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Article ; Online: Metabolic and Immune Markers for Precise Monitoring of COVID-19 Severity and Treatment

André F. Rendeiro / Charles Kyriakos Vorkas / Jan Krumsiek / Harjot K. Singh / Shashi N. Kapadia / Luca Vincenzo Cappelli / Maria Teresa Cacciapuoti / Giorgio Inghirami / Olivier Elemento / Mirella Salvatore

Frontiers in Immunology, Vol

2022 Volume 12

Abstract: Deep understanding of the SARS-CoV-2 effects on host molecular pathways is paramount for the discovery of early biomarkers of outcome of coronavirus disease 2019 (COVID-19) and the identification of novel therapeutic targets. In that light, we generated ... ...

Abstract	Deep understanding of the SARS-CoV-2 effects on host molecular pathways is paramount for the discovery of early biomarkers of outcome of coronavirus disease 2019 (COVID-19) and the identification of novel therapeutic targets. In that light, we generated metabolomic data from COVID-19 patient blood using high-throughput targeted nuclear magnetic resonance (NMR) spectroscopy and high-dimensional flow cytometry. We find considerable changes in serum metabolome composition of COVID-19 patients associated with disease severity, and response to tocilizumab treatment. We built a clinically annotated, biologically-interpretable space for precise time-resolved disease monitoring and characterize the temporal dynamics of metabolomic change along the clinical course of COVID-19 patients and in response to therapy. Finally, we leverage joint immuno-metabolic measurements to provide a novel approach for patient stratification and early prediction of severe disease. Our results show that high-dimensional metabolomic and joint immune-metabolic readouts provide rich information content for elucidation of the host’s response to infection and empower discovery of novel metabolic-driven therapies, as well as precise and efficient clinical action.
Keywords	COVID-19 ; metabolism ; immunology ; infection biology ; precision medicine ; Immunologic diseases. Allergy ; RC581-607
Subject code	610
Language	English
Publishing date	2022-01-01T00:00:00Z
Publisher	Frontiers Media S.A.
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Interferon mediated prophylactic protection against respiratory viruses conferred by a prototype live attenuated influenza virus vaccine lacking non-structural protein 1

Raveen Rathnasinghe / Mirella Salvatore / Hongyong Zheng / Sonia Jangra / Thomas Kehrer / Ignacio Mena / Michael Schotsaert / Thomas Muster / Peter Palese / Adolfo García-Sastre

Scientific Reports, Vol 11, Iss 1, Pp 1-

2021 Volume 12

Abstract: Abstract The influenza A non-structural protein 1 (NS1) is known for its ability to hinder the synthesis of type I interferon (IFN) during viral infection. Influenza viruses lacking NS1 (ΔNS1) are under clinical development as live attenuated human ... ...

Abstract	Abstract The influenza A non-structural protein 1 (NS1) is known for its ability to hinder the synthesis of type I interferon (IFN) during viral infection. Influenza viruses lacking NS1 (ΔNS1) are under clinical development as live attenuated human influenza virus vaccines and induce potent influenza virus-specific humoral and cellular adaptive immune responses. Attenuation of ΔNS1 influenza viruses is due to their high IFN inducing properties, that limit their replication in vivo. This study demonstrates that pre-treatment with a ΔNS1 virus results in an antiviral state which prevents subsequent replication of homologous and heterologous viruses, preventing disease from virus respiratory pathogens, including SARS-CoV-2. Our studies suggest that ΔNS1 influenza viruses could be used for the prophylaxis of influenza, SARS-CoV-2 and other human respiratory viral infections, and that an influenza virus vaccine based on ΔNS1 live attenuated viruses would confer broad protection against influenza virus infection from the moment of administration, first by non-specific innate immune induction, followed by specific adaptive immunity.
Keywords	Medicine ; R ; Science ; Q
Subject code	570
Language	English
Publishing date	2021-11-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Distinct temporal trajectories and risk factors for Post-acute sequelae of SARS-CoV-2 infection

Chen Chen / Sairam Parthasarathy / Jacqueline M. Leung / Michelle J. Wu / Katherine A. Drake / Vanessa K. Ridaura / Howard C. Zisser / William A. Conrad / Victor F. Tapson / James N. Moy / Christopher R. deFilippi / Ivan O. Rosas / Bellur S. Prabhakar / Mujeeb Basit / Mirella Salvatore / Jerry A. Krishnan / Charles C. Kim

Frontiers in Medicine, Vol

2023 Volume 10

Abstract: BackgroundThe understanding of Post-acute sequelae of SARS-CoV-2 infection (PASC) can be improved by longitudinal assessment of symptoms encompassing the acute illness period. To gain insight into the various disease trajectories of PASC, we assessed ... ...

Abstract	BackgroundThe understanding of Post-acute sequelae of SARS-CoV-2 infection (PASC) can be improved by longitudinal assessment of symptoms encompassing the acute illness period. To gain insight into the various disease trajectories of PASC, we assessed symptom evolution and clinical factors associated with the development of PASC over 3 months, starting with the acute illness period.MethodsWe conducted a prospective cohort study to identify parameters associated with PASC. We performed cluster and case control analyses of clinical data, including symptomatology collected over 3 months following infection.ResultsWe identified three phenotypic clusters associated with PASC that could be characterized as remittent, persistent, or incident based on the 3-month change in symptom number compared to study entry: remittent (median; min, max: −4; −17, 3), persistent (−2; −14, 7), or incident (4.5; −5, 17) (p = 0.041 remittent vs. persistent, p < 0.001 remittent vs. incident, p < 0.001 persistent vs. incident). Despite younger age and lower hospitalization rates, the incident phenotype had a greater number of symptoms (15; 8, 24) and a higher proportion of participants with PASC (63.2%) than the persistent (6; 2, 9 and 52.2%) or remittent clusters (1; 0, 6 and 18.7%). Systemic corticosteroid administration during acute infection was also associated with PASC at 3 months [OR (95% CI): 2.23 (1.14, 4.36)].ConclusionAn incident disease phenotype characterized by symptoms that were absent during acute illness and the observed association with high dose steroids during acute illness have potential critical implications for preventing PASC.
Keywords	PASC ; symptom clusters ; long COVID ; SARS-CoV-2 ; COVID-19 ; Medicine (General) ; R5-920
Subject code	610
Language	English
Publishing date	2023-10-01T00:00:00Z
Publisher	Frontiers Media S.A.
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: A Worldwide Assessment of Greenhouse Gas Emissions from Drained Organic Soils

Francesco Nicola Tubiello / Riccardo Biancalani / Mirella Salvatore / Simone Rossi / Giulia Conchedda

Sustainability, Vol 8, Iss 4, p

2016 Volume 371

Abstract: Despite the importance of organic soils, including peatlands, in the global carbon cycle, detailed information on regional and global emissions is scarce. This is due to the difficulty to map, measure, and assess the complex dynamics of land, soil, and ... ...

Abstract	Despite the importance of organic soils, including peatlands, in the global carbon cycle, detailed information on regional and global emissions is scarce. This is due to the difficulty to map, measure, and assess the complex dynamics of land, soil, and water interactions needed to assess the human-driven degradation of organic soils. We produced a new methodology for the comprehensive assessment of drained organic soils in agriculture and the estimation of the associated greenhouse gas emissions. Results indicated that over 25 million hectares of organic soils were drained worldwide for agriculture use, of which about 60% were in boreal and temperate cool areas, 34% in tropical areas, and 5% in warm temperate areas. Total emissions from the drainage were globally significant, totaling nearly one billion tonnes CO2eq annually. Of this, the CO2 component, about 780 million tonnes, represented more than one-fourth of total net CO2 emissions from agriculture, forestry, and land use. The bulk of these emissions came from a few tropical countries in Southeast Asia, and was linked to land clearing and drainage for crop cultivation. Geospatial data relative to this work were disseminated via the FAO geospatial server GeoNetwork, while the national aggregated statistics were disseminated via the FAOSTAT database.
Keywords	organic soils ; peatlands ; drainage ; soil ; climate change ; emissions ; mitigation ; cropland ; grassland ; land cover/land use ; Environmental effects of industries and plants ; TD194-195 ; Renewable energy sources ; TJ807-830 ; Environmental sciences ; GE1-350
Subject code	910
Language	English
Publishing date	2016-04-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: New estimates of CO2 forest emissions and removals: 1990â2015

Federici, Sandro / Francesco N. Tubiello / Mirella Salvatore / Heather Jacobs / Josef Schmidhuber

Forest ecology and management. 2015 Sept. 07, v. 352

2015

Abstract: Using newly available data from the 2015 Forest Resources Assessment (FRA), we refined the information, currently available through the IPCC AR5 and FAOSTAT, on recent trends in global and regional net CO2 emissions and removals from forest land, ... ...

Abstract	Using newly available data from the 2015 Forest Resources Assessment (FRA), we refined the information, currently available through the IPCC AR5 and FAOSTAT, on recent trends in global and regional net CO2 emissions and removals from forest land, including from net forest conversion (used as a proxy for deforestation) and forest remaining forest. The new analysis is based on the simplified forest carbon stock method of the FAOSTAT Emissions database, equivalent to a Tier 1, Approach 1 IPCC methodology, limited to biomass carbon stocks. Our results indicated that CO2 emissions from net forest conversion decreased significantly, from an average of 4.0GtCO2yrâ1 during 2001â2010 to 2.9GtCO2yrâ1 during 2011â2015. More than half of the estimated reductions over the last five years, some 0.6GtCO2yrâ1, took place in Brazil. Detailed analyses further indicated that remaining forests continued to function as a net carbon sink globally, with an average net removal of â2.2GtCO2yrâ1 during 2001â2010, and â2.1GtCO2yrâ1 during 2011â2015. Annex I Parties represented the bulk of this sink, contributing 60% of the total in 2011â2015, down from 65% in 2001â2010. Compared to previous FAOSTAT assessments for the period 2001â2010, based on the 2010 FRA and published in the IPCC AR5, the use of FRA 2015 data led to estimates of net forest conversion that were consistent with previous ones (4.0 vs. 3.8GtCO2yrâ1), while the estimated forest sinks were 22% larger (â2.2 vs. â1.8GtCO2yrâ1). The net contribution of forests to anthropogenic forcing based on FRA2015 data was thus smaller than previously estimated by the IPCC AR5. Finally, we separated for the first time net emissions and removals from forest land into a sink component and a degradation component. Results indicated that, contrary to CO2 emissions from deforestation, CO2 emissions from forest degradation increased significantly, from 0.4GtCO2yrâ1 in the 1990s, to 1.1GtCO2yrâ1 in 2001â2010 and 1.0GtCO2yrâ1 in 2011â2015. Emissions from forest degradation were thus one-fourth of those from deforestation in 2001â2010, increasing to one-third in 2011â2015.
Keywords	anthropogenic activities ; biomass ; carbon dioxide ; carbon sinks ; databases ; deforestation ; forest resources ; forests ; greenhouse gas emissions ; Brazil
Language	English
Dates of publication	2015-0907
Size	p. 89-98.
Publishing place	Elsevier B.V.
Document type	Article
ZDB-ID	751138-3
ISSN	0378-1127
ISSN	0378-1127
DOI	10.1016/j.foreco.2015.04.022
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Mucosal immunization with integrase-defective lentiviral vectors protects against influenza virus challenge in mice.

Judith M Fontana / Paul J Christos / Zuleika Michelini / Donatella Negri / Andrea Cara / Mirella Salvatore

PLoS ONE, Vol 9, Iss 5, p e

2014 Volume 97270

Abstract: Recent reports highlight the potential for integrase-defective lentiviral vectors (IDLV) to be developed as vaccines due to their ability to elicit cell-mediated and humoral immune responses after intramuscular administration. Differently from their ... ...

Abstract	Recent reports highlight the potential for integrase-defective lentiviral vectors (IDLV) to be developed as vaccines due to their ability to elicit cell-mediated and humoral immune responses after intramuscular administration. Differently from their integrase-competent counterpart, whose utility for vaccine development is limited by the potential for insertional mutagenesis, IDLV possess a mutation in their integrase gene that prevents genomic integration. Instead, they are maintained as episomal DNA circles that retain the ability to stably express functional proteins. Despite their favorable profile, it is unknown whether IDLV elicit immune responses after intranasal administration, a route that could be advantageous in the case of infection with a respiratory agent. Using influenza as a model, we constructed IDLV expressing the influenza virus nucleoprotein (IDLV-NP), and tested their ability to generate NP-specific immune responses and protect from challenge in vivo. We found that administration of IDLV-NP elicited NP-specific T cell and antibody responses in BALB/c mice. Importantly, IDLV-NP was protective against homologous and heterosubtypic influenza virus challenge only when given by the intranasal route. This is the first report demonstrating that IDLV can induce protective immunity after intranasal administration, and suggests that IDLV may represent a promising vaccine platform against infectious agents.
Keywords	Medicine ; R ; Science ; Q
Language	English
Publishing date	2014-01-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: Active opioid use does not attenuate the humoral responses to inactivated influenza vaccine

Moroz, Ekaterina / Adolfo García-Sastre / Ann Bordwine Beeder / Brandon Aden / Brian R. Edlin / Jianda Yuan / Mirella Salvatore / Randy A. Albrecht

Vaccine. 2016 Mar. 08, v. 34, no. 11

2016

Abstract: Influenza vaccination is recommended for vulnerable individuals, including active drug users, to prevent influenza complications and decrease influenza spread. Recent studies suggest that opioids negatively regulate immune responses in experimental ... ...

Abstract	Influenza vaccination is recommended for vulnerable individuals, including active drug users, to prevent influenza complications and decrease influenza spread. Recent studies suggest that opioids negatively regulate immune responses in experimental models, but the extent to which opioid use will affect the humoral responses to influenza vaccine in humans is unknown. This information is critical in maximizing vaccination efforts.To determine whether there is a difference in antibody response after influenza vaccination in heroin or methadone users compared to control subjects.We studied active heroin users, subjects on methadone maintenance treatment (MMT) and subjects that did not use any drugs before and 1 and 4 weeks after vaccination with trivalent influenza vaccine (TIV). We measured hemagglutination inhibition and microneutralization titers, and we compared geometric mean titers (GMT), and rates of seroprotection and seroconversion for each of the vaccine strains among the 3 groups of subjects.Heroin users, subjects on MMT and non-user controls mount a similarly robust serologic response to TIV. GMT and rates of seroprotection and seroconversion were not significantly different among groups.Our results suggest that opioid use do not significantly alter antibody responses to influenza vaccine supporting the vaccination effort in these populations.
Keywords	antibodies ; hemagglutination ; heroin ; humans ; humoral immunity ; influenza ; methadone ; models ; seroconversion ; vaccination ; vaccines
Language	English
Dates of publication	2016-0308
Size	p. 1363-1369.
Publishing place	Elsevier Ltd
Document type	Article
ZDB-ID	605674-x
ISSN	1873-2518 ; 0264-410X
ISSN (online)	1873-2518
ISSN	0264-410X
DOI	10.1016/j.vaccine.2016.01.051
Database	NAL-Catalogue (AGRICOLA)

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Article: Greenhouse gas mitigation potential of the world’s grazing lands: Modeling soil carbon and nitrogen fluxes of mitigation practices

Henderson, Benjamin B / Alessandra Falcucci / Dennis S. Ojima / Mirella Salvatore / Pierre J. Gerber / Richard T. Conant / Tom E. Hilinski

Agriculture, ecosystems & environment. 2015 Sept. 01, v. 207

2015

Abstract: This study provides estimates of the net GHG mitigation potential of a selected range of management practices in the world’s native and cultivated grazing lands. The Century and Daycent models are used to calculate the changes in soil carbon stocks, soil ...

Abstract	This study provides estimates of the net GHG mitigation potential of a selected range of management practices in the world’s native and cultivated grazing lands. The Century and Daycent models are used to calculate the changes in soil carbon stocks, soil N2O emissions, and forage removals by ruminants associated with these practices. GLEAM is used in combination with these models to establish grazing area boundaries and to parameterize links between forage consumption, animal production and animal GHG emissions. This study provides an alternative to the usual approach of extrapolating from a small number of field studies and by modeling the linkage between soil, forage and animals it sheds new light on the net mitigation potential of C sequestration practices in the world’s grazing lands. Three different mitigation practices are assessed in this study, namely, improved grazing management, legume sowing and N fertilization. We estimate that optimization of grazing pressure could sequester 148Tg CO2yr−1. The soil C sequestration potential of 203Tg CO2yr−1 for legume sowing was higher than for improved grazing management, despite being applied over a much smaller total area. However, N2O emissions from legumes were estimated to offset 28% of its global C sequestration benefits, in CO2 equivalent terms. Conversely, N2O emissions from N fertilization exceeded soil C sequestration, in all regions. Our estimated potential for increasing C stocks though in grazing lands is lower than earlier worldwide estimates (Smith et al., 2007; Lal, 2004), mainly due to the much smaller grazing land area over which we estimate mitigation practices to be effective. A big concern is the high risk of the practices, particularly legumes, increasing soil-based GHGs if applied outside of this relatively small effective area. More work is needed to develop indicators, based on biophysical and management characteristics of grazing lands, to identify amenable areas before these practices can be considered ready for large scale implementation. The additional ruminant GHG emissions associated with higher forage output are likely to substantially reduce the mitigation potential of these practices, but could contribute to more GHG-efficient livestock production.
Keywords	carbon ; carbon dioxide ; carbon sequestration ; carbon sinks ; field experimentation ; forage ; grazing intensity ; grazing lands ; grazing management ; greenhouse gas emissions ; greenhouse gases ; legumes ; livestock production ; models ; nitrogen ; nitrous oxide ; range management ; risk ; ruminants ; soil ; sowing
Language	English
Dates of publication	2015-0901
Size	p. 91-100.
Publishing place	Elsevier B.V.
Document type	Article
ZDB-ID	602345-9
ISSN	1873-2305 ; 0167-8809
ISSN (online)	1873-2305
ISSN	0167-8809
DOI	10.1016/j.agee.2015.03.029
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Host, Viral, and Environmental Transcriptome Profiles of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2)

Daniel J Butler / Christopher Mozsary / Cem Meydan / David C Danko / Jonathan Foox / Joel Rosiene / Alon Shaiber / Ebrahim Afshinnekoo / Matthew MacKay / Fritz J Sedlazeck / Nikolay A Ivanov / Maria A Sierra / Diana Pohle / Michael Zeitz / Vijendra Ramlall / Undina Gisladottir / Craig D Westover / Krista Ryon / Benjamin Young /

Chandrima Bhattacharya / Phyllis Ruggiero / Bradley W Langhorst / Nathan A Tanner / Justyn Gawrys / Dmitry Meleshko / Dong Xu / Jenny Xiang / Angelika Iftner / Daniela Bezdan / John Sipley / Lin Cong / Arryn Craney / Priya Velu / Ari Melnick / Iman A Hajirasouliha / Thomas Iftner / Mirella Salvatore / Massimo Loda / Lars F Westblade / Shawn Levy / Melissa Cushing / Nicholas P Tatonetti / Marcin Imielinski / Hanna Rennert / Christopher Mason

Abstract: The pandemic from the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) led to >170,000 deaths, including >14,500 in New York City (NYC) alone. This pandemic highlighted a pressing clinical and public health need for rapid, scalable ... ...

Abstract	The pandemic from the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) led to >170,000 deaths, including >14,500 in New York City (NYC) alone. This pandemic highlighted a pressing clinical and public health need for rapid, scalable diagnostics that can detect SARS-CoV-2 infection, interrogate strain evolution, and map host response in patients. To address these challenges, we designed a fast (30 minute) colorimetric test to identify SARS-CoV-2 infection and simultaneously developed a large-scale shotgun metatranscriptomic profiling platform for nasopharyngeal swabs. Both technologies were used to profile 338 clinical specimens tested for SARS-CoV-2 and 86 NYC subway samples, creating a broad molecular picture of the COVID-19 epidemic in NYC. Our results nominate a novel, NYC-enriched SARS-CoV-2 subclade, reveal specific host responses in ACE pathways, and find medication risks associated with SARS-CoV-2 infection and ACE inhibitors. Our findings have immediate applications to SARS-CoV-2 diagnostics, public health monitoring, and therapeutic development.
Keywords	covid19
Publisher	biorxiv
Document type	Article ; Online
DOI	10.1101/2020.04.20.048066
Database	COVID19

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Article: The invertebrate fauna of dune and machair sites in Scotland. Vol II Part (3) The Moray Firth site dossiers. Report to the Nature Conservancy Council.

Francesco N. Tubiello / Mirella Salvatore / Simone Rossi / Aless / ro Ferrara / Nuala Fitton / Pete Smith

Document type	Article
Database	AGRIS - International Information System for the Agricultural Sciences and Technology

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