Mobile DNA最新文献_第9页

Correction: Characterization of transposable elements within the Bemisia tabaci species complex 更正:烟粉虱物种复合体内转座因子的表征

IF 4.9 2区生物学 Q1 GENETICS & HEREDITY

Mobile DNA

Pub Date : 2022-02-02 DOI: 10.21203/rs.3.rs-1312818/v1

Juan Paolo A. Sicat, Paul Visendi, Steven O. Sewe, S. Bouvaine, S. Seal

Background Whiteflies are agricultural pests that have caused worldwide negative impacts that have led to severe financial losses. The Bemisia tabaci whitefly species complex is the most damaging in terms of their broad crop host range and its ability to serve as vector for over 300 plant viruses. Whitefly genomes of the species complex provide valuable genomic data; however, transposable elements (TEs) within the species complex remain unexplored. This study provides the first accurate exploration of TE content within the B. tabaci species complex.Results This study identified an average of 40.61% of the genomes of three whitefly species (MEAM1, MEDQ, and SSA-ECA) consists of TEs. Majority of the TEs identified were DNA transposons (22.85% average) while SINEs (0.14% average) were the least represented. This study also compared the TE content the three whitefly genomes with three other hemipteran genomes and found a significant difference in the presence of DNA transposons and LINEs. A total of 63 TE superfamilies were identified to be present across the three whitefly species (39 DNA transposons, six LTR, 16 LINE, and two SINE) of which 11 TE superfamilies were identified to not be present in the three other hemipteran genomes (nine DNA transposon, and two LINE). This study is the first to characterize TEs found within different B. tabaci species and has created a standardized annotation workflow that could be used to analyze future whitefly genomes.Conclusion This study is the first to characterize the landscape of TEs within the B. tabaci species complex. The characterization of these elements within the three whitefly genomes shows that TEs occupy a significant portion of the whitefly genome, majority of which are DNA transposons. This study also identified TE superfamilies of note and provides a framework for future TE studies within the species complex.

背景白蝇是一种农业害虫，已在全球范围内造成负面影响，并导致严重的经济损失。烟粉虱（Bemisia tabaci whitefly）物种复合体具有广泛的作物宿主范围和作为300多种植物病毒载体的能力，是最具破坏性的。该物种复合体的白蝇基因组提供了有价值的基因组数据；然而，物种复合体中的转座元件（TE）仍未被探索。本研究首次对烟粉虱物种复合体中的TE含量进行了准确的探索。结果本研究确定三种粉虱（MEAM1、MEDQ和SSA-ECA）的基因组中平均40.61%由TE组成。鉴定的大多数TE是DNA转座子（平均22.85%），而SINE（平均0.14%）的代表性最低。这项研究还将三个粉蝶基因组的TE含量与其他三个半翅目基因组进行了比较，发现DNA转座子和LINE的存在存在存在显著差异。共有63个TE超家族被鉴定存在于三个粉蝶物种中（39个DNA转座子、6个LTR、16个LINE和2个SINE），其中11个TE超家庭被鉴定不存在于其他三个半翅目基因组中（9个DNA转座子和2个LINE）。这项研究首次对不同烟粉虱物种中发现的TE进行了表征，并创建了一个标准化的注释工作流程，可用于分析未来的粉虱基因组。结论本研究首次对烟粉虱群落中的TE景观进行了表征。三个粉虱基因组中这些元素的特征表明，TE占据了粉虱基因组的重要部分，其中大多数是DNA转座子。这项研究还确定了值得注意的TE超家族，并为未来在物种复合体中进行TE研究提供了框架。

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引用次数: 0

KRAB zinc finger protein ZNF676 controls the transcriptional influence of LTR12-related endogenous retrovirus sequences. KRAB 锌指蛋白 ZNF676 控制着 LTR12 相关内源性逆转录病毒序列的转录影响。

IF 4.9 2区生物学 Q1 GENETICS & HEREDITY

Mobile DNA

Pub Date : 2022-01-18 DOI: 10.1186/s13100-021-00260-0

Alexandra Iouranova, Delphine Grun, Tamara Rossy, Julien Duc, Alexandre Coudray, Michael Imbeault, Jonas de Tribolet-Hardy, Priscilla Turelli, Alexandre Persat, Didier Trono

Background: Transposable element-embedded regulatory sequences (TEeRS) and their KRAB-containing zinc finger protein (KZFP) controllers are increasingly recognized as modulators of gene expression. We aim to characterize the contribution of this system to gene regulation in early human development and germ cells.

Results: Here, after studying genes driven by the long terminal repeat (LTR) of endogenous retroviruses, we identify the ape-restricted ZNF676 as the sequence-specific repressor of a subset of contemporary LTR12 integrants responsible for a large fraction of transpochimeric gene transcripts (TcGTs) generated during human early embryogenesis. We go on to reveal that the binding of this KZFP correlates with the epigenetic marking of these TEeRS in the germline, and is crucial to the control of genes involved in ciliogenesis/flagellogenesis, a biological process that dates back to the last common ancestor of eukaryotes.

Conclusion: These results illustrate how KZFPs and their TE targets contribute to the evolutionary turnover of transcription networks and participate in the transgenerational inheritance of epigenetic traits.

背景：可转座元件嵌入调控序列（TEeRS）及其含KRAB锌指蛋白（KZFP）的调控因子越来越被认为是基因表达的调控因子。我们的目的是描述这一系统对人类早期发育和生殖细胞中基因调控的贡献：结果：在对内源性逆转录病毒长末端重复序列（LTR）驱动的基因进行研究后，我们发现猿限制性 ZNF676 是当代 LTR12 整合子集的序列特异性抑制因子，它负责人类早期胚胎发育过程中产生的大部分跨单体基因转录本（TcGTs）。我们接着揭示了这种 KZFP 的结合与这些 TEeRS 在生殖系中的表观遗传标记相关，并且对控制参与纤毛生成/鞭毛生成的基因至关重要，这一生物过程可追溯到真核生物的最后一个共同祖先：这些结果说明了 KZFPs 及其 TE 靶标是如何促进转录网络的进化更替并参与表观遗传特征的跨代遗传的。

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引用次数: 0

Exploring Material Design Space with a Deep-Learning Guided Genetic Algorithm 用深度学习引导遗传算法探索材料设计空间

IF 4.9 2区生物学 Q1 GENETICS & HEREDITY

Mobile DNA

Pub Date : 2022-01-01 DOI: 10.4230/LIPIcs.DNA.28.4

Kuan-Lin Chen, Rebecca Schulman

Designing complex, dynamic yet multi-functional materials and devices is challenging because the design spaces for these materials have numerous interdependent and often conflicting constraints. Taking inspiration from advances in artificial intelligence and their applications in material discovery, we propose a computational method for designing metamorphic DNA-co-polymerized hydrogel structures. The method consists of a coarse-grained simulation and a deep learning-guided optimization system for exploring the immense design space of these structures. Here, we develop a simple numeric simulation of DNA-co-polymerized hydrogel shape change and seek to find designs for structured hydrogels that can fold into the shapes of different Arabic numerals in different actuation states. We train a convolutional neural network to classify and score the geometric outputs of the coarse-grained simulation to provide autonomous feedback for design optimization. We then construct a genetic algorithm that generates and selects large batches of material designs that compete with one another to evolve and converge on optimal objective-matching designs. We show that we are able to explore the large design space and learn important parameters and traits. We identify vital relationships between the material scale size and the range of shape change that can be achieved by individual domains and we elucidate trade-offs between different design parameters. Finally, we discover material designs capable of transforming into multiple different digits in different actuation states.

设计复杂、动态但多功能的材料和设备是具有挑战性的，因为这些材料的设计空间有许多相互依存且经常相互冲突的限制。从人工智能的进步及其在材料发现中的应用中获得灵感，我们提出了一种设计变质dna共聚合水凝胶结构的计算方法。该方法由粗粒度模拟和深度学习引导优化系统组成，用于探索这些结构的巨大设计空间。在这里，我们开发了dna共聚合水凝胶形状变化的简单数值模拟，并寻求在不同驱动状态下可以折叠成不同阿拉伯数字形状的结构水凝胶的设计。我们训练卷积神经网络对粗粒度模拟的几何输出进行分类和评分，为设计优化提供自主反馈。然后，我们构建了一个遗传算法，该算法生成并选择大量相互竞争的材料设计，以进化并收敛于最优目标匹配设计。我们表明，我们能够探索更大的设计空间，并学习重要的参数和特征。我们确定了材料尺寸和单个领域可以实现的形状变化范围之间的重要关系，并阐明了不同设计参数之间的权衡。最后，我们发现材料设计能够在不同的驱动状态下转换成多个不同的数字。

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引用次数: 0

Modelling and Optimisation of a DNA Stack Nano-Device Using Probabilistic Model Checking 使用概率模型检查的DNA堆叠纳米器件的建模和优化

IF 4.9 2区生物学 Q1 GENETICS & HEREDITY

Mobile DNA

Pub Date : 2022-01-01 DOI: 10.4230/LIPIcs.DNA.28.5

Bowen Li, N. Mackenzie, Ben Shirt-Ediss, N. Krasnogor, P. Zuliani

A DNA stack nano-device is a bio-computing system that can read and write molecular signals based on DNA-DNA hybridisation and strand displacement. In vitro implementation of the DNA stack faces a number of challenges affecting the performance of the system. In this work, we apply probabilistic model checking to analyse and optimise the DNA stack system. We develop a model framework based on continuous-time Markov chains to quantitatively describe the system behaviour. We use the PRISM probabilistic model checker to answer two important questions: 1) What is the minimum required incubation time to store a signal? And 2) How can we maximise the yield of the system? The results suggest that the incubation time can be reduced from 30 minutes to 5-15 minutes depending on the stack operation stage. In addition, the optimised model shows a 40% increase in the target stack yield. project “Synthetic Portabolomics: Leading the way at the crossroads of the Digital and the Bio Economies” (EP/N031962/1). Krasnogor was supported by the Royal Academy of Engineering under the Chairs in Emerging Technologies scheme.

DNA堆叠纳米器件是一种基于DNA-DNA杂交和链位移的分子信号读写生物计算系统。DNA堆栈的体外实现面临许多影响系统性能的挑战。在这项工作中，我们应用概率模型检查来分析和优化DNA堆栈系统。我们开发了一个基于连续时间马尔可夫链的模型框架来定量描述系统行为。我们使用PRISM概率模型检查器来回答两个重要问题:1)存储信号所需的最小潜伏期是多少?2)我们如何使系统的收益最大化?结果表明，根据堆垛阶段的不同，孵育时间可从30分钟缩短至5-15分钟。此外，优化后的模型显示目标堆产量提高了40%。项目“合成组合组学:在数字经济和生物经济的十字路口引领道路”(EP/N031962/1)。Krasnogor得到了皇家工程院新兴技术项目主席的支持。

引用次数: 1

A Coupled Reconfiguration Mechanism for Single-Stranded DNA Strand Displacement Systems 单链DNA链置换系统的耦合重配置机制

IF 4.9 2区生物学 Q1 GENETICS & HEREDITY

Mobile DNA

Pub Date : 2022-01-01 DOI: 10.4230/LIPIcs.DNA.28.3

H. Johnson, A. Condon

DNA Strand Displacement (DSD) systems model basic reaction rules, such as toehold-mediated strand displacement and 4-way branch migration, that modify complexes of bound DNA strands. DSD systems have been widely used to design and reason about the correctness of molecular programs, including implementations of logic circuits, neural networks, and Chemical Reaction Networks. Such implementations employ a valuable toolkit of mechanisms – sequences of basic reaction rules – that achieve catalysis, reduce errors (e.g., due to leak), or simulate simple computational units such as logic gates, both in solution and on surfaces. Expanding the DSD toolkit of DSD mechanisms can lead to new and better ways of programming with DNA. Here we introduce a new mechanism, which we call controlled reconfiguration . We describe one example where two single-stranded DSD complexes interact, changing the bonds in both complexes in a way that would not be possible for each independently on its own via the basic reaction rules allowed by the model. We use coupled reconfiguration to refer to instances of controlled reconfiguration in which two reactants change each other in this way. We note that our DSD model disallows pseudoknots and that properties of our coupled reconfiguration construction rely on this restriction of the model. A key feature of our coupled reconfiguration example, which distinguishes it from mechanisms (such as 3-way strand displacement or 4-way branch migration) that are typically used to implement molecular programs, is that the reactants are single-stranded. Leveraging this feature, we show how to use coupled reconfiguration to implement Chemical Reaction Networks (CRNs), with a DSD system that has both single-stranded signals (which represent the species of the CRN) and single-stranded fuels (which drive the CRN reactions). Our implementation also has other desirable properties; for example it is capable of implementing reversible CRNs and uses just two distinct toeholds. We discuss drawbacks of our implementation, particularly the reliance on pseudoknot-freeness for correctness, and suggest directions for future research that can provide further insight on the capabilities and limitations of controlled reconfiguration. computing (DSD) systems. a particularly well-studied abstract model of well-mixed chemical systems, in which many interesting programs can be and have been written [2, 3, 28, 36, 41]. Moreover, arbitrary CRNs can be transformed into DSD systems that implement the original CRN [7, 10, 30, 37, 39].

DNA链位移(DSD)系统模拟了基本的反应规则，如支点介导的链位移和4向分支迁移，这些反应规则修饰了结合DNA链的复合物。DSD系统已被广泛用于设计和推理分子程序的正确性，包括逻辑电路、神经网络和化学反应网络的实现。这样的实现采用了一个有价值的机制工具包——基本反应规则序列——来实现催化，减少错误(例如，由于泄漏)，或模拟简单的计算单元，如逻辑门，无论是在溶液中还是在表面上。扩展DSD机制的DSD工具包可以带来新的、更好的DNA编程方法。这里我们引入一种新的机制，我们称之为受控重构。我们描述了一个例子，其中两个单链DSD配合物相互作用，改变了两个配合物中的键，通过模型允许的基本反应规则，每个配合物都不可能独立地改变键。我们使用耦合重构来指两个反应物以这种方式相互改变的受控重构实例。我们注意到我们的DSD模型不允许假结，并且我们的耦合重构结构的性质依赖于模型的这一限制。我们的耦合重构示例的一个关键特征是，反应物是单链的，这与通常用于实现分子程序的机制(如3向链位移或4向分支迁移)不同。利用这一特性，我们展示了如何使用耦合重构来实现化学反应网络(CRN)，其中DSD系统同时具有单链信号(代表CRN的种类)和单链燃料(驱动CRN反应)。我们的实现还具有其他理想的属性;例如，它能够实现可逆的crn，并且只使用两个不同的支点。我们讨论了我们实现的缺点，特别是对伪结无性的依赖，并提出了未来研究的方向，可以进一步了解受控重构的能力和局限性。计算机系统。一种对混合良好的化学系统进行了特别深入研究的抽象模型，在这种模型中可以编写出许多有趣的程序[2,3,28,36,41]。此外，任意CRN都可以转化为实现原始CRN的DSD系统[7,10,30,37,39]。

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引用次数: 1

Fast and Robust Strand Displacement Cascades via Systematic Design Strategies 快速和强大的链位移级联通过系统的设计策略

IF 4.9 2区生物学 Q1 GENETICS & HEREDITY

Mobile DNA

Pub Date : 2022-01-01 DOI: 10.4230/LIPIcs.DNA.28.1

T. Kennedy, Cadence Pearce, Chris Thachuk

A barrier to wider adoption of molecular computation is the difficulty of implementing arbitrary chemical reaction networks (CRNs) that are robust and replicate the kinetics of designed behavior. DNA Strand Displacement (DSD) cascades have been a favored technology for this purpose due to their potential to emulate arbitrary CRNs and known principles to tune their reaction rates. Progress on leakless cascades has demonstrated that DSDs can be arbitrarily robust to spurious “leak” reactions when incorporating systematic domain level redundancy. These improvements in robustness result in slower kinetics of designed reactions. Existing work has demonstrated the kinetic and thermodynamic effects of sequence mismatch introduction and elimination during displacement. We present a systematic, sequence modification strategy for optimizing the kinetics of leakless cascades without practical cost to their robustness. An in-depth case study explores the effects of this optimization when applied to a typical leakless translator cascade. Thermodynamic analysis of energy barriers and kinetic experimental data support that DSD cascades can be fast and robust.

分子计算广泛应用的一个障碍是实现任意化学反应网络(crn)的困难，这些网络是稳健的，可以复制设计行为的动力学。DNA链位移(DSD)级联由于其模拟任意crn的潜力和调节其反应速率的已知原理，因此一直是一种受欢迎的技术。无泄漏级联的进展表明，当纳入系统域级冗余时，dsd可以对虚假的“泄漏”反应具有任意鲁棒性。鲁棒性的这些改进导致设计反应的动力学变慢。现有的工作已经证明了置换过程中序列失配的引入和消除对动力学和热力学的影响。我们提出了一种系统的、序列修改策略来优化无泄漏级联的动力学，而不会对其鲁棒性造成实际损失。一个深入的案例研究探讨了这种优化在应用于典型的无泄漏翻译器级联时的效果。能量势垒的热力学分析和动力学实验数据支持了DSD级联的快速和鲁棒性。

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引用次数: 1

Migrators within migrators: exploring transposable element dynamics in the monarch butterfly, Danaus plexippus 迁徙者中的迁徙者:探索帝王蝶的转座因子动力学

IF 4.9 2区生物学 Q1 GENETICS & HEREDITY

Mobile DNA

Pub Date : 2021-09-28 DOI: 10.1101/2021.09.28.462135

Tobias Baril, Alex Hayward

Lepidoptera (butterflies and moths) are an important model system in ecology and evolution. A high-quality chromosomal genome assembly is available for the monarch butterfly (Danaus plexippus), but it lacks an in-depth transposable element (TE) annotation, presenting an opportunity to explore monarch TE dynamics and the impact of TEs on shaping the monarch genome. We find 6.21% of the monarch genome is comprised of TEs, a reduction of 6.85% compared to the original TE annotation performed on the draft genome assembly. Monarch TE content is low compared to two closely related species with available genomes, Danaus chrysippus (33.97% TE) and Danaus melanippus (11.87% TE). The biggest TE contributions to genome size in the monarch are LINEs and Penelope-like elements, and three newly identified families, r2-hero_dPle (LINE), penelope-1_dPle (Penelope-like), and hase2-1_dPle (SINE), collectively contribute 34.92% of total TE content. We find evidence of recent TE activity, with two novel Tc1 families rapidly expanding over recent timescales (tc1-1_dPle, tc1-2_dPle). LINE fragments show signatures of genomic deletions indicating a high rate of TE turnover. We investigate associations between TEs and wing colouration and immune genes and identify a three-fold increase in TE content around immune genes compared to other host genes. We provide a detailed TE annotation and analysis for the monarch genome, revealing a considerably smaller TE contribution to genome content compared to two closely related Danaus species with available genome assemblies. We identify highly successful novel DNA TE families rapidly expanding over recent timescales, and ongoing signatures of both TE expansion and removal highlight the dynamic nature of repeat content in the monarch genome. Our findings also suggest that insect immune genes are promising candidates for future interrogation of TE-mediated host adaptation.

鳞翅目(蝴蝶和飞蛾)是生态学和进化中重要的模式系统。高质量的黑脉金斑蝶(Danaus plexippus)染色体基因组组装是可用的，但它缺乏深入的转座元件(TE)注释，这为探索黑脉金斑蝶TE动力学和TE对形成黑脉金斑蝶基因组的影响提供了机会。我们发现6.21%的黑脉金斑蝶基因组由TE组成，与在基因组组装草图上进行的原始TE注释相比，减少了6.85%。黑脉金斑蝶(Danaus chrysippus)和黑脉金斑蝶(Danaus melanippus)的TE含量分别为33.97%和11.87%。TE对黑脉王基因组大小贡献最大的是LINEs和Penelope-like元件，其中新发现的r2-hero_dPle (LINE)、penelope-1_dPle (Penelope-like)和hase2-1_dPle (SINE)三个家族共贡献了34.92%的TE总含量。我们发现了最近TE活动的证据，两个新的Tc1家族在最近的时间尺度上迅速扩张(Tc1 - 1_dple, Tc1 - 2_dple)。LINE片段显示基因组缺失的特征，表明TE的高周转率。我们研究了TE与翅膀颜色和免疫基因之间的关系，并发现与其他宿主基因相比，免疫基因周围TE含量增加了三倍。我们对黑脉金斑蝶基因组进行了详细的TE注释和分析，发现与两种具有可用基因组片段的密切相关的Danaus物种相比，黑脉金斑蝶对基因组内容的贡献要小得多。我们发现了在最近的时间尺度上迅速扩展的非常成功的新DNA TE家族，并且TE扩展和去除的持续特征突出了帝王蝶基因组中重复内容的动态性质。我们的研究结果还表明，昆虫免疫基因是未来te介导的宿主适应研究的有希望的候选者。

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引用次数: 15

Unbiased proteomic mapping of the LINE-1 promoter using CRISPR Cas9. 利用 CRISPR Cas9 绘制 LINE-1 启动子的无偏蛋白质组图谱。

IF 4.7 2区生物学 Q1 GENETICS & HEREDITY

Mobile DNA

Pub Date : 2021-08-23 DOI: 10.1186/s13100-021-00249-9

Erica M Briggs, Paolo Mita, Xiaoji Sun, Susan Ha, Nikita Vasilyev, Zev R Leopold, Evgeny Nudler, Jef D Boeke, Susan K Logan

Background: The autonomous retroelement Long Interspersed Element-1 (LINE-1) mobilizes though a copy and paste mechanism using an RNA intermediate (retrotransposition). Throughout human evolution, around 500,000 LINE-1 sequences have accumulated in the genome. Most of these sequences belong to ancestral LINE-1 subfamilies, including L1PA2-L1PA7, and can no longer mobilize. Only a small fraction of LINE-1 sequences, approximately 80 to 100 copies belonging to the L1Hs subfamily, are complete and still capable of retrotransposition. While silenced in most cells, many questions remain regarding LINE-1 dysregulation in cancer cells.

Results: Here, we optimized CRISPR Cas9 gRNAs to specifically target the regulatory sequence of the L1Hs 5'UTR promoter. We identified three gRNAs that were more specific to L1Hs, with limited binding to older LINE-1 sequences (L1PA2-L1PA7). We also adapted the C-BERST method (dCas9-APEX2 Biotinylation at genomic Elements by Restricted Spatial Tagging) to identify LINE-1 transcriptional regulators in cancer cells. Our LINE-1 C-BERST screen revealed both known and novel LINE-1 transcriptional regulators, including CTCF, YY1 and DUSP1.

Conclusion: Our optimization and evaluation of gRNA specificity and application of the C-BERST method creates a tool for studying the regulatory mechanisms of LINE-1 in cancer. Further, we identified the dual specificity protein phosphatase, DUSP1, as a novel regulator of LINE-1 transcription.

背景：自主性逆转录因子长穿插元件-1（LINE-1）通过复制和粘贴机制，利用 RNA 中间体（逆转录）进行调动。在整个人类进化过程中，基因组中积累了约 500,000 个 LINE-1 序列。这些序列中的大部分属于祖先的 LINE-1 亚家族，包括 L1PA2-L1PA7，已经无法再移动。只有一小部分属于L1Hs亚家族的LINE-1序列（约80至100个拷贝）是完整的，仍能进行逆转录。虽然LINE-1在大多数细胞中处于沉默状态，但关于癌细胞中LINE-1的失调仍存在许多问题：在这里，我们对CRISPR Cas9 gRNA进行了优化，以特异性靶向L1Hs 5'UTR启动子的调控序列。我们发现了三种对L1Hs更具特异性的gRNA，它们与较早的LINE-1序列（L1PA2-L1PA7）的结合有限。我们还采用了C-BERST方法（dCas9-APEX2 Biotinylation at genomic Elements by Restricted Spatial Tagging）来鉴定癌细胞中的LINE-1转录调节因子。我们的LINE-1 C-BERST筛选发现了已知的和新的LINE-1转录调控因子，包括CTCF、YY1和DUSP1：结论：我们对 gRNA 特异性的优化和评估以及 C-BERST 方法的应用为研究 LINE-1 在癌症中的调控机制提供了一种工具。此外，我们还发现双重特异性蛋白磷酸酶 DUSP1 是 LINE-1 转录的新型调控因子。

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引用次数: 0

TE Hub: A community-oriented space for sharing and connecting tools, data, resources, and methods for transposable element annotation. TE Hub:面向社区的空间，用于共享和连接可转置元素注释的工具、数据、资源和方法。

IF 4.9 2区生物学 Q1 GENETICS & HEREDITY

Mobile DNA

Pub Date : 2021-06-21 DOI: 10.1186/s13100-021-00244-0

Tyler A Elliott, Tony Heitkam, Robert Hubley, Hadi Quesneville, Alexander Suh, Travis J Wheeler

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.

转座因子(te)广泛存在于大多数真核生物基因组中，在进化和功能上发挥着强大而多样的作用。对它们独特生物学的研究推动了大量数据库、软件、分类系统和注释指南的创建。可用的与te相关的方法和资源的多样性引起了兼容性问题，对于寻求直接指导或材料的研究人员和传播者来说可能是压倒性的。为了应对这些挑战，我们启动了一个新的资源TE Hub，它提供了一个空间，让TE社区的成员可以协作记录和创建资源和方法。该空间包括(1)一个以开放的wiki框架(https://tehub.org)组织的网站，(2)一个通过Twitter账户和Slack频道进行的对话框架，以及(3)双月一次的Hub Update视频聊天平台的开发。除了作为集中式存储库和通信平台之外，TE Hub还为改进各种工具和协议的集成、标准化和有效性奠定了基础。我们邀请TE社区，包括TE识别和分析方面的新手和专家，加入我们，扩大我们面向社区的资源。

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引用次数: 7

Molecular Machines from Topological Linkages 拓扑连杆的分子机器

IF 4.9 2区生物学 Q1 GENETICS & HEREDITY

Mobile DNA

Pub Date : 2021-01-01 DOI: 10.4230/LIPIcs.DNA.27.7

Keenan Breik, Austin Luchsinger, D. Soloveichik

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

生命是建立在极其复杂的分子机器之上的，它们的行为结合了机械和化学作用。从第一性原理制造类似复杂的奈米装置，仍是生物工程尚未实现的目标。在本文中，我们形式化了一个结合化学键的机械运动(机械连杆)的简单模型。该模型使用具有双链刚性链接和单链柔性关节和结合位点的DNA进行自然实现。令人惊讶的是，我们证明了在一个理想化的拓扑模型中保留了许多复杂的行为，该模型只考虑了连杆的图连通性。我们展示了许多工件，包括布尔逻辑、催化剂、燃料马达和化学-机械耦合，所有这些都可以在拓扑模型中被理解和推理。所获得的各种行为支持了拓扑化学键在理解和工程复杂分子行为中的应用。2012 ACM学科分类:计算理论→计算模型;计算理论→计算几何

引用次数: 1