A flexible representation of omic knowledge for thorough analysis of microarray data

BACKGROUND: In order to understand microarray data reasonably in the context of other existing biological knowledge, it is necessary to conduct a thorough examination of the data utilizing every aspect of available omic knowledge libraries. So far, a number of bioinformatics tools have been developed. However, each of them is restricted to deal with one type of omic knowledge, e.g., pathways, interactions or gene ontology. Now that the varieties of omic knowledge are expanding, analysis tools need a way to deal with any type of omic knowledge. Hence, we have designed the Omic Space Markup Language (OSML) that can represent a wide range of omic knowledge, and also, we have developed a tool named GSCope3, which can statistically analyze microarray data in comparison with the OSML-formatted omic knowledge data. RESULTS: In order to test the applicability of OSML to represent a variety of omic knowledge specifically useful for analysis of Arabidopsis thaliana microarray data, we have constructed a Biological Knowledge Library (BiKLi) by converting eight different types of omic knowledge into OSML-formatted datasets. We applied GSCope3 and BiKLi to previously reported A. thaliana microarray data, so as to extract any additional insights from the data. As a result, we have discovered a new insight that lignin formation resists drought stress and activates transcription of many water channel genes to oppose drought stress; and most of the 20S proteasome subunit genes show similar expression profiles under drought stress. In addition to this novel discovery, similar findings previously reported were also quickly confirmed using GSCope3 and BiKLi. CONCLUSION: GSCope3 can statistically analyze microarray data in the context of any OSML-represented omic knowledge. OSML is not restricted to a specific data type structure, but it can represent a wide range of omic knowledge. It allows us to convert new types of omic knowledge into datasets that can be used for microarray data analysis with GSCope3. In addition to BiKLi, by collecting various types of omic knowledge as OSML libraries, it becomes possible for us to conduct detailed thorough analysis from various biological viewpoints. GSCope3 and BiKLi are available for academic users at our web site

Reappraisal of the toxicity test method using the green alga Ulva pertusa Kjellman (Chlorophyta),

This study was aimed to develop an objective way of quantifying the reproductive status of the green macroalga, Ulva pertusa using a vital stain and programmed automated analysis (by Image J program). The EC50 values (with 95% CI), the concentrations of toxicants inducing a reduction of 50% in sporulation after 96 h exposure, from the newly developed method were similar to those obtained by the conventional method: 0.651 (0.598-0.705) mg l(-1) for Cd, 0.144 (0.110-0.162) mg l(-1) for Cu, 0.180 (0.165-0.195) mg l(-1) for atrazine, 0.076 (0.049-0.094) mg l(-1) for diuron and 30.6 (26.5-34.4) ml l(-1) for DMSO, respectively. When the EC50 values from this study were compared to that those from literatures, the sensitivity for some toxicants was similar or higher than that of U. fasciata (1.930 mg l(-1) for germination for Cd), U. armoricana (0.250 mg l(-1) for Fv/Fm for Cu), U. reticulata (0.126-1.585 mg l(-1) for growth for Cu), and U. intestinalis (0.650 mg l(-1) for Fv/Fm for atrazine). The subjective views of the experimental performers can be eliminated using the newly developed method. The Ulva method gave consistent responses to Cu and Cd of internationally allowable ranges for effluents, implying that the method is a useful tool for monitoring industrial wastewaters containing these metals

Lithography-Free Fabrication of Large Area Subwavelength Antireflection Structures Using Thermally Dewetted Pt/Pd Alloy Etch Mask

We have demonstrated lithography-free, simple, and large area fabrication method for subwavelength antireflection structures (SAS) to achieve low reflectance of silicon (Si) surface. Thin film of Pt/Pd alloy on a Si substrate is melted and agglomerated into hemispheric nanodots by thermal dewetting process, and the array of the nanodots is used as etch mask for reactive ion etching (RIE) to form SAS on the Si surface. Two critical parameters, the temperature of thermal dewetting processes and the duration of RIE, have been experimentally studied to achieve very low reflectance from SAS. All the SAS have well-tapered shapes that the refractive index may be changed continuously and monotonously in the direction of incident light. In the wavelength range from 350 to 1800 nm, the measured reflectance of the fabricated SAS averages out to 5%. Especially in the wavelength range from 550 to 650 nm, which falls within visible light, the measured reflectance is under 0.01%

Tapered catheter-based transurethral photoacoustic and ultrasonic endoscopy of the urinary system

Early diagnosis is critical for treating bladder cancer, as this cancer is very aggressive and lethal if detected too late. To address this important clinical issue, a photoacoustic tomography (PAT)-based transabdominal imaging approach was suggested in previous reports, in which its in vivo feasibility was also demonstrated based on a small animal model. However, successful translation of this approach to real clinical settings would be challenging because the human bladder is located at a depth that far exceeds the typical penetration depth of PAT (???3 cm for in vivo cases). In this study, we developed a tapered catheter-based, transurethral photoacoustic and ultrasonic endoscopic probe with a 2.8 mm outer diameter to investigate whether the well-known benefits of PAT can be harnessed to resolve unmet urological issues, including early diagnosis of bladder cancer. To demonstrate the in vivo imaging capability of the proposed imaging probe, we performed a rabbit model-based urinary system imaging experiment and acquired a 3D microvasculature map distributed in the wall of the urinary system, which is a first in PAT, to the best of our knowledge. We believe that the results strongly support the use of this transurethral imaging approach as a feasible strategy for addressing urological diagnosis issues

Development of a Technology Assessment Model by Patents and Customers' Review Data

Recent years have seen an increasing number of patent disputes due to excessive competition in the global market and a reduced technology life-cycle; this has increased the risk of investment in technology development. While many global companies have started developing a methodology to identify promising technologies and assess for decisions, the existing methodology still has some limitations. Post hoc assessments of the new technology are not being performed, especially to determine whether the suggested technologies turned out to be promising. For example, in existing quantitative patent analysis, a patent's citation information has served as an important metric for quality assessment, but this analysis cannot be applied to recently registered patents because such information accumulates over time. Therefore, we propose a new technology assessment model that can replace citation information and positively affect technological development based on post hoc analysis of the patents for promising technologies. Additionally, we collect customer reviews on a target technology to extract keywords that show the customers' needs, and we determine how many keywords are covered in the new technology. Finally, we construct a portfolio (based on a technology assessment from patent information) and a customer-based marketability assessment (based on review data), and we use them to visualize the characteristics of the new technologies

Application of a programmed semi-automated Ulva pertusa bioassay for testing single toxicants and stream water quality

A toxicity test based on inhibition of reproduction in the green macroalga Ulva pertusa involves quantifying the change in thallus color as reproduction progresses. However, interpretation of this color change is reliant on the skill level of the examiner. This study aimed to validate a new toxicity test based on inhibition of reproduction in the green macroalga U. pertusa using a vital stain and programmed semi-automated analysis (using Image J) of the change in thallus color. The toxicity rank by inverse EC50 values was: irgarol (0.048 mg L-1) > Ag (0.132 mg L-1) > As (0.172 mg L-1) > simazine (0.378 mg L-1) > formaldehyde (0.442 mg L-1) > DCOIT (0.783 mg L-1) > ZnPT (3.556 mg L-1) > medetomidine (11.600 mg L-1) > phenol (29.316 mg L-1) > methanol (2,736 mg L-1) > ethanol (3,306 mg L-1). The sensitivity of the U. pertusa test to stream waters was similar to or lower than those of the commonly-used Lemna minor and Daphnia magna bioassays. The U. pertusa bioassay is sensitive to, and suitable for, testing various toxicants including metals, volatile organic compounds, herbicide, antifouling agents and phenol and can also be applied to testing freshwater quality after salinity adjustment

Activation of Hypoxia-Inducible Factor-1α Signaling Pathway Has the Protective Effect of Intervertebral Disc Degeneration

Intervertebral discs (IVDs) have poor nutrient diffusion, because the nucleus pulposus (NP) lacks direct vascular supply and likely generates adenosine triphosphate by anaerobic glycolysis. Regulation of glycolysis is mediated by hypoxia-inducible factor-1α (HIF-1α), a transcription factor that responds to local oxygen tension. Constitutively active HIF-1α (CA HIF-1α) was created by point mutation and determined the protective role of HIF-1α in IVD degeneration. Under fluoroscopy, rat caudal IVD segments were stabbed by a needle puncture, and pcDNA3- HIF-1α wild-type (WT) or pcDNA3-CA HIF-1α was transfected into NP cell lines. The constitutive activity of CA HIF-1α was analyzed using a luciferase assay after cell lysis. Next, IVD tissue samples were retrieved from five patients with degenerative lumbar spinal stenosis at the time of surgery, and NP cells were cultured. NP cells were transfected with CA HIF-1α, and relevant gene expression was measured. HIF-1α protein levels in the nucleus were significantly higher, and transcriptional activity was 10.3-fold higher in NP cells with CA HIF-1α than in those with HIF-1α WT. Gene transfer of CA HIF-1α into NP cells enhanced the expression of Glut-1, Glut-3, aggrecan, type II collagen, and Sox9. Moreover, CA HIF-1α reduced the apoptosis of NP cells induced by the Fas ligand. The HIF-1α and collagen 2 expression levels were notably increased in the NP cells of the CA HIF-1α transfected segments in histology and immunohistochemistry study. Collectively, these results suggest that activation of HIF-1α signaling pathway may play a protective role against IVD degeneration and could be used as a future therapeutic agent

Assessment of various toxicity endpoints in duckweed (Lemna minor) at the physiological, biochemical, and molecular levels as a measure of diuron stress

Simple Summary The presence of diuron in a variety of environments has been reported worldwide to exert serious harm to human health and the ecosystem. HPLC and mass spectrometry are highly specific and sensitive methods for herbicide detection, but they have several drawbacks including complex sample preparation procedures, the need for expensive chemicals and equipment, and interference from secondary contaminants during analysis. In addition, these purely chemical approaches do not provide ecologically meaningful information on temporal changes in terms of exposure or the interactive effects of pollutants. In order to compensate for these limitations, biological assays have been used to assess pollutant-induced ecological risks. Lemna minor is an attractive experimental model organism that has been used for decades for the prospective risk assessment of pesticides. In the current study, we examined the effects of diuron on L. minor using different endpoints at the physiological (growth and photosynthetic efficiency), biochemical (pigment biosynthesis and reactive oxygen species (ROS) levels), and molecular (gene transcription) levels. Our findings provide important insight into the relative sensitivity of different endpoints for diuron toxicity assessment. In addition, they shed light on the toxicity mechanisms of diuron in a model aquatic macrophyte species. The common, broad-spectrum herbicide diuron poses some risks to the environment due to its long persistence and high toxicity. Therefore, the effective monitoring of diuron residues will inform efforts to assess its impacts on ecosystems. In this study, we evaluated the toxicity targets of diuron in the model aquatic macrophyte Lemna minor at the physiological (growth and photosynthetic efficiency), biochemical (pigment biosynthesis and reactive oxygen species (ROS) levels), and molecular (rbcL transcript) levels. The toxicity of diuron was detectable after 48 h of exposure and the order of sensitivity of toxicity endpoints was gene transcription > maximum electron transport rate (ETRmax) > non-photochemical quenching (NPQ) > maximum quantum yield (F-v/F-m) > ROS > fresh weight > chlorophyll b > chlorophyll a > total frond area > carotenoids. Under diuron stress, pigment, ROS, and gene transcript levels increased while frond area, fresh weight, and photosynthesis (F-v/F-m and ETRmax) gradually decreased with the increasing duration of exposure. Notably, ROS levels, F-v/F-m, frond area, and fresh weight were highly correlated with diuron concentration. The growth endpoints (frond area and fresh weight) showed a strong negative correlation with ROS levels and a positive correlation with F-v/F-m and ETRmax. These findings shed light on the relative sensitivity of different endpoints for the assessment of diuron toxicity

First in vivo rat colorectum imaging result of the integrated photoacoustic and ultrasonic endoscopic mini-probe system

We have successfully acquired first in vivo images from a rat colorectum by using the 3.0-mm outer diameter integrated photoacoustic and ultrasonic endoscopic mini-probe system that we introduced in 2019 ABC conference. As previously presented, the system featured the ~1.8-m long torque coil-based proximal actuation mechanism, which enables intra-instrument channel use, and the quasi-optical-resolution photoacoustic imaging capability. In the recent progress, we could confirm that, although the ultrasound image provided deeper imaging, only the photoacoustic image revealed a high-resolution microvasculature distributed in the rat colorectum. The result suggests that our technique could provide more convincing information in relation to the diagnosis of various types of gastrointestinal cancers based on the photoacoustically added vasculature information