scholarly journals Gain and Loss of Small RNA Classes—Characterization of Small RNAs in the Parasitic Nematode Family Strongyloididae

2017 ◽  
Vol 9 (10) ◽  
pp. 2826-2843 ◽  
Author(s):  
Anja Holz ◽  
Adrian Streit
Keyword(s):  
Small Rna ◽  
Small Rnas ◽  
Parasitic Nematode ◽  
Gain And Loss

scholarly journals Sequence-independent characterization of viruses based on the pattern of viral small RNAs produced by the host

2015 ◽  
Vol 43 (13) ◽  
pp. 6191-6206 ◽  
Author(s):  
Eric Roberto Guimarães Rocha Aguiar ◽  
Roenick Proveti Olmo ◽  
Simona Paro ◽  
Flavia Viana Ferreira ◽  
Isaque João da Silva de Faria ◽  
...  
Keyword(s):  
Small Rna ◽  
Small Rnas ◽  
Large Scale ◽  
Virus Detection ◽  
Virus Surveillance ◽  
Size Profile ◽  
Reference Databases ◽  
Similarity Searches ◽  
Viral Sequences

Abstract Virus surveillance in vector insects is potentially of great benefit to public health. Large-scale sequencing of small and long RNAs has previously been used to detect viruses, but without any formal comparison of different strategies. Furthermore, the identification of viral sequences largely depends on similarity searches against reference databases. Here, we developed a sequence-independent strategy based on virus-derived small RNAs produced by the host response, such as the RNA interference pathway. In insects, we compared sequences of small and long RNAs, demonstrating that viral sequences are enriched in the small RNA fraction. We also noted that the small RNA size profile is a unique signature for each virus and can be used to identify novel viral sequences without known relatives in reference databases. Using this strategy, we characterized six novel viruses in the viromes of laboratory fruit flies and wild populations of two insect vectors: mosquitoes and sandflies. We also show that the small RNA profile could be used to infer viral tropism for ovaries among other aspects of virus biology. Additionally, our results suggest that virus detection utilizing small RNAs can also be applied to vertebrates, although not as efficiently as to plants and insects.

scholarly journals Nematode Small RNA Pathways in the Absence of piRNAs

2021 ◽  
Author(s):  
Maxim Zagoskin ◽  
Jianbin Wang ◽  
Ashley T. Neff ◽  
Giovana M.B. Veronezi ◽  
Richard E. Davis
Keyword(s):  
Small Rna ◽  
Small Rnas ◽  
Parasitic Nematode ◽  
Repetitive Sequences ◽  
C Elegans ◽  
Early Embryos ◽  
Specific Mrnas ◽  
Rna Pathways ◽  
Pirna Pathway ◽  
Mature Mrnas

Small RNA pathways play diverse regulatory roles in the nematode C. elegans. However, our understanding of small RNA pathways, their conservation, and their roles in other nematodes is limited. Here, we analyzed small RNA pathways in the parasitic nematode Ascaris. Ascaris has ten Argonautes with five worm-specific Argonautes (WAGOs) that are associated with secondary 5'-triphosphate small RNAs (22-24G-RNAs). These Ascaris WAGOs and their small RNAs target repetitive sequences (WAGO-1, WAGO-2, WAGO-3, and NRDE-3) or mature mRNAs (CSR-1, NRDE-3, and WAGO-3) and are similar to the C. elegans mutator, nuclear, and CSR-1 small RNA pathways. Ascaris CSR-1 likely functions to "license" gene expression in the absence of an Ascaris piRNA pathway. Ascaris ALG-4 and its associated 26G-RNAs target and appear to repress specific mRNAs during meiosis in the testes. Notably, Ascaris WAGOs (WAGO-3 and NRDE-3) small RNAs change their targets between repetitive sequences and mRNAs during spermatogenesis or in early embryos illustrating target plasticity of these WAGOs. We provide a unique and comprehensive view of mRNA and small RNA expression throughout nematode spermatogenesis that illustrates the dynamics and flexibility of small RNA pathways. Overall, our study provides key insights into the conservation and divergence of nematode small RNA pathways.

Characterization of small RNAs in early zebrafish PGCs

2021 ◽  
Author(s):  
Xiaoyuan Zhang ◽  
Yiping Li ◽  
Yunbin Zhang ◽  
Shifeng Li
Keyword(s):  
Small Rnas

scholarly journals Identification and characterization of two novel classes of small RNAs in the mouse germline: retrotransposon-derived siRNAs in oocytes and germline small RNAs in testes

2006 ◽  
Vol 20 (13) ◽  
pp. 1732-1743 ◽  
Author(s):  
Toshiaki Watanabe ◽  
Atsushi Takeda ◽  
Tomoyuki Tsukiyama ◽  
Kazuyuki Mise ◽  
Tetsuro Okuno ◽  
...  
Keyword(s):  
Small Rnas ◽  
Identification And Characterization

scholarly journals Mechanism of Stochastic Resonance in a Quorum Sensing Network Regulated by Small RNAs

2013 ◽  
Vol 2013 ◽  
pp. 1-6 ◽  
Author(s):  
Ya-nan Zhu ◽  
Jianwei Shen ◽  
Yong Xu
Keyword(s):  
Quorum Sensing ◽  
Stochastic Resonance ◽  
Small Rna ◽  
Small Rnas ◽  
Cell Communication ◽  
The Other ◽  
Important Process ◽  
Positive Role ◽  
Bacterial Quorum Sensing ◽  
Bacterial Quorum

Bacterial quorum sensing (QS) is an important process of cell communication and more and more attention is paid to it. Moreover, the noises are ubiquitous in nature and often play positive role. In this paper, we investigate how the noise enhances the QS though the stochastic resonance (SR) and explain the mechanism of SR in this quorum sensing network. In addition, we also discuss the interaction between the small RNA and the other genes in this network and discover the biological importance.

scholarly journals Intertissue small RNA communication mediates the acquisition and inheritance of hormesis in Caenorhabditis elegans

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Emiko Okabe ◽  
Masaharu Uno ◽  
Saya Kishimoto ◽  
Eisuke Nishida
Keyword(s):  
Caenorhabditis Elegans ◽  
Small Rna ◽  
Stress Resistance ◽  
Environmental Conditions ◽  
Production System ◽  
Small Rnas ◽  
Communication Systems ◽  
Rna Transport ◽  
Phenotypic Changes ◽  
Induced Stress

AbstractEnvironmental conditions can cause phenotypic changes, part of which can be inherited by subsequent generations via soma-to-germline communication. However, the signaling molecules or pathways that mediate intertissue communication remain unclear. Here, we show that intertissue small RNA communication systems play a key role in the acquisition and inheritance of hormesis effects – stress-induced stress resistance – in Caenorhabditis elegans. The miRNA-processing enzyme DRSH-1 is involved in both the acquisition and the inheritance of hormesis, whereas worm-specific Argonaute (WAGO) proteins, which function with endo-siRNAs, are involved only in its inheritance. Further analyses demonstrate that the miRNA production system in the neuron and the small RNA transport machinery in the intestine are both essential for its acquisition and that both the transport of small RNAs in the germline and the germline Argonaute HRDE-1 complex are required for its inheritance. Our results thus demonstrate that overlapping and distinct roles of small RNA systems in the acquisition and inheritance of hormesis effects.

scholarly journals Systematic characterization of artificial small RNA-mediated inhibition of Escherichia coli growth

RNA Biology ◽  
2017 ◽  
Vol 14 (2) ◽  
pp. 206-218 ◽  
Author(s):  
Emiko Noro ◽  
Masaru Mori ◽  
Gakuto Makino ◽  
Yuki Takai ◽  
Sumiko Ohnuma ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Small Rna ◽  
Coli Growth

scholarly journals The Importance of the Small RNA Chaperone Hfq for Growth of Epidemic Yersinia pestis, but Not Yersinia pseudotuberculosis, with Implications for Plague Biology

2010 ◽  
Vol 192 (16) ◽  
pp. 4239-4245 ◽  
Author(s):  
Guangchun Bai ◽  
Andrey Golubov ◽  
Eric A. Smith ◽  
Kathleen A. McDonough
Keyword(s):  
Yersinia Pestis ◽  
Small Rna ◽  
Small Rnas ◽  
Yersinia Pseudotuberculosis ◽  
Etiologic Agent ◽  
Growth Restriction ◽  
Rna Chaperone ◽  
Unique Biology ◽  
Severe Growth

ABSTRACT Yersinia pestis, the etiologic agent of plague, has only recently evolved from Yersinia pseudotuberculosis. hfq deletion caused severe growth restriction at 37°C in Y. pestis but not in Y. pseudotuberculosis. Strains from all epidemic plague biovars were similarly affected, implicating Hfq, and likely small RNAs (sRNAs), in the unique biology of the plague bacillus.

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