The sequence of the human genome

Identification and characterization of the human parkin gene promoter

Compound mutations and homozygous loss of function of the parkin gene causes juvenile and early onset, autosomal recessive parkinsonism. Pathologically, the disease is associated with loss of dopaminergic neurons in the substantia nigra pars compacta and locus ceruleus, usually without Lewy body pathology. Hemizygous families have been described that may harbor mutations outside of the open reading frame. The parkin gene promoter has yet to be characterized, and therein, mutations in hemizygous families may plausibly be identified. To identify the promoter of the parkin gene, the transcription start site was defined by a combination of primer extension and 5' RACE. Five kilobases of DNA 5' to the parkin start codon were directly sequenced from a BAC containing parkin exon 1 and evaluated for promoter motifs. The parkin promoter lacks TATA or CAAT boxes and appears to share homology to the alpha-synuclein promoter. Deletion constructs demonstrated core promoter activity and tissue specific enhancing regions in HEK-293T and SH-SY5Y cells.

The hidden code in genomics: a tool for gene discovery

Among new insights coming from the completion of sequencing of the human genome, reported in Nature and Science, are clues of how evolution has increased the complexity of species, and in particular how the genetic code has enabled this process. It is clear that life has not only evolved by increasing the number of genes, but also by ingeniously evolving an efficient code for expressing diversity in the building blocks (i.e. the amino acids). The rules of nucleic acid base pairing and the classification of amino acids according to hydrophobicity/hydrophilicity relationships define a binary DNA code, which determines the general biophysical characteristics of proteins. Sense and antisense strands can encode protein segments having inverted and complementary hydropathy. The underlying binary code controls association and dissociation of proteins and presumably represents a primordial code that might have emerged in the early stages of self-organizing biochemical cycles. It is the purpose of this communication to provide a perspective of the code in the context of a binary language from its primordial origin to its present day format and to propose to use this code as a genomic mining tool.

Genetic analysis of endocytosis in Caenorhabditis elegans: coelomocyte uptake defective mutants

The coelomocytes of Caenorhabditis elegans are scavenger cells that continuously and nonspecifically endocytose fluid from the pseudocoelom (body cavity). Green fluorescent protein (GFP) secreted into the pseudocoelom from body wall muscle cells is endocytosed and degraded by coelomocytes. We show that toxin-mediated ablation of coelomocytes results in viable animals that fail to endocytose pseudocoelomic GFP, indicating that endocytosis by coelomocytes is not essential for growth or survival of C. elegans under normal laboratory conditions. We examined known viable endocytosis mutants, and performed RNAi for other known endocytosis genes, for coelomocyte uptake defective (Cup) phenotypes. We also screened for new genes involved in endocytosis by isolating viable mutants with Cup defects; this screen identified 14 different genes, many with multiple alleles. A variety of Cup terminal phenotypes were observed, consistent with defects at various steps in the endocytic pathway. Available molecular information indicates that the Cup mutant screen has identified novel components of the endocytosis machinery that are conserved in mammals but not in Saccharomyces cerevisiae, the only other organism for which large-scale genetic screens for endocytosis mutants have been performed.

Beyond the genome: turning data into knowledge

Since the publication of the draft sequence of the human genome in April 2001 (1,2), the pressure on life scientists to annotate and gain useful knowledge from the millions of As, Gs, Cs and Ts, is ever increasing. Now that the initial hype has passed, the life sciences field demands the technologies and computer power that can produce and analyze data in a high-throughput manner for drug discovery and disease diagnosis. Cambridge Healthtech Institute's Beyond Genome 2001 conference(1) (17-22 June 2001, San Francisco, CA, USA) brought together the latest research in these technologies in a 'tri-conference' that encompassed the 10th Annual Conference of Bioinformatics and Genome Research, the 3rd Annual Conference of In Silico Biology and the 5th Annual Conference of Proteomics.

Expression and phylogeny of claudins in vertebrate primordia

Claudins, the major transmembrane proteins of tight junctions, are members of the tetraspanin superfamily of proteins that mediate cellular adhesion and migration. Their functional importance is demonstrated by mutations in claudin genes that eliminate tight junctions in myelin and the testis, abolish Mg(2+) resorption in the kidney, and cause autosomal recessive deafness. Here we report that two paralogs among 15 claudin genes in the zebrafish, Danio rerio, are expressed in the otic and lateral-line placodes at their earliest stages of development. Related claudins in amphibians and mammals are expressed in a similar manner in vertebrate primordia such as sensory placodes, branchial arches, and limb buds. We also show that the claudin gene family may have expanded along the chordate stem lineage from urochordates to gnathostomes, in parallel with the elaboration of vertebrate characters. We propose that tight junctions not only form barriers in mature epithelia, but also participate in vertebrate morphogenesis.

The interplay of biology and technology

Technologies for biological research arise in multiple ways-through serendipity, through inspired insights, and through incremental advances-and they are tightly coupled to progress in engineering. Underlying the complex dynamics of technology and biology are the different motivations of those who work in the two realms. Consideration of how methodologies emerge has implications for the planning of interdisciplinary centers and the training of the next generation of scientists.

Mutations in Mlph, encoding a member of the Rab effector family, cause the melanosome transport defects observed in leaden mice

The d, ash, and ln coat color mutations provide a unique model system for the study of vesicle transport in mammals. All three mutant loci encode genes that are required for the polarized transport of melanosomes, the specialized, pigment-containing organelles of melanocytes, to the neighboring keratinocytes and eventually into coat hairs. Genetic studies suggest that these genes function in the same or overlapping pathways and are supported by biochemical studies showing that d encodes an actin-based melanosome transport motor, MyoVa, whereas ash encodes Rab27a, a protein that localizes to the melanosome and is postulated to serve as the MyoVa receptor. Here we show that ln encodes melanophilin (Mlph), a previously undescribed protein with homology to Rab effectors such as granuphilin, Slp3-a, and rabphilin-3A. Like all of these effectors, Mlph possesses two Zn(2+)-binding CX(2)CX(13,14)CX(2)C motifs and a short aromatic-rich amino acid region that is critical for Rab binding. However, Mlph does not contain the two Ca(2+)-binding C(2) domains found in these and other proteins involved in vesicle transport, suggesting that it represents a previously unrecognized class of Rab effectors. Collectively, our data show that Mlph is a critical component of the melanosome transport machinery and suggest that Mlph might function as part of a transport complex with Rab27a and MyoVa.

Characterization of tissue- and cell-type-specific expression of a novel human septin family gene, Bradeion

Expression changes in subsets of genes occur in the course of altering cell fates, i.e., aging, cell death, and carcinogenesis. These changes simultaneously provide the good candidate as a biomarker for monitoring cancer. We have identified a novel human septin family gene, Bradeion, from adult brain cDNA library by a monoclonal antibody CE5. Northern blot and in situ hybridization analysis showed that Bradeion has two distinct transcripts, approximately 2.2 and 1.7 kb length (alpha and beta, respectively) mainly in brain and slightly in heart, and no expression in any fetal organs. Haplotype analysis placed the gene location at 17q23. The gene contains GTPase motifs highly conserved in the septin family genes that are essential for cytokinesis and cell separation. The transcript of beta form lacks a hydrophobic region, which suggests that this form arises from a single Bradeion gene through unique RNA splicing. Interestingly, this brain-specific Bradeion gene is also expressed in two human cancers, colorectal cancer and malignant melanoma. Ectopic expression of normal Bradeion alpha and beta transcripts were confirmed both in patients' tumor samples and in in vitro cultured human cancer cell lines. Thus the Bradeion provides valuable tools as a tumor-specific and selective marker.

Identification and characterization of two novel calpain large subunit genes

Calpains are a family of related proteins, some of which have been shown to function as calcium-dependent cysteine proteases. CAPN1 and CAPN2, the most well characterized calpains, consist of a large (80 kDa) and a small (30 kDa) subunit. In mammals, 11 different paralogous genes encoding calpain large subunits have been identified. We report the identification of two further genes, CAPN13 and CAPN14, potentially encoding calpain large subunits. Radiation hybrid mapping localized both genes within a region mapped to 2p21-2p22. The CAPN13 mRNA exhibits a restricted tissue distribution with low levels of expression detected only in human testis and lung while CAPN14 mRNA could not be detected in any of the 76 tissues examined. Examination of the human genome sequence in the public and private consortia databases did not detect any further members of this gene family. Thus, there would seem to be 13 large subunit calpain genes in the human genome. Phylogenetic analysis reveals that the putative calpain large subunit proteins can be divided into three major groups. The 13 human large subunit genes and the single small subunit gene are located in eight syntenic groups on chromosomes 1, 2, 3, 6, 11, 15, 19 and X.

Gene expression screening of human mast cells and eosinophils using high-density oligonucleotide probe arrays: abundant expression of major basic protein in mast cells

Mast cells (MCs) and eosinophils are thought to play important roles in evoking allergic inflammation. Cell-type--specific gene expression was screened among 12,000 genes in human MCs and eosinophils with the use of high-density oligonucleotide probe arrays. In comparison with other leukocytes, MCs expressed 140 cell-type--specific transcripts, whereas eosinophils expressed only 34. Among the transcripts for expected MC-specific proteins such as tryptase, major basic protein (MBP), which had been thought to be eosinophil specific, was ranked fourth in terms of amounts of increased MC-specific messenger RNA. Mature eosinophils were almost lacking this transcript. MCs obtained from 4 different sources (ie, lung, skin, adult peripheral blood progenitor--derived and cord blood progenitor--derived MCs, and eosinophils) were found to have high protein levels of MBP in their granules with the use of flow cytometric and confocal laser scanning microscopic analyses. The present finding that MCs can produce abundant MBP is crucial because many reports regarding allergic pathogenesis have been based on earlier findings that MBP was almost unique to eosinophils and not produced by MCs. (Blood. 2001;98:1127-1134)

Multiplex polymerase chain reaction (PCR) with color-tagged module-shuffling primers for comparing gene expression levels in various cells

A method based on the multiplex polymerase chain reaction (PCR) and gel electrophoresis for the comparative analysis of gene expression levels was developed. Using the method many cDNA fragments from different sources can be compared simultaneously. Competitive PCR amplification of expressed genes from different sources was performed by using 'module-shuffling primers' (MPSs). The MPSs (labeled with different fluorophores) consist of sequence modules of 3 or 4 nt. The modules are arranged in different orders in each primer; therefore, the base sequences of the primers are different but their melting temperatures are identical. The genes expressed in different sources are ligated with tags complementary with the MPSs. Tag-ligated fragments are mixed in one tube and amplified at the same amplification efficiency by the MPSs. Amplified fragments are detected separately by multiple-color gel electrophoresis. This method can detect different amounts of each expressed gene, up to a difference in amounts of 30%, and its detection limit is 0.1 amol per assay.

Virtual anthropology (VA): a call for glasnost in paleoanthropology

The adventurous scientist, with a hat protecting him from the fierce sun as he travels from one remote place to another, hunting for fossils of our ancestors, has been a part of the romantic imagination associated with anthropological research in the 20th Century. This picture of the paleoanthropologist still retains a grain of truth. Indeed, many new sites were discovered under troublesome conditions in the recent past and have added substantial information about our origins. But on another front, probably less sensational but no less important, are contributions stemming from the analysis of the already discovered fossils. With the latter, a rapid evolution in anthropologic research took place concurrently with advances in computer technology. After ambitious activities by a handful of researchers in some specialized laboratories, a methodologic inventory evolved to extract critical information about fossilized specimens, most of it preserved in the largely inaccessible interior as unrevealed anatomic structures. Many methodologies have become established but, for various reasons, access to both the actual and the digitized fossils is still limited. It is time for more transparency, for a glasnost in paleoanthropology. Herein are presented some answers to the question of how a high-tech approach to anthropology can be integrated into a predominantly conservative field of research, and what are the main challenges for development in the future.

An Eulerian path approach to DNA fragment assembly

For the last 20 years, fragment assembly in DNA sequencing followed the "overlap-layout-consensus" paradigm that is used in all currently available assembly tools. Although this approach proved useful in assembling clones, it faces difficulties in genomic shotgun assembly. We abandon the classical "overlap-layout-consensus" approach in favor of a new euler algorithm that, for the first time, resolves the 20-year-old "repeat problem" in fragment assembly. Our main result is the reduction of the fragment assembly to a variation of the classical Eulerian path problem that allows one to generate accurate solutions of large-scale sequencing problems. euler, in contrast to the celera assembler, does not mask such repeats but uses them instead as a powerful fragment assembly tool.

A polymorphic genomic duplication on human chromosome 15 is a susceptibility factor for panic and phobic disorders

Anxiety disorders are complex and common psychiatric illnesses associated with considerable morbidity and social cost. We have studied the molecular basis of the cooccurrence of panic and phobic disorders with joint laxity. We have identified an interstitial duplication of human chromosome 15q24-26 (named DUP25), which is significantly associated with panic/agoraphobia/social phobia/joint laxity in families, and with panic disorder in nonfamilial cases. Mosaicism, different forms of DUP25 within the same family, and absence of segregation of 15q24-26 markers with DUP25 and the psychiatric phenotypes suggest a non-Mendelian mechanism of disease-causing mutation. We propose that DUP25, which is present in 7% control subjects, is a susceptibility factor for a clinical phenotype that includes panic and phobic disorders and joint laxity.

Mouse genomics: making sense of the sequence

Interpretation of the human genome sequence relies on studies of model genetic organisms. Mouse genetics and genomics will help to identify all the genes, and to determine their function.

Identification of tumor suppressor candidate genes by physical and sequence mapping of the TSLC1 region of human chromosome 11q23

Loss of heterozygosity for a locus on human chromosome 11q22-23 is observed at high frequency in non-small cell lung carcinoma (NSCLC). Introduction of a 1.1 Mb fragmented yeast artificial chromosome (YAC) mapping to this region completely suppresses the tumorigenic properties of a human NSCLC cell line, A549. Smaller fragmented YACs give partial but not complete suppression. To further localize the gene(s) responsible for this partial suppression, a bacterial artificial chromosome (BAC) and P1-based artificial chromosome (PAC) contig was constructed, completely spanning the candidate region. End sequence generated in the construction of the BAC/PAC contig identified a previously unmapped EST and served to order genomic sequence contigs from the publicly available Celera Genomics (CG) and Human Genome Project (HGP) efforts. Comparison showed that CG provided larger contigs, while HGP provided more coverage. Neither CG nor HGP provided complete sequence coverage, alone or in combination. The sequence was used to map 110 ESTs and to predict new genes, including two GenScan gene predictions that overlapped ESTs and were shown to be differentially expressed in tumorigenic and suppressed A549 cell lines.

Sequence analysis of the human kallikrein gene locus identifies a unique polymorphic minisatellite element

Minisatellites are repetitive sequences of DNA that are present throughout the genome. Although the origin and function of these minisatellites is still unknown, they found clinical applications as markers of many diseases, including cancer. Also, they are useful tools for DNA fingerprinting and linkage analysis. Kallikreins are serine proteases that appear to be involved in many diseases including brain disorders and malignancy. We have recently characterized the human kallikrein gene locus on chromosome 19q13.4, which includes 15 kallikrein genes. In this study, we examined the kallikrein locus ( approximately 300 Kb) for all known repeat elements. About 50% of this genomic area is occupied by different repeat elements. We also identified unique minisatellite elements that are restricted to chromosome 19q13. Ten clusters of these minisatellites are distributed along the locus on either DNA strand. The clusters are located in the promoters and enhancers of genes, in introns, and in untranslated regions of the mRNA. Analysis of these elements indicates that they are polymorphic, thus they can be useful in linkage analysis and DNA fingerprinting. Our preliminary results indicate also that the distribution of the different alleles of these minisatellites might be associated with malignancy.

Myotonic dystrophy type 2 caused by a CCTG expansion in intron 1 of ZNF9

Myotonic dystrophy (DM), the most common form of muscular dystrophy in adults, can be caused by a mutation on either chromosome 19q13 (DM1) or 3q21 (DM2/PROMM). DM1 is caused by a CTG expansion in the 3' untranslated region of the dystrophia myotonica-protein kinase gene (DMPK). Several mechanisms have been invoked to explain how this mutation, which does not alter the protein-coding portion of a gene, causes the specific constellation of clinical features characteristic of DM. We now report that DM2 is caused by a CCTG expansion (mean approximately 5000 repeats) located in intron 1 of the zinc finger protein 9 (ZNF9) gene. Parallels between these mutations indicate that microsatellite expansions in RNA can be pathogenic and cause the multisystemic features of DM1 and DM2.

Rapid functional analysis of protein-protein interactions by fluorescent C-terminal labeling and single-molecule imaging

Detection of protein-protein interactions is a fundamental step to understanding gene function. Here we report a sensitive and rapid method for assaying protein-protein interactions at the single-molecule level. Protein molecules were synthesized in a cell-free translation system in the presence of Cy5-puro, a fluorescent puromycin, using mRNA without a stop codon. The interaction of proteins thus prepared was visualized using a single-molecule imaging technique. As a demonstration of this method, a motor protein, kinesin, was labeled with Cy5-puro at an efficiency of about 90%, and the processive movement of kinesin along microtubules was observed by using total internal reflection microscopy. It took only 2 h from the synthesis of proteins to the functional analysis. This method is applicable to the functional analysis of various kinds of proteins.

Molecular characterization of two natural hotspots in the Drosophila buzzatii genome induced by transposon insertions

Transposable elements (TEs) have been implicated in the generation of genetic rearrangements, but their potential to mediate changes in the organization and architecture of host genomes could be even greater than previously thought. Here, we describe the naturally occurring structural and nucleotide variation around two TE insertions in the genome of Drosophila buzzatii. The studied regions correspond to the breakpoints of a widespread chromosomal inversion generated by ectopic recombination between oppositely oriented copies of a TE named Galileo. A detailed molecular analysis by Southern hybridization, PCR amplification, and DNA sequencing of 7.1 kb surrounding the inversion breakpoints in 39 D. buzzatii lines revealed an unprecedented degree of restructuring, consisting of 22 insertions of ten previously undescribed TEs, 13 deletions, 1 duplication, and 1 small inversion. All of these alterations occurred exclusively in inverted chromosomes and appear to have accumulated after the insertion of the Galileo elements, within or close to them. The nucleotide variation at the studied regions is six times lower in inverted than in noninverted chromosomes, suggesting that most of the observed changes originated in only 84,000 years. Galileo elements thus seemed to promote the transformation of these, otherwise normal, chromosomal regions in genetically unstable hotspots and highly efficient traps for transposon insertions. The particular features of two new Galileo copies found indicate that this TE belongs to the Foldback family. Together, our results strengthen the importance of TEs, and especially DNA transposons, as inducers of genome plasticity in evolution.

Role of individual neurons and neural networks in cognitive functioning of the brain: a new insight

The prevailing concept in modern neuroscience is that neuron networks play a dominant role in the functioning of the nervous system, whereas the role of individual neurons is rather insignificant. This concept suggests that "individuality" of single neurons is primarily determined by their place in a network rather than their intrinsic properties. Here I argue that individual neurons may play an important, if not decisive, role in performing cognitive functions of the brain. This tentative viewpoint is supported by experimental and clinical insights into disorders of cognitive functions and by genetic studies of cognitive abilities and disabilities. The results obtained in these studies indicate that many specific cognitive functions are carried out by groups of highly specialized neurons whose roles in performing these functions are genetically predetermined and their activity could not be substituted by the activity of other neurons. In this context, the main role of neural networks and intercellular interactions is to form dynamic ensembles of neurons involved in performing a given cognitive function.

Plant evolution and development in a post-genomic context

Large-scale gene-sequencing projects that have been undertaken in animals have involved organisms from contrasting taxonomic groups, such as worm, fly and mammal. By contrast, similar botanical projects have focused exclusively on flowering plants. This has made it difficult to carry out fundamental research on how plants have evolved from simple to complex forms - a task that has been very successful in animals. However, in the flowering plants, the many completely or partially sequenced genomes now becoming available will provide a powerful tool to investigate the details of evolution in one group of related organisms.

Shifting paradigms in gene-mapping methodology for complex traits

The analysis of genetic linkage has been highly successful in the mapping of the genes responsible for Mendelian diseases. In the past decade, attempts have been made to extend this approach to multifactorial disorders and other health-related traits. It has proved difficult, however, to obtain strong and replicable linkage findings for the common forms of heritable diseases. This, together with the rapid pace of development of molecular technology and expansion of genome sequence information, has resulted in significant shifts in research paradigm. There is an increasing recognition of the need to understand the population genetics and biometrical properties of clinically relevant traits so that phenotypes can be defined in such a way that maximises the chances of successful gene mapping. There is a trend towards systematic association analysis with increasing sophistication in the analysis of pooled DNA samples and multi-locus haplotypes, and in the use of unlinked background markers to protect against spurious associations. We can expect increasing integration between genetics, epidemiology and clinical trials leading to genetically informative designs that will not only identify susceptibility genes but also clarify how the environment influences their effects and how they may modify the response to therapeutic interventions.

Estimating the efficacy and efficiency of cascade genetic screening

Screening for genetic variants that predispose individuals or their offspring to disease may be performed at the general population level or may instead be targeted at the relatives of previously identified carriers. The latter strategy has come to be known as "cascade genetic screening." Since the carrier risk of close relatives of known carriers is generally higher than the population risk, cascade screening is more efficient than population screening, in the sense that fewer individuals have to be genotyped per detected carrier. The efficacy of cascade screening, as measured by the overall proportion of carriers detected in a given population, is, however, lower than that of population-wide screening, and the respective inclusion rates vary according to the population frequency and mode of inheritance of the predisposing variants. For dominant mutations, we have developed equations that allow the inclusion rates of cascade screening to be calculated in an iterative fashion, depending upon screening depth and penetrance. For recessive mutations, we derived only equations for the screening of siblings and the children of patients. Owing to their mathematical complexity, it was necessary to study more extended screening strategies by simulation. Cascade screening turned out to result in low inclusion rates (<1%) when aimed at the identification of heterozygous carriers of rare recessive variants. Considerably higher rates are achievable, however, when screening is performed to detect covert homozygotes for frequent recessive mutations with reduced penetrance. This situation is exemplified by hereditary hemochromatosis, for which up to 40% of at-risk individuals may be identifiable through screening of first- to third-degree relatives of overt carriers (i.e., patients); the efficiency of this screening strategy was found to be approximately 50 times higher than that of population-wide screening. For dominant mutations, inclusion rates of cascade screening were estimated to be higher than for recessive variants. Thus, some 80% of all carriers of the factor V Leiden mutation would be detected if screening were to be targeted specifically at first- to third-degree relatives of patients with venous thrombosis. The relative cost efficiency of cascade as compared with population-wide screening (i.e., the overall savings in the extra managerial cost of the condition) is also likely to be higher for dominant than for recessive mutations. This notwithstanding, once screening has become cost-effective at the population level, it can be expected that cascade screening would only transiently represent an economically viable option.

Mapping protein-protein interactions with combinatorial biology methods

Extremely diverse, DNA-encoded libraries of peptides and proteins have been constructed that include a linkage between each polypeptide and the encoding DNA. Library members can be selected by virtue of a particular binding specificity, and their protein sequence can be deduced from the sequence of the cognate DNA. Such combinatorial biology methods have proven invaluable in both identifying natural protein-protein interactions and also in mapping the specificities and energetics of these interactions in fine detail.

Sequence variation and linkage disequilibrium in the human T-cell receptor beta (TCRB) locus

The T-cell receptor (TCR) plays a central role in the immune system, and > 90% of human T cells present a receptor that consists of the alpha TCR subunit (TCRA) and the beta subunit (TCRB). Here we report an analysis of 63 variable genes (BV), spanning 553 kb of TCRB that yielded 279 single-nucleotide polymorphisms (SNPs). Samples were drawn from 10 individuals and represent four populations-African American, Chinese, Mexican, and Northern European. We found nine variants that produce nonfunctional BV segments, removing those genes from the TCRB genomic repertoire. There was significant heterogeneity among population samples in SNP frequency (including the BV-inactivating sites), indicating the need for multiple-population samples for adequate variant discovery. In addition, we observed considerable linkage disequilibrium (LD) (r(2) > 0.1) over distances of approximately 30 kb in TCRB, and, in general, the distribution of r(2) as a function of physical distance was in close agreement with neutral coalescent simulations. LD in TCRB showed considerable spatial variation across the locus, being concentrated in "blocks" of LD; however, coalescent simulations of the locus illustrated that the heterogeneity of LD we observed in TCRB did not differ markedly from that expected from neutral processes. Finally, examination of the extended genotypes for each subject demonstrated homozygous stretches of >100 kb in the locus of several individuals. These results provide the basis for optimization of locuswide SNP typing in TCRB for studies of genotype-phenotype association.

Genomics, complexity and drug discovery: insights from Boolean network models of cellular regulation

The completion of the first draft of the human genome sequence has revived the old notion that there is no one-to-one mapping between genotype and phenotype. It is now becoming clear that to elucidate the fundamental principles that govern how genomic information translates into organismal complexity, we must overcome the current habit of ad hoc explanations and instead embrace novel, formal concepts that will involve computer modelling. Most modelling approaches aim at recreating a living system via computer simulation, by including as much details as possible. In contrast, the Boolean network model reviewed here represents an abstraction and a coarse-graining, such that it can serve as a simple, efficient tool for the extraction of the very basic design principles of molecular regulatory networks, without having to deal with all the biochemical details. We demonstrate here that such a discrete network model can help to examine how genome-wide molecular interactions generate the coherent, rule-like behaviour of a cell - the first level of integration in the multi-scale complexity of the living organism. Hereby the various cell fates, such as differentiation, proliferation and apoptosis, are treated as attractor states of the network. This modelling language allows us to integrate qualitative gene and protein interaction data to explain a series of hitherto non-intuitive cell behaviours. As the human genome project starts to reveal the limits of the current simplistic 'one gene - one function - one target' paradigm, the development of conceptual tools to increase our understanding of how the intricate interplay of genes gives rise to a global 'biological observable' will open a new perspective for post-genomic drug target discovery.

The role of eosinophils in asthma: Sarastro or the Queen of the Night?

Eosinophils used to be thought of as regulators of allergic inflammation, but there is now evidence to the contrary; eosinophils have been found to be the major effector cells responsible for the late asthmatic response (LAR), airway hyperresponsiveness (AHR) and, at least in part, airway remodeling by releasing leukotrienes and highly basic and cytotoxic proteins such as major basic protein (MBP). However, a recent clinical trial using humanized anti-interleukin-5 monoclonal antibody found a failure to reduce AHR and the LAR, whereas the antibody entirely abolished tissue eosinophilia. In addition, abundant MBP has recently been found in mast cells as well as in eosinophils by our transcriptome (the whole transcripts that a cell expresses) screening of all leukocyte types. Eosinophils are indeed unlikely to be involved in the LAR and may not be unique cytotoxic cells in asthma. It is now necessary to determine the real role of eosinophils and whether early intervention to block eosinophil recruitment into the asthmatic lung does prevent airway remodeling and AHR.

From symptomatic treatments to causative therapy?

The search for genes that predispose individuals to develop common chronic diseases such as asthma, diabetes and Alzheimer's promises to give insights into their molecular pathogenesis. This will lead to the development of therapies that modulate the pathology, rather than the physiology of these diseases. As academia and the pharmaceutical industry increasingly focus on this challenge, the genetic dissection of Alzheimer's is spearheading attempts to shift the therapeutic paradigm away from symptomatic to curative treatments.

Evolution and development of the vertebrate ear

This review outlines major aspects of development and evolution of the ear, specifically addressing issues of cell fate commitment and the emerging molecular governance of these decisions. Available data support the notion of homology of subsets of mechanosensors across phyla (proprioreceptive mechanosensory neurons in insects, hair cells in vertebrates). It is argued that this conservation is primarily related to the specific transducing environment needed to achieve mechanosensation. Achieving this requires highly conserved transcription factors that regulate the expression of the relevant structural genes for mechanosensory transduction. While conserved at the level of some cell fate assignment genes (atonal and its mammalian homologue), the ear has also radically reorganized its development by implementing genes used for cell fate assignment in other parts of the developing nervous systems (e.g., neurogenin 1) and by evolving novel sets of genes specifically associated with the novel formation of sensory neurons that contact hair cells (neurotrophins and their receptors). Numerous genes have been identified that regulate morphogenesis, but there is only one common feature that emerges at the moment: the ear appears to have co-opted genes from a large variety of other parts of the developing body (forebrain, limbs, kidneys) and establishes, in combination with existing transcription factors, an environment in which those genes govern novel, ear-related morphogenetic aspects. The ear thus represents a unique mix of highly conserved developmental elements combined with co-opted and newly evolved developmental elements.

Genome analysis with gene-indexing databases

The recent release of the draft sequence and the eventual completion of the human genome present the scientific community with a rich source of data to mine. Yet, these data are content poor in the absence of additional correlative information. Expressed sequence tag (EST) datasets and their associated gene indices have existed for many years, and represent the first attempt at understanding the complexity of the genome. These datasets remain extremely important as information sources and, in particular, as tools for analyzing the completed genomes. Here, we discuss the nature of ESTs and their associated tools and gene-indexing databases. In particular, we will compare three EST gene indices (UNIGENE, Merck Gene Index Version 2.0 and Doubletwist CAT), discuss how these gene indices are applied for both genome analysis and drug discovery, and demonstrate their importance as a complementary dataset to the annotated human genome.

Protein interaction databases

Life depends on the interaction of proteins. The availability of the complete human genome sequence has highlighted the need for a tool to analyse protein interactions and several databases have been compiled for this purpose. These databases document, categorize, and analyze interacting proteins and the cellular functions of the interactions.

Sequence variation within the fragile X locus

The human genome provides a reference sequence, which is a template for resequencing studies that aim to discover and interpret the record of common ancestry that exists in extant genomes. To understand the nature and pattern of variation and linkage disequilibrium comprising this history, we present a study of approximately 31 kb spanning an approximately 70 kb region of FMR1, sequenced in a sample of 20 humans (worldwide sample) and four great apes (chimp, bonobo, and gorilla). Twenty-five polymorphic sites and two insertion/deletions, distributed in 11 unique haplotypes, were identified among humans. Africans are the only geographic group that do not share any haplotypes with other groups. Parsimony analysis reveals two main clades and suggests that the four major human geographic groups are distributed throughout the phylogenetic tree and within each major clade. An African sample appears to be most closely related to the common ancestor shared with the three other geographic groups. Nucleotide diversity, pi, for this sample is 2.63 +/- 6.28 x 10(-4). The mutation rate, mu is 6.48 x 10(-10) per base pair per year, giving an ancestral population size of approximately 6200 and a time to the most recent common ancestor of approximately 320,000 +/- 72,000 per base pair per year. Linkage disequilibrium (LD) at the FMR1 locus, evaluated by conventional LD analysis and by the length of segment shared between any two chromosomes, is extensive across the region.

Strategies for the systematic sequencing of complex genomes

Recent spectacular advances in the technologies and strategies for DNA sequencing have profoundly accelerated the detailed analysis of genomes from myriad organisms. The past few years alone have seen the publication of near-complete or draft versions of the genome sequence of several well-studied, multicellular organisms - most notably, the human. As well as providing data of fundamental biological significance, these landmark accomplishments have yielded important strategic insights that are guiding current and future genome-sequencing projects.

Gene expression profiling in human fetal liver and identification of tissue- and developmental-stage-specific genes through compiled expression profiles and efficient cloning of full-length cDNAs

Fetal liver intriguingly consists of hepatic parenchymal cells and hematopoietic stem/progenitor cells. Human fetal liver aged 22 wk of gestation (HFL22w) corresponds to the turning point between immigration and emigration of the hematopoietic system. To gain further molecular insight into its developmental and functional characteristics, HFL22w was studied by generating expressed sequence tags (ESTs) and by analyzing the compiled expression profiles of liver at different developmental stages. A total of 13,077 ESTs were sequenced from a 3'-directed cDNA library of HFL22w, and classified as follows: 5819 (44.5%) matched to known genes; 5460 (41.8%) exhibited no significant homology to known genes; and the remaining 1798 (13.7%) were genomic sequences of unknown function, mitochondrial genomic sequences, or repetitive sequences. Integration of ESTs of known human genes generated a profile including 1660 genes that could be divided into 15 gene categories according to their functions. Genes related to general housekeeping, ESTs associated with hematopoiesis, and liver-specific genes were highly expressed. Genes for signal transduction and those associated with diseases, abnormalities, or transcription regulation were also noticeably active. By comparing the expression profiles, we identified six gene groups that were associated with different developmental stages of human fetal liver, tumorigenesis, different physiological functions of Itoh cells against the other types of hepatic cells, and fetal hematopoiesis. The gene expression profile therefore reflected the unique functional characteristics of HFL22w remarkably. Meanwhile, 110 full-length cDNAs of novel genes were cloned and sequenced. These novel genes might contribute to our understanding of the unique functional characteristics of the human fetal liver at 22 wk.