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https://www.readbyqxmd.com/read/28096376/myosin-driven-transport-network-in-plants
#1
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...
January 17, 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
#2
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...
January 4, 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
#3
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
#4
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
#5
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
#6
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
#7
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
#8
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
#9
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
#10
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
https://www.readbyqxmd.com/read/27819663/two-fundamentally-different-classes-of-microbial-genes
#11
Yuri I Wolf, Kira S Makarova, Alexander E Lobkovsky, Eugene V Koonin
The evolution of bacterial and archaeal genomes is highly dynamic and involves extensive horizontal gene transfer and gene loss(1-4). Furthermore, many microbial species appear to have open pangenomes, where each newly sequenced genome contains more than 10% ORFans, that is, genes without detectable homologues in other species(5,6). Here, we report a quantitative analysis of microbial genome evolution by fitting the parameters of a simple, steady-state evolutionary model to the comparative genomic data on the gene content and gene order similarity between archaeal genomes...
November 7, 2016: Nature Microbiology
https://www.readbyqxmd.com/read/27805547/cost-effectiveness-of-increasing-access-to-contraception-during-the-zika-virus-outbreak-puerto-rico-2016
#12
Rui Li, Katharine B Simmons, Jeanne Bertolli, Brenda Rivera-Garcia, Shanna Cox, Lisa Romero, Lisa M Koonin, Miguel Valencia-Prado, Nabal Bracero, Denise J Jamieson, Wanda Barfield, Cynthia A Moore, Cara T Mai, Lauren C Korhonen, Meghan T Frey, Janice Perez-Padilla, Ricardo Torres-Muñoz, Scott D Grosse
We modeled the potential cost-effectiveness of increasing access to contraception in Puerto Rico during a Zika virus outbreak. The intervention is projected to cost an additional $33.5 million in family planning services and is likely to be cost-saving for the healthcare system overall. It could reduce Zika virus-related costs by $65.2 million ($2.8 million from less Zika virus testing and monitoring and $62.3 million from avoided costs of Zika virus-associated microcephaly [ZAM]). The estimates are influenced by the contraception methods used, the frequency of ZAM, and the lifetime incremental cost of ZAM...
January 2017: Emerging Infectious Diseases
https://www.readbyqxmd.com/read/27799560/evolutionary-switches-between-two-serine-codon-sets-are-driven-by-selection
#13
Igor B Rogozin, Frida Belinky, Vladimir Pavlenko, Svetlana A Shabalina, David M Kristensen, Eugene V Koonin
Serine is the only amino acid that is encoded by two disjoint codon sets so that a tandem substitution of two nucleotides is required to switch between the two sets. Previously published evidence suggests that, for the most evolutionarily conserved serines, the codon set switch occurs by simultaneous substitution of two nucleotides. Here we report a genome-wide reconstruction of the evolution of serine codons in triplets of closely related species from diverse prokaryotes and eukaryotes. The results indicate that the great majority of codon set switches proceed by two consecutive nucleotide substitutions, via a threonine or cysteine intermediate, and are driven by selection...
November 15, 2016: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/27789703/prokaryotic-virus-orthologous-groups-pvogs-a-resource-for-comparative-genomics-and-protein-family-annotation
#14
Ana Laura Grazziotin, Eugene V Koonin, David M Kristensen
Viruses are the most abundant and diverse biological entities on earth, and while most of this diversity remains completely unexplored, advances in genome sequencing have provided unprecedented glimpses into the virosphere. The Prokaryotic Virus Orthologous Groups (pVOGs, formerly called Phage Orthologous Groups, POGs) resource has aided in this task over the past decade by using automated methods to keep pace with the rapid increase in genomic data. The uses of pVOGs include functional annotation of viral proteins, identification of genes and viruses in uncharacterized DNA samples, phylogenetic analysis, large-scale comparative genomics projects, and more...
January 4, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/27737689/unexpected-links-reflect-the-noise-in-networks
#15
Anatoly Yambartsev, Michael A Perlin, Yevgeniy Kovchegov, Natalia Shulzhenko, Karina L Mine, Xiaoxi Dong, Andrey Morgun
BACKGROUND: Gene covariation networks are commonly used to study biological processes. The inference of gene covariation networks from observational data can be challenging, especially considering the large number of players involved and the small number of biological replicates available for analysis. RESULTS: We propose a new statistical method for estimating the number of erroneous edges in reconstructed networks that strongly enhances commonly used inference approaches...
October 13, 2016: Biology Direct
https://www.readbyqxmd.com/read/27702904/theory-of-prokaryotic-genome-evolution
#16
Itamar Sela, Yuri I Wolf, Eugene V Koonin
Bacteria and archaea typically possess small genomes that are tightly packed with protein-coding genes. The compactness of prokaryotic genomes is commonly perceived as evidence of adaptive genome streamlining caused by strong purifying selection in large microbial populations. In such populations, even the small cost incurred by nonfunctional DNA because of extra energy and time expenditure is thought to be sufficient for this extra genetic material to be eliminated by selection. However, contrary to the predictions of this model, there exists a consistent, positive correlation between the strength of selection at the protein sequence level, measured as the ratio of nonsynonymous to synonymous substitution rates, and microbial genome size...
October 11, 2016: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/27681128/bipartite-network-analysis-of-the-archaeal-virosphere-evolutionary-connections-between-viruses-and-capsidless-mobile-elements
#17
Jaime Iranzo, Eugene V Koonin, David Prangishvili, Mart Krupovic
: Archaea and particularly hyperthermophilic crenarchaea are hosts to many unusual viruses with diverse virion shapes and distinct gene compositions. As is typical of viruses in general, there are no universal genes in the archaeal virosphere. Therefore, to obtain a comprehensive picture of the evolutionary relationships between viruses, network analysis methods are more productive than traditional phylogenetic approaches. Here we present a comprehensive comparative analysis of genomes and proteomes from all currently known taxonomically classified and unclassified, cultivated and uncultivated archaeal viruses...
December 15, 2016: Journal of Virology
https://www.readbyqxmd.com/read/27630115/cpf1-nucleases-demonstrate-robust-activity-to-induce-dna-modification-by-exploiting-homology-directed-repair-pathways-in-mammalian-cells
#18
Eszter Tóth, Nóra Weinhardt, Petra Bencsura, Krisztina Huszár, Péter I Kulcsár, András Tálas, Elfrieda Fodor, Ervin Welker
BACKGROUND: Cpf1 nucleases have recently been repurposed for site-specific genome modification. Two members of the Cpf1 family, the AsCpf1 from Acidaminococcus sp. and the LbCpf1 from Lachnospiraceae bacterium were shown to induce higher indel frequencies than SpCas9 when examining four randomly-selected target sequences for each type of nuclease. Whether they are a real match for Cas9 nucleases, however, remains to be verified. RESULTS: Here, we used AsCpf1 and LbCpf1 to induce homology directed repair, either single strand annealing (SSA) or homologous recombination (HR), in N2a mouse neuroblastoma cells...
2016: Biology Direct
https://www.readbyqxmd.com/read/27508073/horizontal-gene-transfer-essentiality-and-evolvability-in-prokaryotes-and-roles-in-evolutionary-transitions
#19
REVIEW
Eugene V Koonin
The wide spread of gene exchange and loss in the prokaryotic world has prompted the concept of 'lateral genomics' to the point of an outright denial of the relevance of phylogenetic trees for evolution. However, the pronounced coherence congruence of the topologies of numerous gene trees, particularly those for (nearly) universal genes, translates into the notion of a statistical tree of life (STOL), which reflects a central trend of vertical evolution. The STOL can be employed as a framework for reconstruction of the evolutionary processes in the prokaryotic world...
2016: F1000Research
https://www.readbyqxmd.com/read/27503291/inevitability-of-genetic-parasites
#20
Jaime Iranzo, Pere Puigbo, Alexander E Lobkovsky, Yuri I Wolf, Eugene V Koonin
Almost all cellular life forms are hosts to diverse genetic parasites with various levels of autonomy including plasmids, transposons and viruses. Theoretical modeling of the evolution of primordial replicators indicates that parasites ('cheaters') necessarily evolve in such systems and can be kept at bay primarily via compartmentalization. Given the (near) ubiquity, abundance and diversity of genetic parasites, the question becomes pertinent: are such parasites intrinsic to life? At least in prokaryotes, the persistence of parasites is linked to the rate of horizontal gene transfer (HGT)...
August 8, 2016: Genome Biology and Evolution
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