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https://www.readbyqxmd.com/read/29129923/ist1-regulates-escrt-iii-assembly-and-function-during-multivesicular-endosome-biogenesis-in-caenorhabditis-elegans-embryos
#1
E B Frankel, Raakhee Shankar, James J Moresco, John R Yates, Niels Volkmann, Anjon Audhya
Degradation of most integral membrane proteins is directed by the endosomal sorting complex required for transport (ESCRT) machinery, which selectively targets ubiquitin-modified cargoes into intralumenal vesicles (ILVs) within multivesicular endosomes (MVEs). To better understand the mechanisms underlying ESCRT-mediated formation of ILVs, we exploited the rapid, de novo biogenesis of MVEs during the oocyte-to-embryo transition in C. elegans. In contrast to previous models suggesting that ILVs form individually, we demonstrate that they remain tethered to one another subsequent to internalization, arguing that they bud continuously from stable subdomains...
November 13, 2017: Nature Communications
https://www.readbyqxmd.com/read/29091720/loss-of-the-caenorhabditis-elegans-pocket-protein-lin-35-reveals-muvb-s-innate-function-as-the-repressor-of-dream-target-genes
#2
Paul D Goetsch, Jacob M Garrigues, Susan Strome
The DREAM (Dp/Retinoblastoma(Rb)-like/E2F/MuvB) transcriptional repressor complex acts as a gatekeeper of the mammalian cell cycle by establishing and maintaining cellular quiescence. How DREAM's three functional components, the E2F-DP heterodimer, the Rb-like pocket protein, and the MuvB subcomplex, form and function at target gene promoters remains unknown. The current model invokes that the pocket protein links E2F-DP and MuvB and is essential for gene repression. We tested this model by assessing how the conserved yet less redundant DREAM system in Caenorhabditis elegans is affected by absence of the sole C...
November 2017: PLoS Genetics
https://www.readbyqxmd.com/read/29076351/activity-of-gallic-acid-and-its-ester-derivatives-in-caenorhabditis-elegans-and-zebrafish-danio-rerio-models
#3
Junya de Lacorte Singulani, Liliana Scorzoni, Paulo César Gomes, Ana Carolina Nazaré, Carlos Roberto Polaquini, Luis Octávio Regasini, Ana Marisa Fusco-Almeida, Maria José Soares Mendes-Giannini
AIM: Gallic acid and its ester derivatives have shown antifungal activity in vitro. This study was performed to investigate their activity against Candida albicans and their toxicity in the animal models Caenorhabditis elegans and zebrafish embryos. RESULTS: The compounds protected worms from C. albicans infection. The dodecyl gallate was the most effective. In zebrafish embryo, gallic acid and dodecyl gallate were the least toxic. CONCLUSION: Gallic acid and its ester derivatives have potential for in vivo use against C...
October 2017: Future Medicinal Chemistry
https://www.readbyqxmd.com/read/29075433/differences-in-the-genetic-control-of-early-egg-development-and-reproduction-between-c-elegans-and-its-parthenogenetic-relative-d-coronatus
#4
Christopher Kraus, Philipp H Schiffer, Hiroshi Kagoshima, Hideaki Hiraki, Theresa Vogt, Michael Kroiher, Yuji Kohara, Einhard Schierenberg
BACKGROUND: The free-living nematode Diploscapter coronatus is the closest known relative of Caenorhabditis elegans with parthenogenetic reproduction. It shows several developmental idiosyncracies, for example concerning the mode of reproduction, embryonic axis formation and early cleavage pattern (Lahl et al. in Int J Dev Biol 50:393-397, 2006). Our recent genome analysis (Hiraki et al. in BMC Genomics 18:478, 2017) provides a solid foundation to better understand the molecular basis of developmental idiosyncrasies in this species in an evolutionary context by comparison with selected other nematodes...
2017: EvoDevo
https://www.readbyqxmd.com/read/29074739/genome-wide-discovery-of-active-regulatory-elements-and-transcription-factor-footprints-in-caenorhabditis-elegans-using-dnase-seq
#5
Paul Sternberg, Margaret Ho, Porfirio Quintero-Cadena
Deep sequencing of size-selected DNase I-treated chromatin (DNase-seq) allows high resolution measurement of chromatin accessibility to DNase I cleavage, permitting identification of de novo active cis-regulatory modules (CRMs) and individual transcription factor (TF) binding sites. We adapted DNase-seq to nuclei isolated from C. elegans embryos and L1 arrest larvae to generate high-resolution maps of TF binding. Over half of embryonic DNase I hypersensitive sites (DHSs) were annotated as noncoding, with 24% in intergenic, 12% in promoters and 28% in introns, with similar statistics observed in L1 arrest larvae...
October 26, 2017: Genome Research
https://www.readbyqxmd.com/read/29058002/a-microfluidic-microinjector-for-toxicological-and-developmental-studies-in-drosophila-embryos
#6
Reza Ghaemi, Pouya Arefi, Ana Stosic, Meryl Acker, Qanber Raza, J Roger Jacobs, Ponnambalam Ravi Selvaganapathy
Microinjection is an established and reliable method to deliver biological reagents such as transgenic constructs and drugs, to specific locations inside organisms such as the Drosophila embryo and C. elegans worm. In this paper, a simple compliant mechanism based PDMS-microinjection system has been demonstrated. Unlike conventional microinjectors, this unique system could allow one to precisely insert a long taper microneedle laterally and at various positions inside the length of the Drosophila embryo (up to 250 μm) with the resolution of 5 μm...
November 7, 2017: Lab on a Chip
https://www.readbyqxmd.com/read/29049853/nutrient-driven-o-glcnac-in-proteostasis-and-neurodegeneration
#7
REVIEW
Ilhan Akan, Stephanie Olivier-Van Stichelen, Michelle R Bond, John A Hanover
Proteostasis is essential in the mammalian brain where post-mitotic cells must function for decades to maintain synaptic contacts and memory. The brain is dependent on glucose and other metabolites for proper function and is spared from metabolic deficits even during starvation. In this review, we outline how the nutrient sensitive nucleocytoplasmic posttranslational modification O-linked N-acetylglucosamine (O-GlcNAc) regulates protein homeostasis. The O-GlcNAc modification is highly abundant in the mammalian brain, and has been linked to proteopathies, including neurodegenerative diseases such as Alzheimer's, Parkinson's, and Huntington's...
October 19, 2017: Journal of Neurochemistry
https://www.readbyqxmd.com/read/29048526/comparative-transcriptomics-of-steinernema-and-caenorhabditis-single-embryos-reveals-orthologous-gene-expression-convergence-during-late-embryogenesis
#8
Marissa Macchietto, Dristi Angdembey, Negar Heidarpour, Lorrayne Serra, Bryan Rodriguez, Nicole El-Ali, Ali Mortazavi
Cells express distinct sets of genes in a precise spatio-temporal manner during embryonic development. There is a wealth of information on the deterministic embryonic development of Caenorhabditis elegans, but much less is known about embryonic development in nematodes from other taxa, especially at the molecular level. We are interested in insect pathogenic nematodes from the genus Steinernema as models of parasitism and symbiosis as well as a satellite model for evolution in comparison to C. elegans. To explore gene expression differences across taxa, we sequenced the transcriptomes of single embryos of two Steinernema species and two Caenorhabditis species at 11 stages during embryonic development and found several interesting features...
October 1, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/29043078/a-gap-that-divides
#9
REVIEW
Angika Basant, Michael Glotzer
Cytokinesis in metazoan cells is mediated by an actomyosin-based contractile ring that assembles in response to activation of the small GTPase RhoA. The guanine nucleotide exchange factor that activates RhoA during cytokinesis, ECT-2, is highly regulated. In most metazoan cells, with the notable exception of the early Caenorhabditis elegans embryo, RhoA activation and furrow ingression require the centralspindlin complex. This exception is due to the existence of a parallel pathway for RhoA activation in C...
2017: F1000Research
https://www.readbyqxmd.com/read/29030842/microrna-detection-by-whole-mount-in-situ-hybridization-in-c-elegans
#10
Yoshiki Andachi, Yuji Kohara
MicroRNAs (miRNAs) loaded on argonaute proteins guide RNA-induced silencing complexes to target mRNAs. An excellent method to decipher the spatiotemporal expression patterns of miRNAs is whole-mount in situ hybridization (WISH), which has been successfully used in vertebrate embryos but still remains unavailable for many animal species. Here, we describe a WISH method for miRNA detection in Caenorhabditis elegans at both embryonic and post-embryonic stages. Strategies devised for detection include fixation of animals with carbodiimide at a high temperature and subsequent partial digestion of the fixed animals with an extremely high concentration of proteinase...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29030390/apc-c-fzr-1-controls-sas-5-levels-to-regulate-centrosome-duplication-in-caenorhabditis-elegans
#11
Jeffrey C Medley, Lauren E DeMeyer, Megan M Kabara, Mi Hye Song
As the primary microtubule-organizing center, centrosomes play a key role in establishing mitotic bipolar spindles that secure correct transmission of genomic content. For the fidelity of cell division, centrosome number must be strictly controlled by duplicating only once per cell cycle. Proper levels of centrosome proteins are shown to be critical for normal centrosome number and function. Overexpressing core centrosome factors leads to extra centrosomes, while depleting these factors results in centrosome duplication failure...
October 13, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28994576/combined-computed-nanotomography-and-nanoscopic-x-ray-fluorescence-imaging-of-cobalt-nanoparticles-in-caenorhabditis-elegans
#12
Simone Cagno, Dag Anders Brede, Gert Nuyts, Frederik Vanmeert, Alexandra Pacureanu, Remi Tucoulou, Peter Cloetens, Gerald Falkenberg, Koen Janssens, Brit Salbu, Ole Christian Lind
Synchrotron radiation phase-contrast computed nanotomography (nano-CT) and two- and three-dimensional (2D and 3D) nanoscopic X-ray fluorescence (nano-XRF) were used to investigate the internal distribution of engineered cobalt nanoparticles (Co NPs) in exposed individuals of the nematode Caenorhabditis elegans. Whole nematodes and selected tissues and organs were 3D-rendered: anatomical 3D renderings with 50 nm voxel size enabled the visualization of spherical nanoparticle aggregates with size up to 200 nm within intact C...
November 7, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28974388/-machine-learning-to-analyze-in-vivo-microscopy-support-vector-machines
#13
REVIEW
Michael F Z Wang, Rodrigo Fernandez-Gonzalez
The development of new microscopy techniques for super-resolved, long-term monitoring of cellular and subcellular dynamics in living organisms is revealing new fundamental aspects of tissue development and repair. However, new microscopy approaches present several challenges. In addition to unprecedented requirements for data storage, the analysis of high resolution, time-lapse images is too complex to be done manually. Machine learning techniques are ideally suited for the (semi-)automated analysis of multidimensional image data...
September 30, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28960439/physical-limits-on-the-precision-of-mitotic-spindle-positioning-by-microtubule-pushing-forces-mechanics-of-mitotic-spindle-positioning
#14
REVIEW
Jonathon Howard, Carlos Garzon-Coral
Tissues are shaped and patterned by mechanical and chemical processes. A key mechanical process is the positioning of the mitotic spindle, which determines the size and location of the daughter cells within the tissue. Recent force and position-fluctuation measurements indicate that pushing forces, mediated by the polymerization of astral microtubules against- the cell cortex, maintain the mitotic spindle at the cell center in Caenorhabditis elegans embryos. The magnitude of the centering forces suggests that the physical limit on the accuracy and precision of this centering mechanism is determined by the number of pushing microtubules rather than by thermally driven fluctuations...
September 28, 2017: BioEssays: News and Reviews in Molecular, Cellular and Developmental Biology
https://www.readbyqxmd.com/read/28960081/a-systematic-proteogenomic-approach-to-exploring-a-novel-function-for-nherf1-in-human-reproductive-disorder-lessons-for-exploring-missing-proteins
#15
Keun Na, Heon Shin, Jin-Young Cho, Sang Hee Jung, Jaeseung Lim, Jong-Sun Lim, Eun Ah Kim, Hye Sun Kim, Ah Reum Kang, Ji Hye Kim, Jeong Min Shin, Seul-Ki Jeong, Chae-Yeon Kim, Jun Young Park, Hyung-Min Chung, Gilbert S Omenn, William S Hancock, Young-Ki Paik
One of the major goals of the Chromosome-Centric Human Proteome Project (C-HPP) is to fill the knowledge gaps between human genomic information and the corresponding proteomic information. These gaps are due to "missing" proteins (MPs)-predicted proteins with insufficient evidence from mass spectrometry (MS), biochemical, structural or antibody analyses-that currently account for 2,579 of the 20,159 predicted human proteins (neXtProt, 2017-02). We address some of the lessons learned from the inconsistent annotations of missing proteins in databases (DB) and demonstrate a systematic proteogenomic approach designed to explore a potential new function of a known protein...
September 29, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28943090/genome-architecture-and-evolution-of-a-unichromosomal-asexual-nematode
#16
Hélène Fradin, Karin Kiontke, Charles Zegar, Michelle Gutwein, Jessica Lucas, Mikhail Kovtun, David L Corcoran, L Ryan Baugh, David H A Fitch, Fabio Piano, Kristin C Gunsalus
Asexual reproduction in animals, though rare, is the main or exclusive mode of reproduction in some long-lived lineages. The longevity of asexual clades may be correlated with the maintenance of heterozygosity by mechanisms that rearrange genomes and reduce recombination. Asexual species thus provide an opportunity to gain insight into the relationship between molecular changes, genome architecture, and cellular processes. Here we report the genome sequence of the parthenogenetic nematode Diploscapter pachys with only one chromosome pair...
October 9, 2017: Current Biology: CB
https://www.readbyqxmd.com/read/28940692/dpff-1-transcription-factor-deficiency-causes-the-aberrant-activation-of-mpk-1-and-meiotic-defects-in-the-caenorhabditis-elegans-germline
#17
Emmanuel Villanueva-Chimal, Laura S Salinas, Laura P Fernández-Cardenas, Gabriela Huelgas-Morales, Alejandro Cabrera-Wrooman, Rosa E Navarro
The d4 family of transcription factors consists of three members in mammals. DPF1/neuro-d4 is expressed mainly in neurons and the peripheral nervous system, and is important for brain development. DPF2/requiem/ubi-d4 is expressed ubiquitously and presumably functions as an apoptotic factor, especially during the deprivation of trophic factors. DPF3/cer-d4 is expressed in neurons and in the heart, and is important for heart development and function in zebrafish. In Drosophila, there is only one member, dd4, whose function is still unknown, but it is expressed in many tissues and is particularly abundant in the brain of developing embryos and in adults...
September 23, 2017: Genesis: the Journal of Genetics and Development
https://www.readbyqxmd.com/read/28903999/cdc42-regulates-junctional-actin-but-not-cell-polarization-in-the-caenorhabditis-elegans-epidermis
#18
Yuliya Zilberman, Joshua Abrams, Dorian C Anderson, Jeremy Nance
During morphogenesis, adherens junctions (AJs) remodel to allow changes in cell shape and position while preserving adhesion. Here, we examine the function of Rho guanosine triphosphatase CDC-42 in AJ formation and regulation during Caenorhabditis elegans embryo elongation, a process driven by asymmetric epidermal cell shape changes. cdc-42 mutant embryos arrest during elongation with epidermal ruptures. Unexpectedly, we find using time-lapse fluorescence imaging that cdc-42 is not required for epidermal cell polarization or junction assembly, but rather is needed for proper junctional actin regulation during elongation...
November 6, 2017: Journal of Cell Biology
https://www.readbyqxmd.com/read/28842483/cell-cell-adhesion-in-metazoans-relies-on-evolutionarily-conserved-features-of-the-%C3%AE-catenin%C3%A2-%C3%AE-catenin-binding-interface
#19
Xiangqiang Shao, Hyunook Kang, Timothy Loveless, Gyu Rie Lee, Chaok Seok, William I Weis, Hee-Jung Choi, Jeff Hardin
Stable tissue integrity during embryonic development relies on the function of the cadherin·catenin complex (CCC). The Caenorhabditis elegans CCC is a useful paradigm for analyzing in vivo requirements for specific interactions among the core components of the CCC, and it provides a unique opportunity to examine evolutionarily conserved mechanisms that govern the interaction between α- and β-catenin. HMP-1, unlike its mammalian homolog α-catenin, is constitutively monomeric, and its binding affinity for HMP-2/β-catenin is higher than that of α-catenin for β-catenin...
October 6, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28839200/physical-determinants-of-asymmetric-cell-divisions-in-the-early-development-of-caenorhabditis-elegans
#20
Rolf Fickentscher, Matthias Weiss
Asymmetric cell divisions are of fundamental importance for the development of multicellular organisms, e.g. for the generation of founder cells. Prime examples are asymmetric cell divisions in germline precursors during the early embryogenesis of the transparent roundworm Caenorhabditis elegans, one of the major developmental model organisms. However, due to a lack of quantitative data it has remained unclear how frequent unequal daughter cell sizes emerge in the worm's early embryogenesis, and whether these originate from sterical or biochemical cues...
August 24, 2017: Scientific Reports
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