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WormBook : the online review of C. elegans biology最新文献

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Assaying mechanosensation. 分析mechanosensation。
WormBook : the online review of C. elegans biology Pub Date : 2014-07-31 DOI: 10.1895/wormbook.1.172.1
Martin Chalfie, Anne C Hart, Catharine H Rankin, Miriam B Goodman
{"title":"Assaying mechanosensation.","authors":"Martin Chalfie,&nbsp;Anne C Hart,&nbsp;Catharine H Rankin,&nbsp;Miriam B Goodman","doi":"10.1895/wormbook.1.172.1","DOIUrl":"https://doi.org/10.1895/wormbook.1.172.1","url":null,"abstract":"<p><p>C. elegans detect and respond to diverse mechanical stimuli using neuronal circuitry that has been defined by decades of work by C. elegans researchers. In this WormMethods chapter, we review and comment on the techniques currently used to assess mechanosensory response. This methods review is intended both as an introduction for those new to the field and a convenient compendium for the expert. A brief discussion of commonly used mechanosensory assays is provided, along with a discussion of the neural circuits involved, consideration of critical protocol details, and references to the primary literature. </p>","PeriodicalId":75344,"journal":{"name":"WormBook : the online review of C. elegans biology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2014-07-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4448936/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"32562182","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 43
Mass spectrometry-based shotgun proteomic analysis of C. elegans protein complexes. 基于质谱法的秀丽隐杆线虫蛋白复合物的鸟枪蛋白质组学分析。
WormBook : the online review of C. elegans biology Pub Date : 2014-06-24 DOI: 10.1895/wormbook.1.171.1
Bryan R Fonslow, James J Moresco, Patricia G Tu, Antti P Aalto, Amy E Pasquinelli, Andrew G Dillin, John R Yates
{"title":"Mass spectrometry-based shotgun proteomic analysis of C. elegans protein complexes.","authors":"Bryan R Fonslow,&nbsp;James J Moresco,&nbsp;Patricia G Tu,&nbsp;Antti P Aalto,&nbsp;Amy E Pasquinelli,&nbsp;Andrew G Dillin,&nbsp;John R Yates","doi":"10.1895/wormbook.1.171.1","DOIUrl":"https://doi.org/10.1895/wormbook.1.171.1","url":null,"abstract":"<p><p>Mass spectrometry (MS)-based shotgun proteomics is an enabling technology for the study of C. elegans proteins. When coupled with co-immunoprecipitation (CoIP), new interactions and functions among proteins can be discovered. We provide a general background on protein complexes and methods for their analysis, along with the lifecycle and interaction types of proteins that ultimately define the identifiable components of protein complexes. We highlight traditional biochemical methods to evaluate whether the complexes are sufficiently pure and abundant for analysis with shotgun proteomics. We present two CoIP-MS case studies of protein complexes from C. elegans, using both endogenous and fusion protein antibodies to illustrate the important aspects of their analyses. We discuss results from mass spectrometers with differences in mass accuracy and resolution, along with the relevant information that can be extracted from the data generated, such as protein relative abundance, post-translational modifications, and identification confidence. Finally, we illustrate how comparative analysis can reveal candidate binding partners for biological follow-up and validation. This chapter should act as a complement and extension to the WormBook chapter Biochemistry and molecular biology, which describes tandem affinity purification (TAP) of protein complexes for analysis by mass spectrometry. </p>","PeriodicalId":75344,"journal":{"name":"WormBook : the online review of C. elegans biology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2014-06-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4716738/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"32457455","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 18
Endogenous RNAi pathways in C. elegans. elegans 的内源性 RNAi 途径。
WormBook : the online review of C. elegans biology Pub Date : 2014-05-07 DOI: 10.1895/wormbook.1.170.1
Allison C Billi, Sylvia E J Fischer, John K Kim
{"title":"Endogenous RNAi pathways in C. elegans.","authors":"Allison C Billi, Sylvia E J Fischer, John K Kim","doi":"10.1895/wormbook.1.170.1","DOIUrl":"10.1895/wormbook.1.170.1","url":null,"abstract":"<p><p>In addition to several hundred microRNAs, C. elegans produces thousands of other small RNAs targeting coding genes, pseudogenes, transposons, and other noncoding RNAs. Here we review what is currently known about these endogenous small interfering RNAs (siRNAs) and piwi-interacting RNAs (piRNAs), providing an overview of their biogenesis, their associated protein factors, and their effects on mRNA dynamics and chromatin structure. Additionally, we describe how the molecular actions of these classes of endogenous small RNAs connect to their physiological roles in the organism. </p>","PeriodicalId":75344,"journal":{"name":"WormBook : the online review of C. elegans biology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2014-05-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4781133/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"32331652","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Isolation of C. elegans and related nematodes. 秀丽隐杆线虫及其相关线虫的分离。
WormBook : the online review of C. elegans biology Pub Date : 2014-05-02 DOI: 10.1895/wormbook.1.115.2
Antoine Barrière, Marie-Anne Félix
{"title":"Isolation of C. elegans and related nematodes.","authors":"Antoine Barrière,&nbsp;Marie-Anne Félix","doi":"10.1895/wormbook.1.115.2","DOIUrl":"https://doi.org/10.1895/wormbook.1.115.2","url":null,"abstract":"Isolating Caenorhabditis and other nematodes from the wild first requires field sampling (reviewed in Section 1). The easiest and most efficient way to recover the animals from any substrate is to place the sample onto a standard C. elegans culture plate (Section 2.1). Alternative methods used by nematologists to recover soil nematodes (Sections 2.2, 2.3, and 2.4) are in our hands more difficult to implement and only yield a fraction of the individuals in the sample. A tricky step is to recognize your species of interest out of the zoo of nematode species that comes with a typical sample (Section 3). Culture (Section 4) and freezing (Section 5) conditions are then reviewed. Finally, we briefly summarize the organization and timing of an isolation experiment (Section 6), as well as the available collections (Section 7). Bear in mind that this chapter is strongly focused towards the isolation of Caenorhabditis elegans and close relatives.","PeriodicalId":75344,"journal":{"name":"WormBook : the online review of C. elegans biology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2014-05-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"32322125","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 8
C. elegans as a model for membrane traffic. 秀丽隐杆线虫作为膜交通的模型。
WormBook : the online review of C. elegans biology Pub Date : 2014-04-25 DOI: 10.1895/wormbook.1.77.2
Ken Sato, Anne Norris, Miyuki Sato, Barth D Grant
{"title":"C. elegans as a model for membrane traffic.","authors":"Ken Sato,&nbsp;Anne Norris,&nbsp;Miyuki Sato,&nbsp;Barth D Grant","doi":"10.1895/wormbook.1.77.2","DOIUrl":"https://doi.org/10.1895/wormbook.1.77.2","url":null,"abstract":"<p><p>The counterbalancing action of the endocytosis and secretory pathways maintains a dynamic equilibrium that regulates the composition of the plasma membrane, allowing it to maintain homeostasis and to change rapidly in response to alterations in the extracellular environment and/or intracellular metabolism. These pathways are intimately integrated with intercellular signaling systems and play critical roles in all cells. Studies in Caenorhabditis elegans have revealed diverse roles of membrane trafficking in physiology and development and have also provided molecular insight into the fundamental mechanisms that direct cargo sorting, vesicle budding, and membrane fisson and fusion. In this review, we summarize progress in understanding membrane trafficking mechanisms derived from work in C. elegans, focusing mainly on work done in non-neuronal cell-types, especially the germline, early embryo, coelomocytes, and intestine. </p>","PeriodicalId":75344,"journal":{"name":"WormBook : the online review of C. elegans biology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2014-04-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4096984/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"32298101","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 78
Nematode sperm motility. 线虫精子活力。
WormBook : the online review of C. elegans biology Pub Date : 2014-04-04 DOI: 10.1895/wormbook.1.68.2
Harold E Smith
{"title":"Nematode sperm motility.","authors":"Harold E Smith","doi":"10.1895/wormbook.1.68.2","DOIUrl":"https://doi.org/10.1895/wormbook.1.68.2","url":null,"abstract":"<p><p>Form follows function, and this maxim holds particularly true for the nematode sperm cell. Motility is essential for fertilization, and the process of spermatogenesis culminates in the production of a crawling spermatozoon with an extended pseudopod. However, the morphological similarity to amoeboid cells of other organisms is not conserved at the molecular level. Instead of utilizing the actin cytoskeleton and motor proteins, the pseudopod moves via the regulated assembly and disassembly of filaments composed of the major sperm protein (MSP). The current work reviews the structure and dynamics of MSP filament formation, the critical role of pH in MSP assembly, and the components that regulate this process. The combination of cytological, biochemical, and genetic approaches in this relatively simple system make nematode sperm an attractive model for investigating the mechanics of amoeboid cell motility. </p>","PeriodicalId":75344,"journal":{"name":"WormBook : the online review of C. elegans biology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2014-04-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5402208/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"32247692","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 26
Modern techniques for the analysis of chromatin and nuclear organization in C. elegans. 秀丽隐杆线虫染色质和核组织分析的现代技术。
WormBook : the online review of C. elegans biology Pub Date : 2014-04-02 DOI: 10.1895/wormbook.1.169.1
Peter Askjaer, Sevinç Ercan, Peter Meister
{"title":"Modern techniques for the analysis of chromatin and nuclear organization in C. elegans.","authors":"Peter Askjaer,&nbsp;Sevinç Ercan,&nbsp;Peter Meister","doi":"10.1895/wormbook.1.169.1","DOIUrl":"https://doi.org/10.1895/wormbook.1.169.1","url":null,"abstract":"<p><p>In recent years, Caenorhabditis elegans has emerged as a new model to investigate the relationships between nuclear architecture, cellular differentiation, and organismal development. On one hand, C. elegans with its fixed lineage and transparent body is a great model organism to observe gene functions in vivo in specific cell types using microscopy. On the other hand, two different techniques have been applied in nematodes to identify binding sites for chromatin-associated proteins genome-wide: chromatin immunoprecipitation (ChIP), and Dam-mediated identification (DamID). We summarize here all three techniques together as they are complementary. We also highlight strengths and differences of the individual approaches. </p>","PeriodicalId":75344,"journal":{"name":"WormBook : the online review of C. elegans biology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2014-04-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4781626/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"32240291","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 32
Thermotaxis navigation behavior. 热致性导航行为。
WormBook : the online review of C. elegans biology Pub Date : 2014-02-20 DOI: 10.1895/wormbook.1.168.1
Miriam B Goodman, Mason Klein, Samuel Lasse, Linjiao Luo, Ikue Mori, Aravi Samuel, Piali Sengupta, Dong Wang
{"title":"Thermotaxis navigation behavior.","authors":"Miriam B Goodman,&nbsp;Mason Klein,&nbsp;Samuel Lasse,&nbsp;Linjiao Luo,&nbsp;Ikue Mori,&nbsp;Aravi Samuel,&nbsp;Piali Sengupta,&nbsp;Dong Wang","doi":"10.1895/wormbook.1.168.1","DOIUrl":"https://doi.org/10.1895/wormbook.1.168.1","url":null,"abstract":"<p><p>This chapter describes four different protocols used to assay thermotaxis navigation behavior of single, or populations of, C. elegans hermaphrodites on spatial thermal gradients within the physiological temperature range (15-25°C). A method to assay avoidance of noxious temperatures is also described. </p>","PeriodicalId":75344,"journal":{"name":"WormBook : the online review of C. elegans biology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2014-02-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5410636/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"32149622","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 18
Forward and reverse mutagenesis in C. elegans. 秀丽隐杆线虫的正向和反向诱变。
WormBook : the online review of C. elegans biology Pub Date : 2014-01-17 DOI: 10.1895/wormbook.1.167.1
Lena M Kutscher, Shai Shaham
{"title":"Forward and reverse mutagenesis in C. elegans.","authors":"Lena M Kutscher,&nbsp;Shai Shaham","doi":"10.1895/wormbook.1.167.1","DOIUrl":"https://doi.org/10.1895/wormbook.1.167.1","url":null,"abstract":"Mutagenesis drives natural selection. In the lab, mutations allow gene function to be deciphered. C. elegans is highly amendable to functional genetics because of its short generation time, ease of use, and wealth of available gene-alteration techniques. Here we provide an overview of historical and contemporary methods for mutagenesis in C. elegans, and discuss principles and strategies for forward (genome-wide mutagenesis) and reverse (target-selected and gene-specific mutagenesis) genetic studies in this animal.","PeriodicalId":75344,"journal":{"name":"WormBook : the online review of C. elegans biology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2014-01-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4078664/pdf/nihms-585447.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"32049678","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 81
C. elegans gene transformation by microparticle bombardment. 微粒子轰击秀丽隐杆线虫基因转化。
WormBook : the online review of C. elegans biology Pub Date : 2013-12-30 DOI: 10.1895/wormbook.1.166.1
Peter J Schweinsberg, Barth D Grant
{"title":"C. elegans gene transformation by microparticle bombardment.","authors":"Peter J Schweinsberg,&nbsp;Barth D Grant","doi":"10.1895/wormbook.1.166.1","DOIUrl":"https://doi.org/10.1895/wormbook.1.166.1","url":null,"abstract":"","PeriodicalId":75344,"journal":{"name":"WormBook : the online review of C. elegans biology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2013-12-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4050979/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"32004465","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 31
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