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PubMed1997

Sequencing of cDNA clones that encode bovine ferritin H and L chains.

The molecular weight of the liver-type subunit (L) of bovine ferritin is much larger than that of the heart-type subunit (H) as determined by SDS-PAGE (L, 20.5 kDa; H, 18.4 kDa). The migration of these two subunits on SDS-PAGE gels, relative to each other, is opposite to that reported for ferritin L and H subunits in other mammalian species (L, 19 kDa; H, 21 kDa). To determine the cause of this anomaly, full-length cDNA clones of the bovine L and H chains were isolated from a bovine spleen gamma gt11 cDNA library and sequenced. The amino acid sequences of the L and H chains of bovine ferritin, deduced from their cDNA sequences, contained open reading frames coding for 174 and 180 amino acid residues with calculated molecular weights of 19,856 and 20,920 Da, respectively. The deduced amino acid sequence of the L chain shows 86%, 84%, 87%, 83% and 83% homology with the amino acid sequences of horse, human, rabbit, rat and mouse L chains, respectively. The H chain displays a higher homology with the human, rat and mouse H chains (91%, 92% and 93%, respectively). In addition, the bovine L chain did not contain the extra octapeptide present in rodent L chains, and bovine, L and H chains did not react with concanavalin A. The bovine L and H chains expressed using a baculovirus expression system showed almost the same mobilities as those of bovine spleen ferritin, respectively, by SDS-PAGE. These results suggest that the much slower mobility of the bovine L chain compared with other mammalian L chains on SDS-PAGE cannot be attributed to insertion(s) of amino acid(s) or peptide(s) into the L chain, to the deletion(s) of them of it or to the addition of carbohydrate chains(s) but may result from significant differences in the binding affinity of SDS for bovine ferritin L chains.

Amino Acid Sequence↗

PubMed2006

Identification of bacteria in endodontic infections by sequence analysis of 16S rDNA clone libraries.

A significant proportion of oral bacteria are unable to undergo cultivation by existing techniques. In this regard, the microbiota from root canals still requires complementary characterization. The present study aimed at the identification of bacteria by sequence analysis of 16S rDNA clone libraries from seven endodontically infected teeth. Samples were collected from the root canals, subjected to the PCR with universal 16S rDNA primers, cloned and partially sequenced. Clones were clustered into groups of closely related sequences (phylotypes) and identification to the species level was performed by comparative analysis with the GenBank, EMBL and DDBJ databases, according to a 98% minimum identity. All samples were positive for bacteria and the number of phylotypes detected per subject varied from two to 14. The majority of taxa (65.2%) belonged to the phylum Firmicutes of the Gram-positive bacteria, followed by Proteobacteria (10.9%), Spirochaetes (4.3%), Bacteroidetes (6.5%), Actinobacteria (2.2%) and Deferribacteres (2.2%). A total of 46 distinct taxonomic units was identified. Four clones with low similarity to sequences previously deposited in the databases were sequenced to nearly full extent and were classified taxonomically as novel representatives of the order Clostridiales, including a putative novel species of Mogibacterium. The identification of novel phylotypes associated with endodontic infections suggests that the endodontium may still harbour a relevant proportion of uncharacterized taxa.

Adolescent↗

PubMed1998

Molecular cloning of platelet factor XI, an alternative splicing product of the plasma factor XI gene.

Platelet factor XI is associated with the platelet plasma membrane and has an apparent Mr (220,000 nonreduced, 55,000 reduced) different from that of plasma factor XI. However, the site of synthesis and the nature of platelet factor XI are not known. Using reverse transcriptase polymerase chain reaction, 12 out of 13 exons (all except exon V) coding for mature plasma factor XI were amplified from human platelet mRNA. The sequence of each of these exons was identical to that of plasma factor XI. In situ amplification and hybridization of factor XI mRNA was positive for exon III and negative for exon V in platelets and negative for both exons in other blood cells. By Northern hybridization, a factor XI mRNA transcript of approximately 1.9 kilobases was detected in megakaryocytic cells, and one of approximately 2.1 kilobases was detected in liver cells. Factor XI cDNA was cloned from a megakaryocyte library and sequenced. Exon V was absent, and the splicing of exon IV to exon VI maintained the open reading frame without alteration of the amino acid sequence except for the deletion of amino acids Ala91-Arg144 within the amino-terminal portion of the Apple 2 domain. Thus, platelet factor XI is an alternative splicing product of the factor XI gene, localized to platelets and megakaryocytes but absent from other blood cells.

Alternative Splicing↗

PubMed2004

[Cloning and analysis of six full-length cDNA similar to sheep KAP6-1 from cashmere goat].

Cashmere is the fiber of kings, produced from the cashmere goat (Capra hircus). Cashmere fabric has little squama. Due to its lightness cashmere feels smooth and silky. An intriguing feature of cashmere structure is multiplicity of the hair keratin proteins with distinctive amino acid compositions. To study the role and regulation of one of these keratins, we used the SMART ( switching mechanism at 5' end of RNA transcript) technology to construct a cDNA library of skin tissue from an Inner Mongolia male cashmere goat. A total of 636 cDNA sequences were obtained by randomly sequenced from 5' of cDNA library. Sequence comparison with the GenBank database confirmed that there are 41 sequences showed high nucleotide sequence identity in the coding region with sheep keratin associated protein 6-1 (KAP6-1). They represent six different cDNAs (The accession numbers in GenBenk are AY310749, AY310750, AY310751, AY310752, AY310753 and AY310754, respectively). They are full-length cDNAs according to the known KAP6-1 genomic gene sequences of sheep. From the nucleotide sequences the open reading frames were identified, that encoded six basic proteins of 82, 84, 71, 71, 83, 83 amino acids, respectively, with a combined glycine and tyrosine content of about 60%. Compared analysis showed that the KAPs from goats shared more than 55.4% identities in nucleotide sequences and more than 79.8% identities in amino acid sequences with each other, and shared highest identities (81.9% approximately 98.8%) with KAP6-1 from sheep. The KAP6s from different animal species shared more than 50% identities in amino acid sequences with each other.

Amino Acid Sequence↗

PubMed1986

Isolation of a rat parvalbumin gene and full length cDNA.

The complete sequence of the rat parvalbumin mRNA was determined by sequencing a near full length cDNA clone and a primer extension product of the 5' untranslated region of this clone. The parvalbumin sequence contained 72 nucleotides of the 5' untranslated region, 333 nucleotides of the coding sequence, and 183 nucleotides of the 3' untranslated sequence in the case of the shorter parvalbumin messenger RNA or 556 nucleotides in the case of the larger parvalbumin messenger RNA. The two RNAs were derived from a single primary transcript since two clones were sequenced which were identical except for the site of polyadenylation. The polyadenylation signal of the shorter, more abundant RNA was AATAAA while the putative signal for the larger RNA was GATAAA. A 32-base pair sequence comprising part of the 5' untranslated region and the first seven codons of the parvalbumin cDNA was 81% homologous to a region of the chicken calmodulin cDNA encoding part of the first Ca2+-binding domain. This homology indicates that this portion of the parvalbumin mRNA may have evolved from a primordial first domain. A parvalbumin genomic clone which hybridized to probes derived from both the coding and 3' untranslated region of the cDNA was cloned from a rat genomic library. Partial sequencing identified an uninterrupted stretch of 585 base pairs identical to the 3' end of the parvalbumin cDNA. Two introns were localized in the genomic clone. Their position with respect to the parvalbumin amino acid sequence corresponded to the intron locations found in genes of several other Ca2+-binding proteins. This result indicates that, despite the deletion of one Ca2+-binding domain, the remainder of the parvalbumin gene has maintained the structural pattern of the Ca2+-binding protein gene family.

Amino Acid Sequence↗

PubMed2005

Combined laser capture microdissection and serial analysis of gene expression from human tissue samples.

Cell-specific gene expression profiling from heterogeneous human tissues is confounded by cell purification limitations. Here, we describe a technique to generate gene expression profiles of pure populations of prostate cancer cells obtained from fresh-frozen prostatectomy specimens and small initial quantities of RNA by combining laser capture microdissection and microserial analysis of gene expression (LCM-microSAGE). Two microSAGE libraries were obtained from approximately 100,000 laser pulses, estimated to contain fewer than 3 x 10(5) cells and 20-30 ng mRNA. Two libraries were sequenced to a depth of 10,111 and 10,463 unique tags from normal and cancer cells, representing 6453 and 6923 genes, respectively. Most transcripts were expressed at similar levels, but cancer cells compared with normal cells had increased expression of 385 tags and decreased expression of 389 tags. A total of 20 genes were differentially expressed (P<0.05); five of these genes were upregulated and 15 were downregulated in cancer cells. Quantitative reverse transcriptase-polymerase chain reaction results from three selected genes corroborated the existence of cell-specific gene expression in LCM-microSAGE-derived libraries. In conclusion, the LCM-microSAGE approach demonstrates that large-scale expression profiles of known and unknown transcripts can be generated from pure populations of target cells obtained from human tissue samples comprised of heterogeneous mixtures of cell types.

Gene Expression Profiling↗

PubMed2004

Phylogenetic and ecological analysis of novel marine stramenopiles.

Culture-independent molecular analyses of open-sea microorganisms have revealed the existence and apparent abundance of novel eukaryotic lineages, opening new avenues for phylogenetic, evolutionary, and ecological research. Novel marine stramenopiles, identified by 18S ribosomal DNA sequences within the basal part of the stramenopile radiation but unrelated to any previously known group, constituted one of the most important novel lineages in these open-sea samples. Here we carry out a comparative analysis of novel stramenopiles, including new sequences from coastal genetic libraries presented here and sequences from recent reports from the open ocean and marine anoxic sites. Novel stramenopiles were found in all major habitats, generally accounting for a significant proportion of clones in genetic libraries. Phylogenetic analyses indicated the existence of 12 independent clusters. Some of these were restricted to anoxic or deep-sea environments, but the majority were typical components of coastal and open-sea waters. We specifically identified four clusters that were well represented in most marine surface waters (together they accounted for 74% of the novel stramenopile clones) and are the obvious targets for future research. Many sequences were retrieved from geographically distant regions, indicating that some organisms were cosmopolitan. Our study expands our knowledge on the phylogenetic diversity and distribution of novel marine stramenopiles and confirms that they are fundamental members of the marine eukaryotic picoplankton.

Animals↗

PubMed2006

Antigens for the selection of pan-variable number of tandem repeats motif-specific human antibodies against Mucin-1.

Epitopes found on Mucin-1 are differentially expressed on tumour versus normal tissue. Such epitopes have also been shown to have a potential in immunotherapy and tumour detection. The major epitope explored in this context is located within the variable number of tandem repeats. It has however recently been demonstrated that this epitope exists in several sequence variants. The standard sequence is highly antigenic while the most common sequence variant is much less so. We have now explored routes employing defined synthetic antigens to ensure the development of human recombinant antibody specificities targeting both sequence variants of this epitope. These antibodies may serve as a platform for the development of human antibodies for efficient targeting of Mucin-1 in human disease.

Antibodies, Monoclonal↗

PubMed2001

Core-directed protein design.

For various reasons, it seems sensible to redesign or design proteins from the inside out. Past approaches in this field have involved iterations of mutagenesis and characterisation to 'evolve' designs. Increasingly, combinatorial approaches are being taken to select 'fit' sequences from libraries of variant proteins. In particular, in silico methods have been used to good effect. More recently, experimental methods have been developed and improved. We are now in a position to redesign stability and function into natural protein frameworks confidently and to attempt de novo designs for more ambitious targets.

Algorithms↗

PubMed2002

Construction of a cDNA fragment library from SH-SY5Y cells using restriction display PCR.

A complementary DNA (cDNA) fragment library from SH-SY5Y cells is constructed using a restriction display polymerase chain reaction (RD-PCR) technique. Messenger RNA (mRNA) is extracted from SH-SY5Y cells and single-strand cDNA synthesised using an anchored oligo primer (dT18). The second strand is produced by nick translation. The double strands are cleaved with the restriction enzyme Sau3AI and the fragments ligated with universal linker. The products are amplified with universal primers and selected primers, ligated into the pMDI8-T vector, and then sequenced. The library constructed contained 136 subgroups, each comprising seven to 12 cDNA fragments. RD-PCR proved a simple, effective way to construct a cDNA library, and this will contribute to the investigation of gene expression in the neuron in future microarray studies.

DNA, Complementary↗

PubMed1999

Identification, characterisation and cDNA cloning of two caseins from the common brushtail possum (Trichosurus vulpecula)1.

Two major caseins have been isolated from the milk of the common brushtailed possum (Trichosurus vulpecula). These have been identified as alpha- and beta-casein on the basis of the similarity of their N-terminal sequences to those of the caseins of another marsupial (Macropus eugenii). Both proteins appear to exist in multiple forms. Possum alpha-casein is glycosylated mainly in the form of sialic acid residues and was shown by electrospray mass spectrometry to have multiply phosphorylated forms of three families with molecular masses 22700 and 23200 Da that may represent genetic variants. Two-dimensional electrophoresis showed that beta-casein exists as a complex of five or six proteins of identical N-terminal sequence but differing pI. Electrospray mass spectrometry indicated that the beta-caseins also are multiply phosphorylated with masses between 32300 and 32600 Da. A subfamily with mass values 1530 greater was also detected. The patterns were not affected by stage of lactation and quantitative analysis of two-dimensional gels of whole milk shows that alpha- and beta-caseins are present at a constant ratio throughout lactation. cDNA clones for the possum alpha- and beta-caseins have been isolated from an early lactation mammary cDNA library and sequenced.

Amino Acid Sequence↗

PubMed2006

Design of a novel plasminogen activator based on the structure of hirudin.

Using a phage library, seven peptide sequences with high affinity to human microplasminogen were obtained. Caseinolytic assay indicated that only the synthesized peptide P07 had slight fibrinolytic activity. To enhance its plasminogen activation ability, peptide P07 was fused into loop 32-35 of hirudin. In vitro assay demonstrated that this hirudin-like fusion protein can activate human plasminogen and retain the function of thrombin inhibition. Fusing the sequence ''SPDASRL'' into hirudin generated a plasminogen activation activity 100 times higher than peptide P07 in chromogenic and radial caseinolytic assay. This significant functional improvement might originate from a more specific active structure due to the hirudin scaffold.

Amino Acid Sequence↗

PubMed1997

Developmental gene expression of procollagen III in bovine extraembryonic membranes during early pregnancy.

A major secretory protein produced by bovine chorioallantoic membranes, in vitro, was previously identified as the carboxyl-propeptide of alpha-1 type III collagen. In the present study, the protein and gene expression of procollagen III by bovine chorioallantois between days 17 and 45 of pregnancy was investigated. In addition, differential usage of multiple transcription termination sites by chorioallantois was examined. Two-dimensional PAGE of proteins synthesized and released by whole conceptuses or isolated chorioallantoic membranes into culture medium demonstrated that the C-terminal of procollagen III was not detectable before day 21 of pregnancy and concentrations increased thereafter. Developmental gene expression was determined by Northern blot analysis using a probe (A) that preceded all five polyadenylation sites of the previously sequenced clone 9.22. Procollagen III mRNA expression was undetectable at day 17, low on day 20, and increased through day 36. Two major transcripts of 5.9 and 4.9 kb were identified, the latter of which was expressed more prominently. A second probe (B), which terminated between poly-A sites 2 and 3, was designed to identify transcripts that terminated at poly-A site 1 or 2. This probe bound to the 5.9-kb mRNA only. Two additional procollagen III cDNA clones were isolated from our bovine conceptus cDNA library and sequenced. One, designated 9.29, terminated at poly-A site 5. The other, designated 11.7, terminated at poly-A site 2, indicating that the bovine conceptus uses these stop sites in procollagen III transcription. Results from this study demonstrate that procollagen III gene and protein expression coincide with the development of the allantois, which progressively fuses with the chorion forming the chorioallantois placenta. In addition, multiple termination sites are used in procollagen III transcription.

Animals↗

PubMed2001

From consensus sequence peptide to high affinity ligand, a "library scan" strategy.

A wide variety of proteins have been shown to recognize and bind to specific amino acid sequences on other proteins. These sequences can be readily identified using combinatorial peptide libraries. However, peptides containing these preferred sequences ("consensus sequence peptides") typically display only modest affinities for the consensus sequence-binding site on the intact protein. In this report, we describe a parallel synthesis strategy that transforms consensus sequence peptides into high affinity ligands. The work described herein has focused on the Lck SH2 domain, which binds the consensus peptide acetyl-Tyr(P)-Glu-Glu-Ile-amide with a K(D) of 1.3 micrometer. We employed a strategy that creates a series of spatially focused libraries that challenge specific subsites on the target protein with a diverse array of functionality. The final lead compound identified in this study displayed a 3300-fold higher affinity for the Lck SH2 domain than the starting consensus sequence peptide.

Amino Acid Sequence↗

PubMed1997

Human chromosome pellicle antibody recognizing centromere protein-C (CENP-C), the main component of the kinetochore.

Recently the antichromosome antisera from several scleroderma patients have been found to recognize the pellicle of metaphase and anaphase chromosomes. In order to identify the pellicle components, we used these antichromosome antisera to screen a human embryonic cDNA library. The sequences of the positive clones are identical to the cDNA gene sequence of CENP-C (centromere protein C), a human centromere autoantigen. This result suggests that CENP-C is a component of the pellicle of human metaphase and anaphase chromosomes.

Anaphase↗

PubMed1993

Characterisation of a highly repeated DNA sequence from Mycobacterium bovis.

We report characterisation of a novel repeat sequence from a Mycobacterium bovis genomic library. The highly repeated sequence belongs to a family consisting of a 24 base pair (bp) direct repeat (DR), that appears to be organized into clusters on the chromosome. We classify the 24-bp DR into the group of prokaryotic DNA repeats known as the interspersed repetitive sequence elements. The 24-bp DR will be of potential use as a DNA fingerprinting tool in epidemiological studies of M. bovis.

Base Sequence↗

PubMed1999

Altered gene expression in fetal Down syndrome brain as revealed by the gene hunting technique of subtractive hybridization.

Information on gene expression in brain of patients with Down Syndrome (DS, trisomy 21) is limited and molecular biological research is focussing on mapping and sequencing chromosome 21. The information on gene expression in DS available follows the current concept of a gene dosage effect due to a third copy of chromosome 21 claiming overexpression of genes encoded on this chromosome. Based upon the availability of fetal brain and recent technology of gene hunting, we decided to use subtractive hybridization to evaluate differences in gene expression between DS and control brains. Subtractive hybridization was applied on two fetal brains with DS and two age and sex matched controls, 23rd week of gestation, and mRNA steady state levels were evaluated generating a subtractive library. Subtracted sequences were identified by gene bank and assigned by alignments to individual genes. We found a series of up- and downregulated sequences consisting of chromosomal transcripts, enzymes of intermediary metabolism, hormones, transporters/channels and transcription factors (TFs). We show that trisomy 21 or aneuploidy leads to the deterioration of gene expression and the derangement of transcripts describes the impairment of transport, carriers, channels, signaling, known metabolic and hormone imbalances. The dys-coordinated expression of transcription factors including homeobox genes, POU-domain TFs, helix-loop-helix-motifs, LIM domain containing TFs, leucine zippers, forkhead genes, maybe of pathophysiological significance for abnormal brain development and wiring found in patients with DS. This is the first description of the concomitant expression of a large series of sequences indicating disruption of the concerted action of genes in this disorder.

Amino Acid Sequence↗

PubMed1999

Gene expression in fetal Down syndrome brain as revealed by subtractive hybridization.

Information on gene expression in brain of patients with Down Syndrome (DS, trisomy 21) is limited and molecular biological research is focussing on mapping and sequencing chromosome 21. The information on gene expression in DS available follows the current concept of a gene dosage effect due to a third copy of chromosome 21 claiming overexpression of genes encoded on this chromosome. Based upon the availability of fetal brain and recent technology of gene hunting, we decided to use subtractive hybridization to evaluate differences in gene expression between DS and control brains. Subtractive hybridization was applied on two fetal brains with DS and two age and sex matched controls, 23rd week of gestation, and mRNA steady state levels were evaluated generating a subtractive library. Subtracted sequences were identified by gene bank and assigned by alignments to individual genes. We found a series of up- and downregulated sequences consisting of chromosomal transcripts, enzymes of intermediary metabolism, hormones, transporters/channels and transcription factors (TFs). We show that trisomy 21 or aneuploidy leads to the deterioration of gene expression and the derangement of transcripts described describes the involvement of chromosomes other than chromosome 21, explains impairment of transport, carriers, channels, signaling, known metabolic and hormones imbalances. The dys-coordinated expression of transcription factors including homeobox genes, POU-domain TFs, helix-loop-helix-motifs, LIM domain containing TFs, leucine zippers, forkhead genes, maybe of pathophysiological significance for abnormal brain development and wiring found in patients with DS. This is the first description of the concomitant expression of a large series of sequences indicating disruption of the concerted action of genes in that disorder.

Animals↗