Rapid and reliable extraction of genomic DNA from various wild-type and transgenic plants

BACKGROUND: DNA extraction methods for PCR-quality DNA from calluses and plants are not time efficient, since they require that the tissues be ground in liquid nitrogen, followed by precipitation of the DNA pellet in ethanol, washing and drying the pellet, etc. The need for a rapid and simple procedure is urgent, especially when hundreds of samples need to be analyzed. Here, we describe a simple and efficient method of isolating high-quality genomic DNA for PCR amplification and enzyme digestion from calluses, various wild-type and transgenic plants. RESULTS: We developed new rapid and reliable genomic DNA extraction method. With our developed method, plant genomic DNA extraction could be performed within 30 min. The method was as follows. Plant tissue was homogenized with salt DNA extraction buffer using hand-operated homogenizer and extracted by phenol:chloroform:isoamyl alcohol (25:24:1). After centrifugation, the supernatant was directly used for DNA template for PCR, resulting in successful amplification for RAPD from various sources of plants and specific foreign genes from transgenic plants. After precipitating the supernatant, the DNA was completely digested by restriction enzymes. CONCLUSION: This DNA extraction procedure promises simplicity, speed, and efficiency, both in terms of time and the amount of plant sample required. In addition, this method does not require expensive facilities for plant genomic DNA extraction

An integrated database-pipeline system for studying single nucleotide polymorphisms and diseases

<p>Abstract</p> <p>Background</p> <p>Studies on the relationship between disease and genetic variations such as single nucleotide polymorphisms (SNPs) are important. Genetic variations can cause disease by influencing important biological regulation processes. Despite the needs for analyzing SNP and disease correlation, most existing databases provide information only on functional variants at specific locations on the genome, or deal with only a few genes associated with disease. There is no combined resource to widely support gene-, SNP-, and disease-related information, and to capture relationships among such data. Therefore, we developed an integrated database-pipeline system for studying SNPs and diseases.</p> <p>Results</p> <p>To implement the pipeline system for the integrated database, we first unified complicated and redundant disease terms and gene names using the Unified Medical Language System (UMLS) for classification and noun modification, and the HUGO Gene Nomenclature Committee (HGNC) and NCBI gene databases. Next, we collected and integrated representative databases for three categories of information. For genes and proteins, we examined the NCBI mRNA, UniProt, UCSC Table Track and MitoDat databases. For genetic variants we used the dbSNP, JSNP, ALFRED, and HGVbase databases. For disease, we employed OMIM, GAD, and HGMD databases. The database-pipeline system provides a disease thesaurus, including genes and SNPs associated with disease. The search results for these categories are available on the web page <url>http://diseasome.kobic.re.kr/</url>, and a genome browser is also available to highlight findings, as well as to permit the convenient review of potentially deleterious SNPs among genes strongly associated with specific diseases and clinical phenotypes.</p> <p>Conclusion</p> <p>Our system is designed to capture the relationships between SNPs associated with disease and disease-causing genes. The integrated database-pipeline provides a list of candidate genes and SNP markers for evaluation in both epidemiological and molecular biological approaches to diseases-gene association studies. Furthermore, researchers then can decide semi-automatically the data set for association studies while considering the relationships between genetic variation and diseases. The database can also be economical for disease-association studies, as well as to facilitate an understanding of the processes which cause disease. Currently, the database contains 14,674 SNP records and 109,715 gene records associated with human diseases and it is updated at regular intervals.</p

2D perovskite stabilized phase-pure formamidinium perovskite solar cells.

Compositional engineering has been used to overcome difficulties in fabricating high-quality phase-pure formamidinium perovskite films together with its ambient instability. However, this comes alongside an undesirable increase in bandgap that sacrifices the device photocurrent. Here we report the fabrication of phase-pure formamidinium-lead tri-iodide perovskite films with excellent optoelectronic quality and stability. Incorporation of 1.67 mol% of 2D phenylethylammonium lead iodide into the precursor solution enables the formation of phase-pure formamidinium perovskite with an order of magnitude enhanced photoluminescence lifetime. The 2D perovskite spontaneously forms at grain boundaries to protect the formamidinium perovskite from moisture and suppress ion migration. A stabilized power conversion efficiency (PCE) of 20.64% (certified stabilized PCE of 19.77%) is achieved with a short-circuit current density exceeding 24 mA cm-2 and an open-circuit voltage of 1.130 V, corresponding to a loss-in-potential of 0.35 V, and significantly enhanced operational stability

Effectiveness of the Novel Herbal Medicine, KIOM-MA, and Its Bioconversion Product, KIOM-MA128, on the Treatment of Atopic Dermatitis

This study was conducted to determine if oral administration of the novel herbal medicine, KIOM-MA, and its Lactobacillus acidophilus-fermented product, KIOM-MA128, has therapeutic properties for the treatment of atopic dermatitis (AD). Using AD-induced BALB/c mice by Ovalbumin and aluminum hydroxide, the effectiveness of KIOM-MA and KIOM-MA128 on AD was evaluated. Oral administration of KIOM-MA and KIOM-MA128 reduced major clinical signs of AD including erythema/darkening, edema/papulation, excoriations, lichenification/prurigo, and dryness. Interestingly, KIOM-MA128 more significantly improved AD-related symptoms including decrease of IgE level in the plasma as well as reduction of scratching behavior, skin severity in the AD BALB/c model. HPLC analysis showed the significant changes in the constituent patterns between KIOM-MA and KIOM-MA128. Our results suggest that both KIOM-MA and KIOM-MA128 have potential for therapeutic reagent for the treatment of AD, and further, the efficacy is significantly enhanced by L. acidophilus fermentation via increases in its indicator molecule

Strain-gradient-induced magnetic anisotropy in straight-stripe mixed-phase bismuth ferrites: An insight into flexomagnetic phenomenon

Implementation of antiferromagnetic compounds as active elements in spintronics has been hindered by their insensitive nature against external perturbations which causes difficulties in switching among different antiferromagnetic spin configurations. Electrically-controllable strain gradient can become a key parameter to tune the antiferromagnetic states of multiferroic materials. We have discovered a correlation between an electrically-written straight-stripe mixed-phase boundary and an in-plane antiferromagnetic spin axis in highly-elongated La-5%-doped BiFeO$_{3}$ thin films by performing polarization-dependent photoemission electron microscopy in conjunction with cluster model calculations. Model Hamiltonian calculation for the single-ion anisotropy including the spin-orbit interaction has been performed to figure out the physical origin of the link between the strain gradient present in the mixed phase area and its antiferromagnetic spin axis. Our findings enable estimation of the strain-gradient-induced magnetic anisotropy energy per Fe ion at around 5$\times$10$^{-12}$ eV m, and provide a new pathway towards an electric-field-induced 90$^{\circ}$ rotation of antiferromagnetic spin axis at room temperature by flexomagnetism.Comment: 32 pages, 5 figure

Effect of far-red light on the production and diversity of ginsenosides in leaves of Panax ginseng Meyer

Abstract Ginsenosides are the most valuable and pharmacologically active triterpenoid saponins found in Panax ginseng. Although light quality affects ginsenoside content, little is known about the underlying genetic and regulatory mechanisms. Additionally, the correlation between the adaptability of ginseng to shade and ginsenoside biosynthesis remains poorly understood. In the present study, transcriptome analysis of ginseng seedlings using RNA sequencing revealed that the expression of ginsenoside biosynthesis genes, including PgHMGR, PgFPS, PgSS, and PgUGT, was enhanced in shade conditions but downregulated by red light, indicating that far-red light might play an essential role in ginsenoside production. Further, gene expression analysis in adventitious roots and 2-year-old plants using qRT-PCR showed that the light quality-mediated expression patterns of ginsenoside genes varied with tissue and age. However, unlike the transcriptome, there was no difference in the total ginsenoside content in seedlings among various light conditions. Nevertheless, the amount of major protopanaxadiol-type ginsenosides increased under shade and red light conditions. Unlike seedlings and adventitious roots, there was a decrease in the expression of PgHMGR, PgFPS, PgSS, and PgDDS in 2-year-old plants, along with an increase in the ginsenoside content, under far-red light. Taken together, our findings suggest that far-red light is an important environmental factor for ginsenoside biosynthesis and diversification and provide information that can improve the quality of ginseng produced for medicinal purposes