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2019
Roma-Rodrigues, C, Fernandes {AR}, Baptista {PV}.  2019.  Counteracting the effect of leukemia exosomes by antiangiogenic gold nanoparticles. International journal of nanomedicine. 14:6843–6854.: Dove Medical Press Abstract

Purpose: Progression of chronic myeloid leukemia (CML) is frequently associated with increased angiogenesis at the bone marrow mediated by exosomes. The capability of gold nanoparticles (AuNPs) functionalized with antiangiogenic peptides to hinder the formation of new blood vessels has been demonstrated in a chorioallantoic membrane (CAM) model. Methods: Exosomes of K562 CML cell line were isolated and their angiogenic effect assessed in a CAM model. AuNPs functionalized with antiangiogenic peptides were used to block the angiogenic effect of CML-derived exosomes, assessed by evaluation of expression levels of key modulators involved in angiogenic pathways - VEGFA, VEGFR1 (also known as FLT1) and IL8. Results: Exosomes isolated from K562 cells promoted the doubling of newly formed vessels associated with the increase of VEGFR1 expression. This is a concentration and timedependent effect. The AuNPs functionalized with antiangiogenic peptides were capable to block the angiogenic effect by modulating VEGFR1 associated pathway. Conclusion: Exosomes derived from blast cells are capable to trigger (neo)-angiogenesis, a key factor for the progression and spreading of cancer, in particular in CML. AuNPs functionalized with specific antiangiogenic peptides are capable to block the effect of the exosomes produced by malignant cells via modulation of the intrinsic VEGFR pathway. Together, these data highlight the potential of nanomedicine-based strategies against cancer proliferation.

Tulcidas, A, Lourenço NMT, Antunes R, Santos B, Pawlowski S, Rocha F.  2019.  Crystal habit modification and polymorphic stability assessment of a long-acting β2-adrenergic agonist. CrystEngComm. 21:3460-3470.: The Royal Society of Chemistry AbstractWebsite

Properties such as particle orientation{,} flowability{,} packing{,} compaction{,} syringeability{,} suspension stability and dissolution are the most influenced by changes in the crystal habit and polymorphic form of a drug substance. The crystal habit of a drug substance (long-acting β2-adrenergic agonist (LABA)){,} as well as its purity and polymorphic stability{,} was studied after performing slurry tests with 1{,}2-dimethoxyethane : heptane solution at 50 °C. In these slurry tests{,} the product was kept suspended and undissolved{,} with agitation{,} for polymorphic conversion evaluation. Since no significant modifications were observed in the crystal shape and dimensions at 50 °C{,} a new slurry test was performed at a temperature above the melting point of the starting material (80 °C). In the latter test{,} it was possible to obtain crystals with increased dimensions by 480% compared with the starting material. Additionally{,} the desired polymorphic form (form I) was obtained as well as an acceptable purity of approximately 99%. These are promising results{,} not only for downstream purposes{,} but also concerning the bioavailability of the drug substance. This work shows that working at a temperature higher than the melting point of the compound seems to modify the crystal habit of the product.

Ambrosi, E, Bartlett P, Berg AI, Brivio S, Burr G, Deswal S, Deuermeier J, Haga M-A, Kiazadeh A, Kissling G, Kozicki M, Foroutan-Nejad C, Gale E, Gonzalez-Velo Y, Goossens A, Goux L, Hasegawa T, Hilgenkamp H, Huang R, Ibrahim S, Ielmini D, Kenyon AJ, Kolosov V, Li Y, Majumdar S, Milano G, Prodromakis T, Raeishosseini N, Rana V, Ricciardi C, Santamaria M, Shluger A, Valov I, Waser R, Stanley Williams R, Wouters D, Yang Y, Zaffora A.  2019.  Electrochemical metallization ReRAMs (ECM) - Experiments and modelling: General discussion. Faraday Discussions. 213:115-120. AbstractWebsite
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Fernandes, MJ, Moreira MM, Paíga P, Dias D, Bernardo M, Carvalho M, Lapa N, Fonseca I, Morais S, Figueiredo S, Delerue-Matos C.  2019.  Evaluation of the adsorption potential of biochars prepared from forest and agri-food wastes for the removal of fluoxetine. Bioresource Technology. 292:121973. AbstractWebsite

Twelve biochars from forest and agri-food wastes (pruning of Quercus ilex, Eucalyptus grandis, Pinus pinaster, Quercus suber, Malus pumila, Prunus spinosa, Cydonia oblonga, Eriobotrya japonica, Juglans regia, Actinidia deliciosa, Citrus sinensis and Vitis vinifera) were investigated as potential low-cost and renewable adsorbents for removal of a commonly used pharmaceutical, fluoxetine. Preliminary adsorption experiments allowed to select the most promising adsorbents, Quercus ilex, Cydonia oblonga, Eucalyptus, Juglans regia and Vitis vinifera pruning material. They were characterized by proximate, elemental and mineral analysis, thermogravimetric analysis, Fourier transform infrared spectroscopy, determination of specific surface area and pH at the point of zero charge. Batch and equilibrium studies were performed, and the influence of pH was evaluated. The equilibrium was reached in less than 15 min in all systems. The maximum adsorption capacity obtained was 6.41 mg/g for the Eucalyptus biochar, which also demonstrated a good behavior in continuous mode (packed column).

Pinto, CAM, Palomar T, Alves LC, da Silva SHM, Monteiro RC, Macedo MF, Vilarigues MG.  2019.  Fungal biodeterioration of stained-glass windows in monuments from Belém do Pará (Brazil). International Biodeterioration & Biodegradation. 138:106-113. AbstractWebsite

The most prominent historical buildings in Belém do Pará (Northern Brazil) have modernist stained-glass windows, which were commissioned from Europe since the end of the 19th century. Some of them present biodegradation; however, there is no information about the microbial activity on them. The present work is focused on the biodeterioration by fungi on some of these Modern stained-glass windows. The fungal communities were collected, isolated and then identified by means of molecular methods. Additionally, a laboratory-based biodeterioration experiment was carried out to assess the fungal activity on replica glass samples with three different chemical compositions. The replica samples were inoculated with a four-fungal species mixture and incubated under optimal growth conditions for 5 months. Optical microscopy, μ-PIXE, SEM-EDS and FTIR-ATR were performed to evaluate the biodeterioration of the soda-lime silicate glasses. This multidisciplinary approach showed that the inoculated spores (Aspergillus arenarioides, Fusarium oxysporum, Hortaea werneckii, and Trichoderma longibrachiatum) were able to form substantial mycelia in all replica glass samples. The main alterations observed were small crystals, hyphae fingerprints and a slight decrease on the glass surface smoothness. Despite the aforementioned damages, the soda-lime silicate glass compositions showed high resistance against the inoculated fungal species.

Castanheiro, JE, Vital J, Fonseca IM, Ramos AM.  2019.  Glycerol conversion into biofuel additives by acetalization with pentanal over heteropolyacids immobilized on zeolites. Catalysis Today. AbstractWebsite

Dodecamolydbophosphoric acid (HPMo) immobilized on USY zeolite was used as a catalyst for the acetalization of glycerol with pentanal at 70 °C. Catalysts were prepared with different amounts of heteropolyacid, and the most active sample was the HPMo2@Y catalyst (1.1 wt.%). The products of glycerol acetalization with pentanal were (2-butyl-1,3-dioxolan-4-yl)methanol, a five-member ring compound, and 2-butyl-1,3-dioxan-5-ol, a six-member ring compound. Good values of selectivity for the five-member ring compound (80–85%) were obtained with all materials. The reaction conditions were optimized using HPMo2@Y as a catalyst. The optimal conditions were determined to be 70 °C reaction temperature with 0.3 g catalyst and a 1:2.5 M ratio of glycerol to pentanal. The catalytic stability of HPMo2@Y was studied. The acetalization of glycerol with pentanal was performed using the same sample. High catalytic activity for HPMo2@Y was observed.

Mota, C, Esmaeeli M, Coelho C, Santos-Silva T, Wolff M, Foti A, Leimkühler S, Romão MJ.  2019.  Human aldehyde oxidase (hAOX1): structure determination of the Moco-free form of the natural variant G1269R and biophysical studies of single nucleotide polymorphisms. FEBS Open Bio. 9:925-934., Number 5 AbstractWebsite

Human aldehyde oxidase (hAOX1) is a molybdenum enzyme with high toxicological importance, but its physiological role is still unknown. hAOX1 metabolizes different classes of xenobiotics and is one of the main drug-metabolizing enzymes in the liver, along with cytochrome P450. hAOX1 oxidizes and inactivates a large number of drug molecules and has been responsible for the failure of several phase I clinical trials. The interindividual variability of drug-metabolizing enzymes caused by single nucleotide polymorphisms (SNPs) is highly relevant in pharmaceutical treatments. In this study, we present the crystal structure of the inactive variant G1269R, revealing the first structure of a molybdenum cofactor (Moco)-free form of hAOX1. These data allowed to model, for the first time, the flexible Gate 1 that controls access to the active site. Furthermore, we inspected the thermostability of wild-type hAOX1 and hAOX1 with various SNPs (L438V, R1231H, G1269R or S1271L) by CD spectroscopy and ThermoFAD, revealing that amino acid exchanges close to the Moco site can impact protein stability up to 10 °C. These results correlated with biochemical and structural data and enhance our understanding of hAOX1 and the effect of SNPs in the gene encoding this enzyme in the human population. Enzymes Aldehyde oxidase (EC1.2.3.1); xanthine dehydrogenase (EC1.17.1.4); xanthine oxidase (EC1.1.3.2). Databases Structural data are available in the Protein Data Bank under the accession number 6Q6Q.

Sanchez-Sobrado, O, Mendes MJ, Haque S, Mateus T, Aguas H, Fortunato E, Martins R.  2019.  Lightwave trapping in thin film solar cells with improved photonic-structured front contacts. J. Mater. Chem. C. 7:6456-6464.: The Royal Society of Chemistry AbstractWebsite

Photonic microstructures placed at the topside of photovoltaic cells are currently one of the preferred light management solutions to obtain efficiency enhancement due to the increment of the optical absorption produced in the active medium of the devices. Herein{,} we present the results concerning a practical{,} low-cost and scalable approach to integrate metal-oxide based light trapping microstructures on the front contact of amorphous silicon thin film solar cells. A colloidal lithography method was used to pattern the wavelength-sized pyramidal-like features composing the structures{,} made of two different transparent materials{,} TiO2 and IZO{,} allowing the detailed study of the influence of their geometrical parameters on the optoelectronic properties of the devices. These top coating structures are deposited as a post-process after the solar cell fabrication{,} thus facilitating and broadening their industrial applicability. Measurements of the light absorption{,} external quantum efficiency and I–V curves revealed that the structured coatings provide strong broadband improvements in the generated current{,} due to the suppression of reflected light at short wavelengths and the increment of the optical path length of the longer wavelengths (via light scattering){,} within the amorphous silicon layer. As a result{,} in the four types of structures analyzed in this study{,} remarkable increments were achieved in the cells’ efficiencies (up to 14.4%) and generated currents (up to 21.5%){,} with respect to the flat reference cells.

Abdulmawjood, {BR }, Roma-Rodrigues C, Fernandes {AR}, Baptista {PV}.  2019.  Liquid biopsies in myeloid malignancies. Cancer Drug Resistance. 2:1044–1061., Number 4: OAE Publishing Abstract

Hematologic malignancies are the most common type of cancer affecting children and young adults, and encompass diseases, such as leukemia, lymphoma, and myeloma, all of which impact blood associated tissues such as the bone marrow, lymphatic system, and blood cells. Clinical diagnostics of these malignancies relies heavily on the use of bone marrow samples, which is painful, debilitating, and not free from risks for leukemia patients. Liquid biopsies are based on minimally invasive assessment of markers in the blood (and other fluids) and have the potential to improve the efficacy of diagnostic/therapeutic strategies in leukemia patients, providing a useful tool for the real time molecular profiling of patients. The most promising noninvasive biomarkers are circulating tumor cells, circulating tumor DNA, microRNAs, and exosomes. Herein, we discuss the role of assessing these circulating biomarkers for the understanding of tumor progression and metastasis, tumor progression dynamics through treatment and for follow-up.

Deuermeier, J, Kiazadeh A, Klein A, Martins R, Fortunato E.  2019.  Multi-level cell properties of a bilayer Cu2O/Al2O3 resistive switching device. Nanomaterials. 9, Number 2 AbstractWebsite
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Surra, E, Nogueira MC, Bernardo M, Lapa N, Esteves I, Fonseca I.  2019.  New adsorbents from maize cob wastes and anaerobic digestate for H2S removal from biogas. Waste Management. 94:136-145. AbstractWebsite

Two activated carbons (ACs) were prepared by physical activation of Maize Cob Waste (MCW) with CO2, during 2 and 3 h (MCW(PA)2h and MCW(PA)3h, respectively). Two other ACs were prepared by chemical activation: a) MCW(LD) – MCW was impregnated with anaerobic liquid digestate (LD) and carbonized under N2 atmosphere; and b) CAR-MCW(LD) – previously carbonized MCW was impregnated with LD and carbonized under N2 atmosphere. All ACs were fully characterized for textural and chemical properties, and then used in dynamic H2S removal assays from real biogas samples. Regarding H2S removal, the ACs that were physically activated behaved much better than the impregnated ones: MCW(PA)3h and MCW(PA)2h showed H2S uptake capacities of 15.5 and 0.65 mg g−1, respectively, while MCW(LD) and CAR-MCW(LD) showed values of 0.47 and 0.25 mg g−1, respectively. This may indicate that textural properties (surface area and microporosity) are more important than mineral content in H2S removal. Effectively, both surface area and micropore volume were much higher for the samples of MCW(PA)3h (SBET = 820 m2 g−1 and Vmicro = 0.32 cm3 g−1) and MCW(PA)2h (SBET = 630 m2 g−1 and Vmicro = 0.21 cm3 g−1) than for the ACs that were chemically activated (SBET = 38.0 m2 g−1 and Vmicro = 0.01 cm3 g−1 for MCW(LD); SBET = 8.0 m2 g−1 and Vmicro = 0.01 cm3 g−1 for CAR-MCW(LD)). High oxygen content in MCW(PA)3h favoured the catalytic oxidation reaction of H2S, promoting its removal. The use of MCW as precursor and LD as activating agent of the ACs may contribute for the integrated management of maize wastes and to diversify the applications of anaerobic digestate.

Pérez-Mayoral, E, Matos I, Bernardo M, Fonseca IM.  2019.  New and Advanced Porous Carbon Materials in Fine Chemical Synthesis. Emerging Precursors of Porous Carbons. Catalysts. 9, Number 2 AbstractWebsite

The efficiency of porous carbons in fine chemical synthesis, among other application fields, has been demonstrated since both the porous structure and chemical surface provide the appropriated chemical environment favoring a great variety of relevant chemical transformations. In recent years, metal organic frameworks (MOFs) and covalent organic frameworks (COFs) have emerged as interesting opportunities in the preparation of porous carbons with improved physico-chemical properties. Direct calcination of MOFs or COFs, in the presence or not of others carbon or heteroatom sources, could be considered an easy and practical approach for the synthesis of highly dispersed heteroatom-doped porous carbons but also new porous carbons in which single atoms of metallic species are present, showing a great development of the porosity; both characteristics of supreme importance for catalytic applications. The goal of this review is to provide an overview of the traditional methodologies for the synthesis of new porous carbon structures together with emerging ones that use MOFs or COFs as carbon precursors. As mentioned below, the catalytic application in fine chemical synthesis of these kinds of materials is at present barely explored, but probably will expand in the near future.

Alexandre, M, Chapa M, Haque S, Mendes MJ, Águas H, Fortunato E, Martins R.  2019.  Optimum Luminescent Down-Shifting Properties for High Efficiency and Stable Perovskite Solar Cells. ACS Applied Energy Materials. 2:2930-2938., Number 4 AbstractWebsite

In recent years, the discovery of the excellent optical and electrical properties of perovskite solar cells (PSCs) made them a main focus of research in photovoltaics, with efficiency records increasing astonishingly fast since their inception. However, problems associated with the stability of these devices are hindering their market application. UV degradation is one of the most severe issues, chiefly caused by TiO2’s photogenerated electrons that decompose the perovskite absorber material, coupled with the additional intrinsic degradation of this material under UV exposure. The solution presented here can minimize this effect while boosting the cells’ generated photocurrent, by making use of combined light-trapping and luminescent down-shifting effects capable of changing the harmful UV radiation to higher wavelengths that do not affect the stability and can be effectively “trapped” in the cell. This work focuses in the optimization of the photocurrent gains that can be attained by emulating the changed spectrum resulting from applying down-shifting media as encapsulant in photonic-enhanced PSCs, as well as the reduction in the harmful effects of UV radiation on the devices. Such optimized photonic solution allows current enhancement while reducing the harmful UV photocarrier generation both in the TiO2 (by 1 order of magnitude) and in the perovskite (by 80%) relative to a standard PSC without light management.

Haque, S, Mendes MJ, Sanchez-Sobrado O, Águas H, Fortunato E, Martins R.  2019.  Photonic-structured TiO2 for high-efficiency, flexible and stable Perovskite solar cells. Nano Energy. 59:91-101. AbstractWebsite

Optical solutions are promising for Perovskite solar cell (PSC) technology, not only to increase efficiency, but also to allow thinner absorber layers (higher flexibility) and improve stability. This work optimized the combined anti-reflection and scattering properties of two types of light trapping (LT) structures, based on TiO2 semi-spheroidal geometries with honeycomb periodicity, for application in PSCs with substrate configuration and different perovskite layer thicknesses. Their optically lossless material (TiO2) allows the structures to be patterned in the final processing steps, integrated in the cells’ top n contact, therefore not increasing the surface area of the PV layers and not degrading the electric performance via recombination. Therefore, this strategy circumvents the typical compromise of state-of-the-art LT approaches between optical improvements and electrical deterioration, which is particularly relevant for PSCs since their main recombination is caused by surface defects. When patterned on the cells’ front, the wave-optical micro-features composing the LT structures yield up to 21% and 27% photocurrent enhancement in PSCs with conventional (500 nm thick) and ultra-thin (250 nm) perovskite layers, respectively; which are improvements close to those predicted by theoretical Lambertian limits. In addition, such features are shown to provide an important encapsulation role, preventing the cells’ degradation from UV penetration.

Morawiec, S, Mendes MJ, Priolo F, Crupi I.  2019.  Plasmonic nanostructures for light trapping in thin-film solar cells. Materials Science in Semiconductor Processing. 92:10-18. AbstractWebsite

The optical properties of localized surface plasmon resonances (LSPR) sustained by self-assembled silver nanoparticles are of great interest for enhancing light trapping in thin film photovoltaics. First, we report on a systematic investigation of the structural and the optical properties of silver nanostructures fabricated by a solid-state dewetting process on various substrates. Our study allows to identify fabrication conditions in which circular, uniformly spaced nanoparticles are obtainable. The optimized NPs are then integrated into plasmonic back reflector (PBR) structures. Second, we demonstrate a novel procedure, involving a combination of opto-electronic spectroscopic techniques, allowing for the quantification of useful and parasitic absorption in thin photovoltaic absorber deposited on top of the PBR. We achieve a significant broadband useful absorption enhancement of 90% for 0.9 µm thick μc-Si:H film and demonstrate that optical losses due to plasmonic scattering are insignificant below 730 nm. Finally, we present a successful implementation of a plasmonic light trapping scheme in a thin film a-Si:H solar cell. The quantum efficiency spectra of the devices show a pronounced broadband enhancement resulting in remarkably high short circuit current densities (Jsc).

Godino-Ojer, M, Blazquez-García R, Matos I, Bernardo M, Fonseca IM, Mayoral PE.  2019.  Porous carbons-derived from vegetal biomass in the synthesis of quinoxalines. Mechanistic insights. Catalysis Today. AbstractWebsite

We report herein for the first-time acid biomass-derived carbons from vegetal biomass, with high developed porosity, prepared through integrating method comprising pyrolysis and surface phosphonation, able to efficiently catalyze the synthesis of quinoxalines from 1,2-diamines and α-hydroxi ketones, under aerobic conditions. The obtained results indicate that the reaction is mainly driven by a combination of acid function strength and textural properties in terms of conversion and selectivity. Furthermore, our experimental and theoretical observations suggest that the preferred reaction pathway for this transformation, in the presence of the investigated acid carbon catalysts, involves cascade reactions including imination reaction between reactants, successive imine-enamine and keto-enol tautomerisms, heterocyclization followed by dehydration, and aromatization. While the acid sites seem to be a relevant role in each reaction step, the system formed by activated carbon and molecular oxygen could be behind the last oxidative reaction to give the corresponding nitrogen heterocycles.

Salgueiro, CA, Dantas JM, Morgado L.  2019.  Principles of Nuclear Magnetic Resonance and Selected Biological Applications. Radiation in Bioanalysis: Spectroscopic Techniques and Theoretical Methods. (Pereira, Alice S., Tavares, Pedro, Limão-Vieira, Paulo, Eds.).:245–286., Cham: Springer International Publishing Abstract

Nuclear Magnetic Resonance (NMR) spectroscopy is extremely powerful to study distinct biological systems ranging from biomolecules to specific metabolites. This chapter presents the basic concepts of the technique and illustrates its potential to study such systems. Similarly, to other spectroscopic techniques, the theoretical background of NMR is sustained by detailed mathematics and physical chemistry concepts, which were kept to the minimum. The intent is to introduce the fundamentals of the technique to science students from different backgrounds. The basic concepts of NMR spectroscopy are briefly presented in the first section, and the following sections describe applications in the biosciences field, using electron transfer proteins as model, particularly cytochromes. The heme groups endow cytochromes with particular features making them excellent examples to illustrate the high versatility of NMR spectroscopy. The main methodologies underlying protein solution structure determination are discussed in the second section. This is followed by a description of the main experiments explored to structurally map protein-protein or protein-ligand interface regions in molecular complexes. Finally, it is shown how NMR spectroscopy can assist in the functional characterization of multiheme cytochromes.

Pawlowski, S, Crespo JG, Velizarov S.  2019.  Profiled Ion Exchange Membranes: A Comprehensible Review. International Journal of Molecular Sciences. 20, Number 1 AbstractWebsite

Profiled membranes (also known as corrugated membranes, micro-structured membranes, patterned membranes, membranes with designed topography or notched membranes) are gaining increasing academic and industrial attention and recognition as a viable alternative to flat membranes. So far, profiled ion exchange membranes have shown to significantly improve the performance of reverse electrodialysis (RED), and particularly, electrodialysis (ED) by eliminating the spacer shadow effect and by inducing hydrodynamic changes, leading to ion transport rate enhancement. The beneficial effects of profiled ion exchange membranes are strongly dependent on the shape of their profiles (corrugations/patterns) as well as on the flow rate and salts’ concentration in the feed streams. The enormous degree of freedom to create new profile geometries offers an exciting opportunity to improve even more their performance. Additionally, the advent of new manufacturing methods in the membrane field, such as 3D printing, is anticipated to allow a faster and an easier way to create profiled membranes with different and complex geometries.

Tulcidas, A, Santos B, Pawlowski S, Rocha F.  2019.  Quality by Statistical Control in Crystallization—Assessment of Mixing Conditions and Probability of Obtaining the Desired Particle Size. Industrial & Engineering Chemistry Research. 58:20162-20172., Number 43 AbstractWebsite

Reactor hydrodynamics can play a significant role in antisolvent crystallizations. In this work, the impact of suspension height/clearance ratio (H/C) and power per volume (PV) on the particle size distribution (PSD) parameters Dv10, Dv50, and Dv90 of an active pharmaceutical ingredient (API) were evaluated. The API solution was added near the liquid surface of the antisolvent with a buret, at a rate of approximately 5 mL/min, between the impeller and the reactor’s wall. Statistical models were developed, and it was found that PSD parameters seem to be influenced by the H/C and PV. A relationship between the PSD parameters and the nucleation rate was also witnessed. Furthermore, different mathematical methodologies (indicator function and Monte Carlo simulations) were used to obtain a design space comprising the probability of success of having PSD parameters within specification. An operating region comprising the probability of success was estimated, which can aid in minimizing the risk of failure in antisolvent crystallization processes and consequently help reduce the financial losses caused by out-of-specification batches.

Correia, VG, Pinheiro BA, Carvalho AL, Palma AS.  2019.  Resistance to Aminoglycosides. Antibiotic Drug Resistance. :1-38.: John Wiley & Sons, Ltd Abstract

Summary The emergence of bacterial resistance to different antibiotics in clinical use, together with the knowledge on the mechanisms by which bacteria resist the action of aminoglycosides, have contributed to the renewed interest in these molecules as potential antimicrobials. Here, we give an overview on natural and semisynthetic aminoglycosides and their structural features and modes of action, focusing on the structural insight underlying resistance mechanisms. Developments on carbohydrate chemistry and microarray technology are highlighted as powerful approaches toward generation of new aminoglycosides and for screening their interactions with RNAs and proteins. The link between antibiotic uptake and the human gut microbiome is also addressed, focusing on gut microbiome function and composition, antibiotic-induced alterations in host health, and antibiotic resistance. In addition, strategies to modulate human microbiome responses to antibiotics are discussed as novel approaches for aminoglycoside usage and for the effectiveness of antibiotic therapy.

Tulcidas, A, Nascimento S, Santos B, Alvarez C, Pawlowski S, Rocha F.  2019.  Statistical methodology for scale-up of an anti-solvent crystallization process in the pharmaceutical industry. Separation and Purification Technology. 213:56-62. AbstractWebsite

The scale-up of crystallization processes is a challenging step in production of active pharmaceutical ingredients (APIs). When moving from lab to industrial scale, the mixing conditions tend to modify due to the different geometry and agitation performance, which is particularly important in anti-solvent crystallizations where the size of the crystals depends on the mixing and incorporation of the anti-solvent in the solution. In this work, the results obtained in anti-solvent lab-scale crystallization experiments were used to develop multivariate statistical models predicting Particle Size Distribution (PSD) parameters (Dv10, Dv50 and Dv90) in function of predictors such as percentage of volume, power per volume and tip speed. Firstly, the collinearity among the predictors was assessed by Variance Inflation Factor (VIF) diagnosis. Subsequently, least squares method was employed to find correlations among the predictors and output variables. The optimization of the models was executed by testing quadratic, logarithmic and square root terms of the predictors and removing the least statistically significant regression coefficient. The quality of the fitting was evaluated in terms of adjusted R2 (R2adj). The modelled Dv10, Dv50 and Dv90 values presented a good fitting to the experimental data, with R2adj higher than 0.79, either when using power per volume or tip speed along the percentage of volume as predictors. Afterwards, the particle size distribution parameters of industrial scale production were predicted using the previously developed models. The deviations between predicted and experimental values were lower than 17%. This demonstrates that multivariate statistical models developed in lab-scale conditions can be successfully used to predict particle size distribution in industrial-size vessels.

Alves-Barroco, C, Roma-Rodrigues C, Raposo LR, Brás C, Diniz M, Caço J, Costa PM, Santos-Sanches I, Fernandes AR.  2019.  Streptococcus dysgalactiae subsp. dysgalactiae isolated from milk of the bovine udder as emerging pathogens: In vitro and in vivo infection of human cells and zebrafish as biological models. MicrobiologyOpen. 8:e00623., Number 1 AbstractWebsite

Abstract Streptococcus dysgalactiae subsp. dysgalactiae (SDSD) is a major cause of bovine mastitis and has been regarded as an animal-restricted pathogen, although rare infections have been described in humans. Previous studies revealed the presence of virulence genes encoded by phages of the human pathogen Group A Streptococcus pyogenes (GAS) in SDSD isolated from the milk of bovine udder with mastitis. The isolates SDSD VSD5 and VSD13 could adhere and internalize human primary keratinocyte cells, suggesting a possible human infection potential of bovine isolates. In this work, the in vitro and in vivo potential of SDSD to internalize/adhere human cells of the respiratory track and zebrafish as biological models was evaluated. Our results showed that, in vitro, bovine SDSD strains could interact and internalize human respiratory cell lines and that this internalization was dependent on an active transport mechanism and that, in vivo, SDSD are able to cause invasive infections producing zebrafish morbidity and mortality. The infectious potential of these isolates showed to be isolate-specific and appeared to be independent of the presence or absence of GAS phage-encoded virulence genes. Although the infection ability of the bovine SDSD strains was not as strong as the human pathogenic S. pyogenes in the zebrafish model, results suggested that these SDSD isolates are able to interact with human cells and infect zebrafish, a vertebrate infectious model, emerging as pathogens with zoonotic capability.

Dantas, JM, Portela PC, Fernandes AP, Londer YY, Yang X, Duke NEC, Schiffer M, Pokkuluri RP, Salgueiro CA.  2019.  Structural and Functional Relevance of the Conserved Residue V13 in the Triheme Cytochrome PpcA from Geobacter sulfurreducens. The Journal of Physical Chemistry B. 123:3050-3060., Number 14 AbstractWebsite

The triheme cytochrome PpcA from Geobacter sulfurreducens is highly abundant under several growth conditions and is important for extracellular electron transfer. PpcA plays a central role in transferring electrons resulting from the cytoplasmic oxidation of carbon compounds to the cell exterior. This cytochrome is designed to couple electron and proton transfer at physiological pH, a process achieved via the selection of dominant microstates during the redox cycle of the protein, which are ultimately regulated by a well-established order of oxidation of the heme groups. The three hemes are covered only by a polypeptide chain of 71 residues and are located in the small hydrophobic core of the protein. In this work, we used NMR and X-ray crystallography to investigate the structural and functional role of a conserved valine residue (V13) located within van der Waals contact of hemes III and IV. The residue was replaced by alanine (V13A), isoleucine (V13I), serine (V13S), and threonine (V13T) to probe the effects of the side chain volume and polarity. All mutants were found to be as equally thermally stable as the native protein. The V13A and V13T mutants produced crystals and their structures were determined. The side chain of the threonine residue introduced in V13T showed two conformations, but otherwise the two structures did not show significant changes from the native structure. Analysis of the redox behavior of the four mutants showed that for the hydrophobic replacements (V13A and V13I) the redox properties, and hence the order of oxidation of the hemes, were unaffected in spite of the larger side chain, isoleucine, showing two conformations with minor changes of the protein in the heme core. On the other hand, the polar replacements (V13S and V13T) showed the presence of two more distinctive conformations, and the oxidation order of the hemes was altered. Overall, it is striking that a single residue with proper size and polarity, V13, was naturally selected to ensure a unique conformation of the protein and the order of oxidation of the hemes, endowing the cytochrome PpcA with the optimal functional properties necessary to ensure effectiveness in the extracellular electron transfer respiratory pathways of G. sulfurreducens.

Berg, AI, Brivio S, Brown S, Burr G, Deswal S, Deuermeier J, Gale E, Hwang H, Ielmini D, Indiveri G, Kenyon AJ, Kiazadeh A, Köymen I, Kozicki M, Li Y, Mannion D, Prodromakis T, Ricciardi C, Siegel S, Speckbacher M, Valov I, Wang W, Williams RS, Wouters D, Yang Y.  2019.  Synaptic and neuromorphic functions: General discussion. Faraday Discussions. 213:553-578. AbstractWebsite
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Coelho, C, Muthukumaran J, Santos-Silva T, Romão MJ.  2019.  Systematic exploration of predicted destabilizing nonsynonymous single nucleotide polymorphisms (nsSNPs) of human aldehyde oxidase: A Bio-informatics study. Pharmacology Research & Perspectives. 7:e00538., Number 6 AbstractWebsite

Abstract Aldehyde Oxidase (hAOX1) is a cytosolic enzyme involved in the metabolism of drugs and xenobiotic compounds. The enzyme belongs to the xanthine oxidase (XO) family of Mo containing enzyme and is a homo-dimer of two 150 kDa monomers. Nonsynonymous Single Nucleotide Polymorphisms (nsSNPs) of hAOX1 have been reported as affecting the ability of the enzyme to metabolize different substrates. Some of these nsSNPs have been biochemically and structurally characterized but the lack of a systematic and comprehensive study regarding all described and validated nsSNPs is urgent, due to the increasing importance of the enzyme in drug development, personalized medicine and therapy, as well as in pharmacogenetic studies. The objective of the present work was to collect all described nsSNPs of hAOX1 and utilize a series of bioinformatics tools to predict their effect on protein structure stability with putative implications on phenotypic functional consequences. Of 526 nsSNPs reported in NCBI-dbSNP, 119 are identified as deleterious whereas 92 are identified as nondeleterious variants. The stability analysis was performed for 119 deleterious variants and the results suggest that 104 nsSNPs may be responsible for destabilizing the protein structure, whereas five variants may increase the protein stability. Four nsSNPs do not have any impact on protein structure (neutral nsSNPs) of hAOX1. The prediction results of the remaining six nsSNPs are nonconclusive. The in silico results were compared with available experimental data. This methodology can also be used to identify and prioritize the stabilizing and destabilizing variants in other enzymes involved in drug metabolism.