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Mpamhanga CD, Kounatidis I. The utility of Drosophila melanogaster as a fungal infection model. Front Immunol 2024; 15:1349027. [PMID: 38550600 PMCID: PMC10973011 DOI: 10.3389/fimmu.2024.1349027] [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] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 02/27/2024] [Indexed: 04/02/2024] Open
Abstract
Invasive fungal diseases have profound effects upon human health and are on increase globally. The World Health Organization (WHO) in 2022 published the fungal priority list calling for improved public health interventions and advance research. Drosophila melanogaster presents an excellent model system to dissect host-pathogen interactions and has been proved valuable to study immunopathogenesis of fungal diseases. In this review we highlight the recent advances in fungal-Drosophila interplay with an emphasis on the recently published WHO's fungal priority list and we focus on available tools and technologies.
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Affiliation(s)
- Chengetai D Mpamhanga
- School of Life Health and Chemical Sciences, The Open University, Milton Keynes, United Kingdom
| | - Ilias Kounatidis
- School of Life Health and Chemical Sciences, The Open University, Milton Keynes, United Kingdom
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2
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Bhola PT, Mishra R, Posey JE, Hamilton LE, Graham GE, Punetha J, Lupski JR, Boycott KM, D'Amours D, Kernohan KD. Phenotypic heterogeneity associated with KIF21A: Two new cases and review of the literature. Am J Med Genet A 2024; 194:e63455. [PMID: 37921537 DOI: 10.1002/ajmg.a.63455] [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: 07/17/2023] [Revised: 10/06/2023] [Accepted: 10/13/2023] [Indexed: 11/04/2023]
Abstract
Our understanding of genetic and phenotypic heterogeneity associated with the clinical spectrum of rare diseases continues to expand. Thorough phenotypic descriptions and model organism functional studies are valuable tools in dissecting the biology of the disease process. Kinesin genes are well known to be associated with specific disease phenotypes and a subset of kinesin genes, including KIF21A, have been associated with more than one disease. Here we report two patients with KIF21A variants identified by exome sequencing; one with biallelic variants, supporting a novel KIF21A related syndrome with recessive inheritance and the second report of this condition, and another with a heterozygous de novo variant allele representing a phenotypic expansion of the condition described to date. We provide detailed phenotypic information on both families, including a novel neuropathology finding of neuroaxonal dystrophy associated with biallelic variants in KIF21A. Additionally, we studied the dominant variant in Saccharomyces cerevisiae to assess variant pathogenicity and found that this variant appears to impair protein function. KIF21A associated disease has mounting evidence for phenotypic heterogeneity; further patients and study of an allelic series are required to define the phenotypic spectrum and further explore the molecular etiology for each of these conditions.
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Affiliation(s)
- Priya T Bhola
- Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, Canada
| | - Radha Mishra
- Department of Cellular and Molecular Medicine, Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, Canada
| | - Jennifer E Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Leslie E Hamilton
- Department of Pathology and Laboratory Medicine, Children's Hospital of Eastern Ontario and University of Ottawa, Ottawa, Canada
| | - Gail E Graham
- Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, Canada
| | - Jaya Punetha
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA
- Texas Children's Hospital, Houston, Texas, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
| | - Kym M Boycott
- Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, Canada
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Canada
| | - Damien D'Amours
- Department of Cellular and Molecular Medicine, Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, Canada
| | - Kristin D Kernohan
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Canada
- Newborn Screening Ontario (NSO), Ottawa, Canada
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3
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Schröter L, Jentsch L, Maglioni S, Muñoz-Juan A, Wahle T, Limke A, von Mikecz A, Laromaine A, Ventura N. A Multisystemic Approach Revealed Aminated Polystyrene Nanoparticles-Induced Neurotoxicity. Small 2024; 20:e2302907. [PMID: 37899301 DOI: 10.1002/smll.202302907] [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: 04/06/2023] [Revised: 10/12/2023] [Indexed: 10/31/2023]
Abstract
Exposure to plastic nanoparticles has dramatically increased in the last 50 years, and there is evidence that plastic nanoparticles can be absorbed by organisms and cross the blood-brain-barrier (BBB). However, their toxic effects, especially on the nervous system, have not yet been extensively investigated, and most of the knowledge is based on studies using different conditions and systems, thus hard to compare. In this work, physicochemical properties of non-modified polystyrene (PS) and amine-functionalized PS (PS-NH2 ) nanoparticles are initially characterized. Advantage of a multisystemic approach is then taken to compare plastic nanoparticles effects in vitro, through cytotoxic readouts in mammalian cell culture, and in vivo, through behavioral readouts in the nematode Caenorhabditis elegans (C. elegans), a powerful 3R-complying model organism for toxicology studies. In vitro experiments in neuroblastoma cells indicate a specific cytotoxic effect of PS-NH2 particles, including a decreased neuronal differentiation and an increased Amyloid β (Aβ) secretion, a sensitive readout correlating with Alzheimer's disease pathology. In parallel, only in vivo treatments with PS-NH2 particles affect C. elegans development, decrease lifespan, and reveal higher sensitivity of animals expressing human Aβ compared to wild-type animals. In summary, the multisystemic approach discloses a neurotoxic effect induced by aminated polystyrene nanoparticles.
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Affiliation(s)
- Laura Schröter
- IUF-Leibniz Research Institute for Environmental Medicine, 40225, Duesseldorf, Germany
- Institute for Clinical Chemistry and Laboratory Diagnostic, Medical Faculty, Heinrich Heine University, 40225, Duesseldorf, Germany
| | - Lena Jentsch
- IUF-Leibniz Research Institute for Environmental Medicine, 40225, Duesseldorf, Germany
- Institute for Clinical Chemistry and Laboratory Diagnostic, Medical Faculty, Heinrich Heine University, 40225, Duesseldorf, Germany
| | - Silvia Maglioni
- IUF-Leibniz Research Institute for Environmental Medicine, 40225, Duesseldorf, Germany
- Institute for Clinical Chemistry and Laboratory Diagnostic, Medical Faculty, Heinrich Heine University, 40225, Duesseldorf, Germany
| | - Amanda Muñoz-Juan
- Institut de Ciència de Materials de Barcelona, ICMAB-CSIC, Campus UAB, Bellaterra, Barcelona, 08193, Spain
| | - Tina Wahle
- IUF-Leibniz Research Institute for Environmental Medicine, 40225, Duesseldorf, Germany
| | - Annette Limke
- IUF-Leibniz Research Institute for Environmental Medicine, 40225, Duesseldorf, Germany
| | - Anna von Mikecz
- IUF-Leibniz Research Institute for Environmental Medicine, 40225, Duesseldorf, Germany
| | - Anna Laromaine
- Institut de Ciència de Materials de Barcelona, ICMAB-CSIC, Campus UAB, Bellaterra, Barcelona, 08193, Spain
| | - Natascia Ventura
- IUF-Leibniz Research Institute for Environmental Medicine, 40225, Duesseldorf, Germany
- Institute for Clinical Chemistry and Laboratory Diagnostic, Medical Faculty, Heinrich Heine University, 40225, Duesseldorf, Germany
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4
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Hammer M, Krzyzaniak C, Bahramnejad E, Smelser K, Hack J, Watkins J, Ronaldson P. Sex differences in physiological response to increased neuronal excitability in a knockin mouse model of pediatric epilepsy. Clin Sci (Lond) 2024; 138:205-223. [PMID: 38348743 PMCID: PMC10881277 DOI: 10.1042/cs20231572] [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: 11/29/2023] [Revised: 02/01/2024] [Accepted: 02/09/2024] [Indexed: 02/22/2024]
Abstract
BACKGROUND Epilepsy is a common neurological disease; however, few if any of the currently marketed antiseizure medications prevent or cure epilepsy. Discovery of pathological processes in the early stages of epileptogenesis has been challenging given the common use of preclinical models that induce seizures in physiologically normal animals. Moreover, despite known sex dimorphism in neurological diseases, females are rarely included in preclinical epilepsy models. METHODS We characterized sex differences in mice carrying a pathogenic knockin variant (p.N1768D) in the Scn8a gene that causes spontaneous tonic-clonic seizures (TCs) at ∼3 months of age and found that heterozygous females are more resilient than males in mortality and morbidity. To investigate the cellular mechanisms that underlie female resilience, we utilized blood-brain barrier (BBB) and hippocampal transcriptomic analyses in heterozygous mice before seizure onset (pre-TC) and in mice that experienced ∼20 TCs (post-TC). RESULTS In the pre-TC latent phase, both sexes exhibited leaky BBB; however, patterns of gene expression were sexually dimorphic. Females exhibited enhanced oxidative phosphorylation and protein biogenesis, while males activated gliosis and CREB signaling. After seizure onset (chronic phase), females exhibited a metabolic switch to lipid metabolism, while males exhibited increased gliosis and BBB dysfunction and a strong activation of neuroinflammatory pathways. CONCLUSION The results underscore the central role of oxidative stress and BBB permeability in the early stages of epileptogenesis, as well as sex dimorphism in response to increasing neuronal hyperexcitability. Our results also highlight the need to include both sexes in preclinical studies to effectively translate results of drug efficacy studies.
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Affiliation(s)
- Michael F. Hammer
- BIO5 Institute, University of Arizona, Tucson, Arizona, U.S.A
- Department of Neurology, University of Arizona, Tucson, Arizona, U.S.A
| | | | - Erfan Bahramnejad
- BIO5 Institute, University of Arizona, Tucson, Arizona, U.S.A
- Department of Pharmacology, University of Arizona, Tucson, Arizona, U.S.A
| | | | - Joshua B. Hack
- BIO5 Institute, University of Arizona, Tucson, Arizona, U.S.A
| | - Joseph C. Watkins
- Department of Mathematics, University of Arizona, Tucson, Arizona, U.S.A
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Kato TA. Editorial: Emerging talents in toxicology. Front Toxicol 2024; 6:1369297. [PMID: 38362109 PMCID: PMC10867310 DOI: 10.3389/ftox.2024.1369297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Accepted: 01/24/2024] [Indexed: 02/17/2024] Open
Affiliation(s)
- Takamitsu A. Kato
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO, United States
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Pinsino A, Sevilla N. Editorial: Women in comparative immunology. Front Immunol 2024; 14:1358322. [PMID: 38264666 PMCID: PMC10804235 DOI: 10.3389/fimmu.2023.1358322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Accepted: 12/26/2023] [Indexed: 01/25/2024] Open
Affiliation(s)
- Annalisa Pinsino
- Institute of Translational Pharmacology (IFT), National Research Council (CNR), Palermo, Italy
| | - Noemí Sevilla
- Centro de Investigación en Sanidad Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Consejo Superior de Investigaciones Científicas (CISA-INIA-CSIC), Madrid, Spain
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Santos-Silva T, dos Santos Fabris D, de Oliveira CL, Guimarães FS, Gomes FV. Prefrontal and Hippocampal Parvalbumin Interneurons in Animal Models for Schizophrenia: A Systematic Review and Meta-analysis. Schizophr Bull 2024; 50:210-223. [PMID: 37584417 PMCID: PMC10754178 DOI: 10.1093/schbul/sbad123] [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] [Indexed: 08/17/2023]
Abstract
BACKGROUND Consistent with postmortem findings in patients, most animal models for schizophrenia (SCZ) present abnormal levels of parvalbumin (PV), a marker of fast-spiking GABAergic interneurons, in the prefrontal cortex (PFC) and hippocampus (HIP). However, there are discrepancies in the literature. PV reductions lead to a functional loss of PV interneurons, which is proposed to underly SCZ symptoms. Given its complex etiology, different categories of animal models have been developed to study SCZ, which may distinctly impact PV levels in rodent brain areas. STUDY DESIGN We performed a quantitative meta-analysis on PV-positive cell number/density and expression levels in the PFC and HIP of animal models for SCZ based on pharmacological, neurodevelopmental, and genetic manipulations. RESULTS Our results confirmed that PV levels are significantly reduced in the PFC and HIP regardless of the animal model. By categorizing into subgroups, we found that all pharmacological models based on NMDA receptor antagonism decreased PV-positive cell number/density or PV expression levels in both brain areas examined. In neurodevelopmental models, abnormal PV levels were confirmed in both brain areas in maternal immune activation models and HIP of the methylazoxymethanol acetate model. In genetic models, negative effects were found in neuregulin 1 and ERBB4 mutant mice in both brain regions and the PFC of dysbindin mutant mice. Regarding sex differences, male rodents exhibited PV reductions in both brain regions only in pharmacological models, while few studies have been conducted in females. CONCLUSION Overall, our findings support deficits in prefrontal and hippocampal PV interneurons in animal models for SCZ.
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Affiliation(s)
- Thamyris Santos-Silva
- Department of Pharmacology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
| | - Débora dos Santos Fabris
- Department of Neuroscience and Behavioral Sciences, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
| | - Cilene Lino de Oliveira
- Department of Physiological Sciences, Center of Biological Sciences, University of Santa Catarina, Florianópolis,Brazil
| | - Francisco S Guimarães
- Department of Pharmacology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
| | - Felipe V Gomes
- Department of Pharmacology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
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Bobrovskikh AV, Zubairova US, Doroshkov AV. Fishing Innate Immune System Properties through the Transcriptomic Single-Cell Data of Teleostei. Biology (Basel) 2023; 12:1516. [PMID: 38132342 PMCID: PMC10740722 DOI: 10.3390/biology12121516] [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: 10/13/2023] [Revised: 11/20/2023] [Accepted: 11/22/2023] [Indexed: 12/23/2023]
Abstract
The innate immune system is the first line of defense in multicellular organisms. Danio rerio is widely considered a promising model for IIS-related research, with the most amount of scRNAseq data available among Teleostei. We summarized the scRNAseq and spatial transcriptomics experiments related to the IIS for zebrafish and other Teleostei from the GEO NCBI and the Single-Cell Expression Atlas. We found a considerable number of scRNAseq experiments at different stages of zebrafish development in organs such as the kidney, liver, stomach, heart, and brain. These datasets could be further used to conduct large-scale meta-analyses and to compare the IIS of zebrafish with the mammalian one. However, only a small number of scRNAseq datasets are available for other fish (turbot, salmon, cavefish, and dark sleeper). Since fish biology is very diverse, it would be a major mistake to use zebrafish alone in fish immunology studies. In particular, there is a special need for new scRNAseq experiments involving nonmodel Teleostei, e.g., long-lived species, cancer-resistant fish, and various fish ecotypes.
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Affiliation(s)
- Aleksandr V. Bobrovskikh
- Department of Physics, Novosibirsk State University, 630090 Novosibirsk, Russia
- The Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia; (U.S.Z.); (A.V.D.)
| | - Ulyana S. Zubairova
- The Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia; (U.S.Z.); (A.V.D.)
- Department of Information Technologies, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Alexey V. Doroshkov
- The Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia; (U.S.Z.); (A.V.D.)
- Department of Genomics and Bioinformatics, Institute of Fundamental Biology and Biotechnology, Siberian Federal University, 660036 Krasnoyarsk, Russia
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Barwell T, Seroude L. Polyglutamine disease in peripheral tissues. Hum Mol Genet 2023; 32:3303-3311. [PMID: 37642359 DOI: 10.1093/hmg/ddad138] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 08/21/2023] [Accepted: 08/24/2023] [Indexed: 08/31/2023] Open
Abstract
This year is a milestone anniversary of the discovery that Huntington's disease is caused by the presence of expanded polyglutamine repeats in the huntingtin gene leading to the formation of huntingtin aggregates. 30 years have elapsed and there is still no cure and the only FDA-approved treatment to alleviate the debilitating locomotor impairments presents several adverse effects. It has long been neglected that the huntingtin gene is almost ubiquitously expressed in many tissues outside of the nervous system. Growing evidence indicates that these peripheral tissues can contribute to the symptoms of the disease. New findings in Drosophila have shown that the selective expression of mutant huntingtin in muscle or fat is sufficient to cause detrimental effects in the absence of any neurodegeneration. In addition, it was discovered that a completely different tissue distribution of Htt aggregates in Drosophila muscles is responsible for a drastic aggravation of the detrimental effects. This review examines the peripheral tissues that express huntingtin with an added focus on the nature and distribution of the aggregates, if any.
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Affiliation(s)
- Taylor Barwell
- Department of Biology, Queen's University, 116 Barrie St, Kingston, ON K7L 3N6, Canada
| | - Laurent Seroude
- Department of Biology, Queen's University, 116 Barrie St, Kingston, ON K7L 3N6, Canada
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10
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Yu Y, Wang S, Wang Z, Gao R, Lee J. Arabidopsis thaliana: a powerful model organism to explore histone modifications and their upstream regulations. Epigenetics 2023; 18:2211362. [PMID: 37196184 DOI: 10.1080/15592294.2023.2211362] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 04/07/2023] [Accepted: 04/28/2023] [Indexed: 05/19/2023] Open
Abstract
Histones are subjected to extensive covalent modifications that affect inter-nucleosomal interactions as well as alter chromatin structure and DNA accessibility. Through switching the corresponding histone modifications, the level of transcription and diverse downstream biological processes can be regulated. Although animal systems are widely used in studying histone modifications, the signalling processes that occur outside the nucleus prior to histone modifications have not been well understood due to the limitations including non viable mutants, partial lethality, and infertility of survivors. Here, we review the benefits of using Arabidopsis thaliana as the model organism to study histone modifications and their upstream regulations. Similarities among histones and key histone modifiers such as the Polycomb group (PcG) and Trithorax group (TrxG) in Drosophila, Human, and Arabidopsis are examined. Furthermore, prolonged cold-induced vernalization system has been well-studied and revealed the relationship between the controllable environment input (duration of vernalization), its chromatin modifications of FLOWERING LOCUS C (FLC), following gene expression, and the corresponding phenotypes. Such evidence suggests that research on Arabidopsis can bring insights into incomplete signalling pathways outside of the histone box, which can be achieved through viable reverse genetic screenings based on the phenotypes instead of direct monitoring of histone modifications among individual mutants. The potential upstream regulators in Arabidopsis can provide cues or directions for animal research based on the similarities between them.
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Affiliation(s)
- Yang Yu
- Division of Natural and Applied Sciences, Duke Kunshan University, Kunshan, Jiangsu, China
| | - Sihan Wang
- Division of Natural and Applied Sciences, Duke Kunshan University, Kunshan, Jiangsu, China
| | - Ziqin Wang
- Division of Natural and Applied Sciences, Duke Kunshan University, Kunshan, Jiangsu, China
| | - Renwei Gao
- Division of Natural and Applied Sciences, Duke Kunshan University, Kunshan, Jiangsu, China
| | - Joohyun Lee
- Division of Natural and Applied Sciences, Duke Kunshan University, Kunshan, Jiangsu, China
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Brasher MS, Mize TJ, Thomas AL, Hoeffer CA, Ehringer MA, Evans LM. Testing associations between human anxiety and genes previously implicated by mouse anxiety models. Genes Brain Behav 2023; 22:e12851. [PMID: 37259642 PMCID: PMC10733569 DOI: 10.1111/gbb.12851] [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: 05/02/2023] [Accepted: 05/19/2023] [Indexed: 06/02/2023]
Abstract
Anxiety disorders are common and can be debilitating, with effective treatments remaining hampered by an incomplete understanding of the underlying genetic etiology. Improvements have been made in understanding the genetic influences on mouse behavioral models of anxiety, yet it is unclear the extent to which genes identified in these experimental systems contribute to genetic variation in human anxiety phenotypes. Leveraging new and existing large-scale human genome-wide association studies, we tested whether sets of genes previously identified in mouse anxiety-like behavior studies contribute to a range of human anxiety disorders. When tested as individual genes, 13 mouse-identified genes were associated with human anxiety phenotypes, suggesting an overlap of individual genes contributing to both mouse models of anxiety-like behaviors and human anxiety traits. When genes were tested as sets, we did identify 14 significant associations between mouse gene sets and human anxiety, but the majority of gene sets showed no significant association with human anxiety phenotypes. These few significant associations indicate a need to identify and develop more translatable mouse models by identifying sets of genes that "match" between model systems and specific human phenotypes of interest. We suggest that continuing to develop improved behavioral paradigms and finer-scale experimental data, for instance from individual neuronal subtypes or cell-type-specific expression data, is likely to improve our understanding of the genetic etiology and underlying functional changes in anxiety disorders.
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Affiliation(s)
- Maizy S. Brasher
- Department of Ecology and Evolutionary BiologyUniversity of Colorado BoulderBoulderColoradoUSA
- Institute for Behavioral GeneticsBoulderColoradoUSA
| | - Travis J. Mize
- Department of Ecology and Evolutionary BiologyUniversity of Colorado BoulderBoulderColoradoUSA
- Institute for Behavioral GeneticsBoulderColoradoUSA
| | | | - Charles A. Hoeffer
- Institute for Behavioral GeneticsBoulderColoradoUSA
- Department of Integrative PhysiologyUniversity of Colorado BoulderBoulderColoradoUSA
| | - Marissa A. Ehringer
- Institute for Behavioral GeneticsBoulderColoradoUSA
- Department of Integrative PhysiologyUniversity of Colorado BoulderBoulderColoradoUSA
| | - Luke M. Evans
- Department of Ecology and Evolutionary BiologyUniversity of Colorado BoulderBoulderColoradoUSA
- Institute for Behavioral GeneticsBoulderColoradoUSA
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12
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Elizalde MJ, Gorelick DA. Mechanistic toxicology in light of genetic compensation. Toxicol Sci 2023; 197:kfad113. [PMID: 37941503 PMCID: PMC10823772 DOI: 10.1093/toxsci/kfad113] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2023] Open
Abstract
Mechanistic toxicology seeks to identify the molecular and cellular mechanisms by which toxicants exert their deleterious effects. One powerful approach is to generate mutations in genes that respond to a particular toxicant, and then test how such mutations change the effects of the toxicant. CRISPR is a rapid and versatile approach to generate mutations in cultured cells and in animal models. Many studies use CRISPR to generate short insertions or deletions in a target gene and then assume that the resulting mutation, such as a premature termination codon, causes a loss of functional protein. However, recent studies demonstrate that this assumption is flawed. Cells can compensate for short insertion and deletion mutations, leading toxicologists to draw erroneous conclusions from mutant studies. In this review, we will discuss mechanisms by which a mutation in one gene may be rescued by compensatory activity. We will discuss how CRISPR insertion and deletion mutations are susceptible to compensation by transcriptional adaptation, alternative splicing, and rescue by maternally derived gene products. We will review evidence that measuring levels of messenger RNA transcribed from a mutated gene is an unreliable indicator of the severity of the mutation. Finally, we provide guidelines for using CRISPR to generate mutations that avoid compensation.
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Affiliation(s)
- Mary Jane Elizalde
- Department of Molecular & Cellular Biology, Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX 77030, United States
| | - Daniel A Gorelick
- Department of Molecular & Cellular Biology, Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX 77030, United States
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13
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Rapti G. Regulation of axon pathfinding by astroglia across genetic model organisms. Front Cell Neurosci 2023; 17:1241957. [PMID: 37941606 PMCID: PMC10628440 DOI: 10.3389/fncel.2023.1241957] [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] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2023] [Accepted: 09/07/2023] [Indexed: 11/10/2023] Open
Abstract
Glia and neurons are intimately associated throughout bilaterian nervous systems, and were early proposed to interact for patterning circuit assembly. The investigations of circuit formation progressed from early hypotheses of intermediate guideposts and a "glia blueprint", to recent genetic and cell manipulations, and visualizations in vivo. An array of molecular factors are implicated in axon pathfinding but their number appears small relatively to circuit complexity. Comprehending this circuit complexity requires to identify unknown factors and dissect molecular topographies. Glia contribute to both aspects and certain studies provide molecular and functional insights into these contributions. Here, I survey glial roles in guiding axon navigation in vivo, emphasizing analogies, differences and open questions across major genetic models. I highlight studies pioneering the topic, and dissect recent findings that further advance our current molecular understanding. Circuits of the vertebrate forebrain, visual system and neural tube in zebrafish, mouse and chick, the Drosophila ventral cord and the C. elegans brain-like neuropil emerge as major contexts to study glial cell functions in axon navigation. I present astroglial cell types in these models, and their molecular and cellular interactions that drive axon guidance. I underline shared principles across models, conceptual or technical complications, and open questions that await investigation. Glia of the radial-astrocyte lineage, emerge as regulators of axon pathfinding, often employing common molecular factors across models. Yet this survey also highlights different involvements of glia in embryonic navigation or pioneer axon pathfinding, and unknowns in the molecular underpinnings of glial cell functions. Future cellular and molecular investigations should complete the comprehensive view of glial roles in circuit assembly.
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Affiliation(s)
- Georgia Rapti
- Developmental Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
- Epigenetics and Neurobiology Unit, European Molecular Biology Laboratory, Rome, Italy
- Interdisciplinary Center of Neurosciences, Heidelberg University, Heidelberg, Germany
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Ferjani A, Tsukagoshi H, Vassileva V. Editorial: Model organisms in plant science: Arabidopsis thaliana. Front Plant Sci 2023; 14:1279230. [PMID: 37767288 PMCID: PMC10520703 DOI: 10.3389/fpls.2023.1279230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 08/28/2023] [Indexed: 09/29/2023]
Affiliation(s)
- Ali Ferjani
- Department of Biology, Tokyo Gakugei University, Tokyo, Japan
| | | | - Valya Vassileva
- Department of Molecular Biology and Genetics, Institute of Plant Physiology and Genetics, Bulgarian Academy of Sciences, Sofia, Bulgaria
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15
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Brundel BJJM, Jopling C, Efimov IR, Charpentier F, Etzion Y. Editorial: Experimental models and model organisms in cardiac electrophysiology: opportunities and challenges. Front Physiol 2023; 14:1254596. [PMID: 37745238 PMCID: PMC10512071 DOI: 10.3389/fphys.2023.1254596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 07/24/2023] [Indexed: 09/26/2023] Open
Affiliation(s)
- Bianca J. J. M. Brundel
- Department of Physiology, Amsterdam Cardiovascular Sciences, Amsterdam University Medical Centers, VU Universiteit, Amsterdam, Netherlands
| | - Chris Jopling
- Institute of Functional Genomics, University of Montpellier, CNRS, INSERM, LabEx ICST, Montpellier, France
| | - Igor R. Efimov
- Department of Biomedical Engineering, Northwestern University, Chicago, IL, United States
- Department of Medicine, Northwestern University, Chicago, IL, United States
| | | | - Yoram Etzion
- Department of Physiology and Cell Biology, Ben-Gurion University of the Negev, Beer-Sheva, Israel
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16
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Kolotuev I. Work smart, not hard: How array tomography can help increase the ultrastructure data output. J Microsc 2023. [PMID: 37626455 DOI: 10.1111/jmi.13217] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2023] [Revised: 08/16/2023] [Accepted: 08/17/2023] [Indexed: 08/27/2023]
Abstract
Transmission electron microscopy has been essential for understanding cell biology for over six decades. Volume electron microscopy tools, such as serial block face and focused ion beam scanning electron microscopy acquisition, brought a new era to ultrastructure analysis. 'Array Tomography' (AT) refers to sequential image acquisition of resin-embedded sample sections on a large support (coverslip, glass slide, silicon wafers) for immunolabelling with multiple fluorescent labels, occasionally combined with ultrastructure observation. Subsequently, the term was applied to generating and imaging a series of sections to acquire a 3D representation of a structure using scanning electron microscopy (SEM). Although this is a valuable application, the potential of AT is to facilitate many tasks that are difficult or even impossible to obtain by Transmission Electron Microscopy (TEM). Due to the straightforward nature and versatility of AT sample preparation and image acquisition, the technique can be applied practically to any biological sample for selected sections or volume electron microscopy analysis. Furthermore, in addition to the benefits described here, AT is compatible with morphological analysis, multiplex immunolabelling, immune-gold labelling, and correlative light and electron microscopy workflow applicable for single cells, tissue and small organisms. This versatility makes AT attractive not only for basic research but as a diagnostic tool with a simplified routine.
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Affiliation(s)
- Irina Kolotuev
- Electron Microscopy Facility, University of Lausanne, Lausanne, Switzerland
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17
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Abstract
Methanogenic archaea are the only organisms that produce CH4 as part of their energy-generating metabolism. They are ubiquitous in oxidant-depleted, anoxic environments such as aquatic sediments, anaerobic digesters, inundated agricultural fields, the rumen of cattle, and the hindgut of termites, where they catalyze the terminal reactions in the degradation of organic matter. Methanogenesis is the only metabolism that is restricted to members of the domain Archaea. Here, we discuss the importance of model organisms in the history of methanogen research, including their role in the discovery of the archaea and in the biochemical and genetic characterization of methanogenesis. We also discuss outstanding questions in the field and newly emerging model systems that will expand our understanding of this uniquely archaeal metabolism.
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Affiliation(s)
- Kyle C. Costa
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, Minnesota, USA
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18
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Pulgar VM, Guibert C, Faissal Ahmed AS, Trask AJ. Editorial: Model organisms and experimental models: opportunities and challenges in vascular physiology research. Front Physiol 2023; 14:1271220. [PMID: 37675279 PMCID: PMC10478243 DOI: 10.3389/fphys.2023.1271220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 08/16/2023] [Indexed: 09/08/2023] Open
Affiliation(s)
- Victor M. Pulgar
- Department of Pharmaceutical and Clinical Sciences, Campbell University, Buies-Creek, NC, United States
- Department of Obstetrics and Gynecology, Wake Forest School of Medicine, Winston-Salem, NC, United States
| | - Christelle Guibert
- Université de Bordeaux, Institut National de la Santé et de la Recherche Médicale (INSERM) and Centre de Recherche Cardio-Thoracique de Bordeaux (CRCTB), U1045, Pessac, France
| | | | - Aaron J. Trask
- Center for Cardiovascular Research, The Research Institute at Nationwide Children’s Hospital, Columbus, OH, United States
- Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH, United States
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19
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Gryganskyi AP, Golan J, Muszewska A, Idnurm A, Dolatabadi S, Mondo SJ, Kutovenko VB, Kutovenko VO, Gajdeczka MT, Anishchenko IM, Pawlowska J, Tran NV, Ebersberger I, Voigt K, Wang Y, Chang Y, Pawlowska TE, Heitman J, Vilgalys R, Bonito G, Benny GL, Smith ME, Reynolds N, James TY, Grigoriev IV, Spatafora JW, Stajich JE. Sequencing the Genomes of the First Terrestrial Fungal Lineages: What Have We Learned? Microorganisms 2023; 11:1830. [PMID: 37513002 PMCID: PMC10386755 DOI: 10.3390/microorganisms11071830] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 07/13/2023] [Accepted: 07/16/2023] [Indexed: 07/30/2023] Open
Abstract
The first genome sequenced of a eukaryotic organism was for Saccharomyces cerevisiae, as reported in 1996, but it was more than 10 years before any of the zygomycete fungi, which are the early-diverging terrestrial fungi currently placed in the phyla Mucoromycota and Zoopagomycota, were sequenced. The genome for Rhizopus delemar was completed in 2008; currently, more than 1000 zygomycete genomes have been sequenced. Genomic data from these early-diverging terrestrial fungi revealed deep phylogenetic separation of the two major clades-primarily plant-associated saprotrophic and mycorrhizal Mucoromycota versus the primarily mycoparasitic or animal-associated parasites and commensals in the Zoopagomycota. Genomic studies provide many valuable insights into how these fungi evolved in response to the challenges of living on land, including adaptations to sensing light and gravity, development of hyphal growth, and co-existence with the first terrestrial plants. Genome sequence data have facilitated studies of genome architecture, including a history of genome duplications and horizontal gene transfer events, distribution and organization of mating type loci, rDNA genes and transposable elements, methylation processes, and genes useful for various industrial applications. Pathogenicity genes and specialized secondary metabolites have also been detected in soil saprobes and pathogenic fungi. Novel endosymbiotic bacteria and viruses have been discovered during several zygomycete genome projects. Overall, genomic information has helped to resolve a plethora of research questions, from the placement of zygomycetes on the evolutionary tree of life and in natural ecosystems, to the applied biotechnological and medical questions.
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Affiliation(s)
- Andrii P. Gryganskyi
- Division of Biological & Nanoscale Technologies, UES, Inc., Dayton, OH 45432, USA
| | - Jacob Golan
- Department of Botany, University of Wisconsin-Madison, Madison, WI 53706, USA;
| | - Anna Muszewska
- Institute of Biochemistry & Biophysics, Polish Academy of Sciences, 01-224 Warsaw, Poland;
| | - Alexander Idnurm
- School of BioSciences, University of Melbourne, Parkville, VIC 3010, Australia;
| | - Somayeh Dolatabadi
- Biology Department, Hakim Sabzevari University, Sabzevar 96179-76487, Iran;
| | - Stephen J. Mondo
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; (S.J.M.); (I.V.G.)
| | - Vira B. Kutovenko
- Department of Agrobiology, National University of Life & Environmental Sciences, 03041 Kyiv, Ukraine; (V.B.K.)
| | - Volodymyr O. Kutovenko
- Department of Agrobiology, National University of Life & Environmental Sciences, 03041 Kyiv, Ukraine; (V.B.K.)
| | | | - Iryna M. Anishchenko
- MG Kholodny Institute of Botany, National Academy of Sciences, 01030 Kyiv, Ukraine;
| | - Julia Pawlowska
- Institute of Evolutionary Biology, Faculty of Biology, Biological & Chemical Research Centre, University of Warsaw, 02-089 Warsaw, Poland;
| | - Ngoc Vinh Tran
- Plant Pathology Department, University of Florida, Gainesville, FL 32611, USA; (N.V.T.); (G.L.B.); (M.E.S.)
| | - Ingo Ebersberger
- Leibniz Institute for Natural Product Research & Infection Biology, 07745 Jena, Germany; (I.E.); (K.V.)
| | - Kerstin Voigt
- Leibniz Institute for Natural Product Research & Infection Biology, 07745 Jena, Germany; (I.E.); (K.V.)
| | - Yan Wang
- Department of Ecology & Evolutionary Biology, University of Toronto, Toronto, ON M5S 1A1, Canada;
- Department of Biological Sciences, University of Toronto Scarborough, Toronto, ON M1C 1A4, Canada
| | - Ying Chang
- Department of Biological Sciences, National University of Singapore, Singapore 119077, Singapore;
| | - Teresa E. Pawlowska
- School of Integrative Plant Science, Cornell University, Ithaca, NY 14850, USA; (T.E.P.); (N.R.)
| | - Joseph Heitman
- Department of Molecular Genetics & Microbiology, Duke University School of Medicine, Durham, NC 27710, USA;
| | - Rytas Vilgalys
- Biology Department, Duke University, Durham, NC 27708, USA;
| | - Gregory Bonito
- Department of Plant, Soil & Microbial Sciences, Michigan State University, East Lansing, MI 48824, USA;
| | - Gerald L. Benny
- Plant Pathology Department, University of Florida, Gainesville, FL 32611, USA; (N.V.T.); (G.L.B.); (M.E.S.)
| | - Matthew E. Smith
- Plant Pathology Department, University of Florida, Gainesville, FL 32611, USA; (N.V.T.); (G.L.B.); (M.E.S.)
| | - Nicole Reynolds
- School of Integrative Plant Science, Cornell University, Ithaca, NY 14850, USA; (T.E.P.); (N.R.)
| | - Timothy Y. James
- Department of Ecology & Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA;
| | - Igor V. Grigoriev
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; (S.J.M.); (I.V.G.)
- Department of Plant & Microbial Biology, University of California, Berkeley, CA 94720, USA
| | - Joseph W. Spatafora
- Department of Botany & Plant Pathology, Oregon State University, Corvallis, OR 97331, USA;
| | - Jason E. Stajich
- Department of Microbiology & Plant Pathology, University of California, Riverside, CA 93106, USA;
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20
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Xue B, Rhee SY. Status of genome function annotation in model organisms and crops. Plant Direct 2023; 7:e499. [PMID: 37426891 PMCID: PMC10326244 DOI: 10.1002/pld3.499] [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] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 04/21/2023] [Accepted: 05/08/2023] [Indexed: 07/11/2023]
Abstract
Since the entry into genome-enabled biology several decades ago, much progress has been made in determining, describing, and disseminating the functions of genes and their products. Yet, this information is still difficult to access for many scientists and for most genomes. To provide easy access and a graphical summary of the status of genome function annotation for model organisms and bioenergy and food crop species, we created a web application (https://genomeannotation.rheelab.org) to visualize, search, and download genome annotation data for 28 species. The summary graphics and data tables will be updated semi-annually, and snapshots will be archived to provide a historical record of the progress of genome function annotation efforts. Clear and simple visualization of up-to-date genome function annotation status, including the extent of what is unknown, will help address the grand challenge of elucidating the functions of all genes in organisms.
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Affiliation(s)
- Bo Xue
- Department of Plant BiologyCarnegie Institution for ScienceStanfordCaliforniaUSA
- Present address:
Plant Resilience InstituteMichigan State UniversityEast LansingMI 4882
| | - Seung Y. Rhee
- Department of Plant BiologyCarnegie Institution for ScienceStanfordCaliforniaUSA
- Present address:
Plant Resilience InstituteMichigan State UniversityEast LansingMI 4882
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21
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Saadi I, Goering JP, Hufft-Martinez BM, Tran PV. SPECC1L: a cytoskeletal protein that regulates embryonic tissue dynamics. Biochem Soc Trans 2023:BST20220461. [PMID: 37345651 PMCID: PMC10404473 DOI: 10.1042/bst20220461] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 06/12/2023] [Accepted: 06/13/2023] [Indexed: 06/23/2023]
Abstract
Many structural birth defects occur due to failure of tissue movement and fusion events during embryogenesis. Examples of such birth defects include failure of closure of the neural tube, palate, and ventral body wall. Actomyosin forces play a pivotal role in these closure processes, making proteins that regulate actomyosin dynamics a priority when studying the etiology of structural birth defects. SPECC1L (sperm antigen with calponin homology and coiled-coil domains 1 like) cytoskeletal protein associates with microtubules, filamentous actin, non-muscle myosin II (NMII), as well as membrane-associated components of adherens junctions. Patients with SPECC1L mutations show a range of structural birth defects affecting craniofacial development (hypertelorism, cleft palate), ventral body wall (omphalocele), and internal organs (diaphragmatic hernia, bicornuate uterus). Characterization of mouse models indicates that these syndromic mutations utilize a gain-of-function mechanism to affect intra- and supra-cellular actin organization. Interestingly, SPECC1L deficiency appears to affect the efficiency of tissue dynamics, making it an important cytoskeletal regulator to study tissue movement and fusion events during embryonic development. Here we summarize the SPECC1L-related syndrome mutations, phenotypes of Specc1l mouse models, and cellular functions of SPECC1L that highlight how it may regulate embryonic tissue dynamics.
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Affiliation(s)
- Irfan Saadi
- Department of Cell Biology and Physiology, University of Kansas Medical Center, Kansas City, KS, U.S.A
- Institute for Reproductive and Developmental Sciences, University of Kansas Medical Center, Kansas City, KS, U.S.A
| | - Jeremy P Goering
- Department of Cell Biology and Physiology, University of Kansas Medical Center, Kansas City, KS, U.S.A
| | - Brittany M Hufft-Martinez
- Department of Cell Biology and Physiology, University of Kansas Medical Center, Kansas City, KS, U.S.A
| | - Pamela V Tran
- Department of Cell Biology and Physiology, University of Kansas Medical Center, Kansas City, KS, U.S.A
- Jared Grantham Kidney Institute, University of Kansas Medical Center, Kansas City, KS, U.S.A
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22
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Imperadore P, Jones KM, Morgan JR, De Sio F, Stahnisch FW. Editorial: Regeneration from cells to limbs: past, present, and future. Front Cell Dev Biol 2023; 11:1229613. [PMID: 37389352 PMCID: PMC10303884 DOI: 10.3389/fcell.2023.1229613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Accepted: 06/01/2023] [Indexed: 07/01/2023] Open
Affiliation(s)
- Pamela Imperadore
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Napoli, Italy
- Association for Cephalopod Research—CephRes, Napoli, Italy
| | - Kathryn Maxson Jones
- Center for Medical Ethics and Health Policy, Baylor College of Medicine, Houston, TX, United States
- Department of History, Purdue University, West Lafayette, IN, United States
| | - Jennifer R. Morgan
- The Eugene Bell Center for Regenerative Biology and Tissue Engineering, Marine Biological Laboratory, Woods Hole, MA, United States
| | - Fabio De Sio
- Institut für Geschichte, Theorie und Ethik der Medizin, Centre for Life and Society, Medizinische Fakultät, Heinrich Heine Universität Düsseldorf, Düsseldorf, Germany
| | - Frank W. Stahnisch
- Alberta Medical Foundation/Hannah Professor in the History of Medicine and Health Care, University of Calgary, Calgary, AB, Canada
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Abstract
Targeted protein degradation, with its rapid protein depletion kinetics, allows the measurement of acute changes in the cell. The auxin-inducible degron (AID) system, rapidly degrades AID-tagged proteins only in the presence of auxin. The AID system being inducible makes the study of essential genes and dynamic processes like cell differentiation, cell cycle and genome organization feasible. The AID degradation system has been adapted to yeast, protozoans, C. elegans, Drosophila, zebrafish, mouse and mammalian cell lines. Using the AID system, researchers have unveiled novel functions for essential proteins at developmental stages that were previously difficult to investigate due to early lethality. This comprehensive review discusses the development, advancements, applications and drawbacks of the AID system and compares it with other available protein degradation systems.
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Affiliation(s)
- Kundurthi Phanindhar
- CSIR-Centre for Cellular & Molecular Biology (CCMB), Uppal Road, Hyderabad, 500007, India
| | - Rakesh K Mishra
- CSIR-Centre for Cellular & Molecular Biology (CCMB), Uppal Road, Hyderabad, 500007, India
- Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, 201002, India
- Tata Institute for Genetics & Society (TIGS), Bangalore, 560065, India
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24
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Maxson Jones K, Morgan JR. Lampreys and spinal cord regeneration: "a very special claim on the interest of zoologists," 1830s-present. Front Cell Dev Biol 2023; 11:1113961. [PMID: 37228651 PMCID: PMC10203415 DOI: 10.3389/fcell.2023.1113961] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 04/24/2023] [Indexed: 05/27/2023] Open
Abstract
Employing history of science methods, including analyses of the scientific literature, archival documents, and interviews with scientists, this paper presents a history of lampreys in neurobiology from the 1830s to the present. We emphasize the lamprey's roles in helping to elucidate spinal cord regeneration mechanisms. Two attributes have long perpetuated studies of lampreys in neurobiology. First, they possess large neurons, including multiple classes of stereotypically located, 'identified' giant neurons in the brain, which project their large axons into the spinal cord. These giant neurons and their axonal fibers have facilitated electrophysiological recordings and imaging across biological scales, ranging from molecular to circuit-level analyses of nervous system structures and functions and including their roles in behavioral output. Second, lampreys have long been considered amongst the most basal extant vertebrates on the planet, so they have facilitated comparative studies pointing to conserved and derived characteristics of vertebrate nervous systems. These features attracted neurologists and zoologists to studies of lampreys between the 1830s and 1930s. But, the same two attributes also facilitated the rise of the lamprey in neural regeneration research after 1959, when biologists first wrote about the spontaneous, robust regeneration of some identified CNS axons in larvae after spinal cord injuries, coupled with recovery of normal swimming. Not only did large neurons promote fresh insights in the field, enabling studies incorporating multiple scales with existing and new technologies. But investigators also were able to attach a broad scope of relevance to their studies, interpreting them as suggesting conserved features of successful, and sometimes even unsuccessful, CNS regeneration. Lamprey research demonstrated that functional recovery takes place without the reformation of the original neuronal connections, for instance, by way of imperfect axonal regrowth and compensatory plasticity. Moreover, research performed in the lamprey model revealed that factors intrinsic to neurons are integral in promoting or hindering regeneration. As this work has helped illuminate why basal vertebrates accomplish CNS regeneration so well, whereas mammals do it so poorly, this history presents a case study in how biological and medical value have been, and could continue to be, gleaned from a non-traditional model organism for which molecular tools have been developed only relatively recently.
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Affiliation(s)
- Kathryn Maxson Jones
- Center for Medical Ethics and Health Policy, Baylor College of Medicine, Houston, TX, United States
- Department of History, Purdue University, West Lafayette, IN, United States
- Marine Biological Laboratory, The Eugene Bell Center for Regenerative Biology and Tissue Engineering, Woods Hole, MA, United States
| | - Jennifer R. Morgan
- Marine Biological Laboratory, The Eugene Bell Center for Regenerative Biology and Tissue Engineering, Woods Hole, MA, United States
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25
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Lo RS, Cromie GA, Tang M, Teng K, Owens K, Sirr A, Kutz JN, Morizono H, Caldovic L, Ah Mew N, Gropman A, Dudley AM. The functional impact of 1,570 individual amino acid substitutions in human OTC. Am J Hum Genet 2023; 110:863-879. [PMID: 37146589 PMCID: PMC10183466 DOI: 10.1016/j.ajhg.2023.03.019] [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: 11/15/2022] [Accepted: 03/30/2023] [Indexed: 05/07/2023] Open
Abstract
Deleterious mutations in the X-linked gene encoding ornithine transcarbamylase (OTC) cause the most common urea cycle disorder, OTC deficiency. This rare but highly actionable disease can present with severe neonatal onset in males or with later onset in either sex. Individuals with neonatal onset appear normal at birth but rapidly develop hyperammonemia, which can progress to cerebral edema, coma, and death, outcomes ameliorated by rapid diagnosis and treatment. Here, we develop a high-throughput functional assay for human OTC and individually measure the impact of 1,570 variants, 84% of all SNV-accessible missense mutations. Comparison to existing clinical significance calls, demonstrated that our assay distinguishes known benign from pathogenic variants and variants with neonatal onset from late-onset disease presentation. This functional stratification allowed us to identify score ranges corresponding to clinically relevant levels of impairment of OTC activity. Examining the results of our assay in the context of protein structure further allowed us to identify a 13 amino acid domain, the SMG loop, whose function appears to be required in human cells but not in yeast. Finally, inclusion of our data as PS3 evidence under the current ACMG guidelines, in a pilot reclassification of 34 variants with complete loss of activity, would change the classification of 22 from variants of unknown significance to clinically actionable likely pathogenic variants. These results illustrate how large-scale functional assays are especially powerful when applied to rare genetic diseases.
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Affiliation(s)
- Russell S Lo
- Pacific Northwest Research Institute, Seattle, WA, USA
| | | | - Michelle Tang
- Pacific Northwest Research Institute, Seattle, WA, USA
| | - Kevin Teng
- Pacific Northwest Research Institute, Seattle, WA, USA
| | - Katherine Owens
- Pacific Northwest Research Institute, Seattle, WA, USA; Department of Applied Mathematics, University of Washington, Seattle, WA, USA
| | - Amy Sirr
- Pacific Northwest Research Institute, Seattle, WA, USA
| | - J Nathan Kutz
- Department of Applied Mathematics, University of Washington, Seattle, WA, USA
| | - Hiroki Morizono
- Center for Genetic Medicine Research, Children's National Research Institute, Children's National Hospital, Washington, DC, USA; Department of Genomics and Precision Medicine, School of Medicine and Health Sciences, The George Washington University, Washington, DC, USA
| | - Ljubica Caldovic
- Center for Genetic Medicine Research, Children's National Research Institute, Children's National Hospital, Washington, DC, USA; Department of Genomics and Precision Medicine, School of Medicine and Health Sciences, The George Washington University, Washington, DC, USA
| | - Nicholas Ah Mew
- Center for Genetic Medicine Research, Children's National Research Institute, Children's National Hospital, Washington, DC, USA; Department of Genomics and Precision Medicine, School of Medicine and Health Sciences, The George Washington University, Washington, DC, USA
| | - Andrea Gropman
- Center for Genetic Medicine Research, Children's National Research Institute, Children's National Hospital, Washington, DC, USA; Department of Genomics and Precision Medicine, School of Medicine and Health Sciences, The George Washington University, Washington, DC, USA; Department of Neurology, Division of Neurogenetics and Neurodevelopmental Disabilities, Children's National Hospital, Washington, DC, USA; Center for Neuroscience Research, Children's National Research Institute, Children's National Hospital, Washington, DC, USA
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26
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Petrov PB, Considine JM, Izzi V, Naba A. Matrisome AnalyzeR: A suite of tools to annotate and quantify ECM molecules in big datasets across organisms. bioRxiv 2023:2023.04.18.537378. [PMID: 37131773 PMCID: PMC10153148 DOI: 10.1101/2023.04.18.537378] [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] [Indexed: 05/04/2023]
Abstract
The extracellular matrix (ECM) is a complex meshwork of proteins that forms the scaffold of all tissues in multicellular organisms. It plays critical roles in all aspects of life: from orchestrating cell migration during development, to supporting tissue repair. It also plays critical roles in the etiology or progression of diseases. To study this compartment, we defined the compendium of all genes encoding ECM and ECM-associated proteins for multiple organisms. We termed this compendium the "matrisome" and further classified matrisome components into different structural or functional categories. This nomenclature is now largely adopted by the research community to annotate -omics datasets and has contributed to advance both fundamental and translational ECM research. Here, we report the development of Matrisome AnalyzeR, a suite of tools including a web-based application ( https://sites.google.com/uic.edu/matrisome/tools/matrisome-analyzer ) and an R package ( https://github.com/Matrisome/MatrisomeAnalyzeR ). The web application can be used by anyone interested in annotating, classifying, and tabulating matrisome molecules in large datasets without requiring programming knowledge. The companion R package is available to more experienced users, interested in processing larger datasets or in additional data visualization options. SUMMARY STATEMENT Matrisome AnalyzeR is a suite of tools, including a web-based app and an R package, designed to facilitate the annotation and quantification of extracellular matrix components in big datasets.
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Affiliation(s)
- Petar B. Petrov
- Infotech Institute, University of Oulu, FI-90014 Oulu, Finland
| | - James M. Considine
- Department of Physiology and Biophysics, University of Illinois Chicago, Chicago, IL 60612, USA
| | - Valerio Izzi
- Faculty of Biochemistry and Molecular Medicine & Faculty of Medicine, BioIM Unit, University of Oulu, FI-90014 Oulu, Finland
- Foundation for the Finnish Cancer Institute, Tukholmankatu 8, Helsinki, Finland
| | - Alexandra Naba
- Department of Physiology and Biophysics, University of Illinois Chicago, Chicago, IL 60612, USA
- University of Illinois Cancer Center, Chicago, IL 60612, USA
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27
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Hu Y, Comjean A, Attrill H, Antonazzo G, Thurmond J, Li F, Chao T, Mohr SE, Brown NH, Perrimon N. PANGEA: A New Gene Set Enrichment Tool for Drosophila and Common Research Organisms. bioRxiv 2023:2023.02.20.529262. [PMID: 36865134 PMCID: PMC9980003 DOI: 10.1101/2023.02.20.529262] [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] [Indexed: 02/24/2023]
Abstract
Gene set enrichment analysis (GSEA) plays an important role in large-scale data analysis, helping scientists discover the underlying biological patterns over-represented in a gene list resulting from, for example, an 'omics' study. Gene Ontology (GO) annotation is the most frequently used classification mechanism for gene set definition. Here we present a new GSEA tool, PANGEA (PAthway, Network and Gene-set Enrichment Analysis; https://www.flyrnai.org/tools/pangea/ ), developed to allow a more flexible and configurable approach to data analysis using a variety of classification sets. PANGEA allows GO analysis to be performed on different sets of GO annotations, for example excluding high-throughput studies. Beyond GO, gene sets for pathway annotation and protein complex data from various resources as well as expression and disease annotation from the Alliance of Genome Resources (Alliance). In addition, visualisations of results are enhanced by providing an option to view network of gene set to gene relationships. The tool also allows comparison of multiple input gene lists and accompanying visualisation tools for quick and easy comparison. This new tool will facilitate GSEA for Drosophila and other major model organisms based on high-quality annotated information available for these species.
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Affiliation(s)
- Yanhui Hu
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Harvard University, Boston, MA 02115, USA
- Drosophila RNAi Screening Center, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Aram Comjean
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Harvard University, Boston, MA 02115, USA
- Drosophila RNAi Screening Center, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Helen Attrill
- Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3DY, UK
| | - Giulia Antonazzo
- Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3DY, UK
| | - Jim Thurmond
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
| | - Fangge Li
- Drosophila RNAi Screening Center, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Tiffany Chao
- Drosophila RNAi Screening Center, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Stephanie E. Mohr
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Harvard University, Boston, MA 02115, USA
- Drosophila RNAi Screening Center, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Nicholas H. Brown
- Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3DY, UK
| | - Norbert Perrimon
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Harvard University, Boston, MA 02115, USA
- Drosophila RNAi Screening Center, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
- Howard Hughes Medical Institute, Boston, MA 02138, USA
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28
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Prasad T, Iyer S, Chatterjee S, Kumar M. In vivo models to study neurogenesis and associated neurodevelopmental disorders-Microcephaly and autism spectrum disorder. WIREs Mech Dis 2023:e1603. [PMID: 36754084 DOI: 10.1002/wsbm.1603] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 12/14/2022] [Accepted: 01/24/2023] [Indexed: 02/10/2023]
Abstract
The genesis and functioning of the central nervous system are one of the most intricate and intriguing aspects of embryogenesis. The big lacuna in the field of human CNS development is the lack of accessibility of the human brain for direct observation during embryonic and fetal development. Thus, it is imperative to establish alternative animal models to gain deep mechanistic insights into neurodevelopment, establishment of neural circuitry, and its function. Neurodevelopmental events such as neural specification, differentiation, and generation of neuronal and non-neuronal cell types have been comprehensively studied using a variety of animal models and in vitro model systems derived from human cells. The experimentations on animal models have revealed novel, mechanistic insights into neurogenesis, formation of neural networks, and function. The models, thus serve as indispensable tools to understand the molecular basis of neurodevelopmental disorders (NDDs) arising from aberrations during embryonic development. Here, we review the spectrum of in vivo models such as fruitfly, zebrafish, frog, mice, and nonhuman primates to study neurogenesis and NDDs like microcephaly and Autism Spectrum Disorder. We also discuss nonconventional models such as ascidians and the recent technological advances in the field to study neurogenesis, disease mechanisms, and pathophysiology of human NDDs. This article is categorized under: Cancer > Stem Cells and Development Congenital Diseases > Stem Cells and Development Neurological Diseases > Stem Cells and Development Congenital Diseases > Genetics/Genomics/Epigenetics.
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Affiliation(s)
- Tuhina Prasad
- CSIR-Centre for Cellular and Molecular Biology (CSIR-CCMB), Hyderabad, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Sharada Iyer
- CSIR-Centre for Cellular and Molecular Biology (CSIR-CCMB), Hyderabad, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Sayoni Chatterjee
- CSIR-Centre for Cellular and Molecular Biology (CSIR-CCMB), Hyderabad, India
| | - Megha Kumar
- CSIR-Centre for Cellular and Molecular Biology (CSIR-CCMB), Hyderabad, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
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29
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Park S, Lee J, Kim J, Kim D, Lee JH, Pack SP, Seo M. Benchmark study for evaluating the quality of reference genomes and gene annotations in 114 species. Front Vet Sci 2023; 10:1128570. [PMID: 36896291 PMCID: PMC9988948 DOI: 10.3389/fvets.2023.1128570] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 02/02/2023] [Indexed: 02/23/2023] Open
Abstract
Introduction For reference genomes and gene annotations are key materials that can determine the limits of the molecular biology research of a species; however, systematic research on their quality assessment remains insufficient. Methods We collected reference assemblies, gene annotations, and 3,420 RNA-sequencing (RNA-seq) data from 114 species and selected effective indicators to simultaneously evaluate the reference genome quality of various species, including statistics that can be obtained empirically during the mapping process of short reads. Furthermore, we newly presented and applied transcript diversity and quantification success rates that can relatively evaluate the quality of gene annotations of various species. Finally, we proposed a next-generation sequencing (NGS) applicability index by integrating a total of 10 effective indicators that can evaluate the genome and gene annotation of a specific species. Results and discussion Based on these effective evaluation indicators, we successfully evaluated and demonstrated the relative accessibility of NGS applications in all species, which will directly contribute to determining the technological boundaries in each species. Simultaneously, we expect that it will be a key indicator to examine the direction of future development through relative quality evaluation of genomes and gene annotations in each species, including countless organisms whose genomes and gene annotations will be constructed in the future.
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Affiliation(s)
- Sinwoo Park
- Department of Computer and Information Science, Korea University, Sejong City, Republic of Korea
| | - Jinbaek Lee
- Department of Computer Convergence Software, Korea University, Sejong City, Republic of Korea
| | - Jaeryeong Kim
- Department of Computer and Information Science, Korea University, Sejong City, Republic of Korea
| | - Dohyeon Kim
- Department of Computer and Information Science, Korea University, Sejong City, Republic of Korea
| | - Jin Hyup Lee
- Department of Food and Biotechnology, Korea University, Sejong City, Republic of Korea
| | - Seung Pil Pack
- Department of Biotechnology and Bioinformatics, Korea University, Sejong City, Republic of Korea
| | - Minseok Seo
- Department of Computer and Information Science, Korea University, Sejong City, Republic of Korea.,Department of Computer Convergence Software, Korea University, Sejong City, Republic of Korea
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30
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Ortuño-Sahagún D, Riesgo-Escovar JR. Editorial: Emerging frontiers in developmental biology in Latin America. Front Neurosci 2023; 17:1129291. [PMID: 37152601 PMCID: PMC10159055 DOI: 10.3389/fnins.2023.1129291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 04/03/2023] [Indexed: 05/09/2023] Open
Affiliation(s)
- Daniel Ortuño-Sahagún
- Laboratorio de Neuroinmunobiología Molecular, Instituto de Investigación en Ciencias Biomédicas, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Jalisco, Mexico
- *Correspondence: Daniel Ortuño-Sahagún
| | - Juan Rafael Riesgo-Escovar
- Developmental Neurobiology and Neurophysiology, Instituto de Neurobiología, Campus UNAM Juriquilla, Universidad Nacional Autónoma de Mexico, Santiago de Querétaro, Mexico
- Juan Rafael Riesgo-Escovar
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31
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Pasko VI, Churkina AS, Shakhov AS, Kotlobay AA, Alieva IB. Modeling of Neurodegenerative Diseases: 'Step by Step' and 'Network' Organization of the Complexes of Model Systems. Int J Mol Sci 2022; 24:ijms24010604. [PMID: 36614047 PMCID: PMC9820769 DOI: 10.3390/ijms24010604] [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] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 12/17/2022] [Accepted: 12/25/2022] [Indexed: 12/31/2022] Open
Abstract
Neurodegenerative diseases have acquired the status of one of the leading causes of death in developed countries, which requires creating new model systems capable of accurately reproducing the mechanisms underlying these pathologies. Here we analyzed modern model systems and their contribution to the solution of unexplored manifestations of neuropathological processes. Each model has unique properties that make it the optimal tool for modeling certain aspects of neurodegenerative disorders. We concluded that to optimize research, it is necessary to combine models into complexes that include organisms and artificial systems of different organizational levels. Such complexes can be organized in two ways. The first method can be described as "step by step", where each model for studying a certain characteristic is a separate step that allows using the information obtained in the modeling process for the gradual study of increasingly complex processes in subsequent models. The second way is a 'network' approach. Studies are carried out with several types of models simultaneously, and experiments with each specific type are adjusted in conformity with the data obtained from other models. In our opinion, the 'network' approach to combining individual model systems seems more promising for fundamental biology as well as diagnostics and therapy.
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Affiliation(s)
| | - Aleksandra Sergeevna Churkina
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 1–73, Leninskye Gory, 119992 Moscow, Russia
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 1–40, Leninskye Gory, 119992 Moscow, Russia
| | - Anton Sergeevich Shakhov
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 1–40, Leninskye Gory, 119992 Moscow, Russia
| | - Anatoly Alexeevich Kotlobay
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 1a Malaya Pirogovskaya St., 119435 Moscow, Russia
| | - Irina Borisovna Alieva
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 1–40, Leninskye Gory, 119992 Moscow, Russia
- Correspondence:
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32
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Kunizheva SS, Volobaev VP, Plotnikova MY, Kupriyanova DA, Kuznetsova IL, Tyazhelova TV, Rogaev EI. Current Trends and Approaches to the Search for Genetic Determinants of Aging and Longevity. RUSS J GENET+ 2022; 58:1427-1443. [PMID: 36590179 PMCID: PMC9794410 DOI: 10.1134/s1022795422120067] [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] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 07/06/2022] [Accepted: 07/07/2022] [Indexed: 12/29/2022]
Abstract
Aging is a natural process of extinction of the body and the main aspect that determines the life expectancy for individuals who have survived to the post-reproductive period. The process of aging is accompanied by certain physiological, immune, and metabolic changes in the body, as well as the development of age-related diseases. The contribution of genetic factors to human life expectancy is estimated at about 25-30%. Despite the success in identifying genes and metabolic pathways that may be involved in the life extension process in model organisms, the key question remains to what extent these data can be extrapolated to humans, for example, because of the complexity of its biological and sociocultural systems, as well as possible species differences in life expectancy and causes of mortality. New molecular genetic methods have significantly expanded the possibilities for searching for genetic factors of human life expectancy and identifying metabolic pathways of aging, the interaction of genes and transcription factors, the regulation of gene expression at the level of transcription, and epigenetic modifications. The review presents the latest research and current strategies for studying the genetic basis of human aging and longevity: the study of individual candidate genes in genetic population studies, variations identified by the GWAS method, immunogenetic differences in aging, and genomic studies to identify factors of "healthy aging." Understanding the mechanisms of the interaction between factors affecting the life expectancy and the possibility of their regulation can become the basis for developing comprehensive measures to achieve healthy longevity. Supplementary Information The online version contains supplementary material available at 10.1134/S1022795422120067.
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Affiliation(s)
- S. S. Kunizheva
- Center for Genetics and Life Sciences, Sirius University of Science and Technology, 354340 Sochi, Russia
- Moscow State University, 119234 Moscow, Russia
- Vavilov Institute of General Genetics, Russian Academy of Sciences, 119991 Moscow, Russia
| | - V. P. Volobaev
- Center for Genetics and Life Sciences, Sirius University of Science and Technology, 354340 Sochi, Russia
| | - M. Yu. Plotnikova
- Center for Genetics and Life Sciences, Sirius University of Science and Technology, 354340 Sochi, Russia
- Moscow State University, 119234 Moscow, Russia
| | - D. A. Kupriyanova
- Center for Genetics and Life Sciences, Sirius University of Science and Technology, 354340 Sochi, Russia
| | - I. L. Kuznetsova
- Center for Genetics and Life Sciences, Sirius University of Science and Technology, 354340 Sochi, Russia
- Vavilov Institute of General Genetics, Russian Academy of Sciences, 119991 Moscow, Russia
| | - T. V. Tyazhelova
- Vavilov Institute of General Genetics, Russian Academy of Sciences, 119991 Moscow, Russia
| | - E. I. Rogaev
- Center for Genetics and Life Sciences, Sirius University of Science and Technology, 354340 Sochi, Russia
- Moscow State University, 119234 Moscow, Russia
- Vavilov Institute of General Genetics, Russian Academy of Sciences, 119991 Moscow, Russia
- University of Massachusetts Chan Medical School, 01545 Shrewsbury, MA United States
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33
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Uc A, Strandvik B, Yao J, Liu X, Yi Y, Sun X, Welti R, Engelhardt JF, Norris AW. The fatty acid imbalance of cystic fibrosis exists at birth independent of feeding in pig and ferret models. Clin Sci (Lond) 2022; 136:1773-91. [PMID: 36416119 DOI: 10.1042/CS20220450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 11/18/2022] [Accepted: 11/22/2022] [Indexed: 11/24/2022]
Abstract
Persons with cystic fibrosis (CF) exhibit a unique alteration of fatty acid composition, marked especially among polyunsaturates by relative deficiency of linoleic acid and excess of Mead acid. Relative deficiency of docosahexaenoic acid is variably found. However, the initial development of these abnormalities is not understood. We examined fatty acid composition in young CF ferrets and pigs, finding abnormalities from the day of birth onward including relative deficiency of linoleic acid in both species. Fatty acid composition abnormalities were present in both liver and serum phospholipids of newborn CF piglets even prior to feeding, including reduced linoleic acid and increased Mead acid. Serum fatty acid composition evolved over the first weeks of life in both non-CF and CF ferrets, though differences between CF and non-CF persisted. Although red blood cell phospholipid fatty acid composition was normal in newborn animals, it became perturbed in juvenile CF ferrets including relative deficiencies of linoleic and docosahexaenoic acids and excess of Mead acid. In summary, fatty acid composition abnormalities in CF pigs and ferrets exist from a young age including at birth independent of feeding and overlap extensively with the abnormalities found in humans with CF. That the abnormalities exist prior to feeding implies that dietary measures alone will not address the mechanisms of imbalance.
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Puntin G, Sweet M, Fraune S, Medina M, Sharp K, Weis VM, Ziegler M. Harnessing the Power of Model Organisms To Unravel Microbial Functions in the Coral Holobiont. Microbiol Mol Biol Rev 2022; 86:e0005322. [PMID: 36287022 PMCID: PMC9769930 DOI: 10.1128/mmbr.00053-22] [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] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Stony corals build the framework of coral reefs, ecosystems of immense ecological and economic importance. The existence of these ecosystems is threatened by climate change and other anthropogenic stressors that manifest in microbial dysbiosis such as coral bleaching and disease, often leading to coral mortality. Despite a significant amount of research, the mechanisms ultimately underlying these destructive phenomena, and what could prevent or mitigate them, remain to be resolved. This is mostly due to practical challenges in experimentation on corals and the highly complex nature of the coral holobiont that also includes bacteria, archaea, protists, and viruses. While the overall importance of these partners is well recognized, their specific contributions to holobiont functioning and their interspecific dynamics remain largely unexplored. Here, we review the potential of adopting model organisms as more tractable systems to address these knowledge gaps. We draw on parallels from the broader biological and biomedical fields to guide the establishment, implementation, and integration of new and emerging model organisms with the aim of addressing the specific needs of coral research. We evaluate the cnidarian models Hydra, Aiptasia, Cassiopea, and Astrangia poculata; review the fast-evolving field of coral tissue and cell cultures; and propose a framework for the establishment of "true" tropical reef-building coral models. Based on this assessment, we also suggest future research to address key aspects limiting our ability to understand and hence improve the response of reef-building corals to future ocean conditions.
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Affiliation(s)
- Giulia Puntin
- Department of Animal Ecology and Systematics, Marine Holobiomics Lab, Justus Liebig University Giessen, Giessen, Germany
| | - Michael Sweet
- Aquatic Research Facility, Environmental Sustainability Research Centre, University of Derby, Derby, United Kingdom
| | - Sebastian Fraune
- Institute for Zoology and Organismic Interactions, Heinrich-Heine University Düsseldorf, Düsseldorf, Germany
| | - Mónica Medina
- Department of Biology, Pennsylvania State University, State College, Pennsylvania, USA
| | - Koty Sharp
- Department of Biology, Marine Biology, and Environmental Science, Roger Williams University, Bristol, Rhode Island, USA
| | - Virginia M. Weis
- Department of Integrative Biology, Oregon State University, Corvallis, Oregon, USA
| | - Maren Ziegler
- Department of Animal Ecology and Systematics, Marine Holobiomics Lab, Justus Liebig University Giessen, Giessen, Germany
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35
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Impellitteri F, Curpăn AS, Plăvan G, Ciobica A, Faggio C. Hemocytes: A Useful Tool for Assessing the Toxicity of Microplastics, Heavy Metals, and Pesticides on Aquatic Invertebrates. Int J Environ Res Public Health 2022; 19:16830. [PMID: 36554710 PMCID: PMC9779202 DOI: 10.3390/ijerph192416830] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2022] [Revised: 12/10/2022] [Accepted: 12/13/2022] [Indexed: 05/09/2023]
Abstract
Invertebrates have long been an important tool for assessing water pollution due to their characteristics as intermediate consumers in aquatic ecosystem food chains. Most of the time, the effects of contaminants are measured by their effect on oxidative status or by mortality, although there already exists an easier tool-hemocytes. Hemocytes are circulating cells with a very important role in the immune system of invertebrates, which can be found within the hemolymph, analogous to the blood in vertebrates. The collection of hemolymph samples is easy, fast, minimally invasive, and poses no danger to the life of invertebrates. The purpose of this review was to highlight the advantages of using hemolymph for toxicity assays of various substances, including heavy metals, micro- and nano-plastics, pesticides, hydrocarbons, and oil spills. A literature search was conducted for this purpose using the most common and most often used databases, with a focus on the most recent and relevant studies. Bivalve mollusks, crustaceans, and gastropods were chosen for this investigation. This review found a growing number of studies choosing to use hemolymph as the standard methodology for toxicology assays, confirming their qualities as reliable tools.
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Affiliation(s)
- Federica Impellitteri
- Department of Veterinary Sciences, Polo Universitario dell’Annunziata, University of Messina, 98168 Messina, Italy
| | - Alexandrina-Stefania Curpăn
- Department of Biology, Faculty of Biology, “Alexandru Ioan Cuza” University of Iasi, Carol I Avenue, 20A, 700505 Iasi, Romania
| | - Gabriel Plăvan
- Department of Biology, Faculty of Biology, “Alexandru Ioan Cuza” University of Iasi, Carol I Avenue, 20A, 700505 Iasi, Romania
| | - Alin Ciobica
- Department of Research, Faculty of Biology, “Alexandru Ioan Cuza” University of Iasi, Carol I Avenue, 20A, 700506 Iasi, Romania
| | - Caterina Faggio
- Department of Chemical, Biological, Pharmaceutical, and Environmental Sciences, University of Messina, Viale Ferdinando Stagno D’Alcontres 31, 98166 Messina, Italy
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36
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Jhu MY, Sinha NR. Cuscuta species: Model organisms for haustorium development in stem holoparasitic plants. Front Plant Sci 2022; 13:1086384. [PMID: 36578337 PMCID: PMC9792094 DOI: 10.3389/fpls.2022.1086384] [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] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 11/28/2022] [Indexed: 06/17/2023]
Abstract
Parasitic plants are notorious for causing serious agricultural losses in many countries. Specialized intrusive organs, haustoria, confer on parasitic plants the ability to acquire water and nutrients from their host plants. Investigating the mechanism involved in haustorium development not only reveals the fascinating mystery of how autotrophic plants evolved parasitism but also provides the foundation for developing more effective methods to control the agricultural damage caused by parasitic plants. Cuscuta species, also known as dodders, are one of the most well-known and widely spread stem holoparasitic plants. Although progress has been made recently in understanding the evolution and development of haustoria in root parasitic plants, more and more studies indicate that the behaviors between root and stem haustorium formation are distinct, and the mechanisms involved in the formation of these organs remain largely unknown. Unlike most endoparasites and root holoparasitic plants, which have high host-specificity and self- or kin-recognition to avoid forming haustoria on themselves or closely related species, auto-parasitism and hyper-parasitism are commonly observed among Cuscuta species. In this review, we summarize the current understanding of haustorium development in dodders and the unique characteristics of their parasitizing behaviors. We also outline the advantages of using Cuscuta species as model organisms for haustorium development in stem holoparasitic plants, the current unknown mysteries and limitations in the Cuscuta system, and potential future research directions to overcome these challenges.
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Affiliation(s)
- Min-Yao Jhu
- Crop Science Centre, Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | - Neelima R. Sinha
- Department of Plant Biology, University of California, Davis, CA, United States
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37
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May L, Bartolo B, Harrison D, Guzik T, Drummond G, Figtree G, Ritchie R, Rye KA, de Haan J. Translating atherosclerosis research from bench to bedside: navigating the barriers for effective preclinical drug discovery. Clin Sci (Lond) 2022; 136:1731-1758. [PMID: 36459456 PMCID: PMC9727216 DOI: 10.1042/cs20210862] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 10/21/2022] [Accepted: 11/04/2022] [Indexed: 08/10/2023]
Abstract
Cardiovascular disease (CVD) remains the leading cause of death worldwide. An ongoing challenge remains the development of novel pharmacotherapies to treat CVD, particularly atherosclerosis. Effective mechanism-informed development and translation of new drugs requires a deep understanding of the known and currently unknown biological mechanisms underpinning atherosclerosis, accompanied by optimization of traditional drug discovery approaches. Current animal models do not precisely recapitulate the pathobiology underpinning human CVD. Accordingly, a fundamental limitation in early-stage drug discovery has been the lack of consensus regarding an appropriate experimental in vivo model that can mimic human atherosclerosis. However, when coupled with a clear understanding of the specific advantages and limitations of the model employed, preclinical animal models remain a crucial component for evaluating pharmacological interventions. Within this perspective, we will provide an overview of the mechanisms and modalities of atherosclerotic drugs, including those in the preclinical and early clinical development stage. Additionally, we highlight recent preclinical models that have improved our understanding of atherosclerosis and associated clinical consequences and propose model adaptations to facilitate the development of new and effective treatments.
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Affiliation(s)
- Lauren T. May
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria 3052, Australia
| | | | - David G. Harrison
- Division of Clinical Pharmacology, Department of Medicine, Vanderbilt University Medical Center, Nashville TN, U.S.A
| | - Tomasz Guzik
- Institute of Cardiovascular and Medical Sciences, University of Glasgow, U.K
- Department of Medicine, Jagiellonian University Medical College, Krakow, Poland
| | - Grant R. Drummond
- Centre for Cardiovascular Biology and Disease Research, Department of Microbiology, Anatomy, Physiology and Pharmacology, La Trobe University, Melbourne, Victoria, Australia
| | - Gemma A. Figtree
- Kolling Research Institute, University of Sydney, Sydney, Australia
- Imaging and Phenotyping Laboratory, Charles Perkins Centre and Faculty of Medicine and Health, University of Sydney, Sydney, Australia
| | - Rebecca H. Ritchie
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia
| | - Kerry-Anne Rye
- Lipid Research Group, School of Medical Sciences, Faculty of Medicine, University of New South Wales, Sydney 2052, Australia
| | - Judy B. de Haan
- Cardiovascular Inflammation and Redox Biology Lab, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
- Department of Chemistry and Biotechnology, Swinburne University of Technology, Hawthorn, Victoria 3122, Australia
- Department Cardiometabolic Health, University of Melbourne, Parkville, Victoria 3010, Australia
- Department of Physiology, Anatomy and Microbiology, La Trobe University, Bundoora, Victoria 3086, Australia
- Department of Immunology and Pathology, Central Clinical School, Monash University, Melbourne, Victoria 3004, Australia
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38
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Auer JMT, Murphy LC, Xiao D, Li DU, Wheeler AP. Non-fitting FLIM-FRET facilitates analysis of protein interactions in live zebrafish embryos. J Microsc 2022. [PMID: 36448983 DOI: 10.1111/jmi.13162] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 11/18/2022] [Accepted: 11/21/2022] [Indexed: 12/05/2022]
Abstract
Molecular interactions are key to all cellular processes, and particularly interesting to investigate in the context of gene regulation. Protein-protein interactions are challenging to examine in vivo as they are dynamic, and require spatially and temporally resolved studies to interrogate them. Foerster Resonance Energy Transfer (FRET) is a highly sensitive imaging method, which can interrogate molecular interactions. FRET can be detected by Fluorescence Lifetime Imaging Microscopy (FLIM-FRET), which is more robust to concentration variations and photobleaching than intensity-based FRET but typically needs long acquisition times to achieve high photon counts. New variants of non-fitting lifetime-based FRET perform well in samples with lower signal and require less intensive instrument calibration and analysis, making these methods ideal for probing protein-protein interactions in more complex live 3D samples. Here we show that a non-fitting FLIM-FRET variant, based on the Average Arrival Time of photons per pixel (AAT- FRET), is a sensitive and simple way to detect and measure protein-protein interactions in live early stage zebrafish embryos.
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Affiliation(s)
- Julia M T Auer
- MRC Human Genetics Unit, Institute of Genetics and Cancer, The University of Edinburgh, Edinburgh, UK
| | - Laura C Murphy
- MRC Human Genetics Unit, Institute of Genetics and Cancer, The University of Edinburgh, Edinburgh, UK
| | - Dong Xiao
- Department of Biomedical Engineering, University of Strathclyde, Glasgow, UK
| | - David U Li
- Department of Biomedical Engineering, University of Strathclyde, Glasgow, UK
| | - Ann P Wheeler
- MRC Human Genetics Unit, Institute of Genetics and Cancer, The University of Edinburgh, Edinburgh, UK
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39
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Collins MN, Mesce KA. A review of the bioeffects of low-intensity focused ultrasound and the benefits of a cellular approach. Front Physiol 2022; 13:1047324. [PMID: 36439246 PMCID: PMC9685663 DOI: 10.3389/fphys.2022.1047324] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2022] [Accepted: 10/25/2022] [Indexed: 10/28/2023] Open
Abstract
This review article highlights the historical developments and current state of knowledge of an important neuromodulation technology: low-intensity focused ultrasound. Because compelling studies have shown that focused ultrasound can modulate neuronal activity non-invasively, especially in deep brain structures with high spatial specificity, there has been a renewed interest in attempting to understand the specific bioeffects of focused ultrasound at the cellular level. Such information is needed to facilitate the safe and effective use of focused ultrasound to treat a number of brain and nervous system disorders in humans. Unfortunately, to date, there appears to be no singular biological mechanism to account for the actions of focused ultrasound, and it is becoming increasingly clear that different types of nerve cells will respond to focused ultrasound differentially based on the complement of their ion channels, other membrane biophysical properties, and arrangement of synaptic connections. Furthermore, neurons are apparently not equally susceptible to the mechanical, thermal and cavitation-related consequences of focused ultrasound application-to complicate matters further, many studies often use distinctly different focused ultrasound stimulus parameters to achieve a reliable response in neural activity. In this review, we consider the benefits of studying more experimentally tractable invertebrate preparations, with an emphasis on the medicinal leech, where neurons can be studied as unique individual cells and be synaptically isolated from the indirect effects of focused ultrasound stimulation on mechanosensitive afferents. In the leech, we have concluded that heat is the primary effector of focused ultrasound neuromodulation, especially on motoneurons in which we observed a focused ultrasound-mediated blockade of action potentials. We discuss that the mechanical bioeffects of focused ultrasound, which are frequently described in the literature, are less reliably achieved as compared to thermal ones, and that observations ascribed to mechanical responses may be confounded by activation of synaptically-coupled sensory structures or artifacts associated with electrode resonance. Ultimately, both the mechanical and thermal components of focused ultrasound have significant potential to contribute to the sculpting of specific neural outcomes. Because focused ultrasound can generate significant modulation at a temperature <5°C, which is believed to be safe for moderate durations, we support the idea that focused ultrasound should be considered as a thermal neuromodulation technology for clinical use, especially targeting neural pathways in the peripheral nervous system.
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Affiliation(s)
- Morgan N. Collins
- Graduate Program in Neuroscience, University of Minnesota, Saint Paul, MN, United States
| | - Karen A. Mesce
- Department of Entomology and Graduate Program in Neuroscience, University of Minnesota, Saint Paul, MN, United States
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40
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Sukhikh IS, Biryukov MY, Blinov AG. [Transgenesis in Worms: Candidates for an Ideal Model]. Mol Biol (Mosk) 2022; 56:983-989. [PMID: 36475483 DOI: 10.31857/s0026898422060210] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 06/28/2022] [Indexed: 12/13/2022]
Abstract
Transgenesis is an important and often irreplaceable method to study numerous processes of animal life. To create animal transgenic lines, it is necessary to have a suitable model organism that has necessary traits for efficient and affordable transgenesis. The concise review characterizes the existing model organisms of different taxa for which an efficient transgenesis protocol has been developed. Special attention is paid to flatworms and, in particular, Macrostomum lignano as a promising model organism for studying aging, regeneration, and carcinogenesis.
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Affiliation(s)
- I S Sukhikh
- Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, Novosibirsk, 630090 Russia.,
| | - M Yu Biryukov
- Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, Novosibirsk, 630090 Russia
| | - A G Blinov
- Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, Novosibirsk, 630090 Russia.,blinov @bionet.nsc.ru
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Abstract
Laser-induced hypertension in nonhuman primates is used to mimic human glaucoma, the leading cause of irreversible blindness. In this protocol, we detail steps for laser-induced ocular hypertension in nonhuman primates by laser photocoagulation of the trabecular meshwork and subsequent intracameral injection. We further describe recording and evaluation of intraocular pressure changes and peripapillary retinal nerve fiber layer thickness. This protocol can assist researchers improve the success rate and repeatability of the procedure and reduce the number of nonhuman primates needed. For complete details on the use and execution of this protocol, please refer to Sun et al. (2022). Detailed description for general and ophthalmological examination before experiment Protocol to generate laser-induced chronic ocular hypertension in rhesus monkeys Laser photocoagulation of the trabecular meshwork followed by intracameral injection Approach is highly reproducible and offers a tool to test potential treatment strategies
Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics.
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Affiliation(s)
- Difang Sun
- Eye Institute of Shandong First Medical University, Qingdao Eye Hospital of Shandong First Medical University, State Key Laboratory Cultivation Base, Shandong Provincial Key Laboratory of Ophthalmology, School of Ophthalmology, Shandong First Medical University, Qingdao 266071, China,Department of Ophthalmology, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, China,Corresponding author
| | - Bin Wang
- Department of Sports Medicine, The Affiliated Hospital of Qingdao University, Qingdao 266003, China
| | - Zhenlan Yang
- Department of Ophthalmology, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, China
| | - Zongyi Zhan
- Department of Ophthalmology, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, China,Corresponding author
| | - Jun Li
- Eye Institute of Shandong First Medical University, Qingdao Eye Hospital of Shandong First Medical University, State Key Laboratory Cultivation Base, Shandong Provincial Key Laboratory of Ophthalmology, School of Ophthalmology, Shandong First Medical University, Qingdao 266071, China,Corresponding author
| | - Yuqing Lan
- Department of Ophthalmology, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, China,Corresponding author
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42
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Onorato G, Fardella F, Lewinska A, Gobbo F, Tommasini G, Wnuk M, Tino A, Moros M, Antognazza MR, Tortiglione C. Optical Control of Tissue Regeneration through Photostimulation of Organic Semiconducting Nanoparticles. Adv Healthc Mater 2022; 11:e2200366. [PMID: 35861262 DOI: 10.1002/adhm.202200366] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 07/04/2022] [Indexed: 01/27/2023]
Abstract
Next generation bioengineering strives to identify crucial cues that trigger regeneration of damaged tissues, and to control the cells that execute these programs with biomaterials and devices. Molecular and biophysical mechanisms driving embryogenesis may inspire novel tools to reactivate developmental programs in situ. Here nanoparticles based on conjugated polymers are employed for optical control of regenerating tissues by using an animal with unlimited regenerative potential, the polyp Hydra, as in vivo model, and human keratinocytes as an in vitro model to investigate skin repair. By integrating animal, cellular, molecular, and biochemical approaches, nanoparticles based on poly-3-hexylthiophene (P3HT) are shown able to enhance regeneration kinetics, stem cell proliferation, and biomolecule oxidation levels. Opposite outputs are obtained with PCPDTBT-NPs (Poly[2,6-(4,4-bis-(2-ethylhexyl)-4H-cyclopenta [2,1-b;3,4-b'] dithiophene)-alt-4,7(2,1,3-benzothiadiazole)], causing a beneficial effect on Hydra regeneration but not on the migratory capability of keratinocytes. These results suggest that the artificial modulation of the redox potential in injured tissues may represent a powerful modality to control their regenerative potential. Importantly, the possibility to fine-tuning materials' photocatalytic efficiency may enable a biphasic modulation over a wide dynamic range, which can be exploited to augment the tissue regenerative capacity or inhibit the unlimited potential of cancerous cells in pathological contexts.
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Affiliation(s)
- Giada Onorato
- Istituto di Scienze Applicate e Sistemi Intelligenti "E. Caianiello", Consiglio Nazionale delle Ricerche, Via Campi Flegrei 34, Pozzuoli, 80078, Italy.,Institute of Biosciences and Bioresources, National Research Council, Via Pietro Castellino 111, Napoli, Italy
| | - Federica Fardella
- Istituto di Scienze Applicate e Sistemi Intelligenti "E. Caianiello", Consiglio Nazionale delle Ricerche, Via Campi Flegrei 34, Pozzuoli, 80078, Italy.,Instituto de Nanociencia y Materiales de Aragón, C/Mariano Esquillor 15, Zaragoza, 50018, Spain
| | - Anna Lewinska
- Department of Biotechnology, Institute of Biology and Biotechnology, Faculty of Biotechnology, University of Rzeszow, Pigonia 1, Rzeszow, 35-310, Poland
| | - Federico Gobbo
- Center for Nano Science and Technology @PoliMi, Istituto Italiano di Tecnologia, Via Pascoli 70/3, Milano, 20133, Italy.,Politecnico di Milano, Dip. di Fisica, P.zza L. Da Vinci 32, Milano, 20133, Italy
| | - Giuseppina Tommasini
- Istituto di Scienze Applicate e Sistemi Intelligenti "E. Caianiello", Consiglio Nazionale delle Ricerche, Via Campi Flegrei 34, Pozzuoli, 80078, Italy.,Instituto de Nanociencia y Materiales de Aragón, C/Mariano Esquillor 15, Zaragoza, 50018, Spain
| | - Maciej Wnuk
- Department of Biology, Faculty of Biotechnology, University of Rzeszow, Pigonia 1, Rzeszow, 35-310, Poland
| | - Angela Tino
- Istituto di Scienze Applicate e Sistemi Intelligenti "E. Caianiello", Consiglio Nazionale delle Ricerche, Via Campi Flegrei 34, Pozzuoli, 80078, Italy
| | - Maria Moros
- Instituto de Nanociencia y Materiales de Aragón, C/Mariano Esquillor 15, Zaragoza, 50018, Spain
| | - Maria Rosa Antognazza
- Center for Nano Science and Technology @PoliMi, Istituto Italiano di Tecnologia, Via Pascoli 70/3, Milano, 20133, Italy
| | - Claudia Tortiglione
- Istituto di Scienze Applicate e Sistemi Intelligenti "E. Caianiello", Consiglio Nazionale delle Ricerche, Via Campi Flegrei 34, Pozzuoli, 80078, Italy
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Schröter L, Ventura N. Nanoplastic Toxicity: Insights and Challenges from Experimental Model Systems. Small 2022; 18:e2201680. [PMID: 35810458 DOI: 10.1002/smll.202201680] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 05/05/2022] [Indexed: 06/15/2023]
Abstract
Nanoplastic particles (NPs) can be produced or derived from the degradation of several daily used products and can therefore be found in the air, water, and food. Every day, these microscopic particles are confronted by different routes of exposure. Recent investigations have shown the internalization of these particles, differing in size and modification, in vivo in aquatic organisms and terrestrial organisms, as well as in vitro in different human cell lines. During the last years, the number of studies investigating the effects of NPs using widely different model systems and experimental approaches is exponentially growing, thus providing information about NPs, especially about polystyrene particle toxicity on health. To facilitate the grasping of the most relevant information, an overview is provided on the toxic effects of NPs coming from studies in cellular systems and in vivo in model organisms and on aspects which can be of particular relevance for particle toxicity (e.g., particle internalization mechanisms and structural modifications). Major achievements and gaps in the field as well as the point of view on how more systematic studies and exploitation of in vivo model organisms may improve the knowledge on important aspects of NPs are also pointed out.
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Affiliation(s)
- Laura Schröter
- IUF-Leibniz Institute for Environmental Medicine at the Heinrich Heine University Düsseldorf, Auf'm Hennekamp 50, 40225, Düsseldorf, Germany
| | - Natascia Ventura
- Institute of Clinical Chemistry and Laboratory Diagnostic, Heinrich Heine University Düsseldorf, Moorenstr 5, 40225, Düsseldorf, Germany
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44
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Masocha VF, Liu H, Zhan P, Wang K, Zeng A, Shen S, Schneider H. Bacterial Microbiome in the Phyllo-Endosphere of Highly Specialized Rock Spleenwort. Front Plant Sci 2022; 13:891155. [PMID: 35874023 PMCID: PMC9302946 DOI: 10.3389/fpls.2022.891155] [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] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 05/30/2022] [Indexed: 06/15/2023]
Abstract
Bacteria communities associated with plants have been given increasing consideration because they are arguably beneficial to their host plants. To understand the ecological and evolutionary impact of these mutualistic associations, it is important to explore the vast unknown territory of bacterial genomic diversity and their functional contributions associated with the major branches of the tree-of-life. Arguably, this aim can be achieved by profiling bacterial communities by applying high throughput sequencing approaches, besides establishing model plant organisms to test key predictions. This study utilized the Illumina Miseq reads of bacterial 16S rRNA sequences to determine the bacterial diversity associated with the endosphere of the leaves of the highly specialized rock spleenwort Asplenium delavayi (Aspleniaceae). By documenting the bacterial communities associated with ferns collected in natural occurrence and cultivation, this study discovered the most species-rich bacterial communities associated with terrestrial ferns reported until now. Despite the substantial variations of species diversity and composition among accessions, a set of 28 bacterial OTUs was found to be shared among all accessions. Functional analyses recovered evidence to support the predictions that changes in bacterial community compositions correspond to functional differentiation. Given the ease of cultivating this species, Asplenium delavayi is introduced here as a model organism to explore the ecological and evolutionary benefits created by mutualistic associations between bacteria and ferns.
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Affiliation(s)
- Valerie F. Masocha
- Centre for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Beijing, China
| | - Hongmei Liu
- Centre for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Beijing, China
| | - Pingshan Zhan
- Centre for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Beijing, China
| | - Kaikai Wang
- Centre for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Ao Zeng
- School of Biological and Chemical Sciences, Pu’er University, Pu’er, China
| | - Sike Shen
- Centre for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Harald Schneider
- Centre for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Beijing, China
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45
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Nano PR, Bhaduri A. Evaluation of advances in cortical development using model systems. Dev Neurobiol 2022; 82:408-427. [PMID: 35644985 PMCID: PMC10924780 DOI: 10.1002/dneu.22879] [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: 01/05/2022] [Revised: 04/26/2022] [Accepted: 04/30/2022] [Indexed: 11/11/2022]
Abstract
Compared with that of even the closest primates, the human cortex displays a high degree of specialization and expansion that largely emerges developmentally. Although decades of research in the mouse and other model systems has revealed core tenets of cortical development that are well preserved across mammalian species, small deviations in transcription factor expression, novel cell types in primates and/or humans, and unique cortical architecture distinguish the human cortex. Importantly, many of the genes and signaling pathways thought to drive human-specific cortical expansion also leave the brain vulnerable to disease, as the misregulation of these factors is highly correlated with neurodevelopmental and neuropsychiatric disorders. However, creating a comprehensive understanding of human-specific cognition and disease remains challenging. Here, we review key stages of cortical development and highlight known or possible differences between model systems and the developing human brain. By identifying the developmental trajectories that may facilitate uniquely human traits, we highlight open questions in need of approaches to examine these processes in a human context and reveal translatable insights into human developmental disorders.
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Affiliation(s)
- Patricia R Nano
- Department of Biological Chemistry, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, USA
| | - Aparna Bhaduri
- Department of Biological Chemistry, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, USA
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46
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Harnish JM, Li L, Rogic S, Poirier-Morency G, Kim SY, Boycott KM, Wangler MF, Bellen HJ, Hieter P, Pavlidis P, Liu Z, Yamamoto S. ModelMatcher: A scientist-centric online platform to facilitate collaborations between stakeholders of rare and undiagnosed disease research. Hum Mutat 2022; 43:743-759. [PMID: 35224820 PMCID: PMC9133126 DOI: 10.1002/humu.24364] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [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: 09/30/2021] [Revised: 02/12/2022] [Accepted: 02/23/2022] [Indexed: 11/08/2022]
Abstract
Next-generation sequencing is a prevalent diagnostic tool for undiagnosed diseases and has played a significant role in rare disease gene discovery. Although this technology resolves some cases, others are given a list of possibly damaging genetic variants necessitating functional studies. Productive collaborations between scientists, clinicians, and patients (affected individuals) can help resolve such medical mysteries and provide insights into in vivo function of human genes. Furthermore, facilitating interactions between scientists and research funders, including nonprofit organizations or commercial entities, can dramatically reduce the time to translate discoveries from bench to bedside. Several systems designed to connect clinicians and researchers with a shared gene of interest have been successful. However, these platforms exclude some stakeholders based on their role or geography. Here we describe ModelMatcher, a global online matchmaking tool designed to facilitate cross-disciplinary collaborations, especially between scientists and other stakeholders of rare and undiagnosed disease research. ModelMatcher is integrated into the Rare Diseases Models and Mechanisms Network and Matchmaker Exchange, allowing users to identify potential collaborators in other registries. This living database decreases the time from when a scientist or clinician is making discoveries regarding their genes of interest, to when they identify collaborators and sponsors to facilitate translational and therapeutic research.
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Affiliation(s)
- J. Michael Harnish
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX, 77030, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital (TCH), Houston, TX, 77030, USA
| | - Lucian Li
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital (TCH), Houston, TX, 77030, USA
- Department of Pediatrics, Division of Neurology and Developmental Neuroscience, BCM, Houston, TX, 77030, USA
| | - Sanja Rogic
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T1Z4, Canada
- Department of Psychiatry, University of British Columbia, Vancouver, BC V6T1Z4, Canada
| | - Guillaume Poirier-Morency
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T1Z4, Canada
- Department of Psychiatry, University of British Columbia, Vancouver, BC V6T1Z4, Canada
| | - Seon-Young Kim
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital (TCH), Houston, TX, 77030, USA
- Department of Pediatrics, Division of Neurology and Developmental Neuroscience, BCM, Houston, TX, 77030, USA
| | | | - Kym M. Boycott
- Children’s Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON K1H8L1, Canada
| | - Michael F. Wangler
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX, 77030, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital (TCH), Houston, TX, 77030, USA
- Development, Disease Models & Therapeutics Graduate Program, BCM, Houston, TX, 77030, USA
| | - Hugo J. Bellen
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX, 77030, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital (TCH), Houston, TX, 77030, USA
- Development, Disease Models & Therapeutics Graduate Program, BCM, Houston, TX, 77030, USA
- Department of Neuroscience, BCM, Houston, TX, 77030, USA
| | - Philip Hieter
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T1Z4, Canada
| | - Paul Pavlidis
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T1Z4, Canada
- Department of Psychiatry, University of British Columbia, Vancouver, BC V6T1Z4, Canada
| | - Zhandong Liu
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital (TCH), Houston, TX, 77030, USA
- Department of Pediatrics, Division of Neurology and Developmental Neuroscience, BCM, Houston, TX, 77030, USA
- Quantitative and Computational Biosciences Graduate Program, BCM, Houston, TX, 77030, USA
| | - Shinya Yamamoto
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX, 77030, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital (TCH), Houston, TX, 77030, USA
- Development, Disease Models & Therapeutics Graduate Program, BCM, Houston, TX, 77030, USA
- Department of Neuroscience, BCM, Houston, TX, 77030, USA
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47
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Powers N, Huang GN. Visualization of regenerating and repairing hearts. Clin Sci (Lond) 2022; 136:787-98. [PMID: 35621122 DOI: 10.1042/CS20211116] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 05/03/2022] [Accepted: 05/05/2022] [Indexed: 02/01/2023]
Abstract
With heart failure continuing to become more prevalent, investigating the mechanisms of heart injury and repair holds much incentive. In contrast with adult mammals, other organisms such as teleost fish, urodele amphibians, and even neonatal mammals are capable of robust cardiac regeneration to replenish lost or damaged myocardial tissue. Long-term high-resolution intravital imaging of the behaviors and interactions of different cardiac cell types in their native environment could yield unprecedented insights into heart regeneration and repair. However, this task remains challenging for the heart due to its rhythmic contraction and anatomical location. Here, we summarize recent advances in live imaging of heart regeneration and repair, discuss the advantages and limitations of current systems, and suggest future directions for novel imaging technology development.
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48
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Swart Z, Duong TA, Wingfield BD, Postma A, Slippers B. The relevance of studying insect-nematode interactions for human disease. Pathog Glob Health 2022; 116:140-145. [PMID: 34726122 PMCID: PMC9090338 DOI: 10.1080/20477724.2021.1996796] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
Abstract
Vertebrate-parasitic nematodes cause debilitating, chronic infections in millions of people worldwide. The burden of these so-called 'neglected tropical diseases' is often carried by poorer socioeconomic communities in part because research on parasitic nematodes and their vertebrate hosts is challenging and costly. However, complex biological and pathological processes can be modeled in simpler organisms. Here, we consider how insight into the interactions between entomopathogenic nematodes (EPN), their insect hosts and bacterial symbionts may reveal novel treatment targets for parasitic nematode infections. We argue that a combination of approaches that target nematodes, as well as the interaction of pathogens with insect vectors and bacterial symbionts, offer potentially effective, but underexplored opportunities.
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Affiliation(s)
- Zorada Swart
- Department of Biochemistry Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, South Africa
| | - Tuan A. Duong
- Department of Biochemistry Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, South Africa
| | - Brenda D. Wingfield
- Department of Biochemistry Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, South Africa
| | - Alisa Postma
- Department of Biochemistry Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, South Africa
| | - Bernard Slippers
- Department of Biochemistry Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, South Africa
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49
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Haynes EM, Ulland TK, Eliceiri KW. A Model of Discovery: The Role of Imaging Established and Emerging Non-mammalian Models in Neuroscience. Front Mol Neurosci 2022; 15:867010. [PMID: 35493325 PMCID: PMC9046975 DOI: 10.3389/fnmol.2022.867010] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 03/18/2022] [Indexed: 11/24/2022] Open
Abstract
Rodents have been the dominant animal models in neurobiology and neurological disease research over the past 60 years. The prevalent use of rats and mice in neuroscience research has been driven by several key attributes including their organ physiology being more similar to humans, the availability of a broad variety of behavioral tests and genetic tools, and widely accessible reagents. However, despite the many advances in understanding neurobiology that have been achieved using rodent models, there remain key limitations in the questions that can be addressed in these and other mammalian models. In particular, in vivo imaging in mammals at the cell-resolution level remains technically difficult and demands large investments in time and cost. The simpler nervous systems of many non-mammalian models allow for precise mapping of circuits and even the whole brain with impressive subcellular resolution. The types of non-mammalian neuroscience models available spans vertebrates and non-vertebrates, so that an appropriate model for most cell biological questions in neurodegenerative disease likely exists. A push to diversify the models used in neuroscience research could help address current gaps in knowledge, complement existing rodent-based bodies of work, and bring new insight into our understanding of human disease. Moreover, there are inherent aspects of many non-mammalian models such as lifespan and tissue transparency that can make them specifically advantageous for neuroscience studies. Crispr/Cas9 gene editing and decreased cost of genome sequencing combined with advances in optical microscopy enhances the utility of new animal models to address specific questions. This review seeks to synthesize current knowledge of established and emerging non-mammalian model organisms with advances in cellular-resolution in vivo imaging techniques to suggest new approaches to understand neurodegeneration and neurobiological processes. We will summarize current tools and in vivo imaging approaches at the single cell scale that could help lead to increased consideration of non-mammalian models in neuroscience research.
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Affiliation(s)
- Elizabeth M. Haynes
- Morgridge Institute for Research, Madison, WI, United States
- Center for Quantitative Cell Imaging, University of Wisconsin-Madison, Madison, WI, United States
| | - Tyler K. Ulland
- Department of Pathology, University of Wisconsin-Madison, Madison, WI, United States
| | - Kevin W. Eliceiri
- Morgridge Institute for Research, Madison, WI, United States
- Center for Quantitative Cell Imaging, University of Wisconsin-Madison, Madison, WI, United States
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, WI, United States
- Department of Medical Physics, University of Wisconsin-Madison, Madison, WI, United States
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Son M, Kim DY, Kim CH. Disease Modeling of Rare Neurological Disorders in Zebrafish. Int J Mol Sci 2022; 23:3946. [PMID: 35409306 DOI: 10.3390/ijms23073946] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Revised: 03/31/2022] [Accepted: 03/31/2022] [Indexed: 02/06/2023] Open
Abstract
Rare diseases are those which affect a small number of people compared to the general population. However, many patients with a rare disease remain undiagnosed, and a large majority of rare diseases still have no form of viable treatment. Approximately 40% of rare diseases include neurologic and neurodevelopmental disorders. In order to understand the characteristics of rare neurological disorders and identify causative genes, various model organisms have been utilized extensively. In this review, the characteristics of model organisms, such as roundworms, fruit flies, and zebrafish, are examined, with an emphasis on zebrafish disease modeling in rare neurological disorders.
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