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  • Bacterial but Not Fungal Rhizosphere Community Composition Differ among Perennial Grass Ecotypes under Abiotic Environmental Stress 

    Sarkar, Soumyadev; Kamke, Abigail; Ward, Kaitlyn; Rudick, Aoesta K.; Baer, Sara G.; Ran, QingHong; Feehan, Brandi; Thapa, Shiva; Anderson, Lauren; Galliart, Matthew; Jumpponen, Ari; Johnson, Loretta; Lee, Sonny T. M. (American Society for Microbiology, 2022-04-20)
    Environmental change, especially frequent droughts, is predicted to detrimentally impact the North American perennial grasslands. Consistent dry spells will affect plant communities as well as their associated rhizobiomes, ...
  • GWYRE: A Resource for Mapping Variants onto Experimental and Modeled Structures of Human Protein Complexes 

    Malladi, Sukhaswami; Powell, Harold R.; David, Alessia; Islam, Suhail A.; Copeland, Matthew M.; Kundrotas, Petras J.; Sternberg, Michael J. E.; Vakser, Ilya A. (2022-06-15)
    Rapid progress in structural modeling of proteins and their interactions is powered by advances in knowledge-based methodologies along with better understanding of physical principles of protein structure and function. The ...
  • Peptide nanosponges designed for rapid uptake by leukocytes and neural stem cells 

    Yapa, Asanka S.; Wang, Hongwang; Wendel, Sebastian O.; Shrestha, Tej. B.; Kariyawasam, Nilusha L.; Kalubowilage, Madumali; Perera, Ayomi S.; Pyle, Marla; Basel, Matthew T.; Malalasekera, Aruni P.; Manawadu, Harshi; Yu, Jing; Toledo, Yubisela; Ortega, Raquel; Thapa, Prem S.; Smith, Paul E.; Troyer, Deryl L.; Bossmann, Stefan H. (Royal Society of Chemistry, 2018-04-30)
    The structure of novel binary nanosponges consisting of (cholesterol-(K/D)nDEVDGC)3-trimaleimide units possessing a trigonal maleimide linker, to which either lysine (K)20 or aspartic acid (D)20 are tethered, has been ...
  • Discovery of small molecule inhibitors of Plasmodium falciparum apicoplast DNA polymerase 

    Kaur, Supreet; Nieto, Nicholas S.; McDonald, Peter; Beck, Josh R.; Honzatko, Richard B.; Roy, Anuradha; Nelson, Scott W. (Taylor & Francis Open Access, 2022-05-05)
    Malaria is caused by infection with protozoan parasites of the Plasmodium genus, which is part of the phylum Apicomplexa. Most organisms in this phylum contain a relic plastid called the apicoplast. The apicoplast genome ...
  • DOCKGROUND membrane protein-protein set 

    Kotthoff, Ian; Kundrotas, Petras J.; Vakser, Ilya A. (Public Library of Science, 2022-05-17)
    Membrane proteins are significantly underrepresented in Protein Data Bank despite their essential role in cellular mechanisms and the major progress in experimental protein structure determination. Thus, computational ...
  • Hotspots for social and ecological impacts from freshwater stress and storage loss 

    Huggins, Xander; Gleeson, Tom; Kummu, Matti; Zipper, Samuel C.; Wada, Yoshihide; Troy, Tara J.; Famiglietti, James S. (MDPI, 2022-01-21)
    Humans and ecosystems are deeply connected to, and through, the hydrological cycle. However, impacts of hydrological change on social and ecological systems are infrequently evaluated together at the global scale. Here, ...
  • Repurposing Avasimibe to Inhibit Bacterial Glycosyltransferases 

    Hasan, Md Kamrul; El Qaidi, Samir; McDonald, Peter; Roy, Anuradha; Hardwidge, Philip R. (MDPI, 2022-03-17)
    We are interested in identifying and characterizing small molecule inhibitors of bacterial virulence factors for their potential use as anti-virulence inhibitors. We identified from high-throughput screening assays a ...
  • The American Congress Digital Archives Portal Project White Paper 

    Emerling, Danielle; Brumage, Jody; Gard, Sarah D'Antonio; Williamson, Travis (2022-04)
    This white paper documents the work of the American Congress Digital Archives Portal project to aggregate congressional archives into a single, online platform and make them more broadly available. Congressional archives ...
  • Geomorphology variables predict fish assemblages for forested and endorheic rivers of two continents 

    Shields, Robert; Pyron, Mark; Arsenault, Emily R.; Thorp, James H.; Minder, Mario; Artz, Caleb; Costello, John; Otgonganbat, Amarbat; Mendsaikhan, Bud; Altangerel, Solongo; Maasri, Alain (Wiley Open Access, 2021-11-26)
    Stream fishes are restricted to specific environments with appropriate habitats for feeding and reproduction. Interactions between streams and surrounding landscapes influence the availability and type of fish habitat, ...
  • Novel Compound C150 Inhibits Pancreatic Cancer Cell Epithelial-to-Mesenchymal Transition and Tumor Growth in Mice 

    Wang, Tao; Chen, Ping; Dong, Ruochen; Weir, Scott; Baltezor, Michael; Schoenen, Frank J.; Chen, Qi (Frontiers Media, 2021-12-15)
    Pancreatic cancer cell epithelial-to-mesenchymal transition (EMT) is an important contributor to cell invasion and tumor progression. Therefore, targeting EMT may be beneficial for pancreatic cancer treatment. The aim of ...
  • Binding Analysis Using Accelerated Molecular Dynamics Simulations and Future Perspectives 

    Pawnikar, Shristi; Bhattarai, Apurba; Wang, Jinan; Miao, Yinglong (Dove Medical Press, 2021-02-20)
    Biomolecular recognition such as binding of small molecules, nucleic acids, peptides and proteins to their target receptors plays key roles in cellular function and has been targeted for therapeutic drug design. Molecular ...
  • Overcoming Wnt–β-catenin dependent anticancer therapy resistance in leukaemia stem cells 

    Perry, John M.; Tao, Fang; Roy, Anuradha; Lin, Tara; He, Xi C.; Chen, Shiyuan; Lu, Xiuling; Nemechek, Jacqelyn; Ruan, Linhao; Yu, Xiazhen; Dukes, Debra; Moran, Andrea; Pace, Jennifer; Schroeder, Kealan; Zhao, Meng; Venkatraman, Aparna; Qian, Pengxu; Li, Zhenrui; Hembree, Mark; Paulson, Ariel; He, Zhiquan; Xu, Dong; Tran, Thanh-Huyen; Deshmukh, Prashant; Nguyen, Chi Thanh; Kasi, Rajeswari M.; Ryan, Robin; Broward, Melinda; Ding, Sheng; Guest, Erin; August, Keith; Gamis, Alan S.; Godwin, Andrew; Sittampalam, G. Sitta; Weir, Scott J.; Li, Linheng (Nature Research, 2020-04-20)
    Leukaemia stem cells (LSCs) underlie cancer therapy resistance but targeting these cells remains difficult. The Wnt–β-catenin and PI3K–Akt pathways cooperate to promote tumorigenesis and resistance to therapy. In a mouse ...
  • Community structure of soil fungi in a novel perennial crop monoculture, annual agriculture, and native prairie reconstruction 

    McKenna, Thomas P.; Crews, Timothy E.; Kemp, Laura; Sikes, Benjamin A. (Public Library of Science, 2020-01-30)
    The use of perennial crop species in agricultural systems may increase ecosystem services and sustainability. Because soil microbial communities play a major role in many processes on which ecosystem services and sustainability ...
  • The complete mitogenome of Leptestheria brevirostris Barnard, 1924, a rock pool clam shrimp (Branchiopoda: Spinicaudata) from Central District, Botswana 

    Emami-Khoyi, Arsalan; Tladi, Murphy; Dalu, Tatenda; Teske, Peter R.; van Vuuren, Bettine Jansen; Rogers, D. Christopher; Nyamukondiwa, Casper; Wasserman, Ryan J. (Taylor & Francis Open Access, 2021-02-17)
    Spinicaudatan clam shrimp are a widespread and diverse group of branchiopod crustaceans, yet few mitochondrial genomes have been published for this taxonomic group. Here, we present the mitogenome of Leptestheria brevirostris ...
  • Efficient purification and assembly of ribonucleoprotein complex for interaction analysis by MST assay coupled with GaMD simulations 

    Gao, Yunrong; Cao, Dongdong; Pawnikar, Shristi; Akhter, Sana; Miao, Yinglong; Liang, Bo (Cell Press, 2021-03-19)
    Here, we describe a generic protocol for monitoring protein-RNA interaction using a cleavable GFP fusion of a recombinant RNA-binding protein. We detail each expression and purification step, including high salt and heparin ...
  • YM155 Inhibits NleB and SseK Arginine Glycosyltransferase Activity 

    Zhu, Congrui; El Qaidi, Samir; McDonald, Peter; Roy, Anuradha; Hardwidge, Philip R. (MDPI, 2021-02-23)
    The type III secretion system effector proteins NleB and SseK are glycosyltransferases that glycosylate protein substrates on arginine residues. We conducted high-throughput screening assays on 42,498 compounds to identify ...
  • Repurposing p97 inhibitors for chemical modulation of the bacterial ClpB–DnaK bichaperone system 

    Glaza, Przemyslaw; Ranaweera, Chathurange B.; Shiva, Sunitha; Roy, Anuradha; Geisbrecht, Brian V.; Schoenen, Frank J.; Zolkiewski, Michal (Elsevier, 2020-11-13)
    The ClpB–DnaK bichaperone system reactivates aggregated cellular proteins and is essential for survival of bacteria, fungi, protozoa, and plants under stress. AAA+ ATPase ClpB is a promising target for the development of ...
  • A clinically relevant polymorphism in the Na+/taurocholate cotransporting polypeptide (NTCP) occurs at a rheostat position 

    Ruggiero, Melissa J.; Malhotra, Shipra; Fenton, Aron W.; Swint-Kruse, Liskin; Karanicolas, John; Hagenbuch, Bruno (Elsevier, 2020-11-09)
    Conventionally, most amino acid substitutions at “important” protein positions are expected to abolish function. However, in several soluble-globular proteins, we identified a class of nonconserved positions for which ...
  • Costameric integrin and sarcoglycan protein levels are altered in a Drosophila model for Limb-girdle muscular dystrophy type 2H 

    Bawa, Simranjot; Gameros, Samantha; Baumann, Kenny; Brooks, David S.; Kollhoff, Joseph A.; Zolkiewski, Michal; Cecconi, Andrea David Re; Panini, Nicolò; Russo, Massimo; Piccirillo, Rosanna; Johnson, David K.; Kashipathy, Maithri M.; Battaile, Kevin P.; Lovell, Scott; Bouyain, Samuel E. A.; Kawakami, Jessica; Geisbrecht, Erika R. (Springer Nature, 2021-01-28)
    Mutations in two different domains of the ubiquitously expressed TRIM32 protein give rise to two clinically separate diseases, one of which is Limb-girdle muscular dystrophy type 2H (LGMD2H). Uncovering the muscle-specific ...
  • Pathways and Mechanism of Caffeine Binding to Human Adenosine A2A Receptor 

    Do, Hung N.; Akhter, Sana; Miao, Yinglong (Frontiers Media, 2021-04-27)
    Caffeine (CFF) is a common antagonist to the four subtypes of adenosine G-protein-coupled receptors (GPCRs), which are critical drug targets for treating heart failure, cancer, and neurological diseases. However, the ...

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