Bacterial community structure of the marine diatom Haslea ostrearia

The marine diatom Haslea ostrearia produces a water-soluble blue-pigment named marennine of economic interest (e.g. in aquaculture for the greening of oysters). Up to date the studies devoted to ecological conditions under which this microalga develops never took into account the bacterial-H. ostrearia relationships. In this study the bacterial community was analysed by PCR-TTGE before and after H. ostrearia isolation cells recovered from 4 localities, to distinguish the relative part of the biotope and the biocenose and eventually to describe the temporal dynamic of the structure of the bacterial community. The bacterial structure of the phycosphere differed strongly from that of the bulk sediment. The similarity between bacteria recovered from the biofilm and the suspended bacteria did not exceed 10% (vs. > 90% amongst biofilms). The differences in genetic fingerprints, more especially high between two H. ostrearia isolates showed also the highest differences in the bacterial structure as the result of specific metabolomics profiles. The non-targeted metabolomic investigation showed that these profiles were more distinct in case of bacteria-alga associations than for the H. ostrearia monoculture. At the scale of a culture cycle in laboratory conditions, the bacterial community was specific to the growth stage. When H. ostrearia was subcultured for 9 months, a shift in the bacterial structure was shown from 3-months subculturing and the bacterial structure stabilized afterwards (70-86% similarities). A first insight of the relationships between H. ostrearia and its surrounding bacteria was shown for a better understanding of the ecological feature of this diatom.

First metabolomic approach of the epiphytic bacteria-marine diatom Haslea ostrearia relationships

The marine diatom Haslea ostrearia [1] produces a water-soluble blue-pigment named marennine [2] of economic interest. But the lack of knowledge of the ecological conditions, under which this microalga develops in its natural ecosystem, more especially bacteria H. ostrearia interactions, prevents any optimization of its culture in well-controlled conditions. The structure of the bacterial community was analyzed by PCR-TTGE before and after the isolation of H. ostrearia cells recovered from 4 localities, to distinguish the relative part of the biotope and the biocenose and eventually to describe the temporal dynamic of the structure of the bacterial community at two time-scales. The differences in genetic fingerprints, more especially high between two H. ostrearia isolates (HO-R and HO-BM) showed also the highest differences in the bacterial structure [3] as the result of specific metabolomics profiles. The non-targeted metabolomic investigation showed that these profiles were more distinct in case of bacteria-alga associations than for the H. ostrearia monoculture Here we present a Q-TOF LC/MS metabolomic fingerprinting approach [3]: - to investigate differential metabolites of axenic versus non axenic H. ostrearia cultures. - to focus on the specific metabolites of a bacterial surrounding associated with the activation or inhibition of the microalga growing. The Agilent suite of data processing software makes feature finding, statistical analysis, and identification easier. This enables rapid transformation of complex raw data into biologically relevant metabolite information.

Preliminary metabolomic approach on the bacterial structure community of Haslea ostrearia

The marine diatom Haslea ostrearia [1] produces a water-soluble blue-pigment named marennine [2] of economic interest. But the lack of knowledge of the ecological conditions, under which this microalga develops in its natural ecosystem, more especially bacteria H. ostrearia interactions, prevents any optimization of its culture in well-controlled conditions. The structure of the bacterial community was analyzed by PCR-TTGE before and after the isolation of H. ostrearia cells recovered from 4 localities, to distinguish the relative part of the biotope and the biocenose and eventually to describe the temporal dynamic of the structure of the bacterial community at two time-scales. The differences in genetic fingerprints, more especially high between two H. ostrearia isolates (HO-R and HO-BM) showed also the highest differences in the bacterial structure [3] as the result of specific metabolomics profiles. The non-targeted metabolomic investigation showed that these profiles were more distinct in case of bacteria-alga associations than for the H. ostrearia monoculture Here we present a Q-TOF LC/MS metabolomic fingerprinting approach [3]: - to investigate differential metabolites of axenic versus non axenic H. ostrearia cultures. - to focus on the specific metabolites of a bacterial surrounding associated with the activation or inhibition of the microalga growing. The Agilent suite of data processing software makes feature finding, statistical analysis, and identification easier. This enables rapid transformation of complex raw data into biologically relevant metabolite information.

Polymeric alginate nanoparticles containing the local anesthetic bupivacaine

Bupivacaine (BVC; S75-R25, NovaBupiwater-soluble linear polysaccharide. The present study reports the development of alginate/bis(2-ethylhexyl) sulfosuccinate (AOT) and alginate/chitosan nanoparticle formulations containing BVC (0.5%). The amounts of BVC associated in the alginate/AOT and alginate/chitosan nanoparticles were 87 +/- 1.5 and 76 +/- 0.9%, respectively. The average diameters and zeta potentials of the nanoparticles were measured for 30 days, and the results demonstrated the good stability of these particles in solution. The in vitro release kinetics showed a different behavior for the release profile of BVC in solution, compared with BVC-loaded alginate nanoparticles. In vitro and in vivo assays showed that alginate-chitosan BVC (BVC(ALG-CHIT)) and alginate-AOT BVC (BVC(ALG-AOT)) presented low cytotoxicity in 3T3-fibroblasts, enhanced the intensity, and prolonged the duration of motor and sensory blockades in a sciatic nerve blockade model.

Síntese, aplicação e avaliação do efeito do teor de fósforo da celulose fosfatada em argamassa de alvenaria com aditivo comercial a base de hidroxi-etil-metil celulose (HEMC)

Generally, cellulose ethers improves mortar properties such as water retention, workability and setting time, along with adherence to the substrate. However, a major disadvantage of the addition of cellulose ethers in mortars is the delay in hydration of the cement. In this paper a cellulose phosphate (Cp) was synthesized water soluble and has been evaluated the effect of their incorporation into mortar based on Portland cement. Cellulose phosphate obtained was characterized by spectrophotometry Fourier transform infrared (FTIR), X-ray diffraction (XRD), elemental analysis and scanning electron microscopy (SEM). Mortar compositions were formulated with varying phosphorus content in cellulose and cellulose phosphate concentrations, when used in partial or total replacement of the commercial additive based hydroxyethyl methyl cellulose (HEMC). The mortars formulated with additives were prepared and characterized by: testing in the fresh state (consistency index, water retention, bulk density and air content incorporated) and in the hardened state (absorption by capillarity, density, flexural and compression strength). In mixtures the proportion of sand:cement of 1:5 (v / v) and factor a / c = 1.31 and water were held constant. Overall, the results showed that the celluloses phosphates employed in mortars added acted significantly when partially substituting the commercial additive. With regard to consistency index, water retention and bulk density in the fresh state and absorption by capillarity and bulk density apparent in the hardened state, showed no appreciable differences as compared to the commercial additive. The incorporated air content in the fresh state reduced markedly, but did not affect other properties. The mortars with cellulose phosphate, partially replacing the commercial additive showed an improvement of the properties of flexural strength and compressive strength

Temporal Control of Ion Channel Activation

Ion channels are a large class of integral membrane proteins that allow for the diffusion of ions across a cellular membrane and are found in all forms of life. Pentameric ligand-gated ion channels (pLGICs) comprise a large family of proteins that include the nicotinic acetylcholine receptor (nAChR) and the γ-aminobutyric acid (GABA) receptor. These ion channels are responsible for the fast synaptic transmission that occurs in humans and as a result are of fundamental biological importance. pLGICs bind ligands (neurotransmitters), and upon ligand-binding undergo activation. The activation event causes an ion channel to enter a new physical state that is able to conduct ions. Ion channels allow for the flux of ions across the membrane through a pore that is formed upon ion channel activation. For pLGICs to function properly both ligand-binding and ion channel activation must occur. The ligand-binding event has been studied extensively over the past few decades, and a detailed mechanism of binding has emerged. During activation the ion channel must undergo structural rearrangements that allow the protein to enter a conformation in which ions can flow through. Despite this great and ubiquitous importance, a fundamental understanding of the ion channel activation mechanism and kinetics, as well as concomitant structural arrangements, remains elusive.

This dissertation describes efforts that have been made to temporally control the activation of ligand-gated ion channels. Temporal control of ion channel activation provides a means by which to activate ion channels when desired. The majority of this work examines the use of light to activate ion channels. Several photocages were examined in this thesis; photocages are molecules that release a ligand under irradiation, and, for the work described here, the released ligand then activates the ion channel. First, a new water-soluble photoacid was developed for the activation of proton-sensitive ion channels. Activation of acid-sensing ion channels, ASIC2a and GLIC, was observed only upon irradiation. Next, a variety of Ru²⁺ photocages were also developed for the release of amine ligands. The Ru²⁺ systems interacted in a deleterious manner with a representative subset of biologically essential ion channels. The rapid mixing of ion channels with agonist was also examined. A detection system was built to monitor ion channels activation in the rapid mixing experiments. I have shown that liposomes, and functionally-reconstituted ELIC, are not destroyed during the mixing process. The work presented here provides the means to deliver agonist to ligand-gated ion channels in a controlled fashion.

Do improved pastures affect enzymatic activity and C and N dynamics in soils of the montado system ?

Vast montado areas are threatened by degradation, as the result of a long history of land use changes. Since improved pastures have been installed aiming soil quality improvement and system sustainability, it is crucial to evaluate the effects of these management changes on soil organic matter status and soil biological activity, as soil quality indicators. Therefore, a 35-yr old improved pasture and a natural pasture were studied, considering areas beneath tree canopy and in the open. Total organic C, total N, hot water soluble (HWS) and particulate (POM) C, microbial biomass C (MBC) and N (MBN), C mineralization rate (CMR) and net N mineralization rate (NMR) were determined. In addition, for a 1-yr period, soil β-glucosidase, urease, proteases and acid phosphomonoesterase were periodically determined. Improved pasture promoted the increase of soil C and N through POM-C increment, particularly beneath the trees canopies. The two study pastures did not show differences regarding soil microbial biomass, but variations in CMR, HWS-C and N availability (proteases and urease activities) suggest divergent soil microbial communities. Tree regulator role on C, N and P transformation processes in soil was confirmed

DESIGN, SYNTHESIS AND APPLICATIONS OF FLUORESCENT AND ELECTROCHEMICAL PROBES

“Seeing is believing” the proverb well suits for fluorescent imaging probes. Since we can selectively and sensitively visualize small biomolecules, organelles such as lysosomes, neutral molecules, metal ions, anions through cellular imaging, fluorescent probes can help shed light on the physiological and pathophysiological path ways. Since these biomolecules are produced in low concentrations in the biochemical pathways, general analytical techniques either fail to detect or are not sensitive enough to differentiate the relative concentrations. During my Ph.D. study, I exploited synthetic organic techniques to design and synthesize fluorescent probes with desirable properties such as high water solubility, high sensitivity and with varying fluorescent quantum yields. I synthesized a highly water soluble BOIDPY-based turn-on fluorescent probe for endogenous nitric oxide. I also synthesized a series of cell membrane permeable near infrared (NIR) pH activatable fluorescent probes for lysosomal pH sensing. Fluorescent dyes are molecular tools for designing fluorescent bio imaging probes. This prompted me to design and synthesize a hybrid fluorescent dye with a functionalizable chlorine atom and tested the chlorine re-activity for fluorescent probe design. Carbohydrate and protein interactions are key for many biological processes, such as viral and bacterial infections, cell recognition and adhesion, and immune response. Among several analytical techniques aimed to study these interactions, electrochemical bio sensing is more efficient due to its low cost, ease of operation, and possibility for miniaturization. During my Ph.D., I synthesized mannose bearing aniline molecule which is successfully tested as electrochemical bio sensor. A Ferrocene-mannose conjugate with an anchoring group is synthesized, which can be used as a potential electrochemical biosensor.

A BACKING DEVICE BASED ON AN EMBEDDED STIFFENER AND RETRACTABLE INSERTION TOOL FOR THIN-FILM COCHLEAR ARRAYS

Intracochlear trauma from surgical insertion of bulky electrode arrays and inadequate pitch perception are areas of concern with current hand-assembled commercial cochlear implants. Parylene thin-film arrays with higher electrode densities and lower profiles are a potential solution, but lack rigidity and hence depend on manually fabricated permanently attached polyethylene terephthalate (PET) tubing based bulky backing devices. As a solution, we investigated a new backing device with two sub-systems. The first sub-system is a thin poly(lactic acid) (PLA) stiffener that will be embedded in the parylene array. The second sub-system is an attaching and detaching mechanism, utilizing a poly(N-vinylpyrrolidone)-block-poly(d,l-lactide) (PVP-b-PDLLA) copolymer-based biodegradable and water soluble adhesive, that will help to retract the PET insertion tool after implantation. As a proof-of-concept of sub-system one, a microfabrication process for patterning PLA stiffeners embedded in parylene has been developed. Conventional hotembossing, mechanical micromachining, and standard cleanroom processes were integrated for patterning fully released and discrete stiffeners coated with parylene. The released embedded stiffeners were thermoformed to demonstrate that imparting perimodiolar shapes to stiffener-embedded arrays will be possible. The developed process when integrated with the array fabrication process will allow fabrication of stiffener-embedded arrays in a single process. As a proof-of-concept of sub-system two, the feasibility of the attaching and detaching mechanism was demonstrated by adhering 1x and 1.5x scale PET tube-based insertion tools and PLA stiffeners embedded in parylene using the copolymer adhesive. The attached devices survived qualitative adhesion tests, thermoforming, and flexing. The viability of the detaching mechanism was tested by aging the assemblies in-vitro in phosphate buffer solution. The average detachment times, 2.6 minutes and 10 minutes for 1x and 1.5x scale devices respectively, were found to be clinically relevant with respect to the reported array insertion times during surgical implantation. Eventually, the stiffener-embedded arrays would not need to be permanently attached to current insertion tools which are left behind after implantation and congest the cochlear scala tympani chamber. Finally, a simulation-based approach for accelerated failure analysis of PLA stiffeners and characterization of PVP-b-PDLLA copolymer adhesive has been explored. The residual functional life of embedded PLA stiffeners exposed to body-fluid and thereby subjected to degradation and erosion has been estimated by simulating PLA stiffeners with different parylene coating failure types and different PLA types for a given parylene coating failure type. For characterizing the PVP-b-PDLLA copolymer adhesive, several formulations of the copolymer adhesive were simulated and compared based on the insertion tool detachment times that were predicted from the dissolution, degradation, and erosion behavior of the simulated adhesive formulations. Results indicate that the simulation-based approaches could be used to reduce the total number of time consuming and expensive in-vitro tests that must be conducted.

Microfluidics based manufacture of liposomes simultaneously entrapping hydrophilic and lipophilic drugs

Despite the substantial body of research investigating the use of liposomes, niosomes and other bilayer vesicles for drug delivery, the translation of these systems into licensed products remains limited. Indeed, recent shortages in the supply of liposomal products demonstrate the need for new scalable production methods for liposomes. Therefore, the aim of our research has been to consider the application of microfluidics in the manufacture of liposomes containing either or both a water soluble and a lipid soluble drug to promote co-delivery of drugs. For the first time, we demonstrate the entrapment of a hydrophilic and a lipophilic drug (metformin and glipizide respectively) both individually, and in combination, using a scalable microfluidics manufacturing system. In terms of the operating parameters, the choice of solvents, lipid concentration and aqueous:solvent ratio all impact on liposome size with vesicle diameter ranging from ∼90 to 300 nm. In terms of drug loading, microfluidics production promoted high loading within ∼100 nm vesicles for both the water soluble drug (20–25% of initial amount added) and the bilayer embedded drug (40–42% of initial amount added) with co-loading of the drugs making no impact on entrapment efficacy. However, co-loading of glipizide and metformin within the same liposome formulation did impact on the drug release profiles; in both instances the presence of both drugs in the one formulation promoted faster (up to 2 fold) release compared to liposomes containing a single drug alone. Overall, these results demonstrate the application of microfluidics to prepare liposomal systems incorporating either or both an aqueous soluble drug and a bilayer loaded drug.

Defensive role of allelopathic secondary compounds in plants I: testing two independent general hypotheses

This study tests two general and independent hypotheses with the basic assumption that phytoactive secondary compounds produced by plants evolved primarily as plant defences against competitor plant species. The first hypothesis is that the production and main way of release of phytoactive compounds reflect an adaptive response to climatic conditions. Thus, higher phytoactivity by volatile compounds prevails in plants of hot, dry environments, whereas higher phytoactivity by water-soluble compounds is preponderant in plants from wetter environments. The second hypothesis is that synergy between plant phytoactive compounds is widespread, due to the resulting higher energy efficiency and economy of resources. The first hypothesis was tested on germination and early growth of cucumber treated with either water extracts or volatiles from leaves or vegetative shoot tops of four Mediterranean-type shrubs. The second hypothesis was tested on germination of subterranean clover treated with either water extracts of leaves or vegetative shoot tops of one tree and of three Mediterranean-type shrubs or with each of the three fractions obtained from water extracts. Our data do not support either hypotheses. We found no evidence for higher phytoactivity in volatile compounds released by plants that thrive in hot, dry Mediterranean-type environments. We also found no evidence for the predominance of synergy among the constituents of fractions. To the contrary, we found either antagonism or no interaction of effects among allelopathic compounds.

Effects of nitrogen level on purslane antioxidant activity.

The high antioxidant activity of purslane, Portulaca oleracea L., gives it a high nutritional and functional value. The commercial production of purslane has increased in Portugal, making it necessary to know the effects of inputs, mainly nitrogen, on the antioxidant activity. The main goal of this study was to evaluate the influence of nitrogen application on purslane antioxidant activity. The experiment was carried out with for treatments: 30, 60 and 90 kg/ha of nitrogen. Plants of golden-leaf purslane were grown in Styrofoam-boxes filled with substrate and fertigated two times per week, over four weeks with ammonium nitrate solution (16.9% NO3-N and 16.7 NH4+-N). The increase in the nitrogen level decreased the water-soluble proteins content. However the ascorbate, phenols content as well as antioxidant activity measured by FRAP method was not affected by nitrogen level. Plants shoot antioxidant activity, measured by DPPH method decreased significantly in the treatment with 90 kg N/ha (26.20 g/g gallic acid). On the other hand, plant shoot antioxidant activity mediated by peroxidases was higher in treatment 30 kg N/ha (0.459 µmol min-1/mg prot.). Application of 60 kg N/ha allowed a vigorous plant growth without disturb its antioxidants and conservation properties.

Emerging plant-based proteins: comparison from extraction to functional properties and food application

The increasing demand for alternatives to meat food products, which is linked to ethical and environmental reasons, highlights the necessity of using different protein sources. Plant proteins provide a valid option, thanks to the relative low costs, high availability and wide supply sources. The current process used to produce plant concentrates and isolates is the alkaline extraction followed by isoelectric precipitation. However, despite the high purity of the proteins, it presents some drawbacks. Innovative protein extraction processes are emerging, with the aim of reducing the environmental impact and the costs, as well as improving the functional properties. In this study, the traditional wet protein extraction and another simplified wet process were used to obtain protein-rich extracts out of different plants. The sources considered in the project were de-oiled sunflower and canola, chickpea, lentils, and the camelina meal, an emerging oleaginous seed interesting for its high content of omega 3. The extracts obtained from the two processes were then analysed for their capacities to hold water and fat, to form gel and a stable foam. Results highlighted strong differences concerning the protein content, yield and functionalities. The extracts obtained with the alkaline process confirmed the literature data about the four plant sources (sunflower, canola, chickpea and lentils) and allow to obtain a camelina concentrate with a protein content of 63 % and a protein recovery of 41 %. The second easiest process was not effective to obtain a protein enrichment in oleaginous sources, whereas an enrichment of 10 and 15 % was obtained in chickpea and lentils, respectively. The functional properties were also completely different: the easiest process produced protein ingredients completely water-soluble at pH 7, with a discrete foaming capacity compared to the extracts obtained with alkaline process. These characteristics could make these extracts suitable for the plant milk-analogue products.

A novel hybrid thermochemical-biological refinery integrated with power-to-X approach for obtaining biopolymers

In this study, a novel hybrid thermochemical-biological refinery integrated with power-to-x approach was developed for obtaining biopolymers (namely polyhydroxyalkanoates, PHA). Within this concept, a trilogy process schema comprising of, (i) thermochemical conversion via integrated pyrolysis-gasification technologies, (ii) anaerobic fermentation of the bioavailable products obtained through either thermochemistry or water-electrolysis for volatile fatty acids (VFA) production, (iii) and VFA-to-PHA bioconversion via an original microaerophilic-aerobic process was developed. During the first stage of proposed biorefinery where lignocellulosic (wooden) biomass was converted into, theoretically fermentable products (i.e. bioavailables) which were defined as syngas and water-soluble fraction of pyrolytic liquid (WS); biochar as a biocatalyst material; and a dense-oil as a liquid fuel. Within integrated pyrolysis - gasification process, biomass was efficiently converted into fermentable intermediates representing up to 66% of biomass chemical energy content in chemical oxygen demand (COD) basis. In the secondary stage, namely anaerobic fermentation for obtaining VFA rich streams, three different downstream process were investigated. First fermentation test was acidogenic bioconversion of WS materials obtained through pyrolysis of biomass within an original biochar-packed bioreactor, it was sustained up to 0.6 gCOD/L-day volumetric productivity (VP). Second, C1 rich syngas materials as the gaseous fraction of pyrolysis-gasification stage, was fermented within a novel char-based biofilm sparger reactor (CBSR), where up to 9.8 gCOD/L-day VP was detected. Third was homoacetogenic bioconversion within the innovative power-to-x pathway for obtaining commodities via renewable energy sources. More specifically, water-electrolysis derived H2 and CO2 as a primary greenhouse gas was successfully bio-utilized by anaerobic mixed cultures into VFA within CBSR system (VP: 18.2 gCOD/L-day). In the last stage of the developed biorefinery schema, VFA is converted into biopolymers within a new continuous microaerophilic-aerobic microplant, where up to 60% of PHA containing sludges was obtained.

Analytical pyrolysis to study microplastics and other polymers in the environment

Synthetic polymers constitute a wide class of materials which has enhanced the quality of human life, providing comforts and innovations. Anyway, the increasing production and the incorrect waste management, are leading to the occurrence of polymers in the environment, generating concern. To understand the extent of this issue, analytical investigation holds an essential position. Standardised methods have not established yet, and additional studies are required to improve the present knowledge. The main aim of this thesis was to provide comprehensive information about the potential of pyrolysis coupled with gas-chromatography and mass spectrometry (Py-GC-MS) for polymers investigation, from their characterisation to their identification and quantification in complex matrices. Water-soluble (poly(dimethylsiloxanes), PDMS bearing poly(ethylene glycol), PEG, side chains) and water-insoluble polymers (microplastics, MPs, and bioplastics) were studied. The different studies revealed the possibility to identify heterogeneous classes of polymers, fingerprinting the presence of PDMS copolymers and distinguishing chemically different polyurethanes (PURs). The occurrence of secondary reactions in pyrolysis of polymer mixtures was observed as possible drawback. Pyrolysis products indicative of secondary reactions and their reaction mechanisms were identified. Py-GC-MS also revealed its fundamental role for the identification of polymers composing commercial bioplastics items based. The results aided to identify chemicals that have the potential to migrate in sea waters. Investigations of environmental samples demonstrated the capability of Py-GC-MS to provide reliable, reproducible and comparable results about polymers in complex matrices (PEG-PDMS in sewage sludges and PURs and other MPs in road dusts and spider webs). Criticisms were especially found in quantitation, such as the retrieval reference materials, the construction of reliable calibration protocols and the occurrence of bias due to interferences between pyrolysis products. This thesis pursues the greater purpose to develop harmonised and standardised methods for environmental investigations of polymers, that is fundamental to assess the real state of the environment.