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https://www.readbyqxmd.com/read/29036602/n6-adenine-dna-methylation-is-associated-with-the-linker-dna-of-h2a-z-containing-well-positioned-nucleosomes-in-pol-ii-transcribed-genes-in-tetrahymena
#1
Yuanyuan Wang, Xiao Chen, Yalan Sheng, Yifan Liu, Shan Gao
DNA N6-methyladenine (6mA) is newly rediscovered as a potential epigenetic mark across a more diverse range of eukaryotes than previously realized. As a unicellular model organism, Tetrahymena thermophila is among the first eukaryotes reported to contain 6mA modification. However, lack of comprehensive information about 6mA distribution hinders further investigations into its function and regulatory mechanism. In this study, we provide the first genome-wide, base pair-resolution map of 6mA in Tetrahymena by applying single-molecule real-time (SMRT) sequencing...
October 3, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29022372/machine-learning-based-models-to-predict-modes-of-toxic-action-of-phenols-to-tetrahymena-pyriformis
#2
J A Castillo-Garit, G M Casañola-Martin, S J Barigye, H Pham-The, F Torrens, A Torreblanca
The phenols are structurally heterogeneous pollutants and they present a variety of modes of toxic action (MOA), including polar narcotics, weak acid respiratory uncouplers, pro-electrophiles, and soft electrophiles. Because it is often difficult to determine correctly the mechanism of action of a compound, quantitative structure-activity relationship (QSAR) methods, which have proved their interest in toxicity prediction, can be used. In this work, several QSAR models for the prediction of MOA of 221 phenols to the ciliated protozoan Tetrahymena pyriformis, using Chemistry Development Kit descriptors, are reported...
September 2017: SAR and QSAR in Environmental Research
https://www.readbyqxmd.com/read/29021213/whats-hows-and-whys-of-programmed-dna-elimination-in-tetrahymena
#3
REVIEW
Tomoko Noto, Kazufumi Mochizuki
Programmed genome rearrangements in ciliates provide fascinating examples of flexible epigenetic genome regulations and important insights into the interaction between transposable elements (TEs) and host genomes. DNA elimination in Tetrahymena thermophila removes approximately 12 000 internal eliminated sequences (IESs), which correspond to one-third of the genome, when the somatic macronucleus (MAC) differentiates from the germline micronucleus (MIC). More than half of the IESs, many of which show high similarity to TEs, are targeted for elimination in cis by the small RNA-mediated genome comparison of the MIC to the MAC...
October 2017: Open Biology
https://www.readbyqxmd.com/read/28977712/evolution-of-density-dependent-movement-during-experimental-range-expansions
#4
Emanuel A Fronhofer, Sereina Gut, Florian Altermatt
Range expansions and biological invasions are prime examples of transient processes that are likely impacted by rapid evolutionary changes. As a spatial process, range expansions are driven by dispersal and movement behaviour. While it is widely accepted that dispersal and movement may be context-dependent, for instance density-dependent, and best represented by reaction norms, the evolution of density-dependent movement during range expansions has received little experimental attention. We therefore tested current theory predicting the evolution of increased movement at low densities at range margins using highly replicated and controlled range expansion experiments across multiple genotypes of the protist model system Tetrahymena thermophila...
October 4, 2017: Journal of Evolutionary Biology
https://www.readbyqxmd.com/read/28967947/roles-for-rpos-in-survival-of-escherichia-coli-during-protozoan-predation-and-in-reduced-moisture-conditions-highlight-its-importance-in-soil-environments
#5
Yinka Somorin, Guillaume Bouchard, Joseph Gallagher, Florence Abram, Fiona Brennan, Conor O'Byrne
The soil is a complex ecosystem where interactions between biotic and abiotic factors determine the survival and fate of microbial inhabitants of the system. Having previously shown that Escherichia coli requires the general stress response regulator, RpoS, to survive long term in soil, it was important to determine what specific conditions in this environment necessitate a functional RpoS. This study investigated the susceptibility of soil-persistent E. coli to predation by the single-celled eukaryotes Acanthamoeba polyphaga and Tetrahymena pyriformis, and the role RpoS plays in resisting this predation...
October 16, 2017: FEMS Microbiology Letters
https://www.readbyqxmd.com/read/28954739/an-evolutionarily-conserved-phosphatidate-phosphatase-maintains-lipid-droplet-number-and-er-morphology-but-not-nuclear-morphology
#6
Anoop Narayana Pillai, Sushmita Shukla, Abdur Rahaman
Phosphatidic acid phosphatases are involved in the biosynthesis of phospholipids and triacylglycerol, and also act as transcriptional regulators. Studies to ascertain its role in lipid metabolism and membrane biogenesis are restricted only to Opisthokonta and Archaeplastida. Herein, we report the role of phosphatidate phosphatase (PAH) in Tetrahymena thermophila, belonging to the Alveolata clade. We identified two PAH homologs in Tetrahymena, TtPAH1, and TtPAH2 Loss of function of TtPAH1 results in reduced lipid droplet number and increase in ER content...
September 27, 2017: Biology Open
https://www.readbyqxmd.com/read/28934495/a-germline-limited-piggybac-transposase-gene-is-required-for-precise-excision-in-tetrahymena-genome-rearrangement
#7
Lifang Feng, Guangying Wang, Eileen P Hamilton, Jie Xiong, Guanxiong Yan, Kai Chen, Xiao Chen, Wen Dui, Amber Plemens, Lara Khadr, Arjune Dhanekula, Mina Juma, Hung Quang Dang, Geoffrey M Kapler, Eduardo Orias, Wei Miao, Yifan Liu
Developmentally programmed genome rearrangement accompanies differentiation of the silent germline micronucleus into the transcriptionally active somatic macronucleus in the ciliated protozoan Tetrahymena thermophila. Internal eliminated sequences (IES) are excised, followed by rejoining of MAC-destined sequences, while fragmentation occurs at conserved chromosome breakage sequences, generating macronuclear chromosomes. Some macronuclear chromosomes, referred to as non-maintained chromosomes (NMC), are lost soon after differentiation...
September 19, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28916309/uptake-of-cholesterol-by-tetrahymena-thermophila-is-mainly-due-to-phagocytosis
#8
María Eugenia Elguero, María Luz Sanchez Granel, María Guadalupe Montes, Nicolás G Cid, Nicolás O Favale, Clara B Nudel, Alejandro D Nusblat
No abstract text is available yet for this article.
September 12, 2017: Revista Argentina de Microbiología
https://www.readbyqxmd.com/read/28851837/rna-structure-inference-through-chemical-mapping-after-accidental-or-intentional-mutations
#9
Clarence Y Cheng, Wipapat Kladwang, Joseph D Yesselman, Rhiju Das
Despite the critical roles RNA structures play in regulating gene expression, sequencing-based methods for experimentally determining RNA base pairs have remained inaccurate. Here, we describe a multidimensional chemical-mapping method called "mutate-and-map read out through next-generation sequencing" (M2-seq) that takes advantage of sparsely mutated nucleotides to induce structural perturbations at partner nucleotides and then detects these events through dimethyl sulfate (DMS) probing and mutational profiling...
September 12, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28846184/yeast-and-other-lower-eukaryotic-organisms-for-studies-of-vps13-proteins-in-health-and-disease
#10
REVIEW
Weronika Rzepnikowska, Krzysztof Flis, Sandra Muñoz-Braceras, Regina Menezes, Ricardo Escalante, Teresa Zoladek
Human Vps13 proteins are associated with several diseases, including the neurodegenerative disorder Chorea-acanthocytosis (ChAc), yet the biology of these proteins is still poorly understood. Studies in Saccharomyces cerevisiae, Dictyostelium discoideum, Tetrahymena thermophila and Drosophila melanogaster point to the involvement of Vps13 in cytoskeleton organization, vesicular trafficking, autophagy, phagocytosis, endocytosis, proteostasis, sporulation and mitochondrial functioning. Recent findings show that yeast Vps13 binds to phosphatidylinositol lipids via 4 different regions and functions at membrane contact sites, enlarging the list of Vps13 functions...
August 28, 2017: Traffic
https://www.readbyqxmd.com/read/28803330/bime2-a-novel-gene-required-for-interhomolog-meiotic-recombination-in-the-protist-model-organism-tetrahymena
#11
Anura Shodhan, Maria Novatchkova, Josef Loidl
Meiotic recombination is initiated by DNA double-strand breaks (DSBs). Most DSBs are converted into nonreciprocal exchanges (gene conversions) or crossovers (COs) between sister chromatids. Only a minority of DSBs are processed toward interhomolog COs, the precursors of the chiasmata that connect homologous chromosomes. Dmc1, the meiosis-specific paralog of the universal recombination protein Rad51, is required for interhomolog COs; in its absence, univalents are primarily formed. Here, we report a ciliate-specific novel meiotic gene, BIME2, which also promotes interhomolog crossing over...
August 12, 2017: Chromosome Research
https://www.readbyqxmd.com/read/28773114/toxicity-of-nine-doped-rare-earth-metal-oxides-and-respective-individual-metals-to-aquatic-microorganisms-vibrio-fischeri-and-tetrahymena-thermophila
#12
Imbi Kurvet, Katre Juganson, Heiki Vija, Mariliis Sihtmäe, Irina Blinova, Guttorm Syvertsen-Wiig, Anne Kahru
Despite the increasing use of rare earth elements (REEs) and oxides (REOs) in various technologies, the information on their ecotoxicological hazard is scarce. Here, the effects of La(3+), Ce(3+), Pr(3+), Nd(3+), Gd(3+), CeO₂, and eight doped REOs to marine bacteria Vibrio fischeri and freshwater protozoa Tetrahymena thermophila were studied in parallel with REO dopant metals (Co(2+), Fe(3+), Mn(2+), Ni(2+), Sr(2+)). The highest concentrations of REOs tested were 100 mg/L with protozoa in deionized water and 500 mg/L with bacteria in 2% NaCl...
July 5, 2017: Materials
https://www.readbyqxmd.com/read/28735853/a-comparative-study-of-genome-organization-and-epigenetic-mechanisms-in-model-ciliates-with-an-emphasis-on-tetrahymena-paramecium-and-oxytricha
#13
REVIEW
Yurui Wang, Yuanyuan Wang, Yalan Sheng, Jie Huang, Xiao Chen, Khaled A S Al-Rasheid, Shan Gao
As a group of unicellular eukaryotes, ciliates offer a unique system to explore epigenetic regulation, mostly due to their nuclear dualism. Ciliates launched a successful radiation after their early evolutionary branching, therefore harboring an unexpectedly rich pool of diverse biological functions and mechanisms. In this review, we compare distinct features of different ciliates in mating type determination, genome organization, DNA methylation, and removal of internal eliminated sequences (IES), with emphasis on Tetrahymena, Paramecium and Oxytricha...
July 1, 2017: European Journal of Protistology
https://www.readbyqxmd.com/read/28732250/structural-biology-of-telomerase-and-its-interaction-at-telomeres
#14
REVIEW
Yaqiang Wang, Juli Feigon
Telomerase is an RNP that synthesizes the 3' ends of linear chromosomes and is an important regulator of telomere length. It contains a single long non-coding telomerase RNA (TER), telomerase reverse transcriptase (TERT), and other proteins that vary among organisms. Recent progress in structural biology of telomerase includes reports of the first cryo-electron microscopy structure of telomerase, from Tetrahymena, new crystal structures of TERT domains, telomerase RNA structures and models, and identification in Tetrahymena telomerase holoenzyme of human homologues of telomere-associated proteins that have provided a more unified view of telomerase interaction at telomeres as well as insights into the role of telomerase RNA in activity and assembly...
July 18, 2017: Current Opinion in Structural Biology
https://www.readbyqxmd.com/read/28730449/rational-engineering-of-a-modular-group-i-ribozyme-to-control-its-activity-by-self-dimerization
#15
Takahiro Tanaka, Yoshiya Ikawa, Shigeyoshi Matsumura
We designed and constructed a dimer of the Tetrahymena group I ribozyme the activity of which is regulated by self-dimerization. This dimer was rationally designed by utilizing the P5abc and ΔP5abc domains as large RNA motifs. This strategy enabled us to install large ribozyme functions into an RNA structure. This is a step toward expanding the field of RNA nanotechnology beyond the limitation of using only relatively small functional motifs. Self-dimerization can also be rationally programmed by modular engineering of RNA interaction motifs...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28726394/human-cst-prefers-g-rich-but-not-necessarily-telomeric-sequences
#16
Robert A Hom, Deborah S Wuttke
The human CST (CTC1-STN1-TEN1) heterotrimeric complex plays roles in both telomere maintenance and DNA replication through its ability to interact with single-stranded DNA (ssDNA) of a variety of sequences. The precise sequence specificity required to execute these functions is unknown. Telomere-binding proteins have been shown to specifically recognize key telomeric sequence motifs within ssDNA while accommodating nonspecifically recognized sequences through conformationally plastic interfaces. To better understand the role CST plays in these processes, we have produced a highly purified heterotrimer and elucidated the sequence requirements for CST recognition of ssDNA in vitro...
August 15, 2017: Biochemistry
https://www.readbyqxmd.com/read/28715961/genetics-and-epigenetics-of-mating-type-determination-in-paramecium-and-tetrahymena
#17
Eduardo Orias, Deepankar Pratap Singh, Eric Meyer
While sex is an ancient and highly conserved eukaryotic invention, self-incompatibility systems such as mating types or sexes appear to be derived limitations that show considerable evolutionary plasticity. Within a single class of ciliates, Paramecium and Tetrahymena species have long been known to present a wide variety of mating type numbers and modes of inheritance, but only recently have the genes involved been identified. Although similar transmembrane proteins mediate self/nonself recognition in both ciliates, the mechanisms of mating type determination differ widely, ranging from Mendelian systems to developmental nuclear differentiation, either stochastic or maternally inherited...
July 17, 2017: Annual Review of Microbiology
https://www.readbyqxmd.com/read/28702015/inhibition-of-the-rumen-ciliate-entodinium-caudatum-by-antibiotics
#18
Tansol Park, Tea Meulia, Jeffrey L Firkins, Zhongtang Yu
Axenic cultures of free-living aerobic ciliates, such as Tetrahymena thermophila and Paramecium aurelia, have been established and routinely used in laboratory research, greatly facilitating, or enabling characterization of their metabolism, physiology, and ecology. Ruminal protozoa are anaerobic ciliates, and they play important roles in feed digestion and fermentation. Although, repeatedly attempted, no laboratory-maintainable axenic culture of ruminal ciliates has been established. When axenic ciliate cultures are developed, antibiotics are required to eliminate the accompanying bacteria...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28692189/diversification-of-hp1-like-chromo-domain-proteins-in-tetrahymena-thermophila
#19
Emily A Wiley, Scott Horrell, Alyssa Yoshino, Cara C Schornak, Claire Bagnani, Douglas L Chalker
Proteins that possess a chromo domain are well-known for their roles in heterochromatin assembly and maintenance. The Heterochromatin Protein 1 (HP1) family, with a chromo domain and carboxy-terminal chromo shadow domain, targets heterochromatin through interaction with histone H3 methylated on lysine 9 (H3K9me2/3). The structural and functional diversity of these proteins observed in both fission yeast and metazoans correlate with chromatin specialization. To expand these studies, we examined chromo domain proteins in the ciliate Tetrahymena thermophila, which has functionally diverse and developmentally regulated heterochromatin domains...
July 10, 2017: Journal of Eukaryotic Microbiology
https://www.readbyqxmd.com/read/28685161/behavioral-effects-of-a-chemorepellent-receptor-knockout-mutation-in-tetrahymena-thermophila
#20
Dianxiong Zou, Todd M Hennessey
A conditioned supernatant from Tetrahymena thermophila contains a powerful chemorepellent for wild-type cells, and a gene called G37 is required for this response. This is the first genomic identification of a chemorepellent receptor in any eukaryotic unicellular organism. This conditioned supernatant factor (CSF) is small (<1 kDa), and its repellent effect is resistant to boiling, protease treatment, and nuclease digestion. External BAPTA eliminated the CSF response, suggesting that Ca(2+) entry is required for the classical avoiding reactions (AR) used for chemorepulsion...
July 2017: MSphere
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