publications 2023-2022

2023

Däullary T, Imdahl F, Dietrich O, Hepp L, Krammer T, Fey C, Neuhaus W, Metzger M, Vogel J, Westermann AJ, Saliba AE, Zdzieblo D (2023)
A primary cell-based in vitro model of the human small intestine reveals host Olfactomedin-4 induction in response to Salmonella Typhimurium infection
Gut Microbes 15(1):2186109

Dischinger U, Kötzner L, Kovatcheva-Datchary P, Kleinschmidt H, Haas C, Perez J, Presek C, Koschker AC, Miras AD, Hankir MK, Vogel J, Germer CT, Fassnacht M, Herrmann MJ, Seyfried F (2023)
Hypothalamic integrity is necessary for sustained weight loss after bariatric surgery: A prospective, cross-sectional study
Metabolism 138:155341

Fuchs M, Lamm-Schmidt V, Lenče T, Sulzer J, Bublitz A, Wackenreuter J, Gerovac M, Strowig T, Faber F (2023)
A network of small RNAs regulates sporulation initiation in Clostridioides difficile
EMBO Journal doi: 10.15252/embj.2022112858 (Online ahead of print)

Hadjeras L*, Bartel J*, Maier LK*, Maaß S, Vogel V, Svensson SL, Eggenhofer F, Gelhausen R, Müller T, Alkhnbashi OS, Backofen R, Becher D, Sharma CM, Marchfelder A (2023)
Revealing the small proteome of Haloferax volcanii by combining ribosome profiling and small-protein optimised mass spectrometry
µLife (4)uqad001

Hadjeras L, Heiniger B, Maaß S, Scheuer R, Gelhausen R, Azarderakhsh S, Barth-Weber S, Backofen R, Becher D, Ahrens C#, Sharma CM#, Evguenieva-Hackenberg E# (2022)
Unraveling the small proteome of the plant symbiont Sinorhizobium meliloti by ribosome profiling and proteogenomics
µLife (4)uqad012

Hankir MK, Kovatcheva-Datchary P, Springer R, Hoffmann A, Vogel J, Seyfried F, Arora T (2023)
Gut Microbiota Contribution to Weight-Independent Glycemic Improvements after Gastric Bypass Surgery
Microbiology Spectrum doi: 10.1128/spectrum.05109-22 (Epub ahead of print)

Homberger C, Hayward RJ, Barquist L, Vogel J (2023)
Improved bacterial single-cell RNA-seq through automated MATQ-seq and Cas9-based removal of rRNA reads
mBio 14(2):e0355722

Homberger C, Saliba AE, Vogel J (2023)
A MATQ-seq-Based Protocol for Single-Cell RNA-seq in Bacteria
Methods in Molecular Biology 2584:105-12

Hung S, Kasperkowitz A, Kurz F, Dreher L, Diessner J, Ibrahim ES, Schwarz S, Ohlsen K*, Hertlein T* (2023)
Next-generation humanized NSG-SGM3 mice are highly susceptible to Staphylococcus aureus infection
Frontiers in Immunology 14:1127709

Jiao C, Rechstadt C, König F, Homberger C, Yu J, Vogel J, Westermann AJ, Sharma CM, Beisel CL (2023)
RNA recording in single bacterial cells using reprogrammed tracrRNAs
Nature Biotechnology doi: 10.1038/s41587-022-01604-8 (Online ahead of print)

Jung JJ, Popella L, Do PT, Pfau P, Vogel J, Barquist L (2023)
Design and off-target prediction for antisense oligomers targeting bacterial mRNAs with the MASON webserver
RNA rna.079263.122

Kirchner L, Marciniak T, Ziebuhr W, Scherf-Clavel O, Holzgrabe U (2023)
Development, validation and application of a selective and sensitive LC-MS/MS method for the quantification of daptomycin in a suspension of Mammaliicoccus sciuri in Mueller-Hinton broth
Journal of Pharmaceutical and Biomedical Analysis 227:115293

Masota NE, Ohlsen K, Meinel L, Holzgrabe U (2023)
Nature-inspired synthesis of antibacterial glucovanillin derivatives
Fitoterapia 167:105475

Masota NE, Zehe M, Vogg G, Ohlsen K, Meinel L, Holzgrabe U (2023)
Searching for new agents against Enterobacteriaceae from nature: approaches, potential plant species, isolated compounds, and their respective properties
Phytochemistry Reviews doi.org/10.1007/s11101-023-09902-y

Michaux C, Gerovac M, Hansen EE, Barquist L, Vogel J (2023)
Grad-seq analysis of Enterococcus faecalis and Enterococcus faecium provides a global view of RNA and protein complexes in these two opportunistic pathogens
microLife (4)uqac027

Raschig M, Ramírez-Zavala B, Wiest J, Saedtler M, Gutmann M, Holzgrabe U, Morschhäuser J, Meinel L (2023)
Azobenzene derivatives with activity against drug-resistant Candida albicans and Candida auris
Archiv der Pharmazie 356(2):e2200463

Winter SE, Faber F, Bäumler AJ (2023)
Durchfallerreger und die Homöostase der Mikrobiota
Biospektrum 2/2023

2022

Aguilar C, Pauzuolis M, Pompaiah M, Vafadarnejad E, Arampatzi P, Fischer M, Narres D, Neyazi M, Kayisoglu Ö, Sell T, Blüthgen N, Morkel M, Wiegering A, Germer CT, Kircher S, Rosenwald A, Saliba AE, Bartfeld S (2022)
Helicobacter pylori shows tropism to gastric differentiated pit cells dependent on urea chemotaxis
Nature Communications 5;13(1):5878

Ataide MA, Knöpper K, Cruz de Casas P, Ugur M, Eickhoff S, Zou M, Shaikh H, Trivedi A, Grafen A, Yang T, Prinz I, Ohlsen K, Gomez de Agüero M, Beilhack A, Huehn J, Gaya M, Saliba AE, Gasteiger G, Kastenmüller W (2022)
Lymphatic migration of unconventional T cells promotes site-specific immunity in distinct lymph nodes
Immunity 11;55(10):1813-1828.e9

Barthels F, Meyr J, Hammerschmidt SJ, Marciniak T, Rader HJ, Ziebuhr W, Engels B, Schirmeister T (2022)
2-Sulfonylpyrimidines as Privileged Warheads for the Development of S. aureus Sortase A Inhibitors
Frontiers in Molecular Biosciences 8:804970

Bornet E, Westermann AJ (2022)
The ambivalent role of Bacteroides in enteric infections
Trends in Microbiology 30(2):104-108

Brandt P, Gerwien F, Wagner L, Krüger T, Ramıírez-Zavala B, Mirhakkak MH, Schäuble S, Kniemeyer O, Panagiotou G, Brakhage AA, Morschhäuser J, Vylkova S (2022)
Candida albicans SR-like protein kinases regulate different cellular processes: Sky1 is involved in control of ion homeostasis, while Sky2 is important for dipeptide utilization
Frontiers in Cellular and Infection Microbiology 12:850531

Cordero M, García-Fernández J, Acosta IC, Yepes A, Avendano-Ortiz J, Lisowski C, Oesterreicht B, Ohlsen K, Lopez-Collazo E, Förstner KU, Eulalio A, Lopez D (2022)
The induction of natural competence adapts staphylococcal metabolism to infection
Nature Communications 21;13(1):1525

Doorley LA, Rybak JM, Berkow EL, Zhang Q, Morschhäuser J, Rogers PD (2022)
Candida parapsilosis Mdr1B and Cdr1B are drivers of Mrr1-mediated clinical fluconazole resistance
Antimicrobial Agents and Chemotherapy 66:e0028922

Gelhausen R, Müller T, Svensson SL, Alkhnbashi OS, Sharma CM, Eggenhofer F, Backofen R (2022)
RiboReport - benchmarking tools for ribosome profiling-based identification of open reading frames in bacteria
Briefings in Bioinformatics 23(2):bbab549

Gomez-Raya-Vilanova MV, Leskinen K, Bhattacharjee A, Virta P, Rosenqvist P, Smith JLR, Bayfield OW, Homberger C, Kerrinnes T, Vogel J, Pajunen MI, Skurnik M (2022)
The DNA polymerase of bacteriophage YerA41 replicates its T-modified DNA in a primer-independent manner
Nucleic Acids Research 50(7):3985-3997

Halloy F, Biscans A, Bujold KE, Debacker A, Hill AC, Lacroix A, Luige O, Strömberg R, Sundstrom L, Vogel J, Ghidini A (2022)
Innovative developments and emerging technologies in RNA therapeutics
RNA Biology 19(1):313-332

Herrera-Uribe J, Zaldívar-López S, Aguilar C, Entrenas-García C, Bautista R, Claros MG, Garrido JJ (2022)
Study of microRNA expression in Salmonella Typhimurium-infected porcine ileum reveals miR-194a-5p as an important regulator of the TLR4-mediated inflammatory response
Veterinary Research 53(1):35

Hör J, Jung J, Ðurica-Mitić S, Barquist L, Vogel J (2022)
INRI-seq enables global cell-free analysis of translation initiation and off-target effects of antisense inhibitors
Nucleic Acids Research 14:gkac838

Hung S, Dreher L, Diessner J, Schwarz S, Ohlsen K, Hertlein T (2022)
MRSA Infection in the Thigh Muscle Leads to Systemic Disease, Strong Inflammation, and Loss of Human Monocytes in Humanized Mice
Frontiers in Immunology 13:892053

Ibrahim ES, Ohlsen K (2022)
The Old Yellow Enzyme OfrA Fosters Staphylococcus aureus Survival via Affecting Thiol-Dependent Redox Homeostasis
Frontiers in Microbiology 13:888140

Liao C, Sharma S, Svensson SL, Kibe A, Weinberg Z, Alkhnbashi OS, Bischler T, Backofen R, Caliskan N, Sharma CM, Beisel CL (2022)
Spacer prioritization in CRISPR-Cas9 immunity is enabled by the leader RNA
Nature Microbiology 7(4):530-541

Matera G, Altuvia Y, Gerovac M, El Mouali Y, Margalit H, Vogel J (2022)
Global RNA interactome of Salmonella discovers a 5' UTR sponge for the MicF small RNA that connects membrane permeability to transport capacity
Molecular Cell 82(3):629-644.e4

Omran R, Ramírez-Zavala B, Aji Tebung W, Yao S, Feng J, Law C, Dumeaux V, Morschhäuser J, Whiteway M (20222)
The zinc cluster transcription factor Rha1 is a positive filamentation regulator in Candida albicans
Genetics 220:iyab155

Ponath F, Zhu Y, Cosi V, Vogel J (2022)
Expanding the genetic toolkit helps dissect a global stress response in the early-branching species Fusobacterium nucleatum
PNAS 2 4;119(40)

Popella L, Jung J, Do PT, Hayward RJ, Barquist L, Vogel J (2022)
Comprehensive analysis of PNA-based antisense antibiotics targeting various essential genes in uropathogenic Escherichia coli
Nucleic Acids Research 50(11):6435–52

Prezza G, Ryan D, Mädler G, Reichardt S, Barquist L, Westermann AJ (2022)
Comparative genomics provides structural and functional insights into Bacteroides RNA biology
Molecular Microbiology 117(1):67-85

Ramírez-Zavala B, Krüger I, Dunker C, Jacobsen ID, Morschhäuser J (2022)
The protein kinase Ire1 has a Hac1-independent essential role in iron uptake and virulence of Candida albicans
PLoS Pathogens 18(2): e1010283

Schneider C, Erhard F, Binotti B, Buchberger A, Vogel J, Fischer U (2022)
An unusual mode of baseline translation adjusts cellular protein synthesis capacity to metabolic needs
Cell Reports 11;41(2):111467

Schuster EM, Epple MW, Bremser A, Lucht K, Zimmermann J, Polyzou A, Ballabio A, Trompouki E, Vogel J, Büscher J, Westermann AJ, Rambold AS (2022)
Lysosomal signaling induces mitochondrial itaconate synthesis to suppress virulent bacterial growth states in macrophages
Nature Metabolism 4(7):856-866

Seethaler M, Hertlein T, Hopke E, Köhling P, Ohlsen K, Lalk M, Hilgeroth A (2022)
Novel Effective Fluorinated Benzothiophene-Indole Hybrid Antibacterials against S. aureus and MRSA Strains
Pharmaceuticals (Basel) 13;15(9):1138

Solar Venero EC, Matera G, Vogel J, López NI^#, Tribelli PM^# (2022)
Small RNAs in the Antarctic bacterium Pseudomonas extremaustralis responsive to oxygen availability and oxidative stress
Environmental Microbiology Reports Online ahead of print

Umstätter F, Werner J, Zerlin L, Mühlberg E, Kleist C, Klika KD, Hertlein T, Beijer B, Domhan C, Zimmermann S, Ohlsen K, Haberkorn U, Mier W, Uhl P(2022)
Impact of Linker Modification and PEGylation of Vancomycin Conjugates on Structure-Activity Relationships and Pharmacokinetics
Pharmaceuticals (Basel) 28;15(2):159

Vazquez-Laslop N, Sharma CM, Mankin A, Buskirk AR (2022)
Identifying small ORFs in prokaryotes with ribosome profiling
Journal of Bacteriology 18;204(1):e0029421

Yair Y, Michaux C, Biran D, Bernhard J, Vogel J, Barquist L, Ron EZ (2022)
Cellular RNA Targets of Cold Shock Proteins CspC and CspE and Their Importance for Serum Resistance in Septicemic Escherichia coli
mSystems e0008622