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Selected AbstractsComparative genomic and expression analysis of group B1 sox genes in zebrafish indicates their diversification during vertebrate evolutionDEVELOPMENTAL DYNAMICS, Issue 3 2006Yuich Okuda Abstract Group B1 Sox genes encode HMG domain transcription factors that play major roles in neural development. We have identified six zebrafish B1 sox genes, which include pan-vertebrate sox1a/b, sox2, and sox3, and also fish-specific sox19a/b. SOX19A/B proteins show a transcriptional activation potential that is similar to other B1 SOX proteins. The expression of sox19a and sox3 begins at approximately the 1,000-cell stage during embryogenesis and becomes confined to the future ectoderm by the shield stage. This is reminiscent of the epiblastic expression of Sox2 and/or Sox3 in amniotes. As development progresses, these six B1 sox genes display unique expression patterns that overlap distinctly from one region to another. sox19a expression is widespread in the early neuroectoderm, resembling pan-neural Sox2 expression in amniotes, whereas zebrafish sox2 shows anterior-restricted expression. Comparative genomics suggests that sox19a/b and mammalian Sox15 (group G) have an orthologous relationship and that the B1/G Sox genes arose from a common ancestral gene through two rounds of genome duplication. It seems likely, therefore, that each B1/G Sox gene has gained a distinct expression profile and function during vertebrate evolution. Developmental Dynamics 235:811,825, 2006. © 2006 Wiley-Liss, Inc. [source] Dynamics of marine bacterial and phytoplankton populations using multiplex liquid bead array technologyENVIRONMENTAL MICROBIOLOGY, Issue 4 2010Xavier Mayali Summary Heterotrophic bacteria and phytoplankton dominate the biomass and play major roles in the biogeochemical cycles of the surface ocean. Here, we designed and tested a fast, high-throughput and multiplexed hybridization-based assay to detect populations of marine heterotrophic bacteria and phytoplankton based on their small subunit ribosomal DNA sequences. The assay is based on established liquid bead array technology, an approach that is gaining acceptance in biomedical research but remains underutilized in ecology. End-labelled PCR products are hybridized to taxon-specific oligonucleotide probes attached to fluorescently coded beads followed by flow cytometric detection. We used ribosomal DNA environmental clone libraries (a total of 450 clones) and cultured isolates to design and test 26 bacterial and 10 eukaryotic probes specific to various ribotypes and genera of heterotrophic bacteria and eukaryotic phytoplankton. Pure environmental clones or cultures were used as controls and demonstrated specificity of the probes to their target taxa. The quantitative nature of the assay was demonstrated by a significant relationship between the number of target molecules and fluorescence signal. Clone library sequencing and bead array fluorescence from the same sample provided consistent results. We then applied the assay to a 37-day time series of coastal surface seawater samples from the Southern California Bight to examine the temporal dynamics of microbial communities on the scale of days to weeks. As expected, several bacterial phylotypes were positively correlated with total bacterial abundances and chlorophyll a concentrations, but others were negatively correlated. Bacterial taxa belonging to the same broad taxonomic groups did not necessarily correlate with one another, confirming recent results suggesting that inferring ecological role from broad taxonomic identity may not always be accurate. [source] Cross-species divergence of the major recognition pathways of ubiquitylated substrates for ubiquitin/26S proteasome-mediated proteolysisFEBS JOURNAL, Issue 3 2010Antony S. Fatimababy The recognition of ubiquitylated substrates is an essential element of ubiquitin/26S proteasome-mediated proteolysis (UPP), which is mediated directly by the proteasome subunit RPN10 and/or RPN13, or indirectly by ubiquitin receptors containing ubiquitin-like and ubiquitin-associated domains. By pull-down and mutagenesis assays, we detected cross-species divergence of the major recognition pathways. RPN10 plays a major role in direct recognition in Arabidopsis and yeast based on the strong affinity for the long and K48-linked ubiquitin chains. In contrast, both the RPN10 and RPN13 homologs play major roles in humans. For indirect recognition, the RAD23 and DSK2 homologs (except for the human DSK2 homolog) are major receptors. The human RAD23 homolog is targeted to the 26S proteasome by the RPN10 and RPN13 homologs. In comparison, Arabidopsis uses UIM1 and UIM3 of RPN10 to bind DSK2 and RAD23, respectively. Yeast uses UIM in RPN10 and LRR in RPN1. Overall, multiple proteasome subunits are responsible for the direct and/or indirect recognition of ubiquitylated substrates in yeast and humans. In contrast, a single proteasome subunit, RPN10, is critical for both the direct and indirect recognition pathways in Arabidopsis. In agreement with these results, the accumulation of ubiquitylated substrates and severe pleiotropic phenotypes of vegetative and reproductive growth are associated with the loss of RPN10 function in an Arabidopsis T-DNA insertion mutant. This implies that the targeting and proteolysis of the critical regulators involved are affected. These results support a cross-species mechanistic and functional divergence of the major recognition pathways for ubiquitylated substrates of UPP. Structured digital abstract ,,A list of the large number of protein-protein interactions described in this article is available via the MINT article ID MINT-7307429 [source] TCDD suppresses insulin-responsive glucose transporter (GLUT-4) gene expression through C/EBP nuclear transcription factors in 3T3-L1 adipocytesJOURNAL OF BIOCHEMICAL AND MOLECULAR TOXICOLOGY, Issue 2 2006Phillip Chin-Chen Liu Abstract TCDD is known to reduce significantly the level of the functionally active form of glucose transporter type 4 (GLUT4) in vivo in adipose tissue and muscles. To study the mechanistic basis of this phenomenon, we conducted transient transfection and DNA deletion analysis in 3T3-L1 cells using chloramphenicol acetyltransferase (CAT) reporter plasmids containing the GLUT4 promoter joined to the bacterial CAT. It was found that in transfected control samples, CAT activity was significantly higher in cells transfected with p469CAT and p273CAT than those with p78CAT, indicating that the region between ,78 and ,273 contained elements that play major roles in transactivation of this gene. Treatment with TCDD decreased CAT activity with p469CAT and p273CAT, but not with p78CAT, indicating the same region to contain the element(s) affected by TCDD. A gel-shift (EMSA) analysis result indicated that TCDD shows the profound effect only on the nuclear proteins binding to the [32P]-labeled probe containing C/EBP response element equivalent of the ,265 to ,242 stretch of the GLUT4 promoter. The results of supershift analysis showed that TCDD caused a decrease in the tier of C/EBP, and an increase in that of C/EBP, among the proteins bound to this C/EBP response element. We studied the effect of TCDD in cells overexpressing either C/EBP,, C/EBP,, or C/EBP, through transient transfection of p273CAT or p469CAT. The results clearly showed that the effect of TCDD to suppress the CAT activity of p273 or p469 disappeared in those cells overexpressing C/EBP, or C/EBP,. These results implicate the C/EBP proteins to be the main mediator of suppressive action of TCDD on GLUT4 gene expression in 3T3-L1 cells. © 2006 Wiley Periodicals, Inc. J Biochem Mol Toxicol 20:79,87, 2006; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/jbt.20120 [source] Fine-scale environmental variation and structure of understorey plant communities in two old-growth pine forestsJOURNAL OF ECOLOGY, Issue 2 2003Lee E. Frelich Summary 1Although it is well established that nitrogen and light play major roles in structuring plant communities across the landscape, it is not as clear how they structure communities within forest stands. Virtually nothing is known about within-stand structure of understorey communities of herbs and small shrubs in near-boreal forests. 2We tested the hypothesis that fine-scale (5,20 m) variability in N and light structure forest-floor plant communities in two old-growth mixed Pinus resinosa and Pinus strobus forests in north-eastern Minnesota, USA. 3In each forest, all trees > 1.4 m tall were mapped on a 0.75,1.0 ha area. A grid of subplots 5,10 m apart was established (total n = 147), and N mineralization (µg g,1 soil day,1), soil depth (cm), light (% canopy openness), and percentage cover of all herbs and small shrubs were measured on each subplot. 4Cluster analysis showed that the dominant understorey species fall into three groups. Group 1 is unrelated to N and light, and is negatively associated with a midstorey of the small tree Acer rubrum and the most abundant tall shrub Corylus cornuta. Group 2 reaches maximum abundance in places (mostly gaps) with relatively high light, but is unrelated to within-stand variation in N availability. Group 3 consists of a single species, Aster macrophyllus, and reaches maximum abundance in areas with low N availability and low abundance of Corylus, but higher than average abundance of P. strobus and Betula papyrifera overstorey trees. 5N and light have a moderate influence on understorey plant community structure. The plant species do arrange themselves along N and light gradients, but the gradients are likely to be too narrow to allow the degree of differentiation seen at the landscape level. Spatial patterning of the species groups is probably influenced by other factors, including disturbance history, chance and neighbourhood effects such as clonal reproduction. [source] The role of osteoclast differentiation in aseptic loosening,JOURNAL OF ORTHOPAEDIC RESEARCH, Issue 1 2002Edward M. Greenfields The major cause of orthopaedic implant loosening is thought to be accelerated osteoclastic bone resorption due to the action of cytokines produced in response to phagocytosis of implant-derived wear particles. This accelerated osteoclastic bone resorption could be due to increases in any of the following processes: recruitment of osteoclast precursors to the local microenvironment, differentiation of precursors into mature multinucleated osteoclasts, activation of mature osteoclasts, and/or survival of osteoclasts. Our studies have focused on differentiation and survival to complement work by others who have focused on recruitment of precursors and activation. Taken together, our studies and those of other investigators provide strong evidence that increased recruitment of osteoclast precursors and their subsequent differentiation play major roles in wear particle-induced osteolysis. In contrast, increased osteoclast activation and survival appear to play minor roles. These studies suggest that development of therapeutic interventions that reduce either recruitment or differentiation of osteoclast precursors would improve the performance of orthopaedic implants. © 2002 Orthopaedic Research Society. Published by Elsevier Science Ltd. All rights reserved. [source] Differences in the crystal structures of two dialkyl diester triphenylphosphonium ylidsACTA CRYSTALLOGRAPHICA SECTION C, Issue 4 2007María Teresa Garland Hydrogen bonding and crystal packing play major roles in determining the conformations of ethyl methyl 2-(triphenylphosphoranylidene)malonate, Ph3P=C(CO2CH3)CO2CH2CH3 or C24H23O4P, (I), and dimethyl 2-(triphenylphosphoranylidene)malonate, Ph3P=C(CO2CH3)2 or C23H21O4P, (II). In (I), the acyl O atom of the ethyl ester group is anti to the P atom, while the O atom of the methyl ester group is syn. In (II), the dimethyl diester is a 1:1 mixture of anti,anti and syn,anti conformers. [source] Mediation of interleukin-1,,induced transforming growth factor ,1 expression by activator protein 4 transcription factor in primary cultures of bovine articular chondrocytes: Possible cooperation with activator protein 1ARTHRITIS & RHEUMATISM, Issue 6 2003R. Andriamanalijaona Objective Interleukin-1 (IL-1) and transforming growth factor ,1 (TGF,1) play major roles in osteoarticular diseases, exerting opposite effects on both the catabolism and anabolism of cartilage matrix. Previous findings suggest that IL-1 and TGF,1 could function in a feedback interaction. However, the effect exerted by IL-1 on expression of TGF, by articular chondrocytes is, so far, poorly understood. The present study was carried out to determine the influence of IL-1, on the expression of TGF,1 by bovine articular chondrocytes (BACs) in primary culture. Methods BAC primary cultures were treated with IL-1,, and TGF,1 messenger RNA (mRNA) steady-state levels and protein expression were measured by real-time reverse transcription,polymerase chain reaction and enzyme-linked immunosorbent assay, respectively. Transient transfection of TGF,1 gene promoter constructs was performed to delineate the DNA sequences that mediate the IL-1, effect. Electrophoretic mobility shift assays (EMSAs) and supershift analysis were used to characterize the transcription factors binding to these sequences. Results Cultured BACs responded to IL-1, exposure by exhibiting an increase of TGF,1 expression at both the mRNA and protein levels. The effect was found to be mediated by a major 80-bp sequence located between ,732 and ,652 upstream of the transcription initiation site. EMSA and supershift analysis revealed that the transcription factors activator protein 4 (AP-4) and AP-1 specifically bound to the ,720/,696 part of this sequence under IL-1, treatment. Overexpression of AP-4 in the BAC cultures resulted in stimulation of the transcriptional activity of the ,732/+11 TGF,1 promoter construct through the same IL-1,,responsive element. Conclusion IL-1, induces an increase of TGF,1 in articular chondrocytes through activation of AP-4 and AP-1 binding to the TGF,1 gene promoter. These findings may help us understand the role of IL-1, in the disease process. Notwithstanding its deleterious effect on cartilage, IL-1 could initiate the repair response displayed by injured cartilage in the early stages of osteoarthritis through its ability to enhance TGF,1 expression by local chondrocytes. [source] Role of mitochondrial ion channels in cell deathBIOFACTORS, Issue 4 2010Shin-Young Ryu Abstract Ion channels located in the outer and inner mitochondrial membranes are key regulators of cellular signaling for life and death. Permeabilization of mitochondrial membranes is one of the most critical steps in the progression of several cell death pathways. The mitochondrial apoptosis-induced channel (MAC) and the mitochondrial permeability transition pore (mPTP) play major roles in these processes. Here, the most recent progress and current perspectives about the roles of MAC and mPTP in mitochondrial membrane permeabilization during cell death are presented. The crosstalk signaling of MAC and mPTP formation/activation mediated by cytosolic Ca2+ signaling, Bcl-2 family proteins, and other mitochondrial ion channels is also discussed. Understanding the mechanisms that regulate opening and closing of MAC and mPTP has revealed new therapeutic targets that potentially could control cell death in pathologies such as cancer, ischemia/reperfusion injuries, and neurodegenerative diseases. [source] Hedgehog and Fgf signaling pathways regulate the development of tphR -expressing serotonergic raphe neurons in zebrafish embryosDEVELOPMENTAL NEUROBIOLOGY, Issue 3 2004H. Teraoka Abstract Serotonin (5HT) plays major roles in the physiological regulation of many behavioral processes, including sleep, feeding, and mood, but the genetic mechanisms by which serotonergic neurons arise during development are poorly understood. In the present study, we have investigated the development of serotonergic neurons in the zebrafish. Neurons exhibiting 5HT-immunoreactivity (5HT-IR) are detected from 45 h postfertilization (hpf) in the ventral hindbrain raphe, the hypothalamus, pineal organ, and pretectal area. Tryptophan hydroxylases encode rate-limiting enzymes that function in the synthesis of 5HT. As part of this study, we cloned and analyzed a novel zebrafish tph gene named tphR. Unlike two other zebrafish tph genes (tphD1 and tphD2), tphR is expressed in serotonergic raphe neurons, similar to tph genes in mammalian species. tphR is also expressed in the pineal organ where it is likely to be involved in the pathway leading to synthesis of melatonin. To better understand the signaling pathways involved in the induction of the serotonergic phenotype, we analyzed tphR expression and 5HT-IR in embryos in which either Hh or Fgf signals are abrogated. Hindbrain 5HT neurons are severely reduced in mutants lacking activity of either Ace/Fgf8 or the transcription factor Noi/Pax2.1, which regulates expression of ace/fgf8, and probably other genes encoding signaling proteins. Similarly, serotonergic raphe neurons are absent in embryos lacking Hh activity confirming a conserved role for Hh signals in the induction of these cells. Conversely, over-activation of the Hh pathway increases the number of serotonergic neurons. As in mammals, our results are consistent with the transcription factors Nk2.2 and Gata3 acting downstream of Hh activity in the development of serotonergic raphe neurons. Our results show that the pathways involved in induction of hindbrain serotonergic neurons are likely to be conserved in all vertebrates and help establish the zebrafish as a model system to study this important neuronal class. © 2004 Wiley Periodicals, Inc. J Neurobiol 60: 275,288, 2004 [source] | |||||||||||||