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"Tree of life"

Uwe Hossfeld, Georgy S Levit
No abstract text is available yet for this article.
November 30, 2016: Nature
Nathaniel Bowerman, Nathan Tintle, Matthew Dejongh, Aaron A Best
With continued rapid growth in the number and quality of fully sequenced and accurately annotated bacterial genomes, we have unprecedented opportunities to understand metabolic diversity. We selected 101 diverse and representative completely sequenced bacteria and implemented a manual curation effort to identify 846 unique metabolic variants present in these bacteria. The presence or absence of these variants act as a metabolic signature for each of the bacteria, which can then be used to understand similarities and differences between and across bacterial groups...
2016: Pacific Symposium on Biocomputing
Cheong Xin Chan, Robert G Beiko, Mark A Ragan
Lateral genetic transfer (LGT) is the process by which genetic material moves between organisms (and viruses) in the biosphere. Among the many approaches developed for the inference of LGT events from DNA sequence data, methods based on the comparison of phylogenetic trees remain the gold standard for many types of problem. Identifying LGT events from sequenced genomes typically involves a series of steps in which homologous sequences are identified and aligned, phylogenetic trees are inferred, and their topologies are compared to identify unexpected or conflicting relationships...
2017: Methods in Molecular Biology
Guifré Torruella, David Moreira, Purificación López-García
Apusomonads are a mysterious group of heterotrophic gliding biflagellates branching deeply in the eukaryotic tree of life as sister group to opisthokonts (including animals, fungi and a variety of unicellular protists). Despite their evolutionary interest, their diversity and ecology remain largely unknown, with very few described species and environmental sequences in databases. Most environmental 18S rRNA gene-based studies generally fail to identify apusomonad sequences, which might be due to primer bias, low abundance and/or to the fact that their biotopes remain poorly explored...
November 28, 2016: Environmental Microbiology Reports
Laura R Novick, Kefyn M Catley
The ability to interpret and reason from Tree of Life (ToL) diagrams has become a vital component of science literacy in the 21st century. This article reports on the effectiveness of a research-based curriculum, including an instructional booklet, laboratory, and lectures, to teach the fundamentals of such tree thinking in an introductory biology class for science majors. We present the results of a study involving 117 undergraduates who received either our new research-based tree-thinking curriculum or business-as-usual instruction...
2016: CBE Life Sciences Education
Fernando Rodriguez-Pascual, David Anthony Slatter
Collagens constitute a large family of extracellular matrix (ECM) proteins that play a fundamental role in supporting the structure of various tissues in multicellular animals. The mechanical strength of fibrillar collagens is highly dependent on the formation of covalent cross-links between individual fibrils, a process initiated by the enzymatic action of members of the lysyl oxidase (LOX) family. Fibrillar collagens are present in a wide variety of animals, therefore often being associated with metazoan evolution, where the emergence of an ancestral collagen chain has been proposed to lead to the formation of different clades...
November 23, 2016: Scientific Reports
Ulrike Vavra, Christiane Veit, Richard Strasser
Glycosylation is essential for all trees of life. N-glycosylation is one of the most common covalent protein modifications and influences a large variety of cellular processes including protein folding, quality control and protein-receptor interactions. Despite recent progress in understanding of N-glycan biosynthesis, our knowledge of N-glycan function on individual plant proteins is still very limited. In this respect, plant hormone receptors are an interesting group of proteins as several of these proteins are present at distinct sites in the secretory pathway or at the plasma membrane and have numerous potential N-glycosylation sites...
2017: Methods in Molecular Biology
Antonella Tramacere, Telmo Pievani, Pier F Ferrari
Considering the properties of mirror neurons (MNs) in terms of development and phylogeny, we offer a novel, unifying, and testable account of their evolution according to the available data and try to unify apparently discordant research, including the plasticity of MNs during development, their adaptive value and their phylogenetic relationships and continuity. We hypothesize that the MN system reflects a set of interrelated traits, each with an independent natural history due to unique selective pressures, and propose that there are at least three evolutionarily significant trends that gave raise to three subtypes: hand visuomotor, mouth visuomotor, and audio-vocal...
November 16, 2016: Biological Reviews of the Cambridge Philosophical Society
Steven Dodsworth, Maïté Guignard, Oriane Hidalgo, Jaume Pellicer
Genome size varies enormously across the eukaryotic tree of life (c. 66,000-fold), with the largest reported nuclear genomes found in vertebrates (e.g. salamanders, lungfish) and angiosperms (e.g. mistletoe, fritillaries). Yet despite this huge diversity, most genomes are considerably smaller than the largest reported (c. 150 Gb), with the mean size of both vertebrate and plant genomes being similar, c. 5 Gb. This article is protected by copyright. All rights reserved.
November 12, 2016: Evolution; International Journal of Organic Evolution
Elizabeth Pennisi
No abstract text is available yet for this article.
November 18, 2016: Science
Beatriz Mello, Qiqing Tao, Koichiro Tamura, Sudhir Kumar
Ongoing advances in sequencing technology have led to an explosive expansion in the available molecular data for building increasingly larger and more comprehensive timetrees. However, Bayesian relaxed-clock approaches frequently used to infer these timetrees impose a large computational burden and discourage critical assessment of the robustness of inferred times to model assumptions, influence of calibrations, and selection of optimal data subsets. We analyzed eight large, recently published, empirical datasets to compare time estimates produced by RelTime (a non-Bayesian method) with those reported by using Bayesian approaches that require many priors and are computationally demanding...
November 11, 2016: Molecular Biology and Evolution
David Koslicki, Daniel Falush
Metagenomic profiling is challenging in part because of the highly uneven sampling of the tree of life by genome sequencing projects and the limitations imposed by performing phylogenetic inference at fixed taxonomic ranks. We present the algorithm MetaPalette, which uses long k-mer sizes (k = 30, 50) to fit a k-mer "palette" of a given sample to the k-mer palette of reference organisms. By modeling the k-mer palettes of unknown organisms, the method also gives an indication of the presence, abundance, and evolutionary relatedness of novel organisms present in the sample...
May 2016: MSystems
Pascal O Title, Daniel L Rabosky
Advances in the generation, retrieval and analysis of phylogenetic data have enabled researchers to create phylogenies that contain many thousands of taxa. These "macrophylogenies" - large trees that typically derive from megaphylogeny, supermatrix, or supertree approaches - provide researchers with an unprecedented ability to conduct evolutionary analyses across broad phylogenetic scales. Many studies have now used these phylogenies to explore the dynamics of speciation, extinction, and phenotypic evolution across large swaths of the tree of life...
November 7, 2016: Systematic Biology
Masami Hasegawa
A circular phylogeny with photos or drawings of species is named a phylogeny mandala. This is one of the ways for illustrating the Tree of Life, and is suitable to show visually how the biodiversity has developed in the course of evolution as clarified by the molecular phylogenetics. To demonstrate the recent progress of molecular phylogenetics, six phylogeny mandalas for various taxonomic groups of life were presented; i.e., (1) Eukaryota, (2) Metazoa, (3) Hexapoda, (4) Tetrapoda, (5) Eutheria, and (6) Primates...
November 2, 2016: Molecular Phylogenetics and Evolution
Jonathan Lombard
After being a matter of hot debate for years, the presence of lipid membranes in the last common ancestor of extant organisms (i.e., the cenancestor) now begins to be generally accepted. By contrast, cenancestral cell walls have attracted less attention, probably owing to the large diversity of cell walls that exist in the three domains of life. Many prokaryotic cell walls, however, are synthesized using glycosylation pathways with similar polyisoprenol lipid carriers and topology (i.e., orientation across the cell membranes)...
2016: PeerJ
Chiaki Yamanishi, Mohamed Mahdi Alshahni, Ayako Sano, Ikuo Nakamura, Koichi Makimura
Molecular evolution has dominated taxonomic studies for decades, replacing traditional methods for identification and classification. However, there is a need for better markers to resolve the problems that have limited their usefulness. In this report, we introduce the protein tag (Ptag) sequence, a highly polymorphic amino acid sequence within the C-terminal region of the largest subunit of RNA polymerase I, as a new systematic tag sequence for delineating the evolutionary history of medically important fungi...
November 2, 2016: Medical Mycology: Official Publication of the International Society for Human and Animal Mycology
Arpita Sarkar, Jean-Nicolas Volff, Chantal Vaury
P-element-induced wimpy testis (PIWI)-interacting RNAs (piRNAs) are small, noncoding RNAs known for silencing transposable elements (TEs) in the germline of animals. Most genomes host TEs, which are notorious for mobilizing themselves and endangering survival of the host if not controlled. By silencing TEs in the germline, piRNAs prevent harmful mutations from being passed on to the next generation. How piRNAs are generated and how they silence TEs were the focus of researchers ever since their discovery. Now a spate of recent papers are beginning to tell us that piRNAs can play roles beyond TE silencing and are involved in diverse cellular processes from mRNA regulation to development or genome rearrangement...
October 31, 2016: FASEB Journal: Official Publication of the Federation of American Societies for Experimental Biology
Douglas Chesters
While comprehensive phylogenies have proven an invaluable tool in ecology and evolution, their construction is made increasingly challenging both by the scale and structure of publically available sequences. The distinct partition between gene-rich (genomic) and species-rich (DNA barcode) data is a feature of data that has been largely overlooked, yet presents a key obstacle to scaling supermatrix analysis.I present a phyloinformatics framework for draft construction of a species-level phylogeny of insects (Class Insecta)...
October 26, 2016: Systematic Biology
Claudiu T Supuran
The enzyme carbonic anhydrase (CA, EC is found in numerous organisms across the tree of life, with seven distinct classes known to date. CA inhibition can be exploited for the treatment of edema, glaucoma, seizures, obesity, cancer and infectious diseases. A myriad of CA inhibitor (CAI) classes and inhibition mechanisms have been identified over the past decade, mainly through structure-based drug design approaches. Five different CA inhibition mechanisms are presently known. Areas covered: Recent advances in structure-based CAI design are reviewed, with periodic table-based organization of inhibitor classes...
November 9, 2016: Expert Opinion on Drug Discovery
Gonzalo Giribet
Ctenophores, one of the most basal branches in the tree of life, have been found to have a through-gut, complete with mouth and anus. Basal animals are surprisingly complex and simplification has been rampant in animal evolution.
October 24, 2016: Current Biology: CB
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