Illuminating the structure and dynamics of chromatin by fluorescence labeling

BACKGROUND： Visualization of chromosomal loci location and dynamics is crucial for understanding many fundamental intra-nuclear processes such as DNA transcription, replication, and repair. OBJECTIVE： Here, we will describe the development of fluorescence labeling methods for chromatin imaging, including traditional as well as emerging chromatin labeling techniques in both fixed and live cells. We will also discuss current issues and provide a perspective on future developments and applications of the chromatin labeling technology. METHODS： A systematic literature search was performed using the PubMed. Studies published over the past 50 years were considered for review. More than 100 articles were cited in this review. RESULTS： Taking into account sensitivity, specificity, and spatiotemporal resolution, fluorescence labeling and imaging has been the most prevalent approach for chromatin visualization. Among all the fluorescent labeling tools, the adoption ofgenome editing tools, such as TALE and CRISPR, have great potential for the labeling and imaging of chromatin. CONCLUSION： Although a number of chromatin labeling techniques are available for both fixed and live cells, much more effort is still clearly required to develop fluorescence labeling methods capable of targeting arbitrary sequences non-intrusively to allow long-term, multiplexing, and high-throughput imaging of genomic loci and chromatin structures. The emerging technological advances will outline a next-generation effort toward the comprehensive delineation of chromatin at single-cell level with single-molecule resolution.

Solid-state NMR spectroscopy at ultrahigh resolution for structural and dynamical studies of MOFs

To characterize the structure and dynamics of metal--organic frameworks(MOFs)indepth at the molecular level,it is necessary to pursue high-resolution solid-state magic angle spinning(MAS)nuclear magnetic resonance(NMR)spectroscopy.Spectral resolution is usually affected by the quality of materials and various experimental conditions,of which magic angle(MA)accuracy is a crucial determinant.The current industrial criteria for MA calibration based on the common standard of KBr were found insufficient in guaranteeing optimal resolution MAS NMR for highly ordered MOFs.To drive towards higher-resolution MAS NMR spectroscopy,we propose_a calibration protocol for more accurate MA with a higher-precision criterion based on 79Br MAS NMR of KBr,where the linewidth ratio of the fifth-order spinning sideband to the central band of KBr should be less than 1.00.As a result,ultrahigh-resolution 13C cross-polarization(CP)MAS NMR of MOF-5 is achieved with minimal linewidths as low as 4 Hz,and therefore MOF-5 can be used as a new standard convenient for verifying MA accuracy and also optimizing 13c CP conditions.Maintaining high-precision MA under variable temperature(VT)was found challenging on certain commercial MAS NMR probes,as was systematically investigated by VT NMR using KBr and MOF-5.Nevertheless,ultrahigh-resolution MAS NMR spectroscopy with stable MA under VT is employed to reveal fine structures and linker dynamics of a series of Zn-based MOFs with highly regulated structures.The ultrahigh-resolution NMR methodcan be generally applied to study a broad range of MOFs and other materials.

LAMOST Experiment for Galactic Understanding and Exploration (LEGUE)——The survey's science plan

We describe the current plans for a spectroscopic survey of millions of stars in the Milky Way galaxy using the Guo Shou Jing Telescope （GSJT, formerly calledthe Large sky Area Multi-Object fiber Spectroscopic Telescope -- LAMOST）. The survey will obtain spectra for 2.5 million stars brighter than r 〈 19 during dark/grey time, and 5 million stars brighter than r 〈 17 or J 〈 16 on nights that are moonlit or have low transparency. The survey will begin in the fall of 2012, and will run for at least four years. The telescope＇s design constrains the optimal declination range for observations to 10~ 〈 di 〈 50~, and site conditions lead to an emphasis on stars in the direction of the Galactic anticenter. The survey is divided into three parts with different target selection strategies： disk, anticenter, and spheroid. The resulting dataset will be used to study the merger history of the Milky Way, the substructure and evolution of the disks, the nature of the first generation of stars through identification of the lowest metallicity stars, and star formation through study of open clusters and OB associations. Detailed design of the LAMOST Experiment for Galactic Understanding and Exploration （LEGUE） survey will be completed in summer 2012, after a review of the results of the pilot survey.

Modeling the Newtonian dynamics for rotation curve analysis of thin-disk galaxies

We present an efficient, robust computational method for modeling the Newtonian dynamics for rotation curve analysis of thin-disk galaxies. With appropriate mathematical treatments, the apparent numerical difficulties associated with singularities in computing elliptic integrals are completely removed. Using a boundary element discretization procedure, the governing equations are transformed into a linear algebra matrix equation that can be solved by straightforward Gauss elimination in one step without further iterations. The numerical code implemented according to our algorithm can accurately determine the surface mass density distribution in a disk galaxy from a measured rotation curve （or vice versa）. For a disk galaxy with a typical flat rotation curve, our modeling results show that the surface mass density monotonically decreases from the galactic center toward the periphery, according to Newtonian dynamics. In a large portion of the galaxy, the surface mass density follows an approximately exponential law of decay with respect to the galactic radial coordinate. Yet the radial scale length for the surface mass density seems to be generally larger than that of the measured brightness distribution, suggesting an increasing mass-tolight ratio with the radial distance in a disk galaxy. In a nondimensionalized form, our mathematical system contains a dimensionless parameter which we call the ＂galactic rotation number＂ that represents the gross ratio of centrifugal force and gravitational force. The value of this galactic rotation number is determined as part of the numerial solution. Through a systematic computational analysis, we have illustrated that the galactic rotation number remains within 4-10% of 1.70 for a wide variety of rotation curves. This implies that the total mass in a disk galaxy is proportional to V02 Rg, with V0 denoting the characteristic rotation velocity （such as the ＂flat＂ value in a typical ro- tation curve） and Rg the radius of the galactic disk. The predicted total galactic mass of the Milky Way is in good agreement with the star-count data.

Stellar Abundance and Galactic Chemical Evolution through LAMOST Spectroscopic Survey

A project of a spectroscopic survey of Galactic structure and evolution with a Large sky Area Multi-Object fiber Spectroscopic Telescope （LAMOST） is presented. The spectroscopic survey consists of two observational modes for various targets in our Galaxy. One is a major survey of the Milky Way aimed at a systematic study of the stellar abundance and Galactic chemical evolution through low resolution （R = 1000 2000） spectroscopy. Another is a follow-up observation with medium resolution （R = 10000） spectrographs aimed at detailed studies of the selected stars with different chemical composition, kinematics and dynamics.

Structures of GMC W37

We carried out observations toward the giant molecular cloud W 37 with the J = 1 - 0 transitions of 12CO, 13CO and C180 using the 13.7 m single-dish telescope at the Delingha station of Purple Mountain Observatory. Based on these CO lines, we calculated the column densities and cloud masses for molecular clouds with radial velocities around ＋20 km s-1. The gas mass of W 37, calculated from 13CO emission, is 1.7 × 10^5 M, above the criterion to be considered a giant molecular cloud. The dense ridge of W 37 is a dense filament, which is supercritical in terms of linear mass ratio. Dense clumps found by C180 emission are aligned along the dense ridge at regular intervals of about 2.8 pc, similar to the clump separation caused by large-scale ＇sausage instability＇. We confirm the identification of the giant molecular filament （GMF） G 18.0-16.8 and find a new giant filament, G 16.5-15.8, located ~ 0.7° to the west of G 18.0-16.8. Both GMFs are not gravitationally bound, as indicated by their low linear mass ratio （- 80 M pc-l）. We compared the gas temperature map with the dust temperature map from Herschel images, and found similar structures. The spatial distributions of class I objects and the dense clumps are reminiscent of triggered star formation occurring in the northwestern part of W 37, which is close to NGC 6611.

Made-to-measure galaxy modelling utilising absorption line strength data

We enhance the Syer ＆ Tremaine made-to-measure （M2M） particle method of stellar dynamical modelling to model simultaneously both kinematic data and absorption line strength data, thus creating a ＇chemo-M2M＇ modelling scheme. We apply the enhanced method to four galaxies （NGC 1248, NGC 3838, NGC 4452, NGC 4551） observed using the SAURON integral-field spectrograph as part of the ATLAS3D programme. We are able to reproduce successfully the 2D line strength data achieving mean X2 per bin values of ≈ 1 with 〉 95% of particles having converged weights. Because M2M uses a 3D particle system, we are also able to examine the underlying 3D line strength distributions. The extent to which these dis- tributions are plausible representations of real galaxies requires further consideration. Overall, we consider the modelling exercise to be a promising first step in developing a ＇chemo-M2M＇ modelling system and in understanding some of the issues to be addressed. While the made-to-measure techniques developed have been applied to absorption line strength data, they are in fact general and may be of value in modelling other aspects of galaxies.

Peculiar in-plane velocities in the outer disc of the Milky Way

We present the peculiar in-plane velocities derived from LAMOST red clump stars, which are purified and separated by a novel approach into two groups with different ages. The samples are mostly contributed around the Galactic anti-center direction so that we are able to map the radial profiles of the radial and azimuthal velocities in the outer disc. From variations of the in-plane velocities with Galactocentric radius for the younger and older populations, we find that both radial and azimuthal velocities are not axisymmetric at 8 〈 R 〈 14 kpc. The two red clump populations show that the mean radial velocity is negative within R - 9 kpc and positive beyond. This is likely because of the perturbation induced by the rotating bar. The cross-zero radius, R -9 kpc, essentially indicates the rough location of the Outer Lindblad Resonance radius. Given the circular speed of 238 km s^-1, the pattern speed of the bar can be approximated as 45 km s^-1 kpc^-1. The young red clump stars show larger mean radial velocity than the old population by about 3km s^-1 between R-9 and 12kpc. This is possibly because the younger population is more sensitive to the perturbation than the older one. The radial profiles of the mean azimuthal velocity for the two populations show an interesting U-shape, i.e. at R 〈 10.Skpc, the azimuthal velocity declines with R by about 10km s^-1, while at R 〉 10.5 kpc it increases with R to 240 - 245 km s^-1. It is not clear why the mean azimuthal velocity shows this U-shape along the Galactic anti-center direction. Moreover, the azimuthal velocity for the younger population is slightly larger than that for the older one and the difference moderately declines with R. Beyond R0-12 kpc, the azimuthal velocities for the two populations are indistinguishable.

Revisiting the dichotomy of early-type galaxies

We study the relationship between isophotal shapes, central light profiles and kinematic properties of early-type galaxies （ETGs） based on a compiled sample of 184 ETGs. These sample galaxies are included in Data Release 8 of the Sloan Digital Sky Survey and have central light profiles and kinematic properties available from the literature, which were compiled from observations by the Hubble Space Telescope and the ATLAS3D integral-field spectrograph, respectively. We find that there is only a weak correlation between the isophotal shape （a4/a） and the central light profile （within 1 kpc） of ETGs. About two-fifths of ＂core＂ galaxies have disky isophotes, and one-third of ＂power-law＂ galaxies are boxy. Our statistical results also show that there are weak correlations between galaxy luminosity and dynamical mass with a4/a, but such correlations are tighter with a central light profile. Moreover, no clear link has been found between the isophotal shape and the Sersic index. Comparisons show that there are similar correlations between a4/a and ellipticity, and between a4/a and specific angular momentum ARo/2 for ＂power-law＂ ETGs, but there are no such correlations for ＂core＂ ETGs. Therefore, we speculate that the bimodal classifications of ETGs are not as simple as previously thought, though we also find that the disky ETGs with highest a4/a are more elongated and fast rotators.

Global Axisymmetric Stability Analysis for a Composite System of Two Gravitationally Coupled Scale-Free Discs

For a composite system of gravitationally coupled stellar and gaseous discs, we have carried out a linear stability analysis for axisyrnmetric coplanar perturbations using the two-fluid formalism. The background stellar and gaseous discs are taken to be scale-free with all physical variables varying as powers of the cylindrical radius r with compatible exponents. The unstable modes set in as neutral modes or stationary perturbation configurations with angular frequency f33 = 0. The axisyrnmetric stable range is bounded by two marginal stability curves derived from stationary perturbation configurations. Because of the gravitational coupling between the stellar arid the gaseous discs, one only needs to consider the parameter regime of the stellar disc. There exist two unstable regimes in general: a collapse regime corresponding to large-scale perturbations and a ring-fragmentation regime corresponding to short-wavelength perturbations. The composite system will collapse if it rotates too slowly and will succumb to ring-fragmentation instabilities if it rotates sufficiently fast. The overall stable range against axisyrnmetric perturbations is determined by a necessary D-criterion involving the effective Mach number squared Ds2 (the squared ratio of the stellar disc rotation speed to the stellar velocity dispersion up to a numerical factor). Different mass ratio S and sound speed ratio η of the gaseous and stellar disc components will alter the overall stability. For spiral galaxies or circumnuclear discs, we further include the dynamical effect of a massive dark matter halo. Astrophysical applications to disc galaxies, proto-stellar discs and circumnuclear discs are given as examples.

Dynamical properties of water in living cells

With the aim of studying the effect of water dynamics on the properties of biological systems, in this paper, we present a quasi-elastic neutron scattering study on three different types of living cells, differing both in their morphological and tumor properties. The measured scattering signal, which essentially originates from hydrogen atoms present in the investigated systems, has been analyzed using a global fitting strategy using an optimized theoretical model that considers various classes of hydrogen atoms and allows disentangling diffusive and rotational motions. The approach has been carefully validated by checking the reliability of the calculation of parameters and their 99% confidence intervals. We demonstrate that quasi-elastic neutron scattering is a suitable experimental technique to characterize the dynamics of intracellular water in the angstrom/picosecond space/time scale and to investigate the effect of water dynamics on cellular biodiversity.