scholarly journals High-Definition Electronic Genome Maps from Single Molecule Data

2017 ◽  
Author(s):  
John S. Oliver ◽  
Anthony Catalano ◽  
Jennifer R. Davis ◽  
Boris S. Grinberg ◽  
Timothy E. Hutchins ◽  
...  

With the advent of routine short-read genome sequencing has come a growing recognition of the importance of long-range, structural information in applications ranging from sequence assembly to the detection of structural variation. Here we describe the Nabsys solid-state detector capable of detecting tags on single molecules of DNA 100s of kilobases in length as they translocate through the detector at a velocity greater than 1 megabase pair per second. Sequence-specific tags are detected with a high signal-to-noise ratio. The physical distance between tags is determined after accounting for viscous drag-induced intramolecular velocity fluctuations. The accurate measurement of the physical distance between tags on each molecule and the ability of the detector to resolve distances between tags of less than 300 base-pairs enables the construction of high-density genome maps.

1980 ◽  
Vol 88 ◽  
pp. 53-57 ◽  
Author(s):  
Francis Fekel ◽  
Claud H. Lacy ◽  
J. Tomkin

The recent installation of a solid-state 1024-element silicon photodiode array detector (Reticon) at the coude focus of the 2.7 m McDonald Observatory reflector has greatly extended its limits of observation for binary and multiple systems which have weak and/or broad-lined components. This detector can produce extremely high signal-to-noise ratio observations and has high quantum efficiency over the wavelength region 3000-11000Å. The observational programs of three users of this device are described below.


2018 ◽  
Author(s):  
Gerti Beliu ◽  
Andreas Kurz ◽  
Alexander Kuhlemann ◽  
Lisa Behringer-Pliess ◽  
Natalia Wolf ◽  
...  

Genetic code expansion (GCE) technology allows the specific incorporation of functionalized noncanonical amino acids (ncAAs) into proteins. Here, we investigated the Diels-Alder reaction between trans-cyclooct-2-ene (TCO)-modified ncAAs, and 22 known and novel 1,2,4,5-tetrazine-dye conjugates spanning the entire visible wavelength range. A hallmark of this reaction is its fluorogenicity - the tetrazine moiety can elicit substantial quenching of the dye. We discovered that photoinduced electron transfer (PET) from the excited dye to tetrazine as the main quenching mechanism in red-absorbing oxazine and rhodamine derivatives. Upon reaction with dienophiles quenching interactions are reduced resulting in a considerable increase in fluorescence intensity. Efficient and specific labeling of all tetrazine-dyes investigated permits super-resolution microscopy with high signal-to-noise ratio even at the single-molecule level. The different cell permeability of tetrazine-dyes can be used advantageously for specific intra- and extracellular labeling of proteins and highly sensitive fluorescence imaging experiments in fixed and living cells.


2020 ◽  
Author(s):  
Sven A. Szilagyi ◽  
Moritz Burmeister ◽  
Q. Tyrell Davis ◽  
Gero L. Hermsdorf ◽  
Suman De ◽  
...  

AbstractObservation of highly dynamic processes inside living cells at the single molecule level is key for a quantitative understanding of biological systems. However, imaging of single molecules in living cells usually is limited by the spatial and temporal resolution, photobleaching and the signal-to-background ratio. To overcome these limitations, light-sheet microscopes with thin selective plane illumination have recently been developed. For example, a reflected light-sheet design combines the illumination by a thin light-sheet with a high numerical aperture objective for single-molecule detection. Here, we developed a reflected light-sheet microscope with active optics for fast, high contrast, two-color acquisition of z-stacks. We demonstrate fast volume scanning by imaging a two-color giant unilamellar vesicle (GUV) hemisphere. In addition, the high signal-to-noise ratio enabled the imaging and tracking of single lipids in the cap of a GUV. In the long term, the enhanced reflected scanning light sheet microscope enables fast 3D scanning of artificial membrane systems and cells with single-molecule sensitivity and thereby will provide quantitative and molecular insight into the operation of cells.


2021 ◽  
Author(s):  
Tslil Gabrieli ◽  
Yael Michaeli ◽  
Sigal Avraham ◽  
Dmitry Torchinsky ◽  
Matyas Juhasz ◽  
...  

ABSTRACTDNA methylation, specifically, methylation of cytosine (C) nucleotides at the 5-carbon position (5-mC), is the most studied and among the most significant epigenetic modifications. Here we developed a chemoenzymatic procedure to fluorescently label non-methylated cytosines in the CpG context allowing epigenetic profiling of single DNA molecules spanning hundreds of thousands of base pairs. For this method, a CpG methyltransferase was used to transfer an azide to cytosines from a synthetic S-adenosyl-l-methionine cofactor analog. A fluorophore was then clicked onto the DNA, reporting on the amount and position of non-methylated CpGs. We found that labeling efficiency was increased two-fold by the addition of a nucleosidase that degrades the inactive by-product of the azide-cofactor after labeling, and prevents its inhibitory effect. We first used the method to determine the decline in global DNA methylation in chronic lymphocytic leukemia patients and then performed whole genome methylation mapping of the model plant Arabidopsis thaliana. Our genome maps show high concordance with published methylation maps produced by bisulfite sequencing. Although mapping resolution is limited by optical detection to 500-1000 base pairs, the labeled DNA molecules produced by this approach are hundreds of thousands of base pairs long, allowing access to long repetitive and structurally variable genomic regions.


Author(s):  
Dorel Picovici ◽  
David Denieffe ◽  
Brian Carrig

Most of the existent games consist of multiple players, connected over a network, collaborating and competing in a virtual world. In this world, each player typically controls a single virtual entity. Communication between players can be achieved by sharing entity state information, such as positioning using synchronisation messages. These messages are periodically transmitted across the connecting network, and update the remote state of the virtual entity, which is the state replicated on other players’ computers. If the games are using the Internet as a connecting network, latency, jitter, and packet loss, can have a significant impact upon the service experienced by application user (end-user). More specifically, latency or delay can by introduced by various types of delays, such as propagation, serialisation, and queuing delays. Jitter is the variation in latency experienced by consecutive packets. Not all of the packets in a given flow will take the same path through the network. The time taken to traverse different routes is likely to vary due to factors such as their different physical distance, the number of hops, or physical link properties. On lower bandwidth links, which have a greater serialization delay, variation in packet lengths can introduce jitter. The size distribution and arrival patterns of other traffic flows on shared links may influence the queuing delay experienced by packets in one particular flow and is, in itself, a source of jitter. There are a number of different points on the network where packets may be lost. At the physical layer, all links experience some rate of data corruption, known as the bit error rate (BER). This may be caused by a high signal-to-noise ratio (SNR) during digital to analog conversion processes, which causes erroneous encoding or decoding of data, or it may be caused by faulty hardware. Forward error correction (FEC) is sometimes used at the link layer to recover from one- or two-bit errors. A cyclic redundancy check (CRC) may be applied to detect whether or not errors are included in the frame. Occasionally, transient congestion, with the subsequent queuing of packets, is so severe that it causes the routing queue buffer to overflow. When this occurs, newly arriving packets will be dropped until there is sufficient space in the buffer to place new packets. On other occasions, dynamic routing changes or route flapping may result in a temporarily incomplete network path, which causes losses.


2017 ◽  
Author(s):  
Michael D. Kaiser ◽  
Jennifer R. Davis ◽  
Boris S. Grinberg ◽  
John S. Oliver ◽  
Jay M. Sage ◽  
...  

The importance of structural variation in human disease and the difficulty of detecting structural variants larger than 50 base pairs has led to the development of several long-read sequencing technologies and optical mapping platforms. Frequently, multiple technologies and ad hoc methods are required to obtain a consensus regarding the location, size and nature of a structural variant, with no approach able to reliably bridge the gap of variant sizes between the domain of short-read approaches and the largest rearrangements observed with optical mapping.To address this unmet need, we have developed a new software package,SV-Verify™, which utilizes data collected with the Nabsys High Definition Mapping(HD-Mapping™) system, to perform hypothesis-based verification of putative deletions. We demonstrate that whole genome maps, constructed from electronic detection of tagged DNA, hundreds of kilobases in length, can be used effectively to facilitate calling of structural variants ranging in size from 300 base pairs to hundreds of kilobase pairs.SV-Verifyimplements hypothesis-based verification of putative structural variants using a set of support vector machines and is capable of concurrently testing several thousand independent hypotheses. We describe support vector machine training, utilizing a well-characterized human genome, and application of the resulting classifiers to another human genome, demonstrating high sensitivity and specificity for deletions ≥300 base pairs.


Author(s):  
Ya Chen ◽  
Geoffrey Letchworth ◽  
John White

Low-temperature high-resolution scanning electron microscopy (cryo-HRSEM) has been successfully utilized to image biological macromolecular complexes at nanometer resolution. Recently, imaging of individual viral particles such as reovirus using cryo-HRSEM or simian virus (SIV) using HRSEM, HV-STEM and AFM have been reported. Although conventional electron microscopy (e.g., negative staining, replica, embedding and section), or cryo-TEM technique are widely used in studying of the architectures of viral particles, scanning electron microscopy presents two major advantages. First, secondary electron signal of SEM represents mostly surface topographic features. The topographic details of a biological assembly can be viewed directly and will not be obscured by signals from the opposite surface or from internal structures. Second, SEM may produce high contrast and signal-to-noise ratio images. As a result of this important feature, it is capable of visualizing not only individual virus particles, but also asymmetric or flexible structures. The 2-3 nm resolution obtained using high resolution cryo-SEM made it possible to provide useful surface structural information of macromolecule complexes within cells and tissues. In this study, cryo-HRSEM is utilized to visualize the distribution of glycoproteins of a herpesvirus.


2020 ◽  
Vol 64 (1-4) ◽  
pp. 951-958
Author(s):  
Tianhao Liu ◽  
Yu Jin ◽  
Cuixiang Pei ◽  
Jie Han ◽  
Zhenmao Chen

Small-diameter tubes that are widely used in petroleum industries and power plants experience corrosion during long-term services. In this paper, a compact inserted guided-wave EMAT with a pulsed electromagnet is proposed for small-diameter tube inspection. The proposed transducer is noncontact, compact with high signal-to-noise ratio and unattractive to ferromagnetic tubes. The proposed EMAT is designed with coils-only configuration, which consists of a pulsed electromagnet and a meander pulser/receiver coil. Both the numerical simulation and experimental results validate its feasibility on generating and receiving L(0,2) mode guided wave. The parameters for driving the proposed EMAT are optimized by performance testing. Finally, feasibility on quantification evaluation for corrosion defects was verified by experiments.


2018 ◽  
Author(s):  
Satish Kodali ◽  
Liangshan Chen ◽  
Yuting Wei ◽  
Tanya Schaeffer ◽  
Chong Khiam Oh

Abstract Optical beam induced resistance change (OBIRCH) is a very well-adapted technique for static fault isolation in the semiconductor industry. Novel low current OBIRCH amplifier is used to facilitate safe test condition requirements for advanced nodes. This paper shows the differences between the earlier and novel generation OBIRCH amplifiers. Ring oscillator high standby leakage samples are analyzed using the novel generation amplifier. High signal to noise ratio at applied low bias and current levels on device under test are shown on various samples. Further, a metric to demonstrate the SNR to device performance is also discussed. OBIRCH analysis is performed on all the three samples for nanoprobing of, and physical characterization on, the leakage. The resulting spots were calibrated and classified. It is noted that the calibration metric can be successfully used for the first time to estimate the relative threshold voltage of individual transistors in advanced process nodes.


Nanophotonics ◽  
2020 ◽  
Vol 9 (8) ◽  
pp. 2569-2576 ◽  
Author(s):  
Lu Li ◽  
Lihui Pang ◽  
Qiyi Zhao ◽  
Yao Wang ◽  
Wenjun Liu

AbstractTransition metal dichalcogenides have been widely utilized as nonlinear optical materials for laser pulse generation applications. Herein, we study the nonlinear optical properties of a VS2-based optical device and its application as a new saturable absorber (SA) for high-power pulse generation. Few-layer VS2 nanosheets are deposited on the tapered region of a microfiber to form an SA device, which shows a modulation depth of 40.52%. After incorporating the microfiber-VS2 SA into an Er-doped fiber laser cavity, passively Q-switched pulse trains could be obtained with repetition rates varying from 95 to 233 kHz. Under the pump power of 890 mW, the largest output power and shortest pulse duration are measured to be 43 mW and 854 ns, respectively. The high signal-to-noise ratio of 60 dB confirms the excellent stability of the Q-switching state. To the best of our knolowdge, this is the first illustration of using VS2 as an SA. Our experimental results demonstrate that VS2 nanomaterials have a large potential for nonlinear optics applications.


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