{"entity": "researcher", "timestamp": "2026-08-14T13:18:35.310Z", "family": "Burgess", "given": "Shawn M", "initials": "SM", "orcid": "0000-0003-1147-0596", "affiliations": ["Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, 20892, USA."], "links": {"self": {"href": "https://publications.scilifelab.se/researcher/bf85532f49bc4208b7e456d4ee2e8f76.json"}, "display": {"href": "https://publications.scilifelab.se/researcher/bf85532f49bc4208b7e456d4ee2e8f76"}}, "publications": [{"entity": "publication", "iuid": "397f0c6069f74329b30503eecca169d2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/397f0c6069f74329b30503eecca169d2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/397f0c6069f74329b30503eecca169d2"}}, "title": "Low mutation rate in epaulette sharks is consistent with a slow rate of evolution in sharks.", "authors": [{"family": "Sendell-Price", "given": "Ashley T", "initials": "AT", "orcid": "0000-0002-1227-8929", "researcher": {"href": "https://publications.scilifelab.se/researcher/c2d5fb40391442c8a62c20b1ca9a3295.json"}}, {"family": "Tulenko", "given": "Frank J", "initials": "FJ"}, {"family": "Pettersson", "given": "Mats", "initials": "M", "orcid": "0000-0002-7372-9076", "researcher": {"href": "https://publications.scilifelab.se/researcher/27011c7fbb8a44dda536a4fc876675b0.json"}}, {"family": "Kang", "given": "Du", "initials": "D", "orcid": "0000-0002-1497-8945", "researcher": {"href": "https://publications.scilifelab.se/researcher/7eda8755c14042289ac7196edeffca01.json"}}, {"family": "Montandon", "given": "Margo", "initials": "M", "orcid": "0000-0002-1707-0190", "researcher": {"href": "https://publications.scilifelab.se/researcher/db6f9463614b43c1aa3d41114a8f5086.json"}}, {"family": "Winkler", "given": "Sylke", "initials": "S", "orcid": "0000-0002-0915-3316", "researcher": {"href": "https://publications.scilifelab.se/researcher/f292bbf542f244278bef19506b21b031.json"}}, {"family": "Kulb", "given": "Kathleen", "initials": "K"}, {"family": "Naylor", "given": "Gavin P", "initials": "GP"}, {"family": "Phillippy", "given": "Adam", "initials": "A", "orcid": "0000-0003-2983-8934", "researcher": {"href": "https://publications.scilifelab.se/researcher/eadfad6b448a4438abee6a1b2f842b35.json"}}, {"family": "Fedrigo", "given": "Olivier", "initials": "O"}, {"family": "Mountcastle", "given": "Jacquelyn", "initials": "J"}, {"family": "Balacco", "given": "Jennifer R", "initials": "JR"}, {"family": "Dutra", "given": "Amalia", "initials": "A"}, {"family": "Dale", "given": "Rebecca E", "initials": "RE"}, {"family": "Haase", "given": "Bettina", "initials": "B"}, {"family": "Jarvis", "given": "Erich D", "initials": "ED", "orcid": "0000-0001-8931-5049", "researcher": {"href": "https://publications.scilifelab.se/researcher/d565d5e1788e484d9d2da61af12f2120.json"}}, {"family": "Myers", "given": "Gene", "initials": "G", "orcid": "0000-0002-6580-7839", "researcher": {"href": "https://publications.scilifelab.se/researcher/f9e5a63cadcf4ab995f3e989bc38c024.json"}}, {"family": "Burgess", "given": "Shawn M", "initials": "SM", "orcid": "0000-0003-1147-0596", "researcher": {"href": "https://publications.scilifelab.se/researcher/bf85532f49bc4208b7e456d4ee2e8f76.json"}}, {"family": "Currie", "given": "Peter D", "initials": "PD", "orcid": "0000-0001-8874-8862", "researcher": {"href": "https://publications.scilifelab.se/researcher/13638faa71f94e13b088922cdfa01bb3.json"}}, {"family": "Andersson", "given": "Leif", "initials": "L", "orcid": "0000-0002-4085-6968", "researcher": {"href": "https://publications.scilifelab.se/researcher/bd3343c12f994b1fabcae23027d3a76d.json"}}, {"family": "Schartl", "given": "Manfred", "initials": "M", "orcid": "0000-0001-9882-5948", "researcher": {"href": "https://publications.scilifelab.se/researcher/5f97783b5013409ebc1a6bd2df5ca92c.json"}}], "type": "journal article", "published": "2023-10-19", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "14", "issue": "1", "pages": "6628", "issn-l": "2041-1723"}, "abstract": "Sharks occupy diverse ecological niches and play critical roles in marine ecosystems, often acting as apex predators. They are considered a slow-evolving lineage and have been suggested to exhibit exceptionally low cancer rates. These two features could be explained by a low nuclear mutation rate. Here, we provide a direct estimate of the nuclear mutation rate in the epaulette shark (Hemiscyllium ocellatum). We generate a high-quality reference genome, and resequence the whole genomes of parents and nine offspring to detect de novo mutations. Using stringent criteria, we estimate a mutation rate of 7\u00d710-10 per base pair, per generation. This represents one of the lowest directly estimated mutation rates for any vertebrate clade, indicating that this basal vertebrate group is indeed a slowly evolving lineage whose ability to restore genetic diversity following a sustained population bottleneck may be hampered by a low mutation rate.", "doi": "10.1038/s41467-023-42238-x", "pmid": "37857613", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10587355"}, {"db": "pii", "key": "10.1038/s41467-023-42238-x"}], "notes": [], "created": "2023-12-18T15:04:16.059Z", "modified": "2024-01-16T13:48:31.927Z"}, {"entity": "publication", "iuid": "6b2cc1f6c66b4fe5baafa285bceb1e14", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6b2cc1f6c66b4fe5baafa285bceb1e14.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6b2cc1f6c66b4fe5baafa285bceb1e14"}}, "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.scilifelab.se/researcher/e1415531d8fe4ea7991035665c58e8ba.json"}}, {"family": "Varshney", "given": "Gaurav K", "initials": "GK", "orcid": "0000-0002-0429-1904", "researcher": {"href": "https://publications.scilifelab.se/researcher/a5b107029a9844de8b103873831b54f2.json"}}, {"family": "Waldmann", "given": "Laura", "initials": "L", "orcid": "0000-0002-3619-0796", "researcher": {"href": "https://publications.scilifelab.se/researcher/360d0e0c567f4bf1ae6967f4dedfad1a.json"}}, {"family": "Snitting", "given": "Daniel", "initials": "D", "orcid": "0000-0001-9704-6336", "researcher": {"href": "https://publications.scilifelab.se/researcher/7f99ef381b0b483ea34d05742e38314c.json"}}, {"family": "Allalou", "given": "Amin", "initials": "A", "orcid": "0000-0003-4028-8443", "researcher": {"href": "https://publications.scilifelab.se/researcher/98fffa8e99254fb597bf07dea61d8e37.json"}}, {"family": "Zhang", "given": "Hanqing", "initials": "H"}, {"family": "Ghanem", "given": "Abdurrahman", "initials": "A", "orcid": "0000-0002-4388-6222", "researcher": {"href": "https://publications.scilifelab.se/researcher/08da887bb77d4024a363c81876f3c353.json"}}, {"family": "\u00d6hman M\u00e4gi", "given": "Caroline", "initials": "C", "orcid": "0000-0003-2709-9541", "researcher": {"href": "https://publications.scilifelab.se/researcher/1e91cc9f7f5e4e6da24c6f7f9b4437f1.json"}}, {"family": "Dierker", "given": "Tabea", "initials": "T", "orcid": "0000-0003-1991-2723", "researcher": {"href": "https://publications.scilifelab.se/researcher/51eabac50a584797ba34d0405389eb94.json"}}, {"family": "Kjell\u00e9n", "given": "Lena", "initials": "L"}, {"family": "Burgess", "given": "Shawn M", "initials": "SM", "orcid": "0000-0003-1147-0596", "researcher": {"href": "https://publications.scilifelab.se/researcher/bf85532f49bc4208b7e456d4ee2e8f76.json"}}, {"family": "Ledin", "given": "Johan", "initials": "J", "orcid": "0000-0002-7319-7735", "researcher": {"href": "https://publications.scilifelab.se/researcher/92e482abc18c49d881d3bf0132b3fbcd.json"}}], "type": "journal article", "published": "2022-02-00", "journal": {"title": "PLoS Genet.", "issn": "1553-7404", "issn-l": "1553-7390", "volume": "18", "issue": "2", "pages": "e1010067"}, "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": {"BioImage Informatics": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC8896900"}, {"db": "pii", "key": "PGENETICS-D-21-00836"}], "notes": [], "created": "2022-12-01T15:56:03.295Z", "modified": "2022-12-01T15:56:12.937Z"}, {"entity": "publication", "iuid": "ee18a396f79f4e90a668a1318fc73ed8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ee18a396f79f4e90a668a1318fc73ed8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ee18a396f79f4e90a668a1318fc73ed8"}}, "title": "Amyloid precursor protein-b facilitates cell adhesion during early development in zebrafish.", "authors": [{"family": "Banote", "given": "Rakesh Kumar", "initials": "RK"}, {"family": "Chebli", "given": "Jasmine", "initials": "J"}, {"family": "\u015eat\u0131r", "given": "Tu\u011f\u00e7e Munise", "initials": "TM"}, {"family": "Varshney", "given": "Gaurav K", "initials": "GK", "orcid": "0000-0002-0429-1904", "researcher": {"href": "https://publications.scilifelab.se/researcher/a5b107029a9844de8b103873831b54f2.json"}}, {"family": "Camacho", "given": "Rafael", "initials": "R", "orcid": "0000-0003-2325-6407", "researcher": {"href": "https://publications.scilifelab.se/researcher/6a7a8cfe28634821984b078ce3246343.json"}}, {"family": "Ledin", "given": "Johan", "initials": "J", "orcid": "0000-0002-7319-7735", "researcher": {"href": "https://publications.scilifelab.se/researcher/92e482abc18c49d881d3bf0132b3fbcd.json"}}, {"family": "Burgess", "given": "Shawn M", "initials": "SM", "orcid": "0000-0003-1147-0596", "researcher": {"href": "https://publications.scilifelab.se/researcher/bf85532f49bc4208b7e456d4ee2e8f76.json"}}, {"family": "Abramsson", "given": "Alexandra", "initials": "A", "orcid": "0000-0002-4715-9225", "researcher": {"href": "https://publications.scilifelab.se/researcher/7abde12dab2e4d338bc6e55933f07531.json"}}, {"family": "Zetterberg", "given": "Henrik", "initials": "H"}], "type": "journal article", "published": "2020-06-23", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "10", "issue": "1", "pages": "10127", "issn-l": "2045-2322"}, "abstract": "Understanding the biological function of amyloid beta (A\u03b2) precursor protein (APP) beyond its role in Alzheimer's disease is emerging. Yet, its function during embryonic development is poorly understood. The zebrafish APP orthologue, Appb, is strongly expressed during early development but thus far has only been studied via morpholino-mediated knockdown. Zebrafish enables analysis of cellular processes in an ontogenic context, which is limited in many other vertebrates. We characterized zebrafish carrying a homozygous mutation that introduces a premature stop in exon 2 of the appb gene. We report that appb mutants are significantly smaller until 2 dpf and display perturbed enveloping layer (EVL) integrity and cell protrusions at the blastula stage. Moreover, appb mutants surviving beyond 48 hpf exhibited no behavioral defects at 6 dpf and developed into healthy and fertile adults. The expression of the app family member, appa, was also found to be altered in appb mutants. Taken together, we show that appb is involved in the initial development of zebrafish by supporting the integrity of the EVL, likely by mediating cell adhesion properties. The loss of Appb might then be compensated for by other app family members to maintain normal development.", "doi": "10.1038/s41598-020-66584-8", "pmid": "32576936", "labels": {"Genome Engineering Zebrafish": "Collaborative", "Integrated Microscopy Technologies Gothenburg": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC7311384"}, {"db": "pii", "key": "10.1038/s41598-020-66584-8"}], "notes": [], "created": "2020-06-24T09:03:55.674Z", "modified": "2023-02-16T08:03:52.996Z"}, {"entity": "publication", "iuid": "1114e0886af841b58cd91654ec49c796", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1114e0886af841b58cd91654ec49c796.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1114e0886af841b58cd91654ec49c796"}}, "title": "A high-throughput functional genomics workflow based on CRISPR/Cas9-mediated targeted mutagenesis in zebrafish.", "authors": [{"family": "Varshney", "given": "Gaurav K", "initials": "GK"}, {"family": "Carrington", "given": "Blake", "initials": "B"}, {"family": "Pei", "given": "Wuhong", "initials": "W"}, {"family": "Bishop", "given": "Kevin", "initials": "K"}, {"family": "Chen", "given": "Zelin", "initials": "Z"}, {"family": "Fan", "given": "Chunxin", "initials": "C"}, {"family": "Xu", "given": "Lisha", "initials": "L"}, {"family": "Jones", "given": "Marypat", "initials": "M"}, {"family": "LaFave", "given": "Matthew C", "initials": "MC", "orcid": "0000-0001-9165-041X", "researcher": {"href": "https://publications.scilifelab.se/researcher/9bc2b970f77c4479886070a56418227f.json"}}, {"family": "Ledin", "given": "Johan", "initials": "J", "orcid": "0000-0002-7319-7735", "researcher": {"href": "https://publications.scilifelab.se/researcher/92e482abc18c49d881d3bf0132b3fbcd.json"}}, {"family": "Sood", "given": "Raman", "initials": "R"}, {"family": "Burgess", "given": "Shawn M", "initials": "SM", "orcid": "0000-0003-1147-0596", "researcher": {"href": "https://publications.scilifelab.se/researcher/bf85532f49bc4208b7e456d4ee2e8f76.json"}}], "type": "journal article", "published": "2016-12-00", "journal": {"volume": "11", "issn": "1750-2799", "issue": "12", "pages": "2357-2375", "title": "Nat Protoc", "issn-l": null}, "abstract": "The zebrafish is a popular model organism for studying development and disease, and genetically modified zebrafish provide an essential tool for functional genomic studies. Numerous publications have demonstrated the efficacy of gene targeting in zebrafish using CRISPR/Cas9, and they have included descriptions of a variety of tools and methods for guide RNA synthesis and mutant identification. However, most of the published techniques are not readily scalable to increase throughput. We recently described a CRISPR/Cas9-based high-throughput mutagenesis and phenotyping pipeline in zebrafish. Here, we present a complete workflow for this pipeline, including target selection; cloning-free single-guide RNA (sgRNA) synthesis; microinjection; validation of the target-specific activity of the sgRNAs; founder screening to identify germline-transmitting mutations by fluorescence PCR; determination of the exact lesion by Sanger or next-generation sequencing (including software for analysis); and genotyping in the F1 or subsequent generations. Using these methods, sgRNAs can be evaluated in 3 d, zebrafish germline-transmitting mutations can be identified within 3 months and stable lines can be established within 6 months. Realistically, two researchers can target tens to hundreds of genes per year using this protocol.", "doi": "10.1038/nprot.2016.141", "pmid": "27809318", "labels": {"Genome Engineering Zebrafish": "Technology development"}, "xrefs": [{"db": "pii", "key": "nprot.2016.141"}, {"db": "pmc", "key": "PMC5630457"}, {"db": "mid", "key": "NIHMS905110"}], "notes": [], "created": "2017-05-08T07:59:55.363Z", "modified": "2021-07-06T14:27:46.329Z"}]}