Uma visão reformada da Árvore da Vida de Darwin: micróbios expandem essa árvore!

A new view of the tree of life

Laura A. Hug, Brett J. Baker, Karthik Anantharaman, Christopher T. Brown, Alexander J. Probst, Cindy J. Castelle, Cristina N. Butterfield, Alex W. Hernsdorf, Yuki Amano, Kotaro Ise, Yohey Suzuki, Natasha Dudek, David A. Relman, Kari M. Finstad, Ronald Amundson, Brian C. Thomas & Jillian F. Banfield

Nature Microbiology Article number: 16048 (2016)

doi:10.1038/nmicrobiol.2016.48

Download Citation

Environmental microbiologyPhylogenetics

Received: 25 January 2016 Accepted: 10 March 2016

Published online: 11 April 2016

Abstract

The tree of life is one of the most important organizing principles in biology1. Gene surveys suggest the existence of an enormous number of branches 2, but even an approximation of the full scale of the tree has remained elusive. Recent depictions of the tree of life have focused either on the nature of deep evolutionary relationships 3,​4,​5 or on the known, well-classified diversity of life with an emphasis on eukaryotes 6. These approaches overlook the dramatic change in our understanding of life's diversity resulting from genomic sampling of previously unexamined environments. New methods to generate genome sequences illuminate the identity of organisms and their metabolic capacities, placing them in community and ecosystem contexts 7,8. Here, we use new genomic data from over 1,000 uncultivated and little known organisms, together with published sequences, to infer a dramatically expanded version of the tree of life, with Bacteria, Archaea and Eukarya included. The depiction is both a global overview and a snapshot of the diversity within each major lineage. The results reveal the dominance of bacterial diversification and underline the importance of organisms lacking isolated representatives, with substantial evolution concentrated in a major radiation of such organisms. This tree highlights major lineages currently underrepresented in biogeochemical models and identifies radiations that are probably important for future evolutionary analyses.

Early approaches to describe the tree of life distinguished organisms based on their physical characteristics and metabolic features. Molecular methods dramatically broadened the diversity that could be included in the tree because they circumvented the need for direct observation and experimentation by relying on sequenced genes as markers for lineages. Gene surveys, typically using the small subunit ribosomal RNA (SSU rRNA) gene, provided a remarkable and novel view of the biological world 1,9,10, but questions about the structure and extent of diversity remain. Organisms from novel lineages have eluded surveys, because many are invisible to these methods due to sequence divergence relative to the primers commonly used for gene amplification 7,11. Furthermore, unusual sequences, including those with unexpected insertions, may be discarded as artefacts 7.

Whole genome reconstruction was first accomplished in 1995 (ref. 12), with a near-exponential increase in the number of draft genomes reported each subsequent year. There are 30,437 genomes from all three domains of life—Bacteria, Archaea and Eukarya—which are currently available in the Joint Genome Institute's Integrated Microbial Genomes database (accessed 24 September 2015). Contributing to this expansion in genome numbers are single cell genomics  13 and metagenomics studies. Metagenomics is a shotgun sequencing-based method in which DNA isolated directly from the environment is sequenced, and the reconstructed genome fragments are assigned to draft genomes 14. New bioinformatics methods yield complete and near-complete genome sequences, without a reliance on cultivation or reference genomes 7,15. These genome- (rather than gene) based approaches provide information about metabolic potential and a variety of phylogenetically informative sequences that can be used to classify organisms 16. Here, we have constructed a tree of life by making use of genomes from public databases and 1,011 newly reconstructed genomes that we recovered from a variety of environments (see Methods).

To render this tree of life, we aligned and concatenated a set of 16 ribosomal protein sequences from each organism. This approach yields a higher-resolution tree than is obtained from a single gene, such as the widely used 16S rRNA gene16. The use of ribosomal proteins avoids artefacts that would arise from phylogenies constructed using genes with unrelated functions and subject to different evolutionary processes. Another important advantage of the chosen ribosomal proteins is that they tend to be syntenic and co-located in a small genomic region in Bacteria and Archaea, reducing binning errors that could substantially perturb the geometry of the tree. Included in this tree is one representative per genus for all genera for which high-quality draft and complete genomes exist (3,083 organisms in total).

Despite the methodological challenges, we have included representatives of all three domains of life. Our primary focus relates to the status of Bacteria and Archaea, as these organisms have been most difficult to profile using macroscopic approaches, and substantial progress has been made recently with acquisition of new genome sequences 7,8,13. The placement of Eukarya relative to Bacteria and Archaea is controversial 1,4,5,17,18. Eukaryotes are believed to be evolutionary chimaeras that arose via endosymbiotic fusion, probably involving bacterial and archaeal cells 19. Here, we do not attempt to confidently resolve the placement of the Eukarya. We position them using sequences of a subset of their nuclear-encoded ribosomal proteins, an approach that classifies them based on the inheritance of their information systems as opposed to lipid or other cellular structures 5.

Figure 1 presents a new view of the tree of life. This is one of a relatively small number of three-domain trees constructed from molecular information so far, and the first comprehensive tree to be published since the development of genome-resolved metagenomics. We highlight all major lineages with genomic representation, most of which are phylum-level branches (see Supplementary Fig. 1 for full bootstrap support values). However, we separately identify the Classes of the Proteobacteria, because the phylum is not monophyletic (for example, the Deltaproteobacteria branch away from the other Proteobacteria, as previously reported2,20).

FREE PDF GRATIS: Nature Microbiology

Como sobreviver a uma extinção em massa: viva arriscadamente e morra jovem!

Breeding Young as a Survival Strategy during Earth’s Greatest Mass Extinction

Jennifer Botha-Brink, Daryl Codron, Adam K. Huttenlocker, Kenneth D. Angielczyk & Marcello Ruta

Scientific Reports 6, Article number: 24053 (2016)

doi:10.1038/srep24053

Download Citation

Ecological modelling Evolutionary ecology Palaeoecology Palaeontology

Received: 12 October 2015 Accepted: 18 March 2016

Published online: 05 April 2016

An early Triassic Lystrosaurus murrayi specimen, National Museum Bloemfontein, South Africa - Jennifer Botha-Brink.

Source/Fonte

Abstract

Studies of the effects of mass extinctions on ancient ecosystems have focused on changes in taxic diversity, morphological disparity, abundance, behaviour and resource availability as key determinants of group survival. Crucially, the contribution of life history traits to survival during terrestrial mass extinctions has not been investigated, despite the critical role of such traits for population viability. We use bone microstructure and body size data to investigate the palaeoecological implications of changes in life history strategies in the therapsid forerunners of mammals before and after the Permo-Triassic Mass Extinction (PTME), the most catastrophic crisis in Phanerozoic history. Our results are consistent with truncated development, shortened life expectancies, elevated mortality rates and higher extinction risks amongst post-extinction species. Various simulations of ecological dynamics indicate that an earlier onset of reproduction leading to shortened generation times could explain the persistence of therapsids in the unpredictable, resource-limited Early Triassic environments, and help explain observed body size distributions of some disaster taxa (e.g., Lystrosaurus). Our study accounts for differential survival in mammal ancestors after the PTME and provides a methodological framework for quantifying survival strategies in other vertebrates during major biotic crises.

+++++

FREE PDF GRATIS: Scientific Reports Sup. Info.

A arquitetura da máquina fímbria do tipo IVa: mero acaso, fortuita necessidade ou design inteligente?

Architecture of the type IVa pilus machine

Yi-Wei Chang1,2, Lee A. Rettberg2, Anke Treuner-Lange3, Janet Iwasa4, Lotte Søgaard-Andersen3, Grant J. Jensen1,2,*

1California Institute of Technology, Pasadena, CA 91125, USA.

2Howard Hughes Medical Institute, Pasadena, CA 91125, USA.

3Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany.

4University of Utah, Salt Lake City, UT 84112, USA.

↵*Corresponding author. E-mail: jensen@caltech.edu

Science 11 Mar 2016:Vol. 351, Issue 6278, 

DOI: 10.1126/science.aad2001

How the bacterial pilus works

Many bacteria, including important pathogens, move by projecting grappling-hook–like extensions called type IV pili from their cell bodies. After these pili attach to other cells or objects in their environment, the bacteria retract the pili to pull themselves forward. Chang et al. used electron cryotomography of intact cells to image the protein machines that extend and retract the pili, revealing where each protein component resides. Putting the known structures of the individual proteins in place like pieces of a three-dimensional puzzle revealed insights into how the machine works, including evidence that ATP hydrolysis by cytoplasmic motors rotates a membrane-embedded adaptor that slips pilin subunits back and forth from the membrane onto the pilus.

Science, this issue p. 10.1126/science.aad2001

Structured Abstract

INTRODUCTION

Type IVa pili are bacterial cell surface structures that perform critical functions in motility, surface adhesion, virulence, and biofilm formation. Type IVa pili are anchored in the cell envelope and pull cells forward through cycles of extension, adhesion to surfaces, and retraction, all powered by the type IVa pilus machine (T4PM). Although the structures and connectivities of the 10 core T4PM proteins and minor pilins have already been determined, the overall architecture of the T4PM and its extension and retraction mechanisms have not.

RATIONALE

To elucidate the architecture of the intact T4PM, we directly imaged T4PMs within intact Myxococcus xanthus cells by cryo–electron tomography. Mutants that either lacked T4PM components or contained individual T4PM proteins fused to a tag were then imaged. Difference maps revealed the locations of all components of the T4PM machine. Hypothetical models were then built by fitting the known atomic structures of the components together in their relative positions.

RESULTS

Both piliated and nonpiliated T4PMs are multilayered structures that span the entire cell envelope. T4PMs include an outer membrane pore, three interconnected periplasmic ring structures and another in the cytoplasm, a cytoplasmic disc and dome, and a periplasmic stem. The PilQ secretin forms the outer membrane pore; TsaP forms a periplasmic ring around PilQ; periplasmic domains of PilQ together with PilP constitute the mid-periplasmic ring; and the globular domains of PilO and PilN constitute the lower periplasmic ring and connect via coiled coils across the inner membrane to PilM, which forms the cytoplasmic ring. The cytoplasmic domains of the inner membrane protein PilC form the cytoplasmic dome on the T4PM axis inside the PilM ring. The short stem in the nonpiliated state is composed of minor pilins and PilA, the major subunit of the pilus. In the piliated state, the pilus extends from the cell exterior through the PilQ pore and the periplasmic rings to PilC in the inner membrane. In the piliated structure, the hexameric adenosine triphosphatases (ATPases) PilB and PilT bind in a mutually exclusive manner to the base of the T4PM, where they appear as the cytoplasmic disc during extensions and retractions, respectively.

Next, we asked whether the known atomic structures of the proteins could be fit within the map where our imaging results indicated, while still satisfying all known constraints of size, connectivities, and interfaces. This successful effort resulted in “pseudo-atomic” working models of both states of the T4PM. The models suggest that through ATP hydrolysis, PilB rotates PilC, incrementally moving it into positions that facilitate incorporation of new PilA subunits one by one from the inner membrane onto the base of the growing helical pilus. Pilus retraction is driven by replacement of PilB with PilT, which rotates PilC into positions that promote PilA departure from the base of the pilus back into the membrane.

CONCLUSION

We determined the architecture of the T4PM in the piliated and nonpiliated states and mapped all known components onto this architecture, producing a complete structural map of the T4PM. The results illustrate how the structure and function of macromolecular complexes that defy purification and traditional structural approaches can nonetheless be interrogated through cryo–electron tomography of intact cells and model building.

Abstract

Type IVa pili are filamentous cell surface structures observed in many bacteria. They pull cells forward by extending, adhering to surfaces, and then retracting. We used cryo–electron tomography of intact Myxococcus xanthus cells to visualize type IVa pili and the protein machine that assembles and retracts them (the type IVa pilus machine, or T4PM) in situ, in both the piliated and nonpiliated states, at a resolution of 3 to 4 nanometers. We found that T4PM comprises an outer membrane pore, four interconnected ring structures in the periplasm and cytoplasm, a cytoplasmic disc and dome, and a periplasmic stem. By systematically imaging mutants lacking defined T4PM proteins or with individual proteins fused to tags, we mapped the locations of all 10 T4PM core components and the minor pilins, thereby providing insights into pilus assembly, structure, and function.

+++++

Professores, pesquisadores e alunos de universidades públicas e privadas com acesso ao Portal de Periódicos CAPES/MEC podem ler gratuitamente este artigo da Science e de mais 30.000 publicações científicas.

+++++

PERGUNTA CAUSTICANTE DESTE BLOGGER:

No Abstract os autores não mencionaram o fato, Fato, FATO da evolução das fímbrias. Antes, se limitaram tão somente a descrever a complexidade de máquina biológica que são as fímbrias.

Ora, e Darwin e seus atuais discípulos fundamentalistas não conseguem explicar a extrema complexidade arquitetônica de uma "simples" fímbria, podem explicar a diversidade e complexidade de toda história evolutiva das espécies?

Pano rápido!

Resposta substanciada pelas montanhas de evidências consideradas pelo rigor do contexto de justificação teórica: NÃO!

Fui! Darwin kaput desde 1859!!!

Marcos Eberlin receberá medalha J. J. Thomson em agosto de 2016

Eberlin recebe medalha J. J. Thomson em agosto

31/03/2016 - 07:10

Texto Silvio Anunciação Imagens Antoninho Perri Edição de Imagens Paulo José Cavalheri

O professor da Unicamp Marcos Nogueira Eberlin será o primeiro cientista sul-americano a receber a medalha J. J. Thomson, conferida bianualmente pela Fundação Internacional de Espectrometria de Massa (IMSF, na sigla em inglês). A escolha de Marcos Eberlin foi feita após votação dos representantes de 39 sociedades de espectrometria de massa afiliadas. Conforme a IMSF seu nome foi escolhido entre 17 candidatos indicados graças aos relevantes serviços para o desenvolvimento e propagação da espectrometria de massas. A medalha será entregue em agosto na cidade de Toronto, no Canadá, durante a 21ª Conferência Internacional de Espectrometria de Massas.

...

Leia mais aqui: UNICAMP

+++++

O Prof. Dr. Marcos Eberlin é presidente da SBDI - Sociedade Brasileira do Design Inteligente.

Montagem da sequência de leitura extensa do genoma de gorila

Long-read sequence assembly of the gorilla genome

David Gordon1,2,*, John Huddleston1,2,*, Mark J. P. Chaisson1,*, Christopher M. Hill1,*, Zev N. Kronenberg1,*, Katherine M. Munson1, Maika Malig1, Archana Raja1,2, Ian Fiddes3, LaDeana W. Hillier4, Christopher Dunn5, Carl Baker1, Joel Armstrong3, Mark Diekhans3, Benedict Paten3, Jay Shendure1,2, Richard K. Wilson4, David Haussler3, Chen-Shan Chin5, Evan E. Eichler1,2,†

+ Author Affiliations

↵†Corresponding author. E-mail: eee@gs.washington.edu

↵* These authors contributed equally to this work.

Science 01 Apr 2016: Vol. 352, Issue 6281, 

DOI: 10.1126/science.aae0344

Improving on the gorilla genome

Access to complete, high-quality genomes of nonhuman primates will also help us understand human biology. Gordon et al. used long-read sequencing technology to improve genome data on our close relative the gorilla. Sequencing from a single individual decreased assembly fragmentation and recovered previously missed genes and noncoding loci. Mapping short-read sequences from additional gorillas helped reconstruct a “pan” gorilla sequence documenting genetic variation. Comparison with human genomes revealed species-specific differences ranging in size from one to thousands of bases in length, including some that are likely to affect gene regulation.

Science, this issue p. 10.1126/science.aae0344

Structured Abstract

INTRODUCTION

The accurate sequence and assembly of genomes is critical to our understanding of evolution and genetic variation. Despite advances in short-read sequencing technology that have decreased cost and increased throughput, whole-genome assembly of mammalian genomes remains problematic because of the presence of repetitive DNA.

RATIONALE

The goal of this study was to sequence and assemble the genome of the western lowland gorilla by using primarily single-molecule, real-time (SMRT) sequencing technology and a novel assembly algorithm that takes advantage of long (>10 kbp) sequence reads. We specifically compare the properties of this assembly to gorilla genome assemblies that were generated by using more routine short sequence read approaches in order to determine the value and biological impact of a long-read genome assembly.

RESULTS

We generated 74.8-fold SMRT whole-genome shotgun sequence from peripheral blood DNA isolated from a western lowland gorilla (Gorilla gorilla gorilla) named Susie. We applied a string graph assembly algorithm, Falcon, and consensus algorithm, Quiver, to generate a 3.1-Gbp assembly with a contig N50 of 9.6 Mbp. Short-read sequence data from an additional six gorilla genomes was mapped so as to reduce indel errors and improve the accuracy of the final assembly. We estimate that 98.9% of the gorilla euchromatin has been assembled into 1854 sequence contigs. The assembly represents an improvement in contiguity: >800-fold with respect to the published gorilla genome assembly and >180-fold with respect to a more recently released upgrade of the gorilla assembly. Most of the sequence gaps are now closed, considerably increasing the yield of complete gene models. We estimate that 87% of the missing exons and 94% of the incomplete genes are recovered. We find that the sequence of most full-length common repeats is resolved, with the most significant gains occurring for the longest and most G+C–rich retrotransposons. Although complex regions such as the major histocompatibility locus are accurately sequenced and assembled, both heterochromatin and large, high-identity segmental duplications are not because read lengths are insufficiently long to traverse these repetitive structures. The long-read assembly produces a much finer map of structural variation down to 50 bp in length, facilitating the discovery of thousands of lineage-specific structural variant differences that have occurred since divergence from the human and chimpanzee lineages. This includes the disruption of specific genes and loss of predicted regulatory regions between the two species. We show that use of the new gorilla genome assembly changes estimates of divergence and diversity, resulting in subtle but substantial effects on previous population genetic inferences, such as the timing of species bottlenecks and changes in the effective population size over the course of evolution.

CONCLUSION

The genome assembly that results from using the long-read data provides a more complete picture of gene content, structural variation, and repeat biology, improving population genetic and evolutionary inferences. Long-read sequencing technology now makes it practical for individual laboratories to generate high-quality reference genomes for complex mammalian genomes.

FREE PDF GRATIS: Science

Há 305 milhões de anos atrás - quase uma aranha explica a origem dos aracnídeos

Almost a spider: a 305-million-year-old fossil arachnid and spider origins

Russell J. Garwood, Jason A. Dunlop, Paul A. Selden, Alan R. T. Spencer, Robert C. Atwood, Nghia T. Vo, Michael Drakopoulos

Published 30 March 2016.DOI: 10.1098/rspb.2016.0125

Abstract

Spiders are an important animal group, with a long history. Details of their origins remain limited, with little knowledge of their stem group, and no insights into the sequence of character acquisition during spider evolution. We describe a new fossil arachnid, Idmonarachne brasieri gen. et sp. nov. from the Late Carboniferous (Stephanian, ca 305–299 Ma) of Montceau-les-Mines, France. It is three-dimensionally preserved within a siderite concretion, allowing both laboratory- and synchrotron-based phase-contrast computed tomography reconstruction. The latter is a first for siderite-hosted fossils and has allowed us to investigate fine anatomical details. Although distinctly spider-like in habitus, this remarkable fossil lacks a key diagnostic character of Araneae: spinnerets on the underside of the opisthosoma. It also lacks a flagelliform telson found in the recently recognized, spider-related, Devonian–Permian Uraraneida. Cladistic analysis resolves our new fossil as sister group to the spiders: the spider stem-group comprises the uraraneids and I. brasieri. While we are unable to demonstrate the presence of spigots in this fossil, the recovered phylogeny suggests the earliest character to evolve on the spider stem-group is the secretion of silk. This would have been followed by the loss of a flagelliform telson, and then the ability to spin silk using spinnerets. This last innovation defines the true spiders, significantly post-dates the origins of silk, and may be a key to the group's success. The Montceau-les-Mines locality has previously yielded a mesothele spider (with spinnerets). Evidently, Late Palaeozoic spiders lived alongside Palaeozoic arachnid grades which approached the spider condition, but did not express the full suite of crown-group autapomorphies.

FREE PDF GRATIS: Proc. R. Soc. B

Filogenômica: desembaralhando a Árvore da Vida das aranhas

Spider phylogenomics: untangling the Spider Tree of Life

Evolutionary StudiesTaxonomyZoology

Nicole L. Garrison1, Juanita Rodriguez1, Ingi Agnarsson2, Jonathan A. Coddington3, Charles E. Griswold4, Christopher A. Hamilton1, Marshal Hedin5, Kevin M. Kocot6, Joel M. Ledford7, Jason E. Bond​1

Published February 23, 2016

PubMed 26925338

Author and article information

1 Department of Biological Sciences and Auburn University Museum of Natural History, Auburn University, Auburn, AL, United States

2 Department of Biology, University of Vermont, Burlington, VT, United States

3 Department of Entomology, National Museum of Natural History, Smithsonian Institution, Washingtion, DC, United States

4 Arachnology, California Academy of Sciences, San Francisco, CA, United States

5 Department of Biology, San Diego State University, San Diego, CA, United States

6 Department of Biological Sciences and Alabama Museum of Natural History, University of Alabama—Tuscaloosa, Tuscaloosa, AL, United States

7 Department of Plant Biology, University of California, Davis, Davis, CA, United States

DOI 10.7717/peerj.1719

Published 2016-02-23 Accepted 2016-01-31 Received 

2015-11-06

Academic Editor Scott Edwards

Subject Areas Evolutionary Studies, Taxonomy, Zoology

Keywords

Arachnida, Molecular systematics, Araneae, Spider phylogeny, Web evolution

Copyright © 2016 Garrison et al.

Licence

This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ) and either DOI or URL of the article must be cited.

Cite this article

Garrison NL, Rodriguez J, Agnarsson I, Coddington JA, Griswold CE, Hamilton CA, Hedin M, Kocot KM, Ledford JM, Bond JE. (2016) Spider phylogenomics: untangling the Spider Tree of Life. PeerJ 4:e1719 https://doi.org/10.7717/peerj.1719

The authors have chosen to make the review history of this article public.

Abstract

Spiders (Order Araneae) are massively abundant generalist arthropod predators that are found in nearly every ecosystem on the planet and have persisted for over 380 million years. Spiders have long served as evolutionary models for studying complex mating and web spinning behaviors, key innovation and adaptive radiation hypotheses, and have been inspiration for important theories like sexual selection by female choice. Unfortunately, past major attempts to reconstruct spider phylogeny typically employing the “usual suspect” genes have been unable to produce a well-supported phylogenetic framework for the entire order. To further resolve spider evolutionary relationships we have assembled a transcriptome-based data set comprising 70 ingroup spider taxa. Using maximum likelihood and shortcut coalescence-based approaches, we analyze eight data sets, the largest of which contains 3,398 gene regions and 696,652 amino acid sites forming the largest phylogenomic analysis of spider relationships produced to date. Contrary to long held beliefs that the orb web is the crowning achievement of spider evolution, ancestral state reconstructions of web type support a phylogenetically ancient origin of the orb web, and diversification analyses show that the mostly ground-dwelling, web-less RTA clade diversified faster than orb weavers. Consistent with molecular dating estimates we report herein, this may reflect a major increase in biomass of non-flying insects during the Cretaceous Terrestrial Revolution 125–90 million years ago favoring diversification of spiders that feed on cursorial rather than flying prey. Our results also have major implications for our understanding of spider systematics. Phylogenomic analyses corroborate several well-accepted high level groupings: Opisthothele, Mygalomorphae, Atypoidina, Avicularoidea, Theraphosoidina, Araneomorphae, Entelegynae, Araneoidea, the RTA clade, Dionycha and the Lycosoidea. Alternatively, our results challenge the monophyly of Eresoidea, Orbiculariae, and Deinopoidea. The composition of the major paleocribellate and neocribellate clades, the basal divisions of Araneomorphae, appear to be falsified. Traditional Haplogynae is in need of revision, as our findings appear to support the newly conceived concept of Synspermiata. The sister pairing of filistatids with hypochilids implies that some peculiar features of each family may in fact be synapomorphic for the pair. Leptonetids now are seen as a possible sister group to the Entelegynae, illustrating possible intermediates in the evolution of the more complex entelegyne genitalic condition, spinning organs and respiratory organs.

Cite this as

Garrison NL, Rodriguez J, Agnarsson I, Coddington JA, Griswold CE, Hamilton CA, Hedin M, Kocot KM, Ledford JM, Bond JE. (2016) Spider phylogenomics: untangling the Spider Tree of Life. PeerJ 4:e1719 https://doi.org/10.7717/peerj.1719

FREE PDF GRATIS: PeerJ

Organismos hospedeiros da malária na era dos dinossauros!

What Fossils Reveal About the Protozoa Progenitors, Geographic Provinces, and Early Hosts of Malarial Organisms

George Poinar Jr.

DOI: http://dx.doi.org/10.1093/ae/tmw006 22-25 

First published online: 11 March 2016

In 1991, Robert S. Desowitz asked, “Did the primitive malaria begin as a parasite of some prehistoric reptile that later was picked up by a mosquito, or was it first a parasite of the mosquito that later became established in the reptile?” This question has been debated for years and is addressed in the present work in light of the fossil record of malarial organisms (Haemosporidia). The general consensus is that malaria evolved as a parasite of vertebrates (Manwell 1961, Desportes and Schrével 2013, Mattingly 1983); however, Huff (1945) felt that the malaria progenitor originated with the vector, and in their discussion of malaria evolution, Di Fiore et al. (2009) recognized that in the digenetic malarial life cycle, the vector is the definitive host and the vertebrate the intermediate host. This question has also been addressed with molecular data, but thus far, only very small DNA segments have been analyzed, resulting in incongruous and poorly resolved gene trees (Di Fiore et al. 2009). In the present analysis, fossils are used to determine the progenitors, ancient hosts, and original geographic provinces of malarial organisms.

FREE PDF GRATIS: American Entomologist

Bocas de peixe como estruturas de engenharia para filtração vórtice através de etapas: mero acaso, fortuita necessidade ou design inteligente???

Fish mouths as engineering structures for vortical cross-step filtration

S. Laurie Sanderson, Erin Roberts, Jillian Lineburg & Hannah Brooks

Affiliations Contributions Corresponding author

Nature Communications 7, Article number: 11092 doi:10.1038/ncomms11092

Received 07 September 2015 Accepted 17 February 2016 Published 29 March 2016

Abstract

Suspension-feeding fishes such as goldfish and whale sharks retain prey without clogging their oral filters, whereas clogging is a major expense in industrial crossflow filtration of beer, dairy foods and biotechnology products. Fishes’ abilities to retain particles that are smaller than the pore size of the gill-raker filter, including extraction of particles despite large holes in the filter, also remain unexplained. Here we show that unexplored combinations of engineering structures (backward-facing steps forming d-type ribs on the porous surface of a cone) cause fluid dynamic phenomena distinct from current biological and industrial filter operations. This vortical cross-step filtration model prevents clogging and explains the transport of tiny concentrated particles to the oesophagus using a hydrodynamic tongue. Mass transfer caused by vortices along d-type ribs in crossflow is applicable to filter-feeding duck beak lamellae and whale baleen plates, as well as the fluid mechanics of ventilation at fish gill filaments.

Subject terms: Biological sciences Zoology Fluids and plasma physics

FREE PDF GRATIS: Nature Communications

Arquitetura molecular do sub-complexo do spliceossoma humano: mero acaso, fortuita necessidade ou design inteligente???

Molecular architecture of the human U4/U6.U5 tri-snRNP

Dmitry E. Agafonov1,*, Berthold Kastner1,*, Olexandr Dybkov1,*, Romina V. Hofele2,3,†, Wen-Ti Liu4,5, Henning Urlaub2,3,‡, Reinhard Lührmann1,‡, Holger Stark4,5,‡

- Author Affiliations

1Department of Cellular Biochemistry, Max Planck Institute for Biophysical Chemistry, D-37077 Göttingen, Germany.

2Bioanalytical Mass Spectrometry, Max Planck Institute for Biophysical Chemistry, D-37077 Göttingen, Germany.

3Bioanalytics Group, Institute for Clinical Chemistry, University Medical Center Göttingen, D-37075 Göttingen, Germany.

4Department of 3D Electron Cryomicroscopy, Georg-August Universität Göttingen, D-37077 Göttingen, Germany.

5Department of Structural Dynamics, Max Planck Institute for Biophysical Chemistry, D-37077 Göttingen, Germany.

↵‡Corresponding author. E-mail: reinhard.luehrmann@mpi-bpc.mpg.de (R.L.); hstark1@gwdg.de (H.S.); henning.urlaub@mpibpc.mpg.de (H.U.)

↵* These authors contributed equally to this work.

↵† Present address: Medimmune, Gaithersburg, MD, USA.

Science 25 Mar 2016:

Vol. 351, Issue 6280, pp. 1416-1420

DOI: 10.1126/science.aad2085

A human spliceosomal subcomplex

The spliceosome is an RNA and protein molecular machine that cuts out introns from messenger RNAs. Agafonov et al. used cryo-electron microscopy to determine the structure of the largest intermediate subcomplex on the assembly pathway for the human spliceosome (see the Perspective by Cate). The structure shows substantial differences from the equivalent yeast complex. It also reveals how the subcomplex must dock onto the rest of the spliceosome and hints at the structural changes the complex must go through to form the mature spliceosome.

Science, this issue p. 1416; see also p. 1390

Source/Fonte

Abstract

The U4/U6.U5 triple small nuclear ribonucleoprotein (tri-snRNP) is a major spliceosome building block. We obtained a three-dimensional structure of the 1.8-megadalton human tri-snRNP at a resolution of 7 angstroms using single-particle cryo–electron microscopy (cryo-EM). We fit all known high-resolution structures of tri-snRNP components into the EM density map and validated them by protein cross-linking. Our model reveals how the spatial organization of Brr2 RNA helicase prevents premature U4/U6 RNA unwinding in isolated human tri-snRNPs and how the ubiquitin C-terminal hydrolase–like protein Sad1 likely tethers the helicase Brr2 to its preactivation position. Comparison of our model with cryo-EM three-dimensional structures of the Saccharomyces cerevisiae tri-snRNP and Schizosaccharomyces pombe spliceosome indicates that Brr2 undergoes a marked conformational change during spliceosome activation, and that the scaffolding protein Prp8 is also rearranged to accommodate the spliceosome’s catalytic RNA network.

+++++

Professores, pesquisadores e alunos de universidades públicas e privadas com acesso ao Portal de Periódicos CAPES/MEC podem ler gratuitamente este artigo da Science e de mais 30.000 publicações científicass.

Um Big Bang em biologia estrutural do spliceossoma: mero acaso, fortuita necessidade ou design inteligente???

A Big Bang in spliceosome structural biology

Jamie H. D. Cate

- Author Affiliations

Departments of Molecular and Cell Biology and Chemistry, University of California, Berkeley, CA 94720, USA, and Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.

E-mail: jcate@lbl.gov

Science 25 Mar 2016: Vol. 351, Issue 6280, pp. 1390-1392

DOI: 10.1126/science.aaf4465

Source/Fonte

Summary

Look at a protein-coding gene in the genome of any eukaryote—be it animal, plant, fungus, or protist—and you will likely find the coding region fragmented by intervening sequences known as introns. When the gene is transcribed, these introns have to be removed from the pre-messenger RNA (pre-mRNA) before a protein can be made. How these introns are removed has been studied intensively for decades without the aid of a three-dimensional map of the highly dynamic machine at the heart of the process: the spliceosome. On page 1416 of this issue, Agafonov et al. report the first molecular-resolution reconstruction of a central assembly of the human spliceosome, the U4/U6.U5 triple small nuclear ribonucleoprotein (tri-snRNP) complex, using cryo-electron microscopy (cryo-EM) (1). Together with high-resolution cryo-EM reconstructions of spliceosome assemblies from fungi (2-5) and the x-ray crystal structure of the U1 snRNP (6), these structural models of the splicing machinery launch a new era in understanding eukaryotic gene regulation.

+++++

Professores, pesquisadores e alunos de universidades públicas e privadas com acesso ao Portal de Periódicos CAPES/MEC podem ler gratuitamente este artigo da Science e de mais 30.000 publicações científicas. 

O transcriptoma de peixe dipnoico: um vislumbre nos eventos da evolução molecular na transição da água para a terra

The Lungfish Transcriptome: A Glimpse into Molecular Evolution Events at the Transition from Water to Land

Maria Assunta Biscotti, Marco Gerdol, Adriana Canapa, Mariko Forconi, Ettore Olmo, Alberto Pallavicini, Marco Barucca & Manfred Schartl

Scientific Reports 6, Article number: 21571 (2016)

doi:10.1038/srep21571

Download Citation

Evolutionary genetics Molecular evolution Phylogenetics

Received: 06 September 2015 Accepted: 20 January 2016

Published online: 24 February 2016

Abstract

Lungfish and coelacanths are the only living sarcopterygian fish. The phylogenetic relationship of lungfish to the last common ancestor of tetrapods and their close morphological similarity to their fossil ancestors make this species uniquely interesting. However their genome size, the largest among vertebrates, is hampering the generation of a whole genome sequence. To provide a partial solution to the problem, a high-coverage lungfish reference transcriptome was generated and assembled. The present findings indicate that lungfish, not coelacanths, are the closest relatives to land-adapted vertebrates. Whereas protein-coding genes evolve at a very slow rate, possibly reflecting a “living fossil” status, transposable elements appear to be active and show high diversity, suggesting a role for them in the remarkable expansion of the lungfish genome. Analyses of single genes and gene families documented changes connected to the water to land transition and demonstrated the value of the lungfish reference transcriptome for comparative studies of vertebrate evolution.

FREE PDF GRATIS: Scientific Reports 

Complexidade no design e na síntese de um genoma mínimo bacteriano: mero acaso, fortuita necessidade ou design inteligente?

Design and synthesis of a minimal bacterial genome

Clyde A. Hutchison III1,*,†, Ray-Yuan Chuang1,†,‡, Vladimir N. Noskov1, Nacyra Assad-Garcia1, Thomas J. Deerinck2, Mark H. Ellisman2, John Gill3, Krishna Kannan3, Bogumil J. Karas1, Li Ma1, James F. Pelletier4,§, Zhi-Qing Qi3, R. Alexander Richter1, Elizabeth A. Strychalski4, Lijie Sun1,||, Yo Suzuki1, Billyana Tsvetanova3, Kim S. Wise1, Hamilton O. Smith1,3, John I. Glass1, Chuck Merryman1, Daniel G. Gibson1,3, J. Craig Venter1,3,*

+ Author Affiliations

↵*Corresponding author. E-mail: chutchis@jcvi.org (C.A.H.); jcventer@jcvi.org (J.C.V.)

↵† These authors contributed equally to this work.

↵‡ Present address: American Type Culture Collection, 10801 University Boulevard, Manassas, VA 20110, USA.

↵§ Present address: Center for Bits and Atoms, Massachusetts Institute of Technology, Room E15-401, 20 Ames Street, Cambridge, MA 02139, USA.

↵|| Present address: CBRITE, 11575 Sorrento Valley Road, Suite 204, San Diego, CA 92121, USA.

Science 25 Mar 2016: Vol. 351, Issue 6280, 

DOI: 10.1126/science.aad6253

Source/Fonte

Designing and building a minimal genome

A goal in biology is to understand the molecular and biological function of every gene in a cell. One way to approach this is to build a minimal genome that includes only the genes essential for life. In 2010, a 1079-kb genome based on the genome of Mycoplasma mycoides (JCV-syn1.0) was chemically synthesized and supported cell growth when transplanted into cytoplasm. Hutchison III et al. used a design, build, and test cycle to reduce this genome to 531 kb (473 genes). The resulting JCV-syn3.0 retains genes involved in key processes such as transcription and translation, but also contains 149 genes of unknown function.

Science, this issue p. 10.1126/science.aad6253

Structured Abstract

INTRODUCTION

In 1984, the simplest cells capable of autonomous growth, the mycoplasmas, were proposed as models for understanding the basic principles of life. In 1995, we reported the first complete cellular genome sequences (Haemophilus influenza, 1815 genes, and Mycoplasma genitalium, 525 genes). Comparison of these sequences revealed a conserved core of about 250 essential genes, much smaller than either genome. In 1999, we introduced the method of global transposon mutagenesis and experimentally demonstrated that M. genitalium contains many genes that are nonessential for growth in the laboratory, even though it has the smallest genome known for an autonomously replicating cell found in nature. This implied that it should be possible to produce a minimal cell that is simpler than any natural one. Whole genomes can now be built from chemically synthesized oligonucleotides and brought to life by installation into a receptive cellular environment. We have applied whole-genome design and synthesis to the problem of minimizing a cellular genome.

RATIONALE

Since the first genome sequences, there has been much work in many bacterial models to identify nonessential genes and define core sets of conserved genetic functions, using the methods of comparative genomics. Often, more than one gene product can perform a particular essential function. In such cases, neither gene will be essential, and neither will necessarily be conserved. Consequently, these approaches cannot, by themselves, identify a set of genes that is sufficient to constitute a viable genome. We set out to define a minimal cellular genome experimentally by designing and building one, then testing it for viability. Our goal is a cell so simple that we can determine the molecular and biological function of every gene.

RESULTS

Whole-genome design and synthesis were used to minimize the 1079–kilobase pair (kbp) synthetic genome of M. mycoides JCVI-syn1.0. An initial design, based on collective knowledge of molecular biology in combination with limited transposon mutagenesis data, failed to produce a viable cell. Improved transposon mutagenesis methods revealed a class of quasi-essential genes that are needed for robust growth, explaining the failure of our initial design. Three more cycles of design, synthesis, and testing, with retention of quasi-essential genes, produced JCVI-syn3.0 (531 kbp, 473 genes). Its genome is smaller than that of any autonomously replicating cell found in nature. JCVI-syn3.0 has a doubling time of ~180 min, produces colonies that are morphologically similar to those of JCVI-syn1.0, and appears to be polymorphic when examined microscopically.

CONCLUSION

The minimal cell concept appears simple at first glance but becomes more complex upon close inspection. In addition to essential and nonessential genes, there are many quasi-essential genes, which are not absolutely critical for viability but are nevertheless required for robust growth. Consequently, during the process of genome minimization, there is a trade-off between genome size and growth rate. JCVI-syn3.0 is a working approximation of a minimal cellular genome, a compromise between small genome size and a workable growth rate for an experimental organism. It retains almost all the genes that are involved in the synthesis and processing of macromolecules. Unexpectedly, it also contains 149 genes with unknown biological functions, suggesting the presence of undiscovered functions that are essential for life. JCVI-syn3.0 is a versatile platform for investigating the core functions of life and for exploring whole-genome design.

...

Abstract

We used whole-genome design and complete chemical synthesis to minimize the 1079–kilobase pair synthetic genome of Mycoplasma mycoides JCVI-syn1.0. An initial design, based on collective knowledge of molecular biology combined with limited transposon mutagenesis data, failed to produce a viable cell. Improved transposon mutagenesis methods revealed a class of quasi-essential genes that are needed for robust growth, explaining the failure of our initial design. Three cycles of design, synthesis, and testing, with retention of quasi-essential genes, produced JCVI-syn3.0 (531 kilobase pairs, 473 genes), which has a genome smaller than that of any autonomously replicating cell found in nature. JCVI-syn3.0 retains almost all genes involved in the synthesis and processing of macromolecules. Unexpectedly, it also contains 149 genes with unknown biological functions. JCVI-syn3.0 is a versatile platform for investigating the core functions of life and for exploring whole-genome design.

FREE PDF GRATIS : Science

Cintura pélvica semelhante a tetrápode em um peixe de caverna que anda

Tetrapod-like pelvic girdle in a walking cavefish

Brooke E. Flammang, Apinun Suvarnaraksha, Julie Markiewicz & Daphne Soares

Scientific Reports 6, Article number: 23711 (2016)

doi:10.1038/srep23711

Download Citation

Animal behaviour Biomechanics Ichthyology

Received: 15 December 2015 Accepted: 14 March 2016

Published online: 24 March 2016

Source/Fonte

Abstract

Fishes have adapted a number of different behaviors to move out of the water, but none have been described as being able to walk on land with a tetrapod-like gait. Here we show that the blind cavefish Cryptotora thamicola walks and climbs waterfalls with a salamander-like diagonal-couplets lateral sequence gait and has evolved a robust pelvic girdle that shares morphological features associated with terrestrial vertebrates. In all other fishes, the pelvic bones are suspended in a muscular sling or loosely attached to the pectoral girdle anteriorly. In contrast, the pelvic girdle of Cryptotora is a large, broad puboischiadic plate that is joined to the iliac process of a hypertrophied sacral rib; fusion of these bones in tetrapods creates an acetabulum. The vertebral column in the sacral area has large anterior and posterior zygapophyses, transverse processes, and broad neural spines, all of which are associated with terrestrial organisms. The diagonal-couplet lateral sequence gait was accomplished by rotation of the pectoral and pelvic girdles creating a standing wave of the axial body. These findings are significant because they represent the first example of behavioural and morphological adaptation in an extant fish that converges on the tetrapodal walking behaviour and morphology.

FREE PDF GRATIS: Scientific Reports