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PubMed1999

Cloning and expression of a nitroaryl reductase gene from Streptomyces aminophilus strain MCMB411 in E. coli JM109 and Streptomyces lividans TK64.

A partial genomic library was prepared in E. coli JM109 using pBR322 as vector and 2.4 kb Sau 3A I chromosomal fragment, encoding a nitroaryl reductase (nbr A) gene, from Streptomyces aminophilus strain MCMB 411. From the library, 2.4 kb fragment was recloned in E. coli JM109 and S. lividans TK64 using pUC18 and pIJ702 as vectors respectively. The recombinant plasmids pSD103 and pSD105 expressed the reductase gene and exported the enzyme in periplasmic space of E. coli and in cytoplasm of S. lividans TK64. The proteins expressed by E. coli and S. lividans had the same molecular mass (70 kD) as that expressed by parent strain, which suggested that the enzyme was processed similarly by all strains. Activities of the enzymes cloned in E. coli JM109 and S. lividans TK64 containing recombinant plasmids pSD103 and pSD105 respectively were optimum at 30 degrees C and pH 9 and requirement of cofactors was same as that of the parent strain.

Bacterial Proteins↗

PubMed2006

[Cloning and identification of cellulase genes from uncultured microorganisms in pulp sediments from paper mill effluent].

The metagenomic DNA of pulp sediments from paper mill effluent was extracted and purified. The 16S rDNA was amplified using the purified metagenomic DNA as template and a 16S rDNA library was prepared. Sequence analysis of 16S rDNA clones showed that diverse of uncultured bacteria inhabit in this environment, which can be classified into 4 clusters as Spirochaetes, Proteobacteria, Bacteroidetes and Firmicutes. A metagenomic library containing 10000 clones was constructed into cosmid vector, and the capacity of inserted DNA of which was 3.53 x 10(8) bp. Functional screening of the library resulted in isolation of two independent clones expressing endoglucanase activity, three independent clones expressing exoglucanase activity and two independent clones expressing beta-glucosidase activity. One clone expressing strongest enzyme activity from each activity category was chosen to be further analyzed. Three novel cellulase genes designated as umcel5L, umcel5M and umbgl3D were identified by subcloning, sequencing and expression. The umcel5L encodes an endoglucanase belonging to glycosyl hydrolase family 5, which is most related to an endoglucanase from Bradyrhizobium japonicum at 43% identity and 59% similarity. The umcel5M encodes a cellodextrinase belonging to glycosyl hydrolase family 5, which is most similar to a cellodextrinase from Fibrobacter succinogenes at 48% identity and 69% similarity. The umbgl3D encodes a putative beta-glucosidase belonging to glycosyl hydrolase family 3, which shares highest homology with a beta-glucosidase from Thermotoga maritima at 46% identity and 61% similarity. It is the first time to reveal the bacterial diversity of pulp sediments from paper mill effluent and clone novel cellulase genes from the bacteria by culture-independent method.

Bacteria↗

PubMed2006

The combinatorial approach to asymmetric hydrogenation: phosphoramidite libraries, ruthenacycles, and artificial enzymes.

For a more general implementation of asymmetric catalysis in the production of fine chemicals, the screening for new catalysts and ligands must be dramatically accelerated. This is possible with a high-throughput experimentation (HTE) approach. However, implementation of this technology requires the rapid preparation of libraries of ligands/catalysts and consequently dictates the use of simple ligands that can be readily synthesised in a robot. In this concept article, we describe how the development of new ligands based on monodentate phosphoramidites enabled the development of an integral HTE protocol for asymmetric hydrogenation. This "instant ligand library" protocol makes it possible to synthesise 96 ligands in one day and screen them the next day. Further diversity is possible by using mixtures of monodentate ligands. This concept has already led to an industrial application. Other concepts, still under development, are based on chiral ruthenacycles as new transfer hydrogenation catalysts and the use of enzymes as ligands for transition-metal complexes.

Catalysis↗

PubMed2000

Tmp21-I, a vesicular trafficking protein, is differentially expressed during induction of the ureter and metanephros.

PURPOSE: To identify genes participating in the reciprocal induction of the metanephros and ureter. MATERIALS AND METHODS: Embryonic day 14 Sprague-Dawley rat kidneys and ureters were microdissected into differentiating mesenchyme, ureteric buds, and extrarenal ureter and prepared for RT/PCR differential display. Differentially displayed cDNAs were reamplified, cloned, and sequenced. Expression was verified in the embryonic, newborn or adult kidneys by Northern blot hybridization or RT/PCR using sequence specific primers. A newborn rat kidney cDNA library was prepared and screened with probes of interest. Positive clones were screened, sequenced and compared to the GenBank/EMBL databases. A rabbit polyclonal antibody was raised to a synthetic peptide of the Tmp21-I protein and was used for immunohistochemistry. RESULTS: From the cDNAs differentially displayed by the ureteric buds cDNA B11, is 254 bp in length. The gene for B11 is expressed in adult and newborn kidneys as two transcripts (3.4 kb and 1.3 kb). More importantly, RT/PCR on E14 kidneys using B11 sequence specific primers identified expression in the embryonic kidney at the beginning of induction. B11 cDNA library screening yielded clones with inserts of 1.3 kb. This sequence encodes Tmp21-I, a vesicular trafficking protein. Immunohistochemistry demonstrates that Tmp21-I is abundant in the nephrogenic cortex of the newborn kidney and as a nephron matures, the protein levels decline. The protein is essentially absent in the adult rat kidney. CONCLUSIONS: Tmp21-I is a developmentally regulated gene expressed during kidney induction. Localized within the nephrogenic zone, it may direct the intracellular trafficking or secretion of proteins responsible for nephrogenesis.

Animals↗

PubMedDate not supplied

Optimizing photo-embossed gratings: a gradient library approach.

Methodologies for the rapid screening of coating systems were developed and applied to photopolymer lacquers for photoembossing applications. Continuous and discrete gradient libraries were prepared with a gradient in grating period along the short axis and along the long axis, a gradient in exposure energy, development temperature, film thickness, photoinitiator concentration, or monomer to polymer mass ratio. Discrete gradient libraries consisted of arrays of rectangular films made by pipetting a certain amount of sample onto a chemically patterned substrate consisting of hydrophilic patches surrounded by hydrophobic, fluorinated barriers. The shape and height of the photoembossed gratings were measured using an automated AFM. Optimum grating height was obtained for a 20-microm period at intermediate exposure energies, photoinitiator concentrations, or both. Height improves with development temperature (max 110 degrees C), monomer-to-polymer ratio (max 55 wt % monomer), and film thickness. Surface topography can also be optimized, depending on any specific application.

Calorimetry, Differential Scanning↗

PubMed2006

Hydrazone- and hydrazide-containing N-substituted glycines as peptoid surrogates for expedited library synthesis: application to the preparation of Tsg101-directed HIV-1 budding antagonists.

Replacing the Pro6 in the p6(Gag)-derived 9-mer "P-E-P-T-A-P-P-E-E" with N-substituted glycine (NSG) residues is problematic. However, incorporation of hydrazone amides ("peptoid hydrazones") can be readily achieved in library fashion. Furthermore, reduction of these hydrazones to N-substituted "peptoid hydrazides" affords a facile route to library diversification. This approach is demonstrated by application to Tsg101-binding compounds designed as potential HIV budding antagonists. [reaction: see text]

Amino Acid Sequence↗

PubMed2005

Synthesis of mono- and dihydroxylated furanoses, pyranoses, and an oxepanose for the preparation of natural product analogue libraries.

[structures: see text] Numerous biologically active natural products contain furanoses and pyranoses with mono- and dihydroxylated substituents. However, much of the structure-activity studies on such molecules is gathered on the aglycons without attention to the corresponding carbohydrate components. Consequently, there are few synthetic procedures that enable the rapid preparation of mono- and dihydroxyfuranoses and mono- and dihydroxypyranoses and no report for a 3,4-dihydroxyoxepanose. In this article we report the practical synthesis of orthogonally protected five-, six-, and seven-membered carbohydrate derivatives. The succinct manner in which these molecules were synthesized allows the rapid preparation of analogues aimed at discovering the role of ring size and individual hydroxyl moieties on the pyranose skeleton.

Biological Factors↗

PubMed1986

An improved technique for the efficient construction of gene libraries by partial filling-in of cohesive ends.

For the preparation of gene libraries, DNA from lambda EMBL3 phage was digested with SalI and EcoRI, and the cohesive ends partially filled-in by addition of dTTP, dCTP and Klenow fragment of DNA polymerase I (PolIk). Genomic DNA was cleaved partially with Sau3A and subsequently incubated with dATP, dGTP and PolIk. The phage and genomic DNAs were then mixed and ligated. The recombinant DNAs were packaged in vitro. The efficiency of packaging was 10(5)-10(6) of infectious phage lambda particles per microgram of the genomic DNA (as compared to approx. 10(7) per microgram for the wild-type lambda DNA). This procedure is very rapid and requires only microgram quantities of genomic DNA for preparing an entire gene library. The other important advantage is that multiple independent insertions of genomic DNA cannot occur in a single recombinant phage and self-ligation of phage DNA is blocked. It is also applicable for other SalI-containing vectors.

Cloning, Molecular↗

PubMed2006

Identification of genes involved in interactions between Biomphalaria glabrata and Schistosoma mansoni by suppression subtractive hybridization.

Biomphalaria glabrata is an intermediate snail host for Schistosoma mansoni, a medically important schistosome. In order to identify transcripts involved in snail-schistosome interactions, subtractive cDNA libraries were prepared, using suppression subtractive hybridization (SSH) between a parasite-exposed schistosome-resistant and a susceptible strain of B. glabrata, and also between schistosome-exposed and unexposed snails from the resistant snail line. Separate libraries were made from both haemocytes and the haemopoietic organ. Subtraction was performed in both directions enriching for cDNAs differentially expressed between parasite-exposed resistant and susceptible samples and up or down-regulated in the resistant line after challenge. The resulting eight libraries were screened and eight genes, differentially expressed between the haemocytes of resistant and susceptible snail strains, were identified and confirmed with reverse transcriptase PCR, including two transcripts expected to be involved in the stress response mechanism for regulating the damaging oxidative burst pathways involved in cytotoxic killing of the parasite: the iron-storage and immunoregulatory molecule, ferritin, and HtrA2, a serine protease involved in the cellular stress response. Transcripts with elevated levels in the resistant strain, had the same expression patterns in the subtracted libraries and unsubtracted controls; higher levels in exposed resistant snails compared to susceptible ones and down-regulated in exposed compared with unexposed resistant snails. Differential expression of two of the transcripts with no known function from the susceptible strain, was independently confirmed in a repeat exposure experiment.

Animals↗

PubMed2002

Glycogen-accumulating organisms in laboratory-scale and full-scale wastewater treatment processes.

Laboratory-scale sequencing batch reactors (SBRs) as models for wastewater treatment processes were used to identify glycogen-accumulating organisms (GAOs), which are thought to be responsible for the deterioration of enhanced biological phosphorus removal (EBPR). The SBRs (called Q and T), operated under alternating anaerobic-aerobic conditions typical for EBPR, generated mixed microbial communities (sludges) demonstrating the GAO phenotype. Intracellular glycogen and poly-beta-hydroxyalkanoate (PHA) transformations typical of efficient EBPR occurred but polyphosphate was not bioaccumulated and the sludges contained 1.8% P (sludge Q) and 1.5% P (sludge T). 16S rDNA clone libraries were prepared from DNA extracted from the Q and T sludges. Clone inserts were grouped into operational taxonomic units (OTUs) by restriction fragment length polymorphism banding profiles. OTU representatives were sequenced and phylogenetically analysed. The Q sludge library comprised four OTUs and all six determined sequences were 99.7% identical, forming a cluster in the gamma-Proteobacteria radiation. The T sludge library comprised eight OTUs and the majority of clones were Acidobacteria subphylum 4 (49% of the library) and candidate phylum OP10 (39% of the library). One OTU (two clones, of which one was sequenced) was in the gamma-Proteobacteria radiation with 95% sequence identity to the Q sludge clones. Oligonucleotide probes (called GAOQ431 and GAOQ989) were designed from the gamma-Proteobacteria clone sequences for use in fluorescence in situ hybridization (FISH); 92% of the Q sludge bacteria and 28% of the T sludge bacteria bound these probes in FISH. FISH and post-FISH chemical staining for PHA were used to determine that bacteria from a novel gamma-Proteobacteria cluster were phenotypically GAOs in one laboratory-scale SBR and two full-scale wastewater treatment plants. It is suggested that the GAOs from the novel cluster in the gamma-Proteobacteria radiation be named 'Candidatus Competibacter phosphatis'.

Bacteria↗

PubMed1994

A human T-cell receptor recognizes 'O'-linked sugars from the hinge region of human IgA1 and IgD.

A receptor which binds secretory IgA (sIgA) is expressed on human T cells from patients with systemic lupus erythematosus, rheumatoid arthritis, Behcet's syndrome and IgA nephropathy and on normal T cells following phytohaemagglutinin (PHA) stimulation. The specificity of this receptor was initially probed with a panel of normal serum immunoglobulins in competitive inhibition assays with sIgA using two-colour immunofluorescence. While the receptor showed the strongest affinity for IgA1 (IC(50)10(-6) M), IgD which has a similarly glycosylated hinge region to IgA1, also bound to the receptor (IC50 10(-5) M). IgA2, which lacks the 'O'-glycosylated hinge region, did not significantly inhibit the binding at these concentrations suggesting that the IgA determinants for this receptor might be the oligosaccharides present in the hinge region of IgA1. IgA1 has up to 10 'O'-linked oligosaccharides and four N-linked oligosaccharides per molecule. In order to probe the role of the 'O'-linked hinge sugars in the binding event, a sugar library was prepared from IgA1 by a procedure designed to release 'O'-linked oligosaccharides preferentially, and to retain them in the natural closed ring formation. The sugars were released by hydrazinolysis at 65 degrees and the resulting oligosaccharide library analysed by high voltage paper electrophoresis (HVE) and P4 gel permeation chromatography. Competitive inhibition studies demonstrated that both the library and the individual 'O'-linked sugars associated with IgA1 were implicated in the binding of IgA1 to this receptor (IC50 between 1 x 10(-5) M and 6 x 10(-5) M). Within this range the individual sugars showed small differences in their affinity for the receptor in the following order: Gal beta 3GalNAc = NeuNAc2 alpha 3(6)Gal beta 3GalNAc > NeuNAc2 alpha 3(6)Gal beta 3[NeuNAc2 alpha 6]GalNAc > or = GalNAc.

Binding, Competitive↗

PubMed2001

Functionalized Polymers-Emerging Versatile Tools for Solution-Phase Chemistry and Automated Parallel Synthesis.

As part of the dramatic changes associated with the need for preparing compound libraries in pharmaceutical and agrochemical research laboratories, industry searches for new technologies that allow for the automation of synthetic processes. Since the pioneering work by Merrifield polymeric supports have been identified to play a key role in this field however, polymer-assisted solution-phase synthesis which utilizes immobilized reagents and catalysts has only recently begun to flourish. Polymer-assisted solution-phase synthesis has various advantages over conventional solution-phase chemistry, such as the ease of separation of the supported species from a reaction mixture by filtration and washing, the opportunity to use an excess of the reagent to force the reaction to completion without causing workup problems, and the adaptability to continuous-flow processes. Various strategies for employing functionalized polymers stoichiometrically have been developed. Apart from reagents that are covalently or ionically attached to the polymeric backbone and which are released into solution in the presence of a suitable substrate, scavenger reagents play an increasingly important role in purifying reaction mixtures. Employing functionalized polymers in solution-phase synthesis has been shown to be extremely useful in automated parallel synthesis and multistep sequences. So far, compound libraries containing as many as 88 members have been generated by using several polymer-bound reagents one after another. Furthermore, it has been demonstrated that complex natural products like the alkaloids (+/-)-oxomaritidine and (+/-)-epimaritidine can be prepared by a sequence of five and six consecutive polymer-assisted steps, respectively, and the potent analgesic compound (+/-)-epibatidine in twelve linear steps ten of which are based on functionalized polymers. These developments reveal the great future prospects of polymer-assisted solution-phase synthesis.

Journal Article↗

PubMed2003

Quick gene expression profiling of promyelocytic cell line HL-60.

OBJECTIVE: A number of techniques have been developed to perform gene expression profiling. We report preliminary results from our exploratory study, using sequential analysis of gene expression (SAGE) technique, to profile the undifferentiated and differentiated HL-60 cells in line with our interest to characterize the cancer phenotype. The aim of the study is to evaluate the technique and to understand the molecular bases of these 2 states of cells. METHODS: HL-60 cells were differentiated after treatment with dimethyl sulfoxide. Tag libraries were prepared from the messenger RNAs of the undifferentiated and differentiated cells according to the SAGE protocol. The search for genes corresponding to the tags was carried out using SAGE software. The tags and the genes from the 2 libraries were compared for their levels of expression. The study was carried out at the King Faisal Specialist Hospital and Research Centre, Riyadh, Kingdom of Saudi Arabia during the year 2001. RESULTS: A comparison of tags from the 2 libraries revealed that 151 tags corresponding to 57 genes expressed differentially: 60 tags were elevated and 59 were repressed in the undifferentiated cells. Thirty-two tags were equally expressed in both types of cells. Of the corresponding genes, 25 were expressed at higher, 17 at lower, while 15 were expressed at comparable levels in both cell types. In the profile of undifferentiated cells, the genes involved in mitochondrial function and protein synthesis were prominent, while in the differentiated cells, the genes coding for proteins associated with cell membranes, signal transduction and for cell specific functions were prominent. The genes, expressed equally in both the cell types, were concerned with the maintenance of the living state. CONCLUSION: Sequential analysis of gene expression is a useful technique for gene expression profiling. As previously indicated by others, a dedicated team can generate useful data within reasonable time limits.

Cell Differentiation↗

PubMed1994

Identification of genes overexpressed in tumors through preferential expression screening in trophoblasts.

Early trophoblastic cells share several features with neoplastic cells. Based on that observation, we attempted to identify genes overexpressed in tumors by analyzing genes preferentially expressed in trophoblasts. A subtracted library enriched in complementary DNA from early cytotrophoblasts was constructed, and the expression level of selected recombinants was analyzed on a large panel of normal and tumor tissues. The library was prepared using a polymerase chain reaction-based complementary DNA subtraction method with 6-week amenorrhea cytotrophoblast endoplasmic reticulum-bound RNA as target, and a mixture of complementary DNA prepared from terminal placenta and activated T-lymphocytes as driver. Two rounds of screening were performed to isolate clones preferentially expressed in early placenta. From a total number of recombinant clones estimated at 32,000 in the subtracted library, 594 inserts were analyzed by Southern blot and 21 sequences were isolated as corresponding to genes highly expressed in early placenta. Eleven encoded known molecules, such as carcinoembryonic antigen, human chorionic gonadotropin, and mitochondrial rRNAs. Ten sequences represented novel genes. Northern blot analysis confirmed that most of these genes were preferentially expressed in early trophoblast in comparison to terminal placenta. Three clones that gave detectable hybridization signals on total RNA were extensively studied and were found to be overexpressed in various tumors. Two of these clones, designated B9 and E4, were later identified as corresponding to genes coding for the putative ribosomal protein S18 and the bifunctional enzyme ADE2H1 involved in purine biosynthesis, respectively. Expression of the third clone, E9, was increased up to 10-fold in breast cancer tissues in comparison with normal counterparts. Present results confirm that many genes expressed in the trophoblast are overexpressed in malignant cells. This approach could provide a general targeted method for the identification of genes overexpressed in various neoplastic cell types.

Base Sequence↗

PubMed1991

Analysis of a circular derivative of Saccharomyces cerevisiae chromosome III: a physical map and identification and location of ARS elements.

DNA was isolated from a circular derivative of chromosome III to prepare a library of recombinant plasmids enriched in chromosome III sequences. An ordered set of recombinant plasmids and bacteriophages carrying the contiguous 210-kilobase region of chromosome III between the HML and MAT loci was identified, and a complete restriction map was prepared with BamHI and EcoRI. Using the high frequency transformation assay and extensive subcloning, 13 ARS elements were mapped in the cloned region. Comparison of the physical maps of chromosome III from three strains revealed that the chromosomes differ in the number and positions of Ty elements and also show restriction site polymorphisms. A comparison of the physical map with the genetic map shows that meiotic recombination rates vary at least tenfold along the length of the chromosome.

Chromosomes, Fungal↗

PubMed2006

European Federation of Neurological Societies/Peripheral Nerve Society Guideline on management of paraproteinemic demyelinating neuropathies. Report of a joint task force of the European Federation of Neurological Societies and the Peripheral Nerve Society.

BACKGROUND: Paraprotein-associated neuropathies have heterogeneous clinical, neurophysiological, neuropathological, and hematological features. OBJECTIVES: The aim of this guideline was to prepare evidence-based and consensus guidelines on the clinical management of patients with both a demyelinating neuropathy and a paraprotein [paraproteinemic demyelinating neuropathy (PDN)]. METHODS: Disease experts and a representative of patients considered references retrieved from MEDLINE and the Cochrane Library and prepared statements that were agreed in an iterative fashion. RECOMMENDATIONS: In the absence of adequate data, evidence-based recommendations were not possible, but the Task Force agreed on the following good practice points: (1) patients with PDN should be investigated for a malignant plasma cell dyscrasia; (2) the paraprotein is more likely to be causing the neuropathy if the paraprotein is immunoglobulin M (IgM), antibodies are present in serum or on biopsy, or the clinical phenotype is chronic distal sensory neuropathy; (3) patients with IgM PDN usually have predominantly distal and sensory impairment, with prolonged distal motor latencies, and often anti-myelin-associated glycoprotein antibodies; (4) IgM PDN sometimes responds to immunotherapies. Their potential benefit should be balanced against their possible side effects and the usually slow disease progression; (5) IgG and IgA PDN may be indistinguishable from chronic inflammatory demyelinating polyradiculoneuropathy clinically, electrophysiologically, and in response to treatment; and (6) for POEMS syndrome, local irradiation or resection of an isolated plasmacytoma, or melphalan with or without corticosteroids, should be considered, with hemato-oncology advice.

Europe↗

PubMed1986

Molecular cloning of the murine adenosine deaminase gene from a genetically enriched source: identification and characterization of the promoter region.

A genomic library was prepared with DNA from a genetically enriched mouse cell line in which amplified copies of the adenosine deaminase (ADA) gene account for over 5% of the genome. Overlapping cosmid clones encompassing the entire ADA structural gene were isolated from this genomic library and used for subsequent structural and functional analyses. Nuclease protection and primer extension analyses served to identify the location of multiple transcription initiation sites at the 5' end of the structural gene. Promoter activity was found by functional analyses to reside within a 240-base-pair fragment which contains the transcription initiation sites. Sequences upstream of the transcription initiation sites are very G + C rich (77%) and include a 22 nucleotide stretch of deoxyguanylate residues and two potential Sp1 transcription factor-binding sites. Comparison of the mouse and human ADA gene promoters revealed the presence of several regions that are highly conserved with regard to both sequence content and location and may represent genetic elements which are involved in ADA gene expression.

Acetyltransferases↗

PubMed2005

High speed development work by preparation of an "in-hand" library of NMR-quantified degradation products.

Standard materials of impurities are needed in pharmaceutical development such as for validating impurity analytical methods. Most often the impurities possess structures, which are difficult and very time consuming to synthesize. In the present work, we demonstrate that a library of degradation products of ragaglitazar--a novel tricyclic-gamma-alkyloxyphenylpropionic acid with hypolipidemic and antidiabetic activity--observed in stability indicating samples of a solid dosage formulation by LC-MS can be produced in a one pot oxidation reaction. The library entities were isolated in small quantities (microg-mg) by preparative HPLC and structurally characterized by NMR spectroscopy and mass spectrometry. The concentrations of the library entities were determined in solution by NMR using an internal standard method. The library was successfully used in the validation work of a newly developed purity method for the drug product providing useful response factors and relative retention times (RRTs) of the degradation products.

Chromatography, High Pressure Liquid↗