Integration of biological networks and gene expression data using Cytoscape

Cytoscape is a free software package for visualizing, modeling and analyzing molecular and genetic interaction networks. This protocol explains how to use Cytoscape to analyze the results of mRNA expression profiling, and other functional genomics and proteomics experiments, in the context of an interaction network obtained for genes of interest. Five major steps are described: (i) obtaining a gene or protein network, (ii) displaying the network using layout algorithms, (iii) integrating with gene expression and other functional attributes, (iv) identifying putative complexes and functional modules and (v) identifying enriched Gene Ontology annotations in the network. These steps provide a broad sample of the types of analyses performed by Cytoscape.     

Peptide mapping and assessment of cryoprotective activity of 26/27-kDa dehydrin from soybean seeds

To characterize the molecular weight diversity of seed dehydrin among soybean cultivars, 26/27-kDa soybean dehydrins were purified and compared in peptide mapping patterns, partial amino acid sequences, and cryoprotective activity on enzyme. In reverse phase chromatograms of their trypsin digests, we detected several distinctive peaks, one of which was attributed to a part of the internal glycine-rich region. Partial amino acid sequences of peptide fragments from trypsin and S. aureus V8 protease cleavage were found to be identical to the Mat9 translation. The CP50 of purified 26/27-kDa dehydrins were estimated to be 0.30 and 0.11 microM, respectively.     

Efficient monitoring of maize orange leafhopper, <Emphasis Type="Italic">Cicadulina bipunctata</Emphasis> (Hemiptera: Cicadellidae), and small brown planthopper, <Emphasis Type="Italic">Laodelphax striatellus</Emphasis> (Hemiptera: Delphacidae), in forage maize fields using yellow sticky traps

The monitoring of insect pests in fields of forage maize is difficult because plants are tall and grow at a high density. We investigated the effectiveness of colored sticky traps and appropriate conditions for monitoring insect pests in forage maize fields. Large numbers of the maize orange leafhopper, Cicadulina bipunctata Melichar (Hemiptera: Cicadellidae), and the small brown planthopper, Laodelphax striatellus Fallen (Hemiptera: Delphacidae), were collected during the experimental period with yellow and blue sticky traps placed in summer crop forage maize fields. A greater number of insects were trapped in yellow traps relative to blue traps. Traps located at a lower height (40 cm above the ground) attracted larger numbers of C. bipunctata, whereas L. striatellus did not demonstrate a height-dependent preference. These results indicated that yellow-colored sticky traps located at low height are effective for collecting C. bipunctata and L. striatellus simultaneously. Seasonal occurrence data obtained by the yellow sticky traps showed clearer seasonal occurrences than that obtained by two previously developed methods, suction and light traps, indicating that sticky traps are effective for monitoring the seasonal occurrence of these two insects in forage maize fields.     

Simple SNP typing assay using a base-discriminating fluorescent probe

We have developed a new concept involving a single-step homogeneous method for single-nucleotide polymorphism (SNP) typing. In this method, a probe containing base-discriminating fluorescent (BDF) bases is added to a sample solution. BDF base-containing DNA usually shows only a weak fluorescence, but emits a strong blue fluorescence when it recognizes a target base at a specific site in a hybridized strand. By utilizing this feature, a simple mix-and-read SNP typing assay was achieved without any tedious probe-designing or washing processes for exclusion of hybridization error or any addition of DNA-modifying enzymes. This is very different from conventional methods. We simultaneously analyzed a number of samples with ease, with a high accuracy, using our BDF assay.     

scRNA-seq Analysis of Hemocytes of Penaeid Shrimp Under Virus Infection

Marine Biotechnology - The classification of cells in non-model organisms has lagged behind the classification of cells in model organisms that have established cluster of differentiation marker...     

α-Aminoisobutyric Acid as the Constituent Amino Acid of Protein

α-Aminoisobutyric acid is the only tertiary amino acid which is reported to occur in the proteins. Nevertheless, this amino acid has not been yet isolated from the proteins. Recently we succeeded in isolating this amino acid as white prismy crystalline substance from both acid and pepsin hydrolysate of horse hind leg muscle proteins, and this crystal was identified to be α-amino-isobutyric acid by elementary analysis, properties of this derivates, etc.     

Characterization and imprinting status of OBPH1/Obph1 gene: implications for an extended imprinting domain in human and mouse

Human 11p15.5, as well as its orthologous mouse 7F4/F5, is known as the imprinting domain extending from IPL/Ipl to H19. OBPH1 and Obph1 are located beyond the presumed imprinting boundary on the IPL/Ipl side. We determined full-length cDNAs and complete genomic structures of both orthologues. We also investigated their precise imprinting and methylation status. The orthologues resembled each other in genomic structure and in the position of the 5' CpG island and were expressed ubiquitously. OBPH1 and Obph1 were predominantly expressed from the maternal allele only in placenta, with hypo- and not differentially methylated 5' CpG islands in both species. These results suggested that the imprinting domain would extend beyond the presumed imprinting boundary and that methylation of the 5' CpG island was not associated with the imprinting status in either species. It remains to be elucidated whether the gene is under the control of the KIP2/LIT1 subdomain or is regulated by a specific mechanism. Analysis of the precise genomic sequence around the region should help resolve this question.     

Stimulatory effect of epidermal growth factor on prostaglandin E2 production in mouse fibrosarcoma cell line (HSDM1 C1)

Using HSDM1 C1 cell line derived from the mouse fibrosarcoma which synthesizes and secretes prostaglandin (PG) E2, specific binding sites for epidermal growth factor (EGF), a potent growth stimulator of many tissues, and its effect on PGE2 production by cultured tumor cells were studied. HSDM1 C1 cell line possessed specific, high-affinity receptors for EGF: Kd (5.5 X 10(-10 M) and binding capacity (17,650 sites/cell). EGF significantly stimulated PGE2 production in HSDM1 C1 line cultured in serum-free medium for 24 h in a dose-dependent manner; a 2.5-fold increase over control was induced by as little as 0.1 ng/ml and the maximal effect (3.5-fold increase) by 1 ng/ml. Its stimulatory effect on PGE2 production was completely blocked by indomethacin, an inhibitor of PG biosynthesis. These data suggest that EGF may be involved in modulation of synthesis and/or secretion of PGE2, a potent bone-resorbing factor, by the tumors which may partly contribute to hypercalcemia in certain types of neoplasms.