Browsing Research Articles (Biochemistry) by Title

Browsing Research Articles (Biochemistry) by Title

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  • The RIPper, a web-based tool for genome-wide quantification of repeat-induced point (RIP) mutations 
    Van Wyk, Stephanie; Harrison, Christopher H.; Wingfield, Brenda D.; De Vos, Lieschen; Van der Merwe, Nicolaas Albertus (Albie); Steenkamp, Emma Theodora (PeerJ, 2019-08)
    BACKGROUND. The RIPper (http://theripper.hawk.rocks) is a set of web-based tools designed for analyses of Repeat-Induced Point (RIP) mutations in the genome sequences of Ascomycota. The RIP pathway is a fungal genome ...
  • Roadmap for naming uncultivated Archaea and Bacteria 
    Murray, Alison E.; Freudenstein, John; Gribaldo, Simonetta; Hatzenpichler, Roland; Hugenholtz, Philip; Kampfer, Peter; Konstantinidis, Konstantinos T.; Lane, Christopher E.; Papke, R. Thane; Parks, Donovan H.; Rossello-Mora, Ramon; Stott, Matthew B.; Sutcliffe, Iain C.; Thrash, J. Cameron; Venter, S.N. (Stephanus Nicolaas); Whitman, William B.; Acinas, Silvia G.; Amann, Rudolf I.; Anantharaman, Karthik; Armengaud, Jean; Baker, Brett J.; Barco, Roman A.; Bode, Helge B.; Boyd, Eric S.; Brady, Carrie Louise; Carini, Paul; Chain, Patrick S.G.; Colman, Daniel R.; DeAngelis, Kristen M.; De los Rios, Maria Asuncion; Estrada-de los Santos, Paulina; Dunlap, Christopher A.; Eisen, Jonathan A.; Emerson, David; Ettema, Thijs J.G.; Eveillard, Damien; Girguis, Peter R.; Hentschel, Ute; Hollibaugh, James T.; Hug, Laura A.; Inskeep, William P.; Ivanova, Elena P.; Klenk, Hans-Peter; Li, Wen-Jun; Lloyd, Karen G.; Loffler, Frank E.; Makhalanyane, Thulani Peter; Moser, Duane P.; Nunoura, Takuro; Palmer, Marike; Parro, Victor; Pedrós-Alio, Carlos; Probst, Alexander J.; Smits, Theo H.M.; Steen, Andrew D.; Steenkamp, Emma Theodora; Spang, Anja; Stewart, Frank J.; Tiedje, James M.; Vandamme, Peter; Wagner, Michael; Wang, Feng-Ping; Yarza, Pablo; Hedlund, Brian P.; Reysenbach, Anna-Louise (Nature Research, 2020-06-08)
    The assembly of single-amplified genomes (SAGs) and metagenome-assembled genomes (MAGs) has led to a surge in genome-based discoveries of members affiliated with Archaea and Bacteria, bringing with it a need to develop ...
  • Robust forensic matching of confiscated horns to individual poached African rhinoceros 
    Harper, Cindy Kim; Ludwig, Anette; Clarke, Amy B.; Makgopela, Kagiso; Yurchenko, Andrey; Guthrie, Alan John; Dobrynin, Pavel; Tamazian, Gaik; Emslie, Richard; Van Heerden, Marile; Hofmeyr, Markus; Potter, Roderick; Roets, Johannes; Beytell, Piet; Otiende, Moses; Kariuki, Linus; Du Toit, Raoul; Anderson, Natasha; Okori, Joseph; Antonik, Alexey; Koepfli, Klaus-Peter; Thompson, P.N. (Peter N.); O’Brien, Stephen J. (Elsevier (Cell Press), 2018)
    Black and white rhinoceros (Diceros bicornis and Ceratotherium simum) are iconic African species that are classified by the International Union for the Conservation of Nature (IUCN) as Critically Endangered and ...
  • The role of aDNA in understanding the coevolutionary patterns of human sexually transmitted infections 
    Pimenoff, Ville N.; Houldcroft, Charlotte J.; Rifkin, Riaan F.; Underdown, Simon (MDPI, 2018-07)
    Analysis of pathogen genome data sequenced from clinical and historical samples has made it possible to perform phylogenetic analyses of sexually transmitted infections on a global scale, and to estimate the diversity, ...
  • Role of the horizontal gene exchange in evolution of pathogenic Mycobacteria 
    Reva, Oleg N.; Korotetskiy, Ilya S.; Ilin, A. (BioMed Central, 2015-02)
    BACKGROUND : Mycobacterium tuberculosis is one of the most dangerous human pathogens, the causative agent of tuberculosis. While this pathogen is considered as extremely clonal and resistant to horizontal gene exchange, there ...
  • Roles of plant volatiles in defence against microbial pathogens and microbial exploitation of volatiles 
    Hammerbacher, Almuth; Coutinho, Teresa A.; Gershenzon, Jonathan (Wiley, 2019-10)
    Plants emit a large variety of volatile organic compounds during infection by pathogenic microbes, including terpenes, aromatics, nitrogen‐containing compounds, and fatty acid derivatives, as well as the volatile plant ...
  • Rosellinia necatrix infection induces differential gene expression between tolerant and susceptible avocado rootstocks 
    Zumaquero, Adela; Martınez-Ferri, Elsa; Matas, Antonio J.; Reeksting, Bianca J.; Olivier, Nicholas Abraham; Pliego-Alfaro, Fernando; Barcelo, Araceli; Van den Berg, Noelani (Public Library of Science, 2019-02)
    Rosellinia necatrix is the causal agent of avocado white root rot (WRR). Control of this soilborne disease is difficult, and the use of tolerant rootstocks may present an effective method to lessen its impact. To date, ...
  • Savicalin, a lipocalin from hemocytes of the soft tick, Ornithodoros savignyi 
    Cheng, Paul H.; Mans, Ben J. (Barend Johannes); Neitz, Albert Walter Herman; Gaspar, Anabella Regina Marques (Springer, 2010-11)
    Savicalin, is a lipocalin found in the hemocytes of the soft tick, Ornithodoros savignyi. It could be assigned to the tick lipocalin family based on BLAST analysis. Savicalin is the first non-salivary gland lipocalin ...
  • Sciarid pests (Diptera: Sciaridae) from undercover crop production in South Africa 
    Katumanyane, Agil; Kanzi, Aquillah M.; Malan, Antoinette P. (Academy of Science of South Africa, 2020-03)
    Fungus gnats (sciarids) are among the most important pests in undercover crop production. They cause direct physical damage to plant roots, transfer fungal pathogens and create entry points for soil-borne plant pathogens. ...
  • The seagrass methylome is associated with variation in photosynthetic performance among clonal shoots 
    Jueterbock, Alexander; Boström, Christoffe; Coyer, James A.; Olsen, Jeanine L.; Kopp, Martina; Dhanasiri, Anusha K.S.; Smolina, Irina; Arnaud-Haond, Sophie; Van de Peer, Yves; Hoarau, Galice (Frontiers Media, 2020-09)
    Evolutionary theory predicts that clonal organisms are more susceptible to extinction than sexually reproducing organisms, due to low genetic variation and slow rates of evolution. In agreement, conservation management ...
  • Seeing is believing 
    Schubert, Wolf-Dieter (Lynnwood Ridge: Academy of Science South Africa, 2014)
    Have you ever wondered how something small like a virus or a bacterium can infect a person and cause anything from minor irritations such as a sore throat, to more severe symptoms like fever and measles, or even kill? ...
  • Selection of marker genes for genetic barcoding of microorganisms and binning of metagenomic reads by Barcoder software tools 
    Rotimi, A.M. (Adeola); Pierneef, Rian Ewald; Reva, Oleg N. (BioMed Central, 2018-08-30)
    BACKGROUND : Metagenomic approaches have revealed the complexity of environmental microbiomes with the advancement in whole genome sequencing displaying a significant level of genetic heterogeneity on the species level. ...
  • Sequence data reflect the introduction pathways of the Sirex woodwasp parasitoid, Ibalia leucospoides (Ibaliidae, Hymenoptera) 
    Hurley, Brett Phillip; Fitza, Katrin N.E.; Wingfield, Michael J.; Slippers, Bernard (Wiley, 2020-05)
    The parasitoid wasp Ibalia leucospoides is native to the northern hemisphere and has been introduced to the southern hemisphere as a biological control agent for the invasive woodwasp Sirex noctilio. Two subspecies of the ...
  • Sequence of the hyperplastic genome of the naturally competent Thermus scotoductus SA-01 
    Gounder, Kamini; Brzuszkiewicz, Elzbieta; Liesegang, Heiko; Wollherr, Antje; Daniel, Rolf; Gottschalk, Gerhard; Reva, Oleg N.; Kumwenda, Benjamin; Srivastava, Malay; Bricio, Carlos; Berenguer, Jose; Van Heerden, Esta; Litthauer, Derek (BioMed Central, 2011)
    BACKGROUND: Many strains of Thermus have been isolated from hot environments around the world. Thermus scotoductus SA-01 was isolated from fissure water collected 3.2 km below surface in a South African gold mine. ...
  • Sexual reproduction in populations of Austropuccinia psidii 
    McTaggart, Alistair R.; Du Plessis, Esna; Roux, Jolanda; Barnes, Irene; Fraser, Stuart; Granados, Ginna Marcela; Ho, Wellcome W.H.; Shuey, Louise S.; Drenth, Andre (Springer, 2020-02)
    Austropuccinia psidii is a rust fungus that has expanded its known geographic distribution and host range on Myrtaceae. Invasions by rust fungi are often caused by asexual urediniospores that give rise to populations with ...
  • Short communication : effects of a 17-beta estradiol analogue on gene expression and morphology in a breast epithelial adenocarcinoma cell line : a potential antiproliferative agent 
    Visagie, M.H. (Michelle Helen); Stander, Barend Andre; Birkholtz, Lyn-Marie; Joubert, Annie M. (Biomedical Research Press, 2013)
    2-Methoxyestradiol is a 17-beta estradiol derivative with antitumor activity. Due to low bioavailability, a new estrogen analogue was in silico-designed. The latter, a sulphamoylated analogue of 2-methoxyestradiol, was ...
  • Shotgun metagenomic analysis of kombucha mutualistic community exposed to Mars‐like environment outside the International Space Station 
    Goes-Neto, Aristoteles; Kukharenko, Olga; Orlovska, Iryna; Podolich, Olga; Imchen, Madangchanok; Kumavath, Ranjith; Kato, Rodrigo Bentes; Santana de Carvalho, Daniel; Tiwari, Sandeep; Brenig, Bertram; Azevedo, Vasco; Reva, Oleg N.; De Vera, Jean-Pierre P.; Kozyrovska, Natalia; Barh, Debmalya (Wiley, 2021-07)
    Kombucha is a multispecies microbial ecosystem mainly composed of acetic acid bacteria and osmophilic acid‐tolerant yeasts, which is used to produce a probiotic drink. Furthermore, Kombucha Mutualistic Community (KMC) has ...
  • Sky islands as foci for divergence of fig trees and their pollinators in southwest China 
    Deng, Jun-Yin; Fu, Rong-Hua; Compton, Stephen G.; Liu, Mei; Wang, Qin; Yuan, Chuan; Zhang, Lu-Shui; Chen, Yan (Wiley, 2020-02)
    The dynamics of populations and their divergence over time have shaped current levels of biodiversity and in the case of the “sky islands” of mountainous southwest (SW) China have resulted in an area of exceptional botanical ...
  • Small RNA profiling in Pinus pinaster reveals the transcriptome of developing seeds and highlights differences between zygotic and somatic embryos 
    Rodrigues, Andreia S.; Chaves, Ines; Costa, Bruno Vasques; Lin, Yao-Cheng; Lopes, Susana; Milhinhos, Ana; Van de Peer, Yves; Migue, Celia M. (Nature Research, 2019-08)
    Regulation of seed development by small non-coding RNAs (sRNAs) is an important mechanism controlling a crucial phase of the life cycle of seed plants. In this work, sRNAs from seed tissues (zygotic embryos and megagametophytes) ...
  • Solar salterns as model systems to study the units of bacterial diversity that matter for ecosystem functioning 
    Konstantinidis, Konstantinos T.; Viver, Tomeu; Conrad, Roth E.; Venter, S.N. (Stephanus Nicolaas); Rossello-Mora, Ramon (Elsevier, 2022-02)
    Microbial communities often harbor overwhelming species and gene diversity, making it challenging to determine the important units to study this diversity. We argue that the reduced, and thus tractable, microbial diversity ...