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Mcguire JA, Huang X, Reilly SB, Iskandar DT, Wang-Claypool CY, Werning S, Chong RA, Lawalata SZS, Stubbs AL, Frederick JH, Brown RM, Evans BJ, Arifin U, Riyanto A, Hamidy A, Arida E, Koo MS, Supriatna J, Andayani N, Hall R. Species Delimitation, Phylogenomics, and Biogeography of Sulawesi Flying Lizards: A Diversification History Complicated by Ancient Hybridization, Cryptic Species, and Arrested Speciation. Syst Biol 2023; 72:885-911. [PMID: 37074804 PMCID: PMC10405571 DOI: 10.1093/sysbio/syad020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Revised: 03/14/2023] [Accepted: 04/13/2023] [Indexed: 04/20/2023] Open
Abstract
The biota of Sulawesi is noted for its high degree of endemism and for its substantial levels of in situ biological diversification. While the island's long period of isolation and dynamic tectonic history have been implicated as drivers of the regional diversification, this has rarely been tested in the context of an explicit geological framework. Here, we provide a tectonically informed biogeographical framework that we use to explore the diversification history of Sulawesi flying lizards (the Draco lineatus Group), a radiation that is endemic to Sulawesi and its surrounding islands. We employ a framework for inferring cryptic speciation that involves phylogeographic and genetic clustering analyses as a means of identifying potential species followed by population demographic assessment of divergence-timing and rates of bi-directional migration as means of confirming lineage independence (and thus species status). Using this approach, phylogenetic and population genetic analyses of mitochondrial sequence data obtained for 613 samples, a 50-SNP data set for 370 samples, and a 1249-locus exon-capture data set for 106 samples indicate that the current taxonomy substantially understates the true number of Sulawesi Draco species, that both cryptic and arrested speciations have taken place, and that ancient hybridization confounds phylogenetic analyses that do not explicitly account for reticulation. The Draco lineatus Group appears to comprise 15 species-9 on Sulawesi proper and 6 on peripheral islands. The common ancestor of this group colonized Sulawesi ~11 Ma when proto-Sulawesi was likely composed of two ancestral islands, and began to radiate ~6 Ma as new islands formed and were colonized via overwater dispersal. The enlargement and amalgamation of many of these proto-islands into modern Sulawesi, especially during the past 3 Ma, set in motion dynamic species interactions as once-isolated lineages came into secondary contact, some of which resulted in lineage merger, and others surviving to the present. [Genomics; Indonesia; introgression; mitochondria; phylogenetics; phylogeography; population genetics; reptiles.].
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Affiliation(s)
- Jimmy A Mcguire
- Museum of Vertebrate Zoology, University of California, Berkeley, CA 94720, USA
- Department of Integrative Biology, University of California, Berkeley, CA 94720, USA
| | - Xiaoting Huang
- College of Marine Life Sciences, Ocean University of China, No. 5 Yushan Road, Qindao, Shandong, 266003, PR China
| | - Sean B Reilly
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA 95060, USA
| | - Djoko T Iskandar
- School of Life Sciences and Technology, Institut Teknologi Bandung, Bandung, Indonesia
| | - Cynthia Y Wang-Claypool
- Museum of Vertebrate Zoology, University of California, Berkeley, CA 94720, USA
- Department of Integrative Biology, University of California, Berkeley, CA 94720, USA
| | - Sarah Werning
- Department of Anatomy, Des Moines University, 3200 Grand Avenue, Des Moines, IA 50312-4198, USA
| | - Rebecca A Chong
- Department of Biology, University of Hawaii at Manoa, Honolulu, HI 96822, USA
| | - Shobi Z S Lawalata
- Museum of Vertebrate Zoology, University of California, Berkeley, CA 94720, USA
- Department of Integrative Biology, University of California, Berkeley, CA 94720, USA
- United in Diversity Foundation, Jalan Hayam Wuruk, Jakarta, Indonesia
| | - Alexander L Stubbs
- Museum of Vertebrate Zoology, University of California, Berkeley, CA 94720, USA
- Department of Integrative Biology, University of California, Berkeley, CA 94720, USA
| | - Jeffrey H Frederick
- Museum of Vertebrate Zoology, University of California, Berkeley, CA 94720, USA
- Department of Integrative Biology, University of California, Berkeley, CA 94720, USA
| | - Rafe M Brown
- Biodiversity Institute and Department of Ecology and Evolutionary Biology, 1345 Jayhawk Blvd., University of Kansas, Lawrence, KS 66045, USA
| | - Ben J Evans
- Biology Department, McMaster University, Hamilton, Ontario, Canada
| | - Umilaela Arifin
- Museum of Vertebrate Zoology, University of California, Berkeley, CA 94720, USA
- School of Life Sciences and Technology, Institut Teknologi Bandung, Bandung, Indonesia
- Center for Taxonomy and Morphology, Zoologisches Museum Hamburg, Leibniz Institute for the Analysis of Biodiversity Change, Martin-Luther-King-Platz 3, R230 20146 Hamburg, Germany
| | - Awal Riyanto
- Laboratory of Herpetology, Museum Zoologicum Bogoriense, Research Center for Biosystematics and Evolution, National Research and Innovation Agency of Indonesia (BRIN), Cibinong 16911, Indonesia
| | - Amir Hamidy
- Laboratory of Herpetology, Museum Zoologicum Bogoriense, Research Center for Biosystematics and Evolution, National Research and Innovation Agency of Indonesia (BRIN), Cibinong 16911, Indonesia
| | - Evy Arida
- Research Center for Applied Zoology, National Research and Innovation Agency of Indonesia (BRIN), Cibinong 16911, Indonesia
| | - Michelle S Koo
- Museum of Vertebrate Zoology, University of California, Berkeley, CA 94720, USA
| | - Jatna Supriatna
- Department of Biology, Institute for Sustainable Earth and Resources (I-SER), Gedung Laboratorium Multidisiplin, and Research Center for Climate Change (RCCC-UI), Gedung Laboratorium Multidisiplin, Faculty of Mathematics and Natural Sciences, Universitas Indonesia, Depok 16424, Indonesia
| | - Noviar Andayani
- Department of Biology, Institute for Sustainable Earth and Resources (I-SER), Gedung Laboratorium Multidisiplin, and Research Center for Climate Change (RCCC-UI), Gedung Laboratorium Multidisiplin, Faculty of Mathematics and Natural Sciences, Universitas Indonesia, Depok 16424, Indonesia
| | - Robert Hall
- SE Asia Research Group (SEARG), Department of Earth Sciences, Royal Holloway University of London, Egham, Surrey TW20 0EX, UK
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Quirk DA, Johnson ME, Anderson DE, Smuck M, Sun R, Matthew R, Bailey J, Marras WS, Bell KM, Darwin J, Bowden AE. Biomechanical Phenotyping of Chronic Low Back Pain: Protocol for BACPAC. Pain Med 2023; 24:S48-S60. [PMID: 36315101 PMCID: PMC10403313 DOI: 10.1093/pm/pnac163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 10/12/2022] [Accepted: 10/21/2022] [Indexed: 04/27/2023]
Abstract
OBJECTIVE Biomechanics represents the common final output through which all biopsychosocial constructs of back pain must pass, making it a rich target for phenotyping. To exploit this feature, several sites within the NIH Back Pain Consortium (BACPAC) have developed biomechanics measurement and phenotyping tools. The overall aims of this article were to: 1) provide a narrative review of biomechanics as a phenotyping tool; 2) describe the diverse array of tools and outcome measures that exist within BACPAC; and 3) highlight how leveraging these technologies with the other data collected within BACPAC could elucidate the relationship between biomechanics and other metrics used to characterize low back pain (LBP). METHODS The narrative review highlights how biomechanical outcomes can discriminate between those with and without LBP, as well as among levels of severity of LBP. It also addresses how biomechanical outcomes track with functional improvements in LBP. Additionally, we present the clinical use case for biomechanical outcome measures that can be met via emerging technologies. RESULTS To answer the need for measuring biomechanical performance, our "Results" section describes the spectrum of technologies that have been developed and are being used within BACPAC. CONCLUSION AND FUTURE DIRECTIONS The outcome measures collected by these technologies will be an integral part of longitudinal and cross-sectional studies conducted in BACPAC. Linking these measures with other biopsychosocial data collected within BACPAC increases our potential to use biomechanics as a tool for understanding the mechanisms of LBP, phenotyping unique LBP subgroups, and matching these individuals with an appropriate treatment paradigm.
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Affiliation(s)
- D Adam Quirk
- Harvard School of Engineering and Applied Science, Harvard University, Cambridge, Massachusetts
| | - Marit E Johnson
- Department of Orthopaedic Surgery, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Dennis E Anderson
- Center for Orthopaedic Studies, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, Massachusetts
| | - Matthew Smuck
- Department of Orthopaedic Surgery, Stanford University School of Medicine, Stanford, California
| | - Ruopeng Sun
- Department of Orthopaedic Surgery, Stanford University School of Medicine, Stanford, California
| | - Robert Matthew
- Department of Physical Therapy and Rehabilitation Sciences, University of California, San Francisco, California
| | - Jeannie Bailey
- Department of Orthopaedic Surgery, University of California, San Francisco, California
| | - William S Marras
- Department of Integrated Systems Engineering, The Ohio State University, Columbus, Ohio
| | - Kevin M Bell
- Department of Bioengineering, Swanson School of Engineering, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Jessa Darwin
- Department of Physical Medicine and Rehabilitation, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Anton E Bowden
- Department of Mechanical Engineering, Brigham Young University, Provo, Utah, USA
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Hernandez V, Jordan RS, Hill IM, Xu B, Zhai C, Wu D, Lee H, Misiaszek J, Shirzad K, Martinez MF, Kusoglu A, Yeo J, Wang Y. Deformation Rate-Adaptive Conducting Polymers and Composites. Small 2023; 19:e2207100. [PMID: 37098606 DOI: 10.1002/smll.202207100] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 02/25/2023] [Indexed: 06/19/2023]
Abstract
Materials are more easily damaged during accidents that involve rapid deformation. Here, a design strategy is described for electronic materials comprised of conducting polymers that defies this orthodox property, making their extensibility and toughness dynamically adaptive to deformation rates. This counterintuitive property is achieved through a morphology of interconnected nanoscopic core-shell micelles, where the chemical interactions are stronger within the shells than the cores. As a result, the interlinked shells retain material integrity under strain, while the rate of dissociation of the cores controls the extent of micelle elongation, which is a process that adapts to deformation rates. A prototype based on polyaniline shows a 7.5-fold increase in ultimate elongation and a 163-fold increase in toughness when deformed at increasing rates from 2.5 to 10 000% min-1 . This concept can be generalized to other conducting polymers and highly conductive composites to create "self-protective" soft electronic materials with enhanced durability under dynamic movement or deformation.
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Affiliation(s)
- Victor Hernandez
- Department of Materials Science and Engineering, University of California, Merced, Merced, CA, 95343, USA
| | - Robert S Jordan
- Department of Materials Science and Engineering, University of California, Merced, Merced, CA, 95343, USA
| | - Ian M Hill
- Department of Materials Science and Engineering, University of California, Merced, Merced, CA, 95343, USA
| | - Bohao Xu
- Department of Materials Science and Engineering, University of California, Merced, Merced, CA, 95343, USA
| | - Chenxi Zhai
- Sibley School of Mechanical and Aerospace Engineering, Cornell University, Ithaca, NY, 14850, USA
| | - Di Wu
- Department of Materials Science and Engineering, University of California, Merced, Merced, CA, 95343, USA
| | - Hansong Lee
- Department of Materials Science and Engineering, University of California, Merced, Merced, CA, 95343, USA
| | - John Misiaszek
- Department of Materials Science and Engineering, University of California, Merced, Merced, CA, 95343, USA
| | - Kiana Shirzad
- Department of Materials Science and Engineering, University of California, Merced, Merced, CA, 95343, USA
| | - Miguel F Martinez
- Department of Chemistry and Biochemistry, University of California, Merced, Merced, CA, 95343, USA
| | - Ahmet Kusoglu
- Lawrence Berkeley National Lab, Berkeley, CA, 94720, USA
| | - Jingjie Yeo
- Sibley School of Mechanical and Aerospace Engineering, Cornell University, Ithaca, NY, 14850, USA
| | - Yue Wang
- Department of Materials Science and Engineering, University of California, Merced, Merced, CA, 95343, USA
- Department of Chemistry and Biochemistry, University of California, Merced, Merced, CA, 95343, USA
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Liu C, Le BH, Xu W, Yang CH, Chen YH, Zhao L. Dual chemical labeling enables nucleotide-resolution mapping of DNA abasic sites and common alkylation damage in human mitochondrial DNA. Nucleic Acids Res 2023; 51:e73. [PMID: 37293974 PMCID: PMC10359467 DOI: 10.1093/nar/gkad502] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 05/01/2023] [Accepted: 05/26/2023] [Indexed: 06/10/2023] Open
Abstract
Mitochondrial DNA (mtDNA) modifications play an emerging role in innate immunity and inflammatory diseases. Nonetheless, relatively little is known regarding the locations of mtDNA modifications. Such information is critically important for deciphering their roles in mtDNA instability, mtDNA-mediated immune and inflammatory responses, and mitochondrial disorders. The affinity probe-based enrichment of lesion-containing DNA represents a key strategy for sequencing DNA modifications. Existing methods are limited in the enrichment specificity of abasic (AP) sites, a prevalent DNA modification and repair intermediate. Herein, we devise a novel approach, termed dual chemical labeling-assisted sequencing (DCL-seq), for mapping AP sites. DCL-seq features two designer compounds for enriching and mapping AP sites specifically at single-nucleotide resolution. For proof of principle, we mapped AP sites in mtDNA from HeLa cells under different biological conditions. The resulting AP site maps coincide with mtDNA regions with low TFAM (mitochondrial transcription factor A) coverage and with potential G-quadruplex-forming sequences. In addition, we demonstrated the broader applicability of the method in sequencing other DNA modifications in mtDNA, such as N7-methyl-2'-deoxyguanosine and N3-methyl-2'-deoxyadenosine, when coupled with a lesion-specific repair enzyme. Together, DCL-seq holds the promise to sequence multiple DNA modifications in various biological samples.
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Affiliation(s)
- Chaoxing Liu
- Department of Chemistry, University of California, Riverside, Riverside, CA 92521, USA
| | - Brandon H Le
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, Riverside, CA 92521, USA
| | - Wenyan Xu
- Department of Chemistry, University of California, Riverside, Riverside, CA 92521, USA
| | - Ching-Hsin Yang
- Environmental Toxicology Graduate Program, University of California, Riverside, Riverside, CA 92521, USA
| | - Yu Hsuan Chen
- Department of Chemistry, University of California, Riverside, Riverside, CA 92521, USA
| | - Linlin Zhao
- Department of Chemistry, University of California, Riverside, Riverside, CA 92521, USA
- Environmental Toxicology Graduate Program, University of California, Riverside, Riverside, CA 92521, USA
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Repina NA, Johnson HJ, Bao X, Zimmermann JA, Joy DA, Bi SZ, Kane RS, Schaffer DV. Optogenetic control of Wnt signaling models cell-intrinsic embryogenic patterning using 2D human pluripotent stem cell culture. Development 2023; 150:dev201386. [PMID: 37401411 PMCID: PMC10399980 DOI: 10.1242/dev.201386] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 06/21/2023] [Indexed: 07/05/2023]
Abstract
In embryonic stem cell (ESC) models for early development, spatially and temporally varying patterns of signaling and cell types emerge spontaneously. However, mechanistic insight into this dynamic self-organization is limited by a lack of methods for spatiotemporal control of signaling, and the relevance of signal dynamics and cell-to-cell variability to pattern emergence remains unknown. Here, we combine optogenetic stimulation, imaging and transcriptomic approaches to study self-organization of human ESCs (hESC) in two-dimensional (2D) culture. Morphogen dynamics were controlled via optogenetic activation of canonical Wnt/β-catenin signaling (optoWnt), which drove broad transcriptional changes and mesendoderm differentiation at high efficiency (>99% cells). When activated within cell subpopulations, optoWnt induced cell self-organization into distinct epithelial and mesenchymal domains, mediated by changes in cell migration, an epithelial to mesenchymal-like transition and TGFβ signaling. Furthermore, we demonstrate that such optogenetic control of cell subpopulations can be used to uncover signaling feedback mechanisms between neighboring cell types. These findings reveal that cell-to-cell variability in Wnt signaling is sufficient to generate tissue-scale patterning and establish a hESC model system for investigating feedback mechanisms relevant to early human embryogenesis.
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Affiliation(s)
- Nicole A. Repina
- Department of Bioengineering, University of California, Berkeley, CA 94720, USA
- Graduate Program in Bioengineering, University of California, San Francisco and University of California, Berkeley, CA 94720, USA
| | - Hunter J. Johnson
- Department of Bioengineering, University of California, Berkeley, CA 94720, USA
- Graduate Program in Bioengineering, University of California, San Francisco and University of California, Berkeley, CA 94720, USA
| | - Xiaoping Bao
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA 94720, USA
| | - Joshua A. Zimmermann
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA 94720, USA
| | - David A. Joy
- Graduate Program in Bioengineering, University of California, San Francisco and University of California, Berkeley, CA 94720, USA
- Gladstone Institute of Cardiovascular Disease, Gladstone Institutes, San Francisco, CA 94158, USA
| | - Shirley Z. Bi
- Department of Bioengineering, University of California, Berkeley, CA 94720, USA
| | - Ravi S. Kane
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - David V. Schaffer
- Department of Bioengineering, University of California, Berkeley, CA 94720, USA
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA 94720, USA
- Helen Wills Neuroscience Institute, University of California, Berkeley, CA 94720, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
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Zhou K, Song Z, Rostomian N, Dodge JL, Stern MC, Setiawan VW, Terrault NA, Cockburn MG, Liu L. Association of nativity with survival among adults with hepatocellular carcinoma. J Natl Cancer Inst 2023; 115:861-869. [PMID: 37160726 PMCID: PMC10323898 DOI: 10.1093/jnci/djad067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 02/13/2023] [Accepted: 04/13/2023] [Indexed: 05/11/2023] Open
Abstract
INTRODUCTION Immigrants comprise a considerable proportion of those diagnosed with hepatocellular carcinoma (HCC) in the United States. Nativity or birthplace affects incidence and risk factors for HCC, but little is known about its influence on survival after diagnosis. METHODS We identified 51 533 adults with HCC with available birthplace in the California Cancer Registry between 1988 and 2017. HCC cases were categorized as foreign born or US born and stratified by mutually exclusive race and ethnicity groups. Primary outcome was all-cause mortality. Race and ethnicity-specific Cox regression propensity score-weighted models evaluated the relationship between nativity and death as well as region of birth among foreign-born patients. RESULTS A total of 40% of all HCC cases were foreign born, and 92.2%, 45.2%, 9.1%, and 5.8% of Asian/Pacific Islander (API), Hispanic, White, and Black patients were foreign born, respectively. Five-year survival rates were higher in foreign-born patients compared with US-born patients: 12.9% vs 9.6% for White patients, 11.7% vs 9.8% for Hispanic patients, 12.8% vs 8.1% for Black patients, and 16.4% vs 12.4% for API patients. Nativity was associated with survival, with better survival in foreign-born patients: White patients: hazard ratio (HR) = 0.86 (95% confidence interval [CI] = 0.81 to 0.90), Hispanic patients: HR = 0.90 (95% CI = 0.86 to 0.93), Black patients: HR = 0.89 (95% CI = 0.76 to 1.05), and API patients: HR = 0.94 (95% CI = 0.88 to 1.00). Among foreign-born patients, lower mortality was observed in those from Central and South America compared with Mexico for Hispanic patients, East Asia compared with Southeast Asia for API patients, and East Europe and Greater Middle East compared with West/South/North Europe for White patients. CONCLUSION Foreign-born patients with HCC have better survival than US-born patients. Further investigation into the mechanisms of this survival disparity by nativity is needed.
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Affiliation(s)
- Kali Zhou
- Department of Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
- Research Center for Liver Diseases, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Ziwei Song
- Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | | | - Jennifer L Dodge
- Department of Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
- Research Center for Liver Diseases, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
- Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Mariana C Stern
- Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
- Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - V Wendy Setiawan
- Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
- Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Norah A Terrault
- Department of Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
- Research Center for Liver Diseases, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Myles G Cockburn
- Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
- Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Lihua Liu
- Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
- Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
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Cerqueira PG, Meyer D, Zhang L, Mallory B, Liu J, Hua Fu BX, Zhang X, Heyer WD. Saccharomyces cerevisiae DNA polymerase IV overcomes Rad51 inhibition of DNA polymerase δ in Rad52-mediated direct-repeat recombination. Nucleic Acids Res 2023; 51:5547-5564. [PMID: 37070185 PMCID: PMC10287921 DOI: 10.1093/nar/gkad281] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 03/29/2023] [Accepted: 04/06/2023] [Indexed: 04/19/2023] Open
Abstract
Saccharomyces cerevisiae DNA polymerase IV (Pol4) like its homolog, human DNA polymerase lambda (Polλ), is involved in Non-Homologous End-Joining and Microhomology-Mediated Repair. Using genetic analysis, we identified an additional role of Pol4 also in homology-directed DNA repair, specifically in Rad52-dependent/Rad51-independent direct-repeat recombination. Our results reveal that the requirement for Pol4 in repeat recombination was suppressed by the absence of Rad51, suggesting that Pol4 counteracts the Rad51 inhibition of Rad52-mediated repeat recombination events. Using purified proteins and model substrates, we reconstituted in vitro reactions emulating DNA synthesis during direct-repeat recombination and show that Rad51 directly inhibits Polδ DNA synthesis. Interestingly, although Pol4 was not capable of performing extensive DNA synthesis by itself, it aided Polδ in overcoming the DNA synthesis inhibition by Rad51. In addition, Pol4 dependency and stimulation of Polδ DNA synthesis in the presence of Rad51 occurred in reactions containing Rad52 and RPA where DNA strand-annealing was necessary. Mechanistically, yeast Pol4 displaces Rad51 from ssDNA independent of DNA synthesis. Together our in vitro and in vivo data suggest that Rad51 suppresses Rad52-dependent/Rad51-independent direct-repeat recombination by binding to the primer-template and that Rad51 removal by Pol4 is critical for strand-annealing dependent DNA synthesis.
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Affiliation(s)
- Paula G Cerqueira
- Department of Microbiology and Molecular Genetics, University of California, Davis, One Shields Avenue, Davis, CA 95616-8665, USA
| | - Damon Meyer
- Department of Microbiology and Molecular Genetics, University of California, Davis, One Shields Avenue, Davis, CA 95616-8665, USA
| | - Lilin Zhang
- Department of Microbiology and Molecular Genetics, University of California, Davis, One Shields Avenue, Davis, CA 95616-8665, USA
| | - Benjamin Mallory
- Department of Microbiology and Molecular Genetics, University of California, Davis, One Shields Avenue, Davis, CA 95616-8665, USA
| | - Jie Liu
- Department of Microbiology and Molecular Genetics, University of California, Davis, One Shields Avenue, Davis, CA 95616-8665, USA
| | - Becky Xu Hua Fu
- Department of Microbiology and Molecular Genetics, University of California, Davis, One Shields Avenue, Davis, CA 95616-8665, USA
| | - Xiaoping Zhang
- Department of Microbiology and Molecular Genetics, University of California, Davis, One Shields Avenue, Davis, CA 95616-8665, USA
| | - Wolf-Dietrich Heyer
- Department of Microbiology and Molecular Genetics, University of California, Davis, One Shields Avenue, Davis, CA 95616-8665, USA
- Department of Molecular and Cellular Biology, University of California, Davis, One Shields Avenue, Davis, CA 95616-8665, USA
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Richmond JQ, McGuire JA, Escalona M, Marimuthu MPA, Nguyen O, Sacco S, Beraut E, Toffelmier E, Fisher RN, Wang IJ, Shaffer HB. Reference genome of an iconic lizard in western North America, Blainville's horned lizard Phrynosoma blainvillii. J Hered 2023; 114:410-417. [PMID: 37195437 DOI: 10.1093/jhered/esad032] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 05/19/2023] [Indexed: 05/18/2023] Open
Abstract
Genome assemblies are increasingly being used to identify adaptive genetic variation that can help prioritize the population management of protected species. This approach may be particularly relevant to species like Blainville's horned lizard, Phrynosoma blainvillii, due to its specialized diet on noxious harvester ants, numerous adaptative traits for avoiding predation (e.g. cranial horns, dorsoventrally compressed body, cryptic coloration, and blood squirting from the orbital sinuses), and status as Species of Special Concern in California. Rangewide decline since the early 20th century, the basis of its conservation status, has been driven mainly by habitat conversion, over-collecting, and invasion of a non-native ant that displaces its native ant prey base. Here, we report on a scaffold-level genome assembly for P. blainvillii as part of the California Conservation Genomics Project (CCGP), produced using Pacific Biosciences HiFi long reads and Hi-C chromatin-proximity sequencing technology. The de novo assembly has 78 scaffolds, a total length of ~2.21 Gb, a scaffold N50 length of ~352 Mb, and BUSCO score of 97.4%. This is the second species of Phrynosoma for which a reference genome has been assembled and represents a considerable improvement in terms of contiguity and completeness. Combined with the landscape genomics data being compiled by the CCGP, this assembly will help strategize efforts to maintain and/or restore local genetic diversity, where interventions like genetic rescue, translocation, and strategic land preservation may be the only means by which P. blainvillii and other low-vagility species can survive in the fragmented habitats of California.
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Affiliation(s)
- Jonathan Q Richmond
- U.S. Geological Survey, Western Ecological Research Center, San Diego, CA, United States
| | - Jimmy A McGuire
- Museum of Vertebrate Zoology, University of California, Berkeley, Berkeley, CA, United States
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA, United States
| | - Merly Escalona
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA, United States
| | - Mohan P A Marimuthu
- DNA Technologies and Expression Analysis Core Laboratory, Genome Center, University of California, Davis, Davis, CA, United States
| | - Oanh Nguyen
- DNA Technologies and Expression Analysis Core Laboratory, Genome Center, University of California, Davis, Davis, CA, United States
| | - Samuel Sacco
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA, United States
| | - Eric Beraut
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA, United States
| | - Erin Toffelmier
- Department of Ecology & Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, United States
- La Kretz Center for California Conservation Science, Institute of the Environment and Sustainability, University of California, Los Angeles, Los Angeles, CA, United States
| | - Robert N Fisher
- U.S. Geological Survey, Western Ecological Research Center, San Diego, CA, United States
| | - Ian J Wang
- Museum of Vertebrate Zoology, University of California, Berkeley, Berkeley, CA, United States
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, Berkeley, CA, United States
| | - H Bradley Shaffer
- Department of Ecology & Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, United States
- La Kretz Center for California Conservation Science, Institute of the Environment and Sustainability, University of California, Los Angeles, Los Angeles, CA, United States
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Hall LA, Wang IJ, Escalona M, Beraut E, Sacco S, Sahasrabudhe R, Nguyen O, Toffelmier E, Shaffer HB, Beissinger SR. Reference genome of the Virginia rail, Rallus limicola. J Hered 2023; 114:428-435. [PMID: 37105531 PMCID: PMC10287147 DOI: 10.1093/jhered/esad026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 04/27/2023] [Indexed: 04/29/2023] Open
Abstract
The Virginia rail, Rallus limicola, is a member of the family Rallidae, which also includes many other species of secretive and poorly studied wetland birds. It is recognized as a single species throughout its broad distribution in North America where it is exploited as a game bird, often with generous harvest limits, despite a lack of systematic population surveys and evidence of declines in many areas due to wetland loss and degradation. To help advance understanding of the phylogeography, biology, and ecology of this elusive species, we report the first reference genome assembly for the Virginia rail, produced as part of the California Conservation Genomics Project (CCGP). We produced a de novo genome assembly using Pacific Biosciences HiFi long reads and Hi-C chromatin-proximity sequencing technology with an estimated sequencing error rate of 0.191%. The assembly consists of 1,102 scaffolds spanning 1.39 Gb, with a contig N50 of 11.0 Mb, scaffold N50 of 25.3 Mb, largest contig of 45 Mb, and largest scaffold of 128.4 Mb. It has a high BUSCO completeness score of 96.9% and represents the first genome assembly available for the genus Rallus. This genome assembly will help resolve questions about the complex evolutionary history of rails and evaluate the potential of rails for adaptive evolution in the face of growing threats from climate change and habitat loss and fragmentation. It will also provide a valuable resource for rail conservation efforts by quantifying Virginia rail vagility, population connectivity, and effective population sizes.
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Affiliation(s)
- Laurie A Hall
- Department of Environmental Science, Policy & Management, University of California, Berkeley, Berkeley, CA 94720, United States
- Museum of Vertebrate Zoology, University of California, Berkeley, Berkeley, CA 94720, United States
| | - Ian J Wang
- Department of Environmental Science, Policy & Management, University of California, Berkeley, Berkeley, CA 94720, United States
- Museum of Vertebrate Zoology, University of California, Berkeley, Berkeley, CA 94720, United States
| | - Merly Escalona
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA 95064, United States
| | - Eric Beraut
- Department of Ecology & Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA 95064, United States
| | - Samuel Sacco
- Department of Ecology & Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA 95064, United States
| | - Ruta Sahasrabudhe
- DNA Technologies and Expression Analysis Core Laboratory, Genome Center, University of California, Davis, Davis, CA 95616, United States
| | - Oanh Nguyen
- DNA Technologies and Expression Analysis Core Laboratory, Genome Center, University of California, Davis, Davis, CA 95616, United States
| | - Erin Toffelmier
- Department of Ecology & Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA 90095, United States
- La Kretz Center for California Conservation Science, Institute of the Environment & Sustainability, University of California, Los Angeles, Los Angeles, CA 90095, United States
| | - H Bradley Shaffer
- Department of Ecology & Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA 90095, United States
- La Kretz Center for California Conservation Science, Institute of the Environment & Sustainability, University of California, Los Angeles, Los Angeles, CA 90095, United States
| | - Steven R Beissinger
- Department of Environmental Science, Policy & Management, University of California, Berkeley, Berkeley, CA 94720, United States
- Museum of Vertebrate Zoology, University of California, Berkeley, Berkeley, CA 94720, United States
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Hall LA, Wang IJ, Escalona M, Beraut E, Sacco S, Sahasrabudhe R, Nguyen O, Toffelmier E, Shaffer HB, Beissinger SR. Reference genome of the black rail, Laterallus jamaicensis. J Hered 2023; 114:436-443. [PMID: 37119047 PMCID: PMC10287143 DOI: 10.1093/jhered/esad025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 04/27/2023] [Indexed: 04/30/2023] Open
Abstract
The black rail, Laterallus jamaicensis, is one of the most secretive and poorly understood birds in the Americas. Two of its five subspecies breed in North America: the Eastern black rail (L. j. jamaicensis), found primarily in the southern and mid-Atlantic states, and the California black rail (L. j. coturniculus), inhabiting California and Arizona, are recognized across the highly disjunct distribution. Population declines, due primarily to wetland loss and degradation, have resulted in conservation status listings for both subspecies. To help advance understanding of the phylogeography, biology, and ecology of this elusive species, we report the first reference genome assembly for the black rail, produced as part of the California Conservation Genomics Project (CCGP). We produced a de novo genome assembly using Pacific Biosciences HiFi long reads and Hi-C chromatin-proximity sequencing technology with an estimated sequencing error rate of 0.182%. The assembly consists of 964 scaffolds spanning 1.39 Gb, with a contig N50 of 7.4 Mb, scaffold N50 of 21.4 Mb, largest contig of 44.8 Mb, and largest scaffold of 101.2 Mb. The assembly has a high BUSCO completeness score of 96.8% and represents the first genome assembly available for the genus Laterallus. This genome assembly can help resolve questions about the complex evolutionary history of rails, assess black rail vagility and population connectivity, estimate effective population sizes, and evaluate the potential of rails for adaptive evolution in the face of growing threats from climate change, habitat loss and fragmentation, and disease.
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Affiliation(s)
- Laurie A Hall
- Department of Environmental Science, Policy and Management, University of California, Berkeley, CA 94720, United States
- Museum of Vertebrate Zoology, University of California, Berkeley, CA 94720, United States
| | - Ian J Wang
- Department of Environmental Science, Policy and Management, University of California, Berkeley, CA 94720, United States
- Museum of Vertebrate Zoology, University of California, Berkeley, CA 94720, United States
| | - Merly Escalona
- Department of Biomolecular Engineering, University of California, Santa Cruz, CA 95064, United States
| | - Eric Beraut
- Department of Ecology and Evolutionary Biology, University of Califin JHornia, Santa Cruz, CA 95064, United States
| | - Samuel Sacco
- Department of Ecology and Evolutionary Biology, University of Califin JHornia, Santa Cruz, CA 95064, United States
| | - Ruta Sahasrabudhe
- DNA Technologies and Expression Analysis Core Laboratory, Genome Center, University of California, Davis, CA 95616, United States
| | - Oanh Nguyen
- DNA Technologies and Expression Analysis Core Laboratory, Genome Center, University of California, Davis, CA 95616, United States
| | - Erin Toffelmier
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095, United States
- La Kretz Center for California Conservation Science, Institute of the Environment and Sustainability, University of California, Los Angeles, CA 90095, United States
| | - H Bradley Shaffer
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095, United States
- La Kretz Center for California Conservation Science, Institute of the Environment and Sustainability, University of California, Los Angeles, CA 90095, United States
| | - Steven R Beissinger
- Department of Environmental Science, Policy and Management, University of California, Berkeley, CA 94720, United States
- Museum of Vertebrate Zoology, University of California, Berkeley, CA 94720, United States
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Benham PM, Cicero C, Escalona M, Beraut E, Marimuthu MPA, Nguyen O, Nachman MW, Bowie RCK. A highly contiguous genome assembly for the California quail (Callipepla californica). J Hered 2023; 114:418-427. [PMID: 36763048 PMCID: PMC10287149 DOI: 10.1093/jhered/esad008] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 02/09/2023] [Indexed: 02/11/2023] Open
Abstract
The California quail (Callipepla californica) is an iconic native bird of scrub and oak woodlands in California and the Baja Peninsula of Mexico. Here, we report a draft reference assembly for the species generated from PacBio HiFi long read and Omni-C chromatin-proximity sequencing data as part of the California Conservation Genomics Project (CCGP). Sequenced reads were assembled into 321 scaffolds totaling 1.08 Gb in length. Assembly metrics indicate a highly contiguous and complete assembly with a contig N50 of 5.5 Mb, scaffold N50 of 19.4 Mb, and BUSCO completeness score of 96.5%. Transposable elements (TEs) occupy 16.5% of the genome, more than previous Odontophoridae quail assemblies but in line with estimates of TE content for recent long-read assemblies of chicken and Peking duck. Together these metrics indicate that the present assembly is more complete than prior reference assemblies generated for Odontophoridae quail. This reference will serve as an essential resource for studies on local adaptation, phylogeography, and conservation genetics in this species of significant biological and recreational interest.
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Affiliation(s)
- Phred M Benham
- Museum of Vertebrate Zoology, University of California Berkeley, Berkeley, CA, United States
- Department of Integrative Biology, University of California Berkeley, Berkeley, CA, United States
| | - Carla Cicero
- Museum of Vertebrate Zoology, University of California Berkeley, Berkeley, CA, United States
| | - Merly Escalona
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, United States
| | - Eric Beraut
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA, United States
- Museum of Vertebrate Zoology, University of California Berkeley, Berkeley, CA, United States
| | - Mohan P A Marimuthu
- DNA Technologies and Expression Analysis Core Laboratory, Genome Center, University of California-Davis, Davis, CA, United States
- Museum of Vertebrate Zoology, University of California Berkeley, Berkeley, CA, United States
| | - Oanh Nguyen
- DNA Technologies and Expression Analysis Core Laboratory, Genome Center, University of California-Davis, Davis, CA, United States
- Museum of Vertebrate Zoology, University of California Berkeley, Berkeley, CA, United States
| | - Michael W Nachman
- Museum of Vertebrate Zoology, University of California Berkeley, Berkeley, CA, United States
- Department of Integrative Biology, University of California Berkeley, Berkeley, CA, United States
| | - Rauri C K Bowie
- Museum of Vertebrate Zoology, University of California Berkeley, Berkeley, CA, United States
- Department of Integrative Biology, University of California Berkeley, Berkeley, CA, United States
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62
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Grether GF, Beninde J, Beraut E, Chumchim N, Escalona M, MacDonald ZG, Miller C, Sahasrabudhe R, Shedlock AM, Toffelmier E, Shaffer HB. Reference genome for the American rubyspot damselfly, Hetaerina americana. J Hered 2023; 114:385-394. [PMID: 37195415 PMCID: PMC10287145 DOI: 10.1093/jhered/esad031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 05/07/2023] [Indexed: 05/18/2023] Open
Abstract
Damselflies and dragonflies (Order: Odonata) play important roles in both aquatic and terrestrial food webs and can serve as sentinels of ecosystem health and predictors of population trends in other taxa. The habitat requirements and limited dispersal of lotic damselflies make them especially sensitive to habitat loss and fragmentation. As such, landscape genomic studies of these taxa can help focus conservation efforts on watersheds with high levels of genetic diversity, local adaptation, and even cryptic endemism. Here, as part of the California Conservation Genomics Project (CCGP), we report the first reference genome for the American rubyspot damselfly, Hetaerina americana, a species associated with springs, streams and rivers throughout California. Following the CCGP assembly pipeline, we produced two de novo genome assemblies. The primary assembly includes 1,630,044,487 base pairs, with a contig N50 of 5.4 Mb, a scaffold N50 of 86.2 Mb, and a BUSCO completeness score of 97.6%. This is the seventh Odonata genome to be made publicly available and the first for the subfamily Hetaerininae. This reference genome fills an important phylogenetic gap in our understanding of Odonata genome evolution, and provides a genomic resource for a host of interesting ecological, evolutionary, and conservation questions for which the rubyspot damselfly genus Hetaerina is an important model system.
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Affiliation(s)
- Gregory F Grether
- Department of Ecology and Evolutionary Biology, University of California Los Angeles, Los Angeles, CA 90095-1606, United States
- La Kretz Center for California Conservation Science, Institute of the Environment and Sustainability, University of California Los Angeles, Los Angeles, CA 90095-7239, United States
| | - Joscha Beninde
- La Kretz Center for California Conservation Science, Institute of the Environment and Sustainability, University of California Los Angeles, Los Angeles, CA 90095-7239, United States
| | - Eric Beraut
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA 95064, United States
| | - Noravit Chumchim
- DNA Technologies and Expression Analysis Core Laboratory, University of California Davis, Davis, CA 95616, United States
| | - Merly Escalona
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, United States
| | - Zachary G MacDonald
- La Kretz Center for California Conservation Science, Institute of the Environment and Sustainability, University of California Los Angeles, Los Angeles, CA 90095-7239, United States
| | - Courtney Miller
- Department of Ecology and Evolutionary Biology, University of California Los Angeles, Los Angeles, CA 90095-1606, United States
- La Kretz Center for California Conservation Science, Institute of the Environment and Sustainability, University of California Los Angeles, Los Angeles, CA 90095-7239, United States
| | - Ruta Sahasrabudhe
- DNA Technologies and Expression Analysis Core Laboratory, University of California Davis, Davis, CA 95616, United States
| | - Andrew M Shedlock
- Department of Biology, College of Charleston, Charleston, SC 29424, United States
| | - Erin Toffelmier
- Department of Ecology and Evolutionary Biology, University of California Los Angeles, Los Angeles, CA 90095-1606, United States
- La Kretz Center for California Conservation Science, Institute of the Environment and Sustainability, University of California Los Angeles, Los Angeles, CA 90095-7239, United States
| | - H Bradley Shaffer
- Department of Ecology and Evolutionary Biology, University of California Los Angeles, Los Angeles, CA 90095-1606, United States
- La Kretz Center for California Conservation Science, Institute of the Environment and Sustainability, University of California Los Angeles, Los Angeles, CA 90095-7239, United States
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Adams SA, Graham NR, Holmquist AJ, Sheffer MM, Steigerwald EC, Sahasrabudhe R, Nguyen O, Beraut E, Fairbairn C, Sacco S, Seligmann W, Escalona M, Shaffer HB, Toffelmier E, Gillespie RG. Reference genome of the long-jawed orb-weaver, Tetragnatha versicolor (Araneae: Tetragnathidae). J Hered 2023; 114:395-403. [PMID: 37042574 PMCID: PMC10287146 DOI: 10.1093/jhered/esad013] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 02/27/2023] [Indexed: 04/13/2023] Open
Abstract
Climate-driven changes in hydrological regimes are of global importance and are particularly significant in riparian ecosystems. Riparian ecosystems in California provide refuge to many native and vulnerable species within a xeric landscape. California Tetragnatha spiders play a key role in riparian ecosystems, serving as a link between terrestrial and aquatic elements. Their tight reliance on water paired with the widespread distributions of many species make them ideal candidates to better understand the relative role of waterways versus geographic distance in shaping the population structure of riparian species. To assist in better understanding population structure, we constructed a reference genome assembly for Tetragnatha versicolor using long-read sequencing, scaffolded with proximity ligation Omni-C data. The near-chromosome-level assembly is comprised of 174 scaffolds spanning 1.06 Gb pairs, with a scaffold N50 of 64.1 Mb pairs and BUSCO completeness of 97.6%. This reference genome will facilitate future study of T. versicolor population structure associated with the rapidly changing environment of California.
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Affiliation(s)
- Seira A Adams
- Department of Environmental Science, Policy and Management, University of California, Berkeley, CA, United States
- Center for Population Biology, University of California, Davis, CA, United States
- Department of Evolution and Ecology, University of California, Davis, CA, United States
| | - Natalie R Graham
- Department of Environmental Science, Policy and Management, University of California, Berkeley, CA, United States
| | - Anna J Holmquist
- Department of Environmental Science, Policy and Management, University of California, Berkeley, CA, United States
| | - Monica M Sheffer
- Department of Biology, University of Washington, Seattle, WA, United States
- eScience Institute, University of Washington, Seattle, WA, United States
| | - Emma C Steigerwald
- Department of Environmental Science, Policy and Management, University of California, Berkeley, CA, United States
- Museum of Vertebrate Zoology, University of California, Berkeley, CA, United States
| | - Ruta Sahasrabudhe
- DNA Technologies and Expression Analysis Core Laboratory, Genome Center, University of California, Davis, CA, United States
| | - Oanh Nguyen
- DNA Technologies and Expression Analysis Core Laboratory, Genome Center, University of California, Davis, CA, United States
| | - Eric Beraut
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA, United States
| | - Colin Fairbairn
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA, United States
| | - Samuel Sacco
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA, United States
| | - William Seligmann
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA, United States
| | - Merly Escalona
- Department of Biomolecular Engineering, University of California, Santa Cruz, CA, United States
| | - H Bradley Shaffer
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, United States
- La Kretz Center for California Conservation Science, Institute for Environment and Sustainability, University of California, Los Angeles, CA, United States
| | - Erin Toffelmier
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, United States
- La Kretz Center for California Conservation Science, Institute for Environment and Sustainability, University of California, Los Angeles, CA, United States
| | - Rosemary G Gillespie
- Department of Environmental Science, Policy and Management, University of California, Berkeley, CA, United States
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Chesler NC, Barabino GA. BME2.1: The Need for a Systems Approach to Addressing Race-Based Disparities in Health and Health Care. BME Front 2023; 4:0023. [PMID: 37849658 PMCID: PMC10284143 DOI: 10.34133/bmef.0023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 06/01/2023] [Indexed: 10/19/2023] Open
Affiliation(s)
- Naomi C. Chesler
- Edwards Lifesciences Foundation Cardiovascular Innovation and Research Center and Department of Biomedical Engineering, Samueli School of Engineering, University of California, Irvine, CA, USA
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Adegboyega MT, Jhanjar S, Grote MN, Weaver TD. Predicting the shape, size, and placement of adult human pubic symphyses. Am J Biol Anthropol 2023; 181:182-194. [PMID: 36939148 DOI: 10.1002/ajpa.24725] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Revised: 02/03/2023] [Accepted: 02/27/2023] [Indexed: 05/18/2023]
Abstract
OBJECTIVES When reconstructing fossil pelves, the articulation of the pelvic bones largely relies on subjective decisions by researchers. Different positionings at the pubic symphysis can affect the overall morphology of the pelvis and the subsequent biological interpretation associated with that individual or species. This study aims to reduce this subjectivity using quantitative models to predict pubic symphysis morphology. METHODS We collected 3D landmarks and semilandmarks on the pubic symphysis and adjacent aspects on the CT scans of 103 adults. Using geometric morphometrics we, (1) quantified pubic symphysis morphology, (2) trained simple and two-stage least-squares linear regression models to predict pubic symphysis shape, and (3) assessed the shape variation in the sample. The model with the lowest prediction error was identified as the best model. Principal components analysis was used to explore the effects of each variable on shape and hypothetical shapes were generated from the model to illustrate these effects. RESULTS The best model is a two-stage least-squares model that predicts pubic symphysis size at the first stage using additive effects of sex and age, then subsequently interacts pubic symphysis size with sex and age at the second stage to predict pubic symphysis shape. Other models with low prediction errors included variables reflecting pelvic size and breadth. CONCLUSION Linear regression modeling can be used to systematically predict pubic symphysis morphology. This method can be used in addition to other techniques to improve fossil reconstructions by more accurately estimating the morphology of this region of the pelvis.
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Affiliation(s)
- Mayowa T Adegboyega
- Department of Evolutionary Anthropology, Duke University, Durham, North Carolina, USA
- Department of Anthropology, University of California, Davis, California, USA
| | - Sara Jhanjar
- Department of Anthropology, University of California, Davis, California, USA
- College of Osteopathic Medicine, California Health Sciences University, Clovis, California, USA
| | - Mark N Grote
- Department of Anthropology, University of California, Davis, California, USA
| | - Timothy D Weaver
- Department of Anthropology, University of California, Davis, California, USA
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66
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Kilian JG, Mejias-Ortega M, Hsu HW, Herman DA, Vidal J, Arechavala RJ, Renusch S, Dalal H, Hasen I, Ting A, Rodriguez-Ortiz CJ, Lim SL, Lin X, Vu J, Saito T, Saido TC, Kleinman MT, Kitazawa M. Exposure to quasi-ultrafine particulate matter accelerates memory impairment and Alzheimer's disease-like neuropathology in the AppNL-G-F knock-in mouse model. Toxicol Sci 2023; 193:175-191. [PMID: 37074955 PMCID: PMC10230292 DOI: 10.1093/toxsci/kfad036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/20/2023] Open
Abstract
Exposure to traffic-related air pollution consisting of particulate matter (PM) is associated with cognitive decline leading to Alzheimer's disease (AD). In this study, we sought to examine the neurotoxic effects of exposure to ultrafine PM and how it exacerbates neuronal loss and AD-like neuropathology in wildtype (WT) mice and a knock-in mouse model of AD (AppNL-G-F/+-KI) when the exposure occurs at a prepathologic stage or at a later age with the presence of neuropathology. AppNL-G-F/+-KI and WT mice were exposed to concentrated ultrafine PM from local ambient air in Irvine, California, for 12 weeks, starting at 3 or 9 months of age. Particulate matter-exposed animals received concentrated ultrafine PM up to 8 times above the ambient levels, whereas control animals were exposed to purified air. Particulate matter exposure resulted in a marked impairment of memory tasks in prepathologic AppNL-G-F/+-KI mice without measurable changes in amyloid-β pathology, synaptic degeneration, and neuroinflammation. At aged, both WT and AppNL-G-F/+-KI mice exposed to PM showed a significant memory impairment along with neuronal loss. In AppNL-G-F/+-KI mice, we also detected an increased amyloid-β buildup and potentially harmful glial activation including ferritin-positive microglia and C3-positive astrocytes. Such glial activation could promote the cascade of degenerative consequences in the brain. Our results suggest that exposure to PM impairs cognitive function at both ages while exacerbation of AD-related pathology and neuronal loss may depend on the stage of pathology, aging, and/or state of glial activation. Further studies will be required to unveil the neurotoxic role of glial activation activated by PM exposure.
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Affiliation(s)
- Jason G Kilian
- Department of Environmental and Occupational Health, Center for Occupational and Environmental Health (COEH), University of California, Irvine, California 92697-1830, USA
- Institute for Memory Impairmants and Neurological Disorders (UCI MIND), University of California, Irvine, California 92697, USA
| | - Marina Mejias-Ortega
- Department of Environmental and Occupational Health, Center for Occupational and Environmental Health (COEH), University of California, Irvine, California 92697-1830, USA
- Department of Cell Biology, Genetics and Physiology, Facultad de Ciencias, Instituto de Investigacion Biomedica de Malaga-IBIMA, Universidad de Malaga, Malaga, Spain
- Centro de Investigación Biomedica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Madrid, Spain
| | - Heng-Wei Hsu
- Department of Environmental and Occupational Health, Center for Occupational and Environmental Health (COEH), University of California, Irvine, California 92697-1830, USA
- Institute for Memory Impairmants and Neurological Disorders (UCI MIND), University of California, Irvine, California 92697, USA
| | - David A Herman
- Department of Environmental and Occupational Health, Center for Occupational and Environmental Health (COEH), University of California, Irvine, California 92697-1830, USA
| | - Janielle Vidal
- Department of Environmental and Occupational Health, Center for Occupational and Environmental Health (COEH), University of California, Irvine, California 92697-1830, USA
- Institute for Memory Impairmants and Neurological Disorders (UCI MIND), University of California, Irvine, California 92697, USA
| | - Rebecca J Arechavala
- Department of Environmental and Occupational Health, Center for Occupational and Environmental Health (COEH), University of California, Irvine, California 92697-1830, USA
| | - Samantha Renusch
- Department of Environmental and Occupational Health, Center for Occupational and Environmental Health (COEH), University of California, Irvine, California 92697-1830, USA
| | - Hansal Dalal
- Department of Environmental and Occupational Health, Center for Occupational and Environmental Health (COEH), University of California, Irvine, California 92697-1830, USA
| | - Irene Hasen
- Department of Environmental and Occupational Health, Center for Occupational and Environmental Health (COEH), University of California, Irvine, California 92697-1830, USA
| | - Amanda Ting
- Department of Environmental and Occupational Health, Center for Occupational and Environmental Health (COEH), University of California, Irvine, California 92697-1830, USA
| | - Carlos J Rodriguez-Ortiz
- Department of Environmental and Occupational Health, Center for Occupational and Environmental Health (COEH), University of California, Irvine, California 92697-1830, USA
- Institute for Memory Impairmants and Neurological Disorders (UCI MIND), University of California, Irvine, California 92697, USA
| | - Siok-Lam Lim
- Department of Environmental and Occupational Health, Center for Occupational and Environmental Health (COEH), University of California, Irvine, California 92697-1830, USA
- Institute for Memory Impairmants and Neurological Disorders (UCI MIND), University of California, Irvine, California 92697, USA
| | - Xiaomeng Lin
- Department of Environmental and Occupational Health, Center for Occupational and Environmental Health (COEH), University of California, Irvine, California 92697-1830, USA
| | - Joan Vu
- Department of Environmental and Occupational Health, Center for Occupational and Environmental Health (COEH), University of California, Irvine, California 92697-1830, USA
- Institute for Memory Impairmants and Neurological Disorders (UCI MIND), University of California, Irvine, California 92697, USA
| | - Takashi Saito
- Department of Neurocognitive Science, Institute of Brain Science, Nagoya City University, Nagoya, Japan
| | - Takaomi C Saido
- Laboratory for Proteolytic Neuroscience, RIKEN Center for Brain Science, Wako, Japan
| | - Michael T Kleinman
- Department of Environmental and Occupational Health, Center for Occupational and Environmental Health (COEH), University of California, Irvine, California 92697-1830, USA
| | - Masashi Kitazawa
- Department of Environmental and Occupational Health, Center for Occupational and Environmental Health (COEH), University of California, Irvine, California 92697-1830, USA
- Institute for Memory Impairmants and Neurological Disorders (UCI MIND), University of California, Irvine, California 92697, USA
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Balasubramani PP, Diaz-Delgado J, Grennan G, Alim F, Zafar-Khan M, Maric V, Ramanathan D, Mishra J. Distinct neural activations correlate with maximization of reward magnitude versus frequency. Cereb Cortex 2023; 33:6038-6050. [PMID: 36573422 PMCID: PMC10422923 DOI: 10.1093/cercor/bhac482] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 11/15/2022] [Accepted: 11/17/2022] [Indexed: 12/29/2022] Open
Abstract
Choice selection strategies and decision-making are typically investigated using multiple-choice gambling paradigms that require participants to maximize expected value of rewards. However, research shows that performance in such paradigms suffers from individual biases towards the frequency of gains such that users often choose smaller frequent gains over larger rarely occurring gains, also referred to as melioration. To understand the basis of this subjective tradeoff, we used a simple 2-choice reward task paradigm in 186 healthy human adult subjects sampled across the adult lifespan. Cortical source reconstruction of simultaneously recorded electroencephalography suggested distinct neural correlates for maximizing reward magnitude versus frequency. We found that activations in the parahippocampal and entorhinal areas, which are typically linked to memory function, specifically correlated with maximization of reward magnitude. In contrast, maximization of reward frequency was correlated with activations in the lateral orbitofrontal cortices and operculum, typical areas involved in reward processing. These findings reveal distinct neural processes serving reward frequency versus magnitude maximization that can have clinical translational utility to optimize decision-making.
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Affiliation(s)
- Pragathi Priyadharsini Balasubramani
- Neural Engineering and Translation Labs, Department of Psychiatry, University of California, San Diego, La Jolla, CA, United States
- Department of Cognitive Science, Indian Institute of Technology Kanpur, Kanpur 208016, India
| | - Juan Diaz-Delgado
- Neural Engineering and Translation Labs, Department of Psychiatry, University of California, San Diego, La Jolla, CA, United States
| | - Gillian Grennan
- Neural Engineering and Translation Labs, Department of Psychiatry, University of California, San Diego, La Jolla, CA, United States
| | - Fahad Alim
- Neural Engineering and Translation Labs, Department of Psychiatry, University of California, San Diego, La Jolla, CA, United States
| | - Mariam Zafar-Khan
- Neural Engineering and Translation Labs, Department of Psychiatry, University of California, San Diego, La Jolla, CA, United States
| | - Vojislav Maric
- Neural Engineering and Translation Labs, Department of Psychiatry, University of California, San Diego, La Jolla, CA, United States
| | - Dhakshin Ramanathan
- Neural Engineering and Translation Labs, Department of Psychiatry, University of California, San Diego, La Jolla, CA, United States
- Department of Mental Health, VA San Diego Medical Center, San Diego, CA, United States
- Center of Excellence for Stress and Mental Health, VA San Diego Medical Center, San Diego, CA, United States
| | - Jyoti Mishra
- Neural Engineering and Translation Labs, Department of Psychiatry, University of California, San Diego, La Jolla, CA, United States
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68
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Dranow DB, Le Pabic P, Schilling TF. The non-canonical Wnt receptor Ror2 is required for cartilage cell polarity and morphogenesis of the craniofacial skeleton in zebrafish. Development 2023; 150:dev201273. [PMID: 37039156 PMCID: PMC10163346 DOI: 10.1242/dev.201273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 03/21/2023] [Indexed: 04/12/2023]
Abstract
Non-canonical/β-catenin-independent Wnt signaling plays crucial roles in tissue/cell polarity in epithelia, but its functions have been less well studied in mesenchymal tissues, such as the skeleton. Mutations in non-canonical Wnt signaling pathway genes cause human skeletal diseases such as Robinow syndrome and Brachydactyly Type B1, which disrupt bone growth throughout the endochondral skeleton. Ror2 is one of several non-canonical Wnt receptor/co-receptors. Here, we show that ror2-/- mutant zebrafish have craniofacial skeletal defects, including disruptions of chondrocyte polarity. ror1-/- mutants appear to be phenotypically wild type, but loss of both ror1 and ror2 leads to more severe cartilage defects, indicating partial redundancy. Skeletal defects in ror1/2 double mutants resemble those of wnt5b-/- mutants, suggesting that Wnt5b is the primary Ror ligand in zebrafish. Surprisingly, the proline-rich domain of Ror2, but not its kinase domain, is required to rescue its function in mosaic transgenic experiments in ror2-/- mutants. These results suggest that endochondral bone defects in ROR-related human syndromes reflect defects in cartilage polarity and morphogenesis.
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Affiliation(s)
- Daniel B. Dranow
- Department of Developmental and Cell Biology, University of California, Irvine, CA 92697, USA
| | - Pierre Le Pabic
- Department of Biology & Marine Biology, University of North Carolina, Wilmington, NC 28403, USA
| | - Thomas F. Schilling
- Department of Developmental and Cell Biology, University of California, Irvine, CA 92697, USA
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69
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Oh DL, Schumacher K, Yang J, Wang K, Lin K, Gomez SL, Shariff-Marco S. Disparities in cancer incidence by rurality in California. J Natl Cancer Inst 2023; 115:385-393. [PMID: 36622036 PMCID: PMC10086626 DOI: 10.1093/jnci/djac238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 10/14/2022] [Accepted: 12/20/2022] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND Cancer rates in rural areas across the United States have different patterns than in urban areas. This study examines associations between rurality and incidence for the top 5 cancers in California and evaluates whether these associations vary jointly by sex, race, and ethnicity. METHODS We used 2015-2019 California Cancer Registry data to compare incidence rate ratios (IRRs) and trends for breast, prostate, lung, colorectal, and skin (melanoma) cancers. We leveraged census tract aggregation zones and 7 levels of percentage rural population (0%, >0% to <10%, 10% to <20%, 20% to <30%, 30% to <40%, 40% to <50%, and 50+%). RESULTS Zones with higher proportions of rural population were significantly associated with lower incidence of female breast cancer and prostate cancer, though the trends were not statistically significant overall. Zones with higher proportions of rural population were significantly associated with higher incidence of lung cancer and melanoma. There were no statistically significant trends for colorectal cancer overall. Comparing areas with 50% and over rural population with areas with 0% rural population, the IRR for lung cancer in Hispanic females was higher (IRR = 1.43, 95% confidence interval [CI] = 1.17 to 1.74) than in Hispanic males (IRR = 0.90, 95% CI = 0.72 to 1.11). Also, in areas with 50% or more rural population, the IRR for melanoma was higher in Hispanic females (IRR = 1.75, 95% CI = 1.23 to 2.45) than non-Hispanic White females (IRR = 0.87, 95% CI = 0.80 to 0.95). CONCLUSIONS Our findings show that rurality is associated with cancer incidence and underscore the importance of jointly examining rural disparities with sex, race, and ethnicity by cancer site.
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Affiliation(s)
- Debora L Oh
- Department of Epidemiology and Biostatistics, University of California, San Francisco, USA
- Greater Bay Area Cancer Registry, University of California, San Francisco, USA
| | - Karen Schumacher
- Department of Physiological Nursing, University of California, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, USA
| | - Juan Yang
- Department of Epidemiology and Biostatistics, University of California, San Francisco, USA
- Greater Bay Area Cancer Registry, University of California, San Francisco, USA
| | - Katarina Wang
- Department of Epidemiology and Biostatistics, University of California, San Francisco, USA
| | - Katherine Lin
- Department of Epidemiology and Biostatistics, University of California, San Francisco, USA
- Greater Bay Area Cancer Registry, University of California, San Francisco, USA
| | - Scarlett Lin Gomez
- Department of Epidemiology and Biostatistics, University of California, San Francisco, USA
- Greater Bay Area Cancer Registry, University of California, San Francisco, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, USA
| | - Salma Shariff-Marco
- Department of Epidemiology and Biostatistics, University of California, San Francisco, USA
- Greater Bay Area Cancer Registry, University of California, San Francisco, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, USA
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70
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Rezk-Hanna M, Talhout R, Jordt SE. Sugars and Sweeteners in Tobacco and Nicotine Products: Food and Drug Administration's Regulatory Implications. Nicotine Tob Res 2023; 25:838-840. [PMID: 36148496 PMCID: PMC10032193 DOI: 10.1093/ntr/ntac222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 09/13/2022] [Accepted: 09/20/2022] [Indexed: 11/13/2022]
Affiliation(s)
- Mary Rezk-Hanna
- School of Nursing, University of California, Los Angeles, Los Angeles, CA, USA
| | - Reinskje Talhout
- Centre for Health Protection, National Institute for Public Health and the Environment, Bilthoven, Utrecht, The Netherlands
| | - Sven-Eric Jordt
- Department of Anesthesiology, Duke University School of Medicine, Durham, NC, USA
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71
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Wright DB, Escalona M, Marimuthu MPA, Sahasrabudhe R, Nguyen O, Sacco S, Beraut E, Toffelmier E, Miller C, Shaffer HB, Bernardi G. Reference genome of the Woolly Sculpin, Clinocottus analis. J Hered 2023; 114:60-67. [PMID: 36107748 PMCID: PMC10019020 DOI: 10.1093/jhered/esac055] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 09/14/2022] [Indexed: 11/13/2022] Open
Abstract
Sculpins (Family Cottidae) are generally cold-temperate intertidal reef fishes most commonly found in the North Pacific. As part of the California Conservation Genomics Project (CCGP), we sequenced the genome of the Woolly Sculpin, Clinocottus analis, to establish a genomic model for understanding phylogeographic structure of inshore marine taxa along the California coast. These patterns, in turn, should further inform the design of marine protected areas using dispersal models based on genomic data. The small genome of C. analis is typical of marine fishes at less than 1 Gb (genome size = 538 Mb), and our assembly is near-chromosome level (contig N50 = 9.1 Mb, scaffold N50 = 21 Mb, BUSCO completeness = 97.9%). Within the context of the CCGP, the Woolly Sculpin genome will be used as a reference for future whole-genome resequencing projects aimed at enhancing our knowledge of the population structure of the species, and efficacy of marine protected areas across the state.
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Affiliation(s)
- Daniel B Wright
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, United States
| | - Merly Escalona
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, United States
| | - Mohan P A Marimuthu
- DNA Technologies and Expression Analysis Core Laboratory, Genome Center, University of California-Davis, Davis, CA, United States
| | - Ruta Sahasrabudhe
- DNA Technologies and Expression Analysis Core Laboratory, Genome Center, University of California-Davis, Davis, CA, United States
| | - Oanh Nguyen
- DNA Technologies and Expression Analysis Core Laboratory, Genome Center, University of California-Davis, Davis, CA, United States
| | - Samuel Sacco
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, United States
| | - Eric Beraut
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, United States
| | - Erin Toffelmier
- Department of Ecology & Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, United States
| | - Courtney Miller
- Department of Ecology & Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, United States
| | - H Bradley Shaffer
- Department of Ecology & Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, United States
- La Kretz Center for California Conservation Science, Institute of the Environment and Sustainability, University of California, Los Angeles, Los Angeles, CA, United States
| | - Giacomo Bernardi
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, United States
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72
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Ballare KM, Escalona M, Barr K, Seligmann W, Sacco S, Sahasrabudhe RM, Nguyen O, Wyckoff C, Smith TB, Shapiro B. A reference genome assembly of the declining tricolored blackbird, Agelaius tricolor. J Hered 2023; 114:44-51. [PMID: 36099176 PMCID: PMC10019024 DOI: 10.1093/jhered/esac053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 09/12/2022] [Indexed: 11/13/2022] Open
Abstract
The tricolored blackbird, Agelaius tricolor, is a gregarious species that forms enormous breeding and foraging colonies in wetland and agricultural habitats, primarily in California, USA. Once extremely abundant, species numbers have declined dramatically in the past century, largely due to losses of breeding and foraging habitats. Tricolored blackbirds are currently listed as Endangered by the IUCN, and Threatened under the California Endangered Species Act. Increased genetic information is needed to detail the evolutionary consequences of a species-wide bottleneck and inform conservation management. Here, we present a contiguous tricolored blackbird reference genome, assembled with PacBio HiFi long reads and Dovetail Omni-C data to generate a scaffold-level assembly containing multiple chromosome-length scaffolds. This genome adds a valuable resource for important evolutionary and conservation research on tricolored blackbirds and related species.
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Affiliation(s)
| | | | - Kelly Barr
- Department of Ecology and Evolutionary Biology, University of California Los Angeles, Los Angeles, CA, United States
- Center for Tropical Research, Institute of the Environment and Sustainability, University of California, Los Angeles, Los Angeles, CA, United States
| | - William Seligmann
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, United States
| | - Samuel Sacco
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, United States
| | - Ruta Madhusudan Sahasrabudhe
- UC Davis Genome Center, DNA Technologies and Expression Analysis Cores, University of California, Davis, Davis, CA, United States
| | - Oanh Nguyen
- UC Davis Genome Center, DNA Technologies and Expression Analysis Cores, University of California, Davis, Davis, CA, United States
| | | | - Thomas B Smith
- Department of Ecology and Evolutionary Biology, University of California Los Angeles, Los Angeles, CA, United States
- Center for Tropical Research, Institute of the Environment and Sustainability, University of California, Los Angeles, Los Angeles, CA, United States
| | - Beth Shapiro
- Address correspondence to B. Shapiro at the address above, or e-mail:
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73
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Wright DB, Escalona M, Marimuthu MPA, Sahasrabudhe R, Nguyen O, Sacco S, Beraut E, Toffelmier E, Miller C, Shaffer HB, Bernardi G, German DP. Reference genome of the Monkeyface Prickleback, Cebidichthys violaceus. J Hered 2023; 114:52-59. [PMID: 36321765 PMCID: PMC10019021 DOI: 10.1093/jhered/esac054] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 09/13/2022] [Indexed: 11/06/2022] Open
Abstract
Pricklebacks (Family Stichaeidae) are generally cold-temperate fishes most commonly found in the north Pacific. As part of the California Conservation Genomics Project (CCGP), we sequenced the genome of the Monkeyface Prickleback, Cebidichthys violaceus, to establish a genomic model for understanding phylogeographic patterns of marine organisms in California. These patterns, in turn, may inform the design of marine protected areas using dispersal models based on forthcoming population genomic data. The genome of C. violaceus is typical of many marine fishes at less than 1 Gb (genome size = 575.6 Mb), and our assembly is near-chromosome level (contig N50 = 1 Mb, scaffold N50 = 16.4 Mb, BUSCO completeness = 93.2%). Within the context of the CCGP, the genome will be used as a reference for future whole genome resequencing projects, enhancing our knowledge of the population structure of the species and more generally, the efficacy of marine protected areas as a primary conservation tool across California's marine ecosystems.
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Affiliation(s)
- Daniel B Wright
- Address correspondence to D.B. Wright at the address above, or e-mail:
| | - Merly Escalona
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, United States
| | - Mohan P A Marimuthu
- DNA Technologies and Expression Analysis Core Laboratory, Genome Center, University of California-Davis, Davis, CA, United States
| | - Ruta Sahasrabudhe
- DNA Technologies and Expression Analysis Core Laboratory, Genome Center, University of California-Davis, Davis, CA, United States
| | - Oanh Nguyen
- DNA Technologies and Expression Analysis Core Laboratory, Genome Center, University of California-Davis, Davis, CA, United States
| | - Samuel Sacco
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, United States
| | - Eric Beraut
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, United States
| | - Erin Toffelmier
- Department of Ecology & Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, United States
| | - Courtney Miller
- Department of Ecology & Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, United States
| | - H Bradley Shaffer
- Department of Ecology & Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, United States
- La Kretz Center for California Conservation Science, Institute of the Environment and Sustainability, University of California, Los Angeles, Los Angeles, CA, United States
| | - Giacomo Bernardi
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, United States
| | - Donovan P German
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, CA, United States
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Kieran Blair SR, Schreier A, Escalona M, Finger AJ, Joslin SEK, Sahasrabudhe R, Marimuthu MPA, Nguyen O, Chumchim N, Morris ER, Mangelson H, Hull J. A chromosome-level reference genome for the Versatile Fairy Shrimp, Branchinecta lindahli. J Hered 2023; 114:74-80. [PMID: 36223244 PMCID: PMC10019023 DOI: 10.1093/jhered/esac057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Accepted: 10/10/2022] [Indexed: 11/14/2022] Open
Abstract
We present the novel reference genome of the Versatile Fairy Shrimp, Branchinecta lindahli. The Versatile Fairy Shrimp is a freshwater anostracan crustacean found across the western United States from Iowa to Oregon and from Alberta to Baja California. It is an ephemeral pool specialist, living in prairie potholes, irrigation ditches, tire treads, vernal pools, and other temporary freshwater wetlands. Anostracan fairy shrimp are facing global declines with 3 species in California on the Endangered Species list. This species was included in the California Conservation Genomics Project to provide an easily accessible reference genome, and to provide whole-genome resources for a generalist species, which may lead to new insights into Anostracan resiliency in the face of climate change. The final gapped genome comprises 15 chromosome-length scaffolds covering 98.63% of the 384.8 Mb sequence length, and an additional 55 unscaffolded contigs.
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Affiliation(s)
| | - Andrea Schreier
- Genomic Variation Laboratory, Department of Animal Science, University of California, Davis, Davis, CA, United States
| | - Merly Escalona
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA, United States
| | - Amanda J Finger
- Genomic Variation Laboratory, Department of Animal Science, University of California, Davis, Davis, CA, United States
| | - Shannon E K Joslin
- U.S. National Park Service, Yosemite National Park, El Portal, CA, United States
| | - Ruta Sahasrabudhe
- DNA Technologies and Expression Analysis Cores, UC Davis Genome Center, University of California, Davis, Davis, CA, United States
| | - Mohan P A Marimuthu
- DNA Technologies and Expression Analysis Cores, UC Davis Genome Center, University of California, Davis, Davis, CA, United States
| | - Oanh Nguyen
- DNA Technologies and Expression Analysis Cores, UC Davis Genome Center, University of California, Davis, Davis, CA, United States
| | - Noravit Chumchim
- DNA Technologies and Expression Analysis Cores, UC Davis Genome Center, University of California, Davis, Davis, CA, United States
| | | | | | - Joshua Hull
- U.S. Fish and Wildlife Service, Sacramento Fish and Wildlife Office, Sacramento, CA, United States
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75
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Kieran Blair SR, Schreier A, Escalona M, Finger AJ, Joslin SEK, Sahasrabudhe R, Marimuthu MPA, Nguyen O, Chumchim N, Morris ER, Mangelson H, Hull J. A draft reference genome of the Vernal Pool Fairy Shrimp, Branchinecta lynchi. J Hered 2023; 114:81-87. [PMID: 36222891 PMCID: PMC10019022 DOI: 10.1093/jhered/esac056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 10/10/2022] [Indexed: 11/12/2022] Open
Abstract
We present the reference genome of the Vernal Pool Fairy Shrimp Branchinecta lynchi. This branchiopod crustacean is endemic to California's freshwater ephemeral ponds. It faces enormous habitat loss and fragmentation as urbanization and agriculture have fundamentally changed the vernal pool landscape over the past 3 centuries. The assembled genome consists of 22 chromosome-length scaffolds that account for 96.85% of the total sequence. One hundred and ninety-five unscaffolded contigs comprise the rest of the genome's 575.6 Mb length. The genome is substantially complete with a BUSCO score of 90.0%. There is no immediately identifiable sex chromosome, typical for this class of organism. This new resource will permit researchers to better understand the adaptive capacity of this imperiled species, as well as answer lingering questions about anostracan physiology, sex determination, and development.
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Affiliation(s)
| | - Andrea Schreier
- Genomic Variation Laboratory, Department of Animal Science, University of California, Davis, Davis, CA, United States
| | - Merly Escalona
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA, United States
| | - Amanda J Finger
- Genomic Variation Laboratory, Department of Animal Science, University of California, Davis, Davis, CA, United States
| | - Shannon E K Joslin
- U.S. National Park Service, Yosemite National Park, El Portal, CA, United States
| | - Ruta Sahasrabudhe
- DNA Technologies and Expression Analysis Cores, UC Davis Genome Center, University of California, Davis, Davis, CA, United States
| | - Mohan P A Marimuthu
- DNA Technologies and Expression Analysis Cores, UC Davis Genome Center, University of California, Davis, Davis, CA, United States
| | - Oanh Nguyen
- DNA Technologies and Expression Analysis Cores, UC Davis Genome Center, University of California, Davis, Davis, CA, United States
| | - Noravit Chumchim
- DNA Technologies and Expression Analysis Cores, UC Davis Genome Center, University of California, Davis, Davis, CA, United States
| | | | | | - Joshua Hull
- U.S. Fish and Wildlife Service, Sacramento Fish and Wildlife Office, Sacramento, CA, United States
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Seibert TM, Pagadala MS, Lynch J, Karunamuni R, Carter H, Rose BS, Hauger RL. Response to Haiman, Kote-Jarai, Darst et al. J Natl Cancer Inst 2023; 115:343-344. [PMID: 36629482 PMCID: PMC9996213 DOI: 10.1093/jnci/djad006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 12/07/2022] [Indexed: 01/12/2023] Open
Affiliation(s)
- Tyler M Seibert
- Research Service, VA San Diego Healthcare System, San Diego, CA, USA
- Department of Radiation Medicine and Applied Sciences, University of California San Diego, La Jolla, CA, USA
- Department of Radiology, University of California San Diego, La Jolla, CA, USA
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
| | - Meghana S Pagadala
- Research Service, VA San Diego Healthcare System, San Diego, CA, USA
- Medical Scientist Training Program, University of California San Diego, La Jolla, CA, USA
- Biomedical Science Program, University of California San Diego, La Jolla, CA, USA
| | - Julie Lynch
- VA Informatics and Computing Infrastructure, VA Salt Lake City Healthcare System (VINCI), Salt Lake City, UT, USA
- Department of Internal Medicine, Division of Epidemiology, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Roshan Karunamuni
- Department of Radiation Medicine and Applied Sciences, University of California San Diego, La Jolla, CA, USA
| | - Hannah Carter
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Brent S Rose
- Research Service, VA San Diego Healthcare System, San Diego, CA, USA
- Department of Radiation Medicine and Applied Sciences, University of California San Diego, La Jolla, CA, USA
- Department of Urology, University of California San Diego, La Jolla, CA, USA
| | - Richard L Hauger
- Research Service, VA San Diego Healthcare System, San Diego, CA, USA
- Center for Behavioral Genetics of Aging, University of California San Diego, La Jolla, CA, USA
- Center of Excellence for Stress and Mental Health (CESAMH), VA San Diego Healthcare System, San Diego, CA, USA
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77
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Demir M, Russelburg LP, Lin WJ, Trasviña-Arenas C, Huang B, Yuen P, Horvath M, David S. Structural snapshots of base excision by the cancer-associated variant MutY N146S reveal a retaining mechanism. Nucleic Acids Res 2023; 51:1034-1049. [PMID: 36631987 PMCID: PMC9943663 DOI: 10.1093/nar/gkac1246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 11/18/2022] [Accepted: 12/16/2022] [Indexed: 01/13/2023] Open
Abstract
DNA glycosylase MutY plays a critical role in suppression of mutations resulted from oxidative damage, as highlighted by cancer-association of the human enzyme. MutY requires a highly conserved catalytic Asp residue for excision of adenines misinserted opposite 8-oxo-7,8-dihydroguanine (OG). A nearby Asn residue hydrogen bonds to the catalytic Asp in structures of MutY and its mutation to Ser is an inherited variant in human MUTYH associated with colorectal cancer. We captured structural snapshots of N146S Geobacillus stearothermophilus MutY bound to DNA containing a substrate, a transition state analog and enzyme-catalyzed abasic site products to provide insight into the base excision mechanism of MutY and the role of Asn. Surprisingly, despite the ability of N146S to excise adenine and purine (P) in vitro, albeit at slow rates, N146S-OG:P complex showed a calcium coordinated to the purine base altering its conformation to inhibit hydrolysis. We obtained crystal structures of N146S Gs MutY bound to its abasic site product by removing the calcium from crystals of N146S-OG:P complex to initiate catalysis in crystallo or by crystallization in the absence of calcium. The product structures of N146S feature enzyme-generated β-anomer abasic sites that support a retaining mechanism for MutY-catalyzed base excision.
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Affiliation(s)
- Merve Demir
- Department of Chemistry, University of California, Davis, CA 95616, USA
| | - L Peyton Russelburg
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112, USA
| | - Wen-Jen Lin
- Department of Chemistry, University of California, Davis, CA 95616, USA
| | | | - Beili Huang
- Department of Chemistry, University of California, Davis, CA 95616, USA
| | - Philip K Yuen
- Department of Chemistry, University of California, Davis, CA 95616, USA
| | - Martin P Horvath
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112, USA
| | - Sheila S David
- Department of Chemistry, University of California, Davis, CA 95616, USA
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78
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Cachay ER, Gilbert T, Deiss R, Mathews WC. Shared Decision-Making Concerning Anal Cancer Screening in Persons With Human Immunodeficiency Virus. Clin Infect Dis 2023; 76:582-591. [PMID: 35723270 PMCID: PMC10226749 DOI: 10.1093/cid/ciac491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 05/31/2022] [Accepted: 06/09/2022] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND Anal high-grade squamous intraepithelial lesion (aHSIL) is the immediate precursor of anal cancer. Anal cytology is a recommended screening test to identify aHSIL among people with human immunodeficiency virus (HIV; PWH). Heterogeneity of risk for invasive anal cancer among PWH suggests the value of a shared decision-making framework regarding screening. METHODS Using a longitudinal HIV cohort with a comprehensive anal cancer screening program, we estimated the adjusted probabilities of having aHSIL on the first anal cytology. We used logistic regression models with inverse probability weighting to account for differential screening in the cohort and to construct a predicted probability nomogram for aHSIL. Sensitivity analysis was performed to estimate aHSIL prevalence corrected for misclassification bias. RESULTS Of 8139 PWH under care between 2007 and 2020, 4105 (49.8%) underwent at least 1 anal cytology test. First-time cytology aHSIL was present in 502 (12.2%) PWH. The adjusted probability of having aHSIL varied from 5% to 18% depending on patient characteristics. Prespecified factors in the aHSIL prediction model included nadir CD4 cell count, ethnicity, race, age, sex, gender identity, and HIV risk factors. The ability of the model to discriminate cytological aHSIL was modest, with an area under the curve of 0.63 (95% confidence interval, .60-.65). CONCLUSIONS PWH are at increased risk for aHSIL and invasive anal cancer. Risk, however, varies by patient characteristics. Individual risk factor profiles predictive of aHSIL can be modeled and operationalized as nomograms to facilitate shared decision-making conversations concerning anal cancer screening.
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Affiliation(s)
- Edward R Cachay
- Department of Medicine, Owen Clinic, University of California–San Diego, San Diego, California, USA
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California–San Diego, San Diego, California, USA
| | - Tari Gilbert
- Department of Medicine, Owen Clinic, University of California–San Diego, San Diego, California, USA
| | - Robert Deiss
- Department of Medicine, Owen Clinic, University of California–San Diego, San Diego, California, USA
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California–San Diego, San Diego, California, USA
| | - Wm Christopher Mathews
- Department of Medicine, Owen Clinic, University of California–San Diego, San Diego, California, USA
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79
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George RM, Firulli BA, Podicheti R, Rusch DB, Mannion BJ, Pennacchio LA, Osterwalder M, Firulli AB. Single cell evaluation of endocardial Hand2 gene regulatory networks reveals HAND2-dependent pathways that impact cardiac morphogenesis. Development 2023; 150:dev201341. [PMID: 36620995 PMCID: PMC10110492 DOI: 10.1242/dev.201341] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 12/26/2022] [Indexed: 01/10/2023]
Abstract
The transcription factor HAND2 plays essential roles during cardiogenesis. Hand2 endocardial deletion (H2CKO) results in tricuspid atresia or double inlet left ventricle with accompanying intraventricular septum defects, hypo-trabeculated ventricles and an increased density of coronary lumens. To understand the regulatory mechanisms of these phenotypes, single cell transcriptome analysis of mouse E11.5 H2CKO hearts was performed revealing a number of disrupted endocardial regulatory pathways. Using HAND2 DNA occupancy data, we identify several HAND2-dependent enhancers, including two endothelial enhancers for the shear-stress master regulator KLF2. A 1.8 kb enhancer located 50 kb upstream of the Klf2 TSS imparts specific endothelial/endocardial expression within the vasculature and endocardium. This enhancer is HAND2-dependent for ventricular endocardium expression but HAND2-independent for Klf2 vascular and valve expression. Deletion of this Klf2 enhancer results in reduced Klf2 expression within ventricular endocardium. These data reveal that HAND2 functions within endocardial gene regulatory networks including shear-stress response.
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Affiliation(s)
- Rajani M. George
- Herman B Wells Center for Pediatric Research, Departments of Pediatrics, Anatomy and Medical and Molecular Genetics, Indiana Medical School, Indianapolis, IN 46202, USA
| | - Beth A. Firulli
- Herman B Wells Center for Pediatric Research, Departments of Pediatrics, Anatomy and Medical and Molecular Genetics, Indiana Medical School, Indianapolis, IN 46202, USA
| | - Ram Podicheti
- Center for Genomics and Bioinformatics, Indiana University, Bloomington, IN 47405, USA
| | - Douglas B. Rusch
- Center for Genomics and Bioinformatics, Indiana University, Bloomington, IN 47405, USA
| | - Brandon J. Mannion
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Comparative Biochemistry Program, University of California, Berkeley, CA 94720, USA
| | - Len A. Pennacchio
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Comparative Biochemistry Program, University of California, Berkeley, CA 94720, USA
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Marco Osterwalder
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Department for BioMedical Research (DBMR), University of Bern, Bern 3008, Switzerland
- Department of Cardiology, Bern University Hospital, Bern 3010, Switzerland
| | - Anthony B. Firulli
- Herman B Wells Center for Pediatric Research, Departments of Pediatrics, Anatomy and Medical and Molecular Genetics, Indiana Medical School, Indianapolis, IN 46202, USA
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80
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Pagadala MS, Lynch J, Karunamuni R, Alba PR, Lee KM, Agiri FY, Anglin T, Carter H, Gaziano JM, Jasuja GK, Deka R, Rose BS, Panizzon MS, Hauger RL, Seibert TM. Polygenic risk of any, metastatic, and fatal prostate cancer in the Million Veteran Program. J Natl Cancer Inst 2023; 115:190-199. [PMID: 36305680 PMCID: PMC9905969 DOI: 10.1093/jnci/djac199] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 07/13/2022] [Accepted: 10/26/2022] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND Genetic scores may provide an objective measure of prostate cancer risk and thus inform screening decisions. We evaluated whether a polygenic hazard score based on 290 genetic variants (PHS290) is associated with prostate cancer risk in a diverse population, including Black men, who have higher average risk of prostate cancer death but are often treated as a homogeneously high-risk group. METHODS This was a retrospective analysis of the Million Veteran Program, a national, population-based cohort study of US military veterans conducted 2011-2021. Cox proportional hazards analyses tested for association of genetic and other risk factors (including self-reported race and ethnicity and family history) with age at death from prostate cancer, age at diagnosis of metastatic (nodal or distant) prostate cancer, and age at diagnosis of any prostate cancer. RESULTS A total of 590 750 male participants were included. Median age at last follow-up was 69 years. PHS290 was associated with fatal prostate cancer in the full cohort and for each racial and ethnic group (P < .001). Comparing men in the highest 20% of PHS290 with those in the lowest 20% (based on percentiles from an independent training cohort), the hazard ratio for fatal prostate cancer was 4.42 (95% confidence interval = 3.91 to 5.02). When accounting for guideline-recommended risk factors (family history, race, and ethnicity), PHS290 remained a strong independent predictor of any, metastatic, and fatal prostate cancer. CONCLUSIONS PHS290 stratified US veterans of diverse ancestry for lifetime risk of prostate cancer, including metastatic and fatal cancer. Predicting genetic risk of lethal prostate cancer with PHS290 might inform individualized decisions about prostate cancer screening.
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Affiliation(s)
- Meghana S Pagadala
- Research Service, VA San Diego Healthcare System, San Diego, CA, USA
- Medical Scientist Training Program, University of California San Diego, La Jolla, CA, USA
- Biomedical Science Program, University of California San Diego, La Jolla, CA, USA
| | - Julie Lynch
- VA Informatics and Computing Infrastructure, VA Salt Lake City Healthcare System (VINCI), Salt Lake City, UT, USA
- Department of Internal Medicine, Division of Epidemiology, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Roshan Karunamuni
- Department of Radiation Medicine and Applied Sciences, University of California San Diego, La Jolla, CA, USA
| | - Patrick R Alba
- VA Informatics and Computing Infrastructure, VA Salt Lake City Healthcare System (VINCI), Salt Lake City, UT, USA
- Department of Internal Medicine, Division of Epidemiology, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Kyung Min Lee
- VA Informatics and Computing Infrastructure, VA Salt Lake City Healthcare System (VINCI), Salt Lake City, UT, USA
- Department of Internal Medicine, Division of Epidemiology, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Fatai Y Agiri
- VA Informatics and Computing Infrastructure, VA Salt Lake City Healthcare System (VINCI), Salt Lake City, UT, USA
| | - Tori Anglin
- VA Informatics and Computing Infrastructure, VA Salt Lake City Healthcare System (VINCI), Salt Lake City, UT, USA
- Department of Internal Medicine, Division of Epidemiology, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Hannah Carter
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - J Michael Gaziano
- Massachusetts Veterans Epidemiology Research and Information Center (MAVERIC), VA Boston Healthcare System, Boston, MA, USA
- Department of Medicine, Brigham and Women’s Hospital, Boston, MA, USA
| | - Guneet Kaur Jasuja
- Center for Healthcare Organization and Implementation Research (CHOIR), VA Bedford Healthcare System, Bedford, MA, USA
- Section of General Internal Medicine, Boston University School of Medicine, Boston, MA, USA; Department of Urology, University of California San Diego, La Jolla, CA, USA
| | - Rishi Deka
- Research Service, VA San Diego Healthcare System, San Diego, CA, USA
- Department of Radiation Medicine and Applied Sciences, University of California San Diego, La Jolla, CA, USA
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
| | - Brent S Rose
- Research Service, VA San Diego Healthcare System, San Diego, CA, USA
- Department of Radiation Medicine and Applied Sciences, University of California San Diego, La Jolla, CA, USA
- Section of General Internal Medicine, Boston University School of Medicine, Boston, MA, USA; Department of Urology, University of California San Diego, La Jolla, CA, USA
| | - Matthew S Panizzon
- Research Service, VA San Diego Healthcare System, San Diego, CA, USA
- Center for Behavioral Genetics of Aging, University of California San Diego, La Jolla, CA, USA
| | - Richard L Hauger
- Research Service, VA San Diego Healthcare System, San Diego, CA, USA
- Center for Behavioral Genetics of Aging, University of California San Diego, La Jolla, CA, USA
- Center of Excellence for Stress and Mental Health (CESAMH), VA San Diego Healthcare System, San Diego, CA, USA
| | - Tyler M Seibert
- Research Service, VA San Diego Healthcare System, San Diego, CA, USA
- Department of Radiation Medicine and Applied Sciences, University of California San Diego, La Jolla, CA, USA
- Department of Radiology, University of California San Diego, La Jolla, CA, USA
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
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81
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Canchola A, Langmo S, Meletz R, Lum M, Lin YH. External Factors Modulating Vaping-Induced Thermal Degradation of Vitamin E Acetate. Chem Res Toxicol 2023; 36:83-93. [PMID: 36534744 PMCID: PMC9846828 DOI: 10.1021/acs.chemrestox.2c00298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Indexed: 12/23/2022]
Abstract
Despite previous studies indicating the thermal stability of vitamin E acetate (VEA) at low temperatures, VEA has been shown to readily decompose into various degradation products such as alkenes, long-chain alcohols, and carbonyls such as duroquinone (DQ) at vaping temperatures of <200 °C. While most models simulate the thermal decomposition of e-liquids under pyrolysis conditions, numerous factors, including vaping behavior, device construction, and the surrounding environment, may impact the thermal degradation process. In this study, we investigated the role of the presence of molecular oxygen (O2) and transition metals in promoting thermal oxidation of e-liquids, resulting in greater degradation than predicted by pure pyrolysis. Thermal degradation of VEA was performed in inert (N2) and oxidizing atmospheres (clean air) in the absence and presence of Ni-Cr and Cu-Ni alloy nanopowders, metals commonly found in the heating coil and body of e-cigarettes. VEA degradation was analyzed using thermogravimetric analysis (TGA) and gas chromatography/mass spectrometry (GC/MS). While the presence of O2 was found to significantly enhance the degradation of VEA at both high (356 °C) and low (176 °C) temperatures, the addition of Cu-Ni to oxidizing atmospheres was found to greatly enhance VEA degradation, resulting in the formation of numerous degradation products previously identified in VEA vaping emissions. O2 and Cu-Ni nanopowder together were also found to significantly increase the production of OH radicals, which has implications for e-liquid degradation pathways as well as the potential risk of oxidative damage to biological systems in real-world vaping scenarios. Ultimately, the results presented in this study highlight the importance of oxidation pathways in VEA thermal degradation and may aid in the prediction of thermal degradation products from e-liquids.
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Affiliation(s)
- Alexa Canchola
- Environmental
Toxicology Graduate Program, University
of California, Riverside, California 92521, United States
| | - Siri Langmo
- Department
of Evolution, Ecology, and Organismal Biology, University of California, Riverside, California 92521, United States
| | - Ruth Meletz
- Department
of Environmental Sciences, University of
California, Riverside, California 92521, United States
| | - Michael Lum
- Department
of Environmental Sciences, University of
California, Riverside, California 92521, United States
| | - Ying-Hsuan Lin
- Environmental
Toxicology Graduate Program, University
of California, Riverside, California 92521, United States
- Department
of Environmental Sciences, University of
California, Riverside, California 92521, United States
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82
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Keeley PW, Patel PS, Ryu MS, Reese BE. Neurog2 regulates Isl1 to modulate horizontal cell number. Development 2023; 150:dev201315. [PMID: 36537573 PMCID: PMC10108602 DOI: 10.1242/dev.201315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 12/06/2022] [Indexed: 12/24/2022]
Abstract
The population sizes of different retinal cell types vary between different strains of mice, and that variation can be mapped to genomic loci in order to identify its polygenic origin. In some cases, controlling genes act independently, whereas in other instances, they exhibit epistasis. Here, we identify an epistatic interaction revealed through the mapping of quantitative trait loci from a panel of recombinant inbred strains of mice. The population of retinal horizontal cells exhibits a twofold variation in number, mapping to quantitative trait loci on chromosomes 3 and 13, where these loci are shown to interact epistatically. We identify a prospective genetic interaction underlying this, mediated by the bHLH transcription factor Neurog2, at the chromosome 3 locus, functioning to repress the LIM homeodomain transcription factor Isl1, at the chromosome 13 locus. Using single and double conditional knockout mice, we confirm the countervailing actions of each gene, and validate in vitro a crucial role for two single nucleotide polymorphisms in the 5'UTR of Isl1, one of which yields a novel E-box, mediating the repressive action of Neurog2.
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Affiliation(s)
- Patrick W. Keeley
- Neuroscience Research Institute, University of California at Santa Barbara, Santa Barbara, CA 93106-5060, USA
| | - Pooja S. Patel
- Neuroscience Research Institute, University of California at Santa Barbara, Santa Barbara, CA 93106-5060, USA
| | - Matthew S. Ryu
- Neuroscience Research Institute, University of California at Santa Barbara, Santa Barbara, CA 93106-5060, USA
| | - Benjamin E. Reese
- Neuroscience Research Institute, University of California at Santa Barbara, Santa Barbara, CA 93106-5060, USA
- Department of Psychological and Brain Sciences, University of California at Santa Barbara, Santa Barbara, CA 93106-5060, USA
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83
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Messina MS, Quargnali G, Chang CJ. Activity-Based Sensing for Chemistry-Enabled Biology: Illuminating Principles, Probes, and Prospects for Boronate Reagents for Studying Hydrogen Peroxide. ACS Bio Med Chem Au 2022; 2:548-564. [PMID: 36573097 PMCID: PMC9782337 DOI: 10.1021/acsbiomedchemau.2c00052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 09/29/2022] [Accepted: 09/30/2022] [Indexed: 11/07/2022]
Abstract
Activity-based sensing (ABS) offers a general approach that exploits chemical reactivity as a method for selective detection and manipulation of biological analytes. Here, we illustrate the value of this chemical platform to enable new biological discovery through a case study in the design and application of ABS reagents for studying hydrogen peroxide (H2O2), a major type of reactive oxygen species (ROS) that regulates a diverse array of vital cellular signaling processes to sustain life. Specifically, we summarize advances in the use of activity-based boronate probes for the detection of H2O2 featuring high molecular selectivity over other ROS, with an emphasis on tailoring designs in chemical structure to promote new biological principles of redox signaling.
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Affiliation(s)
- Marco S. Messina
- Department
of Chemistry and Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California 94720, United States
- Department
of Chemistry and Biochemistry, University
of Delaware, Newark, Delaware 19716, United States
| | - Gianluca Quargnali
- Department
of Chemistry and Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California 94720, United States
| | - Christopher J. Chang
- Department
of Chemistry and Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California 94720, United States
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84
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Ayón C, Ellis BD, Hagan MJ, Enriquez LE, Offidani-Bertrand C. Mental health help-seeking among Latina/o/x undocumented college students. Cultur Divers Ethnic Minor Psychol 2022:2023-28142-001. [PMID: 36521136 DOI: 10.1037/cdp0000573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
OBJECTIVES Informed by a social-ecological framework, this study nested undocumented students' individual mental health needs within micro-level campus factors and the macro-level immigration policy context to examine how these are associated with undocumented Latina/o/x college students' use of on-campus mental health services. METHOD A large-scale survey was administered to 1,277 undocumented college students attending 4-year public universities in California. Only Latina/o/x respondents were included in this study (N = 1,181). Fifty percent of students attended a UC system (n = 589). On average, students were 21.84 years old (SE = .15), and most were women (75.3%, n = 890). RESULTS Greater level of mental health symptoms and perceived mental health need, and greater use of campus-wide resources and undocumented student services predicted greater likelihood of using on-campus mental health services. Greater perceptions of social exclusion due to the immigration policy context predicted lower use of mental health services. CONCLUSIONS Results indicate that a greater use of resources and an inclusive campus environment, as well as efforts to minimize policy-related feelings of social exclusion, may facilitate undocumented students' professional mental health help-seeking. These findings emphasize the need to take multiple and multi-level ecological factors into account when considering mental health service use, particularly in the case of undocumented immigrants and likely other structurally marginalized groups. (PsycInfo Database Record (c) 2022 APA, all rights reserved).
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85
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Jung AY, Ahearn TU, Behrens S, Middha P, Bolla MK, Wang Q, Arndt V, Aronson KJ, Augustinsson A, Beane Freeman LE, Becher H, Brenner H, Canzian F, Carey LA, Czene K, Eliassen AH, Eriksson M, Evans DG, Figueroa JD, Fritschi L, Gabrielson M, Giles GG, Guénel P, Hadjisavvas A, Haiman CA, Håkansson N, Hall P, Hamann U, Hoppe R, Hopper JL, Howell A, Hunter DJ, Hüsing A, Kaaks R, Kosma VM, Koutros S, Kraft P, Lacey JV, Le Marchand L, Lissowska J, Loizidou MA, Mannermaa A, Maurer T, Murphy RA, Olshan AF, Olsson H, Patel AV, Perou CM, Rennert G, Shibli R, Shu XO, Southey MC, Stone J, Tamimi RM, Teras LR, Troester MA, Truong T, Vachon CM, Wang SS, Wolk A, Wu AH, Yang XR, Zheng W, Dunning AM, Pharoah PDP, Easton DF, Milne RL, Chatterjee N, Schmidt MK, García-Closas M, Chang-Claude J. Distinct Reproductive Risk Profiles for Intrinsic-Like Breast Cancer Subtypes: Pooled Analysis of Population-Based Studies. J Natl Cancer Inst 2022; 114:1706-1719. [PMID: 35723569 PMCID: PMC9949579 DOI: 10.1093/jnci/djac117] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 03/22/2022] [Accepted: 05/03/2022] [Indexed: 01/11/2023] Open
Abstract
BACKGROUND Reproductive factors have been shown to be differentially associated with risk of estrogen receptor (ER)-positive and ER-negative breast cancer. However, their associations with intrinsic-like subtypes are less clear. METHODS Analyses included up to 23 353 cases and 71 072 controls pooled from 31 population-based case-control or cohort studies in the Breast Cancer Association Consortium across 16 countries on 4 continents. Polytomous logistic regression was used to estimate the association between reproductive factors and risk of breast cancer by intrinsic-like subtypes (luminal A-like, luminal B-like, luminal B-HER2-like, HER2-enriched-like, and triple-negative breast cancer) and by invasiveness. All statistical tests were 2-sided. RESULTS Compared with nulliparous women, parous women had a lower risk of luminal A-like, luminal B-like, luminal B-HER2-like, and HER2-enriched-like disease. This association was apparent only after approximately 10 years since last birth and became stronger with increasing time (odds ratio [OR] = 0.59, 95% confidence interval [CI] = 0.49 to 0.71; and OR = 0.36, 95% CI = 0.28 to 0.46 for multiparous women with luminal A-like tumors 20 to less than 25 years after last birth and 45 to less than 50 years after last birth, respectively). In contrast, parous women had a higher risk of triple-negative breast cancer right after their last birth (for multiparous women: OR = 3.12, 95% CI = 2.02 to 4.83) that was attenuated with time but persisted for decades (OR = 1.03, 95% CI = 0.79 to 1.34, for multiparous women 25 to less than 30 years after last birth). Older age at first birth (Pheterogeneity < .001 for triple-negative compared with luminal A-like breast cancer) and breastfeeding (Pheterogeneity < .001 for triple-negative compared with luminal A-like breast cancer) were associated with lower risk of triple-negative breast cancer but not with other disease subtypes. Younger age at menarche was associated with higher risk of all subtypes; older age at menopause was associated with higher risk of luminal A-like but not triple-negative breast cancer. Associations for in situ tumors were similar to luminal A-like. CONCLUSIONS This large and comprehensive study demonstrates a distinct reproductive risk factor profile for triple-negative breast cancer compared with other subtypes, with implications for the understanding of disease etiology and risk prediction.
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Affiliation(s)
- Audrey Y Jung
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Cancer Epidemiology Group, University Medical Center Hamburg-Eppendorf, University Cancer Center Hamburg (UCCH), Hamburg, Germany
| | - Thomas U Ahearn
- Department of Health and Human Services, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Sabine Behrens
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Pooja Middha
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Manjeet K Bolla
- Department of Public Health and Primary Care, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, UK
| | - Qin Wang
- Department of Public Health and Primary Care, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, UK
| | - Volker Arndt
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Kristan J Aronson
- Department of Public Health Sciences, and Cancer Research Institute, Queen’s University, Kingston, ON, Canada
| | | | - Laura E Beane Freeman
- Department of Health and Human Services, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Heiko Becher
- Institute for Medical Biometry and Epidemiology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Division of Preventive Oncology, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), Heidelberg, Germany
- German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Federico Canzian
- Genomic Epidemiology Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Lisa A Carey
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - CTS Consortium
- Department of Computational and Quantitative Medicine, City of Hope, Duarte, CA, USA
- City of Hope Comprehensive Cancer Center, City of Hope, Duarte, CA, USA
| | - Kamila Czene
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - A Heather Eliassen
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Mikael Eriksson
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - D Gareth Evans
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
- Manchester Academic Health Science Centre, North West Genomics Laboratory Hub, Manchester Centre for Genomic Medicine, St Mary’s Hospital, Manchester University NHS Foundation Trust, Manchester, UK
| | - Jonine D Figueroa
- Department of Health and Human Services, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
- Usher Institute of Population Health Sciences and Informatics, The University of Edinburgh, Edinburgh, UK
- Cancer Research UK Edinburgh Centre, The University of Edinburgh, Edinburgh, UK
| | - Lin Fritschi
- School of Population Health, Curtin University, Perth, Western Australia, Australia
| | - Marike Gabrielson
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Graham G Giles
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Victoria, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, Victoria, Australia
| | - Pascal Guénel
- Institut national de la santé et de la recherche médicale (INSERM), University Paris-Saclay, Center for Research in Epidemiology and Population Health (CESP), Team Exposome and Heredity, Villejuif, France
| | - Andreas Hadjisavvas
- Department of Electron Microscopy/Molecular Pathology, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
- The Cyprus Institute of Neurology and Genetics, Cyprus School of Molecular Medicine, Nicosia, Cyprus
| | - Christopher A Haiman
- Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Niclas Håkansson
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Per Hall
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
- Department of Oncology, Södersjukhuset, Stockholm, Sweden
| | - Ute Hamann
- Molecular Genetics of Breast Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Reiner Hoppe
- Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology, Stuttgart, Germany
- University of Tübingen, Tübingen, Germany
| | - John L Hopper
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
| | - Anthony Howell
- Division of Cancer Sciences, University of Manchester, Manchester, UK
| | - David J Hunter
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Anika Hüsing
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Rudolf Kaaks
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Veli-Matti Kosma
- Translational Cancer Research Area, University of Eastern Finland, Kuopio, Finland
- Institute of Clinical Medicine, Pathology and Forensic Medicine, University of Eastern Finland, Kuopio, Finland
- Biobank of Eastern Finland, Kuopio University Hospital, Kuopio, Finland
| | - Stella Koutros
- Department of Health and Human Services, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Peter Kraft
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Program in Genetic Epidemiology and Statistical Genetics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - James V Lacey
- Department of Computational and Quantitative Medicine, City of Hope, Duarte, CA, USA
- City of Hope Comprehensive Cancer Center, City of Hope, Duarte, CA, USA
| | - Loic Le Marchand
- Epidemiology Program, University of Hawaii Cancer Center, Honolulu, HI, USA
| | - Jolanta Lissowska
- Department of Cancer Epidemiology and Prevention, M. Sklodowska-Curie National Research Oncology Institute, Warsaw, Poland
| | - Maria A Loizidou
- Department of Electron Microscopy/Molecular Pathology, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
- The Cyprus Institute of Neurology and Genetics, Cyprus School of Molecular Medicine, Nicosia, Cyprus
| | - Arto Mannermaa
- Translational Cancer Research Area, University of Eastern Finland, Kuopio, Finland
- Institute of Clinical Medicine, Pathology and Forensic Medicine, University of Eastern Finland, Kuopio, Finland
- Biobank of Eastern Finland, Kuopio University Hospital, Kuopio, Finland
| | - Tabea Maurer
- Cancer Epidemiology Group, University Medical Center Hamburg-Eppendorf, University Cancer Center Hamburg (UCCH), Hamburg, Germany
| | - Rachel A Murphy
- School of Population and Public Health, University of British Columbia, Vancouver, BC, Canada
- BC Cancer Agency, Cancer Control Research, Vancouver, BC, Canada
| | - Andrew F Olshan
- Department of Epidemiology, Gillings School of Global Public Health and UNC Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Håkan Olsson
- Department of Clinical Sciences, Lund University, Lund, Sweden
| | - Alpa V Patel
- Department of Population Science, American Cancer Society, Atlanta, GA, USA
| | - Charles M Perou
- Department of Genetics, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Gad Rennert
- Carmel Medical Center and Technion Faculty of Medicine, Clalit National Cancer Control Center, Haifa, Israel
| | - Rana Shibli
- Carmel Medical Center and Technion Faculty of Medicine, Clalit National Cancer Control Center, Haifa, Israel
| | - Xiao-Ou Shu
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Melissa C Southey
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Victoria, Australia
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, Victoria, Australia
- Department of Clinical Pathology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Jennifer Stone
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
- Genetic Epidemiology Group, School of Population and Global Health, University of Western Australia, Perth, Western Australia, Australia
| | - Rulla M Tamimi
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Department of Population Health Sciences, Weill Cornell Medicine, New York, NY, USA
| | - Lauren R Teras
- Department of Population Science, American Cancer Society, Atlanta, GA, USA
| | - Melissa A Troester
- Department of Epidemiology, Gillings School of Global Public Health and UNC Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Thérèse Truong
- Institut national de la santé et de la recherche médicale (INSERM), University Paris-Saclay, Center for Research in Epidemiology and Population Health (CESP), Team Exposome and Heredity, Villejuif, France
| | - Celine M Vachon
- Department of Quantitative Health Sciences, Division of Epidemiology, Mayo Clinic, Rochester, MN, USA
| | - Sophia S Wang
- Department of Computational and Quantitative Medicine, City of Hope, Duarte, CA, USA
- City of Hope Comprehensive Cancer Center, City of Hope, Duarte, CA, USA
| | - Alicja Wolk
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
- Department of Surgical Sciences, Uppsala University, Uppsala, Sweden
| | - Anna H Wu
- Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Xiaohong R Yang
- Department of Health and Human Services, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Wei Zheng
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Alison M Dunning
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Paul D P Pharoah
- Department of Public Health and Primary Care, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, UK
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Douglas F Easton
- Department of Public Health and Primary Care, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, UK
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Roger L Milne
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Victoria, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, Victoria, Australia
| | - Nilanjan Chatterjee
- Department of Health and Human Services, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
- Department of Biostatistics, Bloomberg School of Public Health, John Hopkins University, Baltimore, MD, USA
- Department of Oncology, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Marjanka K Schmidt
- Division of Molecular Pathology, The Netherlands Cancer Institute—Antoni van Leeuwenhoek Hospital, Amsterdam, the Netherlands
- Division of Psychosocial Research and Epidemiology, The Netherlands Cancer Institute—Antoni van Leeuwenhoek Hospital, Amsterdam, the Netherlands
| | - Montserrat García-Closas
- Department of Health and Human Services, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Jenny Chang-Claude
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Cancer Epidemiology Group, University Medical Center Hamburg-Eppendorf, University Cancer Center Hamburg (UCCH), Hamburg, Germany
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86
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Bernardi G, Toy JA, Escalona M, Marimuthu MPA, Sahasrabudhe R, Nguyen O, Sacco S, Beraut E, Toffelmier E, Miller C, Shaffer HB. Reference Genome of the Black Surfperch, Embiotoca jacksoni (Embiotocidae, Perciformes), a California Kelp Forest Fish That Lacks a Pelagic Larval Stage. J Hered 2022; 113:657-664. [PMID: 35809222 PMCID: PMC9709976 DOI: 10.1093/jhered/esac034] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 07/07/2022] [Indexed: 11/13/2022] Open
Abstract
Surfperches (Family Embiotocidae) are viviparous temperate reef fishes that brood their young. This life history trait translates into limited dispersal, strong population structure, and an unusually strong potential for local adaptation in a marine fish. As part of the California Conservation Genomics Project (CCGP), we sequenced the genome of the Black Surfperch, Embiotoca jacksoni, to establish a genomic model for understanding phylogeographic patterns of marine organisms in California. These patterns, in turn, may inform the design of marine protected areas using dispersal models based on genomic data. The genome of E. jacksoni is typical of marine fishes at less than 1Gb (genome size = 635 Mb), and our assembly is near-chromosome level (contig N50 = 6.5Mb, scaffold N50 = 15.5 Mb, BUSCO = 98.1%). Within the context of the CCGP, the genome will be used as a reference for future whole genome resequencing projects aimed at enhancing our knowledge of the population structure of the species, and efficacy of Marine Protected Areas across the state.
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Affiliation(s)
- Giacomo Bernardi
- Department of Ecology and Evolutionary Biology, University of California–Santa Cruz, Santa Cruz, CA, USA
| | - Jason A Toy
- Department of Ecology and Evolutionary Biology, University of California–Santa Cruz, Santa Cruz, CA, USA
| | - Merly Escalona
- Department of Biomolecular Engineering, University of California–Santa Cruz, Santa Cruz, CA, USA
| | - Mohan P A Marimuthu
- DNA Technologies and Expression Analysis Core Laboratory, Genome Center, University of California–Davis, Davis, CA, USA
| | - Ruta Sahasrabudhe
- DNA Technologies and Expression Analysis Core Laboratory, Genome Center, University of California–Davis, Davis, CA, USA
| | - Oanh Nguyen
- DNA Technologies and Expression Analysis Core Laboratory, Genome Center, University of California–Davis, Davis, CA, USA
| | - Samuel Sacco
- Department of Ecology and Evolutionary Biology, University of California–Santa Cruz, Santa Cruz, CA, USA
| | - Eric Beraut
- Department of Ecology and Evolutionary Biology, University of California–Santa Cruz, Santa Cruz, CA, USA
| | - Erin Toffelmier
- Department of Ecology and Evolutionary Biology, University of California–Los Angeles, Los Angeles, CA, USA
| | - Courtney Miller
- Department of Ecology and Evolutionary Biology, University of California–Los Angeles, Los Angeles, CA, USA
| | - H Bradley Shaffer
- Department of Ecology and Evolutionary Biology, University of California–Los Angeles, Los Angeles, CA, USA
- La Kretz Center for California Conservation Science, Institute of the Environment and Sustainability, University of California–Los Angeles, Los Angeles, CA, USA
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87
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Leão TF, Wang M, da Silva R, Gurevich A, Bauermeister A, Gomes PWP, Brejnrod A, Glukhov E, Aron AT, Louwen JJR, Kim HW, Reher R, Fiore MF, van der Hooft JJJ, Gerwick L, Gerwick WH, Bandeira N, Dorrestein PC. NPOmix: A machine learning classifier to connect mass spectrometry fragmentation data to biosynthetic gene clusters. PNAS Nexus 2022; 1:pgac257. [PMID: 36712343 PMCID: PMC9802219 DOI: 10.1093/pnasnexus/pgac257] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 10/18/2022] [Accepted: 11/25/2022] [Indexed: 06/02/2023]
Abstract
Microbial specialized metabolites are an important source of and inspiration for many pharmaceuticals, biotechnological products and play key roles in ecological processes. Untargeted metabolomics using liquid chromatography coupled with tandem mass spectrometry is an efficient technique to access metabolites from fractions and even environmental crude extracts. Nevertheless, metabolomics is limited in predicting structures or bioactivities for cryptic metabolites. Efficiently linking the biosynthetic potential inferred from (meta)genomics to the specialized metabolome would accelerate drug discovery programs by allowing metabolomics to make use of genetic predictions. Here, we present a k-nearest neighbor classifier to systematically connect mass spectrometry fragmentation spectra to their corresponding biosynthetic gene clusters (independent of their chemical class). Our new pattern-based genome mining pipeline links biosynthetic genes to metabolites that they encode for, as detected via mass spectrometry from bacterial cultures or environmental microbiomes. Using paired datasets that include validated genes-mass spectral links from the Paired Omics Data Platform, we demonstrate this approach by automatically linking 18 previously known mass spectra (17 for which the biosynthesis gene clusters can be found at the MIBiG database plus palmyramide A) to their corresponding previously experimentally validated biosynthetic genes (e.g., via nuclear magnetic resonance or genetic engineering). We illustrated a computational example of how to use our Natural Products Mixed Omics (NPOmix) tool for siderophore mining that can be reproduced by the users. We conclude that NPOmix minimizes the need for culturing (it worked well on microbiomes) and facilitates specialized metabolite prioritization based on integrative omics mining.
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Affiliation(s)
- Tiago F Leão
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA 92093, USA
- Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba 13400-970, SP, Brazil
| | - Mingxun Wang
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA 92093, USA
- Center for Computational Mass Spectrometry, University of California San Diego, La Jolla, CA 92093, USA
| | - Ricardo da Silva
- NPPNS, Physic and Chemistry Department, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto 14040-900, Brazil
| | - Alexey Gurevich
- Center for Algorithmic Biotechnology, St. Petersburg State University, St Petersburg 199004, Russia
| | - Anelize Bauermeister
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Paulo Wender P Gomes
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Asker Brejnrod
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Evgenia Glukhov
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92093, USA
| | - Allegra T Aron
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA 92093, USA
- Department of Chemistry and Biochemistry, University of Denver, Denver, CO 80210, USA
| | - Joris J R Louwen
- Bioinformatics Group, Wageningen University, 6708 PB Wageningen, The Netherlands
| | - Hyun Woo Kim
- College of Pharmacy and Integrated Research Institute for Drug Development, Dongguk University, Gyeonggi-do 10326, Korea
| | - Raphael Reher
- Institute of Pharmaceutical Biology and Biotechnology, University of Marburg, 35043 Marburg, Germany
| | - Marli F Fiore
- Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba 13400-970, SP, Brazil
| | | | - Lena Gerwick
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92093, USA
| | - William H Gerwick
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA 92093, USA
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92093, USA
| | - Nuno Bandeira
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA 92093, USA
- Center for Computational Mass Spectrometry, University of California San Diego, La Jolla, CA 92093, USA
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88
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Ohhara Y, Yamanaka N. Internal sensory neurons regulate stage-specific growth in Drosophila. Development 2022; 149:dev200440. [PMID: 36227580 PMCID: PMC10496149 DOI: 10.1242/dev.200440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 09/22/2022] [Indexed: 09/15/2023]
Abstract
Animals control their developmental schedule in accordance with internal states and external environments. In Drosophila larvae, it is well established that nutrient status is sensed by different internal organs, which in turn regulate production of insulin-like peptides and thereby control growth. In contrast, the impact of the chemosensory system on larval development remains largely unclear. Here, we performed a genetic screen to identify gustatory receptor (Gr) neurons regulating growth and development, and found that Gr28a-expressing neurons are required for proper progression of larval growth. Gr28a is expressed in a subset of peripheral internal sensory neurons, which directly extend their axons to insulin-producing cells (IPCs) in the central nervous system. Silencing of Gr28a-expressing neurons blocked insulin-like peptide release from IPCs and suppressed larval growth during the mid-larval period. These results indicate that Gr28a-expressing neurons promote larval development by directly regulating growth-promoting endocrine signaling in a stage-specific manner.
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Affiliation(s)
- Yuya Ohhara
- School of Food and Nutritional Sciences, University of Shizuoka, Shizuoka 422-8526, Japan
- Graduate School of Integrated Pharmaceutical and Nutritional Sciences, University of Shizuoka, Shizuoka 422-8526, Japan
| | - Naoki Yamanaka
- Department of Entomology, Institute for Integrative Genome Biology, University of California, Riverside, Riverside, CA 92521, USA
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89
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Koganti PP, Tu LN, Selvaraj V. Functional metabolite reserves and lipid homeostasis revealed by the MA-10 Leydig cell metabolome. PNAS Nexus 2022; 1:pgac215. [PMID: 36714831 PMCID: PMC9802464 DOI: 10.1093/pnasnexus/pgac215] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 09/23/2022] [Indexed: 02/01/2023]
Abstract
In Leydig cells, intrinsic factors that determine cellular steroidogenic efficiency is of functional interest to decipher and monitor pathophysiology in many contexts. Nevertheless, beyond basic regulation of cholesterol storage and mobilization, systems biology interpretation of the metabolite networks in steroidogenic function is deficient. To reconstruct and describe the different molecular systems regulating steroidogenesis, we profiled the metabolites in resting MA-10 Leydig cells. Our results identified 283-annotated components (82 neutral lipids, 154 membrane lipids, and 47 other metabolites). Neutral lipids were represented by an abundance of triacyglycerols (97.1%), and low levels of cholesterol esters (2.0%). Membrane lipids were represented by an abundance of glycerophospholipids (77.8%), followed by sphingolipids (22.2%). Acylcarnitines, nucleosides, amino acids and their derivatives were the other metabolite classes identified. Among nonlipid metabolites, we recognized substantial reserves of aspartic acid, choline, creatine, betaine, glutamine, homoserine, isoleucine, and pantothenic acid none of which have been previously considered as a requirement in steroidogenic function. Individually limiting use of betaine, choline, or pantothenic acid, during luteinizing hormone-induced steroidogenesis in MA-10 cells resulted in substantial decreases to acute steroidogenic capacity, explained by intermediary metabolite imbalances affecting homeostasis. As such, our dataset represents the current level of baseline characterization and unravels the functional resting state of steroidogenic MA-10 Leydig cells. In identifying metabolite stockpiles and causal mechanisms, these results serve to further comprehend the cellular setup and regulation of steroid biosynthesis.
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Affiliation(s)
- Prasanthi P Koganti
- Department of Animal Science, College of Agriculture and Life Sciences, Cornell University, Ithaca, NY 14853, USA
| | - Lan N Tu
- Department of Animal Science, College of Agriculture and Life Sciences, Cornell University, Ithaca, NY 14853, USA
| | - Vimal Selvaraj
- Department of Animal Science, College of Agriculture and Life Sciences, Cornell University, Ithaca, NY 14853, USA
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90
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Ben Simon E, Vallat R, Rossi A, Walker MP. Sleep loss leads to the withdrawal of human helping across individuals, groups, and large-scale societies. PLoS Biol 2022; 20:e3001733. [PMID: 35998121 PMCID: PMC9398015 DOI: 10.1371/journal.pbio.3001733] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 06/29/2022] [Indexed: 11/19/2022] Open
Abstract
Humans help each other. This fundamental feature of homo sapiens has been one of the most powerful forces sculpting the advent of modern civilizations. But what determines whether humans choose to help one another? Across 3 replicating studies, here, we demonstrate that sleep loss represents one previously unrecognized factor dictating whether humans choose to help each other, observed at 3 different scales (within individuals, across individuals, and across societies). First, at an individual level, 1 night of sleep loss triggers the withdrawal of help from one individual to another. Moreover, fMRI findings revealed that the withdrawal of human helping is associated with deactivation of key nodes within the social cognition brain network that facilitates prosociality. Second, at a group level, ecological night-to-night reductions in sleep across several nights predict corresponding next-day reductions in the choice to help others during day-to-day interactions. Third, at a large-scale national level, we demonstrate that 1 h of lost sleep opportunity, inflicted by the transition to Daylight Saving Time, reduces real-world altruistic helping through the act of donation giving, established through the analysis of over 3 million charitable donations. Therefore, inadequate sleep represents a significant influential force determining whether humans choose to help one another, observable across micro- and macroscopic levels of civilized interaction. The implications of this effect may be non-trivial when considering the essentiality of human helping in the maintenance of cooperative, civil society, combined with the reported decline in sufficient sleep in many first-world nations.
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Affiliation(s)
- Eti Ben Simon
- Center for Human Sleep Science, Department of Psychology, University of California, Berkeley, California, United States of America
| | - Raphael Vallat
- Center for Human Sleep Science, Department of Psychology, University of California, Berkeley, California, United States of America
| | - Aubrey Rossi
- Center for Human Sleep Science, Department of Psychology, University of California, Berkeley, California, United States of America
| | - Matthew P. Walker
- Center for Human Sleep Science, Department of Psychology, University of California, Berkeley, California, United States of America
- Helen Wills Neuroscience Institute, University of California, Berkeley, California, United States of America
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91
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Tournebize R, Chu G, Moorjani P. Reconstructing the history of founder events using genome-wide patterns of allele sharing across individuals. PLoS Genet 2022; 18:e1010243. [PMID: 35737729 PMCID: PMC9223333 DOI: 10.1371/journal.pgen.1010243] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2022] [Accepted: 05/08/2022] [Indexed: 11/30/2022] Open
Abstract
Founder events play a critical role in shaping genetic diversity, fitness and disease risk in a population. Yet our understanding of the prevalence and distribution of founder events in humans and other species remains incomplete, as most existing methods require large sample sizes or phased genomes. Thus, we developed ASCEND that measures the correlation in allele sharing between pairs of individuals across the genome to infer the age and strength of founder events. We show that ASCEND can reliably estimate the parameters of founder events under a range of demographic scenarios. We then apply ASCEND to two species with contrasting evolutionary histories: ~460 worldwide human populations and ~40 modern dog breeds. In humans, we find that over half of the analyzed populations have evidence for recent founder events, associated with geographic isolation, modes of sustenance, or cultural practices such as endogamy. Notably, island populations have lower population sizes than continental groups and most hunter-gatherer, nomadic and indigenous groups have evidence of recent founder events. Many present-day groups––including Native Americans, Oceanians and South Asians––have experienced more extreme founder events than Ashkenazi Jews who have high rates of recessive diseases due their known history of founder events. Using ancient genomes, we show that the strength of founder events differs markedly across geographic regions and time––with three major founder events related to the peopling of Americas and a trend in decreasing strength of founder events in Europe following the Neolithic transition and steppe migrations. In dogs, we estimate extreme founder events in most breeds that occurred in the last 25 generations, concordant with the establishment of many dog breeds during the Victorian times. Our analysis highlights a widespread history of founder events in humans and dogs and elucidates some of the demographic and cultural practices related to these events. A founder event occurs when small numbers of ancestral individuals give rise to a large fraction of the population. Founder events reduce genetic variation and increase the risk of recessive diseases. Despite their importance in evolutionary and disease studies, we still only have a limited comprehension of their prevalence and properties in humans and other species, as most existing methods require large sample sizes or phased genomes. Here, we present a flexible method, ASCEND, to infer the timing and the strength of founder events that is suitable for sparse datasets with few samples or limited coverage. ASCEND provides reliable estimates across a wide range of demographic scenarios. By applying it to data from two species (humans and dogs), we document a widespread history of recent founder events in both species and provide insights about the demographic processes related to these events. Our analysis helps to identify groups with strong founder events that should be prioritized for future studies as they offer a unique opportunity for biological discovery and reducing disease burden through mapping of recessive disease-causing genes and pathways, as previously shown in studies of Ashkenazi Jews and Finns.
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Affiliation(s)
- Rémi Tournebize
- Department of Molecular and Cell Biology, University of California, Berkeley, California, United States of America
- Center for Computational Biology, University of California, Berkeley, California, United States of America
- * E-mail: (RT); (PM)
| | - Gillian Chu
- Department of Electrical Engineering and Computer Science, University of California, Berkeley, California, United States of America
| | - Priya Moorjani
- Department of Molecular and Cell Biology, University of California, Berkeley, California, United States of America
- Center for Computational Biology, University of California, Berkeley, California, United States of America
- * E-mail: (RT); (PM)
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92
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Volk RF, Montaño JL, Warrington SE, Hofmann KL, Zaro BW. Proteomic characterization of phagocytic primary human monocyte-derived macrophages. RSC Chem Biol 2022; 3:783-793. [PMID: 35755185 PMCID: PMC9175098 DOI: 10.1039/d2cb00076h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Accepted: 05/12/2022] [Indexed: 11/21/2022] Open
Abstract
Macrophages play a vital role in the innate immune system, identifying and destroying unwanted cells. However, it has been difficult to attain a comprehensive understanding of macrophage protein abundance due to technical limitations. In addition, it remains unclear how changes in proteome composition are linked to phagocytic activity. In this study we developed methods to derive human macrophages and prepare them for mass spectrometry analysis in order to more-deeply understand the proteomic consequences of macrophage stimulation. Interferon gamma (IF-g), an immune stimulating cytokine, was used to induce macrophage activation, increasing phagocytosis of cancer cells by 2-fold. These conditions were used to perform comparative shotgun proteomics between resting macrophages and stimulated macrophages with increased phagocytic activity. Our analysis revealed that macrophages bias their protein production toward biological processes associated with phagocytosis and antigen processing in response to stimulation. We confirmed our findings by antibody-based western blotting experiments, validating both previously reported and novel proteins of interest. In addition to whole protein changes, we evaluated active protein synthesis by treating cells with the methionine surrogate probe homopropargylglycine (HPG). We saw increased rates of HPG incorporation during phagocytosis-inducing stimulation, suggesting protein synthesis rates are altered by stimulation. Together our findings provide the most comprehensive proteomic insight to date into primary human macrophages. We anticipate that this data can be used as a launchpoint to generate new hypotheses about innate immune function.
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Affiliation(s)
- Regan F Volk
- Department of Pharmaceutical Chemistry, Cardiovascular Research Institute, Quantitative Biosciences Institute, and Helen Diller Family Comprehensive Cancer Centre, University of California San Francisco CA USA
| | - José L Montaño
- Department of Pharmaceutical Chemistry, Cardiovascular Research Institute, Quantitative Biosciences Institute, and Helen Diller Family Comprehensive Cancer Centre, University of California San Francisco CA USA
| | - Sara E Warrington
- Department of Pharmaceutical Chemistry, Cardiovascular Research Institute, Quantitative Biosciences Institute, and Helen Diller Family Comprehensive Cancer Centre, University of California San Francisco CA USA
| | - Katherine L Hofmann
- Department of Pharmaceutical Chemistry, Cardiovascular Research Institute, Quantitative Biosciences Institute, and Helen Diller Family Comprehensive Cancer Centre, University of California San Francisco CA USA
| | - Balyn W Zaro
- Department of Pharmaceutical Chemistry, Cardiovascular Research Institute, Quantitative Biosciences Institute, and Helen Diller Family Comprehensive Cancer Centre, University of California San Francisco CA USA
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93
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Suparpprom C, Vilaivan T. Perspectives on conformationally constrained peptide nucleic acid (PNA): insights into the structural design, properties and applications. RSC Chem Biol 2022; 3:648-697. [PMID: 35755191 PMCID: PMC9175113 DOI: 10.1039/d2cb00017b] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 03/17/2022] [Indexed: 11/21/2022] Open
Abstract
Peptide nucleic acid or PNA is a synthetic DNA mimic that contains a sequence of nucleobases attached to a peptide-like backbone derived from N-2-aminoethylglycine. The semi-rigid PNA backbone acts as a scaffold that arranges the nucleobases in a proper orientation and spacing so that they can pair with their complementary bases on another DNA, RNA, or even PNA strand perfectly well through the standard Watson-Crick base-pairing. The electrostatically neutral backbone of PNA contributes to its many unique properties that make PNA an outstanding member of the xeno-nucleic acid family. Not only PNA can recognize its complementary nucleic acid strand with high affinity, but it does so with excellent specificity that surpasses the specificity of natural nucleic acids and their analogs. Nevertheless, there is still room for further improvements of the original PNA in terms of stability and specificity of base-pairing, direction of binding, and selectivity for different types of nucleic acids, among others. This review focuses on attempts towards the rational design of new generation PNAs with superior performance by introducing conformational constraints such as a ring or a chiral substituent in the PNA backbone. A large collection of conformationally rigid PNAs developed during the past three decades are analyzed and compared in terms of molecular design and properties in relation to structural data if available. Applications of selected modified PNA in various areas such as targeting of structured nucleic acid targets, supramolecular scaffold, biosensing and bioimaging, and gene regulation will be highlighted to demonstrate how the conformation constraint can improve the performance of the PNA. Challenges and future of the research in the area of constrained PNA will also be discussed.
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Affiliation(s)
- Chaturong Suparpprom
- Department of Chemistry and Center of Excellence for Innovation in Chemistry, Faculty of Science, Naresuan University, Tah-Poe District, Muang Phitsanulok 65000 Thailand
- Organic Synthesis Research Unit, Department of Chemistry, Faculty of Science, Chulalongkorn University Phayathai Road Pathumwan Bangkok 10330 Thailand
| | - Tirayut Vilaivan
- Department of Chemistry and Center of Excellence for Innovation in Chemistry, Faculty of Science, Naresuan University, Tah-Poe District, Muang Phitsanulok 65000 Thailand
- Organic Synthesis Research Unit, Department of Chemistry, Faculty of Science, Chulalongkorn University Phayathai Road Pathumwan Bangkok 10330 Thailand
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94
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Azimova D, Herrera N, Duvenage L, Voorhies M, Rodriguez RA, English BC, Hoving JC, Rosenberg O, Sil A. Cbp1, a fungal virulence factor under positive selection, forms an effector complex that drives macrophage lysis. PLoS Pathog 2022; 18:e1010417. [PMID: 35731824 PMCID: PMC9255746 DOI: 10.1371/journal.ppat.1010417] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 07/05/2022] [Accepted: 03/07/2022] [Indexed: 12/03/2022] Open
Abstract
Intracellular pathogens secrete effectors to manipulate their host cells. Histoplasma capsulatum (Hc) is a fungal intracellular pathogen of humans that grows in a yeast form in the host. Hc yeasts are phagocytosed by macrophages, where fungal intracellular replication precedes macrophage lysis. The most abundant virulence factor secreted by Hc yeast cells is Calcium Binding Protein 1 (Cbp1), which is absolutely required for macrophage lysis. Here we take an evolutionary, structural, and cell biological approach to understand Cbp1 function. We find that Cbp1 is present only in the genomes of closely related dimorphic fungal species of the Ajellomycetaceae family that lead primarily intracellular lifestyles in their mammalian hosts (Histoplasma, Paracoccidioides, and Emergomyces), but not conserved in the extracellular fungal pathogen Blastomyces dermatitidis. We observe a high rate of fixation of non-synonymous substitutions in the Cbp1 coding sequences, indicating that Cbp1 is under positive selection. We determine the de novo structures of Hc H88 Cbp1 and the Paracoccidioides americana (Pb03) Cbp1, revealing a novel "binocular" fold consisting of a helical dimer arrangement wherein two helices from each monomer contribute to a four-helix bundle. In contrast to Pb03 Cbp1, we show that Emergomyces Cbp1 orthologs are unable to stimulate macrophage lysis when expressed in the Hc cbp1 mutant. Consistent with this result, we find that wild-type Emergomyces africanus yeast are able to grow within primary macrophages but are incapable of lysing them. Finally, we use subcellular fractionation of infected macrophages and indirect immunofluorescence to show that Cbp1 localizes to the macrophage cytosol during Hc infection, making this the first instance of a phagosomal human fungal pathogen directing an effector into the cytosol of the host cell. We additionally show that Cbp1 forms a complex with Yps-3, another known Hc virulence factor that accesses the cytosol. Taken together, these data imply that Cbp1 is a fungal virulence factor under positive selection that localizes to the cytosol to trigger host cell lysis.
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Affiliation(s)
- Dinara Azimova
- University of California San Francisco, San Francisco, California, United States of America
| | - Nadia Herrera
- University of California San Francisco, San Francisco, California, United States of America
| | - Lucian Duvenage
- AFRICA Medical Mycology Research Unit, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Mark Voorhies
- University of California San Francisco, San Francisco, California, United States of America
| | - Rosa A. Rodriguez
- University of California San Francisco, San Francisco, California, United States of America
| | - Bevin C. English
- University of California Davis, Davis, California, United States of America
| | - Jennifer C. Hoving
- AFRICA Medical Mycology Research Unit, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Oren Rosenberg
- University of California San Francisco, San Francisco, California, United States of America
| | - Anita Sil
- University of California San Francisco, San Francisco, California, United States of America
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95
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Lofgren LA, Lorch JM, Cramer RA, Blehert DS, Berlowski-Zier BM, Winzeler ME, Gutierrez-Perez C, Kordana NE, Stajich JE. Avian-associated Aspergillus fumigatus displays broad phylogenetic distribution, no evidence for host specificity, and multiple genotypes within epizootic events. G3 (Bethesda) 2022; 12:jkac075. [PMID: 35377435 PMCID: PMC9073692 DOI: 10.1093/g3journal/jkac075] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Accepted: 03/27/2022] [Indexed: 06/14/2023]
Abstract
Birds are highly susceptible to aspergillosis, which can manifest as a primary infection in both domestic and wild birds. Aspergillosis in wild birds causes mortalities ranging in scale from single animals to large-scale epizootic events. However, pathogenicity factors associated with aspergillosis in wild birds have not been examined. Specifically, it is unknown whether wild bird-infecting strains are host-adapted (i.e. phylogenetically related). Similarly, it is unknown whether epizootics are driven by contact with clonal strains that possess unique pathogenic or virulence properties, or by distinct and equally pathogenic strains. Here, we use a diverse collection of Aspergillus fumigatus isolates taken from aspergillosis-associated avian carcasses, representing 24 bird species from a wide geographic range, and representing individual bird mortalities as well as epizootic events. These isolates were sequenced and analyzed along with 130 phylogenetically diverse human clinical isolates to investigate the genetic diversity and phylogenetic placement of avian-associated A. fumigatus, the geographic and host distribution of avian isolates, evidence for clonal outbreaks among wild birds, and the frequency of azole resistance in avian isolates. We found that avian isolates were phylogenetically diverse, with no clear distinction from human clinical isolates, and no sign of host or geographic specificity. Avian isolates from the same epizootic events were diverse and phylogenetically distant, suggesting that avian aspergillosis is not contagious among wild birds and that outbreaks are likely driven by environmental spore loads or host comorbidities. Finally, all avian isolates were susceptible to Voriconazole and none contained the canonical azole resistance gene variants.
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Affiliation(s)
- Lotus A Lofgren
- Department of Microbiology and Plant Pathology, University of California Riverside, Riverside, CA 92521, USA
- Institute for Integrative Genome Biology, University of California Riverside, Riverside, CA 92521, USA
- Department of Biology, Duke University, Durham, NC 27708, USA
| | - Jeffrey M Lorch
- U.S. Geological Survey—National Wildlife Health Center, Madison, WI 53711, USA
| | - Robert A Cramer
- Department of Microbiology and Immunology, Geisel School of Medicine, Dartmouth College, Hanover, NH 03755, USA
| | - David S Blehert
- U.S. Geological Survey—National Wildlife Health Center, Madison, WI 53711, USA
| | | | - Megan E Winzeler
- U.S. Geological Survey—National Wildlife Health Center, Madison, WI 53711, USA
| | - Cecilia Gutierrez-Perez
- Department of Microbiology and Immunology, Geisel School of Medicine, Dartmouth College, Hanover, NH 03755, USA
| | - Nicole E Kordana
- Department of Microbiology and Immunology, Geisel School of Medicine, Dartmouth College, Hanover, NH 03755, USA
| | - Jason E Stajich
- Department of Microbiology and Plant Pathology, University of California Riverside, Riverside, CA 92521, USA
- Institute for Integrative Genome Biology, University of California Riverside, Riverside, CA 92521, USA
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96
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Tee BL, Watson Pereira C, Lukic S, Bajorek LP, Allen IE, Miller ZA, Casaletto KB, Miller BL, Gorno-Tempini ML. Neuroanatomical correlations of visuospatial processing in primary progressive aphasia. Brain Commun 2022; 4:fcac060. [PMID: 35386217 PMCID: PMC8977647 DOI: 10.1093/braincomms/fcac060] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 12/10/2021] [Accepted: 03/10/2022] [Indexed: 11/14/2022] Open
Abstract
Clinical phenotyping of primary progressive aphasia has largely focused on speech and language presentations, leaving other cognitive domains under-examined. This study investigated the diagnostic utility of visuospatial profiles and examined their neural basis among the three main primary progressive aphasia variants. We studied the neuropsychological performances of 118 primary progressive aphasia participants and 30 cognitively normal controls, across 11 measures of visuospatial cognition, and investigated their neural correlates via voxel-based morphometry analysis using visuospatial composite scores derived from principal component analysis. The principal component analysis identified three main factors: visuospatial-executive, visuospatial-memory and visuomotor components. Logopenic variant primary progressive aphasia performed significantly worst across all components; nonfluent/agrammatic variant primary progressive aphasia showed deficits in the visuospatial-executive and visuomotor components compared with controls; and the semantic variant primary progressive aphasia scored significantly lower than nonfluent/agrammatic variant primary progressive aphasia and control in the visuospatial-memory component. Grey matter volumes over the right parieto-occipital cortices correlated with visuospatial-executive performance; volumetric changes in the right anterior parahippocampal gyrus and amygdala were associated with visuospatial-memory function, and visuomotor composite scores correlated significantly with the grey matter volume at the right precentral gyrus. Discriminant function analysis identified three visuospatial measures: Visual Object and Space Perception and Benson figure copy and recall test, which classified 79.7% (94/118) of primary progressive aphasia into their specific variant. This study shows that each primary progressive aphasia variant also carries a distinctive visuospatial cognitive profile that corresponds with grey matter volumetric changes and in turn can be largely represented by their performance on the visuomotor, visuospatial-memory and executive functions.
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Affiliation(s)
- Boon Lead Tee
- Memory and Aging Center, University of California at San Francisco, San Francisco, CA, USA
- Department of Neurology, Dyslexia Center, University of California, San Francisco, CA, USA
- Global Brain Health Institute, University of California, San Francisco, CA, USA
- Department of Neurology, Buddhist Tzu Chi General Hospital, Hualien, Taiwan
- Tzu Chi University, No. 701號, Section 3, Zhongyang Rd, Hualien City, Hualien County, Taiwan 970
| | - Christa Watson Pereira
- Memory and Aging Center, University of California at San Francisco, San Francisco, CA, USA
- Department of Neurology, Dyslexia Center, University of California, San Francisco, CA, USA
| | - Sladjana Lukic
- Memory and Aging Center, University of California at San Francisco, San Francisco, CA, USA
- Department of Neurology, Dyslexia Center, University of California, San Francisco, CA, USA
| | - Lynn P. Bajorek
- Memory and Aging Center, University of California at San Francisco, San Francisco, CA, USA
- Department of Neurology, Dyslexia Center, University of California, San Francisco, CA, USA
| | - Isabel Elaine Allen
- Department of Epidemiology and Biostatistics, University of California, San Francisco, CA, USA
| | - Zachary A. Miller
- Memory and Aging Center, University of California at San Francisco, San Francisco, CA, USA
- Department of Neurology, Dyslexia Center, University of California, San Francisco, CA, USA
| | - Kaitlin B. Casaletto
- Memory and Aging Center, University of California at San Francisco, San Francisco, CA, USA
| | - Bruce L. Miller
- Memory and Aging Center, University of California at San Francisco, San Francisco, CA, USA
| | - Maria Luisa Gorno-Tempini
- Memory and Aging Center, University of California at San Francisco, San Francisco, CA, USA
- Department of Neurology, Dyslexia Center, University of California, San Francisco, CA, USA
- Global Brain Health Institute, University of California, San Francisco, CA, USA
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97
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Trott JF, Schennink A, Horigan KC, Lemay DG, Cohen JR, Famula TR, Dragon JA, Hovey RC. Unique Transcriptomic Changes Underlie Hormonal Interactions During Mammary Histomorphogenesis in Female Pigs. Endocrinology 2022; 163:bqab256. [PMID: 34918063 PMCID: PMC10409904 DOI: 10.1210/endocr/bqab256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Indexed: 11/19/2022]
Abstract
Successful lactation and the risk for developing breast cancer depend on growth and differentiation of the mammary gland (MG) epithelium that is regulated by ovarian steroids (17β-estradiol [E] and progesterone [P]) and pituitary-derived prolactin (PRL). Given that the MG of pigs share histomorphogenic features present in the normal human breast, we sought to define the transcriptional responses within the MG of pigs following exposure to all combinations of these hormones. Hormone-ablated female pigs were administered combinations of E, medroxyprogesterone 17-acetate (source of P), and either haloperidol (to induce PRL) or 2-bromo-α-ergocryptine. We subsequently monitored phenotypic changes in the MG including mitosis, receptors for E and P (ESR1 and PGR), level of phosphorylated STAT5 (pSTAT5), and the frequency of terminal ductal lobular unit (TDLU) subtypes; these changes were then associated with all transcriptomic changes. Estrogen altered the expression of approximately 20% of all genes that were mostly associated with mitosis, whereas PRL stimulated elements of fatty acid metabolism and an inflammatory response. Several outcomes, including increased pSTAT5, highlighted the ability of E to enhance PRL action. Regression of transcriptomic changes against several MG phenotypes revealed 1669 genes correlated with proliferation, among which 29 were E inducible. Additional gene expression signatures were associated with TDLU formation and the frequency of ESR1 or PGR. These data provide a link between the hormone-regulated genome and phenome of the MG in a species having a complex histoarchitecture like that in the human breast, and highlight an underexplored synergy between the actions of E and PRL during MG development.
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Affiliation(s)
- Josephine F Trott
- Department of Animal Science, University of California, Davis, Davis, California 95616, USA
| | - Anke Schennink
- Department of Animal Science, University of California, Davis, Davis, California 95616, USA
| | - Katherine C Horigan
- Department of Animal Science, University of Vermont, Burlington, Vermont 05405, USA
| | - Danielle G Lemay
- US Department of Agriculture ARS Western Human Nutrition Research Center, Davis, California 95616, USA
| | - Julia R Cohen
- Department of Animal Science, University of California, Davis, Davis, California 95616, USA
| | - Thomas R Famula
- Department of Animal Science, University of California, Davis, Davis, California 95616, USA
| | - Julie A Dragon
- Vermont Integrative Genomics Resource, University of Vermont, Burlington, Vermont 05405, USA
| | - Russell C Hovey
- Department of Animal Science, University of California, Davis, Davis, California 95616, USA
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98
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Kelesidis T, Zhang Y, Tran E, Sosa G, Middlekauff HR. Instigators of COVID-19 in Immune Cells Are Increased in Tobacco Cigarette Smokers and Electronic Cigarette Vapers Compared With Nonsmokers. Nicotine Tob Res 2022; 24:413-415. [PMID: 34410424 PMCID: PMC8513409 DOI: 10.1093/ntr/ntab168] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 08/17/2021] [Indexed: 12/25/2022]
Abstract
INTRODUCTION The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), the virus responsible for the COVID-19 pandemic, gains entry into the host cell when its Spike protein is cleaved by host proteases TMPRSS2 and furin, thereby markedly increasing viral affinity for its receptor, angiotensin-converting enzyme-2 (ACE2). In rodent and diseased human lungs, tobacco cigarette (TCIG) smoke increases ACE2, but the effect of electronic cigarette vaping (ECIG) is unknown. It is unknown whether nicotine (in both TCIGs and ECIGs) or non-nicotine constituents unique to TCIG smoke increase expression of key proteins in COVID-19 pathogenesis. METHODS Immune (CD45+) cells collected before the pandemic in otherwise healthy young people, including TCIG smokers (n = 9), ECIG vapers (n = 12), or nonsmokers (NS) (n = 12), were studied. Using flow cytometry, expression of key proteins in COVID-19 pathogenesis were compared among these groups. RESULTS TCIG smokers and ECIG vapers had similar smoking or vaping burdens as indicated by similar plasma cotinine levels. TCIG smokers compared with NS had a significantly increased percentage of cells that were positive for ACE2 (10-fold, p < .001), TMPRSS2 (5-fold, p < .001), and ADAM17 (2.5-fold, p < .001). Additionally, the mean fluorescence intensity (MFI) consistently showed greater mean ACE2 (2.2-fold, p < .001), TMPRSS2 (1.5-fold, p < .001), furin (1.1-fold, p < .05), and ADAM17 (2-fold, p < .001) in TCIG smokers compared with NS. In ECIG vapers, furin MFI was increased (1.15-fold, p < .05) and TMPRSS2 MFI tended to be increased (1.1-fold, p = .077) compared with NS. CONCLUSIONS The finding that key instigators of COVID-19 infection are lower in ECIG vapers compared with TCIG smokers is intriguing and warrants additional investigation to determine if switching to ECIGs is an effective harm reduction strategy. However, the trend toward increased proteases in ECIG vapers remains concerning. IMPLICATIONS (1) This is the first human study to report a marked increase in proteins critical for COVID-19 infection, including ACE2, TMPRSS2, and ADAM17, in immune cells from healthy tobacco cigarette smokers without lung disease compared with e-cigarette vapers and nonsmokers. (2) These findings warrant additional investigation to determine whether switching to electronic cigarettes may be an effective harm reduction strategy in smokers addicted to nicotine who are unable or unwilling to quit. (3) The increase in proteases in electronic cigarette vapers remains concerning.
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Affiliation(s)
- Theodoros Kelesidis
- Department of Medicine, Division of Infectious Disease, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Yuyan Zhang
- Department of Medicine, Division of Infectious Disease, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Elizabeth Tran
- Department of Medicine, Division of Cardiology, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Grace Sosa
- Department of Medicine, Division of Infectious Disease, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Holly R Middlekauff
- Department of Medicine, Division of Cardiology, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
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99
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Groen SC, Joly-Lopez Z, Platts AE, Natividad M, Fresquez Z, Mauck WM, Quintana MR, Cabral CLU, Torres RO, Satija R, Purugganan MD, Henry A. Evolutionary systems biology reveals patterns of rice adaptation to drought-prone agro-ecosystems. Plant Cell 2022; 34:759-783. [PMID: 34791424 PMCID: PMC8824591 DOI: 10.1093/plcell/koab275] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 11/02/2021] [Indexed: 05/24/2023]
Abstract
Rice (Oryza sativa) was domesticated around 10,000 years ago and has developed into a staple for half of humanity. The crop evolved and is currently grown in stably wet and intermittently dry agro-ecosystems, but patterns of adaptation to differences in water availability remain poorly understood. While previous field studies have evaluated plant developmental adaptations to water deficit, adaptive variation in functional and hydraulic components, particularly in relation to gene expression, has received less attention. Here, we take an evolutionary systems biology approach to characterize adaptive drought resistance traits across roots and shoots. We find that rice harbors heritable variation in molecular, physiological, and morphological traits that is linked to higher fitness under drought. We identify modules of co-expressed genes that are associated with adaptive drought avoidance and tolerance mechanisms. These expression modules showed evidence of polygenic adaptation in rice subgroups harboring accessions that evolved in drought-prone agro-ecosystems. Fitness-linked expression patterns allowed us to identify the drought-adaptive nature of optimizing photosynthesis and interactions with arbuscular mycorrhizal fungi. Taken together, our study provides an unprecedented, integrative view of rice adaptation to water-limited field conditions.
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Affiliation(s)
- Simon C Groen
- Author for correspondence: (S.C.G.), (M.D.P.), (A.H.)
| | | | | | - Mignon Natividad
- International Rice Research Institute, Los Baños, Laguna, Philippines, USA
| | - Zoë Fresquez
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, USA
| | | | | | - Carlo Leo U Cabral
- International Rice Research Institute, Los Baños, Laguna, Philippines, USA
| | - Rolando O Torres
- International Rice Research Institute, Los Baños, Laguna, Philippines, USA
| | - Rahul Satija
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, USA
- New York Genome Center, New York, USA
| | | | - Amelia Henry
- Author for correspondence: (S.C.G.), (M.D.P.), (A.H.)
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100
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Nez Henderson P, Lee JP, Soto C, O′Leary R, Rutan E, D′Silva J, Waa A, Henderson ZP, Nez SS, Maddox R. Decolonization of Tobacco in Indigenous Communities of Turtle Island (North America). Nicotine Tob Res 2022; 24:289-291. [PMID: 34516637 PMCID: PMC8807169 DOI: 10.1093/ntr/ntab180] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 09/12/2021] [Indexed: 11/13/2022]
Affiliation(s)
- Patricia Nez Henderson
- Navajo Nation (Diné), Rapid City, SD, USA
- Black Hills Center for American Indian Health, Rapid City, SD, USA
| | - Juliet P Lee
- Pacific Institute for Research and Evaluation-California, Prevention Research Center, Berkeley, CA, USA
| | - Claradina Soto
- Navajo Nation (Diné)/ Jemez Pueblo, Los Angeles, CA, USA
- University of Southern California, Keck School of Medicine, Los Angeles, CA, USA
| | - Rae O′Leary
- Turtle Mountain Band of Chippewa, Timber Lake, SD, USA
- Missouri Breaks Research Industries, Inc., Timber Lake, SD, USA
| | - Emma Rutan
- Black Hills Center for American Indian Health, Rapid City, SD, USA
| | | | - Andrew Waa
- Ngāti Hine/Ngāpuhi, Wellington, New Zealand
- Eru Pomare Māori Health Research Unit, University of Otago, Wellington, New Zealand
| | - Zahlanii P Henderson
- Navajo Nation (Diné), Rapid City, SD, USA
- Black Hills Center for American Indian Health, Rapid City, SD, USA
| | - Shanoa S Nez
- Navajo Nation (Diné), Rapid City, SD, USA
- Black Hills Center for American Indian Health, Rapid City, SD, USA
| | - Raglan Maddox
- Modewa Clan, Papua New Guinea, Canberra, Australian Capital Territory, Australia
- Aboriginal and Torres Strait Islander Health, National Centre for Epidemiology and Population Health, Australian Nation University, Canberra, Australian Capital Territory, Australia
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