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  1. Article ; Online: Proteome profiling of nasopharynx reveals pathophysiological signature of COVID-19 disease severity

    Ooi, Amanda / Esau, Luke E. / Pugachev, Artyom / Groen, Arnoud / Mfarrej, Sara / Salunke, Rahul P. / Subudhi, Amit K. / Ben-Rached, Fathia / Alofi, Fadwa / Alsomali, Afrah / Alquthami, Khaled / Khogeer, Asim / Hashem, Anwar M. / Almontashiri, Naif / Magistretti, Pierre J. / Hala, Sharif / Pain, Arnab

    bioRxiv

    Abstract: An aberrant innate immune system caused by the beta coronavirus SARS-CoV-2 is a characteristic manifestation of severe coronavirus disease 2019 (COVID-19). Here, we performed proteome profiling of nasopharyngeal (NP) swabs from 273 hospitalized patients ... ...

    Abstract An aberrant innate immune system caused by the beta coronavirus SARS-CoV-2 is a characteristic manifestation of severe coronavirus disease 2019 (COVID-19). Here, we performed proteome profiling of nasopharyngeal (NP) swabs from 273 hospitalized patients with mild and severe COVID-19 symptoms, including non-survivors. We identified depletion in STAT1-mediated type I interferon response, retinol metabolism and NRF2 antioxidant system that are associated with disease severity in our patient demography. We found that the dysregulation of glucocorticoid signaling and renin-angiotensin-aldosterone system (RAAS) contribute to the pathophysiology of COVID-19 fatality. Hyperactivation of host innate immune system was observed in severe patients, marked by elevated proteins involved in neutrophil degranulation and platelet aggregation. Our study using high-throughput proteomics on the nasopharynx of COVID-19 patients provides additional evidence on the SARS-CoV-2-induced pathophysiological signatures of disease severity and fatality.
    Keywords covid19
    Language English
    Publishing date 2023-07-10
    Publisher Cold Spring Harbor Laboratory
    Document type Article ; Online
    DOI 10.1101/2023.07.09.548285
    Database COVID19

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  2. Article ; Online: Proteome profiling of nasopharynx reveals pathophysiological signature of COVID-19 disease severity

    Ooi, Amanda / Esau, Luke Emmanuel / Pugachev, Artyom / Groen, Arnoud / Sara Mfarrej, Rached / Salunke, Rahul P. / Subudhi, Amit Kumar / Ben-Rached, Fathia / Alofi, Fadwa / Alsomali, Afrah / Khogeer, Asim / Hashem, Anwar M / Almontashiri, Naif / Magistretti, Pierre J / Hala, Sharif / Pain, Arnab

    bioRxiv

    Abstract: An aberrant innate immune system caused by the beta coronavirus SARS-CoV-2 is a characteristic manifestation of severe coronavirus disease 2019 (COVID-19). Here, we performed proteome profiling of nasopharyngeal (NP) swabs from 273 hospitalized patients ... ...

    Abstract An aberrant innate immune system caused by the beta coronavirus SARS-CoV-2 is a characteristic manifestation of severe coronavirus disease 2019 (COVID-19). Here, we performed proteome profiling of nasopharyngeal (NP) swabs from 273 hospitalized patients with mild and severe COVID-19 symptoms, including non-survivors. We identified depletion in STAT1-mediated type I interferon response, retinol metabolism and NRF2 antioxidant system that are associated with disease severity in our patient demography. We found that the dysregulation of glucocorticoid signaling and renin-angiotensin-aldosterone system (RAAS) contribute to the pathophysiology of COVID-19 fatality. Hyperactivation of host innate immune system was observed in severe patients, marked by elevated proteins involved in neutrophil degranulation and platelet aggregation. Our study using high-throughput proteomics on the nasopharynx of COVID-19 patients provides additional evidence on the SARS-CoV-2-induced pathophysiological signatures of disease severity and fatality.
    Keywords covid19
    Language English
    Publishing date 2023-07-10
    Publisher Cold Spring Harbor Laboratory
    Document type Article ; Online
    DOI 10.1101/2023.07.09.548285
    Database COVID19

    Full text online

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  3. Article ; Online: DNA-binding protein PfAP2-P regulates parasite pathogenesis during malaria parasite blood stages.

    Subudhi, Amit Kumar / Green, Judith L / Satyam, Rohit / Salunke, Rahul P / Lenz, Todd / Shuaib, Muhammad / Isaioglou, Ioannis / Abel, Steven / Gupta, Mohit / Esau, Luke / Mourier, Tobias / Nugmanova, Raushan / Mfarrej, Sara / Shivapurkar, Rupali / Stead, Zenaida / Rached, Fathia Ben / Ostwal, Yogesh / Sougrat, Rachid / Dada, Ashraf /
    Kadamany, Abdullah Fuaad / Fischle, Wolfgang / Merzaban, Jasmeen / Knuepfer, Ellen / Ferguson, David J P / Gupta, Ishaan / Le Roch, Karine G / Holder, Anthony A / Pain, Arnab

    Nature microbiology

    2023  Volume 8, Issue 11, Page(s) 2154–2169

    Abstract: Malaria-associated pathogenesis such as parasite invasion, egress, host cell remodelling and antigenic variation requires concerted action by many proteins, but the molecular regulation is poorly understood. Here we have characterized an essential ... ...

    Abstract Malaria-associated pathogenesis such as parasite invasion, egress, host cell remodelling and antigenic variation requires concerted action by many proteins, but the molecular regulation is poorly understood. Here we have characterized an essential Plasmodium-specific Apicomplexan AP2 transcription factor in Plasmodium falciparum (PfAP2-P; pathogenesis) during the blood-stage development with two peaks of expression. An inducible knockout of gene function showed that PfAP2-P is essential for trophozoite development, and critical for var gene regulation, merozoite development and parasite egress. Chromatin immunoprecipitation sequencing data collected at timepoints matching the two peaks of pfap2-p expression demonstrate PfAP2-P binding to promoters of genes controlling trophozoite development, host cell remodelling, antigenic variation and pathogenicity. Single-cell RNA sequencing and fluorescence-activated cell sorting revealed de-repression of most var genes in Δpfap2-p parasites. Δpfap2-p parasites also overexpress early gametocyte marker genes, indicating a regulatory role in sexual stage conversion. We conclude that PfAP2-P is an essential upstream transcriptional regulator at two distinct stages of the intra-erythrocytic development cycle.
    MeSH term(s) Animals ; Parasites ; Malaria/parasitology ; Gene Expression Regulation ; Plasmodium falciparum/genetics ; Plasmodium
    Language English
    Publishing date 2023-10-26
    Publishing country England
    Document type Journal Article
    ISSN 2058-5276
    ISSN (online) 2058-5276
    DOI 10.1038/s41564-023-01497-6
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article: PfAP2-MRP DNA-binding protein is a master regulator of parasite pathogenesis during malaria parasite blood stages.

    Subudhi, Amit Kumar / Green, Judith L / Satyam, Rohit / Lenz, Todd / Salunke, Rahul P / Shuaib, Muhammad / Isaioglou, Ioannis / Abel, Steven / Gupta, Mohit / Esau, Luke / Mourier, Tobias / Nugmanova, Raushan / Mfarrej, Sara / Sivapurkar, Rupali / Stead, Zenaida / Rached, Fathia Ben / Otswal, Yogesh / Sougrat, Rachid / Dada, Ashraf /
    Kadamany, Abdullah Fuaad / Fischle, Wolfgang / Merzaban, Jasmeen / Knuepfer, Ellen / Ferguson, David J P / Gupta, Ishaan / Le Roch, Karine G / Holder, Anthony A / Pain, Arnab

    bioRxiv : the preprint server for biology

    2023  

    Abstract: Malaria pathogenicity results from the parasite's ability to invade, multiply within and then egress from the host red blood cell (RBC). Infected RBCs are remodeled, expressing antigenic variant proteins (such as PfEMP1, coded by ... ...

    Abstract Malaria pathogenicity results from the parasite's ability to invade, multiply within and then egress from the host red blood cell (RBC). Infected RBCs are remodeled, expressing antigenic variant proteins (such as PfEMP1, coded by the
    Language English
    Publishing date 2023-05-24
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2023.05.23.541898
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    Inter-library loan at ZB MED

    Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

  5. Article ; Online: SARS-CoV-2 genomes from Saudi Arabia implicate nucleocapsid mutations in host response and increased viral load.

    Mourier, Tobias / Shuaib, Muhammad / Hala, Sharif / Mfarrej, Sara / Alofi, Fadwa / Naeem, Raeece / Alsomali, Afrah / Jorgensen, David / Subudhi, Amit Kumar / Ben Rached, Fathia / Guan, Qingtian / Salunke, Rahul P / Ooi, Amanda / Esau, Luke / Douvropoulou, Olga / Nugmanova, Raushan / Perumal, Sadhasivam / Zhang, Huoming / Rajan, Issaac /
    Al-Omari, Awad / Salih, Samer / Shamsan, Abbas / Al Mutair, Abbas / Taha, Jumana / Alahmadi, Abdulaziz / Khotani, Nashwa / Alhamss, Abdelrahman / Mahmoud, Ahmed / Alquthami, Khaled / Dageeg, Abdullah / Khogeer, Asim / Hashem, Anwar M / Moraga, Paula / Volz, Eric / Almontashiri, Naif / Pain, Arnab

    Nature communications

    2022  Volume 13, Issue 1, Page(s) 601

    Abstract: Monitoring SARS-CoV-2 spread and evolution through genome sequencing is essential in handling the COVID-19 pandemic. Here, we sequenced 892 SARS-CoV-2 genomes collected from patients in Saudi Arabia from March to August 2020. We show that two consecutive ...

    Abstract Monitoring SARS-CoV-2 spread and evolution through genome sequencing is essential in handling the COVID-19 pandemic. Here, we sequenced 892 SARS-CoV-2 genomes collected from patients in Saudi Arabia from March to August 2020. We show that two consecutive mutations (R203K/G204R) in the nucleocapsid (N) protein are associated with higher viral loads in COVID-19 patients. Our comparative biochemical analysis reveals that the mutant N protein displays enhanced viral RNA binding and differential interaction with key host proteins. We found increased interaction of GSK3A kinase simultaneously with hyper-phosphorylation of the adjacent serine site (S206) in the mutant N protein. Furthermore, the host cell transcriptome analysis suggests that the mutant N protein produces dysregulated interferon response genes. Here, we provide crucial information in linking the R203K/G204R mutations in the N protein to modulations of host-virus interactions and underline the potential of the nucleocapsid protein as a drug target during infection.
    MeSH term(s) COVID-19/enzymology ; COVID-19/genetics ; COVID-19/virology ; Coronavirus Nucleocapsid Proteins/genetics ; Coronavirus Nucleocapsid Proteins/metabolism ; Genome, Viral ; Glycogen Synthase Kinase 3/genetics ; Glycogen Synthase Kinase 3/metabolism ; Host-Pathogen Interactions ; Humans ; Mutation, Missense ; Nucleocapsid/genetics ; Nucleocapsid/metabolism ; Phosphorylation ; Phylogeny ; Protein Binding ; SARS-CoV-2/classification ; SARS-CoV-2/genetics ; SARS-CoV-2/physiology ; Saudi Arabia ; Viral Load ; Virus Replication
    Chemical Substances Coronavirus Nucleocapsid Proteins ; Glycogen Synthase Kinase 3 (EC 2.7.11.26)
    Language English
    Publishing date 2022-02-01
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2553671-0
    ISSN 2041-1723 ; 2041-1723
    ISSN (online) 2041-1723
    ISSN 2041-1723
    DOI 10.1038/s41467-022-28287-8
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Bioisosteric replacement of dihydropyrazole of 4S-(-)-3-(4-chlorophenyl)-N-methyl-N'-[(4-chlorophenyl)-sulfonyl]-4-phenyl-4,5-dihydro-1H-pyrazole-1-caboxamidine (SLV-319) a potent CB1 receptor antagonist by imidazole and oxazole.

    Srivastava, Brijesh Kumar / Soni, Rina / Joharapurkar, Amit / Sairam, Kalapatapu V V M / Patel, Jayendra Z / Goswami, Amitgiri / Shedage, Sandeep A / Kar, Sidhartha S / Salunke, Rahul P / Gugale, Shivaji B / Dhawas, Amol / Kadam, Pravin / Mishra, Bhupendra / Sadhwani, Nisha / Unadkat, Vishal B / Mitra, Prasenjit / Jain, Mukul R / Patel, Pankaj R

    Bioorganic & medicinal chemistry letters

    2008  Volume 18, Issue 3, Page(s) 963–968

    Abstract: Design, synthesis and conformational analysis of few imidazole and oxazole as bioisosters of 4S-(-)-3-(4-chlorophenyl)-N-methyl-N'-[(4-chlorophenyl)-sulfonyl]-4-phenyl-4,5-dihydro-1H-pyrazole-1-caboxamidine (SLV-319) 2 is reported. Computer assisted ... ...

    Abstract Design, synthesis and conformational analysis of few imidazole and oxazole as bioisosters of 4S-(-)-3-(4-chlorophenyl)-N-methyl-N'-[(4-chlorophenyl)-sulfonyl]-4-phenyl-4,5-dihydro-1H-pyrazole-1-caboxamidine (SLV-319) 2 is reported. Computer assisted conformational analysis gave a direct clue for the loss of CB1 antagonistic activity of the ligands without a fine docking simulation for the homology model.
    MeSH term(s) Animals ; Combinatorial Chemistry Techniques ; Cricetinae ; Cricetulus ; Drug Design ; Humans ; Imidazoles/chemical synthesis ; Imidazoles/chemistry ; Imidazoles/pharmacology ; Models, Molecular ; Molecular Structure ; Oxazoles/chemical synthesis ; Oxazoles/chemistry ; Oxazoles/pharmacology ; Pyrazoles/chemical synthesis ; Pyrazoles/chemistry ; Pyrazoles/pharmacology ; Receptor, Cannabinoid, CB1/antagonists & inhibitors ; Structure-Activity Relationship ; Sulfonamides/chemical synthesis ; Sulfonamides/chemistry ; Sulfonamides/pharmacology
    Chemical Substances 3-(4-chlorophenyl)-N-methyl-N'-((4-chlorophenyl)sulfonyl)-4-phenyl-4,5-dihydro-1H-pyrazole-1-carboxamidine ; Imidazoles ; Oxazoles ; Pyrazoles ; Receptor, Cannabinoid, CB1 ; Sulfonamides
    Language English
    Publishing date 2008-02-01
    Publishing country England
    Document type Journal Article
    ZDB-ID 1063195-1
    ISSN 1464-3405 ; 0960-894X
    ISSN (online) 1464-3405
    ISSN 0960-894X
    DOI 10.1016/j.bmcl.2007.12.036
    Database MEDical Literature Analysis and Retrieval System OnLINE

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