An adverse interaction between warfarin and capecitabine: a case report and review of the literature

Warfarin is one of the most commonly used oral anticoagulants in the clinic. It is well established that a wide range of antineoplastic drugs interact with warfarin, resulting in altered coagulation parameters and/or bleeding sequelae. While altered coagulation parameters have been observed in patients taking the oral 5-fluorouracil prodrug, capecitabine, in combination with warfarin, no report to date has described clinically overt evidence of bleeding. Herein, we report 2 cancer patients who presented with bleeding episodes that most likely resulted from an adverse interaction between capecitabine and warfarin after 6 weeks of concomitant therapy. In each case, there was a marked elevation in both the prothrombin time and international normalized ratio (> 10), with subsequent gastrointestinal bleeding. The exact mechanism of this interaction is yet unknown, but it is possible that capecitabine might, in some manner, reduce the hepatic metabolism of warfarin. Close monitoring of coagulation parameters is recommended for all patients receiving concomitant warfarin and capecitabine, with appropriate adjustment of warfarin dosage. The nature and extent of this interaction requires further investigation.

The promoter connection

The availability of the complete genomic sequence of yeast now enables elucidation of molecular mechanisms governing gene expression patterns. New results from the yeast genome and recent advances in predicting and finding human promoters support the use of similar combinatorial approaches to study genome-wide transcriptional regulation in humans.

Fluorimetric determination of copper(II) in aqueous solution using lucifer yellow CH as selective metal reagent

Lucifer yellow CH is shown to be a highly selective fluorescent reagent for the determination of Cu(III) in the microg L(-1) concentration range. The fluorophore is statically quenched by Cu(II); the carbohydrazide group was assigned as the complexing part of the dye molecule. A total range of Cu(II) determination from 0.06 mg L(-1) (1 micromol L(-1)) to 6.3 mg L(-2) (100 micromol L(-1)) with a limit of detection of 0.019 mg L(-1) (0.3 micromol L(-1)) was obtained, along with surprisingly high selectivity. There was no interference from alkaline and earth alkaline metal ions. The cross sensitivity to heavy metal ions was evaluated by the separate solution method and by competitive binding experiments. Calibration plots are shown for Cu(II) determination at different pH and the dissociation constant was determined. The application of the reagent was demonstrated by the determination of the Cu(II) content of tap water samples.

Regulation of plant growth by cytokinin

Cytokinins are a class of plant-specific hormones that play a central role during the cell cycle and influence numerous developmental programs. Because of the lack of biosynthetic and signaling mutants, the regulatory roles of cytokinins are not well understood. We genetically engineered cytokinin oxidase expression in transgenic tobacco plants to reduce their endogenous cytokinin content. Cytokinin-deficient plants developed stunted shoots with smaller apical meristems. The plastochrone was prolonged, and leaf cell production was only 3-4% that of wild type, indicating an absolute requirement of cytokinins for leaf growth. In contrast, root meristems of transgenic plants were enlarged and gave rise to faster growing and more branched roots. These results suggest that cytokinins are an important regulatory factor of plant meristem activity and morphogenesis, with opposing roles in shoots and roots.

Muscle actin genes: a first step towards computational classification of tissue specific promoters

Tissue-specific gene expression is governed by enhancer and promoter sequences determining the specificity most probably by their internal organization of transcription factor binding sites. In case of muscle-specific gene expression excellent compilations of sequence regions responsible for the tissue-specificity are available. We took advantage of such a compilation in order to elucidate organizational features that are directly correlated with promoter specificity. We chose a systematic approach solely based on a sequence collection known to consist of specific regulatory regions which can in principle be applied to every precompiled set of such sequences. We were able to show that these sequences contained a detectable subgroup (actin promoters) for which it was possible to construct a highly specific promoter model recognizing the majority of all known actin sequences. The model was robust with respect to different training sets, almost 100% specific and sensitive enough to be suitable for database searches. We believe this pilot study demonstrates the general applicability of our approach as well as the concept of modular promoter organization.

Molecular and in silico characterization of a promoter module and C/EBP element that mediate LPS-induced RANTES/CCL5 expression in monocytic cells

The chemokine RANTES/CCL5 is a proinflammatory agent produced by a variety of tissues in response to specific stimuli. In human monocytes, RANTES/CCL5 transcription is up-regulated rapidly and transiently in response to LPS. We describe here two regions that help control LPS-driven transcription from the human RANTES/CCL5 promoter in monocytic cells. These sites were analyzed by using DNase I footprinting, transient transfection assays, site-directed mutagenesis, and EMSA. RANTES site E (R(E), -125/-99) constitutively binds C/EBP proteins in monocytic Mono Mac 6 cells. Mutation of region R(E) led to a significant (40%-50%) reduction in LPS-induced promoter reporter activity. Region R(AB) is composed of tandem kB-like elements R(A) and R(B) (-73/-34). These sites working in concert act as an LPS-responsive promoter module. R(A) constitutively binds Sp1, and Rel p50/p65 following LPS stimulation. Either factor can mediate transcriptional effects at R(A). Induced Rel p50/p50 binding to site R(B) is required for LPS regulation of RANTES/CCL5 transcription. A series of computer models based on the RANTES/CCL5 promoter were generated to represent the organization of these functional elements. The models could identify LPS-regulated promoters in human, other vertebrate, and viral sequences in various databases.

Target gene identification from expression array data by promoter analysis

DNA microchips and expression arrays yield enormous amounts of data linking cDNA sequences to gene expression patterns. This now allows the characterization of gene expression in normal and diseased tissues as well as the response of tissues to the application of therapeutic reagents. Software currently exists to analyze DNA array/chip data with respect to corresponding mRNA sequences, which facilitates the precise determination of when and where certain groups of genes are expressed. The information concerning transcriptional regulatory networks responsible for the observed expression patterns is not contained within the cDNA sequences used to generate the arrays, but resides often within the promoter sequences of the individual genes (and/or enhancers). The complete sequence of the human genome will provide the molecular basis for the identification of such regulatory regions. Promoter sequences for specific cDNAs can be obtained reliably from genomic sequences simply by exon mapping. Promoter prediction tools can also be used to locate promoters directly in the genomic sequence in many cases in which cDNAs are 5'-incomplete. Once sufficient numbers of promoter sequences have been obtained, the comparative promoter analysis of the co-regulated genes and groups of genes can be applied in order to generate models describing the higher order levels of the transcription factor binding site organization within these promoter regions. As evident from several examples, this approach can identify promoter modules responsible for the common regulation of promoters solely by the application of bioinformatics methods. Such modules represent the molecular mechanisms through which regulatory networks influence gene expression. Another advantage of this approach is that it also provides a powerful alternative for elucidating functional features of genes with no detectable sequence similarity, by linking them to other genes on the basis of their common promoter structures.

First pass annotation of promoters on human chromosome 22

The publication of the first almost complete sequence of a human chromosome (chromosome 22) is a major milestone in human genomics. Together with the sequence, an excellent annotation of genes was published which certainly will serve as an information resource for numerous future projects. We noted that the annotation did not cover regulatory regions; in particular, no promoter annotation has been provided. Here we present an analysis of the complete published chromosome 22 sequence for promoters. A recent breakthrough in specific in silico prediction of promoter regions enabled us to attempt large-scale prediction of promoter regions on chromosome 22. Scanning of sequence databases revealed only 20 experimentally verified promoters, of which 10 were correctly predicted by our approach. Nearly 40% of our 465 predicted promoter regions are supported by the currently available gene annotation. Promoter finding also provides a biologically meaningful method for "chromosomal scaffolding", by which long genomic sequences can be divided into segments starting with a gene. As one example, the combination of promoter region prediction with exon/intron structure predictions greatly enhances the specificity of de novo gene finding. The present study demonstrates that it is possible to identify promoters in silico on the chromosomal level with sufficient reliability for experimental planning and indicates that a wealth of information about regulatory regions can be extracted from current large-scale (megabase) sequencing projects. Results are available on-line at http://genomatix.gsf.de/chr22/.

Comparative analysis of the genomic organization of Pax9 and its conserved physical association with Nkx2-9 in the human, mouse, and pufferfish genomes

As a first step towards the identification of cis-regulatory elements of Pax9 by means of comparative genomics, we have analyzed genome regions encompassing the Pax9 gene in three vertebrate species, humans, mice (Mus musculus), and the Japanese pufferfish (Fugu rubripes). We show the genomic organization of Pax9 and its physical association with Nkx2-9 conserved in the three species. We discuss about possible implications of the conserved synteny between Pax9 and Nkx2-9 in a context of vertebrate evolution. This report also includes the first description of the primary structures of Fugu Pax9 and Nkx2-9. Furthermore, we report the identification of a novel upstream exon and putative transcription start sites in mouse Pax9. Our results suggest that transcription of Pax9 may be initiated at two alternative start sites and driven by TATA-less promoters.

Cluster analysis and promoter modelling as bioinformatics tools for the identification of target genes from expression array data

Expression arrays yield enormous amounts of data linking genes, via their cDNA sequences, to gene expression patterns. This now allows the characterisation of gene expression in normal and diseased tissues, as well as the response of tissues to the application of therapeutic reagents. Expression array data can be analysed with respect to the underlying protein sequences, which facilitates the precise determination of when and where certain groups of genes are expressed. More recent developments of clustering algorithms take additional parameters of the experimental set-up into account, focusing more directly on co-regulated set of genes. However, the information concerning transcriptional regulatory networks responsible for the observed expression patterns is not contained within the cDNA sequences used to generate the arrays. Regulation of expression is determined to a large extent by the promoter sequences of the individual genes (and/or enhancers). The complete sequence of the human genome now provides the molecular basis for the identification of many regulatory regions. Promoter sequences for specific cDNAs can be obtained reliably from genomic sequences by exon mapping. In the many cases in which cDNAs are 5'-incomplete, high quality promoter prediction tools can be used to locate promoters directly in the genomic sequence. Once sufficient numbers of promoter sequences have been obtained, a comparative promoter analysis of the co-regulated genes and groups of genes can be applied in order to generate models describing the higher order levels of transcription factor binding site organisation within these promoter regions. Such modules represent the molecular mechanisms through which regulatory networks influence gene expression, and candidates can be determined solely by bioinformatics. This approach also provides a powerful alternative for elucidating the functional features of genes with no detectable sequence similarity, by linking them to other genes on the basis of their common promoter structures.

Chiroptic recognition of potassium ion

The high specificity in the recognition and specific binding of potassium ion by the depsipeptide valinomycin (VM) is exploited for its recognition and quantitation using both circular dichroism (CD) and optical rotation dispersion (ORD). The specific rotation of VM is comparably small (2.34 deg ml g(-1) cm(-1)), so that an 8 microM (= 8.89 mg ml(-1)) solution of VM in 95% ethanol rotates polarized light of Lambda = 426 nm passing a 2 cm cuvette by 0.076 degrees only. It is shown, however, that VM undergoes large changes in both ORD and CD on binding to potassium ion. VM, potassium ion and the anionic dye merocyanine 540 form a ternary complex (VM/K/MC) which displays an induced CD with a positive maximum at 488 nm and a negative maximum at 470 nm. The ternary complex also displays fluorescence that is weaker by about 30% when compared to that of the dye alone. The induced CD of the ternary complex is interpreted in terms of the large conformational change which VM is known to undergo on binding potassium ion, thereby forming the prerequisite for a van der Waals interaction between its outwardly directed lipophilic domains and the lipophilic domains of the anionic dye. The method is likely to be applicable to the fluorescent detection of all kinds of ions for which chiral receptors are known, e.g. in studies on the role of ions in biological systems including ion channels.

Experimental data of a single promoter can be used for in silico detection of genes with related regulation in the absence of sequence similarity

Gene expression is presently a major focus in genome analysis, and the experimental data on regulatory mechanisms and functional transcription factor binding sites are steadily growing. However, the annotation of transcriptional regulation of sequences cannot keep pace with the exponential growth of sequence databases. Employing detailed experimental data of a single promoter or enhancer to predict genes with similar regulation would provide a powerful method to link the literature about transcriptional regulation and sequence databases. To this end, we used information on individual functional transcription factor binding sites to compose in silico promoter and enhancer models of muscle-specific genes and to analyze the rodents section of EMBL with these models. Exhaustive evaluation of all hits revealed every second to third match to be a muscle-associated gene. Moreover, functionally related regulatory regions were detected by our model-based approach even in the absence of sequence similarity. We believe that this new approach is a substanial extension to database analysis by BLAST or FASTA, which are restricted to sequence similarity.

A family of peptidoglycan recognition proteins in the fruit fly Drosophila melanogaster

Peptidoglycans from bacterial cell walls trigger immune responses in insects and mammals. A peptidoglycan recognition protein, PGRP, has been cloned from moths as well as vertebrates and has been shown to participate in peptidoglycan-mediated activation of prophenoloxidase in the silk moth. Here we report that Drosophila expresses 12 PGRP genes, distributed in 8 chromosomal loci on the 3 major chromosomes. By analyzing cDNA clones and genomic databases, we grouped them into two classes: PGRP-SA, SB1, SB2, SC1A, SC1B, SC2, and SD, with short transcripts and short 5'-untranslated regions; and PGRP-LA, LB, LC, LD, and LE, with long transcripts and long 5'-untranslated regions. The predicted structures indicate that the first group encodes extracellular proteins and the second group, intracellular and membrane-spanning proteins. Most PGRP genes are expressed in all postembryonic stages. Peptidoglycan injections strongly induce five of the genes. Transcripts from the different PGRP genes were found in immune competent organs such as fat body, gut, and hemocytes. We demonstrate that at least PGRP-SA and SC1B can bind peptidoglycan, and a function in immunity is likely for this family.

A calix[4]arene based calcium-selective optode membrane: measuring the absorbance maximum wavelength shift

An absorbance based calcium ion sensor is presented which applies a new immobilized chromogenic calix[4]arene. The membrane consists of a hydrogel/1,3-pentanedial mixture and the 1,3-bis(indoaniline)-derived 2,4-bis-[(ethylcarbonyl)methoxyl-calix[4]arene as calcium receptor. The indicator entrapped within the gel was not rapidly washed out. Upon calcium complexation a bathochromic shift up to 70 nm was observed along with an increase of the absorption coefficient. The dynamic range of calcium measurements is from 3 to 10 mM with a point of inflection of the calibration curve at a calcium concentration of about 7 mM. The concentration of calcium ions can be calculated from either absorbance at a distinct wavelength or--preferably when indicator leaching occurs--from the wavelength shift of the absorbance occurring when calcium levels are increased.

Identification and functional modelling of DNA sequence elements of transcription

Identification of transcriptional elements in large sequences is a very difficult task, as individual transcription elements (eg transcription factor binding sites,TF-sites) are not clearly correlated with regions exerting transcription control. However, elucidation of the molecular organisation of genomic regions responsible for the control of gene expression is an essential part of the efforts to annotate the genomic sequences, especially within the Human Genome Project. The task for bioinformatics in this context is twofold. The first step required is the approximate localisation of regulatory sequences in large anonymous DNA sequences. Once those regions are located, the second task is the identification of individual transcriptional control elements and correlation of a subset of such elements with transcriptional functions. Part of this second task can be achieved by constructing organisational models of regulatory regions like promoters which can reveal elements important for a gene class or the coexpression of a set of genes. Comparative genomics in non-coding regions (eg phylogenetic footprinting) is a very promising approach that allows identification of potential new regulatory elements which may be used in modelling approaches.

Optical sensor for seawater salinity

An optical sensor for the measurement of salinity in seawater has been developed. It is based on a chloride-quenchable fluorescent probe (lucigenin) immobilized on a Nafion film. Two approaches for measuring salinity via chloride concentration are presented. In the first, a change in salinity corresponds to a change in the fluorescence intensity of lucigenin. In the second, the fluorescence intensity information is converted into a phase angle information by adding an inert phosphorescent reference luminophore (a ruthenium complex entrapped in poly(acrylonitrile) beads). Under these conditions, the chloride-dependent fluorescence intensity of lucigenin can be converted into a chloride-dependent fluorescence phase shift which serves as the analytical information. This scheme is referred to as dual lifetime referencing (DLR). The sensor was used to determine the salinity in seawater and brackish water of the North Sea.

A pseudoautosomal boundary-like element adjacent to the SSAV1 locus at 18q21

Pseudoautosomal boundary-like (PABL) elements have been found at transition sites between genomic regions with different GC-contents. A new PAB related sequence was found immediately adjacent to the S71 provirus on human chromosome 18q21.1-2 (officially designated the SSAV1 locus). The S71 PABL element was full-length as defined by comparison with elements identified at the pseudoautosomal boundaries of the sex chromosomes and in the MHC region. The 3'-ends of all PABL elements showed significant homology to functional CpG-islands, indicating that this similarity is a new common feature of PABL elements.

Role of Stat3 in lipopolysaccharide-induced IL-10 gene expression

IL-10 is a unique cytokine because it is anti-inflammatory and immunosuppressive. IL-10 is regulated at the level of transcription, but the critical motifs and the relevant transcription factors controlling this gene have remained elusive to date. We now report that a sequence at -120 bp in the human IL-10 promoter binds Stat3 but no other Stat proteins. Mutation of this motif abrogates LPS-induced trans-activation. Overexpression of dominant negative Stat3 suppresses promoter activity, while wild-type Stat3 leads to an enhancement of this activity. Our results show that Stat3, by binding to a single motif in the IL-10 promoter, is controlling expression of the human IL-10 gene.

Hydrophilic sensor membrane based on cation-selective protic chromoionophore

The first potassium optode based on a protic chromoionophore immobilized in a hydrogel matrix is presented. The highly selective protic chromoionophore consists of a cryptohemispherand moiety and a trinitroanilino chromophore part. The acidifying power of potassium ions over sodium ions is 0.6 pH units. This correlates with the findings in solution. In contrast to several crown and aza-crown based chromophores the highly pre-organized moiety allows ion detection even in aqueous environment. The detection limit for potassium ions at pH 7.7 is 5 microM.

Experimental analysis and computer prediction of CTF/NFI transcription factor DNA binding sites

Accurate prediction of transcription factor binding sites is needed to unravel the function and regulation of genes discovered in genome sequencing projects. To evaluate current computer prediction tools, we have begun a systematic study of the sequence-specific DNA-binding of a transcription factor belonging to the CTF/NFI family. Using a systematic collection of rationally designed oligonucleotides combined with an in vitro DNA binding assay, we found that the sequence specificity of this protein cannot be represented by a simple consensus sequence or weight matrix. For instance, CTF/NFI uses a flexible DNA binding mode that allows for variations of the binding site length. From the experimental data, we derived a novel prediction method using a generalised profile as a binding site predictor. Experimental evaluation of the generalised profile indicated that it accurately predicts the binding affinity of the transcription factor to natural or synthetic DNA sequences. Furthermore, the in vitro measured binding affinities of a subset of oligonucleotides were found to correlate with their transcriptional activities in transfected cells. The combined computational-experimental approach exemplified in this work thus resulted in an accurate prediction method for CTF/NFI binding sites potentially functioning as regulatory regions in vivo.