Functional genomics and the study of development, variation and evolution

The developmental and genetic trajectory of coloration in the guppy (Poecilia reticulata)

Examining the association between trait variation and development is crucial for understanding the evolution of phenotypic differences. Male guppy ornamental caudal fin coloration is one trait that shows a striking degree of variation within and between guppy populations. Males initially have no caudal fin coloration, then gradually develop it as they reach sexual maturity. For males, there is a trade-off between female preference for caudal fin coloration and increased visibility to predators. This trade-off may reach unique endpoints in males from different predation regimes. Caudal fin coloration includes black melanin, orange/yellow pteridines or carotenoids, and shimmering iridescence. This study examined the phenotypic trajectory and genetics associated with color development. We found that black coloration always developed first, followed by orange/yellow, then iridescence. The ordering and timing of color appearance was the same regardless of predation regime. The increased expression of melanin synthesis genes correlated well with the visual appearance of black coloration, but there was no correlation between carotenoids or pteridine synthesis gene expression and the appearance of orange/yellow. The lack of orange/yellow coloration in earlier male caudal fin developmental stages may be due to reduced expression of genes underlying the development of orange/yellow xanthophores.

The ancestral levels of transcription and the evolution of sexual phenotypes in filamentous fungi

Changes in gene expression have been hypothesized to play an important role in the evolution of divergent morphologies. To test this hypothesis in a model system, we examined differences in fruiting body morphology of five filamentous fungi in the Sordariomycetes, culturing them in a common garden environment and profiling genome-wide gene expression at five developmental stages. We reconstructed ancestral gene expression phenotypes, identifying genes with the largest evolved increases in gene expression across development. Conducting knockouts and performing phenotypic analysis in two divergent species typically demonstrated altered fruiting body development in the species that had evolved increased expression. Our evolutionary approach to finding relevant genes proved far more efficient than other gene deletion studies targeting whole genomes or gene families. Combining gene expression measurements with knockout phenotypes facilitated the refinement of Bayesian networks of the genes underlying fruiting body development, regulation of which is one of the least understood processes of multicellular development.

RADICAL-INDUCED FRAGMENTATION OF PHOSPHOLIPID CATIONS USING METASTABLE ATOM-ACTIVATED DISSOCIATION MASS SPECTROMETRY (MAD-MS)

The fragmentation pattern of several protonated 1+ phosphatidylcholines (PCs) were studied using low energy collision induced dissociation (CID) and helium metastable atom-activated dissociation (He-MAD). He-MAD of the protonated compounds produced a dominant phosphocholine head group at m/z 184 as well as typical sn-1 and sn-2 glycerol fragments such as [M+H-R_x-1CHC=O]⁺ and [M+H-R_x-1CO₂H]⁺. Within the aliphatic chain, He-MAD showed fragments consistent with high-energy collision induced dissociation (HE-CID) and products/pathways consistent with Penning ionization of the 1+ precursor ions to their respective radical dications. These Penning ionization products included both singly and doubly charged radical fragments, and the fragment ions are related to the number and position of double bonds in the acyl chains. Fragments created through HE-CID-like fragmentation followed classic charge remote fragmentation pathways including ladder-like fragmentation along the acyl chain, except for additional or missing peaks due to predictable rearrangement reactions. He-MAD therefore shows utility in being able to effectively fragment singly charged lipids into a variety of useful product ions using both radical and high-energy processes in the confines of a 3D ion trap.

Transcriptional pathways associated with the slow growth phenotype of transformed Anaplasma marginale

Background

The ability to genetically manipulate bacteria has been fundamentally important for both basic biological discovery and translational research to develop new vaccines and antibiotics. Experimental alteration of the genetic content of prokaryotic pathogens has revealed both expected functional relationships and unexpected phenotypic consequences. Slow growth phenotypes have been reported for multiple transformed bacterial species, including extracellular and intracellular pathogens. Understanding the genes and pathways responsible for the slow growth phenotype provides the opportunity to develop attenuated vaccines as well as bacteriostatic antibiotics. Transformed Anaplasma marginale, a rickettsial pathogen, exhibits slow growth in vitro and in vivo as compared to the parent wild type strain, providing the opportunity to identify the underlying genes and pathways associated with this phenotype.

Results

Whole genome transcriptional profiling allowed for identification of specific genes and pathways altered in transformed A. marginale. Genes found immediately upstream and downstream of the insertion site, including a four gene operon encoding key outer membrane proteins, were not differentially transcribed between wild type and transformed A. marginale. This lack of significant difference in transcription of flanking genes and the large size of the insert relative to the genome were consistent with a trans rather than a cis effect. Transcriptional profiling across the complete genome identified the most differentially transcribed genes, including an iron transporter, an RNA cleaving enzyme and several genes involved in translation. In order to confirm the trend seen in translation-related genes, K-means clustering and Gene Set Enrichment Analysis (GSEA) were applied. These algorithms allowed evaluation of the behavior of genes as groups that share transcriptional status or biological function. Clustering and GSEA confirmed the initial observations and found additional pathways altered in transformed A. marginale. Three pathways were significantly altered as compared to the wild type: translation, translation elongation, and purine biosynthesis.

Conclusions

Identification of perturbed genes and networks through genome wide transcriptional profiling highlights the relevance of pathways such as nucleotide biosynthesis, translation, and translation elongation in the growth phenotype of obligate intracellular bacteria. These genes and pathways provide specific targets for development of slow growing attenuated vaccines and for bacteriostatic antibiotics.

Swedish mutation within amyloid precursor protein modulates global gene expression towards the pathogenesis of Alzheimer's disease

The Swedish mutation (K595N/M596L) of amyloid precursor protein (APP-swe) has been known to increase abnormal cleavage of cellular APP by Beta-secretase (BACE), which causes tau protein hyperphosphorylation and early-onset Alzheimer's disease (AD). Here, we analyzed the effect of APP-swe in global gene expression using deep transcriptome sequencing technique. We found 283 genes were down-regulated and 348 genes were up-regulated in APP-swe expressing H4-swe cells compared to H4 wild-type cells from a total of approximately 74 million reads of 38 base pairs from each transcriptome. Two independent mechanisms such as kinase and phosphatase signaling cascades leading hyperphosphorylation of tau protein were regulated by the expression of APP-swe. Expressions of catalytic subunit as well as several regulatory subunits of protein phosphatases 2A were decreased. In contrast, expressions of tau-phosphorylating glycogen synthase kinase 3ß (GSK-3ß), cyclin dependent kinase 5 (CDK5), and cAMP-dependent protein kinase A (PKA) catalytic subunit were increased. Moreover, the expression of AD-related Aquaporin 1 and presenilin 2 expression was regulated by APP-swe. Taken together, we propose that the expression of APP-swe modulates global gene expression directed to AD pathogenesis.

Translog, a web browser for studying the expression divergence of homologous genes

Background

Increasing amount of data from comparative genomics, and newly developed technologies producing accurate gene expression data facilitate the study of the expression divergence of homologous genes. Previous studies have individually highlighted factors that contribute to the expression divergence of duplicate genes, e.g. promoter changes, exon structure heterogeneity, asymmetric histone modifications and genomic neighborhood conservation. However, there is a lack of a tool to integrate multiple factors and visualize their variety among homologous genes in a straightforward way.

Results

We introduce Translog (a web-based tool for Transcriptome comparison of homologous genes) that assists in the comparison of homologous genes by displaying the loci in three different views: promoter view for studying the sharing/turnover of transcription initiations, exon structure for displaying the exon-intron structure changes, and genomic neighborhood to show the macro-synteny conservation in a larger scale. CAGE data for transcription initiation are mapped for each transcript and can be used to study transcription turnover and expression changes. Alignment anchors between homologous loci can be used to define the precise homologous transcripts. We demonstrate how these views can be used to visualize the changes of homologous genes during evolution, particularly after the 2R and 3R whole genome duplication.

Conclusion

We have developed a web-based tool for assisting in the transcriptome comparison of homologous genes, facilitating the study of expression divergence.

Survival in acute and severe low o environment: use of a genetic model system

Hypoxia whether present during physiologic states (e.g., embryogenesis) or during pathologic states (e.g., obstructive sleep apnea and sickle cell anemia), challenges the vertebrate or invertebrate organism. Clearly, hypoxia can lead to sublethal cell injury or death and consequently organ or systemic injury and failure, depending on severity. We discovered that the adult Drosophila melanogaster is tolerant to a low O(2) environment, withstanding approximately 3-4 hours of total O(2) deprivation or anoxia without showing any evidence of cell injury. This opened major avenues for us since the Drosophila has been used so effectively in so many relevant research areas. We investigated the changes in gene expression in D. melanogaster after severe (1% O(2)) intermittent or constant hypoxia treatment for 2.5 hours. Our microarray analysis has identified multiple gene families that are up- or downregulated in response to acute constant (CH) and intermittent hypoxia (IH). We observed that even for short-term the gene expression response to IH and CH varied not only in the number of genes but also type of gene families. Furthermore, by utilizing powerful Drosophila genetic tools we studied the role of single genes (up- or downregulated in arrays) in survival under either paradigm in adult flies. We observed significant increased adult survival (as compared to controls) of P-element lines for Hsp70 and Hsp23 genes during CH and Mdr49 and l (2)08717 genes during IH. This suggests that the increased transcript levels as observed in array data after either paradigm play an important role under severe hypoxia. Indeed, we found for example that over-expressing Hsp70 in vivo in specific fly organs (such as heart) significantly increased adult survival during CH as compared to controls. These data provide further clues about the mechanisms by which intermittent and constant hypoxia lead to cell injury and morbidity or adaptation and survival.

Characterizing natural variation using next-generation sequencing technologies

Progress in evolutionary genomics is tightly coupled with the development of new technologies to collect high-throughput data. The availability of next-generation sequencing technologies has the potential to revolutionize genomic research and enable us to focus on a large number of outstanding questions that previously could not be addressed effectively. Indeed, we are now able to study genetic variation on a genome-wide scale, characterize gene regulatory processes at unprecedented resolution, and soon, we expect that individual laboratories might be able to rapidly sequence new genomes. However, at present, the analysis of next-generation sequencing data is challenging, in particular because most sequencing platforms provide short reads, which are difficult to align and assemble. In addition, only little is known about sources of variation that are associated with next-generation sequencing study designs. A better understanding of the sources of error and bias in sequencing data is essential, especially in the context of studies of variation at dynamic quantitative traits.

The impact of genomic neighborhood on the evolution of human and chimpanzee transcriptome

Divergence of gene expression can result in phenotypic variation, which contributes to the evolution of new species. Although the influence of trans- and cis-regulatory mutations is well known, the genome-wide impact of changes in genomic neighborhood of genes on expression divergence between species remains largely unexplored. Here, we compare the neighborhood of orthologous genes (within a window of 2 MB) in human and chimpanzee with the expression levels of their transcripts from several equivalent tissues and demonstrate that genes with altered neighborhood are more likely to undergo expression divergence than genes with conserved neighborhood. We observe the same trend when expression divergence data were analyzed from six different brain parts that are equivalent between human and chimpanzee. Additionally, we find enrichment for genes with altered neighborhood to be expressed in a tissue-specific manner in the human brain. These results suggest that expression divergence induced by this mechanism could have contributed to the phenotypic differences between human and chimpanzee. We propose that, in addition to other molecular mechanisms, change in genomic neighborhood is an important factor that drives transcriptome evolution.

RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays

Ultra-high-throughput sequencing is emerging as an attractive alternative to microarrays for genotyping, analysis of methylation patterns, and identification of transcription factor binding sites. Here, we describe an application of the Illumina sequencing (formerly Solexa sequencing) platform to study mRNA expression levels. Our goals were to estimate technical variance associated with Illumina sequencing in this context and to compare its ability to identify differentially expressed genes with existing array technologies. To do so, we estimated gene expression differences between liver and kidney RNA samples using multiple sequencing replicates, and compared the sequencing data to results obtained from Affymetrix arrays using the same RNA samples. We find that the Illumina sequencing data are highly replicable, with relatively little technical variation, and thus, for many purposes, it may suffice to sequence each mRNA sample only once (i.e., using one lane). The information in a single lane of Illumina sequencing data appears comparable to that in a single array in enabling identification of differentially expressed genes, while allowing for additional analyses such as detection of low-expressed genes, alternative splice variants, and novel transcripts. Based on our observations, we propose an empirical protocol and a statistical framework for the analysis of gene expression using ultra-high-throughput sequencing technology.

Gene response profiles for Daphnia pulex exposed to the environmental stressor cadmium reveals novel crustacean metallothioneins

Background

Genomic research tools such as microarrays are proving to be important resources to study the complex regulation of genes that respond to environmental perturbations. A first generation cDNA microarray was developed for the environmental indicator species Daphnia pulex, to identify genes whose regulation is modulated following exposure to the metal stressor cadmium. Our experiments revealed interesting changes in gene transcription that suggest their biological roles and their potentially toxicological features in responding to this important environmental contaminant.

Results

Our microarray identified genes reported in the literature to be regulated in response to cadmium exposure, suggested functional attributes for genes that share no sequence similarity to proteins in the public databases, and pointed to genes that are likely members of expanded gene families in the Daphnia genome. Genes identified on the microarray also were associated with cadmium induced phenotypes and population-level outcomes that we experimentally determined. A subset of genes regulated in response to cadmium exposure was independently validated using quantitative-realtime (Q-RT)-PCR. These microarray studies led to the discovery of three genes coding for the metal detoxication protein metallothionein (MT). The gene structures and predicted translated sequences of D. pulex MTs clearly place them in this gene family. Yet, they share little homology with previously characterized MTs.

Conclusion

The genomic information obtained from this study represents an important first step in characterizing microarray patterns that may be diagnostic to specific environmental contaminants and give insights into their toxicological mechanisms, while also providing a practical tool for evolutionary, ecological, and toxicological functional gene discovery studies. Advances in Daphnia genomics will enable the further development of this species as a model organism for the environmental sciences.

Functional genomics of the pregnant uterus: from expectations to reality, a compilation of studies in the myometrium

Background

Studies on the human myometrium have reported on different microarrays containing different sets of genes or ESTs. However each study profiled only a small number of patients due to various constraints. More profiling information would be an addition to our knowledge base of parturition.

Methods

We compiled from five human studies, transcriptional differences between the non pregnant myometrium (NP), preterm myometrium (PTNIL), term myometrium not in labor (TNIL) and term myometrium in labor (TIL). Software modules developed by the Draghici's group at Wayne State University (Detroit, MI, USA) were used to propose a hierarchical list of several KEGG pathways most likely adjusted to changes observed in microarray experiments.

Results

The differential expression of 118 genes could be dispatched in 14 main KEGG pathways that were the most representative of the changes seen in NP and PTNIL, versus TNIL or TIL. Despite the potential of multiple pitfalls inherent to the use of the microarray technology, gene module analysis of the myometrial transcriptome reveals the activation of precise signaling pathways, some of which may have been under evaluated.

Conclusion

The remodelling and maturation processes that the uterus undergoes in pregnancy appear clearly as phenomena which last during the full course of gestation. It is attested by the nature of the main signaling pathways represented, in the comparison of the PTNIL versus TNIL uterus. Comparatively, the onset of labor is a phenomenon which remains less well characterized by these methods of analysis, possibly because it is a phenomenon occurring in too short a window to have been grasped by the studies carried out up to now.

Experimental selection for Drosophila survival in extremely low O(2) environment

BACKGROUND

Cellular hypoxia, if severe enough, results usually in injury or cell death. Our research in this area has focused on the molecular mechanisms underlying hypoxic tissue injury to explore strategies to prevent injury or enhance tolerance. The current experiments were designed to determine the genetic basis for adaptation to long term low O(2) environments.

METHODOLOGY/PRINCIPAL FINDINGS

With long term experimental selection over many generations, we obtained a Drosophila melanogaster strain that can live perpetually in extremely low, normally lethal, O(2) condition (as low as 4% O(2)). This strain shows a dramatic phenotypic divergence from controls, including a decreased recovery time from anoxic stupor, a higher rate of O(2 )consumption in hypoxic conditions, and a decreased body size and mass due to decreased cell number and size. Expression arrays showed that about 4% of the Drosophila genome altered in expression and about half of the alteration was down-regulation. The contribution of some altered transcripts to hypoxia tolerance was examined by testing the survival of available corresponding P-element insertions (and their excisions) under extremely low O(2) conditions. We found that down-regulation of several candidate genes including Best1, broad, CG7102, dunce, lin19-like and sec6 conferred severe hypoxia tolerance in Drosophila.

CONCLUSIONS/SIGNIFICANCE

We have identified a number of genes that play an important role in the survival of a selected Drosophila strain in extremely low O(2) conditions, selected by decreasing O(2) availability over many generations. Because of conservation of pathways, we believe that such genes are critical in hypoxia adaptation in physiological or pathological conditions not only in Drosophila but also in mammals.

Parallel single nucleotide polymorphism genotyping by surface invasive cleavage with universal detection

Large-scale investigations of sequence variation within the human species will provide information about the basis of heritable variation in disease susceptibility and human migration. The surface invader assay (an adaptation of the invasive cleavage reaction to an array format) is capable of exquisitely sensitive and specific detection of genetic variation. It is shown here that this genotyping technology can be multiplexed in a DNA array format, permitting the parallel analysis of a panel of single nucleotide polymorphisms (SNPs) directly from an unamplified genomic DNA target. In addition, a "universal" mode of detection was developed that makes use of a mixture of degenerate templates for DNA ligation to the surface-bound cleaved oligonucleotides and thereby makes this strategy amenable to any desired SNP site or combination of SNP sites, without regard to their particular DNA sequences. This approach was demonstrated on a proof-of-principle scale using small DNA arrays to genotype 6 SNP markers in the PTPN1 gene and 10 mutations in the cystic fibrosis transmembrane conductance regulator gene. This ability to analyze many different genetic variations in parallel, directly from unamplified human genomic DNA samples, lays the groundwork for the development of high-density arrays able to analyze hundreds of thousands or even millions of SNPs.

Genome-wide patterns of expression in Drosophila pure species and hybrid males. II. Examination of multiple-species hybridizations, platforms, and life cycle stages

Species often produce sterile hybrids early in their evolutionary divergence, and some evidence suggests that hybrid sterility may be associated with deviations or disruptions in gene expression. In support of this idea, many studies have shown that a high proportion of male-biased genes are underexpressed, compared with non-sex-biased genes, in sterile F1 male hybrids of Drosophila species. In this study, we examined and compared patterns of misexpression in sterile F1 male hybrids of Drosophila simulans and 2 of its sibling species, Drosophila mauritiana and Drosophila sechellia, at both the larval and adult life stages. We analyzed hybrids using both commercial Drosophila melanogaster microarrays and arrays we developed from reverse transcriptase-polymerase chain reactions of spermatogenesis and reproduction-related transcripts from these species (sperm array). Although the majority of misexpressed transcripts were underexpressed, a disproportionate number of the overexpressed transcripts were located on the X chromosome. We detected a high overlap in the genes misexpressed between the 2 species pairs, and our sperm array was better at detecting such misexpression than the D. melanogaster array, suggesting possible weaknesses in the use of an array designed from another species. We found only minimal misexpression in the larval samples with the sperm array, suggesting that disruptions in spermatogenesis occur after this life stage. Further study of these misexpressed loci may allow us to identify precisely where disruptions in the spermatogenesis pathway occur.

Adaptation to environmental stress: a rare or frequent driver of speciation?

Recent results of evolutionary genomics and other research programmes indicate an important role for environment-dependent selection in speciation, but the conceptual frameworks of speciation genetics and environmental stress physiology have not been fully integrated. Only a small number of model systems have been established for cross-disciplinary studies of this type in animals and plants. In these taxa (e.g. Drosophila and Arabidopsis/Arabis), studies of the mechanistic basis of various stress responses are increasingly combined with attempts to understand their evolutionary consequences. Our understanding of the role of environmental stress in speciation would benefit from studies of a larger variety of taxa. We pinpoint areas for future study and predict that in many taxa 'broad' hybrid zones maintained by ecological selection will be valuable venues for addressing the link between environmental stress, adaptation, and speciation.

Multi-species microarrays reveal the effect of sequence divergence on gene expression profiles

Interspecies comparisons of gene expression levels will increase our understanding of the evolution of transcriptional mechanisms and help to identify targets of natural selection. This approach holds particular promise for apes, as many human-specific adaptations are thought to result from differences in gene expression rather than in coding sequence. To date, however, all studies directly comparing interspecies gene expression have been performed on single-species arrays, so that it has been impossible to distinguish differential hybridization due to sequence mismatches from underlying expression differences. To evaluate the severity of this potential problem, we constructed a new multiprimate cDNA array using probes from human, chimpanzee, orangutan, and rhesus. We find a large effect of sequence divergence on hybridization signal, even in the closest pair of species, human and chimpanzee. By comparing single-species array analyses with results from multispecies arrays, we examine how estimates of differential gene expression are affected by sequence divergence. Our results indicate that naive use of single-species arrays in direct interspecies comparisons can yield spurious results.

Functional genomics thickens the biological plot

New functional genomic tools are enabling researchers to draw on a large cast of 'non-model' organisms to help set the stage for ecological and evolutionary discovery.

Development and phenotypic correlations: the evolution of tooth shape in Sorex araneus

Do morphogenetic processes cause common patterns of phenotypic covariation, and do those patterns evolve over microevolutionary timescales? Evolution of molar shape variance-covariance (P) matrixes was studied in five populations of the common shrew, Sorex araneus. P matrix evolution was assessed using matrix correlation, matrix disparity, and common principal component analysis (CPCA). Significant changes in covariance structure were found among the populations, but the differences were small. A computer model was used to estimate the theoretical covariance introduced into the phenotype by developmental interactions. Molar developmental processes explained some of the covariance in the shrew samples, especially as measured by matrix correlation, but the proportion was relatively small. Developmental principal components (PCs) were only infrequently associable with common principal components. The results suggest that molar shape P matrixes can evolve quickly in a manner only loosely constrained by development, and that their shared covariance is probably dominated by factors more proximate than development. Rarefaction showed that sample size severely affected P comparisons when n < 15 for matrix correlation and disparity, and when n < 30 for CPCA. Among CPCA evaluation criteria, Akaike Information Criterion performed better than jump-up at n < 30, but worse at n > 30.

Changes in gene expression as biochemical adaptations to environmental change: a tribute to Peter Hochachka

Changes in gene expression are likely to play a critical role in both acclimation and adaptation to a changing environment. There is a rapidly growing body of literature implicating quantitative changes in gene expression during acclimation to environmental change, but less is known about the role of qualitative changes in gene expression, such as switching between alternative isoforms. Alternative isoforms can arise via gene duplication, alternative splicing, or alternative promoter usage. Organisms that have undergone recent genome duplication events may make use of environment-specific isoforms coded by multiple genes, but their role in other organisms is less well known. However, recent data suggest that isoforms arising from alternative splicing may be an under-appreciated source of physiological variation. The role of changes in gene expression during evolutionary adaptation has received comparatively limited attention, but novel approaches to addressing the adaptive significance of changes in gene expression have been applied to a few cases of differences in gene expression among taxa. Recent advances in genomics, including microarray technology, knock-out and knock-down approaches, and the wealth of data coming from large-scale sequencing projects have provided (and will continue to provide at ever increasing rates) new insights into these classic questions in comparative biochemistry.

E pluribus unum, ex uno plura: quantitative and single-gene perspectives on the study of behavior

Genetic studies of behavior have traditionally come in two flavors: quantitative genetic studies of natural variants and single-gene studies of induced mutants. Each employed different techniques and methods of analysis toward the common, ultimate goal of understanding how genes influence behavior. With the advent of new genomic technologies, and also the realization that mechanisms underlying behavior involve a considerable degree of complex gene interaction, the traditionally separate strands of behavior genetics are merging into a single, synthetic strategy.

Darwin to DNA, molecules to morphology: the end of classical population genetics and the road ahead

Molecular reductionism has permeated all of biology and because of successive new technical breakthroughs it has succeeded in unraveling the structural details of genes and genomes. The molecular revolution has reached its reductionist limit, i.e., the study of component parts in isolation, and is ready to come full circle through genomics, proteomics, and gene expression studies back to the phenotype and bring evolutionary biology to confront the Darwinian paradigm, the relationship between gene, organism, and environment. Classical experimental population genetics, dealing with genetic polymorphism and estimation of selection coefficients on a gene-by-gene basis, is coming to an end and a new era of interdisciplinary and interactive biology focusing on dynamic relationships among gene, organism, and environment has begun. In the new population genetics, there will be a shift in focus from single genes to gene networks, from gene-structure to gene-regulation, from additivity to epistasis, and from simple phenotypes to gene-interaction networks and the evolution of complex and modular systems.

The evolution of molecular genetic pathways and networks

There is growing interest in the evolutionary dynamics of molecular genetic pathways and networks, and the extent to which the molecular evolution of a gene depends on its position within a pathway or network, as well as over-all network topology. Investigations on the relationships between network organization, topological architecture and evolutionary dynamics provide intriguing hints as to how networks evolve. Recent studies also suggest that genetic pathway and network structures may influence the action of evolutionary forces, and may play a role in maintaining phenotypic robustness in organisms.

Surface Amplification of Invasive Cleavage Products

A major focus of current efforts in genomics is to elucidate the genetic variations extent within the human population, and to study the effects of these variations upon the human system. The most common type of genetic variations are the single nucleotide polymorphisms (SNPs), which occur every 500-1000 nt in the genome. Large-scale population association studies to study the biological or medical significance of such variations may require the analysis of hundreds of thousands of SNPs on thousands of individuals. We are pursuing development of an approach to large-scale SNP analysis that combines the specificity of invasive cleavage reactions with the parallelism of high density DNA arrays. A surface-immobilized probe oligonucleotide is specifically cleaved in the presence of a complementary target sequence in unamplified human genomic DNA, yielding a 5' phosphate group. High sensitivity detection of this reaction product on the surface is achieved by the use of rolling circle amplification, with an approximate concentration detection limit of 10 fM target DNA. This combination of very specific surface cleavage and highly sensitive surface detection will make possible the rapid and parallel analysis of genetic variations across large populations.

Application of microarray technology in environmental and comparative physiology

DNA microarray technology is revolutionizing many aspects of biological research, allowing the expression of many thousands of gene transcripts to be monitored simultaneously. This provides powerful tools for the genome-wide correlation of gene transcript levels with physiological responses and alterations in physiological states. To date, microarray analyses have been applied almost exclusively to a few model species for which the abundant gene sequence data permit the fabrication of whole-genome microarrays. However, many interesting physiological traits and responses are poorly expressed or absent in model species and may be better illustrated in nonmodel organisms. Comparative approaches to understanding function traditionally focus on species that by virtue of their unusual adaptations, lifestyles, and phylogeny are particularly suited to address a specific biological process or problem. In this review, we show that microarray technology can be successfully applied to these nonmodel species and used to generate new insights of comparative and evolutionary significance into animal function.

Evolution of gene expression in the Drosophila melanogaster subgroup

Little is known about broad patterns of variation and evolution of gene expression during any developmental process. Here we investigate variation in genome-wide gene expression among Drosophila simulans, Drosophila yakuba and four strains of Drosophila melanogaster during a major developmental transition--the start of metamorphosis. Differences in gene activity between these lineages follow a phylogenetic pattern, and 27% of all of the genes in these genomes differ in their developmental gene expression between at least two strains or species. We identify, on a gene-by-gene basis, the evolutionary forces that shape this variation and show that, both within the transcriptional network that controls metamorphosis and across the whole genome, the expression changes of transcription factor genes are relatively stable, whereas those of their downstream targets are more likely to have evolved. Our results demonstrate extensive evolution of developmental gene expression among closely related species.

Evolution of drug resistance in Candida albicans

The widespread deployment of antimicrobial agents in medicine and agriculture is nearly always followed by the evolution of resistance to these agents in the pathogen. With the limited availability of antifungal drugs and the increasing incidence of opportunistic fungal infections, the emergence of drug resistance in fungal pathogens poses a serious public health concern. Antifungal drug resistance has been studied most extensively with the yeast Candida albicans owing to its importance as an opportunistic pathogen and its experimental tractability relative to other medically important fungal pathogens. The emergence of antifungal drug resistance is an evolutionary process that proceeds on temporal, spatial, and genomic scales. This process can be observed through epidemiological studies of patients and through population-genetic studies of pathogen populations. Population-genetic studies rely on sampling of the pathogen in patient populations, serial isolations of the pathogen from individual patients, or experimental evolution of the pathogen in nutrient media or in animal models. Predicting the evolution of drug resistance is fundamental to prolonging the efficacy of existing drugs and to strategically developing and deploying novel drugs.

Imaging optical sensor arrays

Imaging optical fibres have been etched to prepare microwell arrays. These microwells have been loaded with sensing materials such as bead-based sensors and living cells to create high-density sensor arrays. The extremely small sizes and volumes of the wells enable high sensitivity and high information content sensing capabilities.

Identification of genes involved in Drosophila melanogaster geotaxis, a complex behavioral trait

Identifying the genes involved in polygenic traits has been difficult. In the 1950s and 1960s, laboratory selection experiments for extreme geotaxic behavior in fruit flies established for the first time that a complex behavioral trait has a genetic basis. But the specific genes responsible for the behavior have never been identified using this classical model. To identify the individual genes involved in geotaxic response, we used cDNA microarrays to identify candidate genes and assessed fly lines mutant in these genes for behavioral confirmation. We have thus determined the identities of several genes that contribute to the complex, polygenic behavior of geotaxis.

Have microarrays failed to deliver for developmental biology?

Comprehensive microarrays covering large numbers of the predicted expressed transcripts for some invertebrates and vertebrates have been available for some time. Despite predictions that this technology will transform biology, to date there have been few published studies using microarrays to generate novel insights in developmental biology.