Mobile DNA最新文献

{"title":"TE Hub: A community-oriented space for sharing and connecting tools, data, resources, and methods for transposable element annotation.","authors":"Tyler A Elliott,&nbsp;Tony Heitkam,&nbsp;Robert Hubley,&nbsp;Hadi Quesneville,&nbsp;Alexander Suh,&nbsp;Travis J Wheeler","doi":"10.1186/s13100-021-00244-0","DOIUrl":"https://doi.org/10.1186/s13100-021-00244-0","url":null,"abstract":"<p><p>Transposable elements (TEs) play powerful and varied evolutionary and functional roles, and are widespread in most eukaryotic genomes. Research into their unique biology has driven the creation of a large collection of databases, software, classification systems, and annotation guidelines. The diversity of available TE-related methods and resources raises compatibility concerns and can be overwhelming to researchers and communicators seeking straightforward guidance or materials. To address these challenges, we have initiated a new resource, TE Hub, that provides a space where members of the TE community can collaborate to document and create resources and methods. The space consists of (1) a website organized with an open wiki framework,  https://tehub.org , (2) a conversation framework via a Twitter account and a Slack channel, and (3) bi-monthly Hub Update video chats on the platform's development. In addition to serving as a centralized repository and communication platform, TE Hub lays the foundation for improved integration, standardization, and effectiveness of diverse tools and protocols. We invite the TE community, both novices and experts in TE identification and analysis, to join us in expanding our community-oriented resource.</p>","PeriodicalId":18854,"journal":{"name":"Mobile DNA","volume":"12 1","pages":"16"},"PeriodicalIF":4.9,"publicationDate":"2021-06-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s13100-021-00244-0","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10338325","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"ENSnano: A 3D Modeling Software for DNA Nanostructures","authors":"N. Lévy, N. Schabanel","doi":"10.4230/LIPIcs.DNA.27.5","DOIUrl":"https://doi.org/10.4230/LIPIcs.DNA.27.5","url":null,"abstract":"7 Since the 1990s, increasingly complex nanostructures have been reliably obtained out of self-assembled 8 DNA strands: from “simple” 2D shapes to 3D gears and articulated nano-objects, and even computing 9 structures. The success of the assembly of these structures relies on a fine tuning of their structure 10 to match the peculiar geometry of DNA helices. Various softwares have been developed to help 11 the designer. These softwares provide essentially four kind of tools: an abstract representation of 12 DNA helices (e.g. cadnano, scadnano, DNApen, 3DNA, Hex-tiles); a 3D view of the design (e.g., 13 vHelix, Adenita, oxDNAviewer); fully automated design (e.g., BScOR, Daedalus, Perdix, Talos, 14 Athena), generally dedicated to a specific kind of design, such as wireframe origami; and coarse grain 15 or thermodynamical physics simulations (e.g., oxDNA, MrDNA, SNUPI, Nupack, ViennaRNA,...). 16 MagicDNA combines some of these approaches to ease the design of configurable DNA origamis. 17 We present our first step in the direction of conciliating all these different approaches and 18 purposes into one single reliable GUI solution: the first fully usable version (design from scratch to 19 export) of our general purpose 3D DNA nanostructure design software ENSnano . We believe that 20 its intuitive, swift and yet powerful graphical interface, combining 2D and 3D editable views, allows 21 fast and precise editing of DNA nanostructures. It also handles editing of large 2D/3D structures 22 smoothly, and imports from the most common solutions. Our software extends the concept of 23 grids introduced in cadnano . Grids allow to abstract and articulated the different parts of a design. 24 ENSnano also provides new design tools which speeds up considerably the design of complex large 3D 25 structures, most notably: a 2D split view , which allows to edit intricate 3D structures which cannot 26 easily be mapped in a 2D view, and a copy, paste & repeat functionality, which takes advantage 27 of the grids to design swiftly large repetitive chunks of a structure. ENSnano has been validated 28 experimentally, as proven by the AFM images of a DNA origami entirely designed in ENSnano . 29 ENSnano is a light-weight ready-to-run independent single-file app, running seamlessly in most of 30 the operating systems (Windows 10, MacOS 10.13+ and Linux). Precompiled versions for Windows 31 and MacOS are ready to download on ENSnano website. As of writing this paper, our software is 32 being actively developed to extend its capacities in various directions discussed in this article. Still, 33 its 3D and 2D editing interface is already meeting our usability goals. Because of its stability and 34 ease of use, we believe that ENSnano could already be integrated in anyone’s design chain, when 35 precise editing of a larger nanostructure is needed.","PeriodicalId":18854,"journal":{"name":"Mobile DNA","volume":"18 1","pages":"5:1-5:23"},"PeriodicalIF":4.9,"publicationDate":"2021-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"74501231","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Molecular Machines from Topological Linkages","authors":"Keenan Breik, Austin Luchsinger, D. Soloveichik","doi":"10.4230/LIPIcs.DNA.27.7","DOIUrl":"https://doi.org/10.4230/LIPIcs.DNA.27.7","url":null,"abstract":"Life is built upon amazingly sophisticated molecular machines whose behavior combines mechanical and chemical action. Engineering of similarly complex nanoscale devices from first principles remains an as yet unrealized goal of bioengineering. In this paper we formalize a simple model of mechanical motion (mechanical linkages) combined with chemical bonding. The model has a natural implementation using DNA with double-stranded rigid links, and single-stranded flexible joints and binding sites. Surprisingly, we show that much of the complex behavior is preserved in an idealized topological model which considers solely the graph connectivity of the linkages. We show a number of artifacts including Boolean logic, catalysts, a fueled motor, and chemo-mechanical coupling, all of which can be understood and reasoned about in the topological model. The variety of achieved behaviors supports the use of topological chemical linkages in understanding and engineering complex molecular behaviors. 2012 ACM Subject Classification Theory of computation → Models of computation; Theory of computation → Computational geometry","PeriodicalId":18854,"journal":{"name":"Mobile DNA","volume":"226 1","pages":"7:1-7:20"},"PeriodicalIF":4.9,"publicationDate":"2021-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"88783620","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Robust Digital Molecular Design of Binarized Neural Networks","authors":"Johannes Linder, Yuan-Jyue Chen, David Wong, Georg Seelig, L. Ceze, K. Strauss","doi":"10.4230/LIPIcs.DNA.27.1","DOIUrl":"https://doi.org/10.4230/LIPIcs.DNA.27.1","url":null,"abstract":"Molecular programming – a paradigm wherein molecules are engineered to perform computation – shows great potential for applications in nanotechnology, disease diagnostics and smart therapeutics. A key challenge is to identify systematic approaches for compiling abstract models of computation to molecules. Due to their wide applicability, one of the most useful abstractions to realize is neural networks. In prior work, real-valued weights were achieved by individually controlling the concentrations of the corresponding “weight” molecules. However, large-scale preparation of reactants with precise concentrations quickly becomes intractable. Here, we propose to bypass this fundamental problem using Binarized Neural Networks (BNNs), a model that is highly scalable in a molecular setting due to the small number of distinct weight values. We devise a noise-tolerant digital molecular circuit that compactly implements a majority voting operation on binary-valued inputs to compute the neuron output. The network is also rate-independent, meaning the speed at which individual reactions occur does not affect the computation, further increasing robustness to noise. We first demonstrate our design on the MNIST classification task by simulating the system as idealized chemical reactions. Next, we map the reactions to DNA strand displacement cascades, providing simulation results that demonstrate the practical feasibility of our approach. We perform extensive noise tolerance simulations, showing that digital molecular neurons are notably more robust to noise in the concentrations of chemical reactants compared to their analog counterparts. Finally, we provide initial experimental results of a single binarized neuron. Our work suggests a solid framework for building even more complex neural network computation. 2012 ACM Subject Classification Theory of computation → Models of computation; Applied computing","PeriodicalId":18854,"journal":{"name":"Mobile DNA","volume":"14 1","pages":"1:1-1:20"},"PeriodicalIF":4.9,"publicationDate":"2021-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"81810808","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Reactamole: Functional Reactive Molecular Programming","authors":"T. Klinge, James I. Lathrop, Peter-Michael Osera, Allison Rogers","doi":"10.4230/LIPIcs.DNA.27.10","DOIUrl":"https://doi.org/10.4230/LIPIcs.DNA.27.10","url":null,"abstract":"Chemical reaction networks (CRNs) are an important tool for molecular programming, a field that is rapidly expanding our ability to deploy computer programs into biological systems for a variety of applications. However, CRNs are also difficult to work with due to their massively parallel nature, leading to the need for higher-level languages that allow for easier computation with CRNs. Recently, research has been conducted into a variety of higher-level languages for deterministic CRNs but modeling CRN parallelism, managing error accumulation, and finding natural CRN representations are ongoing challenges. We introduce Reactamole, a higher-level language for deterministic CRNs that utilizes the functional reactive programming (FRP) paradigm to represent CRNs as a reactive dataflow network. Reactamole equates a CRN with a functional reactive program, implementing the key primitives of the FRP paradigm directly as CRNs. The functional nature of Reactamole makes reasoning about molecular programs easier, and its strong static typing allows us to ensure that a CRN is well-formed by virtue of being well-typed. In this paper, we describe the design of Reactamole and how we use CRNs to represent the common datatypes and operations found in FRP. We also demonstrate the potential of this functional reactive approach to molecular programming by giving an extended example where a CRN is constructed using FRP to modulate and demodulate an amplitude modulated signal. 2012 ACM Subject Classification Software and its engineering → Functional languages; Software and its engineering → Data flow languages","PeriodicalId":18854,"journal":{"name":"Mobile DNA","volume":"98 1","pages":"10:1-10:20"},"PeriodicalIF":4.9,"publicationDate":"2021-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"75024415","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Directed Non-Cooperative Tile Assembly Is Decidable","authors":"Pierre-Etienne Meunier, Damien Regnault","doi":"10.4230/LIPIcs.DNA.27.6","DOIUrl":"https://doi.org/10.4230/LIPIcs.DNA.27.6","url":null,"abstract":"We provide a complete characterisation of all final states of a model called directed non-cooperative tile self-assembly , also called directed temperature 1 tile assembly , which proves that this model cannot possibly perform Turing computation. This model is a deterministic version of the more general undirected model, whose computational power is still open. Our result uses recent results in the domain, and solves a conjecture formalised in 2011. We believe that this is a major step towards understanding the full model. Temperature 1 tile assembly can be seen as a two-dimensional extension of finite automata, where geometry provides a form of memory and synchronisation, yet the full power of these “geometric blockings” was still largely unknown until recently (note that nontrivial algorithms which are able to build larger structures than the naive constructions have been found).","PeriodicalId":18854,"journal":{"name":"Mobile DNA","volume":"1 1","pages":"6:1-6:21"},"PeriodicalIF":4.9,"publicationDate":"2021-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"89163484","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"New Ther1-derived SINE Squam3 in scaled reptiles","authors":"N. Vassetzky, S. A. Kosushkin, V. Korchagin, A. Ryskov","doi":"10.21203/rs.3.rs-132339/v1","DOIUrl":"https://doi.org/10.21203/rs.3.rs-132339/v1","url":null,"abstract":"Background SINEs comprise a significant part of animal genomes and are used to study the evolution of diverse taxa. Despite significant advances in SINE studies in vertebrates and higher eukaryotes in general, their own evolution is poorly understood. Results We have discovered and described in detail a new Squam3 SINE specific for scaled reptiles (Squamata). The subfamilies of this SINE demonstrate different distribution in the genomes of squamates, which together with the data on similar SINEs in the tuatara allowed us to propose a scenario of their evolution in the context of reptilian evolution. Conclusions Ancestral SINEs preserved in small numbers in most genomes can give rise to taxa-specific SINE families. Analysis of this aspect of SINEs can shed light on the history and mechanisms of SINE variation in reptilian genomes.","PeriodicalId":18854,"journal":{"name":"Mobile DNA","volume":"12 1","pages":""},"PeriodicalIF":4.9,"publicationDate":"2020-12-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"42350982","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"SeqURE - a new copy-capture based method for sequencing of unknown Retroposition events.","authors":"Alexander Y Komkov,&nbsp;Shamil Z Urazbakhtin,&nbsp;Maria V Saliutina,&nbsp;Ekaterina A Komech,&nbsp;Yuri A Shelygin,&nbsp;Gaiaz A Nugmanov,&nbsp;Vitaliy P Shubin,&nbsp;Anastasia O Smirnova,&nbsp;Mikhail Y Bobrov,&nbsp;Alexey S Tsukanov,&nbsp;Anastasia V Snezhkina,&nbsp;Anna V Kudryavtseva,&nbsp;Yuri B Lebedev,&nbsp;Ilgar Z Mamedov","doi":"10.1186/s13100-020-00228-6","DOIUrl":"https://doi.org/10.1186/s13100-020-00228-6","url":null,"abstract":"<p><strong>Background: </strong>Retroelements (REs) occupy a significant part of all eukaryotic genomes including humans. The majority of retroelements in the human genome are inactive and unable to retrotranspose. Dozens of active copies are repressed in most normal tissues by various cellular mechanisms. These copies can become active in normal germline and brain tissues or in cancer, leading to new retroposition events. The consequences of such events and their role in normal cell functioning and carcinogenesis are not yet fully understood. If new insertions occur in a small portion of cells they can be found only with the use of specific methods based on RE enrichment and high-throughput sequencing. The downside of the high sensitivity of such methods is the presence of various artifacts imitating real insertions, which in many cases cannot be validated due to lack of the initial template DNA. For this reason, adequate assessment of rare (< 1%) subclonal cancer specific RE insertions is complicated.</p><p><strong>Results: </strong>Here we describe a new copy-capture technique which we implemented in a method called SeqURE for Sequencing Unknown of Retroposition Events that allows for efficient and reliable identification of new genomic RE insertions. The method is based on the capture of copies of target molecules (copy-capture), selective amplification and sequencing of genomic regions adjacent to active RE insertions from both sides. Importantly, the template genomic DNA remains intact and can be used for validation experiments. In addition, we applied a novel system for testing method sensitivity and precisely showed the ability of the developed method to reliably detect insertions present in 1 out of 100 cells and a substantial portion of insertions present in 1 out of 1000 cells. Using advantages of the method we showed the absence of somatic Alu insertions in colorectal cancer samples bearing tumor-specific L1HS insertions.</p><p><strong>Conclusions: </strong>This study presents the first description and implementation of the copy-capture technique and provides the first methodological basis for the quantitative assessment of RE insertions present in a small portion of cells.</p>","PeriodicalId":18854,"journal":{"name":"Mobile DNA","volume":"11 1","pages":"33"},"PeriodicalIF":4.9,"publicationDate":"2020-12-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s13100-020-00228-6","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38371629","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Intruder (DD38E), a recently evolved sibling family of DD34E/Tc1 transposons in animals.","authors":"Bo Gao,&nbsp;Wencheng Zong,&nbsp;Csaba Miskey,&nbsp;Numan Ullah,&nbsp;Mohamed Diaby,&nbsp;Cai Chen,&nbsp;Xiaoyan Wang,&nbsp;Zoltán Ivics,&nbsp;Chengyi Song","doi":"10.1186/s13100-020-00227-7","DOIUrl":"https://doi.org/10.1186/s13100-020-00227-7","url":null,"abstract":"<p><strong>Background: </strong>A family of Tc1/mariner transposons with a characteristic DD38E triad of catalytic amino acid residues, named Intruder (IT), was previously discovered in sturgeon genomes, but their evolutionary landscapes remain largely unknown.</p><p><strong>Results: </strong>Here, we comprehensively investigated the evolutionary profiles of ITs, and evaluated their cut-and-paste activities in cells. ITs exhibited a narrow taxonomic distribution pattern in the animal kingdom, with invasions into two invertebrate phyla (Arthropoda and Cnidaria) and three vertebrate lineages (Actinopterygii, Agnatha, and Anura): very similar to that of the DD36E/IC family. Some animal orders and species seem to be more hospitable to Tc1/mariner transposons, one order of Amphibia and seven Actinopterygian orders are the most common orders with horizontal transfer events and have been invaded by all four families (DD38E/IT, DD35E/TR, DD36E/IC and DD37E/TRT) of Tc1/mariner transposons, and eight Actinopterygii species were identified as the major hosts of these families. Intact ITs have a total length of 1.5-1.7 kb containing a transposase gene flanked by terminal inverted repeats (TIRs). The phylogenetic tree and sequence identity showed that IT transposases were most closely related to DD34E/Tc1. ITs have been involved in multiple events of horizontal transfer in vertebrates and have invaded most lineages recently (< 5 million years ago) based on insertion age analysis. Accordingly, ITs presented high average sequence identity (86-95%) across most vertebrate species, suggesting that some are putatively active. ITs can transpose in human HeLa cells, and the transposition efficiency of consensus TIRs was higher than that of the TIRs of natural isolates.</p><p><strong>Conclusions: </strong>We conclude that DD38E/IT originated from DD34E/Tc1 and can be detected in two invertebrate phyla (Arthropoda and Cnidaria), and in three vertebrate lineages (Actinopterygii, Agnatha and Anura). IT has experienced multiple HT events in animals, dominated by recent amplifications in most species and has high identity among vertebrate taxa. Our reconstructed IT transposon vector designed according to the sequence from the \"cat\" genome showed high cut-and-paste activity. The data suggest that IT has been acquired recently and is active in many species. This study is meaningful for understanding the evolution of the Tc1/mariner superfamily members and their hosts.</p>","PeriodicalId":18854,"journal":{"name":"Mobile DNA","volume":"11 1","pages":"32"},"PeriodicalIF":4.9,"publicationDate":"2020-12-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s13100-020-00227-7","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38359348","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Correction to: Characterising a human endogenous retrovirus(HERV)-derived tumour-associated antigen: enriched RNA-Seq analysis of HERV-K(HML-2) in mantle cell lymphoma cell lines.","authors":"Witold Tatkiewicz,&nbsp;James Dickie,&nbsp;Franchesca Bedford,&nbsp;Alexander Jones,&nbsp;Mark Atkin,&nbsp;Michele Kiernan,&nbsp;Emmanuel Atangana Maze,&nbsp;Bora Agit,&nbsp;Garry Farnham,&nbsp;Alexander Kanapin,&nbsp;Robert Belshaw","doi":"10.1186/s13100-020-00226-8","DOIUrl":"https://doi.org/10.1186/s13100-020-00226-8","url":null,"abstract":"<p><p>An amendment to this paper has been published and can be accessed via the original article.</p>","PeriodicalId":18854,"journal":{"name":"Mobile DNA","volume":"11 1","pages":"31"},"PeriodicalIF":4.9,"publicationDate":"2020-11-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s13100-020-00226-8","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38349912","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}