Nitrite biosensing via selective enzymes—a long but promising route

Sensors 2010, 10, 11530-11555

Production and characterization of Chitin-Glucan Complex by Komagataella pastoris

This thesis was focused on the production, extraction and characterization of chitin:β-glucan complex (CGC). In this process, glycerol byproduct from the biodiesel industry was used as carbon source. The selected CGC producing yeast was Komagataella pastoris (formerly known as Pichia pastoris), due the fact that to achieved high cell densities using as carbon source glycerol from the biodiesel industry. Firstly, a screening of K. pastoris strains was performed in shake flask assays, in order to select the strain of K. pastoris with better performance, in terms of growth, using glycerol as a carbon source. K. pastoris strain DSM 70877 achieved higher final cell densities (92-97 g/l), using pure glycerol (99%, w/v) and in glycerol from the biodiesel industry (86%, w/v), respectively, compared to DSM 70382 strain (74-82 g/l). Based on these shake flask assays results, the wild type DSM 70877 strain was selected to proceed for cultivation in a 2 l bioreactor, using glycerol byproduct (40 g/l), as sole carbon source. Biomass production by K. pastoris was performed under controlled temperature and pH (30.0 ºC and 5.0, respectively). More than 100 g/l biomass was obtained in less than 48 h. The yield of biomass on a glycerol basis was 0.55 g/g during the batch phase and 0.63 g/g during the fed-batch phase. In order to optimize the downstream process, by increasing extraction and purification efficiency of CGC from K. pastoris biomass, several assays were performed. It was found that extraction with 5 M NaOH at 65 ºC, during 2 hours, associated to neutralization with HCl, followed by successive washing steps with deionised water until conductivity of ≤20μS/cm, increased CGC purity. The obtained copolymer, CGCpure, had a chitin:glucan molar ratio of 25:75 mol% close to commercial CGC samples extracted from A. niger mycelium, kiOsmetine from Kitozyme (30:70 mol%). CGCpure was characterized by solid-state Nuclear Magnetic Resonance (NMR) spectroscopy and Differential Scanning Calorimetry (DCS), revealing a CGC with higher purity than a CGC commercial (kiOsmetine). In order to optimize CGC production, a set of batch cultivation experiments was performed to evaluate the effect of pH (3.5–6.5) and temperature (20–40 ºC) on the specific cell growth rate, CGC production and polymer composition. Statistical tools (response surface methodology and central composite design) were used. The CGC content in the biomass and the volumetric productivity (rp) were not significantly affected within the tested pH and temperature ranges. In contrast, the effect of pH and temperature on the CGC molar ratio was more pronounced. The highest chitin: β-glucan molar ratio (> 14:86) was obtained for the mid-range pH (4.5-5.8) and temperatures (26–33 ºC). The ability of K. pastoris to synthesize CGC with different molar ratios as a function of pH and temperature is a feature that can be exploited to obtain tailored polymer compositions.(...)

Molecular tools in the diagnostic and epidemiology of infections caused by members of Mycobacterium avium Complex

Mycobacterium avium Complex (MAC) comprises microorganisms that affect a wide range of animals including humans. The most relevant are Mycobacterium avium subspecies hominissuis (Mah) with a high impact on public health affecting mainly immunocompromised individuals and Mycobacterium avium subspecies paratuberculosis (Map) causing paratuberculosis in animals with a high economic impact worldwide. In this work, we characterized 28 human and 67 porcine Mah isolates and evaluated the relationship among them by Multiple-Locus Variable number tandem repeat Analysis (MLVA). We concluded that Mah population presented a high genetic diversity and no correlations were inferred based on geographical origin, host or biological sample. For the first time in Portugal Map strains, from asymptomatic bovine faecal samples were isolated highlighting the need of more reliable and rapid diagnostic methods for Map direct detection. Therefore, we developed an IS900 nested real time PCR with high sensitivity and specificity associated with optimized DNA extraction methodologies for faecal and milk samples. We detected 83% of 155 faecal samples from goats, cattle and sheep, and 26% of 98 milk samples from cattle, positive for Map IS900 nested real time PCR. A novel SNPs (single nucleotide polymorphisms) assay to Map characterization based on a Whole Genome Sequencing analysis was developed to elucidate the genetic relationship between strains. Based on sequential detection of 14 SNPs and on a decision tree we were able to differentiate 14 phylogenetic groups with a higher discriminatory power compared to other typing methods. A pigmented Map strain was isolated and characterized evidencing for the first time to our knowledge the existence of pigmented Type C strains. With this work, we intended to improve the ante mortem direct molecular detection of Map, to conscientiously aware for the existence of Map animal infections widespread in Portugal and to contribute to the improvement of Map and Mah epidemiological studies.

Chromian spinels in the basalts from the Lisbon volcanic complex (portugal) and their petrogenetic implications

Chromian spinels are common in the late Cretaceous alkali basalts of the Lisbon volcanic Complex in Portugal. They occur as unzoned inclusions in magnesian olivines of all basalt types and as large spectacularly zoned grains in the groundmass of porphyritic basalts. Microprobe analysis indicate complex cationic exchange in the groundmass zoned spinels due to simple peritectic reactions and in response to changing composition of the basalt liquid. The variation of cationic distribution in zoned chromian-Spinels, reflects very accurately the changing chemistry of the cooling silicate melt and the paragenetical relations of mineral oxides and silicates. Crystallization of initial chromian spinels occurred at T~1200°C and fO2~10-8.5 atm. earlier or contemporaneously with magnesian olivine. The titanomagnetite mantles of zoned chromian spinels crystallized at T~1200°C and much lower fO2.

Synechocystis ferredoxin/ferredoxin-NADP+-reductase/NADP+ complex: Structural model obtained by NMR-restrained docking

FEBS Letters 579 (2005) 4585–4590

A further investigation of the cytochrome b5–cytochrome c complex

J Biol Inorg Chem (2003) 8: 777–786

Synthesis, characterization and reactivity of new cobalt, palladium and nickel complexes bearing α-diimines and P, O ligands

This work describes the synthesis and characterization of a series of new α-diimine and P,O, β-keto and acetamide phosphines ligands, and their complexation to Ni(II), Co(II),Co(III) and Pd(II) to obtain a series of new compounds aiming to study their structural characteristics and to test their catalytic activity. All the compounds synthesized were characterized by the usual spectroscopic and spectrometric techniques: Elemental Analysis, MALDI-TOF-MS spectrometry, IR, UV-vis, 1H, 13C and 31P NMR spectroscopies. Some of the paramagnetic compounds were also characterized by EPR. For the majority of the compounds it was possible to solve their solid state structure by single crystal X-ray diffraction. Tests for olefin polymerization were performed in order to determine the catalytic activity of the Co(II) complexes. Chapter I presents a brief introduction to homogenous catalysis, highlighting the reactions catalyzed by the type of compounds described in this thesis, namely olefin polymerization and oligomerization and reactions catalyzed by the complexes bearing α-diimines and P,O type ligands. Chapter II is dedicated to the description of the synthesis of new α-diimines cobalt (II) complexes, of general formula [CoX2(α-diimine)], where X = Cl or I and the α-diimines are bis(aryl)acenaphthenequinonediimine) (Ar-BIAN) and 1,4-diaryl-2,3-dimethyl-1,4-diaza-1,3-butadiene (Ar-DAB). Structures solved by single crystal X-ray diffraction were obtained for all the described complexes. For some of the compounds, X-band EPR measurements were performed on polycrystalline samples, showing a high-spin Co(II) (S = 3/2) ion, in a distorted axial environment. EPR single crystal experiments on two of the compounds allowed us to determine the g tensor orientation in the molecular structure. In Chapter III we continue with the synthesis and characterization of more cobalt (II)complexes bearing α-diimines of general formula [CoX2(α-diimine)], with X = Cl or I and α-diimines are bis(aryl)acenaphthenequinonediimine) (Ar-BIAN) and 1,4-diaryl-2,3-dimethyl- 1,4-diaza-1,3-butadiene (Ar-DAB). The structures of three of the new compounds synthesized were determined by single crystal X-ray diffraction. A NMR paramagnetic characterization of all the compounds described is presented. Ethylene polymerization tests were done to determine the catalytic activity of several of the Co(II) complexes described in Chapter II and III and their results are shown. In Chapter IV a new rigid bidentate ligand, bis(1-naphthylimino)acenaphthene, and its complexes with Zn(II) and Pd(II), were synthesized. Both the ligand and its complexes show syn and anti isomers. Structures of the ligand and the anti isomer of the Pd(II) complex were solved by single crystal X-ray diffraction. All the compounds were characterized by elemental analysis, MALDI-TOF-MS spectrometry, and by IR, UV-vis, 1H, 13C, 1H-1H COSY, 1H-13C HSQC, 1H-13C HSQC-TOCSY and 1H-1H NOESY NMR when necessary. DFT studies showed that both conformers of [PdCl2(BIAN)] are isoenergetics and can be obtain experimentally. However, we can predict that the isomerization process is not available in square-planar complex, but is possible for the free ligand. The molecular geometry is very similar in both isomers, and only different orientations for naphthyl groups can be expected. Chapter V describes the synthesis of new P, O type ligands, β-keto phosphine, R2PCH2C(O)Ph, and acetamide phosphine R2PNHC(O)Me, as well as a series of new cobalt(III) complexes namely [(η5-C5H5)CoI2{Ph2PCH2C(O)Ph}], and [(η5- C5H5)CoI2{Ph2PNHC(O)Me}]. Treating these Co(III) compounds with an excess of Et3N, resulted in complexes η2-phosphinoenolate [(η5-C5H5)CoI{Ph2PCH…C(…O)Ph}] and η2- acetamide phosphine [(η5-C5H5)CoI{Ph2PN…C(…O)Me}]. Nickel (II) complexes were also obtained: cis-[Ni(Ph2PN…C(…O)Me)2] and cis-[Ni((i-Pr)2PN…C(…O)Me)2]. Their geometry and isomerism were discussed. Seven structures of the compounds described in this chapter were determined by single crystal X-ray diffraction. The general conclusions of this work can be found in Chapter VI.

Primary bioreceptivity of limestones from the mediterranean basin to phototrophic microorganisms

Dissertação apresentada para a obtenção do grau de Doutor em Conservação e Restauro pela Universidade Nova de Lisboa, Faculdade de Ciências e Tecnologia

Functional domains of Bacillus subtilis transcription factor AraR and identification of aminoacids important for nucleoprotein complex assembly and effector-binding.

Journal of Bacteriology (Apr 2006) 3024-3036

Growth of phototrophic biofilms from limestone monuments under laboratory conditions

International Biodeterioration & Biodegradation,xxx (2009) 1–8

The Sinemurian ammonites of the Lusitanian Basin (Portugal): an example of complex endemic evolutioin

Palaeodiversity 3: 59–87; Stuttgart 30 December 2010

The alternative complex III from Rhodothermus marinus - a prototype of a new family of quinol: electron acceptor oxidoreductase

Dissertation presented to obtain a PhD degree in Biochemistry at the Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa

Energy transduction by respiratory complex I

Dissertation presented to obtain a PhD degree in Biochemistry at the Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa

Dynamic and interaction of cytochrome c with Pf1 virus

Dissertação apresentada na Faculdade de Ciências e Tecnologia da Universidade Nova de Lisboa para obtenção do grau de Mestre em BioOrgânica

Cochineal, a precious source of red: cochineal dyes characterization by high performance liquid chromatography with diode array detection and principal component analysis

Presented at Faculdade de Ciências e Tecnologias, Universidade de Lisboa, to obtain the Master Degree in Conservation and Restoration of Textiles