A case of pulmonary sarcoidosis with usual interstitial pneumonia-like lesions distributed predominantly in the lower lung fields]

In 2000, in a 75-year-old man, nodular and reticular opacities were detected in both lower lung fields. He was admitted to our hospital for further examination of these abnormal shadows. Bronchoscopic examination revealed pulmonary sarcoidosis. Prednisolone was prescribed because cardiac sarcoidosis was diagnosed as a clinical complication. In April 2002, the patient visited our hospital for dyspnea on effort. Chest radiography and computed tomography showed nodular and reticular opacities in the right upper lobe, and video-assisted thoracoscopic surgery was performed on the basis of a histological diagnosis. The histological findings of the biopsied specimens revealed a lesion of the type seen in usual interstitial pneumonia, whereas non-caseous granulomas were not detected. His symptoms and chest radiographic findings improved and stabilized with prednisolone and azathioprine. In the present case of pulmonary sarcoidosis, the reticular and nodular opacities predominantly distributed in both lower lung fields, and the histological findings obtained by video-assisted thoracoscopic surgery showed a usual interstitial pneumonia-like lesion. These findings may assist in the understanding of the process of development of pulmonary sarcoidosis.     

Transient conformational fluctuation of TePixD during a reaction

Knowledge of the dynamical behavior of proteins, and in particular their conformational fluctuations, is essential to understanding the mechanisms underlying their reactions. Here, transient enhancement of the isothermal partial molar compressibility, which is directly related to the conformational fluctuation, during a chemical reaction of a blue light sensor protein from the thermophilic cyanobacterium Thermosynechococcus elongatus BP-1 (TePixD, Tll0078) was investigated in a time-resolved manner. The UV-Vis absorption spectrum of TePixD did not change with the application of high pressure. Conversely, the transient grating signal intensities representing the volume change depended significantly on the pressure. This result implies that the compressibility changes during the reaction. From the pressure dependence of the amplitude, the compressibility change of two short-lived intermediate (I₁ and I₂) states were determined to be +(5.6 ± 0.6) × 10⁻² cm³⋅mol⁻¹⋅MPa⁻¹ for I₁ and +(6.6 ± 0.7)×10⁻² cm³⋅mol⁻¹⋅MPa⁻¹ for I₂. This result showed that the structural fluctuation of intermediates was enhanced during the reaction. To clarify the relationship between the fluctuation and the reaction, the compressibility of multiply excited TePixD was investigated. The isothermal compressibility of I₁ and I₂ intermediates of TePixD showed a monotonic decrease with increasing excitation laser power, and this tendency correlated with the reactivity of the protein. This result indicates that the TePixD decamer cannot react when its structural fluctuation is small. We concluded that the enhanced compressibility is an important factor for triggering the reaction of TePixD. To our knowledge, this is the first report showing enhanced fluctuations of intermediate species during a protein reaction, supporting the importance of fluctuations.Proteins often transfer information through changes in domain–domain (or intermolecular) interactions. Photosensor proteins are an important example. They have light-sensing domains and function by using the light-driven changes in domain–domain interactions (1). The sensor of blue light using FAD (BLUF) domain is a light-sensing module found widely among the bacterial kingdom (2). The BLUF domain initiates its photoreaction by the light excitation of the flavin moiety inside the protein, which changes the domain–domain interaction, causing a quaternary structural change and finally transmitting biological signals (3, 4). It has been an important research topic to elucidate how the initial photochemistry occurring in the vicinity of the chromophore leads to the subsequent large conformation change in other domains, which are generally apart from the chromophore.It may be reasonable to consider that the conformation change in the BLUF domain is the driving force in its subsequent reaction; that is, the change in domain–domain interaction. However, sometimes, clear conformational changes have not been observed for the BLUF domain; its conformation is very similar before and after photo-excitation (5–13). The circular dichroism (CD) spectra of BLUF proteins AppA and PixD from thermophilic cyanobacterium Thermosynechococcus elongatus BP-1 (TePixD) did not change on illumination (5, 13). Similarly, solution NMR studies of AppA and BlrB showed only small chemical shifts on excitation (9, 10). The solution NMR structure of BlrP1 showed a clear change, but this was limited in its C-terminal extension region and not core BLUF (11). Furthermore, the diffusion coefficient (D) of the BLUF domain of YcgF was not changed by photo-excitation (12), although D is sensitive to global conformational changes. These results imply that a minor structural change occurs in the BLUF domain. In such cases, how does the BLUF domain control its interdomain interaction? Recently, a molecular dynamics (MD) simulation on another light-sensing domain, the light-oxygen-voltage (LOV) sensing domain, suggested that fluctuation of the LOV core structure could be a key to understanding the mechanism of information transfer (14–16).Because proteins work at room temperature, they are exposed to thermal fluctuations. The importance of such structural fluctuations for biomolecular reactions has been also pointed out: for example, enzymatic activity (17–20). Experimental detections of such conformation fluctuations using single molecular detection (21) or NMR techniques such as the hydrogen-deuterium (H-D) exchange, relaxation dispersion method, and high-pressure NMR (22–24) have succeeded. However, these techniques could not detect the fluctuation of short-lived transient species. Indeed, single molecule spectroscopy can trace the fluctuation in real time, but it is still rather difficult to detect rapid fluctuations for a short-lived intermediate during a reaction. Therefore, information about the fluctuation of intermediates is thus far limited.A thermodynamic measurement is another way to characterize the fluctuation of proteins. In particular, the partial molar isothermal compressibility [K¯T=−(∂V¯/∂P)T] is essential, because this property is directly linked to the mean-square fluctuations of the protein partial molar volume by 〈(V¯−〈V¯〉)2〉≡〈δV¯2〉=kBTK¯T (25). (Here, <X> means the averaged value of a quantity of X.) Therefore, isothermal compressibility is thought to reflect the structural fluctuation of molecules (26). However, experimental measurement of this parameter of proteins in a dilute solution is quite difficult. Indeed, this quantity has been determined indirectly from the theoretical equation using the adiabatic compressibility of a protein solution, which was determined by the sound velocity in the solution (26–31). Although the relation between volume fluctuations and isothermal compressibility is rigorously correct only with respect to the intrinsic part of the volume compressibility, and not the partial molar volume compressibility (32), we considered that this partial molar volume compressibility is still useful for characterizing the fluctuation of the protein structure including its interacting water molecules. In fact, the relationship between β¯T and the volume fluctuation has been often used to discuss the fluctuation of proteins (17, 26–28), and the strong correlation of β¯T of reactants with the functioning for some enzymes (17, 33, 34) has been reported. These studies show the functional importance of the structural fluctuation represented by β¯T. However, thermodynamic techniques lack time resolution, and it has been impossible to measure the fluctuations of short-lived intermediate species.Recently, we developed a time-resolving method for assessing thermodynamic properties using the pulsed laser induced transient grating (TG) method. Using this method, we thus far succeeded in measuring the enthalpy change (ΔH) (35–38), partial molar volume change (ΔV¯) (12, 35, 37), thermal expansion change (Δα¯th) (12, 37), and heat capacity change (ΔC_p) (36–38) for short-lived species. Therefore, in principle, the partial molar isothermal compressibility change (ΔK¯T) of a short-lived intermediate become observable if we conduct the TG experiment under the high-pressure condition and detect ΔV¯ with varying external pressure.There are several difficulties in applying the traditional high-pressure cell to the TG method to measure thermodynamic parameters quantitatively. The most serious problem is ensuring the quantitative performance of the intensity of TG signals measured under the high-pressure condition. On this point, our group has developed a new high-pressure cell specially designed for TG spectroscopy (39) and overcome this problem. In this paper, by applying this high-pressure TG system to the BLUF protein TePixD, we report the first measurement, to our knowledge, of ΔK¯T of short-lived intermediates to investigate the mechanism underlying signal transmission by BLUF proteins, from the view point of the transient fluctuation.TePixD is a homolog of the BLUF protein PixD, which regulates the phototaxis of cyanobacterium (40) and exists in a thermophilic cyanobacterium Thermocynechococcus elongates BP-1 (Tll0078). TePixD is a relatively small (17 kDa) protein that consists only of the BLUF domain with two extended helices in the C-terminal region. In crystals and solutions, it forms a decamer that consists of two pentameric rings (41). The photochemistry of TePixD is typical among BLUF proteins (42–45); on blue light illumination, the absorption spectrum shifts toward red by about 10 nm within a nanosecond. The absorption spectrum does not change further, and the dark state is recovered with a time constant of ∼5 s at room temperature (40, 43). The spectral red shift was explained by the rearrangement of the hydrogen bond network around the chromophore (6, 46–48). The TG method has revealed the dynamic photoreaction mechanism, which cannot be detected by conventional spectroscopic methods. The TG signal of TePixD (Fig. S1) showed that there are two spectrally silent reaction phases: a partial molar volume expansion with the time constant of ∼40 μs and the diffusion coefficient (D) change with a time constant of ∼4 ms. Furthermore, it was reported that the pentamer and decamer states of TePixD are in equilibrium and that the final photoproduct of the decamer is pentamers generated by its dissociation (13, 49). On the basis of these studies, the reaction scheme has been identified as shown in Fig. 1. Here, I₁ is the intermediate of the spectrally red-shifted species (generated within a nanosecond) and I₂ is the one created on the subsequent volume expansion process of +4 cm³⋅mol⁻¹ (∼40 μs). Furthermore, an experiment of the excitation laser power dependence of its TG signal revealed that the TePixD decamer undergoes the original dissociation reaction when only one monomer in the decamer is excited (50). In this study, we investigated the transient compressibility of the intermediates I₁ and I₂ of the photoreaction of TePixD and found a direct link between their fluctuation and reactivity.Open in a separate windowFig. 1.Schematic illustration of the photoreaction of TePixD. Yellow circles represent the TePixD monomer in the ground state, which constructs the decamer and pentamer states. In the dark state, these two forms are in equilibrium. The excited, spectral red-shifted state of the TePixD monomer is indicated by a red circle. The square represents the I₂ state of the monomer, which is created by the volume expansion process.     

Extensive gene deletions in Japanese patients with Diamond-Blackfan anemia

Fifty percent of Diamond-Blackfan anemia (DBA) patients possess mutations in genes coding for ribosomal proteins (RPs). To identify new mutations, we investigated large deletions in the RP genes RPL5, RPL11, RPL35A, RPS7, RPS10, RPS17, RPS19, RPS24, and RPS26. We developed an easy method based on quantitative-PCR in which the threshold cycle correlates to gene copy number. Using this approach, we were able to diagnose 7 of 27 Japanese patients (25.9%) possessing mutations that were not detected by sequencing. Among these large deletions, similar results were obtained with 6 of 7 patients screened with a single nucleotide polymorphism array. We found an extensive intragenic deletion in RPS19, including exons 1-3. We also found 1 proband with an RPL5 deletion, 1 patient with an RPL35A deletion, 3 with RPS17 deletions, and 1 with an RPS19 deletion. In particular, the large deletions in the RPL5 and RPS17 alleles are novel. All patients with a large deletion had a growth retardation phenotype. Our data suggest that large deletions in RP genes comprise a sizable fraction of DBA patients in Japan. In addition, our novel approach may become a useful tool for screening gene copy numbers of known DBA genes.     

Effects of vascular endothelial growth factor-C and -D on osteoclast differentiation and function in human peripheral blood mononuclear cells

ObjectiveThe purpose of this study was to clarify the interaction of vascular endothelial growth factors (VEGFs)-C and -D with cell surface foetal liver kinase-1 (Flk-1) and fms-like tyrosine kinase-4 (Flt-4) receptors in the induction and activity of osteoclasts in cultured human peripheral blood mononuclear cells (PBMCs).DesignPBMCs were cultured on chamber slides or on ivory discs for 2 or 3 weeks in the presence of macrophage-colony stimulating factor (M-CSF), VEGF-A, -C or -D, or placental growth factor (PlGF) with or without receptor activator of nuclear factor kappa-B ligand (RANKL). The number of osteoclasts in each group was counted and the area of ivory resorption was measured. In addition, osteoclast differentiation was further analysed under the same conditions, but with the addition of specific neutralizing antibodies against Flk-1 and Flt-4.ResultsRANKL was essential for the induction of osteoclasts in PBMCs. However, significant differences were found in the number of osteoclasts induced by VEGF-A, -C, -D or M-CSF with RANKL compared with control groups lacking or containing RANKL. Blocking of either Flk-1 or Flt-4 resulted in a reduction in the enhancement of osteoclast differentiation in PBMCs by VEGF-C or -D with RANKL. The osteoclasts induced by VEGF-A, -C, -D or M-CSF with RANKL formed significantly larger resorption lacunae than those formed by osteoclasts induced by RANKL alone.ConclusionsThis study showed that VEGF-C and -D play a role in the induction of osteoclast differentiation through both Flk-1 and Flt-4 receptors and influence the area of the ivory resorption in PBMCs.