171,581 research outputs found
Perianal ultrasound (PAUS): visualization of sphincter muscles and comparison with digital-rectal examination (DRE) in females
No full textAbstract Background The aim of this study was to determine the reproducibility and tolerance of perianal ultrasound (PAUS) and detect differences in sphincter muscles between various measuring positions and different maneuvers. PAUS was compared to digital-rectal examination (DRE) to see if sphincter contraction is visible and gradable in ultrasound volumes. Methods Fifty women underwent a medical history, DRU and PAUS by two uro-gynecologists in a prospective trial. PAUS volumes were measured via different parameters in different maneuvers. Examiners’ DRE impressions of sphincter tone were scaled with the DRESS-score. All patients completed a questionnaire. Results Thirty-five patients with complete PAUS and DRE were included in the study. Fifteen patients were excluded due to poor ultrasound volume quality or sphincter defects. Comparison of sphincter muscle thickness at different positions in PAUS showed significant differences between 6 and 12 o’clock positions (12 > 6 o’clock) and diameters (horizontal > vertical). No difference was found between the examiners. In comparison of rest and contraction only the vertical diameter changed. There was a negative but not significant correlation between PAUS measurements and DRESS-scores. Twenty-six patients completed the questionnaire that revealed women preferred PAUS over DRE. Conclusion PAUS is a reproducible and good tool to visualize the anal canal. It is comfortable for patients and easily handled by examiners. Sphincter muscle contraction is iso-volumetric. Vertical diameter changes during contraction leading the anal canal change its shape to oval due to external influence. PAUS is the ideal additional tool to visualize relevant structures that are palpable on DRE
dre-miR-100-3p and dre-miR-16b affect viability of ZF4 cells and embryonic development of zebrafish.
No full text(A-B) ZF4 cells were transfected with indicated mimics or inhibitor, 24 hours later the cells were exposed to 10°C for 36 hours, then cell viability was examined. (C-D) Zebrafish embryos were microinjected with indicated mimics or inhibitor, 24 hours later the expression of miR-100-3p was detected by qRT-PCR (C), and viability of embryos was determined (n = 120) (D). *: p <0.05, **: p <0.01, ***: p <0.001. NC, negative control.</p
DRE-1/FBXO11-Dependent Degradation of BLMP-1/BLIMP-1 Governs C. elegans Developmental Timing and Maturation
No full textSummaryDevelopmental timing genes catalyze stem cell progression and animal maturation programs across taxa. Caenorhabditis elegans DRE-1/FBXO11 functions in an SCF E3-ubiquitin ligase complex to regulate the transition to adult programs, but its cognate proteolytic substrates are unknown. Here, we identify the conserved transcription factor BLMP-1 as a substrate of the SCFDRE-1/FBXO11 complex. blmp-1 deletion suppressed dre-1 mutant phenotypes and exhibited developmental timing defects opposite to dre-1. blmp-1 also opposed dre-1 for other life history traits, including entry into the dauer diapause and longevity. BLMP-1 protein was strikingly elevated upon dre-1 depletion and dysregulated in a stage- and tissue-specific manner. The role of DRE-1 in regulating BLMP-1 stability is evolutionary conserved, as we observed direct protein interaction and degradation function for worm and human counterparts. Taken together, posttranslational regulation of BLMP-1/BLIMP-1 by DRE-1/FBXO11 coordinates C. elegans developmental timing and other life history traits, suggesting that this two-protein module mediates metazoan maturation processes
DRE-1: An Evolutionarily Conserved F Box Protein that Regulates C. elegans Developmental Age
No full textSummaryDuring metazoan development, cells acquire both positional and temporal identities. The Caenorhabditis elegans heterochronic loci are global regulators of larval temporal fates. Most encode conserved transcriptional and translational factors, which affect stage-appropriate programs in various tissues. Here, we describe dre-1, a heterochronic gene, whose mutant phenotypes include precocious terminal differentiation of epidermal stem cells and altered temporal patterning of gonadal outgrowth. Genetic interactions with other heterochronic loci place dre-1 in the larval-to-adult switch. dre-1 encodes a highly conserved F box protein, suggesting a role in an SCF ubiquitin ligase complex. Accordingly, RNAi knockdown of the C. elegans SKP1-like homolog SKR-1, the cullin CUL-1, and ring finger RBX homologs yielded similar heterochronic phenotypes. DRE-1 and SKR-1 form a complex, as do the human orthologs, hFBXO11 and SKP1, revealing a phyletically ancient interaction. The identification of core components involved in SCF-mediated modification and/or proteolysis suggests an important level of regulation in the heterochronic hierarchy
Positional Cloning of the <i>dre</i> Mutant
No full text<div><p>(A) Schematic representation of assembled contig 11890 of the Zv2 genome assembly. SSLP markers z5395 and z25745 and newly identified SSLPs 11890.2A and 11890.2 were closely linked with the <i>dre</i> locus. Remaining recombinants of a complete panel of 765 mutant embryos are indicated. Four genes were predicted in the region of marker 11890.2A that encode Su(fu), TRC8, ubiquitin conjugating enzyme E2, and β-mannosidase precursor protein.</p><p>(B) The <i>dre</i> mutation is a C to an A substitution, changing a threonine to a lysine.</p><p>(C) Multiple alignment of Su(fu) homologs revealed that the induced mutation changes an amino acid in a highly conserved region of Su(fu).</p></div
Going Beyond Counting First Authors in Author Co-citation Analysis
No full textThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Coordination of Developmental Timing and Maturation by the F-box Protein DRE-1/FBXO11
No full textSpatiotemporal control of cellular events is key to developmental progression in all organisms. Accordingly the abundance of regulatory proteins must be tightly controlled in a highly time- and tissue-specific manner. Pioneering work in the small roundworm Caenorhabditis elegans (C. elegans) has uncovered a network of genes, termed the heterochronic loci, which govern temporal coordination of developmental processes. Importantly this heterochronic network is remarkably conserved across species. There are currently over 30 identified heterochronic loci, which encode various transcriptional, translational and post-translational regulators including the first discovered microRNAs lin-4 and let-7.
In 2007 our laboratory discovered a novel heterochronic gene, dre-1, which specifies late larval development in the C. elegans epidermis and gonad. Interestingly dre-1 encodes a highly conserved F-box protein; F-box proteins typically function as substrate recognition components of SCF E3-ubiquitin ligase complexes, thus conferring substrate specificity to the ubiquitin proteasome system (UPS). The initial analysis of DRE-1 and its mammalian homolog FBXO11 revealed their interaction with SCF complex components, suggesting conservation also on the functional level. Mutation of C. elegans dre-1 leads to a diverse array of developmental alterations including precocious terminal differentiation of epidermal blast cells, molting defects and alterations in gonadal outgrowth. Likewise, haploinsuffiency of Fbxo11 has been linked to craniofacial malformations such as cleft palates, as well as otitis media, an inflammation of the middle ear, in both mice and men. Furthermore, FBXO11 was recently shown to function as a tumor suppressor in lymphoid malignancies by controlling turnover of the oncoprotein BCL6. However, the DRE-1/FBXO11 substrate(s) coordinating developmental progression still remain to be elucidated. Thus the central questions of my thesis are: what are the substrates of DRE-1/FBXO11 in the heterochronic circuit, and how do they illuminate developmental timing events?
In an effort to identify novel substrates of the SCFDRE-1/FBXO11 E3-ubiquitin ligase complex involved in developmental timing, I pursued an RNAi-based suppressor approach in C. elegans. I reasoned that client substrates should aberrantly accumulate in dre-1 mutants and cause developmental alterations across tissues. If so, then knockdown of such substrates would ameliorate related phenotypes. Here, I identified the highly conserved zinc-finger transcriptional repressor BLMP-1 as a new substrate of the SCFDRE-1 complex. Several lines of evidence reveal that BLMP-1 is a substrate of the SCFDRE-1 complex in developmental timing circuits. First, blmp-1 loss of function strongly suppressed dre-1 heterochronic phenotypes in epidermis and gonad and blmp-1 mutation itself exhibited developmental timing defects opposite to dre-1. blmp-1 also opposed dre-1 for other life history traits such as entry into the dauer diapause and adult longevity. Second, BLMP-1 protein was strikingly elevated upon depletion of dre-1 and other SCF complex components, as well as by inhibition of the proteasome. Moreover, BLMP-1 was regulated in a time- and tissue-specific manner by dre-1, consistent with corresponding phenotypes. Third, DRE-1 and BLMP-1 physically interacted in vivo in C. elegans and in vitro in a cell-based system. Importantly the role of DRE-1 in regulating BLMP-1 stability is evolutionary conserved, as direct protein interaction and degradation function was also observed for the human counterparts FBXO11 and BLIMP-1.
In addition to blmp-1, I also investigated genetic interactions of dre-1 and cdt-2 in C. elegans, since CDT2 was recently identified as a FBXO11 substrate in mammalian systems. I found cdt-2 to genetically interact with dre-1 for specific processes in the epidermis. In particular gaps in an adult-specific cuticular structure occurring in dre-1 mutants could arise from elevated CDT-2 levels and a subsequent failure of cell cycle exit of epidermal blast cells, which synthesize these structures. My findings are in line with mammalian studies that established CDT2, which itself is part of an E3-ubiqitin ligase complex, as a critical cell cycle regulator by targeting substrates such as the CDK inhibitor p21 for proteasomal degradation.
Altogether I conclude that dre-1 mutants’ diverse developmental alterations arise from aberrant accumulation of distinct target proteins. In particular, my work shows that spatiotemporal control of BLMP-1 protein by DRE-1 coordinates developmental timing and other life history traits in C. elegans. DRE-1, on the one hand, restrains BLMP-1 abundance in the epidermis to prevent precocious terminal differentiation and, on the other hand, triggers BLMP-1 degradation in distal tip cells to initiate dorso-ventral migratory events. The notion that DRE-1/BLMP-1 work together for multiple processes suggests these proteins comprise a two-protein module that may mediate related metazoan maturation processes. Taken together, my work fundamentally contributes to the understanding of developmental timing coordination by DRE-1/FBXO11 in C. elegans and might help to shed light on related processes in higher organisms
Model-Driven Techniques for Evaluating the QoS of Middleware Configurations for DRE Systems
No full textThis paper provides two contributions to R&D on modeldriven development (MDD) techniques that help codify the impact of middleware configurations on end-to-end distributed real-time and embedded (DRE) system quality of service (QoS). First, we describe how MDD techniques can help select middleware configuration parameters that satisfy key functional and QoS requirements of DRE systems. Second, we apply our MDD techniques to empirically evaluate the end-to-end QoS of representative DRE systems in the avionics and industrial manufacturing domains. Our results show how MDD techniques significantly enhance conventional ad hoc processes used by developers to configure middleware that meets the QoS needs of DRE systems
<i>CBF</i> (<i>C-REPEAT/DRE BINDING FACTOR</i>) co-expression cluster is induced by submergence in maize.
No full text<p>(a.) <i>CBF</i> co-expression network generated form genes differentially expressed at 24 h in comparisons between submerged and control plants. Each gene in the network is represented as a circle. (b.) Genes highlighted in the heatmap are represented by grey circles, while that with a red outline indicates the seed gene for the network. The heatmap highlights the expression of a subset of genes in B73, B97, Mo18W and M162W after 24 h of submergence. (c.) Expression of highlighted genes at 72 h after submergence. All genes showed significant differences in expression between submerged and control plants (FDR <0.001). The scale indicates log<sub>2</sub> fold-change. Up-regulation indicates higher expression in submerged samples. <i>CBF2</i>: <i>C-REPEAT/DRE BINDING FACTOR2</i>; <i>CBF3</i>: <i>C-REPEAT/DRE BINDING FACTOR3</i>; <i>ERF7</i>: <i>ETHYLENE RESPONSE FACTOR7</i>; <i>RRTF1</i>: <i>REDOX REPONSIVE TRANSCRIPTION FACTOR1</i></p
DRE-1/FBXO11, a Conserved F Box Protein, Regulates Apoptosis in C. elegans and is Mutated in Human Lymphoma
No full textIn the course of metazoan embryonic and post-embryonic development, more cells are generated than exist in the mature organism, and these cells are deleted by the process of programmed cell death. In addition, cells can be pushed toward death when they accumulate genetic errors, are virally-infected or are otherwise deemed potentially-harmful to the overall organism. Caenorhabditis elegans has proved to be an excellent model system for elucidating the genetic underpinnings of cell death, and research has shown that the core machinery, made up of the egl-1, ced-9, ced-4 and ced-3 genes, is conserved across metazoans, and their homologues are crucial for such diseases as cancer, neurodegeneration and autoimmunity. We used the C. elegans tail-spike cell as a model to uncover dre-1/FBXO11 as a conserved apoptotic regulator that controls tail-spike cell death and also plays a role in human lymphoma. The tail-spike cell is unique among cells fated for programmed cell death in two ways. First, unlike most dying C. elegans cells, the tail-spike cell lives for several hours before its demise, and during this time differentiates. In comparison, most cells die minutes after birth as undifferentiated cells. Second, while tail-spike cell death requires both the CED-3 caspase and CED-4/Apaf-1 adaptor proteins, the BH3-only protein EGL-1 is dispensable. Thus, other gene(s) substitute for egl-1\u27s role as a regulator of caspase activation in this cell, and we set out to identify the relevant gene or genes. A screen for mutants in which the tail-spike cell survives inappropriately yielded a mutant, ns39, in which the ced-3 caspase is transcribed as normal, but fails to become activated. We mapped and cloned this mutant, and found that dre-1 (daf-12-redundant-1) is required for caspase activation in the tail-spike cell. Expression of the dre-1 cDNA in the tail-spike cell rescues the dre-1(ns39) defect in a cell autonomous manner, and expression studies show that dre-1 is expressed in the tail-spike cell. Partial loss-of-function alleles of dre-1, when combined with weak loss-of-function alleles of ced-3 and ced-4, a null allele of egl-1, or a weak gain-of-function allele of ced-9 exhibit a synergistic loss of tailspike cell death. A null allele of ced-9, however, when combined with a strong loss-of-function dre-1 allele, suppresses the tail-spike cell death phenotype of the dre-1(ns39). This epistatic relationship shows that dre-1 acts upstream of, or in parallel to ced-9. These results show that dre-1 has a central role in tail-spike cell death, and are consistent with it acting in place of egl-1 to promote tail-spike cell death. DRE-1 is an F box protein, and we showed via RNAi and genetic experiments that DRE-1 acts in an SCF complex with CUL-1 and SKR-1 to regulate tail-spike cell death, and present evidence that DRE-1 and CED-9 bind to each other in vitro. These results suggest a model in which the dre-1 SCF complex ubiquitinates CED-9 to eliminate its anti-apoptotic function and open the way for the cell to die. A collaboration with Louis Staudt and Lixin Rui at the National Cancer Institute revealed that dre-1ʼs human homologue, FBXO11 is mutated or deleted in 5% of germinal center-like diffuse large B cell lymphomas, and that reintroduction of the gene into lymphoma cell lines that have deleted it induces apoptosis. In addition, FBXO11 binds to BCL2 in lymphoma cell lines and induces the degradation of BCL2, and expression of BCL2 rescues the toxicity of FBXO11. Taken together, our results establish dre-1/FBXO11 as a regulator of apoptosis in C. elegans and human lymphoma, and suggest a model in which DRE-1/FBXO11 ubiquitinates and degrades BCL2, a major anti-apoptotic protein
- …
