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https://www.readbyqxmd.com/read/27929391/a-hyperspectral-survey-of-new-york-city-lighting-technology
#1
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
#2
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
#3
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
#4
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...
November 29, 2016: 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
#5
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
#6
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
#7
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 15, 2017: Emerging Infectious Diseases
https://www.readbyqxmd.com/read/27799560/evolutionary-switches-between-two-serine-codon-sets-are-driven-by-selection
#8
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
#9
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...
October 26, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27737689/unexpected-links-reflect-the-noise-in-networks
#10
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
#11
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
#12
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
#13
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
#14
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
#15
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
https://www.readbyqxmd.com/read/27493190/diverse-evolutionary-roots-and-mechanistic-variations-of-the-crispr-cas-systems
#16
REVIEW
Prarthana Mohanraju, Kira S Makarova, Bernd Zetsche, Feng Zhang, Eugene V Koonin, John van der Oost
Adaptive immunity had been long thought of as an exclusive feature of animals. However, the discovery of the CRISPR-Cas defense system, present in almost half of prokaryotic genomes, proves otherwise. Because of the everlasting parasite-host arms race, CRISPR-Cas has rapidly evolved through horizontal transfer of complete loci or individual modules, resulting in extreme structural and functional diversity. CRISPR-Cas systems are divided into two distinct classes that each consist of three types and multiple subtypes...
August 5, 2016: Science
https://www.readbyqxmd.com/read/27486193/the-double-stranded-dna-virosphere-as-a-modular-hierarchical-network-of-gene-sharing
#17
Jaime Iranzo, Mart Krupovic, Eugene V Koonin
UNLABELLED: Virus genomes are prone to extensive gene loss, gain, and exchange and share no universal genes. Therefore, in a broad-scale study of virus evolution, gene and genome network analyses can complement traditional phylogenetics. We performed an exhaustive comparative analysis of the genomes of double-stranded DNA (dsDNA) viruses by using the bipartite network approach and found a robust hierarchical modularity in the dsDNA virosphere. Bipartite networks consist of two classes of nodes, with nodes in one class, in this case genomes, being connected via nodes of the second class, in this case genes...
2016: MBio
https://www.readbyqxmd.com/read/27466388/role-of-mrna-structure-in-the-control-of-protein-folding
#18
Guilhem Faure, Aleksey Y Ogurtsov, Svetlana A Shabalina, Eugene V Koonin
Specific structures in mRNA modulate translation rate and thus can affect protein folding. Using the protein structures from two eukaryotes and three prokaryotes, we explore the connections between the protein compactness, inferred from solvent accessibility, and mRNA structure, inferred from mRNA folding energy (ΔG). In both prokaryotes and eukaryotes, the ΔG value of the most stable 30 nucleotide segment of the mRNA (ΔGmin) strongly, positively correlates with protein solvent accessibility. Thus, mRNAs containing exceptionally stable secondary structure elements typically encode compact proteins...
July 27, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27431520/viruses-and-mobile-elements-as-drivers-of-evolutionary-transitions
#19
REVIEW
Eugene V Koonin
The history of life is punctuated by evolutionary transitions which engender emergence of new levels of biological organization that involves selection acting at increasingly complex ensembles of biological entities. Major evolutionary transitions include the origin of prokaryotic and then eukaryotic cells, multicellular organisms and eusocial animals. All or nearly all cellular life forms are hosts to diverse selfish genetic elements with various levels of autonomy including plasmids, transposons and viruses...
August 19, 2016: Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences
https://www.readbyqxmd.com/read/27386933/early-identification-and-prevention-of-the-spread-of-ebola-united-states
#20
Chris A Van Beneden, Harald Pietz, Robert D Kirkcaldy, Lisa M Koonin, Timothy M Uyeki, Alexandra M Oster, Deborah A Levy, Maleeka Glover, Matthew J Arduino, Toby L Merlin, David T Kuhar, Christine Kosmos, Beth P Bell
In response to the 2014-2016 Ebola virus disease (Ebola) epidemic in West Africa, CDC prepared for the potential introduction of Ebola into the United States. The immediate goals were to rapidly identify and isolate any cases of Ebola, prevent transmission, and promote timely treatment of affected patients. CDC's technical expertise and the collaboration of multiple partners in state, local, and municipal public health departments; health care facilities; emergency medical services; and U.S. government agencies were essential to the domestic preparedness and response to the Ebola epidemic and relied on longstanding partnerships...
2016: MMWR Supplements
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