Recent Submissions

  • IMPUTOR : phylogenetically aware software for imputation of errors in next-generation sequencing 

    Jobin, Matthew; Schurz, Haiko; Henn, Brenna M. (Oxford University Press, 2018)
    ENGLISH ABSTRACT: We introduce IMPUTOR, software for phylogenetically aware imputation of missing haploid nonrecombining genomic data. Targeted for next-generation sequencing data, IMPUTOR uses the principle of parsimony ...
  • Unexpected genomic and phenotypic diversity of mycobacterium africanum lineage 5 affects drug resistance, protein secretion, and immunogenicity 

    Ates, Louis S.; Dippenaar, Anzaan; Sayes, Fadel; Pawlik, Alexandre; Bouchier, Christiane; Ma, Laurence; Warren, Robin M.; Sougakoff, Wladimir; Majlessi, Laleh; Van Heijs, Jeroen W. J.; Brossier, Florence; Brosch, Roland (Oxford University Press, 2018)
    ENGLISH ABSTRACT: Mycobacterium africanum consists of Lineages L5 and L6 of the Mycobacterium tuberculosis complex (MTBC) and causes human tuberculosis in specific regions of Western Africa, but is generally not transmitted ...
  • Comprehensive characterization of the attenuated double auxotroph mycobacterium tuberculosisΔleuDΔpanCD as an alternative to H37Rv 

    Mouton, Jomien M.; Heunis, Tiaan; Dippenaar, Anzaan; Gallant, James L.; Kleynhans, Leanie; Sampson, Samantha L. (Frontiers Media, 2019)
    ENGLISH ABSTRACT: Although currently available model organisms such as Mycobacterium smegmatis and Mycobacterium bovis Bacillus Calmette-Guérin (BCG) have significantly contributed to our understanding of tuberculosis (TB) ...
  • PD-1 expression on mycobacterium tuberculosis-specific CD4 T cells is associated with bacterial load in human tuberculosis 

    Day, Cheryl L.; Abrahams, Deborah A.; Bunjun, Rubina; Stone, Lynnett; De Kock, Marwou; Walzl, Gerhard; Wilkinson, Robert J.; Burgers, Wendy A.; Hanekom, Willem A. (Frontiers Media, 2018)
    ENGLISH ABSTRACT: Persistent antigen stimulation in chronic infections has been associated with antigen-specific T cell dysfunction and upregulation of inhibitory receptors, including programmed cell death protein 1 (PD-1). ...
  • Complement component C1q as serum biomarker to detect active tuberculosis 

    Lubbers, Rosalie; Sutherland, Jayne S.; Goletti, Delia; De Paus, Roelof A.; Van Moorsel, Coline H. M.; Veltkamp, Marcel; Vestjens, Stefan M. T.; Bos, Willem J. W.; Petrone, Linda; Del Nonno, Franca; Bajema, Ingeborg M.; Dijkman, Karin; Verreck, Frank A. W.; Walzl, Gerhard; Gelderman, Kyra A.; Groeneveld, Geert H.; Geluk, Annemieke; Ottenhoff, Tom H. M.; Joosten, Simone A.; Trouw, Leendert A. (Frontiers Media, 2018)
    Background: Tuberculosis (TB) remains a major threat to global health. Currently, diagnosis of active TB is hampered by the lack of specific biomarkers that discriminate active TB disease from other (lung) diseases or ...
  • Neutrophils : innate effectors of TB resistance? 

    Kroon, Elouise E.; Coussens, Anna K.; Kinnear, Craig; Orlova, Marianna; Moller, Marlo; Seeger, Allison; Wilkinson, Robert J.; Hoal, Eileen G.; Schurr, Erwin (Frontiers Media, 2018)
    ENGLISH ABSTRACT: Certain individuals are able to resist Mycobacterium tuberculosis infection despite persistent and intense exposure. These persons do not exhibit adaptive immune priming as measured by tuberculin skin ...
  • A serum circulating miRNA signature for short-term risk of progression to active tuberculosis among household contacts 

    Duffy, Fergal J.; Thompson, Ethan; Downing, Katrina; Suliman, Sara; Mayanja-Kizza, Harriet; Boom, W. Henry; Thiel, Bonnie; Weiner III, January; Kaufmann, Stefan H. E.; Dover, Drew; Tabb, David L.; Dockrell, Hazel M.; Ottenhoff, Tom H. M.; Tromp, Gerard; Scriba, Thomas J.; Zak, Daniel E.; Walzl, Gerhard; GC6-74 Consortium (Frontiers Media, 2018)
    ENGLISH ABSTRACT: Biomarkers that predict who among recently Mycobacterium tuberculosis (MTB)-exposed individuals will progress to active tuberculosis are urgently needed. Intracellular microRNAs (miRNAs) regulate the host ...
  • Monocytic myeloid-derived suppressor cells in chronic infections 

    Dorhoi, Anca; Du Plessis, Nelita (Frontiers Media, 2018)
    ENGLISH ABSTRACT: Heterogeneous populations of myeloid regulatory cells (MRC), including monocytes, macrophages, dendritic cells, and neutrophils, are found in cancer and infectious diseases. The inflammatory environment ...
  • IL-22 : an underestimated player in natural resistance to tuberculosis? 

    Ronacher, Katharina; Sinha, Roma; Cestari, Michelle (Frontiers Media, 2018)
    ENGLISH ABSTRACT: Approximately 10% of individuals latently infected with Mycobacterium tuberculosis (Mtb) develop active tuberculosis (TB) during their lifetime. Although it is well recognized that T-helper 1 immune ...
  • New insights on water buffalo genomic diversity and post-domestication migration routes from medium density SNP chip data 

    Colli, Licia; Milanesi, Marco; Vajana, Elia; Iamartino, Daniela; Bomba, Lorenzo; Puglisi, Francesco; Del Corvo, Marcello; Nicolazzi, Ezequiel L.; Ahmed, Sahar S. E.; Herrera, Jesus R. V.; Cruz, Libertado; Zhang, Shujun; Liang, Aixin; Hua, Guohua; Yang, Liguo; Hao, Xingjie; Zuo, Fuyuan; Lai, Song-Jia; Wang, Shuilian; Liu, Ruyu; Gong, Yundeng; Mokhber, Mahdi; Mao, Yongjiang; Guan, Feng; Vlaic, Augustin; Vlaic, Bogdan; Ramunno, Luigi; Cosenza, Gianfranco; Ahmad, Ali; Soysal, Ihsan; Unal, Emel O.; Ketudat-Cairns, Mariena; Garcia, Jose F.; Utsunomiya, Yuri T.; Baruselli, Pietro S.; Amaral, Maria E. J.; Parnpai, Rangsun; Drummond, Marcela G.; Galbusera, Peter; Burton, James; Hoal, Eileen; Yusnizar, Yulnawati; Sumantri, Cece; Moioli, Bianca; Valentini, Alessio; Stella, Alessandra; Williams, John L.; Ajmone-Marsan, Paolo (Frontiers Media, 2018)
    ENGLISH ABSTRACT: The domestic water buffalo is native to the Asian continent but through historical migrations and recent importations, nowadays has a worldwide distribution. The two types of water buffalo, i.e., river ...
  • Patients with concurrent tuberculosis and diabetes have a pro-atherogenic plasma lipid profile 

    Vrieling, Frank; Ronacher, Katharina; Kleynhans, Leanie; Van Den Akker, Erik; Walzl, Gerhard; Ottenhoff, Tom H. M.; Joosten, Simone A. (Elsevier, 2018)
    Background: Type 2 diabetes mellitus (DM) is a major risk factor for development of tuberculosis (TB), however the underlyingmolecular foundations are unclear. Since lipids play a central role in the development of both ...
  • Application of cerebrospinal fluid host protein biosignatures in the diagnosis of tuberculous meningitis in children from a high burden setting 

    Manyelo, Charles M.; Solomons, Regan S.; Snyders, Candice I.; Manngo, Portia M.; Mutavhatsindi, Hygon; Kriel, Belinda; Stanley, Kim; Walzl, Gerhard; Chegou, Novel N. (Hindawi, 2019-04)
    Background. The diagnosis of tuberculous meningitis (TBM) especially in children is challenging. New tests are urgently needed for the diagnosis of the disease, especially in resource-limited settings. Methods. We collected ...
  • Performance and immune characteristics of bronchoalveolar lavage by research bronchoscopy in pulmonary tuberculosis and other lung diseases in the Western Cape, South Africa 

    Young, Carly; Ahlers, Petri; Hiemstra, Andriette M.; Loxton, Andre G.; Gutschmidt, Andrea; Malherbe, Stephanus T.; Walzl, Gerhard; Du Plessis, Nelita (BMC (part of Springer Nature), 2019-06-01)
    Background: Tuberculosis (TB) remains a debilitating, deadly disease that warrants innovative research tools to fully understand the pathogenesis and host immune responses, particularly at the site of infection and disease. ...
  • HIV-1 subtype C envelope function becomes less sensitive to N-glycosylation deletion during disease progression 

    Lumngwena, Evelyn N.; Shuping, Liliwe; Bernitz, Netanya; Woodman, Zenda (BMC (part of Springer Nature), 2019-06-17)
    Objective: As part of a larger study to understand how Envelope N-glycosylation influences HIV-1 pathogenesis, we selected a participant infected with a single Subtype C variant and determined whether deletion of specific ...
  • The neuromyelitis optica presentation and the aquaporin-4 antibody in HIV-seropositive and seronegative patients in KwaZulu-Natal, South Africa 

    Bhigjee, Ahmed I.; Moodley, Anandan A.; Roos, Izanne; Wells, Cait-Lynn; Ramdial, Pratistadevi; Esser, Monika (AOSIS Publishing, 2017)
    Background: The association of the anti-aquaporin-4 (AQP-4) water channel antibody with neuromyelitis optica (NMO) syndrome has been described from various parts of the world. There has been no large study describing this ...
  • Smooth muscle cell-specific Notch1 haploinsufficiency restricts the progression of abdominal aortic aneurysm by modulating CTGF expression 

    Sachdeva, Jaspreet; Mahajan, Advitiya; Cheng, Jeeyun; Baeten, Jeremy T.; Lilly, Brenda; Kuivaniemi, Helena; Hans, Chetan P. (Public Library of Science, 2017)
    Aims: Infiltration of macrophages and apoptosis of vascular smooth muscle cells (VSMCs) promote the development of abdominal aortic aneurysm (AAA). Previously, we demonstrated that global Notch1 deficiency prevents the ...
  • A sex-stratified genome-wide association study of tuberculosis using a multi-ethnic genotyping array 

    Schurz, Haiko; Kinnear, Craig J.; Gignoux, Chris; Wojcik, Genevieve; Van Helden, Paul D.; Tromp, Gerard; Henn, Brenna; Hoal, Eileen G.; Moller, Marlo (Frontiers Media, 2019)
    Tuberculosis (TB), caused by Mycobacterium tuberculosis, is a complex disease with a known human genetic component. Males seem to be more affected than females and in most countries the TB notification rate is twice as ...
  • Evaluating the accuracy of imputation methods in a five-way admixed population 

    Schurz, Haiko; Muller, Stephanie J.; Van Helden, Paul David; Tromp, Gerard; Hoal, Eileen G.; Kinnear, Craig J.; Moller, Marlo (Frontiers Media, 2019)
    Genotype imputation is a powerful tool for increasing statistical power in an association analysis. Meta-analysis of multiple study datasets also requires a substantial overlap of SNPs for a successful association analysis, ...
  • Experimental Mycobacterium bovis infection in three white rhinoceroses (Ceratotherium simum) : Susceptibility, clinical and anatomical pathology 

    Michel, Anita L.; Lane, Emily P.; De Klerk-Lorist, Lin-Mari; Hofmeyr, Markus; Van Der Heijden, Elisabeth M. D. L.; Botha, Louise; Van Helden, Paul; Miller, Michele; Buss, Peter (Public Library of Science, 2017)
    Tuberculosis caused by Mycobacterium bovis is endemic in the African buffalo (Syncerus caffer) population in the Kruger National Park and other conservation areas in South Africa. The disease has been diagnosed in a total ...
  • Paratuberculosis in a domestic dog in South Africa 

    Miller, Michele A.; Davey, Sewellyn C.; Van Helden, Lesley S.; Kettner, Frank; Weltan, Sandy M.; Last, Rick; Grewar, John D.; Botha, Louise; Van Helden, Paul D. (AOSIS Publishing, 2017)
    This case report shows that Mycobacterium avium subsp. paratuberculosis (MAP) infection can cause clinical disease in domestic dogs, and should be considered as a differential diagnosis for gastrointestinal inflammatory ...

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