Publications

2020

Chloroquine fumardiamides as novel quorum sensing inhibitors

Beus, M., Savijoki, K., Patel, J., Yli-Kauhaluoma, J., Fallarero, A. & Zorc, B., 6 Jun 2020, (Accepted/In press) In : Bioorganic & Medicinal Chemistry Letters. 30, 16, 8 p., 127336.

Research output: Contribution to journalArticleScientificpeer-review

Complete Genome Sequences and Methylome Analyses of Cutibacterium acnes subsp. acnes Strains DSM 16379 and DSM 1897T

Deptula, P., Laine, P., Auvinen, P., Paulin, L., Roberts, R. J., Johnston, C. D. & Varmanen, P., 16 Jul 2020, In : Microbiology Resource Announcements. 9, 29, 3 p., e00705-20.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
File
Open Access
File

Skin microbiome in cutaneous T cell lymphoma by 16S and whole genome shotgun sequencing

Salava, A., Deptula, P., Lyyski, A., Laine, P., Paulin, L., Väkevä, L., Ranki, A., Auvinen, P. & Lauerma, A., 28 Apr 2020, In : Journal of Investigative Dermatology.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
File

Evaluation of quorum sensing inhibitory activity of bis-primaquine derivatives

Pavić, K., Patel, J., Savijoki, K., Fallarero, A., Yli-Kauhaluoma, J., Rajić, Z. & Zorc, B., 4 Apr 2019.

Research output: Conference materialsPoster

Growth Mode and Carbon Source Impact the Surfaceome Dynamics of Lactobacillus rhamnosus GG

Savijoki, K., Nyman, T. A., Kainulainen, V., Miettinen, I., Siljamäki, P., Fallarero, A., Sandholm, J., Satokari, R. & Varmanen, P., 5 Jun 2019, In : Frontiers in Microbiology. 10, 17 p., 1272.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
File

Quinoline fumardiamides as novel quorum sensing inhibitors

Rajić, Z., Patel, J., Savijoki, K., Fallarero, A., Yli-Kauhaluoma, J., Beus, M. & Zorc, B., 19 Jun 2019.

Research output: Conference materialsPoster

Red-Brown Pigmentation of Acidipropionibacterium jensenii Is Tied to Haemolytic Activity and cyl-Like Gene Cluster

Deptula, P., Loivamaa, I., Smolander, O-P., Laine, P., Roberts, R. J., Piironen, V., Paulin, L., Savijoki, K., Auvinen, P. & Varmanen, P., Nov 2019, In : Microorganisms. 7, 11, 15 p., 512.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
File

Structural and Functional Dynamics of Staphylococcus aureus Biofilms and Biofilm Matrix Proteins on Different Clinical Materials

Hiltunen, A., Savijoki, K., Nyman, T., Miettinen, I., Ihalainen, P., Peltonen, J. & Fallarero, A., 20 Nov 2019, In : Microorganisms. 7, 12, 27 p., 584.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
File

Synthesis and biological evaluation of hybrid quinolone-based quaternary ammonium antibacterial agents

Fedorowicz, J., Saczewski, J., Konopacka, A., Waleron, K., Lejnowski, D., Ciura, K., Tomasic, T., Skok, Z., Savijoki, K., Morawska, M., Gilbert-Girard, S. & Fallarero, A., 1 Oct 2019, In : European Journal of Medicinal Chemistry. 179, p. 576-590 15 p.

Research output: Contribution to journalArticleScientificpeer-review

2018

3-Flavonols as Novel Quorum Sensing Inhibitors

Patel, J. Z., Seifert, T., Skogman, M., Savijoki, K. K., Fallarero Linares, A., Luthman, K. & Yli-Kauhaluoma, J. T., 2018.

Research output: Conference materialsPoster

Acidipropionibacterium virtanenii sp. nov., isolated from malted barley

Deptula, P., Smolander, O-P. A., Laine, P. K. S., Roberts, R. J., Edelmann, J. M., Peltola, P., Piironen, V. I., Paulin, L. G., Storgårds, E., Savijoki, K., Laitila, A., Auvinen, P. O. V. & Varmanen, P. K., Oct 2018, In : International Journal of Systematic and Evolutionary Microbiology. 68, 10, p. 3175-3183 9 p.

Research output: Contribution to journalArticleScientificpeer-review

Comparative Proteomic Analysis of Hymenolepis diminuta Cysticercoid and Adult Stages

Sulima, A., Savijoki, K., Bien, J., Nareaho, A., Salamatin, R., Conn, D. B. & Mlocicki, D., 15 Jan 2018, In : Frontiers in Microbiology. 8, 14 p., 2672.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
File

In situ fortification of vitamin B12 in wheat flour and wheat bran by fermentation with Propionibacterium freudenreichii

Xie, C., Coda, R., Chamlagain, B., Edelmann, M., Deptula, P., Varmanen, P., Piironen, V. & Katina, K., 4 May 2018, In : Journal of Cereal Science. 81, p. 133-139 7 p.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
File

In situ production of active vitamin B12 in cereal matrices using Propionibacterium freudenreichii

Chamlagain, B., Sugito, T. A., Deptula, P., Edelmann, M., Kariluoto, S., Varmanen, P. & Piironen, V., Jan 2018, In : Food Science & Nutrition. 6, 1, p. 67-76 10 p.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
File

Secretome profiling of Propionibacterium freudenreichii reveals highly variable responses even among the closely related strains

Frohnmeyer, E. G., Deptula, P., Nyman, T. A., Laine, P. K. S., Vihinen, A. H., Paulin, L. G., Auvinen, P. O. V., Jokitalo, E. S., Piironen, V. I., Varmanen, P. K. & Savijoki, K. K., May 2018, In : Microbial Biotechnology. 11, 3, p. 510-526 17 p.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
File
2017

A multifaceted study of Propionibacterium freudenreichii, the food-grade producer of active vitamin B12

Deptula, P., 21 Jun 2017, Helsinki: University of Helsinki. 76 p.

Research output: ThesisDoctoral ThesisCollection of Articles

Open Access

Aspergillus flavus growth inhibition by Lactobacillus strains isolated from traditional fermented Kenyan milk and maize products

Ahlberg, S., Joutsjoki, V., Laurikkala, S., Varmanen, P. & Korhonen, H., Apr 2017, In : Archives of Microbiology. 199, 3, p. 457-464 8 p.

Research output: Contribution to journalArticleScientificpeer-review

De novo assembly of genomes from long sequence reads reveals uncharted territories of Propionibacterium freudenreichii

Deptula, P., Laine, P. K., Roberts, R. J., Smolander, O-P., Vihinen, H., Piironen, V., Paulin, L., Jokitalo, E., Savijoki, K., Auvinen, P. & Varmanen, P., 16 Oct 2017, In : BMC Genomics. 18, 24 p., 790.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
File
Open Access
File

Identification of immunogenic proteins of the cysticercoid of Hymenolepis diminuta

Sulima, A., Bien, J., Savijoki, K., Nareaho, A., Salamatin, R., Conn, D. B. & Mlocicki, D., 21 Nov 2017, In : Parasites & vectors. 10, 577, 12 p., 577.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
File
2016

Bakteerit keskeisessä roolissa Viikin maitoteknologiatutkimuksessa

Alatossava, J. T. & Varmanen, P. K., 2016, In : Kehittyvä Elintarvike. 5, p. 46-48 3 p.

Research output: Contribution to journalArticleScientific

Effect of the lower ligand precursors on vitamin B12 production by food-grade Propionibacteria

Chamlagain, B., Deptula, P., Edelmann, M., Kariluoto, S., Grattepanche, F., Lacroix, C., Varmanen, P. & Piironen, V., 2016, In : LWT-Food Science and Technology. 72, p. 117-124 8 p.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
File
Open Access
File

Mass spectrometry analysis of the excretory-secretory (E-S) products of the model cestode Hymenolepis diminuta reveals their immunogenic properties and the presence of new E-S proteins in cestodes

Bien, J., Salamatin, R., Sulima, A., Savijoki, K., Conn, D. B., Näreaho, A. & Mlocicki, D., Mar 2016, In : Acta Parasitologica. 61, 2, p. 429-442 14 p.

Research output: Contribution to journalArticleScientificpeer-review

Ribosomal dimerization factor YfiA is the major protein synthesized after abrupt glucose depletion in Lactococcus lactis

Breüner, A., Frees, D., Varmanen, P., Boguta, A. M., Hammer, K., Martinussen, J. & Kilstrup, M., Oct 2016, In : Microbiology. 162, 10, p. 1829-1839 11 p.

Research output: Contribution to journalArticleScientificpeer-review

Stress Physiology of Lactic Acid Bacteria

Papadimitriou, K., Alegría, Á., Bron, P. A., de Angelis, M., Gobbetti, M., Kleerebezem, M., Lemos, J. A., Linares, D. M., Ross, P., Stanton, C., Turroni, F., van Sinderen, D., Varmanen, P., Ventura, M., Zúñiga, M., Tsakalidou, E. & Kok, J., 27 Jul 2016, In : Microbiology and Molecular Biology Reviews. 80, 3, p. 837-890 54 p.

Research output: Contribution to journalArticleScientificpeer-review

The Cell Wall Polymer Lipoteichoic Acid Becomes Nonessential in Staphylococcus aureus Cells Lacking the ClpX Chaperone

Bæk, K. T., Bowman, L., Millership, C., Søgaard, M. D., Kaever, V., Siljamäki, P. M., Savijoki, K. K., Varmanen, P. K., Nyman, T. A., Gründling, A. & Frees, D., 9 Aug 2016, In : mBio. 7, 4, 11 p., e01228-16.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
File
2015

A Streptococcus uberis transposon mutant screen reveals a negative role for LiaR homologue in biofilm formation

Salomäki, T., Karonen, T., Siljamäki, P., Savijoki, K., Nyman, T. A., Varmanen, P. & Iivanainen, A., Jan 2015, In : Journal of Applied Microbiology. 118, 1, p. 1-10 10 p.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
File

Complete genome sequence of Propionibacterium freudenreichii DSM 20271T

Koskinen, P., Deptula, P., Smolander, O-P., Tamene, F., Kammonen, J., Savijoki, K., Paulin, L., Piironen, V., Auvinen, P. & Varmanen, P., 2015, In : Standards in Genomic Sciences. 10, p. 1-6 6 p., 83.

Research output: Contribution to journalArticleScientificpeer-review

Uncovering Surface-Exposed Antigens of Lactobacillus rhamnosus by Cell Shaving Proteomics and Two-Dimensional Immunoblotting

Espino, E., Koskenniemi, K., Mato Rodriguez, L., Nyman, T., Reunanen, J., Koponen, J., Öhman, T. J., Siljamäki, P., Alatossava, T., Varmanen, P. K. & Savijoki, K., 2015, In : Journal of Proteome Research. 14, 2, p. 1010-1024 15 p.

Research output: Contribution to journalArticleScientificpeer-review

Ezrin Is Down-Regulated in Diabetic Kidney Glomeruli and Regulates Actin Reorganization and Glucose Uptake via GLUT1 in Cultured Podocytes

Wasik, A. A., Koskelainen, S., Hyvonen, M. E., Musante, L., Lehtonen, E., Koskenniemi, K., Tienari, J., Vaheri, A., Kerjaschki, D., Szalay, C., Revesz, C., Varmanen, P., Nyman, T. A., Hamar, P., Holthofer, H. & Lehtonen, S., Jun 2014, In : The American Journal of Pathology. 184, 6, p. 1727-1739 13 p.

Research output: Contribution to journalArticleScientificpeer-review

Fabricating bacterial biofilms via artificial nano(bio)components, ArtFilm (Academy of Finland project: 1.9.2013-31.8.2017)

Vuorela, P., Fallarero, A., Johnson, M., Airenne, T., Kulomaa, M., Riihimäki, T., Lindfelt, M., Holmberg, N., Peltonen, J., Ihalainen, P., Varmanen, P. & Savijoki, K., 2014, In : Dosis : farmaseuttinen aikakauskirja. 30, 3, p. 216 1 p.

Research output: Contribution to journalArticleProfessional

Genomics and deep proteome profiling of Staphylococcus epidermidis for uncovering adaptation and virulence mechanisms.

Varmanen, P. K., Siljamäki, P., Nyman, T. & Savijoki, K., 2014, Farm animal proteomics 2014: Proceedings of the 5th Management Committee Meeting and 4th Meeting of Working Groups 1,2 & 3 of COST Action FA 1002 . de Almeida, A., Ceciliani, F., Eckersall, D., Miller, I., Renaut, J., Roncada, P. & Turk, R. (eds.). Wageningen: Wageningen Academic Publishers, p. 214-216 3 p.

Research output: Chapter in Book/Report/Conference proceedingConference contributionScientific

Genomics and Proteomics Provide New Insight into the Commensal and Pathogenic Lifestyles of Bovine- and Human-Associated Staphylococcus epidermidis Strains

Savijoki, K., Iivanainen, A., Siljamaki, P., Laine, P. K., Paulin, L., Karonen (os. Miettinen), T., Pyörälä, S., Kankainen, M., Nyman, T. A., Salomaki, T., Koskinen, P., Holm, L., Simojoki, H., Taponen, S., Sukura, A., Kalkkinen, N., Auvinen, P. & Varmanen, P., Aug 2014, In : Journal of Proteome Research. 13, 8, p. 3748-3762 15 p.

Research output: Contribution to journalArticleScientificpeer-review

2013

Probiotics in cheese

Varmanen, P. K. & Savijoki, K., 2013, Cheese Ripening: Quality, Safety and Health Aspects. Randazzo, C. L., Caggia, C. & Neviani, E. (eds.). Nova Science Publishers, p. 215-224 10 p.

Research output: Chapter in Book/Report/Conference proceedingChapterScientificpeer-review

2012

Comparative analysis of excretory-secretory antigens of Trichinella spiralis and Trichinella britovi muscle larvae by two-dimensional difference gel electrophoresis and immunoblotting

Bien, J., Näreaho, A., Varmanen, P., Gozdzik, K., Moskwa, B., Cabaj, W., Nyman, T. A. & Savijoki, K., 2012, In : Proteome Science. 10, 10, p. - 10 p.

Research output: Contribution to journalArticleScientificpeer-review

Comparative exoproteomics of Staphylococcus epidermidis of human and bovine origin to identify bacterial factors involved in adaptation into bovine host

Savijoki, K., Siljamäki, P., Lietzen, N., Varmanen, P. K., Kankainen, M. & Nyman, T., 2012, Farm animal proteomics: Proceedings of the 3rd Managing Commitee Meeting and 2nd Meeting of Working Groups 1, 2 & 3 of COST Action FA1002. Rodrigues, P., Eckersall, D. & de Almeida, A. (eds.). Wageningen: Wageningen Academic Publishers, p. 111-115 5 p.

Research output: Chapter in Book/Report/Conference proceedingConference contributionScientific

Effect of acid stress on protein expression and phosphorylation in Lactobacillus rhamnosus GG

Koponen, J., Laakso, K., Koskenniemi, K., Kankainen, M., Savijoki, K., Nyman, T. A., de Vos, W. M., Tynkkynen, S., Kalkkinen, N. & Varmanen, P., 2012, In : Journal of Proteomics. 75, 4, p. 1357-1374 18 p.

Research output: Contribution to journalArticleScientificpeer-review

New Insights into Staphylococcus aureus Stress Tolerance and Virulence Regulation from an Analysis of the Role of the ClpP Protease in the Strains Newman, COL, and SA564

Frees, D., Andersen, J. H., Hemmingsen, L., Koskenniemi, K., Baek, K. T., Muhammed, M. K., Gudeta, D. D., Nyman, T. A., Sukura, A., Varmanen, P. & Savijoki, K., 2012, In : Journal of Proteome Research. 11, 1, p. 95-108 14 p.

Research output: Contribution to journalArticleScientificpeer-review

Proteomics of foes and friends adapted to milk environment: focus on Gram-positive bovine mastitis bacteria and probiotics

Varmanen, P. K., Koskenniemi, K., Siljamäki, P., Nyman, T. & Savijoki, K., 2012, Farm animal proteomics: Proceedings of the 3rd Managing Commitee Meeting and 2nd Meeting of Working Groups 1, 2 & 3 of COST Action FA1002. Rodrigues, P., Eckersall, D. & de Almeida, A. (eds.). Wageningen: Wageningen Academic Publishers, p. 40-45 6 p.

Research output: Chapter in Book/Report/Conference proceedingConference contributionScientific

2011

Alpha- and beta-casein components of host milk induce biofilm formation in the mastitis bacterium Streptococcus uberis

Varhimo, E., Varmanen, P., Fallarero, A., Skogman, M., Pyorala, S., Iivanainen, A., Sukura, A., Vuorela, P. & Savijoki, K., 2011, In : Veterinary Microbiology. 149, 3-4, p. 381-389 9 p.

Research output: Contribution to journalArticleScientificpeer-review