An improved method for constructing a full-length enriched cDNA library using small amounts of total RNA as a starting material

We have developed an improved method for constructing a full-length cDNA library using small quantity of material by modifying the original oligo-capping method. In our devised method, total RNAs are used in sequential oligo-capping steps directly without preliminary mRNA purification. Using this method, we constructed full- length cDNA libraries from 100 mg of total RNA. These libraries contained 8x10(5) to 8x10(6) independent clones with average insert sizes of 2.0 kb. Moreover, the number of full-length cDNAs containing the translation initiation codon ATG in the constructed libraries was estimated to 60-70%. In addition, 54% of the known cDNAs had a longer 5' end than the corresponding genes in the public database. Our results show that the method can be effectively used to construct full-length enriched cDNA libraries, especially, if starting material is limited.     

Isolation of rice allergenic cDNA clones from a rice cDNA library by immunoscreening with a polyclonal antibody specific to 16 kD rice allergenic protein

Clinical cases of type-1 hypersensitive reaction to rice (Oryza sativa) have been reported in western countries as well as in Japan. Among rice proteins, 14-16 kD globulin proteins encoded by multiple gene family have been identified as major rice allergens. In this study, a rice cDNA library was constructed using lambda UniZap vector and screened with a rat anti-16 kD globulin protein polyclonal antibody in order to isolate Korean rice allergenic cDNA clones. Five independent cDNA clones, termed RAK1-5, were obtained after second rounds of plaque assay and immunoblot analysis. These clones encoded 13-19 kD recombinant proteins upon IPTG induction, which were identified by the polyclonal antibody in immunoblot analysis. DNA sequencing analysis showed that RAK1-4 have 99% sequence homology with RA5b, and RAK5 is closely related with RA14c. This result indicated that RA5b gene is widely distributed in our cDNA library among other possible rice allergenic genes, and more study is needed to isolate heterogeneous or novel rice allergen genes.     

Influence of Cotton Cationization on Pigment Layer Characteristics in Digital Printing

The paper examines the influence of cotton cationization on the print quality in terms of penetration, colour yield and colour depth, which have been analysed in comparison to cotton untreated and pretreated with conventional acrylate binder. The process of cationization during mercerization was performed with a cationizing agent Rewin DWR (CHT Bezema). Standard (non-cationized) and cationized fabric, with and without additional layering of binder have been printed by digital inkjet pigment printing method. Moisture management testing (MMT) and dynamic contact angle measurement (drop shape analyzer–DSA30S) were performed on standard and cationized fabric, with and without binder, both with and without pigment layer. After printing, the objective values of colour depth (K/S) and colour parameters L*, C* and h° were analysed. The samples were also analysed by the method of microscopic imaging using a DinoLite microscope. Printed samples were tested to washing fastness, and the results are presented in terms of total colour difference (dECMC), according to CMC(l:c) equation, after the 1st, 3rd, 5th, 7th and 10th washing cycles. Results showed that the cotton cationization will improve the uniformity and coverage of the printed area as well as increase the K/S value. For the samples with binder, the positive effect of cationization on the stability and bond strength between the polymer layer as a pigment carrier with the cotton fabric was confirmed.     

Separation and analysis of peptides and proteins from Vipera lebetina snake venom

Our studies of Levantine viper venom have demonstrated that the venom is a rich source of biomedically important proteins and peptides. The venom contains metalloproteases: thrombolytic, fibrin-degrading lebetase, an endothelial cell apoptosis inducing metalloprotease (VLAIP), factor X activator (VLFXA); serine proteases: factor V activator, bradykinin-releasing serine proteases, β-fibrinogenase, α-fibrinogenase and chymotrypsin-like protease and different other enzymes such as phosphodiesterase, 5`-nucleotidase, ribonuclease, phospholipase A2s and L-amino acid oxidase. Among nonenzymatic components venom contains: nerve growth factor, vascular endothelial growth factor, disintegrins, C-type lectins.Here we report the isolation and characterization of proteins and peptides from Vipera lebetina venom using size exclusion, ion exchange, hydrophobic interaction and affinity chromatography, HPLC, UPLC and MALDI-TOF MS methods. N-terminal sequences and internal sequences of tryptic peptides of different proteins were determined using Edman sequencing and LC-ESI-MS/MS techniques. On the basis of fragmental sequences of proteins the oligonucleotides were designed and used as primers for cDNA cloning. Using cDNA library of the venom gland of a single snake the cDNAs coding proteins were cloned and sequenced. Protein sequences were deduced from cDNA sequences.The substrate specificity of venom proteases against insulin B-chain, bradykinin, substance P, and 6-10 amino acid residues containing peptides synthesized according to potential cleavage regions of fibrinogen, factor X, factor IX, factor V, α₂-macroglobulin bait region and pregnancy zone protein were studied using MALDI-TOF mass spectrometry technique.     

Design and synthesis of a diverse morpholine template library

Efficient and general procedures have been developed for the solution-phase preparation of substituted morpholine derivatives, and a library has been produced around generic structure 1. This library was designed with proprietary modeling software for use as a general screening library. The 30 R1 reagents were phenols, and the 275 R2 reagents were taken from five different reagent classes, giving a variety of product classes in the final library of 8250 potential products. All of the library members were generated from a common intermediate, mesylate (5), which was synthesized efficiently, in bulk, in three steps from N-benzylethanolamine (2). High-throughput chemistry using robotics was carried out to produce the 7907 library members, which were individually characterized by reversed-phase LC/MS analysis.     

Solid-phase synthesis development of a thymidinyl and 2′-deoxyuridinyl Ugi library for anti-bacterial agent screening

A solid-phase synthesis has been developed to make a thymidinyl and 2′-deoxyuridinyl Ugi library starting from 5′-azidonucleosides loaded onto polystyrene butyl diethylsilane (PS-DES) resin. Library synthesis development including: Ugi reaction optimization; selection of building blocks and optimization to 96-well filter plate synthesis are reported. A 1344 member library was synthesized for anti-bacterial screening.     

Effect of monascus pigment derivatives on the electrophoretic mobility of bacteria, and the cell adsorption and antibacterial activities of pigments

Various amino acid derivatives of monascus pigments were synthesized. The effects of pigment derivatives on the pigment adsorption ratio, electrophoretic mobility (EPM) of bacterial cells, and antibacterial activity were investigated under varying conditions of pigment type, pigment concentration, pH, and ionic strength. Two hydrophobic and two hydrophilic derivatives were selected as model pigments. There was a close relationship between the antimicrobial activity and the pigment adsorption ratio. Against Escherichia coli, the hydrophobic l-Tyr and l-Phe derivatives (log P = 3.18 and 3.57) exhibited high antimicrobial activities (MIC = 8 and 16 mg/L) and high cellular adsorption ratios (9.6 and 10.9 mg/L). The hydrophilic l-Glu and l-Asn derivatives (log P = 1.40 and 0.47) exhibited low activities (MIC = 64 and 128 mg/L) and low adsorption ratios (4.7 and 4.0 mg/L). The electrophoretic mobility of 11 different bacteria varied between −1.93 × 10⁻⁸ and −1.19 × 10⁻⁸ m² V⁻¹ s⁻¹ regardless of Gram⁺ or Gram⁻. The l-Phe derivative showed low MIC values (high antimicrobial activities) against bacteria with a high electrophoretic mobility. A positive linearity between the pigment adsorption ratio and the electrophoretic mobility was established. When the four pigment derivatives were added to E. coli solutions, the electrophoretic mobility of cells in all cases sharply increased with an increasing pigment concentration. The mobility value was high for hydrophobic pigment derivatives in descending order of l-Phe (0.8 × 10⁻⁸ m² V⁻¹ s⁻¹), l-Tyr (0.68 × 10⁻⁸ m² V⁻¹ s⁻¹), l-Glu (0.46 × 10⁻⁸ m² V⁻¹ s⁻¹), and l-Asn (0.44 × 10⁻⁸ m² V⁻¹ s⁻¹). Additional adsorption of the hydrophobic derivatives probably occurred due to a hydrophobic interaction between the pigment and the pigment-coated cells. The electrophoretic mobility decreased gradually with an increasing pH and/or ionic strength with both addition and no addition of the pigment derivatives. The pattern of change of the pigment adsorption ratio under varying pH and/or ionic strength values was similar to the pattern for electrophoretic mobility.     

Solid-phase synthesis of a thymidinyl dipeptide urea library

A thymidinyl dipeptide urea library with structural similarity to the nucleoside peptide class of antibiotics was designed and synthesized. To generate the library, a solid-phase synthesis was developed starting from 5'-azidothymidine attached to a polystyrene butyl diethylsilane (PS-DES) resin support. This study describes the prelibrary solid-phase synthesis development including maximum loading capacity optimization, selection of orthogonal functionalized side-chain protection strategies, synthesis of a 64-member test library, and optimization of the final cleavage step. Using the optimized procedures, we synthesized a 1000-member library in a 50 micromol quantity using IRORI-directed sorting technology in MiniKans, producing the target library in good yields and purity.     

A method for isolating functional RNA from callus of Dendrobium candidum contented rich polysaccharides

Isolation of high-quality RNA from Dendrobium candidum is particularly difficult. D. candidum contains considerable amounts of polysaccharides that coprecipitate with RNA, which render RNA unsuitable for either cDNA synthesis and/or PCR amplification. In this paper, a rapid and efficient method was described for functional RNA isolation from the callus of D. candidum. The procedure included: (i) an extraction with phenol and isopropyl alcohol, to remove proteins and polyphenols; (ii) purifications by lithium chloride, pre-cooled (−20 °C) ethanol successively to remove polysaccharides. The method resulted in high-quality RNA suitable for DDRT-PCR and cDNA library analysis finally.     

Altered sequence specificity identified from a library of DNA-binding small molecules

BACKGROUND: The ability to target specific DNA sequences using small molecules has major implications for basic research and medicine. Previous studies revealed that a bis-intercalating molecule containing two 1,4,5,8-napthalenetetracarboxylic diimides separated by a lysine-tris-glycine linker binds to DNA cooperatively, in pairs, with a preference for G + C-rich sequences. Here we investigate the binding properties of a library of bis-intercalating molecules that have partially randomized peptide linkers. RESULTS: A library of bis-intercalating derivatives with varied peptide linkers was screened for sequence specificity using DNase I footprinting on a 231 base pair (bp) restriction fragment. The library mixtures produced footprints that were generally similar to the parent bis-intercalator, which bound within a 15 bp G + C-rich repeat above 125 nM. Nevertheless, subtle differences in cleavage enhancement bands followed by library deconvolution revealed a derivative with novel specificity. A lysine-tris-beta-alanine derivative was found to bind preferentially within a 19 bp palindrome, without substantial loss of affinity. CONCLUSIONS: Synthetically simple changes in the bis-intercalating compounds can produce derivatives with novel sequence specificity. The large size and symmetrical nature of the preferred binding sites suggest that cooperativity may be retained despite modified sequence specificity. Such findings, combined with structural data, could be used to develop versatile DNA ligands of modest molecular weight that target relatively long DNA sequences in a selective manner.     

Synthesis of a library of glycosylated flavonols

Flavonols are an important class of natural products isolated from plants. Some glycosylated flavonols showed very interesting biological activities. A library of flavonols has been made through Algar-Flynn-Oyamada reaction from 2′-hydroxyacetophenones and benzaldehydes. Glycosylation of these flavonols with various glycosyl donors affords a library of glycosylated flavonols. These compounds are potentially useful pharmacologically active compounds and will be studied for biological activities.     

A STRATEGY FOR ISOLATING DIFFERENTIATIONINDUCING COMPLEMENTARY DNAs FROM HUMAN ESOPHAGEAL CANCER CELL LINE TREATED WITH RETINOIC ACID

Treatment of the human esophageal cancer cell line EC8712 with retinoic acid (RA) stopped the cell growth significantly and gave rise to terminal differentiation of the cells characterized by increased expression of involucrin gene. Two cDNA libraries were constructed from the parental and RA-treated cells respectively. Repeated subtractive hybridization of single-stranded plasmid DNA prepared from pooled colonies of cDNA library of the parental cells with cDNA probe generated from the RA-treated cells exhausted sequences common to both libraries of the cell. The unhybridized cDNA probe represented, therefore, the genes activated after RA-treatment. By using these enriched cDNAs as probe to screen the cDNA library constructed from the RA-treated cells thirty-nine positive colonies were obtained, of which two were specifically due to RA-induction. One of these two cDNA clones, designated as pRA538, has undergone further analysis and shown differentiation-inducing effect on parental cancer cells. A novel     

A strategy for isolating differentiation-inducing complementary DNAs from human esophageal cancer cell line treated with retinoic acid.

Treatment of the human esophageal cancer cell line EC8712 with retinoic acid (RA) stopped the cell growth significantly and gave rise to terminal differentiation of the cells characterized by increased expression of involucrin gene. Two cDNA libraries were constructed from the parental and RA-treated cells respectively. Repeated subtractive hybridization of single-stranded plasmid DNA prepared from pooled colonies of cDNA library of the parental cells with cDNA probe generated from the RA-treated cells exhausted sequences common to both libraries of the cell. The unhybridized cDNA probe represented, therefore, the genes activated after RA-treatment. By using these enriched cDNAs as probe to screen the cDNA library constructed from the RA-treated cells thirty-nine positive colonies were obtained, of which two were specifically due to RA-induction. One of these two cDNA clones, designated as pRA538, has undergone further analysis and shown differentiation-inducing effect on parental cancer cells. A novel strategy for cloning genes involved in terminal differentiation of cancer cells is developed.     

Thermoluminescence characteristics of minerals from irradiated potatoes of different origins of production

Thermoluminescence (TL) characteristics were investigated for minerals, which were separated from potatoes irradiated at 0–1 kGy of different origins of production in Korea. The polyminerals analyzed by X-ray diffractometer were mainly composed of quartz and feldspar, and showed varied contents with producing origins, that contributed to typical TL responses to irradiation. The glow curve of irradiated samples at 0.05–1 kGy peaked at approximately 200°C with high intensity, but that of non-irradiated potatoes was observed at approximately 300°C with low intensity. Discrimination between irradiated (more than 0.05 kGy) and non-irradiated samples was possible just on the basis of the first glow curve, however, normalization of results through a re-irradiation step greatly improved their reliability. The signal intensity of TL decreased with the lapse of post-irradiation time under different storage conditions (0±0.5°C/dark room, 25±5°C/dark room and 25±5°C/naturally lighted room) but was still distinguishable from that of the non-irradiated sample even after one year.     

Analysis of the chemical composition of cotton seed coat by Fourier-transform infrared (FT-IR) microspectroscopy

To improve knowledge on the biodegradation of cotton seed coat fragments in bioscouring, in this study Fourier-transform infrared (FT-IR) microspectroscopy was performed to analyze the composition of cotton seed coat. Microscope observation showed that cotton seed coat has a five-layer structure: epidermal layer, outer pigment layer, colorless layer, palisade layer, and inner pigment layer. Analysis of the FT-IR spectra from each layer shows that cutin, wax, cellulose, and pectin are the main components of the epidermal layer, while pectin and hemicellulose are the main constituents of the palisade layer, as well as aromatic and polyphenol, which are commonly considered as lignins. The main component of the outer and inner pigment layers is lignin. The results suggest that cellulase, pectinase, xylanase, and lignin oxidase are suitable for degradation of cotton seed coat. In addition, cutinase might be very promising in improving the enzymatic degradation of cotton seed coat.     

Effect of Laser Phototherapy on Enzymatic Activity of Salivary Glands of Hamsters Treated with 5‐Fluorouracil

The chemotherapeutic agent 5‐Fluorouracil (5‐FU) can induce salivary gland hypofunction (SGH); however, previous studies did not reach final conclusions on the influence of this drug on glandular tissue. Thus, the aim of this study was to investigate the effect of 5‐FU on submandibular (SMs) and sublingual glands (SLs), as well as, the effect of laser phototherapy (LPT) on SGH induced by 5‐FU. Eighty‐five hamsters were divided into three groups: control (C), chemotherapy (CT) and laser (L), and the SGH was induced by two injections of 5‐FU in groups CT and L. The irradiation was performed using a diode (λ780 nm/20 mW/5 J cm^?2/0.2 J and 10 s per point/spot size of 0.04 cm²) and applied daily. On the euthanasia day, SMs and SLs were removed and biochemical analyses were carried out. The lactate dehydrogenase activity was increased in group CT when compared with group C for SLs and SMs (P < 0.05). In addition, the peroxidase and catalase activities were increased and superoxide dismutase was decreased by 5‐FU (P < 0.05). However, LPT appears to be a protective mechanism against oxidative stress, tending to alter the activity of these antioxidant enzymes, suggesting LPT as a promising therapy to modulate the 5‐FU harmful effect.     

Efficient one-pot synthesis of highly substituted thiophene library from 1,3-dicarbonyl compounds

A facile and efficient one-pot synthesis of highly substituted thiophenes has been developed and employed for the preparation of a small focused library. Treatment of 1,3-dicarbonyl compounds 1 with CS2 in the presence of K2CO3 in DMF at room temperature, followed by stepwise addition of alkyl bromides 2 and methylene active bromides 3, provided via intramolecular cyclization 2,3,4,5-tetrasubstituted thiophenes 4 in yields of 77-94%. This protocol, combining construction and modification of the thiophene ring, increases the structural diversity of final products from readily available materials. A mechanism for the one-pot synthesis of thiophenes of type 4 has been proposed. A small focused library of thiophenes is prepared using the sequential addition of reagents to achieve unique substitution in the 2 and 5 position of the thiophene ring.     

Purification, Characterization, and Molecular Cloning of a Novel Antifungal Lectin From the Roots of Ophioglossum pedunculosum

A novel mannan-specific lectin was isolated from the roots of a traditional Chinese herbal medicine, Ophioglossum pedunculosum through ion-exchange chromatography and gel filtration. With a molecular mass of 19,835.7 Da demonstrated by MALDI-TOF analysis, this novel agglutinin was designated as O. pedunculosum agglutinin (OPA), specifically agglutinating human O erythrocytes and rabbit erythrocytes. The hemagglutination could be strongly inhibited by mannan and thyroglobulin, the activity of which was stable in pH range of 4.0-8.0 and at temperatures below 50 °C. Chemical modification studies indicated that tryptophan and arginine residues were essential for its hemagglutinating activity. Meanwhile, it showed antifungal activities toward Sclerotium rolfsii and Fusarium graminearum. In addition, to amplify cDNA of OPA by 3'/5'-rapid amplification of cDNA ends (RACE), the N-terminal 30 amino acids sequence of OPA was determined, and degenerate primers were designed. The obtained full-length cDNA of OPA contained 885 bp with an open-reading frame of 600 bp encoding a precursor protein of 199 amino acids, while the mature protein had 170 amino acids.