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  1. Article ; Online: Unique fibrinogen-binding motifs in the nucleocapsid phosphoprotein of SARS CoV-2: Potential implications in host-pathogen interactions.

    Sangith, Nikhil

    Medical hypotheses

    2020  Volume 144, Page(s) 110030

    Abstract: Novel Coronavirus (SARS CoV-2), the etiological agent for the highly contagious Corona virus disease-2019 (COVID-19) pandemic has threatened global health and economy infecting around 5.8 million people and causing over 359,200 deaths (as of 28th May ... ...

    Abstract Novel Coronavirus (SARS CoV-2), the etiological agent for the highly contagious Corona virus disease-2019 (COVID-19) pandemic has threatened global health and economy infecting around 5.8 million people and causing over 359,200 deaths (as of 28th May 2020, https://www.worldometers.info/coronavirus/). The clinical manifestations of infected patients generally range from asymptomatic or mild to severe illness, or even death. The ability of the virus to evade the host immune response have been major reasons for high morbidity and mortality. One of the important clinical observations under conditions of critical illness show increased risk of developing disseminated intravascular coagulation. Molecular mechanisms of how SARS CoV-2 induces such conditions still remain unclear. This report describes the presence of two unique motifs in the SARS CoV-2 nucleocapsid phosphoprotein (N-protein) that can potentially interact with fibrinogen and possibly prothrombin. This is based on an established function of secretory proteins in Staphylococcus aureus (S. aureus)-coagulase, Efb (Extracellular fibrinogen binding) and vWBP (von Willebrand factor Binding Protein), which are known to regulate the blood clotting cascade and the functions of host immune response. It is hypothesized that having protein interaction motifs that are homologous to these S. aureus proteins, the N-protein of this virus can mimic their functions, which may in turn play a crucial role in formation of blood clots in the host and help the virus evade host immune response. However, this hypothesis needs to be tested in vitro. Considering the overwhelming increase in the incidence of SARS CoV-2 infection globally, this information may be useful for further investigation and could help in deducing new therapeutic strategies to combat advanced stages of this disease.
    MeSH term(s) Amino Acid Motifs ; Bacterial Proteins/chemistry ; COVID-19/metabolism ; COVID-19/virology ; Coronavirus Nucleocapsid Proteins/chemistry ; Fibrinogen/chemistry ; Host-Pathogen Interactions/immunology ; Humans ; Immune System ; Models, Theoretical ; Peptides/chemistry ; Phosphoproteins/chemistry ; Protein Binding ; Protein Domains ; SARS-CoV-2 ; Staphylococcus aureus/enzymology ; von Willebrand Factor/chemistry
    Chemical Substances Bacterial Proteins ; Coronavirus Nucleocapsid Proteins ; Efb protein, Staphylococcus aureus ; Peptides ; Phosphoproteins ; nucleocapsid phosphoprotein, SARS-CoV-2 ; von Willebrand Factor ; Fibrinogen (9001-32-5)
    Keywords covid19
    Language English
    Publishing date 2020-06-24
    Publishing country United States
    Document type Journal Article
    ZDB-ID 193145-3
    ISSN 1532-2777 ; 0306-9877
    ISSN (online) 1532-2777
    ISSN 0306-9877
    DOI 10.1016/j.mehy.2020.110030
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Unique fibrinogen-binding motifs in the nucleocapsid phosphoprotein of SARS CoV-2

    Sangith, Nikhil

    Medical Hypotheses

    Potential implications in host-pathogen interactions

    2020  Volume 144, Page(s) 110030

    Keywords General Medicine ; covid19
    Language English
    Publisher Elsevier BV
    Publishing country us
    Document type Article ; Online
    ZDB-ID 193145-3
    ISSN 1532-2777 ; 0306-9877
    ISSN (online) 1532-2777
    ISSN 0306-9877
    DOI 10.1016/j.mehy.2020.110030
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  3. Article: Unique fibrinogen-binding motifs in the nucleocapsid phosphoprotein of SARS CoV-2: Potential implications in host-pathogen interactions

    Sangith, Nikhil

    Med Hypotheses

    Abstract: Novel Coronavirus (SARS CoV-2), the etiological agent for the highly contagious Corona virus disease-2019 (COVID-19) pandemic has threatened global health and economy infecting around 5.8 million people and causing over 359,200 deaths (as of 28th May ... ...

    Abstract Novel Coronavirus (SARS CoV-2), the etiological agent for the highly contagious Corona virus disease-2019 (COVID-19) pandemic has threatened global health and economy infecting around 5.8 million people and causing over 359,200 deaths (as of 28th May 2020, https://www.worldometers.info/coronavirus/). The clinical manifestations of infected patients generally range from asymptomatic or mild to severe illness, or even death. The ability of the virus to evade the host immune response have been major reasons for high morbidity and mortality. One of the important clinical observations under conditions of critical illness show increased risk of developing disseminated intravascular coagulation. Molecular mechanisms of how SARS CoV-2 induces such conditions still remain unclear. This report describes the presence of two unique motifs in the SARS CoV-2 nucleocapsid phosphoprotein (N-protein) that can potentially interact with fibrinogen and possibly prothrombin. This is based on an established function of secretory proteins in Staphylococcus aureus (S. aureus)-coagulase, Efb (Extracellular fibrinogen binding) and vWBP (von Willebrand factor Binding Protein), which are known to regulate the blood clotting cascade and the functions of host immune response. It is hypothesized that having protein interaction motifs that are homologous to these S. aureus proteins, the N-protein of this virus can mimic their functions, which may in turn play a crucial role in formation of blood clots in the host and help the virus evade host immune response. However, this hypothesis needs to be tested in vitro. Considering the overwhelming increase in the incidence of SARS CoV-2 infection globally, this information may be useful for further investigation and could help in deducing new therapeutic strategies to combat advanced stages of this disease.
    Keywords covid19
    Publisher WHO
    Document type Article
    Note WHO #Covidence: #612684
    Database COVID19

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  4. Article ; Online: Stringency of bacterial prolipoprotein signal peptidase (LspA) in recognition of signal peptides - Structure-function correlation.

    Sangith, Nikhil / Sankaran, Krishnan

    Biochemical and biophysical research communications

    2017  Volume 488, Issue 2, Page(s) 413–417

    Abstract: Bacterial lipid modification of proteins is an essential post-translational event committed by Phosphatidylglycerol: prolipoprotein diacylglyceryl transferase (Lgt) by catalysing diacyglyceryl transfer from Phosphatidylglycerol to cysteine present in the ...

    Abstract Bacterial lipid modification of proteins is an essential post-translational event committed by Phosphatidylglycerol: prolipoprotein diacylglyceryl transferase (Lgt) by catalysing diacyglyceryl transfer from Phosphatidylglycerol to cysteine present in the characteristic 'lipobox' ([LVI]
    MeSH term(s) Anti-Bacterial Agents/chemistry ; Anti-Bacterial Agents/pharmacology ; Bacterial Outer Membrane Proteins/antagonists & inhibitors ; Bacterial Outer Membrane Proteins/chemistry ; Bacterial Outer Membrane Proteins/metabolism ; Gram-Negative Bacteria/drug effects ; Gram-Negative Bacteria/metabolism ; Models, Molecular ; Molecular Structure ; Peptides/chemistry ; Peptides/pharmacology ; Protein Sorting Signals ; Structure-Activity Relationship
    Chemical Substances Anti-Bacterial Agents ; Bacterial Outer Membrane Proteins ; Peptides ; Protein Sorting Signals ; prolipoprotein signal peptide ; globomycin (67076-74-8)
    Language English
    Publishing date 2017-06-24
    Publishing country United States
    Document type Journal Article
    ZDB-ID 205723-2
    ISSN 1090-2104 ; 0006-291X ; 0006-291X
    ISSN (online) 1090-2104 ; 0006-291X
    ISSN 0006-291X
    DOI 10.1016/j.bbrc.2017.05.069
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Evidence to Suggest Bacterial Lipoprotein Diacylglyceryl Transferase (Lgt) is a Weakly Associated Inner Membrane Protein.

    Sangith, Nikhil / Kumar, Subramani / Sankaran, Krishnan

    The Journal of membrane biology

    2019  Volume 252, Issue 6, Page(s) 563–575

    Abstract: The unique and ubiquitous bacterial lipoprotein biosynthesis pathway is an attractive new antibiotic target. Crystal structures of its three biosynthetic enzymes have been solved recently. The first enzyme, Phosphatidylglycerol:proLipoprotein ... ...

    Abstract The unique and ubiquitous bacterial lipoprotein biosynthesis pathway is an attractive new antibiotic target. Crystal structures of its three biosynthetic enzymes have been solved recently. The first enzyme, Phosphatidylglycerol:proLipoprotein diacylglyceryl Transferase (Lgt), which initiates the post-translational modification at the metabolic interface of protein biosynthesis, phospholipid biosynthesis, protein secretion and lipid modification was reported to be a seven-transmembrane helical structure with a catalytic periplasmic head. Its complete solubilization in water or mild detergent in a fully active state, its chromatographic behaviour as an active monomer in the absence of detergent and recovery of active whole-length protein after proteolytic treatment of spheroplasts cast serious doubts about its proposed membrane association and orientation. Rather, it could be a seven-helical bundle partially embedded in the inner membrane's inner leaflet aided by hydrophobic interaction. In fact, there are examples where originally reported seven-transmembrane proteins were later shown to be seven-helical peripheral membrane proteins based on solubilization criterion and re-analysis. Validated computational tool, Membrane Optimal Docking Area (MODA), also predicted a weaker association of Lgt's helices with the membrane compared to typical transmembrane proteins. This insight is crucial to Lgt-based antibiotic design.
    MeSH term(s) Bacterial Proteins/metabolism ; Escherichia coli/metabolism ; Hydrophobic and Hydrophilic Interactions ; Lipoproteins/metabolism ; Membrane Proteins/metabolism ; Protein Sorting Signals/physiology ; Transferases/metabolism
    Chemical Substances Bacterial Proteins ; Lipoproteins ; Membrane Proteins ; Protein Sorting Signals ; Transferases (EC 2.-) ; phosphatidylglycerol glyceryl transferase (EC 2.4.99.-)
    Language English
    Publishing date 2019-06-29
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 3082-x
    ISSN 1432-1424 ; 0022-2631
    ISSN (online) 1432-1424
    ISSN 0022-2631
    DOI 10.1007/s00232-019-00076-3
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article: Stringency of bacterial prolipoprotein signal peptidase (LspA) in recognition of signal peptides – Structure-function correlation

    Sangith, Nikhil / Krishnan Sankaran

    Biochemical and biophysical research communications. 2017,

    2017  

    Abstract: Bacterial lipid modification of proteins is an essential post-translational event committed by Phosphatidylglycerol: prolipoprotein diacylglyceryl transferase (Lgt) by catalysing diacyglyceryl transfer from Phosphatidylglycerol to cysteine present in the ...

    Abstract Bacterial lipid modification of proteins is an essential post-translational event committed by Phosphatidylglycerol: prolipoprotein diacylglyceryl transferase (Lgt) by catalysing diacyglyceryl transfer from Phosphatidylglycerol to cysteine present in the characteristic ‘lipobox’ ([LVI] (−3) [ASTVI] (−2) [GAS] (−1) C (+1)) of prolipoprotein signal peptides. This is then followed by the cleavage of the signal peptide by lipoprotein-specific signal peptidase (LspA). It had been known for long that threonine at the −1 position allows diacylglyceryl modification by Lgt, but not signal peptide cleavage by LspA. We have addressed this unexplained stringency by computational analysis of the recently published 3D structure of LspA with its competitive inhibitor as well as transition state analogue, globomycin using PyMoL viewing tool and VADAR (Volume, Area, Dihedral Angle Reporter) web server. The propensity to form hydrogen bond (2.9a) between the hydroxyl group of threonine (not possible with serine) and the NH of the lipid-modified cysteine, possible only in the transition state, will prevent the protonation of NH of the leaving peptide and therefore its cleavage. This knowledge could be useful for designing inhibitors of this essential pathway in bacteria or for engineering LspA.
    Keywords bacteria ; cysteine ; engineering ; hydrogen bonding ; Internet ; lipids ; proteins ; serine ; signal peptide ; threonine
    Language English
    Size p. .
    Publishing place Elsevier Inc.
    Document type Article
    Note Pre-press version
    ZDB-ID 205723-2
    ISSN 0006-291X ; 0006-291X
    ISSN (online) 0006-291X
    ISSN 0006-291X
    DOI 10.1016/j.bbrc.2017.05.069
    Database NAL-Catalogue (AGRICOLA)

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  7. Article ; Online: Active sulfite oxidase domain of Salmonella enterica pathogenic protein small intestine invasive factor E (SiiE): a potential diagnostic target.

    Paramasivam, Oviya R / Trivedi, Swati / Sangith, Nikhil / Sankaran, Krishnan

    Applied microbiology and biotechnology

    2019  Volume 103, Issue 14, Page(s) 5679–5688

    Abstract: Serovars of Salmonella enterica are common food-borne bacterial pathogens. Salmonella typhi, which causes typhoid, is the most dangerous of them. Though detailed molecular pathogenesis studies reveal many virulence factors, inability to identify their ... ...

    Abstract Serovars of Salmonella enterica are common food-borne bacterial pathogens. Salmonella typhi, which causes typhoid, is the most dangerous of them. Though detailed molecular pathogenesis studies reveal many virulence factors, inability to identify their biochemical functions hampers the development of diagnostic methods and therapeutic leads. Lack of quicker diagnosis is an impediment in starting early antibiotic treatment to reduce the severe morbidity and mortality in typhoid. In this study, employing bioinformatic prediction, biochemical analysis, and recombinantly cloning the active region, we show that extracellularly secreted virulence-associated protein, small intestinal invasion factor E (SiiE), possesses a sulfite oxidase (SO) domain that catalyzes the conversion of sodium sulfite to sodium sulfate using tungsten as the cofactor. This activity common to Salmonella enterica serovars seems to be specific to them from bioinformatic analysis of available bacterial genomes. Along with the ability of this large non-fimbrial adhesin of 600 kDa binding to sialic acid on the host cells, this activity could aid in subverting the host defense mechanism by destroying sulfites released by the immune cells and colonize the host gastrointestinal epithelium. Being an extracellular enzyme, it could be an ideal candidate for developing diagnostics of S. enterica, particularly S. typhi.
    MeSH term(s) Adhesins, Bacterial/metabolism ; Bacterial Adhesion ; Computational Biology ; Salmonella enterica/enzymology ; Salmonella enterica/genetics ; Salmonella enterica/pathogenicity ; Salmonella typhimurium ; Sulfates/metabolism ; Sulfite Oxidase/genetics ; Sulfite Oxidase/metabolism ; Sulfites/metabolism ; Tungsten/metabolism ; Virulence ; Virulence Factors/metabolism
    Chemical Substances Adhesins, Bacterial ; Sulfates ; Sulfites ; Virulence Factors ; sodium sulfate (0YPR65R21J) ; Sulfite Oxidase (EC 1.8.3.1) ; Tungsten (V9306CXO6G) ; sodium sulfite (VTK01UQK3G)
    Language English
    Publishing date 2019-05-18
    Publishing country Germany
    Document type Journal Article
    ZDB-ID 392453-1
    ISSN 1432-0614 ; 0171-1741 ; 0175-7598
    ISSN (online) 1432-0614
    ISSN 0171-1741 ; 0175-7598
    DOI 10.1007/s00253-019-09894-w
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: Molecular evolution of single chain fragment variable (scFv) for diagnosis of lymphatic filariasis.

    Mahalakshmi, Natarajan / Ravishankaran, Rajendran / Kamatchi, Ramakrishnan / Sangith, Nikhil / Kaliraj, Perumal / Meenakshisundaram, Sankaranarayanan

    Molecular biology reports

    2019  Volume 46, Issue 5, Page(s) 5409–5418

    Abstract: Endemic countries with lymphatic filariasis are striving towards the Global Program to Eliminate Lymphatic Filariasis (GPELF) by 2020. Efficient and cost-effective diagnostic tools to assess active filarial infection are critical to eradicate lymphatic ... ...

    Abstract Endemic countries with lymphatic filariasis are striving towards the Global Program to Eliminate Lymphatic Filariasis (GPELF) by 2020. Efficient and cost-effective diagnostic tools to assess active filarial infection are critical to eradicate lymphatic filariasis. Detection of circulating filarial antigens in sera is one of the precise methods to identify this infection. Monoclonal antibodies and single chain fragment variable (scFv) against Wuchereria bancrofti antigen SXP1 have been developed for antigen detection. Molecular cloning of scFv for recombinant expression has laid a platform for developing novel genetic constructs with enhanced reactivity. In this study, a simple procedure is developed to create diverse libraries of scFv based on a single DNA framework with all the requisites for an in vitro protein synthesis and ribosomal display. Error Prone-PCR was performed to incorporate random mutations and screened by ribosome display technique to isolate evolved scFv. Evolved scFv with six mutations showed tenfold increase in affinity compared to wild-type scFv for rWbSXP1. In silico studies showed that four mutations introduced unique molecular interactions between the evolved scFv and SXP1. Reactivity with asserted clinical samples of endemic normals (EN), microfilariaemic (MF), chronic pathology (CP) and non-endemic normals (NEN) showed significant augment (59.69%, p < 0.0001) in reactivity to MF samples with evolved scFv in comparison to wild-type scFv. Sensitivity of scFv was increased from 15.62 ng to 195 pg by evolved scFv in serum samples. This evolutionary method coupled with ribosome display has facilitated us to improve the reactivity of the ScFv without diminishing the specificity.
    MeSH term(s) Animals ; Antibodies, Monoclonal/immunology ; Antigens, Helminth/immunology ; Elephantiasis, Filarial/diagnosis ; Elephantiasis, Filarial/genetics ; Enzyme-Linked Immunosorbent Assay/methods ; Evolution, Molecular ; Helminth Proteins/immunology ; Protein Engineering/methods ; Single-Chain Antibodies/genetics ; Single-Chain Antibodies/metabolism ; Wuchereria bancrofti/immunology ; Wuchereria bancrofti/pathogenicity
    Chemical Substances Antibodies, Monoclonal ; Antigens, Helminth ; Helminth Proteins ; Single-Chain Antibodies
    Language English
    Publishing date 2019-09-11
    Publishing country Netherlands
    Document type Journal Article
    ZDB-ID 186544-4
    ISSN 1573-4978 ; 0301-4851
    ISSN (online) 1573-4978
    ISSN 0301-4851
    DOI 10.1007/s11033-019-04995-1
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article: Molecular evolution of single chain fragment variable (scFv) for diagnosis of lymphatic filariasis

    Mahalakshmi, Natarajan / Ravishankaran, Rajendran / Kamatchi, Ramakrishnan / Sangith, Nikhil / Kaliraj, Perumal / Meenakshisundaram, Sankaranarayanan

    Molecular biology reports. 2019 Oct., v. 46, no. 5

    2019  

    Abstract: Endemic countries with lymphatic filariasis are striving towards the Global Program to Eliminate Lymphatic Filariasis (GPELF) by 2020. Efficient and cost-effective diagnostic tools to assess active filarial infection are critical to eradicate lymphatic ... ...

    Abstract Endemic countries with lymphatic filariasis are striving towards the Global Program to Eliminate Lymphatic Filariasis (GPELF) by 2020. Efficient and cost-effective diagnostic tools to assess active filarial infection are critical to eradicate lymphatic filariasis. Detection of circulating filarial antigens in sera is one of the precise methods to identify this infection. Monoclonal antibodies and single chain fragment variable (scFv) against Wuchereria bancrofti antigen SXP1 have been developed for antigen detection. Molecular cloning of scFv for recombinant expression has laid a platform for developing novel genetic constructs with enhanced reactivity. In this study, a simple procedure is developed to create diverse libraries of scFv based on a single DNA framework with all the requisites for an in vitro protein synthesis and ribosomal display. Error Prone-PCR was performed to incorporate random mutations and screened by ribosome display technique to isolate evolved scFv. Evolved scFv with six mutations showed tenfold increase in affinity compared to wild-type scFv for rWbSXP1. In silico studies showed that four mutations introduced unique molecular interactions between the evolved scFv and SXP1. Reactivity with asserted clinical samples of endemic normals (EN), microfilariaemic (MF), chronic pathology (CP) and non-endemic normals (NEN) showed significant augment (59.69%, p < 0.0001) in reactivity to MF samples with evolved scFv in comparison to wild-type scFv. Sensitivity of scFv was increased from 15.62 ng to 195 pg by evolved scFv in serum samples. This evolutionary method coupled with ribosome display has facilitated us to improve the reactivity of the ScFv without diminishing the specificity.
    Keywords Bancroftian filariasis ; DNA ; Wuchereria bancrofti ; antigen detection ; antigens ; blood serum ; computer simulation ; cost effectiveness ; evolution ; molecular biology ; ribosomes
    Language English
    Dates of publication 2019-10
    Size p. 5409-5418.
    Publishing place Springer Netherlands
    Document type Article
    Note NAL-AP-2-clean
    ZDB-ID 186544-4
    ISSN 1573-4978 ; 0301-4851
    ISSN (online) 1573-4978
    ISSN 0301-4851
    DOI 10.1007/s11033-019-04995-1
    Database NAL-Catalogue (AGRICOLA)

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  10. Article: Active sulfite oxidase domain of Salmonella enterica pathogenic protein small intestine invasive factor E (SiiE): a potential diagnostic target

    Paramasivam, Oviya R / Sangith, Nikhil / Sankaran, Krishnan / Trivedi, Swati

    Applied microbiology and biotechnology. 2019 July, v. 103, no. 14

    2019  

    Abstract: Serovars of Salmonella enterica are common food-borne bacterial pathogens. Salmonella typhi, which causes typhoid, is the most dangerous of them. Though detailed molecular pathogenesis studies reveal many virulence factors, inability to identify their ... ...

    Abstract Serovars of Salmonella enterica are common food-borne bacterial pathogens. Salmonella typhi, which causes typhoid, is the most dangerous of them. Though detailed molecular pathogenesis studies reveal many virulence factors, inability to identify their biochemical functions hampers the development of diagnostic methods and therapeutic leads. Lack of quicker diagnosis is an impediment in starting early antibiotic treatment to reduce the severe morbidity and mortality in typhoid. In this study, employing bioinformatic prediction, biochemical analysis, and recombinantly cloning the active region, we show that extracellularly secreted virulence-associated protein, small intestinal invasion factor E (SiiE), possesses a sulfite oxidase (SO) domain that catalyzes the conversion of sodium sulfite to sodium sulfate using tungsten as the cofactor. This activity common to Salmonella enterica serovars seems to be specific to them from bioinformatic analysis of available bacterial genomes. Along with the ability of this large non-fimbrial adhesin of 600 kDa binding to sialic acid on the host cells, this activity could aid in subverting the host defense mechanism by destroying sulfites released by the immune cells and colonize the host gastrointestinal epithelium. Being an extracellular enzyme, it could be an ideal candidate for developing diagnostics of S. enterica, particularly S. typhi.
    Keywords adhesins ; antibiotics ; bioinformatics ; catalytic activity ; diagnostic techniques ; epithelium ; extracellular enzymes ; foodborne bacterial pathogens ; genome ; morbidity ; mortality ; pathogenesis ; prediction ; Salmonella Typhi ; serotypes ; sialic acid ; small intestine ; sodium sulfate ; sodium sulfite ; sulfite oxidase ; therapeutics ; tungsten ; typhoid fever ; virulence
    Language English
    Dates of publication 2019-07
    Size p. 5679-5688.
    Publishing place Springer Berlin Heidelberg
    Document type Article
    ZDB-ID 392453-1
    ISSN 1432-0614 ; 0171-1741 ; 0175-7598
    ISSN (online) 1432-0614
    ISSN 0171-1741 ; 0175-7598
    DOI 10.1007/s00253-019-09894-w
    Database NAL-Catalogue (AGRICOLA)

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