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Article ; Online: Specific Interactions and Environment Flexibility Tune Protein Stability under Extreme Crowding.

Katava, Marina / Stirnemann, Guillaume / Pachetti, Maria / Capaccioli, Simone / Paciaroni, Alessandro / Sterpone, Fabio

The journal of physical chemistry. B

2021 Volume 125, Issue 23, Page(s) 6103–6111

Abstract: Macromolecular crowding influences protein mobility and ... ...

Abstract	Macromolecular crowding influences protein mobility and stability
MeSH term(s)	Macromolecular Substances ; Muramidase ; Protein Stability ; Proteins ; Static Electricity
Chemical Substances	Macromolecular Substances ; Proteins ; Muramidase (EC 3.2.1.17)
Language	English
Publishing date	2021-06-08
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1520-5207
ISSN (online)	1520-5207
DOI	10.1021/acs.jpcb.1c01511
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: SARS-CoV-2: March toward adaptation.

Benedetti, Francesca / Pachetti, Maria / Marini, Bruna / Ippodrino, Rudy / Ciccozzi, Massimo / Zella, Davide

Journal of medical virology

2020 Volume 92, Issue 11, Page(s) 2274–2276

MeSH term(s)	COVID-19/epidemiology ; COVID-19/prevention & control ; COVID-19/virology ; Genetic Variation ; Genome, Viral/genetics ; Humans ; Mutation/physiology ; Physical Distancing ; SARS-CoV-2/genetics ; SARS-CoV-2/pathogenicity ; SARS-CoV-2/physiology
Keywords	covid19
Language	English
Publishing date	2020-07-11
Publishing country	United States
Document type	Journal Article
ZDB-ID	752392-0
ISSN	1096-9071 ; 0146-6615
ISSN (online)	1096-9071
ISSN	0146-6615
DOI	10.1002/jmv.26233
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Zs.A 1320: Show issues

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Article ; Online: Strategies and Perspectives for UV Resonance Raman Applicability in Clinical Analyses of Human Sperm RNA.

Pachetti, Maria / D'Amico, Francesco / Zupin, Luisa / Luppi, Stefania / Martinelli, Monica / Crovella, Sergio / Ricci, Giuseppe / Pascolo, Lorella

International journal of molecular sciences

2021 Volume 22, Issue 23

Abstract: Developing a deeper knowledge about the impact of DNA and RNA epigenetic mutations on sperm production and fertilization performance is essential for selecting best quality samples in Assisted Reproductive Technologies (ART). Indeed, sperm RNAs adenine ... ...

Abstract	Developing a deeper knowledge about the impact of DNA and RNA epigenetic mutations on sperm production and fertilization performance is essential for selecting best quality samples in Assisted Reproductive Technologies (ART). Indeed, sperm RNAs adenine and guanine are likely to be methylated in low quality RNA sperm samples and their study requires the employment of techniques able to isolate high quality nucleic acids. UV resonance Raman spectroscopy represents a valuable tool that is able to monitor peculiar molecular modifications occurring predominantly in nucleic acids, being less sensitive to the presence of other biological compounds. In this work, we used an UV Resonance Raman (UVRR) setup coupled to a synchrotron radiation source tuned at 250 nm, in order to enhance sperm RNAs adenine and guanine vibrational signals, reducing also the impact of a fluorescence background typically occurring at lower energies. Despite that our protocol should be further optimized and further analyses are requested, our results support the concept that UVRR can be applied for setting inexpensive tools to be employed for semen quality assessment in ART.
MeSH term(s)	Adenine/chemistry ; Cell Line ; Guanine/chemistry ; Humans ; Infertility, Male/genetics ; Male ; RNA/analysis ; Reproductive Techniques, Assisted ; Semen Analysis/methods ; Spectrum Analysis, Raman/methods ; Spermatozoa/physiology ; Ultraviolet Rays
Chemical Substances	Guanine (5Z93L87A1R) ; RNA (63231-63-0) ; Adenine (JAC85A2161)
Language	English
Publishing date	2021-12-04
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/ijms222313134
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Article ; Online: UV Resonance Raman explores protein structural modification upon fibrillation and ligand interaction.

Pachetti, Maria / D'Amico, Francesco / Pascolo, Lorella / Pucciarelli, Stefania / Gessini, Alessandro / Parisse, Pietro / Vaccari, Lisa / Masciovecchio, Claudio

Biophysical journal

2021 Volume 120, Issue 20, Page(s) 4575–4589

Abstract: Amyloids are proteinaceous deposits considered an underlying pathological hallmark of several degenerative diseases. The mechanism of amyloid formation and its inhibition still represent challenging issues, especially when protein structure cannot be ... ...

Abstract	Amyloids are proteinaceous deposits considered an underlying pathological hallmark of several degenerative diseases. The mechanism of amyloid formation and its inhibition still represent challenging issues, especially when protein structure cannot be investigated by classical biophysical techniques as for the intrinsically disordered proteins (IDPs). In this view, the need to find an alternative way for providing molecular and structural information regarding IDPs prompted us to set a novel, to our knowledge, approach focused on UV Resonance Raman (UVRR) spectroscopy. To test its applicability, we study the fibrillation of hen-egg white lysozyme (HEWL) and insulin as well as their interaction with resveratrol, employing also intrinsic fluorescence spectroscopy, Fourier transform infrared (FTIR) spectroscopy, and atomic force microscopy (AFM). The increasing of the β-sheet structure content at the end of protein fibrillation probed by FTIR occurs simultaneously with a major solvent exposure of tryptophan (Trp) and tyrosine (Tyr) residues of HEWL and insulin, respectively, as revealed by UVRR and intrinsic fluorescence spectroscopy. However, because the latter technique is successfully used when proteins naturally contain Trp residues, it shows poor performances in the case of insulin, and the information regarding its tertiary structure is exclusively provided by UVRR spectroscopy. The presence of an increased concentration of resveratrol induces mild changes in the secondary structure of both protein fibrils while remodeling HEWL fibril length and promoting the formation of amorphous aggregates in the case of insulin. Although the intrinsic fluorescence spectra of proteins are hidden by resveratrol signal, UVRR Trp and Tyr bands are resonantly enhanced, showing a good sensitivity to the presence of resveratrol and marking a modification in the noncovalent interactions in which they are involved. Our findings demonstrate that UVRR is successfully employed in the study of aggregation-prone proteins and of their interaction with ligands, especially in the case of Trp-lacking proteins.
MeSH term(s)	Amyloid ; Animals ; Chickens ; Female ; Intrinsically Disordered Proteins ; Ligands ; Protein Structure, Secondary
Chemical Substances	Amyloid ; Intrinsically Disordered Proteins ; Ligands
Language	English
Publishing date	2021-08-30
Publishing country	United States
Document type	Journal Article
ZDB-ID	218078-9
ISSN	1542-0086 ; 0006-3495
ISSN (online)	1542-0086
ISSN	0006-3495
DOI	10.1016/j.bpj.2021.08.032
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Zs.A 235: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular Jg. 1995 - 2021: Lesesall (1.OG) ab Jg. 2022: Lesesaal (EG)
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Article ; Online: Evaluation of self-sampling-based cervical cancer screening strategy using HPV Selfy CE-IVD test coupled with home-collection kit: a clinical study in Italy.

Feltri, Giulia / Valenti, Giulio / Isidoro, Erica / Kaur, Jaspreett / Treleani, Marianna / Bartelloni, Aurora / Mauro, Claudia / Spiga, Federica / Ticich, Giulia / Di Napoli, Michela / Biagi, Claudia / Pachetti, Maria / Centonze, Sandro / Castriciano, Santina / Zanchiello, Sara / Giudici, Fabiola / Gerin, Daniela / Zanconati, Fabrizio

European journal of medical research

2023 Volume 28, Issue 1, Page(s) 582

Abstract: Background: Primary human papillomaviruses (HPV) cervical cancer screening can be strengthened by offering home-collection of biological specimen as a valuable option to increase screening coverage. As recommended by World Health Organization (WHO), ... ...

Abstract	Background: Primary human papillomaviruses (HPV) cervical cancer screening can be strengthened by offering home-collection of biological specimen as a valuable option to increase screening coverage. As recommended by World Health Organization (WHO), screening programs should consider whether the inclusion of HPV self-sampling as a complementary option within their existing screening algorithms could address the gaps in current coverage. However, few HPV screening tests are validated for self-sampling according to international guidelines. This study aimed to test a self-sampling-based screening strategy, complementary to the main screening program based on clinician-collected cervical samples. The study took place in Trieste, Italy, and it aimed to evaluate the feasibility of self-testing at home under an opt-in system during COVID-19 pandemic in order to exploit self-sampling to reduce the screening delay generated by the lockdown. Methods: 500 women, who should have received the screening call in 2020, were asked, via phone call, to participate in the study. To whom agreed, a home-collection kit, including a vaginal dry swab for specimen collection, was sent. The recipients performed the sample self-collection and sent back the swab through traditional mail using a prepaid envelope. Once received by the hospital, the samples were analyzed with HPV Selfy (Ulisse BioMed, Italy), a CE-IVD HPV screening test specifically validated for self-collection. Results were further compared using cobas Results: 80% women sent back their swab, showing one of the highest return rate obtained in comparable studies. 34 HPV-positive women were followed up and underwent the Pap test, that revealed 8 low squamous intraepithelial lesions (LSIL) cases, later triaged to colposcopy. HPV Selfy was confirmed to be an adequate test for self-sampling-based screening. Conclusions: This study further confirmed the feasibility of self-test at home screening strategy based on self-sampling with an opt-in system as a support method to enhance cervical cancer screening coverage in Italy. Enrolled women showed a high appreciation for this approach. HPV Selfy test demonstrated to be a valuable assay for cervical cancer screening based on home self-collection. Trial registration: ASUGI Trieste n. 16008/2018 and amendment 02-11/09/2020.
MeSH term(s)	Female ; Humans ; Male ; Uterine Cervical Neoplasms/diagnosis ; Uterine Cervical Neoplasms/epidemiology ; Papillomavirus Infections/diagnosis ; Papillomavirus Infections/pathology ; Early Detection of Cancer ; Pandemics ; Papillomaviridae ; Specimen Handling/methods
Language	English
Publishing date	2023-12-11
Publishing country	England
Document type	Journal Article
ZDB-ID	1329381-3
ISSN	2047-783X ; 0949-2321
ISSN (online)	2047-783X
ISSN	0949-2321
DOI	10.1186/s40001-023-01263-8
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Zs.A 4636: Show issues

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Article: Specific Interactions and Environment Flexibility Tune Protein Stability under Extreme Crowding

Katava, Marina / Stirnemann, Guillaume / Pachetti, Maria / Capaccioli, Simone / Paciaroni, Alessandro / Sterpone, Fabio

Journal of physical chemistry. 2021 June 08, v. 125, no. 23

2021

Abstract: Macromolecular crowding influences protein mobility and stability in vivo. A precise description of the crowding effect on protein thermal stability requires the estimate of the combined effects of excluded volume, specific protein–environment ... ...

Abstract	Macromolecular crowding influences protein mobility and stability in vivo. A precise description of the crowding effect on protein thermal stability requires the estimate of the combined effects of excluded volume, specific protein–environment interactions, as well as the thermal response of the crowders. Here, we explore an ideal model system, the lysozyme protein in powder state, to dissect the factors controlling the melting of the protein under extreme crowding. By deploying state-of-the art molecular simulations, supported by calorimetric experiments, we assess the role of the environment flexibility and of intermolecular electrostatic interactions. In particular, we show that the temperature-dependent flexibility of the macromolecular crowders, along with specific interactions, significantly alleviates the stabilizing contributions of the static volume effect.
Keywords	calorimetry ; lysozyme ; thermal stability
Language	English
Dates of publication	2021-0608
Size	p. 6103-6111.
Publishing place	American Chemical Society
Document type	Article
Note	NAL-AP-2-clean
ISSN	1520-5207
DOI	10.1021/acs.jpcb.1c01511
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Detention and mapping of iron and toxic environmental elements in human ovarian endometriosis: A suggested combined role.

Pascolo, Lorella / Pachetti, Maria / Camillo, Anna / Cernogoraz, Alice / Rizzardi, Clara / Mikus, Katarina Vogel / Zanconati, Fabrizio / Salomé, Murielle / Suárez, Vanessa Tardillo / Romano, Federico / Zito, Gabriella / Gianoncelli, Alessandra / Ricci, Giuseppe

The Science of the total environment

2022 Volume 864, Page(s) 161028

Abstract: Background: Endometriosis is a disease affecting 10-15 % of women worldwide, consisting in the ectopic growth of endometrial cells outside the uterine cavity. Whist the pathogenetic mechanisms of endometriosis remain elusive and contemplating even ... ...

Abstract	Background: Endometriosis is a disease affecting 10-15 % of women worldwide, consisting in the ectopic growth of endometrial cells outside the uterine cavity. Whist the pathogenetic mechanisms of endometriosis remain elusive and contemplating even environmental causes, iron deposits are common in endometrial lesions, indicating an altered iron metabolism at this level. This study was undertaken to reveal a possible relationship between iron dysmetabolism and accumulation of environmental metals. Methods: By combining histological and histochemical analysis (H&E and Perl's staining) with μ- and nano- synchrotron-based (SR-based) X-ray Fluorescence (XRF) microscopy, we investigated the distribution of iron and other elements in the ovarian endometriomas of 12 endometriosis patients and in 7 healthy endometrium samples. Results: XRF microscopy expanded the findings obtained by Perl's staining, revealing with an exceptional sensitivity intracellular features of iron accumulation in the epithelial endometrium, stroma and macrophages of the endometriotic lesions. XRF evidenced that iron was specifically accumulated in multiple micro aggregates, reaching concentrations up to 10-20 % p/p. Moreover, by XRF analysis we revealed for the first time the retention of a number of exogenous and potentially toxic metals such as Pb, Br, Ti, Al Cr, Si and Rb partially or totally co-localizing with iron. Conclusion: μXRF reveals accumulation and colocalization of iron and environmental metals in human ovarian endometriosis, suggesting a role in the pathogenesis of endometriosis.
MeSH term(s)	Humans ; Female ; Endometriosis/metabolism ; Endometriosis/pathology ; Iron/toxicity ; Iron/metabolism ; Endometrium/metabolism ; Endometrium/pathology ; Uterine Diseases/metabolism ; Uterine Diseases/pathology ; Epithelial Cells/pathology
Chemical Substances	Iron (E1UOL152H7)
Language	English
Publishing date	2022-12-20
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	121506-1
ISSN	1879-1026 ; 0048-9697
ISSN (online)	1879-1026
ISSN	0048-9697
DOI	10.1016/j.scitotenv.2022.161028
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Article: SARS-CoV-2: March toward adaptation

Benedetti, Francesca / Pachetti, Maria / Marini, Bruna / Ippodrino, Rudy / Ciccozzi, Massimo / Zella, Davide

J. med. virol

Keywords	covid19
Publisher	WHO
Document type	Article
Note	WHO #Covidence: #618700
Database	COVID19

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Article ; Online: SARS‐CoV‐2

Benedetti, Francesca / Pachetti, Maria / Marini, Bruna / Ippodrino, Rudy / Ciccozzi, Massimo / Zella, Davide

Journal of Medical Virology

March toward adaptation

2020 Volume 92, Issue 11, Page(s) 2274–2276

Keywords	Virology ; Infectious Diseases ; covid19
Language	English
Publisher	Wiley
Publishing country	us
Document type	Article ; Online
ZDB-ID	752392-0
ISSN	1096-9071 ; 0146-6615
ISSN (online)	1096-9071
ISSN	0146-6615
DOI	10.1002/jmv.26233
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: Machine and Deep Learning Prediction Of Prostate Cancer Aggressiveness Using Multiparametric MRI.

Bertelli, Elena / Mercatelli, Laura / Marzi, Chiara / Pachetti, Eva / Baccini, Michela / Barucci, Andrea / Colantonio, Sara / Gherardini, Luca / Lattavo, Lorenzo / Pascali, Maria Antonietta / Agostini, Simone / Miele, Vittorio

Frontiers in oncology

2022 Volume 11, Page(s) 802964

Abstract: Prostate cancer (PCa) is the most frequent male malignancy and the assessment of PCa aggressiveness, for which a biopsy is required, is fundamental for patient management. Currently, multiparametric (mp) MRI is strongly recommended before biopsy. ... ...

Abstract	Prostate cancer (PCa) is the most frequent male malignancy and the assessment of PCa aggressiveness, for which a biopsy is required, is fundamental for patient management. Currently, multiparametric (mp) MRI is strongly recommended before biopsy. Quantitative assessment of mpMRI might provide the radiologist with an objective and noninvasive tool for supporting the decision-making in clinical practice and decreasing intra- and inter-reader variability. In this view, high dimensional radiomics features and Machine Learning (ML) techniques, along with Deep Learning (DL) methods working on raw images directly, could assist the radiologist in the clinical workflow. The aim of this study was to develop and validate ML/DL frameworks on mpMRI data to characterize PCas according to their aggressiveness. We optimized several ML/DL frameworks on T2w, ADC and T2w+ADC data, using a patient-based nested validation scheme. The dataset was composed of 112 patients (132 peripheral lesions with Prostate Imaging Reporting and Data System (PI-RADS) score ≥ 3) acquired following both PI-RADS 2.0 and 2.1 guidelines. Firstly, ML/DL frameworks trained and validated on PI-RADS 2.0 data were tested on both PI-RADS 2.0 and 2.1 data. Then, we trained, validated and tested ML/DL frameworks on a multi PI-RADS dataset. We reported the performances in terms of Area Under the Receiver Operating curve (AUROC), specificity and sensitivity. The ML/DL frameworks trained on T2w data achieved the overall best performance. Notably, ML and DL frameworks trained and validated on PI-RADS 2.0 data obtained median AUROC values equal to 0.750 and 0.875, respectively, on unseen PI-RADS 2.0 test set. Similarly, ML/DL frameworks trained and validated on multi PI-RADS T2w data showed median AUROC values equal to 0.795 and 0.750, respectively, on unseen multi PI-RADS test set. Conversely, all the ML/DL frameworks trained and validated on PI-RADS 2.0 data, achieved AUROC values no better than the chance level when tested on PI-RADS 2.1 data. Both ML/DL techniques applied on mpMRI seem to be a valid aid in predicting PCa aggressiveness. In particular, ML/DL frameworks fed with T2w images data (objective, fast and non-invasive) show good performances and might support decision-making in patient diagnostic and therapeutic management, reducing intra- and inter-reader variability.
Language	English
Publishing date	2022-01-13
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2649216-7
ISSN	2234-943X
ISSN	2234-943X
DOI	10.3389/fonc.2021.802964
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