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  1. Article ; Online: Understanding Stress Response to High-Arsenic Gold-Bearing Sulfide Concentrate in Extremely Metal-Resistant Acidophile Sulfobacillus thermotolerans

    Anna Panyushkina / Daria Matyushkina / Olga Pobeguts

    Microorganisms, Vol 8, Iss 1076, p

    2020  Volume 1076

    Abstract: Biooxidation of gold-bearing arsenopyrite concentrates, using acidophilic microbial communities, is among the largest commercial biohydrometallurgical processes. However, molecular mechanisms of microbial responses to sulfide raw materials have not been ... ...

    Abstract Biooxidation of gold-bearing arsenopyrite concentrates, using acidophilic microbial communities, is among the largest commercial biohydrometallurgical processes. However, molecular mechanisms of microbial responses to sulfide raw materials have not been widely studied. The goal of this research was to gain insight into the defense strategies of the acidophilic bacterium Sulfobacillus thermotolerans , which dominates microbial communities functioning in industrial biooxidation processes at >35 °C, against the toxic effect of the high-arsenic gold-bearing sulfide concentrate. In addition to extreme metal resistance, this acidophile proved to be one of the most As-tolerant microorganisms. Comparative proteomic analysis indicated that 30 out of 33 differentially expressed proteins were upregulated in response to the ore concentrate, while the synthesis level of the functional proteins required for cell survival was not negatively affected. Despite a high level of cellular metal(loid) accumulation, no specific metal(loid)-resistant systems were regulated. Instead, several proteins involved in the metabolic pathways and stress response, including MBL fold metallo-hydrolase, sulfide:quinone oxidoreductase, and GroEL chaperonin, may play crucial roles in resistance to the sulfide ore concentrate and arsenic, in particular. This study provides the first data on the microbial responses to sulfide ore concentrates and advances our understanding of defense mechanisms against toxic compounds in acidophiles.
    Keywords acidophiles ; Sulfobacillus thermotolerans ; sulfide concentrate ; arsenic ; resistance ; differential proteomics ; Biology (General) ; QH301-705.5
    Language English
    Publishing date 2020-07-01T00:00:00Z
    Publisher MDPI AG
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  2. Article ; Online: Microarray Profiling of Vaccination-Induced Antibody Responses to SARS-CoV-2 Variants of Interest and Concern

    Julia Svetlova / Dmitry Gustin / Valentin Manuvera / Dmitriy Shirokov / Varvara Shokina / Kirill Prusakov / Konstantin Aldarov / Daria Kharlampieva / Daria Matyushkina / Julia Bespyatykh / Anna Varizhuk / Vassili Lazarev / Tatiana Vedekhina

    International Journal of Molecular Sciences, Vol 23, Iss 13220, p

    2022  Volume 13220

    Abstract: Mutations in surface proteins enable emerging variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) to escape a substantial fraction of neutralizing antibodies and may thus weaken vaccine-driven immunity. To compare available vaccines ... ...

    Abstract Mutations in surface proteins enable emerging variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) to escape a substantial fraction of neutralizing antibodies and may thus weaken vaccine-driven immunity. To compare available vaccines and justify revaccination, rapid evaluation of antibody (Ab) responses to currently circulating SARS-CoV-2 variants of interest (VOI) and concern (VOC) is needed. Here, we developed a multiplex protein microarray-based system for rapid profiling of anti-SARS-CoV-2 Ab levels in human sera. The microarray system was validated using sera samples from SARS-CoV-2-free donors and those diagnosed with COVID-19 based on PCR and enzyme immunoassays. Microarray-based profiling of vaccinated donors revealed a substantial difference in anti-VOC Ab levels elicited by the replication-deficient adenovirus vector-base (Sputnik V) and whole-virion (CoviVac Russia COVID-19) vaccines. Whole-virion vaccine-induced Abs showed minor but statistically significant cross-reactivity with the human blood coagulation factor 1 (fibrinogen) and thrombin. However, their effects on blood clotting were negligible, according to thrombin time tests, providing evidence against the concept of pronounced cross-reactivity-related side effects of the vaccine. Importantly, all samples were collected in the pre-Omicron period but showed noticeable responses to the receptor-binding domain (RBD) of the Omicron spike protein. Thus, using the new express Ab-profiling system, we confirmed the inter-variant cross-reactivity of the anti-SARS-CoV-2 Abs and demonstrated the relative potency of the vaccines against new VOCs.
    Keywords microarrays ; coronavirus infection ; COVID-19 ; SARS-CoV-2 ; antibodies ; Sputnik V ; Biology (General) ; QH301-705.5 ; Chemistry ; QD1-999
    Subject code 500
    Language English
    Publishing date 2022-10-01T00:00:00Z
    Publisher MDPI AG
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  3. Article ; Online: Data-independent proteome profile of Mycoplasma gallisepticum under normal conditions and heat stress

    Ivan Butenko / Olga Pobeguts / Daria Matyushkina / Sergey Kovalchuk / Nickolay Anikanov / Gleb Fisunov / Vadim Govorun

    Data in Brief, Vol 16, Iss , Pp 700-

    2018  Volume 704

    Abstract: The data reported is a large-scale untargeted proteome profile for Mycoplasma gallisepticum – a model organism for studying both regulation in genome-reduced bacteria and intracellular infection (Mazin et al., 2014) [1,2]. While seminal whole-proteome ... ...

    Abstract The data reported is a large-scale untargeted proteome profile for Mycoplasma gallisepticum – a model organism for studying both regulation in genome-reduced bacteria and intracellular infection (Mazin et al., 2014) [1,2]. While seminal whole-proteome studies were performed on Mycoplasma genitalium [3] and a few proteome datasets are available for Mycoplasma pneumoniae, no data-independent (DIA) proteome profiling has been published for bacteria of Mycoplasma genus. Since DIA-based proteome profiling allows to extract evidence on presence and quantity of any protein of interest in a post-acquisition manner and the data presented is describing a model which is suitable to study both proteome regulation in general and details of mycoplasma infection process [4], the proteome profiling data presented here is of value for deep annotation. The data was deposited to the PRIDE repository (PXD008198).
    Keywords Computer applications to medicine. Medical informatics ; R858-859.7 ; Science (General) ; Q1-390
    Language English
    Publishing date 2018-02-01T00:00:00Z
    Publisher Elsevier
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  4. Article ; Online: Data on genome analysis of Mycoplasma gallisepticum during intracellular infection

    Daria Matyushkina / Olga Pobeguts / Irina Garanina / Vladislav Babenko / Maria Vakhitova / Gleb Fisunov / Vadim Govorun

    Data in Brief, Vol 10, Iss C, Pp 264-

    2017  Volume 268

    Abstract: The genus Mycoplasma relates to Gram-positive bacteria that lack a cell wall and are capable to cause chronic disease in humans and animals. Among the agents of infection and disease in domestic poultry and wild birds, Mycoplasma gallisepticum is the ... ...

    Abstract The genus Mycoplasma relates to Gram-positive bacteria that lack a cell wall and are capable to cause chronic disease in humans and animals. Among the agents of infection and disease in domestic poultry and wild birds, Mycoplasma gallisepticum is the most important mycoplasma species, causing considerable losses in the poultry industry. In the present paper, we provide data on adaptation of M. gallisepticum to the eukaryotic host cells on the genomic level. The major changes were predominantly localized in the VlhA-hemagglutinin genes which are important components of pathogenesis. The ability of mycoplasmas to change dramatically the repertoire of surface antigens and to vary the immunogenicity of these components allows them to remain undetected by the immune system of the host. The data presented in this article are related to the article entitled “Phase Transition of the Bacterium upon Invasion of a Host Cell as a Mechanism of Adaptation: a Mycoplasma gallisepticum Model.” (Matyushkina et al., 2016) [1]. Data posted in repository https://www.ncbi.nlm.nih.gov/bioproject/315515. Bioproject ID: PRJNA315515.
    Keywords Host-pathogen interaction ; Mycoplasma ; Genome ; Vlh antiges ; Nucleotide polymorphism ; Computer applications to medicine. Medical informatics ; R858-859.7 ; Science (General) ; Q1-390
    Subject code 630
    Language English
    Publishing date 2017-02-01T00:00:00Z
    Publisher Elsevier
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  5. Article ; Online: Response induced in Mycoplasma gallisepticum under heat shock might be relevant to infection process

    Ivan Butenko / Anna Vanyushkina / Olga Pobeguts / Daria Matyushkina / Sergey Kovalchuk / Alexey Gorbachev / Nicolay Anikanov / Gleb Fisunov / Vadim Govorun

    Scientific Reports, Vol 7, Iss 1, Pp 1-

    2017  Volume 12

    Abstract: Abstract Despite the fact the term “proteome” was proposed to characterize a set of proteins in one of mycoplasma species, proteome response to various exposures in this bacteria are still obscure. Commonly, authors studying proteomic response on ... ...

    Abstract Abstract Despite the fact the term “proteome” was proposed to characterize a set of proteins in one of mycoplasma species, proteome response to various exposures in this bacteria are still obscure. Commonly, authors studying proteomic response on perturbation models in mycoplasmas use single approach and do not confirm their findings by alternative methods. Consequently, the results of proteomic analysis should be validated by complementary techniques. In this study we utilized three complementary approaches (SWATH, MRM, 2D-DIGE) to assess response of Mycoplasma gallisepticum under heat stress on proteomic level and combined these findings with metabolic response and the results of transcriptional profiling. We divide response into two modes – one is directly related to heat stress and other is triggered during heat stress, but not directly relevant to it. The latter includes accumulation of ATP and shedding of antigens. Both of these phenomena may be relevant to evasion of host’s immune system and dissemination during mycoplasmosis in vivo.
    Keywords Medicine ; R ; Science ; Q
    Language English
    Publishing date 2017-09-01T00:00:00Z
    Publisher Nature Publishing Group
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  6. Article ; Online: 16S rRNA gene sequencing data of the upper respiratory tract microbiome in the SARS-CoV-2 infected patients

    Julia Galeeva / Vladislav Babenko / Ramiz Bakhtyev / Vladimir Baklaushev / Larisa Balykova / Pavel Bashkirov / Julia Bespyatykh / Anna Blagonravova / Daria Boldyreva / Dmitry Fedorov / Ilshat Gafurov / Raushaniya Gaifullina / Elena Galova / Alina Gospodaryk / Elena Ilina / Konstantin Ivanov / Daria Kharlampieva / Polina Khromova / Ksenia Klimina /
    Konstantin Kolontarev / Nadezhda Kolyshkina / Andrey Koritsky / Vyacheslav Kuropatkin / Vasily Lazarev / Alexander Manolov / Valentin Manuvera / Daria Matyushkina / Maxim Morozov / Ekaterina Moskaleva / Varvara Musarova / Oleg Ogarkov / Elizaveta Orlova / Alexander Pavlenko / Alla Petrova / Natalia Pozhenko / Dmitry Pushkar / Alexander Rumyantsev / Sergey Rumyantsev / Vladimir Rumyantsev / Lyubov Rychkova / Alexander Samoilov / Irina Shirokova / Vyacheslav Sinkov / Svetlana Solovieva / Elizaveta Starikova / Polina Tikhonova / Galina Trifonova / Alexander Troitsky / Alexander Tulichev / Yuri Udalov / Anna Varizhuk / Alexander Vasiliev / Vladimir Veselovsky / Rinat Vereshchagin / Alexey Volnukhin / Gaukhar Yusubalieva / Vadim Govorun

    Data in Brief, Vol 40, Iss , Pp 107770- (2022)

    2022  

    Abstract: The SARS-CoV-2 pandemic is a big challenge for humanity. The COVID-19 severity differs significantly from patient to patient, and it is important to study the factors protecting from severe forms of the disease. Respiratory microbiota may influence the ... ...

    Abstract The SARS-CoV-2 pandemic is a big challenge for humanity. The COVID-19 severity differs significantly from patient to patient, and it is important to study the factors protecting from severe forms of the disease. Respiratory microbiota may influence the patient's susceptibility to infection and disease severity due to its ability to modulate the immune system response of the host organism.This data article describes the microbiome dataset from the upper respiratory tract of SARS-CoV-2 positive patients from Russia. This dataset reports the microbial community profile of 335 human nasopharyngeal swabs collected between 2020-05 and 2021-03 during the first and the second epidemic waves. Samples were collected from both inpatients and outpatients in 4 cities of the Russian Federation (Moscow, Kazan, Irkutsk, Nizhny Novgorod) and sequenced using the 16S rRNA gene amplicon sequencing of V3-V4 region. Data contains information about the patient such as age, sex, hospitalization status, percent of damaged lung tissue, oxygen saturation (SpO2), respiratory rate, need for supplemental oxygen, chest computer tomography severity score, SARS-CoV-2 lineage, and also information about smoking and comorbidities.The amplicon sequencing data were deposited at NCBI SRA as BioProject PRJNA751478.
    Keywords SARS-CoV-2 ; Microbiome ; 16S ; Upper respiratory tract ; Computer applications to medicine. Medical informatics ; R858-859.7 ; Science (General) ; Q1-390
    Language English
    Publishing date 2022-02-01T00:00:00Z
    Publisher Elsevier
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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