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PubMed1990

Cloning and sequencing of mammalian glutathione reductase cDNA.

The molecular cloning of a partial cDNA to mouse glutathione reductase mRNA and of a full-length cDNA to the mRNA of the human enzyme is described. An initial cDNA clone designated lambda GRM-B11 was isolated by plaque-screening of an induced mouse cDNA expression library in the lambda gt11 vector with a rabbit antibody probe to human glutathione reductase. 125Iodine-labelled whole anti-rabbit immunoglobulin was used as second antibody. EcoRI digestion of the lambda GRM-B11 clone released a 720-bp fragment which was identified as a partial mouse glutathione reductase cDNA by the following techniques. (a) Escherichia coli Y1089 lysogenized with lambda GRM-B11 could be induced to synthesize a recombinant polypeptide whose antigenicity to anti-(glutathione reductase) serum was established by SDS/polyacrylamide gel electrophoresis and subsequent immunoblotting. (b) The GRM-B11 sequence, recloned in the Bluescript vector to give the plasmid pGRM-B11, was found to code for a polypeptide consisting of 242 amino acid residues exhibiting 82% identities with the known amino acid sequence of the human glutathione reductase from position 77 to 318. The insert of the pGRM-B11 plasmid was used as a bona fide nucleic acid probe to screen mouse and human cDNA libraries prepared in the lambda gt11 or in the lambda gt10 vector. The first full-length cDNA clone (lambda GRH-Mev10) was identified in a human cDNA library based on RNA of human placental cells. Its insert was composed of three EcoRI fragments of 720, 613 and 336 bp. The three fragments were recloned in the Bluescript vector and sequenced. The largest fragment (pGRH-B) is colinear with the mouse sequence cloned in the pGRM-B11 plasmid. The fragment of intermediate size (pGRH-CT) comprises the 3' end of the mRNA and the poly(A) tail while the short fragment (pGRH-NT) corresponds to the 5' region of the mRNA. The amino acid sequence deduced from the nucleotide sequences of the three subclones is identical with the known sequence of the mature glutathione reductase from human erythrocytes in all 478 positions.

Amino Acid Sequence↗

PubMed1986

Molecular characterization of the purity of seven human chromosome-specific DNA libraries.

We have characterized at the molecular level seven chromosome-specific libraries constructed in phage lambda Charon 21A from flow-sorted human chromosomes. The purity of libraries prepared from chromosomes sorted from hamster X human cells was estimated by species-specific hybridization and ranged from 48% to 83% of clones containing human inserts. Among libraries of chromosomes from human cells, mass screenings were made for repetitive sequences and 20 clones from the #18 and #20 libraries were analyzed in detail. Ten to fifteen percent of all clones contain sequences which can be mapped; 80-100% of these derive from the intended chromosome of origin, demonstrating very high purity and a 35 X enrichment of chromosome-specific sequences over a total genomic library. The two libraries contain a high, though dissimilar, percent of repeat-containing clones; the #18 library has 55% repetitive clones and the #20 library 85%. This dissimilarity may be due to a difference in insert size distribution, since the #18 library has smaller inserts than the #20. This could be caused by variation in extent of digestion of insert DNA and/or differences in sequence organization between the two chromosomes. A method more sensitive than conventional plaque-lift screening was used to detect repetitive inserts; in this way nearly all repetitive clones could be eliminated before purification of their DNAs.

Animals↗

PubMed1999

Combinatorial libraries by portioning and mixing.

Combinatorial chemistry--due to its radically new synthetic methods--can be considered a forerunner of chemistry in the next century. One of the most important methods is the portioning-mixing (split-mix) synthesis which embodies the combinatorial principle. It is easily realized. Both manual and automatic devices have been described. Some features that contribute to its popularity include: it produces all possible structural combinations of the monomers, it has outstanding productivity, it leads to the formation of individual compounds in nearly equimolar quantities (affected by statistics and incomplete reactions), and it can be applied to all classes of organic compounds. Since an enormously large number of compounds can be produced in principle in a relatively short time, some practical considerations are discussed that can be useful in library design. Encoding organic libraries by peptide or nucleotide sequences or with binary tags are also described together with methods for tagging macroscopic support units with electronic chips, two dimensional bar codes or colored resin and capsule caps. Among the deconvolution strategies, the iteration method, positional scanning, omission libraries, the Selectide and the Pharmacopeia methods are mentioned. A collection of libraries prepared by portioning-mixing is also included in graphical format.

Organic Chemicals↗

PubMed2003

The construction of an EST database for Bombyx mori and its application.

To build a foundation for the complete genome analysis of Bombyx mori, we have constructed an EST database. Because gene expression patterns deeply depend on tissues as well as developmental stages, we analyzed many cDNA libraries prepared from various tissues and different developmental stages to cover the entire set of Bombyx genes. So far, the Bombyx EST database contains 35,000 ESTs from 36 cDNA libraries, which are grouped into approximately 11,000 nonredundant ESTs with the average length of 1.25 kb. The comparison with FlyBase suggests that the present EST database, SilkBase, covers >55% of all genes of Bombyx. The fraction of library-specific ESTs in each cDNA library indicates that we have not yet reached saturation, showing the validity of our strategy for constructing an EST database to cover all genes. To tackle the coming saturation problem, we have checked two methods, subtraction and normalization, to increase coverage and decrease the number of housekeeping genes, resulting in a 5-11% increase of library-specific ESTs. The identification of a number of genes and comprehensive cloning of gene families have already emerged from the SilkBase search. Direct links of SilkBase with FlyBase and WormBase provide ready identification of candidate Lepidoptera-specific genes.

Amino Acid Sequence↗

PubMed1983

Soybean nodulin genes: Analysis of cDNA clones reveals several major tissue-specific sequences in nitrogen-fixing root nodules.

Plant gene products that could play a role in the process of symbiotic nitrogen fixation in leguminous plants were detected by screening a cDNA library prepared from soybean nodule poly(A)(+) RNA. About 13% of the 5,700 clones screened contained sequences detectable with a root cDNA probe while about 2,100 clones (37% of the library) contained sequences that were detectable only with nodule cDNA. Five unique sequence species, accounting for more than half of the 2,100 nodule-specific clones, were identified by cross-hybridization experiments. The most abundant species, represented by 860 clones, encodes the well-characterized protein, leghemoglobin (Lb). The other four species, designated NodA, NodB, NodC, and NodD, are represented by 350, 55, 61, and 6 clones, respectively. Each of these four species was found to be encoded by the plant nuclear genome at low copy number. The transcripts corresponding to the nodule-specific clones represented 12-15% (Lb), 6% (NodA), and 0.5-1.1% (NodB, NodC, and NodD) mole fraction of nodule polysomal mRNAs but could not be detected in root polysomal RNA. Hybrid-selection of nodule mRNAs by representative clones and in vitro translation indicated that polypeptides of M(r) 44,000, 27,000, 24,000, and 100,000-120,000 are encoded by NodA, NodB, NodC, and NodD sequences, respectively. These polypeptides reacted with antiserum prepared against total soluble nodule proteins suggesting that the cloned sequences encode nodule-specific proteins, nodulins.

Journal Article↗

PubMed1984

Molecular cloning of a cDNA for the chicken progesterone receptor B antigen.

A cDNA for the chicken progesterone receptor B subunit antigen (Mr, 108,000) has been isolated from a cDNA library prepared from size-selected chicken oviduct poly(A)+RNA. A specific monoclonal antibody raised against hen progesterone receptor B subunit (alpha PR-B) was used to screen the library. Recombinant clones reacting with the antibody by virtue of antigen expression were used in hybrid-selected translation. A single clone, pPRB-1, hybridized specifically to a mRNA that yielded a Mr 108,000 protein when translated in vitro and which was immunoprecipitable by the alpha PR-B antibody. This cDNA represents a 470-base-pair portion of the PR-B nucleotide sequence. Additional clones have been subsequently isolated from the recombinant library using the insert from pPRB-1 as a specific probe. A mRNA size of approximately 3000 nucleotides was determined for the chicken progesterone receptor B subunit by formaldehyde/agarose gel electrophoresis and blot hybridization using pPRB-1 as a probe. Preliminary studies show that withdrawal of hormone from chickens treated chronically with estrogen leads to a dramatic decrease in the cellular RNA concentration of receptor B, indicating that target tissue levels of receptor B RNA are under hormonal control.

Animals↗

PubMed1998

Design of self-coded combinatorial libraries to facilitate direct analysis of ligands by mass spectrometry.

The direct analysis of selected components from combinatorial libraries by sensitive methods such as mass spectrometry is potentially more efficient than deconvolution and tagging strategies since additional steps of resynthesis or introduction of molecular tags are avoided. A substituent selection procedure is described that eliminates the mass degeneracy commonly observed in libraries prepared by "split-and-mix" methods, without recourse to high-resolution mass measurements. A set of simple rules guides the choice of substituents such that all components of the library have unique nominal masses. Additional rules extend the scope by ensuring that characteristic isotopic mass patterns distinguish isobaric components. The method is applicable to libraries having from two to four varying substituent groups and can encode from a few hundred to several thousand components. No restrictions are imposed on the manner in which the "self-coded" library is synthesized or screened.

Drug Design↗

PubMed1995

Human autoantibody recognition of DNA.

Combinatorial IgG Fab phage display libraries prepared from a systemic lupus erythematosus (SLE) donor and a healthy donor were affinity selected against human placental DNA. Human monoclonal antibody Fab fragments specific for DNA were isolated from both libraries, although Fabs of the highest affinity were isolated only from the lupus library. Generally, apparent affinities of the Fabs for human placental DNA, purified double-stranded DNA, and denatured DNA were approximately equivalent. Surface plasmon resonance indicated Fab binding constants for a double-stranded oligodeoxynucleotide of 0.2-1.3 x 10(8) M-1. The higher-affinity Fabs, as ranked by binding to human placental DNA or to the oligonucleotide probe, tested positive in the Crithidia luciliae assay commonly used in the diagnosis of SLE, and interestingly the genes encoding the heavy-chain variable regions of these antibodies displayed evidence of only minimal somatic hypermutation. The heavy chains of the SLE Fabs were characterized by a predominance of basic residues toward the N terminus of complementarity-determining region 3 (CDR3). The crucial role of heavy-chain CDR3 (HCDR3) in high-affinity DNA recognition was suggested by the creation of DNA binding in an unrelated antibody by HCDR3 transplantation from SLE antibodies. We propose that high-affinity DNA-binding antibodies can arise in SLE without extensive somatic hypermutation in the variable-region genes because of the expression of inappropriate HCDR3s.

Amino Acid Sequence↗

PubMed1987

Role of carbohydrate in the function of human granulocyte-macrophage colony-stimulating factor.

cDNA clones for the human hematopoietic regulator granulocyte-macrophage colony-stimulating factor (hGM-CSF) were isolated from a lamba gt11 cDNA library prepared from RNA of COS cells transiently expressing the gene for hGM-CSF. As the RNA was a rich source of hGM-CSF mRNA, approximately 0.1% of the clones of this library contained hGM-CSF sequences. All of the clones analyzed were full length and were correctly processed. When subcloned into an expression vector and transfected into COS cells, the cDNA clones direct the synthesis of higher levels of the growth factor than the gene from which they were derived. The cDNA for native hGM-CSF was used to generate structural mutants which lack N-linked carbohydrate, O-linked carbohydrate, or both. Although the mutant proteins had differing specific activities, the nonglycosylated forms reproduce many, if not all, of the physiologic functions of authentic hGM-CSF. The role of carbohydrate in the secretion and function of hGM-CSF is discussed.

Animals↗

PubMed1994

The origin of the diversity of crotoxin isoforms in the venom of Crotalus durissus terrificus.

Crotoxin, the main toxin from the venom of the South American rattlesnake Crotalus durissus terrificus, is a beta-neurotoxin which consists of the non-covalent association of two subunits: a phospholipase A2 subunit B (CB), and a non-enzymic subunit A (CA). We have previously purified and characterized several isoforms of each subunit of crotoxin in the venom collected from numerous snakes. Furthermore, three cDNAs encoding two CB isoforms and the precursor, pro-CA, of subunit A have been isolated from a cDNA library prepared from a single venom gland of Crotalus durissus terrificus. The aim of this study is to analyse an individual snake venom from an animal that has been used to construct a cDNA library. Several isoforms of subunit A and two isoforms of subunit B were isolated and compared to purified and characterized subunit isoforms from pooled venom. The result of this study showed that the multiplicity and the diversity of crotoxin isoforms result from post-translational modifications occurring on a precursor and from the expression of different messenger RNAs present in an individual snake. It allowed for the identification of the two CB isoforms encoding cDNAs expressed in the individual venom with two isoforms from pooled venom, CBc and probably CBa2, that belong to two classes of crotoxin complexes which can be distinguished biochemically and pharmacologically.

Amino Acid Sequence↗

PubMed1986

Cloning of the chicken progesterone receptor.

Monospecific antibodies directed against the chicken progesterone receptor (PR) form B were used to screen a randomly primed phage lambda gt11 cDNA expression library prepared from size-fractionated chicken oviduct mRNA. Two independent immunoreactive clones, lambda cPR1 and lambda cPR2, were isolated. Antibodies selected from anti-PR form B antiserum on matrices of lambda cPR1 and lambda cPR2 fusion proteins detected two proteins on electrophoretic immunoblots of crude and purified PR preparations. These proteins had the same apparent molecular weights as did PR forms A and B crosslinked with the tritiated progestin R 5020. Thus, lambda cPR1 and lambda cPR2 fusion proteins contain epitopes present in both PR forms A and B. A cDNA clone, lambda cPR3, containing the inserts of both lambda cPR1 and lambda cPR2, was isolated from a randomly primed lambda gt10 oviduct cDNA library, indicating that both cDNA inserts were derived from the same oviduct mRNA. Additional evidence that these cDNAs correspond to PR mRNA was provided by sequencing the lambda cPR3 cDNA insert, since it was found to encode the sequence of three tryptic peptides prepared from purified PR form B. A fourth and a fifth cDNA clone, lambda cPR4 and lambda cPR5, were sequentially isolated from the same lambda gt10 cDNA library beginning with a probe derived from the 3' end of the lambda cPR3 insert. Partial DNA sequencing of lambda cPR4 and lambda cPR5 revealed the presence of a sequence coding for a cysteine-rich domain that is strikingly homologous to the amino acid sequences present in the putative DNA-binding domain of the human and chicken estrogen receptors, human glucocorticoid receptor, and v-erbA gene product of the avian erythroblastosis virus.

Amino Acid Sequence↗

PubMedDate not supplied

A solid-phase labeling strategy for the preparation of technetium and rhenium bifunctional chelate complexes and associated peptide conjugates.

A new solid-phase labeling strategy for the preparation of (99m)Tc and Re chelate complexes and associated peptide derivatives, was developed. Resin-bound monoamide monoamine (MAMA) chelates were prepared in such a manner that upon the addition of a suitable Re(V) and Tc(V) precursor the target metal complexes were selectively released from the resin. The desired products were isolated from unreacted ligand by a simple filtration/solid-phase extraction procedure. In addition to the preparation of a series of functionalized ligands, a peptide conjugate was constructed from one of the resin-bound chelates using a conventional automated peptide synthesizer. The yields of the Re chelate complexes were typically greater than 70%, while the maximum yield for reactions run at the tracer level using (99m)Tc was 50%. The reported approach has a number of attractive features, including the opportunity to prepare libraries of novel agents, the ability to isolate macroscopic amounts of Re complexes for use in in vitro screening studies and as well-characterized standards for tracer level work, and the ability to produce (99m)Tc complexes that are free of any unreacted starting material without having to employ preparative HPLC.

Amines↗

PubMed2003

Characterization of a gene from chromosome 1B encoding the large subunit of ADPglucose pyrophosphorylase from wheat: evolutionary divergence and differential expression of Agp2 genes between leaves and developing endosperm.

A full-length genomic clone containing the gene encoding the large subunit of the ADPglucose pyrophosphorylase (Agp2), was isolated from a genomic library prepared from etiolated shoots of hexaploid wheat (Triticum aestivum L., cv, Chinese Spring). The coding region of this gene is identical to one of the cDNA clones previously isolated from a developing wheat grain cDNA library and is therefore an actively transcribed gene. The sequence represented by the cDNA spans 4.8 kb of the genomic clone and contains 15 introns. 2852 bp of DNA flanking the transcription start site of the gene was cloned upstream of the GUS (beta-glucuronidase) reporter gene. This Agp2::GUS construct and promoter deletions were used to study the pattern of reporter gene expression in both transgenic tobacco and wheat plants. Histochemical analysis of GUS expression in transgenic tobacco demonstrated that the reporter gene was expressed in guard cells of leaves and throughout the seed. In transgenic wheat, reporter gene expression was confined to the endosperm and aleurone with no expression in leaves. The cloned Agp2 gene was located to chromosome 1B by gene-specific PCR with nullisomic-tetrasomic lines. Northern analysis demonstrated that the Agp2 genes are differentially expressed in leaves and developing endosperm; while all three classes of Agp2 genes are transcribed in developing wheat grain endosperm, only one is transcribed in leaves. The differences between the Agp2 genes are discussed in relation to the evolution of hexaploid wheat.

Journal Article↗

PubMed1990

The predicted amino acid sequence of a centrosphere protein in dividing sea urchin eggs is similar to elongation factor (EF-1 alpha).

Monoclonal antibody (SU5), prepared from isolated mitotic spindles of sea urchin eggs, stained centrospheres preferentially and recognized a 50K (K = 10(3) Mr) polypeptide on immunoblots. Three positive clones were isolated by screening a lambda gt11 cDNA expression library prepared from sea urchin egg mRNA with SU5. One clone containing a 1.8-kb (1 kb = 10(3) base-pairs) insert was selected for further characterization. The beta-galactosidase fusion protein encoded by the cDNA clone had an apparent relative molecular mass of 150K, indicating that the inserted cDNA produced an estimated 34K of polypeptide. A single 2.2-kb RNA transcript was detected in sea urchin embryos using the cDNA clone as a probe. The cDNA fragment was sequenced and the nucleotide sequence was used to predict the amino acid sequence of the open reading frames in the clone. The putative gene product shows striking similarity to the peptide chain elongation factor (EF-1 alpha) from yeast, fungus, shrimp, insect, mouse and human.

Amino Acid Sequence↗

PubMed1986

Molecular cloning and expression in Escherichia coli of the cDNA coding for rabbit tumor necrosis factor.

cDNA clones containing the entire sequence of the precursor of rabbit tumor necrosis factor (TNF) were identified from a cDNA library prepared using poly(A)+RNA of lipopolysaccharide-induced rabbit alveolar cells. Synthetic oligodeoxynucleotides based on the amino acid sequence of rabbit TNF were selected by RNA blot hybridization and used as probes to screen this library. The DNA sequence and the amino acid sequence deduced from it showed very high homology to the reported DNA and amino acid sequences of human TNF. A plasmid containing the tac promoter and cDNA sequence coding for the 154-amino-acid sequence of mature rabbit TNF protein was constructed and expressed in Escherichia coli. The polypeptide produced had the characteristics of purified rabbit serum TNF and caused a necrotic response in a transplanted syngeneic tumor in mice.

Amino Acid Sequence↗

PubMed1986

The EMBL data library.

The EMBL Data Library was the first internationally supported central resource for nucleic acid sequence data. Working in close collaboration with its American counterpart, GenBank (1), the library prepares and makes available to the scientific community a comprehensive collection of the published nucleic acid sequences. This paper describes briefly the contents of the database, how it is available, and possible future enhancements of Data Library services.

Animals↗

PubMed1993

Identification, characterization, and analysis of cDNA and genomic sequences encoding two different small heat shock proteins in Hordeum vulgare.

In vitro translation of mRNAs prepared from barley (Hordeum vulgare) seedlings (cv. Onice) exposed at 40 degrees C directed the synthesis of major heat shock proteins (HSPs) with molecular masses of 80-90, 70, 42 and 16-22 kDa. A cDNA library prepared from the 40 degrees C mRNAs and screened by differential hybridization led to the isolation of heat shock specific sequences. One of these (Hv hsp18) was confirmed by hybrid-arrested and hybrid-released translation as encoding for an 18-kDa HSP. The barley hsp18 sequence has an open reading frame encoding a 160 amino acid residue 18-kDa protein that is 63% identical to wheat 16.9-kDa HSP (clone C5-8), 54% identical to soybean (Glycine max) 17.5-kDa HSP, and 49% identical to Arabidopsis thaliana 17.6-kDa HSP. Lower similarities were found with class II plant small HSPs such as soybean 17.9-kDa HSP (27%), Pisum sativum 17.7-kDa HSP (30%), wheat (Triticum aestivum) 17.3-kDa HSP (clone Ta hsp 17.3) (30%), and with animal small HSPs and alpha-crystallins. The Hv hsp18 sequence was used to pick up Hv hsp17 genomic sequence encoding for another class I 17-kDa HSP. By computer analysis of the nucleotide sequence the TATA box, two heat shock promoter elements, a metal-ion response element, and the polyadenylation signals were identified. Barley HSP18 has an additional cysteine-rich region when compared with HSP17 mapping at the carboxy terminal end.

Amino Acid Sequence↗

PubMed2005

Novel microbial diversity adherent to plant biomass in the herbivore gastrointestinal tract, as revealed by ribosomal intergenic spacer analysis and rrs gene sequencing.

It is well recognized that a dynamic biofilm develops upon plant biomass in the herbivore gastrointestinal tract, but this component of the microbiome has not previously been specifically sampled, or directly compared with the biodiversity present in the planktonic fraction of digesta. In this study, the digesta collected from four sheep fed two different diets was separated into three fractions: the planktonic phase, and the microbial populations either weakly or tightly adherent to plant biomass. The community DNA prepared from each fraction was then subjected to both ribosomal intergenic spacer analysis (RISA) and denaturing gradient gel electrophoresis (DGGE). Both types of analysis showed that dietary factors influence community structure, and that the adherent fractions produced more complex profiles. The RIS-clone libraries prepared from the planktonic and adherent populations were then subjected to restriction fragment length polymorphism (RFLP) and DNA sequence analyses, which resulted in a far greater degree of discrimination among the fractions. Although many of the sequenced clones from the adherent populations were assigned to various clusters within the low G+C Gram-positive bacteria, the clone libraries from animals consuming an all-grass diet were largely comprised of novel lineages of Clostridium, while in animals consuming the starch-containing diet, Selenomonas and Ruminococcus spp. were the dominant low G+C Gram-positive bacteria. Additionally, the libraries from hay-fed animals also contained clones most similar to asaccharolytic Clostridia, and other Gram-positive bacteria that specialize in the transformation of plant phenolic compounds and the formation of cinnamic, phenylacetic and phenylpropionic acids. These results reveal, for the first time, the phylogeny of adherent subpopulations that specialize in the transformation of plant lignins and other secondary compounds, which potentiate polysaccharide hydrolysis by other members of the biofilm.

Animals↗