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Insights into the Structures, Inhibitors, and Improvement Strategies of Glucose Oxidase. Int J Mol Sci 2022; 23:ijms23179841. [PMID: 36077243 PMCID: PMC9456440 DOI: 10.3390/ijms23179841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2022] [Revised: 08/18/2022] [Accepted: 08/26/2022] [Indexed: 11/17/2022] Open
Abstract
Glucose oxidase, which uses molecular oxygen as an electron acceptor to specifically catalyze the conversion of β-d-glucose to gluconic acid and hydrogen peroxide (H2O2), has been considered an important enzyme in increasing environmental sustainability and food security. However, achieving the high yield, low price and high activity required for commercial viability remains challenging. In this review, we first present a brief introduction, looking at the sources, characteristics, catalytic process, and applications of glucose oxidase. Then, the predictive structures of glucose oxidase from two different sources are comparatively discussed. We summarize the inhibitors of glucose oxidase. Finally, we highlight how the production of glucose oxidase can be improved by optimizing the culture conditions and microbial metabolic engineering.
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Abstract
For many years, the laboratory mouse has been the favored model organism to study mammalian development, biology and disease. Among its advantages for these studies are its close concordance with human biology, the syntenic relationship between the mouse and other mammalian genomes, the existence of many inbred strains, its short gestation period, its relatively low cost for housing and husbandry, and the wide array of tools for genome modification, mutagenesis, and for cryopreserving embryos, sperm and eggs. The advent of CRISPR genome modification techniques has considerably broadened the landscape of model organisms available for study, including other mammalian species. However, the mouse remains the most popular and utilized system to model human development, biology, and disease processes. In this review, we will briefly summarize the long history of mice as a preferred mammalian genetic and model system, and review current large-scale mutagenesis efforts using genome modification to produce improved models for mammalian development and disease.
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Affiliation(s)
- Thomas Gridley
- Center for Clinical and Translational Research, Maine Medical Center Research Institute, Scarborough, ME, United States.
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3
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Li QV, Rosen BP, Huangfu D. Decoding pluripotency: Genetic screens to interrogate the acquisition, maintenance, and exit of pluripotency. WILEY INTERDISCIPLINARY REVIEWS. SYSTEMS BIOLOGY AND MEDICINE 2020; 12:e1464. [PMID: 31407519 PMCID: PMC6898739 DOI: 10.1002/wsbm.1464] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Revised: 05/31/2019] [Accepted: 07/17/2019] [Indexed: 01/25/2023]
Abstract
Pluripotent stem cells have the ability to unlimitedly self-renew and differentiate to any somatic cell lineage. A number of systems biology approaches have been used to define this pluripotent state. Complementary to systems level characterization, genetic screens offer a unique avenue to functionally interrogate the pluripotent state and identify the key players in pluripotency acquisition and maintenance, exit of pluripotency, and lineage differentiation. Here we review how genetic screens have helped us decode pluripotency regulation. We will summarize results from RNA interference (RNAi) based screens, discuss recent advances in CRISPR/Cas-based genetic perturbation methods, and how these advances have made it possible to more comprehensively interrogate pluripotency and differentiation through genetic screens. Such investigations will not only provide a better understanding of this unique developmental state, but may enhance our ability to use pluripotent stem cells as an experimental model to study human development and disease progression. Functional interrogation of pluripotency also provides a valuable roadmap for utilizing genetic perturbation to gain systems level understanding of additional cellular states, from later stages of development to pathological disease states. This article is categorized under: Developmental Biology > Stem Cell Biology and Regeneration Developmental Biology > Developmental Processes in Health and Disease Biological Mechanisms > Cell Fates.
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Affiliation(s)
- Qing V. Li
- Sloan Kettering Institute, 1275 York Avenue, New York, New York 10065, USA
- Louis V. Gerstner Jr. Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, New York 10065, USA
- These authors contributed equally
| | - Bess P. Rosen
- Sloan Kettering Institute, 1275 York Avenue, New York, New York 10065, USA
- Weill Graduate School of Medical Sciences at Cornell University, 1300 York Avenue, New York, New York 10065, USA
- These authors contributed equally
| | - Danwei Huangfu
- Sloan Kettering Institute, 1275 York Avenue, New York, New York 10065, USA
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4
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Mouse models and strain-dependency of Chédiak-Higashi syndrome-associated neurologic dysfunction. Sci Rep 2019; 9:6752. [PMID: 31043676 PMCID: PMC6494809 DOI: 10.1038/s41598-019-42159-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Accepted: 03/18/2019] [Indexed: 12/20/2022] Open
Abstract
Chédiak-Higashi syndrome (CHS) is a lethal disorder caused by mutations in the LYST gene that involves progressive neurologic dysfunction. Lyst-mutant mice exhibit neurologic phenotypes that are sensitive to genetic background. On the DBA/2J-, but not on the C57BL/6J-background, Lyst-mutant mice exhibit overt tremor phenotypes associated with loss of cerebellar Purkinje cells. Here, we tested whether assays for ataxia could measure this observed strain-dependency, and if so, establish parameters for empowering phenotype- and candidate-driven approaches to identify genetic modifier(s). A composite phenotypic scoring system distinguished phenotypes in Lyst-mutants and uncovered a previously unrecognized background difference between wild-type C57BL/6J and DBA/2J mice. Accelerating rotarod performance also distinguished phenotypes in Lyst-mutants, but at more advanced ages. These results establish that genetic background, Lyst genotype, and age significantly influence the severity of CHS-associated neurologic deficits. Purkinje cell quantifications likewise distinguished phenotypes of Lyst-mutant mice, as well as background differences between wild-type C57BL/6J and DBA/2J mice. To aid identification of potential genetic modifier genes causing these effects, we searched public datasets for cerebellar-expressed genes that are differentially expressed and/or contain potentially detrimental genetic variants. From these approaches, Nos1, Prdx2, Cbln3, Gnb1, Pttg1 were confirmed to be differentially expressed and leading candidates.
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Jain D, Puno MR, Meydan C, Lailler N, Mason CE, Lima CD, Anderson KV, Keeney S. ketu mutant mice uncover an essential meiotic function for the ancient RNA helicase YTHDC2. eLife 2018; 7:30919. [PMID: 29360036 PMCID: PMC5832417 DOI: 10.7554/elife.30919] [Citation(s) in RCA: 113] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Accepted: 01/22/2018] [Indexed: 02/06/2023] Open
Abstract
Mechanisms regulating mammalian meiotic progression are poorly understood. Here we identify mouse YTHDC2 as a critical component. A screen yielded a sterile mutant, ‘ketu’, caused by a Ythdc2 missense mutation. Mutant germ cells enter meiosis but proceed prematurely to aberrant metaphase and apoptosis, and display defects in transitioning from spermatogonial to meiotic gene expression programs. ketu phenocopies mutants lacking MEIOC, a YTHDC2 partner. Consistent with roles in post-transcriptional regulation, YTHDC2 is cytoplasmic, has 3′→5′ RNA helicase activity in vitro, and has similarity within its YTH domain to an N6-methyladenosine recognition pocket. Orthologs are present throughout metazoans, but are diverged in nematodes and, more dramatically, Drosophilidae, where Bgcn is descended from a Ythdc2 gene duplication. We also uncover similarity between MEIOC and Bam, a Bgcn partner unique to schizophoran flies. We propose that regulation of gene expression by YTHDC2-MEIOC is an evolutionarily ancient strategy for controlling the germline transition into meiosis.
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Affiliation(s)
- Devanshi Jain
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, United States
| | - M Rhyan Puno
- Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, United States.,Howard Hughes Medical Institute, Memorial Sloan Kettering Cancer Center, New York, United States
| | - Cem Meydan
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, United States.,The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, United States
| | - Nathalie Lailler
- Integrated Genomics Operation, Memorial Sloan Kettering Cancer Center, New York, United States
| | - Christopher E Mason
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, United States.,The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, United States.,The Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, United States
| | - Christopher D Lima
- Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, United States.,Howard Hughes Medical Institute, Memorial Sloan Kettering Cancer Center, New York, United States
| | - Kathryn V Anderson
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, United States
| | - Scott Keeney
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, United States.,Howard Hughes Medical Institute, Memorial Sloan Kettering Cancer Center, New York, United States
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6
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Meyer KJ, Anderson MG. Genetic modifiers as relevant biological variables of eye disorders. Hum Mol Genet 2017; 26:R58-R67. [PMID: 28482014 DOI: 10.1093/hmg/ddx180] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Accepted: 05/05/2017] [Indexed: 12/19/2022] Open
Abstract
From early in the study of mammalian genetics, it was clear that modifiers can have a striking influence on phenotypes. Today, several modifiers have now been studied in enough detail to allow a glimpse of how they function and influence our perspective of disease. With respect to diseases of the eye, some modifiers are an important source of phenotypic variation that can elucidate how genes function in networks to collectively shape ocular anatomy and physiology, thus influencing our understanding of basic biology. Other modifiers represent an opportunity for new therapeutic targets, whose manipulation could be used to mitigate ophthalmic disease. Here, we review progress in the study of genetic modifiers of eye disorders, with examples from mice and humans that together illustrate the ubiquitous nature of genetic modifiers and why they are relevant biological variables in experimental design. Special emphasis is given to ophthalmic modifiers in mice, especially those relevant to selection of genetic background and those that might inadvertently be a source of experimental variability. These modifiers are capable of influencing interpretations of many experiments using targeted genome manipulations such as knockouts or transgenics. Whereas there are fewer examples of modifiers of eye disorders in humans with a molecular identification, there is ample evidence that they exist and should be considered as a relevant biological variable in human genetic studies as well.
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Affiliation(s)
- Kacie J Meyer
- Department of Molecular Physiology and Biophysics.,Stephen A. Wynn Institute for Vision Research, University of Iowa, Iowa City, IA 52242, USA
| | - Michael G Anderson
- Department of Molecular Physiology and Biophysics.,Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA.,Stephen A. Wynn Institute for Vision Research, University of Iowa, Iowa City, IA 52242, USA.,Center for Prevention and Treatment of Visual Loss, Iowa City Veterans Administration Medical Center, Iowa City, IA 52242, USA
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Jain D, Meydan C, Lange J, Claeys Bouuaert C, Lailler N, Mason CE, Anderson KV, Keeney S. rahu is a mutant allele of Dnmt3c, encoding a DNA methyltransferase homolog required for meiosis and transposon repression in the mouse male germline. PLoS Genet 2017; 13:e1006964. [PMID: 28854222 PMCID: PMC5607212 DOI: 10.1371/journal.pgen.1006964] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Revised: 09/20/2017] [Accepted: 08/07/2017] [Indexed: 12/30/2022] Open
Abstract
Transcriptional silencing by heritable cytosine-5 methylation is an ancient strategy to repress transposable elements. It was previously thought that mammals possess four DNA methyltransferase paralogs-Dnmt1, Dnmt3a, Dnmt3b and Dnmt3l-that establish and maintain cytosine-5 methylation. Here we identify a fifth paralog, Dnmt3c, that is essential for retrotransposon methylation and repression in the mouse male germline. From a phenotype-based forward genetics screen, we isolated a mutant mouse called 'rahu', which displays severe defects in double-strand-break repair and homologous chromosome synapsis during male meiosis, resulting in sterility. rahu is an allele of a transcription unit (Gm14490, renamed Dnmt3c) that was previously mis-annotated as a Dnmt3-family pseudogene. Dnmt3c encodes a cytosine methyltransferase homolog, and Dnmt3crahu mutants harbor a non-synonymous mutation of a conserved residue within one of its cytosine methyltransferase motifs, similar to a mutation in human DNMT3B observed in patients with immunodeficiency, centromeric instability and facial anomalies syndrome. The rahu mutation lies at a potential dimerization interface and near the potential DNA binding interface, suggesting that it compromises protein-protein and/or protein-DNA interactions required for normal DNMT3C function. Dnmt3crahu mutant males fail to establish normal methylation within LINE and LTR retrotransposon sequences in the germline and accumulate higher levels of transposon-derived transcripts and proteins, particularly from distinct L1 and ERVK retrotransposon families. Phylogenetic analysis indicates that Dnmt3c arose during rodent evolution by tandem duplication of Dnmt3b, after the divergence of the Dipodoidea and Muroidea superfamilies. These findings provide insight into the evolutionary dynamics and functional specialization of the transposon suppression machinery critical for mammalian sexual reproduction and epigenetic regulation.
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Affiliation(s)
- Devanshi Jain
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, United States of America
| | - Cem Meydan
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, United States of America
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College, New York, United States of America
| | - Julian Lange
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, United States of America
- Howard Hughes Medical Institute, Memorial Sloan Kettering Cancer Center, New York, United States of America
| | - Corentin Claeys Bouuaert
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, United States of America
- Howard Hughes Medical Institute, Memorial Sloan Kettering Cancer Center, New York, United States of America
| | - Nathalie Lailler
- Integrated Genomics Operation, Memorial Sloan Kettering Cancer Center, New York, United States of America
| | - Christopher E. Mason
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, United States of America
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College, New York, United States of America
- The Feil Family Brain and Mind Research Institute, Weill Cornell Medical College, New York, United States of America
| | - Kathryn V. Anderson
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, United States of America
| | - Scott Keeney
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, United States of America
- Howard Hughes Medical Institute, Memorial Sloan Kettering Cancer Center, New York, United States of America
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8
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Feng W, Choi I, Clouthier DE, Niswander L, Williams T. The Ptch1(DL) mouse: a new model to study lambdoid craniosynostosis and basal cell nevus syndrome-associated skeletal defects. Genesis 2013; 51:677-89. [PMID: 23897749 DOI: 10.1002/dvg.22416] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2013] [Accepted: 07/16/2013] [Indexed: 12/19/2022]
Abstract
Mouse models provide valuable opportunities for probing the underlying pathology of human birth defects. By using an N-ethyl-N-nitrosourea-based screen for recessive mutations affecting craniofacial anatomy, we isolated a mouse strain, Dogface-like (DL), with abnormal skull and snout morphology. Examination of the skull indicated that these mice developed craniosynostosis of the lambdoid suture. Further analysis revealed skeletal defects related to the pathology of basal cell nevus syndrome (BCNS) including defects in development of the limbs, scapula, ribcage, secondary palate, cranial base, and cranial vault. In humans, BCNS is often associated with mutations in the Hedgehog receptor PTCH1 and genetic mapping in DL identified a point mutation at a splice donor site in Ptch1. By using genetic complementation analysis we determined that DL is a hypomorphic allele of Ptch1, leading to increased Hedgehog signaling. Two aberrant transcripts are generated by the mutated Ptch1(DL) gene, which would be predicted to reduce significantly the levels of functional Patched1 protein. This new Ptch1 allele broadens the mouse genetic reagents available to study the Hedgehog pathway and provides a valuable means to study the underlying skeletal abnormalities in BCNS. In addition, these results strengthen the connection between elevated Hedgehog signaling and craniosynostosis.
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Affiliation(s)
- Weiguo Feng
- Department of Craniofacial Biology and Cell and Developmental Biology, University of Colorado Anschutz Medical Campus, Aurora, Colorado
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Multiplex Chromosomal Exome Sequencing Accelerates Identification of ENU-Induced Mutations in the Mouse. G3-GENES GENOMES GENETICS 2012; 2:143-50. [PMID: 22384391 PMCID: PMC3276189 DOI: 10.1534/g3.111.001669] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2011] [Accepted: 11/21/2011] [Indexed: 12/22/2022]
Abstract
Forward genetic screens in Mus musculus have proved powerfully informative by revealing unsuspected mechanisms governing basic biological processes. This approach uses potent chemical mutagens, such as N-ethyl-N-nitrosourea (ENU), to randomly induce mutations in mice, which are then bred and phenotypically screened to identify lines that disrupt a specific biological process of interest. Although identifying a mutation using the rich resources of mouse genetics is straightforward, it is unfortunately neither fast nor cheap. Here we show that detecting newly induced causal variants in a forward genetic screen can be accelerated dramatically using a methodology that combines multiplex chromosome-specific exome capture, next-generation sequencing, rapid mapping, sequence annotation, and variation filtering. The key innovation of our method is multiplex capture and sequence that allows the simultaneous survey of both mutant, parental, and background strains in a single experiment. By comparing variants identified in mutant offspring with those found in dbSNP, the unmutagenized background strains, and parental lines, induced causative mutations can be distinguished immediately from preexisting variation or experimental artifact. Here we demonstrate this approach to find the causative mutations induced in four novel ENU lines identified from a recent ENU screen. In all four cases, after applying our method, we found six or fewer putative mutations (and sometimes only a single one). Determining the causative variant was then easily achieved through standard segregation approaches. We have developed this process into a community resource that will speed up individual labs’ ability to identify the genetic lesion in mutant mouse lines; all of our reagents and software tools are open source and available to the broader scientific community.
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Lois C, Groves JO. Genetics in non-genetic model systems. Curr Opin Neurobiol 2011; 22:79-85. [PMID: 22119141 DOI: 10.1016/j.conb.2011.11.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2011] [Revised: 10/31/2011] [Accepted: 11/01/2011] [Indexed: 01/29/2023]
Abstract
The past few decades have seen the field of genetic engineering evolve at a rapid pace, with neuroscientists now equipped with a wide range of tools for the manipulation of an animal's genome in order to study brain function. However, the number of species to which these technologies have been applied, namely the fruit fly, C. elegans, zebrafish and mouse, remains relatively few. This review will discuss the variety of approaches to genetic modification that have been developed in such traditional 'genetic systems', and highlight the progress that has been made to translate these technologies to alternative species such as rats, monkeys and birds, where certain neurobiological questions may be better studied.
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Affiliation(s)
- Carlos Lois
- Department of Neurobiology, University of Massachusetts Medical School, Worcester, 364 Plantation Street, MA 01655, USA.
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11
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Foldi CJ, Eyles DW, Flatscher-Bader T, McGrath JJ, Burne THJ. New perspectives on rodent models of advanced paternal age: relevance to autism. Front Behav Neurosci 2011; 5:32. [PMID: 21734873 PMCID: PMC3124931 DOI: 10.3389/fnbeh.2011.00032] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2011] [Accepted: 06/14/2011] [Indexed: 12/29/2022] Open
Abstract
Offspring of older fathers have an increased risk of various adverse health outcomes, including autism and schizophrenia. With respect to biological mechanisms for this association, there are many more germline cell divisions in the life history of a sperm relative to that of an oocyte. This leads to more opportunities for copy error mutations in germ cells from older fathers. Evidence also suggests that epigenetic patterning in the sperm from older men is altered. Rodent models provide an experimental platform to examine the association between paternal age and brain development. Several rodent models of advanced paternal age (APA) have been published with relevance to intermediate phenotypes related to autism. All four published APA models vary in key features creating a lack of consistency with respect to behavioral phenotypes. A consideration of common phenotypes that emerge from these APA-related mouse models may be informative in the exploration of the molecular and neurobiological correlates of APA.
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Affiliation(s)
- Claire J Foldi
- Queensland Brain Institute, The University of Queensland St Lucia, QLD, Australia
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12
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Foldi CJ, Eyles DW, McGrath JJ, Burne THJ. Advanced paternal age is associated with alterations in discrete behavioural domains and cortical neuroanatomy of C57BL/6J mice. Eur J Neurosci 2010; 31:556-64. [DOI: 10.1111/j.1460-9568.2010.07074.x] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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13
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Goetz SC, Ocbina PJR, Anderson KV. The primary cilium as a Hedgehog signal transduction machine. Methods Cell Biol 2009; 94:199-222. [PMID: 20362092 DOI: 10.1016/s0091-679x(08)94010-3] [Citation(s) in RCA: 128] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
The Hedgehog (Hh) signal transduction pathway is essential for the development and patterning of numerous organ systems, and has important roles in a variety of human cancers. Genetic screens for mouse embryonic patterning mutants first showed a connection between mammalian Hh signaling and intraflagellar transport (IFT), a process required for construction of the primary cilium, a small cellular projection found on most vertebrate cells. Additional genetic and cell biological studies have provided very strong evidence that mammalian Hh signaling depends on the primary cilium. Here, we review the evidence that defines the integral roles that IFT proteins and cilia play in the regulation of the Hh signal transduction pathway in vertebrates. We discuss the mechanisms that control localization of Hh pathway proteins to the cilium, focusing on the transmembrane protein Smoothened (Smo), which moves into the cilium in response to Hh ligand. The phenotypes caused by loss of cilia-associated proteins are complex, which suggests that cilia and IFT play active roles in mediating Hh signaling rather than serving simply as a compartment in which pathway components are concentrated. Hh signaling in Drosophila does not depend on cilia, but there appear to be ancient links between cilia and components of the Hh pathway that may reveal how this fundamental difference between the Drosophila and mammalian Hh pathways arose in evolution.
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Affiliation(s)
- Sarah C Goetz
- Developmental Biology Program, Sloan-Kettering Institute, 1275 York Avenue, New York, New York 10065, USA
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14
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Khokha MK, Krylov V, Reilly MJ, Gall JG, Bhattacharya D, Cheung CYJ, Kaufman S, Lam DK, Macha J, Ngo C, Prakash N, Schmidt P, Tlapakova T, Trivedi T, Tumova L, Abu-Daya A, Geach T, Vendrell E, Ironfield H, Sinzelle L, Sater AK, Wells DE, Harland RM, Zimmerman LB. Rapid gynogenetic mapping of Xenopus tropicalis mutations to chromosomes. Dev Dyn 2009; 238:1398-46. [PMID: 19441086 DOI: 10.1002/dvdy.21965] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
Pilot forward genetic screens in Xenopus tropicalis have isolated over 60 recessive mutations. Here we present a simple method for mapping mutations to chromosomes using gynogenesis and centromeric markers. When coupled with available genomic resources, gross mapping facilitates evaluation of candidate genes as well as higher resolution linkage studies. Using gynogenesis, we have mapped the genetic locations of the 10 X. tropicalis centromeres, and performed fluorescence in situ hybridization to validate these locations cytologically. We demonstrate the use of this very small set of centromeric markers to map mutations efficiently to specific chromosomes. Developmental Dynamics 238:1398-1406, 2009. (c) 2009 Wiley-Liss, Inc.
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Affiliation(s)
- Mustafa K Khokha
- Department of Pediatrics and Genetics, Yale University School of Medicine, New Haven, Connecticut, USA
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15
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Abstract
Neural tube defects (NTDs) are among the most common structural birth defects observed in humans. Mouse models provide an excellent experimental system to study the underlying causes of NTDs. These models not only allow for identification of the genes required for neurulation, they provide tractable systems for uncovering the developmental, pathological and molecular mechanisms underlying NTDs. In addition, mouse models are essential for elucidating the mechanisms of gene-environment and gene-gene interactions that contribute to the multifactorial inheritance of NTDs. In some cases these studies have led to development of approaches to prevent NTDs and provide an understanding of the underlying molecular mechanism of these therapies prevent NTDs.
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Affiliation(s)
- Irene E Zohn
- Children's Research Institute, Children's National Medical Center, Washington, DC, USA
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16
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Saha S, Barnett AG, Foldi C, Burne TH, Eyles DW, Buka SL, McGrath JJ. Advanced paternal age is associated with impaired neurocognitive outcomes during infancy and childhood. PLoS Med 2009; 6:e40. [PMID: 19278291 PMCID: PMC2653549 DOI: 10.1371/journal.pmed.1000040] [Citation(s) in RCA: 134] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/08/2008] [Accepted: 01/15/2009] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Advanced paternal age (APA) is associated with an increased risk of neurodevelopmental disorders such as autism and schizophrenia, as well as with dyslexia and reduced intelligence. The aim of this study was to examine the relationship between paternal age and performance on neurocognitive measures during infancy and childhood. METHODS AND FINDINGS A sample of singleton children (n = 33,437) was drawn from the US Collaborative Perinatal Project. The outcome measures were assessed at 8 mo, 4 y, and 7 y (Bayley scales, Stanford Binet Intelligence Scale, Graham-Ernhart Block Sort Test, Wechsler Intelligence Scale for Children, Wide Range Achievement Test). The main analyses examined the relationship between neurocognitive measures and paternal or maternal age when adjusted for potential confounding factors. Advanced paternal age showed significant associations with poorer scores on all of the neurocognitive measures apart from the Bayley Motor score. The findings were broadly consistent in direction and effect size at all three ages. In contrast, advanced maternal age was generally associated with better scores on these same measures. CONCLUSIONS The offspring of older fathers show subtle impairments on tests of neurocognitive ability during infancy and childhood. In light of secular trends related to delayed fatherhood, the clinical implications and the mechanisms underlying these findings warrant closer scrutiny.
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Affiliation(s)
- Sukanta Saha
- Queensland Centre for Mental Health Research, The Park Centre for Mental Health, Richlands, Australia
| | - Adrian G Barnett
- Institute of Health and Biomedical Innovation and School of Public Health, Queensland University of Technology, Kelvin Grove, Australia
| | - Claire Foldi
- Queensland Brain Institute, The University of Queensland, St. Lucia, Australia
| | - Thomas H Burne
- Queensland Centre for Mental Health Research, The Park Centre for Mental Health, Richlands, Australia
- Queensland Brain Institute, The University of Queensland, St. Lucia, Australia
| | - Darryl W Eyles
- Queensland Centre for Mental Health Research, The Park Centre for Mental Health, Richlands, Australia
- Queensland Brain Institute, The University of Queensland, St. Lucia, Australia
| | - Stephen L Buka
- Department of Community Health, Brown University, Providence, Rhode Island, United States of America
| | - John J McGrath
- Queensland Centre for Mental Health Research, The Park Centre for Mental Health, Richlands, Australia
- Queensland Brain Institute, The University of Queensland, St. Lucia, Australia
- Department of Psychiatry, The University of Queensland, St. Lucia, Australia
- * To whom correspondence should be addressed. E-mail:
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Patterson VL, Damrau C, Paudyal A, Reeve B, Grimes DT, Stewart ME, Williams DJ, Siggers P, Greenfield A, Murdoch JN. Mouse hitchhiker mutants have spina bifida, dorso-ventral patterning defects and polydactyly: identification of Tulp3 as a novel negative regulator of the Sonic hedgehog pathway. Hum Mol Genet 2009; 18:1719-39. [PMID: 19223390 PMCID: PMC2671985 DOI: 10.1093/hmg/ddp075] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
The mammalian Sonic hedgehog (Shh) signalling pathway is essential for embryonic development and the patterning of multiple organs. Disruption or activation of Shh signalling leads to multiple birth defects, including holoprosencephaly, neural tube defects and polydactyly, and in adults results in tumours of the skin or central nervous system. Genetic approaches with model organisms continue to identify novel components of the pathway, including key molecules that function as positive or negative regulators of Shh signalling. Data presented here define Tulp3 as a novel negative regulator of the Shh pathway. We have identified a new mouse mutant that is a strongly hypomorphic allele of Tulp3 and which exhibits expansion of ventral markers in the caudal spinal cord, as well as neural tube defects and preaxial polydactyly, consistent with increased Shh signalling. We demonstrate that Tulp3 acts genetically downstream of Shh and Smoothened (Smo) in neural tube patterning and exhibits a genetic interaction with Gli3 in limb development. We show that Tulp3 does not appear to alter expression or processing of Gli3, and we demonstrate that transcriptional regulation of other negative regulators (Rab23, Fkbp8, Thm1, Sufu and PKA) is not affected. We discuss the possible mechanism of action of Tulp3 in Shh-mediated signalling in light of these new data.
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Affiliation(s)
- Victoria L Patterson
- Mammalian Genetics Unit, MRC Harwell, Harwell Science and Innovation Campus, Oxon, UK
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Simpson F, Kerr MC, Wicking C. Trafficking, development and hedgehog. Mech Dev 2009; 126:279-88. [PMID: 19368798 DOI: 10.1016/j.mod.2009.01.007] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2007] [Revised: 01/22/2009] [Accepted: 01/26/2009] [Indexed: 11/27/2022]
Abstract
Embryogenesis is mediated by a relatively small number of developmental signaling pathways, and the morphogens, receptors and transcription factors integral to these cascades are considered the master regulators of development. However, superimposed on this is an additional layer of control by complex intracellular trafficking networks. The importance of trafficking in controlling the processes of morphogenesis and development is highlighted by recent data regarding the transport and localisation of the morphogen sonic hedgehog (Shh) and the machinery that leads to its secretion, modification, cellular internalisation and signal transduction. Here we review the regulation of hedgehog signaling by intracellular trafficking, including the role of the primary cilium and lipids in mediating pathway activity.
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Affiliation(s)
- Fiona Simpson
- The University of Queensland, Institute for Molecular Bioscience, Qld, Australia
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Aigner B, Rathkolb B, Herbach N, Hrabé de Angelis M, Wanke R, Wolf E. Diabetes models by screen for hyperglycemia in phenotype-driven ENU mouse mutagenesis projects. Am J Physiol Endocrinol Metab 2008; 294:E232-40. [PMID: 18056790 DOI: 10.1152/ajpendo.00592.2007] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
More than 150 million people suffer from diabetes mellitus worldwide, and this number is expected to rise substantially within the next decades. Despite its high prevalence, the pathogenesis of diabetes mellitus is not completely understood. Therefore, appropriate experimental models are essential tools to gain more insight into the genetics and pathogenesis of the disease. Here, we describe the current efforts to establish novel diabetes models derived from unbiased, phenotype-driven, large-scale N-ethyl-N-nitrosourea (ENU) mouse mutagenesis projects started a decade ago using hyperglycemia as a high-throughput screen parameter. Mouse lines were established according to their hyperglycemia phenotype over several generations, thereby revealing a mutation as cause for the aberrant phenotype. Chromosomal assignment of the causative mutation and subsequent candidate gene analysis led to the detection of the mutations that resulted in novel alleles of genes already known to be involved in glucose homeostasis, like glucokinase, insulin 2, and insulin receptor. Additional ENU-induced hyperglycemia lines are under genetic analysis. Improvements in screen for diabetic animals are implemented to detect more subtle phenotypes. Moreover, diet challenge assays are being employed to uncover interactions between genetic and environmental factors in the pathogenesis of diabetes mellitus. The new mouse mutants recovered in phenotype-driven ENU mouse mutagenesis projects complement the available models generated by targeted mutagenesis of candidate genes, all together providing the large resource of models required for a systematic dissection of the pathogenesis of diabetes mellitus.
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Affiliation(s)
- Bernhard Aigner
- Institute of Molecular Animal Breeding and Biotechnology, Hackerstrasse 27, Oberschleissheim, Germany.
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Persson J, Vance RE. Genetics-squared: combining host and pathogen genetics in the analysis of innate immunity and bacterial virulence. Immunogenetics 2007; 59:761-78. [PMID: 17874090 DOI: 10.1007/s00251-007-0248-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2007] [Accepted: 08/20/2007] [Indexed: 12/16/2022]
Abstract
The interaction of bacterial pathogens with their hosts' innate immune systems can be extremely complex and is often difficult to disentangle experimentally. Using mouse models of bacterial infections, several laboratories have successfully applied genetic approaches to identify novel host genes required for innate immune defense. In addition, a variety of creative bacterial genetic schemes have been developed to identify key bacterial genes involved in triggering or evading host immunity. In cases where both the host and pathogen are amenable to genetic manipulation, a combination of host and pathogen genetic approaches can be used. Focusing on bacterial infections of mice, this review summarizes the benefits and limitations of applying genetic analysis to the study of host-pathogen interactions. In particular, we consider how prokaryotic and eukaryotic genetic strategies can be combined, or "squared," to yield new insights in host-pathogen biology.
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Mutational pattern and frequency of induced nucleotide changes in mouse ENU mutagenesis. BMC Mol Biol 2007; 8:52. [PMID: 17584492 PMCID: PMC1914352 DOI: 10.1186/1471-2199-8-52] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2006] [Accepted: 06/20/2007] [Indexed: 11/16/2022] Open
Abstract
Background With the advent of sequence-based approaches in the mutagenesis studies, it is now possible to directly evaluate the genome-wide pattern of experimentally induced DNA sequence changes for a diverse array of organisms. To gain a more comprehensive understanding of the mutational bias inherent in mouse ENU mutagenesis, this study describes a detailed evaluation of the induced mutational pattern obtained from a sequence-based screen of ENU-mutagenized mice. Results Based on a large-scale screening data, we derive the sequence-based estimates of the nucleotide-specific pattern and frequency of ENU-induced base replacement mutation in the mouse germline, which are then combined with the pattern of codon usage in the mouse coding sequences to infer the spectrum of amino acid changes obtained by ENU mutagenesis. We detect a statistically significant difference between the mutational patterns in phenotype- versus sequence-based screens, which presumably reflects differential phenotypic effects caused by different amino acid replacements. We also demonstrate that the mutations exhibit strong strand asymmetry, and that this imbalance is generated by transcription, most likely as a by-product of transcription-coupled DNA repair in the germline. Conclusion The results clearly illustrate the biased nature of ENU-induced mutations. We expect that a precise understanding of the mutational pattern and frequency of induced nucleotide changes would be of practical importance when designing sequence-based screening strategies to generate mutant mouse strains harboring amino acid variants at specific loci. More generally, by enhancing the collection of experimentally induced mutations in unambiguously defined genomic regions, sequence-based mutagenesis studies will further illuminate the molecular basis of mutagenic and repair mechanisms that preferentially produce a certain class of mutational changes over others.
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Handrigan GR, Buchtová M, Richman JM. Gene discovery in craniofacial development and disease--cashing in your chips. Clin Genet 2007; 71:109-19. [PMID: 17250659 DOI: 10.1111/j.1399-0004.2007.00761.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
An unbiased, polygenic approach is needed to unravel the complex molecular bases of craniofacial development and disease. DNA microarrays, the current paradigm of genome-wide analysis, permit the simultaneous study of many thousands of genes, the ready identification of candidate molecules and pathways, and the compilation of gene expression profiles for whole systems--pathologic and embryonic alike. We survey the existing literature applying microarrays to craniofacial biology and highlight the value of animal models, particularly mice and chickens, to understanding molecular regulation in the craniofacial complex. We also emphasize the importance of functional studies and high-throughput assays to extracting useful data from microarray output. It is our goal to help put researchers and clinicians on the same page as microarray technology moves into the forefront of craniofacial biology.
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Affiliation(s)
- G R Handrigan
- Department of Oral Health Sciences, Life Sciences Institute, University of British Columbia, Vancouver, B.C., Canada
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