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https://www.readbyqxmd.com/read/28408723/nucleic-acid-detection-with-crispr-cas13a-c2c2
#1
Jonathan S Gootenberg, Omar O Abudayyeh, Jeong Wook Lee, Patrick Essletzbichler, Aaron J Dy, Julia Joung, Vanessa Verdine, Nina Donghia, Nichole M Daringer, Catherine A Freije, Cameron Myhrvold, Roby P Bhattacharyya, Jonathan Livny, Aviv Regev, Eugene V Koonin, Deborah T Hung, Pardis C Sabeti, James J Collins, Feng Zhang
Rapid, inexpensive, and sensitive nucleic acid detection may aid point-of-care pathogen detection, genotyping, and disease monitoring. The RNA-guided, RNA-targeting CRISPR effector Cas13a (previously known as C2c2) exhibits a "collateral effect" of promiscuous RNAse activity upon target recognition. We combine the collateral effect of Cas13a with isothermal amplification to establish a CRISPR-based diagnostic (CRISPR-Dx), providing rapid DNA or RNA detection with attomolar sensitivity and single-base mismatch specificity...
April 13, 2017: Science
https://www.readbyqxmd.com/read/28386012/giant-viruses-with-an-expanded-complement-of-translation-system-components
#2
Frederik Schulz, Natalya Yutin, Natalia N Ivanova, Davi R Ortega, Tae Kwon Lee, Julia Vierheilig, Holger Daims, Matthias Horn, Michael Wagner, Grant J Jensen, Nikos C Kyrpides, Eugene V Koonin, Tanja Woyke
The discovery of giant viruses blurred the sharp division between viruses and cellular life. Giant virus genomes encode proteins considered as signatures of cellular organisms, particularly translation system components, prompting hypotheses that these viruses derived from a fourth domain of cellular life. Here we report the discovery of a group of giant viruses (Klosneuviruses) in metagenomic data. Compared with other giant viruses, the Klosneuviruses encode an expanded translation machinery, including aminoacyl transfer RNA synthetases with specificities for all 20 amino acids...
April 7, 2017: Science
https://www.readbyqxmd.com/read/28376755/reconstruction-of-the-evolution-of-microbial-defense-systems
#3
Pere Puigbò, Kira S Makarova, David M Kristensen, Yuri I Wolf, Eugene V Koonin
BACKGROUND: Evolution of bacterial and archaeal genomes is a highly dynamic process that involves intensive loss of genes as well as gene gain via horizontal transfer, with a lesser contribution from gene duplication. The rates of these processes can be estimated by comparing genomes that are linked by an evolutionary tree. These estimated rates of genome dynamics events substantially differ for different functional classes of genes. The genes involved in defense against viruses and other invading DNA are among those that are gained and lost at the highest rates...
April 4, 2017: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/28356531/homologous-capsid-proteins-testify-to-the-common-ancestry-of-retroviruses-caulimoviruses-pseudoviruses-and-metaviruses
#4
Mart Krupovic, Eugene V Koonin
Reverse-transcribing viruses are classified into 5 different families, Retroviridae, Metaviridae, Pseudoviridae, Caulimoviridae and Hepadnaviridae (1).….
March 29, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28265094/multiple-origins-of-viral-capsid-proteins-from-cellular-ancestors
#5
Mart Krupovic, Eugene V Koonin
Viruses are the most abundant biological entities on earth and show remarkable diversity of genome sequences, replication and expression strategies, and virion structures. Evolutionary genomics of viruses revealed many unexpected connections but the general scenario(s) for the evolution of the virosphere remains a matter of intense debate among proponents of the cellular regression, escaped genes, and primordial virus world hypotheses. A comprehensive sequence and structure analysis of major virion proteins indicates that they evolved on about 20 independent occasions, and in some of these cases likely ancestors are identifiable among the proteins of cellular organisms...
March 21, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28245845/adaptive-multiscapes-an-up-to-date-metaphor-to-visualize-molecular-adaptation
#6
EDITORIAL
Pablo Catalán, Clemente F Arias, Jose A Cuesta, Susanna Manrubia
BACKGROUND: Wright's metaphor of the fitness landscape has shaped and conditioned our view of the adaptation of populations for almost a century. Since its inception, and including criticism raised by Wright himself, the concept has been surrounded by controversy. Among others, the debate stems from the intrinsic difficulty to capture important features of the space of genotypes, such as its high dimensionality or the existence of abundant ridges, in a visually appealing two-dimensional picture...
February 28, 2017: Biology Direct
https://www.readbyqxmd.com/read/28187792/evolution-of-rna-and-dna-guided-antivirus-defense-systems-in-prokaryotes-and-eukaryotes-common-ancestry-vs-convergence
#7
REVIEW
Eugene V Koonin
Complementarity between nucleic acid molecules is central to biological information transfer processes. Apart from the basal processes of replication, transcription and translation, complementarity is also employed by multiple defense and regulatory systems. All cellular life forms possess defense systems against viruses and mobile genetic elements, and in most of them some of the defense mechanisms involve small guide RNAs or DNAs that recognize parasite genomes and trigger their inactivation. The nucleic acid-guided defense systems include prokaryotic Argonaute (pAgo)-centered innate immunity and CRISPR-Cas adaptive immunity as well as diverse branches of RNA interference (RNAi) in eukaryotes...
February 10, 2017: Biology Direct
https://www.readbyqxmd.com/read/28134265/consensus-statement-virus-taxonomy-in-the-age-of-metagenomics
#8
REVIEW
Peter Simmonds, Mike J Adams, Mária Benkő, Mya Breitbart, J Rodney Brister, Eric B Carstens, Andrew J Davison, Eric Delwart, Alexander E Gorbalenya, Balázs Harrach, Roger Hull, Andrew M Q King, Eugene V Koonin, Mart Krupovic, Jens H Kuhn, Elliot J Lefkowitz, Max L Nibert, Richard Orton, Marilyn J Roossinck, Sead Sabanadzovic, Matthew B Sullivan, Curtis A Suttle, Robert B Tesh, René A van der Vlugt, Arvind Varsani, F Murilo Zerbini
The number and diversity of viral sequences that are identified in metagenomic data far exceeds that of experimentally characterized virus isolates. In a recent workshop, a panel of experts discussed the proposal that, with appropriate quality control, viruses that are known only from metagenomic data can, and should be, incorporated into the official classification scheme of the International Committee on Taxonomy of Viruses (ICTV). Although a taxonomy that is based on metagenomic sequence data alone represents a substantial departure from the traditional reliance on phenotypic properties, the development of a robust framework for sequence-based virus taxonomy is indispensable for the comprehensive characterization of the global virome...
March 2017: Nature Reviews. Microbiology
https://www.readbyqxmd.com/read/28115717/profile-of-eugene-v-koonin
#9
Paul Gabrielsen
No abstract text is available yet for this article.
January 31, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28111461/diversity-and-evolution-of-class-2-crispr-cas-systems
#10
REVIEW
Sergey Shmakov, Aaron Smargon, David Scott, David Cox, Neena Pyzocha, Winston Yan, Omar O Abudayyeh, Jonathan S Gootenberg, Kira S Makarova, Yuri I Wolf, Konstantin Severinov, Feng Zhang, Eugene V Koonin
Class 2 CRISPR-Cas systems are characterized by effector modules that consist of a single multidomain protein, such as Cas9 or Cpf1. We designed a computational pipeline for the discovery of novel class 2 variants and used it to identify six new CRISPR-Cas subtypes. The diverse properties of these new systems provide potential for the development of versatile tools for genome editing and regulation. In this Analysis article, we present a comprehensive census of class 2 types and class 2 subtypes in complete and draft bacterial and archaeal genomes, outline evolutionary scenarios for the independent origin of different class 2 CRISPR-Cas systems from mobile genetic elements, and propose an amended classification and nomenclature of CRISPR-Cas...
March 2017: Nature Reviews. Microbiology
https://www.readbyqxmd.com/read/28096376/myosin-driven-transport-network-in-plants
#11
Elizabeth G Kurth, Valera V Peremyslov, Hannah L Turner, Kira S Makarova, Jaime Iranzo, Sergei L Mekhedov, Eugene V Koonin, Valerian V Dolja
We investigate the myosin XI-driven transport network in Arabidopsis using protein-protein interaction, subcellular localization, gene knockout, and bioinformatics analyses. The two major groups of nodes in this network are myosins XI and their membrane-anchored receptors (MyoB) that, together, drive endomembrane trafficking and cytoplasmic streaming in the plant cells. The network shows high node connectivity and is dominated by generalists, with a smaller fraction of more specialized myosins and receptors...
February 21, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28065598/cas13b-is-a-type-vi-b-crispr-associated-rna-guided-rnase-differentially-regulated-by-accessory-proteins-csx27-and-csx28
#12
Aaron A Smargon, David B T Cox, Neena K Pyzocha, Kaijie Zheng, Ian M Slaymaker, Jonathan S Gootenberg, Omar A Abudayyeh, Patrick Essletzbichler, Sergey Shmakov, Kira S Makarova, Eugene V Koonin, Feng Zhang
CRISPR-Cas adaptive immune systems defend microbes against foreign nucleic acids via RNA-guided endonucleases. Using a computational sequence database mining approach, we identify two class 2 CRISPR-Cas systems (subtype VI-B) that lack Cas1 and Cas2 and encompass a single large effector protein, Cas13b, along with one of two previously uncharacterized associated proteins, Csx27 and Csx28. We establish that these CRISPR-Cas systems can achieve RNA interference when heterologously expressed. Through a combination of biochemical and genetic experiments, we show that Cas13b processes its own CRISPR array with short and long direct repeats, cleaves target RNA, and exhibits collateral RNase activity...
February 16, 2017: Molecular Cell
https://www.readbyqxmd.com/read/28053163/atgc-database-and-atgc-cogs-an-updated-resource-for-micro-and-macro-evolutionary-studies-of-prokaryotic-genomes-and-protein-family-annotation
#13
David M Kristensen, Yuri I Wolf, Eugene V Koonin
The Alignable Tight Genomic Clusters (ATGCs) database is a collection of closely related bacterial and archaeal genomes that provides several tools to aid research into evolutionary processes in the microbial world. Each ATGC is a taxonomy-independent cluster of 2 or more completely sequenced genomes that meet the objective criteria of a high degree of local gene order (synteny) and a small number of synonymous substitutions in the protein-coding genes. As such, each ATGC is suited for analysis of microevolutionary variations within a cohesive group of organisms (e...
January 4, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28031045/expansion-of-the-molecular-and-morphological-diversity-of-acanthamoebidae-centramoebida-amoebozoa-and-identification-of-a-novel-life-cycle-type-within-the-group
#14
Alexander K Tice, Lora L Shadwick, Anna Maria Fiore-Donno, Stefan Geisen, Seungho Kang, Gabriel A Schuler, Frederick W Spiegel, Katherine A Wilkinson, Michael Bonkowski, Kenneth Dumack, Daniel J G Lahr, Eckhard Voelcker, Steffen Clauß, Junling Zhang, Matthew W Brown
BACKGROUND: Acanthamoebidae is a "family" level amoebozoan group composed of the genera Acanthamoeba, Protacanthamoeba, and very recently Luapeleamoeba. This clade of amoebozoans has received considerable attention from the broader scientific community as Acanthamoeba spp. represent both model organisms and human pathogens. While the classical composition of the group (Acanthamoeba + Protacanthamoeba) has been well accepted due to the morphological and ultrastructural similarities of its members, the Acanthamoebidae has never been highly statistically supported in single gene phylogenetic reconstructions of Amoebozoa either by maximum likelihood (ML) or Bayesian analyses...
December 28, 2016: Biology Direct
https://www.readbyqxmd.com/read/28010725/splendor-and-misery-of-adaptation-or-the-importance-of-neutral-null-for-understanding-evolution
#15
Eugene V Koonin
The study of any biological features, including genomic sequences, typically revolves around the question: what is this for? However, population genetic theory, combined with the data of comparative genomics, clearly indicates that such a "pan-adaptationist" approach is a fallacy. The proper question is: how has this sequence evolved? And the proper null hypothesis posits that it is a result of neutral evolution: that is, it survives by sheer chance provided that it is not deleterious enough to be efficiently purged by purifying selection...
December 23, 2016: BMC Biology
https://www.readbyqxmd.com/read/27929391/a-hyperspectral-survey-of-new-york-city-lighting-technology
#16
Gregory Dobler, Masoud Ghandehari, Steven E Koonin, Mohit S Sharma
Using side-facing observations of the New York City (NYC) skyline, we identify lighting technologies via spectral signatures measured with Visible and Near Infrared (VNIR) hyperspectral imaging. The instrument is a scanning, single slit spectrograph with 872 spectral channels from 0.4-1.0 μ m. With a single scan, we are able to clearly match the detected spectral signatures of 13 templates of known lighting types. However, many of the observed lighting spectra do not match those that have been measured in the laboratory...
December 5, 2016: Sensors
https://www.readbyqxmd.com/read/27929010/virology-a-parasite-s-parasite-saves-host-s-neighbours
#17
COMMENT
Eugene V Koonin, Mart Krupovic
No abstract text is available yet for this article.
December 7, 2016: Nature
https://www.readbyqxmd.com/read/27924834/activation-induced-deaminase-mutational-signature-overlaps-with-cpg-methylation-sites-in-follicular-lymphoma-and-other-cancers
#18
Igor B Rogozin, Artem G Lada, Alexander Goncearenco, Michael R Green, Subhajyoti De, German Nudelman, Anna R Panchenko, Eugene V Koonin, Youri I Pavlov
Follicular lymphoma (FL) is an uncurable cancer characterized by progressive severity of relapses. We analyzed sequence context specificity of mutations in the B cells from a large cohort of FL patients. We revealed substantial excess of mutations within a novel hybrid nucleotide motif: the signature of somatic hypermutation (SHM) enzyme, Activation Induced Deaminase (AID), which overlaps the CpG methylation site. This finding implies that in FL the SHM machinery acts at genomic sites containing methylated cytosine...
December 7, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27896818/coupling-immunity-and-programmed-cell-suicide-in-prokaryotes-life-or-death-choices
#19
Eugene V Koonin, Feng Zhang
Host-pathogen arms race is a universal, central aspect of the evolution of life. Most organisms evolved several distinct yet interacting strategies of anti-pathogen defense including resistance to parasite invasion, innate and adaptive immunity, and programmed cell death (PCD). The PCD is the means of last resort, a suicidal response to infection that is activated when resistance and immunity fail. An infected cell faces a decision between active defense and altruistic suicide or dormancy induction, depending on whether immunity is "deemed" capable of preventing parasite reproduction and consequent infection of other cells...
January 2017: BioEssays: News and Reviews in Molecular, Cellular and Developmental Biology
https://www.readbyqxmd.com/read/27857066/positive-and-strongly-relaxed-purifying-selection-drive-the-evolution-of-repeats-in-proteins
#20
Erez Persi, Yuri I Wolf, Eugene V Koonin
Protein repeats are considered hotspots of protein evolution, associated with acquisition of new functions and novel phenotypic traits, including disease. Paradoxically, however, repeats are often strongly conserved through long spans of evolution. To resolve this conundrum, it is necessary to directly compare paralogous (horizontal) evolution of repeats within proteins with their orthologous (vertical) evolution through speciation. Here we develop a rigorous methodology to identify highly periodic repeats with significant sequence similarity, for which evolutionary rates and selection (dN/dS) can be estimated, and systematically characterize their evolution...
November 18, 2016: Nature Communications
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