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  1. AU="Subudhi, Amit K"
  2. AU="Rebecca Moore"
  3. AU="Pagali, Sandeep"
  4. AU="Sun, Lova"
  5. AU="Etienne, Z. B."

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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: Malaria parasites regulate intra-erythrocytic development duration via serpentine receptor 10 to coordinate with host rhythms.

    Subudhi, Amit K / O'Donnell, Aidan J / Ramaprasad, Abhinay / Abkallo, Hussein M / Kaushik, Abhinav / Ansari, Hifzur R / Abdel-Haleem, Alyaa M / Ben Rached, Fathia / Kaneko, Osamu / Culleton, Richard / Reece, Sarah E / Pain, Arnab

    Nature communications

    2020  Volume 11, Issue 1, Page(s) 2763

    Abstract: Malaria parasites complete their intra-erythrocytic developmental cycle (IDC) in multiples of 24 h suggesting a circadian basis, but the mechanism controlling this periodicity is unknown. Combining in vivo and in vitro approaches utilizing rodent and ... ...

    Abstract Malaria parasites complete their intra-erythrocytic developmental cycle (IDC) in multiples of 24 h suggesting a circadian basis, but the mechanism controlling this periodicity is unknown. Combining in vivo and in vitro approaches utilizing rodent and human malaria parasites, we reveal that: (i) 57% of Plasmodium chabaudi genes exhibit daily rhythms in transcription; (ii) 58% of these genes lose transcriptional rhythmicity when the IDC is out-of-synchrony with host rhythms; (iii) 6% of Plasmodium falciparum genes show 24 h rhythms in expression under free-running conditions; (iv) Serpentine receptor 10 (SR10) has a 24 h transcriptional rhythm and disrupting it in rodent malaria parasites shortens the IDC by 2-3 h; (v) Multiple processes including DNA replication, and the ubiquitin and proteasome pathways, are affected by loss of coordination with host rhythms and by disruption of SR10. Our results reveal malaria parasites are at least partly responsible for scheduling the IDC and coordinating their development with host daily rhythms.
    MeSH term(s) Animals ; Caenorhabditis elegans Proteins ; Circadian Rhythm/physiology ; Disease Models, Animal ; Erythropoiesis/physiology ; Female ; Gene Expression ; Host-Parasite Interactions/genetics ; Host-Parasite Interactions/physiology ; Humans ; Malaria/metabolism ; Malaria/parasitology ; Mice ; Mice, Knockout ; Plasmodium chabaudi/genetics ; Plasmodium chabaudi/growth & development ; Plasmodium falciparum/genetics ; Plasmodium falciparum/growth & development ; Protozoan Proteins/genetics ; Protozoan Proteins/metabolism ; Receptors, G-Protein-Coupled/genetics ; Receptors, G-Protein-Coupled/metabolism ; Rodentia ; Secologanin Tryptamine Alkaloids/metabolism ; Transcriptome
    Chemical Substances Caenorhabditis elegans Proteins ; Protozoan Proteins ; Receptors, G-Protein-Coupled ; SRD-1 protein, C elegans ; Secologanin Tryptamine Alkaloids ; serpentine (alkaloid) (B503RKE34F)
    Language English
    Publishing date 2020-06-02
    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/s41467-020-16593-y
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article: iSCAN: An RT-LAMP-coupled CRISPR-Cas12 module for rapid, sensitive detection of SARS-CoV-2

    Ali, Zahir / Aman, Rashid / Mahas, Ahmed / Rao, Gundra Sivakrishna / Tehseen, Muhammad / Marsic, Tin / Salunke, Rahul / Subudhi, Amit K / Hala, Sharif M / Hamdan, Samir M / Pain, Arnab / Alofi, Fadwa S / Alsomali, Afrah / Hashem, Anwar M / Khogeer, Asim / Almontashiri, Naif A.M / Abedalthagafi, Malak / Hassan, Norhan / Mahfouz, Magdy M

    Virus research. 2020 Oct. 15, v. 288

    2020  

    Abstract: The COVID-19 pandemic caused by SARS-CoV-2 affects all aspects of human life. Detection platforms that are efficient, rapid, accurate, specific, sensitive, and user friendly are urgently needed to manage and control the spread of SARS-CoV-2. RT-qPCR ... ...

    Abstract The COVID-19 pandemic caused by SARS-CoV-2 affects all aspects of human life. Detection platforms that are efficient, rapid, accurate, specific, sensitive, and user friendly are urgently needed to manage and control the spread of SARS-CoV-2. RT-qPCR based methods are the gold standard for SARS-CoV-2 detection. However, these methods require trained personnel, sophisticated infrastructure, and a long turnaround time, thereby limiting their usefulness. Reverse transcription-loop-mediated isothermal amplification (RT-LAMP), a one-step nucleic acid amplification method conducted at a single temperature, has been used for colorimetric virus detection. CRISPR-Cas12 and CRISPR-Cas13 systems, which possess collateral activity against ssDNA and RNA, respectively, have also been harnessed for virus detection. Here, we built an efficient, rapid, specific, sensitive, user-friendly SARS-CoV-2 detection module that combines the robust virus amplification of RT-LAMP with the specific detection ability of SARS-CoV-2 by CRISPR-Cas12. Furthermore, we combined the RT-LAMP-CRISPR-Cas12 module with lateral flow cells to enable highly efficient point-of-care SARS-CoV-2 detection. Our iSCAN SARS-CoV-2 detection module, which exhibits the critical features of a robust molecular diagnostic device, should facilitate the effective management and control of COVID-19.
    Keywords COVID-19 infection ; RNA ; Severe acute respiratory syndrome coronavirus 2 ; colorimetry ; diagnostic techniques ; gene amplification ; human resources ; humans ; infrastructure ; point-of-care systems ; quantitative polymerase chain reaction ; reverse transcriptase polymerase chain reaction ; reverse transcription loop-mediated isothermal amplification ; single-stranded DNA ; temperature ; viruses
    Language English
    Dates of publication 2020-1015
    Publishing place Elsevier B.V.
    Document type Article
    ZDB-ID 605780-9
    ISSN 1872-7492 ; 0168-1702
    ISSN (online) 1872-7492
    ISSN 0168-1702
    DOI 10.1016/j.virusres.2020.198129
    Database NAL-Catalogue (AGRICOLA)

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  4. Article ; Online: Accelerating Early Antituberculosis Drug Discovery by Creating Mycobacterial Indicator Strains That Predict Mode of Action.

    Boot, Maikel / Commandeur, Susanna / Subudhi, Amit K / Bahira, Meriem / Smith, Trever C / Abdallah, Abdallah M / van Gemert, Mae / Lelièvre, Joël / Ballell, Lluís / Aldridge, Bree B / Pain, Arnab / Speer, Alexander / Bitter, Wilbert

    Antimicrobial agents and chemotherapy

    2018  Volume 62, Issue 7

    Abstract: Due to the rise of drug-resistant forms of tuberculosis, there is an urgent need for novel antibiotics to effectively combat these cases and shorten treatment regimens. Recently, drug screens using whole-cell analyses have been shown to be successful. ... ...

    Abstract Due to the rise of drug-resistant forms of tuberculosis, there is an urgent need for novel antibiotics to effectively combat these cases and shorten treatment regimens. Recently, drug screens using whole-cell analyses have been shown to be successful. However, current high-throughput screens focus mostly on
    MeSH term(s) Animals ; Antitubercular Agents/pharmacology ; Base Sequence ; Cell Line ; Ciprofloxacin/pharmacology ; Drug Discovery/methods ; Ethambutol/pharmacology ; Humans ; Isoniazid/pharmacology ; Macrophages/drug effects ; Mice ; Mycobacterium marinum/drug effects ; Mycobacterium marinum/genetics ; Mycobacterium tuberculosis/drug effects ; Mycobacterium tuberculosis/genetics ; RAW 264.7 Cells ; RNA, Bacterial/genetics ; Rifampin/pharmacology ; Sequence Analysis, RNA ; Streptomycin/pharmacology ; Transcription, Genetic/drug effects ; Transcription, Genetic/genetics ; Tuberculosis, Pulmonary/drug therapy ; Tuberculosis, Pulmonary/microbiology
    Chemical Substances Antitubercular Agents ; RNA, Bacterial ; Ciprofloxacin (5E8K9I0O4U) ; Ethambutol (8G167061QZ) ; Isoniazid (V83O1VOZ8L) ; Rifampin (VJT6J7R4TR) ; Streptomycin (Y45QSO73OB)
    Language English
    Publishing date 2018-06-26
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 217602-6
    ISSN 1098-6596 ; 0066-4804
    ISSN (online) 1098-6596
    ISSN 0066-4804
    DOI 10.1128/AAC.00083-18
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Creation and preclinical evaluation of genetically attenuated malaria parasites arresting growth late in the liver.

    Franke-Fayard, Blandine / Marin-Mogollon, Catherin / Geurten, Fiona J A / Chevalley-Maurel, Séverine / Ramesar, Jai / Kroeze, Hans / Baalbergen, Els / Wessels, Els / Baron, Ludivine / Soulard, Valérie / Martinson, Thomas / Aleshnick, Maya / Huijs, Antonius T G / Subudhi, Amit K / Miyazaki, Yukiko / Othman, Ahmad Syibli / Kolli, Surendra Kumar / Lamers, Olivia A C / Roques, Magali /
    Stanway, Rebecca R / Murphy, Sean C / Foquet, Lander / Moita, Diana / Mendes, António M / Prudêncio, Miguel / Dechering, Koen J / Heussler, Volker T / Pain, Arnab / Wilder, Brandon K / Roestenberg, Meta / Janse, Chris J

    NPJ vaccines

    2022  Volume 7, Issue 1, Page(s) 139

    Abstract: Whole-sporozoite (WSp) malaria vaccines induce protective immune responses in animal malaria models and in humans. A recent clinical trial with a WSp vaccine comprising genetically attenuated parasites (GAP) which arrest growth early in the liver (PfSPZ- ... ...

    Abstract Whole-sporozoite (WSp) malaria vaccines induce protective immune responses in animal malaria models and in humans. A recent clinical trial with a WSp vaccine comprising genetically attenuated parasites (GAP) which arrest growth early in the liver (PfSPZ-GA1), showed that GAPs can be safely administered to humans and immunogenicity is comparable to radiation-attenuated PfSPZ Vaccine. GAPs that arrest late in the liver stage (LA-GAP) have potential for increased potency as shown in rodent malaria models. Here we describe the generation of four putative P. falciparum LA-GAPs, generated by CRISPR/Cas9-mediated gene deletion. One out of four gene-deletion mutants produced sporozoites in sufficient numbers for further preclinical evaluation. This mutant, PfΔmei2, lacking the mei2-like RNA gene, showed late liver growth arrest in human liver-chimeric mice with human erythrocytes, absence of unwanted genetic alterations and sensitivity to antimalarial drugs. These features of PfΔmei2 make it a promising vaccine candidate, supporting further clinical evaluation. PfΔmei2 (GA2) has passed regulatory approval for safety and efficacy testing in humans based on the findings reported in this study.
    Language English
    Publishing date 2022-11-04
    Publishing country England
    Document type Journal Article
    ISSN 2059-0105
    ISSN (online) 2059-0105
    DOI 10.1038/s41541-022-00558-x
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: iSCAN: An RT-LAMP-coupled CRISPR-Cas12 module for rapid, sensitive detection of SARS-CoV-2.

    Ali, Zahir / Aman, Rashid / Mahas, Ahmed / Rao, Gundra Sivakrishna / Tehseen, Muhammad / Marsic, Tin / Salunke, Rahul / Subudhi, Amit K / Hala, Sharif M / Hamdan, Samir M / Pain, Arnab / Alofi, Fadwa S / Alsomali, Afrah / Hashem, Anwar M / Khogeer, Asim / Almontashiri, Naif A M / Abedalthagafi, Malak / Hassan, Norhan / Mahfouz, Magdy M

    Virus research

    2020  Volume 288, Page(s) 198129

    Abstract: The COVID-19 pandemic caused by SARS-CoV-2 affects all aspects of human life. Detection platforms that are efficient, rapid, accurate, specific, sensitive, and user friendly are urgently needed to manage and control the spread of SARS-CoV-2. RT-qPCR ... ...

    Abstract The COVID-19 pandemic caused by SARS-CoV-2 affects all aspects of human life. Detection platforms that are efficient, rapid, accurate, specific, sensitive, and user friendly are urgently needed to manage and control the spread of SARS-CoV-2. RT-qPCR based methods are the gold standard for SARS-CoV-2 detection. However, these methods require trained personnel, sophisticated infrastructure, and a long turnaround time, thereby limiting their usefulness. Reverse transcription-loop-mediated isothermal amplification (RT-LAMP), a one-step nucleic acid amplification method conducted at a single temperature, has been used for colorimetric virus detection. CRISPR-Cas12 and CRISPR-Cas13 systems, which possess collateral activity against ssDNA and RNA, respectively, have also been harnessed for virus detection. Here, we built an efficient, rapid, specific, sensitive, user-friendly SARS-CoV-2 detection module that combines the robust virus amplification of RT-LAMP with the specific detection ability of SARS-CoV-2 by CRISPR-Cas12. Furthermore, we combined the RT-LAMP-CRISPR-Cas12 module with lateral flow cells to enable highly efficient point-of-care SARS-CoV-2 detection. Our iSCAN SARS-CoV-2 detection module, which exhibits the critical features of a robust molecular diagnostic device, should facilitate the effective management and control of COVID-19.
    MeSH term(s) Betacoronavirus/genetics ; COVID-19 ; COVID-19 Testing ; CRISPR-Cas Systems ; Clinical Laboratory Techniques/instrumentation ; Clinical Laboratory Techniques/methods ; Colorimetry/instrumentation ; Colorimetry/methods ; Coronavirus Infections/diagnosis ; Coronavirus Infections/virology ; Endodeoxyribonucleases/chemistry ; Humans ; Molecular Diagnostic Techniques/instrumentation ; Molecular Diagnostic Techniques/methods ; Nucleic Acid Amplification Techniques/instrumentation ; Nucleic Acid Amplification Techniques/methods ; Pandemics ; Pneumonia, Viral/diagnosis ; Pneumonia, Viral/virology ; Point-of-Care Systems ; Rheology ; SARS-CoV-2 ; Sensitivity and Specificity
    Chemical Substances Endodeoxyribonucleases (EC 3.1.-)
    Keywords covid19
    Language English
    Publishing date 2020-08-18
    Publishing country Netherlands
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 605780-9
    ISSN 1872-7492 ; 0168-1702
    ISSN (online) 1872-7492
    ISSN 0168-1702
    DOI 10.1016/j.virusres.2020.198129
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article: iSCAN: An RT-LAMP-coupled CRISPR-Cas12 module for rapid, sensitive detection of SARS-CoV-2

    Ali, Zahir / Aman, Rashid / Mahas, Ahmed / Rao, Gundra Sivakrishna / Tehseen, Muhammad / Marsic, Tin / Salunke, Rahul / Subudhi, Amit K / Hala, Sharif M / Hamdan, Samir M / Pain, Arnab / Alofi, Fadwa S / Alsomali, Afrah / Hashem, Anwar M / Khogeer, Asim / Almontashiri, Naif A M / Abedalthagafi, Malak / Hassan, Norhan / Mahfouz, Magdy M

    Virus Res

    Abstract: The COVID-19 pandemic caused by SARS-CoV-2 affects all aspects of human life. Detection platforms that are efficient, rapid, accurate, specific, sensitive, and user friendly are urgently needed to manage and control the spread of SARS-CoV-2. RT-qPCR ... ...

    Abstract The COVID-19 pandemic caused by SARS-CoV-2 affects all aspects of human life. Detection platforms that are efficient, rapid, accurate, specific, sensitive, and user friendly are urgently needed to manage and control the spread of SARS-CoV-2. RT-qPCR based methods are the gold standard for SARS-CoV-2 detection. However, these methods require trained personnel, sophisticated infrastructure, and a long turnaround time, thereby limiting their usefulness. Reverse transcription-loop-mediated isothermal amplification (RT-LAMP), a one-step nucleic acid amplification method conducted at a single temperature, has been used for colorimetric virus detection. CRISPR-Cas12 and CRISPR-Cas13 systems, which possess collateral activity against ssDNA and RNA, respectively, have also been harnessed for virus detection. Here, we built an efficient, rapid, specific, sensitive, user-friendly SARS-CoV-2 detection module that combines the robust virus amplification of RT-LAMP with the specific detection ability of SARS-CoV-2 by CRISPR-Cas12. Furthermore, we combined the RT-LAMP-CRISPR-Cas12 module with lateral flow cells to enable highly efficient point-of-care SARS-CoV-2 detection. Our iSCAN SARS-CoV-2 detection module, which exhibits the critical features of a robust molecular diagnostic device, should facilitate the effective management and control of COVID-19.
    Keywords covid19
    Publisher WHO
    Document type Article
    Note WHO #Covidence: #719033
    Database COVID19

    Kategorien

  8. Article ; Online: iSCAN

    Ali, Zahir / Aman, Rashid / Mahas, Ahmed / Rao, Gundra Sivakrishna / Tehseen, Muhammad / Marsic, Tin / Salunke, Rahul / Subudhi, Amit K. / Hala, Sharif M. / Hamdan, Samir M. / Pain, Arnab / Alofi, Fadwa S. / Alsomali, Afrah / Hashem, Anwar M. / Khogeer, Asim / Almontashiri, Naif A.M. / Abedalthagafi, Malak / Hassan, Norhan / Mahfouz, Magdy M.

    Virus Research

    An RT-LAMP-coupled CRISPR-Cas12 module for rapid, sensitive detection of SARS-CoV-2

    2020  Volume 288, Page(s) 198129

    Keywords Cancer Research ; Virology ; Infectious Diseases ; covid19
    Language English
    Publisher Elsevier BV
    Publishing country us
    Document type Article ; Online
    ZDB-ID 605780-9
    ISSN 1872-7492 ; 0168-1702
    ISSN (online) 1872-7492
    ISSN 0168-1702
    DOI 10.1016/j.virusres.2020.198129
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  9. Article ; Online: Development and evaluation of a 28S rRNA gene-based nested PCR assay for P. falciparum and P. vivax.

    Pakalapati, Deepak / Garg, Shilpi / Middha, Sheetal / Acharya, Jyoti / Subudhi, Amit K / Boopathi, Arunachalam P / Saxena, Vishal / Kochar, Sanjay K / Kochar, Dhanpat K / Das, Ashis

    Pathogens and global health

    2013  Volume 107, Issue 4, Page(s) 180–188

    Abstract: The 28S rRNA gene was amplified and sequenced from P. falciparum and P. vivax isolates collected from northwest India. Based upon the sequence diversity of the Plasmodium 28SrRNA gene in comparison with its human counterpart, various nested polymerase ... ...

    Abstract The 28S rRNA gene was amplified and sequenced from P. falciparum and P. vivax isolates collected from northwest India. Based upon the sequence diversity of the Plasmodium 28SrRNA gene in comparison with its human counterpart, various nested polymerase chain reaction (PCR) primers were designed from the 3R region of the 28SrRNA gene and evaluated on field isolates. This is the first report demonstrating the utility of this gene for species-specific diagnosis of malaria for these two species, prevalent in India. The initial evaluation on 363 clinical isolates indicated that, in comparison with microscopy, which showed sensitivity and specificity of 85·39% and 100% respectively, the sensitivity and specificity of the nested PCR assay was found to be 99·08% and 100% respectively. This assay was also successful in detecting mixed infections that are undetected by microscopy. Our results demonstrate the utility of the 28S rRNA gene as a diagnostic target for the detection of the major plasmodial species infecting humans.
    MeSH term(s) Coinfection/diagnosis ; Coinfection/parasitology ; DNA Primers/genetics ; DNA, Protozoan/chemistry ; DNA, Protozoan/genetics ; Genes, rRNA ; Humans ; India ; Malaria/diagnosis ; Malaria/parasitology ; Molecular Diagnostic Techniques/methods ; Parasitology/methods ; Plasmodium falciparum/classification ; Plasmodium falciparum/genetics ; Plasmodium vivax/classification ; Plasmodium vivax/genetics ; Polymerase Chain Reaction/methods ; RNA, Ribosomal, 28S/genetics ; Sensitivity and Specificity ; Sequence Analysis, DNA
    Chemical Substances DNA Primers ; DNA, Protozoan ; RNA, Ribosomal, 28S
    Language English
    Publishing date 2013-06-29
    Publishing country England
    Document type Evaluation Study ; Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2625162-0
    ISSN 2047-7732 ; 2047-7724
    ISSN (online) 2047-7732
    ISSN 2047-7724
    DOI 10.1179/2047773213Y.0000000090
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article: Plasmodium vivax apicoplast genome: A comparative analysis of major genes from Indian field isolates

    Saxena, Vishal / Garg, Shilpi / Tripathi, Jyotsna / Sharma, Sonal / Pakalapati, Deepak / Subudhi, Amit K / Boopathi, P.A / Saggu, Gagandeep S / Kochar, Sanjay K / Kochar, Dhanpat K / Das, Ashis

    Acta tropica. 2012 Apr., v. 122, no. 1

    2012  

    Abstract: The apicomplexan parasite Plasmodium vivax is responsible for causing more than 70% of human malaria cases in Central and South America, Southeastern Asia and the Indian subcontinent. The rising severity of the disease and the increasing incidences of ... ...

    Abstract The apicomplexan parasite Plasmodium vivax is responsible for causing more than 70% of human malaria cases in Central and South America, Southeastern Asia and the Indian subcontinent. The rising severity of the disease and the increasing incidences of resistance shown by this parasite towards usual therapeutic regimens have necessitated investigation of putative novel drug targets to combat this disease. The apicoplast, an organelle of procaryotic origin, and its circular genome carrying genes of possible functional importance, are being looked upon as potential drug targets. The genes on this circular genome are believed to be highly conserved among all Plasmodium species. Till date, the plastid genome of P. falciparum, P. berghei and P. chabaudi have been detailed while partial sequences of some genes from other parasites including P. vivax have been studied for identifying evolutionary positions of these parasites. The functional aspects and significance of most of these genes are still hypothetical. In one of our previous reports, we have detailed the complete sequence, as well as structural and functional characteristics of the Elongation factor encoding tufA gene from the plastid genome of P. vivax. We present here the sequences of large and small subunit rRNA (lsu and ssu rRNA) genes, sufB (ORF470) gene, RNA polymerase (rpo B, C) subunit genes and clpC (casienolytic protease) gene from the plastid genome of P. vivax. A comparative analysis of these genes between P. vivax and P. falciparum reveals approximately 5–16% differences. A codon usage analysis of major plastid genes has shown a high frequency of codons rich in A/T at any or all of the three positions in all the species. TTA, AAT, AAA, TAT, and ATA are the major preferred codons. The sequences, functional domains and structural analysis of respective proteins do not show any variations in the active sites. A comparative analysis of these Indian P. vivax plastid genome encoded genes has also been done to understand the evolutionary position of the Indian parasite in comparison to other Plasmodium species.
    Keywords DNA-directed RNA polymerase ; Plasmodium vivax ; active sites ; codons ; correlation ; disease severity ; drugs ; functional properties ; humans ; major genes ; malaria ; parasites ; plastid DNA ; proteinases ; proteins ; ribosomal RNA ; Asia ; South America
    Language English
    Dates of publication 2012-04
    Size p. 138-149.
    Publishing place Elsevier B.V.
    Document type Article
    ZDB-ID 210415-5
    ISSN 1873-6254 ; 0001-706X
    ISSN (online) 1873-6254
    ISSN 0001-706X
    DOI 10.1016/j.actatropica.2012.01.007
    Database NAL-Catalogue (AGRICOLA)

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