Cada vez mais complexidade em máquinas moleculares: mero acaso, fortuita necessidade ou design inteligente?

Controlling Motion at the Nanoscale: Rise of the Molecular Machines

John M. Abendroth†, Oleksandr S. Bushuyev‡, Paul S. Weiss*†§, and Christopher J. Barrett*†‡

† California NanoSystems Institute and Department of Chemistry & Biochemistry, University of California, Los Angeles, Los Angeles, California 90095, United States

‡ Department of Chemistry, McGill University, Montreal, QC, Canada

§ Department of Materials Science & Engineering, University of California, Los Angeles, Los Angeles, California 90095, United States

ACS Nano, 2015, 9 (8), pp 7746–7768

DOI: 10.1021/acsnano.5b03367

Publication Date (Web): July 14, 2015

Copyright © 2015 American Chemical Society

*Address correspondence to psw@cnsi.ucla.edu, christopher.barrett@mcgill.ca.

ACS Editors' Choice - This is an open access article published under an ACS AuthorChoice License, which permits copying and redistribution of the article or any adaptations for non-commercial purposes.

Abstract

As our understanding and control of intra- and intermolecular interactions evolve, ever more complex molecular systems are synthesized and assembled that are capable of performing work or completing sophisticated tasks at the molecular scale. Commonly referred to as molecular machines, these dynamic systems comprise an astonishingly diverse class of motifs and are designed to respond to a plethora of actuation stimuli. In this Review, we outline the conditions that distinguish simple switches and rotors from machines and draw from a variety of fields to highlight some of the most exciting recent examples of opportunities for driven molecular mechanics. Emphasis is placed on the need for controllable and hierarchical assembly of these molecular components to display measurable effects at the micro-, meso-, and macroscales. As in Nature, this strategy will lead to dramatic amplification of the work performed via the collective action of many machines organized in linear chains, on functionalized surfaces, or in three-dimensional assemblies.

Keywords:

amphidynamic crystals; azobenzene; DNA nanotechnology; hierarchical assembly; mechanically interlocked molecules; molecular machines; molecular switches; photomechanical crystals; rotors and motors; thermo/photosalient crystals

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Contrariando a teoria da evolução de Darwin, os polvos, as lulas e os chocos desafiam o "dogma central" da genética editando seus proteomas!

Trade-off between Transcriptome Plasticity and Genome Evolution in Cephalopods

Noa Liscovitch-Brauer, Shahar Alon, Hagit T. Porath, Boaz Elstein, Ron Unger, Tamar Ziv, Arie Admon, Erez Y. Levanon, Joshua J.C. Rosenthal 8, Eli Eisenberg.

8Lead Contact

DOI: http://dx.doi.org/10.1016/j.cell.2017.03.025 

Publication History

Published: April 6, 2017 Accepted: March 16, 2017

Received in revised form: February 2, 2017 Received: December 5, 2016

Source/Fonte: Tom Kleindinst

Highlights

• Unlike other taxa, cephalopods diversify their proteomes extensively by RNA editing

• Extensive recoding is specific to the behaviorally complex coleiods

• Unlike mammals, cephalopod recoding is evolutionarily conserved and often adaptive

• Transcriptome diversification comes at the expense of slowed-down genome evolution

Summary

RNA editing, a post-transcriptional process, allows the diversification of proteomes beyond the genomic blueprint; however it is infrequently used among animals for this purpose. Recent reports suggesting increased levels of RNA editing in squids thus raise the question of the nature and effects of these events. We here show that RNA editing is particularly common in behaviorally sophisticated coleoid cephalopods, with tens of thousands of evolutionarily conserved sites. Editing is enriched in the nervous system, affecting molecules pertinent for excitability and neuronal morphology. The genomic sequence flanking editing sites is highly conserved, suggesting that the process confers a selective advantage. Due to the large number of sites, the surrounding conservation greatly reduces the number of mutations and genomic polymorphisms in protein-coding regions. This trade-off between genome evolution and transcriptome plasticity highlights the importance of RNA recoding as a strategy for diversifying proteins, particularly those associated with neural function.

FREE PDF GRATIS: Cell

O Ovatiovermis cribratus, um lobopodiano do período Cambriano, não tinha uma carapaça protetora dura

Cambrian suspension-feeding lobopodians and the early radiation of panarthropods

Jean-Bernard CaronEmail authorView ORCID ID profile and Cédric Aria

BMC Evolutionary Biology BMC series – open, inclusive and trusted 201717:29

DOI: 10.1186/s12862-016-0858-y © The Author(s). 2017 

Received: 26 May 2016 Accepted: 17 December 2016Published: 31 January 2017

Source/Fonte: Lars Fields, Phlesch Bubble Productions © Royal Ontario Museum

Abstract

Background

Arthropoda, Tardigrada and Onychophora evolved from lobopodians, a paraphyletic group of disparate Palaeozoic vermiform animals with soft legs. Although the morphological diversity that this group encompasses likely illustrates the importance of niche diversification in the early radiation of panarthropods, the ecology of lobopodians remains poorly characterized.

Results

Here we describe a new luolishaniid taxon from the middle Cambrian Burgess Shale (Walcott Quarry) in British Columbia, Canada, whose specialized morphology epitomizes the suspension-feeding ecology of this clade, and is convergent with some modern marine animals, such as caprellid crustaceans. This species possesses two long pairs and four shorter pairs of elongate spinose lobopods at the front, each bearing two slender claws, and three pairs of stout lobopods bearing single, strong, hook-like anterior-facing claws at the back. The trunk is remarkably bare, widening rearwards, and, at the front, extends beyond the first pair of lobopods into a small “head” bearing a pair of visual organs and a short proboscis with numerous teeth. Based on a critical reappraisal of character coding in lobopodians and using Bayesian and parsimony-based tree searches, two alternative scenarios for early panarthropod evolution are retrieved. In both cases, hallucigeniids and luolishaniids are found to be extinct radiative stem group panarthropods, in contrast to previous analyses supporting a position of hallucigeniids as part of total-group Onychophora. Our Bayesian topology finds luolishaniids and hallucigeniids to form two successive clades at the base of Panarthropoda. Disparity analyses suggest that luolishaniids, hallucigeniids and total-group Onychophora each occupy a distinct region of morphospace.

Conclusions

Hallucigeniids and luolishaniids were comparably diverse and successful, representing two major lobopodian clades in the early Palaeozoic, and both evolved body plans adapted to different forms of suspension feeding. A Bayesian approach to cladistics supports the view that a semi-sessile, suspension-feeding lifestyle characterized the origin and rise of Panarthropoda from cycloneuralian body plans.

Keywords

Onychophora Velvet worm Cambrian evolutionary radiation Stem-group Disparity

FREE PDF GRATIS: BMC Evolutionary Biology

StudySwap: plataforma online objetiva facilitar a replicação de pesquisas

StudySwap: A platform for interlab replication, collaboration, and research resource exchange.

Nós topológicos e links em proteínas: mero acaso, fortuita necessidade ou design inteligente?

Topological knots and links in proteins

Pawel Dabrowski-Tumanski a,b and Joanna I. Sulkowska a,b,1  

Author Affiliations

aFaculty of Chemistry, University of Warsaw, 02-093, Warsaw, Poland;

bCentre of New Technologies, University of Warsaw, 02-097, Warsaw, Poland

Edited by George H. Lorimer, University of Maryland, College Park, MD, and approved February 1, 2017 (received for review September 23, 2016)

Significance

Twenty years after a discovery of knotted proteins, we found that some single-protein chains can form links, which have even more complex structures than knots. We derive conditions that proteins need to meet to form links. We search through the entire Protein Data Bank and identify several chains that form a Hopf link and a Solomon link. The link motif has not been recognized before; however, it is clearly of important functional significance in proteins. In this article, we relate topological properties of proteins with links to their function and stability and show that the link topology is characteristic of eukaryotes only.

Abstract

Twenty years after their discovery, knots in proteins are now quite well understood. They are believed to be functionally advantageous and provide extra stability to protein chains. In this work, we go one step further and search for links—entangled structures, more complex than knots, which consist of several components. We derive conditions that proteins need to meet to be able to form links. We search through the entire Protein Data Bank and identify several sequentially nonhomologous chains that form a Hopf link and a Solomon link. We relate topological properties of these proteins to their function and stability and show that the link topology is characteristic of eukaryotes only. We also explain how the presence of links affects the folding pathways of proteins. Finally, we define necessary conditions to form Borromean rings in proteins and show that no structure in the Protein Data Bank forms a link of this type.

folding catenanes slipknot lasso disulphide bridge

Footnotes

1To whom correspondence should be addressed. Email: jsulkowska@chem.uw.edu.pl.

Author contributions: P.D.-T. and J.I.S. designed research; P.D.-T. performed research; P.D.-T. and J.I.S. analyzed data; and P.D.-T. and J.I.S. wrote the paper.

The authors declare no conflict of interest.

This article is a PNAS Direct Submission.

This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10.1073/pnas.1615862114/-/DCSupplemental.

Freely available online through the PNAS open access option.

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Usando a biologia sintética para explorar princípios de desenvolvimento

Using synthetic biology to explore principles of development

Jamie Davies

Development 2017 144: 1146-1158; doi: 10.1242/dev.144196

Abstract

Developmental biology is mainly analytical: researchers study embryos, suggest hypotheses and test them through experimental perturbation. From the results of many experiments, the community distils the principles thought to underlie embryogenesis. Verifying these principles, however, is a challenge. One promising approach is to use synthetic biology techniques to engineer simple genetic or cellular systems that follow these principles and to see whether they perform as expected. As I review here, this approach has already been used to test ideas of patterning, differentiation and morphogenesis. It is also being applied to evo-devo studies to explore alternative mechanisms of development and ‘roads not taken’ by natural evolution.

FREE PDF GRATIS: Development

CRISPR detecta regulação de genes funcionais no genoma humano

CRISPR–Cas9 epigenome editing enables high-throughput screening for functional regulatory elements in the human genome

Tyler S Klann, Joshua B Black, Malathi Chellappan, Alexias Safi, Lingyun Song, Isaac B Hilton, Gregory E Crawford, Timothy E Reddy & Charles A Gersbach

Affiliations Contributions Corresponding authors

Nature Biotechnology (2017) doi:10.1038/nbt.3853

Received 19 September 2016 Accepted 17 March 2017 Published online 03 April 2017

Source/Fonte: © BRYAN SATALINO

Abstract

Large genome-mapping consortia and thousands of genome-wide association studies have identified non-protein-coding elements in the genome as having a central role in various biological processes. However, decoding the functions of the millions of putative regulatory elements discovered in these studies remains challenging. CRISPR–Cas9-based epigenome editing technologies have enabled precise perturbation of the activity of specific regulatory elements. Here we describe CRISPR–Cas9-based epigenomic regulatory element screening (CERES) for improved high-throughput screening of regulatory element activity in the native genomic context. Using dCas9KRAB repressor and dCas9p300 activator constructs and lentiviral single guide RNA libraries to target DNase I hypersensitive sites surrounding a gene of interest, we carried out both loss- and gain-of-function screens to identify regulatory elements for the β-globin and HER2 loci in human cells. CERES readily identified known and previously unidentified regulatory elements, some of which were dependent on cell type or direction of perturbation. This technology allows the high-throughput functional annotation of putative regulatory elements in their native chromosomal context.

Subject terms: Epigenomics Gene expression profiling

Subscription or payment needed/Requer assinatura ou pagamento:

Nature Biotechnology

Cientistas desenvolvem novo método para 'impressão digital' do HIV

Global site-specific N-glycosylation analysis of HIV envelope glycoprotein

Liwei Cao, Jolene K. Diedrich, Daniel W. Kulp, Matthias Pauthner, Lin He, Sung-Kyu Robin Park, Devin Sok, Ching Yao Su, Claire M. Delahunty, Sergey Menis, Raiees Andrabi, Javier Guenaga, Erik Georgeson, Michael Kubitz, Yumiko Adachi, Dennis R. Burton, William R. Schief, John R. Yates III & James C. Paulson

Nature Communications 8, Article number: 14954 (2017)

doi:10.1038/ncomms14954 ReadCube 

Download Citation

Glycomics HIV infections Mass spectrometry Virology

Received: 12 October 2016 Accepted: 15 February 2017 Published online: 28 March 2017

Abstract

HIV-1 envelope glycoprotein (Env) is the sole target for broadly neutralizing antibodies (bnAbs) and the focus for design of an antibody-based HIV vaccine. The Env trimer is covered by ∼90N-linked glycans, which shield the underlying protein from immune surveillance. bNAbs to HIV develop during infection, with many showing dependence on glycans for binding to Env. The ability to routinely assess the glycan type at each glycosylation site may facilitate design of improved vaccine candidates. Here we present a general mass spectrometry-based proteomics strategy that uses specific endoglycosidases to introduce mass signatures that distinguish peptide glycosites that are unoccupied or occupied by high-mannose/hybrid or complex-type glycans. The method yields >95% sequence coverage for Env, provides semi-quantitative analysis of the glycosylation status at each glycosite. We find that most glycosites in recombinant Env trimers are fully occupied by glycans, varying in the proportion of high-mannose/hybrid and complex-type glycans.

Acknowledgements

We thank Dr Ian A. Wilson and Dr Peter S. Lee for providing recombinant influenza virus haemagglutinin. This work was supported by NIH R01AI113867 (J.C.P., J.Y., W.R.S.); NIH UM1 AI100663 (D.R.B.); the International AIDS Vaccine Initiative (W.R.S., D.R.B.); and NIH P41 GM103533 (J.Y.).

Author information

Affiliations

Department of Cell and Molecular Biology, The Scripps Research Institute, La Jolla, California 92037, USA

Liwei Cao & James C. Paulson

Department of Chemical Physiology, The Scripps Research Institute, La Jolla, California 92037, USA

Jolene K. Diedrich, Lin He, Sung-Kyu Robin Park, Claire M. Delahunty, John R. Yates III & James C. Paulson

Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, California 92037, USA

Daniel W. Kulp, Matthias Pauthner, Devin Sok, Ching Yao Su, Raiees Andrabi, Javier Guenaga, Erik Georgeson, Michael Kubitz, Dennis R. Burton, William R. Schief & James C. Paulson

Department of the IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, California 92037, USA

Daniel W. Kulp, Matthias Pauthner, Devin Sok, Sergey Menis, Yumiko Adachi, Dennis R. Burton & William R. Schief

Contributions

L.C., J.R.Y. and J.C.P. designed the research. L.C. prepared samples for MS analysis. J.K.D., L.C. and C.M.D. performed the MS analysis. L.C., L.H. and S.R.P. analysed the data. D.W.K., M.M., D.S., C.Y.S., S.M., R.A., J.G., E.G., M.K. and Y.A. expressed and purified Env proteins. D.R.B., W.R.S., J.R.Y. and J.C.P. supervised the project. L.C. and J.C.P. wrote the manuscript.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to James C. Paulson.

FREE PDF GRATIS: Nature Communications Sup. Info. Peer Review File

Discovery-Mackenzie: 5-6 de maio de 2017.

Citações? Seus problemas acabaram: I4OC

Initiative for Open Citations

The Initiative for Open Citations I4OC is a collaboration between scholarly publishers, researchers, and other interested parties to promote the unrestricted availability of scholarly citation data.

About

Citations are the links that knit together our scientific and cultural knowledge. They are primary data that provide both provenance and an explanation for how we know facts. They allow us to attribute and credit scientific contributions, and they enable the evaluation of research and its impacts. In sum, citations are the most important vehicle for the discovery, dissemination, and evaluation of all scholarly knowledge.

As the number of scholarly publications is estimated to double every nine years, citations – and the computational systems that track them – enable researchers and the public to keep abreast of significant developments in any given field. For this to be possible, it is essential to have unrestricted access to bibliographic and citation data in machine-readable form.

The present scholarly communication system inadequately exposes the knowledge networks that already exist within our literature. Citation data are not usually freely available to access, they are often subject to inconsistent, hard-to-parse licenses, and they are usually not machine-readable.

An initiative to open up citation data

The aim of this initiative is to promote the availability of data on citations that are structured, separable, and open.

Structured means the data representing each publication and each citation instance are expressed in common, machine-readable formats, and that these data can be accessed programmatically. Separable means the citation instances can be accessed and analyzed without the need to access the source bibliographic products (such as journal articles and books) in which the citations are created. Open means the data are freely accessible and reusable.

Key benefits of achieving this aim include:

The establishment of a global public web of linked scholarly citation data to enhance the discoverability of published content, both subscription access and open access. This will particularly benefit individuals who are not members of academic institutions with subscriptions to commercial citation databases.

The ability to build new services over the open citation data, for the benefit of publishers, researchers, funding agencies, academic institutions and the general public, as well as enhancing existing services.

The creation of a public citation graph to explore connections between knowledge fields, and to follow the evolution of ideas and scholarly disciplines.

Reference distribution

Many publishers currently deposit reference lists from their journal articles to Crossref as part of their participation in Crossref’s Cited-by service. To open their references, along with the other bibliographic metadata that publishers send to Crossref, publishers need to turn on reference distribution for all of the Digital Object Identifier (DOI) prefixes they manage. This step allows references within the Crossref members’ articles to be distributed without restriction through all of Crossref's Metadata Delivery services, including the REST API and bulk metadata dumps, to any interested party. See below for additional information on reference distribution and on how to participate in Crossref’s Cited-by service.

Participating publishers

Before I4OC started, publishers releasing references in the open accounted for just 1% of citation metadata collected annually by Crossref. Following discussions over the past months, several subscription-access and open-access publishers have recently made the decision to release reference list metadata publicly. These include: American Geophysical Union, Association for Computing Machinery, BMJ, Cambridge University Press, Cold Spring Harbor Laboratory Press, EMBO Press, Royal Society of Chemistry, SAGE Publishing, Springer Nature, Taylor & Francis, and Wiley. These publishers join other publishers who have been opening their references through Crossref for some time.

The following list includes the names of all the publishers who have chosen to deposit and open up citation data as of March 30, 2017. I4OC will keep this list updated.

American Geophysical Union

Association for Computing Machinery

BMJ

Cambridge University Press

Co-Action Publishing

Cold Spring Harbor Laboratory Press

Copernicus GmbH

eLife

EMBO Press

Faculty of 1000, Ltd.

Frontiers Media SA

Geological Society of London

Hamad bin Khalifa University Press (HBKU Press)

Hindawi

International Union of Crystallography

Leibniz Institute for Psychology Information

MIT Press

PeerJ

Pensoft Publishers

Portland Press

Public Library of Science

Royal Society of Chemistry

SAGE Publishing

Springer Nature

Taylor & Francis Group

The Rockefeller University Press

The Royal Society

Ubiquity Press, Ltd.

Wiley

80% de contaminação de sequenciamento de amostras cruzadas!

Patterns of cross-contamination in a multispecies population genomic project: detection, quantification, impact, and solutions

Marion Ballenghien, Nicolas Faivre and Nicolas Galtier Email author

BMC Biology201715:25

DOI: 10.1186/s12915-017-0366-6 © Galtier et al. 2017 

 

Received: 6 December 2016 Accepted: 13 March 2017 Published: 29 March 2017

Source/Fonte: Sauri Nash - Flickr

Abstract

Background

Contamination is a well-known but often neglected problem in molecular biology. Here, we investigated the prevalence of cross-contamination among 446 samples from 116 distinct species of animals, which were processed in the same laboratory and subjected to subcontracted transcriptome sequencing.

Results

Using cytochrome oxidase 1 as a barcode, we identified a minimum of 782 events of between-species contamination, with approximately 80% of our samples being affected. An analysis of laboratory metadata revealed a strong effect of the sequencing center: nearly all the detected events of between-species contamination involved species that were sent the same day to the same company. We introduce new methods to address the amount of within-species, between-individual contamination, and to correct for this problem when calling genotypes from base read counts.

Conclusions

We report evidence for pervasive within-species contamination in this data set, and show that classical population genomic statistics, such as synonymous diversity, the ratio of non-synonymous to synonymous diversity, inbreeding coefficient FIT, and Tajima’s D, are sensitive to this problem to various extents. Control analyses suggest that our published results are probably robust to the problem of contamination. Recommendations on how to prevent or avoid contamination in large-scale population genomics/molecular ecology are provided based on this analysis.

Keywords RNAseq Transcriptome Animals SNP calling Genotyping Within-species

FREE PDF GRATIS: BMC Biology

O enigma da informação genética: a Academia não tem como responder via teoria da evolução de Darwin!!!

Ebook grátis: Molecular Mechanisms and Physiological Significance of Organelle Interactions and Cooperation

Molecular Mechanisms and Physiological Significance of Organelle Interactions and Cooperation

Edited by: Michael Schrader, Markus Islinger

Publisher: Frontiers Media SA

ISBN: 9782889451043

Product Name: Frontiers Research Topic Ebook

Source/Fonte: Front. Cell Dev. Biol.

Eukaryotic cells contain distinct membrane-bound organelles, which compartmentalise cellular proteins to fulfil a variety of vital functions. Many organelles have long been regarded as isolated and static entities (e.g., peroxisomes, mitochondria, lipid droplets), but it is now evident that they display dynamic changes, interact with each other, share certain proteins and show metabolic cooperation and cross-talk. Despite great advances in the identification and characterisation of essential components and molecular mechanisms associated with the biogenesis and function of organelles, information on how organelles interact and are incorporated into metabolic pathways and signaling networks is just beginning to emerge. Organelle cooperation requires sophisticated targeting systems which regulate the proper distribution of shared proteins to more than one organelle. Organelle motility and membrane remodeling support organelle interaction and contact. This contact can be mediated by membrane proteins residing on different organelles which can serve as molecular tethers to physically link different organelles together. They can also contribute to the exchange of metabolites and ions, or act in the assembly of signaling platforms. In this regard organelle communication events have been associated with important cellular functions such as apoptosis, antiviral defense, organelle division/biogenesis, ROS metabolism and signaling, and various metabolic pathways such as breakdown of fatty acids or cholesterol biosynthesis. 

In this research topic we will focus on recent novel findings on the underlying molecular mechanisms and physiological significance of organelle interaction and cooperation with a particular focus on mitochondria, peroxisomes, endoplasmic reticulum, lysosomes and lipid droplets and their impact on the regulation of cellular homeostasis. Our understanding of how organelles physically interact and use cellular signaling systems to coordinate functional networks between each other is still in its infancy. Nevertheless recent discoveries of defined membrane structures such as the mitochondria-ER associated membranes (MAM) are revealing how membrane domains enriched in specific proteins transmit signals across organelle boundaries, allowing one organelle to influence the function of another. In addition to its role as a mediator between mitochondria and the ER, contacts between the MAM and peroxisomes contribute to antiviral signaling, and specialised regions of the ER are supposed to initiate peroxisome biogenesis, whereas intimate contacts between peroxisomes, lipid droplets and the ER mediate lipid metabolism. In line with these observations it is tempting to speculate that further physical contact sites between other organelles exist. Alternatively, novel regulated vesicle trafficking pathways between organelles (e.g., mitochondria to peroxisomes or lysosomes) have been discovered implying another mode of organelle communication. Identifying the key molecular players of such specialised membrane structures will be a prerequisite to understand how organelle communication is physically accomplished and will lead to the identification of new regulatory networks. In addition to the direct transmission of interorganellar information, cytosolic messenger systems (e.g., kinase/phosphatase systems or redox signaling) may contribute to the coordination of organelle functions. This research topic will integrate new findings from both modes of communication and will provide new perspectives for the functional significance of cross-talk among organelles. 

We would like to thank all the researchers who contributed their valuable work to this research topic. Furthermore, we are grateful to the reviewers and Associate Editors who contributed valuable comments and positive criticism to improve the contributions.

Science > Cell and Developmental Biology > Mitochondrial Research

Science > Physiology > Mitochondrial Research

Keywords: membrane contact sites, organelle dynamics, Peroxisomes, Mitochondria, Endoplasmic Reticulum, Intracellular signaling, Organelle communication, lipid droplet

FREE EBOOK GRATIS: Frontiers 21.7 MBs

Pesquisas CRISPR tornam confusos os resultados de pesquisas genéticas mais antigas

CRISPR/Cas9 mutagenesis invalidates a putative cancer dependency targeted in on-going clinical trials

Ann Lin Christopher J Giuliano Nicole M Sayles Jason M Sheltzer 

Cold Spring Harbor Laboratory, United States; Stony Brook University, United States

DOI: http://dx.doi.org/10.7554/eLife.24179  

Published March 24, 2017 

Cite as eLife 2017;6:e24179

Source/Fonte: Advanced Analytical

Abstract

The Maternal Embryonic Leucine Zipper Kinase (MELK) has been reported to be a genetic dependency in several cancer types. MELK RNAi and small-molecule inhibitors of MELK block the proliferation of various cancer cell lines, and MELK knockdown has been described as particularly effective against the highly-aggressive basal/triple-negative subtype of breast cancer. Based on these preclinical results, the MELK inhibitor OTS167 is currently being tested as a novel chemotherapy agent in several clinical trials. Here, we report that mutagenizing MELK with CRISPR/Cas9 has no effect on the fitness of basal breast cancer cell lines or cell lines from six other cancer types. Cells that harbor null mutations in MELK exhibit wild-type doubling times, cytokinesis, and anchorage-independent growth. Furthermore, MELK-knockout lines remain sensitive to OTS167, suggesting that this drug blocks cell division through an off-target mechanism. In total, our results undermine the rationale for a series of current clinical trials and provide an experimental approach for the use of CRISPR/Cas9 in preclinical target validation that can be broadly applied.

DOI: http://dx.doi.org/10.7554/eLife.24179.001

eLife digest

Like a person who is dependent on coffee to be productive, cancer cells are dependent on the products of certain genes in order to dominate their environment and grow. Cancer cells will stop growing and die when the activity of these gene products is blocked. These genes are known as cancer dependencies or “addictions”. As a result, researchers are constantly looking for cancer dependencies and developing drugs to block their activity.

It was previously believed that a gene called MELK was an addiction in certain types of breast cancer. In fact, pharmaceutical companies had developed a drug to block the activity of MELK, and this drug is currently being tested in human patients. However, Lin, Giuliano et al. have now taken a second look at the role of MELK in breast cancer, and have come to a different conclusion.

Using a gene editing technology called CRISPR/Cas9, Lin, Giuliano et al. removed MELK activity from several cancer cell lines. This did not stop cancer cells from multiplying, suggesting that MELK is not actually a cancer addiction.

Additionally, when breast cancer cells that do not produce MELK were exposed to the drug that is supposed to block MELK activity, the drug still stopped cell growth. Since the drug works when MELK is not present in the cell, the drug must be binding to other proteins. This suggests that MELK is not the actual target of the drug.

Lin, Giuliano et al. suggest that, in the future, CRISPR/Cas9 technology could be used to better identify cancer dependencies and drug targets before cancer drugs are given to human patients.

DOI: http://dx.doi.org/10.7554/eLife.24179.002

FREE PDF GRATIS: eLIFE

+++++

See article/Vide artigo: 

CRISPR studies muddy results of older gene research

Scientists face tough decisions when the latest gene-editing findings don’t match up with the results of other techniques.

Heidi Ledford

05 April 2017 Nature

Análise genômica de 63.220 tumores cancerígenos indica a inviabilidade de uma vacina universal contra o câncer.

Genomic analysis of 63,220 tumors reveals insights into tumor uniqueness and targeted cancer immunotherapy strategies

Ryan J. Hartmaier Email author, Jehad Charo, David Fabrizio, Michael E. Goldberg, Lee A. Albacker, William Pao and Juliann Chmielecki

Genome Medicine20179:16

DOI: 10.1186/s13073-017-0408-2 © The Author(s). 2017 

Received: 2 July 2016Accepted: 25 January 2017Published: 24 February 2017

Imagem © Wikimedia Commons/Dr. Cecil Fox

Abstract

Background

The integration of genomics with immunotherapy has potential value for cancer vaccine development. Given the clinical successes of immune checkpoint modulators, interest in cancer vaccines as therapeutic options has been revived. Current data suggest that each tumor contains a unique set of mutations (mutanome), thus requiring the creation of individualized cancer vaccines. However, rigorous analysis of non-individualized cancer immunotherapy approaches across multiple cancer types and in the context of known driver alterations has yet to be reported. We therefore set out to determine the feasibility of a generalizable cancer vaccine strategy based on targeting multiple neoantigens in an HLA-A/B subtype-directed manner.

Methods

A cancer gene-focused, hybrid capture-based genomic analysis was performed on 63,220 unique tumors. Neoantigens were predicted using a combined peptide processing and MHC-I binding prediction tool (IEDB) for all recurrent (>10 tumors) missense alterations and non-frameshift indels for the two most common HLA-A/B subtypes in North American/European populations.

Results

Despite being overwhelmingly unique overall, many mutanomes (~45%) contain at least one mutation from a set of ten mutations chosen to maximize the number of unique tumors. This held true for tumors driven by KRAS G12C (n = 1799), PIK3CA E545K (n = 1713), or EGFR L858R (n = 478) alterations, which define distinct sample subsets. We therefore hypothesized that sets of carefully selected mutations/neoantigens may allow the development of broadly applicable semi-universal cancer vaccines. To test the feasibility of such an approach, antigen processing and MHC-I binding prediction was applied for HLA subtypes A*01:01/B*08:01 and A*02:01/B*44:02. In tumors with a specific HLA type, 0.7 and 2.5% harbored at least one of a set of ten neoantigens predicted to bind to each subtype, respectively. In comparison, KRAS G12C-driven tumors produced similar results (0.8 and 2.6% for each HLA subtype, respectively), indicating that neoantigen targets still remain highly diverse even within the context of major driver mutations.

Conclusions

This “best case scenario” analysis of a large tumor set across multiple cancer types and in the context of driver alterations reveals that semi-universal, HLA-specific cancer vaccine strategies will be relevant to only a small subset of the general population. Similar analysis of whole exome/genome sequencing, although not currently feasible at scale in a clinical setting, will likely uncover further diversity.

Keywords: Neoantigens Cancer vaccines Genomic profiling Poly-epitope

Discovery Institute Brasil na Universidade Presbiteriana Mackenzie - São Paulo, SP

Núcleo de Pesquisa Mackenzie em Ciência, Fé e Sociedade – Discovery-Mackenzie

O Discovery-Mackenzie é um núcleo de pesquisa interdisciplinar da Universidade Presbiteriana Mackenzie que promove estudos científicos focados em complexidade e informação na busca de evidências que apontem para a ação de processos naturais ou design inteligente na natureza, explorando as implicações dessas descobertas para a relação entre ciência e sociedade, incluindo a fé. Para este fim, o Discovery-Mackenzie coordena ações que fomentem a pesquisa científica e sua divulgação, organiza encontros científicos e cursos de capacitação e produz materiais de divulgação científica e de cunho educacional, mantendo intercâmbio de conhecimento e pessoal com o Discovery Institute – USA e outros centros afiliados.

Evento de Inauguração

Press Release Discovery-Mackenzie 5-6 Maio 2017 | Inauguração do Discovery-Mackenzie

Na sexta a noite, 5 de Maio, as 18h, será inaugurada a sede do Discovery-Mackenzie, que acomodará uma biblioteca, sala de treinamento e workshops, e sala de leitura e escritórios. A inauguração da sede será seguida de uma cerimônia de inauguração (entrada franca para inscritos) iniciada as 19h30 no auditório da Escola Americana.

Nesses eventos, uma delegação de renomados nomes do DI-USA estará presente, entre eles o presidente do Discovery Institute-USA, Steven J. Buri e três de seus principais pesquisadores afiliados: Michel Behe, Douglas Axe e Brian Miller.

Michel Behe é famoso no mundo todo pelo seu Best Seller “A Caixa Preta de Darwin”, livro que lançou as teses do Design Inteligente moderno, mostrando ser a TDI referendada pela bioquímica moderna, catalisando assim uma ampla discussão sobre a viabilidade da Evolução Darwiniana. Douglas Axe se tornou hoje também um dos grandes defensores da TDI por intermédio de seu livro recentemente publicado, outro Best Seller intitulado “Undeniable: How Biology Confirms Our Intuition Life is Designed", sendo também diretor do "Biologic Institute”, um centro de pesquisas associado ao DI-USA. Em seu livro, Douglas Axe argumenta que o DI, à luz da Biologia moderna, é evidente e inquestionável, sendo ainda coincidente com a nossa intuição. Já Brian Miller é Ph.D em Física e dá palestras em todo o mundo sobre o DI e a suas implicações para a visão de mundo cristã.

Na cerimônia, que contará com a participação e palavras de várias autoridades e diretores da Universidade Presbiteriana Mackenzie, e da Sociedade Brasileira do Design Inteligente – TDI BRASIL, além de várias outras autoridades, serão apresentados os objetivos do Discovery-Mackenzie, suas metas e relevância no debate hoje reaquecido entre fé e ciência. Na noite de sexta, Michel Behe e Douglas Axe também proferirão palestras referentes ao tema fé e ciência.

No sábado, dia 6, um curso intensivo de treinamento em Design Inteligente será oferecido para convidados, e conjuntamente pelos pesquisadores do DI-USA e Discovery-Mackenzie, com o objetivo de treinar professores e palestrantes sobre os princípios gerais do Design Inteligente e sua viabilidade frente à evolução Darwiniana.

Convidados

Douglas Axe

É o autor do Livro Undeniable: How Biology Confirms Our Intuition Life is Designed e Diretor do "Biologic Institute", um centro de pesquisas patrocinado pelo Centro de Ciência e Cultura do Discovery Institute (DI-USA). Axe se formou doutor na Caltech e foi pós-doc e pesquisador na Inglaterra na Universidade de Cambridge, no Cambridge Medical Research Council Centre e no Instituto Babraham em Cambridge. Suas pesquisas se valem de experimentos e simulações computacionais para examinar os restrições funcionais e estruturais da Evolução de proteínas e sistemas proteicos.

Michael J. Behe

É Professor de Ciências Biológicas na Lehigh University, Pensilvânia - USA e um Membro Senior do DI-USA. Ele se formou doutor em Bioquímica pela Universidade da Pensilvânia. Seu livro "A Caixa Preta de Darwin: O Desafio Bioquímico para a Evolução" ajudou a inspirar o movimento moderno do Design Inteligente na Biologia e foi eleito pela National Review como um dos 100 mais importantes livros de não-ficção do século 20. Behe escreveu acerca de sua defesa do DI no The New York Times e tem dado palestras sobre DI ao redor do mundo em várias universidades.

Steven J. Buri

É o presidente do DI-USA, o elo intelectual do movimento moderno do Design Inteligente, sendo também um centro de pesquisas em áreas como a tecnologia, educação, bioética, e liberdade econômica. Buri foi também Diretor Executivo do Stewardship Partners, uma organização americana de livre mercado e fez parte também da equipe do senador americano Slade Gorton. Ele também foi prefeito da cidade de Newcastle perto de Seatle-USA. Em 2010, foi escolhido pelo American Council of Young Political Leaders para participar de uma delegação de políticos americanos ao Nepal.

Brian Miller

É coordenador de pesquisas do DI-USA. Ele tem doutorado em Física pela Duke University, e tem proferido palestras ao redor do mundo em universidades em tópicos como o DI e a visão de mundo cristã. Ele tem sido também consultor de igrejas, organizações e empresas em desenvolvimento estratégico e organizacional, e tem sido também consultor do Aslan Guild, um guia start-up para inventores, guia esse que se dedica a trazer inovação para o mercado de trabalho.

Programação

Local: Auditório da Escola Americana – Mackenzie São Paulo

Sexta 05 de Maio

18h - Inauguração do escritório Discovery-Mackenzie.

19h30 - Cerimônia de Abertura do Evento - Participação da Reitoria da UPM, Chancelaria, Presidência do IPM e Presidente do Discovery Institute – USA, Steven J. Buri, e demais autoridades convidadas.

20h15 - Apresentação do DI - Mackenzie. Planos e metas: Marcos N. Eberlin Presidente da TDI BRASIL.

20h30 - Palestra de Abertura 1- Michael Behe - "Celebrando os 20 anos da Complexidade Irredutível: O primeiro grande pilar da Teoria do Design Inteligente".

21h00 - Palestra de Abertura 2 - Douglas Axe - "Irrefutável: Como a bioquímica confirma a nossa intuição de que fomos planejados".

21h30 - Palavra de Encerramento.

Sábado 06 de Maio

9h – 17h - Curso para convidados sobre a Teoria do Design Inteligente:

O curso será ministrado pelos pioneiros e grandes nomes da TDI nos USA e no Brasil – entre eles Steven J. Buri (presidente do DI-USA), Michel Behe (autor do best-seller A Caixa preta de Darwin), Douglas Axe (autor do best-seller Undeniable) e Brian Miller (coordenador do Center for Science and Culture do DI-USA), Marcos N. Eberlin (presidente executivo da TDI-BRASIL) e Enézio Almeida Filho (presidente emérito da TDI-BRASIL). Terá como objetivo expor de forma correta e precisa os principais postulados da Teoria do Design Inteligente e assim treinar professores, palestrantes e líderes para se pronunciar, proferir palestras e aulas sobre a TDI.

Inscrever aqui

Núcleo de Pesquisa Mackenzie em Ciência, Fé e Sociedade

Auditório da Escola Americana – Mackenzie São Paulo

Rua da Consolação 930, São Paulo, SP 01302-907