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  1. Article ; Online: Alternate atxA and acpA dependent response of Bacillus anthracis to serum, HCO3- and CO2.

    Glinert, Itai / Bar-David, Elad / Ben-Shmuel, Amir / Sittner, Assa / Puni, Reut / Laredo, Shira / Kobiler, David / Weiss, Shay / Levy, Haim

    PloS one

    2023  Volume 18, Issue 2, Page(s) e0281879

    Abstract: Bacillus anthracis overcomes host immune responses by producing capsule and secreting toxins. Production of these virulence factors in response to entering the host environment was shown to be regulated by atxA, the major virulence regulator, known to be ...

    Abstract Bacillus anthracis overcomes host immune responses by producing capsule and secreting toxins. Production of these virulence factors in response to entering the host environment was shown to be regulated by atxA, the major virulence regulator, known to be activated by HCO3- and CO2. While toxin production is regulated directly by atxA, capsule production is independently mediated by two regulators; acpA and acpB. In addition, it was demonstrated that acpA has at least two promotors, one of them shared with atxA. We used a genetic approach to study capsule and toxin production under different conditions. Unlike previous works utilizing NBY, CA or R-HCO3- medium under CO2 enriched conditions, we used a sDMEM-based medium. Thus, toxin and capsule production can be induced in ambient or CO2 enriched atmosphere. Using this system, we could differentiate between induction by 10% NRS, 10% CO2 or 0.75% HCO3-. In response to high CO2, capsule production is induced by acpA based response in an atxA-independent manner, with little to no toxin (protective antigen PA) production. atxA based response is activated in response to serum independently of CO2, inducing toxin and capsule production in an acpA or acpB dependent manner. HCO3- was also found to activate atxA based response, but in non-physiological concentrations. Our findings may help explain the first stages of inhalational infection, in which spores germinating in dendritic cells require protection (by encapsulation) without affecting cell migration to the draining lymph-node by toxin secretion.
    MeSH term(s) Bacillus anthracis ; Bacterial Proteins/genetics ; Bacterial Toxins/genetics ; Carbon Dioxide/pharmacology ; Gene Expression Regulation, Bacterial ; Antigens, Bacterial/genetics
    Chemical Substances Bacterial Proteins ; Bacterial Toxins ; Carbon Dioxide (142M471B3J) ; Antigens, Bacterial
    Language English
    Publishing date 2023-02-16
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2267670-3
    ISSN 1932-6203 ; 1932-6203
    ISSN (online) 1932-6203
    ISSN 1932-6203
    DOI 10.1371/journal.pone.0281879
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: In Vitro and In Vivo Therapeutic Potential of 6,6'-Dihydroxythiobinupharidine (DTBN) from

    Weiss, Shay / Waidha, Kamran / Rajendran, Saravanakumar / Benharroch, Daniel / Khalilia, Jannat / Levy, Haim / Bar-David, Elad / Golan-Goldhirsh, Avi / Gopas, Jacob / Ben-Shmuel, Amir

    International journal of molecular sciences

    2023  Volume 24, Issue 9

    Abstract: We have previously published research on the anti-viral properties of an alkaloid mixture extracted ... ...

    Abstract We have previously published research on the anti-viral properties of an alkaloid mixture extracted from
    MeSH term(s) Mice ; Animals ; SARS-CoV-2 ; Nuphar/chemistry ; COVID-19 ; Alkaloids/pharmacology ; Alkaloids/therapeutic use ; Alkaloids/chemistry ; Plant Extracts/pharmacology ; Anti-Inflammatory Agents/pharmacology ; Mice, Transgenic
    Chemical Substances dihydroxythiobinupharidine (30343-70-5) ; K-18 conjugate ; Alkaloids ; Plant Extracts ; Anti-Inflammatory Agents
    Language English
    Publishing date 2023-05-05
    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/ijms24098327
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  3. Article ; Online: Alternate atxA and acpA dependent response of Bacillus anthracis to serum, HCO3- and CO2.

    Itai Glinert / Elad Bar-David / Amir Ben-Shmuel / Assa Sittner / Reut Puni / Shira Laredo / David Kobiler / Shay Weiss / Haim Levy

    PLoS ONE, Vol 18, Iss 2, p e

    2023  Volume 0281879

    Abstract: Bacillus anthracis overcomes host immune responses by producing capsule and secreting toxins. Production of these virulence factors in response to entering the host environment was shown to be regulated by atxA, the major virulence regulator, known to be ...

    Abstract Bacillus anthracis overcomes host immune responses by producing capsule and secreting toxins. Production of these virulence factors in response to entering the host environment was shown to be regulated by atxA, the major virulence regulator, known to be activated by HCO3- and CO2. While toxin production is regulated directly by atxA, capsule production is independently mediated by two regulators; acpA and acpB. In addition, it was demonstrated that acpA has at least two promotors, one of them shared with atxA. We used a genetic approach to study capsule and toxin production under different conditions. Unlike previous works utilizing NBY, CA or R-HCO3- medium under CO2 enriched conditions, we used a sDMEM-based medium. Thus, toxin and capsule production can be induced in ambient or CO2 enriched atmosphere. Using this system, we could differentiate between induction by 10% NRS, 10% CO2 or 0.75% HCO3-. In response to high CO2, capsule production is induced by acpA based response in an atxA-independent manner, with little to no toxin (protective antigen PA) production. atxA based response is activated in response to serum independently of CO2, inducing toxin and capsule production in an acpA or acpB dependent manner. HCO3- was also found to activate atxA based response, but in non-physiological concentrations. Our findings may help explain the first stages of inhalational infection, in which spores germinating in dendritic cells require protection (by encapsulation) without affecting cell migration to the draining lymph-node by toxin secretion.
    Keywords Medicine ; R ; Science ; Q
    Language English
    Publishing date 2023-01-01T00:00:00Z
    Publisher Public Library of Science (PLoS)
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  4. Article ; Online: Turning high-throughput structural biology into predictive inhibitor design.

    Saar, Kadi L / McCorkindale, William / Fearon, Daren / Boby, Melissa / Barr, Haim / Ben-Shmuel, Amir / London, Nir / von Delft, Frank / Chodera, John D / Lee, Alpha A

    Proceedings of the National Academy of Sciences of the United States of America

    2023  Volume 120, Issue 11, Page(s) e2214168120

    Abstract: A common challenge in drug design pertains to finding chemical modifications to a ligand that increases its affinity to the target protein. An underutilized advance is the increase in structural biology throughput, which has progressed from an artisanal ... ...

    Abstract A common challenge in drug design pertains to finding chemical modifications to a ligand that increases its affinity to the target protein. An underutilized advance is the increase in structural biology throughput, which has progressed from an artisanal endeavor to a monthly throughput of hundreds of different ligands against a protein in modern synchrotrons. However, the missing piece is a framework that turns high-throughput crystallography data into predictive models for ligand design. Here, we designed a simple machine learning approach that predicts protein-ligand affinity from experimental structures of diverse ligands against a single protein paired with biochemical measurements. Our key insight is using physics-based energy descriptors to represent protein-ligand complexes and a learning-to-rank approach that infers the relevant differences between binding modes. We ran a high-throughput crystallography campaign against the SARS-CoV-2 main protease (M
    MeSH term(s) Humans ; Ligands ; COVID-19 ; SARS-CoV-2 ; Antiviral Agents ; Biology
    Chemical Substances Ligands ; Antiviral Agents
    Language English
    Publishing date 2023-03-06
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 209104-5
    ISSN 1091-6490 ; 0027-8424
    ISSN (online) 1091-6490
    ISSN 0027-8424
    DOI 10.1073/pnas.2214168120
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Specific and Rapid SARS-CoV-2 Identification Based on LC-MS/MS Analysis.

    Schuster, Ofir / Zvi, Anat / Rosen, Osnat / Achdout, Hagit / Ben-Shmuel, Amir / Shifman, Ohad / Yitzhaki, Shmuel / Laskar, Orly / Feldberg, Liron

    ACS omega

    2021  Volume 6, Issue 5, Page(s) 3525–3534

    Abstract: SARS-CoV-2, the etiologic agent of the COVID-19 pandemic, emerged as the cause of a global crisis. Rapid and reliable clinical diagnosis is essential for effectively controlling transmission. The gold standard assay for SARS-CoV-2 identification is the ... ...

    Abstract SARS-CoV-2, the etiologic agent of the COVID-19 pandemic, emerged as the cause of a global crisis. Rapid and reliable clinical diagnosis is essential for effectively controlling transmission. The gold standard assay for SARS-CoV-2 identification is the highly sensitive real-time quantitative polymerase chain reaction (RT-qPCR); however, this assay depends on specialized reagents and may suffer from false results. Thus, additional assays based on different approaches could be beneficial. Here, we present a novel method for SARS-CoV-2 identification based on mass spectrometry. The approach we implemented combines a multistep procedure for the rational down-selection of a set of reliable markers out of all optional
    Language English
    Publishing date 2021-01-26
    Publishing country United States
    Document type Journal Article
    ISSN 2470-1343
    ISSN (online) 2470-1343
    DOI 10.1021/acsomega.0c04691
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Role of acpA and acpB in Bacillus anthracis capsule accumulation and toxin independent pathogenicity in rabbits.

    Sittner, Assa / Bar-David, Elad / Glinert, Itai / Ben-Shmuel, Amir / Schlomovitz, Josef / Levy, Haim / Weiss, Shay

    Microbial pathogenesis

    2021  Volume 155, Page(s) 104904

    Abstract: The poly- δ- d-glutamic acid capsule of Bacillus anthracis plays a major role in this bacterium pathogenicity. Capsule synthesis relies on a 5 gene operon; capB, C, A, D and E that are regulated by acpA and acpB, that respond to the major virulence ... ...

    Abstract The poly- δ- d-glutamic acid capsule of Bacillus anthracis plays a major role in this bacterium pathogenicity. Capsule synthesis relies on a 5 gene operon; capB, C, A, D and E that are regulated by acpA and acpB, that respond to the major virulence regulator - atxA. We took a genetic approach to examine the involvement of acpA and acpB in capsule production in vitro and on B. anthracis virulence in vivo. To complement the effect of the mutations on capsule accumulation in vitro, we applied our toxin independent systemic infection method to study their effects in vivo. We found that though the roles of acpA and axpB are redundant in vitro, deleting acpA had a significant effect on pathogenicity, mainly on the time to death. As expected, deletion of both acpA and acpB resulted in loss of capsule accumulation in vitro and full attenuation in vivo, indicating that capsule production depends exclusively on acpA/B regulation. To identify additional effects of acpA and acpB on pathogenicity via non-capsule related virulence pathways, we bypassed acpA/B regulation by inserting the pagA promotor upstream to the cap operon, diverting regulation directly to atxA. This resulted in restoration of capsule accumulation in vitro and virulence (in intravenous or subcutaneous inoculation) in vivo. To test for additional pXO2-based genes involved in capsule production, we cloned the pagA
    MeSH term(s) Animals ; Bacillus anthracis/genetics ; Bacterial Capsules/genetics ; Bacterial Capsules/metabolism ; Bacterial Proteins/genetics ; Bacterial Proteins/metabolism ; Gene Expression Regulation, Bacterial ; Rabbits ; Trans-Activators/genetics ; Virulence
    Chemical Substances Bacterial Proteins ; Trans-Activators
    Language English
    Publishing date 2021-04-28
    Publishing country England
    Document type Journal Article
    ZDB-ID 632772-2
    ISSN 1096-1208 ; 0882-4010
    ISSN (online) 1096-1208
    ISSN 0882-4010
    DOI 10.1016/j.micpath.2021.104904
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  7. Article ; Online: Specific and Rapid SARS-CoV‑2 Identification Based on LC-MS/MS Analysis

    Ofir Schuster / Anat Zvi / Osnat Rosen / Hagit Achdout / Amir Ben-Shmuel / Ohad Shifman / Shmuel Yitzhaki / Orly Laskar / Liron Feldberg

    ACS Omega, Vol 6, Iss 5, Pp 3525-

    2021  Volume 3534

    Keywords Chemistry ; QD1-999
    Language English
    Publishing date 2021-01-01T00:00:00Z
    Publisher American Chemical Society
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  8. Article ; Online: Revisiting SARS-CoV-2 environmental contamination by patients with COVID-19: The Omicron variant does not differ from previous strains.

    Glinert, Itai / Ben-Shmuel, Amir / Szwartcwort-Cohen, Moran / Beth-Din, Adi / Laskar, Orly / Barlev-Gross, Moria / Melamed, Sharon / Arbell, Noga / Levy, Haim / Horowitz, Netanel A / Weiss, Shay

    International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases

    2022  Volume 118, Page(s) 211–213

    Abstract: SARS-CoV-2 Omicron strain emergence raised concerns that its enhanced infectivity is partly due to altered spread/contamination modalities. We therefore sampled high-contact surfaces and air in close proximity to patients who were verified as infected ... ...

    Abstract SARS-CoV-2 Omicron strain emergence raised concerns that its enhanced infectivity is partly due to altered spread/contamination modalities. We therefore sampled high-contact surfaces and air in close proximity to patients who were verified as infected with the Omicron strain, using identical protocols applied to sample patients positive to the original or Alpha strains. Cumulatively, for all 3 strains, viral RNA was detected in 90 of 168 surfaces and 6 of 49 air samples (mean cycle threshold [Ct]=35.2±2.5). No infective virus was identified. No significant differences in prevalence were found between strains.
    MeSH term(s) COVID-19 ; Humans ; RNA, Viral/genetics ; SARS-CoV-2 ; Specimen Handling
    Chemical Substances RNA, Viral
    Language English
    Publishing date 2022-03-05
    Publishing country Canada
    Document type Journal Article
    ZDB-ID 1331197-9
    ISSN 1878-3511 ; 1201-9712
    ISSN (online) 1878-3511
    ISSN 1201-9712
    DOI 10.1016/j.ijid.2022.03.001
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  9. Article ; Online: A Novel Quantitative Multi-Component Serological Assay for SARS-CoV-2 Vaccine Evaluation.

    Fisher, Morly / Manor, Alon / Abramovitch, Hagar / Fatelevich, Ella / Afrimov, Yafa / Bilinsky, Gal / Lupu, Edith / Ben-Shmuel, Amir / Glinert, Itai / Madar-Balakirski, Noa / Marcus, Hadar / Mechaly, Adva

    Analytical chemistry

    2022  Volume 94, Issue 10, Page(s) 4380–4389

    Abstract: A multi-component microarray, applying a novel analysis algorithm, was developed for quantitative evaluation of the SARS-CoV-2 vaccines' immunogenicity. The array enables simultaneous quantitation of IgG, IgM, and IgA, specific to the SARS-CoV-2 spike, ... ...

    Abstract A multi-component microarray, applying a novel analysis algorithm, was developed for quantitative evaluation of the SARS-CoV-2 vaccines' immunogenicity. The array enables simultaneous quantitation of IgG, IgM, and IgA, specific to the SARS-CoV-2 spike, receptor binding domain, and nucleocapsid proteins. The developed methodology is based on calculating an apparent immunoglobulin signal from the linear range of the fluorescent read-outs generated by scanning the microarray slides at different exposure times. A dedicated algorithm, employing a rigorous set of embedded conditions, then generates a normalized signal for each of the unique assays. Qualification of the multi-component array performance (evaluating linearity, extended dynamic-range, specificity, precision, and accuracy) was carried out with an in-house COVID-19, qRT-PCR positive serum, as well as pre-pandemic commercial negative sera. Results were compared to the WHO international standard for anti-SARS-CoV-2 immunoglobulins. Specific IgG, IgM, and IgA signals obtained by this array enabled successful discrimination between SARS-CoV-2 q-RT-PCR positive (seroconverted SARS-CoV-2 patients) and negative (naïve) samples. This array is currently used for evaluation of the humoral response to BriLife, the VSV-based Israeli vaccine during phase I/II clinical trials.
    MeSH term(s) Antibodies, Viral ; COVID-19/diagnosis ; COVID-19/prevention & control ; COVID-19 Vaccines ; Humans ; Immunoglobulin G ; Immunoglobulin M ; SARS-CoV-2/genetics ; Sensitivity and Specificity
    Chemical Substances Antibodies, Viral ; COVID-19 Vaccines ; Immunoglobulin G ; Immunoglobulin M
    Language English
    Publishing date 2022-03-01
    Publishing country United States
    Document type Journal Article
    ZDB-ID 1508-8
    ISSN 1520-6882 ; 0003-2700
    ISSN (online) 1520-6882
    ISSN 0003-2700
    DOI 10.1021/acs.analchem.1c05264
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  10. Article ; Online: Development of an immunofluorescence assay for detection of SARS-CoV-2.

    Atiya-Nasagi, Yafit / Milrot, Elad / Makdasi, Efi / Schuster, Ofir / Shmaya, Shlomo / Simon, Irit / Ben-Shmuel, Amir / Beth-Din, Adi / Weiss, Shay / Laskar, Orly

    Archives of virology

    2022  Volume 167, Issue 4, Page(s) 1041–1049

    Abstract: SARS-CoV-2, the etiologic agent of the COVID-19 pandemic, emerged as the cause of a global crisis in 2019. Currently, the main method for identification of SARS-CoV-2 is a reverse transcription (RT)-PCR assay designed to detect viral RNA in oropharyngeal ...

    Abstract SARS-CoV-2, the etiologic agent of the COVID-19 pandemic, emerged as the cause of a global crisis in 2019. Currently, the main method for identification of SARS-CoV-2 is a reverse transcription (RT)-PCR assay designed to detect viral RNA in oropharyngeal (OP) or nasopharyngeal (NP) samples. While the PCR assay is considered highly specific and sensitive, this method cannot determine the infectivity of the sample, which may assist in evaluation of virus transmissibility from patients and breaking transmission chains. Thus, cell-culture-based approaches such as cytopathic effect (CPE) assays are routinely employed for the identification of infectious viruses in NP/OP samples. Despite their high sensitivity, CPE assays take several days and require additional diagnostic tests in order to verify the identity of the pathogen. We have therefore developed a rapid immunofluorescence assay (IFA) for the specific detection of SARS-CoV-2 in NP/OP samples following cell culture infection. Initially, IFA was carried out on Vero E6 cultures infected with SARS-CoV-2 at defined concentrations, and infection was monitored at different time points. This test was able to yield positive signals in cultures infected with 10 pfu/ml at 12 hours postinfection (PI). Increasing the incubation time to 24 hours reduced the detectable infective dose to 1 pfu/ml. These IFA signals occur before the development of CPE. When compared to the CPE test, IFA has the advantages of specificity, rapid detection, and sensitivity, as demonstrated in this work.
    MeSH term(s) COVID-19/diagnosis ; Fluorescent Antibody Technique ; Humans ; Nasopharynx ; Pandemics ; RNA, Viral/genetics ; SARS-CoV-2 ; Sensitivity and Specificity
    Chemical Substances RNA, Viral
    Language English
    Publishing date 2022-02-22
    Publishing country Austria
    Document type Journal Article
    ZDB-ID 7491-3
    ISSN 1432-8798 ; 0304-8608
    ISSN (online) 1432-8798
    ISSN 0304-8608
    DOI 10.1007/s00705-022-05392-z
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