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PubMedDate not supplied

[Plan for finding homologies in nucleotide sequence databases using preliminarily calculated sequence samples].

A scheme of fast similarity search of nucleotide sequences is suggested based on sequence imaging, which results in chunks of information much less than original sequence but more specialized for comparison. Three methods were developed using three different imaging functions. The first is based on identity of local sites of up to twelve nucleotides, the second is based on statistical homology of local 42 nucleotide fragments, and the third is based on the homology of 100-150 nucleotide fragments and models the comparison of restriction maps. Each of them requires the library of sequence images. The total size of such a library is less than the size of sequences stored in compressed form. The sequences are aligned allowing local homology searches. The method reduces total time for a similarity search about 100-fold. The programs can be easily included in any software, which allows user to define his own set of sequences. One of the programs is implemented within DNA-SUN software and is used in Institute of Molecular Genetics and Institute of Molecular Biology.

Amino Acid Sequence↗

PubMed2024

Phage Immunoprecipitation and Sequencing-a Versatile Technique for Mapping the Antibody Reactome.

Characterizing the antibody reactome for circulating antibodies provide insight into pathogen exposure, allergies, and autoimmune diseases. This is important for biomarker discovery, clinical diagnosis, and prognosis of disease progression, as well as population-level insights into the immune system. The emerging technology phage display immunoprecipitation and sequencing (PhIP-seq) is a high-throughput method for identifying antigens/epitopes of the antibody reactome. In PhIP-seq, libraries with sequences of defined lengths and overlapping segments are bioinformatically designed using naturally occurring proteins and cloned into phage genomes to be displayed on the surface. These libraries are used in immunoprecipitation experiments of circulating antibodies. This can be done with parallel samples from multiple sources, and the DNA inserts from the bound phages are barcoded and subjected to next-generation sequencing for hit determination. PhIP-seq is a powerful technique for characterizing the antibody reactome that has undergone rapid advances in recent years. In this review, we comprehensively describe the history of PhIP-seq and discuss recent advances in library design and applications.

Humans↗

PubMed2004

Generation and analysis of expressed sequence tags from Trypanosoma cruzi trypomastigote and amastigote cDNA libraries.

We have generated 2771 expressed sequence tags (ESTs) from two cDNA libraries of Trypanosoma cruzi CL-Brener. The libraries were constructed from trypomastigote and amastigotes, using a spliced leader primer to synthesize the cDNA second strand, thus selecting for full-length cDNAs. Since the libraries were not normalized nor pre-screened, we compared the representation of transcripts between the two using a statistical test and identify a subset of transcripts that show apparent differential representation. A non-redundant set of 1619 reconstructed transcripts was generated by sequence clustering. This dataset was used to perform similarity searches against protein and nucleotide databases. Based on these searches, 339 sequences could be assigned a putative identity. One thousand one-hundred and sixteen sequences in the non-redundant clustered dataset (68.8%) are new expression tags, not represented in the T. cruzi epimastigote ESTs that are in the public databases. Additional information is provided online at http://genoma.unsam.edu.ar/projects/tram. To the best of our knowledge these are the first ESTs reported for the life cycle stages of T. cruzi that occur in the vertebrate host.

Animals↗

PubMed2002

Phylogenetic characterization of microbial communities that reductively dechlorinate TCE based upon a combination of molecular techniques.

An anaerobic microbial consortium (referred to as ANAS) that reductively dechlorinates trichloroethene (TCE) completely to ethene with the transient production of cisdichloroethene (cDCE) and vinyl chloride was enriched from contaminated soil obtained from Alameda Naval Air Station. ANAS uses lactate as its electron donor and has been functionally stable for over 2 years. Following a brief exposure to oxygen, a subculture (designated VCC) derived from ANAS could dechlorinate TCE only to vinyl chloride with lactate as its electron donor. Three molecular methods were used concurrently to characterize the community structure of ANAS and VCC: clone library construction/clone sequencing, terminal restriction fragment length polymorphism (T-RFLP) analysis, and fluorescent in situ hybridization (FISH) with rRNA probes. The community structure of ANAS did not change significantly over the course of a single feeding/dechlorination cycle, and only minor fluctuations occurred over many feeding cycles spanning the course of 1 year. Clone libraries and T-RFLP analyses suggested that ANAS was dominated by populations belonging to three phylogenetic groups: Dehalococcoides species, Desulfovibrio species, and members of the Clostridiaceae (within the low G + C Gram-positives). FISH results suggest that members of the Cytophaga/Flavobacterium/Bacteroides (CFB) cluster and high G + C Gram-positives (HGCs) were numerically important in ANAS despite their under-representation in the clone libraries. Parallel analyses of VCC samples suggested that Dehalococcoides species and Clostridiaceae were only minor populations in this community. Instead, VCC had increased populations of organisms in the beta and gamma subclasses of the Proteobacteria as well as significant populations of organisms in the CFB cluster. It is possible that symbiotic interactions are occurring between some of ANAS's phylogenetic groups under the enrichment conditions, including interspecies hydrogen transfer from Desulfovibrio species to Dehalococcoides species. However, the nucleic acid-based analyses performed here would need to be supplemented with chemical species data in order to test any hypotheses about functional roles of various community members. Additionally, these results suggest that an organism outside the Dehalococcoides genus may be capable of dechlorinating cDCE to vinyl chloride.

Bacteria↗

PubMed1992

Molecular cloning of a G-protein alpha i subunit from the lobster olfactory organ.

A G-protein alpha subunit was cloned from a lobster olfactory organ cDNA library and sequenced. The clone encodes an alpha i subunit based on the 80% identity its predicted amino acid sequence shares with mammalian alpha i subunits. On Northern blots of polyadenylated RNA, the clone hybridized to a 5 kb species from several tissues.

Amino Acid Sequence↗

PubMed2006

Analysis of EST and lectin expressions in hemocytes of Manila clams (Ruditapes philippinarum) (Bivalvia: Mollusca) infected with Perkinsus olseni.

The hemocytes of invertebrates play key roles in both cellular and humoral immune reactions by phagocytosis or delivering immune factors such as lectin and anti-microbial peptides. Bacterial infection causes changes in components such as lectins, anti-bacterial peptides, and lysosomal enzymes of plasma or hemolymph in molluscs. Previously, we found that infection with the protozoan parasite, Perkinsus, increases lectin synthesis in hemocytes. In order to investigate the patterns of genes expressed in Manila clams (Ruditapes philippinarum) infected with the protozoan parasite Perkinsus olseni, we constructed a cDNA library and sequenced 1850 clones (expressed sequence tags). A total of 79 ESTs, were related to 29 functional immune genes such as C-type lectin, lysozyme, and cystatin B, in Manila clams. Lectins were the largest group of immune-function ESTs found in our Manila clams library. Among 7 lectin clones, two full length cDNAs of lectins were cloned. MCL-3, which is a simple C-type lectin composed of 151 amino acids, has a relatively short signal sequence of 17aa and single carbohydrate-recognition domain (CRD) of approximately 130 residues. It is highly homologous to eel C-type lectin. The sequence of mc-sialic acid-binding lectin consists of 168 amino acid residues with molecular weight of 19.2 and shows high homology to sialic acid-binding lectin from the snail, Cepaea hortensis. The expression of 7 different lectins in hemocytes was analyzed by RT-PCR using gene-specific primers. Hemocytes from Perkinsus-infected clam expressed different sets of lectins than with Vibrio infection. These results demonstrate that several lectins are involved in Manila clam innate immunity and different challenges induce expression of different lectins.

Amino Acid Sequence↗

PubMed1994

The complete structure of human class IV alcohol dehydrogenase (retinol dehydrogenase) determined from the ADH7 gene.

A novel human alcohol dehydrogenase (ADH) gene called ADH7 has been characterized and determined to encode class IV ADH, an ADH isozyme which is very active as a retinol dehydrogenase. A nearly full-length cDNA for ADH7 was isolated from a human stomach cDNA library, and a 5' genomic clone containing exons 1 and 2 was isolated from a human genomic library. DNA sequence analysis of the cDNA and genomic clones revealed the complete coding region of the gene and the deduced full-length amino acid sequence of human class IV ADH composed of 373 amino acids following the initiator methionine. The class IV identity of the sequence was confirmed by agreement with previously determined sequences for several human stomach class IV ADH peptides. Alignment of the full-length predicted amino acid sequence of human class IV ADH with the full-length sequences of the other four known human ADH classes revealed sequence identities of 69% (class I), 59% (class II), 61% (class III), and 60% (class V). The higher sequence identity shared with human class I ADH suggests that the genes for ADH classes I and IV may have diverged from a common ancestor after the separation of the other classes, and may still share common physiological functions. Discussed is the possibility that one of these functions is retinol oxidation for the synthesis of retinoic acid, a hormone important for cellular differentiation.

Alcohol Oxidoreductases↗

PubMed1997

Structures of genes encoding phospholipase A2 inhibitors from the serum of Trimeresurus flavoviridis snake.

Inhibitors (PLIs) against snake venom gland phospholipases A2 (PLA2s) have been found in their sera. A cDNA encoding a PLI from Trimeresurus flavoviridis (Tf, habu snake, Crotalinae) serum, cPLI-A, was isolated from the Tf liver cDNA library and sequenced. Northern blot analysis with cPLI-A showed that PLIs are expressed only in liver. Genes for PLIs, gPLI-A and gPLI-B, were isolated from the Tf genomic DNA library and their nucleotide (nt) sequences were determined. The genes consisted of four exons and three introns, and exon 4 encoded the carbohydrate recognition domain (CRD)-like motif. Comparison of the nt sequences between gPLI-A and gPLI-B showed that these genes are highly homologous, including introns, except that exon 3 is rich in nonsynonymous nt substitutions which are almost four times as frequent as synonymous nt substitutions. This evolutionary feature of PLI genes is different from that of venom gland PLA2 isozyme genes in which nonsynonymous nt substitutions are spread over the entire mature protein-coding region.

Amino Acid Sequence↗

PubMed1996

Characterization of a polyubiquitin gene in T. thermophila and of ubiquitin gene expression during sexual reproduction and under stress conditions.

A 5-unit polyubiquitin gene, TTU3, was isolated from a T. thermophila genomic library and sequenced. This gene presents an extra triplet coding for Phe, a AGAGA motif and a putative HSE element in its 5'-non-coding region. The ubiquitin gene expression in this ciliate was investigated by Northern blot hybridization in conjugating cells or cells under stress conditions. Exponentially growing cells express two ubiquitin mRNAs of 0.75 and 1.8 kb and a new species of 1.4 kb is induced under hyperthermic stress. During sexual reproduction of the cells (conjugation) the 1.8-kb mRNA is still transcribed whereas the steady-state population of the 0.75 mRNA transcripts is strongly diminished. Southern blot analysis suggests that ubiquitin in T. thermophila constitutes a large family of about ten members.

Amino Acid Sequence↗

PubMed1991

Cloning and sequence analysis of the human liver rhodanese: comparison with the bovine and chicken enzymes.

The cDNA for the human rhodanese (thiosulfate: cyanide sulfurtransferase, EC 2.8.1.1), a nuclearly encoded protein of the mitochondrial matrix, was isolated from a human fetal liver cDNA library. Nucleotide sequence revealed an open reading frame coding for a polypeptide of 295 amino acids, which presented a 57% and 58% identity with the bovine and avian rhodanese, respectively. The analysis of the 5'-ends of the coding region gave no evidence for the presence of a cleavable signal sequence as found in other mitochondrial proteins. A comparison with two available amino acid sequences (cow and chicken) showed that sequence similarity is not restricted to the alpha-helices and beta-structures motifs which are remarkably superimposable in the two halves of bovine rhodanese, but extends to adjacent regions.

Adrenal Glands↗

PubMedDate not supplied

[A method for the preparation of normalized cDNA libraries enriched with full-length sequences].

We developed a new method for the preparation of normalized cDNA libraries enriched with full-length sequences. It is based on the properties of the recently characterized duplex-specific nuclease from the hepatopancreas of the Kamchatka crab. The duplex-specific nuclease is thermostable, it effectively cleaves double-stranded DNA and is inactive toward single-stranded DNA (Shagin et al., Genome Res., 2002, vol. 12, pp. 1935-1942). Our method enables the normalization of cDNA samples enriched with full-length sequences without use of laborious and ineffective stages of physical separation. The efficiency of the method was demonstrated in model experiments using cDNA samples from several human tissues.

Animals↗

PubMed1993

Isolation and sequence analysis of variant forms of human transcobalamin II.

Two cDNA clones (1.9 kb and 1.5 kb, respectively) encoding full length human TC II have been isolated from a human endothelial cell cDNA library and sequenced. The differences between the two clones are the length of the 5' end and the 3' end non-coding regions and the codon at position 198 and 219. Both the clones differ from the recently isolated (human endothelial cell) cDNA for TC II (Platica, O., Janecko, R., Quadros, E.V., Regee, A., Romain, R. and Rothenberg, S.P. (1991) J. Biol. Chem. 266, 7860-7863) in codon 259 and 376 and in their calculated pI values. In vitro transcription followed by translation in a reticulocyte lysate system and SDS-PAGE revealed that the isolated cDNA clones encode a protein of 43 kDa. Upon treatment with canine pancreatic microsomes, the molecular mass of the in vitro translated product was reduced to 41.5 kDa, indicating the presence of an approximately 1.5 kDa signal peptide. This translation product was immunoprecipitated with rabbit anti-serum to human TC II and was able to bind to Cbl-Sepharose beads. The amino acid sequence alignment of TC II with that of other Cbl binding proteins (rat intrinsic factor, human transcobalamin I and porcine haptocorrin) revealed only 33% overall homology. However, there were four regions of greater than 80% homology and two regions of about 60% homology. These regions encompass the majority of the hydrophobic areas of the Cbl-binders. Based on these studies, we suggest that structural basis for the expression of different polymorphic forms of TC II may be due to single point mutations and that TC II, like other mammalian Cbl-binders, have evolved from a common ancestral gene. Furthermore, the Cbl-binding functional domain most probably resides in a hydrophobic pocket which is formed by all or some of the six regions of high homology.

Amino Acid Sequence↗

PubMed1994

Nucleotide sequence encoding human pancreatic ribonuclease.

A cDNA coding for human pancreatic ribonuclease was isolated from a pancreas cDNA library and sequenced. This cDNA (1620 bp) includes an entire open reading frame encoding mature protein (128 aa) following a signal peptide (28 aa) as well as 5'- and 3'-untranslated regions.

Amino Acid Sequence↗

PubMed2025

Targeted Next-Generation Sequencing in Rare Diseases.

Targeted next-generation sequencing (NGS) in rare disease focuses on genetic analysis of specific regions in genome that are linked to a rare disease. In addition to library preparation, sequencing, and data analysis, targeted NGS includes an additional step of target enrichment of selected genes and regions. It allows for more sensitive and profound sequencing, as it is a fast and cost-effective approach with less data burden and is therefore often a method of choice for identifying rare variants in known genes, especially in diagnostics of rare diseases. Several in silico tools address the pathogenicity predictions of rare variants of unknown significance (VUS) and can therefore facilitate clinical interpretation.

Rare Diseases↗

PubMed2000

Construction and characterization of a Schistosoma mansoni bacterial artificial chromosome library.

A bacterial artificial chromosome (BAC) library has been established from genomic DNA isolated from the trematode parasite of human, Schistosoma mansoni. This library consists of more than 21,000 recombinant clones carrying inserts in the pBeloBAC11 vector. The mean insert size was 100 kb, representing an approximate 7.95-fold genome coverage. Library screening with eight chromosome-specific or single-copy gene probes yielded between 1 and 9 positive clones, and none of those tested was absent from the library. End sequences were obtained for 93 randomly selected clones, and 37 showed sequence identity to S. mansoni sequences (ESTs, genes, or repetitive sequences). A preliminary analysis by fluorescence in situ hybridization localized 8 clones on schistosome chromosomes 1 (2 clones), 2, 3, 5, Z, and W (3 clones). This library provides a new resource for the physical mapping and sequencing of the genome of this important human pathogen.

Animals↗

PubMed1993

Expression of two different forms of cDNA for thromboxane synthase in insect cells and site-directed mutagenesis of a critical cysteine residue.

cDNA coding for human placental thromboxane synthase (EC 5.3.99.5) was amplified by PCR from a human placental cDNA library and sequenced. This cDNA and a shorter cDNA isolated from a human lung cDNA library with a deletion of 163 bp near the 3' end were expressed in Spodoptera frugiperda (Sf9) insect cells using a baculovirus expression system. The cDNA from human placenta was expressed as an active enzyme (60 kDa) with a specific activity higher than those reported from other cell types, whereas the shorter cDNA was expressed in an inactive form (52 kDa). The active recombinant enzyme appeared to be unglycosylated as the molecular mass and the enzyme activity were not altered in the presence of tunicamycin. Site-directed mutagenesis was performed to convert a cysteine at position 480 in thromboxane synthase to a serine. This cysteine is found to be highly conserved in related cytochrome P-450 enzymes. The mutant enzyme was found to be inactive, although Western blot, immunoprecipitation and SDS/PAGE analysis indicated that the mutant enzyme was expressed at a level comparable with the wild-type enzyme. These results suggest that Cys-480 is essential for the enzyme catalytic activity and that the short-form cDNA may be a non-functional transcript.

Amino Acid Sequence↗

PubMed1993

Phospholipid hydroperoxide glutathione peroxidase: full-length pig blastocyst cDNA sequence and regulation by selenium status.

We have isolated and sequenced an apparent full-length cDNA clone for phospholipid hydroperoxide glutathione peroxidase (Genbank accession number L12743) from a pig blastocyst cDNA library. The sequence encodes a polypeptide of 170 amino acids, including a TGA-encoded selenocysteine at residue 46, with a calculated M(r) of 19,492 Da. Use of this clone in Northern blot analysis of Se-deficient rat liver revealed that phospholipid hydroperoxide glutathione peroxidase mRNA levels were little affected by Se deficiency, whereas classical glutathione peroxidase mRNA levels were decreased by 90% in the same samples. Lastly, liver phospholipid hydroperoxide glutathione peroxidase mRNA levels were not elevated in female rats, in contrast to classical glutathione peroxidase.

Amino Acid Sequence↗

PubMed1994

Molecular cloning of a Drosophila melanogaster gene coding for an homologue of human carboxypeptidase E.

PCR primers derived from two functional domains of vertebrate carboxypeptidase E (CPE) were used to generate a probe for screening a size-selected Drosophila melanogaster genomic library. A sequence representing about 50% of the expected complete sequence was obtained by translation of the two open reading frames present on a 1.6 kb DNA genomic fragment. This partial sequence, homologous to human CPE, CPM, and CPN, contained the conserved arginine and zinc binding domains. Similarities to the human enzymes were found with stretches that were equally divergent from the three vertebrate carboxypeptidases. Northern blot analysis revealed the presence of a 6.9 kb transcript for this gene in Drosophila embryos. I postulate that insects possess a single protein fulfilling CPE, CPM, and CPN functions.

Amino Acid Sequence↗