{"entity": "researcher", "timestamp": "2026-09-23T21:37:54.089Z", "family": "Allalou", "given": "Amin", "initials": "A", "orcid": "0000-0003-4028-8443", "affiliations": ["Division of Visual Information and Interaction, Department of Information Technology, Uppsala University, S-75105 Uppsala, Sweden.", "BioImage Informatics Facility at SciLifeLab, S-75105 Uppsala, Sweden."], "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/researcher/48a26837e4ce48dfada540aa1dbd23cf.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/researcher/48a26837e4ce48dfada540aa1dbd23cf"}}, "publications": [{"entity": "publication", "iuid": "b133fe25e23448d59edc6b20d0a38b30", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/b133fe25e23448d59edc6b20d0a38b30.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/b133fe25e23448d59edc6b20d0a38b30"}}, "title": "Chondroitin/dermatan sulfate glycosyltransferase genes are essential for craniofacial development.", "authors": [{"family": "Habicher", "given": "Judith", "initials": "J", "orcid": "0000-0002-8691-8650", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4788622ebc424f4e96c8100b99b2294a.json"}}, {"family": "Varshney", "given": "Gaurav K", "initials": "GK", "orcid": "0000-0002-0429-1904", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/427982d66baf4bfab438a1766071036d.json"}}, {"family": "Waldmann", "given": "Laura", "initials": "L", "orcid": "0000-0002-3619-0796", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e7053118951d4bbda72058715017046a.json"}}, {"family": "Snitting", "given": "Daniel", "initials": "D", "orcid": "0000-0001-9704-6336", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7947d4b34495440cb4b0acdbf49bfffb.json"}}, {"family": "Allalou", "given": "Amin", "initials": "A", "orcid": "0000-0003-4028-8443", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/48a26837e4ce48dfada540aa1dbd23cf.json"}}, {"family": "Zhang", "given": "Hanqing", "initials": "H"}, {"family": "Ghanem", "given": "Abdurrahman", "initials": "A", "orcid": "0000-0002-4388-6222", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/71ba79d7402b477ba257510c62900d3b.json"}}, {"family": "\u00d6hman M\u00e4gi", "given": "Caroline", "initials": "C", "orcid": "0000-0003-2709-9541", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2bbc858437bd45f79964add760b31bf6.json"}}, {"family": "Dierker", "given": "Tabea", "initials": "T", "orcid": "0000-0003-1991-2723", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c9ff3f39bc9b48a08cb0f0ad2583f487.json"}}, {"family": "Kjell\u00e9n", "given": "Lena", "initials": "L"}, {"family": "Burgess", "given": "Shawn M", "initials": "SM", "orcid": "0000-0003-1147-0596", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/68cb29ca7d284d7292a0793852d86598.json"}}, {"family": "Ledin", "given": "Johan", "initials": "J", "orcid": "0000-0002-7319-7735", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/08f88f10e2de4379ac9114baf4bddd3d.json"}}], "type": "journal article", "published": "2022-02-00", "journal": {"title": "PLoS Genet", "issn": "1553-7404", "volume": "18", "issue": "2", "pages": "e1010067", "issn-l": "1553-7390"}, "abstract": "Chondroitin/dermatan sulfate (CS/DS) proteoglycans are indispensable for animal development and homeostasis but the large number of enzymes involved in their biosynthesis have made CS/DS function a challenging problem to study genetically. In our study, we generated loss-of-function alleles in zebrafish genes encoding CS/DS biosynthetic enzymes and characterized the effect on development in single and double mutants. Homozygous mutants in chsy1, csgalnact1a, csgalnat2, chpfa, ust and chst7, respectively, develop to adults. However, csgalnact1a-/- fish develop distinct craniofacial defects while the chsy1-/- skeletal phenotype is milder and the remaining mutants display no gross morphological abnormalities. These results suggest a high redundancy for the CS/DS biosynthetic enzymes and to further reduce CS/DS biosynthesis we combined mutant alleles. The craniofacial phenotype is further enhanced in csgalnact1a-/-;chsy1-/- adults and csgalnact1a-/-;csgalnact2-/- larvae. While csgalnact1a-/-;csgalnact2-/- was the most affected allele combination in our study, CS/DS is still not completely abolished. Transcriptome analysis of chsy1-/-, csgalnact1a-/- and csgalnact1a-/-;csgalnact2-/- larvae revealed that the expression had changed in a similar way in the three mutant lines but no differential expression was found in any of fifty GAG biosynthesis enzymes identified. Thus, zebrafish larvae do not increase transcription of GAG biosynthesis genes as a consequence of decreased CS/DS biosynthesis. The new zebrafish lines develop phenotypes similar to clinical characteristics of several human congenital disorders making the mutants potentially useful to study disease mechanisms and treatment.", "doi": "10.1371/journal.pgen.1010067", "pmid": "35192612", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC8896900"}, {"db": "pii", "key": "PGENETICS-D-21-00836"}], "notes": [], "created": "2026-09-23T12:17:33.422Z", "modified": "2026-09-23T12:17:33.586Z"}, {"entity": "publication", "iuid": "c383a2ad27c54e9f9beb13dc6d39dc0b", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/c383a2ad27c54e9f9beb13dc6d39dc0b.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/c383a2ad27c54e9f9beb13dc6d39dc0b"}}, "title": "The broad role of Nkx3.2 in the development of the zebrafish axial skeleton.", "authors": [{"family": "Waldmann", "given": "Laura", "initials": "L"}, {"family": "Leyhr", "given": "Jake", "initials": "J"}, {"family": "Zhang", "given": "Hanqing", "initials": "H"}, {"family": "\u00d6hman-M\u00e4gi", "given": "Caroline", "initials": "C"}, {"family": "Allalou", "given": "Amin", "initials": "A", "orcid": "0000-0003-4028-8443", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/48a26837e4ce48dfada540aa1dbd23cf.json"}}, {"family": "Haitina", "given": "Tatjana", "initials": "T", "orcid": "0000-0002-8754-5534", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7eeca9472b8e4f29b8f62819946cf1bf.json"}}], "type": "journal article", "published": "2021-08-19", "journal": {"title": "PLoS ONE", "issn": "1932-6203", "volume": "16", "issue": "8", "pages": "e0255953", "issn-l": "1932-6203"}, "abstract": "The transcription factor Nkx3.2 (Bapx1) is an important chondrocyte maturation inhibitor. Previous Nkx3.2 knockdown and overexpression studies in non-mammalian gnathostomes have focused on its role in primary jaw joint development, while the function of this gene in broader skeletal development is not fully described. We generated a mutant allele of nkx3.2 in zebrafish with CRISPR/Cas9 and applied a range of techniques to characterize skeletal phenotypes at developmental stages from larva to adult, revealing loss of the jaw joint, fusions in bones of the occiput, morphological changes in the Weberian apparatus, and the loss or deformation of bony elements derived from basiventral cartilages of the vertebrae. Axial phenotypes are reminiscent of Nkx3.2 knockout in mammals, suggesting that the function of this gene in axial skeletal development is ancestral to osteichthyans. Our results highlight the broad role of nkx3.2 in zebrafish skeletal development and its context-specific functions in different skeletal elements.", "doi": "10.1371/journal.pone.0255953", "pmid": "34411150", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC8376051"}, {"db": "pii", "key": "PONE-D-21-00397"}], "notes": [], "created": "2026-09-23T11:58:55.260Z", "modified": "2026-09-23T11:58:55.353Z"}, {"entity": "publication", "iuid": "91a6a0ea1584437680e64e6d6c7d50e9", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/91a6a0ea1584437680e64e6d6c7d50e9.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/91a6a0ea1584437680e64e6d6c7d50e9"}}, "title": "zOPT: an open source optical projection tomography system and methods for rapid 3D zebrafish imaging.", "authors": [{"family": "Zhang", "given": "Hanqing", "initials": "H"}, {"family": "Waldmann", "given": "Laura", "initials": "L"}, {"family": "Manuel", "given": "Remy", "initials": "R"}, {"family": "Boije", "given": "Henrik", "initials": "H"}, {"family": "Haitina", "given": "Tatjana", "initials": "T"}, {"family": "Allalou", "given": "Amin", "initials": "A", "orcid": "0000-0003-4028-8443", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/48a26837e4ce48dfada540aa1dbd23cf.json"}}], "type": "journal article", "published": "2020-08-01", "journal": {"title": "Biomed Opt Express", "issn": "2156-7085", "volume": "11", "issue": "8", "pages": "4290-4305", "issn-l": "2156-7085"}, "abstract": "Optical projection tomography (OPT) is a 3D imaging alternative to conventional microscopy which allows imaging of millimeter-sized object with isotropic micrometer resolution. The zebrafish is an established model organism and an important tool used in genetic and chemical screening. The size and optical transparency of the embryo and larva makes them well suited for imaging using OPT. Here, we present an open-source implementation of an OPT platform, built around a customized sample stage, 3D-printed parts and open source algorithms optimized for the system. We developed a versatile automated workflow including a two-step image processing approach for correcting the center of rotation and generating accurate 3D reconstructions. Our results demonstrate high-quality 3D reconstruction using synthetic data as well as real data of live and fixed zebrafish. The presented 3D-printable OPT platform represents a fully open design, low-cost and rapid loading and unloading of samples. Our system offers the opportunity for researchers with different backgrounds to setup and run OPT for large scale experiments, particularly in studies using zebrafish larvae as their key model organism.", "doi": "10.1364/BOE.393519", "pmid": "32923043", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC7449731"}, {"db": "pii", "key": "393519"}], "notes": [], "created": "2026-09-23T11:49:56.450Z", "modified": "2026-09-23T11:49:56.514Z"}]}