Small-angle X-ray scattering (SAXS) is used to demonstrate the presence of density fluctuations in ambient water on a physical length-scale of Ϸ1 nm; this is retained with decreasing temperature while the magnitude is enhanced. In contrast, the magnitude of fluctuations in a normal liquid, such as CCl4, exhibits no enhancement with decreasing temperature, as is also the case for water from molecular dynamics simulations under ambient conditions. Based on X-ray emission spectroscopy and X-ray Raman scattering data we propose that the density difference contrast in SAXS is due to fluctuations between tetrahedral-like and hydrogen-bond distorted structures related to, respectively, low and high density water. We combine our experimental observations to propose a model of water as a temperature-dependent, fluctuating equilibrium between the two types of local structures driven by incommensurate requirements for minimizing enthalpy (strong near-tetrahedral hydrogen-bonds) and maximizing entropy (nondirectional H-bonds and disorder). The present results provide experimental evidence that the extreme differences anticipated in the hydrogen-bonding environment in the deeply supercooled regime surprisingly remain in bulk water even at conditions ranging from ambient up to close to the boiling point.density fluctuations ͉ liquid-liquid hypothesis ͉ small angle X-ray scattering ͉ water structure ͉ X-ray spectroscopy L iquid water shows many anomalies in its thermodynamic properties such as compressibility, density variation and heat capacity (1-4). In the low-temperature regime, below the freezing point, these properties deviate strongly from normal and theories, related to a liquid-liquid phase transition between high and low density water, have been proposed to account for these anomalies (5). Although the anomalies are extreme in the supercooled region they are also present at ambient conditions where most of waters' physical, chemical and biological processes of importance occur. In contrast, water at ambient conditions has traditionally been considered as a homogeneous distribution of near-tetrahedral hydrogen-bonded (H-bonded) structures with thermal fluctuations increasing with temperature. This picture has been challenged by recent studies based on X-ray Raman (XRS) and conventional X-ray absorption spectroscopy (XAS) (6), and X-ray emission spectroscopy (XES) (7), suggesting two distinct local structures with tetrahedral as a minority and a highly hydrogen-bond (H-bond) distorted asymmetrical as the majority. In particular the proposed predominant asymmetrical structure has caused intense debate in the last years (see refs. 7 and 8 for detailed discussion).SAXS and small-angle neutron scattering (SANS) provide the most direct probes of density variations or fluctuations on large length scales in a liquid. Through an enhancement of the structure factor at low momentum transfer, Q, small deviations from the average electron density at different length scales can be reliably identified (9). Previous SAXS studies of w...

DNA-protein crosslinks (DPCs)-where proteins are covalently trapped on the DNA strand-block the progression of replication and transcription machineries and hence hamper the faithful transfer of genetic information. However, the repair mechanism of DPCs remains largely elusive. Here we have analyzed the roles of nucleotide excision repair (NER) and homologous recombination (HR) in the repair of DPCs both in vitro and in vivo using a bacterial system. Several lines of biochemical and genetic evidence show that both NER and HR commit to the repair or tolerance of DPCs, but differentially. NER repairs DPCs with crosslinked proteins of sizes less than 12-14 kDa, whereas oversized DPCs are processed exclusively by RecBCD-dependent HR. These results highlight how NER and HR are coordinated when cells need to deal with unusually bulky DNA lesions such as DPCs.

As an aggressive pathogen, Staphylococcus aureus poses a significant public health threat and is becoming increasingly resistant to currently available antibiotics, including vancomycin, the drug of last resort for gram-positive bacterial infections. S. aureus with intermediate levels of resistance to vancomycin (vancomycin-intermediate S. aureus [VISA]) was first identified in 1996. The resistance mechanism of VISA, however, has not yet been clarified. We have previously shown that cell wall thickening is a common feature of VISA, and we have proposed that a thickened cell wall is a phenotypic determinant for vancomycin resistance in VISA (L. Cui, X. Ma, K. Sato, et al., J. Clin. Microbiol. 41:5-14, 2003). Here we show the occurrence of an anomalous diffusion of vancomycin through the VISA cell wall, which is caused by clogging of the cell wall with vancomycin itself. A series of experiments demonstrates that the thickened cell wall of VISA could protect ongoing peptidoglycan biosynthesis in the cytoplasmic membrane from vancomycin inhibition, allowing the cells to continue producing nascent cell wall peptidoglycan and thus making the cells resistant to vancomycin. We conclude that the cooperative effect of the clogging and cell wall thickening enables VISA to prevent vancomycin from reaching its true target in the cytoplasmic membrane, exhibiting a new class of antibiotic resistance in gram-positive pathogens.

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High-resolution O 1s resonant inelastic x-ray scattering spectra of liquid H2O, D2O, and HDO, obtained by excitation near the preedge resonance show, in the elastic line region, well-separated multiple vibrational structures corresponding to the internal OH stretch vibration in the ground state of water. The energy of the first-order vibrational excitation is strongly blueshifted with respect to the main band in the infrared or Raman spectra of water, indicating that water molecules with a highly weakened or broken donating hydrogen bond are correlated with the preedge structure in the x-ray absorption spectrum. The vibrational profile of preedge excited HDO water is well fitted with 50%±20% greater OH-stretch contribution compared to OD, which strongly supports a preference for OH being the weakened or broken H-bond in agreement with the well-known picture that D2O makes stronger H-bonds than H2O. Accompanying path-integral molecular dynamics simulations show that this is particularly the case for strongly asymmetrically H-bonded molecules, i.e., those that are selected by preedge excitation.

Thrombopoietin (TPO) is implicated as a primary regulator of megakaryopoiesis and thrombopoiesis through binding to the cytokine receptor c-Mpl (the product of the c-mpl proto-oncogene). In an effort to determine the pathophysiological role of TPO-c-Mpl system in essential thrombocythemia (ET), we have examined the levels of serum TPO and the expression and function of platelet c-Mpl in 17 patients with ET. In spite of extreme thrombocytosis, serum TPO levels were slightly elevated or within normal range in most, if not all, patients with ET (mean ± SD, 1.31 ± 1.64 fmol/mL), as compared with normal subjects (0.76 ± 0.21 fmol/mL). Flow cytometric and Western blot analyses revealed that the expression of platelet c-Mpl was strikingly reduced in all patients with ET. Furthermore, the expression of platelet c-mpl mRNA was found to be significantly decreased in the ET patients tested. In contrast, almost identical levels of GPIIb/IIIa protein and mRNA were expressed in platelets from ET patients and normal controls. In addition to expression level, activation state of platelet c-Mpl was investigated in ET patients. Immunoblotting with anti-phosphotyrosine antibody showed that no aberrant protein-tyrosine phosphorylation was observed in platelets of ET patients before treatment with TPO, and the levels of TPO-induced protein-tyrosine phosphorylation, including c-Mpl-tyrosyl phosphorylation, roughly paralleled those of c-Mpl expression, suggesting that c-Mpl–mediated signaling pathway was not constitutively activated in platelets of ET patients. These results suggested that the TPO-c-Mpl system may not be directly linked to pathogenesis of ET, and that gene(s) mutated in ET may be important in regulating the levels of c-mpl gene expression in addition to the growth and differentiation of multipotential hematopoietic stem cells.

An extremely high resolution flat field type slit less soft x-ray emission spectrometer has been designed and constructed for the long undulator beamline BL07LSU in SPring-8. By optimizing the ruling parameters of two cylindrical gratings, a high energy resolution ΔE < 100 meV and/or an E∕ΔE ~ 10 000 are expected for the energy range of 350 eV - 750 eV taking into account the broadening by the spatial resolution (25 μm) of a CCD detector. A coma-free operation mode proposed by Strocov et al., is also applied to eliminate both defocus and coma aberrations. The spectrometer demonstrated experimentally that E/ΔE = 10 050 and 8046 for N 1s (402.1 eV) and Mn 2p (641.8 eV) edges, respectively.