Enhancer-driven transcription of MCM8 by E2F4 promotes ATR pathway activation and glioma stem cell characteristics.

BACKGROUND: Glioma stem cells (GSCs) are responsible for glioma recurrence and drug resistance, yet the mechanisms underlying their maintenance remains unclear. This study aimed to identify enhancer-controlled genes involved in GSCs maintenance and elucidate the mechanisms underlying their regulation. METHODS: We analyzed RNA-seq data and H3K27ac ChIP-seq data from GSE119776 to identify differentially expressed genes and enhancers, respectively. Gene Ontology analysis was performed for functional enrichment. Transcription factors were predicted using the Toolkit for Cistrome Data Browser. Prognostic analysis and gene expression correlation was conducted using the Chinese Glioma Genome Atlas (CGGA) data. Two GSC cell lines, GSC-A172 and GSC-U138MG, were isolated from A172 and U138MG cell lines. qRT-PCR was used to detect gene transcription levels. ChIP-qPCR was used to detect H3K27ac of enhancers, and binding of E2F4 to target gene enhancers. Western blot was used to analyze protein levels of p-ATR and γH2AX. Sphere formation, limiting dilution and cell growth assays were used to analyze GSCs growth and self-renewal. RESULTS: We found that upregulated genes in GSCs were associated with ataxia-telangiectasia-mutated-and-Rad3-related kinase (ATR) pathway activation, and that seven enhancer-controlled genes related to ATR pathway activation (LIN9, MCM8, CEP72, POLA1, DBF4, NDE1, and CDKN2C) were identified. Expression of these genes corresponded to poor prognosis in glioma patients. E2F4 was identified as a transcription factor that regulates enhancer-controlled genes related to the ATR pathway activation, with MCM8 having the highest hazard ratio among genes positively correlated with E2F4 expression. E2F4 bound to MCM8 enhancers to promote its transcription. Overexpression of MCM8 partially restored the inhibition of GSCs self-renewal, cell growth, and the ATR pathway activation caused by E2F4 knockdown. CONCLUSION: Our study demonstrated that E2F4-mediated enhancer activation of MCM8 promotes the ATR pathway activation and GSCs characteristics. These findings offer promising targets for the development of new therapies for gliomas.

Ground observation result of an OH radical hyper-resolution spectrometer for the middle and upper atmosphere.

OH radicals in the upper and middle atmosphere are important oxidants and play an important role in atmospheric photochemistry. A hyper-resolution spectrometer based on 308 nm glow was developed for obtaining OH radical concentration data in the upper and middle atmosphere. In order to verify the performance of the OH radical hyper-resolution spectrometer, several comprehensive ground experiments were carried out in this paper. The spectrometer observes OH radicals produced by a photochemistry reactor chamber to verify the detection ability of the instrument for characteristic signals. A solar observation experiment is used to evaluate the hyper-resolution spectroscopic ability of the spectrometer and the on-orbit field-of-slice-view function. In order to evaluate the detection ability of weak atmospheric background radiation, the experimental study of solar scattering light observation was carried out. The experimental results show that the spectrometer has the characteristics of ultrahigh spectral resolution (0.0086 nm), high sensitivity, and high signal-to-noise ratio. The ground observation results are consistent with the theoretical simulation values.

Polarization sensitivity error analysis and measurement of a greenhouse gas monitoring instrument.

Greenhouse gas monitoring instruments (GMI) are spatial heterodyne spectroscopy (SHS) sensors that monitor greenhouse gases (GHG) from space. Due to several kinds of polarization-sensitive optical elements in GMIs, to some extent, the instrument becomes a polarization-sensitive sensor. Its polarization sensitivity will reduce the radiometric accuracy and spectral inversion accuracy of GHG column concentration. Theoretical radiation response models for analyzing the polarization sensitivity of a GMI, which is mainly affected by a scanning mirror beam splitter and diffraction gratings, are presented in this paper. Based on these models and the polarization performance testing, the theoretical and experimental results of the main spectral band of a GMI, covering the wavelength range of 1.568-1.583 µm for carbon dioxide (CO2) detection, have been given. The result shows that the linear polarization sensitivity is less than 0.65% and 1.32% in the nadir (45°, 0°) and in the oblique view direction (45±20°, ±31°), respectively, and that it meets the qualification requirement for an absolute radiometric calibration accuracy better than 5%. The absolute radiometric calibration accuracy directly affects the accuracy of GHG concentration retrieval.

Data processing error analysis based on Doppler asymmetric spatial heterodyne measurement.

The Doppler asymmetric spatial heterodyne (DASH) interferometer provides the capability to retrieve wind speed in the upper atmosphere. The data processing leads to a significant retrieving error with the development of wind precision. The influence of window parameters on the isolated interferogram is analyzed theoretically. Based on the derivation, the system is established, and the interferogram with a small shift is sampled. The phase and wind speed are calculated under various window types and window width values. We conclude that, by choosing the Nuttall window with a small width, the wind retrieving error can be minimized.

The Research of Flatfielding Correction Method for Spatial Heterodyne Spectrometer at Systematic Level.

It can't satisfy the requirement of correction for response non-uniformity at systematic levelif only if the array detector for spatial heterodyne spectrometer is corrected. Traditional methods, such as irradiation with uniform source and column-flat-fielding, are not suitable for spatial heterodyne spectrometer. The article expounds convection arm-blocking method for spatial heterodyne spectrometer briefly at first. This method leads to kinds of mismatches including pixel and sub-pixel level shift and rotation in a single arm data after gluing gratings. The effect of registration accuracy of flatfielding coefficients has been analyzed for the experimental breadboard. The result shows that the registration accuracy of flatfielding coefficients needs to be better than 0.1 pixel for the breadboard. The shift at pixel level is calculated by solving the rotational degree by using logarithm-polar coordinate and phase correlation method for the requirement of registration. The shift at sub-pixel level is estimated with DFT based on matrix multiplication. The flow path of flatfielding method at systematic level is concluded. The integral condition of interferometer after actual gluing is modulated by adjusting the positions of gratings slightly. The flatfielding flow path is applied to the data acquired from the modulated interferometer after gluing. Then, the result is compared with the spectrum after the correction with totally matched signal arm data. The final result shows that the spectral deviation is 0.6% between the two spectra compared with the spectral deviation of 4.1% without correction. The accuracy of recovered spectrum after correction has been improved markedly. This can be the foundation for the follow data processing.

[Error Correction of Spectral Calibration for Hyper-Spectral Atmosphere CO2 Monitoring Instrument].

The detection of hyper-spectral atmosphere CO2 needs remote sensor to be characterized and calibrated precisely while spectral calibration is the most basic work. The high uncertainty of wavelength calibration coefficient is a big problem as to the traditional laboratory calibration methods. In order to solve this problem, the research of error correction of spectral calibration based on gas absorption principle is carried out. The method is in accordance with the using conditions of instrument and it improves the practicability of the calibration coefficient. First, theoretical spectrum and error components are simulated by using radiative transfer. Then, the experiment of atmosphere CO2 absorption spectrum measurement is performed based on the atmosphere environmental simulation calibration house. Last, spectral error is corrected and optimized with LM algorithm. The result of spectral calibration of error correction shows that the mean value of spectral error deviation decreases from 0.03 cm-1 before correction to 0.008 cm-1 after correction, and systematic and mutable errors are removed. The spectral calibration precision on the ground is improved significantly, which lays the foundation for the subsequent greenhouse gas retrieval.

[Data Processing Method of Asymmetric Spatial Heterodyne Interferogram for Wind Measurement].

By using doppler asymmetric spatial heterodyne spectroscopy and doppler effect, the wind speed can be achieved through detecting the interferogram of airglow in the upper atmosphere. This paper mainly analyses the data processing method of the interferogram and then derive the interferometer phase in order to get the wind speed. Comparing with the traditional spatial heterodyne spectroscopy, not only the noise and error of the system should be taken into consideration, but the window function that used to isolate the spectrum has a great influence during the data processing. Then the effect of window type and window width on phase difference of interferogram and the wind error curve are simulated through software. On basis of this the wind error curve under the noise of system and flat field factor are simulated by choosing appropriate window function. The window function simulation indicates that although the joining of window leads to a distortion of the interferogam and phase, the wind speed error can be less than 0.5% with Hanning window in the appropriate optical path difference. The noise of the system simulation indicates that the wind speed error increases with the noise, so it is necessary to control the system noise and preprocess the sampling data. The research on data processing method has great theoretical significance and practical value for designing the system parameter and improving the precision of spatial heterodyne wind detection.

[The Research of Spatial Heterodyne Raman Spectroscopy with Standoff Detection].

Spatial heterodyne Raman spectroscopy (SHRS) is a new type of Raman spectroscopic detection technique with characteristics of high optical throughout, high spectral resolution, and no moving parts. SHRS is very suitable for the planetary exploration missions, which can be used to the analysis of minerals and find the biomarkers maybe exist on the surface of planetary. The authors have applied the technique to the standoff Raman spectroscopic detection, analyzed the main characteristics, including spectral resolution, bandpass and signal to noise (SNR), of standoff SHRS and proved it through experiments. The basic theory of standoff SHRS has been described briefly while a breadboard has been designed, built and calibrated. On the basis, the Raman spectra of some inorganic solids, organic liquids and some natural minerals have been achieved at a distance of 10 m, the SNR of the breadboard has been estimated. Due to the poor adjustment and the defects of the optical elements, the breadboard is far away from an ideal system. But the results show that the SNR is better than 5 for most of the main Raman peaks of the samples, which can meet the basic requirement of clear positive detection of typical Raman peaks and the feasibility of standoff SHRS has been proved. SHRS can overcome the main defects of dispersive grating Raman spectrometers and Fourier transform Raman spectrometers and it has a great application prospect on the detection and analysis of the planetary surface. The work of the authors can prove the potentiality of SHRS on standoff detection and can provide reference for the engineering realization of standoff SHRS.

[Study on the Spectral Characteristics of the Narrow-Band Filter in SHS].

The spectral response of spatial heterodyne spectroscopy (SHS) is determined by the spectrum property of narrow-band filter. As discussed in previous studies, the symmetric heterodyned interferogram of high frequency waves modulated by SHS and lack of sample lead to spectral confusion, which is associated with the true and ghost spectra. Because of the deviation from theoretical index of narrow-band filter in the process of coating, the boarded spectral response and middle wave shift are presented, and conditions in the theoretical Littrow wavelength made the effective wavelength range of SHS reduced. According to the measured curve of filter, a new wavenumber of zero spatial frequency can be reset by tunable laser, and it is easy for SHS to improve the spectral aliasing distortion. The results show that it is utilized to the maximum extent of the effective bandwidth by adjusting the grating angle of rotation to change the Littrow wavelength of the basic frequency, and the spectral region increased to 14.9 nm from original 12.9 nm.

[Study on a new method for instrumental line shape measurement of spatial heterodyne interference spectrometer].

Spatial heterodyne spectroscopy(SHS)is a novel method for hyper-spectral analysis, and instrument line shape function is one of the basic performance parameters, which should be precisely characterized. Based on the analysis of the influence factors(apodization, limited angle, abaxial detector element) and special requirement for measuring method and source, the present paper put forward a new method for measuring with tunable monochromatic light source, and designed experimental equipment with tunable laser and integrating sphere eliminating speckle. Selecting typical spectral range within band range for high spectral resolution scanning (0. 1nm step), the energy distribution of spectrum was obtained according to error correction, spectral reconstruction and normalization. In addition, rule curve for FWHM and wavelength was obtained by the full spectral range scanning interferogram. Finally, theoretical spectrum, ILS convolution simulated spectrum (LBL calculated), and measured carbon dioxide absorption spectrum by ground-based experiment are in good agreement. The result shows that the instrument line shape function exhibits high accuracy.

[Thermal effect on optical properties of spatial heterodyne spectroscopy].

To study the thermal effort on optical properties of spatial heterodyne spectroscopy (SHS), the relation between the change in temperature and the degradation of optical properties was analyzed, including collimator lens, imaging lens and interferometer unit. The theoretical model was verified and corrected by simulation and thermal-optical test, which was established to describe the relation between spectral-line shift and groove density change of gratings. The results show that spectrum measurements are not affected by small temperature changes in the instrument since the primary effects. are a slight defocus of the focal plane array in collimating lens and re-imaging lens under the temperature from 15 to 25 °C. Spectral-line shift obtained by the thermal optical analysis is well coincident with the ones calculated by thermal optical experiment because of the temperature chan- ges of interferometer unit. The Littrow wavelength accuracy is better than 2.3 nm unless the temperature change is less than 2.5 °C under the interferometer unit by use of the material BK7.

[Study on calibration method of spatial heterodyne spectrometer].

Spatial heterodyne spectroscopy (SHS) is a novel method for hyperspectral analysis, but the calibration methods have not been thoroughly studied. The present paper gives some basic theories of SHS, and investigates the laboratory calibration methods, including spectral calibration and radiometric calibration. According to emission lines and the relation between detector size and system bandwidth, we designed the spectral calibration plan for SHS, which uses tunable laser and halogen lamp. Experiments show that the actual spectral range and resolution of our instrument is the same as it was designed, and the spectral shift is less by stability testing. For radiometric calibration, we measured the system's stability by using integrating sphere, and its responses were also calibrated by using standard lamp and diffuser. The experimental results, after validation, proved that our method can be used for SHS calibration. This is a fundamental work for quantified retrieval.