Look at a list of IC publications: 2021, 2020, 2019, 2018, 2017, 2016, 2015, 2014
2021 |
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Esposti, Lorenzo Degli; Adamiano, Alessio; Siliqi, Dritan; Giannini, Cinzia; Iafisco, Michele The effect of chemical structure of carboxylate molecules on hydroxyapatite nanoparticles. A structural and morphological study Journal Article Bioactive Materials, 6 (8), pp. 2360-2371, 2021, ISSN: 2452-199X. @article{DEGLIESPOSTI20212360, title = {The effect of chemical structure of carboxylate molecules on hydroxyapatite nanoparticles. A structural and morphological study}, author = {Lorenzo Degli Esposti and Alessio Adamiano and Dritan Siliqi and Cinzia Giannini and Michele Iafisco}, url = {https://www.sciencedirect.com/science/article/pii/S2452199X21000141}, doi = {10.1016/j.bioactmat.2021.01.010}, issn = {2452-199X}, year = {2021}, date = {2021-08-01}, journal = {Bioactive Materials}, volume = {6}, number = {8}, pages = {2360-2371}, abstract = {Being the most abundant non-macromolecular organic component of bone, the role of citrate (Cit) in hydroxyapatite (HA) crystallization is of high relevance. In this work we have investigated the influence of hydroxycitrate (CitOH) and glutarate (Glr) on HA crystallization in terms of particle growth, composition, and morphology in comparison to Cit. CitOH and Glr have been selected for this work because they share the same backbone structure of Cit but bear different functional groups in the central region. Our data has revealed that CitOH strongly inhibits HA crystallization more efficiently than Cit. CitOH-HA nanoparticles are composed of platy, elongated particles similar to those of Cit-HA but they are ca. twice smaller and have a lower crystal order. On the other hand, Glr does not inhibit HA crystallization as Cit, but leads to the formation of OCP platelets that convert with maturation time to HA nanorods with larger aspect ratio than Cit-HA. In comparison to Cit-HA samples, Glr-HA nanoparticles have bigger dimensions, and higher structural order. Overall, our data reveal that the central carboxyl group of Cit is involved in the selective binding with HA crystal surface and in regulating HA crystal growth. The results of this work highlight new possibilities to control the formation of HA for designing advanced bioactive materials and give new insights on the role of the structure of Cit in regulating the HA morphology.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Being the most abundant non-macromolecular organic component of bone, the role of citrate (Cit) in hydroxyapatite (HA) crystallization is of high relevance. In this work we have investigated the influence of hydroxycitrate (CitOH) and glutarate (Glr) on HA crystallization in terms of particle growth, composition, and morphology in comparison to Cit. CitOH and Glr have been selected for this work because they share the same backbone structure of Cit but bear different functional groups in the central region. Our data has revealed that CitOH strongly inhibits HA crystallization more efficiently than Cit. CitOH-HA nanoparticles are composed of platy, elongated particles similar to those of Cit-HA but they are ca. twice smaller and have a lower crystal order. On the other hand, Glr does not inhibit HA crystallization as Cit, but leads to the formation of OCP platelets that convert with maturation time to HA nanorods with larger aspect ratio than Cit-HA. In comparison to Cit-HA samples, Glr-HA nanoparticles have bigger dimensions, and higher structural order. Overall, our data reveal that the central carboxyl group of Cit is involved in the selective binding with HA crystal surface and in regulating HA crystal growth. The results of this work highlight new possibilities to control the formation of HA for designing advanced bioactive materials and give new insights on the role of the structure of Cit in regulating the HA morphology. | |
Balogh, Bettina Diána; Szakács, Bence; Natale, Giuseppe Di; Tabbì, Giovanni; Pappalardo, Giuseppe; Sóvágó, Imre; Várnagy, Katalin Journal of Inorganic Biochemistry, 217 , pp. 111358, 2021, ISSN: 0162-0134. @article{BALOGH2021111358, title = {Copper (II) binding properties of an octapeptide fragment from the R3 region of tau protein: A combined potentiometric, spectroscopic and mass spectrometric study}, author = {Bettina Di\'{a}na Balogh and Bence Szak\'{a}cs and Giuseppe Di Natale and Giovanni Tabb\`{i} and Giuseppe Pappalardo and Imre S\'{o}v\'{a}g\'{o} and Katalin V\'{a}rnagy}, url = {https://www.sciencedirect.com/science/article/pii/S0162013421000052}, doi = {10.1016/j.jinorgbio.2021.111358}, issn = {0162-0134}, year = {2021}, date = {2021-04-01}, journal = {Journal of Inorganic Biochemistry}, volume = {217}, pages = {111358}, abstract = {The copper(II) complexes of a peptide fragment of the R3 domain of tau protein (tau(326\textendash333) Ac-GNIHHKPG-NH2) and its mutants (Ac-GNGHHKPG-NH2, Ac-GNIHHKAG-NH2, Ac-GNGAHKPG-NH2 and Ac-GNGHAKPG-NH2) have been studied by potentiometric and spectroscopic (UV\textendashVis, CD) methods. ESR spectroscopy and mass spectrometry were also used to prove the coordination mode of the mononuclear complexes and the formation of dinuclear species, respectively. It has been demonstrated that the (326\textendash333) fragment of tau protein is a versatile and effective ligand for copper(II) coordination. The versatility of copper(II) binding is related to the presence of two adjacent histidyl residues in the sequence, which results in the coexistence of mononuclear, bis(ligand) and dinuclear complexes at different metal to ligand ratios. The 1:1 mononuclear complexes are, however, the dominant species with all peptides and the imidazole-N and one to three deprotonated amide nitrogen atoms towards the N-terminal side of the histidyl residue have been suggested as metal binding sites. This binding mode allows the formation of coordination isomers because any of the two histidine moieties can be the primary anchoring site. It is evident from the CD spectroscopic measurements that the isomers are present in almost equal concentration. The copper(II) binding affinity of the native fragment of tau protein is comparable to that of a similar 2-histidine fragment of amyloid-β mutant, Ac-SGAEGHHQK-NH2 but the comparison with an independent histidyl residue (H32) from the N-terminal region of the protein reveals the predominance of H32 over the histidines in the R3 domain.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The copper(II) complexes of a peptide fragment of the R3 domain of tau protein (tau(326–333) Ac-GNIHHKPG-NH2) and its mutants (Ac-GNGHHKPG-NH2, Ac-GNIHHKAG-NH2, Ac-GNGAHKPG-NH2 and Ac-GNGHAKPG-NH2) have been studied by potentiometric and spectroscopic (UV–Vis, CD) methods. ESR spectroscopy and mass spectrometry were also used to prove the coordination mode of the mononuclear complexes and the formation of dinuclear species, respectively. It has been demonstrated that the (326–333) fragment of tau protein is a versatile and effective ligand for copper(II) coordination. The versatility of copper(II) binding is related to the presence of two adjacent histidyl residues in the sequence, which results in the coexistence of mononuclear, bis(ligand) and dinuclear complexes at different metal to ligand ratios. The 1:1 mononuclear complexes are, however, the dominant species with all peptides and the imidazole-N and one to three deprotonated amide nitrogen atoms towards the N-terminal side of the histidyl residue have been suggested as metal binding sites. This binding mode allows the formation of coordination isomers because any of the two histidine moieties can be the primary anchoring site. It is evident from the CD spectroscopic measurements that the isomers are present in almost equal concentration. The copper(II) binding affinity of the native fragment of tau protein is comparable to that of a similar 2-histidine fragment of amyloid-β mutant, Ac-SGAEGHHQK-NH2 but the comparison with an independent histidyl residue (H32) from the N-terminal region of the protein reveals the predominance of H32 over the histidines in the R3 domain. | |
Antonacci, Amina; Bertalan, Ivo; Giardi, Maria Teresa; Scognamiglio, Viviana; Turemis, Mehmet; Fisher, Dirk; Johanningmeier, Udo Enhancing resistance of Chlamydomonas reinhardtii to oxidative stress fusing constructs of heterologous antioxidant peptides into D1 protein Journal Article Algal Research, 54 , pp. 102184, 2021, ISSN: 2211-9264. @article{ANTONACCI2021102184, title = {Enhancing resistance of Chlamydomonas reinhardtii to oxidative stress fusing constructs of heterologous antioxidant peptides into D1 protein}, author = {Amina Antonacci and Ivo Bertalan and Maria Teresa Giardi and Viviana Scognamiglio and Mehmet Turemis and Dirk Fisher and Udo Johanningmeier}, url = {https://www.sciencedirect.com/science/article/pii/S2211926421000035}, doi = {doi.org/10.1016/j.algal.2021.102184}, issn = {2211-9264}, year = {2021}, date = {2021-04-01}, journal = {Algal Research}, volume = {54}, pages = {102184}, abstract = {Algae emerge as leading actors for the development of new strategies to cope oxidative stress, thanks to their availability for genetic manipulation and simple cultivation. This study reports the design of novel mutant strains of the green photosynthetic alga Chlamydomonas reinhardtii, as a model system, able to produce bioactive peptides with high antioxidant capacity by means of a custom-made expression system. The D1 protein of Photosystem II is highly abundant in the chloroplast with a rapid steady-state turnover; the final step of D1 protein processing is thus exploited for the continuous release of antioxidant peptides into the organism. Three antioxidant peptides, isolated from different food sources, were successfully expressed in C. reinhardtii. We show that the in vitro antioxidant activity of algae extract is lower in transgenic lines, while the in vivo antioxidant activity is highly evident towards radical oxygen-generating substances than in the control strain. Moreover, the antioxidant mutant releasing the peptide designed from Hoki fish, showed a longer shelf-life and a better resistance to high light and heat stress than the control. These features can be exploited in the vision of the development of robust biocomponents for bioassay applications. In particular, we described the design of an optical bioassay for herbicides detection, showing the high potential of the proposed mutant strains as robust and sensitive biological recognition elements.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Algae emerge as leading actors for the development of new strategies to cope oxidative stress, thanks to their availability for genetic manipulation and simple cultivation. This study reports the design of novel mutant strains of the green photosynthetic alga Chlamydomonas reinhardtii, as a model system, able to produce bioactive peptides with high antioxidant capacity by means of a custom-made expression system. The D1 protein of Photosystem II is highly abundant in the chloroplast with a rapid steady-state turnover; the final step of D1 protein processing is thus exploited for the continuous release of antioxidant peptides into the organism. Three antioxidant peptides, isolated from different food sources, were successfully expressed in C. reinhardtii. We show that the in vitro antioxidant activity of algae extract is lower in transgenic lines, while the in vivo antioxidant activity is highly evident towards radical oxygen-generating substances than in the control strain. Moreover, the antioxidant mutant releasing the peptide designed from Hoki fish, showed a longer shelf-life and a better resistance to high light and heat stress than the control. These features can be exploited in the vision of the development of robust biocomponents for bioassay applications. In particular, we described the design of an optical bioassay for herbicides detection, showing the high potential of the proposed mutant strains as robust and sensitive biological recognition elements. | |
Giardi, Maria Teresa; Zappi, Daniele; Turemis, Mehmet; Varani, Gabriele; Celso, Fabrizio Lo; Barone, Giampaolo; Calandra, Pietro; Antonacci, Amina; Scognamiglio, Viviana Talanta, 224 , pp. 121854, 2021, ISSN: 0039-9140. @article{GIARDI2021121854, title = {Quantum dots functionalised artificial peptides bioinspired to the D1 protein from the Photosystem II of Chlamydomonas reinhardtii for endocrine disruptor optosensing}, author = {Maria Teresa Giardi and Daniele Zappi and Mehmet Turemis and Gabriele Varani and Fabrizio Lo Celso and Giampaolo Barone and Pietro Calandra and Amina Antonacci and Viviana Scognamiglio}, url = {http://www.sciencedirect.com/science/article/pii/S0039914020311450}, doi = {10.1016/j.talanta.2020.121854}, issn = {0039-9140}, year = {2021}, date = {2021-03-01}, journal = {Talanta}, volume = {224}, pages = {121854}, abstract = {Herein we describe the design and synthesis of novel artificial peptides mimicking the plastoquinone binding niche of the D1 protein from the green photosynthetic alga Chlamydomonas reinhardtii, also able to bind herbicides. In particular, molecular dynamics (MD) simulations were performed to model in silico the behaviour of three peptides, D1Pep70-H, D1Pep70-S264K and D1Pep70-S268C, as genetic variants with different affinity towards the photosynthetic herbicide atrazine. Then the photosynthetic peptides were functionalised with quantum dots for the development of a hybrid optosensor for the detection of atrazine, one of the most employed herbicides for weed control in agriculture as well as considered as a putative endocrine disruptor case study. The excellent agreement between computational and experimental results self consistently shows resistance or super-sensitivity toward the atrazine target, with detection limits in the μg/L concentration range, meeting the requirements of E.U. legislation.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Herein we describe the design and synthesis of novel artificial peptides mimicking the plastoquinone binding niche of the D1 protein from the green photosynthetic alga Chlamydomonas reinhardtii, also able to bind herbicides. In particular, molecular dynamics (MD) simulations were performed to model in silico the behaviour of three peptides, D1Pep70-H, D1Pep70-S264K and D1Pep70-S268C, as genetic variants with different affinity towards the photosynthetic herbicide atrazine. Then the photosynthetic peptides were functionalised with quantum dots for the development of a hybrid optosensor for the detection of atrazine, one of the most employed herbicides for weed control in agriculture as well as considered as a putative endocrine disruptor case study. The excellent agreement between computational and experimental results self consistently shows resistance or super-sensitivity toward the atrazine target, with detection limits in the μg/L concentration range, meeting the requirements of E.U. legislation. | |
Miciaccia, Morena; Belviso, Benny Danilo; Iaselli, Mariaclara; Cingolani, Gino; Ferorelli, Savina; Cappellari, Marianna; Polosa, Paola Loguercio; Perrone, Maria Grazia; Caliandro, Rocco; Scilimati, Antonio Three-dimensional structure of human cyclooxygenase (h COX)-1 Journal Article Scientific reports, 11 (1), pp. 1–18, 2021. @article{miciaccia2021three, title = {Three-dimensional structure of human cyclooxygenase (h COX)-1}, author = {Morena Miciaccia and Benny Danilo Belviso and Mariaclara Iaselli and Gino Cingolani and Savina Ferorelli and Marianna Cappellari and Paola Loguercio Polosa and Maria Grazia Perrone and Rocco Caliandro and Antonio Scilimati}, doi = {10.1038/s41598-021-83438-z}, year = {2021}, date = {2021-02-22}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {1--18}, publisher = {Nature Publishing Group}, abstract = {The beneficial effects of Cyclooxygenases (COX) inhibitors on human health have been known for thousands of years. Nevertheless, COXs, particularly COX-1, have been linked to a plethora of human diseases such as cancer, heart failure, neurological and neurodegenerative diseases only recently. COXs catalyze the first step in the biosynthesis of prostaglandins (PGs) and are among the most important mediators of inflammation. All published structural work on COX-1 deals with the ovine isoenzyme, which is easier to produce in milligram-quantities than the human enzyme and crystallizes readily. Here, we report the long-sought structure of the human cyclooxygenase-1 (hCOX-1) that we refined to an R/Rfree of 20.82/26.37, at 3.36 r{A} resolution. hCOX-1 structure provides a detailed picture of the enzyme active site and the residues crucial for inhibitor/substrate binding and catalytic activity. We compared hCOX-1 crystal structure with the ovine COX-1 and human COX-2 structures by using metrics based on Cartesian coordinates, backbone dihedral angles, and solvent accessibility coupled with multivariate methods. Differences and similarities among structures are discussed, with emphasis on the motifs responsible for the diversification of the various enzymes (primary structure, stability, catalytic activity, and specificity). The structure of hCOX-1 represents an essential step towards the development of new and more selective COX-1 inhibitors of enhanced therapeutic potential.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The beneficial effects of Cyclooxygenases (COX) inhibitors on human health have been known for thousands of years. Nevertheless, COXs, particularly COX-1, have been linked to a plethora of human diseases such as cancer, heart failure, neurological and neurodegenerative diseases only recently. COXs catalyze the first step in the biosynthesis of prostaglandins (PGs) and are among the most important mediators of inflammation. All published structural work on COX-1 deals with the ovine isoenzyme, which is easier to produce in milligram-quantities than the human enzyme and crystallizes readily. Here, we report the long-sought structure of the human cyclooxygenase-1 (hCOX-1) that we refined to an R/Rfree of 20.82/26.37, at 3.36 Å resolution. hCOX-1 structure provides a detailed picture of the enzyme active site and the residues crucial for inhibitor/substrate binding and catalytic activity. We compared hCOX-1 crystal structure with the ovine COX-1 and human COX-2 structures by using metrics based on Cartesian coordinates, backbone dihedral angles, and solvent accessibility coupled with multivariate methods. Differences and similarities among structures are discussed, with emphasis on the motifs responsible for the diversification of the various enzymes (primary structure, stability, catalytic activity, and specificity). The structure of hCOX-1 represents an essential step towards the development of new and more selective COX-1 inhibitors of enhanced therapeutic potential. | |
Toso, Stefano; Baranov, Dmitry; Altamura, Davide; Scattarella, Francesco; Dahl, Jakob; Wang, Xingzhi; Marras, Sergio; Alivisatos, Paul A; Singer, Andrej; Giannini, Cinzia; Manna, Liberato Multilayer Diffraction Reveals That Colloidal Superlattices Approach the Structural Perfection of Single Crystals Journal Article ACS Nano, 0 (0), 2021, (PMID: 33481560). @article{doi:10.1021/acsnano.0c08929, title = {Multilayer Diffraction Reveals That Colloidal Superlattices Approach the Structural Perfection of Single Crystals}, author = {Stefano Toso and Dmitry Baranov and Davide Altamura and Francesco Scattarella and Jakob Dahl and Xingzhi Wang and Sergio Marras and Paul A Alivisatos and Andrej Singer and Cinzia Giannini and Liberato Manna}, url = {https://doi.org/10.1021/acsnano.0c08929}, doi = {10.1021/acsnano.0c08929}, year = {2021}, date = {2021-01-22}, journal = {ACS Nano}, volume = {0}, number = {0}, abstract = {Colloidal superlattices are fascinating materials made of ordered nanocrystals, yet they are rarely called “atomically precise”. That is unsurprising, given how challenging it is to quantify the degree of structural order in these materials. However, once that order crosses a certain threshold, the constructive interference of X-rays diffracted by the nanocrystals dominates the diffraction pattern, offering a wealth of structural information. By treating nanocrystals as scattering sources forming a self-probing interferometer, we developed a multilayer diffraction method that enabled the accurate determination of the nanocrystal size, interparticle spacing, and their fluctuations for samples of self-assembled CsPbBr3 and PbS nanomaterials. The multilayer diffraction method requires only a laboratory-grade diffractometer and an open-source fitting algorithm for data analysis. The average nanocrystal displacement of 0.33 to 1.43 r{A} in the studied superlattices provides a figure of merit for their structural perfection and approaches the atomic displacement parameters found in traditional crystals.}, note = {PMID: 33481560}, keywords = {}, pubstate = {published}, tppubtype = {article} } Colloidal superlattices are fascinating materials made of ordered nanocrystals, yet they are rarely called “atomically precise”. That is unsurprising, given how challenging it is to quantify the degree of structural order in these materials. However, once that order crosses a certain threshold, the constructive interference of X-rays diffracted by the nanocrystals dominates the diffraction pattern, offering a wealth of structural information. By treating nanocrystals as scattering sources forming a self-probing interferometer, we developed a multilayer diffraction method that enabled the accurate determination of the nanocrystal size, interparticle spacing, and their fluctuations for samples of self-assembled CsPbBr3 and PbS nanomaterials. The multilayer diffraction method requires only a laboratory-grade diffractometer and an open-source fitting algorithm for data analysis. The average nanocrystal displacement of 0.33 to 1.43 Å in the studied superlattices provides a figure of merit for their structural perfection and approaches the atomic displacement parameters found in traditional crystals. | |
Chatgilialoglu, Chryssostomos; Ferreri, Carla; Krokidis, Marios G; Masi, Annalisa; Terzidis, Michael A On the relevance of hydroxyl radical to purine DNA damage Journal Article Free Radical Research, 0 (0), pp. 1-21, 2021, (PMID: 33494618). @article{doi:10.1080/10715762.2021.1876855, title = {On the relevance of hydroxyl radical to purine DNA damage}, author = {Chryssostomos Chatgilialoglu and Carla Ferreri and Marios G Krokidis and Annalisa Masi and Michael A Terzidis}, url = {https://doi.org/10.1080/10715762.2021.1876855}, doi = {10.1080/10715762.2021.1876855}, year = {2021}, date = {2021-01-01}, journal = {Free Radical Research}, volume = {0}, number = {0}, pages = {1-21}, publisher = {Taylor & Francis}, abstract = {Abstract Hydroxyl radical (HO•) is the most reactive toward DNA among the reactive oxygen species (ROS) generated in aerobic organisms by cellular metabolisms. HO• is generated also by exogenous sources such as ionizing radiations. In this review we focus on the purine DNA damage by HO• radicals. In particular, emphasis is given on mechanistic aspects for the various lesion formation and their interconnections. Although the majority of the purine DNA lesions like 8-oxo-purine (8-oxo-Pu) are generated by various ROS (including HO•), the formation of 5′,8-cyclopurine (cPu) lesions in vitro and in vivo relies exclusively on the HO• attack. Methodologies generally utilized for the purine lesions quantification in biological samples are reported and critically discussed. Recent results on cPu and 8-oxo-Pu lesions quantification in various types of biological specimens associated with the cellular repair efficiency as well as with distinct pathologies are presented, providing some insights on their biological significance.}, note = {PMID: 33494618}, keywords = {}, pubstate = {published}, tppubtype = {article} } Abstract Hydroxyl radical (HO•) is the most reactive toward DNA among the reactive oxygen species (ROS) generated in aerobic organisms by cellular metabolisms. HO• is generated also by exogenous sources such as ionizing radiations. In this review we focus on the purine DNA damage by HO• radicals. In particular, emphasis is given on mechanistic aspects for the various lesion formation and their interconnections. Although the majority of the purine DNA lesions like 8-oxo-purine (8-oxo-Pu) are generated by various ROS (including HO•), the formation of 5′,8-cyclopurine (cPu) lesions in vitro and in vivo relies exclusively on the HO• attack. Methodologies generally utilized for the purine lesions quantification in biological samples are reported and critically discussed. Recent results on cPu and 8-oxo-Pu lesions quantification in various types of biological specimens associated with the cellular repair efficiency as well as with distinct pathologies are presented, providing some insights on their biological significance. | |
Guccione, Pietro; Lopresti, Mattia; Milanesio, Marco; Caliandro, Rocco Multivariate Analysis Applications in X-ray Diffraction Journal Article Crystals, 11 (1), 2021, ISSN: 2073-4352. @article{cryst11010012, title = {Multivariate Analysis Applications in X-ray Diffraction}, author = {Pietro Guccione and Mattia Lopresti and Marco Milanesio and Rocco Caliandro}, url = {https://www.mdpi.com/2073-4352/11/1/12}, doi = {10.3390/cryst11010012}, issn = {2073-4352}, year = {2021}, date = {2021-01-01}, journal = {Crystals}, volume = {11}, number = {1}, abstract = {Multivariate analysis (MA) is becoming a fundamental tool for processing in an efficient way the large amount of data collected in X-ray diffraction experiments. Multi-wedge data collections can increase the data quality in case of tiny protein crystals; in situ or operando setups allow investigating changes on powder samples occurring during repeated fast measurements; pump and probe experiments at X-ray free-electron laser (XFEL) sources supply structural characterization of fast photo-excitation processes. In all these cases, MA can facilitate the extraction of relevant information hidden in data, disclosing the possibility of automatic data processing even in absence of a priori structural knowledge. MA methods recently used in the field of X-ray diffraction are here reviewed and described, giving hints about theoretical background and possible applications. The use of MA in the framework of the modulated enhanced diffraction technique is described in detail.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Multivariate analysis (MA) is becoming a fundamental tool for processing in an efficient way the large amount of data collected in X-ray diffraction experiments. Multi-wedge data collections can increase the data quality in case of tiny protein crystals; in situ or operando setups allow investigating changes on powder samples occurring during repeated fast measurements; pump and probe experiments at X-ray free-electron laser (XFEL) sources supply structural characterization of fast photo-excitation processes. In all these cases, MA can facilitate the extraction of relevant information hidden in data, disclosing the possibility of automatic data processing even in absence of a priori structural knowledge. MA methods recently used in the field of X-ray diffraction are here reviewed and described, giving hints about theoretical background and possible applications. The use of MA in the framework of the modulated enhanced diffraction technique is described in detail. | |
Vohra, Varun; Matsunaga, Yumi; Takada, Tomoaki; Kiyokawa, Ayumu; Barba, Luisa; Porzio, William Small, 17 (2), pp. 2004168, 2021. @article{https://doi.org/10.1002/smll.202004168, title = {Impact of the Electron Acceptor Nature on the Durability and Nanomorphological Stability of Bulk Heterojunction Active Layers for Organic Solar Cells}, author = {Varun Vohra and Yumi Matsunaga and Tomoaki Takada and Ayumu Kiyokawa and Luisa Barba and William Porzio}, url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/smll.202004168}, doi = {https://doi.org/10.1002/smll.202004168}, year = {2021}, date = {2021-01-01}, journal = {Small}, volume = {17}, number = {2}, pages = {2004168}, abstract = {Abstract A systematic study is conducted to compare the performances and stability of active layers employing a high performance electron donor (PBDB-T) combined with state-of-the-art fullerene (PC71BM), nonfullerene (ITIC), and polymer (N2200) electron acceptors. The impact of the chemical nature of the acceptor on the durability of organic solar cells (OSCs) is elucidated by monitoring their photovoltaic performances under light exposure or dark conditions in the presence of oxygen. PC71BM molecules exhibit a higher resistance toward oxidation compared to nonfullerene acceptors. Unencapsulated PBDB-T:PC71BM OSCs display relatively stable performances at room temperature when stored in air for 3 months. However, when exposed to temperatures above 80 °C, their active materials demix causing notable reductions in the short-circuit densities. Such detrimental demixing can also be seen for PBDB-T:ITIC active layers above 120 °C. Although N2200 chains irreversibly degrade when exposed to air, thermally induced demixing does not occur in PBDB-T:N2200 active layers annealed up to 200 °C. In summary, fullerene OSCs may be the best currently available choice for unencapsulated room temperature applications but if oxidation of the polymer acceptors can be avoided, all polymer active layers should enable the fabrication of highly durable OSCs with lifetimes matching the requirements for OSC commercialization.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Abstract A systematic study is conducted to compare the performances and stability of active layers employing a high performance electron donor (PBDB-T) combined with state-of-the-art fullerene (PC71BM), nonfullerene (ITIC), and polymer (N2200) electron acceptors. The impact of the chemical nature of the acceptor on the durability of organic solar cells (OSCs) is elucidated by monitoring their photovoltaic performances under light exposure or dark conditions in the presence of oxygen. PC71BM molecules exhibit a higher resistance toward oxidation compared to nonfullerene acceptors. Unencapsulated PBDB-T:PC71BM OSCs display relatively stable performances at room temperature when stored in air for 3 months. However, when exposed to temperatures above 80 °C, their active materials demix causing notable reductions in the short-circuit densities. Such detrimental demixing can also be seen for PBDB-T:ITIC active layers above 120 °C. Although N2200 chains irreversibly degrade when exposed to air, thermally induced demixing does not occur in PBDB-T:N2200 active layers annealed up to 200 °C. In summary, fullerene OSCs may be the best currently available choice for unencapsulated room temperature applications but if oxidation of the polymer acceptors can be avoided, all polymer active layers should enable the fabrication of highly durable OSCs with lifetimes matching the requirements for OSC commercialization. | |
Zappi, D; Coronado, E; Soljan, V; Basile, G; Varani, G; Turemis, M; Giardi, M T Talanta, 221 , 2021, (cited By 0). @article{Zappi2021, title = {A microbial sensor platform based on bacterial bioluminescence (luxAB) and green fluorescent protein (gfp) reporters for in situ monitoring of toxicity of wastewater nitrification process dynamics}, author = {D Zappi and E Coronado and V Soljan and G Basile and G Varani and M Turemis and M T Giardi}, doi = {10.1016/j.talanta.2020.121438}, year = {2021}, date = {2021-01-01}, journal = {Talanta}, volume = {221}, abstract = {To avoid the upset of nitrification process in wastewater treatment plants, monitoring of influent toxic chemicals is essential for stable operation. Toxic chemical compounds can interfere with the biological nitrogen removal, thus affecting plant efficiency and effluent water quality. Here we report the development of fluorescence and bioluminescence bioassays, based on E. coli engineered to contain the promoter region of ammonia oxidation pathway (AmoA1) of Nitrosomonas europaea and a reporter gene (lux or gfp). The fluorescence or bioluminescence signal was measured with newly designed optical devices. The microbial sensors were tested and validated at different concentrations of nitrification-inhibiting compounds such as allylthiourea, phenol, and mercury. The signal decrease was immediate and proportional to inhibitor concentration. The developed bacterial bioassays could detect the inhibition of the nitrification process in wastewater for allylthiourea concentrations of 1 μg/L for E. coli pMosaico-Pamo-gfp and 0.5 μg/L for E. coli pMosaico-Pamo-luxAB. The results were confirmed using water from a wastewater plant, containing nitrification-inhibiting compounds. © 2020 Elsevier B.V.}, note = {cited By 0}, keywords = {}, pubstate = {published}, tppubtype = {article} } To avoid the upset of nitrification process in wastewater treatment plants, monitoring of influent toxic chemicals is essential for stable operation. Toxic chemical compounds can interfere with the biological nitrogen removal, thus affecting plant efficiency and effluent water quality. Here we report the development of fluorescence and bioluminescence bioassays, based on E. coli engineered to contain the promoter region of ammonia oxidation pathway (AmoA1) of Nitrosomonas europaea and a reporter gene (lux or gfp). The fluorescence or bioluminescence signal was measured with newly designed optical devices. The microbial sensors were tested and validated at different concentrations of nitrification-inhibiting compounds such as allylthiourea, phenol, and mercury. The signal decrease was immediate and proportional to inhibitor concentration. The developed bacterial bioassays could detect the inhibition of the nitrification process in wastewater for allylthiourea concentrations of 1 μg/L for E. coli pMosaico-Pamo-gfp and 0.5 μg/L for E. coli pMosaico-Pamo-luxAB. The results were confirmed using water from a wastewater plant, containing nitrification-inhibiting compounds. © 2020 Elsevier B.V. | |
Scattarella, Francesco; Altamura, Emiliano; Albanese, Paola; Siliqi, Dritan; Ladisa, Massimo; Mavelli, Fabio; Giannini, Cinzia; Altamura, Davide Table-top combined scanning X-ray small angle scattering and transmission microscopies of lipid vesicles dispersed in free-standing gel Journal Article RSC Adv., 11 , pp. 484-492, 2021. @article{D0RA08581B, title = {Table-top combined scanning X-ray small angle scattering and transmission microscopies of lipid vesicles dispersed in free-standing gel}, author = {Francesco Scattarella and Emiliano Altamura and Paola Albanese and Dritan Siliqi and Massimo Ladisa and Fabio Mavelli and Cinzia Giannini and Davide Altamura}, url = {http://dx.doi.org/10.1039/D0RA08581B}, doi = {10.1039/D0RA08581B}, year = {2021}, date = {2021-01-01}, journal = {RSC Adv.}, volume = {11}, pages = {484-492}, publisher = {The Royal Society of Chemistry}, abstract = {A mm thick free-standing gel containing lipid vesicles made of 2-oleoyl-1-palmitoyl-sn-glycero-3-phosphocholine (POPC) was studied by scanning Small Angle X-ray Scattering (SAXS) and X-ray Transmission (XT) microscopies. Raster scanning relatively large volumes{,} besides reducing the risk of radiation damage{,} allows signal integration{,} improving the signal-to-noise ratio (SNR){,} as well as high statistical significance of the dataset. The persistence of lipid vesicles in gel was demonstrated{,} while mapping their spatial distribution and concentration gradients. Information about lipid aggregation and packing{,} as well as about gel density gradients{,} was obtained. A posteriori confirmation of lipid presence in well-defined sample areas was obtained by studying the dried sample{,} featuring clear Bragg peaks from stacked bilayers. The comparison between wet and dry samples allowed it to be proved that lipids do not significantly migrate within the gel even upon drying{,} whereas bilayer curvature is lost by removing water{,} resulting in lipids packed in ordered lamellae. Suitable algorithms were successfully employed for enhancing transmission microscopy sensitivity to low absorbing objects{,} and allowing full SAXS intensity normalization as a general approach. In particular{,} data reduction includes normalization of the SAXS intensity against the local sample thickness derived from absorption contrast maps. The proposed study was demonstrated by a room-sized instrumentation{,} although equipped with a high brilliance X-ray micro-source{,} and is expected to be applicable to a wide variety of organic{,} inorganic{,} and multicomponent systems{,} including biomaterials. The employed routines for data reduction and microscopy{,} including Gaussian filter for contrast enhancement of low absorbing objects and a region growing segmentation algorithm to exclude no-sample regions{,} have been implemented and made freely available through the updated in-house developed software SUNBIM.}, keywords = {}, pubstate = {published}, tppubtype = {article} } A mm thick free-standing gel containing lipid vesicles made of 2-oleoyl-1-palmitoyl-sn-glycero-3-phosphocholine (POPC) was studied by scanning Small Angle X-ray Scattering (SAXS) and X-ray Transmission (XT) microscopies. Raster scanning relatively large volumes{,} besides reducing the risk of radiation damage{,} allows signal integration{,} improving the signal-to-noise ratio (SNR){,} as well as high statistical significance of the dataset. The persistence of lipid vesicles in gel was demonstrated{,} while mapping their spatial distribution and concentration gradients. Information about lipid aggregation and packing{,} as well as about gel density gradients{,} was obtained. A posteriori confirmation of lipid presence in well-defined sample areas was obtained by studying the dried sample{,} featuring clear Bragg peaks from stacked bilayers. The comparison between wet and dry samples allowed it to be proved that lipids do not significantly migrate within the gel even upon drying{,} whereas bilayer curvature is lost by removing water{,} resulting in lipids packed in ordered lamellae. Suitable algorithms were successfully employed for enhancing transmission microscopy sensitivity to low absorbing objects{,} and allowing full SAXS intensity normalization as a general approach. In particular{,} data reduction includes normalization of the SAXS intensity against the local sample thickness derived from absorption contrast maps. The proposed study was demonstrated by a room-sized instrumentation{,} although equipped with a high brilliance X-ray micro-source{,} and is expected to be applicable to a wide variety of organic{,} inorganic{,} and multicomponent systems{,} including biomaterials. The employed routines for data reduction and microscopy{,} including Gaussian filter for contrast enhancement of low absorbing objects and a region growing segmentation algorithm to exclude no-sample regions{,} have been implemented and made freely available through the updated in-house developed software SUNBIM. | |
Spanu, D; Nemenyi, A; Marelli, M; Binda, G; Guagliardi, A; Bertolotti, F; Giussani, B; Recchia, S Thin Solid Films, 717 , 2021, ISSN: 00406090, (cited By 0). @article{Spanu2021, title = {Development of a Scanning Chemical Vapour Deposition Reactor for the realization of patterned and non-patterned depositions: a preliminary overview}, author = {D Spanu and A Nemenyi and M Marelli and G Binda and A Guagliardi and F Bertolotti and B Giussani and S Recchia}, doi = {10.1016/j.tsf.2020.138446}, issn = {00406090}, year = {2021}, date = {2021-01-01}, journal = {Thin Solid Films}, volume = {717}, publisher = {Elsevier B.V.}, abstract = {The development of a prototype apparatus to perform patterned Chemical Vapour Deposition (CVD) on planar substrates is presented. The system consists of a fixed head which produces and drives a tiny spot of vapors of a suitable organometallic precursor over the substrate, which is mounted on a heatable and movable stage. WO3 deposition from W(CO)6 precursor was chosen as a model for a preliminary evaluation, to show how the main operational parameters affects the morphology and the photocatalytic performances of the deposited layer. As the result, due to the programmable movement of the holder, it is possible to perform any desired patterned deposition, finely controlling the X and Y movements, the head-substrate distance and the scan speed. The width of the deposited lines strongly depends on the morphology of the substrate (porous vs. flat): with porous substrates it ranges from 1 mm to 3.5 mm and can be tuned through the head-substrate distance. The minimum achievable thickness is about 10 nm and, starting from this minimum value, any desired thickness can be produced by means of the utilization of multiple scans. The capability of CVD to cover all the available surface even on structured substrates, is tested on a challenging surface made of hematite nanoplatelets vertically aligned over a Fluorine-doped tin oxide glass. The intimate contact between WO3 and hematite is assessed through photoelectrocatalytic and chronoamperometric measurements. Interestingly, texture analysis reveals that WO3 crystals, with domains of about 80-100 nm, are preferentially oriented with the (200) and (002) planes of the orthorhombic structure laying parallel to the substrate. © 2020}, note = {cited By 0}, keywords = {}, pubstate = {published}, tppubtype = {article} } The development of a prototype apparatus to perform patterned Chemical Vapour Deposition (CVD) on planar substrates is presented. The system consists of a fixed head which produces and drives a tiny spot of vapors of a suitable organometallic precursor over the substrate, which is mounted on a heatable and movable stage. WO3 deposition from W(CO)6 precursor was chosen as a model for a preliminary evaluation, to show how the main operational parameters affects the morphology and the photocatalytic performances of the deposited layer. As the result, due to the programmable movement of the holder, it is possible to perform any desired patterned deposition, finely controlling the X and Y movements, the head-substrate distance and the scan speed. The width of the deposited lines strongly depends on the morphology of the substrate (porous vs. flat): with porous substrates it ranges from 1 mm to 3.5 mm and can be tuned through the head-substrate distance. The minimum achievable thickness is about 10 nm and, starting from this minimum value, any desired thickness can be produced by means of the utilization of multiple scans. The capability of CVD to cover all the available surface even on structured substrates, is tested on a challenging surface made of hematite nanoplatelets vertically aligned over a Fluorine-doped tin oxide glass. The intimate contact between WO3 and hematite is assessed through photoelectrocatalytic and chronoamperometric measurements. Interestingly, texture analysis reveals that WO3 crystals, with domains of about 80-100 nm, are preferentially oriented with the (200) and (002) planes of the orthorhombic structure laying parallel to the substrate. © 2020 | |
Gijsbers, A; Sánchez‐puig, N; Gao, Y; Peters, P J; Ravelli, R B G; Siliqi, D Structural analysis of the partially disordered protein espk from mycobacterium tuberculosis Journal Article Crystals, 11 (1), pp. 1-16, 2021, ISSN: 20734352, (cited By 0). @article{Gijsbers20211, title = {Structural analysis of the partially disordered protein espk from mycobacterium tuberculosis}, author = {A Gijsbers and N S\'{a}nchez‐puig and Y Gao and P J Peters and R B G Ravelli and D Siliqi}, doi = {10.3390/cryst11010018}, issn = {20734352}, year = {2021}, date = {2021-01-01}, journal = {Crystals}, volume = {11}, number = {1}, pages = {1-16}, publisher = {MDPI AG}, abstract = {For centuries, tuberculosis has been a worldwide burden for human health, and gaps in our understanding of its pathogenesis have hampered the development of new treatments. ESX‐1 is a complex machinery responsible for the secretion of virulence factors that manipulate the host response. Despite the importance of these secreted proteins for pathogenicity, only a few of them have been structurally and functionally characterised. Here, we describe a structural study of the ESX‐secretion associated protein K (EspK), a 74 kDa protein known to be essential for the secretion of other substrates and the cytolytic effects of ESX‐1. Small‐Angle X‐ray Scattering (SAXS) data show that EspK is a long molecule with a maximal dimension of 228 r{A}. It consists of two independent folded regions at each end of the protein connected by a flexible unstructured region driving the protein to coexist as an ensemble of conformations. Limited proteolysis identified a 26 kDa globular domain at the C‐terminus of the protein consisting of a mixture of α‐helices and β‐strands, as shown by circular dichroism (CD) and SAXS. In contrast, the N‐terminal portion is mainly helical with an elongated shape. Sequence conservation suggests that this architecture is preserved amongst the different mycobacteria species, proposing specific roles for the N‐ and C‐terminal domains assisted by the middle flexible linker. © 2020 by the authors. Licensee MDPI, Basel, Switzerland.}, note = {cited By 0}, keywords = {}, pubstate = {published}, tppubtype = {article} } For centuries, tuberculosis has been a worldwide burden for human health, and gaps in our understanding of its pathogenesis have hampered the development of new treatments. ESX‐1 is a complex machinery responsible for the secretion of virulence factors that manipulate the host response. Despite the importance of these secreted proteins for pathogenicity, only a few of them have been structurally and functionally characterised. Here, we describe a structural study of the ESX‐secretion associated protein K (EspK), a 74 kDa protein known to be essential for the secretion of other substrates and the cytolytic effects of ESX‐1. Small‐Angle X‐ray Scattering (SAXS) data show that EspK is a long molecule with a maximal dimension of 228 Å. It consists of two independent folded regions at each end of the protein connected by a flexible unstructured region driving the protein to coexist as an ensemble of conformations. Limited proteolysis identified a 26 kDa globular domain at the C‐terminus of the protein consisting of a mixture of α‐helices and β‐strands, as shown by circular dichroism (CD) and SAXS. In contrast, the N‐terminal portion is mainly helical with an elongated shape. Sequence conservation suggests that this architecture is preserved amongst the different mycobacteria species, proposing specific roles for the N‐ and C‐terminal domains assisted by the middle flexible linker. © 2020 by the authors. Licensee MDPI, Basel, Switzerland. | |
2020 |
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Zhang, Peng; Moretti, Manola; Allione, Marco; Tian, Yuansi; Ordonez-Loza, Javier; Altamura, Davide; Giannini, Cinzia; Torre, Bruno; Das, Gobind; Li, Erqiang; Thoroddsen, Sigurdur T; Sarathy, Mani S; Autiero, Ida; Giugni, Andrea; Gentile, Francesco; Malara, Natalia; Marini, Monica; Fabrizio, Enzo Di A droplet reactor on a super-hydrophobic surface allows control and characterization of amyloid fibril growth Journal Article Communications Biology, 3 (1), pp. 457, 2020, ISSN: 2399-3642. @article{zhang_droplet_2020, title = {A droplet reactor on a super-hydrophobic surface allows control and characterization of amyloid fibril growth}, author = {Peng Zhang and Manola Moretti and Marco Allione and Yuansi Tian and Javier Ordonez-Loza and Davide Altamura and Cinzia Giannini and Bruno Torre and Gobind Das and Erqiang Li and Sigurdur T Thoroddsen and Mani S Sarathy and Ida Autiero and Andrea Giugni and Francesco Gentile and Natalia Malara and Monica Marini and Enzo Di Fabrizio}, url = {http://www.nature.com/articles/s42003-020-01187-7}, doi = {10.1038/s42003-020-01187-7}, issn = {2399-3642}, year = {2020}, date = {2020-12-01}, urldate = {2020-09-23}, journal = {Communications Biology}, volume = {3}, number = {1}, pages = {457}, keywords = {}, pubstate = {published}, tppubtype = {article} } | |
Montes-de-Oca-Ávalos, Juan Manuel; Altamura, Davide; Herrera, María Lidia; Huck-Iriart, Cristián; Scattarella, Francesco; Siliqi, Dritan; Giannini, Cinzia; Candal, Roberto Jorge Physical and structural properties of whey protein concentrate - Corn oil - TiO2 nanocomposite films for edible food-packaging Journal Article Food Packaging and Shelf Life, 26 , pp. 100590, 2020, ISSN: 2214-2894. @article{MONTESDEOCAAVALOS2020100590, title = {Physical and structural properties of whey protein concentrate - Corn oil - TiO2 nanocomposite films for edible food-packaging}, author = {Juan Manuel Montes-de-Oca-\'{A}valos and Davide Altamura and Mar\'{i}a Lidia Herrera and Cristi\'{a}n Huck-Iriart and Francesco Scattarella and Dritan Siliqi and Cinzia Giannini and Roberto Jorge Candal}, url = {http://www.sciencedirect.com/science/article/pii/S2214289420306086}, doi = {10.1016/j.fpsl.2020.100590}, issn = {2214-2894}, year = {2020}, date = {2020-12-01}, journal = {Food Packaging and Shelf Life}, volume = {26}, pages = {100590}, abstract = {Interest in polymer technology based on biodegradable and edible films has increased dramatically, in hopes of creating a circular economy with little to no environmental impact. In this study nanocomposite films with a glycerol/WPC ratio of 4/5 were prepared from emulsions containing 2.5, 5.0, or 7.5 wt.% WPC and 2 wt.% corn oil. Films also contained a load of 0.5 wt.% TiO2. Emulsions were prepared with two different droplet sizes: conventional (from 300 to 700 nm) and nano (from 60 to 80 nm). Films were analyzed for color, water vapor permeability, thermogravimetric, mechanical/tensile properties, infrared behavior, and structure. Advanced X-ray microscopy based on small and wide-angle scattering contrast was used to investigate the nanocomponents in the films, allowing the identification of the main scattering species. Film that was prepared from starting systems with nano droplets (60 nm), the highest protein concentration (7.5 wt.% WPC), and TiO2 loading had the greatest E’ (elastic modulus, 19.2 MPa), E (Young modulus, 19.4 MPa), and εb (elongation at break, 119 %) values. This nano-based film had suitable physical properties for cheese packaging and other similar applications. In all films, data showed a close correlation between film structure and mechanical/tensile properties.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Interest in polymer technology based on biodegradable and edible films has increased dramatically, in hopes of creating a circular economy with little to no environmental impact. In this study nanocomposite films with a glycerol/WPC ratio of 4/5 were prepared from emulsions containing 2.5, 5.0, or 7.5 wt.% WPC and 2 wt.% corn oil. Films also contained a load of 0.5 wt.% TiO2. Emulsions were prepared with two different droplet sizes: conventional (from 300 to 700 nm) and nano (from 60 to 80 nm). Films were analyzed for color, water vapor permeability, thermogravimetric, mechanical/tensile properties, infrared behavior, and structure. Advanced X-ray microscopy based on small and wide-angle scattering contrast was used to investigate the nanocomponents in the films, allowing the identification of the main scattering species. Film that was prepared from starting systems with nano droplets (60 nm), the highest protein concentration (7.5 wt.% WPC), and TiO2 loading had the greatest E’ (elastic modulus, 19.2 MPa), E (Young modulus, 19.4 MPa), and εb (elongation at break, 119 %) values. This nano-based film had suitable physical properties for cheese packaging and other similar applications. In all films, data showed a close correlation between film structure and mechanical/tensile properties. | |