{"entity": "researcher", "timestamp": "2026-10-14T01:33:02.384Z", "family": "Ankarklev", "given": "Johan", "initials": "J", "orcid": "0000-0003-3170-8493", "affiliations": ["Molecular Biosciences, the Wenner-Gren Institute, Stockholm University, Sweden."], "links": {"self": {"href": "https://publications.scilifelab.se/researcher/dcf5386930e34157bf76970b16bffc02.json"}, "display": {"href": "https://publications.scilifelab.se/researcher/dcf5386930e34157bf76970b16bffc02"}}, "publications": [{"entity": "publication", "iuid": "09b2174874b74c20886dd68920d6961e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/09b2174874b74c20886dd68920d6961e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/09b2174874b74c20886dd68920d6961e"}}, "title": "Single-cell transcriptomics reveal transcriptional programs underlying male and female cell fate during Plasmodium falciparum gametocytogenesis.", "authors": [{"family": "Mohammed", "given": "Mubasher", "initials": "M"}, {"family": "Dziedziech", "given": "Alexis", "initials": "A"}, {"family": "Macedo", "given": "Diego", "initials": "D"}, {"family": "Huppertz", "given": "Frederik", "initials": "F"}, {"family": "Veith", "given": "Ylva", "initials": "Y", "orcid": "0000-0002-1810-8808", "researcher": {"href": "https://publications.scilifelab.se/researcher/9e316fdf93964e89a0606e68da08c336.json"}}, {"family": "Postel", "given": "Zo\u00e9", "initials": "Z", "orcid": "0000-0003-0502-2375", "researcher": {"href": "https://publications.scilifelab.se/researcher/0481ff1051564262af4e5384cbd17ac3.json"}}, {"family": "Christ", "given": "Elena", "initials": "E"}, {"family": "Scheytt", "given": "Richard", "initials": "R", "orcid": "0009-0004-1405-6360", "researcher": {"href": "https://publications.scilifelab.se/researcher/3866987412724150b6af427c16dd17cf.json"}}, {"family": "Slotte", "given": "Tanja", "initials": "T", "orcid": "0000-0001-6020-5102", "researcher": {"href": "https://publications.scilifelab.se/researcher/67c69ee78bae41478465a7e5fa63b946.json"}}, {"family": "Henriksson", "given": "Johan", "initials": "J", "orcid": "0000-0002-7745-2844", "researcher": {"href": "https://publications.scilifelab.se/researcher/44339821900646b3881d4b4dfd09e8d5.json"}}, {"family": "Ankarklev", "given": "Johan", "initials": "J", "orcid": "0000-0003-3170-8493", "researcher": {"href": "https://publications.scilifelab.se/researcher/dcf5386930e34157bf76970b16bffc02.json"}}], "type": "journal article", "published": "2024-08-26", "journal": {"title": "Nat Commun", "issn": "2041-1723", "issn-l": "2041-1723", "volume": "15", "issue": "1", "pages": "7177"}, "abstract": "The Plasmodium falciparum life cycle includes obligate transition between a human and mosquito host. Gametocytes are responsible for transmission from the human to the mosquito vector where gamete fusion followed by meiosis occurs. To elucidate how male and female gametocytes differentiate in the absence of sex chromosomes, we perform FACS-based cell enrichment of a P. falciparum gametocyte reporter line followed by single-cell RNA-seq. In our analyses we define the transcriptional programs and predict candidate driver genes underlying male and female development, including genes from the ApiAP2 family of transcription factors. A motif-driven, gene regulatory network analysis indicates that AP2-G5 specifically modulates male development. Additionally, genes linked to the inner membrane complex, involved in morphological changes, are uniquely expressed in the female lineage. The transcriptional programs of male and female development detailed herein allow for further exploration of the evolution of sex in eukaryotes and provide targets for future development of transmission blocking therapies.", "doi": "10.1038/s41467-024-51201-3", "pmid": "39187486", "labels": {"Bioinformatics Support for Computational Resources": "Service", "National Genomics Infrastructure": null, "NGI Stockholm (Genomics Production)": null, "NGI Short read": null}, "xrefs": [{"db": "pmc", "key": "PMC11347709"}, {"db": "pii", "key": "10.1038/s41467-024-51201-3"}], "notes": [], "created": "2024-11-25T10:17:42.276Z", "modified": "2025-07-18T10:45:32.069Z"}, {"entity": "publication", "iuid": "c0cac7649e664f42a2dad23b77043ae7", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c0cac7649e664f42a2dad23b77043ae7.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c0cac7649e664f42a2dad23b77043ae7"}}, "title": "Host-pathogen interactions in the Plasmodium-infected mouse liver at spatial and single-cell resolution.", "authors": [{"family": "Hildebrandt", "given": "Franziska", "initials": "F", "orcid": "0000-0002-2673-1704", "researcher": {"href": "https://publications.scilifelab.se/researcher/4c69d2d421d64a11a719a6fd55c1977a.json"}}, {"family": "Iturritza", "given": "Miren Urrutia", "initials": "MU", "orcid": "0000-0002-3989-1803", "researcher": {"href": "https://publications.scilifelab.se/researcher/65bc5beb14634ef9af3d153c19355794.json"}}, {"family": "Zwicker", "given": "Christian", "initials": "C"}, {"family": "Vanneste", "given": "Bavo", "initials": "B"}, {"family": "Van Hul", "given": "No\u00e9mi", "initials": "N", "orcid": "0000-0003-1410-8808", "researcher": {"href": "https://publications.scilifelab.se/researcher/ce1f79e0359b45c9991d14649ad4bc2b.json"}}, {"family": "Semle", "given": "Elisa", "initials": "E"}, {"family": "Quin", "given": "Jaclyn", "initials": "J"}, {"family": "Pascini", "given": "Tales", "initials": "T"}, {"family": "Saarenp\u00e4\u00e4", "given": "Sami", "initials": "S", "orcid": "0000-0003-4731-6857", "researcher": {"href": "https://publications.scilifelab.se/researcher/ee6979cdfc0b4e4285f9d810c39bb7b7.json"}}, {"family": "He", "given": "Mengxiao", "initials": "M", "orcid": "0000-0001-5905-8467", "researcher": {"href": "https://publications.scilifelab.se/researcher/79045a6ac62b4f8ea64233619eb6bfc9.json"}}, {"family": "Andersson", "given": "Emma R", "initials": "ER", "orcid": "0000-0002-8608-625X", "researcher": {"href": "https://publications.scilifelab.se/researcher/1c7313cdcd5f41d4a567a6c315aac3a1.json"}}, {"family": "Scott", "given": "Charlotte L", "initials": "CL", "orcid": "0000-0003-4914-6580", "researcher": {"href": "https://publications.scilifelab.se/researcher/75d25f2a77f9444bb6e57ade9a1388a3.json"}}, {"family": "Vega-Rodriguez", "given": "Joel", "initials": "J", "orcid": "0000-0002-9576-0058", "researcher": {"href": "https://publications.scilifelab.se/researcher/a89fc53ed4fb4e179636b66ae8d1caa3.json"}}, {"family": "Lundeberg", "given": "Joakim", "initials": "J", "orcid": "0000-0003-4313-1601", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a4e6ca0f29b4ead8569e2729481c3e0.json"}}, {"family": "Ankarklev", "given": "Johan", "initials": "J", "orcid": "0000-0003-3170-8493", "researcher": {"href": "https://publications.scilifelab.se/researcher/dcf5386930e34157bf76970b16bffc02.json"}}], "type": "journal article", "published": "2024-08-19", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "15", "issue": "1", "pages": "7105", "issn-l": "2041-1723"}, "abstract": "Upon infecting its vertebrate host, the malaria parasite initially invades the liver where it undergoes massive replication, whilst remaining clinically silent. The coordination of host responses across the complex liver tissue during malaria infection remains unexplored. Here, we perform spatial transcriptomics in combination with single-nuclei RNA sequencing over multiple time points to delineate host-pathogen interactions across Plasmodium berghei-infected liver tissues. Our data reveals significant changes in spatial gene expression in the malaria-infected tissues. These include changes related to lipid metabolism in the proximity to sites of Plasmodium infection, distinct inflammation programs between lobular zones, and regions with enrichment of different inflammatory cells, which we term 'inflammatory hotspots'. We also observe significant upregulation of genes involved in inflammation in the control liver tissues of mice injected with mosquito salivary gland components. However, this response is considerably delayed compared to that observed in P. berghei-infected mice. Our study establishes a benchmark for investigating transcriptome changes during host-parasite interactions in tissues, it provides informative insights regarding in vivo study design linked to infection and offers a useful tool for the discovery and validation of de novo intervention strategies aimed at malaria liver stage infection.", "doi": "10.1038/s41467-024-51418-2", "pmid": "39160174", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11333755"}, {"db": "pii", "key": "10.1038/s41467-024-51418-2"}], "notes": [], "created": "2024-11-25T10:17:47.545Z", "modified": "2024-11-25T10:17:47.707Z"}, {"entity": "publication", "iuid": "d62091617279400ebe9fd264e641f6bc", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d62091617279400ebe9fd264e641f6bc.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d62091617279400ebe9fd264e641f6bc"}}, "title": "Single-Cell Transcriptomics To Define Plasmodium falciparum Stage Transition in the Mosquito Midgut.", "authors": [{"family": "Mohammed", "given": "Mubasher", "initials": "M"}, {"family": "Dziedziech", "given": "Alexis", "initials": "A"}, {"family": "Sekar", "given": "Vaishnovi", "initials": "V"}, {"family": "Ernest", "given": "Medard", "initials": "M"}, {"family": "Alves E Silva", "given": "Thiago Luiz", "initials": "TL"}, {"family": "Balan", "given": "Balu", "initials": "B"}, {"family": "Emami", "given": "S Noushin", "initials": "SN"}, {"family": "Biryukova", "given": "Inna", "initials": "I"}, {"family": "Friedl\u00e4nder", "given": "Marc R", "initials": "MR"}, {"family": "Jex", "given": "Aaron", "initials": "A", "orcid": "0000-0002-1285-7947", "researcher": {"href": "https://publications.scilifelab.se/researcher/cd00075176a841c1ad916a094a182f6c.json"}}, {"family": "Jacobs-Lorena", "given": "Marcelo", "initials": "M"}, {"family": "Henriksson", "given": "Johan", "initials": "J"}, {"family": "Vega-Rodriguez", "given": "Joel", "initials": "J"}, {"family": "Ankarklev", "given": "Johan", "initials": "J", "orcid": "0000-0003-3170-8493", "researcher": {"href": "https://publications.scilifelab.se/researcher/dcf5386930e34157bf76970b16bffc02.json"}}], "type": "journal article", "published": "2023-02-27", "journal": {"title": "Microbiol Spectr", "issn": "2165-0497", "volume": "11", "issue": "2", "pages": "e0367122", "issn-l": null}, "abstract": "Malaria inflicts the highest rate of morbidity and mortality among the vector-borne diseases. The dramatic bottleneck of parasite numbers that occurs in the gut of the obligatory mosquito vector provides a promising target for novel control strategies. Using single-cell transcriptomics, we analyzed Plasmodium falciparum development in the mosquito gut, from unfertilized female gametes through the first 20 h after blood feeding, including the zygote and ookinete stages. This study revealed the temporal gene expression of the ApiAP2 family of transcription factors and of parasite stress genes in response to the harsh environment of the mosquito midgut. Further, employing structural protein prediction analyses, we found several upregulated genes predicted to encode intrinsically disordered proteins (IDPs), a category of proteins known for their importance in regulation of transcription, translation, and protein-protein interactions. IDPs are known for their antigenic properties and may serve as suitable targets for antibody- or peptide-based transmission suppression strategies. In total, this study uncovers the P. falciparum transcriptome from early to late parasite development in the mosquito midgut, inside its natural vector, which provides an important resource for future malaria transmission-blocking initiatives. IMPORTANCE The malaria parasite Plasmodium falciparum causes more than half a million deaths per year. The current treatment regimen targets the symptom-causing blood stage inside the human host. However, recent incentives in the field call for novel interventions to block parasite transmission from humans to the mosquito vector. Therefore, we need to better understand the parasite biology during its development inside the mosquito, including a deeper understanding of the expression of genes controlling parasite progression during these stages. Here, we have generated single-cell transcriptome data, covering P. falciparum's development, from gamete to ookinete inside the mosquito midgut, uncovering previously untapped parasite biology, including a repertoire of novel biomarkers to be explored in future transmission-blocking efforts. We anticipate that our study provides an important resource, which can be further explored to improve our understanding of the parasite biology as well as aid in guiding future malaria intervention strategies.", "doi": "10.1128/spectrum.03671-22", "pmid": "36847501", "labels": {"Microbial Single Cell Genomics": "Service", "Bioinformatics Support for Computational Resources": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10100735"}], "notes": [], "created": "2023-10-06T12:15:41.309Z", "modified": "2024-10-16T07:05:39.782Z"}, {"entity": "publication", "iuid": "8cbacd9195c24dc99bee025eebec1ab8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8cbacd9195c24dc99bee025eebec1ab8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8cbacd9195c24dc99bee025eebec1ab8"}}, "title": "Spatial Transcriptomics to define transcriptional patterns of zonation and structural components in the mouse liver.", "authors": [{"family": "Hildebrandt", "given": "Franziska", "initials": "F", "orcid": "0000-0002-2673-1704", "researcher": {"href": "https://publications.scilifelab.se/researcher/4c69d2d421d64a11a719a6fd55c1977a.json"}}, {"family": "Andersson", "given": "Alma", "initials": "A"}, {"family": "Saarenp\u00e4\u00e4", "given": "Sami", "initials": "S"}, {"family": "Larsson", "given": "Ludvig", "initials": "L", "orcid": "0000-0003-4209-2911", "researcher": {"href": "https://publications.scilifelab.se/researcher/e9ffc7de05a040c48011a6ba639d5851.json"}}, {"family": "Van Hul", "given": "No\u00e9mi", "initials": "N", "orcid": "0000-0003-1410-8808", "researcher": {"href": "https://publications.scilifelab.se/researcher/ce1f79e0359b45c9991d14649ad4bc2b.json"}}, {"family": "Kanatani", "given": "Sachie", "initials": "S"}, {"family": "Masek", "given": "Jan", "initials": "J", "orcid": "0000-0003-2904-3808", "researcher": {"href": "https://publications.scilifelab.se/researcher/23cbd5352a924afcb2fa82185b237cbd.json"}}, {"family": "Ellis", "given": "Ewa", "initials": "E", "orcid": "0000-0002-3057-5337", "researcher": {"href": "https://publications.scilifelab.se/researcher/82ef7cf7903140cfbb7ff8d6f4961dde.json"}}, {"family": "Barragan", "given": "Antonio", "initials": "A", "orcid": "0000-0001-7746-9964", "researcher": {"href": "https://publications.scilifelab.se/researcher/4eefb95f00db42e3891769f384269c6c.json"}}, {"family": "Mollbrink", "given": "Annelie", "initials": "A"}, {"family": "Andersson", "given": "Emma R", "initials": "ER", "orcid": "0000-0002-8608-625X", "researcher": {"href": "https://publications.scilifelab.se/researcher/1c7313cdcd5f41d4a567a6c315aac3a1.json"}}, {"family": "Lundeberg", "given": "Joakim", "initials": "J", "orcid": "0000-0003-4313-1601", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a4e6ca0f29b4ead8569e2729481c3e0.json"}}, {"family": "Ankarklev", "given": "Johan", "initials": "J", "orcid": "0000-0003-3170-8493", "researcher": {"href": "https://publications.scilifelab.se/researcher/dcf5386930e34157bf76970b16bffc02.json"}}], "type": "journal article", "published": "2021-12-02", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "12", "issue": "1", "pages": "7046", "issn-l": "2041-1723"}, "abstract": "Reconstruction of heterogeneity through single cell transcriptional profiling has greatly advanced our understanding of the spatial liver transcriptome in recent years. However, global transcriptional differences across lobular units remain elusive in physical space. Here, we apply Spatial Transcriptomics to perform transcriptomic analysis across sectioned liver tissue. We confirm that the heterogeneity in this complex tissue is predominantly determined by lobular zonation. By introducing novel computational approaches, we enable transcriptional gradient measurements between tissue structures, including several lobules in a variety of orientations. Further, our data suggests the presence of previously transcriptionally uncharacterized structures within liver tissue, contributing to the overall spatial heterogeneity of the organ. This study demonstrates how comprehensive spatial transcriptomic technologies can be used to delineate extensive spatial gene expression patterns in the liver, indicating its future impact for studies of liver function, development and regeneration as well as its potential in pre-clinical and clinical pathology.", "doi": "10.1038/s41467-021-27354-w", "pmid": "34857782", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-021-27354-w"}, {"db": "pmc", "key": "PMC8640072"}], "notes": [], "created": "2022-11-09T15:54:10.121Z", "modified": "2024-01-16T13:48:38.011Z"}, {"entity": "publication", "iuid": "4bfa34257a69416590d769c5a7af7e95", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4bfa34257a69416590d769c5a7af7e95.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4bfa34257a69416590d769c5a7af7e95"}}, "title": "Transcriptome profiling of Giardia intestinalis using strand-specific RNA-seq.", "authors": [{"family": "Franz\u00e9n", "given": "Oscar", "initials": "O"}, {"family": "Jerlstr\u00f6m-Hultqvist", "given": "Jon", "initials": "J"}, {"family": "Einarsson", "given": "Elin", "initials": "E"}, {"family": "Ankarklev", "given": "Johan", "initials": "J", "orcid": "0000-0003-3170-8493", "researcher": {"href": "https://publications.scilifelab.se/researcher/dcf5386930e34157bf76970b16bffc02.json"}}, {"family": "Ferella", "given": "Marcela", "initials": "M"}, {"family": "Andersson", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Sv\u00e4rd", "given": "Staffan G", "initials": "SG"}], "type": "journal article", "published": "2013-03-28", "journal": {"volume": "9", "issn": "1553-7358", "issue": "3", "pages": "e1003000", "title": "PLoS Comput. Biol.", "issn-l": "1553-734X"}, "abstract": "Giardia intestinalis is a common cause of diarrheal disease and it consists of eight genetically distinct genotypes or assemblages (A-H). Only assemblages A and B infect humans and are suggested to represent two different Giardia species. Correlations exist between assemblage type and host-specificity and to some extent symptoms. Phenotypical differences have been documented between assemblages and genome sequences are available for A, B and E. We have characterized and compared the polyadenylated transcriptomes of assemblages A, B and E. Four genetically different isolates were studied (WB (AI), AS175 (AII), P15 (E) and GS (B)) using paired-end, strand-specific RNA-seq. Most of the genome was transcribed in trophozoites grown in vitro, but at vastly different levels. RNA-seq confirmed many of the present annotations and refined the current genome annotation. Gene expression divergence was found to recapitulate the known phylogeny, and uncovered lineage-specific differences in expression. Polyadenylation sites were mapped for over 70% of the genes and revealed many examples of conserved and unexpectedly long 3' UTRs. 28 open reading frames were found in a non-transcribed gene cluster on chromosome 5 of the WB isolate. Analysis of allele-specific expression revealed a correlation between allele-dosage and allele expression in the GS isolate. Previously reported cis-splicing events were confirmed and global mapping of cis-splicing identified only one novel intron. These observations can possibly explain differences in host-preference and symptoms, and it will be the basis for further studies of Giardia pathogenesis and biology.", "doi": "10.1371/journal.pcbi.1003000", "pmid": "23555231", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [{"db": "pii", "key": "PCOMPBIOL-D-12-01572"}, {"db": "pmc", "key": "PMC3610916"}, {"db": "GEO", "key": "GSE36490"}], "notes": [], "created": "2017-05-04T15:01:26.084Z", "modified": "2021-07-07T13:58:48.946Z"}]}