The complete chloroplast genome sequence of the medicinal plant, Dracocephalum rupestre (Lamiaceae).

Dracocephalum rupestre (tribe Mentheae; Lamiaceae) is a perennial herb from Korea and China with high ornamental and medicinal value. Here, we report its complete chloroplast genome to provide insight into the phylogenetic relationships of Dracocephalum. The genome is 151,230 bp long, with two inverted repeat regions (25,643 bp each) that separate a large single-copy region (82,536 bp) and a small single-copy region (17,408 bp). It contains 133 genes that encode 88 proteins, eight rRNAs, and 37 tRNAs. The maximum-likelihood phylogenetic analysis strongly supported Dracocephalum monophyly, showing that the genus forms a sister group with the subtribe Menthinae in the tribe Mentheae.

Clinical Implication of Individually Tailored Segmentation Method for Distorted Hypothalamus in Craniopharyngioma.

Objective: Several attempts have been done to capture damaged hypothalamus (HT) using volumetric measurements to predict the development of hypothalamic obesity in patients with craniopharyngioma (CP). This study was to develop a novel method of HT volume measurement and examine the associations between postoperative HT volume and clinical parameters in patients with CP. Methods: We included 78 patients with adult-onset CP who underwent surgical resection. Postoperative HT volume was measured using T1- and T2-weighted magnetic resonance imaging (MRI) with a slice thickness of 3 mm, and corrected for temporal lobe volume. We collected data on pre- and postoperative body weights, which were measured at the time of HT volume measurements. Results: The corrected postoperative HT volume measured using T1- and T2-weighted images was significantly correlated (r=0.51 [95% confidence interval (CI) 0.32 to 0.67], P<0.01). However, HT volume was overestimated using T1-weighted images owing to obscured MR signal of the thalamus in patients with severe HT damage. Therefore, we used T2-weighted images to evaluate its clinical implications in 72 patients with available medical data. Postoperative HT volume was negatively associated with preoperative body weight and preoperative tumor volume (r=-0.25 [95% CI -0.45 to -0.04], P=0.04 and r=-0.26 [95% CI -0.40 to -0.15], P=0.03, respectively). In the subgroup analysis of CP patients who underwent primary surgery (n=56), pre- and postoperative body weights were negatively associated with HT volume (r=-0.30 [95% CI -0.53 to -0.03], P=0.03 and r=-0.29 [95% CI -0.53 to -0.02], P=0.03, respectively). Conclusions: Adult-onset CP patients showed negative associations between postoperative HT volume and preoperative/postoperative body weight using a new method of HT volume measurement based on T2-weighted images.

Sequencing and Comparative Analysis of the Chloroplast Genome of Angelica polymorpha and the Development of a Novel Indel Marker for Species Identification.

The genus Angelica (Apiaceae) comprises valuable herbal medicines. In this study, we determined the complete chloroplast (CP) genome sequence of A. polymorpha and compared it with that of Ligusticum officinale (GenBank accession no. NC039760). The CP genomes of A. polymorpha and L. officinale were 148,430 and 147,127 bp in length, respectively, with 37.6% GC content. Both CP genomes harbored 113 unique functional genes, including 79 protein-coding, four rRNA, and 30 tRNA genes. Comparative analysis of the two CP genomes revealed conserved genome structure, gene content, and gene order. However, highly variable regions, sufficient to distinguish between A. polymorpha and L. officinale, were identified in hypothetical chloroplast open reading frame1 (ycf1) and ycf2 genic regions. Nucleotide diversity (Pi) analysis indicated that ycf4⁻chloroplast envelope membrane protein (cemA) intergenic region was highly variable between the two species. Phylogenetic analysis revealed that A. polymorpha and L. officinale were well clustered at family Apiaceae. The ycf4-cemA intergenic region in A. polymorpha carried a 418 bp deletion compared with L. officinale. This region was used for the development of a novel indel marker, LYCE, which successfully discriminated between A. polymorpha and L. officinale accessions. Our results provide important taxonomic and phylogenetic information on herbal medicines and facilitate their authentication using the indel marker.

The genome of the giant Nomura's jellyfish sheds light on the early evolution of active predation.

BACKGROUND: Unique among cnidarians, jellyfish have remarkable morphological and biochemical innovations that allow them to actively hunt in the water column and were some of the first animals to become free-swimming. The class Scyphozoa, or true jellyfish, are characterized by a predominant medusa life-stage consisting of a bell and venomous tentacles used for hunting and defense, as well as using pulsed jet propulsion for mobility. Here, we present the genome of the giant Nomura's jellyfish (Nemopilema nomurai) to understand the genetic basis of these key innovations. RESULTS: We sequenced the genome and transcriptomes of the bell and tentacles of the giant Nomura's jellyfish as well as transcriptomes across tissues and developmental stages of the Sanderia malayensis jellyfish. Analyses of the Nemopilema and other cnidarian genomes revealed adaptations associated with swimming, marked by codon bias in muscle contraction and expansion of neurotransmitter genes, along with expanded Myosin type II family and venom domains, possibly contributing to jellyfish mobility and active predation. We also identified gene family expansions of Wnt and posterior Hox genes and discovered the important role of retinoic acid signaling in this ancient lineage of metazoans, which together may be related to the unique jellyfish body plan (medusa formation). CONCLUSIONS: Taken together, the Nemopilema jellyfish genome and transcriptomes genetically confirm their unique morphological and physiological traits, which may have contributed to the success of jellyfish as early multi-cellular predators.

Alcanivorax gelatiniphagus sp. nov., a marine bacterium isolated from tidal flat sediments enriched with crude oil.

A Gram-reaction-negative, rod-shaped marine bacterium, designated MEBiC08158(T), was isolated from sediments collected from Taean County, Korea, near the Hebei Spirit tanker oil spill accident. 16S rRNA gene sequence analysis revealed that strain MEBiC08158(T) was closely related to Alcanivorax marinus R8-12(T) (99.5% similarity) but was distinguishable from other members of the genus Alcanivorax (93.7-97.1%). The DNA-DNA hybridization value between strain MEBiC08158(T) and A. marinus R8-12(T) was 58.4%. Growth of strain MEBiC08158(T) was observed at 15-43 °C (optimum 37-40 °C), at pH 6.0-9.5 (optimum pH 7.0-8.0) and with 0.5-16% NaCl (optimum 1.5-3.0%). The dominant fatty acids were C16 : 0, C19 : 0 cyclo ω8c, C12 : 0, C18 : 1ω7c, C12 : 0 3-OH and summed feature 3 (comprising C15 : 0 2-OH and/or C16 : 1ω7c). Several phenotypic characteristics differentiate strain MEBiC08158(T) from phylogenetically close members of the genus Alcanivorax. Therefore, strain MEBiC08158(T) should be classified as representing a novel species of the genus Alcanivorax, for which the name Alcanivorax gelatiniphagus sp. nov. is proposed. The type strain is MEBiC08158(T) ( = KCCM 42990(T) = JCM 18425(T)).

A highly sensitive and label free biosensing platform for wireless sensor node system.

In this paper, we propose a radio-frequency (RF) biosensor platform based on oscillation frequency deviation at 2.4 GHz. Its feasibility is experimentally demonstrated with the well-known biomolecular binding systems such as biotin-streptavidin and deoxyribonucleic acid (DNA) hybridization. For a basic principle of our biosensing system, the impedance of a resonator with the biomolecular immobilization is at first varied so that the corresponding change results in frequency change of an oscillator. Especially, to enhance the sensitivity of the proposed system, a surface acoustic wave (SAW) filter having a high-Q factor (~2000) is utilized. From the resulting component, even a small change of oscillation frequency can be transformed into a large output amplitude variation. According to the experimental results, it is found that our system shows the low detectable limit (~1 ng/ml) and fast response time (~real-time) for different target biomolecules, i.e. streptavidin and complementary DNA (cDNA). As a result, we find that our device is an effective biosensing system that can be used for a label-free and real-time measurement of the biomolecular binding events.

[Clinicopathologic characteristics of superficial gastric cancer diagnosed at primary health care institutions in 2011].

BACKGROUND/AIMS: Stomach cancer is prevalent in Korea. The purpose of this study was to evaluate the characteristics of superficial gastric cancers detected at SOK Sokpeynhan Internal Medical Network, the nationwide primary health care institutions. METHODS: We prospectively analysed the clinicopathologic and endoscopic characteristics of 218 superficial gastric cancer patients diagnosed using gastric endoscopy at SOK network from January 2011 through December 2011. RESULTS: The mean age was 58.5 years old and male to female ratio was 1.7 : 1. Asymptomatic patients were most common (45.0%). The macroscopic classification revealed that simple types (63.8%) were more common than complex types (36.2%). The most common type was IIc (28.4%) and other types were as follows; IIb (16.1%), IIb+IIc (13.3%), IIa (10.6%), III (9.2%), IIa+IIc (7.3%), IIc+IIa (6.0%), IIc+IIb (5.0%). The most commonly involved sites were the body (53.1%) and greater curvature (32.6%) of the stomach. The size of lesion was less than 1 cm (69.3%) and less than 5 mm (33.5%) in diameter. The most common pathologic type was tubular adenocarcinoma (75.7%). Helicobacter pylori infection rate was 50.2%. Fifty five percent of the cases were diagnosed via endoscopy of National Health Insurance Corporation screenings. CONCLUSIONS: Superficial gastric cancers in 2011 at primary health care SOK network were different from those of previous reports. Type IIc was most common but type IIb was more prevalent and the body and greater curvature of the stomach were the most commonly involved sites. Therefore, careful observation of the proximal gastric mucosa and mucosal color change is needed.

The effect of Baicalein on hippocampal neuronal damage and metalloproteinase activity following transient global cerebral ischaemia.

Baicalein, a flavonoid derived from Scutellaria baicalensis Georgi, is known to protect neural tissue from damage. Several studies have found that baicalein reduces brain infarction following focal brain ischaemia. However, there are few reports on the protective effects of baicalein following global brain ischaemia. Therefore, the current study was designed to address the effects of baicalein on neuronal damage and matrix metalloproteinase (MMP; gelatinase) activity in the hippocampus after transient global ischaemia. C57BL/6 mice were subjected to transient global brain ischaemia for 20 min and sacrificed 72 h after ischaemic insult. Baicalein (200 mg/kg, once daily, as a suspension in 0.5% carboxymethylcellulose) or an equal volume of vehicle was orally administered to the mice from 7 days prior to the ischaemic insult until sacrifice. After global ischaemia neuronal damage was significant in CA1 and CA2 pyramidal cell layers. In baicalein-treated mice, neuronal damage from the ischaemic insult was significantly less than that in vehicle-treated mice. Baicalein administration also inhibited MMP-9 activity in the hippocampus. These data demonstrate that baicalein reduces hippocampal neuronal damage after transient global ischaemia. Besides its possible protective mechanisms, the protective role of baicalein against global ischaemia may operate, at least in part, through the inhibition of MMP-9 activity.

Hispidin isolated from Phellinus linteus protects against hydrogen peroxide-induced oxidative stress in pancreatic MIN6N ß-cells.

Reactive oxygen species (ROS) have been shown to cause DNA damage, protein denaturation, loss of antioxidative enzyme activity, and lipid peroxidation. Thus, ROS are associated with tissue damage and are considered to be prime contributing factors in inflammation, diabetes, aging, and cancer. In this study, we investigated whether or not hispidin protects pancreatic MIN6N ß-cells from oxidative stress caused by hydrogen peroxide. Treatment of MIN6N ß-cells with 0.5 mM hydrogen peroxide for 4 hours caused significant loss of cell viability and an increase in the number of apoptotic cells. However, pretreatment of MIN6N ß-cells with hispidin for 24 hours reduced loss of cell viability and decreased the number of apoptotic cells. In addition, 70 µM hispidin significantly scavenged intracellular ROS and inhibited apoptosis and caspase-3 induced by hydrogen peroxide. Furthermore, the generation of thiobarbituric acid-reactive substances was inhibited in the presence of hispidin in a dose-dependent manner. Also, 70 µM hispidin significantly increased insulin secretion in hydrogen peroxide-treated MIN6N ß-cells. These results suggest that hispidin may be effective for protecting MIN6N ß-cells from ROS toxicity in diabetes.

Novel lipolytic enzymes identified from metagenomic library of deep-sea sediment.

Metagenomic library was constructed from a deep-sea sediment sample and screened for lipolytic activity. Open-reading frames of six positive clones showed only 33-58% amino acid identities to the known proteins. One of them was assigned to a new group while others were grouped into Families I and V or EstD Family. By employing a combination of approaches such as removing the signal sequence, coexpression of chaperone genes, and low temperature induction, we obtained five soluble recombinant proteins in Escherichia coli. The purified enzymes had optimum temperatures of 30-35°C and the cold-activity property. Among them, one enzyme showed lipase activity by preferentially hydrolyzing p-nitrophenyl palmitate and p-nitrophenyl stearate and high salt resistance with up to 4 M NaCl. Our research demonstrates the feasibility of developing novel lipolytic enzymes from marine environments by the combination of functional metagenomic approach and protein expression technology.

Hispidin produced from Phellinus linteus protects pancreatic beta-cells from damage by hydrogen peroxide.

Phellinus linteus, which is a traditional medicinal mushroom used in Asian countries for the treatment of various diseases, has attracted a lot of attention due to its antioxidant, anti-inflammatory, anti-mutagenicity, and cell-mediated immunity properties in addition to its ability to inhibit tumor growth and metastasis. However, the antidiabetic efficacy of P. linteus has not yet been examined. In this study, hispidin from P. linteus exhibited quenching effects against DPPH radicals, superoxide radicals, and hydrogen peroxide in a dose-dependent manner. Intracellular reactive oxygen species scavenging activity of hispidin was approximately 55% at a concentration of 30 microM. In addition, hispidin was shown to inhibit hydrogen peroxide-induced apoptosis and increased insulin secretion in hydrogen peroxide-treated cells. These combined results indicate that hispidin may act as an antidiabetic and that this property occurs through preventing beta-cells from the toxic action of reactive oxygen species in diabetes.

A 9-month-old phosphaturic mesenchymal tumor mimicking the intractable rickets.

Phosphaturic mesenchymal tumor is an extremely rare disease and is frequently associated with oncogenic osteomalacia showing paraneoplastic syndrome, which is characterized by phosphaturia, hypophosphatemia, normocalcemia, and decreased levels of 1,25-dihydroxyvitamin D3 associated with a tumor. A 2-year-old boy, who had a soft tissue tumor on his right thigh and previously diagnosed as myositis ossificans at 9-months-old, was presented with rachitic rosary and mildly enlarged tumor. Biochemical investigations showed hypophosphatemia, hyperphosphaturia, and an increased alkaline phosphatase level of 440 U/l (25-100 U/l), suggesting rickets, which was resistant to vitamin D dietary supplementation. We were certain of intractable rickets because of oncogenic hypophosphatemia and thus decided to excise the soft tissue mass. We observed laboratory improvement of rickets after 2 weeks. On the basis of surgical and histopathological examinations, the tumor was finally diagnosed as the phosphaturic mesenchymal tumor.

Characterization of ragweed pollen adhesion to polyamides and polystyrene using atomic force microscopy.

Pollen is a leading contributor to asthma and allergies, yet pollen adhesion to common indoor surfaces is not well understood. We report the adhesive behavior of short ragweed (A. artemisiifolia) pollen grains with Nylon 6 (N6) and Nylon 6,6 (N66), chosen due to their use in synthetic carpet, and three control surfaces: polyamide 12 (PA12), polystyrene (PS), and silicon. The forces were measured by using atomic force microscopy (AFM) under controlled humidity, where single pollen grains were attached to tipless AFM cantilevers. Pollen grains had an average adhesion of 10 +/- 3 nN with the surfaces, independent of surface type or relative humidity from 20% to 60%. van der Waals forces are the primary molecular attraction driving pollen adhesion to these surfaces. The results also indicate that ragweed pollen contacts the polymer surface via its exine surface spikes, and the total adhesion force scales with the number of contacts. The pollen surface spikes are strong, resisting fracture and compliance up to a load of 0.5 GPa.

Cloning and characterization of a new cold-active lipase from a deep-sea sediment metagenome.

To search for new cold-active lipases, a metagenomic library was constructed using cold-sea sediment samples at Edison Seamount and was screened for lipolytic activities by plating on a tricaprylin medium. Subsequently, a fosmid clone was selected, and the whole sequence of 36 kb insert of the fosmid clone was determined by shotgun sequencing. The sequence analysis revealed the presence of 25 open reading frames (ORF), and ORF20 (EML1) showed similarities to lipases. Phylogenetic analysis of EML1 suggested that the protein belonged to a new family of esterase/lipase together with LipG. The EML1 gene was expressed in Escherichia coli, and purified by metal-chelating chromatography. The optimum activity of the purified EML1 (rEML1) occurred at pH 8.0 and 25 degrees C, respectively, and rEML1 displayed more than 50% activity at 5 degrees C. The activation energy for the hydrolysis of olive oil was determined to be 3.28 kcal/mol, indicating that EML1 is a cold-active lipase. rEML1 preferentially hydrolyzed triacylglycerols acyl-group chains with long chain lengths of > or = 8 carbon atoms and displayed hydrolyzing activities toward various natural oil substrates. rEML1 was resistant to various detergents such as Triton X-100 and Tween 80. This study represents an example which developed a new cold-active lipase from a deep-sea sediment metagenome.