DNA damage response: Damage by Helicobacter pylori

DNA损伤反应:幽门螺杆菌损伤

Infection with the gastric bacterium Helicobacter pylori can cause chromosomal instability (CIN) and promote tumorigenesis. Koeppel et al. compared the DNA damage response (DDR) following H. pylori infection with that induced by other genotoxic treatments in human gastric cells and observed reduced

[详细]

  • Nature Reviews Molecular Cell Biology 16, 391 (2015)
  • 5年前
  • Research Highlight

Dynamical behavior of Borospherene: A Nanobubble

对borospherene动力学行为:一个气泡

The global minimum structure of borospherene (B40) is a cage, comprising two hexagonal and four heptagonal rings. Born-Oppenheimer Molecular Dynamics simulations show that continuous conversions in between six and seven membered rings take place. The activation energy barrier for such a transformation is found to be 14.3 kcal·mol−1. The completely delocalized σ- and π-frameworks, as well as the conservation of the bonding pattern during rearrangement, facilitate the dynamical behavior of B40. B40 is predicted to act as a support-free spherical two-dimensional liquid at moderate temperature. In other words, B40 could be called as a nanobubble.

[详细]

  • Scientific Reports 5
  • 5年前
  • Article

A unique in vivo approach for investigating antimicrobial materials utilizing fistulated animals

一个独特的体内方法为研究抗菌材料利用瘘管动物

Unique in vivo tests were conducted through the use of a fistulated ruminant, providing an ideal environment with a diverse and vibrant microbial community. Utilizing such a procedure can be especially invaluable for investigating the performance of antimicrobial materials related to human and animal related infections. In this pilot study, it is shown that the rumen of a fistulated animal provides an excellent live laboratory for assessing the properties of antimicrobial materials. We investigate microbial colonization onto model nanocomposites based on silver (Ag) nanoparticles at different concentrations into polydimethylsiloxane (PDMS). With implantable devices posing a major risk for hospital-acquired infections, the present study provides a viable solution to understand microbial colonization with the potential to reduce the incidence of infection through the introduction of Ag nanoparticles at the optimum concentrations. In vitro measurements were also conducted to show the validity of the approach. An optimal loading of 0.25 wt% Ag is found to show the greatest antimicrobial activity and observed through the in vivo tests to reduce the microbial diversity colonizing the surface.

[详细]

  • Scientific Reports 5
  • 5年前
  • Article

Conservation of Olfactory Avoidance in Drosophila Species and Identification of Repellents for Drosophila suzukii

在果蝇和樱桃果蝇驱虫剂鉴定嗅障保护

Flying insects use olfaction to navigate towards fruits in complex odor environments with remarkable accuracy. Some fruits change odor profiles substantially during ripening and related species can prefer different stages. In Drosophila species attractive odorants have been studied extensively, but little is understood about the role of avoidance pathways. In order to examine the role of the avoidance cue CO2 emitted from fruit on behavior of two species with different ripening stage preferences, we investigated the CO2-detection pathway in Drosophila melanogaster and Drosophila suzukii, a harmful pest of fruits. Avoidance to CO2 is not conserved in D. suzukii suggesting a behavioral adaptation that could facilitate attraction to younger fruit with higher CO2 emission levels. We investigated known innate avoidance pathways from five species at different evolutionary distances: D. melanogaster, D. yakuba, D. suzukii, D. pseudoobscura and D. virilis. Surprisingly, only DEET shows strong repellency across all species, whereas CO2, citronellal and ethyl 3-hydroxybutyrate show only limited conservation. These findings guide us to test recently discovered safe DEET substitutes, and we identify one that protects fruits from D. suzukii thus providing a new behavioral strategy for controlling agricultural pests.

[详细]

  • Scientific Reports 5
  • 5年前
  • Article

Optical regulation of cell chain

细胞光学调节链

Formation of cell chains is a straightforward and efficient method to study the cell interaction. By regulating the contact sequence and interaction distance, the influence of different extracellular cues on the cell interaction can be investigated. However, it faces great challenges in stable retaining and precise regulation of cell chain, especially in cell culture with relatively low cell concentration. Here we demonstrated an optical method to realize the precise regulation of cell chain, including removing or adding a single cell, adjusting interaction distance, and changing cell contact sequence. After injecting a 980-nm wavelength laser beam into a tapered optical fiber probe (FP), a cell chain of Escherichia colis (E. colis) is formed under the optical gradient force. By manipulating another FP close to the cell chain, a targeted E. coli cell can be trapped by the FP and removed from the chain. Further, the targeted cell can be added back to the chain at different positions to change the cell contact sequence. The experiments were interpreted by numerical simulations and the impact of cell sizes and shapes on this method was analyzed.

[详细]

  • Scientific Reports 5
  • 5年前
  • Article

GONAD: Genome-editing via Oviductal Nucleic Acids Delivery system: a novel microinjection independent genome engineering method in mice

性腺:基因组编辑通过输卵管核酸递送系统:一个新的独立的基因工程小鼠注射方法

Microinjection is considered the gold standard technique for delivery of nucleic acids (NAs; transgenes or genome editing tools such as CRISPR/Cas9 systems) into embryos, for creating genetically modified organisms. It requires sophisticated equipment as wel as well-trained and highly skilled personnel to perform the micro-injection technique. Here, we describe a novel and simple microinjection-independent technique, called Genome-editing via Oviductal Nucleic Acids Delivery (GONAD). Using GONAD, we show that NAs (e.g., eGFP mRNA or Cas9 mRNA/sgRNAs) can be effectively delivered to pre-implantation embryos within the intact mouse oviduct by a simple electroporation method, and result in the desired genetic modification in the embryos. Thus GONAD can bypass many complex steps in transgenic technology such as isolation of zygotes, microinjection of NAs into them, and their subsequent transfer to pseudo-pregnant animals. Furthermore, this method can potentially be used for genome editing in species other than mice.

[详细]

  • Scientific Reports 5
  • 5年前
  • Article

Quantum coherence and correlations in quantum system

在量子系统中的量子相干和相关性

Criteria of measure quantifying quantum coherence, a unique property of quantum system, are proposed recently. In this paper, we first give an uncertainty-like expression relating the coherence and the entropy of quantum system. This finding allows us to discuss the relations between the entanglement and the coherence. Further, we discuss in detail the relations among the coherence, the discord and the deficit in the bipartite quantum system. We show that, the one-way quantum deficit is equal to the sum between quantum discord and the relative entropy of coherence of measured subsystem.

[详细]

  • Scientific Reports 5
  • 5年前
  • Article

Implementation of quantum state manipulation in a dissipative cavity

耗散腔中量子态操作的实现

We discuss a method to perform dissipation-assisted quantum state manipulation in a cavity. We show that atomic spontaneous emission and cavity decay might be exploited to drive many atoms into many-body steady-state entanglement. Our protocol offers a dramatic improvement in fidelity when noise strength increases. Moreover, the dephasing noise is suppressed effectively by showing that high-fidelity target state can be obtained in a dissipative environment.

[详细]

  • Scientific Reports 5
  • 5年前
  • Article

Improving prediction of secondary structure, local backbone angles, and solvent accessible surface area of proteins by iterative deep learning

提高二级结构预测,本地骨干的角度,并通过迭代深度学习蛋白质溶剂可及表面积

Direct prediction of protein structure from sequence is a challenging problem. An effective approach is to break it up into independent sub-problems. These sub-problems such as prediction of protein secondary structure can then be solved independently. In a previous study, we found that an iterative use of predicted secondary structure and backbone torsion angles can further improve secondary structure and torsion angle prediction. In this study, we expand the iterative features to include solvent accessible surface area and backbone angles and dihedrals based on Cα atoms. By using a deep learning neural network in three iterations, we achieved 82% accuracy for secondary structure prediction, 0.76 for the correlation coefficient between predicted and actual solvent accessible surface area, 19° and 30° for mean absolute errors of backbone φ and ψ angles, respectively, and 8° and 32° for mean absolute errors of Cα-based θ and τ angles, respectively, for an independent test dataset of 1199 proteins. The accuracy of the method is slightly lower for 72 CASP 11 targets but much higher than those of model structures from current state-of-the-art techniques. This suggests the potentially beneficial use of these predicted properties for model assessment and ranking.

[详细]

  • Scientific Reports 5
  • 5年前
  • Article

SNSMIL, a real-time single molecule identification and localization algorithm for super-resolution fluorescence microscopy

snsmil,实时单分子识别与定位算法的超分辨率荧光显微镜

Single molecule localization based super-resolution fluorescence microscopy offers significantly higher spatial resolution than predicted by Abbe’s resolution limit for far field optical microscopy. Such super-resolution images are reconstructed from wide-field or total internal reflection single molecule fluorescence recordings. Discrimination between emission of single fluorescent molecules and background noise fluctuations remains a great challenge in current data analysis. Here we present a real-time, and robust single molecule identification and localization algorithm, SNSMIL (Shot Noise based Single Molecule Identification and Localization). This algorithm is based on the intrinsic nature of noise, i.e., its Poisson or shot noise characteristics and a new identification criterion, QSNSMIL, is defined. SNSMIL improves the identification accuracy of single fluorescent molecules in experimental or simulated datasets with high and inhomogeneous background. The implementation of SNSMIL relies on a graphics processing unit (GPU), making real-time analysis feasible as shown for real experimental and simulated datasets.

[详细]

  • Scientific Reports 5
  • 5年前
  • Article

Bloodstain Pattern Analysis: implementation of a fluid dynamic model for position determination of victims

血迹形态分析:对受害者的位置确定的流体动力学模型的实现

Bloodstain Pattern Analysis is a forensic discipline in which, among others, the position of victims can be determined at crime scenes on which blood has been shed. To determine where the blood source was investigators use a straight-line approximation for the trajectory, ignoring effects of gravity and drag and thus overestimating the height of the source. We determined how accurately the location of the origin can be estimated when including gravity and drag into the trajectory reconstruction. We created eight bloodstain patterns at one meter distance from the wall. The origin’s location was determined for each pattern with: the straight-line approximation, our method including gravity, and our method including both gravity and drag. The latter two methods require the volume and impact velocity of each bloodstain, which we are able to determine with a 3D scanner and advanced fluid dynamics, respectively. We conclude that by including gravity and drag in the trajectory calculation, the origin’s location can be determined roughly four times more accurately than with the straight-line approximation. Our study enables investigators to determine if the victim was sitting or standing, or it might be possible to connect wounds on the body to specific patterns, which is important for crime scene reconstruction.

[详细]

  • Scientific Reports 5
  • 5年前
  • Article

Bandage: interactive visualisation of de novo genome assemblies

绷带:从头基因组组装的交互式可视化

Summary: While de novo assembly graphs contain assembled contigs (nodes), the connections between those contigs (edges) are difficult for users to access. Bandage (a Bioinformatics Application for Navigating De novo Assembly Graphs Easily) is a tool for visualising assembly graphs with connections. Users can zoom in to specific areas of the graph and interact with it by moving nodes, adding labels, changing colours and extracting sequences. BLAST searches can be performed within the Bandage GUI and the hits are displayed as highlights in the graph. By displaying connections between contigs, Bandage presents new possibilities for analysing de novo assemblies that are not possible through investigation of contigs alone.

Availability and implementation: Source code and binaries are freely available at https://github.com/rrwick/Bandage. Bandage is implemented in C++ and supported on Linux, OS X and Windows.

Contact: rrwick@gmail.com

Supplementary Information:A full feature list and screenshots are available at Bioinformatics online and http://rrwick.github.io/Bandage.

[详细]

  • Bioinformatics
  • 5年前
  • APPLICATIONS NOTE

forna (force-directed RNA): Simple and Effective Online RNA Secondary Structure Diagrams

福纳(力导向RNA):简单而有效的在线RNA二级结构图

Motivation: The secondary structure of RNA is integral to the variety of functions it carries out in the cell and its depiction allows researchers to develop hypotheses about which nucleotides and base pairs are functionally relevant. Current approaches to visualizing secondary structure provide an adequate platform for the conversion of static text-based representations to two dimensional images, but are limited in their offer of interactivity as well as their ability to display larger structures, multiple structures and pseudoknotted structures.

Results: In this paper we present forna, a web-based tool for displaying RNA secondary structure which allows users to easily convert sequences and secondary structures to clean, concise and customizable visualizations. It supports, among other features, the simultaneous visualization of multiple structures, the display of pseudoknotted structures, the interactive editing of the displayed structures, and the automatic generation of secondary structure diagrams from PDB files. It requires no software installation apart from a modern web browser.

Availability: The web interface of forna is available at http://rna.tbi.univie.ac.at/forna while the source code is available on github at www.github.com/pkerpedjiev/forna.

Contact: pkerp@tbi.univie.ac.at

[详细]

  • Bioinformatics
  • 5年前
  • APPLICATIONS NOTE

Sincell: an R/Bioconductor package for statistical assessment of cell-state hierarchies from single-cell RNA-seq

sincell:一种从单细胞的RNA序列的细胞状态层次的统计评估R/Bioconductor包

Summary: Cell differentiation processes are achieved through a continuum of hierarchical intermediate cell-states that might be captured by single-cell RNA seq. Existing computational approaches for the assessment of cell-state hierarchies from single-cell data might be formalized under a general framework composed of i) a metric to assess cell-to-cell similarities (with or without a dimensionality reduction step), and ii) a graph-building algorithm (optionally making use of a cell clustering step). The Sincell R package implements a methodological toolbox allowing flexible workflows under such a framework. Furthermore, Sincell contributes new algorithms to provide cell-state hierarchies with statistical support while accounting for stochastic factors in single-cell RNA seq. Graphical representations and functional association tests are provided to interpret hierarchies. The functionalities of Sincell are illustrated in a real case study, which demonstrates its ability to discriminate noisy from stable cell-state hierarchies.

Availability and implementation:

Sincell is an open-source R/Bioconductor package available at http://bioconductor.org/packages/3.1/bioc/html/sincell.html. A detailed manual and vignette is provided with the package.

Contact: antonio.rausell@isb-sib.ch

Supplementary Information: Supplementary data are available at Bioinformatics online.

[详细]

  • Bioinformatics
  • 5年前
  • APPLICATIONS NOTE

SAMHD1 is a single-stranded nucleic acid binding protein with no active site-associated nuclease activity

SAMHD1蛋白是一种单链核酸结合蛋白没有活性位点相关的核酸酶活性

The HIV-1 restriction factor SAMHD1 is a tetrameric enzyme activated by guanine nucleotides with dNTP triphosphate hydrolase activity (dNTPase). In addition to this established activity, there have been a series of conflicting reports as to whether the enzyme also possesses single-stranded DNA and/or RNA 3'-5' exonuclease activity. SAMHD1 was purified using three chromatography steps, over which the DNase activity was largely separated from the dNTPase activity, but the RNase activity persisted. Surprisingly, we found that catalytic and nucleotide activator site mutants of SAMHD1 with no dNTPase activity retained the exonuclease activities. Thus, the exonuclease activity cannot be associated with any known dNTP binding site. Monomeric SAMHD1 was found to bind preferentially to single-stranded RNA, while the tetrameric form required for dNTPase action bound weakly. ssRNA binding, but not ssDNA, induces higher-order oligomeric states that are distinct from the tetrameric form that binds dNTPs. We conclude that the trace exonuclease activities detected in SAMHD1 preparations arise from persistent contaminants that co-purify with SAMHD1 and not from the HD active site. An in vivo model is suggested where SAMHD1 alternates between the mutually exclusive functions of ssRNA binding and dNTP hydrolysis depending on dNTP pool levels and the presence of viral ssRNA.

[详细]

  • Nucleic Acids Research
  • 5年前
  • Nucleic Acid Enzymes

Multiplexed highly-accurate DNA sequencing of closely-related HIV-1 variants using continuous long reads from single molecule, real-time sequencing

多路高精度密切相关的HIV-1 DNA测序使用连续长单分子测序读取,实时

Single Molecule, Real-Time (SMRT®) Sequencing (Pacific Biosciences, Menlo Park, CA, USA) provides the longest continuous DNA sequencing reads currently available. However, the relatively high error rate in the raw read data requires novel analysis methods to deconvolute sequences derived from complex samples. Here, we present a workflow of novel computer algorithms able to reconstruct viral variant genomes present in mixtures with an accuracy of >QV50. This approach relies exclusively on Continuous Long Reads (CLR), which are the raw reads generated during SMRT Sequencing. We successfully implement this workflow for simultaneous sequencing of mixtures containing up to forty different >9 kb HIV-1 full genomes. This was achieved using a single SMRT Cell for each mixture and desktop computing power. This novel approach opens the possibility of solving complex sequencing tasks that currently lack a solution.

[详细]

  • Nucleic Acids Research
  • 5年前
  • Methods Online

Ribosomal protein L10(L12)4 autoregulates expression of the Bacillus subtilis rplJL operon by a transcription attenuation mechanism

核糖体蛋白L10(L12)的转录衰减机制rpljl操纵子的枯草芽孢杆菌4 autoregulates表达

Ribosomal protein genes are often controlled by autoregulatory mechanisms in which a protein encoded in the operon can either bind to newly synthesized rRNA during rapid growth or to a similar target in its mRNA during poor growth conditions. The rplJL operon encodes the ribosomal L10(L12)4 complex. In Escherichia coli L10(L12)4 represses its translation by binding to the rplJL leader transcript. We identified three RNA structures in the Bacillus subtilis rplJL leader transcript that function as an anti-antiterminator, antiterminator or intrinsic terminator. Expression studies with transcriptional and translational fusions indicated that L10(L12)4 represses rplJL expression at the transcriptional level. RNA binding studies demonstrated that L10(L12)4 stabilizes the anti-antiterminator structure, while in vitro transcription results indicated that L10(L12)4 promotes termination. Disruption of anti-antiterminator, antiterminator or terminator function by competitor oligonucleotides in vitro and by mutations in vivo demonstrated that each structure functions as predicted. Thus, rplJL expression is regulated by an autogenous transcription attenuation mechanism in which L10(L12)4 binding to the anti-antiterminator structure promotes termination. We also found that translation of a leader peptide increases rplJL expression, presumably by inhibiting Rho-dependent termination. Thus, the rplJL operon of B. subtilis is regulated by transcription attenuation and antitermination mechanisms.

[详细]

  • Nucleic Acids Research
  • 5年前
  • RNA

Induced folding in RNA recognition by Arabidopsis thaliana DCL1

通过拟南芥DCL1诱导的RNA识别折叠

DCL1 is the ribonuclease that carries out miRNA biogenesis in plants. The enzyme has two tandem double stranded RNA binding domains (dsRBDs) in its C-terminus. Here we show that the first of these domains binds precursor RNA fragments when isolated and cooperates with the second domain in the recognition of substrate RNA. Remarkably, despite showing RNA binding activity, this domain is intrinsically disordered. We found that it acquires a folded conformation when bound to its substrate, being the first report of a complete dsRBD folding upon binding. The free unfolded form shows tendency to adopt folded conformations, and goes through an unfolded bound state prior to the folding event. The significance of these results is discussed by comparison with the behavior of other dsRBDs.

[详细]

  • Nucleic Acids Research
  • 5年前
  • Structural Biology

Ca2+ enrichment in culture medium potentiates effect of oligonucleotides

钙的富集培养基中的增强作用的寡核苷酸

Antisense and RNAi-related oligonucleotides have gained attention as laboratory tools and therapeutic agents based on their ability to manipulate biological events in vitro and in vivo. We show that Ca2+ enrichment of medium (CEM) potentiates the in vitro activity of multiple types of oligonucleotides, independent of their net charge and modifications, in various cells. In addition, CEM reflects in vivo silencing activity more consistently than conventional transfection methods. Microscopic analysis reveals that CEM provides a subcellular localization pattern of oligonucleotides resembling that obtained by unassisted transfection, but with quantitative improvement. Highly monodispersed nanoparticles ~100 nm in size are found in Ca2+-enriched serum-containing medium regardless of the presence or absence of oligonucleotides. Transmission electron microscopy analysis reveals that the 100-nm particles are in fact an ensemble of much smaller nanoparticles ( ~ 15 nm). The presence of these nanoparticles is critical for the efficient uptake of various oligonucleotides. In contrast, CEM is ineffective for plasmids, which are readily transfected via the conventional calcium phosphate method. Collectively, CEM enables a more accurate prediction of the systemic activity of therapeutic oligonucleotides, while enhancing the broad usability of oligonucleotides in the laboratory.

[详细]

  • Nucleic Acids Research
  • 5年前
  • Methods Online

Transcription blockage by stable H-DNA analogs in vitro

转录阻滞在体外稳定H-DNA类似物

DNA sequences that can form unusual secondary structures are implicated in regulating gene expression and causing genomic instability. H-palindromes are an important class of such DNA sequences that can form an intramolecular triplex structure, H-DNA. Within an H-palindrome, the H-DNA and canonical B-DNA are in a dynamic equilibrium that shifts toward H-DNA with increased negative supercoiling. The interplay between H- and B-DNA and the fact that the process of transcription affects supercoiling makes it difficult to elucidate the effects of H-DNA upon transcription. We constructed a stable structural analog of H-DNA that cannot flip into B-DNA, and studied the effects of this structure on transcription by T7 RNA polymerase in vitro. We found multiple transcription blockage sites adjacent to and within sequences engaged in this triplex structure. Triplex-mediated transcription blockage varied significantly with changes in ambient conditions: it was exacerbated in the presence of Mn2+ or by increased concentrations of K+ and Li+. Analysis of the detailed pattern of the blockage suggests that RNA polymerase is sterically hindered by H-DNA and has difficulties in unwinding triplex DNA. The implications of these findings for the biological roles of triple-stranded DNA structures are discussed.

[详细]

  • Nucleic Acids Research
  • 5年前
  • Molecular Biology