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Article ; Online: Zika virus remodelled ER membranes contain proviral factors involved in redox and methylation pathways.

Denolly, Solène / Stukalov, Alexey / Barayeu, Uladzimir / Rosinski, Alina N / Kritsiligkou, Paraskevi / Joecks, Sebastian / Dick, Tobias P / Pichlmair, Andreas / Bartenschlager, Ralf

Nature communications

2023 Volume 14, Issue 1, Page(s) 8045

Abstract: Zika virus (ZIKV) has emerged as a global health issue, yet neither antiviral therapy nor a vaccine are available. ZIKV is an enveloped RNA virus, replicating in the cytoplasm in close association with ER membranes. Here, we isolate ER membranes from ... ...

Abstract	Zika virus (ZIKV) has emerged as a global health issue, yet neither antiviral therapy nor a vaccine are available. ZIKV is an enveloped RNA virus, replicating in the cytoplasm in close association with ER membranes. Here, we isolate ER membranes from ZIKV-infected cells and determine their proteome. Forty-six host cell factors are enriched in ZIKV remodeled membranes, several of these having a role in redox and methylation pathways. Four proteins are characterized in detail: thioredoxin reductase 1 (TXNRD1) contributing to folding of disulfide bond containing proteins and modulating ZIKV secretion; aldo-keto reductase family 1 member C3 (AKR1C3), regulating capsid protein abundance and thus, ZIKV assembly; biliverdin reductase B (BLVRB) involved in ZIKV induced lipid peroxidation and increasing stability of viral transmembrane proteins; adenosylhomocysteinase (AHCY) indirectly promoting m
MeSH term(s)	Humans ; Zika Virus/genetics ; Zika Virus Infection ; Methylation ; Proviruses ; Virus Replication/physiology ; Viral Proteins/metabolism ; Oxidation-Reduction
Chemical Substances	Viral Proteins
Language	English
Publishing date	2023-12-05
Publishing country	England
Document type	Journal Article
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-023-43665-6
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Zika virus remodelled ER membranes contain proviral factors involved in redox and methylation pathways

Solène Denolly / Alexey Stukalov / Uladzimir Barayeu / Alina N. Rosinski / Paraskevi Kritsiligkou / Sebastian Joecks / Tobias P. Dick / Andreas Pichlmair / Ralf Bartenschlager

Nature Communications, Vol 14, Iss 1, Pp 1-

2023 Volume 20

Abstract: Abstract Zika virus (ZIKV) has emerged as a global health issue, yet neither antiviral therapy nor a vaccine are available. ZIKV is an enveloped RNA virus, replicating in the cytoplasm in close association with ER membranes. Here, we isolate ER membranes ...

Abstract	Abstract Zika virus (ZIKV) has emerged as a global health issue, yet neither antiviral therapy nor a vaccine are available. ZIKV is an enveloped RNA virus, replicating in the cytoplasm in close association with ER membranes. Here, we isolate ER membranes from ZIKV-infected cells and determine their proteome. Forty-six host cell factors are enriched in ZIKV remodeled membranes, several of these having a role in redox and methylation pathways. Four proteins are characterized in detail: thioredoxin reductase 1 (TXNRD1) contributing to folding of disulfide bond containing proteins and modulating ZIKV secretion; aldo-keto reductase family 1 member C3 (AKR1C3), regulating capsid protein abundance and thus, ZIKV assembly; biliverdin reductase B (BLVRB) involved in ZIKV induced lipid peroxidation and increasing stability of viral transmembrane proteins; adenosylhomocysteinase (AHCY) indirectly promoting m6A methylation of ZIKV RNA by decreasing the level of S- adenosyl homocysteine and thus, immune evasion. These results highlight the involvement of redox and methylation enzymes in the ZIKV life cycle and their accumulation at virally remodeled ER membranes.
Keywords	Science ; Q
Subject code	570
Language	English
Publishing date	2023-12-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: Identification of Novel Biomarkers for Alzheimer's Disease and Related Dementias Using Unbiased Plasma Proteomics.

Lacar, Benjamin / Ferdosi, Shadi / Alavi, Amir / Stukalov, Alexey / Venkataraman, Guhan R / de Geus, Matthijs / Dodge, Hiroko / Wu, Chao-Yi / Kivisakk, Pia / Das, Sudeshna / Guturu, Harendra / Hyman, Brad / Batzoglou, Serafim / Arnold, Steven E / Siddiqui, Asim

bioRxiv : the preprint server for biology

2024

Abstract: Alzheimer's disease (AD) and related dementias (ADRD) is a complex disease with multiple pathophysiological drivers that determine clinical symptomology and disease progression. These diseases develop insidiously over time, through many pathways and ... ...

Abstract	Alzheimer's disease (AD) and related dementias (ADRD) is a complex disease with multiple pathophysiological drivers that determine clinical symptomology and disease progression. These diseases develop insidiously over time, through many pathways and disease mechanisms and continue to have a huge societal impact for affected individuals and their families. While emerging blood-based biomarkers, such as plasma p-tau181 and p-tau217, accurately detect Alzheimer neuropthology and are associated with faster cognitive decline, the full extension of plasma proteomic changes in ADRD remains unknown. Earlier detection and better classification of the different subtypes may provide opportunities for earlier, more targeted interventions, and perhaps a higher likelihood of successful therapeutic development. In this study, we aim to leverage unbiased mass spectrometry proteomics to identify novel, blood-based biomarkers associated with cognitive decline. 1,786 plasma samples from 1,005 patients were collected over 12 years from partcipants in the Massachusetts Alzheimer's Disease Research Center Longitudinal Cohort Study. Patient metadata includes demographics, final diagnoses, and clinical dementia rating (CDR) scores taken concurrently. The Proteograph
Language	English
Publishing date	2024-01-08
Publishing country	United States
Document type	Preprint
DOI	10.1101/2024.01.05.574446
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Article ; Online: Gambling with Flu: "All in" to Maximize Reward.

Stukalov, Alexey / Pichlmair, Andreas

Cell host & microbe

2015 Volume 18, Issue 6, Page(s) 643–645

Abstract: In this issue of Cell Host & Microbe, Tripathi et al. (2015) report an in-depth meta-analysis of eight influenza virus siRNA screens combined with viral-host protein interactome data. The integration of the different omics datasets highlights candidate ... ...

Abstract	In this issue of Cell Host & Microbe, Tripathi et al. (2015) report an in-depth meta-analysis of eight influenza virus siRNA screens combined with viral-host protein interactome data. The integration of the different omics datasets highlights candidate genes and pathways for further investigation and potential therapeutic targeting in the future.
MeSH term(s)	Gambling ; Humans ; Orthomyxoviridae/genetics ; RNA, Small Interfering ; Reward ; Viral Proteins/metabolism
Chemical Substances	RNA, Small Interfering ; Viral Proteins
Language	English
Publishing date	2015-12-07
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Comment
ZDB-ID	2278004-X
ISSN	1934-6069 ; 1931-3128
ISSN (online)	1934-6069
ISSN	1931-3128
DOI	10.1016/j.chom.2015.11.010
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Article ; Online: Deep, unbiased and quantitative mass spectrometry-based plasma proteome analysis of individual responses to mRNA COVID-19 vaccine

Huang, Ting / Campos, Alex Rosa / Wang, Jian / Stukalov, Alexey / Díaz, Ramón / Maurya, Svetlana / Motamedchaboki, Khatereh / Hornburg, Daniel / Saciloto-de-Oliveira, Laura R. / Innocente-Alves, Camila / Calegari-Alves, Yohana P. / Batzoglou, Serafim / Beys-da-Silva, Walter O. / Santi, Lucélia

bioRxiv

Abstract: Global campaign against COVID-19 have vaccinated a significant portion of the world population in recent years. Combating the COVID-19 pandemic with mRNA vaccines played a pivotal role in the global immunization effort. However, individual responses to a ...

Abstract	Global campaign against COVID-19 have vaccinated a significant portion of the world population in recent years. Combating the COVID-19 pandemic with mRNA vaccines played a pivotal role in the global immunization effort. However, individual responses to a vaccine are diverse and lead to varying vaccination efficacy. Despite significant progress, a complete understanding of the molecular mechanisms driving the individual immune response to the COVID-19 vaccine remains elusive. To address this gap, we combined a novel nanoparticle-based proteomic workflow with tandem mass tag (TMT) labeling, to quantitatively assess the proteomic changes in a cohort of 12 volunteers following two doses of the Pfizer-BioNTech mRNA COVID-19 vaccine. This optimized protocol seamlessly integrates comprehensive proteome analysis with enhanced throughput by leveraging the enrichment of low-abundant plasma proteins by engineered nanoparticles. Our data demonstrate the ability of this nanoparticle-based workflow to quantify over 3,000 proteins from 48 human plasma samples, providing the deepest view into COVID-19 vaccine-related plasma proteome study. We identified 69 proteins exhibiting a boosted response to the vaccine after the second dose. Additionally, 74 proteins were differentially regulated between seven volunteers, who contracted COVID-19 despite receiving two doses of the vaccine, and the ones who did not contract COVID-19. These findings offer valuable insights into individual variability in response to vaccination, demonstrating the potential of personalized medicine approaches in vaccine development.
Keywords	covid19
Language	English
Publishing date	2024-04-23
Publisher	Cold Spring Harbor Laboratory
Document type	Article ; Online
DOI	10.1101/2024.04.22.589104
Database	COVID19

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Article ; Online: Deep, unbiased and quantitative mass spectrometry-based plasma proteome analysis of individual responses to mRNA COVID-19 vaccine

Huang, Ting / Campos, Alex Rosa / Wang, Jian / Stukalov, Alexey / Diaz, Ramon / Maurya, Svetlana / Motamedchaboki, Khatereh / Hornburg, Daniel / Saciloto-de-Oliveira, Laura R. / Innocente-Alves, Camila / Calegari-Alves, Yohana P. / Batzoglou, Serafim / Beys-da-Silva, Walter O. / Santi, Lucelia

bioRxiv

Abstract	Global campaign against COVID-19 have vaccinated a significant portion of the world population in recent years. Combating the COVID-19 pandemic with mRNA vaccines played a pivotal role in the global immunization effort. However, individual responses to a vaccine are diverse and lead to varying vaccination efficacy. Despite significant progress, a complete understanding of the molecular mechanisms driving the individual immune response to the COVID-19 vaccine remains elusive. To address this gap, we combined a novel nanoparticle-based proteomic workflow with tandem mass tag (TMT) labeling, to quantitatively assess the proteomic changes in a cohort of 12 volunteers following two doses of the Pfizer-BioNTech mRNA COVID-19 vaccine. This optimized protocol seamlessly integrates comprehensive proteome analysis with enhanced throughput by leveraging the enrichment of low-abundant plasma proteins by engineered nanoparticles. Our data demonstrate the ability of this nanoparticle-based workflow to quantify over 3,000 proteins from 48 human plasma samples, providing the deepest view into COVID-19 vaccine-related plasma proteome study. We identified 69 proteins exhibiting a boosted response to the vaccine after the second dose. Additionally, 74 proteins were differentially regulated between seven volunteers, who contracted COVID-19 despite receiving two doses of the vaccine, and the ones who did not contract COVID-19. These findings offer valuable insights into individual variability in response to vaccination, demonstrating the potential of personalized medicine approaches in vaccine development.
Keywords	covid19
Language	English
Publishing date	2024-04-23
Publisher	Cold Spring Harbor Laboratory
Document type	Article ; Online
DOI	10.1101/2024.04.22.589104
Database	COVID19

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Article ; Online: dagLogo: An R/Bioconductor package for identifying and visualizing differential amino acid group usage in proteomics data.

Ou, Jianhong / Liu, Haibo / Nirala, Niraj K / Stukalov, Alexey / Acharya, Usha / Green, Michael R / Zhu, Lihua Julie

PloS one

2020 Volume 15, Issue 11, Page(s) e0242030

Abstract: Sequence logos have been widely used as graphical representations of conserved nucleic acid and protein motifs. Due to the complexity of the amino acid (AA) alphabet, rich post-translational modification, and diverse subcellular localization of proteins, ...

Abstract	Sequence logos have been widely used as graphical representations of conserved nucleic acid and protein motifs. Due to the complexity of the amino acid (AA) alphabet, rich post-translational modification, and diverse subcellular localization of proteins, few versatile tools are available for effective identification and visualization of protein motifs. In addition, various reduced AA alphabets based on physicochemical, structural, or functional properties have been valuable in the study of protein alignment, folding, structure prediction, and evolution. However, there is lack of tools for applying reduced AA alphabets to the identification and visualization of statistically significant motifs. To fill this gap, we developed an R/Bioconductor package dagLogo, which has several advantages over existing tools. First, dagLogo allows various formats for input sets and provides comprehensive options to build optimal background models. It implements different reduced AA alphabets to group AAs of similar properties. Furthermore, dagLogo provides statistical and visual solutions for differential AA (or AA group) usage analysis of both large and small data sets. Case studies showed that dagLogo can better identify and visualize conserved protein sequence patterns from different types of inputs and can potentially reveal the biological patterns that could be missed by other logo generators.
MeSH term(s)	Algorithms ; Amino Acid Motifs/genetics ; Amino Acids/genetics ; Conserved Sequence/genetics ; Databases, Protein ; Humans ; Position-Specific Scoring Matrices ; Proteins/genetics ; Proteomics/methods ; Sequence Alignment/methods ; Software
Chemical Substances	Amino Acids ; Proteins
Language	English
Publishing date	2020-11-06
Publishing country	United States
Document type	Journal Article
ISSN	1932-6203
ISSN (online)	1932-6203
DOI	10.1371/journal.pone.0242030
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Protein Coronas on Functionalized Nanoparticles Enable Quantitative and Precise Large-Scale Deep Plasma Proteomics.

bioRxiv : the preprint server for biology

2023

Abstract: Background: The wide dynamic range of circulating proteins coupled with the diversity of proteoforms present in plasma has historically impeded comprehensive and quantitative characterization of the plasma proteome at scale. Automated nanoparticle (NP) ... ...

Abstract	Background: The wide dynamic range of circulating proteins coupled with the diversity of proteoforms present in plasma has historically impeded comprehensive and quantitative characterization of the plasma proteome at scale. Automated nanoparticle (NP) protein corona-based proteomics workflows can efficiently compress the dynamic range of protein abundances into a mass spectrometry (MS)-accessible detection range. This enhances the depth and scalability of quantitative MS-based methods, which can elucidate the molecular mechanisms of biological processes, discover new protein biomarkers, and improve comprehensiveness of MS-based diagnostics. Methods: Investigating multi-species spike-in experiments and a cohort, we investigated fold-change accuracy, linearity, precision, and statistical power for the using the Proteograph Results: We show that NP-based workflows enable accurate identification (false discovery rate of 1%) of more than 6,000 proteins from plasma (Orbitrap Astral) and, compared to a gold standard neat plasma workflow that is limited to the detection of hundreds of plasma proteins, facilitate quantification of more proteins with accurate fold-changes, high linearity, and precision. Furthermore, we demonstrate high statistical power for the discovery of biomarkers in small- and large-scale cohorts. Conclusions: The automated NP workflow enables high-throughput, deep, and quantitative plasma proteomics investigation with sufficient power to discover new biomarker signatures with a peptide level resolution.
Language	English
Publishing date	2023-08-29
Publishing country	United States
Document type	Preprint
DOI	10.1101/2023.08.28.555225
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: dagLogo

Jianhong Ou / Haibo Liu / Niraj K Nirala / Alexey Stukalov / Usha Acharya / Michael R Green / Lihua Julie Zhu

PLoS ONE, Vol 15, Iss 11, p e

An R/Bioconductor package for identifying and visualizing differential amino acid group usage in proteomics data.

2020 Volume 0242030

Abstract	Sequence logos have been widely used as graphical representations of conserved nucleic acid and protein motifs. Due to the complexity of the amino acid (AA) alphabet, rich post-translational modification, and diverse subcellular localization of proteins, few versatile tools are available for effective identification and visualization of protein motifs. In addition, various reduced AA alphabets based on physicochemical, structural, or functional properties have been valuable in the study of protein alignment, folding, structure prediction, and evolution. However, there is lack of tools for applying reduced AA alphabets to the identification and visualization of statistically significant motifs. To fill this gap, we developed an R/Bioconductor package dagLogo, which has several advantages over existing tools. First, dagLogo allows various formats for input sets and provides comprehensive options to build optimal background models. It implements different reduced AA alphabets to group AAs of similar properties. Furthermore, dagLogo provides statistical and visual solutions for differential AA (or AA group) usage analysis of both large and small data sets. Case studies showed that dagLogo can better identify and visualize conserved protein sequence patterns from different types of inputs and can potentially reveal the biological patterns that could be missed by other logo generators.
Keywords	Medicine ; R ; Science ; Q
Subject code	612
Language	English
Publishing date	2020-01-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Burials of the Early Iron Age of the Kurgans Cemetery “Bogomolnye Peski-I”

Alexey A. Timofeev / Damir S. Soloviov / Georgiy V. Stukalov / Dmitriy V. Vasiliev / Victor Yu. Bochkarev

Нижневолжский археологический вестник, Vol 19, Iss 2, Pp 279-

2020 Volume 305

Abstract: The article is dedicated to the publication of the materials of burials from the Early Iron Age, discovered during excavations of a crumbling kurgan which is a part of the cemetery “Bogomolnye Peski-I” close to the village of Nikolskoye, Enotaevsky ... ...

Abstract	The article is dedicated to the publication of the materials of burials from the Early Iron Age, discovered during excavations of a crumbling kurgan which is a part of the cemetery “Bogomolnye Peski-I” close to the village of Nikolskoye, Enotaevsky district, Astrakhan region. In total, 14 burials were investigated during the rescue excavations, two of them relate to the Middle Ages, other seven belong to the Bronze Age. The article describes in detail 5 burials of the Early Iron Age. The dating of the burials is defined based on the materials and details of the burial rite. The earliest burial (No. 2) dates back to the Savromat era. It contained a decapitated rams carcase and a molded pot which is typical of assumed era. The rest of the burials belong to the Middle Sarmatian period (1st – 2nd centuries AD). One of the Middle Sarmatian burials was completely destroyed by robbers in ancient times. It was possible to find a lot of gold stripes of clothes among its containment, as well as a bronze cauldron with a tamga. Plaques and stripes are not typical of either the Savromat or the early Sarmatian cultures. Indeed, they are widely used in prestigious burials of the Middle Sarmatian culture. The burials No. 5 and No. 13, accompanied by a rich inventory, are of the greatest interest. A set of gold decorations for a funeral veil and a belt set of gold with turquoise inserts were found in burial No.5, which belong to the products of the Sarmatian polychrome style, typical of the Middle Sarmatian period. In addition, a gilded bronze dish related to Roman provincial dishes and an alabaster vessel were discovered there – a typical find of the Middle Sarmatian era. In burial No. 12, the most interesting findings, in addition to a large number of various beads, are intaglio gemstones made of red glass with plots of ancient mythology depicted on them, which are unique in their own way. Moreover, an interesting vessel shaped as a bird (duck) was found there as well. The close analogs to the latter are known in cemeteries of ...
Keywords	early iron age ; barrow ; lower volga region ; sarmatians ; burial rite ; History of Civilization ; CB3-482 ; Archaeology ; CC1-960 ; Anthropology ; GN1-890
Subject code	930
Language	English
Publishing date	2020-12-01T00:00:00Z
Publisher	Volgograd State University
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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