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https://www.readbyqxmd.com/read/28502981/mechanisms-of-gene-flow-in-archaea
#1
REVIEW
Alexander Wagner, Rachel J Whitaker, David J Krause, Jan-Hendrik Heilers, Marleen van Wolferen, Chris van der Does, Sonja-Verena Albers
Archaea are diverse, ecologically important, single-celled microorganisms. They have unique functions and features, such as methanogenesis and the composition of their cell envelope, although many characteristics are shared with the other domains of life, either through ancestry or through promiscuous horizontal gene transfer. The exchange of genetic material is a major driving force for genome evolution across the tree of life and has a role in archaeal speciation, adaptation and maintenance of diversity. In this Review, we discuss our current knowledge of archaeal mechanisms of DNA transfer and highlight the role of gene transfer in archaeal evolution...
May 15, 2017: Nature Reviews. Microbiology
https://www.readbyqxmd.com/read/28502748/cytochrome-p450-diversity-in-the-tree-of-life
#2
David R Nelson
Sequencing in all areas of the tree of life has produced >300,000 cytochrome P450 (CYP) sequences that have been mined and collected. Nomenclature has been assigned to >41,000 CYP sequences and the majority of the remainder has been sorted by BLAST searches into clans, families and subfamilies in preparation for naming. The P450 sequence space is being systematically explored and filled in. Well-studied groups like vertebrates are covered in greater depth while new insights are being added into uncharted territories like horseshoe crab (Limulus polyphemus), tardigrades (Hypsibius dujardini), velvet worm (Euperipatoides_rowelli), and basal land plants like hornworts, liverworts and mosses...
May 10, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28496163/reshaping-the-tree-of-life
#3
Eva Heinz, Daryl Domman
This month's Genome Watch highlights how metagenomics is continuing to reveal the diversity of microorganisms in the environment and how it is challenging and expanding our understanding of how life evolved on Earth.
May 12, 2017: Nature Reviews. Microbiology
https://www.readbyqxmd.com/read/28493998/metabolomics-analysis-finding-out-metabolic-building-blocks
#4
Ricardo Alberich, José A Castro, Mercè Llabrés, Pere Palmer-Rodríguez
In this paper we propose a new methodology for the analysis of metabolic networks. We use the notion of strongly connected components of a graph, called in this context metabolic building blocks. Every strongly connected component is contracted to a single node in such a way that the resulting graph is a directed acyclic graph, called a metabolic DAG, with a considerably reduced number of nodes. The property of being a directed acyclic graph brings out a background graph topology that reveals the connectivity of the metabolic network, as well as bridges, isolated nodes and cut nodes...
2017: PloS One
https://www.readbyqxmd.com/read/28484436/comparative-genomic-analysis-of-the-class-epsilonproteobacteria-and-proposed-reclassification-to-epsilonbacteraeota-phyl-nov
#5
David W Waite, Inka Vanwonterghem, Christian Rinke, Donovan H Parks, Ying Zhang, Ken Takai, Stefan M Sievert, Jörg Simon, Barbara J Campbell, Thomas E Hanson, Tanja Woyke, Martin G Klotz, Philip Hugenholtz
The Epsilonproteobacteria is the fifth validly described class of the phylum Proteobacteria, known primarily for clinical relevance and for chemolithotrophy in various terrestrial and marine environments, including deep-sea hydrothermal vents. As 16S rRNA gene repositories have expanded and protein marker analysis become more common, the phylogenetic placement of this class has become less certain. A number of recent analyses of the bacterial tree of life using both 16S rRNA and concatenated marker gene analyses have failed to recover the Epsilonproteobacteria as monophyletic with all other classes of Proteobacteria...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28472434/lineage-diversity-and-size-disparity-in-musteloidea-testing-patterns-of-adaptive-radiation-using-molecular-and-fossil-based-methods
#6
Chris J Law, Graham J Slater, Rita S Mehta
Adaptive radiation is hypothesized to be a primary mechanism that drives the remarkable species diversity and morphological disparity across the Tree of Life. Tests for adaptive radiation in extant taxa are traditionally estimated from calibrated molecular phylogenies with little input from extinct taxa. With 85 putative species in 33 genera and over 400 described extinct species, the carnivoran superfamily Musteloidea is a prime candidate to investigate patterns of adaptive radiation using both extant- and fossil-based macroevolutionary methods...
May 4, 2017: Systematic Biology
https://www.readbyqxmd.com/read/28468938/the-role-of-ca-2-signaling-in-parkinson-s-disease
#7
REVIEW
Sofia V Zaichick, Kaitlyn M McGrath, Gabriela Caraveo
Across all kingdoms in the tree of life, calcium (Ca(2+)) is an essential element used by cells to respond and adapt to constantly changing environments. In multicellular organisms, it plays fundamental roles during fertilization, development and adulthood. The inability of cells to regulate Ca(2+) can lead to pathological conditions that ultimately culminate in cell death. One such pathological condition is manifested in Parkinson's disease, the second most common neurological disorder in humans, which is characterized by the aggregation of the protein, α-synuclein...
May 1, 2017: Disease Models & Mechanisms
https://www.readbyqxmd.com/read/28467886/species-boundaries-in-the-absence-of-morphological-ecological-or-geographical-differentiation-in-the-red-sea-octocoral-genus-ovabunda-alcyonacea-xeniidae
#8
Catherine S McFadden, Roxanne Haverkort-Yeh, Alexandra M Reynolds, Anna Halàsz, Andrea M Quattrini, Zac H Forsman, Yehuda Benayahu, Robert J Toonen
The development of coalescent-based and other multilocus methods for species delimitation has facilitated the identification of cryptic species complexes across the tree of life. A recent taxonomic revision of the ecologically important soft coral genus Ovabunda validated 11morphospecies, all with type localities and overlapping geographic ranges in the Red Sea. A subsequent molecular phylogenetic analysis using mitochondrial and 28S nrDNA genes divided the genus into just two clades, with no apparent genetic distinctions among morphospecies...
April 30, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/28461155/akaryotes-and-eukaryotes-are-independent-descendants-of-a-universal-common-ancestor
#9
Ajith Harish, Charles G Kurland
We reconstructed a global tree of life (ToL) with non-reversible and non-stationary models of genome evolution that root trees intrinsically. We implemented Bayesian model selection tests and compared the statistical support for four conflicting ToL hypotheses. We show that reconstructions obtained with a Bayesian implementation (Klopfstein et al., 2015) is consistent with reconstructions obtained with an empirical Sankoff parsimony (ESP) implementation (Harish et al. 2013). Both are based on the genome contents of coding sequences for protein domains (superfamilies) from hundreds of genomes...
April 28, 2017: Biochimie
https://www.readbyqxmd.com/read/28428864/integrating-biogeography-threat-and-evolutionary-data-to-explore-extinction-crisis-in-the-taxonomic-group-of-cycads
#10
Kowiyou Yessoufou, Barnabas H Daru, Respinah Tafirei, Hosam O Elansary, Isaac Rampedi
Will the ongoing extinction crisis cause a severe loss of evolutionary information accumulated over millions of years on the tree of life? This question has been largely explored, particularly for vertebrates and angiosperms. However, no equivalent effort has been devoted to gymnosperms. Here, we address this question focusing on cycads, the gymnosperm group exhibiting the highest proportion of threatened species in the plant kingdom. We assembled the first complete phylogeny of cycads and assessed how species loss under three scenarios would impact the cycad tree of life...
April 2017: Ecology and Evolution
https://www.readbyqxmd.com/read/28410373/parallel-reorganization-of-protein-function-in-the-spindle-checkpoint-pathway-through-evolutionary-paths-in-the-fitness-landscape-that-appear-neutral-in-laboratory-experiments
#11
Alex N Nguyen Ba, Bob Strome, Selma Osman, Elizabeth-Ann Legere, Taraneh Zarin, Alan M Moses
Regulatory networks often increase in complexity during evolution through gene duplication and divergence of component proteins. Two models that explain this increase in complexity are: 1) adaptive changes after gene duplication, such as resolution of adaptive conflicts, and 2) non-adaptive processes such as duplication, degeneration and complementation. Both of these models predict complementary changes in the retained duplicates, but they can be distinguished by direct fitness measurements in organisms with short generation times...
April 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28388929/novel-soil-inhabiting-clades-fill-gaps-in-the-fungal-tree-of-life
#12
Leho Tedersoo, Mohammad Bahram, Rasmus Puusepp, R Henrik Nilsson, Timothy Y James
BACKGROUND: Fungi are a diverse eukaryotic group of degraders, pathogens, and symbionts, with many lineages known only from DNA sequences in soil, sediments, air, and water. RESULTS: We provide rough phylogenetic placement and principal niche analysis for >40 previously unrecognized fungal groups at the order and class level from global soil samples based on combined 18S (nSSU) and 28S (nLSU) rRNA gene sequences. Especially, Rozellomycota (Cryptomycota), Zygomycota s...
April 8, 2017: Microbiome
https://www.readbyqxmd.com/read/28381628/a-puzzling-homology-a-brittle-star-using-a-putative-cnidarian-type-luciferase-for-bioluminescence
#13
Jérôme Delroisse, Esther Ullrich-Lüter, Stefanie Blaue, Olga Ortega-Martinez, Igor Eeckhaut, Patrick Flammang, Jérôme Mallefet
Bioluminescence relies on the oxidation of a luciferin substrate catalysed by a luciferase enzyme. Luciferins and luciferases are generic terms used to describe a large variety of substrates and enzymes. Whereas luciferins can be shared by phylogenetically distant organisms which feed on organisms producing them, luciferases have been thought to be lineage-specific enzymes. Numerous light emission systems would then have co-emerged independently along the tree of life resulting in a plethora of non-homologous luciferases...
April 2017: Open Biology
https://www.readbyqxmd.com/read/28376330/animal-evolution-last-word-on-sponges-first
#14
D Timothy J Littlewood
A major problem in understanding animal evolution is where early branching phyla, especially sponges and comb jellies (sea gooseberries), sit in the tree of life. A new study seeks to overcome this problem by sampling more species and data cleansing.
April 3, 2017: Current Biology: CB
https://www.readbyqxmd.com/read/28369655/why-do-phylogenomic-data-sets-yield-conflicting-trees-data-type-influences-the-avian-tree-of-life-more-than-taxon-sampling
#15
Sushma Reddy, Rebecca T Kimball, Akanksha Pandey, Peter A Hosner, Michael J Braun, Shannon J Hackett, Kin-Lan Han, John Harshman, Christopher J Huddleston, Sarah Kingston, Ben D Marks, Kathleen J Miglia, William S Moore, Frederick H Sheldon, Christopher C Witt, Tamaki Yuri, Edward L Braun
Phylogenomics, the use of large-scale data matrices in phylogenetic analyses, has been viewed as the ultimate solution to the problem of resolving difficult nodes in the tree of life. However, it has become clear that analyses of these large genomic datasets can also result in conflicting estimates of phylogeny. Here we use the early divergences in Neoaves, the largest clade of extant birds, as a 'model system' to understand the basis for incongruence among phylogenomic trees. We were motivated by the observation that trees from two recent avian phylogenomic studies exhibit conflicts...
March 27, 2017: Systematic Biology
https://www.readbyqxmd.com/read/28369123/distribution-and-evolution-of-stable-single-%C3%AE-helices-sah-domains-in-myosin-motor-proteins
#16
Dominic Simm, Klas Hatje, Martin Kollmar
Stable single-alpha helices (SAHs) are versatile structural elements in many prokaryotic and eukaryotic proteins acting as semi-flexible linkers and constant force springs. This way SAH-domains function as part of the lever of many different myosins. Canonical myosin levers consist of one or several IQ-motifs to which light chains such as calmodulin bind. SAH-domains provide flexibility in length and stiffness to the myosin levers, and may be particularly suited for myosins working in crowded cellular environments...
2017: PloS One
https://www.readbyqxmd.com/read/28368387/retroelement-guided-protein-diversification-abounds-in-vast-lineages-of-bacteria-and-archaea
#17
Blair G Paul, David Burstein, Cindy J Castelle, Sumit Handa, Diego Arambula, Elizabeth Czornyj, Brian C Thomas, Partho Ghosh, Jeff F Miller, Jillian F Banfield, David L Valentine
Major radiations of enigmatic Bacteria and Archaea with large inventories of uncharacterized proteins are a striking feature of the Tree of Life(1-5). The processes that led to functional diversity in these lineages, which may contribute to a host-dependent lifestyle, are poorly understood. Here, we show that diversity-generating retroelements (DGRs), which guide site-specific protein hypervariability(6-8), are prominent features of genomically reduced organisms from the bacterial candidate phyla radiation (CPR) and as yet uncultivated phyla belonging to the DPANN (Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota and Nanohaloarchaea) archaeal superphylum...
April 3, 2017: Nature Microbiology
https://www.readbyqxmd.com/read/28361695/silva-rdp-greengenes-ncbi-and-ott-how-do-these-taxonomies-compare
#18
Monika Balvočiūtė, Daniel H Huson
BACKGROUND: A key step in microbiome sequencing analysis is read assignment to taxonomic units. This is often performed using one of four taxonomic classifications, namely SILVA, RDP, Greengenes or NCBI. It is unclear how similar these are and how to compare analysis results that are based on different taxonomies. RESULTS: We provide a method and software for mapping taxonomic entities from one taxonomy onto another. We use it to compare the four taxonomies and the Open Tree of life Taxonomy (OTT)...
March 14, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28319149/walking-and-talking-the-tree-of-life-why-and-how-to-teach-about-biodiversity
#19
Cissy J Ballen, Harry W Greene
Taxonomic details of diversity are an essential scaffolding for biology education, yet outdated methods for teaching the tree of life (TOL), as implied by textbook content and usage, are still commonly employed. Here, we show that the traditional approach only vaguely represents evolutionary relationships, fails to denote major events in the history of life, and relies heavily on memorizing near-meaningless taxonomic ranks. Conversely, a clade-based strategy-focused on common ancestry, monophyletic groups, and derived functional traits-is explicitly based on Darwin's "descent with modification," provides students with a rational system for organizing the details of biodiversity, and readily lends itself to active learning techniques...
March 2017: PLoS Biology
https://www.readbyqxmd.com/read/28298477/central-role-of-the-trehalose-biosynthesis-pathway-in-the-pathogenesis-of-human-fungal-infections-opportunities-and-challenges-for-therapeutic-development
#20
REVIEW
Arsa Thammahong, Srisombat Puttikamonkul, John R Perfect, Richard G Brennan, Robert A Cramer
Invasive fungal infections cause significant morbidity and mortality in part due to a limited antifungal drug arsenal. One therapeutic challenge faced by clinicians is the significant host toxicity associated with antifungal drugs. Another challenge is the fungistatic mechanism of action of some drugs. Consequently, the identification of fungus-specific drug targets essential for fitness in vivo remains a significant goal of medical mycology research. The trehalose biosynthetic pathway is found in a wide variety of organisms, including human-pathogenic fungi, but not in humans...
June 2017: Microbiology and Molecular Biology Reviews: MMBR
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