Similar Sequence Patterns Research Articles

Discovering patterns in outpatient neurology appointments using state sequence analysis

BackgroundOutpatient services in the UK, and in particular outpatient neurology services, are under considerable pressure with an ever-increasing gap between capacity and demand. To improve services, we first need to understand the current situation. This study aims to explore the patterns of appointment type seen in outpatient neurology, in order to identify potential opportunities for change.MethodsWe use State Sequence Analysis (SSA) on routinely collected data from a single neurology outpatient clinic. SSA is an exploratory methodology which allows patterns within sequences of appointments to be discovered. We analyse sequences of appointments for the 18 months following a new appointment. Using SSA we create groups of similar appointment sequence patterns, and then analyse these clusters to determine if there are particular sequences common to different diagnostic categories.ResultsOf 1315 patients 887 patients had only one appointment. Among the 428 patients who had more than one appointment a 6 monthly cycle of appointments was apparent. SSA revealed that there were 11 distinct clusters of appointment sequence patterns. Further analysis showed that there are 3 diagnosis categories which have significant influence over which cluster a patient falls into: seizure/epilepsy, movement disorders, and headache.ConclusionsNeurology outpatient appointment sequences show great diversity, but there are some patterns which are common to specific diagnostic categories. Information about these common patterns could be used to inform the structure of future outpatient appointments.

A Comprehensive Analysis of the Genetic Diversity of Plasmodium falciparum Histidine-Rich Protein 2 (PfHRP2) in the Brazilian Amazon

Early diagnosis and treatment are fundamental to the control and elimination of malaria. In many endemic areas, routine diagnosis is primarily performed microscopically, although rapid diagnostic tests (RDTs) provide a useful point-of-care tool. Most of the commercially available RDTs detect histidine-rich protein 2 (HRP2) of Plasmodium falciparum in the blood of infected individuals. Nonetheless, parasite isolates lacking the pfhrp2 gene are relatively frequent in some endemic regions, thereby hampering the diagnosis of malaria using HRP2-based RDTs. To track the efficacy of RDTs in areas of the Brazilian Amazon, we assessed pfhrp2 deletions in 132 P. falciparum samples collected from four malaria-endemic states in Brazil. Our findings show low to moderate levels of pfhrp2 deletion in different regions of the Brazilian Amazon. Overall, during the period covered by this study (2002-2020), we found that 10% of the P. falciparum isolates were characterized by a pfhrp2 deletion. Notably, however, the presence of pfhrp2-negative isolates has not been translated into a reduction in RDT efficacy, which in part may be explained by the presence of polyclonal infections. A further important finding was the discrepancy in the proportion of pfhrp2 deletions detected using two assessed protocols (conventional PCR versus nested PCR), which reinforces the need to perform a carefully planned laboratory workflow to assess gene deletion. This is the first study to perform a comprehensive analysis of PfHRP2 sequence diversity in Brazilian isolates of P. falciparum. We identified 10 PfHRP2 sequence patterns, which were found to be exclusive of each of the assessed regions. Despite the small number of PfHRP2 sequences available from South America, we found that the PfHRP2 sequences identified in Brazil and neighboring French Guiana show similar sequence patterns. Our findings highlight the importance of continuously monitoring the occurrence and spread of parasites with pfrhp2 deletions, while also taking into account the limitations of PCR-based testing methods associated with accuracy and the complexity of infections.

Properties of protein unfolded states suggest broad selection for expanded conformational ensembles

Much attention is being paid to conformational biases in the ensembles of intrinsically disordered proteins. However, it is currently unknown whether or how conformational biases within the disordered ensembles of foldable proteins affect function in vivo. Recently, we demonstrated that water can be a good solvent for unfolded polypeptide chains, even those with a hydrophobic and charged sequence composition typical of folded proteins. These results run counter to the generally accepted model that protein folding begins with hydrophobicity-driven chain collapse. Here we investigate what other features, beyond amino acid composition, govern chain collapse. We found that local clustering of hydrophobic and/or charged residues leads to significant collapse of the unfolded ensemble of pertactin, a secreted autotransporter virulence protein from Bordetella pertussis, as measured by small angle X-ray scattering (SAXS). Sequence patterns that lead to collapse also correlate with increased intermolecular polypeptide chain association and aggregation. Crucially, sequence patterns that support an expanded conformational ensemble enhance pertactin secretion to the bacterial cell surface. Similar sequence pattern features are enriched across the large and diverse family of autotransporter virulence proteins, suggesting sequence patterns that favor an expanded conformational ensemble are under selection for efficient autotransporter protein secretion, a necessary prerequisite for virulence. More broadly, we found that sequence patterns that lead to more expanded conformational ensembles are enriched across water-soluble proteins in general, suggesting protein sequences are under selection to regulate collapse and minimize protein aggregation, in addition to their roles in stabilizing folded protein structures.

Permanent tooth emergence: Timing and sequence in a sample of Black Southern African children.

This study investigates mean age, sequence, and temporal trends of permanent tooth emergence in Black Southern African children and compares the findings with other population samples. This community-based cross-sectional study involved 639 Black Southern African children between 5 and 20 years of age. Probit analysis was used to derive the mean age at emergence of the permanent teeth. Sex and cross-population comparisons were undertaken to determine similarities and differences in emergence timing and sequence. Females emerged all teeth earlier except for M3s (p < .05). Black Southern Africans have earlier mean ages of emergence compared to population samples from the USA, Europe, Australia, and Asia. Sexual dimorphism was detected in the mandibular I1/M1 emergence sequence (females, M1 I1 ; males, I1 M1 ). The sequence in males is similar in both jaws to males from other sub-Saharan African, USA, and European samples. Females show a similar sequence pattern in the maxilla with other sub-Saharan African, and also Australian and US females of European ancestry. There is a high frequency of polymorphism in the P1P2C1 emergence sequence, with significantly more P2P1C1 maxillary sequences seen among males. Polymorphic variation was common for the I1 M1 sequence in both males and females. Mean age of tooth emergence among Black Southern African children is similar to children from most other sub-Saharan African populations. No temporal change was seen in the mean age of emergence. Earlier permanent tooth emergence in Black Southern Africans is part of a general sub-Saharan pattern that is distinct from European and Asian populations.

History of CRISPR-Cas from Encounter with a Mysterious Repeated Sequence to Genome Editing Technology.

Clustered regularly interspaced short palindromic repeat (CRISPR)-Cas systems are well-known acquired immunity systems that are widespread in archaea and bacteria. The RNA-guided nucleases from CRISPR-Cas systems are currently regarded as the most reliable tools for genome editing and engineering. The first hint of their existence came in 1987, when an unusual repetitive DNA sequence, which subsequently was defined as a CRISPR, was discovered in the Escherichia coli genome during an analysis of genes involved in phosphate metabolism. Similar sequence patterns were then reported in a range of other bacteria as well as in halophilic archaea, suggesting an important role for such evolutionarily conserved clusters of repeated sequences. A critical step toward functional characterization of the CRISPR-Cas systems was the recognition of a link between CRISPRs and the associated Cas proteins, which were initially hypothesized to be involved in DNA repair in hyperthermophilic archaea. Comparative genomics, structural biology, and advanced biochemistry could then work hand in hand, not only culminating in the explosion of genome editing tools based on CRISPR-Cas9 and other class II CRISPR-Cas systems but also providing insights into the origin and evolution of this system from mobile genetic elements denoted casposons. To celebrate the 30th anniversary of the discovery of CRISPR, this minireview briefly discusses the fascinating history of CRISPR-Cas systems, from the original observation of an enigmatic sequence in E. coli to genome editing in humans.

Unique Combinations of βαβ-Units and Π-Like Modules in Proteins and Specific Features of Their Amino Acid Sequences

Possible combinations of βαβ-units and Π-like modules in proteins in both right- and left-handed forms have been analyzed in detail. The correlation between the mutual arrangement of the structural elements in the polypeptide chain and their handedness has been shown. In the βαβП combinations, which is encountered most frequently in proteins, the П-module follows the βαβ unit along the chain and both elements are right-handed. In the Пβαβ combinations, where the П-module is located at the N end and the βαβ-unit follows it, the former is left-handed and the latter is right-handed. In relatively rare combinations of the left-handed βαβ-units and right-handed П-modules, the βαβ-unit follows П-module in the chain. The combinations of left-handed П-modules and the left-handed βαβ-units are unobservable in proteins. It has also been shown that the П-modules with a β-strand-α-helix-arch-β-strand structure are observed in proteins only in a right-handed form and half of them (51%) contains cis-prolines in their arches. These arches of nonhomologous proteins, as well as the positions of cis-prolines, nearly coincide when superimposed. The superimposed П-modules also demonstrate that their overall folds are very similar. Structural alignment of their amino acid sequences has shown that the П-modules have very similar sequence patterns of the key hydrophobic, hydrophilic, glycine, and cis-proline residues.

IPromoter-2L: a two-layer predictor for identifying promoters and their types by multi-window-based PseKNC.

Being responsible for initiating transaction of a particular gene in genome, promoter is a short region of DNA. Promoters have various types with different functions. Owing to their importance in biological process, it is highly desired to develop computational tools for timely identifying promoters and their types. Such a challenge has become particularly critical and urgent in facing the avalanche of DNA sequences discovered in the postgenomic age. Although some prediction methods were developed, they can only be used to discriminate a specific type of promoters from non-promoters. None of them has the ability to identify the types of promoters. This is due to the facts that different types of promoters may share quite similar consensus sequence pattern, and that the promoters of same type may have considerably different consensus sequences. To overcome such difficulty, using the multi-window-based PseKNC (pseudo K-tuple nucleotide composition) approach to incorporate the short-, middle-, and long-range sequence information, we have developed a two-layer seamless predictor named as 'iPromoter-2 L'. The first layer serves to identify a query DNA sequence as a promoter or non-promoter, and the second layer to predict which of the following six types the identified promoter belongs to: σ24, σ28, σ32, σ38, σ54 and σ70. For the convenience of most experimental scientists, a user-friendly and publicly accessible web-server for the powerful new predictor has been established at http://bioinformatics.hitsz.edu.cn/iPromoter-2L/. It is anticipated that iPromoter-2 L will become a very useful high throughput tool for genome analysis. bliu@hit.edu.cn or dshuang@tongji.edu.cn or kcchou@gordonlifescience.org. Supplementary data are available at Bioinformatics online.

Structural Variation in Fstn Exon 3 Gene and Its Association With Growth Traits In Chicken

Follistatin gene is a member of transforming growth factor-β super family involved in muscle growth. The present study was carried out to characterize the nucleotide variability in the exonic (coding) region of FSTN gene in boiler (PD-1) line and control layer chicken lines. A PCR product of 219 bp of exon-3 was amplified and nucleotide variability was studied using PCR-SSCP technique. The PCR products were sequenced to confirm the variability in coding sequence. The present study revealed that the exon3 sequence of FSTN gene was monomorphic having similar sequence pattern in all individuals. Growth data was also analyzed, the growth performance of male and female differed significantly at six week of age. It is concluded that exon3 of FSTN gene was monomorphic without showing any variation in the nucleotide composition both in broiler and layer chicken lines. The codon did not show any effect on variation in growth traits in chicken.

Discovery and information-theoretic characterization of transcription factor binding sites that act cooperatively

Transcription factor binding to the surface of DNA regulatory regions is one of the primary causes of regulating gene expression levels. A probabilistic approach to model protein–DNA interactions at the sequence level is through position weight matrices (PWMs) that estimate the joint probability of a DNA binding site sequence by assuming positional independence within the DNA sequence. Here we construct conditional PWMs that depend on the motif signatures in the flanking DNA sequence, by conditioning known binding site loci on the presence or absence of additional binding sites in the flanking sequence of each siteʼs locus. Pooling known sites with similar flanking sequence patterns allows for the estimation of the conditional distribution function over the binding site sequences. We apply our model to the Dorsal transcription factor binding sites active in patterning the Dorsal–Ventral axis of Drosophila development. We find that those binding sites that cooperate with nearby Twist sites on average contain about 0.5 bits of information about the presence of Twist transcription factor binding sites in the flanking sequence. We also find that Dorsal binding site detectors conditioned on flanking sequence information make better predictions about what is a Dorsal site relative to background DNA than detection without information about flanking sequence features.

Dynamic Time Warping for Music Retrieval Using Time Series Modeling of Musical Emotions

Musical signals have rich temporal information not only at the physical level but at the emotion level. The listeners may wish to find music excerpts that have similar sequence patterns of musical emotions with given excerpts. Most state-of-the-art systems for emotion-based music retrieval concentrate on static analysis of musical emotions, and ignore dynamic analysis and modeling of musical emotions over time. This paper presents a novel approach to perform music retrieval based on time-varying musical emotion dynamics. A three-dimensional musical emotion model—Resonance-Arousal-Valence (RAV)—is used, and emotions of a piece of music are represented by musical emotion dynamics in a time series. A multiple dynamic textures (MDT) model is proposed to model music and emotion dynamics over time, and expectation maximization (EM) algorithm along with Kalman filtering and smoothing is used to estimate model parameters. Two smoothing methods—Rauch-Tung-Striebel (RTS) and minimum-variance smoothing (MVS)—to robust model are investigated and compared to find an optimal solution to enhance prediction. To find similar sequence patterns of musical emotions, subsequence dynamic time warping (DTW) for emotion dynamics matching is presented. Experimental results demonstrate the benefits of MDT to predict time-varying musical emotions, and our proposed method for music retrieval based on emotion dynamics outperforms retrieval methods based on acoustic features.

Elucidating gene function and function evolution through comparison of co-expression networks of plants.

The analysis of gene expression data has shown that transcriptionally coordinated (co-expressed) genes are often functionally related, enabling scientists to use expression data in gene function prediction. This Focused Review discusses our original paper (Large-scale co-expression approach to dissect secondary cell wall formation across plant species, Frontiers in Plant Science 2:23). In this paper we applied cross-species analysis to co-expression networks of genes involved in cellulose biosynthesis. We showed that the co-expression networks from different species are highly similar, indicating that whole biological pathways are conserved across species. This finding has two important implications. First, the analysis can transfer gene function annotation from well-studied plants, such as Arabidopsis, to other, uncharacterized plant species. As the analysis finds genes that have similar sequence and similar expression pattern across different organisms, functionally equivalent genes can be identified. Second, since co-expression analyses are often noisy, a comparative analysis should have higher performance, as parts of co-expression networks that are conserved are more likely to be functionally relevant. In this Focused Review, we outline the comparative analysis done in the original paper and comment on the recent advances and approaches that allow comparative analyses of co-function networks. We hypothesize that in comparison to simple co-expression analysis, comparative analysis would yield more accurate gene function predictions. Finally, by combining comparative analysis with genomic information of green plants, we propose a possible composition of cellulose biosynthesis machinery during earlier stages of plant evolution.

Estimating the composition of species in metagenomes by clustering of next-generation read sequences

Faster and cheaper sequencing technologies together with the ability to sequence uncultured microbes collected from any environment present us an opportunity to distill meaningful information from the millions of new genomic sequences from environmental samples, called metagenome. Contrary to conventional cultured microbes, however, the metagenomic data is extremely heterogeneous and noisy. Therefore the separation of the sets of sequenced genomic fragments that belong to different microbes is essential for successful assembly of microbial genomes. In this paper, we present a novel clustering method for a given metagenomic dataset. The metagenomic dataset has some distinguished features because (i) it is possible that similar sequence patterns may exist in different species and (ii) each species has different number of individuals in the given metagenomic dataset. Our method overcomes these obstacles by using the Gaussian mixture model and analysis of mixture profiles, and taking advantage of genomic signatures extracted from the metagenomic dataset. Unlike conventional clustering methods where clusters are discovered through global similarities of data instances, our method builds clusters by combining the data instances sharing local similarities captured by mixture analysis. By considering shared mixture components, our method is able to create clusters of genomic sequences although they are globally distinct each other. We applied our method to an artificial metagenomic dataset comprised of simulated 47 million reads from 25 real microbial genomes, and analyzed the resulting clusters in terms of the number of clusters, the number of participating species and dominant species in each cluster. Even though our approach cannot address all challenges in the field of metagenome sequence clustering, we believe that out method can contribute to take a step forward to achieve the goals.

Construction of microRNA functional families by a mixture model of position weight matrices

MicroRNAs (miRNAs) are small regulatory molecules that repress the translational processes of their target genes by binding to their 3′ untranslated regions (3′ UTRs). Because the target genes are predominantly determined by their sequence complementarity to the miRNA seed regions (nucleotides 2–7) which are evolutionarily conserved, it is inferred that the target relationships and functions of the miRNA family members are conserved across many species. Therefore, detecting the relevant miRNA families with confidence would help to clarify the conserved miRNA functions, and elucidate miRNA-mediated biological processes. We present a mixture model of position weight matrices for constructing miRNA functional families. This model systematically finds not only evolutionarily conserved miRNA family members but also functionally related miRNAs, as it simultaneously generates position weight matrices representing the conserved sequences. Using mammalian miRNA sequences, in our experiments, we identified potential miRNA groups characterized by similar sequence patterns that have common functions. We validated our results using score measures and by the analysis of the conserved targets. Our method would provide a way to comprehensively identify conserved miRNA functions.

Identification of Context-Dependent Motifs by Contrasting ChIP Binding Data

DNA binding proteins play crucial roles in the regulation of gene expression. Transcription factors (TFs) activate or repress genes directly while other proteins influence chromatin structure for transcription. Binding sites of a TF exhibit a similar sequence pattern called a motif. However, a one-to-one map does not exist between each TF and motif. Many TFs in a protein family may recognize the same motif with subtle nucleotide differences leading to different binding affinities. Additionally, a particular TF may bind different motifs under certain conditions, for example in the presence of different co-regulators. The availability of genome-wide binding data of multiple collaborative TFs makes it possible to detect such context-dependent motifs. We developed a contrast motif finder (CMF) for the de novo identification of motifs that are differentially enriched in two sets of sequences. Applying this method to a number of TF binding datasets from mouse embryonic stem cells, we demonstrate that CMF achieves substantially higher accuracy than several well-known motif finding methods. By contrasting sequences bound by distinct sets of TFs, CMF identified two different motifs that may be recognized by Oct4 dependent on the presence of another co-regulator and detected subtle motif signals that may be associated with potential competitive binding between Sox2 and Tcf3. The software CMF is freely available for academic use at www.stat.ucla.edu/∼zhou/CMF.

Vertical transmission of X4-tropic and dual-tropic HIV-1 in five Ugandan mother–infant pairs

We previously reported the existence of CXCR4-using HIV-1 in 6-14 week-old Ugandan infants. Whether these viruses were transmitted from the mother perinatally or evolved after transmission is not known. In the current study, we investigated the origin of the CXCR4-using viruses in these infants by comparing HIV-1 envelope clones from the infants to those from their mothers at or near the time of delivery. Envelope clones were isolated from five Ugandan infant plasma samples that harbored CXCR4-using viruses, collected at the time of HIV diagnosis (four at birth, one at week 6), and from their mothers at delivery. Coreceptor usage and phylogenetic relatedness of HIV-1 populations in mother-infant pairs were analyzed in detail using the Trofile assay and sequence analysis of envelope clones, respectively. X4-tropic clones were identified in two mother-infant pairs and dual-tropic clones were found in three pairs, either alone or in combination with R5-tropic viruses. Dual-tropic clones varied in their ability to infect CXCR4-expressing cells. In each mother-infant pair, X4-tropic or dual-tropic clones shared similar phenotypic profiles and V3 sequence patterns; gp160 sequences of X4-tropic and dual-tropic clones from infants were phylogenetically indistinguishable from those of their mothers. The virus populations were phylogenetically homogenous in three infants and segregated according to coreceptor tropism in the remaining two infants. This study demonstrates that X4-tropic and dual-tropic HIV-1 can be transmitted from mother to infant, before, during or shortly after delivery, and establishes vertical transmission as an important source of CXCR4-using viruses in infants.

A Conserved Hydrophobic Tetrad near the C Terminus of the Secretory Na+-K+-2Cl- Cotransporter (NKCC1) Is Required for Its Correct Intracellular Processing

Little is known about the intracellular folding and trafficking of integral membrane proteins. Here we identify a hydrophobic amino acid tetrad (ILLV) close to the C terminus of the secretory Na+-K+-2Cl- cotransporter (NKCC1) that is important for the proper intracellular processing of this protein. This tetrad appears in a C-terminal sequence pattern that is conserved across species in a number of members of the NKCC1 gene family (slc12) of electroneutral salt transporters. We studied the effects of various mutations of these amino acids on NKCC1 transiently transfected into HEK-293 cells. Our results show that mutation of two of these residues to alanine leads to a >50% reduction in expression and complex glycosylation levels and that multiple mutations to alanine have cumulative effects. By contrast, scrambling of these amino acids, or mutation of other nearby conserved C-terminal residues, has little effect on these parameters. Mutation of ILLV to AAAA reduces complex glycosylation of NKCC1 by approximately 90% and results in a protein that does not form stable dimers and is retained in the endoplasmic reticulum in a highly aggregated state. Our results are consistent with the hypothesis that mutation of the hydrophobic tetrad ILLV to AAAA leads to the ab initio misfolding and concomitant aggregation of this NKCC1 mutant, resulting in its retention in the endoplasmic reticulum.

Peptides mediating interaction networks: new leads at last

A growing number of protein interactions are found to be mediated by a large globular region in one protein binding to a comparatively short, peptide stretch in another. Regions that bind a common protein often show a similar sequence pattern or linear motif that mediates the binding. The past year has seen reports of new techniques that can uncover these motifs directly from interaction data. These studies have suggested that the fraction of interactions mediated by these regions is greater than previously anticipated. Concurrently, other work has demonstrated that it is possible to target these interactions using small molecules. Together these developments hold great promise for future efforts to target chemically precise details of complex systems.

The GxxxG motif: A framework for transmembrane helix-helix association

In order to identify strong transmembrane helix packing motifs, we have selected transmembrane domains exhibiting high-affinity homo-oligomerization from a randomized sequence library based on the right-handed dimerization motif of glycophorin A. Sequences were isolated using the TOXCAT system, which measures transmembrane helix-helix association in the Escherichia coli inner membrane. Strong selection was applied to a large range of sequences (∼10 7 possibilities) and resulted in the identification of sequence patterns that mediate high-affinity helix-helix association. The most frequent motif isolated, GxxxG, occurs in over 80 % of the isolates. Additional correlations suggest that flanking residues act in concert with the GxxxG motif, and that size complementarity is maintained at the interface, consistent with the idea that the identified sequence patterns represent packing motifs. The convergent identification of similar sequence patterns from an analysis of the transmembrane domains in the SwissProt sequence database suggests that these packing motifs are frequently utilized in naturally occurring helical membrane proteins.

NIH announces funding for structural genomics centres

The National Institute of General Medical Sciences (NIGMS****For further information on NIGMS funding: http://www.nih.gov/nigms/funding/psi.html; Bethesda, MD, USA), one of the US National Institutes of Health, is set to spend up to US $18 million each year for up to five years on the emerging field of structural genomics. The funding is part of the institute’s Protein Structure Initiative (PSI) and will be awarded to up to six US research centres.Unlike functional genomics, which investigates the cellular and phenotypic functions of genes, structural genomics investigates gene function in terms of the consequences of molecular shape. The aim is to solve the three-dimensional structure of every protein encoded by the human genome, using X-ray crystallography and nuclear magnetic resonance (NMR) spectroscopy. Protein structure determination is renowned for being slow and empirical. ‘Fortunately, with recent technological advances and new public funding we now have the opportunity to scale up these techniques and increase the throughput of this process’, says Chris Sander, Chief Information Science Officer, Millennium Predictive Medicine and Visiting Professor, Massachusetts Institute of Technology (Cambridge, MA, USA). The use of synchroton radiation in crystallography, cryocrystallography, selenomethionine for phasing, more powerful NMR machines and other advances, together with improved computational techniques that facilitate automation, make the goal of characterizing all 100 000 human proteins a real possibility.‘We can also increase the efficiency of the process by targeting families of proteins rather than individual proteins and by preventing duplication of effort,’ Sander explains. ‘We can group proteins into families with similar sequence patterns and somewhat related function and then pick one or more from each family to characterize. Initial targets will be proteins encoded by genes of, for example, medical or evolutionary interest,’ he says. Once the structure of a protein is known, techniques such as model building by homology and molecular replacement enable the three-dimensional shape of other members of its family to be elucidated. Relationships between the shapes of protein folds help narrow down the function of each molecule and provide information to build new computational tools to predict the function of other proteins.The location of binding sites and the determination of specificity, catalytic activity, and regulatory mechanisms that involve conformational changes and covalent modifications are likely to be of particular interest in the design of new drugs. Moreover, ‘if we can interpret genetic variations between individuals and map those changes in protein shapes, we can do a better job in targeting drugs at specific patient populations or redesigning drugs to reduce the side-effects that affect certain groups of people,’ says Sander.A PSI website (http://www.structuralgenomics.org/) has been created to encourage scientists working in this field to share their results and prevent them duplicating their efforts. ‘In addition to that we are also trying to organize discussions between key experimenters in the USA, Europe, and Japan to get implicit support for a systematic approach to this problem. We also hope to announce a structural genomics project that will follow in the footsteps of the Human Genome Project and encourage open exchange of information,’ says Sander. ‘Given the right level of public funding, a very rough estimate of the time scale for such a project would be 10 000 proteins in the next five years,’ concludes Sander.

Mineralized hydrothermal solution cavities in the Co-As A�t Ahmane mine (Bou Azzer, Morocco)

In the F53 Ait Ahmane Cobalt-deposit (Bou Azzer, Anti-Atlas, Morocco) a new type of “contact mineralization” is described. It is carbonate hosted but displays similar depositional sequence and fluid inclusion patterns to the well-known vein mineralization from the same mine. Field studies suggest that such a “contact mineralization” formed early by infilling solution cavities in formerly calcified serpentinite.