Arvind Sundaram

• Kijewski, Anne Cecilie Riihonen; Witsø, Ingun Lund; Sundaram, Arvind; Brynildsrud, Ola Brønstad; Pettersen, Kristin Sæbø & Anonsen, Eirik Byrkjeflot [Show all 8 contributors for this article] (2024). Transcriptomic and proteomic analysis of the virulence inducing effect of ciprofloxacin on enterohemorrhagic Escherichia coli. PLOS ONE. ISSN 1932-6203. 19(5). doi: 10.1371/journal.pone.0298746.
• Misceo, Doriana; Senaratne, Lokuliyanage Dona Samudita; Mero, Inger-Lise; Sundaram, Arvind; Bjørnstad, Pål Marius & Szczałuba, Krzysztof [Show all 12 contributors for this article] (2023). Novel Loss of Function Variants in CENPF Including a Large Intragenic Deletion in Patients with Strømme Syndrome. Genes. ISSN 2073-4425. 14(11), p. 1–11. doi: 10.3390/genes14111985. Full text in Research Archive
• Bjørnstad, Pål Marius; Aaløkken, Ragnhild Margrethe; Åsheim, June; Sundaram, Arvind; Nangota Felde, Caroline & Østby, Gina Henriette [Show all 15 contributors for this article] (2023). A 39 kb structural variant causing Lynch Syndrome detected by optical genome mapping and nanopore sequencing. European Journal of Human Genetics. ISSN 1018-4813. 00(xx). doi: 10.1038/s41431-023-01494-7. Full text in Research Archive
• Lekva, Tove; Sundaram, Arvind; Roland, Marie Cecilie; Åsheim, June; Michelsen, Annika Elisabet & Norwitz, Errol R. [Show all 9 contributors for this article] (2023). Platelet and mitochondrial RNA is decreased in plasma-derived extracellular vesicles in women with preeclampsia—an exploratory study. BMC Medicine. ISSN 1741-7015. 21(1). doi: 10.1186/s12916-023-03178-x. Full text in Research Archive
• Spildrejorde, Mari; Samara, Athina; Sharma, Ankush; Leithaug, Magnus; Falck, Martin Bengt Alfred & Modafferi, Stefania [Show all 12 contributors for this article] (2023). Multi-omics approach reveals dysregulated genes during hESCs neuronal differentiation exposure to paracetamol. iScience. ISSN 2589-0042. 26:107755(10), p. 1–29. doi: 10.1016/j.isci.2023.107755. Full text in Research Archive
• Lazado, Carlo C.; Iversen, Marianne; Johansen, Lill-Heidi; Brenne, Hanne Britt; Sundaram, Arvind & Ytteborg, Elisabeth (2023). Nasal responses to elevated temperature and Francisella noatunensis infection in Atlantic cod (Gadus morhua). Genomics. ISSN 0888-7543. 115(6). doi: 10.1016/j.ygeno.2023.110735. Full text in Research Archive Show summary

  We report the histological and transcriptomic changes in the olfactory organ of Atlantic cod exposed to Francisella noatunensis. Experimental infection was performed at either 12oC or 17oC. Infected fish presented the classic gross pathologies of francisellosis. Nasal morpho-phenotypic parameters were not significantly affected by temperature and infection, except for the number of mucus cells in the 12oC group seven weeks after the challenge. A higher number of genes were altered through time in the group reared at 17oC. At termination, the nasal transcriptome of infected fish in both groups was similar to the control. When both infected groups were compared, 754 DEGs were identified, many of which were involved in signalling, defence, transmembrane and enzymatic processes. In conclusion, the study reveals that elevated temperature could trigger responses in the olfactory organ of Atlantic cod and shape the nasal response to F. noatunensis infection.

• Slattery, Orla; Dahle, Maria; Sundaram, Arvind; Nowak, Barbara; Gjessing, Mona Cecilie & Solhaug, Anita (2023). Functional and molecular characterization of the Atlantic salmon gill epithelium cell line ASG-10; a tool for in vitro gill research. Frontiers in Molecular Biosciences. ISSN 2296-889X. 10, p. 1–23. doi: 10.3389/fmolb.2023.1242879.
• Falch, Camilla Maria; Arlien-Søborg, Mai Christiansen; Dal, Jakob; Sundaram, Arvind; Michelsen, Annika Elisabet & Ueland, Thor [Show all 11 contributors for this article] (2023). Gene expression profiling of subcutaneous adipose tissue reveals new biomarkers in acromegaly. European Journal of Endocrinology (EJE). ISSN 0804-4643. 188(3), p. 310–321. doi: 10.1093/ejendo/lvad031. Full text in Research Archive
• Lazado, Carlo C.; Iversen, Marianne & Sundaram, Arvind (2023). Comparative basal transcriptome profiles of the olfactory rosette and gills of Atlantic salmon (Salmo salar) unveil shared and distinct immunological features. Genomics. ISSN 0888-7543. 115(3). doi: 10.1016/j.ygeno.2023.110632. Full text in Research Archive Show summary

  The molecular repertoire of the mucosa-associated lymphoid tissue (MALT) in the olfactory rosette in most teleost fish is unknown. Here we present the basal transcriptome of the olfactory rosette of Atlantic salmon (Salmo salar). To investigate its mucosal immune features, we performed a comparative transcriptomic analysis with the gills, one of the most studied organs possessing MALT. Pathway enrichment revealed that cytokine-cytokine interaction and the neuroactive ligand-receptor interaction pathways were at the core of the shared similarity between the two organs. The immunological features of the two organs were further characterised by the overrepresentation of several immune-related pathways, particularly important for pathogen recognition. The immunological differences between the two organs were underlined with the differential regulation of markers for interleukins, extracellular matrix, antimicrobial peptides, and complement. The basal transcriptome of Atlantic salmon olfactory rosette is a valuable molecular toolbox that will advance our understanding of nasal immunity in teleost fish.

• Bjørneset, J.; Blévin, P.; Bjørnstad, P.M.; Dalmo, R.A.; Goksøyr, A. & Harju, M. [Show all 12 contributors for this article] (2023). Establishment of killer whale (Orcinus orca) primary fibroblast cell cultures and their transcriptomic responses to pollutant exposure. Environment International. ISSN 0160-4120. 174. doi: 10.1016/j.envint.2023.107915. Full text in Research Archive Show summary

  Populations of killer whale (Orcinus orca) contain some of the most polluted animals on Earth. Yet, the knowledge on effects of chemical pollutants is limited in this species. Cell cultures and in vitro exposure experiments are pertinent tools to study effects of pollutants in free-ranging marine mammals. To investigate transcriptional responses to pollutants in killer whale cells, we collected skin biopsies of killer whales from the Northern Norwegian fjords and successfully established primary fibroblast cell cultures from the dermis of 4 out of 5 of them. Cells from the individual with the highest cell yield were exposed to three different concentrations of a mixture of persistent organic pollutants (POPs) that reflects the composition of the 10 most abundant POPs found in Norwegian killer whales (p,p’-DDE, trans-nonachlor, PCB52, 99, 101, 118, 138, 153, 180, 187). Transcriptional responses of 13 selected target genes were studied using digital droplet PCR, and whole transcriptome responses were investigated utilizing RNA sequencing. Among the target genes analysed, CYP1A1 was significantly downregulated in the cells exposed to medium (11.6 µM) and high (116 µM) concentrations of the pollutant mixture, while seven genes involved in endocrine functions showed a non-significant tendency to be upregulated at the highest exposure concentration. Bioinformatic analyses of RNA-seq data indicated that 13 and 43 genes were differentially expressed in the cells exposed to low and high concentrations of the mixture, respectively, in comparison to solvent control. Subsequent pathway and functional analyses of the differentially expressed genes indicated that the enriched pathways were mainly related to lipid metabolism, myogenesis and glucocorticoid receptor regulation. The current study results support previous correlative studies and provide cause-effect relationships, which is highly relevant for chemical and environmental management.

• Lukacs, Morten; Nymo, Ingebjørg Helena; Madslien, Knut; Våge, Jørn; Veiberg, Vebjørn & Rolandsen, Christer Moe [Show all 9 contributors for this article] (2023). Functional immune diversity in reindeer reveals a high Arctic population at risk. Frontiers in Ecology and Evolution. ISSN 2296-701X. 10(1058674). doi: 10.3389/fevo.2022.1058674. Full text in Research Archive Show summary

  Climate changes the geographic range of both species as well as pathogens, causing a potential increase in the vulnerability of populations or species with limited genetic diversity. With advances in high throughput sequencing (HTS) technologies, we can now define functional expressed genetic diversity of wild species at a larger scale and identify populations at risk. Previous studies have used genomic DNA to define major histocompatibility complex (MHC) class II diversity in reindeer. Varying numbers of expressed genes found in many ungulates strongly argues for using cDNA in MHC typing strategies to ensure that diversity estimates relate to functional genes. We have used available reindeer genomes to identify candidate genes and established an HTS approach to define expressed MHC class I and class II diversity. To capture a broad diversity we included samples from wild reindeer from Southern Norway, semi-domesticated reindeer from Northern Norway and reindeer from the high Artic archipelago Svalbard. Our data show a medium MHC diversity in semi-domesticated and wild Norwegian mainland reindeer, and low MHC diversity reindeer in Svalbard reindeer. The low immune diversity in Svalbard reindeer provides a potential risk if the pathogenic pressure changes in response to altered environmental conditions due to climate change, or increased human-related activity. climate change, MHC, reindeer, immune diversity, Svalbard, Norway

• Yadav, Ajay; Verhaegen, Steven; Filis, Panagiotis; Domanska, Diana; Lyle, Robert & Sundaram, Arvind [Show all 14 contributors for this article] (2022). Exposure to a human relevant mixture of persistent organic pollutants or to perfluorooctane sulfonic acid alone dysregulates the developing cerebellum of chicken embryo. Environment International. ISSN 0160-4120. 166, p. 1–13. doi: 10.1016/j.envint.2022.107379. Full text in Research Archive Show summary

  Prenatal exposure to persistent organic pollutants (POPs) is associated with neurodevelopmental disorders. In the present study, we explored whether a human-relevant POP mixture affects the development of chicken embryo cerebellum. We used a defined mixture of 29 POPs, with chemical composition and concentrations based on blood levels in the Scandinavian population. We also evaluated exposure to a prominent compound in the mixture, perfluorooctane sulfonic acid (PFOS), alone. Embryos (n = 7–9 per exposure group) were exposed by injection directly into the allantois at embryonic day 13 (E13). Cerebella were isolated at E17 and subjected to morphological, RNA-seq and shot-gun proteomics analyses. There was a reduction in thickness of the molecular layer of cerebellar cortex in both exposure scenarios. Exposure to the POP mixture significantly affected expression of 65 of 13,800 transcripts, and 43 of 2,568 proteins, when compared to solvent control. PFOS alone affected expression of 80 of 13,859 transcripts, and 69 of 2,555 proteins. Twenty-five genes and 15 proteins were common for both exposure groups. These findings point to alterations in molecular events linked to retinoid X receptor (RXR) signalling, neuronal cell proliferation and migration, cellular stress responses including unfolded protein response, lipid metabolism, and myelination. Exposure to the POP mixture increased methionine oxidation, whereas PFOS decreased oxidation. Several of the altered genes and proteins are involved in a wide variety of neurological disorders. We conclude that POP exposure can interfere with fundamental aspects of neurodevelopment, altering molecular pathways that are associated with adverse neurocognitive and behavioural outcomes.

• Grimholt, Unni; Sundaram, Arvind; Arnason_Bøe, Cathrine; Dahle, Maria & Lukacs, Morten Ferenc (2022). Tetraploid Ancestry Provided Atlantic Salmon With Two Paralogue Functional T Cell Receptor Beta Regions Whereof One Is Completely Novel. Frontiers in Immunology. ISSN 1664-3224. 13(930312). doi: 10.3389/fimmu.2022.930312. Show summary

  Protective cellular immune responses have been difficult to study in fish, due to lack of basic understanding of their T cell populations, and tools to study them. Cellular immunity is thus mostly ignored in vaccination and infection studies compared to humoral responses. High throughput sequencing, as well as access to well assembled genomes, now advances studies of cellular responses. Here we have used such resources to describe organization of T cell receptor beta genes in Atlantic salmon. Salmonids experienced a unique whole genome duplication approximately 94 million years ago, which provided these species with many functional duplicate genes, where some duplicates have evolved new functions or sub-functions of the original gene copy. This is also the case for T cell receptor beta, where Atlantic salmon has retained two paralogue T cell receptor beta regions on chromosomes 01 and 09. Compared to catfish and zebrafish, the genomic organization in both regions is unique, each chromosomal region organized with dual variable- diversity- joining- constant genes in a head to head orientation. Sequence identity of the chromosomal constant sequences between TRB01 and TRB09 is suggestive of rapid diversification, with only 67 percent as opposed to the average 82-90 percent for other duplicated genes. Using virus challenged samples we find both regions expressing bona fide functional T cell receptor beta molecules. Adding the 292 variable T cell receptor alpha genes to the 100 variable TRB genes from 14 subgroups, Atlantic salmon has one of the most diverse T cell receptor alpha beta repertoire of any vertebrate studied so far. Perhaps salmonid cellular immunity is more advanced than we have imagined.

• Ribarska, Teodora Plamenova; Bjørnstad, Pål Marius; Sundaram, Arvind & Gilfillan, Gregor (2022). Optimization of enzymatic fragmentation is crucial to maximize genome coverage: a comparison of library preparation methods for Illumina sequencing. BMC Genomics. ISSN 1471-2164. 23(92). doi: 10.1186/s12864-022-08316-y. Show summary

  Background: Novel commercial kits for whole genome library preparation for next-generation sequencing on Illumina platforms promise shorter workfows, lower inputs and cost savings. Time savings are achieved by employing enzymatic DNA fragmentation and by combining end-repair and tailing reactions. Fewer cleanup steps also allow greater DNA input fexibility (1 ng-1 μg), PCR-free options from 100 ng DNA, and lower price as compared to the well-established sonication and tagmentation-based DNA library preparation kits. Results: We compared the performance of four enzymatic fragmentation-based DNA library preparation kits (from New England Biolabs, Roche, Swift Biosciences and Quantabio) to a tagmentation-based kit (Illumina) using low input DNA amounts (10 ng) and PCR-free reactions with 100 ng DNA. With four technical replicates of each input amount and kit, we compared the kits’ fragmentation sequence-bias as well as performance parameters such as sequence coverage and the clinically relevant detection of single nucleotide and indel variants. While all kits produced high quality sequence data and demonstrated similar performance, several enzymatic fragmentation methods produced library insert sizes which deviated from those intended. Libraries with longer insert lengths performed better in terms of coverage, SNV and indel detection. Lower performance of shorter-insert libraries could be explained by loss of sequence coverage to overlapping paired-end reads, exacerbated by the preferential sequencing of shorter fragments on Illumina sequencers. We also observed that libraries prepared with minimal or no PCR performed best with regard to indel detection. Conclusions: The enzymatic fragmentation-based DNA library preparation kits from NEB, Roche, Swift and Quanta-bio are good alternatives to the tagmentation based Nextera DNA fex kit from Illumina, ofering reproducible results using fexible DNA inputs, quick workfows and lower prices. Libraries with insert DNA fragments longer than the cumulative sum of both read lengths avoid read overlap, thus produce more informative data that leads to strongly improved genome coverage and consequently also increased sensitivity and precision of SNP and indel detection. In order to best utilize such enzymatic fragmentation reagents, researchers should be prepared to invest time to optimize fragmentation conditions for their particular samples.

• Diaz-Lundahl, Anna Sofia; Sundaram, Arvind Y.M.; Gillund, Per; Gilfillan, Gregor; Olsaker, Ingrid & Krogenæs, Anette Kristine (2022). Gene Expression in Embryos From Norwegian Red Bulls With High or Low Non Return Rate: An RNA-Seq Study of in vivo-Produced Single Embryos. Frontiers in Genetics. ISSN 1664-8021. 12(780113). doi: 10.3389/fgene.2021.780113. Full text in Research Archive Show summary

  During the last decade, paternal effects on embryo development have been found to have greater importance than previously believed. In domestic cattle, embryo mortality is an issue of concern, causing huge economical losses for the dairy cattle industry. In attempts to reveal the paternal influence on embryo death, recent approaches have used transcriptome profiling of the embryo to find genes and pathways affected by different phenotypes in the bull. For practical and economic reasons, most such studies have used in vitro produced embryos. The aim of the present study was to investigate the differences in the global transcriptome of in vivo produced embryos, derived from sires with either high or low field fertility measured as the non-return rate (NRR) on day 56 after first AI of the inseminated cows. Superovulated heifers (n= 14) in the age span of 12–15 months were artificially inseminated with semen from either high fertility (n = 6) or low fertility (n = 6) bulls. On day seven after insemination, embryos were retrieved through uterine flushing. Embryos with first grade quality and IETS stage 5 (early blastocyst), 6 (blastocyst) or 7 (expanded blastocyst) were selected for further processing. In total, RNA extracted from 24 embryos was sequenced using Illumina sequencing, followed by differential expression analysis and gene set enrichment analysis. We found 62 genes differentially expressed between the two groups (adj.p-value<0.05), of which several genes and their linked pathways could explain the different developmental capacity. Transcripts highly expressed in the embryos from low fertility bulls were related to sterol metabolism and terpenoid backbone synthesis, while transcripts highly expressed in the high fertility embryos were linked to anti-apoptosis and the regulation of cytokine signaling. The leukocyte transendothelial migration and insulin signaling pathways were associated with enrichments in both groups. We also found some highly expressed transcripts in both groups which can be considered as new candidates in the regulation of embryo development. The present study is an important step in defining the paternal influence in embryonic development. Our results suggest that the sire’s genetic contribution affects several important processes linked to pre-and peri implantation regulation in the developing embryo.

• Løvdal, Trond Karsten; Brandal, Lin Cathrine T.; Sundaram, Arvind; Naseer, Umaer; Roth, Bjørn & Lunestad, Bjørn Tore (2021). Small-Scale Comparative Genomic Analysis of Listeria monocytogenes Isolated from Environments of Salmon Processing Plants and Human Cases in Norway. Hygiene. ISSN 2673-947X. 1, p. 43–55. doi: 10.3390/hygiene1010005. Full text in Research Archive Show summary

  Listeria monocytogenes is a food-borne bacterium that give rise to the potentially life-threatening disease listeriosis. Listeriosis has been mandatorily notifiable in Norway since 1991. All clinical L. monocytogenes isolates are sent to the Norwegian Institute of Public Health (NIPH) for typing. Since 2005 Multi-Locus Variable number tandem repeats Analysis (MLVA) has been used for typing but was recently replaced by whole genome sequencing using core genome Multi-Locus Sequence Typing (cgMLST). In the present study, L. monocytogenes isolates collected at salmon processing plants in Norway in 2007 (n = 12) and 2015 (n = 14) were first subject to MLVA. Twelve clinical L. monocytogenes isolates with matching MLVA profile and sampling time were selected from the strain collection at NIPH. Twenty-one isolates from the salmon processing plants and all clinical isolates (n = 12) were whole genome sequenced and compared using cgMLST and in silico detection of virulence genes. cgMLST revealed four pairs of environmental–human isolates with ≤10 allelic differences over 1708 genes, indicating that they may be assigned as clonal, with the implication that they are descended from the same recent ancestor. No relevant difference in carriage of virulence genes was found between environmental or human isolates. The present study shows that L. monocytogenes strains that genetically resemble contemporary isolates from human listeriosis circulate in Norwegian salmon slaughterhouses, and carry the same virulence genes.

• Lind, Andreas; Barlinn, Regine; Landaas, Elisabeth Toverud; Andresen, Lise Lima; Jakobsen, Kirsti & Fladeby, Cathrine [Show all 13 contributors for this article] (2021). Rapid SARS-CoV-2 variant monitoring using PCR confirmed by whole genome sequencing in a high-volume diagnostic laboratory. Journal of Clinical Virology. ISSN 1386-6532. 141. doi: 10.1016/j.jcv.2021.104906. Full text in Research Archive
• Helgeland, Hanna; Gabrielsen, Ingvild Synnøve Matre; Akselsen, Helle; Meenakshi Sundaram, Arvind Yegambaram; Flåm, Siri Tennebø & Lie, Benedicte Alexandra (2020). Transcriptome profiling of human thymic CD4+ and CD8+ T cells compared to primary peripheral T cells. BMC Genomics. ISSN 1471-2164. 21(350). doi: 10.1186/s12864-020-6755-1. Full text in Research Archive Show summary

  Background: The thymus is a highly specialized organ of the immune system where T cell precursors develop and differentiate into self-tolerant CD4+ or CD8+ T cells. No studies to date have investigated how the human transcriptome profiles differ, between T cells still residing in the thymus and T cells in the periphery. Results: We have performed high-throughput RNA sequencing to characterize the transcriptomes of primary single positive (SP) CD4+ and CD8+ T cells from infant thymic tissue, as well as primary CD4+ and CD8+ T cells from infant and adult peripheral blood, to enable the comparisons across tissues and ages. In addition, we have assessed the expression of candidate genes related to autoimmune diseases in thymic CD4+ and CD8+ T cells. The thymic T cells showed the largest number of uniquely expressed genes, suggesting a more diverse transcription in thymic T cells. Comparing T cells of thymic and blood origin, revealed more differentially expressed genes, than between infant and adult blood. Functional enrichment analysis revealed an over-representation of genes involved in cell cycle and replication in thymic T cells, whereas infant blood T cells were dominated by immune related terms. Comparing adult and infant blood T cells, the former was enriched for inflammatory response, cytokine production and biological adhesion, while upregulated genes in infant blood T cells were associated with cell cycle, cell death and gene expression. Conclusion: This study provides valuable insight into the transcriptomes of the human primary SP T cells still residing within the thymus, and offers a unique comparison to primary blood derived T cells. Interestingly, the majority of autoimmune disease associated genes were expressed in one or more T cell subset, however ~ 11% of these were not expressed in frequently studied adult peripheral blood.

• Heinicke, Fatima; Zhong, Xiangfu; Zucknick, Karola Manuela; Breidenbach, Johannes; Sundaram, Arvind Yegambaram Meenakshi & Flåm, Siri Tennebø [Show all 11 contributors for this article] (2020). An extension to: Systematic assessment of commercially available low-input miRNA library preparation kits. RNA Biology. ISSN 1547-6286. 17(9), p. 1284–1292. doi: 10.1080/15476286.2020.1761081. Full text in Research Archive Show summary

  High-throughput sequencing has emerged as the favoured method to study microRNA (miRNA) expression, but biases introduced during library preparation have been reported. We recently compared the performance (sensitivity, reliability, titration response and differential expression) of six commercially-available kits on synthetic miRNAs and human RNA, where library preparation was performed by the vendors. We hereby supplement this study with data from two further commonly used kits (NEBNext, NEXTflex) whose manufacturers initially declined to participate. NEXTflex demonstrated the highest sensitivity, which may reflect its use of partially-randomized adapter sequences, but overall performance was lower than the QIAseq and TailorMix kits. NEBNext showed intermediate performance. We reaffirm that biases are kit specific, complicating the comparison of miRNA datasets generated using different kits.

• Eieland, Alexander K.; Normann, Kjersti R.; Sundaram, Arvind Y. M.; Nyman, Tuula A.; Øystese, Kristin A. B. & Lekva, Tove [Show all 9 contributors for this article] (2020). Distinct pattern of endoplasmic reticulum protein processing and extracellular matrix proteins in functioning and silent corticotroph pituitary adenomas. Cancers. ISSN 2072-6694. 12(10), p. 1–20. doi: 10.3390/cancers12102980. Full text in Research Archive
• Grimholt, Unni; Fosse, Johanna H. & Meenakshi Sundaram, Arvind Yegambaram (2020). Selective Stimulation of Duplicated Atlantic Salmon MHC Pathway Genes by Interferon-Gamma. Frontiers in Immunology. ISSN 1664-3224. 11. doi: 10.3389/fimmu.2020.571650. Show summary

  Induction of cellular immune responses rely on Major histocompatibility complex (MHC) molecules presenting pathogenic peptides to T cells. Peptide processing, transport, loading and editing is a constitutive process in most cell types, but is accelerated upon infection. Recently, an unexpected complexity in the number of functional genes involved in MHC class I peptide cleavage, peptide transport, peptide loading and editing was found in teleosts, originating from the second and third whole genome duplication events. Salmonids have expanded upon this with functional duplicates also from a fourth unique salmonid whole genome duplication. However, little is known about how individual gene duplicates respond in the context of stimulation. Here we set out to investigate how interferon gamma (IFNg) regulates the transcription of immune genes in Atlantic salmon with particular focus on gene duplicates and MHC pathways. We identified a range of response patterns in Atlantic salmon gene duplicates, with upregulation of all duplicates for some genes, like interferon regulatory factor 1 (IRF1) and interferon induced protein 44-like (IFI44.L), but only induction of one or a few duplicates of other genes, such as TAPBP and ERAP2. A master regulator turned out to be the IRF1 and not the enhanceosome as seen in mammals. If IRF1 also collaborates with CIITA and possibly NLRC5 in regulating IFNg induction of MHCI and MHCII expression in Atlantic salmon, as in zebrafish, remains to be established. Altogether, our results show the importance of deciphering between gene duplicates, as they often respond very differently to stimulation and may have different biological functions.

• Håkenåsen, Ingrid Marie; Øverland, Margareth; Ånestad, Ragnhild; Åkesson, Caroline Piercey; Meenakshi Sundaram, Arvind Yegambaram & Press, Charles McLean [Show all 7 contributors for this article] (2020). Gene expression and gastrointestinal function is altered in piglet small intestine by weaning and inclusion of Cyberlindnera jadinii yeast as a protein source. Journal of Functional Foods. ISSN 1756-4646. 73. doi: 10.1016/j.jff.2020.104118. Full text in Research Archive Show summary

  This study investigated the effect of feeding Cyberlindnera jadinii yeast on the development of gastrointestinal function and health in piglets during the first two challenging weeks after weaning. Changes in gastrointestinal function were mainly attributed to weaning, and not to dietary treatment. The post-weaning (PW) transcriptome profiles differed between dietary treatments showing an overall higher number of differentially expressed genes (DEGs) in control piglets than in yeast-fed piglets. DEGs in jejunum and ileum were compared between sampling timepoints within each feeding group and divided into clusters with similar expression trends. Pathway enrichment analysis was run on each cluster to reveal PW physiological changes. Weaning induced downregulation of several immune functions in the control piglets, which was not as evident in the yeast fed piglets. The results indicate that feeding C. jadinii yeast can improve PW gut homeostasis and give more robust piglets.

• Agusti-Ridaura, Celia; Bakke, Marit Jørgensen; Helgesen, Kari Marie Olli; Sundaram, Arvind Y. M.; Bakke, Sigrid Jørgensen & Kaur, Kiranpreet [Show all 7 contributors for this article] (2020). Candidate genes for monitoring hydrogen peroxide resistance in the salmon louse, Lepeophtheirus salmonis. Parasites & Vectors. ISSN 1756-3305. 13. doi: 10.1186/s13071-020-04211-1. Full text in Research Archive Show summary

  Abstract Background: Hydrogen peroxide (H2O2) is one of the delousing agents used to control sea lice infestations in salmo‑ nid aquaculture. However, some Lepeophtheirus salmonis populations have developed resistance towards H2O2. An increased gene expression and activity of catalase, an enzyme that breaks down H2O2, have been detected in resistant lice, being therefore introduced as a resistance marker in the salmon industry. In the present study the aim was to vali‑ date the use of catalase expression as a marker and to identify new candidate genes as additional markers to catalase,related to H2O2 resistance in L. salmonis. Methods: A sensitive and an H2O2 resistant laboratory strain (P0 generation, not exposed to H2O2 for several years) were batch crossed to generate a cohort with a wide range of H2O2 sensitivities (F2 generation). F2 adult females were then exposed to H2O2 to separate sensitive and resistant individuals. Those F2 lice, the P0 lice and feld-collected resistant lice (exposed to H2O2 in the feld) were used in an RNA sequencing study. Results: Catalase was upregulated in resistant lice exposed to H2O2 compared to sensitive lice. This was, however, not the case for unexposed resistant P0 lice. Several other genes were found diferentially expressed between sensitive and resistant lice, but most of them seemed to be related to H2O2 exposure. However, fve genes were consistently up- or downregulated in the resistant lice independent of exposure history. The upregulated genes were: one gene in the DNA polymerase family, one gene encoding a Nesprin-like protein and an unannotated gene encoding a small protein. The downregulated genes encoded endoplasmic reticulum resident protein 29 and an aquaporin (Glp1_v2). Conclusions: Catalase expression seems to be induced by H2O2 exposure, since it was not upregulated in unex‑ posed resistant lice. This may pose a challenge for its use as a resistance marker. The fve new genes associated with resistance are put forward as complementary candidate genes. The most promising was Glp1_v2, an aquaglycerop‑ orin that may serve as a passing channel for H2O2. Lower channel number can reduce the infux or distribution of H2O2 in the salmon louse, being directly involved in the resistance mechanism.

• Pettersen, Kristin Sæbø; Meenakshi Sundaram, Arvind Yegambaram; Skjerdal, Olaug Taran; Wasteson, Yngvild; Kijewski, Anne Cecilie Riihonen & Lindbäck, Toril [Show all 7 contributors for this article] (2019). Exposure to Broad-Spectrum Visible Light Causes Major Transcriptomic Changes in Listeria monocytogenes EGDe. Applied and Environmental Microbiology. ISSN 0099-2240. 85(22), p. 1–14. doi: 10.1128/AEM.01462-19. Show summary

  Listeria monocytogenes, the causative agent of the serious foodborne disease listeriosis, can rapidly adapt to a wide range of environmental stresses, including visible light. This study shows that exposure of the L. monocytogenes EGDe strain to low-intensity, broad-spectrum visible light inhibited bacterial growth and caused altered multicellular behavior during growth on semisolid agar compared to when the bacteria were grown in complete darkness. These light-dependent changes were observed regardless of the presence of the blue light receptor (Lmo0799) and the stressosome regulator sigma B (SigB), which have been suggested to be important for the ability of L. monocytogenes to respond to blue light. A genome-wide transcriptional analysis revealed that exposure of L. monocytogenes EGDe to broad-spectrum visible light caused altered expression of 2,409 genes belonging to 18 metabolic pathways compared to bacteria grown in darkness. The light-dependent differentially expressed genes are involved in functions such as glycan metabolism, cell wall synthesis, chemotaxis, flagellar synthesis, and resistance to oxidative stress. Exposure to light conferred reduced bacterial motility in semisolid agar, which correlates well with the light-dependent reduction in transcript levels of flagellar and chemotaxis genes. Similar light-induced reduction in growth and motility was also observed in two different L. monocytogenes food isolates, suggesting that these responses are typical for L. monocytogenes. Together, the results show that even relatively small doses of broad-spectrumvisible light cause genome-wide transcriptional changes, reduced growth, and motility in L. monocytogenes.

• Meenakshi Sundaram, Arvind Yegambaram; Garseth, Åse Helen; Maccari, Guiseppe & Grimholt, Unni (2019). An Illumina approach to MHC typing of Atlantic salmon. Immunogenetics. ISSN 0093-7711. 72, p. 89–100. doi: 10.1007/s00251-019-01143-8.
• Heinicke, Fatima; Zhong, Xiangfu; Zucknick, Manuela; Breidenbach, Johannes; Sundaram, Arvind Yegambaram Meenakshi & Flåm, Siri Tennebø [Show all 21 contributors for this article] (2019). Systematic assessment of commercially available low-input miRNA library preparation kits. RNA Biology. ISSN 1547-6286. 17(1), p. 75–86. doi: 10.1080/15476286.2019.1667741. Full text in Research Archive Show summary

  High-throughput sequencing is increasingly favoured to assay the presence and abundance of microRNAs (miRNAs) in biological samples, even from low RNA amounts, and a number of commercial vendors now offer kits that allow miRNA sequencing from sub-nanogram (ng) inputs. Although biases introduced during library preparation have been documented, the relative performance of current reagent kits has not been investigated in detail. Here, six commercial kits capable of handling <100ng total RNA input were used for library preparation, performed by kit manufactures, on synthetic miRNAs of known quantities and human total RNA samples. We compared the performance of miRNA detection sensitivity, reliability, titration response and the ability to detect differentially expressed miRNAs. In addition, we assessed the use of unique molecular identifiers (UMI) sequence tags in one kit. We observed differences in detection sensitivity and ability to identify differentially expressed miRNAs between the kits, but none were able to detect the full repertoire of synthetic miRNAs. The reliability within the replicates of all kits was good, while larger differences were observed between the kits, although none could accurately quantify the relative levels of the majority of miRNAs. UMI tags, at least within the input ranges tested, offered little advantage to improve data utility. In conclusion, biases in miRNA abundance are heavily influenced by the kit used for library preparation, suggesting that comparisons of datasets prepared by different procedures should be made with caution. This article is intended to assist researchers select the most appropriate kit for their experimental conditions.

• Gabrielsen, Ingvild Synnøve Matre; Helgeland, Hanna; Akselsen, Helle; Aass, Hans Christian Dalsbotten; Meenakshi Sundaram, Arvind Yegambaram & Snowhite, Isaac V. [Show all 9 contributors for this article] (2019). Transcriptomes of antigen presenting cells in human thymus. PLOS ONE. ISSN 1932-6203. 14:e0218858(7), p. 1–18. doi: 10.1371/journal.pone.0218858. Full text in Research Archive
• Skugor, Adrijana; Kjos, Nils Petter; Meenakshi Sundaram, Arvind Yegambaram; Mydland, Liv Torunn; Ånestad, Ragnhild & Tauson, Anne Helene [Show all 7 contributors for this article] (2019). Effects of long-term feeding of rapeseed meal on skeletal muscle transcriptome, production efficiency and meat quality traits in Norwegian Landrace growing-finishing pigs. PLOS ONE. ISSN 1932-6203. 14(8). doi: 10.1371/journal.pone.0220441. Full text in Research Archive Show summary

  This study was performed to investigate the effects of dietary inclusion of 20% rapeseed meal (RSM) as an alternative to soybean meal (SBM) in a three-month feeding Experiment with growing finishing pigs. Dietary alteration affected growth performance, several carcass traits and transcriptional responses in the skeletal muscle, but did not affect measured meat quality traits. In general, pigs fed the RSM test diet exhibited reduced growth performance compared to pigs on SBM control diet. Significant transcriptional changes in the skeletal muscle of growing pigs fed RSM diet were likely the consequence of an increased amount of fiber and higher polyunsaturated fatty acids, and presence of bioactive phytochemicals, such as glucosinolates. RNAseq pipeline using Tophat2-Cuffdiff identified 57 upregulated and 63 downregulated genes in RSM compared to SBM pigs. Significantly enriched among downregulated pathways was p53–mediated signalling involved in cellular proliferation, while activation of negative growth regulators (IER5, KLF10, BTG2, KLF11, RETREG1, PRUNE2) in RSM fed pigs provided further evidence for reduced proliferation and increased cellular death, in accordance with the observed reduction in performance traits. Upregulation of well-known metabolic controllers (PDK4, UCP3, ESRRG and ESRRB), involved in energy homeostasis (glucose and lipid metabolism, and mitochondrial function), suggested less available energy and nutrients in RSM pigs. Furthermore, several genes supported more pronounced proteolysis (ABTB1, OTUD1, PADI2, SPP1) and reduced protein synthesis (THBS1, HSF4, AP1S2) in RSM muscle tissue. In parallel, higher levels of NR4A3, PDK4 and FGF21, and a drop in adropin, ELOVL6 and CIDEC/FSP27 indicated increased lipolysis and fatty acid oxidation, reflective of lower dressing percentage. Finally, pigs exposed to RSM showed greater expression level of genes responsive to oxidative stress, indicated by upregulation of GPX1, GPX2, and TXNIP.

• Bizuayehu, Teshome Tilahun; Mommens, Maren; Meenakshi Sundaram, Arvind Yegambaram; Dhanasiri, Anusha Krishanthi Shyama & Babiak, Igor (2019). Postovulatory maternal transcriptome in Atlantic salmon and its relation to developmental potential of embryos. BMC Genomics. ISSN 1471-2164. 20(1). doi: 10.1186/s12864-019-5667-4. Full text in Research Archive Show summary

  Background Early development of an oviparous organism is based on maternally stocked structural, nutritional and regulatory components. These components influence the future developmental potential of an embryo, which is referred to as egg quality. Until zygotic genome activation, translational activity in a fish early embryo is limited to parentally inherited transcripts only. In this study, we asked whether egg transcriptome is associated with egg quality in Atlantic salmon (Salmo salar), which is capable of storing ovulated eggs in its abdominal cavity for a long time before spawning. Results We analyzed messenger RNA (mRNA) and micro RNA (miRNA) transcriptomes throughout the post-ovulatory egg retention period in batches of eggs from two quality groups, good and poor, classified based on the future developmental performance. We identified 28,551 protein-coding genes and 125 microRNA families, with 200 mRNAs and 5 miRNAs showing differential abundance between egg quality groups and/or among postovulatory ages. Transcriptome dynamics during the egg retention period was different in the two egg quality groups. We identified only a single gene, hepcidin-1, as a potential marker for Atlantic salmon egg quality evaluation. Conclusion The overlapping effect of post-ovulatory age on intrinsic egg developmental competence makes the quantification of egg quality difficult when based on transcripts abundance only.

• Karlsen, Tommy Aleksander; Meenakshi Sundaram, Arvind Yegambaram & Brinchmann, Jan E. (2019). Single-Cell RNA Sequencing of In Vitro Expanded Chondrocytes: MSC-Like Cells With No Evidence of Distinct Subsets. Cartilage. ISSN 1947-6035. doi: 10.1177/1947603519847746.
• Choquet, Marvin ; Smolina, Irina Vladimirovna; Dhanasiri, Anusha Krishanthi Shyama; Blanco-Bercial, Leocadio; Kopp, Martina Elisabeth Luise & Jüterbock, Alexander Oliver [Show all 8 contributors for this article] (2019). Towards population genomics in non-model species with large genomes: a case study of the marine zooplankton Calanus finmarchicus. Royal Society Open Science. ISSN 2054-5703. 6(2). doi: 10.1098/rsos.180608. Full text in Research Archive
• Eguiluz-Gracia, Ibon; Malmström, Kristiina; Dheyauldeen, Sinan; Lohi, Jouko; Sajantila, Antti & Aaløkken, Ragnhild [Show all 11 contributors for this article] (2018). Monocytes accumulate in the airways of children with fatal asthma. Clinical and Experimental Allergy. ISSN 0954-7894. 48(12), p. 1631–1639. doi: 10.1111/cea.13265. Full text in Research Archive Show summary

  Background Activated T helper type 2 (Th2) cells are believed to play a pivotal role in allergic airway inflammation, but which cells attract and activate Th2 cells locally have not been fully determined. Recently, it was shown in an experimental human model of allergic rhinitis (AR) that activated monocytes rapidly accumulate in the nasal mucosa after local allergen challenge, where they promote recruitment of Th2 cells and eosinophils. Objective To investigate whether monocytes are recruited to the lungs in paediatric asthma. Methods Tissue samples obtained from children and adolescents with fatal asthma attack (n = 12), age‐matched non‐atopic controls (n = 9) and allergen‐challenged AR patients (n = 8) were subjected to in situ immunostaining. Results Monocytes, identified as CD68+S100A8/A9+ cells, were significantly increased in the lower airway mucosa and in the alveoli of fatal asthma patients compared with control individuals. Interestingly, cellular aggregates containing CD68+S100A8/A9+ monocytes obstructing the lumen of bronchioles were found in asthmatics (8 out of 12) but not in controls. Analysing tissue specimens from challenged AR patients, we confirmed that co‐staining with CD68 and S100A8/A9 was a valid method to identify recently recruited monocytes. We also showed that the vast majority of accumulating monocytes both in the lungs and in the nasal mucosa expressed matrix metalloproteinase 10, suggesting that this protein may be involved in their migration within the tissue. Conclusions and clinical relevance Monocytes accumulated in the lungs of children and adolescents with fatal asthma attack. This finding strongly suggests that monocytes are directly involved in the immunopathology of asthma and that these pro‐inflammatory cells are potential targets for therapy.

• Bakke, Marit Jørgensen; Agusti-Ridaura, Celia; Bruusgaard, Jo C.; Meenakshi Sundaram, Arvind Yegambaram & Horsberg, Tor Einar (2018). Deltamethrin resistance in the salmon louse, Lepeophtheirus salmonis (Krøyer): Maternal inheritance and reduced apoptosis . Scientific Reports. ISSN 2045-2322. 8. doi: 10.1038/s41598-018-26420-6. Full text in Research Archive
• Sarropoulou, Elena; Meenakshi Sundaram, Arvind Yegambaram; Kaitetzidou, Elisavet; Kotoulas, Georgios; Gilfillan, Gregor Duncan & Papandroulakis, Nikos [Show all 8 contributors for this article] (2017). Full genome survey and dynamics of gene expression in the greater amberjack Seriola dumerili. GigaScience. ISSN 2047-217X. 6(12), p. 1–13. doi: 10.1093/gigascience/gix108.
• Falch, Camilla Maria; Meenakshi Sundaram, Arvind Yegambaram; Øystese, Kristin Astrid Berland; Normann, Kjersti Ringvoll; Lekva, Tove & Silamikelis, Ivars [Show all 10 contributors for this article] (2017). Gene expression profiling of fast- and slow-growing non-functioning gonadotroph pituitary adenomas. European Journal of Endocrinology (EJE). ISSN 0804-4643. 178(3), p. 295–307. doi: 10.1530/EJE-17-0702.
• de Muinck, Eric; Trosvik, Pål; Gilfillan, Gregor Duncan; Hov, Johannes Espolin Roksund & Sundaram, Arvind (2017). A novel ultra high-throughput 16S rRNA gene amplicon sequencing library preparation method for the Illumina HiSeq platform. Microbiome. ISSN 2049-2618. doi: 10.1186/s40168-017-0279-1.
• Fuglerud, Bettina Maria; Lemma, Roza Berhanu; Wanichawan, Pimthanya; Sundaram, Arvind; Eskeland, Ragnhild & Gabrielsen, Odd Stokke (2017). A c-Myb mutant causes deregulated differentiation due to impaired histone binding and abrogated pioneer factor function. Nucleic Acids Research (NAR). ISSN 0305-1048. 45(13), p. 7681–7696. doi: 10.1093/nar/gkx364. Full text in Research Archive
• Sundaram, Arvind; Tengs, Torstein & Grimholt, Unni (2017). Issues with RNA-Seq analysis in non-model organisms: a Salmonid example. Developmental and Comparative Immunology. ISSN 0145-305X. 75, p. 38–47. doi: 10.1016/j.dci.2017.02.006.
• Sundaram, Arvind; Hughes, Timothy; Biondi, Shea; Bolduc, Nathalie; Bowman, Sarah K & Camilli, Andrew [Show all 17 contributors for this article] (2016). A comparative study of ChIP-seq sequencing library preparation methods. BMC Genomics. ISSN 1471-2164. 17(1). doi: 10.1186/s12864-016-3135-y.
• Sarropoulou, Elena; Tsalafouta, Alexandra; Sundaram, Arvind; Gilfillan, Gregor Duncan; Kotoulas, Georgios & Papandroulakis, Nikos [Show all 7 contributors for this article] (2016). Transcriptomic changes in relation to early-life events in the gilthead sea bream (Sparus aurata). BMC Genomics. ISSN 1471-2164. 17:506, p. 1–14. doi: 10.1186/s12864-016-2874-0.
• Smolina, Irina; Kollias, Spyros; Møller, Eva Friis; Lindeque, Penelope K.; Sundaram, Arvind & Fernandes, Jorge [Show all 7 contributors for this article] (2015). Contrasting transcriptome response to thermal stress in two key zooplankton species, Calanus finmarchicus and C. glacialis. Marine Ecology Progress Series. ISSN 0171-8630. 534, p. 79–93. doi: 10.3354/meps11398. Full text in Research Archive
• Campos, Catarina; Sundaram, Arvind; Valente, L. M. P.; Conceicao, Luis E.C.; Engrola, Sofia & Fernandes, Jorge (2014). Thermal plasticity of the miRNA transcriptome during Senegalese sole development. BMC Genomics. ISSN 1471-2164. 15(525). doi: 10.1186/1471-2164-15-525. Full text in Research Archive Show summary

  Background Several miRNAs are known to control myogenesis in vertebrates. Some of them are specifically expressed in muscle while others have a broader tissue expression but are still involved in establishing the muscle phenotype. In teleosts, water temperature markedly affects embryonic development and larval growth. It has been previously shown that higher embryonic temperatures promoted faster development and increased size of Senegalese sole (Solea senegalensis) larvae relatively to a lower temperature. The role of miRNAs in thermal-plasticity of growth is hitherto unknown. Hence, we have used high-throughput SOLiD sequencing to determine potential changes in the miRNA transcriptome in Senegalese sole embryos that were incubated at 15 ºC or 21 ºC until hatching and then reared at a common temperature of 21 ºC. Results We have identified 320 conserved miRNAs in Senegalese sole, of which 48 had not been previously described in teleosts. mir-17a-5p, mir-26a, mir-130c, mir-206-3p, mir-181a-5p, mir-181a-3p and mir-199a-5p expression levels were further validated by RT- qPCR. The majority of miRNAs were dynamically expressed during early development, with peaks of expression at pre-metamorphosis or metamorphosis. Also, a higher incubation temperature (21 ºC) was associated with expression of some miRNAs positively related with growth (e.g., miR-17a, miR-181-5p and miR-206) during segmentation and at hatching. Target prediction revealed that these miRNAs may regulate myogenesis through MAPK and mTOR pathways. Expression of miRNAs involved in lipid metabolism and energy production (e.g., miR-122) also differed between temperatures. A miRNA that can potentially target calpain (miR-181-3p), and therefore negatively regulate myogenesis, was preferentially expressed during segmentation at 15 ºC compared to 21 ºC. Conclusions Temperature has a strong influence on expression of miRNAs during embryonic and larval development in fish. Higher expression levels of miR-17a, miR-181-5p and miR-206-3p and down-regulation of miR-181a-3p at 21 ºC may promote myogenesis and are in agreement with previous studies in Senegalese sole, which reported enhanced growth at higher embryonic temperatures compared to 15 ºC. Moreover, miRNAs involved in lipid metabolism and energy production may also contribute to increased larval growth at 21 ºC compared to 15 ºC. Taken together, our data indicate that miRNAs may play a role in temperature-induced phenotypic plasticity of growth in teleosts.

• Sundaram, Arvind; Viswanath, Kiron; Dopazo, Joaquin & Fernandes, Jorge (2012). Diversification of the expanded teleost-specific toll-like receptor family in Atlantic cod, Gadus morhua. BMC Evolutionary Biology. ISSN 1471-2148. 12(1). doi: 10.1186/1471-2148-12-256. Full text in Research Archive
• Sundaram, Arvind; Consuegra, S; Viswanath, Kiron & Fernandes, Jorge (2012). Positive selection pressure within teleost toll-like receptors tlr21 and tlr22 subfamilies and their response to temperature stress and microbial components in zebrafish. Molecular Biology Reports. ISSN 0301-4851. 39(9), p. 8965–8975. doi: 10.1007/s11033-012-1765-y.
• Myant, Kevin; Termanis, Ausma; Sundaram, Arvind; Boe, Tristin; Li, Chao & Merusi, Cara [Show all 9 contributors for this article] (2011). LSH and G9a/GLP complex are required for developmentally programmed DNA methylation. Genome Research. ISSN 1088-9051. 21, p. 83–94. doi: 10.1101/gr.108498.110. Full text in Research Archive

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• Bjørnstad, Pål Marius; aaløkken, Ragnhild Margrethe; Åsheim, June; Sundaram, Arvind; Nangota Felde, Caroline & Østby, Gina Henriette [Show all 15 contributors for this article] (2024). Publisher Correction: A 39 kb structural variant causing Lynch syndrome detected by optical genome mapping and nanopore sequencing (European Journal of Human Genetics, (2023), 10.1038/s41431-023-01494-7). European Journal of Human Genetics. ISSN 1018-4813. doi: 10.1038/s41431-023-01519-1.
• Tsoulia, Thomais; Sundaram, Arvind; Braaen, Stine; Wessel, Øystein; Rimstad, Espen & Dahle, Maria Krudtå (2023). Transcriptome responses of Atlantic salmon blood cells to Piscine orthoreovirus variants.
• Grimholt, Unni; Sundaram, Arvind; Bøe, Cathrine Arnason; Dahle, Maria K. & Lukacs, Morten Ferenc (2022). Two diverse T cell receptor beta regions in Atlantic salmon potentially serving different functions.
• Grimholt, Unni; Sundaram, Arvind; Bøe, Cathrine Arnason; Dahle, Maria & Lukacs, Morten Ferenc (2022). Two diverse T cell receptor beta regions in Atlantic salmon potentially serving different functions.
• Tsoulia, Thomais; Sundaram, Arvind; Rimstad, Espen; Wessel, Øystein & Dahle, Maria (2022). Comparison of whole blood transcriptome responses of Atlantic salmon infected by three Piscine orthoreovirus variants.
• Solhaug, Anita; Sindre, Hilde; Gjessing, Mona Cecilie; Dahle, Maria; Ivanova, Lada & Fæste, Christiane Kruse [Show all 17 contributors for this article] (2022). Karakterisering av en cellemodell for studier av miljøfaktorer på gjellefunksjonen til Atlantisk laks.
• Tsoulia, Thomais; Sundaram, Arvind; Braaen, Stine; Haugland, Øyvind; Rimstad, Espen & Wessel, Øystein [Show all 7 contributors for this article] (2022). Early transcriptome response to Piscine orthoreovirus -1 in Atlantic salmon erythrocytes, compared to salmon kidney cell lines.
• Grimholt, Unni; Garseth, Åse Helen & Sundaram, Arvind Yegambaram Meenakshi (2020). Kartlegging av Immunologisk mangfold i villlaks - behov og muligheter.
• Sundaram, Arvind Yegambaram Meenakshi; Garseth, Åse Helen; Maccari, Giuseppe & Grimholt, Unni (2020). Correction to: An Illumina approach to MHC typing of Atlantic salmon. Immunogenetics. ISSN 0093-7711. 72(1-2), p. 133–133. doi: 10.1007/s00251-019-01152-7.
• Pettersen, Kristin Sæbø; Meenakshi Sundaram, Arvind Yegambaram; Aspholm, Marina; Wasteson, Yngvild; Skjerdal, Olaug Taran & Lindbäck, Toril [Show all 7 contributors for this article] (2018). Hvordan påvirkes Listeria monocytogenes av synlig lys?
• Pettersen, Kristin Sæbø; Meenakshi Sundaram, Arvind Yegambaram; Skjerdal, Olaug Taran; Wasteson, Yngvild; Lindbäck, Toril & Kijewski, Anne Cecilie Riihonen [Show all 7 contributors for this article] (2018). Shining light on L. monocytogenes – a transcriptome analysis .
• Lunestad, Bjørn Tore; Brandal, Lin Cathrine T.; Meenakshi Sundaram, Arvind Yegambaram; Naseer, Mohammed Umaer & Løvdal, Trond (2018). Comparative genome analysis of Listeria monocytogenes isolated from salmon processing environments and clinical cases.
• Løvdal, Trond; Brandal, Lin Thorstensen; Sundaram, Arvind Y.M.; Naseer, Mohammed Umaer & Lunestad, Bjørn Tore (2017). Whole Genome Sequencing of Listeria Monocytogenes Strains Isolated from Salmon Processing Plants; Typing and Detection of Virulence and Resistance Genes and Comparison to Isolates Associated with Human Listeriosis.
• Lazado, Carlo Cabacang; Nagasawa, Kazue; Babiak, Igor; Fernandes, Jorge; Gianetto, Alessia & Sundaram, Arvind (2013). The gonadal miRNA transcriptome of Atlantic cod: Does sexual maturation alter the microRNA repertoire?
• Fernandes, Jorge; Sundaram, Arvind; Kiron, V. & Jørgensen, Jorunn B (2013). Regulation of the innate immune response by microRNAs in zebrafish. Fish and Shellfish Immunology. ISSN 1050-4648. 34(6), p. 1706–1706.
• Sundaram, Arvind; Viswanath, Kiron & Fernandes, Jorge (2012). Evidence of selection pressure within multiple toll-like receptor 22 paralogues in Atlantic cod.
• Sundaram, Arvind; Viswanath, Kiron & Fernandes, Jorge (2012). Multiple toll-like receptor 22 paralogues in Atlantic cod.
• Sundaram, Arvind; Viswanath, Kiron; Dopazo, Joaquin & Fernandes, Jorge (2011). MicroRNA profiling of zebrafish embryos following antigenic stimulation. Show summary

  MicroRNAs (miRNA) are a class of small, 22-24 nucleotide RNAs that play a crucial role in controlling gene expression by fine tuning mRNA translation, thus regulating many fundamental biological processes. In order to establish the role played by individual miRNAs in the innate immune response, their expression changes with antigenic stimulation was quantified in zebrafish (Danio rerio) larvae by microarray analysis. Three day old zebrafish larvae were stimulated with lipopolysaccharide from Salmonella typhimurium or peptidoglycan from Staphylococcus aureus. The Agilent 15k microarray containing probes for all 358 known zebrafish miRNAs was used to quantify their expression. Differential miRNA expression in response to the above two immuno-stimulants was examined and significantly regulated miRNAs exhibiting a greater than 2-fold change were mapped to the immune response pathway. A subset of 20 differentially expressed miRNAs was selected for validation by real-time PCR.

• Sundaram, Arvind & Fernandes, Jorge (2010). Selection pressure in fish-specific Toll-like receptors. Show summary

  Toll-like receptors (TLRs) play a central role in recognising pathogen-associated molecular patterns and activating a downstream immune response in teleost fish. Fish-specific TLRs (tlr21, tlr22a, tlr22b, tlr23) have been identified in various teleost species for which mammalian orthologues do not exist or are present as a non-functional pseudogene. Fish-specific TLRs are important as they may play a crucial role in host defence, since teleosts have a more primitive adaptive immune system, constrained by environmental factors. It is likely that positive natural selection is shaping the evolutionary pattern of fish-specific TLRs, which might be associated with adaptation to new habitats and rapidly evolving pathogens. We present the results of likelihood selection tests to ascertain the type and functional implications of the selection pressure acting on tlr21, tlr22 and tlr23.

• Sundaram, Arvind & Fernandes, Jorge (2009). Zebrafish TLR network response to different bacterial infections - a bioinformatic analysis. Show summary

  Our knowledge regarding the genetic networks that regulate the specificity of the innate immune response is extremely limited. Toll-like receptors (TLRs) are evolutionarily conserved components of the innate immune system that play a vital role in pathogen recognition by detecting pathogen associated molecular patterns. They are also responsible for triggering pathways that result in relatively specific immune responses. Zebrafish is particularly useful model system to study innate immunity, since they take 4 to 6 weeks to develop a fully functional adaptive immune response. Time-course microarray data from zebrafish embryos challenged independently with Salmonella typhimurium and Mycobacterium marinum have been recently published. Here we present the bioinformatic analysis of their transcriptomes, with particular focus on the expression of the genes found in the TLR pathways and we highlight the similarities and differences within and between the two studies.

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