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At least 847 records · Page 47Linked to original sources
PubMed2003

DNA sequence-based "bar codes" for tracking the origins of expressed sequence tags from a maize cDNA library constructed using multiple mRNA sources.

To enhance gene discovery, expressed sequence tag (EST) projects often make use of cDNA libraries produced using diverse mixtures of mRNAs. As such, expression data are lost because the origins of the resulting ESTs cannot be determined. Alternatively, multiple libraries can be prepared, each from a more restricted source of mRNAs. Although this approach allows the origins of ESTs to be determined, it requires the production of multiple libraries. A hybrid approach is reported here. A cDNA library was prepared using 21 different pools of maize (Zea mays) mRNAs. DNA sequence "bar codes" were added during first-strand cDNA synthesis to uniquely identify the mRNA source pool from which individual cDNAs were derived. Using a decoding algorithm that included error correction, it was possible to identify the source mRNA pool of more than 97% of the ESTs. The frequency at which a bar code is represented in an EST contig should be proportional to the abundance of the corresponding mRNA in the source pool. Consistent with this, all ESTs derived from several genes (zein and adh1) that are known to be exclusively expressed in kernels or preferentially expressed under anaerobic conditions, respectively, were exclusively tagged with bar codes associated with mRNA pools prepared from kernel and anaerobically treated seedlings, respectively. Hence, by allowing for the retention of expression data, the bar coding of cDNA libraries can enhance the value of EST projects.

Base Sequence↗
PubMed1995

Characterization and modeling of membrane proteins using sequence analysis.

The current libraries of amino acid sequences of membrane proteins are a valuable resource for the analysis of elements common to these proteins. Multiple-sequence alignment techniques and the identification of conserved features of transmembrane segments have improved the prediction of membrane protein topology. Molecular modeling in combination with structural studies or site-directed mutagenesis is proving to be a powerful link between theory and experiment. Unfortunately, the number of high-resolution structures of intrinsic membrane proteins, although increased recently, presents a restricted and perhaps biased view of membrane protein structure.

Amino Acid Sequence↗
PubMed2002

A serial analysis of gene expression in sun-damaged human skin.

To study the phenotypic changes in human skin associated with repeated sun exposure at the transcription level, we have undertaken a comparative serial analysis of gene expression of sun-damaged preauricular skin and sun-protected postauricular skin as well as sun-protected epidermis. Serial analyses of gene expression libraries, containing multiple mRNA-derived tag recombinants, were made to poly(A+)RNA isolated from human postauricular skin and preauricular skin, as well as epidermal nick biopsy samples. 5330 mRNA-derived cDNA tags from the postauricular serial analysis of gene expression library were sequenced and these tag sequences were compared to cDNA sequences identified from 5105 tags analyzed from a preauricular serial analysis of gene expression library. Of the total of 4742 different tags represented in both libraries we found 34 tags with at least a 4-fold difference of tag abundance between the libraries. Among the mRNAs with altered steady-state(1) levels in sun-damaged skin, we detected those encoding keratin 1, macrophage inhibitory factor, and calmodulin-like skin protein. In addition, a comparison of cDNA sequences identified in the serial analysis of gene expression libraries obtained from the epidermal biopsy samples (5257 cDNA tags) and from both full-thickness skin samples indicated that many genes with altered steady-state transcript levels upon sun exposure were expressed in epidermal keratinocytes. These results suggest a major role for the epidermis in the pathomechanism of largely dermal changes in chronically sun-exposed skin.

Adult↗
PubMed1990

Cloning and sequence analysis of a cDNA encoding a precursor for rat C-type natriuretic peptide (CNP).

Recent identification of a C-type natriuretic peptide (CNP) in porcine brain strongly suggested that a third member of the natriuretic peptide family still remains to be identified in other species of mammals. A cDNA encoding a precursor for rat CNP was cloned from a rat brain cDNA library and sequenced. The precursor was a 126-residue peptide, carrying a 23-residue signal sequence at the N-terminus and the known porcine CNP-53 sequence at the C-terminus. By RNA blot analysis, rat CNP mRNA was found to be expressed exclusively in the brain, implying that CNP may function in the central nervous system as a neuropeptide.

Amino Acid Sequence↗
PubMed2003

Construction of a BAC library and generation of BAC end sequence-tagged connectors for genome sequencing of the African malaria mosquito Anopheles gambiae.

A Bacterial Artificial Chromosome (BAC) genomic DNA library of Anopheles gambiae, the major human malaria vector in sub-Saharan Africa, was constructed and characterized. This library (ND-TAM) is composed of 30,720 BAC clones in eighty 384-well plates. The estimated average insert size of the library is 133 kb, with an overall genome coverage of approximately 14-fold. The ends of approximately two-thirds of the clones in the library were sequenced, yielding 32,340 pair-mate ends. A statistical analysis (G-test) of the results of PCR screening of the library indicated a random distribution of BACs in the genome, although one gap encompassing the white locus on the X-chromosome was identified. Furthermore, combined with another previously constructed BAC library (ND-1), ~2,000 BACs have been physically mapped by polytene chromosomal in situ hybridization. These BAC end pair mates and physically mapped BACs have been useful for both the assembly of a fully sequenced A. gambiae genome and for linking the assembled sequence to the three polytene chromosomes. This ND-TAM library is now publicly available at both http://www.malaria.mr4.org/mr4pages/index.html/ and http://hbz.tamu.edu/, providing a valuable resource to the mosquito research community.

Animals↗
PubMed2003

A census of rRNA genes and linked genomic sequences within a soil metagenomic library.

We have analyzed the diversity of microbial genomes represented in a library of metagenomic DNA from soil. A total of 24,400 bacterial artificial chromosome (BAC) clones were screened for 16S rRNA genes. The sequences obtained from BAC clones were compared with a collection generated by direct PCR amplification and cloning of 16S rRNA genes from the same soil. The results indicated that the BAC library had substantially lower representation of bacteria among the Bacillus, alpha-Proteobacteria, and CFB groups; greater representation among the beta- and gamma-Proteobacteria, and OP10 divisions; and no rRNA genes from the domains Eukaryota and Archaea. In addition to rRNA genes recovered from the bacterial divisions Proteobacteria, Verrucomicrobia, Firmicutes, Cytophagales, and OP11, we identified many rRNA genes from the BAC library affiliated with the bacterial division Acidobacterium; all of these sequences were affiliated with subdivisions that lack cultured representatives. The complete sequence of one BAC clone derived from a member of the Acidobacterium division revealed a complete rRNA operon and 20 other open reading frames, including predicted gene products involved in cell division, cell cycling, folic acid biosynthesis, substrate metabolism, amino acid uptake, DNA repair, and transcriptional regulation. This study is the first step in using genomics to reveal the physiology of as-yet-uncultured members of the Acidobacterium division.

Bacteria↗
PubMed1990

Characterization of a novel nodulin gene in soybean that shares sequence similarity to the gene for nodulin-24.

A gene encoding for nodulin-16 (N-16) was isolated from a soybean genomic library. Nucleotide sequence analysis of the cDNA and the genomic clone of N-16 indicated that the coding region of this gene is 330 bp long and is interrupted by a single intron of 494 bp. The coding region of the N-16 gene shows a high degree of localized sequence similarity with the coding sequence of soybean nodulin-24 (N-24). Sequence similarity between the two genes is limited to the coding region of 90 bp in the first exon and the first 54 bp in the second exon of the N-16 gene which is repeated as the 2nd, 3rd, and 4th exons in the N-24 gene. The N-24 gene has been postulated to be a result of repeated duplication of an insertion element consisting of the 54 bp exon and the flanking intron sequences. In the absence of sequence similarity in the regions flanking the 54 bp sequence between the N-16 and N-24 genes, the N-16 gene does not appear to be the ancestral gene. Both N-16 and N-24 have a similar hydrophobic amino terminal end suggesting that N-16 like N-24 is targeted to the peribacteroid membrane. Southern analysis of soybean genomic DNA shows the presence of other related sequences to the N-16 gene, one of which is found to be closely linked to it. Analysis of the temporal accumulation of the N-16 transcripts during nodule development in effective and ineffective nodules suggests that N-16 and related genes might differ from leghemoglobin and some other late nodulin genes in their mechanism of regulation.

Amino Acid Sequence↗
PubMedDate not supplied

Characterization of iron-dependent endogenous superoxide dismutase of Plasmodium falciparum.

Two main superoxide dismutase activities at isoelectric points (pI) 6.2 and 6.8 and two minor at pI 5.6 and 6.4 were found in crude extracts of Plasmodium falciparum. These activities were cyanide-resistant and hydrogen peroxide-sensitive and represented 20-30% of the total SOD activity found in the crude extract. A fragment of 424 bp, amplified from genomic DNA from P. falciparum, was cloned and sequenced. The deduced amino acid sequence identified this fragment as a coding region of an SOD gene. A cDNA corresponding to SOD was then isolated from a P. falciparum cDNA library and sequenced. The deduced amino acid sequence of SOD (197 aa) was compared with 32 known Feor Mn-SODs by the 'DARWIN' system. This analysis showed that the parasitic enzyme was related to typical Fe-SODs. The SOD subunit was purified and the N-terminal sequence, determined up to 29 residues, corresponded to that of cDNA isolated. The iron-dependent SOD activity found in Plasmodium falciparum represents the first level of the antioxidant defence system of the parasite. It is also the first SOD characterized in the parasitic Apicomplexa phylum whose sequence can be compared to equivalent iron-dependent enzymes known in other protozoa and bacteria.

Amino Acid Sequence↗
PubMed2003

Potential bias of fungal 18S rDNA and internal transcribed spacer polymerase chain reaction primers for estimating fungal biodiversity in soil.

Four fungal 18S rDNA and internal transcribed spacer (ITS) polymerase chain reaction (PCR) primer pairs were tested for their specificity towards target fungal DNA in soil DNA extracts, and their ability to assess the diversity of fungal communities in a natural grassland soil was compared. Amplified PCR products were cloned, and approximately 50 clones from each library were sequenced. Phylogenetic analysis and database searches indicated that each of the sequenced cloned DNA fragments was of fungal origin for each primer pair, with the exception of the sequences generated using the 18S rDNA primers nu-SSU-0817 and nu-SSU-1196, where 35 of the 50 sequenced clones represented soil invertebrates. Although some of the primers have previously been suggested to be biased towards certain fungal taxonomic groups, the ratio of sequences representing each of the four main fungal phyla, Ascomycota, Basidiomycota, Chytridiomycota and Zygomycota, was similar for each of the primer pairs, suggesting that primer bias may be less significant than previously thought. Collector's curves were plotted to estimate the coverage obtained for each of the clone libraries after clustering the sequences into operational taxonomic units at a level of 99% sequence similarity. The curves indicated that good coverage of diversity was achieved, with the exception of the clone library constructed using primers nu-SSU-0817 and nu-SSU-1196, on account of the high number of non-fungal sequences obtained. The work demonstrates the usefulness of 18S rDNA and ITS PCR primers for assessing fungal diversity in environmental samples, and it also highlights some potential limitations of the approach with respect to PCR primer specificity and bias.

Bias↗
PubMed1995

Xenopus laevis ribosomal protein L22: full-length cDNA sequence and expression analysis.

A cDNA clone was isolated from a Xenopus laevis embryo library and sequenced. Primer extension experiments indicated the full-length nature of the insert and the encoded product was identified on a two dimensional gel as ribosomal protein (r-protein) L22. The 510-bp L22 cDNA sequence presents short untranslated regions and a 5'-end polypyrimidine tract found in all other vertebrate r-protein mRNA (rp mRNA) so far analyzed. Both the nucleotide (nt) and the deduced amino acid (aa) sequences have been compared with the homologous sequences from other species. The L22 nt sequence is about 70% similar to the mammalian L27a rp mRNA and about 60% homologous to the Drosophila, Tetrahymena and yeast corresponding mRNAs. The 148-aa sequence presents a higher conservation, being 90% similar to the mammalian sequence and more than 70% to the other species. Expression analysis showed that, both during X. laevis embryogenesis and in X. laevis cultured cells during growth-rate changes, L22 synthesis is translationally regulated. Therefore X. laevis L22 mRNA is a new example of the correlation between the polypyrimidine terminal tract and the translational regulation observed in other rp mRNAs.

Amino Acid Sequence↗
PubMedDate not supplied

Automated mass spectrometric sequence determination of cyclic peptide library members.

Cyclic peptides have come under scrutiny as potential antimicrobial therapeutic agents. Combinatorial split-and-pool synthesis of cyclic peptides can afford single compound per well libraries for antimicrobial screening, new lead identification, and construction of quantitative structure-activity relationships (QSAR). Here, we report a new sequencing protocol for rapid identification of the members of a cyclic peptide library based on automated computer analysis of mass spectra, obviating the need for library encoding/decoding strategies. Furthermore, the software readily integrates with common spreadsheet and database packages to facilitate data visualization and archiving. The utility of the new MS-sequencing approach is demonstrated using sonic spray ionization ion trap MS and MS/MS spectrometry on a single compound per bead cyclic peptide library and validated with individually synthesized pure cyclic D,L-alpha-peptides.

Automation↗
PubMed1990

Defective chlorophyll a/b-binding protein genes in the genome of a homosporous fern.

The majority of homosporous ferns have a chromosome number that is severalfold greater than that of diploid seed plants. These fern species have therefore been generally considered to be of polyploid origin. Enzyme electrophoretic investigations have demonstrated, however, that within fern genera, species having the lowest chromosome numbers (n = 27-52) have the number of isozymes typical of diploid seed plants; there is no isozyme evidence for polyploidy of these plants. We have constructed a genomic DNA library from Polystichum munitum (n = 41), a homosporous fern, and have screened the library for sequences homologous to the chlorophyll a/b-binding (CAB) protein genes of higher plants. The majority of the sequences isolated and characterized by nucleotide sequence determination represent defective CAB genes. This result is in contrast to the situation in the genomes of diploid angiosperms, where most, and sometimes all, copies of the CAB gene family represent functional members. Several hypotheses could explain the existence of multiple defective CAB genes in P. munitum. (i) The defective CAB genes are the result of "gene silencing" following polyploidy. (ii) P. munitum has not gone through a polyploidization event, but several, and perhaps the majority, of its CAB genes have mutated to a nonfunctional state (a phenomenon not yet observed in any of the genomes of non-fern plants so far examined). (iii) Some defective CAB genes have been specifically amplified in the genome of P. munitum.

Amino Acid Sequence↗
PubMed1998

Characterization of the 5' flanking region of the Xenopus laevis transforming growth factor-beta 5 (TGF-beta 5) gene.

Transforming growth factors-beta are potent regulators of cellular proliferation, differentiation and morphogenesis. 2.41 kb of the 5' flanking region of the transforming growth factor-beta 5 (TGF-beta 5) gene has been isolated from a Xenopus laevis genomic library and sequenced. The transcription start site of this gene was determined by 5' RACE method. Promoter activity was demonstrated by transient transfection experiments using luciferase reporter gene constructs in XTC cells. A number of putative recognition sites for transcription factors were found in the 5' flanking region of the TGF-beta 5 gene.

Amino Acid Sequence↗
PubMed1995

Isolation and characterization of the gene encoding the surface membrane 3'-nucleotidase/nuclease of Leishmania donovani.

Leishmania donovani and related trypanosomatid protozoa possess an externally oriented surface membrane enzyme capable of hydrolyzing both 3'-nucleotides and nucleic acids. By virtue of these activities, this 3'-nucleotidase/nuclease (3'-NT/Nu), previously shown to be analogous to fungal and plant class-I single-strand-specific nucleases, is thought to play a critical role in the salvage of purines, essential for the survival of these organisms. The 43-kDa 3'-NT/Nu was purified from L. donovani promastigotes and trypsin treated. Four of the released tryptic peptide fragments yielded amino-acid sequence information (Pept-1 to Pept-4) which provided the basis for the preparation of oligonucleotide primers used for PCR amplification of an approx. 300-bp DNA fragment. This fragment was cloned, sequenced and used to probe a genomic L. donovani cosmid library. Nucleotide sequence analysis of a 4.5-kb SmaI fragment, isolated from a cosmid clone, revealed an open reading frame (ORF) of 1434 nt encoding a 477-amino-acid protein. Pept-1 to Pept-4 were mapped onto the ORF-deduced protein sequence. Peptides corresponding to Pept-1 to Pept-4 were synthesized and used to immunize rabbits. The resulting anti-peptide antibodies recognized the 43-kDa protein on Western blots and immunoprecipitated the native 3'-nucleotidase activity from L. donovani membrane extracts. Further, the ORF-deduced protein shared significant sequence identity with the S1 and P1 fungal nucleases of Aspergillus oryzae and Penicillium citrinum, respectively. Cumulatively, these results demonstrated that the ORF corresponded to a gene for the L. donovani 3'-nucleotidase/nuclease. In Northern blots a nucleotide probe specific for the 3'-NT/Nu gene hybridized to a single 2.5-kb messenger RNA. Results of Southern blot analyses were consistent with the 3'-NT/Nu being encoded by a single copy gene. These data constitute the first report of the gene for this unique trypanosomatid surface membrane enzyme.

Amino Acid Sequence↗
PubMed2004

Efficient purification of unique antibodies using peptide affinity-matrix columns.

Phage display technology was used to identify peptide ligands with unique specificity for a monoclonal model antibody, MK16, that recognises the human multiple sclerosis associated MHC class II molecule DR2 in complex with a myelin basic protein (MBP)-derived peptide corresponding to residue 85-99. Several peptide epitopes were identified and all of them recognised specifically MK16. One peptide, ER6.1, was selected and linked to beaded agarose and demonstrated excellent performance as a peptide affinity chromatography matrix. This epitope matrix was efficient in the purification of MK16 Fab fragments and had no affinity for other antibodies. Using this peptide matrix MK16 IgG could be purified from cell culture supernatants thereby separating MK16 IgG from bovine IgG normally present in the enriched growth media used for such cells. Investigations of the fine specificity of the ER6.1 peptide demonstrated that it recognised a unique epitope within the heavy chain CDR3 region of the MK16 antibody. Thus, variants of MK16 antibody, which had retained the specificity and affinity of the original antibody but had slightly different amino acid composition in the CDR3 region, were not recognised by the ER6.1 peptide.

Amino Acid Sequence↗
PubMed2001

SK3 is an important component of K(+) channels mediating the afterhyperpolarization in cultured rat SCG neurones.

1. Our aim was to identify the small-conductance Ca(2+)-activated K(+) channel(s) (SK) underlying the apamin-sensitive afterhyperpolarization (AHP) in rat superior cervical ganglion (SCG) neurones. 2. Degenerate oligonucleotide primers designed to the putative calmodulin-binding domain conserved in all mammalian SK channel sequences were employed to detect SK DNA in a cDNA library from rat SCG. Only a single band, corresponding to a fragment of the rSK3 gene, was amplified. 3. Northern blot analysis employing a PCR-generated rSK3 fragment showed the presence of mRNA coding for SK3 in SCG as well in other rat peripheral tissues including adrenal gland and liver. 4. The same rSK3 fragment enabled the isolation of a full-length rSK3 cDNA from the library. Its sequence was closely similar to, but not identical with, that of the previously reported rSK3 gene. 5. Expression of the rSK3 gene in mammalian cell lines (CHO, HEK cells) caused the appearance of a K(+) conductance with SK channel properties. 6. The application of selective SK blocking agents (including apamin, scyllatoxin and newer non-peptidic compounds) showed these homomeric SK3 channels to have essentially the same pharmacological characteristics as the SCG afterhyperpolarization, but to differ from those of homomeric SK1 and SK2 channels. 7. Immunohistochemistry using a rSK3 antipeptide antibody revealed the presence of SK3 protein in the cell bodies and processes of cultured SCG neurones. 8. Taken together, these results identify SK3 as a major component of the SK channels responsible for the afterhyperpolarization of cultured rat SCG neurones.

Alkanes↗
PubMed2005

A site-specific insertion sequence in flax genotrophs induced by environment.

A single-copy 5.7 kilobase (kb) DNA fragment, termed Linum Insertion Sequence 1 (LIS-1), has been identified and characterized. This is one of the DNA changes associated with the environmentally induced heritable changes resulting in stable lines termed genotrophs in flax (Linum usitatissimum). The insertion sequence and its insertion site have been cloned from genomic libraries and sequenced. PCR products across the insertion and surrounding regions have also been cloned and sequenced. The 5.7 kb DNA fragment is inserted into a 3.7 kb EcoRI fragment in the plastic line (Pl) with the generation of a 3 base pair duplication at the insertion site, as well as additional sequence changes. The identical insertion was also found in other genotrophs and flax varieties. The intact element was not present in Pl but appeared to be generated by a reproducible series of complex rearrangements or insertion events. LIS-1 is the result of a targeted, highly specific, complex insertion event that occurs during the formation of some of the genotrophs, and occurs naturally in many flax and linseed varieties.

Chromosomes, Plant↗