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Article ; Online: A Survey on the Expression of the Ubiquitin Proteasome System Components HECT- and RBR-E3 Ubiquitin Ligases and E2 Ubiquitin-Conjugating and E1 Ubiquitin-Activating Enzymes during Human Brain Development.

Magnati, Stefano / Alladio, Eugenio / Bracco, Enrico

International journal of molecular sciences

2024 Volume 25, Issue 4

Abstract: Human brain development involves a tightly regulated sequence of events that starts shortly after conception and continues up to adolescence. Before birth, neurogenesis occurs, implying an extensive differentiation process, sustained by changes in the ... ...

Abstract	Human brain development involves a tightly regulated sequence of events that starts shortly after conception and continues up to adolescence. Before birth, neurogenesis occurs, implying an extensive differentiation process, sustained by changes in the gene expression profile alongside proteome remodeling, regulated by the ubiquitin proteasome system (UPS) and autophagy. The latter processes rely on the selective tagging with ubiquitin of the proteins that must be disposed of. E3 ubiquitin ligases accomplish the selective recognition of the target proteins. At the late stage of neurogenesis, the brain starts to take shape, and neurons migrate to their designated locations. After birth, neuronal myelination occurs, and, in parallel, neurons form connections among each other throughout the synaptogenesis process. Due to the malfunctioning of UPS components, aberrant brain development at the very early stages leads to neurodevelopmental disorders. Through deep data mining and analysis and by taking advantage of machine learning-based models, we mapped the transcriptomic profile of the genes encoding HECT- and ring-between-ring (RBR)-E3 ubiquitin ligases as well as E2 ubiquitin-conjugating and E1 ubiquitin-activating enzymes during human brain development, from early post-conception to adulthood. The inquiry outcomes unveiled some implications for neurodevelopment-related disorders.
MeSH term(s)	Humans ; Ubiquitin-Protein Ligases/genetics ; Ubiquitin-Protein Ligases/metabolism ; Ubiquitin-Activating Enzymes/metabolism ; Ubiquitin/genetics ; Ubiquitin/metabolism ; Proteasome Endopeptidase Complex/metabolism ; Ubiquitination ; Ubiquitin-Conjugating Enzymes/genetics ; Ubiquitin-Conjugating Enzymes/metabolism ; Brain/metabolism
Chemical Substances	Ubiquitin-Protein Ligases (EC 2.3.2.27) ; Ubiquitin-Activating Enzymes (EC 6.2.1.45) ; Ubiquitin ; Proteasome Endopeptidase Complex (EC 3.4.25.1) ; Ubiquitin-Conjugating Enzymes (EC 2.3.2.23)
Language	English
Publishing date	2024-02-17
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2019364-6
ISSN	1422-0067 ; 1422-0067 ; 1661-6596
ISSN (online)	1422-0067
ISSN	1422-0067 ; 1661-6596
DOI	10.3390/ijms25042361
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Method development for the quantification of nine nitazene analogs and brorphine in Dried Blood Spots utilizing liquid chromatography - tandem mass spectrometry.

Ververi, Christina / Galletto, Martina / Massano, Marta / Alladio, Eugenio / Vincenti, Marco / Salomone, Alberto

Journal of pharmaceutical and biomedical analysis

2024 Volume 241, Page(s) 115975

Abstract: The detection of nitazenes in biological fluids is increasingly needed as they are repeatedly reported in intoxication and overdose cases. A simple method for the quantification of low levels of nine nitazene analogs and brorphine in Dried Blood Spots ( ... ...

Abstract	The detection of nitazenes in biological fluids is increasingly needed as they are repeatedly reported in intoxication and overdose cases. A simple method for the quantification of low levels of nine nitazene analogs and brorphine in Dried Blood Spots (DBS) was developed and validated. 10 μL of spiked whole blood is deposited on a Capitainer®B card and allowed to dry. The spot is punched out, and extracted with 500 μL methanol:acetonitrile (3:1 v/v) added with 1.5 μL of fentanyl-D5 as the internal standard. After stirring, sonication, and centrifugation of the vial, the solvent is dried under nitrogen, the extract is reconstituted in 30 μL methanol, and 1 μL is injected into a UHPLC-MS/MS instrument. The method validation showed linear calibration in the 1-50 ng/mL range, LOD values ranging between 0.3 ng/mL (isotonitazene) and 0.5 ng/mL (brorphine), average CV% and bias% within 15 % and 10 % for all compounds, respectively. The matrix effect due to blood and filter paper components was within 85-115 % while recovery was between 15-20 %. Stability tests against time and temperature showed no significant variations for storage periods up to 28 days. Room temperature proved to represent the best samples storage conditions. UHPLC-MS/MS proved capable to reliably identify all target analytes at low concentration even in small specimen volumes, as those obtained from DBS cards, which in turn confirmed to be effective and sustainable micro-sampling devices. This procedure improves the efficiency of toxicological testing and provides an innovative approach for the identification of the nitazene class of illicit compounds.
MeSH term(s)	Tandem Mass Spectrometry/methods ; Methanol ; Dried Blood Spot Testing/methods ; Chromatography, Liquid/methods ; Reproducibility of Results ; Chromatography, High Pressure Liquid/methods ; Imidazoles ; Piperidines
Chemical Substances	brorphine (38H2BE6LU4) ; Methanol (Y4S76JWI15) ; Imidazoles ; Piperidines
Language	English
Publishing date	2024-01-12
Publishing country	England
Document type	Journal Article
ZDB-ID	604917-5
ISSN	1873-264X ; 0731-7085
ISSN (online)	1873-264X
ISSN	0731-7085
DOI	10.1016/j.jpba.2024.115975
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Article: Application of Chemometrics Tools to the Study of the Fe(III)-Tannic Acid Interaction.

Berto, Silvia / Alladio, Eugenio

Frontiers in chemistry

2020 Volume 8, Page(s) 614171

Abstract: Chemometric techniques were applied to the study of the interaction of iron(III) and tannic acid (TA). Modeling the interaction of Fe(III)-TA is a challenge, as can be the modeling of the metal complexation upon natural macromolecules without a well- ... ...

Abstract	Chemometric techniques were applied to the study of the interaction of iron(III) and tannic acid (TA). Modeling the interaction of Fe(III)-TA is a challenge, as can be the modeling of the metal complexation upon natural macromolecules without a well-defined molecular structure. The chemical formula for commercial TA is often given as C
Language	English
Publishing date	2020-12-11
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2711776-5
ISSN	2296-2646
ISSN	2296-2646
DOI	10.3389/fchem.2020.614171
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Article ; Online: Biogeographical ancestry, variable selection, and PLS-DA method: a new panel to assess ancestry in forensic samples via MPS technology.

Pilli, Elena / Morelli, Stefania / Poggiali, Brando / Alladio, Eugenio

Forensic science international. Genetics

2022 Volume 62, Page(s) 102806

Abstract: As evidenced by the large number of articles recently published in the literature, forensic scientists are making great efforts to infer externally visible features and biogeographical ancestry (BGA) from DNA analysis. Just as phenotypic, ancestry ... ...

Abstract	As evidenced by the large number of articles recently published in the literature, forensic scientists are making great efforts to infer externally visible features and biogeographical ancestry (BGA) from DNA analysis. Just as phenotypic, ancestry information obtained from DNA can provide investigative leads to identify the victims (missing/unidentified persons, crime/armed conflict/mass disaster victims) or trace their perpetrators when no matches were found with the reference profile or in the database. Recently, the advent of Massively Parallel Sequencing technologies associated with the possibility of harnessing high-throughput genetic data allowed us to investigate the associations between phenotypic and genomic variations in worldwide human populations and develop new BGA forensic tools capable of simultaneously analyzing up to millions of markers if for example the ancient DNA approach of hybridization capture was adopted to target SNPs of interest. In the present study, a selection of more than 3000 SNPs was performed to create a new BGA panel and the accuracy of the new panel to infer ancestry from unknown samples was evaluated by the PLS-DA method. Subsequently, the panel created was assessed using three variable selection techniques (Backward variable elimination, Genetic Algorithm and Regularized elimination procedure), and the best SNPs in terms of inferring bio-geographical ancestry at inter- and intra-continental level were selected to obtain panels to predict BGA with a reduced number of selected markers to be applied in routine forensic cases where PCR amplification is the best choice to target SNPs.
Language	English
Publishing date	2022-11-12
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	2493339-9
ISSN	1878-0326 ; 1872-4973
ISSN (online)	1878-0326
ISSN	1872-4973
DOI	10.1016/j.fsigen.2022.102806
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Article ; Online: Multivariate statistical approach and machine learning for the evaluation of biogeographical ancestry inference in the forensic field.

Alladio, Eugenio / Poggiali, Brando / Cosenza, Giulia / Pilli, Elena

Scientific reports

2022 Volume 12, Issue 1, Page(s) 8974

Abstract: The biogeographical ancestry (BGA) of a trace or a person/skeleton refers to the component of ethnicity, constituted of biological and cultural elements, that is biologically determined. Nowadays, many individuals are interested in exploring their ... ...

Abstract	The biogeographical ancestry (BGA) of a trace or a person/skeleton refers to the component of ethnicity, constituted of biological and cultural elements, that is biologically determined. Nowadays, many individuals are interested in exploring their genealogy, and the capability to distinguish biogeographic information about population groups and subgroups via DNA analysis plays an essential role in several fields such as in forensics. In fact, for investigative and intelligence purposes, it is beneficial to inference the biogeographical origins of perpetrators of crimes or victims of unsolved cold cases when no reference profile from perpetrators or database hits for comparative purposes are available. Current approaches for biogeographical ancestry estimation using SNPs data are usually based on PCA and Structure software. The present study provides an alternative method that involves multivariate data analysis and machine learning strategies to evaluate BGA discriminating power of unknown samples using different commercial panels. Starting from 1000 Genomes project, Simons Genome Diversity Project and Human Genome Diversity Project datasets involving African, American, Asian, European and Oceania individuals, and moving towards further and more geographically restricted populations, powerful multivariate techniques such as Partial Least Squares-Discriminant Analysis (PLS-DA) and machine learning techniques such as XGBoost were employed, and their discriminating power was compared. PLS-DA method provided more robust classifications than XGBoost method, showing that the adopted approach might be an interesting tool for forensic experts to infer BGA information from the DNA profile of unknown individuals, but also highlighting that the commercial forensic panels could be inadequate to discriminate populations at intra-continental level.
MeSH term(s)	Forensic Genetics/methods ; Genetics, Population ; Genotype ; Humans ; Machine Learning ; Racial Groups/genetics
Language	English
Publishing date	2022-05-28
Publishing country	England
Document type	Journal Article
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-022-12903-0
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Article ; Online: Identification by GC-MS Analysis of Organics in Manufactured Articles through a D-Optimal Design

Monica Romagnoli / Valeria Polliotto / Eugenio Alladio / Marco Pazzi

Applied Sciences, Vol 12, Iss 14, p

2022 Volume 7320

Abstract: Many manufactured articles are made of composite materials often bonded by a phenolic resin. Through a D-optimal design, we optimized a method to characterize phenolic resins after the extraction process by GC-MS analysis. The study was conducted on ... ...

Abstract	Many manufactured articles are made of composite materials often bonded by a phenolic resin. Through a D-optimal design, we optimized a method to characterize phenolic resins after the extraction process by GC-MS analysis. The study was conducted on three different phenolic resins and four manufactured articles with the same inorganic composition and different analyzed binders. Moreover, three cardanol resins that differ in their production systems were analyzed to see if there were differences between them. Through Soxhlet extraction with dichloromethane or acetone, it is possible to differentiate the raw materials through characteristic compounds and to identify them in the manufactured articles.
Keywords	phenolic resin ; cardanol resin ; characterization ; GC-MS ; D-optimal design ; Technology ; T ; Engineering (General). Civil engineering (General) ; TA1-2040 ; Biology (General) ; QH301-705.5 ; Physics ; QC1-999 ; Chemistry ; QD1-999
Subject code	670
Language	English
Publishing date	2022-07-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Multivariate statistical approach and machine learning for the evaluation of biogeographical ancestry inference in the forensic field

Eugenio Alladio / Brando Poggiali / Giulia Cosenza / Elena Pilli

Scientific Reports, Vol 12, Iss 1, Pp 1-

2022 Volume 17

Abstract: Abstract The biogeographical ancestry (BGA) of a trace or a person/skeleton refers to the component of ethnicity, constituted of biological and cultural elements, that is biologically determined. Nowadays, many individuals are interested in exploring ... ...

Abstract	Abstract The biogeographical ancestry (BGA) of a trace or a person/skeleton refers to the component of ethnicity, constituted of biological and cultural elements, that is biologically determined. Nowadays, many individuals are interested in exploring their genealogy, and the capability to distinguish biogeographic information about population groups and subgroups via DNA analysis plays an essential role in several fields such as in forensics. In fact, for investigative and intelligence purposes, it is beneficial to inference the biogeographical origins of perpetrators of crimes or victims of unsolved cold cases when no reference profile from perpetrators or database hits for comparative purposes are available. Current approaches for biogeographical ancestry estimation using SNPs data are usually based on PCA and Structure software. The present study provides an alternative method that involves multivariate data analysis and machine learning strategies to evaluate BGA discriminating power of unknown samples using different commercial panels. Starting from 1000 Genomes project, Simons Genome Diversity Project and Human Genome Diversity Project datasets involving African, American, Asian, European and Oceania individuals, and moving towards further and more geographically restricted populations, powerful multivariate techniques such as Partial Least Squares-Discriminant Analysis (PLS-DA) and machine learning techniques such as XGBoost were employed, and their discriminating power was compared. PLS-DA method provided more robust classifications than XGBoost method, showing that the adopted approach might be an interesting tool for forensic experts to infer BGA information from the DNA profile of unknown individuals, but also highlighting that the commercial forensic panels could be inadequate to discriminate populations at intra-continental level.
Keywords	Medicine ; R ; Science ; Q
Subject code	310
Language	English
Publishing date	2022-05-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Wastewater surveillance of 105 pharmaceutical drugs and metabolites by means of ultra-high-performance liquid-chromatography-tandem high resolution mass spectrometry.

Massano, Marta / Salomone, Alberto / Gerace, Enrico / Alladio, Eugenio / Vincenti, Marco / Minella, Marco

Journal of chromatography. A

2023 Volume 1693, Page(s) 463896

Abstract: Water pollution from pharmaceutical drugs is becoming an environmental issue of increasing concern, making water quality monitoring a crucial priority to safeguard public health. In particular, the presence of antidepressants, benzodiazepines, ... ...

Abstract	Water pollution from pharmaceutical drugs is becoming an environmental issue of increasing concern, making water quality monitoring a crucial priority to safeguard public health. In particular, the presence of antidepressants, benzodiazepines, antiepileptics, and antipsychotics require specific attention as they are known to be harmful to aquatic biota. In this study, a multi-class comprehensive method for the detection of 105 pharmaceutical residues in small (30 mL) water samples was developed according to fit-for-purpose criteria and then applied to provide wide screening of samples obtained from four Wastewater Treatment Plants (WWTPs) in northern Italy. The filtered samples (0.22 µm filters) were extracted by SPE, and then eluted. 5 µL of the concentrated samples were analyzed by a UHPLC-QTOF-HRMS method validated for screening purposes. Adequate sensitivity was recorded for all target analytes, with limits of detection below 5 ng/L for 76 out of 105 analytes. A total of 23 out of the 105 targeted pharmaceutical drugs was detected in all samples. Several further compounds were detected over wide concentration intervals, ranging from ng/L to µg/L. In addition, the retrospective analysis of full-scan QTOF-HRMS data was exploited to carry out an untargeted screening of some drugs' metabolites. As a proof of concept, it was investigated the presence of the carbamazepine metabolites, which is among the most frequently detected contaminants of emerging concern in wastewater. Thanks to this approach, 10,11-dihydro-10-hydroxycarbamazepine, 10,11-dihydro-10,11-dihydroxycarbamazepine and carbamazepine-10,11-epoxide were identified, the latter requiring particular attention, since it exhibits antiepileptic properties similar to carbamazepine and potential neurotoxic effects in living organism.
MeSH term(s)	Chromatography, High Pressure Liquid/methods ; Wastewater ; Wastewater-Based Epidemiological Monitoring ; Retrospective Studies ; Mass Spectrometry/methods ; Carbamazepine/analysis ; Pharmaceutical Preparations ; Water Pollutants, Chemical/analysis
Chemical Substances	Wastewater ; Carbamazepine (33CM23913M) ; Pharmaceutical Preparations ; Water Pollutants, Chemical
Language	English
Publishing date	2023-02-26
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	1171488-8
ISSN	1873-3778 ; 0021-9673
ISSN (online)	1873-3778
ISSN	0021-9673
DOI	10.1016/j.chroma.2023.463896
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Article ; Online: Application of Chemometrics Tools to the Study of the Fe(III)–Tannic Acid Interaction

Silvia Berto / Eugenio Alladio

Frontiers in Chemistry, Vol

2020 Volume 8

Abstract: Chemometric techniques were applied to the study of the interaction of iron(III) and tannic acid (TA). Modeling the interaction of Fe(III)–TA is a challenge, as can be the modeling of the metal complexation upon natural macromolecules without a well- ... ...

Abstract	Chemometric techniques were applied to the study of the interaction of iron(III) and tannic acid (TA). Modeling the interaction of Fe(III)–TA is a challenge, as can be the modeling of the metal complexation upon natural macromolecules without a well-defined molecular structure. The chemical formula for commercial TA is often given as C76H52O46, but in fact, it is a mixture of polygalloyl glucoses or polygalloyl quinic acid esters with the number of galloyl moieties per molecule ranging from 2 up to 12. Therefore, the data treatment cannot be based on just the stoichiometric approach. In this work, the redox behavior and the coordination capability of the TA toward Fe(III) were studied by UV-vis spectrophotometry and fluorescence spectroscopy. Multivariate Curve Resolution-Alternating Least Squares (MCR-ALS) and Parallel Factor Analysis (PARAFAC) were used for the data treatment, respectively. The pH range in which there is the redox stability of the system Fe(III)–TA was evaluated. The binding capability of TA toward Fe(III), the spectral features of coordination compounds, and the concentration profiles of the species in solution as a function of pH were defined. Moreover, the stability of the interaction between TA and Fe(III) was interpreted through the chemical models usually employed to depict the interaction of metal cations with humic substances and quantified using the concentration profiles estimated by MCR-ALS.
Keywords	tannic acid ; iron(III) ; chemometric techniques ; spectrophotometry ; fluorescence ; coordination compounds ; Chemistry ; QD1-999
Subject code	540
Language	English
Publishing date	2020-12-01T00:00:00Z
Publisher	Frontiers Media S.A.
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Development of Machine Learning Algorithm to Predict the Risk of Incontinence After Robot-Assisted Radical Prostatectomy.

Amparore, Daniele / De Cillis, Sabrina / Alladio, Eugenio / Sica, Michele / Piramide, Federico / Verri, Paolo / Checcucci, Enrico / Piana, Alberto / Quarà, Alberto / Cisero, Edoardo / Manfredi, Matteo / Di Dio, Michele / Fiori, Cristian / Porpiglia, Francesco

Journal of endourology

2024

Abstract: Introduction: ...

Abstract	Introduction:
Language	English
Publishing date	2024-03-21
Publishing country	United States
Document type	Journal Article
ZDB-ID	356931-7
ISSN	1557-900X ; 0892-7790
ISSN (online)	1557-900X
ISSN	0892-7790
DOI	10.1089/end.2024.0057
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