A Survey of Established Veterinary Clinical Skills Laboratories from Europe and North America:Present Practices and Recent Developments

Hierarchical clustering analysis of all dysregulated genes. (TIF 11970 kb

Using GPU acceleration and a novel artificial neural networks approach for ultra-fast fluorescence lifetime imaging microscopy analysis

Fluorescence lifetime imaging microscopy (FLIM) which is capable of visualizing local molecular and physiological parameters in living cells, plays a significant role in biological sciences, chemistry, and medical research. In order to unveil dynamic cellular processes, it is necessary to develop high-speed FLIM technology. Thanks to the development of highly parallel time-to-digital convertor (TDC) arrays, especially when integrated with single-photon avalanche diodes (SPADs), the acquisition rate of high-resolution fluorescence lifetime imaging has been dramatically improved. On the other hand, these technological advances and advanced data acquisition systems have generated massive data, which significantly increases the difficulty of FLIM analysis. Traditional FLIM systems rely on time-consuming iterative algorithms to retrieve the FLIM parameters. Therefore, lifetime analysis has become a bottleneck for high-speed FLIM applications, let alone real-time or video-rate FLIM systems. Although some simple algorithms have been proposed, most of them are only able to resolve a simple FLIM decay model. On the other hand, existing FLIM systems based on CPU processing do not make use of available parallel acceleration. In order to tackle the existing problems, my study focused on introducing the state-of-art general purpose graphics processing units (GPUs) to the FLIM analysis, and building a data processing system based on both CPU and GPUs. With a large amount of parallel cores, the GPUs are able to significantly speed up lifetime analysis compared to CPU-only processing. In addition to transform the existing algorithms into GPU computing, I have developed a new high-speed and GPU friendly algorithm based on an artificial neural network (ANN). The proposed GPU-ANN-FLIM method has dramatically improved the efficiency of FLIM analysis, which is at least 1000-folder faster than some traditional algorithms, meaning that it has great potential to fuel current revolutions in high-speed high-resolution FLIM applications

Quadrupole Central Transition ¹⁷O NMR Spectroscopy of Biological Macromolecules in Aqueous Solution

We demonstrate a general nuclear magnetic resonance (NMR) spectroscopic approach in obtaining high-resolution 17O (spin-5/2) NMR spectra for biological macromolecules in aqueous solution. This approach, termed quadrupole central transition (QCT) NMR, is based on the multiexponential relaxation properties of half-integer quadrupolar nuclei in molecules undergoing slow isotropic tumbling motion. Under such a circumstance, Redfield’s relaxation theory predicts that the central transition, mI = +1/2 ↔ −1/2, can exhibit relatively long transverse relaxation time constants, thus giving rise to relatively narrow spectral lines. Using three robust protein−ligand complexes of size ranging from 65 to 240 kDa, we have obtained 17O QCT NMR spectra with unprecedented resolution, allowing the chemical environment around the targeted oxygen atoms to be directly probed for the first time. The new QCT approach increases the size limit of molecular systems previously attainable by solution 17O NMR by nearly 3 orders of magnitude (1000-fold). We have also shown that, when both quadrupole and shielding anisotropy interactions are operative, 17O QCT NMR spectra display an analogous transverse relaxation optimized spectroscopy type behavior in that the condition for optimal resolution depends on the applied magnetic field. We conclude that, with the currently available moderate and ultrahigh magnetic fields (14 T and higher), this 17O QCT NMR approach is applicable to a wide variety of biological macromolecules. The new 17O NMR parameters so obtained for biological molecules are complementary to those obtained from 1H, 13C, and 15N NMR studies

Direct NMR Detection of Alkali Metal Ions Bound to G-Quadruplex DNA

We describe a general multinuclear (1H, 23Na, 87Rb) NMR approach for direct detection of alkali metal ions bound to G-quadruplex DNA. This study is motivated by our recent discovery that alkali metal ions (Na+, K+, Rb+) tightly bound to G-quadruplex DNA are actually “NMR visible” in solution (Wong, A.; Ida, R.; Wu, G. Biochem. Biophys. Res. Commun. 2005, 337, 363). Here solution and solid-state NMR methods are developed for studying ion binding to the classic G-quadruplex structures formed by three DNA oligomers:  d(TG4T), d(G4T3G4), and d(G4T4G4). The present study yields the following major findings. (1) Alkali metal ions tightly bound to G-quadruplex DNA can be directly observed by NMR in solution. (2) Competitive ion binding to the G-quadruplex channel site can be directly monitored by simultaneous NMR detection of the two competing ions. (3) Na+ ions are found to locate in the diagonal T4 loop region of the G-quadruplex formed by two strands of d(G4T4G4). This is the first time that direct NMR evidence has been found for alkali metal ion binding to the diagonal T4 loop in solution. We propose that the loop Na+ ion is located above the terminal G-quartet, coordinating to four guanine O6 atoms from the terminal G-quartet and one O2 atom from a loop thymine base and one water molecule. This Na+ ion coordination is supported by quantum chemical calculations on 23Na chemical shifts. Variable-temperature 23Na NMR results have revealed that the channel and loop Na+ ions in d(G4T4G4) exhibit very different ion mobilities. The loop Na+ ions have a residence lifetime of 220 μs at 15 °C, whereas the residence lifetime of Na+ ions residing inside the G-quadruplex channel is 2 orders of magnitude longer. (4) We have found direct 23Na NMR evidence that mixed K+ and Na+ ions occupy the d(G4T4G4) G-quadruplex channel when both Na+ and K+ ions are present in solution. (5) The high spectral resolution observed in this study is unprecedented in solution 23Na NMR studies of biological macromolecules. Our results strongly suggest that multinuclear NMR is a viable technique for studying ion binding to G-quadruplex DNA

Selective Binding of Monovalent Cations to the Stacking G-Quartet Structure Formed by Guanosine 5‘-Monophosphate: A Solid-State NMR Study

We report a solid-state multinuclear (23Na, 15N, 13C, and 31P) NMR study on the relative affinity of monovalent cations for a stacking G-quartet structure formed by guanosine 5‘-monophosphate (5‘-GMP) self-association at pH 8. Two major types of cations are bound to the 5‘-GMP structure:  one at the surface and the other within the channel cavity between two G-quartets. The channel cation is coordinated to eight carbonyl oxygen atoms from the guanine bases, whereas the surface cation is close to the phosphate group and likely to be only partially hydrated. On the basis of solid-state 23Na NMR results from a series of ion titration experiments, we have obtained quantitative thermodynamic parameters concerning the relative cation binding affinity for each of the two major binding sites. For the channel cavity site, the values of the free energy difference (ΔG° at 25 °C) for ion competition between M+ and Na+ ions are K+ (−1.9 kcal mol-1), NH4+ (−1.8 kcal mol-1), Rb+ (−0.3 kcal mol-1), and Cs+ (1.8 kcal mol-1). For the surface site, the values ΔG° are K+ (2.5 kcal mol-1), NH4+ (−1.3 kcal mol-1), Rb+ (1.1 kcal mol-1), and Cs+ (0.9 kcal mol-1). Solid-state NMR data suggest that the affinity of monovalent cations for the 5‘-GMP structure follows the order NH4+ > Na+ > Cs+ > Rb+ > K+ at the surface site and K+ > NH4+ > Rb+ > Na+ > Cs+ > Li+ at the channel cavity site. We have found that the cation-induced stability of a 5‘-GMP structure is determined only by the affinity of monovalent cations for the channel site and that the binding of monovalent cations to phosphate groups plays no role in 5‘-GMP self-ordered structure. We have demonstrated that solid-state 23Na and 15N NMR can be used simultaneously to provide mutually complementary information about competitive binding between Na+ and NH4+ ions

A Modified Townes-Dailey Model for Interpretation and Visualization of Nuclear Quadrupole Coupling Tensors in Molecules

We propose a modified Townes–Dailey (TD) model to help interpret and visualize experimentally measurable nuclear quadrupole coupling tensors (thus the electric field gradient tensors) in molecules. We show that within the framework of the TD model each principal component of the nuclear quadrupole coupling tensor is directly related to a new quantity termed as the valence p-orbital population anisotropy (VPPA or ΔP) in the same direction. Although the proposed model is a simple reformulation of the original TD model thus does not introduce new physics, the concept of VPPA makes it possible to directly interpret as well as visualize in a much straightforward way the experimentally determined nuclear quadrupole coupling tensors in molecules. We illustrate the utilization of VPPA using nuclear quadrupole coupling tensors for 11B, 14N, 17O, 35Cl, 79Br, and 127I nuclei in a variety of molecules. We propose to use VPPA or ΔP ellipsoid representation as a means of visualizing/displaying nuclear quadrupole coupling tensors in the molecular frame. We show the usefulness of the VPPA concept in providing a unifying explanation for seemingly different types of molecular interactions such as hydrogen bonding, halogen bonding, and frustrated Lewis pairs. We further suggest that VPPA can be used as a universal measure of the ability of any element in the entire p-block of the periodic table (groups 13–16) to interact with nucleophiles (e.g., formation of chalcogen, pnictogen, tetrel, and triel bonds)

Helical Structure of Disodium 5′-Guanosine Monophosphate Self-Assembly in Neutral Solution

Helical Structure of Disodium 5′-Guanosine Monophosphate Self-Assembly in Neutral Solutio

N²-Functionalized Blue Luminescent Guanosines by 2,2′-Dipyridylamino and 2-(2′-Pyridyl)benzimidazolyl Chelate Groups and Their Interactions with Zn(II) Ions

The syntheses of new blue luminescent N2-modified guanosine derivatives with chromophores p-4,4′-biphenyl-NPh2 (1a), p-4,4′-biphenyl-N(2-py)2 (1b), and p-4,4′-biphenyl-2-(2′-pyridyl)benzimidazolyl (1c), respectively, have been achieved. These new N2-guanosines are moderate blue emitters with λmax = 395 nm (1a), 370 nm (1b), and 403 nm (1c) and Φ = 0.13, 0.07, and 0.10 in tetrahydrofuran, respectively. Spectroscopic studies and density-functional theory calculations established that the guanine moiety and the new chromophore in all three molecules are involved in the luminescent process. We have also established that guanosines 1a−1c can interact with metal ions such as Zn(II). The interactions of Zn(II) ions with the three guanosines were examined via absorption, fluorescence, circular dichroism (CD), and NMR spectroscopic analyses. We have found that these guanosines display a distinct fluorescent response toward Zn(II) ions which can be attributed to the presence of the chelate chromophore N(2-py)2 in 1b and 2-py-benzimidazolyl in 1c. For 1a and 1b, the addition of Zn(II) ions causes straight fluorescent quenching while for 1c the addition of Zn(II) ions causes quenching initially, which is followed by a distinct spectral red shift and the intensity enhancement of the new emission peak. NMR and CD studies demonstrated that the Zn(II) ions bind preferentially to the guanine moiety in 1a and 1b but to the 2-(2′-py)benzimidazolyl chelate site in 1c. Moreover, the anion-dependent CD response of 1a−1c toward Zn(II) salts points to the possible involvement of intramolecular hydrogen bonding between the acetate bound to the Zn(II) ion and the hydroxyl groups of the guanosine

Communities detection in top1 destination network for each decade between 1960 and 2000.

<p>The nodes having the same colour are members of the same component, while the same background shows that they belong to the same community.</p

Complete International Migration Network in the years 1960 and 2000.

<p>The plots in the figure shows the direct weighted version of the CIMN that highlights the top-ranked destination of each country. The colours of the links represent the proportion of migrant stock in the maximum migrant stock after country of destination [<i>wij</i> / max <i>i</i>(<i>wij</i>)] from light yellow (low-proportion links) to red (high-proportion links). The thickness of the links is proportional to the normalized migrants stocks [<i>wij</i> / max(<i>wij</i>)].</p