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PubMed1998

Striking evolutionary conservation of a cis-element related to nuclear receptor target sites and present in TR2 orphan receptor genes.

A systematic scanning of nucleic acid databases for DNA elements made of combinations of RGGTCA nuclear receptor half sites, has revealed that identical 19 nucleotide-long motifs composed of two inverted RGGTCA sites with a spacing of 7 nucleotides (IR7), are present upstream of the regions coding for the human TR2 and of the sea urchin SpSHR2 orphan receptors. We have developed an experimental strategy based on PCR, to check if this IR7 could correspond to an unusually long cis-element, conserved along evolution and regulating the TR2 genes. We found that indeed IR7 is present in the 5' untranslated region of TR2 genes from all species tested, including Xenopus, rainbow trout, zebrafish and mouse. The exact conservation throughout the animal kingdom of such a long, non repetitive and non coding genomic region, highly suggests that it should ensure important biological functions. In addition, this work has allowed the identification of a new, non coding, upstream exon in the mouse TR2 gene present in testicular TR2 mRNAs.

Animals↗
PubMed2000

A statistical mechanical model for predicting B-DNA curvature and flexibility.

A statistical mechanical model taking into account the symmetric twisting, tilting, sliding fluctuations and asymmetric rolling fluctuations has been proposed to predict the macroscopic curvature and flexibility of B-DNA. Based on the statistical data of structural parameters of double helix in nucleic acid database and the related theoretical analysis, the equilibrium angular parameters (Omega, rho and tau) describing the orientation of successive base-pair planes, the translation parameters (D(y)) along the long axis of neighboring base-pair step and the corresponding force constants are arranged for ten dimers appropriately. Under the assumption of independent angular parameters, independent base-pair steps and a simple energy function, we can calculate the macroscopic curvature and the flexibility of DNA sequences through the transformation matrix and the Boltzmann ensemble average. The predictions on curvature and flexibility of DNA have been compared with the corresponding experimental data. The agreement is remarkably good. It is demonstrated that the lowering of the temperature does increase the DNA curvature.

Animals↗
PubMed1996

Soluble acid invertase determines the hexose-to-sucrose ratio in cold-stored potato tubers.

Cold storage of potato (Solanum tuberosum L.) tubers is known to cause accumulation of reducing sugars. Hexose accumulation has been shown to be cultivar-dependent and proposed to be the result of sucrose hydrolysis via invertase. To study whether hexose accumulation is indeed related to the amount of invertase activities, two different approaches were used: (i) neutral and acidic invertase activities as well as soluble sugars were measured in cold-stored tubers of 24 potato cultivars differing in the cold-induced accumulation of reducing sugars and (ii) antisense potato plants with reduced soluble acid invertase activities were created and the soluble sugar accumulation in cold-stored tubers was studied. The cold-induced hexose accumulation in tubers from the different potato cultivars varied strongly (up to eightfold). Large differences were also detected with respect to soluble acid (50-fold) and neutral (5-fold) invertase activities among the different cultivars. Although there was almost no correlation between the total amount of invertase activity and the accumulation of reducing sugars there was a striking correlation between the hexose/sucrose ratio and the extractable soluble invertase activity. To exclude the possibility that other cultivar-specific features could account for the obtained results, the antisense approach was used to decrease the amount of soluble acid invertase activity in a uniform genetic background. To this end the cDNA of a cold-inducible soluble acid invertase (EMBL nucleic-acid database accession no. X70368) was cloned from the cultivar Desirée, and transgenic potato plants were created expressing this cDNA in the antisense orientation under control of the constitutive 35S cauliflower mosaic virus promotor. Analysis of the harvested and cold-stored tubers showed that inhibition of the soluble acid invertase activity leads to a decreased hexose and an increased sucrose content compared with controls. As was already found for the different potato cultivars the hexose/sucrose ratio decreased with decreasing invertase activities but the total amount of soluble sugars did not significantly change. From these data we conclude that invertases do not control the total amount of soluble sugars in cold-stored potato tubers but are involved in the regulation of the ratio of hexose to sucrose.

Cold Temperature↗
PubMed2001

Stimulation of MCM3 gene expression in osteoblast by low level laser irradiation.

Biostimulatory effect of cell proliferation and bone formation by laser irradiation has been reported, however, very little is known about the molecular basis of mechanisms. We previously constructed the cDNA library of mouse osteoblastic cells (MC3T3-E1) which enhanced gene expression by laser irradiation using a subtracted gene cloning procedure. In the present study, we focused on a gene clone, designated as MCL-140, which exhibited the high homology of DNA sequence with mouse minichromosome maintenance (MCM) 3 gene. MCM3 is involved in the initiation of DNA replication as licensing factor in eukaryotic cells. Nucleotide sequence of MCL-140 insert was determined and assessed in the nucleic acid databases. The transcription level of MCL-140 was examined by Northern blot analysis. The DNA sequences of clone MCL-140 insert exhibited 96.2% homology with MCM 3 gene coding P1 protein. Higher MCM3 mRNA levels were observed in laser-irradiated cells compared to the levels in non-irradiated cells: furthermore, radiolabelled thymidine incorporation was increased by laser irradiation. These findings suggest that low-level laser irradiation may enhance DNA replication and play a role in stimulating proliferation of osteoblast through the enhancement of the MCM3 gene expression.

Animals↗
PubMed1992

Genes selectively expressed in the infectious (metacyclic) stage of Leishmania major promastigotes encode a potential basic-zipper structural motif.

Complementary DNA clones representing transcripts selectively expressed in the non-dividing, infective (metacyclic) stage of Leishmania major promastigotes (MP) were identified by differential and subtractive screening. The majority of the selected clones hybridized on Northern blots to a set of transcripts highly expressed by MP, but to a much lower extent in proliferating and stationary-phase attenuated promastigotes. Stationary, but not log-phase cultures, of each of 5 L. major strains showing a potential for differentiation to metacyclics, expressed these transcripts (MAT-1; MP-associated transcripts). From sequence analysis of full-length cDNA clones corresponding to the predominating MAT-1 species, an open reading frame encoding a 139 aa polypeptide (15.4 kDa) was predicted and supported by immunoprecipitation by kala-azar sera of reticulocyte extract translation products using in vitro transcribed RNA. Although no significant primary sequence homology to database nucleic acid and protein sequences was found, the sequence displays similarities to the basic-zipper families of transcription regulatory proteins.

Amino Acid Sequence↗
PubMed2006

Bioinformatics database infrastructure for biotechnology research.

Many databases are available that provide valuable data resources for the biotechnological researcher. According to their core data, they can be divided into different types. Some databases provide primary data, like all published nucleotide sequences, others deal with protein sequences. In addition to these two basic types of databases, a huge number of more specialized resources are available, like databases about protein structures, protein identification, special features of genes and/or proteins, or certain organisms. Furthermore, some resources offer integrated views on different types of data, allowing the user to do easy customized queries over large datasets and to compare different types of data.

Animals↗
PubMed2006

Multifunctional regulators of cell growth are differentially expressed in anergic murine B cells.

Defective anergy is a major cause of failed tolerance and is amenable to therapeutic manipulation. To better define the molecular basis of anergy in B cells tolerized by matrix self-antigen, we used complementary approaches of representational difference analysis (RDA) and microarray to identify genes differentially transcribed in anergic as compared to non-tolerant B cells isolated from a well-characterized murine autoantibody transgenic model. Forty RDA clones representing 16 genes were isolated from receptor-stimulated B cells and independently confirmed as differentially expressed in tolerant cells using custom microarray, dot blotting and/or quantitative PCR. Differential expression was conserved in tolerant cells from two different transgenic founder lineages and from two genetically disparate backgrounds. Prominent among recovered gene fragments were genes encoding multifunctional proteins not previously implicated in B cell biology, but with roles in biologic processes fundamental to the tolerance phenotype, including cell growth, proliferation and differentiation. RDA also identified a novel transcript not previously reported in nucleic acid databases. To further explore dependence on receptor stimulation and to identify additional genes, commercial oligonucleotide arrays were probed with labeled B cell transcripts and analyzed for genes differentially expressed in resting as well as stimulated cells and in both B6 and MRL mouse strains. Arrays identified differential expression of a subset of RDA genes as well as 46 additional genes, including subsets engaged in signal transduction, transcriptional regulation, cell growth and apoptosis. Immunoblotting confirmed differential protein expression for galectin-3 and galectin-1, two interactive members of the galectin family, suggesting a novel role for galectins as regulators of immune tolerance.

Animals↗
PubMed2006

Serendipitous discovery and X-ray structure of a human phosphate binding apolipoprotein.

We report the serendipitous discovery of a human plasma phosphate binding protein (HPBP). This 38 kDa protein is copurified with the enzyme paraoxonase. Its X-ray structure is similar to the prokaryotic phosphate solute binding proteins (SBPs) associated with ATP binding cassette transmembrane transporters, though phosphate-SBPs have never been characterized or predicted from nucleic acid databases in eukaryotes. However, HPBP belongs to the family of ubiquitous eukaryotic proteins named DING, meaning that phosphate-SBPs are also widespread in eukaryotes. The systematic absence of complete genes for eukaryotic phosphate-SBP from databases is intriguing, but the astonishing 90% sequence conservation between genes belonging to evolutionary distant species suggests that the corresponding proteins play an important function. HPBP is the only known transporter capable of binding phosphate ions in human plasma and may become a new predictor of or a potential therapeutic agent for phosphate-related diseases such as atherosclerosis.

Amino Acid Sequence↗
PubMed2000

SPAC: identification of polypeptides using their amino-acid composition.

We describe here new software able to retrieve from protein or nucleic acid databases, the sequence corresponding to a protein or peptide whose only amino acid composition and molecular weight are known. This algorithm is particularly devoted to the retrieval of partial sequences, a task that other available software performs poorly. Its accuracy for the attribution of a protein fragment to a sequence could represent an easy and economical first tool upstream the use of more sophisticated and expensive methods in proteomic research. SPAC (Sequence Protein Alignment with Composition) is a shareware available software on web site http://www.univ-tln.fr/ approximately grillas/SPAC/. This web site also presents help and a detailed description of the algorithm and interface.

Algorithms↗
PubMed1999

Identification of Leptospira biflexa by real-time homogeneous detection of rapid cycle PCR product.

Sequence analysis of 16S rRNA genes extracted from nucleic acids databases enabled the identification of a Leptospira biflexa (L. biflexa) signature sequence, against which a reverse primer designated L613, was designed. This primer, when used in conjunction with a universal bacterial specific forward primer designated Fd1, enabled the development of a LightCycler-based PCR protocol in which fluorescence emission due to binding of SYBR Green I dye to amplified products could be detected and monitored. A melting temperature (Tm), determined from the melting curve of the amplified product immediately following the termination of thermal cycling, confirmed that the product was that of L. biflexa. Agarose gel electrophoresis therefore was not necessary for identification of PCR products. The PCR protocol was very rapid, and consisted of 30 cycles with a duration of 20 s for each cycle with the monitoring of the melting curve requiring an additional 3 min. The whole protocol was completed in less than 20 min. The PCR protocol was also specific and enabled the identification of 18 strains of L. biflexa, whilst excluding 14 strains of L. interrogans and Leptonema illini. Two examples of its utility in improving work flow of a Leptospira reference laboratory are presented in this article. The use of a simple boiling method for extraction of DNA from all the members of the Leptospiraceae family DNA further simplifies the procedure and makes its use conducive to diagnostic laboratories.

Base Sequence↗
PubMed2003

From biological databases to platforms for biomedical discovery.

The use of high-throughput DNA sequencing and proteomic methods has led to an unprecedented increase in the amount of genomic and proteomic data. Application of computing technologies and development of computational tools to analyze and present these data has not kept pace with the accumulation of information. Here, we discuss the use of different database systems to store biological information and mention some of the key emerging computing technologies that are likely to have a key role in the future of bioinformatics.

Algorithms↗
PubMed2003

How incorrect annotations evolve--the case of short ORFs.

The draft of the human genome sequence is still incomplete. The outstanding tasks include filling in some gaps, finalizing the assembly of short sequences, improving sequence accuracy and correctly identifying coding regions. However, a closely related problem that receives little attention is the substantial number of incorrect annotations that have penetrated some of the widely used databases. This article illustrates this problem using the example of ubiquitin genes, and draws some conclusions that apply to false annotations in other short open reading frames (ORFs). Although the focus is on the human genome, other genomes are equally prone to similar propagation of false annotations.

Databases, Nucleic Acid↗
PubMed2003

Identification of novel anti-angiogenic factors by in silico functional gene screening method.

Angiogenesis, the formation of new blood vessels out of pre-existing capillaries, occurs in a variety of pathophysiological conditions, and is regulated by a balance of angiogenic activators and inhibitors. To identify novel angiogenic factors, we developed a gene screening method by combining the prediction analysis of transcription factor (TF) binding site and the chromosomal localization analysis. First, we analyzed the promoter sequences from known angiogenesis-related factors using the MATINSPECTOR program in TRANSFAC database. Interestingly, we found that the binding site of LMO2 complex is highly conserved in the promoter regions of these factors. Second, we analyzed chromosome loci based on the hypothesis that angiogenesis-related factors might be co-localized in a specific chromosomal band. We found that angiogenesis-related factors are localized in specific 14 chromosomal bands including 5q31 and 19q13 using AngioDB and LocusLink database mining. From these two approaches, we identified 32 novel candidates that have the LMO2 complex binding site in their promoter and are located on one of 14 chromosomal bands. Among them, human recombinant troponin T and spectrin markedly inhibited the neovascularization in vivo and in vitro. Collectively, we suggest that the combination of the prediction analysis of TF binding site and the chromosomal localization analysis might be a useful strategy for gene screening of angiogenesis.

Angiogenesis Inducing Agents↗