Over 17 and 160 types of chemical modifications have been identified in DNA and RNA, respectively. The interest in understanding the various biological functions of DNA and RNA modifications has lead ...to the cutting-edged fields of epigenomics and epitranscriptomics. Developing chemical and biological tools to detect specific modifications in the genome or transcriptome has greatly facilitated their study. Here, we review the recent technological advances in this rapidly evolving field. We focus on high-throughput detection methods and biological findings for these modifications, and discuss questions to be addressed as well. We also summarize third-generation sequencing methods, which enable long-read and single-molecule sequencing of DNA and RNA modification.
Bisulfite sequencing has been the gold standard for mapping DNA modifications including 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC) for decades
. However, this harsh chemical treatment ...degrades the majority of the DNA and generates sequencing libraries with low complexity
. Here, we present a bisulfite-free and base-level-resolution sequencing method, TET-assisted pyridine borane sequencing (TAPS), for detection of 5mC and 5hmC. TAPS combines ten-eleven translocation (TET) oxidation of 5mC and 5hmC to 5-carboxylcytosine (5caC) with pyridine borane reduction of 5caC to dihydrouracil (DHU). Subsequent PCR converts DHU to thymine, enabling a C-to-T transition of 5mC and 5hmC. TAPS detects modifications directly with high sensitivity and specificity, without affecting unmodified cytosines. This method is nondestructive, preserving DNA fragments over 10 kilobases long. We applied TAPS to the whole-genome mapping of 5mC and 5hmC in mouse embryonic stem cells and show that, compared with bisulfite sequencing, TAPS results in higher mapping rates, more even coverage and lower sequencing costs, thus enabling higher quality, more comprehensive and cheaper methylome analyses.
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EMUNI, FIS, FZAB, GEOZS, GIS, IJS, IMTLJ, KILJ, KISLJ, MFDPS, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, SBMB, SBNM, UKNU, UL, UM, UPUK, VKSCE, ZAGLJ
Although various methods have been developed for sequencing cytosine modifications, it is still challenging for specific and quantitative sequencing of individual modification at base-resolution. For ...example, to obtain both true 5-methylcytosine (5mC) and true 5-hydroxymethylcytosine (5hmC) information, the two major epigenetic modifications, it usually requires subtraction of two methods, which increases noise and requires high sequencing depth. Recently, we developed TET-assisted pyridine borane sequencing (TAPS) for bisulfite-free direct sequencing of 5mC and 5hmC. Here we demonstrate that two sister methods, TAPSβ and chemical-assisted pyridine borane sequencing (CAPS), can be effectively used for subtraction-free and specific whole-genome sequencing of 5mC and 5hmC, respectively. We also demonstrate pyridine borane sequencing (PS) for whole-genome profiling of 5-formylcytosine and 5-carboxylcytosine, the further oxidized derivatives of 5mC and 5hmC. This work completes the set of versatile borane reduction chemistry-based methods as a comprehensive toolkit for direct and quantitative sequencing of all four cytosine epigenetic modifications.
A new temperature fiber ring laser (FRL) sensor based on a cascaded Sagnac loops fiber structure is proposed and experimentally demonstrated. The optical FRL sensor consists of cascaded Sagnac loops ...by inserting two polarization-maintaining optical fibers (PMF) with slightly different lengths. PMF with length of 56 cm and 75 cm are used in Sagnac loops as a filter and sensing unit in laser cavity. The working principle of the sensor is based on the phase shift (θ) caused by birefringence between two principal polarization modes and enhance the sensitivity by constructing a Vernier-scale. In an appropriate temperature range (25 °C - 31 °C), the detection sensitivity of FRL sensor based on a cascaded Sagnac structure is significantly higher than other FRL sensors. Thanks to the laser sensing system, the sensitivity can be modulated by changing the free spectral range (FSR). The experimental results show that the temperature sensitivity of the cascade Sagnac structure sensor is - 4.031 nm / °C, which is five times higher than that of FRL sensor base on the single Sagnac structure.
Frequency diverse array‐multiple input multiple output (FDA‐MIMO) radar not only has the advantage of waveform diversity but also can realise azimuth‐range correlation map, so it can realise high ...precision azimuth‐range joint estimation and has the ability to distinguish different range unit targets in the same azimuth. However, the existing research mainly adopts uniform linear array (ULA) model and mainly focusses on incoherent targets. At present, the elevation‐range joint estimation algorithm of metre wave FDA‐MIMO radar based on ULA has the problems of sharp decline in angle‐range measurement accuracy of ultra‐low altitude targets and large fluctuation of elevation‐range measurement accuracy with changing elevation. In order to solve the above difficult problems, starting from the perspective of reducing the influence of multipath effect by array structure, this paper innovatively combines sparse array with FDA‐MIMO radar, establishes the low elevation‐range joint estimation model of metre wave FDA‐MIMO radar based on sparse array, and puts forward the low elevation‐range joint estimation method suitable for this model, and it fills the gap of low elevation‐range measurement method based on sparse array metre wave FDA‐MIMO radar. Simulation experiments compare two typical sparse arrays with ULA of equal array elements, which verify the superiority of low elevation‐range measurement performance of monostatic metre wave FDA‐MIMO radar based on sparse array and the effectiveness of the proposed method.
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FZAB, GIS, IJS, KILJ, NLZOH, NUK, OILJ, SBCE, SBMB, UL, UM, UPUK
Optical fiber sensors are of splendid strength for electrical field intensity sensor due to characteristics including the immunity to electromagnetic interference, lightweight, high sensitivity, and ...large bandwidth. In this paper, we proposed an electric field intensity sensor based on Mach-Zehnder interferometer (MZI) based liquid crystal (LC) filled photonic crystal fiber (PCF) embedded in optical fiber ring laser (FRL). The air hole of PCF combines the LC and fiber core together. When LC is introduced into air holes, it can maintain the waveguide based on external parameters. The photonic bandgap effect significantly improved the sensitivity between light and external electrical field intensity. Thanks to the FRL demodulation, a high signal to noise ratio (SNR) spectrum about 35 dB is obtained. Besides, in comparison with traditional LC-PCF structures, the sensitivity of ours is as high as 1.1 nm/Vrms which is about twice than traditional sensors. At the same time, the stability of proposed sensor was verified which fluctuation was 0.15 nm around 2.5 hours. Therefore, our structure is expected to practical applications in remote electric field monitor and such electric modulate electro-optical devices.
A fiber-optic Mach Zehnder interferometer (MZI) refractive index (RI) sensor based on a double peanut-shaped structure in Er-doped fiber with a section of tapered fiber was fabricated using fusion ...splicer and experimentally demonstrated. The double peanut-shaped structures placed at both ends of the sensor function as beam splitting/combining. Besides, the tapered region works as the sensing area. With RI changes, the optical path difference between the core mode and the cladding modes will change correspondingly, resulting in interference spectrum shifting. By monitoring the shift, the measured RI can be obtained. The experimental results show that the RI sensitivity was significantly improved compared with other types of peanut-shaped fiber sensors. By comparing different taper diameters, it is found that the finer the tapered fiber, the higher the sensitivity of measuring RI.High RI sensitivity of 441.56 nm/RIU is obtained in the experiments. Compared with the similar-structure sensor consisted of single-mode fiber (SMF), the sensitivity of the proposed sensor based on Er-doped fiber is 115.22 nm/RIU higher than that of the former. The proposed sensor has the characteristics of a compact structure. In addition, it has potential in environmental, medical, and aerospace monitoring applications.
Abstract
Oxidation of renewable polyol/sugar into formic acid using molecular O
2
over heterogeneous catalysts is still challenging due to the insufficient activation of both O
2
and organic ...substrates on coordination-saturated metal oxides. In this study, we develop a defective MnO
2
catalyst through a coordination number reduction strategy to enhance the aerobic oxidation of various polyols/sugars to formic acid. Compared to common MnO
2
, the tri-coordinated Mn in the defective MnO
2
catalyst displays the electronic reconstruction of surface oxygen charge state and rich surface oxygen vacancies. These oxygen vacancies create more Mn
δ+
Lewis acid site together with nearby oxygen as Lewis base sites. This combined structure behaves much like Frustrated Lewis pairs, serving to facilitate the activation of O
2
, as well as C–C and C–H bonds. As a result, the defective MnO
2
catalyst shows high catalytic activity (turnover frequency: 113.5 h
−1
) and formic acid yield (>80%) comparable to noble metal catalysts for glycerol oxidation. The catalytic system is further extended to the oxidation of other polyols/sugars to formic acid with excellent catalytic performance.
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