#Enzymatic anti- #CRISPRs improve the #bacteriophage #arsenal (Nat Struct Mol Biol., abstract)

[Source: Nature Structural & Molecular Biology, full page: (LINK). Abstract, edited.]

News & Views | Published: 01 April 2019 | CRISPR

Enzymatic anti-CRISPRs improve the bacteriophage arsenal

Shravanti K. Suresh, Karthik Murugan & Dipali G. Sashital

Nature Structural & Molecular Biology (2019)

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Bacteriophage-encoded anti-CRISPR (Acr) proteins were previously thought to inhibit CRISPR-mediated immunity by acting as physical barriers against the binding or cleavage of DNA. Two new studies report that recently discovered type V Acr proteins use enzymatic activities to shut down the Cas12a endonuclease, providing a multi-turnover ‘off switch’ for CRISPR-based immunity and technology.

(…)

Keywords: CRISPR; Biology; Bacteriophages.

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#Natural, incidental, and engineered #nanomaterials and their #impacts on the #Earth #system (Science, abstract)

[Source: Science, full page: (LINK). Abstract, edited.]

Natural, incidental, and engineered nanomaterials and their impacts on the Earth system

Michael F. Hochella Jr.1,2,*, David W. Mogk3, James Ranville4, Irving C. Allen5, George W. Luther6, Linsey C. Marr7, B. Peter McGrail8, Mitsu Murayama9,10,11, Nikolla P. Qafoku2, Kevin M. Rosso12, Nita Sahai13, Paul A. Schroeder14, Peter Vikesland7, Paul Westerhoff15, Yi Yang16

1 Department of Geosciences, Virginia Tech, Blacksburg, VA 24061, USA. 2 Subsurface Science and Technology Group, Energy and Environment Directorate, Pacific Northwest National Laboratory, Richland, WA 99352, USA. 3 Department of Earth Sciences, Montana State University, Bozeman, MT 59717-3480, USA. 4 Department of Chemistry, Colorado School of Mines, Golden, CO 80401, USA. 5 Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Blacksburg, VA 24061, USA. 6 School of Marine Science and Policy, University of Delaware, Lewes, DE 19958, USA. 7 Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, VA 24061, USA. 8 Applied Functional Materials Group, Energy and Environment Directorate, Pacific Northwest National Laboratory, Richland, WA 99352, USA. 9 Department of Materials Science and Engineering, Virginia Tech, Blacksburg, VA 24061, USA. 10 Reactor Materials and Mechanical Design Group, Energy and Environment Directorate, Pacific Northwest National Laboratory, Richland, WA 99352, USA. 11 Institute for Materials Chemistry and Engineering, Kyushu University, Kasuga, Fukuoka 8168580, Japan. 12 Geochemistry Group, Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA 99352, USA. 13 Department of Polymer Science, University of Akron, Akron, OH 44325-3909, USA. 14 Department of Geology, University of Georgia, Athens, GA 30602, USA. 15 School of Sustainable Engineering and Built Environment, Arizona State University, Tempe, AZ 85287, USA. 16 Key Laboratory of Geographic Information Science of the Ministry of Education, School of Geographic Sciences, East China Normal University, Shanghai 200241, China.

*Corresponding author. Email: hochella@vt.edu

Science  29 Mar 2019: Vol. 363, Issue 6434, eaau8299 / DOI: 10.1126/science.aau8299

 

Nanomaterials in the Earth system

Nanomaterials have been part of the Earth system for billions of years, but human activities are changing the nature and amounts of these materials. Hochella Jr. et al. review sources and impacts of natural nanomaterials, which are not created directly through human actions; incidental nanomaterials, which form unintentionally during human activities; and engineered nanomaterials, which are created for specific applications. Knowledge of the properties of all three types as they cycle through the Earth system is essential for understanding and mitigating their long-term impacts on the environment and human health.

Science, this issue p. eaau8299

 

Structured Abstract

BACKGROUND

Natural nanomaterials have always been abundant during Earth’s formation and throughout its evolution over the past 4.54 billion years. Incidental nanomaterials, which arise as a by-product from human activity, have become unintentionally abundant since the beginning of the Industrial Revolution. Nanomaterials can also be engineered to have unusual, tunable properties that can be used to improve products in applications from human health to electronics, and in energy, water, and food production. Engineered nanomaterials are very much a recent phenomenon, not yet a century old, and are just a small mass fraction of the natural and incidental varieties. As with natural and incidental nanomaterials, engineered nanomaterials can have both positive and negative consequences in our environment.

Despite the ubiquity of nanomaterials on Earth, only in the past 20 years or so have their impacts on the Earth system been studied intensively. This is mostly due to a much better understanding of the distinct behavior of materials at the nanoscale and to multiple advances in analytic techniques. This progress continues to expand rapidly as it becomes clear that nanomaterials are relevant from molecular to planetary dimensions and that they operate from the shortest to the longest time scales over the entire Earth system.

ADVANCES

Nanomaterials can be defined as any organic, inorganic, or organometallic material that present chemical, physical, and/or electrical properties that change as a function of the size and shape of the material. This behavior is most often observed in the size range between 1 nm up to a few to several tens of nanometers in at least one dimension. These materials have very high proportions of surface atoms relative to interior ones. Also, they are often subject to property variation as a function of size owing to quantum confinement effects. Nanomaterial growth, dissolution or evaporation, surface reactivity, and aggregation states play key roles in their lifetime, behaviors, and local interactions in both natural and engineered environments, often with global consequences.

It is now possible to recognize and identify critical roles played by nanomaterials in vital Earth system components, including direct human impact. For example, nanomaterial surfaces may have been responsible for promoting the self-assembly of protocells in the origin of life and in the early evolution of bacterial cell walls. Also, weathering reactions on the continents produce various bioavailable iron (oxy)hydroxide natural and incidental nanomaterials, which are transported to the oceans via riverine and atmospheric pathways and which influence ocean surface primary productivity and thus the global carbon cycle. A third example involves nanomaterials in the atmosphere that travel locally, regionally, and globally. When inhaled, the smallest nanoparticles can pass through the alveolar membranes of the lungs and directly enter the bloodstream. From there, they enter vital organs, including the brain, with possible deleterious consequences.

OUTLOOK

Earth system nanoscience requires a convergent approach that combines physical, biological, and social sciences, as well as engineering and economic disciplines. This convergence will drive developments for all types of intelligent and anticipatory conceptual models assisted by new analytical techniques and computational simulations.

Ultimately, scientists must learn how to recognize key roles of natural, incidental, and engineered nanomaterials in the complex Earth system, so that this understanding can be included in models of Earth processes and Earth history, as well as in ethical considerations regarding their positive and negative effects on present and predicted future environmental and human health issues.

 

Abstract

Nanomaterials are critical components in the Earth system’s past, present, and future characteristics and behavior. They have been present since Earth’s origin in great abundance. Life, from the earliest cells to modern humans, has evolved in intimate association with naturally occurring nanomaterials. This synergy began to shift considerably with human industrialization. Particularly since the Industrial Revolution some two-and-a-half centuries ago, incidental nanomaterials (produced unintentionally by human activity) have been continuously produced and distributed worldwide. In some areas, they now rival the amount of naturally occurring nanomaterials. In the past half-century, engineered nanomaterials have been produced in very small amounts relative to the other two types of nanomaterials, but still in large enough quantities to make them a consequential component of the planet. All nanomaterials, regardless of their origin, have distinct chemical and physical properties throughout their size range, clearly setting them apart from their macroscopic equivalents and necessitating careful study. Following major advances in experimental, computational, analytical, and field approaches, it is becoming possible to better assess and understand all types and origins of nanomaterials in the Earth system. It is also now possible to frame their immediate and long-term impact on environmental and human health at local, regional, and global scales.

Keywords: Nanomaterials; Biology; Environmental Pollution.

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Exploring #astrobiology using #insilico #molecular structure #generation (Phil Transact R Soc., abstract)

[Source: Philosophical Transactions of the Royal Society A, full page: (LINK). Abstract, edited.]

Exploring astrobiology using in silico molecular structure generation

Markus Meringer, H. James Cleaves

Published 13 November 2017. DOI: 10.1098/rsta.2016.0344

 

Abstract

The origin of life is typically understood as a transition from inanimate or disorganized matter to self-organized, ‘animate’ matter. This transition probably took place largely in the context of organic compounds, and most approaches, to date, have focused on using the organic chemical composition of modern organisms as the main guide for understanding this process. However, it has gradually come to be appreciated that biochemistry, as we know it, occupies a minute volume of the possible organic ‘chemical space’. As the majority of abiotic syntheses appear to make a large set of compounds not found in biochemistry, as well as an incomplete subset of those that are, it is possible that life began with a significantly different set of components. Chemical graph-based structure generation methods allow for exhaustive in silico enumeration of different compound types and different types of ‘chemical spaces’ beyond those used by biochemistry, which can be explored to help understand the types of compounds biology uses, as well as to understand the nature of abiotic synthesis, and potentially design novel types of living systems.

This article is part of the themed issue ‘Reconceptualizing the origins of life’.

Keywords: Evolution; Biology; Astrobiology.

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Re- #conceptualizing the #origins of #life (Phil Transact R Soc., abstract)

[Source: Philosophical Transactions of the Royal Society A, full page: (LINK). Abstract, edited.]

Re-conceptualizing the origins of life

Sara I. Walker, N. Packard, G. D. Cody

Published 13 November 2017. DOI: 10.1098/rsta.2016.0337

 

Abstract

Over the last several hundred years of scientific progress, we have arrived at a deep understanding of the non-living world. We have not yet achieved an analogous, deep understanding of the living world. The origins of life is our best chance at discovering scientific laws governing life, because it marks the point of departure from the predictable physical and chemical world to the novel, history-dependent living world. This theme issue aims to explore ways to build a deeper understanding of the nature of biology, by modelling the origins of life on a sufficiently abstract level, starting from prebiotic conditions on Earth and possibly on other planets and bridging quantitative frameworks approaching universal aspects of life. The aim of the editors is to stimulate new directions for solving the origins of life. The present introduction represents the point of view of the editors on some of the most promising future directions.

This article is part of the themed issue ‘Reconceptualizing the origins of life’.

Keywords: Evolution; Biology; Astrobiology.

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Rapid #emergence of #life shown by #discovery of 3,700-million-year-old #microbial #structures (Nature, abstract)

[Source: Nature, full page: (LINK). Abstract, edited.]

Rapid emergence of life shown by discovery of 3,700-million-year-old microbial structures

Allen P. Nutman, Vickie C. Bennett, Clark R. L. Friend, Martin J. Van Kranendonk & Allan R. Chivas

Nature 537, 535–538 (22 September 2016) / doi:10.1038/nature19355

Received 11 October 2015 – Accepted 11 August 2016 – Published online 31 August 2016

 

Abstract

Biological activity is a major factor in Earth’s chemical cycles, including facilitating CO2 sequestration and providing climate feedbacks. Thus a key question in Earth’s evolution is when did life arise and impact hydrosphere–atmosphere–lithosphere chemical cycles? Until now, evidence for the oldest life on Earth focused on debated stable isotopic signatures of 3,800–3,700 million year (Myr)-old metamorphosed sedimentary rocks and minerals1, 2 from the Isua supracrustal belt (ISB), southwest Greenland3.

(…)

Keywords: Research; Abstracts; Biology; Biodiversity.

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#Plants Encode a General #siRNA #Suppressor That Is Induced and Suppressed by #Viruses (Plos Biology, abstract)

[Source: PLoS Biology, full page: (LINK). Abstract, edited.]

Open Access / Peer-reviewed / Research Article

Plants Encode a General siRNA Suppressor That Is Induced and Suppressed by Viruses [   R   ]

Nahid Shamandi,  Matthias Zytnicki,  Cyril Charbonnel,  Emilie Elvira-Matelot,  Aurore Bochnakian,  Pascale Comella,  Allison C. Mallory,  … Gersende Lepère,  Julio Sáez-Vásquez,  Hervé Vaucheret

Published: December 22, 2015 / DOI: 10.1371/journal.pbio.1002326

 

Abstract

Small RNAs play essential regulatory roles in genome stability, development, and responses to biotic and abiotic stresses in most eukaryotes. In plants, the RNaseIII enzyme DICER-LIKE1 (DCL1) produces miRNAs, whereas DCL2, DCL3, and DCL4 produce various size classes of siRNAs. Plants also encode RNASE THREE-LIKE (RTL) enzymes that lack DCL-specific domains and whose function is largely unknown. We found that virus infection induces RTL1 expression, suggesting that this enzyme could play a role in plant–virus interaction. To first investigate the biochemical activity of RTL1 independent of virus infection, small RNAs were sequenced from transgenic plants constitutively expressing RTL1. These plants lacked almost all DCL2-, DCL3-, and DCL4-dependent small RNAs, indicating that RTL1 is a general suppressor of plant siRNA pathways. In vivo and in vitro assays revealed that RTL1 prevents siRNA production by cleaving dsRNA prior to DCL2-, DCL3-, and DCL4-processing. The substrate of RTL1 cleavage is likely long-perfect (or near-perfect) dsRNA, consistent with the RTL1-insensitivity of miRNAs, which derive from DCL1-processing of short-imperfect dsRNA. Virus infection induces RTL1 mRNA accumulation, but viral proteins that suppress RNA silencing inhibit RTL1 activity, suggesting that RTL1 has evolved as an inducible antiviral defense that could target dsRNA intermediates of viral replication, but that a broad range of viruses counteract RTL1 using the same protein toolbox used to inhibit antiviral RNA silencing. Together, these results reveal yet another level of complexity in the evolutionary battle between viruses and plant defenses.

 

Author Summary

Most eukaryotes produce essential regulatory molecules called small RNAs. These molecules are produced primarily by a class of RNaseIII enzymes called DICER, which excises small RNA duplexes from long double-stranded (ds)RNA precursor molecules. Plants also encode several RNaseIII enzymes called RNASE THREE-LIKE (RTL), but the function of these proteins is largely unknown. Here, we show that RTL1 represses small RNA production by cleaving dsRNA before DICER can process them. RTL1 appears to specifically act on the templates of a class of small RNAs called siRNAs, but not on miRNA precursors, suggesting that it cleaves long-perfect (or near-perfect) dsRNA, but not short-imperfect dsRNA. We also found that RTL1 expression is induced after virus infection, suggesting that RTL1 could act as an inducible antiviral defense by destroying dsRNA intermediates of viral replication. Our findings suggest that viruses have evolved to inhibit RTL1 activity, ultimately resulting in successful viral infection.

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Citation: Shamandi N, Zytnicki M, Charbonnel C, Elvira-Matelot E, Bochnakian A, Comella P, et al. (2015) Plants Encode a General siRNA Suppressor That Is Induced and Suppressed by Viruses. PLoS Biol 13(12): e1002326. doi:10.1371/journal.pbio.1002326

Academic Editor: Robert A. Martienssen, Cold Spring Harbor Laboratory, UNITED STATES

Received: April 22, 2015; Accepted: November 11, 2015; Published: December 22, 2015

Copyright: © 2015 Shamandi et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited

Data Availability: Relevant data are within the paper and its Supporting Information files except for deep-sequencing data that has been deposited in the Gene Expression Omnibus (GEO) database, www.ncbi.nlm.nih.gov/geo (accession no. GSE49866).

Funding: This work was supported by grants from the French Agence Nationale de la Recherche: ANR-10-LABX-40 (to HV) and ANR-11-BSV6-007 (to HV, MZ, and JSV). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

Competing interests: The authors have declared that no competing interests exist.

Abbreviations: AGO, argonaute; CMV, cucumber mosaic virus; DCL, Dicer-like; dcl234, dcl2 dcl3 dcl4 triple mutant; DRB, dsRNA binding domain; dsRBD, double stranded RNA binding domain; dsRNA, double stranded RNA; endoIR-siRNA, endogenous inverted repeat-derived siRNA; ETS, 3’External Transcribed Spacer; HMW, high molecular weight; LMW, low molecular weight; miRNA, microRNA; p4-siRNA, POLYMERASE IV-dependent siRNA; PTGS, post-transcriptional gene silencing; RDR, RNA-dependent RNA polymerase; RTL, RNASE THREE-LIKE; RT-PCR, reverse transcriptase polymerase chain reaction; siRNA, small interfering RNA; ta-siRNA, trans acting siRNA; TAIR, The Arabidopsis Information Resource; TCV, turnip crinkle virus; TVCV, turnip vein cleaning virus; TYMV, turnip yellow mosaic virus; VSR, viral suppressor of RNA silencing

Keywords: Research; Abstracts; Biology; Virology.

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#Interactions among #bacterial #strains and fluke #genotypes shape #virulence of co-infection (Proc R Soc Bio., abstract)

[Source: Proceedings of the Royal Society, Biological Sciences, full page: (LINK). Abstract, edited.]

Interactions among bacterial strains and fluke genotypes shape virulence of co-infection [   R   ]

Katja-Riikka Louhi, Lotta-Riina Sundberg, Jukka Jokela, Anssi Karvonen

Published 16 December 2015.DOI: 10.1098/rspb.2015.2097

 

Abstract

Most studies of virulence of infection focus on pairwise host–parasite interactions. However, hosts are almost universally co-infected by several parasite strains and/or genotypes of the same or different species. While theory predicts that co-infection favours more virulent parasite genotypes through intensified competition for host resources, knowledge of the effects of genotype by genotype (G × G) interactions between unrelated parasite species on virulence of co-infection is limited. Here, we tested such a relationship by challenging rainbow trout with replicated bacterial strains and fluke genotypes both singly and in all possible pairwise combinations. We found that virulence (host mortality) was higher in co-infections compared with single infections. Importantly, we also found that the overall virulence was dependent on the genetic identity of the co-infecting partners so that the outcome of co-infection could not be predicted from the respective virulence of single infections. Our results imply that G × G interactions among co-infecting parasites may significantly affect host health, add to variance in parasite fitness and thus influence evolutionary dynamics and ecology of disease in unexpected ways.

Received August 31, 2015. Accepted November 11, 2015.

© 2015 The Author(s)

http://royalsocietypublishing.org/licence

Keywords: Research; Abstracts; Biology.

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