BioAssay Research Database (BARD): chemical biology and probe-development enabled by structured metadata and result types

BARD, the BioAssay Research Database (https://bard.nih.gov/) is a public database and suite of tools developed to provide access to bioassay data produced by the NIH Molecular Libraries Program (MLP). Data from 631 MLP projects were migrated to a new structured vocabulary designed to capture bioassay data in a formalized manner, with particular emphasis placed on the description of assay protocols. New data can be submitted to BARD with a user-friendly set of tools that assist in the creation of appropriately formatted datasets and assay definitions. Data published through the BARD application program interface (API) can be accessed by researchers using web-based query tools or a desktop client. Third-party developers wishing to create new tools can use the API to produce stand-alone tools or new plug-ins that can be integrated into BARD. The entire BARD suite of tools therefore supports three classes of researcher: those who wish to publish data, those who wish to mine data for testable hypotheses, and those in the developer community who wish to build tools that leverage this carefully curated chemical biology resource.

Effects of γ-ray irradiation on optical absorption and laser damage performance of KDP crystals containing arsenic impurities

The effects of γ-irradiation on potassium dihydrogen phosphate crystals containing arsenic impurities are investigated with different optical diagnostics, including UV-VIS absorption spectroscopy, photo-thermal common-path interferometer and photoluminescence spectroscopy. The optical absorption spectra indicate that a new broad absorption band near 260 nm appears after γ-irradiation. It is found that the intensity of absorption band increases with the increasing irradiation dose and arsenic impurity concentration. The simulation of radiation defects show that this absorption is assigned to the formation of AsO₄⁴⁻ centers due to arsenic ions substituting for phosphorus ions. Laser-induced damage threshold test is conducted by using 355 nm nanosecond laser pulses. The correlations between arsenic impurity concentration and laser induced damage threshold are presented. The results indicate that the damage performance of the material decreases with the increasing arsenic impurity concentration. Possible mechanisms of the irradiation-induced defects formation under γ-irradiation of KDP crystals are discussed.

Assessment of the hemodynamic profile in periodontal tissues of diabetic subjects with periodontitis by optical spectroscopy

BACKGROUND AND OBJECTIVE

The influence of diabetes mellitus (DM) on the hemodynamics of periodontal tissues has not been assessed previously. The primary objective of this study was to validate optical spectroscopy as a periodontal diagnostic tool for subjects with type 2 DM and chronic periodontitis.

MATERIAL AND METHODS

Using a portable optical near-infrared spectrometer, optical spectra were obtained from healthy (n = 127), gingivitis (n = 115), and periodontitis (n = 109) sites of 65 subjects with type 2 DM and chronic periodontitis. Healthy (n = 65) sites of 15 nondiabetic subjects without periodontitis were used as controls. A modified Beer-Lambert unmixing model that incorporates a nonparametric scattering-loss function was used to determine the relative contribution of deoxygenated hemoglobin and oxygenated hemoglobin (HbO2 ) to the overall spectrum. The balance between tissue oxygen delivery and oxygen utilization in periodontal tissues was assessed.

RESULTS

In diabetic subjects, tissue oxygen saturation and HbO2 concentration were significantly decreased in the periodontitis sites (p < 0.01) compared with the healthy and gingivitis sites. Furthermore, tissue oxygenation in healthy sites of control subjects was significantly higher than that in sites of diabetic subjects (p < 0.01).

CONCLUSION

In summary, the results of this study suggest that optical spectroscopy can monitor the hemodynamic profile in diabetic subjects with chronic periodontitis. Furthermore, healthy sites of diabetic subjects presented lower tissue oxygenation than did those of nondiabetic subjects.

Effects of surface defects on two-dimensional electron gas at NdAlO3/SrTiO3 interface

Density functional theory calculations of NdAlO₃/SrTiO₃ heterostructure show that two-dimensional electron gas (2-DEG) is produced at the interface with a built-in potential of ~0.3 eV per unit cell. The effects of surface defects on the phase stability and electric field of 2-DEG have been investigated. It is found that oxygen vacancy is easily to form on the NdAlO₃(001) surface, with a low threshold displacement energy and a low formation energy. This point defect results in surface reconstruction and the formation of a zigzag -Al-O-Al- chain, which quenches the built-in potential and enhances the carrier density significantly. These results will provide fundamental insights into understanding how surface defects influence the electronic behavior of 2-DEG and tuning their electronic properties through surface modification.

Arsenic trioxide alleviates airway hyperresponsiveness and promotes apoptosis of CD4+ T lymphocytes: evidence for involvement of the ER stress-CHOP pathway

BACKGROUND

Asthma is a chronic inflammatory disorder of the airway. Arsenic trioxide (ATO) is an ancient Chinese medicine, which is used to treat psoriasis, asthma, and acute promyelocytic leukemia.

AIM

We wanted to research the effect of arsenic trioxide on asthma.

METHODS

Using a murine model of asthma, the airway hyperresponsiveness was conducted by the Buxco pulmonary function apparatus. Total cell counts of BALF were counted with a counting chamber. Histopathological analysis of lung tissues was conducted by hematoxylin-eosin or periodic acid-schiff stain. CD4+T cells were purified from the spleen by positive selection, using immunomagnetic beads. Apoptosis measurements were done with Annexin-V/PI staining. Western blot analysis and real time-PCR were performed to assess the expression of C/EBP-homologous protein (CHOP) and glucose-regulated protein 78 (GRP78), respectively. RNA interference was conducted to inhibit the expression of CHOP.

RESULTS

We found that arsenic trioxide treatment alleviated airway hyperresponsiveness and reduced inflammation of the lung in asthmatic mice. Furthermore, arsenic trioxide treatment promoted apoptosis of CD4+T cells in vivo and in vitro. When CD4+T cells were cultured with arsenic trioxide for 5 h at a concentration of 5 μM, the expression of GRP78 and CHOP was increased. Treatment of CD4+T cells with CHOP siRNA, provided partial resistance to arsenic trioxide-induced apoptosis of CD4+T cells

CONCLUSIONS

These data demonstrated that arsenic trioxide can reduce the severity of asthma attacks and induce the apoptosis of CD4+ T cell which the ER stress-CHOP pathway involved.

Influence of the catheter diameter on the investigation of the esophageal motility through solid-state high-resolution manometry

Past studies have shown that catheter diameter is one of the device-dependent problems which influence the manometric results in the conventional water perfusion esophageal manometry. High-resolution solid-state manometry which abandons water perfusion is thought as an improved manometry method benefited from more pressure sensors, and it is gradually widely used in many present esophageal motility studies. There was no research to evaluate the influence of catheter diameter on the solid-state high-resolution manometry results. The aim of this study was to investigate whether solid-state high-resolution catheters of different diameter provide different data and results. Nine asymptomatic volunteers and 18 gastroesophageal reflux disease patients accepted high-resolution manometry examinations with two solid-state catheters of different outer diameter (4.2 mm and 2.7 mm). Every examination contained 5 minutes resting pressure, 10 water swallows and 10 bread swallows. Some important parameters of the esophageal sphincters and esophageal body peristalsis were analyzed. They included the locations and resting pressure of sphincters, the distal contractile integral, the 4-second integrated relaxation pressure etc. Then, these parameters and the diagnosis of each swallow based on them provided by the two different diameter catheters were compared. (i) The 4.2 mm thick catheter provided higher upper esophageal sphincter resting pressure than the 2.7 mm thick catheter (59.4 ± 21.1 mmHg vs. 49.7 ± 21.4 mmHg); (ii) the 2.7 mm thick catheter provided higher 4-second integrated relaxation pressure than the 4.2 mm thick catheter (10.9 ± 4.5 mmHg vs. 8.5 ± 3.8 mmHg) in water swallows; (iii) the mean distal contractile integral of the water and bread swallows in the large diameter catheter were higher than in the small diameter catheter (989.2 ± 650.0 mmHg/cm/s vs. 806.3 ± 563.7 mmHg/cm/s in water swallows, 1762.5 ± 1440.6 mmHg/cm/s vs. 1275.7 ± 982.0 mmHg/cm/s in bread swallows); (iv) on the lower esophageal sphincter resting pressure, most parameters in bread swallows provided by the two catheters were of no statistical significance; (v) the 2.7 mm thick catheter detected more hypotensive peristalsis swallows than the other catheter in water swallows; and (vi) the final diagnosis of about half of the subjects provided by the two catheters were different. The 2.7 mm thick solid-state high-resolution manometry catheter provides somewhat different data from the usually used 4.2 mm thick catheter. It is needed to set up different and independent series of normative value for the solid-state high-resolution manometry catheters of different outer diameter. The normative value and diagnostic criterion got from one catheter is not universal and acceptable for researches with catheter of different diameter.

[Transformation of human bronchial epithelial cells BEP2D induced by ²³⁸Pu α-particles]

BACKGROUND

To establish a model for the study of transformation of human cell by radon and its progeny.

METHODS

BEP2D, a HPV18 immortalized human bronchial epithelial cell line, was irradiated with high-energy α-particles emitted by ²³⁸Pu.

RESULTS

A single 1. 5 Gy dose of α-particles induced transformation of the cells. A series of sequential steps arose among transformed cells, including altered growth kinetics, resistance to serum-induced terminal differentiation, and anchorage-independence growth.

CONCLUSIONS

This cell line may provide a model to study the cellular and molecular changes at various stages in radiation carcinogenesis.

Ghrelin contributes to derangements of glucose metabolism induced by rapamycin in mice

AIMS/HYPOTHESIS

Rapamycin impairs glucose tolerance and insulin sensitivity. Our previous study demonstrated that rapamycin significantly increases the production of gastric ghrelin, which is critical in the regulation of glucose metabolism. Here, we investigated whether ghrelin contributes to derangements of glucose metabolism induced by rapamycin.

METHODS

The effects of rapamycin on glucose metabolism were examined in mice receiving ghrelin receptor antagonist or with Ghsr1a gene knockout. Changes in GLUT4, c-Jun N-terminal kinase (JNK) and phosphorylated ribosomal protein S6 (pS6) were investigated by immunofluorescent staining or western blotting. Related hormones were detected by radioimmunoassay kits.

RESULTS

Rapamycin impaired glucose metabolism and insulin sensitivity not only in normal C57BL/6J mice but also in both obese mice induced by a high fat diet and db/db mice. This was accompanied by elevation of plasma acylated ghrelin. Rapamycin significantly increased the levels of plasma acylated ghrelin in normal C57BL/6J mice, high-fat-diet-induced obese mice and db/db mice. Elevation in plasma acylated ghrelin and derangements of glucose metabolism upon administration of rapamycin were significantly correlated. The deterioration in glucose homeostasis induced by rapamycin was blocked by D: -Lys3-GHRP-6, a ghrelin receptor antagonist, or by deletion of the Ghsr1a gene. Ghrelin receptor antagonism and Ghsr1a knockout blocked the upregulation of JNK activity and downregulation of GLUT4 levels and translocation in the gastrocnemius muscle induced by rapamycin.

CONCLUSIONS/INTERPRETATION

The current study demonstrates that ghrelin contributes to derangements of glucose metabolism induced by rapamycin via altering the content and translocation of GLUT4 in muscles.

The Yangtze-Hydro Project: a Chinese-German environmental program

Water of good quality is one of the basic needs of human life. Worldwide, great efforts are being undertaken for an assured water supply. In this respect, one of the largest water technology projects worldwide is the Yangtze Three Gorges Dam in China. There is a need for extensive scientific and technical understanding of the challenges arising from this large hydrological engineering project. German and Chinese groups from various scientific fields are collaborating to provide knowledge for the sustainable management of the reservoir. In this project description, the Yangtze Three Gorges Dam Project, its goals and challenges, are described in brief, and the contributions of the German research projects are presented.

Exosomes and immune surveillance of neoplastic lesions: a review

The immune system has been reported to suppress the development and progression of neoplastic lesions; however, the exact mechanisms by which neoplastic lesions and the immune system interact are not well understood. Within the last decade, tiny membrane bound particles, approximately 30-100 nm in diameter, have been observed in the blood and other body fluids. These particles, currently called exosomes, are released from many types of tissues including tumors, and they contain and carry many proteins, and mRNAs and microRNA species. We review here how tumors suppress the immune system, especially by the formation of exosomes. Exosomes released from tumors are carried in part by the vascular system to distant cells, which phagocytose them. Depending on the proteins, mRNAs or microRNAs in the exosomes and the cell type, phagocytosis of exosomes may provide a modulating signal to the cell. In the case of exosomes from tumors, uptake of the exosomes by cells of the immune system has been reported to have three main effects: 1) suppression of the number and activity of natural killer cells, 2) suppression of the activity of T cells and 3) suppression of the number and maturation of mature dendritic cells.

Quantum theory for cold avalanche ionization in solids

A theory of photon-assisted impact ionization in solids is presented. Our theory makes a quantum description of the new impact ionization-cold avalanche ionization recently reported by P. P. Rajeev, M. Gertsvolf, P. B. Corkum, and D. M. Rayner [Phys. Rev. Lett. 102, 083001 (2009)]. The present theory agrees with the experiments and can be reduced to the traditional impact ionization expression in the absence of a laser.