Daniel Lundin | lnu.se

Jag jobbar med datorbaserade analyser inom mikrobiell ekologi. Mina studier bygger för det mesta på DNA-sekvensering (metagenom, metatranskriptom och amplikon) av prover tagna i naturen eller genom experiment, i syfte att bättre beskriva mikrobers roll i naturen.

Publikationer

Artikel i tidskrift (Refereegranskat)

Nilsson, E., Bayfield, O.W., Lundin, D., Antson, A.A., Holmfeldt, K. (2020). Diversity and host interactions among virulent and temperate Baltic Sea Flavobacterium phages. Viruses. 12. 1-21.
Pontiller, B., Martinez-Garcia, S., Lundin, D., Pinhassi, J. (2020). Labile Dissolved Organic Matter Compound Characteristics Select for Divergence in Marine Bacterial Activity and Transcription. Frontiers in Microbiology. 11. 1-19.
Joglar, V., Alvarez-Salgado, X.A., Gago-Martinez, A., Leao, J.M., Pérez Martínez, C., et al. (2020). Cobalamin and microbial plankton dynamics along a coastal to offshore transect in the Eastern North Atlantic Ocean. Environmental Microbiology.
Gonzalez-Gaya, B., Martinez-Varela, A., Vila-Costa, M., Casal, P., Cerro-Galvez, E., et al. (2019). Biodegradation as an important sink of aromatic hydrocarbons in the oceans. Nature Geoscience. 12. 119-125+2.
Karlsson, C.M.G., Cerro-Galvez, E., Lundin, D., Karlsson, C., Vila-Costa, M., et al. (2019). Direct effects of organic pollutants on the growth and gene expression of the Baltic Sea model bacterium Rheinheimera sp. BAL341. Microbial Biotechnology. 12. 892-906.
Vila-Costa, M., Sebastian, M., Pizarro, M., Cerro-Galvez, E., Lundin, D., et al. (2019). Microbial consumption of organophosphate esters in seawater under phosphorus limited conditions. Scientific Reports. 9.
Nilsson, E., Li, K., Fridlund, J., Sulcius, S., Bunse, C., et al. (2019). Genomic and Seasonal Variations among Aquatic Phages Infecting the Baltic Sea Gammaproteobacterium Rheinheimera sp. Strain BAL341. Applied and Environmental Microbiology. 85. 1-19.
Högfors-Rönnholm, E., Lopez-Fernandez, M., Christel, S., Brambilla, D., Huntemann, M., et al. (2019). Metagenomes and metatranscriptomes from boreal potential and actual acid sulfate soil materials. Scientific Data. 6. 1-6.
Cerro-Galvez, E., Casal, P., Lundin, D., Pina, B., Pinhassi, J., et al. (2019). Microbial responses to anthropogenic dissolved organic carbon in the Arctic and Antarctic coastal seawaters. Environmental Microbiology. 21. 1466-1481.
Loderer, C., Holmfeldt, K., Lundin, D. (2019). Non-host class II ribonucleotide reductase in Thermus viruses : sequence adaptation and host interaction. PeerJ. 7. 1-17.
Alneberg, J., Sundh, J., Bennke, C., Beier, S., Lundin, D., et al. (2018). BARM and BalticMicrobeDB, a reference metagenome and interface to meta-omic data for the Baltic Sea. Scientific Data. 5.
Salgado, M.G., van Velzen, R., Nguyen, T.V., Battenberg, K., Berry, A.M., et al. (2018). Comparative Analysis of the Nodule Transcriptomes of Ceanothus thyrsiflorus (Rhamnaceae, Rosales) and Datisca glomerate (Datiscaceae, Cucurbitales). Frontiers in Plant Science. 9.
Srinivas, V., Lebrette, H., Lundin, D., Kutin, Y., Sahlin, M., et al. (2018). Metal-free ribonucleotide reduction powered by a DOPA radical in Mycoplasma pathogens. Nature. 563. 416-420.
Grinberg, I.R., Lundin, D., Sahlin, M., Crona, M., Berggren, G., et al. (2018). A glutaredoxin domain fused to the radical-generating subunit of ribonucleotide reductase (RNR) functions as an efficient RNR reductant. Journal of Biological Chemistry. 293. 15889-15900.
Ni, G., Canizales, S., Broman, E., Simone, D., Palwai, V.R., et al. (2018). Microbial Community and Metabolic Activity in Thiocyanate Degrading Low Temperature Microbial Fuel Cells. Frontiers in Microbiology. 9.
Grinberg, I.R., Lundin, D., Hasan, M., Crona, M., Jonna, V.R., et al. (2018). Novel ATP-cone-driven allosteric regulation of ribonucleotide reductase via the radical-generating subunit. eLIFE. 7.
Loderer, C., Jonna, V.R., Crona, M., Grinberg, I.R., Sahlin, M., et al. (2017). A unique cysteine-rich zinc finger domain present in a majority of class II ribonucleotide reductases mediates catalytic turnover. Journal of Biological Chemistry. 292. 19044-19054.
Zhang, S., Masuyer, G., Zhang, J., Shen, Y., Lundin, D., et al. (2017). Identification and characterization of a novel botulinum neurotoxin. Nature Communications. 8.
Lindh, M.V., Sjöstedt, J., Ekstam, B., Casini, M., Lundin, D., et al. (2017). Metapopulation theory identifies biogeographical patterns among core and satellite marine bacteria scaling from tens to thousands of kilometers. Environmental Microbiology. 19. 1222-1236.
Baltar, F., Lundin, D., Palovaara, J., Lekunberri, I., Reinthaler, T., et al. (2016). Prokaryotic Responses to Ammonium and Organic Carbon Reveal Alternative CO2 Fixation Pathways and Importance of Alkaline Phosphatase in the Mesopelagic North Atlantic. Frontiers in Microbiology. 7.
Herlemann, D.P.R., Lundin, D., Andersson, A.F., Labrenz, M., Juergens, K. (2016). Phylogenetic Signals of Salinity and Season in Bacterial Community Composition Across the Salinity Gradient of the Baltic Sea. Frontiers in Microbiology. 7.
Dantoft, W., Lundin, D., Esfahani, S.S., Engström, Y. (2016). The POU/Oct Transcription Factor Pdm1/nub Is Necessary for a Beneficial Gut Microbiota and Normal Lifespan of Drosophila. Journal of Innate Immunity. 8. 412-426.
Bunse, C., Lundin, D., Karlsson, C.M.G., Akram, N., Vila-Costa, M., et al. (2016). Response of marine bacterioplankton pH homeostasis gene expression to elevated CO₂. Nature Climate Change. 6. 483-487.
Thureborn, P., Franzetti, A., Lundin, D., Sjöling, S. (2016). Reconstructing ecosystem functions of the active microbial community of the Baltic Sea oxygen depleted sediments. PeerJ. 4.
Johansson, R., Jonna, V.R., Kumar, R., Nayeri, N., Lundin, D., et al. (2016). Structural Mechanism of Allosteric Activity Regulation in a Ribonucleotide Reductase with Double ATP Cones. Structure. 24. 906-917.
Wu, X., Holmfeldt, K., Hubalek, V., Lundin, D., Åström, M.E., et al. (2016). Microbial metagenomes from three aquifers in the Fennoscandian shield terrestrial deep biosphere reveal metabolic partitioning among populations. The ISME Journal. 10. 1192-1203.
Jonna, V.R., Crona, M., Rofougaran, R., Lundin, D., Johansson, S., et al. (2015). Diversity in Overall Activity Regulation of Ribonucleotide Reductase. Journal of Biological Chemistry. 1-24.
Aurelius, O., Johansson, R., Bågenholm, V., Lundin, D., Tholander, F., et al. (2015). The Crystal Structure of Thermotoga maritima Class III Ribonucleotide Reductase Lacks a Radical Cysteine Pre-Positioned in the Active Site. PLoS ONE. 10.
Lindh, M.V., Lefebure, R., Degerman, R., Lundin, D., Andersson, A., et al. (2015). Consequences of increased terrestrial dissolved organic matter and temperature on bacterioplankton community composition during a Baltic Sea mesocosm experiment. Ambio. 44. S402-S412.
Lindh, M.V., Figueroa, D., Sjöstedt, J., Baltar, F., Lundin, D., et al. (2015). Transplant experiments uncover Baltic Sea basin-specific responses in bacterioplankton community composition and metabolic activities. Frontiers in Microbiology. 6.
Baichoo, S., Botha, G., Jaufeerally-Fakim, Y., Mungloo-Dilmohamud, Z., Lundin, D., et al. (2015). H3ABioNet computational metagenomics workshop in Mauritius : training to analyse microbial diversity for Africa. Standards in Genomic Sciences. 10.
West, C.E., Rydén, P., Lundin, D., Engstrand, L., Tulic, M.K., et al. (2015). Gut microbiome and innate immune response patterns in IgE-associated eczema. Clinical and Experimental Allergy. 45. 1419-1429.
Lundin, D., Berggren, G., Logan, D.T., Sjöberg, B. (2015). The Origin and Evolution of Ribonucleotide Reduction. Life. 5. 604-636.
Poole, A.M., Lundin, D., Rytkoenen, K.T. (2015). The evolution of early cellular systems viewed through the lens of biological interactions. Frontiers in Microbiology. 6.
Lindh, M.V., Sjöstedt, J., Andersson, A.F., Baltar, F., Hugerth, L., et al. (2015). Disentangling seasonal bacterioplankton population dynamics by high-frequency sampling. Environmental Microbiology. 17. 2459-2476.
Dupont, C.L., Larsson, J., Yooseph, S., Ininbergs, K., Goll, J., et al. (2014). Functional Tradeoffs Underpin Salinity-Driven Divergence in Microbial Community Composition. PLoS ONE. 9.
Hugerth, L.W., Muller, E.E.L., Hu, Y.O.O., Lebrun, L.A.M., Roume, H., et al. (2014). Systematic Design of 18S rRNA Gene Primers for Determining Eukaryotic Diversity in Microbial Consortia. PLoS ONE. 9.
Herlemann, D.P.R., Lundin, D., Labrenz, M., Jürgens, K., Zheng, Z., et al. (2013). Metagenomic De Novo Assembly of an Aquatic Representative of the Verrucomicrobial Class Spartobacteria. mBio. 4. 1-9.
Dwivedi, B., Xue, B., Lundin, D., Edwards, R.A., Breitbart, M. (2013). A bioinformatic analysis of ribonucleotide reductase genes in phage genomes and metagenomes. BMC Evolutionary Biology. 13. 1-17.
Crona, M., Avesson, L., Sahlin, M., Lundin, D., Hinas, A., et al. (2013). A Rare Combination of Ribonucleotide Reductases in the Social Amoeba Dictyostelium discoideum. Journal of Biological Chemistry. 288. 8198-8208.
Thureborn, P., Lundin, D., Plathan, J., Poole, A.M., Sjöberg, B., et al. (2013). A Metagenomics Transect into the Deepest Point of the Baltic Sea Reveals Clear Stratification of Microbial Functional Capacities. PLoS ONE. 8.
Silberberg, G., Lundin, D., Navon, R., Öhman, M. (2012). Deregulation of the A-to-I RNA editing mechanism in psychiatric disorders. Human Molecular Genetics. 21. 311-321.
Lundin, D., Poole, A.M., Sjöberg, B., Högbom, M. (2012). Use of Structural Phylogenetic Networks for Classification of the Ferritin-like Superfamily. Journal of Biological Chemistry. 287. 20565-20575.
Lundin, D., Severin, I., Logue, J.B., Östman, Ö., Andersson, A.F., et al. (2012). Which sequencing depth is sufficient to describe patterns in bacterial α- and β-diversity?. Environmental Microbiology Reports. 4. 367-372.
Grimberg, K.B., Beskow, A., Lundin, D., Davis, M.M., Young, P. (2011). Basic Leucine Zipper Protein Cnc-C Is a Substrate and Transcriptional Regulator of the Drosophila 26S Proteasome. Molecular and Cellular Biology. 31. 897-909.
Lundin, D., Gribaldo, S., Torrents, E., Sjöberg, B., Poole, A.M. (2010). Ribonucleotide reduction - horizontal transfer of a required function spans all three domains. BMC Evolutionary Biology. 10.
Ensterö, M., Åkerborg, Ö., Lundin, D., Wang, B., Furey, T.S., et al. (2010). A computational screen for site selective A-to-I editing detects novel sites in neuron specific Hu proteins. BMC Bioinformatics. 11.
Neumann, N., Lundin, D., Poole, A.M. (2010). Comparative Genomic Evidence for a Complete Nuclear Pore Complex in the Last Eukaryotic Common Ancestor. PLoS ONE. 5.
Johansson, R., Torrents, E., Lundin, D., Sprenger, J., Sahlin, M., et al. (2010). High-resolution crystal structures of the flavoprotein NrdI in oxidized and reduced states – an unusual flavodoxin. The FEBS Journal. 277. 4265-4277.
Lundin, D., Torrents, E., Poole, A.M., Sjöberg, B. (2009). RNRdb, a curated database of the universal enzyme family ribonucleotide reductase, reveals a high level of misannotation in sequences deposited to Genbank. BMC Genomics. 10.
Masson, P., Lundin, D., Söderbom, F., Young, P. (2009). Characterization of a REG/PA28 Proteasome Activator Homolog in Dictyostelium discoideum Indicates that the Ubiquitin- and ATP-Independent REGγ Proteasome Is an Ancient Nuclear Protease. Eukaryotic Cell. 8. 844-851.
Tamas, I., Wernegreen, J.J., Nystedt, B., Kauppinen, S.N., Darby, A.C., et al. (2008). Endosymbiont gene functions impaired and rescued by polymerase infidelity at poly(A) tracts. Proceedings of the National Academy of Sciences of the United States of America. 105. 14934-9.

Kapitel i bok, del av antologi (Refereegranskat)

Berggren, G., Lundin, D., Sjöberg, B. (2017). Assembly of Dimanganese and Heterometallic Manganese Proteins. Encyclopedia of Inorganic and Bioinorganic Chemistry. John Wiley & Sons.

Artikel, forskningöversikt (Refereegranskat)

Muthusamy, S.D., Lundin, D., Branca, R.M.M., Baltar, F., Gonzalez, J.M., et al. (2017). Comparative proteomics reveals signature metabolisms of exponentially growing and stationary phase marine bacteria. Environmental Microbiology. Wiley-Blackwell. 19. 2301-2319.

Manuskript (Övrigt vetenskapligt)

Karlsson, C.M.G., Lundin, D., Karlsson, C., Teikari, J.E., Moran, M.A., et al. Different gene expression responses in two Baltic Sea heterotrophic model bacteria to dinoflagellate dissolved organic matter.
Karlsson, C.M.G., Pontiller, B., Teikari, J.E., Traving, S.J., Happel, E.M., et al. Metatranscriptomic analysis uncovers divergent responses of Baltic Sea bacteria to forest and agriculture river loadings.
Holmfeldt, K., Nilsson, E., Simone, D., Lopez-Fernandez, M., Wu, X., et al. The deep terrestrial virosphere.
Bunse, C., Lundin, D., Lindh, M.V., Sjöstedt, J., Israelsson, S., et al. Seasonality and co-occurrences of free-living Baltic Sea bacterioplankton.