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Commun Integr Biol,
2011]
Positioning of centrosomes within cells determines the directionality of cell division, as well as directionality of cellular activities in the interphase. This brief review focuses on similarities (and differences) of centrosome positioning during early divisions in the Caenorhabditis embryo and during the interaction of T lymphocytes with other cells in the course of immune response. In the study of the two phenomena, a synergy of experimentation and numerical mechanical analysis has recently been achieved. The picture that emerges from these studies is one in which simple physical forces under the constraints of the basic cell structure lead to complex, "life-like" mechanical behavior. This behavior includes instability of equilibria, irreversibility of structural transitions and multidimensional, multiperiodic oscillations. This new picture of cell mechanics may form an interesting paradigm for future research.
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J Biol Phys,
2017]
We investigate free energy behavior in the nematode Caenorhabditis elegans during embryonic development. Our approach utilizes publicly available gene expression data, which gives us a picture of developmental changes in protein concentration and, resultantly, chemical potential and free energy. Our results indicate a clear global relationship between Gibbs free energy and time spent in development and provide thermodynamic indicators of the large-scale biological events of cell division and differentiation.
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Genet Mol Res,
2006]
The expressed sequence tag (EST) is an instrument of gene discovery. When available in large numbers, ESTs may be used to estimate gene expression. We analyzed gene expression by EST sampling, using the KOG database, which includes 24,154 proteins from Arabidopsis thaliana (Ath), 17,101 from Caenorhabditis elegans (Cel), 10,517 from Drosophila melanogaster (Dme), and 26,324 from Homo sapiens (Hsa), and 178,538 ESTs for Ath, 215,200 for Cel, 261,404 for Dme, and 1,941,556 for Hsa. BLAST similarity searches were performed to assign KOG annotation to all ESTs. We determined the amount of gene sampling or expression dedicated to each KOG functional category by each model organism. We found that the 25% most-expressed genes are frequently shared among these organisms. The KOG protein classification allowed the EST sampling calculation throughout the glycolysis pathway. We calculated the KOG cluster coverage and inferred that 50 to 80 K ESTs would efficiently cover 80-85% of the KOG database clusters in a transcriptome project. Since KOG is a database biased towards housekeeping genes, this is probably the number of ESTs needed to include the more commonly expressed genes in these organisms. We also examined a still unaddressed question: what is the minimum number of ESTs that should be produced in a transcriptome project?
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Genome Biol,
2007]
ABSTRACT: BACKGROUND: With its fully sequenced genome and simple, well-defined nervous system, the nematode C. elegans offers a unique opportunity to correlate gene expression with neuronal differentiation. The lineal origin, cellular morphology and synaptic connectivity of each of the 302 neurons are known. In many instances, specific behaviors can be attributed to particular neurons or circuits. Here we describe microarray-based methods that monitor gene expression in C. elegans neurons and thereby link comprehensive profiles of neuronal transcription to key developmental and functional properties of the nervous system. RESULTS: We employed complementary microarray-based strategies to profile gene expression in the embryonic and larval nervous systems. In the MAPCeL (Microarray Profiling C. elegans cells) method, we used Fluorescence Activated Cell Sorting (FACS) to isolate GFP-tagged embryonic neurons for microarray analysis. To profile the larval nervous system, we used the mRNA-tagging technique in which an epitope-labeled mRNA binding protein (FLAG-PAB-1) was transgenically expressed in neurons for immunoprecipitation of cell-specific transcripts. These combined approaches identified approximately 2,500 mRNAs that are highly enriched in either the embryonic or larval C. elegans nervous system. These data are validated in part by the detection of gene classes (e.g. transcription factors, ion channels, synaptic vesicle components) with established roles in neuronal development or function. Of particular interest are 19 conserved transcripts of unknown function that are also expressed in the mammalian brain. In addition to utilizing these profiling approaches to define stage-specific gene expression, we also applied the mRNA-tagging method to fingerprint a specific neuron type, the A-class group of cholinergic motor neurons, during early larval development. A comparison of these data to a MAPCeL profile of Embryonic A-class motor neurons identified genes with common functions in both types of A-class motor neurons as well as transcripts with roles specific to each motor neuron type. Conclusion: We describe microarray-based strategies for generating expression profiles of embryonic and larval C. elegans neurons. These methods can be applied to particular neurons at specific developmental stages and therefore provide an unprecedented opportunity to obtain spatially and temporally defined snapshots of gene expression in a simple model nervous system.
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IEICE Transactions on Information & Systems,
1996]
Caenorhabditis elegans during feeding gives good ''moving biological images'', in which motions of several pulsing organs are superposed on its head swing. A powerful method to extract dynamic features is presented. First step is to use a variance picture VAG4 in order to pick up active pixel coordinates of concerned moving objects. Superiority of VAG4 over usual variance picture VAG2 is shown quantitatively by a model of moving particles. Pulsing areas of C. elegans, are exhibited more clearly in VAG4 than VAG2. Second step is use of a new subtraction method to extract main frequency bands. FFT spectra are averaged in active positions where VAG4 is above threshold THVR in the square with 8 X 8 pixels (ONA). The power spectra averaged in the enlarged squares (ELA) are subtracted from those in ONA, in which ELA includes ONA in its centre position. Large peak bands emerge in the subtracted power spectra, The subtraction eliminates the effect of head swing by spatial averagings in ELA. This new emphasizing method is compared to another subtraction method, The characteristic frequency of periodical moving organs coincides well with the values observed by other research groups and our visual estimation of replayed VTR images. Thus the proposed extraction method is verified to work
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Arch Biochem Biophys,
2016]
Zinc is an essential metal that is involved in a wide range of biological processes, and aberrant zinc homeostasis is implicated in multiple human diseases. Cadmium is chemically similar to zinc, but it is a nonessential environmental pollutant. Because zinc deficiency and excess are deleterious, animals require homeostatic mechanisms to maintain zinc levels in response to dietary fluctuations. The nematode Caenorhabditis elegans is emerging as a powerful model system to investigate zinc trafficking and homeostasis as well as cadmium toxicity. Here we review genetic and molecular studies that have combined to generate a picture of zinc homeostasis based on the transcriptional control of zinc transporters in intestinal cells. Furthermore, we summarize studies of cadmium toxicity that reveal intriguing parallels with zinc biology.
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Toxicol Res (Camb),
2015]
Manganese (Mn) is one of the most abundant metals on the earth. It is required for normal cellular activities, but overexposure leads to toxicity. Neurons are more susceptible to Mn-induced toxicity than other cells, and accumulation of Mn in the brain results in Manganism that presents with Parkinson's disease (PD)-like symptoms. In the last decade, a number of Mn transporters have been identified, which improves our understanding of Mn transport in and out of cells. However, the mechanism of Mn-induced neurotoxicity is only partially uncovered, with further research needed to explore the whole picture of Mn-induced toxicity. In this review, we will address recent progress in Mn-induced neurotoxicity from C. elegans to humans, and explore future directions that will help understand the mechanisms of its neurotoxicity.
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FEMS Microbiol Ecol,
2016]
Be it their pervasiveness, experimental tractability or their impact on human health and agriculture, nematode-bacterium associations are far-reaching research subjects. Although the omics hype did not spare them and helped reveal mechanisms of communication and exchange between the associated partners, a huge amount of knowledge still awaits to be harvested from their study. Here, I summarize and compare the kind of research that has been already performed on the model nematode Caenorhabditis elegans and on symbiotic nematodes, both marine and entomopathogenic ones. The emerging picture highlights how complementing genetic studies with ecological ones (in the case of well-established genetic model systems such as C. elegans) and vice versa (in the case of the yet uncultured Stilbonematinae) will deepen our understanding of how microbial symbioses evolved and how they impact our environment.
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Bull World Health Organ,
1962]
The author reviews the distribution, epidemiology, and treatment of filarial infection due to Brugia malayi, with special reference to Malaya. B. malayi infection in man is confined to the Far East between longitudes 75 degrees E and 140 degrees E and is essentially rural. The chief vectors are Mansonia spp., Anopheles hyrcanus group, A. barbirostris group, and Aedes togoi. The epidemiological picture is complicated by the fact that B. malayi and other closely related species have now been found in several species of animals. The existence of an animal reservoir of infection might have important implications for filariasis control. As to the treatment of B. malayi infection, diethylcarbamazine has been found to reduce the microfilaria count and to kill the adult worms; the severe febrile reactions of microfilaria carriers to the initial doses of this drug may be reduced by administration of the steroid prednisolone.
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PLoS One,
2011]
Unraveling the functional dynamics of phosphorylation networks is a crucial step in understanding the way in which biological networks form a living cell. Recently there has been an enormous increase in the number of measured phosphorylation events. Nevertheless, comparative and integrative analysis of phosphoproteomes is confounded by incomplete coverage and biases introduced by different experimental workflows. As a result, we cannot differentiate whether phosphosites indentified in only one or two samples are the result of condition or species specific phosphorylation, or reflect missing data. Here, we evaluate the impact of incomplete phosphoproteomics datasets on comparative analysis, and we present bioinformatics strategies to quantify the impact of different experimental workflows on measured phosphoproteomes. We show that plotting the saturation in observed phosphosites in replicates provides a reproducible picture of the extent of a particular phosphoproteome. Still, we are still far away from a complete picture of the total human phosphoproteome. The impact of different experimental techniques on the similarity between phosphoproteomes can be estimated by comparing datasets from different experimental pipelines to a common reference. Our results show that comparative analysis is most powerful when datasets have been generated using the same experimental workflow. We show this experimentally by measuring the tyrosine phosphoproteome from Caenorhabditis elegans and comparing it to the tyrosine phosphoproteome of HeLa cells, resulting in an overlap of about 4%. This overlap between very different organisms represents a three-fold increase when compared to dataset of older studies, wherein different workflows were used. The strategies we suggest enable an estimation of the impact of differences in experimental workflows on the overlap between datasets. This will allow us to perform comparative analyses not only on datasets specifically generated for this purpose, but also to extract insights through comparative analysis of the ever-increasing wealth of publically available phosphorylation data.