Confinement effect on hydrolysis in small lipid vesicles

In living organisms most chemical reactions take place within the confines of lipid-membrane bound compartments, while confinement within the bounds of a lipid membrane is thought to be a key step in abiogenesis. In previous work we demonstrated that confinement in the aqueous cavity of a lipid vesicle affords protection against hydrolysis, a phenomenon that we term here confinement effect (C _e) and that we attributed to the interaction with the lipid membrane. Here, we show that both the size and the shape of the cavity of the vesicle modulate the C _e. We link this observation to the packing of the lipid following changes in membrane curvature, and formulate a mathematical model that relates the C _e to the radius of a spherical vesicle and the packing parameter of the lipids. These results suggest that the shape of the compartment where a molecule is located plays a major role in controlling the chemical reactivity of non-enzymatic reactions. Moreover, the mathematical treatment we propose offers a useful tool for the design of vesicles with predictable reaction rates of the confined molecules, e.g., drug delivery vesicles with confined prodrugs. The results also show that a crude form of signal transduction, devoid of complex biological machinery, can be achieved by any external stimuli that drastically changes the structure of the membrane, like the osmotic shocks used in the present work.

High-affinity tamoxifen analogues retain extensive positional disorder when bound to calmodulin

Using a combination of NMR and fluorescence measurements, we have investigated the structure and dynamics of the complexes formed between calcium-loaded calmodulin (CaM) and the potent breast cancer inhibitor idoxifene, a derivative of tamoxifen. High-affinity binding (K d ∼ 300  nM) saturates with a 2 : 1 idoxifene : CaM complex. The complex is an ensemble where each idoxifene molecule is predominantly in the vicinity of one of the two hydrophobic patches of CaM but, in contrast with the lower-affinity antagonists TFP, J-8, and W-7, does not substantially occupy the hydrophobic pocket. At least four idoxifene orientations per domain of CaM are necessary to satisfy the intermolecular nuclear Overhauser effect (NOE) restraints, and this requires that the idoxifene molecules switch rapidly between positions. The CaM molecule is predominantly in the form where the N and C-terminal domains are in close proximity, allowing for the idoxifene molecules to contact both domains simultaneously. Hence, the 2 : 1 idoxifene : CaM complex illustrates how high-affinity binding occurs without the loss of extensive positional dynamics.

How the biomimetic assembly of membrane receptors into multivalent domains is regulated by a small ligand

In living cells, communication requires the action of membrane receptors that are activated following very small environmental changes. A binary all-or-nothing behavior follows, making the organism extremely efficient at responding to specific stimuli. Using a minimal system composed of lipid vesicles, chemical models of a membrane receptor and their ligands, we show that bio-mimetic ON/OFF assembly of high avidity, multivalent domains is triggered by small temperature changes. Moreover, the intensity of the ON signal at the onset of the switch is modulated by the presence of small, weakly binding divalent ligands, reminiscent of the action of primary messengers in biological systems. Based on the analysis of spectroscopic data, we develop a mathematical model that rigorously describes the temperature-dependent switching of the membrane receptor assembly and ligand binding. From this we derive an equation that predicts the intensity of the modulation of the ON signal by the ligand-messenger as a function of the pairwise binding parameters, the number of binding sites that it features and the concentration. The behavior of our system, and the model derived, highlight the usefulness of weakly binding ligands in the regulation of membrane receptors and the pitfalls inherent to their binding promiscuity, such as non-specific binding to the membrane. Our model, and the equations derived from it, offer a valuable tool for the study of membrane receptors in both biological and biomimetic settings. The latter can be exploited to program membrane receptor avidity on sensing vesicles, create hierarchical protocell tissues or develop highly specific drug delivery vehicles.

The role of extracellular matrix in mouse and human corneal neovascularization

Corneal neo-vascularization (CNV) is a highly prevalent medical condition which impairs visual acuity. The role of specific proteins in modulating CNV has been extensively reported, although no studies have described the entire human proteome in CNV corneas. In this paper, we performed a proteomic analysis of vascularized vs healthy corneal stroma, in a CNV mouse model and in CNV-affected patients, with a specific focus on extracellular matrix (ECM) proteins. We identified and quantified 2315 murine proteins, 691 human proteins and validated 5 proteins which are differentially expressed in vascularized samples and conserved in mice and humans: tenascin-C and fibronectin-1 were upregulated, while decorin, lumican and collagen-VI were downregulated in CNV samples. Interestingly, among CNV patients, those affected with Acanthamoeba keratitis showed the highest levels of fibronectin-1 and tenascin-C, suggesting a specific role of these two proteins in Acanthamoeba driven corneal CNV. On a broader picture, our findings support the hypothesis that the corneal stroma in CNV samples is disorganized and less compact. We are confident that the dissection of the human corneal proteome may shed new light on the complex pathophysiology of human CNV, and finally lead to improved treatments.

Modulation of the cooperativity in the assembly of multistranded supramolecular polymers

It is highly desirable that supramolecular polymers self-assemble following small changes in the environment. The degree of responsiveness depends on the degree of cooperativity at play during the assembly. Understanding how to modulate and quantify cooperativity is therefore highly desirable for the study and design of responsive polymers. Here we show that the cooperative assembly of a porphyrin-based, double-stranded polymer is triggered by changes in building blocks and in salt concentration. We develop a model that accounts for this responsiveness by assuming the binding of the salt countercations to the double-stranded polymer. Using our assembly model we generate plots that show the increase in concentration of polymer versus the normalized concentration of monomer. These plots are ideally suited to appreciate changes in cooperativity, and show that, for our system, these changes are consistent with the increase in polymer length observed experimentally. Unexpectedly, we find that polymer stability increases when cooperativity decreases. We attribute this behaviour to the fact that increasing salt concentration stabilizes the overall polymer more than the nucleus. In other words, the cooperativity factor α, defined as the ratio between the growth constant K_g and the nucleation constant K_n decreases as the overall stability of the polymer increases. Using our model to simulate the data, we generate cooperativity plots to explore changes in cooperativity for multistranded polymers. We find that, for the same pairwise association constants, the cooperativity sharply increases with the number of strands in the polymer. We attribute this dependence to the fact that the larger the number of strands, the larger is the nucleus necessary to trigger polymer growth. We show therefore that the cooperativity factor α does not properly account for the cooperativity behaviour of multistranded polymers, or any supramolecular polymer with a nucleus composed of more than 2 building blocks, and propose the use of the corrected cooperativity factor α_m. Finally, we show that multistranded polymers display highly cooperative polymerisation with pairwise association constants as low as 10 M^-1 between the building blocks, which should simplify the design of responsive supramolecular polymers.

Ship in a bottle: confinement-promoted self-assembly

Understanding self-assembly in confined spaces is essential to fully understand molecular processes in confined cell compartments and will offer clues on the behaviour of simple confined systems, such as protocells and lipid-vesicle based devices. Using a model system composed of lipid vesicles, a membrane impermeable receptor and a membrane-permeable ligand, we have studied in detail how compartmentalization modulates the interaction between the confined receptor and its ligand. We demonstrate that confinement of one of the building blocks stabilizes complex self-assembled structures to the extent that dilution leads, counterintuitively, to the formation of long range assemblies. The behaviour of the system can be explained by considering a confinement factor that is analogous, although not identical, to the effective molarity for intramolecular binding events. The confinement effect renders complex self-assembled species robust and persistent under conditions where they do not form in bulk solution. Moreover, we show that the formation of stable complex assemblies in systems compartmentalized by semi-permeable membranes does not require the prior confinement of all components, but only that of key membrane impermeable building blocks. To use a macroscopic analogy, lipid vesicles are like ship-in-a bottle constructs that are capable of directing the assembly of the confined ship following the confinement of a few key wooden planks. Therefore, we believe that the confinement effect described here would have played an important role in shaping the increase of chemical complexity within protocells during the first stages of abiogenesis. Additionally, we argue that this effect can be exploited to design increasingly efficient functional devices based on comparatively simple vesicles for applications in biosensing, nanoreactors and drug delivery vehicles.

Concept-based indexing and retrieval of multimedia documents

In this work, we face the problem of multimedia document indexing with reference to a specific application field, the radiological ward where automatic information management by content is an urgent need. Here, a multimedia document is composed of text and images. The keystone of the approach is the image indexing which is performed in an indirect way: the description of the image (made by an expert, in our case a physician) is further synthesised and formalised to be used by the computer. In this Paper, we propose a concept-based indexing of the description of the images which is based on Farradane's work. The basic proposal has been extended to deal with specific requirements of the considered application and to be automatically performed. A first prototype of a multimedia information retrieval system has been implemented with the goal of validating the method in the specific application.

Multivalence cooperativity leading to "all-or-nothing" assembly: the case of nucleation-growth in supramolecular polymers

All-or-nothing molecular assembly events, essential for the efficient regulation of living systems at the molecular level, are emerging properties of complex chemical systems that are largely attributed to the cooperativity of weak interactions. The link between the self-assembly and the interactions responsible for the assembly is however often poorly defined. In this work we demonstrate how the chelate effect (multivalence cooperativity) can play a central role in the regulation of the all-or-nothing assembly of structures (supramolecular polymers here), even if the building blocks are not multivalent. We have studied the formation of double-stranded supramolecular polymers formed from Co-metalloporphyrin and bi-pyridine building blocks. Their cooperative nucleation-elongation assembly can be summarized as a thermodynamic cycle, where the monomer weakly oligomerizes linearly or weakly dimerizes laterally. But thanks to the chelate effect, the lateral dimer readily oligomerizes linearly and the oligomer readily dimerizes laterally, leading to long double stranded polymers. A model based on this simple thermodynamic cycle can be applied to the assembly of polymers with any number of strands, and allows for the determination of the length of the polymer and the all-or-nothing switching concentration from the pairwise binding constants. The model, which is consistent with the behaviour of supramolecular polymers such as microtubules and gelators, clearly shows that all-or-nothing assembly is triggered by a change in the mode of assembly, from non-multivalent to multivalent, when a critical concentration is reached. We believe this model is applicable to many molecular assembly processes, ranging from the formation of cell-cell focal adhesion points to crystallization.

Ochratoxin A as possible factor trigging autism and its male prevalence via epigenetic mechanism

The role of dysbiosis causing leaky gut with xenobiotic production and absorption is increasingly demonstrated in autism spectrum disorder (ASD) pathogenesis. Among xenobiotics, we focused on ochratoxin A (one of the major food contaminating mycotoxin), that in vitro and in vivo exerts a male-specific neurotoxicity probably via microRNA modulation of a specific target gene. Among possible targets, we focused on neuroligin4X. Interestingly, this gene carries some single nucleotide polymorphisms (SNPs) already correlated with the disease and with illegitimate microRNA binding sites and, being located on X-chromosome, could explain the male prevalence. In conclusion, we propose a possible gene-environment interaction triggering ASD explaining the epigenetic neurotoxic mechanism activated by ochratoxin A in genetically predisposed children. This mechanism offers a clue for male prevalence of the disease and may have an important impact on prevention and cure of ASD.

The roughness of the protein energy landscape results in anomalous diffusion of the polypeptide backbone

Recombination of photolysed protein disulfide bonds confirms subdiffusional backbone motion and measures the roughness of the protein's energy landscape.

Self-assembled nanoparticles as multifunctional drugs for anti-microbial therapies

Multifunctional nanoparticles that kill mycobacteria: nano-Trojan horses for photodynamic therapy and anti-TB drug delivery.

Modulation of in-membrane receptor clustering upon binding of multivalent ligands

In living cells and biomimetic systems alike, multivalent ligands in solution can induce clustering of membrane receptors. The link between the receptor clustering and the ligand binding remains, however, poorly defined. Using minimalist divalent ligands, we develop a model that allows quantifying the modulation of receptor clustering by binding of ligands with any number of binding sites. The ligands, with weak binding affinity for the receptor and with binding sites held together by flexible linkers, lead to nearly quantitative clustering upon binding in a wide range of experimental conditions, showing that efficient modulation of receptor clustering does not require pre-organization or large binding affinities per binding site. Simulations show that, in the presence of ligands with five or more binding sites, an on/off clustering response follows a very small change in receptor density in the membrane, which is consistent with the highly cooperative behavior of multivalent biomolecular systems.

Myosin-binding protein C DNA variants in domestic cats (A31P, A74T, R820W) and their association with hypertrophic cardiomyopathy

BACKGROUND

Two mutations in the MYBPC3 gene have been identified in Maine Coon (MCO) and Ragdoll (RD) cats with hypertrophic cardiomyopathy (HCM).

OBJECTIVE

This study examined the frequency of these mutations and of the A74T polymorphism to describe their worldwide distribution and correlation with echocardiography.

ANIMALS

1855 cats representing 28 breeds and random-bred cats worldwide, of which 446 underwent echocardiographic examination.

METHODS

This is a prospective cross-sectional study. Polymorphisms were genotyped by Illumina VeraCode GoldenGate or by direct sequencing. The disease status was defined by echocardiography according to established guidelines. Odds ratios for the joint probability of having HCM and the alleles were calculated by meta-analysis. Functional analysis was simulated.

RESULTS

The MYBPC3 A31P and R820W were restricted to MCO and RD, respectively. Both purebred and random-bred cats had HCM and the incidence increased with age. The A74T polymorphism was not associated with any phenotype. HCM was most prevalent in MCO homozygote for the A31P mutation and the penetrance increased with age. The penetrance of the heterozygote genotype was lower (0.08) compared with the P/P genotype (0.58) in MCO.

CONCLUSIONS AND CLINICAL IMPORTANCE

A31P mutation occurs frequently in MCO cats. The high incidence of HCM in homozygotes for the mutation supports the causal nature of the A31P mutation. Penetrance is incomplete for heterozygotes at A31P locus, at least at a young age. The A74T variant does not appear to be correlated with HCM.

IBDsite: a Galaxy-interacting, integrative database for supporting inflammatory bowel disease high throughput data analysis

BACKGROUND

Inflammatory bowel diseases (IBD) refer to a group of inflammatory conditions concerning colon and small intestine, which cause socially uncomfortable symptoms and often are associated with an increased risk of colon cancer. IBD are complex disorders, which rely on genetic susceptibility, environmental factors, deregulation of the immune system, and host relationship with commensal microbiota. The complexity of these pathologies makes difficult to clearly understand the mechanisms of their onset. Therefore, the study of IBD must be faced exploiting an integrated and multilevel approach, ranging from genes, transcripts and proteins to pathways altered in affected tissues, and carefully considering their regulatory mechanisms, which may intervene in the pathology onset. It is also crucial to have a knowledge base about the symbiotic bacteria that are hosted in the human gut. To date, much data exist regarding IBD and human commensal bacteria, but this information is sparse in literature and no free resource provides a homogeneously and rationally integrated view of biomolecular data related to these pathologies.

METHODS

Human genes altered in IBD have been collected from literature, paying particular interest for the immune system alterations prompted by the interaction with the gut microbiome. This process has been performed manually to assure the reliability of collected data. Heterogeneous metadata from different sources have been automatically formatted and integrated in order to enrich information about these altered genes. A user-friendly web interface has been created for easy access to structured data. Tools such as gene clustering coefficients, all-pairs shortest paths and pathway lengths calculation have been developed to provide data analysis support. Moreover, the implemented resource is compliant to the Galaxy framework, allowing the collected data to be exploited in the context of high throughput bioinformatics analysis.

RESULTS

To fill the lack of a reference resource for 'omics' science analysis in the context of IBD, we developed the IBDsite (available at http://www.itb.cnr.it/ibd), a disease-oriented platform, which collects data related to biomolecular mechanisms involved in the IBD onset. The resource provides a section devoted to human genes identified as altered in IBD, which can be queried at different biomolecular levels and visualised in gene-centred report pages. Furthermore, the system presents information related to the gut microbiota involved in IBD affected patients. The IBDsite is compliant with all Galaxy installations (in particular, it can be accessed from our custom version of Galaxy, http://www.itb.cnr.it/galaxy), in order to facilitate high-throughput data integration and to enable evaluations of the genomic basis of these diseases, complementing the tools embedded in the IBDsite.

CONCLUSIONS

Lots of sparse data exist concerning IBD studies, but no on-line resource homogeneously and rationally integrate and collect them. The IBDsite is an attempt to group available information regarding human genes and microbial aspects related to IBD, by means of a multilevel mining tool. Moreover, it constitutes a knowledge base to filter, annotate and understand new experimental data in order to formulate new scientific hypotheses, thanks to the possibility of integrating genomics aspects by employing the Galaxy framework. Discussed use-cases demonstrate that the developed system is useful to infer not trivial knowledge from the existing widespread data or from novel experiments.

A pulse--radiolysis approach to fast reductive cleavage of a disulfide bond to uncage enzyme activity

The essential thiol of the enzyme papain has been caged by linking to an aromatic thiol. The resulting caged protein is inactive but enzymatic activity is fully restored upon chemical cleavage of the protective disulfide bond. We have exploited the chemistry of this disulfide bond to uncage papain by pulse radiolysis. We have shown that up to 10% of the enzyme activity can be restored by reductive pulse radiolysis. This approach has been tested on a small-molecule model system, and experiments on this model compound show that pulse radiolysis of the mixed cysteine-aromatic disulfide results in selective reduction of the disulfide bond to generate a thiol in 10-20% yield, consistent with the radiolytically restored activity of the caged papain quantified by the biochemical assay.

Network integration of data and analysis of oncology interest

The Human Genome Project has deeply transformed biology and the field has since then expanded to the management, processing, analysis and visualization of large quantities of data from genomics, proteomics, medicinal chemistry and drug screening. This huge amount of data and the heterogeneity of software tools that are used implies the adoption on a very large scale of new, flexible tools that can enable researchers to integrate data and analysis on the network. ICT technology standards and tools, like Web Services and related languages, and workflow management systems, can support the creation and deployment of such systems. While a number of Web Services are appearing and personal workflow management systems are also being more and more offered to researchers, a reference portal enabling the vast majority of unskilled researchers to take profit from these new technologies is still lacking. In this paper, we introduce the rationale for the creation of such a portal and present the architecture and some preliminary results for the development of a portal for the enactment of workflows of interest in oncology.

Amplification of Bifunctional Ligands for Calmodulin from a Dynamic Combinatorial Library

A well known strategy to prepare high affinity ligands for a biological receptor is to link together low affinity ligands. DCC (dynamic combinatorial chemistry) was used to select bifunctional protein ligands with high affinity relative to the corresponding monofunctional ligands. Thiol to disulfide linkage generated a small dynamic library of bifunctional ligands in the presence of calmodulin, a protein with two independently mobile domains. The binding constant of the bifunctional ligand (disulfide) most amplified by the presence of calmodulin is nearly two orders of magnitude higher than that of the corresponding monofunctional ligand (thiol).

High performance GRID based implementation for genomics and protein analysis

Starting from the genomic and proteomic sequence data, a complex computational infrastructure as been established with the objective to develop a GRID based system to to automate the analysis, prediction and annotation processes of genomic DNA. To support of this type of analysis, several algorithms as been used to recognize biological signals involved in the identification of genes and proteins. The system implemented can be use to analyse the content of the large number of genomic sequences. For this reason, the system realized is capable of using a computational architecture specifically designed for intensive computing based on GRID technologies developed throughout the BIOINFOGRID European project. We developed a GRID based workflow to correlate different kind of Bioinformatics data, going from the Genomics Nucleotide to the Protein Sequence. The first step in the workflow consists of submitting a nucleotide sequence that is elaborated by a specific software for gene prediction. In particular this tool performs a search in the nucleotide sequence to find out the key components of gene. The predicted gene is then translated in the corresponding protein sequence. Based on protein sequence is then possible to identify the domains that characterize the protein functionality using specific tools of domain prediction. Protein domains classification are very important in the analysis of the macromolecular functionality. To analyze a whole protein family from large genome of various organism means to elaborate a large amount of data that requires huge computational resources. To analyze all this data we suggest the use of a high performance platform based on grid technology. We have implemented our applications on a wide area grid platform for scientific applications [http://www.grid.it and http://grid-it.cnaf.infn.it] composed of about 1000 CPU's. The grid infrastructure consists in a collection of computing elements and storage elements that jointly concur to define a platform for high performance elaboration. In this study a grid based application is presented to compute the protein domain analysis in a distributed way. This approach has high performance because the protein domains are checked with different software in parallel in different grid sites.

Enhanced Ligand Affinity for Receptors in which Components of the Binding Site Are Independently Mobile

Using calmodulin antagonism as a model, it is demonstrated that, under circumstances in which binding sites are motionally independent, it is possible to create bifunctional ligands that bind with significant affinity enhancement over their monofunctional counterparts. Suitable head groups were identified by using a semiquantitative screen of monofunctional tryptophan analogs. Two bifunctional ligands, which contained two copies of the highest-affinity head group tethered by rigid linkers, were synthesized. The bifunctional ligands bound to calmodulin with a stoichiometry of 1:1 and with an affinity enhancement over their monofunctional counterparts; the latter bound with a stoichiometry of 2:1 ligand:protein. A lower limit to the effective concentrations of the domains of calmodulin relative to each other (0.2-2 mM) was determined. A comparable effective concentration was achieved for bifunctional ligands based on higher-affinity naphthalene sulphonamide derivatives.

Synthesis and Photochemistry of a New Class of Photocleavable Protein Cross-linking Reagents

A new series of photocleavable protein cross-linking reagents based on bis(maleimide) derivatives of diaryl disulfides have been synthesised. They have been functionalised with cysteine and transient absorption spectra for the photolysis reaction have been recorded by using the pump-probe technique with a time resolution of 100 femtoseconds. Photolysis of the disulfide bond yields the corresponding thiyl radicals in less than a picosecond. There is a significant amount of geminate recombination, but some of the radicals escape the solvent cage and the quantum yield for photocleavage is 30 % in water.

Presence of estrogens and estrogen receptor-like proteins in Solanum glaucophyllum

The synthesis of mammalian steroid hormones by plants has been reported. However, their physiological role in plants is controversial. The existence of receptor molecules as those of animal cells could provide clues into a possible steroid mechanism of action. Solanum glaucophyllum callus cultures were found to contain not only 17beta-estradiol and estrone but also abundant estrogen binding sites. These sites were specific for 17beta-estradiol ( approximately 550 fmol/mg protein) and could also be competed by the known estrogen receptor (ER) agonist diethylstilbestrol. Antibodies directed against specific sequences of the classical ER alpha isoform, labelled a approximately 67 kDa band which comigrated with the mammalian ER alpha antigen. ER alpha-like proteins were tested positive as estrogen binders in Ligand blot experiments using 17beta-estradiol macromolecular derivatives as ligands. Our results provide first evidences on the existence of estrogen binding proteins structurally related to the mammalian ER alpha subtype in a higher plant system.

Presence of ATG triplets in 5' untranslated regions of eukaryotic cDNAs correlates with a 'weak' context of the start codon

MOTIVATION

The context of the start codon (typically, AUG) and the features of the 5' Untranslated Regions (5' UTRs) are important for understanding translation regulation in eukaryotic mRNAs and for accurate prediction of the coding region in genomic and cDNA sequences. The presence of AUG triplets in 5' UTRs (upstream AUGs) might effect the initiation rate and, in the context of gene prediction, could reduce the accuracy of the identification of the authentic start. To reveal potential connections between the presence of upstream AUGs and other features of 5' UTRs, such as their length and the start codon context, we undertook a systematic analysis of the available eukaryotic 5' UTR sequences.

RESULTS

We show that a large fraction of 5' UTRs in the available cDNA sequences, 15-53% depending on the organism, contain upstream ATGs. A negative correlation was observed between the information content of the translation start signal and the length of the 5' UTR. Similarly, a negative correlation exists between the 'strength' of the start context and the number of upstream ATGs. Typically, cDNAs containing long 5' UTRs with multiple upstream ATGs have a 'weak' start context, and in contrast, cDNAs containing short 5' UTRs without ATGs have 'strong' starts. These counter-intuitive results may be interpreted in terms of upstream AUGs having an important role in the regulation of translation efficiency by ensuring low basal translation level via double negative control and creating the potential for additional regulatory mechanisms. One of such mechanisms, supported by experimental studies of some mRNAs, includes removal of the AUG-containing portion of the 5' UTR by alternative splicing.

AVAILABILITY

An ATG_ EVALUATOR program is available upon request or at www.itba.mi.cnr.it/webgene.

CONTACT

rogozin@ncbi.nlm.nih.gov, milanesi@itba.mi.cnr.it.

Effect of culture conditions on the synthesis of vitamin D(3) metabolites in Solanum glaucophyllum grown in vitro

In cultured Solanum glaucophyllum we have recently described the operation of a light-independent pathway of 1alpha,25-dihydroxy-vitamin D(3) (1alpha,25(OH)(2)D(3)) biosynthesis which involves similar intermediates as in vertebrates. In this work we investigated factors influencing the formation of 1alpha,25(OH)(2)D(3) and related sterols in S. glaucophyllum grown in vitro in darkness. Callus tissue and cells cultured in Murashige and Skoog medium in the absence of light were employed. Lipids were extracted with chloroform-methanol. The remaining water soluble fraction was incubated with beta-glucosidase to release vitamin D(3) compounds from their glycoconjugated derivatives followed by organic solvent extraction. Vitamin D(3) derivatives were isolated by Sephadex LH-20 and high-performance liquid chromatography (HPLC). HPLC or competitive protein binding assays with intestine 1alpha,25(OH)(2)D(3) receptor and serum vitamin D binding protein were used to quantify the metabolites. The levels of 1alpha,25(OH)(2)D(3) in calli varied according to the tissue explant origin, e.g. stem>leaf>fruit. For all organs, the metabolite was mainly present as free sterol (>80% of total). There were larger amounts of 25(OH)D(3) than 1alpha,25(OH)(2)D(3). It was found that Ca(2+), auxin and kinetin are important factors upregulating 1alpha,25(OH)(2)D(3) synthesis in S. glaucophyllum tissue and cells. Irradiation with UV light increased vitamin D(3) but not 1alpha,25(OH)(2)D(3) levels. In agreement with these results, incubation of cells with [3H]25(OH)D(3) revealed a low conversion rate to [3H]1alpha,25(OH)(2)D(3). The operation of a light-dependent pathway formation of vitamin D(3) coupled to higher expression of 25(OH)D(3)-1alpha-hydroxylase may account for the large concentrations of 1alpha,25(OH)(2)D(3) normally found in differentiated field-grown plants.

Prediction and phylogenetic analysis of mammalian short interspersed elements (SINEs)

The presence of repetitive elements can create serious problems for sequence analysis, especially in the case of homology searches in nucleotide sequence databases. Repetitive elements should be treated carefully by using special programs and databases. In this paper, various aspects of SINE (short interspersed repetitive element) identification, analysis and evolution are discussed.

Nicotiana glauca: another plant species containing vitamin D(3) metabolites

Vitamin D(3)-related compounds have been detected in various plant species, mostly belonging to the Solanaceae. In this work we show that Nicotiana glauca, a widespread member of this taxonomic family, contains 7-dehydrocholesterol, vitamin D(3) and hydroxylated derivatives bearing precursor-product metabolic relationships in vertebrates. Leaves collected in the field and callus cultures were used. By means of specific radioreceptor binding assays and mass spectrometry of purified fractions obtained from plant tissue lipid extracts by Sephadex LH-20 and Sep-Pak C18 chromatography followed by HPLC, we established the presence of 7-dehydrocholesterol, vitamin D(3), 25(OH)-vitamin D(3) and 1alpha,25(OH)(2)-vitamin D(3) (1alpha,25(OH)(2)D(3)), the latter being a hormonally relevant metabolite in animals. These results indicate that N. glauca may represent a useful species in which to characterize the biosynthetic pathway and physiological functions of vitamin D(3) compounds in plants. In addition, tissue culture of N. glauca could become a significant tool for biotechnological production of 1alpha,25(OH)(2)D(3).

[WWWMGS: an integrated server for molecular-genetic studies]

We report an integrative technology for molecular biology studies in the field of transcription regulation by using Internet. A set of databases, programs, and systems are included into WWWMGS Web server. For example, the use of TRRD database information for site prediction is described. Using this method, the computer system SeqAnn was developed. The system performs the "real time" searching for prediction of initiation transcription site position according to database information. WWWMGS is available at URL: http://wwwmgs.bionet.nsc.ru/.

GeneBuilder: interactive in silico prediction of gene structure

MOTIVATION

Prediction of gene structure in newly sequenced DNA becomes very important in large genome sequencing projects. This problem is complicated due to the exon-intron structure of eukaryotic genes and because gene expression is regulated by many different short nucleotide domains. In order to be able to analyse the full gene structure in different organisms, it is necessary to combine information about potential functional signals (promoter region, splice sites, start and stop codons, 3' untranslated region) together with the statistical properties of coding sequences (coding potential), information about homologous proteins, ESTs and repeated elements.

RESULTS

We have developed the GeneBuilder system which is based on prediction of functional signals and coding regions by different approaches in combination with similarity searches in proteins and EST databases. The potential gene structure models are obtained by using a dynamic programming method. The program permits the use of several parameters for gene structure prediction and refinement. During gene model construction, selecting different exon homology levels with a protein sequence selected from a list of homologous proteins can improve the accuracy of the gene structure prediction. In the case of low homology, GeneBuilder is still able to predict the gene structure. The GeneBuilder system has been tested by using the standard set (Burset and Guigo, Genomics, 34, 353-367, 1996) and the performances are: 0.89 sensitivity and 0.91 specificity at the nucleotide level. The total correlation coefficient is 0.88.

AVAILABILITY

The GeneBuilder system is implemented as a part of the WebGene a the URL: http://www.itba.mi. cnr.it/webgene and TRADAT (TRAncription Database and Analysis Tools) launcher URL: http://www.itba.mi.cnr.it/tradat.

Integrated databases and computer systems for studying eukaryotic gene expression

MOTIVATION

The goal of the work was to develop a WWW-oriented computer system providing a maximal integration of informational and software resources on the regulation of gene expression and navigation through them. Rapid growth of the variety and volume of information accumulated in the databases on regulation of gene expression necessarily requires the development of computer systems for automated discovery of the knowledge that can be further used for analysis of regulatory genomic sequences.

RESULTS

The GeneExpress system developed includes the following major informational and software modules: (1) Transcription Regulation (TRRD) module, which contains the databases on transcription regulatory regions of eukaryotic genes and TRRD Viewer for data visualization; (2) Site Activity Prediction (ACTIVITY), the module for analysis of functional site activity and its prediction; (3) Site Recognition module, which comprises (a) B-DNA-VIDEO system for detecting the conformational and physicochemical properties of DNA sites significant for their recognition, (b) Consensus and Weight Matrices (ConsFrec) and (c) Transcription Factor Binding Sites Recognition (TFBSR) systems for detecting conservative contextual regions of functional sites and their recognition; (4) Gene Networks (GeneNet), which contains an object-oriented database accumulating the data on gene networks and signal transduction pathways, and the Java-based Viewer for exploration and visualization of the GeneNet information; (5) mRNA Translation (Leader mRNA), designed to analyze structural and contextual properties of mRNA 5'-untranslated regions (5'-UTRs) and predict their translation efficiency; (6) other program modules designed to study the structure-function organization of regulatory genomic sequences and regulatory proteins.

AVAILABILITY

GeneExpress is available at http://wwwmgs.bionet.nsc. ru/systems/GeneExpress/ and the links to the mirror site(s) can be found at http://wwwmgs.bionet.nsc.ru/mgs/links/mirrors.html+ ++.

Protein-coding regions prediction combining similarity searches and conservative evolutionary properties of protein-coding sequences

The gene identification procedure in a completely new gene with no good homology with protein sequences can be a very complex task. In order to identify the protein-coding region, a new method, 'SYNCOD', based on the analysis of conservative evolutionary properties of coding regions, has been realized. This program is able to identify and use the coding region homologies of the non-annotated (unknown) protein-coding sequences already present in the nucleotide sequence databases by using the alignment produced by BLASTN. The ratio of number mismatches resulting in synonymous codons to the number of mismatches resulting in non-synonymous codons is estimated for each open reading frame. Monte Carlo simulations are then used to estimate the significance of the ratio deviation from random behavior. The SYNCOD program has been tested on generated random sequences and on different control sets. The high accuracy of predicting protein-coding regions (the correlation coefficient, CC, varies from 0.67 to 0.79) and the high specificity (the portion of wrong exons, WE, varies from 0.06 to 0.07) have proved to be important features of the suggested approach. The SYNCOD program is resident on the ITBA-CNR Web Server and can be used via the Internet (URL: www.itba.mi.cnr.it/webgene).

GeneExpress: a computer system for description, analysis, and recognition of regulatory sequences in eukaryotic genome

GeneExpress system has been designed to integrate description, analysis, and recognition of eukaryotic regulatory sequences. The system includes 5 basic units: (1) GeneNet contains an object-oriented database for accumulation of data on gene networks and signal transduction pathways and a Java-based viewer that allows an exploration and visualization of the GeneNet information; (2) Transcription Regulation combines the database on transcription regulatory regions of eukaryotic genes (TRRD) and TRRD Viewer; (3) Transcription Factor Binding Site Recognition contains a compilation of transcription factor binding sites (TFBSC) and programs for their analysis and recognition; (4) mRNA Translation is designed for analysis of structural and contextual features of mRNA 5'UTRs and prediction of their translation efficiency; and (5) ACTIVITY is the module for analysis and site activity prediction of a given nucleotide sequence. Integration of the databases in the GeneExpress is based on the Sequence Retrieval System (SRS) created in the European Bioinformatics Institute.

The subclass approach for mutational spectrum analysis: application of the SEM algorithm

Analysis and comparison of mutational spectra represents an important problem in molecular biology. To analyse a mutational spectra we apply an algorithm based on the SEM subclass approach (Simulation, Expectation, Maximization). The algorithm tries to classify the mutational sites according to different mutation probabilities, and each site should belong to one class. Each class is approximated by binomial distribution and thus any real mutational spectrum is regarded as a mixture of binomial distributions. The separation process runs iteratively. Each iteration includes the simulation, maximization and estimation procedures. To evaluate the quality of the classification results, the X2 test is used. The algorithm has been checked on random spectra with preset parameters and on real mutational spectra. As has been shown, 17 out of 19 analysed real mutational spectra can be divided into two or more classes of sites, of which one contains hotspots of mutation. For the G:C-->A:T mutational spectra induced by Sn1 alkylating mutagenes (11 spectra) the classification accuracy was 0.95. To test different site volumes, each Sn1-induced spectrum was divided into the G-->A and C-->T spectra. The classification accuracy for these spectra was 0.96. From the analysis of classification errors it is possible to suggest that at least part of them cannot be ascribed to the faults of the algorithm but are caused by some special features of the mutagenesis itself. The results of the real data are in good relation with existing knowledge. The approach we present is an attempt to formalize the concept of a "mutational hotspot". The program implementing the SEM algorithm is available on the Web server (http:/(/)www.itba.mi.cnr.it/webmutation).

Sequence and gene content in 35 kb genomic clone mapping in the human Xq27.1 region

This paper presents detailed analysis of the entire sequence of a cosmid clone, 26H7, containing 35 kb of human DNA. This cosmid resides on the q27.1 region of the human X chromosome between, DXS1232 and DXS119 loci. Novel potential small exons were detected for which conventional gene identification strategies (Northern blot analysis and extensive cDNA library screening) proved to be inefficient. Of the standard repetitive elements we found: 8 Alu's making up 6.2% of the sequence; 10 MIR segments (4.1%); 5 LINE1 elements (4.8%), 3 MIR2 (1.0%); 2 MLT (2.9%), and 1 MSTA (0.7%) representing about 20% of the total sequence. The overall GC content was rather low, only 42% and no CpG island was detected using rare restriction enzymes. However, a CpG-rich region was identified. Computer aided analysis of the sequence inferred the presence of three possible genes: one of them was found to be homologous to the U7 RNA family elements; a second is reported in this paper, however at the moment no significant homology has been found in the data bank. The third predicted gene has not as yet been found to be detectable by RT-PCR. We also report in this paper the identification of X-chromosome specific repeated sequences.

Molecular Probe Data Base (MPDB)

In this paper, the current status of the Molecular Probe Data Base (http://www.biotech.ist.unige.it/interlab/ mpdb.html ) is briefly presented together with a short analysis of its activity during 1997. This has been performed by statistically evaluating the 'logs' of the Internet servers that are used for its distribution with reference to the geographical origin of the requests, the words that were utilized to carry out of the searches and the oligonucleotides that were retrieved. Planned enhancements of this database are also described. They include a revision of its data structure and, even more relevant, of its data management procedures.

Analysis of donor splice sites in different eukaryotic organisms

We present here a new algorithm for functional site analysis. It is based on four main assumptions: each variation of nucleotide composition makes a different contribution to the overall binding free energy of interaction between a functional site and another molecule; nonfunctioning site-like regions (pseudosites) are absent or rare in genomes; there may be errors in the sample of sites; and nucleotides of different site positions are considered to be mutually dependent. In this algorithm, the site set is divided into subsets, each described by a certain consensus. Donor splice sites of the human protein-coding genes were analyzed. Comparing the results with other methods of donor splice site prediction has demonstrated a more accurate prediction of consensus sequences AG/GU(A,G), G/GUnAG, /GU(A,G)AG, /GU(A,G)nGU, and G/GUA than is achieved by weight matrix and consensus (A,C)AG/GU(A,G)AGU with mismatches. The probability of the first type error, E1, for the obtained consensus set was about 0.05, and the probability of the second type error, E2, was 0.15. The analysis demonstrated that accuracy of the functional site prediction could be improved if one takes into account correlations between the site positions. The accuracy of prediction by using human consensus sequences was tested on sequences from different organisms. Some differences in consensus sequences for the plant Arabidopsis sp., the invertebrate Caenorhabditis sp., and the fungus Aspergillus sp. were revealed. For the yeast Saccharomyces sp. only one conservative consensus, /GUA(U,A,C)G(U,A,C), was revealed (E1 = 0.03, E2 = 0.03). Yeast is a very interesting model to use for analysis of molecular mechanisms of splicing.

Identification of a U7snRNA homologue mapping to the human Xq27.1 region, between the DXS1232 and DXS119 loci

To contribute to the identification and analysis of novel genes, we undertook the study of a cosmid clone in the Xq27 region of human DNA. The cloned fragment was previously observed to have a high number of evolutionarily conserved sequences. In this genomic stretch of DNA we have identified sequence homologous to the U7 RNA gene including its potential regulatory elements. This paper describes the genomic organisation of this gene and its mapping to the Xq27.1 genomic sub-interval between the DXS1232 and DXS119 loci.

Hamming-Clustering method for signals prediction in 5' and 3' regions of eukaryotic genes

MOTIVATION

Gene expression is regulated by different kinds of short nucleotide domains. These features can either activate or terminate the transcription process. To predict the signal sites in the 5' and 3' gene regions we applied the Hamming-Clustering network (HC) to the TATA box, to the transcription initiation site and to the poly(A) signal determination in DNA sequences. This approach employs a technique deriving from the synthesis of digital networks in order to generate prototypes, or rules, which can be directly analysed or used for the construction of a final neural network.

RESULTS

More than 1000 poly-A signals have been extracted from EMBL database rel. 42 and used to build the training and the test set. A full set of the eukaryotic genes (1252 entry) from the Eukaryotic Promoter Database (EPD rel. 42) have been used for the TATA-box signal and transcription network approach. The results show the applicability of the Hamming-Clustering method to functional signal prediction.

Characterization and fine localization of two new genes in Xq28 using the genomic sequence/EST database screening approach

Two new genes were identified and mapped by searching the EST databases with genomic sequences obtained from putative CpG islands of the rodent-human hybrid X3000. Previous mapping of these CpG islands in the proximity of the host cell factor (HCFC1) and GdX genes automatically localized these two new genes to Xq28 in the interval between the L1 cell adhesion molecule (L1CAM) and the glucose-6-phosphate dehydrogenase (G6PD) loci. Both genes are relatively short, contain an ORF of 261 and 105 amino acids, respectively, and are ubiquitously expressed. Combining sequencing of selected CpG islands, derived from hybrids containing small portions of the human genome, with an EST database search is an easy method of identifying and mapping new genes to specific regions of the genome.

Gene structure prediction using information on homologous protein sequence

In this paper a new approach for the prediction of protein coding gene structures is described. The principal scheme of prediction is as follows: first, the exons with the best potential are predicted in a sequence with unknown functions and a list of potential amino acid fragments coded by these exons is formed. Second, testing the homology between each amino acid fragment from the list and proteins from the SWISS-PROT database of amino acid sequences. One protein with the best homology is chosen out of all the homologous sequences. Third, reconstruction of the exon-intron structure, basing it on its homology with the chosen protein sequences. The method was tested on an independent control set (20 genes). The results were as follows: 21% of real exons were lost and 3% of non-real exons were found. This system can be used to refine the results of gene prediction systems, especially if highly homologous proteins are found in the amino acid sequence database.

Eukaryotic promoter recognition by binding sites for transcription factors

A method for identification of eukaryotic promoters by localization of binding sites for transcription factors has been suggested. The binding sites for a range of transcription factors have been found to be distributed unevenly. Based on these distributions, we have constructed a weight matrix of binding site localization. On the basis of the weight matrix we have, in turn, designed an algorithm for promoter recognition. To increase the accuracy of the method, we have developed a routine that breaks any promoter sample into subsamples. The method to be reported on allows much better recognition accuracy than does the approach based on detection of the TATA box. In particular, the overprediction error is three times lower following our method. The program FunSiteP recognizes promoters from newly uncovered sequences and tentatively identifies the functional class the promoters must belong to. We have introduced the notion of 'regulatory potential' for the degree to which any region of the sequences is similar to the real eukaryotic promoter. By making use of the potential, we have revealed putative transcription start sites and extended regions of transcription regulation.

Computer tool FUNSITE for analysis of eukaryotic regulatory genomic sequences

We present the computer tool FUNSITE for description and analysis of regulatory sequences of eukaryotic genomes. The tool consists of the following main parts: 1) An integrated database for genomic regulatory sequences. The integrated database was designed on the basis of the databases TRANSFAC (Wingender 1994) and TRRD (Kel et al. 1995) that are currently under development. The following functions are performed: i) linkage to the EMBL database; ii) preparing samples of definite types of functional sites with their flanking sequences; iii) preparing samples of promoter sequences; iv) preparing samples of transcription factors classified with regard to structural and functional features of DNA binding and activating domains, functional families of the factors, their tissue specificity and other functional features; v) access to data on mutual disposition of cis-elements within the regulatory regions. 2) The second component of FUNSITE tool is the set of programs for analysis of the structural organization of regulatory sequences: i) Program for revealing of potential transcription factors binding sites based on their consensi; ii) program for revealing of the potential binding sites using homology search with nucleotide sequences of real binding sites; iii) program for analysis of oligonucleotide context features which are characteristic of flank sequences of the binding sites; iv) program for design of recognition method for the functional sites based on generalized weight matrix; v) program for revealing potential composite elements. The results of analysis of the promoter sequences of eukaryotic genes with the FUNSITE are presented, too.

Data bank homology search algorithm with linear computation complexity

A new algorithm for data bank homology search is proposed. The principal advantages of the new algorithm are: (i) linear computation complexity; (ii) low memory requirements; and (iii) high sensitivity to the presence of local region homology. The algorithm first calculates indicative matrices of k-tuple 'realization' in the query sequence and then searches for an appropriate number of matching k-tuples within a narrow range in database sequences. It does not require k-tuple coordinates tabulation and in-memory placement for database sequences. The algorithm is implemented in a program for execution on PC-compatible computers and tested on PIR and GenBank databases with good results. A few modifications designed to improve the selectivity are also discussed. As an application example, the search for homology of the mouse homeotic protein HOX 3.1 is given.