Fluorescence-, isotope- or biotin-labeling of the 5 '-end of single-stranded DNA/RNA using T4 RNA ligase.

A rapid 5'-labeling method of single-stranded DNA/RNA was developed, which is based on the utilization of an adenylated intermediate in the reaction of T4 RNA ligase. This method is commonly useful for fluorescence-, isotope- or biotin-labeling of the 5'-ends of both oligo- and polynucleotides.     

In vitro studies on mangiferin protection against cadmium-induced human renal endothelial damage and cell death via the MAP kinase and NF-κB pathways

The therapeutic effects of the natural antioxidant mangiferin (a xanthonoid and potent oxygen free radical scavenger), which is widely distributed in mango fruit, against CdCl₂-induced toxicity in human renal glomerulus endothelial cells (HRGEC) were investigated. The viability of HREGCs that were treated with CdCl₂ (25?µ?mol) and co-treated with mangiferin (75?µ?mol) for 24?h was measured by crystal violet dye. The exposure of human glomerulus renal endothelial cells to cadmium promotes a polarized apical secretion of IL-6 and IL-8, two pivotal proinflammatory cytokines known to play a significant role in renal inflammation. Proinflammatory cytokine secretion by human renal glomerulus endothelial cells could be the result of cadmium-induced IL-6 secretion via an NF-κB-dependent pathway. However, IL-8 secretion involves the phosphor-JNK phospho-p38 signaling pathway. The results of the current study reveal that mangiferin could prevent both cadmium-induced IL-6 and IL-8 secretion by human glomerulus endothelial cells and be used to prevent renal inflammation.     

Purification and Amino Acid Sequence of MP-III 4R D49 Phospholipase A2 from Bothrops pirajai Snake Venom, a Toxin with Moderate PLA2 and Anticoagulant Activities and High Myotoxic Activity

MP-III 4R PLA₂ was purified from the venom of Bothrops pirajai venom (Bahia's jararacussu) after three chromatographic steps which started with RP-HPLC. The complete amino acid sequence of MP-III 4R PLA₂ from Bothrops pirajai was determined by amino acid sequencing of reduced and carboxymethylated MP-III 4R and the isolated peptides from clostripain and protease V8 digestion. MP-III 4R is a D49 PLA₂ with 121 amino acid residues and has a molecular weight estimated at 13,800 Da, with 14 half-cysteines. This protein showed moderate PLA₂ and anticoagulant activity. This PLA₂ does not have a high degree of homology with other bothropic PLA₂-like myotoxins (~75%) and nonbothropic myotoxins (~60%). MP-III 4R is a new PLA₂, which was isolated using exclusively analytical and preparative HPLC methods. Based on the N-terminal sequence and biological activities, MP-III 4R was identified as similar to piratoxin-III (PrTX-III), which was isolated by conventional chromatography based on molecular exclusion ion exchange chromatography. Clinical manifestations indicate that at the site of toxin injection, there may be pain of variable intensity, because animals continue to lick the limb. No clinical sign indicating general toxicity was noticed. Myotoxicity was observed in gastrocnemius muscle cells after exposure to MP-III 4R, with a high frequency (70%) of affected muscle fibers.     

Sequence analysis of cDNAs encoding precursors of starfish asterosaps

To understand how starfish sperm activating peptides (asterosaps) are synthesized in the ovary, we cloned cDNAs encoding asterosaps and elucidated their nucleotide sequences. The mRNA encoding asterosaps was synthesized only in the oocytes, but not in the follicle cells, and the length was 3.7 kb. The cDNA clones contained multiple isoforms of asterosaps. We assume that asterosap precursors are large prepolypeptide chains with an unusual “rosary‐type” structure made of 10 successive similar stretches of 51–55 residues. Each stretch finishes with a “spacer” of 17–21 residues immediately followed by the sequence of one asterosap isoform. The N‐terminal of this precursor has 19–21 successive glutamine‐rich repeating units. Maturation of the precursor may require endopeptidases that cleave both C‐ and N‐sites of lysine‐arginine. Dev. Genet. 25:130–136, 1999. © 1999 Wiley‐Liss, Inc.     

Molecular design guided by a local map of sequence space: DNA aptamers that inhibit cathepsin E

It has been strongly demanded by a number of people to elevate activities of molecules of a particular function. Currently, there is no general guide available for this purpose. Here we present a novel approach for this; a local sequence space map-directed method for exploring molecules of a higher activity. This approach exploits the knowledge of a local sequence space so far established and obtains the shape of sequence space (map) by intra- and extrapolating the known landscape, which was drawn through the principal coordinates analysis. In this method, we successfully obtained 16 DNA aptamers of cathepsin E (CE) inhibitory activity that have comparable or higher activities than the ancestral ones on which the designed molecules were based. Some of them had a 30% higher activity than the previously reported top one (SFR-6-3). This high efficiency in obtaining functional molecules (16 out of 21 newly designed ones) is by no means usual because most of molecules generated at random are known to have no function, showing the effectiveness of the map-based approach. The selected molecules were confirmed to have the i-motif structure, consistent to the fact that they have a C-rich sequence and their CE-inhibitory activities were measured at an acidic pH, both of which are favorable for the i-motif. This structure of CE-inhibitory aptamers was inferred to contribute to the structural stability but not to the function itself directly.     

Myzobdella platensis (Hirundinida: Piscicolidae) is true parasite of blue crabs (Crustacea: Portunidae)

Leeches exhibit a marked scope of diversity, including different kinds of symbiosis. The aim of the present study was to demonstrate through biochemical and histological analysis that a species of piscicolid leech, Myzobdella platensis, is a true parasite of blue crabs, feeding on their hemolymph and using them as a site for cocoon deposition. In a total of 48 blue crabs collected on October 2007 at 3 sites of the S?o Vicente Estuary, 12 specimens were infested with leeches. Callinectes bocourti (n = 7) was the most infested species with leeches and cocoons; it was chosen for biochemical and histological assays. The immunoblotting assays showed a positive reaction of the proteins in the intestinal samples of leeches collected from crabs using antihemocyanin polyclonal antibody of Ampullaria canaliculata. In addition, leech intestinal samples were recognized by antihemolymph polyclonal antibody of nonparasitized blue crabs. Histological sections of leech gut showed hemocytes and a granular matrix similar to those found in crab blood vessels. Collectively, this evidence strongly suggests a parasitic interaction between the leech M. platensis and the blue crab C. bocourti, in which the former utilizes the latter as a site for cocoon deposition and possibly for dispersal similar to that proposed for Myzobdella lugubris in Callinectes sapidus in North America.     

Seasonal variation of phlorotannin in sargassacean species from the coast of the Sea of Japan

Variations in phlorotannin concentrations among the developmental stages of brown algae have been reported; however, the phlorotannin concentration plasticity associated with fluctuations in environmental factors make it difficult to determine the essential ontogenetic variation. The phlorotannin concentrations in five perennial sargassacean species where newly sprouted branches appear in summer and become fertile the following spring were examined every month during a year; and correlation with the developmental or seasonal environmental factors was determined. Although the phlorotannin fluctuated greatly throughout the year, the fluctuation patterns were relatively similar among the five species: phlorotannin showed a peak during July and August; gradually decreased in the winter; and increased in April. Performing a multiple regression analysis, the phlorotannin concentration did not correlate with thallus size in all species; and phlorotannin amounts were significantly affected by ambient abiotic factors in some species. The phlorotannin contents in newly sprouted branches were always higher than those in the long main branches during all seasons. When the phlorotannin contents were determined monthly for S. fulvellum (Turner) C. Agardh where the thalli were cultured from embryos in outdoor tanks, the phlorotannin concentrations were 3–4% of the dry matter (DM) in the juveniles and decreased to less than 1% of the DM in thalli >7.5 cm in length. However, the phlorotannin in these cultured thalli suddenly increased to 5.3% DM after being transplanted to the inshore coast; and then the concentration gradually decreased. The data show higher phlorotannin concentrations in younger sargassacean algae thalli and fluctuation of the phlorotannin amounts with extrinsic environmental factors.     

Gel shift selection of translation enhancer sequences using messenger RNA display

We designed a new approach for selection of translation enhancer sequences that enables efficient protein synthesis in cell-free systems. The selection is based on a gel shift assay of a messenger RNA (mRNA)–protein fusion product that is synthesized in a cell-free translation system using an mRNA display method. A library of randomized 20-nt-long sequences, with all possible combinations of the four nucleotides, upstream of a coding region was screened by successive rounds of screening in which the translation time of the succeeding round was reduced compared with the previous round. An efficient translation enhancer sequence capable of more rapid initiation of cell-free protein synthesis, with a minimal translation time of 5 min, than a natural longer enhancer sequence (Xenopus β-globin 5′UTR) was selected using rabbit reticulocyte extract as a model cell-free translation system. Furthermore, a successful screening of cap-independent translation enhancer sequence and a significant sequence similarity of the selected candidates validated the efficiency of the combined mRNA display and gel shift assay method for the rapid development of advanced cell-free translation systems.