Characterisation of ZG16p, a unique mammalian lectin from pancreatic zymogen granules

The mechanisms of secretory granule biogenesis and regulated secretion of digestive enzymes in pancreatic acinar cells are still not well understood. To shed light on these processes, which are of biological and clinical importance (e.g., pancreatitis), a better molecular understanding of the components of the granule membrane, their functions and interactions is required. The application of proteomics has largely contributed to the identification of novel zymogen granule (ZG) proteins but was not yet accompanied by a better characterization of their functions. In this study we aimed at a) isolation and identification of novel membrane-associated ZG proteins; b) characterization of the biochemical properties and function of the secretory lectin ZG16p, a membrane-associated protein; c) exploring the potential of ZG16p as a new tool to label the endolysosomal compartment. First, we have performed a suborganellar proteomics approach by combining protein analysis by 2D-PAGE and identification by mass spectrometry, which has led to the identification of novel peripheral ZGM proteins with proteoglycan-binding properties (e.g., chymase, PpiB). Then, we have unveiled new molecular properties and (multiple) functions of the secretory lectin ZG16p. ZG16p is a unique mammalian lectin with glycan and proteoglycan binding properties. Here, I revealed for the first time that ZG16p is highly protease resistant by developing an enterokinase-digestion assay. In addition I revealed that ZG16p binds to a high molecular weight complex at the ZGM (which is also protease resistant) and forms highly stable dimers. In light of these findings I suggest that ZG16p is a key component of a predicted submembranous granule matrix attached to the luminal side of the ZGM that fulfils important functions during sorting and packaging of zymogens. ZG16p, may act as a linker between the matrix and aggregated zymogens due to dimer formation. Furthermore, ZG16p protease resistance might be of higher importance after secretion since it is known that ZG16p binds to pathogenic fungi in the gut. I have further investigated the role of ZG16p binding motifs in its targeting to ZG in AR42J cells, a pancreatic model system. Point mutations of the glycan and the proteoglycan binding motifs did not inhibit the targeting of ZG16p to ZG in AR42J cells. I have also demonstrated that when ZG16p is present in the cytoplasm it interacts with and modulates the endo-lysosomal compartment. Since it is known that impaired autophagy due to lysosomal malfunction is involved in the course of pancreatitis, a potential role of ZG16p in pancreatitis is discussed.

Assessing the effectiveness of chemical treatment with nanomaterials in improving the quality of different industrial effluents

Industrial activities are the major sources of pollution in all environments. Depending on the type of industry, various levels of organic and inorganic pollutants are being continuously discharged into the environment. Although, several kinds of physical, chemical, biological or the combination of methods have been proposed and applied to minimize the impact of industrial effluents, few have proved to be totally effective in terms of removal rates of several contaminants, toxicity reduction or amelioration of physical and chemical properties. Hence, it is imperative to develop new and innovative methodologies for industrial wastewater treatment. In this context nanotechnology arises announcing the offer of new possibilities for the treatment of wastewaters mainly based on the enhanced physical and chemical proprieties of nanomaterials (NMs), which can remarkably increase their adsorption and oxidation potential. Although applications of NMs may bring benefits, their widespread use will also contribute for their introduction into the environment and concerns have been raised about the intentional use of these materials. Further, the same properties that make NMs so appealing can also be responsible for producing ecotoxicological effects. In a first stage, with the objective of selecting NMs for the treatment of organic and inorganic effluents we first assessed the potential toxicity of nanoparticles of nickel oxide (NiO) with two different sizes (100 and 10-20 nm), titanium dioxide (TiO2, < 25 nm) and iron oxide (Fe2O3, ≈ 85x425 nm). The ecotoxicological assessment was performed with a battery of assays using aquatic organisms from different trophic levels. Since TiO2 and Fe2O3 were the NMs that presented lower risks to the aquatic systems, they were selected for the second stage of this work. Thus, the two NMs pre-selected were tested for the treatment of olive mill wastewater (OMW). They were used as catalyst in photodegradation systems (TiO2/UV, Fe2O3/UV, TiO2/H2O2/UV and Fe2O3/H2O2/UV). The treatments with TiO2 or Fe2O3 combined with H2O2 were the most efficient in ameliorating some chemical properties of the effluent. Regarding the toxicity to V. fischeri the highest reduction was recorded for the H2O2/UV system, without NMs. Afterwards a sequential treatment using photocatalytic oxidation with NMs and degradation with white-rot fungi was applied to OMW. This new approach increased the reduction of chemical oxygen demand, phenolic content and ecotoxicity to V. fischeri. However, no reduction in color and aromatic compounds was achieved after 21 days of biological treatment. The photodegradation systems were also applied to treat the kraft pulp mill and mining effluents. For the organic effluent the combination NMs and H2O2 had the best performances in reduction the chemical parameters as well in terms of toxicity reduction. However, for the mine effluent the best (TiO2/UV and Fe2O3/UV) were only able to significantly remove three metals (Zn, Al and Cd). Nonetheless the treatments were able of reducing the toxicity of the effluent. As a final stage, the toxicity of solid wastes formed during wastewater treatment with NMs was assessed with Chironomus riparius larvae, a representative species of the sediment compartment. Certain solid wastes showed the potential to negatively affect C. riparius survival and growth, depending on the type of effluent treated. This work also brings new insights to the use of NMs for the treatment of industrial wastewaters. Although some potential applications have been announced, many evaluations have to be performed before the upscaling of the chemical treatments with NMs.

Codon ambiguities as a mechanism to alter the genetic code in Saccharomyces cerevisiae

Although the genetic code is generally viewed as immutable, alterations to its standard form occur in the three domains of life. A remarkable alteration to the standard genetic code occurs in many fungi of the Saccharomycotina CTG clade where the Leucine CUG codon has been reassigned to Serine by a novel transfer RNA (Ser-tRNACAG). The host laboratory made a major breakthrough by reversing this atypical genetic code alteration in the human pathogen Candida albicans using a combination of tRNA engineering, gene recombination and forced evolution. These results raised the hypothesis that synthetic codon ambiguities combined with experimental evolution may release codons from their frozen state. In this thesis we tested this hypothesis using S. cerevisiae as a model system. We generated ambiguity at specific codons in a two-step approach, involving deletion of tRNA genes followed by expression of non-cognate tRNAs that are able to compensate the deleted tRNA. Driven by the notion that rare codons are more susceptible to reassignment than those that are frequently used, we used two deletion strains where there is no cognate tRNA to decode the rare CUC-Leu codon and AGG-Arg codon. We exploited the vulnerability of the latter by engineering mutant tRNAs that misincorporate Ser at these sites. These recombinant strains were evolved over time using experimental evolution. Although there was a strong negative impact on the growth rate of strains expressing mutant tRNAs at high level, such expression at low level had little effect on cell fitness. We found that not only codon ambiguity, but also destabilization of the endogenous tRNA pool has a strong negative impact in growth rate. After evolution, strains expressing the mutant tRNA at high level recovered significantly in several growth parameters, showing that these strains adapt and exhibit higher tolerance to codon ambiguity. A fluorescent reporter system allowing the monitoring of Ser misincorporation showed that serine was indeed incorporated and possibly codon reassignment was achieved. Beside the overall negative consequences of codon ambiguity, we demonstrated that codons that tolerate the loss of their cognate tRNA can also tolerate high Ser misincorporation. This raises the hypothesis that these codons can be reassigned to standard and eventually to new amino acids for the production of proteins with novel properties, contributing to the field of synthetic biology and biotechnology.

Infection mechanism of Diplodia corticola

Diplodia corticola is regarded as the most virulent fungus involved in cork oak decline, being able to infect not only Quercus species (mainly Q. suber and Q. ilex), but also grapevines (Vitis vinifera) and eucalypts (Eucalyptus sp.). This endophytic fungus is also a pathogen whose virulence usually manifests with the onset of plant stress. Considering that the infection normally culminates in host death, there is a growing ecologic and socio-economic concern about D. corticola propagation. The molecular mechanisms of infection are hitherto largely unknown. Accordingly, the aim of this study was to unveil potential virulence effectors implicated in D. corticola infection. This knowledge is fundamental to outline the molecular framework that permits the fungal invasion and proliferation in plant hosts, causing disease. Since the effectors deployed are mostly proteins, we adopted a proteomic approach. We performed in planta pathogenicity tests to select two D. corticola strains with distinct virulence degrees for our studies. Like other filamentous fungi D. corticola secretes protein at low concentrations in vitro in the presence of high levels of polysaccharides, two characteristics that hamper the fungal secretome analysis. Therefore, we first compared several methods of extracellular protein extraction to assess their performance and compatibility with 1D and 2D electrophoretic separation. TCA-Acetone and TCA-phenol protein precipitation were the most efficient methods and the former was adopted for further studies. The proteins were extracted and separated by 2D-PAGE, proteins were digested with trypsin and the resulting peptides were further analysed by MS/MS. Their identification was performed by de novo sequencing and/or MASCOT search. We were able to identify 80 extracellular and 162 intracellular proteins, a milestone for the Botryosphaeriaceae family that contains only one member with the proteome characterized. We also performed an extensive comparative 2D gel analysis to highlight the differentially expressed proteins during the host mimicry. Moreover, we compared the protein profiles of the two strains with different degrees of virulence. In short, we characterized for the first time the secretome and proteome of D. corticola. The obtained results contribute to the elucidation of some aspects of the biology of the fungus. The avirulent strain contains an assortment of proteins that facilitate the adaptation to diverse substrates and the identified proteins suggest that the fungus degrades the host tissues through Fenton reactions. On the other hand, the virulent strain seems to have adapted its secretome to the host characteristics. Furthermore, the results indicate that this strain metabolizes aminobutyric acid, a molecule that might be the triggering factor of the transition from a latent to a pathogenic state. Lastly, the secretome includes potential pathogenicity effectors, such as deuterolysin (peptidase M35) and cerato-platanin, proteins that might play an active role in the phytopathogenic lifestyle of the fungus. Overall, our results suggest that D. corticola has a hemibiotrophic lifestyle, switching from a biotrophic to a necrotrophic interaction after plant physiologic disturbances.This understanding is essential for further development of effective plant protection measures.

Screening for biological activities with application in aquaculture in halophytes from the Algarve coastline

Infectious diseases often hamper the production of aquatic organisms in aquaculture systems, causing economical losses, environmental problems and consumer safety issues. The conventional way aquaculture producers had to control pathogens was by means of synthetic antibiotics and chemicals. This procedure had consequences in the emergence of more resilient pathogens, drug contamination of seafood products and local ecosystems. To avoid the repercussions of antibiotic use, vaccination has greatly replaced human drugs in western fish farms. However there is still massive unregulated antibiotic use in third world fish farms, so less expensive therapeutic alternatives for drugs are desperately needed. An alternative way to achieve disease control in aquaculture is by using natural bioactive organic compounds with antibiotic, antioxidant and/or immunostimulant properties. Such diverse biomolecules occur in bacteria, algae, fungi, higher plants and other organisms. Fatty acids, nucleotides, monosaccharides, polysaccharides, peptides, polyphenols and terpenoids, are examples of these substances. One promising source of bioactive compounds are salt tolerant plants. Halophytes have more molecular resources and defence mechanisms, when compared with other tracheophytes, to deal with the oxidative stresses of their habitat. Many halophytes have been used as a traditional food and medical supply, especially by African and Asian cultures. This scientific work evaluated the antibiotic, antioxidant, immunostimulant and metal chelating properties of Atriplex halimus L., Arthrocnemum macrostachyum Moric., Carpobrotus edulis L., Juncus acutus L. and Plantago coronopus L., from the Algarve coast. The antibiotic properties were tested against Listonella anguillarum, Photobacterium damselae piscicida and Vibrio fischeri. The immunostimulant properties were tested with cytochrome c and Griess assays on Sparus aurata head-kidney phagocytes. J. acutus ether extract inhibited the growth of P. damselae piscicida. A. macrostachyum, A. halimus, C. edulis, Juncus acutus and P. coronopus displayed antioxidant, copper chelating and iron chelating properties. These plants show potential as sources of bioactive compounds with application in aquaculture and in other fields.

Bacterial peroxide forming enzymes

Dissertação de mestrado, Engenharia Biológica, Faculdade de Ciências e Tecnologia, Universidade do Algarve; Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, 2015

MOHO EN ESPACIOS INTERIORES

This paper written in Spanish gives hints on what to do to control mold after the flooding in October 2015 in South Carolina. Topics include: presence of mold after a flood, signs of mold, people at greatest risk for health effects from mold, possible health effects of mold exposure and cleaning wet or moldy Items after a flood. It also gives web sites for additional information and resources.

Development of new methodologies for C-H insertion

Tese de doutoramento, Farmácia (Química Farmacêutica e Terapêutica), Universidade de Lisboa, Faculdade de Farmácia, 2014

Development of Detection Systems for the Sporangia of Peronospora Destructor

A monoclonal antibody that recognises components of the wall of sporangia of Peronospora destructor was raised. Tests using spores of higher fungi and other species of mildew demonstrated the specificity of the monoclonal. The antibody was used to develop lateral flow devices for sporangia of P. destructor. A competitive lateral flow format was developed which could detect onion downy mildew sporangia. Five-microliter gold anti-mouse IgM solution pre-mixed with 10 μl of P. destructor monoclonal antibody (EMA 242) proved the optimal concentration for detection of sporangia of P. destructor when applied to sample pads of lateral flow devices. Limits of approximately 500 sporangia of P. destructor could be detected by the absence of a test line on the lateral flow device within test samples. Using a scanning densitometer improved the sensitivity of detection. Further development and validation of the test is required if it is to be used for risk assessments of onion downy mildew in the field.

Determination of Alternaria spp. Habitats Using 7-Day Volumetric Spore Trap, Hybrid Single Particle Lagrangian Integrated Trajectory Model and Geographic Information System

There are many species among the Alternaria genus, which hosts on economically important crops causing significant yield losses. Less attention has been paid to fungi hosting on plants constituting substantial components of pastures and meadows. Alternaria spp. spores are also recognised as important allergens. A 7-day volumetric spore trap was used to monitor the concentration of airborne fungal spores. Air samples were collected in Worcester, England (2006–2010). Days with a high spore count were then selected. The longest episode that occurred within a five year study was chosen for modelling. Two source maps presenting distribution of crops under rotation and pastures in the UK were produced. Back trajectories were calculated using the HYSPLIT model. In ArcGIS clusters of trajectories were studied in connection with source maps by including the height above ground level and the speed of the air masses. During the episode no evidence for a long distance transport from the continent of Alternaria spp. spores was detected. The overall direction of the air masses fell within the range from South-West to North. The back trajectories indicated that the most important sources of Alternaria spp. spores were located in the West Midlands of England.

Application of Redundancy Analysis for Aerobiological Data

An aerobiological survey was conducted through five consecutive years (2006–2010) at Worcester (England).The concentration of 20 allergenic fungal spore types was measured using a 7-day volumetric spore trap. The relationship between investigated fungal spore genera and selected meteorological parameters (maximum, minimum, mean and dew point temperatures, rainfall, relative humidity, air pressure,wind direction) was examined using an ordination method(redundancy analysis) to determine which environmental factors favoured their most abundance in the air and whether it would be possible to detect similarities between different genera in their distribution pattern. Redundancy analysis provided additional information about the biology of the studied fungi through the results of the Spearman’s rank correlation. Application of the variance inflation factor in canonical correspondence analysis indicated which explanatory variables were auto-correlated and needed to be excluded from further analyses. Obtained information will be consequently implemented in the selection of factors that will be a foundation for forecasting models for allergenic fungal spores in the future.

Potential Sources of Airborne Alternaria spp. spores in South-west Spain

Fungi belonging to the genus of Alternaria are recognised as being significant plant pathogens, and Alternaria allergens are one of themost important causes of respiratory allergic diseases in Europe. This study aims to provide a detailed and original analysis of Alternaria transport dynamics in Badajoz, SW Spain. This was achieved by examining daily mean and hourly observations of airborne Alternaria spores recorded during days with high airborne concentrations of Alternaria spores (N100 s m−3) from 2009 to 2011, as well as four inventory maps of major Alternaria habitats, the overall synoptic weather situation and analysis of air mass transport using Hybrid Single Particle Lagrangian Integrated Trajectory model and geographic information systems. Land use calculated within a radius of 100 km from Badajoz shows that crops and grasslands are potentially the most important local sources of airborne Alternaria spores recorded at the site. The results of back trajectory analysis showthat, during the examined four episodes, the two main directions where Alternaria source areas were located were: (1) SW–W; and (2) NW–NE. Regional scale and long distance transport could therefore supplement the airborne catch recorded at Badajoz with Alternaria conidia originating from sources such as crops and orchards situated in other parts of the Iberian Peninsula.

Differing methodologies to measure microbe dispersal during hand drying

Background: Having previously investigated the dispersal by different hand drying methods of a chemical indicator, fungi and bacteria on the hands of users, this new study assessed the potential for viral dispersal. Aims/Objectives: To determine differences between hand drying methods in their capacity to disperse viruses on the hands of users to other occupants of public washrooms and into the washroom environment. Method: A harmless virus was used to artificially contaminate the hands of participants prior to using three different hand drying devices (jet air dryer, warm air dryer, paper towel dispenser). Viral dispersal was assessed at different heights and distances from the hand drying devices and also at different times after use by means of an air sampler. Results: The jet air dryer was shown to produce significantly more dispersal of virus than the warm air dryer or paper towels. After use of the jet air dryer, high numbers of virus were detected at a range of heights with maximum numbers between 0.61 and 1.22 metres. Virus was also detected at distances of up to 3 metres from the jet air dryer and in the air for up to 15 minutes after its use. The warm air dryer and paper towel dispenser produced low or zero viral counts at different heights, different distances and times after use. Conclusion: Jet air dryers have a greater potential than other hand drying methods to disperse viruses on the hands and contaminate other occupants of a public washroom and the washroom environment.

The risk of viral dispersal and aerosolization by different hand-drying methods

Background World Health Organization hand hygiene guidelines state that if electric hand dryers are used, they should not aerosolize pathogens. Previous studies have investigated the dispersal by different hand-drying devices of chemical indicators, fungi and bacteria on the hands. This study assessed the aerosolization and dispersal of virus on the hands to determine any differences between hand-drying devices in their potential to contaminate other occupants of public washrooms and the washroom environment. Methods A suspension of MS2, an Escherichia coli bacteriophage virus, was used to artificially contaminate the hands of participants prior to using three different handdrying devices: jet air dryer, warm air dryer, paper towel dispenser. Virus was detected by plaque formation on agar plates layered with the host bacterium. Vertical dispersal of virus was assessed at a fixed distance (0.4 m) and over a range of different heights (0.0 – 1.8 m) from the floor. Horizontal dispersal was assessed at different distances of up to three metres from the hand-drying devices. Virus aerosolization and dispersal was also assessed at different times up to 15 minutes after use by means of air sampling at two distances (0.1 and 1.0 m) and at a distance behind and offset from each of the hand-drying devices. Results Over a range of heights, the jet air dryer was shown to produce over 60 times greater vertical dispersal of virus from the hands than a warm air dryer and over 1300 times greater than paper towels; the maximum being detected between 0.6 and 1.2 metres from the floor. Horizontal dispersal of virus by the jet air dryer was over 20 times greater than a warm air dryer and over 190 times greater than paper towels; virus being detected at distances of up to three metres. Air sampling at three different positions from the hand-drying devices 15 minutes after use showed that the jet air dryer produced over 50-times greater viral contamination of the air than a warm air dryer and over 110-times greater than paper towels. Conclusions Due to their high air speed, jet air dryers aerosolize and disperse more virus over a range of heights, greater distances, and for longer times than other hand drying devices. If hands are inadequately washed, they have a greater potential to contaminate other occupants of a public washroom and the washroom environment. Main messages: Jet air dryers with claimed air speeds of over 600 kph have a greater potential than warm air dryers or paper towels to aerosolize and disperse viruses on the hands of users. The choice of hand-drying device should be carefully considered. Jet air dryers may increase the risk of transmission of human viruses, such as norovirus, particularly if hand washing is inadequate.

Comparison of virus dispersal and aerosolization by different hand-drying devices

Background World Health Organization and EU hand hygiene guidelines state that if electric hand dryers are used, they should not aerosolize pathogens. Previous studies have investigated the dispersal by different hand-drying devices of chemical indicators, fungi and bacteria on the hands. This study assessed the aerosolization and dispersal of virus on the hands to determine any differences between hand-drying devices in their potential to contaminate other occupants of public washrooms and the washroom environment. Methods A suspension of MS2, an Escherichia coli bacteriophage virus, was used to artificially contaminate the hands of participants prior to using three different hand-drying devices: jet air dryer, warm air dryer, paper towel dispenser. Virus was detected by plaque formation on agar plates layered with the host bacterium. Vertical dispersal of virus was assessed at a fixed distance (0.4 m) and over a range of different heights (0.0 – 1.8 m) from the floor. Horizontal dispersal was assessed at different distances of up to three metres from the hand-drying devices. Virus aerosolization and dispersal was also assessed at different times up to 15 minutes after use by means of air sampling at two distances (0.1 and 1.0 m) and at a distance behind and offset from each of the hand-drying devices. Results Over a range of heights, the jet air dryer was shown to produce over 60 times greater vertical dispersal of virus from the hands than a warm air dryer and over 1300 times greater than paper towels; the maximum being detected between 0.6 and 1.2 metres from the floor. Horizontal dispersal of virus by the jet air dryer was over 20 times greater than a warm air dryer and over 190 times greater than paper towels; virus being detected at distances of up to three metres. Air sampling at three different positions from the hand-drying devices 15 minutes after use showed that the jet air dryer produced over 50-times greater viral contamination of the air than a warm air dryer and over 110-times greater than paper towels. Conclusions Due to their high air speed, jet air dryers aerosolize and disperse more virus over a range of heights, greater distances, and for longer times than other hand drying devices. If hands are inadequately washed, they have a greater potential to contaminate other occupants of a public washroom and the washroom environment. Main messages: Jet air dryers with claimed air speeds of over 600 kph have a greater potential than warm air dryers or paper towels to aerosolize and disperse viruses on the hands of users. The choice of hand-drying device should be carefully considered. Jet air dryers may increase the risk of transmission of human viruses, such as norovirus, particularly if hand washing is inadequate.