Publications

comparing low coverage random shotgun sequence data from brassica oleracea and oryza sativa genome sequence for their ability to add to the annotation of arabidopsis thaliana.	since the completion of the arabidopsis thaliana genome sequence, there is an ongoing effort to annotate the genome as accurately as possible. comparing genome sequences of related species complements the current annotation strategies by identifying genes and improving gene structure. a total of 595,321 brassica oleracea shotgun reads were sequenced by tigr (the institute for genome research) and the collaboration of washington university and cold spring harbor. vicogenta (a genome viewer based ...	15805491
genetic testing and common disorders in a public health framework: how to assess relevance and possibilities. background document to the eshg recommendations on genetic testing and common disorders.		21412252
the ecoresponsive genome of daphnia pulex.	we describe the draft genome of the microcrustacean daphnia pulex, which is only 200 megabases and contains at least 30,907 genes. the high gene count is a consequence of an elevated rate of gene duplication resulting in tandem gene clusters. more than a third of daphnia's genes have no detectable homologs in any other available proteome, and the most amplified gene families are specific to the daphnia lineage. the coexpansion of gene families interacting within metabolic pathways suggests that ...	21292972
pd-catalyzed amination as an alternative to nucleophilic aromatic substitution for the synthesis of n-alkyltacrines and analogues.	a reliable pd-catalyzed amination protocol is described for the synthesis of n-alkyltacrines and analogues. the josiphos ligand cypftbu was found to provide optimum yields: 16 examples are given. compared to the typical high-temperature nucleophilic aromatic substitution (nas) routes, pd-catalyzed aminations proceed at significantly lower reaction temperatures, and enable the synthesis of otherwise inaccessible products.	21286231
nk cells and immune "memory".	immunological memory is a hallmark of the adaptive immune system. however, the ability to remember and respond more robustly against a second encounter with the same pathogen has been described in organisms lacking t and b cells. recently, nk cells have been shown to mediate ag-specific recall responses in several different model systems. although nk cells do not rearrange the genes encoding their activating receptors, nk cells experience a selective education process during development, undergo ...	21289313
out of thin air: sensory detection of oxygen and carbon dioxide.	oxygen (o₂) and carbon dioxide (co₂) levels vary in different environments and locally fluctuate during respiration and photosynthesis. recent studies in diverse animals have identified sensory neurons that detect these external variations and direct a variety of behaviors. detection allows animals to stay within a preferred environment as well as identify potential food or dangers. the complexity of sensation is reflected in the fact that neurons compartmentalize detection into increases, decre ...	21262460
functional architecture of olfactory ionotropic glutamate receptors.	ionotropic glutamate receptors (iglurs) are ligand-gated ion channels that mediate chemical communication between neurons at synapses. a variant iglur subfamily, the ionotropic receptors (irs), was recently proposed to detect environmental volatile chemicals in olfactory cilia. here, we elucidate how these peripheral chemosensors have evolved mechanistically from their iglur ancestors. using a drosophila model, we demonstrate that irs act in combinations of up to three subunits, comprising indiv ...	21220098
3d tracking of mating events in wild swarms of the malaria mosquito anopheles gambiae.	we describe an automated tracking system that allows us to reconstruct the 3d kinematics of individual mosquitoes in swarms of anopheles gambiae. the inputs to the tracking system are video streams recorded from a stereo camera system. the tracker uses a two-pass procedure to automatically localize and track mosquitoes within the swarm. a human-in-the-loop step verifies the estimates and connects broken tracks. the tracker performance is illustrated using footage of mating events filmed in mali ...	22254411
nf-κb/rel proteins and the humoral immune responses of drosophila melanogaster.	nuclear factor-κb (nf-κb)/rel transcription factors form an integral part of innate immune defenses and are conserved throughout the animal kingdom. studying the function, mechanism of activation and regulation of these factors is crucial for understanding host responses to microbial infections. the fruit fly drosophila melanogaster has proved to be a valuable model system to study these evolutionarily conserved nf-κb mediated immune responses. drosophila combats pathogens through humoral and ce ...	20852987
function and evolution of sex determination mechanisms, genes and pathways in insects.	animals have evolved a bewildering diversity of mechanisms to determine the two sexes. studies of sex determination genes--their history and function--in non-model insects and drosophila have allowed us to begin to understand the generation of sex determination diversity. one common theme from these studies is that evolved mechanisms produce activities in either males or females to control a shared gene switch that regulates sexual development. only a few small-scale changes in existing and dupl ...	21110346
gene discovery and expression profile analysis through sequencing of expressed sequence tags from different developmental stages of the chytridiomycete blastocladiella emersonii.	blastocladiella emersonii is an aquatic fungus of the chytridiomycete class which diverged early from the fungal lineage and is notable for the morphogenetic processes which occur during its life cycle. its particular taxonomic position makes this fungus an interesting system to be considered when investigating phylogenetic relationships and studying the biology of lower fungi. to contribute to the understanding of the complexity of the b. emersonii genome, we present here a survey of expressed ...	15701807
structural and sequence motifs of protein (histone) methylation enzymes.	with genome sequencing nearing completion for the model organisms used in biomedical research, there is a rapidly growing appreciation that proteomics, the study of covalent modification to proteins, and transcriptional regulation will likely dominate the research headlines in the next decade. protein methylation plays a central role in both of these fields, as several different residues (arg, lys, gln) are methylated in cells and methylation plays a central role in the "histone code" that regul ...	15869391
comparative genome sequencing of drosophila pseudoobscura: chromosomal, gene, and cis-element evolution.	we have sequenced the genome of a second drosophila species, drosophila pseudoobscura, and compared this to the genome sequence of drosophila melanogaster, a primary model organism. throughout evolution the vast majority of drosophila genes have remained on the same chromosome arm, but within each arm gene order has been extensively reshuffled, leading to a minimum of 921 syntenic blocks shared between the species. a repetitive sequence is found in the d. pseudoobscura genome at many junctions b ...	15632085
silkdb: a knowledgebase for silkworm biology and genomics.	the silkworm knowledgebase (silkdb) is a web-based repository for the curation, integration and study of silkworm genetic and genomic data. with the recent accomplishment of a approximately 6x draft genome sequence of the domestic silkworm (bombyx mori), silkdb provides an integrated representation of the large-scale, genome-wide sequence assembly, cdnas, clusters of expressed sequence tags (ests), transposable elements (tes), mutants, single nucleotide polymorphisms (snps) and functional annota ...	15608225
the systers protein family database in 2005.	the systers project aims to provide a meaningful partitioning of the whole protein sequence space by a fully automatic procedure. a refined two-step algorithm assigns each protein to a family and a superfamily. the sequence data underlying systers release 4 now comprise several protein sequence databases derived from completely sequenced genomes (ensembl, tair, sgd and genedb), in addition to the comprehensive swiss-prot/trembl databases. the systers web server (http://systers.molgen.mpg.de) pro ...	15608183
juvenile immune system activation induces a costly upregulation of adult immunity in field crickets gryllus campestris.	inducible immune defence may allow organisms a state-dependent upregulation of costly immunity in order to minimize the risk of anticipated future parasitism. the basic costs of elevated immune activity might involve a reduction in other fitness-related traits as well as an increased risk of immunopathology. in male field crickets gryllus campestris we experimentally investigated the condition-dependent effects of immune system activation in nymphs on immunity and physiological condition during ...	15875571
the identities of sym-2, sym-3 and sym-4, three genes that are synthetically lethal with mec-8 in caenorhabditis elegans.	on the basis of synthetic lethality, five genes in caenorhabditis elegans are known to be redundant with the mec-8 gene, which encodes a protein that contains two copies of an rna recognition motif (rrm) and affects alternative rna splicing. the molecular identities of two of the redundant genes, sym-1 and sym-5, were previously reported. the remaining three genes have now been cloned, and their synthetically lethal phenotypes with mec-8 are described in more detail. animals homozygous for mec-8 ...	15579686
drosophila klarsicht has distinct subcellular localization domains for nuclear envelope and microtubule localization in the eye.	the drosophila klarsicht (klar) gene is required for developmentally regulated migrations of photoreceptor cell nuclei in the eye. klar encodes a large ( approximately 250 kd) protein with only one recognizable amino acid sequence motif, a kash (klar, anc-1, syne-1 homology) domain, at its c terminus. it has been proposed that klar facilitates nuclear migration by linking the nucleus to the microtubule organizing center (mtoc). here we perform genetic and immunohistochemical experiments that pro ...	15579692
drosophila crinkled, mutations of which disrupt morphogenesis and cause lethality, encodes fly myosin viia.	myosin viis provide motor function for a wide range of eukaryotic processes. we demonstrate that mutations in crinkled (ck) disrupt the drosophila myosin viia heavy chain. the ck/myoviia protein is present at a low level throughout fly development and at the same level in heads, thoraxes, and abdomens. severe ck alleles, likely to be molecular nulls, die as embryos or larvae, but all allelic combinations tested thus far yield a small fraction of adult "escapers" that are weak and infertile. scan ...	15579689
reciprocal regulation of glutathione s-transferase spliceforms and the drosophila c-jun n-terminal kinase pathway components.	in mammalian systems, detoxification enzymes of the gst (glutathione s-transferase) family regulate jnk (c-jun n-terminal kinase) signal transduction by interaction with jnk itself or other proteins upstream in the jnk pathway. in the present study, we have studied gsts and their interaction with components of the jnk pathway from diptera. we have evaluated the effects of four delta class anopheles dirus gsts, gstd1-1, gstd2-2, gstd3-3 and gstd4-4, on the activity of full-length recombinant dros ...	15250826
caenorhabditis elegans atx-2 promotes germline proliferation and the oocyte fate.	in the caenorhabditis elegans germline, proliferation is induced by notch-type signaling. entry of germ cells into meiosis is triggered by activity of the gld-1 and gld-2 pathways, which function redundantly to promote meiosis and/or inhibit proliferation. activation of the germline notch-type receptor, glp-1, ultimately inhibits the activities of the gld-1 and gld-2 pathways. we previously identified several ego (enhancer of glp-1) genes that promote germline proliferation and interact genetica ...	15514056
fast and effective prediction of microrna/target duplexes.	micrornas (mirnas) are short rnas that post-transcriptionally regulate the expression of target genes by binding to the target mrnas. although a large number of animal mirnas has been defined, only a few targets are known. in contrast to plant mirnas, which usually bind nearly perfectly to their targets, animal mirnas bind less tightly, with a few nucleotides being unbound, thus producing more complex secondary structures of mirna/target duplexes. here, we present a program, rna-hybrid, that pre ...	15383676
bitis gabonica (gaboon viper) snake venom gland: toward a catalog for the full-length transcripts (cdna) and proteins.	the venom gland of the snake bitis gabonica (gaboon viper) was used for the first time to construct a unidirectional cdna phage library followed by high-throughput sequencing and bioinformatic analysis. hundreds of cdnas were obtained and clustered into contigs. we found mostly novel full-length cdna coding for metalloproteases (p-ii and p-iii classes), lys49-phospholipase a2, serine proteases with essential mutations in the active site, kunitz protease inhibitors, several c-type lectins, bradyk ...	15276202
synaptotagmins are trafficked to distinct subcellular domains including the postsynaptic compartment.	the synaptotagmin family has been implicated in calcium-dependent neurotransmitter release, although synaptotagmin 1 is the only isoform demonstrated to control synaptic vesicle fusion. here, we report the characterization of the six remaining synaptotagmin isoforms encoded in the drosophila genome, including homologues of mammalian synaptotagmins 4, 7, 12, and 14. like synaptotagmin 1, synaptotagmin 4 is ubiquitously present at synapses, but localizes to the postsynaptic compartment. the remain ...	15263020
u2af homology motifs: protein recognition in the rrm world.	recent structures of the heterodimeric splicing factor u2 snrnp auxiliary factor (u2af) have revealed two unexpected examples of rna recognition motif (rrm)-like domains with specialized features for protein recognition. these unusual rrms, called u2af homology motifs (uhms), represent a novel class of protein recognition motifs. defining a set of rules to distinguish traditional rrms from uhms is key to identifying novel uhm family members. here we review the critical sequence features necessar ...	15231733
a phylogeny of caenorhabditis reveals frequent loss of introns during nematode evolution.	since introns were discovered 26 years ago, people have wondered how changes in intron/exon structure occur, and what role these changes play in evolution. to answer these questions, we have begun studying gene structure in nematodes related to caenorhabditis elegans. as a first step, we cloned a set of five genes from six different caenorhabditis species, and used their amino acid sequences to construct the first detailed phylogeny of this genus. our data indicate that nematode introns are lost ...	15231741
principles of microrna-target recognition.	micrornas (mirnas) are short non-coding rnas that regulate gene expression in plants and animals. although their biological importance has become clear, how they recognize and regulate target genes remains less well understood. here, we systematically evaluate the minimal requirements for functional mirna-target duplexes in vivo and distinguish classes of target sites with different functional properties. target sites can be grouped into two broad categories. 5' dominant sites have sufficient co ...	15723116
commentary on cam and nk cells by kazuyoshi takeda and ko okumura.		15257323
emerging genomic and proteomic evidence on relationships among the animal, plant and fungal kingdoms.	sequence-based molecular phylogenies have provided new models of early eukaryotic evolution. this includes the widely accepted hypothesis that animals are related most closely to fungi, and that the two should be grouped together as the opisthokonta. although most published phylogenies have supported an opisthokont relationship, a number of genes contain a tree-building signal that clusters animal and green plant sequences, to the exclusion of fungi. the alternative tree-building signal is espec ...	15629046
genewise and genomewise.	we present two algorithms in this paper: genewise, which predicts gene structure using similar protein sequences, and genomewise, which provides a gene structure final parse across cdna- and est-defined spliced structure. both algorithms are heavily used by the ensembl annotation system. the genewise algorithm was developed from a principled combination of hidden markov models (hmms). both algorithms are highly accurate and can provide both accurate and complete gene structures when used with th ...	15123596
a functional domain of dof that is required for fibroblast growth factor signaling.	signal transduction by fibroblast growth factor (fgf) receptors in drosophila depends upon the intracellular protein dof, which has been proposed to act downstream of the receptors and upstream of ras. dof is the product of a fast-evolving gene whose vertebrate homologs, bcap and bank, are involved in signaling downstream of the b-cell receptor. mapping functional domains within dof revealed that neither of its potential interaction motifs, the ankyrin repeats and the coiled coil, is essential f ...	14993266
redox sensing: orthogonal control in cell cycle and apoptosis signalling.	living systems have three major types of cell signalling systems that are dependent upon high-energy chemicals, redox environment and transmembranal ion-gating mechanisms. development of integrated systems biology descriptions of cell signalling require conceptual models incorporating all three. recent advances in redox biology show that thiol-disulphide redox systems are regulated under dynamic, nonequilibrium conditions, progressively oxidized with the life cycle of cells and distinct in terms ...	20964735
genome-wide patterns of divergence during speciation: the lake whitefish case study.	the nature, size and distribution of the genomic regions underlying divergence and promoting reproductive isolation remain largely unknown. here, we summarize ongoing efforts using young (12 000 yr bp) species pairs of lake whitefish (coregonus clupeaformis) to expand our understanding of the initial genomic patterns of divergence observed during speciation. our results confirmed the predictions that: (i) on average, phenotypic quantitative trait loci (pqtl) show higher f(st) values and are more ...	22201165
pyramus and thisbe: fgf genes that pattern the mesoderm of drosophila embryos.	the heartless (htl) fgf receptor is required for the differentiation of a variety of mesodermal tissues in the drosophila embryo, yet its ligand is not known. here we identify two new fgf genes, thisbe (ths) and pyramus (pyr), which probably encode the elusive ligands for this receptor. the two genes exhibit dynamic patterns of expression in epithelial tissues adjacent to htl-expressing mesoderm derivatives, including the neurogenic ectoderm, stomadeum, and hindgut. embryos that lack ths+ and py ...	15075295
mapping rice field anopheline breeding habitats in mali, west africa, using landsat etm+ sensor data.	the aim of this study was to determine whether remotely sensed data could be used to identify rice-related malaria vector breeding habitats in an irrigated rice growing area near niono, mali. early stages of rice growth show peak larval production, but landsat sensor data are often obstructed by clouds during the early part of the cropping cycle (rainy season). in this study, we examined whether a classification based on two landsat enhanced thematic mapper (etm)+ scenes acquired in the middle o ...	18084628
genome-wide analysis of retrogene polymorphisms in drosophila melanogaster.	gene duplication via retrotransposition has been shown to be an important mechanism in evolution, affecting gene dosage and allowing for the acquisition of new gene functions. although fixed retrotransposed genes have been found in a variety of species, very little effort has been made to identify retrogene polymorphisms. here, we examine 37 illumina-sequenced north american drosophila melanogaster inbred lines and present the first ever data set and analysis of polymorphic retrogenes in drosoph ...	22135405
comparative evolutionary genomics of the stat family of transcription factors.	the stat signaling pathway is one of the seven common pathways that govern cell fate decisions during animal development. comparative genomics revealed multiple incidences of stat gene duplications throughout metazoan evolutionary history. while pseudogenization is a frequent fate of duplicated genes, many of these stat duplications evolved into novel genes through rapid sequence diversification and neofunctionalization. additionally, the core of stat gene regulatory networks, comprising stat1 t ...	24058748
the redox biology of schistosome parasites and applications for drug development.	schistosomiasis caused by schistosoma spp. is a serious public health concern, especially in sub-saharan africa. praziquantel is the only drug currently administrated to treat this disease. however, praziquantel-resistant parasites have been identified in endemic areas and can be generated in the laboratory. therefore, it is essential to find new therapeutics. antioxidants are appealing drug targets. in order to survive in their hosts, schistosomes are challenged by reactive oxygen species from ...	22607149
aqueous neem extract versus neem powder on culex quinquefasciatus: implications for control in anthropogenic habitats.	control programs using conventional insecticides to target anthropogenic mosquito habitats are very expensive because these habitats are widespread, particularly in cities of most african countries. additionally, there are serious environmental concerns regarding large-scale application of most conventional insecticides. clearly there is a need for alternative methods that are more effective, less expensive, and environmentally friendly. one such method would be the application of preparations m ...	22233153
regime shifts and heterogeneous trends in malaria time series from western kenya highlands.	large malaria epidemics in the east african highlands during the mid and late 1990s kindled a stream of research on the role that global warming might have on malaria transmission. most of the inferences using temporal information have been derived from a malaria incidence time series from kericho. here, we report a detailed analysis of 5 monthly time series, between 15 and 41 years long, from west kenya encompassing an altitudinal gradient along lake victoria basin. we found decreasing, but het ...	21996447
mass spectrometric imaging for biomedical tissue analysis.		20423155
characterization of evolutionarily conserved micrornas in amphioxus.	amphioxus is an extant species closest to the ancestry of vertebrates. observation of microrna (mirna) distribution of amphioxus would lend some hints for evolutionary research of vertebrates. in this study, using the publicly available scaffold data of the florida amphioxus (branchiostoma floridae) genome, we screened and characterized homologs of mirnas that had been identified in other species. in total, 68 pieces of such homologs were obtained and classified into 33 families. most of these m ...	20451158
unusual features of the drosophila melanogaster telomere transposable element het-a are conserved in drosophila yakuba telomere elements.	het-a was the first transposable element shown to have a bona fide role in chromosome structure, maintenance of telomeres in drosophila melanogaster. het-a has hallmarks of non-long-terminal-repeat (non-ltr) retrotransposable elements but also has several unique features. we have now isolated het-a elements from drosophila yakuba, showing that the retrotransposon mechanism of telomere maintenance predates the separation of d. melanogaster and d. yakuba (5-15 million years ago). het-a elements fr ...	9520442
codon reassignment and amino acid composition in hemichordate mitochondria.	in the mitochondrial genome of the hemichordate balanoglossus carnosus, the codon aaa, which is assigned to lysine in most metazoans but to asparagine in echinoderms, is absent. furthermore, the lysine trna gene carries an anticodon substitution that renders its gene product unable to decode aaa codons, whereas the asparagine trna gene has not changed to encode a trna with the ability to recognize aaa codons. thus, the hemichordate mitochondrial genome can be regarded as an intermediate in the p ...	9520430
30 years of science and technology: the example of malaria.		24293742
[not available].		13404430
expressed sequence tags from cephalic chemosensory organs of the northern walnut husk fly, rhagoletis suavis, including a putative canonical odorant receptor.	rhagoletis fruit flies are important both as major agricultural pests and as model organisms for the study of adaptation to new host plants and host race formation. response to fruit odor plays a critical role in such adaptation. to better understand olfaction in rhagoletis, an expressed sequence tag (est) study was carried out on the antennae and maxillary palps of rhagoletis suavis (loew) (diptera: tephritidae), a common pest of walnuts in eastern united states. after cdna cloning and sequenci ...	20569128
role of g-proteins in odor-sensing and co2-sensing neurons in drosophila.	a central question in insect chemoreception is whether signaling occurs via g-proteins. two families of seven-transmembrane-domain chemoreceptors, the odor (or) and gustatory receptor (gr) families, have been identified in drosophila (clyne et al., 1999, 2000; vosshall et al., 1999). ors mediate odor responses, whereas two grs, gr21a and gr63a, mediate co2 response (hallem et al., 2004; jones et al., 2007; kwon et al., 2007). using single-sensillum recordings, we systematically investigate the r ...	20357107
solo: a meiotic protein required for centromere cohesion, coorientation, and smc1 localization in drosophila melanogaster.	sister chromatid cohesion is essential to maintain stable connections between homologues and sister chromatids during meiosis and to establish correct centromere orientation patterns on the meiosis i and ii spindles. however, the meiotic cohesion apparatus in drosophila melanogaster remains largely uncharacterized. we describe a novel protein, sisters on the loose (solo), which is essential for meiotic cohesion in drosophila. in solo mutants, sister centromeres separate before prometaphase i, di ...	20142422
thgs: a web-based database of transmembrane helices in genome sequences.	transmembrane helices in genome sequences (thgs) is an interactive web-based database, developed to search the transmembrane helices in the user-interested gene sequences available in the genome database (gdb). the proposed database has provision to search sequence motifs in transmembrane and globular proteins. in addition, the motif can be searched in the other sequence databases (swiss-prot and pir) or in the macromolecular structure database, protein data bank (pdb). further, the 3d structure ...	14681375
the embl nucleotide sequence database.	the embl nucleotide sequence database (http://www.ebi.ac.uk/embl/), maintained at the european bioinformatics institute (ebi), incorporates, organizes and distributes nucleotide sequences from public sources. the database is a part of an international collaboration with ddbj (japan) and genbank (usa). data are exchanged between the collaborating databases on a daily basis to achieve optimal synchrony. the web-based tool, webin, is the preferred system for individual submission of nucleotide sequ ...	14681351
daily rhythms in antennal protein and olfactory sensitivity in the malaria mosquito anopheles gambiae.	we recently characterized 24-hr daily rhythmic patterns of gene expression in anopheles gambiae mosquitoes. these include numerous odorant binding proteins (obps), soluble odorant carrying proteins enriched in olfactory organs. here we demonstrate that multiple rhythmically expressed genes including obps and takeout proteins, involved in regulating blood feeding behavior, have corresponding rhythmic protein levels as measured by quantitative proteomics. this includes agamobp1, previously shown a ...	23986098
the molecular genetics of insecticide resistance.	the past 60 years have seen a revolution in our understanding of the molecular genetics of insecticide resistance. while at first the field was split by arguments about the relative importance of mono- vs. polygenic resistance and field- vs. laboratory-based selection, the application of molecular cloning to insecticide targets and to the metabolic enzymes that degrade insecticides before they reach those targets has brought out an exponential growth in our understanding of the mutations involve ...	23908373
developmental plasticity and the evolution of animal complex life cycles.	metazoan life cycles can be complex in different ways. a number of diverse phenotypes and reproductive events can sequentially occur along the cycle, and at certain stages a variety of developmental and reproductive options can be available to the animal, the choice among which depends on a combination of organismal and environmental conditions. we hypothesize that a diversity of phenotypes arranged in developmental sequence throughout an animal's life cycle may have evolved by genetic assimilat ...	20083638
evolution of sex chromosomes in insects.	sex chromosomes have many unusual features relative to autosomes. y (or w) chromosomes lack genetic recombination, are male- (female-) limited, and show an abundance of genetically inert heterochromatic dna but contain few functional genes. x (or z) chromosomes also show sex-biased transmission (i.e., x chromosomes show female-biased and z-chromosomes show male-biased inheritance) and are hemizygous in the heterogametic sex. their unusual ploidy level and pattern of inheritance imply that sex ch ...	21047257
toward a population genetic framework of developmental evolution: the costs, limits, and consequences of phenotypic plasticity.	adaptive phenotypic plasticity allows organisms to cope with environmental variability, and yet, despite its adaptive significance, phenotypic plasticity is neither ubiquitous nor infinite. in this review, we merge developmental and population genetic perspectives to explore costs and limits on the evolution of plasticity. specifically, we focus on the role of modularity in developmental genetic networks as a mechanism underlying phenotypic plasticity, and apply to it lessons learned from popula ...	20020499
detecting coevolution of functionally related proteins for automated protein annotation.	sequence similarity based protein clustering methods organize proteins into families of similar sequences, a task that continues to be critical for automated protein characterization. however, many protein families cannot be automatically characterized further because little is known about the function of any protein in a family of similar sequences. we present a novel phylogenetic profile comparison (ppc) method called automated protein annotation by coordinate evolution (apace) that facilitate ...	21655203
resilin-based materials for biomedical applications.	resilin, an insect structural protein, exhibits rubber-like elasticity characterized by low stiffness, high extensibility, efficient energy storage, and exceptional resilience and fatigue lifetime. the outstanding mechanical properties of natural resilin have motivated recent research in the engineering of resilin-like polypeptide-based biomaterials, with a wide range of applications including use as bio-rubbers, nanosprings, elements in biosensors, and tissue engineering scaffolds.	23997990
dissecting the regulatory switches of development: lessons from enhancer evolution in drosophila.	cis-regulatory modules are non-protein-coding regions of dna essential for the control of gene expression. one class of regulatory modules is embryonic enhancers, which drive gene expression during development as a result of transcription factor protein binding at the enhancer sequences. recent comparative studies have begun to investigate the evolution of the sequence architecture within enhancers. these analyses are illuminating the way that developmental biologists think about enhancers by re ...	20023155
smelling the difference: controversial ideas in insect olfaction.	in animals, the sense of smell is often used as a powerful way to attract potential mates, to find food and to explore the environment. different animals evolved different systems to detect volatile odorants, tuned to the specific needs of each species. vertebrates and nematodes have been used extensively as models to study the mechanisms of olfaction: the molecular players are olfactory receptors (ors) expressed in olfactory sensory neurons (osns) where they bind to volatile chemicals, acting a ...	19525421
acoustic detection of dna conformation in genetic assays combined with pcr.	application of pcr to multiplexing assays is not trivial; it requires multiple fluorescent labels for amplicon detection and sophisticated software for data interpretation. alternative pcr-free methods exploiting new concepts in nanotechnology exhibit high sensitivities but require multiple labeling and/or amplification steps. here, we propose to simplify the problem of simultaneous analysis of multiple targets in genetic assays by detecting directly the conformation, rather than mass, of target ...	23778520
identification of distinct tyraminergic and octopaminergic neurons innervating the central complex of the desert locust, schistocerca gregaria.	the central complex is a group of modular neuropils in the insect brain with a key role in visual memory, spatial orientation, and motor control. in desert locusts the neurochemical organization of the central complex has been investigated in detail, including the distribution of dopamine-, serotonin-, and histamine-immunoreactive neurons. in the present study we identified neurons immunoreactive with antisera against octopamine, tyramine, and the enzymes required for their synthesis, tyrosine d ...	23595814
activity-dependent gene expression in honey bee mushroom bodies in response to orientation flight.	the natural history of adult worker honey bees (apis mellifera) provides an opportunity to study the molecular basis of learning in an ecological context. foragers must learn to navigate between the hive and floral locations that may be up to miles away. young pre-foragers prepare for this task by performing orientation flights near the hive, during which they begin to learn navigational cues such as the appearance of the hive, the position of landmarks, and the movement of the sun. despite well ...	23678099
deleterious effect of suboptimal diet on rest-activity cycle in anastrepha ludens manifests itself with age.	activity patterns and sleep-wake cycles are among the physiological processes that change most prominently as animals age, and are often good indicators of healthspan. in this study, we used the video-based high-resolution behavioral monitoring system (bms) to monitor the daily activity cycle of tephritid fruit flies anastrepha ludens over their lifetime. surprisingly, there was no dramatic change in activity profile with respect to age if flies were consistently fed with a nutritionally balance ...	23639915
the dance of male anopheles gambiae in wild mating swarms.	an important element of mating in the malaria vector anopheles gambiae giles in nature is the crepuscular mating aggregation (swarm) composed almost entirely of males, where most coupling and insemination is generally believed to occur. in this study, we mathematically characterize the oscillatory movement of male an. gambiae in terms of an established individual-based mechanistic model that parameterizes the attraction of a mosquito toward the center of the swarm using the natural frequency of ...	23802449
two or four bristles: functional evolution of an enhancer of scute in drosophilidae.	changes in cis-regulatory sequences are proposed to underlie much of morphological evolution. yet, little is known about how such modifications translate into phenotypic differences. to address this problem, we focus on the dorsocentral bristles of drosophilidae. in drosophila melanogaster, development of these bristles depends on a cis-regulatory element, the dorsocentral enhancer, to activate scute in a cluster of cells from which two bristles on the posterior scutum arise. a few species howev ...	17105353
genomic insights into the immune system of the sea urchin.	comparative analysis of the sea urchin genome has broad implications for the primitive state of deuterostome host defense and the genetic underpinnings of immunity in vertebrates. the sea urchin has an unprecedented complexity of innate immune recognition receptors relative to other animal species yet characterized. these receptor genes include a vast repertoire of 222 toll-like receptors, a superfamily of more than 200 nacht domain-leucine-rich repeat proteins (similar to nucleotide-binding and ...	17095692
principles of genome evolution in the drosophila melanogaster species group.	that closely related species often differ by chromosomal inversions was discovered by sturtevant and plunkett in 1926. our knowledge of how these inversions originate is still very limited, although a prevailing view is that they are facilitated by ectopic recombination events between inverted repetitive sequences. the availability of genome sequences of related species now allows us to study in detail the mechanisms that generate interspecific inversions. we have analyzed the breakpoint regions ...	17550304
the ig cell adhesion molecule basigin controls compartmentalization and vesicle release at drosophila melanogaster synapses.	synapses can undergo rapid changes in size as well as in their vesicle release function during both plasticity processes and development. this fundamental property of neuronal cells requires the coordinated rearrangement of synaptic membranes and their associated cytoskeleton, yet remarkably little is known of how this coupling is achieved. in a gfp exon-trap screen, we identified drosophila melanogaster basigin (bsg) as an immunoglobulin domain-containing transmembrane protein accumulating at p ...	17548512
molecular evolution of drosophila cdc6, an essential dna replication-licensing gene, suggests an adaptive choice of replication origins.	increased size of eukaryotic genomes necessitated the use of multiple origins of dna replication, and presumably selected for their efficient spacing to ensure rapid dna replication. the sequence of these origins remains undetermined in metazoan genomes, leaving important questions about the selective constraints acting on replication origins unanswered. we have chosen to study the evolution of proteins that recognize and define these origins every cell cycle, as a surrogate to the direct analys ...	18618020
computational and transcriptional evidence for micrornas in the honey bee genome.	non-coding micrornas (mirnas) are key regulators of gene expression in eukaryotes. insect mirnas help regulate the levels of proteins involved with development, metabolism, and other life history traits. the recently sequenced honey bee genome provides an opportunity to detect novel mirnas in both this species and others, and to begin to infer the roles of mirnas in honey bee development.	17543122
7th international workshop on the molecular biology and genetics of the lepidoptera august 20-26, 2006, orthodox academy of crete, kolympari, crete, greece.		20302527
peptides encoded by short orfs control development and define a new eukaryotic gene family.	despite recent advances in developmental biology, and the sequencing and annotation of genomes, key questions regarding the organisation of cells into embryos remain. one possibility is that uncharacterised genes having nonstandard coding arrangements and functions could provide some of the answers. here we present the characterisation of tarsal-less (tal), a new type of noncanonical gene that had been previously classified as a putative noncoding rna. we show that tal controls gene expression a ...	17439302
insecticide-treated nets for the prevention of malaria in pregnancy: a systematic review of randomised controlled trials.	protection from malaria with insecticide-treated bednets (itns) during pregnancy is widely advocated, but evidence of benefit has been inconsistent. we undertook a systematic review of randomised trials.	17388668
the sorcerer ii global ocean sampling expedition: northwest atlantic through eastern tropical pacific.	the world's oceans contain a complex mixture of micro-organisms that are for the most part, uncharacterized both genetically and biochemically. we report here a metagenomic study of the marine planktonic microbiota in which surface (mostly marine) water samples were analyzed as part of the sorcerer ii global ocean sampling expedition. these samples, collected across a several-thousand km transect from the north atlantic through the panama canal and ending in the south pacific yielded an extensiv ...	17355176
the homer family proteins.	the homer family of adaptor proteins consists of three members in mammals, and homologs are also known in other animals but not elsewhere. they are predominantly localized at the postsynaptic density in mammalian neurons and act as adaptor proteins for many postsynaptic density proteins. as a result of alternative splicing each member has several variants, which are classified primarily into the long and short forms. the long homer forms are constitutively expressed and consist of two major doma ...	17316461
glutamate-64, a newly identified residue of the functionally conserved electron-sharing network contributes to catalysis and structural integrity of glutathione transferases.	in anopheles dirus glutathione transferase d3-3, position 64 is occupied by a functionally conserved glutamate residue, which interacts directly with the gamma-glutamate moiety of gsh (glutathione) as part of an electron-sharing network present in all soluble gsts (glutathione transferases). primary sequence alignment of all gst classes suggests that glu64 is one of a few residues that is functionally conserved in the gst superfamily. available crystal structures as well as consideration of the ...	17100654
eph receptor and ephrin signaling in developing and adult brain of the honeybee (apis mellifera).	roles for eph receptor tyrosine kinase and ephrin signaling in vertebrate brain development are well established. their involvement in the modulation of mammalian synaptic structure and physiology is also emerging. however, less is known of their effects on brain development and their function in adult invertebrate nervous systems. here, we report on the characterization of eph receptor and ephrin orthologs in the honeybee, apis mellifera (am), and their role in learning and memory. in situ hybr ...	17443785
mechanisms of odor receptor gene choice in drosophila.	a remarkable problem in neurobiology is how olfactory receptor neurons (orns) select, from among a large odor receptor repertoire, which receptors to express. we use computational algorithms and mutational analysis to define positive and negative regulatory elements that are required for selection of odor receptor (or) genes in the proper olfactory organ of drosophila, and we identify an element that is essential for selection in one orn class. two odor receptors are coexpressed by virtue of the ...	17270733
new genes as drivers of phenotypic evolution.	during the course of evolution, genomes acquire novel genetic elements as sources of functional and phenotypic diversity, including new genes that originated in recent evolution. in the past few years, substantial progress has been made in understanding the evolution and phenotypic effects of new genes. in particular, an emerging picture is that new genes, despite being present in the genomes of only a subset of species, can rapidly evolve indispensable roles in fundamental biological processes, ...	23949544
climate influences on the cost-effectiveness of vector-based interventions against malaria in elimination scenarios.	despite the dependence of mosquito population dynamics on environmental conditions, the associated impact of climate and climate change on present and future malaria remains an area of ongoing debate and uncertainty. here, we develop a novel integration of mosquito, transmission and economic modelling to assess whether the cost-effectiveness of indoor residual spraying (irs) and long-lasting insecticidal nets (llins) against plasmodium falciparum transmission by anopheles gambiae s.s. mosquitoes ...	25688017
drosophila melanogaster as a model system to study mitochondrial biology.	mitochondria play an essential role in cellular homeostasis. although in the last few decades our knowledge of mitochondria has increased substantially, the mechanisms involved in the control of mitochondrial biogenesis remain largely unknown. the powerful genetics of drosophila combined with a wealth of available cell and molecular biology techniques, make this organism an excellent system to study mitochondria. in this chapter we will review briefly the opportunities that drosophila offers as ...	18314716
complex alternative splicing.	alternative splicing is a powerful means of controlling gene expression and increasing protein diversity. most genes express a limited number of mrna isoforms, but there are several examples of genes that use alternative splicing to generate hundreds, thousands and even tens of thousands of isoforms. collectively such genes are considered to undergo complex alternative splicing. the best example is the drosophila down syndrome cell adhesion molecule (dscam) gene, which can generate 38,016 isofor ...	18380340
soluble guanylyl cyclases in invertebrates: targets for no and o(2).		19122779
investigating payment coping mechanisms used for the treatment of uncomplicated malaria to different socio-economic groups in nigeria.	given the enormous economic burden of malaria in nigeria and in sub-saharan africa, it is important to determine how different population groups cope with payment for malaria treatment. this paper provides new information about the differences in household coping mechanisms for expenditures on malaria treatment.	25834529
differences in the subunit interface residues of alternatively spliced glutathione transferases affects catalytic and structural functions.	gsts (glutathione transferases) are multifunctional widespread enzymes. currently there are 13 identified classes within this family. previously most structural characterization has been reported for mammalian alpha, mu and pi class gsts. in the present study we characterize two enzymes from the insect-specific delta class, adgstd3-3 and adgstd4-4. these two proteins are alternatively spliced products from the same gene and have very similar tertiary structures. several major contributions to th ...	16938097
ether-à-go-go family voltage-gated k+ channels evolved in an ancestral metazoan and functionally diversified in a cnidarian-bilaterian ancestor.	we examined the evolutionary origins of the ether-à-go-go (eag) family of voltage-gated k(+) channels, which have a strong influence on the excitability of neurons. the bilaterian eag family comprises three gene subfamilies (eag, erg and elk) distinguished by sequence conservation and functional properties. searches of genome sequence indicate that eag channels are metazoan specific, appearing first in ctenophores. however, phylogenetic analysis including two eag family channels from the ctenoph ...	25696816
chemistry-specific surface adsorption of the barnacle settlement-inducing protein complex.	gregarious settlement in barnacle larvae (cyprids) is induced by a contact pheromone, the settlement-inducing protein complex (sipc). the sipc has been identified both in the cuticle of adult barnacles and in the temporary adhesive secretion (footprint) of cyprids. besides acting as a settlement inducer, the presence of the sipc in footprints points to its additional involvement in the adhesion process. sipc adsorption behaviour was therefore investigated on a series of self-assembled monolayers ...	25657832
gpcr expression in tissues and cells: are the optimal receptors being used as drug targets?	g-protein-coupled receptors [gpcrs, also known as 7-transmembrane (7-tm) receptors] comprise the largest family of membrane receptors in humans and other species and, in addition, represent the greatest number of current drug targets. in this article, we review methods to define gpcr expression and data indicating that individual cells express >100 different gpcrs. results from studies that have quantified expression of these receptors lead us to conclude that the optimal gpcrs may not be curren ...	21488863
environmental, socio-demographic and behavioural determinants of malaria risk in the western kenyan highlands: a case-control study.	to identify risk factors for uncomplicated malaria in highland areas of east africa at higher risk of malaria epidemics, in order to design appropriate interventions.	19772547
a synaptic vesicle-associated ca2+ channel promotes endocytosis and couples exocytosis to endocytosis.	synaptic vesicle (sv) exo- and endocytosis are tightly coupled to sustain neurotransmission in presynaptic terminals, and both are regulated by ca(2+). ca(2+) influx triggered by voltage-gated ca(2+) channels is necessary for sv fusion. however, extracellular ca(2+) has also been shown to be required for endocytosis. the intracellular ca(2+) levels (<1 microm) that trigger endocytosis are typically much lower than those (>10 microm) needed to induce exocytosis, and endocytosis is inhibited when ...	19737521
drosophila minus is required for cell proliferation and influences cyclin e turnover.	turnover of cyclins plays a major role in oscillatory cyclin-dependent kinase (cdk) activity and control of cell cycle progression. here we present a novel cell cycle regulator, called minus, which influences cyclin e turnover in drosophila. minus mutants produce defects in cell proliferation, some of which are attributable to persistence of cyclin e. minus protein can interact physically with cyclin e and the scf archipelago/fbw7/cdc4 ubiquitin-ligase complex. minus does not affect dmyc, anothe ...	19723762
brain photoreceptor pathways contributing to circadian rhythmicity in crayfish.	freshwater crayfish have three known photoreceptive systems: the compound eyes, extraretinal brain photoreceptors, and caudal photoreceptors. the primary goal of the work described here was to explore the contribution of the brain photoreceptors to circadian locomotory activity and define some of the underlying neural pathways. immunocytochemical studies of the brain photoreceptors in the parastacid (southern hemisphere) crayfish cherax destructor reveal their expression of the blue light-sensit ...	19731110
gef1 is a ciliary sec7 gef of tetrahymena thermophila.	ciliary guanine nucleotide exchange factors (gefs) potentially activate g proteins in intraflagellar transport (ift) cargo release. several classes of gefs have been localized to cilia or basal bodies and shown to be functionally important in the prevention of ciliopathies, but ciliary arl-type sec 7 related gefs have not been well characterized. nair et al. [ 1999] identified a paramecium ciliary sec7 gef, psec7. in tetrahymena, gef1p (gef1), tentatively identified by psec7 antibody, possesses ...	19267341
distinct functional specificities are associated with protein isoforms encoded by the drosophila dorsal-ventral patterning gene pipe.	spatially regulated transcription of the pipe gene in ventral cells of the drosophila ovary follicle cell epithelium is a key event that specifies progeny embryo dorsal-ventral (dv) polarity. pipe encodes ten putative protein isoforms, all of which exhibit similarity to vertebrate glycosaminoglycan-modifying enzymes. expression of one of the isoforms, pipe-st2, in follicle cells has previously been shown to be essential for dv patterning. pipe is also expressed in the embryonic salivary gland an ...	19633171
relationship between exposure, clinical malaria, and age in an area of changing transmission intensity.	the relationship between malaria transmission intensity and clinical disease is important for predicting the outcome of control measures that reduce transmission. comparisons of hospital data between areas of differing transmission intensity suggest that the mean age of hospitalized clinical malaria is higher under relatively lower transmission, but the total number of episodes is similar until transmission drops below a threshold, where the risks of hospitalized malaria decline. these observati ...	18689622
hormonal regulation of the humoral innate immune response in drosophila melanogaster.	juvenile hormone (jh) and 20-hydroxy-ecdysone (20e) are highly versatile hormones, coordinating development, growth, reproduction and aging in insects. pulses of 20e provide key signals for initiating developmental and physiological transitions, while jh promotes or inhibits these signals in a stage-specific manner. previous evidence suggests that jh and 20e might modulate innate immunity, but whether and how these hormones interact to regulate the immune response remains unclear. here we show t ...	18689425
progress and prospects toward our understanding of the evolution of dosage compensation.	in many eukaryotic organisms, gender is determined by a pair of heteromorphic sex chromosomes. degeneration of the non-recombining y chromosome is a general facet of sex chromosome evolution. selective pressure to restore expression levels of x-linked genes relative to autosomes accompanies y-chromosome degeneration, thus driving the evolution of dosage compensation mechanisms. this review focuses on evolutionary aspects of dosage compensation, in light of recent advances in comparative and func ...	19626444
proteomics reveals novel drosophila seminal fluid proteins transferred at mating.	across diverse taxa, seminal fluid proteins (sfps) transferred at mating affect the reproductive success of both sexes. such reproductive proteins often evolve under positive selection between species; because of this rapid divergence, sfps are hypothesized to play a role in speciation by contributing to reproductive isolation between populations. in drosophila, individual sfps have been characterized and are known to alter male sperm competitive ability and female post-mating behavior, but a pr ...	18666829
rapid discrimination between anopheles gambiae s.s. and anopheles arabiensis by high-resolution melt (hrm) analysis.	there is a need for more cost-effective options to more accurately discriminate among members of the anopheles gambiae complex, particularly an. gambiae and anopheles arabiensis. these species are morphologically indistinguishable in the adult stage, have overlapping distributions, but are behaviorally and ecologically different, yet both are efficient vectors of malaria in equatorial africa. the method described here, high-resolution melt (hrm) analysis, takes advantage of minute differences in ...	23543777