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Lin C, Shan Y, Wang Z, Peng H, Li R, Wang P, He J, Shen W, Wu Z, Guo M. Molecular and circuit mechanisms underlying avoidance of rapid cooling stimuli in C. elegans. Nat Commun 2024; 15:297. [PMID: 38182628 PMCID: PMC10770330 DOI: 10.1038/s41467-023-44638-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Accepted: 12/21/2023] [Indexed: 01/07/2024] Open
Abstract
The mechanisms by which animals respond to rapid changes in temperature are largely unknown. Here, we found that polymodal ASH sensory neurons mediate rapid cooling-evoked avoidance behavior within the physiological temperature range in C. elegans. ASH employs multiple parallel circuits that consist of stimulatory circuits (AIZ, RIA, AVA) and disinhibitory circuits (AIB, RIM) to respond to rapid cooling. In the stimulatory circuit, AIZ, which is activated by ASH, releases glutamate to act on both GLR-3 and GLR-6 receptors in RIA neurons to promote reversal, and ASH also directly or indirectly stimulates AVA to promote reversal. In the disinhibitory circuit, AIB is stimulated by ASH through the GLR-1 receptor, releasing glutamate to act on AVR-14 to suppress RIM activity. RIM, an inter/motor neuron, inhibits rapid cooling-evoked reversal, and the loop activities thus equally stimulate reversal. Our findings elucidate the molecular and circuit mechanisms underlying the acute temperature stimuli-evoked avoidance behavior.
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Affiliation(s)
- Chenxi Lin
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
- College of Biomedicine and Health, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yuxin Shan
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
- College of Biomedicine and Health, Huazhong Agricultural University, Wuhan, 430070, China
| | - Zhongyi Wang
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
- College of Biomedicine and Health, Huazhong Agricultural University, Wuhan, 430070, China
| | - Hui Peng
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Rong Li
- Key Laboratory of Molecular Biophysics of Ministry of Education, Institute of Biophysics and Biochemistry, and Department of Biophysics and Molecular Physiology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Pingzhou Wang
- Key Laboratory of Molecular Biophysics of Ministry of Education, Institute of Biophysics and Biochemistry, and Department of Biophysics and Molecular Physiology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Junyan He
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Weiwei Shen
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Zhengxing Wu
- Key Laboratory of Molecular Biophysics of Ministry of Education, Institute of Biophysics and Biochemistry, and Department of Biophysics and Molecular Physiology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Min Guo
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China.
- College of Biomedicine and Health, Huazhong Agricultural University, Wuhan, 430070, China.
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Arellano Spadaro J, Hishida Y, Matsunaga Y, van Es‐Remers M, Korthout H, Kim HK, Poppelaars E, Keizer H, Iliopoulou E, van Duijn B, Wildwater M, van Rijnberk L. 3'sialyllactose and 6'sialyllactose enhance performance in endurance-type exercise through metabolic adaptation. Food Sci Nutr 2023; 11:6199-6212. [PMID: 37823127 PMCID: PMC10563706 DOI: 10.1002/fsn3.3559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 05/31/2023] [Accepted: 06/30/2023] [Indexed: 10/13/2023] Open
Abstract
Human milk oligosaccharides (HMOs) belong to a group of multifunctional glycans that are abundantly present in human breast milk. While health effects of neutral oligosaccharides have been investigated extensively, a lot remains unknown regarding health effects of acidic oligosaccharides, such as the two sialyllactoses (SLs), 3'sialyllactose (3'SL), and 6'sialyllactose (6'SL). We utilized Caenorhabditis elegans (C. elegans) to investigate the effects of SLs on exercise performance. Using swimming as an endurance-type exercise, we found that SLs decrease exhaustion, signifying an increase in endurance that is strongest for 6'SL. Through an unbiased metabolomics approach, we identified changes in energy metabolism that correlated with endurance performance. Further investigation suggested that these metabolic changes were related to adaptations of muscle mitochondria that facilitated a shift from beta oxidation to glycogenolysis during exercise. We found that the effect of SLs on endurance performance required AMPK- (aak-1/aak-2) and adenosine receptor (ador-1) signaling. We propose a model where SLs alter the metabolic status in the gut, causing a signal from the intestine to the nervous system toward muscle cells, where metabolic adaptation increases exercise performance. Together, our results underline the potential of SLs in exercise-associated health and contribute to our understanding of the molecular processes involved in nutritionally-induced health benefits.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Bert van Duijn
- Fytagoras B.V.LeidenThe Netherlands
- Institute Biology LeidenLeiden UniversityLeidenThe Netherlands
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3
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Yoshiyama KO, Okamoto NL, Hidema J, Higashitani A. 222 nm far-UVC efficiently introduces nerve damage in Caenorhabditis elegans. PLoS One 2023; 18:e0281162. [PMID: 36719882 PMCID: PMC9888708 DOI: 10.1371/journal.pone.0281162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 01/16/2023] [Indexed: 02/01/2023] Open
Abstract
Far-ultraviolet radiation C light (far-UVC; 222 nm wavelength) has received attention as a safer light for killing pathogenic bacteria and viruses, as no or little DNA damage is observed after irradiation in mammalian skin models. Far-UVC does not penetrate deeply into tissues; therefore, it cannot reach the underlying critical basal cells. However, it was unclear whether far-UVC (222-UVC) irradiation could cause more biological damage at shallower depths than the 254 nm UVC irradiation (254-UVC), which penetrates more deeply. This study investigated the biological effects of 222- and 254-UVC on the small and transparent model organism Caenorhabditis elegans. At the same energy level of irradiation, 222-UVC introduced slightly less cyclobutane pyrimidine dimer damage to naked DNA in solution than 254-UVC. The survival of eggs laid during 0-4 h after irradiation showed a marked decrease with 254-UVC but not 222-UVC. In addition, defect of chromosomal condensation was observed in a full-grown oocyte by 254-UVC irradiation. In contrast, 222-UVC had a significant effect on the loss of motility of C. elegans. The sensory nervous system, which includes dopamine CEP and PVD neurons on the body surface, was severely damaged by 222-UVC, but not by the same dose of 254-UVC. Interestingly, increasing 254-UVC irradiation by about 10-fold causes similar damage to CEP neurons. These results suggest that 222-UVC is less penetrating, so energy transfer occurs more effectively in tissues near the surface, causing more severe damage than 254-UVC.
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Affiliation(s)
| | | | - Jun Hidema
- Graduate School of Life Sciences, Tohoku University, Sendai, Japan
- Division for the Establishment of Frontier Sciences of the Organization for Advanced Studies, Tohoku University, Sendai, Japan
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4
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Cao D. Reverse complementary matches simultaneously promote both back-splicing and exon-skipping. BMC Genomics 2021; 22:586. [PMID: 34344317 PMCID: PMC8330042 DOI: 10.1186/s12864-021-07910-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 07/23/2021] [Indexed: 12/24/2022] Open
Abstract
Background Circular RNAs (circRNAs) play diverse roles in different biological and physiological environments and are always expressed in a tissue-specific manner. Especially, circRNAs are enriched in the brain tissues of almost all investigated species, including humans, mice, Drosophila, etc. Although circRNAs were found in C. elegans, the neuron-specific circRNA data is not available yet. Exon-skipping is found to be correlated to circRNA formation, but the mechanisms that link them together are not clear. Results Here, through large-scale neuron isolation from the first larval (L1) stage of C. elegans followed by RNA sequencing with ribosomal RNA depletion, the neuronal circRNA data in C. elegans were obtained. Hundreds of novel circRNAs were annotated with high accuracy. circRNAs were highly expressed in the neurons of C. elegans and were positively correlated to the levels of their cognate linear mRNAs. Disruption of reverse complementary match (RCM) sequences in circRNA flanking introns effectively abolished circRNA formation. In the zip-2 gene, deletion of either upstream or downstream RCMs almost eliminated the production of both the circular and the skipped transcript. Interestingly, the 13-nt RCM in zip-2 is highly conserved across five nematode ortholog genes, which show conserved exon-skipping patterns. Finally, through in vivo one-by-one mutagenesis of all the splicing sites and branch points required for exon-skipping and back-splicing in the zip-2 gene, I showed that back-splicing still happened without exon-skipping, and vice versa. Conclusions Through protocol optimization, total RNA obtained from sorted neurons is increased to hundreds of nanograms. circRNAs highly expressed in the neurons of C. elegans are more likely to be derived from genes also highly expressed in the neurons. RCMs are abundant in circRNA flanking introns, and RCM-deletion is an efficient way to knockout circRNAs. More importantly, these RCMs are not only required for back-splicing but also promote the skipping of exon(s) to be circularized. Finally, RCMs in circRNA flanking introns can directly promote both exon-skipping and back-splicing, providing a new explanation for the correlation between them. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07910-w.
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Affiliation(s)
- Dong Cao
- Information Processing Biology Unit, Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna, Kunigami, 904-0495, Okinawa, Japan.
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Rogers AK, Phillips CM. RNAi pathways repress reprogramming of C. elegans germ cells during heat stress. Nucleic Acids Res 2020; 48:4256-4273. [PMID: 32187370 PMCID: PMC7192617 DOI: 10.1093/nar/gkaa174] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Revised: 03/02/2020] [Accepted: 03/10/2020] [Indexed: 01/08/2023] Open
Abstract
Repression of cellular reprogramming in germ cells is critical to maintaining cell fate and fertility. When germ cells mis-express somatic genes they can be directly converted into other cell types, resulting in loss of totipotency and reproductive potential. Identifying the molecular mechanisms that coordinate these cell fate decisions is an active area of investigation. Here we show that RNAi pathways play a key role in maintaining germline gene expression and totipotency after heat stress. By examining transcriptional changes that occur in mut-16 mutants, lacking a key protein in the RNAi pathway, at elevated temperature we found that genes normally expressed in the soma are mis-expressed in germ cells. Furthermore, these genes displayed increased chromatin accessibility in the germlines of mut-16 mutants at elevated temperature. These findings indicate that the RNAi pathway plays a key role in preventing aberrant expression of somatic genes in the germline during heat stress. This regulation occurs in part through the maintenance of germline chromatin, likely acting through the nuclear RNAi pathway. Identification of new pathways governing germ cell reprogramming is critical to understanding how cells maintain proper gene expression and may provide key insights into how cell identity is lost in some germ cell tumors.
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Affiliation(s)
- Alicia K Rogers
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Carolyn M Phillips
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
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6
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Sundararajan L, Stern J, Miller DM. Mechanisms that regulate morphogenesis of a highly branched neuron in C. elegans. Dev Biol 2019; 451:53-67. [PMID: 31004567 DOI: 10.1016/j.ydbio.2019.04.002] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 03/09/2019] [Accepted: 04/05/2019] [Indexed: 02/08/2023]
Abstract
The shape of an individual neuron is linked to its function with axons sending signals to other cells and dendrites receiving them. Although much is known of the mechanisms for axonal outgrowth, the striking complexity of dendritic architecture has hindered efforts to uncover pathways that direct dendritic branching. Here we review the results of an experimental strategy that exploits the power of genetic analysis and live cell imaging of the PVD sensory neuron in C. elegans to reveal key molecular drivers of dendrite morphogenesis.
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Affiliation(s)
- Lakshmi Sundararajan
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN 37240, USA
| | - Jamie Stern
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN 37240, USA
| | - David M Miller
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN 37240, USA.
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7
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A conserved neuronal DAF-16/FoxO plays an important role in conveying pheromone signals to elicit repulsion behavior in Caenorhabditis elegans. Sci Rep 2017; 7:7260. [PMID: 28775361 PMCID: PMC5543152 DOI: 10.1038/s41598-017-07313-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Accepted: 06/27/2017] [Indexed: 01/09/2023] Open
Abstract
Animals use pheromones as a conspecific chemical language to respond appropriately to environmental changes. The soil nematode Caenorhabditis elegans secretes ascaroside pheromones throughout the lifecycle, which influences entry into dauer phase in early larvae, in addition to sexual attraction and aggregation. In adult hermaphrodites, pheromone sensory signals perceived by worms usually elicit repulsion as an initial behavioral signature. However, the molecular mechanisms underlying neuronal pheromone sensory process from perception to repulsion in adult hermaphrodites remain poorly understood. Here, we show that pheromone signals perceived by GPA-3 is conveyed through glutamatergic neurotransmission in which neuronal DAF-16/FoxO plays an important modulatory role by controlling glutaminase gene expression. We further provide evidence that this modulatory role for DAF-16/FoxO seems to be conserved evolutionarily by electro-physiological study in mouse primary hippocampal neurons that are responsible for glutamatergic neurotransmission. These findings provide the basis for understanding the nematode pheromone signaling, which seems crucial for adaptation of adult hermaphrodites to changes in environmental condition for survival.
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8
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Angeles-Albores D, N Lee RY, Chan J, Sternberg PW. Tissue enrichment analysis for C. elegans genomics. BMC Bioinformatics 2016; 17:366. [PMID: 27618863 PMCID: PMC5020436 DOI: 10.1186/s12859-016-1229-9] [Citation(s) in RCA: 105] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2016] [Accepted: 08/26/2016] [Indexed: 01/04/2023] Open
Abstract
Background Over the last ten years, there has been explosive development in methods for measuring gene expression. These methods can identify thousands of genes altered between conditions, but understanding these datasets and forming hypotheses based on them remains challenging. One way to analyze these datasets is to associate ontologies (hierarchical, descriptive vocabularies with controlled relations between terms) with genes and to look for enrichment of specific terms. Although Gene Ontology (GO) is available for Caenorhabditis elegans, it does not include anatomical information. Results We have developed a tool for identifying enrichment of C. elegans tissues among gene sets and generated a website GUI where users can access this tool. Since a common drawback to ontology enrichment analyses is its verbosity, we developed a very simple filtering algorithm to reduce the ontology size by an order of magnitude. We adjusted these filters and validated our tool using a set of 30 gold standards from Expression Cluster data in WormBase. We show our tool can even discriminate between embryonic and larval tissues and can even identify tissues down to the single-cell level. We used our tool to identify multiple neuronal tissues that are down-regulated due to pathogen infection in C. elegans. Conclusions Our Tissue Enrichment Analysis (TEA) can be found within WormBase, and can be downloaded using Python’s standard pip installer. It tests a slimmed-down C. elegans tissue ontology for enrichment of specific terms and provides users with a text and graphic representation of the results. Electronic supplementary material The online version of this article (doi:10.1186/s12859-016-1229-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- David Angeles-Albores
- HHMI and California Institute of Technology, Division of Biology and Biological Engineering, 1200 E California Blvd, Pasadena, 91125, USA
| | - Raymond Y N Lee
- HHMI and California Institute of Technology, Division of Biology and Biological Engineering, 1200 E California Blvd, Pasadena, 91125, USA
| | - Juancarlos Chan
- HHMI and California Institute of Technology, Division of Biology and Biological Engineering, 1200 E California Blvd, Pasadena, 91125, USA
| | - Paul W Sternberg
- HHMI and California Institute of Technology, Division of Biology and Biological Engineering, 1200 E California Blvd, Pasadena, 91125, USA.
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9
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Koziol U, Koziol M, Preza M, Costábile A, Brehm K, Castillo E. De novo discovery of neuropeptides in the genomes of parasitic flatworms using a novel comparative approach. Int J Parasitol 2016; 46:709-21. [PMID: 27388856 DOI: 10.1016/j.ijpara.2016.05.007] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Revised: 05/18/2016] [Accepted: 05/20/2016] [Indexed: 12/11/2022]
Abstract
Neuropeptide mediated signalling is an ancient mechanism found in almost all animals and has been proposed as a promising target for the development of novel drugs against helminths. However, identification of neuropeptides from genomic data is challenging, and knowledge of the neuropeptide complement of parasitic flatworms is still fragmentary. In this work, we have developed an evolution-based strategy for the de novo discovery of neuropeptide precursors, based on the detection of localised sequence conservation between possible prohormone convertase cleavage sites. The method detected known neuropeptide precursors with good precision and specificity in the models Drosophila melanogaster and Caenorhabditis elegans. Furthermore, it identified novel putative neuropeptide precursors in nematodes, including the first description of allatotropin homologues in this phylum. Our search for neuropeptide precursors in the genomes of parasitic flatworms resulted in the description of 34 conserved neuropeptide precursor families, including 13 new ones, and of hundreds of new homologues of known neuropeptide precursor families. Most neuropeptide precursor families show a wide phylogenetic distribution among parasitic flatworms and show little similarity to neuropeptide precursors of other bilaterian animals. However, we could also find orthologs of some conserved bilaterian neuropeptides including pyrokinin, crustacean cardioactive peptide, myomodulin, neuropeptide-Y, neuropeptide KY and SIF-amide. Finally, we determined the expression patterns of seven putative neuropeptide precursor genes in the protoscolex of Echinococcus multilocularis. All genes were expressed in the nervous system with different patterns, indicating a hidden complexity of peptidergic signalling in cestodes.
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Affiliation(s)
- Uriel Koziol
- Sección Bioquímica, Facultad de Ciencias, Universidad de la República, Iguá 4225, CP11400 Montevideo, Uruguay.
| | - Miguel Koziol
- Sección Bioquímica, Facultad de Ciencias, Universidad de la República, Iguá 4225, CP11400 Montevideo, Uruguay
| | - Matías Preza
- Sección Bioquímica, Facultad de Ciencias, Universidad de la República, Iguá 4225, CP11400 Montevideo, Uruguay
| | - Alicia Costábile
- Sección Bioquímica, Facultad de Ciencias, Universidad de la República, Iguá 4225, CP11400 Montevideo, Uruguay
| | - Klaus Brehm
- University of Würzburg, Institute for Hygiene and Microbiology, Josef-Schneider-Straße 2 / Bau E1, 97080 Würzburg, Germany
| | - Estela Castillo
- Sección Bioquímica, Facultad de Ciencias, Universidad de la República, Iguá 4225, CP11400 Montevideo, Uruguay
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10
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Berber S, Wood M, Llamosas E, Thaivalappil P, Lee K, Liao BM, Chew YL, Rhodes A, Yucel D, Crossley M, Nicholas HR. Homeodomain-Interacting Protein Kinase (HPK-1) regulates stress responses and ageing in C. elegans. Sci Rep 2016; 6:19582. [PMID: 26791749 PMCID: PMC4726358 DOI: 10.1038/srep19582] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2015] [Accepted: 12/15/2015] [Indexed: 11/22/2022] Open
Abstract
Proteins of the Homeodomain-Interacting Protein Kinase (HIPK) family regulate an array of processes in mammalian systems, such as the DNA damage response, cellular proliferation and apoptosis. The nematode Caenorhabditis elegans has a single HIPK homologue called HPK-1. Previous studies have implicated HPK-1 in longevity control and suggested that this protein may be regulated in a stress-dependent manner. Here we set out to expand these observations by investigating the role of HPK-1 in longevity and in the response to heat and oxidative stress. We find that levels of HPK-1 are regulated by heat stress, and that HPK-1 contributes to survival following heat or oxidative stress. Additionally, we show that HPK-1 is required for normal longevity, with loss of HPK-1 function leading to a faster decline of physiological processes that reflect premature ageing. Through microarray analysis, we have found that HPK-1-regulated genes include those encoding proteins that serve important functions in stress responses such as Phase I and Phase II detoxification enzymes. Consistent with a role in longevity assurance, HPK-1 also regulates the expression of age-regulated genes. Lastly, we show that HPK-1 functions in the same pathway as DAF-16 to regulate longevity and reveal a new role for HPK-1 in development.
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Affiliation(s)
- Slavica Berber
- School of Molecular Bioscience, University of Sydney, Sydney, Australia
| | - Mallory Wood
- School of Molecular Bioscience, University of Sydney, Sydney, Australia
| | - Estelle Llamosas
- School of Molecular Bioscience, University of Sydney, Sydney, Australia
| | | | - Karen Lee
- School of Molecular Bioscience, University of Sydney, Sydney, Australia
| | - Bing Mana Liao
- School of Molecular Bioscience, University of Sydney, Sydney, Australia
| | - Yee Lian Chew
- School of Molecular Bioscience, University of Sydney, Sydney, Australia
| | - Aaron Rhodes
- School of Molecular Bioscience, University of Sydney, Sydney, Australia
| | - Duygu Yucel
- School of Molecular Bioscience, University of Sydney, Sydney, Australia
| | - Merlin Crossley
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Kensington, Australia
| | - Hannah R Nicholas
- School of Molecular Bioscience, University of Sydney, Sydney, Australia
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11
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Campbell AC, Updike DL. CSR-1 and P granules suppress sperm-specific transcription in the C. elegans germline. Development 2015; 142:1745-55. [PMID: 25968310 DOI: 10.1242/dev.121434] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Germ granules (P granules) in C. elegans are required for fertility and function to maintain germ cell identity and pluripotency. Sterility in the absence of P granules is often accompanied by the misexpression of soma-specific proteins and the initiation of somatic differentiation in germ cells. To investigate whether this is caused by the accumulation of somatic transcripts, we performed mRNA-seq on dissected germlines with and without P granules. Strikingly, we found that somatic transcripts do not increase in the young adult germline when P granules are impaired. Instead, we found that impairing P granules causes sperm-specific mRNAs to become highly overexpressed. This includes the accumulation of major sperm protein (MSP) transcripts in germ cells, a phenotype that is suppressed by feminization of the germline. A core component of P granules, the endo-siRNA-binding Argonaute protein CSR-1, has recently been ascribed with the ability to license transcripts for germline expression. However, impairing CSR-1 has very little effect on the accumulation of its mRNA targets. Instead, we found that CSR-1 functions with P granules to prevent MSP and sperm-specific mRNAs from being transcribed in the hermaphrodite germline. These findings suggest that P granules protect germline integrity through two different mechanisms, by (1) preventing the inappropriate expression of somatic proteins at the level of translational regulation, and by (2) functioning with CSR-1 to limit the domain of sperm-specific expression at the level of transcription.
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Affiliation(s)
- Anne C Campbell
- Kathryn W. Davis Center for Regenerative Biology and Medicine, Mount Desert Island Biological Laboratory, Bar Harbor, ME 04672, USA
| | - Dustin L Updike
- Kathryn W. Davis Center for Regenerative Biology and Medicine, Mount Desert Island Biological Laboratory, Bar Harbor, ME 04672, USA
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12
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Antonacci S, Forand D, Wolf M, Tyus C, Barney J, Kellogg L, Simon MA, Kerr G, Wells KL, Younes S, Mortimer NT, Olesnicky EC, Killian DJ. Conserved RNA-binding proteins required for dendrite morphogenesis in Caenorhabditis elegans sensory neurons. G3 (BETHESDA, MD.) 2015; 5:639-53. [PMID: 25673135 PMCID: PMC4390579 DOI: 10.1534/g3.115.017327] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Accepted: 02/09/2015] [Indexed: 01/22/2023]
Abstract
The regulation of dendritic branching is critical for sensory reception, cell-cell communication within the nervous system, learning, memory, and behavior. Defects in dendrite morphology are associated with several neurologic disorders; thus, an understanding of the molecular mechanisms that govern dendrite morphogenesis is important. Recent investigations of dendrite morphogenesis have highlighted the importance of gene regulation at the posttranscriptional level. Because RNA-binding proteins mediate many posttranscriptional mechanisms, we decided to investigate the extent to which conserved RNA-binding proteins contribute to dendrite morphogenesis across phyla. Here we identify a core set of RNA-binding proteins that are important for dendrite morphogenesis in the PVD multidendritic sensory neuron in Caenorhabditis elegans. Homologs of each of these genes were previously identified as important in the Drosophila melanogaster dendritic arborization sensory neurons. Our results suggest that RNA processing, mRNA localization, mRNA stability, and translational control are all important mechanisms that contribute to dendrite morphogenesis, and we present a conserved set of RNA-binding proteins that regulate these processes in diverse animal species. Furthermore, homologs of these genes are expressed in the human brain, suggesting that these RNA-binding proteins are candidate regulators of dendrite development in humans.
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Affiliation(s)
- Simona Antonacci
- Department of Molecular Biology, Colorado College, Colorado Springs, Colorado 80903
| | - Daniel Forand
- Department of Biology, University of Colorado Colorado Springs, Colorado Springs, Colorado 80918
| | - Margaret Wolf
- Department of Molecular Biology, Colorado College, Colorado Springs, Colorado 80903
| | - Courtney Tyus
- Department of Molecular Biology, Colorado College, Colorado Springs, Colorado 80903
| | - Julia Barney
- Department of Molecular Biology, Colorado College, Colorado Springs, Colorado 80903
| | - Leah Kellogg
- Department of Molecular Biology, Colorado College, Colorado Springs, Colorado 80903
| | - Margo A Simon
- Department of Molecular Biology, Colorado College, Colorado Springs, Colorado 80903
| | - Genevieve Kerr
- Department of Molecular Biology, Colorado College, Colorado Springs, Colorado 80903
| | - Kristen L Wells
- Department of Molecular Biology, Colorado College, Colorado Springs, Colorado 80903
| | - Serena Younes
- Department of Biology, University of Colorado Colorado Springs, Colorado Springs, Colorado 80918
| | - Nathan T Mortimer
- Department of Biological Sciences, University of Denver, Denver, Colorado 80208
| | - Eugenia C Olesnicky
- Department of Biology, University of Colorado Colorado Springs, Colorado Springs, Colorado 80918
| | - Darrell J Killian
- Department of Molecular Biology, Colorado College, Colorado Springs, Colorado 80903
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Spencer WC, McWhirter R, Miller T, Strasbourger P, Thompson O, Hillier LW, Waterston RH, Miller DM. Isolation of specific neurons from C. elegans larvae for gene expression profiling. PLoS One 2014; 9:e112102. [PMID: 25372608 PMCID: PMC4221280 DOI: 10.1371/journal.pone.0112102] [Citation(s) in RCA: 70] [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: 08/06/2014] [Accepted: 10/13/2014] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND The simple and well-described structure of the C. elegans nervous system offers an unprecedented opportunity to identify the genetic programs that define the connectivity and function of individual neurons and their circuits. A correspondingly precise gene expression map of C. elegans neurons would facilitate the application of genetic methods toward this goal. Here we describe a powerful new approach, SeqCeL (RNA-Seq of C. elegans cells) for producing gene expression profiles of specific larval C. elegans neurons. METHODS AND RESULTS We have exploited available GFP reporter lines for FACS isolation of specific larval C. elegans neurons for RNA-Seq analysis. Our analysis showed that diverse classes of neurons are accessible to this approach. To demonstrate the applicability of this strategy to rare neuron types, we generated RNA-Seq profiles of the NSM serotonergic neurons that occur as a single bilateral pair of cells in the C. elegans pharynx. These data detected >1,000 NSM enriched transcripts, including the majority of previously known NSM-expressed genes. SIGNIFICANCE This work offers a simple and robust protocol for expression profiling studies of post-embryonic C. elegans neurons and thus provides an important new method for identifying candidate genes for key roles in neuron-specific development and function.
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Affiliation(s)
- W. Clay Spencer
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Rebecca McWhirter
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Tyne Miller
- Program in Neuroscience, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Pnina Strasbourger
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington, United States of America
| | - Owen Thompson
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington, United States of America
| | - LaDeana W. Hillier
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington, United States of America
| | - Robert H. Waterston
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington, United States of America
| | - David M. Miller
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, Tennessee, United States of America
- Program in Neuroscience, Vanderbilt University, Nashville, Tennessee, United States of America
- * E-mail:
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14
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Sugi T, Ohtani Y. Simplified method for cell-specific gene expression analysis in Caenorhabditis elegans. Biochem Biophys Res Commun 2014; 450:330-4. [PMID: 24942876 DOI: 10.1016/j.bbrc.2014.05.124] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2014] [Accepted: 05/25/2014] [Indexed: 10/25/2022]
Abstract
In the neural circuit functional identities of individual neurons are mainly specified by their differential gene expression patterns. Unveiling functional roles of each neuron requires cell-specific interrogation of neural circuitry in the context of gene expressions. The mRNA tagging strategy in Caenorhabditis elegans is a powerful technique, in which cell-specific transcripts can be isolated by co-immunoprecipitating the complexes of mRNAs and epitope-tagged poly(A) binding protein (3× FLAG-PAB-1), expressed in target neurons. However, the conventional protocol requires laborious and time-consuming procedures; chromosomal integration of gene encoding 3× FLAG-PAB-1 and bleaching of obtained integrant animals for the isolation of huge amounts of synchronized animals. In this paper, we have presented a simplified methodology for cell-specific mRNA tagging analysis in C. elegans. We show that mRNA tagging was achieved using transgenic animals expressing 3× FLAG-PAB-1 as an extrachromosomal array under the control of the flp-18 promoter, without the chromosomal integration procedure. Furthermore, we successfully isolated cell-specific mRNAs from adult transgenic animals synchronously grown from eggs laid by gravid adults during a time window of 3h. This simplification facilitates the implementation of cell-specific gene expression analysis of C. elegans, which contributes to the understanding of neural circuitry at a cell-specific resolution.
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Affiliation(s)
- Takuma Sugi
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Yoshida-Honmachi, Sakyo-ku, Kyoto 606-8501, Japan; PRESTO, Japanese Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Japan.
| | - Yasuko Ohtani
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Yoshida-Honmachi, Sakyo-ku, Kyoto 606-8501, Japan
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15
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Evans GE, Martínez-Conejero JA, Phillipson GTM, Sykes PH, Sin IL, Lam EYN, Print CG, Horcajadas JA, Evans JJ. In the secretory endometria of women, luminal epithelia exhibit gene and protein expressions that differ from those of glandular epithelia. Fertil Steril 2014; 102:307-317.e7. [PMID: 24837612 DOI: 10.1016/j.fertnstert.2014.04.005] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2013] [Revised: 04/07/2014] [Accepted: 04/07/2014] [Indexed: 12/15/2022]
Abstract
OBJECTIVE To characterize the transcriptome of luminal epithelia (LE) of fertile secretory endometria and compare the results with those from glandular epithelia (GE). DESIGN Endometrial samples were collected at 2 and 7 days after initial blood LH surge in separate menstrual cycles. LE were obtained with the use of laser microdissection. mRNA was amplified with the use of linear polymerase chain reaction and hybridized to Agilent 4×44 microarrays. Gene analysis was used to identify differentially expressed mRNAs. Immunohistochemistry was used to assess nine proteins. SETTING One IVF clinic. PATIENT(S) Seven Caucasian fertile cycling women. INTERVENTION(S) None. MAIN OUTCOME MEASURE(S) Cycle dating with the use of blood endocrinologic markers, microarrays of laser-microdissected LE, immunohistochemical analysis. RESULT(S) One hundred sixty-one (of 401) differentially expressed mRNAs in LE were identified from the metabolism pathway. Increased selective protein expression in LE at 7 days after initial LH surge was observed. LE mRNA expression was the converse of that in GE. The two cell types each had a different significant biologic pathway identified. CONCLUSION(S) Our results introduce a new concept that LE differentially expressed mRNAs are in the converse direction to that of GE, indicating different biologic processes despite the GE being continuous with the luminal monolayer. This probable distinction of biologic roles has not been noted previously. Further investigations must take cognizance of this observation.
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Affiliation(s)
- Gloria E Evans
- Department of Obstetrics and Gynaecology, University of Otago, Christchurch, New Zealand; Fertility Associates, Christchurch, New Zealand.
| | | | | | - Peter H Sykes
- Department of Obstetrics and Gynaecology, University of Otago, Christchurch, New Zealand
| | - Iris L Sin
- Fertility Associates, Christchurch, New Zealand
| | - Enid Y N Lam
- Department of Molecular Medicine and Pathology and The Bioinformatics Institute, University of Auckland, Auckland, New Zealand
| | - Cristin G Print
- Department of Molecular Medicine and Pathology and The Bioinformatics Institute, University of Auckland, Auckland, New Zealand
| | - José A Horcajadas
- ARAID at I+CS, Hospital Miguel Servet, Zaragoza, Spain; University Pablo de Olavide, Seville, Spain
| | - John J Evans
- Department of Obstetrics and Gynaecology, University of Otago, Christchurch, New Zealand; Centre of Neuroendocrinology and MacDiarmid Institute of Advanced Materials and Nanotechnology, University of Otago, Christchurch, New Zealand
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16
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Smith CJ, O'Brien T, Chatzigeorgiou M, Spencer WC, Feingold-Link E, Husson SJ, Hori S, Mitani S, Gottschalk A, Schafer WR, Miller DM. Sensory neuron fates are distinguished by a transcriptional switch that regulates dendrite branch stabilization. Neuron 2013; 79:266-80. [PMID: 23889932 DOI: 10.1016/j.neuron.2013.05.009] [Citation(s) in RCA: 85] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/01/2013] [Indexed: 10/26/2022]
Abstract
Sensory neurons adopt distinct morphologies and functional modalities to mediate responses to specific stimuli. Transcription factors and their downstream effectors orchestrate this outcome but are incompletely defined. Here, we show that different classes of mechanosensory neurons in C. elegans are distinguished by the combined action of the transcription factors MEC-3, AHR-1, and ZAG-1. Low levels of MEC-3 specify the elaborate branching pattern of PVD nociceptors, whereas high MEC-3 is correlated with the simple morphology of AVM and PVM touch neurons. AHR-1 specifies AVM touch neuron fate by elevating MEC-3 while simultaneously blocking expression of nociceptive genes such as the MEC-3 target, the claudin-like membrane protein HPO-30, that promotes the complex dendritic branching pattern of PVD. ZAG-1 exercises a parallel role to prevent PVM from adopting the PVD fate. The conserved dendritic branching function of the Drosophila AHR-1 homolog, Spineless, argues for similar pathways in mammals.
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Affiliation(s)
- Cody J Smith
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN 37232-8240, USA
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17
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Resau JH, Ho NT, Dykema K, Faber MS, Busik JV, Nickolov RZ, Furge KA, Paneth N, Jewell S, Khoo SK. Evaluation of sex-specific gene expression in archived dried blood spots (DBS). Int J Mol Sci 2012; 13:9599-9608. [PMID: 22949818 PMCID: PMC3431816 DOI: 10.3390/ijms13089599] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Revised: 07/25/2012] [Accepted: 07/30/2012] [Indexed: 11/16/2022] Open
Abstract
Screening newborns for treatable serious conditions is mandated in all US states and many other countries. After screening, Guthrie cards with residual blood (whole spots or portions of spots) are typically stored at ambient temperature in many facilities. The potential of archived dried blood spots (DBS) for at-birth molecular studies in epidemiological and clinical research is substantial. However, it is also challenging as analytes from DBS may be degraded due to preparation and storage conditions. We previously reported an improved assay for obtaining global RNA gene expression from blood spots. Here, we evaluated sex-specific gene expression and its preservation in DBS using oligonucleotide microarray technology. We found X inactivation-specific transcript (XIST), lysine-specific demethylase 5D (KDM5D) (also known as selected cDNA on Y, homolog of mouse (SMCY)), uncharacterized LOC729444 (LOC729444), and testis-specific transcript, Y-linked 21 (TTTY21) to be differentially-expressed by sex of the newborn. Our finding that trait-specific RNA gene expression is preserved in unfrozen DBS, demonstrates the technical feasibility of performing molecular genetic profiling using such samples. With millions of DBS potentially available for research, we see new opportunities in using newborn molecular gene expression to better understand molecular pathogenesis of perinatal diseases.
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Affiliation(s)
- James H. Resau
- Program of Biospecimen Science, Van Andel Research Institute, Grand Rapids, MI 49503, USA; E-Mails: (J.H.R.); (S.J.)
| | - Nhan T. Ho
- Department of Epidemiology & Biostatistics, College of Human Medicine, Michigan State University, East Lansing, MI 48823, USA; E-Mails: (N.T.H.); (N.P.)
| | - Karl Dykema
- Laboratory of Computational Biology, Van Andel Research Institute, Grand Rapids, MI 49503, USA; E-Mails: (K.D.); (K.A.F.)
| | - Matthew S. Faber
- Department of Physiology, Michigan State University, East Lansing, MI 48824, USA; E-Mails: (M.S.F.); (J.V.B.)
| | - Julia V. Busik
- Department of Physiology, Michigan State University, East Lansing, MI 48824, USA; E-Mails: (M.S.F.); (J.V.B.)
| | - Radoslav Z. Nickolov
- Department of Mathematics & Computer Science, Fayetteville State University, Fayetteville, NC 28301, USA; E-Mail:
| | - Kyle A. Furge
- Laboratory of Computational Biology, Van Andel Research Institute, Grand Rapids, MI 49503, USA; E-Mails: (K.D.); (K.A.F.)
| | - Nigel Paneth
- Department of Epidemiology & Biostatistics, College of Human Medicine, Michigan State University, East Lansing, MI 48823, USA; E-Mails: (N.T.H.); (N.P.)
- Department of Pediatrics & Human Development, College of Human Medicine, Michigan State University, East Lansing, MI 48823, USA
| | - Scott Jewell
- Program of Biospecimen Science, Van Andel Research Institute, Grand Rapids, MI 49503, USA; E-Mails: (J.H.R.); (S.J.)
| | - Sok Kean Khoo
- Laboratory of Microarray Technology, Van Andel Research Institute, Grand Rapids, MI 49503, USA
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +1-616-234-5536; Fax: +1-616-234-5537
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18
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Husson SJ, Costa WS, Wabnig S, Stirman JN, Watson JD, Spencer WC, Akerboom J, Looger LL, Treinin M, Miller DM, Lu H, Gottschalk A. Optogenetic analysis of a nociceptor neuron and network reveals ion channels acting downstream of primary sensors. Curr Biol 2012; 22:743-52. [PMID: 22483941 DOI: 10.1016/j.cub.2012.02.066] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2011] [Revised: 01/12/2012] [Accepted: 02/22/2012] [Indexed: 02/02/2023]
Abstract
BACKGROUND Nociception generally evokes rapid withdrawal behavior in order to protect the tissue from harmful insults. Most nociceptive neurons responding to mechanical insults display highly branched dendrites, an anatomy shared by Caenorhabditis elegans FLP and PVD neurons, which mediate harsh touch responses. Although several primary molecular nociceptive sensors have been characterized, less is known about modulation and amplification of noxious signals within nociceptor neurons. First, we analyzed the FLP/PVD network by optogenetics and studied integration of signals from these cells in downstream interneurons. Second, we investigated which genes modulate PVD function, based on prior single-neuron mRNA profiling of PVD. RESULTS Selectively photoactivating PVD, FLP, and downstream interneurons via Channelrhodopsin-2 (ChR2) enabled the functional dissection of this nociceptive network, without interfering signals by other mechanoreceptors. Forward or reverse escape behaviors were determined by PVD and FLP, via integration by command interneurons. To identify mediators of PVD function, acting downstream of primary nocisensor molecules, we knocked down PVD-specific transcripts by RNAi and quantified light-evoked PVD-dependent behavior. Cell-specific disruption of synaptobrevin or voltage-gated Ca(2+) channels (VGCCs) showed that PVD signals chemically to command interneurons. Knocking down the DEG/ENaC channel ASIC-1 and the TRPM channel GTL-1 indicated that ASIC-1 may extend PVD's dynamic range and that GTL-1 may amplify its signals. These channels act cell autonomously in PVD, downstream of primary mechanosensory molecules. CONCLUSIONS Our work implicates TRPM channels in modifying excitability of and DEG/ENaCs in potentiating signal output from a mechano-nociceptor neuron. ASIC-1 and GTL-1 homologs, if functionally conserved, may denote valid targets for novel analgesics.
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Affiliation(s)
- Steven J Husson
- Buchmann Institute for Molecular Life Sciences, Goethe-University Frankfurt, Max von Laue Str. 15, 60438 Frankfurt, Germany
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19
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Smith CJ, Watson JD, VanHoven MK, Colón-Ramos DA, Miller DM. Netrin (UNC-6) mediates dendritic self-avoidance. Nat Neurosci 2012; 15:731-7. [PMID: 22426253 PMCID: PMC3337961 DOI: 10.1038/nn.3065] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2011] [Accepted: 02/10/2012] [Indexed: 12/13/2022]
Abstract
Dendrites from a single neuron may be highly branched but typically do not overlap. This self-avoidance behavior has been shown to depend on cell-specific membrane proteins that trigger mutual repulsion. Here we report the surprising discovery that a diffusible cue, the axon guidance protein UNC-6/Netrin, is required for self-avoidance of sister dendrites from the PVD nociceptive neuron in C. elegans. We used time lapse imaging to show that dendrites fail to withdraw upon mutual contact in the absence of UNC-6/Netrin signaling. We propose a model in which the UNC-40/DCC receptor captures UNC-6/Netrin at the tips of growing dendrites for interaction with UNC-5 on the apposing branch to induce mutual repulsion. UNC-40/DCC also responds to dendritic contact through an additional pathway that is independent of UNC-6/Netrin. Our findings offer a new model for how an evolutionarily conserved morphogenic cue and its cognate receptors can pattern a fundamental feature of dendritic architecture.
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Affiliation(s)
- Cody J Smith
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, Tennessee, USA
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20
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Laser-capture microdissection and transcriptional profiling in archival FFPE tissue in prostate cancer. Methods Mol Biol 2011; 755:291-300. [PMID: 21761313 DOI: 10.1007/978-1-61779-163-5_24] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Prognostic markers can improve prediction of the behaviour of a cancer at the point of diagnosis. A key value of any prognostic marker is at the point of tumour diagnosis. In the context of prostate cancer, this implies profiling in the diagnostic formalin-fixed, paraffin-embedded (FFPE) transrectal ultrasound-guided (TRUS) needle biopsy. TRUS needle biopsies commonly contain both stromal and epithelial cells, and malignant glands are found as isolated foci within this tissue. Using the entire biopsy for genetic analysis inevitably results in a significant contamination of malignant cells with benign tissue. This combination of minimal tumour yields and tissue heterogeneity have so far prohibited prognostic transcript and microarray molecular studies in needle biopsies. Laser-capture microdissection (LCM) allows enriched cell populations to be accurately isolated from heterogeneous tissue, hence facilitating analysis of different components from a single tissue sample. Here, we describe its use in isolating tumour cells in archival FFPE prostate needle biopsies and subsequent application for RNA extraction and quantitative real-time PCR (QPCR).
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21
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Regulation of behavioral plasticity by systemic temperature signaling in Caenorhabditis elegans. Nat Neurosci 2011; 14:984-92. [DOI: 10.1038/nn.2854] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2011] [Accepted: 05/03/2011] [Indexed: 01/09/2023]
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22
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Albeg A, Smith C, Chatzigeorgiou M, Feitelson DG, Hall DH, Schafer WR, Miller DM, Treinin M. C. elegans multi-dendritic sensory neurons: morphology and function. Mol Cell Neurosci 2011; 46:308-17. [PMID: 20971193 PMCID: PMC3018541 DOI: 10.1016/j.mcn.2010.10.001] [Citation(s) in RCA: 117] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2010] [Revised: 10/02/2010] [Accepted: 10/13/2010] [Indexed: 11/28/2022] Open
Abstract
PVD and FLP sensory neurons envelope the body of the C. elegans adult with a highly branched network of thin sensory processes. Both PVD and FLP neurons are mechanosensors. PVD is known to mediate the response to high threshold mechanical stimuli. Thus PVD and FLP neurons are similar in both morphology and function to mammalian nociceptors. To better understand the function of these neurons we generated strains lacking them. Behavioral analysis shows that PVD and FLP regulate movement under normal growth conditions, as animals lacking these neurons demonstrate higher dwelling behavior. In addition, PVD--whose thin branches project across the body-wall muscles--may have a role in proprioception, as ablation of PVD leads to defective posture. Moreover, movement-dependent calcium transients are seen in PVD, a response that requires MEC-10, a subunit of the mechanosensory DEG/ENaC channel that is also required for maintaining wild-type posture. Hence, PVD senses both noxious and innocuous signals to regulate C. elegans behavior, and thus combines the functions of multiple mammalian somatosensory neurons. Finally, strong mechanical stimulation leads to inhibition of egg-laying, and this response also depends on PVD and FLP neurons. Based on all these results we suggest that noxious signals perceived by PVD and FLP promote an escape behavior consisting of increased speed, reduced pauses and reversals, and inhibition of egg-laying.
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Affiliation(s)
- Adi Albeg
- Department of Medical Neurobiology, Institute for Medical Research – Israel-Canada, Hebrew University – Hadassah Medical School, Jerusalem 91120, Israel
| | - Cody Smith
- Department of Cell and Developmental Biology and Program in Neuroscience, Vanderbilt University, Nashville, TN 37232-8240, USA
| | - Marios Chatzigeorgiou
- Cell Biology Division, MRC Laboratory of Molecular Biology, Hills Road, Cambridge UK
| | - Dror G. Feitelson
- Department of Computer Science, Hebrew University, Jerusalem 91904, Israel
| | - David H. Hall
- Department of Neuroscience, Albert Einstein College of Medicine, Bronx, New York 10461, USA
| | - William R. Schafer
- Cell Biology Division, MRC Laboratory of Molecular Biology, Hills Road, Cambridge UK
| | - David M. Miller
- Department of Cell and Developmental Biology and Program in Neuroscience, Vanderbilt University, Nashville, TN 37232-8240, USA
| | - Millet Treinin
- Department of Medical Neurobiology, Institute for Medical Research – Israel-Canada, Hebrew University – Hadassah Medical School, Jerusalem 91120, Israel
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Khoo SK, Dykema K, Vadlapatla NM, LaHaie D, Valle S, Satterthwaite D, Ramirez SA, Carruthers JA, Haak PT, Resau JH. Acquiring genome-wide gene expression profiles in Guthrie card blood spots using microarrays. Pathol Int 2010; 61:1-6. [DOI: 10.1111/j.1440-1827.2010.02611.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Thyagarajan B, Blaszczak AG, Chandler KJ, Watts JL, Johnson WE, Graves BJ. ETS-4 is a transcriptional regulator of life span in Caenorhabditis elegans. PLoS Genet 2010; 6:e1001125. [PMID: 20862312 PMCID: PMC2940738 DOI: 10.1371/journal.pgen.1001125] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2009] [Accepted: 08/13/2010] [Indexed: 01/05/2023] Open
Abstract
Aging is a complex phenotype responsive to a plethora of environmental inputs; yet only a limited number of transcriptional regulators are known to influence life span. How the downstream expression programs mediated by these factors (or others) are coordinated into common or distinct set of aging effectors is an addressable question in model organisms, such as C. elegans. Here, we establish the transcription factor ETS-4, an ortholog of vertebrate SPDEF, as a longevity determinant. Adult worms with ets-4 mutations had a significant extension of mean life span. Restoring ETS-4 activity in the intestine, but not neurons, of ets-4 mutant worms rescued life span to wild-type levels. Using RNAi, we demonstrated that ets-4 is required post-developmentally to regulate adult life span; thus uncoupling the role of ETS-4 in aging from potential functions in worm intestinal development. Seventy ETS-4-regulated genes, identified by gene expression profiling of two distinct ets-4 alleles and analyzed by bioinformatics, were enriched for known longevity effectors that function in lipid transport, lipid metabolism, and innate immunity. Putative target genes were enriched for ones that change expression during normal aging, the majority of which are controlled by the GATA factors. Also, some ETS-4-regulated genes function downstream of the FOXO factor, DAF-16 and the insulin/IGF-1 signaling pathway. However, epistasis and phenotypic analyses indicate that ets-4 functioned in parallel to the insulin/IGF-1 receptor, daf-2 and akt-1/2 kinases. Furthermore, ets-4 required daf-16 to modulate aging, suggesting overlap in function at the level of common targets that affect life span. In conclusion, ETS-4 is a new transcriptional regulator of aging, which shares transcriptional targets with GATA and FOXO factors, suggesting that overlapping pathways direct common sets of lifespan-related genes. Animal life span is regulated in response to developmental and environmental inputs through coordinate changes in gene expression. Thus, longevity determinants include DNA-binding proteins that regulate gene expression by controlling transcription. Here, we explored the physiological role of the transcriptional regulator, ETS-4, in the roundworm Caenorhabditis elegans. Our data showed that worms that lack ETS-4 lived significantly longer, revealing ETS-4′s role in the transcription network that regulates life span. We identified 70 genes whose expression was modulated by ETS-4 that function in lipid transport, lipid metabolism and innate immunity. Some of the ETS-4-regulated genes were also controlled by two other regulators of aging, the FOXO and GATA factors. We concluded that a common set of transcriptional targets orchestrate the network of physiological factors that affect aging. ETS-4 is closely related to the human ETS protein SPDEF that exhibits aberrant expression in breast and prostate tumors. Because the genetic pathways that regulate aging are well conserved in other organisms, including humans, our findings could lead to a better understanding of SPDEF function and longevity regulation in mammals.
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Affiliation(s)
- Bargavi Thyagarajan
- Huntsman Cancer Institute, Department of Oncological Sciences, University of Utah, Salt Lake City, Utah, United States of America
| | - Adam G. Blaszczak
- Huntsman Cancer Institute, Department of Oncological Sciences, University of Utah, Salt Lake City, Utah, United States of America
| | - Katherine J. Chandler
- Huntsman Cancer Institute, Department of Oncological Sciences, University of Utah, Salt Lake City, Utah, United States of America
| | - Jennifer L. Watts
- School of Molecular Biosciences, Washington State University, Pullman, Washington, United States of America
| | - W. Evan Johnson
- Huntsman Cancer Institute, Department of Oncological Sciences, University of Utah, Salt Lake City, Utah, United States of America
- Department of Statistics, Brigham Young University, Provo, Utah, United States of America
| | - Barbara J. Graves
- Huntsman Cancer Institute, Department of Oncological Sciences, University of Utah, Salt Lake City, Utah, United States of America
- * E-mail:
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Smith CJ, Watson JD, Spencer WC, O'Brien T, Cha B, Albeg A, Treinin M, Miller DM. Time-lapse imaging and cell-specific expression profiling reveal dynamic branching and molecular determinants of a multi-dendritic nociceptor in C. elegans. Dev Biol 2010; 345:18-33. [PMID: 20537990 DOI: 10.1016/j.ydbio.2010.05.502] [Citation(s) in RCA: 141] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2010] [Revised: 05/19/2010] [Accepted: 05/19/2010] [Indexed: 10/19/2022]
Abstract
Nociceptive neurons innervate the skin with complex dendritic arbors that respond to pain-evoking stimuli such as harsh mechanical force or extreme temperatures. Here we describe the structure and development of a model nociceptor, the PVD neuron of C. elegans, and identify transcription factors that control morphogenesis of the PVD dendritic arbor. The two PVD neuron cell bodies occupy positions on either the right (PVDR) or left (PVDL) sides of the animal in posterior-lateral locations. Imaging with a GFP reporter revealed a single axon projecting from the PVD soma to the ventral cord and an elaborate, highly branched arbor of dendritic processes that envelop the animal with a web-like array directly beneath the skin. Dendritic branches emerge in a step-wise fashion during larval development and may use an existing network of peripheral nerve cords as guideposts for key branching decisions. Time-lapse imaging revealed that branching is highly dynamic with active extension and withdrawal and that PVD branch overlap is prevented by a contact-dependent self-avoidance, a mechanism that is also employed by sensory neurons in other organisms. With the goal of identifying genes that regulate dendritic morphogenesis, we used the mRNA-tagging method to produce a gene expression profile of PVD during late larval development. This microarray experiment identified>2,000 genes that are 1.5X elevated relative to all larval cells. The enriched transcripts encode a wide range of proteins with potential roles in PVD function (e.g., DEG/ENaC and Trp channels) or development (e.g., UNC-5 and LIN-17/frizzled receptors). We used RNAi and genetic tests to screen 86 transcription factors from this list and identified eleven genes that specify PVD dendritic structure. These transcription factors appear to control discrete steps in PVD morphogenesis and may either promote or limit PVD branching at specific developmental stages. For example, time-lapse imaging revealed that MEC-3 (LIM homeodomain) is required for branch initiation in early larval development whereas EGL-44 (TEAD domain) prevents ectopic PVD branching in the adult. A comparison of PVD-enriched transcripts to a microarray profile of mammalian nociceptors revealed homologous genes with potentially shared nociceptive functions. We conclude that PVD neurons display striking structural, functional and molecular similarities to nociceptive neurons from more complex organisms and can thus provide a useful model system in which to identify evolutionarily conserved determinants of nociceptor fate.
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Affiliation(s)
- Cody J Smith
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN 37232-8240, USA
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26
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Specific roles for DEG/ENaC and TRP channels in touch and thermosensation in C. elegans nociceptors. Nat Neurosci 2010; 13:861-8. [PMID: 20512132 PMCID: PMC2975101 DOI: 10.1038/nn.2581] [Citation(s) in RCA: 177] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2010] [Accepted: 05/17/2010] [Indexed: 11/09/2022]
Abstract
Polymodal nociceptors detect noxious stimuli including harsh touch, toxic chemicals, and extremes of heat and cold. The molecular mechanisms by which nociceptors are able to sense multiple qualitatively distinct stimuli are not well-understood. We show here that the C. elegans PVD neurons are mulitidendritic nociceptors that respond to harsh touch as well as cold temperatures. The harsh touch modality specifically requires the DEG/ENaC proteins MEC-10 and DEGT-1, which represent putative components of a harsh touch mechanotransduction complex. By contrast, responses to cold require the TRPA-1 channel and are MEC-10- and DEGT-1-independent. Heterologous expression of C. elegans TRPA-1 can confer cold responsiveness to other C. elegans neurons or to mammalian cells, indicating that TRPA-1 is itself a cold sensor. These results show that C. elegans nociceptors respond to thermal and mechanical stimuli using distinct sets of molecules, and identify DEG/ENaC channels as potential receptors for mechanical pain.
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27
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Cell sorting-assisted microarray profiling of host cell response to Cryptosporidium parvum infection. Infect Immun 2009; 78:1040-8. [PMID: 20038534 DOI: 10.1128/iai.01009-09] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
To study the transcriptional response of mammalian cells to infection with the intracellular apicomplexan parasite Cryptosporidium parvum, infected and uninfected cells were recovered from C. parvum-infected cell monolayers. This approach, which contrasts with a more conventional experimental design that compares infected to uninfected cell monolayers, enabled the identification of functional categories of genes that are differentially transcribed as a direct consequence of the presence of intracellular parasites. Among several categories of upregulated genes, glycoprotein metabolism was significantly overrepresented. To investigate whether these transcriptional changes affected the composition of the surface of infected cells, cells were probed with fluorescently labeled lectins. Among a panel of seven lectins, soybean agglutinin, which recognizes N-acetyl-d-galactosamine, generated the largest difference in fluorescence between infected and uninfected cells. The origin of the fluorescent signal emitted by infected cells was further investigated and attributed to the overexpression of glycoprotein on the surface of infected cells, as well as the presence of glycoprotein located in the proximity of intracellular parasites.
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Hutter H, Ng MP, Chen N. GExplore: a web server for integrated queries of protein domains, gene expression and mutant phenotypes. BMC Genomics 2009; 10:529. [PMID: 19917126 PMCID: PMC2779824 DOI: 10.1186/1471-2164-10-529] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2009] [Accepted: 11/16/2009] [Indexed: 01/17/2023] Open
Abstract
Background The majority of the genes even in well-studied multi-cellular model organisms have not been functionally characterized yet. Mining the numerous genome wide data sets related to protein function to retrieve potential candidate genes for a particular biological process remains a challenge. Description GExplore has been developed to provide a user-friendly database interface for data mining at the gene expression/protein function level to help in hypothesis development and experiment design. It supports combinatorial searches for proteins with certain domains, tissue- or developmental stage-specific expression patterns, and mutant phenotypes. GExplore operates on a stand-alone database and has fast response times, which is essential for exploratory searches. The interface is not only user-friendly, but also modular so that it accommodates additional data sets in the future. Conclusion GExplore is an online database for quick mining of data related to gene and protein function, providing a multi-gene display of data sets related to the domain composition of proteins as well as expression and phenotype data. GExplore is publicly available at: http://genome.sfu.ca/gexplore/
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Affiliation(s)
- Harald Hutter
- Department of Biological Sciences, Simon Fraser University, Burnaby, Canada.
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29
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Clément-Ziza M, Gentien D, Lyonnet S, Thiery JP, Besmond C, Decraene C. Evaluation of methods for amplification of picogram amounts of total RNA for whole genome expression profiling. BMC Genomics 2009; 10:246. [PMID: 19470167 PMCID: PMC2700135 DOI: 10.1186/1471-2164-10-246] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2008] [Accepted: 05/26/2009] [Indexed: 12/22/2022] Open
Abstract
Background For more than a decade, microarrays have been a powerful and widely used tool to explore the transcriptome of biological systems. However, the amount of biological material from cell sorting or laser capture microdissection is much too small to perform microarray studies. To address this issue, RNA amplification methods have been developed to generate sufficient targets from picogram amounts of total RNA to perform microarray hybridisation. Results In this study, four commercial protocols for amplification of picograms amounts of input RNA for microarray expression profiling were evaluated and compared. The quantitative and qualitative performances of the methods were assessed. Microarrays were hybridised with the amplified targets and the amplification protocols were compared with respect to the quality of expression profiles, reproducibility within a concentration range of input RNA, and sensitivity. The results demonstrate significant differences between these four methods. Conclusion In our hands, the WT-Ovation pico system proposed by Nugen appears to be the most suitable for RNA amplification. This comparative study will be useful to scientists needing to choose an amplification method to carry out microarray experiments involving samples comprising only a few cells and generating picogram amounts of RNA.
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Affiliation(s)
- Mathieu Clément-Ziza
- Institut Curie, Département de Transfert, 26 Rue d'ULM, F-75248, Paris cedex 05, France.
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Helmcke KJ, Syversen T, Miller DM, Aschner M. Characterization of the effects of methylmercury on Caenorhabditis elegans. Toxicol Appl Pharmacol 2009; 240:265-72. [PMID: 19341752 DOI: 10.1016/j.taap.2009.03.013] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2009] [Revised: 03/11/2009] [Accepted: 03/23/2009] [Indexed: 11/19/2022]
Abstract
The rising prevalence of methylmercury (MeHg) in seafood and in the global environment provides an impetus for delineating the mechanism of the toxicity of MeHg. Deleterious effects of MeHg have been widely observed in humans and in other mammals, the most striking of which occur in the nervous system. Here we test the model organism, Caenorhabditis elegans (C. elegans), for MeHg toxicity. The simple, well-defined anatomy of the C. elegans nervous system and its ready visualization with green fluorescent protein (GFP) markers facilitated our study of the effects of methylmercuric chloride (MeHgCl) on neural development. Although MeHgCl was lethal to C. elegans, induced a developmental delay, and decreased pharyngeal pumping, other traits including lifespan, brood size, swimming rate, and nervous system morphology were not obviously perturbed in animals that survived MeHgCl exposure. Despite the limited effects of MeHgCl on C. elegans development and behavior, intracellular mercury (Hg) concentrations (<or=3 ng Hg/mg protein) in MeHgCl-treated nematodes approached levels that are highly toxic to mammals. If MeHgCl reaches these concentrations throughout the animal, this finding indicates that C. elegans cells, particularly neurons, may be less sensitive to MeHgCl toxicity than mammalian cells. We propose, therefore, that C. elegans should be a useful model for discovering intrinsic mechanisms that confer resistance to MeHgCl exposure.
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Affiliation(s)
- Kirsten J Helmcke
- Pharmacology Department, Vanderbilt University Medical Center, Nashville, TN 37232-0414, USA
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Novel developments for improved detection of specific mRNAs by DNA chips. Appl Microbiol Biotechnol 2008; 80:953-63. [PMID: 18784921 DOI: 10.1007/s00253-008-1680-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2008] [Revised: 08/20/2008] [Accepted: 08/21/2008] [Indexed: 10/21/2022]
Abstract
Microarrays have revolutionized gene expression analysis as they allow for highly parallel monitoring of mRNA levels of thousands of genes in a single experiment. Since their introduction some 15 years ago, substantial progress has been achieved with regard to, e.g., faster or more sensitive analyses. In this review, interesting new approaches for a more sensitive detection of specific mRNAs will be highlighted. Particularly, the potential of electrical DNA chip formats that allow for faster mRNA analyses will be discussed.
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