Research Articles (Molecular Biology and Human Genetics)

 

Recent Submissions

  • Epistatic gene-based interaction analyses for glaucoma in eMERGE and NEIGHBOR Consortium 

    Verma, Shefali Setia; Bailey, Jessica N. Cooke; Lucas, Anastasia; Bradford, Yuki; Linneman, James G.; Hauser, Michael A.; Pasquale, Louis R.; Peissig, Peggy L.; Brilliant, Murray H.; McCarty, Catherine A.; Haines, Jonathan L.; Wiggs, Janey L.; Vrabec, Tamara R.; Tromp, Gerard; Ritchie, Marylyn D.; eMERGE Network; NEIGHBOR Consortium (Public Library of Science, 2016)
    Primary open angle glaucoma (POAG) is a complex disease and is one of the major leading causes of blindness worldwide. Genome-wide association studies have successfully identified several common variants associated with ...

  • Translational research for tuberculosis elimination : priorities, challenges, and actions 

    Lienhardt, Christian; Lonnroth, Knut; Menzies, Dick; Balasegaram, Manica; Chakaya, Jeremiah; Cobelens, Frank; Cohn, Jennifer; Denkinger, Claudia M.; Evans, Thomas G.; Kallenius, Gunilla; Kaplan, Gilla; Kumar, Ajay M. V.; Matthiessen, Line; Mgone, Charles S.; Mizrahi, Valerie; Mukadi, Ya-diul; Nguyen, Viet Nhung; Nordstrom, Anders; Sizemore, Christine F.; Spigelman, Melvin; Squire, S. Bertel; Swaminathan, Soumya; Van Helden, Paul D.; Zumla, Alimuddin; Weyer, Karin; Weil, Diana; Raviglione, Mario (Public Library of Science, 2016)
    Summary Points: • The WHO End TB Strategy, endorsed by the World Health Assembly in May 2014, has the ambitious goal of ending the global tuberculosis (TB) epidemic by 2035, with targets of a 95% decline in deaths due ...

  • Altered mitochondrial respiration and other features of mitochondrial function in parkin-mutant fibroblasts from parkinson’s disease patients 

    Haylett, William; Swart, Chrisna; Van Der Westhuizen, Francois; Van Dyk, Hayley; Van Der Merwe, Lize; Van Der Merwe, Celia; Loos, Ben; Carr, Jonathan; Kinnear, Craig; Bardien, Soraya (Hindawi Publishing Corporation, 2016)
    Mutations in the parkin gene are the most common cause of early-onset Parkinson’s disease (PD). Parkin, an E3 ubiquitin ligase, is involved in respiratory chain function, mitophagy, and mitochondrial dynamics. Human cellular ...

  • The use of digital PCR to improve the application of quantitative molecular diagnostic methods for tuberculosis 

    Devonshire, Alison S.; O’Sullivan, Denise M.; Honeyborne, Isobella; Jones, Gerwyn; Karczmarczyk, Maria; Pavsic, Jernej; Gutteridge, Alice; Milavec, Mojca; Mendoza, Pablo; Schimmel, Heinz; Van Heuverswyn, Fran; Gorton, Rebecca; Cirillo, Daniela Maria; Borroni, Emanuele; Harris, Kathryn; Barnard, Marinus; Heydenrych, Anthenette; Ndusilo, Norah; Wallis, Carole L.; Pillay, Keshree; Barry, Thomas; Reddington, Kate; Richter, Elvira; Mozioglu, Erkan; Akyurek, Sema; Yalcınkaya, Burhanettin; Akgoz, Muslum; Zel, Jana; Foy, Carole A.; McHugh, Timothy D.; Huggett, Jim F. (BioMed Central, 2016)
    Background: Real-time PCR (qPCR) based methods, such as the Xpert MTB/RIF, are increasingly being used to diagnose tuberculosis (TB). While qualitative methods are adequate for diagnosis, the therapeutic monitoring of TB ...

  • Shared genetic risk factors of intracranial, abdominal, and thoracic aneurysms 

    Van 't Hof, Femke N. G.; Ruigrok, Ynte M.; Lee, Cue Hyunkyu; Ripke, Stephan; Anderson, Graig; De Andrade, Mariza; Tromp, Gerard (American Heart Association, 2016-07-14)
    Background: Intracranial aneurysms (IAs), abdominal aortic aneurysms (AAAs), and thoracic aortic aneurysms (TAAs) all have a familial predisposition. Given that aneurysm types are known to co‐occur, we hypothesized that ...

  • Exome sequencing identifies a novel TTC37 mutation in the first reported case of Trichohepatoenteric syndrome (THE-S) in South Africa 

    Kinnear, Craig; Glanzmann, Brigitte; Banda, Eric; Schlechter, Nikola; Durrheim, Glenda; Neethling, Annika; Nel, Etienne; Schoeman, Mardelle; Johnson, Glynis; van Helden, Paul D; Hoal, Eileen G; Esser, Monika; Urban, Michael; Moller, Marlo (BioMed Central, 2017-03-14)
    Background Trichohepatoenteric syndrome (THE-S) or phenotypic diarrhoea of infancy is a rare autosomal recessive disorder characterised by severe infantile diarrhoea, facial dysmorphism, immunodeficiency and woolly hair. ...

  • Recombination in pe/ppe genes contributes to genetic variation in Mycobacterium tuberculosis lineages 

    Phelan, Jody E.; Coll, Francesc; Bergval, Indra; Anthony, Richard M.; Warren, Rob; Sampson, Samantha L.; Gey Van Pittius, Nicolaas C.; Glynn, Judith R.; Crampin, Amelia C.; Alves, Adriana; Bessa, Theolis B.; Campino, Susana; Dheda, Keertan; Grandjean, Louis; Hasan, Rumina; Hasan, Zahra; Miranda, Anabela; Moore, David; Panaiotov, Stefan; Perdigao, Joao; Portugal, Isabel; Sheen, Patricia; De Oliveira Sousa, Erivelton; Streicher, Elizabeth M.; Van Helden, Paul D.; Viveiros, Miguel; Hibberd, Martin L.; Pain, Arnab; McNerney, Ruth; Clark, Taane G. (BioMed Central, 2016-02-29)
    Background: Approximately 10 % of the Mycobacterium tuberculosis genome is made up of two families of genes that are poorly characterized due to their high GC content and highly repetitive nature. The PE and PPE families ...

  • Clinical relevance of nontuberculous mycobacteria isolated from sputum in a gold mining workforce in South Africa : an observational, clinical study 

    Van Halsema, Clare L.; Chihota, Violet N.; Gey van Pittius, Nicolaas C.; Fielding, Katherine L.; Lewis, James J.; Van Helden, Paul D.; Churchyard, Gavin J.; Grant, Alison D. (Hindawi, 2015)
    Background.The clinical relevance of nontuberculous mycobacteria (NTM), detected by liquid more than solid culture in sputum specimens from a South African mining workforce, is uncertain. We aimed to describe the current ...

  • A subgroup of latently Mycobacterium tuberculosis infected individuals is characterized by consistently elevated IgA responses to several mycobacterial antigens 

    Baumann, Ralf; Kaempfer, Susanne; Chegou, Novel N.; Oehlmann, Wulf; Spallek, Ralf; Loxton, Andre G.; Van Helden, Paul D.; Black, Gillian F.; Singh, Mahavir; Walzl, Gerhard (Hindawi, 2015)
    Elevated antibody responses to Mycobacterium tuberculosis antigens in individuals with latent infection (LTBI) have previously been linked to an increased risk for progression to active disease. Studies in the field ...

  • Epigenetics and proteomics join transcriptomics in the quest for tuberculosis biomarkers 

    Esterhuyse, Maria M.; Weiner, January; Caron, Etienne; Loxton, Andre G.; Iannaccone, Marco; Wagman, Chandre; Saikali, Philippe; Stanley, Kim; Wolski, Witold E.; Mollenkopf, Hans-Joachim; Schick, Matthias; Aebersold, Ruedi; Linhart, Heinz; Walzl, Gerhard; Kaufmann, Stefan H. E. (American Society for Microbiology, 2015-09-15)
    An estimated one-third of the world’s population is currently latently infected with Mycobacterium tuberculosis. Latent M. tuberculosis infection (LTBI) progresses into active tuberculosis (TB) disease in ~5 to 10% of ...

  • Biochemical and genetic diagnosis of Smith-Lemli- Opitz syndrome in South Africa 

    Solomon, Gabriele Anna Eva; Jones, Graham; De Jong, Greetje; Marais, Adrian David (Health and Medical Publishing Group, 2015)
    Background. The Smith-Lemli-Opitz syndrome (SLOS), due to defective function of 7-dehydrocholesterol reductase, is an autosomal recessive disorder that is more common than other defects in cholesterol biosynthesis. The ...

  • Animal-adapted members of the Mycobacterium tuberculosis complex endemic to the southern African subregion 

    Clarke, Charlene; Van Helden, Paul; Miller, Michele; Parsons, Sven (AOSIS Publishing, 2016-04)
    Members of the Mycobacterium tuberculosis complex (MTC) cause tuberculosis (TB) in both animals and humans. In this article, three animal-adapted MTC strains that are endemic to the southern African subregion – that is, ...

  • A new tool for prioritization of sequence variants from whole exome sequencing data 

    Glanzmann, Brigitte; Herbst, Hendri; Kinnear, Craig J.; Moller, Marlo; Gamieldien, Junaid; Bardien, Soraya (BioMed Central, 2016-07)
    Background: Whole exome sequencing (WES) has provided a means for researchers to gain access to a highly enriched subset of the human genome in which to search for variants that are likely to be pathogenic and possibly provide ...

  • Investigating the role of gene-gene interactions in TB susceptibility 

    Daya, Michelle; Van der Merwe, Lize; Van Helden, Paul D.; Moller, Marlo; Hoal, Eileen G. (Public Library of Science, 2015-04)
    Tuberculosis (TB) is the second leading cause of mortality from infectious disease worldwide. One of the factors involved in developing disease is the genetics of the host, yet the field of TB susceptibility genetics has ...

  • Rapid sequencing of the mycobacterium tuberculosis pncA gene for detection of pyrazinamide susceptibility 

    Streicher, Elizabeth M.; Maharaj, Kashmeel; York, Talita; Van Heerden, Carel; Barnard, Marinus; Diacon, Andreas; Mendel, Carl M.; Bosman, Marlein E.; Hepple, Juli A.; Pym, Alexander S.; Warren, Robin M.; van Helden, Paul D. (American Society for Microbiology, 2014)
    We developed a pyrazinamidase gene DNA-sequencing method to rapidly identify pyrazinamide resistance-causing mutations in GenoLyse-treated, smear-positive sputum specimens. The sensitivity and specificity were 90.9 and ...

  • Whole genome sequencing reveals genomic heterogeneity and antibiotic purification in Mycobacterium tuberculosis isolates 

    Black, P. A.; De Vos, M.; Louw, G. E.; Van der Merwe, R. G.; Dippenaar, A.; Streicher, E. M.; Abdallah, A. M.; Sampson, S. L.; Victor, T. C.; Dolby, T.; Simpson, J. A.; Van Helden, P. D.; Warren, R. M.; Pain, A. (BioMed Central, 2015-10)
    Background: Whole genome sequencing has revolutionised the interrogation of mycobacterial genomes. Recent studies have reported conflicting findings on the genomic stability of Mycobacterium tuberculosis during the evolution ...

  • Positive selection of deleterious alleles through interaction with a sex-ratio suppressor gene in African buffalo : a plausible new mechanism for a high frequency anomaly 

    Van Hooft, Pim; Greyling, Ben J.; Getz, Wayne M.; Van Helden, Paul D.; Zwaan, Bas J.; Bastos, Armanda D. S (PLoS, 2014-11-05)
    Although generally rare, deleterious alleles can become common through genetic drift, hitchhiking or reductions in selective constraints. Here we present a possible new mechanism that explains the attainment of high ...

  • Host cytokine responses induced after overnight stimulation with novel M. tuberculosis infection phase-dependent antigens show promise as diagnostic candidates for TB disease 

    Essone, Paulin N.; Chegou, Novel N.; Loxton, Andre G.; Stanley, Kim; Kriel, Magdalena; Van der Spuy, Gian; Franken, Kees L.; Ottenhoff, Tom H.; Walzl, Gerhard (PLoS, 2014-07-15)
    Background: We previously identified Mycobacterium tuberculosis (M.tb) antigen-induced host markers that showed promise as TB diagnostic candidates in 7-day whole blood culture supernatants. The aim of the present study ...

  • Fat mass and obesity-associated (FTO) gene polymorphisms are associated with physical activity, food intake, eating behaviors, psychological health, and modeled change in body mass index in overweight/obese caucasian adults 

    Harbron, Janetta; Van der Merwe, Lize; Zaahl, Monique G.; Kotze, Maritha J.; Senekal, Marjanne (MDPI, 2014-08-06)
    The fat mass and obesity-associated (FTO) gene is currently recognized as the most robust predictor of polygenic obesity. We investigated associations between the FTO rs1421085 and rs17817449 polymorphisms and the FTO ...

  • Chronic prosopis glandulosa treatment blunts neutrophil infiltration and enhances muscle repair after contusion injury 

    George, Cindy; Smith, Carine; Isaacs, Ashwin W.; Huisamen, Barbara (MDPI, 2015-01)
    Abstract: The current treatment options for soft tissue injuries remain suboptimal and often result in delayed/incomplete recovery of damaged muscle. The current study aimed to evaluate the effects of oral Prosopis ...

  • Using multi-way admixture mapping to elucidate TB susceptibility in the South African Coloured population 

    Daya, Michelle; Van der Merwe, Lize; Gignoux, Christopher R.; Van Helden, Paul D.; Moller, Marlo; Hoal, Eileen G. (BioMed Central, 2014-11)
    Background: The admixed South African Coloured population is ideally suited to the discovery of tuberculosis susceptibility genetic variants and their probable ethnic origins, but previous attempts at finding such variants ...

  • The combination of red palm oil and rooibos show anti-inflammatory effects in rats 

    Katengua-Thamahane, Emma; Marnewick, Jeanine L.; Ajuwon, Olawale R.; Chegou, Novel N.; Szucs, Gergo; Ferdinandy, Peter; Csont, Tamas; Csonka, Csaba; Van Rooyen, Jacques (BioMed Central, 2014-12)
    Background Red palm oil (RPO) and rooibos have been shown to exhibit cardioprotective properties. RPO is rich in essential fatty acids and fat soluble antioxidants while rooibos contains ...

  • Impact of HIV co-infection on plasma level of cytokines and chemokines of pulmonary tuberculosis patients 

    Mihret, Adane; Abebe, Markos; Bekele, Yonas; Aseffa, Abraham; Walzl, Gerhard; Howe, Rawleigh (BioMed Central, 2014-03-04)
    Background The immunologic environment during HIV/M. tuberculosis co-infection is characterized by cytokine and chemokine irregularities that have been shown to increase immune activation, viral replication, ...

  • Mutations in Danish patients with long QT syndrome and the identification of a large founder family with p.F29L in KCNH2 

    Christiansen, Michael; Hedley, Paula L.; Theilade, Juliane; Stoevring, Birgitte; Leren, Trond P.; Eschen, Ole; Sørensen, Karina M.; Tybjærg-Hansen, Anne; Ousager, Lilian B.; Pedersen, Lisbeth N.; Frikke-Schmidt, Ruth; Aidt, Frederik H.; Hansen, Michael G.; Hansen, Jim; Bloch Thomsen, Poul E.; Toft, Egon; Henriksen, Finn L.; Bundgaard, Henning; Jensen, Henrik K.; Kanters, Jorgen K. (BioMed Central, 2014-03)
    Background: Long QT syndrome (LQTS) is a cardiac ion channelopathy which presents clinically with palpitations, syncope or sudden death. More than 700 LQTS-causing mutations have been identified in 13 genes, all of which ...

  • A metabolic biosignature of early response to anti-tuberculosis treatment 

    Mahapatra, Sebabrata; Hess, Ann M.; Johnson, John L.; Eisenach, Kathleen D.; DeGroote, Mary A.; Gitta, Phineas; Joloba, Moses L.; Kaplan, Gilla; Walzl, Gerhard; Boom, W. H.; Belisle, John T. (BioMed Central, 2014-01)
    Background The successful treatment of tuberculosis (TB) requires long-term multidrug chemotherapy. Clinical trials to evaluate new drugs and regimens for TB treatment are protracted due to the slow clearance ...

  • Exome capture from saliva produces high quality genomic and metagenomic data 

    Kidd, Jeffrey M.; Sharpton, Thomas J.; Bobo, Dean; Norman, Paul J.; Martin, Alicia R.; Carpenter, Meredith L.; Sikora, Martin; Gignoux, Christopher R.; Nemat-Gorgani, Neda; Adams, Alexandra; Guadalupe, Moraima; Guo, Xiaosen; Feng, Qiang; Li, Yingrui; Liu, Xiao; Parham, Peter; Hoal, Eileen G.; Feldman, Marcus W.; Pollard, Katherine S.; Wall, Jeffrey D.; Bustamante, Carlos D.; Henn, Brenna M. (BioMed Central, 2014-04)
    Background Targeted capture of genomic regions reduces sequencing cost while generating higher coverage by allowing biomedical researchers to focus on specific loci of interest, such as exons. Targeted capture also ...

  • Combination of gene expression patterns in whole blood discriminate between tuberculosis infection states 

    Mihret, Adane; Loxton, Andre G.; Bekele, Yonas; Kaufmann, Stefan H. E.; Kidd, Martin; Haks, Marielle C.; Ottenhoff, Tom H. M.; Aseffa, Abraham; Howe, Rawleigh; Walzl, Gerhard (BioMed Central, 2014-05)
    Background Genetic factors are involved in susceptibility or protection to tuberculosis (TB). Apart from gene polymorphisms and mutations, changes in levels of gene expression, induced by non-genetic factors, may ...

  • Decreased expression of miR-21, miR-26a, miR-29a, and miR-142-3p in CD4+ T cells and peripheral blood from tuberculosis patients 

    Kleinsteuber, Katja; Heesch, Kerrin; Schattling, Stefanie; Kohns, Malte; Sander-Julch, Claudia; Walzl, Gerhard; Hesseling, Anneke; Mayatepek, Ertan; Fleischer, Bernhard; Marx, Florian M.; Jacobsen, Marc (Public Library of Science, 2013-04-16)
    The vast majority of Mycobacterium tuberculosis (M. tuberculosis) infected individuals are protected from developing tuberculosis and T cells are centrally involved in this process. MicroRNAs (miRNA) regulate T-cell functions ...

  • Differences in primary sites of infection between zoonotic and human tuberculosis : results from a worldwide systematic review 

    Durr, Salome; Muller, Borna; Alonso, Silvia; Hattendorf, Jan; Laisse, Claudio J. M.; Van Helden, Paul D.; Zinsstag, Jakob (Public Library of Science, 2013-08-29)
    Tuberculosis (TB) is one of the most devastating infectious diseases worldwide. Whilst global burden estimates for M. tuberculosis infection (MtTB) are well established, accurate data on the contribution of zoonotic TB ...

  • Analysis of host responses to secreted, latent and reactivation Mycobacterium tuberculosis antigens in a multi-site study of subjects with different TB and HIV infection states in sub-Saharan Africa 

    Sutherland, Jayne S.; Lalor, Maeve K.; Black, Gillian F.; Ambrose, Lyn R.; Loxton, Andre G.; Chegou, Novel N.; Kassa, Desta; Mihret, Adane; Howe, Rawleigh; Mayanja-Kizza, Harriet; Gomez, Marie P.; Donkor, Simon; Franken, Kees; Boom, W. Henry; Thiel, Bonnie A.; Crampin, Amelia C.; Hanekom, Willem; Klein, Michel R.; Parida, Shreemanta K.; Ota, Martin; Walzl, Gerhard; Ottenhoff, Tom H. M.; Dockrell, Hazel M.; Kaufmann, Stefan H. E. (Public Library of Science, 2013-09-10)
    Background: Tuberculosis (TB) remains a global health threat with 9 million new cases and 1.4 million deaths per year. In order to develop a protective vaccine, we need to define the antigens expressed by Mycobacterium ...

View more