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)

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.
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.
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.
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.
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., 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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
Lundin, D., Berggren, G., Logan, D.T., Sjöberg, B. (2015). The Origin and Evolution of Ribonucleotide Reduction. Life. 5. 604-636.
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.
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.
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.
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.
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.
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.
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.
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.
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., 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.
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.
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.
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.
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.
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)

Bunse, C., Lundin, D., Lindh, M.V., Sjöstedt, J., Israelsson, S., et al. Seasonality and co-occurrences of free-living Baltic Sea bacterioplankton.