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Biochemistry: Recent submissions

  • Whole-genome microsynteny-based phylogeny of angiosperms 
    Zhao, Tao; Zwaenepoel, Arthur; Xue, Jia-Yu; Kao, Shu-Min; Li, Zhen; Schranz, M. Eric; Van de Peer, Yves (Nature Research, 2021-06)
    Plant genomes vary greatly in size, organization, and architecture. Such structural differences may be highly relevant for inference of genome evolution dynamics and phylogeny. Indeed, microsynteny—the conservation of ...
  • The genome of the extremophile Artemia provides insight into strategies to cope with extreme environments 
    De Vos, Stephanie; Rombauts, Stephane; Coussement, Louis; Dermauw, Wannes; Vuylsteke, Marnik; Sorgeloos, Patrick; Clegg, James S.; Nambu, Ziro; Van Nieuwerburgh, Filip; Norouzitallab, Parisa; Van Leeuwen, Thomas; De Meyer, Tim; Van Stappen, Gilbert; Van de Peer, Yves; Bossier, Peter (BMC, 2021-08-31)
    BACKGROUND : Brine shrimp Artemia have an unequalled ability to endure extreme salinity and complete anoxia. This study aims to elucidate its strategies to cope with these stressors. RESULTS AND DISCUSSION : Here, we ...
  • The Welwitschia genome reveals a unique biology underpinning extreme longevity in deserts 
    Wan, Tao; Liu, Zhiming; Leitch, Ilia J.; Xin, Haiping; Maggs-Kolling, Gillian; Gong, Yanbing; Li, Zhen; Marais, Eugene; Liao, Yiying; Dai, Can; Liu, Fan; Wu, Qijia; Song, Chi; Zhou, Yadong; Huang, Weichang; Jiang, Kai; Wang, Qi; Yang, Yong; Zhong, Zhixiang; Yang, Ming; Yan, Xue; Hu, Guangwan; Hou, Chen; Su, Yingjuan; Feng, Shixiu; Yang, Ji; Yan, Jijun; Chu, Jinfang; Chen, Fan; Ran, Jinhua; Wang, Xiaoquan; Van de Peer, Yves; Leitch, Andrew R.; Wang, Qingfeng (Nature Research, 2021)
    The gymnosperm Welwitschia mirabilis belongs to the ancient, enigmatic gnetophyte lineage. It is a unique desert plant with extreme longevity and two ever-elongating leaves. We present a chromosome-level assembly of its ...
  • In silico and in vitro screening of antipathogenic properties of Melianthus comosus (Vahl) against Pseudomonas aeruginosa 
    Baloyi, Itumeleng Tsebang; Adeosun, Idowu Jesulayomi; Yusuf, Abdullahi Ahmed; Cosa, Sekelwa (MDPI, 2021-06-05)
    Bacterial quorum sensing (QS) system regulates pathogenesis, virulence, and biofilm formation, and together they contribute to nosocomial infections. Opportunistic pathogens, such as Pseudomonas aeruginosa, rely on QS for ...
  • The epistatic landscape of antibiotic resistance of different clades of Mycobacterium tuberculosis 
    Muzondiwa, Dillon; Hlanze, Hleliwe; Reva, Oleg N. (MDPI, 2021-07-15)
    Drug resistance (DR) remains a global challenge in tuberculosis (TB) control. In order to develop molecular-based diagnostic methods to replace the traditional culture-based diagnostics, there is a need for a thorough ...
  • Lifespan prolonging mechanisms and insulin upregulation without fat accumulation in long-lived reproductives of a higher termite 
    Seite, Sarah; Harrison, Mark C.; Sillam-Dusses, David; Lupoli, Roland; Van Dooren, Tom J.M.; Robert, Alain; Poissonnier, Laure-Anne; Lemainque, Arnaud; Renault, David; Acket, Sebastien; Andrieu, Muriel; Viscarra, Jose; Sul, Hei Sook; De Beer, Z. Wilhelm; Bornberg-Bauer, Erich; Vasseur-Cognet, Mireille (Nature Publishing, 2022-01)
    Kings and queens of eusocial termites can live for decades, while queens sustain a nearly maximal fertility. To investigate the molecular mechanisms underlying their long lifespan, we carried out transcriptomics, lipidomics ...
  • Tracking, targeting, and conserving soil biodiversity 
    Guerra, Carlos A.; Bardgett, Richard D.; Caon, Lucrezia; Crowther, Thomas W.; Delgado-Baquerizo, Manuel; Montanarella, Luca; Navarro, Laetitia M.; Orgiazzi, Alberto; Singh, Brajesh K.; Tedersoo, Leho; Vargas-Rojas, Ronald; Briones, Maria J.I.; Buscot, Francois; Cameron, Erin K.; Cesarz, Simone; Chatzinotas, Antonis; Cowan, Don A.; Djukic, Ika; Van den Hoogen, Johan; Lehmann, Anika; Maestre, Fernando T.; Marin, Cesar; Reitz, Thomas; Rillig, Matthias C.; Smith, Linnea C.; De Vries, Franciska T.; Weigelt, Alexandra; Wall, Diana H.; Eisenhauer, Nico (American Association for the Advancement of Science, 2021-01)
    Nature conservation literature and policy instruments mainly focus on the impacts of human development and the benefits of nature conservation for oceans and aboveground terrestrial organisms (e.g., birds and plants) and ...
  • African horse sickness virus NS4 protein is an important virulence factor and interferes with JAK-STAT signaling during viral infection 
    Wall, Gayle V.; Wright, Isabella M.; Barnardo, Carin; Erasmus, Baltus J.; Van Staden, Vida; Potgieter, A. Christiaan (Elsevier, 2021-06)
    African horse sickness virus (AHSV) non-structural protein NS4 is a nucleocytoplasmic protein that is expressed in the heart, lung, and spleen of infected horses, binds dsDNA, and colocalizes with promyelocytic leukemia ...
  • Genomic characterization of grapevine viruses N and O : novel vitiviruses from South Africa 
    Read, David Alan; Thompson, Genevieve Dawn; Le Cordeur, Nathan; Swanevelder, Dirk; Pietersen, Gerhard (Springer, 2022-02)
  • Exploring the transmission-blocking activity of antiplasmodial 3,6-diarylated imidazopyridazines 
    Coertzen, Dina; Reader, Janette; Van der Watt, Mariette Elizabeth; Leshabane, Meta Kgaogelo; Langeveld, Henrico; Cheuka, Peter M.; Dziwornu, Godwin Akpeko; Chibale, Kelly; Birkholtz, Lyn-Marie (Taylor and Francis, 2021)
    The effectiveness of current antimalarial therapies that cure patients of the pathogenic asexual blood stages is rapidly declining due to the spread of antimalarial drug resistance. This requires the development of novel ...
  • Paraburkholderia youngii sp. nov. and ‘ Paraburkholderia atlantica ’ – Brazilian and Mexican Mimosa -associated rhizobia that were previously known as Paraburkholderia tuberum sv. mimosae 
    Mavima, Lazarus; Beukes, Chrizelle Winsie; Palmer, Marike; De Meyer, Sofie E.; James, Euan K.; Maluk, Marta; Gross, Eduardo; Junior, Fabio Bueno dos Reis; Avontuur, Juanita Rayleen; Chan, Wai Yin; Venter, S.N. (Stephanus Nicolaas); Steenkamp, Emma Theodora (Elsevier, 2021-01)
    Please read abstract in the article.
  • New amidated 3,6-diphenylated imidazopyridazines with potent antiplasmodium activity are dual inhibitors of Plasmodium phosphatidylinositol-4-kinase and cGMP-dependent protein kinase 
    Cheuka, Peter Mubanga; Centani, Luyanda; Arendse, Lauren B.; Fienberg, Stephen; Wambua, Lynn; Renga, Shoneeze S.; Dziwornu, Godwin Akpeko; Kumar, Malkeet; Lawrence, Nina; Taylor, Dale; Wittlin, Sergio; Coertzen, Dina; Reader, Janette; Van der Watt, Mariette Elizabeth; Birkholtz, Lyn-Marie; Chibale, Kelly (American Chemical Society, 2021-01)
    Recent studies on 3,6-diphenylated imidazopyridazines have demonstrated impressive in vitro activity and in vivo efficacy in mouse models of malaria infection. Herein, we report the synthesis and antiplasmodium evaluation ...
  • Extracellular vesicles in teasing apart complex plant-microbiota links : implications for microbiome-based biotechnology 
    Motaung, Thabiso Eric; Steenkamp, Emma Theodora (American Society for Microbiology, 2021-07)
    Extracellular vesicles (EVs) are subcellular carriers of bioactive compounds with a complex array of functional effects on target cells. In mammals, circulating bodily fluid microbiota EVs (mbEVs) deliver cargo from ...
  • Chemogenomic fingerprints associated with stage-specific gametocytocidal compound action against human malaria parasites 
    Niemand, Jandeli; Van Biljon, Riette Andele; Van der Watt, Mariette Elizabeth; Van Heerden, Ashleigh; Reader, Janette; Van Wyk, Roelof Daniel Jacobus; Orchard, Lindsey M.; Chibale, Kelly; Llinas, Manuel; Birkholtz, Lyn-Marie (American Chemical Society, 2021-09)
    Please read abstract in the article.
  • 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 ...
  • The polyphagous shot hole borer beetle : current status of a perfect invader in South Africa 
    Van Rooyen, Elmar; Paap, Trudy; De Beer, Z. Wilhelm; Townsend, Garyn; Fell, Shawn; Nel, Wilma Janine; Morgan, Seamus; Hill, Martin; Gonzalez, Allan; Roets, Francois (Academy of Science of South Africa, 2021-11)
    The polyphagous shot hole borer (PSHB) beetle is a recent invader in South Africa. Together with its fungal symbiont, Fusarium euwallaceae, it can rapidly kill highly susceptible host plants. Its impact is most profound ...
  • Bradyrhizobium altum sp. nov., Bradyrhizobium oropedii sp. nov. and Bradyrhizobium acaciae sp. nov. from South Africa show locally restricted and pantropical nodA phylogeographic patterns 
    Avontuur, Juanita Rayleen; Palmer, Marike; Beukes, Chrizelle Winsie; Chan, Wai Yin; Tasiya, Taponeswa; Van Zyl, Elritha; Coetzee, Martin Petrus Albertus; Stepkowski, Tomasz; Venter, S.N. (Stephanus Nicolaas); Steenkamp, Emma Theodora (Elsevier, 2022-02)
    Please read abstract in the article.
  • Comparison of transcriptional responses and metabolic alterations in three multidrug-resistant model microorganisms, staphylococcus aureus ATCC BAA-39, escherichia coli ATCC BAA196, and acinetobacter baumannii ATCC BAA-1790, on exposure to iodine-containing nano-micelle drug FS-1 
    Korotetskiy, Ilya S.; Shilov, Sergey V.; Kuznetsova, Tatyana V.; Ilin, Aleksandr I.; Joubert, Monique; Taukobong, Setshaba; Reva, Oleg N. (American Society for Microbiology, 2021-03)
    Iodine is one of the oldest antimicrobial agents. Until now, there have been no reports on acquiring resistance to iodine. Recent studies showed promising results on application of iodine-containing nano-micelles, FS-1, ...
  • Fungal Planet description sheets : 1042–1111 
    Crous, Pedro W.; Wingfield, Michael J.; Chooi, Y.-H.; Gilchrist, C.L.M.; Lacey, E.; Pitt, J.I.; Roets, F.; Swart, W.J.; Cano-Lira, J.F.; Valenzuela-Lopez, N.; Hubka, V.; Shivas, R.G.; Stchigel, A.M.; Holdom, D.G.; Jurjevic, Z.; Kachalkin, A.V.; Lebel, T.; Lock, C.; Martín, M.P.; Tan, Y.P.; Tomashevskaya, M.A.; Vitelli, J.S.; Baseia, I.G.; Bhatt, V.K.; Brandrud, T.E.; De Souza, J.T.; Dima, B.; Lacey, H.J.; Lombard, L.; Morte, A.; Papp, V.; Rodríguez, A.; Rodríguez-Andrade, E.; Semwal, K.C.; Tegart, L.; Abad, Z.G.; Akulov, A.; Alvarado, P.; Alves, A.; Andrade, J.P.; Arenas, F.; Asenjo, C.; Ballara, J.; Barrett, M.D.; Berna, L.M.; Berraf-Tebbal, A.; Bianchinotti, M.V.; Bransgrove, K.; Burgess, T.I.; Carmo, F.S.; Chavez, R.; Cmokova, A.; Dearnaley, J.D.W.; De A. Santiago, A.L.C.M.; Freitas-Neto, J.F.; Denman, S.; Douglas, B.; Dovana, F.; Eichmeier, A.; Esteve-Raventos, F.; Farid, A.; Fedosova, A.G.; Ferisin, G.; Ferreira, R.J.; Ferrer, A.; Figueiredo, C.N.; Figueiredo, Y.F.; Reinoso- Fuentealba, C.G.; Garrido-Benavent, I.; Canete-Gibas, C.F.; Gil-Duran, C.; Glushakova, A.M.; Goncalves, M.F.M.; Gonzalez, M.; Gorczak, M.; Gorton, C.; Guard, F.E.; Guarnizo, A.L.; Guarro, J.; Gutierrez, M.; Hamal, P.; Hien, L.T.; Hocking, A.D.; Houbraken, J.; Hunter, G.C.; Inacio, C.A.; Jourdan, M.; Kapitonov, V.I.; Kelly, L.; Khanh, T.N.; Kisło, K.; Kiss, L.; Kiyashko, A.; Kolarík, M.; Kruse, J.; Kubatova, A.; Kucera, V.; Kucerova, I.; Kusan, I.; Lee, H.B.; Levican, G.; Lewis, A.; Liem, N.V.; Liimatainen, K.; Lim, H.J.; Lyons, M.N.; Macia-Vicente, J.G.; Magana- Duenas, V.; Mahiques, R.; Malysheva, E.F.; Marbach, P.A.S.; Marinho, P.; Matocec, N.; McTaggart, A.R.; Mesic, A.; Morin, L.; Munoz-Mohedano, J.M.; Navarro-Rodenas, A.; Nicolli, C.P.; Oliveira, R.L.; Otsing, E.; Ovrebo, C.L.; Pankratov, T.A.; Panos, A.; Paz-Conde, A.; Perez-Sierra, A.; Phosri, C.; Pintos, A.; Posta, A.; Prencipe, S.; Rubio, E.; Saitta, A.; Sales, L.S.; Sanhueza, L.; Shuttleworth, L.A.; Smith, J.; Smith, M.E.; Spadaro, D.; Spetik, M.; Sochor, M.; Sochorova, Z.; Sousa, J.O.; Suwannasa, N.; Tedersoo, L.; Thanh, H.M.; Thao, L.D.; Tkalcec, Z.; Vaghefi, N.; Vaghefi, N.; Venzhik, A.S.; Verbeken, A.; Vizzini, A.; Voyron, S.; Wainhouse, M.; Whalley, A.J.S.; Wrzosek, M.; Zapata, M.; Zeil-Rolfe, I.; Groenewald, Johannes Zacharias (Naturalis Biodiversity Center & Westerdijk Fungal Biodiversity Institute, 2020)
    Novel species of fungi described in this study include those from various countries as follows: Antarctica, Cladosporium arenosum from marine sediment sand. Argentina, Kosmimatamyces alatophylus (incl. Kosmimatamyces gen. ...
  • 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 ...