During 2017 - August 2021, the MIMS Group Leaders, Director and Deputy Director (Leadership), and Clinical Research Fellows published 205 articles in national and international peer-reviewed journals. 124 publications were published by MIMS junior Group Leaders.

MIMS_Full_publications_list_2017-2021.pdf

 

MIMS Publications 2017-2021 (until 08-15-2021)

2021
Published by MIMS Group Leaders
1. Corkery DP, Nadeem A, Aung KM, Hassan A, Liu T, Cervantes-Rivera R, Lystad AH, Wang H, Persson K, Puhar A, Simonsen A, Uhlin BE, Wai SN, Wu YW (2021) Vibrio cholerae cytotoxin MakA induces noncanonical autophagy resulting in the spatial inhibition of canonical autophagy. J Cell Sci. 2021 Feb 23;134(5):jcs252015.
2. Crowe-McAuliffe C, Murina V, Turnbull KJ, Kasari M, Mohamad M, Polte C, Takada H, Vaitkevicius K, Johansson J, Ignatova Z, Atkinson GC, O'Neill AJ, Hauryliuk V, Wilson DN (2021) Structural basis of ABCF-mediated resistance to pleuromutilin, lincosamide, and streptogramin A antibiotics in Gram-positive pathogens. Nature Communications, 2021 12 3577.
3. Crowe-McAuliffe C, Takada H, Murina V, Polte C, Kasvandik S, Tenson T, Ignatova Z, Atkinson G, Wilson DN, Hauryliuk V (2021) Structural Basis for Bacterial Ribosome-Associated Quality Control by RqcH and RqcP. Molecular Cell, 2021 81(1) 115-126.
4. Dernstedt A, Leidig J, Holm A, Kerkman PF, Mjösberg J, Ahlm C, Henriksson J, Hultdin M, Forsell MNE (2021) Regulation of Decay Accelerating Factor primes human germinal center B cells for phagocytosis. Frontiers in immunology. DOI=10.3389/fimmu.2020.599647.
5. Haim-Vilmovsky L, Henriksson J, Walker JA, Miao Z, Natan E, et al. (2021) Mapping RORa expression in resting and activated CD4+ T cells. PLOS one 16(5): e0251233.
6. Jafari S, Henriksson J, Alenius M (2021) Stress and neuronal activity during a critical period regulate odorant receptor expression in Drosophila Melanogaster. PLOS biology. 19(4): e3001101.
7. Jurėnas D, Payelleville A, Roghanian M, Turnbull KJ, Givaudan A, Brillard J, Hauryliuk V, Cascales E (2021) Photorhabdus antibacterial Rhs polymorphic toxin inhibits translation through ADP-ribosylation of 23S ribosomal RNA. Nucleic Acids Res. 2021. doi:10.1093/nar/gkab608.
8. Kerkman PF, Dernstedt A, Tadala L, Mittler E, Dannborg M, Sundling C, Maleki KT, Tauriainen J, Tuiskunen-Bäck A, Wigren Byström J, Ocaya P, Thunberg T, Jangra RK, Román-Sosa G, Guardado-Calvo P, Rey FA, Klingström J, Chandran K, Puhar A, Ahlm C, Forsell MN (2021) Generation of plasma cells and CD27-IgD- B cells during hantavirus infection is associated with distinct pathological findings. Clin Transl Immunology. 2021 Jul 12;10(7):e1313.
9. Kurata T, Brodiazhenko T, Alves Oliveira SR, Roghanian M, Sakaguchi Y, Turnbull KJ, Bulvas O, Takada H, Tamman H, Ainelo A, Pohl R, Rejman D, Tenson T, Suzuki T, Garcia-Pino A, Atkinson GC, Hauryliuk V (2021) RelA-SpoT Homolog toxins pyrophosphorylate the CCA end of tRNA to inhibit protein synthesis. Mol Cell. 2021 Jun 23:S1097-2765(21)00452-4.
10. Mihai IS, Das D, Maršalkaite G, Henriksson J (2021) Meta-Analysis of Gene Popularity: Less Than Half of Gene Citations Stem from Gene Regulatory Networks. MDPI Genes 12(2): 319.
11. Takada H, Crowe-McAuliffe C, Polte C, Sidorova ZY, Murina V, Atkinson GC, Konevega AL, Ignatova Z, Wilson DN, Hauryliuk V (2021) RqcH and RqcP catalyze processive poly-alanine synthesis in a reconstituted ribosome-associated quality control system. Nucleic Acids Res. doi: 10.1093/nar/gkab589.
12. Takada H, Roghanian M, Caballero-Montes J, Van Nerom K, Jimmy S, Kudrin P, Trebini F, Murayama R, Akanuma G, Garcia-Pino A, Hauryliuk V (2021) Ribosome association primes the stringent factor Rel for tRNA-dependent locking in the A-site and activation of (p)ppGpp synthesis. Nucleic Acids Research, 2021 49(1) 444-457.
Review articles:
1. Sixt BS (2021) Host cell death during infection with Chlamydia: a double-edged sword. FEMS Microbiol Rev. 2021 Jan 8;45(1):fuaa043.

Published by MIMS Leadership
1. Avican K, Aldahdooh J, Togninalli M, Mahmud AKMF, Tang J, Borgwardt KM, Rhen M, Fällman M (2021) RNA atlas of human bacterial pathogens uncovers stress dynamics linked to infection. Nat Commun. 2021 Jun 2;12(1):3282.
2. Knöckel J, Dundas K, Yang ASP, Galaway F, Metcalf T, Gemert GV, Sauerwein RW, Rayner JC, Billker O, Wright GJ (2021) Systematic Identification of Plasmodium Falciparum Sporozoite Membrane Protein Interactions Reveals an Essential Role for the p24 Complex in Host Infection. Mol Cell Proteomics. 2021 Jan 27;20:100038.
3. Miguel-Blanco C, Murithi JM, Benavente ED, Angrisano F, Sala KA, van Schalkwyk DA, Vanaerschot M, Schwach F, Fuchter MJ, Billker O, Sutherland CJ, Campino SG, Clark TG, Blagborough AM, Fidock DA, Herreros E, Gamo FJ, Baum J, Delves MJ (2021) The antimalarial efficacy and mechanism of resistance of the novel chemotype DDD01034957. Sci Rep. 2021 Jan 21;11(1):1888.
4. Schneiders S, Hechard T, Edgren T, Avican K, Fällman M, Fahlgren A, Wang H (2021) Spatiotemporal Variations in Growth Rate and Virulence Plasmid Copy Number during Yersinia pseudotuberculosis Infection. Infect Immun. 2021 Mar 17;89(4):e00710-20.
5. Semenas J, Wang T, Sajid Syed Khaja A, Firoj Mahmud A, Simoulis A, Grundström T, Fällman M, Persson JL (2021) Targeted inhibition of ERα signaling and PIP5K1α/Akt pathways in castration-resistant prostate cancer. Mol Oncol. 2021 Apr;15(4):968-986.
6. Tibúrcio M, Hitz E, Niederwieser I, Kelly G, Davies H, Doerig C, Billker O, Voss TS, Treeck M (2021) A 39-Amino-Acid C-Terminal Truncation of GDV1 Disrupts Sexual Commitment in Plasmodium falciparum. mSphere. 2021 May 19;6(3):e01093-20.
Review articles:
1. Chiappino-Pepe A, Pandey V, Billker O (2021) Genome reconstructions of metabolism of Plasmodium RBC and liver stages. Current Opinion in Microbiology. In press.

Published by MIMS Clinical Research Fellows
1. Aldman MH, Rasmussen M, Olaison L, Påhlman LI (2021) Endocarditis due to Staphylococcus lugdunensis-a retrospective national registry-based study. Eur J Clin Microbiol Infect Dis. 2021 May;40(5):1103-1106.
2. Bai X, Narayanan A, Nowak P, Ray S, Neogi U, Sönnerborg A (2021) Whole-Genome Metagenomic Analysis of the Gut Microbiome in HIV-1-Infected Individuals on Antiretroviral Therapy. Front Microbiol. 2021 Jun 25;12:667718. doi: 10.3389/fmicb.2021.667718.
3. Fonseca-Rodríguez O, Gustafsson PE, San Sebastián M, Connolly AF (2021) Spatial clustering and contextual factors associated with hospitalisation and deaths due to COVID-19 in Sweden: a geospatial nationwide ecological study. BMJ Glob Health. 2021 Jul;6(7):e006247. doi: 10.1136/bmjgh-2021-006247.
4. Glans H, Gredmark-Russ S, Olausson M, Falck-Jones S, Varnaite R, Christ W, Maleki KT, Karlberg ML, Broddesson S, Falck-Jones R, Bell M, Johansson N, Färnert A, Smed-Sörensen A, Klingström J, Bråve A (2021) Shedding of infectious SARS-CoV-2 by hospitalized COVID-19 patients in relation to serum antibody responses. BMC Infect Dis. 2021 May 27;21(1):494. doi: 10.1186/s12879-021-06202-8.
5. Katsoularis I, Fonseca-Rodríguez O, Farrington P, Lindmark K, Fors Connolly AM (2021) Risk of acute myocardial infarction and ischaemic stroke following COVID-19 in Sweden: a self-controlled case series and matched cohort study. Lancet. 2021 Jul 29:S0140-6736(21)00896-5. doi: 10.1016/S0140-6736(21)00896-5.
6. Khademi SMH, Gabrielaite M, Paulsson M, Knulst M, Touriki E, Marvig RL, Påhlman LI (2021) Genomic and Phenotypic Evolution of Achromobacter xylosoxidans during Chronic Airway Infections of Patients with Cystic Fibrosis. mSystems. 2021 Jun 29;6(3):e0052321. doi: 10.1128/mSystems.00523-21.
7. Kvedaraite E, Hertwig L, Sinha I, Ponzetta A, Hed Myrberg I, Lourda M, Dzidic M, Akber M, Klingström J, Folkesson E, Muvva JR, Chen P, Gredmark-Russ S, Brighenti S, Norrby-Teglund A, Eriksson LI, Rooyackers O, Aleman S, Strålin K, Ljunggren HG, Ginhoux F, Björkström NK, Henter JI, Svensson M; Karolinska KI/K COVID-19 Study Group (2021) Major alterations in the mononuclear phagocyte landscape associated with COVID-19 severity. Proc Natl Acad Sci U S A. 2021 Feb 9;118(6):e2018587118. doi: 10.1073/pnas.2018587118.
8. Påhlman LI, Manoharan L, Aspelund AS (2021) Divergent airway microbiomes in lung transplant recipients with or without pulmonary infection. Respir Res. 2021 Apr 23;22(1):118. doi: 10.1186/s12931-021-01724-w.
9. Ray S, Narayanan A, Giske CG, Neogi U, Sönnerborg A, Nowak P (2021) Altered Gut Microbiome under Antiretroviral Therapy: Impact of Efavirenz and Zidovudine. ACS Infect Dis. 2021 May 14;7(5):1104-1115. doi: 10.1021/acsinfecdis.0c00536.
10. Sandberg JT, Varnaitė R, Christ W, Chen P, Muvva JR, Maleki KT, García M, Dzidic M, Folkesson E, Skagerberg M, Ahlén G, Frelin L, Sällberg M, Eriksson LI, Rooyackers O, Sönnerborg A, Buggert M, Björkström NK, Aleman S, Strålin K, Klingström J, Ljunggren HG, Blom K, Gredmark-Russ S; Karolinska COVID‐19 Study Group (2021) SARS-CoV-2-specific humoral and cellular immunity persists through 9 months irrespective of COVID-19 severity at hospitalisation. Clin Transl Immunology. 2021 Jul 5;10(7):e1306. doi: 10.1002/cti2.1306.
11. Sperk M, Ambikan AT, Ray S, Singh K, Mikaeloff F, Diez RC, Narayanan A, Vesterbacka J, Nowak P, Sönnerborg A, Neogi U (2021) Fecal metabolome signature in HIV-1 elite control phenotype: Enrichment of dipeptides act as HIV-1 antagonist but Prevotella agonist. J Virol. 2021 Jul 7:JVI0047921.
12. Sperk M, Mikaeloff F, Svensson-Akusjärvi S, Krishnan S, Ponnan SM, Ambikan AT, Nowak P, Sönnerborg A, Neogi U (2021) Distinct lipid profile, low-level inflammation, and increased antioxidant defense signature in HIV-1 elite control status. iScience. 2021 Jan 28;24(2):102111. doi: 10.1016/j.isci.2021.102111.
13. Tranberg A, Klarin B, Johansson J, Påhlman LI (2021) Efficacy of Lactiplantibacillus plantarum 299 and 299v against nosocomial oropharyngeal pathogens in vitro and as an oral prophylactic treatment in a randomized, controlled clinical trial. Microbiologyopen. 2021 Jan;10(1):e1151. doi: 10.1002/mbo3.1151.
Review articles:
1. Blennow O, Vesterbacka J, Nowak P (2021) Tocilizumab bör övervägas i tidigt skede av svår covid-19. Lakartidningen. 2021 Apr 26;118:21047.

 

2020
Published by MIMS Group Leaders
1. Cervantes-Rivera R, Tronnet S, Puhar A (2020) Complete genome sequence and annotation of the laboratory reference strain Shigella flexneri serotype 5a M90T and genome-wide transcriptional start site determination. BMC Genomics 21:285.
2. Cervantes-Rivera R, Puhar A (2020) Whole-genome Identification of Transcriptional Start Sites by Differential RNA-Seq in Bacteria. Bio-protocol 10 (18): e3757.
3. Corkery DP, Nadeem A, Aung KM, Hassan A, Liu T, Cervantes-Rivera R, Lystad AH, Wang H, Persson K, Puhar A, Simonsen A, Uhlin BE, Wai SN, Wu YW (2020) Vibrio cholerae cytotoxin MakA induces noncanonical autophagy resulting in the spatial inhibition of canonical autophagy. J. Cell Sci. jcs.252015 doi: 10.1242/jcs.252015.
4. Ehrenbolger K, Jespersen N, Sharma H, Sokolova YY, Tokarev YS, Vossbrinck CR, Barandun J (2020) Differences in structure and hibernation mechanism highlight diversification of the microsporidian ribosome. PLOS Biology doi.org/10.1371/journal.pbio.3000958.
5. Fluckiger A, Daillère R, Sassi M, Sixt BS, Liu P, Loos F, Richard C, Rabu C, Alou MT, Goubet AG, Lemaitre F, Ferrere G, Derosa L, Duong CPM, Messaoudene M, Gagné A, Joubert P, De Sordi L, Debarbieux L, Simon S, Scarlata CM, Ayyoub M, Palermo B, Facciolo F, Boidot R, Wheeler R, Boneca IG, Sztupinszki Z, Papp K, Csabai I, Pasolli E, Segata N, Lopez-Otin C, Szallasi Z, Andre F, Iebba V, Quiniou V, Klatzmann D, Boukhalil J, Khelaifia S, Raoult D, Albiges L, Escudier B, Eggermont A, Mami-Chouaib F, Nistico P, Ghiringhelli F, Routy B, Labarrière N, Cattoir V, Kroemer G, Zitvogel LK (2020) Cross-reactivity between tumor MHC class I-restricted antigens and an enterococcal bacteriophage. Science 369(6506):936-942
6. Gwon Y-D, Strand M, Lindqvist R, Nilsson E, Saleeb M, Elofsson M, Överby AK, Evander M (2020) Antiviral Activity of Benzavir-2 against Emerging Flaviviruses. Viruses 12(3), 351.
7. Gwon Y-D, Zusinaite E, Merits A, Överby AK, Evander M (2020) N-glycosylation in the Pre-Membrane Protein Is Essential for the Zika Virus Life Cycle. Viruses 12(9), 925.
8. Irie Y, Agnese La Mensa, Murina M, Hauryliuk V, Tenson T, Shingler V (2020) Hfq-assisted RsmA regulation is central to Pseudomonas aeruginosa biofilm polysaccharide PEL expression. Frontiers in Microbiology, 11:482585.
9. Jimmy S, Saha CK, Kurata T, Stavropoulos CG, Oliveira SRA, Koh A, Cepaiskas A, Takada H, Rejman D, Garcia-Pino A, Tenson T, Hauryliuk V, Atkinson GC (2020) A widespread toxin-antitoxin system exploiting growth control via alarmone signaling. Proceedings of the National Academy of Sciences of the United States of America, 117 (19) 10500-10510
10. Kaldalu N, Hauryliuk V, Turnbull K, La Mensa A, Putrins M, Tenson T (2020) In vitro Studies of Persister Cells. Microbiology and Molecular Biology Reviews doi:10.1128/MMBR.00070-20S
11. Keipert S, Lutter D, Schroeder BO, Brandt D, Ståhlman M, Schwarzmayr T, Graf E, Fuchs H, de Angelis MH, Tschöp MH, Rozman J, Jastroch M (2020) Endogenous FGF21-signaling controls paradoxical obesity resistance of UCP1-deficient mice. Nat Commun. 11(1):624
12. Lindqvist R, Rosendal E, Weber E, Asghar N, Schreier S, Lenman A, Johannson M, Dobler G, Bestehorn M, Kröger A, Överby AK (2020) The envelope protein of tick-borne encephalitis virus influences neuron entry, pathogenicity, and vaccine protection. Journal of Neuroinflammation, BMC 17:284.
13. Marr EJ, Milne RM, Anar B, Girling G, Schwach F, Mooney JP, Nahrendorf W, Spence PJ, Cunningham D, Baker DA, Langhorne J, Rayner JC, Billker O, Bushell ES, Thompson J (2020) An enhanced toolkit for the generation of knockout and marker-free fluorescent Plasmodium chabaudi. Wellcome Open Research 5:71.
14. Reimer L, Betzer C, Kofoed RH, Volbracht C, Fog K, Kurhade C, Nilsson E, Överby AK, Jensen PH (2020) PKR kinase directly regulates tau expression and Alzheimer's disease-related tau phosphorylation. Brain Pathology, 31:103-119
15. Rosendal E, Wigren J, Groening R, Yongdae K, Nilsson E, Sharma A, Espaillat A, Hanke L, Thunberg T, McInerney G, Puhar A, Cava F, Karlsson Hedestam GB, Monsen T, Elgh F, Blomkvist B, Marklund I, Ahlm C, Evander M, Normark J, Johansson A, Overby AK, Forsell M (2020) Detection of asymptomatic SARS-CoV-2 exposed individuals by a sensitive S-based ELISA. *medRxiv. 2020 Jun 4:2020.06.02.20120477. *: Preprint
16. Schott BH, Antonia AL, Wang L, Pittman KJ, Sixt BS, Barnes AB, Valdivia RH, Ko DC (2020) Modeling of variables in cellular infection reveals CXCL10 levels are regulated by human genetic variation and the Chlamydia-encoded CPAF protease. Sci Rep: 10(1):18269
17. Schroeder BO, Birchenough GMB, Pradhan M, Nyström EEL, Henricsson M, Hansson GC and Bäckhed F (2020) Obesity-associated microbiota contributes to mucus layer defects in genetically obese mice. J Biol Chem 295: 15712
18. Takada H, Roghanian M, Murina V, Dzhygyr I, Murayama R, Akanuma G, Atkinson GC, Garcia-Pino A, Hauryliuk V (2020) The C-terminal RRM/ACT domain is crucial for fine-tuning the activation of ‘long’ RelA-SpoT Homolog enzymes by ribosomal complexes. Frontiers in Microbiology, 11:277
19. Tamman H, Van Nerom K, Takada H, Vandenberk N, Scholl D, Polikanov Y, Talavera A, Hauryliuk V, Hendrix J, Garcia-Pino A (2020) A nucleotide-switch mechanism mediates opposing catalytic activities of Rel enzymes. Nature Chemical Biology, 16(8):834-840
20. Wallenhammar A, Lindqvist R, Asghar N, Gunaltay S, Fredlund H, Davidsson Å, Andersson S, Överby AK, Johansson M (2020) Revealing new tick-borne encephalitis virus foci by screening antibodies in sheep milk. Parasites & Vectors 13:185.
Review articles:
1. Puértolas-Balint F and Schroeder BO (2020) Does an Apple a Day Also Keep the Microbes Away? The Interplay Between Diet, Microbiota, and Host Defense Peptides at the Intestinal Mucosal Barrier. Front. Immunol. 11:1164. doi: 10.3389/fimmu.2020.01164.
2. Sixt BS (2020) Host cell death during infection with Chlamydia: a double-edged sword. FEMS Microbiol Rev: doi: 10.1093/femsre/fuaa043.
3. Wilson DN, Hauryliuk V, Atkinson GC, O’Neill AJ (2020) Target protection: expanding the paradigm of antibiotic resistance mechanisms. Nature Reviews Microbiology, 18(11):637-648.

Published by MIMS Leadership
1. Adderley JD, von Freyend SJ, Jackson SA, Bird MJ, Burns AL, Anar B, Metcalf T, Semblat J-P, Billker O, Wilson DW, Doerig C (2020) Analysis of erythrocyte signalling pathways during Plasmodium falciparum infection identifies targets for host-directed antimalarial intervention. Nature Communications 11 (1), 1-13.
2. Akkaya M, Bansal A, Sheehan PW, Pena M, Molina-Cruz A, Orchard LM, Cimperman CK, Qi C-F, Ross P, Yazew T, Sturdevant D, Anzick SL, Thiruvengadam G, Otto TD, Billker O, Llinás M, Miller LH, Pierce SK (2020) A single-nucleotide polymorphism in a Plasmodium berghei ApiAP2 transcription factor alters the development of host immunity. Science advances 6 (6), eaaw6957.
3. Akkaya M, Bansal A, Sheehan PW, Pena M, Cimperman CK, Qi CF, Yazew T, Otto TD, Billker O, Miller LH, Pierce SK (2020) Testing the impact of a single nucleotide polymorphism in a Plasmodium berghei ApiAP2 transcription factor on experimental cerebral malaria in mice. Scientific reports 10 (1), 1-11.
4. Firoj Mahmud AKM, Delhomme N, Nandi S, Fällman M (2020) ProkSeq for complete analysis of RNA-Seq data from prokaryotes. Bioinformatics btaa1063, doi:10.1093/bioinformatics/btaa1063.
5. Mahmud AKMF, Nilsson K, Fahlgren A, Navais R, Choudhury R, Avican K, Fällman M (2020) Genome-scale mapping reveals complex regulatory activities of RpoN in Yersinia pseudotuberculosis. mSystems 5:e01006-20. https://doi.org/10.1128/mSystems.01006-20.
6. Marr EJ, Milne RM, Anar B, Girling G, Schwach F, Mooney JP, Nahrendorf W, Spence PJ, Cunningham D, Baker DA, Langhorne J, Rayner JC, Billker O, Bushell ES, Thompson J (2020) An enhanced toolkit for the generation of knockout and marker-free fluorescent Plasmodium chabaudi. Wellcome Open Research 5:71.
7. Raddi G, AB Barletta ABF, Efremov Ma, Ramirez JL, Cantera R, Teichmann SA, Barillas-Mury C, Billker O (2020) Mosquito cellular immunity at single-cell resolution. Science Vol. 369, Issue 6507, pp. 1128-1132.
8. Semenas J, Wang T, Sajid Syed Khaja A, Mahmud AKMF, Simoulis A, Grundström T, Fällman M, Persson JL (2020) Targeted inhibition of ERα signaling and PIP5K1α/Akt pathways in castration-resistant prostate cancer. Molecular Oncology 4:12. https://doi.org/10.1002/1878-0261.12873.
9. Tripathi J, Segeritz CP, Griffiths G, Bushell W, Vallier L, Skarnes WC, Mota MM, Billker O (2020) A Novel Chemically Differentiated Mouse Embryonic Stem Cell-Based Model to Study Liver Stages of Plasmodium berghei. Stem Cell Reports doi.org/10.1016/j.stemcr.2020.04.010
Review articles:
1. Brown KM, Tonkin CJ, Billker O, Sibley LD (2020) Calcium and cyclic nucleotide signaling networks in Toxoplasma gondii. Toxoplasma gondii, 577-605.

Published by MIMS Clinical Research Fellows
1. Aldman MH & Påhlman LI (2020) Evaluation of penicillin G susceptibility testing methods for Staphylococcus lugdunensis. The Journal of antimicrobial chemotherapy. 75 (5): 1206-1211.
2. Aldman MH, Rasmussen M, Olaison L & Påhlman LI (2020) Endocarditis due to Staphylococcus lugdunensis - a retrospective national registry–based study. European Journal of Clinical Microbiology and Infectious Diseases. 196:1.
3. Björck V, Andersson L, Påhlman LI & Bodelsson M (2020) Commercial albumin solution enhances endotoxin-induced vasoplegia and inflammation. Acta Anaesthesiologica Scandinavica. 64 (7), 982-991.
4. Björck V, Påhlman LI, Bodelsson M, Petersson AC & Kander T (2020) Morbidity and mortality in critically ill patients with invasive group A streptococcus infection: an observational study. Critical Care. 24 (1), 302.
5. Cabak A, Hovold G, Petersson AC, Ramstedt M & Påhlman LI (2020) Activity of airway antimicrobial peptides against cystic fibrosis pathogens. Pathogens and Disease. 78, 7, ftaa048.
6. Cederwall S & Påhlman LI (2020) Respiratory adenovirus infections in immunocompetent and immunocompromised adult patients. Epidemiology and Infection. 147, e328.
7. Eimer J, Vesterbacka J, Svensson A-K, Stojanovic B, Wagrell C, Sönnerborg A, Nowak P (2020) Tocilizumab shortens time on mechanical ventilation and length of hospital stay in patients with severe COVID‐19: a retrospective cohort study. Journal of Internal Medicine doi: 10.1111/joim.13162.
8. Frascaroli G, Rossini G, Maltoni V, Bartoletti M, Ortolani P, Gredmark-Russ S, Gelsomino F, Moroni A, Silenzi S, Castellani G, Sambri V, Mastroianni A, Brune W, Varani S (2020) Genetic and Functional Characterization of Toll-Like Receptor Responses in Immunocompetent Patients with CMV Mononucleosis. Front Cell Infect Microbiol. 2020 Aug 7;10:386. doi: 10.3389/fcimb.2020.00386.
9. García M, Kokkinou E, Carrasco García A, Parrot T, Palma Medina LM, Maleki KT, Christ W, Varnaitė R, Filipovic I, Ljunggren HG, Björkström NK, Folkesson E, Rooyackers O, Eriksson LI, Sönnerborg A, Aleman S, Strålin K, Gredmark-Russ S, Klingström J, Mjösberg J; Karolinska KI/K COVID‐19 Study Group (2020) Innate lymphoid cell composition associates with COVID-19 disease severity. Clin Transl Immunology. 2020 Dec 14;9(12):e1224. doi: 10.1002/cti2.1224.
10. Hansson KE, Rosdahl A, Insulander M, Vene S, Lindquist L, Gredmark-Russ S, Askling H (2020) Tick-borne Encephalitis Vaccine Failures: A 10-year Retrospective Study Supporting the Rationale for Adding an Extra Priming Dose in Individuals Starting at Age 50 Years. Clin Infect Dis 01;70(2):245-251.
11. Hansson M, Gustafsson R, Jacquet C, Chebaane N, Thunberg T, Ahlm C, Fors Connolly AM (2020) Cystatin C and α-1-microglobulin predict severe acute kidney injury in patients with hemorrhagic fever with renal syndrome. Pathogens 18: E666.
12. Holmqvist M, Inghammar M, Påhlman L, Boyd J, Åkesson P, Linder A & Kahn F (2020) Risk of bacteremia in patients presenting with shaking chills and vomiting - A prospective cohort study. Epidemiology and Infection 148: e86.
13. Hovold G, Lindberg U, Ljungberg JK, Shannon O & Påhlman LI (2020) BPI-ANCA is expressed in the airways of cystic fibrosis patients and correlates to platelet numbers and Pseudomonas aeruginosa colonization. Respiratory Medicine, 170: 105994.
14. Kulbacka J, Choromańska A, Drąg-Zalesińska M, Nowak P, Baczyńska D, Kotulska M, Bednarz-Misa I, Saczko J, Chwiłkowska A (2020) Proapoptotic activity induced by photodynamic reaction with novel cyanine dyes in caspase-3-deficient human breast adenocarcinoma cell lines (MCF/WT and MCF/DX). Photodiagnosis Photodyn Ther. 2020 Jun;30:101775. doi: 10.1016/j.pdpdt.2020.101775.
15. Nowak P, Maziarz W, Rydosz A, Kowalski K, Ziąbka M, Zakrzewska K (2020) SnO2/TiO2 Thin Film n-n Heterostructures of Improved Sensitivity to NO2. Sensors (Basel). 2020 Nov 29;20(23):6830. doi: 10.3390/s20236830.
16. Parrot T, Gorin JB, Ponzetta A, Maleki KT, Kammann T, Emgård J, Perez-Potti A, Sekine T, Rivera-Ballesteros O; Karolinska COVID-19 Study Group, Gredmark-Russ S, Rooyackers O, Folkesson E, Eriksson LI, Norrby-Teglund A, Ljunggren HG, Björkström NK, Aleman S, Buggert M, Klingström J, Strålin K, Sandberg JK (2020) MAIT cell activation and dynamics associated with COVID-19 disease severity. Sci Immunol. 2020 Sep 28;5(51):eabe1670. doi: 10.1126/sciimmunol.abe1670.
17. Ray S, Narayanan A, Giske CG, Neogi U, Sönnerborg A, and Nowak P (2020) Altered Gut Microbiome under Antiretroviral Therapy: Impact of Efavirenz and Zidovudine. ACS Infectious Diseases DOI: 10.1021/acsinfecdis.0c00536
18. Schmedes C, Grover S, Hisada Y, Goeijenbier M, Hultdin J, Nilsson S, Thunberg T, Ahlm C, Mackman N, Fors Connolly AM (2020) Increased circulating extracellular vesicle tissue factor activity during orthohantavirus infection is associated with intravascular coagulation. J Infec Dis. 222: 1392-1399
19. Sekine T, Perez-Potti A, Rivera-Ballesteros O, Strålin K, Gorin JB, Olsson A, Llewellyn-Lacey S, Kamal H, Bogdanovic G, Muschiol S, Wullimann DJ, Kammann T, Emgård J, Parrot T, Folkesson E; Karolinska COVID-19 Study Group, Rooyackers O, Eriksson LI, Henter JI, Sönnerborg A, Allander T, Albert J, Nielsen M, Klingström J, Gredmark-Russ S, Björkström NK, Sandberg JK, Price DA, Ljunggren HG, Aleman S, Buggert M (2020) Robust T Cell Immunity in Convalescent Individuals with Asymptomatic or Mild COVID-19. Cell. 2020 Oct 1;183(1):158-168.e14. doi: 10.1016/j.cell.2020.08.017.
20. Sekine T, Perez-Potti A, Nguyen S, Gorin J-B, Wu VH, Gostick E, Llewellyn-Lacey S, Hammer Q, Falck-Jones S, Vangeti S, Yu M, Smed-Sörensen A, Gaballa A, Uhlin M, Sandberg JK, Brander C, Nowak P, Goepfert PA, Price DA, Betts MR, Buggert M (2020) TOX is expressed by exhausted and polyfunctional human effector memory CD8 T cells. Sci Immunol 07;5(49).
21. Sperk M, Ambikan A, Ray S, Singh K, Mikaeloff F, Diez RC, Narayanan A, Vesterbacka J, Nowak P, Sönnerborg A, Neogi U (2020) Novel mechanism of HIV elite control by enriching gut dipeptides as HIV-1 antagonist but Prevotella agonist. doi:10.21203/rs.3.rs-100746/v1.
22. Sperk M, Mikaeloff F, Svensson-Akusjärvi S, Krishnan S, Ponnan SM, Ambikan AT, Nowak P, Sönnerborg A, Neogi U (2020) Distinct Lipid Profile, Low-Level Inflammation and Increased Antioxidant Defense as a Signature in HIV-1 Elite Control Status. bioRxiv 10.1101/2020.07.02.183756*2021, iScience 24,102111
23. Tranberg A, Klarin B, Johansson J & Påhlman LI (2020) Efficacy of Lactiplantibacillus plantarum 299 and 299v against nosocomial oropharyngeal pathogens in vitro and as an oral prophylactic treatment in a randomized, controlled clinical trial. Microbiology Open. doi.org/10.1002/mbo3.1151.
24. Varnaitė R, García M, Glans H, Maleki KT, Sandberg JT, Tynell J, Christ W, Lagerqvist N, Asgeirsson H, Ljunggren H-G, Ahlén G, Frelin L, Sällberg M, Blom K, Klingström J, Gredmark-Russ S (2020) Expansion of SARS-CoV-2-Specific Antibody-Secreting Cells and Generation of Neutralizing Antibodies in Hospitalized COVID-19 Patients. J Immunol 11;205(9):2437-2446
25. Varnaitė R, Blom K, Lampen MH, Vene S, Thunberg S, Lindquist L, Ljunggren H-G, Rombo L, Askling HH and Gredmark-Russ S (2020) Magnitude and Functional Profile of the Human CD4+ T Cell Response throughout Primary Immunization with Tick-Borne Encephalitis Virus Vaccine. J Immunol 02;204(4):914-922
26. Woźniak M, Mrówczyńska L, Kwaśniewska-Sip P, Waśkiewicz A, Nowak P, Ratajczak I (2020) Effect of the Solvent on Propolis Phenolic Profile and its Antifungal, Antioxidant, and In Vitro Cytoprotective Activity in Human Erythrocytes Under Oxidative Stress. Molecules. 2020 Sep 17;25(18):4266. doi: 10.3390/molecules25184266.
Review articles:
1. Kan B, Ahl M, Blennow O, Eriksson P, Nowak P, Parke Å, Stojanovic B, Tovatt T, Vesterbacka J (2020) Tidiga erfarenheter av steroidbehandling vid covid-19. Lakartidningen 10 6;117.
2. Nowak P, Liszniański P, Nowak J (2020) Nawracające częstoskurcze komorowe jako przyczyna dekompensacji układu krążenia w przypadku różnych chorób współtowarzyszących [Recurrent ventricular tachycardia as a cause of circulatory decompensation in the case of various comorbid diseases]. Pol Merkur Lekarski. 2020 Apr 22;48(284):97-99.

 

2019
Published by MIMS Group Leaders
1. Amon JD, Yadav AK, Ramirez-Guadiana FH, Meeske AJ, Cava F, Rudner DZ (2019) SwsB and SafA are required for CwlJ-dependent spore germination in Bacillus subtilis. J Bacteriol. pii: JB.00668-19.
2. Barandun J, Hunziker M, Vossbrinck CR, Klinge S (2019) Evolutionary compaction and adaptation visualized by the structure of the dormant microsporidian ribosome. Nature Microbiology 4, 1798–1804.
3. Bernardo-García N, Sánchez-Murcia PA, Espaillat A, Martínez-Caballero S, Cava F, Hermoso JA, Gago F (2019) Cold-induced aldimine bond cleavage by Tris in Bacillus subtilis alanine racemase. Org Biomol Chem. 17(17):4350-4358.
4. Birchenough GMB, Schroeder BO, Bäckhed F and Hansson, GC (2019) Dietary destabilisation of the balance between the microbiota and the colonic mucus barrier. Gut Microbes 10:2, 246-250.
5. Chauhan D, Srivastava PA, Ritzl B, Yennamalli RM, Cava F, Priyadarshini R (2019) Amino Acid-Dependent Alterations in Cell Wall and Cell Morphology of Deinococcus indicus DR1. Front Microbiol. 10:1449.
6. Erttmann SF, Gekara NO (2019) Hydrogen peroxide release by bacteria suppresses inflammasome-dependent innate immunity. Nature Communications 10: 3493.
7. Filcek K, Vielfort K, Muraleedharan S, Henriksson J, Valdivia RH, Bavoil PM, Sixt BS (2019) Insertional mutagenesis in the zoonotic pathogen Chlamydia caviae. PLoS One 14(11):e0224324.
8. Fleurie A, Zoued A, Alvarez L, Hines KM, Cava F, Xu L, Davis BM, Waldor MK (2019) A Vibrio cholerae BolA-Like Protein Is Required for Proper Cell Shape and Cell Envelope Integrity. MBio. 10(4). pii: e00790-19.
9. Gallagher LA, Shears RK, Fingleton C, Alvarez L, Waters EM, Clarke J, Bricio-Moreno L, Campbell C, Yadav AK, Razvi F, O’Neill E, O’Neill AJ, Cava F, Fey PD, Kadioglu A, O’Gara JP (2019) Impaired alanine transport or exposure to d-cycloserine increases the susceptibility of MRSA to β-lactam antibiotics. J Infect Dis. pii: jiz542. doi: 10.1093/infdis/jiz542.
10. Gekara NO, Jiang H (2019) The innate immune DNA sensor cGAS: A membrane, cytosolic, or nuclear protein? Sci Signal. 2019 May 14;12(581):eaax3521.
11. Henriksson J, Chen X, Gomes T, Ullah U, Meyer KB, Miragaia R, Duddy R, Pramanik K, Yusa K, Lahesmaa R, Teichmann SA (2019) Genome-wide CRISPR screens in T helper cells reveal pervasive cross-talk between activation and differentiation. Cell. 176:4.
12. Hillier C, Pardo M, Yu L, Bushell E, Sanderson T, Metcalf T, Herd C, Anar B, Rayner JC, Billker O, Choudhary JS (2019) Landscape of the Plasmodium Interactome Reveals Both Conserved and Species-Specific Functionality. Cell Rep. 28(6):1635-1647.e5.
13. Howell M, Aliashkevich A, Sundararajan K, Daniel JJ, Lariviere PJ, Goley ED, Cava F, Brown PJB (2019) Agrobacterium tumefaciens divisome proteins regulate the transition from polar growth to cell division. Molecular Microbiology 111: 1074-1092.
14. Hsu YP, Hall E, Booher G, Murphy B, Radkov AD, Yablonowski J, Mulcahey C, Alvarez L, Cava F, Brun YV, Kuru E, VanNieuwenhze MS (2019) Fluorogenic D-amino acids enable real-time monitoring of peptidoglycan biosynthesis and high-throughput transpeptidation assays. Nat Chem. 11(4):335-341.
15. Hunziker M, Barandun J, Buzovetsky O, Steckler C, Molina H, Klinge S (2019) Conformational switches control early maturation of the eukaryotic small ribosomal subunit. Elife 2019;8:e45185.
16. Irazoki O, Hernandez SB, Cava F (2019) Peptidoglycan Muropeptides: Release, Perception, and Functions as Signaling Molecules. Front Microbiol. 10:500. doi:10.3389/fmicb.2019.00500.
17. Jacquier N, Yadav AK, Pillonel T, Viollier PH, Cava F, Greub G (2019) A SpoIID Homolog Cleaves Glycan Strands at the Chlamydial Division Septum. MBio. 10(4). pii: e01128-19.
18. Jiang H, Panda S, Gekara NO (2019) Comet and micronucleus assays for analyzing DNA damage and genome integrity. Methods Enzymol. 2019;625:299-307.
19. Jiang H, Xue X, Panda S, Kawale A, Hooy RM, Liang F, Sohn J, Sung P, Gekara NO (2019) Chromatin-bound cGAS is an inhibitor of DNA repair and hence accelerates genome destabilization and cell death. EMBO J. 2019 Oct 4;38(21):e102718. doi: 10.15252/embj.2019102718.
20. Jõers A, Vind K, Hernández SB, Maruste R, Pereira M, Brauer A, Remm M, Cava F, Tenson T (2019) Muropeptides Stimulate Growth Resumption from Stationary Phase in Escherichia coli. Sci Rep. 9(1):18043.
21. Kaldalu N, Maiväli Ü, Hauryliuk V, Tenson T (2019) Reanalysis of Proteomics Results Fails To Detect MazF-Mediated Stress Proteins. mBio, 10(3):e00949-19.
22. Kasari V, Margus T, Atkinson GC, Johansson MJO, Hauryliuk V (2019) Ribosome profiling analysis of eEF3-depleted Saccharomyces cerevisiae. Scientific Reports, 9:3037.
23. Kasari V, Pochopien AA, Margus T, Murina V, Turnbull K, Zhou Y, Nissan T, Graf M, Nováček J, Atkinson GC, Johansson MJO, Wilson DN, Hauryliuk V (2019) A role for the Saccharomyces cerevisiae ABCF protein New1 in translation termination/recycling. Nucleic Acids Research, 47(16):8807-8820.
24. Kuru E, Radkov A, Meng X, Egan A, Alvarez L, Dowson A, Booher G, Breukink E, Roper DI, Cava F, Vollmer W, Brun Y, VanNieuwenhze MS (2019) Mechanisms of Incorporation for D-Amino Acid Probes That Target Peptidoglycan Biosynthesis. ACS Chem Biol. 14(12):2745-2756.
25. Murphy SG, Alvarez L, Adams MC, Liu S, Chappie JS, Cava F, Dörr T (2019) Endopeptidase Regulation as a Novel Function of the Zur-Dependent Zinc Starvation Response. mBio 19;10(1). pii:e02620-18. doi: 10:e02620-18.
26. Panda S, Jiang H, Gekara NO (2019) TUBE and UbiCRest assays for elucidating polyubiquitin modifications in protein complexes. Methods Enzymol. 2019;625:339-350.
27. Rodrigues R, Danskog K, Överby AK, Arnberg N (2019) Characterizing the cellular attachment receptor for Langat virus. PLoS ONE, Vol. 14 doi:10.1371/journal.pone.0217359.
28. Sharma A, Puhar A (2019) Gentamicin Protection Assay to Determine the Number of Intracellular Bacteria during Infection of Human TC7 Intestinal Epithelial Cells by Shigella flexneri. Bio-protocol 9 (13): e3292.
29. Sharma A, Puhar A (2019) Plaque Assay to Determine Invasion and Intercellular Dissemination of Shigella flexneri in TC7 Human Intestinal Epithelial Cells. Bio-Protocol 9 (13): e3293.
30. Sixt BS, Núñez-Otero C, Kepp O, Valdivia RH, Kroemer G (2019) Chlamydia trachomatis fails to protect its growth niche against pro-apoptotic insults. Cell Death Differ. 2019 Aug;26(8):1485-1500.
31. Stanway RR, Bushell E, Chiappino-Pepe A, Roques M, Sanderson T, Franke-Fayard B, Caldelari R, Golomingi M, Nyonda M, Pandey V, Schwach F, Chevalley S, Ramesar J, Metcalf T, Herd C, Burda P-C, Rayner JC, Soldati-Favre D, Janse CJ, Hatzimanikatis V, Billker O, Heussler VT (2019) Genome-Scale Identification of Essential Metabolic Processes for Targeting the Plasmodium Liver Stage. Cell 14;179 (5):1112-1128.
32. Swacha P, Gekara NO, Erttmann SF (2019) Biochemical and microscopic analysis of inflammasome complex formation. Methods Enzymol. 2019;625:287-298. doi: 10.1016/bs.mie.2019.05.014.
33. Torrens G, Hernández SB, Ayala JA, Moya B, Juan C, Cava F, Oliver A (2019) Regulation of AmpC-Driven β-Lactam Resistance in Pseudomonas aeruginosa: Different Pathways, Different Signaling. mSystems 4(6). pii: e00524-19.
34. Turnbull KJ, Dzhygyr I, Lindemose S, Hauryliuk V, Roghanian M (2019) Intramolecular interactions dominate the autoregulation of Escherichia coli stringent factor RelA. Frontiers in Microbiology, 10:1966.
35. Uckeley ZM, Moeller R, Kühn LI, Nilsson E, Robens C, Lasswitz L, Lindqvist R, Lenman A, Passos V, Voss Y, Sommerauer C, Kampmann M, Goffinet C, Meissner F, Överby AK, Lozach P-Y, Gerold G (2019) Quantitative Proteomics of Uukuniemi Virus-host Cell Interactions Reveals GBF1 as Proviral Host Factor for Phleboviruses. Molecular & Cellular Proteomics, American Society for Biochemistry and Molecular Biology 18, (12):2401-2417.
36. Van Nerom K, Tamman H, Takada H, Hauryliuk V, Garcia-Pino A (2019) The Rel stringent factor from Thermus thermophilus: crystallization and X-ray analysis. Acta Crystallographica Section F-Structural Biology Communications 75: 561-569.
37. Van Nerom K, Tamman H, Takada H, Hauryliuk V, Garcia-Pino A (2019) Crystallization and X-ray analysis of the Rel stringent factor from Thermus thermophilus. Acta Cryst. F75, 561-569.
38. Volk JK, Nyström EEL, van der Post S, Abad BM, Schroeder BO, Johansson Å, Svensson F, Jäverfelt S, Johansson MEV, Hansson GC, Birchenough GMH (2019) The Nlrp6 inflammasome is not required for baseline colonic inner mucus layer formation or function. J Exp Med. 216 (11):2602-2618.
39. Wendler J, Schroeder BO*, Ehmann D, Koeninger L, Mailänder-Sánchez D, Lemberg C, Wanner S, Schaller S, Stange EF, Malek N, Weidenmaier C, LeibundGut-Landmann S, Wehkamp J (2019) Proteolytic Degradation of reduced Human Beta Defensin 1 generates a Novel Antibiotic Octapeptide. Sci. Rep. 6;9(1):3640.
40. Yau W-L, Nguyen-Dinh V, Larsson E, Lindqvist R, Överby AK, Lundmark R (2019) Model System for the Formation of Tick-Borne Encephalitis Virus Replication Compartments without Viral RNA Replication. Journal of Virology, AMER SOC MICROBIOLOGY, 93(18): e00292-19.
41. Zbornikova E, Knejzlik Z, Hauryliuk V, Krasny L, Rejman D (2019) Analysis of Nucleotide Pools in Bacteria Using HPLC-MS in HILIC Mode. Talanta, 205:120161.
Review articles:
1. Ruzek D, Županc TA, Borde J, Chrdle A, Eyer L, Karganova G, Kholodilov I, Knap N, Kozlovskaya L, Matveev A, Miller AD, Osolodkin DI, Överby AK, Tikunova N, Tkachev S, Zajkowska J (2019) Tick-borne encephalitis in Europe and Russia: review of pathogenesis, clinical features, therapy, and vaccines. Antiviral Research 164:23-51.
2. Schroeder BO (2019) Fight them or feed them: how the intestinal mucus layer manages the gut microbiota. Gast. Report 7(1), 3-12.
3. Stange EF & Schroeder BO (2019) Microbiota and mucosal defense in IBD: an update. Expert Rev. Gastroenterol. Hepatol. 13(10):963-976.

Published by MIMS Leadership
1. Abbara A, Rawson TM, Karah N, El-Amin W, Hatcher J, Tajaldin B, Dar O, Dewachi O, Abu Sitta G, Uhlin BE, Sparrow A (2018) Antimicrobial resistance in the context of the Syrian conflict: Drivers before and after the onset of conflict and key recommendations. Int J Infect Dis 73: 1-6.
2. Abbara A, Rawson TM, Karah N, El-Amin W, Hatcher J, Tajaldin B, Dar O, Dewachi O, Abu Sitta G, Uhlin BE, Sparrow A (2018) A summary and appraisal of existing evidence of antimicrobial resistance in the Syrian conflict. Int J Infect Dis 75: 26-33.
3. Hillier C, Pardo M, Yu L, Bushell E, Sanderson T, Metcalf T, Herd C, Anar B, Rayner JC, Billker O, Choudhary JS (2019) Landscape of the Plasmodium Interactome Reveals Both Conserved and Species-Specific Functionality. Cell Rep. 28(6):1635-1647.e5.
4. Howick VM, Russel AJC, Andrews T, Heaton H, Reid AJ, Natarajan K, Butungi H, Metfcalf T, Verzier LH, Rayner JC, Berriman M, Herren JK, Billker O, Hemberg M, Talman AM, Lawniczak MKN (2019) The Malaria Cell Atlas: Single parasite transcriptomes across the complete Plasmodium life cycle. Science 365 (6455), eaaw2619.
5. Stanway RR, Bushell E, Chiappino-Pepe A, Roques M, Sanderson T, Franke-Fayard B, Caldelari R, Golomingi M, Nyonda M, Pandey V, Schwach F, Chevalley S, Ramesar J, Metcalf T, Herd C, Burda P-C, Rayner JC, Soldati-Favre D, Janse CJ, Hatzimanikatis V, Billker O, Heussler VT (2019) Genome-Scale Identification of Essential Metabolic Processes for Targeting the Plasmodium Liver Stage. Cell 14;179 (5):1112-1128.
6. Taheri N, Fällman M, Wai SN, Fahlgren A (2019) Accumulation of virulence-associated proteins in Campylobacter jejuni Outer Membrane Vesicles at human body temperature. Journal of Proteomics 195: 33-40.

Published by MIMS Clinical Research Fellows
1. Babu H, Ambikan AT, Gabriel EE, Akusjärvi SS, Palaniappan AN, Sundaraj V, Mupanni NR, Sperk M, Cheedarla N, Sridhar R, Tripathy SP, Nowak P, Hanna LE, Neogi U (2019) Systemic Inflammation and the Increased Risk of Inflamm-Aging and Age-Associated Diseases in People Living With HIV on Long Term Suppressive Antiretroviral Therapy. Front Immunol 27;10:1965.
2. Babu H, Sperk M, Ambikan AT, Rachel G, Viswanathan VK, Tripathy SP, Nowak P, Hanna LE, Neogi U (2019) Plasma Metabolic Signature and Abnormalities in HIV-Infected Individuals on Long-Term Successful Antiretroviral Therapy. Metabolites 30;9(10).
3. Nowak A, Hedenstierna M, Ursing J, Lidman C, Nowak P (2019) Efficacy of Routine Fecal Microbiota Transplantation for Treatment of Recurrent Infection: A Retrospective Cohort Study. Int J Microbial 1;2019:7395127.
4. Storm-Larsen C, Stiksrud B, Eriksen C, Nowak P, Holm K, Thalme A, Dyrhol-Riise AM, Brix S, Hov JR, Trøseid M (2019) Microbial translocation revisited: targeting the endotoxic potential of gut microbes in HIV-infected individuals. AIDS. 2019 Mar 15;33(4):645-653. doi: 10.1097/QAD.0000000000002087.

 

2018
Published by MIMS Group Leaders
1. Aliashkevich A, Alvarez L, Cava F (2018) New Insights into the Mechanisms and Biological Roles of D-Amino Acids in Complex Eco-Systems. Front Microbiol 9: 683.
2. Alvarez L, Aliashkevich A, de Pedro MA, Cava F (2018) Bacterial secretion of D-arginine controls environmental microbial biodiversity. Isme J 12: 438-450.
3. Böhme U, Otto TD, Cotton JA, Steinbiss S, Sanders M, Oyola SO, Nicot A, Gandon S, Patra KP, Herd C, Bushell E, Modrzynska KK, Billker O, Vinetz JM, Rivero A, Newbold CI, Berriman M (2018) Complete avian malaria parasite genomes reveal features associated with lineage-specific evolution in birds and mammals. Genome Res. 2018 Apr;28(4):547-560.
4. Brodiazhenko T, Johansson MJO, Takada H, Nissan T, Hauryliuk V, Murina V (2018) Elimination of Ribosome Inactivating Factors Improves the Efficiency of Bacillus subtilis and Saccharomyces cerevisiae Cell-Free Translation Systems. Frontiers in Microbiology 9: 8.
5. Bueno E, Sit B, Waldor MK, Cava F (2018) Anaerobic nitrate reduction divergently governs population expansion of the enteropathogen Vibrio cholerae. Nat Microbiol 3: 1346-1353.
6. Carcamo JRP, Morell ML, Vazquez CA, Vatansever S, Upadhyay AS, Överby AK, Cordo SM, Garcia CC (2018) The interplay between viperin antiviral activity, lipid droplets and Junin mammarenavirus multiplication. Virology 514: 216-229.
7. Chahlafi Z, Alvarez L, Cava F, Berenguer J (2018) The role of conserved proteins DrpA and DrpB in nitrate respiration of Thermus thermophilus. Environmental Microbiology 20: 3851-3861.
8. Crowe-McAuliffe C, Graf M, Huter P, Takada H, Abdelshahid M, Novacek J, Murina V, Atkinson GC, Hauryliuk V, Wilson DN (2018) Structural basis for antibiotic resistance mediated by the Bacillus subtilis ABCF ATPase VmlR. Proceedings of the National Academy of Sciences of the United States of America 115: 8978-8983.
9. Flahou B, Rossi M, Bakker J, Langermans JAM, Heuvelman E, Solnick JV, Martin ME, O'Rourke J, Ngoan LD, Hoa NX, Nakamura M, Överby AK, Matsui H, Ota H, Matsumoto T, Foss DL, Kopta LA, Omotosho O, Franciosini MP, Proietti PC et al. (2018) Evidence for a primate origin of zoonotic Helicobacter suis colonizing domesticated pigs. Isme J 12: 77-86.
10. Goormaghtigh F, Fraikin N, Putrins M, Hallaert T, Hauryliuk V, Garcia-Pino A, Sjoodin A, Kasvandik S, Udekwu K, Tenson T, Kaldalu N, Van Melderen L (2018) Reassessing the Role of Type II Toxin-Antitoxin Systems in Formation of Escherichia coli Type II Persister Cells. Mbio 9: 14.
11. Kouidmi I, Alvarez L, Collet JF, Cava F, Paradis-Bleau C (2018) The Chaperone Activities of DsbG and Spy Restore Peptidoglycan Biosynthesis in the elyC Mutant by Preventing Envelope Protein Aggregation. Journal of Bacteriology 200: e00245-18.
12. Kulen M, Lindgren M, Hansen S, Cairns AG, Grundström C, Begum A, van der Lingen I, Brannström K, Hall M, Sauer UH, Johansson J, Sauer-Eriksson AE and Almqvist F (2018) Structure-Based Design of Inhibitors Targeting PrfA, the Master Virulence Regulator of Listeria monocytogenes. J Med Chem 61(9), 4165-4175.
13. Kumar K, Cava F (2018) Integrating network analysis with chromatography: introducing a novel chemometry-chromatography based analytical procedure to classify the bacterial cell wall collection. Anal Methods 10: 1172-1180.
14. Kumar K, Cava F (2018) Principal coordinate analysis assisted chromatographic analysis of bacterial cell wall collection: A robust classification approach. Analytical Biochemistry 550: 8-14.
15. Kurhade C, Schreier S, Lee YP, Zegenhagen L, Hjertqvist M, Dobler G, Kroger A, Överby AK (2018) Correlation of Severity of Human Tick-Borne Encephalitis Virus Disease and Pathogenicity in Mice. Emerging Infectious Diseases 24: 1709-1712.
16. Lindqvist R, Upadhyay A, Överby AK (2018) Tick-Borne Flaviviruses and the Type I Interferon Response. Viruses 10(7): 340.
17. Lindqvist R, Kurhade C, Gilthorpe JD, Överby AK (2018) Cell-type- and region-specific restriction of neurotropic flavivirus infection by viperin. Journal of Neuroinflammation 15: 11.
18. Lindqvist R, Överby AK (2018) The Role of Viperin in Antiflavivirus Responses. DNA Cell Biol 37: 725-730
19. Lund H, Pieber M, Parsa R, Han JM, Grommisch D, Ewing E, Kular L, Needhamsen M, Espinosa A, Nilsson E, Överby AK, Butovsky O, Jagodic M, Zhang XM, Harris RA (2018) Competitive repopulation of an empty microglial niche yields functionally distinct subsets of microglia-like cells. Nature Communications 9: 13.
20. Manav MC, Beljantseva J, Bojer MS, Tenson T, Ingmer H, Hauryliuk V, Brodersen DE (2018) Structural basis for (p)ppGpp synthesis by the Staphylococcus aureus small alarmone synthetase RelP. Journal of Biological Chemistry 293: 3254-3264.
21. Murina V, Kasari M, Hauryliuk V, Atkinson GC (2018) Antibiotic resistance ABCF proteins reset the peptidyl transferase centre of the ribosome to counter translational arrest. Nucleic Acids Research 46: 3753-3763.
22. Nakamura M, Överby AK, Takakashi S, Murayama SY, Matsui H (2018) Parietal cell damage by viable Helicobacter suis could be closely related to the formation of the gastric MALT lymphoma formation in C57BL/6 Infection Model. Helicobacter 23: 1.
23. Orrego AH, Lopez-Gallego F, Espaillat A, Cava F, Guisan JM, Rocha-Martin J (2018) One‐step Synthesis of α‐Keto Acids from Racemic Amino Acids by A Versatile Immobilized Multienzyme Cell‐free System. ChemCatChem 10: 3002-3011.
24. Panayiotou C, Lindqvist R, Kurhade C, Vonderstein K, Pasto J, Edlund K, Upadhyay AS, Överby AK (2018) Viperin Restricts Zika Virus and Tick-Borne Encephalitis Virus Replication by Targeting NS3 for Proteasomal Degradation. Journal of Virology 92: 13.
25. Panda S, Gekara NO (2018) The deubiquitinase MYSM1 dampens NOD2-mediated inflammation and tissue damage by inactivating the RIP2 complex. Nature Communications 9: 13.
26. Peña Cárcamo JR, Morell ML, Vázquez CA, Vatansever S, Upadhyay AS, Överby AK, Cordo SM, García CC (2018) The interplay between viperin antiviral activity, lipid droplets and Junín mammarenavirus multiplication. Virology. 2018 Jan 15;514:216-229.
27. Quereda JJ, Andersson C, Cossart P, Johansson J and Pizarro-Cerda J (2018) Role in virulence of phospholipases, listeriolysin O and listeriolysin S from epidemic Listeria monocytogenes using the chicken embryo infection model. Vet Res 49(1), 13.
28. Vonderstein K, Nilsson E, Hubel P, Skalman LN, Upadhyay A, Pasto J, Pichlmair A, Lundmark R, Överby AK (2018) Viperin Targets Flavivirus Virulence by Inducing Assembly of Noninfectious Capsid Particles. Journal of Virology 92: 15
29. Yadav AK, Espaillat A, Cava F (2018) Bacterial Strategies to Preserve Cell Wall Integrity Against Environmental Threats. Frontiers in Microbiology 9: 9

Published by MIMS Leadership
1. Böhme U, Otto TD, Cotton JA, Steinbiss S, Sanders M, Oyola SO, Nicot A, Gandon S, Patra KP, Herd C, Bushell E, Modrzynska KK, Billker O, Vinetz JM, Rivero A, Newbold CI, Berriman M (2018) Complete avian malaria parasite genomes reveal features associated with lineage-specific evolution in birds and mammals. Genome Res. 2018 Apr;28(4):547-560.
2. Dongre M, Singh B, Aung KM, Larsson P, Miftakhova R, Persson K, Askarian F, Johanessen M, von Hofsten J, Persson JL, Erhardt M, Tuck S, Uhlin BE, Wai SN (2018) Flagella-mediated secretion of a novel Vibrio cholerae cytotoxin affecting both vertebrate and invertebrate hosts. Communications Biology, Springer Nature Publishing AG 2018, Vol. 1.
3. Dongre M, Singh B, Aung KM, Larsson P, Miftakhova R, Persson K, Askarian F, Johannessen M, von Hofsten J, Persson JL, Erhardt M, Tuck S, Uhlin BE, Wai SN (2018) Flagella-mediated secretion of a novel Vibrio cholerae cytotoxin affecting both vertebrate and invertebrate hosts. Commun Biol 1: 59.
4. Fang H, Gomes AR, Klages N, Pino P, Maco B, Walker EM, Zenonos ZA, Angrisano F, Baum J, Doerig C, Baker DA, Billker O, Brochet M (2018) Epistasis studies reveal redundancy among calcium-dependent protein kinases in motility and invasion of malaria parasites. Nature Communications 9 2018 Oct 12;9(1):4248.
5. Nakao R, Myint SL, Wai SN, Uhlin BE (2018) Enhanced Biofilm Formation and Membrane Vesicle Release by Escherichia coli Expressing a Commonly Occurring Plasmid Gene, kil. Frontiers in Microbiology 9: 18.
6. Taheri N, Mahmud A, Sandblad L, Fällman M, Wai SN, Fahlgren A (2018) Campylobacter jejuni bile exposure influences outer membrane vesicles protein content and bacterial interaction with epithelial cells. Scientific Reports 8: 14.
7. Zhang Z, Aung KM, Uhlin BE, Wai SN (2018) Reversible senescence of human colon cancer cells after blockage of mitosis/cytokinesis caused by the CNF1 cyclomodulin from Escherichia coli. Scientific Reports 8: 11
Review articles:
1. Billker O (2018) CRISPRing the Elephant in the Room. Cell Host Microbe 24: 754-755.

Published by MIMS Clinical Research Fellows
1. Björck V, Påhlman LI, Törnebrant J, Bodelsson M (2018) Streptococcal M1 protein induces hyporesponsiveness and cytokine release from human arteries in a fibrinogen-dependent manner: a translational study. Scand J Trauma Resusc Emerg Med. 2018 Jul 24;26(1):61. doi: 10.1186/s13049-018-0530-1.
2. Buggert M, Nguyen S, McLane LM, Steblyanko M, Anikeeva N, Paquin-Proulx D, Del Rio Estrada PM, Ablanedo-Terrazas Y, Noyan K, Reuter MA, Demers K, Sandberg JK, Eller MA, Streeck H, Jansson M, Nowak P, Sönnerborg A, Canaday DH, Naji A, Wherry EJ, Robb ML, Deeks SG, Reyes-Teran G, Sykulev Y, Karlsson AC, Betts MR (2018) Limited immune surveillance in lymphoid tissue by cytolytic CD4+ T cells during health and HIV disease. PLoS Pathog. 2018 Apr 13;14(4):e1006973. doi: 10.1371/journal.ppat.1006973.
3. Eimer J, Vesterbacka J, Savitcheva I, Press R, Roshanisefat H, Nowak P (2018) Nonopportunistic infection leading to rapidly progressive dementia in a patient with HIV/AIDS: A case report. Medicine (Baltimore). 2018 Mar;97(12):e0162. doi: 10.1097/MD.0000000000010162.
4. Hovold G, Palmcrantz V, Kahn F, Egesten A, Påhlman LI (2018) Heparin-binding protein in sputum as a marker of pulmonary inflammation, lung function, and bacterial load in children with cystic fibrosis. BMC Pulm Med. 2018 Jun 20;18(1):104. doi: 10.1186/s12890-018-0668-7.
5. Missailidis C, Neogi U, Stenvinkel P, Trøseid M, Nowak P, Bergman P (2018) The microbial metabolite trimethylamine-N-oxide in association with inflammation and microbial dysregulation in three HIV cohorts at various disease stages. AIDS. 2018 Jul 31;32(12):1589-1598.
6. Sperk M, Zhang W, Nowak P, Neogi U (2018) Plasma soluble factor following two decades prolonged suppressive antiretroviral therapy in HIV-1-positive males: A cross-sectional study. Medicine (Baltimore). 2018 Feb;97(5):e9759. doi: 10.1097/MD.0000000000009759.
7. Stjärne Aspelund A, Hammarström H, Inghammar M, Larsson H, Hansson L, Riise GC, Friman V, Christensson B, Påhlman LI (2018) Microbiological findings in bronchoalveolar lavage fluid from lung transplant patients in Sweden. Transpl Infect Dis. 2018 Dec;20(6):e12973. doi: 10.1111/tid.12973.
8. Stjärne Aspelund A, Hammarström H, Inghammar M, Larsson H, Hansson L, Christensson B, Påhlman LI (2018) Heparin-binding protein, lysozyme, and inflammatory cytokines in bronchoalveolar lavage fluid as diagnostic tools for pulmonary infection in lung transplanted patients. Am J Transplant. 2018 Feb;18(2):444-452. doi: 10.1111/ajt.14458.
9. Zhang W, Ambikan AT, Sperk M, van Domselaar R, Nowak P, Noyan K, Russom A, Sönnerborg A, Neogi U (2018) Transcriptomics and Targeted Proteomics Analysis to Gain Insights Into the Immune-control Mechanisms of HIV-1 Infected Elite Controllers. EBioMedicine. 2018 Jan;27:40-50. doi: 10.1016/j.ebiom.2017.11.031.
Review articles:
1. Williams B, Boucher C, Bushman F, Carrington-Lawrence S, Collman R, Dandekar S, Dang Q, Malaspina A, Paredes R, Wilson C, Nowak P, Klatt N, Lagenaur L, Landay A (2018) A Summary of the Third Annual HIV Microbiome Workshop. AIDS Res Hum Retroviruses. 2018 Oct;34(10):828-834

 

2017
Published by MIMS Group Leaders
1. Abraham NM, Liu L, Jutras BL, Yadav AK, Narasimhan S, Gopalakrishnan V, Ansari JM, Jefferson KK, Cava F, Jacobs-Wagner C, Fikrig E (2017) Pathogen-mediated manipulation of arthropod microbiota to promote infection. Proc Natl Acad Sci U S A. 114(5):E781-E790.
2. Beljantseva J, Kudrin P, Andresen L, Shingler V, Atkinson GC, Tenson T, Hauryliuk V (2017) Negative allosteric regulation of Enterococcus faecalis small alarmone synthetase RelQ by single-stranded RNA. Proc Natl Acad Sci U S A., doi: 10.1073/pnas.1617868114.
3. Beljantseva J, Kudrin P, Jimmy S, Ehn M, Pohl R, Varik V, Tozawa Y, Shingler V, Tenson T, Rejman D, Hauryliuk V (2017) Molecular mutagenesis of ppGpp: turning a RelA activator into an inhibitor. Scientific Reports 7:41839.
4. Castanheira S, Cestero JJ, Rico-Pérez G, García P, Cava F, Ayala JA, Pucciarelli MG, García-Del Portillo F. A (2017) Specialized Peptidoglycan Synthase Promotes Salmonella Cell Division inside Host Cells. MBio. 8(6). pii: e01685-17.
5. Erttmann SF, Härtlova A, Sloniecka M, Raffi FAM, Hosseinzadeh A, Edgren T, Rofougaran R, Resch U, Fällman M, Ek T, Gekara NO (2017) Loss of the DNA Damage Repair Kinase ATM Impairs Inflammasome-Dependent Anti-Bacterial Innate Immunity. Immunity. 2017 Dec 19;47(6):1210-1211.
6. Howell M, Aliashkevich A, Salisbury AK, Cava F, Bowman GR, Brown PJB (2017) Absence of the Polar Organizing Protein PopZ Results in Reduced and Asymmetric Cell Division in Agrobacterium tumefaciens. J Bacteriol. 199(17). pii: e00101-17.
7. Krajewski, S.S., Isoz, I. and Johansson, J. (2017) Antibacterial and antivirulence effect of 6-N-hydroxylaminopurine in Listeria monocytogenes. Nucleic Acids Res 45(4), 1914-1924.
8. Kudrin P, Varik V, Oliveira SR, Beljantseva J, Del Peso Santos T, Dzhygyr I, Rejman D, Cava F, Tenson T, Hauryliuk V (2017) Subinhibitory Concentrations of Bacteriostatic Antibiotics Induce relA-Dependent and relA-Independent Tolerance to β-Lactams. Antimicrob Agents Chemother. Mar 24;61(4). pii: e02173-16.
9. Kumar K, Cava F (2017) Constraint randomised non-negative factor analysis (CRNNFA): an alternate chemometrics approach for analysing the biochemical data sets. Analyst. 142(11):1916-1928.
10. Kumar K, Espaillat A, Cava F (2017) PG-Metrics: A chemometric-based approach for classifying bacterial peptidoglycan data sets and uncovering their subjacent chemical variability. PLoS One. 12(10):e0186197.
11. Maciejewska B, Roszniowski B, Espaillat A, Kęsik-Szeloch A, Majkowska-Skrobek G, Kropinski AM, Briers Y, Cava F, Lavigne R, Drulis-Kawa Z (2017) Klebsiella phages representing a novel clade of viruses with an unknown DNA modification and biotechnologically interesting enzymes. Appl Microbiol Biotechnol. 101(2):673-684.
12. Maciejewska B, Źrubek K, Espaillat A, Wiśniewska M, Rembacz KP, Cava F, Dubin G, Drulis-Kawa Z (2017) Modular endolysin of Burkholderia AP3 phage has the largest lysozyme-like catalytic subunit discovered to date and no catalytic aspartate residue. Sci Rep. 7(1):14501.
13. Moreno-Guzman M, Garcia-Carmona L, Molinero-Fernandez A, Cava F, Lopez Gil MA, Escarpa A (2017) Bi-enzymatic biosensor for on-site, fast and reliable electrochemical detection of relevant D-amino acids in bacterial samples. Sensors and actuators. B, Chemical 242, 95-101.
14. Putzova D, Panda S, Härtlova A, Stulík J, Gekara NO (2017) Subversion of innate immune responses by Francisella involves the disruption of TRAF3 and TRAF6 signalling complexes. Cell Microbiol. 2017 Nov;19(11). doi: 10.1111/cmi.12769.
15. Terceti MS, Rivas AJ, Alvarez L, Noia M, Cava F, Osorio CR (2017) rstB Regulates Expression of the Photobacterium damselae subsp. damselae Major Virulence Factors Damselysin, Phobalysin P and Phobalysin C. Front Microbiol. 8:582.
16. Upadhyay AS, Stehling O, Panayiotou C, Rösser R, Lill R, Överby AK (2017) Cellular requirements for iron-sulfur cluster insertion into the antiviral radical SAM protein viperin. J Biol Chem. 2017 Aug 18;292(33):13879-13889.
17. van Teeseling MCF, de Pedro MA, Cava F (2017) Determinants of Bacterial Morphology: From Fundamentals to Possibilities for Antimicrobial Targeting. Front Microbiol. 8:1264.
18. Vanderlinde EM, Strozen TG, Hernández SB, Cava F, Howard SP (2017) Alterations in Peptidoglycan Cross-Linking Suppress the Secretin Assembly Defect Caused by Mutation of GspA in the Type II Secretion System. J Bacteriol. 199(8). pii: e00617-16.
19. Varik V, Oliveira SR, Hauryliuk V, Tenson T (2017) HPLC-based quantification of bacterial housekeeping nucleotides and alarmone messengers ppGpp and pppGpp. Scientific Reports 7:11022.
20. Vdovikova, S., Luhr, M., Szalai, P., Nygard Skalman, L., Francis, M.K., Lundmark, R., Engedal, N., Johansson, J. and Wai, S.N. (2017) A Novel Role of Listeria monocytogenes Membrane Vesicles in Inhibition of Autophagy and Cell Death. Front Cell Infect Microbiol 7, 154.
21. Vonderstein K, Nilsson E, Hubel P, Nygård Skalman L, Upadhyay A, Pasto J, Pichlmair A, Lundmark R, Överby AK (2017) Viperin Targets Flavivirus Virulence by Inducing Assembly of Noninfectious Capsid Particles. J Virol. 2017 Dec 14;92(1):e01751-17.
22. Webster SJ, Brode S, Ellis L, Fitzmaurice TJ, Elder MJ, Gekara NO, Tourlomousis P, Bryant C, Clare S, Chee R, Gaston HJS, Goodall JC (2017) Detection of a microbial metabolite by STING regulates inflammasome activation in response to Chlamydia trachomatis infection. PLoS Pathog. 2017 Jun 1;13(6):e1006383.
Review articles:
1. Cava F (2017) Biology of Vibrio cholerae. Editorial overview. Int Microbiol. 20(3):105.
2. Cava F (2017) Divergent functional roles of D-amino acids secreted by Vibrio cholerae. Int Microbiol. 20(3):149-150.
3. Gekara NO (2017) DNA damage-induced immune response: Micronuclei provide key platform. J Cell Biol. 2017 Oct 2;216(10):2999-3001. doi: 10.1083/jcb.201708069.
4. Hauryliuk V, Atkinson GC (2017) Small alarmone synthetases as novel bacterial RNA-binding proteins. RNA Biology doi: 10.1080/15476286.2017.1367889.
5. Ignatov, D. and Johansson, J. (2017) RNA-mediated signal perception in pathogenic bacteria. Wiley Interdiscip Rev RNA 8(6).
6. Krajewski, S.S., Ignatov, D. and Johansson, J. (2017) Two Are Better Than One: Dual Targeting of Riboswitches by Metabolite Analogs. Cell Chem Biol 24(5), 535-537.

Published by MIMS Leadership
1. Dimova LG, Zlatkov N, Verkade HJ, Uhlin BE, Tietge UJF (2017) High- cholesterol diet does not alter gut microbiota composition in mice. Nutrition & Metabolism, 2017, Vol. 14: 15.
2. Erttmann SF, Härtlova A, Sloniecka M, Raffi FAM, Hosseinzadeh A, Edgren T, Rofougaran R, Resch U, Fällman M, Ek T, Gekara NO (2017) Loss of the DNA Damage Repair Kinase ATM Impairs Inflammasome-Dependent Anti-Bacterial Innate Immunity. Immunity. 2017 Dec 19;47(6):1210-1211.
3. Karah N, Jolley KA, Hall RM, Uhlin BE (2017) Database for the ampC alleles in Acinetobacter baumannii. PLOS ONE, 2017, Vol. 12, (5).
4. Singh B, Mortezaei N, Savarino SJ, Uhlin BE, Bullitt E, Andersson M (2017) Antibodies damage the resilience of fimbriae, causing them to be stiff and tangled. Journal of Bacteriology, Vol. 199, (1).

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