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https://www.readbyqxmd.com/read/29456136/a-sex-chromosome-pirna-promotes-robust-dosage-compensation-and-sex-determination-in-c-elegans
#1
Wen Tang, Meetu Seth, Shikui Tu, En-Zhi Shen, Qian Li, Masaki Shirayama, Zhiping Weng, Craig C Mello
In metazoans, Piwi-related Argonaute proteins engage piRNAs (Piwi-interacting small RNAs) to defend the genome against invasive nucleic acids, such as transposable elements. Yet many organisms-including worms and humans-express thousands of piRNAs that do not target transposons, suggesting that piRNA function extends beyond genome defense. Here, we show that the X chromosome-derived piRNA 21ux-1 downregulates XOL-1 (XO Lethal), a master regulator of X chromosome dosage compensation and sex determination in Caenorhabditis elegans...
February 13, 2018: Developmental Cell
https://www.readbyqxmd.com/read/29456100/the-coding-regions-of-germline-mrnas-confer-sensitivity-to-argonaute-regulation-in-c-elegans
#2
Meetu Seth, Masaki Shirayama, Wen Tang, En-Zhi Shen, Shikui Tu, Heng-Chi Lee, Zhiping Weng, Craig C Mello
Protein-coding genes undergo a wide array of regulatory interactions with factors that engage non-coding regions. Open reading frames (ORFs), in contrast, are thought to be constrained by coding function, precluding a major role in gene regulation. Here, we explore Piwi-interacting (pi)RNA-mediated transgene silencing in C. elegans and show that marked differences in the sensitivity to piRNA silencing map to the endogenous sequences within transgene ORFs. Artificially increasing piRNA targeting within the ORF of a resistant transgene can lead to a partial yet stable reduction in expression, revealing that piRNAs not only silence but can also "tune" gene expression...
February 14, 2018: Cell Reports
https://www.readbyqxmd.com/read/29456082/identification-of-pirna-binding-sites-reveals-the-argonaute-regulatory-landscape-of-the-c-elegans-germline
#3
En-Zhi Shen, Hao Chen, Ahmet R Ozturk, Shikui Tu, Masaki Shirayama, Wen Tang, Yue-He Ding, Si-Yuan Dai, Zhiping Weng, Craig C Mello
piRNAs (Piwi-interacting small RNAs) engage Piwi Argonautes to silence transposons and promote fertility in animal germlines. Genetic and computational studies have suggested that C. elegans piRNAs tolerate mismatched pairing and in principle could target every transcript. Here we employ in vivo cross-linking to identify transcriptome-wide interactions between piRNAs and target RNAs. We show that piRNAs engage all germline mRNAs and that piRNA binding follows microRNA-like pairing rules. Targeting correlates better with binding energy than with piRNA abundance, suggesting that piRNA concentration does not limit targeting...
February 10, 2018: Cell
https://www.readbyqxmd.com/read/29452922/structural-biology-of-the-separase-securin-complex-with-crucial-roles-in-chromosome-segregation
#4
REVIEW
Shukun Luo, Liang Tong
The cysteine protease separase opens the cohesin ring by cleaving its kleisin subunit and is a pivotal cell cycle factor for the transition from metaphase to anaphase. It is inhibited by forming a complex with the chaperone securin, and in vertebrates, also by the Cdk1-cyclin B1 complex. Separase is activated upon the destruction of securin or cyclin B1 by the proteasome, after ubiquitination by the anaphase-promoting complex/cyclosome (APC/C). Here we review recent structures of the active protease segment of Chaetomium thermophilum separase in complex with a substrate-mimic inhibitor and full-length Saccharomyces cerevisiae and Caenorhabditis elegans separase in complex with securin...
February 13, 2018: Current Opinion in Structural Biology
https://www.readbyqxmd.com/read/29452354/alpha-synuclein-inhibits-snx3-retromer-mediated-retrograde-recycling-of-iron-transporters-in-s-cerevisiae-and-c-elegans-models-of-parkinson-s-disease
#5
Dhaval Patel, Chuan Xu, Sureshbabu Nagarajan, Zhengchang Liu, Wayne O Hemphill, Runhua Shi, Vladimir N Uversky, Guy A Caldwell, Kim A Caldwell, Stephan N Witt
We probed the role of alpha-synuclein (α-syn) in modulating sorting nexin 3 (Snx3)-retromer-mediated recycling of iron transporters in Saccharomyces cerevisiae and Caenorhabditis elegans. In yeast, the membrane-bound heterodimer Fet3/Ftr1 is the high affinity iron importer. Fet3 is a membrane-bound multicopper ferroxidase, whose ferroxidase domain is orthologous to human ceruloplasmin (Cp), that oxidizes external Fe+2 to Fe+3; the Fe+3 ions then channel through the Ftr1 permease into the cell. When the concentration of external iron is low (< 1 µM), Fet3/Ftr1 is maintained on the plasma membrane by retrograde endocytic-recycling; whereas, when the concentration of external iron is high (> 10 µM), Fet3/Ftr1 is endocytosed and shunted to the vacuole for degradation...
February 14, 2018: Human Molecular Genetics
https://www.readbyqxmd.com/read/29452179/massively-parallel-c-elegans-tracking-provides-multi-dimensional-fingerprints-for-phenotypic-discovery
#6
Michele Perni, Pavan K Challa, Julius B Kirkegaard, Ryan Limbocker, Mandy Koopman, Maarten C Hardenberg, Pietro Sormanni, Thomas Müller, Kadi L Saar, Lianne W Y Roode, Johnny Habchi, Giulia Vecchi, Nilumi W Fernando, Samuel Casford, Ellen A A Nollen, Michele Vendruscolo, Christopher M Dobson, Tuomas P J Knowles
BACKGROUND: The nematode worm C. elegans is a model organism widely used for studies of genetics and of human disease. The health and fitness of the worms can be quantified in different ways, such as by measuring their bending frequency, speed or lifespan. Manual assays, however, are time consuming and limited in their scope providing a strong motivation for automation. NEW METHOD: We describe the development and application of an advanced machine vision system for characterizing the behaviour of C...
February 13, 2018: Journal of Neuroscience Methods
https://www.readbyqxmd.com/read/29448492/carbon-quantum-dots-as-fluorescent-probes-for-imaging-and-detecting-free-radicals-in-c-elegans
#7
Jia Xu, Liping Wang, Ying Mu, Yue Zhang, Mingyang Wang, Qifei Wang, Kai Wang, Shuwen Guan, Jiyang Li, Licheng Wang
Uniform and hydrophilic carbon quantum dots (C-QDs) were synthesized by calcination and NaOH treatment from an organo-templated zeolite precursor. The color of luminescence was determined by the concentration of C-QDs. These variable-color C-QDs were applied for the first time in the imaging of Caenorhabditis elegans (C. elegans) as a model organism. The effects of C-QDs and possible behavioral changes in C. elegans were evaluated under treatment conditions. We could clearly observe distribution of C-QDs in C...
February 1, 2018: Journal of Nanoscience and Nanotechnology
https://www.readbyqxmd.com/read/29447162/early-experiences-mediate-distinct-adult-gene-expression-and-reproductive-programs-in-caenorhabditis-elegans
#8
Maria C Ow, Kirill Borziak, Alexandra M Nichitean, Steve Dorus, Sarah E Hall
Environmental stress during early development in animals can have profound effects on adult phenotypes via programmed changes in gene expression. Using the nematode C. elegans, we demonstrated previously that adults retain a cellular memory of their developmental experience that is manifested by differences in gene expression and life history traits; however, the sophistication of this system in response to different environmental stresses, and how it dictates phenotypic plasticity in adults that contribute to increased fitness in response to distinct environmental challenges, was unknown...
February 15, 2018: PLoS Genetics
https://www.readbyqxmd.com/read/29446199/light-dependent-cytoplasmic-recruitment-enhances-the-dynamic-range-of-a-nuclear-import-photoswitch
#9
Hayretin Yumerefendi, Hui Wang, Daniel J Dickinson, Andrew Lerner, Per Malkus, Bob Goldstein, Klaus Hahn, Brian Kuhlman
Cellular signal transduction is often regulated at multiple steps in order to achieve more complex logic or precise control of a pathway. For instance, some signaling mechanisms couple allosteric activation with localization to achieve high signal to noise. Here, we create a system for light activated nuclear import that incorporates two levels of control. It consists of a nuclear import photoswitch, Light Activated Nuclear Shuttle (LANS), and a protein engineered to preferentially interact with LANS in the dark, Zdk2...
February 14, 2018: Chembiochem: a European Journal of Chemical Biology
https://www.readbyqxmd.com/read/29445761/oxidative-stress-assays-arsenite-and-tbhp-in-caenorhabditis-elegans
#10
Collin Yvès Ewald, John M Hourihan, T Keith Blackwell
Cells and organisms face constant exposure to reactive oxygen species (ROS), either from the environment or as a by-product from internal metabolic processes. To prevent cellular damage from ROS, cells have evolved detoxification mechanisms. The activation of these detoxification mechanisms and their downstream responses represent an overlapping defense response that can be tailored to different sources of ROS to adequately adapt and protect cells. In this protocol, we describe how to measure the sensitivity to oxidative stress from two different sources, arsenite and tBHP, using the nematode C...
July 5, 2017: Bio-protocol
https://www.readbyqxmd.com/read/29444471/optimization-of-the-polysaccharide-hydrolysate-from-auricularia-auricula-with-antioxidant-activity-by-response-surface-methodology
#11
Yaoyao Xu, Meng Shen, Yidan Chen, Yeqing Lou, Ruichao Luo, Jiajia Chen, Yongjun Zhang, Jia Li, Weimin Wang
An efficient acid-hydrolysis method was developed and optimized for the hydrolyses of polysaccharide from Auricularia auricula with the ABTS· scavenging ability as the detective marker. Based on the single factor experimental results, Box-Behnken design (BBD) were applied for the optimization of acid-hydrolysis conditions. The possible antioxidant mechanism of the hydrolyses (AAPs-F) in vivo was performed using the C. elegans model. The acid-hydrolysis conditions were found to be the optimal hydrolyzing time 2...
February 11, 2018: International Journal of Biological Macromolecules
https://www.readbyqxmd.com/read/29443938/the-microbial-zoo-in-the-c-elegans-intestine-bacteria-fungi-and-viruses
#12
REVIEW
Hongbing Jiang, David Wang
C. elegans is an invaluable model organism that has been a driving force in many fundamental biological discoveries. However, it is only in the past two decades that it has been applied to host-pathogen interaction studies. These studies have been facilitated by the discoveries of natural microbes that infect C. elegans , including bacteria, fungi and viruses. Notably, many of these microbes share a common site of infection, the C. elegans intestine. Furthermore, the recent descriptions of a natural gut microbiota in C...
February 14, 2018: Viruses
https://www.readbyqxmd.com/read/29442317/zic-genes-in-nematodes-a-role-in-nervous-system-development-and-wnt-signaling
#13
Guillaume Bordet, Vincent Bertrand
Transcription factors of the Zic family play important roles during animal development, and their misregulation has been implicated in several human diseases. Zic proteins are present in nematodes, and their function has been mostly studied in the model organism C. elegans. C. elegans possesses only one Zic family member, REF-2. Functional studies have shown that this factor plays a key role during the development of the nervous system, epidermis, and excretory system. In addition, they have revealed that the C...
2018: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/29436902/both-live-and-dead-enterococci-activate-caenorhabditis-elegans-host-defense-via-immune-and-stress-pathways
#14
Grace J Yuen, Frederick M Ausubel
The innate immune response of the nematode Caenorhabditis elegans has been extensively studied and a variety of Toll-independent immune response pathways have been identified. Surprisingly little, however, is known about how pathogens activate the C. elegans immune response. Enterococcus faecalis and Enterococcus faecium are closely related enterococcal species that exhibit significantly different levels of virulence in C. elegans infection models. Previous work has shown that activation of the C. elegans immune response by Pseudomonas aeruginosa involves P...
February 13, 2018: Virulence
https://www.readbyqxmd.com/read/29435927/gene-silencing-in-vitro-and-in-vivo-using-intronic-micrornas
#15
Shi-Lung Lin, Shao-Yao Ying
MicroRNAs (miRNAs), small single-stranded regulatory RNAs capable of interfering with intracellular messenger RNAs (mRNAs) that contain either complete or partial complementarity, are useful for the design of new therapies against cancer polymorphism and viral mutation. Numerous miRNAs have been reported to induce RNA interference (RNAi), a post-transcriptional gene-silencing mechanism. Recent evidence also indicates that they are involved in the transcriptional regulation of genome activities. They were first discovered in Caenorhabditis elegans as native RNA fragments that modulate a wide range of genetic regulatory pathways during embryonic development, and are now recognized as small gene silencers transcribed from the noncoding regions of a genome...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29434393/the-mycotoxin-zearalenone-hinders-candida-albicans-biofilm-formation-and-hyphal-morphogenesis
#16
Satish Kumar Rajasekharan, Jin-Hyung Lee, Yueju Zhao, Jintae Lee
Yeast-mold mycobiota inhabit several natural ecosystems, in which symbiotic relationships drive strategic pathoadaptation. Mycotoxins are metabolites produced by diverse mycotoxigenic fungi as a defense against yeasts, though at times yeasts secrete enzymes that degrade, detoxify, or bio-transform mycotoxins. The present study is focused on the in vitro inhibitory effects of zearalenone (ZEN), a F2 mycotoxin produced by several Fusarium and Gibberella species, on different microbial strains. ZEN exhibited no effect on the planktonic growth or biofilms of several Gram positive and negative bacteria at the tested concentrations...
March 2018: Indian Journal of Microbiology
https://www.readbyqxmd.com/read/29433733/daf-16-foxo-in-the-context-of-c-elegans
#17
Heidi A Tissenbaum
In Caenorhabditis elegans, there is a single FOXO transcription factor homolog, encoded by the gene, daf-16. As a central regulator for multiple signaling pathways, DAF-16 integrates these signals which results in modulation of several biological processes including longevity, development, fat storage, stress resistance, innate immunity, and reproduction. Using C. elegans allows for studies of FOXO in the context of the whole animal. Therefore, manipulating levels or the activity of daf-16 results in phenotypic changes...
2018: Current Topics in Developmental Biology
https://www.readbyqxmd.com/read/29432910/lactobacillus-paracasei-28-4-reduces-in-vitro-hyphae-formation-of-candida-albicans-and-prevents-the-filamentation-in-an-experimental-model-of-caenorhabditis-elegans
#18
Patrícia Pimentel de Barros, Liliana Scorzoni, Felipe de Camargo Ribeiro, Luciana Ruano de Oliveira Fugisaki, Beth Burgwyn Fuchs, Eleftherios Mylonakis, Antonio Olavo Cardoso Jorge, Juliana Campos Junqueira, Rodnei Dennis Rossoni
The objective of this study was to evaluate the influence of microbe-microbe interactions to identify a strain of Lactobacillus that could reduce the filamentation of Candida albicans ATCC 18804 using in vitro and in vivo models. Thus presenting a probiotic effect against the fungal pathogen. First, we analyzed the ability of 25 clinical isolates of Lactobacillus to reduce filamentation in C. albicans in vitro. We found that L. paracasei isolate 28.4 exhibited the greatest reduction of C. albicans hyphae (p = 0...
February 9, 2018: Microbial Pathogenesis
https://www.readbyqxmd.com/read/29432681/pharming-for-genes-in-neurotransmission-combining-chemical-and-genetic-approaches-in-c-elegans
#19
Stephen M Blazie, Yishi Jin
Synaptic transmission is central to nervous system function. Chemical and genetic screens are valuable approaches to probe synaptic mechanisms in living animals. The nematode C. elegans is a prime system to apply these methods to discover genes and dissect the cellular pathways underlying neurotransmission. Here, we review key approaches to understand neurotransmission and the action of psychiatric drugs in C. elegans, starting with early studies on cholinergic excitatory signaling at the neuromuscular junction and moving into mechanisms mediated by biogenic amine and psychiatric drugs...
February 12, 2018: ACS Chemical Neuroscience
https://www.readbyqxmd.com/read/29432412/hub-connectivity-neuronal-diversity-and-gene-expression-in-the-caenorhabditis-elegans-connectome
#20
Aurina Arnatkevic Iūtė, Ben D Fulcher, Roger Pocock, Alex Fornito
Studies of nervous system connectivity, in a wide variety of species and at different scales of resolution, have identified several highly conserved motifs of network organization. One such motif is a heterogeneous distribution of connectivity across neural elements, such that some elements act as highly connected and functionally important network hubs. These brain network hubs are also densely interconnected, forming a so-called rich club. Recent work in mouse has identified a distinctive transcriptional signature of neural hubs, characterized by tightly coupled expression of oxidative metabolism genes, with similar genes characterizing macroscale inter-modular hub regions of the human cortex...
February 12, 2018: PLoS Computational Biology
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