaches and reach both determination and quantification of suspect compounds when standards are not available.[cat] La presència de residus antropogènics al medi aquàtic, tant amb els canvis climàtics com a l’augment de les temperatures, crea condicions favorables per al desenvolupament d’organismes no desitjats capaços de produir toxines naturals que es combinen amb els altres contaminants antropogènics coneguts. Les toxines naturals inclouen multitud de metabòlits secundaris tòxics produïts per animals, bacteris, algues fongs i plantes que no solen estar concebuts com a contaminants ambientals que preocupin la qualitat de l’aigua. Entre elles, les toxines naturals produïdes per algues (cianotoxines), fongs (micotoxines) i plantes (fitotoxines) són les més freqüents en entorns d’aigües superficials. Alguns d’ells expliquen diversos efectes tòxics contra el cos humà. Els efectes cancerígens, dermotòxics i neurotòxics s’associen generalment a aquests compostos. La preocupació pels efectes dels cianobacteris sobre la salut humana ha crescut en molts països en els darrers anys per diversos motius. Aquests inclouen casos d’intoxicacions atribuïdes a cianobacteris tòxics i la consciència de la contaminació de les fonts d’aigua (especialment els llacs) que es tradueix en un augment del creixement de la cianobacteria. Malgrat això, la seva presència a les aigües superficials no estava regulada ni limitada de manera uniforme, i només la microcistina-LR altament tòxica estava limitada a 1 µg / L per la Directiva sobre aigua potable (Text consolidat: Directiva 98/83 / CE del Consell, de 3 de novembre de 1998 sobre la qualitat de l’aigua destinada al consum humà) de l’Organització Mundial de la Salut. A més, els estudis sobre la seva aparició, persistència química, flotabilitat i predicció de l'aparició de les flors d'algues al medi ambient encara són escassos. L'avaluació del risc ambiental és difícil i el grau de toxicitat en els ecosistemes d'aigües superficials encara està poc estudiat. La identificació i quantificació són difícils a causa de la manca d’estàndards certificats disponibles i el seu destí a l’entorn es pot descriure mitjançant coeficients de distribució com el repartiment octanol-aigua (Kow). Altres dades capaces de definir altres paràmetres de distribució i partició s’obtenen generalment mitjançant eines de predicció in silico. A més, aquests compostos es troben barrejats amb altres grups de productes químics a baixes concentracions. La majoria dels mètodes publicats per a la seva determinació estan dissenyats específicament per identificar un sol compost o un grup de toxines amb característiques similars, cosa que fa que el procés d’identificació de diferents compostos sigui estressant i requereixi temps mitjançant enfocaments específics. Atès que s’ha determinat la perillositat de les toxines naturals a l’aigua superficial, es van produir i publicar dades valuoses per avaluar-ne la presència i la concentració. S'han informat de diverses tècniques analítiques per a la seva anàlisi quantitativa, entre les quals s'utilitzen MALDI-TOF/MS, LC-ESI/HRMS, LC-ESI-QqQ. No obstant això, a causa dels milers de compostos i de la seva extrema heterogeneïtat, el “suspect screening” ha tingut un paper central com a propòsit de idenficació de compostos desconeguts. Al llarg dels anys, el "suspect screening” va implicar l’ús de metòdiques “in-silico” per a la identificació provisional de toxines naturals, convertint-se en un dels mètodes preferits per a l’anàlisi sospitós de compostos desconeguts en aigües superficials. És de primera importància desenvolupar i optimitzar nous mètodes capaços d’identificar toxines naturals en diversos rangs de polaritats, des de les més hidròfobes fins a les més afines a l’aigua. Les proves es centren generalment en cianotoxines sense implementacions quant a toxines vegetals i les micotoxines que estan molt poc estudiades en aigües superficials. En aquest marc, aquesta tesi té com a objectiu augmentar el coneixement sobre les toxines naturals de les aigües superficials. La primera part de l’estudi es va centrar en els recents avenços en la detecció de toxines naturals que recuperen multitud d’enfocaments analítics per a la seva determinació en aigua superficial i potable. Finalment, s’han introduït dos enfocaments de detecció de sospitosos que utilitzen anàlisis de sospitosos i objectius amb mètodes d’adquisició dependents de dades (DDA) i d’adquisició independent de dades (DIA) que exploren el rendiment per a la determinació de compostos multidirectius. Els compostos provisionals s'han filtrat en primer lloc mitjançant una llista sospitosa de 2784 compostos recuperats per diferents bases de dades disponibles a la literatura. A continuació, es van aplicar els mètodes validats per analitzar mostres d’aigua superficial procedents de diferents llocs d’Europa. La presència de toxines naturals produïdes per les plantes, els fongs i els cianobacteris és una realitat en diferents ambients aquàtics que mostren la seva presència a nivells baixos també en zones inesperades amb condicions no favorables per a la seva producció. Gairebé el 80% de les toxines naturals trobades eren fitotoxines, mentre que només s’han identificat provisionalment poques cianotoxines i micotoxines. La diversitat química es basa generalment en la diversitat botànica i l'antropització de la zona. A més, l'estacionalitat i les precipitacions són paràmetres crucials per entendre la presència de fitotoxines respecte a les cianotoxines que s'han trobat també en estacions inesperades. No obstant això, la quantificació no va ser possible per a totes les toxines naturals, ja que només hi havia 32 estàndards disponibles al nostre estudi. En conclusió, el treball presentat en aquesta tesi va permetre omplir alguns dels buits de l’anàlisi de toxines naturals presentant dos enfocaments per augmentar el coneixement sobre la identificació de toxines naturals en aigües superficials. En el futur, hauria de ser crucial actualitzar el darrer enfocament de determinació amb mètodes de quantificació més nous implementant les metòdiques analítiques fent possible la caracterització i la quantificació amb el mateix mètode

Microengineered Electrochemical Tools for in-situ Monitoring of Marine Environment

Measuring the concentration of different compounds in aquatic ecosystem and understanding their impact on the environment are some of the main objectives in the environmental monitoring field. Trace metals, nutrients, volatile organic compounds (VOCs), biotoxins and algaes are among the most important targets of such assessment. Their quantification at an appropriate time scale is crucial in order to understand their dynamics in the marine biogeochemical processes. In situ continuous monitoring is the key to achieve these objectives. This thesis is focused on the development of new micro-engineered tools for improving the performance of electroanalytical techniques by exploiting microfabrication techniques. The developed devices were fabricated by using different techniques, such as thin-film technology, printing and additive manufacturing techniques. The quantification of nutrients is hampered by the high sodium chloride content present in the seawater. Literature is weak concerning systems which provide a selective removal of chloride with respect to other ions. One of the developed tools of this thesis is an environmentally-friendly microfluidic platform for selective sodium chloride removal prior to nutrients detection: chloride removal occurs upon bulk electrolysis in a thin-layer configuration and a ten times-fold reduction was achieved. Trace metals speciation may vary continuously reflecting changing in aquatic system physicochemical conditions. Their quantification is commonly achieved by voltammetric techniques. Voltammetric probes have been reported in literature for detection of trace metals such as lead, cadmium, copper and zinc. The core of these systems is a miniaturized sensor composed by an array of microelectrodes serving as WE and a CE. The reference electrode is a crucial component for the functioning of such sensors however its integration is still challenging. The second tool developed in the framework of this thesis is a three-electrode on-chip sensor for the detection of trace metals, where RE integration is achieved by using a PVC membrane plasticized with ionic liquids as diffusion barrier on top of a silver/silver chloride electrode. These sensors were capable to detect trace metals, but further improvement is required for their quantification. Marine biotoxins are compounds with toxic activity that accumulate in fish and shellfish. Among the various species of biotoxins, another target of this work is saxitoxin, a low molecular weight neurotoxin. Its detection is hindered by its low concentration, therefore a pre-concentration unit is required. Another herein developed tool is a simple microfluidic platform predisposed for pre-concentration of saxitoxin; its working principle is based on the binding of the saxitoxin to a specific aptamer and its release upon a temperature increase. VOCs, such as hydrocarbons and chlorinated hydrocarbons, are considered as significant indicators of urban and industrial pollution. Mid-infrared fiber-optic evanescent wave sensors constitute one of the most promising approaches for continuous VOCs pollution monitoring in seawater. In this thesis a microfluidic platform designed to optimize the enrichment of the polymer layer coating the fiber with the target analytes is developed. The optimization of the device design allowed the simultaneous detection of ten VOCs species. All the tools developed are intended to be integrated in submersible probes for in situ deployment

Novel approaches to the control of infectious diseases

As part of our ongoing efforts to find new drug leads against infectious diseases, several terrestrial and marine macro- and microorganisms were investigated. Several bioactive molecules, presented below, were isolated from these natural products. The mass-screening of dozens of marine Actinomycetes was completed and several Streptomyces with interesting biological activity profiles identified. A few examples are the Streptomyces code H747 and the Streptomyces code H668, a bacterium from which a new (5) and two known polyethers, the antimalarial agent K41-A (6) and its C-29 analog (7) were isolated. Five new six-membered ring cyclic peroxides: plakinastreloic acid A (8), methyl plakinastreloate A (9), the C-12 epimers of methyl 13, 14-epoxyplakinastreloate (10 & 11), and plakinastreloic acid B (12) were isolated from a marine sponge of the genus Plakinastrella. Compounds 8 and 9 exhibited antifungal activities against Candida albicans (IC50 = 6.5 µg/mL and 3.5 µg/mL, respectively), Aspergillus fumigatus (IC50 = 4.0 µg/mL and 9.0 µg/mL, respectively) and Cryptococcus neoformans (IC50 = 4.0 µg/mL and 9.0 µg/mL, respectively). A moderate antimalarial activity against CQ-resistant and CQ-sensitive strains of Plasmodium falciparum was observed, as well. It was also established that 8 possesses anti-HCV (Hepatitis C Virus) activity. Two other compounds were isolated from HCV active methanol extracts of Inga fagifiolia (twigs) and Diplostephium rhodendroides (leaves). These compounds were identified as 2,3,4,5,6-pentahydroxy-2-(hydroxymethyl)hexanamide (14), the amide of a known molecule and 4,5-dihydroxy-3-[(3,4,5-trihydroxy-6-methyltetrahydro-2H-pyran-2-yl)oxy] pentanoic acid (15). The bioassay-guided approach used for their isolation and structure elucidation is reported here. The potential of scCO2 to inactivate bacteria trapped in the gut of oysters was studied. It was established that exposing oysters to CO2 at 100 bar and 37 °C for 30 minutes and at 172 bar and 60 °C for 60 minutes induced 2-log and 3-log reductions in the APC loads, respectively. The decrease in the microbial load as a result of treatment with scCO2 was found to be significant (P = 0.002). A blind study allowing sensory analysis of treated vs. untreated oysters was also completed; no significant difference in the physical appearance, smell, or texture was recorded