Identification of potential target genes for the tomato fruit-ripening regulator RIN by chromatin immunoprecipitation

<p>Abstract</p> <p>Background</p> <p>During ripening, climacteric fruits increase their ethylene level and subsequently undergo various physiological changes, such as softening, pigmentation and development of aroma and flavor. These changes occur simultaneously and are caused by the highly synchronized expression of numerous genes at the onset of ripening. In tomatoes, the MADS-box transcription factor RIN has been regarded as a key regulator responsible for the onset of ripening by acting upstream of both ethylene- and non-ethylene-mediated controls. However, except for <it>LeACS2</it>, direct targets of RIN have not been clarified, and little is known about the transcriptional cascade for ripening.</p> <p>Results</p> <p>Using immunoprecipitated (IPed) DNA fragments recovered by chromatin immunoprecipitation (ChIP) with anti-RIN antibody from ripening tomato fruit, we analyzed potential binding sites for RIN (CArG-box sites) in the promoters of representative ripening-induced genes by quantitative PCR. Results revealed nearly a 5- to 20-fold enrichment of CArG boxes in the promoters of <it>LeACS2</it>, <it>LeACS4</it>, <it>PG</it>, <it>TBG4</it>, <it>LeEXP1</it>, and <it>LeMAN4 </it>and of <it>RIN </it>itself, indicating direct interaction of RIN with their promoters <it>in vivo</it>. Moreover, sequence analysis and genome mapping of 51 cloned IPed DNAs revealed potential RIN binding sites. Quantitative PCR revealed that four of the potential binding sites were enriched 4- to 17-fold in the IPed DNA pools compared with the controls, indicating direct interaction of RIN with these sites <it>in vivo</it>. Near one of the four CArG boxes we found a gene encoding a protein similar to thioredoxin y1. An increase in the transcript level of this gene was observed with ripening in normal fruit but not in the <it>rin </it>mutant, suggesting that RIN possibly induces its expression.</p> <p>Conclusions</p> <p>The presented results suggest that RIN controls fruit softening and ethylene production by the direct transcriptional regulation of cell-wall-modifying genes and ethylene biosynthesis genes during ripening. Moreover, the binding of RIN to its own promoter suggests the presence of autoregulation for <it>RIN </it>expression. ChIP-based analyses identified a novel RIN-binding CArG-box site that harbors a gene associated with <it>RIN </it>expression in its flanking region. These findings clarify the crucial role of RIN in the transcriptional regulation of ripening initiation and progression.</p

The benefit of a sentinel lymph node biopsy and adjuvant therapy in thick (>4 mm) melanoma: multicenter, retrospective study of 291 Japanese patients

The benefit of a sentinel lymph node (SLN) biopsy and adjuvant therapy for patients with thick (>4 mm) melanoma has not been well studied in the Asian population. We examined the benefit of an SLN biopsy and adjuvant therapy on prognosis in Japanese patients with thick melanoma. A review of the melanoma database collected from 26 institutions in Japan identified 291 patients with thick melanoma between 2005 and 2010. Univariate and multivariate analyses were performed to evaluate the factors predictive of the overall survival (OS) and the disease-free survival (DFS). Of the 242 patients with thick melanoma who underwent an SLN biopsy, the results for 96 (40%) were positive. On multivariate analysis, increased Breslow thickness (relative risk, 1.11; 95% confidence interval, 1.05–1.17; P=0.0002) and SLN metastasis (2.14; 1.04–4.43; P=0.040) were associated with a poor OS. Increased Breslow thickness (1.11; 1.04–1.18; P =0.0018), ulceration (3.11; 1.25–7.72; P=0.014), satellitosis (3.89; 1.62–9.31; P=0.0023), and SLN metastasis (2.24; 1.16–4.36; P=0.017) were associated with DFS. Adjuvant chemotherapy had no impact on either OS or DFS. Adjuvant use of a monthly dermal injection of interferon-β (IFN-β) was associated with a improvement in both OS (0.34; 0.17–0.67; P=0.0022) and DFS (0.42; 0.20–0.86; P=0.018). An SLN biopsy provided useful prognostic information and the adjuvant use of IFN-β improved both OS and DFS in Japanese patients with thick melanoma. These results were consistent with those of previous studies carried out on a white population. Therefore, we suggest that an SLN biopsy and adjuvantIFN should be considered for patients with thick melanoma irrespective of the Breslow thickness or ethnicity

Bigradient Phase Referencing

We propose bigradient phase referencing (BPR), a new radio-observation technique, and report its performance using the Japanese very-long-baseline-interferometry network (JVN). In this method, a weak source is detected by phase-referencing using a primary calibrator, in order to play a role as a secondary calibrator for phase-referencing to a weak target. We will be given the opportunity to select a calibrator from lots of milli-Jansky sources, one of which may be located at the position closer to the target. With such a smaller separation, high-quality phase-referencing can be achieved. Furthermore, a subsequent more-sophisticated calibration can relocate array's focus to a hypothetical point much closer to the target; a higher quality of phase referencing is available. Our demonstrative observations with strong radio sources have proved the capabilities of BPR in terms of image dynamic ranges and astrometric reproducibility. The image dynamic range on a target has been improved with a factor of about six compared to that of normal phase-referencing; the resultant position difference of target's emission between two epochs was only 62+-50 micro-arcsecond, even with less than 2300-km baselines at 8.4 GHz and fast-switching of a target-calibrator pair of a 2.1-degree separation.Comment: 10 pages, 4 figures, accepted for publication in PAS

Transient current spectroscopy of a quantum dot in the Coulomb blockade regime

Transient current spectroscopy is proposed and demonstrated in order to investigate the energy relaxation inside a quantum dot in the Coulomb blockade regime. We employ a fast pulse signal to excite an AlGaAs/GaAs quantum dot to an excited state, and analyze the non-equilibrium transient current as a function of the pulse length. The amplitude and time-constant of the transient current are sensitive to the ground and excited spin states. We find that the spin relaxation time is longer than, at least, a few microsecond.Comment: 5 pages, 3 figure

Tumor-Associated Macrophages: Therapeutic Targets for Skin Cancer

Tumor-associated macrophages (TAMs) and regulatory T cells (Tregs) are significant components of the microenvironment of solid tumors in the majority of cancers. TAMs sequentially develop from monocytes into functional macrophages. In each differentiation stage, TAMs obtain various immunosuppressive functions to maintain the tumor microenvironment (e.g., expression of immune checkpoint molecules, production of Treg-related chemokines and cytokines, production of arginase I). Although the main population of TAMs is immunosuppressive M2 macrophages, TAMs can be modulated into M1-type macrophages in each differential stage, leading to the suppression of tumor growth. Because the administration of certain drugs or stromal factors can stimulate TAMs to produce specific chemokines, leading to the recruitment of various tumor-infiltrating lymphocytes, TAMs can serve as targets for cancer immunotherapy. In this review, we discuss the differentiation, activation, and immunosuppressive function of TAMs, as well as their benefits in cancer immunotherapy

Allowed and forbidden transitions in artificial hydrogen and helium atoms

The strength of radiative transitions in atoms is governed by selection rules. Spectroscopic studies of allowed transitions in hydrogen and helium provided crucial evidence for the Bohr's model of an atom. Forbidden transitions, which are actually allowed by higher-order processes or other mechanisms, indicate how well the quantum numbers describe the system. We apply these tests to the quantum states in semiconductor quantum dots (QDs), which are regarded as artificial atoms. Electrons in a QD occupy quantized states in the same manner as electrons in real atoms. However, unlike real atoms, the confinement potential of the QD is anisotropic, and the electrons can easily couple with phonons of the material. Understanding the selection rules for such QDs is an important issue for the manipulation of quantum states. Here we investigate allowed and forbidden transitions for phonon emission in one- and two-electron QDs (artificial hydrogen and helium atoms) by electrical pump-and-probe experiments, and find that the total spin is an excellent quantum number in artificial atoms. This is attractive for potential applications to spin based information storage.Comment: slightly longer version of Nature 419, 278 (2002

Japanese VLBI Network observations of radio-loud narrow-line Seyfert 1 galaxies

We performed phase-reference very long baseline interferometry (VLBI) observations on five radio-loud narrow-line Seyfert 1 galaxies (NLS1s) at 8.4 GHz with the Japanese VLBI Network (JVN). Each of the five targets (RXS J08066+7248, RXS J16290+4007, RXS J16333+4718, RXS J16446+2619, and B3 1702+457) in milli-Jansky levels were detected and unresolved in milli-arcsecond resolutions, i.e., with brightness temperatures higher than 10^7 K. The nonthermal processes of active galactic nuclei (AGN) activity, rather than starbursts, are predominantly responsible for the radio emissions from these NLS1s. Out of the nine known radio-loud NLS1s, including the ones chosen for this study, we found that the four most radio-loud objects exclusively have inverted spectra. This suggests a possibility that these NLS1s are radio-loud due to Doppler beaming, which can apparently enhance both the radio power and the spectral frequency.Comment: 8 pages, 2 figures, accepted for publication in PAS

VLBI Detections of Parsec-Scale Nonthermal Jets in Radio-Loud Broad Absorption Line Quasars

We conducted radio detection observations at 8.4 GHz for 22 radio-loud broad absorption line (BAL) quasars, selected from the Sloan Digital Sky Survey (SDSS) Third Data Release, by a very-long-baseline interferometry (VLBI) technique. The VLBI instrument we used was developed by the Optically ConnecTed Array for VLBI Exploration project (OCTAVE), which is operated as a subarray of the Japanese VLBI Network (JVN). We aimed at selecting BAL quasars with nonthermal jets suitable for measuring their orientation angles and ages by subsequent detailed VLBI imaging studies to evaluate two controversial issues of whether BAL quasars are viewed nearly edge-on, and of whether BAL quasars are in a short-lived evolutionary phase of quasar population. We detected 20 out of 22 sources using the OCTAVE baselines, implying brightness temperatures greater than 10^5 K, which presumably come from nonthermal jets. Hence, BAL outflows and nonthermal jets can be generated simultaneously in these central engines. We also found four inverted-spectrum sources, which are interpreted as Doppler-beamed, pole-on-viewed relativistic jet sources or young radio sources: single edge-on geometry cannot describe all BAL quasars. We discuss the implications of the OCTAVE observations for investigations for the orientation and evolutionary stage of BAL quasars.Comment: 10 pages, no figure, 3 tables, accepted for publication in PAS

Multifrequency VLBI Observations of the Broad Absorption Line Quasar J1020+4320: Recently Restarted Jet Activity?

This paper reports very-long-baseline interferometry observations of the radio-loud broad absorption line (BAL) quasar J1020+4320 at 1.7, 2.3, 6.7, and 8.4 GHz using the Japanese VLBI network (JVN) and European VLBI network (EVN). The radio morphology is compact with a size of ~10 pc. The convex radio spectrum is stable over the last decade; an observed peak frequency of 3.2 GHz is equivalent to 9.5 GHz in the rest frame, suggesting an age of the order of ~100 years as a radio source, according to an observed correlation between linear size and peak frequency of compact steep spectrum (CSS) and giga-hertz peaked spectrum (GPS) radio sources. A low-frequency radio excess suggests relic of past jet activity. J1020+4320 may be one of the quasars with recurrent and short-lived jet activity during a BAL-outflowing phase.Comment: 7 pages, 2 figures, 2 tables, accepted for publication in PAS